Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001246.1 Corchorus capsularis cultivar CVL-1 contig01246, 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, 748

Length: 1248
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.37


Found at i:558 original size:19 final size:19

Alignment explanation


    Indices: 534--571  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

        524 TACAAAGAAT

                               
        534 TCCATCACAACATAAAAAA
          1 TCCATCACAACATAAAAAA

                               
        553 TCCATCACAACATAAAAAA
          1 TCCATCACAACATAAAAAA

        572 GGGACTTGAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.58, C:0.26, G:0.00, T:0.16


Consensus pattern (19 bp):   
TCCATCACAACATAAAAAA

Found at i:970 original size:20 final size:22

Alignment explanation


    Indices: 934--975  Score: 70
    Period size: 20  Copynumber: 2.0  Consensus size: 22

        924 GCTTGACCAA

                                  
        934 TTACCTAATTAAATAGAAAAAC
          1 TTACCTAATTAAATAGAAAAAC

                                  
        956 TTACC-AATT-AATAGAAAAAC
          1 TTACCTAATTAAATAGAAAAAC

        976 AATTCAAGTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  20   11  0.55
  21    4  0.20
  22    5  0.25

ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26


Consensus pattern (22 bp):   
TTACCTAATTAAATAGAAAAAC

Found at i:1226 original size:26 final size:27

Alignment explanation


    Indices: 1187--1239  Score: 99
    Period size: 26  Copynumber: 2.0  Consensus size: 27

       1177 TTGAATCGAG

                                       
       1187 ATATAAAAAAGAAAGTTACCAATAATT
          1 ATATAAAAAAGAAAGTTACCAATAATT

                                       
       1214 ATAT-AAAAAGAAAGTTACCAATAATT
          1 ATATAAAAAAGAAAGTTACCAATAATT

       1240 TAAATACAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  26   22  0.85
  27    4  0.15

ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26


Consensus pattern (27 bp):   
ATATAAAAAAGAAAGTTACCAATAATT
Done.