Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006736.1 Kokia drynarioides strain JFW-HI SEQ_121334, 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: 16386
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:1107 original size:12 final size:12

Alignment explanation


    Indices: 1090--1124  Score: 52
    Period size: 12  Copynumber: 2.9  Consensus size: 12

       1080 TAGTTGGGGA

                     *  
       1090 GCAGATGCAGAT
          1 GCAGATGCAAAT

                        
       1102 GCAGATGCAAAT
          1 GCAGATGCAAAT

               *       
       1114 GCAAATGCAAA
          1 GCAGATGCAAA

       1125 GGGGTTTGTG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  12   21  1.00

ACGTcount: A:0.43, C:0.17, G:0.26, T:0.14


Consensus pattern (12 bp):   
GCAGATGCAAAT

Found at i:9606 original size:54 final size:54

Alignment explanation


    Indices: 9524--9632  Score: 218
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       9514 ATAACCGGAG

                                                                  
       9524 GCTGGATCTTTGAATATTGATAAAACTCTTCTTCCTTCGACTTTGTTATTTTAT
          1 GCTGGATCTTTGAATATTGATAAAACTCTTCTTCCTTCGACTTTGTTATTTTAT

                                                                  
       9578 GCTGGATCTTTGAATATTGATAAAACTCTTCTTCCTTCGACTTTGTTATTTTAT
          1 GCTGGATCTTTGAATATTGATAAAACTCTTCTTCCTTCGACTTTGTTATTTTAT

             
       9632 G
          1 G

       9633 TTATTTATTT


Statistics
Matches: 55,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  54   55  1.00

ACGTcount: A:0.22, C:0.17, G:0.14, T:0.48


Consensus pattern (54 bp):   
GCTGGATCTTTGAATATTGATAAAACTCTTCTTCCTTCGACTTTGTTATTTTAT

Found at i:9680 original size:17 final size:17

Alignment explanation


    Indices: 9652--9698  Score: 51
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       9642 TTTATTTCGA

                 *            
       9652 CTCTTCAATTTTCTATTT
          1 CTCTTAAATTTTCT-TTT

                        *    
       9670 CT-TTAAATTTTATTTT
          1 CTCTTAAATTTTCTTTT

                    *    
       9686 CTCTTAAAATTTC
          1 CTCTTAAATTTTC

       9699 CCCAGATCAC


Statistics
Matches: 24,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  16    5  0.21
  17   17  0.71
  18    2  0.08

ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60


Consensus pattern (17 bp):   
CTCTTAAATTTTCTTTT

Found at i:12062 original size:51 final size:51

Alignment explanation


    Indices: 11956--12137  Score: 201
    Period size: 51  Copynumber: 3.6  Consensus size: 51

      11946 TTTCATTTAA

                                     *        **   *      *       
      11956 TACTCACGATGACA-TATAGTCATCAGACCTCTTGTTCCGTATAAGAATTCA--
          1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATA-AAGGATTCATT

                      *        *                    * *         
      12007 TACTCACGATAACA-TTGAATCATCGGACCTTTAATCCATCATGGATTCATT
          1 TACTCACGATGACACTT-AGTCATCGGACCTTTAATCCATAAAGGATTCATT

                                        *        *             
      12058 TACTCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATT
          1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT

                                         
      12109 TACTCACGATGACACTTAGTCATCGGACC
          1 TACTCACGATGACACTTAGTCATCGGACC

      12138 CTTTCATTTA


Statistics
Matches: 111,  Mismatches: 16, Indels: 8
        0.82            0.12        0.06

Matches are distributed among these distances:
  49    7  0.06
  50    7  0.06
  51   95  0.86
  52    2  0.02

ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31


Consensus pattern (51 bp):   
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Done.