Multiple sequence alignment - TraesCS2A01G273200

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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 TraesCS2A01G273200 chr2A 100.000 2393 0 0 1 2393 447899692 447897300 0.000000e+00 4420.0
1 TraesCS2A01G273200 chr2A 96.426 1455 52 0 1 1455 679988196 679986742 0.000000e+00 2399.0
2 TraesCS2A01G273200 chr3A 97.537 1502 37 0 1 1502 110312759 110311258 0.000000e+00 2569.0
3 TraesCS2A01G273200 chr4A 98.479 1446 22 0 1 1446 546006792 546005347 0.000000e+00 2549.0
4 TraesCS2A01G273200 chr7A 97.079 1472 40 2 1 1469 7844591 7843120 0.000000e+00 2477.0
5 TraesCS2A01G273200 chr7A 88.326 1499 174 1 1 1499 20254408 20252911 0.000000e+00 1797.0
6 TraesCS2A01G273200 chr7A 88.059 1499 177 2 1 1498 270771073 270772570 0.000000e+00 1775.0
7 TraesCS2A01G273200 chr5A 91.267 1500 131 0 1 1500 707721226 707722725 0.000000e+00 2045.0
8 TraesCS2A01G273200 chr5A 89.103 1505 161 3 1 1504 622529042 622527540 0.000000e+00 1868.0
9 TraesCS2A01G273200 chr6B 85.743 1501 212 2 1 1500 68900866 68902365 0.000000e+00 1585.0
10 TraesCS2A01G273200 chr6B 86.842 76 6 4 1881 1954 16313261 16313334 5.480000e-12 82.4
11 TraesCS2A01G273200 chr2D 96.610 413 13 1 1679 2090 337399128 337399540 0.000000e+00 684.0
12 TraesCS2A01G273200 chr2D 95.775 142 5 1 1503 1644 337398701 337398841 6.650000e-56 228.0
13 TraesCS2A01G273200 chr2D 84.416 231 32 4 2164 2393 181207216 181207443 8.610000e-55 224.0
14 TraesCS2A01G273200 chr2D 82.969 229 39 0 2165 2393 145734753 145734981 8.670000e-50 207.0
15 TraesCS2A01G273200 chr2B 90.929 463 31 3 1632 2093 404741634 404741182 1.570000e-171 612.0
16 TraesCS2A01G273200 chr2B 97.297 148 4 0 1499 1646 404741798 404741651 3.950000e-63 252.0
17 TraesCS2A01G273200 chr5D 84.483 232 32 4 2164 2393 435666016 435666245 2.390000e-55 226.0
18 TraesCS2A01G273200 chr5D 86.634 202 27 0 2192 2393 37894457 37894658 8.610000e-55 224.0
19 TraesCS2A01G273200 chr5D 80.808 297 38 9 2113 2393 69985718 69986011 5.180000e-52 215.0
20 TraesCS2A01G273200 chrUn 84.305 223 32 2 2172 2393 110544659 110544439 5.180000e-52 215.0
21 TraesCS2A01G273200 chr7B 82.759 232 36 4 2164 2393 492753426 492753655 1.120000e-48 204.0
22 TraesCS2A01G273200 chr1D 83.412 211 33 2 2171 2380 439001458 439001667 6.750000e-46 195.0
23 TraesCS2A01G273200 chr7D 82.174 230 36 5 2165 2393 568768168 568768393 2.430000e-45 193.0


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 TraesCS2A01G273200 chr2A 447897300 447899692 2392 True 4420 4420 100.0000 1 2393 1 chr2A.!!$R1 2392
1 TraesCS2A01G273200 chr2A 679986742 679988196 1454 True 2399 2399 96.4260 1 1455 1 chr2A.!!$R2 1454
2 TraesCS2A01G273200 chr3A 110311258 110312759 1501 True 2569 2569 97.5370 1 1502 1 chr3A.!!$R1 1501
3 TraesCS2A01G273200 chr4A 546005347 546006792 1445 True 2549 2549 98.4790 1 1446 1 chr4A.!!$R1 1445
4 TraesCS2A01G273200 chr7A 7843120 7844591 1471 True 2477 2477 97.0790 1 1469 1 chr7A.!!$R1 1468
5 TraesCS2A01G273200 chr7A 20252911 20254408 1497 True 1797 1797 88.3260 1 1499 1 chr7A.!!$R2 1498
6 TraesCS2A01G273200 chr7A 270771073 270772570 1497 False 1775 1775 88.0590 1 1498 1 chr7A.!!$F1 1497
7 TraesCS2A01G273200 chr5A 707721226 707722725 1499 False 2045 2045 91.2670 1 1500 1 chr5A.!!$F1 1499
