Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009196.1 Corchorus capsularis cultivar CVL-1 contig09217, 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: 62031
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:1273 original size:53 final size:53

Alignment explanation


    Indices: 1208--1313  Score: 212
    Period size: 53  Copynumber: 2.0  Consensus size: 53

       1198 CTGTAACCAT

                                                                 
       1208 TTTTTATTCCATGTTTTGAACAATTCATGAATAAAGAATATAAACAACATAAA
          1 TTTTTATTCCATGTTTTGAACAATTCATGAATAAAGAATATAAACAACATAAA

                                                                 
       1261 TTTTTATTCCATGTTTTGAACAATTCATGAATAAAGAATATAAACAACATAAA
          1 TTTTTATTCCATGTTTTGAACAATTCATGAATAAAGAATATAAACAACATAAA

       1314 ATAATACACT


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  53   53  1.00

ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36


Consensus pattern (53 bp):   
TTTTTATTCCATGTTTTGAACAATTCATGAATAAAGAATATAAACAACATAAA

Found at i:5579 original size:17 final size:16

Alignment explanation


    Indices: 5541--5589  Score: 53
    Period size: 17  Copynumber: 2.9  Consensus size: 16

       5531 TGTAATCTTT

                  *        *
       5541 GATCACCGGTGATCTT
          1 GATCACTGGTGATCTA

                              
       5557 GCATCACTGGTGATCGTA
          1 G-ATCACTGGTGATC-TA

                   *       
       5575 GATCACTAGTGATCT
          1 GATCACTGGTGATCT

       5590 GAGGGGTGAT


Statistics
Matches: 28,  Mismatches: 3, Indels: 4
        0.80            0.09        0.11

Matches are distributed among these distances:
  16    2  0.07
  17   24  0.86
  18    2  0.07

ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31


Consensus pattern (16 bp):   
GATCACTGGTGATCTA

Found at i:5758 original size:2 final size:2

Alignment explanation


    Indices: 5753--5778  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       5743 CACACACACG

                                                  
       5753 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

       5779 AAAGATAAAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:6928 original size:2 final size:2

Alignment explanation


    Indices: 6921--6959  Score: 53
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       6911 CTATTGTAAC

                                                   *                   
       6921 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TCA -A TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA T

       6960 TGCTGGCTGC


Statistics
Matches: 33,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.94
   3    1  0.03

ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:29684 original size:12 final size:12

Alignment explanation


    Indices: 29667--29691  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      29657 CTAATCCACT

                        
      29667 TAAGTATAATGA
          1 TAAGTATAATGA

                        
      29679 TAAGTATAATGA
          1 TAAGTATAATGA

             
      29691 T
          1 T

      29692 GAATTTGTCT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36


Consensus pattern (12 bp):   
TAAGTATAATGA

Found at i:51104 original size:13 final size:12

Alignment explanation


    Indices: 51078--51103  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      51068 ACATTCAATC

                        
      51078 TTGAAATTTTTT
          1 TTGAAATTTTTT

                        
      51090 TTGAAATTTTTT
          1 TTGAAATTTTTT

              
      51102 TT
          1 TT

      51104 TTCAAGATGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69


Consensus pattern (12 bp):   
TTGAAATTTTTT

Found at i:55187 original size:13 final size:13

Alignment explanation


    Indices: 55169--55198  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      55159 AGAGTGATGC

                         
      55169 TTTAAGTTCATGG
          1 TTTAAGTTCATGG

                         
      55182 TTTAAGTTCATGG
          1 TTTAAGTTCATGG

                
      55195 TTTA
          1 TTTA

      55199 GTAAGTGTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.23, C:0.07, G:0.20, T:0.50


Consensus pattern (13 bp):   
TTTAAGTTCATGG

Found at i:57493 original size:23 final size:23

Alignment explanation


    Indices: 57462--57508  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      57452 TAGATGGGTG

                       *           
      57462 TTGCAAAATACTGTCCCATTTTT
          1 TTGCAAAATACCGTCCCATTTTT

                *    *     *       
      57485 TTGCTAAATGCCGTCTCATTTTT
          1 TTGCAAAATACCGTCCCATTTTT

             
      57508 T
          1 T

      57509 ACACTTTTGA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47


Consensus pattern (23 bp):   
TTGCAAAATACCGTCCCATTTTT
Done.