Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007297.1 Corchorus capsularis cultivar CVL-1 contig07318, 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: 13207
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:2229 original size:31 final size:31

Alignment explanation


    Indices: 2194--2265  Score: 126
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       2184 CATGCATCCA

                                      *    
       2194 TCATGCATCATCCCTTCTTTTGTATTTGTGC
          1 TCATGCATCATCCCTTCTTTTGTATTAGTGC

                                          *
       2225 TCATGCATCATCCCTTCTTTTGTATTAGTGT
          1 TCATGCATCATCCCTTCTTTTGTATTAGTGC

                      
       2256 TCATGCATCA
          1 TCATGCATCA

       2266 GTCATGCATT


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  31   39  1.00

ACGTcount: A:0.17, C:0.25, G:0.12, T:0.46


Consensus pattern (31 bp):   
TCATGCATCATCCCTTCTTTTGTATTAGTGC

Found at i:4502 original size:53 final size:58

Alignment explanation


    Indices: 4395--4552  Score: 166
    Period size: 62  Copynumber: 2.7  Consensus size: 58

       4385 GACCCCTGAA

                            * *                                           
       4395 TCAAATTATCATCAATCCGAGATCAAGTCA-TCAAAGACCCTTGAATCAAATC-A-AAA-TC
          1 TCAAA-TATCATCAATTCAAGATCAAGTCATTC---GACCCTTGAATCAAATCAACAAACTC

                  *                                                     
       4453 TC-AA-GTCATCAATTCAAGATCAAGTCATTCGACCCTTGAATCAAATCAAATCAAACTC
          1 TCAAATATCATCAATTCAAGATCAAGTCATTCGACCCTTGAATCAAATC-AA-CAAACTC

                                    *                 
       4511 TCAAATTATCATCAAGTTCAAGATTAAGTCATTCGACCCTTG
          1 TCAAA-TATCATCAA-TTCAAGATCAAGTCATTCGACCCTTG

       4553 TCTTGAACCC


Statistics
Matches: 85,  Mismatches: 5, Indels: 16
        0.80            0.05        0.15

Matches are distributed among these distances:
  53   17  0.20
  55   21  0.25
  56    2  0.02
  57    5  0.06
  58    6  0.07
  59    2  0.02
  61    7  0.08
  62   25  0.29

ACGTcount: A:0.39, C:0.24, G:0.09, T:0.27


Consensus pattern (58 bp):   
TCAAATATCATCAATTCAAGATCAAGTCATTCGACCCTTGAATCAAATCAACAAACTC

Found at i:4545 original size:62 final size:58

Alignment explanation


    Indices: 4438--4552  Score: 167
    Period size: 62  Copynumber: 1.9  Consensus size: 58

       4428 AAGACCCTTG

                               *                                      
       4438 AATCAAATCAAAATCTCAAGTCATCAATTCAAGATCAAGTCATTCGACCCTTGAATCA
          1 AATCAAATCAAAATCTCAAATCATCAATTCAAGATCAAGTCATTCGACCCTTGAATCA

                        *                          *                 
       4496 AATCAAATCAAACTCTCAAATTATCATCAAGTTCAAGATTAAGTCATTCGACCCTTG
          1 AATCAAATCAAAATCTC-AA--ATCATCAA-TTCAAGATCAAGTCATTCGACCCTTG

       4553 TCTTGAACCC


Statistics
Matches: 50,  Mismatches: 3, Indels: 4
        0.88            0.05        0.07

Matches are distributed among these distances:
  58   16  0.32
  59    2  0.04
  61    7  0.14
  62   25  0.50

ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28


Consensus pattern (58 bp):   
AATCAAATCAAAATCTCAAATCATCAATTCAAGATCAAGTCATTCGACCCTTGAATCA
Done.