8 TraesCS2A01G273200 chr5A 622527540 622529042 1502 True 1868 1868 89.1030 1 1504 1 chr5A.!!$R1 1503
9 TraesCS2A01G273200 chr6B 68900866 68902365 1499 False 1585 1585 85.7430 1 1500 1 chr6B.!!$F2 1499
10 TraesCS2A01G273200 chr2D 337398701 337399540 839 False 456 684 96.1925 1503 2090 2 chr2D.!!$F3 587
11 TraesCS2A01G273200 chr2B 404741182 404741798 616 True 432 612 94.1130 1499 2093 2 chr2B.!!$R1 594

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
796 797 0.242286 TTGCGTGCTGTTGTTGTTGT 59.758 45.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2442 0.037734 ACCGGTGAAAATGGACCTCC 59.962 55.0 6.12 0.0 0.0 4.3 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
226 227 3.135994 GCGGTTCTTGACTCCTTAACAA 58.864 45.455 0.00 0.00 0.00 2.83
266 267 2.821546 TCGCCTACCAAAATCGATCAG 58.178 47.619 0.00 0.00 0.00 2.90
571 572 4.141959 ACAACAACTTGCCACTGCTAATTT 60.142 37.500 0.00 0.00 38.71 1.82
796 797 0.242286 TTGCGTGCTGTTGTTGTTGT 59.758 45.000 0.00 0.00 0.00 3.32
830 834 2.762535 ACGGACCAATCTGACGAAAT 57.237 45.000 0.00 0.00 34.98 2.17
1531 1537 5.298347 AGAGGTTTACTGAGTGCTTGTAAC 58.702 41.667 0.00 0.00 0.00 2.50
1627 1633 9.609346 ATTAAACGTAGTATGCCAAGTATCTTT 57.391 29.630 0.00 0.00 45.00 2.52
1840 2099 6.099125 TGCTTCACCTGCCTAGTAATATACAA 59.901 38.462 0.00 0.00 0.00 2.41
1957 2216 4.131376 GCCGCTAGCATCACACAT 57.869 55.556 16.45 0.00 42.97 3.21
1958 2217 1.645455 GCCGCTAGCATCACACATG 59.355 57.895 16.45 0.00 42.97 3.21
2070 2329 5.313520 TCACGAATAAAGTATGACGGTGA 57.686 39.130 0.00 0.00 0.00 4.02
2099 2358 2.187946 GAGCATCTCCACCCGGTG 59.812 66.667 10.95 10.95 0.00 4.94
2100 2359 2.284625 AGCATCTCCACCCGGTGA 60.285 61.111 19.81 4.45 39.09 4.02
2101 2360 1.899437 GAGCATCTCCACCCGGTGAA 61.899 60.000 19.81 0.00 38.28 3.18
2102 2361 1.002624 GCATCTCCACCCGGTGAAA 60.003 57.895 19.81 5.82 38.28 2.69
2103 2362 1.026718 GCATCTCCACCCGGTGAAAG 61.027 60.000 19.81 15.05 38.28 2.62
2104 2363 1.026718 CATCTCCACCCGGTGAAAGC 61.027 60.000 19.81 0.00 38.28 3.51
2115 2374 0.378610 GGTGAAAGCGGCATTAGAGC 59.621 55.000 1.45 0.00 0.00 4.09
2116 2375 1.086696 GTGAAAGCGGCATTAGAGCA 58.913 50.000 1.45 0.00 35.83 4.26
2117 2376 1.672881 GTGAAAGCGGCATTAGAGCAT 59.327 47.619 1.45 0.00 35.83 3.79
2118 2377 1.942657 TGAAAGCGGCATTAGAGCATC 59.057 47.619 1.45 0.00 35.83 3.91
2129 2388 3.922893 GAGCATCTGCAGTCGCGC 61.923 66.667 14.67 14.99 45.16 6.86
2132 2391 3.260483 CATCTGCAGTCGCGCCTC 61.260 66.667 14.67 0.00 42.97 4.70
2133 2392 3.763356 ATCTGCAGTCGCGCCTCA 61.763 61.111 14.67 0.00 42.97 3.86
2134 2393 3.300934 ATCTGCAGTCGCGCCTCAA 62.301 57.895 14.67 0.00 42.97 3.02
2135 2394 3.782244 CTGCAGTCGCGCCTCAAC 61.782 66.667 5.25 0.00 42.97 3.18
2136 2395 4.600576 TGCAGTCGCGCCTCAACA 62.601 61.111 0.00 0.00 42.97 3.33
2137 2396 3.782244 GCAGTCGCGCCTCAACAG 61.782 66.667 0.00 0.00 0.00 3.16
2138 2397 3.782244 CAGTCGCGCCTCAACAGC 61.782 66.667 0.00 0.00 0.00 4.40
2169 2428 3.864944 TTTTTAGCGTCTCGGCCG 58.135 55.556 22.12 22.12 0.00 6.13
2170 2429 1.289694 TTTTTAGCGTCTCGGCCGA 59.710 52.632 29.03 29.03 0.00 5.54
2171 2430 0.734942 TTTTTAGCGTCTCGGCCGAG 60.735 55.000 42.89 42.89 43.21 4.63
2172 2431 1.870055 TTTTAGCGTCTCGGCCGAGT 61.870 55.000 44.61 31.92 42.49 4.18
