Multiple sequence alignment - TraesCS3D01G411500

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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 TraesCS3D01G411500 chr3D 100.000 1913 0 0 1 1913 524198505 524200417 0.000000e+00 3533
1 TraesCS3D01G411500 chr3D 100.000 316 0 0 2161 2476 524200665 524200980 3.550000e-163 584
2 TraesCS3D01G411500 chr3D 96.053 304 12 0 2161 2464 365507317 365507014 1.710000e-136 496
3 TraesCS3D01G411500 chr6D 96.979 1920 50 4 1 1913 31859061 31860979 0.000000e+00 3217
4 TraesCS3D01G411500 chr6D 97.059 306 8 1 2161 2466 427235259 427234955 4.720000e-142 514
5 TraesCS3D01G411500 chr6D 96.078 306 11 1 2161 2466 31860629 31860933 4.760000e-137 497
6 TraesCS3D01G411500 chr5D 96.970 1914 53 3 1 1913 365120437 365118528 0.000000e+00 3208
7 TraesCS3D01G411500 chr5D 96.345 1915 65 4 1 1913 304884321 304882410 0.000000e+00 3144
8 TraesCS3D01G411500 chr1D 96.860 1911 53 6 1 1908 471280902 471282808 0.000000e+00 3190
9 TraesCS3D01G411500 chr1D 96.503 1916 63 4 1 1913 457576429 457578343 0.000000e+00 3164
10 TraesCS3D01G411500 chr1D 96.501 1915 60 5 1 1913 395974540 395976449 0.000000e+00 3158
11 TraesCS3D01G411500 chr1D 96.091 307 11 1 2161 2466 464936964 464937270 1.320000e-137 499
12 TraesCS3D01G411500 chr1D 95.765 307 11 2 2161 2466 457577993 457578298 6.150000e-136 494
13 TraesCS3D01G411500 chr2D 96.606 1915 59 5 1 1913 476878771 476880681 0.000000e+00 3171
14 TraesCS3D01G411500 chr2D 96.608 1916 58 6 1 1913 588796856 588794945 0.000000e+00 3171
15 TraesCS3D01G411500 chr2D 96.554 1915 62 4 1 1913 16904395 16906307 0.000000e+00 3168
16 TraesCS3D01G411500 chr2D 96.215 317 11 1 2161 2476 484900696 484901012 3.650000e-143 518
17 TraesCS3D01G411500 chr4D 95.570 316 13 1 2161 2476 484449256 484449570 2.840000e-139 505
18 TraesCS3D01G411500 chr7D 96.078 306 12 0 2161 2466 464036816 464037121 1.320000e-137 499
19 TraesCS3D01G411500 chr4A 96.091 307 10 2 2161 2466 117883273 117883578 1.320000e-137 499


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 TraesCS3D01G411500 chr3D 524198505 524200980 2475 False 2058.5 3533 100.0000 1 2476 2 chr3D.!!$F1 2475
1 TraesCS3D01G411500 chr6D 31859061 31860979 1918 False 1857.0 3217 96.5285 1 2466 2 chr6D.!!$F1 2465
2 TraesCS3D01G411500 chr5D 365118528 365120437 1909 True 3208.0 3208 96.9700 1 1913 1 chr5D.!!$R2 1912
3 TraesCS3D01G411500 chr5D 304882410 304884321 1911 True 3144.0 3144 96.3450 1 1913 1 chr5D.!!$R1 1912
4 TraesCS3D01G411500 chr1D 471280902 471282808 1906 False 3190.0 3190 96.8600 1 1908 1 chr1D.!!$F3 1907
5 TraesCS3D01G411500 chr1D 395974540 395976449 1909 False 3158.0 3158 96.5010 1 1913 1 chr1D.!!$F1 1912
6 TraesCS3D01G411500 chr1D 457576429 457578343 1914 False 1829.0 3164 96.1340 1 2466 2 chr1D.!!$F4 2465
7 TraesCS3D01G411500 chr2D 476878771 476880681 1910 False 3171.0 3171 96.6060 1 1913 1 chr2D.!!$F2 1912
8 TraesCS3D01G411500 chr2D 588794945 588796856 1911 True 3171.0 3171 96.6080 1 1913 1 chr2D.!!$R1 1912
9 TraesCS3D01G411500 chr2D 16904395 16906307 1912 False 3168.0 3168 96.5540 1 1913 1 chr2D.!!$F1 1912

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
563 565 1.304282 CATTGCAGGGGTAGCCACT 59.696 57.895 14.06 4.69 38.09 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 2413 0.107456 CTCCCATCCTGGTTCATCGG 59.893 60.0 0.0 0.0 35.17 4.18 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
