Multiple sequence alignment - TraesCS5D01G059000

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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 TraesCS5D01G059000 chr5D 100.000 1935 0 0 444 2378 55921360 55919426 0.000000e+00 3574.0
1 TraesCS5D01G059000 chr5D 100.000 155 0 0 1 155 55921803 55921649 1.080000e-73 287.0
2 TraesCS5D01G059000 chr5B 93.532 1005 60 4 444 1444 678343807 678342804 0.000000e+00 1491.0
3 TraesCS5D01G059000 chr5B 94.465 795 38 4 1443 2231 58674015 58673221 0.000000e+00 1219.0
4 TraesCS5D01G059000 chr5B 92.258 155 12 0 1 155 678343992 678343838 1.110000e-53 220.0
5 TraesCS5D01G059000 chr5B 90.566 53 4 1 1670 1721 58703790 58703738 4.240000e-08 69.4
6 TraesCS5D01G059000 chr7B 92.644 1006 69 4 444 1445 640870542 640869538 0.000000e+00 1443.0
7 TraesCS5D01G059000 chr7B 93.548 155 10 0 1 155 640870727 640870573 5.110000e-57 231.0
8 TraesCS5D01G059000 chr3B 92.705 987 65 6 466 1446 700076438 700075453 0.000000e+00 1417.0
9 TraesCS5D01G059000 chr6B 91.865 1008 76 5 444 1446 653090545 653091551 0.000000e+00 1402.0
10 TraesCS5D01G059000 chr6B 92.258 155 12 0 1 155 653090361 653090515 1.110000e-53 220.0
11 TraesCS5D01G059000 chr6B 84.559 136 21 0 1 136 544544332 544544467 4.120000e-28 135.0
12 TraesCS5D01G059000 chr2B 92.865 967 63 5 486 1448 790632598 790631634 0.000000e+00 1399.0
13 TraesCS5D01G059000 chr2A 90.120 1002 92 6 445 1441 166824087 166825086 0.000000e+00 1295.0
14 TraesCS5D01G059000 chr2A 90.323 155 15 0 1 155 166823901 166824055 1.110000e-48 204.0
15 TraesCS5D01G059000 chr7A 90.020 1002 95 4 445 1442 57117128 57116128 0.000000e+00 1291.0
16 TraesCS5D01G059000 chr7A 89.601 952 78 8 444 1391 535413323 535412389 0.000000e+00 1190.0
17 TraesCS5D01G059000 chr7A 92.903 155 11 0 1 155 535413508 535413354 2.380000e-55 226.0
18 TraesCS5D01G059000 chr7A 90.323 155 15 0 1 155 57125971 57125817 1.110000e-48 204.0
19 TraesCS5D01G059000 chr3D 93.072 765 51 1 444 1206 613063614 613064378 0.000000e+00 1118.0
20 TraesCS5D01G059000 chr5A 95.726 468 14 2 1443 1909 44893986 44893524 0.000000e+00 749.0
21 TraesCS5D01G059000 chr5A 94.328 476 25 2 1896 2370 44885860 44885386 0.000000e+00 728.0
22 TraesCS5D01G059000 chr5A 90.566 53 4 1 1670 1721 44932855 44932803 4.240000e-08 69.4
23 TraesCS5D01G059000 chr4B 95.973 149 6 0 1 149 517373987 517374135 2.360000e-60 243.0
24 TraesCS5D01G059000 chr2D 86.452 155 21 0 1 155 27822560 27822406 1.130000e-38 171.0


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 TraesCS5D01G059000 chr5D 55919426 55921803 2377 True 1930.5 3574 100.0000 1 2378 2 chr5D.!!$R1 2377
1 TraesCS5D01G059000 chr5B 58673221 58674015 794 True 1219.0 1219 94.4650 1443 2231 1 chr5B.!!$R1 788
2 TraesCS5D01G059000 chr5B 678342804 678343992 1188 True 855.5 1491 92.8950 1 1444 2 chr5B.!!$R3 1443
3 TraesCS5D01G059000 chr7B 640869538 640870727 1189 True 837.0 1443 93.0960 1 1445 2 chr7B.!!$R1 1444
4 TraesCS5D01G059000 chr3B 700075453 700076438 985 True 1417.0 1417 92.7050 466 1446 1 chr3B.!!$R1 980
5 TraesCS5D01G059000 chr6B 653090361 653091551 1190 False 811.0 1402 92.0615 1 1446 2 chr6B.!!$F2 1445
6 TraesCS5D01G059000 chr2B 790631634 790632598 964 True 1399.0 1399 92.8650 486 1448 1 chr2B.!!$R1 962
7 TraesCS5D01G059000 chr2A 166823901 166825086 1185 False 749.5 1295 90.2215 1 1441 2 chr2A.!!$F1 1440
8 TraesCS5D01G059000 chr7A 57116128 57117128 1000 True 1291.0 1291 90.0200 445 1442 1 chr7A.!!$R1 997
9 TraesCS5D01G059000 chr7A 535412389 535413508 1119 True 708.0 1190 91.2520 1 1391 2 chr7A.!!$R3 1390
