Multiple sequence alignment - TraesCS4D01G053400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G053400 chr4D 100.000 6220 0 0 1 6220 29404853 29411072 0.000000e+00 11487.0
1 TraesCS4D01G053400 chr4D 90.641 2810 150 47 418 3148 5680502 5677727 0.000000e+00 3627.0
2 TraesCS4D01G053400 chr4D 94.056 1531 71 11 3233 4752 5677725 5676204 0.000000e+00 2305.0
3 TraesCS4D01G053400 chr4D 90.644 1165 53 20 4869 5993 5676211 5675063 0.000000e+00 1496.0
4 TraesCS4D01G053400 chr4D 92.920 226 16 0 1 226 426774705 426774930 4.650000e-86 329.0
5 TraesCS4D01G053400 chr4A 99.068 5792 39 7 443 6220 573670100 573664310 0.000000e+00 10382.0
6 TraesCS4D01G053400 chr4A 91.172 2832 135 50 3230 5993 597843546 597846330 0.000000e+00 3738.0
7 TraesCS4D01G053400 chr4A 89.939 2773 159 50 445 3148 597840826 597843547 0.000000e+00 3465.0
8 TraesCS4D01G053400 chr4A 97.137 454 13 0 1 454 573683846 573683393 0.000000e+00 767.0
9 TraesCS4D01G053400 chr6B 92.458 2824 125 32 3233 5993 625889120 625886322 0.000000e+00 3954.0
10 TraesCS4D01G053400 chr6B 90.548 2444 139 35 755 3148 625891523 625889122 0.000000e+00 3149.0
11 TraesCS4D01G053400 chr4B 97.953 1661 15 3 2287 3934 41837156 41838810 0.000000e+00 2861.0
12 TraesCS4D01G053400 chr4B 98.951 1335 10 2 4887 6220 41841134 41842465 0.000000e+00 2385.0
13 TraesCS4D01G053400 chr4B 98.611 864 5 4 3917 4773 41840248 41841111 0.000000e+00 1522.0
14 TraesCS4D01G053400 chr4B 94.474 380 4 1 835 1214 41836623 41836985 2.520000e-158 569.0
15 TraesCS4D01G053400 chr4B 98.895 181 2 0 2072 2252 41836981 41837161 2.160000e-84 324.0
16 TraesCS4D01G053400 chr6A 89.831 236 24 0 5 240 86361517 86361282 2.820000e-78 303.0
17 TraesCS4D01G053400 chr6A 97.647 85 2 0 3147 3231 108251274 108251358 5.020000e-31 147.0
18 TraesCS4D01G053400 chr2A 89.474 228 22 2 5 230 758660344 758660117 2.840000e-73 287.0
19 TraesCS4D01G053400 chr2A 95.402 87 4 0 3147 3233 745552763 745552849 8.410000e-29 139.0
20 TraesCS4D01G053400 chr2A 95.294 85 4 0 3147 3231 539325662 539325578 1.090000e-27 135.0
21 TraesCS4D01G053400 chr2A 83.740 123 19 1 108 229 672973705 672973827 1.420000e-21 115.0
22 TraesCS4D01G053400 chr2A 80.315 127 24 1 108 233 90595034 90595160 1.850000e-15 95.3
23 TraesCS4D01G053400 chr2D 86.574 216 18 3 1 216 643175560 643175764 1.740000e-55 228.0
24 TraesCS4D01G053400 chr5D 95.349 86 4 0 3146 3231 532592545 532592460 3.020000e-28 137.0
25 TraesCS4D01G053400 chr5D 93.258 89 6 0 3143 3231 446918259 446918171 1.410000e-26 132.0
26 TraesCS4D01G053400 chr7A 95.294 85 4 0 3147 3231 581850992 581850908 1.090000e-27 135.0
27 TraesCS4D01G053400 chr1A 95.294 85 4 0 3147 3231 209362154 209362070 1.090000e-27 135.0
28 TraesCS4D01G053400 chr3A 82.051 117 20 1 108 224 572149950 572149835 1.430000e-16 99.0
29 TraesCS4D01G053400 chrUn 82.301 113 19 1 113 225 20710496 20710385 5.130000e-16 97.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G053400 chr4D 29404853 29411072 6219 False 11487.0 11487 100.000000 1 6220 1 chr4D.!!$F1 6219
1 TraesCS4D01G053400 chr4D 5675063 5680502 5439 True 2476.0 3627 91.780333 418 5993 3 chr4D.!!$R1 5575
2 TraesCS4D01G053400 chr4A 573664310 573670100 5790 True 10382.0 10382 99.068000 443 6220 1 chr4A.!!$R1 5777
3 TraesCS4D01G053400 chr4A 597840826 597846330 5504 False 3601.5 3738 90.555500 445 5993 2 chr4A.!!$F1 5548
4 TraesCS4D01G053400 chr6B 625886322 625891523 5201 True 3551.5 3954 91.503000 755 5993 2 chr6B.!!$R1 5238
5 TraesCS4D01G053400 chr4B 41836623 41842465 5842 False 1532.2 2861 97.776800 835 6220 5 chr4B.!!$F1 5385

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
371 372 0.391661 AACATCTCAATCGCGTGGCT 60.392 50.000 5.77 0.0 0.00 4.75 F
374 375 0.807667 ATCTCAATCGCGTGGCTGTC 60.808 55.000 5.77 0.0 0.00 3.51 F
2127 2213 0.794605 GATTTTGCGCGAGACAAGCC 60.795 55.000 12.10 0.0 0.00 4.35 F
2543 2640 8.027524 TCTGATGAGGCTCTAATGTAATTCTT 57.972 34.615 16.72 0.0 37.87 2.52 F
3891 4032 5.950883 AGTTGCAGATGAATGAAGTGAATG 58.049 37.500 0.00 0.0 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1872 2.414559 CGGAACTTGCATGTGTCCATTC 60.415 50.000 22.08 10.89 0.00 2.67 R
2543 2640 7.078249 TCAAGCCTTGCCAATATAGAGATAA 57.922 36.000 0.00 0.00 0.00 1.75 R
3891 4032 5.374080 CGATAAATTATGCACCACGACATC 58.626 41.667 0.00 0.00 0.00 3.06 R
4366 5979 1.824852 GGACCAATGGCCCTGTAAAAG 59.175 52.381 0.00 0.00 0.00 2.27 R
6107 7819 9.784531 CTGGGAATGTATGTCATATCTTTTAGT 57.215 33.333 0.00 0.00 35.48 2.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.051606 CAGTCAAACCTGAACAACGTG 57.948 47.619 0.00 0.00 34.23 4.49
23 24 2.417239 GTCAAACCTGAACAACGTGTCA 59.583 45.455 0.00 0.00 31.88 3.58
24 25 3.075148 TCAAACCTGAACAACGTGTCAA 58.925 40.909 0.00 0.00 0.00 3.18
25 26 3.126171 TCAAACCTGAACAACGTGTCAAG 59.874 43.478 0.00 0.00 0.00 3.02
27 28 2.706890 ACCTGAACAACGTGTCAAGTT 58.293 42.857 0.00 0.00 0.00 2.66
28 29 3.078837 ACCTGAACAACGTGTCAAGTTT 58.921 40.909 1.01 0.00 0.00 2.66
29 30 3.504520 ACCTGAACAACGTGTCAAGTTTT 59.495 39.130 1.01 1.07 0.00 2.43
30 31 4.022676 ACCTGAACAACGTGTCAAGTTTTT 60.023 37.500 1.01 2.19 0.00 1.94
31 32 5.181622 ACCTGAACAACGTGTCAAGTTTTTA 59.818 36.000 1.01 0.00 0.00 1.52
32 33 5.737290 CCTGAACAACGTGTCAAGTTTTTAG 59.263 40.000 1.01 6.45 0.00 1.85