2173 2432 2.262471 TTTAGCGTCTCGGCCGAGTC 62.262 60.000 44.61 39.05 42.49 3.36
2186 2445 3.827898 GAGTCGCGTCCCCTGGAG 61.828 72.222 5.77 0.00 29.39 3.86
2192 2451 2.365635 CGTCCCCTGGAGGTCCAT 60.366 66.667 0.00 0.00 46.46 3.41
2193 2452 1.995626 CGTCCCCTGGAGGTCCATT 60.996 63.158 0.00 0.00 46.46 3.16
2194 2453 1.562672 CGTCCCCTGGAGGTCCATTT 61.563 60.000 0.00 0.00 46.46 2.32
2195 2454 0.704664 GTCCCCTGGAGGTCCATTTT 59.295 55.000 0.00 0.00 46.46 1.82
2196 2455 0.999712 TCCCCTGGAGGTCCATTTTC 59.000 55.000 0.00 0.00 46.46 2.29
2197 2456 0.704076 CCCCTGGAGGTCCATTTTCA 59.296 55.000 0.00 0.00 46.46 2.69
2198 2457 1.616994 CCCCTGGAGGTCCATTTTCAC 60.617 57.143 0.00 0.00 46.46 3.18
2199 2458 1.616994 CCCTGGAGGTCCATTTTCACC 60.617 57.143 0.00 0.00 46.46 4.02
2200 2459 1.453155 CTGGAGGTCCATTTTCACCG 58.547 55.000 0.00 0.00 46.46 4.94
2201 2460 0.037590 TGGAGGTCCATTTTCACCGG 59.962 55.000 0.00 0.00 42.01 5.28
2202 2461 0.037734 GGAGGTCCATTTTCACCGGT 59.962 55.000 0.00 0.00 37.79 5.28
2203 2462 1.546998 GGAGGTCCATTTTCACCGGTT 60.547 52.381 2.97 0.00 37.79 4.44
2204 2463 2.290450 GGAGGTCCATTTTCACCGGTTA 60.290 50.000 2.97 0.00 37.79 2.85
2205 2464 3.414269 GAGGTCCATTTTCACCGGTTAA 58.586 45.455 2.97 0.00 37.79 2.01
2206 2465 3.418047 AGGTCCATTTTCACCGGTTAAG 58.582 45.455 2.97 0.00 37.79 1.85
2207 2466 2.094906 GGTCCATTTTCACCGGTTAAGC 60.095 50.000 2.97 0.00 0.00 3.09
2208 2467 2.094906 GTCCATTTTCACCGGTTAAGCC 60.095 50.000 2.97 0.00 0.00 4.35
2209 2468 2.167662 CCATTTTCACCGGTTAAGCCT 58.832 47.619 2.97 0.00 34.25 4.58
2210 2469 2.094752 CCATTTTCACCGGTTAAGCCTG 60.095 50.000 2.97 2.27 34.25 4.85
2211 2470 2.642154 TTTTCACCGGTTAAGCCTGA 57.358 45.000 2.97 0.00 34.25 3.86
2212 2471 2.642154 TTTCACCGGTTAAGCCTGAA 57.358 45.000 2.97 0.00 31.87 3.02
2213 2472 2.642154 TTCACCGGTTAAGCCTGAAA 57.358 45.000 2.97 0.00 31.11 2.69
2214 2473 1.886886 TCACCGGTTAAGCCTGAAAC 58.113 50.000 2.97 0.00 34.25 2.78
2215 2474 1.418637 TCACCGGTTAAGCCTGAAACT 59.581 47.619 2.97 0.00 34.25 2.66
2216 2475 1.535462 CACCGGTTAAGCCTGAAACTG 59.465 52.381 2.97 0.00 34.25 3.16
2217 2476 1.165270 CCGGTTAAGCCTGAAACTGG 58.835 55.000 0.00 4.22 43.71 4.00
2218 2477 1.544759 CCGGTTAAGCCTGAAACTGGT 60.545 52.381 9.07 0.00 44.03 4.00
2219 2478 1.535462 CGGTTAAGCCTGAAACTGGTG 59.465 52.381 0.00 0.00 34.25 4.17
2220 2479 1.269723 GGTTAAGCCTGAAACTGGTGC 59.730 52.381 0.00 0.00 0.00 5.01
2221 2480 1.269723 GTTAAGCCTGAAACTGGTGCC 59.730 52.381 0.00 0.00 0.00 5.01
2222 2481 0.605319 TAAGCCTGAAACTGGTGCCG 60.605 55.000 0.00 0.00 0.00 5.69
2223 2482 3.365265 GCCTGAAACTGGTGCCGG 61.365 66.667 0.00 0.00 0.00 6.13
2224 2483 2.113139 CCTGAAACTGGTGCCGGT 59.887 61.111 1.90 0.00 37.08 5.28
2225 2484 2.260869 CCTGAAACTGGTGCCGGTG 61.261 63.158 1.90 0.00 35.44 4.94
2226 2485 2.203280 TGAAACTGGTGCCGGTGG 60.203 61.111 1.90 0.00 35.44 4.61
2227 2486 2.112297 GAAACTGGTGCCGGTGGA 59.888 61.111 1.90 0.00 35.44 4.02
2228 2487 1.303317 GAAACTGGTGCCGGTGGAT 60.303 57.895 1.90 0.00 35.44 3.41
2229 2488 1.303317 AAACTGGTGCCGGTGGATC 60.303 57.895 1.90 0.00 35.44 3.36
2230 2489 2.764637 AAACTGGTGCCGGTGGATCC 62.765 60.000 4.20 4.20 35.44 3.36
2231 2490 3.716195 CTGGTGCCGGTGGATCCA 61.716 66.667 11.44 11.44 35.57 3.41
2232 2491 3.687321 CTGGTGCCGGTGGATCCAG 62.687 68.421 16.81 4.68 38.15 3.86
