Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008151.1 Corchorus capsularis cultivar CVL-1 contig08172, 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: 41144
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:4350 original size:10 final size:10

Alignment explanation


    Indices: 4332--4361  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       4322 TGGATGAGGA

                *     
       4332 TTCTAGAATT
          1 TTCTGGAATT

                      
       4342 TTCTGGAATT
          1 TTCTGGAATT

                      
       4352 TTCTGGAATT
          1 TTCTGGAATT

       4362 GAGCAGGGAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  10   19  1.00

ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50


Consensus pattern (10 bp):   
TTCTGGAATT

Found at i:23008 original size:59 final size:59

Alignment explanation


    Indices: 22936--23049  Score: 194
    Period size: 59  Copynumber: 1.9  Consensus size: 59

      22926 CATTTTGCCC

                                         * *                            
      22936 CCCAAACTAAAATCAATACAATTTTG-ACTTTGACTTCCAAAATTTAAGACAATTTACCT
          1 CCCAAACTAAAATCAATACAA-TTTGCACCTGGACTTCCAAAATTTAAGACAATTTACCT

                                                                   
      22995 CCCAAACTAAAATCAATACAATTTGCACCTGGACTTCCAAAATTTAAGACAATTT
          1 CCCAAACTAAAATCAATACAATTTGCACCTGGACTTCCAAAATTTAAGACAATTT

      23050 GCCCCTTCCG


Statistics
Matches: 52,  Mismatches: 2, Indels: 2
        0.93            0.04        0.04

Matches are distributed among these distances:
  58    4  0.08
  59   48  0.92

ACGTcount: A:0.41, C:0.23, G:0.06, T:0.30


Consensus pattern (59 bp):   
CCCAAACTAAAATCAATACAATTTGCACCTGGACTTCCAAAATTTAAGACAATTTACCT

Found at i:25361 original size:29 final size:31

Alignment explanation


    Indices: 25329--25403  Score: 77
    Period size: 29  Copynumber: 2.5  Consensus size: 31

      25319 TTGTCTAATT

                                      *    
      25329 GACCTTTAGTCCCTTAAACTT-TAATTTGA-
          1 GACCTTTAGTCCCTTAAACTTGTAATATGAG

                                             
      25358 GACCTTT--TACCTCTTAAACTTGTAATATGAG
          1 GACCTTTAGT-CC-CTTAAACTTGTAATATGAG

                *          
      25389 GACATTTTAGTCCCT
          1 GAC-CTTTAGTCCCT

      25404 CTCAAACGGT


Statistics
Matches: 37,  Mismatches: 2, Indels: 11
        0.74            0.04        0.22

Matches are distributed among these distances:
  27    1  0.03
  28    2  0.05
  29   16  0.43
  30    7  0.19
  31    3  0.08
  32    5  0.14
  33    2  0.05
  34    1  0.03

ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40


Consensus pattern (31 bp):   
GACCTTTAGTCCCTTAAACTTGTAATATGAG

Found at i:36686 original size:14 final size:14

Alignment explanation


    Indices: 36653--36680  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      36643 TGTATTAGAA

                          
      36653 AGTTTATAAGTATT
          1 AGTTTATAAGTATT

                          
      36667 AGTTTATAAGTATT
          1 AGTTTATAAGTATT

      36681 GCTTTAAAAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50


Consensus pattern (14 bp):   
AGTTTATAAGTATT
Done.