Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005620.1 Corchorus capsularis cultivar CVL-1 contig05638, 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: 13552
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


Found at i:40 original size:31 final size:31

Alignment explanation


    Indices: 2--75  Score: 96
    Period size: 31  Copynumber: 2.4  Consensus size: 31

          1 G

                          * * *         *  
          2 CTTTTTTTGTAACGTCGGGGGGGCATATGTC
          1 CTTTTTTTGTAACGCCAGAGGGGCATATATC

                     *                     
         33 CTTTTTTTGCAACGCCAGAGGGGCATATATC
          1 CTTTTTTTGTAACGCCAGAGGGGCATATATC

                         
         64 CTTTTTTT-TAAC
          1 CTTTTTTTGTAAC

         76 ATCTCCCTTT


Statistics
Matches: 37,  Mismatches: 6, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  30    3  0.08
  31   34  0.92

ACGTcount: A:0.18, C:0.19, G:0.23, T:0.41


Consensus pattern (31 bp):   
CTTTTTTTGTAACGCCAGAGGGGCATATATC

Found at i:8460 original size:17 final size:17

Alignment explanation


    Indices: 8438--8480  Score: 86
    Period size: 17  Copynumber: 2.5  Consensus size: 17

       8428 TTCTAGAGGT

                             
       8438 ACCAACTCTGCATATGG
          1 ACCAACTCTGCATATGG

                             
       8455 ACCAACTCTGCATATGG
          1 ACCAACTCTGCATATGG

                     
       8472 ACCAACTCT
          1 ACCAACTCT

       8481 TCACATCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   26  1.00

ACGTcount: A:0.30, C:0.33, G:0.14, T:0.23


Consensus pattern (17 bp):   
ACCAACTCTGCATATGG

Found at i:9101 original size:25 final size:25

Alignment explanation


    Indices: 9067--9116  Score: 91
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       9057 GATTGGTTAG

                        *            
       9067 TAGAGACCGAGCGAGAGTGCTCAAA
          1 TAGAGACCGAGCAAGAGTGCTCAAA

                                     
       9092 TAGAGACCGAGCAAGAGTGCTCAAA
          1 TAGAGACCGAGCAAGAGTGCTCAAA

       9117 GATTGGTTGG


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:0.38, C:0.20, G:0.30, T:0.12


Consensus pattern (25 bp):   
TAGAGACCGAGCAAGAGTGCTCAAA

Found at i:11172 original size:31 final size:31

Alignment explanation


    Indices: 11137--11195  Score: 82
    Period size: 31  Copynumber: 1.9  Consensus size: 31

      11127 TATGTTAGAC

                     *     *               
      11137 AAATAAGGATATAATTGGCGTTTCAAAAATT
          1 AAATAAGGACATAATAGGCGTTTCAAAAATT

                    *         *         
      11168 AAATAAGGGCATAATAGGTGTTTCAAAA
          1 AAATAAGGACATAATAGGCGTTTCAAAA

      11196 GTTTTACAAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   24  1.00

ACGTcount: A:0.46, C:0.07, G:0.19, T:0.29


Consensus pattern (31 bp):   
AAATAAGGACATAATAGGCGTTTCAAAAATT

Found at i:11744 original size:16 final size:15

Alignment explanation


    Indices: 11720--11750  Score: 53
    Period size: 16  Copynumber: 2.0  Consensus size: 15

      11710 AAATTAAGGT

                           
      11720 AACTTAAAATAGAAA
          1 AACTTAAAATAGAAA

                            
      11735 AACTTGAAAATAGAAA
          1 AACTT-AAAATAGAAA

      11751 GAAAAAAAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    5  0.33
  16   10  0.67

ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19


Consensus pattern (15 bp):   
AACTTAAAATAGAAA

Found at i:11988 original size:34 final size:34

Alignment explanation


    Indices: 11950--12033  Score: 89
    Period size: 34  Copynumber: 2.5  Consensus size: 34

      11940 TCTCTTAAAT

                      *    *   *               
      11950 TATTGAAATTTTTGATAGATATGT-CCAACAACTC
          1 TATTG-AATTATTGAAAGAAATGTGCCAACAACTC

                  *                           
      11984 TATTGACTTATTGAAAGAAATGTGCCAACAACTC
          1 TATTGAATTATTGAAAGAAATGTGCCAACAACTC

             * **           
      12018 TCTCAAATTATTGAAA
          1 TATTGAATTATTGAAA

      12034 TATGCCCTCT


Statistics
Matches: 41,  Mismatches: 8, Indels: 2
        0.80            0.16        0.04

Matches are distributed among these distances:
  33   14  0.34
  34   27  0.66

ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35


Consensus pattern (34 bp):   
TATTGAATTATTGAAAGAAATGTGCCAACAACTC

Found at i:12322 original size:16 final size:17

Alignment explanation


    Indices: 12300--12353  Score: 58
    Period size: 16  Copynumber: 3.3  Consensus size: 17

      12290 TTGAGAGGAA

                             
      12300 AGAAATAGGAAGAAAAG
          1 AGAAATAGGAAGAAAAG

                    *   **   
      12317 -GAAATAGCAAGGGAAG
          1 AGAAATAGGAAGAAAAG

                         *   
      12333 AGAAATAGGAA-AGAAG
          1 AGAAATAGGAAGAAAAG

                 
      12349 AGAAA
          1 AGAAA

      12354 GGAAGTCATA


Statistics
Matches: 31,  Mismatches: 5, Indels: 3
        0.79            0.13        0.08

Matches are distributed among these distances:
  16   22  0.71
  17    9  0.29

ACGTcount: A:0.61, C:0.02, G:0.31, T:0.06


Consensus pattern (17 bp):   
AGAAATAGGAAGAAAAG
Done.