Multiple sequence alignment - TraesCS6B01G037800

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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 TraesCS6B01G037800 chr6B 100.000 2453 0 0 1 2453 22425223 22427675 0.000000e+00 4530
1 TraesCS6B01G037800 chr1D 97.276 2203 57 3 1 2201 254497276 254499477 0.000000e+00 3733
2 TraesCS6B01G037800 chr1D 93.827 2203 117 14 1 2201 244484765 244482580 0.000000e+00 3297
3 TraesCS6B01G037800 chr5D 97.231 2203 54 6 1 2201 6202000 6199803 0.000000e+00 3723
4 TraesCS6B01G037800 chr5D 96.708 1519 46 4 683 2199 329162138 329163654 0.000000e+00 2525
5 TraesCS6B01G037800 chr5D 97.272 1393 36 2 810 2201 560872556 560873947 0.000000e+00 2361
6 TraesCS6B01G037800 chr4D 95.822 2202 86 6 1 2201 19915776 19917972 0.000000e+00 3552
7 TraesCS6B01G037800 chr7A 94.094 2201 126 4 1 2201 352194743 352192547 0.000000e+00 3341
8 TraesCS6B01G037800 chr3D 97.019 1845 50 4 1 1842 21903905 21905747 0.000000e+00 3097
9 TraesCS6B01G037800 chr3D 96.154 260 3 2 2201 2453 24161354 24161095 3.770000e-113 418
10 TraesCS6B01G037800 chr1A 95.250 1958 78 7 250 2201 168451039 168449091 0.000000e+00 3086
11 TraesCS6B01G037800 chr1A 97.772 1122 23 2 1 1122 112776754 112775635 0.000000e+00 1932
12 TraesCS6B01G037800 chr7B 97.287 258 2 2 2201 2453 662741829 662742086 1.350000e-117 433
13 TraesCS6B01G037800 chr7B 96.875 256 5 1 2201 2453 397631124 397630869 2.250000e-115 425
14 TraesCS6B01G037800 chr3A 96.887 257 3 2 2202 2453 273159631 273159887 2.250000e-115 425
15 TraesCS6B01G037800 chr3A 96.512 258 3 3 2201 2453 524024374 524024118 2.920000e-114 422
16 TraesCS6B01G037800 chrUn 96.154 260 3 2 2201 2453 425830150 425829891 3.770000e-113 418
17 TraesCS6B01G037800 chr3B 96.139 259 4 2 2201 2453 201488914 201488656 3.770000e-113 418
18 TraesCS6B01G037800 chr2D 96.154 260 3 2 2201 2453 630263054 630262795 3.770000e-113 418
19 TraesCS6B01G037800 chr2B 96.109 257 5 3 2201 2453 683741638 683741383 4.880000e-112 414


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 TraesCS6B01G037800 chr6B 22425223 22427675 2452 False 4530 4530 100.000 1 2453 1 chr6B.!!$F1 2452
1 TraesCS6B01G037800 chr1D 254497276 254499477 2201 False 3733 3733 97.276 1 2201 1 chr1D.!!$F1 2200
2 TraesCS6B01G037800 chr1D 244482580 244484765 2185 True 3297 3297 93.827 1 2201 1 chr1D.!!$R1 2200
3 TraesCS6B01G037800 chr5D 6199803 6202000 2197 True 3723 3723 97.231 1 2201 1 chr5D.!!$R1 2200
4 TraesCS6B01G037800 chr5D 329162138 329163654 1516 False 2525 2525 96.708 683 2199 1 chr5D.!!$F1 1516
5 TraesCS6B01G037800 chr5D 560872556 560873947 1391 False 2361 2361 97.272 810 2201 1 chr5D.!!$F2 1391
6 TraesCS6B01G037800 chr4D 19915776 19917972 2196 False 3552 3552 95.822 1 2201 1 chr4D.!!$F1 2200
7 TraesCS6B01G037800 chr7A 352192547 352194743 2196 True 3341 3341 94.094 1 2201 1 chr7A.!!$R1 2200
8 TraesCS6B01G037800 chr3D 21903905 21905747 1842 False 3097 3097 97.019 1 1842 1 chr3D.!!$F1 1841
9 TraesCS6B01G037800 chr1A 168449091 168451039 1948 True 3086 3086 95.250 250 2201 1 chr1A.!!$R2 1951
10 TraesCS6B01G037800 chr1A 112775635 112776754 1119 True 1932 1932 97.772 1 1122 1 chr1A.!!$R1 1121

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
109 110 2.000447 GTGGAGACAAGGTATGTTCGC 59.000 52.381 0.00 0.0 44.12 4.70 F
