Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007992.1 Hibiscus syriacus cultivar Beakdansim tig00110442_pilon, 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: 1314873
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:5159 original size:14 final size:14
Alignment explanation
Indices: 5137--5177 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
5127 AAAAAAATAA
5137 AAAACAAAAAAAGGC
1 AAAA-AAAAAAAGGC
5152 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
5166 AAAAAAACAAAA
1 AAAAAAA-AAAA
5178 AAAGAGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:5160 original size:22 final size:21
Alignment explanation
Indices: 5128--5180 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 21
5118 TTTTTTTTCA
*
5128 AAAAAATAAAAAACAAAAAAAGGC
1 AAAAAA-AAAAAGCAAAAAAA--C
5152 AAAAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAAA-GCAAAAAAAC
5174 AAAAAAA
1 AAAAAAA
5181 GAGCCAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 8 0.30
23 5 0.19
24 14 0.52
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAAGCAAAAAAAC
Found at i:5198 original size:20 final size:20
Alignment explanation
Indices: 5154--5191 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5144 AAAAAGGCAA
*
5154 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
5174 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
5192 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:14439 original size:13 final size:11
Alignment explanation
Indices: 14417--14482 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
14407 TATCACGCCT
14417 ATATCATCACC
1 ATATCATCACC
14428 ATAGTCCATCACC
1 ATA-T-CATCACC
*
14441 ATTATCA-CGCC
1 A-TATCATCACC
14452 TATATCATCACC
1 -ATATCATCACC
14464 ATATTCCATCACC
1 ATA-T-CATCACC
14477 ATATCA
1 ATATCA
14483 CGCCTATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:14445 original size:36 final size:36
Alignment explanation
Indices: 14405--14499 Score: 165
Period size: 36 Copynumber: 2.7 Consensus size: 36
14395 CCTTACATCA
14405 ATTATCACGCCTATATCATCACCATAGTCCATCACC
1 ATTATCACGCCTATATCATCACCATAGTCCATCACC
*
14441 ATTATCACGCCTATATCATCACCATATTCCATCACC
1 ATTATCACGCCTATATCATCACCATAGTCCATCACC
*
14477 A-TATCACGCCTATATTATCACCA
1 ATTATCACGCCTATATCATCACCA
14500 ACTTATAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 21 0.37
36 36 0.63
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (36 bp):
ATTATCACGCCTATATCATCACCATAGTCCATCACC
Found at i:22844 original size:16 final size:16
Alignment explanation
Indices: 22823--22854 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
22813 TAGTTAGCTC
22823 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
22839 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
22855 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:24282 original size:17 final size:18
Alignment explanation
Indices: 24260--24311 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
24250 AATTGGAGTC
24260 CAAAAAGAAAGAAAAGA-
1 CAAAAAGAAAGAAAAGAT
24277 CAAAAAGAAGAGAAAA-AT
1 CAAAAAGAA-AGAAAAGAT
24295 CAGAAAAG-AAGAAAAGA
1 CA-AAAAGAAAGAAAAGA
24312 AGAAGAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.02
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAGAT
Found at i:24292 original size:11 final size:11
Alignment explanation
Indices: 24267--24338 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
24257 GTCCAAAAAG
24267 AAAGAAAAGACAA
1 AAAGAAAAG--AA
*
24280 AAAGAAGAGAA
1 AAAGAAAAGAA
* *
24291 AAATCAGAA-AA
1 AAA-GAAAAGAA
*
24302 GAAGAAAAGAA
1 AAAGAAAAGAA
*
24313 GAAGAAAAG-A
1 AAAGAAAAGAA
24323 AAAGAAAAGAA
1 AAAGAAAAGAA
24334 AAAGA
1 AAAGA
24339 GAAGTTCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 12 0.25
11 26 0.54
12 2 0.04
13 8 0.17
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:24304 original size:5 final size:5
Alignment explanation
Indices: 24262--24335 Score: 61
Period size: 5 Copynumber: 15.8 Consensus size: 5
24252 TTGGAGTCCA
* * **
24262 AAAAG -AAAG AAAAG -ACA- AAAAG AAGAG AAAA- ATCAG AAAAG --AAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
24306 AAAAG AAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
24336 AGAGAAGTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
3 3 0.06
4 10 0.19
5 36 0.67
6 5 0.09
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:24307 original size:8 final size:8
Alignment explanation
Indices: 24262--24328 Score: 57
Period size: 8 Copynumber: 7.9 Consensus size: 8
24252 TTGGAGTCCA
24262 AAAAGAAAG
1 AAAAG-AAG
24271 AAAAGACA-
1 AAAAGA-AG
24279 AAAAGAAG
1 AAAAGAAG
*
24287 AGAAAAATCAG
1 A-AAAGA--AG
24298 AAAAGAAG
1 AAAAGAAG
24306 AAAAGAAG
1 AAAAGAAG
24314 AAGAA-AAG
1 AA-AAGAAG
24322 AAAAGAA
1 AAAAGAA
24329 AAGAAAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
7 3 0.06
8 27 0.55
9 12 0.24
10 4 0.08
11 3 0.06
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (8 bp):
AAAAGAAG
Found at i:24315 original size:16 final size:17
Alignment explanation
Indices: 24262--24327 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 17
24252 TTGGAGTCCA
24262 AAAAGAAAGAAAAGACA-
1 AAAAG-AAGAAAAGACAG
*
24279 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAGA-CAG
24298 AAAAGAAGAAAAGA-AG
1 AAAAGAAGAAAAGACAG
24314 AAGAA-AAGAAAAGA
1 AA-AAGAAGAAAAGA
24328 AAAGAAAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 17 0.40
17 11 0.26
18 6 0.14
19 9 0.21
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAGACAG
Found at i:24328 original size:16 final size:15
Alignment explanation
Indices: 24262--24335 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 15
24252 TTGGAGTCCA
24262 AAAAG-AAAGAAAAG
1 AAAAGAAAAGAAAAG
* *
24276 -ACA-AAAAGAAGAG
1 AAAAGAAAAGAAAAG
**
24289 AAAA-ATCAGAAAAG
1 AAAAGAAAAGAAAAG
24303 --AAGAAAAGAAGAAG
1 AAAAGAAAAGAA-AAG
24317 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
24332 AAAA
1 AAAA
24336 AGAGAAGTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
12 2 0.04
13 15 0.33
14 12 0.26
15 7 0.15
16 10 0.22
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (15 bp):
AAAAGAAAAGAAAAG
Found at i:24338 original size:16 final size:16
Alignment explanation
Indices: 24303--24335 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
24293 ATCAGAAAAG
24303 AAGAAAAGAAGAAGAA
1 AAGAAAAGAAGAAGAA
24319 AAGAAAAGAA-AAGAA
1 AAGAAAAGAAGAAGAA
24334 AA
1 AA
24336 AGAGAAGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAGAAGAA
Found at i:26455 original size:16 final size:16
Alignment explanation
Indices: 26434--26465 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
26424 TAGTTAGCTC
26434 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
26450 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
26466 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:27891 original size:17 final size:18
Alignment explanation
Indices: 27869--27920 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
27859 AATTGGAGTC
27869 CAAAAAGAAAGAAAAGA-
1 CAAAAAGAAAGAAAAGAT
27886 CAAAAAGAAGAGAAAA-AT
1 CAAAAAGAA-AGAAAAGAT
27904 CAGAAAAG-AAGAAAAGA
1 CA-AAAAGAAAGAAAAGA
27921 AGAAGAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.02
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAGAT
Found at i:27901 original size:11 final size:11
Alignment explanation
Indices: 27876--27947 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
27866 GTCCAAAAAG
27876 AAAGAAAAGACAA
1 AAAGAAAAG--AA
*
27889 AAAGAAGAGAA
1 AAAGAAAAGAA
* *
27900 AAATCAGAA-AA
1 AAA-GAAAAGAA
*
27911 GAAGAAAAGAA
1 AAAGAAAAGAA
*
27922 GAAGAAAAG-A
1 AAAGAAAAGAA
27932 AAAGAAAAGAA
1 AAAGAAAAGAA
27943 AAAGA
1 AAAGA
27948 GAAGTTCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 12 0.25
11 26 0.54
12 2 0.04
13 8 0.17
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:27913 original size:5 final size:5
Alignment explanation
Indices: 27871--27944 Score: 61
Period size: 5 Copynumber: 15.8 Consensus size: 5
27861 TTGGAGTCCA
* * **
27871 AAAAG -AAAG AAAAG -ACA- AAAAG AAGAG AAAA- ATCAG AAAAG --AAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
27915 AAAAG AAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
27945 AGAGAAGTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
3 3 0.06
4 10 0.19
5 36 0.67
6 5 0.09
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:27916 original size:8 final size:8
Alignment explanation
Indices: 27871--27937 Score: 57
Period size: 8 Copynumber: 7.9 Consensus size: 8
27861 TTGGAGTCCA
27871 AAAAGAAAG
1 AAAAG-AAG
27880 AAAAGACA-
1 AAAAGA-AG
27888 AAAAGAAG
1 AAAAGAAG
*
27896 AGAAAAATCAG
1 A-AAAGA--AG
27907 AAAAGAAG
1 AAAAGAAG
27915 AAAAGAAG
1 AAAAGAAG
27923 AAGAA-AAG
1 AA-AAGAAG
27931 AAAAGAA
1 AAAAGAA
27938 AAGAAAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
7 3 0.06
8 27 0.55
9 12 0.24
10 4 0.08
11 3 0.06
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (8 bp):
AAAAGAAG
Found at i:27924 original size:16 final size:17
Alignment explanation
Indices: 27871--27936 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 17
27861 TTGGAGTCCA
27871 AAAAGAAAGAAAAGACA-
1 AAAAG-AAGAAAAGACAG
*
27888 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAGA-CAG
27907 AAAAGAAGAAAAGA-AG
1 AAAAGAAGAAAAGACAG
27923 AAGAA-AAGAAAAGA
1 AA-AAGAAGAAAAGA
27937 AAAGAAAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 17 0.40
17 11 0.26
18 6 0.14
19 9 0.21
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAGACAG
Found at i:27937 original size:16 final size:15
Alignment explanation
Indices: 27871--27944 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 15
