Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020975.1 Corchorus olitorius cultivar O-4 contig21008, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 117838
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:303 original size:21 final size:21
Alignment explanation
Indices: 279--349 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
269 CTTAGGCAAT
*
279 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
300 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
321 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
342 TCCAATGA
1 TCCAATGA
350 TCTCCTAACA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 3 0.06
21 45 0.94
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:2003 original size:21 final size:21
Alignment explanation
Indices: 1977--2019 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1967 GAGAGATAAA
1977 AGGCTCTGTTCAATCCCAATC
1 AGGCTCTGTTCAATCCCAATC
1998 AGGCTCTGTTCAATCCCAATC
1 AGGCTCTGTTCAATCCCAATC
2019 A
1 A
2020 ATAAGTTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.33, G:0.14, T:0.28
Consensus pattern (21 bp):
AGGCTCTGTTCAATCCCAATC
Found at i:7116 original size:12 final size:12
Alignment explanation
Indices: 7099--7144 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
7089 TTCTATATTT
7099 GAAAAAAGAAAA
1 GAAAAAAGAAAA
*
7111 G-AAAAA-AAAG
1 GAAAAAAGAAAA
*
7121 GAAAAAAAAAAA
1 GAAAAAAGAAAA
7133 GAAAAAAGAAAA
1 GAAAAAAGAAAA
7145 AGAAGAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 4 0.14
11 10 0.34
12 15 0.52
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
GAAAAAAGAAAA
Found at i:7124 original size:10 final size:10
Alignment explanation
Indices: 7101--7145 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
7091 CTATATTTGA
7101 AAAAAGAAAAG
1 AAAAA-AAAAG
*
7112 AAAAAAAAGG
1 AAAAAAAAAG
7122 AAAAAAAAA-
1 AAAAAAAAAG
*
7131 AAGAAAAAAG
1 AAAAAAAAAG
7141 AAAAA
1 AAAAA
7146 GAAGAAGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 8 0.28
10 16 0.55
11 5 0.17
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:7125 original size:9 final size:9
Alignment explanation
Indices: 7102--7151 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
7092 TATATTTGAA
7102 AAAAGAAAAG
1 AAAA-AAAAG
7112 AAAAAAAAGG
1 AAAAAAAA-G
*
7122 AAAAAAAAA
1 AAAAAAAAG
7131 AAGAAAAAAG
1 AA-AAAAAAG
*
7141 AAAAAGAAG
1 AAAAAAAAG
7150 AA
1 AA
7152 GATATTTCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 14 0.40
10 21 0.60
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:7153 original size:12 final size:12
Alignment explanation
Indices: 7100--7148 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 12
7090 TCTATATTTG
7100 AAAAAAGAAAAGAA
1 AAAAAAG-AAA-AA
7114 AAAAAAGGAAAAA
1 AAAAAA-GAAAAA
7127 AAAAAAGAAAAA
1 AAAAAAGAAAAA
7139 AGAAAAAGAA
1 A-AAAAAGAA
7149 GAAGATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.21
13 16 0.48
14 9 0.27
15 1 0.03
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:10871 original size:6 final size:6
Alignment explanation
Indices: 10860--10896 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
10850 TGCAGGTGGT
10860 AGTTGG AGTTGG AGTTGG AGTTGG AGTTGG AG-TGG AG
1 AGTTGG AGTTGG AGTTGG AGTTGG AGTTGG AGTTGG AG
10897 AACTGAGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.19, C:0.00, G:0.51, T:0.30
Consensus pattern (6 bp):
AGTTGG
Found at i:10883 original size:18 final size:17
Alignment explanation
Indices: 10855--10896 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
10845 TAGGTTGCAG
10855 GTGGTAGTTGGAGTTGGA
1 GTGG-AGTTGGAGTTGGA
10873 GTTGGAGTTGGAGTTGGA
1 G-TGGAGTTGGAGTTGGA
10891 GTGGAG
1 GTGGAG
10897 AACTGAGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 15 0.65
19 3 0.13
ACGTcount: A:0.17, C:0.00, G:0.52, T:0.31
Consensus pattern (17 bp):
GTGGAGTTGGAGTTGGA
Found at i:13904 original size:19 final size:19
Alignment explanation
Indices: 13864--13900 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
13854 AATTTTTAAG
13864 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
13883 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
13901 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:14211 original size:16 final size:16
Alignment explanation
Indices: 14192--14280 Score: 67
Period size: 16 Copynumber: 5.6 Consensus size: 16
14182 CGGGCTCGGG
14192 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* **
14208 CGGGCTCGGGT-TAAGT
1 CGGGTTCGGGTAT-TTT
*
14224 CGGGTTTGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
14240 CGGGCTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
*
14256 CAGGTTCGGGTATTTTT
1 CGGGTTCGGGTA-TTTT
14273 C-GGTTCGG
1 CGGGTTCGG
14281 TCTCGGGTAG
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
15 2 0.04
16 48 0.87
17 4 0.07
18 1 0.02
ACGTcount: A:0.08, C:0.15, G:0.39, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:14235 original size:32 final size:32
Alignment explanation
Indices: 14192--14271 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
14182 CGGGCTCGGG
14192 CGGGTTCGGGTATTTTCGGGCTCGGGTTAAGT
1 CGGGTTCGGGTATTTTCGGGCTCGGGTTAAGT
* *
14224 CGGGTTTGGGTATTTTCGGGCTCGGGTTATGT
1 CGGGTTCGGGTATTTTCGGGCTCGGGTTAAGT
*
14256 CAGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
14272 TCGGTTCGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.09, C:0.14, G:0.39, T:0.39
Consensus pattern (32 bp):
CGGGTTCGGGTATTTTCGGGCTCGGGTTAAGT
Found at i:14308 original size:23 final size:23
Alignment explanation
Indices: 14274--14321 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
14264 GGTATTTTTC
14274 GGTTCGGTCTCGGGTAGGGTTCG
1 GGTTCGGTCTCGGGTAGGGTTCG
*
14297 GGTTCAGG-CTCGGGTCGGGTTCG
1 GGTTC-GGTCTCGGGTAGGGTTCG
14320 GG
1 GG
14322 CTCGAGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.04, C:0.19, G:0.50, T:0.27
Consensus pattern (23 bp):
GGTTCGGTCTCGGGTAGGGTTCG
Found at i:14477 original size:13 final size:12
Alignment explanation
Indices: 14454--14500 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
14444 AAGTTTATTG
14454 ATAATATATAAT
1 ATAATATATAAT
14466 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
14479 ATAACAT-TATT
1 ATAATATATAAT
14490 ATCAATATATA
1 AT-AATATATA
14501 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:15317 original size:2 final size:2
Alignment explanation
Indices: 15312--15364 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
15302 TTATATAAGT
*
15312 TA TA TA TA TA TA TA TA TA TA TA TT TA -A T- TA TA TA TA TA TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
*
15353 AA T- TA TA TA TA T
1 TA TA TA TA TA TA T
15365 TTGGTAGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
1 3 0.07
2 39 0.91
3 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15333 original size:16 final size:14
Alignment explanation
Indices: 15303--15364 Score: 72
Period size: 14 Copynumber: 4.2 Consensus size: 14
15293 TGCTTTAAGT
15303 TATATAAGTTATATA
1 TATATAA-TTATATA
15318 TATAT-ATATATATA
1 TATATAAT-TATATA
*
15332 TATTTAATTATATA
1 TATATAATTATATA
15346 TATATCAAATTATATA
1 TATAT--AATTATATA
15362 TAT
1 TAT
15365 TTGGTAGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.02
14 21 0.51
15 7 0.17
16 12 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (14 bp):
TATATAATTATATA
Found at i:15615 original size:16 final size:16
Alignment explanation
Indices: 15594--15624 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15584 GGGTTCTGCT
*
15594 TCGGGTATTTTCGGGC
1 TCGGGTAATTTCGGGC
15610 TCGGGTAATTTCGGG
1 TCGGGTAATTTCGGG
15625 TTCAGGTTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.16, G:0.39, T:0.35
Consensus pattern (16 bp):
TCGGGTAATTTCGGGC
Found at i:17598 original size:8 final size:9
Alignment explanation
Indices: 17570--17600 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
17560 TTCCTAAATT
17570 AATTATGGA
1 AATTATGGA
17579 AATTATGGA
1 AATTATGGA
17588 AATTA-GGA
1 AATTATGGA
17596 AATTA
1 AATTA
17601 AAGAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (9 bp):
