Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_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: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 33
Found at i:4239818 original size:12 final size:13
Alignment explanation
Indices: 4239727--4240202 Score: 222
Period size: 14 Copynumber: 35.1 Consensus size: 13
4239717 ATTAGTAATA
4239727 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
4239741 AGTATTAAATCATT
1 ATTA-TAAATCATT
4239755 ATTATAAAT-A--
1 ATTATAAATCATT
4239765 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
4239776 ATAACTAAATAATT
1 ATTA-TAAATCATT
4239790 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
4239804 ATTAT-AATGATT
1 ATTATAAATCATT
4239816 ATTATCAAATCATT
1 ATTAT-AAATCATT
4239830 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
4239849 AAATATTTAAATCATT
1 --AT-TATAAATCATT
4239865 A-T-TAAATCATT
1 ATTATAAATCATT
* *
4239876 TTTAT-AATGATT
1 ATTATAAATCATT
4239888 ATTATCAAATCATT
1 ATTAT-AAATCATT
*
4239902 ATTAT-AATGATT
1 ATTATAAATCATT
4239914 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
4239928 ACTAT-AATGATT
1 ATTATAAATCATT
4239940 ATTATCAAATCATT
1 ATTAT-AAATCATT
4239954 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
4239973 AAATATTTAAATCATT
1 --AT-TATAAATCATT
4239989 A-T-TAAATCATT
1 ATTATAAATCATT
* *
4240000 TTTAT-AATGATT
1 ATTATAAATCATT
4240012 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
4240026 ATTAT-AATGATT
1 ATTATAAATCATT
4240038 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
4240052 ACTAT-AATGATT
1 ATTATAAATCATT
4240064 ATTATCAAATCATT
1 ATTAT-AAATCATT
4240078 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
4240097 AAATATTTAAATCATT
1 --AT-TATAAATCATT
4240113 -TT-TAAATCATT
1 ATTATAAATCATT
* *
4240124 TTTAT-AATGATT
1 ATTATAAATCATT
4240136 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
4240150 ATTAT-AATGATT
1 ATTATAAATCATT
4240162 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
4240176 ACTAT-AATGATT
1 ATTATAAATCATT
4240188 ATTATCAAATCATT
1 ATTAT-AAATCATT
4240202 A
1 A
4240203 CTAAATCATC
Statistics
Matches: 371, Mismatches: 39, Indels: 104
0.72 0.08 0.20
Matches are distributed among these distances:
10 4 0.01
11 42 0.11
12 111 0.30
13 14 0.04
14 122 0.33
15 3 0.01
16 24 0.06
17 3 0.01
18 9 0.02
19 33 0.09
20 3 0.01
21 3 0.01
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:4239825 original size:26 final size:26
Alignment explanation
Indices: 4239727--4240202 Score: 367
Period size: 26 Copynumber: 19.2 Consensus size: 26
4239717 ATTAGTAATA
* * *
4239727 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
4239752 ATTATTATAA--ATAATTA-CTAAATA
1 ATTATTATAATGATTATTATC-AAATC
* * * *
4239776 ATAACTA-AATAATTATTATAAAATC
1 ATTATTATAATGATTATTATCAAATC
4239801 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
4239827 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
4239850 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
4239873 ATTTTTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
4239899 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
4239925 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
4239951 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
4239974 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
4239997 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
4240023 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
4240049 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * *
4240075 ATTACTA-AATCATCAAATCATTAAAT-
1 ATTATTATAATGAT--TATTATCAAATC
*
4240101 A-T-TTA-AATCATT-TT-T-AAATC
1 ATTATTATAATGATTATTATCAAATC
*
4240121 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
4240147 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
4240173 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
4240199 ATTA
1 ATTA
4240203 CTAAATCATC
Statistics
Matches: 362, Mismatches: 58, Indels: 61
0.75 0.12 0.13
Matches are distributed among these distances:
19 4 0.01
20 2 0.01
21 10 0.03
22 7 0.02
23 36 0.10
24 36 0.10
25 40 0.11
26 217 0.60
27 10 0.03
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:4239951 original size:124 final size:124
Alignment explanation
Indices: 4239743--4240260 Score: 918
Period size: 124 Copynumber: 4.2 Consensus size: 124
4239733 AAATCATTAG
* * * * * * *
4239743 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTA-AATAATTATTATAAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
4239805 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
4239864 TATTAAATCATTTTTATAATGATTATTA-TCAAATCATTATTATAATGATTATTATCAAATCATT
1 TATTAAATCATTTTTATAATGATTATTACT-AAATCATTATTATAATGATTATTATCAAATCATT
4239928 ACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
65 ACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
4239988 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
4240053 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
4240112 TTTTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
4240177 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
4240236 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
4240261 ATAAATACAT
Statistics
Matches: 382, Mismatches: 10, Indels: 7
0.96 0.03 0.02
Matches are distributed among these distances:
121 18 0.05
122 1 0.00
123 15 0.04
124 347 0.91
125 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (124 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:4239990 original size:98 final size:97
Alignment explanation
Indices: 4239790--4240055 Score: 296
Period size: 98 Copynumber: 2.7 Consensus size: 97
4239780 CTAAATAATT
* * * *
4239790 ATTATAAAATCATTATTATAATGATTATTATCAAATCATTACTA-AATCATCAAATCATTAAAT-
1 ATTATAAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGAT--TATTATCAAATC
* *
4239853 ATT--TAAATCATTATTAAATCATTTTTATAATGATT
64 ATTACTAAATC--TATCAAATCATTTTTATAA-GATC
*
4239888 ATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTATAAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
4239953 TACTAAATC-ATCAAATCATTAAATATT-TAA-ATC
66 TACTAAATCTATCAAATCATT---T-TTATAAGATC
* * *
4239986 ATTATTAAATCATTTTTATAATGATTATTA-CTAAATCATTATTATAATGATTATTATCAAATCA
1 ATTATAAAATCATTATTATAATGATTATTATC-AAATCATTACTATAATGATTATTATCAAATCA
4240050 TTACTA
65 TTACTA
4240056 TAATGATTAT
Statistics
Matches: 149, Mismatches: 10, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
97 19 0.13
98 113 0.76
99 5 0.03
100 10 0.07
101 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (97 bp):
ATTATAAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
TACTAAATCTATCAAATCATTTTTATAAGATC
Found at i:4240031 original size:150 final size:145
Alignment explanation
Indices: 4239862--4240205 Score: 426
Period size: 150 Copynumber: 2.3 Consensus size: 145
4239852 TATTTAAATC
* *
4239862 ATTATTAAATCATTTTTATAATGATTATTATCAAATCATTATTATAATGATTATTATCAAATCAT
1 ATTA-TAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
* * *
4239927 TACTATAATGAT-TATTATCAAATCATTACTAAATCA-TCAAATCATTAAATATT-TAA-ATCAT
65 TACTA-AATCATAAATCATCAAAT-ATT--TAAATCATTCAAATCATT---T-TTATAAGATCAT
* *
4239988 TATTAAATCATTTTTATAATGATT
122 TACTAAATCATTATTATAATGATT
4240012 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTA-TAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
* * *
4240077 TACTAAATCATCAAATCATTAAATATTTAAATCATTTTTAAATCATTTTTATAATGATTATTACT
65 TACTAAATCAT-AAATCATCAAATATTTAAATCA--TTCAAATCATTTTTATAA-GATCATTACT
4240142 AAATCATTATTATAATGATT
126 AAATCATTATTATAATGATT
*
4240162 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTA
1 ATTAT-AAATCATTATTATAATGATTATTATCAAATCATTACTA
4240206 AATCATCAAA
Statistics
Matches: 173, Mismatches: 12, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
147 2 0.01
148 11 0.06
149 6 0.03
150 137 0.79
151 17 0.10
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (145 bp):
ATTATAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATT
ACTAAATCATAAATCATCAAATATTTAAATCATTCAAATCATTTTTATAAGATCATTACTAAATC
ATTATTATAATGATT
Found at i:4243142 original size:26 final size:25
Alignment explanation
Indices: 4243085--4243143 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
4243075 CTAATAAACC
*
4243085 TAATAATGATTTGATAATTACTATT
1 TAATAATGATTTGATAATTAATATT
* *
4243110 AATATAATGATTTGATATTTAATGATT
1 TA-ATAATGATTTGATAATTAAT-ATT
4243137 TAATAAT
1 TAATAAT
4243144 AATATGATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 1 0.04
26 23 0.82
27 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TAATAATGATTTGATAATTAATATT
Found at i:4244017 original size:28 final size:28
Alignment explanation
Indices: 4243950--4244010 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
4243940 AATTTTTATA
*
4243950 TAATATAATATAACTTAAACTAATAAAC
1 TAATATAATATAACTTAAACTAACAAAC
4243978 TAATATAATATAACTTAAACTAACAAAC
1 TAATATAATATAACTTAAACTAACAAAC
4244006 TAATA
1 TAATA
4244011 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (28 bp):
TAATATAATATAACTTAAACTAACAAAC
Found at i:4244020 original size:21 final size:21
Alignment explanation
Indices: 4243987--4244035 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
4243977 CTAATATAAT
4243987 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
4244008 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
4244029 ATTAACT
1 A-TAACT
4244036 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:4244686 original size:29 final size:29
Alignment explanation
Indices: 4244644--4244734 Score: 164
Period size: 29 Copynumber: 3.1 Consensus size: 29
4244634 AAATACACAC
* *
4244644 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCAACCTCCA
4244673 AGGTCGCCCGGATGCCATGGCAACCTCCA
1 AGGTCGCCCGGATGCCATGGCAACCTCCA
4244702 AGGTCGCCCGGATGCCATGGCAACCTCCA
1 AGGTCGCCCGGATGCCATGGCAACCTCCA
4244731 AGGT
1 AGGT
4244735 TACTGTAGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.20, C:0.35, G:0.30, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCAACCTCCA
Found at i:4253621 original size:14 final size:14
