Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold157
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: 1658850
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 45522 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:199683 original size:10 final size:9
Alignment explanation
Indices: 199664--199711 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
199654 TTTCGGTACG
199664 ATAATTTTT
1 ATAATTTTT
199673 ATAAGTTTTT
1 ATAA-TTTTT
**
199683 ACGATTTTT
1 ATAATTTTT
199692 ATAAATTTTT
1 AT-AATTTTT
*
199702 CTAATTTTT
1 ATAATTTTT
199711 A
1 A
199712 ATAAAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
9 17 0.55
10 14 0.45
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (9 bp):
ATAATTTTT
Found at i:199708 original size:19 final size:20
Alignment explanation
Indices: 199665--199752 Score: 65
Period size: 19 Copynumber: 4.5 Consensus size: 20
199655 TTCGGTACGA
*
199665 TAATTTTTATAAGTTTTTAC
1 TAATTTTTATAAATTTTTAC
*
199685 -GATTTTTATAAATTTTT-C
1 TAATTTTTATAAATTTTTAC
* * *
199703 TAATTTTTAATAAAATTTAAA
1 TAATTTTT-ATAAATTTTTAC
* * *
199724 TATTTTTTATTAAA-ATTTAA
1 TAATTTTTA-TAAATTTTTAC
199744 TAATTTTTA
1 TAATTTTTA
199753 GGTTGTGACA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.02
19 21 0.39
20 21 0.39
21 11 0.20
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TAATTTTTATAAATTTTTAC
Found at i:199730 original size:21 final size:20
Alignment explanation
Indices: 199703--199752 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
199693 TAAATTTTTC
199703 TAATTTTTAATAAAATTTAAA
1 TAATTTTTAATAAAATTT-AA
* *
199724 TATTTTTTATTAAAATTTAA
1 TAATTTTTAATAAAATTTAA
199744 TAATTTTTA
1 TAATTTTTA
199753 GGTTGTGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTTTTAATAAAATTTAA
Found at i:200996 original size:5 final size:5
Alignment explanation
Indices: 200988--201020 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
200978 TATTGAAAAG
200988 AATCA AATCA AATCA AATCA AATCA AATCA AAT
1 AATCA AATCA AATCA AATCA AATCA AATCA AAT
201021 TAGAATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (5 bp):
AATCA
Found at i:209761 original size:44 final size:44
Alignment explanation
Indices: 209687--210345 Score: 458
Period size: 44 Copynumber: 14.6 Consensus size: 44
209677 TCATTCCAAC
* * * *
209687 CCACTTCAACTTCAGGG-GTATAGGAATTGTAATTTCAATCTACT
1 CCACTGCAACTTCAGGGAG-ATAAGATTTGTAATTTCAATCTGCT
* *
209731 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTT-AATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTA-ATTTCAATCTGCT
* * **
209775 CCACTGCAACTTCAGGGAGATAAGATTTGTTATCTTGTAGCTTTAGTCTATT
1 CCACTGCAACTTCAGGGAGATAAGATTTG-TA-ATT-T--C---AATCTGCT
* * *
209827 CCATTGCAACTTTAGGGAGATAAGACTTGCTATGGTAGATTT-AATCCGAC-
1 CCACTGCAACTTCAGGGAGATAAGA--T--T-T-GTA-ATTTCAATCTG-CT
* * ** ** * *
209877 CTACTGCAACTTCAGAGG-TATTGGATTTGTTGTTTCCATTTGCT
1 CCACTGCAACTTCAG-GGAGATAAGATTTGTAATTTCAATCTGCT
* * *
209921 CCACTGCAACTTCAGTGAGATAAGATTTGTAACTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAATTTCAATCTGCT
* * * *
209965 CCACTGCAATTTCAGGGAGATAAGGTTTGTAGCTTT-AATATGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTA-ATTTCAATCTGCT
* * * *
210009 CTACTGCAACTTCAGAGAGATAAGATTTACT-ATCTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTT-GTAAT-TTCAATCTGCT
* * * **
210054 CTACTACAACTTTAGGGAGATAAGATTTGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAATTTCAATCTGCT
* * * * *
210098 TCACTGCAATTTCAGGGGGGATAAGGTTTGTAGCTTT-AATCTGCT
1 CCACTGCAACTTCA-GGGAGATAAGATTTGTA-ATTTCAATCTGCT
* *
210143 CTACTGCAACTTCAGAGAGATAAGATTTGCT-ATCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTG-TAAT-TTCAATCTGCT
**
210188 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAATTTCAATCTGCT
* * * * * *
210232 TCACTGTAATTTCAGGGGGATAAGATTTGCT-ATCTTCAATTTGTT
1 CCACTGCAACTTCAGGGAGATAAGATTTG-TAAT-TTCAATCTGCT
* * * **
210277 CCACTACAACTTTAGGGAGATAAGGTTTGTGGCTTT-AATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGT-AATTTCAATCTGCT
*
210321 CCACTACAACTTCAGGGAGATAAGA
1 CCACTGCAACTTCAGGGAGATAAGA
210346 CTCACCATGA
Statistics
Matches: 480, Mismatches: 99, Indels: 72
0.74 0.15 0.11
Matches are distributed among these distances:
43 7 0.01
44 260 0.54
45 148 0.31
46 5 0.01
48 1 0.00
50 19 0.04
51 2 0.00
52 29 0.06
54 1 0.00
56 2 0.00
57 5 0.01
58 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGTAATTTCAATCTGCT
Found at i:210084 original size:89 final size:89
Alignment explanation
Indices: 209720--210345 Score: 512
Period size: 89 Copynumber: 6.9 Consensus size: 89
209710 GAATTGTAAT
* * * *
209720 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTACTCCACTGCAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCTACTGCAAC
*
209785 TTCAGGGAGATAAGATTTGTTATCTTGTAGC
66 TTTAGGGAGATAAGATTTG----C---TAGC
* * ** * * * * *
209816 TTTAGTCTATTCCATTGCAACTTTAGGGAGATAAGACTTGCTATGGTAGATTTAATCCGAC-CTA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T--T-T-GTAGCTTCAATCTG-CTCTA
* * ** * *
209880 CTGCAACTTCAGAGG-TATTGGATTTG-TTGT
59 CTGCAACTTTAG-GGAGATAAGATTTGCTAGC
* * * * * *
209910 TTCCATTTGCTCCACTGCAACTTCAGTGAGATAAGATTTGTAACTTCAATCTACTCCACTGCAA-
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCTACTGCAAC
*
209974 TTTCAGGGAGATAAGGTTTG-TAGC
66 TTT-AGGGAGATAAGATTTGCTAGC
* * * * * * * *
209998 TTTAATATGCTCTACTGCAACTTCAGAGAGATAAGATTTACTATCTTCAATCTACTCTACTACAA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-GTAGCTTCAATCTGCTCTACTGCAA
210063 CTTTAGGGAGATAAGATTTG-TAGC
65 CTTTAGGGAGATAAGATTTGCTAGC
* * * * *
210087 TTCAATCTGCTTCACTGCAATTTCAGGGGGGATAAGGTTTGTAGCTTTAATCTGCTCTACTGCAA
1 TTCAATCTGCTCCACTGCAACTTCA-GGGAGATAAGATTTGTAGCTTCAATCTGCTCTACTGCAA
* * *
210152 CTTCAGAGAGATAAGATTTGCTATC
65 CTTTAGGGAGATAAGATTTGCTAGC
*
210177 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCT-TCACTGTAA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCT-ACTGCAA
* *
210241 -TTTCAGGGGGATAAGATTTGCTATC
65 CTTT-AGGGAGATAAGATTTGCTAGC
* * * * * * * * *
210266 TTCAATTTGTTCCACTACAACTTTAGGGAGATAAGGTTTGTGGCTTTAATCTGCTCCACTACAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCTACTGCAAC
*
210331 TTCAGGGAGATAAGA
66 TTTAGGGAGATAAGA
210346 CTCACCATGA
Statistics
Matches: 428, Mismatches: 83, Indels: 45
0.77 0.15 0.08
Matches are distributed among these distances:
87 5 0.01
88 65 0.15
89 215 0.50
90 43 0.10
92 1 0.00
94 29 0.07
96 31 0.07
98 1 0.00
100 1 0.00
101 1 0.00
102 33 0.08
103 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (89 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCTACTGCAAC
TTTAGGGAGATAAGATTTGCTAGC
Found at i:210166 original size:134 final size:132
Alignment explanation
Indices: 209917--210345 Score: 588
Period size: 134 Copynumber: 3.2 Consensus size: 132
209907 TGTTTCCATT
* * * * *
209917 TGCTCCACTGCAACTTCAGTGAGATAAGATTTGTAACTTCAATCTACTCCACTGCAATTTCAGGG
1 TGCTCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTTCACTGCAATTTCAGGG
*
209982 AGATAAGGTTTGTAGCTTTAATATGCTCTACTGCAACTTCAGAGAGATAAGATTTACTATCTTCA
66 GGATAAGGTTTGTAGCTTTAATATGCTCTACTGCAACTTCAGAGAGATAAGATTT-CTATCTTCA
210047 ATC
130 ATC
* * *
210050 TACTCTACTACAACTTTAGGGAGATAAGATTTGTAGCTTCAATCTGCTTCACTGCAATTTCAGGG
1 TGCTCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTTCACTGCAATTTCA-GG
*
210115 GGGATAAGGTTTGTAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTC
65 GGGATAAGGTTTGTAGCTTTAATATGCTCTACTGCAACTTCAGAGAGATAAGATTT-CTATCTTC
210180 AATC
129 AATC
* *
210184 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTTCACTGTAATTTCAGGG
1 TGCTCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTTCACTGCAATTTCAGGG
* * * * * * * * * * * ** *
210249 GGATAAGATTTGCTATCTTCAATTTGTTCCACTACAACTTTAGGGAGATAAGGTTTGTGGCTTTA
66 GGATAAGGTTTG-TAGCTTTAATATGCTCTACTGCAACTTCAGAGAGATAAGATTTCTATCTTCA
210314 ATC
130 ATC
210317 TGCTCCACTACAACTTCAGGGAGATAAGA
1 TGCTCCACTACAACTTCAGGGAGATAAGA
210346 CTCACCATGA
Statistics
Matches: 263, Mismatches: 31, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
133 104 0.40
134 159 0.60
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (132 bp):
TGCTCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTTCACTGCAATTTCAGGG
GGATAAGGTTTGTAGCTTTAATATGCTCTACTGCAACTTCAGAGAGATAAGATTTCTATCTTCAA
TC
Found at i:217551 original size:29 final size:30
Alignment explanation
Indices: 217518--217583 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 30
217508 AATTAACCGA
217518 ATTAAA-TAATATATATAATATATTTTT-A-T
1 ATTAAATTAATATA-AT-ATATATTTTTAACT
217547 ATTAAATTTAATATAATATATATTTTTAACT
1 ATTAAA-TTAATATAATATATATTTTTAACT
217578 ATTAAA
1 ATTAAA
217584 AGGAATGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 16 0.48
30 3 0.09
31 14 0.42
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTAAATTAATATAATATATATTTTTAACT
Found at i:217581 original size:31 final size:31
Alignment explanation
Indices: 217524--217583 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
217514 CCGAATTAAA
217524 TAATATATATAATATATTTTTATATTAAATT
1 TAATATATATAATATATTTTTATATTAAATT
217555 TAATATA-AT-ATATATTTTTAACTATTAAA
1 TAATATATATAATATATTTTT-A-TATTAAA
217584 AGGAATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 10 0.37
30 3 0.11
31 14 0.52
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
TAATATATATAATATATTTTTATATTAAATT
Found at i:220060 original size:17 final size:18
Alignment explanation
Indices: 220024--220062 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
220014 ATTACTTTTC
* *
220024 AAAAGTGCTTTTGGGCCA
1 AAAAGTACTTTTGAGCCA
220042 AAAAGTACTTTTGAG-CA
1 AAAAGTACTTTTGAGCCA
220059 AAAA
1 AAAA
220063 TTAAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (18 bp):
AAAAGTACTTTTGAGCCA
Found at i:249246 original size:10 final size:11
Alignment explanation
Indices: 249231--249275 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
249221 TATTAACATG
249231 TTAAATTTT-A
1 TTAAATTTTGA
249241 TTAAATTTAT-A
1 TTAAATTT-TGA
*
249252 ATAAATTTTGA
1 TTAAATTTTGA
249263 TT-AATTTTGA
1 TTAAATTTTGA
249273 TTA
1 TTA
249276 TTTTCGACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 19 0.63
11 11 0.37
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (11 bp):
TTAAATTTTGA
Found at i:253302 original size:28 final size:26
Alignment explanation
Indices: 253243--253302 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
253233 TTTGTTTTAA
*
253243 ACTGAAACTGTTATGGATAGTATATT
1 ACTGAAACTGCTATGGATAGTATATT
253269 -CTGAAACTGCTATAGG-TAGTAATATGT
1 ACTGAAACTGCTAT-GGATAGT-ATAT-T
253296 ACTGAAA
1 ACTGAAA
253303 ACACTTTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 16 0.55
26 6 0.21
27 1 0.03
28 6 0.21
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (26 bp):
