Perl：在数组元素中搜索模式 [英] Perl: Search a pattern across array elements

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问题描述

我是Perl的新手，仍然遇到另一个需要一些帮助和投入的生物信息学问题。


问题简短：


  1. 我有一个文件，其中包含40,000多个 unique DNA序列。唯一是指唯一的序列ID。我会在文章结尾处附加一部分内容，以帮助您显示它的外观。



  2. 我需要将 3个部分。因此，如果特定序列的长度为999个字符，则3个部分中的每个部分都将具有333个字符。



  3. 我需要寻找以下模式通过3个单独的部分：


    $ gpat = [G] {3,5}；
    $ npat = [AZ] {1,25};

    $ pattern = $ gpat。$ npat。$ gpat。$ npat。$ gpat。$ npat。$ gpat;



  4. 如果$ pattern出现在3个部分的第一个部分，则增加$ beginning的计数器，如果$ pattern出现在3个部分的第2个部分部分，增加'middle'的计数器，最后，如果$ pattern在第3部分中出现，则增加'end'的计数器。



  5. 打印开始，中间和结束的计数器，即基本上是每个序列的开始，中间，结束的总和。


    在第一个序列中说，其值分别类似于'2'，'5'，'3'，并且在第二序列中，值为'4'，'1'，'6'，最终计数应为'7,6,9'。



我遇到的问题：


  1. 如果将特定序列分为3部分，则可能的$ pattern将丢失。例如，在类似这样的序列上说：每35个字符的长度：


    gggatgtcgatgcatggggatgcatcgatgcgggg

    actagctagcgggatgctacgatggggatgatgat

    aatatcgcggcgcatatatgctagtctatat $$

    em> $ pattern分为前两个部分    。无论如何说如果$ pattern从第一部分开始到第二部分结束，则增加开始计数。 ？


    ## UPDATE ## 以下问题已得到解决，这归功于Cupidvogel建议的代码


    2。如果序列的长度不能被3整除，如何将其分为3个部分？我尝试使用 int ，但是最后一部分是1-2个
    字符。


    以下是我到目前为止编写的代码。


    它读取文件，显示标题名称和序列，每个序列将被划分为的长度，最后是序列分为3个部分，只要序列长度可以被3整除，就可以很好地工作；对于不能被3整除的序列，最后的第3部分要短1-2个字符。

     ＃从用户
    打印中获取文件名请输入文件名： 
     $ in =<> ;; 
     chomp $ in; 
     
     
    开放（FASTA， $ in）或死亡； 
    而（< FASTA>）
     {
     $ / =>; 
     @array = split'\n'，$ _; 
     $ header = shift @array; ＃Fasta序列的标头
     print \n\nNextNext：\n; 
    打印$ header， \n； 
     
     
     $ seq =加入’，@ array; ＃序列
     $ seq =〜s / \s // g; 
     $ seq =〜s / \ * // g; 
     $ seq =〜s /> // g; 
     print $ seq， \n\n; 
     
     $ num = int（length（$ seq）/ 3）; 
     @arr = unpack（ A $ num A $ num A *，$ seq）; 
    打印"新方法给出了这个：， @ arr; 
    打印 \n第一个元素是：，$ arr [0]; 
     print \n第二个元素是：，$ arr [1]; 
    打印 \n第三个元素是：，$ arr [2]; 
     
     
     
    ＃下面的代码行最初是为了拆分... 
    ＃...将序列分成3部分，尽管未成功
     #my $ split =（长度$ seq）/ 3; 
     #print $ split， \n\n; 
     
     #my $ int = int $ split; 
     #print $ int， \n\n; 
     
     
     #my @ array2 = $ seq =〜/(.{$int})/g; 
     #print join（，，@ array2）， \n\n; 
     
    ＃print $ array2 [0]， \n，$ array2 [1]， \n，$ array2 [2]； 
     
     
    } 
     
     
    出口；

    我一直在尝试使用以下示例文件编写的代码：sample.fa


    'pre> > ABC_123 2
    atgtcgatcgatcggcgggcatgcgcgcgcggatg
    atatatagcgcgcgctatatagcgcgactctacgc
    atgctgctgactagctatagtcgctgactgcgcgt
    gggaaaaagggcccgggccccgttttggggatcta
    ggggatagctgatgctagcatgcatgctgactgca
    个DEF_456 4
    gggatgtcgatgcatggggatgcatcgatgcgggg
    actagctagcgggatgctacgatggggatgatgat
    aatatcgcggcgcatatatgctagtctatatatta
    个GHI_789 1个
    atagctgctagtcgatcggcgcgggtatcgatcgg
    ggatcgatcgatcggggatcgatcgggggatcgat

