Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016383.1 Corchorus capsularis cultivar CVL-1 contig16404, 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: 8973
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:1169 original size:20 final size:19

Alignment explanation


    Indices: 1134--1172  Score: 60
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       1124 AACGAAATAT

                       *       
       1134 TTAATTACCTTGAAAATTA
          1 TTAATTACCTTCAAAATTA

                                
       1153 TTAATTACCTTCCAAAATTA
          1 TTAATTACCTT-CAAAATTA

       1173 AATTACAAGG


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19   11  0.61
  20    7  0.39

ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41


Consensus pattern (19 bp):   
TTAATTACCTTCAAAATTA

Found at i:3726 original size:33 final size:33

Alignment explanation


    Indices: 3675--3783  Score: 191
    Period size: 33  Copynumber: 3.3  Consensus size: 33

       3665 TTCTTTTCAC

                         *                   
       3675 CCAAAACAGAATTGTTTGCAATGCTATGATCAA
          1 CCAAAACAGAATTATTTGCAATGCTATGATCAA

                     *                       
       3708 CCAAAACAGGATTATTTGCAATGCTATGATCAA
          1 CCAAAACAGAATTATTTGCAATGCTATGATCAA

                  *                          
       3741 CCAAAATAGAATTATTTGCAATGCTATGATCAA
          1 CCAAAACAGAATTATTTGCAATGCTATGATCAA

                      
       3774 CCAAAACAGA
          1 CCAAAACAGA

       3784 TTTGTTTTCA


Statistics
Matches: 71,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  33   71  1.00

ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26


Consensus pattern (33 bp):   
CCAAAACAGAATTATTTGCAATGCTATGATCAA

Found at i:4956 original size:25 final size:25

Alignment explanation


    Indices: 4922--4969  Score: 96
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       4912 TGGTGCAATC

                                     
       4922 GATAAGCTTTGTAGTACATGGTTTG
          1 GATAAGCTTTGTAGTACATGGTTTG

                                   
       4947 GATAAGCTTTGTAGTACATGGTT
          1 GATAAGCTTTGTAGTACATGGTT

       4970 AAGTATATCG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   23  1.00

ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40


Consensus pattern (25 bp):   
GATAAGCTTTGTAGTACATGGTTTG

Found at i:6116 original size:17 final size:17

Alignment explanation


    Indices: 6076--6120  Score: 54
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       6066 AGCAGGAAGT

                             *
       6076 AAGAAGAAGGAAAAAAAT
          1 AAGAA-AAGGAAAAAAAA

            **               
       6094 GGGAAAAGGAAAAAAAA
          1 AAGAAAAGGAAAAAAAA

                      
       6111 AAGAAAAGGA
          1 AAGAAAAGGA

       6121 GAATGGATTT


Statistics
Matches: 22,  Mismatches: 5, Indels: 1
        0.79            0.18        0.04

Matches are distributed among these distances:
  17   19  0.86
  18    3  0.14

ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02


Consensus pattern (17 bp):   
AAGAAAAGGAAAAAAAA
Done.