Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013492.1 Corchorus olitorius cultivar O-4 contig13525, 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: 5988
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:598 original size:30 final size:30

Alignment explanation


    Indices: 562--620  Score: 109
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        552 AAGCTGCATT

                                          
        562 TGATCAATGATGTGATCAAATTTGTGGAAA
          1 TGATCAATGATGTGATCAAATTTGTGGAAA

                       *                 
        592 TGATCAATGATTTGATCAAATTTGTGGAA
          1 TGATCAATGATGTGATCAAATTTGTGGAA

        621 CTTATCCATG


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   28  1.00

ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36


Consensus pattern (30 bp):   
TGATCAATGATGTGATCAAATTTGTGGAAA

Found at i:934 original size:82 final size:82

Alignment explanation


    Indices: 797--960  Score: 328
    Period size: 82  Copynumber: 2.0  Consensus size: 82

        787 ATAATTAGTT

                                                                             
        797 AATTTTCTTTAAGTTATTTTGTGTCAGTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATT
          1 AATTTTCTTTAAGTTATTTTGTGTCAGTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATT

                             
        862 CTAGGCAATCACTCTAG
         66 CTAGGCAATCACTCTAG

                                                                             
        879 AATTTTCTTTAAGTTATTTTGTGTCAGTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATT
          1 AATTTTCTTTAAGTTATTTTGTGTCAGTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATT

                             
        944 CTAGGCAATCACTCTAG
         66 CTAGGCAATCACTCTAG

        961 GTAGTTACCC


Statistics
Matches: 82,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  82   82  1.00

ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45


Consensus pattern (82 bp):   
AATTTTCTTTAAGTTATTTTGTGTCAGTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATT
CTAGGCAATCACTCTAG

Found at i:1062 original size:98 final size:98

Alignment explanation


    Indices: 893--1090  Score: 396
    Period size: 98  Copynumber: 2.0  Consensus size: 98

        883 TTCTTTAAGT

                                                                             
        893 TATTTTGTGTCAGTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATTCTAGGCAATCACTC
          1 TATTTTGTGTCAGTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATTCTAGGCAATCACTC

                                             
        958 TAGGTAGTTACCCTTGAACATATCTCTCAGAAG
         66 TAGGTAGTTACCCTTGAACATATCTCTCAGAAG

                                                                             
        991 TATTTTGTGTCAGTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATTCTAGGCAATCACTC
          1 TATTTTGTGTCAGTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATTCTAGGCAATCACTC

                                             
       1056 TAGGTAGTTACCCTTGAACATATCTCTCAGAAG
         66 TAGGTAGTTACCCTTGAACATATCTCTCAGAAG

              
       1089 TA
          1 TA

       1091 ATATTTTCTC


Statistics
Matches: 100,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  98  100  1.00

ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39


Consensus pattern (98 bp):   
TATTTTGTGTCAGTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATTCTAGGCAATCACTC
TAGGTAGTTACCCTTGAACATATCTCTCAGAAG

Found at i:1732 original size:2 final size:2

Alignment explanation


    Indices: 1725--1756  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       1715 TCATTATAGA

                                                           
       1725 AT 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 AT

       1757 TTGCACAAAC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:3498 original size:4 final size:4

Alignment explanation


    Indices: 3467--3491  Score: 50
    Period size: 4  Copynumber: 6.2  Consensus size: 4

       3457 TATTCCTGTG

                                           
       3467 TGTA TGTA TGTA TGTA TGTA TGTA T
          1 TGTA TGTA TGTA TGTA TGTA TGTA T

       3492 ATGTATGACC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   21  1.00

ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52


Consensus pattern (4 bp):   
TGTA
Done.