Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001501.1 Corchorus capsularis cultivar CVL-1 contig01501, 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: 5764
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37


Found at i:639 original size:15 final size:16

Alignment explanation


    Indices: 604--641  Score: 51
    Period size: 15  Copynumber: 2.4  Consensus size: 16

        594 TTCCCCAATT

                       *    
        604 ATCATAAGAATTAGAA
          1 ATCATAAGAATGAGAA

                          * 
        620 ATCATAAGAA-GAGTA
          1 ATCATAAGAATGAGAA

                   
        635 ATCATAA
          1 ATCATAA

        642 AAAAAAGTCT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  15   10  0.50
  16   10  0.50

ACGTcount: A:0.55, C:0.08, G:0.13, T:0.24


Consensus pattern (16 bp):   
ATCATAAGAATGAGAA

Found at i:1325 original size:17 final size:17

Alignment explanation


    Indices: 1298--1345  Score: 51
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       1288 GCTAAGCAAC

                             *
       1298 AATATAAATAAAAAAACT
          1 AATA-AAATAAAAAAACA

                      * *    
       1316 AATAAAATAATATAACA
          1 AATAAAATAAAAAAACA

               *         
       1333 AATTAAATAAAAA
          1 AATAAAATAAAAA

       1346 TAATGTCACA


Statistics
Matches: 24,  Mismatches: 6, Indels: 1
        0.77            0.19        0.03

Matches are distributed among these distances:
  17   20  0.83
  18    4  0.17

ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23


Consensus pattern (17 bp):   
AATAAAATAAAAAAACA

Found at i:3476 original size:306 final size:300

Alignment explanation


    Indices: 2941--3488  Score: 981
    Period size: 307  Copynumber: 1.8  Consensus size: 300

       2931 TTTTAATTAT

                                               *                             
       2941 TCATTTAATTAAGTAGTAGAGTTGAAATTTCACATTGACAACATATGAACATATGATATAACCAC
          1 TCATTTAATTAAGTAGTAGAGTTGAAATTTCACATCGACAACATATGAACATATGATATAACCAC

                                                                             
       3006 GTATTTTTCTCGTATCGTTTGAGTAGCATATATAGAAATTATTAGAAAAAATTGCTTTAATTGGA
         66 GTATTTTTCTCGTATCGTTTGAGTAGCATATATAGAAATTATTAGAAAAAATTGCTTTAATTGGA

                              *               *                              
       3071 ATCGCAATTTCATATATCTCACATTTCCCATATATTACTTTAGTATTCAATTATTCCAAAATTGT
        131 ATCGCAATTTCATATATCACACATTTCCCATATAGTACTTTAGTATTCAATTATTCCAAAATTGT

                                                                             
       3136 CAATATTGTTAAAATCATTCTCATTGAAATTAAGAGTTGAGTATTCCAGCAGCTGCCTCGTTGGT
        196 CAATATTGTTAAAATCATTCTCATTGAAATTAAGAGTTGAGTATTCCAGCAGCTGCCTCGTTGGT

                                                    
       3201 AGACTCACCCATCAAATTTAGGTGCATGATGCATGTCAAA
        261 AGACTCACCCATCAAATTTAGGTGCATGATGCATGTCAAA

                                                                             
       3241 TCATTTAATTAAGTAGTAGAGTTGAAATTTCACATCGACAACATATGAACATATGATATAACCAC
          1 TCATTTAATTAAGTAGTAGAGTTGAAATTTCACATCGACAACATATGAACATATGATATAACCAC

                             *                                               
       3306 GTATCATCAATTTTCTCTTATCGTTTGAGTAGCATATATAGAAATTATTAGAAAAAAATTGCTTT
         66 G--T-AT---TTTTCTCGTATCGTTTGAGTAGCATATATAGAAATTATTAG-AAAAAATTGCTTT

                     *                                                       
       3371 AATTGGAATTGCAATTTCATATATCACACATTTCCCATATAGTACTTTAGTATTCAATTATTCCA
        124 AATTGGAATCGCAATTTCATATATCACACATTTCCCATATAGTACTTTAGTATTCAATTATTCCA

                                                                  
       3436 AAATTGTCAA-ATTGTTAAAATCATTCTCATTGAAATTAAGAGTTGAGTATTCC
        189 AAATTGTCAATATTGTTAAAATCATTCTCATTGAAATTAAGAGTTGAGTATTCC

       3489 GCTATCTCTG


Statistics
Matches: 236,  Mismatches: 5, Indels: 8
        0.95            0.02        0.03

Matches are distributed among these distances:
 300   65  0.28
 302    1  0.00
 303    2  0.01
 306   83  0.35
 307   85  0.36

ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37


Consensus pattern (300 bp):   
TCATTTAATTAAGTAGTAGAGTTGAAATTTCACATCGACAACATATGAACATATGATATAACCAC
GTATTTTTCTCGTATCGTTTGAGTAGCATATATAGAAATTATTAGAAAAAATTGCTTTAATTGGA
ATCGCAATTTCATATATCACACATTTCCCATATAGTACTTTAGTATTCAATTATTCCAAAATTGT
CAATATTGTTAAAATCATTCTCATTGAAATTAAGAGTTGAGTATTCCAGCAGCTGCCTCGTTGGT
AGACTCACCCATCAAATTTAGGTGCATGATGCATGTCAAA
Done.