Multiple sequence alignment - TraesCS3D01G407600

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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 TraesCS3D01G407600 chr3D 100.000 3134 0 0 1 3134 520823226 520826359 0.000000e+00 5788.0
1 TraesCS3D01G407600 chr3D 83.818 1823 152 77 600 2358 520862379 520864122 0.000000e+00 1600.0
2 TraesCS3D01G407600 chr3D 74.504 1008 208 37 1097 2093 454219320 454220289 2.930000e-105 392.0
3 TraesCS3D01G407600 chr3B 90.886 2809 176 42 262 3028 686491406 686494176 0.000000e+00 3696.0
4 TraesCS3D01G407600 chr3B 83.775 1812 146 76 600 2349 686524110 686525835 0.000000e+00 1581.0
5 TraesCS3D01G407600 chr3B 73.515 1027 200 48 1097 2093 596852747 596853731 1.080000e-84 324.0
6 TraesCS3D01G407600 chr3B 74.662 592 119 25 1103 1684 39581671 39581101 1.880000e-57 233.0
7 TraesCS3D01G407600 chr3B 90.722 97 8 1 3039 3134 686494356 686494260 9.120000e-26 128.0
8 TraesCS3D01G407600 chr3A 92.158 1900 89 31 473 2340 656134302 656136173 0.000000e+00 2628.0
9 TraesCS3D01G407600 chr3A 85.208 1751 137 65 600 2333 656253943 656255588 0.000000e+00 1687.0
10 TraesCS3D01G407600 chr3A 84.101 1780 148 80 600 2349 656423593 656425267 0.000000e+00 1594.0
11 TraesCS3D01G407600 chr3A 89.655 783 61 10 1564 2333 656339249 656340024 0.000000e+00 979.0
12 TraesCS3D01G407600 chr3A 96.552 464 15 1 2671 3134 656176619 656177081 0.000000e+00 767.0
13 TraesCS3D01G407600 chr3A 89.074 540 43 10 2149 2677 656260696 656261230 0.000000e+00 656.0
14 TraesCS3D01G407600 chr3A 89.094 541 41 12 2148 2677 656264228 656264761 0.000000e+00 656.0
15 TraesCS3D01G407600 chr3A 89.179 536 41 11 2153 2677 656348579 656349108 0.000000e+00 652.0
16 TraesCS3D01G407600 chr3A 88.704 540 45 10 2149 2677 656344887 656345421 0.000000e+00 645.0
17 TraesCS3D01G407600 chr3A 92.642 299 17 4 2336 2631 656176313 656176609 2.890000e-115 425.0
18 TraesCS3D01G407600 chr3A 91.026 312 24 3 2372 2680 656255587 656255897 4.830000e-113 418.0
19 TraesCS3D01G407600 chr3A 90.705 312 25 3 2372 2680 656340023 656340333 2.250000e-111 412.0
20 TraesCS3D01G407600 chr3A 73.805 1004 214 34 1101 2093 597234724 597233759 4.970000e-93 351.0
21 TraesCS3D01G407600 chr3A 91.753 194 13 3 262 453 656133822 656134014 1.850000e-67 267.0
22 TraesCS3D01G407600 chr3A 88.172 186 19 2 2949 3134 656340364 656340546 5.260000e-53 219.0
23 TraesCS3D01G407600 chr3A 87.634 186 20 2 2949 3134 656255928 656256110 2.450000e-51 213.0
24 TraesCS3D01G407600 chr3A 87.363 182 18 4 2954 3134 656264800 656264977 1.470000e-48 204.0
25 TraesCS3D01G407600 chr3A 86.885 183 18 5 2954 3134 656349147 656349325 1.910000e-47 200.0
26 TraesCS3D01G407600 chr3A 87.805 164 17 3 2954 3116 656345460 656345621 4.130000e-44 189.0
27 TraesCS3D01G407600 chr3A 86.585 164 19 3 2954 3116 656261269 656261430 8.930000e-41 178.0
28 TraesCS3D01G407600 chrUn 92.549 255 18 1 2426 2680 476916014 476915761 6.390000e-97 364.0
29 TraesCS3D01G407600 chrUn 89.147 129 12 2 2954 3081 476915725 476915598 3.240000e-35 159.0
30 TraesCS3D01G407600 chr6D 82.748 313 46 7 2485 2794 429842235 429842542 3.980000e-69 272.0
31 TraesCS3D01G407600 chr1B 75.219 456 98 10 1409 1858 16216867 16217313 5.300000e-48 202.0
32 TraesCS3D01G407600 chr1B 78.846 260 53 2 1424 1682 23978572 23978314 1.160000e-39 174.0
33 TraesCS3D01G407600 chr2D 90.566 53 5 0 2387 2439 82181969 82181917 1.560000e-08 71.3