10 TraesCS5D01G059000 chr3D 613063614 613064378 764 False 1118.0 1118 93.0720 444 1206 1 chr3D.!!$F1 762

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
573 574 0.51079 TGCGTTACTCGTGTGCATTG 59.489 50.0 0.0 0.0 42.13 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 1981 0.034059 CCTTGAGGCGTGAGAGTTGT 59.966 55.0 0.0 0.0 0.0 3.32 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
19 20 2.063015 TTGTGTCGTGGCCTTGGGAT 62.063 55.000 3.32 0.00 0.00 3.85
69 70 4.040217 TGCCTACCATTTTGCAATGACTTT 59.960 37.500 0.00 0.00 42.35 2.66
142 143 1.870580 CGACCGTTGTGGAAGCTTGTA 60.871 52.381 2.10 0.00 42.00 2.41
149 150 3.334583 TGTGGAAGCTTGTATGGTCTC 57.665 47.619 2.10 0.00 0.00 3.36
571 572 0.721154 CATGCGTTACTCGTGTGCAT 59.279 50.000 7.78 7.78 46.43 3.96
573 574 0.510790 TGCGTTACTCGTGTGCATTG 59.489 50.000 0.00 0.00 42.13 2.82
643 646 5.221441 CCCAGAACAGATATTCCATGTACGA 60.221 44.000 0.00 0.00 0.00 3.43
645 648 5.923114 CAGAACAGATATTCCATGTACGAGG 59.077 44.000 0.00 0.00 0.00 4.63
646 649 4.258702 ACAGATATTCCATGTACGAGGC 57.741 45.455 0.00 0.00 0.00 4.70
757 760 5.163854 CGGAATGAACTCACTCATGGTAAAC 60.164 44.000 0.00 0.00 36.16 2.01
795 798 1.188219 TCTCCTGCTCGTTCTTGGCT 61.188 55.000 0.00 0.00 0.00 4.75
892 895 3.373565 CTTCGCAAAGGCCCCCAC 61.374 66.667 0.00 0.00 36.38 4.61
963 966 0.973632 TGGCGTTGTCAGTAGATGGT 59.026 50.000 0.00 0.00 0.00 3.55
1200 1203 1.284785 GGGGATGGTTCATTGGACAGA 59.715 52.381 0.00 0.00 0.00 3.41
1206 1209 0.652592 GTTCATTGGACAGATCGGCG 59.347 55.000 0.00 0.00 0.00 6.46
1218 1221 0.814010 GATCGGCGTATGGGCACTTT 60.814 55.000 6.85 0.00 42.43 2.66
1238 1241 6.483307 CACTTTGTGTCAGAGATCAAAAGGTA 59.517 38.462 0.00 0.00 31.07 3.08
1255 1258 8.112822 TCAAAAGGTATTTGAATGATAGGGTGA 58.887 33.333 1.38 0.00 35.69 4.02
1527 1532 7.798596 ATCACATGCTGGTTAGAATTAAGAG 57.201 36.000 0.00 0.00 0.00 2.85
1561 1566 6.864685 TGATGAAGAACTCATGCAATTTTGAC 59.135 34.615 0.00 0.00 45.23 3.18
1584 1589 6.398095 ACTCGTACACATCTTCAATCAATCA 58.602 36.000 0.00 0.00 0.00 2.57
1587 1592 6.090763 TCGTACACATCTTCAATCAATCACAC 59.909 38.462 0.00 0.00 0.00 3.82
1597 1602 4.688879 TCAATCAATCACACGAGTTACCAC 59.311 41.667 0.00 0.00 0.00 4.16
1607 1612 3.498397 CACGAGTTACCACTGCTTCAAAT 59.502 43.478 0.00 0.00 31.22 2.32
1739 1744 8.668510 TGTAGAAAGAAGGAAATATGAGATGC 57.331 34.615 0.00 0.00 0.00 3.91
1742 1747 4.077300 AGAAGGAAATATGAGATGCGCA 57.923 40.909 14.96 14.96 0.00 6.09
1767 1773 4.174305 GGGATTGTAATGCCCCCG 57.826 61.111 3.98 0.00 40.66 5.73
1881 1888 5.248705 AGAGAAGGAGATACGGGAAAAGTTT 59.751 40.000 0.00 0.00 0.00 2.66
1886 1893 7.012661 AGGAGATACGGGAAAAGTTTCTTTA 57.987 36.000 3.92 0.00 37.35 1.85
1925 1932 4.928661 ATACTGCTTACAACTCTTTGCG 57.071 40.909 0.00 0.00 36.00 4.85
1941 1948 0.254462 TGCGCTTATCCCCATCACAA 59.746 50.000 9.73 0.00 0.00 3.33
1969 1980 3.231160 GCCACACATTAACTTAACGCAC 58.769 45.455 0.00 0.00 0.00 5.34
1970 1981 3.304123 GCCACACATTAACTTAACGCACA 60.304 43.478 0.00 0.00 0.00 4.57
1982 1993 1.762222 AACGCACACAACTCTCACGC 61.762 55.000 0.00 0.00 0.00 5.34
2027 2038 2.362369 ACAGCGGAGGACCCATCTG 61.362 63.158 0.00 0.00 39.59 2.90
2034 2045 1.270907 GAGGACCCATCTGTCAGTGT 58.729 55.000 0.00 0.00 36.97 3.55
2035 2046 1.205893 GAGGACCCATCTGTCAGTGTC 59.794 57.143 0.00 3.42 36.97 3.67
2110 2121 7.836183 ACTAAGAAATGAAGGCAAAGGATACAT 59.164 33.333 0.00 0.00 41.41 2.29
2112 2123 7.814264 AGAAATGAAGGCAAAGGATACATAG 57.186 36.000 0.00 0.00 41.41 2.23
2118 2129 6.385759 TGAAGGCAAAGGATACATAGGAGTAA 59.614 38.462 0.00 0.00 41.41 2.24
