Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 35
Found at i:3899359 original size:23 final size:22
Alignment explanation
Indices: 3899308--3899359 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3899298 TCAATAAGTC
* *
3899308 TGTTTGTATGACACGTTTTTTT
1 TGTTTTTATGACAAGTTTTTTT
**
3899330 TCCTTTTATGACAAGTTTTCTTT
1 TGTTTTTATGACAAGTTTT-TTT
3899353 TGTTTTT
1 TGTTTTT
3899360 TACACCTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.13, C:0.12, G:0.13, T:0.62
Consensus pattern (22 bp):
TGTTTTTATGACAAGTTTTTTT
Found at i:3910022 original size:4 final size:4
Alignment explanation
Indices: 3910013--3910059 Score: 78
Period size: 4 Copynumber: 11.8 Consensus size: 4
3910003 ACTAGATTCA
3910013 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATTA- ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A-TAC ATAC ATA
3910060 TACTGGTAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 2 0.05
4 37 0.90
5 2 0.05
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:3910631 original size:3 final size:3
Alignment explanation
Indices: 3910623--3910656 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3910613 TACCAGTACA
3910623 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
3910657 GGTATACACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3911281 original size:22 final size:22
Alignment explanation
Indices: 3911237--3911281 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3911227 CAACCTCTAT
** *
3911237 AACTTAAAAAGTTGCTCTGTTA
1 AACTTAAAAAGTTAATCTCTTA
*
3911259 AACTTAAAATGTTAATCTCTTA
1 AACTTAAAAAGTTAATCTCTTA
3911281 A
1 A
3911282 TGAAATTCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (22 bp):
AACTTAAAAAGTTAATCTCTTA
Found at i:3912288 original size:15 final size:16
Alignment explanation
Indices: 3912259--3912289 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3912249 AATACCCGAC
3912259 CCGAAAAAATATATAA
1 CCGAAAAAATATATAA
3912275 CCGAAAAAAT-TATAA
1 CCGAAAAAATATATAA
3912290 TTTCACCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (16 bp):
CCGAAAAAATATATAA
Found at i:3912811 original size:3 final size:3
Alignment explanation
Indices: 3912803--3912830 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3912793 TATGATTTTG
3912803 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3912831 GTATCATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3916740 original size:113 final size:114
Alignment explanation
Indices: 3916534--3916740 Score: 303
Period size: 113 Copynumber: 1.8 Consensus size: 114
3916524 AAAAACTTTA
* *
3916534 ACTCATCCAGTTATCACGAAACTTCATTTTATCAAATCCTTAGATTAGATACCAAAGATCGTAAA
1 ACTCATCCAGTTATCACGAAACTTCATTTAATCAAATCCTT--ATTAGATACCAAAGATCATAAA
*
3916599 TAAATACCCAATTCCTGAAAATGACAAATCATCTTAAAGAGCTCAAGTTCT
64 CAAATACCCAATTCCTGAAAATGACAAATCATCTTAAAGAGCTCAAGTTCT
*
3916650 ACTCATCCAGTTATCATGAAACTTCACTTTAATTCAAAT-C-T-TTAGATACCAAAGATCATAAA
1 ACTCATCCAGTTATCACGAAACTTCA-TTTAA-TCAAATCCTTATTAGATACCAAAGATCATAAA
* *
3916712 CAAATACCCAATTCCTGCAAATGGCAAAT
64 CAAATACCCAATTCCTGAAAATGACAAAT
3916741 ATTACACGAT
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
113 46 0.55
116 26 0.31
117 5 0.06
118 6 0.07
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (114 bp):
ACTCATCCAGTTATCACGAAACTTCATTTAATCAAATCCTTATTAGATACCAAAGATCATAAACA
AATACCCAATTCCTGAAAATGACAAATCATCTTAAAGAGCTCAAGTTCT
Found at i:3919193 original size:98 final size:98
Alignment explanation
Indices: 3919080--3919407 Score: 487
Period size: 98 Copynumber: 3.4 Consensus size: 98
3919070 GTTGAAAGAG
* *
3919080 TGAAAACACATTCGCCTTCATCGCATAAAACCCATTCGCCTTCAACCTCCTCGTCTGAAAATCCT
1 TGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCAACCTCCTCGTCTGAAAATCCT
3919145 TCGCACTTTAGAGAGATTTCGAGAGATTTCGTC
66 TCGCACTTTAGAGAGATTTCGAGAGATTTCGTC
* *
3919178 TGAAAACCCATTCGCCTTCATCGCAGAAAATCCGTTCGCCTTCAACCTCCTCGTCTGAAAATCCT
1 TGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCAACCTCCTCGTCTGAAAATCCT
3919243 TCGCACTTT------A----GAGAGATTTCGTC
66 TCGCACTTTAGAGAGATTTCGAGAGATTTCGTC
* * *
3919266 TGAAAACCCATTCGCCTTCATCACAGAAAACTCATTCGCCTTCAACCTCCTCGTCTAAAAATCCT
1 TGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCAACCTCCTCGTCTGAAAATCCT
*
3919331 TCGCACTTTAGAGAGATTTCGAAAGATTTCGTC
66 TCGCACTTTAGAGAGATTTCGAGAGATTTCGTC
* * *
3919364 TGAAAACTCATTCGCCTTCATCGAAGAAAACCCATTAGCCTTCA
1 TGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCA
3919408 TCGCAGAAAA
Statistics
Matches: 205, Mismatches: 15, Indels: 20
0.85 0.06 0.08
Matches are distributed among these distances:
88 82 0.40
92 1 0.00
94 1 0.00
98 121 0.59
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.28
Consensus pattern (98 bp):
TGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCAACCTCCTCGTCTGAAAATCCT
TCGCACTTTAGAGAGATTTCGAGAGATTTCGTC
Found at i:3919314 original size:88 final size:88
Alignment explanation
Indices: 3919165--3919351 Score: 331
Period size: 88 Copynumber: 2.1 Consensus size: 88
3919155 GAGAGATTTC
* *
3919165 GAGAGATTTCGTCTGAAAACCCATTCGCCTTCATCGCAGAAAATCCGTTCGCCTTCAACCTCCTC
1 GAGAGATTTCGTCTGAAAACCCATTCGCCTTCATCACAGAAAATCCATTCGCCTTCAACCTCCTC
*
3919230 GTCTGAAAATCCTTCGCACTTTA
66 GTCTAAAAATCCTTCGCACTTTA
3919253 GAGAGATTTCGTCTGAAAACCCATTCGCCTTCATCACAGAAAA-CTCATTCGCCTTCAACCTCCT
1 GAGAGATTTCGTCTGAAAACCCATTCGCCTTCATCACAGAAAATC-CATTCGCCTTCAACCTCCT
3919317 CGTCTAAAAATCCTTCGCACTTTA
65 CGTCTAAAAATCCTTCGCACTTTA
3919341 GAGAGATTTCG
1 GAGAGATTTCG
3919352 AAAGATTTCG
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
87 1 0.01
88 94 0.99
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.28
Consensus pattern (88 bp):
GAGAGATTTCGTCTGAAAACCCATTCGCCTTCATCACAGAAAATCCATTCGCCTTCAACCTCCTC
GTCTAAAAATCCTTCGCACTTTA
Found at i:3919392 original size:24 final size:24
Alignment explanation
Indices: 3919365--3919431 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
3919355 GATTTCGTCT
3919365 GAAAACTCATTCGCCTTCATCGAA
1 GAAAACTCATTCGCCTTCATCGAA
* * *
3919389 GAAAACCCATTAGCCTTCATCGCA
1 GAAAACTCATTCGCCTTCATCGAA
*
3919413 GAAAATTCATTCGCCTTCA
1 GAAAACTCATTCGCCTTCA
3919432 ACCTCCCCGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (24 bp):
GAAAACTCATTCGCCTTCATCGAA
Found at i:3920678 original size:24 final size:24
Alignment explanation
Indices: 3920651--3920698 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3920641 CAAGAAATTA
*
3920651 CTGAACCCGAAATTAATGAACCAG
1 CTGAACCAGAAATTAATGAACCAG
*
3920675 CTGAGCCAGAAATTAATGAACCAG
1 CTGAACCAGAAATTAATGAACCAG
3920699 AACAAGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (24 bp):
CTGAACCAGAAATTAATGAACCAG
Found at i:3920700 original size:15 final size:15
Alignment explanation
Indices: 3920680--3920790 Score: 82
Period size: 15 Copynumber: 7.4 Consensus size: 15
3920670 ACCAGCTGAG
3920680 CCAGAAATTAATGAA
1 CCAGAAATTAATGAA
* *
3920695 CCAGAACA--AGTTGAG
1 CCAGAA-ATTA-ATGAA
*
3920710 CTAGAAATTAATGAA
1 CCAGAAATTAATGAA
* *
3920725 CCTGGAATTAATGAA
1 CCAGAAATTAATGAA
** ** *
3920740 CCAGAACCTGCTGAG
1 CCAGAAATTAATGAA
3920755 CCAGAAATTAATGAA
1 CCAGAAATTAATGAA
* *
3920770 CCTGAAATTGATGAA
1 CCAGAAATTAATGAA
3920785 CCAGAA
1 CCAGAA
3920791 CCTGCTGAGG
Statistics
Matches: 69, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
14 2 0.03
15 65 0.94
16 2 0.03
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.20
Consensus pattern (15 bp):
CCAGAAATTAATGAA
Found at i:3920755 original size:45 final size:45
Alignment explanation
Indices: 3920683--3920799 Score: 180
Period size: 45 Copynumber: 2.6 Consensus size: 45
3920673 AGCTGAGCCA
** * *
3920683 GAAATTAATGAACCAGAACAAGTTGAGCTAGAAATTAATGAACCT
1 GAAATTAATGAACCAGAACCTGCTGAGCCAGAAATTAATGAACCT
*
3920728 GGAATTAATGAACCAGAACCTGCTGAGCCAGAAATTAATGAACCT
1 GAAATTAATGAACCAGAACCTGCTGAGCCAGAAATTAATGAACCT
*
3920773 GAAATTGATGAACCAGAACCTGCTGAG
1 GAAATTAATGAACCAGAACCTGCTGAG
3920800 GTTAGGATAG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (45 bp):
GAAATTAATGAACCAGAACCTGCTGAGCCAGAAATTAATGAACCT
Found at i:3922703 original size:26 final size:26
Alignment explanation
Indices: 3922674--3922733 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
3922664 CATATTCTTC
3922674 ATGCATACTGTTATTACATATTGCTA
1 ATGCATACTGTTATTACATATTGCTA
* * * *
3922700 ATGCATAATGTTATTGCATATTGTTC
1 ATGCATACTGTTATTACATATTGCTA
3922726 ATGCATAC
1 ATGCATAC
3922734 AGTTGTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (26 bp):
ATGCATACTGTTATTACATATTGCTA
Found at i:3922706 original size:13 final size:13
Alignment explanation
Indices: 3922659--3922732 Score: 58
Period size: 13 Copynumber: 5.7 Consensus size: 13
3922649 GTTAACTTGG
* *
3922659 TAATACATATTCT
1 TAATGCATATTGT
* *
3922672 TCATGCATACTGT
1 TAATGCATATTGT
* * *
3922685 TATTACATATTGC
1 TAATGCATATTGT
*
3922698 TAATGCATAATGT
1 TAATGCATATTGT
*
3922711 TATTGCATATTGT