27861 TTGGAGTCCA
27871 AAAAG-AAAGAAAAG
1 AAAAGAAAAGAAAAG
* *
27885 -ACA-AAAAGAAGAG
1 AAAAGAAAAGAAAAG
**
27898 AAAA-ATCAGAAAAG
1 AAAAGAAAAGAAAAG
27912 --AAGAAAAGAAGAAG
1 AAAAGAAAAGAA-AAG
27926 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
27941 AAAA
1 AAAA
27945 AGAGAAGTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
12 2 0.04
13 15 0.33
14 12 0.26
15 7 0.15
16 10 0.22
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (15 bp):
AAAAGAAAAGAAAAG
Found at i:27947 original size:16 final size:16
Alignment explanation
Indices: 27912--27944 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
27902 ATCAGAAAAG
27912 AAGAAAAGAAGAAGAA
1 AAGAAAAGAAGAAGAA
27928 AAGAAAAGAA-AAGAA
1 AAGAAAAGAAGAAGAA
27943 AA
1 AA
27945 AGAGAAGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAGAAGAA
Found at i:32777 original size:16 final size:16
Alignment explanation
Indices: 32756--32787 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
32746 TAGTTAGCTC
32756 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
32772 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
32788 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:34223 original size:11 final size:10
Alignment explanation
Indices: 34207--34273 Score: 56
Period size: 11 Copynumber: 6.9 Consensus size: 10
34197 ATTGGAGTGC
34207 AAAAAGAAGA
1 AAAAAGAAGA
34217 GAAAAAGAAG-
1 -AAAAAGAAGA
34227 -AAAAGAAGA
1 AAAAAGAAGA
34236 AAAGAAGAA-A
1 AAA-AAGAAGA
34246 AGAAAA-AAG-
1 A-AAAAGAAGA
34255 AAAAA-AAGA
1 AAAAAGAAGA
34264 AAAAGAGAAG
1 AAAA-AGAAG
34274 TTCAAAAAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
8 15 0.31
9 7 0.15
10 7 0.15
11 19 0.40
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAAAGAAGA
Found at i:34230 original size:8 final size:8
Alignment explanation
Indices: 34219--34273 Score: 78
Period size: 8 Copynumber: 7.0 Consensus size: 8
34209 AAAGAAGAGA
34219 AAAAGAAG
1 AAAAGAAG
34227 AAAAGAAG
1 AAAAGAAG
34235 AAAAGAAG
1 AAAAGAAG
34243 AAAAGAA-
1 AAAAGAAG
*
34250 AAAAGAAA
1 AAAAGAAG
34258 AAAAGAA-
1 AAAAGAAG
34265 AAAGAGAAG
1 AAA-AGAAG
34274 TTCAAAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
7 10 0.23
8 34 0.77
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:34238 original size:16 final size:15
Alignment explanation
Indices: 34213--34273 Score: 86
Period size: 16 Copynumber: 3.9 Consensus size: 15
34203 GTGCAAAAAG
34213 AAGAGAAAAAGAAGAA
1 AAGA-AAAAAGAAGAA
34229 AAGAAGAAAAGAAGAA
1 AAGAA-AAAAGAAGAA
*
34245 AAGAAAAAAGAAAAA
1 AAGAAAAAAGAAGAA
34260 AAGAAAAAGAGAAG
1 AAGAAAAA-AGAAG
34274 TTCAAAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
15 18 0.44
16 23 0.56
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAGAAGAA
Found at i:34256 original size:31 final size:32
Alignment explanation
Indices: 34213--34273 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
34203 GTGCAAAAAG
*
34213 AAGAGAAAAAGAAGAAAAGAAGAAA-AGAAGAA
1 AAGAGAAAAAGAAAAAAAGAA-AAAGAGAAGAA
34245 AAGA-AAAAAGAAAAAAAGAAAAAGAGAAG
1 AAGAGAAAAAGAAAAAAAGAAAAAGAGAAG
34274 TTCAAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.11
31 20 0.74
32 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (32 bp):
AAGAGAAAAAGAAAAAAAGAAAAAGAGAAGAA
Found at i:36373 original size:16 final size:16
Alignment explanation
Indices: 36352--36383 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
36342 TAGTTAGCTC
36352 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
36368 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
36384 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:40432 original size:19 final size:18
Alignment explanation
Indices: 40397--40456 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
40387 GAACTTCTCT
40397 TTTTCTT-TTCTTTTCTTC
1 TTTTCTTATT-TTTTCTTC
*
40415 TTTTCTTATTTTTCTCTTG
1 TTTTCTTATTTTT-TCTTC
*
40434 TTTTCTGATTTTTGTCTTC
1 TTTTCTTATTTTT-TCTTC
40453 TTTT
1 TTTT
40457 TGCACTCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 10 0.28
19 26 0.72
ACGTcount: A:0.03, C:0.17, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTCTTATTTTTTCTTC
Found at i:40747 original size:20 final size:20
Alignment explanation
Indices: 40710--40753 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40700 ATGGACTTAA
*
40710 GAAATGAATATATAATAAAG
1 GAAATGAATATAGAATAAAG
*
40730 GAAATGAA-ATAGACATAAAT
1 GAAATGAATATAGA-ATAAAG
40750 GAAA
1 GAAA
40754 GAGATGGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.61, C:0.02, G:0.16, T:0.20
Consensus pattern (20 bp):
GAAATGAATATAGAATAAAG
Found at i:50674 original size:24 final size:24
Alignment explanation
Indices: 50620--50674 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
50610 GAAAAATCAG
*
50620 AAAAG-AAGCACTCAAAAAGAAGA
1 AAAAGAAAACACTCAAAAAGAAGA
**
50643 AATTGAAAACACTC-AAAAGAAGAA
1 AAAAGAAAACACTCAAAAAGAAG-A
50667 AAAAGAAA
1 AAAAGAAA
50675 GAAAAGTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.11, G:0.15, T:0.07
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAAAGAAGA
Found at i:51949 original size:24 final size:24
Alignment explanation
Indices: 51922--51973 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
51912 GACATGTCCT
* * *
51922 TTGACGTTCCAACAGTTATGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
* *
51946 TTGATGTTCAAAAAGATGTGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
51970 TTGA
1 TTGA
51974 AGTGCCAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (24 bp):
TTGACGTTCAAAAAGATATGCCAC
Found at i:55972 original size:25 final size:25
Alignment explanation
Indices: 55913--55973 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
55903 TCTTTGCTTT
* *
55913 TTTCTTTTTCTTTTTGAGTGTTGGAA
1 TTTC-TTTTCTTTTGGAGTGTTGCAA
55939 TTT-TCTTTCTTTTGGAGTGCTT-CAA
1 TTTCT-TTTCTTTTGGAGTG-TTGCAA
55964 TTTCTTTTCT
1 TTTCTTTTCT
55974 GATTTTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 1 0.03
25 23 0.77
26 6 0.20
ACGTcount: A:0.10, C:0.13, G:0.15, T:0.62
Consensus pattern (25 bp):
TTTCTTTTCTTTTGGAGTGTTGCAA
Found at i:61071 original size:30 final size:31
Alignment explanation
Indices: 61035--61094 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
61025 CTTAGCTTTA
**
61035 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
61065 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
61095 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:82316 original size:24 final size:21
Alignment explanation
Indices: 82281--82323 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
82271 GGCTCATTCT
*
82281 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
82304 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
82324 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:88797 original size:35 final size:37
Alignment explanation
Indices: 88751--88830 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
88741 TTTGAGAATT
*
88751 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
88786 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
88823 TGGTGATG
1 TGGTGATG
88831 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:92638 original size:17 final size:18
Alignment explanation
Indices: 92616--92667 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
92606 AATTGGAGTG
92616 CAAAAAGAAAGAAAAGA-
1 CAAAAAGAAAGAAAAGAT
92633 CAAAAAGAAGAGAAAA-AT
1 CAAAAAGAA-AGAAAAGAT
92651 CAGAAAAG-AAGAAAAGA
1 CA-AAAAGAAAGAAAAGA
92668 AGAAGAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.02
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAGAT
Found at i:92648 original size:11 final size:11
Alignment explanation
Indices: 92623--92694 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
92613 GTGCAAAAAG
92623 AAAGAAAAGACAA
1 AAAGAAAAG--AA
*
92636 AAAGAAGAGAA
1 AAAGAAAAGAA
* *
92647 AAATCAGAA-AA
1 AAA-GAAAAGAA
*
92658 GAAGAAAAGAA
1 AAAGAAAAGAA
*
92669 GAAGAAAAG-A
1 AAAGAAAAGAA
92679 AAAGAAAAGAA
1 AAAGAAAAGAA
92690 AAAGA
1 AAAGA
92695 GAAGTTCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 12 0.25
11 26 0.54
12 2 0.04
13 8 0.17
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:92660 original size:5 final size:5
Alignment explanation
Indices: 92618--92691 Score: 61
Period size: 5 Copynumber: 15.8 Consensus size: 5
92608 TTGGAGTGCA
* * **
92618 AAAAG -AAAG AAAAG -ACA- AAAAG AAGAG AAAA- ATCAG AAAAG --AAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
92662 AAAAG AAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
92692 AGAGAAGTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
3 3 0.06
4 10 0.19
5 36 0.67
6 5 0.09
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:92663 original size:8 final size:8
Alignment explanation
Indices: 92618--92684 Score: 57
Period size: 8 Copynumber: 7.9 Consensus size: 8
92608 TTGGAGTGCA
92618 AAAAGAAAG
1 AAAAG-AAG
92627 AAAAGACA-
1 AAAAGA-AG
92635 AAAAGAAG
1 AAAAGAAG
*
92643 AGAAAAATCAG
1 A-AAAGA--AG
92654 AAAAGAAG
1 AAAAGAAG
92662 AAAAGAAG
1 AAAAGAAG
92670 AAGAA-AAG
1 AA-AAGAAG
92678 AAAAGAA
1 AAAAGAA
92685 AAGAAAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
7 3 0.06
8 27 0.55
9 12 0.24
10 4 0.08
11 3 0.06
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (8 bp):
AAAAGAAG
Found at i:92671 original size:16 final size:17
Alignment explanation
Indices: 92618--92683 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 17
92608 TTGGAGTGCA
92618 AAAAGAAAGAAAAGACA-
1 AAAAG-AAGAAAAGACAG
*
92635 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAGA-CAG
92654 AAAAGAAGAAAAGA-AG
1 AAAAGAAGAAAAGACAG
