Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008767.1 Corchorus capsularis cultivar CVL-1 contig08788, 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: 2174
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31


Found at i:1654 original size:33 final size:32

Alignment explanation


    Indices: 1539--1658  Score: 136
    Period size: 33  Copynumber: 3.8  Consensus size: 32

       1529 ATCTCTTTCT

                 *          *       *       
       1539 TTTCACCCAAAACAGATTTATTTTCAATGCTA
          1 TTTCAACCAAAACAGAATTATTTTTAATGCTA

                           *       *        
       1571 --TCAACCAAAACAGGATTATTTGTAATGCTA
          1 TTTCAACCAAAACAGAATTATTTTTAATGCTA

              *                 *            
       1601 TAATCAACCAAAACAGAATTGTTTTTAATGCTA
          1 T-TTCAACCAAAACAGAATTATTTTTAATGCTA

                                *    
       1634 TGTTCAACCAAAACAGAATTGTTTT
          1 T-TTCAACCAAAACAGAATTATTTT

       1659 CATCACAATT


Statistics
Matches: 75,  Mismatches: 10, Indels: 5
        0.83            0.11        0.06

Matches are distributed among these distances:
  30   25  0.33
  33   50  0.67

ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34


Consensus pattern (32 bp):   
TTTCAACCAAAACAGAATTATTTTTAATGCTA

Found at i:1693 original size:66 final size:63

Alignment explanation


    Indices: 1545--1693  Score: 142
    Period size: 66  Copynumber: 2.3  Consensus size: 63

       1535 TTCTTTTCAC

                                                    *            * *    *   
       1545 CCAAAACAGATTTA-TTTTCAATGCTATCAACCAAAACAGGATTATTTGTAATGCTATAATCAA
          1 CCAAAACAGATTTAGTTTT-AATGCTATCAACCAAAACAGAATTATTTGTAATACAATAAGCAA

                      *                                    *     *        *  
       1608 CCAAAACAGAATT-GTTTTTAATGCTATGTTCAACCAAAACAGAATTGTTT-TCATCACAATTAG
          1 CCAAAACAGATTTAG-TTTTAATGCTA---TCAACCAAAACAGAATTATTTGTAAT-ACAATAAG

              *
       1671 CAT
         61 CAA

                                
       1674 CCAAAACAGATTTAGTTTTA
          1 CCAAAACAGATTTAGTTTTA

       1694 TTGCAAACAA


Statistics
Matches: 69,  Mismatches: 10, Indels: 11
        0.77            0.11        0.12

Matches are distributed among these distances:
  63   19  0.28
  64    4  0.06
  65    3  0.04
  66   42  0.61
  67    1  0.01

ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33


Consensus pattern (63 bp):   
CCAAAACAGATTTAGTTTTAATGCTATCAACCAAAACAGAATTATTTGTAATACAATAAGCAA
Done.