Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007115.1 Corchorus capsularis cultivar CVL-1 contig07136, 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: 8346
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:21 original size:2 final size:2

Alignment explanation


    Indices: 14--39  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

          4 CGAATAACAC

                                                  
         14 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

         40 CTAACGAAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:942 original size:31 final size:31

Alignment explanation


    Indices: 907--1013  Score: 125
    Period size: 31  Copynumber: 3.5  Consensus size: 31

        897 TCGGCTAAAT

                                           
        907 GCTCAATTTCGTCCTAAACCTTTAAGCGAGC
          1 GCTCAATTTCGTCCTAAACCTTTAAGCGAGC

                  *  *                      
        938 GCTCAAATTGGTCCTAAACCTTTGAA---AGC
          1 GCTCAATTTCGTCCTAAACCTTT-AAGCGAGC

                     *                      
        967 GCTCAATTTGGTCCTAAACCTTTAAGCG-GTC
          1 GCTCAATTTCGTCCTAAACCTTTAAGCGAG-C

                             
        998 GCTCAA-TTCAGTCCTA
          1 GCTCAATTTC-GTCCTA

       1014 TTTCTGACGA


Statistics
Matches: 66,  Mismatches: 4, Indels: 12
        0.80            0.05        0.15

Matches are distributed among these distances:
  28    2  0.03
  29   25  0.38
  30    3  0.05
  31   34  0.52
  32    2  0.03

ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30


Consensus pattern (31 bp):   
GCTCAATTTCGTCCTAAACCTTTAAGCGAGC

Found at i:977 original size:29 final size:29

Alignment explanation


    Indices: 907--992  Score: 120
    Period size: 29  Copynumber: 2.9  Consensus size: 29

        897 TCGGCTAAAT

                     *                     
        907 GCTCAATTTCGTCCTAAACCTTTAAGCGAGC
          1 GCTCAATTTGGTCCTAAACCTTTAA--GAGC

                  *                       
        938 GCTCAAATTGGTCCTAAACCTTTGAA-AGC
          1 GCTCAATTTGGTCCTAAACCTTT-AAGAGC

                                      
        967 GCTCAATTTGGTCCTAAACCTTTAAG
          1 GCTCAATTTGGTCCTAAACCTTTAAG

        993 CGGTCGCTCA


Statistics
Matches: 50,  Mismatches: 3, Indels: 6
        0.85            0.05        0.10

Matches are distributed among these distances:
  28    2  0.04
  29   25  0.50
  31   21  0.42
  32    2  0.04

ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30


Consensus pattern (29 bp):   
GCTCAATTTGGTCCTAAACCTTTAAGAGC

Found at i:3837 original size:15 final size:15

Alignment explanation


    Indices: 3817--3848  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3807 CAGCACTTTT

                           
       3817 TCTCTGTTTTTCAGC
          1 TCTCTGTTTTTCAGC

                           
       3832 TCTCTGTTTTTCAGC
          1 TCTCTGTTTTTCAGC

              
       3847 TC
          1 TC

       3849 CAAAATAATT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.06, C:0.28, G:0.12, T:0.53


Consensus pattern (15 bp):   
TCTCTGTTTTTCAGC

Found at i:4655 original size:29 final size:30

Alignment explanation


    Indices: 4621--4701  Score: 103
    Period size: 29  Copynumber: 2.7  Consensus size: 30

       4611 GCAACCGCTT

                                        *  
       4621 AAAGGTTTAGGACCAAATT-AAGCGCT-TTC
          1 AAAGGTTTAGGACCAAATTGAA-CGCTCCTC

                      *     *              
       4650 AAAGGTTTAGAACCAATTTGAACGCTCGCTC
          1 AAAGGTTTAGGACCAAATTGAACGCTC-CTC

                                 
       4681 AAAGGTTTAGGACCAAATTGA
          1 AAAGGTTTAGGACCAAATTGA

       4702 GCATTTAGCC


Statistics
Matches: 44,  Mismatches: 5, Indels: 4
        0.83            0.09        0.08

Matches are distributed among these distances:
  29   21  0.48
  30    2  0.05
  31   21  0.48

ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26


Consensus pattern (30 bp):   
AAAGGTTTAGGACCAAATTGAACGCTCCTC

Found at i:5690 original size:21 final size:21

Alignment explanation


    Indices: 5646--5693  Score: 62
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5636 GAATAACAGT

                                 
       5646 TTTGTTCTACTTTATGTGACA
          1 TTTGTTCTACTTTATGTGACA

                               ** 
       5667 TTTGTGTCT-CTTTATGTGGTA
          1 TTTGT-TCTACTTTATGTGACA

                  
       5688 TTTGTT
          1 TTTGTT

       5694 AGTTTGTTAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  20    1  0.04
  21   20  0.83
  22    3  0.12

ACGTcount: A:0.12, C:0.10, G:0.19, T:0.58


Consensus pattern (21 bp):   
TTTGTTCTACTTTATGTGACA

Found at i:8310 original size:2 final size:2

Alignment explanation


    Indices: 8305--8341  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       8295 AGTCGACTAT

                                                                   
       8305 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       8342 TAACC


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

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


Consensus pattern (2 bp):   
TA

Done.