Multiple sequence alignment - TraesCS5D01G444900

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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 TraesCS5D01G444900 chr5D 100.000 2818 0 0 1 2818 495620426 495617609 0.000000e+00 5204.0
1 TraesCS5D01G444900 chr5D 76.190 420 78 20 1374 1782 461912975 461913383 4.760000e-48 202.0
2 TraesCS5D01G444900 chr5D 84.615 78 10 2 1087 1163 495625081 495625005 3.010000e-10 76.8
3 TraesCS5D01G444900 chr5B 91.990 2347 97 46 308 2608 612675283 612672982 0.000000e+00 3208.0
4 TraesCS5D01G444900 chr5B 98.592 213 3 0 2606 2818 612672824 612672612 7.370000e-101 377.0
5 TraesCS5D01G444900 chr5B 75.476 420 81 20 1374 1782 567874352 567874760 4.790000e-43 185.0
6 TraesCS5D01G444900 chr5B 91.304 115 9 1 1 114 680316787 680316901 3.760000e-34 156.0
7 TraesCS5D01G444900 chr5B 84.211 76 10 2 1087 1161 612678809 612678735 3.890000e-09 73.1
8 TraesCS5D01G444900 chr5A 90.959 2013 100 32 727 2719 619683839 619681889 0.000000e+00 2634.0
9 TraesCS5D01G444900 chr5A 75.952 420 79 20 1374 1782 581926703 581927111 2.210000e-46 196.0
10 TraesCS5D01G444900 chr5A 79.902 204 33 8 234 434 619684224 619684026 2.930000e-30 143.0
11 TraesCS5D01G444900 chr5A 98.039 51 1 0 2768 2818 619681885 619681835 3.870000e-14 89.8
12 TraesCS5D01G444900 chr5A 84.211 76 10 2 1087 1161 619688340 619688266 3.890000e-09 73.1
13 TraesCS5D01G444900 chr2B 94.017 117 7 0 1 117 750061567 750061683 8.020000e-41 178.0
14 TraesCS5D01G444900 chr4A 90.435 115 11 0 1 115 689529042 689528928 4.860000e-33 152.0
15 TraesCS5D01G444900 chr3B 93.939 99 4 2 24 120 542923901 542923999 6.290000e-32 148.0
16 TraesCS5D01G444900 chr6A 85.841 113 15 1 2053 2165 518594432 518594321 4.930000e-23 119.0
17 TraesCS5D01G444900 chr6B 90.217 92 6 3 21 111 599728487 599728576 1.770000e-22 117.0
18 TraesCS5D01G444900 chr1A 86.916 107 8 5 12 115 172183066 172182963 6.380000e-22 115.0


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 TraesCS5D01G444900 chr5D 495617609 495620426 2817 True 5204.000000 5204 100.000000 1 2818 1 chr5D.!!$R1 2817
1 TraesCS5D01G444900 chr5B 612672612 612678809 6197 True 1219.366667 3208 91.597667 308 2818 3 chr5B.!!$R1 2510
2 TraesCS5D01G444900 chr5A 619681835 619684224 2389 True 955.600000 2634 89.633333 234 2818 3 chr5A.!!$R2 2584

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
97 98 0.122435 ACCTCCCCAATCCCCTTGTA 59.878 55.0 0.0 0.0 32.61 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 5153 0.391661 GGCAGGCAGAGACGAATGAA 60.392 55.0 0.0 0.0 0.0 2.57 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
19 20 1.680338 GAGGGATTCGTGGGGAATTG 58.320 55.000 0.00 0.00 45.33 2.32
20 21 1.211949 GAGGGATTCGTGGGGAATTGA 59.788 52.381 0.00 0.00 45.33 2.57
21 22 1.212935 AGGGATTCGTGGGGAATTGAG 59.787 52.381 0.00 0.00 45.33 3.02
22 23 1.211949 GGGATTCGTGGGGAATTGAGA 59.788 52.381 0.00 0.00 45.33 3.27
24 25 2.565841 GATTCGTGGGGAATTGAGAGG 58.434 52.381 0.00 0.00 45.33 3.69
26 27 1.879575 TCGTGGGGAATTGAGAGGAT 58.120 50.000 0.00 0.00 0.00 3.24
27 28 2.196595 TCGTGGGGAATTGAGAGGATT 58.803 47.619 0.00 0.00 0.00 3.01
29 30 3.388024 TCGTGGGGAATTGAGAGGATTAG 59.612 47.826 0.00 0.00 0.00 1.73
30 31 3.495100 CGTGGGGAATTGAGAGGATTAGG 60.495 52.174 0.00 0.00 0.00 2.69
32 33 3.459598 TGGGGAATTGAGAGGATTAGGTG 59.540 47.826 0.00 0.00 0.00 4.00
33 34 3.181439 GGGGAATTGAGAGGATTAGGTGG 60.181 52.174 0.00 0.00 0.00 4.61
34 35 3.716872 GGGAATTGAGAGGATTAGGTGGA 59.283 47.826 0.00 0.00 0.00 4.02
35 36 4.202409 GGGAATTGAGAGGATTAGGTGGAG 60.202 50.000 0.00 0.00 0.00 3.86
36 37 4.202409 GGAATTGAGAGGATTAGGTGGAGG 60.202 50.000 0.00 0.00 0.00 4.30
38 39 3.320610 TGAGAGGATTAGGTGGAGGAG 57.679 52.381 0.00 0.00 0.00 3.69
39 40 2.859404 TGAGAGGATTAGGTGGAGGAGA 59.141 50.000 0.00 0.00 0.00 3.71
40 41 3.117322 TGAGAGGATTAGGTGGAGGAGAG 60.117 52.174 0.00 0.00 0.00 3.20
41 42 2.178984 AGAGGATTAGGTGGAGGAGAGG 59.821 54.545 0.00 0.00 0.00 3.69
42 43 1.221781 AGGATTAGGTGGAGGAGAGGG 59.778 57.143 0.00 0.00 0.00 4.30
