Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 73 of 89
Found at i:17430690 original size:25 final size:25
Alignment explanation
Indices: 17430662--17430729 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
17430652 ATTTCTAGTT
*
17430662 TTTTAAAGTTCTC-TCTTTTATTTTC
1 TTTTAAAGTTCTCAT-TTTTATTTTA
* *
17430687 TTTTCAAGTTTTCATTTTTATTTTA
1 TTTTAAAGTTCTCATTTTTATTTTA
*
17430712 TTTT-AAGTT-TTATTTTTA
1 TTTTAAAGTTCTCATTTTTA
17430730 AACATGCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.21
24 5 0.13
25 24 0.63
26 1 0.03
ACGTcount: A:0.19, C:0.09, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTTAAAGTTCTCATTTTTATTTTA
Found at i:17430719 original size:24 final size:24
Alignment explanation
Indices: 17430677--17430729 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
17430667 AAGTTCTCTC
*
17430677 TTTTATTTTCTTTTCAAGTTTTCAT
1 TTTTATTTTATTTTCAAGTTTT-AT
17430702 TTTTATTTTATTTT-AAGTTTTAT
1 TTTTATTTTATTTTCAAGTTTTAT
17430725 TTTTA
1 TTTTA
17430730 AACATGCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 7 0.26
24 7 0.26
25 13 0.48
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTTATTTTATTTTCAAGTTTTAT
Found at i:17430730 original size:13 final size:13
Alignment explanation
Indices: 17430682--17430730 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
17430672 CTCTCTTTTA
* *
17430682 TTTTCTTTTCAAG
1 TTTTATTTTTAAG
17430695 TTTTCATTTTT-A-
1 TTTT-ATTTTTAAG
17430707 TTTTA-TTTTAAG
1 TTTTATTTTTAAG
17430719 TTTTATTTTTAA
1 TTTTATTTTTAA
17430731 ACATGCTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 2 0.07
12 9 0.30
13 11 0.37
14 4 0.13
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTTATTTTTAAG
Found at i:17437350 original size:24 final size:24
Alignment explanation
Indices: 17437308--17437360 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
17437298 AAGTTCAATC
* *
17437308 TTTTCTTTTCTTTTCAAGTTTTCAT
1 TTTTATTTTATTTTCAAGTTTT-AT
17437333 TTTTATTTTATTTT-AAGTTTTAT
1 TTTTATTTTATTTTCAAGTTTTAT
17437356 TTTTA
1 TTTTA
17437361 AACATGCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 7 0.27
24 7 0.27
25 12 0.46
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTTATTTTATTTTCAAGTTTTAT
Found at i:17437361 original size:13 final size:13
Alignment explanation
Indices: 17437313--17437361 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
17437303 CAATCTTTTC
* *
17437313 TTTTCTTTTCAAG
1 TTTTATTTTTAAG
17437326 TTTTCATTTTT-A-
1 TTTT-ATTTTTAAG
17437338 TTTTA-TTTTAAG
1 TTTTATTTTTAAG
17437350 TTTTATTTTTAA
1 TTTTATTTTTAA
17437362 ACATGCTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 2 0.07
12 9 0.30
13 11 0.37
14 4 0.13
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTTATTTTTAAG
Found at i:17440474 original size:64 final size:63
Alignment explanation
Indices: 17440403--17440548 Score: 177
Period size: 64 Copynumber: 2.3 Consensus size: 63
17440393 GGCTGTCCAA
*
17440403 GTGCATCGGTGCATAAATCAGCTTCAATGTTTCAAAATAACCAGAGTGCAACGATGCAT-GTCTT
1 GTGCATCGGTGCATAAATCA-ATTCAATGTTTCAAAATAACCAGAGTGCAACGATGCATGGT-TT
* * * * * *
17440467 TTGCATCGGTGGATAAAATCAATTCGATGTTTTAAAATAGCCAGAGTGCATCGATGCATGGTTT
1 GTGCATCGGTGCAT-AAATCAATTCAATGTTTCAAAATAACCAGAGTGCAACGATGCATGGTTT
* *
17440531 GTGTATCGATGCATAAAT
1 GTGCATCGGTGCATAAAT
17440549 TGCATTCGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
63 4 0.06
64 57 0.83
65 8 0.12
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (63 bp):
GTGCATCGGTGCATAAATCAATTCAATGTTTCAAAATAACCAGAGTGCAACGATGCATGGTTT
Found at i:17443137 original size:20 final size:20
Alignment explanation
Indices: 17443112--17443149 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17443102 GCAGTTTTGA
* *
17443112 GAGTGGTGAGAGAGAGAGAG
1 GAGTGGCGACAGAGAGAGAG
17443132 GAGTGGCGACAGAGAGAG
1 GAGTGGCGACAGAGAGAG
17443150 TTTTAGGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.05, G:0.53, T:0.08
Consensus pattern (20 bp):
GAGTGGCGACAGAGAGAGAG
Found at i:17443241 original size:20 final size:22
Alignment explanation
Indices: 17443216--17443316 Score: 68
Period size: 23 Copynumber: 4.6 Consensus size: 22
17443206 CGATGTATGT
17443216 ATCGATGCAC-TT-AGCAGTGC
1 ATCGATGCACATTAAGCAGTGC
*
17443236 ATCGATGCACATTCAAGGAGTGC
1 ATCGATGCACATT-AAGCAGTGC
* * * *
17443259 ATCGGTGCACCTTTATG--GTGT
1 ATCGATGCA-CATTAAGCAGTGC
*
17443280 ATCGATGCACATTCATAG-GGATGC
1 ATCGATGCACATT-A-AGCAG-TGC
17443304 ATCGATGCACATT
1 ATCGATGCACATT
17443317 CATAGGGATG
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
20 13 0.20
21 14 0.22
22 1 0.02
23 18 0.28
24 18 0.28
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (22 bp):
ATCGATGCACATTAAGCAGTGC
Found at i:17443308 original size:24 final size:24
Alignment explanation
Indices: 17443233--17443345 Score: 137
Period size: 24 Copynumber: 4.9 Consensus size: 24
17443223 CACTTAGCAG
17443233 TGCATCGATGCACATTCA-A-GGA
1 TGCATCGATGCACATTCATAGGGA
* * *
17443255 GTGCATCGGTGCACCTT--TATGG-
1 -TGCATCGATGCACATTCATAGGGA
*
17443277 TGTATCGATGCACATTCATAGGGA
1 TGCATCGATGCACATTCATAGGGA
17443301 TGCATCGATGCACATTCATAGGGA
1 TGCATCGATGCACATTCATAGGGA
*
17443325 TGCATCGATGCACTTTCATAG
1 TGCATCGATGCACATTCATAG
17443346 TGTATCGATG
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
21 13 0.17
22 1 0.01
23 20 0.26
24 43 0.56
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (24 bp):
TGCATCGATGCACATTCATAGGGA
Found at i:17443343 original size:48 final size:46
Alignment explanation
Indices: 17443216--17443345 Score: 135
Period size: 48 Copynumber: 2.8 Consensus size: 46
17443206 CGATGTATGT
*
17443216 ATCGATGCAC--TTAGCAGTGCATCGATGCACATTCA-A-GGAGTGC
1 ATCGATGCACATTTAG-GGTGCATCGATGCACATTCATAGGGAGTGC
* * * *
17443259 ATCGGTGCACCTTTATGGTGTATCGATGCACATTCATAGGGA-TGC
1 ATCGATGCACATTTAGGGTGCATCGATGCACATTCATAGGGAGTGC
*
17443304 ATCGATGCACATTCATAGGGATGCATCGATGCACTTTCATAG
1 ATCGATGCACATT--TAGGG-TGCATCGATGCACATTCATAG
17443346 TGTATCGATG
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
43 9 0.13
44 18 0.25
45 18 0.25
46 3 0.04
47 4 0.06
48 19 0.27
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (46 bp):
ATCGATGCACATTTAGGGTGCATCGATGCACATTCATAGGGAGTGC
Found at i:17449216 original size:63 final size:64
Alignment explanation
Indices: 17449063--17449217 Score: 174
Period size: 63 Copynumber: 2.4 Consensus size: 64
17449053 TGCACTATGG
* *
17449063 TGTGTATCAGTGCATAAATTAGC-TTCGATGTTTCAAAATAACCAGGGTGCATTGATGCATGTCT
1 TGTGTATCAGTGCATAAATT-GCATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGTCT
* * * * **
17449127 GGTGTATCGGTGCATAAAAT-CAATTCGATGTTTTAAAAT-AGTAGAGTGCATCGATGCATGGT-
1 TGTGTATCAGTGCATAAATTGC-ATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCAT-GTC
17449189 T
64 T
*
17449190 TGTGTATCAGTACATAAATTGCATTCGA
1 TGTGTATCAGTGCATAAATTGCATTCGA
17449218 AACGGGTATG
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 39 0.52
64 35 0.47
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (64 bp):
TGTGTATCAGTGCATAAATTGCATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGTCT
Found at i:17452350 original size:30 final size:31
Alignment explanation
Indices: 17452282--17452371 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 31
17452272 GCAAGTTTTA
17452282 AAAGGAAAAGAAAAAATGGTGGAAAGATTAG
1 AAAGGAAAAGAAAAAATGGTGGAAAGATTAG
* * *
17452313 AAAGGAAAATAGAAGATGGTGGAAAGATTAG
1 AAAGGAAAAGAAAAAATGGTGGAAAGATTAG
* * *
17452344 -AAGGAAAAGAAAATATAGTGGATAGATT
1 AAAGGAAAAGAAAAAATGGTGGAAAGATT
17452372 TTGGGTTGTA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 23 0.45
31 28 0.55
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (31 bp):
AAAGGAAAAGAAAAAATGGTGGAAAGATTAG
Found at i:17452683 original size:14 final size:15
Alignment explanation
Indices: 17452664--17452704 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
17452654 TGTCATACAT
17452664 AATTTAATATT-TAA
1 AATTTAATATTATAA
17452678 AATTT-ATATTATAA
1 AATTTAATATTATAA
*
17452692 TATTTATATATTA
1 AATTTA-ATATTA
17452705 GAATAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 5 0.22
14 12 0.52
16 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTAATATTATAA
Found at i:17467078 original size:14 final size:13
Alignment explanation
Indices: 17467048--17467086 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 13
17467038 TTCTTTGTAA
17467048 TTTTT-TTCTTTT
1 TTTTTCTTCTTTT
17467060 TTTTTCTTCTTTT
1 TTTTTCTTCTTTT
17467073 TGTTTTCTTCTTTT
1 T-TTTTCTTCTTTT
17467087 GAGTGCTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 5 0.20
13 8 0.32
14 12 0.48
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (13 bp):
TTTTTCTTCTTTT
Found at i:17467087 original size:13 final size:13
Alignment explanation
Indices: 17467048--17467087 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
17467038 TTCTTTGTAA
* *
17467048 TTTTTTTCTTTTT
1 TTTTCTTCTTTTG
17467061 TTTTCTTCTTTTTG
1 TTTTCTTC-TTTTG
17467075 TTTTCTTCTTTTG
1 TTTTCTTCTTTTG
17467088 AGTGCTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.82
Consensus pattern (13 bp):
TTTTCTTCTTTTG
Found at i:17471111 original size:20 final size:20
Alignment explanation
Indices: 17471083--17471122 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17471073 AACCAATATT
*
17471083 TTCACATTTAAGATTTATAG
1 TTCACATTTAACATTTATAG
* *
17471103 TTCATATTTCACATTTATAG
1 TTCACATTTAACATTTATAG
17471123 CCCAATGTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCACATTTAACATTTATAG
Found at i:17471227 original size:35 final size:35
Alignment explanation
Indices: 17471181--17471262 Score: 146
Period size: 35 Copynumber: 2.3 Consensus size: 35
17471171 GCCCAATAAG
17471181 CACTCCAGGTGCTATCATCAGTAAACAGTGATATA
1 CACTCCAGGTGCTATCATCAGTAAACAGTGATATA
*
17471216 CACTCCAGGTGCTATCATCAGTAAACAGTGATATG
1 CACTCCAGGTGCTATCATCAGTAAACAGTGATATA
*
17471251 CACTCCAAGTGC
1 CACTCCAGGTGC
17471263 CTCATATCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (35 bp):
CACTCCAGGTGCTATCATCAGTAAACAGTGATATA
Found at i:17474787 original size:29 final size:29
Alignment explanation
Indices: 17474737--17474828 Score: 125
Period size: 29 Copynumber: 3.1 Consensus size: 29
17474727 CACAATATAT
17474737 AAGGACT-AAATACCAAAAATAGAAAGTTA
1 AAGGACTAAAATA-CAAAAATAGAAAGTTA
17474766 AAGGACTAAAATA-AAAATATAGAAAGTTA
1 AAGGACTAAAATACAAAA-ATAGAAAGTTA
* *
17474795 AAGGGCTAAAATATAAAAAATAGAAAGTTA
1 AAGGACTAAAATA-CAAAAATAGAAAGTTA
17474825 AAGG
1 AAGG
17474829 GTTGAACTAC
Statistics
Matches: 58, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
28 4 0.07
29 30 0.52
30 20 0.34
31 4 0.07
ACGTcount: A:0.60, C:0.05, G:0.16, T:0.18
Consensus pattern (29 bp):
AAGGACTAAAATACAAAAATAGAAAGTTA
Found at i:17474820 original size:30 final size:29
Alignment explanation
Indices: 17474751--17474829 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
17474741 ACTAAATACC
*
17474751 AAAAATAGAAAGTTAAAGGACTAAAATAA
1 AAAAATAGAAAGTTAAAGGGCTAAAATAA
*
17474780 AAATATAGAAAGTTAAAGGGCTAAAATATA
1 AAAAATAGAAAGTTAAAGGGCTAAAATA-A
17474810 AAAAATAGAAAGTTAAAGGG
1 AAAAATAGAAAGTTAAAGGG
17474830 TTGAACTACA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 26 0.57
30 20 0.43
ACGTcount: A:0.61, C:0.03, G:0.18, T:0.19