2233 2492 4.489771 GGTGCCGGTGGATCCAGG 62.490 72.222 16.81 15.43 35.57 4.45
2238 2497 3.781307 CGGTGGATCCAGGCCGAA 61.781 66.667 30.67 0.00 46.33 4.30
2239 2498 2.124695 GGTGGATCCAGGCCGAAC 60.125 66.667 16.81 0.48 35.97 3.95
2240 2499 2.124695 GTGGATCCAGGCCGAACC 60.125 66.667 16.81 0.00 39.61 3.62
2271 2530 4.398598 GCGCCGTGGCAATCGTTT 62.399 61.111 12.06 0.00 42.06 3.60
2272 2531 2.254051 CGCCGTGGCAATCGTTTT 59.746 55.556 12.06 0.00 42.06 2.43
2273 2532 1.371145 CGCCGTGGCAATCGTTTTT 60.371 52.632 12.06 0.00 42.06 1.94
2274 2533 1.604612 CGCCGTGGCAATCGTTTTTG 61.605 55.000 12.06 0.00 42.06 2.44
2275 2534 1.281566 GCCGTGGCAATCGTTTTTGG 61.282 55.000 5.89 0.00 41.49 3.28
2278 2537 3.155424 GGCAATCGTTTTTGGCGC 58.845 55.556 0.00 0.00 41.50 6.53
2279 2538 2.715849 GGCAATCGTTTTTGGCGCG 61.716 57.895 0.00 0.00 41.50 6.86
2280 2539 1.727723 GCAATCGTTTTTGGCGCGA 60.728 52.632 12.10 0.00 39.02 5.87
2281 2540 1.272114 GCAATCGTTTTTGGCGCGAA 61.272 50.000 12.10 0.00 38.17 4.70
2282 2541 1.124462 CAATCGTTTTTGGCGCGAAA 58.876 45.000 13.91 13.91 38.17 3.46
2283 2542 1.122323 CAATCGTTTTTGGCGCGAAAG 59.878 47.619 17.08 6.95 38.17 2.62
2284 2543 0.386731 ATCGTTTTTGGCGCGAAAGG 60.387 50.000 17.08 14.61 38.17 3.11
2314 2573 4.056125 CTGAGTCAGCGACCGCCA 62.056 66.667 7.33 0.69 43.17 5.69
2315 2574 4.357947 TGAGTCAGCGACCGCCAC 62.358 66.667 11.03 8.23 43.17 5.01
2329 2588 4.477975 CCACGCCTCGTCGTCCTC 62.478 72.222 0.00 0.00 41.21 3.71
2330 2589 3.733960 CACGCCTCGTCGTCCTCA 61.734 66.667 0.00 0.00 41.21 3.86
2331 2590 2.750637 ACGCCTCGTCGTCCTCAT 60.751 61.111 0.00 0.00 38.44 2.90
2332 2591 2.024871 CGCCTCGTCGTCCTCATC 59.975 66.667 0.00 0.00 0.00 2.92
2333 2592 2.024871 GCCTCGTCGTCCTCATCG 59.975 66.667 0.00 0.00 0.00 3.84
2334 2593 2.024871 CCTCGTCGTCCTCATCGC 59.975 66.667 0.00 0.00 0.00 4.58
2335 2594 2.024871 CTCGTCGTCCTCATCGCC 59.975 66.667 0.00 0.00 0.00 5.54
2336 2595 2.437895 TCGTCGTCCTCATCGCCT 60.438 61.111 0.00 0.00 0.00 5.52
2337 2596 2.024871 CGTCGTCCTCATCGCCTC 59.975 66.667 0.00 0.00 0.00 4.70
2338 2597 2.024871 GTCGTCCTCATCGCCTCG 59.975 66.667 0.00 0.00 0.00 4.63
2339 2598 3.209812 TCGTCCTCATCGCCTCGG 61.210 66.667 0.00 0.00 0.00 4.63
2340 2599 3.518998 CGTCCTCATCGCCTCGGT 61.519 66.667 0.00 0.00 0.00 4.69
2341 2600 2.893398 GTCCTCATCGCCTCGGTT 59.107 61.111 0.00 0.00 0.00 4.44
2342 2601 1.218316 GTCCTCATCGCCTCGGTTT 59.782 57.895 0.00 0.00 0.00 3.27
2343 2602 0.806492 GTCCTCATCGCCTCGGTTTC 60.806 60.000 0.00 0.00 0.00 2.78
2344 2603 1.521681 CCTCATCGCCTCGGTTTCC 60.522 63.158 0.00 0.00 0.00 3.13
2345 2604 1.521681 CTCATCGCCTCGGTTTCCC 60.522 63.158 0.00 0.00 0.00 3.97
2366 2625 2.731976 CGCGAGGAATCAATACTAAGGC 59.268 50.000 0.00 0.00 0.00 4.35
2367 2626 3.553096 CGCGAGGAATCAATACTAAGGCT 60.553 47.826 0.00 0.00 0.00 4.58
2368 2627 3.743396 GCGAGGAATCAATACTAAGGCTG 59.257 47.826 0.00 0.00 0.00 4.85
2369 2628 3.743396 CGAGGAATCAATACTAAGGCTGC 59.257 47.826 0.00 0.00 0.00 5.25
2370 2629 4.068599 GAGGAATCAATACTAAGGCTGCC 58.931 47.826 11.65 11.65 0.00 4.85
2371 2630 2.808543 GGAATCAATACTAAGGCTGCCG 59.191 50.000 13.96 1.26 0.00 5.69
2372 2631 1.884235 ATCAATACTAAGGCTGCCGC 58.116 50.000 13.96 0.00 0.00 6.53
2373 2632 0.830648 TCAATACTAAGGCTGCCGCT 59.169 50.000 13.96 7.31 36.09 5.52
