Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007211.1 Corchorus capsularis cultivar CVL-1 contig07232, 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: 6543
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35


Found at i:835 original size:3 final size:3

Alignment explanation


    Indices: 829--868  Score: 64
    Period size: 3  Copynumber: 13.7  Consensus size: 3

        819 ATAATAATAA

                                                            *     
        829 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT GAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA

        869 CCCACCACCC


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   2    2  0.06
   3   32  0.94

ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65


Consensus pattern (3 bp):   
TAT

Found at i:2033 original size:1 final size:1

Alignment explanation


    Indices: 2027--2056  Score: 60
    Period size: 1  Copynumber: 30.0  Consensus size: 1

       2017 TCTTTTATGC

                                          
       2027 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       2057 CATCCATAGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   29  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:3277 original size:53 final size:52

Alignment explanation


    Indices: 3198--3299  Score: 152
    Period size: 53  Copynumber: 1.9  Consensus size: 52

       3188 AAATGATTTG

                           *                                     
       3198 ATCACCTGTGGTGATTTTGGGTGGTGATCTCAGATCA-CCCTGTTTGGTTGAA
          1 ATCACCTGTGGTGATCTTGGGTGGTGATCTCAGATCAGCCC-GTTTGGTTGAA

                       *                    *                 
       3250 ATCACCTGTTGTTGATCTTGGGTGGTGATCTCTGATCAGCCCGTTTGGTT
          1 ATCACCTG-TGGTGATCTTGGGTGGTGATCTCAGATCAGCCCGTTTGGTT

       3300 ACACCTTTTT


Statistics
Matches: 45,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
  52    8  0.18
  53   34  0.76
  54    3  0.07

ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38


Consensus pattern (52 bp):   
ATCACCTGTGGTGATCTTGGGTGGTGATCTCAGATCAGCCCGTTTGGTTGAA

Found at i:4521 original size:6 final size:6

Alignment explanation


    Indices: 4510--4541  Score: 64
    Period size: 6  Copynumber: 5.3  Consensus size: 6

       4500 GAATTTGAGT

                                                 
       4510 TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC TC
          1 TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC TC

       4542 AGGCTCAATC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.16, C:0.34, G:0.31, T:0.19


Consensus pattern (6 bp):   
TCGAGC

Done.