Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 61 of 770
Found at i:17871747 original size:21 final size:20
Alignment explanation
Indices: 17871713--17871780 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
17871703 ACATTCTTGT
17871713 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
17871734 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
17871755 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
17871776 AAAGA
1 AAAGA
17871781 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:17871748 original size:6 final size:5
Alignment explanation
Indices: 17871724--17871780 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
17871714 AAGAGAAAAC
*
17871724 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
17871771 AAAGA AAAGA
1 AAAGA AAAGA
17871781 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:17871755 original size:15 final size:14
Alignment explanation
Indices: 17871724--17871780 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
17871714 AAGAGAAAAC
17871724 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
17871740 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
17871755 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
17871771 AAAGAAAAGA
1 AAAGAAAAGA
17871781 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:17871857 original size:12 final size:12
Alignment explanation
Indices: 17871849--17871873 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17871839 TTTGAAAAGC
17871849 AAAAAGAAAATG
1 AAAAAGAAAATG
17871861 AAAAAGAAAATG
1 AAAAAGAAAATG
17871873 A
1 A
17871874 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:17871870 original size:18 final size:18
Alignment explanation
Indices: 17871843--17871898 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
17871833 AAAGCCTTTG
17871843 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
17871862 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
17871880 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
17871897 AA
1 AA
17871899 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:17871883 original size:30 final size:31
Alignment explanation
Indices: 17871849--17871925 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
17871839 TTTGAAAAGC
*
17871849 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
17871879 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
17871909 AAAAA-AAAATTGAAAAA
1 AAAAAGAAAA-TGAAAAA
17871926 AAGAAACGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 11 0.29
30 23 0.61
31 4 0.11
ACGTcount: A:0.66, C:0.01, G:0.19, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:17874184 original size:30 final size:31
Alignment explanation
Indices: 17874150--17874246 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 31
17874140 AGCTCACTCC
*
17874150 TAGCTC-ACTTTCAACTCATGAGCTAAACCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
* * * * *
17874180 TAGCTCAAC-TTCAACTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
* * *
17874210 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
17874240 TAGCTCA
1 TAGCTCA
17874247 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAACTCACGAGCTAAACCT
Found at i:17876481 original size:30 final size:30
Alignment explanation
Indices: 17876447--17876543 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
17876437 TAAACTAAAA
17876447 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
17876477 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
17876507 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
17876537 TGAGCTA
1 TGAGCTA
17876544 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:17878378 original size:14 final size:14
Alignment explanation
Indices: 17878331--17878378 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
17878321 GTACGAATGG
*
17878331 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
17878345 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
17878359 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
17878373 ATTGGT
1 AATGGT
17878379 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:17880247 original size:11 final size:12
Alignment explanation
Indices: 17880215--17880247 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17880205 GAGTTGTAGC
17880215 AAACTTAATTAT
1 AAACTTAATTAT
*
17880227 AAACTGAATTA-
1 AAACTTAATTAT
17880238 AAACTTAATT
1 AAACTTAATT
17880248 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:17881768 original size:14 final size:14
Alignment explanation
Indices: 17881749--17881793 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
17881739 AACTCATCTT
*
17881749 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
17881763 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
17881776 AATTTAATTTAATG
1 AGTTTAATTTAATG
17881790 AGTT
1 AGTT
17881794 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:17884106 original size:18 final size:18
Alignment explanation
Indices: 17884083--17884132 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
17884073 TGAAAGAAAA
*
17884083 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
17884101 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
17884119 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
17884133 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:17884111 original size:24 final size:24
Alignment explanation
Indices: 17884079--17884157 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 24
17884069 GAAATGAAAG
*
17884079 AAAAGAAAAAGAGATTGAGAGTGA
1 AAAAGAAAAAGAGATTGAGAGAGA
* * *
17884103 AAAAGAAAATGAGATTGAAAAAGA
1 AAAAGAAAAAGAGATTGAGAGAGA
* * *
17884127 GAATGAAAAAGAGTTTGAGAGAGA
1 AAAAGAAAAAGAGATTGAGAGAGA
*
17884151 GAAAGAA
1 AAAAGAA
17884158 TGTGAACAAG
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (24 bp):
AAAAGAAAAAGAGATTGAGAGAGA
Found at i:17887676 original size:15 final size:15
Alignment explanation
Indices: 17887630--17887677 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
17887620 AAACCTACCA
*
17887630 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
17887645 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
17887659 AAACTTCATATCCAT
1 AAACTTCATATCCAT
17887674 AAAC
1 AAAC
17887678 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:17890824 original size:20 final size:21
Alignment explanation
Indices: 17890793--17890849 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
17890783 AGCTCCGTCC
**
17890793 AGCTCAAATCCAGCTTATTC-G
1 AGCTC-AATCCAGCTTAGCCTG
*
17890814 AGCTCAATCCATCTT-GCCTG
1 AGCTCAATCCAGCTTAGCCTG
17890834 AGCTCAATCCAGCTTA
1 AGCTCAATCCAGCTTA
17890850 CTCGGTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 24 0.80
21 5 0.17
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (21 bp):
AGCTCAATCCAGCTTAGCCTG
Found at i:17893374 original size:5 final size:5
Alignment explanation
Indices: 17893364--17893420 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
17893354 AAGAGAAAAC
*
17893364 AAAGA AAAGA AAAGA AAACGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAGA AAA-G-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
17893411 AAAGA AAAGA
1 AAAGA AAAGA
17893421 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:17893387 original size:21 final size:20
Alignment explanation
Indices: 17893363--17893420 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
17893353 AAAGAGAAAA
17893363 CAAAGAAAAGAAAAGAAAACG
1 CAAA-AAAAGAAAAGAAAACG
* *
17893384 CAAAAGAAGAAAAAGAAAATG
1 CAAAAAAAG-AAAAGAAAACG
*
17893405 AAATAAAAAGAAAAGA
1 CAA-AAAAAGAAAAGA
