Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold229
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: 643502
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 5
Found at i:251039 original size:18 final size:17
Alignment explanation
Indices: 251007--251040 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
250997 CATGTGAAAT
251007 AAAATTTATTTTTAAAC
1 AAAATTTATTTTTAAAC
*
251024 AAAATTTTTATTTTAAA
1 AAAATTTAT-TTTTAAA
251041 ATTAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAATTTATTTTTAAAC
Found at i:255417 original size:29 final size:29
Alignment explanation
Indices: 255355--255417 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
255345 TATTGTTATG
*
255355 AAAAAAAATGTTGTAAAAAATTAAAATGT
1 AAAAAAAATATTGTAAAAAATTAAAATGT
*
255384 CAAAAAAATATT-TAAAATAATATAAAAT-T
1 AAAAAAAATATTGTAAAA-AAT-TAAAATGT
255413 AAAAA
1 AAAAA
255418 TGTAATCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 5 0.17
29 18 0.62
30 6 0.21
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (29 bp):
AAAAAAAATATTGTAAAAAATTAAAATGT
Found at i:257891 original size:12 final size:12
Alignment explanation
Indices: 257874--257898 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
257864 TTATTTTTTA
257874 TTTATATTTATG
1 TTTATATTTATG
257886 TTTATATTTATG
1 TTTATATTTATG
257898 T
1 T
257899 CATCCAATAT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTATATTTATG
Found at i:257895 original size:18 final size:17
Alignment explanation
Indices: 257862--257896 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
257852 TATTTATATC
*
257862 ATTTATTTTTTATTTAT
1 ATTTATTTTATATTTAT
257879 ATTTATGTTTATATTTAT
1 ATTTAT-TTTATATTTAT
257897 GTCATCCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTATTTTATATTTAT
Found at i:258365 original size:18 final size:19
Alignment explanation
Indices: 258339--258378 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
258329 TATAAAGATA
*
258339 TTTATTTTATTAATTAT-T
1 TTTAGTTTATTAATTATGT
*
258357 TTTAGTTTATTATTTATGT
1 TTTAGTTTATTAATTATGT
258376 TTT
1 TTT
258379 TTATTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTAGTTTATTAATTATGT
Found at i:258387 original size:18 final size:18
Alignment explanation
Indices: 258339--258389 Score: 50
Period size: 21 Copynumber: 2.7 Consensus size: 18
258329 TATAAAGATA
*
258339 TTTATTTTATTAATTATT
1 TTTATTTTATTTATTATT
258357 TTTAGTTTATTATTTATGT-TT
1 TTTA--TT-TTATTTAT-TATT
258378 TTTATTTTATTT
1 TTTATTTTATTT
258390 TTAAATGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 10 0.36
19 2 0.07
20 2 0.07
21 13 0.46
22 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTATTTTATTTATTATT
Found at i:261376 original size:18 final size:17
Alignment explanation
Indices: 261353--261407 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
261343 TTTTATATAA
261353 TAAAAATTATATAATATG
1 TAAAAATTATATAA-ATG
261371 TAAAAA-TATA-AAAT-
1 TAAAAATTATATAAATG
*
261385 TAATATATTATATAAATG
1 TAA-AAATTATATAAATG
261403 TAAAA
1 TAAAA
261408 TGAGTCGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.10
15 4 0.13
16 6 0.19
17 9 0.29
18 9 0.29
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (17 bp):
TAAAAATTATATAAATG
Found at i:261401 original size:24 final size:26
Alignment explanation
Indices: 261345--261408 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 26
261335 ATATCTATTT
261345 TTATAT-AATA-AAAATTATATAATA
1 TTATATAAATATAAAATTATATAATA
261369 TGTA-A-AAATATAAAATTA-AT-ATA
1 T-TATATAAATATAAAATTATATAATA
*
261392 TTATATAAATGTAAAAT
1 TTATATAAATATAAAAT
261409 GAGTCGAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
22 2 0.06
23 5 0.15
24 18 0.53
25 9 0.26
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (26 bp):
TTATATAAATATAAAATTATATAATA
Found at i:261832 original size:4 final size:4
Alignment explanation
Indices: 261823--261849 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
261813 AAGGTTCATT
261823 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
261850 TATATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:262658 original size:17 final size:17
Alignment explanation
Indices: 262628--262671 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
262618 GGACAAAAGG
*
262628 AAAATAAAGGAAATAAA
1 AAAATAAAGAAAATAAA
* *
262645 AAAATCAAGAAAATAGA
1 AAAATAAAGAAAATAAA
262662 AAAATGAAAG
1 AAAAT-AAAG
262672 GTTATATCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.73, C:0.02, G:0.14, T:0.11
Consensus pattern (17 bp):
AAAATAAAGAAAATAAA
Found at i:268931 original size:30 final size:28
Alignment explanation
Indices: 268536--269082 Score: 339
Period size: 28 Copynumber: 18.3 Consensus size: 28
268526 ACAGTGGTGA
*
268536 TTTGAAAAGGGTTGCCATTGACTTGCATGGGC
1 TTTG-AAAGGG-TGCCACTGACTTG--TGGGC
*
268568 TTTAAAAGGGTGCCACTGACTTGCGTGGGC
1 TTTGAAAGGGTGCCACTGACTT--GTGGGC
** * *
268598 TTTGAAAGAATGCCACTAACTCGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
268626 TTTGAAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
268654 TTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
268682 TTTGAAAAGGTACCACTGACTTGCGTGAGC
1 TTTGAAAGGGTGCCACTGACTT--GTGGGC
* *
268712 TTTAAAAAGAGTGCCACTGACTTGTGTGGGC
1 TTT-GAAAGGGTGCCACTGAC-T-TGTGGGC
* * *
268743 TTTAAAATGGTGCCACTGACTTGTGAGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
268771 TTTGAAAGAGTGCCACTGAATTATGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * **
268799 TTCGCAATGGCCGTGATACTGACTTGTAGGGGC
1 TTTG-AAAGG--GTGCCACTGACTTGT--GGGC
* * * * * *
268832 TTCGAGAGGGTGGGCAAGTGGACATGGGGGGC
1 TTTGAAAGGGT--GCCACT-GAC-TTGTGGGC
* *
268864 TCTG-AAGGGTGGCACTGAACTGTGTAAGGGC
1 TTTGAAAGGGTGCCACTG-ACT-TGT--GGGC
268895 TTTGAAAGGGTGCCACTGACATTGTGGGC
1 TTTGAAAGGGTGCCACTGAC-TTGTGGGC
* *
268924 TTTTGAAAAGAGTGCCGACGGA-TTGTGGGC
1 -TTTG-AAAGGGTGCC-ACTGACTTGTGGGC
* *
268954 TTGGAAAAGAGTTG-CACTAGGACGTTGTGGGC
1 TTTG-AAAG-GGTGCCACT--GAC-TTGTGGGC
*
268986 TTTGAAAGAGGTGCCGACTTGACTTGTTGGGT
1 TTTGAAAG-GGTGCC-AC-TGACTTG-TGGGC
269018 TTTAGAAAGGGTGCCACT-ACTT-TGGGC
1 TTT-GAAAGGGTGCCACTGACTTGTGGGC
** * *
269045 TTTGAAAGAATCTGCCACTGATTTGGGGGC
1 TTTGAAAG--GGTGCCACTGACTTGTGGGC
269075 TTTGAAAG
1 TTTGAAAG
269083 AGTACCTTGG
Statistics
Matches: 408, Mismatches: 68, Indels: 80
0.73 0.12 0.14
Matches are distributed among these distances:
26 5 0.01
27 7 0.02
28 118 0.29
29 30 0.07
30 87 0.21
31 77 0.19
32 62 0.15
33 19 0.05
34 3 0.01
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (28 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGC
Found at i:270832 original size:1 final size:1
Alignment explanation
Indices: 270828--270890 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
270818 TTTTTTGCTA
* * * * * * *
270828 TTTTTTTCTCTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
270891 GGTGTAAAGG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (1 bp):
T
Found at i:270859 original size:25 final size:25
Alignment explanation
Indices: 270831--270890 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
270821 TTTGCTATTT
270831 TTTTCTCTTTTTTTT-TGTTTTTTTG
1 TTTTCT-TTTTTTTTGTGTTTTTTTG
* *
270856 TTTTGTTTTTTTTTGTTTTTTTTTG
1 TTTTCTTTTTTTTTGTGTTTTTTTG
270881 TTTT-TTTTTT
1 TTTTCTTTTTT
270891 GGTGTAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 14 0.44
25 18 0.56
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.88
Consensus pattern (25 bp):
TTTTCTTTTTTTTTGTGTTTTTTTG
Found at i:270889 original size:10 final size:10
