Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 60 of 213
Found at i:16244459 original size:75 final size:75
Alignment explanation
Indices: 16244372--16245210 Score: 1366
Period size: 75 Copynumber: 11.2 Consensus size: 75
16244362 AACCATTTTT
* * * * *
16244372 TTTCTATTTTTCAAAAATCAACTCATAATCTGATAGGTGAGTTGAGCCTCGGGTCACAAGCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
16244437 GTATTTTCAA
66 GTATTTTCAA
* * * * * *
16244447 TTTCTGTTTTTCAAAAATCAACTTATAATCGGAGAGGTGAGTTGAGCATTGGGTTGCAGGCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
16244512 GTATTTTCAA
66 GTATTTTCAA
* *
16244522 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCT-GGGTTGCAGGCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
16244586 GTATTTTCAA
66 GTATTTTCAA
16244596 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
16244661 GTATTTTCAA
66 GTATTTTCAA
*
16244671 TTTCTGTTTTTCAAAAATCAACTCATAATCTGAGAGGTG-GTTTGAGCCTCGGGTCGCACGCTGA
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAG-TTGAGCCTCGGGTCGCACGCTGA
16244735 GGTACTTTT-AA
65 GGTA-TTTTCAA
* *
16244746 TTTCTGTTTTTAAAAAATTAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
16244811 GTATTTTCAA
66 GTATTTTCAA
16244821 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
*
16244886 GTATTTTTAA
66 GTATTTTCAA
* *
16244896 TTTCTGTTTTTCAAAAATCAACTCATAATCTGAGAGGTG-GTTTGAGCCTCGGGTCGCACACTGA
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAG-TTGAGCCTCGGGTCGCACGCTGA
*
16244960 GGTCCTTTT-AA
65 GGT-ATTTTCAA
*
16244971 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACACTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
16245036 GTATTTTCAA
66 GTATTTTCAA
16245046 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
16245111 GTATTTTCAA
66 GTATTTTCAA
* *
16245121 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTTGCACGCCGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
*
16245186 GTGTTTTCAA
66 GTATTTTCAA
* *
16245196 GTTC-CTTTTTCAAAA
1 TTTCTGTTTTTCAAAA
16245211 TTTTTTTTTT
Statistics
Matches: 723, Mismatches: 32, Indels: 19
0.93 0.04 0.02
Matches are distributed among these distances:
74 94 0.13
75 619 0.86
76 10 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (75 bp):
TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
GTATTTTCAA
Found at i:16245533 original size:29 final size:29
Alignment explanation
Indices: 16245495--16245593 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
16245485 AAAATTTTAA
* *
16245495 ATTTTGACCCCTAACTTTTTTAAAATTAT
1 ATTTTAACCCCTAACTTTTTTAAAATTAC
*
16245524 ATTTTAACCCTTAAACTTTTTTAAAATTAC
1 ATTTTAACCCCT-AACTTTTTTAAAATTAC
** *
16245554 ATTTTAACCCCTTAAC-TTCCTAAAATTGC
1 ATTTTAACCCC-TAACTTTTTTAAAATTAC
*
16245583 ACTTTAACCCC
1 ATTTTAACCCC
16245594 AAAAGTTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 30 0.50
30 29 0.48
31 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.42
Consensus pattern (29 bp):
ATTTTAACCCCTAACTTTTTTAAAATTAC
Found at i:16246139 original size:20 final size:21
Alignment explanation
Indices: 16246098--16246163 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
16246088 AAACAAAACG
*
16246098 AGAAG-GAAAAAAGGAGGAAGAA
1 AGAAGAGAAAAAAAGA-G-AGAA
*
16246120 AGGAGA-AAAAAAAGAGAGAA
1 AGAAGAGAAAAAAAGAGAGAA
* *
16246140 AGAAGAGAAGAAAAGA-AAAA
1 AGAAGAGAAAAAAAGAGAGAA
16246160 AGAA
1 AGAA
16246164 AATATGAGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 16 0.43
21 9 0.24
22 12 0.32
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (21 bp):
AGAAGAGAAAAAAAGAGAGAA
Found at i:16246142 original size:24 final size:24
Alignment explanation
Indices: 16246104--16246158 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
16246094 AACGAGAAGG
* *
16246104 AAAAAAGGAGGAAGAA-AGGAGAA
1 AAAAAAGGAGAAAGAAGAGAAGAA
16246127 AAAAAAGAGAGAAAGAAGAGAAGAA
1 AAAAAAG-GAGAAAGAAGAGAAGAA
16246152 AAGAAAA
1 AA-AAAA
16246159 AAGAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 7 0.26
24 8 0.30
25 8 0.30
26 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (24 bp):
AAAAAAGGAGAAAGAAGAGAAGAA
Found at i:16246287 original size:6 final size:6
Alignment explanation
Indices: 16246272--16246326 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
16246262 AAGAAGGAGC
*
16246272 AAAAAGG AAAAAG AAAGAA- AAAGAAG AAAAA- AGAAAG AAAAAAG AAAAAG
1 AAAAA-G AAAAAG AAA-AAG AAA-AAG AAAAAG AAAAAG -AAAAAG AAAAAG
16246322 AAAAA
1 AAAAA
16246327 AATAAAAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
5 4 0.10
6 23 0.55
7 15 0.36
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:16246291 original size:10 final size:10
Alignment explanation
Indices: 16246278--16246328 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
16246268 GAGCAAAAAG
16246278 GAAAAAGAAA
1 GAAAAAGAAA
16246288 GAAAAAG-AA
1 GAAAAAGAAA
16246297 GAAAAAAGAAA
1 G-AAAAAGAAA
16246308 G--AAA-AAA
1 GAAAAAGAAA
16246315 GAAAAAGAAA
1 GAAAAAGAAA
16246325 -AAAA
1 GAAAA
16246329 TAAAAACAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
7 4 0.11
8 3 0.08
9 10 0.28
10 16 0.44
11 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
GAAAAAGAAA
Found at i:16246293 original size:11 final size:11
Alignment explanation
Indices: 16246274--16246318 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
16246264 GAAGGAGCAA
*
16246274 AAAGGAAAAAG
1 AAAGAAAAAAG
16246285 AAAG-AAAAAG
1 AAAGAAAAAAG
16246295 -AAGAAAAAAG
1 AAAGAAAAAAG
16246305 AAAGAAAAAAG
1 AAAGAAAAAAG
16246316 AAA
1 AAA
16246319 AAGAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 3 0.09
10 12 0.38
11 17 0.53
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:16246302 original size:20 final size:18
Alignment explanation
Indices: 16246272--16246328 Score: 73
Period size: 17 Copynumber: 3.2 Consensus size: 18
16246262 AAGAAGGAGC
*
16246272 AAAAAGGAAAAAGAAAGA
1 AAAAAAGAAAAAGAAAGA
16246290 AAAAGAAGAAAAAAGAAAG-
1 AAAA-AAG-AAAAAGAAAGA
16246309 AAAAAAGAAAAAGAAA-A
1 AAAAAAGAAAAAGAAAGA
16246326 AAA
1 AAA
16246329 TAAAAACAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 12 0.34
18 7 0.20
19 6 0.17
20 10 0.29
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAGAAAGA
Found at i:16246307 original size:7 final size:7
Alignment explanation
Indices: 16246272--16246340 Score: 51
Period size: 7 Copynumber: 10.6 Consensus size: 7
16246262 AAGAAGGAGC
*
16246272 AAAAAGG
1 AAAAAGA
16246279 AAAAAGA
1 AAAAAGA
*
16246286 AAGAA-A
1 AAAAAGA
*
16246292 AAGAAGA
1 AAAAAGA
16246299 AAAAAG-
1 AAAAAGA
16246305 --AAAGA
1 AAAAAGA
16246310 AAAAAG-
1 AAAAAGA
16246316 AAAAAGA
1 AAAAAGA
16246323 AAAAA-A
1 AAAAAGA
*
16246329 TAAAAACA
1 -AAAAAGA
16246337 AAAA
1 AAAA
16246341 GGATAGGTCG
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
4 4 0.08
6 13 0.25
7 34 0.65
8 1 0.02
ACGTcount: A:0.83, C:0.01, G:0.14, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:16246308 original size:24 final size:24
Alignment explanation
Indices: 16246273--16246327 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 24
16246263 AGAAGGAGCA
*
16246273 AAAAGGAAAAAGAAAG-AAAAAG-
1 AAAAGAAAAAAGAAAGAAAAAAGA
16246295 --AAGAAAAAAGAAAGAAAAAAGA
1 AAAAGAAAAAAGAAAGAAAAAAGA
16246317 AAAAGAAAAAA
1 AAAAGAAAAAA
16246328 ATAAAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 13 0.46
21 6 0.21
24 9 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (24 bp):
AAAAGAAAAAAGAAAGAAAAAAGA
Found at i:16246339 original size:27 final size:27
Alignment explanation
Indices: 16246285--16246340 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
16246275 AAGGAAAAAG
* *
16246285 AAAGAAAAAGAAGAAAAAAGAAAGAAA
1 AAAGAAAAAGAAGAAAAAAAAAACAAA
16246312 AAAGAAAAAGAA-AAAAATAAAAACAAA
1 AAAGAAAAAGAAGAAAAA-AAAAACAAA
16246339 AA
1 AA
16246341 GGATAGGTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (27 bp):
AAAGAAAAAGAAGAAAAAAAAAACAAA
Found at i:16246504 original size:26 final size:26
Alignment explanation
Indices: 16246468--16246520 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
16246458 AGCCCAATCC
* * *
16246468 AGCAAGCCCAGTAGGCTAACAGTAGT
1 AGCAAGCCCAGCAGGCCAACAGCAGT
*
16246494 AGCAGGCCCAGCAGGCCAACAGCAGT
1 AGCAAGCCCAGCAGGCCAACAGCAGT
16246520 A
1 A
16246521 ATCCGACAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.28, G:0.28, T:0.09
Consensus pattern (26 bp):
AGCAAGCCCAGCAGGCCAACAGCAGT
Found at i:16251983 original size:61 final size:61
Alignment explanation
Indices: 16251878--16251995 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 61
16251868 TGAATCTGTT
* ** *
16251878 AAAATACTCGGTTACTTACATCTGTTTCTTTTTCCATAACAAAGATATAAAATCAAAGAAG
1 AAAATACTCGGTTACTTAAATCAATTTCTTTTTCCAAAACAAAGATATAAAATCAAAGAAG
* * *
16251939 AAAATACTTGGTTATTTAAATCAATTTCTTTTGT-CAAAATAAAGATATAAAATCAAA
1 AAAATACTCGGTTACTTAAATCAATTTCTTTT-TCCAAAACAAAGATATAAAATCAAA
16251996 CGGTAATTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
61 48 0.98
62 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (61 bp):
AAAATACTCGGTTACTTAAATCAATTTCTTTTTCCAAAACAAAGATATAAAATCAAAGAAG
Found at i:16254843 original size:44 final size:45
Alignment explanation
Indices: 16254789--16254894 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
16254779 GATAATGTGT
*
16254789 TTGCAAAACTGAGAAGAT-ATAAGAA-AAGGAAAACACGTAGATGC
1 TTGCAAAACTGAGAAGATAATAAGAACAA-GAAAACACATAGATGC
* *
16254833 TTGCAGAACTGAGAAGATAATAAGAACAAGAAAACACATAGATGT
1 TTGCAAAACTGAGAAGATAATAAGAACAAGAAAACACATAGATGC
16254878 TTGCAAAACTGAGAAGA
1 TTGCAAAACTGAGAAGA
16254895 ACATATTGAC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
44 17 0.30
45 37 0.66
46 2 0.04
ACGTcount: A:0.50, C:0.11, G:0.22, T:0.17
Consensus pattern (45 bp):
TTGCAAAACTGAGAAGATAATAAGAACAAGAAAACACATAGATGC
Found at i:16259915 original size:15 final size:13
Alignment explanation
