Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008084.1 Corchorus capsularis cultivar CVL-1 contig08105, 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: 10991
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34


Found at i:736 original size:31 final size:31

Alignment explanation


    Indices: 679--741  Score: 74
    Period size: 31  Copynumber: 2.0  Consensus size: 31

        669 TTCCTTTGCA

                     * *  *            *   
        679 CACTCTTGTGAGTAGAGGGACTAAAATTGAG
          1 CACTCTTGTAAATAAAGGGACTAAAATGGAG

                                            
        710 CACTCTTGTAAATAAAGGGA-TAAAAATGGAG
          1 CACTCTTGTAAATAAAGGGACT-AAAATGGAG

             
        741 C
          1 C

        742 GGTTTTAAGT


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  30    1  0.04
  31   26  0.96

ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24


Consensus pattern (31 bp):   
CACTCTTGTAAATAAAGGGACTAAAATGGAG

Found at i:1050 original size:31 final size:31

Alignment explanation


    Indices: 1010--1084  Score: 96
    Period size: 31  Copynumber: 2.4  Consensus size: 31

       1000 TTTGTTTTTG

                *                          
       1010 GGCTTAAATTGGTCAACTTTTAAAAGGTTTA
          1 GGCTCAAATTGGTCAACTTTTAAAAGGTTTA

                       **        *         
       1041 GGCTCAAATTGAACAACTTTTGAAAGGTTTA
          1 GGCTCAAATTGGTCAACTTTTAAAAGGTTTA

             **          
       1072 GAATCAAATTGGT
          1 GGCTCAAATTGGT

       1085 GGCTAAAAAT


Statistics
Matches: 36,  Mismatches: 8, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  31   36  1.00

ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35


Consensus pattern (31 bp):   
GGCTCAAATTGGTCAACTTTTAAAAGGTTTA

Found at i:6659 original size:6 final size:6

Alignment explanation


    Indices: 6648--6676  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       6638 AAGGGGAACG

                                              
       6648 GTTTTT GTTTTT GTTTTT GTTTTT -TTTTT
          1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT

       6677 CGGTTGAAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    5  0.22
   6   18  0.78

ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86


Consensus pattern (6 bp):   
GTTTTT

Done.