2123 2134 8.763601 GGCAAAGGATACATAGGAGTAAGATAT 58.236 37.037 0.00 0.00 41.41 1.63
2144 2155 0.475475 TATTCCCGGCGTCTCCTAGA 59.525 55.000 6.01 0.00 0.00 2.43
2161 2172 4.954826 TCCTAGACCTACTTTAGTGAAGCC 59.045 45.833 0.00 0.00 39.04 4.35
2204 2215 0.318275 GAGCAGGCTCCGTAGAATCG 60.318 60.000 10.15 0.00 37.11 3.34
2222 2233 4.955811 ATCGGGTAGCAATATCACTTGA 57.044 40.909 0.00 0.00 0.00 3.02
2231 2242 5.899299 AGCAATATCACTTGATTGGCTTTC 58.101 37.500 0.00 0.00 33.36 2.62
2232 2243 5.655532 AGCAATATCACTTGATTGGCTTTCT 59.344 36.000 0.00 0.00 33.36 2.52
2233 2244 5.975939 GCAATATCACTTGATTGGCTTTCTC 59.024 40.000 0.00 0.00 36.05 2.87
2234 2245 6.501781 CAATATCACTTGATTGGCTTTCTCC 58.498 40.000 0.00 0.00 36.05 3.71
2235 2246 3.795688 TCACTTGATTGGCTTTCTCCT 57.204 42.857 0.00 0.00 0.00 3.69
2236 2247 4.104383 TCACTTGATTGGCTTTCTCCTT 57.896 40.909 0.00 0.00 0.00 3.36
2237 2248 4.074970 TCACTTGATTGGCTTTCTCCTTC 58.925 43.478 0.00 0.00 0.00 3.46
2238 2249 3.077359 ACTTGATTGGCTTTCTCCTTCG 58.923 45.455 0.00 0.00 0.00 3.79
2239 2250 2.859165 TGATTGGCTTTCTCCTTCGT 57.141 45.000 0.00 0.00 0.00 3.85
2240 2251 2.699954 TGATTGGCTTTCTCCTTCGTC 58.300 47.619 0.00 0.00 0.00 4.20
2241 2252 2.303022 TGATTGGCTTTCTCCTTCGTCT 59.697 45.455 0.00 0.00 0.00 4.18
2242 2253 2.169832 TTGGCTTTCTCCTTCGTCTG 57.830 50.000 0.00 0.00 0.00 3.51
2243 2254 0.320771 TGGCTTTCTCCTTCGTCTGC 60.321 55.000 0.00 0.00 0.00 4.26
2244 2255 0.036858 GGCTTTCTCCTTCGTCTGCT 60.037 55.000 0.00 0.00 0.00 4.24
2245 2256 1.355005 GCTTTCTCCTTCGTCTGCTC 58.645 55.000 0.00 0.00 0.00 4.26
2246 2257 1.067213 GCTTTCTCCTTCGTCTGCTCT 60.067 52.381 0.00 0.00 0.00 4.09
2247 2258 2.611722 GCTTTCTCCTTCGTCTGCTCTT 60.612 50.000 0.00 0.00 0.00 2.85
2248 2259 3.658709 CTTTCTCCTTCGTCTGCTCTTT 58.341 45.455 0.00 0.00 0.00 2.52
2249 2260 3.753294 TTCTCCTTCGTCTGCTCTTTT 57.247 42.857 0.00 0.00 0.00 2.27
2250 2261 4.866508 TTCTCCTTCGTCTGCTCTTTTA 57.133 40.909 0.00 0.00 0.00 1.52
2251 2262 5.407407 TTCTCCTTCGTCTGCTCTTTTAT 57.593 39.130 0.00 0.00 0.00 1.40
2252 2263 6.525578 TTCTCCTTCGTCTGCTCTTTTATA 57.474 37.500 0.00 0.00 0.00 0.98
2253 2264 5.892568 TCTCCTTCGTCTGCTCTTTTATAC 58.107 41.667 0.00 0.00 0.00 1.47
2254 2265 5.652891 TCTCCTTCGTCTGCTCTTTTATACT 59.347 40.000 0.00 0.00 0.00 2.12
2255 2266 6.827251 TCTCCTTCGTCTGCTCTTTTATACTA 59.173 38.462 0.00 0.00 0.00 1.82
2256 2267 7.502895 TCTCCTTCGTCTGCTCTTTTATACTAT 59.497 37.037 0.00 0.00 0.00 2.12
2257 2268 7.649973 TCCTTCGTCTGCTCTTTTATACTATC 58.350 38.462 0.00 0.00 0.00 2.08
2258 2269 7.284716 TCCTTCGTCTGCTCTTTTATACTATCA 59.715 37.037 0.00 0.00 0.00 2.15
2259 2270 7.380065 CCTTCGTCTGCTCTTTTATACTATCAC 59.620 40.741 0.00 0.00 0.00 3.06
2260 2271 7.329588 TCGTCTGCTCTTTTATACTATCACA 57.670 36.000 0.00 0.00 0.00 3.58
2261 2272 7.941919 TCGTCTGCTCTTTTATACTATCACAT 58.058 34.615 0.00 0.00 0.00 3.21
2262 2273 9.063615 TCGTCTGCTCTTTTATACTATCACATA 57.936 33.333 0.00 0.00 0.00 2.29
2263 2274 9.335891 CGTCTGCTCTTTTATACTATCACATAG 57.664 37.037 0.00 0.00 38.81 2.23
2264 2275 9.632807 GTCTGCTCTTTTATACTATCACATAGG 57.367 37.037 0.00 0.00 37.18 2.57
2265 2276 9.368416 TCTGCTCTTTTATACTATCACATAGGT 57.632 33.333 0.00 0.00 37.18 3.08
2266 2277 9.988815 CTGCTCTTTTATACTATCACATAGGTT 57.011 33.333 0.00 0.00 37.18 3.50
2267 2278 9.982651 TGCTCTTTTATACTATCACATAGGTTC 57.017 33.333 0.00 0.00 37.18 3.62
2268 2279 9.982651 GCTCTTTTATACTATCACATAGGTTCA 57.017 33.333 0.00 0.00 37.18 3.18
2278 2289 9.373450 ACTATCACATAGGTTCATGTCTTATCT 57.627 33.333 0.00 0.00 37.02 1.98
2281 2292 8.996651 TCACATAGGTTCATGTCTTATCTAGA 57.003 34.615 0.00 0.00 37.02 2.43
