Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011245.1 Corchorus capsularis cultivar CVL-1 contig11266, 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: 17097
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:5060 original size:40 final size:41

Alignment explanation


    Indices: 5004--5084  Score: 128
    Period size: 40  Copynumber: 2.0  Consensus size: 41

       4994 TCCAATTTGT

                                 *                   
       5004 CCCTCCTAATAATTAAGGAAATAAATTAAATTCAGATTTAG
          1 CCCTCCTAATAATTAAGGAAAGAAATTAAATTCAGATTTAG

                              *                *     
       5045 CCCT-CTAATAATTAAGGTAAGAAATTAAATTCAGGTTTAG
          1 CCCTCCTAATAATTAAGGAAAGAAATTAAATTCAGATTTAG

       5085 TCTCTGGTTA


Statistics
Matches: 37,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  40   33  0.89
  41    4  0.11

ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32


Consensus pattern (41 bp):   
CCCTCCTAATAATTAAGGAAAGAAATTAAATTCAGATTTAG

Found at i:8052 original size:26 final size:26

Alignment explanation


    Indices: 8021--8104  Score: 82
    Period size: 26  Copynumber: 3.2  Consensus size: 26

       8011 CTAATACAAT

                                      
       8021 TATCAAACTATTAAATAATGGTCAAG
          1 TATCAAACTATTAAATAATGGTCAAG

                    ** **          *   *
       8047 TATCAAAAAAAAAAAACTAAT--ACAAT
          1 TATC-AAACTATTAAA-TAATGGTCAAG

                                      
       8073 TATCAAACTATTAAATAATGGTCAAG
          1 TATCAAACTATTAAATAATGGTCAAG

                  
       8099 TATCAA
          1 TATCAA

       8105 TAAAGAAAAT


Statistics
Matches: 42,  Mismatches: 12, Indels: 8
        0.68            0.19        0.13

Matches are distributed among these distances:
  24    4  0.10
  25    7  0.17
  26   20  0.48
  27    7  0.17
  28    4  0.10

ACGTcount: A:0.54, C:0.12, G:0.07, T:0.27


Consensus pattern (26 bp):   
TATCAAACTATTAAATAATGGTCAAG

Found at i:8075 original size:52 final size:52

Alignment explanation


    Indices: 8010--8113  Score: 190
    Period size: 52  Copynumber: 2.0  Consensus size: 52

       8000 TTAAACTAAT

                                                                
       8010 ACTAATACAATTATCAAACTATTAAATAATGGTCAAGTATCAAAAAAAAAAA
          1 ACTAATACAATTATCAAACTATTAAATAATGGTCAAGTATCAAAAAAAAAAA

                                                       *   *    
       8062 ACTAATACAATTATCAAACTATTAAATAATGGTCAAGTATCAATAAAGAAAA
          1 ACTAATACAATTATCAAACTATTAAATAATGGTCAAGTATCAAAAAAAAAAA

       8114 TATGTTGGAA


Statistics
Matches: 50,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  52   50  1.00

ACGTcount: A:0.56, C:0.12, G:0.07, T:0.26


Consensus pattern (52 bp):   
ACTAATACAATTATCAAACTATTAAATAATGGTCAAGTATCAAAAAAAAAAA

Found at i:10496 original size:15 final size:16

Alignment explanation


    Indices: 10466--10503  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

      10456 TTTAGAGTGA

                 *          
      10466 TAAAAGCAATTTAAAT
          1 TAAAAACAATTTAAAT

                            
      10482 TAAAAACAA-TTAAAT
          1 TAAAAACAATTTAAAT

                   
      10497 TATAAAA
          1 TA-AAAA

      10504 GCAGACAATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  15    8  0.40
  16   12  0.60

ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29


Consensus pattern (16 bp):   
TAAAAACAATTTAAAT

Found at i:11942 original size:39 final size:39

Alignment explanation


    Indices: 11881--11962  Score: 119
    Period size: 39  Copynumber: 2.1  Consensus size: 39

      11871 ATTTGTTCCT

                             *            *        
      11881 CCTAATAATTAAGGAAATAAATTAAATACAGGTTTAGCC
          1 CCTAATAATTAAGGAAAGAAATTAAATACAAGTTTAGCC

                          *            *       *   
      11920 CCTAATAATTAAGGTAAGAAATTAAATTCAAGTTTGGCC
          1 CCTAATAATTAAGGAAAGAAATTAAATACAAGTTTAGCC

                
      11959 CCTA
          1 CCTA

      11963 GTTACAATTC


Statistics
Matches: 38,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  39   38  1.00

ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29


Consensus pattern (39 bp):   
CCTAATAATTAAGGAAAGAAATTAAATACAAGTTTAGCC

Found at i:14944 original size:2 final size:2

Alignment explanation


    Indices: 14937--14964  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      14927 ATATAGGAGC

                                                     
      14937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      14965 TTGTAGTTCT


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

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.