Multiple sequence alignment - TraesCS7D01G456200

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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 TraesCS7D01G456200 chr7D 100.000 2639 0 0 1 2639 574926493 574923855 0.000000e+00 4874.0
1 TraesCS7D01G456200 chr7D 84.615 1339 134 33 929 2253 574874683 574875963 0.000000e+00 1266.0
2 TraesCS7D01G456200 chr7D 84.841 1293 101 33 971 2253 575074493 575073286 0.000000e+00 1214.0
3 TraesCS7D01G456200 chr7D 86.532 1136 91 23 971 2102 575149723 575148646 0.000000e+00 1194.0
4 TraesCS7D01G456200 chr7D 85.011 894 97 20 971 1852 575218185 575217317 0.000000e+00 874.0
5 TraesCS7D01G456200 chr7D 88.716 257 20 5 1923 2178 575217311 575217063 3.300000e-79 305.0
6 TraesCS7D01G456200 chr7D 90.698 86 5 1 39 121 575151019 575150934 7.720000e-21 111.0
7 TraesCS7D01G456200 chr7D 86.842 76 8 2 510 584 574925910 574925984 1.680000e-12 84.2
8 TraesCS7D01G456200 chr7A 86.178 2127 183 47 1 2086 664602037 664604093 0.000000e+00 2196.0
9 TraesCS7D01G456200 chr7A 88.223 968 68 19 972 1934 664699189 664700115 0.000000e+00 1114.0
10 TraesCS7D01G456200 chr7A 84.609 1150 87 26 1090 2225 664781187 664780114 0.000000e+00 1061.0
11 TraesCS7D01G456200 chr7A 82.827 757 77 26 1912 2639 664700127 664700859 1.720000e-176 628.0
12 TraesCS7D01G456200 chr7B 86.765 1700 150 35 966 2639 635300851 635302501 0.000000e+00 1823.0
13 TraesCS7D01G456200 chr7B 85.703 1231 108 43 971 2178 636433345 636432160 0.000000e+00 1236.0
14 TraesCS7D01G456200 chr7B 88.365 1040 91 15 1188 2225 635749106 635748095 0.000000e+00 1223.0
15 TraesCS7D01G456200 chr7B 89.088 614 49 9 1032 1639 635064933 635065534 0.000000e+00 747.0
16 TraesCS7D01G456200 chr7B 85.872 453 32 14 1806 2253 635935531 635935106 1.110000e-123 453.0
17 TraesCS7D01G456200 chr7B 91.358 81 7 0 1730 1810 635940556 635940476 7.720000e-21 111.0
18 TraesCS7D01G456200 chr7B 94.737 38 2 0 858 895 84394428 84394391 2.840000e-05 60.2
19 TraesCS7D01G456200 chr4B 77.778 162 28 6 816 975 78607617 78607462 2.800000e-15 93.5
20 TraesCS7D01G456200 chr4B 78.986 138 24 4 838 973 78607900 78607766 3.620000e-14 89.8
21 TraesCS7D01G456200 chr1D 77.108 166 32 4 812 976 97132466 97132626 1.010000e-14 91.6
22 TraesCS7D01G456200 chr5B 78.947 114 20 3 861 972 243851121 243851010 1.010000e-09 75.0
23 TraesCS7D01G456200 chr6D 82.192 73 10 2 816 888 420734882 420734813 2.840000e-05 60.2


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 TraesCS7D01G456200 chr7D 574923855 574926493 2638 True 4874.0 4874 100.0000 1 2639 1 chr7D.!!$R1 2638
1 TraesCS7D01G456200 chr7D 574874683 574875963 1280 False 1266.0 1266 84.6150 929 2253 1 chr7D.!!$F1 1324
2 TraesCS7D01G456200 chr7D 575073286 575074493 1207 True 1214.0 1214 84.8410 971 2253 1 chr7D.!!$R2 1282
3 TraesCS7D01G456200 chr7D 575148646 575151019 2373 True 652.5 1194 88.6150 39 2102 2 chr7D.!!$R3 2063
4 TraesCS7D01G456200 chr7D 575217063 575218185 1122 True 589.5 874 86.8635 971 2178 2 chr7D.!!$R4 1207
5 TraesCS7D01G456200 chr7A 664602037 664604093 2056 False 2196.0 2196 86.1780 1 2086 1 chr7A.!!$F1 2085
6 TraesCS7D01G456200 chr7A 664780114 664781187 1073 True 1061.0 1061 84.6090 1090 2225 1 chr7A.!!$R1 1135