    实际的输入文件如下所示：

     > NR_037701 1 
     aggagctatgaatattaatgaaagtggtcctgatgcatgcatattaaaca 
     tg猫b agctgtagttatggctggtggagttcagttagtcagcatctggtggagct 
     gcaagtgttttagtattgtttatttagaggccagtgcttatttagctgct 
     agagaaaaggaaaacttgtggcagttagaacatagtttattcttttaagt 
     gtagggctgcatgacttaacccttgtttggcatggccttaggtcctgttt 
     gtaatttggtatcttgttgccacaaagagtgtgtttggtcagtcttatga 
     cctctattttgacattaatgctggttggttgtgtctaaaccataaaaggg 
     aggggagtataatgaggtgtgtctgacctcttgtcctgtcatggctggga 
     actcagtttctaaggtttttctggggtcctctttgccaagagcgtttcta 
     ttcagttggtggaggggacttaggattttatttttagtttgcagccaggg 
     tcagtacatttcagtcacccccgcccagccctcctgatcctcctgtcatt 
     cctcacatcctgtcattgtcagagattttacagatatagagctgaatcat 
     ttcctgccatctcttttaacacacaggcctcccagatctttctaacccag 
     gacctacttggaaaggcatgctgggtctcttccacagactttaagctctc 
     cctacaccagaatttaggtgagtgctttgaggacatgaagctattcctcc 
     caccaccagtagccttgggctggcccacgccaactgtggagctggagcgg 
     gagggaggagtacagacatggaattttaattctgtaatccagggcttcag 
     ttatgtacaacatccatgccatttgatgattccaccactccttttccatc 
     tcccagaagcctgctttttaatgcccgcttaatattatcagagccg海湾合作委员会
     tggaatcaaactgcctctttcaaaacctgccactatatcctggctttgtg 
     acctcagccaagttgcttgactattctcagtctcagtttctgcacctgtc 
     aaatagggtttatgttaacctaactttcagggctgtcaggattaaatgag 
     catgaaccacataaaatgtttggtgtatagtaagtgtacagtaaatactt 
     ccattatcagtccctgcaattctatttttcttccttctctacacagcccc 
     tgtctggctttaaaatgtcctgccctgctttttatgagtggataccccca 
     gccctatgtggattagcaagttaagtaatgacactcagagacagttccat 
     ctttgtccataacttgctctgtgatccagtgtgcatcactcaaacagact 
     atctcttttctcctacaaaacagacagctgcctctcagataatgttgggg 
     gcataggaggaatgggaagcccgctaagagaacagaagtcaaaaacagtt 
     gggttctagatgggaggaggtgtgcgtgcacatgtatgtttgtgtttcag 
     gtcttggaatctcagcaggtcagtcacattgcagtgtgtcgcttcacctg 
     gctccctcttttaaagattttccttccctctttccaactccctgggtcct 
     ggatcctccaacagtgtcagggttagatgccttttatgggccacttgcat 
     tagtgtcctgatagaggcttaatcactgctcagaaactgccttctgccca 
     ctggcaaagggaggcaggggaaatacatgattctaattaatggtccaggc 
     agagaggacactcagaatttcaggactgaagagtatacatgtgtgtgatg 
     gtaaatgggcaaaaatcatcccttggcttctcatgcat aatgcatgggca 
     cacagactcaaaccctctctcacacacatacacatatacattgttattcc 
     acacacaaggcataatcccagtgtccagtgcacatgcatacacgcacaca 
     ttcccttcctaggccactgtattgctttcctagggcatcttcttataaga 
     caccagtcgtataaggagcccaccccactcatctgagcttatcaaccaat 
     tacattaggaaagactgtatttcctagtaaggtcacattcagtagtactg 
     agggttgggacttcaacacagctttttgggggatcataattcaacccatg 
     acagccactgagattattatatctccagagaataaatgtgtggagttaaa 
     aggaagatacatgtggtacaaggggtggtaaggcaagggtaaaaggggag 
     ggaggggattgaactagacacagacacatgagcaggactttggggagtgt 
     gttttatatctgtcagatgcctagaacagcacctgaaatatgggactcaa 
     tcattttagtccccttctttctataagtgtgtgtgtgcggatatgtgtgc 
     tagatgttcttgctgtgttaggaggtgataaacatttgtccatgttatat 
     aggtggaaagggtcagactactaaattgtgaagacatcatctgtctgcat 
     ttattgagaatgtgaatatgaaacaagctgcaagtattctataaatgttc 
     actgttattagatattgtatgtctttgtgtccttttattcatgaattctt 
     gcacattatgaagaaagagtccatgtggtcagtgtcttacccggtgtagg 
     gtaaatgcacctgatagcaataacttaagcacacctttataatgacccta 
     tatggcagatgctcctgaatgtgtgtttcg agctagaaaatccgggagtg 
     gccaatcggagattcgtttcttatctataatagacatctgagcccctggc 
     ccatcccatgaaacccaggctgtagagaggattgaggccttaagttttgg 
     gttaaatgacagttgccaggtgtcgctcattagggaaaggggttaagtga 
     aaatgctgtataaactgcatgatgtttgcaggcagttgtggttttcctgc 
     ccagcctgccaccaccgggccatgcggatatgttgtccagcccaacacca 
     caggaccatttctgtatgtaagacaattctatccagcccgccacctctgg 
     actccctcccctgtatgtaagccctcaataaaaccccacgtctcttttgc 
     tggcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 
     AAA 
     > NM_198399 1 
     aacagattttaactctgaaaagccatttccagtgtctatagactattgtg 
     agcctggagaagtagcatttagttgggatagcttcactagagctgcctgc 
     caaagacttccttccacaggatcttgtcgcaccagcaactgacaggagct 
     tgggagctcgggagcttgggagagggcttatgtttttaataatgtagctg 
     tcagttcgaagcctggaaatgttgaccctcaaagggcataaaatcttgtt 
     attttaatttgcatctgggagaatgtctgagcaaggagacctgaatcagg 
     caatagcagaggaaggagggactgagcaggagacggccactccagagaac 
     ggcattgttaaatcagaaagtctggatgaagaggagaaactggaactgca 
     gaggcggctggaggctcagaatcaagaaagaagaaaatccaagtcagg AG 
     caggaaaaggtaaactgactcgcagccttgctgtctgtgaggaatcttct 
     gccagaccaggaggtgaaagtcttcaggatcagactctctgaaaactgca 
     aatggaaaggaattcaaaagaatttagattaaaagttaaataaaaagtag 
     gcacagtagtgctgaattttcctcaaaggctctcttttgataaggctgaa 
     ccaaatataatcccaagtatcctctctccttccttgttggagatgtctta 
     cctctcagctccccaaaatgcacttgcctataagaaacacaattgctggt 
     tcatatgaaacttaggaaatagtgaataaggtgcatttaactttggagaa 
     atacttttatggctttggtggagatttctcaatactgcaaaagttgtcca 
     gaaatgaatctgagctgatggtgactttaagttaatattattaatatatc 
     actgcatatttttacccttatttttgctccttacagcaagattagtaggt 
     tataaaaatttaaatttaaacaaaattatttcatgacaaaatgggaaact 
     tcacatcatacttatttttgtttgcctttcaggcatcatattagctttta 
     taaaaaatggtcttgctgctgaaattgtacttattttatcagaggctggg 
     tgcagtcaagacaaaagtaaaatggtttacctgagcccaggggagggaaa 
     attgattaagatatcattatttttgtttggtttggttttgcttttttcct 
     cttactttaattgaaatactctgaattcccctcatggaaacagagagcat 
     tgagagcactttctttaaaaggaccaaaaataaattcctaatagattttg 
     tcctaagagagtgtttttttttctagcatcattttcttta catgccactc 
     atgtcataaggcatggacaggctatctttcagtggccattactatgtttc 
     gtacacatgctttattttacttgggctctgagaaatgtgtggctttcctt 
     cagcattttatttgtgcttctctttttaatggagattgaaaagggagaat 
     aatgtgaatatcacggcttatattattaaatgttgattgatggcttgtaa 
     tgtactgcacacaatatatgttaactctgcagaatgacagaccctgggag 
     aagtaatgccccagttgtcccccactcctaatgccaggcagagaaggaca 
     gcctttatagacttaatctgctttttgtcccatttgacaaggtaccagga 
     ggaaattttttaagggatcaactgtatcacagtgcccactctggacctaa 
     gtctagtgtatccatacaattggtgcagagaaataaggtgtaaatggtgc 
     tttgttcctgctggttccaagctcagaaaccaagactagctttgtaggag 
     agaatgagagcctgcaagcctctctttggattggctgaggagtggtggga 
     gcagggggttgatagaaaacatccagacacacatataagcaagtggccgt 
     gctacctttttagagaataaagaaacagacttttgagtttatatgcaatg 
     ccttcattaggtaccaccggcacttacaaaatgtgcggactgaatcccag 
     agaacactggcagatgtatacagtatatggattgtatcgcttccccaatg 
     tttgtaaattcacagtatttggaaaactgccttcattttccagtgtggga 
     aaaactcttgctacctgtattacttgatctcagacccatacctgatggtt 
     cagtctgtccttaagttaaaagaattttgctt ttctaatgttatactatt 
     tacctgtcagtgtattactgcaacttgaatcactcttttactgttgttgg 
     atataaacttatcctgtaccaatgtatttattaacacttgtattttatta 
     ttgagcatatcaataaaaatattaaaaaataacagattgttttttaccaa 
     aaaaaaaaaaaaa 
    个NR_026816 1 
     caacccactctctgtgctatgacttcattactctttcccagcccagccct 
     gggcaagccccttacgaagtctcaggctacctggatgaccaccctttctt 
     atgatgctgcaaggagggcaggtgggcagagccccgtgcatcctgggctc 
     aggccagggacccaagagcttgggagaagctggttctcagactgaaggcc 
     agagcccagcaccttgtcaccatcccggggagcatcatggcacacaacaa 
     ccagagccaaggctacagctagagagttgactcctctatttgagattgac 
     aggcctcggaagtcaaaataagtggtttcctagaccgggtcgagagcaag 
     tctctattggtcccaactgagttttttcagctggtttttcaaccaaacag 
     cacctcatctcccagtgaggggaagggaaggctgggctgagagcagcaag 
     gctgctcatctcacctctccccacccagccatgccagccgcctcacctgg 
     tggggagaggtgggcctcacctgggtcccctggcagtgctctgtgaaggg 
     tcttgacattgcactgtaataataaaggtgtgtgtgaagtatcaaaaaaa 
    个NR_027917 1个
     atgaagatgattgagcagcacaatcaggaatacagggaagggaaacacag 
     cttcacaatggccatgaac gcctttggagaaatgaccagtgaagaattca 
     ggcaggtggtgaatggctttcaaaaccagaagcacaggaaggggaaagtg 
     ctccaggaacctctgcttcatgacatccgcaaatctgtggattggagaga 
     gaaaggctacgtgactcctgtgaaggatcagtgcagctggggctctgtaa 
     ggacagatgttaggaaaactgagaaactagtttcactgagtgtgcagacc 
     tggtggactgctctaggcttcaaggcaatgttggctgcatttttggagaa 
     ccattattttgcttccagtatgttgccgacaatggaggcctggactctga 
     ggaatccttttcatatgaagaaaagctctggagactggaaagtccaaggt 
     cacagaggtgcatctggtgagagccttcttgctagtggggaatctcagca 
     gagtcctgaggtggcacagtattctgggaagcatcaagtgcagtgtcatc 
     ttatcgaggaggctctgcagatgctaagtggtggggatgaggatcacgat 
     gaagacaaatggccccatgacatgaggaatcatctggctggagaggccca 
     ggtgtag 
    个NR_002777 3 
     cttgtcctttcagaagatcagagacaagtgatatctgtgccaatttggcc 
     ttttcagtgttataattatggtgtcttgggatcccaatatttctcctaat 
     gtttccctgatgtgatactttgagagcccaggatgccagtacaataattg 
     aaattcacaaatgtctggtatcttgtccctcgtgccccatatattatctg 
     tggtttcggagagctcacttgtctcttatcttcagaaatgacagcacatg 
     aaatgttgtttggagccactgtcacatcaactg tagaaaaattaacaggt 
     cagctaagggatataatgtaactttatttgtgatatgagagaaatcttga 
     taaagacttgagagaaaactgggaggaaccttgtttagaagttataagga 
     ggggtaagttatgtgtgtcttggaaggagaatcataaatcttaaaacatg 
     agcctaatagagaacataaaattctaaaagataaagataataataatgat 
     aagccgcagggtggcttatgataatgtgacttctccttaccccagtagcg 
     tcggacatctgtcagctctgaaatgataaaaatgcacaatattgaataca 
     aacaaaggagtcagcactgaaattcattttctctccagattagggaaaga 
     gtaggtatgccctatggtagggcagtaaattgctgaatgatgagatgaaa 
     cagccacctagccatttcccattaaatataatcccatcagcagcagacaa 
     tatctatcctcccctatcccctctatccatatttggaaactgcaccctct 
     tccctatttagcaccctaacaccacttgaattccataaccctgttgttga 
     tctagctctcctcacctctaaacacttctagcattcctttcagatcagga 
     gctcgaaacactctcctttgattttttggaaaagtttctggcttcttcaa 
     ggtcacgttctccgtcctaagaattaaaaaaaaaaaaaaaaacttccaaa 
     cctttgaccttgtgtccgtggaacacccctgacttcctatcatttcaacc 
     cattgaggcacttgaactctcttcttggggatcctgagaagggagagtgc 
     aaactcttgaccctggaggcaaacaaaatgttctcatgtttgccttccca 
     cttactttctgtgagaacgtgggaa gatcttaacctctcagaagcacagt 
     ttcttccttctaaaatgaaataattaacctctccctgtctacattcttaa 
     actcataggacataaaaaaaaaaaaaa 
    个NR_033769 1 
     ggcctctggcgggcctccagccagttagaccatttgactaggacgtgtgc 
     agctcagccagccacagaactggaatttttcaggagcagggggagcatgg 
     agtttggactttgctgagcaactgaagtggagcgcagagcttgctcgctt 
     aggagagggcagcatggatggcaaacaagggggcatggatgggagcaagc 
     ccacggggccaagagactctcctgacaccaggcttctttcaaacccattg 
     atgggtgattctgtgtctgattggtctcctatgcctgaagctgcaatcta 
     cggacatcagctgtctctgaggaacctcatcagccacgggtggcttgtga 
     acatcatcatggcagatcatgtttccccactccatgaagcctgtctcaga 
     ggtcatccctctcgtgtaaagattttattaaagcatggagctcaggtgaa 
     tggcgtgacaacagactggcacactccactgtttaatgtttgtatcagca 
     gcagctgggattatgcttctgcagcatggagccagcgttcaacctgagag 
     tgatctggcatcccccgtccatgaagctgctaggagaggccacgtggagt 
     gtgtcgactctcttacagcttataggggcaaaaatgaccataacatcagc 
     cacgtgggcacttcactgtatttggcttgtgaaaaccagcagatagcctg 
     tgtcaagaagcttctggagtcaggagcagacctgaacccagggagaggtt 
     ccccacttcatgcagtggc cttcatgaaggccctcatgaaggattcccca 
     cttcatgcagtggccaggacagccagtgaagagctggcctgcctgctcat 
     ggattttggagcagacacccaggccaagaatgctgaaggcaaatgtcatg 
     tggagctggtgcctccagagagccctttgatccagctcttcttggagaga 
     gaagggcccccttcttttgatgcagttatgcctagaaatcagaagggctt 
     tggaatccagcagcatcataagataaccaaagtcgtcctcccagaggatc 
     tgaaatggtttctcctacatctttgtatgtatcaatggaatggattcaca 
     aacaatgtgaaaacattattgagtgttgtagccactagaattttaaaatc 
     aagttaggtttatagagtttgactagttttttcgattagatttgtattag 
     ttataaatttgttcatagagtttgactaattttttcgattagatttgtat 
     ttgttaaactctgaagccagagtttaaacacactgcatacgtttgtatga 
