Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012802.1 Kokia drynarioides strain JFW-HI SEQ_127815, 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: 7679
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:2105 original size:48 final size:48

Alignment explanation


    Indices: 2053--2148  Score: 174
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       2043 TATGTATTCC

                                                *           
       2053 GGTTACCAATCTGAAACTCGAGTATAGTTTAGATCGTTTATTCGTGAT
          1 GGTTACCAATCTGAAACTCGAGTATAGTTTAGATCGCTTATTCGTGAT

                      *                                     
       2101 GGTTACCAATTTGAAACTCGAGTATAGTTTAGATCGCTTATTCGTGAT
          1 GGTTACCAATCTGAAACTCGAGTATAGTTTAGATCGCTTATTCGTGAT

       2149 CTAATTGGGT


Statistics
Matches: 46,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  48   46  1.00

ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38


Consensus pattern (48 bp):   
GGTTACCAATCTGAAACTCGAGTATAGTTTAGATCGCTTATTCGTGAT

Found at i:3272 original size:17 final size:18

Alignment explanation


    Indices: 3250--3284  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

       3240 TAATATTTAA

                              
       3250 TACATTTT-TAATATATT
          1 TACATTTTATAATATATT

                         *    
       3267 TACATTTTATAATTTATT
          1 TACATTTTATAATATATT

       3285 CATACACTTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    8  0.50
  18    8  0.50

ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60


Consensus pattern (18 bp):   
TACATTTTATAATATATT

Found at i:3273 original size:26 final size:23

Alignment explanation


    Indices: 3223--3281  Score: 55
    Period size: 26  Copynumber: 2.4  Consensus size: 23

       3213 TATTTTTAAA

                                *   
       3223 TAATAGATTTTTAATATTAATATT
          1 TAATA-ATTTTTAATATTAACATT

                                *     
       3247 TAATACATTTTTAATATATTTACATT
          1 TAATA-ATTTTT-A-ATATTAACATT

             *       
       3273 TTATAATTT
          1 TAATAATTT

       3282 ATTCATACAC


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  24   11  0.38
  25    5  0.17
  26   13  0.45

ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56


Consensus pattern (23 bp):   
TAATAATTTTTAATATTAACATT

Found at i:6286 original size:24 final size:24

Alignment explanation


    Indices: 6236--6285  Score: 68
    Period size: 23  Copynumber: 2.1  Consensus size: 24

       6226 ATAATTTTTT

                              *     
       6236 AAATCTAAAAACATACAACAAATA
          1 AAATCTAAAAACATACAAAAAATA

                                     
       6260 AAAT-TAAAAA-ATATCAAAAAATA
          1 AAATCTAAAAACATA-CAAAAAATA

               
       6283 AAA
          1 AAA

       6286 AACAGTCAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  22    3  0.12
  23   17  0.71
  24    4  0.17

ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18


Consensus pattern (24 bp):   
AAATCTAAAAACATACAAAAAATA

Found at i:6568 original size:32 final size:32

Alignment explanation


    Indices: 6512--6598  Score: 81
    Period size: 32  Copynumber: 2.7  Consensus size: 32

       6502 ATATTTAGTT

                             *  *             
       6512 TTTTTAATTTTT-TTTTGAAATTTTA-ACTAAAC
          1 TTTTT-ATTTTTATTTTCAATTTTTATA-TAAAC

                                         ** 
       6544 TTTTTATTTTTATTTTCAATTTTTATATATGC
          1 TTTTTATTTTTATTTTCAATTTTTATATAAAC

                                    
       6576 -TTTTATTTATTTATTTTCAATTT
          1 TTTTTA-TT-TTTATTTTCAATTT

       6599 ACATATTCTT


Statistics
Matches: 47,  Mismatches: 4, Indels: 7
        0.81            0.07        0.12

Matches are distributed among these distances:
  31   11  0.23
  32   21  0.45
  33   15  0.32

ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67


Consensus pattern (32 bp):   
TTTTTATTTTTATTTTCAATTTTTATATAAAC

Found at i:6610 original size:31 final size:30

Alignment explanation


    Indices: 6545--6635  Score: 96
    Period size: 31  Copynumber: 2.9  Consensus size: 30

       6535 TAACTAAACT

                                     *      
       6545 TTTTA-TTTTTATTTTCAATTTTTATATATGC
          1 TTTTATTTTTTATTTTCAA--TTTACATATGC

                                         * 
       6576 TTTTATTTATTTATTTTCAATTTACATATTC
          1 TTTTATTT-TTTATTTTCAATTTACATATGC

                                *         
       6607 TTTT-TGGTTTTTATTTTCATTTTACATAT
          1 TTTTAT--TTTTTATTTTCAATTTACATAT

       6636 ATATATATTT


Statistics
Matches: 53,  Mismatches: 3, Indels: 8
        0.83            0.05        0.12

Matches are distributed among these distances:
  30    1  0.02
  31   37  0.70
  32    4  0.08
  33   11  0.21

ACGTcount: A:0.22, C:0.08, G:0.03, T:0.67


Consensus pattern (30 bp):   
TTTTATTTTTTATTTTCAATTTACATATGC
Done.