Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 78 of 91
Found at i:17869942 original size:30 final size:30
Alignment explanation
Indices: 17869908--17869981 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
17869898 ATTTTATATA
**
17869908 TTTAATATTAATATATTATATTAGGATCAT
1 TTTAATAAAAATATATTATATTAGGATCAT
17869938 TTTAATAAAAATATATTATATTAGGATCAT
1 TTTAATAAAAATATATTATATTAGGATCAT
17869968 TTTAATAAAAATAT
1 TTTAATAAAAATAT
17869982 TAGTTATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (30 bp):
TTTAATAAAAATATATTATATTAGGATCAT
Found at i:17869990 original size:30 final size:30
Alignment explanation
Indices: 17869908--17869990 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
17869898 ATTTTATATA
** *
17869908 TTTAATATTAATATATTATATTAGGATCAT
1 TTTAATAAAAATATAGTATATTAGGATCAT
*
17869938 TTTAATAAAAATATATTATATTAGGATCAT
1 TTTAATAAAAATATAGTATATTAGGATCAT
17869968 TTTAATAAAAATATTAGT-TATTA
1 TTTAATAAAAATA-TAGTATATTA
17869991 AATTACATTC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 46 0.94
31 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (30 bp):
TTTAATAAAAATATAGTATATTAGGATCAT
Found at i:17870127 original size:25 final size:27
Alignment explanation
Indices: 17870084--17870158 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
17870074 CTTTTATTTC
* *
17870084 AATAATATATAATAAATTATT-AATAAA
1 AATAATAT-TATTTAATTATTCAATAAA
* *
17870111 ATTAATATTATTT-ATTAATTTCATTAAA
1 AATAATATTATTTAATT-A-TTCAATAAA
17870139 AATAATATTATTTAATTATT
1 AATAATATTATTTAATTATT
17870159 GAAAATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
25 3 0.08
26 4 0.10
27 11 0.28
28 18 0.46
29 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (27 bp):
AATAATATTATTTAATTATTCAATAAA
Found at i:17870215 original size:15 final size:15
Alignment explanation
Indices: 17870195--17870250 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
17870185 TATAATATAC
17870195 TATTATTAATTTTAA
1 TATTATTAATTTTAA
17870210 TATTA-TAATTTTTAA
1 TATTATTAA-TTTTAA
17870225 TATT-TTAA---TAA
1 TATTATTAATTTTAA
17870236 TATTATT-ATTTTAA
1 TATTATTAATTTTAA
17870250 T
1 T
17870251 TAGTAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
11 8 0.23
12 2 0.06
14 7 0.20
15 18 0.51
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTAATTTTAA
Found at i:17870230 original size:8 final size:8
Alignment explanation
Indices: 17870203--17870250 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
17870193 ACTATTATTA
17870203 ATTTTAAT
1 ATTTTAAT
*
17870211 ATTATAAT
1 ATTTTAAT
17870219 -TTTTAAT
1 ATTTTAAT
17870226 ATTTTAAT
1 ATTTTAAT
* *
17870234 AATATTATT
1 -ATTTTAAT
17870243 ATTTTAAT
1 ATTTTAAT
17870251 TAGTAATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
7 6 0.19
8 20 0.62
9 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTAAT
Found at i:17870261 original size:25 final size:27
Alignment explanation
Indices: 17870206--17870268 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
17870196 ATTATTAATT
* **
17870206 TTAATATTATAATTTTTAATATTTTAA
1 TTAATATTATTATTTTTAATATAGTAA
17870233 -TAATATTATTA-TTTTAAT-TAGTAA
1 TTAATATTATTATTTTTAATATAGTAA
*
17870257 TTAATATAATTA
1 TTAATATTATTA
17870269 ATAATATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 4 0.13
25 17 0.55
26 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAATATTATTATTTTTAATATAGTAA
Found at i:17870273 original size:37 final size:39
Alignment explanation
Indices: 17870221--17870324 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 39
17870211 ATTATAATTT
* *
17870221 TTAATAT-TTTAATAATATTATTATTTT-AATT-AGTAA
1 TTAATATAATTAATAATATTATTATTTTCAATTAAATAA
* *
17870257 TTAATATAATTAATAATATTATTTTTATTCTATTAAATAA
1 TTAATATAATTAATAATATTATTATT-TTCAATTAAATAA
17870297 TTAATATAAATT-ATAATAATT-TTATTTT
1 TTAATAT-AATTAATAAT-ATTATTATTTT
17870325 GATAAAATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
36 7 0.12
37 16 0.28
38 2 0.04
39 5 0.09
40 20 0.35
41 7 0.12
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (39 bp):
TTAATATAATTAATAATATTATTATTTTCAATTAAATAA
Found at i:17870277 original size:34 final size:31
Alignment explanation
Indices: 17870233--17870302 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 31
17870223 AATATTTTAA
* *
17870233 TAATATTATTATTTTAATTAGTAATTAATATAAT
1 TAATAATATTATTTTAATT-CT-ATTAA-ATAAT
*
17870267 TAATAATATTATTTTTATTCTATTAAATAAT
1 TAATAATATTATTTTAATTCTATTAAATAAT
17870298 TAATA
1 TAATA
17870303 TAAATTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 10 0.30
32 5 0.15
33 1 0.03
34 17 0.52
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
TAATAATATTATTTTAATTCTATTAAATAAT
Found at i:17873037 original size:24 final size:25
Alignment explanation
Indices: 17873010--17873175 Score: 158
Period size: 23 Copynumber: 7.1 Consensus size: 25
17873000 CTACTCATAT
17873010 AATTTG-CACCGAAGTG-CCGCGTAG
1 AATTTGTC-CCGAAGTGACCGCGTAG
17873034 AATTTGTCCCGAAG-GACCGCGTAG
1 AATTTGTCCCGAAGTGACCGCGTAG
*
17873058 AATTTGTCCCGAA-TGACCACGTAG
1 AATTTGTCCCGAAGTGACCGCGTAG
*
17873082 AA-TTGTCCCGAA-TGACCACGTAG
1 AATTTGTCCCGAAGTGACCGCGTAG
* *
17873105 AA-TTATCCCGAA-TGACCACGTAG
1 AATTTGTCCCGAAGTGACCGCGTAG
* * *
17873128 AA-TTGCCCCGAA-TGACCACATAG
1 AATTTGTCCCGAAGTGACCGCGTAG
* *
17873151 -ATTTTTCCCGAAG-GACCTCGTAG
1 AATTTGTCCCGAAGTGACCGCGTAG
17873174 AA
1 AA
17873176 CCCTCGACTC
Statistics
Matches: 127, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
22 1 0.01
23 80 0.63
24 45 0.35
25 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (25 bp):
AATTTGTCCCGAAGTGACCGCGTAG
Found at i:17873091 original size:23 final size:23
Alignment explanation
Indices: 17873029--17873175 Score: 195
Period size: 23 Copynumber: 6.3 Consensus size: 23
17873019 CGAAGTGCCG
* *
17873029 CGTAGAATTTGTCCCGAAGGACCG
1 CGTAGAA-TTGTCCCGAATGACCA
17873053 CGTAGAATTTGTCCCGAATGACCA
1 CGTAGAA-TTGTCCCGAATGACCA
17873077 CGTAGAATTGTCCCGAATGACCA
1 CGTAGAATTGTCCCGAATGACCA
*
17873100 CGTAGAATTATCCCGAATGACCA
1 CGTAGAATTGTCCCGAATGACCA
*
17873123 CGTAGAATTGCCCCGAATGACCA
1 CGTAGAATTGTCCCGAATGACCA
* * * * *
17873146 CATAGATTTTTCCCGAAGGACCT
1 CGTAGAATTGTCCCGAATGACCA
17873169 CGTAGAA
1 CGTAGAA
17873176 CCCTCGACTC
Statistics
Matches: 110, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
23 81 0.74
24 29 0.26
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGTCCCGAATGACCA
Found at i:17881569 original size:64 final size:65
Alignment explanation
Indices: 17881458--17881600 Score: 159
Period size: 64 Copynumber: 2.2 Consensus size: 65
17881448 TTCCCCTTGA
* * * * *
17881458 AGTGCATCGATGCA-TTCTATAGTGCATCGATGCATAAATTACCTTCGATGTTT-TTATTTTAAG
1 AGTGCATCGATGCACTCCTATAGTGCATCGATGCACAAATTACATTCGATGTTTCTT-CTTTAAA
17881521 G
65 G
* * **
17881522 GGATGCATCGATGCACTCCT-TA-TGCATCGATGCACCAATTGTATTCGATGTTTCTTCTTTAAA
1 AG-TGCATCGATGCACTCCTATAGTGCATCGATGCACAAATTACATTCGATGTTTCTTCTTTAAA
17881585 G
65 G
17881586 AGTGCATCGATGCAC
1 AGTGCATCGATGCAC
17881601 ATTGAATATG
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
63 13 0.20
64 34 0.52
65 16 0.24
66 3 0.05
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (65 bp):
AGTGCATCGATGCACTCCTATAGTGCATCGATGCACAAATTACATTCGATGTTTCTTCTTTAAAG
Found at i:17882360 original size:24 final size:24
Alignment explanation
Indices: 17882328--17882453 Score: 125
Period size: 23 Copynumber: 5.4 Consensus size: 24
17882318 AAGGATGTTA
*
17882328 CACGTAGAATTTGTCCTAAAGGAC
1 CACGTAGAATTTGTCCCAAAGGAC
* * *
17882352 CACGGAGAATTTGTCCCGAATGAC
1 CACGTAGAATTTGTCCCAAAGGAC
**
17882376 CACGTAGAATTGTGT--CAAATAAC
1 CACGTAGAATT-TGTCCCAAAGGAC
17882399 CACGTAGAA-TTGTCCCAAAGGAC
1 CACGTAGAATTTGTCCCAAAGGAC
* * * *
17882422 CACATAG-ATTTGTCTCGAAGAAC
1 CACGTAGAATTTGTCCCAAAGGAC
17882445 CACGTAGAA
1 CACGTAGAA
17882454 CCATCGACTC
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
21 3 0.04
22 2 0.02
23 44 0.53
24 31 0.37
25 3 0.04
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (24 bp):
CACGTAGAATTTGTCCCAAAGGAC
Found at i:17882423 original size:46 final size:47
Alignment explanation
Indices: 17882328--17882453 Score: 139
Period size: 46 Copynumber: 2.7 Consensus size: 47
17882318 AAGGATGTTA
* * * *
17882328 CACGTAGAATT-TGTCCTAAAGGACCACGGAGAATTTGTCCCGAATGAC
1 CACGTAGAATTGTGT-C-AAAGAACCACGTAGAATTTGTCCCAAAGGAC
*
17882376 CACGTAGAATTGTGTCAAATAACCACGTAGAA-TTGTCCCAAAGGAC
1 CACGTAGAATTGTGTCAAAGAACCACGTAGAATTTGTCCCAAAGGAC
* * * *
17882422 CACATAGATTTGTCTCGAAGAACCACGTAGAA
1 CACGTAGAATTGTGTCAAAGAACCACGTAGAA
17882454 CCATCGACTC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 39 0.58
47 13 0.19
48 12 0.18
49 3 0.04
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (47 bp):
CACGTAGAATTGTGTCAAAGAACCACGTAGAATTTGTCCCAAAGGAC
Found at i:17890409 original size:12 final size:13
Alignment explanation
Indices: 17890392--17890420 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
17890382 CAAAGAAAAA
17890392 TAAAATAATAT-T
1 TAAAATAATATCT
17890404 TAAAATAATATCT
1 TAAAATAATATCT
17890417 TAAA
1 TAAA
17890421 TCCTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATCT
Found at i:17891897 original size:32 final size:32
Alignment explanation
Indices: 17891811--17891899 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
17891801 TTCATATTAG
* *
17891811 GATGTTGAATCTACAAAGATGCACCAATATTC
1 GATGTTGAATCTACAAAGATGCCCCAACATTC
* * * * *