400 402 2.975799 ACCGCGACATTGCCGTTT 60.976 55.556 8.23 0.00 0.00 3.60
409 411 2.038269 ATTGCCGTTTGATCCGCGT 61.038 52.632 4.92 0.00 0.00 6.01
415 417 4.380781 TTTGATCCGCGTCGCCCA 62.381 61.111 12.44 1.91 0.00 5.36
478 480 1.561542 GATCTCCTCTTGCCTTTCCCA 59.438 52.381 0.00 0.00 0.00 4.37
513 515 5.232463 TCGTTTGCTCTCGTTAGGTATTTT 58.768 37.500 0.00 0.00 0.00 1.82
563 565 1.304282 CATTGCAGGGGTAGCCACT 59.696 57.895 14.06 4.69 38.09 4.00
741 743 1.673993 CAGCCACCGCACCATTGTA 60.674 57.895 0.00 0.00 37.52 2.41
752 754 3.261951 CATTGTACCCCGCGCGAG 61.262 66.667 34.63 24.44 0.00 5.03
1115 1117 3.702048 GGCGGTGTCACCTGGCTA 61.702 66.667 23.58 0.00 35.66 3.93
1179 1181 5.634118 AGAGGTCACAATTGGAAAGAATCA 58.366 37.500 10.83 0.00 0.00 2.57
1180 1182 6.070656 AGAGGTCACAATTGGAAAGAATCAA 58.929 36.000 10.83 0.00 0.00 2.57
1347 1354 5.716228 TGAACTGATTTCTATGCAAATGGGT 59.284 36.000 0.00 0.00 34.97 4.51
1388 1395 3.962063 TGATATCAGTACCTGCCCGTTTA 59.038 43.478 0.00 0.00 0.00 2.01
1414 1421 5.365619 ACGTGTCTGATTAGGAAAGTTTGT 58.634 37.500 0.00 0.00 0.00 2.83
1479 1491 8.126700 CGTGTCTGTTATTTGTTTCCTAAAACT 58.873 33.333 3.06 0.00 44.23 2.66
1813 1827 2.052782 AATAAACCGATGGACCAGGC 57.947 50.000 0.00 0.00 0.00 4.85
2189 2205 7.411486 TTGTTTCCTAAGACAAATTGAACCA 57.589 32.000 0.00 0.00 33.19 3.67
2190 2206 7.411486 TGTTTCCTAAGACAAATTGAACCAA 57.589 32.000 0.00 0.00 0.00 3.67
2191 2207 8.017418 TGTTTCCTAAGACAAATTGAACCAAT 57.983 30.769 0.00 0.00 35.39 3.16
2192 2208 9.137459 TGTTTCCTAAGACAAATTGAACCAATA 57.863 29.630 0.00 0.00 32.43 1.90
2193 2209 9.974980 GTTTCCTAAGACAAATTGAACCAATAA 57.025 29.630 0.00 0.00 32.43 1.40
2197 2213 9.423061 CCTAAGACAAATTGAACCAATAAAAGG 57.577 33.333 0.00 0.00 32.43 3.11
2201 2217 9.710900 AGACAAATTGAACCAATAAAAGGAATC 57.289 29.630 0.00 0.00 32.43 2.52
2202 2218 8.532977 ACAAATTGAACCAATAAAAGGAATCG 57.467 30.769 0.00 0.00 32.43 3.34
2203 2219 8.364142 ACAAATTGAACCAATAAAAGGAATCGA 58.636 29.630 0.00 0.00 32.43 3.59
2204 2220 9.369904 CAAATTGAACCAATAAAAGGAATCGAT 57.630 29.630 0.00 0.00 32.43 3.59
2205 2221 9.942850 AAATTGAACCAATAAAAGGAATCGATT 57.057 25.926 11.20 11.20 32.43 3.34
2206 2222 8.931385 ATTGAACCAATAAAAGGAATCGATTG 57.069 30.769 16.96 0.00 31.77 2.67
2207 2223 7.695480 TGAACCAATAAAAGGAATCGATTGA 57.305 32.000 16.96 0.00 30.62 2.57
2208 2224 8.292444 TGAACCAATAAAAGGAATCGATTGAT 57.708 30.769 16.96 0.06 35.98 2.57
2210 2226 9.586435 GAACCAATAAAAGGAATCGATTGATTT 57.414 29.630 16.96 14.79 44.79 2.17
2211 2227 8.931385 ACCAATAAAAGGAATCGATTGATTTG 57.069 30.769 16.96 8.94 44.79 2.32
2212 2228 7.492344 ACCAATAAAAGGAATCGATTGATTTGC 59.508 33.333 16.96 0.00 44.79 3.68
2213 2229 7.492020 CCAATAAAAGGAATCGATTGATTTGCA 59.508 33.333 16.96 8.16 44.79 4.08
2214 2230 9.037737 CAATAAAAGGAATCGATTGATTTGCAT 57.962 29.630 16.96 9.83 44.79 3.96
2218 2234 9.603921 AAAAGGAATCGATTGATTTGCATAATT 57.396 25.926 16.96 0.00 44.79 1.40
2219 2235 9.603921 AAAGGAATCGATTGATTTGCATAATTT 57.396 25.926 16.96 2.14 44.79 1.82
2226 2242 9.734620 TCGATTGATTTGCATAATTTAAGGAAG 57.265 29.630 0.00 0.00 0.00 3.46
2227 2243 9.520204 CGATTGATTTGCATAATTTAAGGAAGT 57.480 29.630 0.00 0.00 0.00 3.01
2264 2280 9.739276 TGTATTATTTGTTTCCTGAAGATCTGT 57.261 29.630 0.00 0.00 0.00 3.41
2270 2286 9.918630 ATTTGTTTCCTGAAGATCTGTTATTTG 57.081 29.630 0.00 0.00 0.00 2.32
2271 2287 8.463930 TTGTTTCCTGAAGATCTGTTATTTGT 57.536 30.769 0.00 0.00 0.00 2.83