2374 2633 0.940126 CAATACTAAGGCTGCCGCTG 59.060 55.000 13.96 9.50 36.09 5.18
2375 2634 0.179045 AATACTAAGGCTGCCGCTGG 60.179 55.000 13.96 9.24 36.09 4.85
2376 2635 1.338136 ATACTAAGGCTGCCGCTGGT 61.338 55.000 13.96 14.61 36.09 4.00
2377 2636 1.956629 TACTAAGGCTGCCGCTGGTC 61.957 60.000 13.96 0.00 36.09 4.02
2378 2637 3.315142 CTAAGGCTGCCGCTGGTCA 62.315 63.158 13.96 0.00 36.09 4.02
2379 2638 3.315142 TAAGGCTGCCGCTGGTCAG 62.315 63.158 13.96 11.56 36.09 3.51
2382 2641 4.385405 GCTGCCGCTGGTCAGTCT 62.385 66.667 14.83 0.00 32.35 3.24
2383 2642 2.345244 CTGCCGCTGGTCAGTCTT 59.655 61.111 0.00 0.00 0.00 3.01
2384 2643 1.302033 CTGCCGCTGGTCAGTCTTT 60.302 57.895 0.00 0.00 0.00 2.52
2385 2644 1.294659 CTGCCGCTGGTCAGTCTTTC 61.295 60.000 0.00 0.00 0.00 2.62
2386 2645 1.301716 GCCGCTGGTCAGTCTTTCA 60.302 57.895 0.00 0.00 0.00 2.69
2387 2646 0.674895 GCCGCTGGTCAGTCTTTCAT 60.675 55.000 0.00 0.00 0.00 2.57
2388 2647 1.813513 CCGCTGGTCAGTCTTTCATT 58.186 50.000 0.00 0.00 0.00 2.57
2389 2648 1.466167 CCGCTGGTCAGTCTTTCATTG 59.534 52.381 0.00 0.00 0.00 2.82
2390 2649 2.416747 CGCTGGTCAGTCTTTCATTGA 58.583 47.619 0.00 0.00 0.00 2.57
2391 2650 3.005554 CGCTGGTCAGTCTTTCATTGAT 58.994 45.455 0.00 0.00 0.00 2.57
2392 2651 3.438087 CGCTGGTCAGTCTTTCATTGATT 59.562 43.478 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.514401 GAGGATAAGGAACAACCAATCGT 58.486 43.478 0.00 0.00 42.04 3.73
226 227 6.492254 GGCGAAAGACGGACATAAAATAAAT 58.508 36.000 0.00 0.00 42.83 1.40
266 267 1.291132 GATGGCGTCTAGTTTGGCTC 58.709 55.000 0.00 0.00 0.00 4.70
546 547 2.374184 AGCAGTGGCAAGTTGTTGTTA 58.626 42.857 4.48 0.00 44.61 2.41
796 797 2.617021 GGTCCGTTTGCTGGAAATCCTA 60.617 50.000 0.00 0.00 37.23 2.94
830 834 0.928505 TAGTCCGTGGGTGAGGGATA 59.071 55.000 0.00 0.00 40.76 2.59
1531 1537 9.345517 CACAATCAGTTTAAGACAAACATATGG 57.654 33.333 7.80 0.00 32.81 2.74
1660 1697 2.768253 ACAGACAGGAAATCATCGCA 57.232 45.000 0.00 0.00 0.00 5.10
1661 1698 3.786635 ACTACAGACAGGAAATCATCGC 58.213 45.455 0.00 0.00 0.00 4.58
1662 1699 5.518128 CAGAACTACAGACAGGAAATCATCG 59.482 44.000 0.00 0.00 0.00 3.84
1663 1700 6.402222 ACAGAACTACAGACAGGAAATCATC 58.598 40.000 0.00 0.00 0.00 2.92
1664 1701 6.014242 TGACAGAACTACAGACAGGAAATCAT 60.014 38.462 0.00 0.00 0.00 2.45
1665 1702 5.304357 TGACAGAACTACAGACAGGAAATCA 59.696 40.000 0.00 0.00 0.00 2.57
1672 1709 3.650070 TGCTGACAGAACTACAGACAG 57.350 47.619 6.65 0.00 34.07 3.51
1674 1711 4.179926 TGATGCTGACAGAACTACAGAC 57.820 45.455 6.65 0.00 34.07 3.51
1737 1996 6.699575 ATCCATTTTATGAGCAACTACCAC 57.300 37.500 0.00 0.00 0.00 4.16
1840 2099 2.034879 CGTCGCAGCCATGTCCTTT 61.035 57.895 0.00 0.00 0.00 3.11
1946 2205 1.806542 GTTCGGTTCATGTGTGATGCT 59.193 47.619 0.00 0.00 33.56 3.79
1957 2216 2.465860 AATGATGGACGTTCGGTTCA 57.534 45.000 0.00 0.00 38.89 3.18
1958 2217 3.518590 AGTAATGATGGACGTTCGGTTC 58.481 45.455 0.00 0.00 0.00 3.62
2070 2329 2.216898 GAGATGCTCTAATGCCGCTTT 58.783 47.619 0.00 0.00 0.00 3.51
2083 2342 1.488705 TTTCACCGGGTGGAGATGCT 61.489 55.000 26.07 0.00 39.21 3.79
2093 2352 1.714899 CTAATGCCGCTTTCACCGGG 61.715 60.000 6.32 0.00 45.66 5.73
2095 2354 0.652592 CTCTAATGCCGCTTTCACCG 59.347 55.000 0.00 0.00 0.00 4.94