33 34 6.243811 TGAACAACGTGTCAAGTTTTTAGT 57.756 33.333 1.01 0.00 0.00 2.24
34 35 6.308675 TGAACAACGTGTCAAGTTTTTAGTC 58.691 36.000 1.01 0.00 0.00 2.59
35 36 5.866335 ACAACGTGTCAAGTTTTTAGTCA 57.134 34.783 1.01 0.00 0.00 3.41
36 37 6.243811 ACAACGTGTCAAGTTTTTAGTCAA 57.756 33.333 1.01 0.00 0.00 3.18
37 38 6.670233 ACAACGTGTCAAGTTTTTAGTCAAA 58.330 32.000 1.01 0.00 0.00 2.69
38 39 7.140048 ACAACGTGTCAAGTTTTTAGTCAAAA 58.860 30.769 1.01 0.00 31.50 2.44
39 40 7.810759 ACAACGTGTCAAGTTTTTAGTCAAAAT 59.189 29.630 1.01 0.00 36.72 1.82
40 41 7.964545 ACGTGTCAAGTTTTTAGTCAAAATC 57.035 32.000 0.00 0.00 36.72 2.17
41 42 7.531716 ACGTGTCAAGTTTTTAGTCAAAATCA 58.468 30.769 0.00 0.00 36.72 2.57
42 43 8.188139 ACGTGTCAAGTTTTTAGTCAAAATCAT 58.812 29.630 0.00 0.00 36.72 2.45
43 44 8.471457 CGTGTCAAGTTTTTAGTCAAAATCATG 58.529 33.333 0.00 0.00 36.72 3.07
44 45 9.301153 GTGTCAAGTTTTTAGTCAAAATCATGT 57.699 29.630 0.00 0.00 36.72 3.21
45 46 9.515020 TGTCAAGTTTTTAGTCAAAATCATGTC 57.485 29.630 0.00 0.00 36.72 3.06
46 47 8.968242 GTCAAGTTTTTAGTCAAAATCATGTCC 58.032 33.333 0.00 0.00 36.72 4.02
47 48 8.690884 TCAAGTTTTTAGTCAAAATCATGTCCA 58.309 29.630 0.00 0.00 36.72 4.02
48 49 8.755018 CAAGTTTTTAGTCAAAATCATGTCCAC 58.245 33.333 0.00 0.00 36.72 4.02
49 50 8.006298 AGTTTTTAGTCAAAATCATGTCCACA 57.994 30.769 0.00 0.00 36.72 4.17
50 51 8.641541 AGTTTTTAGTCAAAATCATGTCCACAT 58.358 29.630 0.00 0.00 36.72 3.21
51 52 8.915654 GTTTTTAGTCAAAATCATGTCCACATC 58.084 33.333 0.00 0.00 36.72 3.06
52 53 7.757941 TTTAGTCAAAATCATGTCCACATCA 57.242 32.000 0.00 0.00 33.61 3.07
53 54 5.892160 AGTCAAAATCATGTCCACATCAG 57.108 39.130 0.00 0.00 33.61 2.90
54 55 5.563592 AGTCAAAATCATGTCCACATCAGA 58.436 37.500 0.00 0.00 33.61 3.27
55 56 5.413833 AGTCAAAATCATGTCCACATCAGAC 59.586 40.000 0.00 0.00 33.61 3.51
56 57 4.392754 TCAAAATCATGTCCACATCAGACG 59.607 41.667 0.00 0.00 37.04 4.18
57 58 3.893326 AATCATGTCCACATCAGACGA 57.107 42.857 0.00 0.00 37.04 4.20
58 59 3.893326 ATCATGTCCACATCAGACGAA 57.107 42.857 0.00 0.00 37.04 3.85
59 60 3.676291 TCATGTCCACATCAGACGAAA 57.324 42.857 0.00 0.00 37.04 3.46
60 61 4.001618 TCATGTCCACATCAGACGAAAA 57.998 40.909 0.00 0.00 37.04 2.29
61 62 3.745975 TCATGTCCACATCAGACGAAAAC 59.254 43.478 0.00 0.00 37.04 2.43
62 63 2.489971 TGTCCACATCAGACGAAAACC 58.510 47.619 0.00 0.00 37.04 3.27
63 64 2.158885 TGTCCACATCAGACGAAAACCA 60.159 45.455 0.00 0.00 37.04 3.67
64 65 3.074412 GTCCACATCAGACGAAAACCAT 58.926 45.455 0.00 0.00 0.00 3.55
65 66 3.125316 GTCCACATCAGACGAAAACCATC 59.875 47.826 0.00 0.00 0.00 3.51
77 78 4.621223 CGAAAACCATCGTAAACAGTACG 58.379 43.478 0.00 0.00 41.79 3.67
84 85 2.783135 TCGTAAACAGTACGAGGGACT 58.217 47.619 4.58 0.00 43.85 3.85
86 87 2.485426 CGTAAACAGTACGAGGGACTGA 59.515 50.000 14.60 0.00 46.01 3.41
87 88 3.058016 CGTAAACAGTACGAGGGACTGAA 60.058 47.826 14.60 0.00 46.01 3.02
88 89 3.662247 AAACAGTACGAGGGACTGAAG 57.338 47.619 14.60 0.00 46.01 3.02
89 90 2.289592 ACAGTACGAGGGACTGAAGT 57.710 50.000 14.60 0.00 46.01 3.01
90 91 2.595238 ACAGTACGAGGGACTGAAGTT 58.405 47.619 14.60 0.00 46.01 2.66
91 92 3.759581 ACAGTACGAGGGACTGAAGTTA 58.240 45.455 14.60 0.00 46.01 2.24
92 93 4.342359 ACAGTACGAGGGACTGAAGTTAT 58.658 43.478 14.60 0.00 46.01 1.89
93 94 4.398673 ACAGTACGAGGGACTGAAGTTATC 59.601 45.833 14.60 0.00 46.01 1.75
94 95 4.641094 CAGTACGAGGGACTGAAGTTATCT 59.359 45.833 1.67 0.00 46.01 1.98
95 96 4.641094 AGTACGAGGGACTGAAGTTATCTG 59.359 45.833 0.00 0.00 41.55 2.90
96 97 2.761208 ACGAGGGACTGAAGTTATCTGG 59.239 50.000 0.00 0.00 41.55 3.86
97 98 2.761208 CGAGGGACTGAAGTTATCTGGT 59.239 50.000 0.00 0.00 41.55 4.00
98 99 3.195825 CGAGGGACTGAAGTTATCTGGTT 59.804 47.826 0.00 0.00 41.55 3.67
99 100 4.322801 CGAGGGACTGAAGTTATCTGGTTT 60.323 45.833 0.00 0.00 41.55 3.27
100 101 4.911390 AGGGACTGAAGTTATCTGGTTTG 58.089 43.478 0.00 0.00 37.18 2.93
101 102 4.597507 AGGGACTGAAGTTATCTGGTTTGA 59.402 41.667 0.00 0.00 37.18 2.69
102 103 5.073144 AGGGACTGAAGTTATCTGGTTTGAA 59.927 40.000 0.00 0.00 37.18 2.69
103 104 5.768164 GGGACTGAAGTTATCTGGTTTGAAA 59.232 40.000 0.00 0.00 0.00 2.69
104 105 6.264518 GGGACTGAAGTTATCTGGTTTGAAAA 59.735 38.462 0.00 0.00 0.00 2.29
105 106 7.363431 GGACTGAAGTTATCTGGTTTGAAAAG 58.637 38.462 0.00 0.00 0.00 2.27
106 107 7.013369 GGACTGAAGTTATCTGGTTTGAAAAGT 59.987 37.037 0.00 0.00 0.00 2.66
107 108 8.293699 ACTGAAGTTATCTGGTTTGAAAAGTT 57.706 30.769 0.00 0.00 0.00 2.66
108 109 8.190784 ACTGAAGTTATCTGGTTTGAAAAGTTG 58.809 33.333 0.00 0.00 0.00 3.16
109 110 8.287439 TGAAGTTATCTGGTTTGAAAAGTTGA 57.713 30.769 0.00 0.00 0.00 3.18
110 111 8.405531 TGAAGTTATCTGGTTTGAAAAGTTGAG 58.594 33.333 0.00 0.00 0.00 3.02
111 112 8.519799 AAGTTATCTGGTTTGAAAAGTTGAGA 57.480 30.769 0.00 0.00 0.00 3.27
112 113 8.159344 AGTTATCTGGTTTGAAAAGTTGAGAG 57.841 34.615 0.00 0.00 0.00 3.20
113 114 7.993183 AGTTATCTGGTTTGAAAAGTTGAGAGA 59.007 33.333 0.00 0.00 0.00 3.10
114 115 6.625873 ATCTGGTTTGAAAAGTTGAGAGAC 57.374 37.500 0.00 0.00 0.00 3.36
115 116 5.745227 TCTGGTTTGAAAAGTTGAGAGACT 58.255 37.500 0.00 0.00 0.00 3.24
116 117 5.586243 TCTGGTTTGAAAAGTTGAGAGACTG 59.414 40.000 0.00 0.00 0.00 3.51
117 118 5.496556 TGGTTTGAAAAGTTGAGAGACTGA 58.503 37.500 0.00 0.00 0.00 3.41
118 119 5.943416 TGGTTTGAAAAGTTGAGAGACTGAA 59.057 36.000 0.00 0.00 0.00 3.02