43 44 1.220750 GGATTAGGTGGAGGAGAGGGA 59.779 57.143 0.00 0.00 0.00 4.20
44 45 2.158081 GGATTAGGTGGAGGAGAGGGAT 60.158 54.545 0.00 0.00 0.00 3.85
45 46 3.592865 GATTAGGTGGAGGAGAGGGATT 58.407 50.000 0.00 0.00 0.00 3.01
46 47 2.777459 TAGGTGGAGGAGAGGGATTC 57.223 55.000 0.00 0.00 0.00 2.52
47 48 0.719015 AGGTGGAGGAGAGGGATTCA 59.281 55.000 0.00 0.00 0.00 2.57
64 65 5.254339 GATTCACCCAATCCACTCAAATC 57.746 43.478 0.00 0.00 35.66 2.17
67 68 1.007118 ACCCAATCCACTCAAATCCCC 59.993 52.381 0.00 0.00 0.00 4.81
69 70 1.288932 CCAATCCACTCAAATCCCCCT 59.711 52.381 0.00 0.00 0.00 4.79
70 71 2.659428 CAATCCACTCAAATCCCCCTC 58.341 52.381 0.00 0.00 0.00 4.30
73 74 0.548510 CCACTCAAATCCCCCTCTCC 59.451 60.000 0.00 0.00 0.00 3.71
74 75 1.289160 CACTCAAATCCCCCTCTCCA 58.711 55.000 0.00 0.00 0.00 3.86
75 76 1.065126 CACTCAAATCCCCCTCTCCAC 60.065 57.143 0.00 0.00 0.00 4.02
76 77 1.289160 CTCAAATCCCCCTCTCCACA 58.711 55.000 0.00 0.00 0.00 4.17
77 78 1.635487 CTCAAATCCCCCTCTCCACAA 59.365 52.381 0.00 0.00 0.00 3.33
78 79 2.041620 CTCAAATCCCCCTCTCCACAAA 59.958 50.000 0.00 0.00 0.00 2.83
79 80 2.171003 CAAATCCCCCTCTCCACAAAC 58.829 52.381 0.00 0.00 0.00 2.93
80 81 0.704664 AATCCCCCTCTCCACAAACC 59.295 55.000 0.00 0.00 0.00 3.27
81 82 0.178831 ATCCCCCTCTCCACAAACCT 60.179 55.000 0.00 0.00 0.00 3.50
82 83 0.840722 TCCCCCTCTCCACAAACCTC 60.841 60.000 0.00 0.00 0.00 3.85
83 84 1.685820 CCCCTCTCCACAAACCTCC 59.314 63.158 0.00 0.00 0.00 4.30
85 86 1.685820 CCTCTCCACAAACCTCCCC 59.314 63.158 0.00 0.00 0.00 4.81
86 87 1.133809 CCTCTCCACAAACCTCCCCA 61.134 60.000 0.00 0.00 0.00 4.96
87 88 0.771127 CTCTCCACAAACCTCCCCAA 59.229 55.000 0.00 0.00 0.00 4.12
88 89 1.355720 CTCTCCACAAACCTCCCCAAT 59.644 52.381 0.00 0.00 0.00 3.16
89 90 1.354368 TCTCCACAAACCTCCCCAATC 59.646 52.381 0.00 0.00 0.00 2.67
90 91 0.407918 TCCACAAACCTCCCCAATCC 59.592 55.000 0.00 0.00 0.00 3.01
91 92 0.614697 CCACAAACCTCCCCAATCCC 60.615 60.000 0.00 0.00 0.00 3.85
92 93 0.614697 CACAAACCTCCCCAATCCCC 60.615 60.000 0.00 0.00 0.00 4.81
93 94 0.780090 ACAAACCTCCCCAATCCCCT 60.780 55.000 0.00 0.00 0.00 4.79
94 95 0.413434 CAAACCTCCCCAATCCCCTT 59.587 55.000 0.00 0.00 0.00 3.95
95 96 0.413434 AAACCTCCCCAATCCCCTTG 59.587 55.000 0.00 0.00 34.42 3.61
96 97 0.780090 AACCTCCCCAATCCCCTTGT 60.780 55.000 0.00 0.00 32.61 3.16
97 98 0.122435 ACCTCCCCAATCCCCTTGTA 59.878 55.000 0.00 0.00 32.61 2.41
98 99 1.275595 ACCTCCCCAATCCCCTTGTAT 60.276 52.381 0.00 0.00 32.61 2.29
100 101 2.135189 CTCCCCAATCCCCTTGTATCA 58.865 52.381 0.00 0.00 32.61 2.15
101 102 2.513738 CTCCCCAATCCCCTTGTATCAA 59.486 50.000 0.00 0.00 32.61 2.57
102 103 2.929724 TCCCCAATCCCCTTGTATCAAA 59.070 45.455 0.00 0.00 32.61 2.69
104 105 3.642848 CCCCAATCCCCTTGTATCAAATG 59.357 47.826 0.00 0.00 32.61 2.32
105 106 4.545678 CCCAATCCCCTTGTATCAAATGA 58.454 43.478 0.00 0.00 32.61 2.57
107 108 4.586001 CCAATCCCCTTGTATCAAATGAGG 59.414 45.833 0.00 0.00 32.61 3.86
108 109 3.297134 TCCCCTTGTATCAAATGAGGC 57.703 47.619 0.00 0.00 0.00 4.70
109 110 2.091885 TCCCCTTGTATCAAATGAGGCC 60.092 50.000 0.00 0.00 0.00 5.19
111 112 3.138283 CCCCTTGTATCAAATGAGGCCTA 59.862 47.826 4.42 0.00 0.00 3.93
112 113 4.386312 CCCCTTGTATCAAATGAGGCCTAA 60.386 45.833 4.42 0.00 0.00 2.69
113 114 4.823989 CCCTTGTATCAAATGAGGCCTAAG 59.176 45.833 4.42 0.70 0.00 2.18
114 115 4.823989 CCTTGTATCAAATGAGGCCTAAGG 59.176 45.833 4.42 7.30 0.00 2.69
115 116 5.397899 CCTTGTATCAAATGAGGCCTAAGGA 60.398 44.000 15.67 4.81 34.38 3.36
116 117 5.708736 TGTATCAAATGAGGCCTAAGGAA 57.291 39.130 4.42 0.00 0.00 3.36
118 119 4.591321 ATCAAATGAGGCCTAAGGAACA 57.409 40.909 4.42 0.00 0.00 3.18
119 120 4.591321 TCAAATGAGGCCTAAGGAACAT 57.409 40.909 4.42 0.00 0.00 2.71
121 122 4.018506 TCAAATGAGGCCTAAGGAACATCA 60.019 41.667 4.42 0.00 0.00 3.07
123 124 2.551270 TGAGGCCTAAGGAACATCACT 58.449 47.619 4.42 0.00 0.00 3.41
124 125 2.237143 TGAGGCCTAAGGAACATCACTG 59.763 50.000 4.42 0.00 0.00 3.66
125 126 1.561542 AGGCCTAAGGAACATCACTGG 59.438 52.381 1.29 0.00 0.00 4.00