17893421 GAGGCAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 22 0.71
22 5 0.16
ACGTcount: A:0.74, C:0.05, G:0.17, T:0.03
Consensus pattern (20 bp):
CAAAAAAAGAAAAGAAAACG
Found at i:17893500 original size:11 final size:12
Alignment explanation
Indices: 17893468--17893498 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17893458 TTGAGAGAAC
17893468 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17893480 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17893492 TTGAAAA
1 TTGAAAA
17893499 GCAAAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:17893522 original size:18 final size:18
Alignment explanation
Indices: 17893495--17893550 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
17893485 AAAGCCTTTG
*
17893495 AAAAGCAAAAGGAAAATGA
1 AAAAG-AAAACGAAAATGA
* * *
17893514 AAAAGAAAATGAGATTGA
1 AAAAGAAAACGAAAATGA
*
17893532 AAAAGAGAACGAAAA-GA
1 AAAAGAAAACGAAAATGA
17893549 AA
1 AA
17893551 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.68, C:0.04, G:0.21, T:0.07
Consensus pattern (18 bp):
AAAAGAAAACGAAAATGA
Found at i:17893546 original size:30 final size:31
Alignment explanation
Indices: 17893512--17893582 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
17893502 AAAGGAAAAT
*
17893512 GAAAAAGAAA-ATGAGATTGAAAAAG-AGAAC
1 GAAAAAGAAATATGAGAGTGAAAAAGAAG-AC
* *
17893542 G-AAAAGAAATTTGAGAGTGAAAAAGAAGAT
1 GAAAAAGAAATATGAGAGTGAAAAAGAAGAC
17893572 GAAAAAGAAAT
1 GAAAAAGAAAT
17893583 TAAAACAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 8 0.23
30 16 0.46
31 11 0.31
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.13
Consensus pattern (31 bp):
GAAAAAGAAATATGAGAGTGAAAAAGAAGAC
Found at i:17893914 original size:30 final size:30
Alignment explanation
Indices: 17893819--17893915 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
17893809 AGCTCACTCC
* * *
17893819 TAGCTC-ACTTTCAACTCACAAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
17893849 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
17893879 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
17893909 TAGCTCA
1 TAGCTCA
17893916 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:17897156 original size:14 final size:14
Alignment explanation
Indices: 17897135--17897178 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
17897125 AAACTTTATA
17897135 TCCATAAACCCATC
1 TCCATAAACCCATC
* * *
17897149 TGCATAAACTTCATA
1 TCCATAAAC-CCATC
17897164 TCCATAAACCCATC
1 TCCATAAACCCATC
17897178 T
1 T
17897179 TTGAATCCTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.36, C:0.34, G:0.02, T:0.27
Consensus pattern (14 bp):
TCCATAAACCCATC
Found at i:17897171 original size:15 final size:15
Alignment explanation
Indices: 17897125--17897172 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
17897115 AAACCTACAA
*
17897125 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
17897140 AAAC-CCATCTGCAT
1 AAACTTCATATCCAT
17897154 AAACTTCATATCCAT
1 AAACTTCATATCCAT
17897169 AAAC
1 AAAC
17897173 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:17901287 original size:21 final size:20
Alignment explanation
Indices: 17901232--17901308 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 20
17901222 AAGAAAACAA
*
17901232 GAAATGAAAGAAAAAGAGTGT
1 GAAA-GAAAGAAAAAGAGAGT
*
17901253 GAAAGAGAGCAAAAAGAGAGT
1 GAAAGAAAG-AAAAAGAGAGT
* *
17901274 GAGAA-AAAGAAAAACGAAATT
1 GA-AAGAAAGAAAAA-GAGAGT
17901295 G-AA-AAAGAAAAAGA
1 GAAAGAAAGAAAAAGA
17901309 ATTTGATCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.04
19 11 0.23
20 9 0.19
21 24 0.50
22 2 0.04
ACGTcount: A:0.64, C:0.03, G:0.26, T:0.08
Consensus pattern (20 bp):
GAAAGAAAGAAAAAGAGAGT
Found at i:17901305 original size:18 final size:17
Alignment explanation
Indices: 17901276--17901336 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
17901266 AAGAGAGTGA
17901276 GAAAAAGAAAAACGAAATT
1 GAAAAAG-AAAA-GAAATT
*
17901295 GAAAAAGAAAAAGAATTT
1 GAAAAAG-AAAAGAAATT
**
17901313 GATCAAGAAAAGAAAATT
1 GAAAAAGAAAAG-AAATT
17901331 GAAAAA
1 GAAAAA
17901337 AAGAGTGAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
17 5 0.14
18 18 0.51
19 12 0.34
ACGTcount: A:0.67, C:0.03, G:0.16, T:0.13
Consensus pattern (17 bp):
GAAAAAGAAAAGAAATT
Found at i:17905379 original size:31 final size:32
Alignment explanation
Indices: 17905326--17905385 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
17905316 AATTCGTTCA
*
17905326 CACCTATGTTCACATGGCAAGACTATTCGGTT
1 CACCTATGTTCACATAGCAAGACTATTCGGTT
*
17905358 CACCT-TGTTCACACTAG-AAGACTCTTCG
1 CACCTATGTTCACA-TAGCAAGACTATTCG
17905386 ACATTCGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (32 bp):
CACCTATGTTCACATAGCAAGACTATTCGGTT
Found at i:17907911 original size:30 final size:30
Alignment explanation
Indices: 17907828--17907924 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
17907818 TAAACTAAAA
* * *
17907828 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
* * * * * *
17907858 TGAGTTGAGGGTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
17907888 TGAGCTAAGGTTTAGCTCGTAAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
17907917 ATGAGCTA
1 -TGAGCTA
17907925 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
Found at i:17910716 original size:17 final size:18
Alignment explanation
Indices: 17910658--17910741 Score: 79
Period size: 17 Copynumber: 4.9 Consensus size: 18
17910648 CATTTTCATT
17910658 TTCTTTTTCTTCTTT-TTA
1 TTCTTTTTCTT-TTTCTTA
* *
17910676 -T-TTTCTCATTTTCTT-
1 TTCTTTTTCTTTTTCTTA
* *
17910691 TTCTCTTTCTTTTTGTTA
1 TTCTTTTTCTTTTTCTTA
*
17910709 TT-TTTTTCTTTTTCTTT
1 TTCTTTTTCTTTTTCTTA
17910726 TTCTTTTTCTTTTTCT
1 TTCTTTTTCTTTTTCT
17910742 CATTTTTCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
15 3 0.06
16 9 0.17
17 25 0.48
18 15 0.29
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTTCTTA
Found at i:17910740 original size:47 final size:46
Alignment explanation
Indices: 17910650--17910769 Score: 127
Period size: 47 Copynumber: 2.5 Consensus size: 46
17910640 TTTCACTTCA
* *
17910650 TTTTCATTTTCTTTTTCTTCTTTTTATTTTCTCATTTTCTTTTCTC-T
1 TTTTC-TTTTATTTTT-TTCTTTTTCTTTTCTCATTTTCTTTTCTCAT
* *
17910697 TTCTTTTTGTTATTTTTTTCTTTTTCTTTT-TCTTTTTCTTTTTCTCAT
1 TT-TTCTT-TTATTTTTTTCTTTTTCTTTTCTCATTTTC-TTTTCTCAT
*
17910745 TTTTCTTTTCTTTTCTTTCTTTTTC
1 TTTTCTTTTATTTT-TTTCTTTTTC
17910770 AACTTCATTC
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
46 13 0.21
47 37 0.60
48 12 0.19
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (46 bp):
TTTTCTTTTATTTTTTTCTTTTTCTTTTCTCATTTTCTTTTCTCAT
Found at i:17910764 original size:35 final size:34
Alignment explanation
Indices: 17910651--17910769 Score: 105
Period size: 35 Copynumber: 3.3 Consensus size: 34
17910641 TTCACTTCAT
* *
17910651 TTTCATTTTCTTTTTCTTCTTTTTATTTTCTCATTTTC
1 TTTCTTTTTCTTTTTC-TCATTTT-TTTT-TC-TTTTC
* * * *
17910689 TTTTCTCTTTCTTTTTGTTATTTTTTTCTT-TTTCTT
1 -TTTCTTTTTCTTTTTCTCATTTTTTT-TTCTTT-TC
17910725 TTTCTTTTTCTTTTTCTCATTTTTCTTTTCTTTTC
1 TTTCTTTTTCTTTTTCTCATTTTT-TTTTCTTTTC
17910760 TTTCTTTTTC
1 TTTCTTTTTC
17910770 AACTTCATTC
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
35 37 0.56
36 6 0.09
37 4 0.06
38 6 0.09
39 13 0.20
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.77
Consensus pattern (34 bp):
TTTCTTTTTCTTTTTCTCATTTTTTTTTCTTTTC
Found at i:17910784 original size:68 final size:63
Alignment explanation
Indices: 17910641--17910789 Score: 160
Period size: 62 Copynumber: 2.3 Consensus size: 63
17910631 AATCAAACTT
* * *
17910641 TTCACTTCATTTTCATTTTCTTTTTCTTCTTTTTATTTTCTCATTTTCTTTTCTCTTTCTTTTTG
