Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000890.1 Kokia drynarioides strain JFW-HI SEQ_112013, 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: 45436
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:18011 original size:2 final size:2
Alignment explanation
Indices: 18006--18036 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17996 GTTTAATCCA
18006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18037 AGGTAAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40695 original size:10 final size:10
Alignment explanation
Indices: 40682--40711 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
40672 GTTGAGGTGA
40682 GATGAGATGG
1 GATGAGATGG
40692 GATGAGATGG
1 GATGAGATGG
40702 GATGAGATGG
1 GATGAGATGG
40712 ATTTTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.50, T:0.20
Consensus pattern (10 bp):
GATGAGATGG
Found at i:40697 original size:20 final size:20
Alignment explanation
Indices: 40669--40711 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
40659 AAAGTGAATG
* *
40669 TGGGTTGAGGTGAGATGAGA
1 TGGGATGAGATGAGATGAGA
*
40689 TGGGATGAGATGGGATGAGA
1 TGGGATGAGATGAGATGAGA
40709 TGG
1 TGG
40712 ATTTTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.51, T:0.23
Consensus pattern (20 bp):
TGGGATGAGATGAGATGAGA
Found at i:42256 original size:4 final size:4
Alignment explanation
Indices: 42247--42272 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
42237 TTATTGATAA
42247 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
42273 TCGTTAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:45295 original size:4 final size:4
Alignment explanation
Indices: 45282--45320 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
45272 AAAATTGAAG
*
45282 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAA
45321 GAAGAAGGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:45312 original size:21 final size:20
Alignment explanation
Indices: 45282--45322 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
45272 AAAATTGAAG
45282 GAAAAAAGAAAGAAAAAAGA
1 GAAAAAAGAAAGAAAAAAGA
*
45302 GAAAGAAAGAAAGAAAGAAGA
1 GAAA-AAAGAAAGAAAAAAGA
45323 AGAAGGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
GAAAAAAGAAAGAAAAAAGA
Found at i:45323 original size:28 final size:27
Alignment explanation
Indices: 45282--45337 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
45272 AAAATTGAAG
45282 GAAAAAAGAAAGAAAAAAGAGAAAGAAA
1 GAAAAAAGAAAGAAAAAAGAGAAA-AAA
* *
45310 GAAAGAAAG-AAGAAGAAGGAGAAAAAA
1 GAAA-AAAGAAAGAAAAAAGAGAAAAAA
45337 G
1 G
45338 GGAAGAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 17 0.68
29 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (27 bp):
GAAAAAAGAAAGAAAAAAGAGAAAAAA
Found at i:45343 original size:24 final size:23
Alignment explanation
Indices: 45300--45361 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
45290 AAAGAAAAAA
* *
45300 GAGAAAGAAAGAAA-GAAAGAA-
1 GAGAAAGAAAAAAAGGGAAGAAT
*
45321 GAAGAAGGAGAAAAAAGGGAAGAAT
1 G-AGAAAGA-AAAAAAGGGAAGAAT
45346 GAGAAAGAAAAAAAGG
1 GAGAAAGAAAAAAAGG
45362 TAATGTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 1 0.03
22 6 0.18
23 13 0.39
24 12 0.36
25 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (23 bp):
GAGAAAGAAAAAAAGGGAAGAAT
Found at i:45344 original size:28 final size:25
Alignment explanation
Indices: 45282--45337 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
45272 AAAATTGAAG
45282 GAAA-AAAGAAAGAAAAAAGAGAAA
1 GAAAGAAAGAAAGAAAAAAGAGAAA
45306 GAAAGAAAGAAAGAAGAAGAAGGAGAAA
1 GAAAGAAAGAAAGAA-AA-AA-GAGAAA
45334 -AAAG
1 GAAAG
45338 GGAAGAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.14
25 10 0.36
26 2 0.07
27 6 0.21
28 6 0.21
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (25 bp):
GAAAGAAAGAAAGAAAAAAGAGAAA
Done.