Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015221.1 Corchorus olitorius cultivar O-4 contig15254, 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: 17173
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:5332 original size:19 final size:19

Alignment explanation


    Indices: 5282--5332  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       5272 CATAAAATTT

                               
       5282 TTAATAA-TAATTATTCAA
          1 TTAATAATTAATTATTCAA

              *              *  
       5300 TAAAATAATT-ATTATTTAA
          1 T-TAATAATTAATTATTCAA

                          
       5319 TTAATAATTAATTA
          1 TTAATAATTAATTA

       5333 ATTTCAGCCC


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    8  0.30
  19   18  0.67
  20    1  0.04

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTAATAATTAATTATTCAA

Found at i:5702 original size:13 final size:13

Alignment explanation


    Indices: 5684--5708  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5674 AAGGTAACAA

                         
       5684 CAAAAATCATCAT
          1 CAAAAATCATCAT

                        
       5697 CAAAAATCATCA
          1 CAAAAATCATCA

       5709 CTCATGCCGA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20


Consensus pattern (13 bp):   
CAAAAATCATCAT

Found at i:7271 original size:22 final size:22

Alignment explanation


    Indices: 7222--7272  Score: 68
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       7212 AAATATTACC

                             **   
       7222 ATAATTATTTTTGCCAGCCATA
          1 ATAATTATTTTTGCCAGAAATA

                                   
       7244 ATAATTATTTTTGCCAAGAAATA
          1 ATAATTATTTTTGCC-AGAAATA

                   
       7267 A-AATTA
          1 ATAATTA

       7273 GGGAATAATT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  22   20  0.77
  23    6  0.23

ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39


Consensus pattern (22 bp):   
ATAATTATTTTTGCCAGAAATA

Found at i:8668 original size:6 final size:6

Alignment explanation


    Indices: 8657--8713  Score: 55
    Period size: 6  Copynumber: 9.5  Consensus size: 6

       8647 CCAAGCCAGG

                                                    *    * *         
       8657 AAAAGA AAAAG- AAAA-A AAAAGAA AAAAGGA AAAGGA AGAGGA AAAAGA
          1 AAAAGA AAAAGA AAAAGA AAAAG-A AAAA-GA AAAAGA AAAAGA AAAAGA

                      
       8705 AAAAGA AAA
          1 AAAAGA AAA

       8714 TAAAATAAAA


Statistics
Matches: 43,  Mismatches: 4, Indels: 8
        0.78            0.07        0.15

Matches are distributed among these distances:
   5    8  0.19
   6   25  0.58
   7    9  0.21
   8    1  0.02

ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00


Consensus pattern (6 bp):   
AAAAGA
Done.