Alignment explanation
Indices: 270818--270889 Score: 81
Period size: 10 Copynumber: 6.6 Consensus size: 10
270808 GACCCTTCTA
270818 TTTTTTGCTATT
1 TTTTTTG-T-TT
*
270830 TTTTTCTCTTT
1 TTTTT-TGTTT
270841 TTTTTTGTTTTT
1 TTTTTTG--TTT
270853 TTGTTTTGTTT
1 TT-TTTTGTTT
270864 TTTTTTGTTT
1 TTTTTTGTTT
270874 TTTTTTGTTT
1 TTTTTTGTTT
270884 TTTTTT
1 TTTTTT
270890 TGGTGTAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
10 25 0.46
11 12 0.22
12 11 0.20
13 6 0.11
ACGTcount: A:0.01, C:0.04, G:0.08, T:0.86
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:284930 original size:20 final size:20
Alignment explanation
Indices: 284883--284957 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
284873 AAAAAGACAT
*
284883 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
284902 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * * *
284923 CATGTATCAATATATTGAAA
1 AATGTATCGATACATTCATA
284943 AATGTATCGATACAT
1 AATGTATCGATACAT
284958 CAGGGTATGA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:284951 original size:40 final size:39
Alignment explanation
Indices: 284880--284957 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
284870 GGTAAAAAGA
* * *
284880 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCAATACATTGAAAAATATATCGATACATT
* *
284919 CATACATGTATCAATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCAATACATTGAAAAATATATCGATACAT
284958 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (39 bp):
CATAATGTATCAATACATTGAAAAATATATCGATACATT
Found at i:286189 original size:3 final size:3
Alignment explanation
Indices: 286181--286206 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
286171 TGATAGTTGC
286181 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
286207 AGACAACGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:286504 original size:16 final size:17
Alignment explanation
Indices: 286464--286507 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
286454 ATCATTCGTG
*
286464 TAATTTCACCTTGACAA
1 TAATTTCACTTTGACAA
* *
286481 TAAATTCACTTTGGC-A
1 TAATTTCACTTTGACAA
286497 TAATTTCACTT
1 TAATTTCACTT
286508 CTCTAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (17 bp):
TAATTTCACTTTGACAA
Found at i:288114 original size:2 final size:2
Alignment explanation
Indices: 288109--288141 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
288099 ATATAATTCA
288109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
288142 AAAGAAGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:291273 original size:15 final size:16
Alignment explanation
Indices: 291249--291281 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
291239 ATCTGTAAAG
*
291249 TTATA-TTTTTTTTTT
1 TTATAGTTTTTTCTTT
291264 TTATAGTTTTTTCTTT
1 TTATAGTTTTTTCTTT
291280 TT
1 TT
291282 TCTTTGGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (16 bp):
TTATAGTTTTTTCTTT
Found at i:296270 original size:10 final size:9
Alignment explanation
Indices: 296255--296298 Score: 56
Period size: 8 Copynumber: 5.0 Consensus size: 9
296245 TTAACCATCA
296255 TTTTCTTTT
1 TTTTCTTTT
296264 CTTTTCTTTT
1 -TTTTCTTTT
*
296274 TTTCCTTTT
1 TTTTCTTTT
296283 TTTT-TTTT
1 TTTTCTTTT
296291 TTTT-TTTT
1 TTTTCTTTT
296299 GGGGGTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
8 12 0.38
9 11 0.34
10 9 0.28
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:297258 original size:2 final size:2
Alignment explanation
Indices: 297253--297277 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
297243 GAGTGTGTAC
297253 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
297278 GTTTTTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:301841 original size:10 final size:10
Alignment explanation
Indices: 301826--301852 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
301816 TAATTATAAC
301826 ATATAATTTA
1 ATATAATTTA
301836 ATATAATTTA
1 ATATAATTTA
301846 ATATAAT
1 ATATAAT
301853 ATTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
ATATAATTTA
Found at i:302245 original size:14 final size:14
Alignment explanation
Indices: 302215--302263 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
302205 ATTTTAAAAA
302215 TTTA-TTTT-ATTT
1 TTTATTTTTAATTT
*
302227 CTTATTTTTAATTT
1 TTTATTTTTAATTT
* *
302241 TTTATATTTAAATT
1 TTTATTTTTAATTT
302255 TTTATTTTT
1 TTTATTTTT
302264 TAAATGATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 3 0.10
13 4 0.13
14 23 0.77
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTTTAATTT
Found at i:302256 original size:15 final size:14
Alignment explanation
Indices: 302202--302268 Score: 50
Period size: 15 Copynumber: 4.9 Consensus size: 14
302192 TCACACTTGA
**
302202 TTTATTTTAAA-AA
1 TTTATTTTAAATTT
302215 TTTATTTT--ATTT
1 TTTATTTTAAATTT
* *
302227 CTTATTTTTAATTT
1 TTTATTTTAAATTT
302241 TTTATATTTAAATTT
1 TTTAT-TTTAAATTT
*
302256 TTATTTTTTAAAT
1 TT-TATTTTAAAT
302269 GATATATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 1 0.02
12 7 0.16
13 8 0.19
14 8 0.19
15 17 0.40
16 2 0.05
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATTTTAAATTT
Found at i:302277 original size:22 final size:22
Alignment explanation
Indices: 302229--302277 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
302219 TTTTATTTCT
* *
302229 TATTTTTAATTTTTTATATTTA
1 TATTTTTAATTTTTTAAATATA
*
302251 AATTTTT-ATTTTTTAAATGATA
1 TATTTTTAATTTTTTAAAT-ATA
302273 TATTT
1 TATTT
302278 AAAAAGTAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTTTTAATTTTTTAAATATA
Found at i:304246 original size:20 final size:20
Alignment explanation
Indices: 304218--304292 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
304208 TTTTACCCAG
304218 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
304238 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
304258 ATGTATCAATATATTCTTCA
1 ATGTATCGATACATTTTTCA
304278 ATGTATCGATACATT
1 ATGTATCGATACATT
304293 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:304262 original size:40 final size:39
Alignment explanation
Indices: 304218--304295 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
304208 TTTTACCCAG
* *
304218 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCAATACATTCTTCAATATATCGATACAT-TATGA
* *
304258 ATGTATCAATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCAATACATTCTTCAATATATCGATACATTATG
304296 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (39 bp):
ATGTATCAATACATTCTTCAATATATCGATACATTATGA
Found at i:305264 original size:22 final size:22
Alignment explanation
Indices: 305239--305307 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
305229 TTTTAATATG
305239 TCCAGCA-TCTCATTGAATGTTA
1 TCCAGCAGT-TCATTGAATGTTA
**
305261 TCCATTAGTTCATTGAATGTTA
1 TCCAGCAGTTCATTGAATGTTA
** *
305283 TCCATTAGTTCATTGTATGATTA
1 TCCAGCAGTTCATTGAATG-TTA
305306 TC
1 TC
305308 ACATTTTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 36 0.86
23 6 0.14
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (22 bp):
TCCAGCAGTTCATTGAATGTTA
Found at i:307582 original size:16 final size:16
Alignment explanation
Indices: 307561--307593 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
307551 AAACTCAATA
*
307561 AAAAAATAAAACTATT
1 AAAAAATAAAAATATT
307577 AAAAAATAAAAATATT
1 AAAAAATAAAAATATT
307593 A
1 A
307594 TCTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATAAAAATATT
Found at i:307859 original size:20 final size:21
Alignment explanation
Indices: 307832--307886 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
