Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010241.1 Corchorus olitorius cultivar O-4 contig10273, 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: 3812
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28


Found at i:244 original size:50 final size:47

Alignment explanation


    Indices: 190--302  Score: 118
    Period size: 50  Copynumber: 2.3  Consensus size: 47

        180 TTTCTTTTCC

                                   **     *                   
        190 GTTTTTAATTTTTGTTTTCCGTTTTTTTCTTAAAAAAAAATTTATTTTGG
          1 GTTTTTAATTTTTGTTTTCCG-TCGTTT-TGAAAAAAAAA-TTATTTTGG

                                 *                     *     *
        240 GTTTTTAATTTTGTGTGTTTTGCGTCGTTTTGAAAAAAAAATTGTTTTGT
          1 GTTTTTAA-TTT-T-TGTTTTCCGTCGTTTTGAAAAAAAAATTATTTTGG

                         
        290 GTTTTTAATTTTT
          1 GTTTTTAATTTTT

        303 TTTGAGTCTT


Statistics
Matches: 54,  Mismatches: 6, Indels: 9
        0.78            0.09        0.13

Matches are distributed among these distances:
  47    1  0.02
  48    1  0.02
  49    3  0.06
  50   23  0.43
  51   13  0.24
  52    5  0.09
  53    8  0.15

ACGTcount: A:0.22, C:0.04, G:0.14, T:0.59


Consensus pattern (47 bp):   
GTTTTTAATTTTTGTTTTCCGTCGTTTTGAAAAAAAAATTATTTTGG

Found at i:344 original size:29 final size:26

Alignment explanation


    Indices: 302--360  Score: 73
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        292 TTTTAATTTT

                                         
        302 TTTTGAGTCTTGCGTCAAAGAAAAAAAAA
          1 TTTTGAGTCTTGCGTC---GAAAAAAAAA

                 *  *                 
        331 TTTTGTGTTTTGCGTCGAAAAAAAAA
          1 TTTTGAGTCTTGCGTCGAAAAAAAAA

                
        357 TTTT
          1 TTTT

        361 TCTTGTTCCT


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  26   14  0.50
  29   14  0.50

ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37


Consensus pattern (26 bp):   
TTTTGAGTCTTGCGTCGAAAAAAAAA

Found at i:2718 original size:42 final size:42

Alignment explanation


    Indices: 2672--2762  Score: 119
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       2662 CGAGTATCAC

                           *                * *   *   
       2672 GCCCGGCCATGCCCGGCACCACAAGCCTCAGCTGCGCCTCAT
          1 GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

                              * *         *           
       2714 GCCCGGCCATGCCCGCCATCTCAAGCCTCATCCGAGCCACAT
          1 GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

                   
       2756 GCCCGGC
          1 GCCCGGC

       2763 TAGGACCGGC


Statistics
Matches: 42,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  42   42  1.00

ACGTcount: A:0.16, C:0.48, G:0.23, T:0.12


Consensus pattern (42 bp):   
GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

Found at i:2866 original size:22 final size:21

Alignment explanation


    Indices: 2841--2883  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2831 CCAAGTCATT

                     *            
       2841 ACCGCCCATTCACCGTGCCATC
          1 ACCGCCCATGC-CCGTGCCATC

                *                
       2863 ACCGGCCATGCCCGTGCCATC
          1 ACCGCCCATGCCCGTGCCATC

       2884 GCCATTCCAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   10  0.53
  22    9  0.47

ACGTcount: A:0.16, C:0.49, G:0.19, T:0.16


Consensus pattern (21 bp):   
ACCGCCCATGCCCGTGCCATC

Found at i:3246 original size:14 final size:15

Alignment explanation


    Indices: 3219--3248  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3209 ATCTCTTTAA

                           
       3219 TTTTCCTTGCATTAT
          1 TTTTCCTTGCATTAT

                           
       3234 TTTTCCTTG-ATTAT
          1 TTTTCCTTGCATTAT

             
       3248 T
          1 T

       3249 GCTTTGATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (15 bp):   
TTTTCCTTGCATTAT
Done.