Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2066

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: 9232
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30


Found at i:7419 original size:39 final size:38

Alignment explanation


    Indices: 7334--7517  Score: 196
    Period size: 39  Copynumber: 4.7  Consensus size: 38

       7324 ACTACTTGCT

                                                     
       7334 CAAATGCCTTCGGGACTT-GACCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAG-CCCGGTTA-A-TAACTCGCA

                             *                     
       7374 CAAATGCCTTCGGGACTCAGCCCGGTTCAATAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTT-AATAACTCGCA

             *                                      
       7413 CCAATGCCTTC-GGACTTAG-CCGGATATAATAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGG-T-TAATAACTCGCA

               *           *              * *   *   
       7451 CAATTGCCTTCGGG-TTTAGCCCGGAATTAGTCACTAGCA
          1 CAAATGCCTTCGGGACTTAGCCCGG--TTAATAACTCGCA

                      *                 
       7490 CAAATGCCTTTGGGACTTAGCCCGGTTA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTA

       7518 TCATCCGATA


Statistics
Matches: 124,  Mismatches: 12, Indels: 18
        0.81            0.08        0.12

Matches are distributed among these distances:
  37    4  0.03
  38   35  0.28
  39   47  0.38
  40   36  0.29
  41    2  0.02

ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25


Consensus pattern (38 bp):   
CAAATGCCTTCGGGACTTAGCCCGGTTAATAACTCGCA

Found at i:7470 original size:38 final size:39

Alignment explanation


    Indices: 7309--7511  Score: 166
    Period size: 39  Copynumber: 5.2  Consensus size: 39

       7299 TACCTTCGAA

                                  *  *              
       7309 ATTTAGCCGGATATAACT-ACTTGCTCAAATGCCTTCGGG
          1 ATTTAGCCGGATATAA-TAACTCGCACAAATGCCTTCGGG

                * *    *    *                       
       7348 ACTTGACCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
          1 A-TTTAGCCGGATATAATAACTCGCACAAATGCCTTCGGG

             * *                        *            
       7388 ACTCAGCCCGG-T-TCAATAACTCGCACCAATGCCTTC-GG
          1 ATTTAG-CCGGATAT-AATAACTCGCACAAATGCCTTCGGG

             *                          *          
       7426 ACTTAGCCGGATATAATAACTCGCACAATTGCCTTCGGG
          1 ATTTAGCCGGATATAATAACTCGCACAAATGCCTTCGGG

                             * *   *             *   
       7465 -TTTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTTGGG
          1 ATTTAG-CCGGATA-TAATAACTCGCACAAATGCCTTCGGG

             *      
       7504 ACTTAGCC
          1 ATTTAGCC

       7512 CGGTTATCAT


Statistics
Matches: 133,  Mismatches: 21, Indels: 20
        0.76            0.12        0.11

Matches are distributed among these distances:
  37    4  0.03
  38   34  0.26
  39   56  0.42
  40   39  0.29

ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26


Consensus pattern (39 bp):   
ATTTAGCCGGATATAATAACTCGCACAAATGCCTTCGGG

Found at i:7496 original size:77 final size:77

Alignment explanation


    Indices: 7334--7511  Score: 198
    Period size: 77  Copynumber: 2.3  Consensus size: 77

       7324 ACTACTTGCT

                                *    *    *                                  
       7334 CAAATGCCTTCGGGACTTGACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTCAGCCCGG
          1 CAAATGCCTTC-GGACTT-AGCCGGATATAATAACTCGCACAAATGCCTTCGGGACTCAGCCCGG

                      *   
       7399 TTCAATAACTCGCA
         64 TTCAATAACTAGCA

             *                                       *           * *         
       7413 CCAATGCCTTCGGACTTAGCCGGATATAATAACTCGCACAATTGCCTTCGGG-TTTAGCCCGGAA
          1 CAAATGCCTTCGGACTTAGCCGGATATAATAACTCGCACAAATGCCTTCGGGACTCAGCCCGG--

                * *       
       7477 TT-AGTCACTAGCA
         64 TTCAATAACTAGCA

                       *          
       7490 CAAATGCCTTTGGGACTTAGCC
          1 CAAATGCC-TTCGGACTTAGCC

       7512 CGGTTATCAT


Statistics
Matches: 84,  Mismatches: 12, Indels: 7
        0.82            0.12        0.07

Matches are distributed among these distances:
  76    8  0.10
  77   46  0.55
  78   20  0.24
  79   10  0.12

ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25


Consensus pattern (77 bp):   
CAAATGCCTTCGGACTTAGCCGGATATAATAACTCGCACAAATGCCTTCGGGACTCAGCCCGGTT
CAATAACTAGCA
Done.