Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 12 of 153
Found at i:3983809 original size:14 final size:14
Alignment explanation
Indices: 3983790--3983817 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3983780 GGAACAATCA
3983790 CCCCCTAAATCACC
1 CCCCCTAAATCACC
3983804 CCCCCTAAATCACC
1 CCCCCTAAATCACC
3983818 TACGTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.57, G:0.00, T:0.14
Consensus pattern (14 bp):
CCCCCTAAATCACC
Found at i:3992743 original size:21 final size:21
Alignment explanation
Indices: 3992715--3992763 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
3992705 AATTAAGCTT
3992715 AATA-TTA-TTATATTTTTAA
1 AATATTTATTTATATTTTTAA
* *
3992734 TAATTTTTATTTTTATTTTTAA
1 -AATATTTATTTATATTTTTAA
3992756 AATATTTA
1 AATATTTA
3992764 AAATATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 10 0.42
22 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AATATTTATTTATATTTTTAA
Found at i:3992980 original size:15 final size:15
Alignment explanation
Indices: 3992960--3993016 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
3992950 CATTCAATTT
3992960 AATATTTTAATAATA
1 AATATTTTAATAATA
*
3992975 AATATTCTCTACAATTATA
1 AATATT-T-T--AATAATA
*
3992994 AATATATTAATAATA
1 AATATTTTAATAATA
3993009 AATATTTT
1 AATATTTT
3993017 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 19 0.56
16 1 0.03
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:3997982 original size:27 final size:25
Alignment explanation
Indices: 3997922--3997982 Score: 59
Period size: 27 Copynumber: 2.3 Consensus size: 25
3997912 GAGAATGAAA
*
3997922 AAAAAAAGAAAAAAAAAGTTAAAAG
1 AAAAAAAGAAAAAAAAAGTCAAAAG
* *
3997947 AACATAAAAGAAAAAAAATTGCTCAAAAT
1 AA-A-AAAAGAAAAAAAA-AG-TCAAAAG
3997976 AAAAAAA
1 AAAAAAA
3997983 AATACGGGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 2 0.07
26 1 0.03
27 17 0.59
28 2 0.07
29 7 0.24
ACGTcount: A:0.75, C:0.05, G:0.08, T:0.11
Consensus pattern (25 bp):
AAAAAAAGAAAAAAAAAGTCAAAAG
Found at i:3998200 original size:49 final size:50
Alignment explanation
Indices: 3998143--3998256 Score: 189
Period size: 49 Copynumber: 2.3 Consensus size: 50
3998133 TAGTTTACTC
3998143 TTATTAGTATTGGTTACAACATATTTGTCATGAAA-TTTTTAGCTAATTA
1 TTATTAGTATTGGTTACAACATATTTGTCATGAAAGTTTTTAGCTAATTA
*
3998192 TTATTAGTATTGGTTACAACATATTTGTCTTGAAAGTTTTTAGCTAATTA
1 TTATTAGTATTGGTTACAACATATTTGTCATGAAAGTTTTTAGCTAATTA
*
3998242 TTA--AGTATTTGTTAC
1 TTATTAGTATTGGTTAC
3998257 TTAACTCAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
48 11 0.18
49 34 0.55
50 17 0.27
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (50 bp):
TTATTAGTATTGGTTACAACATATTTGTCATGAAAGTTTTTAGCTAATTA
Found at i:3998945 original size:21 final size:21
Alignment explanation
Indices: 3998921--3998960 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3998911 CCATATTAAA
3998921 TATATATTTGATTAAAAATTG
1 TATATATTTGATTAAAAATTG
3998942 TATATATTTGATTAAAAAT
1 TATATATTTGATTAAAAAT
3998961 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (21 bp):
TATATATTTGATTAAAAATTG
Found at i:4004248 original size:3 final size:3
Alignment explanation
Indices: 4004234--4004267 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4004224 ATTACCAATC
*
4004234 TCA TCA TTA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
4004268 TAAAACTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:4004991 original size:9 final size:10
Alignment explanation
Indices: 4004943--4005001 Score: 55
Period size: 10 Copynumber: 5.5 Consensus size: 10
4004933 AAAAAAATAC
4004943 AAAAATAATT
1 AAAAATAATT
4004953 AAAAATAATCTT
1 AAAAATAA--TT
*
4004965 GAAAAATATTT
1 -AAAAATAATT
*
4004976 ATAAAAAAATT
1 A-AAAATAATT
*
4004987 AAAAATTATT
1 AAAAATAATT
4004997 AAAAA
1 AAAAA
4005002 GTTACTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
10 21 0.52
11 10 0.25
12 2 0.05
13 7 0.17
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
AAAAATAATT
Found at i:4005060 original size:27 final size:26
Alignment explanation
Indices: 4005016--4005066 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
4005006 CTAAAAATCA
* *
4005016 TTTTTAAAAATGCTAAATTATAATTT
1 TTTTTAAAAATGATAAATGATAATTT
*
4005042 TTTTTAAAAATTATAAAATGATAAT
1 TTTTTAAAAATGAT-AAATGATAAT
4005067 CTTGAGACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTTTAAAAATGATAAATGATAATTT
Found at i:4013526 original size:25 final size:25
Alignment explanation
Indices: 4013493--4013562 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
4013483 AGATTTTTAT
* *
4013493 ATTATTTATTTATATAAATATATAA
1 ATTAATTATATATATAAATATATAA
* * *
4013518 ATTAATTATAAAGTAT-ATTATTTAA
1 ATTAATTATATA-TATAAATATATAA
4013543 ATTAATTATAT-TATAAATAT
1 ATTAATTATATATATAAATAT
4013563 TATATTATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
23 3 0.08
24 4 0.11
25 26 0.72
26 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (25 bp):
ATTAATTATATATATAAATATATAA
Found at i:4013546 original size:21 final size:21
Alignment explanation
Indices: 4013490--4013542 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
4013480 CTTAGATTTT
*
4013490 TATATTATTTATTTATATAAA
1 TATATTATTTAATTATATAAA
* * *
4013511 TATATAAATTAATTATA-AAG
1 TATATTATTTAATTATATAAA
4013531 TATATTATTTAA
1 TATATTATTTAA
4013543 ATTAATTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATATTATTTAATTATATAAA
Found at i:4013566 original size:14 final size:15
Alignment explanation
Indices: 4013518--4013572 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 15
4013508 AAATATATAA
4013518 ATTA-ATTATAAAGT
1 ATTATATTATAAAGT
*
4013532 A-TATTATT-TAAATT
1 ATTA-TATTATAAAGT
4013546 AATTATATTATAAA-T
1 -ATTATATTATAAAGT
4013561 ATTATATTATAA
1 ATTATATTATAA
4013573 GAAATAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 2 0.06
14 18 0.51
15 9 0.26
16 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATTATATTATAAAGT
Found at i:4014588 original size:3 final size:3
Alignment explanation
Indices: 4014574--4014620 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
4014564 GTGAGGTAAA
*
4014574 TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4014621 AGATGAGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:4018260 original size:8 final size:10
Alignment explanation
Indices: 4018234--4018273 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
4018224 TTTTAAAATA
4018234 AAATCATATTT
1 AAAT-ATATTT
4018245 AAATATATTT
1 AAATATATTT
4018255 AAATATATTT
1 AAATATATTT
*
4018265 ATATATATT
1 AAATATATT
4018274 ACTTACTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 24 0.86
11 4 0.14
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (10 bp):
AAATATATTT
Found at i:4019621 original size:31 final size:31
Alignment explanation
Indices: 4019547--4019628 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 31
4019537 GGAAAGAAAA
** *
4019547 AAAAACCTT--AATAACCCAATCACTTAAAT
1 AAAAACCTTCAAATAAATCAATAACTTAAAT
*
4019576 AAAAACCTTCAAATAATTCAATAACTTAAAT
1 AAAAACCTTCAAATAAATCAATAACTTAAAT
* ** *
4019607 GAAAATTTTTAAATAAATCAAT
1 AAAAACCTTCAAATAAATCAAT
4019629 GATCATTTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 9 0.21
31 34 0.79
ACGTcount: A:0.54, C:0.16, G:0.01, T:0.29
Consensus pattern (31 bp):
AAAAACCTTCAAATAAATCAATAACTTAAAT
Found at i:4022001 original size:151 final size:151
Alignment explanation
Indices: 4021727--4022027 Score: 593
Period size: 151 Copynumber: 2.0 Consensus size: 151
4021717 CTTTTCTGAT
4021727 CATTACCATCTGCAGTTTGTTTAATGTCAGCTACATAAATAGGGAAGTTCCGATACTCTTATACT
1 CATTACCATCTGCAGTTTGTTTAATGTCAGCTACATAAATAGGGAAGTTCCGATACTCTTATACT
4021792 AATATCCAAAATCCACAAAAAGAAATGAGTTTTCCTTTTTGGCATATCTCATACATTCAATGTCC
66 AATATCCAAAATCCACAAAAAGAAATGAGTTTTCCTTTTTGGCATATCTCATACATTCAATGTCC
*
4021857 GAGTTTTGGAAGAATACAAAC
131 AAGTTTTGGAAGAATACAAAC
4021878 CATTACCATCTGCAGTTTGTTTAATGTCAGCTACATAAATAGGGAAGTTCCGATACTCTTATACT
1 CATTACCATCTGCAGTTTGTTTAATGTCAGCTACATAAATAGGGAAGTTCCGATACTCTTATACT
4021943 AATATCCAAAATCCACAAAAAGAAATGAGTTTTCCTTTTTGGCATATCTCATACATTCAATGTCC
66 AATATCCAAAATCCACAAAAAGAAATGAGTTTTCCTTTTTGGCATATCTCATACATTCAATGTCC
4022008 AAGTTTTGGAAGAATACAAA
131 AAGTTTTGGAAGAATACAAA
4022028 GAACATAAAC
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 149 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (151 bp):
CATTACCATCTGCAGTTTGTTTAATGTCAGCTACATAAATAGGGAAGTTCCGATACTCTTATACT
AATATCCAAAATCCACAAAAAGAAATGAGTTTTCCTTTTTGGCATATCTCATACATTCAATGTCC
AAGTTTTGGAAGAATACAAAC
Found at i:4031134 original size:132 final size:132
Alignment explanation
Indices: 4030897--4031154 Score: 349
Period size: 132 Copynumber: 2.0 Consensus size: 132
4030887 CTTTCCCACC
* * * *
4030897 GATTCGGATTTCACCTTGCTCGAATCATAATAGTGTACACCAGGCACAGTTTTTTCAGATTGCAA
1 GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
* * * *
4030962 TGAACGAAAGGAGTTAGAACTCTTATGATCATCAATGGGATG-TTTGAAGGAAGATTTGCTTCTC
66 CGAACGAAAGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTG-AGGAAGACTTGCTTCTC
4031026 ACT
130 ACT
* * *
4031029 GATTCAGATTTTACCTTACTCGAATCATAATAGTGTGCACCAGGCACAGGTTTTTCATATTCCAA
1 GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
* * * *
4031094 CGAA-GCAATGGAATCAGAAGTTTTATGATCATCGATGGGATGCTTTGAGGAAGACTTGCTT
66 CGAACG-AAAGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGCTT
4031155 GCAGTTGTCA
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
131 1 0.01
132 104 0.95
