Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024686.1 Corchorus olitorius cultivar O-4 contig24719, 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: 11884
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:1267 original size:15 final size:15

Alignment explanation


    Indices: 1241--1278  Score: 51
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       1231 GACCTTTAAT

                           
       1241 TATAAAAA-AAATTA
          1 TATAAAAATAAATTA

                          *
       1255 TATAAAAATAAATTT
          1 TATAAAAATAAATTA

              *      
       1270 TAAAAAAAT
          1 TATAAAAAT

       1279 TATGTTTTGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  14    8  0.38
  15   13  0.62

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (15 bp):   
TATAAAAATAAATTA

Found at i:3372 original size:21 final size:23

Alignment explanation


    Indices: 3328--3375  Score: 66
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       3318 GGCATTCCTG

                                   
       3328 GTTATAAAAGTTTTAAATAACCA
          1 GTTATAAAAGTTTTAAATAACCA

                                    
       3351 GTTATATAAA-TTTT-AA-AACCA
          1 GTTATA-AAAGTTTTAAATAACCA

                
       3372 GTTA
          1 GTTA

       3376 AACAGGTTGG


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  21    9  0.38
  22    2  0.08
  23   10  0.42
  24    3  0.12

ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38


Consensus pattern (23 bp):   
GTTATAAAAGTTTTAAATAACCA

Found at i:3857 original size:16 final size:15

Alignment explanation


    Indices: 3830--3865  Score: 63
    Period size: 16  Copynumber: 2.3  Consensus size: 15

       3820 GGCGTCTCTC

                           
       3830 ATTATATATATTATT
          1 ATTATATATATTATT

                            
       3845 ATTATATTATATTATT
          1 ATTATA-TATATTATT

                 
       3861 ATTAT
          1 ATTAT

       3866 CATTGAGTCC


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15    6  0.30
  16   14  0.70

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (15 bp):   
ATTATATATATTATT

Found at i:5578 original size:17 final size:16

Alignment explanation


    Indices: 5558--5601  Score: 52
    Period size: 17  Copynumber: 2.6  Consensus size: 16

       5548 TTTGGGAAAA

                           * 
       5558 ATAATTTTTTATATATT
          1 ATAATTTTTTAT-TAGT

                *           
       5575 ATAACTTTTTATTAGT
          1 ATAATTTTTTATTAGT

                       
       5591 ATTAATTTTTT
          1 A-TAATTTTTT

       5602 TTTAAGATTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  16    4  0.17
  17   19  0.83

ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64


Consensus pattern (16 bp):   
ATAATTTTTTATTAGT

Found at i:9571 original size:40 final size:40

Alignment explanation


    Indices: 9491--9572  Score: 130
    Period size: 41  Copynumber: 2.0  Consensus size: 40

       9481 TATTTATATC

                        *                *          
       9491 TAGGGGCTAAACTTGAATTTAATTTATTATCTTAATTTAT
          1 TAGGGGCTAAACCTGAATTTAATTTATTACCTTAATTTAT

                                                     
       9531 TAGGGGACTAAACCTGAATTTAATTTATTACCTTAA-TTAT
          1 TAGGGG-CTAAACCTGAATTTAATTTATTACCTTAATTTAT

              
       9571 TA
          1 TA

       9573 AGATTTAAGA


Statistics
Matches: 39,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  40   12  0.31
  41   27  0.69

ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44


Consensus pattern (40 bp):   
TAGGGGCTAAACCTGAATTTAATTTATTACCTTAATTTAT
Done.