Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006741.1 Kokia drynarioides strain JFW-HI SEQ_121339, 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: 5734
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35


Found at i:2090 original size:9 final size:9

Alignment explanation


    Indices: 2076--2119  Score: 54
    Period size: 9  Copynumber: 5.0  Consensus size: 9

       2066 TCTCTCTTTC

                     
       2076 TATTTTTTT
          1 TATTTTTTT

                    *
       2085 TA-TTTTTC
          1 TATTTTTTT

                    *
       2093 TATTTTTTC
          1 TATTTTTTT

                     
       2102 TATTTTTTT
          1 TATTTTTTT

             *       
       2111 TCTTTTTTT
          1 TATTTTTTT

       2120 CTTCTTTTTT


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
   8    7  0.23
   9   24  0.77

ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84


Consensus pattern (9 bp):   
TATTTTTTT

Found at i:2094 original size:17 final size:17

Alignment explanation


    Indices: 2072--2140  Score: 72
    Period size: 17  Copynumber: 4.2  Consensus size: 17

       2062 TTGCTCTCTC

                             
       2072 TTTCTATTTTTTTTATT
          1 TTTCTATTTTTTTTATT

                        *    
       2089 TTTCTATTTTTTCTATT
          1 TTTCTATTTTTTTTATT

                    *        
       2106 TTT-T-TTCTTTTT-TT
          1 TTTCTATTTTTTTTATT

            *    *            
       2120 CTTCTTTTTTTTTGTATT
          1 TTTCTATTTTTTT-TATT

               
       2138 TTT
          1 TTT

       2141 TTCTTTATTT


Statistics
Matches: 42,  Mismatches: 6, Indels: 7
        0.76            0.11        0.13

Matches are distributed among these distances:
  14    4  0.10
  15    7  0.17
  16    7  0.17
  17   20  0.48
  18    4  0.10

ACGTcount: A:0.07, C:0.09, G:0.01, T:0.83


Consensus pattern (17 bp):   
TTTCTATTTTTTTTATT

Found at i:2111 original size:11 final size:11

Alignment explanation


    Indices: 2087--2142  Score: 66
    Period size: 11  Copynumber: 5.4  Consensus size: 11

       2077 ATTTTTTTTA

                       
       2087 TTTTTCTA--T
          1 TTTTTCTATTT

                       
       2096 TTTTTCTATTT
          1 TTTTTCTATTT

                       
       2107 TTTTTCT-TTT
          1 TTTTTCTATTT

                        
       2117 TTTCTTCT-TTT
          1 TTT-TTCTATTT

                 *     
       2128 TTTTTGTATTT
          1 TTTTTCTATTT

                
       2139 TTTT
          1 TTTT

       2143 CTTTATTTAA


Statistics
Matches: 42,  Mismatches: 1, Indels: 6
        0.86            0.02        0.12

Matches are distributed among these distances:
   9    8  0.19
  10    9  0.21
  11   25  0.60

ACGTcount: A:0.05, C:0.09, G:0.02, T:0.84


Consensus pattern (11 bp):   
TTTTTCTATTT

Found at i:5278 original size:12 final size:12

Alignment explanation


    Indices: 5261--5285  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       5251 TTGCCAACGA

                        
       5261 GCAACTCTTCCT
          1 GCAACTCTTCCT

                        
       5273 GCAACTCTTCCT
          1 GCAACTCTTCCT

             
       5285 G
          1 G

       5286 ACAATGATGG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.16, C:0.40, G:0.12, T:0.32


Consensus pattern (12 bp):   
GCAACTCTTCCT
Done.