Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012510.1 Corchorus capsularis cultivar CVL-1 contig12531, 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: 20722
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1590 original size:178 final size:178

Alignment explanation


    Indices: 1288--1638  Score: 517
    Period size: 178  Copynumber: 2.0  Consensus size: 178

       1278 AATTGCCTTA

                                                                             
       1288 TGATTTCCTATTGTTTCCTTTTCTAAAATGGAATCTATATTAGTAACTATCAAAATAAAAGTCAA
          1 TGATTTCCTATTGTTTCCTTTTCTAAAATGGAA-CTATATTAGTAACTATCAAAATAAAAGTCAA

            **                    *                                          
       1353 TTGACCTAATTAAATCAGCCAAGAAATCTAGTAATTATAATTAATAGATTTATTAGGTACAATTT
         65 CAGACCTAATTAAATCAGCCAAAAAATCTAGTAATTATAATTAATAGATTTATTAGGTACAATTT

                         *   *     * * *                       
       1418 ACAAGGTAAGTTGTATTTTATAAGAGAGTAAAAGACTTGTCTACATACCCT
        130 ACAAGGTAAG-T-AATTATATAAAACAATAAAAGACTTGTCTACATACCCT

                                          *              *     *             
       1469 TGATTTCCTATTGTTTCCTTTTCTAAAATGTAA-TATA-TAGTAATTATCAGAATAAAAGTCAAC
          1 TGATTTCCTATTGTTTCCTTTTCTAAAATGGAACTATATTAGTAACTATCAAAATAAAAGTCAAC

                          *             *  *                                 
       1532 AGACCTAATTAAATTAGCCAAAAAATCTGGTGATTATAATTAATAGATTTATTAGGTACAATTTA
         66 AGACCTAATTAAATCAGCCAAAAAATCTAGTAATTATAATTAATAGATTTATTAGGTACAATTTA

             **                                       
       1597 CTGGGTAAGTAATTATATAAAACAATAAAAGACTTGTCTACA
        131 CAAGGTAAGTAATTATATAAAACAATAAAAGACTTGTCTACA

       1639 ACATGTAAGT


Statistics
Matches: 154,  Mismatches: 16, Indels: 5
        0.88            0.09        0.03

Matches are distributed among these distances:
 176   27  0.18
 177    1  0.01
 178   90  0.58
 179    4  0.03
 181   32  0.21

ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36


Consensus pattern (178 bp):   
TGATTTCCTATTGTTTCCTTTTCTAAAATGGAACTATATTAGTAACTATCAAAATAAAAGTCAAC
AGACCTAATTAAATCAGCCAAAAAATCTAGTAATTATAATTAATAGATTTATTAGGTACAATTTA
CAAGGTAAGTAATTATATAAAACAATAAAAGACTTGTCTACATACCCT

Found at i:3134 original size:25 final size:27

Alignment explanation


    Indices: 3106--3169  Score: 69
    Period size: 28  Copynumber: 2.3  Consensus size: 27

       3096 TATTTATACA

                            *          
       3106 ATATTTATTA-AATTAGTATATGGA-T
          1 ATATTTATTATAATTAATATATGGAGT

                         *               
       3131 ATATAATTATTATTATTAATATATGGAGT
          1 ATAT--TTATTATAATTAATATATGGAGT

                      
       3160 ATCATTTATT
          1 AT-ATTTATT

       3170 TATTTATGAT


Statistics
Matches: 32,  Mismatches: 2, Indels: 7
        0.78            0.05        0.17

Matches are distributed among these distances:
  25    4  0.12
  27    6  0.19
  28   17  0.53
  29    3  0.09
  30    2  0.06

ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50


Consensus pattern (27 bp):   
ATATTTATTATAATTAATATATGGAGT

Done.