Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013805.1 Corchorus capsularis cultivar CVL-1 contig13826, 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: 25728
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:11553 original size:59 final size:60

Alignment explanation


    Indices: 11446--11571  Score: 175
    Period size: 59  Copynumber: 2.1  Consensus size: 60

      11436 ACATTTCTTG

                                     *        *         *               
      11446 AGAGG-AAATTGTCTTGATTTTGATGGTTTAAGAGGTGAAAGTTTCAAATAAAAAATTCA
          1 AGAGGAAAATTGTCTTGATTTTGATAGTTTAAGACGTGAAAGTTACAAATAAAAAATTCA

                                               * *            *        *
      11505 AGAGGAAAATTGTCTTGATTTTGATAGTTTAA-ACTTTAAAGTTACAAATTAAAAATTCT
          1 AGAGGAAAATTGTCTTGATTTTGATAGTTTAAGACGTGAAAGTTACAAATAAAAAATTCA

                    
      11564 AGAGGAAA
          1 AGAGGAAA

      11572 GCCATTGGGT


Statistics
Matches: 59,  Mismatches: 7, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  59   34  0.58
  60   25  0.42

ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34


Consensus pattern (60 bp):   
AGAGGAAAATTGTCTTGATTTTGATAGTTTAAGACGTGAAAGTTACAAATAAAAAATTCA

Found at i:11864 original size:67 final size:67

Alignment explanation


    Indices: 11756--11954  Score: 362
    Period size: 67  Copynumber: 3.0  Consensus size: 67

      11746 GTTTCAATTT

                    *                     *                                  
      11756 GTAAATAGAGAAGCCAATGTATTGTATTAGTACGATAATCGTGTGGTGCGGGACTATTCCTCCCG
          1 GTAAATAGGGAAGCCAATGTATTGTATTAGCACGATAATCGTGTGGTGCGGGACTATTCCTCCCG

              
      11821 GC
         66 GC

                                                                       *     
      11823 GTAAATAGGGAAGCCAATGTATTGTATTAGCACGATAATCGTGTGGTGCGGGACTATTCTTCCCG
          1 GTAAATAGGGAAGCCAATGTATTGTATTAGCACGATAATCGTGTGGTGCGGGACTATTCCTCCCG

              
      11888 GC
         66 GC

                                                                 *           
      11890 GTAAATAGGGAAGCCAATGTATTGTATTAGCACGATAATCGTGTGGTGCGGGATTATTCCTCCCG
          1 GTAAATAGGGAAGCCAATGTATTGTATTAGCACGATAATCGTGTGGTGCGGGACTATTCCTCCCG

      11955 ACGTTTGTAA


Statistics
Matches: 127,  Mismatches: 5, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  67  127  1.00

ACGTcount: A:0.26, C:0.18, G:0.28, T:0.29


Consensus pattern (67 bp):   
GTAAATAGGGAAGCCAATGTATTGTATTAGCACGATAATCGTGTGGTGCGGGACTATTCCTCCCG
GC

Found at i:20422 original size:23 final size:23

Alignment explanation


    Indices: 20394--20438  Score: 90
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      20384 CTCTTTCTTG

                                   
      20394 TGAAGTGCAACTCGATCTACCCT
          1 TGAAGTGCAACTCGATCTACCCT

                                  
      20417 TGAAGTGCAACTCGATCTACCC
          1 TGAAGTGCAACTCGATCTACCC

      20439 GAAGCATGAG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24


Consensus pattern (23 bp):   
TGAAGTGCAACTCGATCTACCCT

Found at i:21342 original size:26 final size:26

Alignment explanation


    Indices: 21313--21377  Score: 121
    Period size: 26  Copynumber: 2.5  Consensus size: 26

      21303 ACAATTTAAA

                  *                   
      21313 AGGCTTAAAATTCGTTGCCATATAAT
          1 AGGCTTGAAATTCGTTGCCATATAAT

                                      
      21339 AGGCTTGAAATTCGTTGCCATATAAT
          1 AGGCTTGAAATTCGTTGCCATATAAT

                         
      21365 AGGCTTGAAATTC
          1 AGGCTTGAAATTC

      21378 TGCAAATATC


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  26   38  1.00

ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34


Consensus pattern (26 bp):   
AGGCTTGAAATTCGTTGCCATATAAT

Found at i:25202 original size:40 final size:40

Alignment explanation


    Indices: 25158--25238  Score: 153
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      25148 ATAACATAAC

                      *                             
      25158 AATTCAAACCCAGAAATATAGTCATATTTCAATCCCAGAA
          1 AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA

                                                    
      25198 AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA
          1 AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA

             
      25238 A
          1 A

      25239 TATATAACAT


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  40   40  1.00

ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25


Consensus pattern (40 bp):   
AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA
Done.