Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005629.1 Corchorus capsularis cultivar CVL-1 contig05647, 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: 1710
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36


Found at i:687 original size:32 final size:32

Alignment explanation


    Indices: 651--720  Score: 90
    Period size: 32  Copynumber: 2.2  Consensus size: 32

        641 CAATACGCCA

                  *                           
        651 CTATTTCGCGGCG-CCTAATGAAACCA-ACACCG
          1 CTATTTAGCGGCGTCC-AATGAAA-CAGACACCG

                                        *   
        683 CTATTTAGCGGCGTCCAATGAAACAGACGCCG
          1 CTATTTAGCGGCGTCCAATGAAACAGACACCG

                  
        715 CTATTT
          1 CTATTT

        721 GGGACCCCAG


Statistics
Matches: 34,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  31    2  0.06
  32   30  0.88
  33    2  0.06

ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23


Consensus pattern (32 bp):   
CTATTTAGCGGCGTCCAATGAAACAGACACCG

Found at i:1248 original size:6 final size:6

Alignment explanation


    Indices: 1237--1292  Score: 60
    Period size: 6  Copynumber: 9.5  Consensus size: 6

       1227 ACAGTAAGTT

                               *        *    *         *           
       1237 CTTTTC CTTTTC CTTTTG CTTTTC ATTTTA CTTTT- CATTTC CTTTTC
          1 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC

            *         
       1284 TTTTTC CTT
          1 CTTTTC CTT

       1293 CCGTGAGTTC


Statistics
Matches: 40,  Mismatches: 9, Indels: 2
        0.78            0.18        0.04

Matches are distributed among these distances:
   5    4  0.10
   6   36  0.90

ACGTcount: A:0.05, C:0.25, G:0.02, T:0.68


Consensus pattern (6 bp):   
CTTTTC

Found at i:1374 original size:14 final size:14

Alignment explanation


    Indices: 1355--1388  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       1345 GGTGTAACCG

                   *      
       1355 TAATTTCCTGTCCC
          1 TAATTTCATGTCCC

                          
       1369 TAATTTCATGTCCC
          1 TAATTTCATGTCCC

                  
       1383 TAATTT
          1 TAATTT

       1389 GTAAAACCTA


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

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.21, C:0.26, G:0.06, T:0.47


Consensus pattern (14 bp):   
TAATTTCATGTCCC
Done.