Multiple sequence alignment - TraesCS3D01G269600

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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 TraesCS3D01G269600 chr3D 100.000 4124 0 0 1 4124 374204964 374209087 0.000000e+00 7616.0
1 TraesCS3D01G269600 chr3D 76.226 265 49 13 1944 2204 339253212 339252958 1.200000e-25 128.0
2 TraesCS3D01G269600 chr3A 95.322 3869 123 21 271 4124 496701696 496705521 0.000000e+00 6089.0
3 TraesCS3D01G269600 chr3A 96.296 54 2 0 3947 4000 496705396 496705449 5.680000e-14 89.8
4 TraesCS3D01G269600 chr3B 94.753 3869 139 27 271 4124 487905332 487909151 0.000000e+00 5962.0
5 TraesCS3D01G269600 chr3B 95.385 65 2 1 202 266 810400564 810400627 7.290000e-18 102.0
6 TraesCS3D01G269600 chr3B 94.444 54 2 1 3947 4000 487909027 487909079 9.500000e-12 82.4
7 TraesCS3D01G269600 chr4A 82.161 768 103 21 3157 3918 658261515 658262254 2.710000e-176 628.0
8 TraesCS3D01G269600 chr7B 82.213 759 103 20 3157 3909 164158543 164157811 3.500000e-175 625.0
9 TraesCS3D01G269600 chr2D 80.749 774 91 23 3167 3909 596162982 596163728 6.030000e-153 551.0
10 TraesCS3D01G269600 chr2D 94.186 258 12 3 18 274 565170706 565170961 1.390000e-104 390.0
11 TraesCS3D01G269600 chr2B 80.469 768 100 27 3157 3918 785240117 785240840 3.630000e-150 542.0
12 TraesCS3D01G269600 chr2B 79.793 772 105 30 3157 3918 793487407 793488137 7.910000e-142 514.0
13 TraesCS3D01G269600 chr4B 80.339 768 105 26 3157 3918 16558151 16557424 1.300000e-149 540.0
14 TraesCS3D01G269600 chr6B 80.364 769 102 29 3157 3918 351224964 351224238 4.690000e-149 538.0
15 TraesCS3D01G269600 chr2A 82.137 655 92 15 3157 3807 778620349 778619716 4.690000e-149 538.0
16 TraesCS3D01G269600 chr1D 95.312 256 9 2 18 272 47437003 47436750 1.790000e-108 403.0
17 TraesCS3D01G269600 chr4D 94.510 255 12 2 18 271 39616298 39616045 3.860000e-105 392.0
18 TraesCS3D01G269600 chr4D 96.296 216 8 0 18 233 508427056 508426841 5.070000e-94 355.0
19 TraesCS3D01G269600 chr7D 94.048 252 12 3 18 269 126029238 126028990 3.010000e-101 379.0
20 TraesCS3D01G269600 chr7D 93.307 254 13 3 18 271 292367430 292367679 5.030000e-99 372.0
21 TraesCS3D01G269600 chr7D 92.913 254 14 2 18 271 521897832 521898081 2.340000e-97 366.0
22 TraesCS3D01G269600 chr1B 93.088 217 14 1 18 234 35004369 35004154 2.390000e-82 316.0
23 TraesCS3D01G269600 chrUn 92.991 214 14 1 18 231 386809995 386809783 1.110000e-80 311.0


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 TraesCS3D01G269600 chr3D 374204964 374209087 4123 False 7616.0 7616 100.0000 1 4124 1 chr3D.!!$F1 4123
1 TraesCS3D01G269600 chr3A 496701696 496705521 3825 False 3089.4 6089 95.8090 271 4124 2 chr3A.!!$F1 3853
2 TraesCS3D01G269600 chr3B 487905332 487909151 3819 False 3022.2 5962 94.5985 271 4124 2 chr3B.!!$F2 3853
3 TraesCS3D01G269600 chr4A 658261515 658262254 739 False 628.0 628 82.1610 3157 3918 1 chr4A.!!$F1 761
4 TraesCS3D01G269600 chr7B 164157811 164158543 732 True 625.0 625 82.2130 3157 3909 1 chr7B.!!$R1 752
5 TraesCS3D01G269600 chr2D 596162982 596163728 746 False 551.0 551 80.7490 3167 3909 1 chr2D.!!$F2 742
6 TraesCS3D01G269600 chr2B 785240117 785240840 723 False 542.0 542 80.4690 3157 3918 1 chr2B.!!$F1 761
7 TraesCS3D01G269600 chr2B 793487407 793488137 730 False 514.0 514 79.7930 3157 3918 1 chr2B.!!$F2 761
8 TraesCS3D01G269600 chr4B 16557424 16558151 727 True 540.0 540 80.3390 3157 3918 1 chr4B.!!$R1 761
9 TraesCS3D01G269600 chr6B 351224238 351224964 726 True 538.0 538 80.3640 3157 3918 1 chr6B.!!$R1 761
10 TraesCS3D01G269600 chr2A 778619716 778620349 633 True 538.0 538 82.1370 3157 3807 1 chr2A.!!$R1 650

