Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_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: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 32
Found at i:5487166 original size:41 final size:42
Alignment explanation
Indices: 5487105--5487187 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 42
5487095 CGCAAATCAG
* *
5487105 TTTCCAGATTCGCAACGCGA-TTCTGACTATCGCATTGCGAT
1 TTTCCAAATTCGCAACGCGATTTCTGACTATCGCAATGCGAT
**
5487146 TTTCCAAATTCGCATTGCGATTTTCTGACTATCGCAATGCGA
1 TTTCCAAATTCGCAACGCGA-TTTCTGACTATCGCAATGCGA
5487188 ATATGTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 17 0.47
43 19 0.53
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (42 bp):
TTTCCAAATTCGCAACGCGATTTCTGACTATCGCAATGCGAT
Found at i:5487260 original size:40 final size:40
Alignment explanation
Indices: 5487169--5487322 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
5487159 ATTGCGATTT
* * * *
5487169 TCTGACTATCGCAATGCGAATATGTA-AATCGCAATGCGAA
1 TCTGACTATCGCAATGCGATTATG-ACTATCGCAATGCCAC
* *
5487209 TATGTA-AATCGCAATGCGATTATGACTATCGCAATGCCAC
1 TCTG-ACTATCGCAATGCGATTATGACTATCGCAATGCCAC
5487249 TCTGACTATCGCAATGCGATTATGACTATCGCAATGCCAC
1 TCTGACTATCGCAATGCGATTATGACTATCGCAATGCCAC
* * * *
5487289 TCTGACTATCGCAACGCGGTTCTGACTGTCGCAA
1 TCTGACTATCGCAATGCGATTATGACTATCGCAA
5487323 CACTGAATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
39 2 0.02
40 96 0.97
41 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (40 bp):
TCTGACTATCGCAATGCGATTATGACTATCGCAATGCCAC
Found at i:5488195 original size:24 final size:24
Alignment explanation
Indices: 5488144--5488197 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5488134 ATATTTGAAA
*
5488144 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGAAC
* *
5488168 TTTGATCTTGGTCAATACTCGAAT
1 TTTGATCTTGGTCAATACCCGAAC
5488192 TTTGAT
1 TTTGAT
5488198 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGAAC
Found at i:5490473 original size:12 final size:12
Alignment explanation
Indices: 5490458--5490493 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5490448 AAGAAAAAGA
5490458 CAATCAAAATCG
1 CAATCAAAATCG
*
5490470 CAATCAAAATCC
1 CAATCAAAATCG
*
5490482 CAATCACAATCG
1 CAATCAAAATCG
5490494 GCTTCACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.47, C:0.31, G:0.06, T:0.17
Consensus pattern (12 bp):
CAATCAAAATCG
Found at i:5490804 original size:140 final size:140
Alignment explanation
Indices: 5490547--5490812 Score: 478
Period size: 140 Copynumber: 1.9 Consensus size: 140
5490537 AAACGTTGTA
*
5490547 TTATGTGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGCTTGAACATTGCTA
1 TTATGGGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGCTTGAACATTGCTA
* *
5490612 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGTAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
5490677 TATGTGTATT
131 TATGTGTATT
* * *
5490687 TTATGGGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGTTA
1 TTATGGGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGCTTGAACATTGCTA
5490752 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
5490813 TTATCGCAAC
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 120 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGGGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGCTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:5490812 original size:20 final size:20
Alignment explanation
Indices: 5490787--5491005 Score: 141
Period size: 20 Copynumber: 11.8 Consensus size: 20
5490777 TTACACATTC
*
5490787 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
5490807 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
5490826 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
5490841 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
5490861 ATATGACTATCACAACGC-A
1 ATTTGACTATCGCAACGCGA
*
5490880 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
5490895 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
*
5490915 A----A--ATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
5490929 ATTTGACTATCACAATGCGA
1 ATTTGACTATCGCAACGCGA
* * *
5490949 ATTTGAGTATCACAACGCAA
1 ATTTGACTATCGCAACGCGA
* * *
5490969 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
*
5490989 ACTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
5491006 AGAAAATCGC
Statistics
Matches: 154, Mismatches: 27, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
14 30 0.19
15 6 0.04
16 1 0.01
18 1 0.01
19 6 0.04
20 110 0.71
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:5490882 original size:54 final size:54
Alignment explanation
Indices: 5490787--5490910 Score: 194
Period size: 54 Copynumber: 2.3 Consensus size: 54
5490777 TTACACATTC
* * * * * *
5490787 ATTTGAATATCGCAACGCGAATTTGATTATCGCAACTCAAAAATCGCAACGCGA
1 ATTTGACTATCGCAACACGAATATGACTATCACAACGCAAAAATCGCAACGCGA
5490841 ATTTGACTATCGCAACACGAATATGACTATCACAACGCAAAAATCGCAACGCGA
1 ATTTGACTATCGCAACACGAATATGACTATCACAACGCAAAAATCGCAACGCGA
5490895 ATTTGACTATCGCAAC
1 ATTTGACTATCGCAAC
5490911 GAGAAAATCG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (54 bp):
ATTTGACTATCGCAACACGAATATGACTATCACAACGCAAAAATCGCAACGCGA
Found at i:5490887 original size:34 final size:34
Alignment explanation
Indices: 5490849--5490943 Score: 138
Period size: 34 Copynumber: 2.8 Consensus size: 34
5490839 GAATTTGACT
* *
5490849 ATCGCAACACGAATATGACTATCACAACGCA-AAA
1 ATCGCAACGCGAATTTGACTATCACAACG-AGAAA
*
5490883 ATCGCAACGCGAATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCGAATTTGACTATCACAACGAGAAA
*
5490917 ATCGCAACGTGAATTTGACTATCACAA
1 ATCGCAACGCGAATTTGACTATCACAA
5490944 TGCGAATTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 1 0.02
34 54 0.98
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCACAACGAGAAA
Found at i:5491054 original size:19 final size:20
Alignment explanation
Indices: 5491011--5491054 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5491001 CAACGAGAAA
*
5491011 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
5491031 ATCGCAATGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
5491050 TTCGC
1 ATCGC
5491055 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:5491073 original size:20 final size:20
Alignment explanation
Indices: 5491044--5491101 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
5491034 GCAATGCGAA
5491044 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
5491064 TTGTCTTTCGCATTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
5491084 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
5491102 AAGTGTACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:5493236 original size:20 final size:20
Alignment explanation
Indices: 5493213--5493256 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5493203 CTTAAAATCA
*
5493213 CAACGCGAAAATGATTATCG
1 CAACGCGAAAATGACTATCG
*
5493233 CAACGGGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
5493253 CAAC
1 CAAC
5493257 TAGAGAATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:5495309 original size:20 final size:19
Alignment explanation
Indices: 5495261--5495328 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
5495251 TTCTGAAACT
5495261 TAAAATCGCAACACGAAAA
1 TAAAATCGCAACACGAAAA
5495280 TAAAATCGCAACACGAAAA
1 TAAAATCGCAACACGAAAA
** * *
5495299 TGACTATCGCAACGCGAAAC
1 T-AAAATCGCAACACGAAAA
5495319 TAAAATCGCA
1 TAAAATCGCA
5495329 TTCCGATTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 27 0.64
20 15 0.36
ACGTcount: A:0.50, C:0.24, G:0.13, T:0.13
Consensus pattern (19 bp):
TAAAATCGCAACACGAAAA
Found at i:5495742 original size:22 final size:22
Alignment explanation
Indices: 5495703--5495766 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
5495693 TCTGATAGAT
5495703 GGAGATA--GACGGATTTCGCC
1 GGAGATAGGGACGGATTTCGCC
* *
5495723 GGAGATAGGGACTGATTTCGTC
1 GGAGATAGGGACGGATTTCGCC
* *
5495745 GGAGATGGGGACGGATGTCGCC
1 GGAGATAGGGACGGATTTCGCC
5495767 TTAGAGAGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 7 0.19
22 29 0.81
ACGTcount: A:0.22, C:0.17, G:0.41, T:0.20
Consensus pattern (22 bp):
GGAGATAGGGACGGATTTCGCC
Found at i:5495961 original size:20 final size:20
Alignment explanation
Indices: 5495931--5496009 Score: 95
Period size: 20 Copynumber: 4.0 Consensus size: 20
5495921 GCGCTTTGAA
* *
5495931 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGACAGTCAG
*
5495951 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGACAGTCAG
* * *
5495971 AATCTCTTTGTGACAGTCAG
1 AATCGCGTTGCGACAGTCAG
*
5495991 AATCGCGTTGCGATAGTCA
1 AATCGCGTTGCGACAGTCA
5496010 TACTCACATT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (20 bp):
AATCGCGTTGCGACAGTCAG
Found at i:5496190 original size:21 final size:21
Alignment explanation
Indices: 5496164--5496211 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
5496154 TCATTTTGGC
5496164 AAATCAAAAAAATATTAATTA
1 AAATCAAAAAAATATTAATTA
5496185 AAATCAAAAAAATATTAATTA
1 AAATCAAAAAAATATTAATTA
5496206 AAATCA
1 AAATCA
5496212 TATATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATCAAAAAAATATTAATTA
Found at i:5500002 original size:31 final size:31
Alignment explanation
Indices: 5499953--5500028 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
5499943 GAGGTTTCGG
5499953 GTCGAGTCGAGCTCCATTTCAGAGTTTTTTA
1 GTCGAGTCGAGCTCCATTTCAGAGTTTTTTA
* * * *
5499984 GTCGGGTCGAGTTTCATTTCAGATTTTTTTA
1 GTCGAGTCGAGCTCCATTTCAGAGTTTTTTA
5500015 GTCGAGTCGAGCTC
1 GTCGAGTCGAGCTC
5500029 AGCAATACTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.39
Consensus pattern (31 bp):
GTCGAGTCGAGCTCCATTTCAGAGTTTTTTA
Found at i:5501263 original size:16 final size:18