2282 2293 9.593565 TCACATAGGTTCATGTCTTATCTAGAT 57.406 33.333 10.73 10.73 37.02 1.98
2285 2296 9.868277 CATAGGTTCATGTCTTATCTAGATTCC 57.132 37.037 11.25 0.00 34.79 3.01
2286 2297 7.921041 AGGTTCATGTCTTATCTAGATTCCA 57.079 36.000 11.25 3.42 34.79 3.53
2287 2298 7.961351 AGGTTCATGTCTTATCTAGATTCCAG 58.039 38.462 11.25 5.34 34.79 3.86
2288 2299 7.566879 AGGTTCATGTCTTATCTAGATTCCAGT 59.433 37.037 11.25 0.00 34.79 4.00
2289 2300 7.655328 GGTTCATGTCTTATCTAGATTCCAGTG 59.345 40.741 11.25 4.28 34.79 3.66
2290 2301 8.417106 GTTCATGTCTTATCTAGATTCCAGTGA 58.583 37.037 11.25 6.45 34.79 3.41
2291 2302 8.718158 TCATGTCTTATCTAGATTCCAGTGAT 57.282 34.615 11.25 0.30 34.79 3.06
2292 2303 9.813826 TCATGTCTTATCTAGATTCCAGTGATA 57.186 33.333 11.25 0.47 34.79 2.15
2301 2312 9.911788 ATCTAGATTCCAGTGATAATTTGTTGT 57.088 29.630 0.00 0.00 0.00 3.32
2302 2313 9.739276 TCTAGATTCCAGTGATAATTTGTTGTT 57.261 29.630 0.00 0.00 0.00 2.83
2303 2314 9.778993 CTAGATTCCAGTGATAATTTGTTGTTG 57.221 33.333 0.00 0.00 0.00 3.33
2304 2315 8.408043 AGATTCCAGTGATAATTTGTTGTTGA 57.592 30.769 0.00 0.00 0.00 3.18
2305 2316 8.299570 AGATTCCAGTGATAATTTGTTGTTGAC 58.700 33.333 0.00 0.00 0.00 3.18
2306 2317 6.325919 TCCAGTGATAATTTGTTGTTGACC 57.674 37.500 0.00 0.00 0.00 4.02
2307 2318 6.068010 TCCAGTGATAATTTGTTGTTGACCT 58.932 36.000 0.00 0.00 0.00 3.85
2308 2319 7.227873 TCCAGTGATAATTTGTTGTTGACCTA 58.772 34.615 0.00 0.00 0.00 3.08
2309 2320 7.174253 TCCAGTGATAATTTGTTGTTGACCTAC 59.826 37.037 0.00 0.00 0.00 3.18
2310 2321 7.174946 CCAGTGATAATTTGTTGTTGACCTACT 59.825 37.037 0.00 0.00 0.00 2.57
2311 2322 9.214957 CAGTGATAATTTGTTGTTGACCTACTA 57.785 33.333 0.00 0.00 0.00 1.82
2312 2323 9.216117 AGTGATAATTTGTTGTTGACCTACTAC 57.784 33.333 0.00 0.00 0.00 2.73
2313 2324 9.216117 GTGATAATTTGTTGTTGACCTACTACT 57.784 33.333 0.00 0.00 0.00 2.57
2318 2329 7.956420 TTTGTTGTTGACCTACTACTACATG 57.044 36.000 0.00 0.00 38.79 3.21
2319 2330 6.032956 TGTTGTTGACCTACTACTACATGG 57.967 41.667 0.00 0.00 35.96 3.66
2320 2331 5.776208 TGTTGTTGACCTACTACTACATGGA 59.224 40.000 0.00 0.00 35.96 3.41
2321 2332 5.909621 TGTTGACCTACTACTACATGGAC 57.090 43.478 0.00 0.00 0.00 4.02
2322 2333 5.326900 TGTTGACCTACTACTACATGGACA 58.673 41.667 0.00 0.00 0.00 4.02
2323 2334 5.955959 TGTTGACCTACTACTACATGGACAT 59.044 40.000 0.00 0.00 0.00 3.06
2324 2335 6.127451 TGTTGACCTACTACTACATGGACATG 60.127 42.308 10.57 10.57 44.15 3.21
2325 2336 4.341235 TGACCTACTACTACATGGACATGC 59.659 45.833 11.96 0.00 42.39 4.06
2326 2337 3.318275 ACCTACTACTACATGGACATGCG 59.682 47.826 11.96 6.45 42.39 4.73
2327 2338 3.318275 CCTACTACTACATGGACATGCGT 59.682 47.826 11.96 11.42 42.39 5.24
2328 2339 3.165058 ACTACTACATGGACATGCGTG 57.835 47.619 11.96 3.82 42.39 5.34
2329 2340 2.496070 ACTACTACATGGACATGCGTGT 59.504 45.455 12.38 12.38 42.39 4.49
2330 2341 1.725641 ACTACATGGACATGCGTGTG 58.274 50.000 18.17 4.35 42.39 3.82
2331 2342 1.001974 ACTACATGGACATGCGTGTGT 59.998 47.619 18.17 10.64 42.39 3.72
2332 2343 1.394572 CTACATGGACATGCGTGTGTG 59.605 52.381 18.17 14.24 42.39 3.82
2333 2344 0.534877 ACATGGACATGCGTGTGTGT 60.535 50.000 18.17 14.88 42.39 3.72
2334 2345 0.166597 CATGGACATGCGTGTGTGTC 59.833 55.000 18.17 6.86 43.02 3.67
2335 2346 0.035317 ATGGACATGCGTGTGTGTCT 59.965 50.000 18.17 0.00 43.23 3.41
2336 2347 0.599991 TGGACATGCGTGTGTGTCTC 60.600 55.000 18.17 0.00 43.23 3.36
2337 2348 0.319900 GGACATGCGTGTGTGTCTCT 60.320 55.000 18.17 0.00 43.23 3.10
2338 2349 1.067846 GGACATGCGTGTGTGTCTCTA 60.068 52.381 18.17 0.00 43.23 2.43