233 234 2.031683 GGCAGGTACGCATATTGTGTTC 59.968 50.000 0.00 0.0 41.83 3.18 F
1240 1256 2.180432 AGACCGGGCTACTTTGAAAC 57.820 50.000 9.02 0.0 0.00 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1319 1335 1.374505 GCGCCATGCCAAATGTGTT 60.375 52.632 0.0 0.0 37.76 3.32 R
1374 1390 2.426024 CACTTGAGCATCCAAATCTGGG 59.574 50.000 0.0 0.0 43.71 4.45 R
2297 2317 1.412710 TGGTAAAGCTCCTAGATGGCG 59.587 52.381 0.0 0.0 35.26 5.69 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
109 110 2.000447 GTGGAGACAAGGTATGTTCGC 59.000 52.381 0.00 0.00 44.12 4.70
233 234 2.031683 GGCAGGTACGCATATTGTGTTC 59.968 50.000 0.00 0.00 41.83 3.18
281 282 3.074390 TCTGGCATTGGGTATATTGGGAG 59.926 47.826 0.00 0.00 0.00 4.30
282 283 3.059853 TGGCATTGGGTATATTGGGAGA 58.940 45.455 0.00 0.00 0.00 3.71
463 464 6.243216 TGGACTAACTGGAAAAGTACAAGT 57.757 37.500 0.00 0.00 38.56 3.16
582 589 4.202264 CGGGCTTATTCCATCTTAGTGTCT 60.202 45.833 0.00 0.00 0.00 3.41
977 991 9.218525 ACATCCCATCTTTAGAGATAAAGAAGA 57.781 33.333 12.90 10.78 45.66 2.87
1240 1256 2.180432 AGACCGGGCTACTTTGAAAC 57.820 50.000 9.02 0.00 0.00 2.78
1319 1335 4.630894 TTGCTTTGCTCTTCTTTTTCGA 57.369 36.364 0.00 0.00 0.00 3.71
1374 1390 5.088739 CGAGATGTTTTTGCTGGTATTGAC 58.911 41.667 0.00 0.00 0.00 3.18
1448 1464 1.897560 ACTACAAGGAAACAGGCAGC 58.102 50.000 0.00 0.00 0.00 5.25
1534 1550 6.040842 TCCCATCCTTTCTTTGACTCTTTTTG 59.959 38.462 0.00 0.00 0.00 2.44
1538 1554 9.154847 CATCCTTTCTTTGACTCTTTTTGTTTT 57.845 29.630 0.00 0.00 0.00 2.43
1586 1602 8.780846 ATTACAAATGAATACGTGTGGAAGTA 57.219 30.769 0.00 0.00 27.91 2.24
1638 1655 5.751243 ATGGAAGCATTGGTTTATACGTC 57.249 39.130 2.14 0.00 0.00 4.34
1780 1798 6.042208 CCAGATAGGGGGACTTCTTACTTAAG 59.958 46.154 0.00 0.00 34.65 1.85
1954 1972 9.838339 AGATTACAATGGATCTACGAAAAGATT 57.162 29.630 0.00 0.00 36.33 2.40
2066 2086 1.612676 AACCTAGGCCAAAACGAACC 58.387 50.000 9.30 0.00 0.00 3.62
2268 2288 2.770164 AAAGGAGTCTTCATGTCCCG 57.230 50.000 0.00 0.00 31.82 5.14
2269 2289 1.645710 AAGGAGTCTTCATGTCCCGT 58.354 50.000 0.00 0.00 0.00 5.28
2270 2290 1.645710 AGGAGTCTTCATGTCCCGTT 58.354 50.000 0.00 0.00 0.00 4.44
2271 2291 2.816411 AGGAGTCTTCATGTCCCGTTA 58.184 47.619 0.00 0.00 0.00 3.18
2272 2292 3.375699 AGGAGTCTTCATGTCCCGTTAT 58.624 45.455 0.00 0.00 0.00 1.89
2273 2293 3.385111 AGGAGTCTTCATGTCCCGTTATC 59.615 47.826 0.00 0.00 0.00 1.75
2274 2294 3.372954 GAGTCTTCATGTCCCGTTATCG 58.627 50.000 0.00 0.00 0.00 2.92
2275 2295 3.021695 AGTCTTCATGTCCCGTTATCGA 58.978 45.455 0.00 0.00 39.71 3.59
2276 2296 3.066900 AGTCTTCATGTCCCGTTATCGAG 59.933 47.826 0.00 0.00 39.71 4.04
2277 2297 2.361119 TCTTCATGTCCCGTTATCGAGG 59.639 50.000 0.00 0.00 39.71 4.63
2278 2298 2.061509 TCATGTCCCGTTATCGAGGA 57.938 50.000 0.00 0.00 39.71 3.71
2279 2299 1.679680 TCATGTCCCGTTATCGAGGAC 59.320 52.381 18.99 18.99 46.86 3.85
2280 2300 1.038280 ATGTCCCGTTATCGAGGACC 58.962 55.000 21.18 10.82 46.52 4.46
2281 2301 0.033796 TGTCCCGTTATCGAGGACCT 60.034 55.000 21.18 0.00 46.52 3.85
2282 2302 0.667453 GTCCCGTTATCGAGGACCTC 59.333 60.000 11.87 11.87 44.09 3.85
2311 2331 4.423625 AAAAATACGCCATCTAGGAGCT 57.576 40.909 0.00 0.00 41.55 4.09
2312 2332 4.423625 AAAATACGCCATCTAGGAGCTT 57.576 40.909 0.00 0.00 41.55 3.74
2313 2333 4.423625 AAATACGCCATCTAGGAGCTTT 57.576 40.909 0.00 0.00 41.55 3.51