1 TAATGCATATTGT
*
3922724 TCATGCATA
1 TAATGCATA
3922733 CAGTTGTTGG
Statistics
Matches: 44, Mismatches: 17, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (13 bp):
TAATGCATATTGT
Found at i:3924119 original size:26 final size:26
Alignment explanation
Indices: 3924083--3924132 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
3924073 ACATACATTA
3924083 CATCTTCAATTCTAACACAAGTCTTG
1 CATCTTCAATTCTAACACAAGTCTTG
*
3924109 CATCTTCAATTCTAACACACGTCT
1 CATCTTCAATTCTAACACAAGTCT
3924133 ATTAACCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (26 bp):
CATCTTCAATTCTAACACAAGTCTTG
Found at i:3927636 original size:22 final size:22
Alignment explanation
Indices: 3927611--3927653 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3927601 ACCTTGACCT
3927611 CTTTGACACTTTGTTTATGTGA
1 CTTTGACACTTTGTTTATGTGA
3927633 CTTTGACACTTTGTTTATGTG
1 CTTTGACACTTTGTTTATGTG
3927654 GACCTGTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (22 bp):
CTTTGACACTTTGTTTATGTGA
Found at i:3932243 original size:20 final size:20
Alignment explanation
Indices: 3932218--3932258 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3932208 TTGATGTAAT
3932218 ATTAAAATAT-TAAGAATTAA
1 ATTAAAATATATAA-AATTAA
*
3932238 ATTAAATTATATAAAATTAA
1 ATTAAAATATATAAAATTAA
3932258 A
1 A
3932259 ACAAAAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
ATTAAAATATATAAAATTAA
Found at i:3941012 original size:60 final size:56
Alignment explanation
Indices: 3940889--3941014 Score: 139
Period size: 60 Copynumber: 2.2 Consensus size: 56
3940879 TATAACCTTC
* * * *
3940889 CTTT-TAAATTGGTCCTTAAACTTTTAAATATTCTTCATCCCTAAGCTATGACTCT
1 CTTTCTAAATTAGTCCTTAAACTTTTAAACATTCTTCATCCCTAAGCTAAGACACT
* *
3940944 CATTCTAAATTAGTCCTTAAACTTTTAAGCATTCAAATTTCATCCCTGAA-CTAAGACACT
1 CTTTCTAAATTAGTCCTTAAACTTTTAAACATTC----TTCATCCCT-AAGCTAAGACACT
3941004 CTTTCTAAATT
1 CTTTCTAAATT
3941015 GGTGTCCAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
55 3 0.05
56 26 0.45
60 27 0.47
61 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.40
Consensus pattern (56 bp):
CTTTCTAAATTAGTCCTTAAACTTTTAAACATTCTTCATCCCTAAGCTAAGACACT
Found at i:3943008 original size:27 final size:27
Alignment explanation
Indices: 3942935--3943001 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
3942925 GATGAAGAAG
*
3942935 TTATAAGAAATTAAAGAAAACGGGTTT
1 TTATATGAAATTAAAGAAAACGGGTTT
3942962 TTATATGAAATTAAAGAAAACGGGTTT
1 TTATATGAAATTAAAGAAAACGGGTTT
3942989 TTATATGAAATTA
1 TTATATGAAATTA
3943002 TGGAAAAGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.34
Consensus pattern (27 bp):
TTATATGAAATTAAAGAAAACGGGTTT
Found at i:3947154 original size:106 final size:106
Alignment explanation
Indices: 3947033--3947243 Score: 386
Period size: 106 Copynumber: 2.0 Consensus size: 106
3947023 TTCATATCTC
3947033 TTTCCGTGTTGTAATGTTATTTAATAAAATAAATATAATTTAAAATTGTAAAATATATTTATAAT
1 TTTCCGTGTTGTAATGTTATTTAATAAAATAAATATAATTTAAAATTGTAAAATATATTTATAAT
* ** *
3947098 GTTATTTTAAAAAATTATATCTTAGAATTAAGTATTTATAG
66 ATTATTTTAAAAAAAGATATCTTAGAATAAAGTATTTATAG
3947139 TTTCCGTGTTGTAATGTTATTTAATAAAATAAATATAATTTAAAATTGTAAAATATATTTATAAT
1 TTTCCGTGTTGTAATGTTATTTAATAAAATAAATATAATTTAAAATTGTAAAATATATTTATAAT
3947204 ATTATTTTAAAAAAAGATATCTTAGAATAAAGTATTTATA
66 ATTATTTTAAAAAAAGATATCTTAGAATAAAGTATTTATA
3947244 AGAGCATAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 101 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (106 bp):
TTTCCGTGTTGTAATGTTATTTAATAAAATAAATATAATTTAAAATTGTAAAATATATTTATAAT
ATTATTTTAAAAAAAGATATCTTAGAATAAAGTATTTATAG
Found at i:3952353 original size:8 final size:8
Alignment explanation
Indices: 3952340--3952368 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3952330 GCCAGCGAGT
3952340 TTTTTTTA
1 TTTTTTTA
3952348 TTTTTTTA
1 TTTTTTTA
3952356 TTTTTTTA
1 TTTTTTTA
3952364 TTTTT
1 TTTTT
3952369 GGACTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3962222 original size:51 final size:51
Alignment explanation
Indices: 3962108--3962222 Score: 140
Period size: 51 Copynumber: 2.3 Consensus size: 51
3962098 TCAAAGGATG
* * *
3962108 ACGAAGACGATGATGATAAGAAGTCAAGATATAGAAAAAAGAAAGACAGTA
1 ACGAAGACGATGACGATAAGAAGTCAAGATATAGAAAAAAGAAAAACAATA
* * * * *
3962159 ACGAAGATGATGACGATAAGAAGTCGAGATATAGGAAAAAGAAAAATAATG
1 ACGAAGACGATGACGATAAGAAGTCAAGATATAGAAAAAAGAAAAACAATA
* *
3962210 ATGACGACGATGA
1 ACGAAGACGATGA
3962223 TAACGATGAC
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.52, C:0.08, G:0.25, T:0.15
Consensus pattern (51 bp):
ACGAAGACGATGACGATAAGAAGTCAAGATATAGAAAAAAGAAAAACAATA
Found at i:3962238 original size:57 final size:53
Alignment explanation
Indices: 3962119--3962258 Score: 131
Period size: 51 Copynumber: 2.6 Consensus size: 53
3962109 CGAAGACGAT
* * * *
3962119 GATGATAAGAAGTCAAGATATAGAAAAAAGAAAGACAGTAACGAAGATGATGAC
1 GATGA-AAGAAGTCGAGATATAGAAAAAAGAAAAAAAGTAACGAAGATGATAAC
* * *
3962173 GAT--AAGAAGTCGAGATATAGGAAAAAGAAAAATAATGATGACGACGATGATAAC
1 GATGAAAGAAGTCGAGATATAGAAAAAAGAAAAA-AA-G-TAACGAAGATGATAAC
* * *
3962227 GATGACAAGAAGTCGAGAAATCGTAAAAAGAA
1 GATGA-AAGAAGTCGAGATATAGAAAAAAGAA
3962259 GAATGATTAC
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
51 26 0.37
52 1 0.01
53 1 0.01
54 19 0.27
57 23 0.33
ACGTcount: A:0.53, C:0.08, G:0.24, T:0.15
Consensus pattern (53 bp):
GATGAAAGAAGTCGAGATATAGAAAAAAGAAAAAAAGTAACGAAGATGATAAC
Found at i:3964459 original size:23 final size:23
Alignment explanation
Indices: 3964433--3964477 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3964423 CACCACAGCT
*
3964433 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
3964456 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
3964478 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:3964715 original size:149 final size:149
Alignment explanation
Indices: 3964458--3964753 Score: 547
Period size: 149 Copynumber: 2.0 Consensus size: 149
3964448 AAGTGCCCCG
* *
3964458 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
3964523 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
3964588 TATGTCCCGAAGAACCGTA
131 TATGTCCCGAAGAACCGTA
*
3964607 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTTTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
*
3964672 TATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
*
3964737 TATGTCTCGAAGAACCG
131 TATGTCCCGAAGAACCG
3964754 CGTAGACCCT
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 142 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCGAAGAACCGTA
Found at i:3965596 original size:18 final size:18
Alignment explanation
Indices: 3965573--3965607 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3965563 TCCCATCTAG
3965573 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
3965591 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
3965608 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:3966213 original size:21 final size:21
Alignment explanation
Indices: 3966183--3966227 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3966173 AATTTGTCGT
* *
3966183 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3966204 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3966225 TTG
1 TTG
3966228 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3970134 original size:5 final size:5
Alignment explanation
Indices: 3970124--3970205 Score: 83
Period size: 5 Copynumber: 15.2 Consensus size: 5
3970114 AACGGTCAAC
* *
3970124 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
3970173 GGTCG GGTCG GGTCAAA GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG G
3970206 ACCGGTCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
5 53 0.82
7 12 0.18
ACGTcount: A:0.09, C:0.21, G:0.52, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:3970145 original size:22 final size:22
Alignment explanation
Indices: 3970117--3970205 Score: 169
Period size: 22 Copynumber: 4.0 Consensus size: 22
3970107 AACGGTCAAC
3970117 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3970139 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3970161 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
3970183 GGTCAAAGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3970205 G
1 G
3970206 ACCGGTCAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.10, C:0.21, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:3970246 original size:10 final size:10
Alignment explanation
Indices: 3970233--3970279 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
3970223 AGACCGGTCA
3970233 AACCGGTTCG
1 AACCGGTTCG
3970243 AACCGGTTCG
1 AACCGGTTCG
*
3970253 AACCGG-TCA
1 AACCGGTTCG
3970262 AACCGG-TCAG
1 AACCGGTTC-G
3970272 AACCGGTT
1 AACCGGTT
3970280 GAAAACCGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 10 0.30
10 22 0.67
11 1 0.03
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.17
