Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 8 of 185
Found at i:2199423 original size:22 final size:21
Alignment explanation
Indices: 2199392--2199452 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
2199382 TTTTCAATTT
* *
2199392 TTTAATAAAATCATTAAAAATG
1 TTTAAAAAAATC-TTAAAAATC
*
2199414 TTTAAAAAAA-CTTATAAATC
1 TTTAAAAAAATCTTAAAAATC
*
2199434 TATAAAAAAAT-TGTAAAAA
1 TTTAAAAAAATCT-TAAAAA
2199453 ATTATAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 17 0.53
21 6 0.19
22 9 0.28
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
TTTAAAAAAATCTTAAAAATC
Found at i:2199433 original size:30 final size:27
Alignment explanation
Indices: 2199399--2199470 Score: 65
Period size: 30 Copynumber: 2.5 Consensus size: 27
2199389 TTTTTTAATA
*
2199399 AAATCATTAAAAATGTTTAAAAAAACTTAT
1 AAATCATTAAAAAT-TGT-AAAAAA-TTAT
*
2199429 AAATCTATAAAAAAATTGTAAAAAATTAT
1 AAATC-AT-TAAAAATTGTAAAAAATTAT
2199458 AAAT-ATTATAAAA
1 AAATCATTA-AAAA
2199471 ATCTAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
26 1 0.03
27 6 0.17
29 8 0.22
30 11 0.31
31 4 0.11
32 6 0.17
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (27 bp):
AAATCATTAAAAATTGTAAAAAATTAT
Found at i:2199479 original size:20 final size:21
Alignment explanation
Indices: 2199448--2199504 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 21
2199438 AAAAAATTGT
2199448 AAAAAAT-T-ATAAATATT-A
1 AAAAAATCTAATAAATATTCA
* *
2199466 TAAAAATCTAATAAAAATTCCAA
1 AAAAAATCTAATAAATATT-C-A
2199489 AAAAAATCTAATAAAT
1 AAAAAATCTAATAAAT
2199505 TATGCATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 6 0.20
19 1 0.03
20 8 0.27
23 15 0.50
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAATCTAATAAATATTCA
Found at i:2203259 original size:3 final size:3
Alignment explanation
Indices: 2203251--2203298 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2203241 TTTATGTATC
2203251 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2203299 ATTCTCATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2203429 original size:32 final size:31
Alignment explanation
Indices: 2203379--2203474 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
2203369 TTTAGATAAT
2203379 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
2203410 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
2203442 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
2203473 TT
1 TT
2203475 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:2205785 original size:11 final size:11
Alignment explanation
Indices: 2205765--2205870 Score: 54
Period size: 11 Copynumber: 10.3 Consensus size: 11
2205755 TAAAAATTAA
2205765 AAAAAGTATTTT
1 AAAAA-TATTTT
2205777 AAAAATATTTT
1 AAAAATATTTT
2205788 --AAA-A--TT
1 AAAAATATTTT
* *
2205794 AAAAA-AATTA
1 AAAAATATTTT
2205804 AAAAAGTATTTT
1 AAAAA-TATTTT
*
2205816 AAAAAAATTTT
1 AAAAATATTTT
2205827 --AAA-A-TTT
1 AAAAATATTTT
2205834 AAAAA-ATTTAAT
1 AAAAATATTT--T
*
2205846 AAAAGTATTTT
1 AAAAATATTTT
*
2205857 AAAAGTATTTT
1 AAAAATATTTT
2205868 AAA
1 AAA
2205871 TTAAAAAAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 25
0.72 0.05 0.23
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 6 0.08
9 10 0.13
10 8 0.10
11 26 0.34
12 18 0.23
13 4 0.05
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:2205803 original size:40 final size:40
Alignment explanation
Indices: 2205756--2205886 Score: 196
Period size: 39 Copynumber: 3.3 Consensus size: 40
2205746 AATTTATTTT
2205756 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
*
2205796 AAAAATT-AAAAAAGTATTTTAAAAAAATTTTAAAATTTAA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA-TTAA
* * *
2205836 AAAATTTAATAAAAGTATTTTAAAAGTATTTT-AAATTAA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
2205875 AAAAA-TAAAAAA
1 AAAAATTAAAAAA
2205887 TAATAAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
38 6 0.07
39 35 0.43
40 20 0.24
41 21 0.26
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (40 bp):
AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:2205839 original size:17 final size:17
Alignment explanation
Indices: 2205774--2205842 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 17
2205764 AAAAAAGTAT
2205774 TTTAAAAATATTTTAAAA
1 TTTAAAAA-ATTTTAAAA
* **
2205792 TTAAAAAAATTAAAAAAGTA
1 TTTAAAAAATT-TTAAA--A
2205812 TTTTAAAAAAATTTTAAAA
1 -TTT-AAAAAATTTTAAAA
2205831 TTTAAAAAATTT
1 TTTAAAAAATTT
2205843 AATAAAAGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
17 12 0.30
18 13 0.32
19 1 0.03
20 1 0.03
21 5 0.12
22 8 0.20
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
TTTAAAAAATTTTAAAA
Found at i:2206600 original size:22 final size:22
Alignment explanation
Indices: 2206558--2206598 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2206548 AAGTTGAAAA
2206558 TAATTTTTAAAAATATTTTTAT
1 TAATTTTTAAAAATATTTTTAT
*
2206580 TAATTTTT-AATATATTTTT
1 TAATTTTTAAAAATATTTTT
2206599 TAGATTACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TAATTTTTAAAAATATTTTTAT
Found at i:2210255 original size:19 final size:17
Alignment explanation
Indices: 2210176--2210257 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 17
2210166 TATTAATTGG
**
2210176 TTATAATTTTATAAATCA
1 TTATAATTTT-TAAATTT
**
2210194 TTA-AATTTTTTTATTT
1 TTATAATTTTTAAATTT
*
2210210 TT-TAATATTTAAATTT
1 TTATAATTTTTAAATTT
2210226 TTATAACATTTTTAATAGTTT
1 TTAT-A-ATTTTTAA-A-TTT
2210247 TTATAATTTTT
1 TTATAATTTTT
2210258 TTTAAAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
16 17 0.34
17 7 0.14
18 4 0.08
19 13 0.26
20 2 0.04
21 7 0.14
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (17 bp):
TTATAATTTTTAAATTT
Found at i:2213937 original size:92 final size:95
Alignment explanation
Indices: 2213833--2214023 Score: 228
Period size: 95 Copynumber: 2.0 Consensus size: 95
2213823 TTTAAAAAAT
* * *
2213833 AAAATATATTTAACATAATGATAAATATAA-AAAAAAATATT-T-TTATTATATAATTATTAATT
1 AAAATATATTTAACATAATCATAAATATAATAAAAAAATATTGTATAATTACATAATTATTAATT
*
2213895 TATTTATATAAATAAAGGAGTTATT-AATTA
66 TATTTATATAAATAAAAGAGTT-TTAAATTA
* * * **** * *
2213925 AAAATATTTTTAACATAATCATATATATAATATATTTTTATTGTATAATTACATATTTATTATTT
1 AAAATATATTTAACATAATCATAAATATAATAAAAAAATATTGTATAATTACATAATTATTAATT
2213990 TATTTATATAAATAAAAGAGTTTTAAATTA
66 TATTTATATAAATAAAAGAGTTTTAAATTA
2214020 AAAA
1 AAAA
2214024 GATGAATTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
92 27 0.33
93 6 0.07
94 3 0.04
95 46 0.56
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (95 bp):
AAAATATATTTAACATAATCATAAATATAATAAAAAAATATTGTATAATTACATAATTATTAATT
TATTTATATAAATAAAAGAGTTTTAAATTA
Found at i:2213971 original size:22 final size:23
Alignment explanation
Indices: 2213946--2213997 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
2213936 AACATAATCA
*
2213946 TATATATAATATATTT-TTATTG
1 TATATATAACATATTTATTATTG
* *
2213968 TATA-ATTACATATTTATTATTT
1 TATATATAACATATTTATTATTG
*
2213990 TATTTATA
1 TATATATA
2213998 TAAATAAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 9 0.39
22 12 0.52
23 2 0.09
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TATATATAACATATTTATTATTG
Found at i:2217338 original size:23 final size:23
Alignment explanation
Indices: 2217289--2217339 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2217279 ACAAATGTCC
***
2217289 GTAACCCCTAAATTCATTATCTT
1 GTAACCCCTAAATTCATTATAAA
2217312 GTAACCCCTAAATT-ATTTATAAA
1 GTAACCCCTAAATTCA-TTATAAA
2217335 GTAAC
1 GTAAC
2217340 TTAATGCTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (23 bp):
GTAACCCCTAAATTCATTATAAA
Found at i:2221410 original size:24 final size:24
Alignment explanation
Indices: 2221376--2221452 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
2221366 CATTTAAGTG
2221376 TTAAACGTAATTTTTAACTATCGT
1 TTAAACGTAATTTTTAACTATCGT
* *
2221400 TTAAACTTAA--TTTAA--GT-G-
1 TTAAACGTAATTTTTAACTATCGT
2221418 TTAAACGTAATTTTTAACTATCGT
1 TTAAACGTAATTTTTAACTATCGT
*
2221442 TTAAACTTAAT
1 TTAAACGTAAT
2221453 CTAGGCTAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
18 9 0.21
19 1 0.02
20 6 0.14
22 6 0.14
23 1 0.02
24 19 0.45
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.45
Consensus pattern (24 bp):
TTAAACGTAATTTTTAACTATCGT
Found at i:2221426 original size:42 final size:42
Alignment explanation
Indices: 2221367--2221452 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
2221357 AACTCATGTC
2221367 ATTTAAGTGTTAAACGTAATTTTTAACTATCGTTTAAACTTA
1 ATTTAAGTGTTAAACGTAATTTTTAACTATCGTTTAAACTTA
2221409 ATTTAAGTGTTAAACGTAATTTTTAACTATCGTTTAAACTTA
1 ATTTAAGTGTTAAACGTAATTTTTAACTATCGTTTAAACTTA
2221451 AT
1 AT
2221453 CTAGGCTAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (42 bp):
ATTTAAGTGTTAAACGTAATTTTTAACTATCGTTTAAACTTA
Found at i:2228013 original size:14 final size:14
Alignment explanation
Indices: 2227994--2228026 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2227984 TGTAATATGA
2227994 AAGTTTGACCATTT
1 AAGTTTGACCATTT
*
2228008 AAGTTTGACCGTTT
1 AAGTTTGACCATTT
2228022 AAGTT
1 AAGTT
2228027 CAGTCTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (14 bp):
AAGTTTGACCATTT
Found at i:2231974 original size:33 final size:32
Alignment explanation
Indices: 2231933--2232033 Score: 110
Period size: 33 Copynumber: 3.3 Consensus size: 32
2231923 AAATACGTTA
2231933 TTTTAGTTTGATTTACTCTATTTTTGGACTGT
1 TTTTAGTTTGATTTACTCTATTTTTGGACTGT
*
2231965 TTTTAAGTTTGGA--TA-T-TA-TTTT-G-TTG-
1 TTTT-AGTTT-GATTTACTCTATTTTTGGACTGT
2231991 TTTTAGTTTGATTTACTCTATTTTTGGACTGT
1 TTTTAGTTTGATTTACTCTATTTTTGGACTGT
2232023 TTTTAAGTTTG
1 TTTT-AGTTTG
2232034 GATATTATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 21
0.71 0.03 0.27
Matches are distributed among these distances:
24 2 0.04
25 5 0.09
26 6 0.11
27 3 0.05
28 3 0.05
29 8 0.14
30 3 0.05
31 3 0.05
32 10 0.18
33 11 0.20
34 2 0.04
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (32 bp):
TTTTAGTTTGATTTACTCTATTTTTGGACTGT
Found at i:2231981 original size:27 final size:27
Alignment explanation
Indices: 2231951--2232039 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 27