2314 2334 5.546621 AAATACGCCATCTAGGAGCTTTA 57.453 39.130 0.00 0.00 41.55 1.85
2315 2335 2.892784 ACGCCATCTAGGAGCTTTAC 57.107 50.000 0.00 0.00 41.55 2.01
2316 2336 1.413077 ACGCCATCTAGGAGCTTTACC 59.587 52.381 0.00 0.00 41.55 2.85
2317 2337 1.412710 CGCCATCTAGGAGCTTTACCA 59.587 52.381 0.00 0.00 41.22 3.25
2318 2338 2.546795 CGCCATCTAGGAGCTTTACCAG 60.547 54.545 0.00 0.00 41.22 4.00
2319 2339 2.224402 GCCATCTAGGAGCTTTACCAGG 60.224 54.545 0.00 0.00 41.22 4.45
2320 2340 3.309296 CCATCTAGGAGCTTTACCAGGA 58.691 50.000 0.00 0.00 41.22 3.86
2321 2341 3.070302 CCATCTAGGAGCTTTACCAGGAC 59.930 52.174 0.00 0.00 41.22 3.85
2322 2342 3.759815 TCTAGGAGCTTTACCAGGACT 57.240 47.619 0.00 0.00 0.00 3.85
2323 2343 3.633418 TCTAGGAGCTTTACCAGGACTC 58.367 50.000 0.00 0.00 0.00 3.36
2324 2344 2.327325 AGGAGCTTTACCAGGACTCA 57.673 50.000 0.00 0.00 0.00 3.41
2325 2345 1.903183 AGGAGCTTTACCAGGACTCAC 59.097 52.381 0.00 0.00 0.00 3.51
2326 2346 1.903183 GGAGCTTTACCAGGACTCACT 59.097 52.381 0.00 0.00 0.00 3.41
2327 2347 3.097614 GGAGCTTTACCAGGACTCACTA 58.902 50.000 0.00 0.00 0.00 2.74
2328 2348 3.131400 GGAGCTTTACCAGGACTCACTAG 59.869 52.174 0.00 0.00 0.00 2.57
2329 2349 4.017808 GAGCTTTACCAGGACTCACTAGA 58.982 47.826 0.00 0.00 0.00 2.43
2330 2350 4.417437 AGCTTTACCAGGACTCACTAGAA 58.583 43.478 0.00 0.00 0.00 2.10
2331 2351 4.838986 AGCTTTACCAGGACTCACTAGAAA 59.161 41.667 0.00 0.00 0.00 2.52
2332 2352 5.307196 AGCTTTACCAGGACTCACTAGAAAA 59.693 40.000 0.00 0.00 0.00 2.29
2333 2353 5.995897 GCTTTACCAGGACTCACTAGAAAAA 59.004 40.000 0.00 0.00 0.00 1.94
2334 2354 6.073167 GCTTTACCAGGACTCACTAGAAAAAC 60.073 42.308 0.00 0.00 0.00 2.43
2335 2355 6.488769 TTACCAGGACTCACTAGAAAAACA 57.511 37.500 0.00 0.00 0.00 2.83
2336 2356 4.704965 ACCAGGACTCACTAGAAAAACAC 58.295 43.478 0.00 0.00 0.00 3.32
2337 2357 4.065789 CCAGGACTCACTAGAAAAACACC 58.934 47.826 0.00 0.00 0.00 4.16
2338 2358 4.202367 CCAGGACTCACTAGAAAAACACCT 60.202 45.833 0.00 0.00 0.00 4.00
2339 2359 5.011738 CCAGGACTCACTAGAAAAACACCTA 59.988 44.000 0.00 0.00 0.00 3.08
2340 2360 6.463897 CCAGGACTCACTAGAAAAACACCTAA 60.464 42.308 0.00 0.00 0.00 2.69
2341 2361 6.990349 CAGGACTCACTAGAAAAACACCTAAA 59.010 38.462 0.00 0.00 0.00 1.85
2342 2362 7.661847 CAGGACTCACTAGAAAAACACCTAAAT 59.338 37.037 0.00 0.00 0.00 1.40
2343 2363 7.878644 AGGACTCACTAGAAAAACACCTAAATC 59.121 37.037 0.00 0.00 0.00 2.17
2344 2364 7.119407 GGACTCACTAGAAAAACACCTAAATCC 59.881 40.741 0.00 0.00 0.00 3.01
2345 2365 6.649557 ACTCACTAGAAAAACACCTAAATCCG 59.350 38.462 0.00 0.00 0.00 4.18
2346 2366 5.935789 TCACTAGAAAAACACCTAAATCCGG 59.064 40.000 0.00 0.00 0.00 5.14
2347 2367 5.935789 CACTAGAAAAACACCTAAATCCGGA 59.064 40.000 6.61 6.61 0.00 5.14
2348 2368 6.428771 CACTAGAAAAACACCTAAATCCGGAA 59.571 38.462 9.01 0.00 0.00 4.30
2349 2369 5.959618 AGAAAAACACCTAAATCCGGAAG 57.040 39.130 9.01 0.18 0.00 3.46
2350 2370 5.382616 AGAAAAACACCTAAATCCGGAAGT 58.617 37.500 9.01 0.89 0.00 3.01
2351 2371 6.536447 AGAAAAACACCTAAATCCGGAAGTA 58.464 36.000 9.01 2.31 0.00 2.24
2352 2372 6.999871 AGAAAAACACCTAAATCCGGAAGTAA 59.000 34.615 9.01 0.00 0.00 2.24
2353 2373 7.668469 AGAAAAACACCTAAATCCGGAAGTAAT 59.332 33.333 9.01 0.00 0.00 1.89
2354 2374 6.997239 AAACACCTAAATCCGGAAGTAATC 57.003 37.500 9.01 0.00 0.00 1.75
2355 2375 5.952347 ACACCTAAATCCGGAAGTAATCT 57.048 39.130 9.01 0.00 0.00 2.40
