Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007401.1 Corchorus olitorius cultivar O-4 contig07426, 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: 3482
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32


Found at i:795 original size:20 final size:20

Alignment explanation


    Indices: 772--816  Score: 54
    Period size: 20  Copynumber: 2.2  Consensus size: 20

        762 CTTTTTTTAG

                            *   
        772 TTTTCGTAGGCATATTTTGA
          1 TTTTCGTAGGCATATTCTGA

                **     *        
        792 TTTTATTAGGCTTATTCTGA
          1 TTTTCGTAGGCATATTCTGA

                 
        812 TTTTC
          1 TTTTC

        817 TGTTTCTTTT


Statistics
Matches: 20,  Mismatches: 5, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.18, C:0.11, G:0.16, T:0.56


Consensus pattern (20 bp):   
TTTTCGTAGGCATATTCTGA

Found at i:1115 original size:21 final size:21

Alignment explanation


    Indices: 1091--1133  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1081 AATGGGGCTA

                         *   *   
       1091 TTTAGCCTTTCTGTATCTATC
          1 TTTAGCCTTTCTGAATCGATC

                *                
       1112 TTTATCCTTTCTGAATCGATC
          1 TTTAGCCTTTCTGAATCGATC

             
       1133 T
          1 T

       1134 CTTCTTTGGC


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.16, C:0.23, G:0.09, T:0.51


Consensus pattern (21 bp):   
TTTAGCCTTTCTGAATCGATC

Found at i:2327 original size:26 final size:26

Alignment explanation


    Indices: 2293--2347  Score: 76
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       2283 AAATTACCAA

                                       
       2293 GGGCATTTTGGTCATTCTT-GCCTTAG
          1 GGGCATTTTGGTCATT-TTCGCCTTAG

                *                      
       2319 GGGCGTTTTGGTCATTTTCCGCCTTAG
          1 GGGCATTTTGGTCATTTT-CGCCTTAG

              
       2346 GG
          1 GG

       2348 AGGGGGGGGG


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  25    2  0.08
  26   15  0.58
  27    9  0.35

ACGTcount: A:0.09, C:0.20, G:0.31, T:0.40


Consensus pattern (26 bp):   
GGGCATTTTGGTCATTTTCGCCTTAG
Done.