2272 2288 8.463930 TGTTTCCTGAAGATCTGTTATTTGTT 57.536 30.769 0.00 0.00 0.00 2.83
2273 2289 8.912988 TGTTTCCTGAAGATCTGTTATTTGTTT 58.087 29.630 0.00 0.00 0.00 2.83
2274 2290 9.399403 GTTTCCTGAAGATCTGTTATTTGTTTC 57.601 33.333 0.00 0.00 0.00 2.78
2275 2291 7.687941 TCCTGAAGATCTGTTATTTGTTTCC 57.312 36.000 0.00 0.00 0.00 3.13
2276 2292 7.461749 TCCTGAAGATCTGTTATTTGTTTCCT 58.538 34.615 0.00 0.00 0.00 3.36
2277 2293 8.602424 TCCTGAAGATCTGTTATTTGTTTCCTA 58.398 33.333 0.00 0.00 0.00 2.94
2278 2294 9.231297 CCTGAAGATCTGTTATTTGTTTCCTAA 57.769 33.333 0.00 0.00 0.00 2.69
2305 2321 9.844257 AACAAATTGAACCAATAAAAGGAATCA 57.156 25.926 0.00 0.00 32.43 2.57
2306 2322 9.844257 ACAAATTGAACCAATAAAAGGAATCAA 57.156 25.926 0.00 0.00 38.67 2.57
2315 2331 8.949177 ACCAATAAAAGGAATCAATTGATTTGC 58.051 29.630 29.44 19.43 44.14 3.68
2316 2332 8.948145 CCAATAAAAGGAATCAATTGATTTGCA 58.052 29.630 29.44 14.97 44.14 4.08
2338 2354 8.378172 TGCATAATTTAAGGAAGTTAGATCCG 57.622 34.615 0.00 0.00 42.03 4.18
2339 2355 7.990886 TGCATAATTTAAGGAAGTTAGATCCGT 59.009 33.333 0.00 0.00 42.03 4.69
2340 2356 8.283291 GCATAATTTAAGGAAGTTAGATCCGTG 58.717 37.037 0.00 0.00 42.03 4.94
2341 2357 9.542462 CATAATTTAAGGAAGTTAGATCCGTGA 57.458 33.333 0.00 0.00 42.03 4.35
2344 2360 9.462606 AATTTAAGGAAGTTAGATCCGTGATTT 57.537 29.630 0.00 0.00 42.03 2.17
2345 2361 7.843490 TTAAGGAAGTTAGATCCGTGATTTG 57.157 36.000 0.00 0.00 42.03 2.32
2346 2362 5.422214 AGGAAGTTAGATCCGTGATTTGT 57.578 39.130 0.00 0.00 42.03 2.83
2347 2363 5.805728 AGGAAGTTAGATCCGTGATTTGTT 58.194 37.500 0.00 0.00 42.03 2.83
2348 2364 6.942976 AGGAAGTTAGATCCGTGATTTGTTA 58.057 36.000 0.00 0.00 42.03 2.41
2349 2365 7.565680 AGGAAGTTAGATCCGTGATTTGTTAT 58.434 34.615 0.00 0.00 42.03 1.89
2350 2366 8.701895 AGGAAGTTAGATCCGTGATTTGTTATA 58.298 33.333 0.00 0.00 42.03 0.98
2351 2367 8.979574 GGAAGTTAGATCCGTGATTTGTTATAG 58.020 37.037 0.00 0.00 0.00 1.31
2352 2368 8.888579 AAGTTAGATCCGTGATTTGTTATAGG 57.111 34.615 0.00 0.00 0.00 2.57
2353 2369 8.019656 AGTTAGATCCGTGATTTGTTATAGGT 57.980 34.615 0.00 0.00 0.00 3.08
2354 2370 8.483758 AGTTAGATCCGTGATTTGTTATAGGTT 58.516 33.333 0.00 0.00 0.00 3.50
2355 2371 9.754382 GTTAGATCCGTGATTTGTTATAGGTTA 57.246 33.333 0.00 0.00 0.00 2.85
2356 2372 9.976511 TTAGATCCGTGATTTGTTATAGGTTAG 57.023 33.333 0.00 0.00 0.00 2.34
2357 2373 7.442656 AGATCCGTGATTTGTTATAGGTTAGG 58.557 38.462 0.00 0.00 0.00 2.69
2358 2374 6.795144 TCCGTGATTTGTTATAGGTTAGGA 57.205 37.500 0.00 0.00 0.00 2.94
2359 2375 7.185318 TCCGTGATTTGTTATAGGTTAGGAA 57.815 36.000 0.00 0.00 0.00 3.36
2360 2376 7.622713 TCCGTGATTTGTTATAGGTTAGGAAA 58.377 34.615 0.00 0.00 0.00 3.13
2361 2377 7.767198 TCCGTGATTTGTTATAGGTTAGGAAAG 59.233 37.037 0.00 0.00 0.00 2.62
2362 2378 7.551617 CCGTGATTTGTTATAGGTTAGGAAAGT 59.448 37.037 0.00 0.00 0.00 2.66
2363 2379 8.943002 CGTGATTTGTTATAGGTTAGGAAAGTT 58.057 33.333 0.00 0.00 0.00 2.66
2367 2383 8.857694 TTTGTTATAGGTTAGGAAAGTTCTGG 57.142 34.615 0.00 0.00 0.00 3.86
2368 2384 7.563724 TGTTATAGGTTAGGAAAGTTCTGGT 57.436 36.000 0.00 0.00 0.00 4.00
2369 2385 7.981142 TGTTATAGGTTAGGAAAGTTCTGGTT 58.019 34.615 0.00 0.00 0.00 3.67
2370 2386 7.881232 TGTTATAGGTTAGGAAAGTTCTGGTTG 59.119 37.037 0.00 0.00 0.00 3.77
2371 2387 4.790718 AGGTTAGGAAAGTTCTGGTTGT 57.209 40.909 0.00 0.00 0.00 3.32
2372 2388 5.899631 AGGTTAGGAAAGTTCTGGTTGTA 57.100 39.130 0.00 0.00 0.00 2.41
2373 2389 6.256643 AGGTTAGGAAAGTTCTGGTTGTAA 57.743 37.500 0.00 0.00 0.00 2.41