1 TTCA-TTC-TTTTCTTTTTCTTTTTCTTCTTTCTATTTTCTCATTTTCTTTTCTCTTTCTTTTTC
*
17910706 TT-ATTTTTTTCTTTTTCTTTTTCTT-TTTCT-TTTTCTCATTTTTCTTTTCTTTTCTTTCTTTT
1 TTCATTCTTTTCTTTTTCTTTTTCTTCTTTCTATTTTCTCA-TTTTCTTTTC---TCTTTCTTTT
17910768 TCAAC
62 T---C
17910773 TTCATTCTTTTCTTTTT
1 TTCATTCTTTTCTTTTT
17910790 TTTCAATTGA
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
60 8 0.11
61 14 0.20
62 18 0.25
63 2 0.03
64 12 0.17
65 2 0.03
67 2 0.03
68 13 0.18
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.74
Consensus pattern (63 bp):
TTCATTCTTTTCTTTTTCTTTTTCTTCTTTCTATTTTCTCATTTTCTTTTCTCTTTCTTTTTC
Found at i:17910789 original size:6 final size:6
Alignment explanation
Indices: 17910650--17910769 Score: 91
Period size: 6 Copynumber: 18.8 Consensus size: 6
17910640 TTTCACTTCA
* * *
17910650 TTTTCA TTTTCT TTTTCT TCTTTTT ATTTTCT CATTTTC- TTTTCT CTTTCT
1 TTTTCT TTTTCT TTTTCT T-TTTCT -TTTTCT --TTTTCT TTTTCT TTTTCT
* *
17910701 TTTTGT TATT-T TTTTCT TTTTCT TTTTCT TTTTCTT TTTCTCAT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTT-TC-T TTTTCT
*
17910751 TTTCTTT TCTTTCT TTTTC
1 TTT-TCT T-TTTCT TTTTC
17910770 AACTTCATTC
Statistics
Matches: 94, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
5 9 0.10
6 50 0.53
7 20 0.21
8 15 0.16
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:17913924 original size:27 final size:26
Alignment explanation
Indices: 17913821--17913939 Score: 96
Period size: 27 Copynumber: 4.5 Consensus size: 26
17913811 TAGCAAAGCT
* * ** *
17913821 ACCAGTAATAATAATGCAGCATAGCT
1 ACCAGTAACAGTAATGTGGCATAGCC
* * *
17913847 ACCAGAAACTGTAAATGTGGCAAAGCC
1 ACCAGTAACAGT-AATGTGGCATAGCC
*
17913874 ACCAGTATCAGTAATTGTGGCATAGCC
1 ACCAGTAACAGTAA-TGTGGCATAGCC
* **
17913901 ACCAGTAACAGTGAATGTGACATATTC
1 ACCAGTAACAGT-AATGTGGCATAGCC
17913928 ACCAGT-ACAGTA
1 ACCAGTAACAGTA
17913940 CTTCCTCCAT
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
25 1 0.01
26 15 0.20
27 56 0.76
28 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (26 bp):
ACCAGTAACAGTAATGTGGCATAGCC
Found at i:17914301 original size:107 final size:108
Alignment explanation
Indices: 17914076--17914478 Score: 557
Period size: 107 Copynumber: 3.8 Consensus size: 108
17914066 GGCATAATCA
* *
17914076 TCATTTTACCATACAGGGGC---ACGGTCATTTTACCTTACAGGGGAATTACGGTCATTTTACCC
1 TCATTTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAGGGGCATTACGGTCATTTTACCC
* **
17914138 TTCAGGGGTATTATGGTCATTTTACCCTACAGGGGCATTACAG
66 TACAGGGGTATTACAGTCATTTTACCCTACAGGGGCATTACAG
* *
17914181 TCATTTTACCCTACAGGGGCATTACGGTCATTTTAACC-TACAGGGGTATTACAGTCATTTTACC
1 TCATTTTACCCTACAGGGGCATTACGGTCATTTT-ACCTTACAGGGGCATTACGGTCATTTTACC
* * * *
17914245 CTACA-GGGTATTACGGTCATTTTATCCTAGAGGGGCATTACGG
65 CTACAGGGGTATTACAGTCATTTTACCCTACAGGGGCATTACAG
* * * * * *
17914288 TCATTTAACCCTACAGGAGCATTATGGTCATTTTACCCTACAGAGGCATTACGGTCATCTTACCC
1 TCATTTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAGGGGCATTACGGTCATTTTACCC
*
17914353 TACAGGGGTATT-CAGTCATTTTACCCTACAGGGGCATTGCAG
66 TACAGGGGTATTACAGTCATTTTACCCTACAGGGGCATTACAG
* *
17914395 TCATTTTACCTTACAGGGGCATTACAGTCATTTTACCTTACAGGGGCATTACGGTCATTTTACCC
1 TCATTTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAGGGGCATTACGGTCATTTTACCC
* *
17914460 TATAGAGGTATTACAGTCA
66 TACAGGGGTATTACAGTCA
17914479 AATAACAACC
Statistics
Matches: 261, Mismatches: 30, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
105 19 0.07
106 3 0.01
107 184 0.70
108 52 0.20
109 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (108 bp):
TCATTTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAGGGGCATTACGGTCATTTTACCC
TACAGGGGTATTACAGTCATTTTACCCTACAGGGGCATTACAG
Found at i:17914478 original size:27 final size:27
Alignment explanation
Indices: 17914076--17914461 Score: 512
Period size: 27 Copynumber: 14.5 Consensus size: 27
17914066 GGCATAATCA
*
17914076 TCATTTTACCATACAGGGGC---ACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* *
17914100 TCATTTTACCTTACAGGGGAATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* * *
17914127 TCATTTTACCCTTCAGGGGTATTATGG
1 TCATTTTACCCTACAGGGGCATTACGG
*
17914154 TCATTTTACCCTACAGGGGCATTACAG
1 TCATTTTACCCTACAGGGGCATTACGG
17914181 TCATTTTACCCTACAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* * *
17914208 TCATTTTAACCTACAGGGGTATTACAG
1 TCATTTTACCCTACAGGGGCATTACGG
*
17914235 TCATTTTACCCTACA-GGGTATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* *
17914261 TCATTTTATCCTAGAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* * *
17914288 TCATTTAACCCTACAGGAGCATTATGG
1 TCATTTTACCCTACAGGGGCATTACGG
*
17914315 TCATTTTACCCTACAGAGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* * *
17914342 TCATCTTACCCTACAGGGGTATT-CAG
1 TCATTTTACCCTACAGGGGCATTACGG
* *
17914368 TCATTTTACCCTACAGGGGCATTGCAG
1 TCATTTTACCCTACAGGGGCATTACGG
* *
17914395 TCATTTTACCTTACAGGGGCATTACAG
1 TCATTTTACCCTACAGGGGCATTACGG
*
17914422 TCATTTTACCTTACAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
17914449 TCATTTTACCCTA
1 TCATTTTACCCTA
17914462 TAGAGGTATT
Statistics
Matches: 319, Mismatches: 38, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
24 18 0.06
26 46 0.14
27 255 0.80
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGCATTACGG
Found at i:17919994 original size:7 final size:7
Alignment explanation
Indices: 17919984--17920029 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
17919974 TTCTAAACGT
17919984 TAAACCC
1 TAAACCC
17919991 TAAACCC
1 TAAACCC
17919998 TAAACCC
1 TAAACCC
*
17920005 TAAACTC
1 TAAACCC
*
17920012 TAAAACC
1 TAAACCC
17920019 TAAACCC
1 TAAACCC
17920026 TAAA
1 TAAA
17920030 TCCATGTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:17919995 original size:14 final size:13
Alignment explanation
Indices: 17919976--17920023 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
17919966 ACAAGAATTT
17919976 CTAAACGTTAAACC
1 CTAAAC-TTAAACC
*
17919990 CTAAACCCTAAACC
1 CTAAA-CTTAAACC
*
17920004 CTAAACTCTAAAAC
1 CTAAACT-TAAACC
17920018 CTAAAC
1 CTAAAC
17920024 CCTAAATCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19
Consensus pattern (13 bp):
CTAAACTTAAACC
Found at i:17920818 original size:15 final size:15
Alignment explanation
Indices: 17920798--17920834 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
17920788 TCCATGCATA
17920798 ATATAATTTAAATAT
1 ATATAATTTAAATAT
17920813 ATATAAATTTAAATAT
1 ATAT-AATTTAAATAT
17920829 AT-TAAT
1 ATATAAT
17920835 AATATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 5 0.24
16 13 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATAATTTAAATAT
Found at i:17923815 original size:5 final size:5
Alignment explanation
Indices: 17923805--17923861 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
17923795 CTTTTGCCTC
*
17923805 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
17923852 TCTTT TCTTT
1 TCTTT TCTTT
17923862 GTTTTCTCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:17923845 original size:15 final size:14
Alignment explanation
Indices: 17923805--17923861 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
17923795 CTTTTGCCTC
*
17923805 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
17923820 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
17923835 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
17923852 TCTTTTCTTT
1 TCTTTTCTTT
17923862 GTTTTCTCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:17923862 original size:21 final size:21
Alignment explanation
Indices: 17923805--17923866 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
17923795 CTTTTGCCTC
* *
17923805 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
