Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007409.1 Corchorus olitorius cultivar O-4 contig07434, 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, 676

Length: 1128
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:613 original size:22 final size:22

Alignment explanation


    Indices: 588--648  Score: 79
    Period size: 22  Copynumber: 2.8  Consensus size: 22

        578 TATTTAGTGT

                  *                
        588 GATTATTAAAATTTTATA-GGCA
          1 GATTATCAAAATTTTATACGG-A

                          *    *  
        610 GATTATCAAAATTTCATACTGA
          1 GATTATCAAAATTTTATACGGA

                             
        632 GATTATCAAAATTTTAT
          1 GATTATCAAAATTTTAT

        649 GGTGTGCTTA


Statistics
Matches: 34,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  22   33  0.97
  23    1  0.03

ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41


Consensus pattern (22 bp):   
GATTATCAAAATTTTATACGGA

Found at i:690 original size:22 final size:22

Alignment explanation


    Indices: 665--755  Score: 71
    Period size: 22  Copynumber: 4.2  Consensus size: 22

        655 CTTACCCAAA

                 *                
        665 TTTCACAGTGTGGTTATCGAAT
          1 TTTCATAGTGTGGTTATCGAAT

                    * *          *
        687 TTTCATAGGGAGGTTATCGAAA
          1 TTTCATAGTGTGGTTATCGAAT

                               *   
        709 TTTCATA-T-TAGGTTATCAAAT
          1 TTTCATAGTGT-GGTTATCGAAT

              *  * *              
        730 TTGCAAAATGTGGTTATC-AAT
          1 TTTCATAGTGTGGTTATCGAAT

                 
        751 ATTTC
          1 -TTTC

        756 TACATTGGAG


Statistics
Matches: 54,  Mismatches: 11, Indels: 8
        0.74            0.15        0.11

Matches are distributed among these distances:
  21   17  0.31
  22   36  0.67
  23    1  0.02

ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41


Consensus pattern (22 bp):   
TTTCATAGTGTGGTTATCGAAT

Found at i:723 original size:21 final size:22

Alignment explanation


    Indices: 662--731  Score: 72
    Period size: 22  Copynumber: 3.3  Consensus size: 22

        652 GTGCTTACCC

                    *  * *        
        662 AAATTTCACAGTGTGGTTATCG
          1 AAATTTCATAGGGAGGTTATCG

              *                   
        684 AATTTTCATAGGGAGGTTATCG
          1 AAATTTCATAGGGAGGTTATCG

                       **         
        706 AAATTTCATA-TTAGGTTATC-
          1 AAATTTCATAGGGAGGTTATCG

                  
        726 AAATTT
          1 AAATTT

        732 GCAAAATGTG


Statistics
Matches: 41,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  20    6  0.15
  21    8  0.20
  22   27  0.66

ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40


Consensus pattern (22 bp):   
AAATTTCATAGGGAGGTTATCG
Done.