Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010274.1 Corchorus olitorius cultivar O-4 contig10306, 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: 16506
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36


Found at i:1063 original size:42 final size:43

Alignment explanation


    Indices: 1012--1105  Score: 120
    Period size: 45  Copynumber: 2.2  Consensus size: 43

       1002 AGTGTGTTAC

                              *    **                  
       1012 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
          1 CTAATATTCTATCTCCATATCTAAATAATTCATCAAAATAAAG

                                                         
       1053 CTAATATTCTATTCCTCCATATCTAAATAATTCATCAAAATAAAG
          1 CTAATATTCTA-T-CTCCATATCTAAATAATTCATCAAAATAAAG

            *       
       1098 GTAATATT
          1 CTAATATT

       1106 AATTGTTGTT


Statistics
Matches: 45,  Mismatches: 4, Indels: 4
        0.85            0.08        0.08

Matches are distributed among these distances:
  41    4  0.09
  42    6  0.13
  45   35  0.78

ACGTcount: A:0.40, C:0.19, G:0.05, T:0.35


Consensus pattern (43 bp):   
CTAATATTCTATCTCCATATCTAAATAATTCATCAAAATAAAG

Found at i:5204 original size:21 final size:20

Alignment explanation


    Indices: 5165--5204  Score: 62
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5155 AAAAAAATCC

                     *  *       
       5165 TTAATTAGGTTTCTTAAAAA
          1 TTAATTAGGGTTATTAAAAA

                                
       5185 TTAATTAGGGTTATTAAAAA
          1 TTAATTAGGGTTATTAAAAA

       5205 GTTTATAAGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42


Consensus pattern (20 bp):   
TTAATTAGGGTTATTAAAAA

Found at i:5403 original size:21 final size:21

Alignment explanation


    Indices: 5373--5439  Score: 73
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       5363 TCTAGCAATA

                *                
       5373 TTAATAAAGTCACTAAAAAAC
          1 TTAACAAAGTCACTAAAAAAC

                       *    *     
       5394 TTAA-AGAAGTTACTATAAAAC
          1 TTAACA-AAGTCACTAAAAAAC

                   *          *  
       5415 TTAACAAGGTCACTAAAATAC
          1 TTAACAAAGTCACTAAAAAAC

                
       5436 TTAA
          1 TTAA

       5440 TAAGATTAAG


Statistics
Matches: 38,  Mismatches: 6, Indels: 4
        0.79            0.12        0.08

Matches are distributed among these distances:
  20    1  0.03
  21   36  0.95
  22    1  0.03

ACGTcount: A:0.52, C:0.13, G:0.07, T:0.27


Consensus pattern (21 bp):   
TTAACAAAGTCACTAAAAAAC

Found at i:6929 original size:1 final size:1

Alignment explanation


    Indices: 6925--6954  Score: 60
    Period size: 1  Copynumber: 30.0  Consensus size: 1

       6915 TTTTGCTCAA

                                          
       6925 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       6955 CAAAAATTCC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   29  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:11692 original size:29 final size:29

Alignment explanation


    Indices: 11657--11718  Score: 124
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      11647 TTCTAAGGTC

                                         
      11657 CATTGCACTGTTTGAGTTCTTTTCCTTGT
          1 CATTGCACTGTTTGAGTTCTTTTCCTTGT

                                         
      11686 CATTGCACTGTTTGAGTTCTTTTCCTTGT
          1 CATTGCACTGTTTGAGTTCTTTTCCTTGT

                
      11715 CATT
          1 CATT

      11719 CTTTTTTAGT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   33  1.00

ACGTcount: A:0.11, C:0.21, G:0.16, T:0.52


Consensus pattern (29 bp):   
CATTGCACTGTTTGAGTTCTTTTCCTTGT
Done.