7 TraesCS7D01G456200 chr7A 664699189 664700859 1670 False 871.0 1114 85.5250 972 2639 2 chr7A.!!$F2 1667
8 TraesCS7D01G456200 chr7B 635300851 635302501 1650 False 1823.0 1823 86.7650 966 2639 1 chr7B.!!$F2 1673
9 TraesCS7D01G456200 chr7B 636432160 636433345 1185 True 1236.0 1236 85.7030 971 2178 1 chr7B.!!$R5 1207
10 TraesCS7D01G456200 chr7B 635748095 635749106 1011 True 1223.0 1223 88.3650 1188 2225 1 chr7B.!!$R2 1037
11 TraesCS7D01G456200 chr7B 635064933 635065534 601 False 747.0 747 89.0880 1032 1639 1 chr7B.!!$F1 607

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
337 347 0.391927 TGCTTGATAAACCCGGACGG 60.392 55.0 0.73 3.25 37.81 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 2464 0.527817 CATGGTAGCCGAACGAGGAC 60.528 60.0 0.0 0.0 0.0 3.85 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
70 71 1.033746 GCCTGGCTATGCACACATGT 61.034 55.000 12.43 0.00 37.04 3.21
101 105 1.129917 CTCCATCCCAGCTCTCACAT 58.870 55.000 0.00 0.00 0.00 3.21
140 144 1.270412 TGCTTCCTCCGTTCGCTTTTA 60.270 47.619 0.00 0.00 0.00 1.52
141 145 2.007608 GCTTCCTCCGTTCGCTTTTAT 58.992 47.619 0.00 0.00 0.00 1.40
142 146 2.418976 GCTTCCTCCGTTCGCTTTTATT 59.581 45.455 0.00 0.00 0.00 1.40
143 147 3.619929 GCTTCCTCCGTTCGCTTTTATTA 59.380 43.478 0.00 0.00 0.00 0.98
144 148 4.260253 GCTTCCTCCGTTCGCTTTTATTAG 60.260 45.833 0.00 0.00 0.00 1.73
145 149 3.788937 TCCTCCGTTCGCTTTTATTAGG 58.211 45.455 0.00 0.00 0.00 2.69
146 150 2.287103 CCTCCGTTCGCTTTTATTAGGC 59.713 50.000 0.00 0.00 0.00 3.93
147 151 2.282407 TCCGTTCGCTTTTATTAGGCC 58.718 47.619 0.00 0.00 0.00 5.19
148 152 1.332686 CCGTTCGCTTTTATTAGGCCC 59.667 52.381 0.00 0.00 0.00 5.80
149 153 1.332686 CGTTCGCTTTTATTAGGCCCC 59.667 52.381 0.00 0.00 0.00 5.80
150 154 1.679680 GTTCGCTTTTATTAGGCCCCC 59.320 52.381 0.00 0.00 0.00 5.40
151 155 1.218844 TCGCTTTTATTAGGCCCCCT 58.781 50.000 0.00 0.00 37.71 4.79
152 156 1.142262 TCGCTTTTATTAGGCCCCCTC 59.858 52.381 0.00 0.00 34.61 4.30
153 157 1.133915 CGCTTTTATTAGGCCCCCTCA 60.134 52.381 0.00 0.00 34.61 3.86
154 158 2.307768 GCTTTTATTAGGCCCCCTCAC 58.692 52.381 0.00 0.00 34.61 3.51
155 159 2.357777 GCTTTTATTAGGCCCCCTCACA 60.358 50.000 0.00 0.00 34.61 3.58
156 160 3.691311 GCTTTTATTAGGCCCCCTCACAT 60.691 47.826 0.00 0.00 34.61 3.21
157 161 4.546674 CTTTTATTAGGCCCCCTCACATT 58.453 43.478 0.00 0.00 34.61 2.71
158 162 4.618378 TTTATTAGGCCCCCTCACATTT 57.382 40.909 0.00 0.00 34.61 2.32
159 163 5.735733 TTTATTAGGCCCCCTCACATTTA 57.264 39.130 0.00 0.00 34.61 1.40
160 164 5.735733 TTATTAGGCCCCCTCACATTTAA 57.264 39.130 0.00 0.00 34.61 1.52
161 165 4.618378 ATTAGGCCCCCTCACATTTAAA 57.382 40.909 0.00 0.00 34.61 1.52
162 166 4.405756 TTAGGCCCCCTCACATTTAAAA 57.594 40.909 0.00 0.00 34.61 1.52
163 167 2.536066 AGGCCCCCTCACATTTAAAAC 58.464 47.619 0.00 0.00 0.00 2.43
164 168 2.111792 AGGCCCCCTCACATTTAAAACT 59.888 45.455 0.00 0.00 0.00 2.66
165 169 2.233676 GGCCCCCTCACATTTAAAACTG 59.766 50.000 0.00 0.00 0.00 3.16
166 170 3.161866 GCCCCCTCACATTTAAAACTGA 58.838 45.455 0.00 0.00 0.00 3.41
167 171 3.576550 GCCCCCTCACATTTAAAACTGAA 59.423 43.478 0.00 0.00 0.00 3.02
168 172 4.321974 GCCCCCTCACATTTAAAACTGAAG 60.322 45.833 0.00 0.00 0.00 3.02