2096 2355 0.378610 GCTCTAATGCCGCTTTCACC 59.621 55.000 0.00 0.00 0.00 4.02
2097 2356 1.086696 TGCTCTAATGCCGCTTTCAC 58.913 50.000 0.00 0.00 0.00 3.18
2098 2357 1.942657 GATGCTCTAATGCCGCTTTCA 59.057 47.619 0.00 0.00 0.00 2.69
2099 2358 2.032204 CAGATGCTCTAATGCCGCTTTC 60.032 50.000 0.00 0.00 0.00 2.62
2100 2359 1.945394 CAGATGCTCTAATGCCGCTTT 59.055 47.619 0.00 0.00 0.00 3.51
2101 2360 1.590932 CAGATGCTCTAATGCCGCTT 58.409 50.000 0.00 0.00 0.00 4.68
2102 2361 0.883814 GCAGATGCTCTAATGCCGCT 60.884 55.000 0.00 0.00 38.21 5.52
2103 2362 1.162181 TGCAGATGCTCTAATGCCGC 61.162 55.000 6.35 0.00 42.66 6.53
2104 2363 0.866427 CTGCAGATGCTCTAATGCCG 59.134 55.000 8.42 0.00 42.66 5.69
2105 2364 1.872313 GACTGCAGATGCTCTAATGCC 59.128 52.381 23.35 0.00 42.66 4.40
2106 2365 1.526041 CGACTGCAGATGCTCTAATGC 59.474 52.381 23.35 0.00 42.66 3.56
2107 2366 1.526041 GCGACTGCAGATGCTCTAATG 59.474 52.381 23.35 0.00 42.66 1.90
2108 2367 1.863267 GCGACTGCAGATGCTCTAAT 58.137 50.000 23.35 0.00 42.66 1.73
2109 2368 0.526310 CGCGACTGCAGATGCTCTAA 60.526 55.000 23.35 0.00 42.97 2.10
2110 2369 1.064783 CGCGACTGCAGATGCTCTA 59.935 57.895 23.35 0.00 42.97 2.43
2111 2370 2.202716 CGCGACTGCAGATGCTCT 60.203 61.111 23.35 0.00 42.97 4.09
2112 2371 3.922893 GCGCGACTGCAGATGCTC 61.923 66.667 23.35 14.54 42.97 4.26
2115 2374 3.260483 GAGGCGCGACTGCAGATG 61.260 66.667 25.24 13.16 42.97 2.90
2116 2375 3.300934 TTGAGGCGCGACTGCAGAT 62.301 57.895 25.24 4.35 42.97 2.90
2117 2376 3.989787 TTGAGGCGCGACTGCAGA 61.990 61.111 25.24 0.00 42.97 4.26
2118 2377 3.782244 GTTGAGGCGCGACTGCAG 61.782 66.667 25.24 13.48 42.97 4.41
2119 2378 4.600576 TGTTGAGGCGCGACTGCA 62.601 61.111 25.24 15.45 42.97 4.41
2120 2379 3.782244 CTGTTGAGGCGCGACTGC 61.782 66.667 25.24 12.46 37.91 4.40
2121 2380 3.782244 GCTGTTGAGGCGCGACTG 61.782 66.667 25.24 5.20 34.05 3.51
2152 2411 0.734942 CTCGGCCGAGACGCTAAAAA 60.735 55.000 45.28 12.18 44.53 1.94
2153 2412 1.153901 CTCGGCCGAGACGCTAAAA 60.154 57.895 45.28 12.76 44.53 1.52
2154 2413 2.488355 CTCGGCCGAGACGCTAAA 59.512 61.111 45.28 13.58 44.53 1.85
2169 2428 3.827898 CTCCAGGGGACGCGACTC 61.828 72.222 15.93 6.47 0.00 3.36
2183 2442 0.037734 ACCGGTGAAAATGGACCTCC 59.962 55.000 6.12 0.00 0.00 4.30
2184 2443 1.905637 AACCGGTGAAAATGGACCTC 58.094 50.000 8.52 0.00 0.00 3.85
2185 2444 3.418047 CTTAACCGGTGAAAATGGACCT 58.582 45.455 8.52 0.00 0.00 3.85
2186 2445 2.094906 GCTTAACCGGTGAAAATGGACC 60.095 50.000 8.52 0.00 0.00 4.46
2187 2446 2.094906 GGCTTAACCGGTGAAAATGGAC 60.095 50.000 8.52 0.00 0.00 4.02
2188 2447 2.164338 GGCTTAACCGGTGAAAATGGA 58.836 47.619 8.52 0.00 0.00 3.41
2189 2448 2.094752 CAGGCTTAACCGGTGAAAATGG 60.095 50.000 8.52 0.00 46.52 3.16
2190 2449 2.817258 TCAGGCTTAACCGGTGAAAATG 59.183 45.455 8.52 5.97 46.52 2.32
2191 2450 3.149005 TCAGGCTTAACCGGTGAAAAT 57.851 42.857 8.52 0.00 46.52 1.82
2192 2451 2.642154 TCAGGCTTAACCGGTGAAAA 57.358 45.000 8.52 2.00 46.52 2.29
2193 2452 2.619646 GTTTCAGGCTTAACCGGTGAAA 59.380 45.455 8.52 9.08 46.52 2.69
2194 2453 2.158726 AGTTTCAGGCTTAACCGGTGAA 60.159 45.455 8.52 5.85 46.52 3.18
2195 2454 1.418637 AGTTTCAGGCTTAACCGGTGA 59.581 47.619 8.52 0.00 46.52 4.02
2196 2455 1.535462 CAGTTTCAGGCTTAACCGGTG 59.465 52.381 8.52 0.00 46.52 4.94
2197 2456 1.544759 CCAGTTTCAGGCTTAACCGGT 60.545 52.381 0.00 0.00 46.52 5.28
