Multiple sequence alignment - TraesCS3A01G506600

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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 TraesCS3A01G506600 chr3A 100.000 3182 0 0 1 3182 728055588 728058769 0.000000e+00 5877.0
1 TraesCS3A01G506600 chr3A 89.086 1237 130 4 953 2186 729690612 729691846 0.000000e+00 1531.0
2 TraesCS3A01G506600 chr3A 89.856 1183 120 0 1004 2186 728018602 728017420 0.000000e+00 1520.0
3 TraesCS3A01G506600 chr3A 90.019 1062 106 0 1125 2186 728033572 728032511 0.000000e+00 1375.0
4 TraesCS3A01G506600 chr3A 86.921 1208 140 13 996 2187 728384618 728385823 0.000000e+00 1339.0
5 TraesCS3A01G506600 chr3A 84.050 1210 177 11 996 2191 728458187 728456980 0.000000e+00 1151.0
6 TraesCS3A01G506600 chr3D 95.528 1297 58 0 930 2226 598060818 598062114 0.000000e+00 2074.0
7 TraesCS3A01G506600 chr3D 90.372 1236 115 3 953 2186 598049273 598048040 0.000000e+00 1620.0
8 TraesCS3A01G506600 chr3D 92.308 65 5 0 2228 2292 275632080 275632016 3.380000e-15 93.5
9 TraesCS3A01G506600 chr4B 97.754 935 20 1 1 935 613038653 613037720 0.000000e+00 1609.0
10 TraesCS3A01G506600 chr4B 91.667 48 4 0 2228 2275 438418206 438418159 2.050000e-07 67.6
11 TraesCS3A01G506600 chr3B 89.334 1247 126 6 953 2196 805004700 805003458 0.000000e+00 1559.0
12 TraesCS3A01G506600 chr3B 96.674 932 31 0 1 932 188464614 188463683 0.000000e+00 1550.0
13 TraesCS3A01G506600 chr3B 96.375 938 29 1 1 933 188492682 188491745 0.000000e+00 1539.0
14 TraesCS3A01G506600 chr3B 84.380 1210 173 12 996 2191 805425853 805424646 0.000000e+00 1173.0
15 TraesCS3A01G506600 chr3B 79.894 378 60 12 2564 2932 59760061 59760431 2.430000e-66 263.0
16 TraesCS3A01G506600 chr3B 90.909 165 14 1 1 165 778556083 778556246 1.490000e-53 220.0
17 TraesCS3A01G506600 chr5B 96.567 932 32 0 1 932 418372425 418373356 0.000000e+00 1544.0
18 TraesCS3A01G506600 chr5B 97.368 342 8 1 592 932 430167087 430166746 5.920000e-162 580.0
19 TraesCS3A01G506600 chr1B 95.829 935 39 0 1 935 29269103 29268169 0.000000e+00 1511.0
20 TraesCS3A01G506600 chr1B 91.018 167 12 3 1 164 282111254 282111420 4.130000e-54 222.0
21 TraesCS3A01G506600 chr1B 84.753 223 31 3 2963 3182 42071174 42070952 1.490000e-53 220.0
22 TraesCS3A01G506600 chr1B 96.774 31 1 0 2253 2283 573290 573320 6.000000e-03 52.8
23 TraesCS3A01G506600 chr7D 90.252 595 57 1 1 594 220315833 220315239 0.000000e+00 776.0
24 TraesCS3A01G506600 chr6A 83.886 844 99 24 2368 3182 497397321 497396486 0.000000e+00 771.0
25 TraesCS3A01G506600 chr6A 88.000 575 44 9 2570 3122 585582719 585582148 0.000000e+00 656.0
26 TraesCS3A01G506600 chr6A 97.376 343 8 1 592 933 228523914 228524256 1.650000e-162 582.0
27 TraesCS3A01G506600 chr6A 82.967 182 25 6 2990 3168 445680684 445680506 3.290000e-35 159.0
28 TraesCS3A01G506600 chr6D 88.870 602 43 8 2581 3160 437348226 437347627 0.000000e+00 719.0
29 TraesCS3A01G506600 chr6D 85.986 421 28 16 2601 2998 61006528 61006940 3.790000e-114 422.0
30 TraesCS3A01G506600 chr6D 87.255 204 21 4 2365 2566 61006325 61006525 8.880000e-56 228.0
31 TraesCS3A01G506600 chr6D 94.483 145 7 1 3039 3182 61007139 61007283 4.130000e-54 222.0
32 TraesCS3A01G506600 chr6D 86.928 153 17 3 3033 3182 12668329 12668481 5.460000e-38 169.0