17923826 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
17923847 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
17923867 CTCGTTACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 7 0.21
21 22 0.65
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:17924802 original size:11 final size:11
Alignment explanation
Indices: 17924784--17924824 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
17924774 TTTTCACTTC
17924784 AATTTTTTT-G
1 AATTTTTTTCG
* *
17924794 GATTTTTTTCA
1 AATTTTTTTCG
17924805 AATTTTTTTCG
1 AATTTTTTTCG
17924816 AATTTTTTT
1 AATTTTTTT
17924825 TAACTTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (11 bp):
AATTTTTTTCG
Found at i:17924809 original size:21 final size:22
Alignment explanation
Indices: 17924784--17924824 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
17924774 TTTTCACTTC
*
17924784 AATTTTTTT-GGATTTTTTTCA
1 AATTTTTTTCGAATTTTTTTCA
17924805 AATTTTTTTCGAATTTTTTT
1 AATTTTTTTCGAATTTTTTT
17924825 TAACTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (22 bp):
AATTTTTTTCGAATTTTTTTCA
Found at i:17926177 original size:10 final size:10
Alignment explanation
Indices: 17926164--17926209 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
17926154 AGCTCACTTG
17926164 AGCTCGTTTT
1 AGCTCGTTTT
*
17926174 AGCTCGTTTG
1 AGCTCGTTTT
*
17926184 AGCTCGAATTT
1 AGCTCG-TTTT
*
17926195 AGCTCGTTTC
1 AGCTCGTTTT
17926205 AGCTC
1 AGCTC
17926210 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:17926197 original size:21 final size:20
Alignment explanation
Indices: 17926161--17926209 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
17926151 ATCAGCTCAC
*
17926161 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
17926181 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
17926202 TTCAGCTC
1 TTGAGCTC
17926210 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:17926452 original size:13 final size:13
Alignment explanation
Indices: 17926434--17926462 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17926424 AATAGTTGTG
17926434 TGTTATTTAATTA
1 TGTTATTTAATTA
17926447 TGTTATTTAATTA
1 TGTTATTTAATTA
17926460 TGT
1 TGT
17926463 AGGTTAGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:17928609 original size:21 final size:20
Alignment explanation
Indices: 17928541--17928609 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 20
17928531 GTAAATCAGT
17928541 TGAGAGAAAAAGAAAAGAATGAA
1 TGAGA-AAAAAGAAAAGAA--AA
*
17928564 TGTGAAAAAAG-AAAGAAAA
1 TGAGAAAAAAGAAAAGAAAA
17928583 T--G-AAAAAGAAAAGAAAA
1 TGAGAAAAAAGAAAAGAAAA
17928600 TCGAGAAAAA
1 T-GAGAAAAA
17928610 GAATACAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
16 6 0.15
17 10 0.25
19 3 0.08
20 1 0.03
21 10 0.25
22 6 0.15
23 4 0.10
ACGTcount: A:0.68, C:0.01, G:0.22, T:0.09
Consensus pattern (20 bp):
TGAGAAAAAAGAAAAGAAAA
Found at i:17931707 original size:21 final size:21
Alignment explanation
Indices: 17931681--17931720 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17931671 TTGAGCTCGT
*
17931681 TTTAGCTCGTTTGAGCTCAAA
1 TTTAGCTCGTTTCAGCTCAAA
17931702 TTTAGCTCGTTTCAGCTCA
1 TTTAGCTCGTTTCAGCTCA
17931721 TTCCTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGCTCGTTTCAGCTCAAA
Found at i:17931962 original size:13 final size:13
Alignment explanation
Indices: 17931944--17931972 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17931934 AATAGTTGTG
17931944 TGTTATTTAATTA
1 TGTTATTTAATTA
17931957 TGTTATTTAATTA
1 TGTTATTTAATTA
17931970 TGT
1 TGT
17931973 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:17934190 original size:13 final size:13
Alignment explanation
Indices: 17934172--17934200 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17934162 CGGCTAACCT
17934172 ACATAATTAAATA
1 ACATAATTAAATA
17934185 ACATAATTAAATA
1 ACATAATTAAATA
17934198 ACA
1 ACA
17934201 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:17941784 original size:30 final size:30
Alignment explanation
Indices: 17941688--17941785 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
17941678 TAAGCTCACT
*
17941688 CTTAGCTC-ACTTTCAACTCACGAGCTAAA-
1 CTTAGCTCAACTTT-AGCTCACGAGCTAAAG
* * * **
17941717 CTTAGCTCAACTTCAGCTTAGGAG-TTTAG
1 CTTAGCTCAACTTTAGCTCACGAGCTAAAG
*
17941746 CCTCAGCTCAACTTTAGCTCACGAGCTAAAG
1 -CTTAGCTCAACTTTAGCTCACGAGCTAAAG
17941777 CTTAGCTCA
1 CTTAGCTCA
17941786 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
28 2 0.04
29 15 0.29
30 32 0.62
31 3 0.06
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29
Consensus pattern (30 bp):
CTTAGCTCAACTTTAGCTCACGAGCTAAAG
Found at i:17943481 original size:12 final size:12
Alignment explanation
Indices: 17943464--17943520 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
17943454 TATACAAGCC
17943464 AAAAAAATTTGA
1 AAAAAAATTTGA
*
17943476 AAAAAAA-TTCA
1 AAAAAAATTTGA
*
17943487 AAAAAAATTCGAAA
1 AAAAAAATTTG--A
*
17943501 AGAAAAAATCTGA
1 A-AAAAAATTTGA
17943514 AAAAAAA
1 AAAAAAA
17943521 GTGTTTAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
11 10 0.28
12 14 0.39
13 2 0.06
14 2 0.06
15 8 0.22
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.16
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:17943501 original size:10 final size:11
Alignment explanation
Indices: 17943463--17943506 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
17943453 TTATACAAGC
*
17943463 CAAAAAAATTT
1 CAAAAAAAATT
*
17943474 GAAAAAAAATT
1 CAAAAAAAATT
17943485 CAAAAAAAATT
1 CAAAAAAAATT
17943496 CGAAAAGAAAA
1 C-AAAA-AAAA
17943507 AATCTGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 20 0.71
12 4 0.14
13 4 0.14
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.16
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:17944442 original size:9 final size:10
Alignment explanation
Indices: 17944435--17944491 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
17944425 AAGAGAAAAC
17944435 AAAGAAAAGA
1 AAAGAAAAGA
17944445 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
17944457 AAAGAAGA-A
1 AAAGAAAAGA
17944466 AAAGAAAATGA
1 AAAGAAAA-GA
17944477 AATA-AAAAGA
1 AA-AGAAAAGA
17944487 AAAGA
1 AAAGA
17944492 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:17944458 original size:21 final size:20
Alignment explanation
Indices: 17944424--17944491 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
17944414 ACATTCTTGT
17944424 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
17944445 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
17944466 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
17944487 AAAGA
1 AAAGA
17944492 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:17944459 original size:6 final size:5
Alignment explanation
Indices: 17944435--17944491 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
17944425 AAGAGAAAAC
*
17944435 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
17944482 AAAGA AAAGA
1 AAAGA AAAGA
17944492 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:17944466 original size:15 final size:14
Alignment explanation
Indices: 17944435--17944491 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
17944425 AAGAGAAAAC
17944435 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
17944451 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
17944466 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
17944482 AAAGAAAAGA
1 AAAGAAAAGA
17944492 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:17944564 original size:12 final size:12
Alignment explanation
Indices: 17944556--17944580 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17944546 TTTGAAAAGC
