Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003545.1 Corchorus capsularis cultivar CVL-1 contig03553, 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, 958

Length: 1597
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33


Found at i:37 original size:16 final size:16

Alignment explanation


    Indices: 12--53  Score: 66
    Period size: 16  Copynumber: 2.6  Consensus size: 16

          2 TGTAATTTTT

                 *       *  
         12 TTCTTGGTTGAATCTG
          1 TTCTTTGTTGAATATG

                            
         28 TTCTTTGTTGAATATG
          1 TTCTTTGTTGAATATG

                      
         44 TTCTTTGTTG
          1 TTCTTTGTTG

         54 CTTCTCCAAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  16   24  1.00

ACGTcount: A:0.12, C:0.10, G:0.21, T:0.57


Consensus pattern (16 bp):   
TTCTTTGTTGAATATG

Found at i:1469 original size:161 final size:163

Alignment explanation


    Indices: 1262--1588  Score: 597
    Period size: 163  Copynumber: 2.0  Consensus size: 163

       1252 AGGGTTTATT

                                                                             
       1262 ATGAAATGTGTAACTGTAACCACAATAAAAGCATATAATCATATCATATGATCATAATTACAA-T
          1 ATGAAATGTGTAACTGTAACCACAATAAAAGCATATAATCATATCATATGATCATAATTACAATT

                                                                             
       1326 TTAAATAATTAATTGAGAAGATGG-AAAACATATTAAGTTACAAAATTTAATTTA-GAGTGTAAC
         66 TTAAATAATTAATTGAGAAGATGGAAAAACATATTAAGTTACAAAATTTAATTTAGGA-TGTAAC

                           *                * 
       1389 GTACATGTAAACATCTAATGACAATTAATATAGA
        130 GTACATGTAAACATCCAATGACAATTAATATAAA

                                        *                                    
       1423 ATGAAATGTGTAACTGTAACCACAATAATAGCATATAATCATATCATATGATCATAATTACAATT
          1 ATGAAATGTGTAACTGTAACCACAATAAAAGCATATAATCATATCATATGATCATAATTACAATT

                                                                             
       1488 TTAAATAATTAATTGAGAAGATGGAAAAACATATTAAGTTACAAAATTTAATTTAGGATGTAACG
         66 TTAAATAATTAATTGAGAAGATGGAAAAACATATTAAGTTACAAAATTTAATTTAGGATGTAACG

                                             
       1553 TACATGTAAACATCCAATGACAATTAATATAAA
        131 TACATGTAAACATCCAATGACAATTAATATAAA

               
       1586 ATG
          1 ATG

       1589 TGATTTTTT


Statistics
Matches: 160,  Mismatches: 3, Indels: 4
        0.96            0.02        0.02

Matches are distributed among these distances:
 161   62  0.39
 162   25  0.16
 163   71  0.44
 164    2  0.01

ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31


Consensus pattern (163 bp):   
ATGAAATGTGTAACTGTAACCACAATAAAAGCATATAATCATATCATATGATCATAATTACAATT
TTAAATAATTAATTGAGAAGATGGAAAAACATATTAAGTTACAAAATTTAATTTAGGATGTAACG
TACATGTAAACATCCAATGACAATTAATATAAA

Done.