33 TraesCS3A01G506600 chr6D 86.928 153 17 3 3033 3182 12692674 12692826 5.460000e-38 169.0
34 TraesCS3A01G506600 chrUn 97.953 342 6 1 592 932 342507763 342508104 2.730000e-165 592.0
35 TraesCS3A01G506600 chrUn 97.953 342 6 1 592 932 399642414 399642073 2.730000e-165 592.0
36 TraesCS3A01G506600 chrUn 90.909 165 14 1 1 165 240411567 240411730 1.490000e-53 220.0
37 TraesCS3A01G506600 chr4A 80.651 584 79 18 2388 2949 583720096 583720667 3.790000e-114 422.0
38 TraesCS3A01G506600 chr1A 80.750 587 72 15 2388 2949 475298971 475299541 1.360000e-113 420.0
39 TraesCS3A01G506600 chr5D 85.556 180 24 2 3001 3179 480808377 480808555 1.510000e-43 187.0
40 TraesCS3A01G506600 chr5D 92.500 40 1 2 2254 2292 540574131 540574093 4.430000e-04 56.5
41 TraesCS3A01G506600 chr2D 74.702 336 54 26 2 324 14890360 14890677 1.550000e-23 121.0
42 TraesCS3A01G506600 chr6B 94.595 74 2 1 2368 2439 662128589 662128516 2.590000e-21 113.0
43 TraesCS3A01G506600 chr7A 93.750 48 3 0 2228 2275 1951461 1951508 4.400000e-09 73.1
44 TraesCS3A01G506600 chr5A 90.566 53 5 0 2228 2280 77750094 77750146 1.580000e-08 71.3
45 TraesCS3A01G506600 chr5A 77.876 113 17 8 2782 2891 632571736 632571843 2.650000e-06 63.9


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 TraesCS3A01G506600 chr3A 728055588 728058769 3181 False 5877.000000 5877 100.000000 1 3182 1 chr3A.!!$F1 3181
1 TraesCS3A01G506600 chr3A 729690612 729691846 1234 False 1531.000000 1531 89.086000 953 2186 1 chr3A.!!$F3 1233
2 TraesCS3A01G506600 chr3A 728017420 728018602 1182 True 1520.000000 1520 89.856000 1004 2186 1 chr3A.!!$R1 1182
3 TraesCS3A01G506600 chr3A 728032511 728033572 1061 True 1375.000000 1375 90.019000 1125 2186 1 chr3A.!!$R2 1061
4 TraesCS3A01G506600 chr3A 728384618 728385823 1205 False 1339.000000 1339 86.921000 996 2187 1 chr3A.!!$F2 1191
5 TraesCS3A01G506600 chr3A 728456980 728458187 1207 True 1151.000000 1151 84.050000 996 2191 1 chr3A.!!$R3 1195
6 TraesCS3A01G506600 chr3D 598060818 598062114 1296 False 2074.000000 2074 95.528000 930 2226 1 chr3D.!!$F1 1296
7 TraesCS3A01G506600 chr3D 598048040 598049273 1233 True 1620.000000 1620 90.372000 953 2186 1 chr3D.!!$R2 1233
8 TraesCS3A01G506600 chr4B 613037720 613038653 933 True 1609.000000 1609 97.754000 1 935 1 chr4B.!!$R2 934
9 TraesCS3A01G506600 chr3B 805003458 805004700 1242 True 1559.000000 1559 89.334000 953 2196 1 chr3B.!!$R3 1243
10 TraesCS3A01G506600 chr3B 188463683 188464614 931 True 1550.000000 1550 96.674000 1 932 1 chr3B.!!$R1 931
11 TraesCS3A01G506600 chr3B 188491745 188492682 937 True 1539.000000 1539 96.375000 1 933 1 chr3B.!!$R2 932
12 TraesCS3A01G506600 chr3B 805424646 805425853 1207 True 1173.000000 1173 84.380000 996 2191 1 chr3B.!!$R4 1195
13 TraesCS3A01G506600 chr5B 418372425 418373356 931 False 1544.000000 1544 96.567000 1 932 1 chr5B.!!$F1 931
14 TraesCS3A01G506600 chr1B 29268169 29269103 934 True 1511.000000 1511 95.829000 1 935 1 chr1B.!!$R1 934
15 TraesCS3A01G506600 chr7D 220315239 220315833 594 True 776.000000 776 90.252000 1 594 1 chr7D.!!$R1 593
16 TraesCS3A01G506600 chr6A 497396486 497397321 835 True 771.000000 771 83.886000 2368 3182 1 chr6A.!!$R2 814