ACTGAAACTGCTATGGATAGTATATT
Found at i:258877 original size:29 final size:27
Alignment explanation
Indices: 258839--258893 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
258829 GTGATTAAAT
258839 AAAATCGACA-CAAGCAAAATTTAAAAGAA
1 AAAATCGACAGCAAG--AAA-TTAAAAGAA
*
258868 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
258894 TAACTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 3 0.12
29 9 0.38
30 4 0.17
ACGTcount: A:0.62, C:0.11, G:0.13, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:264387 original size:50 final size:50
Alignment explanation
Indices: 264278--264506 Score: 178
Period size: 50 Copynumber: 4.5 Consensus size: 50
264268 ACATGCCAAA
* * ** * *
264278 GCCATGTCCTAGACATGGTCTTACATGGGATGTTTC-T-T-GTACTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCG-A-TGCCCAT
* * * **
264327 GCCATATCCCAGATATGGACTTACGTGGGAGTTCTCATATCGATGCCCAT
1 GCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGATGCCCAT
* * * *
264377 GCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGGTG-CCAGT
1 GCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGATGCCCA-T
* * *
264427 GCCATGTCCAAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT-A--TC---GATGCCCAT
*
264483 GCCATGTCCCATACATGGTCTTAC
1 GCCATGTCCCAGACATGGTCTTAC
264507 ATAGGATCTC
Statistics
Matches: 142, Mismatches: 27, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
49 31 0.22
50 78 0.55
51 2 0.01
52 1 0.01
53 2 0.01
56 26 0.18
57 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGATGCCCAT
Found at i:264463 original size:100 final size:103
Alignment explanation
Indices: 264320--264506 Score: 236
Period size: 100 Copynumber: 1.8 Consensus size: 103
264310 TTTCTTGTAC
* * * ** *
264320 TGCCAATGCCATATCCCAGATATGGACTTACGTGGGAGTTCTCAT-A-TC-GATGCCCATGCCAT
1 TGCCAATGCCATATCCAAGACATGGACTTACATGGGACCTCTCATAACTCAGATGCCAATGCCAT
264382 GTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
66 GTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
* * *
264420 TGCCAGTGCCATGTCCAAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCCAATGC
1 TGCCAATGCCATATCCAAGACATGGACTTACATGGGACCTCTCATAA-CTC-A-GATGCCAATGC
*
264485 CATGTCCCATACATGGTCTTAC
63 CATGTCCCAAACATGGTCTTAC
264507 ATAGGATCTC
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
100 37 0.52
101 1 0.01
103 2 0.03
106 31 0.44
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (103 bp):
TGCCAATGCCATATCCAAGACATGGACTTACATGGGACCTCTCATAACTCAGATGCCAATGCCAT
GTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
Found at i:272148 original size:63 final size:62
Alignment explanation
Indices: 272066--272217 Score: 162
Period size: 62 Copynumber: 2.4 Consensus size: 62
272056 GGTCACACAG
* * *
272066 CCTGGACACACGCATGTGTCT-TTGGCCCGTGTGCTCCATAATAGCAAACAGTGAGACACACGA
1 CCTGGACACACGCACGTGTCTCTT-G-CCATGTGATCCATAATAGCAAACAGTGAGACACACGA
* * * * * * *
272129 CCTGGACACATGCCCGTGTCTCTTGCCATGTGATCCTTGATGGCAAACAGTGAGTCACATGA
1 CCTGGACACACGCACGTGTCTCTTGCCATGTGATCCATAATAGCAAACAGTGAGACACACGA
** *
272191 CCTGGACACAATCTCGTGTCTCTTGCC
1 CCTGGACACACGCACGTGTCTCTTGCC
272218 CTTGTGGTCC
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
62 54 0.72
63 19 0.25
64 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.24
Consensus pattern (62 bp):
CCTGGACACACGCACGTGTCTCTTGCCATGTGATCCATAATAGCAAACAGTGAGACACACGA
Found at i:279830 original size:9 final size:9
Alignment explanation
Indices: 279811--279848 Score: 67
Period size: 9 Copynumber: 4.1 Consensus size: 9
279801 GGAAAAAACG
279811 AAAGTAAGAA
1 AAAG-AAGAA
279821 AAAGAAGAA
1 AAAGAAGAA
279830 AAAGAAGAA
1 AAAGAAGAA
279839 AAAGAAGAA
1 AAAGAAGAA
279848 A
1 A
279849 TAAAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 24 0.86
10 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:279858 original size:18 final size:18
Alignment explanation
Indices: 279819--279858 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
279809 CGAAAGTAAG
*
279819 AAAAAGAAGAAAAAGAAG
1 AAAAAGAAGAAAAAGAAC
279837 AAAAAGAAGAAATAA-AAC
1 AAAAAGAAGAAA-AAGAAC
279855 AAAA
1 AAAA
279859 TATTGGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (18 bp):
AAAAAGAAGAAAAAGAAC
Found at i:282481 original size:19 final size:22
Alignment explanation
Indices: 282457--282497 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
282447 CAGGCTAACG
282457 AAATATAA-A-TAAA-AGAATA
1 AAATATAAGATTAAAGAGAATA
282476 AAATATAAGATTAAAGAGAATA
1 AAATATAAGATTAAAGAGAATA
282498 CTCATTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 4 0.21
22 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (22 bp):
AAATATAAGATTAAAGAGAATA
Found at i:283435 original size:49 final size:49
Alignment explanation
Indices: 283355--283452 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 49
283345 GAATTATATT
* * * *
283355 AACAAGATATTGTAAATAAGCATACGACTCTAGAAGGATATAGAATTGA
1 AACAAGATAGTGTAAATAAACATAAGACTCTAGAAGGATATACAATTGA
* *
283404 AACAAGATAGTGTAAATAAACATATAG-CTCTAGCATGATATACAATTGA
1 AACAAGATAGTGTAAATAAACATA-AGACTCTAGAAGGATATACAATTGA
283453 CTTACAACTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 41 0.98
50 1 0.02
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (49 bp):
AACAAGATAGTGTAAATAAACATAAGACTCTAGAAGGATATACAATTGA
Found at i:285910 original size:5 final size:5
Alignment explanation
Indices: 285896--285933 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
285886 AAGATTTAAG
285896 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
285934 ATAAAACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:285962 original size:15 final size:15
Alignment explanation
Indices: 285942--285998 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
285932 TAATAAAACA
* *
285942 AATAAAGAATGAATG
1 AATAAAGAAAGAAAG
285957 AATAAAGAAAGAAAG
1 AATAAAGAAAGAAAG
*
285972 AA-AAAGAAATAGAA-
1 AATAAAGAAAGA-AAG
*
285986 AAGAAAGAAAGAA
1 AATAAAGAAAGAA
285999 CAAACGAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 11 0.31
15 25 0.69
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (15 bp):
AATAAAGAAAGAAAG
Found at i:285989 original size:11 final size:10
Alignment explanation
Indices: 285964--286041 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 10
285954 ATGAATAAAG
285964 AAAGAAAGAA
1 AAAGAAAGAA
*
285974 AAAGAAATAGA
1 AAAGAAAGA-A
285985 AAAGAAAGAA
1 AAAGAAAGAA
*
285995 AGAACAAACGAA
1 A-AAGAAA-GAA
* *
286007 ACAGAAGGGAA
1 AAAGAA-AGAA
286018 AAAGAAAGAAA
1 AAAGAAAG-AA
286029 AAAGGAAAGAA
1 AAA-GAAAGAA
286040 AA
1 AA
286042 TGAGAAAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
10 11 0.20
11 34 0.63
12 9 0.17
ACGTcount: A:0.73, C:0.04, G:0.22, T:0.01
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:285990 original size:25 final size:26
Alignment explanation
Indices: 285960--286030 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
285950 ATGAATGAAT
*
285960 AAAGAAAGAAAGAAAAA-GAAATAGA
1 AAAGAAAGAAAGAAAAACGAAACAGA
285985 AAAGAAAGAAAGAACAAACGAAACAGA
1 AAAGAAAGAAAGAA-AAACGAAACAGA
286012 AGGGAA-AAAGAAAGAAAAA
1 A---AAGAAAGAAAGAAAAA
286031 AGGAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 14 0.35
26 3 0.08
27 8 0.20
28 3 0.08
29 10 0.25
30 2 0.05
ACGTcount: A:0.73, C:0.04, G:0.21, T:0.01
Consensus pattern (26 bp):
AAAGAAAGAAAGAAAAACGAAACAGA
Found at i:287242 original size:21 final size:22
Alignment explanation
Indices: 287217--287259 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
287207 AACTATTTGT
*
287217 ATAGCAAGT-ATGAGATTTGAA
1 ATAGCAAGTGATGAGAATTGAA
287238 ATAGCAAGTGATGAGAATTGAA
1 ATAGCAAGTGATGAGAATTGAA
287260 TATGTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.26
Consensus pattern (22 bp):
ATAGCAAGTGATGAGAATTGAA
Found at i:288528 original size:25 final size:25
Alignment explanation
Indices: 288483--288542 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
288473 TTTGAAATAT
* *
288483 ATATTTTTTTCATTTTCGTATTATA
1 ATATTTTTTTCAATTTCGTATTAAA
*
288508 AT-TTTTTTCTCAATTTGGTATTAAA
1 ATATTTTTT-TCAATTTCGTATTAAA
288533 ATATTTTTTT
1 ATATTTTTTT
288543 GTTTGCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 6 0.20
25 18 0.60
26 6 0.20
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63
Consensus pattern (25 bp):
ATATTTTTTTCAATTTCGTATTAAA
Found at i:288877 original size:17 final size:17
Alignment explanation
Indices: 288829--288879 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
288819 TATTTCATGA
*
288829 ATTTTT-TTATATATTT
1 ATTTTTATTATATATAT
*
288845 ATTTTTAATT-TTTATAT
1 ATTTTT-ATTATATATAT
*
288862 ATTTTTATTATGTATAT
1 ATTTTTATTATATATAT
288879 A
1 A
288880 CATTTAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 9 0.31
17 18 0.62
18 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
ATTTTTATTATATATAT
Found at i:289228 original size:17 final size:17
Alignment explanation
Indices: 289206--289239 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
289196 ACCTTGAGAC
289206 AATTTTATTAAGAAGAT
1 AATTTTATTAAGAAGAT
*
289223 AATTTTATTGAGAAGAT
1 AATTTTATTAAGAAGAT
289240 CAACTTCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (17 bp):
AATTTTATTAAGAAGAT
Found at i:290885 original size:31 final size:31
Alignment explanation
Indices: 290850--290916 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
290840 TTAGCAGTCG
* *
290850 AGTGACTTATAT-AAAAATATTCGAATAATTT
1 AGTGACTTAAATGAAAAAT-TTCGAATAATTC
*
290881 AGTGACTTAAATGAAAACTTTCGAATAATTC
1 AGTGACTTAAATGAAAAATTTCGAATAATTC
290912 AGTGA
1 AGTGA
290917 TCAATTTGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAATGAAAAATTTCGAATAATTC
Found at i:294525 original size:35 final size:35
Alignment explanation
Indices: 294486--294567 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
294476 ACTCTCTGTT
294486 TTGGTGTGTTTCAAATAGATTAACTCTTATGAGCA
1 TTGGTGTGTTTCAAATAGATTAACTCTTATGAGCA
* * *
294521 TTGGTGTGTTTCGAATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAAATAGATTAACTCTTATGAGCA
*
294556 TCTCGTGTGTTT
1 T-TGGTGTGTTT
294568 TGGCTAGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 33 0.79
36 9 0.21
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.43
Consensus pattern (35 bp):
TTGGTGTGTTTCAAATAGATTAACTCTTATGAGCA
Found at i:296358 original size:16 final size:16
Alignment explanation
Indices: 296325--296366 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
296315 TACAAATCAA
296325 ATAAATAAACATTTCAT
1 ATAAA-AAACATTTCAT
296342 ATAACAAAACA-TTCAT
1 ATAA-AAAACATTTCAT
296358 ATAAAAAAC
1 ATAAAAAAC
296367 CAATCGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.21
16 9 0.38
17 9 0.38
18 1 0.04
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAAACATTTCAT
Found at i:297689 original size:25 final size:25
Alignment explanation
Indices: 297627--297718 Score: 96
Period size: 25 Copynumber: 3.7 Consensus size: 25
297617 ATACATGTAT
* * * *
297627 GCTCATACGAGCTGTA-AATAGTAA
1 GCTCATGCGAGCTGAATAACAGGAA
* * *
297651 GCTCTTCCGAGCTGAATAACGGGAA
1 GCTCATGCGAGCTGAATAACAGGAA
* *
297676 GCTCATGTGTGCTGAATAACAGGAA
1 GCTCATGCGAGCTGAATAACAGGAA
297701 GCTCATGCGAGCTGAATA
1 GCTCATGCGAGCTGAATA
297719 TCGAAAAGTT
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
24 13 0.24
25 41 0.76
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (25 bp):
GCTCATGCGAGCTGAATAACAGGAA
Found at i:301507 original size:13 final size:13
Alignment explanation
Indices: 301489--301514 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
301479 CGTAAAAGCA
301489 CCAGAGATGATCT
1 CCAGAGATGATCT
301502 CCAGAGATGATCT
1 CCAGAGATGATCT
301515 TGAAACCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
CCAGAGATGATCT
Found at i:302272 original size:21 final size:20
Alignment explanation
Indices: 302243--302281 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
302233 CAATCTCAAA
*
302243 CACATAAATAGAGTACTTAGC
1 CACAGAAATAGAG-ACTTAGC
302264 CACAGAAATAGAGACTTA
1 CACAGAAATAGAGACTTA
302282 ATAATGACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (20 bp):
CACAGAAATAGAGACTTAGC
Found at i:303027 original size:183 final size:183
Alignment explanation
Indices: 302693--303055 Score: 584
Period size: 184 Copynumber: 2.0 Consensus size: 183
302683 GATTGAGTGG
* *
302693 AAACCCAAAATAGGAATTAGTGAGATCACCAAAGCGAGCTAATCTCCCATGCTTAGATTTGATTA
1 AAACCCAAAATAGGAATTAGTGAGATCACCAAAGCGAGCTAATCACCCATGCTTAAATTTGATTA
*
302758 AGTGAGAATTCATTCACCCGAAGTTCACTTTATTTTCGCTATTTTTATTTTCTTTATTATAAAAA
66 AGTGAGAATTCATTCACCCGAAGTTCACTTTATTTTCGCGATTTTTATTTTCTTTATTATAAAAA
* * *
302823 CCCAAAAATCTTATATTTATGTTTTATCGTATTATTATTTATTTAAAGTATTA
131 CCCAAAAATATTATATTTATGTTTTATCATAATATTATTTATTTAAAGTATTA
* * * *
302876 AAACCCAAAATATGAATTAGTTATGCTCATCAAAGCGAGCTAATCACCCATGCTTAAATTTGATT
1 AAACCCAAAATAGGAATTAGTGA-GATCACCAAAGCGAGCTAATCACCCATGCTTAAATTTGATT
* * *
302941 AAGTTAGAATTCATTCACCTGAAGTTCACTTTATTTTCTCGATTTTTATTTT-TTTATTATAAAA
65 AAGTGAGAATTCATTCACCCGAAGTTCACTTTATTTTCGCGATTTTTATTTTCTTTATTATAAAA
*
303005 ACCCAAAAATATTTTATTTATGTTTTATCATAATATTATTTATTTAAAGTA
130 ACCCAAAAATATTATATTTATGTTTTATCATAATATTATTTATTTAAAGTA
303056 CTAATTATAT
Statistics
Matches: 165, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
183 80 0.48
184 85 0.52
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (183 bp):
AAACCCAAAATAGGAATTAGTGAGATCACCAAAGCGAGCTAATCACCCATGCTTAAATTTGATTA
AGTGAGAATTCATTCACCCGAAGTTCACTTTATTTTCGCGATTTTTATTTTCTTTATTATAAAAA
CCCAAAAATATTATATTTATGTTTTATCATAATATTATTTATTTAAAGTATTA
Found at i:314006 original size:207 final size:205
Alignment explanation
Indices: 313650--314121 Score: 775
Period size: 207 Copynumber: 2.3 Consensus size: 205
313640 TGTATATAAA
** * * *
313650 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGT-ATCCACCATATCTT
* * *
313715 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTTCCCCGAGGGGTTGCTAAGTGCTGATTCCCTG
65 TGAAA-GTAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCG
313780 ATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGAAAAGGGGGGTTGCTATGT
129 ATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGAAAA-GGGGGTTGCTATGT
313845 GCTGATTCCCCCG
193 GCTGATTCCCCCG
313858 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TATCCACCATATCTT
313923 TGAAA-TAAACAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCG
65 TGAAAGTAAA-AGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCG
* *
313987 ATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATTTTTGAAATGAAAAGGGGGTTGCTATGTG
129 ATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGAAAAGGGGGTTGCTATGTG
314052 CTGATTCCCCCG
194 CTGATTCCCCCG
* *
314064 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGC-GTATCCACC
314122 GATAACGGTT
Statistics
Matches: 249, Mismatches: 12, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
206 84 0.34
207 101 0.41
208 63 0.25
209 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (205 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTATCCACCATATCTTT
GAAAGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAT
TCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGAAAAGGGGGTTGCTATGTGCT
GATTCCCCCG
Found at i:314122 original size:103 final size:103
Alignment explanation
Indices: 313650--314121 Score: 777
Period size: 103 Copynumber: 4.6 Consensus size: 103
313640 TGTATATAAA
** * * *
313650 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
* *
313714 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTTCCCCG
65 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
313754 AGGGGTTGCTAAGTGCTGATTCCCTGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
313819 TGAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAA-GGGGGTTGCTATGTGCTGATTCCCCCG
313858 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
313923 TGAAAT-AAACAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAA-AGGGGGTTGCTATGTGCTGATTCCCCCG
* *
313961 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
314026 TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
314064 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
314122 GATAACGGTT
Statistics
Matches: 350, Mismatches: 14, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
103 185 0.53
104 164 0.47
105 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:353942 original size:22 final size:21
Alignment explanation
Indices: 353901--353948 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
353891 TAAAACATTA
**
353901 ATTTTTACTTTTGTTTATTTT
1 ATTTTTACTTTTGTAGATTTT
353922 ATTTTTACCTTTTGTAGATTTT
1 ATTTTTA-CTTTTGTAGATTTT
*
353944 GTTTT
1 ATTTT
353949 CCAAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.15, C:0.06, G:0.08, T:0.71
Consensus pattern (21 bp):
ATTTTTACTTTTGTAGATTTT
Found at i:364326 original size:15 final size:14
Alignment explanation
Indices: 364306--364341 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
364296 CTCATTCGAC
364306 TAAGTTAATTTTGAT
1 TAAGTTAATTTT-AT
364321 TAAGTTAATTTTAT
1 TAAGTTAATTTTAT
364335 T-AGTTAA
1 TAAGTTAA
364342 ATCAGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.29
14 3 0.14
15 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (14 bp):
TAAGTTAATTTTAT
Found at i:375368 original size:15 final size:16
Alignment explanation
Indices: 375339--375368 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
375329 CAAACATGCT
375339 TTAACACATTATCAAA
1 TTAACACATTATCAAA
375355 TTAACACA-TATCAA
1 TTAACACATTATCAA
375369 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:378269 original size:25 final size:25
Alignment explanation
Indices: 378199--378258 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
378189 CAGCTGTAAA
*
378199 CGGTAAGCTCATACGAGCTGAATAT
1 CGGTAATCTCATACGAGCTGAATAT
378224 CGAG-AATCTCATACGAGCTGAATAT
1 CG-GTAATCTCATACGAGCTGAATAT
378249 CGGTAATCTC
1 CGGTAATCTC
378259 TCTCGAGCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 1 0.03
25 30 0.94
26 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (25 bp):
CGGTAATCTCATACGAGCTGAATAT
Found at i:379587 original size:15 final size:15
Alignment explanation
Indices: 379564--379610 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
379554 AGTTTGTTTC
*
379564 CAGTTCATTTCAGCT
1 CAGTACATTTCAGCT
379579 CAGTACATTTCCAGCT
1 CAGTACATTT-CAGCT
*
379595 -AGCTCCATTTCAGCT
1 CAG-TACATTTCAGCT
379610 C
1 C
379611 CACCAGCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (15 bp):
CAGTACATTTCAGCT
Found at i:379873 original size:42 final size:42
Alignment explanation
Indices: 379806--379887 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
379796 AATTCAAAAA
* *
379806 GATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTTG
1 GATAAGAACAAGAGTTAAAACGTTTGAATTTCAAACGTTTTG
* *
379848 GATAGGAACAAGAGTTAAAACGTTTGAATTTTAAACGTTT
1 GATAAGAACAAGAGTTAAAACGTTTGAATTTCAAACGTTT
379888 CACACATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.33
Consensus pattern (42 bp):
GATAAGAACAAGAGTTAAAACGTTTGAATTTCAAACGTTTTG
Found at i:380467 original size:20 final size:20
Alignment explanation
Indices: 380438--380475 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
380428 CGTTCTGCAC
*
380438 CAAAAGAAAAAAATAAAAAA
1 CAAAAGAAAAAAACAAAAAA
*
380458 CAAAATAAAAAAACAAAA
1 CAAAAGAAAAAAACAAAA
380476 TAAAAACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.84, C:0.08, G:0.03, T:0.05
Consensus pattern (20 bp):
CAAAAGAAAAAAACAAAAAA
Found at i:380480 original size:11 final size:12
Alignment explanation
Indices: 380447--380491 Score: 74
Period size: 13 Copynumber: 3.8 Consensus size: 12
380437 CCAAAAGAAA
380447 AAAATAAAAAAC
1 AAAATAAAAAAC
380459 AAAATAAAAAAAC
1 AAAAT-AAAAAAC
380472 AAAAT-AAAAAC
1 AAAATAAAAAAC
380483 AAAATAAAA
1 AAAATAAAA
380492 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.35
12 8 0.26
13 12 0.39
ACGTcount: A:0.84, C:0.07, G:0.00, T:0.09
Consensus pattern (12 bp):
AAAATAAAAAAC
Found at i:380485 original size:24 final size:25
Alignment explanation
Indices: 380439--380491 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
380429 GTTCTGCACC
380439 AAAAGAAAAAAATAAAAAACAAAAT
1 AAAAGAAAAAAATAAAAAACAAAAT
380464 AAAA-AAACAAAAT-AAAAACAAAAT
1 AAAAGAAA-AAAATAAAAAACAAAAT
380488 AAAA
1 AAAA
380492 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.85, C:0.06, G:0.02, T:0.08
Consensus pattern (25 bp):
AAAAGAAAAAAATAAAAAACAAAAT
Found at i:390846 original size:51 final size:51
Alignment explanation
Indices: 390677--390867 Score: 189
Period size: 51 Copynumber: 3.8 Consensus size: 51
390667 TGAAAGTGAA
*
390677 AGTGAT-GGTCA-ATTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-
1 AGTGATAGGTCACA-TGTGTAGTACTATGTGCAGGCTACTACGTGTACGA-AT
* * * *
390727 A-TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGAAT
* * * *
390778 AGCT--TCGATCACGTGTGTAGTACTATGTACAGGCTACTACGTGTATCGAAT
1 AG-TGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGAAT
* *
390829 AGTGAT-GGTCACATGTGTAGTACCATGTGTAGGCTACTA
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTA
390868 TGTGAACCGG
Statistics
Matches: 114, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
49 4 0.04
50 37 0.32
51 71 0.62
52 1 0.01
53 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (51 bp):
AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACGAAT
Found at i:390877 original size:102 final size:101
Alignment explanation
Indices: 390690--390877 Score: 272
