Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007019.1 Corchorus capsularis cultivar CVL-1 contig07040, 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: 12102
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:3528 original size:111 final size:108

Alignment explanation


    Indices: 3326--3542  Score: 274
    Period size: 111  Copynumber: 2.0  Consensus size: 108

       3316 ATCTGCTAAC

                                       *    *    *        *                  
       3326 CACCTACTCACATATATGATAAAAAACTGAGAGAAAATAAACTCTATAACTAAAATGATTTGCTA
          1 CACCTACTCACATATATGATAAAAAACAGAGAAAAAAAAAACTCTAAAACTAAAATGATTTGCTA

              *   *          *   *     * *             
       3391 GCCACACATCAAGAACGGTCGGCGCGCTAGCGCGAGCCGATAA
         66 GCAACAAATCAAGAACGCTCGACGCGCCAACGCGAGCCGATAA

                                                                        *    
       3434 CACCTACTCACATATATGATAAGAACCGAA-AGAGAAAAAAAAAACTCTAAAACTAAAATTATTT
          1 CACCTACTCACATATATGATAA-AA---AACAGAGAAAAAAAAAACTCTAAAACTAAAATGATTT

                               *                *        
       3498 GCTAGCAACAAATCAAGAATGCTCGACGCGCCAACGTGAGCCGAT
         62 GCTAGCAACAAATCAAGAACGCTCGACGCGCCAACGCGAGCCGAT

       3543 CACAACTTGT


Statistics
Matches: 92,  Mismatches: 13, Indels: 5
        0.84            0.12        0.05

Matches are distributed among these distances:
 108   22  0.24
 109    2  0.02
 111   66  0.72
 112    2  0.02

ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19


Consensus pattern (108 bp):   
CACCTACTCACATATATGATAAAAAACAGAGAAAAAAAAAACTCTAAAACTAAAATGATTTGCTA
GCAACAAATCAAGAACGCTCGACGCGCCAACGCGAGCCGATAA

Found at i:5607 original size:24 final size:24

Alignment explanation


    Indices: 5575--5621  Score: 94
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5565 ACAAGAAGTA

                                    
       5575 TGTGACTAAGCTTACAACAAAAAG
          1 TGTGACTAAGCTTACAACAAAAAG

                                   
       5599 TGTGACTAAGCTTACAACAAAAA
          1 TGTGACTAAGCTTACAACAAAAA

       5622 AGCAATTGAA


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

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21


Consensus pattern (24 bp):   
TGTGACTAAGCTTACAACAAAAAG

Found at i:9636 original size:31 final size:31

Alignment explanation


    Indices: 9585--9741  Score: 125
    Period size: 31  Copynumber: 5.4  Consensus size: 31

       9575 TGTGCACGTA

                        *  *      **       
       9585 GCATGCCACGTGCCATTTTTTGAAACATGTG
          1 GCATGCCACGTGTCACTTTTTGGTACATGTG

                     *                 *   
       9616 GCATGCCACATGTCACTTTTTGGTACACGTG
          1 GCATGCCACGTGTCACTTTTTGGTACATGTG

              *  *  *                      
       9647 GCGTGACATGTGTCACTTTTTGGTACATGT-
          1 GCATGCCACGTGTCACTTTTTGGTACATGTG

                                          *
       9677 G---G-CAC--G--ACTTTTTGGTACATGTA
          1 GCATGCCACGTGTCACTTTTTGGTACATGTG

              *      *                 *   
       9700 GCGTGCCACATGTCACTTTTTGGTACACGTG
          1 GCATGCCACGTGTCACTTTTTGGTACATGTG

              *        
       9731 GCGTGCCACGT
          1 GCATGCCACGT

       9742 CGGACACCGT


Statistics
Matches: 102,  Mismatches: 15, Indels: 18
        0.76            0.11        0.13

Matches are distributed among these distances:
  22   16  0.16
  23    1  0.01
  24    1  0.01
  26    3  0.03
  27    4  0.04
  29    1  0.01
  30    1  0.01
  31   75  0.74

ACGTcount: A:0.18, C:0.23, G:0.25, T:0.33


Consensus pattern (31 bp):   
GCATGCCACGTGTCACTTTTTGGTACATGTG

Found at i:9688 original size:53 final size:53

Alignment explanation


    Indices: 9630--9732  Score: 152
    Period size: 53  Copynumber: 1.9  Consensus size: 53

       9620 GCCACATGTC

                            *        **                 *        
       9630 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
          1 ACTTTTTGGTACACGTAGCGTGACACATGTCACTTTTTGGTACACGTGGCACG

                         *        *                           
       9683 ACTTTTTGGTACATGTAGCGTGCCACATGTCACTTTTTGGTACACGTGGC
          1 ACTTTTTGGTACACGTAGCGTGACACATGTCACTTTTTGGTACACGTGGC

       9733 GTGCCACGTC


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  53   44  1.00

ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36


Consensus pattern (53 bp):   
ACTTTTTGGTACACGTAGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Done.