Multiple sequence alignment - TraesCS4A01G047300

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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 TraesCS4A01G047300 chr4A 100.000 3164 0 0 1 3164 38683763 38680600 0.000000e+00 5843.0
1 TraesCS4A01G047300 chr4A 84.572 1413 141 32 825 2174 40260697 40262095 0.000000e+00 1330.0
2 TraesCS4A01G047300 chr4A 77.926 1649 231 70 1008 2571 37833677 37835277 0.000000e+00 905.0
3 TraesCS4A01G047300 chr4A 76.923 390 54 24 2526 2895 40262342 40262715 4.170000e-44 189.0
4 TraesCS4A01G047300 chr4A 93.519 108 4 2 2597 2704 38661749 38661645 1.170000e-34 158.0
5 TraesCS4A01G047300 chr4A 86.395 147 13 2 2212 2351 38674392 38674246 1.520000e-33 154.0
6 TraesCS4A01G047300 chr4A 92.063 63 5 0 2176 2238 38681534 38681472 4.350000e-14 89.8
7 TraesCS4A01G047300 chr4A 92.063 63 5 0 2230 2292 38681588 38681526 4.350000e-14 89.8
8 TraesCS4A01G047300 chr4A 95.918 49 2 0 2847 2895 38660953 38660905 2.620000e-11 80.5
9 TraesCS4A01G047300 chr4A 85.507 69 9 1 2826 2893 38001760 38001828 1.570000e-08 71.3
10 TraesCS4A01G047300 chr4D 91.267 1523 70 20 764 2229 426870055 426871571 0.000000e+00 2017.0
11 TraesCS4A01G047300 chr4D 85.573 1414 140 29 808 2174 424169710 424168314 0.000000e+00 1423.0
12 TraesCS4A01G047300 chr4D 84.961 1423 142 28 808 2174 423989974 423988568 0.000000e+00 1376.0
13 TraesCS4A01G047300 chr4D 84.615 1443 140 34 803 2174 57840496 57841927 0.000000e+00 1360.0
14 TraesCS4A01G047300 chr4D 79.193 1264 192 32 953 2174 428558322 428557088 0.000000e+00 811.0
15 TraesCS4A01G047300 chr4D 86.694 744 61 11 1464 2174 424196577 424195839 0.000000e+00 791.0
16 TraesCS4A01G047300 chr4D 89.091 550 43 10 2283 2828 427261748 427262284 0.000000e+00 667.0
17 TraesCS4A01G047300 chr4D 87.531 401 19 8 2283 2682 426871588 426871958 4.850000e-118 435.0
18 TraesCS4A01G047300 chr4D 80.851 611 55 28 1 584 427208067 427208642 1.050000e-114 424.0
19 TraesCS4A01G047300 chr4D 89.318 337 30 5 2826 3162 426873909 426874239 4.880000e-113 418.0
20 TraesCS4A01G047300 chr4D 79.745 627 72 23 615 1198 427208747 427209361 1.370000e-108 403.0
21 TraesCS4A01G047300 chr4D 86.032 315 32 5 1 314 426867851 426868154 8.460000e-86 327.0
22 TraesCS4A01G047300 chr4D 81.281 406 52 18 2255 2652 427323860 427324249 1.100000e-79 307.0
23 TraesCS4A01G047300 chr4D 93.902 164 5 4 2668 2828 426873623 426873784 3.150000e-60 243.0
24 TraesCS4A01G047300 chr4D 84.064 251 23 13 2487 2725 424109073 424108828 3.180000e-55 226.0
25 TraesCS4A01G047300 chr4D 78.899 327 48 18 2225 2548 427269126 427269434 5.350000e-48 202.0
26 TraesCS4A01G047300 chr4D 81.070 243 22 13 2283 2520 428557057 428556834 4.200000e-39 172.0
27 TraesCS4A01G047300 chr4D 93.913 115 4 2 2594 2708 427021206 427021317 1.510000e-38 171.0
28 TraesCS4A01G047300 chr4D 89.552 67 7 0 2829 2895 424194407 424194341 5.620000e-13 86.1
29 TraesCS4A01G047300 chr4D 88.571 70 8 0 2826 2895 427022046 427022115 5.620000e-13 86.1
30 TraesCS4A01G047300 chr4D 92.593 54 4 0 2230 2283 426871518 426871571 9.410000e-11 78.7
31 TraesCS4A01G047300 chr4D 97.727 44 1 0 2186 2229 427261688 427261731 3.380000e-10 76.8
32 TraesCS4A01G047300 chr4D 93.750 48 3 0 2848 2895 426902595 426902642 4.380000e-09 73.1
33 TraesCS4A01G047300 chr4D 93.750 48 3 0 2848 2895 427269745 427269792 4.380000e-09 73.1
34 TraesCS4A01G047300 chr4D 97.143 35 1 0 2258 2292 428557093 428557059 3.410000e-05 60.2