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 TraesCS3D01G407600 chr3D 520823226 520826359 3133 False 5788.000000 5788 100.000000 1 3134 1 chr3D.!!$F2 3133
1 TraesCS3D01G407600 chr3D 520862379 520864122 1743 False 1600.000000 1600 83.818000 600 2358 1 chr3D.!!$F3 1758
2 TraesCS3D01G407600 chr3D 454219320 454220289 969 False 392.000000 392 74.504000 1097 2093 1 chr3D.!!$F1 996
3 TraesCS3D01G407600 chr3B 686491406 686494176 2770 False 3696.000000 3696 90.886000 262 3028 1 chr3B.!!$F2 2766
4 TraesCS3D01G407600 chr3B 686524110 686525835 1725 False 1581.000000 1581 83.775000 600 2349 1 chr3B.!!$F3 1749
5 TraesCS3D01G407600 chr3B 596852747 596853731 984 False 324.000000 324 73.515000 1097 2093 1 chr3B.!!$F1 996
6 TraesCS3D01G407600 chr3B 39581101 39581671 570 True 233.000000 233 74.662000 1103 1684 1 chr3B.!!$R1 581
7 TraesCS3D01G407600 chr3A 656423593 656425267 1674 False 1594.000000 1594 84.101000 600 2349 1 chr3A.!!$F1 1749
8 TraesCS3D01G407600 chr3A 656133822 656136173 2351 False 1447.500000 2628 91.955500 262 2340 2 chr3A.!!$F2 2078
9 TraesCS3D01G407600 chr3A 656253943 656256110 2167 False 772.666667 1687 87.956000 600 3134 3 chr3A.!!$F4 2534
10 TraesCS3D01G407600 chr3A 656176313 656177081 768 False 596.000000 767 94.597000 2336 3134 2 chr3A.!!$F3 798
11 TraesCS3D01G407600 chr3A 656339249 656340546 1297 False 536.666667 979 89.510667 1564 3134 3 chr3A.!!$F6 1570
12 TraesCS3D01G407600 chr3A 656260696 656264977 4281 False 423.500000 656 88.029000 2148 3134 4 chr3A.!!$F5 986
13 TraesCS3D01G407600 chr3A 656344887 656349325 4438 False 421.500000 652 88.143250 2149 3134 4 chr3A.!!$F7 985
14 TraesCS3D01G407600 chr3A 597233759 597234724 965 True 351.000000 351 73.805000 1101 2093 1 chr3A.!!$R1 992

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
141 142 0.033894 ACACCCGTGGACCAAAAGTT 60.034 50.0 0.00 0.00 34.19 2.66 F
162 163 0.034670 CCCTCCAAGAAGCAAGAGGG 60.035 60.0 9.45 9.45 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2406 1.221840 GGCGCCTGAATCCTTCTCA 59.778 57.895 22.15 0.0 0.0 3.27 R
2188 3746 9.474313 TTCAGCTGTAATTTATTTTCACCCTAT 57.526 29.630 14.67 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
36 37 8.426881 TTTTGAACTTTTTGTAAGTAATGGGC 57.573 30.769 0.00 0.00 0.00 5.36
37 38 6.969993 TGAACTTTTTGTAAGTAATGGGCT 57.030 33.333 0.00 0.00 0.00 5.19
40 41 8.915036 TGAACTTTTTGTAAGTAATGGGCTAAA 58.085 29.630 0.00 0.00 0.00 1.85
41 42 9.188588 GAACTTTTTGTAAGTAATGGGCTAAAC 57.811 33.333 0.00 0.00 0.00 2.01
43 44 8.139350 ACTTTTTGTAAGTAATGGGCTAAACAC 58.861 33.333 0.00 0.00 0.00 3.32
44 45 7.826918 TTTTGTAAGTAATGGGCTAAACACT 57.173 32.000 0.00 0.00 0.00 3.55
45 46 7.443259 TTTGTAAGTAATGGGCTAAACACTC 57.557 36.000 0.00 0.00 0.00 3.51
47 48 6.775708 TGTAAGTAATGGGCTAAACACTCTT 58.224 36.000 0.00 0.00 0.00 2.85
49 50 8.545472 TGTAAGTAATGGGCTAAACACTCTTAT 58.455 33.333 0.00 0.00 0.00 1.73
56 57 9.474313 AATGGGCTAAACACTCTTATATTTCAA 57.526 29.630 0.00 0.00 0.00 2.69
57 58 8.871629 TGGGCTAAACACTCTTATATTTCAAA 57.128 30.769 0.00 0.00 0.00 2.69
134 135 3.746900 GTGTATACACCCGTGGACC 57.253 57.895 23.03 0.00 40.85 4.46
135 136 0.896923 GTGTATACACCCGTGGACCA 59.103 55.000 23.03 0.00 40.85 4.02
136 137 1.275856 GTGTATACACCCGTGGACCAA 59.724 52.381 23.03 0.00 40.85 3.67
137 138 1.976404 TGTATACACCCGTGGACCAAA 59.024 47.619 0.08 0.00 34.19 3.28
138 139 2.371179 TGTATACACCCGTGGACCAAAA 59.629 45.455 0.08 0.00 34.19 2.44