Indices: 16259883--16259915 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
16259873 ACAAAAAAAA
16259883 TTATATATATATT
1 TTATATATATATT
*
16259896 TTATATATTTATT
1 TTATATATATATT
16259909 TTATATA
1 TTATATA
16259916 GTCTAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATATATATATT
Found at i:16265124 original size:45 final size:44
Alignment explanation
Indices: 16265054--16265258 Score: 200
Period size: 45 Copynumber: 4.6 Consensus size: 44
16265044 GCTATACGCC
*
16265054 TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGA
1 TAAAATGAGAAAGACCATAGCTGAAAGATGTTATGGCATCATGA
** * **
16265098 TAAAGATGAGAAAGACCATAATTGAAAGATTTTATGGCATCACCA
1 TAAA-ATGAGAAAGACCATAGCTGAAAGATGTTATGGCATCATGA
* *
16265143 TAAAGATGAGTAAA-ACCATAGCTGAAAGACGCTATGGCATCATGA
1 TAAA-ATGAG-AAAGACCATAGCTGAAAGATGTTATGGCATCATGA
* * ** * *
16265188 TATAAATGAGTAAGACCATGGCTGAAAGATACTATGACATCATGG
1 TA-AAATGAGAAAGACCATAGCTGAAAGATGTTATGGCATCATGA
*
16265233 TAACAA-GACTAAA-ACCATAGCTGAAA
1 TAA-AATGA-GAAAGACCATAGCTGAAA
16265259 CAAGAGGATA
Statistics
Matches: 133, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
44 21 0.16
45 107 0.80
46 5 0.04
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (44 bp):
TAAAATGAGAAAGACCATAGCTGAAAGATGTTATGGCATCATGA
Found at i:16265214 original size:90 final size:89
Alignment explanation
Indices: 16265054--16265258 Score: 243
Period size: 90 Copynumber: 2.3 Consensus size: 89
16265044 GCTATACGCC
* * *
16265054 TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATAAAGATGAGAAAGACCATAA
1 TAAAATGAGTAAAACCATAGCTGAAAGACGCTATGGCATCATGATAAAGATGAGAAAGACCATAA
*
16265119 TTGAAAGATTTTATGGCATCACCA
66 CTGAAAGATTTTATGGCATCACCA
*
16265143 TAAAGATGAGTAAAACCATAGCTGAAAGACGCTATGGCATCATGATATAA-ATGAGTAAGACCAT
1 TAAA-ATGAGTAAAACCATAGCTGAAAGACGCTATGGCATCATGATA-AAGATGAGAAAGACCAT
** ** * ***
16265207 GGCTGAAAGATACTATGACATCATGG
64 AACTGAAAGATTTTATGGCATCACCA
*
16265233 TAACAA-GACTAAAACCATAGCTGAAA
1 TAA-AATGAGTAAAACCATAGCTGAAA
16265259 CAAGAGGATA
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
89 23 0.23
90 73 0.74
91 3 0.03
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (89 bp):
TAAAATGAGTAAAACCATAGCTGAAAGACGCTATGGCATCATGATAAAGATGAGAAAGACCATAA
CTGAAAGATTTTATGGCATCACCA
Found at i:16266290 original size:34 final size:34
Alignment explanation
Indices: 16266247--16266314 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
16266237 ACGATGAAAG
*
16266247 GGTTATATACCCGCCAATAAATAAGAATTCACAT
1 GGTTATATACCCGCAAATAAATAAGAATTCACAT
*
16266281 GGTTATATACCCTCAAATAAATAAGAATTCACAT
1 GGTTATATACCCGCAAATAAATAAGAATTCACAT
16266315 TCGTCAAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (34 bp):
GGTTATATACCCGCAAATAAATAAGAATTCACAT
Found at i:16267577 original size:45 final size:44
Alignment explanation
Indices: 16267507--16267727 Score: 156
Period size: 45 Copynumber: 4.9 Consensus size: 44
16267497 GGCTATACGC
*
16267507 ATAAAATGAGTAAGAACGTAGCTAAAAGATTCTATGGCATCATG
1 ATAAAATGAGTAAGACCGTAGCTAAAAGATTCTATGGCATCATG
* * **
16267551 ATAAAGATGAGTAAGACCGTAACTAAAAGATGT-TATGACATCACC
1 ATAAA-ATGAGTAAGACCGTAGCTAAAAGAT-TCTATGGCATCATG
* * * * * **
16267596 ATAAAAATTAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
1 AT-AAAATGAGTAAGACCGTAGCTAAAAGATTCTATGGCATCATG
* * * * * * * *
16267641 ATATAAATGAATAAGACCATGGTTGAAAGATGCTATGACATTATG
1 ATA-AAATGAGTAAGACCGTAGCTAAAAGATTCTATGGCATCATG
* * * * **
16267686 GTAAACATGACTAAGACCATAGCTGAAAGACACTATGGCATC
1 ATAAA-ATGAGTAAGACCGTAGCTAAAAGATTCTATGGCATC
16267728 CTAGTAGTCT
Statistics
Matches: 139, Mismatches: 32, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
44 8 0.06
45 127 0.91
46 4 0.03
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (44 bp):
ATAAAATGAGTAAGACCGTAGCTAAAAGATTCTATGGCATCATG
Found at i:16267670 original size:90 final size:90
Alignment explanation
Indices: 16267538--16267727 Score: 220
Period size: 90 Copynumber: 2.1 Consensus size: 90
16267528 CTAAAAGATT
* * *
16267538 CTATGGCATCATGATAAAGATGAGTAAGACCGTAACTAAAAGATGTTATGACATCACCATAAAAA
1 CTATGGCATCATGATAAAGATGAATAAGACCATAACTAAAAGATGCTATGACATCACCATAAAAA
* * *
16267603 TTAGTAAAACCATAGTTGAAAGACA
66 TGACTAAAACCATAGCTGAAAGACA
*** * * *** *
16267628 CTATGGCATCATGATATAA-ATGAATAAGACCATGGTTGAAAGATGCTATGACATTATGGTAAAC
1 CTATGGCATCATGATA-AAGATGAATAAGACCATAACTAAAAGATGCTATGACATCACCATAAAA
*
16267692 ATGACTAAGACCATAGCTGAAAGACA
65 ATGACTAAAACCATAGCTGAAAGACA
16267718 CTATGGCATC
1 CTATGGCATC
16267728 CTAGTAGTCT
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
90 81 0.98
91 2 0.02
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (90 bp):
CTATGGCATCATGATAAAGATGAATAAGACCATAACTAAAAGATGCTATGACATCACCATAAAAA
TGACTAAAACCATAGCTGAAAGACA
Found at i:16267821 original size:16 final size:16
Alignment explanation
Indices: 16267800--16267831 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16267790 ATCGTGTAAG
16267800 ACCATAGTTGAAAGAT
1 ACCATAGTTGAAAGAT
16267816 ACCATAGTTGAAAGAT
1 ACCATAGTTGAAAGAT
16267832 GCTATGGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (16 bp):
ACCATAGTTGAAAGAT
Found at i:16281159 original size:22 final size:21
Alignment explanation
Indices: 16281128--16281186 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
16281118 CGATCAGTTT
*
16281128 TTTTTATATTTTAAGTTTTT-A
1 TTTTAATATTTTAA-TTTTTAA
*
16281149 TTTTAATTATTGTAATTTTTGAA
1 TTTTAA-TATTTTAATTTTT-AA
*
16281172 TTTTAAAATTTTAAT
1 TTTTAATATTTTAAT
16281187 CTCGATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 10 0.32
22 14 0.45
23 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTAATATTTTAATTTTTAA
Found at i:16285946 original size:19 final size:19
Alignment explanation
Indices: 16285922--16285958 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
16285912 TATGCTGCAC
16285922 TATAAATAAT-TATTTATAA
1 TATAAA-AATATATTTATAA
16285941 TATAAAAATATATTTATA
1 TATAAAAATATATTTATA
16285959 TATTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAAAAATATATTTATAA
Found at i:16286012 original size:31 final size:31
Alignment explanation
Indices: 16285976--16286062 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
16285966 TTTTGAAAGG
16285976 TATACAATTAAATCAAAATTAAAATTTCATA
1 TATACAATTAAATCAAAATTAAAATTTCATA
* * *
16286007 TATAC-ATATAAACCACAATAAAAATTTCATA
1 TATACAAT-TAAATCAAAATTAAAATTTCATA
* * * *
16286038 TTTATAGTTACATC-AAATTAAAATT
1 TATACAATTAAATCAAAATTAAAATT
16286063 CTTGTGTCAA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
30 11 0.25
31 32 0.73
32 1 0.02
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (31 bp):
TATACAATTAAATCAAAATTAAAATTTCATA
Found at i:16287187 original size:22 final size:21
Alignment explanation
Indices: 16287156--16287205 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
16287146 TTAAAATTAA
* *
16287156 AAAAAT-AAATAGAACTCTGAT
1 AAAAATAAAATAAAAC-CTCAT
*
16287177 AAAAATAAAATAAAACCTCCT
1 AAAAATAAAATAAAACCTCAT
16287198 AAAAATAA
1 AAAAATAA
16287206 GTTAAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.64, C:0.12, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAAATAAAATAAAACCTCAT
Found at i:16296730 original size:18 final size:18
Alignment explanation
Indices: 16296703--16296745 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16296693 CGCATAAAAA
* *
16296703 GAAAGCAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
16296721 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
16296739 GAAAGAA
1 GAAAGAA
16296746 GGGGGGAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:16308919 original size:15 final size:16
Alignment explanation
Indices: 16308890--16308919 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16308880 CAAACATGCT
16308890 TTAACACATTATCAAA
1 TTAACACATTATCAAA
16308906 TTAACACA-TATCAA
1 TTAACACATTATCAA
16308920 CATGGCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:16309394 original size:20 final size:19
Alignment explanation
Indices: 16309367--16309408 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
16309357 CTTTCCAAAT
16309367 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
16309386 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
16309406 TTT
1 TTT
16309409 ACTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:16316009 original size:24 final size:24
Alignment explanation
Indices: 16315975--16316060 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
16315965 TACTACAAAA
* *
16315975 CACTTATAGAATACGTAACAAAGG
1 CACTTACAGAATACGCAACAAAGG
*
16315999 TACTTACAGAATACGCCAA-AAAGG
1 CACTTACAGAATACG-CAACAAAGG
* *
16316023 CACTTACAGAATACCCCACAAAGG
1 CACTTACAGAATACGCAACAAAGG
*
16316047 CACTTACGGAATAC
1 CACTTACAGAATAC
16316061 CCTGCTTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 2 0.04
24 49 0.92
25 2 0.04
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.17
Consensus pattern (24 bp):
CACTTACAGAATACGCAACAAAGG
Found at i:16316061 original size:24 final size:24
Alignment explanation
Indices: 16315992--16316062 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
16315982 AGAATACGTA
* *
16315992 ACAAAGGTACTTACAGAATACGCC
1 ACAAAGGCACTTACAGAATACCCC
*
16316016 AAAAAGGCACTTACAGAATACCCC
1 ACAAAGGCACTTACAGAATACCCC
*
16316040 ACAAAGGCACTTACGGAATACCC
1 ACAAAGGCACTTACAGAATACCC
16316063 TGCTTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.42, C:0.28, G:0.15, T:0.14
Consensus pattern (24 bp):
ACAAAGGCACTTACAGAATACCCC
Found at i:16327080 original size:40 final size:40
Alignment explanation
Indices: 16327038--16327112 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
16327028 ATATTTTTAT
*
16327038 TTTTTTTTA-TTTTTTAATTTTAAAATACTTTTAAAATAA
1 TTTTTTTAATTTTTTTAATTTTAAAATACTTTTAAAATAA
**
16327077 TTTTTTTAATTTTTTTAATTTTAAAATTTTTTTAAA
1 TTTTTTTAATTTTTTTAATTTTAAAATACTTTTAAA