Period size: 102 Copynumber: 1.9 Consensus size: 101
390680 GATGGTCAAT
* * *
390690 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTACTATGT
1 TGTGTAGTACTATGTACAGGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTACCATGT
*
390755 GCAGGCTACTATGCGTACCGGATAGCTTCGATCACG
66 GCAGGCTACTATGCGAACCGGATAGCTTCGATCACG
*
390791 TGTGTAGTACTATGTACAGGCTACTACGTGTATC-GAAT-AGTGATGGTCACATGTGTAGTACCA
1 TGTGTAGTACTATGTACAGGCTACTACGTGTACCAGAATGA-T-A-GGTCACATGTGTAGTACCA
* *
390854 TGTGTAGGCTACTATGTGAACCGG
63 TGTGCAGGCTACTATGCGAACCGG
390878 TATCGTTAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
99 1 0.01
100 5 0.06
101 33 0.43
102 38 0.49
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (101 bp):
TGTGTAGTACTATGTACAGGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTACCATGT
GCAGGCTACTATGCGAACCGGATAGCTTCGATCACG
Found at i:399602 original size:23 final size:23
Alignment explanation
Indices: 399544--399602 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
399534 GACGCCACAA
399544 AATATGCCACAAATGCTTTATAG
1 AATATGCCACAAATGCTTTATAG
* ** *
399567 AACACACCCCAAA-GACTTTATAG
1 AATATGCCACAAATG-CTTTATAG
399590 AATATGCCACAAA
1 AATATGCCACAAA
399603 ATCTTTACAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.22
Consensus pattern (23 bp):
AATATGCCACAAATGCTTTATAG
Found at i:399608 original size:23 final size:23
Alignment explanation
Indices: 399544--399609 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
399534 GACGCCACAA
399544 AATATGCCAC-AAATGCTTTATAG
1 AATATGCCACAAAAT-CTTTATAG
* ** *
399567 AACACACCCCAAAGA-CTTTATAG
1 AATATGCCACAAA-ATCTTTATAG
399590 AATATGCCACAAAATCTTTA
1 AATATGCCACAAAATCTTTA
399610 CAAAATATAC
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 1 0.03
23 28 0.88
24 2 0.06
25 1 0.03
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (23 bp):
AATATGCCACAAAATCTTTATAG
Found at i:399631 original size:23 final size:23
Alignment explanation
Indices: 399605--399660 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
399595 GCCACAAAAT
*
399605 CTTTACAAAATATACCATACAGG
1 CTTTACAAAATATACCATAAAGG
* ** *
399628 CTTTGCCGAATATGCCATAAAGG
1 CTTTACAAAATATACCATAAAGG
399651 CTTTACAAAA
1 CTTTACAAAA
399661 CATTCCGCGT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.27
Consensus pattern (23 bp):
CTTTACAAAATATACCATAAAGG
Found at i:412268 original size:16 final size:17
Alignment explanation
Indices: 412224--412275 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
412214 ATTTAATCTT
412224 AATTATAAAAAAGTTAAA
1 AATTATAAAAAAGTT-AA
412242 AATTAT-AAAAA-TTAA
1 AATTATAAAAAAGTTAA
*
412257 AATTATAAAAAATTTAA
1 AATTATAAAAAAGTTAA
412274 AA
1 AA
412276 GTTTCAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.25
16 7 0.22
17 11 0.34
18 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AATTATAAAAAAGTTAA
Found at i:412290 original size:32 final size:33
Alignment explanation
Indices: 412224--412308 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
412214 ATTTAATCTT
* * *
412224 AATTATAAAAAAGTTAAAAATTATAAAAATTAA
1 AATTATAAAAAATTTAAAAGTTATAAAAAGTAA
*
412257 AATTATAAAAAATTTAAAAGTT-TCAAAAGTAA
1 AATTATAAAAAATTTAAAAGTTATAAAAAGTAA
*
412289 AA-TATAAAAACATTTTAAAG
1 AATTATAAAAA-ATTTAAAAG
412309 ATTTTGTACC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 8 0.17
32 18 0.39
33 20 0.43
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (33 bp):
AATTATAAAAAATTTAAAAGTTATAAAAAGTAA
Found at i:416459 original size:27 final size:28
Alignment explanation
Indices: 416429--416487 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
416419 GGTGTTTGAC
*
416429 AGGCAGCA-CCAGTGGAGGGC-TTGTCAT
1 AGGCAGCATCCAGTGGA-GGCTTTGCCAT
* *
416456 AGGCGGCATCTAGTGGAGGCTTTGCCAT
1 AGGCAGCATCCAGTGGAGGCTTTGCCAT
416484 AGGC
1 AGGC
416488 GGTACCCAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.20, C:0.22, G:0.37, T:0.20
Consensus pattern (28 bp):
AGGCAGCATCCAGTGGAGGCTTTGCCAT
Found at i:421414 original size:96 final size:96
Alignment explanation
Indices: 421229--421415 Score: 272
Period size: 96 Copynumber: 1.9 Consensus size: 96
421219 ACTTACTTTC
*
421229 TTCTCTTGTTGGATATTTAATTGGACATTGGAGAACCTTATGATTTTTTGAACTACACCAATAAC
1 TTCTCTTGTTGGATATTTAATTGGACATTAGAGAACCTTATGATTTTTTGAACTACACCAATAAC
* * *
421294 ATTGCATAAAAGCTGATAGTTCAATCTTATT
66 ATTGCACAAAAGCTGAGAGATCAATCTTATT
421325 TTCTCTAT-TTGGATATTTAATTGGACATTAGA-AACCCTTATGATTTTTTGAACTACACCAATA
1 TTCTCT-TGTTGGATATTTAATTGGACATTAGAGAA-CCTTATGATTTTTTGAACTACACCAATA
* *
421388 ACATTTCACAACAAG-TGAGGGATCAATC
64 ACATTGCACAA-AAGCTGAGAGATCAATC
421416 ATACTCCTCT
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
95 2 0.02
96 76 0.93
97 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (96 bp):
TTCTCTTGTTGGATATTTAATTGGACATTAGAGAACCTTATGATTTTTTGAACTACACCAATAAC
ATTGCACAAAAGCTGAGAGATCAATCTTATT
Found at i:423873 original size:14 final size:14
Alignment explanation
Indices: 423854--423880 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
423844 AAAGTTGTAG
423854 TTTAATAAATAAAT
1 TTTAATAAATAAAT
423868 TTTAATAAATAAA
1 TTTAATAAATAAA
423881 CTAAGTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAATAAATAAAT
Found at i:424730 original size:20 final size:19
Alignment explanation
Indices: 424661--424727 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
424651 TCGCACATAC
424661 GTACCCCTGTTGTACTTTG
1 GTACCCCTGTTGTACTTTG
*
424680 GTGCCCCTGTTGTACTTTG
1 GTACCCCTGTTGTACTTTG
*
424699 GTACCCCTGATTGTACTTCG
1 GTACCCCTG-TTGTACTTTG
424719 GTACCCCTG
1 GTACCCCTG
424728 ATTTGCACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 26 0.59
20 18 0.41
ACGTcount: A:0.10, C:0.30, G:0.22, T:0.37
Consensus pattern (19 bp):
GTACCCCTGTTGTACTTTG
Found at i:435866 original size:27 final size:27
Alignment explanation
Indices: 435832--435930 Score: 126
Period size: 27 Copynumber: 3.6 Consensus size: 27
435822 GTCATTTCGA
**
435832 CTTCTAGGGGTATAACGGTCATTTTACC
1 CTTC-AGGGGTATTTCGGTCATTTTACC
* * *
435860 TTTTAGGGGTATTTTGGTCATTTTACC
1 CTTCAGGGGTATTTCGGTCATTTTACC
* *
435887 CTTCGGGGGTATTTCGGCCATTTTACC
1 CTTCAGGGGTATTTCGGTCATTTTACC
435914 CTTCAGGGGTATTTCGG
1 CTTCAGGGGTATTTCGG
435931 ACATCTACCC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
27 58 0.97
28 2 0.03
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.40
Consensus pattern (27 bp):
CTTCAGGGGTATTTCGGTCATTTTACC
Found at i:441787 original size:28 final size:28
Alignment explanation
Indices: 441751--441814 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
441741 CAGTAATAGT
*
441751 ACAGTGTGGGCCTTAG-CTCGATACAGTA
1 ACAGTGTGGGCCTTAGCCT-AATACAGTA
*
441779 ATAGTGTGGGCCTTAGCCTAATACAGTA
1 ACAGTGTGGGCCTTAGCCTAATACAGTA
441807 ACAGTGTG
1 ACAGTGTG
441815 ATAATGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 30 0.94
29 2 0.06
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.27
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCTAATACAGTA
Found at i:441910 original size:27 final size:27
Alignment explanation
Indices: 441880--441954 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 27
441870 TTTCAAGGGT
441880 ATTTCGGTCATTTTACCCTTTGGCAAA
1 ATTTCGGTCATTTTACCCTTTGGCAAA
*** * ****
441907 ATTTTAATCATTTTACCCTTCGGGGGT
1 ATTTCGGTCATTTTACCCTTTGGCAAA
*
441934 ATTTCGGTTATTTTACCCTTT
1 ATTTCGGTCATTTTACCCTTT
441955 ATGGAGGTAT
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.47
Consensus pattern (27 bp):
ATTTCGGTCATTTTACCCTTTGGCAAA
Found at i:446886 original size:35 final size:35
Alignment explanation
Indices: 446847--446969 Score: 165
Period size: 35 Copynumber: 3.5 Consensus size: 35
446837 TTACAGTGTT
*
446847 TCTGGTGTGCTGGATGGTACTGGCTCTTATGAGCA
1 TCTGGTGTGCTGGATGGTACTAGCTCTTATGAGCA
* * * *
446882 TCTGGTGTGTTGGATGGTACTAACTCTTGTAAGCA
1 TCTGGTGTGCTGGATGGTACTAGCTCTTATGAGCA
* *
446917 TCTGGTGTGCTGGGTGGTACTAGCTCTTATGAACA
1 TCTGGTGTGCTGGATGGTACTAGCTCTTATGAGCA
* *
446952 TCTTGTGTGCTGAATGGT
1 TCTGGTGTGCTGGATGGT
446970 TAACTGTGTA
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 74 1.00
ACGTcount: A:0.16, C:0.15, G:0.32, T:0.37
Consensus pattern (35 bp):
TCTGGTGTGCTGGATGGTACTAGCTCTTATGAGCA
Found at i:450148 original size:33 final size:32
Alignment explanation
Indices: 450111--450271 Score: 124
Period size: 33 Copynumber: 4.8 Consensus size: 32
450101 ACATTCGTAG
* **
450111 TGCCATAACCCAGTTATGGTCTTATCATCAAAA
1 TGCCATAGCCCAACTATGGTCTTA-CATCAAAA
* *
450144 TGCCATAGCCCAGCTATGGTCTTACATATAAACA
1 TGCCATAGCCCAACTATGGTCTTACAT-CAAA-A
* * * * *
450178 CTGCCATGGTCCAACTATGGTCTTACGTCTATAG
1 -TGCCATAGCCCAACTATGGTCTTACATC-AAAA
* * * *
450212 TGCCATAACCCAATTATTGTCTTATCATCAGAA
1 TGCCATAGCCCAACTATGGTCTTA-CATCAAAA
* *
450245 TGCTATAGCCCAACTATGGCCTTACAT
1 TGCCATAGCCCAACTATGGTCTTACAT
450272 ATAAACACTT
Statistics
Matches: 100, Mismatches: 23, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
32 6 0.06
33 65 0.65
34 4 0.04
35 25 0.25
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (32 bp):
TGCCATAGCCCAACTATGGTCTTACATCAAAA
Found at i:450196 original size:35 final size:35
Alignment explanation
Indices: 450111--450303 Score: 114
Period size: 33 Copynumber: 5.7 Consensus size: 35
450101 ACATTCGTAG
* ** *
450111 TGCCATAACCCAGTTATGGTCTTATCAT-CAAA-A-
1 TGCCATAGCCCAACTATGGTCTTA-CATATAAACAC
*
450144 TGCCATAGCCCAGCTATGGTCTTACATATAAACAC
1 TGCCATAGCCCAACTATGGTCTTACATATAAACAC
* * * * * *
450179 TGCCATGGTCCAACTATGGTCTTACGTCT--ATAG
1 TGCCATAGCCCAACTATGGTCTTACATATAAACAC
* * * * *
450212 TGCCATAACCCAATTATTGTCTTATCAT-CAGA-A-
1 TGCCATAGCCCAACTATGGTCTTA-CATATAAACAC
* *
450245 TGCTATAGCCCAACTATGGCCTTACATATAAACAC
1 TGCCATAGCCCAACTATGGTCTTACATATAAACAC
* * * *
450280 TTCCATGGTCCAACCATGGTCTTA
1 TGCCATAGCCCAACTATGGTCTTA
450304 TGTTTGAATA
Statistics
Matches: 121, Mismatches: 30, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
32 6 0.05
33 67 0.55
34 5 0.04
35 43 0.36
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (35 bp):
TGCCATAGCCCAACTATGGTCTTACATATAAACAC
Found at i:450221 original size:101 final size:101
Alignment explanation
Indices: 450048--450303 Score: 320
Period size: 101 Copynumber: 2.6 Consensus size: 101
450038 TCATTTTTGT
* * * * * ** * * *
450048 CATAGTCCAACTATGGTCTTACATAT--GCATTGCCATGGCCCTGCCATGGTCGTACAT-TCGTA
1 CATAGCCCAACTATGGCCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTCT-ATA
*
450110 GTGCCATAACCCAGTTATGGTCTTATCATCAAAATGC
65 GTGCCATAACCCAATTATGGTCTTATCATCAAAATGC
* * *
450147 CATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACTATGGTCTTACGTCTATAG
1 CATAGCCCAACTATGGCCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTCTATAG
* *
450212 TGCCATAACCCAATTATTGTCTTATCATCAGAATGC
66 TGCCATAACCCAATTATGGTCTTATCATCAAAATGC
