Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010170.1 Corchorus capsularis cultivar CVL-1 contig10191, 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: 14985
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:1855 original size:131 final size:131

Alignment explanation


    Indices: 1696--1958  Score: 526
    Period size: 131  Copynumber: 2.0  Consensus size: 131

       1686 GCCCTTGAAT

                                                                             
       1696 TTATTATTTTCAAGTAAATAAGTCTGTAAAGTCTCATCTGCCATCAAATAAGTCTATTTGAACTT
          1 TTATTATTTTCAAGTAAATAAGTCTGTAAAGTCTCATCTGCCATCAAATAAGTCTATTTGAACTT

                                                                             
       1761 TTTATTATAATCAAATAAGTCCCTAAACTTTGATTTATGCTCAATTAAACTCTTGATATATATAA
         66 TTTATTATAATCAAATAAGTCCCTAAACTTTGATTTATGCTCAATTAAACTCTTGATATATATAA

             
       1826 C
        131 C

                                                                             
       1827 TTATTATTTTCAAGTAAATAAGTCTGTAAAGTCTCATCTGCCATCAAATAAGTCTATTTGAACTT
          1 TTATTATTTTCAAGTAAATAAGTCTGTAAAGTCTCATCTGCCATCAAATAAGTCTATTTGAACTT

                                                                             
       1892 TTTATTATAATCAAATAAGTCCCTAAACTTTGATTTATGCTCAATTAAACTCTTGATATATATAA
         66 TTTATTATAATCAAATAAGTCCCTAAACTTTGATTTATGCTCAATTAAACTCTTGATATATATAA

             
       1957 C
        131 C

             
       1958 T
          1 T

       1959 AAAATTGATC


Statistics
Matches: 132,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 131  132  1.00

ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41


Consensus pattern (131 bp):   
TTATTATTTTCAAGTAAATAAGTCTGTAAAGTCTCATCTGCCATCAAATAAGTCTATTTGAACTT
TTTATTATAATCAAATAAGTCCCTAAACTTTGATTTATGCTCAATTAAACTCTTGATATATATAA
C

Found at i:4007 original size:5 final size:5

Alignment explanation


    Indices: 3997--4029  Score: 57
    Period size: 5  Copynumber: 6.4  Consensus size: 5

       3987 ATTATTATAC

                                                   
       3997 TAAAA TAAAA TAAAA TAAAA TAAAA TAATAA TA
          1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA TA

       4030 TGGAGCCTTA


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5   23  0.85
   6    4  0.15

ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24


Consensus pattern (5 bp):   
TAAAA

Found at i:4702 original size:31 final size:31

Alignment explanation


    Indices: 4633--4734  Score: 114
    Period size: 31  Copynumber: 3.3  Consensus size: 31

       4623 TCCTTTTGTG

                              *  *      ** 
       4633 CACGTGGCATGCCACGTGCCATTTTTTGAAA
          1 CACGTGGCATGCCACGTGTCACTTTTTGGTA

              *                            
       4664 CATGTGGCATGCCACGTGTCACTTTTTGGTA
          1 CACGTGGCATGCCACGTGTCACTTTTTGGTA

                    *  *  *      *         
       4695 CACGTGGCGTGACATGTGTCAGTTTTTGGTA
          1 CACGTGGCATGCCACGTGTCACTTTTTGGTA

              *      
       4726 CATGTGGCA
          1 CACGTGGCA

       4735 CGACTTTTTG


Statistics
Matches: 59,  Mismatches: 12, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  31   59  1.00

ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32


Consensus pattern (31 bp):   
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Done.