Consensus pattern (10 bp):
AACCGGTTCG
Found at i:3970257 original size:29 final size:30
Alignment explanation
Indices: 3970225--3970299 Score: 102
Period size: 29 Copynumber: 2.5 Consensus size: 30
3970215 ACCGATTCAG
3970225 ACCGGTCAAACCGGTTC-GAACCGGTTCG-A
1 ACCGGTCAAACCGGTTCAGAACCGGTT-GAA
3970254 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTG-AA
*
3970284 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
3970300 TCCAGCAGCC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
28 3 0.07
29 23 0.56
30 14 0.34
31 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (30 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAA
Found at i:3970277 original size:19 final size:19
Alignment explanation
Indices: 3970206--3970298 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 19
3970196 GTCGGGTCGG
*
3970206 ACCGGTCAAACCGATTCAG-
1 ACCGGTCAAACCG-GTCAGA
3970225 ACCGGTCAAACCGGTTC-GA
1 ACCGGTCAAACCGG-TCAGA
*
3970244 ACCGGTTCGAACCGGTCA-A
1 ACCGG-TCAAACCGGTCAGA
* *
3970263 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGG-TCAGA
*
3970284 ACCGGTTAAACCGGT
1 ACCGGTCAAACCGGT
3970299 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.05
19 35 0.56
20 16 0.26
21 8 0.13
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTCAGA
Found at i:3970288 original size:11 final size:9
Alignment explanation
Indices: 3970206--3970299 Score: 62
Period size: 9 Copynumber: 9.8 Consensus size: 9
3970196 GTCGGGTCGG
*
3970206 ACCGGTCAA
1 ACCGGTTAA
* *
3970215 ACCGATTCAG
1 ACCGGTT-AA
*
3970225 ACCGGTCAA
1 ACCGGTTAA
*
3970234 ACCGGTTCGA
1 ACCGGTT-AA
*
3970244 ACCGGTTCGA
1 ACCGGTT-AA
*
3970254 ACCGGTCAA
1 ACCGGTTAA
*
3970263 ACCGGTCAGA
1 ACCGGTTA-A
3970273 ACCGGTTGAAA
1 ACCGGTT--AA
3970284 ACCGGTTAA
1 ACCGGTTAA
3970293 ACCGGTT
1 ACCGGTT
3970300 TCCAGCAGCC
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
9 30 0.43
10 30 0.43
11 8 0.12
12 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:3977477 original size:5 final size:5
Alignment explanation
Indices: 3977467--3977548 Score: 83
Period size: 5 Copynumber: 15.2 Consensus size: 5
3977457 AACGGTCAAC
* *
3977467 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
3977516 GGTCG GGTCG GGTCAAA GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG G
3977549 ACCGGTCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
5 53 0.82
7 12 0.18
ACGTcount: A:0.09, C:0.21, G:0.52, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:3977488 original size:22 final size:22
Alignment explanation
Indices: 3977460--3977548 Score: 169
Period size: 22 Copynumber: 4.0 Consensus size: 22
3977450 AACGGTCAAC
3977460 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3977482 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3977504 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
3977526 GGTCAAAGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3977548 G
1 G
3977549 ACCGGTCAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.10, C:0.21, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:3977561 original size:9 final size:9
Alignment explanation
Indices: 3977549--3977641 Score: 78
Period size: 9 Copynumber: 9.7 Consensus size: 9
3977539 GTCGGGTCGG
3977549 ACCGGTCAA
1 ACCGGTCAA
* *
3977558 ACCGATTCAG
1 ACCG-GTCAA
3977568 ACCGGTCAA
1 ACCGGTCAA
*
3977577 ACCGGTTCGA
1 ACCGG-TCAA
*
3977587 ACCGGTTGAA
1 ACCGG-TCAA
3977597 ACCGGTCAA
1 ACCGGTCAA
3977606 ACCGGTCAGA
1 ACCGGTCA-A
*
3977616 ACCGGTTGAAA
1 ACCGG-T-CAA
*
3977627 ACCGGTTAA
1 ACCGGTCAA
3977636 ACCGGT
1 ACCGGT
3977642 TTCCAGCAGC
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
9 31 0.45
10 30 0.43
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:3977600 original size:29 final size:31
Alignment explanation
Indices: 3977568--3977642 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
3977558 ACCGATTCAG
3977568 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
3977597 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
3977627 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
3977643 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:3977620 original size:19 final size:19
Alignment explanation
Indices: 3977549--3977641 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 19
3977539 GTCGGGTCGG
*
3977549 ACCGGTCAAACCGATTCAG-
1 ACCGGTCAAACCG-GTCAGA
3977568 ACCGGTCAAACCGGTTC-GA
1 ACCGGTCAAACCGG-TCAGA
*
3977587 ACCGGTTGAAACCGGTCA-A
1 ACCGG-TCAAACCGGTCAGA
* *
3977606 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGG-TCAGA
*
3977627 ACCGGTTAAACCGGT
1 ACCGGTCAAACCGGT
3977642 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.05
19 35 0.56
20 16 0.26
21 8 0.13
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTCAGA
Found at i:3979164 original size:23 final size:23
Alignment explanation
Indices: 3979138--3979182 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3979128 CACCACAGCT
*
3979138 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
3979161 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
3979183 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:3979420 original size:149 final size:149
Alignment explanation
Indices: 3979163--3979458 Score: 556
Period size: 149 Copynumber: 2.0 Consensus size: 149
3979153 AAGTGCCCCG
* *
3979163 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
3979228 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
3979293 TATGTCCCGAAGAACCGTA
131 TATGTCCCGAAGAACCGTA
3979312 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
*
3979377 TATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
*
3979442 TATGTCTCGAAGAACCG
131 TATGTCCCGAAGAACCG
3979459 CGTAGACCCT
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 143 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCGAAGAACCGTA
Found at i:3979823 original size:18 final size:18
Alignment explanation
Indices: 3979788--3979825 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3979778 ATTTCATATC
*
3979788 AATTCTTTACCATCACAT
1 AATTCTTTAACATCACAT
3979806 AATTCCTTTAACAT-ACAT
1 AATT-CTTTAACATCACAT
3979824 AA
1 AA
3979826 CATATCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTCTTTAACATCACAT
Found at i:3980293 original size:18 final size:18
Alignment explanation
Indices: 3980270--3980304 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3980260 TCCCATCTAG
3980270 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
3980288 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
3980305 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:3981645 original size:2 final size:2
Alignment explanation
Indices: 3981638--3981680 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3981628 AGAATCTTTC
3981638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3981680 A
1 A
3981681 AACTTGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3982472 original size:18 final size:18
Alignment explanation
Indices: 3982449--3982512 Score: 119
Period size: 18 Copynumber: 3.6 Consensus size: 18
3982439 CAGTGAGTTT
3982449 ATGAGCATCAGGCAAAGG
1 ATGAGCATCAGGCAAAGG
*
3982467 ATGAGCATCAGACAAAGG
1 ATGAGCATCAGGCAAAGG
3982485 ATGAGCATCAGGCAAAGG
1 ATGAGCATCAGGCAAAGG
3982503 ATGAGCATCA
1 ATGAGCATCA
3982513 TCCGGATTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.41, C:0.17, G:0.30, T:0.12
Consensus pattern (18 bp):
ATGAGCATCAGGCAAAGG
Found at i:4001203 original size:33 final size:33
Alignment explanation
Indices: 4001161--4001244 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
4001151 TTAATGAGCA
*
4001161 CATGCATCTATGGGTGTCCATCCATGTCTCTAT
1 CATGCATCTATGGGTATCCATCCATGTCTCTAT
*
4001194 CATGCATCTATAGGTATCCATCCATGTCTCTAT
1 CATGCATCTATGGGTATCCATCCATGTCTCTAT
*
4001227 CATGTATCTATGGGTATC
1 CATGCATCTATGGGTATC
4001245 TTGCACTGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (33 bp):
CATGCATCTATGGGTATCCATCCATGTCTCTAT
Found at i:4001392 original size:21 final size:22
Alignment explanation
Indices: 4001354--4001395 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
4001344 CTGAATATCC
*
4001354 ATATGTAATATATGTTTTAAAT
1 ATATGTAAAATATGTTTTAAAT
*
4001376 ATATG-AAAATATTTTTTAAA
1 ATATGTAAAATATGTTTTAAA
4001396 AAAGATTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
ATATGTAAAATATGTTTTAAAT
Found at i:4009466 original size:2 final size:2
Alignment explanation
Indices: 4009459--4009486 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4009449 CATTATCGTA
4009459 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
4009487 CATCAACACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4011232 original size:2 final size:2
Alignment explanation
Indices: 4011225--4011254 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4011215 TGGAATTATG
4011225 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
