Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010663.1 Corchorus capsularis cultivar CVL-1 contig10684, 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: 10474
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31


Found at i:1628 original size:21 final size:21

Alignment explanation


    Indices: 1585--1629  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1575 ATTGGAAATC

                            * *  
       1585 ATGTCTTGGAGAAACATGGAG
          1 ATGTCTTGGAGAAACAAGAAG

                        **       
       1606 ATGTCTTGGAGATTCAAGAAG
          1 ATGTCTTGGAGAAACAAGAAG

               
       1627 ATG
          1 ATG

       1630 CCACGGATGA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.33, C:0.09, G:0.31, T:0.27


Consensus pattern (21 bp):   
ATGTCTTGGAGAAACAAGAAG

Found at i:2081 original size:21 final size:21

Alignment explanation


    Indices: 2051--2090  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2041 ACAAGTGACC

                 *               
       2051 GGCCATGCGACTTGGAGATCA
          1 GGCCACGCGACTTGGAGATCA

                               
       2072 GGCCACGCGACTTGGAGAT
          1 GGCCACGCGACTTGGAGAT

       2091 GCCCGCGCAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.23, C:0.25, G:0.35, T:0.17


Consensus pattern (21 bp):   
GGCCACGCGACTTGGAGATCA

Found at i:2115 original size:33 final size:33

Alignment explanation


    Indices: 2072--2165  Score: 127
    Period size: 33  Copynumber: 2.8  Consensus size: 33

       2062 TTGGAGATCA

                       *                      
       2072 GGCCACGCGACTTGGAGATGCCC-GCGCAACACC
          1 GGCCACGCGACATGGAGATGCCCGGC-CAACACC

                 *                      *    
       2105 GGCCATGCGACATGGAGATGCCCGGCCATCACC
          1 GGCCACGCGACATGGAGATGCCCGGCCAACACC

                           **           
       2138 GGCCACGCGACATGGCCATGCCCGGCCA
          1 GGCCACGCGACATGGAGATGCCCGGCCA

       2166 CATGACTCGG


Statistics
Matches: 54,  Mismatches: 6, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  33   52  0.96
  34    2  0.04

ACGTcount: A:0.20, C:0.39, G:0.31, T:0.10


Consensus pattern (33 bp):   
GGCCACGCGACATGGAGATGCCCGGCCAACACC

Found at i:4954 original size:12 final size:13

Alignment explanation


    Indices: 4913--4957  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       4903 AATTATTGTT

                         
       4913 TGCTTTATTAATC
          1 TGCTTTATTAATC

                        *
       4926 TGCTTTATTAATT
          1 TGCTTTATTAATC

                         
       4939 TGCTTTA-TAATC
          1 TGCTTTATTAATC

                   
       4951 TGCTTTA
          1 TGCTTTA

       4958 GATTTAGATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   11  0.37
  13   19  0.63

ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56


Consensus pattern (13 bp):   
TGCTTTATTAATC

Found at i:5884 original size:32 final size:32

Alignment explanation


    Indices: 5843--5907  Score: 130
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       5833 TCTTCACTCA

                                            
       5843 TAAGCTCGTCTTGCTCATTAAAGTACAAGACT
          1 TAAGCTCGTCTTGCTCATTAAAGTACAAGACT

                                            
       5875 TAAGCTCGTCTTGCTCATTAAAGTACAAGACT
          1 TAAGCTCGTCTTGCTCATTAAAGTACAAGACT

             
       5907 T
          1 T

       5908 TCTTATTAAC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   33  1.00

ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32


Consensus pattern (32 bp):   
TAAGCTCGTCTTGCTCATTAAAGTACAAGACT
Done.