Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022535.1 Corchorus olitorius cultivar O-4 contig22568, 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: 24826
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:4248 original size:57 final size:55

Alignment explanation


    Indices: 4121--4249  Score: 134
    Period size: 57  Copynumber: 2.3  Consensus size: 55

       4111 AGGTTTTAGA

                  *    *                 *           *  *          
       4121 TTTTATGAATATAG-AAAATAAATATTATCTTTTAAGTAAGGTCTTAAATTCAAG
          1 TTTTATAAATAAAGAAAAATAAATATTATATTTTAAGTAAGATCATAAATTCAAG

               ** *   **                                     *       
       4175 TTTGGTTAATGGAGAAAATATATAATATTATATTTTAAGTAAGATCATATATTCAAG
          1 TTTTATAAATAAAGAAAA-ATA-AATATTATATTTTAAGTAAGATCATAAATTCAAG

                              
       4232 TTTTATAAATAAAGAAAA
          1 TTTTATAAATAAAGAAAA

       4250 CAGATTTTAT


Statistics
Matches: 58,  Mismatches: 14, Indels: 3
        0.77            0.19        0.04

Matches are distributed among these distances:
  54    9  0.16
  55    3  0.05
  56    3  0.05
  57   43  0.74

ACGTcount: A:0.45, C:0.04, G:0.12, T:0.40


Consensus pattern (55 bp):   
TTTTATAAATAAAGAAAAATAAATATTATATTTTAAGTAAGATCATAAATTCAAG

Found at i:15249 original size:13 final size:13

Alignment explanation


    Indices: 15231--15260  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      15221 GAAACTAAAT

                         
      15231 CATAAATAAACTA
          1 CATAAATAAACTA

                         
      15244 CATAAATAAACTA
          1 CATAAATAAACTA

                
      15257 CATA
          1 CATA

      15261 TATACCTACC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23


Consensus pattern (13 bp):   
CATAAATAAACTA

Found at i:22658 original size:20 final size:19

Alignment explanation


    Indices: 22603--22658  Score: 62
    Period size: 17  Copynumber: 2.9  Consensus size: 19

      22593 CATGGTATTT

                               
      22603 TTAATAATAATT-ATTTAA
          1 TTAATAATAATTAATTTAA

                *                
      22621 -TAAAAATAATTATTATTTAA
          1 TTAATAATAATTA--ATTTAA

                              
      22641 TTAATAATTAATTAATTT
          1 TTAATAA-TAATTAATTT

      22659 CAGCCCTTGC


Statistics
Matches: 31,  Mismatches: 2, Indels: 8
        0.76            0.05        0.20

Matches are distributed among these distances:
  17   10  0.32
  20   10  0.32
  21    5  0.16
  22    6  0.19

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (19 bp):   
TTAATAATAATTAATTTAA
Done.