169 173 4.832823 CCCCCTCACATTTAAAACTGAAGT 59.167 41.667 0.00 0.00 0.00 3.01
170 174 5.304357 CCCCCTCACATTTAAAACTGAAGTT 59.696 40.000 0.00 0.00 40.50 2.66
220 229 7.529880 ACGTATGTAGTTAAAATAGTGCCAC 57.470 36.000 0.00 0.00 0.00 5.01
224 233 7.611213 ATGTAGTTAAAATAGTGCCACTGAC 57.389 36.000 7.83 0.00 0.00 3.51
225 234 6.526526 TGTAGTTAAAATAGTGCCACTGACA 58.473 36.000 7.83 0.00 0.00 3.58
226 235 6.993308 TGTAGTTAAAATAGTGCCACTGACAA 59.007 34.615 7.83 0.00 0.00 3.18
229 238 7.593825 AGTTAAAATAGTGCCACTGACAATTC 58.406 34.615 7.83 0.00 0.00 2.17
230 239 7.230510 AGTTAAAATAGTGCCACTGACAATTCA 59.769 33.333 7.83 0.00 0.00 2.57
240 249 4.494690 CCACTGACAATTCATTTCGATCCG 60.495 45.833 0.00 0.00 0.00 4.18
241 250 3.063997 ACTGACAATTCATTTCGATCCGC 59.936 43.478 0.00 0.00 0.00 5.54
243 252 3.627123 TGACAATTCATTTCGATCCGCAT 59.373 39.130 0.00 0.00 0.00 4.73
246 255 4.143835 CAATTCATTTCGATCCGCATACG 58.856 43.478 0.00 0.00 39.67 3.06
321 331 2.435693 GGCCAGATACGAGGGTGCT 61.436 63.158 0.00 0.00 0.00 4.40
329 339 4.508124 CAGATACGAGGGTGCTTGATAAAC 59.492 45.833 0.00 0.00 0.00 2.01
337 347 0.391927 TGCTTGATAAACCCGGACGG 60.392 55.000 0.73 3.25 37.81 4.79
340 350 0.538118 TTGATAAACCCGGACGGAGG 59.462 55.000 13.13 0.00 37.50 4.30
349 359 1.079127 CGGACGGAGGAAGTGCATT 60.079 57.895 0.00 0.00 0.00 3.56
422 936 7.845066 ACAGCTTAGTTTATTTAGTAGCACC 57.155 36.000 0.00 0.00 0.00 5.01
479 998 3.576550 GGGTGCCAAGTATTCTCCAAAAA 59.423 43.478 0.00 0.00 0.00 1.94
499 1181 9.981114 CCAAAAATATGAAAATATACCACTCCC 57.019 33.333 0.00 0.00 0.00 4.30
519 1201 5.584913 TCCCTCTCCTCTGATCCATATTAC 58.415 45.833 0.00 0.00 0.00 1.89
520 1202 5.317262 TCCCTCTCCTCTGATCCATATTACT 59.683 44.000 0.00 0.00 0.00 2.24
528 1210 5.758924 TCTGATCCATATTACTTGACGACG 58.241 41.667 0.00 0.00 0.00 5.12
544 1226 5.108517 TGACGACGGTTTAGTACAACTTTT 58.891 37.500 0.00 0.00 0.00 2.27
570 1252 4.573201 ACAAAAGTTGTACTAAAGCTGCGA 59.427 37.500 0.00 0.00 43.27 5.10
582 1264 3.819564 AAGCTGCGACAGTAATATGGA 57.180 42.857 8.32 0.00 33.43 3.41
612 1321 3.396260 ACTAGAACTGCGGCAAGTAAA 57.604 42.857 3.44 0.00 0.00 2.01
650 1359 4.869861 GTGCACCTGTTTGAAAAATGAAGT 59.130 37.500 5.22 0.00 0.00 3.01
772 1527 4.904251 TGGGTCCAAATTTTGAAATGAGGA 59.096 37.500 10.72 6.21 32.83 3.71
783 1538 2.552315 TGAAATGAGGAAAGCAACGTCC 59.448 45.455 0.00 0.00 0.00 4.79
790 1545 1.608283 GGAAAGCAACGTCCTGTAGCT 60.608 52.381 0.00 0.00 37.08 3.32
795 1550 1.336887 GCAACGTCCTGTAGCTGAAGA 60.337 52.381 0.00 0.00 0.00 2.87
820 1575 6.299922 AGGCTGGCTAAATAAATTCTACTCC 58.700 40.000 0.13 0.00 0.00 3.85
823 1578 6.773200 GCTGGCTAAATAAATTCTACTCCCTT 59.227 38.462 0.00 0.00 0.00 3.95
836 1591 3.679824 ACTCCCTTGGTTTCGAACTAG 57.320 47.619 0.00 0.00 0.00 2.57
837 1592 2.970640 ACTCCCTTGGTTTCGAACTAGT 59.029 45.455 0.00 0.00 0.00 2.57
838 1593 4.154942 ACTCCCTTGGTTTCGAACTAGTA 58.845 43.478 0.00 0.00 0.00 1.82
883 1638 6.496338 TGAATCAGATGTATATAGACGCGT 57.504 37.500 13.85 13.85 0.00 6.01
888 1643 9.856488 AATCAGATGTATATAGACGCGTTTTAT 57.144 29.630 15.53 16.86 0.00 1.40
892 1647 9.125906 AGATGTATATAGACGCGTTTTATTGTC 57.874 33.333 15.53 5.08 0.00 3.18
900 1655 7.360575 AGACGCGTTTTATTGTCTTTAATCT 57.639 32.000 15.53 0.00 38.48 2.40
