Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024910.1 Corchorus olitorius cultivar O-4 contig24943, 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: 17551
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31


Found at i:1264 original size:2 final size:2

Alignment explanation


    Indices: 1259--1287  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       1249 GTAGTTCTAC

                                                       
       1259 AT 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 AT A

       1288 GTGTGGCTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:2147 original size:21 final size:21

Alignment explanation


    Indices: 2123--2168  Score: 67
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       2113 TCTCACAGGG

                                  
       2123 GGTTATCAAAA-ATCATAGGAA
          1 GGTTA-CAAAATATCATAGGAA

                       *         
       2144 GGTTACAAAATTTCATAGGAA
          1 GGTTACAAAATATCATAGGAA

                
       2165 GGTT
          1 GGTT

       2169 TATTAAAATT


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20    5  0.22
  21   18  0.78

ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28


Consensus pattern (21 bp):   
GGTTACAAAATATCATAGGAA

Found at i:3274 original size:28 final size:28

Alignment explanation


    Indices: 3234--3295  Score: 115
    Period size: 28  Copynumber: 2.2  Consensus size: 28

       3224 CCTCTCTTGC

                                        
       3234 CCTTCAGAATTGGTATGTATTAGAAACT
          1 CCTTCAGAATTGGTATGTATTAGAAACT

                                        
       3262 CCTTCAGAATTGGTATGTATTAGAAACT
          1 CCTTCAGAATTGGTATGTATTAGAAACT

             *    
       3290 CTTTCA
          1 CCTTCA

       3296 TTGGAGGTGA


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  28   33  1.00

ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37


Consensus pattern (28 bp):   
CCTTCAGAATTGGTATGTATTAGAAACT

Found at i:8342 original size:43 final size:43

Alignment explanation


    Indices: 8291--8419  Score: 231
    Period size: 43  Copynumber: 3.0  Consensus size: 43

       8281 CTTTGAAAAC

                                     *                 
       8291 TGATGGGAACTTTCCCAATTTGAAATACTTAAATTGAATACTT
          1 TGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTT

                             *                         
       8334 TGATGGGAACTTTCCCAGTTTGAAAAACTTAAATTGAATACTT
          1 TGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTT

                                       *               
       8377 TGATGGGAACTTTCCCAATTTGAAAAATTTAAATTGAATACTT
          1 TGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTT

       8420 CTTCTTTTTT


Statistics
Matches: 82,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  43   82  1.00

ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36


Consensus pattern (43 bp):   
TGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTT

Found at i:9712 original size:20 final size:20

Alignment explanation


    Indices: 9679--9718  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       9669 AAAACTCTCC

                     *     *    
       9679 TTTTTCTATTTTTTTTTGTA
          1 TTTTTCTATATTTTTGTGTA

                   *            
       9699 TTTTTCTGTATTTTTGTGTA
          1 TTTTTCTATATTTTTGTGTA

       9719 ATAAAAAAAA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.10, C:0.05, G:0.10, T:0.75


Consensus pattern (20 bp):   
TTTTTCTATATTTTTGTGTA

Found at i:10079 original size:58 final size:55

Alignment explanation


    Indices: 9989--10123  Score: 218
    Period size: 56  Copynumber: 2.4  Consensus size: 55

       9979 CTTGAAAAAA

                      *                                            * 
       9989 AAACTCTCTGTTA-GGTTTTTTTTTGTGTTTTTCAAAGAAAAAAAGATGAGCTTTTC
          1 AAACTCTCTGCTAGGGTTTTTTTTTGTGTTTTTCAAAG--AAAAAGATGAGCTTTAC

                                                                    
      10045 AAACTCTCTGCTAGGGTCTTTTTTTTGTGTTTTTCAAAGAAAAAGATGAGCTTTAC
          1 AAACTCTCTGCTAGGGT-TTTTTTTTGTGTTTTTCAAAGAAAAAGATGAGCTTTAC

                                   
      10101 AAACTCTCTGCTAGGGTTTTTTT
          1 AAACTCTCTGCTAGGGTTTTTTT

      10124 GCTTGGAAAA


Statistics
Matches: 75,  Mismatches: 2, Indels: 5
        0.91            0.02        0.06

Matches are distributed among these distances:
  55    6  0.08
  56   45  0.60
  57    3  0.04
  58   21  0.28

ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44


Consensus pattern (55 bp):   
AAACTCTCTGCTAGGGTTTTTTTTTGTGTTTTTCAAAGAAAAAGATGAGCTTTAC

Found at i:16176 original size:28 final size:27

Alignment explanation


    Indices: 16145--16206  Score: 90
    Period size: 28  Copynumber: 2.3  Consensus size: 27

      16135 CGTAGTAGAT

                              *         
      16145 TGACGTGTCAACGGGTGATGTGGCAGGA
          1 TGACGTGTCAACGGGTGACGTGGCA-GA

                                        
      16173 TGAC-TGGTCAACGGGTGACGTGGCAGA
          1 TGACGT-GTCAACGGGTGACGTGGCAGA

                   
      16200 TGACGTG
          1 TGACGTG

      16207 GCAGGTTGAC


Statistics
Matches: 31,  Mismatches: 1, Indels: 5
        0.84            0.03        0.14

Matches are distributed among these distances:
  27    8  0.26
  28   23  0.74

ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21


Consensus pattern (27 bp):   
TGACGTGTCAACGGGTGACGTGGCAGA
Done.