92670 AAGAA-AAGAAAAGA
1 AA-AAGAAGAAAAGA
92684 AAAGAAAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 17 0.40
17 11 0.26
18 6 0.14
19 9 0.21
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAGACAG
Found at i:92684 original size:16 final size:15
Alignment explanation
Indices: 92618--92691 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 15
92608 TTGGAGTGCA
92618 AAAAG-AAAGAAAAG
1 AAAAGAAAAGAAAAG
* *
92632 -ACA-AAAAGAAGAG
1 AAAAGAAAAGAAAAG
**
92645 AAAA-ATCAGAAAAG
1 AAAAGAAAAGAAAAG
92659 --AAGAAAAGAAGAAG
1 AAAAGAAAAGAA-AAG
92673 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
92688 AAAA
1 AAAA
92692 AGAGAAGTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
12 2 0.04
13 15 0.33
14 12 0.26
15 7 0.15
16 10 0.22
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (15 bp):
AAAAGAAAAGAAAAG
Found at i:92694 original size:16 final size:16
Alignment explanation
Indices: 92659--92691 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
92649 ATCAGAAAAG
92659 AAGAAAAGAAGAAGAA
1 AAGAAAAGAAGAAGAA
92675 AAGAAAAGAA-AAGAA
1 AAGAAAAGAAGAAGAA
92690 AA
1 AA
92692 AGAGAAGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAGAAGAA
Found at i:98082 original size:17 final size:18
Alignment explanation
Indices: 98057--98109 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
98047 AAAATATAGT
98057 AATGAAATAAAAAAAATGA
1 AATG-AATAAAAAAAATGA
*
98076 AA-GAAT-AAAGAAATGA
1 AATGAATAAAAAAAATGA
98092 AATG-ATAAAAAAAATGA
1 AATGAATAAAAAAAATGA
98109 A
1 A
98110 GATAACTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 13 0.43
17 14 0.47
18 1 0.03
19 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (18 bp):
AATGAATAAAAAAAATGA
Found at i:98099 original size:16 final size:16
Alignment explanation
Indices: 98057--98109 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
98047 AAAATATAGT
98057 AATGAAAT-A-AAAAA
1 AATGAAATGATAAAAA
*
98071 AATGAAA-GAATAAAGA
1 AATGAAATG-ATAAAAA
98087 AATGAAATGATAAAAAA
1 AATGAAATGAT-AAAAA
98104 AATGAA
1 AATGAA
98110 GATAACTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 7 0.22
15 1 0.03
16 13 0.41
17 11 0.34
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (16 bp):
AATGAAATGATAAAAA
Found at i:98768 original size:35 final size:37
Alignment explanation
Indices: 98722--98801 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
98712 TTTGAGAATT
*
98722 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
98757 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
98794 TGGTGATG
1 TGGTGATG
98802 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:100541 original size:21 final size:22
Alignment explanation
Indices: 100507--100550 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
100497 AAAACAACCT
100507 GCAAAGTGAATGGCTCAAAATA
1 GCAAAGTGAATGGCTCAAAATA
100529 GCAAAGT-AATGGCTCAAAATA
1 GCAAAGTGAATGGCTCAAAATA
100550 G
1 G
100551 AATGGTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.18
Consensus pattern (22 bp):
GCAAAGTGAATGGCTCAAAATA
Found at i:106721 original size:16 final size:16
Alignment explanation
Indices: 106700--106731 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
106690 TAGTTAGCTC
106700 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
106716 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
106732 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:109206 original size:15 final size:15
Alignment explanation
Indices: 109186--109215 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
109176 TGTCGTGGCA
109186 GATGCTCTTTCACGC
1 GATGCTCTTTCACGC
*
109201 GATGCTCTTTTACGC
1 GATGCTCTTTCACGC
109216 AGGTACGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.30, G:0.20, T:0.37
Consensus pattern (15 bp):
GATGCTCTTTCACGC
Found at i:119004 original size:19 final size:20
Alignment explanation
Indices: 118980--119019 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
118970 TATCCTTTCT
118980 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
118999 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
119019 T
1 T
119020 ATTATTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:119307 original size:20 final size:19
Alignment explanation
Indices: 119277--119325 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
119267 GGAGTGCAAA
*
119277 AAGAAAGAAAAAGACAAAAG
1 AAGAAA-AAAAACACAAAAG
* *
119297 AAGAGAAAAAATCAGAAAAG
1 AAGA-AAAAAAACACAAAAG
119317 AAGAAAAAA
1 AAGAAAAAA
119326 GAAAAAGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 18 0.72
21 2 0.08
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (19 bp):
AAGAAAAAAAACACAAAAG
Found at i:119336 original size:18 final size:17
Alignment explanation
Indices: 119274--119333 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
119264 ATTGGAGTGC
119274 AAAAAGAAAG-AAAAAG
1 AAAAAGAAAGAAAAAAG
*
119290 ACAAAAGAAGAGAAAAAATC
1 A-AAAAGAA-AGAAAAAA-G
119310 AGAAAAG-AAGAAAAAAG
1 A-AAAAGAAAGAAAAAAG
119327 AAAAAGA
1 AAAAAGA
119334 GAAAGCAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
16 6 0.17
17 8 0.22
18 10 0.28
19 6 0.17
20 6 0.17
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAAG
Found at i:120591 original size:90 final size:91
Alignment explanation
Indices: 120475--120656 Score: 294
Period size: 90 Copynumber: 2.0 Consensus size: 91
120465 GGGAAATGAT
*
120475 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
120539 GGGGCTGTTCATATGCAAAACACATG
66 GGGGCTGGTCATATGCAAAACACATG
* * *
120565 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
**
120630 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCATATGCAAAACACATG
120656 G
1 G
120657 GTGTTCTAGG
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 60 0.71
91 24 0.29
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCATATGCAAAACACATG
Found at i:126060 original size:19 final size:17
Alignment explanation
Indices: 126037--126094 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 17
126027 AAATTTTGGC
126037 TTTTTTTGGCTCTTTTTT
1 TTTTTTTGGC-CTTTTTT
*
126055 TATTTTTTTGCC--TTTT
1 T-TTTTTTGGCCTTTTTT
126071 TTTTTTT-GCCTTTTTT
1 TTTTTTTGGCCTTTTTT
126087 TGTTTTTT
1 T-TTTTTT
126095 TGAAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 3 0.09
15 6 0.17
16 10 0.29
17 6 0.17
18 2 0.06
19 8 0.23
ACGTcount: A:0.02, C:0.10, G:0.09, T:0.79
Consensus pattern (17 bp):
TTTTTTTGGCCTTTTTT
Found at i:126060 original size:20 final size:17
Alignment explanation
Indices: 126037--126096 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 17
126027 AAATTTTGGC
*
126037 TTTTTTTGGCTCTTTTTT
1 TTTTTTTTGC-CTTTTTT
126055 TATTTTTTTGCC---TTT
1 T-TTTTTTTGCCTTTTTT
126070 TTTTTTTTGCCTTTTTT
1 TTTTTTTTGCCTTTTTT
126087 TGTTTTTTTG
1 T-TTTTTTTG
126097 AAAAAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 10 0.28
15 4 0.11
17 4 0.11
18 10 0.28
19 8 0.22
ACGTcount: A:0.02, C:0.10, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTTTTTTGCCTTTTTT
Found at i:126074 original size:14 final size:14
Alignment explanation
Indices: 126052--126092 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
126042 TTGGCTCTTT
126052 TTTTATTTTTTTGCC
1 TTTT-TTTTTTTGCC
126067 TTTTTTTTTTTGCC
1 TTTTTTTTTTTGCC
126081 TTTTTTTGTTTT
1 TTTTTTT-TTTT
126093 TTTGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.80
Consensus pattern (14 bp):
TTTTTTTTTTTGCC
Found at i:130779 original size:20 final size:19
Alignment explanation
Indices: 130756--130793 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
130746 AATTTTGGCT
130756 TTTTTTGGCTCTTTTTTTTA
1 TTTTTTGGC-CTTTTTTTTA
*
130776 TTTTTTTGCCTTTTTTTT
1 TTTTTTGGCCTTTTTTTT
130794 TTTGCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.03, C:0.11, G:0.08, T:0.79
Consensus pattern (19 bp):
TTTTTTGGCCTTTTTTTTA
Found at i:130793 original size:14 final size:14
Alignment explanation
Indices: 130771--130811 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
130761 TGGCTCTTTT
130771 TTTTATTTTTTTGCC
1 TTTT-TTTTTTTGCC
130786 TTTTTTTTTTTGCC
1 TTTTTTTTTTTGCC
130800 TTTTTTTGTTTT
1 TTTTTTT-TTTT
130812 TTTGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.80
Consensus pattern (14 bp):
TTTTTTTTTTTGCC
Found at i:130794 original size:20 final size:21
Alignment explanation
Indices: 130755--130795 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
130745 AAATTTTGGC
*
130755 TTTTTTTGGCTCTTTTTTTTA
1 TTTTTTTGCCTCTTTTTTTTA
*
130776 TTTTTTTGCCTTTTTTTTTT
1 TTTTTTTGCCTCTTTTTTTT
130796 TGCCTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTTTGCCTCTTTTTTTTA
Found at i:134012 original size:8 final size:8
Alignment explanation
Indices: 133999--134039 Score: 64
Period size: 8 Copynumber: 4.9 Consensus size: 8
133989 TTTTTTTTCA
133999 AAAAAAAC
1 AAAAAAAC
134007 AAAAAAAC
1 AAAAAAAC
134015 AAAAAAAC
1 AAAAAAAC
134023 AAAAAAAGGC
1 AAAAAAA--C
134033 AAAAAAA
1 AAAAAAA
134040 AAAGAGCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 23 0.74
10 8 0.26
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:134036 original size:24 final size:24
Alignment explanation
Indices: 133997--134060 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
133987 TTTTTTTTTT
* * *
133997 CAAAAAAAACAAAAAAACAAAAAAA
1 CAAAAAAAGCCAAAAAA-AAAAGAA
* *
134022 CAAAAAAAGGCAAAAAAAAAAGAG
1 CAAAAAAAGCCAAAAAAAAAAGAA
*
134046 CCAAAAAAGCCAAAA
1 CAAAAAAAGCCAAAA
134061 TTTCAAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.78, C:0.14, G:0.08, T:0.00
Consensus pattern (24 bp):
CAAAAAAAGCCAAAAAAAAAAGAA
Found at i:134042 original size:16 final size:16
Alignment explanation
