Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001600.1 Corchorus capsularis cultivar CVL-1 contig01600, 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, 907

Length: 1513
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36

Warning! 3 characters in sequence are not A, C, G, or T


Found at i:152 original size:11 final size:11

Alignment explanation


    Indices: 122--181  Score: 63
    Period size: 10  Copynumber: 5.6  Consensus size: 11

        112 TTGATTTAAT

                      *
        122 ATTTAAAT-GG
          1 ATTTAAATAGA

                       
        132 ATTT-AATAGA
          1 ATTTAAATAGA

                       
        142 ATTTAAATAGA
          1 ATTTAAATAGA

                      **
        153 ATTTTAAAT-TT
          1 A-TTTAAATAGA

                       
        164 ATTTAAATAGA
          1 ATTTAAATAGA

                   
        175 ATTTAAA
          1 ATTTAAA

        182 ATTTAATAAA


Statistics
Matches: 41,  Mismatches: 5, Indels: 7
        0.77            0.09        0.13

Matches are distributed among these distances:
   9    3  0.07
  10   16  0.39
  11   15  0.37
  12    7  0.17

ACGTcount: A:0.48, C:0.00, G:0.08, T:0.43


Consensus pattern (11 bp):   
ATTTAAATAGA

Found at i:164 original size:18 final size:19

Alignment explanation


    Indices: 122--187  Score: 55
    Period size: 22  Copynumber: 3.3  Consensus size: 19

        112 TTGATTTAAT

                      *          
        122 ATTTAAAT-GGATTTAATAGA
          1 ATTTAAATAGAATTTAA-A-A

                                 *
        142 ATTTAAATAGAATTTTAAATTT
          1 ATTTAAATAGAA-TTTAAA--A

                               
        164 ATTTAAATAGAATTT-AAA
          1 ATTTAAATAGAATTTAAAA

                  
        182 ATTTAA
          1 ATTTAA

        188 TAAAAATAAA


Statistics
Matches: 39,  Mismatches: 4, Indels: 8
        0.76            0.08        0.16

Matches are distributed among these distances:
  18    6  0.15
  20   10  0.26
  21    6  0.15
  22   17  0.44

ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44


Consensus pattern (19 bp):   
ATTTAAATAGAATTTAAAA

Found at i:167 original size:22 final size:22

Alignment explanation


    Indices: 142--186  Score: 81
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        132 ATTTAATAGA

                           *      
        142 ATTTAAATAGAATTTTAAATTT
          1 ATTTAAATAGAATTTAAAATTT

                                  
        164 ATTTAAATAGAATTTAAAATTT
          1 ATTTAAATAGAATTTAAAATTT

             
        186 A
          1 A

        187 ATAAAAATAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47


Consensus pattern (22 bp):   
ATTTAAATAGAATTTAAAATTT

Found at i:191 original size:21 final size:22

Alignment explanation


    Indices: 145--191  Score: 69
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        135 TAATAGAATT

                        *        *
        145 TAAATAGAATTTTAAATTTATT
          1 TAAATAGAATTTAAAATTTATA

                                  
        167 TAAATAGAATTTAAAATTTA-A
          1 TAAATAGAATTTAAAATTTATA

                
        188 TAAA
          1 TAAA

        192 AATAAAAAAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21    4  0.17
  22   19  0.83

ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43


Consensus pattern (22 bp):   
TAAATAGAATTTAAAATTTATA

Found at i:1162 original size:16 final size:16

Alignment explanation


    Indices: 1141--1175  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       1131 TATCGGGTAT

                   *        
       1141 TTTATTTCCTAGCGTA
          1 TTTATTTACTAGCGTA

                    *       
       1157 TTTATTTATTAGCGTA
          1 TTTATTTACTAGCGTA

               
       1173 TTT
          1 TTT

       1176 GCTCTTTCTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.20, C:0.11, G:0.11, T:0.57


Consensus pattern (16 bp):   
TTTATTTACTAGCGTA
Done.