17 TraesCS3A01G506600 chr6A 585582148 585582719 571 True 656.000000 656 88.000000 2570 3122 1 chr6A.!!$R3 552
18 TraesCS3A01G506600 chr6D 437347627 437348226 599 True 719.000000 719 88.870000 2581 3160 1 chr6D.!!$R1 579
19 TraesCS3A01G506600 chr6D 61006325 61007283 958 False 290.666667 422 89.241333 2365 3182 3 chr6D.!!$F3 817
20 TraesCS3A01G506600 chr4A 583720096 583720667 571 False 422.000000 422 80.651000 2388 2949 1 chr4A.!!$F1 561
21 TraesCS3A01G506600 chr1A 475298971 475299541 570 False 420.000000 420 80.750000 2388 2949 1 chr1A.!!$F1 561

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
776 778 0.611618 CAGCCTAACATGTGGGCCAA 60.612 55.0 28.48 0.0 46.31 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 2361 0.105224 TGTCAGTCGGCCGAAAGAAA 59.895 50.0 32.93 22.48 0.0 2.52 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 1.075482 CATGTCAGCCCCACACCTT 59.925 57.895 0.00 0.00 0.00 3.50
168 170 4.692475 GCGGCCGTACCCAACTGT 62.692 66.667 28.70 0.00 33.26 3.55
465 467 1.065926 TCTGCCTGCAACAATCGATCT 60.066 47.619 0.00 0.00 0.00 2.75
763 765 2.949177 TTCTTTGCCAAGTCAGCCTA 57.051 45.000 0.00 0.00 0.00 3.93
776 778 0.611618 CAGCCTAACATGTGGGCCAA 60.612 55.000 28.48 0.00 46.31 4.52
786 788 1.604593 GTGGGCCAAGCATGTCAGT 60.605 57.895 8.40 0.00 0.00 3.41
842 850 3.445450 TGCTTTTTGTTACTCACTTGCCA 59.555 39.130 0.00 0.00 0.00 4.92
897 905 6.403866 AAAGTGATGGTTTTGCAGTATTCA 57.596 33.333 0.00 0.00 0.00 2.57
959 967 1.163554 CTTCTCCTTGCTGCTTCACC 58.836 55.000 0.00 0.00 0.00 4.02
1077 1095 1.587054 CGCGTCCTCCTTTCAGAGT 59.413 57.895 0.00 0.00 31.53 3.24
1098 1116 3.210528 GCCCTCGTCGTCGGATCT 61.211 66.667 1.55 0.00 37.69 2.75
1237 1260 2.512286 CCGCCATCACGCATCTGT 60.512 61.111 0.00 0.00 0.00 3.41
1298 1321 1.807165 CACCGCTCACCGACATCAG 60.807 63.158 0.00 0.00 40.02 2.90
1299 1322 2.276116 ACCGCTCACCGACATCAGT 61.276 57.895 0.00 0.00 40.02 3.41
1614 1640 2.842462 TGGTCTGTGCACCGTCCT 60.842 61.111 21.17 0.00 39.62 3.85
1761 1787 3.001902 TTTCAGCGACGCCTCGGAT 62.002 57.895 17.79 0.00 40.53 4.18
1800 1826 2.202987 GAGATCTGGGCAGCCGTG 60.203 66.667 5.00 0.02 0.00 4.94
1818 1844 1.737793 GTGGATCCGTTCGCAAAGAAT 59.262 47.619 7.39 0.00 41.49 2.40
1922 1948 1.124477 GCAGGGTATGAGGGAGAGGG 61.124 65.000 0.00 0.00 0.00 4.30
2009 2035 0.670546 AATGAGCTTGTCACGACGGG 60.671 55.000 0.00 0.00 38.28 5.28
2016 2042 3.771160 GTCACGACGGGGCTCCAT 61.771 66.667 1.96 0.00 0.00 3.41
2196 2222 7.151999 TGTTCCGTGATGCTTTTATATTGTT 57.848 32.000 0.00 0.00 0.00 2.83
2202 2228 9.313323 CCGTGATGCTTTTATATTGTTTATACG 57.687 33.333 0.00 0.00 0.00 3.06
2203 2229 8.827599 CGTGATGCTTTTATATTGTTTATACGC 58.172 33.333 0.00 0.00 0.00 4.42
2213 2239 3.620427 TGTTTATACGCAGTCCCATGT 57.380 42.857 0.00 0.00 43.93 3.21
2226 2252 7.099764 CGCAGTCCCATGTTATAATCTAGAAT 58.900 38.462 0.00 0.00 0.00 2.40
2227 2253 7.063898 CGCAGTCCCATGTTATAATCTAGAATG 59.936 40.741 0.00 0.00 0.00 2.67
2228 2254 7.335422 GCAGTCCCATGTTATAATCTAGAATGG 59.665 40.741 9.52 9.52 34.21 3.16
2232 2258 7.922382 CCCATGTTATAATCTAGAATGGGTCT 58.078 38.462 21.28 0.00 45.13 3.85
2233 2259 7.826252 CCCATGTTATAATCTAGAATGGGTCTG 59.174 40.741 21.28 5.17 45.13 3.51