Alignment explanation
Indices: 4253589--4253639 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
4253579 ACTCTAAGCC
* *
4253589 TAAATCATAAACCC
1 TAAATCTTAAACCT
*
4253603 CAAATCTTAAACCT
1 TAAATCTTAAACCT
*
4253617 TAAATCCTAAA-CT
1 TAAATCTTAAACCT
4253630 TAAATCTTAA
1 TAAATCTTAA
4253640 GCACTAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAATCTTAAACCT
Found at i:4253647 original size:27 final size:26
Alignment explanation
Indices: 4253569--4253653 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 26
4253559 CCCTAACCCA
*
4253569 TAAACTTTAAA-CTCTAAGCCTAAATCA
1 TAAAC-TTAAATCT-TAAGCCTAAATCC
** *
4253596 TAAACCCCAAATCTTAAACCTTAAATCC
1 TAAA-CTTAAATCTTAAGCC-TAAATCC
*
4253624 TAAACTTAAATCTTAAGCACTAAATTC
1 TAAACTTAAATCTTAAGC-CTAAATCC
4253651 TAA
1 TAA
4253654 TCTCTAACCA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
27 32 0.70
28 14 0.30
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (26 bp):
TAAACTTAAATCTTAAGCCTAAATCC
Found at i:4254262 original size:15 final size:16
Alignment explanation
Indices: 4254242--4254274 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4254232 TTCCATATAA
4254242 ATAAATAA-ATAAAAT
1 ATAAATAATATAAAAT
4254257 ATAAATAATTATAAAAT
1 ATAAATAA-TATAAAAT
4254274 A
1 A
4254275 ACAAATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAATAATATAAAAT
Found at i:4256225 original size:3 final size:3
Alignment explanation
Indices: 4256217--4256268 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
4256207 TAATATTATG
* * *
4256217 TAA TAA TAA TAT TAA TAA TTA TAA TAA -AA TTAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
4256262 T-A TAA TA
1 TAA TAA TA
4256269 TAAACGTCAC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:4256242 original size:18 final size:18
Alignment explanation
Indices: 4256219--4256268 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
4256209 ATATTATGTA
4256219 ATAATAATATTAATAATT
1 ATAATAATATTAATAATT
*
4256237 ATAATAAAATTAATAATT
1 ATAATAATATTAATAATT
4256255 ATAATAATA-TAATA
1 ATAATAATATTAATA
4256269 TAAACGTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 5 0.17
18 25 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATAATATTAATAATT
Found at i:4256785 original size:90 final size:89
Alignment explanation
Indices: 4256534--4256797 Score: 307
Period size: 91 Copynumber: 2.9 Consensus size: 89
4256524 GAATTTGTAT
* * * * *
4256534 TACTCCACTACTTTTCCGTGAAGG-TTTCATACTTTGCTGAAAAATCCATTCTACCACTCTTCCA
1 TACTTCACTACTCTTCTGTGAAGGCTTT-ATACTTTGCTGAAAAATCCATTCCACTACTCTTCCA
*
4256598 TAGAGAGTGAATTTTGATCTTATTCC
65 TGGAGAG-GAATTTTGATCTTATTCC
* * * *** ***
4256624 TATTTCACTACTCTTTCTGTGAAGGCTTTATACATTGCTAAAAAATTTGTTCCACTACTCTTTTG
1 TACTTCACTACTC-TTCTGTGAAGGCTTTATACTTTGCTGAAAAATCCATTCCACTACTCTTCCA
4256689 TGGAGAGCGAATTTTGATCTTATTCC
65 TGGAGAG-GAATTTTGATCTTATTCC
* * * *
4256715 TGCTTCACTACTCTTCTGTGAAGGCTTTAAACTTTGTTGAAAAGTCCATTCCACTACTCTTCCAT
1 TACTTCACTACTCTTCTGTGAAGGCTTTATACTTTGCTGAAAAATCCATTCCACTACTCTTCCAT
4256780 GGAGA-GAATTTTGATCTT
66 GGAGAGGAATTTTGATCTT
4256798 GCTTTTGCTT
Statistics
Matches: 143, Mismatches: 29, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
88 13 0.09
90 56 0.39
91 71 0.50
92 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (89 bp):
TACTTCACTACTCTTCTGTGAAGGCTTTATACTTTGCTGAAAAATCCATTCCACTACTCTTCCAT
GGAGAGGAATTTTGATCTTATTCC
Found at i:4257038 original size:20 final size:20
Alignment explanation
Indices: 4257015--4257083 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
4257005 CTAAAGGATC
*
4257015 TACAAATTACCCGAAGGTTT
1 TACAAATGACCCGAAGGTTT
4257035 TACAAATGACCCGAAGGTTT
1 TACAAATGACCCGAAGGTTT
** * *
4257055 TACAAATGATTCGTAGGCTT
1 TACAAATGACCCGAAGGTTT
4257075 TACAAATGA
1 TACAAATGA
4257084 TTCGGAGGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (20 bp):
TACAAATGACCCGAAGGTTT
Found at i:4257059 original size:40 final size:40
Alignment explanation
Indices: 4257015--4257141 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 40
4257005 CTAAAGGATC
* * * *
4257015 TACAAATTACCCGAAGGTTTTACAAATGACCCGAAGGTTT
1 TACAAATTATCCGTAGGCTTTACAAATGACCCGAAGGCTT
* * ** *
4257055 TACAAATGATTCGTAGGCTTTACAAATGATTCGGAGGCTT
1 TACAAATTATCCGTAGGCTTTACAAATGACCCGAAGGCTT
* * *
4257095 TACAAATTATCCGTAGACTTTACAAAAGACCCGTAGGCTT
1 TACAAATTATCCGTAGGCTTTACAAATGACCCGAAGGCTT
4257135 TA-AAATT
1 TACAAATT
4257142 TTGTGAAAAA
Statistics
Matches: 71, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
39 5 0.07
40 66 0.93
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (40 bp):
TACAAATTATCCGTAGGCTTTACAAATGACCCGAAGGCTT
Found at i:4257084 original size:20 final size:20
Alignment explanation
Indices: 4257033--4257140 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
4257023 ACCCGAAGGT
* * *
4257033 TTTACAAATGACCCGAAGGT
1 TTTACAAATGATCCGTAGGC
*
4257053 TTTACAAATGATTCGTAGGC
1 TTTACAAATGATCCGTAGGC
* *
4257073 TTTACAAATGATTCGGAGGC
1 TTTACAAATGATCCGTAGGC
* *
4257093 TTTACAAATTATCCGTAGAC
1 TTTACAAATGATCCGTAGGC
* *
4257113 TTTACAAAAGACCCGTAGGC
1 TTTACAAATGATCCGTAGGC
4257133 TTTA-AAAT
1 TTTACAAAT
4257141 TTTGTGAAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
19 3 0.04
20 71 0.96
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (20 bp):
TTTACAAATGATCCGTAGGC
Found at i:4258145 original size:65 final size:65
Alignment explanation
Indices: 4258026--4258237 Score: 222
Period size: 65 Copynumber: 3.3 Consensus size: 65
4258016 TTTTTCAGAG
* * *
4258026 TGATGCACCGATGCAC-CAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATG
1 TGATGCATCGATGCACTC-AGCCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATG
4258087 CATT
62 CATT
* * * * *
4258091 TCATGCATCAATGCACTTA-CCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCAAATGCA
1 TGATGCATCGATGCACTCAGCCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
4258154 TT
64 TT
* * *
4258156 TGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACTCAGCCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
4258220 TGATGCATCGATGCACTC
1 TGATGCATCGATGCACTC
4258238 TTAGTGCACC
Statistics
Matches: 123, Mismatches: 15, Indels: 18
0.79 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 47 0.38
65 70 0.57
66 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (65 bp):
TGATGCATCGATGCACTCAGCCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:4258235 original size:17 final size:19
Alignment explanation
Indices: 4258207--4258255 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
4258197 TATTTTGAAA
4258207 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
4258225 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
4258244 CACCGATGCACT
1 CATCGATGCACT
4258256 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:4258625 original size:28 final size:28
Alignment explanation
Indices: 4258593--4258647 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
4258583 TTGTACTCAA
4258593 TTGTATTCATTCTTGAGTGTTCTTTTCT
1 TTGTATTCATTCTTGAGTGTTCTTTTCT
4258621 TTGTATTCATTCTTGAGTGTTCTTTTC
1 TTGTATTCATTCTTGAGTGTTCTTTTC
4258648 AAAACTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.60
Consensus pattern (28 bp):
TTGTATTCATTCTTGAGTGTTCTTTTCT
Found at i:4262852 original size:20 final size:20
Alignment explanation
Indices: 4262827--4262880 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
4262817 CGTCCTGAAT
4262827 ATGCATCGATGCATGGGGTC
1 ATGCATCGATGCATGGGGTC
4262847 ATGCATCGATGCATGGGGTC
1 ATGCATCGATGCATGGGGTC
4262867 ATGCATCGATGCAT
1 ATGCATCGATGCAT
4262881 CTGTCGGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.26
Consensus pattern (20 bp):
ATGCATCGATGCATGGGGTC
Found at i:4265725 original size:64 final size:65
Alignment explanation
Indices: 4265566--4265727 Score: 215
Period size: 65 Copynumber: 2.5 Consensus size: 65
4265556 AATTAAATTG
* *
4265566 AACATCGAATGCATTTCATGCATCGATGCACTTACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCGATGCACTGAGGATTTTATGAA
* *
4265631 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACT-ATGGCTATTT-T
1 AACATCGAATGCATTTGATGCATCGATGCACTCA-CCATGCACCGATGCACTGA-GGAT-TTTAT
4265693 -AA
63 GAA
* *
4265695 AACATCGAATGCACTTGATGCATCGGTGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
4265728 TTAGTGCACC
Statistics
Matches: 87, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
64 33 0.38
65 51 0.59
66 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCGATGCACTGAGGATTTTATGAA
Found at i:4265741 original size:64 final size:63
Alignment explanation
Indices: 4265566--4265746 Score: 183
Period size: 65 Copynumber: 2.8 Consensus size: 63
4265556 AATTAAATTG
* *
4265566 AACATCGAATGCATTTCATGCATCGATGCA-CTTACCATGCACCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCTTA--GTGCACCGATGCACT-AGGATTTTATGA
4265630 A
63 A
* *
4265631 AACATCGAATGCATTTGATGCATCGATGCACC--AGCCATGCATCGATGCACTATGGCTATTT-T
1 AACATCGAATGCATTTGATGCATCGATGCACCTTAG---TGCACCGATGCACTA-GGAT-TTTAT
4265693 -AA
61 GAA
* * *
4265695 AACATCGAATGCACTTGATGCATCGGTGCACTCTTAGTGCACCGATGTACTA
1 AACATCGAATGCATTTGATGCATCGATGCAC-CTTAGTGCACCGATGCACTA
4265747 AGGGTCTAAC
Statistics
Matches: 99, Mismatches: 8, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
64 46 0.46
65 47 0.47
66 4 0.04
67 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACCTTAGTGCACCGATGCACTAGGATTTTATGAA
Found at i:4269045 original size:86 final size:85
Alignment explanation
Indices: 4268891--4269052 Score: 261
Period size: 86 Copynumber: 1.9 Consensus size: 85
4268881 TCCACTGCCT
* * * *
4268891 CATTATTCCCTTTATTTCAGAAAATCTGATATAGGTGCTCGAGGTGTTTTTAGAGTTGTACTTGC
1 CATTATTCCCTTTATTTCAGAAAATATGATATAGGTGCCCGAAGTGTTTTCAGAGTTGTACTTGC
4268956 TCTATTCTCTTTAAATTGTCC
66 TCTATTC-CTTTAAATTGTCC
* *
4268977 CATTCTTCCCTTTATTTCAGAAAATATGATATAGGTGCCCGAAGTGTTTTCAGAGTTGTACTTTC
1 CATTATTCCCTTTATTTCAGAAAATATGATATAGGTGCCCGAAGTGTTTTCAGAGTTGTACTTGC
4269042 TCTATTCCTTT
66 TCTATTCCTTT
4269053 TTAAACATGT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 4 0.06
86 66 0.94
