Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006566.1 Corchorus capsularis cultivar CVL-1 contig06587, 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, 861

Length: 1435
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26


Found at i:179 original size:35 final size:35

Alignment explanation


    Indices: 129--199  Score: 106
    Period size: 35  Copynumber: 2.0  Consensus size: 35

        119 TTGTTGGTTG

                 *    *     *            *     
        129 CAAATTGAAGCCGATTTAAAACAGCACTATTGGGC
          1 CAAATCGAAGACGATTCAAAACAGCACTAATGGGC

                                               
        164 CAAATCGAAGACGATTCAAAACAGCACTAATGGGC
          1 CAAATCGAAGACGATTCAAAACAGCACTAATGGGC

             
        199 C
          1 C

        200 CCGAACGGCC


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  35   32  1.00

ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18


Consensus pattern (35 bp):   
CAAATCGAAGACGATTCAAAACAGCACTAATGGGC

Found at i:450 original size:153 final size:154

Alignment explanation


    Indices: 162--741  Score: 826
    Period size: 154  Copynumber: 3.8  Consensus size: 154

        152 GCACTATTGG

                                                       *                *    
        162 GCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAACGGCCCG-AA-AAAAAGCGTTC
          1 GCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTC

                      *                      *  *      *              *    * 
        225 TGAATGAGCTGAAAACTTCACAATGGACTAATCCCATCAAAATAATTATAGTTAGGCCATAAACA
         66 TGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAAA

              *                      
        290 ATGGAAAGAAAAGCTTTG-TGGTTT
        131 ATTGAAAGAAAAGCTTTGTTGG-TT

                                                        **                   
        314 GCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAATTCCCGAAA-AAAAAGTGTTC
          1 GCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTC

              *                                                            * 
        378 TGCATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAATA
         66 TGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAAA

                                     
        443 ATTGAAAGAAAAGCTTTGTTGGATT
        131 ATTGAAAGAAAAGCTTTGTTGG-TT

                                                *                   *  *     
        468 GCCAAATCGAAGACGATTCAAAACAGCACTAATGGGTCCCGAAAGGCCCGAAATAACAATTGTTC
          1 GCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTC

                   *        *                                  *     *       
        533 TGAATGAACTAAAAAAATTCACAATGGACTAATCTCACCAAAATGATTATAATTAGGTCGTAAAA
         66 TGAATGAGCT-AAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAA

                        *           *
        598 AATTGAAAGAAACGCTTTGTTGGTA
        130 AATTGAAAGAAAAGCTTTGTTGGTT

                   *    * *   *                   *                 *       *
        623 GCCAAATTGAAGCCAATTTAAAACAGCACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTT
          1 GCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTC

                    *             *                               
        688 TGAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
         66 TGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTA

        742 TGATATGAAT


Statistics
Matches: 385,  Mismatches: 39, Indels: 6
        0.90            0.09        0.01

Matches are distributed among these distances:
 152   47  0.12
 153   87  0.23
 154   96  0.25
 155   83  0.22
 156   72  0.19

ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23


Consensus pattern (154 bp):   
GCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTC
TGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAAA
ATTGAAAGAAAAGCTTTGTTGGTT
Done.