Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010684.1 Corchorus capsularis cultivar CVL-1 contig10705, 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: 12609
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32


Found at i:59 original size:33 final size:32

Alignment explanation


    Indices: 5--92  Score: 131
    Period size: 33  Copynumber: 2.6  Consensus size: 32

          1 CGAA

                                              
          5 GCCGCCCTCATGGGGCAGGCTTCCCCATGAAAAG
          1 GCCGCCC-CATGGGGC-GGCTTCCCCATGAAAAG

             *                               
         39 GTCGCCCCATGAGGGCGGCTTCCCCATGAAAAG
          1 GCCGCCCCATG-GGGCGGCTTCCCCATGAAAAG

                                 
         72 GCCGCCCCACTGGGGCGGCTT
          1 GCCGCCCCA-TGGGGCGGCTT

         93 AGCCAGGGCA


Statistics
Matches: 50,  Mismatches: 2, Indels: 5
        0.88            0.04        0.09

Matches are distributed among these distances:
  33   38  0.76
  34   12  0.24

ACGTcount: A:0.17, C:0.36, G:0.32, T:0.15


Consensus pattern (32 bp):   
GCCGCCCCATGGGGCGGCTTCCCCATGAAAAG

Found at i:244 original size:33 final size:32

Alignment explanation


    Indices: 194--288  Score: 106
    Period size: 33  Copynumber: 2.9  Consensus size: 32

        184 CCCCACCGGT

                                              
        194 GCCGTCCC-CCTGGGGCGGCTGAGCCATGGCCAA
          1 GCCG-CCCTCCTGGGGCGGCT-AGCCATGGCCAA

                                              
        227 GCCGCCCTCCTGGGGCGGCACTA-CCATGGCCAA
          1 GCCGCCCTCCTGGGGCGG--CTAGCCATGGCCAA

                            *        *    
        260 GCCG-CCTCCCTGGGGTGGCTAGCCGTGGC
          1 GCCGCCCT-CCTGGGGCGGCTAGCCATGGC

        289 AGAGCCGTCC


Statistics
Matches: 55,  Mismatches: 2, Indels: 11
        0.81            0.03        0.16

Matches are distributed among these distances:
  31    3  0.05
  32   12  0.22
  33   37  0.67
  34    1  0.02
  35    2  0.04

ACGTcount: A:0.11, C:0.40, G:0.36, T:0.14


Consensus pattern (32 bp):   
GCCGCCCTCCTGGGGCGGCTAGCCATGGCCAA

Found at i:4715 original size:15 final size:15

Alignment explanation


    Indices: 4695--4729  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       4685 GATTGTCCCT

                   *   *   
       4695 TTAAAAGTATAGTAA
          1 TTAAAAGGATACTAA

                           
       4710 TTAAAAGGATACTAA
          1 TTAAAAGGATACTAA

                 
       4725 TTAAA
          1 TTAAA

       4730 GTGACAATGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.54, C:0.03, G:0.11, T:0.31


Consensus pattern (15 bp):   
TTAAAAGGATACTAA

Found at i:5743 original size:14 final size:14

Alignment explanation


    Indices: 5698--5735  Score: 58
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       5688 AAGATAGCCG

                       *   
       5698 CTCCTCTCTCCCCTT
          1 CTCC-CTCTCCTCTT

                          
       5713 CTCCCTCTCCTCTT
          1 CTCCCTCTCCTCTT

                     
       5727 CTCCCTCTC
          1 CTCCCTCTC

       5736 TAGTTCTCAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  14   18  0.82
  15    4  0.18

ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39


Consensus pattern (14 bp):   
CTCCCTCTCCTCTT

Found at i:10540 original size:2 final size:2

Alignment explanation


    Indices: 10533--10558  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      10523 CGAATCAGAC

                                                  
      10533 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

      10559 GTTTGTTATG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Done.