Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 86 of 133
Found at i:17111233 original size:32 final size:33
Alignment explanation
Indices: 17111197--17111258 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
17111187 TTTGCATGAT
*
17111197 TAATATTATATTTGCATGA-TAATTTATTTGCC
1 TAATATTATATTTGCATGATTAATATATTTGCC
*
17111229 TAATATTTTATTTGCATGATTAATATATTT
1 TAATATTATATTTGCATGATTAATATATTT
17111259 ATATGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.53
Consensus pattern (33 bp):
TAATATTATATTTGCATGATTAATATATTTGCC
Found at i:17111313 original size:21 final size:20
Alignment explanation
Indices: 17111287--17111329 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
17111277 TGCATGATTT
17111287 ATTTAATTACATGATTTATTA
1 ATTTAATTACATGA-TTATTA
*
17111308 ATTTAATTGCATGATTATTA
1 ATTTAATTACATGATTATTA
17111328 AT
1 AT
17111330 ATATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (20 bp):
ATTTAATTACATGATTATTA
Found at i:17111324 original size:17 final size:17
Alignment explanation
Indices: 17111188--17111324 Score: 62
Period size: 17 Copynumber: 7.6 Consensus size: 17
17111178 GTATTTATTT
17111188 TTGCATGATTAATATTATA
1 TTGCATGATTAAT-TTA-A
*
17111207 TTTGCATGA-TAATTTAT
1 -TTGCATGATTAATTTAA
* * * *
17111224 TTGCCT-AATATTTTAT
1 TTGCATGATTAATTTAA
* *
17111240 TTGCATGATTAATATAT
1 TTGCATGATTAATTTAA
** **
17111257 TTATATGAATTTAATTTGC
1 TTGCATG-A-TTAATTTAA
*
17111276 TTGCATGATTTATTTAA
1 TTGCATGATTAATTTAA
*
17111293 TTACATGATTTATTAATTTAA
1 TTGCATG----ATTAATTTAA
17111314 TTGCATGATTA
1 TTGCATGATTA
17111325 TTAATATATT
Statistics
Matches: 89, Mismatches: 20, Indels: 19
0.70 0.16 0.15
Matches are distributed among these distances:
15 1 0.01
16 17 0.19
17 28 0.31
18 5 0.06
19 15 0.17
20 8 0.09
21 15 0.17
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (17 bp):
TTGCATGATTAATTTAA
Found at i:17111335 original size:45 final size:45
Alignment explanation
Indices: 17111286--17111380 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
17111276 TTGCATGATT
*
17111286 TATTTAATTACATGATTTATTAATTTAATTGCATGATTATTAATA
1 TATTTAATTACATGATTTATTAATATAATTGCATGATTATTAATA
* *** *
17111331 TATTTATTTGTGTGATTTATTAATATATTTGCATGATTATTAATA
1 TATTTAATTACATGATTTATTAATATAATTGCATGATTATTAATA
17111376 TATTT
1 TATTT
17111381 GTTTGTGTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (45 bp):
TATTTAATTACATGATTTATTAATATAATTGCATGATTATTAATA
Found at i:17111349 original size:37 final size:38
Alignment explanation
Indices: 17111308--17111409 Score: 98
Period size: 45 Copynumber: 2.5 Consensus size: 38
17111298 TGATTTATTA
17111308 ATTTAATTGCATGATTATTAATATATTTATTTGTGTGATTT
1 ATTTAATTGCATGATTATTAATATATTTATTTGTGTG---T
*
17111349 ATTAATATATTTGCATGATTATTAATATATTTGTTTGTGTG-
1 ATT--TA-A-TTGCATGATTATTAATATATTTATTTGTGTGT
* * *
17111390 ATTTATTTGTATGATAATTA
1 ATTTAATTGCATGATTATTA
17111410 TATTATTGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
37 12 0.23
39 2 0.04
41 6 0.11
43 2 0.04
44 1 0.02
45 30 0.57
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (38 bp):
ATTTAATTGCATGATTATTAATATATTTATTTGTGTGT
Found at i:17111356 original size:25 final size:25
Alignment explanation
Indices: 17111322--17111396 Score: 88
Period size: 21 Copynumber: 3.2 Consensus size: 25
17111312 AATTGCATGA
17111322 TTATTAATATATTTATTTGTGTGAT
1 TTATTAATATATTTATTTGTGTGAT
**
17111347 TTATT-A-ATA--TATTTGCATGA-
1 TTATTAATATATTTATTTGTGTGAT
*
17111367 TTATTAATATATTTGTTTGTGTGAT
1 TTATTAATATATTTATTTGTGTGAT
17111392 TTATT
1 TTATT
17111397 TGTATGATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 5 0.12
21 10 0.25
22 3 0.08
23 3 0.08
24 9 0.22
25 10 0.25
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.59
Consensus pattern (25 bp):
TTATTAATATATTTATTTGTGTGAT
Found at i:17111372 original size:20 final size:21
Alignment explanation
Indices: 17111276--17111381 Score: 89
Period size: 20 Copynumber: 5.1 Consensus size: 21
17111266 TTTAATTTGC
17111276 TTGCATGATTTATT--TA-A-
1 TTGCATGATTTATTAATATAT
* * *
17111293 TTACATGATTTATTAATTTAA
1 TTGCATGATTTATTAATATAT
17111314 TTGCATGA-TTATTAATATATTTAT
1 TTGCATGATTTATT-A-ATA--TAT
**
17111338 TTGTGTGATTTATTAATATAT
1 TTGCATGATTTATTAATATAT
17111359 TTGCATGA-TTATTAATATAT
1 TTGCATGATTTATTAATATAT
17111379 TTG
1 TTG
17111382 TTTGTGTGAT
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
17 13 0.18
19 1 0.01
20 21 0.30
21 17 0.24
22 2 0.03
23 3 0.04
24 9 0.13
25 5 0.07
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (21 bp):
TTGCATGATTTATTAATATAT
Found at i:17111386 original size:45 final size:45
Alignment explanation
Indices: 17111298--17111396 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 45
17111288 TTTAATTACA
*
17111298 TGATTTATTAATTTAATTGCATGATTATTAATATATTTATTTGTG
1 TGATTTATTAATATAATTGCATGATTATTAATATATTTATTTGTG
* *
17111343 TGATTTATTAATATATTTGCATGATTATTAATATATTTGTTTGTG
1 TGATTTATTAATATAATTGCATGATTATTAATATATTTATTTGTG
17111388 TGATTTATT
1 TGATTTATT
17111397 TGTATGATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (45 bp):
TGATTTATTAATATAATTGCATGATTATTAATATATTTATTTGTG
Found at i:17112929 original size:17 final size:18
Alignment explanation
Indices: 17112896--17112930 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17112886 ACTTGTATAT
17112896 ACATTTTTTATCCATGTAA
1 ACATTTTTTAT-CATGTAA
17112915 ACATTTTTTAT-ATGTA
1 ACATTTTTTATCATGTA
17112931 CATTATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (18 bp):
ACATTTTTTATCATGTAA
Found at i:17113028 original size:135 final size:132
Alignment explanation
Indices: 17112630--17113028 Score: 405
Period size: 130 Copynumber: 3.0 Consensus size: 132
17112620 ATGTATTTGC
* * * * * *
17112630 ATATACA-TTTTTATCCATGTAAACATTTTTGTATGCACATTATTTTGTTGGCTTGAAAAAATTT
1 ATATACATTTTTTATCCATGTAAACATTTTTGTATGTACATTATTTTATTTGCTTG-GAGAATCT
* *
17112694 TTGCCTTTTCAATTTTGTACATAG-TTTGGATATGAATTCTTGTTT-TTCACTATGTATTACATA
65 TTGCCTTTTCAGTTTTGTACATAGTTTTGAATATGAATTCTT-TTTGTT-ACTATGTATTACATA
17112757 CATGT
128 CATGT
* * * *** * ** *
17112762 ATTTGCATATAAGAT---TTTATCCATTTTTGTATGTACATTATTTTATTTGCCTAGGAGAATCT
1 ATATACATTTTTTATCCATGTAAACATTTTTGTATGTACATTATTTTATTTG-CTTGGAGAATCT
* * * * * * * *
17112824 TTGCATTTTTAGTTTTGTACATAGTTGTGAATATGAATTCTTGTTGTTATTATGCATTATATACT
65 TTGCCTTTTCAGTTTTGTACATAGTTTTGAATATGAATTCTTTTTGTTACTATGTATTACATACA
17112889 TGT
130 TGT
* * * *
17112892 ATATACATTTTTTATCCATGTAAACATTTTTTATATGTACATTATATCATTTGTTTGGGAGCAAT
1 ATATACATTTTTTATCCATGTAAACA-TTTTTGTATGTACATTATTTTATTTGCTT-GGAG-AAT
* *
17112957 CTTTGCCTTTGCAGTTTTGTACATAGTTTTGAATATGAATTCTTTTTGTTACTATGTATTGCATA
63 CTTTGCCTTTTCAGTTTTGTACATAGTTTTGAATATGAATTCTTTTTGTTACTATGTATTACATA
17113022 CATGT
128 CATGT
17113027 AT
1 AT
17113029 TTGCATGTAA
Statistics
Matches: 207, Mismatches: 50, Indels: 17
0.76 0.18 0.06
Matches are distributed among these distances:
130 81 0.39
131 20 0.10
132 5 0.02
133 9 0.04
134 27 0.13
135 65 0.31
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (132 bp):
ATATACATTTTTTATCCATGTAAACATTTTTGTATGTACATTATTTTATTTGCTTGGAGAATCTT
TGCCTTTTCAGTTTTGTACATAGTTTTGAATATGAATTCTTTTTGTTACTATGTATTACATACAT
GT
Found at i:17114261 original size:9 final size:9
Alignment explanation
Indices: 17114239--17114295 Score: 62
Period size: 10 Copynumber: 6.1 Consensus size: 9
17114229 AAAAAAAGGG
*
17114239 GAAAAGAAAG
1 GAAAA-AAAT
17114249 GAAAAAAAT
1 GAAAAAAAT
17114258 GAAAAAAAAT
1 G-AAAAAAAT
17114268 G-AAAAAAT
1 GAAAAAAAT
*
17114276 GAAAAAAAA
1 GAAAAAAAT
17114285 GATAAAAAAT
1 GA-AAAAAAT
17114295 G
1 G
17114296 TGAAAAGGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 8 0.20
9 12 0.29
10 21 0.51
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:17114261 original size:19 final size:18
Alignment explanation
Indices: 17114239--17114295 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
17114229 AAAAAAAGGG
*
17114239 GAAAAGAAAGGAAAAAAAT
1 GAAAA-AAAAGAAAAAAAT
17114258 GAAAAAAAATG-AAAAAAT
1 GAAAAAAAA-GAAAAAAAT
17114276 GAAAAAAAAGATAAAAAAT
1 GAAAAAAAAGA-AAAAAAT
17114295 G
1 G
17114296 TGAAAAGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 1 0.03
18 19 0.56
19 14 0.41
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (18 bp):
GAAAAAAAAGAAAAAAAT
Found at i:17114301 original size:10 final size:10
Alignment explanation
Indices: 17114227--17114301 Score: 52
Period size: 10 Copynumber: 7.6 Consensus size: 10
17114217 AGTGAAAACA
17114227 TGAAAAAAAGG
1 TGAAAAAAA-G
*
17114238 GGAAAAGAAAG
1 TGAAAA-AAAG
17114249 -GAAAAAAA-
1 TGAAAAAAAG
*
17114257 TGAAAAAAAA
1 TGAAAAAAAG
17114267 TG-AAAAAA-
1 TGAAAAAAAG
17114275 TGAAAAAAAAG
1 TG-AAAAAAAG
*
17114286 AT-AAAAAATG
1 -TGAAAAAAAG
17114296 TGAAAA
1 TGAAAA
17114302 GGAAAATGTC
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
8 2 0.04
9 18 0.33
10 24 0.44
11 6 0.11
12 4 0.07
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (10 bp):
TGAAAAAAAG
Found at i:17114301 original size:19 final size:20
Alignment explanation
Indices: 17114239--17114301 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
17114229 AAAAAAAGGG
* * *
17114239 GAAAAGAAAGGAAAAAA-AT
1 GAAAAAAAATGAAAAAATGT
17114258 GAAAAAAAATGAAAAAATG-
1 GAAAAAAAATGAAAAAATGT
*
17114277 AAAAAAAAGAT-AAAAAATGT
1 GAAAAAAA-ATGAAAAAATGT
17114297 GAAAA
1 GAAAA
17114302 GGAAAATGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 30 0.83
20 6 0.17
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.10
Consensus pattern (20 bp):
GAAAAAAAATGAAAAAATGT
Found at i:17114301 original size:27 final size:27
Alignment explanation
Indices: 17114245--17114307 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
17114235 AGGGGAAAAG
*
17114245 AAAGGAAAAAAATGAAAAAAAATGAAA
1 AAAGGAAAAAAAAGAAAAAAAATGAAA
* * **
17114272 AAATGAAAAAAAAGATAAAAAATGTGA
1 AAAGGAAAAAAAAGAAAAAAAATGAAA
17114299 AAAGGAAAA
1 AAAGGAAAA
17114308 TGTCACTGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.10
Consensus pattern (27 bp):
AAAGGAAAAAAAAGAAAAAAAATGAAA
Found at i:17116054 original size:36 final size:34
Alignment explanation
Indices: 17116014--17116129 Score: 117
Period size: 36 Copynumber: 3.2 Consensus size: 34
17116004 TTCAAATATG
17116014 ATCTTAGATACGAATCTCTACAATTTTTGAATGTGA
1 ATCTT-GATACGAATCTCTA-AATTTTTGAATGTGA
** *
17116050 ATCTTGAATATAAATCTCTGAGATTTTTGAAATGTGA