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
238 239 0.030235 GGGGGCGATTTTTATGCGTC 59.970 55.0 0.00 0.0 0.00 5.19 F
295 296 0.107897 CGCTTGGGTGTAGGTGCATA 60.108 55.0 0.00 0.0 0.00 3.14 F
938 945 0.394216 TAGGCGGAGTTGGCGTAGTA 60.394 55.0 0.00 0.0 39.82 1.82 F
2350 2366 0.040204 ACCATGGCAAAGAAGAGGGG 59.960 55.0 13.04 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 1979 1.486726 GGGGTGAGGTAGGACTTGATG 59.513 57.143 0.00 0.0 0.00 3.07 R
2052 2068 1.987855 TACTTCCTGGTGAGGGCGG 60.988 63.158 0.00 0.0 40.25 6.13 R
2826 2842 0.101759 GTAGAACGTCCTGCCGCATA 59.898 55.000 0.00 0.0 0.00 3.14 R
3383 3425 4.133013 ACACGTGTTTCTTAGACCTGTT 57.867 40.909 17.22 0.0 0.00 3.16 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
28 29 4.606457 GGATGACGAGGAAATTTCTGTG 57.394 45.455 17.42 9.70 0.00 3.66
29 30 4.253685 GGATGACGAGGAAATTTCTGTGA 58.746 43.478 17.42 8.80 0.00 3.58
30 31 4.878397 GGATGACGAGGAAATTTCTGTGAT 59.122 41.667 17.42 12.64 0.00 3.06
31 32 5.220739 GGATGACGAGGAAATTTCTGTGATG 60.221 44.000 17.42 5.30 0.00 3.07
32 33 4.893608 TGACGAGGAAATTTCTGTGATGA 58.106 39.130 17.42 0.00 0.00 2.92
33 34 5.304778 TGACGAGGAAATTTCTGTGATGAA 58.695 37.500 17.42 0.00 0.00 2.57
34 35 5.762711 TGACGAGGAAATTTCTGTGATGAAA 59.237 36.000 17.42 0.00 39.79 2.69
35 36 6.430925 TGACGAGGAAATTTCTGTGATGAAAT 59.569 34.615 17.42 0.00 45.32 2.17
36 37 7.606073 TGACGAGGAAATTTCTGTGATGAAATA 59.394 33.333 17.42 0.00 43.40 1.40
37 38 8.511604 ACGAGGAAATTTCTGTGATGAAATAT 57.488 30.769 17.42 0.00 43.40 1.28
38 39 8.400947 ACGAGGAAATTTCTGTGATGAAATATG 58.599 33.333 17.42 0.00 43.40 1.78
39 40 8.400947 CGAGGAAATTTCTGTGATGAAATATGT 58.599 33.333 17.42 0.00 43.40 2.29
40 41 9.512435 GAGGAAATTTCTGTGATGAAATATGTG 57.488 33.333 17.42 0.00 43.40 3.21
41 42 9.246670 AGGAAATTTCTGTGATGAAATATGTGA 57.753 29.630 17.42 0.00 43.40 3.58
74 75 8.948853 ATATTTATGTTGATAATTGAACGCCG 57.051 30.769 0.00 0.00 0.00 6.46
75 76 6.424176 TTTATGTTGATAATTGAACGCCGA 57.576 33.333 0.00 0.00 0.00 5.54
76 77 4.536364 ATGTTGATAATTGAACGCCGAG 57.464 40.909 0.00 0.00 0.00 4.63
77 78 2.095213 TGTTGATAATTGAACGCCGAGC 59.905 45.455 0.00 0.00 0.00 5.03
78 79 1.295792 TGATAATTGAACGCCGAGCC 58.704 50.000 0.00 0.00 0.00 4.70
79 80 1.295792 GATAATTGAACGCCGAGCCA 58.704 50.000 0.00 0.00 0.00 4.75
80 81 1.003866 GATAATTGAACGCCGAGCCAC 60.004 52.381 0.00 0.00 0.00 5.01
81 82 1.355796 TAATTGAACGCCGAGCCACG 61.356 55.000 0.00 0.00 42.18 4.94
101 102 1.931551 CGAACCACGCCGAATATGG 59.068 57.895 0.00 0.00 39.57 2.74
102 103 1.495584 CGAACCACGCCGAATATGGG 61.496 60.000 0.00 0.00 37.86 4.00
110 111 2.789409 GCCGAATATGGGCCTATTCT 57.211 50.000 22.26 0.00 44.97 2.40
111 112 2.633488 GCCGAATATGGGCCTATTCTC 58.367 52.381 22.26 3.45 44.97 2.87
112 113 2.893637 CCGAATATGGGCCTATTCTCG 58.106 52.381 19.45 19.45 36.42 4.04
113 114 2.271800 CGAATATGGGCCTATTCTCGC 58.728 52.381 22.26 7.55 36.42 5.03
114 115 2.633488 GAATATGGGCCTATTCTCGCC 58.367 52.381 7.02 0.00 44.92 5.54
120 121 2.029838 GGCCTATTCTCGCCCATATG 57.970 55.000 0.00 0.00 39.39 1.78
121 122 1.407437 GGCCTATTCTCGCCCATATGG 60.407 57.143 15.41 15.41 39.39 2.74
132 133 3.965780 CCATATGGGCCTTTTTCGC 57.034 52.632 14.52 0.00 0.00 4.70
133 134 0.389025 CCATATGGGCCTTTTTCGCC 59.611 55.000 14.52 0.00 46.29 5.54
139 140 2.736890 GGCCTTTTTCGCCGAAATG 58.263 52.632 13.68 9.28 36.47 2.32
140 141 0.735978 GGCCTTTTTCGCCGAAATGG 60.736 55.000 20.58 20.58 36.47 3.16
141 142 0.735978 GCCTTTTTCGCCGAAATGGG 60.736 55.000 23.79 21.89 38.63 4.00
147 148 3.674906 CGCCGAAATGGGGTTTCA 58.325 55.556 2.01 0.00 45.24 2.69
