Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005471.1 Kokia drynarioides strain JFW-HI SEQ_119518, 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: 3854
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38


Found at i:1159 original size:25 final size:27

Alignment explanation


    Indices: 1130--1198  Score: 74
    Period size: 26  Copynumber: 2.7  Consensus size: 27

       1120 GCCAGCACTT

                                       
       1130 TAATTGAAATAATTAAATG-TATTA-A
          1 TAATTGAAATAATTAAATGTTATTATA

                     *                  
       1155 TAATTTGAATTAATT-AATGTTATTATA
          1 TAA-TTGAAATAATTAAATGTTATTATA

            *         *       
       1182 GAATT-AAATGATTAAAT
          1 TAATTGAAATAATTAAAT

       1199 TATGTCAAAT


Statistics
Matches: 36,  Mismatches: 4, Indels: 7
        0.77            0.09        0.15

Matches are distributed among these distances:
  25   13  0.36
  26   20  0.56
  27    3  0.08

ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43


Consensus pattern (27 bp):   
TAATTGAAATAATTAAATGTTATTATA

Found at i:1212 original size:15 final size:14

Alignment explanation


    Indices: 1192--1233  Score: 50
    Period size: 14  Copynumber: 3.0  Consensus size: 14

       1182 GAATTAAATG

                        *  
       1192 ATTAAATTATGTCAA
          1 ATTAAATTAT-TAAA

                  *       
       1207 ATTAAAATATTAAA
          1 ATTAAATTATTAAA

                          
       1221 ATTAAA-TATTAAA
          1 ATTAAATTATTAAA

       1234 TATGTGCATA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  13    7  0.28
  14    9  0.36
  15    9  0.36

ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38


Consensus pattern (14 bp):   
ATTAAATTATTAAA

Found at i:1229 original size:13 final size:14

Alignment explanation


    Indices: 1205--1233  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

       1195 AAATTATGTC

                          
       1205 AAATTAAAATATTA
          1 AAATTAAAATATTA

                          
       1219 AAATT-AAATATTA
          1 AAATTAAAATATTA

              
       1232 AA
          1 AA

       1234 TATGTGCATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   10  0.67
  14    5  0.33

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (14 bp):   
AAATTAAAATATTA

Found at i:1910 original size:16 final size:15

Alignment explanation


    Indices: 1873--1935  Score: 63
    Period size: 15  Copynumber: 4.1  Consensus size: 15

       1863 TTATGCTATA

                    *      
       1873 TTGAAAAATTAAGTG
          1 TTGAAAAAATAAGTG

              **            
       1888 CTAAAAAAAATAAGTG
          1 -TTGAAAAAATAAGTG

                        * *
       1904 TTGAAAAAATAAATA
          1 TTGAAAAAATAAGTG

                    *      
       1919 TTGAAAAATTAAGTG
          1 TTGAAAAAATAAGTG

              
       1934 TT
          1 TT

       1936 CAATTTAAGC


Statistics
Matches: 37,  Mismatches: 10, Indels: 1
        0.77            0.21        0.02

Matches are distributed among these distances:
  15   25  0.68
  16   12  0.32

ACGTcount: A:0.54, C:0.02, G:0.14, T:0.30


Consensus pattern (15 bp):   
TTGAAAAAATAAGTG

Found at i:2583 original size:46 final size:46

Alignment explanation


    Indices: 2530--2621  Score: 184
    Period size: 46  Copynumber: 2.0  Consensus size: 46

       2520 AGCTATCAAT

                                                          
       2530 AAATCAGATCATACGAATCATACACATATAATATGTCATTTACTTA
          1 AAATCAGATCATACGAATCATACACATATAATATGTCATTTACTTA

                                                          
       2576 AAATCAGATCATACGAATCATACACATATAATATGTCATTTACTTA
          1 AAATCAGATCATACGAATCATACACATATAATATGTCATTTACTTA

       2622 GAATTAAGAT


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  46   46  1.00

ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33


Consensus pattern (46 bp):   
AAATCAGATCATACGAATCATACACATATAATATGTCATTTACTTA

Found at i:2809 original size:25 final size:24

Alignment explanation


    Indices: 2780--2832  Score: 97
    Period size: 25  Copynumber: 2.2  Consensus size: 24

       2770 TCCTAAGCTT

                                     
       2780 TTTTATTTTACTTCTTGAATTGCAA
          1 TTTTATTTTACTTCTTGAATTGC-A

                                    
       2805 TTTTATTTTACTTCTTGAATTGCA
          1 TTTTATTTTACTTCTTGAATTGCA

                
       2829 TTTT
          1 TTTT

       2833 GTTTCCTATG


Statistics
Matches: 28,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  24    5  0.18
  25   23  0.82

ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60


Consensus pattern (24 bp):   
TTTTATTTTACTTCTTGAATTGCA

Found at i:2905 original size:17 final size:18

Alignment explanation


    Indices: 2872--2908  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       2862 TCTTGTTGCC

                               
       2872 TTCCTCTCTAGCATTTTGT
          1 TTCCTCTCTAG-ATTTTGT

                              
       2891 TTCCTCTCTAG-TTTTGT
          1 TTCCTCTCTAGATTTTGT

             
       2908 T
          1 T

       2909 GCTAAGTTTG


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  17    7  0.39
  19   11  0.61

ACGTcount: A:0.08, C:0.24, G:0.11, T:0.57


Consensus pattern (18 bp):   
TTCCTCTCTAGATTTTGT
Done.