Alignment explanation
Indices: 5501239--5501286 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
5501229 AATAAGAAAT
5501239 TTATTTTTATATTAG-TA
1 TTATTTTTATATTAGTTA
*
5501256 TT-TTTTTA-AATAGTTA
1 TTATTTTTATATTAGTTA
5501272 TTATATTTTATATTA
1 TTAT-TTTTATATTA
5501287 ATATATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.16
16 10 0.40
17 3 0.12
18 5 0.20
19 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
TTATTTTTATATTAGTTA
Found at i:5501293 original size:15 final size:15
Alignment explanation
Indices: 5501273--5501344 Score: 67
Period size: 15 Copynumber: 4.7 Consensus size: 15
5501263 AAATAGTTAT
5501273 TATATTTTATATTAA
1 TATATTTTATATTAA
*
5501288 TATA-TTTATATAAA
1 TATATTTTATATTAA
*
5501302 TATATTTTTTATTAA
1 TATATTTTATATTAA
*
5501317 AATAATATTTATA-TAA
1 TAT-AT-TTTATATTAA
5501333 TTATTATTTTAT
1 -TA-TATTTTAT
5501345 TTAGAATTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 13 0.28
15 14 0.30
16 10 0.22
17 8 0.17
18 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTTTATATTAA
Found at i:5501297 original size:14 final size:14
Alignment explanation
Indices: 5501270--5501308 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5501260 TTTAAATAGT
5501270 TATT-ATAT-TTTA
1 TATTAATATATTTA
5501282 TATTAATATATTTA
1 TATTAATATATTTA
*
5501296 TATAAATATATTT
1 TATTAATATATTT
5501309 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 4 0.17
13 4 0.17
14 16 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTAATATATTTA
Found at i:5501330 original size:32 final size:28
Alignment explanation
Indices: 5501273--5501345 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 28
5501263 AAATAGTTAT
*
5501273 TATATTTTATATTAATATATTTATATAAA
1 TATATTTTTTATTAATATATTTATAT-AA
5501302 TATATTTTTTATTAAAATAATATTTATATAA
1 TATATTTTTTATT--AAT-ATATTTATATAA
5501333 T-TATTATTTTATT
1 TATATT-TTTTATT
5501346 TAGAATTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 12 0.31
30 4 0.10
31 13 0.33
32 10 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TATATTTTTTATTAATATATTTATATAA
Found at i:5503172 original size:21 final size:21
Alignment explanation
Indices: 5503121--5503172 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5503111 TATGCCATCT
*
5503121 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
5503142 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
5503163 CCGCAGGGTT
1 CCGCAGGGTT
5503173 TTATACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:5503746 original size:34 final size:34
Alignment explanation
Indices: 5503695--5503792 Score: 126
Period size: 34 Copynumber: 2.9 Consensus size: 34
5503685 AAATGTTTTT
5503695 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATACAAATTATATTATTCGAAATTTAAAATA
* * * *
5503729 AAAATA-AAAATAGTATTATTCAAAATTTAAATTT
1 AAAATACAAATTA-TATTATTCGAAATTTAAAATA
* *
5503763 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATACAAATTATATTATTCGAAATTTAA
5503793 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.09
34 45 0.82
35 5 0.09
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAATACAAATTATATTATTCGAAATTTAAAATA
Found at i:5504424 original size:128 final size:128
Alignment explanation
Indices: 5504196--5505310 Score: 1842
Period size: 128 Copynumber: 8.7 Consensus size: 128
5504186 ACAATCCATC
*
5504196 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTCACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
5504261 GGAAGGCGCCCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* *
5504324 TAGTGTTCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
5504389 GGAAGGCGCTCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATAAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* * *
5504452 TAGTGTCCCCAAAGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCGGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
5504517 GAAAGGAGCGCCCCCGGGAACGCGCATTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
5504580 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
5504645 GGAAGGCGCGCCCCCAGGAATGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* * *
5504708 TAGTTTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
** * *
5504773 GGAATTCGCGCCCCCGGGAACGCGCCTTCAAGTACCCTGAGAAATAATATGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* *
5504836 TAGTGTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAATATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * *
5504901 AGAAGGCGCGCCCCCAGGAACGTGCCTTCAAGTCCCCTGAGAAATAATAGTTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* * *
5504964 TAGTATCCCCGAGGGACATGAGTGACATAATTGGGCAATGATAACATA-T-TCTG--AACATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
5505025 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* *
5505088 TAGTTTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * *
5505153 GGAAGGCGCACCCTCGGGAACACGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATAAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
5505216 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
5505281 GGAAGGCGCGCCCCCTGGAACGCTCCTTCA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
5505311 TGTGAATAGT
Statistics
Matches: 913, Mismatches: 70, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
124 111 0.12
125 1 0.00
126 8 0.01
127 1 0.00
128 792 0.87
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:5505404 original size:8 final size:8
Alignment explanation
Indices: 5505391--5505431 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
5505381 TCACAAGCTT
5505391 TCAAATTC
1 TCAAATTC
5505399 TCAAATTC
1 TCAAATTC
* *
5505407 ACAAACTC
1 TCAAATTC
5505415 T-AAATTC
1 TCAAATTC
5505422 TCAAATTC
1 TCAAATTC
5505430 TC
1 TC
5505432 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:5511732 original size:20 final size:22
Alignment explanation
Indices: 5511699--5511738 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
5511689 ATTAAAGAAA
5511699 TGACACCACTTTTAAAAAATTT
1 TGACACCACTTTTAAAAAATTT
5511721 TGACACC-C-TTTAAAAAAT
1 TGACACCACTTTTAAAAAAT
5511739 GATCTCACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (22 bp):
TGACACCACTTTTAAAAAATTT
Found at i:5512229 original size:22 final size:21
Alignment explanation
Indices: 5512195--5512238 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
5512185 CGTTTATTTA
*
5512195 TGTTCATTTACGTTCATTTGTG
1 TGTTCATTAACGTTCA-TTGTG
*
5512217 TGTTCGTTAACGTTCATTGTG
1 TGTTCATTAACGTTCATTGTG
5512238 T
1 T
5512239 TCGTTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (21 bp):
TGTTCATTAACGTTCATTGTG
Found at i:5512454 original size:2 final size:2
Alignment explanation
Indices: 5512447--5512509 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
5512437 ATAATTCTTC
5512447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5512489 AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
5512510 GAATGATTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5513216 original size:2 final size:2
Alignment explanation
Indices: 5513209--5513263 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
5513199 AATTAATGTT
5513209 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
5513251 GA TA GA TA TA TA T
1 TA TA TA TA TA TA T
5513264 TGGGTACGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5524773 original size:185 final size:186
Alignment explanation
Indices: 5524461--5524851 Score: 624
Period size: 185 Copynumber: 2.1 Consensus size: 186
5524451 TTTTCTAATT
* * *
5524461 TATATAA-AAATTAAATATTTTATAATTAAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATA
*
5524525 ATTATAAAATATAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATATAAAATTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* * * *
5524590 TTAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCGTATGTTA
131 TTAGATCTTAAATTATTAATTGAATTTTAAATGGTATGGGCTGAACCCATATGTTA
* * * * *
5524646 TATATAATATATTTAATATTTTTTAATTCAGAAAAATATTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATA
*
5524711 ATTATAAAATA-AAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATATAAAATTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* *
5524775 TTGGATCTTAAATTATTAATTGAATTTTAAATGGTATGGGCTGAACTCATATGTTA
131 TTAGATCTTAAATTATTAATTGAATTTTAAATGGTATGGGCTGAACCCATATGTTA
5524831 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
5524852 AAAATTTTAT
Statistics
Matches: 189, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
185 129 0.68
186 60 0.32
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTATAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATATAAAATTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTAGATCTTAAATTATTAATTGAATTTTAAATGGTATGGGCTGAACCCATATGTTA
Found at i:5526117 original size:15 final size:14
Alignment explanation
Indices: 5526094--5526141 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
5526084 AAATTGAAAG
5526094 TTAGAGTAATTAAA
1 TTAGAGTAATTAAA
5526108 TTAGGAGTAATTTGAAA
1 TTA-GAGTAA-TT-AAA
5526125 GTTA-AGTAATTAAA
1 -TTAGAGTAATTAAA
5526139 TTA
1 TTA
5526142 AAAAAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.10
14 6 0.20
15 8 0.27
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.38
Consensus pattern (14 bp):
TTAGAGTAATTAAA
Found at i:5526134 original size:16 final size:17
Alignment explanation
Indices: 5526087--5526135 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
5526077 AATAAAAAAA
5526087 TTGAAAGTTAGAGTAA-
1 TTGAAAGTTAGAGTAAT
5526103 TT-AAA-TTAGGAGTAAT
1 TTGAAAGTTA-GAGTAAT
5526119 TTGAAAGTTA-AGTAAT
1 TTGAAAGTTAGAGTAAT
5526135 T
1 T
5526136 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.10
15 9 0.31
16 11 0.38
