Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008701.1 Corchorus capsularis cultivar CVL-1 contig08722, 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: 57030
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:16926 original size:18 final size:18

Alignment explanation


    Indices: 16903--16938  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      16893 GGCATCTTTA

                              
      16903 AAACGGAAGTCTTCCTGG
          1 AAACGGAAGTCTTCCTGG

                              
      16921 AAACGGAAGTCTTCCTGG
          1 AAACGGAAGTCTTCCTGG

      16939 GCGGCACCCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22


Consensus pattern (18 bp):   
AAACGGAAGTCTTCCTGG

Found at i:25058 original size:18 final size:18

Alignment explanation


    Indices: 25031--25070  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      25021 CCAAAAAAAA

                 *      *     
      25031 AAAGATAAAAAGGGAGAG
          1 AAAGAGAAAAAGAGAGAG

                            * 
      25049 AAAGAGAAAAAGAGAGGG
          1 AAAGAGAAAAAGAGAGAG

                
      25067 AAAG
          1 AAAG

      25071 CTAATTAGCA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03


Consensus pattern (18 bp):   
AAAGAGAAAAAGAGAGAG

Found at i:33398 original size:17 final size:18

Alignment explanation


    Indices: 33376--33409  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

      33366 TGATAATAAA

                              
      33376 TCTTAGGGTTG-CAACAT
          1 TCTTAGGGTTGACAACAT

                   *         
      33393 TCTTAGGTTTGACAACA
          1 TCTTAGGGTTGACAACA

      33410 ATTACACTTG


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17   10  0.67
  18    5  0.33

ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35


Consensus pattern (18 bp):   
TCTTAGGGTTGACAACAT

Found at i:46686 original size:15 final size:17

Alignment explanation


    Indices: 46651--46689  Score: 55
    Period size: 15  Copynumber: 2.4  Consensus size: 17

      46641 GGGAAAAGAG

                       *     
      46651 AACAGAGATGATGGAAA
          1 AACAGAGATGAAGGAAA

                             
      46668 AACAGAGAT-AAGG-AA
          1 AACAGAGATGAAGGAAA

                   
      46683 AACAGAG
          1 AACAGAG

      46690 TTCTCTGTCC


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

Matches are distributed among these distances:
  15    9  0.43
  16    3  0.14
  17    9  0.43

ACGTcount: A:0.56, C:0.08, G:0.28, T:0.08


Consensus pattern (17 bp):   
AACAGAGATGAAGGAAA

Found at i:48650 original size:30 final size:29

Alignment explanation


    Indices: 48577--48654  Score: 111
    Period size: 29  Copynumber: 2.7  Consensus size: 29

      48567 ACTTGAAGCA

                        *  * *           
      48577 TTTGGACGTTTTGCCTCTTGAACTTCAAT
          1 TTTGGACGTTTTACCCCCTGAACTTCAAT

                   *                     
      48606 TTTGGACATTTTACCCCCTGAACTTCAAT
          1 TTTGGACGTTTTACCCCCTGAACTTCAAT

                                
      48635 TTTGGGACGTTTTACCCCCT
          1 TTT-GGACGTTTTACCCCCT

      48655 CAGACTAACG


Statistics
Matches: 43,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  29   28  0.65
  30   15  0.35

ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41


Consensus pattern (29 bp):   
TTTGGACGTTTTACCCCCTGAACTTCAAT
Done.