307822 TTAATTATAA
307832 AATT-TATATTTTATA-ATAT
1 AATTATATATTTTATACATAT
307851 AATTATATATATTT-TAGCATAT
1 AATTATATAT-TTTATA-CATAT
*
307873 TATTATA-ATTTTAT
1 AATTATATATTTTAT
307887 TTTATTAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 4 0.13
20 10 0.33
21 6 0.20
22 10 0.33
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
AATTATATATTTTATACATAT
Found at i:307872 original size:22 final size:22
Alignment explanation
Indices: 307836--307879 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
307826 TTATAAAATT
*
307836 TATATTTTATAATATAATTATA
1 TATATTTTAGAATATAATTATA
* *
307858 TATATTTTAGCATATTATTATA
1 TATATTTTAGAATATAATTATA
307880 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TATATTTTAGAATATAATTATA
Found at i:309967 original size:24 final size:23
Alignment explanation
Indices: 309926--309976 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
309916 ATCATCAAAT
*
309926 ATATATAAAAAATATAAATTATTA
1 ATATATAAAAAATATAAA-TATAA
* * *
309950 ATATATTAAAATTTTAAATATAA
1 ATATATAAAAAATATAAATATAA
309973 ATAT
1 ATAT
309977 GATATATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATATAAAAAATATAAATATAA
Found at i:309969 original size:30 final size:31
Alignment explanation
Indices: 309935--309994 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
309925 TATATATAAA
*
309935 AAATATAAATTATTA-ATATATTAAA-ATTTT
1 AAATATAAA-TATGATATATATTAAATATTTT
309965 AAATATAAATATGATATATATTAAATATTT
1 AAATATAAATATGATATATATTAAATATTT
309995 CATATTAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 4 0.15
30 19 0.70
31 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (31 bp):
AAATATAAATATGATATATATTAAATATTTT
Found at i:310692 original size:19 final size:19
Alignment explanation
Indices: 310668--310716 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
310658 CCCATGTGGG
*
310668 TGAAAAAAATAATTTTTTT
1 TGAAAAAAATAATTTTGTT
*
310687 TGAAAAAAATTATTTTGTT
1 TGAAAAAAATAATTTTGTT
310706 T--AAAAAATAAT
1 TGAAAAAAATAAT
310717 AAGTTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 9 0.33
19 18 0.67
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (19 bp):
TGAAAAAAATAATTTTGTT
Found at i:310883 original size:25 final size:24
Alignment explanation
Indices: 310837--310885 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
310827 TTTGATATTT
* * *
310837 TTTAATTACATATATTTGATTAAA
1 TTTAATAACATAAATTTAATTAAA
310861 TTTAATAACAATAAATTTAATTAAA
1 TTTAATAAC-ATAAATTTAATTAAA
310886 AATTTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (24 bp):
TTTAATAACATAAATTTAATTAAA
Found at i:312493 original size:6 final size:6
Alignment explanation
Indices: 312482--312532 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
312472 TATTAAATAC
* *
312482 ATATAA ATATAA TTATAA TATATAA A-AT-T ATATAA ATAT-A ATATAA
1 ATATAA ATATAA ATATAA -ATATAA ATATAA ATATAA ATATAA ATATAA
312528 ATATA
1 ATATA
312533 TAAATTATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 1 0.03
5 9 0.24
6 22 0.59
7 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:312496 original size:31 final size:29
Alignment explanation
Indices: 312451--312536 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 29
312441 ATTAAAATTT
*
312451 ATATAAA-ATAAATTATTAACT-TATTAAATAC
1 ATATAAATAT-AATTA-TAA-TATATAAAAT-C
*
312482 ATATAAATATAATTATAATATATAAAATT
1 ATATAAATATAATTATAATATATAAAATC
312511 ATATAAATATAA-TATAAATATATAAA
1 ATATAAATATAATTAT-AATATATAAA
312537 TTATCAAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
28 3 0.06
29 23 0.46
30 10 0.20
31 12 0.24
32 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
ATATAAATATAATTATAATATATAAAATC
Found at i:312503 original size:11 final size:11
Alignment explanation
Indices: 312482--312532 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
312472 TATTAAATAC
312482 ATATAAATATA
1 ATATAAATATA
312493 AT-TATAATAT-
1 ATATA-AATATA
312503 ATA-AAAT-T-
1 ATATAAATATA
312511 ATATAAATATA
1 ATATAAATATA
312522 ATATAAATATA
1 ATATAAATATA
312533 TAAATTATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 4 0.11
9 7 0.20
10 6 0.17
11 18 0.51
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAAATATA
Found at i:312512 original size:15 final size:15
Alignment explanation
Indices: 312492--312540 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
312482 ATATAAATAT
312492 AATTATAATATATAA
1 AATTATAATATATAA
* *
312507 AATTAT-ATAAATAT
1 AATTATAATATATAA
312521 AA-TATAA-ATATATA
1 AATTATAATATATA-A
312535 AATTAT
1 AATTAT
312541 CAAATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 7 0.26
14 11 0.41
15 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTATAATATATAA
Found at i:312534 original size:19 final size:18
Alignment explanation
Indices: 312475--312537 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
312465 ATTAACTTAT
*
312475 TAAATACATATAAATATAA
1 TAAATATATATAAATAT-A
312494 TTATAATATATA-AAATTATA
1 -TA-AATATATATAAA-TATA
312514 TAAATATAATATAAATATA
1 TAAATAT-ATATAAATATA
312533 TAAAT
1 TAAAT
312538 TATCAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 5 0.13
19 14 0.37
20 9 0.24
21 10 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATATATATAAATATA
Found at i:312564 original size:27 final size:27
Alignment explanation
Indices: 312482--312564 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 27
312472 TATTAAATAC
312482 ATATAAATATAATTATAATATATAAAATT
1 ATATAAATATAATTA-AATAT-TAAAATT
312511 ATATAAATATAATATAAATA-TATAAATT
1 ATATAAATATAAT-TAAATATTA-AAATT
* *
312539 ATCA-AATTTTAATTAAATATTAAAAT
1 AT-ATAAATATAATTAAATATTAAAAT
312565 AATAATAGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
27 12 0.25
28 16 0.33
29 18 0.38
30 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATAAATATAATTAAATATTAAAATT
Found at i:313568 original size:22 final size:23
Alignment explanation
Indices: 313543--313602 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
313533 TATTTTTGTG
*
313543 TTTATTTTTAAA-ATTAAATAAA
1 TTTATTTATAAATATTAAATAAA
*
313565 TTTATTTATAAATATTAAATGAA
1 TTTATTTATAAATATTAAATAAA
* *
313588 TATATTTATCAATAT
1 TTTATTTATAAATAT
313603 ATAATTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTATTTATAAATATTAAATAAA
Found at i:315656 original size:33 final size:33
Alignment explanation
Indices: 315612--315747 Score: 209
Period size: 33 Copynumber: 4.1 Consensus size: 33
315602 TTGTGCAGTT
315612 TTTAAACTCCATTGCTGGTGTATAAGATAATAA
1 TTTAAACTCCATTGCTGGTGTATAAGATAATAA
*
315645 TCTAAACTCCATTGCTGGTGTATAAGATAATAA
1 TTTAAACTCCATTGCTGGTGTATAAGATAATAA
** * *
315678 TTTAAACTCCATTGCTGGCATGTAAGAGAATAA
1 TTTAAACTCCATTGCTGGTGTATAAGATAATAA
* *
315711 TTTAAACTCTATTGCTGGTGTGTAAGATAATAA
1 TTTAAACTCCATTGCTGGTGTATAAGATAATAA
315744 TTTA
1 TTTA
315748 CAGTTATATA
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 93 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (33 bp):
TTTAAACTCCATTGCTGGTGTATAAGATAATAA
Found at i:321813 original size:2 final size:2
Alignment explanation
Indices: 321806--321835 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
321796 TGTAAGTTAC
*
321806 AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
321836 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:321840 original size:2 final size:2
Alignment explanation
Indices: 321835--321863 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
321825 TATATATATA
321835 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