17 3 0.10
18 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (17 bp):
TTGAAAGTTAGAGTAAT
Found at i:5526846 original size:2 final size:2
Alignment explanation
Indices: 5526833--5526867 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5526823 GATTACAAAT
*
5526833 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5526868 TTGTTGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5528882 original size:31 final size:30
Alignment explanation
Indices: 5528858--5528919 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
5528848 TAAAAAGAGT
5528858 AAATCTTTATTTAAACATACTTAAAAACATC
1 AAATCTTTATTTAAACATA-TTAAAAACATC
*
5528889 AAATCTTTATTTGAACATATTAAAAAACATC
1 AAATCTTTATTTAAACATATT-AAAAACATC
5528920 GCATCCTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (30 bp):
AAATCTTTATTTAAACATATTAAAAACATC
Found at i:5528930 original size:31 final size:31
Alignment explanation
Indices: 5528858--5528930 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
5528848 TAAAAAGAGT
*
5528858 AAATCTTTATTTAAACATACTTAAAAACATC
1 AAATCCTTATTTAAACATACTTAAAAACATC
* *
5528889 AAATCTTTATTTGAACATA-TTAAAAAACATC
1 AAATCCTTATTTAAACATACTT-AAAAACATC
**
5528920 GCATCCTTATT
1 AAATCCTTATT
5528931 CAATTCGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 2 0.05
31 35 0.95
ACGTcount: A:0.44, C:0.16, G:0.03, T:0.37
Consensus pattern (31 bp):
AAATCCTTATTTAAACATACTTAAAAACATC
Found at i:5536823 original size:61 final size:62
Alignment explanation
Indices: 5536747--5536912 Score: 185
Period size: 61 Copynumber: 2.7 Consensus size: 62
5536737 GAAGCGTAGA
* * * ** *
5536747 AGCCACCTGAGGGGAGTGCTCGCA-GGTTTATAAGGACTTACCACAATGCACAAAGCAAATG
1 AGCCACCTTATGGGAGTGCTCACAGGGTCCATAAGGACTTACCACAATGCACAAAGCAAAGG
* ** *
5536808 AGCCACCTTATGGGAGTG-TCATAGGGTCCATAAGTTCTTACCACAATGCACAAAGTAAAGG
1 AGCCACCTTATGGGAGTGCTCACAGGGTCCATAAGGACTTACCACAATGCACAAAGCAAAGG
* * * *
5536869 TGCCACCCTATGGGAGTGC-CACAGGGTCAATAAGGTCTTACCAC
1 AGCCACCTTATGGGAGTGCTCACAGGGTCCATAAGGACTTACCAC
5536913 TAGGCTCATT
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
60 3 0.03
61 85 0.97
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (62 bp):
AGCCACCTTATGGGAGTGCTCACAGGGTCCATAAGGACTTACCACAATGCACAAAGCAAAGG
Found at i:5539010 original size:21 final size:21
Alignment explanation
Indices: 5538984--5539025 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5538974 CCAGAATAGG
* *
5538984 GGGAATTGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5539005 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5539026 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:5539232 original size:29 final size:31
Alignment explanation
Indices: 5539200--5539259 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
5539190 AAATTTTGAA
*
5539200 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5539229 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5539260 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:5540114 original size:24 final size:24
Alignment explanation
Indices: 5540066--5540137 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
5540056 ATCGTATTTA
*
5540066 AAATATA-AAAAAACATCAAGTAAAC
1 AAATATATAAATAA-ATCAA-TAAAC
*
5540091 AAACT-TGTAAATAAATCAATAAAC
1 AAA-TATATAAATAAATCAATAAAC
*
5540115 AAATATATATATAAATCAATAAA
1 AAATATATAAATAAATCAATAAA
5540138 TGAATTTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 1 0.03
24 24 0.60
25 9 0.22
26 6 0.15
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.24
Consensus pattern (24 bp):
AAATATATAAATAAATCAATAAAC
Found at i:5566370 original size:19 final size:19
Alignment explanation
Indices: 5566346--5566401 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
5566336 ATGACCAACA
5566346 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
* * *
5566365 AAATCGTAATACGATATCT
1 AAATCGCAATGCGATCTCT
5566384 AAATCGCAATGCGATCTC
1 AAATCGCAATGCGATCTC
5566402 CAGTATCGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:5566450 original size:20 final size:20
Alignment explanation
Indices: 5566427--5566498 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
5566417 GTTTCCAGAT
*
5566427 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
5566447 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
* *
5566467 TCGCAACGCGATTCTAACTA
1 TCGCAACGCGATTATGACTA
*
5566487 TCACAACGCGAT
1 TCGCAACGCGAT
5566499 AATACAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:5566697 original size:22 final size:22
Alignment explanation
Indices: 5566672--5566722 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
5566662 ACATCCATCC
5566672 CCATCTCCAACGAAATCCGTCT
1 CCATCTCCAACGAAATCCGTCT
* *
5566694 CCATCTCCGACGAAATTCGTCT
1 CCATCTCCAACGAAATCCGTCT
5566716 --ATCTCCA
1 CCATCTCCA
5566723 TCTCTTAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.23
22 20 0.77
ACGTcount: A:0.25, C:0.39, G:0.10, T:0.25
Consensus pattern (22 bp):
CCATCTCCAACGAAATCCGTCT
Found at i:5568073 original size:20 final size:20
Alignment explanation
Indices: 5568026--5568073 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
5568016 GAAATTCAGT
* *
5568026 GTTGCGACAGTTAGAATCGC
1 GTTGCGATAGTCAGAATCGC
5568046 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
5568066 GTTGCGAT
1 GTTGCGAT
5568074 TATGTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:5568087 original size:21 final size:21
Alignment explanation
Indices: 5568061--5568136 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
5568051 GATAGTCAGA
5568061 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
* *
5568082 ATCGCGTTGCAATTATATATT
1 ATCGCGTTGCGATTATGTATT
5568103 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
5568124 ATTACGTTGCGAT
1 ATCGCGTTGCGAT
5568137 AGTCAAAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.42
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:5568534 original size:25 final size:24
Alignment explanation
Indices: 5568499--5568548 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
5568489 TAGTCTACCC
* *
5568499 TCTCCCTTCTTCCTATACATACTCA
1 TCTCCCATCTTCCTATAAATA-TCA
*
5568524 TCTCCCATCTTCTTATAAATATCA
1 TCTCCCATCTTCCTATAAATATCA
5568548 T
1 T
5568549 ACCCAAACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.42
Consensus pattern (24 bp):
TCTCCCATCTTCCTATAAATATCA
Found at i:5571605 original size:37 final size:38
Alignment explanation
Indices: 5571525--5571605 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
5571515 TAAAAGTTGG
* *
5571525 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTAAAAATCAT
*
5571564 -AAAATTTATATATATTT-TTTACAAAATTAAAAAT-AT
1 AAAAATTTATATAT-TTTCTTTAAAAAATTAAAAATCAT
5571600 AAAAAT
1 AAAAAT
5571606 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 2 0.05
37 29 0.78
38 6 0.16
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATTAAAAATCAT
Found at i:5571933 original size:655 final size:653
Alignment explanation
Indices: 5570681--5571934 Score: 1878
Period size: 655 Copynumber: 1.9 Consensus size: 653
5570671 TGGTTCACGG
* * *
5570681 AATGTAAGATTACAAGTGGGAATGTAAGATTACCAGAGAATAGGATTACTGTGAATGTTGTATTT
1 AATGTAAAATTACAAGTGAGAATGTAAGATTACCAGAGAATAGGATTACTGGGAATGTTGTATTT
* *
5570746 TGTGTTTGGTTGGCTTAGCAGGAATGTAAAATTACTGTGTTTGGTTAAAGGAATAAAAGATTATT
66 TGTGTTTGGTTAGCTTAGCAGGAATGTAAAATTACCGTGTTTGGTTAAAGGAATAAAAGATTATT
* *
5570811 GGAATGTATATTTGACCAAATTGTCTTTATTATATATTTGTATAATATTACAAGTTGGAAAATAT
131 GGAATGTATATTTGACCAAATTGTCTTTATTACATATTTGTATAATATTAAAAGTTGGAAAATAT
* *
5570876 TTATATATTTTCTTTAAAAAAATTAAATTTATAATATTTATATATTTTTTACAAAAATAAAAATA
196 TTATATATTTTCTTTAAAAAAATTAAATTCATAAAATTTATATATTTTTTACAAAAATAAAAATA
*
5570941 AAAAAAGTTTAATGAAAGGGTAAAATTTTATTTTAACCCTTGAACTTCATATAAAATTTTAATTA
261 AAAAAAGTTTAATGAAAGAGTAAAATTTTATTTTAACCCTTGAACTTCATATAAAATTTTAATTA
* * *
5571006 TAGATTTTTTGTAAATCTAAAATAATTTAAAGATAAATTTGTAATTTAACATTCGTATAATTTTT
326 TAGATTTTTTGTAAATCTAAAATAATTTAAAGATAAATTTATAATTCAACATTCGTAGAATTTTT
*
5571071 ATTATTCAATGACAGAAGAAATATATTTTTGAAAAAAAATAAAAATTTAAGGACATTTTAGTCCA
391 ATTATTCAATGACAAAAGAAATATATTTTTG----AAAATAAAAATTTAAGGACATTTTAGTCCA
* * **
5571136 AAATGTCGGTAATCCAACAATACCTAAGGAAATGGAGGTAATGACATTCCCGGTAATATATCCCA
452 AAATGTCGGTAATCCAACAATACCTAAAGAAATAGAGGTAATGACATTCCCAATAATATATCCCA
* * * * * **
5571201 AAAAATCCACTATTGGTAATCTTACATTACAGGGAATAGGATTCCCGAGCTAACCAAACGGGGGA
517 AAAAATCCACTATTAGTAATATAAAATTACAGGAAATAGGATTCCCGAGCTAACCAAACGGAAGA
* *
5571266 ATGTGGATTCCATTCCGATGGGAATCCCACATTCCCCCATCCAAACACCCTAAGAGTGCGTTTGG
582 ATATGAATTCCATTCCGATGGGAATCCCACATTCCCCCATCCAAACACCCTAAGAGTGCGTTTGG
5571331 TTTACAT
647 TTTACAT
* * *
5571338 AATGTAAAATTACCAGTGAGAATGTAAGATTACCAGGGAATATGATTACTGGGAATGTTGTATTT
1 AATGTAAAATTACAAGTGAGAATGTAAGATTACCAGAGAATAGGATTACTGGGAATGTTGTATTT
* * *
5571403 TGTGTTTGGTTAGTTTAGCAGGAATGTAAGATTACCGTGTTTGGTTAAATGAATAAAAGATTATT
66 TGTGTTTGGTTAGCTTAGCAGGAATGTAAAATTACCGTGTTTGGTTAAAGGAATAAAAGATTATT
*
5571468 -TAATGTATATTTGACCAAATTGTCTTTATTACATATTTGTATAATATTAAAAGTTGGAAAATAT
131 GGAATGTATATTTGACCAAATTGTCTTTATTACATATTTGTATAATATTAAAAGTTGGAAAATAT
* *
5571532 TTATATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATATATATTTTTTACAAAATTAAAAA
196 TTATATATTTTCTTTAAAAAAATTAAATTCATAAAA-TT-TATATATTTTTTACAAAAATAAAAA
* *
5571597 TATAAAAATGTTTAATGAAAGAGTAAAATTTTATTTTAA-CCTCTGAACTTCATATAACATTTTA
259 TA-AAAAAAGTTTAATGAAAGAGTAAAATTTTATTTTAACCCT-TGAACTTCATATAAAATTTTA
* * *
5571661 ATTATA-ATTTTCTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTATAATTCAACATTTGTAG
322 ATTATAGA--TT-TTTTGTAAATCTAAAATAATTTAAAGATAAATTTATAATTCAACATTCGTAG
* *
5571725 AATTTTTATTATTTAATGACAAAAG-AATGATATTTTTG-AAA-AAAAATTTAA-GAGTATTTTA
