Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1940

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: 30020
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31


Found at i:1936 original size:40 final size:40

Alignment explanation


    Indices: 1760--1982  Score: 236
    Period size: 40  Copynumber: 5.6  Consensus size: 40

       1750 TCCTCGTTCA

                          *  *     *    *      *    
       1760 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

                          *              *          
       1799 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

             *                                      
       1839 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

                                        *  *       *
       1879 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

              *                *      *  * *    *     
       1919 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
          1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG

              *              *      
       1959 AAAGCCTTCGGGACTTAGCCCGGA
          1 AATGCCTTCGGGACTTAACCCGGA

       1983 CAGCATTCAA


Statistics
Matches: 158,  Mismatches: 22, Indels: 7
        0.84            0.12        0.04

Matches are distributed among these distances:
  39   37  0.23
  40  113  0.72
  41    8  0.05

ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25


Consensus pattern (40 bp):   
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

Found at i:9749 original size:40 final size:39

Alignment explanation


    Indices: 9651--9873  Score: 241
    Period size: 40  Copynumber: 5.6  Consensus size: 39

       9641 TCCTCGTTCA

                          *  *     *    *      *   
       9651 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC

                          *              *         
       9690 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC

                                                    
       9729 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
          1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC

                                         *  *       
       9769 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
          1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC

               *                *      *  * *    *    
       9809 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
          1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC

              *              *      
       9850 AAAGCCTTCGGGACTTAGCCCGGA
          1 AATGCCTTCGGGACTTAACCCGGA

       9874 CAGCATTCAA


Statistics
Matches: 160,  Mismatches: 20, Indels: 7
        0.86            0.11        0.04

Matches are distributed among these distances:
  39   37  0.23
  40  115  0.72
  41    8  0.05

ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25


Consensus pattern (39 bp):   
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC

Found at i:9873 original size:120 final size:119

Alignment explanation


    Indices: 9651--9873  Score: 272
    Period size: 120  Copynumber: 1.9  Consensus size: 119

       9641 TCCTCGTTCA

                             *     *                 *                      *
       9651 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
          1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA

                    *       *                                     
       9716 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
         66 TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

                          *                *   *                   *   *     
       9770 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
          1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA

                 *                             *      
       9834 TATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
         64 TATA-ACAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA

       9874 CAGCATTCAA


Statistics
Matches: 87,  Mismatches: 13, Indels: 7
        0.81            0.12        0.07

Matches are distributed among these distances:
 119   37  0.43
 120   44  0.51
 121    6  0.07

ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25


Consensus pattern (119 bp):   
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

Found at i:19537 original size:46 final size:46

Alignment explanation


    Indices: 19484--19595  Score: 170
    Period size: 46  Copynumber: 2.4  Consensus size: 46

      19474 ATTAATAAGT

                                                          
      19484 TAAGTCATTTAATTTGTCTAAATTACTACAACAATTTAAGTTGTCC
          1 TAAGTCATTTAATTTGTCTAAATTACTACAACAATTTAAGTTGTCC

                                     *    *              *
      19530 TAAGTCATTTAATTTGTCTAAATTATTACAGCAATTTAAGTTGTCT
          1 TAAGTCATTTAATTTGTCTAAATTACTACAACAATTTAAGTTGTCC

                * *             
      19576 TAAACTAATTTAATTTGTCT
          1 T-AAGTCATTTAATTTGTCT

      19596 TGTTTACAGC


Statistics
Matches: 60,  Mismatches: 5, Indels: 1
        0.91            0.08        0.02

Matches are distributed among these distances:
  46   44  0.73
  47   16  0.27

ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45


Consensus pattern (46 bp):   
TAAGTCATTTAATTTGTCTAAATTACTACAACAATTTAAGTTGTCC

Found at i:29639 original size:20 final size:20

Alignment explanation


    Indices: 29616--29662  Score: 58
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      29606 GGGTTAAGAT

                            *   
      29616 TGAGCTGAATTGAGCTTGAA
          1 TGAGCTGAATTGAGCTCGAA

                *   *          *
      29636 TGAGTTGACTTGAGCTCGAG
          1 TGAGCTGAATTGAGCTCGAA

                   
      29656 TGAGCTG
          1 TGAGCTG

      29663 GAAACAAGCT


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30


Consensus pattern (20 bp):   
TGAGCTGAATTGAGCTCGAA
Done.