     ttagttagaaggcatgaagacttttttccctgcttggagactgtctaaaa 
     taacagctattgttttgcatatccactgcaggccaagcactttcagcatc 
     atctaattcagccctcacagcaactgggtcaatctgtccaatttcccagg 
     gcaaggatagaggagtcagattcaaatacaggttttctgacgttaactta 
     tgtgatgatttgatcaaagcaggattttccagcatcactatccttgttcc 
     atctctgctatatgggaatgaaaataaagaaatgtatttcaaaaaaataa 
     aaagaaaagaaaaacagagacggtc 
    个NM_016326 3 
     atgcgcgcaagagag cgggaagccgagctgggcgagaagtaggggagggc 
     ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg 
     cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac 
     gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag 
     tgtgaaaggccacgtgaagatgctgcggctggtgtttgcacttgtgacag 
     cagtatgctgtcttgccgacggggcccttatttaccggaagcttctgttc 
     aatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagt 
     tttgtaattttatattactttttagtttgatactaagtattaaacatatt 
     tctgtattcttccacatattttctgcagttattttaactcagtataggag 
     ctagaggaagagatttccgaagtctgcaccccgcgcagagcactactgta 
     acttccaagggagcgctgggagcagcgggatcgggttttccggcacccgg 
     gcctgggtggcagggaagaatgtgccgggatccgcctcagggatctttga 
     atctctttactgcctggctggccggcagctccg 
    个NM_181641 2 
     atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc 
     ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg 
     cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac 
     gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag 
     tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta 
     TGA ccttttttatcatcgcacaagcccctgaaccatatattgttatcact 
     ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag 
     acttgatcgattaatgaagtggttattttggcctttgcttgtgtttgcac 
     ttgtgacagcagtatgctgtcttgccgacggggcccttatttaccggaag 
     cttctgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaa 
     aaaagaagttttgtaattttatattactttttagtttgatactaagtatt 
     aaacatatttctgtattcttccacatattttctgcagttattttaactca 
     gtataggagctagaggaagagatttccgaagtctgcaccccgcgcagagc 
     actactgtaacttccaagggagcgctgggagcagcgggatcgggttttcc 
     ggcacccgggcctgggtggcagggaagaatgtgccgggatccgcctcagg 
     gatctttgaatctctttactgcctggctggccggcagctccg 
    个NM_001144931 1 
     gtttccgttcctctgcccgccatgccgttcctagagctgcacacgaattt 
     ccccgccaaccgagtgcccgcggggctggagaaacggctgtgcgccgtcg 
     ctgcctccatcttgggcaaacctgcagaccttgtgaacgtgacggtacgg 
     ccgggcctggccagggcgctgagcgggtccaccgagccctgcgcgcagct 
     gtccatctcctccatcggcgtagtgggcaccgccgaggacaaccgcagcc 
     acagtgcccacttctttgagtttctcaccaaggagctagccctgggccag 
     gaccggtgcgcaggggtagtaggcccggaatatta ttctaaaacacaatc 
     agagtactccattcctgctaacagtttaaagccaaacacctaggcaggcc 
     atttaggcttctgaatgactgggtcttgaccaggagagctgctgtctagg 
     ttttctcttcctgaccagttcctcaagagaaatgcaaaactagtgattaa 
     cagtaagagtcaggcagggcgcggtggctcacgcctgtaatcccagcact 
     ttgggaggccgag 
    个NR_029429 1 
     ggacaccaccccaaaatttcctagtcctctttgatacgggttcctccaat 
     ctgtagctgccctccatctactgccagagccaagtctgctccaatcacaa 
     caggttcaatcccagcctgtcctccaccttcagaaacgatggacaaacct 
     atggactatcctatgggagtggcagcctgagtgtgttcctgggctatgac 
     actgtgactgttcataacatcgttgtcaataaccaggagtttggcctgag 
     tgagaatgagcccagcgaccccttttactattcagactttgacgggatcc 
     tgggaatggcctacccaaacatggcagaggggaattcccctacagtaatg 
     caggggatgctgcagcagagccagcttactcagcccgtcttcagcttcta 
     cttcacctgccagccaacccgccagtattgtggagagctcatccttggag 
     gtgtggaccccaactttattctggtcagatcatctggacccctgtcagcc 
     cgtaactgtactggcagattgccatcgaggaatttgccatcggtaaccag 
     gccactggcttgtgctctgagggttgccaggccattgtggataccgagac 
     cttcctgc 
    > NR_026551 1 
     tgtggcct gagaggacggccaggactggccagaaaagagagggacgtggc 
     taaacgtgagggggcgtggccaagatggccgcgtgcgggatcctcgggta 
     ccgggagcgaacgaggaggttctggctcagtgcatccactctgggagagc 
     gtggacctggttcctgggggcgatcgccagtcacccatcaacattcggtg 
     gagggacagtgtttatgatcccggcttaaaaccactgaccatctcttatg 
     acccagccacctgcctccacgtctggaataatgggtactctttcctcgtg 
     gaatttgaagattctacagataaatcagctgcacttagtgcattggaacg 
     cagtcaaatttgaaaactttgaggatgcagcactggaagaaaatggtttg 
     gctgtgataggagtatttttaaagatttcggaaacttctggcagcccagt 
     gtctactggaaggcccaagccgcttgccagaaagctgcgccccgcccaaa 
     agcactgggttctgcagtccaggcccttcctcagctcccaggtccaggag 
     aactgcaaggtcacctacttccacaggaagcactgggtccgcatccggcc 
     cctccgcaccactcctcccagctgggactacacccgcatctgcatccaga 
     gagagatggtccccgcccgcatccgcgtcctgagagagatggtccccgag 
     gcctggaggtgctttcccaacaggctgccgctgctgagcaacatcaggcc 
     tgatttctccaaggctcccctggcctacgtgaagcggtggctttggaccg 
     cccgccacccccacagcctgtccgcagcctggtgaccgtgaaaatcgccc 
     cgccagagagcagaggaagcccgacgcccaggccatctgccttcaggtct 
     gtgatgagaaacggagtggcctgttccgttgtgcccaggtctaggccgct 
     gagcagagccctcactcccaggcagagttgtctgaatccttcct 
    个NM_181640 2 
     atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc 
     ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg 
     cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac 
     gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag 
     tgtgaaaggccacgtgaagatgctgcggctggatattatcaactcactgg 
     taacaacagtattcatgctcatcgtatctgtgttggcactgataccagaa 
     accacaacattgacagttggtggaggggtgtttgcacttgtgacagcagt 
     atgctgtcttgccgacggggcccttatttaccggaagcttctgttcaatc 
     ccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagttttg 
     taattttatattactttttagtttgatactaagtattaaacatatttctg 
     tattcttccacatattttctgcagttattttaactcagtataggagctag 
     aggaagagatttccgaagtctgcaccccgcgcagagcactactgtaactt 
     ccaagggagcgctgggagcagcgggatcgggttttccggcacccgggcct 
     gggtggcagggaagaatgtgccgggatccgcctcagggatctttgaatct 
     ctttactgcctggctggccggcagctccg 
    个NM_016951 3 
     atgcgcgcaagagagcgggaagccgagctgggc gagaagtaggggagggc 
     ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg 
     cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac 
     gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag 
     tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta 
     tgaccttttttatcatcgcacaagcccctgaaccatatattgttatcact 
     ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag 
     acttgatcgattaatgaagtggttattttggcctttgcttgatattatca 
     actcactggtaacaacagtattcatgctcatcgtatctgtgttggcactg 
     ataccagaaaccacaacattgacagttggtggaggggtgtttgcacttgt 
     gacagcagtatgctgtcttgccgacggggcccttatttaccggaagcttc 
     tgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaa 
     gaagttttgtaattttatattactttttagtttgatactaagtattaaac 
     atatttctgtattcttccacatattttctgcagttattttaactcagtat 
     aggagctagaggaagagatttccgaagtctgcaccccgcgcagagcacta 
     ctgtaacttccaagggagcgctgggagcagcgggatcgggttttccggca 
     cccgggcctgggtggcagggaagaatgtgccgggatccgcctcagggatc 
     tttgaatctctttactgcctggctggccggcagctccg 
    个NR_002773 1 
     cagcaccacaccagga ccctccagaggctgtgagaaacatcctgcaccca 
     ggtcctctctatctgtttatcattgtctattttgtattctgcattcagaa 
     ccaagagcctgaagacgacccaggagctttagctatggctgtcttcatta 
     ttttgtccctgtttagtgttctggtgacaggcatgggtgaaggtggggct 
     gggagtgagaaaggaggtgagagggaatgtaagctgaaccagcttcccca 
     ttgcccctccgtatctcccagtgcccagccttggacacaccctggccaga 
     gccagctgtttgcagacctgagccgagaggagctgacggctgtgatgcgc 
     tttctgacccagcagctggggccagggctggtggatgcagcccaggccca 
     gccctcggacaactgtgtcttctcagtggagttgcagctgcctcccaagg 
     ctgcagccctggctcacttggacagggggagccccccacctgcccgggag 
     gcactggccatcgtcttctttggcaggcaaccccagcccaacgtgagtga 
     gctggtggtggggccactgcctcacccctcctacatgcgggacgtgactg 
     tggagcgtcatggaggccccctgccctatcaccgacgccccatgttgttc 
     caagagtacctggacatagaccagatgatcttcgacagagagctgcccca 
     ggcttctgggcttctccatcactgttgcttctacaagcgccggggacgga 
     acctggtgacaatgaccacggctccccgtggtctgcaatcaggggaccgg 
     gccacctagtttggcctctactacaacatctcgggcgctgggttcttcct 
     gcaccacgtgggcttggagctgctagtgaaccacaaggcccttgaccctg 
     cccgctgg actatccagaaggtgttctatcaaggccgctactatgacagc 
     ctggcccagctggaggcccagtttgaggccggcctggtgaatgtggtgct 
     gatcccagacaatggcacaggtgggtcctggtccctgaagtcccctgtgc 
     ccccgggtccagctccccctctgcagttccatccccaaggcccccgcttc 
     agtgtccagggaagtcgagtggcctcctcactgtggactttctcctttgg 
     cctcggagcattcagtggcccaaggatctttgacgttcccttccaagggg 
     agagggtggcctatgaagtcagtgtccaggcggccttggccatctatgga 
     ggcaattctccttctgctctacgaagccggtacatagatagtggctttgg 
     cttgggccacttctccacgcccctgacccatggggtggactgcccctacc 
     tggccacctacgtggactggcacttcctttttgagtcccaggccgccaag 
     acaatacgcgatgccttttgtatatttgaacagaaccagggcctccccct 
     gcggcgacaccactcagatctctactcccactactttgggggccttgcgg 
     aaacggtgctggtcatcagatctgtgtctactatgctcaactatgactat 
     gtgtgggatatggtcttccaccctaatggggccatagaaatcagactcca 
     caccaccggctacatcagctcagcattcccctttggtgctgcccagaggt 
     atggaaacaaagtttcagagcacaccctgggcacggtccacacccacagc 
     gcccacttcaaggtggacctggatgtagcaggtaaggcatcctggcagag 
     gcaaaagtgctggaggggtgagctgaagtctccatgcctagctttaaaag 
     ttttcgttgggctgggagcagtagcttatgcctgtaagcccaacactttg 
     ggagactgaggggggtggatcacttgaggtcaggagttcaaaaccagcct 
     ggccaacatggcgaaatcctgtctgtactaaaaatacaaaaattagctgg 
     gcatgggtatgctgtaatcctagctactcgggaggctgaggcaggagaat 
     cacttgaatctgggagtcagaggttgcagtgagctgagattgagccactg 
     cactccatcctgcgtgactgaac 
    个NR_037806 1 
     attcccagtcacccactcactcagaaagccgggagtcatcggacaccttg 
     ctggtcagaggtcctgggggtggttttgaaccatcagagcttggactttt 
     ctgacttccccagcaaggatcttcccacttcctgctccctgtgttcccac 
     cctccagtgttggcacaggcccacccctggctccaccagagccagaagca 
     gaggtagaatcaggcgggccccgggctgcactccgagcagtgttcctggc 
     catctttgctactttcctagagaacccggctgttgccttaaatgtgtgag 
     agggacttggccaaggcaaaagctggggagatgccagtgacaacatacag 
     ttcatgactaggtttaggaattgggcactgagaaaattctcaatatttca 
     gagagtccttcccttatttgggactcttaacacggtatcctcgctagttg 
     gttttaagggaaacactctgctcctgggtgtgagcagaggctctggtctt 
     gccctgtggtttgactctccttagaaccaccgcccaccagaaacataaag 
     gattaaaatcacactaataacccctggatggtcaatctgataataggatc 
     agatttacgtctaccctaattcttaacattgcagctttctctccatctgc 
     agattattcccagtctcccagtaacacgtttctacccagatcctttttca 
     tttccttaagttttgatctccgtcttcctgatgaagcaggcagagctcag 
     aggatcttggcatcacccaccaaagttagctgaaagcagggcactcctgg 
     ataaagcagcttcactcaactctggggaatgctaccattttttttccaaa 
     gtagaaaggaagcacttctgagccagtgaccactgaaagatgaacactct 
     tcctgatcctctcctctagaattcatctcctcctgctagcagccgcgtcc 
     tggaggagcagcggatggggaatccattctgtttcttcctggtgtttagg 
     aagttgccccacacacagattgccccgatgtccaaccagaagaagtgaaa 
     ctgctgctgggtctggagaggtgaagacccgtggccagcttctgttgttg 
     ccatcggccattgctttttgttcgcttgcttttggttttgcaagaagagc 
     ggcctctgtctctgatctgcttcaaatcatcattccatcagtgacagaag 
     tggctgttccatcagtggtcgcagccagttcagctcctgcatccatcccc 
     aagtgttctgagtggaatttgaggcctccccaaccacctaccaaaaaagg 
     agggtgaaatgaaaggaagaagaaaaactcagcattctttcctctgacaa 
     agagtaaaacgacaaggaatatcggcctgaattctcttcccaagaagaaa 
     gaaagcacaccaacgcaggcatttgtcttctgtccatggtgctgaagttt 
     attcactttcaaaccactttcagtaacagcaaattctttagaaaag gaaa 
     atacagggaaagggataaacctcactgacttggaggaaatcaagaggagt 
     gagcacagcatcagaaagccccctggccccagactgcacccgctttcctg 
     gccctaccttgaaatccatcaggtctgcgttggacbggggbb 
     