35 TraesCS4A01G047300 chr4B 88.578 1646 94 26 664 2229 522669103 522670734 0.000000e+00 1912.0
36 TraesCS4A01G047300 chr4B 93.339 1276 52 9 932 2174 527644841 527643566 0.000000e+00 1855.0
37 TraesCS4A01G047300 chr4B 84.639 1634 137 48 616 2173 527781559 527779964 0.000000e+00 1522.0
38 TraesCS4A01G047300 chr4B 85.336 1398 140 34 825 2174 86132209 86130829 0.000000e+00 1386.0
39 TraesCS4A01G047300 chr4B 84.993 1406 151 24 820 2174 520298415 520297019 0.000000e+00 1373.0
40 TraesCS4A01G047300 chr4B 83.485 551 34 17 2201 2722 522670652 522671174 8.000000e-126 460.0
41 TraesCS4A01G047300 chr4B 83.153 463 39 21 2306 2745 86097245 86096799 1.380000e-103 387.0
42 TraesCS4A01G047300 chr4B 86.957 322 37 3 2829 3150 522671610 522671926 1.080000e-94 357.0
43 TraesCS4A01G047300 chr4B 84.874 357 22 12 2283 2633 527748172 527747842 6.540000e-87 331.0
44 TraesCS4A01G047300 chr4B 84.211 285 27 1 1908 2174 86097570 86097286 8.700000e-66 261.0
45 TraesCS4A01G047300 chr4B 89.252 214 16 4 2617 2827 527594483 527594274 8.700000e-66 261.0
46 TraesCS4A01G047300 chr4B 80.000 290 36 15 2283 2564 522683457 522683732 8.950000e-46 195.0
47 TraesCS4A01G047300 chr4B 85.629 167 20 4 607 770 527646757 527646592 4.200000e-39 172.0
48 TraesCS4A01G047300 chr4B 81.057 227 32 9 2255 2477 522684156 522684375 1.510000e-38 171.0
49 TraesCS4A01G047300 chr4B 82.381 210 11 5 2283 2488 527643469 527643282 3.270000e-35 159.0
50 TraesCS4A01G047300 chr4B 92.929 99 7 0 2695 2793 522671171 522671269 9.150000e-31 145.0
51 TraesCS4A01G047300 chr4B 87.288 118 10 4 2482 2595 527620183 527620067 2.560000e-26 130.0
52 TraesCS4A01G047300 chr4B 97.619 42 1 0 2188 2229 527643527 527643486 4.380000e-09 73.1
53 TraesCS4A01G047300 chr3D 89.095 917 64 17 852 1743 543683992 543683087 0.000000e+00 1107.0
54 TraesCS4A01G047300 chr3D 86.774 310 30 5 1 310 543686065 543685767 5.060000e-88 335.0
55 TraesCS4A01G047300 chr3B 87.560 209 20 3 1 207 719383162 719382958 1.470000e-58 237.0
56 TraesCS4A01G047300 chr7B 84.946 93 11 3 2717 2807 103083855 103083764 1.210000e-14 91.6


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 TraesCS4A01G047300 chr4A 38680600 38683763 3163 True 2007.533333 5843 94.708667 1 3164 3 chr4A.!!$R3 3163
1 TraesCS4A01G047300 chr4A 37833677 37835277 1600 False 905.000000 905 77.926000 1008 2571 1 chr4A.!!$F1 1563
2 TraesCS4A01G047300 chr4A 40260697 40262715 2018 False 759.500000 1330 80.747500 825 2895 2 chr4A.!!$F3 2070
3 TraesCS4A01G047300 chr4D 424168314 424169710 1396 True 1423.000000 1423 85.573000 808 2174 1 chr4D.!!$R3 1366
4 TraesCS4A01G047300 chr4D 423988568 423989974 1406 True 1376.000000 1376 84.961000 808 2174 1 chr4D.!!$R1 1366
5 TraesCS4A01G047300 chr4D 57840496 57841927 1431 False 1360.000000 1360 84.615000 803 2174 1 chr4D.!!$F1 1371
6 TraesCS4A01G047300 chr4D 426867851 426874239 6388 False 586.450000 2017 90.107167 1 3162 6 chr4D.!!$F4 3161
7 TraesCS4A01G047300 chr4D 424194341 424196577 2236 True 438.550000 791 88.123000 1464 2895 2 chr4D.!!$R4 1431
8 TraesCS4A01G047300 chr4D 427208067 427209361 1294 False 413.500000 424 80.298000 1 1198 2 chr4D.!!$F6 1197
9 TraesCS4A01G047300 chr4D 427261688 427262284 596 False 371.900000 667 93.409000 2186 2828 2 chr4D.!!$F7 642
10 TraesCS4A01G047300 chr4D 428556834 428558322 1488 True 347.733333 811 85.802000 953 2520 3 chr4D.!!$R5 1567
11 TraesCS4A01G047300 chr4B 527779964 527781559 1595 True 1522.000000 1522 84.639000 616 2173 1 chr4B.!!$R6 1557