321864 CTTTTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:324432 original size:30 final size:30
Alignment explanation
Indices: 324398--324461 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
324388 TCCTGACTTA
*
324398 ATTAAACATAAACTTTGTATTTATGATTTG
1 ATTAAACATAAACTTTATATTTATGATTTG
* * *
324428 ATTAATCATAAGCTTTATCTTTATGATTTG
1 ATTAAACATAAACTTTATATTTATGATTTG
324458 ATTA
1 ATTA
324462 GTTATAGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.48
Consensus pattern (30 bp):
ATTAAACATAAACTTTATATTTATGATTTG
Found at i:324826 original size:17 final size:17
Alignment explanation
Indices: 324804--324852 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
324794 ATATAATATT
324804 AATTATTAAAATATAAA
1 AATTATTAAAATATAAA
324821 AATTA-TATAAATATAAA
1 AATTATTA-AAATATAAA
324838 ATATT-TT-AAATATAA
1 A-ATTATTAAAATATAA
324853 TTATATGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.34
17 15 0.52
18 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTATTAAAATATAAA
Found at i:325435 original size:19 final size:20
Alignment explanation
Indices: 325411--325451 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
325401 TATGTTCATG
325411 ATATATGTACAT-T-TTACAT
1 ATATATGTA-ATATCTTACAT
325430 ATATATGTAATATCTTACAT
1 ATATATGTAATATCTTACAT
325450 AT
1 AT
325452 GATTATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 2 0.10
19 10 0.50
20 8 0.40
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (20 bp):
ATATATGTAATATCTTACAT
Found at i:325460 original size:20 final size:20
Alignment explanation
Indices: 325424--325462 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
325414 TATGTACATT
*
325424 TTACATATATATGTAATATC
1 TTACATATATATATAATATC
325444 TTACATATGAT-TATAATAT
1 TTACATAT-ATATATAATAT
325463 AAAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (20 bp):
TTACATATATATATAATATC
Found at i:326150 original size:23 final size:24
Alignment explanation
Indices: 326098--326150 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
326088 TATGTCGTTG
*
326098 TGTTTATATTATTTTTTCATATCA
1 TGTTCATATTATTTTTTCATATCA
* *
326122 T-ATCATATT-TTTTTTCATGTCA
1 TGTTCATATTATTTTTTCATATCA
326144 TGTTCAT
1 TGTTCAT
326151 GCTCATAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 13 0.54
23 10 0.42
24 1 0.04
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (24 bp):
TGTTCATATTATTTTTTCATATCA
Found at i:326289 original size:29 final size:31
Alignment explanation
Indices: 326256--326314 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
326246 TATATTGTTA
**
326256 AATAAAAATTATTATATT-AATAA-AATATT
1 AATAAAAATTAAAATATTAAATAATAATATT
326285 AATAAAAATTAAAATATTAAATAATAATAT
1 AATAAAAATTAAAATATTAAATAATAATAT
326315 GAGATGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 16 0.62
30 5 0.19
31 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
AATAAAAATTAAAATATTAAATAATAATATT
Found at i:327084 original size:15 final size:14
Alignment explanation
Indices: 327028--327086 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 14
327018 TTTACCCATA
327028 TTATATTTTT-TAAT
1 TTAT-TTTTTATAAT
* *
327042 TTAATTTTTATAAA
1 TTATTTTTTATAAT
*
327056 TT-TTTTTTAAAAT
1 TTATTTTTTATAAT
327069 TTATTTTTTAGTAAT
1 TTATTTTTTA-TAAT
327084 TTA
1 TTA
327087 ATGCATTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
13 15 0.42
14 15 0.42
15 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTATTTTTTATAAT
Found at i:327175 original size:19 final size:19
Alignment explanation
Indices: 327153--327194 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
327143 TACATTATAG
*
327153 TATTATATAT-ATATATATT
1 TATT-TATATGATATATAAT
327172 TATTTATATGATATATAAT
1 TATTTATATGATATATAAT
327191 TATT
1 TATT
327195 CTTTACATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTTATATGATATATAAT
Found at i:327523 original size:2 final size:2
Alignment explanation
Indices: 327510--327547 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
327500 ATTGTGGGAG
327510 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
327548 CTTAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:329123 original size:2 final size:2
Alignment explanation
Indices: 329116--329140 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
329106 GTTTCTGTTT
329116 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
329141 GTTATTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:331274 original size:2 final size:2
Alignment explanation
Indices: 331267--331300 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
331257 TTCAAGCATG
*
331267 GT GT GT GT GT GC GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
331301 TTTTTTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
GT
Found at i:333562 original size:18 final size:18
Alignment explanation
Indices: 333539--333579 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
333529 TTAGAATTGT
333539 AGAATAGTCATTAAGTGG
1 AGAATAGTCATTAAGTGG
333557 AGAATAGTCATTAAGTGG
1 AGAATAGTCATTAAGTGG
333575 AGAAT
1 AGAAT
333580 TGTAGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.27
Consensus pattern (18 bp):
AGAATAGTCATTAAGTGG
Found at i:335589 original size:8 final size:8
Alignment explanation
Indices: 335574--335629 Score: 50
Period size: 8 Copynumber: 7.6 Consensus size: 8
335564 ATTTAAAATT
335574 TTAT-TTA
1 TTATATTA
335581 TTATATTA
1 TTATATTA
*
335589 TTAAATTA
1 TTATATTA
335597 TTAT-TT-
1 TTATATTA
335603 TTATATTA
1 TTATATTA
*
335611 ATAT-TTA
1 TTATATTA
*
335618 TT-TATTT
1 TTATATTA
335625 TTATA
1 TTATA
335630 ATTAAATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
6 5 0.13
7 16 0.41
8 18 0.46
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTATATTA
Found at i:335615 original size:25 final size:26
Alignment explanation
Indices: 335539--335615 Score: 67
Period size: 29 Copynumber: 3.0 Consensus size: 26
335529 TTAAAATTAA
335539 AAAATTTTATTTAAAATTAATATTAAT-TT
1 AAAATTTTATTT---ATT-ATATTAATATT
335568 AAAATTTTATTTATTATA-T--TATT
1 AAAATTTTATTTATTATATTAATATT
335591 -AAATTATTATTT-TTATATTAATATT
1 AAAATT-TTATTTATTATATTAATATT
335616 TATTTATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
22 11 0.26
23 9 0.21
24 1 0.02
25 7 0.16
26 3 0.07
29 12 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AAAATTTTATTTATTATATTAATATT
Found at i:335638 original size:22 final size:21
Alignment explanation
Indices: 335573--335639 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
335563 AATTTAAAAT
*
335573 TTTATTTA-TTATATTATTAAA
1 TTTATTTATTTTTA-TATTAAA
335594 -TTA-TTATTTTTATATTAATA
1 TTTATTTATTTTTATATTAA-A
335614 TTTATTTATTTTTATAATTAAA
1 TTTATTTATTTTTAT-ATTAAA
335636 TTTA
1 TTTA
335640 AATAAAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 9 0.22
20 8 0.20
21 3 0.08
22 15 0.38
23 5 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTATTTATTTTTATATTAAA
Found at i:335714 original size:31 final size:31
Alignment explanation
Indices: 335679--335738 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
335669 ATATTTTATA
**
335679 TTAAATCAAATCAGTTCAAATTTATAAAAAC
1 TTAAATCAAATCAAATCAAATTTATAAAAAC
*
335710 TTAAATTAAATCAAATCAAATTTATAAAA
1 TTAAATCAAATCAAATCAAATTTATAAAA
335739 GTTTTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (31 bp):
TTAAATCAAATCAAATCAAATTTATAAAAAC
Found at i:336882 original size:25 final size:25
Alignment explanation
Indices: 336836--336885 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
336826 TTTTTATATT
*
336836 AATATTTTTAATTAAATTTAAATAAA
