Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012063.1 Corchorus olitorius cultivar O-4 contig12096, 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: 8803
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:3049 original size:108 final size:104

Alignment explanation


    Indices: 2927--3197  Score: 388
    Period size: 107  Copynumber: 2.6  Consensus size: 104

       2917 GGTTTTTTTA

                  *                                                          
       2927 TTATAGTGTTTTAGAAATAAAATATAAAAACTAATTTCACTAAGTTTAGCCCAGAATTAAAATTT
          1 TTATAGGGTTTTAGAAATAAAATAT-AAAACTAATTTCACTAAGTTTAGCCCA-AATTAAAATTT

                           *       *                   
       2992 TATTTTTAATTTAAGTGTAAATTTCAAAATTAATAATTTATTG
         64 TATTTTTAATTTAAGGGTAAATTCCAAAATTAATAA--TATTG

                                    *                                        
       3035 TTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT
          1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAG-CCCAAATTAAAATTTT

                   *                 *             *
       3100 ATTTTTATTTTAAGGGTAAATTCCATAATTAATAATATTT
         65 ATTTTTAATTTAAGGGTAAATTCCAAAATTAATAATATTG

                                                      *    *              
       3140 TTATAGGGTTTTAGAAA-AAAATAT--AACTAA-TTCACTAAATTTAACCCAAATTAAAATT
          1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATT

       3198 AAAATTTTAT


Statistics
Matches: 152,  Mismatches: 10, Indels: 10
        0.88            0.06        0.06

Matches are distributed among these distances:
 100   14  0.09
 101   12  0.08
 102    6  0.04
 104    6  0.04
 105   21  0.14
 107   66  0.43
 108   27  0.18

ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40


Consensus pattern (104 bp):   
TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATTTTA
TTTTTAATTTAAGGGTAAATTCCAAAATTAATAATATTG

Found at i:7454 original size:15 final size:16

Alignment explanation


    Indices: 7436--7473  Score: 69
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       7426 AGGTTGACAA

                            
       7436 AAAACAATTAAAC-AG
          1 AAAACAATTAAACTAG

                            
       7451 AAAACAATTAAACTAG
          1 AAAACAATTAAACTAG

                   
       7467 AAAACAA
          1 AAAACAA

       7474 AGCAAAATAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.68, C:0.13, G:0.05, T:0.13


Consensus pattern (16 bp):   
AAAACAATTAAACTAG

Done.