17891843 GGTGATGAATCTCCAAAAATGCCCCAACATTT
1 GATGTTGAATCTACAAAGATGCCCCAACATTC
*
17891875 GATGTTGAATCTTCAAAGATGCCCC
1 GATGTTGAATCTACAAAGATGCCCC
17891900 CACTCTTCCT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (32 bp):
GATGTTGAATCTACAAAGATGCCCCAACATTC
Found at i:17893184 original size:2 final size:2
Alignment explanation
Indices: 17893177--17893238 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
17893167 ATAACAAGGG
17893177 AT AT AT AT 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 AT AT AT AT
*
17893219 AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
17893239 GGATAAATGA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17895735 original size:47 final size:47
Alignment explanation
Indices: 17895684--17895777 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
17895674 GAAAAAAAAT
17895684 TTAGTACAACTATTTATTTAAAAAATAATCAAAGATAAATAATTAGA
1 TTAGTACAACTATTTATTTAAAAAATAATCAAAGATAAATAATTAGA
*
17895731 TTAGTACAACTATTTCTTTAAAAAATAATCAAAGATAAATAATTAGA
1 TTAGTACAACTATTTATTTAAAAAATAATCAAAGATAAATAATTAGA
17895778 ATCGAATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.52, C:0.07, G:0.06, T:0.34
Consensus pattern (47 bp):
TTAGTACAACTATTTATTTAAAAAATAATCAAAGATAAATAATTAGA
Found at i:17896075 original size:18 final size:19
Alignment explanation
Indices: 17896052--17896088 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
17896042 TTCATTGAAA
17896052 AACCGAAAAA-CCGAACCG
1 AACCGAAAAACCCGAACCG
17896070 AACCGAAAAACCCGAACCG
1 AACCGAAAAACCCGAACCG
17896089 TTAAAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.49, C:0.35, G:0.16, T:0.00
Consensus pattern (19 bp):
AACCGAAAAACCCGAACCG
Found at i:17896086 original size:14 final size:14
Alignment explanation
Indices: 17896065--17896111 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
17896055 CGAAAAACCG
17896065 AACCGAACCGAAAA
1 AACCGAACCGAAAA
*
17896079 ACCCGAACCGTTAAAAA
1 AACCGAACCG---AAAA
17896096 AACCGAACCGAAAA
1 AACCGAACCGAAAA
17896110 AA
1 AA
17896112 TCGGTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 15 0.54
17 13 0.46
ACGTcount: A:0.55, C:0.28, G:0.13, T:0.04
Consensus pattern (14 bp):
AACCGAACCGAAAA
Found at i:17896568 original size:5 final size:5
Alignment explanation
Indices: 17896558--17896604 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
17896548 ACGTTAGATT
* *
17896558 ATAAA ATAAA AGAAA TATCAA ATAAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA -ATAAA AT-AAA ATAAA ATAAA ATAAA ATAAA
17896605 TCAAAGAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 29 0.81
6 7 0.19
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:17896596 original size:16 final size:16
Alignment explanation
Indices: 17896558--17896604 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
17896548 ACGTTAGATT
*
17896558 ATAAAATAAAAGA-AAT
1 ATAAAATAAAA-ATAAA
*
17896574 ATCAAATAAAAATAAA
1 ATAAAATAAAAATAAA
17896590 ATAAAAT-AAAATAAA
1 ATAAAATAAAAATAAA
17896605 TCAAAGAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (16 bp):
ATAAAATAAAAATAAA
Found at i:17896709 original size:60 final size:58
Alignment explanation
Indices: 17896587--17896717 Score: 133
Period size: 60 Copynumber: 2.2 Consensus size: 58
17896577 AAATAAAAAT
* * ** *
17896587 AAAATA-AAATAAAATAAATCAAAGAAGTAAATATTAGATTTTAAAAAATGTTATATAA
1 AAAATATAAA-AAAATAAATCAAAGAAGAAAATATTAAATTTTAAAAAATGAAAAATAA
* *
17896645 AAAATGTTAAAAAAATAAAAT-AAATGAAGAAAATATTAAATTTTAGAAAA-GAAAAATAA
1 AAAAT-ATAAAAAAAT-AAATCAAA-GAAGAAAATATTAAATTTTAAAAAATGAAAAATAA
17896704 TAAAATATAAAAAA
1 -AAAATATAAAAAA
17896718 TGTTAAAAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
58 5 0.08
59 21 0.35
60 34 0.57
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (58 bp):
AAAATATAAAAAAATAAATCAAAGAAGAAAATATTAAATTTTAAAAAATGAAAAATAA
Found at i:17896820 original size:36 final size:37
Alignment explanation
Indices: 17896734--17896805 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
17896724 AAGAGAAAAA
*
17896734 ATAAAACAAAATAAAATAAAAAAGTGGGAAAATAAAG
1 ATAAAAAAAAATAAAATAAAAAAGTGGGAAAATAAAG
* *
17896771 ATGAAACAAAATAAAATAAAAAAG-GGGAAATATAA
1 ATAAAAAAAAATAAAATAAAAAAGTGGGAAA-ATAA
17896806 TAAAATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 6 0.18
37 27 0.82
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (37 bp):
ATAAAAAAAAATAAAATAAAAAAGTGGGAAAATAAAG
Found at i:17896883 original size:18 final size:18
Alignment explanation
Indices: 17896862--17896904 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
17896852 GTTATTTTTA
*
17896862 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
17896880 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
17896898 AAATAAA
1 AAATAAA
17896905 TAATATAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:17898467 original size:47 final size:47
Alignment explanation
Indices: 17898410--17898503 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
17898400 TGAAAAAACG
*
17898410 TTAGTGCAACTATTTATTTAAAAAATAATCAAAGATAAATAATTAGA
1 TTAGTACAACTATTTATTTAAAAAATAATCAAAGATAAATAATTAGA
17898457 TTAGTACAACTATTTATTTAAAAAATAATCAAAGATAAATAATTAGA
1 TTAGTACAACTATTTATTTAAAAAATAATCAAAGATAAATAATTAGA
17898504 ATCTAATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.34
Consensus pattern (47 bp):
TTAGTACAACTATTTATTTAAAAAATAATCAAAGATAAATAATTAGA
Found at i:17899293 original size:5 final size:5
Alignment explanation
Indices: 17899283--17899323 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
17899273 ATGCTAGATT
* *
17899283 ATAAA ATAAA AGAAA TATCAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA -ATAAA ATAAA ATAAA ATAAA ATAAA
17899324 TCAAAGAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 28 0.90
6 3 0.10
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:17899523 original size:36 final size:36
Alignment explanation
Indices: 17899439--17899524 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
17899429 AAGAGAAAAA
* *
17899439 ATAAAACAAAATAAAATAAAAAGTGGGGAAATAAAG
1 ATAAAAAAAAATAAAATAAAAAGAGGGGAAATAAAG
* * *
17899475 ATGAAACAAAATAAAATAAAAA-AGGGGAAATATA-
1 ATAAAAAAAAATAAAATAAAAAGAGGGGAAATAAAG
17899509 ATAAAATAATAAATAA
1 ATAAAA-AA-AAATAA
17899525 TGGTAGTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
34 5 0.12
35 11 0.26
36 27 0.63
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (36 bp):
ATAAAAAAAAATAAAATAAAAAGAGGGGAAATAAAG
Found at i:17899587 original size:18 final size:18
Alignment explanation
Indices: 17899566--17899608 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
17899556 GTTGTTTTTA
*
17899566 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
17899584 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
17899602 AAATAAA
1 AAATAAA
17899609 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:17903126 original size:64 final size:63
Alignment explanation
Indices: 17903021--17903141 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 63
17903011 ATTGTTCAAG
* * * *
17903021 GTGTATCGGTGCACATGAAGTGCATCGATGCACTACTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTT-AAATAAAAACATCGAATGCCATCA
* * * *
17903085 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATTGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTTAAATAAAAACATCGAATG
17903142 GAATTTTTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 16 0.33
64 33 0.67
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTTAAATAAAAACATCGAATGCCATCA
Found at i:17904811 original size:23 final size:23
Alignment explanation
Indices: 17904743--17904811 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
17904733 CAATCTTATA
**
17904743 TGGCACTTCGGTTTATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * *
17904766 CGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
17904789 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
17904812 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:17908085 original size:64 final size:63
Alignment explanation
Indices: 17908010--17908130 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 63
17908000 ATTGTTCAAG
* * *
17908010 GTGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCAAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCAAATGCCATCA
* * * *
17908074 GTGTATCGATGCACAAGTAGTGCATCGATGCGCCCCCTTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCAAATG
17908131 GAATTTATGC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 16 0.32
64 34 0.68
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCAAATGCCATCA
Found at i:17909798 original size:23 final size:23
Alignment explanation
Indices: 17909730--17909798 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
17909720 CAATCTTATA
*
17909730 TGGCACTTCGATGTATTTCTACG
1 TGGCACTTCGGTGTATTTCTACG
* * * *
17909753 CGGCACTACGGTGAAATTCTACG
1 TGGCACTTCGGTGTATTTCTACG
*
17909776 TGGCACTTCGGTGTATTTATACG
1 TGGCACTTCGGTGTATTTCTACG
17909799 AACTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGTATTTCTACG
Found at i:17911644 original size:23 final size:23
Alignment explanation
Indices: 17911607--17911670 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
17911597 CAGCTCCTAT
17911607 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
17911630 AATTGCACCGTAGTGCCTCGTAG
1 AAATGCACCGAAGTGCCACGTAG
*
17911653 AAATACACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
