Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018777.1 Corchorus olitorius cultivar O-4 contig18810, 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: 29934
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:1375 original size:15 final size:16

Alignment explanation


    Indices: 1355--1394  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       1345 AGAGGTTGAA

                            
       1355 AGAAAACAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
       1370 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
       1386 AGAAAACAA
          1 AGAAAACAA

       1395 AACAAACAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:7700 original size:20 final size:21

Alignment explanation


    Indices: 7661--7702  Score: 59
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       7651 CCTCTCATGG

                          **     
       7661 AGCTTGGGATTTTCTTCATCA
          1 AGCTTGGGATTTTCACCATCA

                                 
       7682 AGCTT-GGATTTTCACCATCA
          1 AGCTTGGGATTTTCACCATCA

             
       7702 A
          1 A

       7703 ATATCTCTTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  20   14  0.74
  21    5  0.26

ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38


Consensus pattern (21 bp):   
AGCTTGGGATTTTCACCATCA

Found at i:17004 original size:24 final size:24

Alignment explanation


    Indices: 16968--17019  Score: 70
    Period size: 24  Copynumber: 2.2  Consensus size: 24

      16958 TTAATTTCAA

                                     
      16968 ATTTTAAAAAATAATTAATTGATTT
          1 ATTTTAAAAAATAATTAATT-ATTT

                    *       *       
      16993 ATTTT-AATAATAATTTATTATTT
          1 ATTTTAAAAAATAATTAATTATTT

                
      17016 ATTT
          1 ATTT

      17020 AGTCCCTTCC


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  23    8  0.32
  24   12  0.48
  25    5  0.20

ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56


Consensus pattern (24 bp):   
ATTTTAAAAAATAATTAATTATTT

Found at i:17206 original size:23 final size:24

Alignment explanation


    Indices: 17165--17209  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 24

      17155 CCTTTCTCTT

                                    
      17165 CCTTTTTGTTCTTCAAAACCGAGC
          1 CCTTTTTGTTCTTCAAAACCGAGC

                   *  *           
      17189 CCTTTTTTTTTTTC-AAACCGA
          1 CCTTTTTGTTCTTCAAAACCGA

      17210 CTTACCCCTC


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  23    7  0.37
  24   12  0.63

ACGTcount: A:0.20, C:0.27, G:0.09, T:0.44


Consensus pattern (24 bp):   
CCTTTTTGTTCTTCAAAACCGAGC

Found at i:20103 original size:25 final size:26

Alignment explanation


    Indices: 20027--20107  Score: 76
    Period size: 25  Copynumber: 3.0  Consensus size: 26

      20017 AAGAGAAAAT

                                      * 
      20027 ATTTTTTTTTTCTAAAAACGCAGAAAAA
          1 ATTTTTTTTTTC-AAAAACGCA-AAACA

                          **          *
      20055 ATTTTTTTTTT--ATGACGCAAAAACC
          1 ATTTTTTTTTTCAAAAACGC-AAAACA

                                       
      20080 ATTTTTTTTTTCAAAAACGCAAACACA
          1 ATTTTTTTTTTCAAAAACGCAAA-ACA

             
      20107 A
          1 A

      20108 AATTAAAGAC


Statistics
Matches: 42,  Mismatches: 7, Indels: 9
        0.72            0.12        0.16

Matches are distributed among these distances:
  25   19  0.45
  26    4  0.10
  27    8  0.19
  28   11  0.26

ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40


Consensus pattern (26 bp):   
ATTTTTTTTTTCAAAAACGCAAAACA
Done.