Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_2586

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: 22625
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34


Found at i:11155 original size:22 final size:23

Alignment explanation


    Indices: 11109--11153  Score: 67
    Period size: 21  Copynumber: 2.0  Consensus size: 23

      11099 TTTAATAAAA

                               *   
      11109 TAAAGATTAAATTGAAATTTATT
          1 TAAAGATTAAATTGAAATTAATT

                                   
      11132 TAAA-ATTAAATT-AAATTAATT
          1 TAAAGATTAAATTGAAATTAATT

             
      11153 T
          1 T

      11154 TATTAATTAC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    9  0.43
  22    8  0.38
  23    4  0.19

ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44


Consensus pattern (23 bp):   
TAAAGATTAAATTGAAATTAATT

Found at i:15672 original size:25 final size:25

Alignment explanation


    Indices: 15657--15721  Score: 121
    Period size: 25  Copynumber: 2.6  Consensus size: 25

      15647 AGCACTGACA

                                     
      15657 TGCTAATAATTAGAGAGCAATAACG
          1 TGCTAATAATTAGAGAGCAATAACG

                                     
      15682 TGCTAATAATTAGAGAGCAATAACG
          1 TGCTAATAATTAGAGAGCAATAACG

                      *    
      15707 TGCTAATAATCAGAG
          1 TGCTAATAATTAGAG

      15722 CGCGCGCTAG


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  25   39  1.00

ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25


Consensus pattern (25 bp):   
TGCTAATAATTAGAGAGCAATAACG

Found at i:21241 original size:47 final size:49

Alignment explanation


    Indices: 21170--21342  Score: 178
    Period size: 49  Copynumber: 3.6  Consensus size: 49

      21160 AGGGTATAAT

                                                      *      
      21170 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-CATC-AA
          1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAAATCGAA

             *                                *              *
      21217 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCGAAATCGAG
          1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-AAATCGAA

                 *           *               *                 *
      21266 GCCGACGCCATGTCCCAAACATGGTCTTACACTAGCTC-TCACATATCCG-T
          1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCA-A-AT-CGAA

                       *   *            
      21316 GCCGATGCCATATCCTAGACAT-GTCTT
          1 GCCGATGCCATGTCCCAGACATGGTCTT

      21343 GCATTGGCAC


Statistics
Matches: 105,  Mismatches: 14, Indels: 12
        0.80            0.11        0.09

Matches are distributed among these distances:
  46    3  0.03
  47   35  0.33
  48    4  0.04
  49   41  0.39
  50   20  0.19
  51    2  0.02

ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25


Consensus pattern (49 bp):   
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAAATCGAA

Found at i:21295 original size:49 final size:47

Alignment explanation


    Indices: 21170--21298  Score: 170
    Period size: 47  Copynumber: 2.7  Consensus size: 47

      21160 AGGGTATAAT

                                              *      *     
      21170 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAA
          1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCATCAATCAA

             *                                               *
      21217 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCGAAATCGAG
          1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCATC--AATC-AA

                 *           *               
      21266 GCCGACGCCATGTCCCAAACATGGTCTTACACT
          1 GCCGATGCCATGTCCCAGACATGGTCTTACACT

      21299 AGCTCTCACA


Statistics
Matches: 72,  Mismatches: 7, Indels: 4
        0.87            0.08        0.05

Matches are distributed among these distances:
  46    3  0.04
  47   35  0.49
  48    3  0.04
  49   31  0.43

ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23


Consensus pattern (47 bp):   
GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCATCAATCAA
Done.