139 140 2.194201 ATACACCCGTGGACCAAAAG 57.806 50.000 0.00 0.00 34.19 2.27
140 141 0.838608 TACACCCGTGGACCAAAAGT 59.161 50.000 0.00 0.00 34.19 2.66
141 142 0.033894 ACACCCGTGGACCAAAAGTT 60.034 50.000 0.00 0.00 34.19 2.66
142 143 1.107945 CACCCGTGGACCAAAAGTTT 58.892 50.000 0.00 0.00 0.00 2.66
143 144 1.066454 CACCCGTGGACCAAAAGTTTC 59.934 52.381 0.00 0.00 0.00 2.78
144 145 0.671796 CCCGTGGACCAAAAGTTTCC 59.328 55.000 0.00 0.00 0.00 3.13
145 146 0.671796 CCGTGGACCAAAAGTTTCCC 59.328 55.000 0.00 0.00 0.00 3.97
146 147 1.687563 CGTGGACCAAAAGTTTCCCT 58.312 50.000 0.00 0.00 0.00 4.20
148 149 1.961394 GTGGACCAAAAGTTTCCCTCC 59.039 52.381 0.00 0.00 0.00 4.30
151 152 2.628178 GGACCAAAAGTTTCCCTCCAAG 59.372 50.000 0.00 0.00 0.00 3.61
152 153 3.562182 GACCAAAAGTTTCCCTCCAAGA 58.438 45.455 0.00 0.00 0.00 3.02
153 154 3.958147 GACCAAAAGTTTCCCTCCAAGAA 59.042 43.478 0.00 0.00 0.00 2.52
154 155 3.960755 ACCAAAAGTTTCCCTCCAAGAAG 59.039 43.478 0.00 0.00 0.00 2.85
155 156 3.243873 CCAAAAGTTTCCCTCCAAGAAGC 60.244 47.826 0.00 0.00 0.00 3.86
156 157 3.312736 AAAGTTTCCCTCCAAGAAGCA 57.687 42.857 0.00 0.00 0.00 3.91
157 158 3.312736 AAGTTTCCCTCCAAGAAGCAA 57.687 42.857 0.00 0.00 0.00 3.91
158 159 2.868899 AGTTTCCCTCCAAGAAGCAAG 58.131 47.619 0.00 0.00 0.00 4.01
160 161 2.816672 GTTTCCCTCCAAGAAGCAAGAG 59.183 50.000 0.00 0.00 0.00 2.85
161 162 0.987294 TCCCTCCAAGAAGCAAGAGG 59.013 55.000 0.00 0.00 0.00 3.69
162 163 0.034670 CCCTCCAAGAAGCAAGAGGG 60.035 60.000 9.45 9.45 0.00 4.30
163 164 0.695347 CCTCCAAGAAGCAAGAGGGT 59.305 55.000 0.00 0.00 0.00 4.34
164 165 1.909302 CCTCCAAGAAGCAAGAGGGTA 59.091 52.381 0.00 0.00 0.00 3.69
165 166 2.305927 CCTCCAAGAAGCAAGAGGGTAA 59.694 50.000 0.00 0.00 0.00 2.85
166 167 3.339141 CTCCAAGAAGCAAGAGGGTAAC 58.661 50.000 0.00 0.00 0.00 2.50
167 168 2.979678 TCCAAGAAGCAAGAGGGTAACT 59.020 45.455 0.00 0.00 0.00 2.24
169 170 4.783227 TCCAAGAAGCAAGAGGGTAACTAT 59.217 41.667 0.00 0.00 0.00 2.12
170 171 5.250774 TCCAAGAAGCAAGAGGGTAACTATT 59.749 40.000 0.00 0.00 0.00 1.73
171 172 5.946377 CCAAGAAGCAAGAGGGTAACTATTT 59.054 40.000 0.00 0.00 0.00 1.40
172 173 6.094186 CCAAGAAGCAAGAGGGTAACTATTTC 59.906 42.308 0.00 0.00 0.00 2.17
173 174 5.746284 AGAAGCAAGAGGGTAACTATTTCC 58.254 41.667 0.00 0.00 0.00 3.13
174 175 4.505324 AGCAAGAGGGTAACTATTTCCC 57.495 45.455 0.00 0.00 41.36 3.97
177 178 4.398358 GCAAGAGGGTAACTATTTCCCAAC 59.602 45.833 6.09 0.68 43.31 3.77
178 179 5.566469 CAAGAGGGTAACTATTTCCCAACA 58.434 41.667 6.09 0.00 43.31 3.33
179 180 5.853572 AGAGGGTAACTATTTCCCAACAA 57.146 39.130 6.09 0.00 43.31 2.83
182 183 5.707495 AGGGTAACTATTTCCCAACAAACA 58.293 37.500 6.09 0.00 43.31 2.83
183 184 6.137559 AGGGTAACTATTTCCCAACAAACAA 58.862 36.000 6.09 0.00 43.31 2.83
184 185 6.612049 AGGGTAACTATTTCCCAACAAACAAA 59.388 34.615 6.09 0.00 43.31 2.83
185 186 6.926826 GGGTAACTATTTCCCAACAAACAAAG 59.073 38.462 0.00 0.00 40.79 2.77
186 187 6.422701 GGTAACTATTTCCCAACAAACAAAGC 59.577 38.462 0.00 0.00 0.00 3.51
187 188 5.869649 ACTATTTCCCAACAAACAAAGCT 57.130 34.783 0.00 0.00 0.00 3.74
188 189 6.969993 ACTATTTCCCAACAAACAAAGCTA 57.030 33.333 0.00 0.00 0.00 3.32
189 190 7.539034 ACTATTTCCCAACAAACAAAGCTAT 57.461 32.000 0.00 0.00 0.00 2.97
193 194 7.546778 TTTCCCAACAAACAAAGCTATTTTC 57.453 32.000 0.00 0.00 0.00 2.29
194 195 5.606505 TCCCAACAAACAAAGCTATTTTCC 58.393 37.500 0.00 0.00 0.00 3.13