1 ATCTTG-ATACGAATCTCT-AAATTTTTG-AATGTGA
*
17116087 ATCTTGA-AGGCGAATCTTTAAGATTTTTGAATGTGA
1 ATCTTGATA--CGAATCTCTAA-ATTTTTGAATGTGA
17116123 ATCTTGA
1 ATCTTGA
17116130 AAGTGAACTT
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
35 2 0.03
36 38 0.57
37 27 0.40
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (34 bp):
ATCTTGATACGAATCTCTAAATTTTTGAATGTGA
Found at i:17116130 original size:36 final size:36
Alignment explanation
Indices: 17116036--17116188 Score: 164
Period size: 37 Copynumber: 4.2 Consensus size: 36
17116026 AATCTCTACA
* * * *
17116036 ATTTTTGAATGTGAATCTTGAATATAAATCTCTGAG
1 ATTTTTGAATGTGAATCTTGAATGTGAATCTTTAAG
* *
17116072 ATTTTTGAAATGTGAATCTTGAAGGCGAATCTTTAAG
1 ATTTTTG-AATGTGAATCTTGAATGTGAATCTTTAAG
*
17116109 ATTTTTGAATGTGAATCTTGAAAGTGAA-CTTCTAAG
1 ATTTTTGAATGTGAATCTTGAATGTGAATCTT-TAAG
** * * *
17116145 ATTTTCAAATATGAATCTTTGAATGTGAATCTTAAAA
1 ATTTTTGAATGTGAATC-TTGAATGTGAATCTTTAAG
17116182 ATTTTTG
1 ATTTTTG
17116189 GATGAAAAGC
Statistics
Matches: 97, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
35 3 0.03
36 44 0.45
37 47 0.48
38 3 0.03
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (36 bp):
ATTTTTGAATGTGAATCTTGAATGTGAATCTTTAAG
Found at i:17116147 original size:73 final size:73
Alignment explanation
Indices: 17116002--17116188 Score: 190
Period size: 73 Copynumber: 2.6 Consensus size: 73
17115992 ATCTTTGGAC
* *
17116002 TTTTCAAATATG-ATCTTAGATA--CGAATCTCT-ACAATTTTTGAATGTGAATCTTGAATATAA
1 TTTTCAAATATGAATCTTTGA-AGGCGAATCT-TAAAAATTTTTGAATGTGAATCTTGAATATAA
*
17116063 ATCTCTGAGA
64 ATCTCTAAGA
* * * * *
17116073 TTTTTGAAATGTGAATC-TTGAAGGCGAATCTTTAAGATTTTTGAATGTGAATCTTGAA-AGTGA
1 -TTTTCAAATATGAATCTTTGAAGGCGAATCTTAAAAATTTTTGAATGTGAATCTTGAATA-TAA
17116136 A-CTTCTAAGA
64 ATC-TCTAAGA
* *
17116146 TTTTCAAATATGAATCTTTGAATGTGAATCTTAAAAATTTTTG
1 TTTTCAAATATGAATCTTTGAAGGCGAATCTTAAAAATTTTTG
17116189 GATGAAAAGC
Statistics
Matches: 95, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
71 1 0.01
72 30 0.32
73 64 0.67
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.41
Consensus pattern (73 bp):
TTTTCAAATATGAATCTTTGAAGGCGAATCTTAAAAATTTTTGAATGTGAATCTTGAATATAAAT
CTCTAAGA
Found at i:17116186 original size:37 final size:36
Alignment explanation
Indices: 17116043--17116186 Score: 130
Period size: 36 Copynumber: 3.9 Consensus size: 36
17116033 ACAATTTTTG
* * * *
17116043 AATGTGAATCTTGAATA-TAAATCTCTGAGATTTTTGA
1 AATGTGAATCTTGAA-AGTGAATCTTTAAGA-TTTTCA
* * **
17116080 AATGTGAATCTTGAAGGCGAATCTTTAAGATTTTTG
1 AATGTGAATCTTGAAAGTGAATCTTTAAGATTTTCA
17116116 AATGTGAATCTTGAAAGTGAA-CTTCTAAGATTTTCA
1 AATGTGAATCTTGAAAGTGAATCTT-TAAGATTTTCA
* * * *
17116152 AATATGAATCTTTGAATGTGAATCTTAAAAATTTT
1 AATGTGAATC-TTGAAAGTGAATCTTTAAGATTTT
17116187 TGGATGAAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
35 3 0.03
36 41 0.47
37 41 0.47
38 3 0.03
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (36 bp):
AATGTGAATCTTGAAAGTGAATCTTTAAGATTTTCA
Found at i:17116276 original size:18 final size:18
Alignment explanation
Indices: 17116255--17116298 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
17116245 GAATCTCGAT
* *
17116255 GAATCTTTGAACCTTTGC
1 GAATCTTGGAAACTTTGC
* *
17116273 GAATCGTGGAAACTTTGT
1 GAATCTTGGAAACTTTGC
17116291 GAATCTTG
1 GAATCTTG
17116299 AATATTTTGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (18 bp):
GAATCTTGGAAACTTTGC
Found at i:17116393 original size:22 final size:22
Alignment explanation
Indices: 17116359--17116403 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17116349 AATTCATTGC
* * *
17116359 CATGCATTGCATTCATTACATT
1 CATGCAATACATTCATTAAATT
17116381 CATGCAATACATTCATTAAATT
1 CATGCAATACATTCATTAAATT
17116403 C
1 C
17116404 GTTATGCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (22 bp):
CATGCAATACATTCATTAAATT
Found at i:17116803 original size:22 final size:22
Alignment explanation
Indices: 17116743--17116961 Score: 52
Period size: 22 Copynumber: 10.0 Consensus size: 22
17116733 TCAAGATCTA
* *
17116743 CGAGCATGATTTGTAAGACCTT
1 CGAGCATAATTTATAAGACCTT
* * * *
17116765 C-AGGTATGATCTCTAAGACCTT
1 CGA-GCATAATTTATAAGACCTT
*
17116787 CGAGCATAATTTATAAG-CTTTT
1 CGAGCATAATTTATAAGAC-CTT
* * * *
17116809 CAAGCATAATCTCTAAGACCTC
1 CGAGCATAATTTATAAGACCTT
* * **
17116831 CAAGGCATGATTTGCAAGACCTAT
1 CGA-GCATAATTTATAAGACCT-T
* * *
17116855 -AAGCATAATCTT-CAAGATCTT
1 CGAGCATAAT-TTATAAGACCTT
* * * * *
17116876 CAAACATGATTTGTAAAACCTT
1 CGAGCATAATTTATAAGACCTT
* * * *
17116898 TGGGCATAATTTATAAGATCTC
1 CGAGCATAATTTATAAGACCTT
* * * **
17116920 CGAGTATAATCT-CAAGATGTT
1 CGAGCATAATTTATAAGACCTT
* *
17116941 CGGGTATAATTTATAAGACCT
1 CGAGCATAATTTATAAGACCT
17116962 CAAGGTATGA
Statistics
Matches: 141, Mismatches: 46, Indels: 20
0.68 0.22 0.10
Matches are distributed among these distances:
21 21 0.15
22 100 0.71
23 20 0.14
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (22 bp):
CGAGCATAATTTATAAGACCTT
Found at i:17117041 original size:43 final size:42
Alignment explanation
Indices: 17116993--17117213 Score: 200
Period size: 43 Copynumber: 5.2 Consensus size: 42
17116983 TTTGGTACCT
* *
17116993 TTTTATTTTTCAAAAGTTTTAAAACCCCAATTATGGAGGAGCA
1 TTTTATTTTTCAAAAGTTTTAAAACCTCAGTTATGG-GGAGCA
* * * *
17117036 TTTTATTTTTCAAAAGTTTTAATGA-CTTAGTTGTAGGGGAGCG
1 TTTTATTTTTCAAAAGTTTTAA-AACCTCAGTTAT-GGGGAGCA
* * ** * * *
17117079 TTTTATTTTTCAAAAATTTCAACGCCTTAGTTATGGAAGAGTA
1 TTTTATTTTTCAAAAGTTTTAAAACCTCAGTTATGG-GGAGCA
*
17117122 TTTTATTTTTCAAAA-TTTTCAAAACCTCAGTTGTGGGGAGCA
1 TTTTATTTTTCAAAAGTTTT-AAAACCTCAGTTATGGGGAGCA
* * *
17117164 TTTTATTTTTCCAAAG--TT-AAACCTTAGTTGTGGGGAAGCA
1 TTTTATTTTTCAAAAGTTTTAAAACCTCAGTTATGGGG-AGCA
17117204 TTTTATTTTT
1 TTTTATTTTT
17117214 TTCAAAGTTG
Statistics
Matches: 148, Mismatches: 23, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
39 16 0.11
40 14 0.09
41 2 0.01
42 23 0.16
43 90 0.61
44 3 0.02
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (42 bp):
TTTTATTTTTCAAAAGTTTTAAAACCTCAGTTATGGGGAGCA
Found at i:17118223 original size:16 final size:20
Alignment explanation
Indices: 17118183--17118228 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 20
17118173 TTTTGCATGA
17118183 ATTTGCATGATTAATATTAT
1 ATTTGCATGATTAATATTAT
17118203 ATTTGCATGA-T-A-ATT-T
1 ATTTGCATGATTAATATTAT
17118219 ATTTGCATGA
1 ATTTGCATGA
17118229 ATTCAATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 11 0.42
17 3 0.12
18 1 0.04
19 1 0.04
20 10 0.38
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (20 bp):
ATTTGCATGATTAATATTAT
Found at i:17118361 original size:24 final size:24
Alignment explanation
Indices: 17118268--17118362 Score: 67
Period size: 24 Copynumber: 4.1 Consensus size: 24
17118258 TAATTGCATA
* * *
17118268 ATTATAAATATACTTGTTTGCT-TG
1 ATTATTAATATAATTATTTG-TGTG
* *
17118292 ATTATTAATAT-TTTATTTTTGTG
1 ATTATTAATATAATTATTTGTGTG
**
17118315 A-T-TT-AT-TAATATATTTGCATG
1 ATTATTAATATAAT-TATTTGTGTG
17118336 ATTATTAATATAATTATTTGTGTG
1 ATTATTAATATAATTATTTGTGTG
17118360 ATT
1 ATT
17118363 TATTTGTATG
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
19 1 0.02
20 3 0.06
21 10 0.19
22 3 0.06
23 10 0.19
24 23 0.43
25 4 0.07
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.56
Consensus pattern (24 bp):
ATTATTAATATAATTATTTGTGTG
Found at i:17118394 original size:19 final size:20
Alignment explanation
Indices: 17118363--17118414 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
17118353 TTGTGTGATT
*
17118363 TATTTGTATGATAATT-ATA
1 TATTTGCATGATAATTAATA
17118382 T-TATTGCATGATAATTAATA
1 TAT-TTGCATGATAATTAATA
17118402 TATTTGCATGATA
1 TATTTGCATGATA
17118415 TTTTGGCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 13 0.45
20 14 0.48
21 1 0.03
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (20 bp):
TATTTGCATGATAATTAATA
Found at i:17118463 original size:27 final size:25
Alignment explanation
Indices: 17118401--17118465 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 25
17118391 GATAATTAAT
17118401 ATATTTGCATGA-TATTTTGGCATG
1 ATATTTGCATGATTATTTTGGCATG
* *
17118425 AT-TTTGGTATGATTTTTTTGTTGCATG
1 ATATTT-GCATGATTATTTTG--GCATG
17118452 ATATTTGCATGATT
1 ATATTTGCATGATT
17118466 GCATGACGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 3 0.09
24 7 0.21
25 6 0.18
27 14 0.42
28 3 0.09
ACGTcount: A:0.22, C:0.06, G:0.20, T:0.52
Consensus pattern (25 bp):
ATATTTGCATGATTATTTTGGCATG
Found at i:17121961 original size:52 final size:53
Alignment explanation
Indices: 17121905--17122015 Score: 147
Period size: 52 Copynumber: 2.1 Consensus size: 53
17121895 CATATGAATG
*
17121905 AAATTGTAATAACAATAAAATATATCTTAAAAAAAT-TTA-TAAACAAAA-AAAA
1 AAATTGTAATAACAATAAAATATACCTT-AAAAAATGTTACTAAA-AAAATAAAA
** *
17121957 AAATTGTAATAGTAATAGAATATACCTTAAAAAATGTTACTAAAAAAATAAAA
1 AAATTGTAATAACAATAAAATATACCTTAAAAAATGTTACTAAAAAAATAAAA
17122010 AAATTG
1 AAATTG
17122016 ATGTATAACA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
51 7 0.13
52 31 0.60
53 14 0.27
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.28
Consensus pattern (53 bp):
AAATTGTAATAACAATAAAATATACCTTAAAAAATGTTACTAAAAAAATAAAA
Found at i:17122586 original size:22 final size:22
Alignment explanation
Indices: 17122558--17122610 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
17122548 ATTTTTTGTT
*
17122558 TATAATAAAATATAATTATAAA
1 TATAATAAAATATAAATATAAA
17122580 TATAAT-AAATATAAATATAAA
1 TATAATAAAATATAAATATAAA
17122601 -ATATATAAAA
1 TATA-ATAAAA
17122611 ACAAAAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TATAATAAAATATAAATATAAA
Found at i:17122592 original size:15 final size:15
Alignment explanation
Indices: 17122569--17122609 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
17122559 ATAATAAAAT
*
17122569 ATAATTATAAATATA
1 ATAAATATAAATATA
17122584 ATAAATATAAATATA
1 ATAAATATAAATATA
17122599 A-AATATATAAA
1 ATAA-ATATAAA
17122610 AACAAAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAATATAAATATA
Found at i:17123334 original size:20 final size:21
Alignment explanation
Indices: 17123305--17123343 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
17123295 AATACAGTCA
17123305 AAAATATTTTAAATTTTATCC
1 AAAATATTTTAAATTTTATCC
17123326 AAAAT-TTTTAAATTTTAT
1 AAAATATTTTAAATTTTAT
17123344 GTGAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAATATTTTAAATTTTATCC
Found at i:17124081 original size:2 final size:2
Alignment explanation
Indices: 17124068--17124099 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17124058 AGCGATAGAC
*
17124068 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17124100 TTGCATTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17126557 original size:2 final size:2
Alignment explanation
Indices: 17126550--17126576 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17126540 ATATAGAAAC
17126550 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
17126577 AAGTGTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17127203 original size:19 final size:18
Alignment explanation
Indices: 17127172--17127213 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
17127162 AATTATGATC
17127172 TTATTTTTAATTATTTTA
1 TTATTTTTAATTATTTTA
17127190 GTTATTATTT-ATTATTTTA
1 -TTATT-TTTAATTATTTTA
17127209 TTATT
1 TTATT
17127214 GAAAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.23
19 14 0.64
20 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTATTTTTAATTATTTTA
Found at i:17128055 original size:9 final size:9
Alignment explanation
Indices: 17128041--17128065 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17128031 TATTTATTAG
17128041 AAAATTTAT
1 AAAATTTAT
17128050 AAAATTTAT
1 AAAATTTAT
17128059 AAAATTT
1 AAAATTT
17128066 TTCAGAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTTAT
Found at i:17129988 original size:27 final size:28
Alignment explanation
Indices: 17129948--17130012 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
17129938 ATTGAATTCT
* * *
17129948 TTTTAATTTCTTTTT-GAAAGCAAATCA
1 TTTTAATTTTTTTTTAAAAAGCAAAACA
17129975 TTTTAATTTTTTTTTAAAAAGCAAAACA
1 TTTTAATTTTTTTTTAAAAAGCAAAACA
*
17130003 ATTT-ATTTTT
1 TTTTAATTTTT
17130013 AGGATGAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 20 0.61
28 13 0.39
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (28 bp):
TTTTAATTTTTTTTTAAAAAGCAAAACA
Found at i:17130503 original size:20 final size:20
Alignment explanation
Indices: 17130448--17130510 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
17130438 GGGTCTAGAG
*
17130448 TTAGGGTTTAAGTTTTAAGG-
1 TTAGGGTTTAAG-TTTAGGGT
* * *
17130468 TTAAGGTATGAGGTTTAGGGT
1 TTAGGGT-TTAAGTTTAGGGT
*
17130489 TTAGGGTTTAAGTTTTGGGT
1 TTAGGGTTTAAGTTTAGGGT
17130509 TT
1 TT
17130511 TAAGTTTTGG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 24 0.73
21 9 0.27
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (20 bp):
TTAGGGTTTAAGTTTAGGGT
Found at i:17130508 original size:13 final size:13
Alignment explanation
Indices: 17130451--17130524 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 13
17130441 TCTAGAGTTA
17130451 GGGTTTAAGTTTT
1 GGGTTTAAGTTTT
* * *
17130464 AAGG-TTAAGGTAT
1 -GGGTTTAAGTTTT
* *
17130477 GAGGTTTAGGGTTTA
1 G-GGTTTA-AGTTTT
17130492 GGGTTTAAGTTTT
1 GGGTTTAAGTTTT
17130505 GGGTTTTAAGTTTT
1 GGG-TTTAAGTTTT
17130519 -GGTTTA
1 GGGTTTA
17130525 GGGTTAGCAA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
12 4 0.09
13 18 0.39
14 21 0.46
15 3 0.07
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.47
Consensus pattern (13 bp):
GGGTTTAAGTTTT
Found at i:17130602 original size:19 final size:18
Alignment explanation
Indices: 17130553--17130604 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
17130543 TAGAGACTAG
17130553 GGTTTGGTTTAGGGTTAA
1 GGTTTGGTTTAGGGTTAA
**
17130571 GGTGTTGACTTAGGGTTTAA
1 GGT-TTGGTTTAGGG-TTAA
17130591 GGTTTGGTTTAGGG
1 GGTTTGGTTTAGGG
17130605 CTAGGGTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 3 0.11
19 18 0.64
20 7 0.25
ACGTcount: A:0.15, C:0.02, G:0.40, T:0.42
Consensus pattern (18 bp):
GGTTTGGTTTAGGGTTAA
Found at i:17133231 original size:14 final size:14
Alignment explanation
Indices: 17133214--17133247 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17133204 GTGCAAAATA
**
17133214 TATGTTGCATGTTG
1 TATGTTGCATAATG
17133228 TATGTTGCATAATG
1 TATGTTGCATAATG
17133242 TATGTT
1 TATGTT
17133248 TGAAACTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.50
Consensus pattern (14 bp):
TATGTTGCATAATG
Found at i:17133951 original size:18 final size:18
Alignment explanation
Indices: 17133928--17133991 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
17133918 TGACTCTTGG
17133928 GAATCTTTAAAA-TTTTAT
1 GAATC-TTAAAACTTTTAT
*
17133946 GAATCTTAAAACTTTTAC
1 GAATCTTAAAACTTTTAT
* *
17133964 AAACCTTGAAAA--TTT-T
1 GAATCTT-AAAACTTTTAT
17133980 GAATCTTAAAAC
1 GAATCTTAAAAC
17133992 ACTTTCTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
15 4 0.11
16 5 0.14
17 9 0.24
18 15 0.41
19 4 0.11
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (18 bp):
GAATCTTAAAACTTTTAT
Found at i:17134252 original size:42 final size:42
Alignment explanation
Indices: 17134206--17134309 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
17134196 CTTTCTTGTG
* *
17134206 AATCCAGAGTCTTCTAAACTATGAATCGCTCACTCTGTTATA
1 AATCCAAAGTCTTCTAAACTATGAATCACTCACTCTGTTATA
* ** *
17134248 AATCCAAAGTCTT-TCAAACTATGAATCATTTGCTTTGTTATA
1 AATCCAAAGTCTTCT-AAACTATGAATCACTCACTCTGTTATA
17134290 AATCCAAAGTCATTC-AAACT
1 AATCCAAAGTC-TTCTAAACT
17134310 CTAAATCATT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
41 1 0.02
42 50 0.94
43 2 0.04
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35
Consensus pattern (42 bp):
AATCCAAAGTCTTCTAAACTATGAATCACTCACTCTGTTATA
Found at i:17134317 original size:42 final size:42
Alignment explanation
Indices: 17134241--17134320 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
17134231 TCGCTCACTC
* *
17134241 TGTTATAAATCCAAAGTCTTTCAAACTATGAATCATTTGCTT
1 TGTTATAAATCCAAAGTCATTCAAACTATAAATCATTTGCTT
*
17134283 TGTTATAAATCCAAAGTCATTCAAACTCTAAATCATTT
1 TGTTATAAATCCAAAGTCATTCAAACTATAAATCATTT
17134321 ACTCTATTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.39
Consensus pattern (42 bp):
TGTTATAAATCCAAAGTCATTCAAACTATAAATCATTTGCTT
Found at i:17134350 original size:42 final size:42
Alignment explanation
Indices: 17134304--17134403 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
17134294 CAAAGTCATT
* * *
17134304 CAAACTCTAAATCATTTACTCTATTGTGAATCTAGAGTCCTC
1 CAAACTATAAATCATTTACTCTATTATGAATCTAGAATCCTC
* * * * * *
17134346 CAAACTGTGAATCGTTTACTTTGTTATGAATCTAGAATCTTC
1 CAAACTATAAATCATTTACTCTATTATGAATCTAGAATCCTC
*
17134388 CAAATTATAAATCATT
1 CAAACTATAAATCATT
17134404 CACATGCACA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (42 bp):
CAAACTATAAATCATTTACTCTATTATGAATCTAGAATCCTC
Found at i:17134357 original size:126 final size:125
Alignment explanation
Indices: 17134165--17134403 Score: 282
Period size: 126 Copynumber: 1.9 Consensus size: 125
17134155 CTCAACTATG
* * * ** * * * *
17134165 AATCCAAAGTCTTCCAACTTTGAATTGTTTACTTTCTTGTGAATCCAGAGTCTTCTAAACTATGA
1 AATCCAAAGTCTTCAAACTCTAAATCATTTACTCTATTGTGAATCCAGAGTCCTCCAAACTATGA
* *
17134230 ATCGCTCACTCTGTTATAAATCCA-AAGTCTTTCAAACTATGAATCATTTGCTTTGTTATA
66 ATCGCTCACTCTGTTATAAATCCAGAA-TCTTCCAAACTATAAATCATTTGCTTTGTTATA
* *
17134290 AATCCAAAGTCATTCAAACTCTAAATCATTTACTCTATTGTGAATCTAGAGTCCTCCAAACTGTG
1 AATCCAAAGTC-TTCAAACTCTAAATCATTTACTCTATTGTGAATCCAGAGTCCTCCAAACTATG
* * * * * *
17134355 AATCGTTTACTTTGTTATGAATCTAGAATCTTCCAAATTATAAATCATT
65 AATCGCTCACTCTGTTATAAATCCAGAATCTTCCAAACTATAAATCATT
17134404 CACATGCACA
Statistics
Matches: 93, Mismatches: 19, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
125 11 0.12
126 80 0.86
127 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (125 bp):
AATCCAAAGTCTTCAAACTCTAAATCATTTACTCTATTGTGAATCCAGAGTCCTCCAAACTATGA
ATCGCTCACTCTGTTATAAATCCAGAATCTTCCAAACTATAAATCATTTGCTTTGTTATA
Found at i:17134607 original size:13 final size:13
Alignment explanation
Indices: 17134571--17134759 Score: 115
Period size: 13 Copynumber: 14.2 Consensus size: 13
17134561 CCAAAATTTC
*
17134571 AAACCTTAAACCCT
1 AAACCCTAAA-CCT
* *
17134585 ATACCTTAAACCT
1 AAACCCTAAACCT
17134598 AAACCCTAAA-CT
1 AAACCCTAAACCT
17134610 CAAACCCTAAACCT
1 -AAACCCTAAACCT
*
17134624 -AGCCCTAAACCCT
1 AAACCCTAAA-CCT
**
17134637 AAACTTTAAACCCT
1 AAACCCTAAA-CCT
17134651 -AACCCTAAATCCT
1 AAACCCTAAA-CCT
17134664 AAACCCTAAAGCCAAAT
1 AAACCCTAAA-CC---T
*
17134681 CAAACCTTAAACCT
1 -AAACCCTAAACCT
* *
17134695 AAAGCC-AAATC-
1 AAACCCTAAACCT
17134706 AAACCCTAAACCT
1 AAACCCTAAACCT
*
17134719 AAACTCC-ATACCTT
1 AAAC-CCTAAACC-T
17134733 AAACCCTAAACC-
1 AAACCCTAAACCT
17134745 -AACCCTAAAACCT
1 AAACCCT-AAACCT
17134758 AA
1 AA
17134760 CCTAGACTCT
Statistics
Matches: 139, Mismatches: 19, Indels: 34
0.72 0.10 0.18
Matches are distributed among these distances:
11 11 0.08
12 23 0.17
13 48 0.35
14 45 0.32
17 3 0.02
18 9 0.06
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (13 bp):
AAACCCTAAACCT
Found at i:17134618 original size:20 final size:20
Alignment explanation
Indices: 17134569--17134759 Score: 91
Period size: 20 Copynumber: 9.9 Consensus size: 20
17134559 ACCCAAAATT
* *
17134569 TCAAACCTTAAACCCTATACC
1 TCAAACCCTAAACCCTA-AAC
*
17134590 TTAAA-CCTAAACCCTAAAC
1 TCAAACCCTAAACCCTAAAC
*
17134609 TCAAACCCTAAA-CCT-AGC
1 TCAAACCCTAAACCCTAAAC
* **
17134627 CCTAAACCCTAAACTTTAAAC
1 TC-AAACCCTAAACCCTAAAC
* * *
17134648 CCTAACCCTAAATCCTAAAC
1 TCAAACCCTAAACCCTAAAC
* * *
17134668 CCTAAAGCC-AAA-TC-AAACC
1 TC-AAACCCTAAACCCTAAA-C
* *
17134687 TTAAA-CCTAAAGCC-AAA-
1 TCAAACCCTAAACCCTAAAC
17134704 TCAAACCCTAAA-CCTAAAC
1 TCAAACCCTAAACCCTAAAC
* *
17134723 TCCATACCTTAAACCCTAAAC
1 T-CAAACCCTAAACCCTAAAC
*
17134744 -C-AACCCTAAAACCTAA
1 TCAAACCCTAAACCCTAA
17134760 CCTAGACTCT
Statistics
Matches: 132, Mismatches: 25, Indels: 29
0.71 0.13 0.16
Matches are distributed among these distances:
17 8 0.06
18 33 0.25
19 27 0.20
20 45 0.34
21 19 0.14
ACGTcount: A:0.44, C:0.36, G:0.02, T:0.19
Consensus pattern (20 bp):
TCAAACCCTAAACCCTAAAC
Found at i:17134636 original size:7 final size:7
Alignment explanation
Indices: 17134571--17134744 Score: 106
Period size: 7 Copynumber: 26.7 Consensus size: 7
17134561 CCAAAATTTC
*
17134571 AAACCTT
1 AAACCCT
17134578 AAACCCT
1 AAACCCT
* *
17134585 ATACCTT
1 AAACCCT
17134592 AAA-CCT
1 AAACCCT
17134598 AAACCCT
1 AAACCCT
*
17134605 AAACTC-
1 AAACCCT
17134611 AAACCCT
1 AAACCCT
17134618 AAA-CCT
1 AAACCCT
*
17134624 -AGCCCT
1 AAACCCT
17134630 AAACCCT