AATTATGGA
Found at i:17606 original size:17 final size:18
Alignment explanation
Indices: 17570--17609 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
17560 TTCCTAAATT
**
17570 AATTATGGAAATTATGGA
1 AATTATGGAAATTAAAGA
17588 AATTA-GGAAATTAAAGA
1 AATTATGGAAATTAAAGA
17605 AATTA
1 AATTA
17610 AAATTTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (18 bp):
AATTATGGAAATTAAAGA
Found at i:18923 original size:49 final size:48
Alignment explanation
Indices: 18858--18985 Score: 154
Period size: 49 Copynumber: 2.7 Consensus size: 48
18848 TTACATTTCC
** *
18858 TGCACTTTTTCTCAATTTTTACTACAAAATTGAAATTTT-ATTTTTACT
1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGAAATTTTAATTTTCA-T
***
18906 TGCACATTTTTCTCAATTTTTAAGACAAAATTGTTCTTTTAATTTTCAT
1 TGCAC-TTTTTCTCAATTTTTAAGACAAAATTGAAATTTTAATTTTCAT
*
18955 TGCACTTTTTATCAATTTTT--GACAAAATTGA
1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGA
18986 TTGGCACGCT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
46 10 0.14
48 19 0.27
49 35 0.50
50 6 0.09
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.50
Consensus pattern (48 bp):
TGCACTTTTTCTCAATTTTTAAGACAAAATTGAAATTTTAATTTTCAT
Found at i:21824 original size:8 final size:9
Alignment explanation
Indices: 21796--21826 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
21786 TTCCTAAATT
21796 AATTATGGA
1 AATTATGGA
21805 AATTATGGA
1 AATTATGGA
21814 AATTA-GGA
1 AATTATGGA
21822 AATTA
1 AATTA
21827 AAGAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (9 bp):
AATTATGGA
Found at i:21832 original size:17 final size:18
Alignment explanation
Indices: 21796--21835 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
21786 TTCCTAAATT
**
21796 AATTATGGAAATTATGGA
1 AATTATGGAAATTAAAGA
21814 AATTA-GGAAATTAAAGA
1 AATTATGGAAATTAAAGA
21831 AATTA
1 AATTA
21836 AAATTTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (18 bp):
AATTATGGAAATTAAAGA
Found at i:23165 original size:49 final size:47
Alignment explanation
Indices: 23100--23228 Score: 154
Period size: 49 Copynumber: 2.7 Consensus size: 47
23090 TTACATTTCC
*
23100 TGCACTTTTTCTCAATTTTTACTACAAAATTGAACTTTT-ATTTTTACT
1 TGCACTTTTTCTCAATTTTTA-TACAAAATTGAACTTTTAATTTTCA-T
* * *
23148 TGCACCTTTTTCTCAATTTTTAAGATAAAATTGATCTTTTAATTTTCAT
1 TGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACTTTTAATTTTCAT
*
23197 TGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
23229 TTGGCACGCT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
47 9 0.13
48 19 0.27
49 35 0.50
50 7 0.10
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (47 bp):
TGCACTTTTTCTCAATTTTTATACAAAATTGAACTTTTAATTTTCAT
Found at i:23573 original size:20 final size:20
Alignment explanation
Indices: 23529--23579 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
23519 AATACAACAC
23529 CATTAAATAA-ACATAATACA
1 CATT-AATAATACATAATACA
*
23549 TATTAATAATACA-AATATCA
1 CATTAATAATACATAATA-CA
*
23569 CATTATTAATA
1 CATTAATAATA
23580 AACATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (20 bp):
CATTAATAATACATAATACA
Found at i:28697 original size:19 final size:22
Alignment explanation
Indices: 28663--28702 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
28653 AGTCACCAAC
28663 AATTTGCTCAACATT-GAAGAG
1 AATTTGCTCAACATTGGAAGAG
28684 AATTTGC-C-ACATTGGAAGA
1 AATTTGCTCAACATTGGAAGA
28703 TCGAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (22 bp):
AATTTGCTCAACATTGGAAGAG
Found at i:36066 original size:23 final size:24
Alignment explanation
Indices: 36025--36069 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
36015 TATATATTAG
36025 TGGTCACAAAGCACTGTCGCAAGA
1 TGGTCACAAAGCACTGTCGCAAGA
*
36049 TGGTTACAAA-CACTGTCGCAA
1 TGGTCACAAAGCACTGTCGCAA
36070 ATATTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (24 bp):
TGGTCACAAAGCACTGTCGCAAGA
Found at i:37621 original size:21 final size:21
Alignment explanation
Indices: 37597--37653 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
37587 GAACCCTATT
*
37597 GGATTCAAGTGGTACAAAATA
1 GGATTTAAGTGGTACAAAATA
37618 GGATTTAAGTGGTACAAAATA
1 GGATTTAAGTGGTACAAAATA
37639 GGATTTAAGTGGTAC
1 GGATTTAAGTGGTAC
37654 TAGGGTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (21 bp):
GGATTTAAGTGGTACAAAATA
Found at i:41654 original size:39 final size:39
Alignment explanation
Indices: 41608--41697 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 39
41598 TCAGATAAGT
* *
41608 AAACCTGCTTAGGATCTCCGCTTTGA-ATCCCGTTTAAAC
1 AAACCTGCTTAGGACCTCCGCTTAGAGAT-CCGTTTAAAC
* * *
41647 AAACCTGCTTA-GACCTCTGCTTAGAGATTCGTTTAATC
1 AAACCTGCTTAGGACCTCCGCTTAGAGATCCGTTTAAAC
41685 AAACCTGCTTAGG
1 AAACCTGCTTAGG
41698 TCCTTGTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
38 30 0.68
39 14 0.32
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.31
Consensus pattern (39 bp):
AAACCTGCTTAGGACCTCCGCTTAGAGATCCGTTTAAAC
Found at i:41656 original size:77 final size:77
Alignment explanation
Indices: 41575--41856 Score: 265
Period size: 77 Copynumber: 3.7 Consensus size: 77
41565 TAAGTACACA
* * * * *
41575 TGCTTAGGTCCATGTTTAGAATTTCAG-ATAAGTAAACCTGCTTAGGATCTCCGCTTT-GAATCC
1 TGCTTAGGTCCTTGTTTAGAATTTCCGTTTAAGTAAACCTGCTTAGG-TCTCTG-TTTAGAATCT
41638 CGTTTAAACAAACC
64 CGTTTAAACAAACC
* *
41652 TGCTTA-GACCTCTGCTTAGAGA-TT-CGTTTAA-TCAAACCTGCTTAGGTC-CTTGTTTAGAAC
1 TGCTTAGGTCCT-TGTTTAGA-ATTTCCGTTTAAGT-AAACCTGCTTAGGTCTC-TGTTTAGAA-
* * * *
41712 TTTTGTTTAATCAAATC
61 TCTCGTTTAAACAAACC
* * * * * *
41729 TGTTTAGGTCCTTGTCTAGAACTCCCG-TTAAGTAAACCTGCTTAGGTCTATGTTTAGAATCTCA
1 TGCTTAGGTCCTTGTTTAGAATTTCCGTTTAAGTAAACCTGCTTAGGTCTCTGTTTAGAATCTCG
**
41793 TTTAAGGAAACC
66 TTTAAACAAACC
*
41805 TGCTTAGGTCCTTGTTTAGAATTTCCGTTTAAGCAAACCTGCTTAGGTCTCT
1 TGCTTAGGTCCTTGTTTAGAATTTCCGTTTAAGTAAACCTGCTTAGGTCTCT
41857 ATTCCGCTTA
Statistics
Matches: 163, Mismatches: 29, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
75 4 0.02
76 46 0.28
77 105 0.64
78 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (77 bp):
TGCTTAGGTCCTTGTTTAGAATTTCCGTTTAAGTAAACCTGCTTAGGTCTCTGTTTAGAATCTCG
TTTAAACAAACC
Found at i:41709 original size:38 final size:38
Alignment explanation
Indices: 41638--41853 Score: 201
Period size: 38 Copynumber: 5.6 Consensus size: 38
41628 CTTTGAATCC
* * *
41638 CGTTTAAACAAACCTGCTTA-GACCTCTGCTTAGAGA-TT
1 CGTTTAATCAAACCTGCTTAGGTCCT-TGTTTAGA-ACTT
41676 CGTTTAATCAAACCTGCTTAGGTCCTTGTTTAGAACTTT
1 CGTTTAATCAAACCTGCTTAGGTCCTTGTTTAGAAC-TT
* * * * *
41715 TGTTTAATCAAATCTGTTTAGGTCCTTGTCTAGAACTCC
1 CGTTTAATCAAACCTGCTTAGGTCCTTGTTTAGAACT-T
41754 CG-TTAAGT-AAACCTGCTTAGGT-CTATGTTTAGAA-TCT
1 CGTTTAA-TCAAACCTGCTTAGGTCCT-TGTTTAGAACT-T
* ** *
41791 CATTTAAGGAAACCTGCTTAGGTCCTTGTTTAGAATTT
1 CGTTTAATCAAACCTGCTTAGGTCCTTGTTTAGAACTT
*
41829 CCGTTTAAGCAAACCTGCTTAGGTC
1 -CGTTTAATCAAACCTGCTTAGGTC
41854 TCTATTCCGC
Statistics
Matches: 150, Mismatches: 17, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
37 6 0.04
38 79 0.53
39 65 0.43
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (38 bp):
CGTTTAATCAAACCTGCTTAGGTCCTTGTTTAGAACTT
Found at i:41736 original size:39 final size:39
Alignment explanation
Indices: 41677--41853 Score: 157
Period size: 39 Copynumber: 4.6 Consensus size: 39
41667 TTAGAGATTC
*
41677 GTTTAATCAAACCTGCTTAGGTCCTTGTTTAGAACTTTT
1 GTTTAATCAAACCTGCTTAGGTCCTTGTCTAGAACTTTT
* * ***
41716 GTTTAATCAAATCTGTTTAGGTCCTTGTCTAGAACTCCC
1 GTTTAATCAAACCTGCTTAGGTCCTTGTCTAGAACTTTT
* * *
41755 G-TTAAGT-AAACCTGCTTAGGT-CTATGTTTAGAA-TCTC
1 GTTTAA-TCAAACCTGCTTAGGTCCT-TGTCTAGAACTTTT
* ** * *
41792 ATTTAAGGAAACCTGCTTAGGTCCTTGTTTAGAA-TTTCC
1 GTTTAATCAAACCTGCTTAGGTCCTTGTCTAGAACTTT-T
*
41831 GTTTAAGCAAACCTGCTTAGGTC
1 GTTTAATCAAACCTGCTTAGGTC
41854 TCTATTCCGC
Statistics
Matches: 117, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
37 5 0.04
38 53 0.45
39 59 0.50
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (39 bp):
GTTTAATCAAACCTGCTTAGGTCCTTGTCTAGAACTTTT
Found at i:44226 original size:18 final size:18
