Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001720.1 Kokia drynarioides strain JFW-HI SEQ_113418, 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: 14310
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Found at i:212 original size:22 final size:22
Alignment explanation
Indices: 174--223 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
164 ATTTCAAGTT
* **
174 TTTTTAATATTATAATTTTCCA
1 TTTTTAAAATTATAATTTAACA
196 TTTTTAAAATCTA-AATTTAACA
1 TTTTTAAAAT-TATAATTTAACA
218 TTTTTA
1 TTTTTA
224 TTTTAGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTAAAATTATAATTTAACA
Found at i:5605 original size:16 final size:15
Alignment explanation
Indices: 5585--5655 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
5575 AGTATATATT
5585 TTTATAAATTTTTAA
1 TTTATAAATTTTTAA
* *
5600 TTT-TATTATTATTAA
1 TTTATA-AATTTTTAA
5615 TTTA-AAATTTTATAA
1 TTTATAAATTTT-TAA
*
5630 ATTATAAAATTTTTAA
1 TTTAT-AAATTTTTAA
* *
5646 ATTAAAAATT
1 TTTATAAATT
5656 ATCATTTTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 6 0.13
15 25 0.56
16 7 0.16
17 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATAAATTTTTAA
Found at i:5611 original size:22 final size:22
Alignment explanation
Indices: 5581--5645 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
5571 ATATAGTATA
*
5581 TATTTTTATAAATTTTTAATTT
1 TATTATTATAAATTTTTAATTT
* **
5603 TATTATTATTAATTTAAAATTT
1 TATTATTATAAATTTTTAATTT
*
5625 TATAAATTATAAAATTTTTAA
1 TAT-TATTAT-AAATTTTTAA
5646 ATTAAAAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
22 21 0.64
23 5 0.15
24 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTATTATAAATTTTTAATTT
Found at i:6210 original size:18 final size:16
Alignment explanation
Indices: 6178--6221 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
6168 ATGGAATGAG
6178 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
6194 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
6208 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
6222 ACCCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:6284 original size:6 final size:6
Alignment explanation
Indices: 6273--6301 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
6263 ACGCCTCTCT
6273 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
6302 TTCCCTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:6977 original size:20 final size:21
Alignment explanation
Indices: 6922--6977 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
6912 ATCAATCTAA
6922 AAATTCATAATT-TATGTTTTT
1 AAATT-ATAATTATATGTTTTT
* *
6943 AAGTTATCAA-AATAT-TTTTT
1 AAATTAT-AATTATATGTTTTT
6963 AAATTATAATTATAT
1 AAATTATAATTATAT
6978 AAATTTTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
19 2 0.07
20 17 0.61
21 9 0.32
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (21 bp):
AAATTATAATTATATGTTTTT
Found at i:7046 original size:26 final size:25
Alignment explanation
Indices: 6999--7047 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
6989 TAAAATTTTT
*
6999 AAAAATTCATAAAATTATAAAAATA
1 AAAAATTCATAAAATTACAAAAATA
* *
7024 AAAAATTACCTAAAATTCCAAAAA
1 AAAAATT-CATAAAATTACAAAAA
7048 AGTCGAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAATTCATAAAATTACAAAAATA
Found at i:10072 original size:26 final size:26
Alignment explanation
Indices: 10037--10096 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
10027 CTCCCATAAC
*
10037 AAAACACTTATCTGATGATACACAAG
1 AAAACACTTATCTGATGACACACAAG
* * *
10063 AAAGCACTTATTTGATGACACATAAG
1 AAAACACTTATCTGATGACACACAAG
10089 AAAACACT
1 AAAACACT
10097 CTCATTTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (26 bp):
AAAACACTTATCTGATGACACACAAG
Found at i:11691 original size:18 final size:18
Alignment explanation
Indices: 11660--11708 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
11650 GTTTTATTGT
*
11660 TAATATTATTTTTATTTAAA
1 TAATATT-TATTTA-TTAAA
11680 -AATATTTATTTATTAAA
1 TAATATTTATTTATTAAA
*
11697 TTATATTTATTT
1 TAATATTTATTT
11709 TAATATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 5 0.19
18 15 0.58
19 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAATATTTATTTATTAAA
Found at i:13959 original size:4 final size:4
Alignment explanation
Indices: 13946--13984 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
13936 AAAAATGAAG
*
13946 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAA
13985 GAAGGAAAAA
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:13960 original size:11 final size:11
Alignment explanation
Indices: 13936--13994 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
13926 GGGGACCAAC
* *
13936 AAAAATGAAGG
1 AAAAAAGAAAG
13947 AAAAAAGAAAG
1 AAAAAAGAAAG
13958 AAAAAAG--AG
1 AAAAAAGAAAG
13967 AAAGAAAGAAAG
1 AAA-AAAGAAAG
* *
13979 AAAGAAGAAGG
1 AAAAAAGAAAG
13990 AAAAA
1 AAAAA
13995 GGAGAAGAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 5 0.12
10 4 0.10
11 26 0.65
12 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:13995 original size:21 final size:21
Alignment explanation
Indices: 13936--13995 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
13926 GGGGACCAAC
*
13936 AAAAATGAAGGAAAAAAGAAAG
1 AAAAAAGAAGG-AAAAAGAAAG
*
13958 AAAAAAG-AGAAAGAAAGAAAG
1 AAAAAAGAAGGAA-AAAGAAAG
*
13979 AAAGAAGAAGGAAAAAG
1 AAAAAAGAAGGAAAAAG
13996 GAGAAGAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 2 0.06
21 20 0.62
22 10 0.31
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (21 bp):
AAAAAAGAAGGAAAAAGAAAG
Found at i:13995 original size:25 final size:24
Alignment explanation
Indices: 13946--13995 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
13936 AAAAATGAAG
*
13946 GAAAAAAGAAAGAAAAAAGAGAAA
1 GAAAAAAGAAAGAAAAAAGAAAAA
* *
13970 GAAAGAAAGAAAGAAGAAGGAAAAA
1 GAAA-AAAGAAAGAAAAAAGAAAAA
13995 G
1 G
13996 GAGAAGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (24 bp):
GAAAAAAGAAAGAAAAAAGAAAAA
Found at i:14007 original size:9 final size:9
Alignment explanation
Indices: 13981--14017 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
13971 AAAGAAAGAA
13981 AGAAGAAGG
1 AGAAGAAGG
13990 A-AA-AAGG
1 AGAAGAAGG
13997 AGAAGAAGG
1 AGAAGAAGG
*
14006 AGAAGAATG
1 AGAAGAAGG
14015 AGA
1 AGA
14018 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
7 5 0.20
8 4 0.16
9 16 0.64
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (9 bp):
AGAAGAAGG
Done.