127 128 1.340017 GCCTAAGGAACATCACTGGCA 60.340 52.381 0.00 0.00 38.99 4.92
128 129 2.879756 GCCTAAGGAACATCACTGGCAA 60.880 50.000 0.00 0.00 38.99 4.52
129 130 2.749621 CCTAAGGAACATCACTGGCAAC 59.250 50.000 0.00 0.00 0.00 4.17
131 132 0.396435 AGGAACATCACTGGCAACGA 59.604 50.000 0.00 0.00 42.51 3.85
134 135 0.889186 AACATCACTGGCAACGACCC 60.889 55.000 0.00 0.00 42.51 4.46
135 136 2.040544 CATCACTGGCAACGACCCC 61.041 63.158 0.00 0.00 42.51 4.95
136 137 3.268103 ATCACTGGCAACGACCCCC 62.268 63.158 0.00 0.00 42.51 5.40
147 148 2.993264 GACCCCCGTCGAAGGACA 60.993 66.667 19.75 0.00 43.61 4.02
148 149 2.524887 ACCCCCGTCGAAGGACAA 60.525 61.111 19.75 0.00 43.61 3.18
149 150 2.264794 CCCCCGTCGAAGGACAAG 59.735 66.667 19.75 1.53 43.61 3.16
150 151 2.264794 CCCCGTCGAAGGACAAGG 59.735 66.667 19.75 7.48 43.61 3.61
153 154 1.004918 CCGTCGAAGGACAAGGCTT 60.005 57.895 12.53 0.00 43.61 4.35
154 155 0.602905 CCGTCGAAGGACAAGGCTTT 60.603 55.000 12.53 0.00 43.61 3.51
155 156 0.790814 CGTCGAAGGACAAGGCTTTC 59.209 55.000 0.00 0.00 43.61 2.62
156 157 0.790814 GTCGAAGGACAAGGCTTTCG 59.209 55.000 13.25 13.25 45.22 3.46
157 158 0.949105 TCGAAGGACAAGGCTTTCGC 60.949 55.000 14.43 0.00 44.05 4.70
169 170 1.032114 GCTTTCGCCCACTTATGCCT 61.032 55.000 0.00 0.00 0.00 4.75
170 171 1.017387 CTTTCGCCCACTTATGCCTC 58.983 55.000 0.00 0.00 0.00 4.70
171 172 0.742990 TTTCGCCCACTTATGCCTCG 60.743 55.000 0.00 0.00 0.00 4.63
172 173 3.272334 CGCCCACTTATGCCTCGC 61.272 66.667 0.00 0.00 0.00 5.03
173 174 2.902343 GCCCACTTATGCCTCGCC 60.902 66.667 0.00 0.00 0.00 5.54
174 175 2.589540 CCCACTTATGCCTCGCCA 59.410 61.111 0.00 0.00 0.00 5.69
177 178 0.392998 CCACTTATGCCTCGCCAACT 60.393 55.000 0.00 0.00 0.00 3.16
178 179 1.009829 CACTTATGCCTCGCCAACTC 58.990 55.000 0.00 0.00 0.00 3.01
180 181 1.293924 CTTATGCCTCGCCAACTCTG 58.706 55.000 0.00 0.00 0.00 3.35
182 183 0.175760 TATGCCTCGCCAACTCTGAC 59.824 55.000 0.00 0.00 0.00 3.51
183 184 2.435059 GCCTCGCCAACTCTGACC 60.435 66.667 0.00 0.00 0.00 4.02
184 185 2.948720 GCCTCGCCAACTCTGACCT 61.949 63.158 0.00 0.00 0.00 3.85
185 186 1.605058 GCCTCGCCAACTCTGACCTA 61.605 60.000 0.00 0.00 0.00 3.08
186 187 0.457851 CCTCGCCAACTCTGACCTAG 59.542 60.000 0.00 0.00 0.00 3.02
212 213 0.179004 AGCCAATCCACAACGAACCA 60.179 50.000 0.00 0.00 0.00 3.67
213 214 0.887933 GCCAATCCACAACGAACCAT 59.112 50.000 0.00 0.00 0.00 3.55
215 216 1.885887 CCAATCCACAACGAACCATGT 59.114 47.619 0.00 0.00 0.00 3.21
216 217 2.351641 CCAATCCACAACGAACCATGTG 60.352 50.000 0.00 0.00 45.06 3.21
221 222 1.878953 ACAACGAACCATGTGAGACC 58.121 50.000 0.00 0.00 0.00 3.85
222 223 1.140052 ACAACGAACCATGTGAGACCA 59.860 47.619 0.00 0.00 0.00 4.02
223 224 2.217750 CAACGAACCATGTGAGACCAA 58.782 47.619 0.00 0.00 0.00 3.67
224 225 2.169832 ACGAACCATGTGAGACCAAG 57.830 50.000 0.00 0.00 0.00 3.61
226 227 1.168714 GAACCATGTGAGACCAAGCC 58.831 55.000 0.00 0.00 0.00 4.35
227 228 0.478072 AACCATGTGAGACCAAGCCA 59.522 50.000 0.00 0.00 0.00 4.75
229 230 1.100510 CCATGTGAGACCAAGCCATG 58.899 55.000 0.00 0.00 34.18 3.66
231 232 1.741706 CATGTGAGACCAAGCCATGTC 59.258 52.381 0.00 0.00 0.00 3.06
232 233 1.059098 TGTGAGACCAAGCCATGTCT 58.941 50.000 0.00 0.00 44.25 3.41
238 239 1.377725 CCAAGCCATGTCTCCGCTT 60.378 57.895 0.85 0.85 43.45 4.68
246 247 2.749076 CCATGTCTCCGCTTGAATTTCA 59.251 45.455 0.00 0.00 0.00 2.69
250 251 4.832248 TGTCTCCGCTTGAATTTCATAGT 58.168 39.130 0.00 0.00 0.00 2.12
258 259 4.379394 GCTTGAATTTCATAGTGCGAACCA 60.379 41.667 0.00 0.00 0.00 3.67
263 268 1.847328 TCATAGTGCGAACCAGGAGA 58.153 50.000 0.00 0.00 0.00 3.71
271 276 2.227194 GCGAACCAGGAGAAAAAGGAA 58.773 47.619 0.00 0.00 0.00 3.36
273 278 2.814336 CGAACCAGGAGAAAAAGGAAGG 59.186 50.000 0.00 0.00 0.00 3.46
274 279 3.496160 CGAACCAGGAGAAAAAGGAAGGA 60.496 47.826 0.00 0.00 0.00 3.36
276 281 2.783510 ACCAGGAGAAAAAGGAAGGACA 59.216 45.455 0.00 0.00 0.00 4.02
278 283 3.149981 CAGGAGAAAAAGGAAGGACACC 58.850 50.000 0.00 0.00 0.00 4.16
279 284 2.783510 AGGAGAAAAAGGAAGGACACCA 59.216 45.455 0.00 0.00 0.00 4.17
284 289 0.179029 AAAGGAAGGACACCACACGG 60.179 55.000 0.00 0.00 38.77 4.94