119 120 6.432783 TGGTTTGAAAAGTTGAGAGACTGAAA 59.567 34.615 0.00 0.00 0.00 2.69
120 121 7.122650 TGGTTTGAAAAGTTGAGAGACTGAAAT 59.877 33.333 0.00 0.00 0.00 2.17
121 122 7.976175 GGTTTGAAAAGTTGAGAGACTGAAATT 59.024 33.333 0.00 0.00 0.00 1.82
125 126 9.784531 TGAAAAGTTGAGAGACTGAAATTATCT 57.215 29.630 0.00 0.00 0.00 1.98
127 128 9.784531 AAAAGTTGAGAGACTGAAATTATCTGA 57.215 29.630 0.00 0.00 0.00 3.27
128 129 9.956640 AAAGTTGAGAGACTGAAATTATCTGAT 57.043 29.630 0.00 0.00 0.00 2.90
129 130 9.956640 AAGTTGAGAGACTGAAATTATCTGATT 57.043 29.630 0.00 0.00 0.00 2.57
130 131 9.956640 AGTTGAGAGACTGAAATTATCTGATTT 57.043 29.630 0.00 0.00 32.16 2.17
131 132 9.985318 GTTGAGAGACTGAAATTATCTGATTTG 57.015 33.333 0.00 0.00 29.75 2.32
132 133 9.948964 TTGAGAGACTGAAATTATCTGATTTGA 57.051 29.630 0.00 0.00 29.75 2.69
133 134 9.597170 TGAGAGACTGAAATTATCTGATTTGAG 57.403 33.333 0.00 0.00 36.63 3.02
134 135 9.814899 GAGAGACTGAAATTATCTGATTTGAGA 57.185 33.333 0.00 0.00 34.94 3.27
143 144 9.880157 AAATTATCTGATTTGAGAAATTGTGGG 57.120 29.630 0.00 0.00 0.00 4.61
144 145 8.827832 ATTATCTGATTTGAGAAATTGTGGGA 57.172 30.769 0.00 0.00 0.00 4.37
145 146 5.964958 TCTGATTTGAGAAATTGTGGGAC 57.035 39.130 0.00 0.00 0.00 4.46
146 147 5.634118 TCTGATTTGAGAAATTGTGGGACT 58.366 37.500 0.00 0.00 0.00 3.85
147 148 6.778821 TCTGATTTGAGAAATTGTGGGACTA 58.221 36.000 0.00 0.00 0.00 2.59
148 149 7.230747 TCTGATTTGAGAAATTGTGGGACTAA 58.769 34.615 0.00 0.00 0.00 2.24
149 150 7.391554 TCTGATTTGAGAAATTGTGGGACTAAG 59.608 37.037 0.00 0.00 0.00 2.18
150 151 7.004086 TGATTTGAGAAATTGTGGGACTAAGT 58.996 34.615 0.00 0.00 0.00 2.24
151 152 7.505585 TGATTTGAGAAATTGTGGGACTAAGTT 59.494 33.333 0.00 0.00 0.00 2.66
152 153 7.654022 TTTGAGAAATTGTGGGACTAAGTTT 57.346 32.000 0.00 0.00 0.00 2.66
153 154 7.654022 TTGAGAAATTGTGGGACTAAGTTTT 57.346 32.000 0.00 0.00 0.00 2.43
154 155 8.754991 TTGAGAAATTGTGGGACTAAGTTTTA 57.245 30.769 0.00 0.00 0.00 1.52
155 156 8.161699 TGAGAAATTGTGGGACTAAGTTTTAC 57.838 34.615 0.00 0.00 0.00 2.01
156 157 7.996644 TGAGAAATTGTGGGACTAAGTTTTACT 59.003 33.333 0.00 0.00 0.00 2.24
157 158 8.166422 AGAAATTGTGGGACTAAGTTTTACTG 57.834 34.615 0.00 0.00 0.00 2.74
158 159 6.894339 AATTGTGGGACTAAGTTTTACTGG 57.106 37.500 0.00 0.00 0.00 4.00
159 160 5.376756 TTGTGGGACTAAGTTTTACTGGT 57.623 39.130 0.00 0.00 0.00 4.00
160 161 5.376756 TGTGGGACTAAGTTTTACTGGTT 57.623 39.130 0.00 0.00 0.00 3.67
161 162 5.757988 TGTGGGACTAAGTTTTACTGGTTT 58.242 37.500 0.00 0.00 0.00 3.27
162 163 6.189133 TGTGGGACTAAGTTTTACTGGTTTT 58.811 36.000 0.00 0.00 0.00 2.43
163 164 6.095720 TGTGGGACTAAGTTTTACTGGTTTTG 59.904 38.462 0.00 0.00 0.00 2.44
164 165 6.319405 GTGGGACTAAGTTTTACTGGTTTTGA 59.681 38.462 0.00 0.00 0.00 2.69
165 166 6.890814 TGGGACTAAGTTTTACTGGTTTTGAA 59.109 34.615 0.00 0.00 0.00 2.69
166 167 7.067737 TGGGACTAAGTTTTACTGGTTTTGAAG 59.932 37.037 0.00 0.00 0.00 3.02
167 168 7.067859 GGGACTAAGTTTTACTGGTTTTGAAGT 59.932 37.037 0.00 0.00 0.00 3.01
168 169 8.464404 GGACTAAGTTTTACTGGTTTTGAAGTT 58.536 33.333 0.00 0.00 0.00 2.66
169 170 9.285770 GACTAAGTTTTACTGGTTTTGAAGTTG 57.714 33.333 0.00 0.00 0.00 3.16
170 171 9.016438 ACTAAGTTTTACTGGTTTTGAAGTTGA 57.984 29.630 0.00 0.00 0.00 3.18
171 172 9.849166 CTAAGTTTTACTGGTTTTGAAGTTGAA 57.151 29.630 0.00 0.00 0.00 2.69
173 174 9.549078 AAGTTTTACTGGTTTTGAAGTTGAAAA 57.451 25.926 0.00 0.00 0.00 2.29
174 175 9.549078 AGTTTTACTGGTTTTGAAGTTGAAAAA 57.451 25.926 1.60 0.00 0.00 1.94
175 176 9.588774 GTTTTACTGGTTTTGAAGTTGAAAAAC 57.411 29.630 8.46 8.46 42.75 2.43
176 177 8.888579 TTTACTGGTTTTGAAGTTGAAAAACA 57.111 26.923 15.97 15.97 44.41 2.83
177 178 8.888579 TTACTGGTTTTGAAGTTGAAAAACAA 57.111 26.923 17.21 9.21 44.41 2.83
178 179 7.977789 ACTGGTTTTGAAGTTGAAAAACAAT 57.022 28.000 17.21 6.71 44.41 2.71
179 180 8.389779 ACTGGTTTTGAAGTTGAAAAACAATT 57.610 26.923 17.21 6.63 44.41 2.32
180 181 8.845227 ACTGGTTTTGAAGTTGAAAAACAATTT 58.155 25.926 17.21 4.51 44.41 1.82
206 207 9.939802 TCTATACTTTTGAAAGAGTTAAGGGAC 57.060 33.333 10.26 0.00 39.31 4.46
207 208 7.668525 ATACTTTTGAAAGAGTTAAGGGACG 57.331 36.000 10.26 0.00 39.31 4.79
208 209 5.677567 ACTTTTGAAAGAGTTAAGGGACGA 58.322 37.500 10.26 0.00 39.31 4.20
209 210 6.117488 ACTTTTGAAAGAGTTAAGGGACGAA 58.883 36.000 10.26 0.00 39.31 3.85
210 211 6.600427 ACTTTTGAAAGAGTTAAGGGACGAAA 59.400 34.615 10.26 0.00 39.31 3.46
211 212 7.121611 ACTTTTGAAAGAGTTAAGGGACGAAAA 59.878 33.333 10.26 0.00 39.31 2.29
212 213 7.393841 TTTGAAAGAGTTAAGGGACGAAAAA 57.606 32.000 0.00 0.00 0.00 1.94
213 214 7.576861 TTGAAAGAGTTAAGGGACGAAAAAT 57.423 32.000 0.00 0.00 0.00 1.82
214 215 8.680039 TTGAAAGAGTTAAGGGACGAAAAATA 57.320 30.769 0.00 0.00 0.00 1.40
215 216 8.857694 TGAAAGAGTTAAGGGACGAAAAATAT 57.142 30.769 0.00 0.00 0.00 1.28
216 217 9.947433 TGAAAGAGTTAAGGGACGAAAAATATA 57.053 29.630 0.00 0.00 0.00 0.86
218 219 9.955102 AAAGAGTTAAGGGACGAAAAATATACT 57.045 29.630 0.00 0.00 0.00 2.12
219 220 9.955102 AAGAGTTAAGGGACGAAAAATATACTT 57.045 29.630 0.00 0.00 0.00 2.24
220 221 9.597170 AGAGTTAAGGGACGAAAAATATACTTC 57.403 33.333 0.00 0.00 0.00 3.01
221 222 9.597170 GAGTTAAGGGACGAAAAATATACTTCT 57.403 33.333 0.00 0.00 0.00 2.85
222 223 9.955102 AGTTAAGGGACGAAAAATATACTTCTT 57.045 29.630 0.00 0.00 0.00 2.52
