Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016796.1 Corchorus olitorius cultivar O-4 contig16829, 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: 19631
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32


Found at i:1050 original size:16 final size:16

Alignment explanation


    Indices: 1029--1073  Score: 56
    Period size: 17  Copynumber: 2.8  Consensus size: 16

       1019 TGTTTCGATT

                    **      
       1029 TTCTTTGATTTTTTAA
          1 TTCTTTGAAATTTTAA

                             
       1045 TTCTTTAGAAATTTTAA
          1 TTCTTT-GAAATTTTAA

                         
       1062 TT-TTTGAAATTT
          1 TTCTTTGAAATTT

       1074 GCTTTGGAGA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  15    7  0.27
  16    9  0.35
  17   10  0.38

ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62


Consensus pattern (16 bp):   
TTCTTTGAAATTTTAA

Found at i:3603 original size:48 final size:46

Alignment explanation


    Indices: 3528--3663  Score: 159
    Period size: 48  Copynumber: 2.9  Consensus size: 46

       3518 GAGCGTGCCA

                        *         *                   *     
       3528 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGT-AAAA-AAAAAG

                                                            
       3575 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAAAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAAAAAAAG

            *           *               *             
       3623 TTCAATTTTGTAGTAAAAATTGAGAAAAGGTGC-AGTAAAAA
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAAA

       3664 GTAAATGATT


Statistics
Matches: 79,  Mismatches: 6, Indels: 9
        0.84            0.06        0.10

Matches are distributed among these distances:
  46    8  0.10
  47   15  0.19
  48   46  0.58
  49    9  0.11
  50    1  0.01

ACGTcount: A:0.51, C:0.06, G:0.15, T:0.27


Consensus pattern (46 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAAAAAAG

Found at i:12698 original size:76 final size:76

Alignment explanation


    Indices: 12547--12690  Score: 184
    Period size: 76  Copynumber: 1.9  Consensus size: 76

      12537 ACAAGGGCCC

                                           *                   *    *      * 
      12547 CGACTCCACCTGGGCGCCCACATGGTTGCCTTAAGCACCCATGTGGTTTGCTTGAGGACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTGAAGCACCCATGTGGTTTGCCTGAGCACCCAGAT

                       
      12612 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                           *       
      12623 CGACTCCAGCTGGGTGCCCACATGGTTTGTCTGAAG-ACCCATGT-GTTTCGCCTGATCACCCAG
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTGAAGCACCCATGTGGTTT-GCCTGAGCACCCAG

                 
      12686 ATGGG
         64 ATGGG

      12691 TTGTGTCATA


Statistics
Matches: 58,  Mismatches: 8, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  75    4  0.07
  76   46  0.79
  77    8  0.14

ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTGAAGCACCCATGTGGTTTGCCTGAGCACCCAGAT
GGGCAGTGTCA

Found at i:12915 original size:12 final size:11

Alignment explanation


    Indices: 12887--12918  Score: 64
    Period size: 11  Copynumber: 2.9  Consensus size: 11

      12877 CATAAATCAT

                       
      12887 CCAAAAAGGTC
          1 CCAAAAAGGTC

                       
      12898 CCAAAAAGGTC
          1 CCAAAAAGGTC

                      
      12909 CCAAAAAGGT
          1 CCAAAAAGGT

      12919 ACAAAATTGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   21  1.00

ACGTcount: A:0.47, C:0.25, G:0.19, T:0.09


Consensus pattern (11 bp):   
CCAAAAAGGTC

Found at i:15329 original size:21 final size:21

Alignment explanation


    Indices: 15303--15354  Score: 61
    Period size: 21  Copynumber: 2.5  Consensus size: 21

      15293 AGCAGCTTGC

                         * *      
      15303 GCCTGGGTGCTCAGGTTCTTTA
          1 GCCTGGGTGCTCAAGCT-TTTA

                     *           
      15325 G-CTGGGTGTTCAAGCTTTTA
          1 GCCTGGGTGCTCAAGCTTTTA

                      
      15345 GCCTGGGTGC
          1 GCCTGGGTGC

      15355 CCAGCTAGAG


Statistics
Matches: 25,  Mismatches: 4, Indels: 3
        0.78            0.12        0.09

Matches are distributed among these distances:
  20    5  0.20
  21   19  0.76
  22    1  0.04

ACGTcount: A:0.10, C:0.21, G:0.35, T:0.35


Consensus pattern (21 bp):   
GCCTGGGTGCTCAAGCTTTTA
Done.