285 290 2.668550 GGAAGGACACCACACGGC 60.669 66.667 0.00 0.00 34.57 5.68
286 291 2.668550 GAAGGACACCACACGGCC 60.669 66.667 0.00 0.00 34.57 6.13
287 292 3.469863 GAAGGACACCACACGGCCA 62.470 63.158 2.24 0.00 34.57 5.36
288 293 3.767630 AAGGACACCACACGGCCAC 62.768 63.158 2.24 0.00 34.57 5.01
322 3542 4.202315 TGGTGTACTACTTGTGTTGATGCT 60.202 41.667 0.00 0.00 0.00 3.79
366 3587 2.347490 GCTCCGGAAGCCAGAACA 59.653 61.111 5.23 0.00 45.92 3.18
432 3681 1.210155 GCGACAATGCCAGACAACC 59.790 57.895 0.00 0.00 0.00 3.77
466 3715 1.978455 AAGGCTGGTTGGTGTGTCGA 61.978 55.000 0.00 0.00 0.00 4.20
491 3740 8.738645 ACAAAGAGAGTTCATTTAGAGTTGTT 57.261 30.769 0.00 0.00 0.00 2.83
492 3741 9.832445 ACAAAGAGAGTTCATTTAGAGTTGTTA 57.168 29.630 0.00 0.00 0.00 2.41
514 3763 1.737363 GCTCTTTAGAGGTGACTGGCG 60.737 57.143 8.73 0.00 44.43 5.69
516 3765 1.968493 TCTTTAGAGGTGACTGGCGTT 59.032 47.619 0.00 0.00 44.43 4.84
517 3766 2.069273 CTTTAGAGGTGACTGGCGTTG 58.931 52.381 0.00 0.00 44.43 4.10
518 3767 1.045407 TTAGAGGTGACTGGCGTTGT 58.955 50.000 0.00 0.00 44.43 3.32
544 3793 0.452122 GGACGCGATTTTGTTGGTCG 60.452 55.000 15.93 0.00 38.34 4.79
581 3830 3.181438 ACTTAAGGGGTGTATTGTGTGCA 60.181 43.478 7.53 0.00 0.00 4.57
593 3842 1.511850 TGTGTGCATTCGAGTTGGAG 58.488 50.000 0.00 0.00 0.00 3.86
594 3843 0.166814 GTGTGCATTCGAGTTGGAGC 59.833 55.000 0.00 0.00 0.00 4.70
595 3844 0.250252 TGTGCATTCGAGTTGGAGCA 60.250 50.000 0.00 0.00 0.00 4.26
596 3845 0.874390 GTGCATTCGAGTTGGAGCAA 59.126 50.000 0.00 0.00 33.37 3.91
597 3846 1.135859 GTGCATTCGAGTTGGAGCAAG 60.136 52.381 0.00 0.00 33.37 4.01
598 3847 0.179179 GCATTCGAGTTGGAGCAAGC 60.179 55.000 0.00 0.00 0.00 4.01
599 3848 1.446907 CATTCGAGTTGGAGCAAGCT 58.553 50.000 0.00 0.00 0.00 3.74
600 3849 1.808945 CATTCGAGTTGGAGCAAGCTT 59.191 47.619 0.00 0.00 0.00 3.74
601 3850 1.229428 TTCGAGTTGGAGCAAGCTTG 58.771 50.000 22.44 22.44 0.00 4.01
611 3860 3.490890 CAAGCTTGCTACTCGGCC 58.509 61.111 14.65 0.00 0.00 6.13
647 3896 3.836562 AGCTTGCTGGAATTCTTGGATTT 59.163 39.130 5.23 0.00 0.00 2.17
648 3897 4.285260 AGCTTGCTGGAATTCTTGGATTTT 59.715 37.500 5.23 0.00 0.00 1.82
656 3905 5.163216 TGGAATTCTTGGATTTTGTGCCTTT 60.163 36.000 5.23 0.00 0.00 3.11
692 3943 0.518636 GCAGTTTGCATGCTCTCGAA 59.481 50.000 20.33 0.58 44.26 3.71
772 4027 5.533533 TTCCGTTATTATCAACAACGTGG 57.466 39.130 0.00 0.00 42.55 4.94
819 4074 1.657751 GGCACGGGGAAGCAGATTTC 61.658 60.000 0.00 0.00 0.00 2.17
845 4100 1.069765 CCGCGCCCAGAATAGATGT 59.930 57.895 0.00 0.00 0.00 3.06
909 4164 2.289002 GGAAGCTATTGAGACGCCATTG 59.711 50.000 0.00 0.00 0.00 2.82
986 4249 3.385384 GGCAAGGAAAGGCAGGCC 61.385 66.667 0.97 0.97 0.00 5.19
1294 4585 2.421073 TGCTTCGCTTTCTCATTCATGG 59.579 45.455 0.00 0.00 0.00 3.66
1295 4586 2.223433 GCTTCGCTTTCTCATTCATGGG 60.223 50.000 0.00 0.00 0.00 4.00
1298 4589 3.531538 TCGCTTTCTCATTCATGGGTAC 58.468 45.455 0.00 0.00 0.00 3.34
1568 4865 2.907179 CGAGTTCCTGGGGCCCTTT 61.907 63.158 25.93 2.24 0.00 3.11
1580 4877 2.047274 CCCTTTCTCTTCGCCGCA 60.047 61.111 0.00 0.00 0.00 5.69
1661 4958 1.359117 GCTCGTCTACGGCTGCATA 59.641 57.895 0.50 0.00 40.29 3.14
1856 5153 3.956199 CCAGCCAAACCTAACATGATGAT 59.044 43.478 0.00 0.00 0.00 2.45
1857 5154 4.403432 CCAGCCAAACCTAACATGATGATT 59.597 41.667 0.00 0.00 0.00 2.57
1858 5155 5.450965 CCAGCCAAACCTAACATGATGATTC 60.451 44.000 0.00 0.00 0.00 2.52
1859 5156 5.125900 CAGCCAAACCTAACATGATGATTCA 59.874 40.000 0.00 0.00 36.00 2.57
1860 5157 5.895534 AGCCAAACCTAACATGATGATTCAT 59.104 36.000 0.00 0.00 43.51 2.57
1861 5158 6.381994 AGCCAAACCTAACATGATGATTCATT 59.618 34.615 0.00 0.00 40.70 2.57
1862 5159 6.698766 GCCAAACCTAACATGATGATTCATTC 59.301 38.462 0.00 0.00 40.70 2.67
1863 5160 6.914215 CCAAACCTAACATGATGATTCATTCG 59.086 38.462 0.00 0.00 40.70 3.34
1864 5161 7.415541 CCAAACCTAACATGATGATTCATTCGT 60.416 37.037 0.00 0.00 40.70 3.85
1865 5162 6.851222 ACCTAACATGATGATTCATTCGTC 57.149 37.500 0.00 0.00 40.70 4.20
1866 5163 6.586344 ACCTAACATGATGATTCATTCGTCT 58.414 36.000 0.00 0.00 40.70 4.18
