Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015472.1 Corchorus capsularis cultivar CVL-1 contig15493, 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: 44427
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:720 original size:21 final size:23

Alignment explanation


    Indices: 668--714  Score: 76
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        658 ATCAAAATCG

                     *     *       
        668 AGACAATTTGCCCCCGATGCGAA
          1 AGACAATTTACCCCCAATGCGAA

                                   
        691 AGACAATTTACCCCCAATGCGAA
          1 AGACAATTTACCCCCAATGCGAA

             
        714 A
          1 A

        715 CAATTTTCAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17


Consensus pattern (23 bp):   
AGACAATTTACCCCCAATGCGAA

Found at i:8399 original size:24 final size:25

Alignment explanation


    Indices: 8372--8428  Score: 75
    Period size: 24  Copynumber: 2.4  Consensus size: 25

       8362 TAAATTAATC

                           *          
       8372 TCAAATTATTTTTTATTTA-A-TGTT
          1 TCAAATT-TTTTTTAGTTAGATTGTT

                                     
       8396 TCAAATTTTTTTTAGTTAGATTGTT
          1 TCAAATTTTTTTTAGTTAGATTGTT

                     
       8421 TC-AATTTT
          1 TCAAATTTT

       8429 CTAATTTTTA


Statistics
Matches: 30,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  23   10  0.33
  24   14  0.47
  25    6  0.20

ACGTcount: A:0.26, C:0.05, G:0.07, T:0.61


Consensus pattern (25 bp):   
TCAAATTTTTTTTAGTTAGATTGTT

Found at i:16434 original size:1 final size:1

Alignment explanation


    Indices: 16392--16416  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

      16382 ACCCTTTTCC

                                     
      16392 TTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTT

      16417 CAAATTTAAT


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

Matches are distributed among these distances:
   1   24  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:20659 original size:15 final size:15

Alignment explanation


    Indices: 20639--20669  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      20629 TCTAGAGCTC

                           
      20639 ATCCTGCTGTTGTCA
          1 ATCCTGCTGTTGTCA

                           
      20654 ATCCTGCTGTTGTCA
          1 ATCCTGCTGTTGTCA

             
      20669 A
          1 A

      20670 GAAGCAGCCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39


Consensus pattern (15 bp):   
ATCCTGCTGTTGTCA

Found at i:36200 original size:99 final size:95

Alignment explanation


    Indices: 36037--36216  Score: 254
    Period size: 99  Copynumber: 1.9  Consensus size: 95

      36027 TGAGAACTTG

                                           *   *           *                 
      36037 ATTTGATTTGATTCAAGGGTCGAATGACTTGGTCTTGAATTTGATAATTTAATTCAAGGGTCTTG
          1 ATTTGATTTGATTCAAGGGTCGAATGACTTGATCTCGAATTTGATAAATTAATTCAAGGGTCTTG

                                          
      36102 ACGACTTGATCTTGAATTGATGACTTGGGA
         66 ACGACTTGATCTTGAATTGATGACTTGGGA

                          *                                        *         
      36132 ATTTGATTTGATTCGAGGGTCTTTG-ATGACTTGATCTCGAATTGATGATAAATTGATTCAAGGG
          1 ATTTGATTTGATTCAAGGGTC---GAATGACTTGATCTCGAATT--TGATAAATTAATTCAAGGG

                 *               
      36196 TCTTGGCGACTTGATCTTGAA
         61 TCTTGACGACTTGATCTTGAA

      36217 CAAACAAAAT


Statistics
Matches: 74,  Mismatches: 6, Indels: 6
        0.86            0.07        0.07

Matches are distributed among these distances:
  95   20  0.27
  97   16  0.22
  98    1  0.01
  99   37  0.50

ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39


Consensus pattern (95 bp):   
ATTTGATTTGATTCAAGGGTCGAATGACTTGATCTCGAATTTGATAAATTAATTCAAGGGTCTTG
ACGACTTGATCTTGAATTGATGACTTGGGA
Done.