Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008015.1 Kokia drynarioides strain JFW-HI SEQ_122669, 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: 1905
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38


Found at i:471 original size:3 final size:3

Alignment explanation


    Indices: 412--453  Score: 84
    Period size: 3  Copynumber: 14.0  Consensus size: 3

        402 TTATTAATGT

                                                                   
        412 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

        454 GTAGCACATT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   39  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:1187 original size:18 final size:18

Alignment explanation


    Indices: 1166--1263  Score: 89
    Period size: 17  Copynumber: 5.6  Consensus size: 18

       1156 TAATAAGTTT

                       *    * 
       1166 TAAATTTAAATATAAATC
          1 TAAATTTAAATTTAAAAC

                               
       1184 TAAATTTAAATTTTAAAAC
          1 TAAATTTAAA-TTTAAAAC

                              
       1203 -AAATTTAAATTTAAAA-
          1 TAAATTTAAATTTAAAAC

              *         *     
       1219 TATATTTAAATTCAAAA-
          1 TAAATTTAAATTTAAAAC

             *                 
       1236 TCAATTT-AATCTTAAAA-
          1 TAAATTTAAAT-TTAAAAC

                       
       1253 TAAATCTTAAA
          1 TAAAT-TTAAA

       1264 ATGGGTTTAA


Statistics
Matches: 67,  Mismatches: 8, Indels: 9
        0.80            0.10        0.11

Matches are distributed among these distances:
  16    3  0.04
  17   35  0.52
  18   21  0.31
  19    8  0.12

ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40


Consensus pattern (18 bp):   
TAAATTTAAATTTAAAAC

Found at i:1192 original size:24 final size:24

Alignment explanation


    Indices: 1164--1217  Score: 74
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       1154 TATAATAAGT

                           *         
       1164 TTTAAA-TTTAAATATAAATCTAAA
          1 TTTAAATTTTAAA-ACAAATCTAAA

                               *    
       1188 TTTAAATTTTAAAACAAATTTAAA
          1 TTTAAATTTTAAAACAAATCTAAA

                  
       1212 TTTAAA
          1 TTTAAA

       1218 ATATATTTAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  24   21  0.78
  25    6  0.22

ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43


Consensus pattern (24 bp):   
TTTAAATTTTAAAACAAATCTAAA

Found at i:1219 original size:7 final size:6

Alignment explanation


    Indices: 1164--1230  Score: 57
    Period size: 6  Copynumber: 11.3  Consensus size: 6

       1154 TATAATAAGT

                           *      *                     **          
       1164 TTTAAA TTTAAA TATAAA TCTAAA TTTAAA TTTTAAA -ACAAA TTTAAA
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA

                    *  *           
       1212 TTTAAA -ATATA TTTAAA TT
          1 TTTAAA TTTAAA TTTAAA TT

       1231 CAAAATCAAT


Statistics
Matches: 47,  Mismatches: 11, Indels: 6
        0.73            0.17        0.09

Matches are distributed among these distances:
   5    6  0.13
   6   35  0.74
   7    6  0.13

ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45


Consensus pattern (6 bp):   
TTTAAA
Done.