2339 2350 1.986378 GACATGCGTGTGTGTCTCTAC 59.014 52.381 18.17 0.00 41.10 2.59
2340 2351 1.613925 ACATGCGTGTGTGTCTCTACT 59.386 47.619 11.65 0.00 37.14 2.57
2341 2352 2.254459 CATGCGTGTGTGTCTCTACTC 58.746 52.381 0.00 0.00 0.00 2.59
2342 2353 1.314730 TGCGTGTGTGTCTCTACTCA 58.685 50.000 0.00 0.00 0.00 3.41
2343 2354 1.679153 TGCGTGTGTGTCTCTACTCAA 59.321 47.619 0.00 0.00 31.33 3.02
2344 2355 2.052157 GCGTGTGTGTCTCTACTCAAC 58.948 52.381 0.00 0.00 31.33 3.18
2345 2356 2.287668 GCGTGTGTGTCTCTACTCAACT 60.288 50.000 0.00 0.00 31.33 3.16
2346 2357 3.300857 CGTGTGTGTCTCTACTCAACTG 58.699 50.000 0.00 0.00 31.33 3.16
2347 2358 3.003378 CGTGTGTGTCTCTACTCAACTGA 59.997 47.826 0.00 0.00 31.33 3.41
2348 2359 4.497507 CGTGTGTGTCTCTACTCAACTGAA 60.498 45.833 0.00 0.00 31.33 3.02
2349 2360 4.979197 GTGTGTGTCTCTACTCAACTGAAG 59.021 45.833 0.00 0.00 31.33 3.02
2350 2361 3.984633 GTGTGTCTCTACTCAACTGAAGC 59.015 47.826 0.00 0.00 31.33 3.86
2351 2362 3.891977 TGTGTCTCTACTCAACTGAAGCT 59.108 43.478 0.00 0.00 0.00 3.74
2352 2363 4.022762 TGTGTCTCTACTCAACTGAAGCTC 60.023 45.833 0.00 0.00 0.00 4.09
2353 2364 4.217550 GTGTCTCTACTCAACTGAAGCTCT 59.782 45.833 0.00 0.00 0.00 4.09
2354 2365 4.217334 TGTCTCTACTCAACTGAAGCTCTG 59.783 45.833 0.00 0.00 0.00 3.35
2355 2366 4.457603 GTCTCTACTCAACTGAAGCTCTGA 59.542 45.833 0.00 0.00 0.00 3.27
2356 2367 5.125417 GTCTCTACTCAACTGAAGCTCTGAT 59.875 44.000 0.00 0.00 0.00 2.90
2357 2368 5.125257 TCTCTACTCAACTGAAGCTCTGATG 59.875 44.000 0.00 0.00 0.00 3.07
2358 2369 4.769488 TCTACTCAACTGAAGCTCTGATGT 59.231 41.667 0.00 0.00 0.00 3.06
2359 2370 4.348863 ACTCAACTGAAGCTCTGATGTT 57.651 40.909 0.00 0.00 0.00 2.71
2360 2371 4.063689 ACTCAACTGAAGCTCTGATGTTG 58.936 43.478 9.99 9.99 36.93 3.33
2361 2372 3.405831 TCAACTGAAGCTCTGATGTTGG 58.594 45.455 13.86 2.28 36.45 3.77
2362 2373 2.486472 ACTGAAGCTCTGATGTTGGG 57.514 50.000 0.00 0.00 0.00 4.12
2363 2374 1.980765 ACTGAAGCTCTGATGTTGGGA 59.019 47.619 0.00 0.00 0.00 4.37
2364 2375 2.575279 ACTGAAGCTCTGATGTTGGGAT 59.425 45.455 0.00 0.00 0.00 3.85
2365 2376 3.776969 ACTGAAGCTCTGATGTTGGGATA 59.223 43.478 0.00 0.00 0.00 2.59
2366 2377 4.411540 ACTGAAGCTCTGATGTTGGGATAT 59.588 41.667 0.00 0.00 0.00 1.63
2367 2378 5.604231 ACTGAAGCTCTGATGTTGGGATATA 59.396 40.000 0.00 0.00 0.00 0.86
2368 2379 6.271857 ACTGAAGCTCTGATGTTGGGATATAT 59.728 38.462 0.00 0.00 0.00 0.86
2369 2380 7.455953 ACTGAAGCTCTGATGTTGGGATATATA 59.544 37.037 0.00 0.00 0.00 0.86
2370 2381 7.845037 TGAAGCTCTGATGTTGGGATATATAG 58.155 38.462 0.00 0.00 0.00 1.31
2371 2382 6.232581 AGCTCTGATGTTGGGATATATAGC 57.767 41.667 0.00 0.00 0.00 2.97
2372 2383 5.963253 AGCTCTGATGTTGGGATATATAGCT 59.037 40.000 0.00 0.00 0.00 3.32
2373 2384 6.443206 AGCTCTGATGTTGGGATATATAGCTT 59.557 38.462 0.00 0.00 31.76 3.74
2374 2385 6.538021 GCTCTGATGTTGGGATATATAGCTTG 59.462 42.308 0.00 0.00 0.00 4.01
2375 2386 6.950842 TCTGATGTTGGGATATATAGCTTGG 58.049 40.000 0.00 0.00 0.00 3.61
2376 2387 6.730507 TCTGATGTTGGGATATATAGCTTGGA 59.269 38.462 0.00 0.00 0.00 3.53
2377 2388 7.237471 TCTGATGTTGGGATATATAGCTTGGAA 59.763 37.037 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
471 472 3.659444 CGACGAAACTTCTCAACATTTGC 59.341 43.478 0.00 0.00 0.00 3.68
571 572 2.239402 TCCCAGAACATAGCAGCATCAA 59.761 45.455 0.00 0.00 0.00 2.57
573 574 2.158842 AGTCCCAGAACATAGCAGCATC 60.159 50.000 0.00 0.00 0.00 3.91
585 586 1.040646 CTAGCCGCATAGTCCCAGAA 58.959 55.000 0.00 0.00 0.00 3.02
757 760 4.854587 CTCGAGGGGAGGGATAGG 57.145 66.667 3.91 0.00 39.22 2.57
795 798 7.484993 TTGTTGGAAGGTGTTATAGTAGCTA 57.515 36.000 0.00 0.00 0.00 3.32