* *
450248 TATAGCCCAACTATGGCCTTACATATAAACACTTCCATGGTCCAACCATGGTCTTA
1 CATAGCCCAACTATGGCCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTA
450304 TGTTTGAATA
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
99 24 0.18
101 110 0.81
102 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (101 bp):
CATAGCCCAACTATGGCCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTCTATAG
TGCCATAACCCAATTATGGTCTTATCATCAAAATGC
Found at i:451606 original size:15 final size:15
Alignment explanation
Indices: 451586--451614 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
451576 GAGGTCTCGA
451586 TTATCAAATCAAAAT
1 TTATCAAATCAAAAT
451601 TTATCAAATCAAAA
1 TTATCAAATCAAAA
451615 CCTTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (15 bp):
TTATCAAATCAAAAT
Found at i:457806 original size:13 final size:13
Alignment explanation
Indices: 457788--457812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
457778 TAAGTTATAT
457788 GTGTGAAAATTTC
1 GTGTGAAAATTTC
457801 GTGTGAAAATTT
1 GTGTGAAAATTT
457813 GATAGTTTGA
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:465632 original size:13 final size:13
Alignment explanation
Indices: 465614--465638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
465604 TAAGTTATAT
465614 GTGTGAAAATTTC
1 GTGTGAAAATTTC
465627 GTGTGAAAATTT
1 GTGTGAAAATTT
465639 GATAGTTTGA
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:467141 original size:41 final size:41
Alignment explanation
Indices: 467096--467198 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
467086 GGCTATGTGC
* *
467096 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * * *
467137 CTAGCAGGCTTAATGCCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* *
467178 CTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
467199 TATCAAATCA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
Found at i:467839 original size:95 final size:95
Alignment explanation
Indices: 467676--467865 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
467666 TTCATGGTGA
467676 ACGAAATCAGCAAGGGGGAAGCCTTAGTTAGGGTTTTCAAGCTTCCAAGCTCTAGAGTAAGTGAT
1 ACGAAATCAGCAAGGGGGAAGCCTTAGTTAGGGTTTTCAAGCTTCCAAGCTCTAGAGTAAGTGAT
467741 CCCAAGCCCCGTTTTTAATGTTTTTACGTC
66 CCCAAGCCCCGTTTTTAATGTTTTTACGTC
467771 ACGAAATCAGCAAGGGGGAAGCCTTAGTTAGGGTTTTCAAGCTTCCAAGCTCTAGAGTAAGTGAT
1 ACGAAATCAGCAAGGGGGAAGCCTTAGTTAGGGTTTTCAAGCTTCCAAGCTCTAGAGTAAGTGAT
467836 CCCAAGCCCCGTTTTTAATGTTTTTACGTC
66 CCCAAGCCCCGTTTTTAATGTTTTTACGTC
467866 TTTAGAGTCC
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (95 bp):
ACGAAATCAGCAAGGGGGAAGCCTTAGTTAGGGTTTTCAAGCTTCCAAGCTCTAGAGTAAGTGAT
CCCAAGCCCCGTTTTTAATGTTTTTACGTC
Found at i:476788 original size:15 final size:16
Alignment explanation
Indices: 476760--476796 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
476750 CCAAGCTTAT
476760 TATATTTAAATATATA
1 TATATTTAAATATATA
476776 TATATTT-AATATATA
1 TATATTTAAATATATA
*
476791 TGTATT
1 TATATT
476797 GAATTTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TATATTTAAATATATA
Found at i:477001 original size:124 final size:126
Alignment explanation
Indices: 476833--477084 Score: 490
Period size: 124 Copynumber: 2.0 Consensus size: 126
476823 GTAATGCCTC
476833 GTAACCCTAATTCGGTGACAAATATGGGTAAGGGGTGTTACACAAACTACCTTTATGTAAGGTCC
1 GTAACCCTAATTCGGTGACAAATATGGGTAAGGGGTGTTACACAAACTACCTTTATGTAAGGTCC
476898 TATACATTTAAGTTCAACCATATCATAAGACGATTTCCATGTACACA-C-TTCATCACATA
66 TATACATTTAAGTTCAACCATATCATAAGACGATTTCCATGTACACACCATTCATCACATA
476957 GTAACCCTAATTCGGTGACAAATATGGGTAAGGGGTGTTACACAAACTACCTTTATGTAAGGTCC
1 GTAACCCTAATTCGGTGACAAATATGGGTAAGGGGTGTTACACAAACTACCTTTATGTAAGGTCC
477022 TATACATTTAAGTTCAACCATATCATAAGACGATTTCCATGTACACACCATTCATCACATA
66 TATACATTTAAGTTCAACCATATCATAAGACGATTTCCATGTACACACCATTCATCACATA
477083 GT
1 GT
477085 TATTTTGTTA
Statistics
Matches: 126, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
124 112 0.89
125 1 0.01
126 13 0.10
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (126 bp):
GTAACCCTAATTCGGTGACAAATATGGGTAAGGGGTGTTACACAAACTACCTTTATGTAAGGTCC
TATACATTTAAGTTCAACCATATCATAAGACGATTTCCATGTACACACCATTCATCACATA
Found at i:495286 original size:28 final size:29
Alignment explanation
Indices: 495254--495310 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
495244 AAATAATTAA
495254 AGTGCACTTAAAATATG-ACATGTTGAAT
1 AGTGCACTTAAAATATGAACATGTTGAAT
495282 AGTGCACTTAAAATATGAACATGTTGAAT
1 AGTGCACTTAAAATATGAACATGTTGAAT
495311 TTTAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (29 bp):
AGTGCACTTAAAATATGAACATGTTGAAT
Found at i:495327 original size:12 final size:12
Alignment explanation
Indices: 495310--495335 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
495300 ACATGTTGAA
495310 TTTTAATTAATT
1 TTTTAATTAATT
495322 TTTTAATTAATT
1 TTTTAATTAATT
495334 TT
1 TT
495336 GATGAATATT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTAATTAATT
Found at i:503672 original size:27 final size:27
Alignment explanation
Indices: 503573--503726 Score: 118
Period size: 27 Copynumber: 5.7 Consensus size: 27
503563 ATATCTGGAC
**
503573 CGAAATACCCCCAAAGGGTAAAATGAT
1 CGAAATACCCCCGTAGGGTAAAATGAT
* **
503600 TGAAATACCATCG-ATGGGTAAAATGAT
1 CGAAATACCCCCGTA-GGGTAAAATGAT
* * ** *
503627 TGAAATGCCCTTG-ATGGGTAAAATTAT
1 CGAAATACCCCCGTA-GGGTAAAATGAT
*
503654 CGAAATACCCCCGTAGGGTAGAAT-A-
1 CGAAATACCCCCGTAGGGTAAAATGAT
* * *
503679 CTGAAATACCCCCATAGGGTAAAATAAC
1 C-GAAATACCCCCGTAGGGTAAAATGAT
*
503707 CGTAATACCCCCGTAGGGTA
1 CGAAATACCCCCGTAGGGTA
503727 TACCCTCATA
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
25 1 0.01
26 23 0.22
27 79 0.75
28 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (27 bp):
CGAAATACCCCCGTAGGGTAAAATGAT
Found at i:503673 original size:54 final size:53
Alignment explanation
Indices: 503574--503726 Score: 148
Period size: 53 Copynumber: 2.9 Consensus size: 53
503564 TATCTGGACC
* * * ** *
503574 GAAATACCCCCAAAGGGTAAAATGATTGAAATACCATCG-ATGGGTAAAATGATT
1 GAAATACCCCCATAGGGTAAAATAATCGAAATACCCCCGTA-GGGTAAAAT-ACT
* ** * *
503628 GAAATGCCCTTGAT-GGGTAAAATTATCGAAATACCCCCGTAGGGTAGAATACT
1 GAAATACCC-CCATAGGGTAAAATAATCGAAATACCCCCGTAGGGTAAAATACT
* *
503681 GAAATACCCCCATAGGGTAAAATAACCGTAATACCCCCGTAGGGTA
1 GAAATACCCCCATAGGGTAAAATAATCGAAATACCCCCGTAGGGTA
503727 TACCCTCATA
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
52 2 0.03
53 39 0.49
54 37 0.46
55 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (53 bp):
GAAATACCCCCATAGGGTAAAATAATCGAAATACCCCCGTAGGGTAAAATACT
Found at i:503976 original size:27 final size:27
Alignment explanation
Indices: 503920--503977 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
503910 GGAACTACTG
* * *
503920 TACTCGTGGCTCTGCCACAATCACTGT
1 TACTAGTGGCTCGGCCACAATCACTAT
503947 TACTAGTGGCTCGGCCACATAT-ACTAT
1 TACTAGTGGCTCGGCCACA-ATCACTAT
503974 TACT
1 TACT
503978 GGCAGCTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.31
Consensus pattern (27 bp):
TACTAGTGGCTCGGCCACAATCACTAT
Found at i:503997 original size:26 final size:26
Alignment explanation
Indices: 503967--504017 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
503957 TCGGCCACAT
* *
503967 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATCACTGGCAACTTTGCTGCG
* *
503993 ATACTGTCGCTGGCAACTTTGCTGC
1 ATACTATCACTGGCAACTTTGCTGC
504018 AATGCTACTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (26 bp):
ATACTATCACTGGCAACTTTGCTGCG
Found at i:504064 original size:32 final size:32
Alignment explanation
Indices: 504023--504229 Score: 193
Period size: 32 Copynumber: 6.5 Consensus size: 32
504013 GCTGCAATGC
*
504023 TACTGATGGCTTTGTGACGATCATAGT-ACCGT
1 TACTGATGGCTTTGTGCCGATCATA-TCACCGT
*
504055 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
** * * * * * *
504087 TACCAACGGC-TGGTTACTGATCATTTCACTGT
1 TACTGATGGCTTTG-TGCCGATCATATCACCGT
* * * * *
504119 TATTAATGGCTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
* * *
504151 TACTGAGGGCTTTGTGCCGATCATGTTACCGT
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
* * *
504183 TACTGATGGCTGTGTGTCGATCATATCACTGT
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
504215 TACTGATGGCTTTGT
1 TACTGATGGCTTTGT
504230 ACTAATCACA
Statistics
Matches: 138, Mismatches: 34, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
31 3 0.02
32 134 0.97
33 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATCACCGT
Found at i:504194 original size:96 final size:96
Alignment explanation
Indices: 504023--504225 Score: 241
Period size: 96 Copynumber: 2.1 Consensus size: 96
504013 GCTGCAATGC
* * * *
504023 TACTGATGGCTTTGTGACGATCATAGTACCGTTACTGATGGCTTTGTGCCGATCATATTACCGTT
1 TACTAATGGCTGTGTGACGATCATAGTACCGCTACTGAGGGCTTTGTGCCGATCATATTACCGTT
*
504088 ACCAACGGCTG-GT-TACTGATCATTTCACTGT
66 ACCAACGGCTGTGTGT-C-GATCATATCACTGT
* * * *
504119 TATTAATGGCTGTGTGCCGATCATA-TCACTGCTACTGAGGGCTTTGTGCCGATCATGTTACCGT
1 TACTAATGGCTGTGTGACGATCATAGT-ACCGCTACTGAGGGCTTTGTGCCGATCATATTACCGT
** *
504183 TACTGATGGCTGTGTGTCGATCATATCACTGT
65 TACCAACGGCTGTGTGTCGATCATATCACTGT
*
504215 TACTGATGGCT
1 TACTAATGGCT
504226 TTGTACTAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
95 1 0.01
96 85 0.94
97 3 0.03
98 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (96 bp):
TACTAATGGCTGTGTGACGATCATAGTACCGCTACTGAGGGCTTTGTGCCGATCATATTACCGTT
ACCAACGGCTGTGTGTCGATCATATCACTGT
Found at i:504246 original size:32 final size:31
Alignment explanation
Indices: 504176--504259 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
504166 GCCGATCATG
* * *
504176 TTACCGTTACTGATGGCTGTGTGTCGATCATA
1 TTACTGTTACTGATGGCT-TGTGTCAATCACA
*
504208 TCACTGTTACTGATGGCTT-TGTACTAATCACA
1 TTACTGTTACTGATGGCTTGTGT-C-AATCACA
*
504240 TTACTG-TACTTATGGCTTGT
1 TTACTGTTACTGATGGCTTGT
504260 AGCCATTCTG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
30 3 0.07
31 13 0.30
32 27 0.63
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (31 bp):
TTACTGTTACTGATGGCTTGTGTCAATCACA
Found at i:505535 original size:20 final size:20
Alignment explanation
Indices: 505512--505582 Score: 81
Period size: 20 Copynumber: 3.4 Consensus size: 20
505502 AAATTTTAAT
505512 TTTATTATCTAATTTTTCAA
1 TTTATTATCTAATTTTTCAA
*
505532 TTTATTAATTATTAATATTTT-AA
1 TTTATT-A-T-CTAAT-TTTTCAA
505555 TTTTATTATCTAATTTTTCAA
1 -TTTATTATCTAATTTTTCAA
505576 TTTATTA
1 TTTATTA
505583 AATTATTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
20 17 0.40
21 7 0.16
22 2 0.05
23 7 0.16
24 10 0.23
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTATCTAATTTTTCAA
Found at i:505555 original size:44 final size:45
Alignment explanation
Indices: 505504--505598 Score: 183
Period size: 44 Copynumber: 2.1 Consensus size: 45