133 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (132 bp):
GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
CGAACGAAAGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGCTTCTCA
CT
Found at i:4031303 original size:150 final size:150
Alignment explanation
Indices: 4031029--4031364 Score: 399
Period size: 150 Copynumber: 2.2 Consensus size: 150
4031019 GCTTCTCACT
* * *
4031029 GATTCAGATTTTACCTTACTCGAATCATAATAGTGTGCACCAGGCACAGGTTTTTCATATTCCAA
1 GATTCAGATTTTACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTTTTCATATTCCAA
* * *
4031094 CGAAGCAATGGAATCAGAAGTTTTATGATCATCGATGGGATGCTTTGAGGAAGACTTGCTTG-CA
66 CGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGCTTGCCA
* * *
4031158 GTTGTCAGAATCTTTCCCACC
131 -CTGCCAAAATCTTTCCCACC
* * *
4031179 GATTCGGATTTTACCTTACTAGAATCATAATAGTGTACACCAGATACA-GTTTGTTCGTATTCCA
1 GATTCAGATTTTACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTT-TTCATATTCCA
* * ** * *
4031243 ATGAAGCAGTGGAATTGGAACTCTTATGGTCATCAATGGGATG-TTTGAAGGAAGATTTGCTTGC
65 ACGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTG-AGGAAGACTTGCTTGC
**
4031307 CACTGCCAAAATCTTTCCCGTC
129 CACTGCCAAAATCTTTCCCACC
* * * * *
4031329 AATTCAGATTTCATCTTGCTTGAATCATAATAGTGT
1 GATTCAGATTTTACCTTACTAGAATCATAATAGTGT
4031365 TTTGCCATAT
Statistics
Matches: 157, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
149 8 0.05
150 147 0.94
151 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (150 bp):
GATTCAGATTTTACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTTTTCATATTCCAA
CGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGCTTGCCA
CTGCCAAAATCTTTCCCACC
Found at i:4037822 original size:9 final size:9
Alignment explanation
Indices: 4037808--4037841 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
4037798 TTCTATTCTG
4037808 TTTCTTTTC
1 TTTCTTTTC
4037817 TTTCTTTT-
1 TTTCTTTTC
*
4037825 TTTCTATTC
1 TTTCTTTTC
4037834 TTTCTTTT
1 TTTCTTTT
4037842 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:4037834 original size:17 final size:17
Alignment explanation
Indices: 4037808--4037841 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4037798 TTCTATTCTG
*
4037808 TTTCTTTTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
4037825 TTTCTATTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
4037842 GTTTTATGTA
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:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTATTCTTTCTTTT
Found at i:4037863 original size:5 final size:5
Alignment explanation
Indices: 4037850--4037922 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
4037840 TTGTTTTATG
4037850 TATATA TATAA TATAA TATAA TAT-A T-TAA TGATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
4037898 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
4037923 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:4037875 original size:19 final size:19
Alignment explanation
Indices: 4037851--4037893 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
4037841 TGTTTTATGT
4037851 ATATATATAAT-ATAATATA
1 ATATAT-TAATGATAATATA
4037870 ATATATTAATGATAATATA
1 ATATATTAATGATAATATA
4037889 ATATA
1 ATATA
4037894 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATATTAATGATAATATA
Found at i:4037903 original size:24 final size:24
Alignment explanation
Indices: 4037857--4037921 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
4037847 ATGTATATAT
* * *
4037857 ATAATATAATATAATATATTAATG
1 ATAATATAATATAATAAAATAATC
4037881 ATAATATAATATAA-AAACATAATC
1 ATAATATAATATAATAAA-ATAATC
*
4037905 ATTACTATAATATAATA
1 A-TAATATAATATAATA
4037922 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 19 0.56
25 12 0.35
26 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATC
Found at i:4041109 original size:33 final size:34
Alignment explanation
Indices: 4041052--4041116 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 34
4041042 CAAACACCAG
4041052 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTAC-GAAAAGT
4041087 AAAATATTTT-CAG-AAATCATTTTACGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACGAAAA
4041117 ACATTTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 5 0.17
33 12 0.40
34 3 0.10
35 10 0.33
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.34
Consensus pattern (34 bp):
AAAATATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:4044961 original size:18 final size:18
Alignment explanation
Indices: 4044938--4044998 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
4044928 TTAAAATAAT
4044938 TAAAAATTAAAATATTTA
1 TAAAAATTAAAATATTTA
*
4044956 TAAAAATTCCAAAT-TTTA
1 TAAAAATT-AAAATATTTA
***
4044974 TATATTTTTAAAATA-TTA
1 TA-AAAATTAAAATATTTA
4044992 TAAAAAT
1 TAAAAAT
4044999 CTTAAAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 7
0.68 0.17 0.15
Matches are distributed among these distances:
17 2 0.06
18 23 0.72
19 7 0.22
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAAATTAAAATATTTA
Found at i:4045005 original size:19 final size:19
Alignment explanation
Indices: 4044981--4045027 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
4044971 TTATATATTT
*
4044981 TTAAAATATTATAAAAATC
1 TTAAAAAATTATAAAAATC
* *
4045000 TTAAAAAATTCTAAAAATA
1 TTAAAAAATTATAAAAATC
4045019 TATAAAAAA
1 T-TAAAAAA
4045028 GTTAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAAAAAATTATAAAAATC
Found at i:4045033 original size:19 final size:19
Alignment explanation
Indices: 4044992--4045033 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
4044982 TAAAATATTA
* *
4044992 TAAAAATCTTAAAAAATTC
1 TAAAAATATTAAAAAAGTC
4045011 TAAAAATATATAAAAAAGT-
1 TAAAAATAT-TAAAAAAGTC
4045030 TAAA
1 TAAA
4045034 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (19 bp):
TAAAAATATTAAAAAAGTC
Found at i:4053763 original size:18 final size:18
Alignment explanation
Indices: 4053740--4053798 Score: 118
Period size: 18 Copynumber: 3.3 Consensus size: 18
4053730 CGAGATTGAC
4053740 AACTCATCCCTTAAAGTT
1 AACTCATCCCTTAAAGTT
4053758 AACTCATCCCTTAAAGTT
1 AACTCATCCCTTAAAGTT
4053776 AACTCATCCCTTAAAGTT
1 AACTCATCCCTTAAAGTT
4053794 AACTC
1 AACTC
4053799 GATTTCAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (18 bp):
AACTCATCCCTTAAAGTT
Found at i:4054226 original size:12 final size:12
Alignment explanation
Indices: 4054209--4054238 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4054199 AAAAAATCCA
4054209 AATTTAATTTCC
1 AATTTAATTTCC
*
4054221 AATTTAATTTCT
1 AATTTAATTTCC
4054233 AATTTA
1 AATTTA
4054239 TTTAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:4055414 original size:33 final size:33
Alignment explanation
Indices: 4055376--4055440 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
4055366 TTAAAATATA
*
4055376 TATATT-ATATATTATGTTTACTTA-AATAATAAG
1 TATATTGATATATTAT-ATTA-TTATAATAATAAG
*
4055409 TATATTGTTATATTATATTATTATAATAATAA
1 TATATTGATATATTATATTATTATAATAATAA
4055441 AACAAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 3 0.11
33 17 0.61
34 8 0.29
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (33 bp):
TATATTGATATATTATATTATTATAATAATAAG
Found at i:4062116 original size:17 final size:18
Alignment explanation
Indices: 4062091--4062126 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4062081 TCTCTCTCTC
4062091 TTTTCTAG-TTTTACTTT
1 TTTTCTAGTTTTTACTTT
*
4062108 TTTTTTAGTTTTTACTTT
1 TTTTCTAGTTTTTACTTT
4062126 T
1 T
4062127 AAAAGTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.11, C:0.08, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTCTAGTTTTTACTTT
Found at i:4062622 original size:21 final size:21
Alignment explanation
Indices: 4062596--4062637 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4062586 CATATCCTCC
4062596 TCCTGAATTGAGATGCAACCT
1 TCCTGAATTGAGATGCAACCT
4062617 TCCTGAATTGAGATGCAACCT
1 TCCTGAATTGAGATGCAACCT
4062638 AATCTGCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (21 bp):
TCCTGAATTGAGATGCAACCT
Found at i:4066248 original size:14 final size:14
Alignment explanation
Indices: 4066225--4066265 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
4066215 GGTTATAATG
*
4066225 TTTAGATATTTTAT
1 TTTAAATATTTTAT
*
4066239 TTTAATTATTTTA-
1 TTTAAATATTTTAT
4066252 TTTAAATATTTTAT
1 TTTAAATATTTTAT
4066266 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTAAATATTTTAT
Found at i:4066261 original size:13 final size:13
Alignment explanation
Indices: 4066225--4066270 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
4066215 GGTTATAATG
*
4066225 TTTAGATATTTTA
1 TTTAAATATTTTA
*
4066238 TTTTAATTATTTTA
1 -TTTAAATATTTTA
4066252 TTTAAATATTTTA
1 TTTAAATATTTTA
*
4066265 TATAAA
1 TTTAAA
4066271 AATAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTAAATATTTTA
Found at i:4073370 original size:5 final size:6
Alignment explanation
Indices: 4073352--4073377 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4073342 AAATTATTAA
4073352 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
4073378 TTATATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:4077226 original size:35 final size:35
Alignment explanation
Indices: 4077187--4077256 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
4077177 AGTGAATCAA
*
4077187 GTTGGTCTTCTTCAAGAGCTAACTCATACAAGTCT
1 GTTGGTCTTCTTCAAGAACTAACTCATACAAGTCT
4077222 GTTGGTCTTCTTCAAGAACTAACTCATACAAGTCT
1 GTTGGTCTTCTTCAAGAACTAACTCATACAAGTCT
4077257 ATTGAGATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (35 bp):