     
    感谢您抽出宝贵的时间解决我的问题！
    解决方案
    我没有将序列分为三部分，而是通过查找完整序列中所有出现的 $ pattern 并确定模式的哪三分之一来实现的
     
     
     
    内置变量 $-[0] 包含最近的开始的偏移量成功匹配。
     
     
     
    下面的代码可以满足我的要求。它通过累加每个序列（在找到新序列ID或到达文件末尾时结束）并将其传递给 process_seq 子例程来工作。
     
     
     
    该子例程获取序列的长度，并计算字符串每三分之一结尾的偏移量。惯用的 sprintf'％.0f'，$ value 用于将小数值取整到最接近的字符位置。
     
     
     
    对于序列中每次出现的 $ regex ，都会调整 @counts 数组。  @counts 要增加的元素是通过比较匹配项在 $-[0] 中的开始位置来确定的
     
     
     
    处理完每个序列后， @counts 被累加到 @totals 中，以给出所有序列的总体数字。
     
     
     
    程序在以下情况下的输出显示使用示例数据。总计为（9，1，6）。
     使用严格; 
    使用警告； 
     
    我的$ gpat =‘[G] {3,5}’； 
    我的$ npat =‘[A-Z] {1,25}’； 
     my $ pattern = $ gpat。$ npat。$ gpat。$ npat。$ gpat。$ npat。$ gpat; 
    我的$ regex = qr / $ pattern / i; 
     
    打开我的$ fh，<， sequences.txt或死亡$ !; 
     
     my（$ id，$ seq）; 
     my @totals =（0，0，0）; 
     
    而（< $ fh>））{
     
     chomp; 
     
     if（/ ^>（\w +）/）{
     process_seq（$ seq）如果$ id; 
     $ id = $ 1; 
     $ seq =’； 
    打印 $ id\n； 
    } 
     elsif（$ id）{
     $ seq。= $ _; 
     process_seq（$ seq）如果eof; 
    } 
    } 
     
