Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011863.1 Corchorus capsularis cultivar CVL-1 contig11884, 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: 7459
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30


Found at i:401 original size:16 final size:16

Alignment explanation


    Indices: 376--418  Score: 54
    Period size: 16  Copynumber: 2.8  Consensus size: 16

        366 AGGAATAGGC

                            
        376 AATCAATCAAAGCAAT
          1 AATCAATCAAAGCAAT

                 *          
        392 AATCATTCAAAGCAA-
          1 AATCAATCAAAGCAAT

                         
        407 AA-CAATGCAAAG
          1 AATCAAT-CAAAG

        419 AAAAGAAAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  14    3  0.12
  15    7  0.29
  16   14  0.58

ACGTcount: A:0.56, C:0.19, G:0.09, T:0.16


Consensus pattern (16 bp):   
AATCAATCAAAGCAAT

Found at i:1750 original size:112 final size:112

Alignment explanation


    Indices: 1553--1777  Score: 432
    Period size: 112  Copynumber: 2.0  Consensus size: 112

       1543 AAAGGAGTCT

                                                                             
       1553 TGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACCTGAAT
          1 TGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACCTGAAT

                                                       *   
       1618 CACCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATACATC
         66 CACCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATC

                                                                       *     
       1665 TGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACTTGAAT
          1 TGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACCTGAAT

                                                           
       1730 CACCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATC
         66 CACCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATC

             
       1777 T
          1 T

       1778 TCCTTCGTTC


Statistics
Matches: 111,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 112  111  1.00

ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29


Consensus pattern (112 bp):   
TGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACCTGAAT
CACCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATC

Found at i:2540 original size:33 final size:32

Alignment explanation


    Indices: 2453--2593  Score: 131
    Period size: 33  Copynumber: 4.3  Consensus size: 32

       2443 AAAGGATCGT

                                 **         **
       2453 GTGGCCGGTTGTGGCCGGGCAAGGCCGA-GTCAA
          1 GTGGCCGG-TGTGGCCGGGCATCGCC-ATGTCGC

                         *        *          
       2486 GTGGCCGGGTGTGACCGGGCATGGCCATGTCGC
          1 GTGGCC-GGTGTGGCCGGGCATCGCCATGTCGC

                                   *         
       2519 GTGGCCGGTGATGGCCGGGCATCTCCATGTCGC
          1 GTGGCCGGTG-TGGCCGGGCATCGCCATGTCGC

            *          *           *   *     
       2552 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
          1 GTGGCCGGTGTGGC-CGGGCATCGCCATGTCGC

                     
       2585 GTGGCCGGT
          1 GTGGCCGGT

       2594 CACTCGCGCC


Statistics
Matches: 93,  Mismatches: 11, Indels: 8
        0.83            0.10        0.07

Matches are distributed among these distances:
  32    8  0.09
  33   83  0.89
  34    2  0.02

ACGTcount: A:0.11, C:0.28, G:0.43, T:0.19


Consensus pattern (32 bp):   
GTGGCCGGTGTGGCCGGGCATCGCCATGTCGC

Found at i:7441 original size:30 final size:30

Alignment explanation


    Indices: 7389--7447  Score: 84
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       7379 CAAGGGGGAG

                             *            
       7389 GGAATGATGCGCCCAAGGCTTATCATGGAA
          1 GGAATGATGCGCCCAAGACTTATCATGGAA

                                    *     
       7419 GGAATGATGCG-CCAAGAACTTATTATGGA
          1 GGAATGATGCGCCCAAG-ACTTATCATGGA

       7448 CTTGAAGACA


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  29    5  0.19
  30   21  0.81

ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22


Consensus pattern (30 bp):   
GGAATGATGCGCCCAAGACTTATCATGGAA
Done.