Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007068.1 Corchorus capsularis cultivar CVL-1 contig07089, 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: 26855
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:3929 original size:6 final size:6

Alignment explanation


    Indices: 3918--3949  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       3908 TCTATTCTGC

                                                  
       3918 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT

       3950 GCTTTGCTTT


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

Matches are distributed among these distances:
   5    4  0.15
   6   22  0.85

ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:8515 original size:7 final size:7

Alignment explanation


    Indices: 8503--8535  Score: 66
    Period size: 7  Copynumber: 4.7  Consensus size: 7

       8493 TCAACTTTAA

                   
       8503 TATATGT
          1 TATATGT

                   
       8510 TATATGT
          1 TATATGT

                   
       8517 TATATGT
          1 TATATGT

                   
       8524 TATATGT
          1 TATATGT

                 
       8531 TATAT
          1 TATAT

       8536 AGATGTTATA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   26  1.00

ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58


Consensus pattern (7 bp):   
TATATGT

Found at i:12028 original size:31 final size:31

Alignment explanation


    Indices: 11988--12062  Score: 89
    Period size: 31  Copynumber: 2.4  Consensus size: 31

      11978 TTATTAATTA

                *       *                   
      11988 GACTCAATTGATTCAATC-TGACAAGTAGAGG
          1 GACTAAATTGATCCAATCTTG-CAAGTAGAGG

                *      *              *    
      12019 GACTGAATTGACCCAATCTTGCAAGTGGAGG
          1 GACTAAATTGATCCAATCTTGCAAGTAGAGG

                         
      12050 GACTAAATTGATC
          1 GACTAAATTGATC

      12063 AGTTTTTTAG


Statistics
Matches: 37,  Mismatches: 6, Indels: 2
        0.82            0.13        0.04

Matches are distributed among these distances:
  31   35  0.95
  32    2  0.05

ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25


Consensus pattern (31 bp):   
GACTAAATTGATCCAATCTTGCAAGTAGAGG

Found at i:12803 original size:24 final size:24

Alignment explanation


    Indices: 12740--12805  Score: 62
    Period size: 24  Copynumber: 2.7  Consensus size: 24

      12730 ATATGTTGCT

                          *  *       *
      12740 TTTTCTTATCAATGATTATTGGGTTT
          1 TTTTCTT-TC-ATGTTTTTTGGGTTA

                      *              
      12766 TCTTTCTTT-TTGTTTTTTGGGTTA
          1 T-TTTCTTTCATGTTTTTTGGGTTA

                            
      12790 TTTTCTTTCATGTTTT
          1 TTTTCTTTCATGTTTT

      12806 GTAAAATGTT


Statistics
Matches: 33,  Mismatches: 5, Indels: 6
        0.75            0.11        0.14

Matches are distributed among these distances:
  23    7  0.21
  24   18  0.55
  26    2  0.06
  27    6  0.18

ACGTcount: A:0.11, C:0.09, G:0.14, T:0.67


Consensus pattern (24 bp):   
TTTTCTTTCATGTTTTTTGGGTTA

Found at i:15238 original size:30 final size:30

Alignment explanation


    Indices: 15204--15260  Score: 105
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      15194 AAGCTATATA

                                          
      15204 TTCTACCTAACTTCTAATATCTATTGCATG
          1 TTCTACCTAACTTCTAATATCTATTGCATG

                      *                
      15234 TTCTACCTAATTTCTAATATCTATTGC
          1 TTCTACCTAACTTCTAATATCTATTGC

      15261 TGCTTGGCAA


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

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.26, C:0.23, G:0.05, T:0.46


Consensus pattern (30 bp):   
TTCTACCTAACTTCTAATATCTATTGCATG

Found at i:24209 original size:2 final size:2

Alignment explanation


    Indices: 24202--24226  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      24192 CTTTTCCTAA

                                                 
      24202 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

      24227 AGGCTTTTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.