Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007809.1 Corchorus capsularis cultivar CVL-1 contig07830, 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: 17339
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:3551 original size:22 final size:22

Alignment explanation


    Indices: 3509--3566  Score: 55
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       3499 TTTATGTTTG

                    *       *      
       3509 GGCTTTGATGCTTATATTTAGAT
          1 GGCTTTG-GGCTTATACTTAGAT

                                 * 
       3532 GG-TTTGGGCTTAATACTTAGTT
          1 GGCTTTGGGCTT-ATACTTAGAT

                         
       3554 GGTCTTTGGGCTT
          1 GG-CTTTGGGCTT

       3567 TGTTATTTCA


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  21    4  0.14
  22   14  0.48
  23    2  0.07
  24    9  0.31

ACGTcount: A:0.16, C:0.10, G:0.28, T:0.47


Consensus pattern (22 bp):   
GGCTTTGGGCTTATACTTAGAT

Found at i:6627 original size:18 final size:19

Alignment explanation


    Indices: 6598--6636  Score: 62
    Period size: 18  Copynumber: 2.1  Consensus size: 19

       6588 CAAGATTAAA

                        *      
       6598 AAAAGAAAAAACTAGAAAG
          1 AAAAGAAAAAACGAGAAAG

                               
       6617 AAAAG-AAAAACGAGAAAG
          1 AAAAGAAAAAACGAGAAAG

              
       6635 AA
          1 AA

       6637 TTAGTAGAAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18   14  0.74
  19    5  0.26

ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03


Consensus pattern (19 bp):   
AAAAGAAAAAACGAGAAAG

Found at i:15743 original size:17 final size:17

Alignment explanation


    Indices: 15711--15742  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

      15701 GGGTTAAGAG

                             
      15711 GAGAAGAAAAAGAAAAT
          1 GAGAAGAAAAAGAAAAT

                            
      15728 GAGAAG-AAAAGAAAA
          1 GAGAAGAAAAAGAAAA

      15743 AAGGAGCTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    9  0.60
  17    6  0.40

ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03


Consensus pattern (17 bp):   
GAGAAGAAAAAGAAAAT

Found at i:17082 original size:16 final size:16

Alignment explanation


    Indices: 17063--17097  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      17053 GACTCGAAAA

                    *       
      17063 ACCCAAAATCCGAATG
          1 ACCCAAAACCCGAATG

                         *  
      17079 ACCCAAAACCCGAGTG
          1 ACCCAAAACCCGAATG

               
      17095 ACC
          1 ACC

      17098 TGAAGCCAAA


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

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.40, C:0.37, G:0.14, T:0.09


Consensus pattern (16 bp):   
ACCCAAAACCCGAATG
Done.