GTTGGTCTTCTTCAAGAACTAACTCATACAAGTCT
Found at i:4077866 original size:136 final size:136
Alignment explanation
Indices: 4077622--4077896 Score: 505
Period size: 136 Copynumber: 2.0 Consensus size: 136
4077612 ACTCTTTCAC
*
4077622 TCTAGGTGTTGGAGATGGACTATGCTCTGAAACTTCAGCTAAATACTTATGCTCCACAAAACTCT
1 TCTAGATGTTGGAGATGGACTATGCTCTGAAACTTCAGCTAAATACTTATGCTCCACAAAACTCT
*
4077687 TTACATCAGAATTCTTAGATTCCCCATCATCTGACGCAACTTCTTGGGAGATGCTGCGTGCTAAT
66 TTACATCAGAATTCTTAGATTCCCCATCATCTGACGCAACTTCTTGGGAGATGCTGCATGCTAAT
4077752 TTTTCT
131 TTTTCT
**
4077758 TCTAGATGTTGGAGATGGACTATGCTCTGAAACTTCAGCTAAATACTTATGCTTTACAAAACTCT
1 TCTAGATGTTGGAGATGGACTATGCTCTGAAACTTCAGCTAAATACTTATGCTCCACAAAACTCT
*
4077823 TTACATCAGAATTCTTAGATTCCCCATCGTCTGACGCAACTTCTTGGGAGATGCTGCATGCTAAT
66 TTACATCAGAATTCTTAGATTCCCCATCATCTGACGCAACTTCTTGGGAGATGCTGCATGCTAAT
4077888 TTTTCT
131 TTTTCT
4077894 TCT
1 TCT
4077897 GTCTGGTTAT
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 134 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (136 bp):
TCTAGATGTTGGAGATGGACTATGCTCTGAAACTTCAGCTAAATACTTATGCTCCACAAAACTCT
TTACATCAGAATTCTTAGATTCCCCATCATCTGACGCAACTTCTTGGGAGATGCTGCATGCTAAT
TTTTCT
Found at i:4089460 original size:25 final size:25
Alignment explanation
Indices: 4089432--4089481 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4089422 CAGGTAAGGC
4089432 TCCTTCTCCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
* * *
4089457 TCCTTTTTCTTCTTCTGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
4089482 CTTCTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.04, C:0.34, G:0.04, T:0.58
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCGTTCTTCAT
Found at i:4092410 original size:21 final size:21
Alignment explanation
Indices: 4092386--4092438 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
4092376 CGCTGTTTCT
* *
4092386 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
4092407 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
4092428 AATCTCACCGC
1 AATCTCACCGC
4092439 CACTGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:4097728 original size:96 final size:96
Alignment explanation
Indices: 4097564--4097757 Score: 280
Period size: 96 Copynumber: 2.0 Consensus size: 96
4097554 GGGATGTTGC
* * * * * *
4097564 TGCTGTGTAGGAGGCATTGGGAAGTGTTGACTTGGAGCCTCCTGAGTTTGGCCAGGCGGTGGATA
1 TGCTGAGTAGGAGGCATCGAGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGCGGAGGATA
4097629 GTAAGCATCTCGCTGAGGGACAGAAGGAACT
66 GTAAGCATCTCGCTGAGGGACAGAAGGAACT
* * * * *
4097660 TGCTGAGTAGGAGGCATCGAGAATTGCTGACTTGGAATCTCCTGAGTTTGGGCAGGGGGAGTATA
1 TGCTGAGTAGGAGGCATCGAGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGCGGAGGATA
*
4097725 GTAAGCATCTCGTTGAGGGACAGAAGGAACT
66 GTAAGCATCTCGCTGAGGGACAGAAGGAACT
4097756 TG
1 TG
4097758 GCTCTGAGGG
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 86 1.00
ACGTcount: A:0.24, C:0.15, G:0.37, T:0.24
Consensus pattern (96 bp):
TGCTGAGTAGGAGGCATCGAGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGCGGAGGATA
GTAAGCATCTCGCTGAGGGACAGAAGGAACT
Found at i:4101755 original size:17 final size:16
Alignment explanation
Indices: 4101729--4101769 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
4101719 AGAAATAAGA
4101729 TTTT-TATTTTTTACT
1 TTTTCTATTTTTTACT
*
4101744 TTTTGCTATTTTTTAGT
1 TTTT-CTATTTTTTACT
4101761 TTTTCTATT
1 TTTTCTATT
4101770 CTATCACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 5 0.22
17 14 0.61
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTTCTATTTTTTACT
Found at i:4104481 original size:24 final size:24
Alignment explanation
Indices: 4104454--4104505 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4104444 TTAGTAAGTC
*
4104454 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
4104478 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
4104502 AAAT
1 AAAT
4104506 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:4106451 original size:24 final size:24
Alignment explanation
Indices: 4106424--4106475 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4106414 TTAGTAAGTC
*
4106424 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
4106448 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
4106472 AAAT
1 AAAT
4106476 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:4106659 original size:25 final size:26
Alignment explanation
Indices: 4106629--4106682 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
4106619 CAAAAATTTT
** *
4106629 AATTTTTTAACCATTAATTGAAC-TA
1 AATTTTTTAAAAATTAACTGAACTTA
4106654 AATTTTTTAAAAATTAACTGAACTTA
1 AATTTTTTAAAAATTAACTGAACTTA
4106680 AAT
1 AAT
4106683 ATTTCGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (26 bp):
AATTTTTTAAAAATTAACTGAACTTA
Found at i:4109681 original size:58 final size:58
Alignment explanation
Indices: 4109616--4109733 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
4109606 GATCATAATA
4109616 AATTACATAAATAAATAAGCAAATGTCTGTCTCTTTCGGCGTACCTATTTTAGTTTTG
1 AATTACATAAATAAATAAGCAAATGTCTGTCTCTTTCGGCGTACCTATTTTAGTTTTG
4109674 AATTACATAAATAAATAAGCAAATGTCTGTCTCTTTCGGCGTACCTATTTTAGTTTTG
1 AATTACATAAATAAATAAGCAAATGTCTGTCTCTTTCGGCGTACCTATTTTAGTTTTG
4109732 AA
1 AA
4109734 ACAAGGGTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (58 bp):
AATTACATAAATAAATAAGCAAATGTCTGTCTCTTTCGGCGTACCTATTTTAGTTTTG
Found at i:4111225 original size:30 final size:29
Alignment explanation
Indices: 4111191--4111275 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
4111181 TTATATGAAG
4111191 TAAAAAATTAAAATAATTATCAAATATATT
1 TAAAAAATT-AAATAATTATCAAATATATT
* * **
4111221 TAAAATATTAAAT-GTTAAAAAAATATATT
1 TAAAAAATTAAATAATT-ATCAAATATATT
* *
4111250 TAAAAACTTTAATAATTTATCAAATA
1 TAAAAAATTAAATAA-TTATCAAATA
4111276 CACCTAAATG
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 14 0.33
31 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.38
Consensus pattern (29 bp):
TAAAAAATTAAATAATTATCAAATATATT
Found at i:4111297 original size:39 final size:39
Alignment explanation
Indices: 4111254--4111331 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
4111244 TATATTTAAA
4111254 AACTTTAATAATTTATCAAATACACCTAAATGTGACAGT
1 AACTTTAATAATTTATCAAATACACCTAAATGTGACAGT
4111293 AACTTTAATAATTTATCAAATACACCTAAATGTGACAGT
1 AACTTTAATAATTTATCAAATACACCTAAATGTGACAGT
4111332 CTTCACTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (39 bp):
AACTTTAATAATTTATCAAATACACCTAAATGTGACAGT
Found at i:4113356 original size:11 final size:11
Alignment explanation
Indices: 4113335--4113373 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
4113325 TATTCTGTTA
4113335 TTATTTCGTTG
1 TTATTTCGTTG
4113346 TTGATTT-GTTG
1 TT-ATTTCGTTG
4113357 TTATTTCGTTG
1 TTATTTCGTTG
*
4113368 CTATTT
1 TTATTT
4113374 TGCTGTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.10, C:0.08, G:0.18, T:0.64
Consensus pattern (11 bp):
TTATTTCGTTG
Found at i:4113375 original size:22 final size:22
Alignment explanation
Indices: 4113325--4113385 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
4113315 TTAAATCTTT
* * *
4113325 TATTCTGTTATTATTTCGTTGT
1 TATTTTGTTGTTATTTCGTTGC
4113347 TGA-TTTGTTGTTATTTCGTTGC
1 T-ATTTTGTTGTTATTTCGTTGC
* *
4113369 TATTTTGCTGTGATTTC
1 TATTTTGTTGTTATTTC
4113386 ATTACTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.11, C:0.10, G:0.18, T:0.61
Consensus pattern (22 bp):
TATTTTGTTGTTATTTCGTTGC
Found at i:4113393 original size:22 final size:22
Alignment explanation
Indices: 4113350--4113393 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4113340 TCGTTGTTGA
* * * *
4113350 TTTGTTGTTATTTCGTTGCTAT
1 TTTGCTGTGATTTCATTACTAT
4113372 TTTGCTGTGATTTCATTACTAT
1 TTTGCTGTGATTTCATTACTAT
4113394 AAAGTTACTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (22 bp):
TTTGCTGTGATTTCATTACTAT
Found at i:4114791 original size:29 final size:30
Alignment explanation
Indices: 4114728--4114791 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
4114718 TTACAATTTG
*
4114728 GTCACTAAACTATTCAAATGGTTTCATTTAA
1 GTCACTAAACTATTCAAA-GATTTCATTTAA
*
4114759 GTCACTGAACTATTCAAA-ATTTCATTTAA
1 GTCACTAAACTATTCAAAGATTTCATTTAA
4114788 GTCA
1 GTCA
4114792 TTGGGCTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 14 0.45
31 17 0.55
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (30 bp):
GTCACTAAACTATTCAAAGATTTCATTTAA
Found at i:4123280 original size:30 final size:30
Alignment explanation
Indices: 4123246--4123306 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
4123236 ACATTATAAG
4123246 AAGAACCATAAGTTTCTTCATGTGATTGTT
1 AAGAACCATAAGTTTCTTCATGTGATTGTT
4123276 AAGAACCATAAGTTTCTTCATGTGATTGTT
1 AAGAACCATAAGTTTCTTCATGTGATTGTT
4123306 A
1 A
4123307 CAAAATATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.39
Consensus pattern (30 bp):
AAGAACCATAAGTTTCTTCATGTGATTGTT
Found at i:4134999 original size:335 final size:341
Alignment explanation
Indices: 4134380--4135035 Score: 920
Period size: 335 Copynumber: 1.9 Consensus size: 341
4134370 GATTTTCTTG
** * * * *
4134380 TACTAATTCATTATTTGTTAGGTTAAGTTGAGCTCCCTTAATTAAGCAAACCAAAGCTTTTTTTT
1 TACTAATTCATTATTTGTTAGGTTAAACTGACCGCCATTAATGAAGCAAACCAAAGCTTTTTTTT
* * *
4134445 TTAAAGTTGTTAGACTAAAAATTGGGTTGAGTTAATAAAGTAGGTATTTTTTATTTTCAAGCAAT
66 TTAAAGTAGTTAGACTAAAAATTGGGTTGACTTAATAAAGCAGGTATTTTTTATTTTCAAGCAAT
* * *
4134510 TAAATTGGTAATTTTTCAAATTTTGGGTTGTTTTATTTCTTTCTTTCTTTTTTTTACTTAATTAA