505494 TTTCTCCTAA
505504 ATTTTAATTTTATTATCTAATTTTTCAATTTATT-AATTATTAAT
1 ATTTTAATTTTATTATCTAATTTTTCAATTTATTAAATTATTAAT
505548 ATTTTAATTTTATTATCTAATTTTTCAATTTATTAAATTATTAAT
1 ATTTTAATTTTATTATCTAATTTTTCAATTTATTAAATTATTAAT
505593 ATTTTA
1 ATTTTA
505599 TATTAATTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 34 0.68
45 16 0.32
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (45 bp):
ATTTTAATTTTATTATCTAATTTTTCAATTTATTAAATTATTAAT
Found at i:505580 original size:17 final size:15
Alignment explanation
Indices: 505516--505583 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 15
505506 TTTAATTTTA
505516 TTATCTAATTTTTCAAT
1 TTAT-TAATTTTT-AAT
*
505533 TTATTAATTATTAAT
1 TTATTAATTTTTAAT
505548 ATT-TTAA-TTTT-A-
1 -TTATTAATTTTTAAT
505560 TTATCTAATTTTTCAAT
1 TTAT-TAATTTTT-AAT
505577 TTATTAA
1 TTATTAA
505584 ATTATTAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 15
0.71 0.03 0.25
Matches are distributed among these distances:
11 2 0.05
12 1 0.02
13 4 0.10
14 7 0.17
15 7 0.17
16 13 0.31
17 8 0.19
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTAATTTTTAAT
Found at i:517591 original size:27 final size:27
Alignment explanation
Indices: 517553--517655 Score: 152
Period size: 27 Copynumber: 3.8 Consensus size: 27
517543 TCATTAACTA
* *
517553 TACTGAAGTACCCTCGATGGGTAAAAT
1 TACTGAAATACCCTCAATGGGTAAAAT
*
517580 TACTGAAATACCCTTAATGGGTAAAAT
1 TACTGAAATACCCTCAATGGGTAAAAT
* *
517607 TACCGAAATACCCTCAATGGATAAAAT
1 TACTGAAATACCCTCAATGGGTAAAAT
*
517634 TATTGAAATACCCTCAATGGGT
1 TACTGAAATACCCTCAATGGGT
517656 CCTAATGGGT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (27 bp):
TACTGAAATACCCTCAATGGGTAAAAT
Found at i:517855 original size:27 final size:26
Alignment explanation
Indices: 517825--517878 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
517815 ATTGTTTCTA
517825 GTGGCTCTGCCACA-ATTACTGTTACTG
1 GTGGCTCTGCCACATA-TACTG-TACTG
*
517852 GTGGCTTTGCCACATATACTGTACTG
1 GTGGCTCTGCCACATATACTGTACTG
517878 G
1 G
517879 CAGCTTTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 18 0.72
28 1 0.04
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (26 bp):
GTGGCTCTGCCACATATACTGTACTG
Found at i:517884 original size:26 final size:27
Alignment explanation
Indices: 517832--517887 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
517822 CTAGTGGCTC
**
517832 TGCCACAATTACTGTTACTGGTGGCTT
1 TGCCACAATTACTGTTACTGGCAGCTT
517859 TGCCAC-ATATACTG-TACTGGCAGCTT
1 TGCCACAAT-TACTGTTACTGGCAGCTT
517885 TGC
1 TGC
517888 TGTGTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (27 bp):
TGCCACAATTACTGTTACTGGCAGCTT
Found at i:518954 original size:25 final size:25
Alignment explanation
Indices: 518921--519210 Score: 196
Period size: 25 Copynumber: 11.6 Consensus size: 25
518911 AAATTATTTG
518921 AAAAGCCTTTGTGGTAAACTCTCTA
1 AAAAGCCTTTGTGGTAAACTCTCTA
* * * * *
518946 AAAATCCTTTGTGGCAAAATCTTTG
1 AAAAGCCTTTGTGGTAAACTCTCTA
* * *
518971 AAAAGCCTTTGTGGCAAACTCTATG
1 AAAAGCCTTTGTGGTAAACTCTCTA
* ** *
518996 AAATGCCTTTGTGGCGAACTCTCTG
1 AAAAGCCTTTGTGGTAAACTCTCTA
* * *
519021 AAAAGCCTTTATGGTGAACTGTCTA
1 AAAAGCCTTTGTGGTAAACTCTCTA
* * * *
519046 AAAAGCCTTTGAGGCAAACCCTCTG
1 AAAAGCCTTTGTGGTAAACTCTCTA
* * *
519071 AAAAGCCTTGGTGGTGAACTCTTTA
1 AAAAGCCTTTGTGGTAAACTCTCTA
*
519096 AAAAGCCTTTGCT-GTGAAA-TCTTTGA
1 AAAAGCCTTTG-TGGT-AAACTCTCT-A
* *
519122 AAAA-CATTTGTGGTGAACTCTCTA
1 AAAAGCCTTTGTGGTAAACTCTCTA
* * *
519146 AAAAGCCGTTGTGACG-AATC-CTATA
1 AAAAGCCTTTGTG--GTAAACTCTCTA
* *
519171 GAAAGCCTTTGTGGCT-AACTCTCTCT
1 AAAAGCCTTTGTGG-TAAACTCTCT-A
*
519197 GAAAGCCTTTGTGG
1 AAAAGCCTTTGTGG
519211 AAAGATGCTA
Statistics
Matches: 208, Mismatches: 45, Indels: 23
0.75 0.16 0.08
Matches are distributed among these distances:
23 1 0.00
24 10 0.05
25 172 0.83
26 24 0.12
27 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (25 bp):
AAAAGCCTTTGTGGTAAACTCTCTA
Found at i:518992 original size:50 final size:49
Alignment explanation
Indices: 518917--519210 Score: 270
Period size: 50 Copynumber: 5.9 Consensus size: 49
518907 CACGAAATTA
* *
518917 TTTGAAAAGCCTTTGTGGTAAACTCTCTAAAAATCCTTTGTGGCAAAATC
1 TTTGAAAAGCCTTTGTGGTGAACTCTCTAAAAAGCCTTTGTGGC-AAATC
** * * * *
518967 TTTGAAAAGCCTTTGTGGCAAACTCTATGAAATGCCTTTGTGGCGAACTC
1 TTTGAAAAGCCTTTGTGGTGAACTCTCTAAAAAGCCTTTGTGGC-AAATC
* * * * *
519017 TCTGAAAAGCCTTTATGGTGAACTGTCTAAAAAGCCTTTGAGGCAAACCC
1 TTTGAAAAGCCTTTGTGGTGAACTCTCTAAAAAGCCTTTGTGGCAAA-TC
* * *
519067 TCTGAAAAGCCTTGGTGGTGAACTCTTTAAAAAGCCTTTGCTGTG-AAATC
1 TTTGAAAAGCCTTTGTGGTGAACTCTCTAAAAAGCCTTTG-TG-GCAAATC
* * * * *
519117 TTTGAAAAACATTTGTGGTGAACTCTCTAAAAAGCCGTTGTGACGAATCC
1 TTTGAAAAGCCTTTGTGGTGAACTCTCTAAAAAGCCTTTGTGGCAAAT-C
* **
519167 TAT-AGAAAGCCTTTGTGGCT-AACTCTCTCTGAAAGCCTTTGTGG
1 TTTGA-AAAGCCTTTGTGG-TGAACTCTCT-AAAAAGCCTTTGTGG
519211 AAAGATGCTA
Statistics
Matches: 197, Mismatches: 39, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
49 8 0.04
50 172 0.87
51 16 0.08
52 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (49 bp):
TTTGAAAAGCCTTTGTGGTGAACTCTCTAAAAAGCCTTTGTGGCAAATC
Found at i:519150 original size:75 final size:74
Alignment explanation
Indices: 518919--519183 Score: 241
Period size: 75 Copynumber: 3.5 Consensus size: 74
518909 CGAAATTATT
* * *
518919 TGAAAAGCCTTTGTGGTAAACTCTCTAAAAATCCTTTGTG-GCAAAATCTTTGAAAAGCCTTTGT
1 TGAAAAGCCTTTGTGGTGAACTCTCTAAAAAGCCTTTGTGTG--AAATCTTTGAAAAACCTTTGT
*
518983 GGCAAACTCTA
64 GGCAAACTCTC
* * * * * * * *
518994 TGAAATGCCTTTGTGGCGAACTCTCTGAAAAGCCTTTATGGTGAACTGTCT-AAAAAGCCTTTGA
1 TGAAAAGCCTTTGTGGTGAACTCTCTAAAAAGCCTTTGT-GTGAAATCTTTGAAAAA-CCTTTGT
*
519058 GGCAAACCCTC
64 GGCAAACTCTC
* * *
519069 TGAAAAGCCTTGGTGGTGAACTCTTTAAAAAGCCTTTGCTGTGAAATCTTTGAAAAACATTTGTG
1 TGAAAAGCCTTTGTGGTGAACTCTCTAAAAAGCCTTTG-TGTGAAATCTTTGAAAAACCTTTGTG
**
519134 GTGAACTCTC
65 GCAAACTCTC
* * **
519144 TAAAAAGCCGTTGTGACGAA-TC-CTATAGAAAGCCTTTGTG
1 TGAAAAGCCTTTGTGGTGAACTCTCTA-A-AAAGCCTTTGTG
519184 GCTAACTCTC
Statistics
Matches: 150, Mismatches: 33, Indels: 15
0.76 0.17 0.08
Matches are distributed among these distances:
73 2 0.01
74 9 0.06
75 131 0.87
76 7 0.05
77 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (74 bp):
TGAAAAGCCTTTGTGGTGAACTCTCTAAAAAGCCTTTGTGTGAAATCTTTGAAAAACCTTTGTGG
CAAACTCTC
Found at i:536246 original size:27 final size:27
Alignment explanation
Indices: 536202--536744 Score: 518
Period size: 27 Copynumber: 19.9 Consensus size: 27
536192 ACATGCAACA
536202 AAATACCCCCATAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
** * *
536229 AAATACCCTTATAAGGTAAAATGACAG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
536256 AAATA-CCCCATAGGGCAAAATGGCCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
536282 AAATACCCCCATAGGGTAGAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
536309 AAATACCCCCATAGGATAAAATGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
536336 AAATACCCTCATAGGGTAAAATGGCCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
536363 AAATACCCTCATAGGGTAAAATGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
* **
536390 AAATA-CCCCATAGGGTAGAATGACTA
1 AAATACCCCCATAGGGTAAAATGACCG
* **
536416 AAATACCCTCATAGGGTAAAATGACTA
1 AAATACCCCCATAGGGTAAAATGACCG
* *
536443 AAATACCCCTATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
536470 AAATACCCTCATAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * * * *
536497 AAATGCCCCTAT-GAGGTCAAATTATCG
1 AAATACCCCCATAG-GGTAAAATGACCG
* * * * *
536524 AAATACCCCTATGGGGTCAAATTATCG
1 AAATACCCCCATAGGGTAAAATGACCG
** * *
536551 AAATACCCTTATGGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
536578 AAATACCCCTATACCCCCATAAGGTAAAATGATCG
1 --A-A-----ATACCCCCATAGGGTAAAATGACCG
* * **
536613 AAATACCCCTATAGGGTAGAATGATTG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
536640 AAATACCCCTATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
536667 AAATACCCCTATAGGGTAGAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
536694 GAATA-CCCCATAGGGTAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGACCG
*
536720 AAATACCCGCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
536745 TGTTTTAACC
Statistics
Matches: 438, Mismatches: 65, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
26 65 0.15
27 347 0.79
28 1 0.00
29 1 0.00
30 1 0.00
32 1 0.00
33 1 0.00
35 21 0.05
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGACCG
Found at i:536399 original size:107 final size:107
Alignment explanation
Indices: 536202--536743 Score: 582
Period size: 107 Copynumber: 5.0 Consensus size: 107
536192 ACATGCAACA
* * *
536202 AAATACCCCCATAGGGTAAAATGACCGAAATACCCTTATAAGGTAAAATGA-CAGAAATACCC-C
1 AAATACCCCCATAGGGTAAAATGACTGAAATACCCTCATAGGGTAAAATGATC-GAAATACCCTC
* *
536265 ATAGGGCAAAATGGCCGAAATACCCCCATAGGGTAGAATGATCG
65 ATAGGGTAAAATGACCGAAATA-CCCCATAGGGTAGAATGATCG
* **
536309 AAATACCCCCATAGGATAAAATGACTGAAATACCCTCATAGGGTAAAATGGCCGAAATACCCTCA
1 AAATACCCCCATAGGGTAAAATGACTGAAATACCCTCATAGGGTAAAATGATCGAAATACCCTCA
* *
536374 TAGGGTAAAATGACTGAAATACCCCATAGGGTAGAATGA-CTA
66 TAGGGTAAAATGACCGAAATACCCCATAGGGTAGAATGATC-G
* *
536416 AAATACCCTCATAGGGTAAAATGACTAAAATACCC-CTATAGGGTAAAATGATCGAAATACCCTC
1 AAATACCCCCATAGGGTAAAATGACTGAAATACCCTC-ATAGGGTAAAATGATCGAAATACCCTC
* *
536480 ATAGGGTAAAATGACCGAAATGCCCC-TATGAGGTCA-AATTATCG
65 ATAGGGTAAAATGACCGAAATACCCCATA-G-GGT-AGAATGATCG
* * * * * *
536524 AAATACCCCTATGGGGTCAAATTA-TCGAAATACCCTTATGGGGTAAAATGATCGAAATACCCCT
1 AAATACCCCCATAGGGTAAAATGACT-GAAATACCCTCATAGGGTAAAATGATCGAAATA-CCC-
* * *
536588 ATACCCCCATAAGGTAAAATGATCGAAATACCCCTATAGGGTAGAATGATTG
63 -T-----CATAGGGTAAAATGACCGAAATACCCC-ATAGGGTAGAATGATCG
* * *
536640 AAATACCCCTATAGGGTAAAATGA-TCGAAATACCC-CTATAGGGTAGAATGATCGGAATACCC-
1 AAATACCCCCATAGGGTAAAATGACT-GAAATACCCTC-ATAGGGTAAAATGATCGAAATACCCT
* *
536702 CATAGGGTAAAATGACCAAAATACCCGCATAGGGTAAAATGA
64 CATAGGGTAAAATGACCGAAATACCC-CATAGGGTAGAATGA
536744 CTGTTTTAAC
Statistics
Matches: 370, Mismatches: 42, Indels: 46
0.81 0.09 0.10
Matches are distributed among these distances:
106 4 0.01
107 192 0.52
108 77 0.21
109 5 0.01
111 1 0.00
115 4 0.01
116 84 0.23
117 1 0.00
118 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (107 bp):
AAATACCCCCATAGGGTAAAATGACTGAAATACCCTCATAGGGTAAAATGATCGAAATACCCTCA
TAGGGTAAAATGACCGAAATACCCCATAGGGTAGAATGATCG
Found at i:536620 original size:143 final size:142
Alignment explanation
Indices: 536202--536727 Score: 496
Period size: 134 Copynumber: 3.8 Consensus size: 142
536192 ACATGCAACA
* * *
536202 AAATACCCCCATAGGGTAAAATGACCGAAATACCCTTATAAGGTAAAATGA-CAGAAATACCCC-
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATC-GAAATACCCCT
* * ** * * *