991 1747 3.967332 ACATTCCATTCCAAGCAAAGG 57.033 42.857 0.00 0.00 0.00 3.11
1022 1783 5.913137 ATGCCAACCGAGAAAAATAATGA 57.087 34.783 0.00 0.00 0.00 2.57
1030 1791 5.648092 ACCGAGAAAAATAATGACAAGAGGG 59.352 40.000 0.00 0.00 0.00 4.30
1037 1798 0.773644 AATGACAAGAGGGCCTGTGT 59.226 50.000 12.95 15.70 0.00 3.72
1639 2430 1.411977 ACTCCGCGCTCTACTACTAGA 59.588 52.381 5.56 0.00 0.00 2.43
1640 2431 2.063266 CTCCGCGCTCTACTACTAGAG 58.937 57.143 5.56 2.87 46.42 2.43
1641 2432 1.149987 CCGCGCTCTACTACTAGAGG 58.850 60.000 5.56 0.00 44.55 3.69
1646 2437 2.809696 CGCTCTACTACTAGAGGCCTTC 59.190 54.545 6.77 0.00 44.55 3.46
1647 2438 3.151554 GCTCTACTACTAGAGGCCTTCC 58.848 54.545 6.77 0.00 44.55 3.46
1648 2439 3.435313 GCTCTACTACTAGAGGCCTTCCA 60.435 52.174 6.77 0.00 44.55 3.53
1670 2464 2.678934 TTCTCCCCCGTCTCACCG 60.679 66.667 0.00 0.00 0.00 4.94
1765 2581 3.927163 AAAATGCCAGCTGCTGCGC 62.927 57.895 26.04 26.04 45.42 6.09
1822 2650 1.678970 GAGGTCACATGGGGTTGGC 60.679 63.158 0.00 0.00 0.00 4.52
1871 2699 2.775911 TTCTACTGCAGCTCAGCAAT 57.224 45.000 15.27 0.00 46.76 3.56
1916 2744 5.891551 TGGGAATTAGGGCTGTAATTTCTTC 59.108 40.000 9.57 0.00 33.60 2.87
1919 2747 7.124298 GGGAATTAGGGCTGTAATTTCTTCTTT 59.876 37.037 9.57 0.00 33.60 2.52
1921 2749 9.574458 GAATTAGGGCTGTAATTTCTTCTTTTC 57.426 33.333 6.78 0.00 33.60 2.29
1999 2879 3.242867 TGGAGCTTCTTCTTCCTCTTCA 58.757 45.455 0.00 0.00 0.00 3.02
2018 2898 4.860802 TCATTGGCTAGGGATTTTGAGA 57.139 40.909 0.00 0.00 0.00 3.27
2019 2899 4.526970 TCATTGGCTAGGGATTTTGAGAC 58.473 43.478 0.00 0.00 0.00 3.36
2116 3008 4.631773 CCAGGATCTGGTGCTGTG 57.368 61.111 8.67 0.00 45.82 3.66
2117 3009 1.681666 CCAGGATCTGGTGCTGTGT 59.318 57.895 8.67 0.00 45.82 3.72
2122 3014 2.234908 AGGATCTGGTGCTGTGTAGAAC 59.765 50.000 0.00 0.00 0.00 3.01
2199 3096 1.933181 GCGCACAATGATGCACTACTA 59.067 47.619 0.30 0.00 46.47 1.82
2200 3097 2.545526 GCGCACAATGATGCACTACTAT 59.454 45.455 0.30 0.00 46.47 2.12
2201 3098 3.605461 GCGCACAATGATGCACTACTATG 60.605 47.826 0.30 0.00 46.47 2.23
2202 3099 3.605461 CGCACAATGATGCACTACTATGC 60.605 47.826 0.00 0.00 46.47 3.14
2238 3135 5.314923 TGGTAGTACCGCTACTAAACAAG 57.685 43.478 14.67 0.00 46.99 3.16
2240 3137 5.243730 TGGTAGTACCGCTACTAAACAAGTT 59.756 40.000 14.67 0.00 46.99 2.66
2245 3142 2.423577 CGCTACTAAACAAGTTGGGCT 58.576 47.619 7.96 0.00 39.80 5.19
2257 3154 1.547372 AGTTGGGCTTGTGATGCATTC 59.453 47.619 0.00 0.00 0.00 2.67
2267 3164 3.972133 TGTGATGCATTCCCTTCAGAAT 58.028 40.909 0.00 0.00 36.92 2.40
2275 3173 0.700564 TCCCTTCAGAATTGCTGCCT 59.299 50.000 0.00 0.00 44.52 4.75
2284 3182 4.525487 TCAGAATTGCTGCCTGAAAATCTT 59.475 37.500 4.21 0.00 44.52 2.40
2285 3183 5.711506 TCAGAATTGCTGCCTGAAAATCTTA 59.288 36.000 4.21 0.00 44.52 2.10
2286 3184 6.379133 TCAGAATTGCTGCCTGAAAATCTTAT 59.621 34.615 4.21 0.00 44.52 1.73
2287 3185 7.557358 TCAGAATTGCTGCCTGAAAATCTTATA 59.443 33.333 4.21 0.00 44.52 0.98
2288 3186 7.861372 CAGAATTGCTGCCTGAAAATCTTATAG 59.139 37.037 0.00 0.00 37.90 1.31
2290 3188 6.683974 TTGCTGCCTGAAAATCTTATAGTC 57.316 37.500 0.00 0.00 0.00 2.59
2291 3189 5.744171 TGCTGCCTGAAAATCTTATAGTCA 58.256 37.500 0.00 0.00 0.00 3.41
2298 3203 7.466590 GCCTGAAAATCTTATAGTCAGTTCAGC 60.467 40.741 0.00 0.00 39.45 4.26