2231941 TGATTTACTC
2231951 TATTTTTGGACTGTTTTTAAGTTTGGA
1 TATTTTTGGACTGTTTTTAAGTTTGGA
* * *
2231978 TATTATTTTG-TTG-TTTT-AGTTTGATTTA
1 TATT-TTTGGACTGTTTTTAAGTTTG---GA
2232006 CTCTATTTTTGGACTGTTTTTAAGTTTGGA
1 ---TATTTTTGGACTGTTTTTAAGTTTGGA
2232036 TATT
1 TATT
2232040 ATTTTGTTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 20
0.64 0.08 0.28
Matches are distributed among these distances:
25 6 0.13
26 4 0.09
27 10 0.22
28 5 0.11
30 5 0.11
31 6 0.13
32 4 0.09
33 6 0.13
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.60
Consensus pattern (27 bp):
TATTTTTGGACTGTTTTTAAGTTTGGA
Found at i:2232023 original size:58 final size:58
Alignment explanation
Indices: 2231933--2232052 Score: 240
Period size: 58 Copynumber: 2.1 Consensus size: 58
2231923 AAATACGTTA
2231933 TTTTAGTTTGATTTACTCTATTTTTGGACTGTTTTTAAGTTTGGATATTATTTTGTTG
1 TTTTAGTTTGATTTACTCTATTTTTGGACTGTTTTTAAGTTTGGATATTATTTTGTTG
2231991 TTTTAGTTTGATTTACTCTATTTTTGGACTGTTTTTAAGTTTGGATATTATTTTGTTG
1 TTTTAGTTTGATTTACTCTATTTTTGGACTGTTTTTAAGTTTGGATATTATTTTGTTG
2232049 TTTT
1 TTTT
2232053 GCTTTCCGCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.17, C:0.05, G:0.17, T:0.62
Consensus pattern (58 bp):
TTTTAGTTTGATTTACTCTATTTTTGGACTGTTTTTAAGTTTGGATATTATTTTGTTG
Found at i:2232050 original size:27 final size:27
Alignment explanation
Indices: 2231962--2232052 Score: 89
Period size: 27 Copynumber: 3.2 Consensus size: 27
2231952 ATTTTTGGAC
2231962 TGTTTTTAAGTTTGGATATTATTTTGT
1 TGTTTTTAAGTTTGGATATTATTTTGT
*
2231989 TG-TTTT-AGTTT-GATTTACTCTATTTTTGGAC
1 TGTTTTTAAGTTTGGA--TA-T-TA-TTTT-G-T
2232020 TGTTTTTAAGTTTGGATATTATTTTGT
1 TGTTTTTAAGTTTGGATATTATTTTGT
2232047 TGTTTT
1 TGTTTT
2232053 GCTTTCCGCT
Statistics
Matches: 52, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
24 2 0.04
25 5 0.10
26 6 0.12
27 9 0.17
28 3 0.06
29 8 0.15
30 3 0.06
31 3 0.06
32 6 0.12
33 5 0.10
34 2 0.04
ACGTcount: A:0.16, C:0.03, G:0.18, T:0.63
Consensus pattern (27 bp):
TGTTTTTAAGTTTGGATATTATTTTGT
Found at i:2235047 original size:14 final size:13
Alignment explanation
Indices: 2235013--2235054 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
2235003 ACATTCAAGC
2235013 TTAAATTA-TAAA
1 TTAAATTATTAAA
*
2235025 TTTAATTATTAAA
1 TTAAATTATTAAA
2235038 TCTAAATTATTAAA
1 T-TAAATTATTAAA
2235052 TTA
1 TTA
2235055 TAAATTTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 7 0.27
13 7 0.27
14 12 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTATTAAA
Found at i:2237707 original size:17 final size:17
Alignment explanation
Indices: 2237678--2237723 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
2237668 ATACTACAAA
2237678 AATTATTTCGATTAATT
1 AATTATTTCGATTAATT
2237695 AATTAATTT-GATTAATT
1 AATT-ATTTCGATTAATT
*
2237712 ACTTGATTTCGA
1 AATT-ATTTCGA
2237724 ACCGAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.50
Consensus pattern (17 bp):
AATTATTTCGATTAATT
Found at i:2239314 original size:18 final size:18
Alignment explanation
Indices: 2239291--2239344 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
2239281 AAATCGTGTC
2239291 ATTCATTTTCAAAACATT
1 ATTCATTTTCAAAACATT
* *
2239309 ATTCATTTAT-AAACCTTT
1 ATTCATTT-TCAAAACATT
*
2239327 ATTCAATTTCAAAACATT
1 ATTCATTTTCAAAACATT
2239345 TTTTTATTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 1 0.03
18 27 0.93
19 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTCATTTTCAAAACATT
Found at i:2249305 original size:24 final size:25
Alignment explanation
Indices: 2249263--2249311 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
2249253 CAAAATTAAA
* *
2249263 ATAATAATTTAATATATTTTAAAACC
1 ATAATAA-TTAATAAATTTAAAAACC
2249289 ATAATAA-TAATAAATTTAAAAAC
1 ATAATAATTAATAAATTTAAAAAC
2249312 ACCCTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
26 7 0.33
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATAATTAATAAATTTAAAAACC
Found at i:2251002 original size:44 final size:43
Alignment explanation
Indices: 2250906--2251027 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 43
2250896 ACTTGATGCG
* * * * *
2250906 ATCTGCTCTACTGCAACTTCAGAGATATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATTAATTCA
* *
2250950 AT-TCGCTCCACTACAACTTCAGGGAGATAGGATTATTGAATTCA
1 ATCT-GCTCCACTGCAACTTCAGGGAGATAAGATTATT-AATTCA
*
2250994 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
2251028 TTCTTCTTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
43 5 0.08
44 59 0.91
45 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTAATTCA
Found at i:2253592 original size:21 final size:22
Alignment explanation
Indices: 2253553--2253593 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2253543 GTCAATGTAG
2253553 GATTAAAATTAACTTTTTAAGA
1 GATTAAAATTAACTTTTTAAGA
*
2253575 GATTAGAATTAA-TTTTTAA
1 GATTAAAATTAACTTTTTAA
2253594 TGAAAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (22 bp):
GATTAAAATTAACTTTTTAAGA
Found at i:2253897 original size:22 final size:23
Alignment explanation
Indices: 2253853--2253900 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
2253843 TTAGCCAATG
*
2253853 AGGGATTAAAATTTACTTTTTTA
1 AGGGATTAAAATTTAATTTTTTA
*
2253876 AGGGGTTAAAA-TTAATTTTTTA
1 AGGGATTAAAATTTAATTTTTTA
2253898 AGG
1 AGG
2253901 AAATAGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (23 bp):
AGGGATTAAAATTTAATTTTTTA
Found at i:2254255 original size:152 final size:153
Alignment explanation
Indices: 2253976--2254277 Score: 441
Period size: 152 Copynumber: 2.0 Consensus size: 153
2253966 ATGAAAATAG
* * * *
2253976 TGAAAGTGAGCTATAAAAGTATTATCTAGTTAATGTGGGAGTAAAATTAACTTTTTAAATGAAAA
1 TGAAAGCGAGCTATAAAAGTATTATCTAGTCAATATGAGAGTAAAATTAACTTTTTAAATGAAAA
* * * * *
2254041 TAGTGAAGAAATTGTCACTTATTTATAAGGTAAATATGAGATATGGGAGTATTCTCCGGTCAAT-
66 TAGTAAAGAAATTGTCACTTATTTATAACGTAAATATGAGATACGAGAGTATTCTCCCGTCAATG
2254105 ATGGAATTAAAATTAACTTTTTTA
131 ATGG-ATTAAAATTAACTTTTTTA
2254129 TGAAAGCGAGCTATAAAAGTATTATCTAGTCAATATGAGA-TAAAAATTAACTTTTT-AATG-AA
1 TGAAAGCGAGCTATAAAAGTATTATCTAGTCAATATGAGAGT-AAAATTAACTTTTTAAATGAAA
* *
2254191 ATCAGTAAAGAAGTTGTCACTTATTTATAACGTAAATGTGAGATACGAGAGTATTCTCCCGTCAA
65 AT-AGTAAAGAAATTGTCACTTATTTATAACGTAAATATGAGATACGAGAGTATTCTCCCGTCAA
*
2254256 TGTTGGATTAAAATTAACTTTT
129 TGATGGATTAAAATTAACTTTT
2254278 AACCTTTTAA
Statistics
Matches: 134, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
151 4 0.03
152 77 0.57
153 53 0.40
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (153 bp):
TGAAAGCGAGCTATAAAAGTATTATCTAGTCAATATGAGAGTAAAATTAACTTTTTAAATGAAAA
TAGTAAAGAAATTGTCACTTATTTATAACGTAAATATGAGATACGAGAGTATTCTCCCGTCAATG
ATGGATTAAAATTAACTTTTTTA
Found at i:2259980 original size:13 final size:13
Alignment explanation
Indices: 2259955--2259995 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2259945 GTGTATGGTG
2259955 TTTAAATATTATTT
1 TTTAAA-ATTATTT
*
2259969 TTTAAAATTATTC
1 TTTAAAATTATTT
2259982 TTT-AAA-TATTT
1 TTTAAAATTATTT
2259993 TTT
1 TTT
2259996 TACTAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 7 0.28
12 3 0.12
13 9 0.36
14 6 0.24
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAAAATTATTT
Found at i:2263624 original size:31 final size:31
Alignment explanation
Indices: 2263586--2263649 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
2263576 AAAACTATAG
2263586 ACCAAGCAATATCATATACAACACGGTACTA
1 ACCAAGCAATATCATATACAACACGGTACTA
2263617 ACCAAGCAATATCATATACAACACGGTACTA
1 ACCAAGCAATATCATATACAACACGGTACTA
2263648 AC
1 AC
2263650 ATGACACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.27, G:0.09, T:0.19
Consensus pattern (31 bp):
ACCAAGCAATATCATATACAACACGGTACTA
Found at i:2268710 original size:12 final size:12
Alignment explanation
Indices: 2268693--2268718 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2268683 TGTCACGAAA
2268693 ATTTAGTAGCAT
1 ATTTAGTAGCAT
2268705 ATTTAGTAGCAT
1 ATTTAGTAGCAT
2268717 AT
1 AT
2268719 GCTCTTAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATTTAGTAGCAT
Found at i:2271728 original size:2 final size:2
Alignment explanation
Indices: 2271721--2271761 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2271711 TCCTTCTCAT
2271721 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2271762 AATTATTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2284793 original size:21 final size:18
Alignment explanation
Indices: 2284769--2284816 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 18
2284759 AATCCCCATT
*
2284769 TTCATCATCATCCTCCCTCCC
1 TTCATCATCATCAT--CT-CC
2284790 TTCATCATCATCATCTCC
1 TTCATCATCATCATCTCC
2284808 TTCATCATC
1 TTCATCATC
2284817 CGTGTAATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.42
19 2 0.08
21 13 0.50
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.38
Consensus pattern (18 bp):
TTCATCATCATCATCTCC
Found at i:2284794 original size:18 final size:18
Alignment explanation
Indices: 2284773--2284817 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2284763 CCCATTTTCA
*
2284773 TCATCATCCTC-CCTCCCT
1 TCATCATCCTCATCT-CCT
*
2284791 TCATCATCATCATCTCCT
1 TCATCATCCTCATCTCCT
2284809 TCATCATCC
1 TCATCATCC
2284818 GTGTAATCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.36
Consensus pattern (18 bp):
TCATCATCCTCATCTCCT
Found at i:2291532 original size:28 final size:28
Alignment explanation
Indices: 2291500--2291555 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2291490 CCATTTCCAA
2291500 ATTGGACCTATATCAATAGATTTCTCCT
1 ATTGGACCTATATCAATAGATTTCTCCT
2291528 ATTGGACCTATATCAATAGATTTCTCCT
1 ATTGGACCTATATCAATAGATTTCTCCT
2291556 TCTTAAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (28 bp):
ATTGGACCTATATCAATAGATTTCTCCT
Found at i:2295595 original size:24 final size:24
Alignment explanation
Indices: 2295554--2295639 Score: 66
Period size: 25 Copynumber: 3.5 Consensus size: 24
2295544 GTCACAACTA
* * *
2295554 ATCGGGATGCTTCGAAGAGCTAT-T
1 ATCGGGAAGC-TCGAAGAACCATAT
2295578 ATCGGGAAGCTCGCAAGAACCATAT
1 ATCGGGAAGCTCG-AAGAACCATAT
* **
2295603 AACGGGAAGCTCGAGAGGGCCATAT