2374 2390 6.849151 AGGTTAGGAAAGTTCTGGTTGTAAT 58.151 36.000 0.00 0.00 0.00 1.89
2375 2391 7.981142 AGGTTAGGAAAGTTCTGGTTGTAATA 58.019 34.615 0.00 0.00 0.00 0.98
2376 2392 8.442374 AGGTTAGGAAAGTTCTGGTTGTAATAA 58.558 33.333 0.00 0.00 0.00 1.40
2377 2393 9.070179 GGTTAGGAAAGTTCTGGTTGTAATAAA 57.930 33.333 0.00 0.00 0.00 1.40
2380 2396 8.622948 AGGAAAGTTCTGGTTGTAATAAAGAG 57.377 34.615 0.00 0.00 0.00 2.85
2381 2397 8.218488 AGGAAAGTTCTGGTTGTAATAAAGAGT 58.782 33.333 0.00 0.00 0.00 3.24
2382 2398 8.290325 GGAAAGTTCTGGTTGTAATAAAGAGTG 58.710 37.037 0.00 0.00 0.00 3.51
2383 2399 8.974060 AAAGTTCTGGTTGTAATAAAGAGTGA 57.026 30.769 0.00 0.00 0.00 3.41
2384 2400 8.974060 AAGTTCTGGTTGTAATAAAGAGTGAA 57.026 30.769 0.00 0.00 0.00 3.18
2385 2401 8.608844 AGTTCTGGTTGTAATAAAGAGTGAAG 57.391 34.615 0.00 0.00 0.00 3.02
2386 2402 8.429641 AGTTCTGGTTGTAATAAAGAGTGAAGA 58.570 33.333 0.00 0.00 0.00 2.87
2387 2403 8.713271 GTTCTGGTTGTAATAAAGAGTGAAGAG 58.287 37.037 0.00 0.00 0.00 2.85
2388 2404 8.190326 TCTGGTTGTAATAAAGAGTGAAGAGA 57.810 34.615 0.00 0.00 0.00 3.10
2389 2405 8.647796 TCTGGTTGTAATAAAGAGTGAAGAGAA 58.352 33.333 0.00 0.00 0.00 2.87
2390 2406 9.273016 CTGGTTGTAATAAAGAGTGAAGAGAAA 57.727 33.333 0.00 0.00 0.00 2.52
2391 2407 9.621629 TGGTTGTAATAAAGAGTGAAGAGAAAA 57.378 29.630 0.00 0.00 0.00 2.29
2400 2416 8.446599 AAAGAGTGAAGAGAAAAATAAACCGA 57.553 30.769 0.00 0.00 0.00 4.69
2401 2417 8.622948 AAGAGTGAAGAGAAAAATAAACCGAT 57.377 30.769 0.00 0.00 0.00 4.18
2402 2418 8.034058 AGAGTGAAGAGAAAAATAAACCGATG 57.966 34.615 0.00 0.00 0.00 3.84
2403 2419 7.878127 AGAGTGAAGAGAAAAATAAACCGATGA 59.122 33.333 0.00 0.00 0.00 2.92
2404 2420 8.391075 AGTGAAGAGAAAAATAAACCGATGAA 57.609 30.769 0.00 0.00 0.00 2.57
2405 2421 8.290325 AGTGAAGAGAAAAATAAACCGATGAAC 58.710 33.333 0.00 0.00 0.00 3.18
2406 2422 7.537649 GTGAAGAGAAAAATAAACCGATGAACC 59.462 37.037 0.00 0.00 0.00 3.62
2407 2423 7.229707 TGAAGAGAAAAATAAACCGATGAACCA 59.770 33.333 0.00 0.00 0.00 3.67
2408 2424 7.145932 AGAGAAAAATAAACCGATGAACCAG 57.854 36.000 0.00 0.00 0.00 4.00
2409 2425 6.151144 AGAGAAAAATAAACCGATGAACCAGG 59.849 38.462 0.00 0.00 0.00 4.45
2410 2426 6.007703 AGAAAAATAAACCGATGAACCAGGA 58.992 36.000 0.00 0.00 0.00 3.86
2411 2427 6.663523 AGAAAAATAAACCGATGAACCAGGAT 59.336 34.615 0.00 0.00 0.00 3.24
2412 2428 5.835113 AAATAAACCGATGAACCAGGATG 57.165 39.130 0.00 0.00 0.00 3.51
2423 2439 3.099170 CAGGATGGGAGGGGGTGG 61.099 72.222 0.00 0.00 0.00 4.61
2424 2440 3.637544 AGGATGGGAGGGGGTGGT 61.638 66.667 0.00 0.00 0.00 4.16
2425 2441 3.420482 GGATGGGAGGGGGTGGTG 61.420 72.222 0.00 0.00 0.00 4.17
2426 2442 3.420482 GATGGGAGGGGGTGGTGG 61.420 72.222 0.00 0.00 0.00 4.61
2430 2446 4.348495 GGAGGGGGTGGTGGGAGA 62.348 72.222 0.00 0.00 0.00 3.71
2431 2447 2.204090 GAGGGGGTGGTGGGAGAA 60.204 66.667 0.00 0.00 0.00 2.87
2432 2448 2.204151 AGGGGGTGGTGGGAGAAG 60.204 66.667 0.00 0.00 0.00 2.85
2433 2449 2.204090 GGGGGTGGTGGGAGAAGA 60.204 66.667 0.00 0.00 0.00 2.87
2434 2450 2.301738 GGGGGTGGTGGGAGAAGAG 61.302 68.421 0.00 0.00 0.00 2.85
2435 2451 1.229529 GGGGTGGTGGGAGAAGAGA 60.230 63.158 0.00 0.00 0.00 3.10
2436 2452 1.554583 GGGGTGGTGGGAGAAGAGAC 61.555 65.000 0.00 0.00 0.00 3.36
2437 2453 1.592223 GGTGGTGGGAGAAGAGACG 59.408 63.158 0.00 0.00 0.00 4.18
2438 2454 0.898789 GGTGGTGGGAGAAGAGACGA 60.899 60.000 0.00 0.00 0.00 4.20
2439 2455 0.966920 GTGGTGGGAGAAGAGACGAA 59.033 55.000 0.00 0.00 0.00 3.85