384 AATTTTTATTATTCAATGACAAAAGAAAT-ATATTTTTGAAAATAAAAATTTAAGGA-CATTTTA
* *
5571786 GTCCAAAATGTCGGTAATCTAATAATACCTAAAGAAATAGAGGTAATGACATTCCCAATAATATA
447 GTCCAAAATGTCGGTAATCCAACAATACCTAAAGAAATAGAGGTAATGACATTCCCAATAATATA
* * *
5571851 TCCCAAAAAATTCACTATTAGTAATATAAAATTATC-GGAAAT-GAGATTCTCGTGCTAACCAAA
512 TCCCAAAAAATCCACTATTAGTAATATAAAATTA-CAGGAAATAG-GATTCCCGAGCTAACCAAA
5571914 CGGAAGAATATGAATTCCATT
575 CGGAAGAATATGAATTCCATT
5571935 TTCATATAAA
Statistics
Matches: 538, Mismatches: 48, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
654 3 0.01
655 143 0.27
656 98 0.18
657 121 0.22
658 30 0.06
659 60 0.11
660 5 0.01
661 78 0.14
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (653 bp):
AATGTAAAATTACAAGTGAGAATGTAAGATTACCAGAGAATAGGATTACTGGGAATGTTGTATTT
TGTGTTTGGTTAGCTTAGCAGGAATGTAAAATTACCGTGTTTGGTTAAAGGAATAAAAGATTATT
GGAATGTATATTTGACCAAATTGTCTTTATTACATATTTGTATAATATTAAAAGTTGGAAAATAT
TTATATATTTTCTTTAAAAAAATTAAATTCATAAAATTTATATATTTTTTACAAAAATAAAAATA
AAAAAAGTTTAATGAAAGAGTAAAATTTTATTTTAACCCTTGAACTTCATATAAAATTTTAATTA
TAGATTTTTTGTAAATCTAAAATAATTTAAAGATAAATTTATAATTCAACATTCGTAGAATTTTT
ATTATTCAATGACAAAAGAAATATATTTTTGAAAATAAAAATTTAAGGACATTTTAGTCCAAAAT
GTCGGTAATCCAACAATACCTAAAGAAATAGAGGTAATGACATTCCCAATAATATATCCCAAAAA
ATCCACTATTAGTAATATAAAATTACAGGAAATAGGATTCCCGAGCTAACCAAACGGAAGAATAT
GAATTCCATTCCGATGGGAATCCCACATTCCCCCATCCAAACACCCTAAGAGTGCGTTTGGTTTA
CAT
Found at i:5576446 original size:21 final size:20
Alignment explanation
Indices: 5576420--5576517 Score: 90
Period size: 21 Copynumber: 4.8 Consensus size: 20
5576410 ATCAGTTTCC
5576420 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
5576441 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
5576460 ACAAATTCGCATTGCGATTTTAG
1 A-AAA-TCGCAACGCGATTTT-G
* *
5576483 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
5576503 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
5576518 ACACATAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 38 0.60
22 3 0.05
23 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:5576507 original size:20 final size:20
Alignment explanation
Indices: 5576420--5576555 Score: 80
Period size: 20 Copynumber: 6.7 Consensus size: 20
5576410 ATCAGTTTCC
* *
5576420 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAAT-ATG
*
5576441 AAAATCGCAATGCG-ATA-G
1 AAAATCGCAACGCGAATATG
** * *
5576459 TACAAATTCGCATTGCGATTTTAG
1 -A-AAA-TCGCAACGCGAATAT-G
5576483 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATATG
* *
5576503 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATG
* **
5576522 ATAAATCGCAACGCGTATCCG
1 A-AAATCGCAACGCGAATATG
*
5576543 TAAATCGCAACGC
1 AAAATCGCAACGC
5576556 ATATGGGTAA
Statistics
Matches: 90, Mismatches: 17, Indels: 17
0.73 0.14 0.14
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 48 0.53
21 33 0.37
22 4 0.04
23 1 0.01
24 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:5576565 original size:20 final size:20
Alignment explanation
Indices: 5576484--5576713 Score: 196
Period size: 20 Copynumber: 11.5 Consensus size: 20
5576474 CGATTTTAGA
* ** *
5576484 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
5576504 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
5576524 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* **
5576544 AAATCGCAACGCATATGGGT
1 AAATCGCAACGCGTATCCGT
*
5576564 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5576584 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
5576604 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
5576624 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * * *
5576644 AAATCACAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
5576664 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
5576684 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
5576704 AAATCACAAC
1 AAATCGCAAC
5576714 ACTGAAATTT
Statistics
Matches: 169, Mismatches: 35, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
19 1 0.01
20 166 0.98
21 2 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:5576567 original size:40 final size:40
Alignment explanation
Indices: 5576484--5576713 Score: 241
Period size: 40 Copynumber: 5.8 Consensus size: 40
5576474 CGATTTTAGA
* * * ** *
5576484 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATC-CGT
* * * **
5576524 AAATCGCAACGCGTATCCGTAAATCGCAACGCAT-ATGGGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGT
* * * * * *
5576564 AAATCGCAATGCGTATCCGTATATCGCAACGCGT-ATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGT
5576604 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
*
5576644 AAATCACAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
*
5576684 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCTGTAAATCGCAAC
5576714 ACTGAAATTT
Statistics
Matches: 164, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 163 0.99
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
Found at i:5577413 original size:24 final size:24
Alignment explanation
Indices: 5577374--5577420 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5577364 AAATTTGGTC
5577374 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
5577398 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
5577421 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:5577612 original size:12 final size:12
Alignment explanation
Indices: 5577595--5577619 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5577585 ATATAATCCT
5577595 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5577607 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5577619 G
1 G
5577620 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:5579995 original size:19 final size:19
Alignment explanation
Indices: 5579955--5580052 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
5579945 GATTCTCTCG
5579955 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
5579975 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5579994 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5580008 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5580027 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5580046 TTGCGAT
1 TTGCGAT
5580053 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5580049 original size:52 final size:53
Alignment explanation
Indices: 5579936--5580052 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
5579926 GAAATGAAAA
5579936 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
5579989 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
5580041 TCGCATTGCGAT
1 TCGCATTGCGAT
5580053 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:5580178 original size:14 final size:14
Alignment explanation
Indices: 5580159--5580195 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5580149 CATCAATTAC
5580159 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5580173 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5580187 ACAAATCAA
1 ACAAATCAA
5580196 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5581712 original size:21 final size:21
Alignment explanation
Indices: 5581673--5581713 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5581663 ACTCTCGAGG
* *
5581673 AATGATAGGGGGGGCCTCTTC
1 AATGATAGGAGGGGACTCTTC
*
5581694 AATGATAGGAGTGGACTCTT
1 AATGATAGGAGGGGACTCTT
5581714 GAGGGATGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (21 bp):
AATGATAGGAGGGGACTCTTC
Found at i:5582197 original size:14 final size:14
Alignment explanation
Indices: 5582178--5582234 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5582168 GCGAAATGAA
*
5582178 AATCGCAACGACAG
1 AATCGCAACGAAAG
5582192 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5582209 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5582225 AATCGCAACG
1 AATCGCAACG
5582235 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:5582205 original size:33 final size:33
Alignment explanation
Indices: 5582159--5582251 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
5582149 GCGAAACCAA
*
5582159 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5582192 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5582225 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5582252 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5582216 original size:19 final size:19
Alignment explanation
Indices: 5582122--5582256 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
5582112 TAGTTTACTT
* *
5582122 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
5582142 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
5582161 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5582180 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5582194 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5582213 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5582227 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5582246 TCGCAATGCGA
1 TCGCAACGCGA
5582257 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5582274 original size:19 final size:19
Alignment explanation
Indices: 5582252--5582399 Score: 145
Period size: 19 Copynumber: 8.3 Consensus size: 19
5582242 AAAATCGCAA
5582252 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5582271 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
5582285 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5582304 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
5582318 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
**
5582337 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5582356 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5582375 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5582395 TGCGA