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (85 bp):
CATTATTCCCTTTATTTCAGAAAATATGATATAGGTGCCCGAAGTGTTTTCAGAGTTGTACTTGC
TCTATTCCTTTAAATTGTCC
Found at i:4272606 original size:33 final size:33
Alignment explanation
Indices: 4272569--4272633 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
4272559 CAAATAATTT
*
4272569 AATATAAATACTTACTA-AATAATATTTAATATA
1 AATATAAATA-GTACTATAATAATATTTAATATA
* * *
4272602 AATATTAATAGTCCTATTATAATATTTAATAT
1 AATATAAATAGTACTATAATAATATTTAATAT
4272634 TAAAACCATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (33 bp):
AATATAAATAGTACTATAATAATATTTAATATA
Found at i:4272815 original size:61 final size:61
Alignment explanation
Indices: 4272748--4272875 Score: 247
Period size: 61 Copynumber: 2.1 Consensus size: 61
4272738 TATAATAATA
4272748 AAATTAATTAACCTAATTTGAAATACTACTAGAATTATGTACTAATTATATAATTTAACAT
1 AAATTAATTAACCTAATTTGAAATACTACTAGAATTATGTACTAATTATATAATTTAACAT
*
4272809 AAATTAATTAACCTAATTTGAAATACTACTAGAATTATGTACTAATTATGTAATTTAACAT
1 AAATTAATTAACCTAATTTGAAATACTACTAGAATTATGTACTAATTATATAATTTAACAT
4272870 AAATTA
1 AAATTA
4272876 CTAATACATG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.39
Consensus pattern (61 bp):
AAATTAATTAACCTAATTTGAAATACTACTAGAATTATGTACTAATTATATAATTTAACAT
Found at i:4272894 original size:61 final size:61
Alignment explanation
Indices: 4272748--4272894 Score: 197
Period size: 61 Copynumber: 2.4 Consensus size: 61
4272738 TATAATAATA
* * *
4272748 AAATTAATTAACCTAATTTGAAATACTACTAGAATTATGTACTAATTATATAATTTAACAT
1 AAATTAATAAACATAATTTAAAATACTACTAGAATTATGTACTAATTATATAATTTAACAT
* * * *
4272809 AAATTAATTAACCTAATTTGAAATACTACTAGAATTATGTACTAATTATGTAATTTAACAT
1 AAATTAATAAACATAATTTAAAATACTACTAGAATTATGTACTAATTATATAATTTAACAT
* *
4272870 AAATTACTAATACATGA-TTAAAATA
1 AAATTAATAA-ACATAATTTAAAATA
4272895 GAATTTATTA
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
61 75 0.95
62 4 0.05
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (61 bp):
AAATTAATAAACATAATTTAAAATACTACTAGAATTATGTACTAATTATATAATTTAACAT
Found at i:4273821 original size:16 final size:17
Alignment explanation
Indices: 4273794--4273826 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4273784 GCGGTGGCAA
4273794 AATGATAACCCTAGGGT
1 AATGATAACCCTAGGGT
4273811 AATGA-AACCCTAGGGT
1 AATGATAACCCTAGGGT
4273827 TTATACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.21
Consensus pattern (17 bp):
AATGATAACCCTAGGGT
Found at i:4274091 original size:23 final size:22
Alignment explanation
Indices: 4274061--4274105 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
4274051 CTGGGCTTTG
*
4274061 TAATATTAT-GTAATAATAATAT
1 TAATATTATAATAAT-ATAATAT
4274083 TAATAATTATAATAATATAATAT
1 TAAT-ATTATAATAATATAATAT
4274106 AAACGTCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TAATATTATAATAATATAATAT
Found at i:4275225 original size:21 final size:21
Alignment explanation
Indices: 4275181--4275226 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4275171 TCCCATCCCA
* *
4275181 AAACCCCAAAACCTATACTTT
1 AAACCCCAAAACCTAAACTCT
4275202 AAACCCCAAAACCTAAAAC-CT
1 AAACCCCAAAACCT-AAACTCT
4275223 AAAC
1 AAAC
4275227 ATTAAATCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (21 bp):
AAACCCCAAAACCTAAACTCT
Found at i:4275231 original size:28 final size:29
Alignment explanation
Indices: 4275177--4275232 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
4275167 TTTATCCCAT
* *
4275177 CCCAAAACCCCAAAACCTATACTTTAAAC
1 CCCAAAACCCCAAAACCTAAACATTAAAC
*
4275206 CCCAAAA-CCTAAAACCTAAACATTAAA
1 CCCAAAACCCCAAAACCTAAACATTAAA
4275233 TCCTAAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (29 bp):
CCCAAAACCCCAAAACCTAAACATTAAAC
Found at i:4276610 original size:16 final size:16
Alignment explanation
Indices: 4276591--4276630 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
4276581 TCGTTGTTCG
4276591 TTAAGCTCGTTACTCA
1 TTAAGCTCGTTACTCA
*
4276607 TTAAACTCGTTACTCA
1 TTAAGCTCGTTACTCA
4276623 TTAAGCTC
1 TTAAGCTC
4276631 AATGCTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (16 bp):
TTAAGCTCGTTACTCA
Found at i:4282816 original size:84 final size:83
Alignment explanation
Indices: 4282710--4282881 Score: 206
Period size: 84 Copynumber: 2.1 Consensus size: 83
4282700 TAATCCGACA
* *
4282710 TTTTATTTTATATATATATATATTTATTTATT-TTTTATGTTTCTGTTTCTGTTT-T-TTGTTAT
1 TTTTATTTTATATATATATATATATATATATTCTTTTAT-TTTCTGTTTCTGTTTCTGTT-TTAT
4282772 TATTATATTTTTACCTAACAT
64 TATT-TATTTTTACCTAACAT
* * * * *
4282793 TTTTATTTATTTATATATATATATATATATATTCTTTTCTTTTCTTTTTTTGTTTCTGTTTTGTT
1 TTTTATTT-TATATATATATATATATATATATTCTTTTATTTTCTGTTTCTGTTTCTGTTTTATT
* *
4282858 GTTTTTTTTTACCTAACAT
65 ATTTATTTTTACCTAACAT
4282877 TTTTA
1 TTTTA
4282882 ATAATTTGTG
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
83 8 0.11
84 54 0.71
85 12 0.16
86 2 0.03
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (83 bp):
TTTTATTTTATATATATATATATATATATATTCTTTTATTTTCTGTTTCTGTTTCTGTTTTATTA
TTTATTTTTACCTAACAT
Found at i:4284286 original size:14 final size:14
Alignment explanation
Indices: 4284264--4284298 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
4284254 AATATATTTA
4284264 TTTTT-AAATTAAT
1 TTTTTAAAATTAAT
4284277 TTTTTAAAATTAAT
1 TTTTTAAAATTAAT
4284291 TTTATTAA
1 TTT-TTAA
4284299 GTCTTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 11 0.55
15 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTAAAATTAAT
Found at i:4293673 original size:104 final size:106
Alignment explanation
Indices: 4293503--4293705 Score: 259
Period size: 104 Copynumber: 1.9 Consensus size: 106
4293493 ACCAAGGGTA
* * *
4293503 GAGTATTGATACTCCCTATAAGGGTATCGATACTGAGGTGTTTTTCAAAACATCGAAACCAATTT
1 GAGTATTGATACTCCCTATAAGAGTATCGATACTAAGGTGTTTATCAAAACATCGAAACCAATTT
* *
4293568 TGGTATCGGTACTCAGGGT-AATATCAATACCCACCCCTAG
66 TGGTATCGATACTCAGGGTGAATATCAAAACCCACCCCTAG
* * * * * * *
4293608 GAGTATTGATACTCCC-GTAAGAGTATCGATATTAAAGGT-TTTATCCAAATATCGAAGCTATTT
1 GAGTATTGATACTCCCTATAAGAGTATCGATACT-AAGGTGTTTATCAAAACATCGAAACCAATT
*
4293671 TTGGTATCGATACTCAGGGTGAGTATCAAAACCCA
65 TTGGTATCGATACTCAGGGTGAATATCAAAACCCA
4293706 AGAGTCAATA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
104 51 0.61
105 32 0.39
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (106 bp):
GAGTATTGATACTCCCTATAAGAGTATCGATACTAAGGTGTTTATCAAAACATCGAAACCAATTT
TGGTATCGATACTCAGGGTGAATATCAAAACCCACCCCTAG
Found at i:4297500 original size:104 final size:104
Alignment explanation
Indices: 4297310--4297518 Score: 276
Period size: 104 Copynumber: 2.0 Consensus size: 104
4297300 ACCGCCTAAG
* * * * ** *
4297310 AATGTATCTGAGGTGCGCAGCTTCTTAGTCCATGCAGGGTACAATCATCGCTTTGTTAAGGGATT
1 AATGTATCTGAGGTGCACAGCTTCTTAGGCCATGCAAGGTACAATCATCACTTCATCAAGGGATT
* *
4297375 CTCGATGATAGTAGCATCGTTGACCAAGCTACTACAAAA
66 CTCGATGATAGCAGCACCGTTGACCAAGCTACTACAAAA
* * *
4297414 AATGTATCTGAGGTGCATAGCTTCTTAGGCC-TCGCAAGGTACTATCATCACTTCATCAAGGGTT
1 AATGTATCTGAGGTGCACAGCTTCTTAGGCCAT-GCAAGGTACAATCATCACTTCATCAAGGGAT
* *
4297478 TCTCGATGATAGCAGTACCGTTGACCAAGCTACTGCAAAA
65 TCTCGATGATAGCAGCACCGTTGACCAAGCTACTACAAAA
4297518 A
1 A
4297519 GGAGTCCATT
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
103 1 0.01
104 89 0.99
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (104 bp):
AATGTATCTGAGGTGCACAGCTTCTTAGGCCATGCAAGGTACAATCATCACTTCATCAAGGGATT
CTCGATGATAGCAGCACCGTTGACCAAGCTACTACAAAA
Found at i:4297960 original size:11 final size:11
Alignment explanation
Indices: 4297944--4297968 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4297934 CCTACGTGAA
4297944 GGAACCAATCT
1 GGAACCAATCT
4297955 GGAACCAATCT
1 GGAACCAATCT
4297966 GGA
1 GGA
4297969 TCCTATCCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (11 bp):
GGAACCAATCT
Found at i:4301812 original size:32 final size:27
Alignment explanation
Indices: 4301748--4301801 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
4301738 ATGATTACAA
*
4301748 GAGAAAATAATTAAATTAACTAATTTC
1 GAGAAAACAATTAAATTAACTAATTTC
4301775 GAGAAAACAATTAAATTAACTAATTTC
1 GAGAAAACAATTAAATTAACTAATTTC
4301802 ACACCTAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.31
Consensus pattern (27 bp):
GAGAAAACAATTAAATTAACTAATTTC
Found at i:4303920 original size:41 final size:41
Alignment explanation
Indices: 4303874--4304047 Score: 131
Period size: 40 Copynumber: 4.3 Consensus size: 41
4303864 TTTTTGAACG
*
4303874 AACGCCAG-TAAATATTCGTATTTTAGTGGTGTTTTTATATA
1 AACGCC-GCTAAATATTCGTACTTTAGTGGTGTTTTTATATA
* ** * * *
4303915 AACGCCGCTAAATAAT-GTACTTTAGTGGCATTTTAAGCACA
1 AACGCCGCTAAATATTCGTACTTTAGTGGTGTTTTTA-TATA
* * *
4303956 AACGACGTTAAATATTCTTACTTTAGTGGTG-TTTTATATA
1 AACGCCGCTAAATATTCGTACTTTAGTGGTGTTTTTATATA
** * * *** *
4303996 AATACCACTAAATATT-ATACTTTAGTAACGTTTTTATACA
1 AACGCCGCTAAATATTCGTACTTTAGTGGTGTTTTTATATA
*
4304036 AACACCGCTAAA
1 AACGCCGCTAAA
4304048 AACTCGTAAC
Statistics
Matches: 101, Mismatches: 28, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
39 10 0.10
40 48 0.48
41 32 0.32
42 11 0.11
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (41 bp):
AACGCCGCTAAATATTCGTACTTTAGTGGTGTTTTTATATA
Found at i:4303991 original size:42 final size:41
Alignment explanation
Indices: 4303882--4303991 Score: 114
Period size: 41 Copynumber: 2.7 Consensus size: 41
4303872 CGAACGCCAG
* * * * *
4303882 TAAATATTCGTATTTTAGTGGTGTTTTTATATAAACGCCGC
1 TAAATATTCGTACTTTAGTGGTGTTTTAACACAAACGACGC
* ** *
4303923 TAAATAAT-GTACTTTAGTGGCATTTTAAGCACAAACGACGT
1 TAAATATTCGTACTTTAGTGGTGTTTTAA-CACAAACGACGC
*
4303964 TAAATATTCTTACTTTAGTGGTGTTTTA
1 TAAATATTCGTACTTTAGTGGTGTTTTA
4303992 TATAAATACC
Statistics
Matches: 54, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
40 16 0.30
41 22 0.41
42 16 0.30
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (41 bp):
TAAATATTCGTACTTTAGTGGTGTTTTAACACAAACGACGC
Found at i:4307250 original size:21 final size:20
Alignment explanation
Indices: 4307226--4307294 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
4307216 ATAAACTTTG