148 149 1.960612 CGCCGAAATGGGGTTTCAA 59.039 52.632 2.01 0.00 45.24 2.69
149 150 0.315568 CGCCGAAATGGGGTTTCAAA 59.684 50.000 2.01 0.00 45.24 2.69
150 151 1.269831 CGCCGAAATGGGGTTTCAAAA 60.270 47.619 2.01 0.00 45.24 2.44
151 152 2.412870 GCCGAAATGGGGTTTCAAAAG 58.587 47.619 2.01 0.00 45.24 2.27
152 153 2.224185 GCCGAAATGGGGTTTCAAAAGT 60.224 45.455 2.01 0.00 45.24 2.66
153 154 3.389221 CCGAAATGGGGTTTCAAAAGTG 58.611 45.455 2.01 0.00 45.24 3.16
154 155 3.389221 CGAAATGGGGTTTCAAAAGTGG 58.611 45.455 2.01 0.00 45.24 4.00
155 156 3.738982 GAAATGGGGTTTCAAAAGTGGG 58.261 45.455 0.00 0.00 44.53 4.61
156 157 1.055849 ATGGGGTTTCAAAAGTGGGC 58.944 50.000 0.00 0.00 0.00 5.36
157 158 1.051556 TGGGGTTTCAAAAGTGGGCC 61.052 55.000 0.00 0.00 0.00 5.80
158 159 1.051556 GGGGTTTCAAAAGTGGGCCA 61.052 55.000 0.00 0.00 0.00 5.36
159 160 0.833949 GGGTTTCAAAAGTGGGCCAA 59.166 50.000 8.40 0.00 0.00 4.52
160 161 1.210722 GGGTTTCAAAAGTGGGCCAAA 59.789 47.619 8.40 0.00 0.00 3.28
161 162 2.356227 GGGTTTCAAAAGTGGGCCAAAA 60.356 45.455 8.40 0.18 0.00 2.44
162 163 3.550820 GGTTTCAAAAGTGGGCCAAAAT 58.449 40.909 8.40 0.00 0.00 1.82
163 164 3.563808 GGTTTCAAAAGTGGGCCAAAATC 59.436 43.478 8.40 0.00 0.00 2.17
164 165 2.810439 TCAAAAGTGGGCCAAAATCG 57.190 45.000 8.40 0.00 0.00 3.34
165 166 2.311463 TCAAAAGTGGGCCAAAATCGA 58.689 42.857 8.40 0.00 0.00 3.59
166 167 2.035321 TCAAAAGTGGGCCAAAATCGAC 59.965 45.455 8.40 0.00 0.00 4.20
167 168 0.596082 AAAGTGGGCCAAAATCGACG 59.404 50.000 8.40 0.00 0.00 5.12
168 169 0.250553 AAGTGGGCCAAAATCGACGA 60.251 50.000 8.40 0.00 0.00 4.20
169 170 0.953960 AGTGGGCCAAAATCGACGAC 60.954 55.000 8.40 0.00 0.00 4.34
170 171 0.953960 GTGGGCCAAAATCGACGACT 60.954 55.000 8.40 0.00 0.00 4.18
171 172 0.953471 TGGGCCAAAATCGACGACTG 60.953 55.000 2.13 0.00 0.00 3.51
172 173 1.644786 GGGCCAAAATCGACGACTGG 61.645 60.000 4.39 14.99 0.00 4.00
173 174 1.644786 GGCCAAAATCGACGACTGGG 61.645 60.000 18.88 10.18 0.00 4.45
174 175 1.794222 CCAAAATCGACGACTGGGC 59.206 57.895 0.00 0.00 0.00 5.36
175 176 1.419922 CAAAATCGACGACTGGGCG 59.580 57.895 0.00 0.00 37.29 6.13
177 178 0.244450 AAAATCGACGACTGGGCGTA 59.756 50.000 0.00 0.00 45.72 4.42
178 179 0.244450 AAATCGACGACTGGGCGTAA 59.756 50.000 0.00 0.00 45.72 3.18
179 180 0.244450 AATCGACGACTGGGCGTAAA 59.756 50.000 0.00 0.00 45.72 2.01
180 181 0.244450 ATCGACGACTGGGCGTAAAA 59.756 50.000 0.00 0.00 45.72 1.52
181 182 0.664166 TCGACGACTGGGCGTAAAAC 60.664 55.000 0.08 0.00 45.72 2.43
182 183 1.620413 CGACGACTGGGCGTAAAACC 61.620 60.000 0.08 0.00 45.72 3.27
183 184 1.620413 GACGACTGGGCGTAAAACCG 61.620 60.000 0.08 0.00 45.72 4.44
184 185 1.665599 CGACTGGGCGTAAAACCGT 60.666 57.895 0.00 0.00 0.00 4.83
185 186 1.620413 CGACTGGGCGTAAAACCGTC 61.620 60.000 0.00 0.00 0.00 4.79
188 189 2.747460 GGGCGTAAAACCGTCCCC 60.747 66.667 0.00 0.00 46.75 4.81
189 190 2.032376 GGCGTAAAACCGTCCCCA 59.968 61.111 0.00 0.00 0.00 4.96
190 191 1.600356 GGCGTAAAACCGTCCCCAA 60.600 57.895 0.00 0.00 0.00 4.12
191 192 1.575922 GCGTAAAACCGTCCCCAAC 59.424 57.895 0.00 0.00 0.00 3.77
199 200 3.411351 CGTCCCCAACGCTGAACG 61.411 66.667 0.00 0.00 45.76 3.95
209 210 4.223964 GCTGAACGAATCGCCGGC 62.224 66.667 19.07 19.07 0.00 6.13
210 211 2.509336 CTGAACGAATCGCCGGCT 60.509 61.111 26.68 5.36 0.00 5.52
211 212 2.508439 TGAACGAATCGCCGGCTC 60.508 61.111 26.68 14.82 0.00 4.70
212 213 3.617538 GAACGAATCGCCGGCTCG 61.618 66.667 28.66 28.66 38.53 5.03
235 236 1.886542 CCTAGGGGGCGATTTTTATGC 59.113 52.381 0.00 0.00 0.00 3.14
236 237 1.535462 CTAGGGGGCGATTTTTATGCG 59.465 52.381 0.00 0.00 0.00 4.73
237 238 0.395173 AGGGGGCGATTTTTATGCGT 60.395 50.000 0.00 0.00 0.00 5.24