Consensus pattern (29 bp):
AAAAATAGAAAGTTAAAGGGCTAAAATAA
Found at i:17476759 original size:134 final size:132
Alignment explanation
Indices: 17476481--17476956 Score: 464
Period size: 134 Copynumber: 3.6 Consensus size: 132
17476471 TGAAGAGGTC
* * * * * * *
17476481 TGGTCATCTAAGGATGACACGGCTCCTACGTGATGAGAAGATCTAGTCGGGGGATGACACTGCTC
1 TGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTAGTCGAGGGATGACACGGTTC
* * * * * * *
17476546 ATACATGATTAAGAGTTCTTAGCCATCTTTAGGGAGGGTGATTACACGATTTCTACGCGATAAGG
66 CTACGTGATGAAGAGTTCTTGGCCATCTTTA--GAGGATGATAACACGAGTTCTACGCGATAAGG
*
17476611 ATAG
129 ACAG
* *
17476615 TTGGTTATCTAGTGGTAACACGGCTCCTACGTGATGAGGAGATCTAGTCGAGGGATGACACGGTT
1 -TGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTAGTCGAGGGATGACACGGTT
* **
17476680 CCTA-GTGATGAAGAGTTCTTGGCCATCTTTAAGAAAGATGATAACACGA-TTCATATACGATAA
65 CCTACGTGATGAAGAGTTCTTGGCCATCTTT-AG-AGGATGATAACACGAGTTC-TACGCGATAA
17476743 GGACAG
127 GGACAG
* * * *
17476749 CTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTGTGGTC-AGGGGATGAAACGGT
1 -TGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTAGTCGA-GGGATGACACGGT
* * * * * *
17476813 TCCTACGTGATGAGGAAG--ATAGGCCATCTTT-GGGGATGATAACAC-AGTTCCTACGTGATGA
64 TCCTACGTGATGAAG-AGTTCTTGGCCATCTTTAGAGGATGATAACACGAGTT-CTACGCGATAA
17476874 GGACGAG
127 GGAC-AG
* * * * *
17476881 TGGTTATCTAGGGGTGACACAGCTCATACGTGATGAGGAGGTC-AGGTCGGGGGATGACACAGTT
1 TGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTA-GTCGAGGGATGACACGGTT
*
17476945 CCTACATGATGA
65 CCTACGTGATGA
17476957 GGATAGCATG
Statistics
Matches: 287, Mismatches: 43, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
130 1 0.00
131 89 0.31
132 4 0.01
133 5 0.02
134 119 0.41
135 67 0.23
136 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (132 bp):
TGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTAGTCGAGGGATGACACGGTTC
CTACGTGATGAAGAGTTCTTGGCCATCTTTAGAGGATGATAACACGAGTTCTACGCGATAAGGAC
AG
Found at i:17476973 original size:131 final size:130
Alignment explanation
Indices: 17476742--17476980 Score: 338
Period size: 131 Copynumber: 1.8 Consensus size: 130
17476732 ATATACGATA
* * **
17476742 AGGACAGCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTGTGGTCAGGGGATGA
1 AGGACAGCTGGTTATCTAGGGGTGACACAGCTCATACGTGATGAGGAGGTCAGGTCAGGGGATGA
* * * *
17476807 AACGGTTCCTACGTGATGAGGAAGATAGGCCATCTTTGGGGATGATAACACAGTTCCTACGTGAT
66 AACAGTTCCTACATGATGAGGAAGATA-GCAATCTTTAGGGATGATAACACAGTTCCTACGTGAT
17476872 G
130 G
*
17476873 AGGACGAG-TGGTTATCTAGGGGTGACACAGCTCATACGTGATGAGGAGGTCAGGTCGGGGGATG
1 AGGAC-AGCTGGTTATCTAGGGGTGACACAGCTCATACGTGATGAGGAGGTCAGGTCAGGGGATG
*
17476937 ACACAGTTCCTACATGATGAGGATAGCAT-GCAATCTTTAGGGAT
65 AAACAGTTCCTACATGATGAGGA-AG-ATAGCAATCTTTAGGGAT
17476981 AATGGTTTCA
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
131 89 0.94
132 4 0.04
133 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.35, T:0.23
Consensus pattern (130 bp):
AGGACAGCTGGTTATCTAGGGGTGACACAGCTCATACGTGATGAGGAGGTCAGGTCAGGGGATGA
AACAGTTCCTACATGATGAGGAAGATAGCAATCTTTAGGGATGATAACACAGTTCCTACGTGATG
Found at i:17477150 original size:29 final size:28
Alignment explanation
Indices: 17477042--17477152 Score: 111
Period size: 30 Copynumber: 3.8 Consensus size: 28
17477032 TCAAGGGAGA
*
17477042 CAAA-ATTTATTTCAAG-GAAAACA-ATCT
1 CAAAGATTTTTTTCAAGAG-AAACAGA-CT
17477069 CAAAGATGTTTGTTTCAAGAGAAACAGACT
1 CAAAGAT-TTT-TTTCAAGAGAAACAGACT
*
17477099 CAAAGACTTTTTTTTCAAGAGAAACATACT
1 CAAAGA--TTTTTTTCAAGAGAAACAGACT
*
17477129 CAAAGATTTTTCTTCAAAAGAAAC
1 CAAAGATTTTT-TTCAAGAGAAAC
17477153 TGTCTCAAGA
Statistics
Matches: 73, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
27 4 0.05
28 7 0.10
29 13 0.18
30 43 0.59
31 5 0.07
32 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAGAGAAACAGACT
Found at i:17477290 original size:65 final size:65
Alignment explanation
Indices: 17477111--17477283 Score: 206
Period size: 65 Copynumber: 2.6 Consensus size: 65
17477101 AAGACTTTTT
* * * *
17477111 TTTCAAGAGAAACATACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAGAGAGATAAAACCTT
1 TTTCAAGAGAAATAAACTCAAAGA-TTTTCTTTAAAAGAAACTGTCTCAAGAGAGACAAAACCTT
17477176 G
65 G
* *
17477177 TTTCCAGAG-AATCAAACTCAAAGATTTTTTTTAAAAGAAACTGTCTCAAGAGAGACAAAA-CTT
1 TTTCAAGAGAAAT-AAACTCAAAGATTTTCTTTAAAAGAAACTGTCTCAAGAGAGACAAAACCTT
17477240 G
65 G
* * * *
17477241 TTTCAAAAGAAATAGACTCCAAGACTTTTGTTTAAAGAGAAAC
1 TTTCAAGAGAAATAAACTCAAAGA-TTTTCTTTAAA-AGAAAC
17477284 GACTCAAAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
64 20 0.22
65 48 0.52
66 24 0.26
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (65 bp):
TTTCAAGAGAAATAAACTCAAAGATTTTCTTTAAAAGAAACTGTCTCAAGAGAGACAAAACCTTG
Found at i:17477959 original size:2 final size:2
Alignment explanation
Indices: 17477952--17477990 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
17477942 GATATTTTGT
* *
17477952 TA TA TA TA TA TA TA TA TA TA TT TA T- TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17477991 GTAGTATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:17478110 original size:37 final size:37
Alignment explanation
Indices: 17478023--17478457 Score: 343
Period size: 37 Copynumber: 12.0 Consensus size: 37
17478013 TTTTGACGAA
* * * * *
17478023 ATATAATATATAATTTTCAGAAAATGATTTTCGAAAATTT
1 ATATAATATATAGTTTTTA-AAAA-CATTTT-TAAAAATT
* * *
17478063 ATATATTATATAGTTTTTGAAAACATTTTTAAAAAAT
1 ATATAATATATAGTTTTTAAAAACATTTTTAAAAATT
* *
17478100 ATATAATATATAG-TTTTCAAAACATTTTGAAAACATTT
1 ATATAATATATAGTTTTTAAAAACATTTTTAAAA-A-TT
* * * *
17478138 ATATATTATATAATTTTT-AAAACAATTTTGAAAACTT
1 ATATAATATATAGTTTTTAAAAAC-ATTTTTAAAAATT
* * *
17478175 ATATAATATATACTTTTTTAAAACATTTTTGAGAAATT
1 ATATAATATATAGTTTTTAAAAACATTTTT-AAAAATT
* *
17478213 ATATAATATATAG-TTTCAAAAACATTTTTGAAAAAAT
1 ATATAATATATAGTTTTTAAAAACATTTTT-AAAAATT
17478250 ATATAATATATAG-TTTTAAAAACATTTTTGAAAAATT
1 ATATAATATATAGTTTTTAAAAACATTTTT-AAAAATT
*
17478287 ATATAATATATAG-TTTTAAAAACATTTTT---GA--
1 ATATAATATATAGTTTTTAAAAACATTTTTAAAAATT
* * *
17478318 A-ATAATGTATAGTTTTAAAAAATATTTTTTGAAAAATT
1 ATATAATATATAGTTTTTAAAAACA-TTTTT-AAAAATT
* ** *
17478356 ATATAATATATAG-TTTTAAAAATATTTTTTGGAAACT
1 ATATAATATATAGTTTTTAAAAACA-TTTTTAAAAATT
* *
17478393 -TAT-ATA-ATA-TTTTT-AAAACA-TTTTGAAAACT
1 ATATAATATATAGTTTTTAAAAACATTTTTAAAAATT
* *
17478424 ATATAATGTATAG-TTTTGAAAAC-TTTTTAAAAAT
1 ATATAATATATAGTTTTTAAAAACATTTTTAAAAAT
17478458 ATAATATAGT
Statistics
Matches: 331, Mismatches: 42, Indels: 49
0.78 0.10 0.12
Matches are distributed among these distances:
30 10 0.03
31 20 0.06
32 8 0.02
33 8 0.02
34 14 0.04
35 16 0.05
36 22 0.07
37 129 0.39
38 61 0.18
39 28 0.08
40 15 0.05
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
ATATAATATATAGTTTTTAAAAACATTTTTAAAAATT
Found at i:17478127 original size:112 final size:108
Alignment explanation
Indices: 17477985--17478465 Score: 351
Period size: 112 Copynumber: 4.4 Consensus size: 108
17477975 ATTATATATG
* * * *
17477985 TATATAGTAGTATAGTTTGTGAAAATATTTTTGACGAA-ATATAATATATAATTTTCAGAAAATG
1 TATATAATA-TATAGTTT-TCAAAACATTTTTGA-AAACATATAATATATAATTTT-A-AAAA--
* * *
17478049 ATTTTCGAAAATTTATATATTATATAGTTTTTGAAAACATTTTT-AAAAAA
59 ATTTT-GAAAAATTATATAATATATAGTTTTTAAAAACATTTTTGAAAAAA
17478099 TATATAATATATAGTTTTCAAAACA-TTTTGAAAACATTTATATATTATATAATTTTTAAAACAA
1 TATATAATATATAGTTTTCAAAACATTTTTGAAAACA--TATA-A-TATATAA-TTTTAAAA-AA
* * * * *
17478163 TTTTGAAAACTTATATAATATATACTTTTTTAAAACATTTTTGAGAAAT
60 TTTTGAAAAATTATATAATATATAGTTTTTAAAAACATTTTTGAAAAAA
* *
17478212 TATATAATATATAG-TTTCAAAAACATTTTTGAAAAAATATATAATATATAGTTTTAAAAACATT
1 TATATAATATATAGTTTTC-AAAACATTTTTG--AAAACATATAATATATAATTTTAAAAA-A-T
17478276 TTTGAAAAATTATATAATATATAG-TTTTAAAAACATTTTTG-----A
61 TTTGAAAAATTATATAATATATAGTTTTTAAAAACATTTTTGAAAAAA
* * * * *
17478318 -A-ATAATGTATAGTTTTAAAAAATATTTTTTGAAAAATTATATAATATATAGTTTTAAAAATAT
1 TATATAATATATAGTTTT-CAAAACA-TTTTTG-AAAA-CATATAATATATAATTTTAAAAA-A-
* * *
17478381 TTTTTG-GAAACT-TAT-ATA-ATA-TTTTT-AAAACA-TTTTG-AAAAC
60 -TTTTGAAAAATTATATAATATATAGTTTTTAAAAACATTTTTGAAAAAA
* *
17478423 TATATAATGTATAGTTTTGAAAAC-TTTTT-AAAA-ATATAATATA
1 TATATAATATATAGTTTTCAAAACATTTTTGAAAACATATAATATA
17478466 GTTTAAAAAT
Statistics
Matches: 316, Mismatches: 25, Indels: 66
0.78 0.06 0.16
Matches are distributed among these distances:
100 10 0.03
101 5 0.02
102 10 0.03
103 7 0.02
104 18 0.06
105 17 0.05
106 39 0.12
107 21 0.07
110 3 0.01
111 32 0.10
112 73 0.23
113 42 0.13
114 21 0.07
115 9 0.03
116 9 0.03
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (108 bp):
TATATAATATATAGTTTTCAAAACATTTTTGAAAACATATAATATATAATTTTAAAAAATTTTGA
AAAATTATATAATATATAGTTTTTAAAAACATTTTTGAAAAAA
Found at i:17478144 original size:75 final size:73
Alignment explanation
Indices: 17478023--17478460 Score: 411
Period size: 75 Copynumber: 6.0 Consensus size: 73
17478013 TTTTGACGAA
* * * * * *
17478023 ATATAATATATAATTTTCAGAAAATGATTTTCGAAAATTTATATATTATATAGTTTTTGAAAACA
1 ATATAATATATAGTTTT-A-AAAA-CATTTTTGAAAAATTATATAATATATAG-TTTTAAAAACA
17478088 TTTTTAAAAAAT
62 TTTTTAAAAAAT
* * * *
17478100 ATATAATATATAGTTTTCAAAACA-TTTTGAAAACATTTATATATTATATAATTTTTAAAACAAT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAA-A-TTATATAATATATAGTTTTAAAAAC-AT
* **
17478164 TTTGAAAACTT
63 TTTTAAAAAAT
* * * *
17478175 ATATAATATATACTTTTTTAAAACATTTTTGAGAAATTATATAATATATAGTTTCAAAAACATTT
1 ATATAATATATA-GTTTTAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTT
17478240 TTGAAAAAAT
65 TT-AAAAAAT
17478250 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTT
*
17478315 T----GA-
66 TAAAAAAT
* * *
17478318 A-ATAATGTATAGTTTTAAAAAATATTTTTTGAAAAATTATATAATATATAGTTTTAAAAATATT
1 ATATAATATATAGTTTT-AAAAACA-TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA-T
** *
17478382 TTTTGGAAACT
63 TTTTAAAAAAT
* * * *
17478393 -TAT-ATA-ATA-TTTTTAAAACA-TTTTG-AAAACTATATAATGTATAGTTTTGAAAAC-TTTT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTT
17478451 T-AAAAAT
66 TAAAAAAT
17478458 ATA
1 ATA
17478461 ATATAGTTTA
Statistics
Matches: 306, Mismatches: 39, Indels: 43
0.79 0.10 0.11
Matches are distributed among these distances:
65 4 0.01
66 7 0.02
67 14 0.05
68 32 0.10
69 42 0.14
70 5 0.02
71 5 0.02
72 4 0.01
73 11 0.04
74 67 0.22
75 80 0.26
76 11 0.04
77 24 0.08
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (73 bp):
ATATAATATATAGTTTTAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTT
TAAAAAAT
Found at i:17478373 original size:39 final size:38
Alignment explanation
Indices: 17478319--17478486 Score: 136
Period size: 38 Copynumber: 4.8 Consensus size: 38
17478309 CATTTTTGAA
*
17478319 ATAATGTATAGTTTTAAAAAATATTTTTTGAAAAATTAT
1 ATAATATATAGTTTT-AAAAATATTTTTTGAAAAATTAT
* *
17478358 ATAATATATAGTTTTAAAAATATTTTTTGGAAACTTAT
1 ATAATATATAGTTTTAAAAATATTTTTTGAAAAATTAT
* *
17478396 AT-A-ATAT--TTTT-AAAACA--TTTTG-AAAACTAT
1 ATAATATATAGTTTTAAAAATATTTTTTGAAAAATTAT
* * *
17478426 ATAATGTATAGTTTT-GAAA-ACTTTTT--AAAA--AT
1 ATAATATATAGTTTTAAAAATATTTTTTGAAAAATTAT
17478458 AT-A-ATATAG-TTTAAAAATATTTTTTGAAA
1 ATAATATATAGTTTTAAAAATATTTTTTGAAA
17478487 TATATATTTT
Statistics
Matches: 108, Mismatches: 11, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
