Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003002.1 Kokia drynarioides strain JFW-HI SEQ_115498, 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: 22559
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:210 original size:11 final size:11
Alignment explanation
Indices: 191--241 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
181 CTTCCCCTTC
191 TTCCTTCTTTT
1 TTCCTTCTTTT
* **
202 TTACTTCTTCC
1 TTCCTTCTTTT
213 TT-CTTCTTTCT
1 TTCCTTCTTT-T
*
224 TTCCTTTTTTT
1 TTCCTTCTTTT
235 TTCCTTC
1 TTCCTTC
242 AATTTTCGTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
10 6 0.19
11 19 0.61
12 6 0.19
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (11 bp):
TTCCTTCTTTT
Found at i:6313 original size:19 final size:19
Alignment explanation
Indices: 6291--6338 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
6281 TTTTTAATTA
* *
6291 TTAACATTTTTTTGATATG
1 TTAACACTTGTTTGATATG
*
6310 TTAACACTTGTTTGATCTG
1 TTAACACTTGTTTGATATG
*
6329 TTAGCACTTG
1 TTAACACTTG
6339 GGATTTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (19 bp):
TTAACACTTGTTTGATATG
Found at i:9244 original size:24 final size:21
Alignment explanation
Indices: 9190--9238 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
9180 TGAGGACCCT
9190 AACTCAGCAAGTGAGCAGCAC
1 AACTCAGCAAGTGAGCAGCAC
*
9211 ATCTCAGCAAGTGAGCAGCAC
1 AACTCAGCAAGTGAGCAGCAC
9232 AACTCAG
1 AACTCAG
9239 TTGCAAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.29, G:0.22, T:0.12
Consensus pattern (21 bp):
AACTCAGCAAGTGAGCAGCAC
Found at i:9672 original size:12 final size:12
Alignment explanation
Indices: 9655--9679 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9645 TAAATTGTTT
9655 TTGAACTTTTTG
1 TTGAACTTTTTG
9667 TTGAACTTTTTG
1 TTGAACTTTTTG
9679 T
1 T
9680 AAAGTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TTGAACTTTTTG
Found at i:18414 original size:21 final size:22
Alignment explanation
Indices: 18377--18419 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
18367 CAACAAATGA
*
18377 TTTTAAAATTATAAAAATTATT
1 TTTTAAAAATATAAAAATTATT
18399 TTTTAAAAATAT-AAAATTATT
1 TTTTAAAAATATAAAAATTATT
18420 AAAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTAAAAATATAAAAATTATT
Found at i:20213 original size:16 final size:16
Alignment explanation
Indices: 20194--20243 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
20184 ATAAATTAGT
20194 ATTAAAAACTCTATTC
1 ATTAAAAACTCTATTC
* *
20210 ATTATAATAAAT-TAGT-
1 ATTA-AA-AACTCTATTC
20226 ATTAAAAACTCTATTC
1 ATTAAAAACTCTATTC
20242 AT
1 AT
20244 AGAGCAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 3 0.12
15 5 0.19
16 10 0.38
17 5 0.19
18 3 0.12
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.40
Consensus pattern (16 bp):
ATTAAAAACTCTATTC
Found at i:20214 original size:32 final size:32
Alignment explanation
Indices: 20178--20243 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
20168 GTAAGATTAT
20178 ATTATAATAAATTAGTATTAAAAACTCTATTC
1 ATTATAATAAATTAGTATTAAAAACTCTATTC
20210 ATTATAATAAATTAGTATTAAAAACTCTATTC
1 ATTATAATAAATTAGTATTAAAAACTCTATTC
20242 AT
1 AT
20244 AGAGCAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (32 bp):
ATTATAATAAATTAGTATTAAAAACTCTATTC
Found at i:22443 original size:4 final size:4
Alignment explanation
Indices: 22430--22468 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
22420 AAAATTGAAG
*
22430 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAA
22469 GAAGGAAGAA
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:22460 original size:21 final size:20
Alignment explanation
Indices: 22430--22470 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
22420 AAAATTGAAG
22430 GAAAAAAGAAAGAAAAAAGA
1 GAAAAAAGAAAGAAAAAAGA
*
22450 GAAAGAAAGAAAGAAAGAAGA
1 GAAA-AAAGAAAGAAAAAAGA
22471 AGGAAGAAGG
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:22478 original size:18 final size:17
Alignment explanation
Indices: 22434--22467 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
22424 TTGAAGGAAA
22434 AAAGAAAGAAAAAAGAG
1 AAAGAAAGAAAAAAGAG
22451 AAAGAAAGAAAGAAAGA
1 AAAGAAAGAAA-AAAGA
22468 AGAAGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAGAG
Found at i:22485 original size:16 final size:15
Alignment explanation
Indices: 22466--22495 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
22456 AAGAAAGAAA
22466 GAAGAAGGAAGAAGGG
1 GAAGAAGG-AGAAGGG
22482 GAAGAAGGAGAAGG
1 GAAGAAGGAGAAGG
22496 AAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GAAGAAGGAGAAGGG
Done.