12 TraesCS4A01G047300 chr4B 86130829 86132209 1380 True 1386.000000 1386 85.336000 825 2174 1 chr4B.!!$R1 1349
13 TraesCS4A01G047300 chr4B 520297019 520298415 1396 True 1373.000000 1373 84.993000 820 2174 1 chr4B.!!$R2 1354
14 TraesCS4A01G047300 chr4B 522669103 522671926 2823 False 718.500000 1912 87.987250 664 3150 4 chr4B.!!$F1 2486
15 TraesCS4A01G047300 chr4B 527643282 527646757 3475 True 564.775000 1855 89.742000 607 2488 4 chr4B.!!$R8 1881
16 TraesCS4A01G047300 chr4B 86096799 86097570 771 True 324.000000 387 83.682000 1908 2745 2 chr4B.!!$R7 837
17 TraesCS4A01G047300 chr3D 543683087 543686065 2978 True 721.000000 1107 87.934500 1 1743 2 chr3D.!!$R1 1742

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
456 868 0.261991 TCCTCTGAACTCGGGGCTAT 59.738 55.0 0.0 0.0 0.0 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2270 6077 0.111061 TGGCTCATCCAAGCACAGTT 59.889 50.0 0.0 0.0 43.21 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
44 46 5.249852 TCAACTTAAGTAATACAGTGGCCCT 59.750 40.000 8.92 0.00 0.00 5.19
55 57 2.242043 CAGTGGCCCTGAAGTGATTTT 58.758 47.619 14.21 0.00 44.49 1.82
66 68 5.530915 CCTGAAGTGATTTTTACTCCACACA 59.469 40.000 0.00 0.00 32.35 3.72
71 73 3.509575 TGATTTTTACTCCACACATGCCC 59.490 43.478 0.00 0.00 0.00 5.36
136 138 7.494952 AGCGGTATTAGTAAGAAAACTCATTCC 59.505 37.037 0.00 0.00 0.00 3.01
137 139 7.494952 GCGGTATTAGTAAGAAAACTCATTCCT 59.505 37.037 0.00 0.00 0.00 3.36
138 140 8.818057 CGGTATTAGTAAGAAAACTCATTCCTG 58.182 37.037 0.00 0.00 0.00 3.86
139 141 8.613482 GGTATTAGTAAGAAAACTCATTCCTGC 58.387 37.037 0.00 0.00 0.00 4.85
175 177 4.084287 AGATTTCAGTGTACCGGTAGTGA 58.916 43.478 16.41 15.21 0.00 3.41
180 182 5.357742 TCAGTGTACCGGTAGTGATAGTA 57.642 43.478 16.41 0.00 0.00 1.82
208 210 2.881734 TGGTGCAATGGGTTAATGTGA 58.118 42.857 0.00 0.00 0.00 3.58
271 273 9.739276 TCTAGAAGATTTTTCCTGCTTTTATCA 57.261 29.630 0.00 0.00 0.00 2.15
286 288 5.240403 GCTTTTATCAGGATAGCTTTGAGGG 59.760 44.000 0.00 0.00 0.00 4.30
333 524 8.154856 GGGTATTTTTCCTGCATCTACACTATA 58.845 37.037 0.00 0.00 0.00 1.31
430 841 6.183361 CCCCTTTTCAAGCTATAGAACCCTAT 60.183 42.308 3.21 0.00 38.95 2.57
447 858 5.844601 ACCCTATCTAGTTTCCTCTGAACT 58.155 41.667 0.00 0.00 40.28 3.01
456 868 0.261991 TCCTCTGAACTCGGGGCTAT 59.738 55.000 0.00 0.00 0.00 2.97
511 928 6.358974 TTCCTGATCATGACACTAAGACAA 57.641 37.500 0.00 0.00 0.00 3.18
512 929 6.358974 TCCTGATCATGACACTAAGACAAA 57.641 37.500 0.00 0.00 0.00 2.83
513 930 6.166279 TCCTGATCATGACACTAAGACAAAC 58.834 40.000 0.00 0.00 0.00 2.93
587 1028 4.618927 GCAAGTGCAAAAGGCTGATATGAA 60.619 41.667 0.00 0.00 45.15 2.57
649 1166 0.936600 ATTGCAAGCCAAAACGCAAC 59.063 45.000 4.94 0.00 46.21 4.17
660 1177 1.668101 AAACGCAACCGCCAAGGAAA 61.668 50.000 0.00 0.00 45.00 3.13
663 1180 1.006220 GCAACCGCCAAGGAAAAGG 60.006 57.895 0.00 0.00 45.00 3.11
699 1221 0.482446 ATTCAGACCCCCAAACAGCA 59.518 50.000 0.00 0.00 0.00 4.41
703 1225 2.676471 ACCCCCAAACAGCATCGC 60.676 61.111 0.00 0.00 0.00 4.58
794 2493 2.357952 CTCGGATTGTCGTCTGTGGATA 59.642 50.000 0.00 0.00 0.00 2.59
872 4438 2.143925 GCTCCTGCGTATATTTCCACC 58.856 52.381 0.00 0.00 0.00 4.61
903 4474 1.876664 GATCGATCCATCCGCTCGA 59.123 57.895 14.76 0.00 44.54 4.04
919 4490 3.391382 GACACCCACCTCCCCTCG 61.391 72.222 0.00 0.00 0.00 4.63
1063 4690 2.969806 GCCACCACGACGACGAGTA 61.970 63.158 15.32 0.00 42.66 2.59
1490 5143 3.027170 GTGCCAAGACGATGCACGG 62.027 63.158 12.18 0.00 44.95 4.94
