Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012665.1 Kokia drynarioides strain JFW-HI SEQ_127676, 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: 8858
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:472 original size:24 final size:24
Alignment explanation
Indices: 439--489 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
429 AGAAATAATC
* *
439 TTTCAGTTAAACACTGTTTATTTG
1 TTTCAATTAAACACTGTTTAGTTG
*
463 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACACTGTTTAGTTG
487 TTT
1 TTT
490 GAGTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACACTGTTTAGTTG
Found at i:8027 original size:31 final size:31
Alignment explanation
Indices: 7985--8069 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 31
7975 TTTAAATAGG
* *
7985 TCTTATTTTTTTGTCCAAACTCT-TTTTTCGA
1 TCTTATATTTTT-TCCAAACTCTATTTTTCAA
8016 TCTTATATTTTTTCCCAAACT-TATTTTTCAA
1 TCTTATATTTTTT-CCAAACTCTATTTTTCAA
*
8047 TTTTATATTTTTATCCAAACTCT
1 TCTTATATTTTT-TCCAAACTCT
8070 CTTGTCCAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
30 2 0.04
31 43 0.91
32 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.02, T:0.56
Consensus pattern (31 bp):
TCTTATATTTTTTCCAAACTCTATTTTTCAA
Found at i:8755 original size:4 final size:4
Alignment explanation
Indices: 8735--8821 Score: 68
Period size: 4 Copynumber: 21.2 Consensus size: 4
8725 AAATAAACGG
* * * *
8735 GAAA AAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * * *
8785 GGAA GAAG GAGAG GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
8822 GTAATGTGTT
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
3 3 0.04
4 52 0.78
5 12 0.18
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:8760 original size:17 final size:17
Alignment explanation
Indices: 8735--8821 Score: 83
Period size: 17 Copynumber: 5.3 Consensus size: 17
8725 AAATAAACGG
*
8735 GAAAAAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
8752 GAAAGAAAGAAAGG-AA
1 GAAAGAAAGAAAGGAAA
* *
8768 GAAGGAGAGGAAA-GAAA
1 GAAAGA-AAGAAAGGAAA
* * *
8785 GGAAGAAGGAGAGGAAA
1 GAAAGAAAGAAAGGAAA
8802 GAAAG-AAG-AAGGAAA
1 GAAAGAAAGAAAGGAAA
8817 GAAAG
1 GAAAG
8822 GTAATGTGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
15 11 0.19
16 15 0.26
17 32 0.55
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:8764 original size:21 final size:21
Alignment explanation
Indices: 8740--8821 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
8730 AACGGGAAAA
*
8740 AAAGAAAGGAAAGA-AAGAAAG
1 AAAGAAA-GAAGGAGAAGAAAG
* *
8761 AAAGGAAGAAGGAGAGGAAAG
1 AAAGAAAGAAGGAGAAGAAAG
* *
8782 AAAGGAAGAAGGAGAGGAAAG
1 AAAGAAAGAAGGAGAAGAAAG
8803 AAAG-AAGAAGGA-AAGAAAG
1 AAAGAAAGAAGGAGAAGAAAG
8822 GTAATGTGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
19 6 0.11
20 13 0.23
21 37 0.66
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAGGAGAAGAAAG
Done.