Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009218.1 Corchorus capsularis cultivar CVL-1 contig09239, 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: 27894
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:2916 original size:18 final size:18

Alignment explanation


    Indices: 2883--2917  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2873 GGGGGGTCAG

                    *         
       2883 AAAAGAAATGAAAAAAAA
          1 AAAAGAAAGGAAAAAAAA

                       *     
       2901 AAAAGAAAGGAGAAAAA
          1 AAAAGAAAGGAAAAAAA

       2918 TTAATCAGAG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

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


Consensus pattern (18 bp):   
AAAAGAAAGGAAAAAAAA

Found at i:5490 original size:2 final size:2

Alignment explanation


    Indices: 5483--5536  Score: 65
    Period size: 2  Copynumber: 26.0  Consensus size: 2

       5473 AATAAACTTC

                                                                        *   
       5483 TA TA TA TA TA TA TA TA T- TGA TGA TA TA TA TA TA TA TA TA TC TA
          1 TA TA TA TA TA TA TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA

                           
       5526 TA CTA TA TA TA
          1 TA -TA TA TA TA

       5537 AAAGTACGAG


Statistics
Matches: 47,  Mismatches: 2, Indels: 6
        0.85            0.04        0.11

Matches are distributed among these distances:
   1    1  0.02
   2   40  0.85
   3    6  0.13

ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:5532 original size:23 final size:24

Alignment explanation


    Indices: 5482--5536  Score: 80
    Period size: 23  Copynumber: 2.4  Consensus size: 24

       5472 TAATAAACTT

                                    
       5482 CTATATATATATATATATTGATGA
          1 CTATATATATATATATATTGATGA

                                     
       5506 -TATATATATATATATATCT-AT-A
          1 CTATATATATATATATAT-TGATGA

                     
       5528 CTATATATA
          1 CTATATATA

       5537 AAAGTACGAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
  22    1  0.03
  23   27  0.93
  24    1  0.03

ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47


Consensus pattern (24 bp):   
CTATATATATATATATATTGATGA

Found at i:5875 original size:110 final size:113

Alignment explanation


    Indices: 5740--5963  Score: 350
    Period size: 110  Copynumber: 2.0  Consensus size: 113

       5730 TTTTAACCAA

                                                                             
       5740 AAAAAATTTTAGATATACTAAAATTTTTTCTAATATACAATTTTATTCTACT-AAAAACTCTATT
          1 AAAAAATTTTAGATATACTAAAATTTTTTCTAATATACAATTTTATTCTACTAAAAAACTCTATT

                                                             
       5804 TTCATTTAATTAAA-TCTAATATCTT-TATAA-TTACTTTATTTTTACC
         66 TTCATTTAATTAAATTC-AATATCTTATATAATTTACTTTATTTTTACC

                      *      *                                               
       5850 AAAAAA-TTTGGATATATTAAAAATTTTTTCTAATATACAATTTTATTCTACTAAAAAACTCTAT
          1 AAAAAATTTTAGATATACT-AAAATTTTTTCTAATATACAATTTTATTCTACTAAAAAACTCTAT

                                   *           **            
       5914 TTTCATTTAATTAAATTCAATATTTTATATAATTTTTTTTATTTTTACC
         65 TTTCATTTAATTAAATTCAATATCTTATATAATTTACTTTATTTTTACC

             
       5963 A
          1 A

       5964 TTTTAATTTA


Statistics
Matches: 104,  Mismatches: 5, Indels: 7
        0.90            0.04        0.06

Matches are distributed among these distances:
 109   10  0.10
 110   39  0.38
 111   33  0.32
 112    7  0.07
 113   15  0.14

ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49


Consensus pattern (113 bp):   
AAAAAATTTTAGATATACTAAAATTTTTTCTAATATACAATTTTATTCTACTAAAAAACTCTATT
TTCATTTAATTAAATTCAATATCTTATATAATTTACTTTATTTTTACC
Done.