4011255 GTTGTAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4011636 original size:2 final size:2
Alignment explanation
Indices: 4011629--4011670 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4011619 TAGTTAAAGA
4011629 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4011671 TAATACGCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4028526 original size:22 final size:22
Alignment explanation
Indices: 4028472--4028535 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
4028462 AAGAATAAAC
* *
4028472 ACGTGTCACAAAGACATAGAAAA
1 ACGTGTCATAAAGACA-AAAAAA
** *
4028495 ATATGCCATAAAGACAAAAAAA
1 ACGTGTCATAAAGACAAAAAAA
*
4028517 ACGTGTCATAAAGATAAAA
1 ACGTGTCATAAAGACAAAA
4028536 TTATTCTTAT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
22 20 0.62
23 12 0.38
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.16
Consensus pattern (22 bp):
ACGTGTCATAAAGACAAAAAAA
Found at i:4030222 original size:21 final size:21
Alignment explanation
Indices: 4030198--4030237 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4030188 CAATACTCGG
4030198 GTCTAATATGTGAATAAAGTT
1 GTCTAATATGTGAATAAAGTT
*
4030219 GTCTACTATGTGAATAAAG
1 GTCTAATATGTGAATAAAG
4030238 GGATGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (21 bp):
GTCTAATATGTGAATAAAGTT
Found at i:4035092 original size:3 final size:3
Alignment explanation
Indices: 4035086--4035147 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
4035076 TCATTTAAAT
** * *
4035086 TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4035134 TATA TTA TTTA TTA
1 T-TA TTA -TTA TTA
4035148 AATATTACAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:4035098 original size:15 final size:15
Alignment explanation
Indices: 4035080--4035125 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4035070 TTTTTTTCAT
4035080 TTAAATTTATTATTA
1 TTAAATTTATTATTA
*
4035095 TTAAAATTATTATTA
1 TTAAATTTATTATTA
*
4035110 TT-AGTATTATTATTA
1 TTAAAT-TTATTATTA
4035125 T
1 T
4035126 AATTATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 1 0.04
15 26 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TTAAATTTATTATTA
Found at i:4037301 original size:20 final size:21
Alignment explanation
Indices: 4037278--4037329 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
4037268 AGAAATTAAA
4037278 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
4037298 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
4037320 -ATT-ATTTATT
1 AATTCATTTATT
4037330 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:4044406 original size:82 final size:82
Alignment explanation
Indices: 4044281--4044566 Score: 545
Period size: 82 Copynumber: 3.5 Consensus size: 82
4044271 GAATGTGCTC
4044281 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTT
4044346 AGAAGATGAATTTATCA
66 AGAAGATGAATTTATCA
*
4044363 AAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTT
*
4044428 AGAAGATGAATTTGTCA
66 AGAAGATGAATTTATCA
*
4044445 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTTAGTTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTT
4044510 AGAAGATGAATTTATCA
66 AGAAGATGAATTTATCA
4044527 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
4044567 ATTCAGTAGG
Statistics
Matches: 199, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 199 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (82 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTT
AGAAGATGAATTTATCA
Found at i:4047128 original size:22 final size:22
Alignment explanation
Indices: 4047099--4047153 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
4047089 ATCTACACTC
4047099 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
4047121 TTTAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
4047143 TTCAAAGATGA
1 TTCAAAGATGA
4047154 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:4047813 original size:76 final size:76
Alignment explanation
Indices: 4047665--4048384 Score: 1341
Period size: 76 Copynumber: 9.5 Consensus size: 76
4047655 CTATTTCCCA
* *
4047665 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGAAGCTTTTTGATATTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
4047730 AATCCTTCGGGT
65 AAGCCTTCGGGT
4047742 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4047807 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
4047818 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
4047883 ATCCTTCGGGT
66 AGCCTTCGGGT
*
4047894 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
4047959 ATCCTTCGGGT
66 AGCCTTCGGGT
4047970 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4048035 AGCCTTCGGGT
66 AGCCTTCGGGT
4048046 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4048111 AGCCTTCGGGT
66 AGCCTTCGGGT
4048122 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4048187 AGCCTTCGGGT
66 AGCCTTCGGGT
4048198 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4048263 AGCCTTCGGGT
66 AGCCTTCGGGT
4048274 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4048339 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
4048350 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
4048385 CATTTCCATC
Statistics
Matches: 632, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
76 600 0.95
77 32 0.05
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:4048518 original size:3 final size:3
Alignment explanation
Indices: 4048512--4048573 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
4048502 TCATTTAAAT
** * *
4048512 TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4048560 TATA TTA TTTA TTA
1 T-TA TTA -TTA TTA
4048574 AATATTACAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:4048524 original size:15 final size:15
Alignment explanation
Indices: 4048506--4048551 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4048496 TTTTTTTCAT
4048506 TTAAATTTATTATTA
1 TTAAATTTATTATTA
*
4048521 TTAAAATTATTATTA
1 TTAAATTTATTATTA
*
4048536 TT-AGTATTATTATTA
1 TTAAAT-TTATTATTA
4048551 T
1 T
4048552 AATTATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 1 0.04
15 26 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TTAAATTTATTATTA
Found at i:4067009 original size:106 final size:106
Alignment explanation
Indices: 4066824--4067032 Score: 400
Period size: 106 Copynumber: 2.0 Consensus size: 106
4066814 ATGTGCACAT
* *
4066824 CAATGCTCACAGTTTGTTTTGCGCCGGAGGTGCCTGACTCCTCTTTCTCGTAGTCGGTTCATACA
1 CAATGCTCACAGTTTGTTTAGCGCCGGAGGTGCCTGACTCCTCTTTCTCATAGTCGGTTCATACA
4066889 TCCTAGGTCCTCTCCCTTTTACAGCCTTAGAAGCATGGCTC
66 TCCTAGGTCCTCTCCCTTTTACAGCCTTAGAAGCATGGCTC
4066930 CAATGCTCACAGTTTGTTTAGCGCCGGAGGTGCCTGACTCCTCTTTCTCATAGTCGGTTCATACA
1 CAATGCTCACAGTTTGTTTAGCGCCGGAGGTGCCTGACTCCTCTTTCTCATAGTCGGTTCATACA
4066995 TCCTAGGTCCTCTCCCTTTTACAGCCTTAGAAGCATGG
66 TCCTAGGTCCTCTCCCTTTTACAGCCTTAGAAGCATGG
4067033 TTCTGATTAT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 101 1.00
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.33
Consensus pattern (106 bp):
CAATGCTCACAGTTTGTTTAGCGCCGGAGGTGCCTGACTCCTCTTTCTCATAGTCGGTTCATACA
TCCTAGGTCCTCTCCCTTTTACAGCCTTAGAAGCATGGCTC
Found at i:4076767 original size:175 final size:176
Alignment explanation
Indices: 4076573--4076925 Score: 699
Period size: 175 Copynumber: 2.0 Consensus size: 176
4076563 ACCAGTTGTG
4076573 CATGATTTAACCAAAAGTAATTACCTCCGGGAACCTTTTATATATCCAACTGCCCAAACTCTCTC
1 CATGATTTAACCAAAAGTAATTACCTCCGGGAACCTTTTATATATCCAACTGCCCAAACTCTCTC
4076638 AAGACCATAATTCAATGTATTTTCAAGCCTGAAAACAAATGAATTGGTCAAAAAAATC-AAAGCT
66 AAGACCATAATTCAATGTATTTTCAAGCCTGAAAACAAATGAATTGGTCAAAAAAATCAAAAGCT
4076702 TGAAGAATTTGAAGATATCACCGCATACATAAAAGCCTATTAAGAT
131 TGAAGAATTTGAAGATATCACCGCATACATAAAAGCCTATTAAGAT
4076748 CATGATTTAACCAAAAGTAATTACCTCCGGGAACCTTTTATATATCCAACTGCCCAAACTCTCTC
1 CATGATTTAACCAAAAGTAATTACCTCCGGGAACCTTTTATATATCCAACTGCCCAAACTCTCTC
4076813 AAGACCATAATTCAATGTATTTTCAAGCCTGAAAACAAATGAATTGGTCAAAAAAATCAAAAGCT
66 AAGACCATAATTCAATGTATTTTCAAGCCTGAAAACAAATGAATTGGTCAAAAAAATCAAAAGCT
4076878 TGAAGAATTTGAAGATATCACCGCATACATAAAAGCCTATTAAGAT
131 TGAAGAATTTGAAGATATCACCGCATACATAAAAGCCTATTAAGAT
4076924 CA
1 CA
4076926 AAATATCCTA
Statistics
Matches: 177, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
175 123 0.69
176 54 0.31
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.27
Consensus pattern (176 bp):
CATGATTTAACCAAAAGTAATTACCTCCGGGAACCTTTTATATATCCAACTGCCCAAACTCTCTC
AAGACCATAATTCAATGTATTTTCAAGCCTGAAAACAAATGAATTGGTCAAAAAAATCAAAAGCT
TGAAGAATTTGAAGATATCACCGCATACATAAAAGCCTATTAAGAT
Found at i:4082780 original size:15 final size:15
Alignment explanation
Indices: 4082759--4082799 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4082749 GTGGTTTAAT
4082759 GTTTTATGAGTTCTGA
1 GTTTTATGAGTT-TGA
4082775 -TTTTATG-G-TTGA
1 GTTTTATGAGTTTGA
4082787 GTTTTATGAGTTT
1 GTTTTATGAGTTT
