Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010236.1 Corchorus olitorius cultivar O-4 contig10268, 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: 5097
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36


Found at i:2558 original size:74 final size:74

Alignment explanation


    Indices: 2473--2611  Score: 244
    Period size: 74  Copynumber: 1.9  Consensus size: 74

       2463 AACCTTTTTT

                                          *              *                   
       2473 TTTATATATAAAAAGTTA-CTAAAATCATCTAAGAGCGCAATTAGGTTTGTAGAAAGCATCATAG
          1 TTTATATATAAAAAGTTATC-AAAATCATCCAAGAGCGCAATTAGCTTTGTAGAAAGCATCATAG

                      
       2537 CGCAATTAGG
         65 CGCAATTAGG

                                                                             
       2547 TTTATATATAAAAAGTTATCAAAATCATCCAAGAGCGCAATTAGCTTTGTAGAAAGCATCATAGC
          1 TTTATATATAAAAAGTTATCAAAATCATCCAAGAGCGCAATTAGCTTTGTAGAAAGCATCATAGC

       2612 TATTTTAATA


Statistics
Matches: 62,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  74   61  0.98
  75    1  0.02

ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29


Consensus pattern (74 bp):   
TTTATATATAAAAAGTTATCAAAATCATCCAAGAGCGCAATTAGCTTTGTAGAAAGCATCATAGC
GCAATTAGG

Found at i:3184 original size:98 final size:98

Alignment explanation


    Indices: 3067--3251  Score: 300
    Period size: 98  Copynumber: 1.9  Consensus size: 98

       3057 AAATTGATAA

                                                                             
       3067 TCTTCTTCCACCAGAGATCGATAATC-TTCTTAATTGATTAATATTCAACTTCGTTCTTAATAAC
          1 TCTTCTTCCACCAGAGATCGATAA-CATTCTTAATTGATTAATATTCAACTTCGTTCTTAATAAC

                                              
       3131 CCTGTAGTTTTTTTAGTAAATTCTTTCTTCTTCT
         65 CCTGTAGTTTTTTTAGTAAATTCTTTCTTCTTCT

                   *  *                               *  *                *  
       3165 TCTTCTTGCATCAGAGATCGATAACATTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGCC
          1 TCTTCTTCCACCAGAGATCGATAACATTCTTAATTGATTAATATTCAACTTCGTTCTTAATAACC

            *                     
       3230 TTGTAGTTTTTTTAGTAAATTC
         66 CTGTAGTTTTTTTAGTAAATTC

       3252 AAATAAGAAA


Statistics
Matches: 80,  Mismatches: 6, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  97    1  0.01
  98   79  0.99

ACGTcount: A:0.25, C:0.18, G:0.10, T:0.46


Consensus pattern (98 bp):   
TCTTCTTCCACCAGAGATCGATAACATTCTTAATTGATTAATATTCAACTTCGTTCTTAATAACC
CTGTAGTTTTTTTAGTAAATTCTTTCTTCTTCT

Found at i:4319 original size:19 final size:20

Alignment explanation


    Indices: 4292--4329  Score: 53
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       4282 TACTATTATT

                                 
       4292 TTTTGAATTT-AATATTTTAC
          1 TTTTGAATTTCAAT-TTTTAC

                               
       4312 TTTT-AATTTCAATTTTTA
          1 TTTTGAATTTCAATTTTTA

       4330 AATGTCAATA


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  19   10  0.59
  20    7  0.41

ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63


Consensus pattern (20 bp):   
TTTTGAATTTCAATTTTTAC
Done.