1 TGCGA
5582400 AAGTAAACTA
Statistics
Matches: 109, Mismatches: 9, Indels: 21
0.78 0.06 0.15
Matches are distributed among these distances:
14 22 0.20
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 67 0.61
20 13 0.12
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:5582294 original size:33 final size:33
Alignment explanation
Indices: 5582252--5582380 Score: 163
Period size: 33 Copynumber: 3.8 Consensus size: 33
5582242 AAAATCGCAA
5582252 TGCGATTTTGGTTTCGCGTTGCGATCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATCTTGTCGT
5582285 TGCGATTTTGGTTTCGCGTTGCGAT-TCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATCT-TGTCGT
**
5582318 TGCGATTTTCATTTCGCGTTGCGATTTTCATT-TCGCGT
1 TGCGATTTTGGTTTCGCGTTGCGA---TC-TTGT--CGT
5582356 TGCGATTTTGGTTTCGCGTTGCGAT
1 TGCGATTTTGGTTTCGCGTTGCGAT
5582381 TTTAAGTTTC
Statistics
Matches: 84, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
32 1 0.01
33 53 0.63
35 1 0.01
36 2 0.02
37 1 0.01
38 26 0.31
ACGTcount: A:0.08, C:0.19, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATCTTGTCGT
Found at i:5582701 original size:93 final size:93
Alignment explanation
Indices: 5582443--5582915 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
5582433 TTGAATGGAT
5582443 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5582508 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
5582536 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5582600 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5582628 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5582693 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5582721 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5582786 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5582814 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5582879 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5582907 AAATTTACT
1 AAATTTACT
5582916 AAGCAATCTA
Statistics
Matches: 376, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 91 0.24
93 285 0.76
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5584613 original size:14 final size:14
Alignment explanation
Indices: 5584594--5584683 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
5584584 TTGAAATGAA
5584594 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5584608 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
5584625 ACAATCGCAACAAGAG
1 --AATCGCAACGAGAG
*
5584641 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
5584660 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5584674 AATCGCAACG
1 AATCGCAACG
5584684 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 1 0.02
16 7 0.11
17 7 0.11
18 1 0.02
19 18 0.29
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5584631 original size:33 final size:33
Alignment explanation
Indices: 5584586--5584700 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
5584576 TCTTTTGGTT
5584586 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
5584619 GAGATGACAATCGCAACAAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
5584652 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5584685 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
5584701 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5584632 original size:19 final size:19
Alignment explanation
Indices: 5584608--5584705 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
5584598 GCAACGAGAG
*
5584608 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAC
*
5584627 AATCGCAA--C--AA-GAG
1 AATCGCAACGCGAAATGAC
5584641 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAC
*
5584660 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAC
*
5584674 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAC
*
5584693 AATCGCAATGCGA
1 AATCGCAACGCGA
5584706 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 3 0.05
19 32 0.51
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:5584736 original size:14 final size:14
Alignment explanation
Indices: 5584717--5584773 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5584707 TTTGGTTTCG
5584717 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5584731 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5584750 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5584764 CGTTGCGATT
1 CGTTGCGATT
5584774 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5584749 original size:33 final size:33
Alignment explanation
Indices: 5584701--5584781 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
5584691 AAAATCGCAA
**
5584701 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5584734 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
5584767 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
5584782 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:5584784 original size:21 final size:21
Alignment explanation
Indices: 5584758--5584833 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
5584748 CGCGTTGCGA
5584758 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
5584779 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
5584799 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
5584820 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
5584834 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:5584814 original size:41 final size:41
Alignment explanation
Indices: 5584757--5584834 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
5584747 TCGCGTTGCG
*
5584757 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
5584798 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
5584835 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:5584960 original size:33 final size:33
Alignment explanation
Indices: 5584913--5584983 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
5584903 AATACTAACT
* *
5584913 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* * *
5584946 TGAAAATCGCAACGACAGAATCGTAACGTGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
5584979 TGAAA
1 TGAAA
5584984 TCTAAGTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.15, G:0.24, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:5585217 original size:22 final size:22
Alignment explanation
Indices: 5585165--5585219 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5585155 TGGTTGTGAG
**
5585165 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
5585187 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
5585209 GGATTTCTTCG
1 GGATTTCTTCG
5585220 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:5585385 original size:39 final size:40
Alignment explanation
Indices: 5585342--5585423 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
5585332 TACGCGTAGC
*
5585342 GATTATAATGGCGCTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGAT-TCGCGTTGCGATTTACG
** * *
5585381 GATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
5585421 GAT
1 GAT
5585424 ACGTGTTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.39
40 20 0.56
41 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (40 bp):
GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:5585528 original size:20 final size:20
Alignment explanation
Indices: 5585365--5585557 Score: 210
Period size: 20 Copynumber: 9.7 Consensus size: 20
5585355 CTTTAAATAT
5585365 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
* * *
5585386 -TCGTTGCGATTTACAGATT
1 CGCGTTGCGATTTACGGATA
*
5585405 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5585425 CGTGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
5585445 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
5585465 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5585485 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5585505 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
5585525 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
5585545 CGCGTTGCGATTT
1 CGCGTTGCGATTT
5585558 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
19 1 0.01
20 143 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5585551 original size:60 final size:60
Alignment explanation
Indices: 5585364--5585679 Score: 191
Period size: 60 Copynumber: 5.2 Consensus size: 60
5585354 GCTTTAAATA
* * * **
5585364 TCGCGTTGCGATTTACGGATTATCG--TTGCGATTTACAG-ATTCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGA-TA-CGCATTGCGATTTA-TGTATTCGCGTTGCGATTTTCATAT
* * * *** * * **
5585424 ACGTGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
* * * *
5585484 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
* * * * * *
5585544 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TGTACTATCGCATTGCGATTTTCAATAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-ATAT
* * ** * *
5585607 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTAT-T
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCATAT
5585666 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
5585680 TGTTGGTCAT
Statistics
Matches: 208, Mismatches: 36, Indels: 25
0.77 0.13 0.09
Matches are distributed among these distances:
58 2 0.01
59 18 0.09
60 113 0.54
61 27 0.13
62 25 0.12
63 21 0.10
64 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
Found at i:5585558 original size:20 final size:19
Alignment explanation
Indices: 5585505--5585621 Score: 74
Period size: 21 Copynumber: 5.7 Consensus size: 19
5585495 TTTACGGATA
* **
5585505 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTT-TATAAT
*
5585525 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTT-ATAAT
*
5585545 CGCGTTGCGATTTTGGAAAAT
1 CGCGTTGCGATTTT--ATAAT