17911671 TATAAGATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:17914589 original size:24 final size:24
Alignment explanation
Indices: 17914557--17914641 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
17914547 TATATCAGAA
* *
17914557 ATCAAAACAGAATTCAGATAAGAT
1 ATCAAAACAAAATCCAGATAAGAT
* *
17914581 ATCAAAACAAAATCCAGATTAGAA
1 ATCAAAACAAAATCCAGATAAGAT
* * * * *
17914605 ATCAGAACAGAATCCAGGTCAGGT
1 ATCAAAACAAAATCCAGATAAGAT
*
17914629 ATCAGAACAAAAT
1 ATCAAAACAAAAT
17914642 TCAAATCGGA
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGATAAGAT
Found at i:17914654 original size:48 final size:48
Alignment explanation
Indices: 17914550--17914658 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
17914540 AAATGGATAT
* * *
17914550 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAAAACAAAATCCAG
1 ATCAGAAATCAGAACAGAATCCAGATAAGATATCAAAACAAAATCCAA
* * * * * *
17914598 ATTAGAAATCAGAACAGAATCCAGGTCAGGTATCAGAACAAAATTCAA
1 ATCAGAAATCAGAACAGAATCCAGATAAGATATCAAAACAAAATCCAA
*
17914646 ATCGGAAATCAGA
1 ATCAGAAATCAGA
17914659 TAAAACATTC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATCCAGATAAGATATCAAAACAAAATCCAA
Found at i:17918720 original size:24 final size:24
Alignment explanation
Indices: 17918693--17918780 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
17918683 AAACGGATAT
*
17918693 ATCAGAAATC-GAAACAGAATTCAG
1 ATCAGAAATCAG-AACAGAATCCAG
* * *
17918717 ATCAGATATCATAACAAAATCCAG
1 ATCAGAAATCAGAACAGAATCCAG
17918741 ATCAGAAATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATCCAG
* **
17918765 GTCAGGTATCAGAACA
1 ATCAGAAATCAGAACA
17918781 TAATTCAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATCCAG
Found at i:17918799 original size:48 final size:48
Alignment explanation
Indices: 17918693--17918795 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 48
17918683 AAACGGATAT
* * *
17918693 ATCAGAAATC-GAAACAGAATTCAGATCAGATATCATAACAAAATCCAG
1 ATCAGAAATCAG-AACAGAATCCAGATCAGATATCAGAACAAAATCCAA
* * * *
17918741 ATCAGAAATCAGAACAGAATCCAGGTCAGGTATCAGAACATAATTCAA
1 ATCAGAAATCAGAACAGAATCCAGATCAGATATCAGAACAAAATCCAA
17918789 ATC-GAAA
1 ATCAGAAA
17918796 ATCAAATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
47 4 0.09
48 42 0.89
49 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATCCAGATCAGATATCAGAACAAAATCCAA
Found at i:17922855 original size:67 final size:67
Alignment explanation
Indices: 17922747--17922881 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
17922737 AGTCTCCTCA
17922747 CTCCCTTTGGGTTCGTGTGTTAAGCGAGATATACAAGATGGTTGAGCTCTACCCTCTCTCAACTG
1 CTCCCTTTGGGTTCGTGTGTTAAGCGAGATATACAAGATGGTTGAGCTCTACCCTCTCTCAACTG
17922812 CT
66 CT
17922814 CTCCCTTTGGGTTCGTGTGTTAAGCGAGATATACAAGATGGTTGAGCTCTACCCTCTCTCAACTG
1 CTCCCTTTGGGTTCGTGTGTTAAGCGAGATATACAAGATGGTTGAGCTCTACCCTCTCTCAACTG
17922879 CT
66 CT
17922881 C
1 C
17922882 GTTTCAATAG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (67 bp):
CTCCCTTTGGGTTCGTGTGTTAAGCGAGATATACAAGATGGTTGAGCTCTACCCTCTCTCAACTG
CT
Found at i:17927334 original size:13 final size:13
Alignment explanation
Indices: 17927316--17927362 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
17927306 TTTGTCAGTA
17927316 AGGCATAATAGTG
1 AGGCATAATAGTG
17927329 AGGCATAATAGTG
1 AGGCATAATAGTG
*
17927342 AGGCATACTAGGTG
1 AGGCATAATA-GTG
17927356 AGTGCAT
1 AG-GCAT
17927363 TTATTATGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 22 0.71
14 5 0.16
15 4 0.13
ACGTcount: A:0.34, C:0.11, G:0.32, T:0.23
Consensus pattern (13 bp):
AGGCATAATAGTG
Found at i:17928709 original size:3 final size:3
Alignment explanation
Indices: 17928703--17928834 Score: 57
Period size: 3 Copynumber: 41.7 Consensus size: 3
17928693 GAGTAGTAGC
* * * * * *
17928703 TAA TAA TAAA TAT TAAA TCA TAA TGA TAA TAT TAA TAA TAT TAA CAAA
1 TAA TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
* * * * * * *
17928751 TAA CAA TAA TAT TCA TAA TAA TAA TAA TAAA TAG TAA TAG TCAG TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA
* * *
17928798 TAA TAA TAC TAA TTAA TAA TTAA TAG TAA TAA AAA TA
1 TAA TAA TAA TAA -TAA TAA -TAA TAA TAA TAA TAA TA
17928835 TTAGTAATTA
Statistics
Matches: 92, Mismatches: 30, Indels: 14
0.68 0.22 0.10
Matches are distributed among these distances:
3 73 0.79
4 19 0.21
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:17928829 original size:29 final size:28
Alignment explanation
Indices: 17928766--17928860 Score: 81
Period size: 29 Copynumber: 3.4 Consensus size: 28
17928756 ATAATATTCA
* *
17928766 TAATAATAATAATAAATAGTAA-TAGTCAG
1 TAATAATAAT-ATAATTAGTAATTAAT-AG
* *
17928795 TGATAATAATACTAATTAATAATTAATAG
1 TAATAATAATA-TAATTAGTAATTAATAG
*
17928824 TAATAA-AA-AT-ATTAGTAATTATTAG
1 TAATAATAATATAATTAGTAATTAATAG
17928849 TAATAAATAATA
1 TAAT-AATAATA
17928861 ACTAGTAACC
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
25 17 0.31
26 3 0.06
27 3 0.06
28 4 0.07
29 24 0.44
30 3 0.06
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (28 bp):
TAATAATAATATAATTAGTAATTAATAG
Found at i:17928842 original size:25 final size:26
Alignment explanation
Indices: 17928809--17928860 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
17928799 AATAATACTA
17928809 ATTAATAATTAATAGTAATAAA-AAT
1 ATTAATAATTAATAGTAATAAATAAT
* *
17928834 ATTAGTAATTATTAGTAATAAATAAT
1 ATTAATAATTAATAGTAATAAATAAT
17928860 A
1 A
17928861 ACTAGTAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (26 bp):
ATTAATAATTAATAGTAATAAATAAT
Found at i:17930329 original size:3 final size:3
Alignment explanation
Indices: 17930305--17930385 Score: 69
Period size: 3 Copynumber: 27.7 Consensus size: 3
17930295 TTATATTAAA
* *
17930305 ATT A-T ATT ATT TTT ATT GTT ATT ATT ATT ATT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
17930351 ATA ACT ATT A-T ACT ATA ATAC ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT AT
17930386 GTTACATATT
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
2 6 0.10
3 54 0.87
4 2 0.03
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:17931226 original size:40 final size:40
Alignment explanation
Indices: 17931166--17931257 Score: 148
Period size: 40 Copynumber: 2.3 Consensus size: 40
17931156 ATTGCACAAA
*
17931166 AGTGATGAGGTCGAGCATTGCTTACCTAATAACGCACCGT
1 AGTGATGAGGTCGAGCATTGCTCACCTAATAACGCACCGT
* *
17931206 AGTGTTGAGGTCGAGCATTGCTCACCTAATAATGCACCGT
1 AGTGATGAGGTCGAGCATTGCTCACCTAATAACGCACCGT
*
17931246 AGTGCTGAGGTC
1 AGTGATGAGGTC
17931258 AGGTTTTACC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
AGTGATGAGGTCGAGCATTGCTCACCTAATAACGCACCGT
Found at i:17939081 original size:21 final size:21
Alignment explanation
Indices: 17939040--17939081 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17939030 ATAGTGGAAA
* **
17939040 AGCTTCAACTATTGGTGTTAC
1 AGCTCCAACTATTGGCATTAC
17939061 AGCTCCAACTATTGGCATTAC
1 AGCTCCAACTATTGGCATTAC
17939082 CTCTGAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (21 bp):
AGCTCCAACTATTGGCATTAC
Found at i:17943340 original size:31 final size:31
Alignment explanation
Indices: 17943302--17943457 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
17943292 CCCGAAGGAC
* *
17943302 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
17943333 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
17943364 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
17943395 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
17943426 CAGTCCATATGTTCCGAAGAACATACGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
17943457 C
1 C
17943458 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:17943661 original size:23 final size:24
Alignment explanation
Indices: 17943635--17943682 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
17943625 ATATACTTGT
*
17943635 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
17943658 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
17943682 T
1 T
17943683 AGGCCATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:17947111 original size:31 final size:31
Alignment explanation
Indices: 17947073--17947228 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
17947063 CCCGAAGGAC
* *
17947073 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
17947104 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
17947135 CAGTCCATATGTTCCAAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
17947166 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
17947197 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
17947228 C
1 C
17947229 CCTCGACCCT
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:17947432 original size:23 final size:24
Alignment explanation
Indices: 17947406--17947452 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
17947396 ATATACTTGT
*
17947406 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
17947429 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
17947453 CAGGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:17947995 original size:21 final size:21
Alignment explanation
Indices: 17947965--17948008 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
17947955 ATTCTGTCGT
* *
17947965 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
17947986 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
17948007 TT
1 TT