16327113 TTTTTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 8 0.25
40 24 0.75
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (40 bp):
TTTTTTTAATTTTTTTAATTTTAAAATACTTTTAAAATAA
Found at i:16327088 original size:9 final size:9
Alignment explanation
Indices: 16327074--16327119 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
16327064 ACTTTTAAAA
16327074 TAATTTTTT
1 TAATTTTTT
16327083 TAATTTTTT
1 TAATTTTTT
*
16327092 TAA-TTTTA
1 TAATTTTTT
*
16327100 AAATTTTTT
1 TAATTTTTT
16327109 TAAATTTTTT
1 T-AATTTTTT
16327119 T
1 T
16327120 TAAAATACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
8 6 0.19
9 16 0.52
10 9 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TAATTTTTT
Found at i:16327109 original size:11 final size:11
Alignment explanation
Indices: 16327095--16327144 Score: 64
Period size: 11 Copynumber: 4.3 Consensus size: 11
16327085 ATTTTTTTAA
16327095 TTTTAAAATTT
1 TTTTAAAATTT
*
16327106 TTTTAAATTTT
1 TTTTAAAATTT
16327117 TTTTAAAATACTTT
1 TTTT-AAA-A-TTT
16327131 TTTTAAAATTT
1 TTTTAAAATTT
16327142 TTT
1 TTT
16327145 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 20 0.59
12 4 0.12
13 3 0.09
14 7 0.21
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:16327111 original size:26 final size:25
Alignment explanation
Indices: 16327075--16327163 Score: 92
Period size: 25 Copynumber: 3.4 Consensus size: 25
16327065 CTTTTAAAAT
16327075 AATTTTTTTAATTTTTTTAATTTTAA
1 AATTTTTTTAA-TTTTTTAATTTTAA
* *
16327101 AATTTTTTTAAATTTTT--TTTAAA
1 AATTTTTTTAATTTTTTAATTTTAA
16327124 ATACTTTTTTTAAAATTTTTTAATTTTAA
1 A-A-TTTTTTT--AATTTTTTAATTTTAA
*
16327153 AATATTTTTAA
1 AATTTTTTTAA
16327164 AATACTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
23 6 0.12
24 1 0.02
25 14 0.27
26 11 0.21
27 13 0.25
28 1 0.02
29 6 0.12
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (25 bp):
AATTTTTTTAATTTTTTAATTTTAA
Found at i:16327121 original size:51 final size:52
Alignment explanation
Indices: 16327055--16327194 Score: 173
Period size: 52 Copynumber: 2.7 Consensus size: 52
16327045 TATTTTTTAA
16327055 TTTTAAAATAC--TTTTAAAATAATTTTTTTAATTTTTTTAATTTTAAAAT-T
1 TTTTAAAATACTTTTTTAAAAT-ATTTTTTTAATTTTTTTAATTTTAAAATAT
* * *
16327105 TTTTTAAAT-TTTTTTTAAAATACTTTTTTTAAAATTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTTAAAATA-TTTTTTT-AATTTTTTTAATTTTAAAATAT
*
16327158 TTTTAAAATACTTTTTTAAACT-TTTATTTTAATTTTT
1 TTTTAAAATACTTTTTTAAAATATTT-TTTTAATTTTT
16327195 AAAATAAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
50 9 0.12
51 16 0.21
52 28 0.37
53 13 0.17
54 10 0.13
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (52 bp):
TTTTAAAATACTTTTTTAAAATATTTTTTTAATTTTTTTAATTTTAAAATAT
Found at i:16327151 original size:41 final size:40
Alignment explanation
Indices: 16327106--16327200 Score: 118
Period size: 41 Copynumber: 2.2 Consensus size: 40
16327096 TTTAAAATTT
* *
16327106 TTTTAAATTTTTTTTAAAATACTTTTTTTAAAATTTTTTAA
1 TTTTAAAATATTTTTAAAATAC-TTTTTTAAAATTTTTTAA
*
16327147 TTTTAAAATATTTTTAAAATACTTTTTTAAACTTTTATTTTAA
1 TTTTAAAATATTTTTAAAATACTTTTTTAAA--ATT-TTTTAA
16327190 TTTTTAAAATA
1 -TTTTAAAATA
16327201 AATTTTTGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
40 9 0.19
41 20 0.43
42 2 0.04
43 6 0.13
44 10 0.21
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (40 bp):
TTTTAAAATATTTTTAAAATACTTTTTTAAAATTTTTTAA
Found at i:16327161 original size:11 final size:11
Alignment explanation
Indices: 16327095--16327173 Score: 53
Period size: 11 Copynumber: 7.4 Consensus size: 11
16327085 ATTTTTTTAA
*
16327095 TTTTAAAATTT
1 TTTTAAAATAT
* *
16327106 TTTTAAATTTT
1 TTTTAAAATAT
16327117 TTTTAAAATACTTT
1 TTTTAAAATA---T
16327131 TTTTAAAAT-T
1 TTTTAAAATAT
16327141 TTTT---A-A-
1 TTTTAAAATAT
16327147 TTTTAAAATAT
1 TTTTAAAATAT
16327158 TTTTAAAATACT
1 TTTTAAAATA-T
16327170 TTTT
1 TTTT
16327174 TAAACTTTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
6 4 0.07
7 1 0.02
9 1 0.02
10 6 0.11
11 28 0.51
12 5 0.09
14 10 0.18
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:16327567 original size:19 final size:18
Alignment explanation
Indices: 16327540--16327578 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
16327530 AATTGCGTGT
* *
16327540 TGAATAGAAATAAACGAAA
1 TGAAAAGAAA-AAAAGAAA
16327559 TGAAAAGAAAAAAAGAAA
1 TGAAAAGAAAAAAAGAAA
16327577 TG
1 TG
16327579 GGAAACATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.18, T:0.13
Consensus pattern (18 bp):
TGAAAAGAAAAAAAGAAA
Found at i:16330685 original size:41 final size:41
Alignment explanation
Indices: 16330623--16330730 Score: 171
Period size: 41 Copynumber: 2.6 Consensus size: 41
16330613 TGATCTAGTA
*
16330623 CACCGACATTAAGCCTGCTAGACATATAGTCTGAAATATTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATATTT
* *
16330664 CACCGGCATTAAGCCTACTAGACGTATAGTCTGAAATATTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATATTT
* *
16330705 CACTGGCATTAAGCCTGCTAGGCATA
1 CACCGGCATTAAGCCTGCTAGACATA
16330731 AGCTTAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:16342942 original size:37 final size:37
Alignment explanation
Indices: 16342891--16342974 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
16342881 GAAACATCAT
* **
16342891 GTTTCGATACTAAACTAAAATAATAAATCTAGTTTCC
1 GTTTCGATATTAAACTAAAATAATAAATCTAAATTCC
* *
16342928 GTTTCAATATTAAACTAAAATAATAAGTCTAAATTCC
1 GTTTCGATATTAAACTAAAATAATAAATCTAAATTCC
16342965 GTTTCGATAT
1 GTTTCGATAT
16342975 AAATTTCAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.37
Consensus pattern (37 bp):
GTTTCGATATTAAACTAAAATAATAAATCTAAATTCC
Found at i:16346358 original size:2 final size:2
Alignment explanation
Indices: 16346345--16346378 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
16346335 TAAATAAGAA
*
16346345 AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16346379 TGATGGGTGT
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:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16349705 original size:22 final size:21
Alignment explanation
Indices: 16349646--16349706 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
16349636 AAACAATTAA
* *
16349646 AATTTCAATTAAACATCATTAC
1 AATTT-AATTAAAAATCATAAC
**
16349668 AATTATAATTCCAAATGCATAAC
1 AATT-TAATTAAAAAT-CATAAC
16349691 AATTTAATTAAAAATC
1 AATTTAATTAAAAATC
16349707 TGTATGAACT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 1 0.03
22 20 0.65
23 10 0.32
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (21 bp):
AATTTAATTAAAAATCATAAC
Found at i:16353022 original size:30 final size:30
Alignment explanation
Indices: 16352982--16353049 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
16352972 TTAAAGGATC
* *
16352982 TGAAAATGCAAATGTG-ATTGATTACAGGGTA
1 TGAATATGCAAATGTGAATGGA--ACAGGGTA
16353013 TG-ATATGCAAATGTGAATGGAACAGGGTA
1 TGAATATGCAAATGTGAATGGAACAGGGTA
16353042 TGAATATG
1 TGAATATG
16353050 TTAATATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 10 0.30
30 17 0.52
31 6 0.18
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAATATGCAAATGTGAATGGAACAGGGTA
Found at i:16357966 original size:24 final size:24
Alignment explanation
Indices: 16357933--16357978 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16357923 ATTGATATAA
* **
16357933 TGGTATCCTTTTTGACCTTTTCAT
1 TGGTAACCTTTTCCACCTTTTCAT
16357957 TGGTAACCTTTTCCACCTTTTC
1 TGGTAACCTTTTCCACCTTTTC
16357979 TTTGTTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.26, G:0.11, T:0.50
Consensus pattern (24 bp):
TGGTAACCTTTTCCACCTTTTCAT
Found at i:16358864 original size:13 final size:13
Alignment explanation
Indices: 16358844--16358875 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16358834 TTGACTCATA
16358844 AATATTAATTAAT
1 AATATTAATTAAT
*
16358857 AGTATTAATTAAT
1 AATATTAATTAAT
16358870 AATATT
1 AATATT
16358876 TATGAACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AATATTAATTAAT
Found at i:16363394 original size:36 final size:36
Alignment explanation
Indices: 16363353--16363428 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
16363343 TAATTTAACC
16363353 TTAATCATGCTTAGTGGATGTTCCCATCACTATCTA
1 TTAATCATGCTTAGTGGATGTTCCCATCACTATCTA
* *
16363389 TTAATCATGCTTAGTGGATGTTGCCATCACTGTCTA
1 TTAATCATGCTTAGTGGATGTTCCCATCACTATCTA
16363425 TTAA
1 TTAA
16363429 CTTCACATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (36 bp):
TTAATCATGCTTAGTGGATGTTCCCATCACTATCTA
Found at i:16367667 original size:13 final size:13
Alignment explanation
Indices: 16367649--16367674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16367639 AAAATTGGAC
16367649 AGATGATAAATAA
1 AGATGATAAATAA
16367662 AGATGATAAATAA
1 AGATGATAAATAA
16367675 TAAAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
AGATGATAAATAA
Found at i:16368783 original size:24 final size:24
Alignment explanation
Indices: 16368728--16368783 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
16368718 GGCTCTTTTG
* * *
16368728 TGAGCTTCTTGATATTGGCTCGCT
1 TGAGCTTCTCGATATTGGCTCACA
* *
16368752 TGAACTTCTCGATATTGGGTCACA
1 TGAGCTTCTCGATATTGGCTCACA
16368776 TGAGCTTC
1 TGAGCTTC
16368784 CTGTTATATG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (24 bp):
TGAGCTTCTCGATATTGGCTCACA
Found at i:16379804 original size:24 final size:24
Alignment explanation
Indices: 16379777--16379827 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
16379767 ATACTAAAAA
16379777 TCAGGAAAATAAAAATCTGATTTG
1 TCAGGAAAATAAAAATCTGATTTG
16379801 TCAGGAAAATAAAAATCTGATTTG
1 TCAGGAAAATAAAAATCTGATTTG
16379825 TCA
1 TCA
16379828 TTCTCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (24 bp):
TCAGGAAAATAAAAATCTGATTTG
Found at i:16380693 original size:369 final size:367
Alignment explanation
Indices: 16379144--16380639 Score: 1588
Period size: 392 Copynumber: 4.0 Consensus size: 367