2234 2260 8.597167 CCATGTTATAATCTAGAATGGGTCTGA 58.403 37.037 8.83 0.00 37.12 3.27
2235 2261 9.429359 CATGTTATAATCTAGAATGGGTCTGAC 57.571 37.037 0.00 0.00 37.12 3.51
2236 2262 8.783660 TGTTATAATCTAGAATGGGTCTGACT 57.216 34.615 7.85 0.00 37.12 3.41
2237 2263 9.877222 TGTTATAATCTAGAATGGGTCTGACTA 57.123 33.333 7.85 0.00 37.12 2.59
2243 2269 8.588290 ATCTAGAATGGGTCTGACTATATCAC 57.412 38.462 7.85 0.00 37.12 3.06
2244 2270 7.526918 TCTAGAATGGGTCTGACTATATCACA 58.473 38.462 7.85 0.00 37.12 3.58
2245 2271 6.412362 AGAATGGGTCTGACTATATCACAC 57.588 41.667 7.85 0.00 34.29 3.82
2246 2272 5.305644 AGAATGGGTCTGACTATATCACACC 59.694 44.000 7.85 0.00 43.80 4.16
2247 2273 4.265856 TGGGTCTGACTATATCACACCT 57.734 45.455 7.85 0.00 43.95 4.00
2248 2274 5.397553 TGGGTCTGACTATATCACACCTA 57.602 43.478 7.85 0.00 43.95 3.08
2249 2275 5.386060 TGGGTCTGACTATATCACACCTAG 58.614 45.833 7.85 0.00 43.95 3.02
2250 2276 5.133830 TGGGTCTGACTATATCACACCTAGA 59.866 44.000 7.85 0.00 43.95 2.43
2251 2277 5.474189 GGGTCTGACTATATCACACCTAGAC 59.526 48.000 7.85 0.00 43.95 2.59
2252 2278 5.179742 GGTCTGACTATATCACACCTAGACG 59.820 48.000 7.85 0.00 41.85 4.18
2253 2279 5.759273 GTCTGACTATATCACACCTAGACGT 59.241 44.000 0.00 0.00 32.37 4.34
2254 2280 5.758784 TCTGACTATATCACACCTAGACGTG 59.241 44.000 0.00 5.41 39.75 4.49
2255 2281 5.677567 TGACTATATCACACCTAGACGTGA 58.322 41.667 14.23 14.23 45.62 4.35
2256 2282 5.758784 TGACTATATCACACCTAGACGTGAG 59.241 44.000 16.22 5.58 44.83 3.51
2257 2283 5.926663 ACTATATCACACCTAGACGTGAGA 58.073 41.667 16.22 13.26 44.83 3.27
2258 2284 6.535540 ACTATATCACACCTAGACGTGAGAT 58.464 40.000 19.10 19.10 44.83 2.75
2259 2285 7.677892 ACTATATCACACCTAGACGTGAGATA 58.322 38.462 19.23 19.23 44.74 1.98
2261 2287 9.168451 CTATATCACACCTAGACGTGAGATATT 57.832 37.037 23.55 14.68 46.18 1.28
2263 2289 9.688091 ATATCACACCTAGACGTGAGATATTAT 57.312 33.333 17.93 10.14 46.18 1.28
2264 2290 7.436430 TCACACCTAGACGTGAGATATTATC 57.564 40.000 9.39 0.00 37.23 1.75
2265 2291 7.225011 TCACACCTAGACGTGAGATATTATCT 58.775 38.462 5.88 5.88 43.70 1.98
2283 2309 7.993821 ATTATCTCACATCTAAGTTGTGACG 57.006 36.000 9.39 7.03 46.31 4.35
2284 2310 4.848562 TCTCACATCTAAGTTGTGACGT 57.151 40.909 9.39 0.00 46.31 4.34
2285 2311 4.795268 TCTCACATCTAAGTTGTGACGTC 58.205 43.478 9.11 9.11 46.31 4.34
2286 2312 4.277423 TCTCACATCTAAGTTGTGACGTCA 59.723 41.667 15.76 15.76 46.31 4.35
2287 2313 4.546570 TCACATCTAAGTTGTGACGTCAG 58.453 43.478 20.73 5.35 46.31 3.51
2288 2314 4.037565 TCACATCTAAGTTGTGACGTCAGT 59.962 41.667 20.73 6.20 46.31 3.41
2289 2315 5.239963 TCACATCTAAGTTGTGACGTCAGTA 59.760 40.000 20.73 8.54 46.31 2.74
2290 2316 5.569441 CACATCTAAGTTGTGACGTCAGTAG 59.431 44.000 20.73 14.56 45.83 2.57
2291 2317 5.472478 ACATCTAAGTTGTGACGTCAGTAGA 59.528 40.000 20.73 18.81 0.00 2.59
2292 2318 6.151312 ACATCTAAGTTGTGACGTCAGTAGAT 59.849 38.462 20.73 20.00 0.00 1.98
2293 2319 6.570672 TCTAAGTTGTGACGTCAGTAGATT 57.429 37.500 20.73 12.61 0.00 2.40
2294 2320 6.379386 TCTAAGTTGTGACGTCAGTAGATTG 58.621 40.000 20.73 7.97 0.00 2.67
2295 2321 4.585955 AGTTGTGACGTCAGTAGATTGT 57.414 40.909 20.73 0.00 0.00 2.71
2296 2322 4.945246 AGTTGTGACGTCAGTAGATTGTT 58.055 39.130 20.73 0.00 0.00 2.83
