Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006378.1 Kokia drynarioides strain JFW-HI SEQ_120954, 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: 18002
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35


Found at i:3035 original size:13 final size:13

Alignment explanation


    Indices: 3019--3090  Score: 56
    Period size: 14  Copynumber: 5.4  Consensus size: 13

       3009 TCTAAATTTA

                     *   
       3019 ATATTTAATCTTT
          1 ATATTTAATTTTT

                          
       3032 ATATTTTAATTTTT
          1 ATA-TTTAATTTTT

                *   *   *
       3046 A-ATATAAATTTA
          1 ATATTTAATTTTT

             *           
       3058 ACATTTAATTTTT
          1 ATATTTAATTTTT

                          *
       3071 ATATTTTAACTTTTA
          1 ATA-TTTAA-TTTTT

                 
       3086 ATATT
          1 ATATT

       3091 GTTAAGCCTT


Statistics
Matches: 46,  Mismatches: 9, Indels: 7
        0.74            0.15        0.11

Matches are distributed among these distances:
  12    8  0.17
  13   14  0.30
  14   17  0.37
  15    7  0.15

ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60


Consensus pattern (13 bp):   
ATATTTAATTTTT

Found at i:3054 original size:39 final size:39

Alignment explanation


    Indices: 3011--3089  Score: 131
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       3001 TTATCATATC

                     *                    *        
       3011 TAAATTTAATATTTAATCTTTATATTTTAATTTTTAATA
          1 TAAATTTAACATTTAATCTTTATATTTTAACTTTTAATA

                             *                     
       3050 TAAATTTAACATTTAATTTTTATATTTTAACTTTTAATA
          1 TAAATTTAACATTTAATCTTTATATTTTAACTTTTAATA

             
       3089 T
          1 T

       3090 TGTTAAGCCT


Statistics
Matches: 37,  Mismatches: 3, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  39   37  1.00

ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58


Consensus pattern (39 bp):   
TAAATTTAACATTTAATCTTTATATTTTAACTTTTAATA

Found at i:4232 original size:19 final size:18

Alignment explanation


    Indices: 4182--4232  Score: 50
    Period size: 19  Copynumber: 2.7  Consensus size: 18

       4172 TTAAATATTT

                              
       4182 AAAAATTAAAAATTTATA
          1 AAAAATTAAAAATTTATA

                 *              
       4200 AAAATCTTATAAAA-TTATA
          1 AAAA-ATTA-AAAATTTATA

                          
       4219 AAGAAATTACAAAA
          1 AA-AAATTA-AAAA

       4233 AATATATGTC


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    4  0.15
  19   17  0.63
  20    6  0.22

ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29


Consensus pattern (18 bp):   
AAAAATTAAAAATTTATA

Found at i:4756 original size:24 final size:23

Alignment explanation


    Indices: 4729--4777  Score: 71
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       4719 TTTTTTCTAA

                   *                
       4729 TTTTTATTTGTCTTTGTGACACGC
          1 TTTTTATCTGTC-TTGTGACACGC

                 *                 
       4753 TTTTTCTCTGTCTTGTGACACGC
          1 TTTTTATCTGTCTTGTGACACGC

              
       4776 TT
          1 TT

       4778 CTGCCTTTTG


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  23   13  0.57
  24   10  0.43

ACGTcount: A:0.10, C:0.20, G:0.16, T:0.53


Consensus pattern (23 bp):   
TTTTTATCTGTCTTGTGACACGC

Found at i:4820 original size:17 final size:18

Alignment explanation


    Indices: 4798--4832  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

       4788 GCACGTTTTC

                              
       4798 ATCTACATTCGT-GATAG
          1 ATCTACATTCGTGGATAG

                  *           
       4815 ATCTACGTTCGTGGATAG
          1 ATCTACATTCGTGGATAG

       4833 TTTTCTCACA


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

Matches are distributed among these distances:
  17   11  0.69
  18    5  0.31

ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34


Consensus pattern (18 bp):   
ATCTACATTCGTGGATAG

Found at i:13756 original size:21 final size:21

Alignment explanation


    Indices: 13732--13772  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      13722 ATAATAATTT

                                  
      13732 TAAAT-TTTTATGATATAAAAA
          1 TAAATATTTTAT-ATATAAAAA

                          *     
      13753 TAAATATTTTATATTTAAAA
          1 TAAATATTTTATATATAAAA

      13773 TAGTGAAAAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21   12  0.67
  22    6  0.33

ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46


Consensus pattern (21 bp):   
TAAATATTTTATATATAAAAA
Done.