Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002726.1 Kokia drynarioides strain JFW-HI SEQ_115029, 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: 4232
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38


Found at i:517 original size:24 final size:24

Alignment explanation


    Indices: 490--552  Score: 76
    Period size: 22  Copynumber: 2.7  Consensus size: 24

        480 GAAATTAAAT

                         *          
        490 TATATATTTTTATTATTGTAAAAA
          1 TATATATTTTTATAATTGTAAAAA

                             *   *  
        514 TATA-A-TTTTATAATTTTAATAA
          1 TATATATTTTTATAATTGTAAAAA

             *               
        536 TTTATATTTTTATAATT
          1 TATATATTTTTATAATT

        553 TTTAAAGTGT


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  22   17  0.52
  23    2  0.06
  24   14  0.42

ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59


Consensus pattern (24 bp):   
TATATATTTTTATAATTGTAAAAA

Found at i:537 original size:9 final size:8

Alignment explanation


    Indices: 514--554  Score: 57
    Period size: 8  Copynumber: 5.1  Consensus size: 8

        504 ATTGTAAAAA

                    
        514 TATAATTT
          1 TATAATTT

                    
        522 TATAATTT
          1 TATAATTT

                     
        530 TAATAA-TT
          1 T-ATAATTT

                *   
        538 TATATTTT
          1 TATAATTT

                    
        546 TATAATTT
          1 TATAATTT

             
        554 T
          1 T

        555 TAAAGTGTTA


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
   7    3  0.10
   8   22  0.76
   9    4  0.14

ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63


Consensus pattern (8 bp):   
TATAATTT

Found at i:553 original size:24 final size:23

Alignment explanation


    Indices: 486--554  Score: 77
    Period size: 24  Copynumber: 3.0  Consensus size: 23

        476 AAGCGAAATT

                             *   *  
        486 AAATTATATATTTTTATTATTGTA
          1 AAATT-TATATTTTTATAATTTTA

                *    *             
        510 AAA-ATATAATTTTATAATTTTA
          1 AAATTTATATTTTTATAATTTTA

                                   
        532 ATAATTTATATTTTTATAATTTT
          1 A-AATTTATATTTTTATAATTTT

        555 TAAAGTGTTA


Statistics
Matches: 37,  Mismatches: 6, Indels: 4
        0.79            0.13        0.09

Matches are distributed among these distances:
  22   16  0.43
  23    2  0.05
  24   19  0.51

ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58


Consensus pattern (23 bp):   
AAATTTATATTTTTATAATTTTA

Found at i:1174 original size:11 final size:11

Alignment explanation


    Indices: 1151--1184  Score: 50
    Period size: 11  Copynumber: 3.0  Consensus size: 11

       1141 GGATGGATCA

                        
       1151 ATTAAATAAATT
          1 ATTAAA-AAATT

                       
       1163 ATTAAAAAATT
          1 ATTAAAAAATT

             *         
       1174 AATAAAAAATT
          1 ATTAAAAAATT

       1185 TAAAGATAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  11   15  0.71
  12    6  0.29

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (11 bp):   
ATTAAAAAATT

Found at i:3515 original size:73 final size:73

Alignment explanation


    Indices: 3436--3595  Score: 248
    Period size: 73  Copynumber: 2.2  Consensus size: 73

       3426 ATATTTTATT

                               ***        *           *                      
       3436 ATATATATCAACAAGTGTTGTGGATTGAATCTTAAATCGATCTATATCAATATCGTTTTAAACAT
          1 ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGATCGATATCAATATCGTTTTAAACAT

                    
       3501 TGTATCAA
         66 TGTATCAA

                                                   *                    *    
       3509 ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGGTCGATATCAATATCGTTTTAGACAT
          1 ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGATCGATATCAATATCGTTTTAAACAT

                    
       3574 TGTATCAA
         66 TGTATCAA

                  *       
       3582 ATATATGTCAACAA
          1 ATATATATCAACAA

       3596 ATGATAAATT


Statistics
Matches: 79,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  73   79  1.00

ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36


Consensus pattern (73 bp):   
ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGATCGATATCAATATCGTTTTAAACAT
TGTATCAA
Done.