Alignment explanation
Indices: 44203--44260 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 18
44193 GGAGATACCA
*
44203 AAAAAAAGGAGTTCATAC
1 AAAAAAAGCAGTTCATAC
44221 -AAAAAA-CAGTTCATAC
1 AAAAAAAGCAGTTCATAC
* *
44237 CAAAAAAGCAGTTGATACC
1 AAAAAAAGCAGTTCATA-C
44256 AAAAA
1 AAAAA
44261 TTTCATACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 9 0.26
17 12 0.35
18 8 0.24
19 5 0.15
ACGTcount: A:0.57, C:0.16, G:0.12, T:0.16
Consensus pattern (18 bp):
AAAAAAAGCAGTTCATAC
Found at i:44231 original size:16 final size:16
Alignment explanation
Indices: 44212--44274 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
44202 AAAAAAAAGG
44212 AGTTCATACAAAAAAC
1 AGTTCATACAAAAAAC
44228 AGTTCATACCAAAAAAGC
1 AGTTCATA-CAAAAAA-C
* *
44246 AGTTGATAC-CAAAA-
1 AGTTCATACAAAAAAC
*
44260 ATTTCATACAAAAAA
1 AGTTCATACAAAAAA
44275 AAACAGTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 7 0.18
15 4 0.10
16 12 0.31
17 8 0.21
18 8 0.21
ACGTcount: A:0.54, C:0.17, G:0.08, T:0.21
Consensus pattern (16 bp):
AGTTCATACAAAAAAC
Found at i:44260 original size:34 final size:34
Alignment explanation
Indices: 44201--44295 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 34
44191 GGGGAGATAC
* *
44201 CAAAAAAAAGGAGTTCATACAAAAAACAGTTCATA
1 CAAAAAAAAGCAGTTCATACCAAAAA-AGTTCATA
* * *
44236 C-CAAAAAAGCAGTTGATACC-AAAAATTTCATA
1 CAAAAAAAAGCAGTTCATACCAAAAAAGTTCATA
* *
44268 CAAAAAAAAACAGTTCATACCCAAAAAG
1 CAAAAAAAAGCAGTTCATACCAAAAAAG
44296 AAGAGAGTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
32 8 0.16
33 20 0.41
34 20 0.41
35 1 0.02
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.17
Consensus pattern (34 bp):
CAAAAAAAAGCAGTTCATACCAAAAAAGTTCATA
Found at i:44293 original size:18 final size:17
Alignment explanation
Indices: 44212--44294 Score: 75
Period size: 18 Copynumber: 4.9 Consensus size: 17
44202 AAAAAAAAGG
44212 AGTTCATA-CAAAAAAC
1 AGTTCATACCAAAAAAC
44228 AGTTCATACCAAAAAAGC
1 AGTTCATACCAAAAAA-C
*
44246 AGTTGATACC--AAAA-
1 AGTTCATACCAAAAAAC
* *
44260 ATTTCATACAAAAAAAAAC
1 AGTTCATAC--CAAAAAAC
44279 AGTTCATACCCAAAAA
1 AGTTCATA-CCAAAAA
44295 GAAGAGAGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
14 7 0.13
16 12 0.23
17 7 0.13
18 19 0.36
19 7 0.13
20 1 0.02
ACGTcount: A:0.54, C:0.19, G:0.07, T:0.19
Consensus pattern (17 bp):
AGTTCATACCAAAAAAC
Found at i:45667 original size:2 final size:2
Alignment explanation
Indices: 45660--45702 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
45650 GTTAATATGC
*
45660 AT AT AT AT AT AT GT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45701 AT
1 AT
45703 TTGGGCTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59633 original size:19 final size:17
Alignment explanation
Indices: 59605--59644 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
59595 ATGACTCCTC
*
59605 TTCTTGTTGTTGATTTGAT
1 TTCTTCTTGTTG--TTGAT
59624 TTCTTCTTGTTGTTGAT
1 TTCTTCTTGTTGTTGAT
59641 TTCT
1 TTCT
59645 GGCTCTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.07, C:0.10, G:0.17, T:0.65
Consensus pattern (17 bp):
TTCTTCTTGTTGTTGAT
Found at i:59849 original size:34 final size:35
Alignment explanation
Indices: 59793--59858 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
59783 AAAGGAAAAT
* *
59793 ATTTTTTTTCTTTTCTTTGAAAACGCAAGAAACAAA
1 ATTTTTTTTCTCTTCTTAGAAAACGCAA-AAACAAA
59829 ATTTTTTTTC-CTT-TTAGAAAACGCAAAAAC
1 ATTTTTTTTCTCTTCTTAGAAAACGCAAAAAC
59859 TCTTTCTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 4 0.14
34 12 0.43
35 2 0.07
36 10 0.36
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (35 bp):
ATTTTTTTTCTCTTCTTAGAAAACGCAAAAACAAA
Found at i:64853 original size:22 final size:22
Alignment explanation
Indices: 64771--65166 Score: 135
Period size: 22 Copynumber: 18.1 Consensus size: 22
64761 CACACAATGC
* *
64771 AATTTCAATAACCTTC-CTGTGA
1 AATTTCGATAACC-TCACTATGA
*
64793 AATTTCGATAA-C-CACTATGG
1 AATTTCGATAACCTCACTATGA
* * *
64813 AATTTTGGT-A-CTCCCTATGA
1 AATTTCGATAACCTCACTATGA
64833 AATTTCGATAACCAT-ACTATGA
1 AATTTCGATAACC-TCACTATGA
* *
64855 AACTTT-GAT-AGCTCACTATAA
1 AA-TTTCGATAACCTCACTATGA
64876 AATTTCGATAACCTC-CGTATGA
1 AATTTCGATAACCTCAC-TATGA
* ** *
64898 AATTTTGATAATGTCCCTATGA
1 AATTTCGATAACCTCACTATGA
** *
64920 AATTTCGATAATTTTC-CTATTA
1 AATTTCGATAA-CCTCACTATGA
* * * *
64942 AACTAT-GATAATCTCTCTATTAA
1 AA-TTTCGATAACCTCACTA-TGA
* * *
64965 AAATTCGATAACCACAGTATGA
1 AATTTCGATAACCTCACTATGA
*
64987 AATATTTG-T-ACCTC-CTTATGAA
1 AAT-TTCGATAACCTCAC-TATG-A
* * *
65009 AATTT-TATAACCACACTATTA
1 AATTTCGATAACCTCACTATGA
* * * *
65030 AATTTTGGTAACCTCGCTAAGA
1 AATTTCGATAACCTCACTATGA
* * **
65052 AATTTTGATAACATTC-CTAAAAA
1 AATTTCGATAAC-CTCACT-ATGA
* * *
65075 AATTTTGAGAACAATC-CTATGA
1 AATTTCGATAAC-CTCACTATGA
* *
65097 AATTTTGATAACCTCCCTATGA
1 AATTTCGATAACCTCACTATGA
** * *
65119 AATTTTTAATAATCTCCCTATGA
1 AA-TTTCGATAACCTCACTATGA
*
65142 AATTTTC-ATAACCACACTATGA
1 AA-TTTCGATAACCTCACTATGA
65164 AAT
1 AAT
65167 AACCTCGCTA
Statistics
Matches: 289, Mismatches: 58, Indels: 55
0.72 0.14 0.14
Matches are distributed among these distances:
19 3 0.01
20 28 0.10
21 39 0.13
22 147 0.51
23 72 0.25
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
AATTTCGATAACCTCACTATGA
Found at i:64885 original size:21 final size:20
Alignment explanation
Indices: 64792--64888 Score: 63
Period size: 20 Copynumber: 4.7 Consensus size: 20
64782 CCTTCCTGTG
*
64792 AAATTTCGATAACCACTATG
1 AAATTTCGATAACCACTATA
* * * * *
64812 GAATTTTGGT-ACTCCCTATG
1 AAATTTCGATAAC-CACTATA
64832 AAATTTCGATAACCATACTATGA
1 AAATTTCGATAACC--ACTAT-A
* *
64855 AACTTT-GATAGCTCACTATA
1 AAATTTCGATAAC-CACTATA
64875 AAATTTCGATAACC
1 AAATTTCGATAACC
64889 TCCGTATGAA
Statistics
Matches: 57, Mismatches: 13, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
19 2 0.04
20 28 0.49
21 12 0.21
22 9 0.16
23 6 0.11
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (20 bp):
AAATTTCGATAACCACTATA
Found at i:64886 original size:43 final size:42
Alignment explanation
Indices: 64790--64930 Score: 171
Period size: 43 Copynumber: 3.3 Consensus size: 42
64780 AACCTTCCTG
* *
64790 TGAAATTTCGATAACC-ACTATGGAATTTTGGTA-CTCCCTA
1 TGAAATTTCGATAACCTACTATGAAATTTTGATAGCTCCCTA
* *
64830 TGAAATTTCGATAACCATACTATGAAACTTTGATAGCTCACTA
1 TGAAATTTCGATAACC-TACTATGAAATTTTGATAGCTCCCTA
* *
64873 TAAAATTTCGATAACCTCCGTATGAAATTTTGATAATG-TCCCTA
1 TGAAATTTCGATAACCTAC-TATGAAATTTTGAT-A-GCTCCCTA
64917 TGAAATTTCGATAA
1 TGAAATTTCGATAA
64931 TTTTCCTATT
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
40 16 0.19
42 16 0.19
43 34 0.40
44 19 0.22
45 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (42 bp):
TGAAATTTCGATAACCTACTATGAAATTTTGATAGCTCCCTA
Found at i:65139 original size:45 final size:44
Alignment explanation
Indices: 64790--65166 Score: 226
Period size: 45 Copynumber: 8.6 Consensus size: 44
64780 AACCTTCCTG
* *
64790 TGAAATTTCGATAA-C-CACTATGGAATTTTGGT-A-CTCCCTA
1 TGAAATTTCGATAACCTCACTATGAAATTTTGATAATCTCCCTA
* * *
64830 TGAAATTTCGATAACCAT-ACTATGAAACTTTGAT-AGCTCACTA
1 TGAAATTTCGATAACC-TCACTATGAAATTTTGATAATCTCCCTA
* *
64873 TAAAATTTCGATAACCTC-CGTATGAAATTTTGATAATGTCCCTA
1 TGAAATTTCGATAACCTCAC-TATGAAATTTTGATAATCTCCCTA
** * * * *
64917 TGAAATTTCGATAATTTTC-CTATTAAACTATGATAATCTCTCTA
1 TGAAATTTCGATAA-CCTCACTATGAAATTTTGATAATCTCCCTA
* * * * * *
64961 TTAAAAATTCGATAACCACAGTATGAAATATTTG-T-ACCTCCTTA
1 -TGAAATTTCGATAACCTCACTATGAAAT-TTTGATAATCTCCCTA
* * * * * *
65005 TGAAAATTT-TATAACCACACTATTAAATTTTGGTAACCTCGCTA
1 TG-AAATTTCGATAACCTCACTATGAAATTTTGATAATCTCCCTA
* * * ** *
65049 AGAAATTTTGATAACATTC-CTAAAAAAATTTTGAGAA-CAAT-CCTA
1 TGAAATTTCGATAAC-CTCACT-ATGAAATTTTGATAATC--TCCCTA
* * *
65094 TGAAATTTTGATAACCTCCCTATGAAATTTTTAATAATCTCCCTA
1 TGAAATTTCGATAACCTCACTATGAAA-TTTTGATAATCTCCCTA
*
65139 TGAAATTTTC-ATAACCACACTATGAAAT
1 TGAAA-TTTCGATAACCTCACTATGAAAT
65167 AACCTCGCTA
Statistics
Matches: 259, Mismatches: 54, Indels: 44
0.73 0.15 0.12
Matches are distributed among these distances:
40 14 0.05
41 1 0.00