131 TAAATTGGTAATTTTTCAAATTTTGGGTTGTTTTA--T-TTTCTTTCGTTTTTTTACTGAATCAA
4134575 ACACATGGATAACGTCAGAAAATGTTACAACGAAAAGTAAAACTGTAAAAGATAAAATTACACAA
193 ACACATGGATAACGTCAGAAAATGTTACAACGAAAAGTAAAACTGTAAAAGATAAAATTACACAA
* *
4134640 TGTGTAAACATTGAGAGCTCAATTTTTAGAATCAAAACTAAATTGACACAATGTATAAATGACAA
258 TATGTAAACATTGAGAGCTCAATTTTTAGAATCAAAACTAAATTGACACAATGTACAAATGACAA
4134705 ATTTAATAGCTCTGAGTGA
323 ATTTAATAGCTCTGAGTGA
* * *
4134724 TACTAATTCATTGTTTGTTAGGTTAAACTGACCGCCATTGAA-GAAGTAAATCAAAGCTTCTTCT
1 TACTAATTCATTATTTGTTAGGTTAAACTGACCGCCATT-AATGAAGCAAACCAAAGCTT-TT-T
* * *
4134788 TTTTT-AAGTAGTTAGACTTACAATTGGGTTGACTTAATGAAGCA-G-A-TTTTT-TTTTCAAGC
63 TTTTTAAAGTAGTTAGACTAAAAATTGGGTTGACTTAATAAAGCAGGTATTTTTTATTTTCAAGC
*
4134848 AATTAAATT-GTCTATTTTTCAAATTTTGGGTTGTTTTA-TTTC-TT-GTTTTTTTACTGAATCA
128 AATTAAATTGGT-AATTTTTCAAATTTTGGGTTGTTTTATTTTCTTTCGTTTTTTTACTGAATCA
* *
4134909 AACACATGGATAACGTCAG-AAATGGTTACAACGAAAAGTAAAACTGTAAAAGATCAAATTGCAC
192 AACACATGGATAACGTCAGAAAAT-GTTACAACGAAAAGTAAAACTGTAAAAGATAAAATTACAC
* * * *
4134973 AATATGTAAACGTTGAGGGTTCAATTTTTAGAATCAAAACTAAATTGGCACAATGTACAAATG
256 AATATGTAAACATTGAGAGCTCAATTTTTAGAATCAAAACTAAATTGACACAATGTACAAATG
4135036 TCAAGGGTTA
Statistics
Matches: 280, Mismatches: 27, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
334 4 0.01
335 128 0.46
336 2 0.01
337 4 0.01
340 2 0.01
341 43 0.15
342 5 0.02
343 1 0.00
344 48 0.17
345 37 0.13
346 6 0.02
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (341 bp):
TACTAATTCATTATTTGTTAGGTTAAACTGACCGCCATTAATGAAGCAAACCAAAGCTTTTTTTT
TTAAAGTAGTTAGACTAAAAATTGGGTTGACTTAATAAAGCAGGTATTTTTTATTTTCAAGCAAT
TAAATTGGTAATTTTTCAAATTTTGGGTTGTTTTATTTTCTTTCGTTTTTTTACTGAATCAAACA
CATGGATAACGTCAGAAAATGTTACAACGAAAAGTAAAACTGTAAAAGATAAAATTACACAATAT
GTAAACATTGAGAGCTCAATTTTTAGAATCAAAACTAAATTGACACAATGTACAAATGACAAATT
TAATAGCTCTGAGTGA
Found at i:4140333 original size:13 final size:14
Alignment explanation
Indices: 4140315--4140347 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4140305 AAAATTTATA
4140315 ATAAATAACA-TTT
1 ATAAATAACATTTT
*
4140328 ATAAATAATATTTT
1 ATAAATAACATTTT
4140342 ATAAAT
1 ATAAAT
4140348 TATCCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAAATAACATTTT
Found at i:4140334 original size:17 final size:17
Alignment explanation
Indices: 4140298--4140338 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
4140288 TAAGTAAAAC
4140298 ATAATATAAAATTTATA
1 ATAATATAAAATTTATA
*
4140315 ATAA-ATAACATTTATAA
1 ATAATATAAAATTTAT-A
4140332 ATAATAT
1 ATAATAT
4140339 TTTATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 10 0.48
17 9 0.43
18 2 0.10
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATATAAAATTTATA
Found at i:4143108 original size:20 final size:20
Alignment explanation
Indices: 4143085--4143194 Score: 80
Period size: 20 Copynumber: 5.5 Consensus size: 20
4143075 TGATATATCG
4143085 AAATTTCTAA-ACTTATACCA
1 AAATTTCTAAGA-TTATACCA
* ** **
4143105 AAATTTTTAAGGCTATATAA
1 AAATTTCTAAGATTATACCA
* * *
4143125 AAAATTCTAAGATTTTATCA
1 AAATTTCTAAGATTATACCA
4143145 AAATTTCTAATGATT-TACCA
1 AAATTTCTAA-GATTATACCA
* * *
4143165 AAATTTCTAAAAGTATACCT
1 AAATTTCTAAGATTATACCA
*
4143185 ATATTTCTAA
1 AAATTTCTAA
4143195 AGTTTTCCTT
Statistics
Matches: 70, Mismatches: 17, Indels: 6
0.75 0.18 0.06
Matches are distributed among these distances:
19 2 0.03
20 64 0.91
21 4 0.06
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.39
Consensus pattern (20 bp):
AAATTTCTAAGATTATACCA
Found at i:4143261 original size:20 final size:19
Alignment explanation
Indices: 4143236--4143316 Score: 74
Period size: 20 Copynumber: 4.1 Consensus size: 19
4143226 TCAATATTTT
* *
4143236 ATTATACTAAAATTCTTAAG
1 ATTATACAAAAATT-ATAAG
4143256 ATTATACCAAAAATTATAAG
1 ATTATA-CAAAAATTATAAG
*
4143276 GTTATACAAAAATTTATAATG
1 ATTATACAAAAA-TTATAA-G
*
4143297 ATTA-AGCAAAATTTATAAG
1 ATTATA-CAAAAATTATAAG
4143316 A
1 A
4143317 ATTTATTAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
19 8 0.15
20 28 0.54
21 16 0.31
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (19 bp):
ATTATACAAAAATTATAAG
Found at i:4143307 original size:40 final size:40
Alignment explanation
Indices: 4143237--4143315 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
4143227 CAATATTTTA
*
4143237 TTATACTAAAATTCTTAAGATTATACCAAAAATTATAAGG
1 TTATACAAAAATTCTTAAGATTATACCAAAAATTATAAGG
* *
4143277 TTATACAAAAATT-TATAATGATTA-AGCAAAATTTATAAG
1 TTATACAAAAATTCT-TAA-GATTATACCAAAAATTATAAG
4143316 AATTTATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 1 0.03
40 28 0.82
41 5 0.15
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (40 bp):
TTATACAAAAATTCTTAAGATTATACCAAAAATTATAAGG
Found at i:4143689 original size:17 final size:17
Alignment explanation
Indices: 4143659--4143692 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4143649 ATATTGATTG
**
4143659 ATATATTTTTTATAAAT
1 ATATATTTAATATAAAT
4143676 ATATATTTAATATAAAT
1 ATATATTTAATATAAAT
4143693 TATTTTTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATTTAATATAAAT
Found at i:4151744 original size:20 final size:23
Alignment explanation
Indices: 4151699--4151745 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 23
4151689 ATCTAAAAGG
4151699 TTATCATTTTCAAAATATTAATT
1 TTATCATTTTCAAAATATTAATT
*
4151722 TTATCA-TTT-AAAATA-TGATT
1 TTATCATTTTCAAAATATTAATT
4151742 TTAT
1 TTAT
4151746 TTGTTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 6 0.26
22 3 0.13
23 6 0.26
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATCATTTTCAAAATATTAATT
Found at i:4169851 original size:126 final size:126
Alignment explanation
Indices: 4169709--4169997 Score: 488
Period size: 126 Copynumber: 2.3 Consensus size: 126
4169699 GTGTTAATTT
**
4169709 AAAAAAGCTCCCACGTGGACGCTTTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGAC
1 AAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGAC
* *
4169774 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTA
66 GTTTCTAAGAAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTA
* * * *
4169835 AAAAAAGCTCCCACGTGGTCGCGCTTTTGCTACAATAGCTCCTGAAAAAATAATTTTGAGTAGAC
1 AAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGAC
*
4169900 GTTTCTAAGAAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
66 GTTTCTAAGAAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTA
*
4169961 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTA
1 AAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTA
4169998 ACTTCTGTTT
Statistics
Matches: 151, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 151 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (126 bp):
AAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGAC
GTTTCTAAGAAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTA
Found at i:4171535 original size:840 final size:839
Alignment explanation
Indices: 4169917--4171597 Score: 3020
Period size: 840 Copynumber: 2.0 Consensus size: 839
4169907 AGAAAATAGT
4169917 GTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGACG
1 GTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGACG
* * *
4169982 CGCTTTTGCTACAGTAACTTCTGTTTTGCTTGAGGCTATAAATGAAGCAAAATTTTTTCTCATAT
66 CGCTTTTGCTACAGTAACTCCTGTTTGGCTTGAGGCTATAAATGAAGCAAAATTTTTTCTCAGAT
*
4170047 TGCATAAGTTACAGCAAAAAAATTTAGAGAGTCTAAGAATGATAGAAATTGAAGATGAGTGAACG
131 TGCATAAGTTACAGCAAAAAAATTTAGAGAGTCTAAGAAGGATAGAAATTGAAGATGAGTGAACG
* *
4170112 TATTAGTGCTGTTATTTACTATGATGGTAAGGTTCGTCACACCGAGAACGGTGTTATTTTTTTAT
196 TATTAGTGCTATTATTTACTATGATGGTAAGATTCGTCACACCGAGAACGGTGTTATTTTTTTAT
*
4170177 CGAATAATACAGTGCGACTGGTTTTTAACCAGAATATAGATTTGACAGAACTTCGTAAAAGAATT
261 CGAAGAATACAGTGCGACTGGTTTTTAACCAGAATATAGATTTGACAGAACTTCGTAAAAGAATT
4170242 AGCGTAAAATATTCGGAACAACGCCAATGAAAGTTCTGTCTATTACGTATCGATTTTGTTATTCT
326 AGCGTAAAATATTCGGAACAACGCCAATGAAAGTTCTGTCTATTACGTATCGATTTTGTTATTCT
* * *
4170307 GTTGATCCTGTGACATATAACTCGTTCGACGTAAAAGGTGTTCGTAGCTTGGAGGTAATGGTGCA
391 GTTGATCCGGTGACATATAACTCGTTCGACGTAAAAAGTGTTCGTAGCTTGGAGGCAATGGTGCA
* * * ** * *
4170372 GACTCGTCTCATTAGTGGAGCACCTTATATGGAGTTATATGTATAATTTACATTGCCAAATGATG
456 GACTCGTCTCACTAGTGGAACACATTATATACAGTTATATGTACAATTTACATCGCCAAATGATG
*
4170437 CACTTGCAACTGTTGTTCGAGAGGTATACATGACCCCTGCTTAACACTCGGTTAGTGGGTTACAA
521 CACTTGCAACTGTTGTTCGAGAGGTATACATGACCCCTGCTCAACACTCGGTTAGTGGGTTACAA
*
4170502 AATACGGAACAACCCATGTTTAGTAGCGGTATGGAATACACATCCCCTGCACAACACTCTGTCAG
586 AATACGGAACAACCCATGTTTAGTAGCGGTATGGAATACACATCCCCTGCACAACACTCTATCAG
*
4170567 TGGATGGGGCATGCACCTCGGTGGGTCGATGTTTGATGCTGGAAATACGTATTGGAGAACGGCAT
651 TGGATGGGGCATGCACCTCAGTGGGTCGATGTTTGATGCTGGAAATACGTATTGGAGAACGGCAT
*
4170632 CAACTTCTAGTGGTTGGCAATCTACATCCAATTGGGGACGTTATGAAATGCCTAGAAGAAGGGAT
716 CAACTTCTAGTGGTTGGCAATCTACATCCAATTGGGGACGTTATGAAACGCCTAGAAGAAGGGAT
* * * *
4170697 GATGTACTCTTTACAACGTCCACCGGTGAGGGGACCTCGTACGTTGCAGATGATGGTGG
781 GATGTACTCTCTACAACGTCCACCAGTAAGGGGACCTCATACGTTGCAGATGATGGTGG
4170756 GTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGACG
1 GTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGACG
* *
4170821 CGCTTTTGCTACAGTAGCTCCTGTTTGGCTTGAGGCTATAAATGAAGCAAATTTTTTTCTCAGAT
66 CGCTTTTGCTACAGTAACTCCTGTTTGGCTTGAGGCTATAAATGAAGCAAAATTTTTTCTCAGAT
4170886 TGCATAAGTTACAGCAAAAAAAATTTAGAGAGTCTAAGAAGGATAGAAATTGAAGATGAGTGAAC
131 TGCATAAGTTACAGC-AAAAAAATTTAGAGAGTCTAAGAAGGATAGAAATTGAAGATGAGTGAAC
* * *
4170951 GTATTAGTGTTATTATTTACTATGATGGTGAGATTCGTCACATCGAGAACGGTGTTATTTTTTTA
