Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004463.1 Corchorus capsularis cultivar CVL-1 contig04471, 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, 640

Length: 1067
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32


Found at i:880 original size:27 final size:27

Alignment explanation


    Indices: 842--1064  Score: 293
    Period size: 27  Copynumber: 7.8  Consensus size: 27

        832 TCTGCAAGAA

                                       
        842 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
        869 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
        896 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                            *    *   *       
        923 CTCCGAATCATAAATGATCCGCTGACGCTCATC
          1 CTCCGAATCAT---T-CT-C-TTGAAGCTCATC

                                       
        956 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
        983 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                            *    *           
       1010 CTCCGAATCATAAATGATCCGCTGAAGCTCATC
          1 CTCCGAATCAT---T-CT-C-TTGAAGCTCATC

                                  
       1043 CTCCGAATCATTCTCTTGAAGC
          1 CTCCGAATCATTCTCTTGAAGC

       1065 CTC


Statistics
Matches: 174,  Mismatches: 10, Indels: 24
        0.84            0.05        0.12

Matches are distributed among these distances:
  27  119  0.68
  28    2  0.01
  29    2  0.01
  30    4  0.02
  31    2  0.01
  32    2  0.01
  33   43  0.25

ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30


Consensus pattern (27 bp):   
CTCCGAATCATTCTCTTGAAGCTCATC

Found at i:982 original size:87 final size:87

Alignment explanation


    Indices: 858--1064  Score: 405
    Period size: 87  Copynumber: 2.4  Consensus size: 87

        848 ATCATTCTCT

                                                                             
        858 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
        923 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

               *                                                             
        945 TGACGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
       1010 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

                                             
       1032 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGC

       1065 CTC


Statistics
Matches: 118,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  87  118  1.00

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


Consensus pattern (87 bp):   
TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
CTCCGAATCATAAATGATCCGC

Found at i:1036 original size:60 final size:54

Alignment explanation


    Indices: 842--1064  Score: 293
    Period size: 60  Copynumber: 3.9  Consensus size: 54

        832 TCTGCAAGAA

                                                                  
        842 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                                       *    *   *       
        896 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATAAATGATCCGCTGACGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT---T-CT-C-TTGAAGCTCATC

                                                                  
        956 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                            *    *                                 
       1010 CTCCGAATCATAAATGATCCGCTGAAGCTCATCCTCCGAATCATTCTCTTGAAGC
          1 CTCCGAATCAT---T-CT-C-TTGAAGCTCATCCTCCGAATCATTCTCTTGAAGC

       1065 CTC


Statistics
Matches: 149,  Mismatches: 8, Indels: 18
        0.85            0.05        0.10

Matches are distributed among these distances:
  54   59  0.40
  55    1  0.01
  56    1  0.01
  57    3  0.02
  58    2  0.01
  59    2  0.01
  60   81  0.54

ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30


Consensus pattern (54 bp):   
CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
Done.