Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006944.1 Kokia drynarioides strain JFW-HI SEQ_121549, 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: 8512
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37


Found at i:702 original size:66 final size:66

Alignment explanation


    Indices: 596--727  Score: 264
    Period size: 66  Copynumber: 2.0  Consensus size: 66

        586 GCCGACTCTG

                                                                             
        596 AAGCAAATTTCCATCAAGATTAAAGATCTCCTTTTGATTTCTTTGAAGTTTATTATGAGTTTTGT
          1 AAGCAAATTTCCATCAAGATTAAAGATCTCCTTTTGATTTCTTTGAAGTTTATTATGAGTTTTGT

             
        661 T
         66 T

                                                                             
        662 AAGCAAATTTCCATCAAGATTAAAGATCTCCTTTTGATTTCTTTGAAGTTTATTATGAGTTTTGT
          1 AAGCAAATTTCCATCAAGATTAAAGATCTCCTTTTGATTTCTTTGAAGTTTATTATGAGTTTTGT

             
        727 T
         66 T

        728 TTGTTTCTTG


Statistics
Matches: 66,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  66   66  1.00

ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45


Consensus pattern (66 bp):   
AAGCAAATTTCCATCAAGATTAAAGATCTCCTTTTGATTTCTTTGAAGTTTATTATGAGTTTTGT
T

Found at i:2450 original size:2 final size:2

Alignment explanation


    Indices: 2437--2511  Score: 60
    Period size: 2  Copynumber: 37.0  Consensus size: 2

       2427 ATACTGTTAC

                      *              *           *  *          *     *    
       2437 AT AT AT AC AT AT AT AT AC AT AT AT AC AC AT AT AT GT AT GT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                      *                 *  *                
       2479 AT AT AT AC AT AT AT AT AT AC AC AT AT AT CAT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT

       2512 CTGATTCCAC


Statistics
Matches: 58,  Mismatches: 14, Indels: 2
        0.78            0.19        0.03

Matches are distributed among these distances:
   2   56  0.97
   3    2  0.03

ACGTcount: A:0.47, C:0.11, G:0.03, T:0.40


Consensus pattern (2 bp):   
AT

Found at i:2506 original size:10 final size:10

Alignment explanation


    Indices: 2437--2495  Score: 73
    Period size: 10  Copynumber: 5.7  Consensus size: 10

       2427 ATACTGTTAC

                      
       2437 ATATATACAT
          1 ATATATACAT

                      
       2447 ATATATACAT
          1 ATATATACAT

                 *    
       2457 ATATACACAT
          1 ATATATACAT

                    **  
       2467 ATATGTATGTAT
          1 ATA--TATACAT

                      
       2479 ATATATACAT
          1 ATATATACAT

                   
       2489 ATATATA
          1 ATATATA

       2496 TACACATATA


Statistics
Matches: 41,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
  10   34  0.83
  12    7  0.17

ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41


Consensus pattern (10 bp):   
ATATATACAT

Found at i:3472 original size:9 final size:9

Alignment explanation


    Indices: 3458--3482  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

       3448 TATAATTGAC

                     
       3458 ATTATTTTA
          1 ATTATTTTA

                     
       3467 ATTATTTTA
          1 ATTATTTTA

                   
       3476 ATTATTT
          1 ATTATTT

       3483 ATTTGTTACT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (9 bp):   
ATTATTTTA

Found at i:3518 original size:18 final size:20

Alignment explanation


    Indices: 3495--3536  Score: 61
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       3485 TTGTTACTCA

                                
       3495 TTTTAT-TGTT-TACTATAT
          1 TTTTATATGTTGTACTATAT

                          *     
       3513 TTTTATATGTTGTATTATAT
          1 TTTTATATGTTGTACTATAT

                
       3533 TTTT
          1 TTTT

       3537 TTCCTTTTCT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  18    6  0.29
  19    4  0.19
  20   11  0.52

ACGTcount: A:0.21, C:0.02, G:0.07, T:0.69


Consensus pattern (20 bp):   
TTTTATATGTTGTACTATAT

Found at i:5337 original size:23 final size:21

Alignment explanation


    Indices: 5296--5354  Score: 64
    Period size: 23  Copynumber: 2.6  Consensus size: 21

       5286 TTTTCATATA

                               *    
       5296 TTTTAAATTTAGTATTTTTTTTAT
          1 TTTTAAATTTA--A-TTTTATTAT

                                   
       5320 TTTTAGGAATTTAATTTTATTAT
          1 TTTTA--AATTTAATTTTATTAT

                        
       5343 TTTTAAATTTAA
          1 TTTTAAATTTAA

       5355 ATATATAAAT


Statistics
Matches: 32,  Mismatches: 1, Indels: 7
        0.80            0.03        0.17

Matches are distributed among these distances:
  21    7  0.22
  23   13  0.41
  24    6  0.19
  26    6  0.19

ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64


Consensus pattern (21 bp):   
TTTTAAATTTAATTTTATTAT
Done.