42 20 0.08
43 58 0.22
44 74 0.29
45 84 0.32
46 8 0.03
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (44 bp):
TGAAATTTCGATAACCTCACTATGAAATTTTGATAATCTCCCTA
Found at i:65162 original size:67 final size:64
Alignment explanation
Indices: 64998--65166 Score: 160
Period size: 67 Copynumber: 2.5 Consensus size: 64
64988 ATATTTGTAC
* * * * *
64998 CTCCTTATGAAAATTTTATAACCACACTATTAAATTTTGGTAACCTCGCTAAGAAATTTTGATAA
1 CTCCCTATG-AAATTTTATAACCACACTATGAAATTTTGATAACCTCCCTAAGAAATTTTAATAA
* ** * * *
65063 CATTCCTAAAAAAATTTTGAGAACAATC-CTATGAAATTTTGATAACCTCCCTATGAAATTTTTA
1 C-TCCCT-ATGAAATTTT-ATAACCA-CACTATGAAATTTTGATAACCTCCCTAAGAAA-TTTTA
65127 ATAA
61 ATAA
65131 TCTCCCTATGAAATTTTCATAACCACACTATGAAAT
1 -CTCCCTATGAAATTTT-ATAACCACACTATGAAAT
65167 AACCTCGCTA
Statistics
Matches: 80, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
65 1 0.01
66 11 0.14
67 54 0.68
68 13 0.16
69 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (64 bp):
CTCCCTATGAAATTTTATAACCACACTATGAAATTTTGATAACCTCCCTAAGAAATTTTAATAA
Found at i:65257 original size:22 final size:23
Alignment explanation
Indices: 65179--65263 Score: 95
Period size: 22 Copynumber: 3.8 Consensus size: 23
65169 CCTCGCTATA
* *
65179 AAATCTTGTTAATC-ACAGTATG
1 AAATTTTGATAATCTACAGTATG
*
65201 AAATTTTGATAA-CTACACTATG
1 AAATTTTGATAATCTACAGTATG
* *
65223 AAAATTTGATAATCT-GAGTATG
1 AAATTTTGATAATCTACAGTATG
65245 AAATTTTGATAATCATACA
1 AAATTTTGATAATC-TACA
65264 AAGACAACAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 1 0.02
22 46 0.90
23 3 0.06
24 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAATCTACAGTATG
Found at i:71938 original size:40 final size:40
Alignment explanation
Indices: 71876--72193 Score: 307
Period size: 40 Copynumber: 7.7 Consensus size: 40
71866 AACATGACAA
*** *
71876 AAACAACACCTTCCGACAGGGAAGGG-AAAATTGGGAACTT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAA-TGGGAAATT
71916 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGGGAAATT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGGGAAATT
*
71956 AAACAACACCTTCCGGTGGGGAAGGGCAAAACGGGAAATAGGT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGGGAAAT---T
* * *
71999 AGACAACACCTTCCGGTGGGGAAGGGCAGAATAGGAAATT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGGGAAATT
* * * * * *
72039 AAACAATACCTTCTGGTGAGGAAGGGCAAAACAGGAAAAAGGT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAA-TGG-GAAA-TT
* * * *
72082 AGACAACACCTTCCGATAGGGAAGGGCAAAACTGGAAAATAGGT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAA-TGGGAAAT---T
* * * *
72126 AGACAACACCTTCGGGTGGGGAAGGGCAGAATTGG-AATT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGGGAAATT
* *
72165 TAATAACACCTTCCGGTGGGGAAGGGCAA
1 AAACAACACCTTCCGGTGGGGAAGGGCAA
72194 GACAGGAAAA
Statistics
Matches: 231, Mismatches: 37, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
39 25 0.11
40 96 0.42
41 5 0.02
42 10 0.04
43 67 0.29
44 28 0.12
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.15
Consensus pattern (40 bp):
AAACAACACCTTCCGGTGGGGAAGGGCAAAATGGGAAATT
Found at i:72036 original size:83 final size:84
Alignment explanation
Indices: 71918--72232 Score: 338
Period size: 83 Copynumber: 3.8 Consensus size: 84
71908 GGGAACTTAA
* *
71918 ACAACACCTTCCGGTGGGGAAGGGCAAAAT-GGGAAATTAAACAACACCTTCCGGTGGGGAAGGG
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATAGGAAAATTAAACAACACCTTCCGGTGAGGAAGGG
*
71982 CAAAACGGGAAATAGGTAG
66 CAAAACAGGAAATAGGTAG
* * *
72001 ACAACACCTTCCGGTGGGGAAGGGCAGAATAGG-AAATTAAACAATACCTTCTGGTGAGGAAGGG
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATAGGAAAATTAAACAACACCTTCCGGTGAGGAAGGG
*
72065 CAAAACAGGAAAAAGGTAG
66 CAAAACAGGAAATAGGTAG
* * * * *
72084 ACAACACCTTCCGATAGGGAAGGGCAAAACT-GGAAAATAGGTAGACAACACCTTCGGGTGGGGA
1 ACAACACCTTCCGGTGGGGAAGGGCAAAA-TAGGAAAAT---TAAACAACACCTTCCGGTGAGGA
* ** *
72148 AGGGCAGAATTGG-AAT--TTA-
62 AGGGCAAAACAGGAAATAGGTAG
* * * * *
72167 ATAACACCTTCCGGTGGGGAAGGGCAAGACAGGAAAAAGGTAGACAACACCTTCCGGTGAGGAAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATAGG-AAAA-TTAAACAACACCTTCCGGTGAGGAAG
72232 G
64 G
72233 CCAATTTTGG
Statistics
Matches: 197, Mismatches: 26, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
82 24 0.12
83 129 0.65
84 13 0.07
86 2 0.01
87 29 0.15
ACGTcount: A:0.37, C:0.17, G:0.31, T:0.14
Consensus pattern (84 bp):
ACAACACCTTCCGGTGGGGAAGGGCAAAATAGGAAAATTAAACAACACCTTCCGGTGAGGAAGGG
CAAAACAGGAAATAGGTAG
Found at i:72188 original size:126 final size:125
Alignment explanation
Indices: 71878--72222 Score: 455
Period size: 126 Copynumber: 2.8 Consensus size: 125
71868 CATGACAAAA
*** *
71878 ACAACACCTTCCGACAGGGAAGGG-AAAATTGGGAACTTAAACAACACCTTCCGGTGGGGAAGGG
1 ACAACACCTTCCGGTGGGGAAGGGCAGAATT-GGAA-TTAAACAACACCTTCCGGTGGGGAAGGG
* * * * * * *
71942 CAAAA-TGG-GAAA-TTAAACAACACCTTCCGGTGGGGAAGGGCAAAACGGGAAATAGGTAG
64 CAAAACAGGAAAAAGGTAGACAACACCTTCCGATAGGGAAGGGCAAAACGGAAAATAGGTAG
* * * *
72001 ACAACACCTTCCGGTGGGGAAGGGCAGAATAGGAAATTAAACAATACCTTCTGGTGAGGAAGGGC
1 ACAACACCTTCCGGTGGGGAAGGGCAGAATTGG-AATTAAACAACACCTTCCGGTGGGGAAGGGC
72066 AAAACAGGAAAAAGGTAGACAACACCTTCCGATAGGGAAGGGCAAAACTGGAAAATAGGTAG
65 AAAACAGGAAAAAGGTAGACAACACCTTCCGATAGGGAAGGGCAAAAC-GGAAAATAGGTAG
* * *
72128 ACAACACCTTCGGGTGGGGAAGGGCAGAATTGGAATTTAATAACACCTTCCGGTGGGGAAGGGCA
1 ACAACACCTTCCGGTGGGGAAGGGCAGAATTGGAATTAAACAACACCTTCCGGTGGGGAAGGGCA
*
72193 AGACAGGAAAAAGGTAGACAACACCTTCCG
66 AAACAGGAAAAAGGTAGACAACACCTTCCG
72223 GTGAGGAAGG
Statistics
Matches: 193, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
123 53 0.27
124 8 0.04
125 3 0.02
126 86 0.45
127 43 0.22
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.14
Consensus pattern (125 bp):
ACAACACCTTCCGGTGGGGAAGGGCAGAATTGGAATTAAACAACACCTTCCGGTGGGGAAGGGCA
AAACAGGAAAAAGGTAGACAACACCTTCCGATAGGGAAGGGCAAAACGGAAAATAGGTAG
Found at i:72245 original size:43 final size:43
Alignment explanation
Indices: 71918--72394 Score: 355
Period size: 43 Copynumber: 10.9 Consensus size: 43
71908 GGGAACTTAA
* * *
71918 ACAACACCTTCCGGTGGGGAAGGGCAAAA-TGG-GAAA-TTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATTGGAAAAAGGTAG
** *
71958 ACAACACCTTCCGGTGGGGAAGGGCAAAACGGGAAATAGGTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATTGGAAAAAGGTAG
* * * *
72001 ACAACACCTTCCGGTGGGGAAGGGCAGAATAGG--AAA-TTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATTGGAAAAAGGTAG
* * * **
72041 ACAATACCTTCTGGTGAGGAAGGGCAAAACAGGAAAAAGGTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATTGGAAAAAGGTAG
* * *
72084 ACAACACCTTCCGATAGGGAAGGGCAAAACTGGAAAATAGGTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATTGGAAAA-AGGTAG
* * **
72128 ACAACACCTTCGGGTGGGGAAGGGCAGAATTGG---AATTTA-
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATTGGAAAAAGGTAG
* * **
72167 ATAACACCTTCCGGTGGGGAAGGGCAAGACAGGAAAAAGGTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATTGGAAAAAGGTAG
* * **
72210 ACAACACCTTCCGGTGAGGAAGGCCAATTTTGGAAAAAGCAGACTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATTGGAAAAAG--G---TAG
* * ** *
72258 ACAACACCTTCCGATGAGGAAGGGCAATTTTGGAAAACGTAGATTTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATTGGAAAA---AG---GTAG
* *
72307 ACAACACCTTCCGATGGGGAAGGGC-AATTTGGGAAAAAGTAGACTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATT-GGAAAAAG--G---TAG
* * *
72355 ACAACACCTTCCGATGGGGAAGGGCAAACTAGGAAAAAGG
1 ACAACACCTTCCGGTGGGGAAGGGCAAAATTGGAAAAAGG
72395 CTAAAATTAA
Statistics
Matches: 355, Mismatches: 57, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
39 27 0.08
40 62 0.17
41 5 0.01
42 9 0.03
43 97 0.27
44 34 0.10
45 2 0.01
46 3 0.01
48 78 0.22
49 36 0.10
51 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.30, T:0.16
Consensus pattern (43 bp):
ACAACACCTTCCGGTGGGGAAGGGCAAAATTGGAAAAAGGTAG
Found at i:72328 original size:49 final size:48
Alignment explanation
Indices: 72207--72490 Score: 302
Period size: 48 Copynumber: 5.8 Consensus size: 48
72197 AGGAAAAAGG
* * *
72207 TAGACAACACCTTCCGGTGAGGAAGGCCAATTTTGGAAAAAGCAGACT