17944556 AAAAAGAAAATG
1 AAAAAGAAAATG
17944568 AAAAAGAAAATG
1 AAAAAGAAAATG
17944580 A
1 A
17944581 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:17944577 original size:18 final size:18
Alignment explanation
Indices: 17944550--17944605 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
17944540 AAAGCCTTTG
17944550 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
17944569 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
17944587 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
17944604 AA
1 AA
17944606 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:17944590 original size:30 final size:31
Alignment explanation
Indices: 17944556--17944637 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
17944546 TTTGAAAAGC
*
17944556 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
17944586 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
17944616 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
17944638 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:17952172 original size:14 final size:14
Alignment explanation
Indices: 17952130--17952174 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
17952120 TTAAAGAAGC
17952130 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
17952144 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
17952157 AACTCATTTAATTA
1 AACTCATTAAATTA
17952171 AACT
1 AACT
17952175 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:17954673 original size:18 final size:18
Alignment explanation
Indices: 17954646--17954695 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
17954636 CAAACTCTTT
17954646 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
17954664 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
17954682 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
17954696 TTTTCTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:17956086 original size:29 final size:29
Alignment explanation
Indices: 17956020--17956078 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
17956010 AAGGATTCAA
*
17956020 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
17956049 AGATGGGTTTAT-GATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
17956077 AG
1 AG
17956079 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:17957100 original size:14 final size:14
Alignment explanation
Indices: 17957058--17957102 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
17957048 TTAAAGAAGC
17957058 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
17957072 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
17957085 AACTCATTTAATTA
1 AACTCATTAAATTA
17957099 AACT
1 AACT
17957103 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:17958422 original size:12 final size:12
Alignment explanation
Indices: 17958407--17958440 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
17958397 TTCTTTTCGT
17958407 TCTCTTTTTCAA
1 TCTCTTTTTCAA
17958419 TCTCTTTTTCAA
1 TCTCTTTTTCAA
*
17958431 TCTCATTTTC
1 TCTCTTTTTC
17958441 TTTTTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTCTTTTTCAA
Found at i:17958475 original size:12 final size:12
Alignment explanation
Indices: 17958460--17958490 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17958450 TTCTTTTTGC
17958460 TTTTCAAAGGCT
1 TTTTCAAAGGCT
17958472 TTTTCAAAGGCT
1 TTTTCAAAGGCT
17958484 TTTTCAA
1 TTTTCAA
17958491 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:17958578 original size:15 final size:15
Alignment explanation
Indices: 17958538--17958579 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
17958528 CTCTTGCCTC
*
17958538 TCTTTTCTTTTTATT
1 TCTTTTCTTTTTACT
17958553 TCATTTTCTTTTT-CT
1 TC-TTTTCTTTTTACT
17958568 TCTTTTGCTTTT
1 TCTTTT-CTTTT
17958580 GGTTTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.17
15 10 0.42
16 10 0.42
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (15 bp):
TCTTTTCTTTTTACT
Found at i:17958601 original size:21 final size:23
Alignment explanation
Indices: 17958567--17958611 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
17958557 TTTCTTTTTC
17958567 TTCTTTTGCTTTTGGTTTT-TCTT
1 TTCTTTTGCTTTT-GTTTTCTCTT
17958590 TTCTTTT-C-TTTGTTTTCTCTT
1 TTCTTTTGCTTTTGTTTTCTCTT
17958611 T
1 T
17958612 ACAAGAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 1 0.05
23 7 0.33
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.76
Consensus pattern (23 bp):
TTCTTTTGCTTTTGTTTTCTCTT
Found at i:17974008 original size:17 final size:17
Alignment explanation
Indices: 17973988--17974021 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17973978 CTATAAGCAC
17973988 AATTAAACAAGTTAAAT
1 AATTAAACAAGTTAAAT
17974005 AATTAAACAAGTTAAAT
1 AATTAAACAAGTTAAAT
17974022 GGCTATAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
AATTAAACAAGTTAAAT
Found at i:17978072 original size:30 final size:30
Alignment explanation
Indices: 17977976--17978060 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
17977966 TAAACTAAAA
*
17977976 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
17978006 TGAGCTGAGGCTAAACTCCTAAGCTCAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
17978036 TGAGCTAAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGGTTTAGCTCGTGAGCT
17978061 GAATATGAGC
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:17980312 original size:5 final size:5
Alignment explanation
Indices: 17980302--17980358 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
17980292 CTCTTGCCTC
*
17980302 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
17980349 TCTTT TCTTT
1 TCTTT TCTTT
17980359 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:17980342 original size:15 final size:14
Alignment explanation
Indices: 17980302--17980358 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
17980292 CTCTTGCCTC
*
17980302 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
17980317 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
17980332 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
17980349 TCTTTTCTTT
1 TCTTTTCTTT
17980359 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:17980368 original size:21 final size:20
Alignment explanation
Indices: 17980300--17980369 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
17980290 GCCTCTTGCC
17980300 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
17980323 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
17980343 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
17980363 TCTCTTT
1 TCTCTTT
17980370 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:17983476 original size:30 final size:29
Alignment explanation
Indices: 17983431--17983502 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
17983421 TTCTTTTGTT
*
17983431 TCAATTTCTTTTTCA-TCTTCTTTTTCACTC
1 TCAATTTC-TTTTCATTC-TCTTTTTCAATC
17983461 TCAAATTTCTTTTCATTCTCTTTTTCAATC
1 TC-AATTTCTTTTCATTCTCTTTTTCAATC
*
17983491 TCATTTTCTTTT
1 TCAATTTCTTTT
17983503 TGCTTTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 9 0.24
30 21 0.55
31 8 0.21
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (29 bp):
TCAATTTCTTTTCATTCTCTTTTTCAATC
Found at i:17983520 original size:11 final size:11
Alignment explanation
Indices: 17983504--17983531 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
17983494 TTTTCTTTTT
17983504 GCTTTTCAAAG
1 GCTTTTCAAAG
17983515 GCTTTTCAAAG
1 GCTTTTCAAAG
17983526 GCTTTT
1 GCTTTT
17983532 TAAGTTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (11 bp):
GCTTTTCAAAG
Found at i:17983604 original size:6 final size:5