1777 5467 1.815212 CGCCGCAGACAATGAGATCG 61.815 60.000 0.00 0.00 0.00 3.69
2038 5741 0.613260 ATGGTTTGCTGCTCCTCGTA 59.387 50.000 0.00 0.00 0.00 3.43
2081 5817 1.266989 CGAAAAGAAGGCACCAAGGAC 59.733 52.381 0.00 0.00 0.00 3.85
2221 6022 5.232414 GGATAAACTCTCGTGATGTAACTGC 59.768 44.000 0.00 0.00 0.00 4.40
2239 6046 1.963515 TGCGCTTGGATGAGCTATCTA 59.036 47.619 9.73 0.00 40.52 1.98
2240 6047 2.564504 TGCGCTTGGATGAGCTATCTAT 59.435 45.455 9.73 0.00 40.52 1.98
2241 6048 2.928757 GCGCTTGGATGAGCTATCTATG 59.071 50.000 0.00 0.00 40.52 2.23
2242 6049 3.616076 GCGCTTGGATGAGCTATCTATGT 60.616 47.826 0.00 0.00 40.52 2.29
2243 6050 4.380973 GCGCTTGGATGAGCTATCTATGTA 60.381 45.833 0.00 0.00 40.52 2.29
2244 6051 5.714047 CGCTTGGATGAGCTATCTATGTAA 58.286 41.667 0.00 0.00 40.52 2.41
2245 6052 6.159293 CGCTTGGATGAGCTATCTATGTAAA 58.841 40.000 0.00 0.00 40.52 2.01
2246 6053 6.815641 CGCTTGGATGAGCTATCTATGTAAAT 59.184 38.462 0.00 0.00 40.52 1.40
2247 6054 7.201504 CGCTTGGATGAGCTATCTATGTAAATG 60.202 40.741 0.00 0.00 40.52 2.32
2248 6055 7.413877 GCTTGGATGAGCTATCTATGTAAATGC 60.414 40.741 0.00 0.00 39.57 3.56
2249 6056 7.250032 TGGATGAGCTATCTATGTAAATGCT 57.750 36.000 0.00 0.00 36.03 3.79
2250 6057 8.366359 TGGATGAGCTATCTATGTAAATGCTA 57.634 34.615 0.00 0.00 36.03 3.49
2251 6058 8.473219 TGGATGAGCTATCTATGTAAATGCTAG 58.527 37.037 0.00 0.00 36.03 3.42
2252 6059 7.925483 GGATGAGCTATCTATGTAAATGCTAGG 59.075 40.741 0.00 0.00 36.03 3.02
2253 6060 8.601047 ATGAGCTATCTATGTAAATGCTAGGA 57.399 34.615 0.00 0.00 0.00 2.94
2254 6061 8.601047 TGAGCTATCTATGTAAATGCTAGGAT 57.399 34.615 0.00 0.00 0.00 3.24
2255 6062 9.700831 TGAGCTATCTATGTAAATGCTAGGATA 57.299 33.333 0.00 0.00 0.00 2.59
2263 6070 9.646427 CTATGTAAATGCTAGGATAAACTCTCC 57.354 37.037 0.00 0.00 0.00 3.71
2264 6071 7.432148 TGTAAATGCTAGGATAAACTCTCCA 57.568 36.000 0.00 0.00 35.08 3.86
2265 6072 7.500992 TGTAAATGCTAGGATAAACTCTCCAG 58.499 38.462 0.00 0.00 35.08 3.86
2266 6073 6.814954 AAATGCTAGGATAAACTCTCCAGA 57.185 37.500 0.00 0.00 35.08 3.86
2267 6074 7.385894 AAATGCTAGGATAAACTCTCCAGAT 57.614 36.000 0.00 0.00 35.08 2.90
2268 6075 5.798125 TGCTAGGATAAACTCTCCAGATG 57.202 43.478 0.00 0.00 35.08 2.90
2269 6076 5.211973 TGCTAGGATAAACTCTCCAGATGT 58.788 41.667 0.00 0.00 35.08 3.06
2270 6077 6.373759 TGCTAGGATAAACTCTCCAGATGTA 58.626 40.000 0.00 0.00 35.08 2.29
2271 6078 6.839134 TGCTAGGATAAACTCTCCAGATGTAA 59.161 38.462 0.00 0.00 35.08 2.41
2272 6079 7.149307 GCTAGGATAAACTCTCCAGATGTAAC 58.851 42.308 0.00 0.00 35.08 2.50
2273 6080 7.014808 GCTAGGATAAACTCTCCAGATGTAACT 59.985 40.741 0.00 0.00 35.08 2.24
2274 6081 7.118496 AGGATAAACTCTCCAGATGTAACTG 57.882 40.000 0.00 0.00 35.08 3.16
2275 6082 6.670027 AGGATAAACTCTCCAGATGTAACTGT 59.330 38.462 0.00 0.00 36.30 3.55
2276 6083 6.758886 GGATAAACTCTCCAGATGTAACTGTG 59.241 42.308 0.00 0.00 36.30 3.66
2277 6084 3.601443 ACTCTCCAGATGTAACTGTGC 57.399 47.619 0.00 0.00 36.30 4.57
2278 6085 3.169099 ACTCTCCAGATGTAACTGTGCT 58.831 45.455 0.00 0.00 36.30 4.40
2279 6086 3.580458 ACTCTCCAGATGTAACTGTGCTT 59.420 43.478 0.00 0.00 36.30 3.91
2280 6087 3.930336 TCTCCAGATGTAACTGTGCTTG 58.070 45.455 0.00 0.00 36.30 4.01
2281 6088 3.005554 CTCCAGATGTAACTGTGCTTGG 58.994 50.000 0.00 0.00 36.30 3.61
2304 6143 6.430283 GGATGAGCCATCAAGTAGAACTTGG 61.430 48.000 17.27 6.04 44.93 3.61
2315 6154 1.079405 GAACTTGGTCGCCGGATCA 60.079 57.895 5.05 0.00 0.00 2.92