2297 2323 5.357257 AGTTGTGACGTCAGTAGATTGTTT 58.643 37.500 20.73 0.00 0.00 2.83
2298 2324 5.815740 AGTTGTGACGTCAGTAGATTGTTTT 59.184 36.000 20.73 0.00 0.00 2.43
2299 2325 5.900339 TGTGACGTCAGTAGATTGTTTTC 57.100 39.130 20.73 2.57 0.00 2.29
2300 2326 5.597806 TGTGACGTCAGTAGATTGTTTTCT 58.402 37.500 20.73 0.00 0.00 2.52
2301 2327 6.046593 TGTGACGTCAGTAGATTGTTTTCTT 58.953 36.000 20.73 0.00 0.00 2.52
2302 2328 7.204604 TGTGACGTCAGTAGATTGTTTTCTTA 58.795 34.615 20.73 0.00 0.00 2.10
2303 2329 7.870954 TGTGACGTCAGTAGATTGTTTTCTTAT 59.129 33.333 20.73 0.00 0.00 1.73
2304 2330 8.709646 GTGACGTCAGTAGATTGTTTTCTTATT 58.290 33.333 20.73 0.00 0.00 1.40
2305 2331 9.268268 TGACGTCAGTAGATTGTTTTCTTATTT 57.732 29.630 15.76 0.00 0.00 1.40
2306 2332 9.530129 GACGTCAGTAGATTGTTTTCTTATTTG 57.470 33.333 11.55 0.00 0.00 2.32
2307 2333 9.052759 ACGTCAGTAGATTGTTTTCTTATTTGT 57.947 29.630 0.00 0.00 0.00 2.83
2308 2334 9.878599 CGTCAGTAGATTGTTTTCTTATTTGTT 57.121 29.630 0.00 0.00 0.00 2.83
2317 2343 9.914923 ATTGTTTTCTTATTTGTTTCTTTTCGC 57.085 25.926 0.00 0.00 0.00 4.70
2318 2344 7.605259 TGTTTTCTTATTTGTTTCTTTTCGCG 58.395 30.769 0.00 0.00 0.00 5.87
2319 2345 7.273815 TGTTTTCTTATTTGTTTCTTTTCGCGT 59.726 29.630 5.77 0.00 0.00 6.01
2320 2346 6.963017 TTCTTATTTGTTTCTTTTCGCGTC 57.037 33.333 5.77 0.00 0.00 5.19
2321 2347 5.134640 TCTTATTTGTTTCTTTTCGCGTCG 58.865 37.500 5.77 0.00 0.00 5.12
2322 2348 2.810028 TTTGTTTCTTTTCGCGTCGT 57.190 40.000 5.77 0.00 0.00 4.34
2323 2349 2.810028 TTGTTTCTTTTCGCGTCGTT 57.190 40.000 5.77 0.00 0.00 3.85
2324 2350 2.810028 TGTTTCTTTTCGCGTCGTTT 57.190 40.000 5.77 0.00 0.00 3.60
2325 2351 2.696255 TGTTTCTTTTCGCGTCGTTTC 58.304 42.857 5.77 0.00 0.00 2.78
2326 2352 2.349275 TGTTTCTTTTCGCGTCGTTTCT 59.651 40.909 5.77 0.00 0.00 2.52
2327 2353 3.181518 TGTTTCTTTTCGCGTCGTTTCTT 60.182 39.130 5.77 0.00 0.00 2.52
2328 2354 3.661758 TTCTTTTCGCGTCGTTTCTTT 57.338 38.095 5.77 0.00 0.00 2.52
2329 2355 3.228878 TCTTTTCGCGTCGTTTCTTTC 57.771 42.857 5.77 0.00 0.00 2.62
2330 2356 2.861935 TCTTTTCGCGTCGTTTCTTTCT 59.138 40.909 5.77 0.00 0.00 2.52
2331 2357 3.307782 TCTTTTCGCGTCGTTTCTTTCTT 59.692 39.130 5.77 0.00 0.00 2.52
2332 2358 3.661758 TTTCGCGTCGTTTCTTTCTTT 57.338 38.095 5.77 0.00 0.00 2.52
2333 2359 3.661758 TTCGCGTCGTTTCTTTCTTTT 57.338 38.095 5.77 0.00 0.00 2.27
2334 2360 3.661758 TCGCGTCGTTTCTTTCTTTTT 57.338 38.095 5.77 0.00 0.00 1.94
2352 2378 1.956297 TTTTTCTTTCGGCCGACTGA 58.044 45.000 31.19 25.07 0.00 3.41
2353 2379 1.223187 TTTTCTTTCGGCCGACTGAC 58.777 50.000 31.19 0.00 0.00 3.51
2354 2380 0.105224 TTTCTTTCGGCCGACTGACA 59.895 50.000 31.19 18.58 0.00 3.58
2355 2381 0.105224 TTCTTTCGGCCGACTGACAA 59.895 50.000 31.19 18.45 0.00 3.18
2356 2382 0.105224 TCTTTCGGCCGACTGACAAA 59.895 50.000 31.19 17.65 0.00 2.83
2357 2383 0.941542 CTTTCGGCCGACTGACAAAA 59.058 50.000 31.19 16.84 0.00 2.44
2358 2384 1.332375 CTTTCGGCCGACTGACAAAAA 59.668 47.619 31.19 16.03 0.00 1.94
2378 2404 4.322057 AAAATGAACTGGCTCCTACCAT 57.678 40.909 0.00 0.00 39.54 3.55
2512 2542 3.988379 TGTGAGCAATTTGAAGTGTCC 57.012 42.857 0.00 0.00 0.00 4.02
2514 2544 3.316029 TGTGAGCAATTTGAAGTGTCCAG 59.684 43.478 0.00 0.00 0.00 3.86