1 AATATTTTT-ATTAAATATAAATAAA
336862 AATATTTTT-TTAATATATAAATAA
1 AATATTTTTATTAA-ATATAAATAA
336886 TAATTAAGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 9 0.41
26 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATATTTTTATTAAATATAAATAAA
Found at i:339358 original size:22 final size:21
Alignment explanation
Indices: 339314--339357 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
339304 TATATACTTT
339314 AATTTTATTTTTAGAGTTTAA
1 AATTTTATTTTTAGAGTTTAA
*
339335 AATTTTATTTTTAGTGTTTAA
1 AATTTTATTTTTAGAGTTTAA
339356 AA
1 AA
339358 AATGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (21 bp):
AATTTTATTTTTAGAGTTTAA
Found at i:341797 original size:13 final size:13
Alignment explanation
Indices: 341781--341810 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
341771 ACAATTCATC
341781 ATGTATCGATACA
1 ATGTATCGATACA
341794 ATGTATCGATACA
1 ATGTATCGATACA
341807 ATGT
1 ATGT
341811 GCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:341806 original size:33 final size:33
Alignment explanation
Indices: 341763--341827 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
341753 TTGAAGCAAC
341763 GTATCAATACAAT-T-CATCATGTATCGATACAAT
1 GTATCAATACAATGTGC--CATGTATCGATACAAT
*
341796 GTATCGATACAATGTGCCATGTATCGATACAA
1 GTATCAATACAATGTGCCATGTATCGATACAA
341828 ATAGTGATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (33 bp):
GTATCAATACAATGTGCCATGTATCGATACAAT
Found at i:341899 original size:20 final size:20
Alignment explanation
Indices: 341857--341902 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
341847 TACCAGTTTC
**
341857 ATGTATCGATACAATTATGA
1 ATGTATCGATACAAGCATGA
341877 ATGTATCGATACAAAGCAT-A
1 ATGTATCGATAC-AAGCATGA
341897 ATGTAT
1 ATGTAT
341903 AAATACATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAAGCATGA
Found at i:342846 original size:33 final size:33
Alignment explanation
Indices: 342799--342865 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
342789 AAGTGCACTA
* *
342799 AAGTGCTCATTCATGCGCTGCGAGAGTGAAGTG
1 AAGTGCTCACTCATGCGCTGCGAAAGTGAAGTG
* *
342832 AAGTGCTTACTCATGTGCTGCGAAAGTGAAGTG
1 AAGTGCTCACTCATGCGCTGCGAAAGTGAAGTG
342865 A
1 A
342866 TCAACTCTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (33 bp):
AAGTGCTCACTCATGCGCTGCGAAAGTGAAGTG
Found at i:348286 original size:34 final size:32
Alignment explanation
Indices: 348224--348286 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
348214 TAGCCAAACT
**
348224 TGTATCGATACACCAAGTATGTATCGATATAA
1 TGTATCGATACACCAAAAATGTATCGATATAA
348256 TGTATCGATACACCAAAAAATTGTATCGATA
1 TGTATCGATACACC-AAAAA-TGTATCGATA
348287 CATTGGCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 14 0.52
33 3 0.11
34 10 0.37
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATATAA
Found at i:354193 original size:13 final size:13
Alignment explanation
Indices: 354175--354213 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
354165 ACATTTTTCT
354175 TTGTATCGATACA
1 TTGTATCGATACA
*
354188 TTGTATCCATACA
1 TTGTATCGATACA
*
354201 CTGTATCGATACA
1 TTGTATCGATACA
354214 AGGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:354286 original size:27 final size:27
Alignment explanation
Indices: 354255--354317 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
354245 ATTAAAAAAC
** *
354255 GGGGTTGGAATATCTTCTCGGAAGAAT
1 GGGGTTGGAATATCCCCTCAGAAGAAT
* *
354282 GGGGTTGGAGTGTCCCCTCAGAAGAAT
1 GGGGTTGGAATATCCCCTCAGAAGAAT
*
354309 GAGGTTGGA
1 GGGGTTGGA
354318 GTGTCCCCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.24, C:0.13, G:0.38, T:0.25
Consensus pattern (27 bp):
GGGGTTGGAATATCCCCTCAGAAGAAT
Found at i:356613 original size:20 final size:20
Alignment explanation
Indices: 356584--356640 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
356574 GTAAAAAGAG
*
356584 AGAATATATCGATGCATTGA
1 AGAATATATCGATACATTGA
*
356604 AGAATGTATCGATACATTGA
1 AGAATATATCGATACATTGA
*
356624 AGAATATATTGATACAT
1 AGAATATATCGATACAT
356641 CTAGGTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATATATCGATACATTGA
Found at i:356671 original size:51 final size:51
Alignment explanation
Indices: 356606--356702 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
356596 TGCATTGAAG
* *
356606 AATGTATCGATACATTGAAGAATATATTGATACATCTAGGTAAAAAGACAT
1 AATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAAGACAT
* * *
356657 AATGTATCGATACATTGAAAAATGTATCGATACATTTTGGTAAAAA
1 AATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAA
356703 TGTGACATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (51 bp):
AATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAAGACAT
Found at i:356681 original size:71 final size:72
Alignment explanation
Indices: 356535--356692 Score: 228
Period size: 71 Copynumber: 2.2 Consensus size: 72
356525 TTTTAACTAG
* * * * *
356535 ATGTATCGTTACATTGAATAATGTATCGATACATCTAGGGTAAAAAGAGAGAATATATCGATGCA
1 ATGTATCGATACATTGAAGAATATATCGATACATCTAGGGTAAAAAGACAGAATATATCGATACA
*
356600 TTGAAGA
66 TTGAAAA
* * *
356607 ATGTATCGATACATTGAAGAATATATTGATACATCTA-GGTAAAAAGACATAATGTATCGATACA
1 ATGTATCGATACATTGAAGAATATATCGATACATCTAGGGTAAAAAGACAGAATATATCGATACA
356671 TTGAAAA
66 TTGAAAA
356678 ATGTATCGATACATT
1 ATGTATCGATACATT
356693 TTGGTAAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 44 0.57
72 33 0.43
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (72 bp):
ATGTATCGATACATTGAAGAATATATCGATACATCTAGGGTAAAAAGACAGAATATATCGATACA
TTGAAAA
Found at i:358645 original size:22 final size:22
Alignment explanation
Indices: 358596--358649 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
358586 ATATTTCCAC
**
358596 TTAAAAACATTTGATTTAAGGT
1 TTAAAAACATTTGATTTAAACT
*
358618 TCAAAAACATTTG-TTTATAACT
1 TTAAAAACATTTGATTTA-AACT
358640 TT-AAAACATT
1 TTAAAAACATT
358650 CATTGATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (22 bp):
TTAAAAACATTTGATTTAAACT
Found at i:362958 original size:20 final size:20
Alignment explanation
Indices: 362901--362979 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
362891 TGAAAAAAGC
362901 ATAGC-TTTAATATAATTTA
1 ATAGCTTTTAATATAATTTA
* * *
362920 ATAGTTTTTGAA-ATGATTTG
1 ATAGCTTTT-AATATAATTTA
*
362940 ATAGCTTTTAATATTATTTTA
1 ATAGCTTTTAATA-TAATTTA
** *
362961 ATAATTTTTTATATAATTT
1 ATAGCTTTTAATATAATTT
362980 TGATAATCTT
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
19 6 0.13
20 23 0.51
21 16 0.36
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (20 bp):
ATAGCTTTTAATATAATTTA
Found at i:362974 original size:21 final size:21
Alignment explanation
Indices: 362906--363002 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 21
362896 AAAGCATAGC
*
362906 TTTAATATAA-TTTAATAGTT
1 TTTAATATAATTTTAATAATT
* * **
362926 TTTGAA-ATGA-TTTGATAGCT
1 TTT-AATATAATTTTAATAATT
*
362946 TTTAATATTATTTTAATAATT
1 TTTAATATAATTTTAATAATT
* * *
362967 TTTTATATAATTTTGATAATC
1 TTTAATATAATTTTAATAATT
*
362988 TTTAATA-CATTTTAA
1 TTTAATATAATTTTAA
363003 ATATAATTTT
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.03
20 26 0.43
21 32 0.53
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (21 bp):
TTTAATATAATTTTAATAATT
Found at i:363007 original size:32 final size:31
Alignment explanation
Indices: 362957--363017 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
362947 TTAATATTAT
**
362957 TTTAATAATTTTTTATATAATTTTGATAATC
1 TTTAATAATTTTAAATATAATTTTGATAATC
362988 TTTAATACATTTTAAATATAATTTTGATAA
1 TTTAATA-ATTTTAAATATAATTTTGATAA
