Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006091.1 Corchorus capsularis cultivar CVL-1 contig06109, 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: 16953
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:126 original size:13 final size:13

Alignment explanation


    Indices: 105--140  Score: 63
    Period size: 13  Copynumber: 2.8  Consensus size: 13

         95 GGGTGATCTG

                *        
        105 AGATTACCACCCA
          1 AGATCACCACCCA

                         
        118 AGATCACCACCCA
          1 AGATCACCACCCA

                      
        131 AGATCACCAC
          1 AGATCACCAC

        141 GGGTGATTTG


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  13   22  1.00

ACGTcount: A:0.39, C:0.42, G:0.08, T:0.11


Consensus pattern (13 bp):   
AGATCACCACCCA

Found at i:419 original size:13 final size:13

Alignment explanation


    Indices: 401--425  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        391 TAATTTTTGA

                         
        401 ATTAATATTAATC
          1 ATTAATATTAATC

                        
        414 ATTAATATTAAT
          1 ATTAATATTAAT

        426 GGTGCCATAG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48


Consensus pattern (13 bp):   
ATTAATATTAATC

Found at i:5798 original size:107 final size:103

Alignment explanation


    Indices: 5666--5941  Score: 412
    Period size: 103  Copynumber: 2.6  Consensus size: 103

       5656 TTTAGAAATA

                                                *                            
       5666 AAATAAAATATAAAACTAATTTCACTAAGTTTAGTCTCAAATTAAAATTGTATTTTTATTTTAAG
          1 AAATAAAATATAAAACTAATTTCACTAAGTTTAG-CCCAAATTAAAATT-TATTTTTATTTTAAG

                    *                                 
       5731 GGTAAATTTCAAAATTAATAATATATTGTTATAGGGTTTTAG
         64 GGTAAATTCCAAAATTAAT-A-ATATTGTTATAGGGTTTTAG

                      *                                       *              
       5773 AAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCAAAATT-AAATTTTTTTTTATTTTAAGG
          1 AAATAAAATATAAAACTAATTTCACTAAGTTTAGCCC-AAATTAAAATTTATTTTTATTTTAAGG

                      *                            
       5837 GTAAATTCCATAATTAATAATATTGTTATAGGGTTTTAG
         65 GTAAATTCCAAAATTAATAATATTGTTATAGGGTTTTAG

                        *                                    * *             
       5876 AAATAAAATATATAACTAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGG
          1 AAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATT-TATTTTTATTTTAAGG

              
       5940 GT
         65 GT

       5942 TAGAAAAATT


Statistics
Matches: 156,  Mismatches: 10, Indels: 10
        0.89            0.06        0.06

Matches are distributed among these distances:
 101    5  0.03
 102   22  0.14
 103   52  0.33
 104    1  0.01
 105   31  0.20
 106    7  0.04
 107   38  0.24

ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40


Consensus pattern (103 bp):   
AAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATTTATTTTTATTTTAAGGG
TAAATTCCAAAATTAATAATATTGTTATAGGGTTTTAG

Found at i:10345 original size:54 final size:57

Alignment explanation


    Indices: 10236--10347  Score: 194
    Period size: 54  Copynumber: 2.0  Consensus size: 57

      10226 TCTTATCATT

                                                                      
      10236 ATAAGTCTTCAATAATGCTGTTCATATTAATACCTGTGTTTCTTAACCCGTATATCAG
          1 ATAAGTCTTCAATAATGCTGTTCA-ATTAATACCTGTGTTTCTTAACCCGTATATCAG

                                                                     
      10294 ATAAGTCTTCAATAATGCTGTTC-A-T-ATACCTGTGTTTCTTAACCCGTATATCAG
          1 ATAAGTCTTCAATAATGCTGTTCAATTAATACCTGTGTTTCTTAACCCGTATATCAG

      10348 TCTAAATAAA


Statistics
Matches: 54,  Mismatches: 0, Indels: 4
        0.93            0.00        0.07

Matches are distributed among these distances:
  54   29  0.54
  55    1  0.02
  56    1  0.02
  58   23  0.43

ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39


Consensus pattern (57 bp):   
ATAAGTCTTCAATAATGCTGTTCAATTAATACCTGTGTTTCTTAACCCGTATATCAG

Found at i:12972 original size:18 final size:17

Alignment explanation


    Indices: 12940--12982  Score: 52
    Period size: 18  Copynumber: 2.5  Consensus size: 17

      12930 GACAAGCGGT

                            * 
      12940 AAAATAAAAATAATGATA
          1 AAAATAAAAATAATG-CA

                              
      12958 AAAATAAAACA-AATGCA
          1 AAAATAAAA-ATAATGCA

                    
      12975 AAAATAAA
          1 AAAATAAA

      12983 CCAATTTGAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  17    9  0.39
  18   13  0.57
  19    1  0.04

ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16


Consensus pattern (17 bp):   
AAAATAAAAATAATGCA
Done.