17948009 ACCCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:17952093 original size:17 final size:17
Alignment explanation
Indices: 17952055--17952125 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
17952045 TATTTTGCCT
17952055 AAAAAAG-AAAGAAAATG
1 AAAAAAGAAAAGAAAA-G
17952072 -AAAAAGAAAAGAAAA-
1 AAAAAAGAAAAGAAAAG
*
17952087 AAGAAAAGAAAA-AATGAG
1 AA-AAAAGAAAAGAA-AAG
* *
17952105 AAAAAATAAAAGAAAAT
1 AAAAAAGAAAAGAAAAG
17952122 AAAA
1 AAAA
17952126 TAAAATGAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
16 9 0.20
17 31 0.70
18 4 0.09
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAAAAGAAAAGAAAAG
Found at i:17952100 original size:12 final size:12
Alignment explanation
Indices: 17952062--17952125 Score: 67
Period size: 12 Copynumber: 5.1 Consensus size: 12
17952052 CCTAAAAAAG
17952062 AAAGAAAATG-AA
1 AAAGAAAA-GAAA
17952074 AAAGAAAAGAAA
1 AAAGAAAAGAAA
17952086 AAAGAAAAGAAA
1 AAAGAAAAGAAA
*
17952098 AAATGAGAAAAAATA
1 AAA-GA-AAAGAA-A
*
17952113 AAAGAAAATAAA
1 AAAGAAAAGAAA
17952125 A
1 A
17952126 TAAAATGAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
11 1 0.02
12 27 0.59
13 7 0.15
14 7 0.15
15 4 0.09
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:17952115 original size:15 final size:15
Alignment explanation
Indices: 17952088--17952134 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
17952078 AAAAGAAAAA
17952088 AGAAAAGAA-AAAATG
1 AGAAAA-AATAAAATG
17952103 AGAAAAAATAAAA-G
1 AGAAAAAATAAAATG
*
17952117 AAAATAAAATAAAATG
1 AGAA-AAAATAAAATG
17952133 AG
1 AG
17952135 GGTTCAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.22
15 19 0.70
16 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (15 bp):
AGAAAAAATAAAATG
Found at i:17953434 original size:113 final size:113
Alignment explanation
Indices: 17953235--17953545 Score: 399
Period size: 113 Copynumber: 2.7 Consensus size: 113
17953225 GTTCGATCCT
* * * * * *
17953235 AATTCAATGGATCAACTCACACAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGACTCTCTT
1 AATTCAATGGATCAATTCCCACAGATCTGATATTCCCTTCAGAATAAGCAGAACAAGTCTCTCTT
* *
17953300 TTCCAAGATTTGATATTCCCTTTAGAGTAAGTGGAACAAGTTTGCCCC
66 TTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCC
* * * * * *
17953348 GATTCAATGAATCAATTCCCCCAGACCTGATATTCCCTTCAGATTAAGCAGAACATGTCTCTCTT
1 AATTCAATGGATCAATTCCCACAGATCTGATATTCCCTTCAGAATAAGCAGAACAAGTCTCTCTT
17953413 TTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCC
66 TTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCC
* * * * * * *
17953461 AATTTAATGGATCAATTCCCTCAGATCTAATATTCCCTTTAGAAAGAAGCAGAACAAATCCCTCT
1 AATTCAATGGATCAATTCCCACAGATCTGATATTCCCTTCAG-AATAAGCAGAACAAGTCTCTCT
*
17953526 CCTT-CAAGATTTGATATTCC
65 -TTTCCAAGATTTGATATTCC
17953546 ATGAGTGACA
Statistics
Matches: 171, Mismatches: 25, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
113 136 0.80
114 33 0.19
115 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (113 bp):
AATTCAATGGATCAATTCCCACAGATCTGATATTCCCTTCAGAATAAGCAGAACAAGTCTCTCTT
TTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCC
Found at i:17953562 original size:113 final size:112
Alignment explanation
Indices: 17953235--17953581 Score: 317
Period size: 113 Copynumber: 3.1 Consensus size: 112
17953225 GTTCGATCCT
* * * * * * * * *
17953235 AATTCAATGGATCAACTCACACAGATCTGATATTCCCTTCAG-AGTAAGCGGAACAGGA-CTCTC
1 AATTCAATGAATCAATTCCCCCAGACCTAATATTCCCTTCAGAAG-AAGCAGAACA-AATCCCTC
* * * *
17953298 TTTTCCAAGATTTGATATTCCCTTTAGAGTAAGTGGAACAAGTTTGCCCC
64 TCTTCCAAGATTTGATATTCCC-ATAGAGTAAGCGGAACAAGTCTGCCCC
* * ** ** * *
17953348 GATTCAATGAATCAATTCCCCCAGACCTGATATTCCCTTCAGATTAAGCAGAACATGTCTCTCTT
1 AATTCAATGAATCAATTCCCCCAGACCTAATATTCCCTTCAGAAGAAGCAGAACAAATCCCTCTC
* *
17953413 TTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCC
66 TTCCAAGATTTGATATTCCCAT-AGAGTAAGCGGAACAAGTCTGCCCC
* * * * *
17953461 AATTTAATGGATCAATTCCCTCAGATCTAATATTCCCTTTAGAAAGAAGCAGAACAAATCCCTCT
1 AATTCAATGAATCAATTCCCCCAGACCTAATATTCCCTTCAG-AAGAAGCAGAACAAATCCCTCT
*
17953526 CCTT-CAAGATTTGATATT-CCAT-GAGTGACAGCGGAACAAGTCTACCCC
65 -CTTCCAAGATTTGATATTCCCATAGAGT-A-AGCGGAACAAGTCTGCCCC
*
17953574 GATTCAAT
1 AATTCAAT
17953582 CTTCCCTAAA
Statistics
Matches: 197, Mismatches: 30, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
111 4 0.02
112 3 0.02
113 157 0.80
114 31 0.16
115 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (112 bp):
AATTCAATGAATCAATTCCCCCAGACCTAATATTCCCTTCAGAAGAAGCAGAACAAATCCCTCTC
TTCCAAGATTTGATATTCCCATAGAGTAAGCGGAACAAGTCTGCCCC
Found at i:17953812 original size:3 final size:3
Alignment explanation
Indices: 17953800--17953909 Score: 129
Period size: 3 Copynumber: 37.7 Consensus size: 3
17953790 TTATATTAAA
*
17953800 ATT A-T ATT ATT ATT ATT GTT ATT ATT ATT ATT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
17953846 ATT A-T ATT ATT ATT ATT ATT GTA AAT ATT A-T ATT ATA ATAC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
17953890 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
17953910 GTTACATATT
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
2 8 0.09
3 81 0.89
4 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:17953821 original size:17 final size:16
Alignment explanation
Indices: 17953801--17953927 Score: 90
Period size: 15 Copynumber: 8.2 Consensus size: 16
17953791 TATATTAAAA
17953801 TTATATTATTATTATT
1 TTATATTATTATTATT
*
17953817 GT-TATTATTATTA--
1 TTATATTATTATTATT
17953830 TTATATTATTATTATT
1 TTATATTATTATTATT
17953846 ATTATATTATTATTATT
1 -TTATATTATTATTATT
* * *
17953863 ATTGTA--AATATTATA
1 -TTATATTATTATTATT
* *
17953878 TTATAATA-CATTATT
1 TTATATTATTATTATT
*
17953893 ATTATTATTATTATTATG
1 -TTA-TATTATTATTATT
*
17953911 TTACA-TATTA-TATT
1 TTATATTATTATTATT
17953925 TTA
1 TTA
17953928 CAGGCCCAAG
Statistics
Matches: 89, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
13 1 0.01
14 21 0.24
15 28 0.31
16 6 0.07
17 28 0.31
18 5 0.06
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
TTATATTATTATTATT
Found at i:17956734 original size:20 final size:20
Alignment explanation
Indices: 17956709--17956746 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
17956699 TTTGGTTCAC
17956709 AGAATGTAAGATTACCAGTG
1 AGAATGTAAGATTACCAGTG
17956729 AGAATGTAAGATTACCAG
1 AGAATGTAAGATTACCAG
17956747 GGAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGTAAGATTACCAGTG
Found at i:17956756 original size:16 final size:19
Alignment explanation
Indices: 17956709--17956758 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
17956699 TTTGGTTCAC
17956709 AGAATGTAAGATTACCAGTG
1 AGAA-GTAAGATTACCAGTG
17956729 AGAATGTAAGATTACCAG-G
1 AGAA-GTAAGATTACCAGTG
17956748 -GAA-TAAGATTA
1 AGAAGTAAGATTA
17956759 ATGAGAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.27
18 3 0.10
19 1 0.03
20 18 0.60
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (19 bp):
AGAAGTAAGATTACCAGTG
Found at i:17959779 original size:25 final size:25
Alignment explanation
Indices: 17959731--17959779 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
17959721 TTGTGACACG
* *
17959731 TTTTCTCTACTCTTGTGGCGCGTTT
1 TTTTCTCTACTCTTGTGACACGTTT
* *
17959756 TTTTGTCTATTCTTGTGACACGTT
1 TTTTCTCTACTCTTGTGACACGTT
17959780 CCTTAAGGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.08, C:0.20, G:0.18, T:0.53
Consensus pattern (25 bp):
TTTTCTCTACTCTTGTGACACGTTT
Found at i:17961656 original size:23 final size:23
Alignment explanation
Indices: 17961621--17961665 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
17961611 TTTTTAACAC
17961621 TTTTTAAATATTTT-TATATTTTA
1 TTTTTAAATATTTTCTA-ATTTTA
17961644 TTTTTAAGA-ATTTTCTAATTTT
1 TTTTTAA-ATATTTTCTAATTTT
17961666 TTATACTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTAAATATTTTCTAATTTTA
Found at i:17961667 original size:32 final size:33
Alignment explanation
Indices: 17961607--17961670 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
17961597 TGTATTTTTA
*
17961607 TTTATTTTTAACACTTTTTAAATATTTTTATAT
1 TTTATTTTTAACAATTTTTAAATATTTTTATAT
*
17961640 TTTATTTTTAAGAATTTTCT-AAT-TTTTTATA
1 TTTATTTTTAACAATTTT-TAAATATTTTTATA
17961671 CTTTCTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 8 0.29
33 19 0.68
34 1 0.04
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (33 bp):
TTTATTTTTAACAATTTTTAAATATTTTTATAT
Found at i:17961695 original size:9 final size:9
Alignment explanation
Indices: 17961599--17961756 Score: 56
Period size: 9 Copynumber: 17.8 Consensus size: 9
17961589 TATTTTAATG
*
17961599 TATTTTTATT
1 TATTTTTA-A
17961609 TATTTTTAA
1 TATTTTTAA
*
17961618 CACTTTTTAAA
1 TA-TTTTT-AA
17961629 TATTTTT-A
1 TATTTTTAA
17961637 TA--TTT--
1 TATTTTTAA
17961642 TATTTTTAA
1 TATTTTTAA
*
17961651 GAATTTTCTAA
1 -TATTTT-TAA
17961662 T-TTTTT-A
1 TATTTTTAA
*
17961669 TACTTTCTAA
1 TA-TTTTTAA
17961679 TA-TTTTAA
1 TATTTTTAA
17961687 TATTTTTAA
1 TATTTTTAA
17961696 T-TCTTTGTGAA
1 TAT-TTT-T-AA
17961707 T-TATTTT--
1 TAT-TTTTAA
17961714 TATTTTTAA
1 TATTTTTAA
*
17961723 TATTTTAAA
1 TATTTTTAA
17961732 TATAATTTTAA
1 TAT--TTTTAA
*
17961743 T-TGTTTAA
1 TATTTTTAA
17961751 -ATTTTT
1 TATTTTT
17961757 TAGAATATTT
Statistics
Matches: 115, Mismatches: 12, Indels: 44
0.67 0.07 0.26
Matches are distributed among these distances:
5 2 0.02
6 3 0.03
7 10 0.09
8 22 0.19
9 30 0.26
10 29 0.25
11 19 0.17
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.64