4307226 ATTTATTATTATGGATTTCAA
1 ATTTATT-TTATGGATTTCAA
*
4307247 ATTTCTTGTTATGGATTTCAA
1 ATTTATT-TTATGGATTTCAA
* * * *
4307268 GTTTGTTTTTTGGATGTCAA
1 ATTTATTTTATGGATTTCAA
*
4307288 GTTTATT
1 ATTTATT
4307295 GGATAATGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.23, C:0.06, G:0.16, T:0.55
Consensus pattern (20 bp):
ATTTATTTTATGGATTTCAA
Found at i:4311158 original size:54 final size:54
Alignment explanation
Indices: 4311092--4311202 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
4311082 TGAGGAAAAT
4311092 TTACACCACAATTTAAATTGTTTCCTGTAAAACTGAATAAACAAAGTTAATAGA
1 TTACACCACAATTTAAATTGTTTCCTGTAAAACTGAATAAACAAAGTTAATAGA
* *
4311146 TTACACCGCAATTTAAATTGTTTCCTGTAAAACTGAATAAACAAAGTTAATGGA
1 TTACACCACAATTTAAATTGTTTCCTGTAAAACTGAATAAACAAAGTTAATAGA
4311200 TTA
1 TTA
4311203 AGTTCACGAC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.32
Consensus pattern (54 bp):
TTACACCACAATTTAAATTGTTTCCTGTAAAACTGAATAAACAAAGTTAATAGA
Found at i:4317823 original size:28 final size:28
Alignment explanation
Indices: 4317770--4317828 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
4317760 AAATTTTACC
*
4317770 GATCTAACACCCTTTCTGATGAGGCGCG
1 GATCTAACACCCTTTCTGATCAGGCGCG
*
4317798 GATCTAGCACCCTTTCTGA-CATGGCGCG
1 GATCTAACACCCTTTCTGATCA-GGCGCG
4317826 GAT
1 GAT
4317829 AGTTATCCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.25
Consensus pattern (28 bp):
GATCTAACACCCTTTCTGATCAGGCGCG
Found at i:4321612 original size:3 final size:3
Alignment explanation
Indices: 4321604--4321657 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
4321594 CTCCTCACTC
* * * *
4321604 TCA TCA TCA TCT TCA TCA TCA TCA CCA TCA CCA TTA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
4321652 TCA TCA
1 TCA TCA
4321658 GGAGCAGGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:4323288 original size:112 final size:112
Alignment explanation
Indices: 4323091--4323314 Score: 376
Period size: 112 Copynumber: 2.0 Consensus size: 112
4323081 GTATGCAAGC
* *
4323091 TCGTGCATACATTTTAACCTGCTCCTCCGAGGCTTTGCTACTCAAACGCTTGAAAGTTACATCCA
1 TCGTGCATACATTTTAACCTACTCCTCCGAGGCGTTGCTACTCAAACGCTTGAAAGTTACATCCA
* *
4323156 ACCAATTTAGCATAATTCGACCACCGTTTAAATTAGGCGGGACATCT
66 ACCAATTTAACATAATTCGACCACCATTTAAATTAGGCGGGACATCT
* *
4323203 TCGTGCATACATTTTATCCTACTGCTCCGAGGCGTTGCTACTCAAACGCTTGAAAGTTACATCCA
1 TCGTGCATACATTTTAACCTACTCCTCCGAGGCGTTGCTACTCAAACGCTTGAAAGTTACATCCA
* *
4323268 ACCAATTTAACGTAATTCGACCACTATTTAAATTAGGCGGGACATCT
66 ACCAATTTAACATAATTCGACCACCATTTAAATTAGGCGGGACATCT
4323315 CCAAGATACT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 104 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (112 bp):
TCGTGCATACATTTTAACCTACTCCTCCGAGGCGTTGCTACTCAAACGCTTGAAAGTTACATCCA
ACCAATTTAACATAATTCGACCACCATTTAAATTAGGCGGGACATCT
Found at i:4332496 original size:13 final size:13
Alignment explanation
Indices: 4332474--4332498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4332464 TCAAAATCAT
4332474 ATCTCAAAAATAA
1 ATCTCAAAAATAA
4332487 ATCTCAAAAATA
1 ATCTCAAAAATA
4332499 TTTAGGGCCA
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (13 bp):
ATCTCAAAAATAA
Found at i:4339645 original size:157 final size:159
Alignment explanation
Indices: 4339343--4339693 Score: 496
Period size: 157 Copynumber: 2.2 Consensus size: 159
4339333 CCTCCACTTC
* * *
4339343 AAGTCCGTTTTTACCAAATTTGAACCACATGTTCCTATACCATAGTAGAATACATGTGTACTTTC
1 AAGTTCGTTTTTACCAAATTTGAACCACATGCTCCTATAACATAGTAGAATACATGTGTACTTTC
* *
4339408 AATTCATCTTTTTGATAACAATTTTTTTTTTATTTTTCAATTTAGTCATTCAATTTTTTATATCC
66 AATTCATCTTTTTGATAACAA-TTTTTTTTTATGTTTCAATTTAGTCATTCAATTTTTCATATCC
**
4339473 TCCTTATTTTTTCAATTCGTCATTTATTTT
130 TCCTTATTCCTTCAATTCGTCATTTATTTT
* *
4339503 AAGTTCGTTTTTACCAAATTTGAGCCACATGCTCCTA-AACATAGTAGAATACATGTGTACTTTT
1 AAGTTCGTTTTTACCAAATTTGAACCACATGCTCCTATAACATAGTAGAATACATGTGTACTTTC
4339567 AATTTC-TCTTTTTGATAACAA-TTTTTTTTATGTTTCAATTTAGTTC-TTCAATTTTTCATAAT
66 AA-TTCATCTTTTTGATAACAATTTTTTTTTATGTTTCAATTTAG-TCATTCAATTTTTCAT-AT
* *
4339629 -CTCCTTATTCCTTCAATTTGTGATTTATTTT
128 CCTCCTTATTCCTTCAATTCGTCATTTATTTT
** *
4339660 AAGTCTATTTTTTATCAAATTTGAACCACATGCT
1 AAGT-TCGTTTTTACCAAATTTGAACCACATGCT
4339694 GATATACTAC
Statistics
Matches: 172, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
157 64 0.37
158 29 0.17
159 42 0.24
160 37 0.22
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.49
Consensus pattern (159 bp):
AAGTTCGTTTTTACCAAATTTGAACCACATGCTCCTATAACATAGTAGAATACATGTGTACTTTC
AATTCATCTTTTTGATAACAATTTTTTTTTATGTTTCAATTTAGTCATTCAATTTTTCATATCCT
CCTTATTCCTTCAATTCGTCATTTATTTT
Found at i:4339938 original size:20 final size:21
Alignment explanation
Indices: 4339900--4339948 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
4339890 TCTTTAAAAT
*
4339900 ATAATATTATGAATTTATTTC
1 ATAATATTATGAATATATTTC
* *
4339921 ATAATTTTA-GAATATATTTG
1 ATAATATTATGAATATATTTC
4339941 AT-ATATTA
1 ATAATATTA
4339949 AATAACATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 5 0.21
20 11 0.46
21 8 0.33
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (21 bp):
ATAATATTATGAATATATTTC
Found at i:4349583 original size:44 final size:44
Alignment explanation
Indices: 4349465--4349583 Score: 136
Period size: 43 Copynumber: 2.7 Consensus size: 44
4349455 GTTGGTTCTG
* * *
4349465 AAAAACGCCGCTAAATGTTCTTACATTTAGTGGTGTTTGTTACC
1 AAAAATGCCGCTAAATGTTCTGACATTTAGTGGCGTTTGTTACC
* *
4349509 -AAAGTGCCGCTAAATGTTCTGACTTTTAGTGGCGTTTGTT-CC
1 AAAAATGCCGCTAAATGTTCTGACATTTAGTGGCGTTTGTTACC
* *
4349551 AAAAAATGCCGTTAAATG-TCATGACATATAGTG
1 -AAAAATGCCGCTAAATGTTC-TGACATTTAGTG
4349584 AGTTTTTTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
42 2 0.03
43 37 0.59
44 24 0.38
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (44 bp):
AAAAATGCCGCTAAATGTTCTGACATTTAGTGGCGTTTGTTACC
Found at i:4349796 original size:21 final size:21
Alignment explanation
Indices: 4349770--4349828 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
4349760 ATTATCCAAT
*
4349770 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
4349791 AAACTTGAAATTCATAACAAC
1 AAACTTGAAATCCATAACAAC
4349812 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
4349829 TAATAAATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:4354561 original size:43 final size:45
Alignment explanation
Indices: 4354513--4354596 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
4354503 TCTAATTTAT
*
4354513 TTATAG-T-TATATTGGTATAGATATGATCTATATTTTATTATCA
1 TTATAGTTGTATATTGGTATAGATATGATCTATAATTTATTATCA
*
4354556 TTATAGTTGTATATTGGTATATATATGATCTATAATTTATT
1 TTATAGTTGTATATTGGTATAGATATGATCTATAATTTATT
4354597 TATAAACCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 6 0.16
44 1 0.03
45 30 0.81
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (45 bp):
TTATAGTTGTATATTGGTATAGATATGATCTATAATTTATTATCA
Found at i:4355309 original size:16 final size:16
Alignment explanation
Indices: 4355288--4355345 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
4355278 CAATCCTAGA
4355288 AAAAAATATAAGGAAT
1 AAAAAATATAAGGAAT
4355304 AAAAAATATAAGGAAT
1 AAAAAATATAAGGAAT
*
4355320 AAAAAATATAAAGAAT
1 AAAAAATATAAGGAAT
*
4355336 CAAACAATAT
1 -AAAAAATAT
4355346 CTTGTTGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
16 31 0.79
17 8 0.21
ACGTcount: A:0.69, C:0.03, G:0.09, T:0.19
Consensus pattern (16 bp):
AAAAAATATAAGGAAT
Found at i:4357055 original size:123 final size:121
Alignment explanation
Indices: 4356803--4357025 Score: 279
Period size: 123 Copynumber: 1.8 Consensus size: 121
4356793 ACTATTGTGA
* *
4356803 CGTTTGTCTAAAAAACGCCATTAAAGAACGATTCTTTTGCGGTGTTTTTTAGAAACACCACTAAA
1 CGTTTGTCTAAAAAACGCCACTAAAGAACGATTATTTTGCGGTGTTTTTTAGAAACACCACTAAA
* * * *
4356868 GTACTAGGTTTTAGCGTCGTTTGTCTAAAAATGCCACAATATATGTACCATATTGCGG
66 GTAC-AGGTTTTAGCGGCATTTGTCTAAAAACGCCAC-ATATAAGTACCATATTGCGG
* * *
4356926 CGTTTGTTTAAAAAA-TCCACTAAAGAACGATTATTTTGCGGTGTTTGTTTAGAAACGCCACTAA
1 CGTTTGTCTAAAAAACGCCACTAAAGAACGATTATTTTGCGGTGTTT-TTTAGAAACACCACTAA
* * *
4356990 AGTA-GGGTTTTGTGGCGGCATTTGTTTAAAAACGCC
65 AGTACAGG-TTT-TAGCGGCATTTGTCTAAAAACGCC
4357026 TCTAAAGTAC
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
121 2 0.02
122 31 0.36
123 53 0.62
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (121 bp):
CGTTTGTCTAAAAAACGCCACTAAAGAACGATTATTTTGCGGTGTTTTTTAGAAACACCACTAAA
GTACAGGTTTTAGCGGCATTTGTCTAAAAACGCCACATATAAGTACCATATTGCGG
Found at i:4360808 original size:21 final size:24
Alignment explanation
Indices: 4360774--4360840 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 24
4360764 TATATATATA
*
4360774 TATTTA-ATTATATT-TTTTTATT
1 TATTTATACTATATTATTTTTATT
**
4360796 TA-TT-TACTATATTCCTTTT-TT
1 TATTTATACTATATTATTTTTATT
*
4360817 TATTTATATTATATTATTTTTATT
1 TATTTATACTATATTATTTTTATT
4360841 ATATATCTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
21 13 0.37
22 8 0.23
23 12 0.34
24 2 0.06
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.70
Consensus pattern (24 bp):
TATTTATACTATATTATTTTTATT
Found at i:4360829 original size:23 final size:22
Alignment explanation
Indices: 4360784--4360853 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
4360774 TATTTAATTA
*
4360784 TATTTTTTTATTTATTTACTATAT
1 TATTTTTTTATTTA--TATTATAT
*
4360808 TCCTTTTTTTATTTATATTATAT
1 T-ATTTTTTTATTTATATTATAT
* *
4360831 TATTTTTATTATATATCTTATAT
1 TATTTTT-TTATTTATATTATAT
4360854 CATTATATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.13
23 21 0.54
24 1 0.03
25 12 0.31
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTTTTTATTTATATTATAT
Found at i:4360835 original size:14 final size:15
Alignment explanation
Indices: 4360817--4360892 Score: 73
Period size: 16 Copynumber: 4.9 Consensus size: 15
4360807 TTCCTTTTTT
4360817 TATTTATATTATAT-
1 TATTTATATTATATA
*
4360831 TATTTTTATTATATA
1 TATTTATATTATATA
*
4360846 TCTTATATCATTATATA
1 TATT-TAT-ATTATATA
*
4360863 TATATATATATATATA
1 TATTTATAT-TATATA
*
4360879 TATATATATGTATA
1 TATTTATAT-TATA
