Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007432.1 Corchorus capsularis cultivar CVL-1 contig07453, 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: 9600
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34


Found at i:1251 original size:14 final size:14

Alignment explanation


    Indices: 1232--1259  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       1222 GCAGCTAAAA

                          
       1232 GCAAGTCATATTGT
          1 GCAAGTCATATTGT

                          
       1246 GCAAGTCATATTGT
          1 GCAAGTCATATTGT

       1260 TAGTTAATAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36


Consensus pattern (14 bp):   
GCAAGTCATATTGT

Found at i:1919 original size:31 final size:31

Alignment explanation


    Indices: 1875--1933  Score: 91
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       1865 GTTAAAAAAC

                    *                      
       1875 TAAGGATATAATAGGTATTTCAAAAGTTAAA
          1 TAAGGATAAAATAGGTATTTCAAAAGTTAAA

                 *          *           
       1906 TAAGGGTAAAATAGGTGTTTCAAAAGTT
          1 TAAGGATAAAATAGGTATTTCAAAAGTT

       1934 TCTCAAAACT


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  31   25  1.00

ACGTcount: A:0.44, C:0.03, G:0.20, T:0.32


Consensus pattern (31 bp):   
TAAGGATAAAATAGGTATTTCAAAAGTTAAA

Found at i:6988 original size:2 final size:2

Alignment explanation


    Indices: 6981--7007  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       6971 CAAGATTAAA

                                                    
       6981 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7008 AATAAAGAGC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:7447 original size:103 final size:103

Alignment explanation


    Indices: 7220--7492  Score: 345
    Period size: 103  Copynumber: 2.7  Consensus size: 103

       7210 CGGATTTTTA

                                *                        * *     *           
       7220 TGTAGTAATTTCCGTTGCAACAATTTATTTTGGCGCAAAATATTTTAACAAGCGGGAATTCAAAT
          1 TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTTGAGCAAGCAGGAATTCAAAT

                        *     *                   
       7285 TTTAATTTCTCATGAAAATTAAATTCGTTGCAAAATTT
         66 TTTAATTTCTCACGAAAACTAAATTCGTTGCAAAATTT

            *        *   *   *              *                *   *           
       7323 GGTAGTAATGTCCTTTGAAAAAATTTATTTTGACGCAAAATATTTGAGCGAGCTGGAATTCAAAT
          1 TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTTGAGCAAGCAGGAATTCAAAT

                    * *              *            
       7388 TTTAATTTGTTACG-AAACTAAATTTGTTGCAAAATTT
         66 TTTAATTTCTCACGAAAACTAAATTCGTTGCAAAATTT

                                    *         *              *               
       7425 TGTAGTAATTTCCGTTGCAAAAA-GTATTTTGGCACAAAATATTTGAGTTAA-CAGGAATTCAAA
          1 TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTTGAG-CAAGCAGGAATTCAAA

                 
       7488 TTTTA
         65 TTTTA

       7493 TTTTATATGG


Statistics
Matches: 144,  Mismatches: 25, Indels: 4
        0.83            0.14        0.02

Matches are distributed among these distances:
 101   37  0.26
 102   41  0.28
 103   66  0.46

ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38


Consensus pattern (103 bp):   
TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTTGAGCAAGCAGGAATTCAAAT
TTTAATTTCTCACGAAAACTAAATTCGTTGCAAAATTT

Done.