Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008755.1 Kokia drynarioides strain JFW-HI SEQ_123438, 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: 12124
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36


Found at i:1257 original size:2 final size:2

Alignment explanation


    Indices: 1250--1276  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1240 TTGTCATTAG

                                                    
       1250 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1277 TAAAAGAAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:1820 original size:17 final size:17

Alignment explanation


    Indices: 1798--1832  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       1788 TTTTCCTAAA

                        *    
       1798 AATGACTAAATTGTGTG
          1 AATGACTAAATTATGTG

                   *         
       1815 AATGACTCAATTATGTG
          1 AATGACTAAATTATGTG

             
       1832 A
          1 A

       1833 TTTAATATGA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34


Consensus pattern (17 bp):   
AATGACTAAATTATGTG

Found at i:3068 original size:21 final size:21

Alignment explanation


    Indices: 3039--3115  Score: 93
    Period size: 21  Copynumber: 3.7  Consensus size: 21

       3029 GGAGTTTTTA

                            *    
       3039 GTATCGGTAGAAGTATGACTT
          1 GTATCGGTAGAAGTATCACTT

              *          *        
       3060 GTTTCGGTAGAA-AAGTCACTT
          1 GTATCGGTAGAAGTA-TCACTT

                        *  *     
       3081 GTATCGGTAGAACTAACACTT
          1 GTATCGGTAGAAGTATCACTT

                          
       3102 GTATCGGTAGAAGT
          1 GTATCGGTAGAAGT

       3116 CTGCACTACT


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

Matches are distributed among these distances:
  20    1  0.02
  21   45  0.96
  22    1  0.02

ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31


Consensus pattern (21 bp):   
GTATCGGTAGAAGTATCACTT

Found at i:5248 original size:29 final size:29

Alignment explanation


    Indices: 5194--5250  Score: 71
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       5184 ACTATCGACA

                             *   *       
       5194 CCACATGGGCGTGTGGTGGACCGTGTGAG
          1 CCACATGGGCGTGTGGTAGACAGTGTGAG

                    *                    
       5223 CCACATGGTCGTGTGGTA-AGCAGTGTGA
          1 CCACATGGGCGTGTGGTAGA-CAGTGTGA

       5251 TGGATCGTGT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  28    1  0.04
  29   23  0.96

ACGTcount: A:0.18, C:0.19, G:0.40, T:0.23


Consensus pattern (29 bp):   
CCACATGGGCGTGTGGTAGACAGTGTGAG

Found at i:6103 original size:14 final size:14

Alignment explanation


    Indices: 6076--6118  Score: 77
    Period size: 14  Copynumber: 3.0  Consensus size: 14

       6066 ACTGCACTGT

                           
       6076 TATAATCACAATGAA
          1 TATAATC-CAATGAA

                          
       6091 TATAATCCAATGAA
          1 TATAATCCAATGAA

                          
       6105 TATAATCCAATGAA
          1 TATAATCCAATGAA

       6119 GAAGTGCCAC


Statistics
Matches: 28,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  14   21  0.75
  15    7  0.25

ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28


Consensus pattern (14 bp):   
TATAATCCAATGAA

Found at i:11685 original size:18 final size:19

Alignment explanation


    Indices: 11653--11689  Score: 58
    Period size: 18  Copynumber: 2.0  Consensus size: 19

      11643 ACTAAAATCA

                      *        
      11653 TATTTAATTTTTTTGTTAC
          1 TATTTAATTTATTTGTTAC

                               
      11672 TATTT-ATTTATTTGTTAC
          1 TATTTAATTTATTTGTTAC

      11690 GTAAAAATTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18   12  0.71
  19    5  0.29

ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68


Consensus pattern (19 bp):   
TATTTAATTTATTTGTTAC
Done.