224 225 7.860918 AAGGGACGAAAAATATACTTCTTCC 57.139 36.000 11.19 11.19 38.59 3.46
225 226 7.196637 AGGGACGAAAAATATACTTCTTCCT 57.803 36.000 15.94 8.26 39.05 3.36
226 227 8.315220 AGGGACGAAAAATATACTTCTTCCTA 57.685 34.615 15.94 0.00 39.05 2.94
227 228 8.765517 AGGGACGAAAAATATACTTCTTCCTAA 58.234 33.333 15.94 0.00 39.05 2.69
228 229 9.387257 GGGACGAAAAATATACTTCTTCCTAAA 57.613 33.333 15.94 0.00 39.05 1.85
261 262 8.972262 ATAATCTAGTGTTGCACTCATATACG 57.028 34.615 4.95 0.00 41.21 3.06
262 263 6.635030 ATCTAGTGTTGCACTCATATACGA 57.365 37.500 4.95 0.00 41.21 3.43
263 264 6.061231 TCTAGTGTTGCACTCATATACGAG 57.939 41.667 4.95 0.00 41.21 4.18
265 266 5.830000 AGTGTTGCACTCATATACGAGTA 57.170 39.130 0.31 0.00 44.49 2.59
266 267 6.203808 AGTGTTGCACTCATATACGAGTAA 57.796 37.500 0.31 0.00 44.49 2.24
267 268 6.627243 AGTGTTGCACTCATATACGAGTAAA 58.373 36.000 0.31 0.00 44.49 2.01
268 269 7.094631 AGTGTTGCACTCATATACGAGTAAAA 58.905 34.615 0.31 0.00 44.49 1.52
269 270 7.275779 AGTGTTGCACTCATATACGAGTAAAAG 59.724 37.037 0.31 0.00 44.49 2.27
270 271 6.533723 TGTTGCACTCATATACGAGTAAAAGG 59.466 38.462 0.31 0.00 44.49 3.11
271 272 6.216801 TGCACTCATATACGAGTAAAAGGT 57.783 37.500 0.31 0.00 44.49 3.50
272 273 6.636705 TGCACTCATATACGAGTAAAAGGTT 58.363 36.000 0.31 0.00 44.49 3.50
273 274 7.101054 TGCACTCATATACGAGTAAAAGGTTT 58.899 34.615 0.31 0.00 44.49 3.27
274 275 7.604927 TGCACTCATATACGAGTAAAAGGTTTT 59.395 33.333 0.31 0.00 44.49 2.43
275 276 9.090692 GCACTCATATACGAGTAAAAGGTTTTA 57.909 33.333 0.31 0.00 44.49 1.52
296 297 3.217599 CGAGACTCGTTTCATGAAGGA 57.782 47.619 16.83 9.32 34.72 3.36
297 298 3.575630 CGAGACTCGTTTCATGAAGGAA 58.424 45.455 16.83 0.00 34.72 3.36
298 299 4.177026 CGAGACTCGTTTCATGAAGGAAT 58.823 43.478 16.83 0.27 34.72 3.01
299 300 5.340803 CGAGACTCGTTTCATGAAGGAATA 58.659 41.667 16.83 0.00 34.72 1.75
300 301 5.805486 CGAGACTCGTTTCATGAAGGAATAA 59.195 40.000 16.83 0.00 34.72 1.40
301 302 6.237595 CGAGACTCGTTTCATGAAGGAATAAC 60.238 42.308 16.83 2.03 34.72 1.89
302 303 6.702329 AGACTCGTTTCATGAAGGAATAACT 58.298 36.000 8.41 2.38 32.25 2.24
303 304 7.162082 AGACTCGTTTCATGAAGGAATAACTT 58.838 34.615 8.41 0.00 32.25 2.66
304 305 8.311836 AGACTCGTTTCATGAAGGAATAACTTA 58.688 33.333 8.41 0.00 32.25 2.24
305 306 9.099454 GACTCGTTTCATGAAGGAATAACTTAT 57.901 33.333 8.41 0.00 32.25 1.73
306 307 8.883731 ACTCGTTTCATGAAGGAATAACTTATG 58.116 33.333 8.41 0.00 32.25 1.90
307 308 8.786826 TCGTTTCATGAAGGAATAACTTATGT 57.213 30.769 8.41 0.00 0.00 2.29
308 309 8.664798 TCGTTTCATGAAGGAATAACTTATGTG 58.335 33.333 8.41 0.00 0.00 3.21
309 310 8.450964 CGTTTCATGAAGGAATAACTTATGTGT 58.549 33.333 8.41 0.00 0.00 3.72
310 311 9.774742 GTTTCATGAAGGAATAACTTATGTGTC 57.225 33.333 8.41 0.00 0.00 3.67
311 312 9.739276 TTTCATGAAGGAATAACTTATGTGTCT 57.261 29.630 8.41 0.00 0.00 3.41
312 313 9.739276 TTCATGAAGGAATAACTTATGTGTCTT 57.261 29.630 3.38 0.00 0.00 3.01
313 314 9.739276 TCATGAAGGAATAACTTATGTGTCTTT 57.261 29.630 0.00 0.00 0.00 2.52
325 326 9.620660 AACTTATGTGTCTTTTATTTTTAGCGG 57.379 29.630 0.00 0.00 0.00 5.52
326 327 8.789762 ACTTATGTGTCTTTTATTTTTAGCGGT 58.210 29.630 0.00 0.00 0.00 5.68
329 330 7.136289 TGTGTCTTTTATTTTTAGCGGTAGG 57.864 36.000 0.00 0.00 0.00 3.18
330 331 6.935771 TGTGTCTTTTATTTTTAGCGGTAGGA 59.064 34.615 0.00 0.00 0.00 2.94
331 332 7.444792 TGTGTCTTTTATTTTTAGCGGTAGGAA 59.555 33.333 0.00 0.00 0.00 3.36
332 333 8.456471 GTGTCTTTTATTTTTAGCGGTAGGAAT 58.544 33.333 0.00 2.53 0.00 3.01
333 334 8.455682 TGTCTTTTATTTTTAGCGGTAGGAATG 58.544 33.333 12.17 0.61 0.00 2.67
334 335 8.671028 GTCTTTTATTTTTAGCGGTAGGAATGA 58.329 33.333 12.17 4.49 0.00 2.57
335 336 8.671028 TCTTTTATTTTTAGCGGTAGGAATGAC 58.329 33.333 12.17 0.00 0.00 3.06
336 337 7.925043 TTTATTTTTAGCGGTAGGAATGACA 57.075 32.000 12.17 0.00 0.00 3.58
337 338 8.514330 TTTATTTTTAGCGGTAGGAATGACAT 57.486 30.769 12.17 0.00 0.00 3.06
338 339 8.514330 TTATTTTTAGCGGTAGGAATGACATT 57.486 30.769 0.00 0.00 0.00 2.71
339 340 6.827586 TTTTTAGCGGTAGGAATGACATTT 57.172 33.333 1.39 0.00 0.00 2.32
340 341 6.827586 TTTTAGCGGTAGGAATGACATTTT 57.172 33.333 1.39 0.00 0.00 1.82
341 342 6.827586 TTTAGCGGTAGGAATGACATTTTT 57.172 33.333 1.39 0.00 0.00 1.94
342 343 7.925043 TTTAGCGGTAGGAATGACATTTTTA 57.075 32.000 1.39 0.00 0.00 1.52
343 344 8.514330 TTTAGCGGTAGGAATGACATTTTTAT 57.486 30.769 1.39 0.00 0.00 1.40
344 345 6.377327 AGCGGTAGGAATGACATTTTTATG 57.623 37.500 1.39 0.00 0.00 1.90
345 346 5.885912 AGCGGTAGGAATGACATTTTTATGT 59.114 36.000 1.39 0.00 37.50 2.29
346 347 7.051623 AGCGGTAGGAATGACATTTTTATGTA 58.948 34.615 1.39 0.00 34.45 2.29
347 348 7.554835 AGCGGTAGGAATGACATTTTTATGTAA 59.445 33.333 1.39 0.00 34.45 2.41
348 349 8.349983 GCGGTAGGAATGACATTTTTATGTAAT 58.650 33.333 1.39 0.00 34.45 1.89
366 367 9.644993 TTATGTAATTTTAACATCTCAATCGCG 57.355 29.630 0.00 0.00 38.49 5.87
367 368 7.067532 TGTAATTTTAACATCTCAATCGCGT 57.932 32.000 5.77 0.00 0.00 6.01
368 369 6.958752 TGTAATTTTAACATCTCAATCGCGTG 59.041 34.615 5.77 0.00 0.00 5.34
369 370 4.335082 TTTTAACATCTCAATCGCGTGG 57.665 40.909 5.77 0.00 0.00 4.94
370 371 1.286501 TAACATCTCAATCGCGTGGC 58.713 50.000 5.77 0.00 0.00 5.01
371 372 0.391661 AACATCTCAATCGCGTGGCT 60.392 50.000 5.77 0.00 0.00 4.75
372 373 1.086067 ACATCTCAATCGCGTGGCTG 61.086 55.000 5.77 0.00 0.00 4.85