195 196 4.754618 CCCAACAAACAAAGCTATTTTCCC 59.245 41.667 0.00 0.00 0.00 3.97
198 199 5.869649 ACAAACAAAGCTATTTTCCCAGT 57.130 34.783 0.00 0.00 0.00 4.00
201 202 6.761242 ACAAACAAAGCTATTTTCCCAGTTTC 59.239 34.615 0.00 0.00 0.00 2.78
202 203 6.478512 AACAAAGCTATTTTCCCAGTTTCA 57.521 33.333 0.00 0.00 0.00 2.69
203 204 6.478512 ACAAAGCTATTTTCCCAGTTTCAA 57.521 33.333 0.00 0.00 0.00 2.69
206 207 7.826744 ACAAAGCTATTTTCCCAGTTTCAAAAA 59.173 29.630 0.00 0.00 0.00 1.94
207 208 7.786178 AAGCTATTTTCCCAGTTTCAAAAAC 57.214 32.000 0.00 0.00 0.00 2.43
208 209 6.883744 AGCTATTTTCCCAGTTTCAAAAACA 58.116 32.000 5.46 0.00 0.00 2.83
209 210 7.508687 AGCTATTTTCCCAGTTTCAAAAACAT 58.491 30.769 5.46 0.00 0.00 2.71
210 211 8.646900 AGCTATTTTCCCAGTTTCAAAAACATA 58.353 29.630 5.46 0.00 0.00 2.29
211 212 9.267084 GCTATTTTCCCAGTTTCAAAAACATAA 57.733 29.630 5.46 0.00 0.00 1.90
215 216 7.889873 TTCCCAGTTTCAAAAACATAAGAGA 57.110 32.000 5.46 0.00 0.00 3.10
216 217 7.510549 TCCCAGTTTCAAAAACATAAGAGAG 57.489 36.000 5.46 0.00 0.00 3.20
217 218 7.287061 TCCCAGTTTCAAAAACATAAGAGAGA 58.713 34.615 5.46 0.00 0.00 3.10
218 219 7.445402 TCCCAGTTTCAAAAACATAAGAGAGAG 59.555 37.037 5.46 0.00 0.00 3.20
220 221 8.840321 CCAGTTTCAAAAACATAAGAGAGAGAA 58.160 33.333 5.46 0.00 0.00 2.87
236 237 8.989653 AGAGAGAGAAAAAGTTTATTAGACGG 57.010 34.615 0.00 0.00 0.00 4.79
237 238 8.804204 AGAGAGAGAAAAAGTTTATTAGACGGA 58.196 33.333 0.00 0.00 0.00 4.69
238 239 8.989653 AGAGAGAAAAAGTTTATTAGACGGAG 57.010 34.615 0.00 0.00 0.00 4.63
239 240 7.546316 AGAGAGAAAAAGTTTATTAGACGGAGC 59.454 37.037 0.00 0.00 0.00 4.70
241 242 7.824779 AGAGAAAAAGTTTATTAGACGGAGCAT 59.175 33.333 0.00 0.00 0.00 3.79
242 243 7.975750 AGAAAAAGTTTATTAGACGGAGCATC 58.024 34.615 0.00 0.00 0.00 3.91
254 255 2.426651 GAGCATCCTACCCGTAGCA 58.573 57.895 0.00 0.00 31.95 3.49
256 257 0.969894 AGCATCCTACCCGTAGCATC 59.030 55.000 0.00 0.00 31.95 3.91
257 258 0.037232 GCATCCTACCCGTAGCATCC 60.037 60.000 0.00 0.00 31.95 3.51
259 260 1.902508 CATCCTACCCGTAGCATCCAT 59.097 52.381 0.00 0.00 31.95 3.41
260 261 1.338107 TCCTACCCGTAGCATCCATG 58.662 55.000 0.00 0.00 31.95 3.66
432 433 0.036577 AAGCACAGCAGCAGTAGGAG 60.037 55.000 0.00 0.00 36.85 3.69
433 434 1.190833 AGCACAGCAGCAGTAGGAGT 61.191 55.000 0.00 0.00 36.85 3.85
434 435 0.321122 GCACAGCAGCAGTAGGAGTT 60.321 55.000 0.00 0.00 0.00 3.01
435 436 1.719600 CACAGCAGCAGTAGGAGTTC 58.280 55.000 0.00 0.00 0.00 3.01
436 437 0.244994 ACAGCAGCAGTAGGAGTTCG 59.755 55.000 0.00 0.00 0.00 3.95
484 768 3.599343 TGTAAGGCTGTAACTGCATCTG 58.401 45.455 0.00 0.00 0.00 2.90
536 820 1.227380 CACCTACGATCAGCAGGCC 60.227 63.158 0.00 0.00 36.84 5.19
560 844 4.884257 GCCGGCGGCGATCAAGTA 62.884 66.667 37.09 0.00 39.62 2.24
582 867 6.882140 AGTAACCCAACATACGAATGAATCAA 59.118 34.615 0.00 0.00 36.54 2.57
583 868 5.560966 ACCCAACATACGAATGAATCAAC 57.439 39.130 0.00 0.00 36.54 3.18
619 937 4.716794 GATGAATCTGCCCTGAATCTTCT 58.283 43.478 0.00 0.00 0.00 2.85
659 979 4.043200 GCACGCAACTTGGGAGCC 62.043 66.667 14.73 1.12 40.05 4.70
829 1153 2.928801 TGCAAAGCTTCTCCACACTA 57.071 45.000 0.00 0.00 0.00 2.74
854 1184 2.323790 CTCGATCGGTCGGACGAC 59.676 66.667 19.53 15.90 46.64 4.34
883 1213 5.784023 TCCACCTATAAATACACCTCCTCA 58.216 41.667 0.00 0.00 0.00 3.86
903 1233 3.118992 TCACTTCTCTTCCACCATCATCG 60.119 47.826 0.00 0.00 0.00 3.84
905 1235 1.866015 TCTCTTCCACCATCATCGGT 58.134 50.000 0.00 0.00 41.07 4.69
