Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000563.1 Corchorus capsularis cultivar CVL-1 contig00563, 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, 623

Length: 1039
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.30


Found at i:467 original size:9 final size:8

Alignment explanation


    Indices: 451--502  Score: 50
    Period size: 9  Copynumber: 6.1  Consensus size: 8

        441 TTTTAAAAAA

                    
        451 AAAATAAT
          1 AAAATAAT

                     
        459 AATAATAAT
          1 AA-AATAAT

                     
        468 AAAATAAAT
          1 AAAAT-AAT

                *   
        477 AAAAAAAT
          1 AAAATAAT

               *     
        485 ATATATAAT
          1 A-AAATAAT

                *   
        494 AAAAAAAT
          1 AAAATAAT

             
        502 A
          1 A

        503 TATAAATTGC


Statistics
Matches: 36,  Mismatches: 5, Indels: 6
        0.77            0.11        0.13

Matches are distributed among these distances:
   8   15  0.42
   9   21  0.58

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (8 bp):   
AAAATAAT

Found at i:492 original size:29 final size:29

Alignment explanation


    Indices: 444--508  Score: 89
    Period size: 29  Copynumber: 2.3  Consensus size: 29

        434 CTTTTTTTTT

                                    *    
        444 TAAA-AAAAAAATAATAATAATAATAAAA
          1 TAAATAAAAAAATAATAATAATAAAAAAA

                                          
        472 TAAATAAAAAAAT-ATATATAATAAAAAAA
          1 TAAATAAAAAAATAATA-ATAATAAAAAAA

              *     
        501 TATATAAA
          1 TAAATAAA

        509 TTGCTGAAAA


Statistics
Matches: 33,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  28    7  0.21
  29   26  0.79

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (29 bp):   
TAAATAAAAAAATAATAATAATAAAAAAA

Found at i:503 original size:17 final size:17

Alignment explanation


    Indices: 446--506  Score: 67
    Period size: 17  Copynumber: 3.8  Consensus size: 17

        436 TTTTTTTTTA

                   *         
        446 AAAAAAAAATA-ATAAT
          1 AAAAAAATATATATAAT

                 *            
        462 AATAATAA-A-ATA-AAT
          1 AA-AAAAATATATATAAT

                             
        477 AAAAAAATATATATAAT
          1 AAAAAAATATATATAAT

                         
        494 AAAAAAATATATA
          1 AAAAAAATATATA

        507 AATTGCTGAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 9
        0.78            0.04        0.18

Matches are distributed among these distances:
  14    4  0.11
  15    7  0.18
  16    7  0.18
  17   20  0.53

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (17 bp):   
AAAAAAATATATATAAT
Done.