1 TAGACAACACCTTCCGATGAGGAAGGGCAATTTTGGAAAAAGTAGACT
* *
72255 TAGACAACACCTTCCGATGAGGAAGGGCAATTTTGGAAAACGTAGATTT
1 TAGACAACACCTTCCGATGAGGAAGGGCAATTTTGGAAAAAGTAGA-CT
* *
72304 TAGACAACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAAGTAGACT
1 TAGACAACACCTTCCGATGAGGAAGGGCAATTTTGGAAAAAGTAGACT
* ** * * *
72352 TAGACAACACCTTCCGATGGGGAAGGGCAAACTAGGAAAAAGGCTAAAAT
1 TAGACAACACCTTCCGATGAGGAAGGGCAATTTTGGAAAAA-G-TAGACT
* * * **
72402 TAAACAACACCTTTCGATGAGGAAGGGCAATTTTGGGAACAAG-ACGAAAA
1 TAGACAACACCTTCCGATGAGGAAGGGCAATTTT-GGAAAAAGTA-G-ACT
* *
72452 TAAACAACACCTTCCGACTG-GGAAGAGGCATTTTTGGAA
1 TAGACAACACCTTCCGA-TGAGGAAG-GGCAATTTTGGAA
72491 TAAAACTTAA
Statistics
Matches: 203, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
48 82 0.40
49 45 0.22
50 60 0.30
51 16 0.08
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.19
Consensus pattern (48 bp):
TAGACAACACCTTCCGATGAGGAAGGGCAATTTTGGAAAAAGTAGACT
Found at i:72390 original size:97 final size:94
Alignment explanation
Indices: 72169--72440 Score: 309
Period size: 97 Copynumber: 2.8 Consensus size: 94
72159 GGAATTTAAT
* * *
72169 AACACCTTCCGGTGGGGAAGGGCAAGAC-AGGAAAA--AG-GTAGACAACACCTTCCGGTGAGGA
1 AACACCTTCCGATGGGGAAGGGCAA-ACTAGGAAAAGTAGATTAGACAACACCTTCCGATGAGGA
* *
72230 AGGCCAATTTTGGAAAAAGCAGACTTAGAC
65 AGGGCAATTTGGGAAAAAGCAGACTTAGAC
* ** * *
72260 AACACCTTCCGATGAGGAAGGGCAATTTTGGAAAACGTAGATTTTAGACAACACCTTCCGATGGG
1 AACACCTTCCGATGGGGAAGGGCAAACTAGGAAAA-GTAGA--TTAGACAACACCTTCCGATGAG
*
72325 GAAGGGCAATTTGGGAAAAAGTAGACTTAGAC
63 GAAGGGCAATTTGGGAAAAAGCAGACTTAGAC
* * *
72357 AACACCTTCCGATGGGGAAGGGCAAACTAGGAAAAAGGCTAAAATTAAACAACACCTTTCGATGA
1 AACACCTTCCGATGGGGAAGGGCAAACTAGG-AAAA-G-T-AGATTAGACAACACCTTCCGATGA
72422 GGAAGGGCAATTTTGGGAA
62 GGAAGGGCAA-TTTGGGAA
72441 CAAGACGAAA
Statistics
Matches: 150, Mismatches: 20, Indels: 14
0.82 0.11 0.08
Matches are distributed among these distances:
91 29 0.19
94 2 0.01
97 75 0.50
98 33 0.22
99 9 0.06
100 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.18
Consensus pattern (94 bp):
AACACCTTCCGATGGGGAAGGGCAAACTAGGAAAAGTAGATTAGACAACACCTTCCGATGAGGAA
GGGCAATTTGGGAAAAAGCAGACTTAGAC
Found at i:73261 original size:50 final size:50
Alignment explanation
Indices: 73207--73301 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
73197 ACTATTAATT
* *
73207 AATCATAAA-TTCCATCGTTTAGTTCAAAGATC-CTATTTTTATTTCGCCTC
1 AATCAAAAAGTTCAATCGTTTA-TTCAAAGATCTC-ATTTTTATTTCGCCTC
* * *
73257 AATCAAAAAGTTTAATCTTTTATTCAAAGATTTCATTTTTATTTC
1 AATCAAAAAGTTCAATCGTTTATTCAAAGATCTCATTTTTATTTC
73302 ACATTTATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
50 28 0.74
51 10 0.26
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (50 bp):
AATCAAAAAGTTCAATCGTTTATTCAAAGATCTCATTTTTATTTCGCCTC
Found at i:73552 original size:151 final size:152
Alignment explanation
Indices: 73342--73973 Score: 864
Period size: 151 Copynumber: 4.2 Consensus size: 152
73332 AAGATTTCCT
* * * * * * *
73342 TTAAAAGTTCAATCCTTTTACTTAAAAATTCAATCTTTATTTATAAATTACTAAAAAGTTTCATC
1 TTAAAAGTTTAAT-CTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATC
* * * *
73407 TTTTAA-TCAAAATTCCAATCTCTATTCACAAATTACTTAAAAGCTTCAAT-TTTTCACTTAAAA
65 TTTTAACTCAAAATTCCAACCTTTATTTACAAATTACTTAAAAG-TTTAATATTTTCACTTAAAA
* *
73470 GTTCAACCTTTATTTACAAATTAC
129 ATCCAACCTTTATTTACAAATTAC
*
73494 CTAAAAGTTTAATCTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCT
1 TTAAAAGTTTAATCTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCT
* * *
73559 TTTAACTCAAAGA-TCCAACCTTTATTTACAAATCACTTAAAAGTTTAAT-CTTTCACTTAAACA
66 TTTAACTCAAA-ATTCCAACCTTTATTTACAAATTACTTAAAAGTTTAATATTTTCACTTAAAAA
* *
73622 TTCAACCTTTATTTATAAATTAC
130 TCCAACCTTTATTTACAAATTAC
*
73645 TTAAAAGTTTAATCTTTTAATCAAAAATCCAATATTTATTTACAAATTACTTAAAAGTTTAATCT
1 TTAAAAGTTTAATCTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCT
* *
73710 TTTAACTCAAAAATT-CAACCTTTATTTACAAATTACTTAAAAGTTTAATATTTT-AATAAAAAA
66 TTTAACTC-AAAATTCCAACCTTTATTTACAAATTACTTAAAAGTTTAATATTTTCACTTAAAAA
*
73773 TCCAATCTTTATTTACAAATTAC
130 TCCAACCTTTATTTACAAATTAC
* * *
73796 TTAAAAGTTTAATCTTTTAACTCAAAAATTCAACCTTTATTTATAAATTACTTAAAAGTTTAATC
1 TTAAAAGTTTAATCTTTTAA-TCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATC
* * * * *
73861 TTTTAA-TCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCTTTTAACTCAAAAA
65 TTTTAACTCAAAATTCCAACCTTTATTTACAAATTACTTAAAAGTTTAATATTTTCACTTAAAAA
* *
73925 TCCAACATTTATTTACAAATTGC
130 TCCAACCTTTATTTACAAATTAC
73948 TTAAAAGTTTAATCTTTTAACTCAAA
1 TTAAAAGTTTAATCTTTTAA-TCAAA
73974 GGTTTCATTT
Statistics
Matches: 433, Mismatches: 39, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
150 5 0.01
151 279 0.64
152 148 0.34
153 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (152 bp):
TTAAAAGTTTAATCTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCT
TTTAACTCAAAATTCCAACCTTTATTTACAAATTACTTAAAAGTTTAATATTTTCACTTAAAAAT
CCAACCTTTATTTACAAATTAC
Found at i:73662 original size:252 final size:252
Alignment explanation
Indices: 73342--73973 Score: 971
Period size: 252 Copynumber: 2.5 Consensus size: 252
73332 AAGATTTCCT
* * *
73342 TTAAAAGTTCAATCCTTTTACTTAAAAATTCAATCTTTATTTATAAATTACTAAAAAGTTTCATC
1 TTAAAAGTTTAAT-CTTTTACTTAAAAATTCAATCTTTATTTATAAATTACTTAAAAGTTTAATC
* * * * * *
73407 TTTTAATCAAAATTCCAATCTCTATTCACAAATTACTTAAAAGCTTCAAT-TTTTCACTTAAAAG
65 TTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAG-TTCAATCTTTTAACTCAAAAA
* *
73471 TTCAACCTTTATTTACAAATTACCTAAAAGTTTAATCTTTTAATCAAAAATCCAATCTTTATTTA
129 TTCAACCTTTATTTACAAATTACCTAAAAGTTTAATATTTTAATAAAAAATCCAATCTTTATTTA
*
73536 CAAATTACTTAAAAGTTTAATCTTTTAACTCAAAGATCCAACCTTTATTTACAAATCAC
194 CAAATTACTTAAAAGTTTAATCTTTTAACTCAAAAATCCAACCTTTATTTACAAATCAC
* * *
73595 TTAAAAGTTTAATCTTTCACTTAAACATTCAACCTTTATTTATAAATTACTTAAAAGTTTAATCT
1 TTAAAAGTTTAATCTTTTACTTAAAAATTCAATCTTTATTTATAAATTACTTAAAAGTTTAATCT
* *
73660 TTTAATCAAAAATCCAATATTTATTTACAAATTACTTAAAAGTTTAATCTTTTAACTCAAAAATT
66 TTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTCAATCTTTTAACTCAAAAATT
*
73725 CAACCTTTATTTACAAATTACTTAAAAGTTTAATATTTTAATAAAAAATCCAATCTTTATTTACA
131 CAACCTTTATTTACAAATTACCTAAAAGTTTAATATTTTAATAAAAAATCCAATCTTTATTTACA
* * *
73790 AATTACTTAAAAGTTTAATCTTTTAACTCAAAAATTCAACCTTTATTTATAAATTAC
196 AATTACTTAAAAGTTTAATCTTTTAACTCAAAAATCCAACCTTTATTTACAAATCAC
* * * *
73847 TTAAAAGTTTAATCTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCT
1 TTAAAAGTTTAATCTTTTACTTAAAAATTCAATCTTTATTTATAAATTACTTAAAAGTTTAATCT
* *
73912 TTTAACTCAAAAATCCAA-CATTTATTTACAAATTGCTTAAAAGTTTAATCTTTTAACTCAAA
66 TTTAA-TCAAAAATCCAATC-TTTATTTACAAATTACTTAAAAGTTCAATCTTTTAACTCAAA
73974 GGTTTCATTT
Statistics
Matches: 346, Mismatches: 30, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
251 5 0.01
252 276 0.80
253 65 0.19
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (252 bp):
TTAAAAGTTTAATCTTTTACTTAAAAATTCAATCTTTATTTATAAATTACTTAAAAGTTTAATCT
TTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTCAATCTTTTAACTCAAAAATT
CAACCTTTATTTACAAATTACCTAAAAGTTTAATATTTTAATAAAAAATCCAATCTTTATTTACA
AATTACTTAAAAGTTTAATCTTTTAACTCAAAAATCCAACCTTTATTTACAAATCAC
Found at i:74018 original size:101 final size:101
Alignment explanation
Indices: 73342--73973 Score: 878
Period size: 101 Copynumber: 6.2 Consensus size: 101
73332 AAGATTTCCT
* * * * * * *
73342 TTAAAAGTTCAATCCTTTTACTTAAAAATTCAATCTTTATTTATAAATTACTAAAAAGTTTCATC
1 TTAAAAGTTTAAT-CTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATC
* * *
73407 TTTTAA-TC-AAAATTCCAATCTCTATTCACAAATTAC
65 TTTTAACTCAAAAATT-CAACCTTTATTTACAAATTAC
* * * * * * *
73443 TTAAAAGCTTCAAT-TTTTCACTTAAAAGTTCAACCTTTATTTACAAATTACCTAAAAGTTTAAT
1 TTAAAAG-TTTAATCTTTT-AATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAAT
* *
73507 CTTTTAA-TCAAAAATCCAATCTTTATTTACAAATTAC
64 CTTTTAACTCAAAAATTCAACCTTTATTTACAAATTAC
* * *
73544 TTAAAAGTTTAATCTTTTAACTCAAAGATCCAACCTTTATTTACAAATCACTTAAAAGTTTAATC
1 TTAAAAGTTTAATCTTTTAA-TCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATC
* * * *
73609 -TTTCACTTAAACATTCAACCTTTATTTATAAATTAC
65 TTTTAACTCAAAAATTCAACCTTTATTTACAAATTAC
*
73645 TTAAAAGTTTAATCTTTTAATCAAAAATCCAATATTTATTTACAAATTACTTAAAAGTTTAATCT
1 TTAAAAGTTTAATCTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCT
73710 TTTAACTCAAAAATTCAACCTTTATTTACAAATTAC
66 TTTAACTCAAAAATTCAACCTTTATTTACAAATTAC
* *
73746 TTAAAAGTTTAATATTTTAATAAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCT
1 TTAAAAGTTTAATCTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCT
*
73811 TTTAACTCAAAAATTCAACCTTTATTTATAAATTAC
66 TTTAACTCAAAAATTCAACCTTTATTTACAAATTAC
73847 TTAAAAGTTTAATCTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCT
1 TTAAAAGTTTAATCTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCT
* * *
73912 TTTAACTCAAAAATCCAACATTTATTTACAAATTGC
66 TTTAACTCAAAAATTCAACCTTTATTTACAAATTAC
73948 TTAAAAGTTTAATCTTTTAACTCAAA
1 TTAAAAGTTTAATCTTTTAA-TCAAA
73974 GGTTTCATTT
Statistics
Matches: 482, Mismatches: 41, Indels: 15
0.90 0.08 0.03
Matches are distributed among these distances:
100 54 0.11
101 412 0.85
102 16 0.03
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (101 bp):
TTAAAAGTTTAATCTTTTAATCAAAAATCCAATCTTTATTTACAAATTACTTAAAAGTTTAATCT
TTTAACTCAAAAATTCAACCTTTATTTACAAATTAC
Found at i:74067 original size:51 final size:50
Alignment explanation
Indices: 73959--74092 Score: 180
Period size: 51 Copynumber: 2.7 Consensus size: 50
73949 TAAAAGTTTA
* * *
73959 ATCTTTTAAC-TCAAAGGTTTCATTTTTATCATAAATCAATAAAAAAATTC
1 ATCTTTTAACAT-AAAGATTACATTTTTATTATAAATCAATAAAAAAATTC
* * * *
74009 ATCTTTTAACATGAAGATTACATTTTCTATTATAAGTCAATTAAAAACTTC
1 ATCTTTTAACATAAAGATTACATTTT-TATTATAAATCAATAAAAAAATTC
74060 ATCTTTTAACATAAAGATTACATTTTTATTATA
1 ATCTTTTAACATAAAGATTACATTTTTATTATA
74093 CCCCACTTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
50 28 0.38
51 46 0.62
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (50 bp):
ATCTTTTAACATAAAGATTACATTTTTATTATAAATCAATAAAAAAATTC
Found at i:75258 original size:29 final size:30
Alignment explanation
Indices: 75226--75284 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
75216 AACTGACCAA
*
75226 TTTTATTAAT-TTTCAAAATCTTCTTTTGG
1 TTTTATTAATCTTCCAAAATCTTCTTTTGG
*
75255 TTTTATTTATCTTCCAAAATCTTCTTTTGG
1 TTTTATTAATCTTCCAAAATCTTCTTTTGG
75285 AATTACCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.22, C:0.14, G:0.07, T:0.58
Consensus pattern (30 bp):
TTTTATTAATCTTCCAAAATCTTCTTTTGG
Found at i:75310 original size:38 final size:38
Alignment explanation
Indices: 75260--75333 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
75250 TTTGGTTTTA
75260 TTTATCTTCCAAAATCTTCTTTTGGAATTACCTAAACT
1 TTTATCTTCCAAAATCTTCTTTTGGAATTACCTAAACT
* * *
75298 TTTATTTTCCAAAATCTTCTTTTGGAGTTACTTAAA
1 TTTATCTTCCAAAATCTTCTTTTGGAATTACCTAAA
75334 AAAAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (38 bp):
TTTATCTTCCAAAATCTTCTTTTGGAATTACCTAAACT
Found at i:78940 original size:27 final size:27
Alignment explanation
Indices: 78897--78970 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 27
78887 GAGTGTACTT
** *
78897 AAAATGACCAATGTGCCCCTAAATATG
1 AAAATGACCAAAATGCCCCTAAATATA
* * * *
78924 CAAATGACCAAAATG-CCCTTAGTGTA
1 AAAATGACCAAAATGCCCCTAAATATA
78950 AAAATGACCAAAATGCCCCTA
1 AAAATGACCAAAATGCCCCTA
78971 GGTGACCCTA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAATATA
Found at i:82729 original size:2 final size:2
Alignment explanation
Indices: 82724--82783 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
82714 ATCTGAAGGT
82724 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
82765 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
82784 ATAAAACACG
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:87102 original size:22 final size:21
Alignment explanation
Indices: 87050--87103 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
87040 TACTTCTTGA
87050 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
87071 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
87090 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
87104 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:89604 original size:21 final size:21
Alignment explanation
Indices: 89580--89669 Score: 153
Period size: 21 Copynumber: 4.3 Consensus size: 21
89570 CTTAGGCAAT
* *
89580 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
89601 TCCAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
89622 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
89643 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
89664 TCCAAT
1 TCCAAT
89670 TGCTACAAAC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Found at i:90518 original size:22 final size:22
Alignment explanation
Indices: 90493--90545 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
90483 TAATCTAACT
90493 AACAATTAA-AATCAACTAAAG-A
1 AACAATTAAGAA--AACTAAAGAA
* *
90515 AACAATCAAGAAAATTAAAGAA
1 AACAATTAAGAAAACTAAAGAA
90537 AACAATTAA
1 AACAATTAA
90546 CAAGATAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 7 0.27
22 17 0.65
23 2 0.08
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (22 bp):
AACAATTAAGAAAACTAAAGAA
Found at i:95252 original size:27 final size:27
Alignment explanation
Indices: 95214--95286 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
95204 TCAAGAATCT
95214 AGGGGCATTTTAGTCATTTGCACATTC
1 AGGGGCATTTTAGTCATTTGCACATTC
*
95241 AGGGGCATTTTAGTCATTTGCATATTC
1 AGGGGCATTTTAGTCATTTGCACATTC
*
95268 AGGGGCATTTTGGTCATTT
1 AGGGGCATTTTAGTCATTT
95287 TAAGTTCACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.40
Consensus pattern (27 bp):
AGGGGCATTTTAGTCATTTGCACATTC
Found at i:95466 original size:48 final size:48
Alignment explanation
Indices: 95395--95492 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
95385 ACATACTTCA
95395 TGGTTTAGCTTCATTCAGTAATTTAGTCTAGTTTTCAATTGACATCTT
1 TGGTTTAGCTTCATTCAGTAATTTAGTCTAGTTTTCAATTGACATCTT
95443 TGGTTTAGCTTCATTCAGTAATTTAGTCTAGTTTTCAATTGACATCTT
1 TGGTTTAGCTTCATTCAGTAATTTAGTCTAGTTTTCAATTGACATCTT
95491 TG
1 TG
95493 TGTTCATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.48
Consensus pattern (48 bp):
TGGTTTAGCTTCATTCAGTAATTTAGTCTAGTTTTCAATTGACATCTT
Found at i:95583 original size:13 final size:13
Alignment explanation
Indices: 95565--95590 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
95555 ATGGTCTTTT
95565 TATTCTCATTAAG
1 TATTCTCATTAAG
95578 TATTCTCATTAAG
1 TATTCTCATTAAG
95591 CATGATCATC
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:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TATTCTCATTAAG
Found at i:98063 original size:40 final size:41
Alignment explanation
Indices: 97985--98069 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 41
97975 GATCAATATG
*
97985 GTCCCTAATTTAGGATTCTATTTACTATTCGATACAATTTA
1 GTCCCTAATTTAGGATTCTATGTACTATTCGATACAATTTA
* * * *
98026 GTCCCTGATTTAGGATTCTA-GTACTATTTGATTCAATTTG
1 GTCCCTAATTTAGGATTCTATGTACTATTCGATACAATTTA
98066 GTCC
1 GTCC
98070 TTCTTTTTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 20 0.51
41 19 0.49
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (41 bp):
GTCCCTAATTTAGGATTCTATGTACTATTCGATACAATTTA
Found at i:101853 original size:30 final size:30
Alignment explanation
Indices: 101796--101870 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
101786 TACCCAAAAA
*
101796 AATCCCTTATGTTTTACTTTTGGGACAAGA-T
1 AATCCCTTATGTTTTA-TTTCGGGACAA-ATT
101827 AATCCCTTATGTTCTT-TTTCGGGACAAATT
1 AATCCCTTATGTT-TTATTTCGGGACAAATT
*
101857 AATCCCTTACGTTT
1 AATCCCTTATGTTT
101871 CAAAAATGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
29 2 0.05
30 23 0.57
31 13 0.32
32 2 0.05
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (30 bp):
AATCCCTTATGTTTTATTTCGGGACAAATT
Found at i:102047 original size:30 final size:31
Alignment explanation
Indices: 102003--102076 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
101993 CCACGTCAGC
* *
102003 AAGGGACTAATTTGTCCC-ATAA-AAAAACAT
1 AAGGGATTATTTTGTCCCGA-AAGAAAAACAT