1 AAACCCT
**
17134637 AAACTTT
1 AAACCCT
17134644 AAACCCT
1 AAACCCT
17134651 -AACCCT
1 AAACCCT
*
17134657 AAATCCT
1 AAACCCT
17134664 AAACCCT
1 AAACCCT
*
17134671 AAAGCC-
1 AAACCCT
*
17134677 AAA-TC-
1 AAACCCT
*
17134682 AAACCTT
1 AAACCCT
17134689 AAA-CCT
1 AAACCCT
*
17134695 AAAGCC-
1 AAACCCT
*
17134701 AAA-TC-
1 AAACCCT
17134706 AAACCCT
1 AAACCCT
17134713 AAA-CCT
1 AAACCCT
17134719 AAACTCC-
1 AAAC-CCT
* *
17134726 ATACCTT
1 AAACCCT
17134733 AAACCCT
1 AAACCCT
17134740 AAACC
1 AAACC
17134745 AACCCTAAAA
Statistics
Matches: 128, Mismatches: 26, Indels: 26
0.71 0.14 0.14
Matches are distributed among these distances:
5 9 0.07
6 41 0.32
7 76 0.59
8 2 0.02
ACGTcount: A:0.44, C:0.36, G:0.02, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:17134697 original size:24 final size:24
Alignment explanation
Indices: 17134661--17134721 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
17134651 AACCCTAAAT
17134661 CCTAAACCCTAAAGCCAAATCAAAC
1 CCTAAA-CCTAAAGCCAAATCAAAC
*
17134686 CTTAAACCTAAAGCCAAATCAAAC
1 CCTAAACCTAAAGCCAAATCAAAC
17134710 CCTAAACCTAAA
1 CCTAAACCTAAA
17134722 CTCCATACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 29 0.85
25 5 0.15
ACGTcount: A:0.49, C:0.33, G:0.03, T:0.15
Consensus pattern (24 bp):
CCTAAACCTAAAGCCAAATCAAAC
Found at i:17137210 original size:19 final size:19
Alignment explanation
Indices: 17137188--17137326 Score: 101
Period size: 19 Copynumber: 7.5 Consensus size: 19
17137178 TGGTTTAGGA
* *
17137188 TTTAGGGTTTCTTAGGTTG
1 TTTAGGGTTTCATAGGTGG
* * *
17137207 TTTAAGGTTT-GTAAAGTGG
1 TTTAGGGTTTCAT-AGGTGG
17137226 TTTAGGGTTTCAT-GTGTGG
1 TTTAGGGTTTCATAG-GTGG
* *
17137245 TTTAAGGTTTCATAGATGG
1 TTTAGGGTTTCATAGGTGG
*
17137264 TTTAGGGTTTCATAGGTGA
1 TTTAGGGTTTCATAGGTGG
* *
17137283 TTTAAGG--T-A-GGGTGG
1 TTTAGGGTTTCATAGGTGG
* *
17137298 TTTAGGGTTGCATGGGTGG
1 TTTAGGGTTTCATAGGTGG
*
17137317 TTTAGAGTTT
1 TTTAGGGTTT
17137327 GAAATTTAGG
Statistics
Matches: 93, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
15 10 0.11
16 1 0.01
17 1 0.01
18 2 0.02
19 77 0.83
20 2 0.02
ACGTcount: A:0.18, C:0.04, G:0.35, T:0.44
Consensus pattern (19 bp):
TTTAGGGTTTCATAGGTGG
Found at i:17137230 original size:38 final size:38
Alignment explanation
Indices: 17137188--17137290 Score: 122
Period size: 38 Copynumber: 2.7 Consensus size: 38
17137178 TGGTTTAGGA
* *
17137188 TTTAGGGTTTCTTAGGTTGTTTAAGGTTTGTAAAG-TGG
1 TTTAGGGTTTCATAGGTTGTTTAAGGTTT-CAAAGATGG
* *
17137226 TTTAGGGTTTCAT-GTGTGGTTTAAGGTTTCATAGATGG
1 TTTAGGGTTTCATAG-GTTGTTTAAGGTTTCAAAGATGG
17137264 TTTAGGGTTTCATAGG-TGATTTAAGGT
1 TTTAGGGTTTCATAGGTTG-TTTAAGGT
17137291 AGGGTGGTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
37 5 0.09
38 50 0.89
39 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (38 bp):
TTTAGGGTTTCATAGGTTGTTTAAGGTTTCAAAGATGG
Found at i:17137254 original size:57 final size:57
Alignment explanation
Indices: 17137163--17137273 Score: 127
Period size: 57 Copynumber: 1.9 Consensus size: 57
17137153 AAGGTCTCAT
* * * * *
17137163 AAGTGGTTTAGGGTTTGGTTTAGGATTTAGGGTTTCTTAGGTTGTTTAAGGTTTGTA
1 AAGTGGTTTAGGGTTTGGTGTAGGATTTAAGGTTTCATAGATGGTTTAAGGTTTGTA
* *
17137220 AAGTGGTTTAGGGTTTCATGTGT-GG-TTTAAGGTTTCATAGATGGTTTAGGGTTT
1 AAGTGGTTTAGGGTTT--GGTGTAGGATTTAAGGTTTCATAGATGGTTTAAGGTTT
17137274 CATAGGTGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
57 40 0.89
58 2 0.04
59 3 0.07
ACGTcount: A:0.18, C:0.03, G:0.33, T:0.46
Consensus pattern (57 bp):
AAGTGGTTTAGGGTTTGGTGTAGGATTTAAGGTTTCATAGATGGTTTAAGGTTTGTA
Found at i:17138325 original size:13 final size:13
Alignment explanation
Indices: 17138307--17138331 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17138297 GATTATACCT
17138307 TCTTTCTTTTTTC
1 TCTTTCTTTTTTC
17138320 TCTTTCTTTTTT
1 TCTTTCTTTTTT
17138332 TTTTTCACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TCTTTCTTTTTTC
Found at i:17146463 original size:26 final size:26
Alignment explanation
Indices: 17146434--17146487 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
17146424 CAATTAAGGT
*
17146434 ATTTCTATACATAAATGCATTAATTG
1 ATTTCTATACAAAAATGCATTAATTG
* * *
17146460 ATTTGTATATAAAAATGCTTTAATTG
1 ATTTCTATACAAAAATGCATTAATTG
17146486 AT
1 AT
17146488 CATATCAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (26 bp):
ATTTCTATACAAAAATGCATTAATTG
Found at i:17155120 original size:14 final size:14
Alignment explanation
Indices: 17155101--17155127 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17155091 ATTGTTGAAA
17155101 TAGGACATCAATGT
1 TAGGACATCAATGT
17155115 TAGGACATCAATG
1 TAGGACATCAATG
17155128 AAGTAAATAT
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:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (14 bp):
TAGGACATCAATGT
Found at i:17158066 original size:64 final size:62
Alignment explanation
Indices: 17157965--17158336 Score: 179
Period size: 62 Copynumber: 6.0 Consensus size: 62
17157955 TCAAACAATC
* * * * * *
17157965 AATCAATTACTACATTGATATGTTTTGTAACGCAGTAATTGATCATTGTATATGCTTTTAAAA
1 AATCAAATACTACATTGCTTTGGTTTATAACGTAGTAATTGATCATTGTATATG-TTTTAAAA
* * *
17158028 TAATCAAATACTACATTGCTTTGGTTTATAACATAGTAATTGAT-ACT-CATATTGTTTTCAAAA
1 -AATCAAATACTACATTGCTTTGGTTTATAACGTAGTAATTGATCATTGTATA-TGTTTT-AAAA
* *** *
17158091 AATCAAATATTGTGTTACTTT-GTTTCATAACGTAGTAATTGATCATTGTCAT-TGTTTTAAAA
1 AATCAAATACTACATTGCTTTGGTTT-ATAACGTAGTAATTGATCATTGT-ATATGTTTTAAAA
* * * * * * * * * *
17158153 CAATTAATTACTACGTTG-TATAGTTCAATAATGCAATAATTGATCA-T-TAT-TGTTTTGAAAC
1 -AATCAAATACTACATTGCTTTGGTT-TATAACGTAGTAATTGATCATTGTATATGTTTT-AAAA
* * * * ** * * * * * * *
17158214 ATTCAATTATTGCATTGCTTCAGTTTATAATGCAATAATTGATAATTGTATTTGTTTCAAAC
1 AATCAAATACTACATTGCTTTGGTTTATAACGTAGTAATTGATCATTGTATATGTTTTAAAA
* * * * * * *
17158276 AATCAAAAATTGCATTGATTT-GTTTCAAAATGTAATAATTGATCATTGTCAT-TGTTTTAAA
1 AATCAAATACTACATTGCTTTGGTTT-ATAACGTAGTAATTGATCATTGT-ATATGTTTTAAA
17158337 TTAATTGATT
Statistics
Matches: 244, Mismatches: 48, Indels: 34
0.75 0.15 0.10
Matches are distributed among these distances:
60 38 0.16
61 18 0.07
62 97 0.40
63 53 0.22
64 36 0.15
65 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.43
Consensus pattern (62 bp):
AATCAAATACTACATTGCTTTGGTTTATAACGTAGTAATTGATCATTGTATATGTTTTAAAA
Found at i:17158193 original size:63 final size:62
Alignment explanation
Indices: 17158126--17158402 Score: 219
Period size: 63 Copynumber: 4.5 Consensus size: 62
17158116 CATAACGTAG
* * *
17158126 TAATTGATCATTGTCATTGTTTTAAAACAATTAATTACTACGTTGTATAGTTCAATAATGCAA
1 TAATTGATCATTGT-ATTGTTTTAAAACAATTAATTATTGCATTGTATAGTTCAATAATGCAA
* *
17158189 TAATTGATCA-T-TATTGTTTTGAAAC-ATTCAATTATTGCATTGCT-TCAGTT-TATAATGCAA
1 TAATTGATCATTGTATTGTTTTAAAACAATT-AATTATTGCATTG-TAT-AGTTCAATAATGCAA
* * * ** * *
17158249 TAATTGATAATTGTATT-TGTTTCAAACAATCAAAAATTGCATTG-ATTTGTTTCAA-AATGTAA
1 TAATTGATCATTGTATTGT-TTTAAAACAATTAATTATTGCATTGTA-TAG-TTCAATAATGCAA
** * ** * * ** *
17158311 TAATTGATCATTGTCATTGTTTTAAATTAATTGATTATTGTGTTGTGTTGTTTTATAACGCAA
1 TAATTGATCATTGT-ATTGTTTTAAAACAATTAATTATTGCATTGTATAGTTCAATAATGCAA
17158374 TAATTGATCATTGTAATTGTTTTAAAACA
1 TAATTGATCATTGT-ATTGTTTTAAAACA
17158403 GTGTTCTATA
Statistics
Matches: 168, Mismatches: 31, Indels: 30
0.73 0.14 0.13
Matches are distributed among these distances:
59 3 0.02
60 41 0.24
61 9 0.05
62 48 0.29
63 66 0.39
64 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (62 bp):
TAATTGATCATTGTATTGTTTTAAAACAATTAATTATTGCATTGTATAGTTCAATAATGCAA
Found at i:17158214 original size:60 final size:63
Alignment explanation
Indices: 17158126--17158802 Score: 166
Period size: 63 Copynumber: 10.6 Consensus size: 63
17158116 CATAACGTAG
*
17158126 TAATTGATCATTGTCATTGTTTTAAAACAATT-AATTACTACGTTG-TAT-AGTTCAATAATGCA
1 TAATTGATCATTGTCATTGTTTTAAAAC-ATTCAATTACTACATTGCT-TCAGTT-AATAATGCA
17158188 A
63 A
* * * *
17158189 TAATTGATCA-T-T-ATTGTTTTGAAACATTCAATTATTGCATTGCTTCAGTTTATAATGCAA
1 TAATTGATCATTGTCATTGTTTTAAAACATTCAATTACTACATTGCTTCAGTTAATAATGCAA
* * * ** * * * * *
17158249 TAATTGATAATTGT-ATT-TGTTTCAAACAATCAAAAATTGCATTGATT-TGTTTCAA-AATGTA
1 TAATTGATCATTGTCATTGT-TTTAAAACATTCAATTACTACATTGCTTCAG-TT-AATAATGCA
17158310 A
63 A
* * *** * * *
17158311 TAATTGATCATTGTCATTGTTTTAAATTA-ATT-GATTATTGTGTTG-TGT-TGTTTTATAACGC
1 TAATTGATCATTGTCATTGTTTTAAA--ACATTCAATTACTACATTGCT-TCAG-TTAATAATGC
17158372 AA
62 AA
* * * * * *
17158374 TAATTGATCATTGTAATTGTTTTAAAACAGTGTTCTA-TATTTCGA-TGCTT-TGTTTTATAATG
1 TAATTGATCATTGTCATTGTTTTAAAACA---TTCAATTACTAC-ATTGCTTCAG-TTAATAATG
*
17158436 TAA
61 CAA
* * * * * * * * ** *
17158439 TATTTGTTTGATAGTAATTG-TTTACAAACAATCAATTATTACGA-TGCTT-TGTTTTCTAATGT
1 TAATTG-ATCATTGTCATTGTTTTA-AAACATTCAATTACTAC-ATTGCTTCAG-TTAATAATGC
*
17158501 AG
62 AA
* * * *** * * * *
17158503 TAATTGATCATTATAATTATTTTAAAAC-TATCAATTACTGTGTT-CATTTATTTTATAATGCAG
1 TAATTGATCATTGTCATTGTTTTAAAACAT-TCAATTACTACATTGC-TTCAGTTAATAATGCAA
* * ** * * *
17158566 TAATTGATCATTGTAATTGTTTTTCAAAACAATCTAATTACTATGTTGCTTTATTTTATAATGCA
1 TAATTGATCATTGTCATTG-TTTT-AAAACATTC-AATTACTACATTGCTTCAGTTAATAATGCA
*
17158631 G
63 A
* * * * * **
17158632 TAATTGATCATCGTAATTGCTTTTTAAAACAATCCAATTACTACATTGCTT-TGTTTTATAACAC
1 TAATTGATCATTGTCATTG--TTTTAAAAC-ATTCAATTACTACATTGCTTCAG-TTAATAATGC
17158696 AA
62 AA
* * * * * * * * *
17158698 CAATTAATTATTG-AATTTTTTTAAAATAATTCATTTACTACATTGCTT-TGTTTTATAATGCAA
1 TAATTGATCATTGTCATTGTTTTAAAA-CATTCAATTACTACATTGCTTCAG-TTAATAATGCAA
*
17158761 TAATTGATCATAGT-ATTTGTATTTTAAAAC-TATCAATTACTA
1 TAATTGATCATTGTCA-TTG--TTTTAAAACAT-TCAATTACTA
17158803 TGATGCTTTG
Statistics
Matches: 484, Mismatches: 87, Indels: 84
0.74 0.13 0.13
Matches are distributed among these distances:
59 3 0.01
60 41 0.08
61 10 0.02
62 53 0.11
63 165 0.34
64 44 0.09
65 52 0.11
66 108 0.22
67 8 0.02
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (63 bp):
TAATTGATCATTGTCATTGTTTTAAAACATTCAATTACTACATTGCTTCAGTTAATAATGCAA
Found at i:17158562 original size:63 final size:66
Alignment explanation
Indices: 17158464--17158837 Score: 286
Period size: 66 Copynumber: 5.8 Consensus size: 66
17158454 AATTGTTTAC
* * * * * *
17158464 AAACAATC-AATTATTACGATGCTTTGTTTTCTAATGTAGTAATTGATCATTATAATT-ATTTT-
1 AAACAATCTAATTACTATGTTGCTTTATTTTATAATGCAGTAATTGATCATTATAATTGATTTTC
17158526 A
66 A
* * * *