892 895 0.250038 CGAGGTGCATGTATCCCAGG 60.250 60.000 0.00 0.00 0.00 4.45
931 934 1.836999 AACGCCACCTGATGCACCTA 61.837 55.000 0.00 0.00 0.00 3.08
993 996 3.384789 TGTCTCGAAGAATCATTCCCGAT 59.615 43.478 11.48 0.00 35.66 4.18
1200 1203 1.095228 CAAAGTGCCCATACGCCGAT 61.095 55.000 0.00 0.00 0.00 4.18
1206 1209 2.744202 CTCTGACACAAAGTGCCCATAC 59.256 50.000 0.00 0.00 36.98 2.39
1218 1221 7.223584 TCAAATACCTTTTGATCTCTGACACA 58.776 34.615 0.00 0.00 33.90 3.72
1238 1241 9.305555 CAGGAATAATCACCCTATCATTCAAAT 57.694 33.333 0.00 0.00 0.00 2.32
1527 1532 7.279536 TGCATGAGTTCTTCATCAGAAATACTC 59.720 37.037 0.00 0.00 44.76 2.59
1561 1566 6.311200 TGTGATTGATTGAAGATGTGTACGAG 59.689 38.462 0.00 0.00 0.00 4.18
1584 1589 1.411246 TGAAGCAGTGGTAACTCGTGT 59.589 47.619 0.00 0.00 32.98 4.49
1587 1592 3.125316 GGATTTGAAGCAGTGGTAACTCG 59.875 47.826 0.00 0.00 32.98 4.18
1597 1602 2.034939 TGCACAACTGGATTTGAAGCAG 59.965 45.455 0.00 0.00 36.69 4.24
1607 1612 4.069304 GTTGGTACTTATGCACAACTGGA 58.931 43.478 6.80 0.00 38.60 3.86
1742 1747 1.750682 GCATTACAATCCCCCGCTTCT 60.751 52.381 0.00 0.00 0.00 2.85
1767 1773 0.629058 TAAATCCTTGTCCAGGGCCC 59.371 55.000 16.46 16.46 44.12 5.80
1897 1904 6.531503 AGAGTTGTAAGCAGTATAGCAAGA 57.468 37.500 0.00 0.00 36.85 3.02
1902 1909 5.500931 GCGCAAAGAGTTGTAAGCAGTATAG 60.501 44.000 0.30 0.00 37.06 1.31
1925 1932 3.088532 TGTGTTTGTGATGGGGATAAGC 58.911 45.455 0.00 0.00 0.00 3.09
1941 1948 2.294074 AGTTAATGTGTGGCGTGTGTT 58.706 42.857 0.00 0.00 0.00 3.32
1969 1980 1.143305 CTTGAGGCGTGAGAGTTGTG 58.857 55.000 0.00 0.00 0.00 3.33
1970 1981 0.034059 CCTTGAGGCGTGAGAGTTGT 59.966 55.000 0.00 0.00 0.00 3.32
2014 2025 0.539051 CACTGACAGATGGGTCCTCC 59.461 60.000 10.08 0.00 36.97 4.30
2027 2038 0.108615 CGTGGATCCCTGACACTGAC 60.109 60.000 9.90 0.00 33.13 3.51
2034 2045 0.396556 TCCGAATCGTGGATCCCTGA 60.397 55.000 9.90 7.43 0.00 3.86
2035 2046 0.464036 TTCCGAATCGTGGATCCCTG 59.536 55.000 9.90 1.05 34.91 4.45
2057 2068 0.802494 CAGGTACGGACATGGCAAAC 59.198 55.000 4.02 0.00 33.66 2.93
2110 2121 6.127793 GCCGGGAATAGATATCTTACTCCTA 58.872 44.000 11.25 0.00 0.00 2.94
2112 2123 4.202030 CGCCGGGAATAGATATCTTACTCC 60.202 50.000 11.25 13.46 0.00 3.85
2118 2129 3.018149 GAGACGCCGGGAATAGATATCT 58.982 50.000 10.73 10.73 0.00 1.98
2123 2134 0.475475 TAGGAGACGCCGGGAATAGA 59.525 55.000 2.18 0.00 43.43 1.98
2126 2137 1.108132 GTCTAGGAGACGCCGGGAAT 61.108 60.000 2.18 0.00 43.43 3.01
2161 2172 1.676967 GCCTCCCTTCCTTGCAGTG 60.677 63.158 0.00 0.00 0.00 3.66
2195 2206 4.857588 GTGATATTGCTACCCGATTCTACG 59.142 45.833 0.00 0.00 0.00 3.51
2204 2215 4.022849 GCCAATCAAGTGATATTGCTACCC 60.023 45.833 0.00 0.00 33.73 3.69
2222 2233 2.704572 CAGACGAAGGAGAAAGCCAAT 58.295 47.619 0.00 0.00 0.00 3.16
2231 2242 5.897050 AGTATAAAAGAGCAGACGAAGGAG 58.103 41.667 0.00 0.00 0.00 3.69
2232 2243 5.916661 AGTATAAAAGAGCAGACGAAGGA 57.083 39.130 0.00 0.00 0.00 3.36
2233 2244 7.380065 GTGATAGTATAAAAGAGCAGACGAAGG 59.620 40.741 0.00 0.00 0.00 3.46
2234 2245 7.915923 TGTGATAGTATAAAAGAGCAGACGAAG 59.084 37.037 0.00 0.00 0.00 3.79
2235 2246 7.768240 TGTGATAGTATAAAAGAGCAGACGAA 58.232 34.615 0.00 0.00 0.00 3.85
2236 2247 7.329588 TGTGATAGTATAAAAGAGCAGACGA 57.670 36.000 0.00 0.00 0.00 4.20
2237 2248 9.335891 CTATGTGATAGTATAAAAGAGCAGACG 57.664 37.037 0.00 0.00 0.00 4.18
2238 2249 9.632807 CCTATGTGATAGTATAAAAGAGCAGAC 57.367 37.037 0.00 0.00 0.00 3.51
2239 2250 9.368416 ACCTATGTGATAGTATAAAAGAGCAGA 57.632 33.333 0.00 0.00 0.00 4.26
2240 2251 9.988815 AACCTATGTGATAGTATAAAAGAGCAG 57.011 33.333 0.00 0.00 0.00 4.24