2440 2456 1.343465 GTGGTGGGAGAAGAGACGAAA 59.657 52.381 0.00 0.00 0.00 3.46
2441 2457 2.043992 TGGTGGGAGAAGAGACGAAAA 58.956 47.619 0.00 0.00 0.00 2.29
2442 2458 2.436542 TGGTGGGAGAAGAGACGAAAAA 59.563 45.455 0.00 0.00 0.00 1.94
2462 2478 5.977171 AAAAACCAGCGAAAATAAACCAC 57.023 34.783 0.00 0.00 0.00 4.16
2463 2479 2.981400 ACCAGCGAAAATAAACCACG 57.019 45.000 0.00 0.00 0.00 4.94
2464 2480 1.538075 ACCAGCGAAAATAAACCACGG 59.462 47.619 0.00 0.00 0.00 4.94
2465 2481 1.807742 CCAGCGAAAATAAACCACGGA 59.192 47.619 0.00 0.00 0.00 4.69
2466 2482 2.159572 CCAGCGAAAATAAACCACGGAG 60.160 50.000 0.00 0.00 0.00 4.63
2467 2483 2.739913 CAGCGAAAATAAACCACGGAGA 59.260 45.455 0.00 0.00 0.00 3.71
2468 2484 2.740447 AGCGAAAATAAACCACGGAGAC 59.260 45.455 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 1.448540 CTTCGATGCCAGCGAGGTT 60.449 57.895 4.84 0.00 39.14 3.50
415 417 0.985490 GGGGAAGACATGGGAGCTCT 60.985 60.000 14.64 0.00 0.00 4.09
478 480 1.073923 AGCAAACGAGAGGGGAAACAT 59.926 47.619 0.00 0.00 0.00 2.71
563 565 1.330655 GGGTCAATCCGAGGAGCTCA 61.331 60.000 17.19 0.00 37.00 4.26
737 739 4.424566 GTCTCGCGCGGGGTACAA 62.425 66.667 31.95 6.94 0.00 2.41
861 863 4.547859 GCAGAAGATGGCCACGAT 57.452 55.556 8.16 0.00 0.00 3.73
1011 1013 3.361977 ACATTTGTCCACGGCGGC 61.362 61.111 13.24 0.00 33.14 6.53
1115 1117 1.280710 TCGCATAAACACCTCCACCAT 59.719 47.619 0.00 0.00 0.00 3.55
1388 1395 5.407407 ACTTTCCTAATCAGACACGTCAT 57.593 39.130 0.00 0.00 0.00 3.06
1754 1767 9.629878 TTTATTACAACCAGAACTTTCCTAACA 57.370 29.630 0.00 0.00 0.00 2.41
1847 1861 1.345410 CGCGGTTTATTTTTGCTGGG 58.655 50.000 0.00 0.00 0.00 4.45
2164 2180 7.841956 TGGTTCAATTTGTCTTAGGAAACAAA 58.158 30.769 3.45 3.45 46.16 2.83
2165 2181 7.411486 TGGTTCAATTTGTCTTAGGAAACAA 57.589 32.000 0.00 0.00 29.84 2.83
2166 2182 7.411486 TTGGTTCAATTTGTCTTAGGAAACA 57.589 32.000 0.00 0.00 30.79 2.83
2167 2183 9.974980 TTATTGGTTCAATTTGTCTTAGGAAAC 57.025 29.630 0.00 0.00 35.54 2.78
2171 2187 9.423061 CCTTTTATTGGTTCAATTTGTCTTAGG 57.577 33.333 0.00 0.00 35.54 2.69
2175 2191 9.710900 GATTCCTTTTATTGGTTCAATTTGTCT 57.289 29.630 0.00 0.00 35.54 3.41
2176 2192 8.647226 CGATTCCTTTTATTGGTTCAATTTGTC 58.353 33.333 0.00 0.00 35.54 3.18
2177 2193 8.364142 TCGATTCCTTTTATTGGTTCAATTTGT 58.636 29.630 0.00 0.00 35.54 2.83
2178 2194 8.755696 TCGATTCCTTTTATTGGTTCAATTTG 57.244 30.769 0.00 0.00 35.54 2.32
2179 2195 9.942850 AATCGATTCCTTTTATTGGTTCAATTT 57.057 25.926 4.39 0.00 35.54 1.82
2180 2196 9.369904 CAATCGATTCCTTTTATTGGTTCAATT 57.630 29.630 7.92 0.00 35.54 2.32
2181 2197 8.748412 TCAATCGATTCCTTTTATTGGTTCAAT 58.252 29.630 7.92 0.00 37.80 2.57
2182 2198 8.116651 TCAATCGATTCCTTTTATTGGTTCAA 57.883 30.769 7.92 0.00 0.00 2.69
2183 2199 7.695480 TCAATCGATTCCTTTTATTGGTTCA 57.305 32.000 7.92 0.00 0.00 3.18
2184 2200 9.586435 AAATCAATCGATTCCTTTTATTGGTTC 57.414 29.630 7.92 0.00 41.12 3.62
2185 2201 9.369904 CAAATCAATCGATTCCTTTTATTGGTT 57.630 29.630 7.92 0.00 41.12 3.67
2186 2202 7.492344 GCAAATCAATCGATTCCTTTTATTGGT 59.508 33.333 7.92 0.00 41.12 3.67
2187 2203 7.492020 TGCAAATCAATCGATTCCTTTTATTGG 59.508 33.333 7.92 1.25 41.12 3.16
2188 2204 8.410030 TGCAAATCAATCGATTCCTTTTATTG 57.590 30.769 7.92 8.01 41.12 1.90
2192 2208 9.603921 AATTATGCAAATCAATCGATTCCTTTT 57.396 25.926 7.92 5.75 41.12 2.27
2193 2209 9.603921 AAATTATGCAAATCAATCGATTCCTTT 57.396 25.926 7.92 8.03 41.12 3.11