1 ATCGGGAAGCTCGA-AGAACCATAT
* *
2295628 ATCAGGATGCTC
1 ATCGGGAAGCTC
2295640 ATGAGAGCTA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.06
24 17 0.34
25 30 0.60
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.20
Consensus pattern (24 bp):
ATCGGGAAGCTCGAAGAACCATAT
Found at i:2300743 original size:15 final size:13
Alignment explanation
Indices: 2300694--2300746 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
2300684 TATTAACTTA
* *
2300694 TATTCTTAAAATA
1 TATTTTTAAAATT
2300707 TATTTTTAAAATT
1 TATTTTTAAAATT
2300720 TATACTTTTACTAAATT
1 TAT--TTTTA--AAATT
2300737 TATTTTTAAA
1 TATTTTTAAA
2300747 CTAAATAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 16 0.47
15 10 0.29
17 8 0.24
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTTTAAAATT
Found at i:2307157 original size:16 final size:18
Alignment explanation
Indices: 2307129--2307163 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2307119 AATATTATTT
2307129 ATTAAATTAA-TTTCTCA
1 ATTAAATTAATTTTCTCA
2307146 ATTAAA-TAATTTTCTCA
1 ATTAAATTAATTTTCTCA
2307163 A
1 A
2307164 CCAATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAAATTAATTTTCTCA
Found at i:2317979 original size:17 final size:18
Alignment explanation
Indices: 2317947--2317985 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2317937 TAAGTTAGAA
* *
2317947 ATATATATATAAACAATT
1 ATATATATAAAAACAAAT
2317965 ATATA-ATAAAAACAAAT
1 ATATATATAAAAACAAAT
2317982 ATAT
1 ATAT
2317986 CTAATTCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATATATAAAAACAAAT
Found at i:2318081 original size:17 final size:17
Alignment explanation
Indices: 2318026--2318078 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
2318016 ACATAAGAAT
*
2318026 AATAATATTAATA-CATA
1 AATAATAATAATAGC-TA
2318043 TAATAATAATAATAGCTA
1 -AATAATAATAATAGCTA
*
2318061 AATAATAA-AATTGCTA
1 AATAATAATAATAGCTA
2318077 AA
1 AA
2318079 ATACGGACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 9 0.28
17 8 0.25
18 14 0.44
19 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (17 bp):
AATAATAATAATAGCTA
Found at i:2319306 original size:3 final size:3
Alignment explanation
Indices: 2319298--2319332 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2319288 TGGGCTGTAC
2319298 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2319333 ATCTTTCCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2323291 original size:3 final size:3
Alignment explanation
Indices: 2323283--2323309 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2323273 AAAGAAAAAC
2323283 ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA
2323310 CAATTCGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:2330219 original size:13 final size:13
Alignment explanation
Indices: 2330189--2330221 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2330179 ACAATAATTT
*
2330189 ATTTCACCCTTTA
1 ATTTTACCCTTTA
2330202 ATTTTACCCTTTA
1 ATTTTACCCTTTA
2330215 ATTTTAC
1 ATTTTAC
2330222 AAAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTACCCTTTA
Found at i:2330455 original size:29 final size:26
Alignment explanation
Indices: 2330394--2330456 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 26
2330384 TTAATTAATT
*
2330394 TTTTAAAATTTAAAAATTTAAAAATA
1 TTTTAAAATTTAAAAATTAAAAAATA
*
2330420 TTATAAAATCATTAAAACATTAAAAAATA
1 TTTTAAAAT--TTAAAA-ATTAAAAAATA
2330449 TTTTAAAA
1 TTTTAAAA
2330457 GATATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.26
28 6 0.19
29 17 0.55
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
TTTTAAAATTTAAAAATTAAAAAATA
Found at i:2332281 original size:21 final size:20
Alignment explanation
Indices: 2332255--2332294 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2332245 ACAAAAAAAG
2332255 AAAAAAAGATTTAAGTACCT
1 AAAAAAAGATTTAAGTACCT
2332275 AAAAAAAGATTTAAGTACCT
1 AAAAAAAGATTTAAGTACCT
2332295 TGGATGTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (20 bp):
AAAAAAAGATTTAAGTACCT
Found at i:2341599 original size:23 final size:23
Alignment explanation
Indices: 2341538--2341599 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
2341528 CAACAGGCGA
*
2341538 CGACATCACAACGAGAAGGCTTC
1 CGACATCACAACGAGGAGGCTTC
** * * * *
2341561 TAACGTCACGATGAGGAGGTTTC
1 CGACATCACAACGAGGAGGCTTC
2341584 CGACATCACAACGAGG
1 CGACATCACAACGAGG
2341600 GCGAATATGA
Statistics
Matches: 27, Mismatches: 12, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (23 bp):
CGACATCACAACGAGGAGGCTTC
Found at i:2343134 original size:20 final size:20
Alignment explanation
Indices: 2343109--2343167 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
2343099 CTAAAATTAA
2343109 AAAAATTATAAAATTATTTT
1 AAAAATTATAAAATTATTTT
2343129 AAAAATTA-AAAATTATTTT
1 AAAAATTATAAAATTATTTT
*
2343148 AAAACA-TATAAAAATATTTT
1 AAAA-ATTATAAAATTATTTT
2343168 TATATATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTATAAAATTATTTT
Found at i:2352414 original size:21 final size:21
Alignment explanation
Indices: 2352388--2352442 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2352378 TTGTTTTTAT
2352388 TTATTATTTTCATTACTATTA
1 TTATTATTTTCATTACTATTA
**
2352409 TTATTACATT-ATTTACTATTA
1 TTATTATTTTCA-TTACTATTA
*
2352430 TTATTATTATCAT
1 TTATTATTTTCAT
2352443 ATTTTCTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTATTTTCATTACTATTA
Found at i:2352436 original size:24 final size:24
Alignment explanation
Indices: 2352404--2352451 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2352394 TTTTCATTAC
2352404 TATTATTATTA-CATTATTTACTAT
1 TATTATTATTATCA-TATTTACTAT
*
2352428 TATTATTATTATCATATTTTCTAT
1 TATTATTATTATCATATTTACTAT
2352452 ACATATACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTATTATTATCATATTTACTAT
Found at i:2352658 original size:9 final size:8
Alignment explanation
Indices: 2352644--2352676 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2352634 ATTTTTAACT
2352644 TTTATATA
1 TTTATATA
2352652 CTTTATAT-
1 -TTTATATA
2352660 TTTATATA
1 TTTATATA
2352668 TTTATATA
1 TTTATATA
2352676 T
1 T
2352677 ACTTATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.30
8 9 0.39
9 7 0.30
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTATATA
Found at i:2368181 original size:9 final size:9
Alignment explanation
Indices: 2368169--2368226 Score: 53
Period size: 9 Copynumber: 5.8 Consensus size: 9
2368159 GGCAAAAAAC
2368169 TCTCAAATT
1 TCTCAAATT
2368178 TCTCCCTAAATT
1 TCT--C-AAATT
*
2368190 TCTCAAAGT
1 TCTCAAATT
2368199 TCTCAAATT
1 TCTCAAATT
2368208 TCTCCTTAAATT
1 TCT-C--AAATT
2368220 TCTCAAA
1 TCTCAAA
2368227 GCTCTCTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
9 21 0.51
10 2 0.05
11 2 0.05
12 16 0.39
ACGTcount: A:0.31, C:0.26, G:0.02, T:0.41
Consensus pattern (9 bp):
TCTCAAATT
Found at i:2368205 original size:30 final size:30
Alignment explanation
Indices: 2368168--2368232 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
2368158 TGGCAAAAAA
2368168 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
* *
2368198 TTCTCAAATTTCTCCTTAAATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
2368228 CTCTC
1 CTCTC
2368233 TTTAATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.29, G:0.03, T:0.40
Consensus pattern (30 bp):
CTCTCAAATTTCTCCCTAAATTTCTCAAAG
Found at i:2368232 original size:21 final size:21
Alignment explanation
Indices: 2368198--2368237 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2368188 TTTCTCAAAG
**
2368198 TTCTCAAATTTCTCCTTAAAT
1 TTCTCAAAGCTCTCCTTAAAT
*
2368219 TTCTCAAAGCTCTCTTTAA
1 TTCTCAAAGCTCTCCTTAA
2368238 TTAATTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.25, G:0.03, T:0.45
Consensus pattern (21 bp):
TTCTCAAAGCTCTCCTTAAAT
Found at i:2368457 original size:15 final size:16
Alignment explanation
Indices: 2368423--2368454 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2368413 TTTTCTTATG
2368423 TTATTTTAATTAATTT
1 TTATTTTAATTAATTT
2368439 TTATTTT-A-TAATTT
1 TTATTTTAATTAATTT
2368453 TT
1 TT
2368455 TATAACAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATTTTAATTAATTT
Found at i:2369392 original size:7 final size:7
Alignment explanation
Indices: 2369380--2369404 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2369370 AGTTGTTTCA
2369380 TATTTAG
1 TATTTAG
2369387 TATTTAG
1 TATTTAG
2369394 TATTTAG
1 TATTTAG
2369401 TATT
1 TATT
2369405 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:2370453 original size:58 final size:59
Alignment explanation
Indices: 2370343--2370457 Score: 137
Period size: 58 Copynumber: 2.0 Consensus size: 59
2370333 GTACAAACTT
****
2370343 TTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTAATATTTTAATAGTAAATTA
1 TTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTAATAAGGCAATAG-AAATTA
* *
2370403 TTTTTATATT-TTT-ATTTAATAAAATAGAA-TTTTTTTTGAATAAGGCAATAGAAAT
1 TTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTT-AATAAGGCAATAGAAAT
2370458 AATGCAACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
57 11 0.23
58 24 0.50
59 3 0.06
60 10 0.21
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (59 bp):
TTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTAATAAGGCAATAGAAATTA
Found at i:2373577 original size:126 final size:126
Alignment explanation
Indices: 2373422--2373943 Score: 814
Period size: 126 Copynumber: 4.1 Consensus size: 126
2373412 GGCCAAACAT
* * *
2373422 GAACTACTGCAAAAAAATAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
2373487 CTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAA
* *
2373548 GAACTACTGTAGAAAAAGAACGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
*** * * *
2373613 CTGCTTGAATTGTTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAA
* * *
2373674 GAACTACTGTAGAAAAAGAGCATCCATGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
* *
2373739 CTGCTTGAA-CTATTTTTGACACTATTTGTTTAAAACTGTCTTCTCAAAATTATTTTTTC-A
66 CTGCTTGAAGC-ATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAA
*
2373799 GTAACTACTATAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCAT
1 G-AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCAT
* * * *
2373864 CCGGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACTATCTTCTCAAAATTATTTTTTCAG
65 CCTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAA
2373926 GAACTACTGTAGAGAAAA
1 GAACTACTGTAGA-AAAA
2373944 ATCCTTATTG
Statistics
Matches: 357, Mismatches: 34, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
125 1 0.00
126 350 0.98
127 6 0.02
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
CTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAA
Found at i:2374222 original size:15 final size:15
Alignment explanation
Indices: 2374202--2374240 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2374192 TTAGTTTAAC
*
2374202 AAAACCCTAAACCTA
1 AAAACCCTAAACCAA
*
2374217 AAAACCCTAAATCAA
1 AAAACCCTAAACCAA
2374232 AAAACCCTA
1 AAAACCCTA
2374241 GGGACTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAACCCTAAACCAA
Found at i:2376524 original size:85 final size:84
Alignment explanation
Indices: 2376418--2376572 Score: 229
Period size: 85 Copynumber: 1.8 Consensus size: 84
2376408 AAGCTGCCTA
* * *
2376418 TGTTGGAAAATCGGTTTGAAAAGAGTGAAAATAAGCAGAAAGAAATTTTTAAATTTTTCAATGAA
1 TGTTGGAAAATCGATTTGAAAAGAGTGAAAATAAGCAGAAAGAAA-ATTTAAAATTTTCAATGAA
2376483 ACCAACTAGTTGTGATAATG
65 ACCAACTAGTTGTGATAATG
* * * **
2376503 TGTTGGAAAATCGATTTGAAAATAGTGAAAATAAGCATAATGAAAATTTAAAATTTTCTTTGAAA
1 TGTTGGAAAATCGATTTGAAAAGAGTGAAAATAAGCAGAAAGAAAATTTAAAATTTTCAATGAAA
2376568 CCAAC
66 CCAAC
2376573 CGGATATGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
84 21 0.34
85 41 0.66
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (84 bp):
TGTTGGAAAATCGATTTGAAAAGAGTGAAAATAAGCAGAAAGAAAATTTAAAATTTTCAATGAAA
CCAACTAGTTGTGATAATG
Found at i:2380309 original size:22 final size:22
Alignment explanation
Indices: 2380274--2380325 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2380264 CTTTTTTAAC
*
2380274 TAATAATTAT-AAAT-TAAATT
1 TAATAATTTTCAAATATAAATT
*
2380294 ATAATTATTTTCAAATATAAATT
1 -TAATAATTTTCAAATATAAATT
2380317 TAATAATTT
1 TAATAATTT
2380326 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 8 0.31
22 12 0.46
23 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATTTTCAAATATAAATT
Found at i:2384694 original size:104 final size:104
Alignment explanation
Indices: 2384514--2384712 Score: 319
Period size: 104 Copynumber: 1.9 Consensus size: 104
2384504 ATCGAGCTCG
* * * *
2384514 TAAGAATAAAATAGGAAGATTAATAGCGTTAGTGTAAAAATATCTTAAAGATTGATTAAGTAATT
1 TAAGAATAAAATAGGAAGATGAATAGAGTTAGTGTAAAAATATATTAAAGATAGATTAAGTAATT
* *
2384579 TAACCGGGAAAATTGTTAATTAAAGCTCAGGGACTCTCA
66 TAACCGAGAAAATCGTTAATTAAAGCTCAGGGACTCTCA
*
2384618 TAAGAATAAAATAGGAAGATGAATAGAGTTAGTGTAATAATATATTAAAGATCAG-TTAAGTAAT
1 TAAGAATAAAATAGGAAGATGAATAGAGTTAGTGTAAAAATATATTAAAGAT-AGATTAAGTAAT
2384682 TTAACCGAGAAAATCGTTAATTAAAGCTCAG
65 TTAACCGAGAAAATCGTTAATTAAAGCTCAG
2384713 TGGCTAAATT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
104 86 0.99
105 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (104 bp):
TAAGAATAAAATAGGAAGATGAATAGAGTTAGTGTAAAAATATATTAAAGATAGATTAAGTAATT
TAACCGAGAAAATCGTTAATTAAAGCTCAGGGACTCTCA
Found at i:2385957 original size:28 final size:29
Alignment explanation
Indices: 2385927--2385983 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2385917 ACCGACCGAA
**
2385927 TTTACTGAAAAAATTTCGGTTCGGTTAAT
1 TTTACTGAAAAAATTTCAATTCGGTTAAT
**
2385956 TTTTTTGAAAAAATTTCAATTCGGTTAA
1 TTTACTGAAAAAATTTCAATTCGGTTAA
2385984 CAGTTAAAAA
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:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (29 bp):
TTTACTGAAAAAATTTCAATTCGGTTAAT
Found at i:2401170 original size:12 final size:12
Alignment explanation
Indices: 2401155--2401179 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2401145 GCTAATTTTA
2401155 TGTTACTATTGT
1 TGTTACTATTGT
2401167 TGTTACTATTGT
1 TGTTACTATTGT
2401179 T
1 T
2401180 AAGTATGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TGTTACTATTGT
Found at i:2403392 original size:11 final size:12
Alignment explanation
Indices: 2403363--2403395 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2403353 AATTGAATTG
*
2403363 AATTTTATTTCT
1 AATTTAATTTCT
2403375 AATTTAATTTCT
1 AATTTAATTTCT
2403387 AA-TTAATTT
1 AATTTAATTT
2403396 TGATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (12 bp):
AATTTAATTTCT
Found at i:2409064 original size:12 final size:12
Alignment explanation
Indices: 2409024--2409067 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 12
2409014 CCATTTTCTA
2409024 AATAAAATA-TT
1 AATAAAATATTT
2409035 AAT-AAATATTT
1 AATAAAATATTT
2409046 AAGTAAAATATTT
1 AA-TAAAATATTT
*
2409059 TATAAAATA
1 AATAAAATA
2409068 ATTTTTAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 5 0.17
11 7 0.24
12 8 0.28
13 9 0.31
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
AATAAAATATTT
Found at i:2411472 original size:13 final size:13
Alignment explanation
Indices: 2411454--2411481 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2411444 ACCCGTATGT
2411454 GACACTTATATCA
1 GACACTTATATCA
2411467 GACACTTATATCA
1 GACACTTATATCA
2411480 GA
1 GA
2411482 GTCCAAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (13 bp):
GACACTTATATCA
Found at i:2413176 original size:13 final size:14
Alignment explanation
Indices: 2413150--2413181 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2413140 GATCAAGGCA
2413150 CCCACCCCCACCCC
1 CCCACCCCCACCCC
2413164 CCCACCCCC-CCCC
1 CCCACCCCCACCCC
2413177 CCCAC
1 CCCAC
2413182 TTGCCTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.12, C:0.88, G:0.00, T:0.00
Consensus pattern (14 bp):
CCCACCCCCACCCC
Found at i:2419923 original size:167 final size:166
Alignment explanation
Indices: 2419648--2419987 Score: 644
Period size: 167 Copynumber: 2.0 Consensus size: 166
2419638 GACAAACTCG
*
2419648 ACCACCATCAGAAGCAATGTAAACACACCGCTGATCAATATTTTTGATCTCAAGCATCAGTAAAA
1 ACCACCATCAGAAGCAATGTAAACACACCGCTGATCAATATATTTGATCTCAAGCATCAGTAAAA
2419713 ATTTAAAATAAAAGAAAAAAAATACAGTACACAGGAGCAATGAAAACCACTAGTCCCATCTGCAC
66 ATTTAAAATAAAAGAAAAAAAATACAGTACACAGGAGCAATGAAAACCACTAGTCCCATCTGCAC
2419778 TCTAGTCTAATTTCAACATGATCATAGAAAACGAAT
131 TCTAGTCTAATTTCAACATGATCATAGAAAACGAAT
*
2419814 ACCACCATCAGAAGCAATGTAAACACACCGCTGATCAATATATTTGAATCTCAAGGATCAGTAAA
1 ACCACCATCAGAAGCAATGTAAACACACCGCTGATCAATATATTTG-ATCTCAAGCATCAGTAAA
2419879 AATTTAAAATAAAAGAAAAAAAATACAGTACACAGGAGCAATGAAAACCACTAGTCCCATCTGCA
65 AATTTAAAATAAAAGAAAAAAAATACAGTACACAGGAGCAATGAAAACCACTAGTCCCATCTGCA
2419944 CTCTAGTCTAATTTCAACATGATCATAGAAAACGAAT
130 CTCTAGTCTAATTTCAACATGATCATAGAAAACGAAT
*
2419981 ACAACCA
1 ACCACCA
2419988 AATATGGAGA
Statistics
Matches: 170, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
166 45 0.26
167 125 0.74
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (166 bp):
ACCACCATCAGAAGCAATGTAAACACACCGCTGATCAATATATTTGATCTCAAGCATCAGTAAAA
ATTTAAAATAAAAGAAAAAAAATACAGTACACAGGAGCAATGAAAACCACTAGTCCCATCTGCAC
TCTAGTCTAATTTCAACATGATCATAGAAAACGAAT
Found at i:2420143 original size:123 final size:123
Alignment explanation
Indices: 2419919--2420163 Score: 339
Period size: 123 Copynumber: 2.0 Consensus size: 123
2419909 CACAGGAGCA
* * *
2419919 ATGAAAACCACTAGTCCCATCTGCACTCTAGTCTAATTTCAACATGATCATAGAAAACGAATACA
1 ATGAAAACCACTAGTCACATCTGCACTCTAGTCCAATTTCAACATGATCATAGAAAACAAATACA
**** * * *
2419984 ACCAAATATGGAGACAGCAATGTGCTGGTTCAAAAGGGATTATATTAGGACATGCACG
66 ACCAAATATGGAGACAGCAAACAACTGGTTCAAAAGGGATTAGAATAGAACATGCACG
* *
2420042 ATGAAAACCACTAGTTACATCTGCACTCTAGTCCAATTTCAACATGATCATAGAAAACAAATAGA
1 ATGAAAACCACTAGTCACATCTGCACTCTAGTCCAATTTCAACATGATCATAGAAAACAAATACA
* **
2420107 ACCAGATATGGAGACAGCAACACAACT-GTTTGAAAGGGATTAGAATAGAACATGCAC
66 ACCAAATATGGAGACAGCAA-ACAACTGGTTCAAAAGGGATTAGAATAGAACATGCAC
2420164 TCAGTGGGAT
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 104 0.98
124 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.22
Consensus pattern (123 bp):
ATGAAAACCACTAGTCACATCTGCACTCTAGTCCAATTTCAACATGATCATAGAAAACAAATACA
ACCAAATATGGAGACAGCAAACAACTGGTTCAAAAGGGATTAGAATAGAACATGCACG
Found at i:2427948 original size:5 final size:5
Alignment explanation
Indices: 2427938--2427974 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
2427928 AATGAGCATG
2427938 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA
2427975 AGGCCTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:2433658 original size:22 final size:23
Alignment explanation
Indices: 2433610--2433672 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
2433600 TTTACCTTTT
2433610 TTTTA-ATTTATTAAATAATATA
1 TTTTATATTTATTAAATAATATA
*
2433632 TTTTATATTT-TTAAA-AATATG
1 TTTTATATTTATTAAATAATATA
* *
2433653 TATT-TATTAATTAAATAATA
1 TTTTATATTTATTAAATAATA
2433673 ATTAGTCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 4 0.11
21 13 0.37
22 14 0.40
23 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTATATTTATTAAATAATATA
Found at i:2434758 original size:15 final size:15
Alignment explanation
Indices: 2434708--2434759 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2434698 CCAGAACAGG
* *
2434708 ATAGAGCAGAACAGA
1 ATAGAGCAAAACTGA
*
2434723 GTAGAGCAAAACTGA
1 ATAGAGCAAAACTGA
*
2434738 ACAGAGCAAAA-TGGA
1 ATAGAGCAAAACT-GA
2434753 ATAGAGC
1 ATAGAGC
2434760 TACGCAAAGG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 1 0.03
15 29 0.97
ACGTcount: A:0.50, C:0.13, G:0.27, T:0.10
Consensus pattern (15 bp):
ATAGAGCAAAACTGA
Found at i:2435651 original size:12 final size:13
Alignment explanation
Indices: 2435633--2435670 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2435623 TAAAAATCAT
2435633 AAAAA-TTATAAA
1 AAAAAGTTATAAA
* *
2435645 CAAAATTTATAAA
1 AAAAAGTTATAAA
2435658 AAAAAGTTATAAA
1 AAAAAGTTATAAA
2435671 TTTTTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (13 bp):
AAAAAGTTATAAA
Found at i:2435658 original size:9 final size:9
Alignment explanation
Indices: 2435607--2435644 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2435597 AAGCCATTTT