Consensus pattern (9 bp):
TATTTTTAA
Found at i:17961766 original size:27 final size:25
Alignment explanation
Indices: 17961621--17961785 Score: 77
Period size: 27 Copynumber: 6.2 Consensus size: 25
17961611 TTTTTAACAC
*
17961621 TTTTTA-AATATTTTTATATTTT-AT
1 TTTTTAGAATATTTTAAT-TTTTAAT
* *
17961645 TTTTAAGAAT-TTTCTAATTTTTTAT
1 TTTTTAGAATATTT-TAATTTTTAAT
** **
17961670 ACTTTCTAATATTTTAATATTTTTAAT
1 TTTTTAGAATATTTT-A-ATTTTTAAT
*
17961697 TCTTTGT-GAATTATTTTTATTTTTAAT
1 T-TTT-TAGAA-TATTTTAATTTTTAAT
* *
17961724 ATTTTAAATATAATTTTAATTGTTTAAAT
1 TTTTTAGA-AT-ATTTTAATT-TTT-AAT
*
17961753 TTTTTAGAATATTTTCTATTTTCTAAT
1 TTTTTAGAATATTTT-AATTTT-TAAT
17961780 TATTTT
1 T-TTTT
17961786 CATTTTTTTA
Statistics
Matches: 106, Mismatches: 18, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
24 12 0.11
25 15 0.14
26 9 0.08
27 37 0.35
28 17 0.16
29 16 0.15
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.64
Consensus pattern (25 bp):
TTTTTAGAATATTTTAATTTTTAAT
Found at i:17969400 original size:2 final size:2
Alignment explanation
Indices: 17969393--17969418 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17969383 AGTAGTAATT
17969393 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
17969419 AGACTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17969488 original size:28 final size:29
Alignment explanation
Indices: 17969427--17969517 Score: 71
Period size: 28 Copynumber: 3.1 Consensus size: 29
17969417 TAAGACTAAG
17969427 ATAATAA-TAAAAAATAATAATAATTAAA
1 ATAATAATTAAAAAATAATAATAATTAAA
* * *
17969455 ACAATAATTAAAATATAA-AAGTAA-TAAT
1 ATAATAATTAAAAAATAATAA-TAATTAAA
*** *
17969483 ATAATAATATTGTAAATAAATAATGATTAAA
1 ATAATAAT-TAAAAAAT-AATAATAATTAAA
17969514 ATAA
1 ATAA
17969518 AAGAAATTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
28 18 0.38
29 16 0.34
30 4 0.09
31 9 0.19
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (29 bp):
ATAATAATTAAAAAATAATAATAATTAAA
Found at i:17970839 original size:3 final size:3
Alignment explanation
Indices: 17970833--17970867 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17970823 TTTTTTTATT
17970833 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17970868 TGTAAACTGA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:17971164 original size:45 final size:45
Alignment explanation
Indices: 17971099--17971548 Score: 729
Period size: 45 Copynumber: 10.0 Consensus size: 45
17971089 TCAAAAAGCT
*
17971099 CCCGAAGGCTTTTGAAAACATCATGCACTAAAGGGCTTACAGATGA
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * *
17971145 CCCGAAGGTTTTGAAAACATAATGCACTGAAGGACTTACAAATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
17971190 CCCGAAGGTTTTGAAAACATTATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
**
17971235 CATGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
17971280 CCCGAAGGTTTTGAAAACATCATGCATTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
** * *
17971325 CCCGAATATTTTGAAAATATCATGCACTGAAGAGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
17971370 CCCGAAGGTTTTGAAAATATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
17971415 CCCGAAGGTTTTGAAAATATCATGCACTGAAGGGCTTAAAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
17971460 TCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
17971505 CTCGAATGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
17971549 TGGGAAATAG
Statistics
Matches: 376, Mismatches: 28, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
45 368 0.98
46 8 0.02
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:17972236 original size:22 final size:22
Alignment explanation
Indices: 17972208--17972289 Score: 137
Period size: 22 Copynumber: 3.7 Consensus size: 22
17972198 AATAAAGCTT
*
17972208 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
17972230 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
17972252 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
17972274 TCATCTTTGAAGAGAG
1 TCATCTTTGAAAAGAG
17972290 TAGATATGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:17972760 original size:54 final size:54
Alignment explanation
Indices: 17972599--17972761 Score: 211
Period size: 54 Copynumber: 3.0 Consensus size: 54
17972589 CCATAACTGG
* * *
17972599 TTCGTAAAACACTTGTCAATACATTCATCTTTTCCTGTGGTTTCTGCCCAGATG
1 TTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTGCCCAGATT
* * * * * *
17972653 TTCGCAAAATATTTGACAACACATTCATAC-TTTCATGTAGCTTCTGCCCAGATT
1 TTCGTAAAACATTTGACAATACATTCAT-CTTTTCCTGTGGTTTCTGCCCAGATT
* *
17972707 TTCGTAAAGCATTTGACAATACATTCATCTTTTCCTGTGGTTTCTGTCCAGATT
1 TTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTGCCCAGATT
17972761 T
1 T
17972762 CTGGTTAGGG
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 88 0.98
55 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (54 bp):
TTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTGCCCAGATT
Found at i:17973356 original size:3 final size:3
Alignment explanation
Indices: 17973348--17973404 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
17973338 TTCATTTTCA
* *
17973348 TAT TAT TAT TAT TAT TAT TA- TAA TAT GA- TAT TA- TAT TA- TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
17973393 ATAT TAT TAT TA
1 -TAT TAT TAT TA
17973405 AATAAAAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
2 7 0.15
3 32 0.70
4 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:17973381 original size:16 final size:16
Alignment explanation
Indices: 17973347--17973402 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
17973337 TTTCATTTTC
17973347 ATATTATTAT-TAT-T
1 ATATTATTATATATAT
*
17973361 ATTATTATAATATGATAT
1 A-TATTATTATAT-ATAT
17973379 -TA-TATTATATATAT
1 ATATTATTATATATAT
17973393 ATATTATTAT
1 ATATTATTAT
17973403 TAAATAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 5 0.15
15 17 0.50
16 9 0.26
17 2 0.06
18 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
ATATTATTATATATAT
Found at i:17974694 original size:16 final size:15
Alignment explanation
Indices: 17974664--17974701 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
17974654 TTAATTTCTT
17974664 TTATTTTGATTATTA
1 TTATTTTGATTATTA
*
17974679 TTATTTTGTTTTATTA
1 TTATTTTG-ATTATTA
17974695 TTATTTT
1 TTATTTT
17974702 TGATATATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (15 bp):
TTATTTTGATTATTA
Found at i:17974696 original size:19 final size:20
Alignment explanation
Indices: 17974662--17974699 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
17974652 TTTTAATTTC
17974662 TTTTATTTTGATTATTATTA
1 TTTTATTTTGATTATTATTA
*
17974682 TTTTGTTTT-ATTATTATT
1 TTTTATTTTGATTATTATT
17974700 TTTGATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTATTTTGATTATTATTA
Found at i:17977232 original size:19 final size:20
Alignment explanation
Indices: 17977208--17977245 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17977198 ATCTTTACAT
17977208 TTTTAT-TTTGCATTTGTAC
1 TTTTATGTTTGCATTTGTAC
*
17977227 TTTTATGTTTGCTTTTGTA
1 TTTTATGTTTGCATTTGTA
17977246 TTGCACAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.66
Consensus pattern (20 bp):
TTTTATGTTTGCATTTGTAC
Found at i:17977359 original size:14 final size:13
Alignment explanation
Indices: 17977288--17977362 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
17977278 CATATTTATA
17977288 TTTGCATTTGCAT
1 TTTGCATTTGCAT
17977301 TTTGCATTTTTGCAT
1 TTTGCA--TTTGCAT
* * *
17977316 TTTACGTTTGTAT
1 TTTGCATTTGCAT
*
17977329 TTT-CATTTTCATT
1 TTTGCATTTGCA-T
17977342 TTTGCATTTGCAT
1 TTTGCATTTGCAT
17977355 CTTTGCAT
1 -TTTGCAT
17977363 AATTACATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
12 5 0.10
13 20 0.40
14 14 0.28
15 11 0.22
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (13 bp):
TTTGCATTTGCAT
Found at i:17980679 original size:22 final size:21
Alignment explanation
Indices: 17980627--17980684 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
17980617 ACATCTACAT
*
17980627 TCTTCCATAGATGATAGATTC
1 TCTTCCAAAGATGATAGATTC
*
17980648 TCTCTTCAAAGATGATAGATTC
1 TCT-TCCAAAGATGATAGATTC
17980670 TCTTGCCAAAGATGA
1 TCTT-CCAAAGATGA
17980685 AAGCTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (21 bp):
TCTTCCAAAGATGATAGATTC
Found at i:17981413 original size:45 final size:45
Alignment explanation
Indices: 17981347--17981919 Score: 941
Period size: 45 Copynumber: 12.7 Consensus size: 45
17981337 TATTTCTCAT
* * * *
17981347 ATCTGTAAGTCCTACAATGCATGATGTTTTCAAAACCTTTGAGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
17981392 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
17981437 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* * *
17981482 ATTTGTAAGTCCTACAGTGCATAATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
17981527 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
17981572 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* * *
17981617 ATCTGTAAGTCCTTCAGTGCATGATATTTTCAAAACATTTGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* *
17981662 ATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAACCTTCGAGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* *
17981707 ATCTGTAA-ACCTTTCAGTGCATGATGTTTTCAAAACCTTCAGGTC
1 ATCTGTAAGTCC-TTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
17981752 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
