Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1655

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 14461
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30


Found at i:1635 original size:40 final size:40

Alignment explanation


    Indices: 1551--1694  Score: 134
    Period size: 40  Copynumber: 3.6  Consensus size: 40

       1541 TTGAATGCTG

                 *                       *            
       1551 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACT-AT
          1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT

                                  *           *  *    
       1590 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
          1 -TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT

                 **              *                  
       1631 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
          1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT

                 **                 
       1671 TCCGGGTTAAGTCCCGAAGGCATT
          1 TCCGGACTAAGTCCCGAAGGCATT

       1695 GAATGAGTTA


Statistics
Matches: 87,  Mismatches: 12, Indels: 10
        0.80            0.11        0.09

Matches are distributed among these distances:
  39    1  0.01
  40   74  0.85
  41   12  0.14

ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28


Consensus pattern (40 bp):   
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT

Found at i:9477 original size:40 final size:40

Alignment explanation


    Indices: 9376--9517  Score: 123
    Period size: 40  Copynumber: 3.5  Consensus size: 40

       9366 TTGAATGCTG

                  *                      *            
       9376 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTA-AGTGACT-AT
          1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGA-T-ACTAAT

                   *                                   
       9415 ATCCGGACTTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAT
          1 -TCCGG-GTTAAG-TCCCGAAGGCCTTTGTGCGAGATACTAAT

                                 *  *         **    *
       9457 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TTTTAAAA
          1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACT-AAT

                                 
       9497 TCCGGGTTAAGTCCCGAAGGC
          1 TCCGGGTTAAGTCCCGAAGGC

       9518 ATTGAATGAG


Statistics
Matches: 86,  Mismatches: 9, Indels: 14
        0.79            0.08        0.13

Matches are distributed among these distances:
  39    3  0.03
  40   50  0.58
  41   19  0.22
  42   13  0.15
  43    1  0.01

ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26


Consensus pattern (40 bp):   
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT

Found at i:9541 original size:39 final size:39

Alignment explanation


    Indices: 9457--9567  Score: 116
    Period size: 40  Copynumber: 2.8  Consensus size: 39

       9447 AGATACTAAT

                                      **      *     
       9457 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
          1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA

                                       *         ** 
       9497 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
          1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA

                  *  *                      
       9537 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
          1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG

       9568 GAGCTATATC


Statistics
Matches: 60,  Mismatches: 9, Indels: 4
        0.82            0.12        0.05

Matches are distributed among these distances:
  39   25  0.42
  40   35  0.58

ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24


Consensus pattern (39 bp):   
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA

Found at i:13703 original size:40 final size:40

Alignment explanation


    Indices: 13590--13796  Score: 264
    Period size: 40  Copynumber: 5.3  Consensus size: 40

      13580 CCCTCGTTCA

                          *  *          **         *
      13590 AATGCCTTCGGGACATAGCCCGG-TTTAGTAACT--CACC
          1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG

                                                    
      13627 AATGCCTTC-GGACTTAACCCGGATTTAACAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG

                                                     
      13666 AATGCCTTCGGGAC-TAACCCGGATTTAACAACTTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAACAAC-TCGCACG

                                                    
      13706 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG

                                         ** *       *
      13746 AATG-CTTCGGGACTTAAACCCGGATTTAGTATCTCGCACA
          1 AATGCCTTCGGGACTT-AACCCGGATTTAACAACTCGCACG

              *        
      13786 AAGGCCTTCGG
          1 AATGCCTTCGG

      13797 ATCTTAGTCC


Statistics
Matches: 152,  Mismatches: 10, Indels: 12
        0.87            0.06        0.07

Matches are distributed among these distances:
  36   11  0.07
  37   17  0.11
  39   41  0.27
  40   59  0.39
  41   24  0.16

ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24


Consensus pattern (40 bp):   
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG

Done.