2435607 AAAATT-TA
1 AAAATTATA
2435615 AAAATTATTA
1 AAAATTA-TA
*
2435625 AAAATCATA
1 AAAATTATA
2435634 AAAATTATA
1 AAAATTATA
2435643 AA
1 AA
2435645 CAAAATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 6 0.23
9 12 0.46
10 8 0.31
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:2437044 original size:14 final size:14
Alignment explanation
Indices: 2437025--2437062 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
2437015 ATTCAGTAAC
2437025 ATTATTATTAATCT
1 ATTATTATTAATCT
*
2437039 ATTATTATTAATTT
1 ATTATTATTAATCT
2437053 ATTATTATTA
1 ATTATTATTA
2437063 TCACCGCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTATTATTAATCT
Found at i:2437047 original size:17 final size:17
Alignment explanation
Indices: 2437025--2437063 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2437015 ATTCAGTAAC
2437025 ATTATT-ATTAATCTATT
1 ATTATTAATTAAT-TATT
*
2437042 ATTATTAATTTATTATT
1 ATTATTAATTAATTATT
2437059 ATTAT
1 ATTAT
2437064 CACCGCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTATTAATTAATTATT
Found at i:2437155 original size:22 final size:23
Alignment explanation
Indices: 2437130--2437177 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2437120 TTAATTGCCA
2437130 TTAT-TTACTTATATAA-ATTATT
1 TTATGTTA-TTATATAATATTATT
*
2437152 TTATGTTATTATGTAATATTATT
1 TTATGTTATTATATAATATTATT
2437175 TTA
1 TTA
2437178 GGTTTTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (23 bp):
TTATGTTATTATATAATATTATT
Found at i:2437819 original size:18 final size:17
Alignment explanation
Indices: 2437792--2437826 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2437782 GATTATTGCT
2437792 CTTATGTGTATTGTATTG
1 CTTATGTGTATT-TATTG
*
2437810 CTTATTTGTATTTATTG
1 CTTATGTGTATTTATTG
2437827 ATTCTTTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (17 bp):
CTTATGTGTATTTATTG
Found at i:2437834 original size:17 final size:18
Alignment explanation
Indices: 2437793--2437835 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2437783 ATTATTGCTC
* *
2437793 TTATGTGTATTGTATTGC
1 TTATTTGTATTGTATTGA
2437811 TTATTTGTATT-TATTGA
1 TTATTTGTATTGTATTGA
*
2437828 TTCTTTGT
1 TTATTTGT
2437836 CGCTCATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.16, C:0.05, G:0.16, T:0.63
Consensus pattern (18 bp):
TTATTTGTATTGTATTGA
Found at i:2443717 original size:9 final size:9
Alignment explanation
Indices: 2443685--2443722 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2443675 AAATATGACA
*
2443685 TAAATATAT
1 TAAAAATAT
2443694 TAAAAATAAT
1 TAAAAAT-AT
2443704 T-AAAATAT
1 TAAAAATAT
2443712 TAAAAATAT
1 TAAAAATAT
2443721 TA
1 TA
2443723 CATTAATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 3 0.12
9 20 0.77
10 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAAAAATAT
Found at i:2443999 original size:20 final size:20
Alignment explanation
Indices: 2443958--2444000 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2443948 GTCAAAAAAT
*
2443958 AATGAAATTTATTTACTTAG
1 AATGAAATTTATTTACTAAG
*
2443978 AATGAATTTTATTTTA-TAAG
1 AATGAAATTTA-TTTACTAAG
2443998 AAT
1 AAT
2444001 TACCATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (20 bp):
AATGAAATTTATTTACTAAG
Found at i:2445252 original size:215 final size:215
Alignment explanation
Indices: 2444881--2445313 Score: 866
Period size: 215 Copynumber: 2.0 Consensus size: 215
2444871 TTGGACATTG
2444881 AAATGCCATATTTTGGAAAGGTGTAAATATCAGGCTTAACAGTCAGTTTTAACACATTGAAAGCC
1 AAATGCCATATTTTGGAAAGGTGTAAATATCAGGCTTAACAGTCAGTTTTAACACATTGAAAGCC
2444946 CATTTTTTGGACAATCTATCCTACAGTAATCTTTGGTCATTGTGTTCCCAAGGAAGACAGTTTTC
66 CATTTTTTGGACAATCTATCCTACAGTAATCTTTGGTCATTGTGTTCCCAAGGAAGACAGTTTTC
2445011 GCTTCGGAATTTGATCGAACACTTTGAGTACATGGTCCATGTCACCAAGTTTATTTATACAAGAA
131 GCTTCGGAATTTGATCGAACACTTTGAGTACATGGTCCATGTCACCAAGTTTATTTATACAAGAA
2445076 CATCAAAGTTCAGTAAAAAA
196 CATCAAAGTTCAGTAAAAAA
2445096 AAATGCCATATTTTGGAAAGGTGTAAATATCAGGCTTAACAGTCAGTTTTAACACATTGAAAGCC
1 AAATGCCATATTTTGGAAAGGTGTAAATATCAGGCTTAACAGTCAGTTTTAACACATTGAAAGCC
2445161 CATTTTTTGGACAATCTATCCTACAGTAATCTTTGGTCATTGTGTTCCCAAGGAAGACAGTTTTC
66 CATTTTTTGGACAATCTATCCTACAGTAATCTTTGGTCATTGTGTTCCCAAGGAAGACAGTTTTC
2445226 GCTTCGGAATTTGATCGAACACTTTGAGTACATGGTCCATGTCACCAAGTTTATTTATACAAGAA
131 GCTTCGGAATTTGATCGAACACTTTGAGTACATGGTCCATGTCACCAAGTTTATTTATACAAGAA
2445291 CATCAAAGTTCAGTAAAAAA
196 CATCAAAGTTCAGTAAAAAA
2445311 AAA
1 AAA
2445314 AATGGGTGTT
Statistics
Matches: 218, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
215 218 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (215 bp):
AAATGCCATATTTTGGAAAGGTGTAAATATCAGGCTTAACAGTCAGTTTTAACACATTGAAAGCC
CATTTTTTGGACAATCTATCCTACAGTAATCTTTGGTCATTGTGTTCCCAAGGAAGACAGTTTTC
GCTTCGGAATTTGATCGAACACTTTGAGTACATGGTCCATGTCACCAAGTTTATTTATACAAGAA
CATCAAAGTTCAGTAAAAAA
Found at i:2445801 original size:20 final size:20
Alignment explanation
Indices: 2445749--2445801 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
2445739 AATGAGTTTC
* **
2445749 TTTTTTTTATAAATTTTGAA
1 TTTTTTTCATAAAAATTGAA
* * *
2445769 TATTATTCTTAAAAATTGAA
1 TTTTTTTCATAAAAATTGAA
2445789 TTTTTTTCATAAA
1 TTTTTTTCATAAA
2445802 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (20 bp):
TTTTTTTCATAAAAATTGAA
Found at i:2448079 original size:20 final size:20
Alignment explanation
Indices: 2448051--2448094 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2448041 AAATAGTACC
*
2448051 GATATTTTGACTAA-GGTATA
1 GATACTTTG-CTAATGGTATA
*
2448071 GATACTTTGTTAATGGTATA
1 GATACTTTGCTAATGGTATA
2448091 GATA
1 GATA
2448095 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (20 bp):
GATACTTTGCTAATGGTATA
Found at i:2450230 original size:23 final size:23
Alignment explanation
Indices: 2450204--2450282 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
2450194 TAAAACACTG
*
2450204 AATATAACACGCACAAGGTGCTA
1 AATATAACACGCACAAGGCGCTA
*
2450227 AATATAACACGCATATA-GCGCTA
1 AATATAACACGCACA-AGGCGCTA
* * *
2450250 AATGTAACATGCACAAGGGGCT-
1 AATATAACACGCACAAGGCGCTA
*
2450272 GATATAACACG
1 AATATAACACG
2450283 TGTAAAGCAC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
22 9 0.20
23 35 0.78
24 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (23 bp):
AATATAACACGCACAAGGCGCTA
Found at i:2450258 original size:46 final size:45
Alignment explanation
Indices: 2450181--2450282 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 45
2450171 CAATCACACC
* * *
2450181 AATATAACATGCATAAAACACTGAATATAACACGCACAAGGTGCT
1 AATATAACACGCATAAAACACTAAATATAACACGCACAAGGGGCT
* * * * *
2450226 AAATATAACACGCATATAGCGCTAAATGTAACATGCACAAGGGGCT
1 -AATATAACACGCATAAAACACTAAATATAACACGCACAAGGGGCT
*
2450272 GATATAACACG
1 AATATAACACG
2450283 TGTAAAGCAC
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
45 10 0.21
46 37 0.79
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (45 bp):
AATATAACACGCATAAAACACTAAATATAACACGCACAAGGGGCT
Found at i:2453698 original size:22 final size:20
Alignment explanation
Indices: 2453658--2453696 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2453648 TTAATACCAC
*
2453658 AATATATTAAATATATTTAA
1 AATATATAAAATATATTTAA
2453678 AATATATAATAATATATTT
1 AATATATAA-AATATATTT
2453697 TATCCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATAAAATATATTTAA
Found at i:2454092 original size:289 final size:273
Alignment explanation
Indices: 2453749--2454332 Score: 722
Period size: 273 Copynumber: 2.1 Consensus size: 273
2453739 ATATCTATAT
* * *
2453749 TATTATTTAAGTGTTTTACTGAGTTGGTATTACCGTCAATCGAGTCACCAACTCAATTGTTAAAT
1 TATTATTTAAGTGTTTTACTGAGTTGGTATCACCCTCAAACGAGTCACCAACTCAATTGTTAAAT
* * * * *
2453814 TACGGGAATACTCTCCTATAATTAAGAAAGTTATATTATTCGAGGGTATTTTAATCTTTTTCATT
66 TACGGAAATACCCTCCTATAATTAAAAAAGTTATATTATTCGAGGATA-TTTAAT-ATTTT-A-T
* * *
2453879 TAAAAAACCAATAAAAATATATATATGGTGACCCGTGTTGATTGCATCAATAAAACGTTTAATTT
127 T-AAAAACCAAT---AA-A-AT-TAT-GT----CATGTTAATTGCATCAATAAAACCTTTAATTT
* * * ** * *
2453944 ACCACTCAACTAAAGCTTTGTTTTGATATTTTTATATGTTTTTATTTTATTATGCACATTTTATC
180 ACCACTCAACTAAAGCTTTATTTTAATATTCTTATACATTTTTATTTTATTATGCACACTCTAT-
*
2454009 ACA-TT-CATCAATTGTATATCTATACTTAC
244 A-ATTTCCATCAATTGTACATCTATACTTAC
* *
2454038 TATTATTTAAGTGTTTTATTGAGTTGGTGTCACCCTCAAACGAGTCACCAACTCAATTGTTAAAT
1 TATTATTTAAGTGTTTTACTGAGTTGGTATCACCCTCAAACGAGTCACCAACTCAATTGTTAAAT
* ** * *
2454103 TATGGAAATACCCTTTTGTAATTAAAAAAGTTATATTATTCGAGGATATTTAGTATTTTATTAAA
66 TACGGAAATACCCTCCTATAATTAAAAAAGTTATATTATTCGAGGATATTTAATATTTTATTAAA
* *
2454168 AATCAATAAAATTATGTCATGTTAATTGCATCAATAAAACCTTTAATTTACCACTCAACTAAATC
131 AACCAATAAAATTATGTCATGTTAATTGCATCAATAAAACCTTTAATTTACCACTCAACTAAAGC
2454233 TTTATTTTAATATTCTTATACATTTTTATTTTATTATGCACACTCTATAATTTCCATCAATTGTA
196 TTTATTTTAATATTCTTATACATTTTTATTTTATTATGCACACTCTATAATTTCCATCAATTGTA
*
2454298 CATCTATACTTAT
261 CATCTATACTTAC
*
2454311 TATTATTTAAGTGTTTAACTGA
1 TATTATTTAAGTGTTTTACTGA
2454333 ATTGACGTCA
Statistics
Matches: 262, Mismatches: 31, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
271 1 0.00
272 3 0.01
273 127 0.48
277 2 0.01
278 3 0.01
279 2 0.01
280 1 0.00
281 2 0.01
284 9 0.03
285 2 0.01
286 1 0.00
287 4 0.02
288 5 0.02
289 100 0.38
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (273 bp):
TATTATTTAAGTGTTTTACTGAGTTGGTATCACCCTCAAACGAGTCACCAACTCAATTGTTAAAT
TACGGAAATACCCTCCTATAATTAAAAAAGTTATATTATTCGAGGATATTTAATATTTTATTAAA
AACCAATAAAATTATGTCATGTTAATTGCATCAATAAAACCTTTAATTTACCACTCAACTAAAGC
TTTATTTTAATATTCTTATACATTTTTATTTTATTATGCACACTCTATAATTTCCATCAATTGTA
CATCTATACTTAC
Found at i:2454443 original size:39 final size:41
Alignment explanation
Indices: 2454400--2454486 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 41
2454390 ATTAAAATAA
2454400 TTTAAATTA-AGTATTT-ATAA-TTTTTAAT-AATTTTTAAA-T
1 TTTAAATTATAGT-TTTCATAAGTTTTT--TGAATTTTTAAATT
*
2454439 TTTAAA-AATAGTTTTCATAAGTTTTTTGAATTTTTAAATT
1 TTTAAATTATAGTTTTCATAAGTTTTTTGAATTTTTAAATT
2454479 TTTAAATT
1 TTTAAATT
2454487 TTAAAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
38 5 0.12
39 23 0.57
40 12 0.30