17981797 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
17981842 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTT
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
17981887 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAA
17981920 CACTTCCATC
Statistics
Matches: 492, Mismatches: 34, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
44 2 0.00
45 488 0.99
46 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (45 bp):
ATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
Found at i:17982051 original size:3 final size:3
Alignment explanation
Indices: 17982043--17982105 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
17982033 TTCATTTTTA
17982043 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17982089 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
17982106 AATAAAAAAG
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.07
3 54 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:17983414 original size:16 final size:17
Alignment explanation
Indices: 17983393--17983432 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
17983383 TAACAGTTTG
*
17983393 ATATTTTTCA-TTTAAT
1 ATATTTTGCATTTTAAT
17983409 ATATTTTGCATTTTAAT
1 ATATTTTGCATTTTAAT
17983426 ATTATTT
1 A-TATTT
17983433 CTTTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 7 0.33
18 5 0.24
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (17 bp):
ATATTTTGCATTTTAAT
Found at i:17983462 original size:3 final size:3
Alignment explanation
Indices: 17983454--17983536 Score: 63
Period size: 3 Copynumber: 28.7 Consensus size: 3
17983444 TTTTATTTTG
*
17983454 ATT ATT ATT ATT -TT ATT -TT GTT -TT ATT ATT ATT ATT GATAT ATGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -AT-T AT-T
*
17983499 -TT A-A ATT ATT ATT -TT CATT ATT ATT -TT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT AT
17983537 CTTAAGTCAT
Statistics
Matches: 67, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
2 12 0.18
3 47 0.70
4 7 0.10
5 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17984649 original size:2 final size:2
Alignment explanation
Indices: 17984642--17984713 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
17984632 AATCTCATCC
17984642 AT AT AT AT 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 AT AT AT AT
17984684 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
17984714 CCATGTTCAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17992294 original size:17 final size:18
Alignment explanation
Indices: 17992272--17992305 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17992262 ACAAATAATC
*
17992272 ATCCAA-AATAAAAAAAA
1 ATCCAAGAACAAAAAAAA
17992289 ATCCAAGAACAAAAAAA
1 ATCCAAGAACAAAAAAA
17992306 TGTTTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.74, C:0.15, G:0.03, T:0.09
Consensus pattern (18 bp):
ATCCAAGAACAAAAAAAA
Found at i:17992304 original size:18 final size:17
Alignment explanation
Indices: 17992254--17992305 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
17992244 TCGAAAACAT
*
17992254 AAATCC-AAACAAATAA
1 AAATCCAAAACAAAAAA
** *
17992270 TCATCCAAAATAAAAAA
1 AAATCCAAAACAAAAAA
17992287 AAATCCAAGAACAAAAAA
1 AAATCCAA-AACAAAAAA
17992305 A
1 A
17992306 TGTTTATTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 4 0.15
17 14 0.52
18 9 0.33
ACGTcount: A:0.69, C:0.17, G:0.02, T:0.12
Consensus pattern (17 bp):
AAATCCAAAACAAAAAA
Found at i:17994238 original size:20 final size:20
Alignment explanation
Indices: 17994213--17994300 Score: 149
Period size: 20 Copynumber: 4.4 Consensus size: 20
17994203 ACCCGACGGA
*
17994213 TGCATCGATGCATGGCTCTT
1 TGCATCGATGCATGGCTCTG
17994233 TGCATCGATGCATGGCTCTG
1 TGCATCGATGCATGGCTCTG
* *
17994253 TGCATCGATACATGGATCTG
1 TGCATCGATGCATGGCTCTG
17994273 TGCATCGATGCATGGCTCTG
1 TGCATCGATGCATGGCTCTG
17994293 TGCATCGA
1 TGCATCGA
17994301 GGCACATTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATGGCTCTG
Found at i:17994348 original size:21 final size:21
Alignment explanation
Indices: 17994324--17994395 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
17994314 AGTGCATTGG
17994324 TGCATCTTCATGATGTATCGA
1 TGCATCTTCATGATGTATCGA
*
17994345 TGCA-CATTCATAAGGATGCATCGA
1 TGCATC-TTCAT---GATGTATCGA
* *
17994369 TGCACCTTAAT-AGTGTATCGA
1 TGCATCTTCATGA-TGTATCGA
17994390 TGCATC
1 TGCATC
17994396 ATGCATAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 2 0.05
21 21 0.51
24 17 0.41
25 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (21 bp):
TGCATCTTCATGATGTATCGA
Found at i:17998805 original size:19 final size:19
Alignment explanation
Indices: 17998777--17998823 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
17998767 TGCAAGAGGA
*
17998777 GAGAGCCAATAAGCTCATC
1 GAGAGTCAATAAGCTCATC
17998796 GAGAGTCAATAAGCTCATC
1 GAGAGTCAATAAGCTCATC
17998815 GAGAGTCAA
1 GAGAGTCAA
17998824 GGATTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.17
Consensus pattern (19 bp):
GAGAGTCAATAAGCTCATC
Found at i:18004562 original size:55 final size:55
Alignment explanation
Indices: 18004494--18004639 Score: 220
Period size: 55 Copynumber: 2.7 Consensus size: 55
18004484 TTTGTATGAG
* * *
18004494 TGTGTATCGGTACACTAATGAGTGTATCGATACCCTCAAAACATTGAATGCCATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCCATT
* * *
18004549 TGTGTATCGGTACACTGAGGAGTGTATCGATACCATCAAAACATCGAGTGCTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCCATT
* *
18004604 TGTATATCAGTACACTGAGGAGTGTATCGATACCCT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCT
18004640 TTCCATTTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 82 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCCATT
Found at i:18004672 original size:55 final size:55
Alignment explanation
Indices: 18004494--18004691 Score: 213
Period size: 55 Copynumber: 3.6 Consensus size: 55
18004484 TTTGTATGAG
* * *
18004494 TGTGTATCGGTACACTAATGAGTGTATCGATACCCTCAAAACATTGAATGCCATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATTGAATGCAATT
* * * *
18004549 TGTGTATCGGTACACTGAGGAGTGTATCGATACCATCAAAACATCGAGTGCTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATTGAATGCAATT
* * **** **
18004604 TGTATATCAGTACACTGAGGAGTGTATCGATACCCTTTCCATTTTGAATGCAATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATTGAATGCAATT
* *
18004659 TAG-GTATCGGTACA-TGTGTAG-GTATCGATACCC
1 T-GTGTATCGGTACACTGAGGAGTGTATCGATACCC
18004692 CCAAGTATAA
Statistics
Matches: 120, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
53 12 0.10
54 5 0.04
55 102 0.85
56 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATTGAATGCAATT
Found at i:18005081 original size:21 final size:21
Alignment explanation
Indices: 18005039--18005088 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
18005029 GTGTTAGGAA
**
18005039 AATATGAACTTTGAATATGTG
1 AATATGAACTTAAAATATGTG
18005060 AATATGAACTTCAAAATA-GTG
1 AATATGAACTT-AAAATATGTG
*
18005081 AATGTGAA
1 AATATGAA
18005089 TATACTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (21 bp):
AATATGAACTTAAAATATGTG
Found at i:18011439 original size:55 final size:55
Alignment explanation
Indices: 18011327--18011473 Score: 179
Period size: 55 Copynumber: 2.7 Consensus size: 55
18011317 TTTGTATGAG
* *
18011327 TGTGTATCGGTACACTGAGGAGTTTTATTAATACCCTCAAAACATCGAATTTCATT
1 TGTGTATCGGTACACTGAGGAG-TGTATCAATACCCTCAAAACATCGAATTTCATT
* * *
18011383 TGTGTATCGGTACACTGAGAAGTGTATCAATACCCTCAAAACATTGAGTGTT-ATT
1 TGTGTATCGGTACACTGAGGAGTGTATCAATACCCTCAAAACATCGAAT-TTCATT
* ** * *
18011438 TGTATATCAATACATTGAGGAGTGTATCGATACCCT
1 TGTGTATCGGTACACTGAGGAGTGTATCAATACCCT
18011474 TTCCATTTAG
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
55 56 0.71
56 23 0.29
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTGTATCAATACCCTCAAAACATCGAATTTCATT
Found at i:18011915 original size:21 final size:21
Alignment explanation
Indices: 18011873--18011922 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
18011863 GTGTTAGGAA
* *
18011873 AATATGAACTTTGAACATGTG
1 AATATGAAATTCGAACATGTG
18011894 AATATGAAATTCGAATCA-GTG
1 AATATGAAATTCGAA-CATGTG
*
18011915 AATGTGAA
1 AATATGAA
18011923 TATACTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (21 bp):
AATATGAAATTCGAACATGTG
Found at i:18021647 original size:21 final size:21
Alignment explanation
Indices: 18021621--18021694 Score: 139
Period size: 21 Copynumber: 3.5 Consensus size: 21
18021611 TATTCTTTGA
18021621 GTATCGATACCCAACGGAGGG
1 GTATCGATACCCAACGGAGGG
18021642 GTATCGATACCCAACGGAGGG
1 GTATCGATACCCAACGGAGGG
18021663 GTATCGATACCCAACGGAGGG
1 GTATCGATACCCAACGGAGGG
*
18021684 GTATAGATACC
1 GTATCGATACC
18021695 ATCTTCGAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.30, C:0.23, G:0.31, T:0.16
Consensus pattern (21 bp):
GTATCGATACCCAACGGAGGG
Found at i:18023417 original size:3 final size:3
Alignment explanation
Indices: 18023409--18023549 Score: 282
Period size: 3 Copynumber: 47.0 Consensus size: 3
18023399 TGTCACTATT
18023409 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18023457 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18023505 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18023550 CATCTTCACA
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 138 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18031450 original size:24 final size:24