16379134 AATTTATTAA
* * * *
16379144 AATA-AAAAAGGCAAAATTTTCTAAAATTTCATATTTCAACAAGAATGTAAAATTTCTTAAGAGA
1 AATAGAAAAAGGCAAAATTTCCCAAAA--TCATAATGCAACAAGAATGTAAAATTTCTTAAGAGA
* * * * * *
16379208 TACTATTGATATTAATTCCTATATTTTGAAATATTGATAGAATGTGAAATTACCATCTCATCTAG
64 TAATATTGATACTAATTTCTATATTCTAAAATATTGACAGAATGTGAAATTACCATCTCATCTAG
* * * *
16379273 AAAAATGATTGTATGAAACTGTGGTTCCACGTCATCTTTATCCCTTTCCAATGCGAGAATGACAA
129 AAAAATGATTGTATAAAACTGTAGTTCCACGTCATCTTTATCCATTTCCAATGGGAGAATGACAA
* * * * *
16379338 ATCAGA-TTTTTTCTCCTAACTTTTATCTTTTTCCTCTTGAAAAAAATTCAAATCCAATTAAAAA
194 ATCAAATTTTTTTCTCCTGATTTTTAGCTTTTTCCTCTTG-AAAAAATTCAAATCCAACTAAAAA
* * *
16379402 TACTAAAAATCAAGAGAGAAAAAA-ATGATTTGTCATTCTCCCATTAGAAAGAGATAAAAATGAC
258 TACTAAAAATCAGGAGAGAAAAAATATGATTTATCATTCTCCCATTAAAAAGAGATAAAAATGAC
*** * * * *
16379466 GCGAAATCATAATTTCATATCATCTTTTCTCCTAAAATTTATTAA
323 ATAAAATCACAATTTCATATCATCTTTTCTCCTAAAAGTTATCAT
* * * * * * *
16379511 AATA-AAAAAGACAAAATTTTCTAAAATTTCATATTTCAACAAGAAAGTAAAATTTCTTAATAGA
1 AATAGAAAAAGGCAAAATTTCCCAAAA--TCATAATGCAACAAGAATGTAAAATTTCTTAAGAGA
* * *
16379575 TAA-ATTGATATTAATTCCTATATTCTGAAATATTGACAGAATGTGAAATTACCATCTCATCTAG
64 TAATATTGATACTAATTTCTATATTCTAAAATATTGACAGAATGTGAAATTACCATCTCATCTAG
* * * * * * *
16379639 AGAAATAATAGTATAAAACTGTGGTTCCACGTTATTTTTATCTC-TTTCCAATGGGAAAATGACA
129 AAAAATGATTGTATAAAACTGTAGTTCCACGTCATCTTTATC-CATTTCCAATGGGAGAATGACA
*
16379703 AATCAGATTTTTTTCTCCTGATTTTTAGCTTTTTCCTCTTGAAAAAATTCAAATCCAACTAAAAA
193 AATCAAATTTTTTTCTCCTGATTTTTAGCTTTTTCCTCTTGAAAAAATTCAAATCCAACTAAAAA
* * *
16379768 TACTAAAAATCAGGA-AAATAAAAATCTGATTTGTCAGGAAAATAAAAATCTGATTTGTCATTCT
258 TACTAAAAATCAGGAGAGA-AAAAATATGA--T-T--------T----ATC--A--T-TC--TCC
* * * * * *
16379832 C-TTATTAGAA-AGAGATAAAAATGACGTGAAATTACAATTTCATATCATCTTTTCTCCTAAAAT
300 CATTA--AAAAGAGATA-AAAA-TGACATAAAATCACAATTTCATATCATCTTTTCTCCTAAAAG
16379895 TTAT--T
361 TTATCAT
* ** * * * ** *
16379900 AAAAGAAAAAAGAAAAAATTTTCTAAAATTTCATATTTTAACAAGAATGTAAATTTTCTTAAGAG
1 AATAG-AAAAAGGCAAAATTTCCCAAAA--TCATAATGCAACAAGAATGTAAAATTTCTTAAGAG
*
16379965 ATAATATTGATACTAATTTCTATATTCTGAAATATTGACAGAATGTGAAATTACCATCTCATCTA
63 ATAATATTGATACTAATTTCTATATTCTAAAATATTGACAGAATGTGAAATTACCATCTCATCTA
* * * *
16380030 GAGAAATGATTGTATGAAACTGTGGTTCCATGTCATCTTTATCCATTTCCAATGGGAGAATGACA
128 GAAAAATGATTGTATAAAACTGTAGTTCCACGTCATCTTTATCCATTTCCAATGGGAGAATGACA
* * * *
16380095 AATTAAATTTTTTTTTCCTGATTTTTAGCTTTTTCTTCTTGAAAAAATTCAAATCTAACTAAAAA
193 AATCAAATTTTTTTCTCCTGATTTTTAGCTTTTTCCTCTTGAAAAAATTCAAATCCAACTAAAAA
* *
16380160 TACTAAAAATCAGGAGAGAAAAAATATGATTTGTCATTCTCCCATTAGAAAGAGATAAAAATGAC
258 TACTAAAAATCAGGAGAGAAAAAATATGATTTATCATTCTCCCATTAAAAAGAGATAAAAATGAC
* * * * *
16380225 GTGAAATCACAATTTCATATTATCTTTTCTCCTAAAATTTATTAT
323 ATAAAATCACAATTTCATATCATCTTTTCTCCTAAAAGTTATCAT
* * * * *
16380270 AATAGAATAAGGCAAAATTTTCTAAAATTTCATATTTCAACAAGAATGTAAAATTTCTTAAGAGA
1 AATAGAAAAAGGCAAAATTTCCCAAAA--TCATAATGCAACAAGAATGTAAAATTTCTTAAGAGA
* *
16380335 TACTATTGATATTAA-TTCTTATATTCTAAAATATTGACAGAATGTGAAATTACCATCTCATCTA
64 TAATATTGATACTAATTTC-TATATTCTAAAATATTGACAGAATGTGAAATTACCATCTCATCTA
* * *
16380399 GAAAAATGATTGTATAAAATTGTAGTTCCACGTCATTTTTATCTC-TTTTCAATGGGAGAATGAC
128 GAAAAATGATTGTATAAAACTGTAGTTCCACGTCATCTTTATC-CATTTCCAATGGGAGAATGAC
16380463 AAATCAAA-TTTTTTCTCCT-ACTTTTTAGCTTTTTCCTCTTGAAAAAATTCAAATCCAACTAAA
192 AAATCAAATTTTTTTCTCCTGA-TTTTTAGCTTTTTCCTCTTGAAAAAATTCAAATCCAACTAAA
* * * *
16380526 AATACTAAAAATTA-G-GA-AAAAAATCTGATTTATCATTCTCCTATTAAAAAGAGATAAAAATT
256 AATACTAAAAATCAGGAGAGAAAAAATATGATTTATCATTCTCCCATTAAAAAGAGATAAAAATG
* * *
16380588 ATATAAAATCACAATTTTATATCATCTTTTGTCCTAAACACAGTTATCAT
321 ACATAAAATCACAATTTCATATCATCTTTTCTCCT-AA-A-AGTTATCAT
16380638 AA
1 AA
16380640 AAAAAATTGT
Statistics
Matches: 991, Mismatches: 93, Indels: 89
0.84 0.08 0.08
Matches are distributed among these distances:
365 71 0.07
366 166 0.17
367 100 0.10
368 119 0.12
369 181 0.18
370 14 0.01
371 3 0.00
372 2 0.00
373 1 0.00
375 1 0.00
377 2 0.00
378 1 0.00
381 1 0.00
382 2 0.00
384 1 0.00
386 1 0.00
387 2 0.00
388 3 0.00
389 11 0.01
390 7 0.01
391 102 0.10
392 198 0.20
393 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (367 bp):
AATAGAAAAAGGCAAAATTTCCCAAAATCATAATGCAACAAGAATGTAAAATTTCTTAAGAGATA
ATATTGATACTAATTTCTATATTCTAAAATATTGACAGAATGTGAAATTACCATCTCATCTAGAA
AAATGATTGTATAAAACTGTAGTTCCACGTCATCTTTATCCATTTCCAATGGGAGAATGACAAAT
CAAATTTTTTTCTCCTGATTTTTAGCTTTTTCCTCTTGAAAAAATTCAAATCCAACTAAAAATAC
TAAAAATCAGGAGAGAAAAAATATGATTTATCATTCTCCCATTAAAAAGAGATAAAAATGACATA
AAATCACAATTTCATATCATCTTTTCTCCTAAAAGTTATCAT
Found at i:16386816 original size:30 final size:31
Alignment explanation
Indices: 16386777--16386834 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
16386767 ATTTGGTCAC
*
16386777 TAAATTATTCAAAA-TTTCCATTTAAGTTAT
1 TAAACTATTCAAAAGTTTCCATTTAAGTTAT
**
16386807 TAAACTATTCAAAAGTTTTTATTTAAGT
1 TAAACTATTCAAAAGTTTCCATTTAAGT
16386835 CACTAAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (31 bp):
TAAACTATTCAAAAGTTTCCATTTAAGTTAT
Found at i:16392756 original size:18 final size:18
Alignment explanation
Indices: 16392733--16392770 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16392723 TAGTTAGTTG
* *
16392733 ATTAAAGAAAAGGACTAA
1 ATTAAAAAAAAGGACAAA
16392751 ATTAAAAAAAAGGACAAA
1 ATTAAAAAAAAGGACAAA
16392769 AT
1 AT
16392771 ATAGAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.66, C:0.05, G:0.13, T:0.16
Consensus pattern (18 bp):
ATTAAAAAAAAGGACAAA
Found at i:16400125 original size:42 final size:42
Alignment explanation
Indices: 16400079--16400201 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
16400069 TAACCCTTCC
* *
16400079 GGGTTTTAGTTCAACTCTTTTGAGCTCCAGTTTAACCCTAAT
1 GGGTTTTAGTTCAGCTCTTATGAGCTCCAGTTTAACCCTAAT
* * * * * * * *
16400121 GGGTTTCAATTTAGCTCTTCTAAGCTTCAGATTAACCCTTAT
1 GGGTTTTAGTTCAGCTCTTATGAGCTCCAGTTTAACCCTAAT
* * *
16400163 GGGTTTTCGTTCAGCTCCTATGAGCTTCC-GTTCAACCCT
1 GGGTTTTAGTTCAGCTCTTATGAGC-TCCAGTTTAACCCT
16400202 TACAGGTTTC
Statistics
Matches: 61, Mismatches: 19, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
42 59 0.97
43 2 0.03
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (42 bp):
GGGTTTTAGTTCAGCTCTTATGAGCTCCAGTTTAACCCTAAT
Found at i:16400210 original size:84 final size:84
Alignment explanation
Indices: 16400062--16400218 Score: 199
Period size: 84 Copynumber: 1.9 Consensus size: 84
16400052 TCATATGAGT
* * * * **
16400062 TTCAGATTAACCCTTCCGGGTTTTAGTTCAACTCTTTTGAGCTCCAGTTTAACCCTAATGGGTTT
1 TTCAGATTAACCCTTACGGGTTTTAGTTCAACTCCTATGAGCTCCAGTTCAACCCTAACAGGTTT
16400127 CAATTTAGCTCTTCTAAGC
66 CAATTTAGCTCTTCTAAGC
* * * *
16400146 TTCAGATTAACCCTTATGGGTTTTCGTTCAGCTCCTATGAGCTTCC-GTTCAACCCTTACAGGTT
1 TTCAGATTAACCCTTACGGGTTTTAGTTCAACTCCTATGAGC-TCCAGTTCAACCCTAACAGGTT
*
16400210 TCCATTTAG
65 TCAATTTAG
16400219 TTCGGGATTC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
84 58 0.95
85 3 0.05
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (84 bp):
TTCAGATTAACCCTTACGGGTTTTAGTTCAACTCCTATGAGCTCCAGTTCAACCCTAACAGGTTT
CAATTTAGCTCTTCTAAGC
Found at i:16403359 original size:17 final size:17
Alignment explanation
Indices: 16403337--16403376 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
16403327 AGCAATTAGT
16403337 TCAAAAAGT-TTTTTCTA
1 TCAAAAAGTATTTTT-TA
16403354 TCAAAAAGTATTTTTTA
1 TCAAAAAGTATTTTTTA
16403371 T-AAAAA
1 TCAAAAA
16403377 AATTCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 12 0.55
18 5 0.23
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (17 bp):
TCAAAAAGTATTTTTTA
Found at i:16417460 original size:14 final size:13
Alignment explanation
Indices: 16417418--16417476 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
16417408 AAACTATAAC
16417418 AAAAAA-AACAAA
1 AAAAAATAACAAA
* *
16417430 TAAAAATCACTAAA
1 AAAAAATAAC-AAA
16417444 AAAAAATAACAATA
1 AAAAAATAACAA-A
*
16417458 AAACAATAA-AAA
1 AAAAAATAACAAA
16417470 TAAAAAA
1 -AAAAAA
16417477 AAAAATCTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
12 6 0.16
13 11 0.30
14 20 0.54
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAACAAA
Found at i:16417467 original size:24 final size:25
Alignment explanation
Indices: 16417408--16417476 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
16417398 TTAAGATATG
* *
16417408 AAACTATAACAAAAAAAACAAATAA
1 AAACAATAAAAAAAAAAACAAATAA
*
16417433 AAATCACTAAAAAAAAATAAC-AAT-A
1 AAA-CAATAAAAAAAAA-AACAAATAA
16417458 AAACAATAAAAATAAAAAA
1 AAACAATAAAAA-AAAAAA
16417477 AAAAATCTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
24 10 0.27
25 11 0.30
26 13 0.35
27 3 0.08
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (25 bp):
AAACAATAAAAAAAAAAACAAATAA
Found at i:16446458 original size:17 final size:17
Alignment explanation
Indices: 16446428--16446468 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
16446418 AAAATTGAAT
* *
16446428 TTTTTTATAAAAAATAC
1 TTTTTGATAAAAAAAAC
*
16446445 TTTTTGATAGAAAAAAC
1 TTTTTGATAAAAAAAAC
16446462 TTTTTGA
1 TTTTTGA
16446469 ACTAATTGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (17 bp):
TTTTTGATAAAAAAAAC
Found at i:16449694 original size:42 final size:42
Alignment explanation
Indices: 16449635--16449783 Score: 131
Period size: 42 Copynumber: 3.5 Consensus size: 42
16449625 TGGAAACCTG
* *
16449635 TAAGGGTTGAA-CGGAAGCTCATAGGAGCTGAACGAAAACCCA
1 TAAGGGTT-AATCTGAAGCTCATAAGAGCTGAACGAAAACCCA
* * * *
16449677 TAAGGGTTAATCTGAAGCTTAGAAGAGCTAAATTG-AAACCCA
1 TAAGGGTTAATCTGAAGCTCATAAGAGCTGAA-CGAAAACCCA
* * * * * * *
16449719 TTAGGGTTAAACTGGAGCTCAAAAGAGTTGAACTAAAACCCG
1 TAAGGGTTAATCTGAAGCTCATAAGAGCTGAACGAAAACCCA
* *
16449761 GAAGGGTTAATCTGAAACTCATA
1 TAAGGGTTAATCTGAAGCTCATA
16449784 TGAGTTAATT
Statistics