238 239 0.030235 GGGGGCGATTTTTATGCGTC 59.970 55.000 0.00 0.00 0.00 5.19
239 240 3.544615 GGGCGATTTTTATGCGTCC 57.455 52.632 0.00 0.00 42.93 4.79
240 241 1.021968 GGGCGATTTTTATGCGTCCT 58.978 50.000 0.00 0.00 45.64 3.85
241 242 1.404035 GGGCGATTTTTATGCGTCCTT 59.596 47.619 0.00 0.00 45.64 3.36
242 243 2.450160 GGCGATTTTTATGCGTCCTTG 58.550 47.619 0.00 0.00 0.00 3.61
243 244 2.450160 GCGATTTTTATGCGTCCTTGG 58.550 47.619 0.00 0.00 0.00 3.61
244 245 2.794631 GCGATTTTTATGCGTCCTTGGG 60.795 50.000 0.00 0.00 0.00 4.12
245 246 2.223479 CGATTTTTATGCGTCCTTGGGG 60.223 50.000 0.00 0.00 0.00 4.96
246 247 1.551452 TTTTTATGCGTCCTTGGGGG 58.449 50.000 0.00 0.00 0.00 5.40
267 268 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26
268 269 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
269 270 0.461548 CAACGGCTGGAGATGCTCTA 59.538 55.000 0.00 0.00 0.00 2.43
295 296 0.107897 CGCTTGGGTGTAGGTGCATA 60.108 55.000 0.00 0.00 0.00 3.14
296 297 1.677518 CGCTTGGGTGTAGGTGCATAA 60.678 52.381 0.00 0.00 0.00 1.90
297 298 2.654863 GCTTGGGTGTAGGTGCATAAT 58.345 47.619 0.00 0.00 0.00 1.28
594 599 5.011329 TGAACTACCGAGTAAATTCCACACT 59.989 40.000 0.00 0.00 33.58 3.55
644 650 8.435982 ACTATATTTTTAGAGCTTGCTCATCCT 58.564 33.333 22.44 6.39 0.00 3.24
656 662 4.860802 TGCTCATCCTTATCCTTTTCCA 57.139 40.909 0.00 0.00 0.00 3.53
661 667 6.462067 GCTCATCCTTATCCTTTTCCATTTGG 60.462 42.308 0.00 0.00 0.00 3.28
662 668 5.898972 TCATCCTTATCCTTTTCCATTTGGG 59.101 40.000 0.00 0.00 35.41 4.12
665 671 4.651045 CCTTATCCTTTTCCATTTGGGGAG 59.349 45.833 0.00 0.00 38.42 4.30
729 736 5.652994 GAGAAACGCTCATCCCTCTATAT 57.347 43.478 0.00 0.00 43.38 0.86
738 745 2.044555 CCCTCTATATCCGCGGCGA 61.045 63.158 25.92 11.32 0.00 5.54
740 747 1.025113 CCTCTATATCCGCGGCGAGA 61.025 60.000 25.92 19.11 0.00 4.04
762 769 6.228258 AGATCGTAATGCGGGTTATTAATGT 58.772 36.000 0.00 0.00 41.72 2.71
768 775 4.157849 TGCGGGTTATTAATGTGGATCA 57.842 40.909 0.00 0.00 0.00 2.92
919 926 7.962995 TTGAGGAGATCAACAGTAGTAATCT 57.037 36.000 0.00 0.00 43.09 2.40
938 945 0.394216 TAGGCGGAGTTGGCGTAGTA 60.394 55.000 0.00 0.00 39.82 1.82
1216 1226 1.991230 CCCCTGGAAGTTCGTCCAT 59.009 57.895 7.80 0.00 46.66 3.41
1782 1792 0.620700 GGTACCCTGTCCATGGAGGT 60.621 60.000 23.55 23.55 39.02 3.85
1963 1979 1.376037 CCCTTCGGACCAAGTGCTC 60.376 63.158 0.00 0.00 0.00 4.26
2081 2097 3.073101 GGAAGTACTCCCCGGCGT 61.073 66.667 6.01 0.00 38.44 5.68
2257 2273 4.966005 TGGCGACAGTTCTTCTCG 57.034 55.556 0.00 0.00 35.01 4.04
2350 2366 0.040204 ACCATGGCAAAGAAGAGGGG 59.960 55.000 13.04 0.00 0.00 4.79
2646 2662 0.603707 TCTGGGCGCAAGAAGAACAG 60.604 55.000 10.83 4.11 43.02 3.16
2656 2672 2.280797 AAGAACAGCAGCGCGGAA 60.281 55.556 13.03 0.00 0.00 4.30
2727 2743 3.371097 GAACGCCCGATCCTGCTGA 62.371 63.158 0.00 0.00 0.00 4.26
2773 2789 1.321074 ATCTTGACGAGGACGACCCC 61.321 60.000 0.00 0.00 42.66 4.95
2808 2824 3.751246 CGCACCCCATTGCCACAG 61.751 66.667 0.00 0.00 39.53 3.66
2826 2842 2.636893 ACAGAGCAGGTGAATCTTCAGT 59.363 45.455 0.00 0.00 37.98 3.41
2832 2848 2.868583 CAGGTGAATCTTCAGTATGCGG 59.131 50.000 0.00 0.00 37.98 5.69
2836 2852 1.869767 GAATCTTCAGTATGCGGCAGG 59.130 52.381 9.25 0.00 34.76 4.85
2837 2853 1.123077 ATCTTCAGTATGCGGCAGGA 58.877 50.000 9.25 0.46 34.76 3.86
3025 3041 7.418337 TGCACATCGGATTAGGTACATATAT 57.582 36.000 0.00 0.00 0.00 0.86
3026 3042 8.528044 TGCACATCGGATTAGGTACATATATA 57.472 34.615 0.00 0.00 0.00 0.86
3027 3043 8.630037 TGCACATCGGATTAGGTACATATATAG 58.370 37.037 0.00 0.00 0.00 1.31
3028 3044 8.082852 GCACATCGGATTAGGTACATATATAGG 58.917 40.741 0.00 0.00 0.00 2.57
3029 3045 8.082852 CACATCGGATTAGGTACATATATAGGC 58.917 40.741 0.00 0.00 0.00 3.93
