Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002812.1 Corchorus capsularis cultivar CVL-1 contig02820, 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, 632

Length: 1054
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27


Found at i:125 original size:31 final size:34

Alignment explanation


    Indices: 90--154  Score: 82
    Period size: 36  Copynumber: 1.9  Consensus size: 34

         80 TAAAATAAAT

                                   *          
         90 AACTGGA-GAA-AA-ACCACCCTGGATCATTCTG
          1 AACTGGACGAAGAAGACCACCCTCGATCATTCTG

                                              
        121 AACTGGACTGAAGAATGACCACCCTCGATCATTC
          1 AACTGGAC-GAAGAA-GACCACCCTCGATCATTC

        155 CGACGCAAAT


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

Matches are distributed among these distances:
  31    7  0.25
  33    3  0.11
  34    2  0.07
  36   16  0.57

ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20


Consensus pattern (34 bp):   
AACTGGACGAAGAAGACCACCCTCGATCATTCTG

Found at i:297 original size:35 final size:35

Alignment explanation


    Indices: 232--324  Score: 89
    Period size: 35  Copynumber: 2.7  Consensus size: 35

        222 ATTTCGGACT

                          * *      **        *  
        232 AACTGAAGAAAAGACCACCCTGGGTC-ATTGAAGTA
          1 AACTGAAG-AAAGATCGCCCTGGACCAATTGAAATA

              *       *       *               *
        267 AATTGAAGAATGATCGCCTTGGACCAATTGAAATC
          1 AACTGAAGAAAGATCGCCCTGGACCAATTGAAATA

                                   
        302 AACTGAAGAAAGATCGCCCTGGA
          1 AACTGAAGAAAGATCGCCCTGGA

        325 TCGAGTAACT


Statistics
Matches: 45,  Mismatches: 12, Indels: 2
        0.76            0.20        0.03

Matches are distributed among these distances:
  34   11  0.24
  35   34  0.76

ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19


Consensus pattern (35 bp):   
AACTGAAGAAAGATCGCCCTGGACCAATTGAAATA

Found at i:586 original size:37 final size:35

Alignment explanation


    Indices: 545--634  Score: 94
    Period size: 34  Copynumber: 2.6  Consensus size: 35

        535 TGAGAATGAT

                                                 
        545 CACCCTGGATCAAATTTGAAAGCAACTGAAGAAAGAC
          1 CACCCTGGATCAAA-TTGAAA-CAACTGAAGAAAGAC

                    *   *       ** *      *    
        582 CACCCTGGGTC-CATTGAAATTATTGAAGAGAGAC
          1 CACCCTGGATCAAATTGAAACAACTGAAGAAAGAC

                                
        616 CACCCTGGATC-AATTGAAA
          1 CACCCTGGATCAAATTGAAA

        635 TTTACTGAAT


Statistics
Matches: 45,  Mismatches: 8, Indels: 3
        0.80            0.14        0.05

Matches are distributed among these distances:
  34   28  0.62
  35    6  0.13
  36    1  0.02
  37   10  0.22

ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20


Consensus pattern (35 bp):   
CACCCTGGATCAAATTGAAACAACTGAAGAAAGAC

Found at i:616 original size:34 final size:35

Alignment explanation


    Indices: 569--664  Score: 115
    Period size: 34  Copynumber: 2.8  Consensus size: 35

        559 TTTGAAAGCA

                    *                          
        569 ACTGAAGAAAGACCACCCTGGGTCCATTGAAA-TT
          1 ACTGAAGAGAGACCACCCTGGGTCCATTGAAATTT

             *                   *  *          
        603 ATTGAAGAGAGACCACCCTGGATCAATTGAAATTT
          1 ACTGAAGAGAGACCACCCTGGGTCCATTGAAATTT

                      *         *       
        638 ACTGAATG-GGGACCACCCTAGGTCCAT
          1 ACTGAA-GAGAGACCACCCTGGGTCCAT

        665 CAACTGAATG


Statistics
Matches: 51,  Mismatches: 9, Indels: 3
        0.81            0.14        0.05

Matches are distributed among these distances:
  34   28  0.55
  35   22  0.43
  36    1  0.02

ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22


Consensus pattern (35 bp):   
ACTGAAGAGAGACCACCCTGGGTCCATTGAAATTT
Done.