29 3 0.03
30 16 0.15
31 13 0.12
32 7 0.06
33 8 0.07
34 15 0.14
35 4 0.04
36 4 0.04
37 1 0.01
38 23 0.21
39 14 0.13
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (38 bp):
ATAATATATAGTTTTAAAAATATTTTTTGAAAAATTAT
Found at i:17478376 original size:69 final size:67
Alignment explanation
Indices: 17478252--17478486 Score: 257
Period size: 69 Copynumber: 3.5 Consensus size: 67
17478242 GAAAAAATAT
17478252 ATAATATATAGTTTTAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTTG
1 ATAATATATAGTTTTAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTTG
17478317 AA
66 AA
* * *
17478319 ATAATGTATAGTTTTAAAAAATATTTTTTGAAAAATTATATAATATATAGTTTTAAAAATATTTT
1 ATAATATATAGTTTT-AAAAACA-TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA-TTT
17478384 TTGGAA
63 TT-GAA
* * * * *
17478390 ACTTATATAATA-TTTTTAAAACA-TTTTG-AAAACTATATAATGTATAGTTTTGAAAAC-TTTT
1 A-TAATAT-ATAGTTTTAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTT
17478451 T-AA
64 TGAA
* *
17478454 AAATATAATATAG-TTTAAAAATATTTTTTGAAA
1 ATA-AT-ATATAGTTTTAAAAACA-TTTTTGAAA
17478487 TATATATTTT
Statistics
Matches: 141, Mismatches: 15, Indels: 24
0.78 0.08 0.13
Matches are distributed among these distances:
64 16 0.11
65 2 0.01
66 10 0.07
67 16 0.11
68 31 0.22
69 41 0.29
70 5 0.04
71 9 0.06
72 8 0.06
73 3 0.02
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (67 bp):
ATAATATATAGTTTTAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTTG
AA
Found at i:17478509 original size:3 final size:3
Alignment explanation
Indices: 17478501--17478525 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17478491 TATTTTATAG
17478501 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
17478526 TATTTACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17478578 original size:24 final size:23
Alignment explanation
Indices: 17478501--17478574 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 23
17478491 TATTTTATAG
17478501 TATTA-TTA-TTATTATTA-TTAT
1 TATTATTTACTTATT-TTATTTAT
** *
17478522 TATTTATTTACTTGCTTTATTAAT
1 TA-TTATTTACTTATTTTATTTAT
*
17478546 TAGTTATTTATTTATTTTATTTAT
1 TA-TTATTTACTTATTTTATTTAT
17478570 TATTA
1 TATTA
17478575 ATTTTTTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
21 2 0.05
22 3 0.07
23 9 0.22
24 27 0.66
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (23 bp):
TATTATTTACTTATTTTATTTAT
Found at i:17485795 original size:164 final size:164
Alignment explanation
Indices: 17485014--17486120 Score: 1420
Period size: 165 Copynumber: 6.7 Consensus size: 164
17485004 TTTAAGACAA
* * * * *
17485014 CATTTGCAGCATAACTCAAGGCTAGAAGAGTTATCTGCCAACAAAGACCTTCGAGTTCAACTACG
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * * * * * *
17485079 CTTAGCTCCAAGGCACATCATTTGTAACATAGCTCAAGGT-AAGAAGGGCTATTTTCCAACAAAA
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAA-GTCGAGAAGGGCTA-TCTGC--C-AAA
* * * * * *
17485143 GACCTTCGAGTTCGACTACATTCAGC-TCCAAGGCATAT
126 GACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * * * * *
17485181 CATTTGCAGCATAACGT-AAGACGAGAAGGGTTATCTGCCAACTAAAGACATTTGAGTTCGACTA
1 CATTTACAGCATAAC-TCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTA
* *
17485245 CGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGAC
64 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* *
17485310 CCTCGAGTTTGATCACACTCAGCTTCGAGGGCACAT
129 CCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * *
17485346 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGTCCTTCAAGTTCGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTAC
* *
17485411 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACTAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
*
17485476 CTCGAGTTCGATTACACTCAGCTTCAAGGGCACAT
130 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * * * * *
17485511 CATTTGCATCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTAC
*
17485576 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
17485641 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
130 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
*
17485676 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* *
17485741 CTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCA
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
*
17485806 TCGAGTTCGATTACACTCAGCTTCGAGGGTACAT
131 TCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * *
17485840 CATTTATAGCATAACTCAAGGCTATAAGGGTTATATGTCACCAAAGACCTTCGAGTTCGACTACA
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * * * *
17485905 CTCAACTCAAAGGCACATCATTTGCATCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGTCCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
*
17485970 TCGAGTTCGATTATACTCAGCTTCGAGGGCACAT
131 TCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * * * *
17486004 CATTT---GCATCA-TCAAGGCAAGAAGGGCTAT-TTTCCAACAAAATACCTTCGAGTTCGACTA
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-C-ACCAAAGACCTTCGAGTTCGACTA
* ** * * * *
17486064 CGCTCACCTCCAAGGCACATCATTTATAGCATAGCTCAAGGCAAGAAGGGTTATCTG
64 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
17486121 TCAATAAAAT
Statistics
Matches: 833, Mismatches: 98, Indels: 24
0.87 0.10 0.03
Matches are distributed among these distances:
159 2 0.00
160 17 0.02
161 73 0.09
164 304 0.36
165 331 0.40
166 3 0.00
167 39 0.05
168 64 0.08
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (164 bp):
CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
TCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
Found at i:17486130 original size:84 final size:84
Alignment explanation
Indices: 17485014--17486124 Score: 963
Period size: 84 Copynumber: 13.5 Consensus size: 84
17485004 TTTAAGACAA
* * * * * *
17485014 CATTTGCAGCATAACTCAAGGCTAGAAGAGTTATCTGCCAA-CAAAGACCTTCGAGTTCAACTAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* *
17485078 GCTTAGCTCCAAGGCACAT
66 ACTCAGCTCCAAGGCACAT
* * ** * *
17485097 CATTTGTAACATAGCTCAAGGTAAGAAGGGCTAT-TTTCCAACAAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGT-CAACCAAAGACCTTCGAGTTCGACTA
* *
17485161 CATTCAGCTCCAAGGCATAT
65 CACTCAGCTCCAAGGCACAT
* * * * * * *
17485181 CATTTGCAGCATAACGT-AAGACGAGAAGGGTTATCTGCCAACTAAAGACATTTGAGTTCGACTA
1 CATTTGCAGCATAGC-TCAAGGCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTA
* *
17485245 CGCTCAGCTCCAAGGCGCAT
65 CACTCAGCTCCAAGGCACAT
* * * * *
17485265 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATG----CCAAAGACCCTCGAGTTTGA-TCA
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACT-A
* *
17485325 CACTCAGCTTCGAGGGCACAT
65 CACTCAGC-TCCAAGGCACAT
* * * * * * * *
17485346 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGT-GACCAAAAGTCCTTCAAGTTCGACTA
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACC-AAAGACCTTCGAGTTCGACTA
*
17485410 CGCTCAGCTCCAAGGCACAT
65 CACTCAGCTCCAAGGCACAT
* * * * *
17485430 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--T--ACTAAAGACCCTCGAGTTCGATTAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
*
17485491 ACTCAGCTTCAAGGGCACAT
66 ACTCAGCTCCAA-GGCACAT
* * * * * * *
17485511 CATTTGCATCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
*
17485576 GCTCAGCTCCAAGGCACAT
66 ACTCAGCTCCAAGGCACAT
* * * * *
17485595 CATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* *
17485656 ACTCAGCTTCGAGGGCACAT
66 ACTCAGC-TCCAAGGCACAT
* * * * *
17485676 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* *
17485740 GCTCAGCTCAAAGGCACAT
66 ACTCAGCTCCAAGGCACAT
* * * *
17485759 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCATCGAGTTCGATTAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* * *
17485820 ACTCAGCTTCGAGGGTACAT
66 ACTCAGC-TCCAAGGCACAT
** * * * * *
17485840 CATTTATAGCATAACTCAAGGCTATAAGGGTTATATGTC-ACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* *
17485904 ACTCAACTCAAAGGCACAT
66 ACTCAGCTCCAAGGCACAT
* * * * * * *
17485923 CATTTGCATCATAGCTTAAGTCGAGAAGGGCTATC--T--ACCAAAGTCCCTCGAGTTCGATTAT
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* *
17485984 ACTCAGCTTCGAGGGCACAT
66 ACTCAGC-TCCAAGGCACAT
* * * * *
17486004 CATTTGCATC--A--TCAAGGCAAGAAGGGCTAT-TTTCCAACAAAATACCTTCGAGTTCGACTA
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGT-CAACCAAAGACCTTCGAGTTCGACTA
* *
17486064 CGCTCACCTCCAAGGCACAT
65 CACTCAGCTCCAAGGCACAT
** * *
17486084 CATTTATAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAA
1 CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAA
17486125 TAAAATTATC
Statistics
Matches: 825, Mismatches: 167, Indels: 71
0.78 0.16 0.07
Matches are distributed among these distances:
77 16 0.02
78 1 0.00
79 2 0.00
80 150 0.18
81 202 0.24
82 3 0.00
83 105 0.13
84 288 0.35
85 57 0.07
86 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (84 bp):
CATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
ACTCAGCTCCAAGGCACAT
Found at i:17486695 original size:2 final size:2
Alignment explanation
Indices: 17486688--17486728 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
17486678 TATTTTGTTT
*
17486688 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17486729 GTAATATAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17486887 original size:38 final size:37
Alignment explanation
Indices: 17486761--17487200 Score: 471
Period size: 38 Copynumber: 12.0 Consensus size: 37
17486751 TTTTGACAAA
* *
17486761 ATATAATATATAATTTTCAGAAAACGA-TTTTCAAAAATTT
1 ATATAATATATAGTTTT-A-AAAAC-ATTTTTGAAAAA-TT
* * *
17486801 ATATATTATACAGTTTTTGAAAACATTTTT--AAAATAT
1 ATATAATATATAG-TTTTAAAAACATTTTTGAAAAAT-T
* *
17486838 ATATAATATATAGTTTTGAAAAC-CTTTTGAAAACATTT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAA-A-TT
* * * *
17486876 ATATATTATATAGTTTTTAAAACAATTTTGAAAACTT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATT
* *
17486913 ATATAATATATAGTTTTTTAAAACATTTTTGAGAAATT
1 ATATAATATATAG-TTTTAAAAACATTTTTGAAAAATT
17486951 ATATAATATATAGTTTTAAAAACATTTTTG-AAAATT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATT
17486987 ATATAATATATAGTTTTAAAAACATTTTTTGAAAAATT
1 ATATAATATATAGTTTTAAAAACA-TTTTTGAAAAATT
17487025 ATATAATATATAGTTTTAAAAACATTTTTG--AAATT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATT
*
17487060 ATATAATGTATAGTTTTAAAAAACATTTTTTGAAAAATT
1 ATATAATATATAGTTTT-AAAAACA-TTTTTGAAAAATT
* **
17487099 ATATAATATATAGTTTTAAAAATATTTTTTGAAAGCTT
1 ATATAATATATAGTTTTAAAAACA-TTTTTGAAAAATT
*
17487137 ATAT-A-ATAT--TTTT-AAAACA-TTTTG-AAAACT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATT
* *
17487167 ATATAATGTATAGTTTTGAAAAC-TTTTT-AAAAAT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAAT
17487201 ATAATATAGT
Statistics
Matches: 350, Mismatches: 28, Indels: 49
0.82 0.07 0.11
Matches are distributed among these distances:
30 7 0.02
31 6 0.02
32 3 0.01
33 5 0.01
34 8 0.02
35 38 0.11
36 51 0.15
37 68 0.19
38 110 0.31
39 40 0.11
40 10 0.03
41 4 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATAATATATAGTTTTAAAAACATTTTTGAAAAATT
Found at i:17487016 original size:74 final size:72
Alignment explanation
Indices: 17486761--17487229 Score: 484
Period size: 74 Copynumber: 6.4 Consensus size: 72
17486751 TTTTGACAAA
* * * * *