Matches: 82, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
41 2 0.02
42 79 0.96
43 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (42 bp):
TAAGGGTTAATCTGAAGCTCATAAGAGCTGAACGAAAACCCA
Found at i:16457181 original size:18 final size:19
Alignment explanation
Indices: 16457155--16457193 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
16457145 TAATTTCTAT
*
16457155 ATTTTGTCCTTTTT-TTTA
1 ATTTAGTCCTTTTTCTTTA
16457173 ATTTAGTCCTTTTTCTTTA
1 ATTTAGTCCTTTTTCTTTA
16457192 AT
1 AT
16457194 CAACTAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (19 bp):
ATTTAGTCCTTTTTCTTTA
Found at i:16463160 original size:31 final size:31
Alignment explanation
Indices: 16463122--16463180 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
16463112 TAACTTAGTG
*
16463122 ACTTAAATAAAAACTTTTGAATAGTTTAATA
1 ACTTAAATAAAAACTTTTGAATAATTTAATA
** *
16463153 ACTTAAATGGAAATTTTTGAATAATTTA
1 ACTTAAATAAAAACTTTTGAATAATTTA
16463181 GTGACCAAAT
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:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTTGAATAATTTAATA
Found at i:16469445 original size:26 final size:23
Alignment explanation
Indices: 16469396--16469446 Score: 57
Period size: 26 Copynumber: 2.1 Consensus size: 23
16469386 TTTTTTTATG
*
16469396 ATTTATTTTTAGGGAAATAAAAT
1 ATTTATTTTTAGGGAAAGAAAAT
*
16469419 ATTTGATTTGTTAGGAGAAAGATAAT
1 ATTT-ATTT-TTAGG-GAAAGAAAAT
16469445 AT
1 AT
16469447 GATTGTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 4 0.17
25 5 0.22
26 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (23 bp):
ATTTATTTTTAGGGAAAGAAAAT
Found at i:16479876 original size:17 final size:17
Alignment explanation
Indices: 16479852--16479911 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
16479842 AGATTAAATC
16479852 AAATACTCGTACAAAAG
1 AAATACTCGTACAAAAG
* *
16479869 ATATACTC--ACATTAAATC
1 AAATACTCGTACA--AAA-G
16479887 AAATACTCGTACAAAAG
1 AAATACTCGTACAAAAG
16479904 AAATACTC
1 AAATACTC
16479912 ACAGAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 3 0.09
17 18 0.53
18 10 0.29
20 3 0.09
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (17 bp):
AAATACTCGTACAAAAG
Found at i:16479890 original size:35 final size:35
Alignment explanation
Indices: 16479844--16479914 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
16479834 AATTTAGCAG
*
16479844 ATTAAATCAAATACTCGTACAAAAGATATACTCAC
1 ATTAAATCAAATACTCGTACAAAAGAAATACTCAC
16479879 ATTAAATCAAATACTCGTACAAAAGAAATACTCAC
1 ATTAAATCAAATACTCGTACAAAAGAAATACTCAC
16479914 A
1 A
16479915 GAAAATGTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.24
Consensus pattern (35 bp):
ATTAAATCAAATACTCGTACAAAAGAAATACTCAC
Found at i:16490647 original size:29 final size:30
Alignment explanation
Indices: 16490603--16490671 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
16490593 TTTTTTAAAA
* *
16490603 TTTAAAAAATAAAAA-TATAAAAATATATT
1 TTTAAAAATTAAAAATTATAAAAAAATATT
*
16490632 TTTAAAAATTAGAAATTATAAAAAAATATT
1 TTTAAAAATTAAAAATTATAAAAAAATATT
16490662 TTTAAAAATT
1 TTTAAAAATT
16490672 TAATTATTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 13 0.36
30 23 0.64
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (30 bp):
TTTAAAAATTAAAAATTATAAAAAAATATT
Found at i:16494592 original size:22 final size:22
Alignment explanation
Indices: 16494567--16494658 Score: 112
Period size: 22 Copynumber: 4.2 Consensus size: 22
16494557 AAATTCAATA
* *
16494567 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
16494589 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
16494611 TCAATTCCCTTCAAAATTTCTA
1 TCAATTCCCTTCAAAAATTCTC
* *
16494633 TCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
16494655 TCAA
1 TCAA
16494659 ACTCTCAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:16494674 original size:52 final size:51
Alignment explanation
Indices: 16494608--16494710 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
16494598 TTCAAAATTT
* * *
16494608 CTCTCAATTCCCTT-CAAAATTTCTATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAAAA-TCCTATCAATTTCCTTCAAAAAATCTC-CAAA
*
16494660 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
16494711 TCCATATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
Found at i:16494699 original size:21 final size:22
Alignment explanation
Indices: 16494660--16494701 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16494650 TTCTCTCAAA
16494660 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
16494682 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
16494702 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:16494805 original size:28 final size:28
Alignment explanation
Indices: 16494745--16494805 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
16494735 TAAATTTCAT
*
16494745 TTTTTTAAGAAAATTTTAAAATTTTTTA
1 TTTTTTAAGAAAATTTTAAAATTTTTAA
*
16494773 TTTTTTAA-ATAATTTTAAAATTTTTAA
1 TTTTTTAAGAAAATTTTAAAATTTTTAA
*
16494800 TATTTT
1 TTTTTT
16494806 CAACAATGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTTTAAGAAAATTTTAAAATTTTTAA
Found at i:16494951 original size:24 final size:23
Alignment explanation
Indices: 16494889--16494951 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
16494879 TAAATTTAAA
*
16494889 TTTTAAAT-TTTTTTTAAGATAT
1 TTTTATATATTTTTTTAAGATAT
*
16494911 TTTTATTTATGTATTTTT-AGATAT
1 TTTTATATAT-T-TTTTTAAGATAT
16494935 TTATTAATATATTTTTT
1 TT-TT-ATATATTTTTT
16494952 GTTATAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 6 0.18
23 1 0.03
24 13 0.39
25 8 0.24
26 5 0.15
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (23 bp):
TTTTATATATTTTTTTAAGATAT
Found at i:16497103 original size:17 final size:18
Alignment explanation
Indices: 16497081--16497115 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16497071 TAAAATCCCT
16497081 AACCCT-ACTTAATTAAA
1 AACCCTAACTTAATTAAA
*
16497098 AACCCTAATTTAATTAAA
1 AACCCTAACTTAATTAAA
16497116 TTAAAAACCC
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:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (18 bp):
AACCCTAACTTAATTAAA
Found at i:16497103 original size:23 final size:23
Alignment explanation
Indices: 16497069--16497141 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
16497059 ACATTATTTG
*
16497069 ATTAAAATCCCTAACCCTACTTA
1 ATTAAAAACCCTAACCCTACTTA
** *
16497092 ATTAAAAACCCTAA-TTTAATTAA
1 ATTAAAAACCCTAACCCTACTT-A
16497115 ATTAAAAACCCTAAACCCTACTTA
1 ATTAAAAACCCT-AACCCTACTTA
16497139 ATT
1 ATT
16497142 TAATTAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
22 4 0.10
23 26 0.65
24 6 0.15
25 4 0.10
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (23 bp):
ATTAAAAACCCTAACCCTACTTA
Found at i:16497131 original size:30 final size:30
Alignment explanation
Indices: 16497097--16497175 Score: 122
Period size: 34 Copynumber: 2.5 Consensus size: 30
16497087 ACTTAATTAA
16497097 AAACCCTAATTTAATTAAATTAAAAACCCT
1 AAACCCTAATTTAATTAAATTAAAAACCCT
16497127 AAACCCTACTTAATTTAATTAAATTAAAAACCCT
1 AAA-CC--C-TAATTTAATTAAATTAAAAACCCT
16497161 AAACCCTAATTTAAT
1 AAACCCTAATTTAAT
16497176 CAAGCTAGCC
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
30 12 0.27
31 3 0.07
33 3 0.07
34 27 0.60
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (30 bp):
AAACCCTAATTTAATTAAATTAAAAACCCT
Found at i:16497144 original size:34 final size:34
Alignment explanation
Indices: 16497103--16497168 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
16497093 TTAAAAACCC
16497103 TAATTTAATTAAATTAAAAACCCTAAACCCTACT
1 TAATTTAATTAAATTAAAAACCCTAAACCCTACT
16497137 TAATTTAATTAAATTAAAAACCCTAAACCCTA
1 TAATTTAATTAAATTAAAAACCCTAAACCCTA
16497169 ATTTAATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (34 bp):
TAATTTAATTAAATTAAAAACCCTAAACCCTACT
Found at i:16498813 original size:125 final size:125
Alignment explanation
Indices: 16498591--16498872 Score: 381
Period size: 125 Copynumber: 2.3 Consensus size: 125
16498581 CCACGAGGGC
*
16498591 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGC
1 GCGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGC
* * * * **
16498656 GAAATCACGTCCACAAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 GAAATCACGTCCACAAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
* *
16498716 GCGATTTTATACTATTTCCTCAGAAAACGTCAAAAAAAAATTATTT-CTCACATGACC-ACTGTA
1 GCGATTTGACACTATTTCCTCAG-AAACGTCAAAAAAAAATTATTTCCT-ACATGACCAACTGTA
* * *
16498779 GCGAAATCACGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTAGTAGAA
64 GCGAAATCACGTCCACAAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
** *
16498841 GCGATTTCCCACTATTTAAC-CAGAAACGTCAA
1 GCGATTTGACACTATTT-CCTCAGAAACGTCAA
16498873 CTCGAAAAAA
Statistics
Matches: 138, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
124 9 0.07
125 98 0.71
126 31 0.22
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.28
Consensus pattern (125 bp):
GCGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGC
GAAATCACGTCCACAAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
Found at i:16503710 original size:2 final size:2
Alignment explanation
Indices: 16503703--16503728 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16503693 TCACTTGATT
16503703 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
16503729 AAAAGCTCTT
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:16508791 original size:45 final size:45
Alignment explanation
Indices: 16508729--16508840 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
16508719 CCTGATGTAG
* *
16508729 TTGCTT-C-CACGTTGCTTCCTTTTTTGTTTGGACATAGATTTGA
1 TTGCTTCCACACGTTGCTTCCTTTTTTGTCTGGACATAGATGTGA
*
16508772 TTGCTTCCACACGTTGCTTCCTTTTTTGTCTGGATATAGATGTGA
1 TTGCTTCCACACGTTGCTTCCTTTTTTGTCTGGACATAGATGTGA
*
16508817 TTGCTTCCACACATTGCTTCCTTT
1 TTGCTTCCACACGTTGCTTCCTTT