195 GTATTAGTGCTATTATTTACTATGATGGTAAGATTCGTCACACCGAGAACGGTGTTATTTTTTTA
*
4171016 TCGAAGAATACAGTGCGACTGGTTTTTAACCAGAATATAGATTTGACAGAACTTCGTAAATGAAT
260 TCGAAGAATACAGTGCGACTGGTTTTTAACCAGAATATAGATTTGACAGAACTTCGTAAAAGAAT
**
4171081 TAGCGTAAAATATTCGGAATGACGCCAATGAAAGTTCTGTCTATTACGTATCGATTTTGTTATTC
325 TAGCGTAAAATATTCGGAACAACGCCAATGAAAGTTCTGTCTATTACGTATCGATTTTGTTATTC
4171146 TGTTGATCCGGTGACATATAACTCGTTCGACGTAAAAAGTGTTCGTAGCTTGGAGGCAATGGTGC
390 TGTTGATCCGGTGACATATAACTCGTTCGACGTAAAAAGTGTTCGTAGCTTGGAGGCAATGGTGC
*
4171211 TGACTCGTCTCACTAGTGGAACACATTATATACAGTTATATGTACAATTTACATCGCCAAATGAT
455 AGACTCGTCTCACTAGTGGAACACATTATATACAGTTATATGTACAATTTACATCGCCAAATGAT
4171276 GCACTTGCAACTGTTGTTCGAGAGGTATACATGACCCCTGCTCAACACTCGGTTAGTGGGTTACA
520 GCACTTGCAACTGTTGTTCGAGAGGTATACATGACCCCTGCTCAACACTCGGTTAGTGGGTTACA
*
4171341 AAATACGGAACAGCCCATGTTTAGTAGCGGTATGGAATACACATCCCCTGCACAACACTCTATCA
585 AAATACGGAACAACCCATGTTTAGTAGCGGTATGGAATACACATCCCCTGCACAACACTCTATCA
*
4171406 GTGGATGGGGCATGCACCTCAGTGGGTCGATGTTTGATGCTGGAAATACGTATTGGGGAACGGCA
650 GTGGATGGGGCATGCACCTCAGTGGGTCGATGTTTGATGCTGGAAATACGTATTGGAGAACGGCA
4171471 TCAACTTCTAGTGGTTGGCAATCTACATCCAATTGGGGACGTTATGAAACGCCTAGAAGAAGGGA
715 TCAACTTCTAGTGGTTGGCAATCTACATCCAATTGGGGACGTTATGAAACGCCTAGAAGAAGGGA
*
4171536 TGATGTACTCTCTACGACGTCCACCAGTAAGGGGACCTCATACGTTGCAGATGATGGTGG
780 TGATGTACTCTCTACAACGTCCACCAGTAAGGGGACCTCATACGTTGCAGATGATGGTGG
4171596 GT
1 GT
4171598 TAGAAGATGA
Statistics
Matches: 804, Mismatches: 37, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
839 140 0.17
840 664 0.83
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (839 bp):
GTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGACG
CGCTTTTGCTACAGTAACTCCTGTTTGGCTTGAGGCTATAAATGAAGCAAAATTTTTTCTCAGAT
TGCATAAGTTACAGCAAAAAAATTTAGAGAGTCTAAGAAGGATAGAAATTGAAGATGAGTGAACG
TATTAGTGCTATTATTTACTATGATGGTAAGATTCGTCACACCGAGAACGGTGTTATTTTTTTAT
CGAAGAATACAGTGCGACTGGTTTTTAACCAGAATATAGATTTGACAGAACTTCGTAAAAGAATT
AGCGTAAAATATTCGGAACAACGCCAATGAAAGTTCTGTCTATTACGTATCGATTTTGTTATTCT
GTTGATCCGGTGACATATAACTCGTTCGACGTAAAAAGTGTTCGTAGCTTGGAGGCAATGGTGCA
GACTCGTCTCACTAGTGGAACACATTATATACAGTTATATGTACAATTTACATCGCCAAATGATG
CACTTGCAACTGTTGTTCGAGAGGTATACATGACCCCTGCTCAACACTCGGTTAGTGGGTTACAA
AATACGGAACAACCCATGTTTAGTAGCGGTATGGAATACACATCCCCTGCACAACACTCTATCAG
TGGATGGGGCATGCACCTCAGTGGGTCGATGTTTGATGCTGGAAATACGTATTGGAGAACGGCAT
CAACTTCTAGTGGTTGGCAATCTACATCCAATTGGGGACGTTATGAAACGCCTAGAAGAAGGGAT
GATGTACTCTCTACAACGTCCACCAGTAAGGGGACCTCATACGTTGCAGATGATGGTGG
Found at i:4172298 original size:29 final size:29
Alignment explanation
Indices: 4172243--4172298 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
4172233 CAAAAAAAAT
*
4172243 AAAATTAAAGCTTTTTTTAAAATAATTAA
1 AAAATTAAAGCTTTTTTTAAAAGAATTAA
4172272 AAAATTAAAGC-TTTTTTAAGAAGAATT
1 AAAATTAAAGCTTTTTTTAA-AAGAATT
4172299 TGAGAGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (29 bp):
AAAATTAAAGCTTTTTTTAAAAGAATTAA
Found at i:4172317 original size:11 final size:11
Alignment explanation
Indices: 4172294--4172334 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
4172284 TTTTTAAGAA
*
4172294 GAATTTGAGAG
1 GAATTTGAAAG
*
4172305 GAAATTGAAAG
1 GAATTTGAAAG
*
4172316 GATTTTGAAAG
1 GAATTTGAAAG
4172327 GAATTTGA
1 GAATTTGA
4172335 GAGAATATTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (11 bp):
GAATTTGAAAG
Found at i:4172323 original size:22 final size:22
Alignment explanation
Indices: 4172292--4172356 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
4172282 CTTTTTTAAG
4172292 AAGAA-TTTGAGAGGAAATTGA
1 AAGAATTTTGAGAGGAAATTGA
* * *
4172313 AAGGATTTTGAAAGGAATTTGA
1 AAGAATTTTGAGAGGAAATTGA
* *
4172335 GAGAATATTG-GAGAGAAATTGA
1 AAGAATTTTGAGAG-GAAATTGA
4172357 GAAAAAGGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
21 6 0.18
22 28 0.82
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (22 bp):
AAGAATTTTGAGAGGAAATTGA
Found at i:4174333 original size:20 final size:19
Alignment explanation
Indices: 4174279--4174334 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
4174269 AAATTTATAT
4174279 ATAATTAAT-TATTATTTA
1 ATAATTAATATATTATTTA
4174297 ACTAAATCTAA-AT-TTATTTA
1 A-T-AAT-TAATATATTATTTA
4174317 ATAATATAATATATTATT
1 ATAAT-TAATATATTATT
4174335 ATTTACGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
18 7 0.23
19 4 0.13
20 16 0.52
21 4 0.13
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAATTAATATATTATTTA
Found at i:4178555 original size:18 final size:17
Alignment explanation
Indices: 4178522--4178560 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
4178512 TTTTATAAAT
4178522 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
4178540 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
4178557 TGTG
1 TGTG
4178561 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:4178861 original size:23 final size:23
Alignment explanation
Indices: 4178786--4178861 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
4178776 AGTGTTATTG
*
4178786 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
4178809 TTTAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4178832 AGT-AGTGGTAGCTTCGGCTACAT
1 A-TCAGTGGTAGCTTCGGCTACAT
4178855 ATCAGTG
1 ATCAGTG
4178862 TGACACTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.02
23 43 0.96
24 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:4181730 original size:11 final size:11
Alignment explanation
Indices: 4181716--4181782 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
4181706 ATATTCAAAC
4181716 AATAATAACAA
1 AATAATAACAA
* *
4181727 AATAGTAGCAA
1 AATAATAACAA
*
4181738 AATATTGAA-AA
1 AATAAT-AACAA
*
4181749 AATAATAAGAA
1 AATAATAACAA
*
4181760 AATAATAGCAA
1 AATAATAACAA
*
4181771 AACAATAA-AA
1 AATAATAACAA
4181781 AA
1 AA
4181783 AACAAGAAGA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
10 6 0.13
11 38 0.84
12 1 0.02
ACGTcount: A:0.69, C:0.06, G:0.07, T:0.18
Consensus pattern (11 bp):
AATAATAACAA
Found at i:4181742 original size:33 final size:33
Alignment explanation
Indices: 4181705--4181772 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
4181695 AGAGTTATAC
* *
4181705 AATATTCAAACAATAATAACAAAATAGTAGCAA
1 AATATTCAAAAAATAATAACAAAATAATAGCAA
* *
4181738 AATATTGAAAAAATAATAAGAAAATAATAGCAA
1 AATATTCAAAAAATAATAACAAAATAATAGCAA
4181771 AA
1 AA
4181773 CAATAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.21
Consensus pattern (33 bp):
AATATTCAAAAAATAATAACAAAATAATAGCAA
Found at i:4181782 original size:33 final size:33
Alignment explanation
Indices: 4181716--4181783 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
4181706 ATATTCAAAC
* * * *
4181716 AATAATAACAAAATAGTAGCAAAATATTGAAAA
1 AATAATAACAAAATAATAGCAAAACAATAAAAA
*
4181749 AATAATAAGAAAATAATAGCAAAACAATAAAAA
1 AATAATAACAAAATAATAGCAAAACAATAAAAA
4181782 AA
1 AA
4181784 ACAAGAAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.69, C:0.06, G:0.07, T:0.18
Consensus pattern (33 bp):
AATAATAACAAAATAATAGCAAAACAATAAAAA
Found at i:4188188 original size:32 final size:32
Alignment explanation
Indices: 4188152--4188220 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
4188142 CATGCACACA
4188152 AACATTCATAGGTGAATAAATGACATCCTACT
1 AACATTCATAGGTGAATAAATGACATCCTACT
4188184 AACATTCATAGGTGAATAAATGACATCCTACT
1 AACATTCATAGGTGAATAAATGACATCCTACT
4188216 AACAT
1 AACAT
4188221 ATGGGGCGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (32 bp):
AACATTCATAGGTGAATAAATGACATCCTACT
Found at i:4193068 original size:127 final size:125
Alignment explanation
Indices: 4192784--4193352 Score: 847
Period size: 126 Copynumber: 4.5 Consensus size: 125
4192774 GATAAAATCA
* * * * * * * *
4192784 AAGCAGGATGCT-TTATCAGAAGGATTTCTGAAGTCGCACCCACGTGTACGCGCTTTTGCTATAG
1 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * * *
4192848 TGGGTCCTGTAAAAATAATTTCGAGTTCACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
**
4192909 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCAATTTTGCTACAG
1 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
4192973 TAGGTCCTGGAATAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAATGCTTC
65 TAGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTT-AAAAAACGCTTC
*
4193036 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAAT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * *
4193101 AGGTCCTGAAAGAAATAATTTCGAGTTGATGTTTCGGAGCAAATAGTTTAAAAAACGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
*
4193162 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGTTTTTGCTACAGT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * *
4193227 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTAT-AAAAATGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
* *
4193286 TAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
4193351 AG
66 AG
4193353 CATGTTTGGG
Statistics
Matches: 407, Mismatches: 34, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
124 74 0.18
125 97 0.24
126 119 0.29
127 115 0.28
128 2 0.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
Found at i:4193197 original size:253 final size:249
Alignment explanation
Indices: 4192784--4193348 Score: 882
Period size: 253 Copynumber: 2.3 Consensus size: 249
4192774 GATAAAATCA
* * * * * * * *
4192784 AAGCAGGATGCT-TTATCAGAAGGATTTCTGAAGTCGCACCCACGTGTACGCGCTTTTGCTATAG
1 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAA
* * *
