Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001670.1 Corchorus olitorius cultivar O-4 contig01670, 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, 865

Length: 1442
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38


Found at i:547 original size:106 final size:107

Alignment explanation


    Indices: 437--637  Score: 266
    Period size: 106  Copynumber: 1.9  Consensus size: 107

        427 ACATATCAAC

                           *   *    *                                        
        437 AAGGTTTAACCCCAATTAATAAAATATTTGAAA-TTTTAAA-GAGTAAATCTTGAA-TTTTAAGA
          1 AAGGTTTAACCCCAACTAAAAAAAGATTT-AAATTTTTAAAGGA-TAAATCTTGAATTTTTAAGA

             *                                           
        499 CTCATTCTCAT-AGGATTTTAGAAAAAAAAATAAATAATTTTAAT
         64 CCCATTCTCATAAGG-TTTTAGAAAAAAAAATAAATAATTTTAAT

                    *   *                        *                           
        543 AAGGTTTAGCCCTAACTAAAAAAAGATTTAAATTTTTTAAGGATAAATCTTGAATTTTTAAGACC
          1 AAGGTTTAACCCCAACTAAAAAAAGATTTAAATTTTTAAAGGATAAATCTTGAATTTTTAAGACC

             *    *                       
        608 CTTTCTTATAAGGTTTTAGAAAAAAAAATA
         66 CATTCTCATAAGGTTTTAGAAAAAAAAATA

        638 TACATATATA


Statistics
Matches: 82,  Mismatches: 9, Indels: 7
        0.84            0.09        0.07

Matches are distributed among these distances:
 105    3  0.04
 106   41  0.50
 107   35  0.43
 108    3  0.04

ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36


Consensus pattern (107 bp):   
AAGGTTTAACCCCAACTAAAAAAAGATTTAAATTTTTAAAGGATAAATCTTGAATTTTTAAGACC
CATTCTCATAAGGTTTTAGAAAAAAAAATAAATAATTTTAAT

Found at i:1050 original size:11 final size:11

Alignment explanation


    Indices: 1031--1060  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

       1021 TGGTCTGCTA

                *      
       1031 TTTTCTTTCTT
          1 TTTTTTTTCTT

                       
       1042 TTTTTTTTCTT
          1 TTTTTTTTCTT

                    
       1053 TTTTTTTT
          1 TTTTTTTT

       1061 GAGGAAAAGA


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

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90


Consensus pattern (11 bp):   
TTTTTTTTCTT

Found at i:1051 original size:15 final size:14

Alignment explanation


    Indices: 1031--1060  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       1021 TGGTCTGCTA

                           
       1031 TTTTCTTTCTTTTTT
          1 TTTTCTTT-TTTTTT

                          
       1046 TTTTCTTTTTTTTT
          1 TTTTCTTTTTTTTT

             
       1060 T
          1 T

       1061 GAGGAAAAGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    7  0.47
  15    8  0.53

ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90


Consensus pattern (14 bp):   
TTTTCTTTTTTTTT
Done.