954 1311 2.919856 ACTGCCTCAGTGCCTCGT 60.920 61.111 0.00 0.00 43.63 4.18
1977 2376 2.852075 AAGAACTCGTGGGGGCCA 60.852 61.111 4.39 0.00 0.00 5.36
2007 2406 2.197465 GAGAAGGGGTACATCAGGGTT 58.803 52.381 0.00 0.00 0.00 4.11
2172 3727 7.097192 TCTGCGTGTCTGAATTATTTCTACTT 58.903 34.615 0.00 0.00 32.78 2.24
2235 3796 2.427232 TAAGTGTTTCTCCGTCCACG 57.573 50.000 0.00 0.00 39.44 4.94
2246 3811 2.832818 CCGTCCACGCGCAAGAATTG 62.833 60.000 5.73 0.00 43.43 2.32
2268 3833 0.387929 CGTGTATAGCGTGGGACCAT 59.612 55.000 0.00 0.00 0.00 3.55
2269 3834 1.602165 CGTGTATAGCGTGGGACCATC 60.602 57.143 0.00 0.00 0.00 3.51
2271 3836 2.112190 TGTATAGCGTGGGACCATCAA 58.888 47.619 0.00 0.00 0.00 2.57
2272 3837 2.703536 TGTATAGCGTGGGACCATCAAT 59.296 45.455 0.00 0.00 0.00 2.57
2281 3855 5.163602 GCGTGGGACCATCAATATTTGTTTA 60.164 40.000 0.00 0.00 0.00 2.01
2463 4056 2.750166 ACTAGACGATATGATCCCGCAG 59.250 50.000 0.00 0.00 0.00 5.18
2667 4262 3.459232 TGGTAGAGAATTCTCATGCGG 57.541 47.619 31.79 0.00 45.21 5.69
2739 4334 5.428496 ACAATATTGATGATGTGGAAGCG 57.572 39.130 22.16 0.00 0.00 4.68
2765 4360 9.226345 GCACATGTCAAAATAATTAGAAGTAGC 57.774 33.333 0.00 0.00 0.00 3.58
2787 4382 7.151999 AGCGGAGATAACTCACTTAGATATG 57.848 40.000 2.13 0.00 44.22 1.78
2856 4451 6.648310 TCTTGCTAAAGAACTCATCTGACAAG 59.352 38.462 0.00 0.00 39.52 3.16
2861 4456 4.433186 AGAACTCATCTGACAAGACTCG 57.567 45.455 0.00 0.00 36.88 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.051679 GCCCATTACTTACAAAAAGTTCAAAAT 57.948 29.630 0.00 0.00 0.00 1.82
11 12 8.261522 AGCCCATTACTTACAAAAAGTTCAAAA 58.738 29.630 0.00 0.00 0.00 2.44
12 13 7.787028 AGCCCATTACTTACAAAAAGTTCAAA 58.213 30.769 0.00 0.00 0.00 2.69
15 16 9.188588 GTTTAGCCCATTACTTACAAAAAGTTC 57.811 33.333 0.00 0.00 0.00 3.01
16 17 8.697292 TGTTTAGCCCATTACTTACAAAAAGTT 58.303 29.630 0.00 0.00 0.00 2.66
17 18 8.139350 GTGTTTAGCCCATTACTTACAAAAAGT 58.861 33.333 0.00 0.00 0.00 2.66
18 19 8.357402 AGTGTTTAGCCCATTACTTACAAAAAG 58.643 33.333 0.00 0.00 0.00 2.27
19 20 8.240267 AGTGTTTAGCCCATTACTTACAAAAA 57.760 30.769 0.00 0.00 0.00 1.94
21 22 7.228590 AGAGTGTTTAGCCCATTACTTACAAA 58.771 34.615 0.00 0.00 0.00 2.83
22 23 6.775708 AGAGTGTTTAGCCCATTACTTACAA 58.224 36.000 0.00 0.00 0.00 2.41
24 25 8.959705 ATAAGAGTGTTTAGCCCATTACTTAC 57.040 34.615 0.00 0.00 0.00 2.34
30 31 9.474313 TTGAAATATAAGAGTGTTTAGCCCATT 57.526 29.630 0.00 0.00 0.00 3.16
31 32 9.474313 TTTGAAATATAAGAGTGTTTAGCCCAT 57.526 29.630 0.00 0.00 0.00 4.00
116 117 0.896923 TGGTCCACGGGTGTATACAC 59.103 55.000 25.00 25.00 45.72 2.90
117 118 1.642112 TTGGTCCACGGGTGTATACA 58.358 50.000 0.08 0.08 0.00 2.29
119 120 2.638855 ACTTTTGGTCCACGGGTGTATA 59.361 45.455 0.00 0.00 0.00 1.47
122 123 0.033894 AACTTTTGGTCCACGGGTGT 60.034 50.000 0.00 0.00 0.00 4.16
123 124 1.066454 GAAACTTTTGGTCCACGGGTG 59.934 52.381 0.00 0.00 0.00 4.61
124 125 1.395635 GAAACTTTTGGTCCACGGGT 58.604 50.000 0.00 0.00 0.00 5.28
125 126 0.671796 GGAAACTTTTGGTCCACGGG 59.328 55.000 0.00 0.00 0.00 5.28
127 128 1.607148 GAGGGAAACTTTTGGTCCACG 59.393 52.381 0.00 0.00 32.70 4.94
128 129 1.961394 GGAGGGAAACTTTTGGTCCAC 59.039 52.381 0.00 0.00 32.70 4.02
129 130 1.571457 TGGAGGGAAACTTTTGGTCCA 59.429 47.619 0.00 0.00 32.70 4.02
130 131 2.375014 TGGAGGGAAACTTTTGGTCC 57.625 50.000 0.00 0.00 0.00 4.46
131 132 3.562182 TCTTGGAGGGAAACTTTTGGTC 58.438 45.455 0.00 0.00 0.00 4.02
133 134 3.243873 GCTTCTTGGAGGGAAACTTTTGG 60.244 47.826 0.00 0.00 0.00 3.28
