Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012582.1 Corchorus capsularis cultivar CVL-1 contig12603, 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: 17174
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:1430 original size:2 final size:2

Alignment explanation


    Indices: 1423--1447  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       1413 CTAATAGTTA

                                                 
       1423 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       1448 GCCACTTACA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:3852 original size:178 final size:178

Alignment explanation


    Indices: 3541--3944  Score: 454
    Period size: 178  Copynumber: 2.3  Consensus size: 178

       3531 TCGATCACTT

                *                                   *  *     *               
       3541 GAAAACTAAATTTAATGTTTCAAGTATCAAAAAAGCTTCCGAATAATTAGTTGTTTCGGTTAACG
          1 GAAAGCTAAATTTAATGTTTCAAGTATCAAAAAAGCTTCCAAAAAATTAATTGTTTCGGTTAACG

            *     *          *          *                  **      *         
       3606 GGAATGGACGATCCACTTAATATAACATTACTTTTGCTCAAGATGTCTTATTGAGCTGATTCAAG
         66 AGAATGAACGATCCACTGAATATAACATAACTTTTGCTCAAGATGTCCGATTGAGATGATTCAAG

                           *     *                           
       3671 TGTCT-CATAAAAGGTTATTTTATGATCTACAACTTTCATGCAGGAAGC
        131 TGTCTGC-TAAAAGGCTATTTCATGATCTACAACTTTCATGCAGGAAGC

                                                   *             *         * 
       3719 GAAAGCTAAATTTAATGTTTCAAGTAT-AAAAAATGCTTTCAAAAAATTAATTTTTTCGGTTAGC
          1 GAAAGCTAAATTTAATGTTTCAAGTATCAAAAAA-GCTTCCAAAAAATTAATTGTTTCGGTTAAC

                       *  *                 *        *                     * 
       3783 GAGAATGAACGGTCTACTGAATA-ATACATAATTTTTGCTCTAGATGTCCGATTGAGATGATTTA
         65 GAGAATGAACGATCCACTGAATATA-ACATAACTTTTGCTCAAGATGTCCGATTGAGATGATTCA

                              *    *      *           *    ***
       3847 AGTGTCTGCTAAAAGGCTGTTTCGTGATCTTCAACTTTCATGTAGGACTT
        129 AGTGTCTGCTAAAAGGCTATTTCATGATCTACAACTTTCATGCAGGAAGC

                         *  *      *  *            **       
       3897 GAAAGCTAAATTTGATTTTTCAAATACCAAAAAAGCTTCTGAAAAATT
          1 GAAAGCTAAATTTAATGTTTCAAGTATCAAAAAAGCTTCCAAAAAATT

       3945 TATATTTCGG


Statistics
Matches: 187,  Mismatches: 35, Indels: 8
        0.81            0.15        0.03

Matches are distributed among these distances:
 177    7  0.04
 178  173  0.93
 179    7  0.04

ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35


Consensus pattern (178 bp):   
GAAAGCTAAATTTAATGTTTCAAGTATCAAAAAAGCTTCCAAAAAATTAATTGTTTCGGTTAACG
AGAATGAACGATCCACTGAATATAACATAACTTTTGCTCAAGATGTCCGATTGAGATGATTCAAG
TGTCTGCTAAAAGGCTATTTCATGATCTACAACTTTCATGCAGGAAGC

Found at i:5622 original size:18 final size:18

Alignment explanation


    Indices: 5580--5634  Score: 56
    Period size: 18  Copynumber: 2.9  Consensus size: 18

       5570 ATTATATATA

                   *             
       5580 TTTTAATAATTTCATTTTCTT
          1 TTTTAATTATTT-A-TTT-TT

                *             
       5601 TTTTTATTATTTATTTTT
          1 TTTTAATTATTTATTTTT

                    *       
       5619 TTTTAATTTTTTATTT
          1 TTTTAATTATTTATTT

       5635 CTTAAGAAGT


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  18   16  0.53
  19    3  0.10
  20    1  0.03
  21   10  0.33

ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76


Consensus pattern (18 bp):   
TTTTAATTATTTATTTTT

Found at i:9720 original size:15 final size:15

Alignment explanation


    Indices: 9696--9726  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       9686 TTCAACTTTA

                           
       9696 ATATAATATATATAT
          1 ATATAATATATATAT

                 *         
       9711 ATATATTATATATAT
          1 ATATAATATATATAT

             
       9726 A
          1 A

       9727 GACAGGCCTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (15 bp):   
ATATAATATATATAT

Found at i:13189 original size:27 final size:27

Alignment explanation


    Indices: 13118--13193  Score: 100
    Period size: 28  Copynumber: 2.8  Consensus size: 27

      13108 TAGGGTCACC

                        *              
      13118 CAGGGGCATTTTGGTCATTTTTACATT
          1 CAGGGGCATTTTCGTCATTTTTACATT

                         *               
      13145 CAGAGGGCATTTTTGTCATTCTTT-CATT
          1 CAG-GGGCATTTTCGTCATT-TTTACATT

            *                    
      13173 TAGGGGCATTTTCGTCATTTT
          1 CAGGGGCATTTTCGTCATTTT

      13194 GAGTCCACTA


Statistics
Matches: 44,  Mismatches: 3, Indels: 5
        0.85            0.06        0.10

Matches are distributed among these distances:
  26    2  0.05
  27   18  0.41
  28   21  0.48
  29    3  0.07

ACGTcount: A:0.17, C:0.16, G:0.21, T:0.46


Consensus pattern (27 bp):   
CAGGGGCATTTTCGTCATTTTTACATT
Done.