Multiple sequence alignment - TraesCS4B01G236000

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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 TraesCS4B01G236000 chr4B 100.000 2429 0 0 1 2429 493628621 493631049 0.000000e+00 4486
1 TraesCS4B01G236000 chr4D 90.952 2332 101 35 1 2276 399626559 399628836 0.000000e+00 3037
2 TraesCS4B01G236000 chr4A 87.991 1807 87 46 445 2162 57434042 57435807 0.000000e+00 2015
3 TraesCS4B01G236000 chr4A 92.000 425 17 9 1 415 57433627 57434044 4.500000e-162 580
4 TraesCS4B01G236000 chrUn 95.745 94 4 0 2282 2375 37006362 37006455 4.180000e-33 152
5 TraesCS4B01G236000 chrUn 95.745 94 4 0 2282 2375 38258583 38258676 4.180000e-33 152
6 TraesCS4B01G236000 chrUn 95.745 94 4 0 2282 2375 196709647 196709554 4.180000e-33 152
7 TraesCS4B01G236000 chrUn 94.681 94 5 0 2282 2375 36920986 36921079 1.950000e-31 147
8 TraesCS4B01G236000 chrUn 94.681 94 5 0 2282 2375 37366891 37366798 1.950000e-31 147
9 TraesCS4B01G236000 chrUn 94.681 94 5 0 2282 2375 242182951 242182858 1.950000e-31 147
10 TraesCS4B01G236000 chr5D 94.624 93 5 0 2283 2375 301581403 301581311 7.000000e-31 145
11 TraesCS4B01G236000 chr1D 94.565 92 5 0 2276 2367 268929829 268929920 2.520000e-30 143
12 TraesCS4B01G236000 chr1B 91.089 101 7 2 2273 2372 27294485 27294386 4.210000e-28 135


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 TraesCS4B01G236000 chr4B 493628621 493631049 2428 False 4486.0 4486 100.0000 1 2429 1 chr4B.!!$F1 2428
1 TraesCS4B01G236000 chr4D 399626559 399628836 2277 False 3037.0 3037 90.9520 1 2276 1 chr4D.!!$F1 2275
2 TraesCS4B01G236000 chr4A 57433627 57435807 2180 False 1297.5 2015 89.9955 1 2162 2 chr4A.!!$F1 2161

