Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010951.1 Kokia drynarioides strain JFW-HI SEQ_125919, 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: 8289
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:4815 original size:2 final size:2

Alignment explanation


    Indices: 4810--4846  Score: 56
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       4800 TATATATATA

                                     *        *                    
       4810 TG TG TG TG TG TG TG TG TC TG TG TA TG TG TG TG TG TG T
          1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T

       4847 AAATTTGGGT


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.03, C:0.03, G:0.43, T:0.51


Consensus pattern (2 bp):   
TG

Found at i:7661 original size:182 final size:182

Alignment explanation


    Indices: 7348--7720  Score: 595
    Period size: 182  Copynumber: 2.0  Consensus size: 182

       7338 ACCTTGTTTG

                                                                   *         
       7348 GATTAAATAATTAGTTCATAAGCATCTCAACATTGTTTATGCATGAACAAATGTCGTGGGCCGCA
          1 GATTAAATAATTAGTTCATAAGCATCTCAACATTGTTTATGCATGAACAAATGTCATGGGCCGCA

                                                        *            * *     
       7413 GTTCAAAGCCCATGACAATTGCACAAAATGTGTCCCAAGAAGGTTTATCAATTAGATGGGGCTCA
         66 GTTCAAAGCCCATGACAATTGCACAAAATGTGTCCCAAGAAGGTCTATCAATTAGATCGAGCTCA

                                  *                        *     
       7478 TTTGAC-CGACGAGAACTAACCTGATTCAAAGAGTTGTTGAAGAAGGTTGTTA
        131 TTTGACTC-ACGAGAACTAACCCGATTCAAAGAGTTGTTGAAGAAGGATGTTA

                                   *                                         
       7530 GATTAAATAATTAGTTCATAAGCTTCTCAACATTGTTTATGCATGAACAAATGTCATGGGCCGCA
          1 GATTAAATAATTAGTTCATAAGCATCTCAACATTGTTTATGCATGAACAAATGTCATGGGCCGCA

                       *    *      *              *           *              
       7595 GTTCAAAGCCCGTGACCATTGCATAAAATGTGTCCCAATAAGGTCTATCAGTTAGATCGAGCTCA
         66 GTTCAAAGCCCATGACAATTGCACAAAATGTGTCCCAAGAAGGTCTATCAATTAGATCGAGCTCA

                          *                        *            
       7660 TTTGACTCACGAGAGCTAACCCGATTCAAAGAGTTGTTGGAGAAGGATGTTA
        131 TTTGACTCACGAGAACTAACCCGATTCAAAGAGTTGTTGAAGAAGGATGTTA

                     
       7712 GATTGAAAT
          1 GATT-AAAT

       7721 CTGGATGGTC


Statistics
Matches: 175,  Mismatches: 14, Indels: 3
        0.91            0.07        0.02

Matches are distributed among these distances:
 182  170  0.97
 183    5  0.03

ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28


Consensus pattern (182 bp):   
GATTAAATAATTAGTTCATAAGCATCTCAACATTGTTTATGCATGAACAAATGTCATGGGCCGCA
GTTCAAAGCCCATGACAATTGCACAAAATGTGTCCCAAGAAGGTCTATCAATTAGATCGAGCTCA
TTTGACTCACGAGAACTAACCCGATTCAAAGAGTTGTTGAAGAAGGATGTTA

Found at i:7845 original size:13 final size:14

Alignment explanation


    Indices: 7827--7856  Score: 53
    Period size: 13  Copynumber: 2.2  Consensus size: 14

       7817 TTGATTTGAT

                          
       7827 TTGATTATGTAA-A
          1 TTGATTATGTAATA

                          
       7840 TTGATTATGTAATA
          1 TTGATTATGTAATA

               
       7854 TTG
          1 TTG

       7857 TAAATCCCTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   12  0.75
  14    4  0.25

ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50


Consensus pattern (14 bp):   
TTGATTATGTAATA
Done.