1867 5164 6.703607 ACCTAACATGATGATTCATTCGTCTC 59.296 38.462 0.00 0.00 40.70 3.36
1908 5217 7.310664 TGTATGTATGCTAAACTAGATACCGC 58.689 38.462 0.00 0.00 0.00 5.68
1970 5279 3.668447 ACATGAGTCACTGTGATTGGAC 58.332 45.455 14.37 0.97 0.00 4.02
1973 5282 3.930336 TGAGTCACTGTGATTGGACATC 58.070 45.455 14.37 0.00 32.79 3.06
2118 5429 6.319658 TGGATATGAATTTTCTCAGCAAGGAC 59.680 38.462 0.00 0.00 0.00 3.85
2267 5579 3.018149 TGTTTACACCCACTGAAACACC 58.982 45.455 0.00 0.00 36.99 4.16
2504 5825 1.586154 AAACTTCGCCATTGCCTCGG 61.586 55.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.212935 CTCAATTCCCCACGAATCCCT 59.787 52.381 0.00 0.00 40.47 4.20
2 3 1.211949 TCTCAATTCCCCACGAATCCC 59.788 52.381 0.00 0.00 40.47 3.85
4 5 2.170607 TCCTCTCAATTCCCCACGAATC 59.829 50.000 0.00 0.00 40.47 2.52
5 6 2.196595 TCCTCTCAATTCCCCACGAAT 58.803 47.619 0.00 0.00 43.34 3.34
6 7 1.651737 TCCTCTCAATTCCCCACGAA 58.348 50.000 0.00 0.00 34.14 3.85
7 8 1.879575 ATCCTCTCAATTCCCCACGA 58.120 50.000 0.00 0.00 0.00 4.35
8 9 2.717639 AATCCTCTCAATTCCCCACG 57.282 50.000 0.00 0.00 0.00 4.94
9 10 3.459969 ACCTAATCCTCTCAATTCCCCAC 59.540 47.826 0.00 0.00 0.00 4.61
14 15 4.656112 TCCTCCACCTAATCCTCTCAATTC 59.344 45.833 0.00 0.00 0.00 2.17
15 16 4.635473 TCCTCCACCTAATCCTCTCAATT 58.365 43.478 0.00 0.00 0.00 2.32
16 17 4.078336 TCTCCTCCACCTAATCCTCTCAAT 60.078 45.833 0.00 0.00 0.00 2.57
18 19 2.859404 TCTCCTCCACCTAATCCTCTCA 59.141 50.000 0.00 0.00 0.00 3.27
19 20 3.496331 CTCTCCTCCACCTAATCCTCTC 58.504 54.545 0.00 0.00 0.00 3.20
20 21 2.178984 CCTCTCCTCCACCTAATCCTCT 59.821 54.545 0.00 0.00 0.00 3.69
21 22 2.604139 CCTCTCCTCCACCTAATCCTC 58.396 57.143 0.00 0.00 0.00 3.71
22 23 1.221781 CCCTCTCCTCCACCTAATCCT 59.778 57.143 0.00 0.00 0.00 3.24
24 25 2.777459 TCCCTCTCCTCCACCTAATC 57.223 55.000 0.00 0.00 0.00 1.75
26 27 2.317900 TGAATCCCTCTCCTCCACCTAA 59.682 50.000 0.00 0.00 0.00 2.69
27 28 1.937350 TGAATCCCTCTCCTCCACCTA 59.063 52.381 0.00 0.00 0.00 3.08
29 30 0.833949 GTGAATCCCTCTCCTCCACC 59.166 60.000 0.00 0.00 0.00 4.61
30 31 0.833949 GGTGAATCCCTCTCCTCCAC 59.166 60.000 0.00 0.00 35.21 4.02
42 43 4.098501 GGATTTGAGTGGATTGGGTGAATC 59.901 45.833 0.00 0.00 40.00 2.52
43 44 4.026052 GGATTTGAGTGGATTGGGTGAAT 58.974 43.478 0.00 0.00 0.00 2.57
44 45 3.430453 GGATTTGAGTGGATTGGGTGAA 58.570 45.455 0.00 0.00 0.00 3.18
45 46 2.291540 GGGATTTGAGTGGATTGGGTGA 60.292 50.000 0.00 0.00 0.00 4.02
46 47 2.102578 GGGATTTGAGTGGATTGGGTG 58.897 52.381 0.00 0.00 0.00 4.61
47 48 1.007118 GGGGATTTGAGTGGATTGGGT 59.993 52.381 0.00 0.00 0.00 4.51
50 51 2.243221 AGAGGGGGATTTGAGTGGATTG 59.757 50.000 0.00 0.00 0.00 2.67
51 52 2.511637 GAGAGGGGGATTTGAGTGGATT 59.488 50.000 0.00 0.00 0.00 3.01
52 53 2.131023 GAGAGGGGGATTTGAGTGGAT 58.869 52.381 0.00 0.00 0.00 3.41
55 56 1.065126 GTGGAGAGGGGGATTTGAGTG 60.065 57.143 0.00 0.00 0.00 3.51
56 57 1.290134 GTGGAGAGGGGGATTTGAGT 58.710 55.000 0.00 0.00 0.00 3.41
58 59 1.753903 TTGTGGAGAGGGGGATTTGA 58.246 50.000 0.00 0.00 0.00 2.69
59 60 2.171003 GTTTGTGGAGAGGGGGATTTG 58.829 52.381 0.00 0.00 0.00 2.32
60 61 1.077169 GGTTTGTGGAGAGGGGGATTT 59.923 52.381 0.00 0.00 0.00 2.17
62 63 0.178831 AGGTTTGTGGAGAGGGGGAT 60.179 55.000 0.00 0.00 0.00 3.85
63 64 0.840722 GAGGTTTGTGGAGAGGGGGA 60.841 60.000 0.00 0.00 0.00 4.81
64 65 1.685820 GAGGTTTGTGGAGAGGGGG 59.314 63.158 0.00 0.00 0.00 5.40
67 68 1.133809 TGGGGAGGTTTGTGGAGAGG 61.134 60.000 0.00 0.00 0.00 3.69
69 70 1.354368 GATTGGGGAGGTTTGTGGAGA 59.646 52.381 0.00 0.00 0.00 3.71
70 71 1.616994 GGATTGGGGAGGTTTGTGGAG 60.617 57.143 0.00 0.00 0.00 3.86
73 74 0.614697 GGGGATTGGGGAGGTTTGTG 60.615 60.000 0.00 0.00 0.00 3.33
74 75 0.780090 AGGGGATTGGGGAGGTTTGT 60.780 55.000 0.00 0.00 0.00 2.83
75 76 0.413434 AAGGGGATTGGGGAGGTTTG 59.587 55.000 0.00 0.00 0.00 2.93
76 77 0.413434 CAAGGGGATTGGGGAGGTTT 59.587 55.000 0.00 0.00 35.08 3.27
77 78 0.780090 ACAAGGGGATTGGGGAGGTT 60.780 55.000 0.00 0.00 43.68 3.50
78 79 0.122435 TACAAGGGGATTGGGGAGGT 59.878 55.000 0.00 0.00 43.68 3.85
