Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003605.1 Kokia drynarioides strain JFW-HI SEQ_116491, 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: 3661
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33


Found at i:2439 original size:5 final size:6

Alignment explanation


    Indices: 2422--2466  Score: 54
    Period size: 6  Copynumber: 7.0  Consensus size: 6

       2412 GTGATACATG

                                         *                     
       2422 TGTTTT TGTTTT TGTTTT TGTTACATG TGTTTT TGTTTT TGTTTT
          1 TGTTTT TGTTTT TGTTTT TGTT---TT TGTTTT TGTTTT TGTTTT

       2467 AATCATAACA


Statistics
Matches: 34,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
   6   29  0.85
   9    5  0.15

ACGTcount: A:0.04, C:0.02, G:0.18, T:0.76


Consensus pattern (6 bp):   
TGTTTT

Found at i:2454 original size:15 final size:15

Alignment explanation


    Indices: 2405--2458  Score: 60
    Period size: 15  Copynumber: 3.7  Consensus size: 15

       2395 CCAAATTTTT

                             
       2405 TGTTTTTGTGATACATG
          1 TGTTTTTGT--TACATG

                          *
       2422 TGTTTTTGTT---TT
          1 TGTTTTTGTTACATG

                           
       2434 TGTTTTTGTTACATG
          1 TGTTTTTGTTACATG

                      
       2449 TGTTTTTGTT
          1 TGTTTTTGTT

       2459 TTTGTTTTAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  12   11  0.34
  15   12  0.38
  17    9  0.28

ACGTcount: A:0.09, C:0.04, G:0.20, T:0.67


Consensus pattern (15 bp):   
TGTTTTTGTTACATG

Found at i:2454 original size:27 final size:28

Alignment explanation


    Indices: 2401--2466  Score: 116
    Period size: 27  Copynumber: 2.4  Consensus size: 28

       2391 AGCTCCAAAT

                                         
       2401 TTTTTGTTTTTGTGATACATGTGTTTTTG
          1 TTTTTGTTTTTGT-ATACATGTGTTTTTG

                                        
       2430 TTTTTGTTTTTGT-TACATGTGTTTTTG
          1 TTTTTGTTTTTGTATACATGTGTTTTTG

                      
       2457 TTTTTGTTTT
          1 TTTTTGTTTT

       2467 AATCATAACA


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  27   24  0.65
  29   13  0.35

ACGTcount: A:0.08, C:0.03, G:0.18, T:0.71


Consensus pattern (28 bp):   
TTTTTGTTTTTGTATACATGTGTTTTTG

Found at i:3022 original size:16 final size:16

Alignment explanation


    Indices: 3001--3041  Score: 55
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       2991 ATGAGTGCTT

                      * * * 
       3001 AAAGAAAAAATTGTTA
          1 AAAGAAAAAAATATAA

                            
       3017 AAAGAAAAAAATATAA
          1 AAAGAAAAAAATATAA

                     
       3033 AAAGAAAAA
          1 AAAGAAAAA

       3042 TTCTTTGTAG


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15


Consensus pattern (16 bp):   
AAAGAAAAAAATATAA

Done.