Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009700.1 Corchorus capsularis cultivar CVL-1 contig09721, 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: 6939
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:692 original size:23 final size:23

Alignment explanation


    Indices: 662--713  Score: 95
    Period size: 23  Copynumber: 2.3  Consensus size: 23

        652 ATTCTTGATT

                                   
        662 AGCAAATTTCATTTTATATTTTA
          1 AGCAAATTTCATTTTATATTTTA

                                   
        685 AGCAAATTTCATTTTATATTTTA
          1 AGCAAATTTCATTTTATATTTTA

             *    
        708 AACAAA
          1 AGCAAA

        714 ATGACATCAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  23   28  1.00

ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46


Consensus pattern (23 bp):   
AGCAAATTTCATTTTATATTTTA

Found at i:1193 original size:33 final size:32

Alignment explanation


    Indices: 1155--1226  Score: 83
    Period size: 31  Copynumber: 2.2  Consensus size: 32

       1145 GACAAAAATA

                           *                 
       1155 ACACGTGGGCACACGTACATATAACAAAAGGTG
          1 ACACGTGGGCACAC-CACATATAACAAAAGGTG

                        *    * *  *         
       1188 ACACGT-GGCACGCCACGTGTACCAAAAGGTG
          1 ACACGTGGGCACACCACATATAACAAAAGGTG

                    
       1219 ACACGTGG
          1 ACACGTGG

       1227 CACGCCATGT


Statistics
Matches: 33,  Mismatches: 5, Indels: 3
        0.80            0.12        0.07

Matches are distributed among these distances:
  31   20  0.61
  32    7  0.21
  33    6  0.18

ACGTcount: A:0.33, C:0.25, G:0.28, T:0.14


Consensus pattern (32 bp):   
ACACGTGGGCACACCACATATAACAAAAGGTG

Found at i:1252 original size:30 final size:31

Alignment explanation


    Indices: 1179--1255  Score: 138
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       1169 GTACATATAA

                                           
       1179 CAAAAGGTGACACGTGGCACGCCACGTGTAC
          1 CAAAAGGTGACACGTGGCACGCCACGTGTAC

                                    *      
       1210 CAAAAGGTGACACGTGGCACGCCATGTGTAC
          1 CAAAAGGTGACACGTGGCACGCCACGTGTAC

                            
       1241 CAAAA-GTGACACGTG
          1 CAAAAGGTGACACGTG

       1256 TCATTTTTTT


Statistics
Matches: 45,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  30   10  0.22
  31   35  0.78

ACGTcount: A:0.31, C:0.26, G:0.29, T:0.14


Consensus pattern (31 bp):   
CAAAAGGTGACACGTGGCACGCCACGTGTAC
Done.