2198 2457 1.165270 CCAGTTTCAGGCTTAACCGG 58.835 55.000 0.00 0.00 46.52 5.28
2199 2458 1.535462 CACCAGTTTCAGGCTTAACCG 59.465 52.381 5.82 0.00 46.52 4.44
2200 2459 1.269723 GCACCAGTTTCAGGCTTAACC 59.730 52.381 5.82 0.00 39.61 2.85
2201 2460 1.269723 GGCACCAGTTTCAGGCTTAAC 59.730 52.381 1.90 1.90 0.00 2.01
2202 2461 1.616159 GGCACCAGTTTCAGGCTTAA 58.384 50.000 0.00 0.00 0.00 1.85
2203 2462 0.605319 CGGCACCAGTTTCAGGCTTA 60.605 55.000 0.00 0.00 0.00 3.09
2204 2463 1.898574 CGGCACCAGTTTCAGGCTT 60.899 57.895 0.00 0.00 0.00 4.35
2205 2464 2.281761 CGGCACCAGTTTCAGGCT 60.282 61.111 0.00 0.00 0.00 4.58
2206 2465 3.365265 CCGGCACCAGTTTCAGGC 61.365 66.667 0.00 0.00 0.00 4.85
2207 2466 2.113139 ACCGGCACCAGTTTCAGG 59.887 61.111 0.00 0.00 0.00 3.86
2208 2467 2.260869 CCACCGGCACCAGTTTCAG 61.261 63.158 0.00 0.00 0.00 3.02
2209 2468 2.063015 ATCCACCGGCACCAGTTTCA 62.063 55.000 0.00 0.00 0.00 2.69
2210 2469 1.303317 ATCCACCGGCACCAGTTTC 60.303 57.895 0.00 0.00 0.00 2.78
2211 2470 1.303317 GATCCACCGGCACCAGTTT 60.303 57.895 0.00 0.00 0.00 2.66
2212 2471 2.351276 GATCCACCGGCACCAGTT 59.649 61.111 0.00 0.00 0.00 3.16
2213 2472 3.717294 GGATCCACCGGCACCAGT 61.717 66.667 6.95 0.00 0.00 4.00
2214 2473 3.687321 CTGGATCCACCGGCACCAG 62.687 68.421 11.44 9.90 42.61 4.00
2215 2474 3.716195 CTGGATCCACCGGCACCA 61.716 66.667 11.44 3.29 42.61 4.17
2216 2475 4.489771 CCTGGATCCACCGGCACC 62.490 72.222 11.44 0.00 43.37 5.01
2221 2480 3.781307 TTCGGCCTGGATCCACCG 61.781 66.667 29.26 29.26 46.97 4.94
2222 2481 2.124695 GTTCGGCCTGGATCCACC 60.125 66.667 11.44 11.04 39.54 4.61
2223 2482 2.124695 GGTTCGGCCTGGATCCAC 60.125 66.667 11.44 1.36 0.00 4.02
2254 2513 3.889831 AAAACGATTGCCACGGCGC 62.890 57.895 6.90 0.00 45.51 6.53
2255 2514 1.371145 AAAAACGATTGCCACGGCG 60.371 52.632 4.80 4.80 45.51 6.46
2256 2515 1.281566 CCAAAAACGATTGCCACGGC 61.282 55.000 0.00 0.00 42.35 5.68
2257 2516 1.281566 GCCAAAAACGATTGCCACGG 61.282 55.000 0.00 0.00 34.93 4.94
2258 2517 1.604612 CGCCAAAAACGATTGCCACG 61.605 55.000 0.00 0.00 0.00 4.94
2259 2518 1.885814 GCGCCAAAAACGATTGCCAC 61.886 55.000 0.00 0.00 0.00 5.01
2260 2519 1.663074 GCGCCAAAAACGATTGCCA 60.663 52.632 0.00 0.00 0.00 4.92
2261 2520 2.715849 CGCGCCAAAAACGATTGCC 61.716 57.895 0.00 0.00 0.00 4.52
2262 2521 1.272114 TTCGCGCCAAAAACGATTGC 61.272 50.000 0.00 0.00 35.48 3.56
2263 2522 1.122323 CTTTCGCGCCAAAAACGATTG 59.878 47.619 0.00 0.00 35.48 2.67
2264 2523 1.404477 CTTTCGCGCCAAAAACGATT 58.596 45.000 0.00 0.00 35.48 3.34
2265 2524 0.386731 CCTTTCGCGCCAAAAACGAT 60.387 50.000 0.00 0.00 35.48 3.73
2266 2525 1.009449 CCTTTCGCGCCAAAAACGA 60.009 52.632 0.00 0.00 0.00 3.85
2267 2526 2.014018 CCCTTTCGCGCCAAAAACG 61.014 57.895 0.00 0.00 0.00 3.60
2268 2527 2.307309 GCCCTTTCGCGCCAAAAAC 61.307 57.895 0.00 0.00 0.00 2.43
2269 2528 2.028337 GCCCTTTCGCGCCAAAAA 59.972 55.556 0.00 0.00 0.00 1.94
2270 2529 3.206211 CTGCCCTTTCGCGCCAAAA 62.206 57.895 0.00 1.69 0.00 2.44
2271 2530 3.669344 CTGCCCTTTCGCGCCAAA 61.669 61.111 0.00 0.00 0.00 3.28
2297 2556 4.056125 TGGCGGTCGCTGACTCAG 62.056 66.667 15.04 1.21 41.60 3.35
2298 2557 4.357947 GTGGCGGTCGCTGACTCA 62.358 66.667 15.04 1.43 41.60 3.41
2312 2571 4.477975 GAGGACGACGAGGCGTGG 62.478 72.222 9.36 0.54 45.72 4.94
