Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold237

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: 13303
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32


Found at i:11591 original size:39 final size:39

Alignment explanation


    Indices: 11507--11617  Score: 125
    Period size: 40  Copynumber: 2.8  Consensus size: 39

      11497 AGATACTAAT

                                      **      *     
      11507 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
          1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA

                                       *         *  
      11547 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
          1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA

                  *  *                      
      11587 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
          1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG

      11618 GAGCTATATC


Statistics
Matches: 61,  Mismatches: 8, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  39   25  0.41
  40   36  0.59

ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24


Consensus pattern (39 bp):   
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA

Found at i:11625 original size:40 final size:39

Alignment explanation


    Indices: 11428--11630  Score: 101
    Period size: 40  Copynumber: 5.1  Consensus size: 39

      11418 TGAATGCTGT

                                *   **  *          *
      11428 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTGAAC-GAGTGACTATAA

                *                 *   **              *
      11468 CCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGAT-ACTA-ATT
          1 CCGGGCTAAG-TCCCGAAGG-CATTGAACGAG-TGACTATA-A

                 *                   **      **  *  
      11508 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA
          1 CCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACTATAA

                  *                    *    *       
      11547 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
          1 -CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA

                    *                               *
      11587 CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATAT
          1 CCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATAA

                
      11627 CCGG
          1 CCGG

      11631 TTAAATTCCG


Statistics
Matches: 133,  Mismatches: 19, Indels: 22
        0.76            0.11        0.13

Matches are distributed among these distances:
  39   33  0.25
  40   90  0.68
  41   10  0.08

ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25


Consensus pattern (39 bp):   
CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA

Found at i:13196 original size:21 final size:20

Alignment explanation


    Indices: 13155--13198  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 20

      13145 GCTTTAGCTA

                           *    
      13155 ATTATTTTATTACATGCATT
          1 ATTATTTTATTACATACATT

                         *   *   
      13175 ATTATTTATATTATATATATT
          1 ATTATTT-TATTACATACATT

               
      13196 ATT
          1 ATT

      13199 TGTTGCCCTA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59


Consensus pattern (20 bp):   
ATTATTTTATTACATACATT
Done.