Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004217.1 Corchorus capsularis cultivar CVL-1 contig04225, 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, 781

Length: 1302
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32


Found at i:567 original size:19 final size:20

Alignment explanation


    Indices: 538--576  Score: 62
    Period size: 19  Copynumber: 2.0  Consensus size: 20

        528 TTCAACTTCA

                           *    
        538 AGAACAATTATAAATTAAAT
          1 AGAACAATTATAAATAAAAT

                                
        558 AGAA-AATTATAAATAAAAT
          1 AGAACAATTATAAATAAAAT

        577 TATAATTATT


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

Matches are distributed among these distances:
  19   14  0.78
  20    4  0.22

ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28


Consensus pattern (20 bp):   
AGAACAATTATAAATAAAAT

Found at i:591 original size:14 final size:14

Alignment explanation


    Indices: 574--612  Score: 78
    Period size: 14  Copynumber: 2.8  Consensus size: 14

        564 TTATAAATAA

                          
        574 AATTATAATTATTT
          1 AATTATAATTATTT

                          
        588 AATTATAATTATTT
          1 AATTATAATTATTT

                       
        602 AATTATAATTA
          1 AATTATAATTA

        613 ATGTAAAACA


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

Matches are distributed among these distances:
  14   25  1.00

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (14 bp):   
AATTATAATTATTT

Found at i:698 original size:22 final size:24

Alignment explanation


    Indices: 654--698  Score: 58
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        644 ATATAATAAA

                              *     
        654 ATAAAAAATTATAAATTTTAATAT
          1 ATAAAAAATTATAAATTTAAATAT

                  *                
        678 ATAAAATATTA-AAA-TTAAATA
          1 ATAAAAAATTATAAATTTAAATA

        699 CGGGATATAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  22    6  0.32
  23    3  0.16
  24   10  0.53

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (24 bp):   
ATAAAAAATTATAAATTTAAATAT

Found at i:1147 original size:11 final size:12

Alignment explanation


    Indices: 1125--1157  Score: 50
    Period size: 11  Copynumber: 2.8  Consensus size: 12

       1115 AAAAAGAAAG

                         
       1125 AAATAGAAAATAT
          1 AAATA-AAAATAT

                        
       1138 AAA-AAAAATAT
          1 AAATAAAAATAT

                     
       1149 AAATAAAAA
          1 AAATAAAAA

       1158 GGCGGGAACG


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  11   10  0.53
  12    6  0.32
  13    3  0.16

ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18


Consensus pattern (12 bp):   
AAATAAAAATAT
Done.