Indices: 133997--134042 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
133987 TTTTTTTTTT
133997 CAAAAAAAACAAAAAAA
1 CAAAAAAAA-AAAAAAA
*
134014 CAAAAAAACAAAAAAAGG
1 CAAAAAAA-AAAAAAA-A
134032 CAAAAAAAAAA
1 CAAAAAAAAAA
134043 GAGCCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAAAAAAAA
Found at i:139795 original size:22 final size:23
Alignment explanation
Indices: 139764--139806 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
139754 TAATATAGGA
139764 TGATTAATTATCTT-TTAGGATC
1 TGATTAATTATCTTATTAGGATC
* *
139786 TGATTTATTATTTTATTAGGA
1 TGATTAATTATCTTATTAGGA
139807 ATTAAGGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (23 bp):
TGATTAATTATCTTATTAGGATC
Found at i:146046 original size:30 final size:31
Alignment explanation
Indices: 146010--146069 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
146000 CTTAGCTTTA
**
146010 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
146040 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
146070 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:146965 original size:19 final size:21
Alignment explanation
Indices: 146941--146992 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
146931 CGGCCAAGAG
*
146941 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
146960 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
146981 CATGTATTTTCA
1 CATGTATTTTCA
146993 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:147429 original size:19 final size:20
Alignment explanation
Indices: 147405--147444 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
147395 TATCATTTCT
147405 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
147424 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
147444 T
1 T
147445 ATTATTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:147447 original size:19 final size:18
Alignment explanation
Indices: 147401--147447 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
147391 TCTCTATCAT
147401 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
147418 TTCTTATTATTTCTTTTCA
1 TTCTTA-TATTTCATTTCA
147437 TTACTTATATT
1 TT-CTTATATT
147448 ATTACCCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Found at i:148415 original size:19 final size:20
Alignment explanation
Indices: 148391--148442 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
148381 CGGCCAAGAG
* *
148391 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
148410 CATGTATTTTCATAAAAAAAT
1 CATGTATTTTCAT-AAAAAAT
148431 CATGTATTTTCA
1 CATGTATTTTCA
148443 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
21 17 0.59
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:151950 original size:24 final size:21
Alignment explanation
Indices: 151915--151957 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
151905 GGCTCAGTCT
*
151915 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
151938 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
151958 ATCTTATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:157528 original size:36 final size:36
Alignment explanation
Indices: 157461--157564 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
157451 ATTTATAAGT
157461 TGGTGATAATATAGGCGTGA-AATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
157496 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
* *
157532 TAGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
157565 CAGATTGTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.32, C:0.04, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:162717 original size:14 final size:15
Alignment explanation
Indices: 162700--162728 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
162690 TTACTTTTGA
162700 TTTTC-TTCTTTTTC
1 TTTTCTTTCTTTTTC
162714 TTTTCTTTCTTTTTC
1 TTTTCTTTCTTTTTC
162729 ACTCCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:162783 original size:25 final size:24
Alignment explanation
Indices: 162750--162797 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
162740 GATGTAGGAG
*
162750 TCTTTTTCTT-TTCTCTTTTTTTTT
1 TCTTTTTCTTGTT-GCTTTTTTTTT
162774 TCTTCTTTCTTGTTGCTTTTTTTT
1 TCTT-TTTCTTGTTGCTTTTTTTT
162798 GTAGCACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 15 0.71
26 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (24 bp):
TCTTTTTCTTGTTGCTTTTTTTTT
Found at i:163213 original size:13 final size:12
Alignment explanation
Indices: 163194--163279 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
163184 ATATAGGCGT
163194 GATATGGTGATG
1 GATATGGTGATG
163206 GAATATGGTGAT-
1 G-ATATGGTGATG
*
163218 GATATAGGCG-T-
1 GATAT-GGTGATG
163229 GATAATGGTGATG
1 GAT-ATGGTGATG
163242 GACTATGGTGAT-
1 GA-TATGGTGATG
*
163254 GATATAGGCG-T-
1 GATAT-GGTGATG
163265 GATAATGGTGATG
1 GAT-ATGGTGATG
163278 GA
1 GA
163280 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:163249 original size:36 final size:36
Alignment explanation
Indices: 163176--163280 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
163166 ATTTATAAGT
* *
163176 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
163211 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
163247 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
163281 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:170598 original size:22 final size:21
Alignment explanation
Indices: 170556--170595 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
170546 AAGACTATTT
170556 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
170577 TCATTTTTGT-ATTTTGAAA
1 TCATTTTT-TAATTTTGAAA
170596 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:181115 original size:38 final size:38
Alignment explanation
Indices: 181054--181212 Score: 203
Period size: 38 Copynumber: 4.2 Consensus size: 38
181044 ATATTTATTA
*
181054 AGCAATTCGGTGCATATGATGGGCACGAACTTATGTGT
1 AGCACTTCGGTGCATATGATGGGCACGAACTTATGTGT
* * *
181092 AGCACTTCGGTGCATACGTTGGGCACGACCTTATGTGT
1 AGCACTTCGGTGCATATGATGGGCACGAACTTATGTGT
* * *
181130 AGCACTTCAGTGCAAATGATGGGCACGACCTTATGTGT
1 AGCACTTCGGTGCATATGATGGGCACGAACTTATGTGT
* * *
181168 AGCACTTTGGTGCATATGGTAGGCAC-AACCTTATGTGT
1 AGCACTTCGGTGCATATGATGGGCACGAA-CTTATGTGT
181206 AAGCACT
1 -AGCACT
181213 ACGATGTATA
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
37 1 0.01
38 98 0.93
39 6 0.06
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (38 bp):
AGCACTTCGGTGCATATGATGGGCACGAACTTATGTGT
Found at i:181193 original size:76 final size:77
Alignment explanation
Indices: 181052--181212 Score: 234
Period size: 76 Copynumber: 2.1 Consensus size: 77
181042 TCATATTTAT
* * * * *
181052 TAAGCAATTCGGTGCATATGATGGGCACGAACTTATGTGTAGCACTTCGGTGCATACGTTGGGCA
1 TAAGCACTTCAGTGCAAATGATGGGCACGAACTTATGTGTAGCACTTCGGTGCATACGGTAGGCA
*
181117 CGACCTTATGTG
66 CAACCTTATGTG
* * *
181129 T-AGCACTTCAGTGCAAATGATGGGCACGACCTTATGTGTAGCACTTTGGTGCATATGGTAGGCA
1 TAAGCACTTCAGTGCAAATGATGGGCACGAACTTATGTGTAGCACTTCGGTGCATACGGTAGGCA
181193 CAACCTTATGTG
66 CAACCTTATGTG
181205 TAAGCACT
1 TAAGCACT
181213 ACGATGTATA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
76 67 0.91
77 7 0.09
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (77 bp):
TAAGCACTTCAGTGCAAATGATGGGCACGAACTTATGTGTAGCACTTCGGTGCATACGGTAGGCA
CAACCTTATGTG
Found at i:186593 original size:9 final size:9
Alignment explanation
Indices: 186577--186617 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
186567 AATAAATAAT
186577 TTATTTTTA
1 TTATTTTTA
*
186586 TAATTTTT-
1 TTATTTTTA
*
186594 TTATTTTTC
1 TTATTTTTA
186603 TTATTTTTA
1 TTATTTTTA
186612 TTATTT
1 TTATTT
186618 ACAGACATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (9 bp):
TTATTTTTA
Found at i:186596 original size:17 final size:17
Alignment explanation
Indices: 186576--186617 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
186566 AAATAAATAA
186576 TTTATTTTTATAATTTT
1 TTTATTTTTATAATTTT
* *
186593 TTTATTTTTCTTATTTT
1 TTTATTTTTATAATTTT
186610 TATTATTT
1 T-TTATTT
186618 ACAGACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTTATAATTTT
Found at i:189320 original size:19 final size:20
Alignment explanation
Indices: 189273--189323 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
189263 GAAATCCCTT
**
189273 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
189293 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
189312 TGAAGATACATG
1 TGAAAATACATG
189324 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:190811 original size:55 final size:55
Alignment explanation
Indices: 190699--190814 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 55
190689 TGACACTATA
* * *
190699 TGTG-AAAACTAATAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGGG
* * * *
190753 TGTGCAAAACTAAGAAATTCATAATAAGTTTGTGAATTTCCT-TATTGGTAGTGGG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTT-CTGTATGGGCACTGGG
190808 TGTGCAA
1 TGTGCAA
190815 CTCACGTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
54 4 0.08
55 48 0.91
56 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.37
Consensus pattern (55 bp):
TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGGG
Found at i:190826 original size:55 final size:55
Alignment explanation
Indices: 190699--190836 Score: 133
Period size: 55 Copynumber: 2.5 Consensus size: 55
190689 TGACACTATA
* * *
190699 TGTGAAAACTAA-TAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTGTG
1 TGTGCAAACTAAGTAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGGG
* * * *
190753 TGTGCAAAACTAAG-AAATTCATAATAAGTTTGTGAATTTCCT-TATTGGTAGTGGG
1 TGTGC-AAACTAAGTAAATTCATAATAAGTTTATGAATTT-CTGTATGGGCACTGGG
* *
