Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006068.1 Kokia drynarioides strain JFW-HI SEQ_120548, 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, 603

Length: 1005
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34


Found at i:264 original size:6 final size:6

Alignment explanation


    Indices: 248--302  Score: 53
    Period size: 6  Copynumber: 9.3  Consensus size: 6

        238 ACATTTAAAA

                                                         *   *       
        248 TAAATTT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAA-C TAAATT
          1 TAAA-TT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT

                     
        295 TAAATT TA
          1 TAAATT TA

        303 GAATAATCTT


Statistics
Matches: 40,  Mismatches: 4, Indels: 9
        0.75            0.08        0.17

Matches are distributed among these distances:
   4    2  0.05
   5    5  0.12
   6   27  0.68
   7    6  0.15

ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47


Consensus pattern (6 bp):   
TAAATT

Found at i:273 original size:24 final size:23

Alignment explanation


    Indices: 240--284  Score: 72
    Period size: 24  Copynumber: 1.9  Consensus size: 23

        230 ATACTTAGAC

                                    
        240 ATTTAAAATAAATTTTAAATTTAA
          1 ATTTAAAATAAA-TTTAAATTTAA

                 *               
        264 ATTTATAATAAATTTAAATTT
          1 ATTTAAAATAAATTTAAATTT

        285 CAACTAAATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  23    9  0.45
  24   11  0.55

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


Consensus pattern (23 bp):   
ATTTAAAATAAATTTAAATTTAA

Found at i:275 original size:17 final size:17

Alignment explanation


    Indices: 255--337  Score: 89
    Period size: 17  Copynumber: 4.9  Consensus size: 17

        245 AAATAAATTT

                             
        255 TAAATTTAAATTTATAA
          1 TAAATTTAAATTTATAA

                             *
        272 TAAATTTAAATTTCA-AC
          1 TAAATTTAAATTT-ATAA

                          *  
        289 TAAATTTAAATTTAGAA
          1 TAAATTTAAATTTATAA

                      *    *  
        306 T-AATCTTAATTTTAAAA
          1 TAAAT-TTAAATTTATAA

                     *     
        323 TAAATTTAAGTTTAT
          1 TAAATTTAAATTTAT

        338 TGGGCCCAGA


Statistics
Matches: 56,  Mismatches: 6, Indels: 8
        0.80            0.09        0.11

Matches are distributed among these distances:
  16    4  0.07
  17   48  0.86
  18    4  0.07

ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46


Consensus pattern (17 bp):   
TAAATTTAAATTTATAA

Found at i:295 original size:34 final size:34

Alignment explanation


    Indices: 255--337  Score: 105
    Period size: 34  Copynumber: 2.4  Consensus size: 34

        245 AAATAAATTT

                                           *  *
        255 TAAATTTAAATTTATAATAAAT-TTAAATTTCAAC
          1 TAAATTTAAATTTATAAT-AATCTTAAATTTAAAA

                          *           *       
        289 TAAATTTAAATTTAGAATAATCTTAATTTTAAAA
          1 TAAATTTAAATTTATAATAATCTTAAATTTAAAA

                     *     
        323 TAAATTTAAGTTTAT
          1 TAAATTTAAATTTAT

        338 TGGGCCCAGA


Statistics
Matches: 42,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  33    3  0.07
  34   39  0.93

ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46


Consensus pattern (34 bp):   
TAAATTTAAATTTATAATAATCTTAAATTTAAAA
Done.