2356 2376 6.309389 ACACCTAAATCCGGAAGTAATCTT 57.691 37.500 9.01 0.00 36.51 2.40
2357 2377 7.427989 ACACCTAAATCCGGAAGTAATCTTA 57.572 36.000 9.01 0.00 33.64 2.10
2358 2378 7.854337 ACACCTAAATCCGGAAGTAATCTTAA 58.146 34.615 9.01 0.00 33.64 1.85
2359 2379 8.323567 ACACCTAAATCCGGAAGTAATCTTAAA 58.676 33.333 9.01 0.00 33.64 1.52
2360 2380 9.169592 CACCTAAATCCGGAAGTAATCTTAAAA 57.830 33.333 9.01 0.00 33.64 1.52
2361 2381 9.743581 ACCTAAATCCGGAAGTAATCTTAAAAA 57.256 29.630 9.01 0.00 33.64 1.94
2384 2404 5.411831 AATCAATTCTGGGAAAAAGGAGC 57.588 39.130 0.00 0.00 0.00 4.70
2385 2405 3.843422 TCAATTCTGGGAAAAAGGAGCA 58.157 40.909 0.00 0.00 0.00 4.26
2386 2406 4.222336 TCAATTCTGGGAAAAAGGAGCAA 58.778 39.130 0.00 0.00 0.00 3.91
2387 2407 4.840115 TCAATTCTGGGAAAAAGGAGCAAT 59.160 37.500 0.00 0.00 0.00 3.56
2388 2408 6.015918 TCAATTCTGGGAAAAAGGAGCAATA 58.984 36.000 0.00 0.00 0.00 1.90
2389 2409 6.669154 TCAATTCTGGGAAAAAGGAGCAATAT 59.331 34.615 0.00 0.00 0.00 1.28
2390 2410 6.721704 ATTCTGGGAAAAAGGAGCAATATC 57.278 37.500 0.00 0.00 0.00 1.63
2391 2411 4.199310 TCTGGGAAAAAGGAGCAATATCG 58.801 43.478 0.00 0.00 0.00 2.92
2392 2412 3.947834 CTGGGAAAAAGGAGCAATATCGT 59.052 43.478 0.00 0.00 0.00 3.73
2393 2413 5.104693 TCTGGGAAAAAGGAGCAATATCGTA 60.105 40.000 0.00 0.00 0.00 3.43
2394 2414 5.690865 TGGGAAAAAGGAGCAATATCGTAT 58.309 37.500 0.00 0.00 0.00 3.06
2395 2415 6.126409 TGGGAAAAAGGAGCAATATCGTATT 58.874 36.000 0.00 0.00 0.00 1.89
2396 2416 6.262273 TGGGAAAAAGGAGCAATATCGTATTC 59.738 38.462 0.00 0.00 0.00 1.75
2397 2417 6.363473 GGAAAAAGGAGCAATATCGTATTCG 58.637 40.000 0.00 0.00 38.55 3.34
2398 2418 6.018180 GGAAAAAGGAGCAATATCGTATTCGT 60.018 38.462 0.00 0.00 38.33 3.85
2399 2419 6.526566 AAAAGGAGCAATATCGTATTCGTC 57.473 37.500 0.00 0.00 38.33 4.20
2400 2420 5.455056 AAGGAGCAATATCGTATTCGTCT 57.545 39.130 0.00 0.00 38.33 4.18
2401 2421 5.455056 AGGAGCAATATCGTATTCGTCTT 57.545 39.130 0.00 0.00 38.33 3.01
2402 2422 5.462405 AGGAGCAATATCGTATTCGTCTTC 58.538 41.667 0.00 0.00 38.33 2.87
2403 2423 5.009710 AGGAGCAATATCGTATTCGTCTTCA 59.990 40.000 0.00 0.00 38.33 3.02
2404 2424 5.690409 GGAGCAATATCGTATTCGTCTTCAA 59.310 40.000 0.00 0.00 38.33 2.69
2405 2425 6.129062 GGAGCAATATCGTATTCGTCTTCAAG 60.129 42.308 0.00 0.00 38.33 3.02
2406 2426 6.504398 AGCAATATCGTATTCGTCTTCAAGA 58.496 36.000 0.00 0.00 38.33 3.02
2407 2427 6.978659 AGCAATATCGTATTCGTCTTCAAGAA 59.021 34.615 0.00 0.00 38.33 2.52
2408 2428 7.491372 AGCAATATCGTATTCGTCTTCAAGAAA 59.509 33.333 0.00 0.00 38.33 2.52
2409 2429 8.114290 GCAATATCGTATTCGTCTTCAAGAAAA 58.886 33.333 0.00 0.00 38.33 2.29
2410 2430 9.967245 CAATATCGTATTCGTCTTCAAGAAAAA 57.033 29.630 0.00 0.00 38.33 1.94
2411 2431 9.968743 AATATCGTATTCGTCTTCAAGAAAAAC 57.031 29.630 0.00 0.00 38.33 2.43
2412 2432 6.831727 TCGTATTCGTCTTCAAGAAAAACA 57.168 33.333 0.00 0.00 38.33 2.83
2413 2433 6.873656 TCGTATTCGTCTTCAAGAAAAACAG 58.126 36.000 0.00 0.00 38.33 3.16
2414 2434 6.698329 TCGTATTCGTCTTCAAGAAAAACAGA 59.302 34.615 0.00 0.00 38.33 3.41
2415 2435 7.223193 TCGTATTCGTCTTCAAGAAAAACAGAA 59.777 33.333 0.00 0.00 38.33 3.02
2416 2436 7.849026 CGTATTCGTCTTCAAGAAAAACAGAAA 59.151 33.333 0.00 0.00 0.00 2.52
2417 2437 9.665264 GTATTCGTCTTCAAGAAAAACAGAAAT 57.335 29.630 0.00 0.00 0.00 2.17
2419 2439 7.969387 TCGTCTTCAAGAAAAACAGAAATTG 57.031 32.000 0.00 0.00 0.00 2.32