4192848 TGGGTCCTGTAAAAATAATTTCGAGTTCACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
65 TAGGTCCTGAAAAAATAATTTCGAGTTCACGTTTCGGAGCAAATAGTATAAAAAACGCTTCAAGC
4192913 AGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCAATTTTGCTACAGTAGGT
130 AGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCAATTTTGCTACAGTAGGT
*
4192978 CCTGGAATAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAATGCTTC
195 CCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGAAAATAG--TAAAAAAATGCTTC
*
4193036 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAAT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAAT
* * *
4193101 AGGTCCTGAAAGAAATAATTTCGAGTTGATGTTTCGGAGCAAATAGTTTAAAAAACGCTTCAAGC
66 AGGTCCTGAAA-AAATAATTTCGAGTTCACGTTTCGGAGCAAATAGTATAAAAAACGCTTCAAGC
**
4193166 AGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGTTTTTGCTACAGTAGG
130 AGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCAATTTTGCTACAGTAGG
*
4193230 TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAATGCTTC
194 TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTAAAAAAATGCTTC
*
4193286 TAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACA
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACA
4193349 GTAGCATGTT
Statistics
Matches: 289, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
250 74 0.26
252 95 0.33
253 118 0.41
254 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (249 bp):
AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAAT
AGGTCCTGAAAAAATAATTTCGAGTTCACGTTTCGGAGCAAATAGTATAAAAAACGCTTCAAGCA
GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCAATTTTGCTACAGTAGGTC
CTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTAAAAAAATGCTTC
Found at i:4196075 original size:13 final size:13
Alignment explanation
Indices: 4196027--4196075 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
4196017 AATATAATAA
4196027 ATATTTATTTTTT
1 ATATTTATTTTTT
* *
4196040 ATTTTTTATTTTTA
1 A-TATTTATTTTTT
* *
4196054 AAATATATTTTTT
1 ATATTTATTTTTT
4196067 ATATTTATT
1 ATATTTATT
4196076 AAAAATCGGC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATATTTATTTTTT
Found at i:4196910 original size:21 final size:21
Alignment explanation
Indices: 4196880--4197006 Score: 132
Period size: 21 Copynumber: 6.0 Consensus size: 21
4196870 TCAAATTATA
4196880 TTTAAGTTAAGGGTTAAGGTT
1 TTTAAGTTAAGGGTTAAGGTT
* * *
4196901 TTTAACTTAAGTGTTAGGGTT
1 TTTAAGTTAAGGGTTAAGGTT
* * *
4196922 TTTTATTTAAGGGTTACGGTT
1 TTTAAGTTAAGGGTTAAGGTT
*
4196943 TTAAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGG-TTAAGGTT
4196965 TTTAA-TTCAAGGGTTACA-GTT
1 TTTAAGTT-AAGGGTTA-AGGTT
* *
4196986 TTTAAGTTGAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAAGGTT
4197007 AGGGTTTTTA
Statistics
Matches: 87, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
21 68 0.78
22 19 0.22
ACGTcount: A:0.25, C:0.03, G:0.27, T:0.45
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAAGGTT
Found at i:4196953 original size:42 final size:42
Alignment explanation
Indices: 4196880--4197006 Score: 155
Period size: 43 Copynumber: 3.0 Consensus size: 42
4196870 TCAAATTATA
* * * *
4196880 TTTAAGTTAAGGGTTAAGGTTTTTAACTTAAGTGTTAGGGTT
1 TTTAATTTAAGGGTTACGGTTTTTAAGTTAAGGGTTAGGGTT
* * *
4196922 TTTTATTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAAGGTT
1 TTTAATTTAAGGGTTACGGTTTTTAAGTTAAGGG-TTAGGGTT
* * *
4196965 TTTAATTCAAGGGTTACAGTTTTTAAGTTGAGGGTTAGGGTT
1 TTTAATTTAAGGGTTACGGTTTTTAAGTTAAGGGTTAGGGTT
4197007 AGGGTTTTTA
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 35 0.49
43 36 0.51
ACGTcount: A:0.25, C:0.03, G:0.27, T:0.45
Consensus pattern (42 bp):
TTTAATTTAAGGGTTACGGTTTTTAAGTTAAGGGTTAGGGTT
Found at i:4196987 original size:64 final size:63
Alignment explanation
Indices: 4196883--4197006 Score: 160
Period size: 64 Copynumber: 2.0 Consensus size: 63
4196873 AATTATATTT
* ** * *
4196883 AAGTTAAGGGTTAAGGTTTTTAACTTAAGTGTTAGGGTTTTTTATTTAAGGGTTACGGTTTTA
1 AAGTTAAGGGTTAAGGTTTTTAACTTAAGGGTTACAGTTTTTAAGTTAAGGGTTACGGTTTTA
* *
4196946 AAGTTAAGGGTTTAAGGTTTTTAA-TTCAAGGGTTACAGTTTTTAAGTTGAGGGTTAGGGTT
1 AAGTTAAGGG-TTAAGGTTTTTAACTT-AAGGGTTACAGTTTTTAAGTTAAGGGTTACGGTT
4197007 AGGGTTTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
63 12 0.23
64 40 0.77
ACGTcount: A:0.26, C:0.03, G:0.27, T:0.44
Consensus pattern (63 bp):
AAGTTAAGGGTTAAGGTTTTTAACTTAAGGGTTACAGTTTTTAAGTTAAGGGTTACGGTTTTA
Found at i:4197006 original size:27 final size:27
Alignment explanation
Indices: 4196974--4197027 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4196964 TTTTAATTCA
*
4196974 AGGGTTACAGTTTTTAAGTTGAGGGTT
1 AGGGTTACAGTTTTTAAGTTAAGGGTT
** *
4197001 AGGGTTAGGGTTTTTAGGTTAAGGGTT
1 AGGGTTACAGTTTTTAAGTTAAGGGTT
4197028 TAAGGTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (27 bp):
AGGGTTACAGTTTTTAAGTTAAGGGTT
Found at i:4198492 original size:20 final size:20
Alignment explanation
Indices: 4198455--4198492 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4198445 TTTATTTTTA
*
4198455 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
4198475 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
4198493 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:4199483 original size:51 final size:51
Alignment explanation
Indices: 4199428--4199527 Score: 112
Period size: 51 Copynumber: 2.0 Consensus size: 51
4199418 AATGATTTAA
* *
4199428 AAATAGGGATTTAAGAGAAATTT-AATAGGAACTTGAGAATAAATTGAGATT
1 AAATAGAGATTTAAGAGAAATTTGAA-AGGAACTTGAGAACAAATTGAGATT
* ** * * *
4199479 AAATATAGATTTGGGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGAGATTTAAGAGAAATTTGAAAGGAACTTGAGAACAAATTGAGA
4199528 GGAAATTTGG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.98
52 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.28
Consensus pattern (51 bp):
AAATAGAGATTTAAGAGAAATTTGAAAGGAACTTGAGAACAAATTGAGATT
Found at i:4199512 original size:22 final size:22
Alignment explanation
Indices: 4199487--4199541 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
4199477 TTAAATATAG
4199487 ATTTGGGAGAAATTTG-GAAGG-A
1 ATTTGGGAGAAA-TTGAG-AGGAA
*
4199509 ATTTGAGAGCAAATTGAGAGGAA
1 ATTTGGGAG-AAATTGAGAGGAA
4199532 ATTTGGGAGA
1 ATTTGGGAGA
4199542 GGATTAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.38, C:0.02, G:0.35, T:0.25
Consensus pattern (22 bp):
ATTTGGGAGAAATTGAGAGGAA
Found at i:4202943 original size:23 final size:24
Alignment explanation
Indices: 4202916--4202961 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
4202906 ATTAAATTAG
*
4202916 AAAACTCTTAA-TTTAAAGAAAAT
1 AAAACTCTTAATTTTAAAAAAAAT
4202939 AAAACTCTTAATTTTAAAAAAAA
1 AAAACTCTTAATTTTAAAAAAAA
4202962 ATAATACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAACTCTTAATTTTAAAAAAAAT
Found at i:4204915 original size:18 final size:18
Alignment explanation
Indices: 4204894--4204928 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4204884 ACTTTACTAA
* *
4204894 TCAAGTGATGCCTTCAAC
1 TCAAATGATGCCCTCAAC
4204912 TCAAATGATGCCCTCAA
1 TCAAATGATGCCCTCAA
4204929 ATTCTGTGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (18 bp):
TCAAATGATGCCCTCAAC
Found at i:4207768 original size:63 final size:63
Alignment explanation
Indices: 4207669--4207792 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 63
4207659 ATTAATAGTG
* *
4207669 GGACAATAAATGATTACGGAAACTTGAAAAATGCCACATTTCAGTGCATGCCCTACTCATGTC
1 GGACAATAAATGATTACGGAAACTTGAAAAATGCCACATTTCACTGCATGCCCTACGCATGTC
4207732 GGACAATAAATGATTACGGAAACTTGAAAAATGCCACATTTCACTGCATGCCCTACGCATG
1 GGACAATAAATGATTACGGAAACTTGAAAAATGCCACATTTCACTGCATGCCCTACGCATG
4207793 CCATTTTCAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (63 bp):
GGACAATAAATGATTACGGAAACTTGAAAAATGCCACATTTCACTGCATGCCCTACGCATGTC
Found at i:4208649 original size:22 final size:22
Alignment explanation
Indices: 4208610--4208663 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
4208600 TATAATTTTA
** * *
4208610 AAATATATGTTAAATAATCATT
1 AAATATATAATAAATAATAAAT
*
4208632 AAATATATAATAAGTAATAAAT
1 AAATATATAATAAATAATAAAT
*
4208654 ATATATATAA
1 AAATATATAA
4208664 ATTATATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (22 bp):
AAATATATAATAAATAATAAAT
Found at i:4212329 original size:18 final size:18
Alignment explanation
Indices: 4212277--4212332 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
4212267 TGACAAAAAA
4212277 TTCTCAAATTTCTCCCTAAAT
1 TTCTCAAATTTCT--C-AAAT
**
4212298 TTCTCAAAGCTCTCAAAT
1 TTCTCAAATTTCTCAAAT
4212316 TTCTCAAATTTCTCAAA
1 TTCTCAAATTTCTCAAA
4212333 GCTCTCTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 19 0.61
19 1 0.03
21 11 0.35
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.39
Consensus pattern (18 bp):
TTCTCAAATTTCTCAAAT
Found at i:4212332 original size:27 final size:29
Alignment explanation
Indices: 4212278--4212338 Score: 99
Period size: 27 Copynumber: 2.1 Consensus size: 29
4212268 GACAAAAAAT
4212278 TCTCAAATTTCTCCCTAAATTTCTCAAAGC
1 TCTCAAATTTCT-CCTAAATTTCTCAAAGC
4212308 TCTCAAATTTCT-C-AAATTTCTCAAAGC
1 TCTCAAATTTCTCCTAAATTTCTCAAAGC
4212335 TCTC
1 TCTC
4212339 TTTAATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 18 0.58
28 1 0.03
30 12 0.39
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.38
Consensus pattern (29 bp):
TCTCAAATTTCTCCTAAATTTCTCAAAGC
Found at i:4214107 original size:18 final size:18
Alignment explanation
