Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008590.1 Corchorus capsularis cultivar CVL-1 contig08611, 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: 13555
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33


Found at i:1164 original size:48 final size:48

Alignment explanation


    Indices: 1108--1248  Score: 282
    Period size: 48  Copynumber: 2.9  Consensus size: 48

       1098 CTTGCATAAG

                                                            
       1108 ATATCTCTTCTCCTCTTGCATAAGATCACTTCTTTATGAAAACAGAAA
          1 ATATCTCTTCTCCTCTTGCATAAGATCACTTCTTTATGAAAACAGAAA

                                                            
       1156 ATATCTCTTCTCCTCTTGCATAAGATCACTTCTTTATGAAAACAGAAA
          1 ATATCTCTTCTCCTCTTGCATAAGATCACTTCTTTATGAAAACAGAAA

                                                         
       1204 ATATCTCTTCTCCTCTTGCATAAGATCACTTCTTTATGAAAACAG
          1 ATATCTCTTCTCCTCTTGCATAAGATCACTTCTTTATGAAAACAG

       1249 TCTTAATTAC


Statistics
Matches: 93,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  48   93  1.00

ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36


Consensus pattern (48 bp):   
ATATCTCTTCTCCTCTTGCATAAGATCACTTCTTTATGAAAACAGAAA

Found at i:9727 original size:13 final size:13

Alignment explanation


    Indices: 9709--9743  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

       9699 TTAATTATTG

                         
       9709 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

                         
       9722 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

             *       
       9735 TCTGCTTTA
          1 TTTGCTTTA

       9744 GATTTAGATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60


Consensus pattern (13 bp):   
TTTGCTTTATTAA

Found at i:9751 original size:6 final size:6

Alignment explanation


    Indices: 9740--9771  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       9730 ATTAATCTGC

                                                  
       9740 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT

       9772 GCTTTGCTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    4  0.15
   6   22  0.85

ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:11954 original size:19 final size:18

Alignment explanation


    Indices: 11921--11956  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      11911 TTGAAATAAT

                              
      11921 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      11939 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      11957 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:12778 original size:16 final size:17

Alignment explanation


    Indices: 12748--12782  Score: 54
    Period size: 16  Copynumber: 2.1  Consensus size: 17

      12738 TTTTAAATTT

                      *      
      12748 TTTTCAAAAATTTTTGC
          1 TTTTCAAAAACTTTTGC

                             
      12765 TTTTC-AAAACTTTTGC
          1 TTTTCAAAAACTTTTGC

              
      12781 TT
          1 TT

      12783 CTCTTGTTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  16   12  0.71
  17    5  0.29

ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54


Consensus pattern (17 bp):   
TTTTCAAAAACTTTTGC

Found at i:13342 original size:13 final size:13

Alignment explanation


    Indices: 13324--13349  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      13314 AAGAATTTTT

                         
      13324 CTGTCTCAACCTG
          1 CTGTCTCAACCTG

                         
      13337 CTGTCTCAACCTG
          1 CTGTCTCAACCTG

      13350 TTGTTAGTGA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.15, C:0.38, G:0.15, T:0.31


Consensus pattern (13 bp):   
CTGTCTCAACCTG
Done.