Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003709.1 Kokia drynarioides strain JFW-HI SEQ_116652, 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, 938

Length: 1564
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38


Found at i:283 original size:4 final size:4

Alignment explanation


    Indices: 276--314  Score: 53
    Period size: 4  Copynumber: 9.8  Consensus size: 4

        266 TTCTTCCTTC

                                        *                    
        276 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
          1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC

        315 CTTCATTTTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   3    3  0.10
   4   25  0.81
   5    3  0.10

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (4 bp):   
TTCT

Found at i:303 original size:21 final size:20

Alignment explanation


    Indices: 274--318  Score: 65
    Period size: 21  Copynumber: 2.2  Consensus size: 20

        264 CCTTCTTCCT

                                 
        274 TCTTCTTTCTTTCTTTCTTTC
          1 TCTTCTTTCTTTCTTT-TTTC

                *               
        295 TCTTTTTTCTTTCTTTTTTC
          1 TCTTCTTTCTTTCTTTTTTC

                 
        315 -CTTC
          1 TCTTC

        319 ATTTTTCGTT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  19    3  0.14
  20    4  0.18
  21   15  0.68

ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73


Consensus pattern (20 bp):   
TCTTCTTTCTTTCTTTTTTC

Found at i:311 original size:11 final size:11

Alignment explanation


    Indices: 273--325  Score: 56
    Period size: 11  Copynumber: 4.9  Consensus size: 11

        263 ACCTTCTTCC

                 *     
        273 TTCTTCTTTCT
          1 TTCTTTTTTCT

                        
        284 TTCTTTCTTTC-
          1 TTCTTT-TTTCT

                       
        295 -TCTTTTTTCT
          1 TTCTTTTTTCT

                      *
        305 TTCTTTTTTCC
          1 TTCTTTTTTCT

               *      
        316 TTCATTTTTC
          1 TTCTTTTTTC

        326 GTTTGTCCCC


Statistics
Matches: 36,  Mismatches: 3, Indels: 6
        0.80            0.07        0.13

Matches are distributed among these distances:
   9    4  0.11
  10    5  0.14
  11   23  0.64
  12    4  0.11

ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74


Consensus pattern (11 bp):   
TTCTTTTTTCT

Found at i:323 original size:21 final size:21

Alignment explanation


    Indices: 269--323  Score: 60
    Period size: 21  Copynumber: 2.5  Consensus size: 21

        259 ATTCACCTTC

                                   
        269 TTCCTTCTTCTTTCTTTCTTTCT
          1 TTCCTTC-T-TTTCTTTCTTTCT

                                  
        292 TTCTCTT-TTTTCTTTCTTT-T
          1 TTC-CTTCTTTTCTTTCTTTCT

                        
        312 TTCCTTCATTTT
          1 TTCCTTC-TTTT

        324 TCGTTTGTCC


Statistics
Matches: 29,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
  19    3  0.10
  20    4  0.14
  21   15  0.52
  22    1  0.03
  23    3  0.10
  24    3  0.10

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


Consensus pattern (21 bp):   
TTCCTTCTTTTCTTTCTTTCT
Done.