Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011888.1 Corchorus capsularis cultivar CVL-1 contig11909, 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: 7777
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33


Found at i:400 original size:171 final size:171

Alignment explanation


    Indices: 110--440  Score: 617
    Period size: 171  Copynumber: 1.9  Consensus size: 171

        100 TTTTTTGAGA

                                                                             
        110 ACTTAAACTATTGTAGTTTTATTCTACTAAAAACTCTATCTTGATTTAATTATTAAATCTAATAT
          1 ACTTAAACTATTGTAGTTTTATTCTACTAAAAACTCTATCTTGATTTAATTATTAAATCTAATAT

                                                                             
        175 CTTTATAATTTCTTTATTTTTACCATTTTACTATTTTTCAATAAAAATTTGATATATTAAAATTT
         66 CTTTATAATTTCTTTATTTTTACCATTTTACTATTTTTCAATAAAAATTTGATATATTAAAATTT

                                                     
        240 TTAATATACAGTTTTATTCTACTAAAAACTTAAATGCCCTT
        131 TTAATATACAGTTTTATTCTACTAAAAACTTAAATGCCCTT

                *                                     *    *               * 
        281 ACTTGAACTATTGTAGTTTTATTCTACTAAAAACTCTATCTTTATTTGATTATTAAATCTAATTT
          1 ACTTAAACTATTGTAGTTTTATTCTACTAAAAACTCTATCTTGATTTAATTATTAAATCTAATAT

                                                                             
        346 CTTTATAATTTCTTTATTTTTACCATTTTACTATTTTTCAATAAAAATTTGATATATTAAAATTT
         66 CTTTATAATTTCTTTATTTTTACCATTTTACTATTTTTCAATAAAAATTTGATATATTAAAATTT

                     *                    
        411 TTAATATACTGTTTTATTCTACTAAAAACT
        131 TTAATATACAGTTTTATTCTACTAAAAACT

        441 CTATTTTCAT


Statistics
Matches: 155,  Mismatches: 5, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 171  155  1.00

ACGTcount: A:0.35, C:0.12, G:0.04, T:0.50


Consensus pattern (171 bp):   
ACTTAAACTATTGTAGTTTTATTCTACTAAAAACTCTATCTTGATTTAATTATTAAATCTAATAT
CTTTATAATTTCTTTATTTTTACCATTTTACTATTTTTCAATAAAAATTTGATATATTAAAATTT
TTAATATACAGTTTTATTCTACTAAAAACTTAAATGCCCTT

Found at i:3415 original size:17 final size:17

Alignment explanation


    Indices: 3393--3429  Score: 65
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       3383 GTTATCCAGC

                             
       3393 ACCTCATGCTACCTAGT
          1 ACCTCATGCTACCTAGT

                          *  
       3410 ACCTCATGCTACCTGGT
          1 ACCTCATGCTACCTAGT

               
       3427 ACC
          1 ACC

       3430 ATGAGGGGAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.22, C:0.38, G:0.14, T:0.27


Consensus pattern (17 bp):   
ACCTCATGCTACCTAGT

Found at i:7726 original size:12 final size:12

Alignment explanation


    Indices: 7709--7733  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       7699 GGCAGACACG

                        
       7709 TGCAAATGTATT
          1 TGCAAATGTATT

                        
       7721 TGCAAATGTATT
          1 TGCAAATGTATT

             
       7733 T
          1 T

       7734 AAGTAGTATA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44


Consensus pattern (12 bp):   
TGCAAATGTATT
Done.