Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020623.1 Corchorus olitorius cultivar O-4 contig20656, 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: 9512
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31


Found at i:6721 original size:50 final size:50

Alignment explanation


    Indices: 6577--6774  Score: 177
    Period size: 50  Copynumber: 4.0  Consensus size: 50

       6567 ACCTTTGAGT

                *             *     *  *           *     **   
       6577 TAAAAATTGGATTTTTAATTAAAAGTTCAAACTTTTAAGTAATTTAAGAA
          1 TAAAGATTGGATTTTTAAGTAAAAATTGAAACTTTTAAGAAATTTGGGAA

                     *           *   *           *             
       6627 TAAAGATTGAATTTTTAAGTGGAAATTTGAAAC-TTTGAGAAATTTGGGAA
          1 TAAAGATTGGATTTTTAAGT-AAAAATTGAAACTTTTAAGAAATTTGGGAA

                 *                  *    *          *      *   
       6677 TAAAGGTTGGATTTTTAA-TCAAAGATTGGAACTTTTAAGCAATTTGTGAA
          1 TAAAGATTGGATTTTTAAGT-AAAAATTGAAACTTTTAAGAAATTTGGGAA

                        *     *       *                      
       6727 TAAAGATTGGATCTTTAATTAAAAGAGTG-AACTTTTAAGAAATTTGGG
          1 TAAAGATTGGATTTTTAAGTAAAA-ATTGAAACTTTTAAGAAATTTGGG

       6775 CTAAATGTTC


Statistics
Matches: 118,  Mismatches: 26, Indels: 8
        0.78            0.17        0.05

Matches are distributed among these distances:
  49    9  0.08
  50   96  0.81
  51   13  0.11

ACGTcount: A:0.40, C:0.04, G:0.18, T:0.37


Consensus pattern (50 bp):   
TAAAGATTGGATTTTTAAGTAAAAATTGAAACTTTTAAGAAATTTGGGAA

Found at i:6999 original size:14 final size:14

Alignment explanation


    Indices: 6980--7006  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       6970 CATGCCCGAA

                          
       6980 AATAATAAAAAAGT
          1 AATAATAAAAAAGT

                         
       6994 AATAATAAAAAAG
          1 AATAATAAAAAAG

       7007 AAAAAAAGGG


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

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19


Consensus pattern (14 bp):   
AATAATAAAAAAGT

Found at i:7599 original size:17 final size:17

Alignment explanation


    Indices: 7579--7612  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       7569 GGAAATTCTG

                             
       7579 CTCCAAAAACAATTTGA
          1 CTCCAAAAACAATTTGA

                  *   *      
       7596 CTCCAACAACGATTTGA
          1 CTCCAAAAACAATTTGA

       7613 GCATCATTTA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24


Consensus pattern (17 bp):   
CTCCAAAAACAATTTGA

Found at i:8905 original size:19 final size:17

Alignment explanation


    Indices: 8883--8917  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       8873 TTTCAGGTAT

                             
       8883 ATATATACTGATGTTAA
          1 ATATATACTGATGTTAA

                             
       8900 ATATATACTGATGTTAA
          1 ATATATACTGATGTTAA

             
       8917 A
          1 A

       8918 CGTTTTCAGG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40


Consensus pattern (17 bp):   
ATATATACTGATGTTAA

Found at i:9202 original size:20 final size:19

Alignment explanation


    Indices: 9163--9207  Score: 72
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       9153 TATTAATATC

                               
       9163 TTTTTCCTGCATCCCATTT
          1 TTTTTCCTGCATCCCATTT

                         *     
       9182 TTTTTCCTGCATCTCATTT
          1 TTTTTCCTGCATCCCATTT

                   
       9201 TTCTTTC
          1 TT-TTTC

       9208 TCATGTGCCC


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  19   20  0.83
  20    4  0.17

ACGTcount: A:0.09, C:0.29, G:0.04, T:0.58


Consensus pattern (19 bp):   
TTTTTCCTGCATCCCATTT

Done.