Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012232.1 Corchorus olitorius cultivar O-4 contig12265, 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: 47037
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:10765 original size:15 final size:15

Alignment explanation


    Indices: 10747--10777  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      10737 AAATATGCCA

                *          
      10747 ATAGGAAATACTAAT
          1 ATAGAAAATACTAAT

                           
      10762 ATAGAAAATACTAAT
          1 ATAGAAAATACTAAT

             
      10777 A
          1 A

      10778 ATGATAATGA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26


Consensus pattern (15 bp):   
ATAGAAAATACTAAT

Found at i:12027 original size:23 final size:22

Alignment explanation


    Indices: 11990--12035  Score: 56
    Period size: 23  Copynumber: 2.0  Consensus size: 22

      11980 AAAGAATATA

                    * *            
      11990 AAAGAAAAGAGAAGAGAAGGAAG
          1 AAAGAAAACAAAAGA-AAGGAAG

                            *     
      12013 AAAGAAAACAAAAGAAGGGAAG
          1 AAAGAAAACAAAAGAAAGGAAG

             
      12035 A
          1 A

      12036 GAAAAGAAGG


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  22    7  0.35
  23   13  0.65

ACGTcount: A:0.67, C:0.02, G:0.30, T:0.00


Consensus pattern (22 bp):   
AAAGAAAACAAAAGAAAGGAAG

Found at i:24080 original size:15 final size:15

Alignment explanation


    Indices: 24060--24089  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      24050 ATTGTAGGAA

                           
      24060 AAAATCTGATTTGTC
          1 AAAATCTGATTTGTC

                   *       
      24075 AAAATCTTATTTGTC
          1 AAAATCTGATTTGTC

      24090 GGGACCACAG


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43


Consensus pattern (15 bp):   
AAAATCTGATTTGTC

Found at i:28554 original size:17 final size:17

Alignment explanation


    Indices: 28532--28566  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      28522 TCAGATTTGA

                        *    
      28532 AAGAGAAAGAAAGAAAG
          1 AAGAGAAAGAAAAAAAG

                  *          
      28549 AAGAGAGAGAAAAAAAG
          1 AAGAGAAAGAAAAAAAG

             
      28566 A
          1 A

      28567 GACTGACCAG


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

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00


Consensus pattern (17 bp):   
AAGAGAAAGAAAAAAAG

Found at i:34191 original size:24 final size:24

Alignment explanation


    Indices: 34164--34211  Score: 87
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      34154 TAGAATTTGA

                                    
      34164 AATTTCCTTCTAAATATCTAGACT
          1 AATTTCCTTCTAAATATCTAGACT

                  *                 
      34188 AATTTCTTTCTAAATATCTAGACT
          1 AATTTCCTTCTAAATATCTAGACT

      34212 TTGAATTAGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44


Consensus pattern (24 bp):   
AATTTCCTTCTAAATATCTAGACT

Found at i:38151 original size:22 final size:21

Alignment explanation


    Indices: 38100--38158  Score: 73
    Period size: 21  Copynumber: 2.8  Consensus size: 21

      38090 TGAATATTTT

                       *     *   
      38100 TATGAAATTTTAATAACTACC
          1 TATGAAATTTTGATAACCACC

               *                  
      38121 TATTAAATTTTGATAACCACGC
          1 TATGAAATTTTGATAACCAC-C

                *           
      38143 TATGGAATTTTGATAA
          1 TATGAAATTTTGATAA

      38159 TTTGCCTATG


Statistics
Matches: 32,  Mismatches: 5, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  21   17  0.53
  22   15  0.47

ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39


Consensus pattern (21 bp):   
TATGAAATTTTGATAACCACC
Done.