Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018992.1 Corchorus olitorius cultivar O-4 contig19025, 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: 9762
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33


Found at i:424 original size:13 final size:13

Alignment explanation


    Indices: 406--431  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        396 TCTCTTTTTT

                         
        406 TAAAAAATAAAAA
          1 TAAAAAATAAAAA

                         
        419 TAAAAAATAAAAA
          1 TAAAAAATAAAAA

        432 AATCGAAGCT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15


Consensus pattern (13 bp):   
TAAAAAATAAAAA

Found at i:2024 original size:20 final size:20

Alignment explanation


    Indices: 1999--2036  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1989 TCACCTTTCA

                                
       1999 AATTACTAGCAAATGAAATT
          1 AATTACTAGCAAATGAAATT

                     *        
       2019 AATTACTAGTAAATGAAA
          1 AATTACTAGCAAATGAAA

       2037 AATGCAAATC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.53, C:0.08, G:0.11, T:0.29


Consensus pattern (20 bp):   
AATTACTAGCAAATGAAATT

Found at i:2866 original size:58 final size:59

Alignment explanation


    Indices: 2802--2933  Score: 191
    Period size: 58  Copynumber: 2.3  Consensus size: 59

       2792 CTTTCATGAT

                                                      * *               
       2802 CTGTCTTCAGATT-CA-CTCGTGAGCTGTCTTCAGTCTCAATCTTAAAATCTTTAAGGAA
          1 CTGTCTTCAGATTCCATCT-GTGAGCTGTCTTCAGTCTCAATATCAAAATCTTTAAGGAA

            *                                                    *     
       2860 TTGTCTTCAG-TTCCATCTGTGAGCTGTCTTCAGTCTCAATATCAAAATCTTTCAGGAA
          1 CTGTCTTCAGATTCCATCTGTGAGCTGTCTTCAGTCTCAATATCAAAATCTTTAAGGAA

                             
       2918 CTGTCTTCAGA-TCCAT
          1 CTGTCTTCAGATTCCAT

       2934 TTCTGATGAA


Statistics
Matches: 66,  Mismatches: 5, Indels: 6
        0.86            0.06        0.08

Matches are distributed among these distances:
  57    2  0.03
  58   62  0.94
  59    2  0.03

ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37


Consensus pattern (59 bp):   
CTGTCTTCAGATTCCATCTGTGAGCTGTCTTCAGTCTCAATATCAAAATCTTTAAGGAA

Found at i:4372 original size:1 final size:1

Alignment explanation


    Indices: 4366--4414  Score: 53
    Period size: 1  Copynumber: 49.0  Consensus size: 1

       4356 TTGTTTTGTG

                       *        *     *     *     *          
       4366 TTTTTTTTTTTGTTTTTTTTGTTTTTGTTTTTGTTTTTGTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       4415 GCGACCCGGC


Statistics
Matches: 38,  Mismatches: 10, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
   1   38  1.00

ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90


Consensus pattern (1 bp):   
T

Found at i:4381 original size:6 final size:6

Alignment explanation


    Indices: 4355--4415  Score: 76
    Period size: 6  Copynumber: 10.7  Consensus size: 6

       4345 CAATCTTTGC

                                       *                            
       4355 TTTGTT TTGTGTT TTT-TT TTT-TG TTT-TT TTTGTT TTTGTT TTTGTT
          1 TTTGTT TT-TGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT

                              
       4401 TTTGTT TTT-TT TTTG
          1 TTTGTT TTTGTT TTTG

       4416 CGACCCGGCT


Statistics
Matches: 50,  Mismatches: 2, Indels: 6
        0.86            0.03        0.10

Matches are distributed among these distances:
   5   18  0.36
   6   26  0.52
   7    6  0.12

ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85


Consensus pattern (6 bp):   
TTTGTT

Found at i:4402 original size:27 final size:28

Alignment explanation


    Indices: 4355--4412  Score: 100
    Period size: 27  Copynumber: 2.1  Consensus size: 28

       4345 CAATCTTTGC

                            *           
       4355 TTTGTTTTGTGTTTTTTTTTTTGTTTTT
          1 TTTGTTTTGTGTTTTTGTTTTTGTTTTT

                                        
       4383 TTTGTTTT-TGTTTTTGTTTTTGTTTTT
          1 TTTGTTTTGTGTTTTTGTTTTTGTTTTT

               
       4410 TTT
          1 TTT

       4413 TTGCGACCCG


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  27   21  0.72
  28    8  0.28

ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86


Consensus pattern (28 bp):   
TTTGTTTTGTGTTTTTGTTTTTGTTTTT

Found at i:9700 original size:37 final size:36

Alignment explanation


    Indices: 9647--9756  Score: 103
    Period size: 42  Copynumber: 2.8  Consensus size: 36

       9637 AAGACTAAAT

                       *                     *   
       9647 GGGATCTTTCCTTAAATTGAAAACTTGAAAACTCGAC
          1 GGGATCTTTCCCTAAATT-AAAACTTGAAAACTAGAC

                                     *               *
       9684 GGGATCTTTCCCTAAATTTAAAAATTTTGAAGAAGACTAGAT
          1 GGGATCTTTCCCTAAA-TT-AAAA-CTTG-A-AA-ACTAGAC

             *                             
       9726 GTGATCTTTCCCTAAATTAAAACTCTGAAAA
          1 GGGATCTTTCCCTAAATTAAAACT-TGAAAA

       9757 AAGACA


Statistics
Matches: 60,  Mismatches: 7, Indels: 12
        0.76            0.09        0.15

Matches are distributed among these distances:
  37   16  0.27
  38    8  0.13
  39    5  0.08
  40    7  0.12
  41    4  0.07
  42   20  0.33

ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32


Consensus pattern (36 bp):   
GGGATCTTTCCCTAAATTAAAACTTGAAAACTAGAC
Done.