Indices: 4214084--4214121 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4214074 TGCCAGGTGC
* *
4214084 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTCATAT
4214102 GTATCCTAACCCTCATAT
1 GTATCCTAACCCTCATAT
4214120 GT
1 GT
4214122 TTTCTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (18 bp):
GTATCCTAACCCTCATAT
Found at i:4217855 original size:125 final size:126
Alignment explanation
Indices: 4217632--4217899 Score: 421
Period size: 125 Copynumber: 2.1 Consensus size: 126
4217622 GGTCAAACAT
* *
4217632 GAACTACTGTAGAAAAAGAACGTTGATGTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCGACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
*
4217697 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAG
** * *
4217758 GAACTACTGTAGAAAAAGAGTGTCGACGTGGGAGC-TTTTTCAGTAATTTTGTTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCGACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
* * *
4217822 TTGCTTGAAGTGTTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAG
66 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAG
* *
4217883 GAACTATTATAGAAAAA
1 GAACTACTGTAGAAAAA
4217900 AATAAAATCC
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
125 99 0.76
126 31 0.24
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAACGTCGACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
CTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAG
Found at i:4217999 original size:33 final size:31
Alignment explanation
Indices: 4217955--4218067 Score: 147
Period size: 33 Copynumber: 3.5 Consensus size: 31
4217945 TAAACACAAT
4217955 ATTA-TTTTTAAAAAACTAAACCCTAATTTA
1 ATTATTTTTTAAAAAACTAAACCCTAATTTA
4217985 ATTGATTTTCTTAAAAAACTAAACCCTAATTTA
1 ATT-ATTTT-TTAAAAAACTAAACCCTAATTTA
**
4218018 ATTTATTTATTTAAAACTCCTAAACCCTAATTTA
1 A-TTATTT-TTTAAAA-AACTAAACCCTAATTTA
*
4218052 ATTATTTTTAAAAAAA
1 ATTATTTTTTAAAAAA
4218068 ACACTAAATC
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
30 3 0.04
31 1 0.01
32 9 0.12
33 40 0.56
34 19 0.26
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.42
Consensus pattern (31 bp):
ATTATTTTTTAAAAAACTAAACCCTAATTTA
Found at i:4218160 original size:42 final size:41
Alignment explanation
Indices: 4218113--4218192 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 41
4218103 AACGTAGAAC
* *
4218113 CCTAAATTATTTTAACAAAACCTTAAACCCTACAAACCTAAG
1 CCTAAATTATTATAACAAAACCTT-AACCCTAAAAACCTAAG
*
4218155 CCTAAATTATTATAACAAAATCTTAACCCTAAAAACCT
1 CCTAAATTATTATAACAAAACCTTAACCCTAAAAACCT
4218193 TAAACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 13 0.37
42 22 0.63
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (41 bp):
CCTAAATTATTATAACAAAACCTTAACCCTAAAAACCTAAG
Found at i:4224458 original size:46 final size:46
Alignment explanation
Indices: 4224395--4224495 Score: 157
Period size: 46 Copynumber: 2.2 Consensus size: 46
4224385 ATTGCTATAG
* * * *
4224395 CTCAGTATGATTTTCTTCACGAAAATACCATATCTACTTTTCACAA
1 CTCAATATGATTTTCTTCACCAAAACACCATACCTACTTTTCACAA
*
4224441 CTCAATATGGTTTTCTTCACCAAAACACCATACCTACTTTTCACAA
1 CTCAATATGATTTTCTTCACCAAAACACCATACCTACTTTTCACAA
4224487 CTCAATATG
1 CTCAATATG
4224496 TACCTACTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.35
Consensus pattern (46 bp):
CTCAATATGATTTTCTTCACCAAAACACCATACCTACTTTTCACAA
Found at i:4224500 original size:25 final size:25
Alignment explanation
Indices: 4224471--4224520 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
4224461 CAAAACACCA
4224471 TACCTACTTTTCACAACTCAATATG
1 TACCTACTTTTCACAACTCAATATG
* *
4224496 TACCTACTTTTCATAACTCAGTATG
1 TACCTACTTTTCACAACTCAATATG
4224521 ATTTTCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (25 bp):
TACCTACTTTTCACAACTCAATATG
Found at i:4224507 original size:71 final size:71
Alignment explanation
Indices: 4224428--4224566 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 71
4224418 AATACCATAT
*
4224428 CTACTTTTCACAACTCAATATGGTTTTCTTCACCAAAACACCATACCTACTTTTCACAACTCAAT
1 CTACTTTTCACAACTCAATATGATTTTCTTCACCAAAACACCATACCTACTTTTCACAACTCAAT
4224493 ATGTAC
66 ATGTAC
* * * * * *
4224499 CTACTTTTCATAACTCAGTATGATTTTCTTTACCGAAATACCATACCTACTTTTCACAACTCAGT
1 CTACTTTTCACAACTCAATATGATTTTCTTCACCAAAACACCATACCTACTTTTCACAACTCAAT
4224564 ATG
66 ATG
4224567 ATTTTCTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (71 bp):
CTACTTTTCACAACTCAATATGATTTTCTTCACCAAAACACCATACCTACTTTTCACAACTCAAT
ATGTAC
Found at i:4224549 original size:46 final size:46
Alignment explanation
Indices: 4224496--4224646 Score: 230
Period size: 46 Copynumber: 3.3 Consensus size: 46
4224486 ACTCAATATG
4224496 TACCTACTTTTCATAACTCAGTATGATTTTCTTTACCGAAATACCA
1 TACCTACTTTTCATAACTCAGTATGATTTTCTTTACCGAAATACCA
* * **
4224542 TACCTACTTTTCACAACTCAGTATGATTTTCTTTATCGAAATATTA
1 TACCTACTTTTCATAACTCAGTATGATTTTCTTTACCGAAATACCA
* * *
4224588 TACCTACTTTTCATAACTCAGTATGGTTTTCTTCACTGAAATACCA
1 TACCTACTTTTCATAACTCAGTATGATTTTCTTTACCGAAATACCA
*
4224634 TACCTACGTTTCA
1 TACCTACTTTTCA
4224647 CACTTTGCCA
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 93 1.00
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.40
Consensus pattern (46 bp):
TACCTACTTTTCATAACTCAGTATGATTTTCTTTACCGAAATACCA
Found at i:4224606 original size:117 final size:117
Alignment explanation
Indices: 4224395--4224612 Score: 312
Period size: 117 Copynumber: 1.9 Consensus size: 117
4224385 ATTGCTATAG
* *
4224395 CTCAGTATGATTTTCTTCACGAAAATACCATATCTACTTTTCACAACTCAATATGGTTTTCTTCA
1 CTCAGTATGATTTTCTTCACGAAAATACCATACCTACTTTTCACAACTCAATATGATTTTCTTCA
4224460 CCAAAACACCATACCTACTTTTCACAACTCAATATGTACCTACTTTTCATAA
66 CCAAAACACCATACCTACTTTTCACAACTCAATATGTACCTACTTTTCATAA
* * *
4224512 CTCAGTATGATTTTCTTTACCG-AAATACCATACCTACTTTTCACAACTCAGTATGATTTTCTTT
1 CTCAGTATGATTTTCTTCA-CGAAAATACCATACCTACTTTTCACAACTCAATATGATTTTCTTC
* * * ** * *
4224576 ATCGAAATATTATACCTACTTTTCATAACTCAGTATG
65 ACCAAAACACCATACCTACTTTTCACAACTCAATATG
4224613 GTTTTCTTCA
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
117 86 0.98
118 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.38
Consensus pattern (117 bp):
CTCAGTATGATTTTCTTCACGAAAATACCATACCTACTTTTCACAACTCAATATGATTTTCTTCA
CCAAAACACCATACCTACTTTTCACAACTCAATATGTACCTACTTTTCATAA
Found at i:4232277 original size:21 final size:19
Alignment explanation
Indices: 4232227--4232282 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 19
4232217 AAAGTGTGAC
4232227 ATAATTCAATATTATTAAA
1 ATAATTCAATATTATTAAA
4232246 ATCAATGTCAA-ATTCATTAAA
1 AT-AAT-TCAATATT-ATTAAA
*
4232267 GTATAATTCAACATTA
1 --ATAATTCAATATTA
4232283 ATTTAGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
19 2 0.06
20 6 0.19
21 15 0.48
22 6 0.19
23 2 0.06
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.38
Consensus pattern (19 bp):
ATAATTCAATATTATTAAA
Found at i:4233913 original size:23 final size:23
Alignment explanation
Indices: 4233877--4233936 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
4233867 TTAAGATTGT
*
4233877 TAAATTTAATAAATA-AAAAATTA
1 TAAATTTAA-AAATATAAAAATAA
*
4233900 TAAATTTATAAAATATTAAAATAA
1 TAAATTTA-AAAATATAAAAATAA
4233924 TATAATTTAAAAA
1 TA-AATTTAAAAA
4233937 GTGAAAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 13 0.41
24 13 0.41
25 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAATTTAAAAATATAAAAATAA
Found at i:4233927 original size:18 final size:19
Alignment explanation
Indices: 4233884--4233928 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
4233874 TGTTAAATTT
4233884 AATAA-ATAAAAAATTATA
1 AATAATATAAAAAATTATA
* *
4233902 AAT-TTATAAAATATTA-A
1 AATAATATAAAAAATTATA
4233919 AATAATATAA
1 AATAATATAA
4233929 TTTAAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAATATAAAAAATTATA
Found at i:4234376 original size:25 final size:24
Alignment explanation
Indices: 4234342--4234393 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
4234332 TTAAAATATT
* *
4234342 ATTTGTTTTATTTTAATCACTTTTA
1 ATTTGTTTTAATTTAATCA-TTCTA
*
4234367 ATTTTTTTTAATTTAATCATTCTA
1 ATTTGTTTTAATTTAATCATTCTA
4234391 ATT
1 ATT
4234394 AAAATAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTTGTTTTAATTTAATCATTCTA
Found at i:4244862 original size:23 final size:24
Alignment explanation
Indices: 4244827--4244871 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
4244817 TATTTGAATG
* * *
4244827 AAAATTATATATATGTATATTTTA
1 AAAACTATATATAAGTAAATTTTA
4244851 AAAACTAT-TATAAGTAAATTT
1 AAAACTATATATAAGTAAATTT
4244872 GTATACTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (24 bp):
AAAACTATATATAAGTAAATTTTA
Found at i:4245568 original size:17 final size:17
Alignment explanation
Indices: 4245548--4245580 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4245538 TTTTTAAATA
4245548 ATAATAATTTTT-TTAAG
1 ATAAT-ATTTTTATTAAG
4245565 ATAATATTTTTATTAA
1 ATAATATTTTTATTAA
4245581 AATATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATAATATTTTTATTAAG
Found at i:4253722 original size:18 final size:18
Alignment explanation
Indices: 4253701--4253742 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
4253691 TTATATTCAC
*
4253701 ACTTTTTTTTTCAG-TTTT
1 ACTTTTTGTTT-AGTTTTT
*
4253719 ACTTTATGTTTAGTTTTT
1 ACTTTTTGTTTAGTTTTT
4253737 ACTTTT
1 ACTTTT
4253743 AAAAATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.14, C:0.10, G:0.07, T:0.69
Consensus pattern (18 bp):
ACTTTTTGTTTAGTTTTT
Found at i:4256016 original size:24 final size:24
Alignment explanation