4360893 GATGTATTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
14 13 0.25
15 5 0.10
16 24 0.46
17 10 0.19
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (15 bp):
TATTTATATTATATA
Found at i:4360862 original size:2 final size:2
Alignment explanation
Indices: 4360840--4360892 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
4360830 TTATTTTTAT
*
4360840 TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4360881 TA TA TA TG TA TA
1 TA TA TA TA TA TA
4360893 GATGTATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
1 2 0.04
2 41 0.91
3 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4360969 original size:39 final size:38
Alignment explanation
Indices: 4360922--4361007 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 38
4360912 ATTTACTATG
4360922 TATATATATATTTTCTTAATATTATATTTTATACGTT-TT
1 TATATATATATTTTCTTAATATTATATTTT-TA-GTTATT
* *
4360961 TATATATATATTTTCTTAATATTCTATTTTTATTTATT
1 TATATATATATTTTCTTAATATTATATTTTTAGTTATT
4360999 TATATATAT
1 TATATATAT
4361008 TATATTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
37 2 0.05
38 13 0.30
39 29 0.66
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (38 bp):
TATATATATATTTTCTTAATATTATATTTTTAGTTATT
Found at i:4360999 original size:26 final size:27
Alignment explanation
Indices: 4360979--4361028 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
4360969 TATTTTCTTA
*
4360979 ATATTCTATTTTTA-TTTA-TTTATAT
1 ATATTATATTTTTACTTTATTTTATAT
4361004 ATATTATATTTTTACTTTATTTTAT
1 ATATTATATTTTTACTTTATTTTAT
4361029 TTTTTTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 4 0.18
27 5 0.23
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (27 bp):
ATATTATATTTTTACTTTATTTTATAT
Found at i:4361008 original size:25 final size:26
Alignment explanation
Indices: 4360969--4361042 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
4360959 TTTATATATA
*
4360969 TATTTTCTTAATATTCTATTTTTA-TT
1 TATTTTATT-ATATTCTATTTTTACTT
*
4360995 TA-TTTATATATATTATATTTTTACTT
1 TATTTTAT-TATATTCTATTTTTACTT
* *
4361021 TATTTTATTTTTTTCTATTTTT
1 TATTTTATTATATTCTATTTTT
4361043 TTTCTTAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 17 0.43
26 18 0.45
27 5 0.12
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (26 bp):
TATTTTATTATATTCTATTTTTACTT
Found at i:4361096 original size:36 final size:36
Alignment explanation
Indices: 4361026--4361113 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 36
4361016 TACTTTATTT
* *
4361026 TATTT-TTTTCTATTTTTTTTCTTAATATCGTATATA
1 TATTTATTTTTTATTTTTTTACTTAATATC-TATATA
*
4361062 TATTTATTTTTTATTTGTTTTACTTAGTAT-TATATA
1 TATTTATTTTTTATTT-TTTTACTTAATATCTATATA
*
4361098 TTTATTA-TTTTTATTT
1 TAT-TTATTTTTTATTT
4361114 AGTAAATACT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
36 22 0.49
37 12 0.27
38 11 0.24
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (36 bp):
TATTTATTTTTTATTTTTTTACTTAATATCTATATA
Found at i:4361098 original size:38 final size:37
Alignment explanation
Indices: 4361026--4361113 Score: 92
Period size: 38 Copynumber: 2.4 Consensus size: 37
4361016 TACTTTATTT
* * *
4361026 TATTT-TTTTCTATTTTTTTTCTTAATATCGTATATA
1 TATTTATTTTTTATTTTTTTACTTAATATCATATATA
* * *
4361062 TATTTATTTTTTATTTGTTTTACTTAGTATTATATATT
1 TATTTATTTTTTATTT-TTTTACTTAATATCATATATA
4361100 TA-TTA-TTTTTATTT
1 TATTTATTTTTTATTT
4361114 AGTAAATACT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
36 14 0.32
37 12 0.27
38 18 0.41
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (37 bp):
TATTTATTTTTTATTTTTTTACTTAATATCATATATA
Found at i:4361180 original size:18 final size:17
Alignment explanation
Indices: 4361140--4361184 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
4361130 TATGTACACA
*
4361140 TTATTTTTATTCATTTT
1 TTATTTTTTTTCATTTT
* *
4361157 TAATTTCTTTTTCCTTTT
1 TTATTT-TTTTTCATTTT
4361175 TTATTTTTTT
1 TTATTTTTTT
4361185 ACTCCATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (17 bp):
TTATTTTTTTTCATTTT
Found at i:4365714 original size:10 final size:10
Alignment explanation
Indices: 4365699--4365742 Score: 54
Period size: 10 Copynumber: 4.2 Consensus size: 10
4365689 CAATCCGAAC
4365699 AAAAAGAGAA
1 AAAAAGAGAA
4365709 AAAAAGAGAAAA
1 AAAAAGAG--AA
4365721 TAAAAAGAGAA
1 -AAAAAGAGAA
4365732 AAAAAG-GAA
1 AAAAAGAGAA
4365741 AA
1 AA
4365743 TTGAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.16
10 14 0.45
11 2 0.06
12 2 0.06
13 8 0.26
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (10 bp):
AAAAAGAGAA
Found at i:4365727 original size:13 final size:13
Alignment explanation
Indices: 4365709--4365733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4365699 AAAAAGAGAA
4365709 AAAAAGAGAAAAT
1 AAAAAGAGAAAAT
4365722 AAAAAGAGAAAA
1 AAAAAGAGAAAA
4365734 AAAGGAAAAT
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:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (13 bp):
AAAAAGAGAAAAT
Found at i:4365749 original size:23 final size:23
Alignment explanation
Indices: 4365699--4365743 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
4365689 CAATCCGAAC
4365699 AAAAAGAGAAAAAAAGAGAAAAT
1 AAAAAGAGAAAAAAAGAGAAAAT
4365722 AAAAAGAGAAAAAAAG-GAAAAT
1 AAAAAGAGAAAAAAAGAGAAAAT
4365744 TGAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (23 bp):
AAAAAGAGAAAAAAAGAGAAAAT
Found at i:4365925 original size:69 final size:69
Alignment explanation
Indices: 4365814--4365951 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
4365804 GATTCAAAAT
*
4365814 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
4365879 TCAA
66 TCAA
* *
4365883 ATGAGATTGATCGAGCACAATCATTTCCGAATCACTGAATCACTTCACTTGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
4365948 TCAA
66 TCAA
4365952 GAGAGACACA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
TCAA
Found at i:4366913 original size:32 final size:31
Alignment explanation
Indices: 4366877--4366996 Score: 150
Period size: 32 Copynumber: 3.7 Consensus size: 31
4366867 GGAACAATGA
*
4366877 GGGCATCTTTGAAGATTCAATATCAAATGTTG
1 GGGCATCTTTG-AGATTCAACATCAAATGTTG
* * *
4366909 GGGCAGTTTTTTAGATTTAACATCAAATGTTG
1 GGGCA-TCTTTGAGATTCAACATCAAATGTTG
*
4366941 GGGCATCTTTTGAGATTCAACATCAAATATTG
1 GGGCATC-TTTGAGATTCAACATCAAATGTTG
*
4366973 GGGCATCTTTGGGAATTCAACATC
1 GGGCATCTTTGAG-ATTCAACATC
4366997 CCGATGCTAA
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
31 6 0.08
32 66 0.87
33 4 0.05
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATGTTG
Found at i:4367702 original size:106 final size:106
Alignment explanation
Indices: 4367577--4367789 Score: 257
Period size: 106 Copynumber: 2.0 Consensus size: 106
4367567 CGTGCCACTT
* * *
4367577 GAGACAACACAAGTTCAACTCCATAACG-AAGGGATGACTGGTTGTAAACAAATAATTTCCCAAT
1 GAGACAACACAAGCTCAACTCCACAACGAAAGGG-TGACTGGTTGTAAACAAACAATTTCCCAAT
*
4367641 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
65 TCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* * ** * ** *
4367683 GAGACAACACAAGCTCAACTTCACAGCGAAAGGGTGGTTGGTTGTCAACAAACAATTTCTTAGTT
1 GAGACAACACAAGCTCAACTCCACAACGAAAGGGTGACTGGTTGTAAACAAACAATTTCCCAATT
* * * * *
4367748 CCATAGCCAATTTTAACTTCACGGTGGAGGATATTGGACTC
66 CCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
4367789 G
1 G
4367790 GAACAATACA
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
106 84 0.94
107 5 0.06
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (106 bp):
GAGACAACACAAGCTCAACTCCACAACGAAAGGGTGACTGGTTGTAAACAAACAATTTCCCAATT
CCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
Found at i:4368046 original size:67 final size:68
Alignment explanation
Indices: 4367937--4368085 Score: 189
Period size: 68 Copynumber: 2.2 Consensus size: 68
4367927 ACAGTTTCCA
* * *
4367937 AGTTTCCCTTG-AA-ACAAAATCTTTAAATTTATTTCTACTAAAAC-AAATTTTGTCTCCCTTGA
1 AGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCTACTAAAACAAAATTTTATCTCCCTTGA
4367999 GAC
66 GAC
* *
4368002 AGTTTCTCTTGAAACACAAAATCTTCAAATTTATTT-TCCTTAAAACAAAATTTTATTTCCCTTG
1 AGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCTAC-TAAAACAAAATTTTATCTCCCTTG
4368066 AGAC
65 AGAC
* * *
4368070 CGTTTTTCATGAAACA
1 AGTTTCTCTTGAAACA
4368086 ACAGATATCT
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
65 10 0.14
66 4 0.06
67 26 0.36
68 32 0.44
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.39
Consensus pattern (68 bp):
AGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCTACTAAAACAAAATTTTATCTCCCTTGA
GAC
Found at i:4369001 original size:110 final size:108
Alignment explanation
Indices: 4368795--4369067 Score: 351
Period size: 110 Copynumber: 2.5 Consensus size: 108
4368785 ACGAAGGGGC
*
4368795 TTCCCAG-T-TTCAGAGCCAATTTTAACTTCACAGCGAGGGATATTGGACT-GAAGACAACACAA
1 TTCCCAGTTCTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCG-AGACAACACAA
* *
4368857 GCTCAAATTCATAATGAAGGGGAGACTGATTGTCAACAAACAACT
65 GCTCAAATTCATAACGAAGGGGAGACTGACTGTCAACAAACAA-T
* * * *
4368902 TT-TCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACA
1 TTCCCAG-TTC-TTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * * *
4368966 AGCTCAACTTCATAGCGAAGGGGCGACTGGCTGTCAACAAACAAT
64 AGCTCAAATTCATAACGAAGGGGAGACTGACTGTCAACAAACAAT
* *
4369011 TTCCCAGTTC--CAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCGAAACAA
1 TTCCCAGTTCTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAA
4369068 TACTACCCAC
Statistics
Matches: 143, Mismatches: 17, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
106 45 0.31
107 2 0.01
108 1 0.01
109 6 0.04
110 88 0.62
111 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (108 bp):
TTCCCAGTTCTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
CTCAAATTCATAACGAAGGGGAGACTGACTGTCAACAAACAAT
Found at i:4370503 original size:23 final size:24
Alignment explanation
Indices: 4370446--4370521 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 24
4370436 TATATTTTTA
*
4370446 ATTATATTTTTTTATTTATTTTCTAT
1 ATTA-ATTTTTTTATTTA-TATCTAT
**
4370472 ATTCCTTTTTTTATTTATAT-TAT
1 ATTAATTTTTTTATTTATATCTAT
* *