17486761 ATATAATATATAATTTTCAGAAAACGA-TTTTCAAAAATTTATATATTATACAGTTTTTGAAAAC
1 ATATAATATATAGTTTT---AAAAC-ATTTTTGAAAAA-TTATATAATATATAG-TTTTAAAAAC
17486825 ATTTTT-AAAATAT
60 ATTTTTGAAAAT-T
* * * *
17486838 ATATAATATATAGTTTTGAAAAC-CTTTTGAAAACATTTATATATTATATAGTTTTTAAAACAAT
1 ATATAATATATAGTTTT-AAAACATTTTTGAAAA-A-TTATATAATATATAGTTTTAAAAACATT
17486902 TTTGAAAACTT
63 TTTGAAAA-TT
*
17486913 ATATAATATATAGTTTTTTAAAACATTTTTGAGAAATTATATAATATATAGTTTTAAAAACATTT
1 ATATAATATATAG--TTTTAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTT
17486978 TTGAAAATT
64 TTGAAAATT
17486987 ATATAATATATAGTTTTAAAAACATTTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTT
1 ATATAATATATAGTTTT-AAAACA-TTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTT
17487052 TTG-AAATT
64 TTGAAAATT
* *
17487060 ATATAATGTATAGTTTTAAAAAACATTTTTTGAAAAATTATATAATATATAGTTTTAAAAATATT
1 ATATAATATATAGTTTT--AAAACA-TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA-T
*
17487125 TTTTGAAAGCTT
62 TTTTGAAA-ATT
* * *
17487137 ATAT-A-ATAT--TTTTAAAACA-TTTTG-AAAACTATATAATGTATAGTTTTGAAAAC-TTTTT
1 ATATAATATATAGTTTTAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTT
17487195 -AAAA--
66 GAAAATT
*
17487199 ATAT-A-ATATAGTTTTAAAATATTTTTTGAAA
1 ATATAATATATAGTTTTAAAACA-TTTTTGAAA
17487230 TATATATTTT
Statistics
Matches: 353, Mismatches: 21, Indels: 46
0.84 0.05 0.11
Matches are distributed among these distances:
62 9 0.03
64 9 0.03
65 3 0.01
66 10 0.03
67 2 0.01
68 25 0.07
69 5 0.01
71 6 0.02
72 4 0.01
73 31 0.09
74 123 0.35
75 82 0.23
76 10 0.03
77 34 0.10
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (72 bp):
ATATAATATATAGTTTTAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTT
GAAAATT
Found at i:17487224 original size:30 final size:29
Alignment explanation
Indices: 17487137--17487233 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 29
17487127 TTGAAAGCTT
*
17487137 ATATAATAT--TTTTAAAACATTTTGAAAA
1 ATATAATATAGTTTTAAAA-ATTTTTAAAA
*
17487165 CTATATAATGTATAGTTTTGAAAACTTTTTAAAA
1 --ATATAA--TATAGTTTT-AAAAATTTTTAAAA
**
17487199 ATATAATATAGTTTTAAAATATTTTTTGAA
1 ATATAATATAGTTTTAAAA-ATTTTTAAAA
17487229 ATATA
1 ATATA
17487234 TATTTTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
29 4 0.07
30 27 0.48
32 9 0.16
34 12 0.21
35 4 0.07
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (29 bp):
ATATAATATAGTTTTAAAAATTTTTAAAA
Found at i:17487292 original size:24 final size:23
Alignment explanation
Indices: 17487263--17487313 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
17487253 TATTTTTTTC
17487263 TATTTACTTGA-TTTATTAATTAGT
1 TATTTA-TTGATTTTATTAATTA-T
* *
17487287 TATTTATTTATTTTATTTATTAT
1 TATTTATTGATTTTATTAATTAT
17487310 TATT
1 TATT
17487314 ATTTTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (23 bp):
TATTTATTGATTTTATTAATTAT
Found at i:17487295 original size:28 final size:26
Alignment explanation
Indices: 17487249--17487317 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 26
17487239 TATAGTATTA
*
17487249 TTATTATT-TTTTTCTATTTACTTGAT
1 TTATTATTATTATT-TATTTACTTGAT
* *
17487275 TTATTAATTAGTTATTTATTTATTTTAT
1 TTATT-ATTA-TTATTTATTTACTTGAT
17487303 TTATTATTATTATTT
1 TTATTATTATTATTT
17487318 TTTTTGTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 11 0.30
27 7 0.19
28 15 0.41
29 4 0.11
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (26 bp):
TTATTATTATTATTTATTTACTTGAT
Found at i:17497029 original size:21 final size:21
Alignment explanation
Indices: 17496980--17497029 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 21
17496970 CTCAGAGACG
*
17496980 AGCT-ATT-ACTTTGAAGTAA
1 AGCTCATTGACTTTAAAGTAA
* * *
17496999 GGCACCTTGACTTTAAAGTAA
1 AGCTCATTGACTTTAAAGTAA
17497020 AGCTCATTGA
1 AGCTCATTGA
17497030 TTCTTAATTG
Statistics
Matches: 22, Mismatches: 7, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
19 2 0.09
20 2 0.09
21 18 0.82
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (21 bp):
AGCTCATTGACTTTAAAGTAA
Found at i:17500274 original size:38 final size:37
Alignment explanation
Indices: 17500198--17500276 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
17500188 GTGTTTTGAG
**
17500198 GAAAACTGTCTCAAGTGAGACGAAATTTGTTTTGAGA
1 GAAAACTGTCTCAAGTGAGACGAAATTTGTTCCGAGA
* *
17500235 GAAAATTGTCTTAAGTGAGAC-AACATTTTGTTCCGAGA
1 GAAAACTGTCTCAAGTGAGACGAA-A-TTTGTTCCGAGA
17500273 GAAA
1 GAAA
17500277 CAACATCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 2 0.06
37 20 0.56
38 14 0.39
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (37 bp):
GAAAACTGTCTCAAGTGAGACGAAATTTGTTCCGAGA
Found at i:17500405 original size:32 final size:32
Alignment explanation
Indices: 17500357--17500419 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
17500347 TTCACATCAG
*
17500357 GATGTTTAATTCCCAAAGATACCCTAACATTT
1 GATGTTGAATTCCCAAAGATACCCTAACATTT
* * *
17500389 GATGTTGAATTTCCAAAGATGCCCTATCATT
1 GATGTTGAATTCCCAAAGATACCCTAACATT
17500420 CATCGTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (32 bp):
GATGTTGAATTCCCAAAGATACCCTAACATTT
Found at i:17501467 original size:16 final size:18
Alignment explanation
Indices: 17501435--17501492 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 18
17501425 TTTTCATTGA
*
17501435 TTTTTTCTTTGTTTTTGC
1 TTTTTTCTTTGTATTTGC
17501453 -TTTTTCTTT-TATTTGC
1 TTTTTTCTTTGTATTTGC
*
17501469 TTTTTTCTTTGCTCTTTG-
1 TTTTTTCTTTG-TATTTGC
17501487 TTTTTT
1 TTTTTT
17501493 TTCTTACTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.17
17 18 0.51
18 6 0.17
19 5 0.14
ACGTcount: A:0.02, C:0.12, G:0.09, T:0.78
Consensus pattern (18 bp):
TTTTTTCTTTGTATTTGC
Found at i:17502064 original size:32 final size:32
Alignment explanation
Indices: 17502028--17502092 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
17502018 GACGATGATG
17502028 TGACTTTATTGGCTCAAAGAAAGGTAAGTGTA
1 TGACTTTATTGGCTCAAAGAAAGGTAAGTGTA
17502060 TGACTTTATTGGCTCAAAGAAAGGTAAGTGTA
1 TGACTTTATTGGCTCAAAGAAAGGTAAGTGTA
17502092 T
1 T
17502093 AACATCTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (32 bp):
TGACTTTATTGGCTCAAAGAAAGGTAAGTGTA
Found at i:17503872 original size:27 final size:27
Alignment explanation
Indices: 17503820--17503909 Score: 90
Period size: 27 Copynumber: 3.1 Consensus size: 27
17503810 CACAATATAT
* *
17503820 AAGGACTAAATAGCAAAAATAGAAAGTTA
1 AAGGACTAAA-A-TAAAAATAAAAAGTTA
*
17503849 AAGGACTAAAATAAAAATAAAAAGTTC
1 AAGGACTAAAATAAAAATAAAAAGTTA
* *
17503876 AAGGGCTAAAATAGAAAAAACATAAAGTTA
1 AAGGACTAAAATA-AAAATA-A-AAAGTTA
17503906 AAGG
1 AAGG
17503910 GTTGAACTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
27 25 0.48
28 6 0.12
29 11 0.21
30 10 0.19
ACGTcount: A:0.60, C:0.07, G:0.17, T:0.17
Consensus pattern (27 bp):
AAGGACTAAAATAAAAATAAAAAGTTA
Found at i:17505470 original size:29 final size:29
Alignment explanation
Indices: 17505428--17505606 Score: 286
Period size: 29 Copynumber: 6.1 Consensus size: 29
17505418 ATATTTTGAA
*
17505428 AATTATTTTGAAAAATGTGACATTCTGGG
1 AATTATTTTGAAAAAGGTGACATTCTGGG
* *
17505457 AATTATTTTGAAAAAGATGTCATTCTGGG
1 AATTATTTTGAAAAAGGTGACATTCTGGG
*
17505486 AATTATTTTGAAAAAGGTGACATTCTAGG
1 AATTATTTTGAAAAAGGTGACATTCTGGG
*
17505515 AATTATTTTAAAAAAGGTGACATTCTGGG
1 AATTATTTTGAAAAAGGTGACATTCTGGG
*
17505544 AATTATTTTTGAAAAAGGTGGCATTCTGGG
1 AATTA-TTTTGAAAAAGGTGACATTCTGGG
*
17505574 AATTATTTTGAAAAAGGTGACATTTTGGG
1 AATTATTTTGAAAAAGGTGACATTCTGGG
17505603 AATT
1 AATT
17505607 TTTGAATGTG
Statistics
Matches: 137, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
29 110 0.80
30 27 0.20
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (29 bp):
AATTATTTTGAAAAAGGTGACATTCTGGG
Found at i:17506645 original size:24 final size:25
Alignment explanation
Indices: 17506616--17506662 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
17506606 TAAGATTATG
17506616 GTATAATTTTATGAGA-TTACTGCA
1 GTATAATTTTATGAGATTTACTGCA
17506640 GTATAATTTTATGAGATTTACTG
1 GTATAATTTTATGAGATTTACTG
17506663 GACTATGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (25 bp):
GTATAATTTTATGAGATTTACTGCA
Found at i:17506673 original size:25 final size:24
Alignment explanation
Indices: 17506617--17506673 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
17506607 AAGATTATGG
*
17506617 TATAATTTTATGAGATTACTGCAG
1 TATAATTTTATGAGATTACTGCAC
*
17506641 TATAATTTTATGAGATTTACTGGAC
1 TATAATTTTATGAGA-TTACTGCAC
*
17506666 TATGATTT
1 TATAATTT
17506674 GTTTAGTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.46
Consensus pattern (24 bp):
TATAATTTTATGAGATTACTGCAC
Found at i:17511050 original size:17 final size:17
Alignment explanation
Indices: 17511028--17511063 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17511018 ATTGGGTCGA
17511028 CATGAAGAAGGACATCT
1 CATGAAGAAGGACATCT
* *
17511045 CATGAATAAGGATATCT
1 CATGAAGAAGGACATCT
17511062 CA
1 CA
17511064 GTTTTGTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (17 bp):
CATGAAGAAGGACATCT
Found at i:17513039 original size:19 final size:19
Alignment explanation
Indices: 17512991--17513027 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17512981 GTTTGACTGG
17512991 TTTGACCGGTCTAAACCGA
1 TTTGACCGGTCTAAACCGA
*
17513010 TTTGACCGGTCTGAACCG
1 TTTGACCGGTCTAAACCG
17513028 GATTGACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (19 bp):
TTTGACCGGTCTAAACCGA
Found at i:17513140 original size:29 final size:29
Alignment explanation
Indices: 17513069--17513144 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
17513059 AACCCGACCC
* **
17513069 GGTGATATTTTGAAAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
*
17513098 GGTGACATTCTGGGAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
17513127 GGTGACATTTTGGGAATT
1 GGTGACATTTTGGGAATT
17513145 TTCGAATGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (29 bp):
GGTGACATTTTGGGAATTATTTTGAAAAA
Found at i:17514072 original size:31 final size:31
Alignment explanation
Indices: 17514037--17514184 Score: 138
Period size: 31 Copynumber: 4.7 Consensus size: 31
17514027 GTGACTCTTA
* *
17514037 GGTAGGCTCTACGGCCCTGAGATCTTTCTAG
1 GGTAGGCCCTACGGCCCTAAGATCTTTCTAG
* * *
17514068 GGTAGGCCCTGCGGCCCTGAGATCTTTCTCG
1 GGTAGGCCCTACGGCCCTAAGATCTTTCTAG
* *
17514099 GGTAGGCCCTGCGGCCCTAAGATGTGTTCTTA-
1 GGTAGGCCCTACGGCCCTAAGATCT-TTC-TAG
* * * * *
17514131 GGTAGGCCCCACGGCCCCAAAATCTATCTTG
1 GGTAGGCCCTACGGCCCTAAGATCTTTCTAG
*
17514162 GGTAGGCTCT-CAGGCCCTAAGAT
1 GGTAGGCCCTAC-GGCCCTAAGAT
17514185 GTTCCCTTAG
Statistics
Matches: 96, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
30 2 0.02
31 70 0.73
32 23 0.24
33 1 0.01
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (31 bp):
GGTAGGCCCTACGGCCCTAAGATCTTTCTAG
Found at i:17514146 original size:63 final size:61
Alignment explanation
Indices: 17514037--17514187 Score: 160
Period size: 63 Copynumber: 2.4 Consensus size: 61
17514027 GTGACTCTTA
* * ** ** * *
17514037 GGTAGGCTCTACGGCCCTGAGATCTTTCTAGGGTAGGCCCTGCGGCCCTGAGATCTTTCTCG
1 GGTAGGCTCT-CGGCCCTAAGATGTTTCTAGGGTAGGCCCCACGGCCCCAAAATCTATCTCG
* *
17514099 GGTAGGCCCTGCGGCCCTAAGATGTGTTCTTA-GGTAGGCCCCACGGCCCCAAAATCTATCTTG
1 GGTAGGCTCT-CGGCCCTAAGATGT-TTC-TAGGGTAGGCCCCACGGCCCCAAAATCTATCTCG
17514162 GGTAGGCTCTCAGGCCCTAAGATGTT