363018 CATTTGGTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTAATAATTTTAAATATAATTTTGATAATC
Found at i:365267 original size:44 final size:43
Alignment explanation
Indices: 365213--365318 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 43
365203 TAGGCATAAC
* * *
365213 TTTGGTTGAGTTCCATTACCTTGCAAGCAACTTCGCACTTGATT
1 TTTGTTTGAGTTCCATTACCTTGCAAACAACTTCACACTTGA-T
*
365257 TTTGTTTGAGTTCCATTACTTTGCAAACAACTTCACACTTGAT
1 TTTGTTTGAGTTCCATTACCTTGCAAACAACTTCACACTTGAT
*
365300 TTTCTTT-AGGTTCCATTAC
1 TTTGTTTGA-GTTCCATTAC
365319 TTTGTGATTG
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
42 1 0.02
43 17 0.30
44 38 0.68
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (43 bp):
TTTGTTTGAGTTCCATTACCTTGCAAACAACTTCACACTTGAT
Found at i:370232 original size:18 final size:17
Alignment explanation
Indices: 370206--370259 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
370196 TTGAATAGGT
*
370206 TAATTTTAAAAATTTATA
1 TAATATTAAAAA-TTATA
**
370224 TAATATTAATTATTA-A
1 TAATATTAAAAATTATA
370240 T-ATATTAAAAATTATA
1 TAATATTAAAAATTATA
370256 TAAT
1 TAAT
370260 TATAAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 11 0.38
16 4 0.14
17 5 0.17
18 9 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATATTAAAAATTATA
Found at i:373957 original size:2 final size:2
Alignment explanation
Indices: 373950--373980 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
373940 GTATGGTTTT
373950 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
373981 AGGGTAAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:374366 original size:36 final size:36
Alignment explanation
Indices: 374272--374411 Score: 138
Period size: 36 Copynumber: 3.8 Consensus size: 36
374262 TTCCCTTATT
* *
374272 GGACTTCTGCTGATGCTTCTCCTAGGAGAAGCCCTACCA
1 GGACTTCTGCTAATGCTTCTCC---GAGAAGACCTACCA
* * * * * *
374311 -GAGCTCCTACTTATACTTCTCCGAGAAGGCCTAACA
1 GGA-CTTCTGCTAATGCTTCTCCGAGAAGACCTACCA
* *
374347 GGACTTCTGCTAATGCTTCTCCGAGAAGATCTTCCA
1 GGACTTCTGCTAATGCTTCTCCGAGAAGACCTACCA
*
374383 GGACTTCTGCTAAAGCTTCTCCGAGAAGA
1 GGACTTCTGCTAATGCTTCTCCGAGAAGA
374412 TATTGCAGGA
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
36 65 0.77
37 2 0.02
38 2 0.02
39 15 0.18
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (36 bp):
GGACTTCTGCTAATGCTTCTCCGAGAAGACCTACCA
Found at i:374412 original size:36 final size:36
Alignment explanation
Indices: 374326--374426 Score: 139
Period size: 36 Copynumber: 2.8 Consensus size: 36
374316 CCTACTTATA
** * *
374326 CTTCTCCGAGAAGGCCTAACAGGACTTCTGCTAATG
1 CTTCTCCGAGAAGATCTTACAGGACTTCTGCTAAAG
*
374362 CTTCTCCGAGAAGATCTTCCAGGACTTCTGCTAAAG
1 CTTCTCCGAGAAGATCTTACAGGACTTCTGCTAAAG
* *
374398 CTTCTCCGAGAAGATATTGCAGGACTTCT
1 CTTCTCCGAGAAGATCTTACAGGACTTCT
374427 ACTTACGCTT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.28
Consensus pattern (36 bp):
CTTCTCCGAGAAGATCTTACAGGACTTCTGCTAAAG
Found at i:375931 original size:31 final size:31
Alignment explanation
Indices: 375893--375954 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
375883 TAAACTAAAT
*
375893 CAAATTTAATTTTAATTTGAT-TGACGGTTAA
1 CAAATTTAATTTGAATTTGATCTGA-GGTTAA
375924 CAAATTTAATTTGAATTTGATCTGAGGTTAA
1 CAAATTTAATTTGAATTTGATCTGAGGTTAA
375955 AAAAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (31 bp):
CAAATTTAATTTGAATTTGATCTGAGGTTAA
Found at i:379434 original size:31 final size:31
Alignment explanation
Indices: 379391--379458 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
379381 CAATAGAAAT
* * * *
379391 ATAAATAGTGCATAACTGTGTGCGGATACAG
1 ATAAATAATGCATAAATATGTGCAGATACAG
379422 ATAAATAATGCATAAATATGTGCAGATACAG
1 ATAAATAATGCATAAATATGTGCAGATACAG
379453 ATAAAT
1 ATAAAT
379459 GTGTGTATGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.26
Consensus pattern (31 bp):
ATAAATAATGCATAAATATGTGCAGATACAG
Found at i:379670 original size:17 final size:16
Alignment explanation
Indices: 379634--379680 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
379624 ATATTTTTTA
*
379634 AAATAAAATATAATAAT
1 AAATAAATTATAA-AAT
379651 AAATAAATTATAAAACT
1 AAATAAATTATAAAA-T
*
379668 AAATTAATT-TAAA
1 AAATAAATTATAAA
379681 TAACTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAATTATAAAAT
Found at i:380038 original size:26 final size:26
Alignment explanation
Indices: 380009--380073 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
379999 AGAATACATA
* *
380009 ATATTTATATAA-ATATTTATAATTTT
1 ATATTTACATAATATATTTA-AATATT
* *
380035 ATATATAGATAATATATTTAAATATT
1 ATATTTACATAATATATTTAAATATT
380061 ATATATTACATAA
1 ATAT-TTACATAA
380074 CATTATTTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
ATATTTACATAATATATTTAAATATT
Found at i:380555 original size:17 final size:17
Alignment explanation
Indices: 380516--380564 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 17
380506 CAATGTAAGA
380516 CTATTAATATTAT-TAAT
1 CTATT-ATATTATGTAAT
*
380533 CCATTATATTATGTAAT
1 CTATTATATTATGTAAT
*
380550 GTA-T-TATTATGTAAT
1 CTATTATATTATGTAAT
380565 ATTTAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 11 0.39
16 8 0.29
17 9 0.32
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (17 bp):
CTATTATATTATGTAAT
Found at i:380785 original size:31 final size:31
Alignment explanation
Indices: 380750--380808 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
380740 AAATTACTAT
*
380750 ATATTTTACATTACGACATTACTATATAAAA
1 ATATTTTACATTACGACAGTACTATATAAAA
* * *
380781 ATATTTTACGTTACTATAGTACTATATA
1 ATATTTTACATTACGACAGTACTATATA
380809 CTTATGTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (31 bp):
ATATTTTACATTACGACAGTACTATATAAAA
Found at i:380931 original size:20 final size:22
Alignment explanation
Indices: 380884--380938 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 22
380874 ATTATCTAAC
*
380884 TTGTTTTTTTG-TATGTTGAAA
1 TTGTTATTTTGTTATGTTGAAA
*
380905 TTATTATTTTGTTAT-TT-AAA
1 TTGTTATTTTGTTATGTTGAAA
380925 TTGTTATTTT-TTAT
1 TTGTTATTTTGTTAT
380939 ATTTTAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 12 0.40
21 11 0.37
22 3 0.10
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (22 bp):
TTGTTATTTTGTTATGTTGAAA
Found at i:381818 original size:17 final size:18
Alignment explanation
Indices: 381796--381830 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
381786 GATATGTAAA
381796 TTAAA-TTTATTTTTTTT
1 TTAAATTTTATTTTTTTT
381813 TTAAATTTTATTTTTTTT
1 TTAAATTTTATTTTTTTT
381831 ATATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTAAATTTTATTTTTTTT
Found at i:384779 original size:17 final size:17
Alignment explanation
Indices: 384752--384786 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
384742 TTTTAACACT
384752 AATATAATTAAAAATATA
1 AATATAATTAAAAA-ATA
384770 AATA-AATTAAAAAATA
1 AATATAATTAAAAAATA
384786 A
1 A
384787 TAATTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 9 0.53
18 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATAATTAAAAAATA
Found at i:387813 original size:2 final size:2
Alignment explanation
Indices: 387806--387839 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
387796 CCAATCTCAC
387806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
387840 TCCTTGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:389049 original size:8 final size:9
Alignment explanation
Indices: 389035--389092 Score: 63
Period size: 8 Copynumber: 7.0 Consensus size: 9
389025 ATTTGAATCT
389035 TTAAATATA
1 TTAAATATA
389044 -TAAATA-A
1 TTAAATATA
389051 TTAAA-ATA