4370495 ATTAATTTTATTATATATATCTTAT
1 ATTAATTTTTTTATTTATATC-TAT
4370520 AT
1 AT
4370522 CATTATATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
23 19 0.46
24 2 0.05
25 17 0.41
26 3 0.07
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTAATTTTTTTATTTATATCTAT
Found at i:4370616 original size:2 final size:2
Alignment explanation
Indices: 4370609--4370633 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4370599 TATACGTTTT
4370609 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 T
4370634 TCTTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4370843 original size:18 final size:17
Alignment explanation
Indices: 4370811--4370855 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
4370801 TGTACACATT
4370811 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
4370828 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
4370846 ATTTTTTTAC
1 ATTTTTTTAC
4370856 TCCTTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:4370853 original size:17 final size:17
Alignment explanation
Indices: 4370809--4370855 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
4370799 TATGTACACA
4370809 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
4370826 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
4370844 TTATTTTTTTAC
1 TTATTTTTTTAC
4370856 TCCTTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:4374800 original size:24 final size:24
Alignment explanation
Indices: 4374768--4374819 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4374758 AAAAATTTAA
*
4374768 AAAATATATAATATATAGTTTTTG
1 AAAACATATAATATATAGTTTTTG
* *
4374792 AAAACATATATTGTATAGTTTTTG
1 AAAACATATAATATATAGTTTTTG
4374816 AAAA
1 AAAA
4374820 TATTTTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (24 bp):
AAAACATATAATATATAGTTTTTG
Found at i:4374839 original size:30 final size:30
Alignment explanation
Indices: 4374805--4374868 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
4374795 ACATATATTG
*
4374805 TATAGTTTTTGAAA-ATATTTTGAAAACATA
1 TATAGTTTTTAAAACAT-TTTTGAAAACATA
4374835 TATAGTTTTTAAAACATTTTTGAAAACATA
1 TATAGTTTTTAAAACATTTTTGAAAACATA
4374865 TATA
1 TATA
4374869 AAATATATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (30 bp):
TATAGTTTTTAAAACATTTTTGAAAACATA
Found at i:4376764 original size:30 final size:30
Alignment explanation
Indices: 4376730--4376791 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
4376720 ACCTATTGAC
*
4376730 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTAGAT
4376760 AGTTACCGAGGATCTTTATGACCTCTAGAT
1 AGTTACCGAGGATCTTTATGACCTCTAGAT
4376790 AG
1 AG
4376792 GTCCTTCGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTAGAT
Found at i:4382008 original size:30 final size:30
Alignment explanation
Indices: 4381962--4382033 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
4381952 GTTCTTCGAA
* *
4381962 ACCTATGGACAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
4381992 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
4382022 ACCTCTGGATAG
1 ACCTCTGGATAG
4382034 GTCCTTCGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:4384022 original size:20 final size:19
Alignment explanation
Indices: 4383982--4384028 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
4383972 AGTTTTTCAA
4383982 TTTTAATTT--TTTATATT
1 TTTTAATTTACTTTATATT
*
4383999 TTTTATTTTACTTTATATTT
1 TTTTAATTTACTTTATA-TT
4384019 TTTTAATTTA
1 TTTTAATTTA
4384029 ACCTTTTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
19 6 0.24
20 11 0.44
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTAATTTACTTTATATT
Found at i:4384239 original size:6 final size:6
Alignment explanation
Indices: 4384228--4384254 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4384218 GATCAAATTT
4384228 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
4384255 TCGCAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:4390021 original size:16 final size:17
Alignment explanation
Indices: 4389996--4390029 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4389986 CCGAGGTGTT
4389996 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
4390012 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
4390029 A
1 A
4390030 GAATGAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:4390719 original size:23 final size:24
Alignment explanation
Indices: 4390672--4390721 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
4390662 CCATTAGGGG
*
4390672 CACGTAGAATTTGTCCCGAAAGAC
1 CACGTAGAATATGTCCCGAAAGAC
* *
4390696 CACGTAGAA-ATGTTCCGAATGAC
1 CACGTAGAATATGTCCCGAAAGAC
4390719 CAC
1 CAC
4390722 ATATAACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (24 bp):
CACGTAGAATATGTCCCGAAAGAC
Found at i:4391031 original size:15 final size:15
Alignment explanation
Indices: 4391007--4391037 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4390997 ATCTCTTGAT
4391007 CATTTAATCACATAA
1 CATTTAATCACATAA
*
4391022 CATTTTATCACATAA
1 CATTTAATCACATAA
4391037 C
1 C
4391038 TCATAGTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (15 bp):
CATTTAATCACATAA
Found at i:4392423 original size:46 final size:45
Alignment explanation
Indices: 4392372--4392478 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
4392362 TGCACATACC
* * * *
4392372 ATGCATTGATGCACTGAGGAT-TTTATGAAAACATTGAATGCATTTG
1 ATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTG
* *
4392418 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTG
4392463 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
4392479 TTAATGCACC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 32 0.59
46 19 0.35
47 3 0.06
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTG
Found at i:4398014 original size:23 final size:21
Alignment explanation
Indices: 4397926--4398020 Score: 79
Period size: 21 Copynumber: 4.4 Consensus size: 21
4397916 TTGTGCTTCA
*
4397926 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
* *
4397946 TACATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
*
4397968 TGCATCGATACA-CTATGAAGG
1 TGCATCGATACACCT-TGAATG
*
4397989 TGCACCGATACACGCCTTGAATG
1 TGCATCGATACA--CCTTGAATG
4398012 TGCATCGAT
1 TGCATCGAT
4398021 GCACAAGGCC
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.20
21 18 0.31
22 12 0.20
23 15 0.25
24 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:4399263 original size:45 final size:46
Alignment explanation
Indices: 4399171--4399274 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 46
4399161 TGCATATACC
* * *
4399171 ATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGTATTTG
1 ATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTG
* *
4399217 ATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAATGCACTTG
1 ATGCATCGATGCACTCAGGAT-TTTATGAAAACATCGAATGCACTTG
*
4399262 ATGTATCGATGCA
1 ATGCATCGATGCA
4399275 TTCTTAATGC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 28 0.55
46 20 0.39
47 3 0.06
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTG
Found at i:4402386 original size:16 final size:17
Alignment explanation
Indices: 4402361--4402394 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4402351 CTGAGGTGTC
4402361 ACATTAACTTTT-CAAA
1 ACATTAACTTTTACAAA
*
4402377 ACATTTACTTTTACAAA
1 ACATTAACTTTTACAAA
4402394 A
1 A
4402395 GAATGAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (17 bp):
ACATTAACTTTTACAAA
Found at i:4411541 original size:13 final size:13
Alignment explanation
Indices: 4411525--4411554 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4411515 TTATGACACG
*
4411525 CATTTATGACTTA
1 CATTTACGACTTA
4411538 CATTTACGACTTA
1 CATTTACGACTTA
4411551 CATT
1 CATT
4411555 GCGTGTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
CATTTACGACTTA
Found at i:4415552 original size:20 final size:20
Alignment explanation
Indices: 4415527--4415592 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
4415517 TTCTCAACTT
4415527 ACTCTCAATATTCAGAATTC
1 ACTCTCAATATTCAGAATTC
4415547 ACTCTCAATATTCAGAATTC
1 ACTCTCAATATTCAGAATTC
*
4415567 ACTCTCGATATTCAGAATTC
1 ACTCTCAATATTCAGAATTC
4415587 ACTCTC
1 ACTCTC
4415593 CAAGTGTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (20 bp):
ACTCTCAATATTCAGAATTC
Found at i:4425859 original size:20 final size:21
Alignment explanation
Indices: 4425821--4425859 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4425811 CATTAAGGTC
4425821 TTTGTTGAAGCCATGAAATCT
1 TTTGTTGAAGCCATGAAATCT
*
4425842 TTTGTTGAGGCCAT-AAAT
1 TTTGTTGAAGCCATGAAAT
4425860 TCCTGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (21 bp):
TTTGTTGAAGCCATGAAATCT
Found at i:4438723 original size:2 final size:2
Alignment explanation
Indices: 4438718--4438767 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
4438708 CTTTTGTGTG
4438718 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
4438760 TA TA TA TA
1 TA TA TA TA
4438768 CACATCAAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4441524 original size:12 final size:12
Alignment explanation
Indices: 4441507--4441537 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4441497 TGGATTCAAA
4441507 TCGCGTTTTCGG
1 TCGCGTTTTCGG
4441519 TCGCGTTTTCGG
1 TCGCGTTTTCGG
4441531 TCGCGTT
1 TCGCGTT
4441538 GCGTTTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.26, G:0.32, T:0.42
Consensus pattern (12 bp):
TCGCGTTTTCGG
Found at i:4444606 original size:32 final size:31
Alignment explanation
Indices: 4444566--4444641 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 31
4444556 ATGTCCTATT
*
4444566 GTCGTCGACAACTAACATTAAAGTTAGTATC
1 GTCGTCGACAACTAACATTAAAATTAGTATC
* *
4444597 GTCGGTCGACAATTAACATTAAAATTAGTGTC
1 GTC-GTCGACAACTAACATTAAAATTAGTATC
4444629 GTCGTCGATCAAC
1 GTCGTCGA-CAAC
4444642 AAAAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 8 0.21
32 31 0.79
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (31 bp):
GTCGTCGACAACTAACATTAAAATTAGTATC
Found at i:4448868 original size:2 final size:2
Alignment explanation
Indices: 4448855--4448910 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