373 374 1.086067 CATCTCAATCGCGTGGCTGT 61.086 55.000 5.77 0.00 0.00 4.40
374 375 0.807667 ATCTCAATCGCGTGGCTGTC 60.808 55.000 5.77 0.00 0.00 3.51
375 376 2.792290 CTCAATCGCGTGGCTGTCG 61.792 63.158 5.77 0.00 0.00 4.35
376 377 3.112075 CAATCGCGTGGCTGTCGT 61.112 61.111 5.77 0.00 0.00 4.34
377 378 3.112075 AATCGCGTGGCTGTCGTG 61.112 61.111 5.77 5.00 39.65 4.35
382 383 4.602259 CGTGGCTGTCGTGGGTGT 62.602 66.667 0.00 0.00 0.00 4.16
383 384 2.972505 GTGGCTGTCGTGGGTGTG 60.973 66.667 0.00 0.00 0.00 3.82
384 385 4.927782 TGGCTGTCGTGGGTGTGC 62.928 66.667 0.00 0.00 0.00 4.57
387 388 4.969196 CTGTCGTGGGTGTGCGCT 62.969 66.667 9.73 0.00 0.00 5.92
388 389 4.961511 TGTCGTGGGTGTGCGCTC 62.962 66.667 9.73 5.51 0.00 5.03
401 402 4.430423 CGCTCGCGGCTGTCAAAC 62.430 66.667 6.13 0.00 39.13 2.93
402 403 3.345808 GCTCGCGGCTGTCAAACA 61.346 61.111 6.13 0.00 38.06 2.83
412 413 1.831343 CTGTCAAACAGTGCAGTTGC 58.169 50.000 0.00 0.00 41.19 4.17
413 414 1.132834 CTGTCAAACAGTGCAGTTGCA 59.867 47.619 2.03 2.03 42.29 4.08
430 431 6.693113 GCAGTTGCACTTATTAGAATTTAGGC 59.307 38.462 0.00 0.00 41.59 3.93
431 432 7.415653 GCAGTTGCACTTATTAGAATTTAGGCT 60.416 37.037 0.00 0.00 41.59 4.58
432 433 8.462016 CAGTTGCACTTATTAGAATTTAGGCTT 58.538 33.333 0.00 0.00 0.00 4.35
433 434 9.025041 AGTTGCACTTATTAGAATTTAGGCTTT 57.975 29.630 0.00 0.00 0.00 3.51
434 435 9.639601 GTTGCACTTATTAGAATTTAGGCTTTT 57.360 29.630 0.00 0.00 0.00 2.27
523 526 7.879160 ACTACTTCAAACCGATATTAACCAACA 59.121 33.333 0.00 0.00 0.00 3.33
621 633 7.429340 GCCGTGAGTTTTCATTAATACAGATTG 59.571 37.037 0.00 0.00 35.39 2.67
739 756 2.476051 GCATCGTCTGCGTTGTGG 59.524 61.111 0.00 0.00 41.97 4.17
1809 1872 9.838339 AGTATTATACACTTCCAGAAAGAATGG 57.162 33.333 5.11 0.00 38.44 3.16
2127 2213 0.794605 GATTTTGCGCGAGACAAGCC 60.795 55.000 12.10 0.00 0.00 4.35
2543 2640 8.027524 TCTGATGAGGCTCTAATGTAATTCTT 57.972 34.615 16.72 0.00 37.87 2.52
3891 4032 5.950883 AGTTGCAGATGAATGAAGTGAATG 58.049 37.500 0.00 0.00 0.00 2.67
4366 5979 3.549794 AGAGCTATGCCATTGTTCCTTC 58.450 45.455 0.00 0.00 0.00 3.46
6107 7819 5.428457 AGGAGACTATCACTCTCTCTTCTCA 59.572 44.000 0.00 0.00 40.61 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.418628 ACACGTTGTTCAGGTTTGACTG 59.581 45.455 0.00 0.00 39.84 3.51
2 3 2.417239 TGACACGTTGTTCAGGTTTGAC 59.583 45.455 0.00 0.00 31.71 3.18
3 4 2.701107 TGACACGTTGTTCAGGTTTGA 58.299 42.857 0.00 0.00 0.00 2.69
4 5 3.119990 ACTTGACACGTTGTTCAGGTTTG 60.120 43.478 0.00 0.00 0.00 2.93
8 9 3.757745 AAACTTGACACGTTGTTCAGG 57.242 42.857 0.00 0.00 0.00 3.86
9 10 6.311723 ACTAAAAACTTGACACGTTGTTCAG 58.688 36.000 3.64 4.03 0.00 3.02
11 12 6.308675 TGACTAAAAACTTGACACGTTGTTC 58.691 36.000 3.64 0.00 0.00 3.18
12 13 6.243811 TGACTAAAAACTTGACACGTTGTT 57.756 33.333 5.64 5.64 0.00 2.83
13 14 5.866335 TGACTAAAAACTTGACACGTTGT 57.134 34.783 0.00 0.00 0.00 3.32
14 15 7.555639 TTTTGACTAAAAACTTGACACGTTG 57.444 32.000 0.00 0.00 32.72 4.10
16 17 7.531716 TGATTTTGACTAAAAACTTGACACGT 58.468 30.769 0.00 0.00 40.51 4.49
17 18 7.962934 TGATTTTGACTAAAAACTTGACACG 57.037 32.000 0.00 0.00 40.51 4.49
18 19 9.301153 ACATGATTTTGACTAAAAACTTGACAC 57.699 29.630 0.00 0.00 40.51 3.67
20 21 8.968242 GGACATGATTTTGACTAAAAACTTGAC 58.032 33.333 0.00 8.14 40.51 3.18
23 24 8.474025 TGTGGACATGATTTTGACTAAAAACTT 58.526 29.630 0.00 0.00 40.51 2.66
24 25 8.006298 TGTGGACATGATTTTGACTAAAAACT 57.994 30.769 0.00 0.00 40.51 2.66
25 26 8.816640 ATGTGGACATGATTTTGACTAAAAAC 57.183 30.769 0.00 0.00 36.55 2.43
27 28 8.175925 TGATGTGGACATGATTTTGACTAAAA 57.824 30.769 0.00 0.00 37.15 1.52
28 29 7.665145 TCTGATGTGGACATGATTTTGACTAAA 59.335 33.333 0.00 0.00 36.57 1.85
29 30 7.119699 GTCTGATGTGGACATGATTTTGACTAA 59.880 37.037 0.00 0.00 36.57 2.24
30 31 6.595326 GTCTGATGTGGACATGATTTTGACTA 59.405 38.462 0.00 0.00 36.57 2.59
31 32 5.413833 GTCTGATGTGGACATGATTTTGACT 59.586 40.000 0.00 0.00 36.57 3.41
32 33 5.634896 GTCTGATGTGGACATGATTTTGAC 58.365 41.667 0.00 0.00 36.57 3.18
33 34 4.392754 CGTCTGATGTGGACATGATTTTGA 59.607 41.667 0.00 0.00 36.57 2.69
34 35 4.392754 TCGTCTGATGTGGACATGATTTTG 59.607 41.667 0.00 0.00 36.57 2.44
35 36 4.578871 TCGTCTGATGTGGACATGATTTT 58.421 39.130 0.00 0.00 36.57 1.82
36 37 4.206477 TCGTCTGATGTGGACATGATTT 57.794 40.909 0.00 0.00 36.57 2.17
37 38 3.893326 TCGTCTGATGTGGACATGATT 57.107 42.857 0.00 0.00 36.57 2.57
38 39 3.893326 TTCGTCTGATGTGGACATGAT 57.107 42.857 0.00 0.00 36.57 2.45
39 40 3.676291 TTTCGTCTGATGTGGACATGA 57.324 42.857 0.00 0.00 36.57 3.07
40 41 3.120199 GGTTTTCGTCTGATGTGGACATG 60.120 47.826 0.00 0.00 36.57 3.21
41 42 3.074412 GGTTTTCGTCTGATGTGGACAT 58.926 45.455 0.00 0.00 39.70 3.06
42 43 2.158885 TGGTTTTCGTCTGATGTGGACA 60.159 45.455 0.00 0.00 33.73 4.02
43 44 2.489971 TGGTTTTCGTCTGATGTGGAC 58.510 47.619 0.00 0.00 0.00 4.02
44 45 2.920724 TGGTTTTCGTCTGATGTGGA 57.079 45.000 0.00 0.00 0.00 4.02
45 46 2.094258 CGATGGTTTTCGTCTGATGTGG 59.906 50.000 0.00 0.00 34.46 4.17
46 47 3.374389 CGATGGTTTTCGTCTGATGTG 57.626 47.619 0.00 0.00 34.46 3.21
55 56 4.382457 TCGTACTGTTTACGATGGTTTTCG 59.618 41.667 1.92 0.00 43.85 3.46
56 57 5.164022 CCTCGTACTGTTTACGATGGTTTTC 60.164 44.000 6.30 0.00 46.85 2.29
57 58 4.687483 CCTCGTACTGTTTACGATGGTTTT 59.313 41.667 6.30 0.00 46.85 2.43
58 59 4.240096 CCTCGTACTGTTTACGATGGTTT 58.760 43.478 6.30 0.00 46.85 3.27