Alignment explanation
Indices: 17983582--17983629 Score: 53
Period size: 5 Copynumber: 9.0 Consensus size: 5
17983572 CTTTTGCCTC
17983582 TCTTT TCTTT T-TATT TCGTTT TCTTTT TCTTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TC-TTT TCTTT TCTTT TCTTT
17983630 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
4 1 0.03
5 22 0.56
6 15 0.38
7 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:17983611 original size:22 final size:22
Alignment explanation
Indices: 17983584--17983629 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
17983574 TTTGCCTCTC
17983584 TTTTCTTTTT-ATTTCGTTTTCT
1 TTTTCTTTTTCATTTC-TTTTCT
*
17983606 TTTTCTTTTTCTTTTCTTTTCT
1 TTTTCTTTTTCATTTCTTTTCT
17983628 TT
1 TT
17983630 GTTTTCTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTCTTTTTCATTTCTTTTCT
Found at i:17983640 original size:16 final size:15
Alignment explanation
Indices: 17983584--17983636 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
17983574 TTTGCCTCTC
*
17983584 TTTTCTTTTTATTTCG
1 TTTTCTTTTTCTTT-G
17983600 TTTTCTTTTTCTTT-
1 TTTTCTTTTTCTTTG
*
17983614 TTCTTTTCTTTTCTTTG
1 TT-TTCT-TTTTCTTTG
17983631 TTTTCT
1 TTTTCT
17983637 CTTTACAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 2 0.06
15 3 0.10
16 24 0.77
17 2 0.06
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTCTTTG
Found at i:17986235 original size:30 final size:30
Alignment explanation
Indices: 17986201--17986283 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
17986191 TAAACTAAAA
17986201 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
17986231 TGAGCTGAAGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
17986261 TGAGCTAAGGTTTAGCTCGTGAG
1 TGAGCTAAGCTTTAGCTCGTGAG
17986284 TTGAAAGTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
29 3 0.07
30 34 0.83
31 4 0.10
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:17986863 original size:35 final size:33
Alignment explanation
Indices: 17986824--17986905 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
17986814 CTGTATTGAG
*
17986824 ATGGGCTTAGGCCGAGACTGTTTACTGATACTAAA
1 ATGGGCTTAGGCCG-GACT-ATTACTGATACTAAA
* * **
17986859 ATGGGCTAAGGCCCGGACTATTACTGTTACTATT
1 ATGGGCTTAGG-CCGGACTATTACTGATACTAAA
17986893 ATGGGCTTAGGCC
1 ATGGGCTTAGGCC
17986906 CAGAATGTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.05
34 21 0.52
35 14 0.35
36 3 0.08
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (33 bp):
ATGGGCTTAGGCCGGACTATTACTGATACTAAA
Found at i:17999711 original size:10 final size:10
Alignment explanation
Indices: 17999698--17999732 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
17999688 AAGCTCGGTT
17999698 GAGCTCAAAC
1 GAGCTCAAAC
*
17999708 GAGCTAAAAC
1 GAGCTCAAAC
*
17999718 GAGCTCAAAT
1 GAGCTCAAAC
17999728 GAGCT
1 GAGCT
17999733 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:17999741 original size:20 final size:20
Alignment explanation
Indices: 17999695--17999742 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
17999685 AGTAAGCTCG
17999695 GTTGAGCTCAAACGAGCTAA
1 GTTGAGCTCAAACGAGCTAA
*** * *
17999715 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTAA
17999735 GTTGAGCT
1 GTTGAGCT
17999743 GGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTAA
Found at i:18001355 original size:18 final size:19
Alignment explanation
Indices: 18001332--18001388 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
18001322 TTTATCTCAA
18001332 TTTCTTTTTC-CACTCTTT
1 TTTCTTTTTCACACTCTTT
* *
18001350 TTTCTTGTTCACATTC-TT
1 TTTCTTTTTCACACTCTTT
* *
18001368 TTTCTCTTTCAAACTCTTT
1 TTTCTTTTTCACACTCTTT
18001387 TT
1 TT
18001389 CATTCTCTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 23 0.74
19 8 0.26
ACGTcount: A:0.11, C:0.25, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTCTTTTTCACACTCTTT
Found at i:18001396 original size:12 final size:12
Alignment explanation
Indices: 18001374--18001413 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
18001364 TCTTTTTCTC
*
18001374 TTTCAAACTCTT
1 TTTCAATCTCTT
*
18001386 TTTCATTCTCTT
1 TTTCAATCTCTT
*
18001398 TTTCAATCTCAT
1 TTTCAATCTCTT
18001410 TTTC
1 TTTC
18001414 TTTTTCATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTCAATCTCTT
Found at i:18001415 original size:18 final size:18
Alignment explanation
Indices: 18001388--18001439 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
18001378 AAACTCTTTT
*
18001388 TCATTCTCTTTTTCAATC
1 TCATTTTCTTTTTCAATC
* *
18001406 TCATTTTCTTTTTCATTT
1 TCATTTTCTTTTTCAATC
* *
18001424 TCTTTTTGTTTTTCAA
1 TCATTTTCTTTTTCAA
18001440 AGGCTTTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.19, G:0.02, T:0.65
Consensus pattern (18 bp):
TCATTTTCTTTTTCAATC
Found at i:18001424 original size:24 final size:23
Alignment explanation
Indices: 18001363--18001425 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
18001353 CTTGTTCACA
*
18001363 TTCTTTTTCTCTTTCAAACTCTTT
1 TTCTTTTTCT-TTTCAAACTCATT
* * *
18001387 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTTTC-TTTTCAAACTCATT
18001411 TTCTTTTTCATTTTC
1 TTCTTTTTC-TTTTC
18001426 TTTTTGTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.63
Consensus pattern (23 bp):
TTCTTTTTCTTTTCAAACTCATT
Found at i:18001437 original size:12 final size:12
Alignment explanation
Indices: 18001406--18001430 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18001396 TTTTTCAATC
18001406 TCATTTTCTTTT
1 TCATTTTCTTTT
18001418 TCATTTTCTTTT
1 TCATTTTCTTTT
18001430 T
1 T
18001431 GTTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:18001539 original size:15 final size:14
Alignment explanation
Indices: 18001499--18001555 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 14
18001489 CTTTTGCCTC
*
18001499 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
*
18001514 TCATTTCCTTTTTCT
1 TC-TTTTCTTTTTCT
18001529 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
18001546 TCTTTTCTTT
1 TCTTTTCTTT
18001556 GTTTTCTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
14 3 0.09
15 12 0.34
16 13 0.37
17 7 0.20
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:18007286 original size:19 final size:19
Alignment explanation
Indices: 18007259--18007299 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
18007249 TGAGCTGGTA
* *
18007259 GTGAGCTGGACCTGAGCTG
1 GTGAACTGGAACTGAGCTG
*
18007278 GTGAACTGGAAGTGAGCTG
1 GTGAACTGGAACTGAGCTG
18007297 GTG
1 GTG
18007300 GCGAGCTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.15, G:0.44, T:0.22
Consensus pattern (19 bp):
GTGAACTGGAACTGAGCTG
Found at i:18013993 original size:46 final size:45
Alignment explanation
Indices: 18013943--18014116 Score: 221
Period size: 46 Copynumber: 3.8 Consensus size: 45
18013933 TGTTTGGGCA
18013943 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
18013989 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGA--GATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
18014034 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
18014080 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18014117 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 33 0.30
46 68 0.61
47 4 0.04
48 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:18014048 original size:91 final size:91
Alignment explanation
Indices: 18013939--18014108 Score: 313
Period size: 91 Copynumber: 1.9 Consensus size: 91
18013929 AGGATGTTTG
* *
18013939 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
18014004 TTGAGTCCGAGTTCGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGATGTAACTA
*
