Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018156.1 Corchorus olitorius cultivar O-4 contig18189, 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: 49775
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:4376 original size:14 final size:15

Alignment explanation


    Indices: 4341--4380  Score: 55
    Period size: 16  Copynumber: 2.7  Consensus size: 15

       4331 ATAATAATAT

                           
       4341 ATATAATATATAACA
          1 ATATAATATATAACA

                      *     
       4356 ATAATAATATTTAA-A
          1 AT-ATAATATATAACA

                      
       4371 ATATAATATA
          1 ATATAATATA

       4381 ATCTTAATTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  14    7  0.32
  15    5  0.23
  16   10  0.45

ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38


Consensus pattern (15 bp):   
ATATAATATATAACA

Found at i:16883 original size:21 final size:21

Alignment explanation


    Indices: 16857--16907  Score: 93
    Period size: 21  Copynumber: 2.4  Consensus size: 21

      16847 ATACTTACCA

                                 
      16857 CCACCAGCCTTTTTCTGCTCC
          1 CCACCAGCCTTTTTCTGCTCC

                                 
      16878 CCACCAGCCTTTTTCTGCTCC
          1 CCACCAGCCTTTTTCTGCTCC

              *      
      16899 CCTCCAGCC
          1 CCACCAGCC

      16908 ATATCATCAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   29  1.00

ACGTcount: A:0.10, C:0.51, G:0.10, T:0.29


Consensus pattern (21 bp):   
CCACCAGCCTTTTTCTGCTCC

Found at i:22257 original size:19 final size:19

Alignment explanation


    Indices: 22221--22259  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      22211 AATCCAGGAT

                               
      22221 ATCCACATCAAATGCAAGA
          1 ATCCACATCAAATGCAAGA

                          *     
      22240 ATCCA-ATCAAGATTCAAGA
          1 ATCCACATCAA-ATGCAAGA

             
      22259 A
          1 A

      22260 CCCCACATAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  18    5  0.28
  19   13  0.72

ACGTcount: A:0.49, C:0.23, G:0.10, T:0.18


Consensus pattern (19 bp):   
ATCCACATCAAATGCAAGA

Found at i:31173 original size:19 final size:19

Alignment explanation


    Indices: 31149--31185  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      31139 TCTTGCCACG

                   * *         
      31149 TTTCAAATATAAAAAATTT
          1 TTTCAAAAAAAAAAAATTT

                              
      31168 TTTCAAAAAAAAAAAATT
          1 TTTCAAAAAAAAAAAATT

      31186 ATATATAAAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35


Consensus pattern (19 bp):   
TTTCAAAAAAAAAAAATTT

Found at i:32601 original size:38 final size:40

Alignment explanation


    Indices: 32546--32629  Score: 109
    Period size: 38  Copynumber: 2.1  Consensus size: 40

      32536 AGCAGTATTC

                                                    
      32546 TTCAGATAGTCACAATCTAGTC-TCTTATGCTCTAAAG-T
          1 TTCAGATAGTCACAATCTAGTCTTCTTATGCTCTAAAGTT

                        *      *       *    *   *   
      32584 TTCAGATAGTCATAATCTATTCTTCTTGTGCTTTAATGTT
          1 TTCAGATAGTCACAATCTAGTCTTCTTATGCTCTAAAGTT

                  
      32624 TTCAGA
          1 TTCAGA

      32630 GAGCTATTAT


Statistics
Matches: 39,  Mismatches: 5, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  38   20  0.51
  39   12  0.31
  40    7  0.18

ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43


Consensus pattern (40 bp):   
TTCAGATAGTCACAATCTAGTCTTCTTATGCTCTAAAGTT

Found at i:41487 original size:31 final size:29

Alignment explanation


    Indices: 41452--41512  Score: 95
    Period size: 31  Copynumber: 2.0  Consensus size: 29

      41442 AAATAATACA

                                *          
      41452 TAGTCAAAGACTTTATTTTATATGCTATAAT
          1 TAGTCAAAGACTTTA--TTAGATGCTATAAT

                                         
      41483 TAGTCAAAGACTTTATTAGATGCTATAAT
          1 TAGTCAAAGACTTTATTAGATGCTATAAT

             
      41512 T
          1 T

      41513 TGATTTCTTT


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  29   14  0.48
  31   15  0.52

ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43


Consensus pattern (29 bp):   
TAGTCAAAGACTTTATTAGATGCTATAAT

Found at i:41771 original size:19 final size:19

Alignment explanation


    Indices: 41747--41783  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      41737 GTACAGTACC

                       *       
      41747 TAATCTAATCTGTACAGTG
          1 TAATCTAATCTATACAGTG

                  *           
      41766 TAATCTCATCTATACAGT
          1 TAATCTAATCTATACAGT

      41784 TGTTAAACAG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38


Consensus pattern (19 bp):   
TAATCTAATCTATACAGTG
Done.