    打印 Total：@ totals\n; 
     
     
     
     sub process_seq {
     
     my $ sequence = shift; 
     my $ length =长度$ sequence; 
     
     my @offsets =地图{sprintf'％.0f'，$ length * $ _ / 3} 1..3; 
     
     my @counts =（0，0，0）; 
     
    而（$ sequence =〜/ $ regex / g）{
    我的$ place = $-[0];我的$ i的
    （0..2）{如果$ place> = $ offsets [$ i]，则
    ； 
     $ counts [$ i] ++; 
    最后； 
    } 
    } 
     
    打印 @ counts\n\n; 
     $ totals [$ _] + = $ counts [$ _]为0..2; 
    } 
          
     输出 
      NR_037701 
     0 0 1 
     
     NM_198399 
     1 0 0 
     
     NR_026816 
     1 0 1 
     
     NR_027917 
     0 0 0 
     
     NR_002777 
     0 0 0 
     
     NR_033769 
     1 0 0 
     
     NM_016326 
     1 0 1 
     
     NM_181641 
     1 0 1 
     
     NM_001144931 
     0 0 0 
     
     NR_029429 
     0 1 0 
     
     NR_026551 
     1 0 0 
     
     NM_181640 
     1 0 1 
     
     NM_016951 
     1 0 1 
     
     NR_002773 
     1 0 0 
     
     NR_037806 
     0 0 0 
     
    总计：9 1 6 
          
     
    I am a Perl newbie, stuck with another bioinformatics problem that requires some help and input.
    

    The problem in brief:
      

    1. I have a file, which has over 40,000 unique DNA sequences. By unique, I mean unique sequence id. I am attaching a portion of it at the end of my post to help you show what it looks like.
      

      2. 

    2. I need to divide each of the 40,000 sequences into 3 parts. So if a particular sequence is 999 character long, each of the 3 parts would have 333 characters.
      

      3. 

    3. I need to look for the following pattern through each of the 3 individual parts:
      

      $gpat = [G]{3,5};
$npat = [A-Z]{1,25};
      
$pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat;
      

      4. 

    4. If $pattern appears in the first of the 3 parts, increase the counter of 'beginning', if $pattern occurs in the 2nd of the 3 parts, increase counter of 'middle' and lastly if the $pattern appears in the 3rd part, increase counter of 'end'.
      

      5. 

    5. Print the counters of 'beginning','middle' and 'end' i.e basically summation of 'beginning','middle','end' for each of the sequences.
      

      Say in 1st sequence, the values are like '2','5','3' respectively and in 2nd sequence, the values are '4','1','6', the final count should be '7,6,9'.
      

      6. 

    The issues I am having:
      

    1. If a particular sequence is split into 3 parts, potential $pattern is lost. eg say on a sequence like :
      2. 

    gggatgtcgatgcatggggatgcatcgatgcggggactagctagcgggatgctacgatggggatgatgataatatcgcggcgcatatatgctagtctatatatta
    

    a split into 3 parts produces following 3 sub-parts,each of 35 character length:
    

    gggatgtcgatgcatggggatgcatcgatgcgggg
    
actagctagcgggatgctacgatggggatgatgat
    
aatatcgcggcgcatatatgctagtctatatatta
    

    Hence, $pattern gets split into the first 2 parts. Is there anyway to say "If $pattern begins in 1st part and ends in 2nd part", increase count of "beginning" ?
    

    ##UPDATE## The following issue has been resolved thanks to the code suggested by Cupidvogel
    

    2.How do I divide a sequence into 3 parts if its length is not divisible by 3? I tried using int, but then the last part is 1-2
characters short.
    

    The following is the code I have written so far.
    

    It reads in the file, displays the header name and sequence, the length into which each sequence will be divided and finally the sequence split into 3 parts which works fine provided the sequence length is divisible by 3, for those which aren't, the final 3rd part is 1-2 characters short.
    #Take Filename from user
print "Please enter file name : ";
$in =<>;
chomp $in;
        
        
open (FASTA,"$in") or die ;
while (<FASTA>)
{
$/=">";
@array = split '\n', $_;
$header=shift @array; # Header of the fasta sequence
print "\n\nNext sequence: \n";
print $header,"\n";
            
            
$seq= join '', @array; # sequence
$seq=~s/\s//g;
$seq=~s/\*//g;
$seq=~s/>//g;
print $seq,"\n\n";

$num = int(length($seq)/3);
@arr = unpack("A$num A$num A*",$seq);
print " New method gives this :", @arr;
print "\nThe first element is :", $arr[0]; 
print "\nThe second element is :",$arr[1]; 
print "\nThe third element is :",$arr[2] ;

            
            
#The following lines of code were originally written to split...
#...the sequence into 3 parts, albeit unsuccessfully                    
#my $split = (length $seq)/3;
#print $split,"\n\n";
         
#my $int = int $split;
#print $int,"\n\n";
         
         
#my @array2 = $seq =~ /(.{$int})/g;
#print join (" ", @array2),"\n\n";
        
#print $array2[0],"\n",$array2[1],"\n",$array2[2];
        
            
}
        
        
exit;

    I have been trying the code I have written so far with the following sample file : sample.fa
    >ABC_123 2
atgtcgatcgatcggcgggcatgcgcgcgcggatg
atatatagcgcgcgctatatagcgcgactctacgc
atgctgctgactagctatagtcgctgactgcgcgt
gggaaaaagggcccgggccccgttttggggatcta
ggggatagctgatgctagcatgcatgctgactgca
>DEF_456 4
gggatgtcgatgcatggggatgcatcgatgcgggg
actagctagcgggatgctacgatggggatgatgat
aatatcgcggcgcatatatgctagtctatatatta
>GHI_789 1
atagctgctagtcgatcggcgcgggtatcgatcgg
ggatcgatcgatcggggatcgatcgggggatcgat

