Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015729.1 Corchorus olitorius cultivar O-4 contig15762, 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: 27354
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32


Found at i:17434 original size:6 final size:6

Alignment explanation


    Indices: 17419--17453  Score: 52
    Period size: 6  Copynumber: 5.7  Consensus size: 6

      17409 AAGAGAACCC

                               *                    
      17419 AAAAAGG AAAAAG AAAATG AAAAAG AAAAAG AAAA
          1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAA

      17454 GCAACCCTTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   6   21  0.81
   7    5  0.19

ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03


Consensus pattern (6 bp):   
AAAAAG

Found at i:23284 original size:5 final size:5

Alignment explanation


    Indices: 23270--23299  Score: 51
    Period size: 5  Copynumber: 6.0  Consensus size: 5

      23260 TCAAGTAATT

                        *                      
      23270 AAAGG AAAGG GAAGG AAAGG AAAGG AAAGG
          1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG

      23300 GGAGGGAAGT


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   5   23  1.00

ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00


Consensus pattern (5 bp):   
AAAGG

Found at i:23556 original size:29 final size:29

Alignment explanation


    Indices: 23513--23578  Score: 125
    Period size: 28  Copynumber: 2.3  Consensus size: 29

      23503 GCTTGGTAAT

                                         
      23513 AAAAAAAAATGAAAAAATTAGAAATTTTC
          1 AAAAAAAAATGAAAAAATTAGAAATTTTC

                                         
      23542 AAAAAAAAA-GAAAAAATTAGAAATTTTC
          1 AAAAAAAAATGAAAAAATTAGAAATTTTC

                     
      23570 AAAAAAAAA
          1 AAAAAAAAA

      23579 ATAAAATCTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  28   28  0.76
  29    9  0.24

ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20


Consensus pattern (29 bp):   
AAAAAAAAATGAAAAAATTAGAAATTTTC

Found at i:23585 original size:20 final size:23

Alignment explanation


    Indices: 23547--23598  Score: 65
    Period size: 20  Copynumber: 2.4  Consensus size: 23

      23537 TTTTCAAAAA

                               *   
      23547 AAAAGAAAAAATTAGAAATTTTC
          1 AAAAGAAAAAATTAGAAATCTTC

                                   
      23570 AAAA-AAAAAA-TA-AAATCTTC
          1 AAAAGAAAAAATTAGAAATCTTC

             *       
      23590 ACAAGAAAA
          1 AAAAGAAAA

      23599 GAGATGAGAG


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  20   10  0.38
  21    6  0.23
  22    6  0.23
  23    4  0.15

ACGTcount: A:0.67, C:0.08, G:0.06, T:0.19


Consensus pattern (23 bp):   
AAAAGAAAAAATTAGAAATCTTC

Found at i:23598 original size:22 final size:22

Alignment explanation


    Indices: 23548--23598  Score: 61
    Period size: 21  Copynumber: 2.4  Consensus size: 22

      23538 TTTCAAAAAA

                      *       *   
      23548 AAAGAAAAAATTAGAAATTTTC
          1 AAAGAAAAAAATAGAAATCTTC

                                  
      23570 AAA-AAAAAAATA-AAATCTTC
          1 AAAGAAAAAAATAGAAATCTTC

                     
      23590 ACAAGAAAA
          1 A-AAGAAAA

      23599 GAGATGAGAG


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  20    8  0.32
  21   10  0.40
  22    7  0.28

ACGTcount: A:0.67, C:0.08, G:0.06, T:0.20


Consensus pattern (22 bp):   
AAAGAAAAAAATAGAAATCTTC
Done.