190808 TGTGC-AACTCACGTAAATT-ATAGTAAGTT
1 TGTGCAAACT-AAGTAAATTCATAATAAGTT
190837 GGGAAATTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
53 4 0.06
54 15 0.21
55 50 0.71
56 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (55 bp):
TGTGCAAACTAAGTAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGGG
Found at i:197504 original size:12 final size:12
Alignment explanation
Indices: 197487--197515 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
197477 TCACTCATAG
197487 AAGAATGAGAGA
1 AAGAATGAGAGA
197499 AAGAATGAGAGA
1 AAGAATGAGAGA
197511 AAGAA
1 AAGAA
197516 AAGAAGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.07
Consensus pattern (12 bp):
AAGAATGAGAGA
Found at i:207502 original size:45 final size:45
Alignment explanation
Indices: 207421--207555 Score: 201
Period size: 45 Copynumber: 3.1 Consensus size: 45
207411 TCATTTAATA
*
207421 CCATAAGCTCGTAAGCTTATTTT--C---ATACTTATCATTTGTT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTT
207461 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTT
* *
207506 CCATAAGCTCGTAAGCTTATTTTACCAATACACTTACCA-TTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTT
207550 CCATAA
1 CCATAA
207556 ACTATATTCC
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
40 23 0.26
42 1 0.01
44 10 0.11
45 53 0.61
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTT
Found at i:214253 original size:93 final size:92
Alignment explanation
Indices: 214130--214479 Score: 348
Period size: 93 Copynumber: 3.8 Consensus size: 92
214120 CAACATCTTT
* * *
214130 TCCAAGTTGTTACATTAATGAATGGTAGTTTGAATATAATTGAAATGTCTTACCCAAACACTTTG
1 TCCAAGTTGTTACATTAATGGATGGAAGTTTGAATATAATTGAAATGTCTTA-CTAAACACTTTG
* *
214195 ATACTTACTAATTAAAGAGGTTAACATA
65 ATATTTACTGATTAAAGAGGTTAACATA
* *** * *
214223 TCCATGTTGTTACATTAATGGATGGAAGTTTGAATAGCGTTGAAATGTTTTAATAAAGCACTTTG
1 TCCAAGTTGTTACATTAATGGATGGAAGTTTGAATATAATTGAAATGTCTTACTAAA-CACTTTG
* * *
214288 ATATTTA-TGGACTAAAGATGTTAACGTA
65 ATATTTACT-GATTAAAGAGGTTAACATA
* * * ** * *
214316 TTCAAGTTGTTACTTTAATGGTTAAAAGTTTGAATAGT-GTTGAAATATCTTAGCTAAACACTTT
1 TCCAAGTTGTTACATTAATGGATGGAAGTTTGAATA-TAATTGAAATGTCTTA-CTAAACACTTT
* * * *
214380 GATGTTTACGGATTAATGAGGTTAACTTA
64 GATATTTACTGATTAAAGAGGTTAACATA
* * * *
214409 TCCAAGTAGTTACATTAATGGTTGGAAGATTGAATA-ACATTGAAATGTTTTAACTAAACACTTT
1 TCCAAGTTGTTACATTAATGGATGGAAGTTTGAATATA-ATTGAAATGTCTT-ACTAAACACTTT
214473 GAT-TTTA
64 GATATTTA
214480 GTTTCAATTA
Statistics
Matches: 210, Mismatches: 39, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
92 8 0.04
93 197 0.94
94 5 0.02
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (92 bp):
TCCAAGTTGTTACATTAATGGATGGAAGTTTGAATATAATTGAAATGTCTTACTAAACACTTTGA
TATTTACTGATTAAAGAGGTTAACATA
Found at i:214795 original size:93 final size:93
Alignment explanation
Indices: 214655--215149 Score: 525
Period size: 93 Copynumber: 5.3 Consensus size: 93
214645 TTGAATAACG
* * * * * * *
214655 TTGAAATGCCTTAACTAAACAATTTGATGTGTATGTATTAAGGAGGTTAACTTATCCAAGTTGTT
1 TTGAAATGTCTTAACTAAACACTTTGATGTTTACGGAGTAAAGAGGTTAACTTATCCAAGTTGTT
* *
214720 ACATTAATGGATGGAAATTTGAATAATT
66 ACATTAATGGATGGAAATTTGAATAGTA
* * * * **
214748 TTAAAATTTATTAACTAAACACTTTGATGTTTATGGAGTAAAGAGGTTAACTTATCCAAGCGGTT
1 TTGAAATGTCTTAACTAAACACTTTGATGTTTACGGAGTAAAGAGGTTAACTTATCCAAGTTGTT
* * * *
214813 ACATTAGTGGATGGTAGTTTGAATAGTT
66 ACATTAATGGATGGAAATTTGAATAGTA
* ** * * * *
214841 TTGAAATGTCTTAACTCAACACTTTGACATTTACGGACTAAAAATGTTAACTTATTCAAGTTGTT
1 TTGAAATGTCTTAACTAAACACTTTGATGTTTACGGAGTAAAGAGGTTAACTTATCCAAGTTGTT
* *
214906 ACATTAATGGATGG-AATATTGAATAATG
66 ACATTAATGGATGGAAAT-TTGAATAGTA
* * *
214934 TTGAAATGTCTTAACTAAACATTTTGATGTTTGCGG-GCTAAAGAGGTTAACTTATTCAAGTTGT
1 TTGAAATGTCTTAACTAAACACTTTGATGTTTACGGAG-TAAAGAGGTTAACTTATCCAAGTTGT
* * * *
214998 TACATTAATGGTTAGAAGTTTGAATAGCA
65 TACATTAATGGATGGAAATTTGAATAGTA
* *
215027 TTGAAATGTCTTAA-TAAACACTTTGATGTTCACGG-GATAAAGATGTTAACTTATCCAAGTTGT
1 TTGAAATGTCTTAACTAAACACTTTGATGTTTACGGAG-TAAAGAGGTTAACTTATCCAAGTTGT
* *
215090 TACATTAAT-TATTGGAAGA-TTGAATAGCA
65 TACATTAATGGA-TGGAA-ATTTGAATAGTA
* * *
215119 TTGAAATCTTTTAACTAAGCACTTTGATGTT
1 TTGAAATGTCTTAACTAAACACTTTGATGTT
215150 AGTTTTGATT
Statistics
Matches: 337, Mismatches: 59, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
92 80 0.24
93 255 0.76
94 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (93 bp):
TTGAAATGTCTTAACTAAACACTTTGATGTTTACGGAGTAAAGAGGTTAACTTATCCAAGTTGTT
ACATTAATGGATGGAAATTTGAATAGTA
Found at i:216346 original size:30 final size:33
Alignment explanation
Indices: 216312--216373 Score: 103
Period size: 30 Copynumber: 2.0 Consensus size: 33
216302 AAAAATAATA
216312 AAATTACAAT-AAAAGTCTAA-ATTTT-TATAG
1 AAATTACAATAAAAAGTCTAATATTTTATATAG
216342 AAATTACAATAAAAAGTCTAATATTTTATATA
1 AAATTACAATAAAAAGTCTAATATTTTATATA
216374 TTAGAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 10 0.34
31 10 0.34
32 5 0.17
33 4 0.14
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (33 bp):
AAATTACAATAAAAAGTCTAATATTTTATATAG
Found at i:216442 original size:29 final size:29
Alignment explanation
Indices: 216388--216444 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
216378 AATAAAAGGT
*
216388 AAAACTTTTTACAAATAATAAGAAATACC
1 AAAACTTTTTACAAATAACAAGAAATACC
* * *
216417 AAAACTTTTTATAAATTACAATAAATAC
1 AAAACTTTTTACAAATAACAAGAAATAC
216445 TATTTTCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAACTTTTTACAAATAACAAGAAATACC
Found at i:219628 original size:45 final size:45
Alignment explanation
Indices: 219497--219758 Score: 339
Period size: 45 Copynumber: 5.8 Consensus size: 45
219487 TTCATTGAAA
* * * * *
219497 GCATCCATTCATG-CTTATAATGCACCATTATGCATTTTCATTTATG
1 GCATCCTTTCATGCCTT-TTATACACTATTATACA-TTTCATTTATG
* * *
219543 GCAACCGTTCATGCCTTTTTATACAATATTATACATTTCATTTATG
1 GCATCCTTTCATGCC-TTTTATACACTATTATACATTTCATTTATG
* * * *
219589 GCATCCTTTAATGCCTTTTATACTCTATTAAACAATTCATTTATG
1 GCATCCTTTCATGCCTTTTATACACTATTATACATTTCATTTATG
*
219634 GCAT-CTTTCATTCCTTTTATACACTATTATACATTTCATTTATG
1 GCATCCTTTCATGCCTTTTATACACTATTATACATTTCATTTATG
* *
219678 GCATCCTTTCATGCCTTTTATACTCTATTAGACATTTCATTTATG
1 GCATCCTTTCATGCCTTTTATACACTATTATACATTTCATTTATG
*
219723 GCATCCTTTCATGCCTTTTATACACCATTATACATT
1 GCATCCTTTCATGCCTTTTATACACTATTATACATT
219759 ATTATACATA
Statistics
Matches: 188, Mismatches: 25, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
44 39 0.21
45 100 0.53
46 34 0.18
47 13 0.07
48 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (45 bp):
GCATCCTTTCATGCCTTTTATACACTATTATACATTTCATTTATG
Found at i:219662 original size:89 final size:89
Alignment explanation
Indices: 219533--219758 Score: 353
Period size: 89 Copynumber: 2.5 Consensus size: 89
219523 ATTATGCATT
* * *
219533 TTCATTTATGGCAACCGTTCATGCCTTTTTATACAATATTATACATTTCATTTATGGCATCCTTT
1 TTCATTTATGGC-ATCTTTCATGCC-TTTTATACACTATTATACATTTCATTTATGGCATCCTTT
219598 AATGCCTTTTATACTCTATTAAACAA
64 AATGCCTTTTATACTCTATTAAACAA
* *
219624 TTCATTTATGGCATCTTTCATTCCTTTTATACACTATTATACATTTCATTTATGGCATCCTTTCA
1 TTCATTTATGGCATCTTTCATGCCTTTTATACACTATTATACATTTCATTTATGGCATCCTTTAA
* *
219689 TGCCTTTTATACTCTATTAGACAT
66 TGCCTTTTATACTCTATTAAACAA
*
219713 TTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATACATT
1 TTCATTTATGGCAT-CTTTCATGCCTTTTATACACTATTATACATT
219759 ATTATACATA
Statistics
Matches: 125, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
89 75 0.60
90 38 0.30
91 12 0.10
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (89 bp):
TTCATTTATGGCATCTTTCATGCCTTTTATACACTATTATACATTTCATTTATGGCATCCTTTAA
TGCCTTTTATACTCTATTAAACAA
Found at i:219855 original size:68 final size:68
Alignment explanation
Indices: 219779--219983 Score: 302
Period size: 68 Copynumber: 3.0 Consensus size: 68
219769 TAGTCTTTTA
* * * * * *
219779 CTCAAAGGCATTTAACCTTTCATCTAACTGACATGATTGACACCTTTCCGTCAAATGCACAGCTA
1 CTCAAAGGCAATTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
219844 GGC
66 GGC
* *
219847 CTCAAAGGCAATTAGCCTTTCATCTATCTGGCATAATTGACACCTCTCTGTCAAATGCACAGTTA
1 CTCAAAGGCAATTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
219912 GGC
66 GGC
* * * *
219915 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTAACACCTTTTTGTCAAATACACAGTTA
1 CTCAAAGGCAATTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
219980 GGC
66 GGC
219983 C
1 C
219984 AATAATCTTT
Statistics
Matches: 123, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 123 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (68 bp):
CTCAAAGGCAATTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
GGC
Found at i:220881 original size:55 final size:55
Alignment explanation
Indices: 220163--220863 Score: 897
Period size: 55 Copynumber: 12.8 Consensus size: 55
220153 AGGTAGTTTG
* * * * *
220163 TCAACTCATGATGAATTTCGTGGATTTGTAGACATAGTGCATGTACGGTTATTCA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
** * ** **
220218 TCAACTCATGATGAATTATGT-GATTTGCACACAAAATGTTTGTACAATTATTCA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
** * *
220272 TCAACTCATGATGAATTTTGTGGATTTGCACACATAGTGCATGTACGGTTATTCA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
* * * **
220327 TCAACTCATGATAAATTCCATGGATTTGCACACAAAGTTCCTGTACAATTATTCA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
* * * *
220382 TCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCTTGTACGATTATTCA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
* * * * * * *
220437 TCAACTCATGATGAATTTCATGGATTTGCCCATAAAGCGCTTGTACAGTTATTCA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
* * *