    The actual input file looks like the following:
    >NR_037701 1
aggagctatgaatattaatgaaagtggtcctgatgcatgcatattaaaca
tgcatcttacatatgacacatgttcaccttggggtggagacttaatattt
aaatattgcaatcaggccctatacatcaaaaggtctattcaggacatgaa
ggcactcaagtatgcaatctctgtaaacccgctagaaccagtcatggtcg
gtgggctccttaccaggagaaaattaccgaaatcactcttgtccaatcaa
agctgtagttatggctggtggagttcagttagtcagcatctggtggagct
gcaagtgttttagtattgtttatttagaggccagtgcttatttagctgct
agagaaaaggaaaacttgtggcagttagaacatagtttattcttttaagt
gtagggctgcatgacttaacccttgtttggcatggccttaggtcctgttt
gtaatttggtatcttgttgccacaaagagtgtgtttggtcagtcttatga
cctctattttgacattaatgctggttggttgtgtctaaaccataaaaggg
aggggagtataatgaggtgtgtctgacctcttgtcctgtcatggctggga
actcagtttctaaggtttttctggggtcctctttgccaagagcgtttcta
ttcagttggtggaggggacttaggattttatttttagtttgcagccaggg
tcagtacatttcagtcacccccgcccagccctcctgatcctcctgtcatt
cctcacatcctgtcattgtcagagattttacagatatagagctgaatcat
ttcctgccatctcttttaacacacaggcctcccagatctttctaacccag
gacctacttggaaaggcatgctgggtctcttccacagactttaagctctc
cctacaccagaatttaggtgagtgctttgaggacatgaagctattcctcc
caccaccagtagccttgggctggcccacgccaactgtggagctggagcgg
gagggaggagtacagacatggaattttaattctgtaatccagggcttcag
ttatgtacaacatccatgccatttgatgattccaccactccttttccatc
tcccagaagcctgctttttaatgcccgcttaatattatcagagccgagcc
tggaatcaaactgcctctttcaaaacctgccactatatcctggctttgtg
acctcagccaagttgcttgactattctcagtctcagtttctgcacctgtc
aaatagggtttatgttaacctaactttcagggctgtcaggattaaatgag
catgaaccacataaaatgtttggtgtatagtaagtgtacagtaaatactt
ccattatcagtccctgcaattctatttttcttccttctctacacagcccc
tgtctggctttaaaatgtcctgccctgctttttatgagtggataccccca
gccctatgtggattagcaagttaagtaatgacactcagagacagttccat
ctttgtccataacttgctctgtgatccagtgtgcatcactcaaacagact
atctcttttctcctacaaaacagacagctgcctctcagataatgttgggg
gcataggaggaatgggaagcccgctaagagaacagaagtcaaaaacagtt
gggttctagatgggaggaggtgtgcgtgcacatgtatgtttgtgtttcag
gtcttggaatctcagcaggtcagtcacattgcagtgtgtcgcttcacctg
gctccctcttttaaagattttccttccctctttccaactccctgggtcct
ggatcctccaacagtgtcagggttagatgccttttatgggccacttgcat
tagtgtcctgatagaggcttaatcactgctcagaaactgccttctgccca
ctggcaaagggaggcaggggaaatacatgattctaattaatggtccaggc
agagaggacactcagaatttcaggactgaagagtatacatgtgtgtgatg
gtaaatgggcaaaaatcatcccttggcttctcatgcataatgcatgggca
cacagactcaaaccctctctcacacacatacacatatacattgttattcc
acacacaaggcataatcccagtgtccagtgcacatgcatacacgcacaca
ttcccttcctaggccactgtattgctttcctagggcatcttcttataaga
caccagtcgtataaggagcccaccccactcatctgagcttatcaaccaat
tacattaggaaagactgtatttcctagtaaggtcacattcagtagtactg
agggttgggacttcaacacagctttttgggggatcataattcaacccatg
acagccactgagattattatatctccagagaataaatgtgtggagttaaa
aggaagatacatgtggtacaaggggtggtaaggcaagggtaaaaggggag
ggaggggattgaactagacacagacacatgagcaggactttggggagtgt
gttttatatctgtcagatgcctagaacagcacctgaaatatgggactcaa
tcattttagtccccttctttctataagtgtgtgtgtgcggatatgtgtgc
tagatgttcttgctgtgttaggaggtgataaacatttgtccatgttatat
aggtggaaagggtcagactactaaattgtgaagacatcatctgtctgcat
ttattgagaatgtgaatatgaaacaagctgcaagtattctataaatgttc
actgttattagatattgtatgtctttgtgtccttttattcatgaattctt
gcacattatgaagaaagagtccatgtggtcagtgtcttacccggtgtagg
gtaaatgcacctgatagcaataacttaagcacacctttataatgacccta
tatggcagatgctcctgaatgtgtgtttcgagctagaaaatccgggagtg
gccaatcggagattcgtttcttatctataatagacatctgagcccctggc
ccatcccatgaaacccaggctgtagagaggattgaggccttaagttttgg
gttaaatgacagttgccaggtgtcgctcattagggaaaggggttaagtga
aaatgctgtataaactgcatgatgtttgcaggcagttgtggttttcctgc
ccagcctgccaccaccgggccatgcggatatgttgtccagcccaacacca
caggaccatttctgtatgtaagacaattctatccagcccgccacctctgg
actccctcccctgtatgtaagccctcaataaaaccccacgtctcttttgc
tggcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
aaa
>NM_198399 1
aacagattttaactctgaaaagccatttccagtgtctatagactattgtg
agcctggagaagtagcatttagttgggatagcttcactagagctgcctgc
caaagacttccttccacaggatcttgtcgcaccagcaactgacaggagct
tgggagctcgggagcttgggagagggcttatgtttttaataatgtagctg
tcagttcgaagcctggaaatgttgaccctcaaagggcataaaatcttgtt
attttaatttgcatctgggagaatgtctgagcaaggagacctgaatcagg
caatagcagaggaaggagggactgagcaggagacggccactccagagaac
ggcattgttaaatcagaaagtctggatgaagaggagaaactggaactgca
gaggcggctggaggctcagaatcaagaaagaagaaaatccaagtcaggag
caggaaaaggtaaactgactcgcagccttgctgtctgtgaggaatcttct
gccagaccaggaggtgaaagtcttcaggatcagactctctgaaaactgca
aatggaaaggaattcaaaagaatttagattaaaagttaaataaaaagtag
gcacagtagtgctgaattttcctcaaaggctctcttttgataaggctgaa
ccaaatataatcccaagtatcctctctccttccttgttggagatgtctta
cctctcagctccccaaaatgcacttgcctataagaaacacaattgctggt
tcatatgaaacttaggaaatagtgaataaggtgcatttaactttggagaa
atacttttatggctttggtggagatttctcaatactgcaaaagttgtcca
gaaatgaatctgagctgatggtgactttaagttaatattattaatatatc
actgcatatttttacccttatttttgctccttacagcaagattagtaggt
tataaaaatttaaatttaaacaaaattatttcatgacaaaatgggaaact
tcacatcatacttatttttgtttgcctttcaggcatcatattagctttta
taaaaaatggtcttgctgctgaaattgtacttattttatcagaggctggg
tgcagtcaagacaaaagtaaaatggtttacctgagcccaggggagggaaa
attgattaagatatcattatttttgtttggtttggttttgcttttttcct
cttactttaattgaaatactctgaattcccctcatggaaacagagagcat
tgagagcactttctttaaaaggaccaaaaataaattcctaatagattttg
tcctaagagagtgtttttttttctagcatcattttctttacatgccactc
atgtcataaggcatggacaggctatctttcagtggccattactatgtttc
gtacacatgctttattttacttgggctctgagaaatgtgtggctttcctt
cagcattttatttgtgcttctctttttaatggagattgaaaagggagaat
aatgtgaatatcacggcttatattattaaatgttgattgatggcttgtaa
tgtactgcacacaatatatgttaactctgcagaatgacagaccctgggag
aagtaatgccccagttgtcccccactcctaatgccaggcagagaaggaca
gcctttatagacttaatctgctttttgtcccatttgacaaggtaccagga
ggaaattttttaagggatcaactgtatcacagtgcccactctggacctaa
gtctagtgtatccatacaattggtgcagagaaataaggtgtaaatggtgc
tttgttcctgctggttccaagctcagaaaccaagactagctttgtaggag
agaatgagagcctgcaagcctctctttggattggctgaggagtggtggga
gcagggggttgatagaaaacatccagacacacatataagcaagtggccgt
gctacctttttagagaataaagaaacagacttttgagtttatatgcaatg
ccttcattaggtaccaccggcacttacaaaatgtgcggactgaatcccag
agaacactggcagatgtatacagtatatggattgtatcgcttccccaatg
tttgtaaattcacagtatttggaaaactgccttcattttccagtgtggga
aaaactcttgctacctgtattacttgatctcagacccatacctgatggtt
cagtctgtccttaagttaaaagaattttgcttttctaatgttatactatt
tacctgtcagtgtattactgcaacttgaatcactcttttactgttgttgg
atataaacttatcctgtaccaatgtatttattaacacttgtattttatta
ttgagcatatcaataaaaatattaaaaaataacagattgttttttaccaa
aaaaaaaaaaaaa
>NR_026816 1
caacccactctctgtgctatgacttcattactctttcccagcccagccct
gggcaagccccttacgaagtctcaggctacctggatgaccaccctttctt
atgatgctgcaaggagggcaggtgggcagagccccgtgcatcctgggctc
aggccagggacccaagagcttgggagaagctggttctcagactgaaggcc
agagcccagcaccttgtcaccatcccggggagcatcatggcacacaacaa
ccagagccaaggctacagctagagagttgactcctctatttgagattgac
aggcctcggaagtcaaaataagtggtttcctagaccgggtcgagagcaag
tctctattggtcccaactgagttttttcagctggtttttcaaccaaacag
cacctcatctcccagtgaggggaagggaaggctgggctgagagcagcaag
gctgctcatctcacctctccccacccagccatgccagccgcctcacctgg
tggggagaggtgggcctcacctgggtcccctggcagtgctctgtgaaggg
tcttgacattgcactgtaataataaaggtgtgtgtgaagtatcaaaaaaa
>NR_027917 1
atgaagatgattgagcagcacaatcaggaatacagggaagggaaacacag
cttcacaatggccatgaacgcctttggagaaatgaccagtgaagaattca
ggcaggtggtgaatggctttcaaaaccagaagcacaggaaggggaaagtg
ctccaggaacctctgcttcatgacatccgcaaatctgtggattggagaga
gaaaggctacgtgactcctgtgaaggatcagtgcagctggggctctgtaa
ggacagatgttaggaaaactgagaaactagtttcactgagtgtgcagacc
tggtggactgctctaggcttcaaggcaatgttggctgcatttttggagaa
ccattattttgcttccagtatgttgccgacaatggaggcctggactctga
ggaatccttttcatatgaagaaaagctctggagactggaaagtccaaggt
cacagaggtgcatctggtgagagccttcttgctagtggggaatctcagca
gagtcctgaggtggcacagtattctgggaagcatcaagtgcagtgtcatc
ttatcgaggaggctctgcagatgctaagtggtggggatgaggatcacgat
gaagacaaatggccccatgacatgaggaatcatctggctggagaggccca
ggtgtag
>NR_002777 3
cttgtcctttcagaagatcagagacaagtgatatctgtgccaatttggcc
ttttcagtgttataattatggtgtcttgggatcccaatatttctcctaat
gtttccctgatgtgatactttgagagcccaggatgccagtacaataattg
aaattcacaaatgtctggtatcttgtccctcgtgccccatatattatctg
tggtttcggagagctcacttgtctcttatcttcagaaatgacagcacatg
aaatgttgtttggagccactgtcacatcaactgtagaaaaattaacaggt
cagctaagggatataatgtaactttatttgtgatatgagagaaatcttga
taaagacttgagagaaaactgggaggaaccttgtttagaagttataagga
ggggtaagttatgtgtgtcttggaaggagaatcataaatcttaaaacatg
agcctaatagagaacataaaattctaaaagataaagataataataatgat
aagccgcagggtggcttatgataatgtgacttctccttaccccagtagcg
tcggacatctgtcagctctgaaatgataaaaatgcacaatattgaataca
aacaaaggagtcagcactgaaattcattttctctccagattagggaaaga
gtaggtatgccctatggtagggcagtaaattgctgaatgatgagatgaaa
cagccacctagccatttcccattaaatataatcccatcagcagcagacaa
tatctatcctcccctatcccctctatccatatttggaaactgcaccctct
tccctatttagcaccctaacaccacttgaattccataaccctgttgttga
tctagctctcctcacctctaaacacttctagcattcctttcagatcagga
gctcgaaacactctcctttgattttttggaaaagtttctggcttcttcaa
ggtcacgttctccgtcctaagaattaaaaaaaaaaaaaaaaacttccaaa
cctttgaccttgtgtccgtggaacacccctgacttcctatcatttcaacc
cattgaggcacttgaactctcttcttggggatcctgagaagggagagtgc
aaactcttgaccctggaggcaaacaaaatgttctcatgtttgccttccca
cttactttctgtgagaacgtgggaagatcttaacctctcagaagcacagt
ttcttccttctaaaatgaaataattaacctctccctgtctacattcttaa
actcataggacataaaaaaaaaaaaaa
>NR_033769 1
ggcctctggcgggcctccagccagttagaccatttgactaggacgtgtgc
agctcagccagccacagaactggaatttttcaggagcagggggagcatgg
agtttggactttgctgagcaactgaagtggagcgcagagcttgctcgctt
aggagagggcagcatggatggcaaacaagggggcatggatgggagcaagc
ccacggggccaagagactctcctgacaccaggcttctttcaaacccattg
atgggtgattctgtgtctgattggtctcctatgcctgaagctgcaatcta
cggacatcagctgtctctgaggaacctcatcagccacgggtggcttgtga
acatcatcatggcagatcatgtttccccactccatgaagcctgtctcaga
ggtcatccctctcgtgtaaagattttattaaagcatggagctcaggtgaa
tggcgtgacaacagactggcacactccactgtttaatgtttgtatcagca
gcagctgggattatgcttctgcagcatggagccagcgttcaacctgagag
tgatctggcatcccccgtccatgaagctgctaggagaggccacgtggagt
gtgtcgactctcttacagcttataggggcaaaaatgaccataacatcagc
cacgtgggcacttcactgtatttggcttgtgaaaaccagcagatagcctg
tgtcaagaagcttctggagtcaggagcagacctgaacccagggagaggtt
ccccacttcatgcagtggccttcatgaaggccctcatgaaggattcccca