17158527 AAACTATC-AATTACTGTGTT-CATTTATTTTATAATGCAGTAATTGATCATTGTAATTGTTTTT
1 AAACAATCTAATTACTATGTTGC-TTTATTTTATAATGCAGTAATTGATCATTATAATTGATTTT
17158590 CA
65 CA
** * *
17158592 AAACAATCTAATTACTATGTTGCTTTATTTTATAATGCAGTAATTGATCATCGTAATTGCTTTTT
1 AAACAATCTAATTACTATGTTGCTTTATTTTATAATGCAGTAATTGATCATTATAATTGATTTTC
17158657 A
66 A
* ** * ** ** * * * *
17158658 AAACAATCCAATTACTACATTGCTTTGTTTTATAACACAACAATTAATTATT-GAATT--TTTTT
1 AAACAATCTAATTACTATGTTGCTTTATTTTATAATGCAGTAATTGATCATTATAATTGATTTTC
17158720 A
66 A
* * ** * * *
17158721 AAATAAT-TCATTTACTACATTGCTTTGTTTTATAATGCAATAATTGATCA-TAGTATTTGTATT
1 AAACAATCT-AATTACTATGTTGCTTTATTTTATAATGCAGTAATTGATCATTA-TAATTG-ATT
17158784 TT-A
63 TTCA
* * * **
17158787 AAACTATC-AATTACTATGATGCTTTGTTTTATAATATAGTAATTGATCATT
1 AAACAATCTAATTACTATGTTGCTTTATTTTATAATGCAGTAATTGATCATT
17158838 GAAGCTGCAT
Statistics
Matches: 252, Mismatches: 46, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
62 2 0.01
63 93 0.37
64 7 0.03
65 46 0.18
66 99 0.39
67 5 0.02
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (66 bp):
AAACAATCTAATTACTATGTTGCTTTATTTTATAATGCAGTAATTGATCATTATAATTGATTTTC
A
Found at i:17158605 original size:129 final size:128
Alignment explanation
Indices: 17158452--17158838 Score: 369
Period size: 129 Copynumber: 3.0 Consensus size: 128
17158442 TTGTTTGATA
* * * *
17158452 GTAATTG-TTTAC-AAACAATC-AATTATTACGATGCTTTGTTTTCTAATGTAGTAATTGATCAT
1 GTAATTGTTTTTCAAAACAATCTAATTACTACGATGCTTTGTTTTATAATGCAGTAATTGATCAT
* * *
17158514 TATAATTATTTTAAAACTATCAATTACTGTGTTCATTTATTTTATAATGCAGTAATTGATCATT
66 TATAATTATTTTAAAACTATCAATTACTATGTTC-TTTGTTTTATAATACAGTAATTGATCATT
* * *
17158578 GTAATTGTTTTTCAAAACAATCTAATTACTATGTTGCTTTATTTTATAATGCAGTAATTGATCAT
1 GTAATTGTTTTTCAAAACAATCTAATTACTACGATGCTTTGTTTTATAATGCAGTAATTGATCAT
** * * ** * ** * *
17158643 CGTAATTGCTTTTTAAAACAATCCAATTACTACATTGCTTTGTTTTATAACACAACAATTAATTA
66 TATAATT--ATTTTAAAACTAT-CAATTACTATGTT-CTTTGTTTTATAATACAGTAATTGATCA
17158708 TT
127 TT
* * *
17158710 G-AATT-TTTTT-AAAATAAT-TCATTTACTAC-ATTGCTTTGTTTTATAATGCAATAATTGATC
1 GTAATTGTTTTTCAAAACAATCT-AATTACTACGA-TGCTTTGTTTTATAATGCAGTAATTGATC
* * *
17158770 A-TAGTATTTGTATTTTAAAACTATCAATTACTATGATGCTTTGTTTTATAATATAGTAATTGAT
64 ATTA-TA-AT-TATTTTAAAACTATCAATTACTATG-TTCTTTGTTTTATAATACAGTAATTGAT
17158834 CATT
125 CATT
17158838 G
1 G
17158839 AAGCTGCATT
Statistics
Matches: 207, Mismatches: 41, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
126 7 0.03
127 4 0.02
128 43 0.21
129 97 0.47
130 6 0.03
131 16 0.08
132 33 0.16
133 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.46
Consensus pattern (128 bp):
GTAATTGTTTTTCAAAACAATCTAATTACTACGATGCTTTGTTTTATAATGCAGTAATTGATCAT
TATAATTATTTTAAAACTATCAATTACTATGTTCTTTGTTTTATAATACAGTAATTGATCATT
Found at i:17158702 original size:32 final size:32
Alignment explanation
Indices: 17158653--17158755 Score: 90
Period size: 32 Copynumber: 3.2 Consensus size: 32
17158643 CGTAATTGCT
17158653 TTTTA-AAACAATCCAATTACTACATTGCTTTG
1 TTTTATAAACAAT-CAATTACTACATTGCTTTG
* * *
17158685 TTTTATAACACAA-CAATTAAT-TATTGAATTT-
1 TTTTATAA-ACAATCAATTACTACATTG-CTTTG
* *
17158716 TTTTA-AAATAATTCATTTACTACATTGCTTTG
1 TTTTATAAACAA-TCAATTACTACATTGCTTTG
17158748 TTTTATAA
1 TTTTATAA
17158756 TGCAATAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
29 3 0.05
30 2 0.04
31 18 0.33
32 24 0.44
33 4 0.07
34 4 0.07
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.47
Consensus pattern (32 bp):
TTTTATAAACAATCAATTACTACATTGCTTTG
Found at i:17159605 original size:15 final size:16
Alignment explanation
Indices: 17159585--17159618 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
17159575 TAATGATGAC
17159585 TCATTTTCTTTT-TTT
1 TCATTTTCTTTTGTTT
*
17159600 TCATTTTTTTTTGTTT
1 TCATTTTCTTTTGTTT
17159616 TCA
1 TCA
17159619 ACAGGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (16 bp):
TCATTTTCTTTTGTTT
Found at i:17161865 original size:12 final size:12
Alignment explanation
Indices: 17161848--17161872 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17161838 TACAATCTTT
17161848 ATAATTTTTTTA
1 ATAATTTTTTTA
17161860 ATAATTTTTTTA
1 ATAATTTTTTTA
17161872 A
1 A
17161873 CATATTGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATAATTTTTTTA
Found at i:17169284 original size:21 final size:20
Alignment explanation
Indices: 17169241--17169286 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
17169231 ACTAAATTTC
**
17169241 AAAAATAGTGCATAATCTAG
1 AAAAATAGAACATAATCTAG
*
17169261 AAAAATAGAACATCATCTAG
1 AAAAATAGAACATAATCTAG
*
17169281 GAAAAT
1 AAAAAT
17169287 TAACCAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (20 bp):
AAAAATAGAACATAATCTAG
Found at i:17170426 original size:31 final size:31
Alignment explanation
Indices: 17170388--17170446 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
17170378 AGTTTAGGTC
*
17170388 ATTTGTAT-AAATTATACCAAAAATCCTCCAA
1 ATTTGTATAAAAATAT-CCAAAAATCCTCCAA
*
17170419 ATTTGTATAAAAATATCCAAAATTCCTC
1 ATTTGTATAAAAATATCCAAAAATCCTC
17170447 AATTTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (31 bp):
ATTTGTATAAAAATATCCAAAAATCCTCCAA
Found at i:17171988 original size:26 final size:27
Alignment explanation
Indices: 17171948--17172018 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
17171938 TATTTTTAAA
17171948 AAAAAATTATGAAAAAAATAAGAAAAC-T
1 AAAAAATT-T-AAAAAAATAAGAAAACTT
* * *
17171976 AAAATATTTAAAAATATATGAAAACTT
1 AAAAAATTTAAAAAAATAAGAAAACTT
17172003 AAAAAATTTAAAAAAA
1 AAAAAATTTAAAAAAA
17172019 AAATCTCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 14 0.38
27 16 0.43
28 7 0.19
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (27 bp):
AAAAAATTTAAAAAAATAAGAAAACTT
Found at i:17172050 original size:21 final size:21
Alignment explanation
Indices: 17172003--17172051 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
17171993 ATGAAAACTT
*
17172003 AAAAAATTTAAAAAAAAAATC
1 AAAAAATTTAAAAAAAAAACC
** * *
17172024 TCAAAATTTTAATAAAAAACC
1 AAAAAATTTAAAAAAAAAACC
17172045 AAAAAAT
1 AAAAAAT
17172052 GAAAAATTCA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAAATTTAAAAAAAAAACC
Found at i:17172187 original size:20 final size:21
Alignment explanation
Indices: 17172157--17172207 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
17172147 TTTTTTAAAC
*
17172157 TTTTTGAAAAAGCCTAAA-AT
1 TTTTTAAAAAAGCCTAAACAT
***
17172177 TTTTTAAAAAATTGTAAACAT
1 TTTTTAAAAAAGCCTAAACAT
17172198 TTTTTAAAAA
1 TTTTTAAAAA
17172208 TTATGAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (21 bp):
TTTTTAAAAAAGCCTAAACAT
Found at i:17172221 original size:21 final size:20
Alignment explanation
Indices: 17172171--17172221 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
17172161 TGAAAAAGCC
*
17172171 TAAAATTTTTTAAAAAATTG
1 TAAAATTTTTTAAAAAATTA
17172191 TAAACATTTTTT-AAAAATTA
1 TAAA-ATTTTTTAAAAAATTA
17172211 TGAAAATTTTT
1 T-AAAATTTTT
17172222 CATTGTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
TAAAATTTTTTAAAAAATTA
Found at i:17172275 original size:9 final size:9
Alignment explanation
Indices: 17172244--17172622 Score: 68
Period size: 9 Copynumber: 41.0 Consensus size: 9
17172234 TTGCAAGTTT
17172244 AATTTTTATA
1 AATTTTT-TA
* * *
17172254 TATTTTATG
1 AATTTTTTA
17172263 AATTTTTTA
1 AATTTTTTA
*
17172272 AATTTTTTG
1 AATTTTTTA
* *
17172281 GATTTTTTT
1 AATTTTTTA
*
17172290 AATTTTTCA
1 AATTTTTTA
*
17172299 AAATTTTTA
1 AATTTTTTA
*
17172308 AATTTTTAA
1 AATTTTTTA
17172317 GAGATTTTTTA
1 -A-ATTTTTTA
**
17172328 TAAAATTTT-
1 -AATTTTTTA
*
17172337 AGTTTTTT-
1 AATTTTTTA
*
17172345 -A--TTTTC
1 AATTTTTTA
17172351 AATTTTTTA
1 AATTTTTTA
*
17172360 ACTTTTTAGTA
1 AATTTTT--TA
*
17172371 AATTTATTTTT
1 AA-TT-TTTTA
* *
17172382 TATTTTTAA
1 AATTTTTTA
**
17172391 CAAAATTTT-
1 -AATTTTTTA
17172400 -ATTTTAATTA
1 AATTTT--TTA
*
17172410 AATTTTTTT
1 AATTTTTTA
17172419 AA--TTTTA
1 AATTTTTTA
17172426 AGA-TTTTTA
1 A-ATTTTTTA
**
17172435 AGATTTTTGG
1 A-ATTTTTTA
*
17172445 ATTTTTATTAA
1 AATTTT-TT-A
*
17172456 AATTTTGT-
1 AATTTTTTA
*
17172464 GAT-TTTTA
1 AATTTTTTA
*
17172472 AAATTTTTA
1 AATTTTTTA
*
17172481 ATTTTTTTA
1 AATTTTTTA
*
17172490 AATTTTAT-
1 AATTTTTTA
**
17172498 AATTTTAAA
1 AATTTTTTA
*
17172507 AATATTTTA
1 AATTTTTTA
*
17172516 TA-TTTTTA
1 AATTTTTTA
*
17172524 AATATTTTA
1 AATTTTTTA
*
17172533 TGA-TTTTTA
1 -AATTTTTTA
* *
17172542 AATATGTTA
1 AATTTTTTA
* *
17172551 GATTTTTAAA
1 AATTTTT-TA
*
17172561 AATATTTTA
1 AATTTTTTA
17172570 TAATTTTTTA
1 -AATTTTTTA
*
17172580 GATTTTTTTAA
1 -AATTTTTT-A
17172591 AATTTTTTTAA
1 AA-TTTTTT-A
17172602 AATTGTTTTGA
1 AATT-TTTT-A
17172613 ATATTTTTTA
1 A-ATTTTTTA
17172623 TTTAATATTG
Statistics
Matches: 258, Mismatches: 79, Indels: 64
0.64 0.20 0.16
Matches are distributed among these distances:
5 4 0.02
7 12 0.05
8 23 0.09
9 117 0.45
10 50 0.19
11 44 0.17
12 5 0.02
13 3 0.01
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (9 bp):
AATTTTTTA
Found at i:17172474 original size:17 final size:16
Alignment explanation
Indices: 17172427--17172561 Score: 90
Period size: 17 Copynumber: 7.7 Consensus size: 16
17172417 TTAATTTTAA
*
17172427 GATTTTTAAGATTTTT
1 GATTTTTAAAATTTTT
17172443 GGATTTTTATTAAAATTTTGT
1 -GA--TTT-TTAAAATTTT-T
17172464 GATTTTTAAAATTTTT
1 GATTTTTAAAATTTTT
* *
17172480 AATTTTTTTAAATTTTAT
1 GA-TTTTTAAAATTTT-T
* *
17172498 AATTTTAAAAATATTTT
1 GATTTTTAAAAT-TTTT
*
17172515 ATATTTTTAAATATTTTAT
1 -GATTTTTAAA-ATTTT-T
* *
17172534 GATTTTTAAATATGTTA
1 GATTTTTAAA-ATTTTT
17172551 GATTTTTAAAA
1 GATTTTTAAAA
17172562 ATATTTTATA
Statistics
Matches: 98, Mismatches: 10, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
16 3 0.03
17 43 0.44
18 34 0.35
19 6 0.06
20 11 0.11
21 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (16 bp):
GATTTTTAAAATTTTT
Found at i:17172515 original size:19 final size:18
Alignment explanation
Indices: 17172491--17172576 Score: 93
Period size: 18 Copynumber: 4.7 Consensus size: 18
17172481 ATTTTTTTAA
17172491 ATTTTATAATTTTAAAAAT
1 ATTTTATAATTTT-AAAAT
*
17172510 ATTTTAT-ATTTTTAAAT
1 ATTTTATAATTTTAAAAT
* *
17172527 ATTTTATGATTTTTAAAT
1 ATTTTATAATTTTAAAAT
* * *
17172545 ATGTTAGATTTTTAAAAAT
1 ATTTTATAATTTT-AAAAT
17172564 ATTTTATAATTTT
1 ATTTTATAATTTT
17172577 TTAGATTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
17 11 0.20
18 24 0.43
19 21 0.38