220492 TCAACTCATGATGAATTCCGTGGATTTACACACAAAGTGCATGTATGGTTATTCA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
* * * *
220547 TCAACTCATGTTGAAATCAGTGGATTTGCACACAAAGTGCATGTACGGTTATT--
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
* * *
220600 T-AACTCATTATGAATTCCATGGATTTGCACACAAAGTGCCTATACGGTTATTCA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
* * * * *
220654 TCAACTCATGATGAATTTCGGGGATTTGCACATATAGTGCCTGTACGGTTTTTCA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
*
220709 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCGTGTACGGTTATTCA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
* * *
220764 TCAACTCATGATGAATTCTGTGGATTCGCACACAAAGTGCCTCTACGGTTATTCA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
* *
220819 TCAACTCATGATGAATTCCATGGATTTACACACAAAGTGCCTGTA
1 TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTA
220864 GGAAAATTCA
Statistics
Matches: 558, Mismatches: 84, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
52 44 0.08
53 1 0.00
54 46 0.08
55 467 0.84
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (55 bp):
TCAACTCATGATGAATTCCGTGGATTTGCACACAAAGTGCCTGTACGGTTATTCA
Found at i:221354 original size:20 final size:20
Alignment explanation
Indices: 221329--221385 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 20
221319 CAATGTTTCC
221329 TGGTATCGATACCCCTACCA
1 TGGTATCGATACCCCTACCA
* * *
221349 TGGTATGGATACTACCATACTA
1 TGGTATCGATAC--CCCTACCA
*
221371 TGGTATTGATACCCC
1 TGGTATCGATACCCC
221386 CTTCCGGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 13 0.43
22 17 0.57
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (20 bp):
TGGTATCGATACCCCTACCA
Found at i:221401 original size:95 final size:95
Alignment explanation
Indices: 221271--221459 Score: 252
Period size: 95 Copynumber: 2.0 Consensus size: 95
221261 GACATTTCTT
* * * *
221271 TACTATGGTACCGATACCCCCTTCAGGTATCGATACCAATTTTTGGTTCAATGTTTCCTGGTATC
1 TACTATGGTACCGATACCCCCTTCAGGTATCGATACCAATTTTAGCTTCAATGATGCCTGGTATC
*
221336 GATACCCCTACCATGGTATGGATACTACCA
66 GATACACCTACCATGGTATGGATACTACCA
** * * * * *
221366 TACTATGGTATTGATACCCCCTTCCGGTATTGATACCAATTTTAGCTTCGATGATGCTTGGTATT
1 TACTATGGTACCGATACCCCCTTCAGGTATCGATACCAATTTTAGCTTCAATGATGCCTGGTATC
* *
221431 GATACACTTACCATGGTATTGATACTACC
66 GATACACCTACCATGGTATGGATACTACC
221460 TTGTCGGTAT
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 80 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (95 bp):
TACTATGGTACCGATACCCCCTTCAGGTATCGATACCAATTTTAGCTTCAATGATGCCTGGTATC
GATACACCTACCATGGTATGGATACTACCA
Found at i:228093 original size:8 final size:8
Alignment explanation
Indices: 228082--228145 Score: 78
Period size: 8 Copynumber: 8.0 Consensus size: 8
228072 TTTTTGGCTC
228082 TTTTTTTG
1 TTTTTTTG
228090 TTTTTTTG
1 TTTTTTTG
**
228098 CCTTTTT-
1 TTTTTTTG
228105 TTTTTTTG
1 TTTTTTTG
228113 CCTTTTTTTG
1 --TTTTTTTG
228123 -TTTTTTG
1 TTTTTTTG
228130 TTTTTTTG
1 TTTTTTTG
228138 TTTTTTTG
1 TTTTTTTG
228146 AAAAAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
7 12 0.25
8 28 0.58
10 8 0.17
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (8 bp):
TTTTTTTG
Found at i:228106 original size:20 final size:20
Alignment explanation
Indices: 228071--228111 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
228061 AAATTTTGGC
*
228071 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGCCTCTTTTTTTGT
228091 TTTTTTGCCT-TTTTTTT-T
1 TTTTTTGCCTCTTTTTTTGT
228109 TTT
1 TTT
228112 GCCTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 9 0.45
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (20 bp):
TTTTTTGCCTCTTTTTTTGT
Found at i:228118 original size:33 final size:34
Alignment explanation
Indices: 228071--228145 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 34
228061 AAATTTTGGC
*
228071 TTTTTTGGCTCTTTTTTTGTTTTTTTGCCTTTTT-
1 TTTTTTTGCTCTTTTTTTG-TTTTTTGCCTTTTTG
**
228105 TTTTTTTGC-CTTTTTTTGTTTTTTGTTTTTTTG
1 TTTTTTTGCTCTTTTTTTGTTTTTTGCCTTTTTG
228138 TTTTTTTG
1 TTTTTTTG
228146 AAAAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 12 0.32
33 17 0.46
34 8 0.22
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (34 bp):
TTTTTTTGCTCTTTTTTTGTTTTTTGCCTTTTTG
Found at i:228133 original size:15 final size:16
Alignment explanation
Indices: 228081--228143 Score: 85
Period size: 15 Copynumber: 3.9 Consensus size: 16
228071 TTTTTTGGCT
228081 CTTTTTTTGTTTTTTTG
1 CTTTTTTTG-TTTTTTG
*
228098 CCTTTTTT-TTTTTTG
1 CTTTTTTTGTTTTTTG
228113 CCTTTTTTTGTTTTTTG
1 -CTTTTTTTGTTTTTTG
228130 -TTTTTTTGTTTTTT
1 CTTTTTTTGTTTTTT
228144 TGAAAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
15 21 0.50
16 7 0.17
17 14 0.33
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.83
Consensus pattern (16 bp):
CTTTTTTTGTTTTTTG
Found at i:231212 original size:90 final size:90
Alignment explanation
Indices: 231068--231295 Score: 377
Period size: 90 Copynumber: 2.5 Consensus size: 90
231058 CATTATGCAT
* * * *
231068 TTTCATTTATGGCAACCGTTCATGCCTTTTTATACACTATTATACTTTTCATTTATGGCATCCTT
1 TTTCATTTATGGCATCCTTTCATGCC-TTTTATACACAATTATACATTTCATTTATGGCATCCTT
231133 TCATGCCTTTTATACTCTATTA-AACA
65 TCATGCCTTTTATACTCTATTATAA-A
*
231159 TTTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATACATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTTATACACAATTATACATTTCATTTATGGCATCCTTT
231224 CATGCCTTTTATACTCTATTATAAA
66 CATGCCTTTTATACTCTATTATAAA
*
231249 TTTCATTTATGGCATCCTTTCATGCCTTTTATACAGAATTATACATT
1 TTTCATTTATGGCATCCTTTCATGCCTTTTATACACAATTATACATT
231296 GTTATACATC
Statistics
Matches: 130, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
90 104 0.80
91 26 0.20
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.46
Consensus pattern (90 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTTATACACAATTATACATTTCATTTATGGCATCCTTT
CATGCCTTTTATACTCTATTATAAA
Found at i:231291 original size:45 final size:45
Alignment explanation
Indices: 231068--231283 Score: 335
Period size: 45 Copynumber: 4.8 Consensus size: 45
231058 CATTATGCAT
* * **
231068 TTTCATTTATGGCAACCGTTCATGCCTTTTTATACACTATTATACT
1 TTTCATTTATGGCATCCTTTCATGCC-TTTTATACACTATTATAAA
*
231114 TTTCATTTATGGCATCCTTTCATGCCTTTTATACTCTATTA-AACA
1 TTTCATTTATGGCATCCTTTCATGCCTTTTATACACTATTATAA-A
* *
231159 TTTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATACA
1 TTTCATTTATGGCATCCTTTCATGCCTTTTATACACTATTATAAA
*
231204 TTTCATTTATGGCATCCTTTCATGCCTTTTATACTCTATTATAAA
1 TTTCATTTATGGCATCCTTTCATGCCTTTTATACACTATTATAAA
231249 TTTCATTTATGGCATCCTTTCATGCCTTTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCTTTTATACA
231284 GAATTATACA
Statistics
Matches: 156, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
44 1 0.01
45 130 0.83
46 25 0.16
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.47
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTTATACACTATTATAAA
Found at i:231426 original size:68 final size:68
Alignment explanation
Indices: 231316--231654 Score: 464
Period size: 68 Copynumber: 5.0 Consensus size: 68
231306 TAGTCTTTTA
* * * * * *
231316 CTCAAAGGCATTTAACCTTTCATCTAACTGACATGATTGACACCTTTTTGT-AAGATGCACAGCT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAA-ATGCACAGTT
231380 AGGC
65 AGGC
* * * * *
231384 CTCAAAGGTACTTAGCCTTTCATCTAACTGGCATAATCGACACTTTTATGTCAAATACACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
*
231449 GAC
66 GGC
* * * * *
231452 CTCAAAGGCACTTAGCCTTTTATCTAATTGGCATAATTAACACCTTTATGTCAAATGCACAGTTT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
231517 GGC
66 GGC
* * *
231520 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTAACACCATTCTGTCAAATGCACTGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
231585 GGC
66 GGC
* *
231588 CTCAAAGGCACTTATCCTTTCATCTAAATGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
231653 GG
66 GG
231655 TCATTAATAT
Statistics
Matches: 239, Mismatches: 31, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
68 237 0.99
69 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
GGC
Found at i:232552 original size:55 final size:55
Alignment explanation
Indices: 231807--232542 Score: 843
Period size: 55 Copynumber: 13.4 Consensus size: 55
231797 TTTATTAAGA
** * *
231807 TGCACACGTAGTGCCTATACGG-TAGTTTATCAACTCATGATGAATT-TCGTGGATT
1 TGCACACAAAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCT-GTGGATT
* * ** * * * *
231862 TACACACAAGGTGTTTGTACGGTTATTTATCAACTCTTGGTGAATTCCGTGGATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * ** *
231917 TGAACATAAAGTGCCTGTATAGTTATTCATTAACTCATGATGAATTCCT-TGGATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-CTGTGGATT
* * * * ** *
231972 TGTACACATAGTTCTTGTATAGTTATTCATCAACTCATGATGAATTCAGTGGATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * *
232027 TGCACACAAAATGCTTGTACGATTATTCATCAACTCATGATGAATAT-TCGTGGATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAAT-TCT-GTGGATT
* * ** *
232083 TTCACACAAAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGTATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * * * *
232138 TGCACACAAAGTGCTTGTACGATTATTCATCAACTTATGATGAGTTATGTGGATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * * * *
232193 TGCACGCATAGTGCCTGTATGGTTATTCATCAACTCATTATGAATTATGTGGATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * *
232248 TGCACACAAAGTACCTATACGGTTATTCATCAACTCATGATGAATT-TCATGGATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGATT
* * * * **
232303 TGCACACATAGTGACAGTACGGTTATTCATAAACTCATGATGAATTCCATGGATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * *
232358 TGCACACAAAGTACCTGTAAGGTTATTCATCATCTCATGATGAATTCTGTGGATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * *
232413 TGCACACATAGTGCCTGTACGGTTATTCATCAACTTATGATGAATTCCGTGGATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * *
232468 TGCACACAAAGTGCTTGTATGGTAATTCATCAACTCATGATGAATTCTGTGGATT
1 TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
232523 TGCACACAAAGTGCCTGTAC
1 TGCACACAAAGTGCCTGTAC
232543 AAAAATTCAT
Statistics
Matches: 573, Mismatches: 99, Indels: 18
0.83 0.14 0.03
Matches are distributed among these distances:
54 2 0.00
55 519 0.91
56 52 0.09
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (55 bp):
TGCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
Found at i:234461 original size:93 final size:93
Alignment explanation
Indices: 234298--234471 Score: 267
Period size: 93 Copynumber: 1.9 Consensus size: 93
234288 ACGTGTTTAA
** * *
234298 CTAAACACTTTGATGTTTATGAACTAAAGATGTTAACTTATCCAAGTAGTTACATTAATATATGG
1 CTAAACACTTTGATGTTTACAAACTAAAGAGGTTAACTTATCCAAGTAGTTACATTAATAGATGG
*
234363 TAGTTTGAATACCATTAAAATATCTTGT
66 AAGTTTGAATACCATTAAAATATCTTGT
* ** *
234391 CTAAATACTTTGATGTTTACAAACTAAAGAGGTTAACTTATCCATTTCGTTACATTAATAGATGG
1 CTAAACACTTTGATGTTTACAAACTAAAGAGGTTAACTTATCCAAGTAGTTACATTAATAGATGG
234456 AAGTTTGAATACCATT
66 AAGTTTGAATACCATT
234472 GTCATTAACT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (93 bp):
CTAAACACTTTGATGTTTACAAACTAAAGAGGTTAACTTATCCAAGTAGTTACATTAATAGATGG
AAGTTTGAATACCATTAAAATATCTTGT
Found at i:234737 original size:93 final size:92
Alignment explanation
Indices: 234568--234741 Score: 210
Period size: 93 Copynumber: 1.9 Consensus size: 92
234558 TGCTTACACA
* * *
234568 TTAACTTATCCAAGTTGTTACAGTAACGAATGAAATTTGAATATCGTTGAAATGTTCTAACTAAA
1 TTAACTAATCCAAGTTGTTACAGTAACGAATGAAATTTGAATAGCGTTGAAAAGTTCTAACTAAA
* *
234633 TAGTTTCATGTTTATGGATTGAGGAGG
66 CACTTTCATGTTTATGGATTGAGGAGG
* * *
234660 TTAACTAATCCCAA-TTGTTACATTAATGGATGAAAATTTGAATAGCGTTGAAACCAG-T-TAAC
1 TTAACTAAT-CCAAGTTGTTACAGTAACGAATG-AAATTTGAATAGCGTTGAAA--AGTTCTAAC
*
234722 TAAACACTTTGATGTTTATG
62 TAAACACTTTCATGTTTATG
234742 AACTACTTAG
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
92 23 0.33
93 44 0.64
94 1 0.01
95 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (92 bp):
TTAACTAATCCAAGTTGTTACAGTAACGAATGAAATTTGAATAGCGTTGAAAAGTTCTAACTAAA
CACTTTCATGTTTATGGATTGAGGAGG
Found at i:238420 original size:19 final size:20
Alignment explanation
Indices: 238396--238467 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 20
238386 ATGACAAAAT
238396 GGTATCGATACCATAG-AAG
1 GGTATCGATACCATAGTAAG
*
238415 GGTATCGATACCATAGTATG
1 GGTATCGATACCATAGTAAG
* * *
238435 GTAGTATCAATACCATGGTAGG
1 G--GTATCGATACCATAGTAAG
238457 GGTATCGATAC
1 GGTATCGATAC
238468 TCAGGAGCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.36
20 12 0.27
22 17 0.38
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:238941 original size:45 final size:45
Alignment explanation
Indices: 238876--239260 Score: 502
Period size: 45 Copynumber: 8.6 Consensus size: 45
238866 GAATGAAAAC
*** *
238876 ATAATAATGCATATGGGTGCATTATCAACATGAAAGGATGCAAAA
1 ATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAA
* *
238921 ATAATAATGTATATGTGTGCATTATTGGCATGAAAGGATGCCAAA
1 ATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAA
* * * *
238966 ATAATAATACATATGGGTGCATTATTGGTATGAACGGAGGCCAAA
1 ATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAA
* * *
239011 ATAATAATGCATATGGCTGCATTATTGGTATGAAATGATGCCAAA
1 ATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAA
* * * * *
239056 ATAATAATGCATATGGGAGTATTATCGGCATGACAGGATACCAAA
1 ATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAA
** *
239101 ATAATAATGCATATGGGTGCATTATCAGCATTAAAGGATGCCAAA
1 ATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAA
* *
239146 ATAATAATGCATATGGGTGTATTATTAGCATGAAAGGATGCCAAA
1 ATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAA
* *
239191 ATAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAG
1 ATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AA
* * *
239237 TTGA-AATGAATATGGGTGCATTAT
1 ATAATAATGCATATGGGTGCATTAT
239261 CAGCATAAAA
Statistics
Matches: 298, Mismatches: 41, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 295 0.99
46 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.29
Consensus pattern (45 bp):
ATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAA
Found at i:243474 original size:21 final size:22
Alignment explanation
Indices: 243450--243490 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
243440 TGATTGTTGC
243450 ATATGA-TGTTATCATGAATAT
1 ATATGATTGTTATCATGAATAT
*
243471 ATATGATTTTTATCATGAAT
1 ATATGATTGTTATCATGAAT
243491 GTTATTTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (22 bp):
ATATGATTGTTATCATGAATAT
Found at i:243851 original size:13 final size:13
Alignment explanation
Indices: 243833--243858 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
243823 GGCTATTGTC
243833 TATTGTTTATGGT
1 TATTGTTTATGGT
243846 TATTGTTTATGGT
1 TATTGTTTATGGT
243859 AAATGGTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (13 bp):
TATTGTTTATGGT
Found at i:248910 original size:22 final size:22
Alignment explanation
Indices: 248882--248924 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
248872 TTCATATTAG
248882 GTTGAAGAATTGGATTAAACAA
1 GTTGAAGAATTGGATTAAACAA
248904 GTTGAAGAATTGGATTAAACA
1 GTTGAAGAATTGGATTAAACA
248925 GGTTTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (22 bp):
GTTGAAGAATTGGATTAAACAA
Found at i:251250 original size:21 final size:22
Alignment explanation
Indices: 251226--251266 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
251216 TGATTGTTGC
251226 ATATGA-TGTTATCATGAATAT
1 ATATGATTGTTATCATGAATAT
*
251247 ATATGATTTTTATCATGAAT
1 ATATGATTGTTATCATGAAT
251267 GTTATTTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (22 bp):
ATATGATTGTTATCATGAATAT
Found at i:251511 original size:60 final size:60
Alignment explanation
Indices: 251426--251540 Score: 194
Period size: 60 Copynumber: 1.9 Consensus size: 60
251416 TTGGGAATAC
** * *
251426 ACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTCATATTCGGGAACTGT
1 ACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTCATATTCGGGAACTGT
251486 ACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTCATATTCGGGA
1 ACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTCATATTCGGGA
251541 TTGTACAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (60 bp):
ACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTCATATTCGGGAACTGT
Found at i:255979 original size:20 final size:20
Alignment explanation
Indices: 255954--256004 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
255944 ATTCAATCGA
*
255954 TATCGATATCAAAGGGGAA-G
1 TATCGATACCAAA-GGGAATG
255974 TATCGATACCAAAGGGAATG
1 TATCGATACCAAAGGGAATG
255994 TATCGATACCA
1 TATCGATACCA
256005 TTCAAAACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 5 0.17
20 24 0.83
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.22
Consensus pattern (20 bp):
TATCGATACCAAAGGGAATG
Found at i:256054 original size:19 final size:19
Alignment explanation
Indices: 256026--256138 Score: 109
Period size: 22 Copynumber: 5.6 Consensus size: 19
256016 ATGAAAAAAT
*
256026 GGTATCGATACCAAAGTAG
1 GGTATCGATACCATAGTAG
* *
256045 GGTATTGATAACATAGTATG
1 GGTATCGATACCATAGTA-G
*
256065 GTAGTATCGATACCATGGTAG
1 G--GTATCGATACCATAGTAG
*
256086 GGTATTGATACCATAGTATG
1 GGTATCGATACCATAGTA-G
*
256106 GTAGTATCGATACCATGGTAGG
1 G--GTATCGATACCATAGTA-G
256128 GGTATCGATAC
1 GGTATCGATAC
256139 TGAGGAGCTA
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
19 30 0.39
20 14 0.18
21 2 0.03
22 31 0.40
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:256076 original size:22 final size:22
Alignment explanation
Indices: 256027--256138 Score: 105
Period size: 19 Copynumber: 5.5 Consensus size: 22
256017 TGAAAAAATG
*
256027 GTATCGATACCAAAGTA-GG--
1 GTATCGATACCATAGTATGGTA
* *
256046 GTATTGATAACATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
*
256068 GTATCGATACCATGGTA-GG--
1 GTATCGATACCATAGTATGGTA
*
256087 GTATTGATACCATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
* *
256109 GTATCGATACCATGGTA-GG-G
1 GTATCGATACCATAGTATGGTA
256129 GTATCGATAC
1 GTATCGATAC
256139 TGAGGAGCTA
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
19 29 0.38
20 14 0.18
21 4 0.05
22 29 0.38
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:256121 original size:41 final size:41
Alignment explanation
Indices: 256027--256138 Score: 179
Period size: 41 Copynumber: 2.7 Consensus size: 41
256017 TGAAAAAATG
** *
256027 GTATCGATACCAAAGTAGGGTATTGATAACATAGTATGGTA
1 GTATCGATACCATGGTAGGGTATTGATACCATAGTATGGTA
256068 GTATCGATACCATGGTAGGGTATTGATACCATAGTATGGTA
1 GTATCGATACCATGGTAGGGTATTGATACCATAGTATGGTA
*
256109 GTATCGATACCATGGTAGGGGTATCGATAC
1 GTATCGATACCATGGTA-GGGTATTGATAC
256139 TGAGGAGCTA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 55 0.83
42 11 0.17
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (41 bp):
GTATCGATACCATGGTAGGGTATTGATACCATAGTATGGTA
Found at i:256601 original size:45 final size:45
Alignment explanation
Indices: 256530--256890 Score: 386
Period size: 45 Copynumber: 8.0 Consensus size: 45
256520 GCTCTAAAAC
* * *
256530 GAATGTCAAAATAATAATGCAAATGGGTACATTATCGGCATGAAA
1 GAATGCCAAAATAATAATGCATATGGGTGCATTATCGGCATGAAA
* * *
256575 GAATGTCAAAATAATAATACATATGGGTGCATTATTGGCATGAAA
1 GAATGCCAAAATAATAATGCATATGGGTGCATTATCGGCATGAAA
* * * * *
256620 GGATGCCAAATTAATAATGTATATGGGTCCATTATCAGCATGAAA
1 GAATGCCAAAATAATAATGCATATGGGTGCATTATCGGCATGAAA
* *