2377 6232 5.523552 CCATTATGCACACGTTCAGAGAATA 59.476 40.000 0.00 0.00 0.00 1.75
2378 6233 6.414079 CATTATGCACACGTTCAGAGAATAC 58.586 40.000 0.00 0.00 0.00 1.89
2381 6236 2.341760 GCACACGTTCAGAGAATACGTC 59.658 50.000 0.00 0.00 45.67 4.34
2382 6237 3.561503 CACACGTTCAGAGAATACGTCA 58.438 45.455 0.00 0.00 45.67 4.35
2401 6256 6.602179 ACGTCAAGATGTGTAAATTGTGATG 58.398 36.000 0.00 0.00 0.00 3.07
2402 6257 6.204688 ACGTCAAGATGTGTAAATTGTGATGT 59.795 34.615 0.00 0.00 31.00 3.06
2403 6258 7.386573 ACGTCAAGATGTGTAAATTGTGATGTA 59.613 33.333 0.00 0.00 33.43 2.29
2418 6273 6.255596 TGTGATGTACTAGTGTTGAGAGAC 57.744 41.667 5.39 0.00 0.00 3.36
2425 6280 3.511934 ACTAGTGTTGAGAGACCCATCAC 59.488 47.826 0.00 0.00 35.55 3.06
2465 6334 7.118390 ACAGATGCTCAGTTGTTATTGAGTTAC 59.882 37.037 3.74 0.00 42.17 2.50
2522 6401 9.436957 AATCCGGAGTTGATGATAAATATGTAC 57.563 33.333 11.34 0.00 0.00 2.90
2523 6402 8.190326 TCCGGAGTTGATGATAAATATGTACT 57.810 34.615 0.00 0.00 0.00 2.73
2524 6403 8.088365 TCCGGAGTTGATGATAAATATGTACTG 58.912 37.037 0.00 0.00 0.00 2.74
2588 6471 7.537596 TGAATTGATGGTTAAAATGTCCTGT 57.462 32.000 0.00 0.00 0.00 4.00
2672 6567 5.527582 GGACTTGTTCATGTACTTCAGTGTT 59.472 40.000 4.01 0.00 0.00 3.32
2767 8365 7.289587 AGCGTGGTTTTATTTCAATATTTGC 57.710 32.000 0.00 0.00 0.00 3.68
2840 9386 8.203937 AGGAAGTATATCAGATCTTCGATACG 57.796 38.462 5.20 0.00 37.67 3.06
2876 9422 1.280421 AGACCTGCAGGGAGAATGAAC 59.720 52.381 35.42 14.44 40.27 3.18
2908 9454 5.930135 AGAGCTTAGTTCCTTTCAGTTCAA 58.070 37.500 0.00 0.00 0.00 2.69
2917 9463 6.547141 AGTTCCTTTCAGTTCAATCATGTTCA 59.453 34.615 0.00 0.00 0.00 3.18
2928 9474 8.649591 AGTTCAATCATGTTCATAGATAGAGCT 58.350 33.333 0.00 0.00 0.00 4.09
2931 9477 9.920133 TCAATCATGTTCATAGATAGAGCTAAC 57.080 33.333 0.00 0.00 0.00 2.34
2954 9500 1.210931 CTGCCCATTTGTGTCTGCG 59.789 57.895 0.00 0.00 0.00 5.18
2979 9525 0.033796 CCCCAGTCTCATTGGTGCAT 60.034 55.000 0.00 0.00 33.73 3.96
2992 9538 3.369242 TGGTGCATGGATGATCAGAAA 57.631 42.857 0.09 0.00 0.00 2.52
3001 9547 6.039493 GCATGGATGATCAGAAATTCAGAACT 59.961 38.462 0.09 0.00 0.00 3.01
3009 9555 9.239551 TGATCAGAAATTCAGAACTCAATCATT 57.760 29.630 0.00 0.00 0.00 2.57
3055 9601 5.643379 AACAACAAATATCGAAGTGGCAT 57.357 34.783 0.00 0.00 0.00 4.40
3064 9610 0.449388 CGAAGTGGCATGGAAGAAGC 59.551 55.000 0.00 0.00 0.00 3.86
3099 9645 1.202770 ACCGTTCCTCTCCAAACCTTG 60.203 52.381 0.00 0.00 0.00 3.61
3150 9696 1.841556 ACCTCTCCTCCGCCAACAA 60.842 57.895 0.00 0.00 0.00 2.83
3153 9699 1.373570 CTCTCCTCCGCCAACAATTC 58.626 55.000 0.00 0.00 0.00 2.17
3162 9708 1.794222 CCAACAATTCGCGACTCCC 59.206 57.895 9.15 0.00 0.00 4.30
3163 9709 0.673644 CCAACAATTCGCGACTCCCT 60.674 55.000 9.15 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 19 6.653740 GGCCACTGTATTACTTAAGTTGACTT 59.346 38.462 14.49 1.60 39.85 3.01
37 39 3.826729 AGTAAAAATCACTTCAGGGCCAC 59.173 43.478 6.18 0.00 0.00 5.01
44 46 6.514870 GCATGTGTGGAGTAAAAATCACTTCA 60.515 38.462 0.00 0.00 0.00 3.02
55 57 1.271871 CCAAGGGCATGTGTGGAGTAA 60.272 52.381 0.00 0.00 32.54 2.24
66 68 2.832643 TGATCATCAACCAAGGGCAT 57.167 45.000 0.00 0.00 0.00 4.40
71 73 4.074259 TGTGTCCTTGATCATCAACCAAG 58.926 43.478 0.00 0.00 37.58 3.61
114 116 8.613482 GGCAGGAATGAGTTTTCTTACTAATAC 58.387 37.037 0.00 0.00 0.00 1.89
136 138 1.975407 CTCCTTGTGGCCTTGGCAG 60.975 63.158 14.04 2.03 39.19 4.85
137 139 1.792757 ATCTCCTTGTGGCCTTGGCA 61.793 55.000 14.04 0.00 35.21 4.92
138 140 0.613012 AATCTCCTTGTGGCCTTGGC 60.613 55.000 3.32 2.49 0.00 4.52