1 GGTAGGCTCTC-GGCCCTAAGATGTT
17514188 CCCTTAGGGT
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
62 23 0.31
63 49 0.66
64 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (61 bp):
GGTAGGCTCTCGGCCCTAAGATGTTTCTAGGGTAGGCCCCACGGCCCCAAAATCTATCTCG
Found at i:17514656 original size:64 final size:63
Alignment explanation
Indices: 17514539--17514683 Score: 179
Period size: 64 Copynumber: 2.3 Consensus size: 63
17514529 TTTTCAAAGG
* *
17514539 CATGCACCGATGCATCAGTCCATGCATCGATGCACCTATGATTTAATTGAACATCGAATGCATTT
1 CATGCACCGATGCATCA-TCCATGCATCGATGCACCTAGGATTT-ATTAAACATCGAATGCATTT
17514604 CATGCACCGATGCACTC-TCCATGCATCGATGCACC-AGGCTATTT-TTCAAACATCGAATGCAT
1 CATGCACCGATGCA-TCATCCATGCATCGATGCACCTAGG--ATTTATT-AAACATCGAATGCAT
17514666 TT
62 TT
* *
17514668 TATGCATCGATGCATC
1 CATGCACCGATGCATC
17514684 CTTAGTGCAC
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
63 6 0.08
64 46 0.64
65 18 0.25
66 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (63 bp):
CATGCACCGATGCATCATCCATGCATCGATGCACCTAGGATTTATTAAACATCGAATGCATTT
Found at i:17519850 original size:24 final size:23
Alignment explanation
Indices: 17519822--17519902 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 23
17519812 CACTTAACAA
17519822 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CCTTTGAATG
*
17519846 TGCATCGATGCATCC---GCATG
1 TGCATCGATGCATCCTTTGAATG
* *
17519866 ATGCACCGATGCATGCCTTT-AATA
1 -TGCATCGATGCAT-CCTTTGAATG
17519890 TGCATCGATGCAT
1 TGCATCGATGCAT
17519903 AAGACCATGC
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
20 4 0.09
21 12 0.26
22 2 0.04
23 14 0.30
24 15 0.32
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (23 bp):
TGCATCGATGCATCCTTTGAATG
Found at i:17526808 original size:41 final size:41
Alignment explanation
Indices: 17526691--17527213 Score: 593
Period size: 41 Copynumber: 12.7 Consensus size: 41
17526681 GTGCTTTAGA
* * * * *
17526691 ACAAACGCCGCTAAATACTTGTACTTTAGTAGCATTTTTAGA
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTA-T
*
17526733 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTT-AT
* * *
17526775 ACAAACGTCGATAAAGACT-GTACTTTAGCGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * *
17526815 ACAAATGCCGCTATAGACTCGTACTTTAGCGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * *
17526856 ACAAACGCCACTATAGACTTGTACTTTAGCGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * *
17526897 ACAAACGCCGCTAAAGTCTCGTTCTTTAGTGGCATTTTTAAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTT-AT
17526939 ACAAACGCCGCTATAA-ACTCGTA-TTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTA-AAGACTCGTACTTTAGTGGCGTTTTTAT
* * * *
17526979 ACAAAGGCCGCTAAAGACTCATATTTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * *
17527020 ATAAACGCCGCTAAAGGCTCGTACTTTAGTGGCGTTTTAAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * *
17527061 AAAAACGCCACTATAGACTCGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * *
17527102 ACAAACGCCGCTATAGACTCATACTTTAGTGACGTTTTTTT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* *** * * *
17527143 ACAAACACCGCTGTGGACTCATGCTTTAGTGGTGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * *
17527184 ACAAACGCTGCTATAGACTCATGCTTTAGT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGT
17527214 TGGAGCCCCT
Statistics
Matches: 419, Mismatches: 56, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
39 2 0.00
40 37 0.09
41 305 0.73
42 72 0.17
43 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (41 bp):
ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
Found at i:17531233 original size:43 final size:43
Alignment explanation
Indices: 17531185--17531416 Score: 265
Period size: 42 Copynumber: 5.4 Consensus size: 43
17531175 AGCGTTTTTT
*
17531185 CAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTATC
1 CAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATC
* * * *
17531228 CAAAAA-GTCACTATAGATCTGGCATTTTGCGGCGTTTGTATC
1 CAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATC
* * **
17531270 CAAAAACGCCACTATAGATATGACCTTTTGTTGCGTTTGTATC
1 CAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATC
* * * *
17531313 AAAAAAAGTCGCTATAGATCTAGACCTTTTGCGACGTTTGT-TC
1 CAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTATC
* * *
17531356 C-AAAACCCCGCTATAGATATTGACCTTTTGCGGTGTTTGT-TC
1 CAAAAACGCCGCTATAGAT-CTGACCTTTTGCGGCGTTTGTATC
*
17531398 CAAAAACGCCGCGATAGAT
1 CAAAAACGCCGCTATAGAT
17531417 ATCGTATGGG
Statistics
Matches: 158, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
42 72 0.46
43 70 0.44
44 16 0.10
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (43 bp):
CAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATC
Found at i:17531285 original size:85 final size:85
Alignment explanation
Indices: 17531177--17531403 Score: 282
Period size: 85 Copynumber: 2.7 Consensus size: 85
17531167 TAATTAGCAG
* * *
17531177 CGTTT-TTTCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCCAAAAAGTCACTA
1 CGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAAGTCACTA
* *
17531241 TAGATCT-GGCATTTTGCGG
66 TAGATCTAGACATTTTGCGA
* ** * *
17531260 CGTTTGTATCCAAAAACGCCACTATAGATATGACCTTTTGTTGCGTTTGTATCAAAAAAAGTCGC
1 CGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATC-CAAAAAGTCAC
*
17531325 TATAGATCTAGACCTTTTGCGA
64 TATAGATCTAGACATTTTGCGA
* *
17531347 CGTTTGTTCC-AAAACCCCGCTATAGATATTGACCTTTTGCGGTGTTTGT-TCCAAAAA
1 CGTTTGTTCCAAAAACGCCGCTATAGATA-TGACCTTTTGCGGCGTTTGTATCCAAAAA
17531404 CGCCGCGATA
Statistics
Matches: 122, Mismatches: 17, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
83 5 0.04
84 6 0.05
85 57 0.47
86 38 0.31
87 16 0.13
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (85 bp):
CGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAAGTCACTA
TAGATCTAGACATTTTGCGA
Found at i:17535249 original size:46 final size:46
Alignment explanation
Indices: 17535191--17535282 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
17535181 CCTTCAGTGT
17535191 TGGTCCAACCTGAGTCTGGCAAGACCTACGTGGTTTACAGTGACAC
1 TGGTCCAACCTGAGTCTGGCAAGACCTACGTGGTTTACAGTGACAC
17535237 TGGTCCAACCTGAGTCTGGCAAGACCTACGTGGTTTACAGTGACAC
1 TGGTCCAACCTGAGTCTGGCAAGACCTACGTGGTTTACAGTGACAC
17535283 ATCCTATAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (46 bp):
TGGTCCAACCTGAGTCTGGCAAGACCTACGTGGTTTACAGTGACAC
Found at i:17539321 original size:178 final size:181
Alignment explanation
Indices: 17539022--17539380 Score: 697
Period size: 178 Copynumber: 2.0 Consensus size: 181
17539012 TTATTGTGTC
17539022 CCAATCTAGGATTGACAAGTACTGATCTCCTTGAATTATAAGTTTGGGCTGCAACAAAGATAAGA
1 CCAATCTAGGATTGACAAGTACTGATCTCCTTGAATTATAAGTTTGGGCTGCAACAAAGATAAGA
17539087 AAGAAATATGATTAATGATGGAATAATAAATGGAATAATAAGATAAGTAATGAAATGAAAGAAAA
66 AAGAAATATGATTAATGATGGAATAATAAATGGAATAATAAGATAAGTAATGAAATGAAAGAAAA
17539152 GG-A-ATATATGGTTGTGG-ATTAAGAAGATGTTTATGGTCTTGAGGGATG
131 GGAATATATATGGTTGTGGAATTAAGAAGATGTTTATGGTCTTGAGGGATG
17539200 CCAATCTAGGATTGACAAGTACTGATCTCCTTGAATTATAAGTTTGGGCTGCAACAAAGATAAGA
1 CCAATCTAGGATTGACAAGTACTGATCTCCTTGAATTATAAGTTTGGGCTGCAACAAAGATAAGA
17539265 AAGAAATATGATTAATGATGGAATAATAAATGGAATAATAAGATAAGTAATGAAATGAAAGAAAA
66 AAGAAATATGATTAATGATGGAATAATAAATGGAATAATAAGATAAGTAATGAAATGAAAGAAAA
17539330 GGAATATATATGGTTGTGGAATTAAGAAGATGTTTATGGTCTTGAGGGATG
131 GGAATATATATGGTTGTGGAATTAAGAAGATGTTTATGGTCTTGAGGGATG
17539381 ATGTTGTTGG
Statistics
Matches: 178, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
178 132 0.74
179 1 0.01
180 14 0.08
181 31 0.17
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (181 bp):
CCAATCTAGGATTGACAAGTACTGATCTCCTTGAATTATAAGTTTGGGCTGCAACAAAGATAAGA
AAGAAATATGATTAATGATGGAATAATAAATGGAATAATAAGATAAGTAATGAAATGAAAGAAAA
GGAATATATATGGTTGTGGAATTAAGAAGATGTTTATGGTCTTGAGGGATG
Found at i:17543971 original size:23 final size:23
Alignment explanation
Indices: 17543935--17544023 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 23
17543925 GAGTCAAGGG
*
17543935 TTCTACACGGTCCTTCGGGAAAA
1 TTCTACGCGGTCCTTCGGGAAAA
* * *
17543958 TTCTACGCGATCCTTCGGGATAT
1 TTCTACGCGGTCCTTCGGGAAAA
* *
17543981 TTCTACGTGGTCCTTCGGGAGAA
1 TTCTACGCGGTCCTTCGGGAAAA
* * *
17544004 TACTATGTGGTCCTTCGGGA
1 TTCTACGCGGTCCTTCGGGA
17544024 CATTTGTACA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGAAAA
Found at i:17544666 original size:15 final size:16
Alignment explanation
Indices: 17544646--17544680 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17544636 AATTTTCACT
17544646 ATGTTTT-AAAAGTAA
1 ATGTTTTGAAAAGTAA
*
17544661 ATGTTTTGAAAAGTTA
1 ATGTTTTGAAAAGTAA
17544677 ATGT
1 ATGT
17544681 GACGCCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (16 bp):
ATGTTTTGAAAAGTAA
Found at i:17559241 original size:42 final size:42
Alignment explanation
Indices: 17559170--17559249 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
17559160 TCTTTAATAT
* *
17559170 TAAAAAATAAATAAATATTAATAAGAATAT-GATATTTTTTCC
1 TAAAAAATAAATAAAAATAAATAAGAATATAG-TATTTTTTCC
*
17559212 TAAAAAATATAATAAAAATAAATTA-AATATAGTATTTT
1 TAAAAAATA-AATAAAAATAAATAAGAATATAGTATTTT
17559250 ATTTATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
42 20 0.61
43 13 0.39
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.38
Consensus pattern (42 bp):
TAAAAAATAAATAAAAATAAATAAGAATATAGTATTTTTTCC
Found at i:17559367 original size:143 final size:143
Alignment explanation
Indices: 17559104--17559369 Score: 310
Period size: 143 Copynumber: 1.9 Consensus size: 143
17559094 AAATAGGGCA
*
17559104 TTTATTTATTTAAAAATATTAAAAAATGACAACTAGTTACTTTAAGACAACCCCTTTCTTTAATA
1 TTTATTTATTTAAAAATATCAAAAAATGACAACTAGTTACTTTAAGACAACCCCTTTCTTTAATA
* * * * *
17559169 TTAAAAAATAAATAAATATTAATAAGAATATGATATTTTTTCCTAAAAAATATAATAAAAATAAA
66 TTAAAAAATAAATAAATACTAATAAGAATATGAAATATTTTCATAAAAAAAATAATAAAAATAAA
17559234 TTAAATATAGTAT
131 TTAAATATAGTAT
* * **
17559247 TTTATTTATTTAAAAATATCAGAAAAA-GACATA-TAGTTACTTTAAGATAATCTGTTTC-TTAA
1 TTTATTTATTTAAAAATATCA-AAAAATGACA-ACTAGTTACTTTAAGACAACCCCTTTCTTTAA
* * **
17559309 TATT-AAAAATAAATGAATACTATTATTTAAT-T-AAATATTTTCATATGAAATAAAATAATAA
64 TATTAAAAAATAAATAAATACTAATA-AGAATATGAAATATTTTCATA--AAA-AAAATAATAA
17559370 TTAAATACTA
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
140 10 0.10
141 19 0.18
142 14 0.14
143 54 0.52
144 6 0.06
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (143 bp):
TTTATTTATTTAAAAATATCAAAAAATGACAACTAGTTACTTTAAGACAACCCCTTTCTTTAATA
TTAAAAAATAAATAAATACTAATAAGAATATGAAATATTTTCATAAAAAAAATAATAAAAATAAA
TTAAATATAGTAT
Found at i:17560682 original size:3 final size:3
Alignment explanation
Indices: 17560676--17560728 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
17560666 TATTATTATT
* *
17560676 TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
17560723 AAA TAA
1 TAA TAA
17560729 AAATGAACAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:17561372 original size:41 final size:41
Alignment explanation
Indices: 17561327--17561422 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 41
17561317 AGGTCTTATG
* * * * *
17561327 GATGACCCGAAGGTTTTATCATCTTGTTTGAAAGACTTACA
1 GATGACCCGAAGGTTTAAACATCATGCTCGAAAGACTTACA
* *
17561368 GATGAACCGAAAGATTTAAACATCATGCTCGAAAGACTTACA