536265 ATAGGGCAAAATGGCCGAAATACCCCCATAGGGTAGAATGATC--GA-A-----ATACCCCCAT-
65 ATAGGGTAGAATGATCGAAATA-CCCCATAGGGTAAAATGACCAAAATACCCCTATACCCCCATA
536321 AGGATAAAATGA-CTG
129 AGG-TAAAATGATC-G
*
536336 AAATA-CCCTCATAGGGTAAAATGGCCGAAATA-CCCTCATAGGGTAAAATGA-CTGAAATACCC
1 AAATACCCCT-ATAGGGTAAAATGACCGAAATACCCCT-ATAGGGTAAAATGATC-GAAATACCC
* *
536398 C-ATAGGGTAGAATGA-CTAAAATACCCTCATAGGGTAAAATGACTAAAATACCCC--T------
63 CTATAGGGTAGAATGATC-GAAATACCC-CATAGGGTAAAATGACCAAAATACCCCTATACCCCC
*
536453 ATAGGGTAAAATGATCG
126 ATAAGGTAAAATGATCG
* * *
536470 AAATA-CCCTCATAGGGTAAAATGACCGAAATGCCCCTAT-GAGGTCAAATTATCGAAATACCCC
1 AAATACCCCT-ATAGGGTAAAATGACCGAAATACCCCTATAG-GGTAAAATGATCGAAATACCCC
* * * * * *
536533 TATGGGGTCA-AATTATCGAAATACCCTTATGGGGTAAAATGATCGAAATACCCCTATACCCCCA
64 TATAGGGT-AGAATGATCGAAATACCC-CATAGGGTAAAATGACCAAAATACCCCTATACCCCCA
536597 TAAGGTAAAATGATCG
127 TAAGGTAAAATGATCG
* **
536613 AAATACCCCTATAGGGTAGAATGATTGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCTA
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCTA
*
536678 TAGGGTAGAATGATCGGAATACCCCATAGGGTAAAATGACCAAAATACCC
66 TAGGGTAGAATGATCGAAATACCCCATAGGGTAAAATGACCAAAATACCC
536728 GCATAGGGTA
Statistics
Matches: 322, Mismatches: 40, Indels: 52
0.78 0.10 0.13
Matches are distributed among these distances:
133 11 0.03
134 141 0.44
135 49 0.15
136 3 0.01
137 2 0.01
140 1 0.00
142 23 0.07
143 87 0.27
144 5 0.02
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (142 bp):
AAATACCCCTATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCTA
TAGGGTAGAATGATCGAAATACCCCATAGGGTAAAATGACCAAAATACCCCTATACCCCCATAAG
GTAAAATGATCG
Found at i:536645 original size:170 final size:169
Alignment explanation
Indices: 536282--536743 Score: 502
Period size: 170 Copynumber: 2.8 Consensus size: 169
536272 AAAATGGCCG
* * * * *
536282 AAATACCCCCATAGGGTAGAATGATCGAAATACCCCCATAGGATAAAATGACTGAAATA-CCCTC
1 AAATACCCCTATAGGGTAAAATGATCGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCT-
* ** ** *
536346 ATAGGGTAAAATGGCCGAAATACCCTCATAGGGTAAAATGACTGAAATACCC-CATAGGGTAGAA
65 ATAGGGTAGAATGATCGAAATACCC-CATAGGGTAAAATGACCAAAATACCCGCATAGGGTAAAA
* * *
536410 TGA-C-TAA-A-----ATACCCTCATAGGGTAAAATGACTA
129 TGATCGAAATACCCCTATACCCCCATAAGGTAAAATGACTA
*
536443 AAATACCCCTATAGGGTAAAATGATCGAAATA-CCCTCATAGGGTAAAATGACCGAAATGCCCCT
1 AAATACCCCTATAGGGTAAAATGATCGAAATACCCCT-ATAGGGTAAAATGACCGAAATACCCCT
* * * * * * ** *
536507 AT-GAGGTCA-AATTATCGAAATACCCCTATGGGGTCAAATTATCGAAATACCCTTATGGGGTAA
65 ATAG-GGT-AGAATGATCGAAATACCCC-ATAGGGTAAAATGACCAAAATACCCGCATAGGGTAA
*
536570 AATGATCGAAATACCCCTATACCCCCATAAGGTAAAATGA-TCG
127 AATGATCGAAATACCCCTATACCCCCATAAGGTAAAATGACT-A
* * *
536613 AAATACCCCTATAGGGTAGAATGATTGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCTA
1 AAATACCCCTATAGGGTAAAATGATCGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCTA
*
536678 TAGGGTAGAATGATCGGAATACCCCATAGGGTAAAATGACCAAAATACCCGCATAGGGTAAAATG
66 TAGGGTAGAATGATCGAAATACCCCATAGGGTAAAATGACCAAAATACCCGCATAGGGTAAAATG
536743 A
131 A
536744 CTGTTTTAAC
Statistics
Matches: 248, Mismatches: 35, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
160 5 0.02
161 87 0.35
162 17 0.07
163 1 0.00
164 2 0.01
165 1 0.00
169 35 0.14
170 95 0.38
171 5 0.02
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (169 bp):
AAATACCCCTATAGGGTAAAATGATCGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCTA
TAGGGTAGAATGATCGAAATACCCCATAGGGTAAAATGACCAAAATACCCGCATAGGGTAAAATG
ATCGAAATACCCCTATACCCCCATAAGGTAAAATGACTA
Found at i:536671 original size:89 final size:89
Alignment explanation
Indices: 536510--536679 Score: 261
Period size: 89 Copynumber: 1.9 Consensus size: 89
536500 TGCCCCTATG
* * * * * *
536510 AGGTCAAATTATCGAAATACCCCTATGGGGTCAAATTATCGAAATACCCTTATGGGGTAAAATGA
1 AGGTAAAATGATCGAAATACCCCTATAGGGTCAAATGATCGAAATACCCCTATAGGGTAAAATGA
536575 TCGAAATACCCCTATACCCCCATA
66 TCGAAATACCCCTATACCCCCATA
*
536599 AGGTAAAATGATCGAAATACCCCTATAGGGT-AGAATGATTGAAATACCCCTATAGGGTAAAATG
1 AGGTAAAATGATCGAAATACCCCTATAGGGTCA-AATGATCGAAATACCCCTATAGGGTAAAATG
536663 ATCGAAATACCCCTATA
65 ATCGAAATACCCCTATA
536680 GGGTAGAATG
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 1 0.01
89 72 0.99
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (89 bp):
AGGTAAAATGATCGAAATACCCCTATAGGGTCAAATGATCGAAATACCCCTATAGGGTAAAATGA
TCGAAATACCCCTATACCCCCATA
Found at i:536684 original size:116 final size:116
Alignment explanation
Indices: 536472--536702 Score: 313
Period size: 116 Copynumber: 2.0 Consensus size: 116
536462 AATGATCGAA
* * * * *
536472 ATACCCTCATAGGGTAAAATGACCGAAATGCCCCTATGAGGTCAAATTATCGAAATACCCCTATG
1 ATACCCCCATAAGGTAAAATGACCGAAATACCCCTATGAGGTCAAATGATCGAAATACCCCTATA
* * * *
536537 GGGTCAAATTATCGAAATACCCTTATGGGGTAAAATGATCGAAATACCCCT
66 GGGTAAAATGATCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCT
* *
536588 ATACCCCCATAAGGTAAAATGATCGAAATACCCCTAT-AGGGT-AGAATGATTGAAATACCCCTA
1 ATACCCCCATAAGGTAAAATGACCGAAATACCCCTATGA-GGTCA-AATGATCGAAATACCCCTA
* *
536651 TAGGGTAAAATGATCGAAATACCCCTATAGGGTAGAATGATCGGAATACCCC
64 TAGGGTAAAATGATCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCC
536703 ATAGGGTAAA
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
115 2 0.02
116 98 0.98
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (116 bp):
ATACCCCCATAAGGTAAAATGACCGAAATACCCCTATGAGGTCAAATGATCGAAATACCCCTATA
GGGTAAAATGATCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCT
Found at i:542064 original size:19 final size:20
Alignment explanation
Indices: 542032--542069 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
542022 CAAGCTGACT
542032 TTAGCTCAATTTCAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
542052 TTAGCTC-ATTTCAGCTCC
1 TTAGCTCAATTTCAGCTCC
542070 AATCAGCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.34, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:542077 original size:20 final size:19
Alignment explanation
Indices: 542034--542079 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
542024 AGCTGACTTT
* *
542034 AGCTCAATTTCAGCTCCCTT
1 AGCTC-ATTTCAGCTCCATC
542054 AGCTCATTTCAGCTCCAATC
1 AGCTCATTTCAGCTCC-ATC
542074 AGCTCA
1 AGCTCA
542080 CTTGAGCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.24, C:0.35, G:0.11, T:0.30
Consensus pattern (19 bp):
AGCTCATTTCAGCTCCATC
Found at i:543550 original size:27 final size:27
Alignment explanation
Indices: 543514--543870 Score: 464
Period size: 27 Copynumber: 13.3 Consensus size: 27
543504 AGAGGTCAAT
543514 AAATGACCGAATTACCCCCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * *
543541 AAATGACCGAGTTACCCCCATAGGTTA
1 AAATGACCGAATTACCCCCACAGGGTA
**
543568 AAATGGGCGAATTACCCCCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
*
543595 AAATGACCGAATTACCCCCACAGTGTA
1 AAATGACCGAATTACCCCCACAGGGTA
543622 AAATGACCGAATTACCCCCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* *
543649 AAATGATCGAATTACCCCCACACGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* *
543676 AAATGATCGAATTACCCCCACAAGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
*
543703 AAATGAGCGAATTACCCCCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * *
543730 AAATGATCGAATTA-CCCTATAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* *
543756 AAATGACCGAATTACCCCGATAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
** * *
543783 AAATGACTAAATTACCCCTATAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* *
543810 AAATTACCGAATTACCCCCATAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * * * *
543837 AAATGACCAAAATATCCCTATAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
543864 AAATGAC
1 AAATGAC
543871 TATTATACCC
Statistics
Matches: 295, Mismatches: 34, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
26 23 0.08
27 272 0.92
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATGACCGAATTACCCCCACAGGGTA
Found at i:544279 original size:28 final size:28
Alignment explanation
Indices: 544235--544463 Score: 343
Period size: 28 Copynumber: 8.2 Consensus size: 28
544225 ACTGTATCGA
*
544235 TACTGTATAGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
544263 TACTGCATTGGGTTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
544291 TACTGTATTGAGCTAAGGCCGACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
544319 TACTGAATTGGGCTAAGGCCCACATTAT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
544347 TACTATATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
544375 TACTGTATTCGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
544403 TACTGTATTGGGCTAAGGCCCTCATTAT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
544431 TACTGTATTGGGCTAAGGCCCACACTG-
1 TACTGTATTGGGCTAAGGCCCACATTGT
544458 TACTGT
1 TACTGT
544464 TACTGAATAG
Statistics
Matches: 179, Mismatches: 22, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
27 6 0.03
28 173 0.97
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACATTGT
Found at i:546599 original size:17 final size:17
Alignment explanation
Indices: 546574--546608 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
546564 CCCACTTTCA
*
546574 TTTTTTTTCTTTTCCTC
1 TTTTCTTTCTTTTCCTC
*
546591 TTTTCTTTCTTTTTCTC
1 TTTTCTTTCTTTTCCTC
546608 T
1 T
546609 ATTGAGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCTTTCTTTTCCTC
Found at i:547754 original size:46 final size:46
Alignment explanation
Indices: 547687--547779 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
547677 GGAGAAAGTG
547687 TTTTCTAGTAGTATTACTACAATACTGGAGGTTAAACTTCAATATT
1 TTTTCTAGTAGTATTACTACAATACTGGAGGTTAAACTTCAATATT
*
547733 TTTTCTAGTAGTATTACTACAATACTGGCGGTTAAACTTCAATATT
1 TTTTCTAGTAGTATTACTACAATACTGGAGGTTAAACTTCAATATT
547779 T
1 T
547780 GTTTGGCAGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (46 bp):
TTTTCTAGTAGTATTACTACAATACTGGAGGTTAAACTTCAATATT
Found at i:547959 original size:34 final size:33
Alignment explanation
Indices: 547915--548038 Score: 117
Period size: 34 Copynumber: 3.7 Consensus size: 33
547905 TTCTGATATG
* *
547915 ATATGGCATTCTTATATGATATATGTTTACGAAA
1 ATATGACATTCTGATATGATATATGTTTACG-AA
* *
547949 ATATGACATTCTGACT-TGGTATATGTTTATTGAA
1 ATATGACATTCTGA-TATGATATATGTTTA-CGAA
* * *
547983 ATATGACATTCTGATTTGATAAATGTTT-CTGGTA
1 ATATGACATTCTGATATGATATATGTTTAC--GAA
*
548017 ATGTGACATTCTGATATGATAT
1 ATATGACATTCTGATATGATAT
548039 TTGCATATGT
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
33 1 0.01
34 71 0.96
35 2 0.03
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (33 bp):
ATATGACATTCTGATATGATATATGTTTACGAA
Found at i:548964 original size:16 final size:16
Alignment explanation
Indices: 548940--548990 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
