Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3336

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: 7841
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29


Found at i:1425 original size:39 final size:40

Alignment explanation


    Indices: 1380--1603  Score: 233
    Period size: 40  Copynumber: 5.7  Consensus size: 40

       1370 GCTCCTCGTT

                            *  *     *           *  
       1380 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                          *         
       1420 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

             *                               *      
       1459 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                *                      *      *      
       1499 CAAAGGCCTTCGGG-CTTAACCCGGAACTT-GTATCTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA

                                **      *  * *    *   
       1538 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA

                               *      
       1579 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAACCCGGA

       1604 CAGCATTCAA


Statistics
Matches: 157,  Mismatches: 20, Indels: 14
        0.82            0.10        0.07

Matches are distributed among these distances:
  38    2  0.01
  39   66  0.42
  40   78  0.50
  41   11  0.07

ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

Found at i:1483 original size:79 final size:78

Alignment explanation


    Indices: 1380--1604  Score: 247
    Period size: 79  Copynumber: 2.8  Consensus size: 78

       1370 GCTCCTCGTT

                            *        *                 *                     
       1380 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA

            *             
       1445 TTTAATAACTCGCA
         66 CTT-ATAACTCGCA

             *                 *             *   *                           
       1459 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGG-CTTAACCCGG
          1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAA-GCCTTCGGGACTTAACCCGG

                 *  *      
       1523 AACTTGTATCTCGCA
         65 -ACTTATAACTCGCA

                                 *      *  * *   *                      *    
       1538 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCA-CACAAAGCCTTCGGGACTTAACCCG

               
       1602 GAC
         64 GAC

       1605 AGCATTCAAT


Statistics
Matches: 121,  Mismatches: 20, Indels: 10
        0.80            0.13        0.07

Matches are distributed among these distances:
  78    3  0.02
  79   91  0.75
  80   27  0.22

ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25


Consensus pattern (78 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
CTTATAACTCGCA

Found at i:1612 original size:41 final size:41

Alignment explanation


    Indices: 1535--1612  Score: 97
    Period size: 40  Copynumber: 1.9  Consensus size: 41

       1525 CTTGTATCTC

                                   *     * *         
       1535 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
          1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA

                                                   
       1576 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
          1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA

       1613 ATTAATCATG


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  40   17  0.53
  41   15  0.47

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


Consensus pattern (41 bp):   
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.