79 80 1.425448 GATACAAGGGGATTGGGGAGG 59.575 57.143 0.00 0.00 43.68 4.30
80 81 2.135189 TGATACAAGGGGATTGGGGAG 58.865 52.381 0.00 0.00 43.68 4.30
81 82 2.295269 TGATACAAGGGGATTGGGGA 57.705 50.000 0.00 0.00 43.68 4.81
82 83 3.396685 TTTGATACAAGGGGATTGGGG 57.603 47.619 0.00 0.00 43.68 4.96
83 84 4.545678 TCATTTGATACAAGGGGATTGGG 58.454 43.478 0.00 0.00 43.68 4.12
85 86 4.038402 GCCTCATTTGATACAAGGGGATTG 59.962 45.833 0.00 0.00 45.01 2.67
86 87 4.218312 GCCTCATTTGATACAAGGGGATT 58.782 43.478 0.00 0.00 0.00 3.01
87 88 3.437052 GGCCTCATTTGATACAAGGGGAT 60.437 47.826 0.00 0.00 0.00 3.85
88 89 2.091885 GGCCTCATTTGATACAAGGGGA 60.092 50.000 0.00 0.00 0.00 4.81
89 90 2.091665 AGGCCTCATTTGATACAAGGGG 60.092 50.000 0.00 0.00 0.00 4.79
90 91 3.303351 AGGCCTCATTTGATACAAGGG 57.697 47.619 0.00 0.00 0.00 3.95
91 92 4.823989 CCTTAGGCCTCATTTGATACAAGG 59.176 45.833 9.68 9.10 0.00 3.61
92 93 5.684704 TCCTTAGGCCTCATTTGATACAAG 58.315 41.667 9.68 2.58 0.00 3.16
93 94 5.708736 TCCTTAGGCCTCATTTGATACAA 57.291 39.130 9.68 0.00 0.00 2.41
94 95 5.045213 TGTTCCTTAGGCCTCATTTGATACA 60.045 40.000 9.68 1.91 0.00 2.29
95 96 5.437060 TGTTCCTTAGGCCTCATTTGATAC 58.563 41.667 9.68 0.00 0.00 2.24
96 97 5.708736 TGTTCCTTAGGCCTCATTTGATA 57.291 39.130 9.68 0.00 0.00 2.15
97 98 4.591321 TGTTCCTTAGGCCTCATTTGAT 57.409 40.909 9.68 0.00 0.00 2.57
98 99 4.018506 TGATGTTCCTTAGGCCTCATTTGA 60.019 41.667 9.68 0.00 0.00 2.69
100 101 4.018050 AGTGATGTTCCTTAGGCCTCATTT 60.018 41.667 9.68 0.00 0.00 2.32
101 102 3.525199 AGTGATGTTCCTTAGGCCTCATT 59.475 43.478 9.68 0.00 0.00 2.57
102 103 3.118112 CAGTGATGTTCCTTAGGCCTCAT 60.118 47.826 9.68 5.02 0.00 2.90
104 105 2.420687 CCAGTGATGTTCCTTAGGCCTC 60.421 54.545 9.68 0.00 0.00 4.70
105 106 1.561542 CCAGTGATGTTCCTTAGGCCT 59.438 52.381 11.78 11.78 0.00 5.19
107 108 1.340017 TGCCAGTGATGTTCCTTAGGC 60.340 52.381 0.00 0.00 41.15 3.93
108 109 2.749621 GTTGCCAGTGATGTTCCTTAGG 59.250 50.000 0.00 0.00 0.00 2.69
109 110 2.416547 CGTTGCCAGTGATGTTCCTTAG 59.583 50.000 0.00 0.00 0.00 2.18
111 112 1.202758 TCGTTGCCAGTGATGTTCCTT 60.203 47.619 0.00 0.00 0.00 3.36
112 113 0.396435 TCGTTGCCAGTGATGTTCCT 59.604 50.000 0.00 0.00 0.00 3.36
113 114 0.517316 GTCGTTGCCAGTGATGTTCC 59.483 55.000 0.00 0.00 0.00 3.62
114 115 0.517316 GGTCGTTGCCAGTGATGTTC 59.483 55.000 0.00 0.00 0.00 3.18
115 116 0.889186 GGGTCGTTGCCAGTGATGTT 60.889 55.000 0.00 0.00 0.00 2.71
116 117 1.302511 GGGTCGTTGCCAGTGATGT 60.303 57.895 0.00 0.00 0.00 3.06
118 119 2.351276 GGGGTCGTTGCCAGTGAT 59.649 61.111 0.00 0.00 0.00 3.06
119 120 3.948719 GGGGGTCGTTGCCAGTGA 61.949 66.667 0.00 0.00 0.00 3.41
131 132 2.524887 TTGTCCTTCGACGGGGGT 60.525 61.111 8.26 0.00 42.37 4.95
134 135 2.434359 GCCTTGTCCTTCGACGGG 60.434 66.667 8.26 2.56 42.37 5.28
135 136 0.602905 AAAGCCTTGTCCTTCGACGG 60.603 55.000 0.45 0.45 42.37 4.79
136 137 0.790814 GAAAGCCTTGTCCTTCGACG 59.209 55.000 0.00 0.00 42.37 5.12
138 139 3.210857 CGAAAGCCTTGTCCTTCGA 57.789 52.632 0.00 0.00 0.00 3.71
153 154 1.153449 CGAGGCATAAGTGGGCGAA 60.153 57.895 0.00 0.00 35.71 4.70
154 155 2.499205 CGAGGCATAAGTGGGCGA 59.501 61.111 0.00 0.00 35.71 5.54
155 156 3.272334 GCGAGGCATAAGTGGGCG 61.272 66.667 0.00 0.00 35.71 6.13
156 157 2.902343 GGCGAGGCATAAGTGGGC 60.902 66.667 0.00 0.00 0.00 5.36
157 158 1.077787 TTGGCGAGGCATAAGTGGG 60.078 57.895 0.00 0.00 0.00 4.61
158 159 0.392998 AGTTGGCGAGGCATAAGTGG 60.393 55.000 0.00 0.00 0.00 4.00
160 161 0.905357 AGAGTTGGCGAGGCATAAGT 59.095 50.000 0.00 0.00 0.00 2.24
161 162 1.134699 TCAGAGTTGGCGAGGCATAAG 60.135 52.381 0.00 0.00 0.00 1.73
162 163 0.901827 TCAGAGTTGGCGAGGCATAA 59.098 50.000 0.00 0.00 0.00 1.90
163 164 0.175760 GTCAGAGTTGGCGAGGCATA 59.824 55.000 0.00 0.00 0.00 3.14
164 165 1.078848 GTCAGAGTTGGCGAGGCAT 60.079 57.895 0.00 0.00 0.00 4.40
165 166 2.343758 GTCAGAGTTGGCGAGGCA 59.656 61.111 0.00 0.00 0.00 4.75
166 167 1.605058 TAGGTCAGAGTTGGCGAGGC 61.605 60.000 0.00 0.00 0.00 4.70
167 168 0.457851 CTAGGTCAGAGTTGGCGAGG 59.542 60.000 0.00 0.00 0.00 4.63
