Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007833.1 Corchorus capsularis cultivar CVL-1 contig07854, 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: 16871
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31


Found at i:10348 original size:21 final size:23

Alignment explanation


    Indices: 10323--10367  Score: 67
    Period size: 21  Copynumber: 2.0  Consensus size: 23

      10313 CTAATTGCAC

                                   
      10323 AAAAACCCTAATT-C-CCAAATA
          1 AAAAACCCTAATTACTCCAAATA

                      *            
      10344 AAAAACCCTAGTTACTCCAAATA
          1 AAAAACCCTAATTACTCCAAATA

             
      10367 A
          1 A

      10368 CCTAGATTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21   12  0.57
  22    1  0.05
  23    8  0.38

ACGTcount: A:0.51, C:0.27, G:0.02, T:0.20


Consensus pattern (23 bp):   
AAAAACCCTAATTACTCCAAATA

Found at i:10554 original size:12 final size:13

Alignment explanation


    Indices: 10537--10565  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

      10527 CTGGTCAAAA

                         
      10537 TTTTTTTTTA-AT
          1 TTTTTTTTTATAT

                         
      10549 TTTTTTTTTATAT
          1 TTTTTTTTTATAT

                
      10562 TTTT
          1 TTTT

      10566 CGATATAACT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   10  0.62
  13    6  0.38

ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86


Consensus pattern (13 bp):   
TTTTTTTTTATAT

Found at i:12139 original size:30 final size:28

Alignment explanation


    Indices: 12098--12172  Score: 89
    Period size: 29  Copynumber: 2.6  Consensus size: 28

      12088 TTTGACACCG

                                       *  
      12098 AGTGCA-AACCCGCACTCAATACAATCCCA
          1 AGTGCACAACCCGCACTCAAT-CAA-CACA

                         *    *          
      12127 AGTGCACAACCCGTACTTGAATCAACACA
          1 AGTGCACAACCCGCAC-TCAATCAACACA

                             
      12156 AGTGCACAACCCGCACT
          1 AGTGCACAACCCGCACT

      12173 TGATACACCA


Statistics
Matches: 40,  Mismatches: 4, Indels: 5
        0.82            0.08        0.10

Matches are distributed among these distances:
  28    1  0.03
  29   24  0.60
  30   11  0.28
  31    4  0.10

ACGTcount: A:0.36, C:0.36, G:0.13, T:0.15


Consensus pattern (28 bp):   
AGTGCACAACCCGCACTCAATCAACACA

Found at i:14429 original size:33 final size:33

Alignment explanation


    Indices: 14392--14498  Score: 108
    Period size: 33  Copynumber: 3.2  Consensus size: 33

      14382 AGCACTAGTG

                    *                  *     
      14392 ACCGGCCATGCGACTTGGAGAAGCCCGTCCAAC
          1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

                      *    *     *           
      14425 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

               *          *    * * *         
      14458 ACCAGCCACGCGACATGGACATGTCCGGCC-AC
          1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

                     
      14490 AACCGGCCA
          1 -ACCGGCCA

      14499 TCGCTTGGCG


Statistics
Matches: 61,  Mismatches: 12, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  32    2  0.03
  33   59  0.97

ACGTcount: A:0.24, C:0.39, G:0.27, T:0.09


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
Done.