4082800 TAAAATGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
12 3 0.14
13 8 0.36
14 2 0.09
15 9 0.41
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (15 bp):
GTTTTATGAGTTTGA
Found at i:4092727 original size:12 final size:12
Alignment explanation
Indices: 4092710--4092741 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4092700 TTTGTCATGG
*
4092710 TTGTTCATGGGT
1 TTGTTCACGGGT
4092722 TTGTTCACGGGT
1 TTGTTCACGGGT
4092734 TTGTTCAC
1 TTGTTCAC
4092742 TAATGAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (12 bp):
TTGTTCACGGGT
Found at i:4103912 original size:2 final size:2
Alignment explanation
Indices: 4103905--4103946 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4103895 CAATACCTTT
*
4103905 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4103947 AAGGGAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4106788 original size:15 final size:16
Alignment explanation
Indices: 4106770--4106808 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
4106760 CACTTTTATT
4106770 ATAAATAATTA-AATA
1 ATAAATAATTATAATA
*
4106785 ATAAATAA-TATGATA
1 ATAAATAATTATAATA
4106800 ATAAATAAT
1 ATAAATAAT
4106809 ACATCAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
ATAAATAATTATAATA
Found at i:4106791 original size:7 final size:7
Alignment explanation
Indices: 4106770--4106809 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
4106760 CACTTTTATT
4106770 ATAAATA
1 ATAAATA
4106777 ATTAAATA
1 A-TAAATA
4106785 ATAAATA
1 ATAAATA
*
4106792 ATATGATA
1 ATA-AATA
4106800 ATAAATA
1 ATAAATA
4106807 ATA
1 ATA
4106810 CATCAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (7 bp):
ATAAATA
Found at i:4107824 original size:16 final size:15
Alignment explanation
Indices: 4107803--4107871 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 15
4107793 AAGAAATTTA
4107803 TTTTTATGTTAATATT
1 TTTTTATGTTAATA-T
*
4107819 TTTTTAAATAGTTATTAT
1 TTTTT--AT-GTTAATAT
*
4107837 TTTTTATATTAATA-
1 TTTTTATGTTAATAT
* *
4107851 TATTTATGTAAATAT
1 TTTTTATGTTAATAT
4107866 TATTTT
1 T-TTTT
4107872 TTCATTAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
14 11 0.27
15 6 0.15
16 10 0.24
18 8 0.20
19 6 0.15
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (15 bp):
TTTTTATGTTAATAT
Found at i:4107849 original size:34 final size:34
Alignment explanation
Indices: 4107798--4107873 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
4107788 GTGGTAAGAA
* *
4107798 ATTTATTTTTATGTTAATAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTATATTAATATATTTATGTAAATA-TT
4107832 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTATATTAATATATTTATGTAAATATT
4107867 ATTTTTT
1 ATTTTTT
4107874 CATTAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
34 21 0.57
35 9 0.24
36 7 0.19
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (34 bp):
ATTTTTTTTATATTAATATATTTATGTAAATATT
Found at i:4107879 original size:31 final size:34
Alignment explanation
Indices: 4107831--4107909 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
4107821 TTTAAATAGT
* *
4107831 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTACATTAAATAATATTTATATAAA
*
4107863 TATTATTTTTT-CATTAAAATAATATTTATATAAT
1 TATTATTTTTTACATT-AAATAATATTTATATAAA
4107897 TATTATTTATTTA
1 TATTATTT-TTTA
4107910 GAATTATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
31 3 0.08
32 11 0.28
33 3 0.08
34 19 0.49
35 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (34 bp):
TATTATTTTTTACATTAAATAATATTTATATAAA
Found at i:4107901 original size:34 final size:32
Alignment explanation
Indices: 4107821--4107909 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
4107811 TTAATATTTT
* * *
4107821 TTTAAATAGTTATTATTTTTTATATTAATATA
1 TTTATATAATTATTATTTTTTATATAAATATA
* *
4107853 TTTATGTAAATATTATTTTTTCAT-TAAAATAATA
1 TTTATATAATTATTATTTTTT-ATAT-AAAT-ATA
4107887 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTT-TTTA
4107910 GAATTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 18 0.39
33 5 0.11
34 20 0.43
35 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTATATAATTATTATTTTTTATATAAATATA
Found at i:4108071 original size:17 final size:17
Alignment explanation
Indices: 4108049--4108102 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
4108039 AATGTTAATA
4108049 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
4108066 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
4108083 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
4108100 TTT
1 TTT
4108103 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:4109710 original size:21 final size:21
Alignment explanation
Indices: 4109684--4109777 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
4109674 TATGCCATCT
4109684 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
4109705 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
4109726 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
4109747 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
4109768 CCGCAGGGTT
1 CCGCAGGGTT
4109778 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.28, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:4110359 original size:33 final size:34
Alignment explanation
Indices: 4110300--4110396 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
4110290 AAATGTTTTT
*
4110300 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
4110334 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
4110367 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
4110397 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:4110403 original size:34 final size:33
Alignment explanation
Indices: 4110298--4110403 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
4110288 ATAAATGTTT
*
4110298 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
4110332 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
4110364 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
4110399 TTAAA
1 TTAAA
4110404 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:4111024 original size:128 final size:128
Alignment explanation
Indices: 4110796--4111552 Score: 1363
Period size: 128 Copynumber: 5.9 Consensus size: 128
4110786 TTACCTGATT
*
4110796 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGAAATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
4110861 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAGTAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
4110924 TACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTATC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
4110989 TGATGAAATAATGGAAGGCGCGTCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
4111052 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
4111117 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
4111180 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
4111245 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
4111308 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
4111373 TGACGAAATAATGGAAGGCGCGCCCCCGGGAATGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
4111436 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
4111501 TGACGAAATAATGGAAGGCGCGTCCCCGGAAACGCGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
4111553 ACTCCGATTA
Statistics
Matches: 606, Mismatches: 21, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
127 1 0.00
128 604 1.00
129 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:4111636 original size:8 final size:8
Alignment explanation
Indices: 4111623--4111663 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
4111613 TCACAATCTT
4111623 TCAAATTC
1 TCAAATTC
4111631 TCAAATTC
1 TCAAATTC
* *
4111639 CCAAACTC
1 TCAAATTC
4111647 T-AAATTC
1 TCAAATTC
4111654 TCAAATTC
1 TCAAATTC
4111662 TC
1 TC
4111664 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:4127838 original size:23 final size:24
Alignment explanation
Indices: 4127811--4127863 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
4127801 CATGGAATAA
* *
4127811 TATTTTCAAATTGAA-CATGATAT
1 TATTTTCAAATTGAATAAGGATAT
* *
4127834 TATTTTTAAATTTAATAAGGATAT
1 TATTTTCAAATTGAATAAGGATAT
4127858 TATTTT
1 TATTTT
4127864 TTGAATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (24 bp):
TATTTTCAAATTGAATAAGGATAT
Found at i:4127870 original size:25 final size:24
Alignment explanation
Indices: 4127829--4127876 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
4127819 AATTGAACAT
*
4127829 GATATTATTTTTAAATTTAATAAG
1 GATATTATTTTTAAATTAAATAAG
*
4127853 GATATTATTTTTTGAATTAAATAA
1 GATATTA-TTTTTAAATTAAATAA
4127877 TTCATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (24 bp):
GATATTATTTTTAAATTAAATAAG
Found at i:4131137 original size:13 final size:13
Alignment explanation
Indices: 4131096--4131138 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
4131086 AATTGTTGTT
4131096 TTAATTAGATAAG
