Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022159.1 Corchorus olitorius cultivar O-4 contig22192, 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: 5448
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Found at i:1423 original size:163 final size:161

Alignment explanation


    Indices: 1090--1427  Score: 403
    Period size: 163  Copynumber: 2.1  Consensus size: 161

       1080 TATTTGCAGA

                     *         *                                             
       1090 AAAACGCCGTTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGGAGAGGGAATTT
          1 AAAACGCCGCTATATATTACAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGGAGAGGGAATTT

                       *                             **    *              *  
       1155 TTCCCTCCAAACAAAGAAAAAAAAATCTCTCCCTCCATATATTAAAATAGCGGCGTTTACTGTTC
         66 TTCCCTCCAAAAAAAGAAAAAAAAATCTCTCCCTCCATATACCAAAACAGCGGCGTTTACTGATC

            * *                            
       1220 TAGACGCCACAAATTAACGGCGTCTTGTTCT
        131 AAAACGCCACAAATTAACGGCGTCTTGTTCT

                                   **           **                 *         
       1251 AAAACGCCGCTATATATTACAGGTTTAGAGTTGGAAGCTTTCTTTGTTTTAGTGGGGAGGGAATT
          1 AAAACGCCGCTATATATTACAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAG-GGAGAGGGAATT

                               *                    *      *  *          *   
       1316 TTTCCCTCCAAAAAAAGGAGAAAAAAATCTCTCCCTCCATGTACCAATACGGCGGCGTCTTTCT-
         65 TTTCCCTCCAAAAAAA-GAAAAAAAAATCTCTCCCTCCATATACCAAAACAGCGGCGT-TTACTG

                       *        *               
       1380 ATCAAAACGCCGCTAAATT-GCGGCGTCTCTGTT-T
        128 ATCAAAACGCCAC-AAATTAACGGCGTCT-TGTTCT

            * *           
       1414 CAGACGCCGCTATA
          1 AAAACGCCGCTATA

       1428 GCAAATTTCA


Statistics
Matches: 149,  Mismatches: 23, Indels: 8
        0.83            0.13        0.04

Matches are distributed among these distances:
 161   46  0.31
 162   26  0.17
 163   64  0.43
 164   13  0.09

ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30


Consensus pattern (161 bp):   
AAAACGCCGCTATATATTACAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGGAGAGGGAATTT
TTCCCTCCAAAAAAAGAAAAAAAAATCTCTCCCTCCATATACCAAAACAGCGGCGTTTACTGATC
AAAACGCCACAAATTAACGGCGTCTTGTTCT

Found at i:3628 original size:26 final size:26

Alignment explanation


    Indices: 3565--3628  Score: 103
    Period size: 25  Copynumber: 2.5  Consensus size: 26

       3555 ACAATTCAAA

                                   *  
       3565 AGGCTTAAAATTCATTGCCATATTAT
          1 AGGCTTAAAATTCATTGCCATATAAT

             *                        
       3591 -TGCTTAAAATTCATTGCCATATAAT
          1 AGGCTTAAAATTCATTGCCATATAAT

                         
       3616 AGGCTTAAAATTC
          1 AGGCTTAAAATTC

       3629 TGCAAATATC


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  25   23  0.68
  26   11  0.32

ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38


Consensus pattern (26 bp):   
AGGCTTAAAATTCATTGCCATATAAT
Done.