1 TTAAATATA
389059 TTAAATATA
1 TTAAATATA
* *
389068 CT-CATATA
1 TTAAATATA
389076 TTAAATATA
1 TTAAATATA
389085 -TAAATATA
1 TTAAATATA
389093 ATCGTAATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
7 2 0.05
8 30 0.73
9 9 0.22
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (9 bp):
TTAAATATA
Found at i:389091 original size:17 final size:18
Alignment explanation
Indices: 389036--389092 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
389026 TTTGAATCTT
*
389036 TAAATATA-TAAATA-AT
1 TAAATATATTAAATATAC
389052 TAAA-ATATTAAATATAC
1 TAAATATATTAAATATAC
*
389069 T-CATATATTAAATATA-
1 TAAATATATTAAATATAC
389085 TAAATATA
1 TAAATATA
389093 ATCGTAATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 3 0.09
16 12 0.35
17 19 0.56
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATATATTAAATATAC
Found at i:389133 original size:27 final size:27
Alignment explanation
Indices: 389103--389158 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
389093 ATCGTAATTC
* *
389103 ATTTTCATATTTAAATAATATAATTTT
1 ATTTTCAAATTCAAATAATATAATTTT
*
389130 ATTTTTAAATTCAAATAATATAATTTT
1 ATTTTCAAATTCAAATAATATAATTTT
389157 AT
1 AT
389159 CCGCAAACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTTCAAATTCAAATAATATAATTTT
Found at i:391968 original size:2 final size:2
Alignment explanation
Indices: 391961--392005 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
391951 AGAAAATACA
391961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
392001 AT AT A
1 AT AT A
392006 ACATCAAACC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:397008 original size:27 final size:25
Alignment explanation
Indices: 396976--397025 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
396966 GCTCAATTTG
396976 AATTAAAATTCAAATACAAATAATTGA
1 AATTAAAA-TCAAATACAAA-AATTGA
*
397003 AATTAAAATCAAATATAAAAATT
1 AATTAAAATCAAATACAAAAATT
397026 AACTCATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 10 0.45
27 8 0.36
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (25 bp):
AATTAAAATCAAATACAAAAATTGA
Found at i:401502 original size:26 final size:25
Alignment explanation
Indices: 401443--401508 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 25
401433 AAATTTAATT
* *
401443 ATAAAATATATTAATAATTAATATA
1 ATAAAATATTTTAATAATTAAAATA
*
401468 A-AATTAATATTTTAATATTTTAAAATA
1 ATAA--AATATTTTAATA-ATTAAAATA
401495 ATAAAATATGTTTA
1 ATAAAATAT-TTTA
401509 CGAATCAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
24 2 0.06
25 1 0.03
26 16 0.48
27 12 0.36
28 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATAAAATATTTTAATAATTAAAATA
Found at i:402458 original size:16 final size:17
Alignment explanation
Indices: 402437--402469 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
402427 TTATAAAAAA
*
402437 TTAATTATTA-TTAAAT
1 TTAATTACTATTTAAAT
402453 TTAATTACTATTTAAAT
1 TTAATTACTATTTAAAT
402470 CTTATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAATTACTATTTAAAT
Found at i:411293 original size:40 final size:39
Alignment explanation
Indices: 411235--411325 Score: 107
Period size: 38 Copynumber: 2.3 Consensus size: 39
411225 TTTATGTGTT
*
411235 ATAATTATTTTTTAAATATTATATATTTATATAAAT-TTTA
1 ATAATTATTTATTAAATATTAT-T-TTTATATAAATATTTA
*
411275 ATAATTTATTTATT-AATATTATTTTTATATAATTATTTA
1 ATAA-TTATTTATTAAATATTATTTTTATATAAATATTTA
411314 AT-ATTATATTAT
1 ATAATTAT-TTAT
411326 ATTTTTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
37 4 0.09
38 15 0.33
39 7 0.15
40 12 0.26
41 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (39 bp):
ATAATTATTTATTAAATATTATTTTTATATAAATATTTA
Found at i:411333 original size:23 final size:24
Alignment explanation
Indices: 411251--411334 Score: 77
Period size: 23 Copynumber: 3.6 Consensus size: 24
411241 ATTTTTTAAA
*
411251 TATTATATATTTATATAA-ATT-T
1 TATTATATATTTATTTAATATTAT
* *
411273 TAATAATTTATTTA-TTAATATTAT
1 T-ATTATATATTTATTTAATATTAT
* *
411297 TTTTATATAATTATTTAATATTA-
1 TATTATATATTTATTTAATATTAT
*
411320 TATTATATTTTTATT
1 TATTATATATTTATT
411335 AGTTTTTATA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
22 4 0.08
23 33 0.69
24 11 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTATATATTTATTTAATATTAT
Found at i:411660 original size:38 final size:38
Alignment explanation
Indices: 411610--411746 Score: 123
Period size: 39 Copynumber: 3.8 Consensus size: 38
411600 ATGATTATTA
*
411610 AATATA-AATATAATGTATAAAATAATTAAATATATAT
1 AATATATAATATAATATATAAAATAATTAAATATATAT
* *
411647 AATATATAATATAATATTAAAAAATAATATAAATATAGAAT
1 AATATATAATATAATA-TATAAAATAAT-TAAATATA-TAT
* *
411688 AA-ATAT-ATA-AATATATAAAA-ATTTATATA-ATAT
1 AATATATAATATAATATATAAAATAATTAAATATATAT
411721 AAT-T-T-AT-TAATATATAAAAATAATTA
1 AATATATAATATAATATAT-AAAATAATTA
411747 TTTAATAGAT
Statistics
Matches: 84, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
32 10 0.12
33 9 0.11
34 5 0.06
35 5 0.06
36 2 0.02
37 12 0.14
38 12 0.14
39 13 0.15
40 12 0.14
41 4 0.05
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (38 bp):
AATATATAATATAATATATAAAATAATTAAATATATAT
Found at i:411733 original size:13 final size:14
Alignment explanation
Indices: 411699--411734 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
411689 AATATATAAA
411699 TATATAA-A-AATT
1 TATATAATATAATT
411711 TATATAATATAATT
1 TATATAATATAATT
411725 TAT-TAATATA
1 TATATAATATA
411735 TAAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 8 0.36
14 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATAATATAATT
Found at i:411733 original size:32 final size:31
Alignment explanation
Indices: 411680--411741 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
411670 ATAATATAAA
411680 TATAGAATAAATATATAAATATATAAAAATT
1 TATAGAATAAATATATAAATATATAAAAATT
* * *
411711 TATATAATATAATTTATTAATATATAAAAAT
1 TATAGAATA-AATATATAAATATATAAAAAT
411742 AATTATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (31 bp):
TATAGAATAAATATATAAATATATAAAAATT
Found at i:411736 original size:59 final size:60
Alignment explanation
Indices: 411598--411744 Score: 144
Period size: 59 Copynumber: 2.4 Consensus size: 60
411588 TTTAAATGTT
* *
411598 TAATGATTATTAA-ATATAAATATAATGTATAAAATAATTAAATATATATAATATATAATA
1 TAAT-ATTATTAATATATAAATATAATGAATAAAATAATTAAATATATAAAATATATAATA
**
411658 TAATATTAAAAAATAATATAAATAT-A-GAAT-AAAT-ATATAAATATATAAAAATTTATATAAT
1 TAATATT-ATTAAT-ATATAAATATAATGAATAAAATAAT-TAAATATAT-AAAA--TATATAAT
411719 A
60 A
*
411720 TAAT-TTATTAATATATAAAAATAAT
1 TAATATTATTAATATATAAATATAAT
411745 TATTTAATAG
Statistics
Matches: 71, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
58 2 0.03
59 25 0.35
60 18 0.25
61 3 0.04
62 23 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (60 bp):
TAATATTATTAATATATAAATATAATGAATAAAATAATTAAATATATAAAATATATAATA
Found at i:411745 original size:21 final size:20
Alignment explanation
Indices: 411711--411753 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
411701 TATAAAAATT
*
411711 TATATAATATAATT-TATTAA
1 TATATAAAATAATTAT-TTAA
411731 TATATAAAAATAATTATTTAA
1 TATAT-AAAATAATTATTTAA
411752 TA
1 TA
411754 GATTTAGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 14 0.70
22 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATAAAATAATTATTTAA
Found at i:411932 original size:36 final size:37
Alignment explanation
Indices: 411865--411968 Score: 99
Period size: 36 Copynumber: 2.8 Consensus size: 37
411855 AAAAGTAATA
* ** *
411865 ATTTATATATTTATATATTTTTATGTGTTATAATTATTT