59 60 3.367703 CCCTCGTACTGTTTACGATGGTT 60.368 47.826 15.14 0.00 46.85 3.67
60 61 2.165030 CCCTCGTACTGTTTACGATGGT 59.835 50.000 15.14 0.00 46.85 3.55
61 62 2.805845 CCCTCGTACTGTTTACGATGG 58.194 52.381 11.29 11.29 46.85 3.51
62 63 3.128242 AGTCCCTCGTACTGTTTACGATG 59.872 47.826 6.30 4.30 46.85 3.84
63 64 3.128242 CAGTCCCTCGTACTGTTTACGAT 59.872 47.826 6.30 0.00 46.85 3.73
64 65 2.485426 CAGTCCCTCGTACTGTTTACGA 59.515 50.000 5.77 5.77 46.10 3.43
65 66 2.485426 TCAGTCCCTCGTACTGTTTACG 59.515 50.000 0.00 0.00 43.88 3.18
66 67 4.022503 ACTTCAGTCCCTCGTACTGTTTAC 60.023 45.833 0.00 0.00 43.88 2.01
67 68 4.147321 ACTTCAGTCCCTCGTACTGTTTA 58.853 43.478 0.00 0.00 43.88 2.01
68 69 2.963782 ACTTCAGTCCCTCGTACTGTTT 59.036 45.455 0.00 0.00 43.88 2.83
69 70 2.595238 ACTTCAGTCCCTCGTACTGTT 58.405 47.619 0.00 0.00 43.88 3.16
70 71 2.289592 ACTTCAGTCCCTCGTACTGT 57.710 50.000 0.00 0.00 43.88 3.55
71 72 4.641094 AGATAACTTCAGTCCCTCGTACTG 59.359 45.833 0.00 0.00 44.66 2.74
72 73 4.641094 CAGATAACTTCAGTCCCTCGTACT 59.359 45.833 0.00 0.00 0.00 2.73
73 74 4.202030 CCAGATAACTTCAGTCCCTCGTAC 60.202 50.000 0.00 0.00 0.00 3.67
74 75 3.952323 CCAGATAACTTCAGTCCCTCGTA 59.048 47.826 0.00 0.00 0.00 3.43
75 76 2.761208 CCAGATAACTTCAGTCCCTCGT 59.239 50.000 0.00 0.00 0.00 4.18
76 77 2.761208 ACCAGATAACTTCAGTCCCTCG 59.239 50.000 0.00 0.00 0.00 4.63
77 78 4.828072 AACCAGATAACTTCAGTCCCTC 57.172 45.455 0.00 0.00 0.00 4.30
78 79 4.597507 TCAAACCAGATAACTTCAGTCCCT 59.402 41.667 0.00 0.00 0.00 4.20
79 80 4.906618 TCAAACCAGATAACTTCAGTCCC 58.093 43.478 0.00 0.00 0.00 4.46
80 81 6.877611 TTTCAAACCAGATAACTTCAGTCC 57.122 37.500 0.00 0.00 0.00 3.85
81 82 7.931275 ACTTTTCAAACCAGATAACTTCAGTC 58.069 34.615 0.00 0.00 0.00 3.51
82 83 7.881775 ACTTTTCAAACCAGATAACTTCAGT 57.118 32.000 0.00 0.00 0.00 3.41
83 84 8.405531 TCAACTTTTCAAACCAGATAACTTCAG 58.594 33.333 0.00 0.00 0.00 3.02
84 85 8.287439 TCAACTTTTCAAACCAGATAACTTCA 57.713 30.769 0.00 0.00 0.00 3.02
85 86 8.621286 TCTCAACTTTTCAAACCAGATAACTTC 58.379 33.333 0.00 0.00 0.00 3.01
86 87 8.519799 TCTCAACTTTTCAAACCAGATAACTT 57.480 30.769 0.00 0.00 0.00 2.66
87 88 7.993183 TCTCTCAACTTTTCAAACCAGATAACT 59.007 33.333 0.00 0.00 0.00 2.24
88 89 8.070769 GTCTCTCAACTTTTCAAACCAGATAAC 58.929 37.037 0.00 0.00 0.00 1.89
89 90 7.993183 AGTCTCTCAACTTTTCAAACCAGATAA 59.007 33.333 0.00 0.00 0.00 1.75
90 91 7.442364 CAGTCTCTCAACTTTTCAAACCAGATA 59.558 37.037 0.00 0.00 0.00 1.98
91 92 6.261826 CAGTCTCTCAACTTTTCAAACCAGAT 59.738 38.462 0.00 0.00 0.00 2.90
92 93 5.586243 CAGTCTCTCAACTTTTCAAACCAGA 59.414 40.000 0.00 0.00 0.00 3.86
93 94 5.586243 TCAGTCTCTCAACTTTTCAAACCAG 59.414 40.000 0.00 0.00 0.00 4.00
94 95 5.496556 TCAGTCTCTCAACTTTTCAAACCA 58.503 37.500 0.00 0.00 0.00 3.67
95 96 6.436843 TTCAGTCTCTCAACTTTTCAAACC 57.563 37.500 0.00 0.00 0.00 3.27
96 97 8.917415 AATTTCAGTCTCTCAACTTTTCAAAC 57.083 30.769 0.00 0.00 0.00 2.93
99 100 9.784531 AGATAATTTCAGTCTCTCAACTTTTCA 57.215 29.630 0.00 0.00 0.00 2.69
101 102 9.784531 TCAGATAATTTCAGTCTCTCAACTTTT 57.215 29.630 0.00 0.00 0.00 2.27
102 103 9.956640 ATCAGATAATTTCAGTCTCTCAACTTT 57.043 29.630 0.00 0.00 0.00 2.66
103 104 9.956640 AATCAGATAATTTCAGTCTCTCAACTT 57.043 29.630 0.00 0.00 0.00 2.66
104 105 9.956640 AAATCAGATAATTTCAGTCTCTCAACT 57.043 29.630 0.00 0.00 0.00 3.16
105 106 9.985318 CAAATCAGATAATTTCAGTCTCTCAAC 57.015 33.333 0.00 0.00 0.00 3.18
106 107 9.948964 TCAAATCAGATAATTTCAGTCTCTCAA 57.051 29.630 0.00 0.00 0.00 3.02
107 108 9.597170 CTCAAATCAGATAATTTCAGTCTCTCA 57.403 33.333 0.00 0.00 0.00 3.27
108 109 9.814899 TCTCAAATCAGATAATTTCAGTCTCTC 57.185 33.333 0.00 0.00 0.00 3.20
117 118 9.880157 CCCACAATTTCTCAAATCAGATAATTT 57.120 29.630 0.00 0.00 0.00 1.82
118 119 9.258629 TCCCACAATTTCTCAAATCAGATAATT 57.741 29.630 0.00 0.00 0.00 1.40
119 120 8.689972 GTCCCACAATTTCTCAAATCAGATAAT 58.310 33.333 0.00 0.00 0.00 1.28
120 121 7.890127 AGTCCCACAATTTCTCAAATCAGATAA 59.110 33.333 0.00 0.00 0.00 1.75
121 122 7.405292 AGTCCCACAATTTCTCAAATCAGATA 58.595 34.615 0.00 0.00 0.00 1.98
122 123 6.251471 AGTCCCACAATTTCTCAAATCAGAT 58.749 36.000 0.00 0.00 0.00 2.90
123 124 5.634118 AGTCCCACAATTTCTCAAATCAGA 58.366 37.500 0.00 0.00 0.00 3.27
124 125 5.972107 AGTCCCACAATTTCTCAAATCAG 57.028 39.130 0.00 0.00 0.00 2.90
125 126 7.004086 ACTTAGTCCCACAATTTCTCAAATCA 58.996 34.615 0.00 0.00 0.00 2.57
126 127 7.454260 ACTTAGTCCCACAATTTCTCAAATC 57.546 36.000 0.00 0.00 0.00 2.17
127 128 7.839680 AACTTAGTCCCACAATTTCTCAAAT 57.160 32.000 0.00 0.00 0.00 2.32
128 129 7.654022 AAACTTAGTCCCACAATTTCTCAAA 57.346 32.000 0.00 0.00 0.00 2.69
129 130 7.654022 AAAACTTAGTCCCACAATTTCTCAA 57.346 32.000 0.00 0.00 0.00 3.02
130 131 7.996644 AGTAAAACTTAGTCCCACAATTTCTCA 59.003 33.333 0.00 0.00 0.00 3.27
131 132 8.290325 CAGTAAAACTTAGTCCCACAATTTCTC 58.710 37.037 0.00 0.00 0.00 2.87
132 133 7.230712 CCAGTAAAACTTAGTCCCACAATTTCT 59.769 37.037 0.00 0.00 0.00 2.52
133 134 7.013942 ACCAGTAAAACTTAGTCCCACAATTTC 59.986 37.037 0.00 0.00 0.00 2.17
134 135 6.837048 ACCAGTAAAACTTAGTCCCACAATTT 59.163 34.615 0.00 0.00 0.00 1.82
135 136 6.370453 ACCAGTAAAACTTAGTCCCACAATT 58.630 36.000 0.00 0.00 0.00 2.32
136 137 5.948842 ACCAGTAAAACTTAGTCCCACAAT 58.051 37.500 0.00 0.00 0.00 2.71