Alignment explanation
Indices: 18031435--18031549 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
18031425 CATAATTCAC
* * *
18031435 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
* *
18031459 GTCATGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
18031483 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
18031507 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
18031531 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
18031550 ATCAAATCCA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 2 0.02
24 79 0.95
25 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:18034030 original size:18 final size:18
Alignment explanation
Indices: 18034003--18034066 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
18033993 CAACGGTCAA
*
18034003 CGGGTCGGGTCAACGGAT
1 CGGGTCGGGTCAACGGGT
* *
18034021 CGGATCGGGTCCACGGGT
1 CGGGTCGGGTCAACGGGT
*
18034039 CGGGTCGAGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
18034057 CGGGTCGGGT
1 CGGGTCGGGT
18034067 TGTGACCAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:18036224 original size:24 final size:24
Alignment explanation
Indices: 18036197--18036306 Score: 141
Period size: 24 Copynumber: 4.6 Consensus size: 24
18036187 TTCACGTTAT
* *
18036197 GTATCATATCAAAATCCAGGTCAA
1 GTATCATATCAGAATCCATGTCAA
* * * *
18036221 GTATCAGATTAGAATCCAAGTCCA
1 GTATCATATCAGAATCCATGTCAA
18036245 GTATCATATCAGAATCCATGTC-A
1 GTATCATATCAGAATCCATGTCAA
*
18036268 GATATCATATCAGAATCCATGTTAA
1 G-TATCATATCAGAATCCATGTCAA
18036293 GTATCATATCAGAA
1 GTATCATATCAGAA
18036307 ATCAAATCAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
23 2 0.03
24 71 0.95
25 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (24 bp):
GTATCATATCAGAATCCATGTCAA
Found at i:18037196 original size:20 final size:20
Alignment explanation
Indices: 18037173--18037213 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
18037163 CCATTACATT
18037173 TAAAGGTAGTCCAATACCTA
1 TAAAGGTAGTCCAATACCTA
18037193 TAAAGGTAGTCCAATACCTA
1 TAAAGGTAGTCCAATACCTA
18037213 T
1 T
18037214 GCTTACTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (20 bp):
TAAAGGTAGTCCAATACCTA
Found at i:18038899 original size:142 final size:142
Alignment explanation
Indices: 18038643--18038927 Score: 525
Period size: 142 Copynumber: 2.0 Consensus size: 142
18038633 TCGAGAAATA
*
18038643 GACTGCGGAATCGGATTTGGAACGTCGAAAAATGTCAGGATAGGTATACTCGATCAAAGTCAAAG
1 GACTGCGGAATCGGATTTGGAACGTCGAAAAATGTCAAGATAGGTATACTCGATCAAAGTCAAAG
* * *
18038708 GTAGTTTAATGCCCGATCAAATCCCTTCAAAGTTTTTGTCAACAGTGGTCAACGCCGGTCAACGG
66 GTAGTTTAATGCCCGATCAAAGCCCTTCAAAGTTTTGGTCAACAGTGGTCAACGCCGGTCAACGA
18038773 TCAACGGGTCGG
131 TCAACGGGTCGG
18038785 GACTGCGGAATCGGATTTGGAACGTCGAAAAATGTCAAGATAGGTATACTCGATCAAAGTCAAAG
1 GACTGCGGAATCGGATTTGGAACGTCGAAAAATGTCAAGATAGGTATACTCGATCAAAGTCAAAG
*
18038850 GTCGTTTAATGCCCGATCAAAGCCCTTCAAAGTTTTGGTCAACAGTGGTCAACGCCGGTCAACGA
66 GTAGTTTAATGCCCGATCAAAGCCCTTCAAAGTTTTGGTCAACAGTGGTCAACGCCGGTCAACGA
18038915 TCAACGGGTCGG
131 TCAACGGGTCGG
18038927 G
1 G
18038928 TCAATGGGTC
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 138 1.00
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (142 bp):
GACTGCGGAATCGGATTTGGAACGTCGAAAAATGTCAAGATAGGTATACTCGATCAAAGTCAAAG
GTAGTTTAATGCCCGATCAAAGCCCTTCAAAGTTTTGGTCAACAGTGGTCAACGCCGGTCAACGA
TCAACGGGTCGG
Found at i:18042257 original size:79 final size:79
Alignment explanation
Indices: 18041997--18042250 Score: 411
Period size: 79 Copynumber: 3.2 Consensus size: 79
18041987 TACATGGAAT
18041997 GATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAGA-AATGCATATGGGTGCA
1 GATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGA-ATAATGCATATGGGTGCA
*
18042061 TTATTTGCATGAAAG
65 TTATTGGCATGAAAG
* * *
18042076 GATGACATAGCTGAAATGTATATTGGTACATTGTCAGCATAAAATAATAATGCATATGGGTGCAT
1 GATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGCAT
*
18042141 TATTGGAATGAAAG
66 TATTGGCATGAAAG
* * *
18042155 GATGCCATAGCTGAAATGTATATGGGTACATTATCAGCATAAAAGAATAATGCATATGAGTGTAT
1 GATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGCAT
*
18042220 TATTGGCATGAGAG
66 TATTGGCATGAAAG
18042234 GATGCCATAGCTGAAAT
1 GATGCCATAGCTGAAAT
18042251 CCATATGAGT
Statistics
Matches: 161, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
78 1 0.01
79 160 0.99
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (79 bp):
GATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGCAT
TATTGGCATGAAAG
Found at i:18049012 original size:79 final size:79
Alignment explanation
Indices: 18048917--18049202 Score: 446
Period size: 79 Copynumber: 3.6 Consensus size: 79
18048907 ATATTACATT
*
18048917 AAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGTATAAAAGAATAATGCATATGGGT
1 AAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGT
18048982 GCATTATTGGCATG
66 GCATTATTGGCATG
* *
18048996 AAAGGATGTCATAGCTGAAATGTATATGGGTACATTGTCAACATAAAAGAATAATGCATATGGGT
1 AAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGT
18049061 GCATTATTGGCATG
66 GCATTATTGGCATG
* * * * *
18049075 AAAGGATGTCATAGATGAAATGTTTATGGGTACATTATAAGCATAAAAGAATAATGCATATGGGT
1 AAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGT
18049140 GCATTATTGGCATG
66 GCATTATTGGCATG
* * *** *
18049154 AAATGATGCCATAGCTGAAATGCATATGGGTGTGTTATCAGCATAAAAG
1 AAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAG
18049203 TACATTCTAT
Statistics
Matches: 190, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 190 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (79 bp):
AAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGT
GCATTATTGGCATG
Found at i:18053723 original size:106 final size:106
Alignment explanation
Indices: 18053581--18054113 Score: 695
Period size: 106 Copynumber: 5.1 Consensus size: 106
18053571 AATCCAAGTA
* * * * * * *
18053581 TTGTTTTGAGTCCAATATCGTCCGCAGTGAATTTGAAATTGGTTCTGGAACTGGGAAATTGTTTG
1 TTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTG
* **
18053646 TTGACAGTCAGTTGCCCCTTCGCTGTGAAGTTGAGCTTGTG
66 TTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
* * *
18053687 TTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTG
1 TTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTG
18053746 TTGACAATCAGCCGCCCCTTCG-TCGTGAAGTTGAGCTTGTG
66 TTGACAATCAGCCGCCCCTTCGCT-GTGAAGTTGAGCTTGTG
* * * * * *
18053787 TTGTCTTGGGTCCAAGATCCTTCGCTGGGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTG
1 TTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTG
* *
18053852 TTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGATTGTG
66 TTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
* *
18053893 TTGTCTTGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTTTTTG
1 TTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTG
* * *
18053958 TTGACAA-CTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG
66 TTGACAATC-AGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
* *
18053999 TTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTG
1 TTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTG
* * * * *
18054064 TTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTG
66 TTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
18054105 TTGTCTTGA
1 TTGTCTTGA
18054114 ATGGCACGAT
Statistics
Matches: 377, Mismatches: 40, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
99 1 0.00
100 80 0.21
101 3 0.01
102 5 0.01
104 4 0.01
105 4 0.01
106 278 0.74
107 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (106 bp):
TTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTG
TTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
Found at i:18054499 original size:36 final size:36
Alignment explanation
Indices: 18054449--18054519 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
18054439 TCAAAGTTTA
* *
18054449 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
*
18054485 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAAT
18054520 CTTCTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
Found at i:18054979 original size:18 final size:18
Alignment explanation
Indices: 18054952--18054987 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18054942 TGTTGAATCC
* *
18054952 CCAAAGATGCCCTAATAT
1 CCAAAAATGCCCCAATAT
18054970 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
18054988 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:18056072 original size:16 final size:17
Alignment explanation
Indices: 18056051--18056088 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
18056041 TTTGAATGTG
18056051 CTTTTTG-TCCCTTTTT
1 CTTTTTGATCCCTTTTT
**
18056067 CTTTTTGATTTCTTTTT
1 CTTTTTGATCCCTTTTT
18056084 CTTTT
1 CTTTT
18056089 GTTCTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.03, C:0.18, G:0.05, T:0.74
Consensus pattern (17 bp):
CTTTTTGATCCCTTTTT
Found at i:18056108 original size:9 final size:8
Alignment explanation
Indices: 18056079--18056139 Score: 61
Period size: 8 Copynumber: 7.5 Consensus size: 8
18056069 TTTTGATTTC
18056079 TTTTTCTT
1 TTTTTCTT
*
18056087 TTGTTCTT
1 TTTTTCTT
*
18056095 GTTTCTCTT
1 -TTTTTCTT
18056104 TTTTCTCTT
1 TTTT-TCTT
18056113 TTTTT-TT
1 TTTTTCTT
*
18056120 TTTTGCTT
1 TTTTTCTT
*
18056128 CTTTTCTT
1 TTTTTCTT
18056136 TTTT
1 TTTT
18056140 GTTCTTGATT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