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (41 bp):
TTTAAATTATAGTTTTCATAAGTTTTTTGAATTTTTAAATT
Found at i:2464167 original size:3 final size:3
Alignment explanation
Indices: 2464159--2464185 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2464149 TTAAATTAAC
2464159 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2464186 TGCTGCCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2464815 original size:22 final size:23
Alignment explanation
Indices: 2464764--2464809 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2464754 GAAGCCCAAA
2464764 AACCCATCCCACAAAAACCTTAG
1 AACCCATCCCACAAAAACCTTAG
2464787 AACCCATCCCACAAAAACCTTAG
1 AACCCATCCCACAAAAACCTTAG
2464810 CACCATGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.39, G:0.04, T:0.13
Consensus pattern (23 bp):
AACCCATCCCACAAAAACCTTAG
Found at i:2471790 original size:11 final size:12
Alignment explanation
Indices: 2471765--2471793 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2471755 ATAATTTTAA
2471765 ATTTTAAATAAT
1 ATTTTAAATAAT
2471777 ATTTTAAA-AAT
1 ATTTTAAATAAT
2471788 ATTTTA
1 ATTTTA
2471794 TTTTATTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTTAAATAAT
Found at i:2475306 original size:15 final size:15
Alignment explanation
Indices: 2475260--2475315 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
2475250 ATGTTTTCTG
2475260 AATATTAATTTAATTAAA
1 AATATT-ATTTAA--AAA
2475278 AA-ATTATTTAAAAA
1 AATATTATTTAAAAA
* *
2475292 AATATTTTTTTAAAA
1 AATATTATTTAAAAA
*
2475307 AATAATATT
1 AATATTATT
2475316 ATTATTATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 5 0.15
15 17 0.52
16 6 0.18
17 3 0.09
18 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATTATTTAAAAA
Found at i:2478533 original size:27 final size:27
Alignment explanation
Indices: 2478430--2478540 Score: 132
Period size: 27 Copynumber: 4.1 Consensus size: 27
2478420 AACATGTCAG
* * *
2478430 GAAAGAATAGCTTTTGTGGTGATCTTT
1 GAAAGAATAACCTTTGTGGTGAACTTT
**
2478457 GAAAGAATAACCTTTGTGGTGAGTTTT
1 GAAAGAATAACCTTTGTGGTGAACTTT
*
2478484 GAAAGAATAACCTTTATGGTGAACTTT
1 GAAAGAATAACCTTTGTGGTGAACTTT
* * * *
2478511 AAAAGAATAACCATTGTAGTGAACTCT
1 GAAAGAATAACCTTTGTGGTGAACTTT
2478538 GAA
1 GAA
2478541 TGGACATGCT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (27 bp):
GAAAGAATAACCTTTGTGGTGAACTTT
Found at i:2487756 original size:171 final size:171
Alignment explanation
Indices: 2487471--2487806 Score: 573
Period size: 171 Copynumber: 2.0 Consensus size: 171
2487461 AGGGGGAACA
*
2487471 TATTTGCTTCTCCAAAGAATTACCCAAAACTCAATCCCATGATCCTGTCCCACCTTCACATGATG
1 TATTTGCTGCTCCAAAGAATTACCCAAAACTCAATCCCATGATCCTGTCCCACCTTCACATGATG
* * *
2487536 AGATGGATCAGTTACAGGAACGTAATTGTAGTAGCTCCTTTTCTCCTGCTTCTCTAGATCCTCCA
66 AGATGGATCAGTTACAGGAACGTAATTGTAGCAGCTCCCTTTCTCCTGCTTCTCTAGATCCTACA
* *
2487601 TCCTCAGGTCAGAAGTTCGTATCTCCCATGGCAAAAGTTTG
131 TCCTCAGGTCAAAAGTTCGTATCTCCCATAGCAAAAGTTTG
* *
2487642 TATTTGCTGCTCCAAAGAATTACCCAAAACTCAATCCCATGATCCTGTGCCACCTTCACATGTTG
1 TATTTGCTGCTCCAAAGAATTACCCAAAACTCAATCCCATGATCCTGTCCCACCTTCACATGATG
* *
2487707 AGATGGATCAGTTACGGGATCGTAATTGTAGCAGCTCCCTTTCTCCTGCTTCTCTAGATCCTACA
66 AGATGGATCAGTTACAGGAACGTAATTGTAGCAGCTCCCTTTCTCCTGCTTCTCTAGATCCTACA
*
2487772 TCCTCAGGTCAAAAGTTTGTATCTCCCATAGCAAA
131 TCCTCAGGTCAAAAGTTCGTATCTCCCATAGCAAA
2487807 GGAAAATCAT
Statistics
Matches: 154, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
171 154 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.31
Consensus pattern (171 bp):
TATTTGCTGCTCCAAAGAATTACCCAAAACTCAATCCCATGATCCTGTCCCACCTTCACATGATG
AGATGGATCAGTTACAGGAACGTAATTGTAGCAGCTCCCTTTCTCCTGCTTCTCTAGATCCTACA
TCCTCAGGTCAAAAGTTCGTATCTCCCATAGCAAAAGTTTG
Found at i:2489567 original size:12 final size:12
Alignment explanation
Indices: 2489550--2489581 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2489540 AAAAATTAAT
2489550 TATATTTTTTTA
1 TATATTTTTTTA
2489562 TATATTTTTTTA
1 TATATTTTTTTA
2489574 TA-ATTTTT
1 TATATTTTT
2489582 ATGCTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TATATTTTTTTA
Found at i:2498547 original size:16 final size:15
Alignment explanation
Indices: 2498505--2498547 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
2498495 TTTATATATA
2498505 TATATTTATTAATTT
1 TATATTTATTAATTT
2498520 TATGATTTATTAATTAT
1 TAT-ATTTATTAATT-T
2498537 T-TATTTCATTA
1 TATATTT-ATTA
2498548 TAGTTGGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.28
16 16 0.64
17 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (15 bp):
TATATTTATTAATTT
Found at i:2498776 original size:29 final size:28
Alignment explanation
Indices: 2498722--2498784 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
2498712 CAAGAGAGTC
* * *
2498722 AAAACGAAAGAAAACAAAAAGGGAAAAGG
1 AAAATGAAAGAAAACAAAAAGAG-AAAGA
*
2498751 AAAATGAAAGAAAAGAAAGAA-AGAAAGA
1 AAAATGAAAGAAAACAAA-AAGAGAAAGA
2498779 AAAATG
1 AAAATG
2498785 CCCTCCTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 10 0.34
29 17 0.59
30 2 0.07
ACGTcount: A:0.71, C:0.03, G:0.22, T:0.03
Consensus pattern (28 bp):
AAAATGAAAGAAAACAAAAAGAGAAAGA
Found at i:2499754 original size:29 final size:29
Alignment explanation
Indices: 2499712--2499767 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
2499702 ATTTATGGAG
2499712 TTAGATGAAATAGAAACGTCATGTTCTAC
1 TTAGATGAAATAGAAACGTCATGTTCTAC
2499741 TTAGATGAAATAGAAACGTCATGTTCT
1 TTAGATGAAATAGAAACGTCATGTTCT
2499768 CCTACTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (29 bp):
TTAGATGAAATAGAAACGTCATGTTCTAC
Found at i:2500992 original size:41 final size:40
Alignment explanation
Indices: 2500877--2501261 Score: 457
Period size: 41 Copynumber: 9.4 Consensus size: 40
2500867 CCTTTCGAGG
* **
2500877 CTTTAGCAGCATTTTTGAAAAAGCGCCGCTAACACTCGGGT
1 CTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC-GGT
* * *
2500918 CTTTCGTGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGAGT
1 CTTTAGCGGC-ATTTTTGAAAAAGCGCCGCTAATGCTCG-GT
* * * * *
2500960 TTTTAGCGGCGTTTTTGAAAAACCGTCACTAATGCTCGGCT
1 CTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCGG-T
*
2501001 CTTTAGCGGCGTTTTTG-AAAAGCGCCGCTAATGCTCGTGT
1 CTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCG-GT
* * * * *
2501041 CTTGAGCGACATTTTTGAAAAAGTGTCGCTAATGCTTGGAT
1 CTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCGG-T
* *
2501082 CTTTAGCGGCATTTTTGAAAAAGAGCCGGTAATGCTCAGGT
1 CTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC-GGT
*
2501123 CTTTAACGGCATTTTTGAAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC-GGT
*
2501164 CTTTAGCGGCATTTTTGAAAAAGCGCCTCTAATGCTCGTGT
1 CTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCG-GT
* *
2501205 CTTTAGCGGAATTTTTGAAAAAGCGCCTCTAATGCTCGTGT
1 CTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCG-GT
*
2501246 CTTTAGCGGCGTTTTT
1 CTTTAGCGGCATTTTT
2501262 ATAAAAAAAC
Statistics
Matches: 298, Mismatches: 38, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
40 35 0.12
41 228 0.77
42 35 0.12
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (40 bp):
CTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCGGT
Found at i:2507619 original size:16 final size:16
Alignment explanation
Indices: 2507581--2507645 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
2507571 TTCGCTATAT
* *
2507581 TGGAATGGAGACGTAA
1 TGGAATAGAGGCGTAA
* *
2507597 TGAAATAGAGGCATAA
1 TGGAATAGAGGCGTAA
2507613 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
2507629 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
2507645 T
1 T
2507646 AGATAATTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.40, C:0.06, G:0.34, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:2508103 original size:121 final size:120
Alignment explanation
Indices: 2507859--2508590 Score: 1247
Period size: 121 Copynumber: 6.1 Consensus size: 120
2507849 TTAATCATAT
* *
2507859 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTCATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
2507924 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
2507979 TTTAAAATAATTATTATCAAATATAATTTAATAAAAATATATAATTTAATAAAATTCGTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-T
* *
2508044 TAAATATTCTTAAATAAATTTACTAAAATCATAAAATATAATACTATAAAATATAA
65 TAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
2508100 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
2508165 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
2508220 TTTAAAATAATTATTATTAAAAATATAATTTAGT-AAAATATATAATTTAATAAAATTCTTAATA
1 TTTAAAATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA
2508284 TTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
64 TTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
2508341 TTTAAAATAATAATTATTAAAAATATAATTTAGTAAAAATATATAATTTAATAAAATTCTTAATA
1 TTTAAAATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA
2508406 TTAAATATTCTT--A-GAATTTACTAAAATCATAATATATAATACTATAAAATATAA
64 TTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * *
2508460 TTTAAATTAATTATTTTTAAATATAATCTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
2508525 AAATATTCTTATATAAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
2508580 TTTAAAATAAT
1 TTTAAAATAAT
2508591 AAAATTTGAA
Statistics
Matches: 584, Mismatches: 21, Indels: 14
0.94 0.03 0.02
Matches are distributed among these distances:
117 55 0.09
119 57 0.10
120 183 0.31
121 234 0.40
122 55 0.09
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:2508257 original size:15 final size:16
Alignment explanation
Indices: 2508211--2508274 Score: 64
Period size: 17 Copynumber: 4.2 Consensus size: 16
2508201 ATAATACTAT
2508211 AAAATATAATTTAA-A
1 AAAATATAATTTAATA
* *
2508226 ATAAT-T-A-TTATTA
1 AAAATATAATTTAATA
*
2508239 AAAATATAATTTAGTA
1 AAAATATAATTTAATA
2508255 AAATATATAATTTAATA
1 AAA-ATATAATTTAATA
2508272 AAA
1 AAA
2508275 TTCTTAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
12 3 0.08
13 6 0.15
14 2 0.05
15 5 0.13
16 8 0.21
17 15 0.38
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATATAATTTAATA
Found at i:2508264 original size:17 final size:17
Alignment explanation
Indices: 2508237--2508397 Score: 66
Period size: 17 Copynumber: 9.4 Consensus size: 17
2508227 TAATTATTAT
*
2508237 TAAAA-ATATAATTTAG
1 TAAAATATATAATTTAA
2508253 TAAAATATATAATTTAA
1 TAAAATATATAATTTAA
*
2508270 TAAAAT-TCTTAATATTAAA
1 TAAAATAT-ATAAT-TT-AA
*** * *
2508289 TATTCTTAAATGAATTTAC
1 TA-AAATATAT-AATTTAA
* *
2508308 TAAAAT-CATAATAT-A
1 TAAAATATATAATTTAA
* * *
2508323 TAATACTATAAAATATAA
1 TAA-AATATATAATTTAA
*
2508341 TTTAAAATA-ATAA-TTAT
1 --TAAAATATATAATTTAA
*
2508358 TAAAA-ATATAATTTAG
1 TAAAATATATAATTTAA
2508374 TAAAAATATATAATTTAA
1 T-AAAATATATAATTTAA
2508392 TAAAAT
1 TAAAAT
2508398 TCTTAATATT
Statistics
Matches: 106, Mismatches: 23, Indels: 31
0.66 0.14 0.19
Matches are distributed among these distances:
14 1 0.01
15 12 0.11
16 16 0.15
17 39 0.37
18 18 0.17
19 10 0.09
20 7 0.07
21 3 0.03
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAAATATATAATTTAA
Found at i:2508290 original size:241 final size:240
Alignment explanation
Indices: 2507859--2508590 Score: 1249
Period size: 241 Copynumber: 3.0 Consensus size: 240
2507849 TTAATCATAT
* *
2507859 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTCATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
2507924 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAATTTAAAATAA
66 AAATATTCTTA-ATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAA
* *
2507989 TTATTA-TCAAATATAATTTAATAAAAATATATAATTTAATAAAATTCGTAATATTTAAATATTC
130 TTATTATTAAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-TTAAATATTC
*
2508053 TTAAATAAATTTACTAAAATCATAAAATATAATACTATAAAATATAA
194 TTAAATAAATTTACTAAAATCATAATATATAATACTATAAAATATAA
2508100 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
2508165 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAA
66 AAATATTCTT-AATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAA
*
2508230 TTATTATTAAAAATATAATTTAGT-AAAATATATAATTTAATAAAATTCTTAATATTAAATATTC
130 TTATTATT-AAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTC
*
2508294 TTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
194 TTAAATAAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
2508341 TTTAAAATAATAATTATTAAAAATATAATTTAGTAAAAATATATAATTTAATAAAATTCTTAATA
1 TTTAAAATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA
*
2508406 TTAAATATTCTT-A-GAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAATTA
64 TTAAATATTCTTAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATA
* *
2508469 ATTATT-TTTAAATATAATCTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTC
129 ATTATTATTAAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTC
*
2508533 TTATATAAATTTACTAAAATCATAATATATAATACTATAAAATATAA
194 TTAAATAAATTTACTAAAATCATAATATATAATACTATAAAATATAA
2508580 TTTAAAATAAT
1 TTTAAAATAAT
2508591 AAAATTTGAA
Statistics
Matches: 469, Mismatches: 16, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
238 12 0.03
239 98 0.21
240 55 0.12
241 204 0.43
242 31 0.07
243 69 0.15
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (240 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAAT
TATTATTAAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTT
AAATAAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:2508365 original size:16 final size:16
Alignment explanation
Indices: 2508344--2508388 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2508334 AATATAATTT
*
2508344 AAAATAATAATTATTA
1 AAAATAATAATTAGTA
2508360 AAAAT-ATAATTTAGTA
1 AAAATAATAA-TTAGTA
2508376 AAAATATATAATT
1 AAAATA-ATAATT
2508389 TAATAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.16
16 15 0.60
17 2 0.08
18 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAATAATAATTAGTA
Found at i:2508384 original size:18 final size:17
Alignment explanation
Indices: 2508359--2508396 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2508349 AATAATTATT
*
2508359 AAAAATATAATTTAGTA
1 AAAAATATAATTTAATA
2508376 AAAATATATAATTTAATA
1 AAAA-ATATAATTTAATA
2508394 AAA
1 AAA
2508397 TTCTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATATAATTTAATA
Found at i:2508394 original size:44 final size:41
Alignment explanation
Indices: 2507934--2508403 Score: 174
Period size: 38 Copynumber: 11.6 Consensus size: 41
2507924 AAATATTCTT
* * * *
2507934 ATATGAATTTAATAAAATCA-T-AATATATAA-TACTATAAA
1 ATAT-AATTTAATAAAATTATTAAAAATATAATTAATAAAAA
*
2507973 ATATAATTTAA-AATAATTATTATCAAATATAATTTAATAAAAA
1 ATATAATTTAATAA-AATTATTA-AAAATATAA-TTAATAAAAA
** * * * * ***
2508016 TATATAATTTAATAAAATTCGT-AATATTTAAATATTCTTAA
1 -ATATAATTTAATAAAATTATTAAAAATATAATTAATAAAAA
* * * *
2508057 ATA-AATTTACTAAAATCA-T-AAAATATAA-TACTATAAA
1 ATATAATTTAATAAAATTATTAAAAATATAATTAATAAAAA
*
2508094 ATATAATTTAA-AATAATTATTATTAAATATAATTTAATAAAAA
1 ATATAATTTAATAA-AATTATTA-AAAATATAA-TTAATAAAAA
* * * * ***
2508137 TATATAATTTAATAAAATTCTT-AATAT-TAAATATTCTTAA
1 -ATATAATTTAATAAAATTATTAAAAATATAATTAATAAAAA
* * * * * *
2508177 AT-GAATTTACTAAAATCA-T-AATATATAA-TACTATAAA
1 ATATAATTTAATAAAATTATTAAAAATATAATTAATAAAAA
* * *
2508214 ATATAATTTAAAATAATTATTATTAAAAATATAATTTAGTAAAAT
1 ATATAATTT--AATAA-AATTATTAAAAATATAA-TTAATAAAAA
* * * * ***
2508259 ATATAATTTAATAAAATTCTT-AATAT-TAAATATTCTTAA
1 ATATAATTTAATAAAATTATTAAAAATATAATTAATAAAAA
* * * * * *
2508298 AT-GAATTTACTAAAATCA-T-AATATATAA-TACTATAAA
1 ATATAATTTAATAAAATTATTAAAAATATAATTAATAAAAA
*
2508335 ATATAATTTAAAATAATAATTATTAAAAATATAATTTAGTAAAAA
1 ATATAATTT--AATAA-AATTATTAAAAATATAA-TTAATAAAAA
*
2508380 TATATAATTTAATAAAATTCTTAA
1 -ATATAATTTAATAAAATTATTAA
2508404 TATTAAATAT
Statistics
Matches: 321, Mismatches: 74, Indels: 68
0.69 0.16 0.15
Matches are distributed among these distances:
37 41 0.13
38 69 0.21
39 26 0.08
40 19 0.06
41 34 0.11
42 16 0.05
43 43 0.13
44 38 0.12
45 26 0.08
46 9 0.03
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (41 bp):
ATATAATTTAATAAAATTATTAAAAATATAATTAATAAAAA
Found at i:2508424 original size:53 final size:53
Alignment explanation
Indices: 2508367--2508535 Score: 144
Period size: 60 Copynumber: 3.0 Consensus size: 53
2508357 TTAAAAATAT
* *
2508367 AATTTAGTAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAG
1 AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAA
* * * * *
2508420 AATTTACT-AAAATCATAATATATAATACTATAAAATATAATTTAA-ATTAATTATTTTTAA
1 AATTTAATAAAAAT-AT-ATA-AT-TTA--ATAAAAT-T--CTTAATATTAAATATTCTTAA
2508480 ATATAATCTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTA
1 A-AT--T-TAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTA
2508536 TATAAATTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
52 5 0.06
53 9 0.10
54 3 0.03
55 2 0.02
56 6 0.07
57 12 0.13
58 8 0.09
59 8 0.09
60 13 0.14
61 8 0.09
62 2 0.02
63 4 0.04
64 5 0.06
65 5 0.06
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (53 bp):
AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAA
Found at i:2508635 original size:20 final size:20
Alignment explanation
Indices: 2508588--2508626 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2508578 AATTTAAAAT
*
2508588 AATAAAATTTGAATCGATTA
1 AATAATATTTGAATCGATTA
* *
2508608 AATGATATTTGAATTGATT
1 AATAATATTTGAATCGATT
2508627 TGATAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (20 bp):
AATAATATTTGAATCGATTA
Found at i:2508856 original size:13 final size:13
Alignment explanation
Indices: 2508838--2508865 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2508828 TCATGTTCTT
2508838 ATTGAATTGCTAA
1 ATTGAATTGCTAA
2508851 ATTGAATTGCTAA
1 ATTGAATTGCTAA
2508864 AT
1 AT
2508866 GAGATAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTGAATTGCTAA
Found at i:2511937 original size:14 final size:14
Alignment explanation
Indices: 2511918--2511945 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2511908 AGCAGAAATC
2511918 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
2511932 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
2511946 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:2511943 original size:19 final size:18
Alignment explanation
Indices: 2511921--2511965 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
2511911 AGAAATCTGG
2511921 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
2511940 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
2511957 AGAAAAGAA
1 AGAAAAGAA
2511966 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:2512286 original size:23 final size:23
Alignment explanation
Indices: 2512260--2512869 Score: 304
Period size: 23 Copynumber: 26.8 Consensus size: 23
2512250 TAAATATTGT
*
2512260 AAATTGAAGTGTTTAAGTGCTAC
1 AAATTGAAGTGTTTAAGTGCTGC
*
2512283 AAATTGAAGTATTT-AGTTGCTAG-
1 AAATTGAAGTGTTTAAG-TGCT-GC
*
2512306 AAATTG-AGATGTTTTA-TCGCTG-
1 AAATTGAAG-TGTTTAAGT-GCTGC
* * * * *
2512328 TAATT-AAGGTGTATAAATGTTGT
1 AAATTGAA-GTGTTTAAGTGCTGC
*
2512351 TAATTGATA-TGTTTAAGTGCTGC
1 AAATTGA-AGTGTTTAAGTGCTGC
*
2512374 AAATTTAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
* *
2512397 AAATTTAAGTGTTTAAGTGCTGA
1 AAATTGAAGTGTTTAAGTGCTGC
* *
2512420 AAATTG-AGATGTTTTA-TCGTTG-
1 AAATTGAAG-TGTTTAAGT-GCTGC
* * * * * *
2512442 TAATTGAGGTGTATAAATGTTGT
1 AAATTGAAGTGTTTAAGTGCTGC
* *
2512465 TAATTGATA-AGTTTAAGTGCTGC
1 AAATTGA-AGTGTTTAAGTGCTGC
* *
2512488 GAATTTAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
* *
2512511 AAATTGAAGTGTTTAAGTGTTGT
1 AAATTGAAGTGTTTAAGTGCTGC
*
2512534 AAATTG-AGATGTTTTA-T-C-GC
1 AAATTGAAG-TGTTTAAGTGCTGC
** * * *
2512554 TATAATTGAAGTGTAAAAATGTTGT
1 -A-AATTGAAGTGTTTAAGTGCTGC
*
2512579 TAATTGATA-TGTTTAAGTGCTG-
1 AAATTGA-AGTGTTTAAGTGCTGC
* * *
2512601 AAATTTAAGTGTTTAAATGCTGT
1 AAATTGAAGTGTTTAAGTGCTGC
2512624 AAATTGAAGTG-TTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
*
2512646 AAATTTAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
*
2512669 AAATTG-AGATGTATT-A-TCGCT-T
1 AAATTGAAG-TGT-TTAAGT-GCTGC
* * * * * *
2512691 TAATTGATGTGTATAAATGTTGT
1 AAATTGAAGTGTTTAAGTGCTGC
* * *
2512714 TATTTGATA-TGTTAAAGTGCTGC
1 AAATTGA-AGTGTTTAAGTGCTGC
