Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005925.1 Corchorus capsularis cultivar CVL-1 contig05943, 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: 6972
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:2805 original size:21 final size:21

Alignment explanation


    Indices: 2781--2824  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2771 AAAAACTTGA

                                  
       2781 TTGCTAAGT-ACCGCCCAATTT
          1 TTGCT-AGTCACCGCCCAATTT

                  *         *    
       2802 TTGCTATTCACCGCCCCATTT
          1 TTGCTAGTCACCGCCCAATTT

              
       2823 TT
          1 TT

       2825 CACGCTTTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20    2  0.10
  21   18  0.90

ACGTcount: A:0.18, C:0.32, G:0.11, T:0.39


Consensus pattern (21 bp):   
TTGCTAGTCACCGCCCAATTT

Found at i:3297 original size:15 final size:15

Alignment explanation


    Indices: 3256--3297  Score: 50
    Period size: 14  Copynumber: 2.7  Consensus size: 15

       3246 GGCTCAGTGT

                            *
       3256 AAAAGTGTAAAAAGGGT
          1 AAAAGTGT--AAAGGGC

                           
       3273 AAAA-TGTAAAGGGC
          1 AAAAGTGTAAAGGGC

                       
       3287 AAAAGTGTAAA
          1 AAAAGTGTAAA

       3298 AAGTGGGGCG


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  14   10  0.43
  15    6  0.26
  16    3  0.13
  17    4  0.17

ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17


Consensus pattern (15 bp):   
AAAAGTGTAAAGGGC

Found at i:4775 original size:17 final size:16

Alignment explanation


    Indices: 4735--4785  Score: 66
    Period size: 17  Copynumber: 3.1  Consensus size: 16

       4725 TATGTAATCT

                    *       
       4735 TTGATCACCGGTGATC
          1 TTGATCACTGGTGATC

                             
       4751 TTGCATCACTGGTGATC
          1 TTG-ATCACTGGTGATC

                      *      
       4768 TTAGATCACTAGTGATC
          1 TT-GATCACTGGTGATC

             
       4785 T
          1 T

       4786 GGGGGGTGAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  16    3  0.10
  17   27  0.87
  18    1  0.03

ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35


Consensus pattern (16 bp):   
TTGATCACTGGTGATC
Done.