4448845 AGATGGCCAA
*
4448855 AT AT AT AC 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
4448897 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
4448911 CTTACACATC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4455539 original size:14 final size:14
Alignment explanation
Indices: 4455517--4455557 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4455507 TGGTTAAGTT
*
4455517 GAGTTAACTCGTTC
1 GAGTCAACTCGTTC
*
4455531 GAGTCAACTCGTCC
1 GAGTCAACTCGTTC
*
4455545 GAGTCAACCCGTT
1 GAGTCAACTCGTT
4455558 AACTTTGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (14 bp):
GAGTCAACTCGTTC
Found at i:4457331 original size:36 final size:35
Alignment explanation
Indices: 4457290--4457365 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
4457280 AAGTCTCTGT
4457290 AGGTTCAAC-TCTGATCAAGCTGGTAATTCCTTATAC
1 AGGTTCAACATC-GAT-AAGCTGGTAATTCCTTATAC
** * *
4457326 AGGTTCAACATCGATTGGTTGGTAATTCCTTATAT
1 AGGTTCAACATCGATAAGCTGGTAATTCCTTATAC
4457361 AGGTT
1 AGGTT
4457366 TGTATAAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 21 0.60
36 12 0.34
37 2 0.06
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (35 bp):
AGGTTCAACATCGATAAGCTGGTAATTCCTTATAC
Found at i:4460233 original size:14 final size:14
Alignment explanation
Indices: 4460215--4460244 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4460205 AAAATTAAGA
4460215 AAAAAATATTATTTT
1 AAAAAA-ATTATTTT
4460230 AAAAAAATTATTTT
1 AAAAAAATTATTTT
4460244 A
1 A
4460245 TTGGCCCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAAAAATTATTTT
Found at i:4462283 original size:3 final size:3
Alignment explanation
Indices: 4462277--4462308 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
4462267 ATTTATTATT
4462277 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4462309 AAAAAAGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4462298 original size:14 final size:14
Alignment explanation
Indices: 4462279--4462307 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4462269 TTATTATTTA
4462279 ATAATAATAATAAT
1 ATAATAATAATAAT
4462293 ATAATAATAATAAT
1 ATAATAATAATAAT
4462307 A
1 A
4462308 AAAAAAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:4462732 original size:137 final size:137
Alignment explanation
Indices: 4462484--4463923 Score: 1918
Period size: 137 Copynumber: 10.5 Consensus size: 137
4462474 GGATGCTATT
* * * *
4462484 GTTCCTTCGTGATGAGGACGTCTGGCTATCTAAGGATGACGCGACTTC-ACGTGATGAGGAGTTC
1 GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
*
4462548 TGGTC-AGTGGATGACATTGTTCCTTCGTGATGAGGACATCTGACCATCTTTAAAGATAATTGAG
66 TGGTCGA-TGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATAATTGAG
*
4462612 ATAACATG
130 ATAACACG
* * * * * *
4462620 ATTCCTTTGTGATGAAGACTTCTTGCTATCTAAGGATGACTCGGCTCCTACGTGATTAGGATTTC
1 GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
*
4462685 TGGTCGATGGATGACATTGTTCCTTTGTGATGAGGACATCTGGCCATCTTTAAAGATAATTGAGA
66 TGGTCGATGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATAATTGAGA
4462750 TAACACG
131 TAACACG
* * ** * *
4462757 GTTCCTTCGTGATGAAGACTTCTAGCTATCTAAGGATGACTCAACTCCTACATGATGAGAAGTTC
1 GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
* * *
4462822 TGGTCGATGAATGACATTTTTCCTTCGTGATGATGACATCTGGCCATCTTTAAAGATAATTGAGA
66 TGGTCGATGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATAATTGAGA
* *
4462887 TAGCATG
131 TAACACG
* * * * * * *
4462894 GTTCCTTCATGATGAAGACTTATGGCTATCTAAGGATGACTCGGTTCCTAGGTGATGAGAAATTC
1 GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
* * *
4462959 TGGTTCAATGGATGACATTGTTCATTCGTGATGAGGACATCTAGCCATCTTTAAAGATAATTGAG
66 TGG-TCGATGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATAATTGAG
4463024 ATAACACG
130 ATAACACG
* * * * *
4463032 GTTCCTTCATGATGAGGACTTATGGCTAGCTAAGGATGACTCGGCTCATACGTGATAAGGAGTTC
1 GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
* * * * *
4463097 TGGTCGATGAATAACATTGTTCCTTCATGATGAGGACATCTGACCATCTTTAAATATAATTGAGA
66 TGGTCGATGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATAATTGAGA
4463162 TAACACG
131 TAACACG
* * * * *
4463169 GTTCCTTCATGATGAGGACTTCTGGCTATCTAAGGATAACTCAGCTCTTACGTGATGAGGAGTTT
1 GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
* * *
4463234 TGGTCGATGGATGACATTGTTCCTTCATGATGAGGACATCTAGACATCTTTAAAGATAATTGAGA
66 TGGTCGATGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATAATTGAGA
*
4463299 TAATACG
131 TAACACG
* * ** * * *
4463306 GTTCCTTTGTGATGAGGACTCCAAGCTATCTAAGGATGAGTCAGCTTCTACGTGATGAGGAGTTC
1 GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
* **
4463371 TGGTCGATGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGTAATCTTTAAAGATAATTGAGA
66 TGGTCGATGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATAATTGAGA
4463436 TAACACG
131 TAACACG
* * * * *
4463443 GTTCCTTCGCGATGAGGACGTCTGGCTATCTAAGAATGACTCGGCTCCTACATAATGAGGAGTTC
1 GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
* * * * * * * * *
4463508 TAGTCGACGGGTGACATTGTTCATTCATGATGAAGACGTTTGGCCATCTTTAGAGATAATTGAGA
66 TGGTCGATGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATAATTGAGA
4463573 TAACACG
131 TAACACG
* *
4463580 GTTCCTTCGTGATGAGGAATTCTGGCTATCTAAGAATGACTCGGCTCCTACGTGATGAGGAGTTC
1 GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
* * * *
4463645 TGGTCGATAGATGACATTGTTCCTTCATGATGAGGACGTCTAGTCC-TCTTTAGAA-ATAATTGA
66 TGGTCGATGGATGACATTGTTCCTTCGTGATGAGGACATCT-GGCCATCTTTA-AAGATAATTGA
*
4463708 GATAGCACG
129 GATAACACG
* * * * * * *
4463717 GTTCATTAGTGATGAGGAATTCTGGATATCTAAGAATGACTCAGCTCCTACGTGATGAGGAGTTT
1 GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
* * *
4463782 TGGTCGATGGATGACATTGTTCCTTCTTGATGAGGACGTCTGACCATCTTTAGAA-ATAATTGAG
66 TGGTCGATGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTA-AAGATAATTGAG
4463846 ATAACACG
130 ATAACACG
* * * *
4463854 GTTCATTCGTGATGAGGACGTATGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTA
1 GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
4463919 TGGTC
66 TGGTC
4463924 TTGAGGTTGA
Statistics
Matches: 1153, Mismatches: 145, Indels: 11
0.88 0.11 0.01
Matches are distributed among these distances:
136 43 0.04
137 984 0.85
138 126 0.11
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (137 bp):
GTTCCTTCGTGATGAGGACTTCTGGCTATCTAAGGATGACTCGGCTCCTACGTGATGAGGAGTTC
TGGTCGATGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATAATTGAGA
TAACACG
Found at i:4465232 original size:39 final size:39
Alignment explanation
Indices: 4465130--4465237 Score: 157
Period size: 38 Copynumber: 2.8 Consensus size: 39
4465120 TGCATTTAAA
*
4465130 ATTATTTCTTGTTGATATGAGCCTTCAAAATGCCCCAAC
1 ATTATTTCTTGCTGATATGAGCCTTCAAAATGCCCCAAC
* * *
4465169 ATT-TTT-TATGCTGATATGAACCTTCAAAATGTCCTAAC
1 ATTATTTCT-TGCTGATATGAGCCTTCAAAATGCCCCAAC
4465207 ATTATTTCTTGCTGATATGAGCCTTCAAAAT
1 ATTATTTCTTGCTGATATGAGCCTTCAAAAT
4465238 ATCTCAACAT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
37 1 0.02
38 32 0.52
39 27 0.44
40 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (39 bp):
ATTATTTCTTGCTGATATGAGCCTTCAAAATGCCCCAAC
Found at i:4465246 original size:77 final size:77
Alignment explanation
Indices: 4465099--4465248 Score: 203
Period size: 77 Copynumber: 1.9 Consensus size: 77
4465089 CCCCAACATT
* * * *
4465099 TGCTGATACGAACGTTCAAAATGCATTTAAAATTATTTCTTGTTGATATGAGCCTTCAAAATGCC
1 TGCTGATACGAACCTTCAAAATGCA-CTAAAATTATTTCTTGCTGATATGAGCCTTCAAAATACC
4465164 CCAACATTTTTTA
65 CCAACATTTTTTA
* * *
4465177 TGCTGATATGAACCTTCAAAATGTC-CTAACATTATTTCTTGCTGATATGAGCCTTCAAAATATC
1 TGCTGATACGAACCTTCAAAATG-CACTAAAATTATTTCTTGCTGATATGAGCCTTCAAAATACC
*
4465241 TCAACATT
65 CCAACATT
4465249 CCAAGTTGTA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
77 41 0.65
78 21 0.33
79 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (77 bp):
TGCTGATACGAACCTTCAAAATGCACTAAAATTATTTCTTGCTGATATGAGCCTTCAAAATACCC
CAACATTTTTTA
Found at i:4465247 original size:39 final size:38
Alignment explanation
Indices: 4465130--4465248 Score: 152
Period size: 39 Copynumber: 3.1 Consensus size: 38
4465120 TGCATTTAAA
* *
4465130 ATTATTTCTTGTTGATATGAGCCTTCAAAATGCCCCAAC
1 ATTATTTCTTGCTGATATGAGCCTTCAAAATG-TCCAAC
*
4465169 ATT-TTT-TATGCTGATATGAACCTTCAAAATGTCCTAAC
1 ATTATTTCT-TGCTGATATGAGCCTTCAAAATGTCC-AAC
*
4465207 ATTATTTCTTGCTGATATGAGCCTTCAAAATATCTCAAC
1 ATTATTTCTTGCTGATATGAGCCTTCAAAATGTC-CAAC
4465246 ATT
1 ATT
4465249 CCAAGTTGTA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
37 3 0.04
38 30 0.43
39 35 0.50
40 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (38 bp):
ATTATTTCTTGCTGATATGAGCCTTCAAAATGTCCAAC
Found at i:4469254 original size:40 final size:40
Alignment explanation
Indices: 4469209--4469557 Score: 445
Period size: 40 Copynumber: 8.7 Consensus size: 40
4469199 GATTTTCCAT
* *
4469209 AATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATC-CGTAAATCGCAACGCGTATCCGTA
* * **
4469249 AATCGCAACGTGTATCCGTAAATCGCAATGCGTATGGGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* *
4469289 AATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* *
4469329 AATCGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
*
4469369 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
*
4469409 AATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTA
*
4469449 AATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTA
* * * *
4469489 AATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTA
* * * *
4469529 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
4469558 ACTGAAATTT
Statistics
Matches: 282, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
39 1 0.00
40 279 0.99
41 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
Found at i:4469291 original size:60 final size:60
Alignment explanation
Indices: 4469209--4469557 Score: 445
Period size: 60 Copynumber: 5.8 Consensus size: 60
4469199 GATTTTCCAT
* * *
4469209 AATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATC-CGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* ** * *
