Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009002.1 Kokia drynarioides strain JFW-HI SEQ_123700, 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: 6826
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34


Found at i:2449 original size:69 final size:70

Alignment explanation


    Indices: 2320--2449  Score: 165
    Period size: 69  Copynumber: 1.9  Consensus size: 70

       2310 CCTACGCTTA

                                 *    *         *                  *         
       2320 CAACTGATATCATAAAGGTTTTGCCGGATTAAGAATGCAACCTCCAAAACAACTAGCGAACTTAC
          1 CAACTGATATCATAAAGGTTTCGCCGAATTAAGAATACAACCTCCAAAACAACTAACGAACTTAC

                 
       2385 AATCC
         66 AATCC

                    *                          *              * *         
       2390 CAACTGATGTCATAAAGG-TTCGCC-AATTTAAGATTACAACCTCCAAAATAGCTAACGAAC
          1 CAACTGATATCATAAAGGTTTCGCCGAA-TTAAGAATACAACCTCCAAAACAACTAACGAAC

       2450 CTATGTTCCC


Statistics
Matches: 51,  Mismatches: 8, Indels: 3
        0.82            0.13        0.05

Matches are distributed among these distances:
  68    1  0.02
  69   33  0.65
  70   17  0.33

ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23


Consensus pattern (70 bp):   
CAACTGATATCATAAAGGTTTCGCCGAATTAAGAATACAACCTCCAAAACAACTAACGAACTTAC
AATCC

Found at i:2610 original size:68 final size:69

Alignment explanation


    Indices: 2530--2658  Score: 179
    Period size: 69  Copynumber: 1.9  Consensus size: 69

       2520 ACACTCTCAG

                                      *                        *             
       2530 TTGATGTCATAAA-GGTTCACCGATTGATATCGCAACCTCCAAAATAGCTATCGGACCTACGCTC
          1 TTGATGTCATAAATGGTTCACCGATTAATATCGCAACCTCCAAAATAGCTAGCGGACCTACGCTC

                
       2594 CCAA
         66 CCAA

                 *         *  ** * *                                     
       2598 TTGATTTCATAAATGTTTGTCGGTTTAATATCGCAACCTCCAAAATAGCTAGCGGACCTAC
          1 TTGATGTCATAAATGGTTCACCGATTAATATCGCAACCTCCAAAATAGCTAGCGGACCTAC

       2659 ATTCCCAGCT


Statistics
Matches: 52,  Mismatches: 8, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  68   12  0.23
  69   40  0.77

ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29


Consensus pattern (69 bp):   
TTGATGTCATAAATGGTTCACCGATTAATATCGCAACCTCCAAAATAGCTAGCGGACCTACGCTC
CCAA

Found at i:6146 original size:23 final size:23

Alignment explanation


    Indices: 6117--6189  Score: 92
    Period size: 23  Copynumber: 3.2  Consensus size: 23

       6107 TCATGCGTTA

                       *           
       6117 TATGCTTAAAGGTTAATGTGATT
          1 TATGCTTAAAGATTAATGTGATT

                      *            
       6140 TATGCTTAAATATTAATGTGATT
          1 TATGCTTAAAGATTAATGTGATT

               *      *    * *     
       6163 TATACTTAAATATTACTATGATT
          1 TATGCTTAAAGATTAATGTGATT

                
       6186 TATG
          1 TATG

       6190 TGTATTTATG


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  23   44  1.00

ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47


Consensus pattern (23 bp):   
TATGCTTAAAGATTAATGTGATT
Done.