Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022369.1 Corchorus olitorius cultivar O-4 contig22402, 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: 3191
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:1346 original size:29 final size:29

Alignment explanation


    Indices: 1306--1371  Score: 89
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       1296 ATGAGAACAA

                    *                    
       1306 TTCAT-TTTCTATAGATGTTATGAAATGG
          1 TTCATCTTCCTATAGATGTTATGAAATGG

                         *         *    *
       1334 TTCATCTTCCTATGGATGTTATGGAATGT
          1 TTCATCTTCCTATAGATGTTATGAAATGG

                     
       1363 TTCATCTTC
          1 TTCATCTTC

       1372 TCACATTTAT


Statistics
Matches: 33,  Mismatches: 4, Indels: 1
        0.87            0.11        0.03

Matches are distributed among these distances:
  28    5  0.15
  29   28  0.85

ACGTcount: A:0.23, C:0.14, G:0.17, T:0.47


Consensus pattern (29 bp):   
TTCATCTTCCTATAGATGTTATGAAATGG

Found at i:2108 original size:2 final size:2

Alignment explanation


    Indices: 2101--2130  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       2091 ATTATCAATC

                                                        
       2101 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2131 TTTATAAAAC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:2350 original size:50 final size:47

Alignment explanation


    Indices: 2245--2375  Score: 147
    Period size: 50  Copynumber: 2.7  Consensus size: 47

       2235 GAGCGTGCCA

                              *   *         *  *    *      
       2245 ATCAATTTTGTCAAAAAAATGATAAAAAGTGCGATGAAAATTAAAAG
          1 ATCAATTTTGTCAAAAAATTGAGAAAAAGTGCAATAAAAAATAAAAG

                         *                                    
       2292 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAAATAAAAG
          1 ATCAATTTTGTC-AAAAAATTGAGAAAAAG-TGCAA-TAAAAAATAAAAG

            *                                  
       2342 TTCAATTTTGT-AGCAAAAATTGAGAAAAAGTGCA
          1 ATCAATTTTGTCA--AAAAATTGAGAAAAAGTGCA

       2376 GTGAAAAGTA


Statistics
Matches: 71,  Mismatches: 8, Indels: 8
        0.82            0.09        0.09

Matches are distributed among these distances:
  47   12  0.17
  48   14  0.20
  49    8  0.11
  50   37  0.52

ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27


Consensus pattern (47 bp):   
ATCAATTTTGTCAAAAAATTGAGAAAAAGTGCAATAAAAAATAAAAG
Done.