Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006286.1 Corchorus capsularis cultivar CVL-1 contig06305, 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: 1860
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30


Found at i:1314 original size:27 final size:27

Alignment explanation


    Indices: 1276--1542  Score: 372
    Period size: 27  Copynumber: 9.4  Consensus size: 27

       1266 TCTGCAAGAA

                                       
       1276 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
       1303 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
       1330 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                            *    *           
       1357 CTCCGAATCATAAATGATCCGCTGAAGCTCATC
          1 CTCCGAATCAT---T-CT-C-TTGAAGCTCATC

                                       
       1390 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
       1417 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                            *    *            
       1444 CTCCGAATCATAAATGATCCGCTGAACGCTCATC
          1 CTCCGAATCAT---T-CT-C-TTGAA-GCTCATC

                                       
       1478 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                    *  
       1505 CTCCGAATCATTCTCTTGAAGCTCGTC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                       
       1532 CTCCGAATCAT
          1 CTCCGAATCAT

       1543 AAATGATCCG


Statistics
Matches: 218,  Mismatches: 9, Indels: 26
        0.86            0.04        0.10

Matches are distributed among these distances:
  27  158  0.72
  28    5  0.02
  29    2  0.01
  30    4  0.02
  31    3  0.01
  32    2  0.01
  33   26  0.12
  34   18  0.08

ACGTcount: A:0.24, C:0.33, G:0.12, T:0.31


Consensus pattern (27 bp):   
CTCCGAATCATTCTCTTGAAGCTCATC

Found at i:1416 original size:87 final size:87

Alignment explanation


    Indices: 1292--1554  Score: 508
    Period size: 87  Copynumber: 3.0  Consensus size: 87

       1282 ATCATTCTCT

                                                                             
       1292 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
       1357 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

                                                                             
       1379 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
       1444 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

                                                                           * 
       1466 TGAACGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCGT
          1 TGAA-GCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCAT

                                   
       1531 CCTCCGAATCATAAATGATCCGC
         65 CCTCCGAATCATAAATGATCCGC

             
       1554 T
          1 T

       1555 TGCCCCGAAA


Statistics
Matches: 174,  Mismatches: 1, Indels: 1
        0.99            0.01        0.01

Matches are distributed among these distances:
  87   91  0.52
  88   83  0.48

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


Consensus pattern (87 bp):   
TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
CTCCGAATCATAAATGATCCGC
Done.