1 TTAATTAGATAAG
** * *
4131109 TTAAAGACATATG
1 TTAATTAGATAAG
4131122 TTAATTAGATAAG
1 TTAATTAGATAAG
4131135 TTAA
1 TTAA
4131139 AGTCAAATGG
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (13 bp):
TTAATTAGATAAG
Found at i:4139962 original size:17 final size:17
Alignment explanation
Indices: 4139934--4139974 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
4139924 GAGGATTTTT
*
4139934 TTCGGGTTGCGTTCGGG
1 TTCGGGTCGCGTTCGGG
*
4139951 TTTGGGTCGCGTTCGGG
1 TTCGGGTCGCGTTCGGG
4139968 TTCGGGT
1 TTCGGGT
4139975 TCGGGTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.17, G:0.46, T:0.37
Consensus pattern (17 bp):
TTCGGGTCGCGTTCGGG
Found at i:4139970 original size:6 final size:6
Alignment explanation
Indices: 4139934--4139981 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
4139924 GAGGATTTTT
* * *
4139934 TTCGGG TT-GCG TTCGGG TTTGGG -TCGCG TTCGGG TTCGGG TTCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
4139980 TT
1 TT
4139982 GAATTATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 27 0.79
ACGTcount: A:0.00, C:0.17, G:0.46, T:0.38
Consensus pattern (6 bp):
TTCGGG
Found at i:4139978 original size:12 final size:12
Alignment explanation
Indices: 4139934--4139981 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 12
4139924 GAGGATTTTT
*
4139934 TTCGGGTT-GCG
1 TTCGGGTTCGGG
*
4139945 TTCGGGTTTGGG
1 TTCGGGTTCGGG
*
4139957 -TCGCGTTCGGG
1 TTCGGGTTCGGG
4139968 TTCGGGTTCGGG
1 TTCGGGTTCGGG
4139980 TT
1 TT
4139982 GAATTATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 17 0.55
12 14 0.45
ACGTcount: A:0.00, C:0.17, G:0.46, T:0.38
Consensus pattern (12 bp):
TTCGGGTTCGGG
Found at i:4168194 original size:30 final size:29
Alignment explanation
Indices: 4168160--4168241 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
4168150 AACTTTTGGA
*
4168160 CATTCTAATTTCATCCC-AAATTATGACTCT
1 CATTCTAATTTCATCCCGAAATTATGA--AT
* * * *
4168190 CATTCTAAATTGATCCCTAAACTTTTGAAT
1 CATTCTAATTTCATCCCGAAA-TTATGAAT
4168220 -ATTCTAATTTCATCCCGAAATT
1 CATTCTAATTTCATCCCGAAATT
4168242 CATCCAAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
28 2 0.05
29 17 0.40
30 16 0.37
31 3 0.07
32 5 0.12
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (29 bp):
CATTCTAATTTCATCCCGAAATTATGAAT
Found at i:4168199 original size:59 final size:60
Alignment explanation
Indices: 4168078--4168241 Score: 181
Period size: 59 Copynumber: 2.8 Consensus size: 60
4168068 CCTCAATTTG
* * * * * * * *
4168078 AATTGATCCTTAAATTTTTGAATATTCCAATTTCA-CCCTCATACTATGACTCTCATTTTA
1 AATTGATCCCTAAACTTTTGAACATTCTAATTTCATCCC-GAAATTATGACTCTCATTCTA
* * *
4168138 AATT-AGTCCTTTAACTTTTGGACATTCTAATTTCATCCC-AAATTATGACTCTCATTCTA
1 AATTGA-TCCCTAAACTTTTGAACATTCTAATTTCATCCCGAAATTATGACTCTCATTCTA
*
4168197 AATTGATCCCTAAACTTTTGAATATTCTAATTTCATCCCGAAATT
1 AATTGATCCCTAAACTTTTGAACATTCTAATTTCATCCCGAAATT
4168242 CATCCAAATA
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
59 51 0.58
60 34 0.39
61 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (60 bp):
AATTGATCCCTAAACTTTTGAACATTCTAATTTCATCCCGAAATTATGACTCTCATTCTA
Found at i:4168234 original size:29 final size:28
Alignment explanation
Indices: 4168150--4168235 Score: 75
Period size: 30 Copynumber: 3.0 Consensus size: 28
4168140 TTAGTCCTTT
* *
4168150 AACTTTTGGACATTCTAATTTCATCCCA
1 AACTTTTGAATATTCTAATTTCATCCCA
* * * *
4168178 AA-TTATGACTCTCATTCTAAATTGATCCCTA
1 AACTTTTGA--AT-ATTCTAATTTCATCCC-A
4168209 AACTTTTGAATATTCTAATTTCATCCC
1 AACTTTTGAATATTCTAATTTCATCCC
4168236 GAAATTCATC
Statistics
Matches: 43, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
27 4 0.09
28 2 0.05
29 14 0.33
30 15 0.35
31 3 0.07
32 5 0.12
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (28 bp):
AACTTTTGAATATTCTAATTTCATCCCA
Found at i:4178396 original size:3 final size:3
Alignment explanation
Indices: 4178388--4178413 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4178378 ATGTCTTCAT
4178388 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
4178414 ACTATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:4188403 original size:37 final size:37
Alignment explanation
Indices: 4188332--4188558 Score: 184
Period size: 37 Copynumber: 6.1 Consensus size: 37
4188322 TAGTTTAAAA
* * * *
4188332 AAAACA-TTTTAAAAAATATATATAATATATAATTTTTT
1 AAAACATTTTTGAAAACT-TATAT-ATATATAAGTTTTG
*
4188370 AAAATCA-TTTTGAAAACTTATATATATATAATTTTTG
1 AAAA-CATTTTTGAAAACTTATATATATATAAGTTTTG
* **
4188407 AAAACATTTTTGAAAGCACATATAT-TAT-AGTTTTG
1 AAAACATTTTTGAAAACTTATATATATATAAGTTTTG
* *
4188442 AAAATATTTTTGAAAACATT-TATATATTATATAGTTTTT
1 AAAACATTTTTGAAAAC-TTATATATA-TATA-AGTTTTG
* *
4188481 AAAACA-TTTTGAAAA--TAAATATAATATATAGTTTTT
1 AAAACATTTTTGAAAACTTATATAT-ATATA-AGTTTTG
*
4188517 AAAACATTTTTGAAAACATATATAT-TATATAGTTTTTG
1 AAAACATTTTTGAAAACTTATATATATATA-AG-TTTTG
4188555 AAAA
1 AAAA
4188559 TATATATATA
Statistics
Matches: 160, Mismatches: 16, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
35 27 0.17
36 27 0.17
37 52 0.32
38 26 0.16
39 28 0.17
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
AAAACATTTTTGAAAACTTATATATATATAAGTTTTG
Found at i:4188580 original size:28 final size:26
Alignment explanation
Indices: 4188523--4188584 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
4188513 TTTTAAAACA
4188523 TTTTTGAAAACATATATATTATATAG
1 TTTTTGAAAACATATATATTATATAG
*
4188549 TTTTTGAAAATATATATA-TATTATAG
1 TTTTTGAAAACATATATATTA-TATAG
*
4188575 TTTTTTAAAA
1 TTTTTGAAAA
4188585 AAATATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 2 0.06
26 31 0.94
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (26 bp):
TTTTTGAAAACATATATATTATATAG
Found at i:4188624 original size:67 final size:63
Alignment explanation
Indices: 4188487--4188628 Score: 180
Period size: 63 Copynumber: 2.2 Consensus size: 63
4188477 TTTTAAAACA
* *
4188487 TTTTGAAAATAAATATAATATATAGTTTTTAAAACATTTTTGAAAACATATATATTATATAGT
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAAATTTTTGAAAACATATATATTATATAGT
**
4188550 TTTTGAAAATATATAT-ATATTATAGTTTTTTAAAAAAATATTTT-AGAAATTTATATATTATAT
1 TTTTGAAAATATATATAATA-TATAG-TTTTT-AAAAAAT-TTTTGA-AAACATATATATTATAT
4188613 ATGT
61 A-GT
4188617 TTTTGAAAATAT
1 TTTTGAAAATAT
4188629 TTTTATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
62 3 0.04
63 20 0.29
64 5 0.07
65 7 0.10
66 20 0.29
67 14 0.20
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.48
Consensus pattern (63 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAAAATTTTTGAAAACATATATATTATATAGT
Found at i:4188637 original size:6 final size:6
Alignment explanation
Indices: 4188626--4188692 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
4188616 TTTTTGAAAA
* * *
4188626 TATTTT TATTTT TATTATT TATTAT TATTAT TA-TTT TA-TTT TA-TGT
1 TATTTT TATTTT TATT-TT TATTTT TATTTT TATTTT TATTTT TATTTT
*
4188672 TA-TTT TATTCCT TATTTT TAT
1 TATTTT TATT-TT TATTTT TAT
4188693 GCTTTGTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
5 17 0.33
6 24 0.46
7 11 0.21
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.73
Consensus pattern (6 bp):
TATTTT
Found at i:4188646 original size:13 final size:13
Alignment explanation
Indices: 4188626--4188692 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 13
4188616 TTTTTGAAAA
4188626 TATT-TTTATTTT
1 TATTATTTATTTT
*
4188638 TATTATTTATTAT
1 TATTATTTATTTT
4188651 TATTA-TTATTTT
1 TATTATTTATTTT
*
4188663 ATTTTATGTTA-TTT
1 -TATTAT-TTATTTT
**
4188677 TATTCCTTATTTT
1 TATTATTTATTTT
4188690 TAT
1 TAT
4188693 GCTTTGTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
12 13 0.30
13 25 0.57
14 3 0.07
15 3 0.07
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.73
Consensus pattern (13 bp):
TATTATTTATTTT
Found at i:4188652 original size:10 final size:10
Alignment explanation
Indices: 4188626--4188680 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 10
4188616 TTTTTGAAAA
*
4188626 TATTTTTATT
1 TATTATTATT
4188636 T-TTATTATT
1 TATTATTATT
4188645 TATTATTA-T
1 TATTATTATT
4188654 TATTA-T-TT
1 TATTATTATT
4188662 TATT-TTATGT
1 TATTATTAT-T
4188672 TATT-TTATT
1 TATTATTATT
4188681 CCTTATTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
8 7 0.18
9 16 0.41
10 16 0.41
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (10 bp):
TATTATTATT
Found at i:4188656 original size:16 final size:15
Alignment explanation
Indices: 4188626--4188662 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
4188616 TTTTTGAAAA
*
4188626 TATTTTTATTTTTAT
1 TATTTTTATTATTAT
4188641 TATTTATTATTATTAT
1 TATTT-TTATTATTAT
4188657 TATTTT
1 TATTTT
4188663 ATTTTATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTTTATTATTAT
Found at i:4189800 original size:11 final size:12
Alignment explanation
Indices: 4189780--4189805 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4189770 TCCTCTTTAT