102033 AAGGGATTATTTTGTCCCGAAAGAAAAACAT
1 AAGGGATTATTTTGTCCCGAAAGAAAAACAT
*
102064 AAGGGATTTTTTT
1 AAGGGATTATTTT
102077 TATATTTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 18 0.46
31 21 0.54
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.30
Consensus pattern (31 bp):
AAGGGATTATTTTGTCCCGAAAGAAAAACAT
Found at i:103115 original size:144 final size:144
Alignment explanation
Indices: 102936--103199 Score: 361
Period size: 144 Copynumber: 1.8 Consensus size: 144
102926 TCTTACCCTT
* ** **
102936 ATTTTTCAATTATATATCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTCAATTAAAAACT
1 ATTTTTCAAATATATATCTTAAATAACATTGTTTAAACTTTTACAATTTTACTCAACCAAAAACT
*
103001 CTATTTTTATTTAATCAAA-TCTAATATATTTACAACTATTTTATTTTTACCATTTTACTATTTT
66 CTATTTTTATTTAATCAAATTC-AATAT-TTTACAACTATTTTATCTTTACCATTTTACTATTTT
103065 AATTATATATATTAGA
129 AATTATATATATTAGA
* * * * ** *
103081 ATTTTT-AAATATATTTCTTAAATAACATTTTTTAAACTTTTACAGTTTTATTTTACCAAAAATT
1 ATTTTTCAAATATATATCTTAAATAACATTGTTTAAACTTTTACAATTTTACTCAACCAAAAACT
* *
103145 CTATTTTTATTTAATTAAATTCAATATTTTATAACTATTTTATCTTTACCATTTT
66 CTATTTTTATTTAATCAAATTCAATATTTTACAACTATTTTATCTTTACCATTTT
103200 TTAGAGAATT
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
143 26 0.25
144 69 0.67
145 8 0.08
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (144 bp):
ATTTTTCAAATATATATCTTAAATAACATTGTTTAAACTTTTACAATTTTACTCAACCAAAAACT
CTATTTTTATTTAATCAAATTCAATATTTTACAACTATTTTATCTTTACCATTTTACTATTTTAA
TTATATATATTAGA
Found at i:103423 original size:28 final size:30
Alignment explanation
Indices: 103352--103413 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
103342 ACTAAATACT
103352 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATG-TTTTCTTTTGGGAC
103383 AAAAAAATCCCTTATG-TTT-TTTTGGGAC
1 AAAAAAATCCCTTATGTTTTCTTTTGGGAC
103411 AAA
1 AAA
103414 TTAGTCCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 12 0.39
29 3 0.10
31 16 0.52
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (30 bp):
AAAAAAATCCCTTATGTTTTCTTTTGGGAC
Found at i:103598 original size:32 final size:31
Alignment explanation
Indices: 103557--103633 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 31
103547 CTCATTTTTG
103557 AAACATAAGGGATTAATTTGTCCCGAAAAAAA
1 AAACATAAGGGATTAATTTGTCCC-AAAAAAA
** **
103589 AAACATAAGGGATTCTTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAAAAA
*
103620 AAACATAAAGGATT
1 AAACATAAGGGATT
103634 TTTTTGGGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 18 0.45
32 22 0.55
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (31 bp):
AAACATAAGGGATTAATTTGTCCCAAAAAAA
Found at i:103626 original size:31 final size:32
Alignment explanation
Indices: 103557--103639 Score: 105
Period size: 31 Copynumber: 2.6 Consensus size: 32
103547 CTCATTTTTG
*
103557 AAACATAAGGGATTAATTTGTCCCGAAAAAAA
1 AAACATAAGGGATTATTTTGTCCCGAAAAAAA
* **
103589 AAACATAAGGGATTCTTTTGTCCC-AAAAGCA
1 AAACATAAGGGATTATTTTGTCCCGAAAAAAA
* *
103620 AAACATAAAGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
103640 GGGTATTTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
31 23 0.51
32 22 0.49
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (32 bp):
AAACATAAGGGATTATTTTGTCCCGAAAAAAA
Found at i:105739 original size:123 final size:121
Alignment explanation
Indices: 105516--105760 Score: 454
Period size: 123 Copynumber: 2.0 Consensus size: 121
105506 GATAATTATA
105516 AGAAACAATAATAAGAGGATTTGAAATTACCAAAAAACCAATCCAACCTTAACGTCTCATGATTT
1 AGAAACAATAATAAGAGGATTTGAAATTACCAAAAAACCAATCCAACCTTAACGTCTCATGATTT
*
105581 GGAGAACAAATGAGGAGGGGTATTTTGGTATTTTCATGCTCGGTTTTTCCGTTATTTG
66 GGAGAACAAATGAGGAGGGGTATTTTGGTACTTTCATGCTC-G-TTTTCCGTTATTTG
*
105639 AGAAACAATAATAAGAGGATTTGAAATTACCAAAAAACCAATCCAACCTTAACTTCTCATGATTT
1 AGAAACAATAATAAGAGGATTTGAAATTACCAAAAAACCAATCCAACCTTAACGTCTCATGATTT
105704 GGAGAACAAATGAGGAGGGGTATTTTGGTACTTTCATGCTCGTTTTCCGTTATTTG
66 GGAGAACAAATGAGGAGGGGTATTTTGGTACTTTCATGCTCGTTTTCCGTTATTTG
105760 A
1 A
105761 ATTGATAATT
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
121 15 0.12
122 1 0.01
123 104 0.87
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (121 bp):
AGAAACAATAATAAGAGGATTTGAAATTACCAAAAAACCAATCCAACCTTAACGTCTCATGATTT
GGAGAACAAATGAGGAGGGGTATTTTGGTACTTTCATGCTCGTTTTCCGTTATTTG
Found at i:106699 original size:432 final size:435
Alignment explanation
Indices: 105965--106892 Score: 1093
Period size: 433 Copynumber: 2.1 Consensus size: 435
105955 TATTTGTCCA
*
105965 ATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAATTTTCATGAAGAACTCA
1 ATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGAACTC-
* * * * *
106030 AAAGCCAATTTTAATGTTTTGATTCTAAAAAATGCTTCCGGAATTTTGTGGTTTTGATGGCCGGT
65 AAAGCCAATTTTAATGTTTTAATTCAAAAAAATGCTTCCGAAATTTGGTCGTTTTGATGGCCGGT
* * * * * * *
106095 CAATTTAATATCGTATAATCTTTTGTCCACATATCCGATTGAGGTTATTGAAGTGTCGGTTAAAA
130 CAATTTAATACCATATAATCTTTCGTCCACATATCCAATTAAAGTTATTCAAGTGTCGGTTAAAA
* * * * * *
106160 GGTTATTGCATGATTTACGACTTTCTTGAAGGACCCGAAAGCTAAATTTGATCTACGAGTTTCAT
195 GGTTACTGCATGATCTACAACTTTCATGAAGAACCCGAAAGCTAAATTTGAGCTACGAGTTTCAT
* * * * *
106225 GAAGGGCTCAAAAGGGAGTTTTTATGCTTCAAGATCTCCATTAACAAACATTTTCTTATTTGGAT
260 GAAGGGCTCAAAAGGGAATTTTTATGCTTCAAGATATCCATTAACAAACAATTTATTATTTGAAT
* *
106290 TATTTATCAAATAACCCTCATATTTTTCTACTTTATACTACTTAGTTCTTTACAAATTCTATTTT
325 TAGTTATCAAATAACCCTCATACTTTTCTACTTTATACTACTTAGTTCTTTACAAATTCTATTTT
106355 CATCTGACGTTTAAGATTTATTTTTTTATTCATTGTTTATTGTCTG
390 CATCTGACGTTTAAGATTTATTTTTTTATTCATTGTTTATTGTCTG
* * * * * *
106401 ATTAAGTTGATTCATGTGTCTATTAAAATGTTATTTTATGATCTACAACTTTCATGAAGGACTC-
1 ATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGAACTCA
* * * **
106465 AAG-CAATTTTTTATGTTTTAATTCAAAAAAAT-CTTCCTAAATTTGGTCGTTTTGATTGTTGGT
66 AAGCCAA-TTTTAATGTTTTAATTCAAAAAAATGCTTCCGAAATTTGGTCGTTTTGATGGCCGGT
* * *
106528 CTATTTAATACCATATAGT-TTTCGATCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAA
130 CAATTTAATACCATATAATCTTTCG-TCCACATATCCAATTAAAGTTATTCAAGTGTCGGTTAAA
* * *
106592 AGGTTACTGTATGATCTATAACTTTCATGAAGAACCCGAAAG-TTAATTTGAGCTACGAGTTTCA
194 AGGTTACTGCATGATCTACAACTTTCATGAAGAACCCGAAAGCTAAATTTGAGCTACGAGTTTCA
* * * *
106656 TGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATATCCATTAAGAAATAATTTATTATTTGAA
259 TGAAGGGCTCAAAAGGGAATTTTTATGCTTCAAGATATCCATTAACAAACAATTTATTATTTGAA
* *
106721 TTAGTTATCAAATGACCCTCATACTTTTCTATTTTATATATTTTATGCTACTTAGTTCTTTACAA
324 TTAGTTATCAAATAACCCTCATACTTTTCTA--CT-T-TA---TA--CTACTTAGTTCTTTACAA
* * * * **
106786 ATTCTATCTT-A-CT--CGATTTAACGCTTCATTTTTTATTTTC-TCTGTTCTATTTGTCCA
380 ATTCTATTTTCATCTGACG-TTTAA-GATTTATTTTTT-TATTCAT-TGTT-TA-TTGTCTG
* ** *
106843 ATTAAGGTAATTCAAGTGTCTATTAAAAAATAATTTTATGATCTACAACT
1 ATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACT
106893 CTTTTATAAA
Statistics
Matches: 414, Mismatches: 61, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
432 108 0.26
433 111 0.27
434 26 0.06
435 1 0.00
436 59 0.14
437 2 0.00
438 5 0.01
439 15 0.04
440 9 0.02
441 29 0.07
442 49 0.12
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (435 bp):
ATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGAACTCA
AAGCCAATTTTAATGTTTTAATTCAAAAAAATGCTTCCGAAATTTGGTCGTTTTGATGGCCGGTC
AATTTAATACCATATAATCTTTCGTCCACATATCCAATTAAAGTTATTCAAGTGTCGGTTAAAAG
GTTACTGCATGATCTACAACTTTCATGAAGAACCCGAAAGCTAAATTTGAGCTACGAGTTTCATG
AAGGGCTCAAAAGGGAATTTTTATGCTTCAAGATATCCATTAACAAACAATTTATTATTTGAATT
AGTTATCAAATAACCCTCATACTTTTCTACTTTATACTACTTAGTTCTTTACAAATTCTATTTTC
ATCTGACGTTTAAGATTTATTTTTTTATTCATTGTTTATTGTCTG
Found at i:112498 original size:2 final size:2
Alignment explanation
Indices: 112491--112523 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
112481 CTCACAAATA
112491 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
112524 ATTACCAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:115526 original size:485 final size:478
Alignment explanation
Indices: 114374--115536 Score: 1557
Period size: 479 Copynumber: 2.4 Consensus size: 478