169 170 1.464734 CTCTAGGTCAGAGTTGGCGA 58.535 55.000 0.00 0.00 45.10 5.54
177 178 2.206223 TGGCTCCTACTCTAGGTCAGA 58.794 52.381 0.00 0.00 46.32 3.27
178 179 2.738587 TGGCTCCTACTCTAGGTCAG 57.261 55.000 0.00 0.00 46.32 3.51
180 181 2.894765 GGATTGGCTCCTACTCTAGGTC 59.105 54.545 0.00 0.00 46.32 3.85
182 183 2.630580 GTGGATTGGCTCCTACTCTAGG 59.369 54.545 0.00 0.00 45.21 3.02
183 184 3.300388 TGTGGATTGGCTCCTACTCTAG 58.700 50.000 0.00 0.00 45.21 2.43
184 185 3.398318 TGTGGATTGGCTCCTACTCTA 57.602 47.619 0.00 0.00 45.21 2.43
185 186 2.237392 GTTGTGGATTGGCTCCTACTCT 59.763 50.000 0.00 0.00 45.21 3.24
186 187 2.633488 GTTGTGGATTGGCTCCTACTC 58.367 52.381 0.00 0.00 45.21 2.59
188 189 1.066430 TCGTTGTGGATTGGCTCCTAC 60.066 52.381 0.00 0.00 45.21 3.18
190 191 0.400213 TTCGTTGTGGATTGGCTCCT 59.600 50.000 0.00 0.00 45.21 3.69
191 192 0.521735 GTTCGTTGTGGATTGGCTCC 59.478 55.000 0.00 0.00 45.19 4.70
192 193 0.521735 GGTTCGTTGTGGATTGGCTC 59.478 55.000 0.00 0.00 0.00 4.70
193 194 0.179004 TGGTTCGTTGTGGATTGGCT 60.179 50.000 0.00 0.00 0.00 4.75
194 195 0.887933 ATGGTTCGTTGTGGATTGGC 59.112 50.000 0.00 0.00 0.00 4.52
195 196 1.885887 ACATGGTTCGTTGTGGATTGG 59.114 47.619 0.00 0.00 0.00 3.16
197 198 2.813754 CTCACATGGTTCGTTGTGGATT 59.186 45.455 0.00 0.00 42.72 3.01
198 199 2.038426 TCTCACATGGTTCGTTGTGGAT 59.962 45.455 0.00 0.00 42.72 3.41
199 200 1.414550 TCTCACATGGTTCGTTGTGGA 59.585 47.619 0.00 0.00 42.72 4.02
202 203 1.140052 TGGTCTCACATGGTTCGTTGT 59.860 47.619 0.00 0.00 0.00 3.32
203 204 1.877637 TGGTCTCACATGGTTCGTTG 58.122 50.000 0.00 0.00 0.00 4.10
204 205 2.494059 CTTGGTCTCACATGGTTCGTT 58.506 47.619 0.00 0.00 0.00 3.85
205 206 1.878102 GCTTGGTCTCACATGGTTCGT 60.878 52.381 0.00 0.00 0.00 3.85
206 207 0.798776 GCTTGGTCTCACATGGTTCG 59.201 55.000 0.00 0.00 0.00 3.95
207 208 1.168714 GGCTTGGTCTCACATGGTTC 58.831 55.000 0.00 0.00 0.00 3.62
208 209 0.478072 TGGCTTGGTCTCACATGGTT 59.522 50.000 0.00 0.00 0.00 3.67
209 210 0.700564 ATGGCTTGGTCTCACATGGT 59.299 50.000 0.00 0.00 0.00 3.55
212 213 1.632409 AGACATGGCTTGGTCTCACAT 59.368 47.619 0.00 0.00 40.18 3.21
213 214 1.059098 AGACATGGCTTGGTCTCACA 58.941 50.000 0.00 0.00 40.18 3.58
217 218 1.599047 CGGAGACATGGCTTGGTCT 59.401 57.895 0.41 5.73 46.51 3.85
218 219 2.109126 GCGGAGACATGGCTTGGTC 61.109 63.158 0.41 0.00 0.00 4.02
219 220 2.045926 GCGGAGACATGGCTTGGT 60.046 61.111 0.41 0.00 0.00 3.67
220 221 1.377725 AAGCGGAGACATGGCTTGG 60.378 57.895 0.41 0.00 44.69 3.61
221 222 4.308526 AAGCGGAGACATGGCTTG 57.691 55.556 0.41 0.00 44.69 4.01
223 224 0.254178 ATTCAAGCGGAGACATGGCT 59.746 50.000 0.00 0.00 39.01 4.75
224 225 1.098050 AATTCAAGCGGAGACATGGC 58.902 50.000 0.00 0.00 0.00 4.40
226 227 4.627611 ATGAAATTCAAGCGGAGACATG 57.372 40.909 0.00 0.00 0.00 3.21
227 228 5.295292 CACTATGAAATTCAAGCGGAGACAT 59.705 40.000 0.00 0.00 0.00 3.06
229 230 4.494855 GCACTATGAAATTCAAGCGGAGAC 60.495 45.833 0.00 0.00 0.00 3.36
231 232 3.544834 CGCACTATGAAATTCAAGCGGAG 60.545 47.826 19.79 8.32 35.47 4.63
232 233 2.351418 CGCACTATGAAATTCAAGCGGA 59.649 45.455 19.79 0.00 35.47 5.54
238 239 3.689161 CCTGGTTCGCACTATGAAATTCA 59.311 43.478 0.00 0.00 0.00 2.57
246 247 3.695830 TTTTCTCCTGGTTCGCACTAT 57.304 42.857 0.00 0.00 0.00 2.12
250 251 1.142060 TCCTTTTTCTCCTGGTTCGCA 59.858 47.619 0.00 0.00 0.00 5.10
258 259 2.783510 TGGTGTCCTTCCTTTTTCTCCT 59.216 45.455 0.00 0.00 0.00 3.69
263 268 2.021457 CGTGTGGTGTCCTTCCTTTTT 58.979 47.619 0.00 0.00 0.00 1.94
271 276 4.250305 GTGGCCGTGTGGTGTCCT 62.250 66.667 0.00 0.00 37.67 3.85
273 278 4.250305 AGGTGGCCGTGTGGTGTC 62.250 66.667 0.00 0.00 37.67 3.67
274 279 4.250305 GAGGTGGCCGTGTGGTGT 62.250 66.667 0.00 0.00 37.67 4.16
276 281 3.249189 ATGAGGTGGCCGTGTGGT 61.249 61.111 0.00 0.00 37.67 4.16
278 283 2.034879 GTGATGAGGTGGCCGTGTG 61.035 63.158 0.00 0.00 0.00 3.82
279 284 2.347490 GTGATGAGGTGGCCGTGT 59.653 61.111 0.00 0.00 0.00 4.49
284 289 1.304282 ACCATGGTGATGAGGTGGC 59.696 57.895 18.99 0.00 33.24 5.01
322 3542 2.441164 GTGGTTGTGGTGGTGCCA 60.441 61.111 0.00 0.00 46.95 4.92
