Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010757.1 Corchorus capsularis cultivar CVL-1 contig10778, 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: 28642
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:148 original size:29 final size:27

Alignment explanation


    Indices: 77--148  Score: 63
    Period size: 29  Copynumber: 2.4  Consensus size: 27

         67 TTTTGAAATG

                               *         
         77 TAAGGGATTAATTTGTCCCGAAAAAAACA
          1 TAAGGGATT--TTTGTCCCAAAAAAAACA

               * *                         
        106 TAAAGAATTATTTTGTCCCAAAAGCAAAACA
          1 TAAGGGA-T-TTTTGTCCCAAAA--AAAACA

                        
        137 TAAGGGATTTTT
          1 TAAGGGATTTTT

        149 TTGGGTATTT


Statistics
Matches: 34,  Mismatches: 5, Indels: 8
        0.72            0.11        0.17

Matches are distributed among these distances:
  29   20  0.59
  30    2  0.06
  31   12  0.35

ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29


Consensus pattern (27 bp):   
TAAGGGATTTTTGTCCCAAAAAAAACA

Found at i:6377 original size:30 final size:28

Alignment explanation


    Indices: 6341--6397  Score: 78
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       6331 AGTGTTCTGA

                                          
       6341 ATTTGGAAATTCAAGGAGTAAAATGTCCTG
          1 ATTTGG-AATTC-AGGAGTAAAATGTCCTG

                   *      *            
       6371 ATTTGGAGTTCAGGTGTAAAATGTCCT
          1 ATTTGGAATTCAGGAGTAAAATGTCCT

       6398 TGACGCAATA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  28   15  0.60
  29    4  0.16
  30    6  0.24

ACGTcount: A:0.32, C:0.11, G:0.25, T:0.33


Consensus pattern (28 bp):   
ATTTGGAATTCAGGAGTAAAATGTCCTG

Found at i:9832 original size:30 final size:29

Alignment explanation


    Indices: 9734--9841  Score: 126
    Period size: 29  Copynumber: 3.7  Consensus size: 29

       9724 ACATGTAGTG

                    *      *              
       9734 TTTGGACGTTTTTGTTCCCTGAATTTCAAT
          1 TTTGGAC-ATTTTGTCCCCTGAATTTCAAT

                    *          *  *      
       9764 TTTGGACAATTTGTCCCCTAAACTTCAAT
          1 TTTGGACATTTTGTCCCCTGAATTTCAAT

                           **            
       9793 TTTGGACATTTTGTCTTCTGAATTTCAAT
          1 TTTGGACATTTTGTCCCCTGAATTTCAAT

                          *     
       9822 TTTGGGACATTTTGCCCCCT
          1 TTT-GGACATTTTGTCCCCT

       9842 CAACTAATGA


Statistics
Matches: 64,  Mismatches: 13, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  29   44  0.69
  30   20  0.31

ACGTcount: A:0.19, C:0.20, G:0.15, T:0.45


Consensus pattern (29 bp):   
TTTGGACATTTTGTCCCCTGAATTTCAAT

Found at i:17574 original size:15 final size:15

Alignment explanation


    Indices: 17554--17583  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      17544 CACTAATTTA

                           
      17554 ACCTTTTCATAGTTT
          1 ACCTTTTCATAGTTT

                           
      17569 ACCTTTTCATAGTTT
          1 ACCTTTTCATAGTTT

      17584 GGGCACTTAT


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

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53


Consensus pattern (15 bp):   
ACCTTTTCATAGTTT

Found at i:21238 original size:27 final size:27

Alignment explanation


    Indices: 21207--21262  Score: 112
    Period size: 27  Copynumber: 2.1  Consensus size: 27

      21197 AAATCAAAGT

                                       
      21207 TATATTAAAAAAGTGGGTTTAAGTCCA
          1 TATATTAAAAAAGTGGGTTTAAGTCCA

                                       
      21234 TATATTAAAAAAGTGGGTTTAAGTCCA
          1 TATATTAAAAAAGTGGGTTTAAGTCCA

              
      21261 TA
          1 TA

      21263 AGTGACAATA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34


Consensus pattern (27 bp):   
TATATTAAAAAAGTGGGTTTAAGTCCA
Done.