Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017269.1 Corchorus olitorius cultivar O-4 contig17302, 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, 868

Length: 1448
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.29


Found at i:433 original size:7 final size:7

Alignment explanation


    Indices: 421--461  Score: 50
    Period size: 7  Copynumber: 6.0  Consensus size: 7

        411 CCAGACTTAA

                   
        421 AAAAAAT
          1 AAAAAAT

                   
        428 AAAAAA-
          1 AAAAAAT

                *   
        434 ATAATAA-
          1 A-AAAAAT

                   
        441 AAAAAAT
          1 AAAAAAT

                   
        448 AAAAAAT
          1 AAAAAAT

                   
        455 AAAAAAT
          1 AAAAAAT

        462 TATCCTCTGC


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
   6    5  0.17
   7   25  0.83

ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15


Consensus pattern (7 bp):   
AAAAAAT

Found at i:443 original size:12 final size:12

Alignment explanation


    Indices: 419--458  Score: 50
    Period size: 12  Copynumber: 3.5  Consensus size: 12

        409 TTCCAGACTT

                        
        419 AAAAAA-AAT-A
          1 AAAAAATAATAA

                        
        429 AAAAAATAATAA
          1 AAAAAATAATAA

                        
        441 AAAAAATAA-AA
          1 AAAAAATAATAA

                   
        452 AATAAAA
          1 AA-AAAA

        459 AATTATCCTC


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  10    6  0.22
  11    7  0.26
  12   14  0.52

ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12


Consensus pattern (12 bp):   
AAAAAATAATAA

Found at i:460 original size:9 final size:9

Alignment explanation


    Indices: 418--453  Score: 54
    Period size: 10  Copynumber: 3.8  Consensus size: 9

        408 TTTCCAGACT

                     
        418 TAAAAAAAA
          1 TAAAAAAAA

                       
        427 TAAAAAAATAA
          1 T-AAAAAA-AA

                     
        438 TAAAAAAAA
          1 TAAAAAAAA

                   
        447 TAAAAAA
          1 TAAAAAA

        454 TAAAAAATTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
   9   10  0.40
  10   12  0.48
  11    3  0.12

ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14


Consensus pattern (9 bp):   
TAAAAAAAA

Found at i:606 original size:22 final size:22

Alignment explanation


    Indices: 565--629  Score: 80
    Period size: 22  Copynumber: 3.0  Consensus size: 22

        555 CTGAAGTTGA

                                    
        565 AGAAAATAATGCACTCTGCAAAGT
          1 AGAAAATAATG--CTCTGCAAAGT

            *                     
        589 GGAAAATAATGCTCTGCAAAGT
          1 AGAAAATAATGCTCTGCAAAGT

                  *              
        611 AG-AAAGAAT-CTCTGCAAAG
          1 AGAAAATAATGCTCTGCAAAG

        630 ATGTTTCCAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  20   10  0.26
  21    6  0.16
  22   12  0.32
  24   10  0.26

ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20


Consensus pattern (22 bp):   
AGAAAATAATGCTCTGCAAAGT

Done.