2326 3231 3.681897 GCTGACTGCATATACAGCCATAC 59.318 47.826 17.56 0.00 46.46 2.39
2330 3235 4.635223 ACTGCATATACAGCCATACAGTG 58.365 43.478 2.65 0.00 41.60 3.66
2331 3236 4.101585 ACTGCATATACAGCCATACAGTGT 59.898 41.667 0.00 0.00 41.60 3.55
2332 3237 4.379652 TGCATATACAGCCATACAGTGTG 58.620 43.478 5.88 0.00 0.00 3.82
2333 3238 4.100808 TGCATATACAGCCATACAGTGTGA 59.899 41.667 5.88 0.00 0.00 3.58
2334 3239 4.449068 GCATATACAGCCATACAGTGTGAC 59.551 45.833 5.88 0.00 0.00 3.67
2335 3240 5.740224 GCATATACAGCCATACAGTGTGACT 60.740 44.000 5.88 0.00 0.00 3.41
2366 3278 7.895759 TGGATTTTCCAATACCTTGAAGAAAG 58.104 34.615 0.00 0.00 45.00 2.62
2371 3288 3.193479 CCAATACCTTGAAGAAAGTGGCC 59.807 47.826 0.00 0.00 34.04 5.36
2376 3293 2.555757 CCTTGAAGAAAGTGGCCTGAAG 59.444 50.000 3.32 0.00 33.66 3.02
2377 3294 3.217626 CTTGAAGAAAGTGGCCTGAAGT 58.782 45.455 3.32 0.00 0.00 3.01
2381 3298 3.064900 AGAAAGTGGCCTGAAGTGATC 57.935 47.619 3.32 0.00 0.00 2.92
2387 3304 0.035630 GGCCTGAAGTGATCACTGCT 60.036 55.000 29.96 16.61 41.58 4.24
2389 3306 1.467734 GCCTGAAGTGATCACTGCTTG 59.532 52.381 29.96 22.05 41.58 4.01
2390 3307 2.873245 GCCTGAAGTGATCACTGCTTGA 60.873 50.000 29.96 12.84 41.58 3.02
2391 3308 3.001414 CCTGAAGTGATCACTGCTTGAG 58.999 50.000 29.96 20.32 41.58 3.02
2392 3309 3.556633 CCTGAAGTGATCACTGCTTGAGT 60.557 47.826 29.96 13.76 41.58 3.41
2394 3311 3.323115 TGAAGTGATCACTGCTTGAGTCT 59.677 43.478 29.96 12.35 41.58 3.24
2395 3312 4.202295 TGAAGTGATCACTGCTTGAGTCTT 60.202 41.667 29.96 11.65 41.58 3.01
2396 3313 3.924144 AGTGATCACTGCTTGAGTCTTC 58.076 45.455 27.37 0.00 40.75 2.87
2397 3314 2.665537 GTGATCACTGCTTGAGTCTTCG 59.334 50.000 18.83 0.00 37.77 3.79
2398 3315 2.558359 TGATCACTGCTTGAGTCTTCGA 59.442 45.455 0.00 0.00 37.77 3.71
2399 3316 3.194329 TGATCACTGCTTGAGTCTTCGAT 59.806 43.478 0.00 0.00 37.77 3.59
2407 3324 4.177026 GCTTGAGTCTTCGATGTGTATGT 58.823 43.478 0.00 0.00 0.00 2.29
2408 3325 4.266502 GCTTGAGTCTTCGATGTGTATGTC 59.733 45.833 0.00 0.00 0.00 3.06
2432 3354 1.551883 GCCAAATGCAGTGAAAGGGAT 59.448 47.619 0.00 0.00 40.77 3.85
2433 3355 2.675889 GCCAAATGCAGTGAAAGGGATG 60.676 50.000 0.00 0.00 40.77 3.51
2434 3356 2.827322 CCAAATGCAGTGAAAGGGATGA 59.173 45.455 0.00 0.00 0.00 2.92
2435 3357 3.449737 CCAAATGCAGTGAAAGGGATGAT 59.550 43.478 0.00 0.00 0.00 2.45
2440 3362 2.941720 GCAGTGAAAGGGATGATGAGAC 59.058 50.000 0.00 0.00 0.00 3.36
2452 3374 5.352284 GGATGATGAGACGACAATGTAGTT 58.648 41.667 0.00 0.00 0.00 2.24
2463 3385 4.437390 CGACAATGTAGTTCAGGAATTGGC 60.437 45.833 0.00 0.00 33.72 4.52
2480 3402 0.721718 GGCGAAATCGGACAGAACAG 59.278 55.000 4.84 0.00 40.23 3.16
2532 3454 3.979101 TCTCCTTGCATCACACATACA 57.021 42.857 0.00 0.00 0.00 2.29
2533 3455 3.865446 TCTCCTTGCATCACACATACAG 58.135 45.455 0.00 0.00 0.00 2.74
2534 3456 3.261643 TCTCCTTGCATCACACATACAGT 59.738 43.478 0.00 0.00 0.00 3.55
2535 3457 4.466015 TCTCCTTGCATCACACATACAGTA 59.534 41.667 0.00 0.00 0.00 2.74
2551 3473 7.379797 CACATACAGTATGACTTATGAGAACCG 59.620 40.741 24.81 0.00 39.69 4.44
2569 3491 2.196749 CCGGTCATCACATTCTTCGAG 58.803 52.381 0.00 0.00 0.00 4.04
2594 3518 4.853924 AATGGCATCACGAGAAAAGTTT 57.146 36.364 0.00 0.00 0.00 2.66