2420 2440 6.472163 TCGTCTTCAAGAAAAACAGAAATTGC 59.528 34.615 0.00 0.00 0.00 3.56
2421 2441 6.253298 CGTCTTCAAGAAAAACAGAAATTGCA 59.747 34.615 0.00 0.00 0.00 4.08
2422 2442 7.043192 CGTCTTCAAGAAAAACAGAAATTGCAT 60.043 33.333 0.00 0.00 0.00 3.96
2423 2443 8.606602 GTCTTCAAGAAAAACAGAAATTGCATT 58.393 29.630 0.00 0.00 0.00 3.56
2424 2444 9.165035 TCTTCAAGAAAAACAGAAATTGCATTT 57.835 25.926 0.00 0.00 34.64 2.32
2425 2445 9.777575 CTTCAAGAAAAACAGAAATTGCATTTT 57.222 25.926 6.29 6.29 34.01 1.82
2426 2446 9.771915 TTCAAGAAAAACAGAAATTGCATTTTC 57.228 25.926 21.09 21.09 41.50 2.29
2427 2447 8.944029 TCAAGAAAAACAGAAATTGCATTTTCA 58.056 25.926 27.09 7.28 42.50 2.69
2428 2448 9.724839 CAAGAAAAACAGAAATTGCATTTTCAT 57.275 25.926 27.09 16.52 42.50 2.57
2434 2454 8.851541 AACAGAAATTGCATTTTCATTATGGT 57.148 26.923 27.09 16.75 37.93 3.55
2435 2455 8.483307 ACAGAAATTGCATTTTCATTATGGTC 57.517 30.769 27.09 6.38 37.93 4.02
2436 2456 8.316214 ACAGAAATTGCATTTTCATTATGGTCT 58.684 29.630 27.09 8.19 37.93 3.85
2437 2457 8.600625 CAGAAATTGCATTTTCATTATGGTCTG 58.399 33.333 27.09 14.54 37.93 3.51
2438 2458 8.533657 AGAAATTGCATTTTCATTATGGTCTGA 58.466 29.630 27.09 0.00 37.93 3.27
2439 2459 8.483307 AAATTGCATTTTCATTATGGTCTGAC 57.517 30.769 0.00 0.00 0.00 3.51
2440 2460 6.587206 TTGCATTTTCATTATGGTCTGACA 57.413 33.333 10.38 0.00 0.00 3.58
2441 2461 6.198650 TGCATTTTCATTATGGTCTGACAG 57.801 37.500 10.38 0.00 0.00 3.51
2442 2462 5.945191 TGCATTTTCATTATGGTCTGACAGA 59.055 36.000 10.38 0.00 0.00 3.41
2443 2463 6.433716 TGCATTTTCATTATGGTCTGACAGAA 59.566 34.615 6.76 0.00 0.00 3.02
2444 2464 6.749118 GCATTTTCATTATGGTCTGACAGAAC 59.251 38.462 13.89 13.89 31.00 3.01
2445 2465 6.480524 TTTTCATTATGGTCTGACAGAACG 57.519 37.500 15.64 1.19 33.73 3.95
2446 2466 5.400066 TTCATTATGGTCTGACAGAACGA 57.600 39.130 15.64 3.48 33.73 3.85
2447 2467 4.744570 TCATTATGGTCTGACAGAACGAC 58.255 43.478 15.64 0.08 33.73 4.34
2448 2468 4.219725 TCATTATGGTCTGACAGAACGACA 59.780 41.667 15.64 9.01 33.73 4.35
2449 2469 4.594123 TTATGGTCTGACAGAACGACAA 57.406 40.909 15.64 6.58 33.73 3.18
2450 2470 3.685139 ATGGTCTGACAGAACGACAAT 57.315 42.857 15.64 0.72 33.73 2.71
2451 2471 3.469008 TGGTCTGACAGAACGACAATT 57.531 42.857 15.64 0.00 33.73 2.32
2452 2472 4.594123 TGGTCTGACAGAACGACAATTA 57.406 40.909 15.64 0.00 33.73 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 5.065218 CCTAAACGAGTCATGAAGGGAATTG 59.935 44.000 0.00 0.00 0.00 2.32
233 234 1.000938 GCCAAGAAACACAAGCCAGAG 60.001 52.381 0.00 0.00 0.00 3.35
281 282 7.487829 GTCCGCTCATCAGAGAATATTTCTATC 59.512 40.741 0.00 0.00 44.98 2.08
282 283 7.319646 GTCCGCTCATCAGAGAATATTTCTAT 58.680 38.462 0.00 0.00 44.98 1.98
361 362 1.076549 CCAAAGCAAGCCACCCCTA 59.923 57.895 0.00 0.00 0.00 3.53
463 464 0.402504 ACCCCACGCTGGATTTACAA 59.597 50.000 5.71 0.00 40.96 2.41
582 589 1.753930 TATAGACGTTGAGGCGGACA 58.246 50.000 0.00 0.00 35.98 4.02
618 625 7.448469 ACTGGAAAGTACAGTTTCAATATTGCT 59.552 33.333 10.76 0.00 46.38 3.91
881 895 3.012274 TCTGAATAATCCCCCTTTTGCCA 59.988 43.478 0.00 0.00 0.00 4.92
977 991 1.003223 GGCGTACAAAAAGCTCACGTT 60.003 47.619 0.00 0.00 35.17 3.99
1240 1256 1.666888 GCTGCGAAAAACACCATCAGG 60.667 52.381 0.00 0.00 42.21 3.86
1319 1335 1.374505 GCGCCATGCCAAATGTGTT 60.375 52.632 0.00 0.00 37.76 3.32
1374 1390 2.426024 CACTTGAGCATCCAAATCTGGG 59.574 50.000 0.00 0.00 43.71 4.45