3030 3046 7.783119 ACATCGGATTAGGTACATATATAGGCA 59.217 37.037 0.00 0.00 0.00 4.75
3034 3050 9.477484 CGGATTAGGTACATATATAGGCATTTC 57.523 37.037 0.00 0.00 0.00 2.17
3334 3374 6.430000 ACATAAGCTTCCAAGTGAAAATACGT 59.570 34.615 0.00 0.00 31.06 3.57
3383 3425 7.573656 GCAGATCACATTACAGACATTTGACAA 60.574 37.037 0.00 0.00 0.00 3.18
3696 3750 1.755179 ATGTGTTGGTAGCTGATGGC 58.245 50.000 0.00 0.00 42.19 4.40
3754 3808 6.763715 ACATATCCCAGCTATTGGTTTCTA 57.236 37.500 0.00 0.00 46.25 2.10
3950 4008 9.559732 TGACACTAGTGGAAATAAATCATATGG 57.440 33.333 26.12 0.00 34.19 2.74
4039 4098 6.254281 ACACAAATATAAGCACTGTTCCAC 57.746 37.500 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.056107 ACAGAAATTTCCTCGTCATCCGA 60.056 43.478 14.61 0.00 45.00 4.55
6 7 3.062639 CACAGAAATTTCCTCGTCATCCG 59.937 47.826 14.61 0.00 38.13 4.18
7 8 4.253685 TCACAGAAATTTCCTCGTCATCC 58.746 43.478 14.61 0.00 0.00 3.51
8 9 5.582269 TCATCACAGAAATTTCCTCGTCATC 59.418 40.000 14.61 0.00 0.00 2.92
9 10 5.491070 TCATCACAGAAATTTCCTCGTCAT 58.509 37.500 14.61 0.00 0.00 3.06
10 11 4.893608 TCATCACAGAAATTTCCTCGTCA 58.106 39.130 14.61 0.00 0.00 4.35
11 12 5.862924 TTCATCACAGAAATTTCCTCGTC 57.137 39.130 14.61 0.00 0.00 4.20
12 13 6.824305 ATTTCATCACAGAAATTTCCTCGT 57.176 33.333 14.61 7.08 43.67 4.18
13 14 8.400947 ACATATTTCATCACAGAAATTTCCTCG 58.599 33.333 14.61 6.46 43.67 4.63
14 15 9.512435 CACATATTTCATCACAGAAATTTCCTC 57.488 33.333 14.61 0.00 43.67 3.71
15 16 9.246670 TCACATATTTCATCACAGAAATTTCCT 57.753 29.630 14.61 0.00 43.67 3.36
48 49 9.393249 CGGCGTTCAATTATCAACATAAATATT 57.607 29.630 0.00 0.00 0.00 1.28
49 50 8.779303 TCGGCGTTCAATTATCAACATAAATAT 58.221 29.630 6.85 0.00 0.00 1.28
50 51 8.144155 TCGGCGTTCAATTATCAACATAAATA 57.856 30.769 6.85 0.00 0.00 1.40
51 52 7.022055 TCGGCGTTCAATTATCAACATAAAT 57.978 32.000 6.85 0.00 0.00 1.40
52 53 6.424176 TCGGCGTTCAATTATCAACATAAA 57.576 33.333 6.85 0.00 0.00 1.40
53 54 5.503357 GCTCGGCGTTCAATTATCAACATAA 60.503 40.000 6.85 0.00 0.00 1.90
54 55 4.025229 GCTCGGCGTTCAATTATCAACATA 60.025 41.667 6.85 0.00 0.00 2.29
55 56 3.242739 GCTCGGCGTTCAATTATCAACAT 60.243 43.478 6.85 0.00 0.00 2.71
56 57 2.095213 GCTCGGCGTTCAATTATCAACA 59.905 45.455 6.85 0.00 0.00 3.33
57 58 2.538939 GGCTCGGCGTTCAATTATCAAC 60.539 50.000 6.85 0.00 0.00 3.18
58 59 1.668751 GGCTCGGCGTTCAATTATCAA 59.331 47.619 6.85 0.00 0.00 2.57
59 60 1.295792 GGCTCGGCGTTCAATTATCA 58.704 50.000 6.85 0.00 0.00 2.15
60 61 1.003866 GTGGCTCGGCGTTCAATTATC 60.004 52.381 6.85 0.00 0.00 1.75
61 62 1.014352 GTGGCTCGGCGTTCAATTAT 58.986 50.000 6.85 0.00 0.00 1.28
62 63 1.355796 CGTGGCTCGGCGTTCAATTA 61.356 55.000 6.85 0.00 35.71 1.40
63 64 2.677003 CGTGGCTCGGCGTTCAATT 61.677 57.895 6.85 0.00 35.71 2.32
64 65 3.118454 CGTGGCTCGGCGTTCAAT 61.118 61.111 6.85 0.00 35.71 2.57
83 84 1.495584 CCCATATTCGGCGTGGTTCG 61.496 60.000 6.85 0.00 43.12 3.95
84 85 1.782028 GCCCATATTCGGCGTGGTTC 61.782 60.000 6.85 0.00 36.47 3.62
85 86 1.822186 GCCCATATTCGGCGTGGTT 60.822 57.895 6.85 0.00 36.47 3.67
86 87 2.203153 GCCCATATTCGGCGTGGT 60.203 61.111 6.85 0.00 36.47 4.16
91 92 2.633488 GAGAATAGGCCCATATTCGGC 58.367 52.381 15.47 10.24 43.79 5.54
92 93 2.893637 CGAGAATAGGCCCATATTCGG 58.106 52.381 15.47 10.10 43.79 4.30
93 94 2.271800 GCGAGAATAGGCCCATATTCG 58.728 52.381 15.47 13.38 43.79 3.34
94 95 2.633488 GGCGAGAATAGGCCCATATTC 58.367 52.381 14.20 14.20 43.64 1.75
95 96 2.789409 GGCGAGAATAGGCCCATATT 57.211 50.000 0.00 0.00 43.64 1.28
102 103 2.029838 CCATATGGGCGAGAATAGGC 57.970 55.000 14.52 0.00 34.95 3.93
114 115 0.389025 GGCGAAAAAGGCCCATATGG 59.611 55.000 15.41 15.41 44.97 2.74
