Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020149.1 Corchorus olitorius cultivar O-4 contig20182, 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: 18101
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:12511 original size:11 final size:11

Alignment explanation


    Indices: 12497--12551  Score: 51
    Period size: 11  Copynumber: 5.1  Consensus size: 11

      12487 AGTGTGAATA

                       
      12497 TATTTATTATT
          1 TATTTATTATT

                  *     
      12508 TATTTTCTTA-T
          1 TA-TTTATTATT

                       
      12519 TATTT-TTATT
          1 TATTTATTATT

                    *  
      12529 TATTTATTTTT
          1 TATTTATTATT

              **       
      12540 TAAATATTATT
          1 TATTTATTATT

             
      12551 T
          1 T

      12552 TCGTACTCTA


Statistics
Matches: 36,  Mismatches: 5, Indels: 6
        0.77            0.11        0.13

Matches are distributed among these distances:
   9    3  0.08
  10    9  0.25
  11   18  0.50
  12    6  0.17

ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73


Consensus pattern (11 bp):   
TATTTATTATT

Found at i:12922 original size:16 final size:16

Alignment explanation


    Indices: 12901--12936  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      12891 GAACCCGAAT

                  *         
      12901 CCGAAATTATCTGAAC
          1 CCGAAAATATCTGAAC

                           *
      12917 CCGAAAATATCTGAAT
          1 CCGAAAATATCTGAAC

                
      12933 CCGA
          1 CCGA

      12937 GGCAGCTCGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.39, C:0.25, G:0.14, T:0.22


Consensus pattern (16 bp):   
CCGAAAATATCTGAAC

Found at i:13082 original size:26 final size:23

Alignment explanation


    Indices: 13053--13100  Score: 60
    Period size: 24  Copynumber: 2.0  Consensus size: 23

      13043 TTTACTATTA

                                      
      13053 AATAAAACTATTATATATATGAATAT
          1 AATAAAA-T-TTATATATAT-AATAT

                        *         
      13079 AATAAAATTTATTTATATAATA
          1 AATAAAATTTATATATATAATA

      13101 ATGATCACAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  23    4  0.19
  24    9  0.43
  25    1  0.05
  26    7  0.33

ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42


Consensus pattern (23 bp):   
AATAAAATTTATATATATAATAT

Found at i:13161 original size:2 final size:2

Alignment explanation


    Indices: 13154--13192  Score: 69
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      13144 AAACTATTAA

                                             *                        
      13154 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      13193 ACTTAAAGCA


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:17723 original size:29 final size:29

Alignment explanation


    Indices: 17690--17745  Score: 96
    Period size: 29  Copynumber: 1.9  Consensus size: 29

      17680 GAAAGATAAC

                                          
      17690 TTATTTT-AAGACGCTAAAAAGAAAAAGAA
          1 TTATTTTAAAGA-GCTAAAAAGAAAAAGAA

                                       
      17719 TTATTTTAAAGAGCTAAAAAGAAAAAG
          1 TTATTTTAAAGAGCTAAAAAGAAAAAG

      17746 TTCAACAAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  29   22  0.85
  30    4  0.15

ACGTcount: A:0.55, C:0.05, G:0.14, T:0.25


Consensus pattern (29 bp):   
TTATTTTAAAGAGCTAAAAAGAAAAAGAA

Found at i:17998 original size:72 final size:72

Alignment explanation


    Indices: 17910--18045  Score: 200
    Period size: 72  Copynumber: 1.9  Consensus size: 72

      17900 TAAAATTTTA

                    *                                                  *     
      17910 GGGGACCATATTATAAATTTTCCAGTTTTTTCAGTTGAAATGCATATATATAAAAGAATTCTTGG
          1 GGGGACCAAATTATAAATTTTCCAGTTTTTTCAGTTGAAATGCATATATATAAAAGAATCCTTGG

                   
      17975 CAATTTG
         66 CAATTTG

                *                  **        *     *     *                  
      17982 GGGGGCCAAATTATAAATTTTCCTTTTTTTTCATTTGAAGTGCATGTATATAAAAGAATCCTTG
          1 GGGGACCAAATTATAAATTTTCCAGTTTTTTCAGTTGAAATGCATATATATAAAAGAATCCTTG

      18046 CCCCTGCTGT


Statistics
Matches: 56,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  72   56  1.00

ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40


Consensus pattern (72 bp):   
GGGGACCAAATTATAAATTTTCCAGTTTTTTCAGTTGAAATGCATATATATAAAAGAATCCTTGG
CAATTTG
Done.