Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007746.1 Corchorus olitorius cultivar O-4 contig07772, 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: 2114
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40


Found at i:69 original size:13 final size:13

Alignment explanation


    Indices: 51--76  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

         41 TTGTTGGCTC

                         
         51 ATAGATTAGCATT
          1 ATAGATTAGCATT

                         
         64 ATAGATTAGCATT
          1 ATAGATTAGCATT

         77 TCTGTATTGT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38


Consensus pattern (13 bp):   
ATAGATTAGCATT

Found at i:225 original size:59 final size:57

Alignment explanation


    Indices: 125--252  Score: 186
    Period size: 59  Copynumber: 2.2  Consensus size: 57

        115 TCCTGTGTGT

                   *                             *                     
        125 TTGTAATCCCAA-TCTCTTTAAAAAATGAAAATGATTTTTATCTAAAAAAAAGTAGTAG
          1 TTGTAATTCCAATTCTCTTTAAAAAATGAAAATGATTCTTATCT-AAAAAAA-TAGTAG

                                  *          *                     * 
        183 TTGTAATTCCAATTCTCTTTAAGAAATGAAAATTATTCTTATCTAAAAAAATAGTGG
          1 TTGTAATTCCAATTCTCTTTAAAAAATGAAAATGATTCTTATCTAAAAAAATAGTAG

                         
        240 TTGTAATTCCAAT
          1 TTGTAATTCCAAT

        253 ATCTAAATTT


Statistics
Matches: 64,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  57   18  0.28
  58   18  0.28
  59   28  0.44

ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38


Consensus pattern (57 bp):   
TTGTAATTCCAATTCTCTTTAAAAAATGAAAATGATTCTTATCTAAAAAAATAGTAG

Found at i:1432 original size:128 final size:128

Alignment explanation


    Indices: 1281--1539  Score: 403
    Period size: 128  Copynumber: 2.0  Consensus size: 128

       1271 CATTGTTTAA

                     *                      *  *     *                       
       1281 ATTTTTATAGTTTTACTAAACTAAAAACTCTATTTTTATTTGATAAAATCTAATATCCTTATAAC
          1 ATTTTTATAATTTTACTAAACTAAAAACTCTACTTCTATTTAATAAAATCTAATATCCTTATAAC

                                    *                             *      *  
       1346 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTT-ATATATTAGAATTTTTAATAT
         66 TATTTTATTTTTACCATTTTACTAATTTAATT-AAAAAACTTAATATATTAGAAATTTTAAAAT

                             *                                       *     * 
       1409 ATTTTTATAATTTTACTCAACTAAAAACTCTACTTCTATTTAATAAAATCTAATATCTTTATACC
          1 ATTTTTATAATTTTACTAAACTAAAAACTCTACTTCTATTTAATAAAATCTAATATCCTTATAAC

                                                                            
       1474 TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAAT
         66 TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTA-ATATATTAGAAATTTTAAAAT

              
       1538 AT
          1 AT

       1540 ATTTCTTAAA


Statistics
Matches: 119,  Mismatches: 10, Indels: 3
        0.90            0.08        0.02

Matches are distributed among these distances:
 127    9  0.08
 128   89  0.75
 129   21  0.18

ACGTcount: A:0.39, C:0.10, G:0.02, T:0.48


Consensus pattern (128 bp):   
ATTTTTATAATTTTACTAAACTAAAAACTCTACTTCTATTTAATAAAATCTAATATCCTTATAAC
TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAAATTTTAAAAT
Done.