4189780 TCATTTTTTTCC
1 TCATTTTTTTCC
4189792 TCATTTTTTTCC
1 TCATTTTTTTCC
4189804 TC
1 TC
4189806 CTTGATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.27, G:0.00, T:0.65
Consensus pattern (12 bp):
TCATTTTTTTCC
Found at i:4191505 original size:19 final size:19
Alignment explanation
Indices: 4191481--4191526 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
4191471 ATTTAGACAT
4191481 TTTGCATTTCGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
4191500 TTTGCATTTTGTTATTTTC
1 TTTGCATTTCGTTATTTTC
4191519 TTTGCATT
1 TTTGCATT
4191527 CACATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.11, C:0.13, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTGCATTTCGTTATTTTC
Found at i:4192304 original size:48 final size:48
Alignment explanation
Indices: 4192233--4192329 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
4192223 TTCAGGATAG
4192233 TCTATCGGGCTCAGCCATTCGGTGGTACAACCAGCTAAGCCGATCAAA
1 TCTATCGGGCTCAGCCATTCGGTGGTACAACCAGCTAAGCCGATCAAA
4192281 TCTATCGGGCTCAGCCATTCGGTGGTACAACCAGCTAAGCCGATCAAA
1 TCTATCGGGCTCAGCCATTCGGTGGTACAACCAGCTAAGCCGATCAAA
4192329 T
1 T
4192330 ATCAAGACCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.22
Consensus pattern (48 bp):
TCTATCGGGCTCAGCCATTCGGTGGTACAACCAGCTAAGCCGATCAAA
Found at i:4195087 original size:84 final size:84
Alignment explanation
Indices: 4194895--4196271 Score: 1722
Period size: 84 Copynumber: 16.4 Consensus size: 84
4194885 TAAACAAACT
* * * ** * * *
4194895 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-A--AAAGACCCCCAAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
4194957 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
*
4194977 ATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
4195042 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
** * * * * *
4195061 ATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
4195126 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * * ** * * *
4195145 ATTTGCAGAATAGCTTAAGTCAAGAAGGGATATCTG----CCAAAGACCCCCAAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
4195206 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
*
4195226 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
4195291 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
** * * * * *
4195310 ATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
4195375 CTCAGCT-CAACGGCACATC
66 CTCAGCTCCAA-GGCACATC
* * * ** *
4195394 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTCC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
4195458 GCTCAGCTCCAAGGCACATC
65 GCTCAGCTCCAAGGCACATC
*
4195478 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
4195543 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
** * * * * *
4195562 ATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
4195627 CTCAGCT-CAACGGCACATC
66 CTCAGCTCCAA-GGCACATC
* * * ** *
4195646 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTCC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
4195710 GCTCAGCTCCAAGGCACATC
65 GCTCAGCTCCAAGGCACATC
*
4195730 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
*
4195795 GCTCAGCTCCAAGGCATATC
65 GCTCAGCTCCAAGGCACATC
** * * * * *
4195815 ATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
4195880 CTCAGCT-CAACGGCACATC
66 CTCAGCTCCAA-GGCACATC
* * * ** *
4195899 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTCC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
4195963 GCTCAGCTCCAAGGCACATC
65 GCTCAGCTCCAAGGCACATC
*
4195983 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
4196048 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
** * * * * *
4196067 ATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
4196132 CTCAGCT-CAACGGCACATC
66 CTCAGCTCCAA-GGCACATC
* * * ** *
4196151 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTCC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
4196215 GCTCAGCTCCAAGGCACATC
65 GCTCAGCTCCAAGGCACATC
* *
4196235 ATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGC
4196272 TTAAGACCTT
Statistics
Matches: 1105, Mismatches: 166, Indels: 45
0.84 0.13 0.03
Matches are distributed among these distances:
80 24 0.02
81 43 0.04
82 35 0.03
83 21 0.02
84 835 0.76
85 147 0.13
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATC
Found at i:4195623 original size:252 final size:252
Alignment explanation
Indices: 4194969--4196271 Score: 2382
Period size: 252 Copynumber: 5.2 Consensus size: 252
4194959 CAGCTTCGAG
*
4194969 GGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
4195034 CGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCC
66 CGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCC
* * * *
4195099 AACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGAATAGCTTAA
131 AACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTACAGCATAACTCAA
* * * ** * * * * * *
4195163 GTCAAGAAGGGATATC--TG-CC-AAAGACCCCCAAGTTCGATTACACTCAGCTTCGAG
195 GGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGC-TCCAA
4195218 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
4195283 CGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCC
66 CGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCC
4195348 AACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATAACTCAAG
131 AACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATAACTCAAG
4195413 GCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAA
196 GCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAA
4195470 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
4195535 CGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCC
66 CGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCC
4195600 AACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATAACTCAAG
131 AACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATAACTCAAG
4195665 GCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAA
196 GCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAA
4195722 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAAGACCTTCGAGT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGT
4195787 TCGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGC
65 TCGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGC
4195852 CAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATAACTCAA
130 CAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATAACTCAA
4195917 GGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAA
195 GGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAA
4195975 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
4196040 CGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCC
66 CGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCC
4196105 AACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATAACTCAAG
131 AACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATAACTCAAG
4196170 GCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAA
196 GCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAA
* *
4196227 GGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGC
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
4196272 TTAAGACCTT
Statistics
Matches: 1030, Mismatches: 18, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
248 3 0.00
249 198 0.19
251 2 0.00
252 552 0.54
253 275 0.27
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (252 bp):
GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
CGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTTTGCC
AACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATAACTCAAG
GCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAA
Found at i:4197066 original size:37 final size:37
Alignment explanation
Indices: 4196995--4197221 Score: 184
Period size: 37 Copynumber: 6.1 Consensus size: 37
4196985 TAGTTTAAAA
* * * *
4196995 AAAACA-TTTTAAAAAATATATATAATATATAATTTTTT
1 AAAACATTTTTGAAAACT-TATAT-ATATATAAGTTTTG
*
4197033 AAAATCA-TTTTGAAAACTTATATATATATAATTTTTG
1 AAAA-CATTTTTGAAAACTTATATATATATAAGTTTTG
* **
4197070 AAAACATTTTTGAAAGCACATATAT-TAT-AGTTTTG
1 AAAACATTTTTGAAAACTTATATATATATAAGTTTTG
* *
4197105 AAAATATTTTTGAAAACATT-TATATATTATATAGTTTTT
1 AAAACATTTTTGAAAAC-TTATATATA-TATA-AGTTTTG
* *
4197144 AAAACA-TTTTGAAAA--TAAATATAATATATAGTTTTT
1 AAAACATTTTTGAAAACTTATATAT-ATATA-AGTTTTG
*
4197180 AAAACATTTTTGAAAACATATATAT-TATATAGTTTTTG
1 AAAACATTTTTGAAAACTTATATATATATA-AG-TTTTG
4197218 AAAA
1 AAAA
4197222 TATATATATA
Statistics
Matches: 160, Mismatches: 16, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
35 27 0.17
36 27 0.17
37 52 0.32
38 26 0.16
39 28 0.17
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
AAAACATTTTTGAAAACTTATATATATATAAGTTTTG
Found at i:4197216 original size:26 final size:26
Alignment explanation
Indices: 4197185--4197247 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
