Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009666.1 Corchorus capsularis cultivar CVL-1 contig09687, 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: 2917
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31


Found at i:110 original size:16 final size:16

Alignment explanation


    Indices: 82--158  Score: 93
    Period size: 16  Copynumber: 4.8  Consensus size: 16

         72 TCTGAACCTA

                             
         82 AACCCGAAAAAAACCCG
          1 AACCCG-AAAAAACCCG

                            
         99 AACCCGAAAAAACCCG
          1 AACCCGAAAAAACCCG

               *       * * *
        115 AACTCGAAAAAGCTCA
          1 AACCCGAAAAAACCCG

                             
        131 AACCCGAAAAAAACCCG
          1 AACCCG-AAAAAACCCG

                        
        148 AACCC-AAAAAA
          1 AACCCGAAAAAA

        159 GCTCAAACTT


Statistics
Matches: 51,  Mismatches: 8, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
  15    6  0.12
  16   27  0.53
  17   18  0.35

ACGTcount: A:0.55, C:0.32, G:0.10, T:0.03


Consensus pattern (16 bp):   
AACCCGAAAAAACCCG

Found at i:142 original size:33 final size:33

Alignment explanation


    Indices: 99--177  Score: 115
    Period size: 33  Copynumber: 2.4  Consensus size: 33

         89 AAAAAACCCG

                                * *          
         99 AACCCG-AAAAAACCCGAACTCGAAAAAGCTCA
          1 AACCCGAAAAAAACCCGAACCCAAAAAAGCTCA

                                             
        131 AACCCGAAAAAAACCCGAACCCAAAAAAGCTCA
          1 AACCCGAAAAAAACCCGAACCCAAAAAAGCTCA

               **         
        164 AACTTGAAAAAAAC
          1 AACCCGAAAAAAAC

        178 TAAATCCGAA


Statistics
Matches: 42,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  32    6  0.14
  33   36  0.86

ACGTcount: A:0.54, C:0.29, G:0.10, T:0.06


Consensus pattern (33 bp):   
AACCCGAAAAAAACCCGAACCCAAAAAAGCTCA

Found at i:173 original size:49 final size:49

Alignment explanation


    Indices: 81--174  Score: 145
    Period size: 49  Copynumber: 1.9  Consensus size: 49

         71 GTCTGAACCT

                                             *               
         81 AAACCCGAAAAAAACCCGAACCCGAAAAAACCCGAACTCGAAAAAGCTC
          1 AAACCCGAAAAAAACCCGAACCCGAAAAAACCCAAACTCGAAAAAGCTC

                                            *      *      
        130 AAACCCGAAAAAAACCCGAACCC-AAAAAAGCTCAAACTTGAAAAA
          1 AAACCCGAAAAAAACCCGAACCCGAAAAAA-CCCAAACTCGAAAAA

        175 AACTAAATCC


Statistics
Matches: 41,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  48    6  0.15
  49   35  0.85

ACGTcount: A:0.54, C:0.30, G:0.11, T:0.05


Consensus pattern (49 bp):   
AAACCCGAAAAAAACCCGAACCCGAAAAAACCCAAACTCGAAAAAGCTC

Found at i:187 original size:49 final size:48

Alignment explanation


    Indices: 79--189  Score: 143
    Period size: 49  Copynumber: 2.3  Consensus size: 48

         69 TCGTCTGAAC

                                               *           *
         79 CTAAACCCGAAAAAAACCCGAACCCGAAAAAACCCGAACTCGAAAAAG
          1 CTAAACCCGAAAAAAACCCGAACCCGAAAAAACCCAAACTCGAAAAAA

                                               *      *        
        127 CTCAAACCCGAAAAAAACCCGAACCC-AAAAAAGCTCAAACTTGAAAAAAA
          1 CT-AAACCCGAAAAAAACCCGAACCCGAAAAAA-CCCAAACTCG-AAAAAA

                 *       
        177 CTAAATCCGAAAA
          1 CTAAACCCGAAAA

        190 TTTATGAAAA


Statistics
Matches: 55,  Mismatches: 5, Indels: 5
        0.85            0.08        0.08

Matches are distributed among these distances:
  48    8  0.15
  49   40  0.73
  50    7  0.13

ACGTcount: A:0.54, C:0.29, G:0.10, T:0.07


Consensus pattern (48 bp):   
CTAAACCCGAAAAAAACCCGAACCCGAAAAAACCCAAACTCGAAAAAA

Found at i:363 original size:32 final size:32

Alignment explanation


    Indices: 327--413  Score: 104
    Period size: 32  Copynumber: 2.7  Consensus size: 32

        317 TTTGGCCAAA

                     *          *           
        327 ACCCAAACAGAACCCGAACCTGAATTAACCTG
          1 ACCCAAACACAACCCGAACCCGAATTAACCTG

                   **    *                  
        359 ACCCAAATTCAACTCGAACCCGAATTAACCTG
          1 ACCCAAACACAACCCGAACCCGAATTAACCTG

                            *       
        391 ACCCAAATC-CAACCCAAACCCGA
          1 ACCCAAA-CACAACCCGAACCCGA

        414 CTCAAACCCG


Statistics
Matches: 46,  Mismatches: 8, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  32   46  1.00

ACGTcount: A:0.40, C:0.38, G:0.09, T:0.13


Consensus pattern (32 bp):   
ACCCAAACACAACCCGAACCCGAATTAACCTG
Done.