Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010176.1 Corchorus capsularis cultivar CVL-1 contig10197, whole genome shotgun sequence

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: 22993
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:2205 original size:54 final size:54

Alignment explanation


    Indices: 2144--2251  Score: 189
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       2134 ACATATACCC

                              *                       * *         
       2144 ATTTTCTGAATTAATTTTGTTTTTAAAATTCAAAAATATTCTTTGAACCCCGCA
          1 ATTTTCTGAATTAATTTTATTTTTAAAATTCAAAAATATTCTCTAAACCCCGCA

                                                                  
       2198 ATTTTCTGAATTAATTTTATTTTTAAAATTCAAAAATATTCTCTAAACCCCGCA
          1 ATTTTCTGAATTAATTTTATTTTTAAAATTCAAAAATATTCTCTAAACCCCGCA

       2252 TGTGTAGTTT


Statistics
Matches: 51,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  54   51  1.00

ACGTcount: A:0.35, C:0.16, G:0.06, T:0.44


Consensus pattern (54 bp):   
ATTTTCTGAATTAATTTTATTTTTAAAATTCAAAAATATTCTCTAAACCCCGCA

Found at i:2545 original size:3 final size:3

Alignment explanation


    Indices: 2537--2573  Score: 74
    Period size: 3  Copynumber: 12.3  Consensus size: 3

       2527 ATCCTAAATA

                                                             
       2537 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T

       2574 TTTTAACCAC


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   34  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TAT

Found at i:4835 original size:3 final size:3

Alignment explanation


    Indices: 4827--4867  Score: 82
    Period size: 3  Copynumber: 13.7  Consensus size: 3

       4817 ATCCCTCTCG

                                                                  
       4827 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

       4868 TGCAAATTCT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   38  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:7235 original size:20 final size:20

Alignment explanation


    Indices: 7210--7251  Score: 84
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       7200 AGAGATTGAA

                                
       7210 AGTCTCAAAATTAATTAACT
          1 AGTCTCAAAATTAATTAACT

                                
       7230 AGTCTCAAAATTAATTAACT
          1 AGTCTCAAAATTAATTAACT

              
       7250 AG
          1 AG

       7252 AATAGATTAC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33


Consensus pattern (20 bp):   
AGTCTCAAAATTAATTAACT

Found at i:13164 original size:11 final size:11

Alignment explanation


    Indices: 13148--13172  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

      13138 ATTCAAAAGC

                       
      13148 TTAATATTCTG
          1 TTAATATTCTG

                       
      13159 TTAATATTCTG
          1 TTAATATTCTG

               
      13170 TTA
          1 TTA

      13173 TCCACAACAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56


Consensus pattern (11 bp):   
TTAATATTCTG
Done.