18014030 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
18014095 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
18014109 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (91 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGATGTAACTA
Found at i:18017085 original size:15 final size:15
Alignment explanation
Indices: 18017065--18017133 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
18017055 GTATCTTGGG
18017065 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
18017080 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
18017095 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
18017110 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
18017125 TTTCTTTAT
1 TTTCTTTAT
18017134 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:18017134 original size:30 final size:30
Alignment explanation
Indices: 18017056--18017143 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
18017046 CATAGTATCG
* * * *
18017056 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
18017086 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
18017116 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
18017144 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:18019574 original size:46 final size:45
Alignment explanation
Indices: 18019524--18019699 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
18019514 TGTTTGGGCA
18019524 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
18019570 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
18019617 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
18019663 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18019700 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:18019631 original size:93 final size:93
Alignment explanation
Indices: 18019520--18019691 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
18019510 AGGATGTTTG
* *
18019520 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
18019585 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
18019613 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
18019678 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
18019692 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:18022524 original size:19 final size:19
Alignment explanation
Indices: 18022500--18022539 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
18022490 AGCTCCCATG
18022500 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
18022519 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
18022538 TA
1 TA
18022540 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:18027834 original size:19 final size:19
Alignment explanation
Indices: 18027810--18027849 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
18027800 AGCTCCCATG
18027810 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
18027829 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
18027848 TA
1 TA
18027850 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:18029520 original size:10 final size:9
Alignment explanation
Indices: 18029499--18029540 Score: 61
Period size: 8 Copynumber: 4.8 Consensus size: 9
18029489 TATACAAGTT
18029499 AAAAAAAT-
1 AAAAAAATC
18029507 AAAAAAATC
1 AAAAAAATC
18029516 GAAAAAAATC
1 -AAAAAAATC
18029526 AAAAAAAT-
1 AAAAAAATC
18029534 AAAAAAA
1 AAAAAAA
18029541 AGTGATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 15 0.47
9 8 0.25
10 9 0.28
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:18033571 original size:30 final size:30
Alignment explanation
Indices: 18033485--18033582 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
18033475 TTAAACTAAA
* *
18033485 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
18033515 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
18033545 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
18033575 ATGAGCTA
1 ATGAGCTA
18033583 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:18035856 original size:29 final size:30
Alignment explanation
Indices: 18035786--18035867 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
18035776 CTTTTGTTTC
*
18035786 AATTTCTTTTTCA-TCTTCTTTTTCACTCTCA
1 AATTTC-TTTTCATTC-TCTTTTTCAATCTCA
*
18035817 AATTTCTTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTCATTCTCTTTTTCAATCTCA
* * *
18035846 ATTTTTTTTTCATTTTCTTTTT
1 AATTTCTTTTCATTCTCTTTTT
18035868 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
29 18 0.41
30 18 0.41
31 8 0.18
ACGTcount: A:0.13, C:0.21, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTCATTCTCTTTTTCAATCTCA
Found at i:18035885 original size:12 final size:12
Alignment explanation
Indices: 18035870--18035900 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
18035860 TTCTTTTTGC
18035870 TTTTCAAAGACT
1 TTTTCAAAGACT
*
18035882 TTTTCAAAGGCT
1 TTTTCAAAGACT
18035894 TTTTCAA
1 TTTTCAA
18035901 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGACT
Found at i:18035958 original size:5 final size:5
Alignment explanation
Indices: 18035948--18036004 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
18035938 CTCTTGCCTC
*
18035948 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
18035995 TCTTT TCTTT
1 TCTTT TCTTT
18036005 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:18035988 original size:15 final size:14
Alignment explanation
Indices: 18035948--18036004 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
18035938 CTCTTGCCTC
*
18035948 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
18035963 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
18035978 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
18035995 TCTTTTCTTT
1 TCTTTTCTTT
18036005 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:18036005 original size:21 final size:21
Alignment explanation
Indices: 18035948--18036015 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
18035938 CTCTTGCCTC
* *
18035948 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
18035969 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
18035990 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
18036010 CTCTTT
1 -TCTTT
18036016 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:18037091 original size:320 final size:321
Alignment explanation
Indices: 18036563--18037204 Score: 1250
Period size: 320 Copynumber: 2.0 Consensus size: 321
18036553 TGATACCAGA
18036563 TGATACGAACCACCTCGGGGAGAGTCGAGTCGTATGCTGAGTTGCCCGATCGTCTACGAGAAACT
1 TGATACGAACCACCTCGGGGAGAGTCGAGTCGTATGCTGAGTTGCCCGATCGTCTACGAGAAACT
18036628 ATCGTTCAATTCACTTTTGAAATGAAGTTGATGGAAAAATAGGACGGAAGCTATGTATAATGGTT
66 ATCGTTCAATTCACTTTTGAAATGAAGTTGATGGAAAAATAGGACGGAAGCTATGTATAATGGTT
* *
18036693 CTATGATGGTTTATGGATAAATACAGGTTCGGTTAAATTGGAAGGGAAAGTGAAAGAAGTAAATA
131 CTATGATGGTTTATGGATAAATACAGGTTCGGCTAAATTGGAAGGGAAAGTGAAAAAAGTAAATA
18036758 GAGGATGGATATGGAAGAAAAAGGGTTCTTAAAAGCAAGCACGAACCAATATTAGAAAAATATCG
196 GAGGATGGATATGGAAGAAAAAGGGTTCTTAAAAGCAAGCACGAACCAATATTAGAAAAATATCG
18036823 GCCCAAAATGCTTATAGGCTTTCAAGGTGGAGGATGAAAGTGATAAACCTTGACCCGCTAC
261 GCCCAAAATGCTTATAGGCTTTCAAGGTGGAGGATGAAAGTGATAAACCTTGACCCGCTAC
*
18036884 TGATACGAACTACCTCGGGGAGAGTCGAGTCGTATGCTGAGTTGCCCGATCGTCTACGAGAAACT
1 TGATACGAACCACCTCGGGGAGAGTCGAGTCGTATGCTGAGTTGCCCGATCGTCTACGAGAAACT
18036949 ATCGTTCAATTCACTTTTGAAATGAAGTTGATGGAAAAAT-GGACGGAAGCTATGTATAATGGTT
66 ATCGTTCAATTCACTTTTGAAATGAAGTTGATGGAAAAATAGGACGGAAGCTATGTATAATGGTT
18037013 CTATGATGGTTTATGGATAAATACAGGTTCGGCTAAATTGGAAGGGAAAGTGAAAAAAGTAAATA
131 CTATGATGGTTTATGGATAAATACAGGTTCGGCTAAATTGGAAGGGAAAGTGAAAAAAGTAAATA
18037078 GAGGATGGATATGGAAGAAAAAGGGTTCTTAAAAGCAAGCACGAACCAATATTAGAAAAATATCG