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTTATAATTTTAAAAT
Found at i:17172585 original size:54 final size:52
Alignment explanation
Indices: 17172484--17172585 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 52
17172474 ATTTTTAATT
* *
17172484 TTTTTAAATTTTATAATTTTAAAAATATTTTATATTTTTAAATATTTTATGA
1 TTTTTAAATTTTAGAATTTTAAAAATATTTTATATTTTTAAAGATTTTATGA
* *
17172536 TTTTTAAATATGTTAGATTTTTAAAAATATTTTATAATTTTT-TAGATTTT
1 TTTTTAAAT-T-TTAGAATTTTAAAAATATTTTAT-ATTTTTAAAGATTTT
17172586 TTTAAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
52 9 0.21
53 1 0.02
54 27 0.63
55 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (52 bp):
TTTTTAAATTTTAGAATTTTAAAAATATTTTATATTTTTAAAGATTTTATGA
Found at i:17172587 original size:11 final size:11
Alignment explanation
Indices: 17172553--17172621 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
17172543 ATATGTTAGA
*
17172553 TTTTTAAAAAT
1 TTTTTAAAATT
* *
17172564 ATTTTATAA-T
1 TTTTTAAAATT
*
17172574 TTTTT-AGATT
1 TTTTTAAAATT
17172584 TTTTTAAAATT
1 TTTTTAAAATT
17172595 TTTTTAAAATT
1 TTTTTAAAATT
* *
17172606 GTTTTGAATATT
1 -TTTTTAAAATT
17172618 TTTT
1 TTTT
17172622 ATTTAATATT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
9 1 0.02
10 11 0.23
11 26 0.55
12 9 0.19
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (11 bp):
TTTTTAAAATT
Found at i:17172597 original size:29 final size:27
Alignment explanation
Indices: 17172535--17172597 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
17172525 ATATTTTATG
17172535 ATTTTTAAATATGTTAGATTTTTAAAA
1 ATTTTTAAATATGTTAGATTTTTAAAA
* * *
17172562 ATATTTTATAATTTTTTAGATTTTTTTAAA
1 AT-TTTTA-AATATGTTAGA-TTTTTAAAA
17172592 ATTTTT
1 ATTTTT
17172598 TTAAAATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.07
28 5 0.17
29 13 0.43
30 10 0.33
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (27 bp):
ATTTTTAAATATGTTAGATTTTTAAAA
Found at i:17173257 original size:26 final size:26
Alignment explanation
Indices: 17173219--17173276 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
17173209 CACTTTTACT
17173219 TATTAATCTGGTAAATAACAATTTGG
1 TATTAATCTGGTAAATAACAATTTGG
* *
17173245 TATTAAT-TCGGTACATAACATTTTGG
1 TATTAATCT-GGTAAATAACAATTTGG
17173271 TATTAA
1 TATTAA
17173277 ATTAGGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (26 bp):
TATTAATCTGGTAAATAACAATTTGG
Found at i:17173868 original size:25 final size:25
Alignment explanation
Indices: 17173810--17173868 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
17173800 TTAATTAAGA
*
17173810 TTATATTAATATTTTATCTTAGAAT
1 TTATATTATTATTTTATCTTAGAAT
* **
17173835 TTATTTTATTATTTTAT-TTATTAT
1 TTATATTATTATTTTATCTTAGAAT
17173859 TTATGATTAT
1 TTAT-ATTAT
17173869 GTTAGGATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (25 bp):
TTATATTATTATTTTATCTTAGAAT
Found at i:17175719 original size:14 final size:14
Alignment explanation
Indices: 17175700--17175727 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17175690 TATCACAATT
17175700 TTATTATTTACTTA
1 TTATTATTTACTTA
17175714 TTATTATTTACTTA
1 TTATTATTTACTTA
17175728 ATGGTCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTATTTACTTA
Found at i:17180247 original size:35 final size:35
Alignment explanation
Indices: 17180201--17180275 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
17180191 TTGTTGCCCT
*** * *
17180201 TTCCAAATTTGTCATGTGGTAGCCTGGTGGGCTTC
1 TTCCAAATTTGTCACACGATAGCCTGGTAGGCTTC
17180236 TTCCAAATTTGTCACACGATAGCCTGGTAGGCTTC
1 TTCCAAATTTGTCACACGATAGCCTGGTAGGCTTC
17180271 TTCCA
1 TTCCA
17180276 TCTCCGCCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (35 bp):
TTCCAAATTTGTCACACGATAGCCTGGTAGGCTTC
Found at i:17182496 original size:25 final size:26
Alignment explanation
Indices: 17182453--17182505 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
17182443 TTCAACACAT
17182453 AAAATGATAAAAAGAAATAAGTTTTC
1 AAAATGATAAAAAGAAATAAGTTTTC
*
17182479 AAAATGGT-AAAAGAAATAAGTTTTC
1 AAAATGATAAAAAGAAATAAGTTTTC
17182504 AA
1 AA
17182506 GTGTCTACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (26 bp):
AAAATGATAAAAAGAAATAAGTTTTC
Found at i:17185093 original size:33 final size:32
Alignment explanation
Indices: 17185050--17185112 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
17185040 TTAACATCTT
*
17185050 AAAAAAACAATTAAATTATATCCAAACAATAA
1 AAAAAAACAATGAAATTATATCCAAACAATAA
*
17185082 AAAATAAACAATGAAATTATATTCAAACAAT
1 AAAA-AAACAATGAAATTATATCCAAACAAT
17185113 GAGTAAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.24
Consensus pattern (32 bp):
AAAAAAACAATGAAATTATATCCAAACAATAA
Found at i:17185113 original size:19 final size:19
Alignment explanation
Indices: 17185054--17185114 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
17185044 CATCTTAAAA
* *
17185054 AAACAATTAAATTATATCC
1 AAACAATGAAATTATATTC
*
17185073 AAACAAT-AAA--A-AAT-
1 AAACAATGAAATTATATTC
17185087 AAACAATGAAATTATATTC
1 AAACAATGAAATTATATTC
17185106 AAACAATGA
1 AAACAATGA
17185115 GTAAAAGTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 7 0.21
15 4 0.12
16 1 0.03
17 1 0.03
18 5 0.15
19 16 0.47
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.25
Consensus pattern (19 bp):
AAACAATGAAATTATATTC
Found at i:17186954 original size:18 final size:18
Alignment explanation
Indices: 17186928--17186962 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17186918 TAAAAATTTT
*
17186928 TACTTATAATTAAGAAAA
1 TACTCATAATTAAGAAAA
*
17186946 TACTCATAATTGAGAAA
1 TACTCATAATTAAGAAA
17186963 GATAATCTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (18 bp):
TACTCATAATTAAGAAAA
Found at i:17190008 original size:32 final size:31
Alignment explanation
Indices: 17189967--17190058 Score: 80
Period size: 32 Copynumber: 2.9 Consensus size: 31
17189957 TATTTTACAA
* * *
17189967 AATAGCTATTTATGAAACAACCATTTTCATAG
1 AATAACTATTTATGAAACAACC-TATTCAAAG
**
17189999 AATAACTATTTACAAAACAA-CTATTCAAAG
1 AATAACTATTTATGAAACAACCTATTCAAAG
* *
17190029 AATAACTCTTTCATGGAACAACACT-TTCAA
1 AATAACTATTT-ATGAAACAAC-CTATTCAA
17190059 GGATTAGTTG
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
30 17 0.35
31 7 0.15
32 22 0.46
33 2 0.04
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (31 bp):
AATAACTATTTATGAAACAACCTATTCAAAG
Found at i:17194069 original size:6 final size:6
Alignment explanation
Indices: 17194060--17194091 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
17194050 ATTAATTCTT
17194060 TTTTTC -TTTTC TTTTTC TTTTTC TTTTT- TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
17194092 AGACAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 9 0.36
6 16 0.64
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTC
Found at i:17194082 original size:17 final size:16
Alignment explanation
Indices: 17194060--17194091 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
17194050 ATTAATTCTT
17194060 TTTTTCTTTTCTTTTTC
1 TTTTTCTTTT-TTTTTC
17194077 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTT
17194092 AGACAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTC
Found at i:17194603 original size:26 final size:26
Alignment explanation
Indices: 17194569--17194620 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
17194559 TTGGGATCTA
*
17194569 GGTTTAGGGTTTTGCGTTTAAGGTTT
1 GGTTTAGGGTTTAGCGTTTAAGGTTT
* *
17194595 GGTTTAGGGTTTAGGGTTTTAGGTTT
1 GGTTTAGGGTTTAGCGTTTAAGGTTT
17194621 AAGGTTTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.12, C:0.02, G:0.37, T:0.50
Consensus pattern (26 bp):
GGTTTAGGGTTTAGCGTTTAAGGTTT
Found at i:17194606 original size:19 final size:19
Alignment explanation
Indices: 17194584--17194657 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 19
17194574 AGGGTTTTGC
17194584 GTTTAAGGTTTGGTTTAGG
1 GTTTAAGGTTTGGTTTAGG
*
17194603 GTTT-AGG---GTTTTA-G
1 GTTTAAGGTTTGGTTTAGG
17194617 GTTTAAGGTTTGGTTT-GAG
1 GTTTAAGGTTTGGTTTAG-G
* * *
17194636 ATTTAAGATTTGGTTTTGG
1 GTTTAAGGTTTGGTTTAGG
17194655 GTT
1 GTT
17194658 AGGGTTTAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
14 5 0.12
15 8 0.19
18 7 0.16
19 22 0.51
20 1 0.02
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (19 bp):
GTTTAAGGTTTGGTTTAGG
Found at i:17194611 original size:33 final size:33
Alignment explanation
Indices: 17194569--17194632 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 33
17194559 TTGGGATCTA
17194569 GGTTTAGGGTTTT-GCGTTTAAGGTTTGGTTTAG
1 GGTTTAGGGTTTTAG-GTTTAAGGTTTGGTTTAG
17194602 GGTTTAGGGTTTTAGGTTTAAGGTTTGGTTT
1 GGTTTAGGGTTTTAGGTTTAAGGTTTGGTTT
17194633 GAGATTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.12, C:0.02, G:0.36, T:0.50
Consensus pattern (33 bp):
GGTTTAGGGTTTTAGGTTTAAGGTTTGGTTTAG
Found at i:17194617 original size:8 final size:7
Alignment explanation
Indices: 17194569--17194627 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
17194559 TTGGGATCTA
17194569 GGTTTAG
1 GGTTTAG
*
17194576 GGTTTTG
1 GGTTTAG
* *
17194583 CGTTTAA
1 GGTTTAG
17194590 GGTTT--
1 GGTTTAG
17194595 GGTTTAG
1 GGTTTAG
17194602 GGTTTAG
1 GGTTTAG
17194609 GGTTTTA-
1 GG-TTTAG
*
17194616 GGTTTAA
1 GGTTTAG
17194623 GGTTT
1 GGTTT
17194628 GGTTTGAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
5 5 0.12
6 4 0.09
7 30 0.70
8 4 0.09
ACGTcount: A:0.14, C:0.02, G:0.36, T:0.49
Consensus pattern (7 bp):
GGTTTAG
Found at i:17196541 original size:3 final size:3
Alignment explanation
Indices: 17196491--17196521 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
17196481 ATTTTAAAAG
17196491 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17196522 CAATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17197035 original size:17 final size:17
Alignment explanation
Indices: 17197015--17197048 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17197005 TTTCATATTT
* *
17197015 TAAATAATAAAATTAAA
1 TAAAGAATAAAAATAAA
17197032 TAAAGAATAAAAATAAA
1 TAAAGAATAAAAATAAA
17197049 ATAAGATCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
TAAAGAATAAAAATAAA
Found at i:17199790 original size:12 final size:12
Alignment explanation
Indices: 17199775--17199816 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
17199765 ACTTGAAAAA
17199775 AAAAAGGAAAGG
1 AAAAAGGAAAGG
*
17199787 AAAAAGGATAAAG
1 AAAAAGGA-AAGG
17199800 -AAAAGAGAAAGG
1 AAAAAG-GAAAGG
17199812 AAAAA
1 AAAAA