1 GATGACCCG-AAGGTTTAAACATCATGCTCGAAAGACTTACA
*
17561410 GATGGCCCGAAGG
1 GATGACCCGAAGG
17561423 ACTTATGAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
41 11 0.25
42 33 0.75
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (41 bp):
GATGACCCGAAGGTTTAAACATCATGCTCGAAAGACTTACA
Found at i:17561381 original size:20 final size:20
Alignment explanation
Indices: 17561356--17561427 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
17561346 CATCTTGTTT
17561356 GAAAGACTTACAGATGAACC
1 GAAAGACTTACAGATGAACC
* * * * *
17561376 GAAAGATTTAAACATCATGCTC
1 GAAAGACTTACAGATGA-AC-C
**
17561398 GAAAGACTTACAGATGGCCC
1 GAAAGACTTACAGATGAACC
*
17561418 GAAGGACTTA
1 GAAAGACTTA
17561428 TGAATCAAGA
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
20 23 0.61
21 2 0.05
22 13 0.34
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
GAAAGACTTACAGATGAACC
Found at i:17561683 original size:42 final size:42
Alignment explanation
Indices: 17561587--17561683 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
17561577 AGTTCTTATG
* * *
17561587 GATGACCCAAAGG-TTTTATCATCTTGCTCGAAAGACTTACA
1 GATGACCCAAAGGATTTAAACATCATGCTCGAAAGACTTACA
* * * *
17561628 GATAACCCGAAGGATTTAAACATCATGCTCGAATGACTTACT
1 GATGACCCAAAGGATTTAAACATCATGCTCGAAAGACTTACA
*
17561670 GATGGCCCAAAGGA
1 GATGACCCAAAGGA
17561684 CTTATGAATC
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 11 0.24
42 34 0.76
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (42 bp):
GATGACCCAAAGGATTTAAACATCATGCTCGAAAGACTTACA
Found at i:17562184 original size:259 final size:260
Alignment explanation
Indices: 17561128--17562206 Score: 1631
Period size: 260 Copynumber: 4.2 Consensus size: 260
17561118 AATGACTTAT
* * * * * *
17561128 CATCTTGCTCAAAAGGCTTACAGATGGCCCGAAGAACTGAAGAATCAAGAAACCCTC-AAATGCT
1 CATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTATGAATCAAGAAACCCTCGAAA-GCT
* *
17561192 TAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGTTTAGCTTCCTTTAACAAATCTTTTGAGAT
65 TAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTTTTGAGAT
* * *
17561257 AATTAGGAAACCCTCGAAGGCTTAGTTTTTAAAATCTCATTTGAAAACATCTAGCACTGAAGGTC
130 AATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTC
* * *
17561322 TTATGGATGACCCGAAGGTTTTATCATCTTGTTTGAAAGACTTACAGATGAACCGAAAGATTTAA
195 TTATGGATGACCCGAAGGTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAA
17561387 A
260 A
17561388 CATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTATGAATCAAGAAACCCTCGAAAGCTT
1 CATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTATGAATCAAGAAACCCTCGAAAGCTT
* *
17561453 AGTTTTTTAGTTGTCAAGGAACCCCTTTGTTAGGATTAGCTTCCTTTAACAACTCTTTTGAGATA
66 AGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATA
* * * * * *
17561518 ATTAGGAAACCCCTGAAGGCTTAGTTTCTAAAACCTCATTTGAAAACTTCCAACATTGAAGTTCT
131 ATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCT
* * *
17561583 TATGGATGACCCAAAGGTTTTATCATCTTGCTCGAAAGACTTACAGATAACCCGAAGGATTTAAA
196 TATGGATGACCCGAAGGTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAAA
* * * * * * * **
17561648 CATCATGCTCGAATGACTTACTGATGGCCCAAAGGACTTATGAATCAATAAACACACAAAATATT
1 CATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTATGAATCAAGAAACCCTCGAAAGCTT
** *
17561713 AGTTTCTTAGTTGTCAATAAACCCCTTTGTTAGTCTTAGCTTCCTTTAACAACTCTTTTGAGATA
66 AGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATA
* *
17561778 AGTAGGAAACCCCCGAATGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCT
131 ATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCT
* * * *
17561843 TATGGATGACTCGAAGGTTTTATCTTCTTACTCGAAAGACTTACAGATGACCCAAAAGATTTAAA
196 TATGGATGACCCGAAGGTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAAA
* *
17561908 CATCATGCTCAAAAGACTTACAGATGGCCCGAAGGACTTATGAATTAAGAAACCCTCGAAAGCTT
1 CATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTATGAATCAAGAAACCCTCGAAAGCTT
*
17561973 AGTTTCTTATTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATA
66 AGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATA
* * * * *
17562038 ATTAGGAAA-CCTCGAAGGCTTAGTTTCTAAAATATCATTTAAAAACATCCAGTATTGAAGGTCT
131 ATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCT
* * *
17562102 TATGGATGACGCGAAGGTTTTATCATCTTGCTCGAAAGACTTACAGATGTCCCGAAGGATTTAAA
196 TATGGATGACCCGAAGGTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAAA
* *
17562167 CATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTA
1 CATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTA
17562207 CAATTTCGGG
Statistics
Matches: 734, Mismatches: 84, Indels: 3
0.89 0.10 0.00
Matches are distributed among these distances:
259 145 0.20
260 586 0.80
261 3 0.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (260 bp):
CATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTATGAATCAAGAAACCCTCGAAAGCTT
AGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATA
ATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCT
TATGGATGACCCGAAGGTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAAA
Found at i:17564757 original size:72 final size:72
Alignment explanation
Indices: 17564648--17564783 Score: 227
Period size: 72 Copynumber: 1.9 Consensus size: 72
17564638 ATATAACAAA
* *
17564648 CTAGCTGAATATTATCCATAAAGTCGGGGCGATTAACCAATTGCTTTAAGGGGACAACTCAAGCA
1 CTAGCTGAATATTATCCATAAAGTCGGGGCGAATAACCAATTGCTTCAAGGGGACAACTCAAGCA
17564713 TAACAGG
66 TAACAGG
* * *
17564720 CTAGCTGAATATTATCCATAAAGTCGGGGCTAATAACCAATTGCTTCAGGGGGATAACTCAAGC
1 CTAGCTGAATATTATCCATAAAGTCGGGGCGAATAACCAATTGCTTCAAGGGGACAACTCAAGC
17564784 TTTATTGTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (72 bp):
CTAGCTGAATATTATCCATAAAGTCGGGGCGAATAACCAATTGCTTCAAGGGGACAACTCAAGCA
TAACAGG
Found at i:17567290 original size:6 final size:6
Alignment explanation
Indices: 17567279--17567330 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
17567269 CAAAGATGTG
** *
17567279 AATGCA AATGCA AATGCAA AGATATA AATGCAA AATGAA AATGCA AATGCA
1 AATGCA AATGCA AATGC-A A-ATGCA AATGC-A AATGCA AATGCA AATGCA
17567330 A
1 A
17567331 CGAAGAAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 26 0.70
7 9 0.24
8 2 0.05
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (6 bp):
AATGCA
Found at i:17567322 original size:39 final size:39
Alignment explanation
Indices: 17567225--17567330 Score: 117
Period size: 39 Copynumber: 2.7 Consensus size: 39
17567215 AAATGTAATT
* *
17567225 ATGCAAAGATGCAAAAATGAAAATACAAATACAAACGTAAA
1 ATGCAAAGATG--AAAATGCAAATGCAAATACAAACGTAAA
** *
17567266 ATGCAAAGATGTGAATGCAAATGCAAATGCAAA-GATATAA
1 ATGCAAAGATGAAAATGCAAATGCAAATACAAACG-TA-AA
17567306 ATGCAAA-ATGAAAATGCAAATGCAA
1 ATGCAAAGATGAAAATGCAAATGCAA
17567331 CGAAGAAGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
38 1 0.02
39 35 0.62
40 9 0.16
41 11 0.20
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.17
Consensus pattern (39 bp):
ATGCAAAGATGAAAATGCAAATGCAAATACAAACGTAAA
Found at i:17571044 original size:16 final size:16
Alignment explanation
Indices: 17571017--17571077 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 16
17571007 AATGGGCATG
17571017 TAATATTTATTTATAAT
1 TAATA-TTATTTATAAT
*
17571034 TATTATTATTTAATAA-
1 TAATATTATTT-ATAAT
*
17571050 TAATAATATTTATAAT
1 TAATATTATTTATAAT
17571066 AATAATATTATT
1 --TAATATTATT
17571078 AATATTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
15 4 0.11
16 15 0.42
17 8 0.22
18 9 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATATTATTTATAAT
Found at i:17571050 original size:3 final size:3
Alignment explanation
Indices: 17571044--17571111 Score: 57
Period size: 3 Copynumber: 23.0 Consensus size: 3
17571034 TATTATTATT
* * * * * *
17571044 TAA TAA TAA TAA TAT TTA TAA TAA TAA TAT TAT TAA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
17571092 TAT TAA T-A TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
17571112 AAATGAACAT
Statistics
Matches: 50, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:17571067 original size:18 final size:18
Alignment explanation
Indices: 17571044--17571110 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 18
17571034 TATTATTATT
*
17571044 TAATAATAATAATATTTA
1 TAATAATAATAATATTAA
*
17571062 TAATAATAATATTATTAA
1 TAATAATAATAATATTAA
* *
17571080 TATTTATAATAATATTAA
1 TAATAATAATAATATTAA
*
17571098 T-ATAATAAAAATA
1 TAATAATAATAATA
17571111 AAAATGAACA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 9 0.22
18 32 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATAATAATATTAA
Found at i:17571080 original size:24 final size:24
Alignment explanation
Indices: 17571044--17571104 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
17571034 TATTATTATT
17571044 TAATAATAATAATATTTATAATAA
1 TAATAATAATAATATTTATAATAA
* *
17571068 TAATATTATTAATATTTATAATAA
1 TAATAATAATAATATTTATAATAA
*
17571092 TATTAAT-ATAATA
1 TAATAATAATAATA
17571105 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 5 0.16
24 27 0.84
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATAATAATAATATTTATAATAA
Found at i:17575350 original size:16 final size:16
Alignment explanation
Indices: 17575329--17575362 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17575319 CTTTTAAGTA
17575329 TATATAAAAGAAATTT
1 TATATAAAAGAAATTT
* *
17575345 TATATAAATGTAATTT
1 TATATAAAAGAAATTT
17575361 TA
1 TA
17575363 CTTTAACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TATATAAAAGAAATTT
Found at i:17576626 original size:45 final size:45
Alignment explanation
Indices: 17576565--17576710 Score: 229
Period size: 45 Copynumber: 3.2 Consensus size: 45
17576555 ATTATTCATT
* * *
17576565 ATTTCCATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGC
1 ATTT-CATTTAAGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
17576611 ATTTGATTTAGGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTAAGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
17576656 ATTTCATTTAAGGCATCCCTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTAAGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
17576701 ATTTCATTTA
1 ATTTCATTTA
17576711 TTTAATGAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 89 0.96
46 4 0.04
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (45 bp):
ATTTCATTTAAGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:17583505 original size:45 final size:45
Alignment explanation
Indices: 17583440--17583721 Score: 431
Period size: 45 Copynumber: 6.3 Consensus size: 45
17583430 ATTATTCATT
*
17583440 ATTTCCATTTATGG-ATCCTTTCATGCCTTTAATGCACCGTTATTC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
17583485 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATTC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
17583530 ATTTCATTTATCGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
17583575 ATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
17583620 ATTTCATTTATAGCATCCTTTCATGCCTTTAATGCATCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * * * * *
17583665 ATTTCGTTTATGGCATCTTTTCATCCCTTCAATGTACTGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
17583710 ATTTCATTTATG
1 ATTTCATTTATG
17583722 TAATGAAAAC
Statistics
Matches: 218, Mismatches: 18, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