1563 1579 8.780846 ATTACTTCCACACGTATTCATTTGTA 57.219 30.769 0.00 0.00 0.00 2.41
1638 1655 5.554070 TCCCTAAAGTCGAAACTAAAAGGG 58.446 41.667 11.07 11.07 43.71 3.95
1666 1684 7.362142 GGTTCTTGGAAGAAGATAGCGAAAAAT 60.362 37.037 1.96 0.00 45.01 1.82
1780 1798 3.549299 TCGAAGAACACGGAGACTAAC 57.451 47.619 0.00 0.00 0.00 2.34
1954 1972 9.524106 CTATTCCGTTGTAGATGTAAATACACA 57.476 33.333 0.00 0.00 39.30 3.72
1966 1986 8.959548 TGACTTTGTATACTATTCCGTTGTAGA 58.040 33.333 4.17 0.00 0.00 2.59
2066 2086 2.736144 TCAGTAAACTACCTGCACCG 57.264 50.000 0.00 0.00 0.00 4.94
2247 2267 3.181443 ACGGGACATGAAGACTCCTTTTT 60.181 43.478 0.00 0.00 31.62 1.94
2248 2268 2.372172 ACGGGACATGAAGACTCCTTTT 59.628 45.455 0.00 0.00 31.62 2.27
2249 2269 1.978580 ACGGGACATGAAGACTCCTTT 59.021 47.619 0.00 0.00 31.62 3.11
2250 2270 1.645710 ACGGGACATGAAGACTCCTT 58.354 50.000 0.00 0.00 34.81 3.36
2251 2271 1.645710 AACGGGACATGAAGACTCCT 58.354 50.000 0.00 0.00 0.00 3.69
2252 2272 3.718815 GATAACGGGACATGAAGACTCC 58.281 50.000 0.00 0.00 0.00 3.85
2253 2273 3.066342 TCGATAACGGGACATGAAGACTC 59.934 47.826 0.00 0.00 40.21 3.36
2254 2274 3.021695 TCGATAACGGGACATGAAGACT 58.978 45.455 0.00 0.00 40.21 3.24
2255 2275 3.372954 CTCGATAACGGGACATGAAGAC 58.627 50.000 0.00 0.00 43.41 3.01
2256 2276 2.361119 CCTCGATAACGGGACATGAAGA 59.639 50.000 0.00 0.00 43.41 2.87
2257 2277 2.361119 TCCTCGATAACGGGACATGAAG 59.639 50.000 0.00 0.00 43.41 3.02
2258 2278 2.380941 TCCTCGATAACGGGACATGAA 58.619 47.619 0.00 0.00 43.41 2.57
2259 2279 2.061509 TCCTCGATAACGGGACATGA 57.938 50.000 0.00 0.00 43.41 3.07
2264 2284 3.106738 GAGGTCCTCGATAACGGGA 57.893 57.895 2.28 0.00 43.41 5.14
2290 2310 4.423625 AGCTCCTAGATGGCGTATTTTT 57.576 40.909 0.00 0.00 35.26 1.94
2291 2311 4.423625 AAGCTCCTAGATGGCGTATTTT 57.576 40.909 0.00 0.00 35.26 1.82
2292 2312 4.423625 AAAGCTCCTAGATGGCGTATTT 57.576 40.909 0.00 0.00 35.26 1.40
2293 2313 4.262506 GGTAAAGCTCCTAGATGGCGTATT 60.263 45.833 0.00 0.00 35.26 1.89
2294 2314 3.258622 GGTAAAGCTCCTAGATGGCGTAT 59.741 47.826 0.00 0.00 35.26 3.06
2295 2315 2.626743 GGTAAAGCTCCTAGATGGCGTA 59.373 50.000 0.00 0.00 35.26 4.42
2296 2316 1.413077 GGTAAAGCTCCTAGATGGCGT 59.587 52.381 0.00 0.00 35.26 5.68
2297 2317 1.412710 TGGTAAAGCTCCTAGATGGCG 59.587 52.381 0.00 0.00 35.26 5.69
2298 2318 2.224402 CCTGGTAAAGCTCCTAGATGGC 60.224 54.545 0.00 0.00 35.26 4.40
2299 2319 3.070302 GTCCTGGTAAAGCTCCTAGATGG 59.930 52.174 0.00 0.00 37.10 3.51
2300 2320 3.964031 AGTCCTGGTAAAGCTCCTAGATG 59.036 47.826 0.00 0.00 0.00 2.90
2301 2321 4.219919 GAGTCCTGGTAAAGCTCCTAGAT 58.780 47.826 0.00 0.00 0.00 1.98
2302 2322 3.011369 TGAGTCCTGGTAAAGCTCCTAGA 59.989 47.826 0.00 0.00 0.00 2.43
2303 2323 3.131400 GTGAGTCCTGGTAAAGCTCCTAG 59.869 52.174 0.00 0.00 0.00 3.02
2304 2324 3.097614 GTGAGTCCTGGTAAAGCTCCTA 58.902 50.000 0.00 0.00 0.00 2.94
2305 2325 1.903183 GTGAGTCCTGGTAAAGCTCCT 59.097 52.381 0.00 0.00 0.00 3.69
2306 2326 1.903183 AGTGAGTCCTGGTAAAGCTCC 59.097 52.381 0.00 0.00 0.00 4.70
2307 2327 4.017808 TCTAGTGAGTCCTGGTAAAGCTC 58.982 47.826 0.00 0.00 0.00 4.09
2308 2328 4.048970 TCTAGTGAGTCCTGGTAAAGCT 57.951 45.455 0.00 0.00 0.00 3.74
2309 2329 4.803098 TTCTAGTGAGTCCTGGTAAAGC 57.197 45.455 0.00 0.00 0.00 3.51
2310 2330 6.990349 TGTTTTTCTAGTGAGTCCTGGTAAAG 59.010 38.462 0.00 0.00 0.00 1.85
