Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002057.1 Corchorus capsularis cultivar CVL-1 contig02061, 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, 673

Length: 1123
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30


Found at i:665 original size:27 final size:27

Alignment explanation


    Indices: 627--892  Score: 379
    Period size: 27  Copynumber: 9.4  Consensus size: 27

        617 TCTGCAAGAA

                                       
        627 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                 *                     
        654 CTCCGTATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
        681 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

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

                                       
        741 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
        768 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

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

                                       
        828 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
        855 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                       
        882 CTCCGAATCAT
          1 CTCCGAATCAT

        893 AAATGATCCG


Statistics
Matches: 217,  Mismatches: 10, Indels: 24
        0.86            0.04        0.10

Matches are distributed among these distances:
  27  161  0.74
  28    2  0.01
  29    2  0.01
  30    4  0.02
  31    2  0.01
  32    2  0.01
  33   44  0.20

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


Consensus pattern (27 bp):   
CTCCGAATCATTCTCTTGAAGCTCATC

Found at i:767 original size:87 final size:87

Alignment explanation


    Indices: 643--904  Score: 515
    Period size: 87  Copynumber: 3.0  Consensus size: 87

        633 ATCATTCTCT

                            *                                                
        643 TGAAGCTCATCCTCCGTATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
        708 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

                                                                             
        730 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
        795 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

                                                                             
        817 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
        882 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

             
        904 T
          1 T

        905 TGCCCCGAAA


Statistics
Matches: 174,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  87  174  1.00

ACGTcount: A:0.25, C:0.32, G:0.13, T:0.31


Consensus pattern (87 bp):   
TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
CTCCGAATCATAAATGATCCGC

Found at i:848 original size:114 final size:112

Alignment explanation


    Indices: 627--892  Score: 387
    Period size: 114  Copynumber: 2.3  Consensus size: 112

        617 TCTGCAAGAA

                                            *                                
        627 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGTATCATTCTCTTGAAGCTCATCCTCCGAATCAT
          1 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT

             *  *                                            
        692 TCTCTTGAAGCTCATCCTCCGAATCATAAATGATCCGCTGAAGCTCATC
         66 TATCCTGAAGCTCATCCTCCGAATCAT--ATGATCCGCTGAAGCTCATC

                                                                             
        741 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT
          1 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT

                                                *    *           
        806 AAATGATCCGCTGAAGCTCATCCTCCGAATCAT-T-CT-C-TTGAAGCTCATC
         66 ---T-AT-C-CTGAAGCTCATCCTCCGAATCATATGATCCGCTGAAGCTCATC

                                                  
        855 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT
          1 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT

        893 AAATGATCCG


Statistics
Matches: 141,  Mismatches: 5, Indels: 12
        0.89            0.03        0.08

Matches are distributed among these distances:
 114  113  0.80
 115    1  0.01
 116    1  0.01
 117    2  0.01
 118    1  0.01
 119    1  0.01
 120   22  0.16

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


Consensus pattern (112 bp):   
CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT
TATCCTGAAGCTCATCCTCCGAATCATATGATCCGCTGAAGCTCATC
Done.