Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001818.1 Corchorus capsularis cultivar CVL-1 contig01819, 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: 3248
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32


Found at i:248 original size:20 final size:20

Alignment explanation


    Indices: 211--250  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        201 CTGACGTGGC

                        **      
        211 CTGAAAATTCCATGTGGCCT
          1 CTGAAAATTCCACATGGCCT

                *               
        231 CTGATAATTCCACATGGCCT
          1 CTGAAAATTCCACATGGCCT

        251 ATATTCACGC


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30


Consensus pattern (20 bp):   
CTGAAAATTCCACATGGCCT

Found at i:533 original size:2 final size:2

Alignment explanation


    Indices: 526--555  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

        516 TGAGCTCAAC

                                                        
        526 AT AT 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 AT AT

        556 GCTTTCATAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:2104 original size:21 final size:22

Alignment explanation


    Indices: 2056--2105  Score: 66
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       2046 GGTTGTTAAC

                                 *
       2056 TCAAATAACAAAAAAACAATGT
          1 TCAAATAACAAAAAAACAATGA

             *    *               
       2078 TGAAATGACAAAAAAA-AATGA
          1 TCAAATAACAAAAAAACAATGA

                   
       2099 TCAAATA
          1 TCAAATA

       2106 GTAACCAAAT


Statistics
Matches: 23,  Mismatches: 5, Indels: 1
        0.79            0.17        0.03

Matches are distributed among these distances:
  21    9  0.39
  22   14  0.61

ACGTcount: A:0.64, C:0.10, G:0.08, T:0.18


Consensus pattern (22 bp):   
TCAAATAACAAAAAAACAATGA

Found at i:3112 original size:19 final size:20

Alignment explanation


    Indices: 3084--3121  Score: 69
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       3074 AATTTAAAAC

                                
       3084 AAAATAAAAACTACCCATTT
          1 AAAATAAAAACTACCCATTT

                               
       3104 AAAAT-AAAACTACCCATT
          1 AAAATAAAAACTACCCATT

       3122 AGAGAATAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   13  0.72
  20    5  0.28

ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24


Consensus pattern (20 bp):   
AAAATAAAAACTACCCATTT

Done.