2311 2331 6.764560 GTGTTTTTCTAGTGAGTCCTGGTAAA 59.235 38.462 0.00 0.00 0.00 2.01
2312 2332 6.285990 GTGTTTTTCTAGTGAGTCCTGGTAA 58.714 40.000 0.00 0.00 0.00 2.85
2313 2333 5.221581 GGTGTTTTTCTAGTGAGTCCTGGTA 60.222 44.000 0.00 0.00 0.00 3.25
2314 2334 4.444449 GGTGTTTTTCTAGTGAGTCCTGGT 60.444 45.833 0.00 0.00 0.00 4.00
2315 2335 4.065789 GGTGTTTTTCTAGTGAGTCCTGG 58.934 47.826 0.00 0.00 0.00 4.45
2316 2336 4.962155 AGGTGTTTTTCTAGTGAGTCCTG 58.038 43.478 0.00 0.00 0.00 3.86
2317 2337 6.742559 TTAGGTGTTTTTCTAGTGAGTCCT 57.257 37.500 0.00 0.00 0.00 3.85
2318 2338 7.119407 GGATTTAGGTGTTTTTCTAGTGAGTCC 59.881 40.741 0.00 0.00 0.00 3.85
2319 2339 7.148623 CGGATTTAGGTGTTTTTCTAGTGAGTC 60.149 40.741 0.00 0.00 0.00 3.36
2320 2340 6.649557 CGGATTTAGGTGTTTTTCTAGTGAGT 59.350 38.462 0.00 0.00 0.00 3.41
2321 2341 6.092259 CCGGATTTAGGTGTTTTTCTAGTGAG 59.908 42.308 0.00 0.00 0.00 3.51
2322 2342 5.935789 CCGGATTTAGGTGTTTTTCTAGTGA 59.064 40.000 0.00 0.00 0.00 3.41
2323 2343 5.935789 TCCGGATTTAGGTGTTTTTCTAGTG 59.064 40.000 0.00 0.00 0.00 2.74
2324 2344 6.117975 TCCGGATTTAGGTGTTTTTCTAGT 57.882 37.500 0.00 0.00 0.00 2.57
2325 2345 6.653740 ACTTCCGGATTTAGGTGTTTTTCTAG 59.346 38.462 4.15 0.00 0.00 2.43
2326 2346 6.536447 ACTTCCGGATTTAGGTGTTTTTCTA 58.464 36.000 4.15 0.00 0.00 2.10
2327 2347 5.382616 ACTTCCGGATTTAGGTGTTTTTCT 58.617 37.500 4.15 0.00 0.00 2.52
2328 2348 5.700722 ACTTCCGGATTTAGGTGTTTTTC 57.299 39.130 4.15 0.00 0.00 2.29
2329 2349 7.668469 AGATTACTTCCGGATTTAGGTGTTTTT 59.332 33.333 4.15 0.00 0.00 1.94
2330 2350 7.173032 AGATTACTTCCGGATTTAGGTGTTTT 58.827 34.615 4.15 0.00 0.00 2.43
2331 2351 6.718294 AGATTACTTCCGGATTTAGGTGTTT 58.282 36.000 4.15 0.00 0.00 2.83
2332 2352 6.309389 AGATTACTTCCGGATTTAGGTGTT 57.691 37.500 4.15 0.00 0.00 3.32
2333 2353 5.952347 AGATTACTTCCGGATTTAGGTGT 57.048 39.130 4.15 0.00 0.00 4.16
2334 2354 8.726870 TTTAAGATTACTTCCGGATTTAGGTG 57.273 34.615 4.15 0.00 37.53 4.00
2335 2355 9.743581 TTTTTAAGATTACTTCCGGATTTAGGT 57.256 29.630 4.15 2.38 37.53 3.08
2359 2379 6.712095 GCTCCTTTTTCCCAGAATTGATTTTT 59.288 34.615 0.00 0.00 0.00 1.94
2360 2380 6.183361 TGCTCCTTTTTCCCAGAATTGATTTT 60.183 34.615 0.00 0.00 0.00 1.82
2361 2381 5.307716 TGCTCCTTTTTCCCAGAATTGATTT 59.692 36.000 0.00 0.00 0.00 2.17
2362 2382 4.840115 TGCTCCTTTTTCCCAGAATTGATT 59.160 37.500 0.00 0.00 0.00 2.57
2363 2383 4.419282 TGCTCCTTTTTCCCAGAATTGAT 58.581 39.130 0.00 0.00 0.00 2.57
2364 2384 3.843422 TGCTCCTTTTTCCCAGAATTGA 58.157 40.909 0.00 0.00 0.00 2.57
2365 2385 4.605640 TTGCTCCTTTTTCCCAGAATTG 57.394 40.909 0.00 0.00 0.00 2.32
2366 2386 6.183360 CGATATTGCTCCTTTTTCCCAGAATT 60.183 38.462 0.00 0.00 0.00 2.17
2367 2387 5.300286 CGATATTGCTCCTTTTTCCCAGAAT 59.700 40.000 0.00 0.00 0.00 2.40
2368 2388 4.640201 CGATATTGCTCCTTTTTCCCAGAA 59.360 41.667 0.00 0.00 0.00 3.02
2369 2389 4.199310 CGATATTGCTCCTTTTTCCCAGA 58.801 43.478 0.00 0.00 0.00 3.86
2370 2390 3.947834 ACGATATTGCTCCTTTTTCCCAG 59.052 43.478 0.00 0.00 0.00 4.45
2371 2391 3.963129 ACGATATTGCTCCTTTTTCCCA 58.037 40.909 0.00 0.00 0.00 4.37
2372 2392 6.565999 CGAATACGATATTGCTCCTTTTTCCC 60.566 42.308 0.00 0.00 42.66 3.97
2373 2393 6.018180 ACGAATACGATATTGCTCCTTTTTCC 60.018 38.462 0.00 0.00 42.66 3.13
2374 2394 6.945072 ACGAATACGATATTGCTCCTTTTTC 58.055 36.000 0.00 0.00 42.66 2.29
