Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014821.1 Kokia drynarioides strain JFW-HI SEQ_129863, 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: 35115
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35

Warning! 156 characters in sequence are not A, C, G, or T


Found at i:10029 original size:19 final size:20

Alignment explanation


    Indices: 10002--10040  Score: 53
    Period size: 19  Copynumber: 2.0  Consensus size: 20

       9992 GGAGATTTTT

                                
      10002 AAATAAATTAATGTGTTATA
          1 AAATAAATTAATGTGTTATA

                     *    *     
      10022 AAAT-AATTTATGTTTTATA
          1 AAATAAATTAATGTGTTATA

      10041 GATATATTAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   13  0.76
  20    4  0.24

ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46


Consensus pattern (20 bp):   
AAATAAATTAATGTGTTATA

Found at i:16144 original size:19 final size:20

Alignment explanation


    Indices: 16102--16144  Score: 52
    Period size: 19  Copynumber: 2.2  Consensus size: 20

      16092 TTGTTGAGGT

                   *       *   *
      16102 ATATTGTTATTGTGATGATT
          1 ATATTGTGATTGTGAAGATG

                                
      16122 ATATTGTGA-TGTGAAGATG
          1 ATATTGTGATTGTGAAGATG

                
      16141 ATAT
          1 ATAT

      16145 GATTGAGGTT


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  19   12  0.60
  20    8  0.40

ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47


Consensus pattern (20 bp):   
ATATTGTGATTGTGAAGATG

Found at i:17418 original size:15 final size:13

Alignment explanation


    Indices: 17388--17429  Score: 50
    Period size: 13  Copynumber: 3.2  Consensus size: 13

      17378 GCTCCTTCCA

                      *  
      17388 TTTTC-TCTTATT
          1 TTTTCTTCTTCTT

                  *       
      17400 TTTCTCCTCTTCTT
          1 TTT-TCTTCTTCTT

                         
      17414 TTTTCTTCTTCTT
          1 TTTTCTTCTTCTT

               
      17427 TTT
          1 TTT

      17430 CATGCCCTCT


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  12    3  0.12
  13   14  0.54
  14    9  0.35

ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74


Consensus pattern (13 bp):   
TTTTCTTCTTCTT

Found at i:31226 original size:21 final size:21

Alignment explanation


    Indices: 31202--31243  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      31192 TTTGGGTTTG

                     *           
      31202 AAATAAAATTTAAAAATTAAA
          1 AAATAAAATATAAAAATTAAA

                          *      
      31223 AAATAAAATATAAAGATTAAA
          1 AAATAAAATATAAAAATTAAA

      31244 GATGACCAGA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26


Consensus pattern (21 bp):   
AAATAAAATATAAAAATTAAA
Done.