Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011887.1 Corchorus capsularis cultivar CVL-1 contig11908, 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: 17865
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:1527 original size:10 final size:10

Alignment explanation


    Indices: 1510--1563  Score: 62
    Period size: 10  Copynumber: 5.7  Consensus size: 10

       1500 ATATATTTTT

                      
       1510 TAAT-ATATA
          1 TAATAATATA

                      
       1519 TAATAATAT-
          1 TAATAATATA

                       
       1528 TAGAT-ATATA
          1 TA-ATAATATA

                *     
       1538 TAATTATATA
          1 TAATAATATA

                      
       1548 TAATAATATA
          1 TAATAATATA

                   
       1558 T-ATAAT
          1 TAATAAT

       1564 TATTAAACGG


Statistics
Matches: 40,  Mismatches: 1, Indels: 8
        0.82            0.02        0.16

Matches are distributed among these distances:
   9   17  0.43
  10   23  0.57

ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44


Consensus pattern (10 bp):   
TAATAATATA

Found at i:2456 original size:28 final size:27

Alignment explanation


    Indices: 2422--2477  Score: 69
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       2412 TAGCCAAAGA

                                  *      
       2422 TGCCGC-AGCAACCCAAAAATTGCAAAAT
          1 TGCCGCAAG-AACCC-AAAATTCCAAAAT

                     *                 
       2450 TGCCGCAAGTACCCAAAATTCCAAAAT
          1 TGCCGCAAGAACCCAAAATTCCAAAAT

             
       2477 T
          1 T

       2478 TTCCGCAACT


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  27   13  0.52
  28   10  0.40
  29    2  0.08

ACGTcount: A:0.41, C:0.29, G:0.12, T:0.18


Consensus pattern (27 bp):   
TGCCGCAAGAACCCAAAATTCCAAAAT

Found at i:2497 original size:28 final size:27

Alignment explanation


    Indices: 2437--2497  Score: 68
    Period size: 28  Copynumber: 2.2  Consensus size: 27

       2427 CAGCAACCCA

                  *              *  *  
       2437 AAAATTGCAAAATTGCCGCAAGTACCC
          1 AAAATTCCAAAATTGCCGCAACTAACC

                           *            
       2464 AAAATTCCAAAATTTTCCGCAACTAACC
          1 AAAATTCCAAAA-TTGCCGCAACTAACC

             *    
       2492 AGAATT
          1 AAAATT

       2498 GCAAGAGCCC


Statistics
Matches: 28,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  27   11  0.39
  28   17  0.61

ACGTcount: A:0.43, C:0.25, G:0.10, T:0.23


Consensus pattern (27 bp):   
AAAATTCCAAAATTGCCGCAACTAACC

Found at i:6636 original size:27 final size:27

Alignment explanation


    Indices: 6587--6650  Score: 76
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       6577 CTAGGGTTAT

                           *           
       6587 TTTGGTCATTTGCACGTCCA-GGGGCA
          1 TTTGGTCATTTGCACATCCAGGGGGCA

                              **        
       6613 CTTTGGTCATTTGCACATTTAGGGGGCA
          1 -TTTGGTCATTTGCACATCCAGGGGGCA

                      
       6641 TTTCGGTCAT
          1 TTT-GGTCAT

       6651 CTCAAGTCTA


Statistics
Matches: 32,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  27   20  0.62
  28   12  0.38

ACGTcount: A:0.16, C:0.20, G:0.28, T:0.36


Consensus pattern (27 bp):   
TTTGGTCATTTGCACATCCAGGGGGCA

Found at i:10793 original size:22 final size:22

Alignment explanation


    Indices: 10767--10813  Score: 85
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      10757 ATTTATTCAT

                                  
      10767 TATTAATTAACTATTAATTAGA
          1 TATTAATTAACTATTAATTAGA

                     *            
      10789 TATTAATTAGCTATTAATTAGA
          1 TATTAATTAACTATTAATTAGA

               
      10811 TAT
          1 TAT

      10814 AGTATAATGG


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47


Consensus pattern (22 bp):   
TATTAATTAACTATTAATTAGA

Found at i:10809 original size:11 final size:11

Alignment explanation


    Indices: 10767--10809  Score: 68
    Period size: 11  Copynumber: 3.9  Consensus size: 11

      10757 ATTTATTCAT

                     * 
      10767 TATTAATTAAC
          1 TATTAATTAGC

                      *
      10778 TATTAATTAGA
          1 TATTAATTAGC

                       
      10789 TATTAATTAGC
          1 TATTAATTAGC

                      
      10800 TATTAATTAG
          1 TATTAATTAG

      10810 ATATAGTATA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  11   29  1.00

ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47


Consensus pattern (11 bp):   
TATTAATTAGC

Found at i:15917 original size:2 final size:2

Alignment explanation


    Indices: 15906--15940  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      15896 ACATATGTAG

                                                                 
      15906 AT AT -T 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 AT AT AT

      15941 CTTCTATCTA


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
AT

Done.