Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000059.1 Corchorus olitorius cultivar O-4 contig00059, 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, 611

Length: 1019
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33


Found at i:215 original size:14 final size:12

Alignment explanation


    Indices: 196--234  Score: 51
    Period size: 12  Copynumber: 3.1  Consensus size: 12

        186 ATAAAGAACC

                        
        196 TTTAATAATAAA
          1 TTTAATAATAAA

                         *
        208 TTACTAATAATAAG
          1 TT--TAATAATAAA

                        
        222 TTTAATAATAAA
          1 TTTAATAATAAA

             
        234 T
          1 T

        235 CAATAATTCC


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  12   12  0.52
  14   11  0.48

ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41


Consensus pattern (12 bp):   
TTTAATAATAAA

Found at i:731 original size:20 final size:19

Alignment explanation


    Indices: 706--747  Score: 59
    Period size: 20  Copynumber: 2.2  Consensus size: 19

        696 CTAAAAAGGT

                                 
        706 TTAATAA-AGTTACTACAATA
          1 TTAATAACA-TTACTACAA-A

                               
        726 TTAATAACATTACTACAAA
          1 TTAATAACATTACTACAAA

               
        745 TTA
          1 TTA

        748 TCAAGGTTAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  19    4  0.19
  20   16  0.76
  21    1  0.05

ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36


Consensus pattern (19 bp):   
TTAATAACATTACTACAAA

Found at i:868 original size:21 final size:22

Alignment explanation


    Indices: 844--892  Score: 64
    Period size: 22  Copynumber: 2.3  Consensus size: 22

        834 TGAAATTCAC

                              *   
        844 AATAAGATTA-CTAAAAATCTT
          1 AATAAGATTAGCTAAAAACCTT

                  *    *          
        865 AATAAGGTTAGGTAAAAACCTT
          1 AATAAGATTAGCTAAAAACCTT

                  
        887 AATAAG
          1 AATAAG

        893 GTGACCAAAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  21    9  0.38
  22   15  0.62

ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29


Consensus pattern (22 bp):   
AATAAGATTAGCTAAAAACCTT
Done.