44 9 0.04
45 209 0.96
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:17584253 original size:94 final size:94
Alignment explanation
Indices: 17584085--17584282 Score: 265
Period size: 94 Copynumber: 2.1 Consensus size: 94
17584075 CCCTACCATG
* * * * *
17584085 GTATCGATACTTCTATACTATGGTATAGATACCTCTTTTAGTGTCGATACCATTTCTACATTCTG
1 GTATCGATACTACTATACTATGGTACAGATACCCCTTTCAGTATCGATACCATTTCTACATTCTG
* * *
17584150 TTATTCATGGTATCGATACTTTTCTTATA
66 TAATCCATGGTATCGATACTTTCCTTATA
* *
17584179 GTATCGATACTACTATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTT-TGGCATTC
1 GTATCGATACTACTATACTATGGTACAGATAC-CCCTTTCAGTATCGATACCATTTCT-ACATTC
*
17584243 TG-AATCCATGGTATCGATACTTTCCTTTTA
64 TGTAATCCATGGTATCGATACTTTCCTTATA
17584273 GTATCGATAC
1 GTATCGATAC
17584283 CCCATCAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
94 64 0.70
95 27 0.30
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.41
Consensus pattern (94 bp):
GTATCGATACTACTATACTATGGTACAGATACCCCTTTCAGTATCGATACCATTTCTACATTCTG
TAATCCATGGTATCGATACTTTCCTTATA
Found at i:17587427 original size:14 final size:14
Alignment explanation
Indices: 17587408--17587434 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17587398 AATCTATTCG
17587408 TTCATTTATGTTCA
1 TTCATTTATGTTCA
17587422 TTCATTTATGTTC
1 TTCATTTATGTTC
17587435 TCTAGACCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (14 bp):
TTCATTTATGTTCA
Found at i:17590331 original size:18 final size:18
Alignment explanation
Indices: 17590306--17590345 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
17590296 TTAAAATTGT
*
17590306 AAAT-AATTTCAACATAA
1 AAATAAATTTAAACATAA
*
17590323 AAATAAATTTAAACATTA
1 AAATAAATTTAAACATAA
17590341 AAATA
1 AAATA
17590346 GAAATCAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATAAATTTAAACATAA
Found at i:17601157 original size:14 final size:15
Alignment explanation
Indices: 17601138--17601166 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17601128 TCAAGCATCT
17601138 AACAATCCA-AAACA
1 AACAATCCAGAAACA
17601152 AACAATCCAGAAACA
1 AACAATCCAGAAACA
17601167 TCAAAACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:17609080 original size:26 final size:26
Alignment explanation
Indices: 17609019--17609118 Score: 152
Period size: 26 Copynumber: 3.9 Consensus size: 26
17609009 CATGGTCCTA
*
17609019 TGCATCGATGCATCAAATGGTC-CT-A-
1 TGCATCGATGCATCAAAT-G-CATTGAG
17609044 TGCATCGATGCATCAAATGCATTGAG
1 TGCATCGATGCATCAAATGCATTGAG
17609070 TGCATCGATGCATCAAATGCATTGAG
1 TGCATCGATGCATCAAATGCATTGAG
17609096 TGCATCGATGCATCAAATGCATT
1 TGCATCGATGCATCAAATGCATT
17609119 CGATGTTCAA
Statistics
Matches: 71, Mismatches: 1, Indels: 5
0.92 0.01 0.06
Matches are distributed among these distances:
23 1 0.01
24 2 0.03
25 19 0.27
26 49 0.69
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (26 bp):
TGCATCGATGCATCAAATGCATTGAG
Found at i:17610146 original size:15 final size:15
Alignment explanation
Indices: 17610122--17610156 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17610112 ACAGTCAACG
17610122 GCTCGACTCAACTCA
1 GCTCGACTCAACTCA
*
17610137 GCTCGGCTCAACTCA
1 GCTCGACTCAACTCA
*
17610152 ACTCG
1 GCTCG
17610157 TTTTGAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.40, G:0.17, T:0.20
Consensus pattern (15 bp):
GCTCGACTCAACTCA
Found at i:17611142 original size:17 final size:17
Alignment explanation
Indices: 17611122--17611157 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17611112 CCCACCATGG
17611122 TACCTAACCCGACCCAA
1 TACCTAACCCGACCCAA
**
17611139 TACCTAACTTGACCCAA
1 TACCTAACCCGACCCAA
17611156 TA
1 TA
17611158 TTCGACTCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.39, G:0.06, T:0.19
Consensus pattern (17 bp):
TACCTAACCCGACCCAA
Found at i:17616713 original size:12 final size:12
Alignment explanation
Indices: 17616696--17616722 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17616686 TTAATTGCGA
17616696 AAATTAAAACTT
1 AAATTAAAACTT
17616708 AAATTAAAACTT
1 AAATTAAAACTT
17616720 AAA
1 AAA
17616723 GATTCGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTAAAACTT
Found at i:17618090 original size:4 final size:4
Alignment explanation
Indices: 17618081--17618127 Score: 67
Period size: 4 Copynumber: 11.0 Consensus size: 4
17618071 ACCAAAATAA
17618081 AAAT AAAT AAAT AAAAT AAAT AAAT AAAT AAAT AAATT AAATT AAAT
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAA-T AAA-T AAAT
17618128 TAAAATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 28 0.68
5 13 0.32
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:17618097 original size:5 final size:5
Alignment explanation
Indices: 17618074--17618147 Score: 54
Period size: 5 Copynumber: 15.8 Consensus size: 5
17618064 GACCTAAACC
*
17618074 AAAAT AAAA- ATAAAT -AAAT AAAAT -AAAT -AAAT -AAAT -AAAT AAATT
1 AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* *
17618119 AAATT AAATT AAAAT AAAA- AGAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT A-AAAT AAAA
17618148 ATATATGTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
4 22 0.36
5 38 0.62
6 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:17618107 original size:21 final size:23
Alignment explanation
Indices: 17618075--17618146 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 23
17618065 ACCTAAACCA
*
17618075 AAATAAA-AATAAATAAATAAAAT
1 AAATAAATAA-AATTAAATAAAAT
*
17618098 AAATAAAT-AAA-TAAATAAATT
1 AAATAAATAAAATTAAATAAAAT
*
17618119 AAATTAAATTAAAA-TAAAAAGAAAT
1 AAA-TAAA-TAAAATTAAATA-AAAT
17618144 AAA
1 AAA
17618147 AATATATGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 12 0.29
22 6 0.15
23 9 0.22
24 8 0.20
25 6 0.15
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (23 bp):
AAATAAATAAAATTAAATAAAAT
Found at i:17618375 original size:38 final size:36
Alignment explanation
Indices: 17618218--17618430 Score: 173
Period size: 37 Copynumber: 5.7 Consensus size: 36
17618208 GAAGATTATA
* *
17618218 TATATTATATACGTTTTCAAAAAACCATTTTTAAAAAC
1 TATATTATATATGTTTTC-AAAAACC-GTTTTAAAAAC
* * * **
17618256 TAGA-TATAGAAGTTTTCAAAAAATATGTTTTTTCAAAAAC
1 TATATTATATATGTTTTC-AAAAA-CCG--TTTT-AAAAAC
*
17618296 TATATTATATATGTTTTCAAAAAACCGTTTTAAAAAT
1 TATATTATATATGTTTTC-AAAAACCGTTTTAAAAAC
* * *
17618333 TATA-TATTATACGTTTTTAAAAGTA-TGTTTTCAAAAAC
1 TATATTA-TATATGTTTTCAAAA--ACCGTTTT-AAAAAC
*
17618371 TATATTATATATGTTTTTAAAAACCGTTTTAAAAAC
1 TATATTATATATGTTTTCAAAAACCGTTTTAAAAAC
17618407 TATA-TATTATATGTTTTCAAAAAC
1 TATATTA-TATATGTTTTCAAAAAC
17618431 TATATTATAT
Statistics
Matches: 144, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
35 2 0.01
36 33 0.23
37 45 0.31
38 31 0.22
39 6 0.04
40 10 0.07
41 17 0.12
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (36 bp):
TATATTATATATGTTTTCAAAAACCGTTTTAAAAAC
Found at i:17618405 original size:36 final size:37
Alignment explanation
Indices: 17618285--17618430 Score: 167
Period size: 36 Copynumber: 3.9 Consensus size: 37
17618275 AAAATATGTT
*
17618285 TTTTCAAAAACTATAT-TATATATGTTTTCAAAAAACCG
1 TTTTCAAAAACTATATAT-TATATGTTTT-TAAAAACCG
* * *
17618323 TTTT-AAAAATTATATATTATACGTTTTTAAAAGTA-TG
1 TTTTCAAAAACTATATATTATATGTTTTTAAAA--ACCG
17618360 TTTTCAAAAACTATAT-TATATATGTTTTTAAAAACCG
1 TTTTCAAAAACTATATAT-TATATGTTTTTAAAAACCG
*
17618397 TTTT-AAAAACTATATATTATATGTTTTCAAAAAC
1 TTTTCAAAAACTATATATTATATGTTTTTAAAAAC
17618431 TATATTATAT
Statistics
Matches: 93, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
36 32 0.34
37 31 0.33
38 30 0.32
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (37 bp):
TTTTCAAAAACTATATATTATATGTTTTTAAAAACCG
Found at i:17618424 original size:60 final size:61
Alignment explanation
Indices: 17618356--17618488 Score: 227
Period size: 60 Copynumber: 2.2 Consensus size: 61
17618346 TTTTTAAAAG
*
17618356 TATGTTTTCAAAAACTATATTATATATGTTTTTAAAAACCG-TTTTAAAAACTATATATTA
1 TATGTTTTCAAAAACTATATTATATATGTTTTCAAAAACCGTTTTTAAAAACTATATATTA
*
17618416 TATGTTTTCAAAAACTATATTATATATGTTTTCAAAAACCGTTTTTTAAAACTATATATTA
1 TATGTTTTCAAAAACTATATTATATATGTTTTCAAAAACCGTTTTTAAAAACTATATATTA
17618477 TA--TTTTCAAAAA
1 TATGTTTTCAAAAA
17618489 TGTATTTTCA
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
59 10 0.14
60 40 0.57
61 20 0.29
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (61 bp):
TATGTTTTCAAAAACTATATTATATATGTTTTCAAAAACCGTTTTTAAAAACTATATATTA
Found at i:17618433 original size:24 final size:24
Alignment explanation
Indices: 17618396--17618454 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
17618386 TTTAAAAACC
17618396 GTTTT-AAAAACTATA-TATTATAT
1 GTTTTCAAAAACTATATTA-TATAT
17618419 GTTTTCAAAAACTATATTATATAT
1 GTTTTCAAAAACTATATTATATAT
17618443 GTTTTCAAAAAC
1 GTTTTCAAAAAC
17618455 CGTTTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.15
24 27 0.79
25 2 0.06
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (24 bp):
GTTTTCAAAAACTATATTATATAT
Found at i:17619360 original size:34 final size:33
Alignment explanation
Indices: 17619279--17619373 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
17619269 GGCAAGTTTG
**
17619279 AAAATTCATCTTGGTTGGT-AGCCAACTTATTGG
1 AAAATTCATCTTGGTTGGTGA-CCAACTTATTAA
*
17619312 AAATTTCATCTTGGTTGGTGACCAACTTATTAA
1 AAAATTCATCTTGGTTGGTGACCAACTTATTAA
* *
17619345 AAAATTCATCTTTGGTAGGTGGCCAACTT
1 AAAATTCATC-TTGGTTGGTGACCAACTT
17619374 TGCAAATGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
33 37 0.69
34 17 0.31
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (33 bp):
AAAATTCATCTTGGTTGGTGACCAACTTATTAA
Found at i:17624120 original size:34 final size:33
Alignment explanation
Indices: 17624038--17624133 Score: 165
Period size: 33 Copynumber: 2.9 Consensus size: 33
17624028 GCAACATCCT
17624038 GAAAATTCATCTTGGTTGGTGGCCAACTTATTG
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATTG
*
17624071 GAAATTTCATCTTGGTTGGTGGCCAACTTATTG
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATTG
*
17624104 GAAAATTCATCTTTGGTAGGTGGCCAACTT
1 GAAAATTCATC-TTGGTTGGTGGCCAACTT
17624134 TGCACATGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 42 0.71
34 17 0.29
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (33 bp):
GAAAATTCATCTTGGTTGGTGGCCAACTTATTG
Found at i:17624158 original size:38 final size:34
Alignment explanation
Indices: 17624038--17624158 Score: 129
Period size: 33 Copynumber: 3.5 Consensus size: 34
17624028 GCAACATCCT
* * *
17624038 GAAAATTCATC-TTGGTTGGTGGCCAACTTATTG
1 GAAATTTCATCTTTGGTAGGTGGCCAACTTAATG
* *
17624071 GAAATTTCATC-TTGGTTGGTGGCCAACTTATTG
1 GAAATTTCATCTTTGGTAGGTGGCCAACTTAATG
*
17624104 GAAAATTCATCTTTGGTAGGTGGCCAACTTTGCACATG
1 GAAATTTCATCTTTGGTAGGTGGCCAAC-TT--A-ATG
*
17624142 GGAATTTCATCTTTGGT
1 GAAATTTCATCTTTGGT
17624159 CCCTAAAATA
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
33 42 0.55
34 15 0.19
35 2 0.03
37 1 0.01
38 17 0.22
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (34 bp):
GAAATTTCATCTTTGGTAGGTGGCCAACTTAATG
Found at i:17626473 original size:24 final size:24
Alignment explanation
Indices: 17626443--17626561 Score: 159
Period size: 24 Copynumber: 5.0 Consensus size: 24
17626433 AAACATAATT
* *
17626443 CATGTCAAGTATCATATTAAAATC