256665 -ATATGCCAAAATAATAAAGCATATGGGTGCATTATTGGCATGAAA
1 GA-ATGCCAAAATAATAATGCATATGGGTGCATTATCGGCATGAAA
* * *
256710 GAATGCCAAAAGAATAATGAATATGGGTGCATTATCAGCATGAAA
1 GAATGCCAAAATAATAATGCATATGGGTGCATTATCGGCATGAAA
* * * * *
256755 GGATGCCAAAATAATAATGCATATAGGTGCATTATTGGGACGAAA
1 GAATGCCAAAATAATAATGCATATGGGTGCATTATCGGCATGAAA
*** * *
256800 TG-ATGCCAAAATAATAATGCATATGGGCATATTATCGGTATGGAA
1 -GAATGCCAAAATAATAATGCATATGGGTGCATTATCGGCATGAAA
* ** * * *
256845 GGATGCCATAGTTCA-AATGCATATGGGTGCATTATCAGCATAAAA
1 GAATGCCA-AAATAATAATGCATATGGGTGCATTATCGGCATGAAA
256890 G
1 G
256891 TATGTTATAT
Statistics
Matches: 261, Mismatches: 50, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
44 1 0.00
45 255 0.98
46 5 0.02
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (45 bp):
GAATGCCAAAATAATAATGCATATGGGTGCATTATCGGCATGAAA
Found at i:258851 original size:21 final size:21
Alignment explanation
Indices: 258827--258890 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
258817 ATGATCAATA
*
258827 CCTTGACTGAAAGGATCGATC
1 CCTTGACTAAAAGGATCGATC
* *
258848 CCTTCACAAAAAGGATCGATC
1 CCTTGACTAAAAGGATCGATC
* *
258869 CCTTG-CTTAAATGATCGATC
1 CCTTGACTAAAAGGATCGATC
258889 CC
1 CC
258891 AAACATTCTA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (21 bp):
CCTTGACTAAAAGGATCGATC
Found at i:260295 original size:60 final size:60
Alignment explanation
Indices: 260202--260980 Score: 918
Period size: 60 Copynumber: 13.0 Consensus size: 60
260192 TTGTTTTTAT
* * * * * * *
260202 TCTAACTTGCATTAATAGCACCTTTCGGCCAAAATGCACCGTTAGGCATTTAACATTTAA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
* * * *
260262 TCTAACATGCATTAGTGGCTCCTTTCTGCCAAAATGCATCGTTAGGCATTTAAATTTTCA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
* * * * *
260322 TCAAATTTGCAATAGTGTCACCTTTCTGCCAAAATGAATCATTAGGCATTTAACTTTTCA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
* * * * ** * * *
260382 TCTAAGTTGCATTAATGACACCTTTCTGCCAAAATAAACCGTTAGGCATTTAACATTTAA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
* * * * ***
260442 TGTAACTTGCATTAGTGGCAACTTTCTGCCAAAATGCATTGTTATTAATTTAACTTTTCA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
* * *
260502 TCTAACTTGCAATAGTGGCACCTTTCTACCAAATTGCATCGTTAGGCATTTAAATTTTCA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
* * * * *
260562 TCTAACTTACAATAGTGGCACCTTTCTGCAAAAATGAATAGTTAGGCATTTCACTTTTCA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
* *
260622 TC-AACTTGCAATAGTGGCACATTTCTGCCAAAATGCATCATTAGGCATTTAACTTTTCA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
* * * * *
260681 TCTTACTTGCAATAGTGGCACCTTTCCGCCAAAATACATTGTTAGACATTTAACTTTTCA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
* * * * *
260741 TCTAACTTGCAATAATGG-AGCATATCTTCCAAAATGCATCGTTAGGCGTTTAACTTTTCA
1 TCTAACTTGCAATAGTGGCA-CCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
* * *
260801 TCTAACTTGCAATAGTGACACCTTTCTACTAAAATGCATCGTTAGGCATTTAACTTTTC-
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
** * * *
260860 -CTAAACTTGCAATAGTCACACCTTTCAGCCAAAATGCATCTTTAGACATTTAACTTTTCA
1 TCT-AACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
* * * * * *
260920 GCTAAATTGCAATAGTGTCACCTTTTTGCCAAAATGCATCGTTAGACATTTACCTTTTCA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
260980 T
1 T
260981 TTTATAGCAG
Statistics
Matches: 608, Mismatches: 105, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
58 2 0.00
59 103 0.17
60 500 0.82
61 3 0.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (60 bp):
TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCA
Found at i:260781 original size:239 final size:238
Alignment explanation
Indices: 260202--260980 Score: 941
Period size: 239 Copynumber: 3.3 Consensus size: 238
260192 TTGTTTTTAT
* * * * * * * *
260202 TCTAACTTGCATTAATAGCACCTTTCGGCCAAAATGCACCGTTAGGCATTTAACATTTAATCTAA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGACATTTAACTTTTCATCTAA
* * * * * *
260267 CATGCATTAGTGGCTCCTTTCTGCCAAAATGCATCGTTAGGCATTTAAATTTTCATCAAATTTGC
66 CTTGCAATAGTGG-ACCTTTCTACCAAAATGCATCGTTAGGCATTTAAATTTTCATCTAACTTGC
* * * *
260332 AATAGTGTCACCTTTCTGCCAAAATGAATCA-TTAGGCATTTAACTTTTCATCTAAGTTGCATTA
130 AATAGTGACACCTTTCTGCAAAAATGAAT-AGTTAGGCATTTAACTTTTCATC-AACTTGCAATA
* ** * * * *
260396 ATGACACCTTTCTGCCAAAATAAACCGTTAGGCATTTAACATTTAA
193 GTGACACCTTTCTGCCAAAATGCATCATTAGGCATTTAACTTTTCA
* * * * *
260442 TGTAACTTGCATTAGTGGCAACTTTCTGCCAAAATGCATTGTTATTA-ATTTAACTTTTCATCTA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTA-GACATTTAACTTTTCATCTA
* *
260506 ACTTGCAATAGTGGCACCTTTCTACCAAATTGCATCGTTAGGCATTTAAATTTTCATCTAACTTA
65 ACTTGCAATAGTGG-ACCTTTCTACCAAAATGCATCGTTAGGCATTTAAATTTTCATCTAACTTG
* *
260571 CAATAGTGGCACCTTTCTGCAAAAATGAATAGTTAGGCATTTCACTTTTCATCAACTTGCAATAG
129 CAATAGTGACACCTTTCTGCAAAAATGAATAGTTAGGCATTTAACTTTTCATCAACTTGCAATAG
* *
260636 TGGCACATTTCTGCCAAAATGCATCATTAGGCATTTAACTTTTCA
194 TGACACCTTTCTGCCAAAATGCATCATTAGGCATTTAACTTTTCA
* * * *
260681 TCTTACTTGCAATAGTGGCACCTTTCCGCCAAAATACATTGTTAGACATTTAACTTTTCATCTAA
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGACATTTAACTTTTCATCTAA
* * * * * *
260746 CTTGCAATAATGGAGCATATCTTCCAAAATGCATCGTTAGGCGTTTAACTTTTCATCTAACTTGC
66 CTTGCAATAGTGGA-CCTTTCTACCAAAATGCATCGTTAGGCATTTAAATTTTCATCTAACTTGC
* * * * * *
260811 AATAGTGACACCTTTCTACTAAAATGCATCGTTAGGCATTTAACTTTTCCTAAACTTGCAATAGT
130 AATAGTGACACCTTTCTGCAAAAATGAATAGTTAGGCATTTAACTTTTCATCAACTTGCAATAGT
* * * *
260876 CACACCTTTCAGCCAAAATGCATCTTTAGACATTTAACTTTTCA
195 GACACCTTTCTGCCAAAATGCATCATTAGGCATTTAACTTTTCA
* * * * *
260920 GCTAAATTGCAATAGTGTCACCTTTTTGCCAAAATGCATCGTTAGACATTTACCTTTTCAT
1 TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGACATTTAACTTTTCAT
260981 TTTATAGCAG
Statistics
Matches: 464, Mismatches: 71, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
238 2 0.00
239 305 0.66
240 157 0.34
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (238 bp):
TCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGACATTTAACTTTTCATCTAA
CTTGCAATAGTGGACCTTTCTACCAAAATGCATCGTTAGGCATTTAAATTTTCATCTAACTTGCA
ATAGTGACACCTTTCTGCAAAAATGAATAGTTAGGCATTTAACTTTTCATCAACTTGCAATAGTG
ACACCTTTCTGCCAAAATGCATCATTAGGCATTTAACTTTTCA
Found at i:261401 original size:20 final size:22
Alignment explanation
Indices: 261376--261430 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
261366 AGGTTCAATA
*
261376 GTATCGGTAC-CCT-TACCATG
1 GTATCGATACTCCTATACCATG
*
261396 GTATCGATACTCCTATACTATG
1 GTATCGATACTCCTATACCATG
261418 GTA-CTGATACTCC
1 GTATC-GATACTCC
261431 CTTTCAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 9 0.30
21 4 0.13
22 17 0.57
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (22 bp):
GTATCGATACTCCTATACCATG
Found at i:267680 original size:60 final size:60
Alignment explanation
Indices: 267582--268668 Score: 1372
Period size: 60 Copynumber: 18.1 Consensus size: 60
267572 AATGCACTAT
* * * ** * * *
267582 TTTTCATCCAACTTGCATTAATGGCACCTTTCGGCCAAAATGCACCGTTAGACATTTAAA
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* * * * * *
267642 TTTTCATCTAACTTGCATTATTGGAACATTTCTACCAAAATGCATCATTAGGCATTTAGC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* ** *
267702 TTATCATCTAACTTGCAATAGTGGCACCTTTAAACCAAAATGTATCGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* * * * * * *
267762 -TTTCATCTAACTTGCAATAGTGGCACCTTTCTTCCAAAATACATTGTTACGCAATAAAT
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* * * *
267821 TTTTCATCTAACTTGCAATAGTGTCATCTTTCTACCAAAATGCATCATTAGGCATTTAAT
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* * * *
267881 TTTTCATCTGACTTGCAATAGTGCCACCTTTCTACCGAAATGCATCATTAGGCATTTAAC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
*
267941 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* * * * *
268001 TTTTCATCTAACATGCAATAGTGACACCTTTTTACAAAAAATGCATCTTTAGGCATTTAAC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTAC-CAAAATGCATCGTTAGGCATTTAAC
* * *
268062 TTTTCATCTAACTTGCAATAGTGGCAACTTTCTGCCAAAATGCATCGTTACGCATTTAAC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* * * * *
268122 TTTTCATCTAACTTGCAATAGTGGCACATTTCTTCCAAAATGCATTGTTACGCATTAAAC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* * * * *
268182 TTTTCATTTAACTTGCAATAGTGTCATCTTTCTACCAAAATGCATCATTAGGCATTTAAT
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* * * * * *
268242 TTTTCATCTGACTAGCAATAGTGCCACCTTTCTACCAAATTACATCGTTAGACATTTAAC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* *
268302 TTTTCATCTAACTTGCAATAGTAGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* *
268362 TTTTCATCTAACTTGCAATAGTGACACCTTTTTACCGAAAATGCATCGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACC-AAAATGCATCGTTAGGCATTTAAC
* * * *
268423 TTTTCATCTAACTTGCAATAGTGGCAACTTTCTGCCAAAATGCATCATT-GGGATTTTAAC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCA-TTTAAC
* * * * * * *
268483 TTTTCATCTATCTTGTAATATTTGCACCTTTATGCCAAAATGCATCGTTAGACATTTAAC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* * * * *
268543 TTTTCATCTAAAC-TACAATAGTGACACCTTTATGCCAAAATGTATCGTTAGGCATTTAAC
1 TTTTCATCT-AACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
* * * *
268603 TTTACATCTAACTTGCAATAGTGTCA-CTTTCTACTAAAATGCATCGTTAGGCATTTACC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
268662 TTTTCAT
1 TTTTCAT
268669 TTTAGAGCAG
Statistics
Matches: 886, Mismatches: 134, Indels: 15
0.86 0.13 0.01
Matches are distributed among these distances:
59 88 0.10
60 685 0.77
61 113 0.13
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (60 bp):
TTTTCATCTAACTTGCAATAGTGGCACCTTTCTACCAAAATGCATCGTTAGGCATTTAAC
Done.