Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013773.1 Corchorus olitorius cultivar O-4 contig13806, 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: 14997
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:285 original size:21 final size:20

Alignment explanation


    Indices: 242--282  Score: 82
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        232 ATAAAGAAAA

                                
        242 TAATAAACTTAGTTTTTTGT
          1 TAATAAACTTAGTTTTTTGT

                                
        262 TAATAAACTTAGTTTTTTGT
          1 TAATAAACTTAGTTTTTTGT

             
        282 T
          1 T

        283 TAAGTGTTAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56


Consensus pattern (20 bp):   
TAATAAACTTAGTTTTTTGT

Found at i:1608 original size:60 final size:57

Alignment explanation


    Indices: 1516--1627  Score: 179
    Period size: 60  Copynumber: 1.9  Consensus size: 57

       1506 CTGTTTCCTT

                                      *       *                      
       1516 TCACACAATAAATGTTATAATAAATCTTATCCCCTCTATCTCTACTTAATTATTCTC
          1 TCACACAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATTCTC

                                                                   
       1573 TCACACAATAAATGTTAGTATAATAAATCCTATCCCCCCTATCTCTACTTAATTA
          1 TCACACAATAAATG-T--TATAATAAATCCTATCCCCCCTATCTCTACTTAATTA

       1628 AATAATATTT


Statistics
Matches: 50,  Mismatches: 2, Indels: 3
        0.91            0.04        0.05

Matches are distributed among these distances:
  57   14  0.28
  58    1  0.02
  60   35  0.70

ACGTcount: A:0.35, C:0.25, G:0.03, T:0.38


Consensus pattern (57 bp):   
TCACACAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATTCTC

Found at i:2851 original size:22 final size:22

Alignment explanation


    Indices: 2823--2867  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2813 AGCGTAATGT

                                  
       2823 TAACATGTTCATTTTCCCTTTA
          1 TAACATGTTCATTTTCCCTTTA

                                  
       2845 TAACATGTTCATTTTCCCTTTA
          1 TAACATGTTCATTTTCCCTTTA

             
       2867 T
          1 T

       2868 CCTTTAGCTA


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

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.22, C:0.22, G:0.04, T:0.51


Consensus pattern (22 bp):   
TAACATGTTCATTTTCCCTTTA

Found at i:5494 original size:3 final size:3

Alignment explanation


    Indices: 5486--5559  Score: 112
    Period size: 3  Copynumber: 23.3  Consensus size: 3

       5476 GGGCTTTACC

                                                                           
       5486 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA

                                             
       5534 GAA GAA GGAA GGAA GGAA GGAA GAA G
          1 GAA GAA -GAA -GAA -GAA -GAA GAA G

       5560 GGGAAAAAAT


Statistics
Matches: 70,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
   3   55  0.79
   4   15  0.21

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (3 bp):   
GAA

Done.