Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003909.1 Corchorus capsularis cultivar CVL-1 contig03917, 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, 777

Length: 1296
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31


Found at i:547 original size:139 final size:140

Alignment explanation


    Indices: 287--655  Score: 496
    Period size: 139  Copynumber: 2.6  Consensus size: 140

        277 TTTTTGGCAA

                *          *       ** *          *                           
        287 TTAATTAACGACTAATTTGATTCCCTAATTTATTTAGTATGTTCAATCAATCTATTTTTTTTGCT
          1 TTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAAT-T-TTTTTTTTG-T

                                    *        *                               
        352 AACATAATTACTAATTGATTCATTCATTTATGACAAAATCAAATAATCATCAATCAATTATAACT
         63 AACATAATTACTAATTGATTCATTTATTTATGAAAAAATCAAATAATCATCAATCAATTATAACT

                         
        417 TTGATTGACAAAG
        128 TTGATTGACAAAG

              *                                                              
        430 TTGA-TCAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAA-TTTTTTTTTGTAA
          1 TTAACT-AACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTTTGTAA

            *                 *                               *              
        493 TATAATTACTAATTGATTTATTTATTTATGGAAAAAAT-AAATAATCATCCATCAATTATAACTT
         65 CATAATTACTAATTGATTCATTTATTTAT-GAAAAAATCAAATAATCATCAATCAATTATAACTT

                  *     
        557 TGATTGGCAAAG
        129 TGATTGACAAAG

                                         *      * *                          
        569 TTAACTAA-GAACTAACTTGATTCATTTACTTATTTTGGATGTTCAATCAATTTATTTTTTTGTA
          1 TTAACTAACG-ACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTT-TTTTTTTGTA

                                    
        633 ACATAA-TACTAATTGATTCATTT
         64 ACATAATTACTAATTGATTCATTT

        656 TGTCACGCCC


Statistics
Matches: 202,  Mismatches: 18, Indels: 15
        0.86            0.08        0.06

Matches are distributed among these distances:
 138    1  0.00
 139  107  0.53
 140   35  0.17
 141   16  0.08
 142    1  0.00
 143   42  0.21

ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44


Consensus pattern (140 bp):   
TTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTTTGTAAC
ATAATTACTAATTGATTCATTTATTTATGAAAAAATCAAATAATCATCAATCAATTATAACTTTG
ATTGACAAAG
Done.