2200 2216 9.734620 CTTCCTTAAATTATGCAAATCAATCGA 57.265 29.630 0.00 0.00 0.00 3.59
2201 2217 9.520204 ACTTCCTTAAATTATGCAAATCAATCG 57.480 29.630 0.00 0.00 0.00 3.34
2238 2254 9.739276 ACAGATCTTCAGGAAACAAATAATACA 57.261 29.630 0.00 0.00 0.00 2.29
2244 2260 9.918630 CAAATAACAGATCTTCAGGAAACAAAT 57.081 29.630 0.00 0.00 0.00 2.32
2245 2261 8.912988 ACAAATAACAGATCTTCAGGAAACAAA 58.087 29.630 0.00 0.00 0.00 2.83
2246 2262 8.463930 ACAAATAACAGATCTTCAGGAAACAA 57.536 30.769 0.00 0.00 0.00 2.83
2247 2263 8.463930 AACAAATAACAGATCTTCAGGAAACA 57.536 30.769 0.00 0.00 0.00 2.83
2248 2264 9.399403 GAAACAAATAACAGATCTTCAGGAAAC 57.601 33.333 0.00 0.00 0.00 2.78
2249 2265 8.576442 GGAAACAAATAACAGATCTTCAGGAAA 58.424 33.333 0.00 0.00 0.00 3.13
2250 2266 7.944554 AGGAAACAAATAACAGATCTTCAGGAA 59.055 33.333 0.00 0.00 0.00 3.36
2251 2267 7.461749 AGGAAACAAATAACAGATCTTCAGGA 58.538 34.615 0.00 0.00 0.00 3.86
2252 2268 7.693969 AGGAAACAAATAACAGATCTTCAGG 57.306 36.000 0.00 0.00 0.00 3.86
2279 2295 9.844257 TGATTCCTTTTATTGGTTCAATTTGTT 57.156 25.926 0.00 0.00 35.54 2.83
2280 2296 9.844257 TTGATTCCTTTTATTGGTTCAATTTGT 57.156 25.926 0.00 0.00 35.54 2.83
2289 2305 8.949177 GCAAATCAATTGATTCCTTTTATTGGT 58.051 29.630 29.08 10.23 43.41 3.67
2290 2306 8.948145 TGCAAATCAATTGATTCCTTTTATTGG 58.052 29.630 29.08 8.13 43.41 3.16
2312 2328 8.836413 CGGATCTAACTTCCTTAAATTATGCAA 58.164 33.333 0.00 0.00 0.00 4.08
2313 2329 7.990886 ACGGATCTAACTTCCTTAAATTATGCA 59.009 33.333 0.00 0.00 0.00 3.96
2314 2330 8.283291 CACGGATCTAACTTCCTTAAATTATGC 58.717 37.037 0.00 0.00 0.00 3.14
2315 2331 9.542462 TCACGGATCTAACTTCCTTAAATTATG 57.458 33.333 0.00 0.00 0.00 1.90
2318 2334 9.462606 AAATCACGGATCTAACTTCCTTAAATT 57.537 29.630 0.00 0.00 0.00 1.82
2319 2335 8.893727 CAAATCACGGATCTAACTTCCTTAAAT 58.106 33.333 0.00 0.00 0.00 1.40
2320 2336 7.881232 ACAAATCACGGATCTAACTTCCTTAAA 59.119 33.333 0.00 0.00 0.00 1.52
2321 2337 7.391620 ACAAATCACGGATCTAACTTCCTTAA 58.608 34.615 0.00 0.00 0.00 1.85
2322 2338 6.942976 ACAAATCACGGATCTAACTTCCTTA 58.057 36.000 0.00 0.00 0.00 2.69
2323 2339 5.805728 ACAAATCACGGATCTAACTTCCTT 58.194 37.500 0.00 0.00 0.00 3.36
2324 2340 5.422214 ACAAATCACGGATCTAACTTCCT 57.578 39.130 0.00 0.00 0.00 3.36
2325 2341 7.787725 ATAACAAATCACGGATCTAACTTCC 57.212 36.000 0.00 0.00 0.00 3.46
2326 2342 8.979574 CCTATAACAAATCACGGATCTAACTTC 58.020 37.037 0.00 0.00 0.00 3.01
2327 2343 8.483758 ACCTATAACAAATCACGGATCTAACTT 58.516 33.333 0.00 0.00 0.00 2.66
2328 2344 8.019656 ACCTATAACAAATCACGGATCTAACT 57.980 34.615 0.00 0.00 0.00 2.24
2329 2345 8.658499 AACCTATAACAAATCACGGATCTAAC 57.342 34.615 0.00 0.00 0.00 2.34
2330 2346 9.976511 CTAACCTATAACAAATCACGGATCTAA 57.023 33.333 0.00 0.00 0.00 2.10
2331 2347 8.582437 CCTAACCTATAACAAATCACGGATCTA 58.418 37.037 0.00 0.00 0.00 1.98
2332 2348 7.289317 TCCTAACCTATAACAAATCACGGATCT 59.711 37.037 0.00 0.00 0.00 2.75
2333 2349 7.439381 TCCTAACCTATAACAAATCACGGATC 58.561 38.462 0.00 0.00 0.00 3.36
2334 2350 7.369551 TCCTAACCTATAACAAATCACGGAT 57.630 36.000 0.00 0.00 0.00 4.18
2335 2351 6.795144 TCCTAACCTATAACAAATCACGGA 57.205 37.500 0.00 0.00 0.00 4.69
2336 2352 7.551617 ACTTTCCTAACCTATAACAAATCACGG 59.448 37.037 0.00 0.00 0.00 4.94
2337 2353 8.488651 ACTTTCCTAACCTATAACAAATCACG 57.511 34.615 0.00 0.00 0.00 4.35
2341 2357 9.462606 CCAGAACTTTCCTAACCTATAACAAAT 57.537 33.333 0.00 0.00 0.00 2.32
2342 2358 8.442374 ACCAGAACTTTCCTAACCTATAACAAA 58.558 33.333 0.00 0.00 0.00 2.83