115 116 3.965780 GGCGAAAAAGGCCCATATG 57.034 52.632 0.00 0.00 44.97 1.78
122 123 0.735978 CCCATTTCGGCGAAAAAGGC 60.736 55.000 33.59 0.00 35.11 4.35
123 124 0.108851 CCCCATTTCGGCGAAAAAGG 60.109 55.000 34.99 33.65 35.11 3.11
124 125 0.601057 ACCCCATTTCGGCGAAAAAG 59.399 50.000 34.99 28.23 35.11 2.27
125 126 1.041437 AACCCCATTTCGGCGAAAAA 58.959 45.000 34.99 17.50 35.11 1.94
126 127 1.000052 GAAACCCCATTTCGGCGAAAA 60.000 47.619 34.99 20.36 37.55 2.29
127 128 0.599060 GAAACCCCATTTCGGCGAAA 59.401 50.000 33.79 33.79 37.55 3.46
128 129 2.259281 GAAACCCCATTTCGGCGAA 58.741 52.632 19.83 19.83 37.55 4.70
129 130 3.990466 GAAACCCCATTTCGGCGA 58.010 55.556 4.99 4.99 37.55 5.54
134 135 3.738982 CCCACTTTTGAAACCCCATTTC 58.261 45.455 0.00 0.00 46.07 2.17
135 136 2.158682 GCCCACTTTTGAAACCCCATTT 60.159 45.455 0.00 0.00 0.00 2.32
136 137 1.419762 GCCCACTTTTGAAACCCCATT 59.580 47.619 0.00 0.00 0.00 3.16
137 138 1.055849 GCCCACTTTTGAAACCCCAT 58.944 50.000 0.00 0.00 0.00 4.00
138 139 1.051556 GGCCCACTTTTGAAACCCCA 61.052 55.000 0.00 0.00 0.00 4.96
139 140 1.051556 TGGCCCACTTTTGAAACCCC 61.052 55.000 0.00 0.00 0.00 4.95
140 141 0.833949 TTGGCCCACTTTTGAAACCC 59.166 50.000 0.00 0.00 0.00 4.11
141 142 2.700722 TTTGGCCCACTTTTGAAACC 57.299 45.000 0.00 0.00 0.00 3.27
142 143 3.247411 CGATTTTGGCCCACTTTTGAAAC 59.753 43.478 0.00 0.00 0.00 2.78
143 144 3.133003 TCGATTTTGGCCCACTTTTGAAA 59.867 39.130 0.00 0.00 0.00 2.69
144 145 2.695666 TCGATTTTGGCCCACTTTTGAA 59.304 40.909 0.00 0.00 0.00 2.69
145 146 2.035321 GTCGATTTTGGCCCACTTTTGA 59.965 45.455 0.00 0.00 0.00 2.69
146 147 2.403259 GTCGATTTTGGCCCACTTTTG 58.597 47.619 0.00 0.00 0.00 2.44
147 148 1.000717 CGTCGATTTTGGCCCACTTTT 60.001 47.619 0.00 0.00 0.00 2.27
148 149 0.596082 CGTCGATTTTGGCCCACTTT 59.404 50.000 0.00 0.00 0.00 2.66
149 150 0.250553 TCGTCGATTTTGGCCCACTT 60.251 50.000 0.00 0.00 0.00 3.16
150 151 0.953960 GTCGTCGATTTTGGCCCACT 60.954 55.000 0.00 0.00 0.00 4.00
151 152 0.953960 AGTCGTCGATTTTGGCCCAC 60.954 55.000 0.00 0.00 0.00 4.61
152 153 0.953471 CAGTCGTCGATTTTGGCCCA 60.953 55.000 0.00 0.00 0.00 5.36
153 154 1.644786 CCAGTCGTCGATTTTGGCCC 61.645 60.000 0.00 0.00 0.00 5.80
154 155 1.644786 CCCAGTCGTCGATTTTGGCC 61.645 60.000 14.46 0.00 0.00 5.36
155 156 1.794222 CCCAGTCGTCGATTTTGGC 59.206 57.895 14.46 0.00 0.00 4.52
156 157 1.794222 GCCCAGTCGTCGATTTTGG 59.206 57.895 13.45 13.45 0.00 3.28
157 158 1.289109 ACGCCCAGTCGTCGATTTTG 61.289 55.000 0.00 0.00 38.44 2.44
158 159 0.244450 TACGCCCAGTCGTCGATTTT 59.756 50.000 0.00 0.00 43.15 1.82
159 160 0.244450 TTACGCCCAGTCGTCGATTT 59.756 50.000 0.00 0.00 43.15 2.17
160 161 0.244450 TTTACGCCCAGTCGTCGATT 59.756 50.000 0.00 0.00 43.15 3.34
161 162 0.244450 TTTTACGCCCAGTCGTCGAT 59.756 50.000 0.00 0.00 43.15 3.59
162 163 0.664166 GTTTTACGCCCAGTCGTCGA 60.664 55.000 0.00 0.00 43.15 4.20
163 164 1.620413 GGTTTTACGCCCAGTCGTCG 61.620 60.000 0.00 0.00 43.15 5.12
164 165 1.620413 CGGTTTTACGCCCAGTCGTC 61.620 60.000 0.00 0.00 43.15 4.20
165 166 1.665599 CGGTTTTACGCCCAGTCGT 60.666 57.895 0.00 0.00 45.49 4.34
166 167 1.620413 GACGGTTTTACGCCCAGTCG 61.620 60.000 0.00 0.00 37.37 4.18
167 168 1.293963 GGACGGTTTTACGCCCAGTC 61.294 60.000 0.00 0.00 36.33 3.51
168 169 1.301953 GGACGGTTTTACGCCCAGT 60.302 57.895 0.00 0.00 36.33 4.00
169 170 2.036571 GGGACGGTTTTACGCCCAG 61.037 63.158 11.35 0.00 44.29 4.45
170 171 2.032376 GGGACGGTTTTACGCCCA 59.968 61.111 11.35 0.00 44.29 5.36
171 172 2.747460 GGGGACGGTTTTACGCCC 60.747 66.667 8.79 8.79 44.22 6.13
172 173 1.600356 TTGGGGACGGTTTTACGCC 60.600 57.895 0.00 0.00 37.37 5.68