1 CATGTCAAGTATCATATCAGAATC
* *
17626467 CAGGTCAAGTATCATATTAGAATC
1 CATGTCAAGTATCATATCAGAATC
* * *
17626491 CAAGTCACGTATCAGATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
17626515 CATGT-AAGATATCATATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
17626539 CATGTCAAGTATCATATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
17626562 TCAAATCGAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.02
24 79 0.94
25 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:17629070 original size:17 final size:17
Alignment explanation
Indices: 17629050--17629103 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
17629040 TCGTTGACCT
17629050 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
17629067 ACCCGACCCGTTGACC---G
1 ACCCGACCC---GACCGTTG
17629084 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
17629101 ACC
1 ACC
17629104 GTTGACCGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
14 4 0.13
17 23 0.74
20 4 0.13
ACGTcount: A:0.19, C:0.48, G:0.22, T:0.11
Consensus pattern (17 bp):
ACCCGACCCGACCGTTG
Found at i:17629103 original size:34 final size:34
Alignment explanation
Indices: 17629021--17629103 Score: 139
Period size: 34 Copynumber: 2.4 Consensus size: 34
17629011 ACCGGTTCTA
* * *
17629021 ACCCGACCGTTGACACGACTCGTTGACCTACCCG
1 ACCCGACCGTTGACCCGACCCGTTGACCGACCCG
17629055 ACCCGACCGTTGACCCGACCCGTTGACCGACCCG
1 ACCCGACCGTTGACCCGACCCGTTGACCGACCCG
17629089 ACCCGACCGTTGACC
1 ACCCGACCGTTGACC
17629104 GTTGACCGGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.19, C:0.45, G:0.22, T:0.14
Consensus pattern (34 bp):
ACCCGACCGTTGACCCGACCCGTTGACCGACCCG
Found at i:17629152 original size:29 final size:29
Alignment explanation
Indices: 17629111--17629246 Score: 202
Period size: 29 Copynumber: 4.7 Consensus size: 29
17629101 ACCGTTGACC
* *
17629111 GGGTGCTAGTTTAGTAATTAATTCGAAAC
1 GGGTGCTACTTTAGTAATTAATTCGAAAT
*
17629140 GGGTGCTATTTTAGTAATTAATTCGAAAT
1 GGGTGCTACTTTAGTAATTAATTCGAAAT
*
17629169 GTGTGCTACTTTAGTAATTAATTCGAAAT
1 GGGTGCTACTTTAGTAATTAATTCGAAAT
17629198 GGGTGCTACTTTAGTAATTAATTCGAAAT
1 GGGTGCTACTTTAGTAATTAATTCGAAAT
* *
17629227 AGGTGTTA-TATTAGTAATTA
1 GGGTGCTACT-TTAGTAATTA
17629247 TTTAAAAAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
28 1 0.01
29 98 0.99
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (29 bp):
GGGTGCTACTTTAGTAATTAATTCGAAAT
Found at i:17629259 original size:29 final size:29
Alignment explanation
Indices: 17629208--17629264 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
17629198 GGGTGCTACT
** *
17629208 TTAGTAATTAATTCGAAATAGGTGTTATA
1 TTAGTAATTAATTAAAAAAAGGTGTTATA
*
17629237 TTAGTAATTATTTAAAAAAAGGTGTTAT
1 TTAGTAATTAATTAAAAAAAGGTGTTAT
17629265 TTATGTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (29 bp):
TTAGTAATTAATTAAAAAAAGGTGTTATA
Found at i:17632560 original size:2 final size:2
Alignment explanation
Indices: 17632551--17632586 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
17632541 AACTAAATTT
*
17632551 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17632587 TTGTTTGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17633463 original size:14 final size:13
Alignment explanation
Indices: 17633444--17633475 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
17633434 GAATCAATAC
17633444 TAAAAATAAATAAA
1 TAAAAATAAA-AAA
17633458 TAAAAATAAAAAA
1 TAAAAATAAAAAA
17633471 TAAAA
1 TAAAA
17633476 TTATATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:17635005 original size:2 final size:2
Alignment explanation
Indices: 17634998--17635029 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17634988 CTATGAATGA
17634998 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17635030 AGAGTCCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17635372 original size:155 final size:156
Alignment explanation
Indices: 17635090--17635402 Score: 619
Period size: 155 Copynumber: 2.0 Consensus size: 156
17635080 AAGGTCTCTG
17635090 AGAATCTGATATGTTGCACTGGAATGTCTGGCGATGATAACTCCCCATGATCTTCCCCTAAGAAC
1 AGAATCTGATATGTTGCACTGGAATGTCTGGCGATGATAACTCCCCATGATCTTCCCCTAAGAAC
17635155 CTGCAAATAGAAACACATTTCGAACACTGAGCTTATGAGCTTAGTGCCTCACTAATAATTATATT
66 CTGCAAATAGAAACACATTTCGAACACTGAGCTTATGAGCTTAGTGCCTCACTAATAATTATATT
17635220 GTACTATATGCA-TCATTTAATGAAA
131 GTACTATATGCATTCATTTAATGAAA
17635245 AGAATCTGATATGTTGCACTGGAATGTCTGGCGATGATAACTCCCCATGATCTTCCCCTAAGAAC
1 AGAATCTGATATGTTGCACTGGAATGTCTGGCGATGATAACTCCCCATGATCTTCCCCTAAGAAC
17635310 CTGCAAATAGAAACACATTTCGAACACTGAGCTTATGAGCTTAGTGCCTCACTAATAATTATATT
66 CTGCAAATAGAAACACATTTCGAACACTGAGCTTATGAGCTTAGTGCCTCACTAATAATTATATT
17635375 GTACTATATGCATTCATTTAATGAAA
131 GTACTATATGCATTCATTTAATGAAA
17635401 AG
1 AG
17635403 GCTAGTGTCA
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
155 142 0.90
156 15 0.10
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (156 bp):
AGAATCTGATATGTTGCACTGGAATGTCTGGCGATGATAACTCCCCATGATCTTCCCCTAAGAAC
CTGCAAATAGAAACACATTTCGAACACTGAGCTTATGAGCTTAGTGCCTCACTAATAATTATATT
GTACTATATGCATTCATTTAATGAAA
Found at i:17649194 original size:61 final size:61
Alignment explanation
Indices: 17649115--17649267 Score: 252
Period size: 61 Copynumber: 2.5 Consensus size: 61
17649105 GCTTATGCCA
*
17649115 TAGTGCTTATCCGGATATGACACATCAGGTCATGCCCACCACCTACACTAGGTTTAAACTC
1 TAGTGCTAATCCGGATATGACACATCAGGTCATGCCCACCACCTACACTAGGTTTAAACTC
17649176 TAGTGCTAATCCGGATATGACACATCAGGTCATGCCCACCACCTACACTAGGTTTAAACTC
1 TAGTGCTAATCCGGATATGACACATCAGGTCATGCCCACCACCTACACTAGGTTTAAACTC
* * * * *
17649237 TAGTGTTAATCCGAACATGATACATAAGGTC
1 TAGTGCTAATCCGGATATGACACATCAGGTC
17649268 GTATCCACCT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 86 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (61 bp):
TAGTGCTAATCCGGATATGACACATCAGGTCATGCCCACCACCTACACTAGGTTTAAACTC
Found at i:17649632 original size:24 final size:24
Alignment explanation
Indices: 17649602--17649647 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
17649592 CTTCCTGATT
17649602 ATGTATAAAACATCTATGTACATG
1 ATGTATAAAACATCTATGTACATG
*
17649626 ATGTATAAAAGATCTATGTACA
1 ATGTATAAAACATCTATGTACA
17649648 ATGTCATGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (24 bp):
ATGTATAAAACATCTATGTACATG
Found at i:17651424 original size:29 final size:31
Alignment explanation
Indices: 17651358--17651427 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
17651348 AAATTACCAT
* * * *
17651358 TTTGGTCCCTAAACTTTTCCAAAGTTTATAC
1 TTTGGTCACTAAACTTTTCAAAAATTTATAA
17651389 TTTGGTCACTAAAC-TTT-AAAAATTTATAA
1 TTTGGTCACTAAACTTTTCAAAAATTTATAA
17651418 TTTGGTCACT
1 TTTGGTCACT
17651428 CACTAAATCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
30 3 0.09
31 13 0.37
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (31 bp):
TTTGGTCACTAAACTTTTCAAAAATTTATAA
Found at i:17655546 original size:20 final size:21
Alignment explanation
Indices: 17655521--17655572 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
17655511 TCATCTCAAG
17655521 TAAAAC-TATCATATG-ATATT
1 TAAAACATAT-ATATGTATATT
17655541 TAAAACATATATATGTATA-T
1 TAAAACATATATATGTATATT
17655561 TAAATACATATA
1 TAAA-ACATATA
17655573 CTCAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAAACATATATATGTATATT
Found at i:17656597 original size:24 final size:24
Alignment explanation
Indices: 17656565--17656613 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
17656555 AGTCTTCCTG
17656565 ATGATGTATAAAACATCTATATAC
1 ATGATGTATAAAACATCTATATAC
* *
17656589 ATGATGTATAAAAGATCTATGTAC
1 ATGATGTATAAAACATCTATATAC
17656613 A
1 A
17656614 ATGTCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATATAC
Found at i:17657816 original size:11 final size:11
Alignment explanation
Indices: 17657800--17657824 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17657790 TTTCATGCTA
17657800 AATTTACCTTT
1 AATTTACCTTT
17657811 AATTTACCTTT
1 AATTTACCTTT
17657822 AAT
1 AAT
17657825 GAATATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTACCTTT
Found at i:17658357 original size:30 final size:29
Alignment explanation
Indices: 17658321--17658385 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
17658311 AAATTACTAT
* *
17658321 TTTGGTC-CCTAAACTTTTCAAAGTTTATAC
1 TTTGGTCACCT-AAC-TTTAAAAGTTTATAA
*
17658351 TTTGGTCACCTAACTTTAAAATTTTATAA
1 TTTGGTCACCTAACTTTAAAAGTTTATAA
17658380 TTTGGT
1 TTTGGT
17658386 AACTATACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 18 0.58
30 10 0.32
31 3 0.10
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (29 bp):
TTTGGTCACCTAACTTTAAAAGTTTATAA
Found at i:17658688 original size:24 final size:24
Alignment explanation
Indices: 17658656--17658701 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
17658646 AGTCTTCCTG
17658656 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
17658680 ATGATGTATAAAAGATCTATGT
1 ATGATGTATAAAACATCTATGT
17658702 TCAATGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:17659910 original size:11 final size:11
Alignment explanation
Indices: 17659894--17659918 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17659884 TTTCATGCTA
17659894 AATTTACCTTT
1 AATTTACCTTT
17659905 AATTTACCTTT
1 AATTTACCTTT
17659916 AAT
1 AAT
17659919 GAATATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTACCTTT
Found at i:17660783 original size:24 final size:24
Alignment explanation
Indices: 17660751--17660796 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
17660741 AGTCTTCCTG
17660751 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
17660775 ATGATGTATAAAAGATCTATGT
1 ATGATGTATAAAACATCTATGT
17660797 TCAATGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:17662865 original size:24 final size:24
Alignment explanation
Indices: 17662833--17662878 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
17662823 AGTCTTCCTG
17662833 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
17662857 ATGATGTATAAAAGATCTATGT
1 ATGATGTATAAAACATCTATGT
17662879 TCAATGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:17664945 original size:24 final size:24
Alignment explanation
Indices: 17664913--17664958 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
17664903 AGTCTTCCTG
*
17664913 ATGATGTATAAAATATCTATGTAC
1 ATGATGTATAAAAGATCTATGTAC
17664937 ATGATGTATAAAAGATCTATGT
1 ATGATGTATAAAAGATCTATGT
17664959 TCAATGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (24 bp):
ATGATGTATAAAAGATCTATGTAC
Found at i:17667030 original size:24 final size:24
Alignment explanation
Indices: 17666998--17667043 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
17666988 AGTCTTCCTG
17666998 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
17667022 ATGATGTATAAAAGATCTATGT
1 ATGATGTATAAAACATCTATGT
17667044 TCAATGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:17669107 original size:24 final size:24
Alignment explanation
Indices: 17669075--17669123 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
17669065 AGTCTTCCAG
17669075 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
17669099 ATGATGTATAAAAGATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
17669123 A
1 A
17669124 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Done.