Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000587.1 Corchorus capsularis cultivar CVL-1 contig00587, 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, 630

Length: 1051
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32


Found at i:126 original size:35 final size:36

Alignment explanation


    Indices: 81--596  Score: 455
    Period size: 35  Copynumber: 14.9  Consensus size: 36

         71 AACTCCTCTG

                          *    *   *            
         81 GATCAACTCTGATCATC-GGAAATTTCTTGAAATGA
          1 GATCAACTCTGATCCTCTGAAAACTTCTTGAAATGA

                 *       **    *     *          *
        116 GATCACCTCTGATTGT-TGGAAACTAC-TGAAAATGT
          1 GATCAACTCTGATCCTCTGAAAACTTCTTG-AAATGA

                          *    *     *          *
        151 GATCAACTCTGATCGT-TGGAAACTAC-TGAAAATGC
          1 GATCAACTCTGATCCTCTGAAAACTTCTTG-AAATGA

              *           *           *          *
        186 GACCAACTCTGATCGT-TGGAAAA-TAC-TGAAAATGC
          1 GATCAACTCTGATCCTCT-GAAAACTTCTTG-AAATGA

                          *    *                *
        221 GATCAACTCTGATCGT-TGGAAACTTC-TGAAAATGT
          1 GATCAACTCTGATCCTCTGAAAACTTCTTG-AAATGA

                          *           *          *
        256 GATCAACTCTGATCGT-TGGAAAA-TAC-TGAAAATGC
          1 GATCAACTCTGATCCTCT-GAAAACTTCTTG-AAATGA

                        *                          
        291 GATCAACTCTGTCTGACCTCTGAAAACTTCTTGAAATGA
          1 GATCAACTCTG-AT--CCTCTGAAAACTTCTTGAAATGA

                                          *     
        330 GATC-A-----A--CTCT---AACTTCTTGGAATGA
          1 GATCAACTCTGATCCTCTGAAAACTTCTTGAAATGA

                                          *     
        355 GATCAACTCTGA-CCTCTGAAAACTTCTTGGAATGA
          1 GATCAACTCTGATCCTCTGAAAACTTCTTGAAATGA

                                          *     
        390 GATCAACTCTGA-CCTCTGAAAACTTCTTGCAATGA
          1 GATCAACTCTGATCCTCTGAAAACTTCTTGAAATGA

                                          *     
        425 GATCAACTCTGA-CCTCTGAAAACTTCTTGGAATGA
          1 GATCAACTCTGATCCTCTGAAAACTTCTTGAAATGA

                                                
        460 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
          1 GATCAACTCTGATCCTCTGAAAACTTCTTGAAATGA

                                           *    
        495 GATCAACTCTGAT-CTCTGAAAACTTCTTGATATGA
          1 GATCAACTCTGATCCTCTGAAAACTTCTTGAAATGA

                                          *     
        530 GATCAACTCTGA-CCTCTGAAAACTTCTTGGAATGA
          1 GATCAACTCTGATCCTCTGAAAACTTCTTGAAATGA

                                             
        565 GATCAACTCTGAT-CTCTGAAAACTTCTTGAAA
          1 GATCAACTCTGATCCTCTGAAAACTTCTTGAAA

        597 GACCGCACAG


Statistics
Matches: 426,  Mismatches: 31, Indels: 48
        0.84            0.06        0.10

Matches are distributed among these distances:
  25   18  0.04
  26    1  0.00
  28    4  0.01
  31    1  0.00
  32    4  0.01
  34    6  0.01
  35  361  0.85
  36    9  0.02
  38    8  0.02
  39   12  0.03
  40    2  0.00

ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29


Consensus pattern (36 bp):   
GATCAACTCTGATCCTCTGAAAACTTCTTGAAATGA

Found at i:345 original size:25 final size:25

Alignment explanation


    Indices: 315--364  Score: 91
    Period size: 25  Copynumber: 2.0  Consensus size: 25

        305 GACCTCTGAA

                                     
        315 AACTTCTTGAAATGAGATCAACTCT
          1 AACTTCTTGAAATGAGATCAACTCT

                     *               
        340 AACTTCTTGGAATGAGATCAACTCT
          1 AACTTCTTGAAATGAGATCAACTCT

        365 GACCTCTGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32


Consensus pattern (25 bp):   
AACTTCTTGAAATGAGATCAACTCT

Done.