Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001088.1 Kokia drynarioides strain JFW-HI SEQ_112348, 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, 948

Length: 1581
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


Found at i:157 original size:9 final size:9

Alignment explanation


    Indices: 143--190  Score: 55
    Period size: 9  Copynumber: 5.2  Consensus size: 9

        133 GCAAATGATT

                     
        143 TTAAAATTA
          1 TTAAAATTA

                     
        152 TTAAAATTA
          1 TTAAAATTA

                        
        161 TTTTTAAAA-TA
          1 ---TTAAAATTA

                     
        172 -TAAAATTA
          1 TTAAAATTA

                     
        180 TTAAAATTA
          1 TTAAAATTA

              
        189 TT
          1 TT

        191 TTTTTGACAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 10
        0.77            0.00        0.23

Matches are distributed among these distances:
   7    5  0.15
   8    2  0.06
   9   19  0.56
  11    2  0.06
  12    6  0.18

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


Consensus pattern (9 bp):   
TTAAAATTA

Found at i:177 original size:19 final size:21

Alignment explanation


    Indices: 141--181  Score: 68
    Period size: 19  Copynumber: 2.0  Consensus size: 21

        131 CAGCAAATGA

                                 
        141 TTTTAAAATTATTAAAATTAT
          1 TTTTAAAATTATTAAAATTAT

                                 
        162 TTTTAAAA-TA-TAAAATTAT
          1 TTTTAAAATTATTAAAATTAT

             
        181 T
          1 T

        182 AAAATTATTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  19   10  0.50
  20    2  0.10
  21    8  0.40

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (21 bp):   
TTTTAAAATTATTAAAATTAT

Found at i:994 original size:89 final size:91

Alignment explanation


    Indices: 878--1045  Score: 261
    Period size: 89  Copynumber: 1.9  Consensus size: 91

        868 AAAAATGGAG

                  *  *                                          *            
        878 GAATTTTGGGGGTTTTCGAGAAAGAAAATGAGAAAGCATGAGATTATGTAAGGAAAA-AAA-TTT
          1 GAATTTAGGAGGTTTTCGAGAAAGAAAATGAGAAAGCATGAGATTATGTAAGAAAAACAAATTTT

                                      
        941 TTGGTGTTTGGTTTAGGGTTTAGGGT
         66 TTGGTGTTTGGTTTAGGGTTTAGGGT

                                                     *                       
        967 GAATTTAGGAGGTTTTC-AGGAAAGAAAATGAGAAAGCATGGGATTATGTAAGAAAAACAAATTT
          1 GAATTTAGGAGGTTTTCGA-GAAAGAAAATGAGAAAGCATGAGATTATGTAAGAAAAACAAA-TT

                           
       1031 TTTTGGTGTTTGGTT
         64 TTTTGGTGTTTGGTT

       1046 GTTAAGAAAA


Statistics
Matches: 71,  Mismatches: 4, Indels: 5
        0.89            0.05        0.06

Matches are distributed among these distances:
  88    1  0.01
  89   51  0.72
  90    3  0.04
  92   16  0.23

ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33


Consensus pattern (91 bp):   
GAATTTAGGAGGTTTTCGAGAAAGAAAATGAGAAAGCATGAGATTATGTAAGAAAAACAAATTTT
TTGGTGTTTGGTTTAGGGTTTAGGGT

Found at i:1183 original size:29 final size:31

Alignment explanation


    Indices: 1120--1192  Score: 105
    Period size: 29  Copynumber: 2.4  Consensus size: 31

       1110 ATTAAAATTA

                                           
       1120 TTTAATAATTTTATTATTTCAAAAAAACAAT
          1 TTTAATAATTTTATTATTTCAAAAAAACAAT

                   *            *      *   
       1151 TTTAATATTTTTA-TATTT-TAAAAAATAAT
          1 TTTAATAATTTTATTATTTCAAAAAAACAAT

                         
       1180 TTTAATAATTTTA
          1 TTTAATAATTTTA

       1193 AAATCATTTG


Statistics
Matches: 38,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  29   21  0.55
  30    5  0.13
  31   12  0.32

ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52


Consensus pattern (31 bp):   
TTTAATAATTTTATTATTTCAAAAAAACAAT
Done.