Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012467.1 Corchorus capsularis cultivar CVL-1 contig12488, 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: 37149
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:950 original size:21 final size:20

Alignment explanation


    Indices: 893--952  Score: 59
    Period size: 21  Copynumber: 3.0  Consensus size: 20

        883 CTATTTAGTA

                    *           
        893 ACTGTACATATGAAATT-AC
          1 ACTGTACAGATGAAATTAAC

               *       * *      *
        912 ACTATACAGATTAGATTAGAT
          1 ACTGTACAGATGAAATTA-AC

                                
        933 ACTGTACAGATGAAATTAAC
          1 ACTGTACAGATGAAATTAAC

        953 GGCGATGAAA


Statistics
Matches: 30,  Mismatches: 9, Indels: 3
        0.71            0.21        0.07

Matches are distributed among these distances:
  19   13  0.43
  20    1  0.03
  21   16  0.53

ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30


Consensus pattern (20 bp):   
ACTGTACAGATGAAATTAAC

Found at i:8167 original size:2 final size:2

Alignment explanation


    Indices: 8160--8191  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       8150 AAAAATTGAT

                                                             
       8160 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       8192 GTTGATGTTG


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:13677 original size:2 final size:2

Alignment explanation


    Indices: 13670--13697  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      13660 CATCAAGTAG

                                                     
      13670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      13698 GAGGCAGGCA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:15961 original size:30 final size:30

Alignment explanation


    Indices: 15920--15979  Score: 93
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      15910 TCCAGGCTTG

                                          
      15920 GCTCCAACCCACTTTGCTTTTCCTCTTCTT
          1 GCTCCAACCCACTTTGCTTTTCCTCTTCTT

                *           *       *     
      15950 GCTCGAACCCACTTTGGTTTTCCTTTTCTT
          1 GCTCCAACCCACTTTGCTTTTCCTCTTCTT

      15980 CTTGTTCTTG


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.10, C:0.35, G:0.10, T:0.45


Consensus pattern (30 bp):   
GCTCCAACCCACTTTGCTTTTCCTCTTCTT

Found at i:17656 original size:2 final size:2

Alignment explanation


    Indices: 17649--17683  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      17639 TACTTGTAAT

                                                                 
      17649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      17684 CTACTATTTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:25082 original size:17 final size:17

Alignment explanation


    Indices: 25027--25075  Score: 71
    Period size: 17  Copynumber: 2.9  Consensus size: 17

      25017 CTAGTAATCT

                  *  *       
      25027 AAGATCGCCAGTGATGC
          1 AAGATCACCGGTGATGC

                             
      25044 AAGATCACCGGTGATGC
          1 AAGATCACCGGTGATGC

                    *      
      25061 AAGATCACTGGTGAT
          1 AAGATCACCGGTGAT

      25076 CAAAGATTAC


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  17   29  1.00

ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20


Consensus pattern (17 bp):   
AAGATCACCGGTGATGC

Found at i:27280 original size:78 final size:79

Alignment explanation


    Indices: 27144--27306  Score: 274
    Period size: 78  Copynumber: 2.1  Consensus size: 79

      27134 TGTGATTATA

                                                    *                        
      27144 TCTCATCAAAATTCAATGTTTTTAGTTGATGAGAATCACCCAGATGGTTAAGCAGTGCTCATTCT
          1 TCTCATCAAAATTCAATG-TTTTAGTTGATGAGAATCACCAAGATGGTTAAGCAGTGCTCATTCT

                           
      27209 TAACAGAATCTGACT
         65 TAACAGAATCTGACT

                                      **                        *            
      27224 TCTCATCAAAATTCAATG-TTTAGTTTTTGAGAATCACCAAGATGGTTAAGCGGTGCTCATTCTT
          1 TCTCATCAAAATTCAATGTTTTAGTTGATGAGAATCACCAAGATGGTTAAGCAGTGCTCATTCTT

                          
      27288 AACAGAATCTGACT
         66 AACAGAATCTGACT

                 
      27302 TCTCA
          1 TCTCA

      27307 ATTATTCAGT


Statistics
Matches: 79,  Mismatches: 4, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  78   61  0.77
  80   18  0.23

ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34


Consensus pattern (79 bp):   
TCTCATCAAAATTCAATGTTTTAGTTGATGAGAATCACCAAGATGGTTAAGCAGTGCTCATTCTT
AACAGAATCTGACT
Done.