Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006460.1 Kokia drynarioides strain JFW-HI SEQ_121043, 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: 8480
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:591 original size:17 final size:16

Alignment explanation


    Indices: 563--598  Score: 54
    Period size: 17  Copynumber: 2.2  Consensus size: 16

        553 TTATTATAAA

                            
        563 TTATTATTAATATCAT
          1 TTATTATTAATATCAT

                          *  
        579 TTATTAGTTAATATTAT
          1 TTATTA-TTAATATCAT

               
        596 TTA
          1 TTA

        599 AAATATTTTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  16    6  0.33
  17   12  0.67

ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58


Consensus pattern (16 bp):   
TTATTATTAATATCAT

Found at i:1347 original size:17 final size:17

Alignment explanation


    Indices: 1320--1373  Score: 72
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       1310 TTTTAATTTT

                *            
       1320 ATTTTAATTTAAAATAA
          1 ATTTAAATTTAAAATAA

            *   *            
       1337 GTTTGAATTTAAAATAA
          1 ATTTAAATTTAAAATAA

                         *   
       1354 ATTTAAATTTAAAGTAA
          1 ATTTAAATTTAAAATAA

               
       1371 ATT
          1 ATT

       1374 CAAACTTATT


Statistics
Matches: 32,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  17   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44


Consensus pattern (17 bp):   
ATTTAAATTTAAAATAA

Found at i:8431 original size:294 final size:294

Alignment explanation


    Indices: 7902--8480  Score: 1086
    Period size: 294  Copynumber: 2.0  Consensus size: 294

       7892 CATCTGCTCC

                                                                             
       7902 TTTTGGTCATTAAACACAAGACTTTGATTTAGTAGCCAATTATTCTTTCCCTTTTACCCCGAATA
          1 TTTTGGTCATTAAACACAAGACTTTGATTTAGTAGCCAATTATTCTTTCCCTTTTACCCCGAATA

                                                                *            
       7967 AAGTACATATATTCATAAAAATATGAAAGATGCAAAGCATCATTCAACATGTGGTGGTTTAGTTT
         66 AAGTACATATATTCATAAAAATATGAAAGATGCAAAGCATCATTCAACATGTAGTGGTTTAGTTT

                                                                             
       8032 AAAAAACCACCAAACAAAGTATCCAAATATCAGCACCATTGTCACTTTCAAAGAAGAAGAATATA
        131 AAAAAACCACCAAACAAAGTATCCAAATATCAGCACCATTGTCACTTTCAAAGAAGAAGAATATA

                                             *                               
       8097 AGCACCATTGTCTAGAAGCATAATCTCAATACTTTTCTTGATCTTTTTGGTACATTAGGTAAAAC
        196 AGCACCATTGTCTAGAAGCATAATCTCAATACTGTTCTTGATCTTTTTGGTACATTAGGTAAAAC

                                              
       8162 AATAAAATGGAATTTTAGAGTTAAGAGAAAAAAA
        261 AATAAAATGGAATTTTAGAGTTAAGAGAAAAAAA

                                                                   *         
       8196 TTTTGGTCATTAAACACAAGACTTTGATTTAGTAGCCAATTATTCTTTCCCTTTTTCCCCGAATA
          1 TTTTGGTCATTAAACACAAGACTTTGATTTAGTAGCCAATTATTCTTTCCCTTTTACCCCGAATA

                    *                                                        
       8261 AAGTACATGTATTCATAAAAATATGAAAGATGCAAAGCATCATTCAACATGTAGTGGTTTAGTTT
         66 AAGTACATATATTCATAAAAATATGAAAGATGCAAAGCATCATTCAACATGTAGTGGTTTAGTTT

                    *        *                                        *      
       8326 AAAAAACCCCCAAACAATGTATCCAAATATCAGCACCATTGTCACTTTCAAAGAAGAATAATATA
        131 AAAAAACCACCAAACAAAGTATCCAAATATCAGCACCATTGTCACTTTCAAAGAAGAAGAATATA

                                                                            *
       8391 AGCACCATTGTCTAGAAGCATAATCTCAATACTGTTCTTGATCTTTTTGGTACATTAGGTAAAAT
        196 AGCACCATTGTCTAGAAGCATAATCTCAATACTGTTCTTGATCTTTTTGGTACATTAGGTAAAAC

                                     
       8456 AATAAAATGGAATTTTAGAGTTAAG
        261 AATAAAATGGAATTTTAGAGTTAAG


Statistics
Matches: 277,  Mismatches: 8, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 294  277  1.00

ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32


Consensus pattern (294 bp):   
TTTTGGTCATTAAACACAAGACTTTGATTTAGTAGCCAATTATTCTTTCCCTTTTACCCCGAATA
AAGTACATATATTCATAAAAATATGAAAGATGCAAAGCATCATTCAACATGTAGTGGTTTAGTTT
AAAAAACCACCAAACAAAGTATCCAAATATCAGCACCATTGTCACTTTCAAAGAAGAAGAATATA
AGCACCATTGTCTAGAAGCATAATCTCAATACTGTTCTTGATCTTTTTGGTACATTAGGTAAAAC
AATAAAATGGAATTTTAGAGTTAAGAGAAAAAAA
Done.