Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013618.1 Corchorus olitorius cultivar O-4 contig13651, 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: 29732
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:2592 original size:70 final size:70

Alignment explanation


    Indices: 2479--2619  Score: 273
    Period size: 70  Copynumber: 2.0  Consensus size: 70

       2469 TCTGCTTGAG

                                                                             
       2479 CCTGTTTTTCATGCAACAATTCCTTCTGTAGATCAACTGGGATTTAATCATATGATGATGTTAAG
          1 CCTGTTTTTCATGCAACAATTCCTTCTGTAGATCAACTGGGATTTAATCATATGATGATGTTAAG

                 
       2544 ATTCT
         66 ATTCT

                                          *                                  
       2549 CCTGTTTTTCATGCAACAATTCCTTCTGTATATCAACTGGGATTTAATCATATGATGATGTTAAG
          1 CCTGTTTTTCATGCAACAATTCCTTCTGTAGATCAACTGGGATTTAATCATATGATGATGTTAAG

                 
       2614 ATTCT
         66 ATTCT

             
       2619 C
          1 C

       2620 ATTCATTACC


Statistics
Matches: 70,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  70   70  1.00

ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40


Consensus pattern (70 bp):   
CCTGTTTTTCATGCAACAATTCCTTCTGTAGATCAACTGGGATTTAATCATATGATGATGTTAAG
ATTCT

Found at i:4500 original size:15 final size:16

Alignment explanation


    Indices: 4480--4509  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       4470 TCAGCAGCTC

                            
       4480 AAAAG-CTTAAAGAAG
          1 AAAAGCCTTAAAGAAG

                           
       4495 AAAAGCCTTAAAGAA
          1 AAAAGCCTTAAAGAA

       4510 AATAGTCAAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    5  0.36
  16    9  0.64

ACGTcount: A:0.60, C:0.10, G:0.17, T:0.13


Consensus pattern (16 bp):   
AAAAGCCTTAAAGAAG

Found at i:18206 original size:22 final size:22

Alignment explanation


    Indices: 18181--18236  Score: 69
    Period size: 22  Copynumber: 2.5  Consensus size: 22

      18171 TAGTTTTATG

                    *    *         
      18181 AAATTTTGGTAACTA-CAGTATC
          1 AAATTTTGATAACCACCA-TATC

                                 *
      18203 AAATTTTGATAACCACCATATG
          1 AAATTTTGATAACCACCATATC

                        
      18225 AAATTTTGATAA
          1 AAATTTTGATAA

      18237 TTACCTATAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  22   28  0.93
  23    2  0.07

ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36


Consensus pattern (22 bp):   
AAATTTTGATAACCACCATATC

Found at i:18265 original size:43 final size:44

Alignment explanation


    Indices: 18177--18294  Score: 114
    Period size: 43  Copynumber: 2.7  Consensus size: 44

      18167 TGAATAGTTT

                        *        *   *     *      *     
      18177 TATGAAATTTTGGTAACTACAGTATCAAATTTTGATAACCACCA
          1 TATGAAATTTTGATAACTACACTATAAAATTGTGATAAACACCA

                            *                       *   
      18221 TATGAAATTTTGATAATTAC-CTATAAAATTGTGATAAACTCCA
          1 TATGAAATTTTGATAACTACACTATAAAATTGTGATAAACACCA

              *  * *                  *     
      18264 TAAGAGACTTTGATAACCTA-ACTATGAAATT
          1 TATGAAATTTTGATAA-CTACACTATAAAATT

      18295 TTTTAATAAA


Statistics
Matches: 60,  Mismatches: 12, Indels: 4
        0.79            0.16        0.05

Matches are distributed among these distances:
  43   31  0.52
  44   29  0.48

ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35


Consensus pattern (44 bp):   
TATGAAATTTTGATAACTACACTATAAAATTGTGATAAACACCA

Found at i:28204 original size:19 final size:21

Alignment explanation


    Indices: 28166--28204  Score: 55
    Period size: 19  Copynumber: 2.0  Consensus size: 21

      28156 TTTAGTAACC

                                 
      28166 TAACATCTTTAATAAATTTAG
          1 TAACATCTTTAATAAATTTAG

                         *      
      28187 TAACAT-TTT-ATCAATTTA
          1 TAACATCTTTAATAAATTTA

      28205 ATGAGGAGTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    8  0.47
  20    3  0.18
  21    6  0.35

ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46


Consensus pattern (21 bp):   
TAACATCTTTAATAAATTTAG
Done.