17199817 AAAGTTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (12 bp):
AAAAAGGAAAGG
Found at i:17201071 original size:17 final size:16
Alignment explanation
Indices: 17201046--17201104 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 16
17201036 GAAAAGTCAA
*
17201046 AAAGAAAAAAAAAAAGTG
1 AAAG-AAAAAATAAA-TG
17201064 AAAGAAAAAATAAATG
1 AAAGAAAAAATAAATG
17201080 AAAGAACAAAATAAATG
1 AAAGAA-AAAATAAATG
17201097 AAATGAAA
1 AAA-GAAA
17201105 TAATGGGCGG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
16 8 0.21
17 23 0.61
18 7 0.18
ACGTcount: A:0.75, C:0.02, G:0.14, T:0.10
Consensus pattern (16 bp):
AAAGAAAAAATAAATG
Found at i:17202285 original size:41 final size:40
Alignment explanation
Indices: 17202205--17202285 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 40
17202195 AAAAGAAAGG
**
17202205 AAGAAAAAATGTTTTTAAGAATGGTAATGTGTCTCCTTGT
1 AAGAAAAAATGTTTTTAAGAATGGTAATGCATCTCCTTGT
* * *
17202245 AAGAAAACATGTTTTTTAAGAATGGTGATGCATCTTCTTGT
1 AAGAAAAAATG-TTTTTAAGAATGGTAATGCATCTCCTTGT
17202286 TAAGTATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 10 0.29
41 25 0.71
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (40 bp):
AAGAAAAAATGTTTTTAAGAATGGTAATGCATCTCCTTGT
Found at i:17202662 original size:18 final size:18
Alignment explanation
Indices: 17202639--17202676 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
17202629 ACGAGGATAT
17202639 ATTTTATATAACATTTGC
1 ATTTTATATAACATTTGC
17202657 ATTTTATATAACATTTGC
1 ATTTTATATAACATTTGC
17202675 AT
1 AT
17202677 AAAAGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTTATATAACATTTGC
Found at i:17203215 original size:41 final size:40
Alignment explanation
Indices: 17203169--17203345 Score: 117
Period size: 41 Copynumber: 4.3 Consensus size: 40
17203159 TATCTCTAGA
17203169 CAAAATTTTAAATTTTTGAAAGACTTTCAAAGACTT-TCGAG
1 CAAAATTTTAAATTTTTGAAAGA-TTTCAAAGACTTCT-GAG
* * * *
17203210 CAAAATTTCAATTTTTTAAAATGATTTCCAAAGACTTCTGGG
1 CAAAATTTTAAATTTTTGAAA-GATTT-CAAAGACTTCTGAG
* * * * * *
17203252 TAAAATCTTAAATTTATGAAGGATTTTC-AAGACCTCTAAG
1 CAAAATTTTAAATTTTTGAAAGA-TTTCAAAGACTTCTGAG
** * * **
17203292 CAAACCTTTAAATTTTT-AAAGAATTTCCCAAGACCTCCAAG
1 CAAAATTTTAAATTTTTGAAAG-ATTT-CAAAGACTTCTGAG
*
17203333 CAAAAATTTAAAT
1 CAAAATTTTAAAT
17203346 GATTCGTAAG
Statistics
Matches: 106, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
39 6 0.06
40 23 0.22
41 46 0.43
42 30 0.28
43 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.34
Consensus pattern (40 bp):
CAAAATTTTAAATTTTTGAAAGATTTCAAAGACTTCTGAG
Found at i:17203659 original size:19 final size:18
Alignment explanation
Indices: 17203631--17203667 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
17203621 TTAAATATTC
17203631 TAAAAAAAAACAACAAAA
1 TAAAAAAAAACAACAAAA
17203649 TAAAAACAAAACAACAAAA
1 TAAAAA-AAAACAACAAAA
17203668 AATAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.81, C:0.14, G:0.00, T:0.05
Consensus pattern (18 bp):
TAAAAAAAAACAACAAAA
Found at i:17204031 original size:16 final size:16
Alignment explanation
Indices: 17204010--17204041 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17204000 AAAAAAAAAC
*
17204010 TAAATAATAATAACAA
1 TAAATAAAAATAACAA
17204026 TAAATAAAAATAACAA
1 TAAATAAAAATAACAA
17204042 CAAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (16 bp):
TAAATAAAAATAACAA
Found at i:17205940 original size:3 final size:3
Alignment explanation
Indices: 17205869--17205921 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
17205859 AAATAAAAAG
17205869 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17205917 ATA AT
1 ATA AT
17205922 TTTTTAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17206067 original size:12 final size:12
Alignment explanation
Indices: 17206050--17206082 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
17206040 AATTATTAAA
17206050 TAATAAAAATAT
1 TAATAAAAATAT
17206062 TAATAAAAA-AT
1 TAATAAAAATAT
*
17206073 TTATAAAAAT
1 TAATAAAAAT
17206083 TATAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATAAAAATAT
Found at i:17206200 original size:19 final size:19
Alignment explanation
Indices: 17206176--17206244 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
17206166 CATAAATTTC
* *
17206176 TAAAACTCGAAACCTTAGT
1 TAAAACTCGAAACCCTAGG
**
17206195 TAAAACTATAAACCCTAGG
1 TAAAACTCGAAACCCTAGG
** **
17206214 TAAAACTCTTAACCCTAAA
1 TAAAACTCGAAACCCTAGG
*
17206233 TGAAACTCGAAA
1 TAAAACTCGAAA
17206245 AACCTAAACA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.23
Consensus pattern (19 bp):
TAAAACTCGAAACCCTAGG
Found at i:17207292 original size:20 final size:21
Alignment explanation
Indices: 17207247--17207295 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
17207237 TTCTTGGTTT
* * *
17207247 TAAATCAAAATCAATTATAAG
1 TAAATAAAAATCAATAATAAA
17207268 T-AATAAAAAT-AATAATAAA
1 TAAATAAAAATCAATAATAAA
17207287 TAAATAAAA
1 TAAATAAAA
17207296 GCAAAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 8 0.33
20 15 0.62
21 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAATAAAAATCAATAATAAA
Found at i:17207631 original size:49 final size:49
Alignment explanation
Indices: 17207581--17207848 Score: 273
Period size: 49 Copynumber: 5.6 Consensus size: 49
17207571 TTATTATTAT
** *
17207581 TTTTTTA-AGAAACACTTTCATTAGTTATTCTTTTTAATAATTTTCCTA
1 TTTTTTAGAGAAACACTCCCATTACTTATTCTTTTTAATAATTTTCCTA
*
17207629 TTTTTTA-AGAAAACACTCCCATTACTTATTCTTTTTAATAATTTTCTTA
1 TTTTTTAGAG-AAACACTCCCATTACTTATTCTTTTTAATAATTTTCCTA
* * * * *
17207678 TTTTTTAGGGAAACACTCCC-TT-GTCTATTCCTTTTATTAATTTTCTTA
1 TTTTTTAGAGAAACACTCCCATTACT-TATTCTTTTTAATAATTTTCCTA
* * * * *
17207726 TTTTTTAGAAAAACAGTACCATTACCTATT-TCTTTTAATAATTTTTCTA
1 TTTTTTAGAGAAACACTCCCATTACTTATTCT-TTTTAATAATTTTCCTA
* * *
17207775 CTTTTTA-AGGAAACACACCCATTACCTATTCTTTTTAAT--TTTTCCTA
1 TTTTTTAGA-GAAACACTCCCATTACTTATTCTTTTTAATAATTTTCCTA
* *
17207822 TTTTTGAGAGAAACACTCTCATTACTT
1 TTTTTTAGAGAAACACTCCCATTACTT
17207849 GTTATCCTAT
Statistics
Matches: 182, Mismatches: 29, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
47 28 0.15
48 50 0.27
49 102 0.56
50 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.49
Consensus pattern (49 bp):
TTTTTTAGAGAAACACTCCCATTACTTATTCTTTTTAATAATTTTCCTA
Found at i:17207682 original size:97 final size:95
Alignment explanation
Indices: 17207581--17207848 Score: 276
Period size: 97 Copynumber: 2.8 Consensus size: 95
17207571 TTATTATTAT
*
17207581 TTTTTTAAGAAACACTTTCATTAGTTATTCTTTTTAATAATTTTCCTATTTTTTAAGAAAACACT
1 TTTTTTAAGAAACAC-TCCATTAGTTATTCTTTTTAATAATTTTCCTATTTTTT-AGAAAACACT
17207646 CCCATTACTTA-TTCTTTTTAATAA-TTTTCTTA
64 CCCATTACTTATTTC-TTTTAATAATTTTTC-TA
* * * * * *
17207678 TTTTTTAGGGAAACACTCCCTT-GTCTATTCCTTTTATTAATTTTCTTATTTTTTAGAAAAACAG
1 TTTTTTA-AGAAACACTCCATTAGT-TATTCTTTTTAATAATTTTCCTATTTTTTAG-AAAACAC
* *
17207742 TACCATTACCTATTTCTTTTAATAATTTTTCTA
63 TCCCATTACTTATTTCTTTTAATAATTTTTCTA
* * ** *
17207775 CTTTTTAAGGAAACACACCCATTACCTATTCTTTTTAAT--TTTTCCTATTTTTGAGAGAAACAC
1 TTTTTTAA-GAAACAC-TCCATTAGTTATTCTTTTTAATAATTTTCCTATTTTTTAGA-AAACAC
*
17207838 TCTCATTACTT
63 TCCCATTACTT
17207849 GTTATCCTAT
Statistics
Matches: 139, Mismatches: 23, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
95 1 0.01
96 31 0.22
97 77 0.55
98 30 0.22
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.49
Consensus pattern (95 bp):
TTTTTTAAGAAACACTCCATTAGTTATTCTTTTTAATAATTTTCCTATTTTTTAGAAAACACTCC
CATTACTTATTTCTTTTAATAATTTTTCTA
Found at i:17207918 original size:36 final size:36
Alignment explanation
Indices: 17207832--17207926 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 36
17207822 TTTTTGAGAG
* * * * *
17207832 AAACACTCTCATTACTTGTTATCCTATTTTTTAGGA
1 AAACACTTTAATTACTTGTTCTCCTACTTTATAGGA
* *
17207868 AAATATTTTAATTACTTGTTCTCCTACTTTATAGGA
1 AAACACTTTAATTACTTGTTCTCCTACTTTATAGGA
*
17207904 AAACACCTTT-ATTACTTATTCTC
1 AAACA-CTTTAATTACTTGTTCTC
17207927 TTTCTTTTAG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
36 45 0.94
37 3 0.06
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (36 bp):
AAACACTTTAATTACTTGTTCTCCTACTTTATAGGA
Found at i:17208265 original size:39 final size:40
Alignment explanation
Indices: 17208210--17208289 Score: 144
Period size: 39 Copynumber: 2.0 Consensus size: 40
17208200 GAAACTTATA
*
17208210 TCATACATCTTTAAATTACAAGAACACATATATTTTATTT
1 TCATACATCTTTAAATTACAAGAACAAATATATTTTATTT
17208250 TCATA-ATCTTTAAATTACAAGAACAAATATATTTTATTT
1 TCATACATCTTTAAATTACAAGAACAAATATATTTTATTT
17208289 T
1 T
17208290 TATATATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 34 0.87
40 5 0.13
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (40 bp):
TCATACATCTTTAAATTACAAGAACAAATATATTTTATTT
Found at i:17217845 original size:19 final size:20
Alignment explanation
Indices: 17217812--17217852 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
17217802 TTATTTTTCA
*
17217812 TTTATTTGATATTATGTTAT
1 TTTATTTGATATTATGATAT
*
17217832 TTTATTT-ATTTTATGATAT
1 TTTATTTGATATTATGATAT
17217851 TT
1 TT
17217853 ATTGCTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTATTTGATATTATGATAT
Found at i:17221603 original size:11 final size:11
Alignment explanation
Indices: 17221586--17221624 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
17221576 ATCCCATAAA
17221586 AGATTTGTTTG
1 AGATTTGTTTG
* *
17221597 GGATTTGTTAG
1 AGATTTGTTTG
17221608 AGATTTGTTTG
1 AGATTTGTTTG
17221619 AGATTT
1 AGATTT
17221625 TTCAGATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (11 bp):
AGATTTGTTTG
Found at i:17221740 original size:52 final size:52
Alignment explanation
Indices: 17221651--17221807 Score: 217
Period size: 52 Copynumber: 3.0 Consensus size: 52
17221641 TGGACAAGAA
* **
17221651 GACTTGCAAAAGAAGAATTCTAAGA-GAAAGATTATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAG-GGATTCTTAATAGGTAAGTTT
* *
17221703 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
* * * *
17221755 AACTTACAAGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
17221807 G
1 G
17221808 TATGGTTATA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 87 0.95
53 5 0.05
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.27
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
Found at i:17237153 original size:221 final size:220
Alignment explanation