134 135 3.384467 TGCTTCTTGGAGGGAAACTTTTG 59.616 43.478 0.00 0.00 0.00 2.44
135 136 3.642141 TGCTTCTTGGAGGGAAACTTTT 58.358 40.909 0.00 0.00 0.00 2.27
136 137 3.312736 TGCTTCTTGGAGGGAAACTTT 57.687 42.857 0.00 0.00 0.00 2.66
137 138 3.117512 TCTTGCTTCTTGGAGGGAAACTT 60.118 43.478 0.00 0.00 0.00 2.66
138 139 2.443255 TCTTGCTTCTTGGAGGGAAACT 59.557 45.455 0.00 0.00 0.00 2.66
139 140 2.816672 CTCTTGCTTCTTGGAGGGAAAC 59.183 50.000 0.00 0.00 0.00 2.78
140 141 2.224867 CCTCTTGCTTCTTGGAGGGAAA 60.225 50.000 0.00 0.00 40.98 3.13
141 142 1.352352 CCTCTTGCTTCTTGGAGGGAA 59.648 52.381 0.00 0.00 40.98 3.97
142 143 0.987294 CCTCTTGCTTCTTGGAGGGA 59.013 55.000 0.00 0.00 40.98 4.20
143 144 3.566130 CCTCTTGCTTCTTGGAGGG 57.434 57.895 0.00 0.00 40.98 4.30
144 145 0.695347 ACCCTCTTGCTTCTTGGAGG 59.305 55.000 0.00 0.00 43.42 4.30
145 146 3.008485 AGTTACCCTCTTGCTTCTTGGAG 59.992 47.826 0.00 0.00 0.00 3.86
146 147 2.979678 AGTTACCCTCTTGCTTCTTGGA 59.020 45.455 0.00 0.00 0.00 3.53
148 149 6.094186 GGAAATAGTTACCCTCTTGCTTCTTG 59.906 42.308 0.00 0.00 0.00 3.02
151 152 4.882427 GGGAAATAGTTACCCTCTTGCTTC 59.118 45.833 0.00 0.00 40.39 3.86
152 153 4.291249 TGGGAAATAGTTACCCTCTTGCTT 59.709 41.667 0.75 0.00 43.59 3.91
153 154 3.850173 TGGGAAATAGTTACCCTCTTGCT 59.150 43.478 0.75 0.00 43.59 3.91
154 155 4.230745 TGGGAAATAGTTACCCTCTTGC 57.769 45.455 0.75 0.00 43.59 4.01
155 156 5.566469 TGTTGGGAAATAGTTACCCTCTTG 58.434 41.667 0.75 0.00 43.59 3.02
156 157 5.853572 TGTTGGGAAATAGTTACCCTCTT 57.146 39.130 0.75 0.00 43.59 2.85
157 158 5.853572 TTGTTGGGAAATAGTTACCCTCT 57.146 39.130 0.75 0.00 43.59 3.69
158 159 5.771165 TGTTTGTTGGGAAATAGTTACCCTC 59.229 40.000 0.75 0.00 43.59 4.30
160 161 6.408107 TTGTTTGTTGGGAAATAGTTACCC 57.592 37.500 0.75 2.81 36.82 3.69
161 162 6.422701 GCTTTGTTTGTTGGGAAATAGTTACC 59.577 38.462 0.00 0.00 38.39 2.85
162 163 7.207383 AGCTTTGTTTGTTGGGAAATAGTTAC 58.793 34.615 0.00 0.00 0.00 2.50
163 164 7.354751 AGCTTTGTTTGTTGGGAAATAGTTA 57.645 32.000 0.00 0.00 0.00 2.24
164 165 6.233905 AGCTTTGTTTGTTGGGAAATAGTT 57.766 33.333 0.00 0.00 0.00 2.24
165 166 5.869649 AGCTTTGTTTGTTGGGAAATAGT 57.130 34.783 0.00 0.00 0.00 2.12
166 167 8.831715 AAATAGCTTTGTTTGTTGGGAAATAG 57.168 30.769 0.00 0.00 0.00 1.73
167 168 9.267084 GAAAATAGCTTTGTTTGTTGGGAAATA 57.733 29.630 0.00 0.00 0.00 1.40
169 170 6.540551 GGAAAATAGCTTTGTTTGTTGGGAAA 59.459 34.615 0.00 0.00 0.00 3.13
170 171 6.052360 GGAAAATAGCTTTGTTTGTTGGGAA 58.948 36.000 0.00 0.00 0.00 3.97
171 172 5.454045 GGGAAAATAGCTTTGTTTGTTGGGA 60.454 40.000 0.00 0.00 0.00 4.37
172 173 4.754618 GGGAAAATAGCTTTGTTTGTTGGG 59.245 41.667 0.00 0.00 0.00 4.12
173 174 5.363939 TGGGAAAATAGCTTTGTTTGTTGG 58.636 37.500 0.00 0.00 0.00 3.77
174 175 6.048509 ACTGGGAAAATAGCTTTGTTTGTTG 58.951 36.000 0.00 0.00 0.00 3.33
177 178 6.760770 TGAAACTGGGAAAATAGCTTTGTTTG 59.239 34.615 0.00 0.00 0.00 2.93
178 179 6.883744 TGAAACTGGGAAAATAGCTTTGTTT 58.116 32.000 0.00 0.00 0.00 2.83
179 180 6.478512 TGAAACTGGGAAAATAGCTTTGTT 57.521 33.333 0.00 0.00 0.00 2.83
182 183 7.826744 TGTTTTTGAAACTGGGAAAATAGCTTT 59.173 29.630 0.00 0.00 0.00 3.51
183 184 7.334858 TGTTTTTGAAACTGGGAAAATAGCTT 58.665 30.769 0.00 0.00 0.00 3.74
184 185 6.883744 TGTTTTTGAAACTGGGAAAATAGCT 58.116 32.000 0.00 0.00 0.00 3.32
185 186 7.728847 ATGTTTTTGAAACTGGGAAAATAGC 57.271 32.000 5.30 0.00 0.00 2.97
188 189 9.546428 CTCTTATGTTTTTGAAACTGGGAAAAT 57.454 29.630 5.30 0.00 0.00 1.82
