Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014863.1 Corchorus olitorius cultivar O-4 contig14896, 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: 16815
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33


Found at i:4170 original size:22 final size:21

Alignment explanation


    Indices: 4118--4171  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

       4108 TGCTTCTCGA

                                  
       4118 AATAATTCTTC-AATGATCTTC
          1 AATAA-TCTTCAAATGATCTTC

                          *      
       4139 -A-AATCTTCAAATTATCTTC
          1 AATAATCTTCAAATGATCTTC

                          
       4158 AATAAGTCTTCAAA
          1 AATAA-TCTTCAAA

       4172 CACGAACTTC


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    5  0.18
  19   11  0.39
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39


Consensus pattern (21 bp):   
AATAATCTTCAAATGATCTTC

Found at i:5382 original size:10 final size:12

Alignment explanation


    Indices: 5357--5381  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       5347 TTTCTATATG

                        
       5357 TATTGTCTTATA
          1 TATTGTCTTATA

                        
       5369 TATTGTCTTATA
          1 TATTGTCTTATA

             
       5381 T
          1 T

       5382 TTATAGGTTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60


Consensus pattern (12 bp):   
TATTGTCTTATA

Found at i:7756 original size:24 final size:23

Alignment explanation


    Indices: 7728--7783  Score: 94
    Period size: 24  Copynumber: 2.4  Consensus size: 23

       7718 GGTAGAAGGT

                            *       
       7728 GGAGATGAGATCAGATGTGGAGGG
          1 GGAGATGAGATCAGATCTGGA-GG

                                   
       7752 GGAGATGAGATCAGATCTGGAGG
          1 GGAGATGAGATCAGATCTGGAGG

                     
       7775 GGAGATGAG
          1 GGAGATGAG

       7784 CCGAGATGAG


Statistics
Matches: 31,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  23   11  0.35
  24   20  0.65

ACGTcount: A:0.30, C:0.05, G:0.48, T:0.16


Consensus pattern (23 bp):   
GGAGATGAGATCAGATCTGGAGG

Found at i:10409 original size:16 final size:16

Alignment explanation


    Indices: 10387--10423  Score: 58
    Period size: 16  Copynumber: 2.4  Consensus size: 16

      10377 AAAACAGGGG

                       *    
      10387 ATTAAAAA-AATAGCA
          1 ATTAAAAAGAAAAGCA

                            
      10402 ATTAAAAAGAAAAGCA
          1 ATTAAAAAGAAAAGCA

                  
      10418 ATTAAA
          1 ATTAAA

      10424 CTAAAAATAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  15    8  0.40
  16   12  0.60

ACGTcount: A:0.68, C:0.05, G:0.08, T:0.19


Consensus pattern (16 bp):   
ATTAAAAAGAAAAGCA

Done.