Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006613.1 Kokia drynarioides strain JFW-HI SEQ_121203, 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: 13006
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33


Found at i:1011 original size:11 final size:11

Alignment explanation


    Indices: 982--1015  Score: 50
    Period size: 11  Copynumber: 3.0  Consensus size: 11

        972 CACGTTTAAA

                        
        982 AGCTCGTTTATT
          1 AGCTCGTTTA-T

            *          
        994 GGCTCGTTTAT
          1 AGCTCGTTTAT

                       
       1005 AGCTCGTTTAT
          1 AGCTCGTTTAT

       1016 TTATTAATGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  11   11  0.55
  12    9  0.45

ACGTcount: A:0.15, C:0.18, G:0.21, T:0.47


Consensus pattern (11 bp):   
AGCTCGTTTAT

Found at i:1143 original size:12 final size:12

Alignment explanation


    Indices: 1128--1169  Score: 52
    Period size: 12  Copynumber: 3.6  Consensus size: 12

       1118 GTTTAATTAT

                        
       1128 ATGTTCGTGAAC
          1 ATGTTCGTGAAC

                      *  
       1140 ATGTTCGAT-TA-
          1 ATGTTCG-TGAAC

                        
       1151 ATGTTCGTGAAC
          1 ATGTTCGTGAAC

                   
       1163 ATGTTCG
          1 ATGTTCG

       1170 ATTAAGTTAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 6
        0.76            0.06        0.18

Matches are distributed among these distances:
  10    1  0.04
  11    8  0.32
  12   15  0.60
  13    1  0.04

ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38


Consensus pattern (12 bp):   
ATGTTCGTGAAC

Found at i:1158 original size:23 final size:23

Alignment explanation


    Indices: 1105--1191  Score: 104
    Period size: 23  Copynumber: 3.7  Consensus size: 23

       1095 TCGTTAACAT

                       *    **      
       1105 TGTTCGTGAACGTGTTTAATTATA
          1 TGTTCGTGAACATGTTCGATTA-A

                                   
       1129 TGTTCGTGAACATGTTCGATTAA
          1 TGTTCGTGAACATGTTCGATTAA

                                   
       1152 TGTTCGTGAACATGTTCGATTAA
          1 TGTTCGTGAACATGTTCGATTAA

                 **           
       1175 -GTTAAATGAACATGTTC
          1 TGTT-CGTGAACATGTTC

       1192 ATGAACATTA


Statistics
Matches: 57,  Mismatches: 5, Indels: 3
        0.88            0.08        0.05

Matches are distributed among these distances:
  22    3  0.05
  23   35  0.61
  24   19  0.33

ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40


Consensus pattern (23 bp):   
TGTTCGTGAACATGTTCGATTAA

Found at i:1202 original size:23 final size:23

Alignment explanation


    Indices: 1158--1203  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1148 TTAATGTTCG

                          *  *     
       1158 TGAACATGTTCGATTAAGTTAAA
          1 TGAACATGTTCGATGAAATTAAA

                                    
       1181 TGAACATGTTC-ATGAACATTAAA
          1 TGAACATGTTCGATGAA-ATTAAA

       1204 CAAACGAACA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  22    4  0.20
  23   16  0.80

ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33


Consensus pattern (23 bp):   
TGAACATGTTCGATGAAATTAAA

Found at i:11551 original size:18 final size:18

Alignment explanation


    Indices: 11510--11554  Score: 56
    Period size: 20  Copynumber: 2.4  Consensus size: 18

      11500 ATTAAATAAA

                               
      11510 AATTATTAAAAATGTTGAC
          1 AATTATTAAAAATGTT-AC

                      *        
      11529 AATTATGTAATAATGTT-C
          1 AATTAT-TAAAAATGTTAC

                    
      11547 AATTATTA
          1 AATTATTA

      11555 TTTTTTTTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  17    2  0.08
  18    7  0.29
  19    6  0.25
  20    9  0.38

ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42


Consensus pattern (18 bp):   
AATTATTAAAAATGTTAC
Done.