4469269 AATCGCAATGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* *
4469329 AATCGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* *
4469389 AATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTA
* * * *
4469449 AATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACGCGTATCCGTA
* * * * *
4469509 AATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGT-ATCCGTAAATCGCAACGCGTATCCGTAAATCGCAAC
4469558 ACTGAAATTT
Statistics
Matches: 254, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
59 3 0.01
60 250 0.98
61 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
Found at i:4469539 original size:20 final size:19
Alignment explanation
Indices: 4469227--4469557 Score: 383
Period size: 20 Copynumber: 16.6 Consensus size: 19
4469217 CGCGAACACA
4469227 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
4469247 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
* **
4469267 TAAATCGCAATGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
4469287 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
4469307 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
4469327 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
4469347 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
4469367 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
4469387 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
4469407 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
4469427 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
4469447 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
4469467 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
4469487 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
4469507 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
4469527 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
4469547 TAAATCACAAC
1 TAAATCGCAAC
4469558 ACTGAAATTT
Statistics
Matches: 276, Mismatches: 29, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
19 2 0.01
20 273 0.99
21 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:4470270 original size:24 final size:24
Alignment explanation
Indices: 4470231--4470277 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4470221 AAATTTGGTC
4470231 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
4470255 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
4470278 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:4470469 original size:12 final size:12
Alignment explanation
Indices: 4470452--4470476 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4470442 ATATAATCCT
4470452 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4470464 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4470476 G
1 G
4470477 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:4472804 original size:19 final size:19
Alignment explanation
Indices: 4472782--4473107 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
4472772 CGGAAAATAC
*
4472782 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4472801 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
4472815 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
4472835 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
4472849 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4472868 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4472887 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
4472901 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4472920 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4472939 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
4472953 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4472972 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
4472991 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
4473010 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4473029 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4473048 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
4473062 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4473081 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4473100 AATCGCAA
1 AATCGCAA
4473108 CGAGATAATC
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 12 0.04
18 4 0.01
19 174 0.65
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:4472869 original size:33 final size:34
Alignment explanation
Indices: 4472782--4473107 Score: 321
Period size: 33 Copynumber: 9.2 Consensus size: 34
4472772 CGGAAAATAC
* *
4472782 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
4472815 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
4472849 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
4472887 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
4472920 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
4472953 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
4472991 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
4473029 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
4473061 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
4473100 AATCGCAA
1 AATCGCAA
4473108 CGAGATAATC
Statistics
Matches: 257, Mismatches: 12, Indels: 43
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.01
33 111 0.43
34 32 0.12
35 9 0.04
36 6 0.02
37 4 0.02
38 91 0.35
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:4473043 original size:161 final size:157
Alignment explanation
Indices: 4472810--4473129 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
4472800 AAATCCCAAC
*
4472810 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
4472875 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
4472940 ATCGCAACGAGAGAATCGCAATGCGAA
131 ATCGCAACGAGAGAATCGCAATGCGAA
*
4472967 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGAAAA
4473031 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
61 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
*
4473096 TGAAAATCGCAACGAGATAATCGCAATGCGAA
126 TGAAAATCGCAACGAGAGAATCGCAATGCGAA
4473128 AT
1 AT
4473130 TATAAACGCA
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 3 0.02
160 1 0.01
161 120 0.78
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATGCGAA
Found at i:4473145 original size:52 final size:52
Alignment explanation
Indices: 4472810--4473129 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
4472800 AAATCCCAAC
4472810 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
4472863 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
4472915 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
4472967 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
4473024 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
4473076 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
4473128 AT
1 AT
4473130 TATAAACGCA
Statistics
Matches: 255, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 184 0.72
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:4473245 original size:19 final size:19
Alignment explanation
Indices: 4473136--4473237 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
4473126 AAATTATAAA
4473136 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4473155 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
4473175 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
4473191 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4473208 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4473227 CGCATTGCGAT
1 CGCATTGCGAT
4473238 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:4473363 original size:14 final size:14
Alignment explanation
Indices: 4473344--4473380 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4473334 CATCAATTAC
4473344 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4473358 ACAAATCATCTTTT
1 ACAAATCAACTTTT
4473372 ACAAATCAA
1 ACAAATCAA
4473381 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:4473392 original size:12 final size:12
Alignment explanation
Indices: 4473375--4473447 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
4473365 ATCTTTTACA
4473375 AATCAATTAAAC
1 AATCAATTAAAC
*
4473387 AATCAA--AAATTG
1 AATCAATTAAA--C
**
4473399 AATCAACTTTTAC
1 AATCAA-TTAAAC
4473412 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
4473425 AATCAA-AAAAC
1 AATCAATTAAAC
4473436 AATCAATTAAAC
1 AATCAATTAAAC
4473448 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:4473409 original size:38 final size:38
Alignment explanation
Indices: 4473361--4473433 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
4473351 AACTTTTACA
*
4473361 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
4473399 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
4473434 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:4475289 original size:19 final size:19
Alignment explanation
Indices: 4475249--4475383 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
4475239 TAGTTTACTT
* *
4475249 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
4475269 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
4475288 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4475307 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
4475321 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
4475340 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
4475354 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4475373 TCGCAATGCGA
1 TCGCAACGCGA
4475384 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:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:4475324 original size:14 final size:14
Alignment explanation
Indices: 4475305--4475361 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4475295 GCGAAATGAA
*
4475305 AATCGCAACGACAG
1 AATCGCAACGAAAG
4475319 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
4475336 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
4475352 AATCGCAACG
1 AATCGCAACG
4475362 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:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Done.