Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000756.1 Corchorus capsularis cultivar CVL-1 contig00756, 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: 7707
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:102 original size:53 final size:53

Alignment explanation


    Indices: 22--129  Score: 198
    Period size: 53  Copynumber: 2.0  Consensus size: 53

         12 ATTTCCTTTA

                                                                 
         22 ATTTCCTTTTATCCTTTAATAAGTATTGGACAATTCATTTAGCTTAAATGAGT
          1 ATTTCCTTTTATCCTTTAATAAGTATTGGACAATTCATTTAGCTTAAATGAGT

                                                     *        *  
         75 ATTTCCTTTTATCCTTTAATAAGTATTGGACAATTCATTTATCTTAAATGGGT
          1 ATTTCCTTTTATCCTTTAATAAGTATTGGACAATTCATTTAGCTTAAATGAGT

              
        128 AT
          1 AT

        130 GGATATCTCA


Statistics
Matches: 53,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  53   53  1.00

ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46


Consensus pattern (53 bp):   
ATTTCCTTTTATCCTTTAATAAGTATTGGACAATTCATTTAGCTTAAATGAGT

Found at i:704 original size:73 final size:72

Alignment explanation


    Indices: 587--725  Score: 215
    Period size: 73  Copynumber: 1.9  Consensus size: 72

        577 ATACACATAT

                           *      *         *                                
        587 TTTTACTAATGTTTCTTATGGGTCAATGGACATTTAACATGATTTAATCCAATTGAGATGGGCAC
          1 TTTTACTAATGTTTCATATGGGCCAATGGACACTTAACATGATTTAATCCAATTGAGATGGGCAC

                   
        652 TTACAAA
         66 TTACAAA

                                     *                              * *      
        659 TTTTACTAATGTTTCATATGGGCCGGATGGACACTTAACATGATTTAATCCAATTGGGGTGGGCA
          1 TTTTACTAATGTTTCATATGGGCC-AATGGACACTTAACATGATTTAATCCAATTGAGATGGGCA

              
        724 CT
         65 CT

        726 CAAAATTATT


Statistics
Matches: 60,  Mismatches: 6, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  72   22  0.37
  73   38  0.63

ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36


Consensus pattern (72 bp):   
TTTTACTAATGTTTCATATGGGCCAATGGACACTTAACATGATTTAATCCAATTGAGATGGGCAC
TTACAAA

Found at i:3260 original size:10 final size:10

Alignment explanation


    Indices: 3245--3276  Score: 57
    Period size: 10  Copynumber: 3.3  Consensus size: 10

       3235 TTTAGAAATA

                      
       3245 TATCTATATC
          1 TATCTATATC

                      
       3255 TATCTATATC
          1 TATCTATATC

                      
       3265 TATCTATA-C
          1 TATCTATATC

               
       3274 TAT
          1 TAT

       3277 ATTTAAAAGT


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

Matches are distributed among these distances:
   9    4  0.18
  10   18  0.82

ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50


Consensus pattern (10 bp):   
TATCTATATC
Done.