Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007989.1 Corchorus capsularis cultivar CVL-1 contig08010, 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: 7148
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:2575 original size:6 final size:6

Alignment explanation


    Indices: 2564--2611  Score: 87
    Period size: 6  Copynumber: 7.8  Consensus size: 6

       2554 TTCTTCATTC

                                                                   
       2564 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTTT TCTTTT TCTTT
          1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC-TTTT TCTTTT TCTTT

       2612 CATTTTTTCA


Statistics
Matches: 41,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   6   35  0.85
   7    6  0.15

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (6 bp):   
TCTTTT

Found at i:2587 original size:18 final size:19

Alignment explanation


    Indices: 2564--2611  Score: 89
    Period size: 19  Copynumber: 2.6  Consensus size: 19

       2554 TTCTTCATTC

                               
       2564 TCTTTTTCTTTTTC-TTTT
          1 TCTTTTTCTTTTTCTTTTT

                               
       2582 TCTTTTTCTTTTTCTTTTT
          1 TCTTTTTCTTTTTCTTTTT

                       
       2601 TCTTTTTCTTT
          1 TCTTTTTCTTT

       2612 CATTTTTTCA


Statistics
Matches: 29,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  18   14  0.48
  19   15  0.52

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (19 bp):   
TCTTTTTCTTTTTCTTTTT

Found at i:2617 original size:18 final size:17

Alignment explanation


    Indices: 2564--2620  Score: 69
    Period size: 18  Copynumber: 3.1  Consensus size: 17

       2554 TTCTTCATTC

                       *      
       2564 TCTTTTTCTTTTTCTTTT
          1 TCTTTTTCTTTCT-TTTT

                               
       2582 TCTTTTTCTTTTTCTTTTT
          1 TCTTTTTC--TTTCTTTTT

                              
       2601 TCTTTTTCTTTCATTTTT
          1 TCTTTTTCTTTC-TTTTT

              
       2619 TC
          1 TC

       2621 ATGCACTTGA


Statistics
Matches: 35,  Mismatches: 1, Indels: 6
        0.83            0.02        0.14

Matches are distributed among these distances:
  17    4  0.11
  18   15  0.43
  19   12  0.34
  20    4  0.11

ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81


Consensus pattern (17 bp):   
TCTTTTTCTTTCTTTTT

Found at i:2956 original size:28 final size:28

Alignment explanation


    Indices: 2910--2963  Score: 72
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       2900 CTTCGCCTTT

                        ***             
       2910 CCTTTCACTTTCTTTTTTCAATTTTTTC
          1 CCTTTCACTTTCAACTTTCAATTTTTTC

                                *     
       2938 CCTTTCACTTTCAACTTTCACTTTTT
          1 CCTTTCACTTTCAACTTTCAATTTTT

       2964 CATCCTTTTT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  28   22  1.00

ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59


Consensus pattern (28 bp):   
CCTTTCACTTTCAACTTTCAATTTTTTC
Done.