1 ATTTATA-ATTTATATATTTATAT-AATTATAATAATTT
411904 -TTTA-AATTTATATATTTATATAAATTATAATAATTT
1 ATTTATAATTTATATATTTATAT-AATTATAATAATTT
411940 ATTTATTAATATTAT-T-TTTATATAATTAT
1 ATTTA-TAAT-TTATATATTTATATAATTAT
411969 TTAATATTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
36 26 0.46
37 11 0.20
38 11 0.20
39 4 0.07
40 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (37 bp):
ATTTATAATTTATATATTTATATAATTATAATAATTT
Found at i:411964 original size:31 final size:30
Alignment explanation
Indices: 411929--411988 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
411919 TTATATAAAT
*
411929 TATAATAATTTATTTATTAATATTAT-TTTTA
1 TATAATAATTTA-ATATT-ATATTATATTTTA
*
411960 TATAATTATTTAATATTATATTATATTTT
1 TATAATAATTTAATATTATATTATATTTT
411989 TATTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 7 0.27
30 8 0.31
31 11 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TATAATAATTTAATATTATATTATATTTTA
Found at i:411983 original size:23 final size:23
Alignment explanation
Indices: 411911--411992 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
411901 TTTTTTAAAT
*
411911 TTATATATTTATATAA-ATTATAA
1 TTATATATTTATTTAATATTAT-A
* * *
411934 TAATTTATTTA-TTAATATTATTT
1 TTATATATTTATTTAATATTA-TA
*
411957 TTATATAATTATTTAATATTATA
1 TTATATATTTATTTAATATTATA
*
411980 TTATATTTTTATT
1 TTATATATTTATT
411993 ATTTTTTATA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
22 3 0.07
23 33 0.72
24 10 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATATATTTATTTAATATTATA
Found at i:412332 original size:31 final size:31
Alignment explanation
Indices: 412282--412358 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
412272 ATGATTATTA
* *
412282 AATATAAATATA-ATGTATAA-AATAATTAAAT
1 AATATAAATATATA-ATATAATAATAA-AAAAT
*
412313 -ATATATAATATATAATATAATATTAAAAAAT
1 AATATA-AATATATAATATAATAATAAAAAAT
412344 AATATAAATATATAA
1 AATATAAATATATAA
412359 AATTTTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 5 0.13
31 24 0.62
32 10 0.26
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (31 bp):
AATATAAATATATAATATAATAATAAAAAAT
Found at i:412332 original size:38 final size:40
Alignment explanation
Indices: 412281--412376 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 40
412271 AATGATTATT
*
412281 AAATATA-AATATAAT-GTATAAAATAAT-TAAATATATA
1 AAATATATAATATAATAGTAAAAAATAATATAAATATATA
* *
412318 TAATATATAATATAATATTAAAAAATAATATAAATATATA
1 AAATATATAATATAATAGTAAAAAATAATATAAATATATA
412358 AAATTTTATATAATATAAT
1 AAA---TATATAATATAAT
412377 TTATTAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
37 6 0.12
38 8 0.16
39 10 0.20
40 12 0.24
43 13 0.27
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (40 bp):
AAATATATAATATAATAGTAAAAAATAATATAAATATATA
Found at i:412334 original size:21 final size:21
Alignment explanation
Indices: 412282--412409 Score: 78
Period size: 21 Copynumber: 6.3 Consensus size: 21
412272 ATGATTATTA
*
412282 AATATA-AATATAATGTATA-
1 AATATATAATATAATATATAT
*
412301 AA-ATA-ATTA-AATATATAT
1 AATATATAATATAATATATAT
412319 AATATATAATATAATAT-TA-
1 AATATATAATATAATATATAT
* *
412338 AA-AAATAATATAAATATATAA
1 AATATATAATAT-AATATATAT
*
412359 AATTTTATATAATATAATTTAT-T
1 AA---TATATAATATAATATATAT
* *
412382 AATATATAAAAATAAT-TATTT
1 AATATAT-AATATAATATATAT
412403 AATATAT
1 AATATAT
412410 TTATAAAAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
17 7 0.08
18 16 0.18
19 12 0.14
20 15 0.17
21 22 0.25
23 2 0.02
24 6 0.07
25 8 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (21 bp):
AATATATAATATAATATATAT
Found at i:412386 original size:13 final size:14
Alignment explanation
Indices: 412283--412387 Score: 55
Period size: 13 Copynumber: 7.7 Consensus size: 14
412273 TGATTATTAA
*
412283 ATATAAATATAATGT
1 ATAT-AATATAATTT
412298 ATA-AA-ATAA-TT
1 ATATAATATAATTT
*
412309 AAATATATATAA--T
1 ATATA-ATATAATTT
412322 ATATAATATAATATT
1 ATATAATATAAT-TT
* *
412337 A-A-AAAATAATAT
1 ATATAATATAATTT
* *
412349 AAATATATAAAATTTT
1 ATATA-ATATAA-TTT
412365 ATATAATATAATTT
1 ATATAATATAATTT
412379 AT-TAATATA
1 ATATAATATA
412388 TAAAAATAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 22
0.69 0.10 0.22
Matches are distributed among these distances:
11 3 0.04
12 13 0.19
13 23 0.33
14 11 0.16
15 14 0.20
16 6 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (14 bp):
ATATAATATAATTT
Found at i:412391 original size:32 final size:33
Alignment explanation
Indices: 412349--412464 Score: 121
Period size: 33 Copynumber: 3.5 Consensus size: 33
412339 AAAATAATAT
412349 AAATATATAAAATTTTATATAATATAATTTATTA
1 AAATATA-AAAATTTTATATAATATAATTTATTA
* * * *
412383 ATATATAAAAATAATTATTTAATAT-ATTTATAA
1 AAATATAAAAAT-TTTATATAATATAATTTATTA
* *
412416 AAATATAAAAATTTTATA-AGTA-AAATTATTA
1 AAATATAAAAATTTTATATAATATAATTTATTA
*
412447 AAATCATATAAATTTTAT
1 AAAT-ATAAAAATTTTAT
412465 TTTTTAATTA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
31 13 0.19
32 16 0.24
33 23 0.34
34 16 0.24
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (33 bp):
AAATATAAAAATTTTATATAATATAATTTATTA
Found at i:412471 original size:67 final size:65
Alignment explanation
Indices: 412349--412502 Score: 145
Period size: 66 Copynumber: 2.4 Consensus size: 65
412339 AAAATAATAT
* *
412349 AAATATATAAAATTTTATATAATATAATTTATTAATATATAAAAATAATTATTTAATATATTTAT
1 AAATATATAAAATTTTATATAATATAAATTATTAATATATAAAAATAATTATTTAAT-TAATT-T
412414 AA
64 AA
* ** * *
412416 AAATATA-AAAATTTTATA-AGTA-AAATTATTAAAATCATATAAATTTTATTTTTTAATTAATT
1 AAATATATAAAATTTTATATAATATAAATTATT--AAT-ATATAAAAATAATTATTTAATTAATT
412478 TAA
63 TAA
* **
412481 AAATACATATCATTTTAT-TAAT
1 AAATATATAAAATTTTATATAAT
412503 TTTTTTTAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
64 7 0.10
65 12 0.17
66 28 0.39
67 24 0.34
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (65 bp):
AAATATATAAAATTTTATATAATATAAATTATTAATATATAAAAATAATTATTTAATTAATTTAA
Found at i:413260 original size:24 final size:26
Alignment explanation
Indices: 413232--413288 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
413222 ATTATTTTTT
*
413232 TTAAATTTAATAAAAAAT-AATG-T-A
1 TTAAATAT-ATAAAAAATCAATGATAA
413256 TTAAATATATAAAAAATCAATGATAA
1 TTAAATATATAAAAAATCAATGATAA
413282 TTAAATA
1 TTAAATA
413289 ATTTTTCACT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 9 0.31
24 11 0.38
25 1 0.03
26 8 0.28
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (26 bp):
TTAAATATATAAAAAATCAATGATAA
Found at i:413654 original size:2 final size:2
Alignment explanation
Indices: 413647--413678 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
413637 AATCAAAGAT
413647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
413679 CACACAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:414306 original size:18 final size:17
Alignment explanation
Indices: 414273--414308 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
414263 AATTATAAAT
*
414273 TAAATTCAAATCTTTAA
1 TAAATTCAAATATTTAA
414290 TAAATTCAAAATATTTAA
1 TAAATTC-AAATATTTAA
414308 T
1 T
414309 TAATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTCAAATATTTAA
Found at i:414408 original size:25 final size:25
Alignment explanation
Indices: 414368--414415 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
414358 TGAATAATAA
*
414368 ATAAATTTTAATTTTAAAATATTTAT
1 ATAAATTTTAAATTT-AAATATTTAT
414394 ATAAA-TTTAAATTTAAATATTT
1 ATAAATTTTAAATTTAAATATTT
414416 GATTCATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATAAATTTTAAATTTAAATATTTAT
Done.