7 6 0.14
8 22 0.52
9 14 0.33
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (8 bp):
TTTTTCTT
Found at i:18056112 original size:18 final size:15
Alignment explanation
Indices: 18056075--18056139 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 15
18056065 TTCTTTTTGA
18056075 TTTC-TTTTTCTTTT
1 TTTCTTTTTTCTTTT
*
18056089 GTTCTTGTTTCTCTTTT
1 TTTCTT-TTT-TCTTTT
18056106 TTCTCTTTTTT-TTTT
1 TT-TCTTTTTTCTTTT
18056121 TTTGCTTCTTTTCTTTT
1 TTT-CTT-TTTTCTTTT
18056138 TT
1 TT
18056140 GTTCTTGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 4 0.10
15 10 0.24
16 8 0.19
17 16 0.38
18 4 0.10
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (15 bp):
TTTCTTTTTTCTTTT
Found at i:18056132 original size:15 final size:15
Alignment explanation
Indices: 18056082--18056145 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
18056072 TGATTTCTTT
* * *
18056082 TTCTTTTGTTCTTGT
1 TTCTTTTTTTTTTGC
* *
18056097 TTCTCTTTTTTCT-C
1 TTCTTTTTTTTTTGC
*
18056111 TTTTTTTTTTTTTGC
1 TTCTTTTTTTTTTGC
18056126 TTCTTTTCTTTTTTG-
1 TTCTTTT-TTTTTTGC
18056141 TTCTT
1 TTCTT
18056146 GATTGGATCT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
14 10 0.26
15 21 0.55
16 7 0.18
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (15 bp):
TTCTTTTTTTTTTGC
Found at i:18056136 original size:32 final size:31
Alignment explanation
Indices: 18056063--18056139 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
18056053 TTTTGTCCCT
* *
18056063 TTTTCTTTTTGATTTCTTTTTCTTTTGTTCTTG
1 TTTTCTTTTT--TCTCTTTTTCTTTTGTTCTTC
* *
18056096 TTTCTCTTTTTTCTCTTTTTTTTTTTTTGCTTC
1 TTT-TCTTTTTTCTCTTTTTCTTTTGTT-CTTC
18056129 TTTTCTTTTTT
1 TTTTCTTTTTT
18056140 GTTCTTGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
32 22 0.58
33 9 0.24
34 7 0.18
ACGTcount: A:0.01, C:0.14, G:0.05, T:0.79
Consensus pattern (31 bp):
TTTTCTTTTTTCTCTTTTTCTTTTGTTCTTC
Found at i:18069894 original size:24 final size:24
Alignment explanation
Indices: 18069867--18069973 Score: 117
Period size: 24 Copynumber: 4.5 Consensus size: 24
18069857 GTAAACGGAG
*
18069867 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCATAACAGAATTC
* * *
18069891 ATATCAGATATCATAATAGAATCC
1 ATATCAGAAATCATAACAGAATTC
* *
18069915 ATGTCAAAAATCATAACAGAATTC
1 ATATCAGAAATCATAACAGAATTC
*
18069939 ATATCA-AGTATCATAACAGAATTC
1 ATATCAGA-AATCATAACAGAATTC
* *
18069963 AAATCGGAAAT
1 ATATCAGAAAT
18069974 AAGATAAAAC
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
23 1 0.01
24 65 0.97
25 1 0.01
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (24 bp):
ATATCAGAAATCATAACAGAATTC
Found at i:18069898 original size:12 final size:12
Alignment explanation
Indices: 18069867--18069963 Score: 56
Period size: 12 Copynumber: 8.1 Consensus size: 12
18069857 GTAAACGGAG
*
18069867 ATATCAGAAATC
1 ATATCAGAATTC
* *
18069879 AAAACAGAATTC
1 ATATCAGAATTC
18069891 ATATCAG-ATATC
1 ATATCAGAAT-TC
*
18069903 ATAAT-AGAATCC
1 AT-ATCAGAATTC
* * *
18069915 ATGTCAAAAATC
1 ATATCAGAATTC
*
18069927 ATAACAGAATTC
1 ATATCAGAATTC
*
18069939 ATATCA-AGTATC
1 ATATCAGAAT-TC
*
18069951 ATAACAGAATTC
1 ATATCAGAATTC
18069963 A
1 A
18069964 AATCGGAAAT
Statistics
Matches: 61, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
11 5 0.08
12 50 0.82
13 6 0.10
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.26
Consensus pattern (12 bp):
ATATCAGAATTC
Found at i:18072504 original size:18 final size:19
Alignment explanation
Indices: 18072481--18072524 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
18072471 CAACAGTCAA
18072481 CGGGTCAGCTC-AACGGGT
1 CGGGTCAGCTCAAACGGGT
* *
18072499 CGGGTCAGGTCAAATGGGT
1 CGGGTCAGCTCAAACGGGT
18072518 CGGGTCA
1 CGGGTCA
18072525 AAACTGGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.18, C:0.23, G:0.41, T:0.18
Consensus pattern (19 bp):
CGGGTCAGCTCAAACGGGT
Found at i:18078527 original size:21 final size:20
Alignment explanation
Indices: 18078500--18078597 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
18078490 AATCAGTGTC
18078500 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
18078521 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
18078541 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
18078561 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
18078582 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
18078598 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:18078550 original size:41 final size:41
Alignment explanation
Indices: 18078441--18078597 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
18078431 AAATGACCAA
* **
18078441 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
18078480 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
18078521 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
18078562 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
18078598 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:18078607 original size:20 final size:20
Alignment explanation
Indices: 18078584--18078774 Score: 129
Period size: 20 Copynumber: 9.6 Consensus size: 20
18078574 GCGAATATGA
18078584 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
18078604 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
18078624 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
18078644 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
18078664 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
18078684 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
18078704 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
18078724 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
18078744 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
18078764 AAATCGCAACG
1 AAATCGCAACG
18078775 AGAATCTGTA
Statistics
Matches: 151, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.01
20 147 0.97
21 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:18078628 original size:40 final size:40
Alignment explanation
Indices: 18078564--18078793 Score: 232
Period size: 40 Copynumber: 5.8 Consensus size: 40
18078554 CGATTTTCCA
* ** * *
18078564 AAATCGCAACGCGAATATGAAAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAAC-CGT
* * *
18078604 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGT
* * *
18078644 AAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGT
*
18078684 AAATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAA-CCGT
* * * *
18078724 AAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAA-CCGT
* * * *
18078764 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGCGTATCCGTAAATCGCAAC
18078794 ACTGAAATTT
Statistics
Matches: 168, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 164 0.98
41 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGT
Found at i:18078649 original size:60 final size:59
Alignment explanation
Indices: 18078584--18078793 Score: 233
Period size: 60 Copynumber: 3.5 Consensus size: 59
18078574 GCGAATATGA
* *
18078584 AAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAAC-CGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
** * *
18078644 AAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCG-AACCGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
** * * * *
18078704 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGAT-AATCCGT
1 AAATCGCAACGCGAA-CCGTAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGT
* * *
18078764 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGCGAA-CCGTAAATCGCAAC
18078794 ACTGAAATTT
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
60 127 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (59 bp):
AAATCGCAACGCGAACCGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
Found at i:18078775 original size:20 final size:20
Alignment explanation
Indices: 18078618--18078793 Score: 189
Period size: 20 Copynumber: 8.8 Consensus size: 20
18078608 CGCAATGCGT
*
18078618 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
18078638 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
18078658 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
*
18078678 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
18078698 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
18078718 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
18078738 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
18078758 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
18078778 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
18078794 ACTGAAATTT
Statistics
Matches: 141, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
19 1 0.01
20 139 0.99
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:18079515 original size:24 final size:24
Alignment explanation
Indices: 18079476--18079522 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
18079466 AAATTTGGTC
18079476 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
18079500 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
18079523 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:18079714 original size:12 final size:12
Alignment explanation
Indices: 18079697--18079721 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18079687 ATATAATCCT
18079697 GAAGAAGAAAAA
1 GAAGAAGAAAAA
18079709 GAAGAAGAAAAA
1 GAAGAAGAAAAA
18079721 G
1 G
18079722 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Done.