2598 3522 5.000591 TGGCATCACGAGAAAAGTTTGATA 58.999 37.500 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 4.480115 CTGGGATGGAGTGTGTACCTATA 58.520 47.826 0.00 0.00 0.00 1.31
101 105 2.546368 GCACGTGTTCATTCAGTTACCA 59.454 45.455 18.38 0.00 0.00 3.25
140 144 4.618378 TTTAAATGTGAGGGGGCCTAAT 57.382 40.909 0.84 0.00 31.76 1.73
141 145 4.090819 GTTTTAAATGTGAGGGGGCCTAA 58.909 43.478 0.84 0.00 31.76 2.69
142 146 3.335484 AGTTTTAAATGTGAGGGGGCCTA 59.665 43.478 0.84 0.00 31.76 3.93
143 147 2.111792 AGTTTTAAATGTGAGGGGGCCT 59.888 45.455 0.84 0.00 36.03 5.19
144 148 2.233676 CAGTTTTAAATGTGAGGGGGCC 59.766 50.000 0.00 0.00 0.00 5.80
145 149 3.161866 TCAGTTTTAAATGTGAGGGGGC 58.838 45.455 0.00 0.00 0.00 5.80
146 150 4.832823 ACTTCAGTTTTAAATGTGAGGGGG 59.167 41.667 11.68 3.95 0.00 5.40
147 151 6.405278 AACTTCAGTTTTAAATGTGAGGGG 57.595 37.500 11.68 5.57 33.93 4.79
148 152 8.846211 TCTAAACTTCAGTTTTAAATGTGAGGG 58.154 33.333 10.15 7.22 45.07 4.30
149 153 9.665264 GTCTAAACTTCAGTTTTAAATGTGAGG 57.335 33.333 10.15 7.50 45.07 3.86
161 165 9.120538 ACACAAATGTATGTCTAAACTTCAGTT 57.879 29.630 0.00 0.00 37.26 3.16
162 166 8.677148 ACACAAATGTATGTCTAAACTTCAGT 57.323 30.769 0.00 0.00 37.26 3.41
194 198 8.534778 GTGGCACTATTTTAACTACATACGTAC 58.465 37.037 11.13 0.00 0.00 3.67
197 201 7.490079 TCAGTGGCACTATTTTAACTACATACG 59.510 37.037 21.59 1.44 0.00 3.06
220 229 3.063861 TGCGGATCGAAATGAATTGTCAG 59.936 43.478 0.00 0.00 37.14 3.51
224 233 4.143835 CGTATGCGGATCGAAATGAATTG 58.856 43.478 0.00 0.00 0.00 2.32
225 234 4.389664 CGTATGCGGATCGAAATGAATT 57.610 40.909 0.00 0.00 0.00 2.17
279 289 7.484975 CCCTGACCGCATATTTAATTTTGTAA 58.515 34.615 0.00 0.00 0.00 2.41
288 298 0.840617 TGGCCCTGACCGCATATTTA 59.159 50.000 0.00 0.00 0.00 1.40
295 305 2.109181 GTATCTGGCCCTGACCGC 59.891 66.667 0.00 0.00 0.00 5.68
299 309 1.457643 CCCTCGTATCTGGCCCTGA 60.458 63.158 0.00 0.00 0.00 3.86
321 331 0.538118 CCTCCGTCCGGGTTTATCAA 59.462 55.000 0.00 0.00 37.00 2.57
329 339 4.452733 GCACTTCCTCCGTCCGGG 62.453 72.222 0.00 0.00 35.59 5.73
337 347 1.888512 TGCCTCAAAATGCACTTCCTC 59.111 47.619 0.00 0.00 31.31 3.71
422 936 8.550376 AGCTTGCAATTTAGTAACAACAAAATG 58.450 29.630 0.00 0.00 0.00 2.32
479 998 7.964293 AGGAGAGGGAGTGGTATATTTTCATAT 59.036 37.037 0.00 0.00 0.00 1.78
493 1175 1.063341 TGGATCAGAGGAGAGGGAGTG 60.063 57.143 0.00 0.00 0.00 3.51
495 1177 2.700353 ATGGATCAGAGGAGAGGGAG 57.300 55.000 0.00 0.00 0.00 4.30
499 1181 7.574779 CGTCAAGTAATATGGATCAGAGGAGAG 60.575 44.444 0.00 0.00 0.00 3.20
500 1182 6.207614 CGTCAAGTAATATGGATCAGAGGAGA 59.792 42.308 0.00 0.00 0.00 3.71
501 1183 6.207614 TCGTCAAGTAATATGGATCAGAGGAG 59.792 42.308 0.00 0.00 0.00 3.69
502 1184 6.016192 GTCGTCAAGTAATATGGATCAGAGGA 60.016 42.308 0.00 0.00 0.00 3.71
503 1185 6.153067 GTCGTCAAGTAATATGGATCAGAGG 58.847 44.000 0.00 0.00 0.00 3.69
519 1201 4.293415 AGTTGTACTAAACCGTCGTCAAG 58.707 43.478 0.00 0.00 0.00 3.02
520 1202 4.305989 AGTTGTACTAAACCGTCGTCAA 57.694 40.909 0.00 0.00 0.00 3.18
546 1228 5.754406 TCGCAGCTTTAGTACAACTTTTGTA 59.246 36.000 0.00 0.00 43.27 2.41
553 1235 3.057734 ACTGTCGCAGCTTTAGTACAAC 58.942 45.455 6.74 0.00 34.37 3.32
565 1247 7.715265 AACTTTATCCATATTACTGTCGCAG 57.285 36.000 5.47 5.47 37.52 5.18
