Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012735.1 Corchorus capsularis cultivar CVL-1 contig12756, 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: 7561
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.37


Found at i:444 original size:19 final size:18

Alignment explanation


    Indices: 420--455  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        410 TGAAAATTTC

                               
        420 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
        439 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

        456 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:2726 original size:12 final size:12

Alignment explanation


    Indices: 2704--2733  Score: 53
    Period size: 12  Copynumber: 2.6  Consensus size: 12

       2694 ATTACAATTT

                        
       2704 GATTG-TTGATG
          1 GATTGATTGATG

                        
       2715 GATTGATTGATG
          1 GATTGATTGATG

                   
       2727 GATTGAT
          1 GATTGAT

       2734 CTTTTATTCC


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  11    5  0.28
  12   13  0.72

ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43


Consensus pattern (12 bp):   
GATTGATTGATG

Found at i:4165 original size:32 final size:32

Alignment explanation


    Indices: 4124--4190  Score: 134
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       4114 ATGGTGAGAT

                                            
       4124 TTTGTGCTTTTATATGAAAATTGTTTAGGGTA
          1 TTTGTGCTTTTATATGAAAATTGTTTAGGGTA

                                            
       4156 TTTGTGCTTTTATATGAAAATTGTTTAGGGTA
          1 TTTGTGCTTTTATATGAAAATTGTTTAGGGTA

               
       4188 TTT
          1 TTT

       4191 CTTAAATCTC


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   35  1.00

ACGTcount: A:0.24, C:0.03, G:0.21, T:0.52


Consensus pattern (32 bp):   
TTTGTGCTTTTATATGAAAATTGTTTAGGGTA

Found at i:5290 original size:10 final size:10

Alignment explanation


    Indices: 5275--5299  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       5265 ATTACTCAGC

                      
       5275 CCATATAAGT
          1 CCATATAAGT

                      
       5285 CCATATAAGT
          1 CCATATAAGT

                 
       5295 CCATA
          1 CCATA

       5300 ATTGGAGTTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28


Consensus pattern (10 bp):   
CCATATAAGT
Done.