173 174 1.575922 GTTGGGGACGGTTTTACGC 59.424 57.895 0.00 0.00 37.37 4.42
183 184 0.953960 ATTCGTTCAGCGTTGGGGAC 60.954 55.000 0.00 0.00 42.13 4.46
184 185 0.672401 GATTCGTTCAGCGTTGGGGA 60.672 55.000 0.00 0.00 42.13 4.81
185 186 1.794222 GATTCGTTCAGCGTTGGGG 59.206 57.895 0.00 0.00 42.13 4.96
186 187 1.419922 CGATTCGTTCAGCGTTGGG 59.580 57.895 0.00 0.00 42.13 4.12
187 188 1.225745 GCGATTCGTTCAGCGTTGG 60.226 57.895 8.03 0.00 42.13 3.77
188 189 1.225745 GGCGATTCGTTCAGCGTTG 60.226 57.895 8.03 0.00 42.13 4.10
189 190 2.726691 CGGCGATTCGTTCAGCGTT 61.727 57.895 0.00 0.00 42.13 4.84
190 191 3.179265 CGGCGATTCGTTCAGCGT 61.179 61.111 0.00 0.00 42.13 5.07
191 192 3.913573 CCGGCGATTCGTTCAGCG 61.914 66.667 9.30 0.00 43.01 5.18
192 193 4.223964 GCCGGCGATTCGTTCAGC 62.224 66.667 12.58 0.00 0.00 4.26
193 194 2.509336 AGCCGGCGATTCGTTCAG 60.509 61.111 23.20 0.00 0.00 3.02
194 195 2.508439 GAGCCGGCGATTCGTTCA 60.508 61.111 23.20 0.00 0.00 3.18
195 196 3.617538 CGAGCCGGCGATTCGTTC 61.618 66.667 23.98 13.06 0.00 3.95
215 216 1.886542 GCATAAAAATCGCCCCCTAGG 59.113 52.381 0.06 0.06 39.47 3.02
216 217 1.535462 CGCATAAAAATCGCCCCCTAG 59.465 52.381 0.00 0.00 0.00 3.02
217 218 1.134037 ACGCATAAAAATCGCCCCCTA 60.134 47.619 0.00 0.00 0.00 3.53
218 219 0.395173 ACGCATAAAAATCGCCCCCT 60.395 50.000 0.00 0.00 0.00 4.79
219 220 0.030235 GACGCATAAAAATCGCCCCC 59.970 55.000 0.00 0.00 0.00 5.40
220 221 0.030235 GGACGCATAAAAATCGCCCC 59.970 55.000 0.00 0.00 0.00 5.80
221 222 1.021968 AGGACGCATAAAAATCGCCC 58.978 50.000 0.00 0.00 0.00 6.13
222 223 2.450160 CAAGGACGCATAAAAATCGCC 58.550 47.619 0.00 0.00 0.00 5.54
223 224 2.450160 CCAAGGACGCATAAAAATCGC 58.550 47.619 0.00 0.00 0.00 4.58
224 225 2.223479 CCCCAAGGACGCATAAAAATCG 60.223 50.000 0.00 0.00 33.47 3.34
225 226 2.100749 CCCCCAAGGACGCATAAAAATC 59.899 50.000 0.00 0.00 38.24 2.17
226 227 2.107366 CCCCCAAGGACGCATAAAAAT 58.893 47.619 0.00 0.00 38.24 1.82
227 228 1.551452 CCCCCAAGGACGCATAAAAA 58.449 50.000 0.00 0.00 38.24 1.94
228 229 3.274601 CCCCCAAGGACGCATAAAA 57.725 52.632 0.00 0.00 38.24 1.52
250 251 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
261 262 3.376540 CCAAGCGACTAGTTAGAGCATC 58.623 50.000 0.00 0.00 34.71 3.91
262 263 2.101582 CCCAAGCGACTAGTTAGAGCAT 59.898 50.000 0.00 0.00 34.71 3.79
263 264 1.476891 CCCAAGCGACTAGTTAGAGCA 59.523 52.381 0.00 0.00 34.71 4.26
264 265 1.477295 ACCCAAGCGACTAGTTAGAGC 59.523 52.381 0.00 1.08 0.00 4.09
265 266 2.492484 ACACCCAAGCGACTAGTTAGAG 59.508 50.000 0.00 0.00 0.00 2.43
266 267 2.522185 ACACCCAAGCGACTAGTTAGA 58.478 47.619 0.00 0.00 0.00 2.10
267 268 3.181489 CCTACACCCAAGCGACTAGTTAG 60.181 52.174 0.00 0.00 0.00 2.34
268 269 2.756760 CCTACACCCAAGCGACTAGTTA 59.243 50.000 0.00 0.00 0.00 2.24
269 270 1.549170 CCTACACCCAAGCGACTAGTT 59.451 52.381 0.00 0.00 0.00 2.24
295 296 0.543749 GGTCCTGAGCTGCCACTATT 59.456 55.000 0.00 0.00 0.00 1.73
296 297 0.326048 AGGTCCTGAGCTGCCACTAT 60.326 55.000 0.00 0.00 37.82 2.12
297 298 0.335019 TAGGTCCTGAGCTGCCACTA 59.665 55.000 9.03 0.00 39.78 2.74
462 467 2.295253 CGTGGAACATGTAGGGAGAC 57.705 55.000 0.00 0.00 44.52 3.36
559 564 7.732976 TACTCGGTAGTTCAGCAAAAAGCGA 62.733 44.000 0.00 0.00 42.11 4.93
644 650 4.030216 GCTCCCCAAATGGAAAAGGATAA 58.970 43.478 0.00 0.00 37.39 1.75
665 671 2.698855 TTAGAGGGATGAGCAAGTGC 57.301 50.000 0.00 0.00 42.49 4.40
728 735 1.863662 ATTACGATCTCGCCGCGGAT 61.864 55.000 33.48 14.15 44.43 4.18
729 736 2.549198 ATTACGATCTCGCCGCGGA 61.549 57.895 33.48 8.40 44.43 5.54
762 769 1.002069 AGGCCCAGTCAAATGATCCA 58.998 50.000 0.00 0.00 0.00 3.41
768 775 5.747248 GCAATATCTCTAGGCCCAGTCAAAT 60.747 44.000 0.00 0.00 0.00 2.32