2518 2548 5.181811 TGAGCAATTTGAAGTGTCCAGTATG 59.818 40.000 0.00 0.00 0.00 2.39
2534 2567 7.872993 TGTCCAGTATGTTTCAAAAACACAAAA 59.127 29.630 7.36 0.00 32.37 2.44
2592 2625 6.788930 GTGAATAAACTTTGTAGTTCCGAACG 59.211 38.462 5.62 0.00 43.74 3.95
2693 2726 8.669946 TTTATGAAAATCCCCAAACAGTTTTC 57.330 30.769 0.00 0.00 38.56 2.29
2980 3044 4.260866 GGGATTGTTCTTGTTTTTCGTCGA 60.261 41.667 0.00 0.00 0.00 4.20
2998 3062 4.319477 CGTCGAAAAGAATGTTGGACATGT 60.319 41.667 0.00 0.00 40.61 3.21
2999 3063 4.911610 GTCGAAAAGAATGTTGGACATGTG 59.088 41.667 1.15 0.00 40.35 3.21
3025 3089 1.519751 CCCCACAACGCCAATTTCGA 61.520 55.000 4.12 0.00 0.00 3.71
3037 3259 3.556004 GCCAATTTCGAAATCCAACCCAA 60.556 43.478 22.93 0.00 0.00 4.12
3100 3324 3.438183 GGGGGACAAGACTAGTAGTTGA 58.562 50.000 19.56 0.00 0.00 3.18
3104 3328 5.336610 GGGGACAAGACTAGTAGTTGAGAAC 60.337 48.000 19.56 9.48 0.00 3.01
3164 3388 3.118038 AGTCAAAGGTGGACTTGCAACTA 60.118 43.478 0.00 0.00 42.77 2.24
3169 3393 2.644798 AGGTGGACTTGCAACTAGGATT 59.355 45.455 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.025793 AGAGATGTGAGGAGGAAGACGA 60.026 50.000 0.00 0.00 0.00 4.20
123 125 3.749064 GCCAGTCGTCGAGGAGCA 61.749 66.667 8.30 0.00 0.00 4.26
212 214 3.490759 GTCCTGCGCGACACCATG 61.491 66.667 12.10 0.00 32.74 3.66
300 302 3.364964 TCCCCATCGACCTCCCCT 61.365 66.667 0.00 0.00 0.00 4.79
360 362 0.950116 GGGTAGATCGATTCGTCCGT 59.050 55.000 5.89 0.00 0.00 4.69
416 418 1.293924 CAGAAGCAAGCGGATCGAAT 58.706 50.000 0.00 0.00 0.00 3.34
763 765 1.976898 CATGCTTGGCCCACATGTT 59.023 52.632 17.34 0.00 37.10 2.71
776 778 5.050091 CGACTAAGTGAAAAACTGACATGCT 60.050 40.000 0.00 0.00 39.81 3.79
786 788 1.796459 GAGCCGCGACTAAGTGAAAAA 59.204 47.619 8.23 0.00 0.00 1.94
1029 1038 1.004560 CTGGCTCTTCTTGACGGCA 60.005 57.895 0.00 0.00 0.00 5.69
1071 1089 2.282251 ACGAGGGCGACACTCTGA 60.282 61.111 7.37 0.00 41.64 3.27
1158 1176 2.590114 GGCGTACACCTTCCAGGGT 61.590 63.158 0.00 0.00 40.58 4.34
1225 1248 1.065701 GTCGAGGTACAGATGCGTGAT 59.934 52.381 0.00 0.00 0.00 3.06
1237 1260 2.753043 GTCGGCCAGGTCGAGGTA 60.753 66.667 18.83 0.00 41.35 3.08
1281 1304 2.214181 GACTGATGTCGGTGAGCGGT 62.214 60.000 3.57 0.00 35.19 5.68
1298 1321 1.472276 CGCGGCGTAGAAGACATGAC 61.472 60.000 15.36 0.00 0.00 3.06
1299 1322 1.226575 CGCGGCGTAGAAGACATGA 60.227 57.895 15.36 0.00 0.00 3.07
1614 1640 0.841289 AGAACCCAAAGACCACGGAA 59.159 50.000 0.00 0.00 0.00 4.30
1800 1826 2.006888 TCATTCTTTGCGAACGGATCC 58.993 47.619 0.00 0.00 33.72 3.36
1818 1844 3.455990 TTGCTGCAATTGAAAGCTTCA 57.544 38.095 25.09 12.65 37.82 3.02
2016 2042 3.173540 CCACCAATTGGCGATCTCA 57.826 52.632 24.79 0.00 39.07 3.27
2129 2155 1.098050 AATCCATGCGTTGAAGGAGC 58.902 50.000 0.00 0.00 32.91 4.70
2196 2222 7.903145 AGATTATAACATGGGACTGCGTATAA 58.097 34.615 0.00 0.00 0.00 0.98
2201 2227 6.025749 TCTAGATTATAACATGGGACTGCG 57.974 41.667 0.00 0.00 0.00 5.18
2202 2228 7.335422 CCATTCTAGATTATAACATGGGACTGC 59.665 40.741 8.83 0.00 0.00 4.40
2203 2229 8.783833 CCATTCTAGATTATAACATGGGACTG 57.216 38.462 8.83 0.00 0.00 3.51
2230 2256 5.758784 CACGTCTAGGTGTGATATAGTCAGA 59.241 44.000 8.97 0.00 37.56 3.27
2231 2257 5.758784 TCACGTCTAGGTGTGATATAGTCAG 59.241 44.000 12.21 0.00 40.02 3.51