**
5585566 CGCAATGCGAATTTGTACT-AT
1 CGCGTTGCG-ATTT-TA-TAAT
*
5585587 CGCATTGCGATTTTCAATAAT
1 CGCGTTGCGATTTT--ATAAT
5585608 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
5585622 GGAAACTGAT
Statistics
Matches: 79, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.03
20 35 0.44
21 37 0.47
22 4 0.05
23 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (19 bp):
CGCGTTGCGATTTTATAAT
Found at i:5585574 original size:21 final size:21
Alignment explanation
Indices: 5585544--5585626 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
5585534 ATTTTCATAT
*
5585544 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
5585565 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
5585586 TCGCATTGCGATTTT-CAATAA
1 TCGCATTGCGATTTTGGAA-AA
*
5585607 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
5585627 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:5585617 original size:42 final size:43
Alignment explanation
Indices: 5585524--5585622 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
5585514 ATTTATGTGT
* *
5585524 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
5585565 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAATAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
5585607 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
5585623 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:5587542 original size:15 final size:16
Alignment explanation
Indices: 5587524--5587626 Score: 65
Period size: 15 Copynumber: 6.2 Consensus size: 16
5587514 TTTTTTATCC
5587524 ATTTATTT-TTATTAT
1 ATTTATTTATTATTAT
5587539 ATTTAATAATAATATTATTAT
1 ATTT-AT--T--TATTATTAT
*
5587560 ATTATATTTAATATTAT
1 ATT-TATTTATTATTAT
5587577 -TTTA-TT-TTATTATT
1 ATTTATTTATTATTA-T
5587591 ATTTATATTATTATTAT
1 ATTTAT-TTATTATTAT
*
5587608 -TATTA-TTATTATTAC
1 AT-TTATTTATTATTAT
5587623 ATTT
1 ATTT
5587627 CAGGTCCACT
Statistics
Matches: 71, Mismatches: 3, Indels: 28
0.70 0.03 0.27
Matches are distributed among these distances:
13 5 0.07
14 3 0.04
15 21 0.30
16 6 0.08
17 14 0.20
18 7 0.10
19 1 0.01
20 1 0.01
21 12 0.17
22 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATTTATTATTAT
Found at i:5587557 original size:3 final size:3
Alignment explanation
Indices: 5587551--5587621 Score: 80
Period size: 3 Copynumber: 24.7 Consensus size: 3
5587541 TTAATAATAA
*
5587551 TAT TAT TA- TAT TA- TATT TAA TAT TAT T-T TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
5587593 T-T ATAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA
5587622 CATTTCAGGT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
2 9 0.15
3 47 0.80
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5588912 original size:29 final size:29
Alignment explanation
Indices: 5588875--5588963 Score: 98
Period size: 27 Copynumber: 3.2 Consensus size: 29
5588865 TTTAATTAAA
*
5588875 TATTTTAATTATTATTATTAT-TATTATT
1 TATTTTAATTATTATTAATATATATTATT
5588903 TAATTTTAATTA-TATTAATATATATTATT
1 T-ATTTTAATTATTATTAATATATATTATT
* *
5588932 TA-TTTAATT-TTATAAAT-TAGTAATATT
1 TATTTTAATTATTATTAATATA-TATTATT
5588959 TATTT
1 TATTT
5588964 ATTTTTAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.04
27 21 0.40
28 12 0.23
29 18 0.34
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (29 bp):
TATTTTAATTATTATTAATATATATTATT
Found at i:5588928 original size:10 final size:9
Alignment explanation
Indices: 5588869--5588950 Score: 51
Period size: 9 Copynumber: 8.9 Consensus size: 9
5588859 TATGTGTTTA
*
5588869 ATTAAATAT
1 ATTAATTAT
*
5588878 TTTAATTATT
1 ATTAATTA-T
5588888 ATT-ATTATT
1 ATTAATTA-T
*
5588897 ATTATTTAAT
1 ATTAATT-AT
*
5588907 TTTAATTAT
1 ATTAATTAT
5588916 ATTAATATAT
1 ATTAAT-TAT
*
5588926 ATTATTTAT
1 ATTAATTAT
*
5588935 -TTAATTTT
1 ATTAATTAT
*
5588943 ATAAATTA
1 ATTAATTA
5588951 GTAATATTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
8 6 0.11
9 30 0.54
10 19 0.34
11 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTAATTAT
Found at i:5588965 original size:31 final size:33
Alignment explanation
Indices: 5588876--5588967 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 33
5588866 TTAATTAAAT
*
5588876 ATTTTAATT--ATTATTAT-TATTA-TTATTTA
1 ATTTTAATTAAATTAATATATATTATTTATTTA
*
5588905 ATTTTAATTATATTAATATATATTATTTATTTA
1 ATTTTAATTAAATTAATATATATTATTTATTTA
*
5588938 ATTTT-A-TAAATTAGTA-ATATTTATTTATTT
1 ATTTTAATTAAATTAATATATA-TTATTTATTT
5588968 TTAAATATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
29 9 0.16
30 3 0.05
31 25 0.45
32 6 0.11
33 12 0.22
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (33 bp):
ATTTTAATTAAATTAATATATATTATTTATTTA
Found at i:5589057 original size:2 final size:2
Alignment explanation
Indices: 5589050--5589079 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5589040 ATGCTTTAAA
5589050 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5589080 TTAATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5589877 original size:15 final size:16
Alignment explanation
Indices: 5589859--5589888 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5589849 CTTTCAAATT
5589859 TTTTTATACT-TATAG
1 TTTTTATACTATATAG
5589874 TTTTTATACTATATA
1 TTTTTATACTATATA
5589889 TATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTTTATACTATATAG
Found at i:5593245 original size:15 final size:15
Alignment explanation
Indices: 5593225--5593258 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5593215 GATCAATACC
5593225 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
5593240 TTTTGCATACATTCA
1 TTTTGCATACATGCA
5593255 TTTT
1 TTTT
5593259 TCATTGCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.50
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:5600618 original size:16 final size:15
Alignment explanation
Indices: 5600599--5600640 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
5600589 ATATAATAAG
*
5600599 AAAAAAAAAGAAGGA
1 AAAAAAAAAAAAGGA
5600614 AAAAAAGAAAAAAGGA
1 AAAAAA-AAAAAAGGA
5600630 AAAAATAAAAA
1 AAAAA-AAAAA
5600641 CAAATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 6 0.25
16 17 0.71
17 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAAAAGGA
Found at i:5601021 original size:18 final size:18
Alignment explanation
Indices: 5600998--5601036 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
5600988 AGTTTATCTA
5600998 TTCGAAATTCAATTTATT
1 TTCGAAATTCAATTTATT
5601016 TTCGAAATTCAATTTATT
1 TTCGAAATTCAATTTATT
5601034 TTC
1 TTC
5601037 TTATATAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (18 bp):
TTCGAAATTCAATTTATT
Found at i:5602206 original size:122 final size:122
Alignment explanation
Indices: 5601989--5602799 Score: 1055
Period size: 122 Copynumber: 6.7 Consensus size: 122
5601979 CATTTAATGA
* * *
5601989 ATCAACTTTTCCAG-AGAAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTTATA
1 ATCAACATTTCCAGAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
5602053 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
*
5602111 ATCAACATTTCCAGAAGAGTTCGTAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * *
5602176 TGAGAAGAACTTGTTTAACCTTTTGCTCGACTCTATCGTAGAAGGAGATAGACCAGC
66 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
* *
5602233 ATCAATATTTCCAGAAGAGTTCCTAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * *
5602298 TGAGAAGAACTTGGTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGATCAGC
66 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
* * *
5602355 ATTAACATTTTCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATA
* * * *** *
5602420 ATGAGAAGAACTTGTTTAACCTTTTACTCGAAT-TCAT--C---ACTCGATGGATCAAC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCT-ATCGCAGAAGGAGATAGATCAAC
* * *
5602473 -T-----TTTCCATAGAA-AGTTTATAATGAGAAGAACTTATCTGAATAGGAAGAAGAAGTTCAT
1 ATCAACATTTCC--AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* * * *
5602531 AATGAGAAGAACTTGTTCAACTTTTTGCAT-GACTCTATCACAGAAGGAGATAGACCATC
64 AATGAGAAGAACTTGTTCAACCTTTTGC-TCGACTCTATCGCAGAAGGAGATAGATCAAC
* * * *
5602590 ATCAACTTTTCCAGAGAAAATTCATAATGAGAAGAACTTATCTGAAG-GGTAAGAAGAAGTTCAT
1 ATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGG-AAGAAGAAGTTCAT
* *
5602654 AATGAGAATAACTTGTTCAACCTTTTGCAT-GACTCTATCACAGAAGGAGATAGATCAAC
64 AATGAGAAGAACTTGTTCAACCTTTTGC-TCGACTCTATCGCAGAAGGAGATAGATCAAC
* *
5602713 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAAAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATA
*
5602777 ATGAGAAGAACTTGATCAACCTT
65 ATGAGAAGAACTTGTTCAACCTT
5602800 GCCTTAATTC
Statistics
Matches: 607, Mismatches: 59, Indels: 46
0.85 0.08 0.06
Matches are distributed among these distances:
112 51 0.08
113 28 0.05
114 4 0.01
117 10 0.02
118 11 0.02
121 4 0.01
122 332 0.55
123 165 0.27
124 2 0.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (122 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
Found at i:5602617 original size:123 final size:122
Alignment explanation
Indices: 5602467--5602799 Score: 490
Period size: 123 Copynumber: 2.7 Consensus size: 122
5602457 CACTCGATGG
* *
5602467 ATCAACTTTTCCATAGAAAGTTTATAATGAGAAGAACTTATCTGAATAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAA-AGGAAGAAGAAGTTCATA
* *
5602532 ATGAGAAGAACTTGTTCAACTTTTTGCATGACTCTATCACAGAAGGAGATAGACCATC
65 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGACCAAC
* *
5602590 ATCAACTTTTCCAGAGAAAATTCATAATGAGAAGAACTTATCTGAAGGGTAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAAGG-AAGAAGAAGTTCATA
* *
5602655 ATGAGAATAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
65 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGACCAAC
* ** * *