16508841 GTCTTTTCTT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 6 0.10
44 1 0.02
45 56 0.89
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (45 bp):
TTGCTTCCACACGTTGCTTCCTTTTTTGTCTGGACATAGATGTGA
Found at i:16509812 original size:45 final size:45
Alignment explanation
Indices: 16509737--16509854 Score: 204
Period size: 45 Copynumber: 2.7 Consensus size: 45
16509727 TTTTTGTCCT
* *
16509737 GATGTGGTTGCTT-C-CACGTTGCTTCCTTTTTTGTTTGGACGTA
1 GATGTGGTTGCTTCCACACGTTGCTTCCTTTTTTGTCTGGACATA
16509780 GATGTGGTTGCTTCCACACGTTGCTTCCTTTTTTGTCTGGACATA
1 GATGTGGTTGCTTCCACACGTTGCTTCCTTTTTTGTCTGGACATA
16509825 GATGTGGTTGCTTCCACACGTTGCTTCCTT
1 GATGTGGTTGCTTCCACACGTTGCTTCCTT
16509855 ATTGCTTTTC
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
43 13 0.18
44 1 0.01
45 57 0.80
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.43
Consensus pattern (45 bp):
GATGTGGTTGCTTCCACACGTTGCTTCCTTTTTTGTCTGGACATA
Found at i:16511028 original size:26 final size:23
Alignment explanation
Indices: 16510999--16511056 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
16510989 AACATTTTAA
16510999 AAATTAAAAAATATATATTAAATATT
1 AAATTAAAAAATA-ATA-TAAATA-T
*
16511025 AAATT-CAAAATAATATAAATAT
1 AAATTAAAAAATAATATAAATAT
*
16511047 AATTTAAAAA
1 AAATTAAAAA
16511057 TCTTTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.18
23 9 0.32
24 3 0.11
25 6 0.21
26 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATTAAAAAATAATATAAATAT
Found at i:16520721 original size:19 final size:18
Alignment explanation
Indices: 16520686--16520721 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16520676 AATATTTATA
*
16520686 TTTTTTTATTAATTTAAC
1 TTTTTTTATTAAATTAAC
16520704 TTTTTTTATTAAAATTAA
1 TTTTTTTATT-AAATTAA
16520722 TTCTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTTTTATTAAATTAAC
Found at i:16521613 original size:13 final size:13
Alignment explanation
Indices: 16521595--16521619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16521585 TCTTCTCAAT
16521595 CATTCTAATTTAG
1 CATTCTAATTTAG
16521608 CATTCTAATTTA
1 CATTCTAATTTA
16521620 ATAAAATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (13 bp):
CATTCTAATTTAG
Found at i:16523672 original size:51 final size:51
Alignment explanation
Indices: 16523576--16523672 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
16523566 CGGTATATGA
* **
16523576 CGTAAGACCATAAATGAAAGACGCTATGGCAATCTAGTATGAGGTACGTCG
1 CGTAAGACCATAAATGAAAGACGCGATGGCAATCTAGTACAAGGTACGTCG
* * *
16523627 CGTAAGATCATAGATGAAAGACGCGATGGCAA-CATGGTACAAGGTA
1 CGTAAGACCATAAATGAAAGACGCGATGGCAATC-TAGTACAAGGTA
16523673 TAAGATATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 1 0.03
51 38 0.97
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (51 bp):
CGTAAGACCATAAATGAAAGACGCGATGGCAATCTAGTACAAGGTACGTCG
Found at i:16526269 original size:25 final size:24
Alignment explanation
Indices: 16526241--16526344 Score: 78
Period size: 25 Copynumber: 4.5 Consensus size: 24
16526231 ATAAGATTAT
16526241 TTTAATAGTTTAATATTAAATTAAA
1 TTTAATA-TTTAATATTAAATTAAA
*
16526266 TTTAATACTT-ATATT-AA-TAATA
1 TTTAATATTTAATATTAAATTAA-A
16526288 TTT--TA-TTAAT-TTAATATTAAA
1 TTTAATATTTAATATTAA-ATTAAA
* * * *
16526309 ATGATTATTTTAATATTAAATTTAA
1 TTTAATA-TTTAATATTAAATTAAA
16526334 TTTAATATTTA
1 TTTAATATTTA
16526345 TCTTGTAGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 21
0.69 0.08 0.23
Matches are distributed among these distances:
19 4 0.06
20 5 0.08
21 6 0.10
22 9 0.15
23 7 0.11
24 6 0.10
25 21 0.34
26 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTAATATTTAATATTAAATTAAA
Found at i:16526385 original size:62 final size:59
Alignment explanation
Indices: 16526317--16526434 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 59
16526307 AAATGATTAT
* *
16526317 TTTAATATTAAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATT-ATTTTAATAAGA
1 TTTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTCA-TTTAATAAGA
16526379 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTCATTTAATA
1 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTCATTTAATA
16526435 TTAAAGTGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
59 21 0.40
60 2 0.04
61 1 0.02
62 29 0.55
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (59 bp):
TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTCATTTAATAAGA
Found at i:16528497 original size:35 final size:35
Alignment explanation
Indices: 16528430--16528557 Score: 202
Period size: 35 Copynumber: 3.6 Consensus size: 35
16528420 AGTACATCGA
* *
16528430 TAATCCAACCGAAACACACCAAATGCTCATAAGAGC
1 TAATCCATCTGAAACACACC-AATGCTCATAAGAGC
*
16528466 TAATCTATCTGAAACACACCAATGCTCATAAGAGC
1 TAATCCATCTGAAACACACCAATGCTCATAAGAGC
*
16528501 TAATCCATCCGAAACACACCAATGCTCATAAGAGC
1 TAATCCATCTGAAACACACCAATGCTCATAAGAGC
*
16528536 TAATCCATTTGAAACACACCAA
1 TAATCCATCTGAAACACACCAA
16528558 AACAGAAAGT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 68 0.80
36 17 0.20
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (35 bp):
TAATCCATCTGAAACACACCAATGCTCATAAGAGC
Found at i:16531789 original size:27 final size:27
Alignment explanation
Indices: 16531729--16531789 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
16531719 CGATGTTAGG
*
16531729 GGACGTGGCAGAAAATCACGTCTCTAA
1 GGACGTGGCAGAAAATCACGTCCCTAA
*
16531756 GGACGTGGCAGAAAATCACGTCCCTGA
1 GGACGTGGCAGAAAATCACGTCCCTAA
*
16531783 GGGCGTG
1 GGACGTG
16531790 CTTTGCTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.28, C:0.23, G:0.33, T:0.16
Consensus pattern (27 bp):
GGACGTGGCAGAAAATCACGTCCCTAA
Found at i:16532379 original size:124 final size:125
Alignment explanation
Indices: 16532114--16532400 Score: 452
Period size: 125 Copynumber: 2.3 Consensus size: 125
16532104 ATTTATTAAG
* * * *
16532114 GAAATCGCTCACATGTGAACGTGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* *
16532179 GTTTCTAAGCAAATAGTATAAAAAACACTTGAAGCAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTAAGAAAATAGTATAAAAAACACTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
*
16532239 AAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATATT-GAGTTGA
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAAT-TTCGAGTTGA
* *
16532303 CGTTTCTGAGAAAATAGTAT-AAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
65 CGTTTCTAAGAAAATAGTATAAAAAACACTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
* *
16532363 GAAATCGCTCCCACGTGGACGCGTTTTTACTACAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
16532401 CATGTTTGGA
Statistics
Matches: 149, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
124 73 0.49
125 74 0.50
126 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
GTTTCTAAGAAAATAGTATAAAAAACACTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
Found at i:16535653 original size:49 final size:49
Alignment explanation
Indices: 16535596--16535851 Score: 442
Period size: 49 Copynumber: 5.2 Consensus size: 49
16535586 TAAGAATATT
16535596 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
16535645 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
* *
16535694 AAATATTTTGTATTTTATTAAATGAAATAGTATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
* * *
16535743 AACTATTTTGCA-TTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
* *
16535791 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
16535840 AACTATTTTGTA
1 AACTATTTTGTA
16535852 CAAATATATT
Statistics
Matches: 198, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
48 44 0.22
49 154 0.78
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.41
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
Found at i:16535819 original size:97 final size:98
Alignment explanation
Indices: 16535596--16535849 Score: 438
Period size: 97 Copynumber: 2.6 Consensus size: 98
16535586 TAAGAATATT
*
16535596 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGCATTTT
*
16535661 ATTAAATGAAATAATATCAAAATATTCAAAATA
66 ATTAAATCAAATAATATCAAAATATTCAAAATA
* *
16535694 AAATATTTTGTATTTTATTAAATGAAATAGTATCAAAATATTCAAAATAAACTATTTTGCA-TTT
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGCATTTT
*
16535758 ATTACATCAAATAATATCAAAATATTCAAAATA
66 ATTAAATCAAATAATATCAAAATATTCAAAATA
* *
16535791 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAACTATTTTG
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
16535850 TACAAATATA
Statistics
Matches: 147, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
97 89 0.61
98 58 0.39
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.41
Consensus pattern (98 bp):
AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGCATTTT
ATTAAATCAAATAATATCAAAATATTCAAAATA
Found at i:16538130 original size:11 final size:11
Alignment explanation
Indices: 16538114--16538159 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
16538104 TCTTTTAAAT
16538114 AGGAATTTGAG
1 AGGAATTTGAG
16538125 AGGAATTTGAG
1 AGGAATTTGAG
16538136 A-GAATATT-AG
1 AGGAAT-TTGAG
*
16538146 AGAGAAATTGAG
1 AG-GAATTTGAG
16538158 AG
1 AG
16538160 AAAGGATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.23
11 16 0.53
12 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24
Consensus pattern (11 bp):
AGGAATTTGAG
Found at i:16538158 original size:10 final size:10
Alignment explanation
Indices: 16538120--16538162 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
16538110 AAATAGGAAT
*
16538120 TTGAGAGGAAT
1 TTGAGA-GAAA
16538131 TTGAGAGAATA
1 TTGAGAGAA-A
16538142 TTAGAGAGAAA
1 TT-GAGAGAAA
16538153 TTGAGAGAAA
1 TTGAGAGAAA
16538163 GGATTTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 11 0.38
11 11 0.38
12 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:16541554 original size:11 final size:11
Alignment explanation
Indices: 16541538--16541644 Score: 63
