Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009282.1 Corchorus capsularis cultivar CVL-1 contig09303, 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: 6568
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34


Found at i:3056 original size:27 final size:27

Alignment explanation


    Indices: 3026--3083  Score: 71
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       3016 GACTCATTCC

                        *     *        
       3026 ATTCACCTCTGCTTCCTCTATAACTAT
          1 ATTCACCTCTGCATCCTCCATAACTAT

                *   * *                
       3053 ATTCCCCTGTTCATCCTCCATAACTAT
          1 ATTCACCTCTGCATCCTCCATAACTAT

                
       3080 ATTC
          1 ATTC

       3084 CCCTGTTCAC


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.22, C:0.34, G:0.03, T:0.40


Consensus pattern (27 bp):   
ATTCACCTCTGCATCCTCCATAACTAT

Found at i:3084 original size:27 final size:27

Alignment explanation


    Indices: 3039--3092  Score: 99
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       3029 CACCTCTGCT

                 *                     
       3039 TCCTCTATAACTATATTCCCCTGTTCA
          1 TCCTCCATAACTATATTCCCCTGTTCA

                                       
       3066 TCCTCCATAACTATATTCCCCTGTTCA
          1 TCCTCCATAACTATATTCCCCTGTTCA

       3093 CATTCAATAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.22, C:0.35, G:0.04, T:0.39


Consensus pattern (27 bp):   
TCCTCCATAACTATATTCCCCTGTTCA

Found at i:5155 original size:30 final size:31

Alignment explanation


    Indices: 5119--5183  Score: 89
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       5109 GTGCAAATGG

                                            
       5119 GTCCCTGAAG-TGAACTT-AGTGAGCAATTGA
          1 GTCCCTGAAGTTG-ACTTAAGTGAGCAATTGA

                          *    *           
       5149 GTCCCTGAAGTTGAGTTAATTGAGCAATTGA
          1 GTCCCTGAAGTTGACTTAAGTGAGCAATTGA

                
       5180 GTCC
          1 GTCC

       5184 TTCACCATTT


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

Matches are distributed among these distances:
  30   13  0.42
  31   18  0.58

ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29


Consensus pattern (31 bp):   
GTCCCTGAAGTTGACTTAAGTGAGCAATTGA

Found at i:5396 original size:29 final size:31

Alignment explanation


    Indices: 5345--5425  Score: 85
    Period size: 29  Copynumber: 2.7  Consensus size: 31

       5335 GCTCAGTTAA

                    *      *  *            
       5345 CTCCACTTCAGGGACTAAATTGC-ATATTC-
          1 CTCCACTTGAGGGACCAATTTGCTATATTCG

            * *                       *    
       5374 TTTCACTTGAGGGACCAATTTGCTATGTTCG
          1 CTCCACTTGAGGGACCAATTTGCTATATTCG

                      *          
       5405 CTCCACTTGAAGGACCAATTT
          1 CTCCACTTGAGGGACCAATTT

       5426 TGTACTTTTA


Statistics
Matches: 41,  Mismatches: 9, Indels: 2
        0.79            0.17        0.04

Matches are distributed among these distances:
  29   18  0.44
  30    5  0.12
  31   18  0.44

ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33


Consensus pattern (31 bp):   
CTCCACTTGAGGGACCAATTTGCTATATTCG
Done.