139 141 1.821136 GAAATCTCCTTGTGGCCTTGG 59.179 52.381 3.32 0.48 0.00 3.61
175 177 4.402155 CCATTGCACCAACCATTGTACTAT 59.598 41.667 0.00 0.00 0.00 2.12
180 182 0.686224 CCCATTGCACCAACCATTGT 59.314 50.000 0.00 0.00 0.00 2.71
208 210 1.414919 TCACGTTGCCTCCTTAGTTGT 59.585 47.619 0.00 0.00 0.00 3.32
267 269 3.317406 TGCCCTCAAAGCTATCCTGATA 58.683 45.455 0.00 0.00 0.00 2.15
268 270 2.130193 TGCCCTCAAAGCTATCCTGAT 58.870 47.619 0.00 0.00 0.00 2.90
269 271 1.583556 TGCCCTCAAAGCTATCCTGA 58.416 50.000 0.00 0.00 0.00 3.86
270 272 2.295885 CTTGCCCTCAAAGCTATCCTG 58.704 52.381 0.00 0.00 0.00 3.86
271 273 1.918957 ACTTGCCCTCAAAGCTATCCT 59.081 47.619 0.00 0.00 0.00 3.24
272 274 2.092699 AGACTTGCCCTCAAAGCTATCC 60.093 50.000 0.00 0.00 0.00 2.59
273 275 2.941720 CAGACTTGCCCTCAAAGCTATC 59.058 50.000 0.00 0.00 0.00 2.08
274 276 2.573462 TCAGACTTGCCCTCAAAGCTAT 59.427 45.455 0.00 0.00 0.00 2.97
275 277 1.977854 TCAGACTTGCCCTCAAAGCTA 59.022 47.619 0.00 0.00 0.00 3.32
276 278 0.767375 TCAGACTTGCCCTCAAAGCT 59.233 50.000 0.00 0.00 0.00 3.74
279 281 3.072915 TGAAGATCAGACTTGCCCTCAAA 59.927 43.478 0.00 0.00 0.00 2.69
314 322 8.928448 AGATCTTTATAGTGTAGATGCAGGAAA 58.072 33.333 0.00 0.00 0.00 3.13
333 524 9.213799 GTGAACATCTAACTGAAGAAGATCTTT 57.786 33.333 9.87 0.00 36.73 2.52
352 543 4.224370 AGTTACAACCCGGATAGTGAACAT 59.776 41.667 0.73 0.00 0.00 2.71
430 841 3.090037 CCCGAGTTCAGAGGAAACTAGA 58.910 50.000 0.00 0.00 44.43 2.43
447 858 2.297701 GATTGCAAGAAATAGCCCCGA 58.702 47.619 4.94 0.00 0.00 5.14
456 868 3.401033 TCAGAGTCGGATTGCAAGAAA 57.599 42.857 4.94 0.00 0.00 2.52
542 959 7.888250 TGCCCATCACAATGTAATGTAATAA 57.112 32.000 0.00 0.00 30.84 1.40
543 960 7.559533 ACTTGCCCATCACAATGTAATGTAATA 59.440 33.333 0.00 0.00 30.84 0.98
544 961 6.380846 ACTTGCCCATCACAATGTAATGTAAT 59.619 34.615 0.00 0.00 30.84 1.89
545 962 5.714333 ACTTGCCCATCACAATGTAATGTAA 59.286 36.000 0.00 0.00 30.84 2.41
546 963 5.125257 CACTTGCCCATCACAATGTAATGTA 59.875 40.000 0.00 0.00 30.84 2.29
547 964 4.082081 CACTTGCCCATCACAATGTAATGT 60.082 41.667 0.00 0.00 0.00 2.71
548 965 4.426416 CACTTGCCCATCACAATGTAATG 58.574 43.478 0.00 0.00 0.00 1.90
549 966 3.119029 GCACTTGCCCATCACAATGTAAT 60.119 43.478 0.00 0.00 34.31 1.89
587 1028 4.207165 CCATGATTACATTTCCCTTCGGT 58.793 43.478 0.00 0.00 34.15 4.69
603 1044 3.931907 TTCCCAATCGAGAACCATGAT 57.068 42.857 0.00 0.00 0.00 2.45
604 1045 3.808728 GATTCCCAATCGAGAACCATGA 58.191 45.455 0.00 0.00 0.00 3.07
649 1166 1.616159 TTCTTCCTTTTCCTTGGCGG 58.384 50.000 0.00 0.00 0.00 6.13
676 1198 1.780309 TGTTTGGGGGTCTGAATGTCT 59.220 47.619 0.00 0.00 0.00 3.41
677 1199 2.162681 CTGTTTGGGGGTCTGAATGTC 58.837 52.381 0.00 0.00 0.00 3.06
678 1200 1.823250 GCTGTTTGGGGGTCTGAATGT 60.823 52.381 0.00 0.00 0.00 2.71
679 1201 0.890683 GCTGTTTGGGGGTCTGAATG 59.109 55.000 0.00 0.00 0.00 2.67
680 1202 0.482446 TGCTGTTTGGGGGTCTGAAT 59.518 50.000 0.00 0.00 0.00 2.57
681 1203 0.482446 ATGCTGTTTGGGGGTCTGAA 59.518 50.000 0.00 0.00 0.00 3.02
683 1205 1.308069 CGATGCTGTTTGGGGGTCTG 61.308 60.000 0.00 0.00 0.00 3.51
684 1206 1.002134 CGATGCTGTTTGGGGGTCT 60.002 57.895 0.00 0.00 0.00 3.85
685 1207 2.700773 GCGATGCTGTTTGGGGGTC 61.701 63.158 0.00 0.00 0.00 4.46
686 1208 2.676471 GCGATGCTGTTTGGGGGT 60.676 61.111 0.00 0.00 0.00 4.95
687 1209 3.814268 CGCGATGCTGTTTGGGGG 61.814 66.667 0.00 0.00 0.00 5.40
688 1210 3.039202 GACGCGATGCTGTTTGGGG 62.039 63.158 15.93 0.00 0.00 4.96