2343 2359 7.981142 ACCAGAACTTTCCTAACCTATAACAA 58.019 34.615 0.00 0.00 0.00 2.83
2344 2360 7.563724 ACCAGAACTTTCCTAACCTATAACA 57.436 36.000 0.00 0.00 0.00 2.41
2345 2361 7.881751 ACAACCAGAACTTTCCTAACCTATAAC 59.118 37.037 0.00 0.00 0.00 1.89
2346 2362 7.981142 ACAACCAGAACTTTCCTAACCTATAA 58.019 34.615 0.00 0.00 0.00 0.98
2347 2363 7.563724 ACAACCAGAACTTTCCTAACCTATA 57.436 36.000 0.00 0.00 0.00 1.31
2348 2364 6.449830 ACAACCAGAACTTTCCTAACCTAT 57.550 37.500 0.00 0.00 0.00 2.57
2349 2365 5.899631 ACAACCAGAACTTTCCTAACCTA 57.100 39.130 0.00 0.00 0.00 3.08
2350 2366 4.790718 ACAACCAGAACTTTCCTAACCT 57.209 40.909 0.00 0.00 0.00 3.50
2351 2367 8.625786 TTATTACAACCAGAACTTTCCTAACC 57.374 34.615 0.00 0.00 0.00 2.85
2354 2370 9.720769 CTCTTTATTACAACCAGAACTTTCCTA 57.279 33.333 0.00 0.00 0.00 2.94
2355 2371 8.218488 ACTCTTTATTACAACCAGAACTTTCCT 58.782 33.333 0.00 0.00 0.00 3.36
2356 2372 8.290325 CACTCTTTATTACAACCAGAACTTTCC 58.710 37.037 0.00 0.00 0.00 3.13
2357 2373 9.052759 TCACTCTTTATTACAACCAGAACTTTC 57.947 33.333 0.00 0.00 0.00 2.62
2358 2374 8.974060 TCACTCTTTATTACAACCAGAACTTT 57.026 30.769 0.00 0.00 0.00 2.66
2359 2375 8.974060 TTCACTCTTTATTACAACCAGAACTT 57.026 30.769 0.00 0.00 0.00 2.66
2360 2376 8.429641 TCTTCACTCTTTATTACAACCAGAACT 58.570 33.333 0.00 0.00 0.00 3.01
2361 2377 8.603242 TCTTCACTCTTTATTACAACCAGAAC 57.397 34.615 0.00 0.00 0.00 3.01
2362 2378 8.647796 TCTCTTCACTCTTTATTACAACCAGAA 58.352 33.333 0.00 0.00 0.00 3.02
2363 2379 8.190326 TCTCTTCACTCTTTATTACAACCAGA 57.810 34.615 0.00 0.00 0.00 3.86
2364 2380 8.833231 TTCTCTTCACTCTTTATTACAACCAG 57.167 34.615 0.00 0.00 0.00 4.00
2365 2381 9.621629 TTTTCTCTTCACTCTTTATTACAACCA 57.378 29.630 0.00 0.00 0.00 3.67
2374 2390 9.550406 TCGGTTTATTTTTCTCTTCACTCTTTA 57.450 29.630 0.00 0.00 0.00 1.85
2375 2391 8.446599 TCGGTTTATTTTTCTCTTCACTCTTT 57.553 30.769 0.00 0.00 0.00 2.52
2376 2392 8.507249 CATCGGTTTATTTTTCTCTTCACTCTT 58.493 33.333 0.00 0.00 0.00 2.85
2377 2393 7.878127 TCATCGGTTTATTTTTCTCTTCACTCT 59.122 33.333 0.00 0.00 0.00 3.24
2378 2394 8.029642 TCATCGGTTTATTTTTCTCTTCACTC 57.970 34.615 0.00 0.00 0.00 3.51
2379 2395 7.979444 TCATCGGTTTATTTTTCTCTTCACT 57.021 32.000 0.00 0.00 0.00 3.41
2380 2396 7.537649 GGTTCATCGGTTTATTTTTCTCTTCAC 59.462 37.037 0.00 0.00 0.00 3.18
2381 2397 7.229707 TGGTTCATCGGTTTATTTTTCTCTTCA 59.770 33.333 0.00 0.00 0.00 3.02
2382 2398 7.590279 TGGTTCATCGGTTTATTTTTCTCTTC 58.410 34.615 0.00 0.00 0.00 2.87
2383 2399 7.309194 CCTGGTTCATCGGTTTATTTTTCTCTT 60.309 37.037 0.00 0.00 0.00 2.85
2384 2400 6.151144 CCTGGTTCATCGGTTTATTTTTCTCT 59.849 38.462 0.00 0.00 0.00 3.10
2385 2401 6.150474 TCCTGGTTCATCGGTTTATTTTTCTC 59.850 38.462 0.00 0.00 0.00 2.87
2386 2402 6.007703 TCCTGGTTCATCGGTTTATTTTTCT 58.992 36.000 0.00 0.00 0.00 2.52
2387 2403 6.262193 TCCTGGTTCATCGGTTTATTTTTC 57.738 37.500 0.00 0.00 0.00 2.29
2388 2404 6.350949 CCATCCTGGTTCATCGGTTTATTTTT 60.351 38.462 0.00 0.00 31.35 1.94
2389 2405 5.127031 CCATCCTGGTTCATCGGTTTATTTT 59.873 40.000 0.00 0.00 31.35 1.82
2390 2406 4.644685 CCATCCTGGTTCATCGGTTTATTT 59.355 41.667 0.00 0.00 31.35 1.40
2391 2407 4.207165 CCATCCTGGTTCATCGGTTTATT 58.793 43.478 0.00 0.00 31.35 1.40
2392 2408 3.435026 CCCATCCTGGTTCATCGGTTTAT 60.435 47.826 0.00 0.00 35.17 1.40
2393 2409 2.092646 CCCATCCTGGTTCATCGGTTTA 60.093 50.000 0.00 0.00 35.17 2.01
2394 2410 1.340991 CCCATCCTGGTTCATCGGTTT 60.341 52.381 0.00 0.00 35.17 3.27