Indices: 17236518--17237416 Score: 972
Period size: 220 Copynumber: 4.1 Consensus size: 220
17236508 ATATTATTGT
* * * * * * *
17236518 AACGTAAAAGAATTTTTACATTGAACCTAAA-AATTAAGTCTAAACTAATAAATAAATGTTAACA
1 AACGTAAAAGAATTATTACTTTAAACCCAAAGAA-TAAGTATAAACCAATAAATAAATATTAACA
* * *
17236582 TAAAAAGGTAAAAATTATCGTAAAATTGGTATAATTT-AGCATAAAATGTGTTAGAAATATTATA
65 T-AAAAGGTAAAAATTATCGTAAAATTGATATCATTTGA-CATAAAATGTGTTAGAAGTATTATA
* * * ** * * * *
17236646 ATACCCTAAGAAAGCA-TTGTGATAATTCTAAATGTAATGAAGATAAAAATAAGCATAAAAAGAT
128 ACACCCTAAGAGAG-AGTTGTGACAATTCTAAACATAATAAAGGTAAGAACAAGCATAAAAAGAT
* *
17236710 ATTATTGTAACA-TAAATAATTAAATTGAT
192 ATTATTGTAA-AGTAAATAATTAAATTAAC
* * * * * *
17236739 AACGTGAAAA-AATTATTACTGTAAACCCAAAAAATAATTCA-AAACCAATGAATAAATGTTAAT
1 AACGT-AAAAGAATTATTACTTTAAACCCAAAGAATAAGT-ATAAACCAATAAATAAATATTAAC
* * * * * * * *
17236802 GTAAAAGCTAAGAATTATCATAATATTGGTATCATTTCACATAAAATGTGTTAGAAGTATTGTAA
64 ATAAAAGGTAAAAATTATCGTAAAATTGATATCATTTGACATAAAATGTGTTAGAAGTATTATAA
* * * * **
17236867 CACCCTAAAATAGTGTTGTGACAAATCTAAATGTAATGAAA-GTAAGAACAAG-AGTAAAAAGAT
129 CACCCTAAGAGAGAGTTGTGACAATTCTAAACATAAT-AAAGGTAAGAACAAGCA-TAAAAAGAT
*
17236930 ATTATTGTAAAGTAAATAATTAAATTGAC
192 ATTATTGTAAAGTAAATAATTAAATTAAC
* *
17236959 AATGTAAAAGAATTATTACTTTAAACCCAAAGAATAATTATAAACCAATAAATAAATATTAACAT
1 AACGTAAAAGAATTATTACTTTAAACCCAAAGAATAAGTATAAACCAATAAATAAATATTAACAT
** * * *
17237024 AAAAATATAAAAATTATCGTAAAATTGATATCATTTGGCATAAAATGTATTAGAAGTATTGTAAC
66 -AAAAGGTAAAAATTATCGTAAAATTGATATCATTTGACATAAAATGTGTTAGAAGTATTATAAC
* *
17237089 ACCCTATGAGAGAGTTGTGATAATTCTAAACATAATAAAGGTAAGAACAAGCATAAAAAGATATT
130 ACCCTAAGAGAGAGTTGTGACAATTCTAAACATAATAAAGGTAAGAACAAGCATAAAAAGATATT
* * *
17237154 ATTGTAGAGTGAATAATTAAATTAAT
195 ATTGTAAAGTAAATAATTAAATTAAC
* * * * *
17237180 AACGTAAAAGAGTTATTACCTTGAACCCAAAGAGTAAGTCTAAACCAATAAATAAATATTAACAT
1 AACGTAAAAGAATTATTACTTTAAACCCAAAGAATAAGTATAAACCAATAAATAAATATTAACAT
* * * * *
17237245 AAAATGGTGAAAATTATTGTAAAATTGATATC-TTTGACATAAAAAGTGTTAGAAGTGTCATAAC
66 AAAA-GGTAAAAATTATCGTAAAATTGATATCATTTGACATAAAATGTGTTAGAAGTATTATAAC
* * * * * *
17237309 ACCTTAAGAGAGTGTTGTGACAATTTTAAACATAATGAAGGTAAGAATAAGTATAAAAAGATATT
130 ACCCTAAGAGAGAGTTGTGACAATTCTAAACATAATAAAGGTAAGAACAAGCATAAAAAGATATT
*
17237374 ATTGTAATGTAAATAATTAAATTAAC
195 ATTGTAAAGTAAATAATTAAATTAAC
* *
17237400 AATGTAAAA-AAATATTA
1 AACGTAAAAGAATTATTA
17237417 TTACAAATAA
Statistics
Matches: 575, Mismatches: 89, Indels: 30
0.83 0.13 0.04
Matches are distributed among these distances:
219 13 0.02
220 298 0.52
221 257 0.45
222 7 0.01
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (220 bp):
AACGTAAAAGAATTATTACTTTAAACCCAAAGAATAAGTATAAACCAATAAATAAATATTAACAT
AAAAGGTAAAAATTATCGTAAAATTGATATCATTTGACATAAAATGTGTTAGAAGTATTATAACA
CCCTAAGAGAGAGTTGTGACAATTCTAAACATAATAAAGGTAAGAACAAGCATAAAAAGATATTA
TTGTAAAGTAAATAATTAAATTAAC
Found at i:17237347 original size:441 final size:435
Alignment explanation
Indices: 17236521--17237416 Score: 1061
Period size: 441 Copynumber: 2.0 Consensus size: 435
17236511 TTATTGTAAC
* * * * * *
17236521 GTAAAAGAATTTTTACATTGAACCTAAAAATTAAGTCTAAACTAATAAATAAATGTTAACATAAA
1 GTAAAAGAATTATTACATTAAACCCAAAAATTAAGTATAAACCAATAAATAAATATTAACATAAA
* * * *
17236586 AAGGTAAAAATTATCGTAAAATTGGTATAATTTAGCATAAAATGTGTTAGAAATATTATAATACC
66 AAGATAAAAATTATCGTAAAATT-GTATCATTTAGCATAAAATGTATTAGAAGTATTATAATACC
* * * * *
17236651 CTAAGAAAGCA-TTGTGATAATTCTAAATGTAATGAAGATAAAAATAAGCATAAAAAGATATTAT
130 CTAAGAGAG-AGTTGTGATAATTCTAAACGTAATGAAGGTAAGAACAAGCATAAAAAGATATTAT
* *
17236715 TGTAACATAAATAATTAAATTGATAACGTGAAAAAATTATTA-CTGTAAACCCAAAAAATAATTC
194 TGTAACGTAAATAATTAAATTGATAACGT-AAAAAATTATTACCT-TAAACCCAAAGAATAATTC
* * * ** * *
17236779 AAAACCAATGAATAAATGTTAATGTAAAAGCTAAGAATTATCA-TAATATTGGTATCATTTCACA
257 TAAACCAATAAATAAATATTAACATAAAAGGTAA-AATTAT-AGTAAAATTGGTATC-TTTCACA
* ** * **
17236843 TAAAATGTGTTAGAAGTATTGTAACACCCTAA-AATAGTGTTGTGACAAATCTAAATGTAATGAA
319 TAAAATGTGTTAGAAGTGTCATAACACCCTAAGAA-AGTGTTGTGACAATTCTAAACATAATGAA
17236907 AGTAAGAACAAG-AGTAAAAAGATATTATTGTAAAGTAAATAATTAAATTGACAAT
383 AGTAAGAACAAGCA-TAAAAAGATATTATTGT-AAGTAAATAATTAAATT-ACAAT
* *
17236962 GTAAAAGAATTATTACTTTAAACCCAAAGAA-TAATTATAAACCAATAAATAAATATTAACATAA
1 GTAAAAGAATTATTACATTAAACCCAAA-AATTAAGTATAAACCAATAAATAAATATTAACATAA
* * * *
17237026 AAATATAAAAATTATCGTAAAATTGATATCATTTGGCATAAAATGTATTAGAAGTATTGTAACAC
65 AAAGATAAAAATTATCGTAAAATTG-TATCATTTAGCATAAAATGTATTAGAAGTATTATAATAC
* * *
17237091 CCTATGAGAGAGTTGTGATAATTCTAAACATAATAAAGGTAAGAACAAGCATAAAAAGATATTAT
129 CCTAAGAGAGAGTTGTGATAATTCTAAACGTAATGAAGGTAAGAACAAGCATAAAAAGATATTAT
* * * * * *
17237156 TGTAGA-GTGAATAATTAAATTAATAACGTAAAAGAGTTATTACCTTGAACCCAAAGAGTAAGTC
194 TGTA-ACGTAAATAATTAAATTGATAACGTAAAA-AATTATTACCTTAAACCCAAAGAATAATTC
* * *
17237220 TAAACCAATAAATAAATATTAACATAAAATGGTGAAAATTATTGTAAAATTGATATCTTTGACAT
257 TAAACCAATAAATAAATATTAACATAAAA-GGT-AAAATTATAGTAAAATTGGTATCTTTCACAT
* * * * *
17237285 AAAAAGTGTTAGAAGTGTCATAACACCTTAAGAGAGTGTTGTGACAATTTTAAACATAATGAAGG
320 AAAATGTGTTAGAAGTGTCATAACACCCTAAGAAAGTGTTGTGACAATTCTAAACATAATGAAAG
* *
17237350 TAAGAATAAGTATAAAAAGATATTATTGTAATGTAAATAATTAAATTAACAAT
385 TAAGAACAAGCATAAAAAGATATTATTGTAA-GTAAATAATTAAATT-ACAAT
*
17237403 GTAAAA-AAATATTA
1 GTAAAAGAATTATTA
17237417 TTACAAATAA
Statistics
Matches: 387, Mismatches: 56, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
440 15 0.04
441 344 0.89
442 26 0.07
443 2 0.01
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (435 bp):
GTAAAAGAATTATTACATTAAACCCAAAAATTAAGTATAAACCAATAAATAAATATTAACATAAA
AAGATAAAAATTATCGTAAAATTGTATCATTTAGCATAAAATGTATTAGAAGTATTATAATACCC
TAAGAGAGAGTTGTGATAATTCTAAACGTAATGAAGGTAAGAACAAGCATAAAAAGATATTATTG
TAACGTAAATAATTAAATTGATAACGTAAAAAATTATTACCTTAAACCCAAAGAATAATTCTAAA
CCAATAAATAAATATTAACATAAAAGGTAAAATTATAGTAAAATTGGTATCTTTCACATAAAATG
TGTTAGAAGTGTCATAACACCCTAAGAAAGTGTTGTGACAATTCTAAACATAATGAAAGTAAGAA
CAAGCATAAAAAGATATTATTGTAAGTAAATAATTAAATTACAAT
Found at i:17237422 original size:21 final size:21
Alignment explanation
Indices: 17237362--17237430 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
17237352 AGAATAAGTA
* **
17237362 TAAAAAGATATTATTGTAATG
1 TAAAAAAATATTATTACAATG
* * *
17237383 TAAATAATTA-AATTAACAATG
1 TAAAAAAATATTATT-ACAATG
*
17237404 TAAAAAAATATTATTACAA-A
1 TAAAAAAATATTATTACAATG
17237424 TAAAAAA
1 TAAAAAA
17237431 TAAAAGTTAA
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
20 10 0.28
21 23 0.64
22 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (21 bp):
TAAAAAAATATTATTACAATG
Found at i:17238325 original size:21 final size:21
Alignment explanation
Indices: 17238265--17238333 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
17238255 ACAACAATCA
* *
17238265 TAAAAAGATATTATTATAATG
1 TAAAAAAATATTATTACAATG
* * *
17238286 TAAATAATTA-AATTGACAATG
1 TAAAAAAATATTATT-ACAATG
*
17238307 TAAAAAAATATTATTACAA-A
1 TAAAAAAATATTATTACAATG
17238327 TAAAAAA
1 TAAAAAA
17238334 TAATTCTAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
20 10 0.27
21 24 0.65
22 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (21 bp):
TAAAAAAATATTATTACAATG
Found at i:17238877 original size:67 final size:67
Alignment explanation
Indices: 17238806--17238975 Score: 209
Period size: 67 Copynumber: 2.5 Consensus size: 67
17238796 AGAATAATTG
* * * * *
17238806 TAAAATTTATATAATTTAACATAGAATGTGTTAAATGTATCGTAACGTAAAAATATGAAAATAGT
1 TAAAATTAATATAATTTAACATAAAATGTATTAAAAGTATCATAACGTAAAAATATGAAAATAGT
17238871 CA
66 CA
* * *
17238873 TAAAA-TAGATATAATTTCACGTAAAATGTATTAAAAGTATCATAACGTAAAAATGTGAAAATAG
1 TAAAATTA-ATATAATTTAACATAAAATGTATTAAAAGTATCATAACGTAAAAATATGAAAATAG
17238937 TCA
65 TCA
* **
17238940 TAAAATTAATATTATTTAGTATAAAAT-TGATTAAAA
1 TAAAATTAATATAATTTAACATAAAATGT-ATTAAAA
17238976 TTATTGTAAC
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
66 2 0.02
67 83 0.95
68 2 0.02
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (67 bp):
TAAAATTAATATAATTTAACATAAAATGTATTAAAAGTATCATAACGTAAAAATATGAAAATAGT
CA
Found at i:17239150 original size:23 final size:23
Alignment explanation
Indices: 17239111--17239183 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 23
17239101 TCATAAAAAC
17239111 ATAAAAA-AAAT-TATTAATATAA
1 ATAAAAATAAATAT-TTAATATAA
17239133 ATAAAAATAAATATTTAAT-T--
1 ATAAAAATAAATATTTAATATAA
*
17239153 A-AAAAATAAATATTTACATAAAA
1 ATAAAAATAAATATTTA-ATATAA
17239176 ATATAAAA
1 ATA-AAAA
17239184 ATAATTGTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
19 15 0.36
20 3 0.07
22 8 0.19
23 10 0.24
24 2 0.05
25 4 0.10
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (23 bp):
ATAAAAATAAATATTTAATATAA
Found at i:17239158 original size:20 final size:19
Alignment explanation
Indices: 17239135--17239182 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
17239125 TAATATAAAT
17239135 AAAAATAAATATTTA-ATTA
1 AAAAATAAATATTTACA-TA
17239154 AAAAATAAATATTTACATA
1 AAAAATAAATATTTACATA
17239173 AAAATATAAA
1 AAAA-ATAAA
17239183 AATAATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATAAATATTTACATA
Found at i:17239471 original size:10 final size:10
Alignment explanation
Indices: 17239448--17239492 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
17239438 TATTATTCTT
* *
17239448 ATAATTTATT
1 ATAATATATC
17239458 ATAATATATC
1 ATAATATATC
*
17239468 ATAAAATATC
1 ATAATATATC
*
17239478 ATAATATTTC
1 ATAATATATC
17239488 ATAAT
1 ATAAT
17239493 TTTAAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (10 bp):
ATAATATATC
Found at i:17240274 original size:19 final size:19
Alignment explanation
Indices: 17240250--17240300 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
17240240 TTAATCAAAT
17240250 TTAAATCAAATATCAAACA
1 TTAAATCAAATATCAAACA
* * *
17240269 TTAAATAAAAAATCGAACA
1 TTAAATCAAATATCAAACA
17240288 -TAAACTCAAATAT
1 TTAAA-TCAAATAT
17240301 TTCATTATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (19 bp):
TTAAATCAAATATCAAACA
Found at i:17240565 original size:12 final size:13
Alignment explanation
Indices: 17240548--17240576 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
17240538 ATTATCTTTT
17240548 TTTAAATAT-ATA
1 TTTAAATATAATA
17240560 TTTAAATATAATA
1 TTTAAATATAATA
17240573 TTTA
1 TTTA
17240577 GAAAGAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAAATATAATA
Done.