5602713 ATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAAAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTG-A-AAGGAAGAAGAAGTTCAT
*
5602776 AATGAGAAGAACTTGATCAACCTT
64 AATGAGAAGAACTTGTTCAACCTT
5602800 GCCTTAATTC
Statistics
Matches: 190, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
122 60 0.32
123 127 0.67
124 3 0.02
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (122 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGACCAAC
Found at i:5603188 original size:3 final size:3
Alignment explanation
Indices: 5603180--5603266 Score: 112
Period size: 3 Copynumber: 30.7 Consensus size: 3
5603170 TTATATTCAA
*
5603180 TAT TAT TAT TA- TAT TAT TAT TAA TAT TAT T-T TA- TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
5603224 TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAA TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5603267 CATTTCAGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
2 10 0.13
3 65 0.87
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5603265 original size:41 final size:41
Alignment explanation
Indices: 5603180--5603266 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
5603170 TTATATTCAA
* *
5603180 TATTATTATTATATTATTATTAATATTATTTTATATTATTT
1 TATTATTATTATATTATTATTAATATTATTTTATATAATAT
* *
5603221 TATTATTATTATTTTATTATTATTATTATTATTA-ATAATAT
1 TATTATTATTATATTATTATTAATATTATT-TTATATAATAT
5603262 TATTA
1 TATTA
5603267 CATTTCAGGC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 38 0.93
42 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (41 bp):
TATTATTATTATATTATTATTAATATTATTTTATATAATAT
Found at i:5604497 original size:13 final size:13
Alignment explanation
Indices: 5604426--5604539 Score: 67
Period size: 13 Copynumber: 8.5 Consensus size: 13
5604416 AATTTCATTT
5604426 ATTTTATATTTTA
1 ATTTTATATTTTA
**
5604439 ATACTATAGTTTTA
1 ATTTTATA-TTTTA
5604453 A-TTT-TA-TTT-
1 ATTTTATATTTTA
*
5604462 ATTTTAGTCATTATTT
1 ATTTTA-T-ATT-TTA
5604478 A-TTTATATTTTA
1 ATTTTATATTTTA
5604490 ATTTTATATGTTTA
1 ATTTTATAT-TTTA
**
5604504 ATTAAATATTTTA
1 ATTTTATATTTTA
5604517 ATTATTATTATTATTTA
1 ATT-TTA-TA-T-TTTA
5604534 ATTTTA
1 ATTTTA
5604540 ATTATATTAA
Statistics
Matches: 78, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
9 1 0.01
10 6 0.08
12 6 0.08
13 25 0.32
14 20 0.26
15 8 0.10
16 5 0.06
17 7 0.09
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (13 bp):
ATTTTATATTTTA
Found at i:5604558 original size:32 final size:33
Alignment explanation
Indices: 5604505--5604572 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
5604495 ATATGTTTAA
*
5604505 TTAAATATTTTAATTATTATTA-TTATTTAATT
1 TTAAATATATTAATTATTATTATTTATTTAATT
*
5604537 TTAATTATATTAA-TATATATTATTTATTTAATT
1 TTAAATATATTAATTAT-TATTATTTATTTAATT
5604570 TTA
1 TTA
5604573 TAAATTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 3 0.09
32 16 0.50
33 13 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
TTAAATATATTAATTATTATTATTTATTTAATT
Found at i:5604562 original size:23 final size:23
Alignment explanation
Indices: 5604511--5604555 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5604501 TTAATTAAAT
* *
5604511 ATTTTAATTATTATTATTATTTA
1 ATTTTAATTATTATTAATATATA
5604534 ATTTTAATTA-TATTAATATATA
1 ATTTTAATTATTATTAATATATA
5604556 TTATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTAATTATTATTAATATATA
Found at i:5604594 original size:31 final size:33
Alignment explanation
Indices: 5604514--5604596 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 33
5604504 ATTAAATATT
*
5604514 TTAAT-TATTATTA-TTATTTAATTTTAATTATA
1 TTAATATA-TATTATTTATTTAATTTTAATTAAA
5604546 TTAATATATATTATTTATTTAATTTT-A-TAAA
1 TTAATATATATTATTTATTTAATTTTAATTAAA
*
5604577 TTAGTA-ATATTTATTTATTT
1 TTAATATATA-TTATTTATTT
5604597 TTAAATATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
30 3 0.07
31 18 0.39
32 11 0.24
33 14 0.30
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (33 bp):
TTAATATATATTATTTATTTAATTTTAATTAAA
Found at i:5611677 original size:30 final size:30
Alignment explanation
Indices: 5611642--5611712 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
5611632 TTTTAATGAA
5611642 TATTTAATTCAGAATAATCAAATAAGATGT
1 TATTTAATTCAGAATAATCAAATAAGATGT
** * * *
5611672 TATTTAATTTGGAATAATTAAATTAGATTT
1 TATTTAATTCAGAATAATCAAATAAGATGT
*
5611702 TAATTAATTCA
1 TATTTAATTCA
5611713 TAATTACAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (30 bp):
TATTTAATTCAGAATAATCAAATAAGATGT
Found at i:5615574 original size:6 final size:6
Alignment explanation
Indices: 5615563--5615587 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5615553 TGTTTCAGTC
5615563 GATGAA GATGAA GATGAA GATGAA G
1 GATGAA GATGAA GATGAA GATGAA G
5615588 CACTTGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GATGAA
Found at i:5628224 original size:20 final size:21
Alignment explanation
Indices: 5628195--5628250 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
5628185 TGTTGGACAC
* *
5628195 AAAGTATCGAAACTTT-AGGT
1 AAAGTTTCGAAACTTTGAGAT
5628215 AAAGTTTCGAAACTCTTGAGAT
1 AAAGTTTCGAAACT-TTGAGAT
5628237 -AA-TTTCGAAACTTT
1 AAAGTTTCGAAACTTT
5628251 TTGGGAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 2 0.06
20 23 0.72
21 4 0.12
22 3 0.09
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (21 bp):
AAAGTTTCGAAACTTTGAGAT
Found at i:5629094 original size:2 final size:2
Alignment explanation
Indices: 5629087--5629112 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5629077 TTAAATAATG
5629087 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5629113 GGATAAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5629772 original size:64 final size:64
Alignment explanation
Indices: 5629703--5629923 Score: 225
Period size: 64 Copynumber: 3.5 Consensus size: 64
5629693 TTGAAGGTGT
* **
5629703 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
5629766 C
64 C
* * **
5629767 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* ** * * ** *
5629831 ATCGATGCATAAGG-AGTGCATTGATGCATCCCAGCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* *
5629895 ACCGATGCATTA-ATAGTGCATCGATGCAT
1 ATCGATGCA-TAGGTAGTGCATCGATGCAT
5629924 ACCTTCATTA
Statistics
Matches: 131, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
64 124 0.95
65 7 0.05
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:5630428 original size:31 final size:32
Alignment explanation
Indices: 5630375--5630492 Score: 154
Period size: 32 Copynumber: 3.8 Consensus size: 32
5630365 GTTCTACGGA
*
5630375 ACATATGGATAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
* *
5630407 ACATATGGACAGTA-TACCTATGT-TCTACG-G
1 ACATATGGACAGAATTACCTATGTCT-TTCGAG
5630437 AACATATGGACAGAATTACCTATGTCTTTCGAG
1 -ACATATGGACAGAATTACCTATGTCTTTCGAG
*
5630470 ACATATGGACAGTA-TACCTATGT
1 ACATATGGACAGAATTACCTATGT
5630493 TCTAAGGAAC
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
30 2 0.03
31 34 0.45
32 37 0.49
33 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (32 bp):
ACATATGGACAGAATTACCTATGTCTTTCGAG
Found at i:5630433 original size:63 final size:63
Alignment explanation
Indices: 5630355--5630520 Score: 289
Period size: 63 Copynumber: 2.7 Consensus size: 63
5630345 AGAGTCGAGG
*
5630355 GTATACCTATGTTCTACGGAACATATGGATAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
5630418 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* * *
5630481 GTATACCTATGTTCTAAGGAACATATAGACAG-TTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
5630521 GGTTCTTCGG
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
62 7 0.07
63 92 0.93
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:5630505 original size:31 final size:31
Alignment explanation
Indices: 5630355--5630540 Score: 191
Period size: 31 Copynumber: 5.9 Consensus size: 31
5630345 AGAGTCGAGG
*
5630355 GTATACCTATGTTCTACGGAACATATGGATA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
5630386 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
5630418 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
5630449 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
* *
5630481 GTATACCTATGTTCTAAGGAACATATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
5630512 GTTTACCTAGGTTCTTCGGAACCTATGGA
1 GTATACCTATGTTCTACGGAACATATGGA
5630541 TAGTTGCCGA
Statistics
Matches: 128, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
31 75 0.59
32 53 0.41
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:5630573 original size:30 final size:30
Alignment explanation
Indices: 5630532--5630603 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
5630522 GTTCTTCGGA
* *
5630532 ACCTATGGATAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
*
5630562 GCCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
5630592 ACCTCTGGATAG
1 ACCTCTGGATAG
5630604 GTCCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.32
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:5633922 original size:64 final size:63
Alignment explanation
Indices: 5633805--5634025 Score: 212
Period size: 64 Copynumber: 3.5 Consensus size: 63
5633795 TTGAAGGTGT
** ** * *
5633805 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAATATTGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAT--AAACATCGAATGCAATTCATG
5633868 C
63 C
* **
5633869 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGTAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAT-AAACATCGAATGCAATTCATGC
* ** * ** *
5633933 ATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAA-ACATCGAATGCAATTCATGC
* * *
5633997 ACCGATGCATCAGTAGTGAATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
5634026 ACCTTCATTA