2241 2252 9.982651 GAACCTATGTGATAGTATAAAAGAGCA 57.017 33.333 0.00 0.00 0.00 4.26
2242 2253 9.982651 TGAACCTATGTGATAGTATAAAAGAGC 57.017 33.333 0.00 0.00 0.00 4.09
2252 2263 9.373450 AGATAAGACATGAACCTATGTGATAGT 57.627 33.333 0.00 0.00 41.15 2.12
2255 2266 9.593565 TCTAGATAAGACATGAACCTATGTGAT 57.406 33.333 0.00 0.00 41.15 3.06
2256 2267 8.996651 TCTAGATAAGACATGAACCTATGTGA 57.003 34.615 0.00 0.00 41.15 3.58
2259 2270 9.868277 GGAATCTAGATAAGACATGAACCTATG 57.132 37.037 5.46 0.00 36.93 2.23
2260 2271 9.607333 TGGAATCTAGATAAGACATGAACCTAT 57.393 33.333 5.46 0.00 36.93 2.57
2261 2272 9.083422 CTGGAATCTAGATAAGACATGAACCTA 57.917 37.037 5.46 0.00 36.93 3.08
2262 2273 7.566879 ACTGGAATCTAGATAAGACATGAACCT 59.433 37.037 5.46 0.00 36.93 3.50
2263 2274 7.655328 CACTGGAATCTAGATAAGACATGAACC 59.345 40.741 5.46 0.00 36.93 3.62
2264 2275 8.417106 TCACTGGAATCTAGATAAGACATGAAC 58.583 37.037 5.46 0.00 36.93 3.18
2265 2276 8.539117 TCACTGGAATCTAGATAAGACATGAA 57.461 34.615 5.46 0.00 36.93 2.57
2266 2277 8.718158 ATCACTGGAATCTAGATAAGACATGA 57.282 34.615 5.46 6.79 36.93 3.07
2275 2286 9.911788 ACAACAAATTATCACTGGAATCTAGAT 57.088 29.630 0.00 0.00 0.00 1.98
2276 2287 9.739276 AACAACAAATTATCACTGGAATCTAGA 57.261 29.630 0.00 0.00 0.00 2.43
2277 2288 9.778993 CAACAACAAATTATCACTGGAATCTAG 57.221 33.333 0.00 0.00 0.00 2.43
2278 2289 9.513906 TCAACAACAAATTATCACTGGAATCTA 57.486 29.630 0.00 0.00 0.00 1.98
2279 2290 8.299570 GTCAACAACAAATTATCACTGGAATCT 58.700 33.333 0.00 0.00 0.00 2.40
2280 2291 7.542130 GGTCAACAACAAATTATCACTGGAATC 59.458 37.037 0.00 0.00 0.00 2.52
2281 2292 7.233348 AGGTCAACAACAAATTATCACTGGAAT 59.767 33.333 0.00 0.00 0.00 3.01
2282 2293 6.549364 AGGTCAACAACAAATTATCACTGGAA 59.451 34.615 0.00 0.00 0.00 3.53
2283 2294 6.068010 AGGTCAACAACAAATTATCACTGGA 58.932 36.000 0.00 0.00 0.00 3.86
2284 2295 6.331369 AGGTCAACAACAAATTATCACTGG 57.669 37.500 0.00 0.00 0.00 4.00
2285 2296 8.099364 AGTAGGTCAACAACAAATTATCACTG 57.901 34.615 0.00 0.00 0.00 3.66
2286 2297 9.216117 GTAGTAGGTCAACAACAAATTATCACT 57.784 33.333 0.00 0.00 0.00 3.41
2287 2298 9.216117 AGTAGTAGGTCAACAACAAATTATCAC 57.784 33.333 0.00 0.00 0.00 3.06
2292 2303 8.999431 CATGTAGTAGTAGGTCAACAACAAATT 58.001 33.333 0.00 0.00 0.00 1.82
2293 2304 7.606456 CCATGTAGTAGTAGGTCAACAACAAAT 59.394 37.037 0.00 0.00 0.00 2.32
2294 2305 6.932400 CCATGTAGTAGTAGGTCAACAACAAA 59.068 38.462 0.00 0.00 0.00 2.83
2295 2306 6.268158 TCCATGTAGTAGTAGGTCAACAACAA 59.732 38.462 0.00 0.00 0.00 2.83
2296 2307 5.776208 TCCATGTAGTAGTAGGTCAACAACA 59.224 40.000 0.00 0.00 0.00 3.33
2297 2308 6.098017 GTCCATGTAGTAGTAGGTCAACAAC 58.902 44.000 0.00 0.00 0.00 3.32
2298 2309 5.776208 TGTCCATGTAGTAGTAGGTCAACAA 59.224 40.000 0.00 0.00 0.00 2.83
2299 2310 5.326900 TGTCCATGTAGTAGTAGGTCAACA 58.673 41.667 0.00 0.00 0.00 3.33
2300 2311 5.909621 TGTCCATGTAGTAGTAGGTCAAC 57.090 43.478 0.00 0.00 0.00 3.18
2301 2312 5.163447 GCATGTCCATGTAGTAGTAGGTCAA 60.163 44.000 8.91 0.00 40.80 3.18
2302 2313 4.341235 GCATGTCCATGTAGTAGTAGGTCA 59.659 45.833 8.91 0.00 40.80 4.02
2303 2314 4.556898 CGCATGTCCATGTAGTAGTAGGTC 60.557 50.000 8.91 0.00 40.80 3.85
2304 2315 3.318275 CGCATGTCCATGTAGTAGTAGGT 59.682 47.826 8.91 0.00 40.80 3.08
2305 2316 3.318275 ACGCATGTCCATGTAGTAGTAGG 59.682 47.826 8.91 0.00 40.80 3.18
2306 2317 4.202020 ACACGCATGTCCATGTAGTAGTAG 60.202 45.833 8.91 1.99 40.80 2.57
2307 2318 3.697542 ACACGCATGTCCATGTAGTAGTA 59.302 43.478 8.91 0.00 40.80 1.82
2308 2319 2.496070 ACACGCATGTCCATGTAGTAGT 59.504 45.455 8.91 7.69 40.80 2.73