Indices: 4255984--4256029 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
4255974 TATTCCAATG
4255984 AATTCTGCAGATATTACTATGAAT
1 AATTCTGCAGATATTACTATGAAT
4256008 AATTCTGCAGATATTACTATGA
1 AATTCTGCAGATATTACTATGA
4256030 GCCTGCTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (24 bp):
AATTCTGCAGATATTACTATGAAT
Found at i:4263885 original size:22 final size:22
Alignment explanation
Indices: 4263865--4263909 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
4263855 AAATAATAAC
4263865 TAAAATATTATTATTTTATAAAA
1 TAAAATA-TATTATTTTATAAAA
*
4263888 TAAATTATATTATTTTA-AAAA
1 TAAAATATATTATTTTATAAAA
4263909 T
1 T
4263910 GTTTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 10 0.48
23 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAAAATATATTATTTTATAAAA
Found at i:4264752 original size:7 final size:7
Alignment explanation
Indices: 4264740--4264770 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
4264730 TTTATTTCCC
4264740 TGCCCAG
1 TGCCCAG
4264747 TGCCCAG
1 TGCCCAG
4264754 TGCCCAG
1 TGCCCAG
4264761 TGCCCAG
1 TGCCCAG
4264768 TGC
1 TGC
4264771 AATATAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.42, G:0.29, T:0.16
Consensus pattern (7 bp):
TGCCCAG
Found at i:4269041 original size:27 final size:27
Alignment explanation
Indices: 4269011--4269062 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
4269001 CAAATGCCGA
*
4269011 GTGGAGGTGGGGGTGAAGGTGGAGGAG
1 GTGGAGGTGGGGGGGAAGGTGGAGGAG
*
4269038 GTGGTGGTGGGGGGGAAGGTGGAGG
1 GTGGAGGTGGGGGGGAAGGTGGAGG
4269063 GGGAGGNATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.69, T:0.15
Consensus pattern (27 bp):
GTGGAGGTGGGGGGGAAGGTGGAGGAG
Found at i:4284165 original size:16 final size:16
Alignment explanation
Indices: 4284144--4284192 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
4284134 TTCGCTGTAT
*
4284144 TGGAATAAAGGCGTAA
1 TGGAATAGAGGCGTAA
* *
4284160 TGGAATAGAGACATAA
1 TGGAATAGAGGCGTAA
*
4284176 TGGAATAGATGCGTAA
1 TGGAATAGAGGCGTAA
4284192 T
1 T
4284193 AGAAAATCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.29, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:4284447 original size:18 final size:17
Alignment explanation
Indices: 4284425--4284459 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4284415 TAATTATTAA
*
4284425 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
4284443 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
4284460 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:4284579 original size:26 final size:26
Alignment explanation
Indices: 4284550--4284764 Score: 106
Period size: 26 Copynumber: 8.3 Consensus size: 26
4284540 TTAATCATAT
*
4284550 TTTAACATAATTATTATTAAATATAA
1 TTTAATATAATTATTATTAAATATAA
* * * * *
4284576 TTTAATAAAATATATAAATTTACTAAAA
1 TTTAATATAAT-TAT-TATTAAATATAA
* * * *
4284604 TCATAATATATAATACTATAAAATATAA
1 T-TTAATATA-ATTATTATTAAATATAA
*
4284632 TTTAAAATAATTATTATTAAATATAA
1 TTTAATATAATTATTATTAAATATAA
* * *
4284658 TTTAATAAAAATATATAATTTAATA-AA
1 TTTAAT-ATAAT-TATTATTAAATATAA
* * *
4284685 -AT-ATATAAAT-TTACTAAAATCATAA
1 TTTAATATAATTATTA-TTAAAT-ATAA
*
4284710 --T-ATATAA-TACTA-TAAAGTATAA
1 TTTAATATAATTATTATTAAA-TATAA
* *
4284732 TTTAAAATTATTATTATTAAATATAA
1 TTTAATATAATTATTATTAAATATAA
4284758 TTTAATA
1 TTTAATA
4284765 AAATATATAA
Statistics
Matches: 137, Mismatches: 36, Indels: 32
0.67 0.18 0.16
Matches are distributed among these distances:
22 9 0.07
23 7 0.05
24 14 0.10
25 8 0.06
26 44 0.32
27 19 0.14
28 27 0.20
29 8 0.06
30 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (26 bp):
TTTAATATAATTATTATTAAATATAA
Found at i:4284634 original size:145 final size:145
Alignment explanation
Indices: 4284346--4284635 Score: 435
Period size: 145 Copynumber: 2.0 Consensus size: 145
4284336 ATGATTATTG
* *
4284346 TTATTGTTATTAAATTTTAATAAGATTATTAATATCAGTAATAAATAATTTAATCATATTTTAAC
1 TTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAAC
* *
4284411 ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
66 ATAATAATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCATAATAATCAATAT
***
4284476 TGTTATATGAATTTA
131 TAAAATATGAATTTA
4284491 TTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAAC
1 TTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAAC
* *
4284556 ATAATTATTATTAAATATAATTTAA-TAAAATATATAAATTTACTAAAA-TCATAATATAT-AAT
66 ATAATAATTATTAAATATAATTTAATTAAAATATAT-AATTTAATAAAATTCATAATA-ATCAAT
4284618 ACTATAAAATAT-AATTTA
129 A-T-TAAAATATGAATTTA
4284636 AAATAATTAT
Statistics
Matches: 132, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
144 21 0.16
145 106 0.80
146 5 0.04
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (145 bp):
TTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAAC
ATAATAATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCATAATAATCAATAT
TAAAATATGAATTTA
Found at i:4284683 original size:100 final size:99
Alignment explanation
Indices: 4284570--4284785 Score: 396
Period size: 100 Copynumber: 2.2 Consensus size: 99
4284560 TTATTATTAA
4284570 ATATAATTTAATAAAATATATAAATTTACTAAAATCATAATATATAATACTATAAAATATAATTT
1 ATATAATTTAATAAAATATATAAATTTACTAAAATCATAATATATAATACTATAAAATATAATTT
4284635 AAAATAATTATTATTAAATATAATTTAATAAAAAT
66 AAAATAATTATTATTAAATATAATTTAAT-AAAAT
*
4284670 ATATAATTTAATAAAATATATAAATTTACTAAAATCATAATATATAATACTATAAAGTATAATTT
1 ATATAATTTAATAAAATATATAAATTTACTAAAATCATAATATATAATACTATAAAATATAATTT
*
4284735 AAAATTATTATTATTAAATATAATTTAATAAAAT
66 AAAATAATTATTATTAAATATAATTTAATAAAAT
*
4284769 ATATAATTTGATAAAAT
1 ATATAATTTAATAAAAT
4284786 TCTTAGTATT
Statistics
Matches: 113, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
99 21 0.19
100 92 0.81
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (99 bp):
ATATAATTTAATAAAATATATAAATTTACTAAAATCATAATATATAATACTATAAAATATAATTT
AAAATAATTATTATTAAATATAATTTAATAAAAT
Found at i:4291649 original size:24 final size:24
Alignment explanation
Indices: 4291621--4291672 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
4291611 TTTTTAGAAG
*
4291621 ATTTAATATTTA-TAAGTATAATAT
1 ATTTAATATTTATTAA-CATAATAT
*
4291645 ATTTAATGTTTATTAACATAATAT
1 ATTTAATATTTATTAACATAATAT
4291669 ATTT
1 ATTT
4291673 GACTTTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTTAATATTTATTAACATAATAT
Found at i:4291965 original size:18 final size:18
Alignment explanation
Indices: 4291942--4291977 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4291932 ATCGTCAACA
*
4291942 AAAGACTTTTCTTGTGTC
1 AAAGACTTTTCTTCTGTC
4291960 AAAGACTTTTCTTCTGTC
1 AAAGACTTTTCTTCTGTC
4291978 TCTGTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.44
Consensus pattern (18 bp):
AAAGACTTTTCTTCTGTC
Found at i:4292259 original size:16 final size:17
Alignment explanation
Indices: 4292231--4292262 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4292221 CTTTTTTAAT
4292231 TAATTTTTATTTAAAAA
1 TAATTTTTATTTAAAAA
4292248 TAATTTTT-TTTAAAA
1 TAATTTTTATTTAAAA
4292263 CATACAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTTTTATTTAAAAA
Found at i:4292508 original size:28 final size:30
Alignment explanation
Indices: 4292476--4292532 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
4292466 AGAGATTTAA
*
4292476 ATAATT-ATATAATTATTATT-TAACATAT
1 ATAATTAACATAATTATTATTATAACATAT
*
4292504 ATAATTAACATAATTATTTTTATAACATA
1 ATAATTAACATAATTATTATTATAACATA
4292533 AAAAAATTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.24
29 12 0.48
30 7 0.28
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
ATAATTAACATAATTATTATTATAACATAT
Found at i:4292804 original size:4 final size:4
Alignment explanation
Indices: 4292795--4292822 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4292785 TAAGAGGGAT
4292795 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
4292823 GATGGGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:4295371 original size:157 final size:157
Alignment explanation
Indices: 4295085--4295397 Score: 590
Period size: 157 Copynumber: 2.0 Consensus size: 157
4295075 ATAAAAGATC
4295085 GAGAAAGTGCCATCCAAGCAGAACCTATTACAGAAAAAGAGATGCTTGTCAGAGATACCACCTAA
1 GAGAAAGTGCCATCCAAGCAGAACCTATTACAGAAAAAGAGATGCTTGTCAGAGATACCACCTAA
*
4295150 TGCAGATATAATGGTGAACATTATGGTTGTCTAATAGAGATTATGGCAACAAGGTAGTTCACGAG
66 TGCAGATATAATGGTGAACATTATGGTTGTCAAATAGAGATTATGGCAACAAGGTAGTTCACGAG
*
4295215 ATAGTAGAGGAAATTCTGCAAAAATGT
131 ATAATAGAGGAAATTCTGCAAAAATGT
* *
4295242 GAGAAAGTGCCATCCAAGCAGAACCTATTACAGAAAAAGATATGCTTGTCAGAGATGCCACCTAA
1 GAGAAAGTGCCATCCAAGCAGAACCTATTACAGAAAAAGAGATGCTTGTCAGAGATACCACCTAA
4295307 TGCAGATATAATGGTGAACATTATGGTTGTCAAATAGAGATTATGGCAACAAGGTAGTTCACGAG
66 TGCAGATATAATGGTGAACATTATGGTTGTCAAATAGAGATTATGGCAACAAGGTAGTTCACGAG
4295372 ATAATAGAGGAAATTCTGCAAAAATG
131 ATAATAGAGGAAATTCTGCAAAAATG
4295398 CTAATGAACA
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 152 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (157 bp):
GAGAAAGTGCCATCCAAGCAGAACCTATTACAGAAAAAGAGATGCTTGTCAGAGATACCACCTAA
TGCAGATATAATGGTGAACATTATGGTTGTCAAATAGAGATTATGGCAACAAGGTAGTTCACGAG
ATAATAGAGGAAATTCTGCAAAAATGT
Found at i:4314703 original size:16 final size:17
Alignment explanation
Indices: 4314682--4314720 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
4314672 ATCTTTATAT
4314682 ATTTTTTTATCCCTTCA
1 ATTTTTTTATCCCTTCA
**
4314699 ATTTTTTTATCTTTTCA
1 ATTTTTTTATCCCTTCA
4314716 ATTTT
1 ATTTT
4314721 CTTTCCTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTTTTATCCCTTCA
Done.