548930 GGTTAATTGG
*
548940 AATGAAATAGGGTTGT
1 AATGAAATAGAGTTGT
* *
548956 AATGGAATAGAGCTGT
1 AATGAAATAGAGTTGT
548972 AATGAAATAGAGTTGT
1 AATGAAATAGAGTTGT
548988 AAT
1 AAT
548991 TAGTAATTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.41, C:0.02, G:0.27, T:0.29
Consensus pattern (16 bp):
AATGAAATAGAGTTGT
Found at i:563814 original size:11 final size:11
Alignment explanation
Indices: 563794--563824 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
563784 GTCTCATTAT
*
563794 GCATGTTTTGG
1 GCATGATTTGG
563805 GCATGATTTGG
1 GCATGATTTGG
563816 GCATGATTT
1 GCATGATTT
563825 AGGGTCTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.10, G:0.32, T:0.42
Consensus pattern (11 bp):
GCATGATTTGG
Found at i:566530 original size:50 final size:50
Alignment explanation
Indices: 566475--566668 Score: 176
Period size: 50 Copynumber: 3.9 Consensus size: 50
566465 TATTGAGGTT
* *
566475 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAC
** * * ** * *
566525 ATGAGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCACGGGCACCAAT
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAC
** * * *
566575 ATGAGAACTCCCATGTAAGACCTTATCTGGGATATGGAATTGGCA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCG-AC
* * ** * *
566624 AGGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA
566669 TGTTATTATC
Statistics
Matches: 112, Mismatches: 31, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
49 37 0.33
50 75 0.67
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAC
Found at i:568367 original size:25 final size:25
Alignment explanation
Indices: 568347--568434 Score: 176
Period size: 25 Copynumber: 3.5 Consensus size: 25
568337 ATAGCTCATA
568347 TGAGCATACCGATCTGCAGCTCGAG
1 TGAGCATACCGATCTGCAGCTCGAG
568372 TGAGCATACCGATCTGCAGCTCGAG
1 TGAGCATACCGATCTGCAGCTCGAG
568397 TGAGCATACCGATCTGCAGCTCGAG
1 TGAGCATACCGATCTGCAGCTCGAG
568422 TGAGCATACCGAT
1 TGAGCATACCGAT
568435 TCACAAAGTG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20
Consensus pattern (25 bp):
TGAGCATACCGATCTGCAGCTCGAG
Found at i:568455 original size:50 final size:50
Alignment explanation
Indices: 568324--568434 Score: 161
Period size: 50 Copynumber: 2.2 Consensus size: 50
568314 AGCTCGTATT
* * * *
568324 AGCATATCGATTTATAGCTCATATGAGCATACCGATCTGCAGCTCGAGTG
1 AGCATACCGATCTACAGCTCGTATGAGCATACCGATCTGCAGCTCGAGTG
*
568374 AGCATACCGATCTGCAGCTCG-AGTGAGCATACCGATCTGCAGCTCGAGTG
1 AGCATACCGATCTACAGCTCGTA-TGAGCATACCGATCTGCAGCTCGAGTG
568424 AGCATACCGAT
1 AGCATACCGAT
568435 TCACAAAGTG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 1 0.02
50 54 0.98
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.23
Consensus pattern (50 bp):
AGCATACCGATCTACAGCTCGTATGAGCATACCGATCTGCAGCTCGAGTG
Found at i:579413 original size:13 final size:13
Alignment explanation
Indices: 579395--579421 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
579385 TTACAAACAC
579395 GGTTGGTGAATAT
1 GGTTGGTGAATAT
579408 GGTTGGTGAATAT
1 GGTTGGTGAATAT
579421 G
1 G
579422 TGTTTAGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.37
Consensus pattern (13 bp):
GGTTGGTGAATAT
Found at i:585917 original size:27 final size:27
Alignment explanation
Indices: 585885--585972 Score: 124
Period size: 27 Copynumber: 3.3 Consensus size: 27
585875 ACTATACCGA
*
585885 AATACCTTCAATGGGTAAAATTACCAT
1 AATACCTTCGATGGGTAAAATTACCAT
* *
585912 AATACCCTCGATGGGTAAAATTACCAA
1 AATACCTTCGATGGGTAAAATTACCAT
*
585939 AATACCCTT-GATGGGTATAATTACCAT
1 AATA-CCTTCGATGGGTAAAATTACCAT
585966 AATACCT
1 AATACCT
585973 CCGTTAAGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
26 3 0.06
27 48 0.89
28 3 0.06
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (27 bp):
AATACCTTCGATGGGTAAAATTACCAT
Found at i:586143 original size:27 final size:27
Alignment explanation
Indices: 586105--586170 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
586095 ATAGAGGAAG
* *
586105 TACTGTTTCTGGTGGCTTTGCAACA-A
1 TACTGTTACTGGTGACTTTGCAACATA
*
586131 TTACTGTTACTGGTGACTTTGCCACATA
1 -TACTGTTACTGGTGACTTTGCAACATA
586159 TACTG-TACTGGT
1 TACTGTTACTGGT
586171 AGCTATGCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.20
27 27 0.77
28 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (27 bp):
TACTGTTACTGGTGACTTTGCAACATA
Found at i:589544 original size:25 final size:25
Alignment explanation
Indices: 589516--589609 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
589506 GTTCCAACCC
589516 ACAGCTCGTATGAGCATACCGATTT
1 ACAGCTCGTATGAGCATACCGATTT
* * *
589541 ACAGCTTGTGA-GAGCATATCGATCT
1 ACAGCTCGT-ATGAGCATACCGATTT
* *
589566 GCAGCTCG-AGTGAGCATACCGATTC
1 ACAGCTCGTA-TGAGCATACCGATTT
* *
589591 ACATCTCGTATAAGCATAC
1 ACAGCTCGTATGAGCATAC
589610 ATGTACATGA
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
23 1 0.02
25 51 0.94
26 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
ACAGCTCGTATGAGCATACCGATTT
Found at i:592371 original size:14 final size:15
Alignment explanation
Indices: 592352--592381 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
592342 AAAATTGCTT
592352 AAAAATCAAG-CAAA
1 AAAAATCAAGTCAAA
592366 AAAAATCAAGTCAAA
1 AAAAATCAAGTCAAA
592381 A
1 A
592382 GTCACTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.70, C:0.13, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAAATCAAGTCAAA
Found at i:607105 original size:39 final size:39
Alignment explanation
Indices: 607012--607144 Score: 148
Period size: 39 Copynumber: 3.4 Consensus size: 39
607002 CGTTACACCA
* * *
607012 ACATGAAGCCTACTAGGC-ATCAATCTCGATAAAG--ATCG
1 ACATGAAGCCTGCTAGGCTA-AAAGCTCGAT-AAGTCATCG
607050 ACATGAAGCC-GACTAGGCTAAAAGCTCGATAAGTCATCG
1 ACATGAAGCCTG-CTAGGCTAAAAGCTCGATAAGTCATCG
* * *
607089 AAATGAAGCCTGCTAGGCTAAAAGCTCGATATGTCACCG
1 ACATGAAGCCTGCTAGGCTAAAAGCTCGATAAGTCATCG
*
607128 ACACGAAGCCTGCTAGG
1 ACATGAAGCCTGCTAGG
607145 TGCAGAGCCG
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
37 3 0.04
38 24 0.29
39 54 0.66
40 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.19
Consensus pattern (39 bp):
ACATGAAGCCTGCTAGGCTAAAAGCTCGATAAGTCATCG
Found at i:619248 original size:50 final size:50
Alignment explanation
Indices: 619193--619291 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
619183 TATTGAGGTT
*
619193 ATGAGAGG-TCCCACGTAAGACCATGTCTACGACATGGCTTTGGCACCGAG
1 ATGAGAGGTTCCC-CGTAAGACCATGTCTACGACATGGCATTGGCACCGAG
**
619243 ATGAGAGGTTCCCCGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
1 ATGAGAGGTTCCCCGTAAGACCATGTCTACGACATGGCATTGGCACCGA
619292 TATATGAACA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 41 0.91
51 4 0.09
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTTCCCCGTAAGACCATGTCTACGACATGGCATTGGCACCGAG
Found at i:619376 original size:49 final size:49
Alignment explanation
Indices: 619257--619387 Score: 147
Period size: 49 Copynumber: 2.6 Consensus size: 49
619247 GAGGTTCCCC
* * * *
619257 GTAAGACCATGTCTGGGACATGGCATTGGCACCGATATATGAACATCCCAT
1 GTAAGACCATGTCTGGGATATGGCATTGGCA-C-ATACAGGAACATCCAAT
* *
619308 GTAAGACCATATTTGGGATATGGCATTGGCA-ATACAGGAAACATCCAAT
1 GTAAGACCATGTCTGGGATATGGCATTGGCACATACAGG-AACATCCAAT
* * *
619357 GTAAGACCATGTCTAGGATATGACTTTGGCA
1 GTAAGACCATGTCTGGGATATGGCATTGGCA
619388 TGTTATTATC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
48 5 0.07
49 35 0.51
51 28 0.41
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGATATGGCATTGGCACATACAGGAACATCCAAT
Found at i:619614 original size:20 final size:20
Alignment explanation
Indices: 619589--619627 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
619579 TGAGTTATTT
619589 AAGTAAGCGAGTAAGTAAAC
1 AAGTAAGCGAGTAAGTAAAC
*
619609 AAGTAAGTGAGTAAGTAAA
1 AAGTAAGCGAGTAAGTAAA
619628 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.26, T:0.18
Consensus pattern (20 bp):
AAGTAAGCGAGTAAGTAAAC
Found at i:619636 original size:20 final size:20
Alignment explanation
Indices: 619597--619636 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
619587 TTAAGTAAGC
*
619597 GAGTAAGTAAACAAGTAAGT
1 GAGTAAGTAAACAAGAAAGT
*
619617 GAGTAAGTAAAGAAGAAAGT
1 GAGTAAGTAAACAAGAAAGT
619637 AAAGATCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.28, T:0.17
Consensus pattern (20 bp):
GAGTAAGTAAACAAGAAAGT
Found at i:623514 original size:26 final size:26
Alignment explanation
Indices: 623450--623530 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
623440 TTTACTACAT
* * * *
623450 ATACTGTTACTGCCAGCATTGTTGCA
1 ATACTATTACTGGCAGCTTTGTTGCG
* *
623476 ATACTAATACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGTTGCG
*
623502 ATACTATTACTGGAAGCTTTGTTGCG
1 ATACTATTACTGGCAGCTTTGTTGCG
623528 ATA
1 ATA
623531 TTGGTGTGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGTTGCG
Found at i:627967 original size:188 final size:189
Alignment explanation
Indices: 627650--628020 Score: 735
Period size: 188 Copynumber: 2.0 Consensus size: 189
627640 GGTGGTTGTG
627650 ATTGGGGTGCGAAGGGACTTTCTGTCTAATGTGATCTCCGCATTAAGGGTCAAAAAACTGGTTCA
1 ATTGGGGTGCGAAGGGACTTTCTGTCTAATGTGATCTCCGCATTAAGGGTCAAAAAACTGGTTCA
627715 CAAGGATTATGAGGTGTTTAAAGCCTATATTGGTGTATATGATTTTGAGGGTCCTTTTGTTGGAG
66 CAAGGATTATGAGGTGTTTAAAGCCTATATTGGTGTATATGATTTTGAGGGTCCTTTTGTTGGAG
627780 ATATCAGAACAGTTAAGGATTTTTCTTATGTATTTCCTGATGAGCT-CCTGGGGTTCCT
131 ATATCAGAACAGTTAAGGATTTTTCTTATGTATTTCCTGATGAGCTCCCTGGGGTTCCT
627838 ATTGGGGTGCGAAGGGACTTTCTGTCTAATGTGATCTCCGCATTAAGGGTCAAAAAACTGGTTCA
1 ATTGGGGTGCGAAGGGACTTTCTGTCTAATGTGATCTCCGCATTAAGGGTCAAAAAACTGGTTCA
627903 CAAGGATTATGAGGTGTTTAAAGCCTATATTGGTGTATATGATTTTGAGGGTCCTTTTGTTGGAG
66 CAAGGATTATGAGGTGTTTAAAGCCTATATTGGTGTATATGATTTTGAGGGTCCTTTTGTTGGAG
627968 ATATCAGAACAGTTAAGGATTTTTCTTATGTATTTCCTGATGAGCTCCCTGGG
131 ATATCAGAACAGTTAAGGATTTTTCTTATGTATTTCCTGATGAGCTCCCTGGG
628021 TTGCCTCCGA
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
188 176 0.97
189 6 0.03
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (189 bp):
ATTGGGGTGCGAAGGGACTTTCTGTCTAATGTGATCTCCGCATTAAGGGTCAAAAAACTGGTTCA
CAAGGATTATGAGGTGTTTAAAGCCTATATTGGTGTATATGATTTTGAGGGTCCTTTTGTTGGAG
ATATCAGAACAGTTAAGGATTTTTCTTATGTATTTCCTGATGAGCTCCCTGGGGTTCCT
Found at i:632945 original size:27 final size:26
Alignment explanation
Indices: 632900--632971 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
632890 ATGGAGGAAG
**
632900 TATACTGTACTGGTGGCTTTGCCACA
1 TATACTGTACTGGCAGCTTTGCCACA
*
632926 TATACTGTTACTGGCAGCTTTGCTACA
1 TATACTG-TACTGGCAGCTTTGCCACA
* *
632953 -ATACTAATACTAGCAGCTT
1 TATACT-GTACTGGCAGCTT
632972 CGCTGCGATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 23 0.59
27 16 0.41
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (26 bp):
TATACTGTACTGGCAGCTTTGCCACA
Done.