Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005948.1 Corchorus capsularis cultivar CVL-1 contig05966, 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: 10091
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:564 original size:51 final size:49

Alignment explanation


    Indices: 476--572  Score: 133
    Period size: 51  Copynumber: 1.9  Consensus size: 49

        466 CAGCAACTAT

                                            *                
        476 TTAATTAAAAGTTTAGTATATAAAATCCAACCGAATTAAACACAACTCA
          1 TTAATTAAAAGTTTAGTATATAAAATCCAACCAAATTAAACACAACTCA

                                             *         *     
        525 TTAATTAAAATGTATT-GCTATATAAAATCCAATCAAATTAAAGACAAC
          1 TTAATTAAAA-GT-TTAG-TATATAAAATCCAACCAAATTAAACACAAC

        573 CAACTCACGT


Statistics
Matches: 42,  Mismatches: 3, Indels: 4
        0.86            0.06        0.08

Matches are distributed among these distances:
  49   10  0.24
  50    3  0.07
  51   29  0.69

ACGTcount: A:0.49, C:0.14, G:0.06, T:0.30


Consensus pattern (49 bp):   
TTAATTAAAAGTTTAGTATATAAAATCCAACCAAATTAAACACAACTCA

Found at i:5334 original size:15 final size:15

Alignment explanation


    Indices: 5316--5346  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5306 TTTAAGTTTC

                           
       5316 AGGGACTTAATTGAA
          1 AGGGACTTAATTGAA

                     *     
       5331 AGGGACTTATTTGAA
          1 AGGGACTTAATTGAA

             
       5346 A
          1 A

       5347 AGAAAATAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29


Consensus pattern (15 bp):   
AGGGACTTAATTGAA

Found at i:9587 original size:145 final size:145

Alignment explanation


    Indices: 9324--9619  Score: 592
    Period size: 145  Copynumber: 2.0  Consensus size: 145

       9314 AGAAGATCCT

                                                                             
       9324 TGAACGATTCTAGATGCAAGTTTGCAAACCCATAGACACTCATATCACTAAAGGTGAGACTTTAA
          1 TGAACGATTCTAGATGCAAGTTTGCAAACCCATAGACACTCATATCACTAAAGGTGAGACTTTAA

                                                                             
       9389 GTCTTCAACTGACTCCAAAGACATCTGATGAATAGAAATAGATGGCTCATGTTCCAAACTTAGTG
         66 GTCTTCAACTGACTCCAAAGACATCTGATGAATAGAAATAGATGGCTCATGTTCCAAACTTAGTG

                           
       9454 TTGTTGGCATTCTTA
        131 TTGTTGGCATTCTTA

                                                                             
       9469 TGAACGATTCTAGATGCAAGTTTGCAAACCCATAGACACTCATATCACTAAAGGTGAGACTTTAA
          1 TGAACGATTCTAGATGCAAGTTTGCAAACCCATAGACACTCATATCACTAAAGGTGAGACTTTAA

                                                                             
       9534 GTCTTCAACTGACTCCAAAGACATCTGATGAATAGAAATAGATGGCTCATGTTCCAAACTTAGTG
         66 GTCTTCAACTGACTCCAAAGACATCTGATGAATAGAAATAGATGGCTCATGTTCCAAACTTAGTG

                           
       9599 TTGTTGGCATTCTTA
        131 TTGTTGGCATTCTTA

                  
       9614 TGAACG
          1 TGAACG

       9620 CATGCACTAG


Statistics
Matches: 151,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 145  151  1.00

ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29


Consensus pattern (145 bp):   
TGAACGATTCTAGATGCAAGTTTGCAAACCCATAGACACTCATATCACTAAAGGTGAGACTTTAA
GTCTTCAACTGACTCCAAAGACATCTGATGAATAGAAATAGATGGCTCATGTTCCAAACTTAGTG
TTGTTGGCATTCTTA
Done.