189 190 8.754080 TCTCTTATGTTTTTGAAACTGGGAAAA 58.246 29.630 5.30 0.00 0.00 2.29
193 194 7.445402 TCTCTCTCTTATGTTTTTGAAACTGGG 59.555 37.037 5.30 0.00 0.00 4.45
194 195 8.383318 TCTCTCTCTTATGTTTTTGAAACTGG 57.617 34.615 5.30 0.00 0.00 4.00
210 211 9.425577 CCGTCTAATAAACTTTTTCTCTCTCTT 57.574 33.333 0.00 0.00 0.00 2.85
211 212 8.804204 TCCGTCTAATAAACTTTTTCTCTCTCT 58.196 33.333 0.00 0.00 0.00 3.10
213 214 7.546316 GCTCCGTCTAATAAACTTTTTCTCTCT 59.454 37.037 0.00 0.00 0.00 3.10
215 216 7.159372 TGCTCCGTCTAATAAACTTTTTCTCT 58.841 34.615 0.00 0.00 0.00 3.10
216 217 7.360575 TGCTCCGTCTAATAAACTTTTTCTC 57.639 36.000 0.00 0.00 0.00 2.87
217 218 7.065923 GGATGCTCCGTCTAATAAACTTTTTCT 59.934 37.037 0.00 0.00 0.00 2.52
218 219 7.065923 AGGATGCTCCGTCTAATAAACTTTTTC 59.934 37.037 0.00 0.00 42.75 2.29
220 221 6.415573 AGGATGCTCCGTCTAATAAACTTTT 58.584 36.000 0.00 0.00 42.75 2.27
221 222 5.990668 AGGATGCTCCGTCTAATAAACTTT 58.009 37.500 0.00 0.00 42.75 2.66
222 223 5.615925 AGGATGCTCCGTCTAATAAACTT 57.384 39.130 0.00 0.00 42.75 2.66
223 224 5.010820 GGTAGGATGCTCCGTCTAATAAACT 59.989 44.000 0.00 0.00 42.75 2.66
225 226 4.282703 GGGTAGGATGCTCCGTCTAATAAA 59.717 45.833 0.00 0.00 42.75 1.40
226 227 3.830755 GGGTAGGATGCTCCGTCTAATAA 59.169 47.826 0.00 0.00 42.75 1.40
228 229 2.249139 GGGTAGGATGCTCCGTCTAAT 58.751 52.381 0.00 0.00 42.75 1.73
229 230 1.700955 GGGTAGGATGCTCCGTCTAA 58.299 55.000 0.00 0.00 42.75 2.10
230 231 0.536687 CGGGTAGGATGCTCCGTCTA 60.537 60.000 6.24 0.00 42.75 2.59
231 232 1.828660 CGGGTAGGATGCTCCGTCT 60.829 63.158 6.24 0.00 42.75 4.18
232 233 2.728817 CGGGTAGGATGCTCCGTC 59.271 66.667 6.24 0.00 42.75 4.79
234 235 1.957562 CTACGGGTAGGATGCTCCG 59.042 63.158 12.05 12.05 42.75 4.63
235 236 1.113517 TGCTACGGGTAGGATGCTCC 61.114 60.000 7.87 0.00 36.58 4.70
236 237 0.969894 ATGCTACGGGTAGGATGCTC 59.030 55.000 11.41 0.00 41.68 4.26
237 238 0.969894 GATGCTACGGGTAGGATGCT 59.030 55.000 16.17 0.00 42.98 3.79
238 239 0.037232 GGATGCTACGGGTAGGATGC 60.037 60.000 16.17 15.07 42.98 3.91
239 240 1.338107 TGGATGCTACGGGTAGGATG 58.662 55.000 16.17 0.00 42.98 3.51
241 242 1.338107 CATGGATGCTACGGGTAGGA 58.662 55.000 7.87 5.30 37.89 2.94
242 243 0.321671 CCATGGATGCTACGGGTAGG 59.678 60.000 5.56 0.00 33.87 3.18
243 244 1.273606 CTCCATGGATGCTACGGGTAG 59.726 57.143 16.63 1.45 36.29 3.18
246 247 0.250038 CACTCCATGGATGCTACGGG 60.250 60.000 16.63 3.11 0.00 5.28
247 248 0.752658 TCACTCCATGGATGCTACGG 59.247 55.000 16.63 3.93 0.00 4.02
248 249 2.205074 GTTCACTCCATGGATGCTACG 58.795 52.381 16.63 4.75 0.00 3.51
249 250 2.205074 CGTTCACTCCATGGATGCTAC 58.795 52.381 16.63 14.25 0.00 3.58
251 252 0.745845 GCGTTCACTCCATGGATGCT 60.746 55.000 16.63 0.00 44.59 3.79
252 253 1.723870 GCGTTCACTCCATGGATGC 59.276 57.895 16.63 6.88 41.75 3.91
253 254 1.399440 CTTGCGTTCACTCCATGGATG 59.601 52.381 16.63 15.33 0.00 3.51
254 255 1.742761 CTTGCGTTCACTCCATGGAT 58.257 50.000 16.63 2.66 0.00 3.41
256 257 1.236616 TGCTTGCGTTCACTCCATGG 61.237 55.000 4.97 4.97 0.00 3.66
257 258 0.592637 TTGCTTGCGTTCACTCCATG 59.407 50.000 0.00 0.00 0.00 3.66
259 260 1.444119 GGTTGCTTGCGTTCACTCCA 61.444 55.000 0.00 0.00 0.00 3.86
260 261 1.282875 GGTTGCTTGCGTTCACTCC 59.717 57.895 0.00 0.00 0.00 3.85
359 360 0.746563 ACGGTATTGATGGCGGTTGG 60.747 55.000 0.00 0.00 0.00 3.77
420 421 0.528470 ACTCGAACTCCTACTGCTGC 59.472 55.000 0.00 0.00 0.00 5.25
