Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005271.1 Corchorus capsularis cultivar CVL-1 contig05289, 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: 2063
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.37


Found at i:875 original size:50 final size:50

Alignment explanation


    Indices: 811--1080  Score: 423
    Period size: 50  Copynumber: 5.4  Consensus size: 50

        801 GATCCGACTT

                   *                                   *      
        811 CTTCGAATTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCACTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                 **    *                      
        861 CTTCGAACTGTCTTCCAATTCCTTCTTGAAAGGACCGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                          *      *   *          *             
        911 CTTCGAACTGTCTTTCAATTCCATCATAAAAGGACCATCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                *                                             
        961 CTTCAAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                               *              
       1011 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACAGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

               *           *    
       1061 CTTTGAACTGTCTTCTAATT
          1 CTTCGAACTGTCTTCCAATT

       1081 TCCATTCTTT


Statistics
Matches: 201,  Mismatches: 19, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  50  201  1.00

ACGTcount: A:0.24, C:0.29, G:0.11, T:0.36


Consensus pattern (50 bp):   
CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

Found at i:1295 original size:40 final size:40

Alignment explanation


    Indices: 1209--1296  Score: 106
    Period size: 40  Copynumber: 2.2  Consensus size: 40

       1199 CCTGAAAAAT

                        *         *         *       
       1209 CGTCTTCTGATTGACTTCTGAATATCTAAATCCAATAAAC
          1 CGTCTTCTGATTAACTTCTGAAAATCTAAATCAAATAAAC

             *                          **           
       1249 CTTCTTCTGATTAACTTCTGAAAATCTATTTCTAAAT-AAC
          1 CGTCTTCTGATTAACTTCTGAAAATCTAAATC-AAATAAAC

                    
       1289 CGTCTTCT
          1 CGTCTTCT

       1297 AGTGCATCTT


Statistics
Matches: 40,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  40   37  0.93
  41    3  0.08

ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40


Consensus pattern (40 bp):   
CGTCTTCTGATTAACTTCTGAAAATCTAAATCAAATAAAC

Found at i:1411 original size:64 final size:64

Alignment explanation


    Indices: 1309--1536  Score: 289
    Period size: 64  Copynumber: 3.6  Consensus size: 64

       1299 TGCATCTTTT

                             *   *                     *                     
       1309 AACAAGATCGTCTTCCCCATCGACTTCTGAAAACTCTTGATAACCCATCTTCTGGTGTACTTC-A
          1 AACAAGATCGTCTT-CCGATCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTACTTCTA

             *  *                            *                        *      
       1373 TGACGAGATCGTCTTCCGATCAACTTCTGAAAATTCTTGATAAACCATCTTCTGGTGTGCTTCTA
          1 -AACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTACTTCTA

                         *                              *       *        * *
       1438 AACAAGATCGTCTCCCGATCAACTTCTGAAAACTCTTGATAAACTATCTTCTAGTGTACTTTTT
          1 AACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTACTTCTA

                      *         *      *        
       1502 AACAAGATC-ACTTCCGATCCACTTCTAAAAACTCT
          1 AACAAGATCGTCTTCCGATCAACTTCTGAAAACTCT

       1537 CCCTAGCAGA


Statistics
Matches: 142,  Mismatches: 20, Indels: 4
        0.86            0.12        0.02

Matches are distributed among these distances:
  63   22  0.15
  64  107  0.75
  65   13  0.09

ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33


Consensus pattern (64 bp):   
AACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTACTTCTA
Done.