Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001229.1 Corchorus capsularis cultivar CVL-1 contig01229, 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: 10296
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34


Found at i:5369 original size:121 final size:120

Alignment explanation


    Indices: 5133--5359  Score: 284
    Period size: 119  Copynumber: 1.9  Consensus size: 120

       5123 AGTCTTCAAT

                                           **  *       *                     
       5133 AATCATAAAGAGTTCGGAACTTGTTCTCGAGTTTTTGAGTTTTGTGAATAGAGAAAATCATATTG
          1 AATCATAAAGAGTTCGGAACTTGTTCTCGAGAATTCGAGTTTTATGAATAGAGAAAATCATATTG

              *    *    *            *          *        *          
       5198 CTGGAGGTCGTTGATCGGACTGAACTAGGTTAACTTGTAAATATATAGAAAAAAAA
         66 CTAGAGGACG-TAATCGGACTGAACAAGGTTAACTTATAAATATAAAGAAAAAAAA

                                                                *            
       5254 AATCATAAAGAGTTCGGAACTTGTTCTC-A-AATTCGAGTTTTATGAAT-GTTGAAAATCATATT
          1 AATCATAAAGAGTTCGGAACTTGTTCTCGAGAATTCGAGTTTTATGAATAG-AGAAAATCATATT

                               *                          
       5316 GCTAGA-GAC-TAATCGGATTCGAACAAGGTTAACTTATAAATATA
         65 GCTAGAGGACGTAATCGGACT-GAACAAGGTTAACTTATAAATATA

       5360 CCAAAAGAAA


Statistics
Matches: 93,  Mismatches: 11, Indels: 8
        0.83            0.10        0.07

Matches are distributed among these distances:
 116    8  0.09
 117   22  0.24
 118    3  0.03
 119   31  0.33
 120    1  0.01
 121   28  0.30

ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33


Consensus pattern (120 bp):   
AATCATAAAGAGTTCGGAACTTGTTCTCGAGAATTCGAGTTTTATGAATAGAGAAAATCATATTG
CTAGAGGACGTAATCGGACTGAACAAGGTTAACTTATAAATATAAAGAAAAAAAA

Found at i:7244 original size:17 final size:19

Alignment explanation


    Indices: 7222--7268  Score: 55
    Period size: 17  Copynumber: 2.6  Consensus size: 19

       7212 AAAAACATGA

                               
       7222 TAAAAGTTTCAC-AA-CTG
          1 TAAAAGTTTCACGAATCTG

                   *           
       7239 TAAAAGTAT-ACGAATCTG
          1 TAAAAGTTTCACGAATCTG

                        
       7257 TAAAAAGTTTCA
          1 T-AAAAGTTTCA

       7269 ATTGCCTTCT


Statistics
Matches: 24,  Mismatches: 2, Indels: 5
        0.77            0.06        0.16

Matches are distributed among these distances:
  16    2  0.08
  17   10  0.42
  18    4  0.17
  19    7  0.29
  20    1  0.04

ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30


Consensus pattern (19 bp):   
TAAAAGTTTCACGAATCTG
Done.