Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009407.1 Corchorus capsularis cultivar CVL-1 contig09428, 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: 29499
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:2802 original size:18 final size:18

Alignment explanation


    Indices: 2779--2813  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2769 GGACAATTTA

                              
       2779 CCTAGAAATTGCTCATGG
          1 CCTAGAAATTGCTCATGG

                             
       2797 CCTAGAAATTGCTCATG
          1 CCTAGAAATTGCTCATG

       2814 TCATCAGTTC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29


Consensus pattern (18 bp):   
CCTAGAAATTGCTCATGG

Found at i:2834 original size:152 final size:157

Alignment explanation


    Indices: 2558--2869  Score: 420
    Period size: 152  Copynumber: 2.0  Consensus size: 157

       2548 GTATGGACAT

                      *                                          *           
       2558 TTTCTCCCTCGAACTTTTAATTTGAAAATTTTCACTTATAAACTATCAAAATCTGGACAATTTGA
          1 TTTCTCCCTCAAACTTTTAATTTGAAAATTTTCACTTATAAACTATCAAAATCGGGACAATTT-A

               *       **             *        *         *        *          
       2623 ACAGTGACGTATGTTGACATGGCCCATAAATTGCTGATATCATCATTTCTTAGGGGTAAATTGTC
         65 ACACTGACGTAAATTGACATGGCCCAGAAATTGCTCATATCATCAGTTCTTAGGAGTAAATTGTC

                               *        
       2688 TCGACTTTGATAGTTTAAAGAGTGAAAG
        130 TCGACTTTGATAGTTTAAAAAGTGAAAG

                                                    **                       
       2716 TTTCTCCCTCAAACTTTTAATTTG-AAATTTTCACTTATACGCTATCAAAATCGGGACAATTT-A
          1 TTTCTCCCTCAAACTTTTAATTTGAAAATTTTCACTTATAAACTATCAAAATCGGGACAATTTAA

                            *       *             *                          
       2779 C-CT-A-G-AAATTGCTCATGGCCTAGAAATTGCTCATGTCATCAGTTCTTAGGAGTAAATTGTC
         66 CACTGACGTAAATTG-ACATGGCCCAGAAATTGCTCATATCATCAGTTCTTAGGAGTAAATTGTC

                *                       
       2840 TCGATTTTGATAGTTTAAAAAGTGAAAG
        130 TCGACTTTGATAGTTTAAAAAGTGAAAG

              
       2868 TT
          1 TT

       2870 CCAAATCAAA


Statistics
Matches: 137,  Mismatches: 16, Indels: 8
        0.85            0.10        0.05

Matches are distributed among these distances:
 151    4  0.03
 152   71  0.52
 153    1  0.01
 154    1  0.01
 155    2  0.01
 157   35  0.26
 158   23  0.17

ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37


Consensus pattern (157 bp):   
TTTCTCCCTCAAACTTTTAATTTGAAAATTTTCACTTATAAACTATCAAAATCGGGACAATTTAA
CACTGACGTAAATTGACATGGCCCAGAAATTGCTCATATCATCAGTTCTTAGGAGTAAATTGTCT
CGACTTTGATAGTTTAAAAAGTGAAAG

Found at i:11969 original size:19 final size:19

Alignment explanation


    Indices: 11945--11985  Score: 82
    Period size: 19  Copynumber: 2.2  Consensus size: 19

      11935 GATCAAGCTC

                               
      11945 ATTTGAGTAAGTTAATTTA
          1 ATTTGAGTAAGTTAATTTA

                               
      11964 ATTTGAGTAAGTTAATTTA
          1 ATTTGAGTAAGTTAATTTA

               
      11983 ATT
          1 ATT

      11986 CATCATGTTC


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

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.37, C:0.00, G:0.15, T:0.49


Consensus pattern (19 bp):   
ATTTGAGTAAGTTAATTTA

Found at i:20952 original size:23 final size:23

Alignment explanation


    Indices: 20926--20973  Score: 96
    Period size: 23  Copynumber: 2.1  Consensus size: 23

      20916 TTATAATTTA

                                   
      20926 TAATTTCATCTTTTTATATGAAC
          1 TAATTTCATCTTTTTATATGAAC

                                   
      20949 TAATTTCATCTTTTTATATGAAC
          1 TAATTTCATCTTTTTATATGAAC

              
      20972 TA
          1 TA

      20974 TGAATGTGCC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   25  1.00

ACGTcount: A:0.31, C:0.12, G:0.04, T:0.52


Consensus pattern (23 bp):   
TAATTTCATCTTTTTATATGAAC

Found at i:26110 original size:2 final size:2

Alignment explanation


    Indices: 26105--26134  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      26095 TAGCTTATTG

                                                        
      26105 AT 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 AT

      26135 TTCAGTTTAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:27607 original size:27 final size:24

Alignment explanation


    Indices: 27570--27621  Score: 68
    Period size: 25  Copynumber: 2.0  Consensus size: 24

      27560 CATATTAGAA

                           *          
      27570 TTTTTTAAAATATATTCTTTTACAAT
          1 TTTTTTAAAATA-A-ACTTTTACAAT

                                     
      27596 TTTTTTAGAAATAAACTTTTACAAT
          1 TTTTTTA-AAATAAACTTTTACAAT

             
      27621 T
          1 T

      27622 ATTCTACTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  25   11  0.46
  26    8  0.33
  27    5  0.21

ACGTcount: A:0.37, C:0.08, G:0.02, T:0.54


Consensus pattern (24 bp):   
TTTTTTAAAATAAACTTTTACAAT
Done.