Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006506.1 Corchorus olitorius cultivar O-4 contig06531, 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: 1856
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37


Found at i:178 original size:35 final size:35

Alignment explanation


    Indices: 132--235  Score: 140
    Period size: 35  Copynumber: 3.0  Consensus size: 35

        122 TTTCGTAGGC

                                               
        132 TTTGTTGTTGCTTTGTTGATGGAGAAGAACTTTGT
          1 TTTGTTGTTGCTTTGTTGATGGAGAAGAACTTTGT

                                               
        167 TTTGTTGTTGCTTTGTTGATGGAGAA-AACTTTGT
          1 TTTGTTGTTGCTTTGTTGATGGAGAAGAACTTTGT

              ** *    *                         
        201 TGCAGAT-TTACTTTGCTTGATGGAGAAGAACTTTG
          1 T-TTGTTGTTGCTTTG-TTGATGGAGAAGAACTTTG

        236 CCTTGCCTTG


Statistics
Matches: 62,  Mismatches: 4, Indels: 5
        0.87            0.06        0.07

Matches are distributed among these distances:
  34   16  0.26
  35   39  0.63
  36    7  0.11

ACGTcount: A:0.20, C:0.08, G:0.27, T:0.45


Consensus pattern (35 bp):   
TTTGTTGTTGCTTTGTTGATGGAGAAGAACTTTGT

Found at i:945 original size:44 final size:44

Alignment explanation


    Indices: 882--968  Score: 174
    Period size: 44  Copynumber: 2.0  Consensus size: 44

        872 CGAATTTTGA

                                                        
        882 CTTTAAACTTGGATTTCATGGGACTTGAAATGTCAATGCATTGG
          1 CTTTAAACTTGGATTTCATGGGACTTGAAATGTCAATGCATTGG

                                                       
        926 CTTTAAACTTGGATTTCATGGGACTTGAAATGTCAATGCATTG
          1 CTTTAAACTTGGATTTCATGGGACTTGAAATGTCAATGCATTG

        969 TTTAGGGTTT


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  44   43  1.00

ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37


Consensus pattern (44 bp):   
CTTTAAACTTGGATTTCATGGGACTTGAAATGTCAATGCATTGG

Found at i:1071 original size:46 final size:45

Alignment explanation


    Indices: 976--1199  Score: 281
    Period size: 46  Copynumber: 4.9  Consensus size: 45

        966 TTGTTTAGGG

                             *         *                  
        976 TTTTTATCACCCTCTACTTCTGCATCGCCTTCTTGGCGGGGTTGAT
          1 TTTTTATCACCCTCTACCTCTGCATCGGCTT-TTGGCGGGGTTGAT

                           *     **                       
       1022 TTTTTATCACCCTCTTCCTCTATATCGGCTTTTGGCGGGGTTGATT
          1 TTTTTATCACCCTCTACCTCTGCATCGGCTTTTGGCGGGGTTGA-T

                                  *                       
       1068 TTTTTATCACCCTCTACCTCTGTATCAGGC-TTTGGCGGGGTTGAT
          1 TTTTTATCACCCTCTACCTCTGCATC-GGCTTTTGGCGGGGTTGAT

                     *                  *                   
       1113 TATTTTATCGCCCTCTA-CTCCTGCATCAGCTTCTTGGCGGGGTTGAT
          1 T-TTTTATCACCCTCTACCT-CTGCATCGGCTT-TTGGCGGGGTTGAT

                    *                      *        
       1160 TTTTTATCGCCCTCTACCTCTGCATCGGCTACTTGGCGGG
          1 TTTTTATCACCCTCTACCTCTGCATCGGCT-TTTGGCGGG

       1200 CCACGGGCCA


Statistics
Matches: 158,  Mismatches: 12, Indels: 16
        0.85            0.06        0.09

Matches are distributed among these distances:
  45   19  0.12
  46  119  0.75
  47   20  0.13

ACGTcount: A:0.12, C:0.27, G:0.21, T:0.40


Consensus pattern (45 bp):   
TTTTTATCACCCTCTACCTCTGCATCGGCTTTTGGCGGGGTTGAT

Done.