699 1221 0.456824 CTGTGTACAGCAGACGCGAT 60.457 55.000 15.93 0.00 45.49 4.58
710 1232 1.080366 CGCCGGTTAGCTGTGTACA 60.080 57.895 1.90 0.00 0.00 2.90
713 1236 3.530910 AAGCGCCGGTTAGCTGTGT 62.531 57.895 18.96 4.26 43.78 3.72
785 2483 0.952280 GGCGATCGAGTATCCACAGA 59.048 55.000 21.57 0.00 0.00 3.41
903 4474 4.250170 ACGAGGGGAGGTGGGTGT 62.250 66.667 0.00 0.00 0.00 4.16
1041 4665 4.634133 GTCGTCGTGGTGGCGTGA 62.634 66.667 0.00 0.00 0.00 4.35
1060 4684 0.098376 GACGCCGACGATTGTCTACT 59.902 55.000 11.37 0.00 43.21 2.57
1061 4685 0.864797 GGACGCCGACGATTGTCTAC 60.865 60.000 11.37 2.26 43.21 2.59
1063 4690 2.181021 GGACGCCGACGATTGTCT 59.819 61.111 11.37 0.00 43.21 3.41
1079 4706 4.399395 TGCGGCTCCTCTTGCAGG 62.399 66.667 0.00 0.00 45.15 4.85
1897 5600 1.166531 AACAGTTCCCGCAGCTTGTC 61.167 55.000 0.00 0.00 0.00 3.18
1944 5647 1.363807 GCCTTGCAACACCTGGAAC 59.636 57.895 0.00 0.00 31.22 3.62
2081 5817 2.824041 CCGGCGGGATGAACTTGG 60.824 66.667 20.56 0.00 34.06 3.61
2174 5916 5.641209 CCTAGCATTTACATAGATGGCTCAC 59.359 44.000 0.00 0.00 0.00 3.51
2239 6046 8.034313 TGGAGAGTTTATCCTAGCATTTACAT 57.966 34.615 0.00 0.00 37.74 2.29
2240 6047 7.344612 TCTGGAGAGTTTATCCTAGCATTTACA 59.655 37.037 0.00 0.00 37.74 2.41
2241 6048 7.727181 TCTGGAGAGTTTATCCTAGCATTTAC 58.273 38.462 0.00 0.00 37.74 2.01
2242 6049 7.914427 TCTGGAGAGTTTATCCTAGCATTTA 57.086 36.000 0.00 0.00 37.74 1.40
2243 6050 6.814954 TCTGGAGAGTTTATCCTAGCATTT 57.185 37.500 0.00 0.00 37.74 2.32
2244 6051 6.328672 ACATCTGGAGAGTTTATCCTAGCATT 59.671 38.462 0.00 0.00 37.74 3.56
2245 6052 5.843421 ACATCTGGAGAGTTTATCCTAGCAT 59.157 40.000 0.00 0.00 37.74 3.79
2246 6053 5.211973 ACATCTGGAGAGTTTATCCTAGCA 58.788 41.667 0.00 0.00 37.74 3.49
2247 6054 5.799827 ACATCTGGAGAGTTTATCCTAGC 57.200 43.478 0.00 0.00 37.74 3.42
2248 6055 8.356657 CAGTTACATCTGGAGAGTTTATCCTAG 58.643 40.741 0.00 0.00 37.74 3.02
2249 6056 7.839705 ACAGTTACATCTGGAGAGTTTATCCTA 59.160 37.037 0.00 0.00 39.48 2.94
2250 6057 6.670027 ACAGTTACATCTGGAGAGTTTATCCT 59.330 38.462 0.00 0.00 39.48 3.24
2251 6058 6.758886 CACAGTTACATCTGGAGAGTTTATCC 59.241 42.308 0.00 0.00 39.48 2.59
2252 6059 6.256757 GCACAGTTACATCTGGAGAGTTTATC 59.743 42.308 0.00 0.00 39.48 1.75
2253 6060 6.070538 AGCACAGTTACATCTGGAGAGTTTAT 60.071 38.462 0.00 0.00 39.48 1.40
2254 6061 5.246203 AGCACAGTTACATCTGGAGAGTTTA 59.754 40.000 0.00 0.00 39.48 2.01
2255 6062 4.040952 AGCACAGTTACATCTGGAGAGTTT 59.959 41.667 0.00 0.00 39.48 2.66
2256 6063 3.580458 AGCACAGTTACATCTGGAGAGTT 59.420 43.478 0.00 0.00 39.48 3.01
2257 6064 3.169099 AGCACAGTTACATCTGGAGAGT 58.831 45.455 0.00 0.00 39.48 3.24
2258 6065 3.883830 AGCACAGTTACATCTGGAGAG 57.116 47.619 0.00 0.00 39.48 3.20
2259 6066 3.306989 CCAAGCACAGTTACATCTGGAGA 60.307 47.826 0.00 0.00 39.48 3.71
2260 6067 3.005554 CCAAGCACAGTTACATCTGGAG 58.994 50.000 0.00 0.00 39.48 3.86
2261 6068 2.637382 TCCAAGCACAGTTACATCTGGA 59.363 45.455 0.00 0.00 39.48 3.86
2262 6069 3.057969 TCCAAGCACAGTTACATCTGG 57.942 47.619 0.00 0.00 39.48 3.86
2263 6070 4.256110 TCATCCAAGCACAGTTACATCTG 58.744 43.478 0.00 0.00 40.80 2.90
2264 6071 4.511527 CTCATCCAAGCACAGTTACATCT 58.488 43.478 0.00 0.00 0.00 2.90
2265 6072 3.064545 GCTCATCCAAGCACAGTTACATC 59.935 47.826 0.00 0.00 42.05 3.06
2266 6073 3.012518 GCTCATCCAAGCACAGTTACAT 58.987 45.455 0.00 0.00 42.05 2.29
2267 6074 2.426522 GCTCATCCAAGCACAGTTACA 58.573 47.619 0.00 0.00 42.05 2.41
2268 6075 1.740025 GGCTCATCCAAGCACAGTTAC 59.260 52.381 0.00 0.00 44.35 2.50