2309 2320 2.860136 CACACGCATGTCCATGTAGTAG 59.140 50.000 8.91 7.22 40.80 2.57
2310 2321 2.232696 ACACACGCATGTCCATGTAGTA 59.767 45.455 8.91 0.00 40.80 1.82
2311 2322 1.001974 ACACACGCATGTCCATGTAGT 59.998 47.619 8.91 6.86 40.80 2.73
2312 2323 1.394572 CACACACGCATGTCCATGTAG 59.605 52.381 8.91 6.31 40.80 2.74
2313 2324 1.270571 ACACACACGCATGTCCATGTA 60.271 47.619 8.91 0.00 40.80 2.29
2314 2325 0.534877 ACACACACGCATGTCCATGT 60.535 50.000 8.91 0.00 40.80 3.21
2315 2326 0.166597 GACACACACGCATGTCCATG 59.833 55.000 2.86 2.86 39.49 3.66
2316 2327 0.035317 AGACACACACGCATGTCCAT 59.965 50.000 0.00 0.00 45.28 3.41
2317 2328 0.599991 GAGACACACACGCATGTCCA 60.600 55.000 0.00 0.00 45.28 4.02
2318 2329 0.319900 AGAGACACACACGCATGTCC 60.320 55.000 0.00 0.00 45.28 4.02
2319 2330 1.986378 GTAGAGACACACACGCATGTC 59.014 52.381 0.00 0.00 44.64 3.06
2320 2331 1.613925 AGTAGAGACACACACGCATGT 59.386 47.619 0.00 0.00 40.80 3.21
2321 2332 2.254459 GAGTAGAGACACACACGCATG 58.746 52.381 0.00 0.00 0.00 4.06
2322 2333 1.886542 TGAGTAGAGACACACACGCAT 59.113 47.619 0.00 0.00 0.00 4.73
2323 2334 1.314730 TGAGTAGAGACACACACGCA 58.685 50.000 0.00 0.00 0.00 5.24
2324 2335 2.052157 GTTGAGTAGAGACACACACGC 58.948 52.381 0.00 0.00 0.00 5.34
2325 2336 3.003378 TCAGTTGAGTAGAGACACACACG 59.997 47.826 0.00 0.00 0.00 4.49
2326 2337 4.569761 TCAGTTGAGTAGAGACACACAC 57.430 45.455 0.00 0.00 0.00 3.82
2327 2338 4.499865 GCTTCAGTTGAGTAGAGACACACA 60.500 45.833 0.00 0.00 0.00 3.72
2328 2339 3.984633 GCTTCAGTTGAGTAGAGACACAC 59.015 47.826 0.00 0.00 0.00 3.82
2329 2340 3.891977 AGCTTCAGTTGAGTAGAGACACA 59.108 43.478 0.00 0.00 0.00 3.72
2330 2341 4.217550 AGAGCTTCAGTTGAGTAGAGACAC 59.782 45.833 0.00 0.00 0.00 3.67
2331 2342 4.217334 CAGAGCTTCAGTTGAGTAGAGACA 59.783 45.833 0.00 0.00 0.00 3.41
2332 2343 4.457603 TCAGAGCTTCAGTTGAGTAGAGAC 59.542 45.833 0.00 0.00 0.00 3.36
2333 2344 4.657013 TCAGAGCTTCAGTTGAGTAGAGA 58.343 43.478 0.00 0.00 0.00 3.10
2334 2345 5.105797 ACATCAGAGCTTCAGTTGAGTAGAG 60.106 44.000 0.00 0.00 0.00 2.43
2335 2346 4.769488 ACATCAGAGCTTCAGTTGAGTAGA 59.231 41.667 0.00 0.00 0.00 2.59
2336 2347 5.070770 ACATCAGAGCTTCAGTTGAGTAG 57.929 43.478 0.00 0.00 0.00 2.57
2337 2348 5.233225 CAACATCAGAGCTTCAGTTGAGTA 58.767 41.667 10.86 0.00 38.80 2.59
2338 2349 4.063689 CAACATCAGAGCTTCAGTTGAGT 58.936 43.478 10.86 0.00 38.80 3.41
2339 2350 3.436015 CCAACATCAGAGCTTCAGTTGAG 59.564 47.826 15.43 6.41 38.80 3.02
2340 2351 3.405831 CCAACATCAGAGCTTCAGTTGA 58.594 45.455 15.43 4.79 38.80 3.18
2341 2352 2.486982 CCCAACATCAGAGCTTCAGTTG 59.513 50.000 9.88 9.88 36.89 3.16
2342 2353 2.373169 TCCCAACATCAGAGCTTCAGTT 59.627 45.455 0.00 0.00 0.00 3.16
2343 2354 1.980765 TCCCAACATCAGAGCTTCAGT 59.019 47.619 0.00 0.00 0.00 3.41
2344 2355 2.775911 TCCCAACATCAGAGCTTCAG 57.224 50.000 0.00 0.00 0.00 3.02
2345 2356 6.692849 ATATATCCCAACATCAGAGCTTCA 57.307 37.500 0.00 0.00 0.00 3.02
2346 2357 6.760770 GCTATATATCCCAACATCAGAGCTTC 59.239 42.308 0.00 0.00 0.00 3.86
2347 2358 6.443206 AGCTATATATCCCAACATCAGAGCTT 59.557 38.462 0.00 0.00 31.59 3.74
2348 2359 5.963253 AGCTATATATCCCAACATCAGAGCT 59.037 40.000 0.00 0.00 0.00 4.09
2349 2360 6.232581 AGCTATATATCCCAACATCAGAGC 57.767 41.667 0.00 0.00 0.00 4.09
2350 2361 7.046652 CCAAGCTATATATCCCAACATCAGAG 58.953 42.308 0.00 0.00 0.00 3.35
2351 2362 6.730507 TCCAAGCTATATATCCCAACATCAGA 59.269 38.462 0.00 0.00 0.00 3.27
2352 2363 6.950842 TCCAAGCTATATATCCCAACATCAG 58.049 40.000 0.00 0.00 0.00 2.90
2353 2364 6.950860 TCCAAGCTATATATCCCAACATCA 57.049 37.500 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.