196 GAGGATGGATATGGAAGAAAAAGGGTTCTTAAAAGCAAGCACGAACCAATATTAGAAAAATATCG
18037143 GCCCAAAATGCTTATAGGCTTTCAAGGTGGAGGATGAAAGTGATAAACCTTGACCCGCTAC
261 GCCCAAAATGCTTATAGGCTTTCAAGGTGGAGGATGAAAGTGATAAACCTTGACCCGCTAC
18037204 T
1 T
18037205 TAGCAAAGTA
Statistics
Matches: 318, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
320 214 0.67
321 104 0.33
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.25
Consensus pattern (321 bp):
TGATACGAACCACCTCGGGGAGAGTCGAGTCGTATGCTGAGTTGCCCGATCGTCTACGAGAAACT
ATCGTTCAATTCACTTTTGAAATGAAGTTGATGGAAAAATAGGACGGAAGCTATGTATAATGGTT
CTATGATGGTTTATGGATAAATACAGGTTCGGCTAAATTGGAAGGGAAAGTGAAAAAAGTAAATA
GAGGATGGATATGGAAGAAAAAGGGTTCTTAAAAGCAAGCACGAACCAATATTAGAAAAATATCG
GCCCAAAATGCTTATAGGCTTTCAAGGTGGAGGATGAAAGTGATAAACCTTGACCCGCTAC
Found at i:18038309 original size:31 final size:30
Alignment explanation
Indices: 18038273--18038358 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
18038263 TAAACTAAAA
* * *
18038273 TGAGCTAAGCTTTAGCTCGTGAGCTAAAAGT
1 TGAGCTAAGATTTAGCTCATGAGCT-AAAGC
* * * * *
18038304 TGAGCTGAGATTAAACTCCTAAGCTAAAGC
1 TGAGCTAAGATTTAGCTCATGAGCTAAAGC
*
18038334 TGAGCTAAGTTTTAGCTCATGAGCT
1 TGAGCTAAGATTTAGCTCATGAGCT
18038359 GAATATGAGC
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
30 23 0.55
31 19 0.45
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCATGAGCTAAAGC
Found at i:18042574 original size:19 final size:19
Alignment explanation
Indices: 18042550--18042589 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
18042540 AGCTCCCATG
18042550 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
18042569 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
18042588 TA
1 TA
18042590 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:18043188 original size:31 final size:32
Alignment explanation
Indices: 18043135--18043194 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
18043125 AATTCGTTCA
*
18043135 CACCTATGTTCACATGGCAAGACTATTCAGTT
1 CACCTATGTTCACATAGCAAGACTATTCAGTT
*
18043167 CACCT-TGTTCACACTAG-AAGACTCTTCA
1 CACCTATGTTCACA-TAGCAAGACTATTCA
18043195 ACATTCGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (32 bp):
CACCTATGTTCACATAGCAAGACTATTCAGTT
Found at i:18046932 original size:30 final size:29
Alignment explanation
Indices: 18046878--18046958 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 29
18046868 TTCTTTTGTT
* *
18046878 TCAATTTCTTTTTCATCTTCTTTTTTACTC
1 TCAATTTC-TTTTCATCTTCTTTTTCAATC
*
18046908 TCAAATTTCTTTTCGTTCTT-TTTTTCAATC
1 TC-AATTTCTTTTC-ATCTTCTTTTTCAATC
* *
18046938 TCATTTTCTTTTTCATTTTCT
1 TCAATTTC-TTTTCATCTTCT
18046959 GTTTGCTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
29 8 0.20
30 23 0.56
31 10 0.24
ACGTcount: A:0.14, C:0.21, G:0.01, T:0.64
Consensus pattern (29 bp):
TCAATTTCTTTTCATCTTCTTTTTCAATC
Found at i:18046980 original size:12 final size:12
Alignment explanation
Indices: 18046965--18046994 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
18046955 TTCTGTTTGC
18046965 TTTTCAAAGGCT
1 TTTTCAAAGGCT
18046977 TTTT-AAAGGCT
1 TTTTCAAAGGCT
18046988 TTTTCAA
1 TTTTCAA
18046995 GTTCTCTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:18047052 original size:5 final size:5
Alignment explanation
Indices: 18047042--18047098 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
18047032 CTCTTGCCTC
*
18047042 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
18047089 TCTTT TCTTT
1 TCTTT TCTTT
18047099 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:18047082 original size:15 final size:14
Alignment explanation
Indices: 18047042--18047098 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
18047032 CTCTTGCCTC
*
18047042 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
18047057 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
18047072 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
18047089 TCTTTTCTTT
1 TCTTTTCTTT
18047099 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:18047108 original size:21 final size:20
Alignment explanation
Indices: 18047040--18047109 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
18047030 GCCTCTTGCC
18047040 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
18047063 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
18047083 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
18047103 TCTCTTT
1 TCTCTTT
18047110 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:18048059 original size:24 final size:25
Alignment explanation
Indices: 18048020--18048073 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 25
18048010 CATTAAACAC
*
18048020 TTTTTTTTTCAGATTTTTTTTCGAA
1 TTTTTTTTTCAAATTTTTTTTCGAA
18048045 TTTTTTTTT-AAATTTTTTTTCGAA
1 TTTTTTTTTCAAATTTTTTTTCGAA
18048069 TTTTT
1 TTTTT
18048074 CTTGACTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (25 bp):
TTTTTTTTTCAAATTTTTTTTCGAA
Found at i:18048070 original size:12 final size:12
Alignment explanation
Indices: 18048021--18048073 Score: 72
Period size: 12 Copynumber: 4.4 Consensus size: 12
18048011 ATTAAACACT
18048021 TTTTTTTTC-AGA
1 TTTTTTTTCGA-A
18048033 TTTTTTTTCGAA
1 TTTTTTTTCGAA
**
18048045 TTTTTTTTTAAA
1 TTTTTTTTCGAA
18048057 TTTTTTTTCGAA
1 TTTTTTTTCGAA
18048069 TTTTT
1 TTTTT
18048074 CTTGACTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
12 35 0.97
13 1 0.03
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:18051255 original size:30 final size:30
Alignment explanation
Indices: 18051221--18051317 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
18051211 TAAACTAAAA
18051221 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
18051251 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
18051281 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
18051311 TGAGCTA
1 TGAGCTA
18051318 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:18057802 original size:17 final size:18
Alignment explanation
Indices: 18057780--18057813 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
18057770 TTTGAAAAAG
18057780 AAAGAAAAGA-AAATGAA
1 AAAGAAAAGAGAAATGAA
18057797 AAAGAAAAGAGAAATGA
1 AAAGAAAAGAGAAATGA
18057814 GATAAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (18 bp):
AAAGAAAAGAGAAATGAA
Found at i:18057881 original size:15 final size:14
Alignment explanation
Indices: 18057844--18057886 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
18057834 CAAAAGAGAG
*
18057844 AGAAAAGAAAATG-
1 AGAAAAGAAAAAGA
18057857 AGAAAAGAAAAAGA
1 AGAAAAGAAAAAGA
18057871 AGAACAAGAAAAAGA
1 AGAA-AAGAAAAAGA
18057886 A
1 A
18057887 AATGGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 12 0.44
14 4 0.15
15 11 0.41
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (14 bp):
AGAAAAGAAAAAGA
Found at i:18061812 original size:21 final size:20
Alignment explanation
Indices: 18061768--18061816 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
18061758 TCAGCTCCCA
* *
18061768 TCAGCTCACTTGAGCTTGAT
1 TCAGCTCGCTTGAGCTAGAT
*
18061788 TCAGCTCGTTTGAGCTAGAAT
1 TCAGCTCGCTTGAGCTAG-AT
18061809 TCAGCTCG
1 TCAGCTCG
18061817 ATCTAGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (20 bp):
TCAGCTCGCTTGAGCTAGAT
Found at i:18063078 original size:19 final size:19
Alignment explanation
Indices: 18063054--18063093 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
18063044 AGCTTCCATG
18063054 TAGCTCCGCACCAGCTCAT
1 TAGCTCCGCACCAGCTCAT
* *
18063073 TAGCTCGGGACCAGCTCAT
1 TAGCTCCGCACCAGCTCAT
18063092 TA
1 TA
18063094 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.23
Consensus pattern (19 bp):
TAGCTCCGCACCAGCTCAT
Done.