Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013699.1 Corchorus capsularis cultivar CVL-1 contig13720, 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: 12527
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:1799 original size:3 final size:3

Alignment explanation


    Indices: 1791--1815  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       1781 CTGGCTTTAC

                                             
       1791 TCT TCT TCT TCT TCT TCT TCT TCT T
          1 TCT TCT TCT TCT TCT TCT TCT TCT T

       1816 TTTTTTGGGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (3 bp):   
TCT

Found at i:7019 original size:14 final size:14

Alignment explanation


    Indices: 7000--7027  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       6990 ACAGTCCTCC

                          
       7000 CTCTCTCGTGATGA
          1 CTCTCTCGTGATGA

                          
       7014 CTCTCTCGTGATGA
          1 CTCTCTCGTGATGA

       7028 TGTTATAGAC


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:0.14, C:0.29, G:0.21, T:0.36


Consensus pattern (14 bp):   
CTCTCTCGTGATGA

Found at i:11441 original size:82 final size:81

Alignment explanation


    Indices: 11288--11454  Score: 198
    Period size: 82  Copynumber: 2.0  Consensus size: 81

      11278 AACAACCCAA

                                  *                                     *  **
      11288 TTCGCCATTGGATAGTTCACTTGAAGGAACAACAATATGCTCAGCAACAACCCAATTCTTGGTTT
          1 TTCGCCATTGGATAGTTCAC-TCAAGGAACAACAATATGCTCAGCAACAACCCAATTCTTAGTCC

                    *        
      11353 GATGAATGTCTAACTTC
         65 GATGAATGACTAACTTC

                                                       *                     
      11370 TTCGCCATTGGATAGTTCAC-CAAGGAAC-A-AA-ATGCTCAGTAACAACCCAATTCTCGACATA
          1 TTCGCCATTGGATAGTTCACTCAAGGAACAACAATATGCTCAGCAACAACCCAATTCT-----TA

                                 
      11431 GTCCGATGAATGACTAACTTC
         61 GTCCGATGAATGACTAACTTC

               
      11452 TTC
          1 TTC

      11455 CGATGAATGA


Statistics
Matches: 74,  Mismatches: 6, Indels: 10
        0.82            0.07        0.11

Matches are distributed among these distances:
  77   22  0.30
  78    2  0.03
  79    1  0.01
  80    7  0.09
  82   42  0.57

ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28


Consensus pattern (81 bp):   
TTCGCCATTGGATAGTTCACTCAAGGAACAACAATATGCTCAGCAACAACCCAATTCTTAGTCCG
ATGAATGACTAACTTC

Found at i:11458 original size:21 final size:21

Alignment explanation


    Indices: 11432--11475  Score: 88
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      11422 CTCGACATAG

                                 
      11432 TCCGATGAATGACTAACTTCT
          1 TCCGATGAATGACTAACTTCT

                                 
      11453 TCCGATGAATGACTAACTTCT
          1 TCCGATGAATGACTAACTTCT

              
      11474 TC
          1 TC

      11476 GCCACCTGAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34


Consensus pattern (21 bp):   
TCCGATGAATGACTAACTTCT
Done.