2232 2258 5.677567 TCACGTCTAGGTGTGATATAGTCA 58.322 41.667 12.21 0.00 40.02 3.41
2233 2259 5.990386 TCTCACGTCTAGGTGTGATATAGTC 59.010 44.000 15.36 0.00 43.59 2.59
2234 2260 5.926663 TCTCACGTCTAGGTGTGATATAGT 58.073 41.667 15.36 0.00 43.59 2.12
2239 2265 7.885922 AGATAATATCTCACGTCTAGGTGTGAT 59.114 37.037 18.58 18.58 46.74 3.06
2240 2266 7.225011 AGATAATATCTCACGTCTAGGTGTGA 58.775 38.462 14.56 14.56 42.49 3.58
2241 2267 7.441890 AGATAATATCTCACGTCTAGGTGTG 57.558 40.000 0.00 8.46 39.00 3.82
2267 2293 4.585955 ACTGACGTCACAACTTAGATGT 57.414 40.909 15.76 3.92 36.74 3.06
2268 2294 5.939457 TCTACTGACGTCACAACTTAGATG 58.061 41.667 15.76 3.22 0.00 2.90
2269 2295 6.761099 ATCTACTGACGTCACAACTTAGAT 57.239 37.500 15.76 15.96 0.00 1.98
2270 2296 6.016527 ACAATCTACTGACGTCACAACTTAGA 60.017 38.462 15.76 14.55 0.00 2.10
2271 2297 6.150318 ACAATCTACTGACGTCACAACTTAG 58.850 40.000 15.76 5.61 0.00 2.18
2272 2298 6.080648 ACAATCTACTGACGTCACAACTTA 57.919 37.500 15.76 0.00 0.00 2.24
2273 2299 4.945246 ACAATCTACTGACGTCACAACTT 58.055 39.130 15.76 2.09 0.00 2.66
2274 2300 4.585955 ACAATCTACTGACGTCACAACT 57.414 40.909 15.76 0.00 0.00 3.16
2275 2301 5.652744 AAACAATCTACTGACGTCACAAC 57.347 39.130 15.76 0.00 0.00 3.32
2276 2302 6.046593 AGAAAACAATCTACTGACGTCACAA 58.953 36.000 15.76 4.45 0.00 3.33
2277 2303 5.597806 AGAAAACAATCTACTGACGTCACA 58.402 37.500 15.76 4.45 0.00 3.58
2278 2304 6.526566 AAGAAAACAATCTACTGACGTCAC 57.473 37.500 15.76 0.00 0.00 3.67
2279 2305 8.827177 AATAAGAAAACAATCTACTGACGTCA 57.173 30.769 18.88 18.88 0.00 4.35
2280 2306 9.530129 CAAATAAGAAAACAATCTACTGACGTC 57.470 33.333 9.11 9.11 0.00 4.34
2281 2307 9.052759 ACAAATAAGAAAACAATCTACTGACGT 57.947 29.630 0.00 0.00 0.00 4.34
2282 2308 9.878599 AACAAATAAGAAAACAATCTACTGACG 57.121 29.630 0.00 0.00 0.00 4.35
2291 2317 9.914923 GCGAAAAGAAACAAATAAGAAAACAAT 57.085 25.926 0.00 0.00 0.00 2.71
2292 2318 8.105135 CGCGAAAAGAAACAAATAAGAAAACAA 58.895 29.630 0.00 0.00 0.00 2.83
2293 2319 7.273815 ACGCGAAAAGAAACAAATAAGAAAACA 59.726 29.630 15.93 0.00 0.00 2.83
2294 2320 7.606131 ACGCGAAAAGAAACAAATAAGAAAAC 58.394 30.769 15.93 0.00 0.00 2.43
2295 2321 7.304962 CGACGCGAAAAGAAACAAATAAGAAAA 60.305 33.333 15.93 0.00 0.00 2.29
2296 2322 6.139482 CGACGCGAAAAGAAACAAATAAGAAA 59.861 34.615 15.93 0.00 0.00 2.52
2297 2323 5.617992 CGACGCGAAAAGAAACAAATAAGAA 59.382 36.000 15.93 0.00 0.00 2.52
2298 2324 5.134640 CGACGCGAAAAGAAACAAATAAGA 58.865 37.500 15.93 0.00 0.00 2.10
2299 2325 4.901881 ACGACGCGAAAAGAAACAAATAAG 59.098 37.500 15.93 0.00 0.00 1.73
2300 2326 4.835344 ACGACGCGAAAAGAAACAAATAA 58.165 34.783 15.93 0.00 0.00 1.40
2301 2327 4.455917 ACGACGCGAAAAGAAACAAATA 57.544 36.364 15.93 0.00 0.00 1.40
2302 2328 3.328237 ACGACGCGAAAAGAAACAAAT 57.672 38.095 15.93 0.00 0.00 2.32
2303 2329 2.810028 ACGACGCGAAAAGAAACAAA 57.190 40.000 15.93 0.00 0.00 2.83
2304 2330 2.810028 AACGACGCGAAAAGAAACAA 57.190 40.000 15.93 0.00 0.00 2.83
2305 2331 2.349275 AGAAACGACGCGAAAAGAAACA 59.651 40.909 15.93 0.00 0.00 2.83
2306 2332 2.965239 AGAAACGACGCGAAAAGAAAC 58.035 42.857 15.93 0.00 0.00 2.78
2307 2333 3.661758 AAGAAACGACGCGAAAAGAAA 57.338 38.095 15.93 0.00 0.00 2.52
2308 2334 3.307782 AGAAAGAAACGACGCGAAAAGAA 59.692 39.130 15.93 0.00 0.00 2.52
