Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009957.1 Corchorus capsularis cultivar CVL-1 contig09978, 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: 10589
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--37  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

                                                                   
          1 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

         38 TGTGCAAATT


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

Found at i:3892 original size:285 final size:285

Alignment explanation


    Indices: 3377--3953  Score: 1145
    Period size: 285  Copynumber: 2.0  Consensus size: 285

       3367 CATTACTACA

                                                                             
       3377 TATTGTTACAAGTGCATATTTCTACTTCAACCGTTTCACAGGGATGAAAATGAAAGAAACTCGTA
          1 TATT-TTACAAGTGCATATTTCTACTTCAACCGTTTCACAGGGATGAAAATGAAAGAAACTCGTA

                                                                             
       3442 TTCCATATAATCTATTTTATTGGTGAAAACCCAAACTTCATTTTCAAACTTATGTAGCTTTAAGC
         65 TTCCATATAATCTATTTTATTGGTGAAAACCCAAACTTCATTTTCAAACTTATGTAGCTTTAAGC

                                                                             
       3507 ACATTGTGAAGTGACATTGCTGATTAGCTACCCATAATTTTGGTGTAATCACGTTGTTCTCTCTT
        130 ACATTGTGAAGTGACATTGCTGATTAGCTACCCATAATTTTGGTGTAATCACGTTGTTCTCTCTT

                                                                             
       3572 ATCTATTTGGTATGCACTTGGCTTTGGCTGTTACGTTTTTATAGGCAGCTCTTATCTTGTGCCTC
        195 ATCTATTTGGTATGCACTTGGCTTTGGCTGTTACGTTTTTATAGGCAGCTCTTATCTTGTGCCTC

                                      
       3637 CATACGCTTAGGTTCCTTATGCATTG
        260 CATACGCTTAGGTTCCTTATGCATTG

                                                                             
       3663 TATTTTACAAGTGCATATTTCTACTTCAACCGTTTCACAGGGATGAAAATGAAAGAAACTCGTAT
          1 TATTTTACAAGTGCATATTTCTACTTCAACCGTTTCACAGGGATGAAAATGAAAGAAACTCGTAT

                                                                             
       3728 TCCATATAATCTATTTTATTGGTGAAAACCCAAACTTCATTTTCAAACTTATGTAGCTTTAAGCA
         66 TCCATATAATCTATTTTATTGGTGAAAACCCAAACTTCATTTTCAAACTTATGTAGCTTTAAGCA

                                                                             
       3793 CATTGTGAAGTGACATTGCTGATTAGCTACCCATAATTTTGGTGTAATCACGTTGTTCTCTCTTA
        131 CATTGTGAAGTGACATTGCTGATTAGCTACCCATAATTTTGGTGTAATCACGTTGTTCTCTCTTA

                                                                             
       3858 TCTATTTGGTATGCACTTGGCTTTGGCTGTTACGTTTTTATAGGCAGCTCTTATCTTGTGCCTCC
        196 TCTATTTGGTATGCACTTGGCTTTGGCTGTTACGTTTTTATAGGCAGCTCTTATCTTGTGCCTCC

                                     
       3923 ATACGCTTAGGTTCCTTATGCATTG
        261 ATACGCTTAGGTTCCTTATGCATTG

                  
       3948 TATTTT
          1 TATTTT

       3954 TCCGCAAAGA


Statistics
Matches: 291,  Mismatches: 0, Indels: 1
        1.00            0.00        0.00

Matches are distributed among these distances:
 285  287  0.99
 286    4  0.01

ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39


Consensus pattern (285 bp):   
TATTTTACAAGTGCATATTTCTACTTCAACCGTTTCACAGGGATGAAAATGAAAGAAACTCGTAT
TCCATATAATCTATTTTATTGGTGAAAACCCAAACTTCATTTTCAAACTTATGTAGCTTTAAGCA
CATTGTGAAGTGACATTGCTGATTAGCTACCCATAATTTTGGTGTAATCACGTTGTTCTCTCTTA
TCTATTTGGTATGCACTTGGCTTTGGCTGTTACGTTTTTATAGGCAGCTCTTATCTTGTGCCTCC
ATACGCTTAGGTTCCTTATGCATTG

Found at i:9873 original size:42 final size:42

Alignment explanation


    Indices: 9804--9916  Score: 136
    Period size: 42  Copynumber: 2.7  Consensus size: 42

       9794 ATGAGATGAA

                    *    *   * *  *      *        *   
       9804 TTGGGCCATGCAGTCCATAGCTGTGGTATGAATGGAGACTTG
          1 TTGGGCCACGCAGCCCACATCTATGGTATAAATGGAGAATTG

                                *              *      
       9846 TTGGGCCACGCAGCCCACATTTATGGTATAAATGGGGAATTG
          1 TTGGGCCACGCAGCCCACATCTATGGTATAAATGGAGAATTG

                          *              
       9888 TTGGGCCACGCAGCTCACATCTATGGTAT
          1 TTGGGCCACGCAGCCCACATCTATGGTAT

       9917 TATCAATGGG


Statistics
Matches: 60,  Mismatches: 11, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  42   60  1.00

ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27


Consensus pattern (42 bp):   
TTGGGCCACGCAGCCCACATCTATGGTATAAATGGAGAATTG

Found at i:9940 original size:45 final size:42

Alignment explanation


    Indices: 9844--9941  Score: 133
    Period size: 42  Copynumber: 2.3  Consensus size: 42

       9834 AATGGAGACT

                                  *                  *
       9844 TGTTGGGCCACGCAGCCCACATTTATGGTATAAATGGGGAAT
          1 TGTTGGGCCACGCAGCCCACATCTATGGTATAAATGGGGAAA

                            *                            
       9886 TGTTGGGCCACGCAGCTCACATCTATGGTATTATCAATGGGGAAA
          1 TGTTGGGCCACGCAGCCCACATCTATGGTA-TA--AATGGGGAAA

                *      
       9931 TGTTTGGCCAC
          1 TGTTGGGCCAC

       9942 AGATATTGGC


Statistics
Matches: 49,  Mismatches: 4, Indels: 3
        0.88            0.07        0.05

Matches are distributed among these distances:
  42   28  0.57
  43    2  0.04
  45   19  0.39

ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28


Consensus pattern (42 bp):   
TGTTGGGCCACGCAGCCCACATCTATGGTATAAATGGGGAAA

Found at i:10019 original size:18 final size:18

Alignment explanation


    Indices: 9996--10032  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       9986 ATAATTACCT

                              
       9996 TTCTAAGATGGCAAATTA
          1 TTCTAAGATGGCAAATTA

                              
      10014 TTCTAAGATGGCAAATTA
          1 TTCTAAGATGGCAAATTA

             
      10032 T
          1 T

      10033 ACAATACACC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35


Consensus pattern (18 bp):   
TTCTAAGATGGCAAATTA

Found at i:10538 original size:17 final size:17

Alignment explanation


    Indices: 10516--10549  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      10506 CCGCCCTCAT

                             
      10516 GGGGCGGCTTCACCATG
          1 GGGGCGGCTTCACCATG

                       *     
      10533 GGGGCGGCTTCCCCATG
          1 GGGGCGGCTTCACCATG

      10550 AAAGGCCGCC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.09, C:0.32, G:0.41, T:0.18


Consensus pattern (17 bp):   
GGGGCGGCTTCACCATG
Done.