582 1264 6.812998 TGCCGCAGTTCTAGTATAACTTTAT 58.187 36.000 0.00 0.00 34.99 1.40
596 1305 2.227865 TCCATTTTACTTGCCGCAGTTC 59.772 45.455 0.00 0.00 0.00 3.01
702 1450 4.998979 GCAACAGCGAAACTATAATTGC 57.001 40.909 0.00 0.00 34.98 3.56
717 1465 5.597813 AAATCTAGACAACTTCGCAACAG 57.402 39.130 0.00 0.00 0.00 3.16
730 1478 7.556275 TGGACCCATTTCATACAAAATCTAGAC 59.444 37.037 0.00 0.00 0.00 2.59
783 1538 2.011046 GCCAGCCTTCTTCAGCTACAG 61.011 57.143 0.00 0.00 37.18 2.74
790 1545 6.891908 AGAATTTATTTAGCCAGCCTTCTTCA 59.108 34.615 0.00 0.00 0.00 3.02
795 1550 6.773200 GGAGTAGAATTTATTTAGCCAGCCTT 59.227 38.462 0.00 0.00 0.00 4.35
859 1614 6.909909 ACGCGTCTATATACATCTGATTCAA 58.090 36.000 5.58 0.00 0.00 2.69
940 1695 7.333423 CCTCTGTTCCGATTACAAGACATTTTA 59.667 37.037 0.00 0.00 0.00 1.52
991 1747 4.695217 TCTCGGTTGGCATTTACAAATC 57.305 40.909 0.00 0.00 0.00 2.17
1022 1783 0.034896 CGTTACACAGGCCCTCTTGT 59.965 55.000 0.00 0.00 0.00 3.16
1058 1822 3.995048 GTGGCTCCTTCTTATATAACGGC 59.005 47.826 0.00 0.00 0.00 5.68
1178 1966 1.453379 CCGGAGACCTCGAGGCTTA 60.453 63.158 31.56 0.00 39.32 3.09
1647 2438 3.787001 GACGGGGGAGAAGGGCTG 61.787 72.222 0.00 0.00 0.00 4.85
1648 2439 3.986116 GAGACGGGGGAGAAGGGCT 62.986 68.421 0.00 0.00 0.00 5.19
1670 2464 0.527817 CATGGTAGCCGAACGAGGAC 60.528 60.000 0.00 0.00 0.00 3.85
1684 2478 2.591753 CATCACGCCCTCCATGGT 59.408 61.111 12.58 0.00 0.00 3.55
1765 2581 1.760086 AGGGGCAGATCGGTCAGAG 60.760 63.158 0.00 0.00 0.00 3.35
1916 2744 8.672815 AGAACACTCAGAAAAAGAAGAGAAAAG 58.327 33.333 0.00 0.00 32.59 2.27
1919 2747 8.043710 AGAAGAACACTCAGAAAAAGAAGAGAA 58.956 33.333 0.00 0.00 32.59 2.87
1921 2749 7.784633 AGAAGAACACTCAGAAAAAGAAGAG 57.215 36.000 0.00 0.00 0.00 2.85
1999 2879 3.529319 AGGTCTCAAAATCCCTAGCCAAT 59.471 43.478 0.00 0.00 0.00 3.16
2018 2898 5.590259 GGCTTACATGATGTGTTATCAAGGT 59.410 40.000 8.61 0.00 42.29 3.50
2019 2899 5.277490 CGGCTTACATGATGTGTTATCAAGG 60.277 44.000 8.61 0.00 42.29 3.61
2057 2944 7.486647 AGCAAAATCATCCATTTCACTCATAC 58.513 34.615 0.00 0.00 33.16 2.39
2059 2946 6.540438 AGCAAAATCATCCATTTCACTCAT 57.460 33.333 0.00 0.00 33.16 2.90
2112 2999 1.800586 AGTGCATTGCGTTCTACACAG 59.199 47.619 3.84 0.00 0.00 3.66
2116 3008 1.804151 TGGAAGTGCATTGCGTTCTAC 59.196 47.619 18.00 5.90 30.42 2.59
2117 3009 2.177394 TGGAAGTGCATTGCGTTCTA 57.823 45.000 18.00 12.30 30.42 2.10
2122 3014 0.742505 ATCCATGGAAGTGCATTGCG 59.257 50.000 20.67 0.00 30.42 4.85
2225 3122 2.423577 AGCCCAACTTGTTTAGTAGCG 58.576 47.619 0.00 0.00 35.54 4.26
2236 3133 1.636148 ATGCATCACAAGCCCAACTT 58.364 45.000 0.00 0.00 40.05 2.66
2238 3135 1.404583 GGAATGCATCACAAGCCCAAC 60.405 52.381 0.00 0.00 0.00 3.77
2240 3137 0.971959 GGGAATGCATCACAAGCCCA 60.972 55.000 0.00 0.00 42.47 5.36
2245 3142 3.438216 TCTGAAGGGAATGCATCACAA 57.562 42.857 0.00 0.00 32.04 3.33
2250 3147 3.132289 CAGCAATTCTGAAGGGAATGCAT 59.868 43.478 0.00 0.00 45.72 3.96
2251 3148 2.494471 CAGCAATTCTGAAGGGAATGCA 59.506 45.455 13.48 0.00 45.72 3.96
2257 3154 0.815734 CAGGCAGCAATTCTGAAGGG 59.184 55.000 8.52 0.00 45.72 3.95
2267 3164 6.179756 TGACTATAAGATTTTCAGGCAGCAA 58.820 36.000 0.00 0.00 0.00 3.91
2275 3173 8.314021 TCTGCTGAACTGACTATAAGATTTTCA 58.686 33.333 0.00 0.00 0.00 2.69
