Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020483.1 Corchorus olitorius cultivar O-4 contig20516, 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: 4211
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:516 original size:21 final size:21

Alignment explanation


    Indices: 491--537  Score: 69
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        481 TCTCACAGAG

                                  
        491 AGGTTATCAAAAATT-ATAGGA
          1 AGGTTA-CAAAAATTCATAGGA

                       *         
        512 AGGTTACAAAATTTCATAGGA
          1 AGGTTACAAAAATTCATAGGA

                 
        533 AGGTT
          1 AGGTT

        538 TATTAAAATT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  20    7  0.29
  21   17  0.71

ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30


Consensus pattern (21 bp):   
AGGTTACAAAAATTCATAGGA

Found at i:549 original size:23 final size:23

Alignment explanation


    Indices: 506--576  Score: 92
    Period size: 23  Copynumber: 3.2  Consensus size: 23

        496 ATCAAAAATT

                          *        
        506 ATAGGAAGG-TTA-CAAAATTTC
          1 ATAGGAAGGTTTATTAAAATTTC

                                   
        527 ATAGGAAGGTTTATTAAAATTTC
          1 ATAGGAAGGTTTATTAAAATTTC

               *   *           *   
        550 ATATGAATGTTTATTAAAACTTC
          1 ATAGGAAGGTTTATTAAAATTTC

                
        573 ATAG
          1 ATAG

        577 TTAGGTTATC


Statistics
Matches: 43,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  21    9  0.21
  22    3  0.07
  23   31  0.72

ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37


Consensus pattern (23 bp):   
ATAGGAAGGTTTATTAAAATTTC

Found at i:637 original size:22 final size:22

Alignment explanation


    Indices: 609--671  Score: 74
    Period size: 22  Copynumber: 2.9  Consensus size: 22

        599 TTCATAGGTA

                                   
        609 AATTATCAAAATTCT-ATAACAT
          1 AATTATCAAAATT-TAATAACAT

                               ** 
        631 AATTATCAAAATTTAATAAGGT
          1 AATTATCAAAATTTAATAACAT

             *            *    
        653 AGTTATCAAAATTTCATAA
          1 AATTATCAAAATTTAATAA

        672 AAACATTCAA


Statistics
Matches: 36,  Mismatches: 4, Indels: 2
        0.86            0.10        0.05

Matches are distributed among these distances:
  21    1  0.03
  22   35  0.97

ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37


Consensus pattern (22 bp):   
AATTATCAAAATTTAATAACAT

Found at i:3563 original size:32 final size:32

Alignment explanation


    Indices: 3502--3563  Score: 97
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       3492 GGTTTCAAAC

                             *    * *       
       3502 AGATATCACTCATCTCACAAACTATCTCCTAG
          1 AGATATCACTCATCTCAAAAACCAGCTCCTAG

                                          
       3534 AGATATCACTCATCTCAAAAACCAGCTCCT
          1 AGATATCACTCATCTCAAAAACCAGCTCCT

       3564 GAAGCTACAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.35, C:0.32, G:0.06, T:0.26


Consensus pattern (32 bp):   
AGATATCACTCATCTCAAAAACCAGCTCCTAG

Found at i:3823 original size:5 final size:5

Alignment explanation


    Indices: 3813--3848  Score: 65
    Period size: 5  Copynumber: 7.4  Consensus size: 5

       3803 AATTTCCTAA

                                                        
       3813 TTCTT TTCTT TTCTT TTCTT TTCTT TTC-T TTCTT TT
          1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT

       3849 AAGTTTGGCT


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   4    4  0.13
   5   26  0.87

ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81


Consensus pattern (5 bp):   
TTCTT

Done.