362 3583 2.331451 GCAAGTGGCACGGTGTTC 59.669 61.111 20.57 3.53 43.97 3.18
409 3630 3.818787 CTGGCATTGTCGCTGGCC 61.819 66.667 0.00 0.00 46.58 5.36
417 3638 1.453155 GATCGGTTGTCTGGCATTGT 58.547 50.000 0.00 0.00 0.00 2.71
420 3641 0.107508 CTGGATCGGTTGTCTGGCAT 60.108 55.000 0.00 0.00 0.00 4.40
466 3715 8.738645 AACAACTCTAAATGAACTCTCTTTGT 57.261 30.769 0.00 0.00 0.00 2.83
491 3740 3.133003 GCCAGTCACCTCTAAAGAGCATA 59.867 47.826 1.21 0.00 40.75 3.14
492 3741 2.093235 GCCAGTCACCTCTAAAGAGCAT 60.093 50.000 1.21 0.00 40.75 3.79
514 3763 3.708734 CGCGTCCCGACCAACAAC 61.709 66.667 0.00 0.00 40.02 3.32
544 3793 4.217767 CCCTTAAGTGCTTTGTCCTAAACC 59.782 45.833 0.97 0.00 0.00 3.27
581 3830 1.808945 CAAGCTTGCTCCAACTCGAAT 59.191 47.619 14.65 0.00 0.00 3.34
594 3843 2.456119 CGGCCGAGTAGCAAGCTTG 61.456 63.158 24.07 22.44 0.00 4.01
595 3844 2.125512 CGGCCGAGTAGCAAGCTT 60.126 61.111 24.07 0.00 0.00 3.74
596 3845 4.148825 CCGGCCGAGTAGCAAGCT 62.149 66.667 30.73 0.00 0.00 3.74
598 3847 3.740128 ATGCCGGCCGAGTAGCAAG 62.740 63.158 30.73 8.26 38.99 4.01
599 3848 3.781307 ATGCCGGCCGAGTAGCAA 61.781 61.111 30.73 12.30 38.99 3.91
600 3849 4.529219 CATGCCGGCCGAGTAGCA 62.529 66.667 30.73 27.60 40.00 3.49
601 3850 4.530857 ACATGCCGGCCGAGTAGC 62.531 66.667 30.73 22.33 0.00 3.58
602 3851 2.586079 CACATGCCGGCCGAGTAG 60.586 66.667 30.73 16.31 0.00 2.57
603 3852 4.155733 CCACATGCCGGCCGAGTA 62.156 66.667 30.73 17.10 0.00 2.59
611 3860 4.827087 AGCTCTCGCCACATGCCG 62.827 66.667 0.00 0.00 36.60 5.69
621 3870 2.021355 AGAATTCCAGCAAGCTCTCG 57.979 50.000 0.65 0.00 0.00 4.04
647 3896 5.420421 TGCCATAGCTTTATAAAAGGCACAA 59.580 36.000 17.08 4.04 45.10 3.33
648 3897 4.952957 TGCCATAGCTTTATAAAAGGCACA 59.047 37.500 17.08 5.56 45.10 4.57
656 3905 3.804036 ACTGCGTGCCATAGCTTTATAA 58.196 40.909 0.00 0.00 40.80 0.98
718 3972 2.158638 GGACTGACGGGGACTATACTCT 60.159 54.545 0.00 0.00 0.00 3.24
719 3973 2.158638 AGGACTGACGGGGACTATACTC 60.159 54.545 0.00 0.00 0.00 2.59
720 3974 1.851653 AGGACTGACGGGGACTATACT 59.148 52.381 0.00 0.00 0.00 2.12
772 4027 4.698304 TCTTCACCGTCCAAATAATTCCAC 59.302 41.667 0.00 0.00 0.00 4.02
845 4100 2.550277 TTAGAGGTCATGGCTGGAGA 57.450 50.000 0.00 0.00 0.00 3.71
946 4201 2.402787 GTAGAGGACGACGGACGC 59.597 66.667 0.00 0.00 46.94 5.19
986 4249 2.203394 CCATGGCCTTGGATCGGG 60.203 66.667 29.65 3.93 39.25 5.14
1294 4585 1.064060 GCAACGCATGGAGAATGTACC 59.936 52.381 0.00 0.00 38.65 3.34
1295 4586 2.009774 AGCAACGCATGGAGAATGTAC 58.990 47.619 0.00 0.00 38.65 2.90
1298 4589 1.089112 TCAGCAACGCATGGAGAATG 58.911 50.000 0.00 0.00 39.49 2.67
1580 4877 0.757512 AGAGCATGAGGATGACGCAT 59.242 50.000 0.00 0.00 32.95 4.73
1661 4958 2.105930 GAGAAGATGAGCGCGGCT 59.894 61.111 8.83 5.31 43.88 5.52
1856 5153 0.391661 GGCAGGCAGAGACGAATGAA 60.392 55.000 0.00 0.00 0.00 2.57
1857 5154 1.219124 GGCAGGCAGAGACGAATGA 59.781 57.895 0.00 0.00 0.00 2.57
1858 5155 1.088340 CAGGCAGGCAGAGACGAATG 61.088 60.000 0.00 0.00 0.00 2.67
1859 5156 1.220206 CAGGCAGGCAGAGACGAAT 59.780 57.895 0.00 0.00 0.00 3.34
1860 5157 2.659016 CAGGCAGGCAGAGACGAA 59.341 61.111 0.00 0.00 0.00 3.85
1861 5158 3.385384 CCAGGCAGGCAGAGACGA 61.385 66.667 0.00 0.00 0.00 4.20
1970 5279 7.087409 TGGCAATACTACATTTCTGTTGATG 57.913 36.000 0.00 0.00 36.79 3.07
1973 5282 6.974622 GGATTGGCAATACTACATTTCTGTTG 59.025 38.462 15.33 0.00 36.79 3.33
2021 5332 7.594015 GCTTGTTGATGATCATTCCATATGTTC 59.406 37.037 10.14 0.00 0.00 3.18
2027 5338 4.283337 TGGCTTGTTGATGATCATTCCAT 58.717 39.130 10.14 0.00 0.00 3.41
2118 5429 3.686128 TGTTTGACAAACGAAACGATGG 58.314 40.909 22.59 0.00 44.28 3.51
2267 5579 5.543507 AAGCAGACCCATCTAAGATAGTG 57.456 43.478 0.00 0.00 32.25 2.74
2458 5779 8.974292 AGCTCTTATTTCCCTTATGGTAGATA 57.026 34.615 0.00 0.00 34.77 1.98
2491 5812 2.125310 TGTACCGAGGCAATGGCG 60.125 61.111 0.00 0.00 42.47 5.69
2504 5825 7.806690 TGAATTTGCAAGAGTCATTACTGTAC 58.193 34.615 0.00 0.00 35.56 2.90
2620 6103 2.224744 TGAAGCTGCACAATAACCCAGA 60.225 45.455 1.02 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.