Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008607.1 Kokia drynarioides strain JFW-HI SEQ_123285, 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: 18040
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31


Found at i:1670 original size:122 final size:124

Alignment explanation


    Indices: 1451--1698  Score: 374
    Period size: 123  Copynumber: 2.0  Consensus size: 124

       1441 CTCGAATATT

                                               *            *                
       1451 TTTTCCTTCGAAACCCTTAGATAACTTTAAATCAATCAAACAAAAAAGGCAGGATAGCTTATAGC
          1 TTTTCCTTCGAAACCCTTAGATAACTTTAAATCAACCAAACAAAAAAGCCAGGATAGCTTATAGC

                  *      *      **   *                                 
       1516 ATGAAAGAAAGCTTTTCTAAGTTATTCATTCTTCATAT-AACCCAAAATTCTAACTAGG
         66 ATGAAAAAAAGCTATTCTAAACTATGCATTCTTCATATAAACCCAAAATTCTAACTAGG

                    *         *                          * *                 
       1574 TTTTCCTTTGAAACCCTTGGATAACTTTAAATCAACCAAAC-AAATATCCAGGATAGCTTATAGC
          1 TTTTCCTTCGAAACCCTTAGATAACTTTAAATCAACCAAACAAAAAAGCCAGGATAGCTTATAGC

                                                                *      
       1638 ATGAAAAAAAGCTATTCTAAACTATGCATTCTTCATATAAACCCAAAATTCTGACTAGG
         66 ATGAAAAAAAGCTATTCTAAACTATGCATTCTTCATATAAACCCAAAATTCTAACTAGG

              
       1697 TT
          1 TT

       1699 CAACATGATA


Statistics
Matches: 112,  Mismatches: 12, Indels: 2
        0.89            0.10        0.02

Matches are distributed among these distances:
 122   53  0.47
 123   59  0.53

ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31


Consensus pattern (124 bp):   
TTTTCCTTCGAAACCCTTAGATAACTTTAAATCAACCAAACAAAAAAGCCAGGATAGCTTATAGC
ATGAAAAAAAGCTATTCTAAACTATGCATTCTTCATATAAACCCAAAATTCTAACTAGG

Found at i:4161 original size:23 final size:23

Alignment explanation


    Indices: 4135--4180  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       4125 AGTAGATTAT

                 *                  
       4135 AAAAATACA-GTAAAATATTTTAA
          1 AAAAAAACACGTAAAA-ATTTTAA

                        *          
       4158 AAAAAAACACGTCAAAATTTTAA
          1 AAAAAAACACGTAAAAATTTTAA

       4181 TATACTAGCA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  23   15  0.75
  24    5  0.25

ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26


Consensus pattern (23 bp):   
AAAAAAACACGTAAAAATTTTAA

Found at i:17205 original size:11 final size:11

Alignment explanation


    Indices: 17189--17244  Score: 58
    Period size: 11  Copynumber: 4.9  Consensus size: 11

      17179 TCATACTCCC

                       
      17189 TTTAAATTTAT
          1 TTTAAATTTAT

                       *
      17200 TTTAAATTTAAA
          1 TTTAAATTT-AT

                    * *
      17212 TTTAAATTAAG
          1 TTTAAATTTAT

                  *    
      17223 TTTAAAATTAT
          1 TTTAAATTTAT

                       
      17234 TTTCAAATTTA
          1 TTT-AAATTTA

      17245 AAATTTAAAA


Statistics
Matches: 36,  Mismatches: 7, Indels: 3
        0.78            0.15        0.07

Matches are distributed among these distances:
  11   21  0.58
  12   15  0.42

ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54


Consensus pattern (11 bp):   
TTTAAATTTAT

Found at i:17211 original size:17 final size:17

Alignment explanation


    Indices: 17189--17251  Score: 72
    Period size: 17  Copynumber: 3.6  Consensus size: 17

      17179 TCATACTCCC

                             
      17189 TTTAAATTTATTTTAAA
          1 TTTAAATTTATTTTAAA

                      **    *
      17206 TTTAAATTTAAATTAAG
          1 TTTAAATTTATTTTAAA

                  *           
      17223 TTTAAAATTATTTTCAAA
          1 TTTAAATTTATTTT-AAA

                       
      17241 TTTAAAATTTA
          1 TTT-AAATTTA

      17252 AAATAAATAA


Statistics
Matches: 36,  Mismatches: 8, Indels: 2
        0.78            0.17        0.04

Matches are distributed among these distances:
  17   25  0.69
  18    5  0.14
  19    6  0.17

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52


Consensus pattern (17 bp):   
TTTAAATTTATTTTAAA

Found at i:17221 original size:5 final size:6

Alignment explanation


    Indices: 17189--17253  Score: 55
    Period size: 6  Copynumber: 11.0  Consensus size: 6

      17179 TCATACTCCC

                        *                           *        *    *
      17189 TTTAAA TTT-AT TTTAAA TTTAAA TTTAAA -TTAAG TTTAAA ATT-AT
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA

                                  
      17234 TTTCAAA TTTAAAA TTTAAA
          1 TTT-AAA TTT-AAA TTTAAA

      17254 ATAAATAAAA


Statistics
Matches: 46,  Mismatches: 9, Indels: 8
        0.73            0.14        0.13

Matches are distributed among these distances:
   5   11  0.24
   6   25  0.54
   7   10  0.22

ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51


Consensus pattern (6 bp):   
TTTAAA

Found at i:17259 original size:18 final size:18

Alignment explanation


    Indices: 17201--17259  Score: 59
    Period size: 18  Copynumber: 3.3  Consensus size: 18

      17191 TAAATTTATT

                              
      17201 TTAAATTT-AAATTTAAA
          1 TTAAATTTAAAATTTAAA

                *           **
      17218 TTAAGTTTAAAA-TTATT
          1 TTAAATTTAAAATTTAAA

                               
      17235 TTCAAATTTAAAATTTAAA
          1 TT-AAATTTAAAATTTAAA

            *     
      17254 ATAAAT
          1 TTAAAT

      17260 AAAACCCAAA


Statistics
Matches: 32,  Mismatches: 7, Indels: 5
        0.73            0.16        0.11

Matches are distributed among these distances:
  17   12  0.38
  18   16  0.50
  19    4  0.12

ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46


Consensus pattern (18 bp):   
TTAAATTTAAAATTTAAA
Done.