Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018048.1 Corchorus olitorius cultivar O-4 contig18081, 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: 14693
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:1472 original size:19 final size:18

Alignment explanation


    Indices: 1439--1474  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1429 TGAAAATAAT

                              
       1439 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       1457 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       1475 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:3074 original size:12 final size:12

Alignment explanation


    Indices: 3053--3082  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       3043 AGGAGGTCTA

                 *      
       3053 TAGGGTGGCCTG
          1 TAGGGCGGCCTG

                        
       3065 TAGGGCGGCCTG
          1 TAGGGCGGCCTG

                  
       3077 TAGGGC
          1 TAGGGC

       3083 TTGGTGTGGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.10, C:0.20, G:0.50, T:0.20


Consensus pattern (12 bp):   
TAGGGCGGCCTG

Found at i:9611 original size:22 final size:23

Alignment explanation


    Indices: 9563--9611  Score: 57
    Period size: 22  Copynumber: 2.2  Consensus size: 23

       9553 TTTTTATAGT

                          *    **  
       9563 GCAATTAAAACTAGTCTAACTAA
          1 GCAATTAAAACTAGACTAAAGAA

                                   
       9586 -CAATTAAAACTA-ACTAAAGAA
          1 GCAATTAAAACTAGACTAAAGAA

                 
       9607 GCAAT
          1 GCAAT

       9612 CAAGAAAATT


Statistics
Matches: 22,  Mismatches: 3, Indels: 3
        0.79            0.11        0.11

Matches are distributed among these distances:
  21    6  0.27
  22   16  0.73

ACGTcount: A:0.53, C:0.16, G:0.08, T:0.22


Consensus pattern (23 bp):   
GCAATTAAAACTAGACTAAAGAA

Found at i:10539 original size:161 final size:161

Alignment explanation


    Indices: 10368--10690  Score: 646
    Period size: 161  Copynumber: 2.0  Consensus size: 161

      10358 GACCTAAGGT

                                                                             
      10368 GGCTATTTATAGTGGAAATAACCCTAGGAATTCCAATCCTAACTTGGAAAGAGGTTTAAGTCGGT
          1 GGCTATTTATAGTGGAAATAACCCTAGGAATTCCAATCCTAACTTGGAAAGAGGTTTAAGTCGGT

                                                                             
      10433 TTTGGATCTAACTTAGACTCCAAGTTGGATTAAAAGTCTTCTTAGAGTAGAATCCAAGTTAAAAT
         66 TTTGGATCTAACTTAGACTCCAAGTTGGATTAAAAGTCTTCTTAGAGTAGAATCCAAGTTAAAAT

                                           
      10498 AGGATCCTGAAAAAAATCCTGATTTCGTGCA
        131 AGGATCCTGAAAAAAATCCTGATTTCGTGCA

                                                                             
      10529 GGCTATTTATAGTGGAAATAACCCTAGGAATTCCAATCCTAACTTGGAAAGAGGTTTAAGTCGGT
          1 GGCTATTTATAGTGGAAATAACCCTAGGAATTCCAATCCTAACTTGGAAAGAGGTTTAAGTCGGT

                                                                             
      10594 TTTGGATCTAACTTAGACTCCAAGTTGGATTAAAAGTCTTCTTAGAGTAGAATCCAAGTTAAAAT
         66 TTTGGATCTAACTTAGACTCCAAGTTGGATTAAAAGTCTTCTTAGAGTAGAATCCAAGTTAAAAT

                                           
      10659 AGGATCCTGAAAAAAATCCTGATTTCGTGCA
        131 AGGATCCTGAAAAAAATCCTGATTTCGTGCA

             
      10690 G
          1 G

      10691 AAACTTCAAC


Statistics
Matches: 162,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 161  162  1.00

ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30


Consensus pattern (161 bp):   
GGCTATTTATAGTGGAAATAACCCTAGGAATTCCAATCCTAACTTGGAAAGAGGTTTAAGTCGGT
TTTGGATCTAACTTAGACTCCAAGTTGGATTAAAAGTCTTCTTAGAGTAGAATCCAAGTTAAAAT
AGGATCCTGAAAAAAATCCTGATTTCGTGCA

Found at i:14437 original size:21 final size:20

Alignment explanation


    Indices: 14390--14438  Score: 53
    Period size: 21  Copynumber: 2.4  Consensus size: 20

      14380 TAAAAATAAT

                             *  
      14390 AATTAAAAAGAAAACAATTA
          1 AATTAAAAAGAAAACAAGTA

                      *   *       
      14410 AACTTAAAAATAAAGCAAAGTA
          1 AA-TTAAAAAGAAAAC-AAGTA

                   
      14432 AATTAAA
          1 AATTAAA

      14439 TCTAAACTAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  20    2  0.08
  21   16  0.67
  22    6  0.25

ACGTcount: A:0.67, C:0.06, G:0.06, T:0.20


Consensus pattern (20 bp):   
AATTAAAAAGAAAACAAGTA
Done.