919 926 0.394216 TACTACGCCAACTCCGCCTA 60.394 55.000 0.00 0.00 0.00 3.93
995 1002 7.063544 GGAAAGTCAAGGCTATATATTAGCACG 59.936 40.741 14.68 0.00 42.06 5.34
1216 1226 2.782222 GGCGTAGACATCGGCCTCA 61.782 63.158 0.00 0.00 45.61 3.86
1782 1792 3.062466 CCTGCTCGGAGTCGGACA 61.062 66.667 11.27 0.53 36.95 4.02
1963 1979 1.486726 GGGGTGAGGTAGGACTTGATG 59.513 57.143 0.00 0.00 0.00 3.07
2052 2068 1.987855 TACTTCCTGGTGAGGGCGG 60.988 63.158 0.00 0.00 40.25 6.13
2257 2273 2.716217 CCTTCCTCCTTGGTCATGAAC 58.284 52.381 2.98 2.98 37.07 3.18
2299 2315 2.039480 CTCAACCATGATCCATCCCGAT 59.961 50.000 0.00 0.00 34.37 4.18
2431 2447 0.108329 TGTCGCCGGATTTCCTCTTC 60.108 55.000 5.05 0.00 0.00 2.87
2662 2678 3.561213 CAGCGAGCGCATGGAGTG 61.561 66.667 17.68 1.42 44.88 3.51
2663 2679 4.074526 ACAGCGAGCGCATGGAGT 62.075 61.111 17.68 0.00 44.88 3.85
2664 2680 3.561213 CACAGCGAGCGCATGGAG 61.561 66.667 17.68 0.00 44.88 3.86
2720 2736 0.967887 TCTTCCTCCTCGTCAGCAGG 60.968 60.000 0.00 0.00 0.00 4.85
2727 2743 1.096386 CGATCCGTCTTCCTCCTCGT 61.096 60.000 0.00 0.00 0.00 4.18
2808 2824 3.559242 GCATACTGAAGATTCACCTGCTC 59.441 47.826 10.02 0.00 32.44 4.26
2826 2842 0.101759 GTAGAACGTCCTGCCGCATA 59.898 55.000 0.00 0.00 0.00 3.14
2832 2848 1.000506 TGAACTGGTAGAACGTCCTGC 59.999 52.381 0.00 0.00 0.00 4.85
2836 2852 5.694910 TCAAATCTTGAACTGGTAGAACGTC 59.305 40.000 0.00 0.00 36.59 4.34
2837 2853 5.465724 GTCAAATCTTGAACTGGTAGAACGT 59.534 40.000 0.00 0.00 42.15 3.99
3025 3041 5.221342 ACAATTTGACAAACCGAAATGCCTA 60.221 36.000 1.94 0.00 0.00 3.93
3026 3042 4.057432 CAATTTGACAAACCGAAATGCCT 58.943 39.130 1.94 0.00 0.00 4.75
3027 3043 3.807071 ACAATTTGACAAACCGAAATGCC 59.193 39.130 1.94 0.00 0.00 4.40
3028 3044 5.196825 CAACAATTTGACAAACCGAAATGC 58.803 37.500 1.94 0.00 34.24 3.56
3029 3045 6.343226 ACAACAATTTGACAAACCGAAATG 57.657 33.333 1.94 1.43 36.48 2.32
3030 3046 7.262048 AGTACAACAATTTGACAAACCGAAAT 58.738 30.769 1.94 0.00 36.48 2.17
3034 3050 6.262601 AGAAGTACAACAATTTGACAAACCG 58.737 36.000 1.94 0.00 36.48 4.44
3070 3086 4.786507 TGATCAAGTTGCTGAACGATTTG 58.213 39.130 0.00 0.00 37.15 2.32
3221 3237 4.803613 TGTTGCACTACGTATTATGCTCTG 59.196 41.667 20.63 0.85 38.90 3.35
3334 3374 5.029807 TGAGGTATCGCAATTATGGTTGA 57.970 39.130 0.00 0.00 0.00 3.18
3383 3425 4.133013 ACACGTGTTTCTTAGACCTGTT 57.867 40.909 17.22 0.00 0.00 3.16
3621 3670 9.959721 AGGTTTGTGTAGATTTGTGTAGATTAT 57.040 29.630 0.00 0.00 0.00 1.28
3623 3672 9.787435 TTAGGTTTGTGTAGATTTGTGTAGATT 57.213 29.630 0.00 0.00 0.00 2.40
3624 3673 9.959721 ATTAGGTTTGTGTAGATTTGTGTAGAT 57.040 29.630 0.00 0.00 0.00 1.98
3625 3674 9.214957 CATTAGGTTTGTGTAGATTTGTGTAGA 57.785 33.333 0.00 0.00 0.00 2.59
3626 3675 8.999431 ACATTAGGTTTGTGTAGATTTGTGTAG 58.001 33.333 0.00 0.00 0.00 2.74
3627 3676 8.911918 ACATTAGGTTTGTGTAGATTTGTGTA 57.088 30.769 0.00 0.00 0.00 2.90
3628 3677 7.817418 ACATTAGGTTTGTGTAGATTTGTGT 57.183 32.000 0.00 0.00 0.00 3.72
3629 3678 8.349245 TGAACATTAGGTTTGTGTAGATTTGTG 58.651 33.333 0.00 0.00 40.63 3.33
3630 3679 8.458573 TGAACATTAGGTTTGTGTAGATTTGT 57.541 30.769 0.00 0.00 40.63 2.83
3631 3680 8.023128 CCTGAACATTAGGTTTGTGTAGATTTG 58.977 37.037 0.00 0.00 40.63 2.32
3632 3681 7.724061 ACCTGAACATTAGGTTTGTGTAGATTT 59.276 33.333 0.00 0.00 46.13 2.17
3671 3720 4.882842 TCAGCTACCAACACATTGACTA 57.117 40.909 0.00 0.00 38.15 2.59
3950 4008 6.276847 TGTATTTGTGTTTCCCATTGTGTTC 58.723 36.000 0.00 0.00 0.00 3.18
4039 4098 9.301153 GAATAGGTATTTGCAGTTTTTACCATG 57.699 33.333 12.29 0.00 35.76 3.66


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

AutoCloner maintained by Alex Coulton.