Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008375.1 Kokia drynarioides strain JFW-HI SEQ_123042, 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: 2494
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37


Found at i:239 original size:3 final size:3

Alignment explanation


    Indices: 233--286  Score: 72
    Period size: 3  Copynumber: 17.7  Consensus size: 3

        223 ATCATTAAAA

                         *  * *                                         
        233 ATT ATT ATT AGT GTC ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT

                      
        279 ATT ATT AT
          1 ATT ATT AT

        287 ATAAATATTA


Statistics
Matches: 44,  Mismatches: 6, Indels: 2
        0.85            0.12        0.04

Matches are distributed among these distances:
   3   41  0.93
   4    3  0.07

ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61


Consensus pattern (3 bp):   
ATT

Found at i:253 original size:15 final size:13

Alignment explanation


    Indices: 232--296  Score: 67
    Period size: 15  Copynumber: 4.6  Consensus size: 13

        222 CATCATTAAA

                           
        232 AATTATTATTAGTGT
          1 AATTATTATTA-T-T

            *            
        247 CATTATTATTATT
          1 AATTATTATTATT

                           
        260 ATTATTATTATTATT
          1 A--ATTATTATTATT

                          
        275 AATTATTATTATAT
          1 AATTATTATTAT-T

              *     
        289 AAATATTA
          1 AATTATTA

        297 ATAATAATAT


Statistics
Matches: 44,  Mismatches: 3, Indels: 7
        0.81            0.06        0.13

Matches are distributed among these distances:
  13   12  0.27
  14    9  0.20
  15   23  0.52

ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57


Consensus pattern (13 bp):   
AATTATTATTATT

Found at i:1010 original size:23 final size:23

Alignment explanation


    Indices: 971--1021  Score: 59
    Period size: 22  Copynumber: 2.2  Consensus size: 23

        961 TTAATTTAAT

                 *            *    
        971 TTTAACTTAAAATAAACTTAT-A
          1 TTTAAATTAAAATAAACTCATAA

                       *            
        993 TTTAAATTAAATTCAAACTCATAA
          1 TTTAAATTAAAAT-AAACTCATAA

                 
       1017 TTTAA
          1 TTTAA

       1022 TTTTGAATTT


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

Matches are distributed among these distances:
  22   11  0.46
  23    7  0.29
  24    6  0.25

ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41


Consensus pattern (23 bp):   
TTTAAATTAAAATAAACTCATAA

Found at i:1023 original size:23 final size:21

Alignment explanation


    Indices: 971--1023  Score: 52
    Period size: 23  Copynumber: 2.3  Consensus size: 21

        961 TTAATTTAAT

                              *   
        971 TTTAACTTAAAATAAACTTATA
          1 TTTAA-TTAAAATAAACTCATA

                       *            
        993 TTTAAATTAAATTCAAACTCATAA
          1 TTT-AATTAAAAT-AAACTCAT-A

                   
       1017 TTTAATT
          1 TTTAATT

       1024 TTGAATTTAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  22    9  0.35
  23   13  0.50
  24    4  0.15

ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43


Consensus pattern (21 bp):   
TTTAATTAAAATAAACTCATA
Done.