Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004723.1 Corchorus capsularis cultivar CVL-1 contig04739, 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, 650

Length: 1084
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:210 original size:27 final size:27

Alignment explanation


    Indices: 172--612  Score: 576
    Period size: 27  Copynumber: 15.4  Consensus size: 27

        162 TCTGCAAGAA

                                       
        172 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
        199 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
        226 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                            *    *           
        253 CTCCGAATCATAAATGATCCGCTGAAGCTCATC
          1 CTCCGAATCAT---T-CT-C-TTGAAGCTCATC

                                       
        286 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
        313 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                             *    *           
        340 CTCCGAATCATAAAGTGATCCGCTGAAGCTCATC
          1 CTCCGAATCAT----T-CT-C-TTGAAGCTCATC

                                       
        374 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
        401 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                            *    *           
        428 CTCCGAATCATAAATGATCCGCTGAAGCTCATC
          1 CTCCGAATCAT---T-CT-C-TTGAAGCTCATC

                                       
        461 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
        488 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                            *    *           
        515 CTCCGAATCATAAATGATCCGCTGAAGCTCATC
          1 CTCCGAATCAT---T-CT-C-TTGAAGCTCATC

                                       
        548 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                            *          
        575 CTCCGAATCATTCTCTCGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                       
        602 CTCCGAATCAT
          1 CTCCGAATCAT

        613 AAATGATCCG


Statistics
Matches: 372,  Mismatches: 17, Indels: 50
        0.85            0.04        0.11

Matches are distributed among these distances:
  27  260  0.70
  28    4  0.01
  29    4  0.01
  30    7  0.02
  31    4  0.01
  32    4  0.01
  33   67  0.18
  34   22  0.06

ACGTcount: A:0.25, C:0.33, G:0.12, T:0.30


Consensus pattern (27 bp):   
CTCCGAATCATTCTCTTGAAGCTCATC

Found at i:312 original size:87 final size:87

Alignment explanation


    Indices: 188--624  Score: 856
    Period size: 87  Copynumber: 5.0  Consensus size: 87

        178 ATCATTCTCT

                                                                             
        188 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
        253 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

                                                                             
        275 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                   
        340 CTCCGAATCATAAAGTGATCCGC
         66 CTCCGAATCATAAA-TGATCCGC

                                                                             
        363 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
        428 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

                                                                             
        450 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
        515 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

                                                                  *          
        537 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTCGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
        602 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

             
        624 T
          1 T

        625 TGCCCCGAAA


Statistics
Matches: 348,  Mismatches: 1, Indels: 2
        0.99            0.00        0.01

Matches are distributed among these distances:
  87  261  0.75
  88   87  0.25

ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30


Consensus pattern (87 bp):   
TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
CTCCGAATCATAAATGATCCGC
Done.