2375 2395 6.761714 AGACGAATACGATATTGCTCCTTTTT 59.238 34.615 0.00 0.00 42.66 1.94
2376 2396 6.281405 AGACGAATACGATATTGCTCCTTTT 58.719 36.000 0.00 0.00 42.66 2.27
2377 2397 5.844004 AGACGAATACGATATTGCTCCTTT 58.156 37.500 0.00 0.00 42.66 3.11
2378 2398 5.455056 AGACGAATACGATATTGCTCCTT 57.545 39.130 0.00 0.00 42.66 3.36
2379 2399 5.009710 TGAAGACGAATACGATATTGCTCCT 59.990 40.000 0.00 0.00 42.66 3.69
2380 2400 5.220381 TGAAGACGAATACGATATTGCTCC 58.780 41.667 0.00 0.00 42.66 4.70
2381 2401 6.637254 TCTTGAAGACGAATACGATATTGCTC 59.363 38.462 0.00 0.00 42.66 4.26
2382 2402 6.504398 TCTTGAAGACGAATACGATATTGCT 58.496 36.000 0.00 0.00 42.66 3.91
2383 2403 6.749216 TCTTGAAGACGAATACGATATTGC 57.251 37.500 0.00 0.00 42.66 3.56
2384 2404 9.967245 TTTTTCTTGAAGACGAATACGATATTG 57.033 29.630 0.00 0.00 42.66 1.90
2385 2405 9.968743 GTTTTTCTTGAAGACGAATACGATATT 57.031 29.630 0.00 0.00 42.66 1.28
2386 2406 9.146984 TGTTTTTCTTGAAGACGAATACGATAT 57.853 29.630 0.00 0.00 42.66 1.63
2387 2407 8.523523 TGTTTTTCTTGAAGACGAATACGATA 57.476 30.769 0.00 0.00 42.66 2.92
2388 2408 7.384115 TCTGTTTTTCTTGAAGACGAATACGAT 59.616 33.333 0.00 0.00 42.66 3.73
2389 2409 6.698329 TCTGTTTTTCTTGAAGACGAATACGA 59.302 34.615 0.00 0.00 42.66 3.43
2390 2410 6.873656 TCTGTTTTTCTTGAAGACGAATACG 58.126 36.000 0.00 0.00 45.75 3.06
2391 2411 9.665264 ATTTCTGTTTTTCTTGAAGACGAATAC 57.335 29.630 0.00 0.00 0.00 1.89
2393 2413 9.023967 CAATTTCTGTTTTTCTTGAAGACGAAT 57.976 29.630 0.00 0.00 0.00 3.34
2394 2414 7.009174 GCAATTTCTGTTTTTCTTGAAGACGAA 59.991 33.333 0.00 0.00 0.00 3.85
2395 2415 6.472163 GCAATTTCTGTTTTTCTTGAAGACGA 59.528 34.615 0.00 0.00 0.00 4.20
2396 2416 6.253298 TGCAATTTCTGTTTTTCTTGAAGACG 59.747 34.615 0.00 0.00 0.00 4.18
2397 2417 7.524294 TGCAATTTCTGTTTTTCTTGAAGAC 57.476 32.000 0.00 0.00 0.00 3.01
2398 2418 8.721019 AATGCAATTTCTGTTTTTCTTGAAGA 57.279 26.923 0.00 0.00 26.74 2.87
2415 2435 7.613585 TGTCAGACCATAATGAAAATGCAATT 58.386 30.769 0.00 0.00 38.98 2.32
2416 2436 7.123098 TCTGTCAGACCATAATGAAAATGCAAT 59.877 33.333 0.00 0.00 0.00 3.56
2417 2437 6.433716 TCTGTCAGACCATAATGAAAATGCAA 59.566 34.615 0.00 0.00 0.00 4.08
2418 2438 5.945191 TCTGTCAGACCATAATGAAAATGCA 59.055 36.000 0.00 0.00 0.00 3.96
2419 2439 6.441093 TCTGTCAGACCATAATGAAAATGC 57.559 37.500 0.00 0.00 0.00 3.56
2420 2440 6.963242 CGTTCTGTCAGACCATAATGAAAATG 59.037 38.462 0.78 0.00 0.00 2.32
2421 2441 6.878923 TCGTTCTGTCAGACCATAATGAAAAT 59.121 34.615 0.78 0.00 0.00 1.82
2422 2442 6.147164 GTCGTTCTGTCAGACCATAATGAAAA 59.853 38.462 0.78 0.00 0.00 2.29
2423 2443 5.637810 GTCGTTCTGTCAGACCATAATGAAA 59.362 40.000 0.78 0.00 0.00 2.69
2424 2444 5.168569 GTCGTTCTGTCAGACCATAATGAA 58.831 41.667 0.78 0.00 0.00 2.57
2425 2445 4.219725 TGTCGTTCTGTCAGACCATAATGA 59.780 41.667 0.78 0.00 34.24 2.57
2426 2446 4.494484 TGTCGTTCTGTCAGACCATAATG 58.506 43.478 0.78 0.00 34.24 1.90
2427 2447 4.801330 TGTCGTTCTGTCAGACCATAAT 57.199 40.909 0.78 0.00 34.24 1.28
2428 2448 4.594123 TTGTCGTTCTGTCAGACCATAA 57.406 40.909 0.78 0.00 34.24 1.90
2429 2449 4.801330 ATTGTCGTTCTGTCAGACCATA 57.199 40.909 0.78 0.00 34.24 2.74
2430 2450 3.685139 ATTGTCGTTCTGTCAGACCAT 57.315 42.857 0.78 0.00 34.24 3.55
2431 2451 3.469008 AATTGTCGTTCTGTCAGACCA 57.531 42.857 0.78 0.00 34.24 4.02


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

AutoCloner maintained by Alex Coulton.