2298 3203 4.863689 GCTGTATATGCAGTCAGCTATCTG 59.136 45.833 20.18 11.49 46.35 2.90
2316 3221 4.562757 GGAAAGTCACACTGTATGGCTGTA 60.563 45.833 0.00 0.00 30.75 2.74
2326 3231 5.458041 AAAATCCATGGAAAGTCACACTG 57.542 39.130 20.67 0.00 0.00 3.66
2352 3264 3.330701 TCAGGCCACTTTCTTCAAGGTAT 59.669 43.478 5.01 0.00 36.72 2.73
2353 3265 2.708861 TCAGGCCACTTTCTTCAAGGTA 59.291 45.455 5.01 0.00 36.72 3.08
2356 3268 3.004106 CACTTCAGGCCACTTTCTTCAAG 59.996 47.826 5.01 0.00 38.64 3.02
2366 3278 1.446907 CAGTGATCACTTCAGGCCAC 58.553 55.000 25.84 0.00 40.20 5.01
2371 3288 3.661944 ACTCAAGCAGTGATCACTTCAG 58.338 45.455 25.84 16.09 40.20 3.02
2376 3293 2.665537 CGAAGACTCAAGCAGTGATCAC 59.334 50.000 18.47 18.47 34.41 3.06
2377 3294 2.558359 TCGAAGACTCAAGCAGTGATCA 59.442 45.455 0.00 0.00 34.41 2.92
2381 3298 2.411069 CACATCGAAGACTCAAGCAGTG 59.589 50.000 0.00 0.00 42.51 3.66
2387 3304 4.381612 GGGACATACACATCGAAGACTCAA 60.382 45.833 0.00 0.00 42.51 3.02
2389 3306 3.707793 GGGACATACACATCGAAGACTC 58.292 50.000 0.00 0.00 42.51 3.36
2390 3307 2.099263 CGGGACATACACATCGAAGACT 59.901 50.000 0.00 0.00 42.51 3.24
2391 3308 2.460918 CGGGACATACACATCGAAGAC 58.539 52.381 0.00 0.00 42.51 3.01
2392 3309 1.407618 CCGGGACATACACATCGAAGA 59.592 52.381 0.00 0.00 45.75 2.87
2394 3311 0.179094 GCCGGGACATACACATCGAA 60.179 55.000 2.18 0.00 0.00 3.71
2395 3312 1.440060 GCCGGGACATACACATCGA 59.560 57.895 2.18 0.00 0.00 3.59
2396 3313 1.594293 GGCCGGGACATACACATCG 60.594 63.158 2.18 0.00 0.00 3.84
2397 3314 0.107410 TTGGCCGGGACATACACATC 60.107 55.000 1.80 0.00 0.00 3.06
2398 3315 0.329931 TTTGGCCGGGACATACACAT 59.670 50.000 1.80 0.00 0.00 3.21
2399 3316 0.329931 ATTTGGCCGGGACATACACA 59.670 50.000 1.80 0.00 0.00 3.72
2407 3324 2.676121 CACTGCATTTGGCCGGGA 60.676 61.111 2.18 0.00 43.89 5.14
2408 3325 1.814772 TTTCACTGCATTTGGCCGGG 61.815 55.000 2.18 0.00 43.89 5.73
2432 3354 5.385509 TGAACTACATTGTCGTCTCATCA 57.614 39.130 0.00 0.00 0.00 3.07
2433 3355 4.800993 CCTGAACTACATTGTCGTCTCATC 59.199 45.833 0.00 0.00 0.00 2.92
2434 3356 4.462834 TCCTGAACTACATTGTCGTCTCAT 59.537 41.667 0.00 0.00 0.00 2.90
2435 3357 3.824443 TCCTGAACTACATTGTCGTCTCA 59.176 43.478 0.00 0.34 0.00 3.27
2440 3362 4.437390 GCCAATTCCTGAACTACATTGTCG 60.437 45.833 0.00 0.00 0.00 4.35
2452 3374 1.065782 TCCGATTTCGCCAATTCCTGA 60.066 47.619 0.00 0.00 38.18 3.86
2463 3385 1.126846 GCACTGTTCTGTCCGATTTCG 59.873 52.381 0.00 0.00 39.44 3.46
2480 3402 4.993905 ACAGTAACCAAAAGAAACAGCAC 58.006 39.130 0.00 0.00 0.00 4.40
2532 3454 4.954202 TGACCGGTTCTCATAAGTCATACT 59.046 41.667 9.42 0.00 29.75 2.12
2533 3455 5.258456 TGACCGGTTCTCATAAGTCATAC 57.742 43.478 9.42 0.00 29.75 2.39
2534 3456 5.596772 TGATGACCGGTTCTCATAAGTCATA 59.403 40.000 9.42 0.00 43.13 2.15
2535 3457 4.405680 TGATGACCGGTTCTCATAAGTCAT 59.594 41.667 9.42 2.68 45.11 3.06
2551 3473 5.862924 TTTTCTCGAAGAATGTGATGACC 57.137 39.130 0.00 0.00 33.67 4.02
2569 3491 5.222631 ACTTTTCTCGTGATGCCATTTTTC 58.777 37.500 0.00 0.00 0.00 2.29
2594 3518 7.186570 TGATTGACTCTCTGGAATGTTATCA 57.813 36.000 0.00 0.00 0.00 2.15
2598 3522 4.699257 GCTTGATTGACTCTCTGGAATGTT 59.301 41.667 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.