Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006329.1 Corchorus olitorius cultivar O-4 contig06354, 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, 725

Length: 1209
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33


Found at i:288 original size:14 final size:12

Alignment explanation


    Indices: 269--305  Score: 56
    Period size: 14  Copynumber: 2.9  Consensus size: 12

        259 ATAAAGAACC

                        
        269 TTTAATAATAAG
          1 TTTAATAATAAG

                          
        281 TTACTAATAATAAG
          1 TT--TAATAATAAG

                       
        295 TTTAATAATAA
          1 TTTAATAATAA

        306 ATCAATAATT


Statistics
Matches: 23,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

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

ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41


Consensus pattern (12 bp):   
TTTAATAATAAG

Found at i:785 original size:20 final size:19

Alignment explanation


    Indices: 760--801  Score: 59
    Period size: 20  Copynumber: 2.2  Consensus size: 19

        750 CTAAAAAGGT

                                 
        760 TTAATAA-AGTTACTACAATA
          1 TTAATAACA-TTACTACAA-A

                               
        780 TTAATAACATTACTACAAA
          1 TTAATAACATTACTACAAA

               
        799 TTA
          1 TTA

        802 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:924 original size:21 final size:22

Alignment explanation


    Indices: 898--946  Score: 64
    Period size: 22  Copynumber: 2.3  Consensus size: 22

        888 TGAAATTCAC

                              *   
        898 AATAAGATTA-CTAAAAATCTT
          1 AATAAGATTAGCTAAAAAACTT

                  *    *          
        919 AATAAGGTTAGGTAAAAAACTT
          1 AATAAGATTAGCTAAAAAACTT

                  
        941 AATAAG
          1 AATAAG

        947 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:0.53, C:0.06, G:0.12, T:0.29


Consensus pattern (22 bp):   
AATAAGATTAGCTAAAAAACTT
Done.