2309 2335 2.861935 AGAAAGAAACGACGCGAAAAGA 59.138 40.909 15.93 0.00 0.00 2.52
2310 2336 3.234596 AGAAAGAAACGACGCGAAAAG 57.765 42.857 15.93 2.90 0.00 2.27
2311 2337 3.661758 AAGAAAGAAACGACGCGAAAA 57.338 38.095 15.93 0.00 0.00 2.29
2312 2338 3.661758 AAAGAAAGAAACGACGCGAAA 57.338 38.095 15.93 0.00 0.00 3.46
2313 2339 3.661758 AAAAGAAAGAAACGACGCGAA 57.338 38.095 15.93 0.00 0.00 4.70
2314 2340 3.661758 AAAAAGAAAGAAACGACGCGA 57.338 38.095 15.93 0.00 0.00 5.87
2333 2359 1.600485 GTCAGTCGGCCGAAAGAAAAA 59.400 47.619 32.93 8.50 0.00 1.94
2334 2360 1.223187 GTCAGTCGGCCGAAAGAAAA 58.777 50.000 32.93 9.68 0.00 2.29
2335 2361 0.105224 TGTCAGTCGGCCGAAAGAAA 59.895 50.000 32.93 22.48 0.00 2.52
2336 2362 0.105224 TTGTCAGTCGGCCGAAAGAA 59.895 50.000 32.93 19.62 0.00 2.52
2337 2363 0.105224 TTTGTCAGTCGGCCGAAAGA 59.895 50.000 32.93 26.83 0.00 2.52
2338 2364 0.941542 TTTTGTCAGTCGGCCGAAAG 59.058 50.000 32.93 24.87 0.00 2.62
2339 2365 1.380524 TTTTTGTCAGTCGGCCGAAA 58.619 45.000 32.93 18.02 0.00 3.46
2340 2366 3.082165 TTTTTGTCAGTCGGCCGAA 57.918 47.368 32.93 12.67 0.00 4.30
2341 2367 4.859400 TTTTTGTCAGTCGGCCGA 57.141 50.000 27.28 27.28 0.00 5.54
2356 2382 4.112634 TGGTAGGAGCCAGTTCATTTTT 57.887 40.909 0.00 0.00 33.97 1.94
2357 2383 3.806949 TGGTAGGAGCCAGTTCATTTT 57.193 42.857 0.00 0.00 33.97 1.82
2358 2384 4.273318 GAATGGTAGGAGCCAGTTCATTT 58.727 43.478 0.00 0.00 42.47 2.32
2359 2385 3.372025 GGAATGGTAGGAGCCAGTTCATT 60.372 47.826 0.00 0.00 42.47 2.57
2360 2386 2.173569 GGAATGGTAGGAGCCAGTTCAT 59.826 50.000 0.00 0.00 42.47 2.57
2361 2387 1.559682 GGAATGGTAGGAGCCAGTTCA 59.440 52.381 0.00 0.00 42.47 3.18
2362 2388 1.559682 TGGAATGGTAGGAGCCAGTTC 59.440 52.381 0.00 0.00 42.47 3.01
2363 2389 1.668826 TGGAATGGTAGGAGCCAGTT 58.331 50.000 0.00 0.00 42.47 3.16
2364 2390 1.668826 TTGGAATGGTAGGAGCCAGT 58.331 50.000 0.00 0.00 42.47 4.00
2365 2391 3.648067 TCTATTGGAATGGTAGGAGCCAG 59.352 47.826 0.00 0.00 42.47 4.85
2366 2392 3.664320 TCTATTGGAATGGTAGGAGCCA 58.336 45.455 0.00 0.00 43.48 4.75
2439 2466 7.939782 TGCAAGATTGTTTTCTAATCTCAACA 58.060 30.769 0.00 0.00 42.43 3.33
2442 2469 9.985730 AAATTGCAAGATTGTTTTCTAATCTCA 57.014 25.926 4.94 0.00 42.43 3.27
2497 2526 5.376854 ACATACTGGACACTTCAAATTGC 57.623 39.130 0.00 0.00 0.00 3.56
2562 2595 9.113876 CGGAACTACAAAGTTTATTCACATTTC 57.886 33.333 0.00 0.00 46.09 2.17
2653 2686 9.862585 GATTTTCATAAATTGTTCGTGCTTTTT 57.137 25.926 0.00 0.00 34.16 1.94
2661 2694 7.386299 TGTTTGGGGATTTTCATAAATTGTTCG 59.614 33.333 0.00 0.00 34.16 3.95
2772 2807 7.894376 ATGGTGCAAAAGAATTAATTGACAG 57.106 32.000 5.17 0.00 0.00 3.51
2876 2936 5.697473 TGCCACGAACATTTCTTTGAATA 57.303 34.783 0.00 0.00 0.00 1.75
2933 2997 6.423905 CCTCACAAACTTCTAGAAAATGTCGA 59.576 38.462 6.63 10.16 0.00 4.20
2980 3044 7.378181 GGTAATCACATGTCCAACATTCTTTT 58.622 34.615 0.00 0.00 36.53 2.27
3025 3089 1.468506 GGCGTGGTTGGGTTGGATTT 61.469 55.000 0.00 0.00 0.00 2.17
3037 3259 0.462047 GCTATGCAACTAGGCGTGGT 60.462 55.000 0.00 0.00 34.18 4.16
3100 3324 2.040412 GTTTCATCCCACCCTCAGTTCT 59.960 50.000 0.00 0.00 0.00 3.01
3104 3328 2.558359 GTTTGTTTCATCCCACCCTCAG 59.442 50.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.