Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022909.1 Corchorus olitorius cultivar O-4 contig22942, 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: 13394
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29


Found at i:44 original size:33 final size:33

Alignment explanation


    Indices: 1--66  Score: 123
    Period size: 33  Copynumber: 2.0  Consensus size: 33

                                             
          1 ATTGGACGGCATGACCATGGTCATGCCTCCCTC
          1 ATTGGACGGCATGACCATGGTCATGCCTCCCTC

                 *                           
         34 ATTGGGCGGCATGACCATGGTCATGCCTCCCTC
          1 ATTGGACGGCATGACCATGGTCATGCCTCCCTC

         67 CCTGGTCATG


Statistics
Matches: 32,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   32  1.00

ACGTcount: A:0.17, C:0.33, G:0.26, T:0.24


Consensus pattern (33 bp):   
ATTGGACGGCATGACCATGGTCATGCCTCCCTC

Found at i:151 original size:10 final size:10

Alignment explanation


    Indices: 121--198  Score: 55
    Period size: 10  Copynumber: 8.5  Consensus size: 10

        111 TTTTTTAATT

                     *
        121 ATTAATTATT
          1 ATTAATTATA

                      
        131 ATTAA-T-T-
          1 ATTAATTATA

                      
        138 ATTAATTATA
          1 ATTAATTATA

                  *   
        148 ATTAATAATA
          1 ATTAATTATA

                       
        158 A-TAATT-TAA
          1 ATTAATTAT-A

                  *   
        167 ATTAATAATA
          1 ATTAATTATA

                      
        177 ATT-A--ATA
          1 ATTAATTATA

                  *   
        184 ATTAATAATA
          1 ATTAATTATA

                 
        194 ATTAA
          1 ATTAA

        199 AAAAATAAAA


Statistics
Matches: 56,  Mismatches: 3, Indels: 18
        0.73            0.04        0.23

Matches are distributed among these distances:
   7   11  0.20
   8    4  0.07
   9    9  0.16
  10   31  0.55
  11    1  0.02

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (10 bp):   
ATTAATTATA

Found at i:190 original size:7 final size:7

Alignment explanation


    Indices: 115--192  Score: 72
    Period size: 7  Copynumber: 11.1  Consensus size: 7

        105 TTTTTGTTTT

                 * 
        115 TTAATTA
          1 TTAATAA

                 * 
        122 TTAATTA
          1 TTAATAA

               *   
        129 TTATTAA
          1 TTAATAA

               *   
        136 TTATTAA
          1 TTAATAA

                   
        143 TT-ATAA
          1 TTAATAA

                   
        149 TTAATAA
          1 TTAATAA

                   
        156 -TAATAA
          1 TTAATAA

                      
        162 TTTAAATTAA
          1 -TT-AA-TAA

                   
        172 -TAATAA
          1 TTAATAA

                   
        178 TTAATAA
          1 TTAATAA

                   
        185 TTAATAA
          1 TTAATAA

             
        192 T
          1 T

        193 AATTAAAAAA


Statistics
Matches: 62,  Mismatches: 3, Indels: 12
        0.81            0.04        0.16

Matches are distributed among these distances:
   6   14  0.23
   7   41  0.66
   8    2  0.03
   9    2  0.03
  10    3  0.05

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (7 bp):   
TTAATAA

Found at i:198 original size:17 final size:17

Alignment explanation


    Indices: 115--198  Score: 88
    Period size: 17  Copynumber: 5.2  Consensus size: 17

        105 TTTTTGTTTT

                 *      *  * 
        115 TTAATTATTAATTATTA
          1 TTAATAATTAATAATAA

                 *      *    
        132 TTAATTATTAATTATAA
          1 TTAATAATTAATAATAA

                             
        149 TTAATAA-TAATAAT--
          1 TTAATAATTAATAATAA

                             
        163 TT-A-AATTAATAATAA
          1 TTAATAATTAATAATAA

                             
        178 TTAATAATTAATAATAA
          1 TTAATAATTAATAATAA

                
        195 TTAA
          1 TTAA

        199 AAAAATAAAA


Statistics
Matches: 59,  Mismatches: 3, Indels: 10
        0.82            0.04        0.14

Matches are distributed among these distances:
  12    2  0.03
  13    8  0.14
  14    2  0.03
  15    2  0.03
  16    7  0.12
  17   38  0.64

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


Consensus pattern (17 bp):   
TTAATAATTAATAATAA
Done.