137 138 5.376756 ACCAGTAAAACTTAGTCCCACAA 57.623 39.130 0.00 0.00 0.00 3.33
138 139 5.376756 AACCAGTAAAACTTAGTCCCACA 57.623 39.130 0.00 0.00 0.00 4.17
139 140 6.319405 TCAAAACCAGTAAAACTTAGTCCCAC 59.681 38.462 0.00 0.00 0.00 4.61
140 141 6.424883 TCAAAACCAGTAAAACTTAGTCCCA 58.575 36.000 0.00 0.00 0.00 4.37
141 142 6.947644 TCAAAACCAGTAAAACTTAGTCCC 57.052 37.500 0.00 0.00 0.00 4.46
142 143 7.993101 ACTTCAAAACCAGTAAAACTTAGTCC 58.007 34.615 0.00 0.00 0.00 3.85
143 144 9.285770 CAACTTCAAAACCAGTAAAACTTAGTC 57.714 33.333 0.00 0.00 0.00 2.59
144 145 9.016438 TCAACTTCAAAACCAGTAAAACTTAGT 57.984 29.630 0.00 0.00 0.00 2.24
145 146 9.849166 TTCAACTTCAAAACCAGTAAAACTTAG 57.151 29.630 0.00 0.00 0.00 2.18
147 148 9.549078 TTTTCAACTTCAAAACCAGTAAAACTT 57.451 25.926 0.00 0.00 0.00 2.66
148 149 9.549078 TTTTTCAACTTCAAAACCAGTAAAACT 57.451 25.926 0.00 0.00 0.00 2.66
149 150 9.588774 GTTTTTCAACTTCAAAACCAGTAAAAC 57.411 29.630 0.00 0.00 37.04 2.43
150 151 9.326413 TGTTTTTCAACTTCAAAACCAGTAAAA 57.674 25.926 5.34 0.00 40.65 1.52
151 152 8.888579 TGTTTTTCAACTTCAAAACCAGTAAA 57.111 26.923 5.34 0.00 40.65 2.01
152 153 8.888579 TTGTTTTTCAACTTCAAAACCAGTAA 57.111 26.923 5.34 0.00 40.65 2.24
153 154 9.495572 AATTGTTTTTCAACTTCAAAACCAGTA 57.504 25.926 5.34 0.00 40.65 2.74
154 155 7.977789 ATTGTTTTTCAACTTCAAAACCAGT 57.022 28.000 5.34 0.00 40.65 4.00
155 156 9.328721 GAAATTGTTTTTCAACTTCAAAACCAG 57.671 29.630 5.34 0.00 40.56 4.00
156 157 9.061435 AGAAATTGTTTTTCAACTTCAAAACCA 57.939 25.926 5.34 0.00 42.45 3.67
180 181 9.939802 GTCCCTTAACTCTTTCAAAAGTATAGA 57.060 33.333 2.63 0.00 37.31 1.98
181 182 8.870879 CGTCCCTTAACTCTTTCAAAAGTATAG 58.129 37.037 2.63 0.00 37.31 1.31
182 183 8.587608 TCGTCCCTTAACTCTTTCAAAAGTATA 58.412 33.333 2.63 0.00 37.31 1.47
183 184 7.447594 TCGTCCCTTAACTCTTTCAAAAGTAT 58.552 34.615 2.63 0.00 37.31 2.12
184 185 6.819284 TCGTCCCTTAACTCTTTCAAAAGTA 58.181 36.000 2.63 0.00 37.31 2.24
185 186 5.677567 TCGTCCCTTAACTCTTTCAAAAGT 58.322 37.500 2.63 0.00 37.31 2.66
186 187 6.613755 TTCGTCCCTTAACTCTTTCAAAAG 57.386 37.500 0.00 0.00 37.36 2.27
187 188 7.393841 TTTTCGTCCCTTAACTCTTTCAAAA 57.606 32.000 0.00 0.00 0.00 2.44
188 189 7.393841 TTTTTCGTCCCTTAACTCTTTCAAA 57.606 32.000 0.00 0.00 0.00 2.69
189 190 7.576861 ATTTTTCGTCCCTTAACTCTTTCAA 57.423 32.000 0.00 0.00 0.00 2.69
190 191 8.857694 ATATTTTTCGTCCCTTAACTCTTTCA 57.142 30.769 0.00 0.00 0.00 2.69
192 193 9.955102 AGTATATTTTTCGTCCCTTAACTCTTT 57.045 29.630 0.00 0.00 0.00 2.52
193 194 9.955102 AAGTATATTTTTCGTCCCTTAACTCTT 57.045 29.630 0.00 0.00 0.00 2.85
194 195 9.597170 GAAGTATATTTTTCGTCCCTTAACTCT 57.403 33.333 0.00 0.00 0.00 3.24
195 196 9.597170 AGAAGTATATTTTTCGTCCCTTAACTC 57.403 33.333 0.00 0.00 0.00 3.01
196 197 9.955102 AAGAAGTATATTTTTCGTCCCTTAACT 57.045 29.630 0.00 0.00 0.00 2.24
198 199 9.387257 GGAAGAAGTATATTTTTCGTCCCTTAA 57.613 33.333 16.26 0.00 42.47 1.85
199 200 8.765517 AGGAAGAAGTATATTTTTCGTCCCTTA 58.234 33.333 20.18 0.00 46.52 2.69
200 201 7.631007 AGGAAGAAGTATATTTTTCGTCCCTT 58.369 34.615 20.18 8.67 46.52 3.95
201 202 7.196637 AGGAAGAAGTATATTTTTCGTCCCT 57.803 36.000 20.18 12.60 46.52 4.20
202 203 8.953368 TTAGGAAGAAGTATATTTTTCGTCCC 57.047 34.615 20.18 11.28 46.52 4.46
236 237 8.793592 TCGTATATGAGTGCAACACTAGATTAT 58.206 33.333 0.00 0.00 45.44 1.28
237 238 8.161699 TCGTATATGAGTGCAACACTAGATTA 57.838 34.615 0.00 0.00 45.44 1.75
238 239 7.039313 TCGTATATGAGTGCAACACTAGATT 57.961 36.000 0.00 0.00 45.44 2.40
239 240 6.635030 TCGTATATGAGTGCAACACTAGAT 57.365 37.500 0.00 0.00 45.44 1.98
240 241 6.061231 CTCGTATATGAGTGCAACACTAGA 57.939 41.667 13.05 0.00 45.44 2.43
252 253 9.507280 TCGTAAAACCTTTTACTCGTATATGAG 57.493 33.333 18.61 18.61 46.33 2.90
253 254 9.507280 CTCGTAAAACCTTTTACTCGTATATGA 57.493 33.333 15.38 0.00 46.33 2.15
254 255 9.507280 TCTCGTAAAACCTTTTACTCGTATATG 57.493 33.333 15.38 0.00 46.33 1.78
255 256 9.508567 GTCTCGTAAAACCTTTTACTCGTATAT 57.491 33.333 15.38 0.00 46.33 0.86
256 257 8.730680 AGTCTCGTAAAACCTTTTACTCGTATA 58.269 33.333 15.38 0.00 46.33 1.47
257 258 7.597386 AGTCTCGTAAAACCTTTTACTCGTAT 58.403 34.615 15.38 1.20 46.33 3.06
258 259 6.970484 AGTCTCGTAAAACCTTTTACTCGTA 58.030 36.000 15.38 2.41 46.33 3.43
259 260 5.836347 AGTCTCGTAAAACCTTTTACTCGT 58.164 37.500 15.38 0.00 46.33 4.18
260 261 5.058977 CGAGTCTCGTAAAACCTTTTACTCG 59.941 44.000 14.27 14.63 46.33 4.18
261 262 6.373359 CGAGTCTCGTAAAACCTTTTACTC 57.627 41.667 14.27 8.75 46.33 2.59
276 277 3.217599 TCCTTCATGAAACGAGTCTCG 57.782 47.619 20.57 20.57 46.93 4.04
277 278 6.814146 AGTTATTCCTTCATGAAACGAGTCTC 59.186 38.462 9.88 0.00 0.00 3.36
278 279 6.702329 AGTTATTCCTTCATGAAACGAGTCT 58.298 36.000 9.88 0.94 0.00 3.24
279 280 6.969828 AGTTATTCCTTCATGAAACGAGTC 57.030 37.500 9.88 0.00 0.00 3.36
280 281 8.883731 CATAAGTTATTCCTTCATGAAACGAGT 58.116 33.333 9.88 7.40 0.00 4.18
281 282 8.883731 ACATAAGTTATTCCTTCATGAAACGAG 58.116 33.333 9.88 0.00 0.00 4.18
282 283 8.664798 CACATAAGTTATTCCTTCATGAAACGA 58.335 33.333 9.88 5.25 0.00 3.85
283 284 8.450964 ACACATAAGTTATTCCTTCATGAAACG 58.549 33.333 9.88 2.80 0.00 3.60
284 285 9.774742 GACACATAAGTTATTCCTTCATGAAAC 57.225 33.333 9.88 3.64 0.00 2.78
285 286 9.739276 AGACACATAAGTTATTCCTTCATGAAA 57.261 29.630 9.88 0.00 0.00 2.69
