Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005836.1 Kokia drynarioides strain JFW-HI SEQ_120127, 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: 7893
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30


Found at i:1212 original size:29 final size:31

Alignment explanation


    Indices: 1180--1254  Score: 84
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       1170 ATTTTAAACG

                                *          
       1180 AACTTTAAATAAAAA-TT-ATATAACTCAAT
          1 AACTTTAAATAAAAACTTCAAATAACTCAAT

                                      *  *  
       1209 AACTTT-AATAAAAACTTTCAAATAATTCTAT
          1 AACTTTAAATAAAAAC-TTCAAATAACTCAAT

                     *     
       1240 AACTTTAAAAAAAAA
          1 AACTTTAAATAAAAA

       1255 AAAACACCAT


Statistics
Matches: 38,  Mismatches: 4, Indels: 5
        0.81            0.09        0.11

Matches are distributed among these distances:
  28    8  0.21
  29    6  0.16
  30    2  0.05
  31   15  0.39
  32    7  0.18

ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33


Consensus pattern (31 bp):   
AACTTTAAATAAAAACTTCAAATAACTCAAT

Found at i:1484 original size:13 final size:13

Alignment explanation


    Indices: 1466--1492  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       1456 ATATGAAACC

                         
       1466 AATATAACCAGAT
          1 AATATAACCAGAT

                         
       1479 AATATAACCAGAT
          1 AATATAACCAGAT

             
       1492 A
          1 A

       1493 TCAAAATCAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22


Consensus pattern (13 bp):   
AATATAACCAGAT

Found at i:7239 original size:59 final size:60

Alignment explanation


    Indices: 7137--7285  Score: 180
    Period size: 60  Copynumber: 2.5  Consensus size: 60

       7127 TTTAGGTCCT

                  *                                                      
       7137 TTAAAAGTTGATAAAA-AAAAATTTGGACCCTTAAAAGCTAAAAA-TTTTTTTGGA-CCCC
          1 TTAAAAATTGA-AAAACAAAAATTTGGACCCTTAAAAGCTAAAAATTTTTTTTGGAGCCCC

                      *                 * *       *                       
       7195 TTAAAAATTTTAAAAACAAAAATTT-GAGCTTTAAAAGTTAAAAAATTTTTTTTGGAGCCCC
          1 TTAAAAA-TTGAAAAACAAAAATTTGGACCCTTAAAAGCT-AAAAATTTTTTTTGGAGCCCC

                              * *         
       7256 TTAAAAATTGAAAAACAATATTTTGGACCC
          1 TTAAAAATTGAAAAACAAAAATTTGGACCC

       7286 CTTTTAGCCT


Statistics
Matches: 75,  Mismatches: 10, Indels: 9
        0.80            0.11        0.10

Matches are distributed among these distances:
  58   21  0.28
  59   16  0.21
  60   24  0.32
  61   14  0.19

ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33


Consensus pattern (60 bp):   
TTAAAAATTGAAAAACAAAAATTTGGACCCTTAAAAGCTAAAAATTTTTTTTGGAGCCCC

Found at i:7270 original size:60 final size:58

Alignment explanation


    Indices: 7119--7285  Score: 178
    Period size: 58  Copynumber: 2.8  Consensus size: 58

       7109 AAAGTTGGAG

                           *  *      *                                  
       7119 AAAATTTTTTTAGG-TCCTTTAAAAGTTGATAAAA-AAAAATTTGGACCCTTAAAAGCTA
          1 AAAATTTTTTT-GGACCCCTTAAAAATTGA-AAAACAAAAATTTGGACCCTTAAAAGCTA

                                        *                 * *       *   
       7177 AAAATTTTTTTGGACCCCTTAAAAATTTTAAAAACAAAAATTT-GAGCTTTAAAAGTTAA
          1 AAAATTTTTTTGGACCCCTTAAAAA-TTGAAAAACAAAAATTTGGACCCTTAAAAGCT-A

                                                  * *         
       7236 AAAATTTTTTTTGGAGCCCCTTAAAAATTGAAAAACAATATTTTGGACCC
          1 AAAA-TTTTTTTGGA-CCCCTTAAAAATTGAAAAACAAAAATTTGGACCC

       7286 CTTTTAGCCT


Statistics
Matches: 90,  Mismatches: 12, Indels: 11
        0.80            0.11        0.10

Matches are distributed among these distances:
  57    2  0.02
  58   34  0.38
  59   16  0.18
  60   24  0.27
  61   14  0.16

ACGTcount: A:0.43, C:0.12, G:0.11, T:0.35


Consensus pattern (58 bp):   
AAAATTTTTTTGGACCCCTTAAAAATTGAAAAACAAAAATTTGGACCCTTAAAAGCTA
Done.