Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3684

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: 33231
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31


Found at i:3378 original size:19 final size:21

Alignment explanation


    Indices: 3351--3390  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3341 GTGTATATGC

                                 
       3351 ATATCTGAA-T-TGAATTTGT
          1 ATATCTGAATTATGAATTTGT

                *                
       3370 ATATGTGAATTATGAATTTGT
          1 ATATCTGAATTATGAATTTGT

       3391 TATTATATGA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19    8  0.44
  20    1  0.06
  21    9  0.50

ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47


Consensus pattern (21 bp):   
ATATCTGAATTATGAATTTGT

Found at i:15683 original size:40 final size:39

Alignment explanation


    Indices: 15526--15706  Score: 294
    Period size: 39  Copynumber: 4.6  Consensus size: 39

      15516 ACTACTTGCT

                                    *              
      15526 CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCA

                                                   
      15565 CAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCA
          1 CAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCA

                                                   
      15604 CAAATGCCTTCGGACTTAG-CCGGATATAGTAACTCGCA
          1 CAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCA

                                             *   *   
      15642 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCA
          1 CAAATGCCTTC-GGACTTAGCCCGGATA-TAGTAACTCGCA

                                     
      15682 CAAATGCCTTCGGGACTTAGCCCGG
          1 CAAATGCCTTC-GGACTTAGCCCGG

      15707 TTATCATCCG


Statistics
Matches: 136,  Mismatches: 3, Indels: 5
        0.94            0.02        0.03

Matches are distributed among these distances:
  38   30  0.22
  39   66  0.49
  40   40  0.29

ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23


Consensus pattern (39 bp):   
CAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCA

Found at i:18339 original size:40 final size:40

Alignment explanation


    Indices: 18253--18444  Score: 271
    Period size: 40  Copynumber: 4.8  Consensus size: 40

      18243 GGATATAGCT

                  *                        *        
      18253 ACTCGCCCAAATGCCTTCGGGAC-TAGCCCGATCATAGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTCATAGTA

                                      *             
      18292 ACTCGCACAAATGCCTTCGGGACTTAACCCGGTCATAGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTCATAGTA

                                      *      *      
      18332 ACTCGCACAAATGCCTTCGGGACTTAACCCGGTTATAGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTCATAGTA

                 *    *                        *    *
      18372 ACTCGTACAATTGCCTTCGGGACTTAGCCCGGAT-TTAGTC
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TCATAGTA

               *                             
      18412 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGT
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGT

      18445 TATTATCCGA


Statistics
Matches: 139,  Mismatches: 12, Indels: 4
        0.90            0.08        0.03

Matches are distributed among these distances:
  39   23  0.17
  40  115  0.83
  41    1  0.01

ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24


Consensus pattern (40 bp):   
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTCATAGTA

Found at i:26916 original size:40 final size:40

Alignment explanation


    Indices: 26870--27014  Score: 211
    Period size: 40  Copynumber: 3.6  Consensus size: 40

      26860 ACTACTTGCT

                      *         *    *              
      26870 CAAATGCCTTTGGGACTTAGTCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                                                 *  
      26910 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                                      *      *   *   
      26950 CAAATGCCTTCGGGACTTAGCCC-GAAATTAGTCACTAGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA

                                     
      26990 CAAATGCCTTCGGGACTTAGCCCGG
          1 CAAATGCCTTCGGGACTTAGCCCGG

      27015 TTATCATCCG


Statistics
Matches: 95,  Mismatches: 8, Indels: 3
        0.90            0.08        0.03

Matches are distributed among these distances:
  39    3  0.03
  40   91  0.96
  41    1  0.01

ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

Found at i:32360 original size:44 final size:41

Alignment explanation


    Indices: 32312--32406  Score: 93
    Period size: 44  Copynumber: 2.2  Consensus size: 41

      32302 AAATGTTTAG

                         *                           *   
      32312 CCAAAGCTATAATGA-TATCACACACTTAGTGGCATCACATTAAA
          1 CCAAAGCTAT-ATCAGTATCACACACTTAGT-GC--CACATAAAA

                 *    *       **                     
      32356 CCAAAACTATCTCAGTATTGCACACTTAGTGCCACATAAAA
          1 CCAAAGCTATATCAGTATCACACACTTAGTGCCACATAAAA

                      
      32397 CCAAAGCTAT
          1 CCAAAGCTAT

      32407 TACAATTCGT


Statistics
Matches: 43,  Mismatches: 7, Indels: 5
        0.78            0.13        0.09

Matches are distributed among these distances:
  41   17  0.40
  43    4  0.09
  44   22  0.51

ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24


Consensus pattern (41 bp):   
CCAAAGCTATATCAGTATCACACACTTAGTGCCACATAAAA
Done.