Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001971.1 Corchorus olitorius cultivar O-4 contig01971, 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: 9348
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35


Found at i:5587 original size:36 final size:36

Alignment explanation


    Indices: 5547--5620  Score: 121
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       5537 GGTTATAGAC

                     *                          
       5547 AGTTTGAGGGATTCTTATTAGGGTGAAAATTGGGTG
          1 AGTTTGAGGAATTCTTATTAGGGTGAAAATTGGGTG

                         *            *         
       5583 AGTTTGAGGAATTGTTATTAGGGTGAGAATTGGGTG
          1 AGTTTGAGGAATTCTTATTAGGGTGAAAATTGGGTG

              
       5619 AG
          1 AG

       5621 GGTTGAGCCC


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  36   35  1.00

ACGTcount: A:0.26, C:0.01, G:0.38, T:0.35


Consensus pattern (36 bp):   
AGTTTGAGGAATTCTTATTAGGGTGAAAATTGGGTG

Found at i:6653 original size:24 final size:24

Alignment explanation


    Indices: 6604--6669  Score: 62
    Period size: 24  Copynumber: 2.8  Consensus size: 24

       6594 CACCACTTCC

                  *           *     
       6604 TCTTCCTCCTCCTCCTCCTCTGCT
          1 TCTTCCACCTCCTCCTCCCCTGCT

                    *                
       6628 TCTTCCACTTCCTCCTCCCCAT-CT
          1 TCTTCCACCTCCTCCTCCCC-TGCT

               *  *   *       
       6652 TCTGCCGCCTTCTCCTCC
          1 TCTTCCACCTCCTCCTCC

       6670 TCCACGTGTT


Statistics
Matches: 34,  Mismatches: 7, Indels: 2
        0.79            0.16        0.05

Matches are distributed among these distances:
  24   33  0.97
  25    1  0.03

ACGTcount: A:0.03, C:0.55, G:0.05, T:0.38


Consensus pattern (24 bp):   
TCTTCCACCTCCTCCTCCCCTGCT

Found at i:9320 original size:2 final size:2

Alignment explanation


    Indices: 9303--9343  Score: 59
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       9293 ATAAATGCTC

                                                                           
       9303 AT AT -T AT AT A- AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       9344 TATCT


Statistics
Matches: 36,  Mismatches: 0, Indels: 6
        0.86            0.00        0.14

Matches are distributed among these distances:
   1    2  0.06
   2   33  0.92
   3    1  0.03

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (2 bp):   
AT

Done.