2512737 AAATTGAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
2512760 AAATTG-AGATGTCTT-A-TCGCTG-
1 AAATTGAAG-TGT-TTAAGT-GCTGC
* * * * * *
2512782 TAATTGATGTGTATAAATGTTGT
1 AAATTGAAGTGTTTAAGTGCTGC
* * *
2512805 TAATTGATA-TGTTAAAGTGTTGC
1 AAATTGA-AGTGTTTAAGTGCTGC
* *
2512828 AAATTGAAGTGTTTAAATGCTGT
1 AAATTGAAGTGTTTAAGTGCTGC
*
2512851 AAATTGAAGTGTTAAAGTG
1 AAATTGAAGTGTTTAAGTG
2512870 TTACTTTCCA
Statistics
Matches: 453, Mismatches: 86, Indels: 96
0.71 0.14 0.15
Matches are distributed among these distances:
20 1 0.00
21 4 0.01
22 117 0.26
23 322 0.71
24 7 0.02
25 2 0.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (23 bp):
AAATTGAAGTGTTTAAGTGCTGC
Found at i:2512401 original size:91 final size:91
Alignment explanation
Indices: 2512243--2512857 Score: 451
Period size: 91 Copynumber: 6.8 Consensus size: 91
2512233 AACATGCTCT
* * * * *
2512243 AGGTGTTTAAATATTGTAAATTGA-AGTGTTTAAGTGCTACAAATTGAAGTATTT-AGTTGCTAG
1 AGGTGTATAAATGTTGTTAATTGATA-TGTTTAAGTGCTGCAAATTGAAGTGTTTAAG-TGCT-G
* *
2512306 -AAATTGAGATGTTTTA-TCGCTGTAATTA
63 CAAATTGAGATGTTTAAGT-GCTGAAATTA
*
2512334 AGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGTGTTTAAGTGCTGCAA
1 AGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAA
* *
2512399 ATTTA-AGTGTTTAAGTGCTGAAAATTG
66 ATTGAGA-TGTTTAAGTGCTG-AAATTA
* ** ** * * * ** *
2512426 AGATGT-TTTATCGTTG-TAATTGAGGTGTATAAATGTTGTTAATTGATA-AGTTTAAGTGCTGC
1 AGGTGTATAAAT-GTTGTTAATTGATATGTTTAAGTGCTGCAAATTGA-AGTGTTTAAGTGCTGC
* *
2512488 GAATTTA-AGTGTTTAAGTGCTGCAAATTGA
64 AAATTGAGA-TGTTTAAGTGCTG-AAATT-A
* * * * * ** * * *
2512518 A-GTGTTTAAGTGTTGTAAATTGAGATGTTTTA-T-C-GCTATAATTGAAGTGTAAAAATGTTGT
1 AGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGC-A-AATTGAAGTGTTTAAGTGCTGC
* *
2512579 TAATTGATATGTTTAAGTGCTGAAATTTA
64 AAATTGAGATGTTTAAGTGCTGAAA-TTA
* * * *
2512608 A-GTGTTTAAATGCTGTAAATTGA-A-GTGTTAAGTGCTGCAAATTTAAGTGTTTAAGTGCTGCA
1 AGGTGTATAAATGTTGTTAATTGATATGT-TTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCA
** *
2512670 AATTGAGATGTATT-A-TCGCTTTAATTG
65 AATTGAGATGT-TTAAGT-GCTGAAATTA
* * *
2512697 ATGTGTATAAATGTTGTTATTTGATATGTTAAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAA
1 AGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAA
* *
2512762 ATTGAGATGTCTT-A-TCGCTGTAATTG
66 ATTGAGATGT-TTAAGT-GCTGAAATTA
* * * * *
2512788 ATGTGTATAAATGTTGTTAATTGATATGTTAAAGTGTTGCAAATTGAAGTGTTTAAATGCTGTAA
1 AGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAA
2512853 ATTGA
66 ATTGA
2512858 AGTGTTAAAG
Statistics
Matches: 429, Mismatches: 70, Indels: 50
0.78 0.13 0.09
Matches are distributed among these distances:
88 2 0.00
89 9 0.02
90 79 0.18
91 301 0.70
92 38 0.09
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (91 bp):
AGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAA
ATTGAGATGTTTAAGTGCTGAAATTA
Found at i:2512446 original size:114 final size:114
Alignment explanation
Indices: 2512260--2512869 Score: 736
Period size: 114 Copynumber: 5.4 Consensus size: 114
2512250 TAAATATTGT
* * *
2512260 AAATTGAAGTGTTTAAGTGCTACAAATTGAAGTATTT-AGTTGCT-AGAAATTGAGATGTTTTAT
1 AAATTTAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAG-TGCTGA-AAATTGAGATGTTTTAT
*
2512323 CGCTGTAATTAAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGC
64 CGCTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGC
*
2512374 AAATTTAAGTGTTTAAGTGCTGCAAATTTAAGTGTTTAAGTGCTGAAAATTGAGATGTTTTATCG
1 AAATTTAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGAAAATTGAGATGTTTTATCG
* *
2512439 TTGTAATTGAGGTGTATAAATGTTGTTAATTGATAAGTTTAAGTGCTGC
66 CTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGC
* * *
2512488 GAATTTAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGTTGTAAATTGAGATGTTTTATCG
1 AAATTTAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGAAAATTGAGATGTTTTATCG
* * *
2512553 CTATAATTGAAGTGTAAAAATGTTGTTAATTGATATGTTTAAGTGCTG-
66 CTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGC
* * * * *
2512601 AAATTTAAGTGTTTAAATGCTGTAAATTGAAGTG-TTAAGTGCTGCAAATTTA-AGTGTTTAAGT
1 AAATTTAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGAAAATTGAGA-TGTTTTA-T
* * * * * * * *
2512664 -GCTGCAAATTGAGATGTAT-TATCGCT-TTAATTGATGTGTATAAATGTTG-
64 CGCTG-TAATTGAGGTGTATAAAT-GTTGTTAATTGATATGTTTAAGTGCTGC
** * * *
2512713 TTATTTGATA-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGATGTCTTAT
1 AAATTT-A-AGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGAAAATTGAGATGTTTTAT
* * *
2512777 CGCTGTAATTGATGTGTATAAATGTTGTTAATTGATATGTTAAAGTGTTGC
64 CGCTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGC
* * * *
2512828 AAATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTG
1 AAATTTAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTG
2512870 TTACTTTCCA
Statistics
Matches: 423, Mismatches: 58, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
111 1 0.00
112 49 0.12
113 82 0.19
114 284 0.67
115 7 0.02
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (114 bp):
AAATTTAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGAAAATTGAGATGTTTTATCG
CTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGC
Found at i:2512577 original size:45 final size:45
Alignment explanation
Indices: 2512245--2512857 Score: 353
Period size: 45 Copynumber: 13.5 Consensus size: 45
2512235 CATGCTCTAG
* *
2512245 GTGTTTAAATATTGTAAATTGA-AGTGTTTAAGTGCTACAAATTGAA
1 GTGTTTAAATGTTGTAAATTGAGA-TGTTTAAGTGCT-GAAATTGAA
* ** * * *
2512291 GTATTTAGTTGCTAG-AAATTGAGATGTTTTA-TCGCTGTAATT-AA
1 GTGTTTAAATG-TTGTAAATTGAGATGTTTAAGT-GCTGAAATTGAA
* * * *
2512335 GGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAA
1 -GTGTTTAAATGTTGTAAATTGAGATGTTTAAGTGCTG-AAATTGAA
* * * *
2512382 GTGTTTAAGTGCTGCAAATTTA-AGTGTTTAAGTGCTGAAAATTG-A
1 GTGTTTAAATGTTGTAAATTGAGA-TGTTTAAGTGCTG-AAATTGAA
* * * * * *
2512427 GATGTTT-TATCGTTGT-AATTGAGGTGTATAAATGTTGTTAATTGATA
1 G-TGTTTAAAT-GTTGTAAATTGAGATGTTTAAGTGCTG-AAATTGA-A
* * * ** *
2512474 -AGTTTAAGTGCTGCGAATTTA-AGTGTTTAAGTGCTGCAAATTGAA
1 GTGTTTAAATGTTGTAAATTGAGA-TGTTTAAGTGCTG-AAATTGAA
* *
2512519 GTGTTTAAGTGTTGTAAATTGAGATGTTTTA-TCGCT-ATAATTGAA
1 GTGTTTAAATGTTGTAAATTGAGATGTTTAAGT-GCTGA-AATTGAA
** * * *
2512564 GTGTAAAAATGTTGTTAATTGATATGTTTAAGTGCTGAAATTTAA
1 GTGTTTAAATGTTGTAAATTGAGATGTTTAAGTGCTGAAATTGAA
* *
2512609 GTGTTTAAATGCTGTAAATTGA-A-GTGTTAAGTGCTGCAAATTTAA
1 GTGTTTAAATGTTGTAAATTGAGATGT-TTAAGTGCTG-AAATTGAA
* * * ** *
2512654 GTGTTTAAGTGCTGCAAATTGAGATGTATT-A-TCGCTTTAATTGAT
1 GTGTTTAAATGTTGTAAATTGAGATGT-TTAAGT-GCTGAAATTGAA
* * * * *
2512699 GTGTATAAATGTTGTTATTTGATATGTTAAAGTGCTGCAAATTGAA
1 GTGTTTAAATGTTGTAAATTGAGATGTTTAAGTGCTG-AAATTGAA
* * * * *
2512745 GTGTTTAAGTGCTGCAAATTGAGATGTCTT-A-TCGCTGTAATTGAT
1 GTGTTTAAATGTTGTAAATTGAGATGT-TTAAGT-GCTGAAATTGAA
* * * * *
2512790 GTGTATAAATGTTGTTAATTGATATGTTAAAGTGTTGCAAATTGAA
1 GTGTTTAAATGTTGTAAATTGAGATGTTTAAGTGCTG-AAATTGAA
*
2512836 GTGTTTAAATGCTGTAAATTGA
1 GTGTTTAAATGTTGTAAATTGA
2512858 AGTGTTAAAG
Statistics
Matches: 425, Mismatches: 106, Indels: 72
0.70 0.18 0.12
Matches are distributed among these distances:
43 2 0.00
44 18 0.04
45 211 0.50
46 182 0.43
47 12 0.03
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (45 bp):
GTGTTTAAATGTTGTAAATTGAGATGTTTAAGTGCTGAAATTGAA
Found at i:2512613 original size:22 final size:23
Alignment explanation
Indices: 2512588--2512673 Score: 131
Period size: 22 Copynumber: 3.8 Consensus size: 23
2512578 TTAATTGATA
2512588 TGTTTAAGTGCTG-AAATTTAAG
1 TGTTTAAGTGCTGCAAATTTAAG
* * *
2512610 TGTTTAAATGCTGTAAATTGAAG
1 TGTTTAAGTGCTGCAAATTTAAG
2512633 TG-TTAAGTGCTGCAAATTTAAG
1 TGTTTAAGTGCTGCAAATTTAAG
2512655 TGTTTAAGTGCTGCAAATT
1 TGTTTAAGTGCTGCAAATT
2512674 GAGATGTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
22 31 0.54
23 26 0.46
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (23 bp):
TGTTTAAGTGCTGCAAATTTAAG
Found at i:2512673 original size:135 final size:137
Alignment explanation
Indices: 2512475--2512766 Score: 444
Period size: 135 Copynumber: 2.1 Consensus size: 137
2512465 TAATTGATAA
* * * *
2512475 GTTTAAGTGCTGCGAATTTAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGTTGTAAATTG
1 GTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTG
* *
2512540 AGATGTTTTATCGCTATAATTGAAGTGTAAAAATGTTGTTAATTGATATGTTTAAGTGCTG-AAA
66 AGATGTATTATCGCTATAATTGAAGTGTAAAAATGTTGTTAATTGATATGTTAAAGTGCTGCAAA
*
2512604 TTTAAGT
131 TTGAAGT
* * *
2512611 GTTTAAATGCTGTAAATTGAAGTG-TTAAGTGCTGCAAATTTAAGTGTTTAAGTGCTGCAAATTG
1 GTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTG
* * * *
2512675 AGATGTATTATCGCTTTAATTGATGTGTATAAATGTTGTTATTTGATATGTTAAAGTGCTGCAAA
66 AGATGTATTATCGCTATAATTGAAGTGTAAAAATGTTGTTAATTGATATGTTAAAGTGCTGCAAA
2512740 TTGAAGT
131 TTGAAGT
2512747 GTTTAAGTGCTGCAAATTGA
1 GTTTAAGTGCTGCAAATTGA
2512767 GATGTCTTAT
Statistics
Matches: 139, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
135 92 0.66
136 47 0.34
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (137 bp):
GTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTG
AGATGTATTATCGCTATAATTGAAGTGTAAAAATGTTGTTAATTGATATGTTAAAGTGCTGCAAA
TTGAAGT
Found at i:2513833 original size:43 final size:43
Alignment explanation
Indices: 2513777--2513964 Score: 245
Period size: 43 Copynumber: 4.3 Consensus size: 43
2513767 TTTTTGTGAC
* * *
2513777 CTTTAGTGGCGTTTTTGGAGAAAGCGCCGCTAAAGGTCTTGTT
1 CTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCTTGGT
* * * *
2513820 CTTTAGCAGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCTTGTT
1 CTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCTTGGT
* *
2513863 CTTTAGCGGTGTTTGTGGTA-AAAGCGCCGCTAAAGGTCATGGT
1 CTTTAGCGGCGTTTGTGG-AGAAAGCGCCGCTAAAGGTCTTGGT
*
2513906 CTTTAGCGGCGTTTGTGG-GAAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTGGAG-AAAGCGCCGCTAAAGGTCTTGGT
2513949 CTTTAGCGGCGCTTTG
1 CTTTAGCGGCG-TTTG
2513965 CTAAAAGCCT
Statistics
Matches: 130, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
43 126 0.97
44 4 0.03
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCTTGGT
Done.