Statistics
Matches: 131, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
63 2 0.02
64 125 0.95
65 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (63 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAACATCGAATGCAATTCATGC
Found at i:5634515 original size:32 final size:31
Alignment explanation
Indices: 5634479--5634596 Score: 150
Period size: 32 Copynumber: 3.7 Consensus size: 31
5634469 GTTCTACGGA
5634479 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAA-TACCTATGTCTTTCGAG
* *
5634511 ACATATGGACAGTATACCTATGT-TCTACG-G
1 ACATATGGACAGAATACCTATGTCT-TTCGAG
*
5634541 AACATATGGACAGAATTACCTATGTCTTTCAAG
1 -ACATATGGACAGAA-TACCTATGTCTTTCGAG
*
5634574 ACATATGGACAGTATACCTATGT
1 ACATATGGACAGAATACCTATGT
5634597 TCTAAGGAAC
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
30 2 0.03
31 34 0.45
32 37 0.49
33 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (31 bp):
ACATATGGACAGAATACCTATGTCTTTCGAG
Found at i:5634537 original size:63 final size:63
Alignment explanation
Indices: 5634459--5634624 Score: 298
Period size: 63 Copynumber: 2.7 Consensus size: 63
5634449 AGAGTCGAGG
*
5634459 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCAAGACATATGGACA
5634522 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCAAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCAAGACATATGGACA
* *
5634585 GTATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
5634625 GGTTCTTCGG
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 7 0.07
63 93 0.93
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCAAGACATATGGACA
Found at i:5634630 original size:31 final size:31
Alignment explanation
Indices: 5634462--5634649 Score: 186
Period size: 31 Copynumber: 6.0 Consensus size: 31
5634452 GTCGAGGGTA
*
5634462 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
5634494 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
5634525 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* * *
5634557 TACCTATG-TCTTTC-AAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
5634588 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * * *
5634619 TACCTAGGTTCTTCGGAACCTATGGATAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
5634650 GCCGAGGATC
Statistics
Matches: 128, Mismatches: 19, Indels: 19
0.77 0.11 0.11
Matches are distributed among these distances:
31 77 0.60
32 51 0.40
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:5634677 original size:30 final size:30
Alignment explanation
Indices: 5634635--5634707 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
5634625 GGTTCTTCGG
* *
5634635 AACCTATGGATAGTTGCCGAGGATCTTTAT
1 AACCTCTGGATAGTTACCGAGGATCTTTAT
*
5634665 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 AACCTCTGGATAGTTACCGAGGATCTTTAT
5634695 AACCTCTGGATAG
1 AACCTCTGGATAG
5634708 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (30 bp):
AACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:5637279 original size:18 final size:18
Alignment explanation
Indices: 5637256--5637298 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5637246 GCTTGAGATA
*
5637256 ACCTAAAAAAAATAAAAT
1 ACCTAAAAAAAATAAAAC
**
5637274 ACCTAAAGGAAATAAAAC
1 ACCTAAAAAAAATAAAAC
5637292 ACCTAAA
1 ACCTAAA
5637299 TAAACCTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.65, C:0.16, G:0.05, T:0.14
Consensus pattern (18 bp):
ACCTAAAAAAAATAAAAC
Found at i:5637474 original size:205 final size:211
Alignment explanation
Indices: 5637119--5637538 Score: 798
Period size: 205 Copynumber: 2.0 Consensus size: 211
5637109 AGAAATCATG
5637119 CTTAGCATATAAAAGACGGAAAAAAATAAAAAAGATGAAAAATAAAAATAATCTTTGTAAAAATC
1 CTTAGCATATAAAAGACGGAAAAAAATAAAAAAGATGAAAAATAAAAATAATCTTTGTAAAAATC
5637184 CCAAAGCTAATTAAATCCAAAAGCAGAACATTTGTCAAGCTTCACCTTAATGAGTATTTTTAGCT
66 CCAAAGCTAATTAAATCCAAAAGCAGAACATTTGTCAAGCTTCACCTTAATGAGTATTTTTAGCT
5637249 TGAGATAACCTAAAAAAAATAAAATACCTAAAGGAAATAAAACACCT-AA-ATAAACCTAAGCAC
131 TGAGATAACCTAAAAAAAATAAAATACCTAAAGGAAATAAAACACCTAAAGATAAACCTAAGCAC
5637312 ATTCAAATACTTAAA-
196 ATTCAAATACTTAAAT
5637327 CTTAGCATATAAAAGACGGAAAAAAAT-AAAAA-ATG-AAAATAAAAATAATCTTTGTAAAAATC
1 CTTAGCATATAAAAGACGGAAAAAAATAAAAAAGATGAAAAATAAAAATAATCTTTGTAAAAATC
5637389 CCAAAGCTAATTAAATCCAAAAGCAGAACATTTGTCAAGCTTCACCTTAATGAGTATTTTTAGCT
66 CCAAAGCTAATTAAATCCAAAAGCAGAACATTTGTCAAGCTTCACCTTAATGAGTATTTTTAGCT
5637454 TGAGATAACCTAAAAAAAATAAAATACCTAAAGGAAATAAAACACCTAAAGATAAACCTAAGCAC
131 TGAGATAACCTAAAAAAAATAAAATACCTAAAGGAAATAAAACACCTAAAGATAAACCTAAGCAC
5637519 ATTCAAATACTTAAAT
196 ATTCAAATACTTAAAT
5637535 CTTA
1 CTTA
5637539 ATTAATTGCA
Statistics
Matches: 209, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
205 139 0.67
206 5 0.02
207 34 0.16
208 31 0.15
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (211 bp):
CTTAGCATATAAAAGACGGAAAAAAATAAAAAAGATGAAAAATAAAAATAATCTTTGTAAAAATC
CCAAAGCTAATTAAATCCAAAAGCAGAACATTTGTCAAGCTTCACCTTAATGAGTATTTTTAGCT
TGAGATAACCTAAAAAAAATAAAATACCTAAAGGAAATAAAACACCTAAAGATAAACCTAAGCAC
ATTCAAATACTTAAAT
Found at i:5637484 original size:18 final size:18
Alignment explanation
Indices: 5637461--5637503 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5637451 GCTTGAGATA
*
5637461 ACCTAAAAAAAATAAAAT
1 ACCTAAAAAAAATAAAAC
**
5637479 ACCTAAAGGAAATAAAAC
1 ACCTAAAAAAAATAAAAC
5637497 ACCTAAA
1 ACCTAAA
5637504 GATAAACCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.65, C:0.16, G:0.05, T:0.14
Consensus pattern (18 bp):
ACCTAAAAAAAATAAAAC
Found at i:5637504 original size:18 final size:18
Alignment explanation
Indices: 5637470--5637504 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5637460 AACCTAAAAA
*
5637470 AAATAAAATACCTAAAGG
1 AAATAAAACACCTAAAGG
5637488 AAATAAAACACCTAAAG
1 AAATAAAACACCTAAAG
5637505 ATAAACCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.14, G:0.09, T:0.14
Consensus pattern (18 bp):
AAATAAAACACCTAAAGG
Found at i:5638401 original size:13 final size:13
Alignment explanation
Indices: 5638385--5638410 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5638375 CTTTACCTTT
5638385 AGGCTTTTTCTTC
1 AGGCTTTTTCTTC
5638398 AGGCTTTTTCTTC
1 AGGCTTTTTCTTC
5638411 TAGGACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.15, T:0.54
Consensus pattern (13 bp):
AGGCTTTTTCTTC
Found at i:5640161 original size:29 final size:29
Alignment explanation
Indices: 5640116--5640173 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
5640106 GTGTTGGCCG
*
5640116 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
5640145 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
5640174 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:5640226 original size:10 final size:10
Alignment explanation
Indices: 5640213--5640263 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 10
5640203 ACACGTTGGG
5640213 CATCCGAGGC
1 CATCCGAGGC
5640223 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
5640237 CATCCGAGAG-
1 CATCCGAG-GC
5640247 CATCCGAGGC
1 CATCCGAGGC
5640257 CATCCGA
1 CATCCGA
5640264 CCGATGCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
9 1 0.03
10 21 0.60
11 3 0.09
13 2 0.06
14 8 0.23
ACGTcount: A:0.24, C:0.39, G:0.27, T:0.10
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:5640235 original size:14 final size:14
Alignment explanation
Indices: 5640216--5640282 Score: 62
Period size: 14 Copynumber: 4.4 Consensus size: 14
5640206 CGTTGGGCAT
5640216 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
5640230 CCGAGGCCATCCGAGAGCA
1 CCGAGGCCATCC----G-A
5640249 TCCGAGGCCATCCGA
1 -CCGAGGCCATCCGA
*
5640264 CCGATGCCATCCGA
1 CCGAGGCCATCCGA
*
5640278 ACGAG
1 CCGAG
5640283 CTATGCGAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 28 0.64
15 1 0.02
16 1 0.02
18 1 0.02
19 1 0.02
20 12 0.27
ACGTcount: A:0.24, C:0.39, G:0.28, T:0.09
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:5640250 original size:34 final size:36
Alignment explanation
Indices: 5640212--5640300 Score: 128
Period size: 34 Copynumber: 2.5 Consensus size: 36
5640202 AACACGTTGG
5640212 GCATCCGAGGCCATCCGACCGAGGCCATCCG-A-GA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGA
*
5640246 GCATCCGAGGCCATCCGACCGATGCCATCCGAACGA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGA
* *
5640282 GCTATGCGAGGGCATCCGA
1 GC-ATCCGAGGCCATCCGA
5640301 GGGCAACTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
34 30 0.61
35 1 0.02
36 4 0.08
37 14 0.29
ACGTcount: A:0.24, C:0.36, G:0.29, T:0.11
Consensus pattern (36 bp):
GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGA
Found at i:5640346 original size:33 final size:33
Alignment explanation
Indices: 5640274--5640348 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
5640264 CCGATGCCAT
* *
5640274 CCGAACGAGCTATGCGAGGGCATCCGAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
*
5640307 CTGAGCGAGCTATGCGAGGGAATCCGAGGG-AA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
5640339 GCCGAGCGAG
1 -CCGAGCGAG
5640349 GGTAGGTCGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.27, C:0.24, G:0.40, T:0.09
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
Found at i:5640385 original size:29 final size:29
Alignment explanation
Indices: 5640352--5640407 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5640342 GAGCGAGGGT
* *
5640352 AGGTCGCTCGGAGTGCACGGCGACCTACA
1 AGGTCGCCCGGAGGGCACGGCGACCTACA
* *
5640381 AGGTCGCCCGTAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCACGGCGACCTA
5640408 TGTGTTGGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.20, C:0.30, G:0.36, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCACGGCGACCTACA
Done.