Period size: 11 Copynumber: 10.4 Consensus size: 11
16541528 ATTTGTTTAA
16541538 TTTTAAAATAT
1 TTTTAAAATAT
16541549 TTTTAAAATACT
1 TTTTAAAATA-T
**
16541561 TTTT--TTTAT
1 TTTTAAAATAT
*
16541570 TTTT--TA-AT
1 TTTTAAAATAT
16541578 -TTTAAAATAT
1 TTTTAAAATAT
16541588 TTTTAAAATACT
1 TTTTAAAATA-T
16541600 TTTT-AAAT-T
1 TTTTAAAATAT
** *
16541609 TTTT--TTTAA
1 TTTTAAAATAT
16541618 TTTTAAAATAT
1 TTTTAAAATAT
16541629 TTTTAAAATACT
1 TTTTAAAATA-T
16541641 TTTT
1 TTTT
16541645 TTAATTTTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
7 3 0.04
8 3 0.04
9 16 0.21
10 4 0.05
11 35 0.46
12 15 0.20
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:16541622 original size:30 final size:32
Alignment explanation
Indices: 16541586--16541659 Score: 109
Period size: 30 Copynumber: 2.4 Consensus size: 32
16541576 ATTTTAAAAT
*
16541586 ATTTTTAAAATACTTTTT-AAAT-TTTTTTTTA
1 ATTTTTAAAATA-TTTTTAAAATACTTTTTTTA
16541617 A-TTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATATTTTTAAAATACTTTTTTTA
16541648 ATTTTTAAAATA
1 ATTTTTAAAATA
16541660 AATTTTTGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 5 0.13
30 14 0.36
31 10 0.26
32 10 0.26
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (32 bp):
ATTTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:16541626 original size:41 final size:41
Alignment explanation
Indices: 16541521--16541653 Score: 195
Period size: 39 Copynumber: 3.3 Consensus size: 41
16541511 ATATATTTAT
*
16541521 TTTTTAAA--TTTGTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTAAATTTTTTTTTAATTTTAAAATATTTTTAAAATAC
16541560 TTTTT---TTTATTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTAAATTT-TTTTTTAATTTTAAAATATTTTTAAAATAC
16541599 TTTTTAAATTTTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTAAATTTTTTTTTAATTTTAAAATATTTTTAAAATAC
*
16541640 TTTTTTTAATTTTT
1 -TTTTTAAATTTTT
16541654 AAAATAAATT
Statistics
Matches: 85, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
38 1 0.01
39 39 0.46
41 30 0.35
42 15 0.18
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (41 bp):
TTTTTAAATTTTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:16541665 original size:21 final size:21
Alignment explanation
Indices: 16541627--16541666 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16541617 ATTTTAAAAT
**
16541627 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
16541648 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
16541667 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:16541673 original size:22 final size:20
Alignment explanation
Indices: 16541626--16541679 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
16541616 AATTTTAAAA
* *
16541626 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
16541646 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
16541669 TATTTATTAAA
1 TATTT-TTAAA
16541680 CAAATGGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.04
21 11 0.39
22 10 0.36
23 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:16542621 original size:20 final size:20
Alignment explanation
Indices: 16542584--16542621 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16542574 TATTTTAAAA
*
16542584 AAAAATTATTTAATATATAT
1 AAAAATTATTTAAAATATAT
16542604 AAAAA-TATTTACAAATAT
1 AAAAATTATTTA-AAATAT
16542622 CAAACAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATTATTTAAAATATAT
Found at i:16548400 original size:21 final size:21
Alignment explanation
Indices: 16548374--16548414 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16548364 TGGGTGGATT
16548374 AGCTCTCACGAGCTTCTGTTC
1 AGCTCTCACGAGCTTCTGTTC
* *
16548395 AGCTCTTATGAGCTTCTGTT
1 AGCTCTCACGAGCTTCTGTT
16548415 GGTGTATTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.39
Consensus pattern (21 bp):
AGCTCTCACGAGCTTCTGTTC
Found at i:16550726 original size:13 final size:14
Alignment explanation
Indices: 16550708--16550738 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
16550698 AACCCCTTTT
16550708 ATAATAATAA-ATA
1 ATAATAATAACATA
16550721 ATAATAATAACATA
1 ATAATAATAACATA
16550735 ATAA
1 ATAA
16550739 AATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAATAATAACATA
Found at i:16554238 original size:26 final size:25
Alignment explanation
Indices: 16554157--16554238 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
16554147 CAACTACCTA
* *
16554157 TAAATAATTCAAATAAAAT-TATATT
1 TAAAAAATTAAAATAAAATCTA-ATT
*
16554182 TAGAAAATTAAAAT--AATCTAACTT
1 TAAAAAATTAAAATAAAATCTAA-TT
*
16554206 CGTAAAAGATTAAAATAAAATCTAATT
1 --TAAAAAATTAAAATAAAATCTAATT
16554233 TAAAAA
1 TAAAAA
16554239 TAAATATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
23 4 0.09
24 4 0.09
25 16 0.36
26 12 0.27
27 2 0.04
28 7 0.16
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (25 bp):
TAAAAAATTAAAATAAAATCTAATT
Found at i:16556883 original size:31 final size:32
Alignment explanation
Indices: 16556841--16556937 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 32
16556831 TAGTATCTTT
*
16556841 AAAGTTTTGGTTTCACCCAATAAGTCTTTTTG
1 AAAGTTCTGGTTTCACCCAATAAGTCTTTTTG
* **
16556873 AAAG-TCTGGTTTCAACC---AAGTTCATTTTCA
1 AAAGTTCTGGTTTCACCCAATAAG-TC-TTTTTG
* *
16556903 AAAGTTCTAGTTTCACCTAATAAGTCTTTTTG
1 AAAGTTCTGGTTTCACCCAATAAGTCTTTTTG
16556935 AAA
1 AAA
16556938 ACTCATCTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 3 0.06
29 2 0.04
30 8 0.16
31 21 0.42
32 11 0.22
33 2 0.04
34 3 0.06
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (32 bp):
AAAGTTCTGGTTTCACCCAATAAGTCTTTTTG
Found at i:16557098 original size:60 final size:62
Alignment explanation
Indices: 16557004--16557175 Score: 179
Period size: 60 Copynumber: 2.8 Consensus size: 62
16556994 ATCCTGTTTC
*
16557004 ATTTTCAAAAGTTTTGGTTCTATCC-AGTAAGTATTTTTGAAAGTTTGGTTCCG-C-AAATTT
1 ATTTTCAAAAGTTCTGGTTCTA-CCTAGTAAGTATTTTTGAAAGTTTGGTTCCGTCTAAATTT
* * * ** **
16557064 ATTTTCAAAAGTTCTAGTTCCACCTAGTAGGTATTTTTGAAAGACTGGTTCCGTCTAGGTTT
1 ATTTTCAAAAGTTCTGGTTCTACCTAGTAAGTATTTTTGAAAGTTTGGTTCCGTCTAAATTT
** * * * * *
16557126 GCTTTCAAAAGTTCTGGTTCTGCTTAGTATGTATTTATGAAACTTTGGTT
1 ATTTTCAAAAGTTCTGGTTCTACCTAGTAAGTATTTTTGAAAGTTTGGTT
16557176 TCACCTAGGT
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
59 2 0.02
60 44 0.49
61 1 0.01
62 43 0.48
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (62 bp):
ATTTTCAAAAGTTCTGGTTCTACCTAGTAAGTATTTTTGAAAGTTTGGTTCCGTCTAAATTT
Found at i:16557175 original size:62 final size:59
Alignment explanation
Indices: 16557006--16557175 Score: 151
Period size: 62 Copynumber: 2.8 Consensus size: 59
16556996 CCTGTTTCAT
* * * *
16557006 TTTCAAAAGTTTTGGTTCTATCCAGTAAGTATTTTTGAAAGTTTGGTTCCGCAAATTTAT
1 TTTCAAAAGTTCTGGTTCTCT-TAGTAAGTATTTTTGAAAGTTTGGTTCCGCAAATTTAC
* * * * ** ** *
16557066 TTTCAAAAGTTCTAGTTCCACCTAGTAGGTATTTTTGAAAGACTGGTTCCGTCTAGGTTTGC
1 TTTCAAAAGTTCTGGTT-CTCTTAGTAAGTATTTTTGAAAGTTTGGTTCCG-C-AAATTTAC
* * *
16557128 TTTCAAAAGTTCTGGTTCTGCTTAGTATGTATTTATGAAACTTTGGTT
1 TTTCAAAAGTTCTGGTTCT-CTTAGTAAGTATTTTTGAAAGTTTGGTT
16557176 TCACCTAGGT
Statistics
Matches: 85, Mismatches: 21, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
60 40 0.47
61 3 0.04
62 42 0.49
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.44
Consensus pattern (59 bp):
TTTCAAAAGTTCTGGTTCTCTTAGTAAGTATTTTTGAAAGTTTGGTTCCGCAAATTTAC
Found at i:16558663 original size:16 final size:16
Alignment explanation
Indices: 16558641--16558700 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
16558631 CTGATTATAA
16558641 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
* * * *
16558657 CTTTATTACATTGCAA
1 CTCTATTCCATTACAG
16558673 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
*
16558689 CCCTATTCCATT
1 CTCTATTCCATT
16558701 CTAGTGAACC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:16562188 original size:24 final size:23
Alignment explanation
Indices: 16562139--16562188 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
16562129 ATAAAGTAGT
* *
16562139 TATATATTATTTTTATAATATTA
1 TATATATGATTTTTATAATATCA
16562162 TATATTATGATTTTTATTAAT-TCA
1 TATA-TATGATTTTTA-TAATATCA
16562186 TAT
1 TAT
16562189 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TATATATGATTTTTATAATATCA
Found at i:16562508 original size:16 final size:16
Alignment explanation
Indices: 16562487--16562537 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
16562477 TGAATTACTG
*
16562487 ATTACAATTCTATTCT
1 ATTACAGTTCTATTCT
* *
16562503 ATTACAGCTCTATTCC
1 ATTACAGTTCTATTCT
16562519 ATTACAGTTCTATTCT
1 ATTACAGTTCTATTCT
16562535 ATT
1 ATT
16562538 CTCCCCAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (16 bp):
ATTACAGTTCTATTCT
Found at i:16562961 original size:4 final size:4
Alignment explanation
Indices: 16562954--16562981 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
16562944 TTAAAATAGG
16562954 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
16562982 CAAAGATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:16567491 original size:28 final size:29
Alignment explanation
Indices: 16567432--16567493 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
16567422 AAAAAAGTTT
*
16567432 TTTTTTTAATATTTATTGAAATGGGTTGA
1 TTTTTTGAATATTTATTGAAATGGGTTGA
* *
16567461 TTTTTTGATTATTTATTGGAATGGGTT-A
1 TTTTTTGAATATTTATTGAAATGGGTTGA
16567489 TTTTT
1 TTTTT
16567494 CAAGAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.23, C:0.00, G:0.18, T:0.60
Consensus pattern (29 bp):
TTTTTTGAATATTTATTGAAATGGGTTGA
Found at i:16569436 original size:10 final size:10
Alignment explanation
Indices: 16569421--16569447 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
16569411 TAAAATTATC
16569421 AAATTATGTA
1 AAATTATGTA
16569431 AAATTATGTA
1 AAATTATGTA
16569441 AAATTAT
1 AAATTAT
16569448 TAAGCCAAAA