2313 2572 2.921538 GATGAGGACGACGAGGCGTG 62.922 65.000 9.36 0.00 45.72 5.34
2315 2574 2.024871 GATGAGGACGACGAGGCG 59.975 66.667 0.00 0.00 37.29 5.52
2316 2575 2.024871 CGATGAGGACGACGAGGC 59.975 66.667 0.00 0.00 0.00 4.70
2317 2576 2.024871 GCGATGAGGACGACGAGG 59.975 66.667 0.00 0.00 0.00 4.63
2318 2577 2.024871 GGCGATGAGGACGACGAG 59.975 66.667 0.00 0.00 0.00 4.18
2319 2578 2.437895 AGGCGATGAGGACGACGA 60.438 61.111 0.00 0.00 44.04 4.20
2320 2579 2.024871 GAGGCGATGAGGACGACG 59.975 66.667 0.00 0.00 44.04 5.12
2321 2580 2.024871 CGAGGCGATGAGGACGAC 59.975 66.667 0.00 0.00 39.24 4.34
2322 2581 3.209812 CCGAGGCGATGAGGACGA 61.210 66.667 0.00 0.00 0.00 4.20
2323 2582 2.558554 AAACCGAGGCGATGAGGACG 62.559 60.000 0.00 0.00 0.00 4.79
2324 2583 0.806492 GAAACCGAGGCGATGAGGAC 60.806 60.000 0.00 0.00 0.00 3.85
2325 2584 1.515954 GAAACCGAGGCGATGAGGA 59.484 57.895 0.00 0.00 0.00 3.71
2326 2585 1.521681 GGAAACCGAGGCGATGAGG 60.522 63.158 0.00 0.00 0.00 3.86
2327 2586 1.521681 GGGAAACCGAGGCGATGAG 60.522 63.158 0.00 0.00 43.64 2.90
2328 2587 2.582436 GGGAAACCGAGGCGATGA 59.418 61.111 0.00 0.00 43.64 2.92
2342 2601 1.410004 AGTATTGATTCCTCGCGGGA 58.590 50.000 8.08 10.34 43.41 5.14
2343 2602 3.318017 CTTAGTATTGATTCCTCGCGGG 58.682 50.000 6.13 0.59 0.00 6.13
2344 2603 3.318017 CCTTAGTATTGATTCCTCGCGG 58.682 50.000 6.13 0.00 0.00 6.46
2345 2604 2.731976 GCCTTAGTATTGATTCCTCGCG 59.268 50.000 0.00 0.00 0.00 5.87
2346 2605 3.743396 CAGCCTTAGTATTGATTCCTCGC 59.257 47.826 0.00 0.00 0.00 5.03
2347 2606 3.743396 GCAGCCTTAGTATTGATTCCTCG 59.257 47.826 0.00 0.00 0.00 4.63
2348 2607 4.068599 GGCAGCCTTAGTATTGATTCCTC 58.931 47.826 3.29 0.00 0.00 3.71
2349 2608 3.495100 CGGCAGCCTTAGTATTGATTCCT 60.495 47.826 10.54 0.00 0.00 3.36
2350 2609 2.808543 CGGCAGCCTTAGTATTGATTCC 59.191 50.000 10.54 0.00 0.00 3.01
2351 2610 2.224314 GCGGCAGCCTTAGTATTGATTC 59.776 50.000 10.54 0.00 37.42 2.52
2352 2611 2.158755 AGCGGCAGCCTTAGTATTGATT 60.159 45.455 10.54 0.00 46.67 2.57
2353 2612 1.417890 AGCGGCAGCCTTAGTATTGAT 59.582 47.619 10.54 0.00 46.67 2.57
2354 2613 0.830648 AGCGGCAGCCTTAGTATTGA 59.169 50.000 10.54 0.00 46.67 2.57
2355 2614 0.940126 CAGCGGCAGCCTTAGTATTG 59.060 55.000 10.54 0.00 46.67 1.90
2356 2615 0.179045 CCAGCGGCAGCCTTAGTATT 60.179 55.000 10.54 0.00 46.67 1.89
2357 2616 1.338136 ACCAGCGGCAGCCTTAGTAT 61.338 55.000 10.54 0.00 46.67 2.12
2358 2617 1.956629 GACCAGCGGCAGCCTTAGTA 61.957 60.000 10.54 0.00 46.67 1.82
2359 2618 3.316573 GACCAGCGGCAGCCTTAGT 62.317 63.158 10.54 1.04 46.67 2.24
2360 2619 2.512515 GACCAGCGGCAGCCTTAG 60.513 66.667 10.54 0.00 46.67 2.18
2361 2620 3.315142 CTGACCAGCGGCAGCCTTA 62.315 63.158 10.54 0.00 46.67 2.69
2362 2621 4.711949 CTGACCAGCGGCAGCCTT 62.712 66.667 10.54 0.00 46.67 4.35
2365 2624 3.890936 AAGACTGACCAGCGGCAGC 62.891 63.158 0.00 0.00 45.58 5.25
2366 2625 1.294659 GAAAGACTGACCAGCGGCAG 61.295 60.000 1.45 13.19 34.62 4.85
2367 2626 1.301716 GAAAGACTGACCAGCGGCA 60.302 57.895 1.45 0.00 0.00 5.69
2368 2627 0.674895 ATGAAAGACTGACCAGCGGC 60.675 55.000 0.00 0.00 0.00 6.53
2369 2628 1.466167 CAATGAAAGACTGACCAGCGG 59.534 52.381 0.00 0.00 0.00 5.52
2370 2629 2.416747 TCAATGAAAGACTGACCAGCG 58.583 47.619 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.