cttcatgcagtggccaggacagccagtgaagagctggcctgcctgctcat
ggattttggagcagacacccaggccaagaatgctgaaggcaaatgtcatg
tggagctggtgcctccagagagccctttgatccagctcttcttggagaga
gaagggcccccttcttttgatgcagttatgcctagaaatcagaagggctt
tggaatccagcagcatcataagataaccaaagtcgtcctcccagaggatc
tgaaatggtttctcctacatctttgtatgtatcaatggaatggattcaca
aacaatgtgaaaacattattgagtgttgtagccactagaattttaaaatc
aagttaggtttatagagtttgactagttttttcgattagatttgtattag
ttataaatttgttcatagagtttgactaattttttcgattagatttgtat
ttgttaaactctgaagccagagtttaaacacactgcatacgtttgtatga
ttagttagaaggcatgaagacttttttccctgcttggagactgtctaaaa
taacagctattgttttgcatatccactgcaggccaagcactttcagcatc
atctaattcagccctcacagcaactgggtcaatctgtccaatttcccagg
gcaaggatagaggagtcagattcaaatacaggttttctgacgttaactta
tgtgatgatttgatcaaagcaggattttccagcatcactatccttgttcc
atctctgctatatgggaatgaaaataaagaaatgtatttcaaaaaaataa
aaagaaaagaaaaacagagacggtc
>NM_016326 3
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggtgtttgcacttgtgacag
cagtatgctgtcttgccgacggggcccttatttaccggaagcttctgttc
aatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagt
tttgtaattttatattactttttagtttgatactaagtattaaacatatt
tctgtattcttccacatattttctgcagttattttaactcagtataggag
ctagaggaagagatttccgaagtctgcaccccgcgcagagcactactgta
acttccaagggagcgctgggagcagcgggatcgggttttccggcacccgg
gcctgggtggcagggaagaatgtgccgggatccgcctcagggatctttga
atctctttactgcctggctggccggcagctccg
>NM_181641 2
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta
tgaccttttttatcatcgcacaagcccctgaaccatatattgttatcact
ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag
acttgatcgattaatgaagtggttattttggcctttgcttgtgtttgcac
ttgtgacagcagtatgctgtcttgccgacggggcccttatttaccggaag
cttctgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaa
aaaagaagttttgtaattttatattactttttagtttgatactaagtatt
aaacatatttctgtattcttccacatattttctgcagttattttaactca
gtataggagctagaggaagagatttccgaagtctgcaccccgcgcagagc
actactgtaacttccaagggagcgctgggagcagcgggatcgggttttcc
ggcacccgggcctgggtggcagggaagaatgtgccgggatccgcctcagg
gatctttgaatctctttactgcctggctggccggcagctccg
>NM_001144931 1
gtttccgttcctctgcccgccatgccgttcctagagctgcacacgaattt
ccccgccaaccgagtgcccgcggggctggagaaacggctgtgcgccgtcg
ctgcctccatcttgggcaaacctgcagaccttgtgaacgtgacggtacgg
ccgggcctggccagggcgctgagcgggtccaccgagccctgcgcgcagct
gtccatctcctccatcggcgtagtgggcaccgccgaggacaaccgcagcc
acagtgcccacttctttgagtttctcaccaaggagctagccctgggccag
gaccggtgcgcaggggtagtaggcccggaatattattctaaaacacaatc
agagtactccattcctgctaacagtttaaagccaaacacctaggcaggcc
atttaggcttctgaatgactgggtcttgaccaggagagctgctgtctagg
ttttctcttcctgaccagttcctcaagagaaatgcaaaactagtgattaa
cagtaagagtcaggcagggcgcggtggctcacgcctgtaatcccagcact
ttgggaggccgag
>NR_029429 1
ggacaccaccccaaaatttcctagtcctctttgatacgggttcctccaat
ctgtagctgccctccatctactgccagagccaagtctgctccaatcacaa
caggttcaatcccagcctgtcctccaccttcagaaacgatggacaaacct
atggactatcctatgggagtggcagcctgagtgtgttcctgggctatgac
actgtgactgttcataacatcgttgtcaataaccaggagtttggcctgag
tgagaatgagcccagcgaccccttttactattcagactttgacgggatcc
tgggaatggcctacccaaacatggcagaggggaattcccctacagtaatg
caggggatgctgcagcagagccagcttactcagcccgtcttcagcttcta
cttcacctgccagccaacccgccagtattgtggagagctcatccttggag
gtgtggaccccaactttattctggtcagatcatctggacccctgtcagcc
cgtaactgtactggcagattgccatcgaggaatttgccatcggtaaccag
gccactggcttgtgctctgagggttgccaggccattgtggataccgagac
cttcctgc
>NR_026551 1
tgtggcctgagaggacggccaggactggccagaaaagagagggacgtggc
taaacgtgagggggcgtggccaagatggccgcgtgcgggatcctcgggta
ccgggagcgaacgaggaggttctggctcagtgcatccactctgggagagc
gtggacctggttcctgggggcgatcgccagtcacccatcaacattcggtg
gagggacagtgtttatgatcccggcttaaaaccactgaccatctcttatg
acccagccacctgcctccacgtctggaataatgggtactctttcctcgtg
gaatttgaagattctacagataaatcagctgcacttagtgcattggaacg
cagtcaaatttgaaaactttgaggatgcagcactggaagaaaatggtttg
gctgtgataggagtatttttaaagatttcggaaacttctggcagcccagt
gtctactggaaggcccaagccgcttgccagaaagctgcgccccgcccaaa
agcactgggttctgcagtccaggcccttcctcagctcccaggtccaggag
aactgcaaggtcacctacttccacaggaagcactgggtccgcatccggcc
cctccgcaccactcctcccagctgggactacacccgcatctgcatccaga
gagagatggtccccgcccgcatccgcgtcctgagagagatggtccccgag
gcctggaggtgctttcccaacaggctgccgctgctgagcaacatcaggcc
tgatttctccaaggctcccctggcctacgtgaagcggtggctttggaccg
cccgccacccccacagcctgtccgcagcctggtgaccgtgaaaatcgccc
cgccagagagcagaggaagcccgacgcccaggccatctgccttcaggtct
gtgatgagaaacggagtggcctgttccgttgtgcccaggtctaggccgct
gagcagagccctcactcccaggcagagttgtctgaatccttcct
>NM_181640 2
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggatattatcaactcactgg
taacaacagtattcatgctcatcgtatctgtgttggcactgataccagaa
accacaacattgacagttggtggaggggtgtttgcacttgtgacagcagt
atgctgtcttgccgacggggcccttatttaccggaagcttctgttcaatc
ccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagttttg
taattttatattactttttagtttgatactaagtattaaacatatttctg
tattcttccacatattttctgcagttattttaactcagtataggagctag
aggaagagatttccgaagtctgcaccccgcgcagagcactactgtaactt
ccaagggagcgctgggagcagcgggatcgggttttccggcacccgggcct
gggtggcagggaagaatgtgccgggatccgcctcagggatctttgaatct
ctttactgcctggctggccggcagctccg
>NM_016951 3
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta
tgaccttttttatcatcgcacaagcccctgaaccatatattgttatcact
ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag
acttgatcgattaatgaagtggttattttggcctttgcttgatattatca
actcactggtaacaacagtattcatgctcatcgtatctgtgttggcactg
ataccagaaaccacaacattgacagttggtggaggggtgtttgcacttgt
gacagcagtatgctgtcttgccgacggggcccttatttaccggaagcttc
tgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaa
gaagttttgtaattttatattactttttagtttgatactaagtattaaac
atatttctgtattcttccacatattttctgcagttattttaactcagtat
aggagctagaggaagagatttccgaagtctgcaccccgcgcagagcacta
ctgtaacttccaagggagcgctgggagcagcgggatcgggttttccggca
cccgggcctgggtggcagggaagaatgtgccgggatccgcctcagggatc
tttgaatctctttactgcctggctggccggcagctccg
>NR_002773 1
cagcaccacaccaggaccctccagaggctgtgagaaacatcctgcaccca
ggtcctctctatctgtttatcattgtctattttgtattctgcattcagaa
ccaagagcctgaagacgacccaggagctttagctatggctgtcttcatta
ttttgtccctgtttagtgttctggtgacaggcatgggtgaaggtggggct
gggagtgagaaaggaggtgagagggaatgtaagctgaaccagcttcccca
ttgcccctccgtatctcccagtgcccagccttggacacaccctggccaga
gccagctgtttgcagacctgagccgagaggagctgacggctgtgatgcgc
tttctgacccagcagctggggccagggctggtggatgcagcccaggccca
gccctcggacaactgtgtcttctcagtggagttgcagctgcctcccaagg
ctgcagccctggctcacttggacagggggagccccccacctgcccgggag
gcactggccatcgtcttctttggcaggcaaccccagcccaacgtgagtga
gctggtggtggggccactgcctcacccctcctacatgcgggacgtgactg
tggagcgtcatggaggccccctgccctatcaccgacgccccatgttgttc
caagagtacctggacatagaccagatgatcttcgacagagagctgcccca
ggcttctgggcttctccatcactgttgcttctacaagcgccggggacgga
acctggtgacaatgaccacggctccccgtggtctgcaatcaggggaccgg
gccacctagtttggcctctactacaacatctcgggcgctgggttcttcct
gcaccacgtgggcttggagctgctagtgaaccacaaggcccttgaccctg
cccgctggactatccagaaggtgttctatcaaggccgctactatgacagc
ctggcccagctggaggcccagtttgaggccggcctggtgaatgtggtgct
gatcccagacaatggcacaggtgggtcctggtccctgaagtcccctgtgc
ccccgggtccagctccccctctgcagttccatccccaaggcccccgcttc
agtgtccagggaagtcgagtggcctcctcactgtggactttctcctttgg
cctcggagcattcagtggcccaaggatctttgacgttcccttccaagggg
agagggtggcctatgaagtcagtgtccaggcggccttggccatctatgga
ggcaattctccttctgctctacgaagccggtacatagatagtggctttgg
cttgggccacttctccacgcccctgacccatggggtggactgcccctacc
tggccacctacgtggactggcacttcctttttgagtcccaggccgccaag
acaatacgcgatgccttttgtatatttgaacagaaccagggcctccccct
gcggcgacaccactcagatctctactcccactactttgggggccttgcgg
aaacggtgctggtcatcagatctgtgtctactatgctcaactatgactat
gtgtgggatatggtcttccaccctaatggggccatagaaatcagactcca
caccaccggctacatcagctcagcattcccctttggtgctgcccagaggt
atggaaacaaagtttcagagcacaccctgggcacggtccacacccacagc
gcccacttcaaggtggacctggatgtagcaggtaaggcatcctggcagag
gcaaaagtgctggaggggtgagctgaagtctccatgcctagctttaaaag
ttttcgttgggctgggagcagtagcttatgcctgtaagcccaacactttg
ggagactgaggggggtggatcacttgaggtcaggagttcaaaaccagcct
ggccaacatggcgaaatcctgtctgtactaaaaatacaaaaattagctgg
gcatgggtatgctgtaatcctagctactcgggaggctgaggcaggagaat
cacttgaatctgggagtcagaggttgcagtgagctgagattgagccactg
cactccatcctgcgtgactgaac
>NR_037806 1
attcccagtcacccactcactcagaaagccgggagtcatcggacaccttg
ctggtcagaggtcctgggggtggttttgaaccatcagagcttggactttt
ctgacttccccagcaaggatcttcccacttcctgctccctgtgttcccac
cctccagtgttggcacaggcccacccctggctccaccagagccagaagca
gaggtagaatcaggcgggccccgggctgcactccgagcagtgttcctggc
catctttgctactttcctagagaacccggctgttgccttaaatgtgtgag
agggacttggccaaggcaaaagctggggagatgccagtgacaacatacag
ttcatgactaggtttaggaattgggcactgagaaaattctcaatatttca
gagagtccttcccttatttgggactcttaacacggtatcctcgctagttg
gttttaagggaaacactctgctcctgggtgtgagcagaggctctggtctt
gccctgtggtttgactctccttagaaccaccgcccaccagaaacataaag
gattaaaatcacactaataacccctggatggtcaatctgataataggatc
agatttacgtctaccctaattcttaacattgcagctttctctccatctgc
agattattcccagtctcccagtaacacgtttctacccagatcctttttca
tttccttaagttttgatctccgtcttcctgatgaagcaggcagagctcag
aggatcttggcatcacccaccaaagttagctgaaagcagggcactcctgg
ataaagcagcttcactcaactctggggaatgctaccattttttttccaaa
gtagaaaggaagcacttctgagccagtgaccactgaaagatgaacactct
tcctgatcctctcctctagaattcatctcctcctgctagcagccgcgtcc
tggaggagcagcggatggggaatccattctgtttcttcctggtgtttagg
aagttgccccacacacagattgccccgatgtccaaccagaagaagtgaaa
ctgctgctgggtctggagaggtgaagacccgtggccagcttctgttgttg
ccatcggccattgctttttgttcgcttgcttttggttttgcaagaagagc
ggcctctgtctctgatctgcttcaaatcatcattccatcagtgacagaag
tggctgttccatcagtggtcgcagccagttcagctcctgcatccatcccc
aagtgttctgagtggaatttgaggcctccccaaccacctaccaaaaaagg
agggtgaaatgaaaggaagaagaaaaactcagcattctttcctctgacaa
agagtaaaacgacaaggaatatcggcctgaattctcttcccaagaagaaa
gaaagcacaccaacgcaggcatttgtcttctgtccatggtgctgaagttt
attcactttcaaaccactttcagtaacagcaaattctttagaaaaggaaa
atacagggaaagggataaacctcactgacttggaggaaatcaagaggagt
gagcacagcatcagaaagccccctggccccagactgcacccgctttcctg
gccctaccttgaaatccatcaggtctgcgttggacacggcattgtacatg
ggattagctctg