2269 6076 1.350684 TGGCTCATCCAAGCACAGTTA 59.649 47.619 0.00 0.00 43.21 2.24
2270 6077 0.111061 TGGCTCATCCAAGCACAGTT 59.889 50.000 0.00 0.00 43.21 3.16
2271 6078 1.763120 TGGCTCATCCAAGCACAGT 59.237 52.632 0.00 0.00 43.21 3.55
2272 6079 4.728409 TGGCTCATCCAAGCACAG 57.272 55.556 0.00 0.00 43.21 3.66
2277 6084 7.078215 AAGTTCTACTTGATGGCTCATCCAAG 61.078 42.308 11.25 14.32 42.07 3.61
2278 6085 5.280676 AAGTTCTACTTGATGGCTCATCCAA 60.281 40.000 11.25 6.40 42.07 3.53
2279 6086 4.225942 AAGTTCTACTTGATGGCTCATCCA 59.774 41.667 11.25 2.00 42.61 3.41
2280 6087 4.414337 AGTTCTACTTGATGGCTCATCC 57.586 45.455 11.25 0.00 39.87 3.51
2304 6143 0.600255 CTAATGGGTGATCCGGCGAC 60.600 60.000 9.30 0.00 38.76 5.19
2315 6154 0.611896 GCAGGCCAACACTAATGGGT 60.612 55.000 5.01 0.00 38.44 4.51
2377 6232 6.204688 ACATCACAATTTACACATCTTGACGT 59.795 34.615 0.00 0.00 0.00 4.34
2378 6233 6.602179 ACATCACAATTTACACATCTTGACG 58.398 36.000 0.00 0.00 0.00 4.35
2380 6235 8.846943 AGTACATCACAATTTACACATCTTGA 57.153 30.769 0.00 0.00 0.00 3.02
2382 6237 9.944376 ACTAGTACATCACAATTTACACATCTT 57.056 29.630 0.00 0.00 0.00 2.40
2401 6256 4.705507 TGATGGGTCTCTCAACACTAGTAC 59.294 45.833 0.00 0.00 0.00 2.73
2402 6257 4.705507 GTGATGGGTCTCTCAACACTAGTA 59.294 45.833 0.00 0.00 35.79 1.82
2403 6258 3.511934 GTGATGGGTCTCTCAACACTAGT 59.488 47.826 3.41 0.00 35.79 2.57
2418 6273 1.321474 AACAACAGCACTGTGATGGG 58.679 50.000 27.30 20.85 44.13 4.00
2465 6334 2.124011 AACGCACAAATTGAGCACTG 57.876 45.000 15.07 2.29 33.49 3.66
2490 6361 4.027674 TCATCAACTCCGGATTTTGGAA 57.972 40.909 20.42 7.61 34.44 3.53
2491 6362 3.712016 TCATCAACTCCGGATTTTGGA 57.288 42.857 20.42 10.50 0.00 3.53
2492 6363 6.449635 TTTATCATCAACTCCGGATTTTGG 57.550 37.500 20.42 6.16 0.00 3.28
2522 6401 6.204688 TCTGTTGCTTAGAACATTTGTACCAG 59.795 38.462 0.00 0.00 35.32 4.00
2523 6402 6.058833 TCTGTTGCTTAGAACATTTGTACCA 58.941 36.000 0.00 0.00 35.32 3.25
2524 6403 6.554334 TCTGTTGCTTAGAACATTTGTACC 57.446 37.500 0.00 0.00 35.32 3.34
2588 6471 3.954200 TCATGAAATCTGCACCAGCTAA 58.046 40.909 0.00 0.00 42.74 3.09
2767 8365 6.814644 TCGAATATAAGTGGTGTGGTTTAGTG 59.185 38.462 0.00 0.00 0.00 2.74
2824 8425 5.974158 CAGTTTGACGTATCGAAGATCTGAT 59.026 40.000 0.00 0.00 45.12 2.90
2840 9386 3.561725 CAGGTCTTCTTCCACAGTTTGAC 59.438 47.826 0.00 0.00 0.00 3.18
2876 9422 6.581171 AAGGAACTAAGCTCTTGAATTTGG 57.419 37.500 0.00 0.00 38.49 3.28
2908 9454 9.872721 CATGTTAGCTCTATCTATGAACATGAT 57.127 33.333 20.77 0.00 44.37 2.45
2917 9463 4.081198 GGCAGCCATGTTAGCTCTATCTAT 60.081 45.833 6.55 0.00 38.95 1.98
2928 9474 1.549620 CACAAATGGGCAGCCATGTTA 59.450 47.619 15.19 0.00 0.00 2.41
2931 9477 0.108520 GACACAAATGGGCAGCCATG 60.109 55.000 15.19 8.92 0.00 3.66
2944 9490 1.891919 GGGCTTCACGCAGACACAA 60.892 57.895 0.00 0.00 41.67 3.33
2954 9500 1.457346 CAATGAGACTGGGGCTTCAC 58.543 55.000 0.00 0.00 0.00 3.18
2979 9525 6.714278 TGAGTTCTGAATTTCTGATCATCCA 58.286 36.000 13.53 7.81 0.00 3.41
3036 9582 4.269183 TCCATGCCACTTCGATATTTGTT 58.731 39.130 0.00 0.00 0.00 2.83
3055 9601 2.557452 GGGAAAAGGATGGCTTCTTCCA 60.557 50.000 16.59 0.00 40.97 3.53
3064 9610 0.251608 ACGGTTGGGGAAAAGGATGG 60.252 55.000 0.00 0.00 0.00 3.51
3099 9645 1.202580 CGTCCATGAATCACCTCTCCC 60.203 57.143 0.00 0.00 0.00 4.30
3107 9653 1.289276 CACGATGCGTCCATGAATCA 58.711 50.000 0.00 0.00 38.32 2.57
3127 9673 3.775654 GCGGAGGAGAGGTGGTGG 61.776 72.222 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.