2395 2411 0.255890 CCCATCCTGGTTCATCGGTT 59.744 55.000 0.00 0.00 35.17 4.44
2396 2412 0.620410 TCCCATCCTGGTTCATCGGT 60.620 55.000 0.00 0.00 35.17 4.69
2397 2413 0.107456 CTCCCATCCTGGTTCATCGG 59.893 60.000 0.00 0.00 35.17 4.18
2398 2414 0.107456 CCTCCCATCCTGGTTCATCG 59.893 60.000 0.00 0.00 35.17 3.84
2399 2415 0.475906 CCCTCCCATCCTGGTTCATC 59.524 60.000 0.00 0.00 35.17 2.92
2400 2416 0.995675 CCCCTCCCATCCTGGTTCAT 60.996 60.000 0.00 0.00 35.17 2.57
2401 2417 1.619363 CCCCTCCCATCCTGGTTCA 60.619 63.158 0.00 0.00 35.17 3.18
2402 2418 2.386935 CCCCCTCCCATCCTGGTTC 61.387 68.421 0.00 0.00 35.17 3.62
2403 2419 2.287194 CCCCCTCCCATCCTGGTT 60.287 66.667 0.00 0.00 35.17 3.67
2404 2420 3.637544 ACCCCCTCCCATCCTGGT 61.638 66.667 0.00 0.00 35.17 4.00
2405 2421 3.099170 CACCCCCTCCCATCCTGG 61.099 72.222 0.00 0.00 37.25 4.45
2406 2422 3.099170 CCACCCCCTCCCATCCTG 61.099 72.222 0.00 0.00 0.00 3.86
2407 2423 3.637544 ACCACCCCCTCCCATCCT 61.638 66.667 0.00 0.00 0.00 3.24
2408 2424 3.420482 CACCACCCCCTCCCATCC 61.420 72.222 0.00 0.00 0.00 3.51
2409 2425 3.420482 CCACCACCCCCTCCCATC 61.420 72.222 0.00 0.00 0.00 3.51
2413 2429 3.883822 TTCTCCCACCACCCCCTCC 62.884 68.421 0.00 0.00 0.00 4.30
2414 2430 2.204090 TTCTCCCACCACCCCCTC 60.204 66.667 0.00 0.00 0.00 4.30
2415 2431 2.204151 CTTCTCCCACCACCCCCT 60.204 66.667 0.00 0.00 0.00 4.79
2416 2432 2.204090 TCTTCTCCCACCACCCCC 60.204 66.667 0.00 0.00 0.00 5.40
2417 2433 1.229529 TCTCTTCTCCCACCACCCC 60.230 63.158 0.00 0.00 0.00 4.95
2418 2434 1.889530 CGTCTCTTCTCCCACCACCC 61.890 65.000 0.00 0.00 0.00 4.61
2419 2435 0.898789 TCGTCTCTTCTCCCACCACC 60.899 60.000 0.00 0.00 0.00 4.61
2420 2436 0.966920 TTCGTCTCTTCTCCCACCAC 59.033 55.000 0.00 0.00 0.00 4.16
2421 2437 1.712056 TTTCGTCTCTTCTCCCACCA 58.288 50.000 0.00 0.00 0.00 4.17
2422 2438 2.833631 TTTTCGTCTCTTCTCCCACC 57.166 50.000 0.00 0.00 0.00 4.61
2440 2456 4.504826 CGTGGTTTATTTTCGCTGGTTTTT 59.495 37.500 0.00 0.00 0.00 1.94
2441 2457 4.045783 CGTGGTTTATTTTCGCTGGTTTT 58.954 39.130 0.00 0.00 0.00 2.43
2442 2458 3.551250 CCGTGGTTTATTTTCGCTGGTTT 60.551 43.478 0.00 0.00 0.00 3.27
2443 2459 2.030628 CCGTGGTTTATTTTCGCTGGTT 60.031 45.455 0.00 0.00 0.00 3.67
2444 2460 1.538075 CCGTGGTTTATTTTCGCTGGT 59.462 47.619 0.00 0.00 0.00 4.00
2445 2461 1.807742 TCCGTGGTTTATTTTCGCTGG 59.192 47.619 0.00 0.00 0.00 4.85
2446 2462 2.739913 TCTCCGTGGTTTATTTTCGCTG 59.260 45.455 0.00 0.00 0.00 5.18
2447 2463 2.740447 GTCTCCGTGGTTTATTTTCGCT 59.260 45.455 0.00 0.00 0.00 4.93
2448 2464 2.473376 CGTCTCCGTGGTTTATTTTCGC 60.473 50.000 0.00 0.00 0.00 4.70
2449 2465 2.988493 TCGTCTCCGTGGTTTATTTTCG 59.012 45.455 0.00 0.00 35.01 3.46
2450 2466 5.121142 TGAATCGTCTCCGTGGTTTATTTTC 59.879 40.000 0.00 0.00 35.01 2.29
2451 2467 4.998672 TGAATCGTCTCCGTGGTTTATTTT 59.001 37.500 0.00 0.00 35.01 1.82
2452 2468 4.390909 GTGAATCGTCTCCGTGGTTTATTT 59.609 41.667 0.00 0.00 35.01 1.40
2453 2469 3.930848 GTGAATCGTCTCCGTGGTTTATT 59.069 43.478 0.00 0.00 35.01 1.40
2454 2470 3.518590 GTGAATCGTCTCCGTGGTTTAT 58.481 45.455 0.00 0.00 35.01 1.40
2455 2471 2.950433 GTGAATCGTCTCCGTGGTTTA 58.050 47.619 0.00 0.00 35.01 2.01
2456 2472 1.792006 GTGAATCGTCTCCGTGGTTT 58.208 50.000 0.00 0.00 35.01 3.27
2457 2473 3.509388 GTGAATCGTCTCCGTGGTT 57.491 52.632 0.00 0.00 35.01 3.67


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

AutoCloner maintained by Alex Coulton.