    Any help and input would be deeply appreciated.
    

    Thank you for taking the time to go through my problem!
     解决方案 
    Rather than splitting the sequence into three parts, the way I see this working is to find all occurrences of $pattern in the complete sequence and determine in which third the pattern starts.
    


    The built-in variable $-[0] contains the offset of the start of the most recent successful match.
    


    The code below does what I think you want. It works by accumulating each sequence (which ends either when a new sequence ID is found or the end of file is reached) and passing it to the process_seq subroutine.
    


    The subroutine takes the length of the sequence and caclulates the offset of the end of each third of the string. The idiomatic sprintf '%.0f', $value is used to round fractional values to the nearest character position.
    


    The @counts array is adjusted for each occurrence of $regex in the sequence. The element of @counts to be incremented is established by comparing the starting position of the match in $-[0] with the end offset of each of the three segments of the sequence.
    


    Once each sequence has been processed the values in @counts are accumulated into @totals to give overall figures for all sequences.
    


    The output of the program when using your sample data is shown. The grand total is (9, 1, 6).
    use strict;
use warnings;

my $gpat = '[G]{3,5}';
my $npat = '[A-Z]{1,25}';
my $pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat; 
my $regex = qr/$pattern/i;

open my $fh, '<', 'sequences.txt' or die $!;

my ($id, $seq);
my @totals = (0, 0, 0);

while (<$fh>) {

  chomp;

  if (/^>(\w+)/) {
    process_seq($seq) if $id;
    $id = $1;
    $seq = '';
    print "$id\n";
  }
  elsif ($id) {
    $seq .= $_;
    process_seq($seq) if eof;
  }
}

print "Total: @totals\n";



sub process_seq {

  my $sequence = shift;
  my $length = length $sequence;

  my @offsets = map {sprintf '%.0f', $length * $_ / 3} 1..3;

  my @counts = (0, 0, 0);

  while ($sequence =~ /$regex/g) {
    my $place = $-[0];
    for my $i (0..2) {
      next if $place >= $offsets[$i];
      $counts[$i]++;
      last;
    }
  }

  print "@counts\n\n";
  $totals[$_] += $counts[$_] for 0..2;
}

    output
    NR_037701
0 0 1

NM_198399
1 0 0

NR_026816
1 0 1

NR_027917
0 0 0

NR_002777
0 0 0

NR_033769
1 0 0

NM_016326
1 0 1

NM_181641
1 0 1

NM_001144931
0 0 0

NR_029429
0 1 0

NR_026551
1 0 0

NM_181640
1 0 1

NM_016951
1 0 1

NR_002773
1 0 0

NR_037806
0 0 0

Total: 9 1 6

    

                        
    这篇关于Perl：在数组元素中搜索模式的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！
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