114364 TCACATTCCC
*
114374 AAATAATAATTGGCTCTTCACTGGTGCCCCTAGTGCACCCGTTAGCCAAACCATTTGTCTAATTG
1 AAATAATAATTGGCTCTTCACGGGTGCCCCTAGTGCACCCGTTAGCCAAACCATTTGTCTAATTG
* * * *
114439 TGATACGCTTTGGTCGAATTAATAACTTCACATGTGG-------A-ATTAATATATCTAAATTAA
66 TAATAAGTTTTGGTGGAATTAATAACTTCACATGTGGAATTAATATATTAATATATCTAAATTAA
*
114496 AATATTAATTATTCAAATTGAGATGATGATGACTGTAGAAATTGATTGATATTGGGAATGTAGTA
131 AATATTAATTATTCCAATTGAGATGATGATGAC-GTAGAAATTGATTGATATTGGGAATGTAGTA
* * *
114561 TTGTACGTTGAAGTTTTAAAAAAGAATTAAAAATAATAATGATTCAGGTCAAATTCGGATTAGTC
195 TTGTACGTTGAAATTCTAAAAAAGAATTAAAAATAATAATGATTCAGGTCAAACTCGGATTAGTC
** *
114626 AAAGCTTTCAATAATAATATTTGGGGCTAAATTCTAATAAATGATGGTTAACTTTTACTAATTTC
260 AAAGCTTTCAATAATAATATTTGGGGCTAAATTCTAATAAATGATGGTTAACTAATACTAATTTA
* * * * *
114691 TTTTATTTAATTTCTAAAATCCTATAACACATTAGGTTTAAATTTTAATATTCACATTTAAAATC
325 TTTAATTCAATTTCTAAAATCCTATAACACATTAGGTTTAAATTTTAAGATTCACACTTAAAATA
* * * *
114756 AATAAATATTATAATTCAATAATTATTACAGGGGCATTATTGTCTTACAACAATTGGGAGACTTA
390 AATAAATATTATAATTCAATAATAATTACACGGG-ATTATTGTCTTACAACAATTAGGAGACATA
114821 CTCTGTGCTTTTAGCACAAACTCCA
454 CTCTGTGCTTTTAGCACAAACTCCA
* * *
114846 AAATAATAATTGGCTCATCACGGGTG-CCCTAG-GAAACCCGTTAGCCAAACCATTTGTTTAATT
1 AAATAATAATTGGCTCTTCACGGGTGCCCCTAGTG-CACCCGTTAGCCAAACCATTTGTCTAATT
** * * ** * * * * *
114909 GCCATATGTGTTGCCGTAATTAATAACTTCACTTATGAAATTAATATATTAATTTATCTAAATTA
65 GTAATAAGTTTTGGTGGAATTAATAACTTCACATGTGGAATTAATATATTAATATATCTAAATTA
*
114974 AAATATTAATTATTCCAATTGAGATGATGATGATCGTAGAAATTGATAGATATTGGGAATGTAGT
130 AAATATTAATTATTCCAATTGAGATGATGATGA-CGTAGAAATTGATTGATATTGGGAATGTAGT
*
115039 ATTATACGTTGAAATTCTAAAAAAGAATTAAAAATAATAATGATTCAGGTCAAACTCGGATTAGT
194 ATTGTACGTTGAAATTCTAAAAAAGAATTAAAAATAATAATGATTCAGGTCAAACTCGGATTAGT
* * * * * *
115104 CAGAGCTTTCAATAATGATA-TTGAGGGCTAAATTCTATTAAATTATGGTTAGCTAATATTAATT
259 CAAAGCTTTCAATAATAATATTTG-GGGCTAAATTCTAATAAATGATGGTTAACTAATACTAATT
* * *
115168 TATTTAATTCAATTTCTAAAATCCTATAACA-A-TATGTTTAAATTTTAAGATTTACCCTTAAAA
323 TATTTAATTCAATTTCTAAAATCCTATAACACATTAGGTTTAAATTTTAAGATTCACACTTAAAA
* *
115231 TAAATAAATATTGTAATTCAAGGCTAAACAATAATTATTACGGG-TGTATTGTCTTACAACAATT
388 TAAATAAATATTATAATTCAA---T----AATAATTA-CACGGGAT-TATTGTCTTACAACAATT
* *
115295 AGGAGACATATTTTGTGCTTTTAGCACAAACTCCA
444 AGGAGACATACTCTGTGCTTTTAGCACAAACTCCA
* * **
115330 AAATAATAATTGGCTCTTAACGGGTGCCCCT-GTTGCACCCGTTAGCAAAACTGTTTGTCTAATA
1 AAATAATAATTGGCTCTTCACGGGTGCCCCTAG-TGCACCCGTTAGCCAAACCATTTGTCTAAT-
115394 T-TAATAAGTTTTGGTGGAATTAATAACTTCACATGTGGAATTAATATATTAATATATCTAAATT
64 TGTAATAAGTTTTGGTGGAATTAATAACTTCACATGTGGAATTAATATATTAATATATCTAAATT
* *
115458 AAAATATAAATTATTCCAATTGAGATGATGATGACAGTAGAAATTGATTGATATTGGGAATATAG
129 AAAATATTAATTATTCCAATTGAGATGATGATGAC-GTAGAAATTGATTGATATTGGGAATGTAG
115523 TATTGTACGTTGAA
193 TATTGTACGTTGAA
115537 TAATGATGTT
Statistics
Matches: 596, Mismatches: 70, Indels: 37
0.85 0.10 0.05
Matches are distributed among these distances:
470 1 0.00
471 59 0.10
472 24 0.04
477 45 0.08
478 5 0.01
479 219 0.37
480 2 0.00
483 1 0.00
484 82 0.14
485 156 0.26
486 2 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (478 bp):
AAATAATAATTGGCTCTTCACGGGTGCCCCTAGTGCACCCGTTAGCCAAACCATTTGTCTAATTG
TAATAAGTTTTGGTGGAATTAATAACTTCACATGTGGAATTAATATATTAATATATCTAAATTAA
AATATTAATTATTCCAATTGAGATGATGATGACGTAGAAATTGATTGATATTGGGAATGTAGTAT
TGTACGTTGAAATTCTAAAAAAGAATTAAAAATAATAATGATTCAGGTCAAACTCGGATTAGTCA
AAGCTTTCAATAATAATATTTGGGGCTAAATTCTAATAAATGATGGTTAACTAATACTAATTTAT
TTAATTCAATTTCTAAAATCCTATAACACATTAGGTTTAAATTTTAAGATTCACACTTAAAATAA
ATAAATATTATAATTCAATAATAATTACACGGGATTATTGTCTTACAACAATTAGGAGACATACT
CTGTGCTTTTAGCACAAACTCCA
Found at i:116804 original size:21 final size:21
Alignment explanation
Indices: 116757--116804 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
116747 TGTGATAAGC
*
116757 TTTAGTGGAATTAATAATTTCA
1 TTTA-TGGAATTAATAATTTAA
*
116779 CTTATGGAATTAAT-ATATTAA
1 TTTATGGAATTAATAAT-TTAA
116800 TTTAT
1 TTTAT
116805 CTAAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.09
21 17 0.77
22 3 0.14
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (21 bp):
TTTATGGAATTAATAATTTAA
Found at i:117264 original size:21 final size:21
Alignment explanation
Indices: 117223--117264 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
117213 AAGCTCTGGC
* *
117223 GAAATTAATAACTTCACTTAT
1 GAAATTAATAACTTAAATTAT
117244 GAAATTAATATA-TTAAATTAT
1 GAAATTAATA-ACTTAAATTAT
117265 CTAACTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (21 bp):
GAAATTAATAACTTAAATTAT
Found at i:117540 original size:468 final size:469
Alignment explanation
Indices: 116938--117837 Score: 1276
Period size: 469 Copynumber: 1.9 Consensus size: 469
116928 AATGATATTT
* * *
116938 GGGGCTAAATTCTATTAAATGATGGTTAACTTTTACTAATTTCTTTTATTTAATTTCTAAAATCC
1 GGGGCTAAATTCTATAAAATGATGGTTAACTTGTACTAATTTATTTTATTTAATTTCTAAAATCC
* *
117003 TATAACAATAGGTTTAAAATTTTAAGATTTACCCTTATAATCAATAAATATTATAATTTAAGGCT
66 TATAACAATAGGTTTAAAATTTTAAGATTTACCCTTAAAATCAATAAATATTATAATTCAAGGCT
* ** *
117068 AAACAATAATTATTAC-AGGAGCATTATTGTCTAACAATAATTAGGAGACATACTCTGTGTTTTT
131 AAACAATAATTATTACAAGG-GCATTATTGTCTAACAACAATTAGGAGACATACTCTACGCTTTT
* * * *
117132 AGCAGAAACTCCAAAATAATAATTGCCTCATCATGGGTGCCCCTAG-GAATCCCGTTAGCCAAAC
195 AGCACAAACTCCAAAATAATAATTGCCTCATCACGGGTGCCACTAGTGAA-CCCGTTAGACAAAC
*
117196 CGTTTGAT-TAA-TGTGATAAGCTCTGGCGAAATTAATAACTTCACT-TATGAAATTAATATATT
259 CGTTTG-TCTAATTGTGATAAGCTCTGGCGAAATTAATAACTTCA-TATATGAAATTAATATACT
* * * *
117258 AA-ATTATCTAACTTAAAATACT-AACTATTCTAATTGAGATGATGATGATCGTAGAAATTTATT
322 AATA-TATCTAAATTAAAATA-TAAACTATTCCAATTGAGATGATGATGACCGTAGAAATTGATT
117321 GACATTGGAAATATAGTATTGTACATTGAAGTTCTAAAAAAGAATTAAAAATAATAATATGATTC
385 GACATTGGAAATATAGTATTGTACATTGAAGTTCTAAAAAAGAATTAAAAATAATAATATGATTC
117386 AGGACAAATTCGGATTACTA
450 AGGACAAATTCGGATTACTA
* * * *
117406 GGGGCTAAATTCTATAAAAATTATGGTTAACTTGTATTAATTTATTTTATTTTATTTCTAATATC
1 GGGGCTAAATTCTAT-AAAATGATGGTTAACTTGTACTAATTTATTTTATTTAATTTCTAAAATC
* *
117471 CTATAACAATATGTTT-AAATTTTAAGATTTACCGTTAAAATCAATAAATATTATAATTCAAGGC
65 CTATAACAATAGGTTTAAAATTTTAAGATTTACCCTTAAAATCAATAAATATTATAATTCAAGGC
* * *
117535 TAAACAATAATTATTACAAGGGTATTATTGTCTTACAACAATTAGGAGACATACTTTACGCTTTT
130 TAAACAATAATTATTACAAGGGCATTATTGTCTAACAACAATTAGGAGACATACTCTACGCTTTT
* * * * * *
117600 AGCACAAATTCCCAAATAATAATTGGCTCTTCACGGGTGCCACTGGTGCACCCGTTAGACAAACC
195 AGCACAAACTCCAAAATAATAATTGCCTCATCACGGGTGCCACTAGTGAACCCGTTAGACAAACC
* * * * * *
117665 GTTTGTCTAATTGTGATAAGTTTTGGTGGAATTAATAACTTCATATGTGGAATTAATATACTAAT
260 GTTTGTCTAATTGTGATAAGCTCTGGCGAAATTAATAACTTCATATATGAAATTAATATACTAAT
* *
117730 ATATCTAAATTAAAATATAAATTATTCCAATTGAGATGATGATGACCGTAGAAATTGATTGATAT
325 ATATCTAAATTAAAATATAAACTATTCCAATTGAGATGATGATGACCGTAGAAATTGATTGACAT
* * * *
117795 TGGGAATGTAGTATTGTACGTTGAAGTTCTAAAAAATAATTAA
390 TGGAAATATAGTATTGTACATTGAAGTTCTAAAAAAGAATTAA
117838 T
Statistics
Matches: 379, Mismatches: 45, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
467 1 0.00
468 176 0.46
469 201 0.53
470 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (469 bp):
GGGGCTAAATTCTATAAAATGATGGTTAACTTGTACTAATTTATTTTATTTAATTTCTAAAATCC
TATAACAATAGGTTTAAAATTTTAAGATTTACCCTTAAAATCAATAAATATTATAATTCAAGGCT
AAACAATAATTATTACAAGGGCATTATTGTCTAACAACAATTAGGAGACATACTCTACGCTTTTA
GCACAAACTCCAAAATAATAATTGCCTCATCACGGGTGCCACTAGTGAACCCGTTAGACAAACCG
TTTGTCTAATTGTGATAAGCTCTGGCGAAATTAATAACTTCATATATGAAATTAATATACTAATA
TATCTAAATTAAAATATAAACTATTCCAATTGAGATGATGATGACCGTAGAAATTGATTGACATT
GGAAATATAGTATTGTACATTGAAGTTCTAAAAAAGAATTAAAAATAATAATATGATTCAGGACA
AATTCGGATTACTA
Found at i:117731 original size:21 final size:21
Alignment explanation
Indices: 117690--117731 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
117680 ATAAGTTTTG
*
117690 GTGGAATTAATAACTTCATAT
1 GTGGAATTAATAACTTAATAT
117711 GTGGAATTAATATAC-TAATAT
1 GTGGAATTAATA-ACTTAATAT
117732 ATCTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (21 bp):
GTGGAATTAATAACTTAATAT
Done.