4197175 TTTTTAAAAC
4197185 ATTTTTGAAAACATATATAT-TATATA
1 ATTTTTGAAAACATATATATAT-TATA
* *
4197211 GTTTTTGAAAATATATATATATTATA
1 ATTTTTGAAAACATATATATATTATA
*
4197237 ATTTTTTAAAA
1 ATTTTTGAAAA
4197248 AAATATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 31 0.97
27 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (26 bp):
ATTTTTGAAAACATATATATATTATA
Found at i:4197228 original size:28 final size:27
Alignment explanation
Indices: 4197192--4197253 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
4197182 AACATTTTTG
* *
4197192 AAAACATATATATTATATAGTTTTTGAA
1 AAAATATATATATTATA-AGTTTTTAAA
* *
4197220 AATATATATATATTATAATTTTTTAAA
1 AAAATATATATATTATAAGTTTTTAAA
4197247 AAAATAT
1 AAAATAT
4197254 TTTAGAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (27 bp):
AAAATATATATATTATAAGTTTTTAAA
Found at i:4197300 original size:6 final size:6
Alignment explanation
Indices: 4197289--4197355 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
4197279 GTTTTGAAAA
* * *
4197289 TATTTT TATTTT TATTATT TATTAT TATTAT TA-TTT TA-TTT TA-TGT
1 TATTTT TATTTT TATT-TT TATTTT TATTTT TATTTT TATTTT TATTTT
*
4197335 TA-TTT TATTCCT TATTTT TAT
1 TATTTT TATT-TT TATTTT TAT
4197356 GCTTTGTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
5 17 0.33
6 24 0.46
7 11 0.21
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.73
Consensus pattern (6 bp):
TATTTT
Found at i:4197311 original size:13 final size:13
Alignment explanation
Indices: 4197289--4197355 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 13
4197279 GTTTTGAAAA
4197289 TATT-TTTATTTT
1 TATTATTTATTTT
*
4197301 TATTATTTATTAT
1 TATTATTTATTTT
4197314 TATTA-TTATTTT
1 TATTATTTATTTT
*
4197326 ATTTTATGTTA-TTT
1 -TATTAT-TTATTTT
**
4197340 TATTCCTTATTTT
1 TATTATTTATTTT
4197353 TAT
1 TAT
4197356 GCTTTGTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
12 13 0.30
13 25 0.57
14 3 0.07
15 3 0.07
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.73
Consensus pattern (13 bp):
TATTATTTATTTT
Found at i:4197315 original size:10 final size:10
Alignment explanation
Indices: 4197289--4197343 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 10
4197279 GTTTTGAAAA
*
4197289 TATTTTTATT
1 TATTATTATT
4197299 T-TTATTATT
1 TATTATTATT
4197308 TATTATTA-T
1 TATTATTATT
4197317 TATTA-T-TT
1 TATTATTATT
4197325 TATT-TTATGT
1 TATTATTAT-T
4197335 TATT-TTATT
1 TATTATTATT
4197344 CCTTATTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
8 7 0.18
9 16 0.41
10 16 0.41
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (10 bp):
TATTATTATT
Found at i:4197319 original size:16 final size:15
Alignment explanation
Indices: 4197289--4197325 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
4197279 GTTTTGAAAA
*
4197289 TATTTTTATTTTTAT
1 TATTTTTATTATTAT
4197304 TATTTATTATTATTAT
1 TATTT-TTATTATTAT
4197320 TATTTT
1 TATTTT
4197326 ATTTTATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTTTATTATTAT
Found at i:4198662 original size:20 final size:20
Alignment explanation
Indices: 4198637--4198676 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4198627 TTGTTTTTTA
*
4198637 TTTATTTAATATTTTTCCTC
1 TTTATTCAATATTTTTCCTC
* *
4198657 TTTATTCATTTTTTTTCCTC
1 TTTATTCAATATTTTTCCTC
4198677 ATTTTTTTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATTCAATATTTTTCCTC
Found at i:4198821 original size:12 final size:12
Alignment explanation
Indices: 4198804--4198828 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4198794 TCGAATCGGG
4198804 TAATTTAAATTT
1 TAATTTAAATTT
4198816 TAATTTAAATTT
1 TAATTTAAATTT
4198828 T
1 T
4198829 TCAATTTTCG
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAATTTAAATTT
Found at i:4215115 original size:23 final size:24
Alignment explanation
Indices: 4215069--4215133 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 24
4215059 TGCATTTCTG
*
4215069 TGCTGAATCATTCAGCA-TTGTTT
1 TGCTGAATCAGTCAGCACTTGTTT
*
4215092 TGCTGAATCAGTCGGCACTT-TTT
1 TGCTGAATCAGTCAGCACTTGTTT
*
4215115 TGTTGAATCAGTCAGCACT
1 TGCTGAATCAGTCAGCACT
4215134 GAATCATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 35 0.95
24 2 0.05
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (24 bp):
TGCTGAATCAGTCAGCACTTGTTT
Found at i:4221809 original size:20 final size:20
Alignment explanation
Indices: 4221780--4221836 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
4221770 CGTTTGGTTT
4221780 ATAA-AATATAAGATTATTA
1 ATAAGAATATAAGATTATTA
*
4221799 ATAAGAATATAAGATTACTA
1 ATAAGAATATAAGATTATTA
** *
4221819 ATGGGAATAAAAGATTAT
1 ATAAGAATATAAGATTAT
4221837 CAGGGAATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.32
Consensus pattern (20 bp):
ATAAGAATATAAGATTATTA
Found at i:4223255 original size:21 final size:21
Alignment explanation
Indices: 4223231--4223270 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4223221 AAAATGTAAA
4223231 AAAAAATAATAA-TAAAATACC
1 AAAAAATAA-AATTAAAATACC
*
4223252 AAAAATTAAAATTAAAATA
1 AAAAAATAAAATTAAAATA
4223271 TATATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATAAAATTAAAATACC
Found at i:4225481 original size:2 final size:2
Alignment explanation
Indices: 4225472--4225509 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
4225462 AAAATATAAA
4225472 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4225510 CGGGGCGGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4227934 original size:2 final size:2
Alignment explanation
Indices: 4227927--4227954 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4227917 TTAACAAGAC
4227927 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4227955 GTATCTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4229333 original size:28 final size:28
Alignment explanation
Indices: 4229295--4229372 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
4229285 GAGTAAGTCC
*
4229295 TCCTTCACCTACATAATCACTTTCTAAG
1 TCCTCCACCTACATAATCACTTTCTAAG
4229323 TCCTCCACCTACATAATCACTTTCTAAG
1 TCCTCCACCTACATAATCACTTTCTAAG
4229351 ---TCCACCTACATAATCACTTTCT
1 TCCTCCACCTACATAATCACTTTCT
4229373 GTTCGTCTGT
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
25 22 0.45
28 27 0.55
ACGTcount: A:0.28, C:0.35, G:0.03, T:0.35
Consensus pattern (28 bp):
TCCTCCACCTACATAATCACTTTCTAAG
Found at i:4229813 original size:10 final size:10
Alignment explanation
Indices: 4229793--4229843 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
4229783 TGTGTGTGTT
*
4229793 TATACACATA
1 TATATACATA
*
4229803 TACATACATA
1 TATATACATA
*
4229813 TATATATATA
1 TATATACATA
*
4229823 TATATATATA
1 TATATACATA
*
4229833 TATATATATA
1 TATATACATA
4229843 T
1 T
4229844 GTTTTCAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATACATA
Found at i:4229817 original size:2 final size:2
Alignment explanation
Indices: 4229800--4229843 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
4229790 GTTTATACAC
* *
4229800 AT AT AC AT AC 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
4229842 AT
1 AT
4229844 GTTTTCAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4249129 original size:34 final size:33
Alignment explanation
Indices: 4249086--4249165 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 33
4249076 ATTGTCCAGA
*
4249086 GGGAACAGATTCCCCCAGGGGGTATCGATTCCGC
1 GGGAACAGATTCCCCCA-GGGGTATCGATTCCCC
*
4249120 GGGAACAGATTTCCCCTAGGGGTATCGATTCCCC
1 GGGAACAGA-TTCCCCCAGGGGTATCGATTCCCC
*
4249154 GGGTACAGATTC
1 GGGAACAGATTC
4249166 TCTTGTATGG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 3 0.07
34 32 0.76
35 7 0.17
ACGTcount: A:0.21, C:0.28, G:0.30, T:0.21
Consensus pattern (33 bp):
GGGAACAGATTCCCCCAGGGGTATCGATTCCCC
Found at i:4249306 original size:21 final size:21
Alignment explanation
Indices: 4249280--4249321 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4249270 ATTTGAATAT
4249280 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
4249301 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
4249322 CCATTCTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:4251008 original size:38 final size:40
Alignment explanation
Indices: 4250945--4251024 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
4250935 AGACCACGTG
4250945 ATAAAAAATTATATATTATTCTCTCTTTTTTTCCTTCAAT
1 ATAAAAAATTATATATTATTCTCTCTTTTTTTCCTTCAAT
4250985 ATAAAAAATTATATATTATTCTCTCTTTTTTTCCTTCAAT
1 ATAAAAAATTATATATTATTCTCTCTTTTTTTCCTTCAAT
4251025 CATGCGGCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (40 bp):
ATAAAAAATTATATATTATTCTCTCTTTTTTTCCTTCAAT
Found at i:4251456 original size:13 final size:13
Alignment explanation
Indices: 4251438--4251466 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4251428 ATTTGATAAC
4251438 ATATTTAAACAAA
1 ATATTTAAACAAA
4251451 ATATTTAAACAAA
1 ATATTTAAACAAA
4251464 ATA
1 ATA
4251467 ATAAGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATTTAAACAAA
Done.