Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006243.1 Kokia drynarioides strain JFW-HI SEQ_120814, 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: 7122
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32


Found at i:5005 original size:67 final size:66

Alignment explanation


    Indices: 4892--5043  Score: 214
    Period size: 67  Copynumber: 2.3  Consensus size: 66

       4882 ATACCGTATT

                   *                          *      *          *    *       
       4892 TACAATATTAAACTTTTGTAAATGCAAATGAATGGTGATTCTAATATAGTTATCATGGTGATTCC
          1 TACAATACTAAA-TTTTGTAAATGCAAATGAATGATGATTCCAATATAGTTACCATGATGATTCC

              
       4957 AA
         65 AA

                                          *                                * 
       4959 TACAATACTAAGATTTTGTAAATGCAAATGGATGATGATTCCAATATAGTTACCATGATGATTTC
          1 TACAATACTAA-ATTTTGTAAATGCAAATGAATGATGATTCCAATATAGTTACCATGATGATTCC

              
       5024 AA
         65 AA

                              
       5026 TACAATACTAAAATTTTG
          1 TACAATACT-AAATTTTG

       5044 CAAAGAAATG


Statistics
Matches: 76,  Mismatches: 7, Indels: 4
        0.87            0.08        0.05

Matches are distributed among these distances:
  67   73  0.96
  68    3  0.04

ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36


Consensus pattern (66 bp):   
TACAATACTAAATTTTGTAAATGCAAATGAATGATGATTCCAATATAGTTACCATGATGATTCCA
A

Found at i:5061 original size:61 final size:62

Alignment explanation


    Indices: 4914--5064  Score: 180
    Period size: 67  Copynumber: 2.4  Consensus size: 62

       4904 CTTTTGTAAA

                           *    *          *    *                    *    
       4914 TGCAAATG-AATGGTGATTCTAATATAGTTATCATGGTGATTCCAATACAATACTAAGATTT
          1 TGCAAATGAAATGGTAATTCCAATATAGTTACCATGATGATTCCAATACAATACTAAAATTT

              *                                            *                 
       4975 TGTAAATGCAAATGGATGATGATTCCAATATAGTTACCATGATGATTTCAATACAATACTAAAAT
          1 TGCAAATG-AAATGG-T-A--ATTCCAATATAGTTACCATGATGATTCCAATACAATACTAAAAT

              
       5040 TT
         61 TT

                                    
       5042 TGCAAA-GAAATGGTAATTCCAAT
          1 TGCAAATGAAATGGTAATTCCAAT

       5065 TTTGATAAAA


Statistics
Matches: 76,  Mismatches: 8, Indels: 12
        0.79            0.08        0.12

Matches are distributed among these distances:
  61   15  0.20
  63    6  0.08
  64    2  0.03
  65    6  0.08
  66    1  0.01
  67   46  0.61

ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34


Consensus pattern (62 bp):   
TGCAAATGAAATGGTAATTCCAATATAGTTACCATGATGATTCCAATACAATACTAAAATTT

Found at i:5467 original size:41 final size:41

Alignment explanation


    Indices: 5410--5505  Score: 149
    Period size: 41  Copynumber: 2.3  Consensus size: 41

       5400 GAATTTTATT

                   *                                  
       5410 TTAACAAAAATTCTAGTCACCTAATTCTAACAATCT-TCACC
          1 TTAACAAGAATTCTAGTCACCTAATTCTAACAATCTCT-ACC

                                          *          
       5451 TTAACAAGAATTCTAGTCACCTAATTCTAATAATCTCTACC
          1 TTAACAAGAATTCTAGTCACCTAATTCTAACAATCTCTACC

              *           
       5492 TTGACAAGAATTCT
          1 TTAACAAGAATTCT

       5506 CTACGAACAA


Statistics
Matches: 51,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
  41   50  0.98
  42    1  0.02

ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33


Consensus pattern (41 bp):   
TTAACAAGAATTCTAGTCACCTAATTCTAACAATCTCTACC
Done.