286 287 9.739276 AAGACACATAAGTTATTCCTTCATGAA 57.261 29.630 8.12 8.12 0.00 2.57
287 288 9.739276 AAAGACACATAAGTTATTCCTTCATGA 57.261 29.630 0.00 0.00 0.00 3.07
299 300 9.620660 CCGCTAAAAATAAAAGACACATAAGTT 57.379 29.630 0.00 0.00 0.00 2.66
300 301 8.789762 ACCGCTAAAAATAAAAGACACATAAGT 58.210 29.630 0.00 0.00 0.00 2.24
303 304 8.885722 CCTACCGCTAAAAATAAAAGACACATA 58.114 33.333 0.00 0.00 0.00 2.29
304 305 7.608761 TCCTACCGCTAAAAATAAAAGACACAT 59.391 33.333 0.00 0.00 0.00 3.21
305 306 6.935771 TCCTACCGCTAAAAATAAAAGACACA 59.064 34.615 0.00 0.00 0.00 3.72
306 307 7.368480 TCCTACCGCTAAAAATAAAAGACAC 57.632 36.000 0.00 0.00 0.00 3.67
307 308 7.982761 TTCCTACCGCTAAAAATAAAAGACA 57.017 32.000 0.00 0.00 0.00 3.41
308 309 8.671028 TCATTCCTACCGCTAAAAATAAAAGAC 58.329 33.333 0.00 0.00 0.00 3.01
309 310 8.671028 GTCATTCCTACCGCTAAAAATAAAAGA 58.329 33.333 0.00 0.00 0.00 2.52
310 311 8.455682 TGTCATTCCTACCGCTAAAAATAAAAG 58.544 33.333 0.00 0.00 0.00 2.27
311 312 8.338072 TGTCATTCCTACCGCTAAAAATAAAA 57.662 30.769 0.00 0.00 0.00 1.52
312 313 7.925043 TGTCATTCCTACCGCTAAAAATAAA 57.075 32.000 0.00 0.00 0.00 1.40
313 314 8.514330 AATGTCATTCCTACCGCTAAAAATAA 57.486 30.769 0.00 0.00 0.00 1.40
314 315 8.514330 AAATGTCATTCCTACCGCTAAAAATA 57.486 30.769 0.00 0.00 0.00 1.40
315 316 7.404671 AAATGTCATTCCTACCGCTAAAAAT 57.595 32.000 0.00 0.00 0.00 1.82
316 317 6.827586 AAATGTCATTCCTACCGCTAAAAA 57.172 33.333 0.00 0.00 0.00 1.94
317 318 6.827586 AAAATGTCATTCCTACCGCTAAAA 57.172 33.333 0.00 0.00 0.00 1.52
318 319 6.827586 AAAAATGTCATTCCTACCGCTAAA 57.172 33.333 0.00 0.00 0.00 1.85
319 320 7.554835 ACATAAAAATGTCATTCCTACCGCTAA 59.445 33.333 0.00 0.00 0.00 3.09
320 321 7.051623 ACATAAAAATGTCATTCCTACCGCTA 58.948 34.615 0.00 0.00 0.00 4.26
321 322 5.885912 ACATAAAAATGTCATTCCTACCGCT 59.114 36.000 0.00 0.00 0.00 5.52
322 323 6.131544 ACATAAAAATGTCATTCCTACCGC 57.868 37.500 0.00 0.00 0.00 5.68
340 341 9.644993 CGCGATTGAGATGTTAAAATTACATAA 57.355 29.630 0.00 0.00 36.41 1.90
341 342 8.822855 ACGCGATTGAGATGTTAAAATTACATA 58.177 29.630 15.93 0.00 36.41 2.29
342 343 7.639850 CACGCGATTGAGATGTTAAAATTACAT 59.360 33.333 15.93 0.00 38.86 2.29
343 344 6.958752 CACGCGATTGAGATGTTAAAATTACA 59.041 34.615 15.93 0.00 0.00 2.41
344 345 6.410914 CCACGCGATTGAGATGTTAAAATTAC 59.589 38.462 15.93 0.00 0.00 1.89
345 346 6.482835 CCACGCGATTGAGATGTTAAAATTA 58.517 36.000 15.93 0.00 0.00 1.40
346 347 5.331902 CCACGCGATTGAGATGTTAAAATT 58.668 37.500 15.93 0.00 0.00 1.82
347 348 4.730613 GCCACGCGATTGAGATGTTAAAAT 60.731 41.667 15.93 0.00 0.00 1.82
348 349 3.425625 GCCACGCGATTGAGATGTTAAAA 60.426 43.478 15.93 0.00 0.00 1.52
349 350 2.095213 GCCACGCGATTGAGATGTTAAA 59.905 45.455 15.93 0.00 0.00 1.52
350 351 1.663643 GCCACGCGATTGAGATGTTAA 59.336 47.619 15.93 0.00 0.00 2.01
351 352 1.134818 AGCCACGCGATTGAGATGTTA 60.135 47.619 15.93 0.00 0.00 2.41
352 353 0.391661 AGCCACGCGATTGAGATGTT 60.392 50.000 15.93 0.00 0.00 2.71
353 354 1.086067 CAGCCACGCGATTGAGATGT 61.086 55.000 15.93 0.00 0.00 3.06
354 355 1.086067 ACAGCCACGCGATTGAGATG 61.086 55.000 15.93 7.72 0.00 2.90
355 356 0.807667 GACAGCCACGCGATTGAGAT 60.808 55.000 15.93 0.00 0.00 2.75
356 357 1.446099 GACAGCCACGCGATTGAGA 60.446 57.895 15.93 0.00 0.00 3.27
357 358 2.792290 CGACAGCCACGCGATTGAG 61.792 63.158 15.93 1.55 0.00 3.02
358 359 2.809174 CGACAGCCACGCGATTGA 60.809 61.111 15.93 0.00 0.00 2.57
359 360 3.112075 ACGACAGCCACGCGATTG 61.112 61.111 15.93 0.00 0.00 2.67
360 361 3.112075 CACGACAGCCACGCGATT 61.112 61.111 15.93 0.00 0.00 3.34
365 366 4.602259 ACACCCACGACAGCCACG 62.602 66.667 0.00 0.00 0.00 4.94
366 367 2.972505 CACACCCACGACAGCCAC 60.973 66.667 0.00 0.00 0.00 5.01
367 368 4.927782 GCACACCCACGACAGCCA 62.928 66.667 0.00 0.00 0.00 4.75
370 371 4.969196 AGCGCACACCCACGACAG 62.969 66.667 11.47 0.00 0.00 3.51
371 372 4.961511 GAGCGCACACCCACGACA 62.962 66.667 11.47 0.00 0.00 4.35
385 386 3.300667 CTGTTTGACAGCCGCGAGC 62.301 63.158 8.23 9.98 39.62 5.03
386 387 2.856032 CTGTTTGACAGCCGCGAG 59.144 61.111 8.23 0.00 39.62 5.03
408 409 9.639601 AAAAGCCTAAATTCTAATAAGTGCAAC 57.360 29.630 0.00 0.00 0.00 4.17
434 435 7.414762 GCCCACGCAAAAATCTAGTATAGAAAA 60.415 37.037 0.00 0.00 42.83 2.29
435 436 6.037830 GCCCACGCAAAAATCTAGTATAGAAA 59.962 38.462 0.00 0.00 42.83 2.52
436 437 5.526111 GCCCACGCAAAAATCTAGTATAGAA 59.474 40.000 0.00 0.00 42.83 2.10
437 438 5.054477 GCCCACGCAAAAATCTAGTATAGA 58.946 41.667 0.00 0.00 43.40 1.98
438 439 4.814234 TGCCCACGCAAAAATCTAGTATAG 59.186 41.667 0.00 0.00 43.74 1.31
439 440 4.771903 TGCCCACGCAAAAATCTAGTATA 58.228 39.130 0.00 0.00 43.74 1.47
440 441 3.616219 TGCCCACGCAAAAATCTAGTAT 58.384 40.909 0.00 0.00 43.74 2.12
635 652 5.958428 TCGTTATCGATAAAAATGTCGCTG 58.042 37.500 19.11 2.66 41.35 5.18
739 756 4.609691 TTTCTTTGATAAATCGGCCGAC 57.390 40.909 33.75 18.44 0.00 4.79
1809 1872 2.414559 CGGAACTTGCATGTGTCCATTC 60.415 50.000 22.08 10.89 0.00 2.67
2543 2640 7.078249 TCAAGCCTTGCCAATATAGAGATAA 57.922 36.000 0.00 0.00 0.00 1.75
3891 4032 5.374080 CGATAAATTATGCACCACGACATC 58.626 41.667 0.00 0.00 0.00 3.06
4366 5979 1.824852 GGACCAATGGCCCTGTAAAAG 59.175 52.381 0.00 0.00 0.00 2.27
6107 7819 9.784531 CTGGGAATGTATGTCATATCTTTTAGT 57.215 33.333 0.00 0.00 35.48 2.24


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.