Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010646.1 Corchorus capsularis cultivar CVL-1 contig10667, 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: 23279
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:1793 original size:19 final size:19

Alignment explanation


    Indices: 1769--1805  Score: 58
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       1759 CTTAGAATTA

                                
       1769 GAGTAG-TCTTGTAACTTAG
          1 GAGTAGTTCTT-TAACTTAG

                              
       1788 GAGTAGTTCTTTAACTTA
          1 GAGTAGTTCTTTAACTTA

       1806 ACATTTTCCC


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  19   13  0.76
  20    4  0.24

ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41


Consensus pattern (19 bp):   
GAGTAGTTCTTTAACTTAG

Found at i:6850 original size:21 final size:21

Alignment explanation


    Indices: 6810--6852  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       6800 TGCATACACT

                                 
       6810 AAATTTGGTATCAGTATTTTC
          1 AAATTTGGTATCAGTATTTTC

                            *     
       6831 AAATATTGGTATCAGTTTTTTC
          1 AAAT-TTGGTATCAGTATTTTC

       6853 CTTTCAAACC


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  21    4  0.20
  22   16  0.80

ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49


Consensus pattern (21 bp):   
AAATTTGGTATCAGTATTTTC

Found at i:12596 original size:30 final size:30

Alignment explanation


    Indices: 12520--12599  Score: 115
    Period size: 30  Copynumber: 2.7  Consensus size: 30

      12510 CAAAGGATCA

                            *             
      12520 AATGACATCTTTGGTGAGATTCCTCCATCC
          1 AATGACATCTTTGGTGCGATTCCTCCATCC

                *                         
      12550 AATGGCATCTTTGGTGCGATTCCTCCATCC
          1 AATGACATCTTTGGTGCGATTCCTCCATCC

             *   **             
      12580 ATTGATGTCTTTGGTGCGAT
          1 AATGACATCTTTGGTGCGAT

      12600 CCCATCTCCT


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  30   44  1.00

ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36


Consensus pattern (30 bp):   
AATGACATCTTTGGTGCGATTCCTCCATCC

Found at i:13485 original size:2 final size:2

Alignment explanation


    Indices: 13478--13513  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      13468 ATCCTCACAA

                                       *                         
      13478 GT GT GT GT GT GT GT GT GT TT GT GT GT GT GT GT GT GT
          1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT

      13514 ATACCTTGTT


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

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
GT

Found at i:16592 original size:30 final size:30

Alignment explanation


    Indices: 16558--16618  Score: 104
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      16548 GTTCGAGATT

                                      *   
      16558 TTCCAAAGTTTTTGAAGTTTGGGTTCTAAG
          1 TTCCAAAGTTTTTGAAGTTTGGGTTCAAAG

                 *                        
      16588 TTCCAGAGTTTTTGAAGTTTGGGTTCAAAG
          1 TTCCAAAGTTTTTGAAGTTTGGGTTCAAAG

             
      16618 T
          1 T

      16619 CGAATAAAGG


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

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.23, C:0.10, G:0.25, T:0.43


Consensus pattern (30 bp):   
TTCCAAAGTTTTTGAAGTTTGGGTTCAAAG

Found at i:22648 original size:13 final size:13

Alignment explanation


    Indices: 22630--22657  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      22620 ATATCTATTT

                         
      22630 AAAAAAAATAAAA
          1 AAAAAAAATAAAA

                         
      22643 AAAAAAAATAAAA
          1 AAAAAAAATAAAA

              
      22656 AA
          1 AA

      22658 CTAACCCAGT


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

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07


Consensus pattern (13 bp):   
AAAAAAAATAAAA
Done.