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:0.07, T:0.41
Consensus pattern (10 bp):
AAATTATGTA
Found at i:16569587 original size:122 final size:121
Alignment explanation
Indices: 16569366--16569607 Score: 326
Period size: 122 Copynumber: 2.0 Consensus size: 121
16569356 ACATTATGTA
* * *
16569366 AAATTATGTAAGATTATTAAGTTCCAAAATTTTGTTAATGGTTAGTAAAATTATCAAATTATGTA
1 AAATTATGTAAAATTATTAAGATCCAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGTA
* ***
16569431 AAATTATGTAAAATTATTAAGCCAAAATTTTTTTAATTAAATTAGATAAAATTATC
66 AAATTATGTAAAACTATTAAGCCAAAAAAATTTTAATTAAATTAGATAAAATTATC
***
16569487 AAATTATGTAAAATTATTAA-ATCCAAAAATTGTGTTAATGGTTAGGGT-TTTTTATCAAATTAT
1 AAATTATGTAAAATTATTAAGATCC-AAAATTGTGTTAATGGTTA--GTAAAATTATCAAATTAT
* * *
16569550 TTAAACTTATGTAAAACTATTAAGCCAAAAAAATTTTAATTAAATTAGGTAAAATTAT
63 GTAAAATTATGTAAAACTATTAAGCCAAAAAAATTTTAATTAAATTAGATAAAATTAT
16569608 TAAGTCCAAA
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
120 3 0.03
121 37 0.35
122 63 0.60
123 2 0.02
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (121 bp):
AAATTATGTAAAATTATTAAGATCCAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGTA
AAATTATGTAAAACTATTAAGCCAAAAAAATTTTAATTAAATTAGATAAAATTATC
Found at i:16569660 original size:55 final size:55
Alignment explanation
Indices: 16569591--16569716 Score: 234
Period size: 55 Copynumber: 2.3 Consensus size: 55
16569581 AATTTTAATT
*
16569591 AAATTAGGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
*
16569646 AAATTATGTAAAATTATTAAGTCCAACAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
16569701 AAATTATGTAAAATTA
1 AAATTATGTAAAATTA
16569717 GGTTAGGGTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 69 1.00
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:16569747 original size:18 final size:18
Alignment explanation
Indices: 16569724--16569765 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
16569714 TTAGGTTAGG
16569724 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
16569742 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
16569760 ATTAGG
1 GTTAGG
16569766 TTAGGGTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:16569774 original size:29 final size:29
Alignment explanation
Indices: 16569742--16570064 Score: 323
Period size: 29 Copynumber: 10.8 Consensus size: 29
16569732 TTTTAATTAA
16569742 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
16569771 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
16569800 GTTAGGGTTTTTAATTAAGTTAGGGTTAGG
1 GTTAGGGTTTTTAATTAAATTA-GGTTAGG
* * *
16569830 GTTAGGATTTTTAAGTAAGTTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
16569859 GTTAGGGTTTTTAATTAAGTTAGGATTTTTAATTAG
1 GTTAGGGTTTTTAATTAAATTAGG----TT-A--GG
** * * *
16569895 GTTA-GGTTAGGGTAAGGGTT--TTTA-ATTA-A
1 GTTAGGGTT--TTTAA---TTAAATTAGGTTAGG
* **
16569924 CTTAGGGTTTTTAATTAGGTTAGGGTTAGG
1 GTTAGGGTTTTTAATTAAATTA-GGTTAGG
16569954 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
16569983 GTTAGAGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
16570012 GTAAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
16570041 GTTAGAGTTTTTAATTAAGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGG
16570065 GTTTTTAATT
Statistics
Matches: 249, Mismatches: 26, Indels: 38
0.80 0.08 0.12
Matches are distributed among these distances:
25 2 0.01
27 3 0.01
28 3 0.01
29 168 0.67
30 50 0.20
32 1 0.00
33 4 0.02
34 1 0.00
35 4 0.02
36 5 0.02
37 3 0.01
38 3 0.01
40 2 0.01
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.44
Consensus pattern (29 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGG
Found at i:16569822 original size:47 final size:47
Alignment explanation
Indices: 16569771--16570035 Score: 224
Period size: 47 Copynumber: 5.1 Consensus size: 47
16569761 TTAGGTTAGG
16569771 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
*
16569818 GTTAGGGTTAGGGTTAGGATTTTTAAGTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTT---TTTA--A---TT-A--AA-TTAGGTTAGGGTTAGGGTTTTTAATTAA
* ** *
16569877 GTTAGGATTTTTAATTAGGTTAGGTTAGGGTAAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
* **
16569924 CTTAGGGTTTTTAATTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTAGGGTTTTTAATT--A--A
*
16569976 GGTTAGGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAA
1 -GTTA--G---G-GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
*
16570030 ATTAGG
1 GTTAGG
16570036 TTAGGGTTAG
Statistics
Matches: 180, Mismatches: 14, Indels: 47
0.75 0.06 0.20
Matches are distributed among these distances:
47 56 0.31
48 23 0.13
50 5 0.03
51 3 0.02
52 2 0.01
53 6 0.03
54 2 0.01
55 3 0.02
56 5 0.03
58 25 0.14
59 50 0.28
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.44
Consensus pattern (47 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
Found at i:16569882 original size:18 final size:18
Alignment explanation
Indices: 16569858--16569950 Score: 83
Period size: 18 Copynumber: 5.6 Consensus size: 18
16569848 GTTAGGTTAG
16569858 GGTTAGGGTTTTTAATTA
1 GGTTAGGGTTTTTAATTA
* *
16569876 AGTTAGGATTTTTAATTA
1 GGTTAGGGTTTTTAATTA
*
16569894 GGTTA-GG---TT-A--G
1 GGTTAGGGTTTTTAATTA
*
16569905 GGTAAGGGTTTTTAATTA
1 GGTTAGGGTTTTTAATTA
**
16569923 ACTTAGGGTTTTTAATTA
1 GGTTAGGGTTTTTAATTA
16569941 GGTTAGGGTT
1 GGTTAGGGTT
16569951 AGGGTTAGGG
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
11 4 0.07
12 2 0.04
13 1 0.02
14 2 0.04
15 2 0.04
16 1 0.02
17 1 0.02
18 43 0.77
ACGTcount: A:0.25, C:0.01, G:0.28, T:0.46
Consensus pattern (18 bp):
GGTTAGGGTTTTTAATTA
Found at i:16570068 original size:18 final size:18
Alignment explanation
Indices: 16570041--16570136 Score: 98
Period size: 18 Copynumber: 5.7 Consensus size: 18
16570031 TTAGGTTAGG
*
16570041 GTTAGAGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
16570059 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
**
16570077 GTTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
16570088 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
16570106 GTTAGGGTTTTTAAATAA
1 GTTAGGGTTTTTAATTAA
*
16570124 ATTAGGGTTTTTA
1 GTTAGGGTTTTTA
16570137 TTACATCAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
11 4 0.06
12 2 0.03
13 1 0.02
14 2 0.03
15 2 0.03
16 1 0.02
17 2 0.03
18 50 0.78
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:16570084 original size:47 final size:47
Alignment explanation
Indices: 16570015--16570129 Score: 203
Period size: 47 Copynumber: 2.4 Consensus size: 47
16570005 GGTTAGGGTA
16570015 AGGGTTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAGTT
1 AGGGTTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAGTT
* *
16570062 AGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTT
1 AGGGTTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAGTT
*
16570109 AGGGTTTTTAAATAAATTAGG
1 AGGGTTTTTAATTAAATTAGG
16570130 GTTTTTATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 64 1.00
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (47 bp):
AGGGTTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAGTT
Found at i:16570131 original size:182 final size:183
Alignment explanation
Indices: 16569714--16570132 Score: 698
Period size: 182 Copynumber: 2.3 Consensus size: 183
16569704 TTATGTAAAA
16569714 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTAGGG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGGTTAGGGTTAGGG
* * *
16569778 TTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTAGGGTTAGGATTTTTA
66 TTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGGTTAGGGTAAGGATTTTTA
* * *
16569843 AGTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGATTTTTAATTAGG
131 AGTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAGTTAGGATTTTTAATTAAG
* * **
16569896 TTAGGTTAGGGTAAGGGTTTTTAATTAACTTAGGGTTTTTAATTAGGTTAGGGTTAGGGTTAGGG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGGTTAGGGTTAGGG
*
16569961 TTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTA-GGTTAGGGTAAGGGTTTTTA
66 TTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGGTTAGGGTAAGGATTTTTA
* *
16570025 ATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAGTTAGGGTTTTTAATTAAG
131 AGTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAGTTAGGATTTTTAATTAAG
*
16570078 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAAATAAATTAGGGTT
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGGTT
16570133 TTTATTACAT
Statistics
Matches: 218, Mismatches: 18, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
182 162 0.74
183 56 0.26
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.45
Consensus pattern (183 bp):
TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGGTTAGGGTTAGGG
TTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGGTTAGGGTAAGGATTTTTA
AGTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAGTTAGGATTTTTAATTAAG
Found at i:16570184 original size:25 final size:26
Alignment explanation
Indices: 16570132--16570195 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
16570122 AAATTAGGGT
*
16570132 TTTTATTACATCAAATTGAACTTCTA
1 TTTTATTACATCAAATTAAACTTCTA
* *
16570158 TTTTATTATATTAAA-TAAACTTCTA
1 TTTTATTACATCAAATTAAACTTCTA
16570183 TTTTATTACATCA
1 TTTTATTACATCA
16570196 GATAATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 20 0.61
26 13 0.39
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTATTACATCAAATTAAACTTCTA
Found at i:16570628 original size:18 final size:18
Alignment explanation
Indices: 16570601--16570635 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16570591 CGAAAAAGGA
* *
16570601 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
16570619 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
16570636 AAACACACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Done.