432 433 2.978013 TCATCGCATACGTACTCGAAC 58.022 47.619 20.07 0.00 41.18 3.95
433 434 3.614588 CTTCATCGCATACGTACTCGAA 58.385 45.455 20.07 6.79 41.18 3.71
434 435 2.601504 GCTTCATCGCATACGTACTCGA 60.602 50.000 18.97 18.97 41.18 4.04
435 436 1.709203 GCTTCATCGCATACGTACTCG 59.291 52.381 0.00 4.60 41.18 4.18
436 437 2.727777 TGCTTCATCGCATACGTACTC 58.272 47.619 0.00 0.00 41.18 2.59
464 748 2.352960 GCAGATGCAGTTACAGCCTTAC 59.647 50.000 0.00 0.00 41.59 2.34
465 749 2.632377 GCAGATGCAGTTACAGCCTTA 58.368 47.619 0.00 0.00 41.59 2.69
466 750 1.457346 GCAGATGCAGTTACAGCCTT 58.543 50.000 0.00 0.00 41.59 4.35
467 751 3.165606 GCAGATGCAGTTACAGCCT 57.834 52.632 0.00 0.00 41.59 4.58
484 768 0.734942 TGCTACGCCGTAGAACTTGC 60.735 55.000 27.27 12.28 38.29 4.01
509 793 1.269166 GATCGTAGGTGTGCAGTTCG 58.731 55.000 0.00 0.00 0.00 3.95
551 835 4.426416 TCGTATGTTGGGTTACTTGATCG 58.574 43.478 0.00 0.00 0.00 3.69
560 844 5.105917 GGTTGATTCATTCGTATGTTGGGTT 60.106 40.000 1.75 0.00 33.34 4.11
597 905 4.716794 AGAAGATTCAGGGCAGATTCATC 58.283 43.478 0.00 0.00 0.00 2.92
619 937 0.034863 GGTGGTATTTGGGAGGCGAA 60.035 55.000 0.00 0.00 0.00 4.70
659 979 2.031012 TCGAGGTGGTTGCAGCTG 59.969 61.111 10.11 10.11 32.51 4.24
852 1182 6.388278 GTGTATTTATAGGTGGAGATCGGTC 58.612 44.000 0.00 0.00 0.00 4.79
854 1184 5.480772 AGGTGTATTTATAGGTGGAGATCGG 59.519 44.000 0.00 0.00 0.00 4.18
883 1213 2.169352 CCGATGATGGTGGAAGAGAAGT 59.831 50.000 0.00 0.00 0.00 3.01
903 1233 1.732732 CGTTGGAGTGTGAGATCGACC 60.733 57.143 0.00 0.00 0.00 4.79
905 1235 1.199327 GACGTTGGAGTGTGAGATCGA 59.801 52.381 0.00 0.00 0.00 3.59
949 1306 2.226912 GAGCTGTAGTGGCTATACGAGG 59.773 54.545 0.00 0.00 40.40 4.63
950 1307 2.096169 CGAGCTGTAGTGGCTATACGAG 60.096 54.545 0.00 0.00 40.40 4.18
952 1309 1.602851 ACGAGCTGTAGTGGCTATACG 59.397 52.381 0.00 0.00 40.40 3.06
953 1310 3.001395 CACGAGCTGTAGTGGCTATAC 57.999 52.381 0.00 0.00 40.40 1.47
1086 1455 2.599281 TCGTTGTCCTCCAGCGGA 60.599 61.111 0.00 0.00 46.40 5.54
2007 2406 1.221840 GGCGCCTGAATCCTTCTCA 59.778 57.895 22.15 0.00 0.00 3.27
2188 3746 9.474313 TTCAGCTGTAATTTATTTTCACCCTAT 57.526 29.630 14.67 0.00 0.00 2.57
2222 3783 3.793775 TTGCGCGTGGACGGAGAAA 62.794 57.895 8.43 0.00 40.23 2.52
2235 3796 0.793861 TACACGTCCAATTCTTGCGC 59.206 50.000 0.00 0.00 0.00 6.09
2246 3811 0.248784 GTCCCACGCTATACACGTCC 60.249 60.000 0.00 0.00 42.96 4.79
2248 3813 0.966875 TGGTCCCACGCTATACACGT 60.967 55.000 0.00 0.00 46.42 4.49
2254 3819 4.640771 AATATTGATGGTCCCACGCTAT 57.359 40.909 0.00 0.00 0.00 2.97
2322 3905 4.576463 AGCAAGCTTACATACATTACCAGC 59.424 41.667 0.00 0.00 0.00 4.85
2410 4000 8.443953 AAAGTACTCCATCTGCTTCATAATTC 57.556 34.615 0.00 0.00 0.00 2.17
2645 4240 4.141620 ACCGCATGAGAATTCTCTACCATT 60.142 41.667 30.45 12.54 43.25 3.16
2667 4262 3.120269 CCACTAGTATCCGTGCGATCTAC 60.120 52.174 0.00 0.00 31.92 2.59
2739 4334 9.226345 GCTACTTCTAATTATTTTGACATGTGC 57.774 33.333 1.15 0.00 0.00 4.57
2765 4360 8.670135 CCTACATATCTAAGTGAGTTATCTCCG 58.330 40.741 0.00 0.00 39.75 4.63
2856 4451 5.356882 TGATGAAATTGACAAACCGAGTC 57.643 39.130 0.00 0.00 36.55 3.36
2861 4456 7.116805 GGTTGAGATTGATGAAATTGACAAACC 59.883 37.037 0.00 0.00 0.00 3.27
2937 4532 3.011032 AGAAGGGTGAAGCCTTCATGATT 59.989 43.478 32.11 15.90 43.23 2.57
2938 4533 2.579860 AGAAGGGTGAAGCCTTCATGAT 59.420 45.455 32.11 16.20 43.23 2.45


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

AutoCloner maintained by Alex Coulton.