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
989 1051 0.119155 ACCAGTCCCTGATCCCAGAA 59.881 55.0 0.0 0.0 43.02 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 2245 0.036952 ACGGAGGCATGTTCTCTGTG 60.037 55.0 22.87 13.57 45.86 3.66 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
95 97 3.022406 ACGTACCTAGTGAATCCTGTCC 58.978 50.000 0.00 0.00 0.00 4.02
100 105 3.515901 ACCTAGTGAATCCTGTCCAGAAC 59.484 47.826 0.00 0.00 0.00 3.01
102 107 3.971245 AGTGAATCCTGTCCAGAACTC 57.029 47.619 0.00 0.00 0.00 3.01
103 108 3.242867 AGTGAATCCTGTCCAGAACTCA 58.757 45.455 0.00 0.00 0.00 3.41
104 109 3.843027 AGTGAATCCTGTCCAGAACTCAT 59.157 43.478 0.00 0.00 0.00 2.90
106 111 3.054875 TGAATCCTGTCCAGAACTCATGG 60.055 47.826 0.00 0.00 39.33 3.66
107 112 2.325661 TCCTGTCCAGAACTCATGGA 57.674 50.000 0.00 0.00 44.63 3.41
402 417 4.671590 TCGCGAGGGTGGGAGACA 62.672 66.667 3.71 0.00 0.00 3.41
418 433 3.497584 GGAGACATCCATCCTTCCCATTC 60.498 52.174 0.00 0.00 45.87 2.67
428 443 1.740025 CCTTCCCATTCGAGAAACTGC 59.260 52.381 0.00 0.00 0.00 4.40
432 447 1.339055 CCCATTCGAGAAACTGCTCCA 60.339 52.381 0.00 0.00 0.00 3.86
443 462 0.471617 ACTGCTCCAGGATGTATGCC 59.528 55.000 0.00 0.00 35.51 4.40
605 638 1.934589 GCCATCTGCACGTACATACA 58.065 50.000 0.00 0.00 40.77 2.29
724 778 2.033550 CAGTACTATGGACAGAGACGGC 59.966 54.545 0.00 0.00 0.00 5.68
752 806 4.201576 CGCGAAATTTATCTTACCGAAGC 58.798 43.478 0.00 0.00 32.21 3.86
788 842 4.159857 GCGTCGTCATCAGAAGATATACC 58.840 47.826 0.00 0.00 34.80 2.73
928 990 6.989169 CAGCCATCAGTTCCCTATATATAAGC 59.011 42.308 0.00 0.00 0.00 3.09
948 1010 1.582968 CATGGGCGGATGCTTATGC 59.417 57.895 0.00 0.00 42.25 3.14
954 1016 1.063806 GCGGATGCTTATGCTCGTAG 58.936 55.000 1.96 0.00 40.48 3.51
975 1037 1.631898 ACCGCCACCTAATTAACCAGT 59.368 47.619 0.00 0.00 0.00 4.00
989 1051 0.119155 ACCAGTCCCTGATCCCAGAA 59.881 55.000 0.00 0.00 43.02 3.02
994 1056 1.134670 GTCCCTGATCCCAGAAAGACG 60.135 57.143 0.00 0.00 43.02 4.18
1041 1111 2.684843 GGCACTCTTCTTGCTGGCG 61.685 63.158 0.00 0.00 40.07 5.69
1106 1176 2.607811 CTACACCAGGATCCAGCCA 58.392 57.895 15.82 0.00 0.00 4.75
1111 1181 1.379044 CCAGGATCCAGCCACCAAC 60.379 63.158 15.82 0.00 0.00 3.77
1133 1203 5.464168 ACAATCACAGGTACGTACAGTAAC 58.536 41.667 26.02 9.22 43.28 2.50
1137 1207 4.022935 TCACAGGTACGTACAGTAACCAAG 60.023 45.833 26.02 10.26 43.99 3.61
1176 1246 4.760530 ACTTCATAATGCAGACTGGCTA 57.239 40.909 4.26 0.00 34.04 3.93
1191 1261 1.137513 GGCTATGGCAATCGTACGTC 58.862 55.000 16.05 3.32 40.87 4.34
1192 1262 1.269621 GGCTATGGCAATCGTACGTCT 60.270 52.381 16.05 0.89 40.87 4.18
1193 1263 2.052157 GCTATGGCAATCGTACGTCTC 58.948 52.381 16.05 3.31 38.54 3.36
1194 1264 2.307929 CTATGGCAATCGTACGTCTCG 58.692 52.381 16.05 0.00 0.00 4.04
1196 1266 0.241749 TGGCAATCGTACGTCTCGTT 59.758 50.000 16.05 1.39 41.54 3.85
1198 1268 2.095314 TGGCAATCGTACGTCTCGTTAA 60.095 45.455 16.05 0.00 41.54 2.01
1199 1269 3.111098 GGCAATCGTACGTCTCGTTAAT 58.889 45.455 16.05 0.00 41.54 1.40
1202 1272 5.229887 GGCAATCGTACGTCTCGTTAATTTA 59.770 40.000 16.05 0.00 41.54 1.40
1226 1296 2.231964 TGGTCACTTTATAACGCTCGGT 59.768 45.455 0.00 0.00 0.00 4.69
1419 1489 2.053747 ACATCTACACCCAGGGGAAA 57.946 50.000 11.37 0.00 38.96 3.13
1432 1502 2.749621 CAGGGGAAACACAACTAGATGC 59.250 50.000 0.00 0.00 34.58 3.91
1467 1545 1.802365 GAAACCGTTGGTGCTTACGAT 59.198 47.619 0.00 0.00 40.03 3.73
1606 1687 6.607600 TGTGAATTACAGCTATAGTCACCTCT 59.392 38.462 15.39 0.00 34.40 3.69
1618 1699 7.042658 GCTATAGTCACCTCTTTGTATTTTCCG 60.043 40.741 0.84 0.00 0.00 4.30
1619 1700 3.751698 AGTCACCTCTTTGTATTTTCCGC 59.248 43.478 0.00 0.00 0.00 5.54
1625 1706 3.801293 TCTTTGTATTTTCCGCGTTTCG 58.199 40.909 4.92 0.00 38.08 3.46
1661 1742 4.436242 TGTATCTGTTCTGGACTCGAAC 57.564 45.455 0.00 0.00 40.79 3.95
1678 1759 9.692749 GGACTCGAACTTTTATCATCATGTATA 57.307 33.333 0.00 0.00 0.00 1.47
1803 1912 3.698040 AGTTAGACAACCCGACGTCATAT 59.302 43.478 17.16 0.00 35.05 1.78
1804 1913 4.883585 AGTTAGACAACCCGACGTCATATA 59.116 41.667 17.16 0.00 35.05 0.86
1942 2051 5.065731 GTCATAGTTCCTTTTGCTCCATCTG 59.934 44.000 0.00 0.00 0.00 2.90
2112 2237 2.098233 CGCACGGTCGCCACTTAAT 61.098 57.895 0.00 0.00 0.00 1.40
2117 2242 3.231160 CACGGTCGCCACTTAATTTTTC 58.769 45.455 0.00 0.00 0.00 2.29
2118 2243 3.058501 CACGGTCGCCACTTAATTTTTCT 60.059 43.478 0.00 0.00 0.00 2.52
2120 2245 4.156182 CGGTCGCCACTTAATTTTTCTTC 58.844 43.478 0.00 0.00 0.00 2.87
2121 2246 4.319911 CGGTCGCCACTTAATTTTTCTTCA 60.320 41.667 0.00 0.00 0.00 3.02
2122 2247 4.915667 GGTCGCCACTTAATTTTTCTTCAC 59.084 41.667 0.00 0.00 0.00 3.18
2156 2281 7.784037 TGCCTCCGTTCTTTATAACTGTATAA 58.216 34.615 0.00 0.00 31.59 0.98
2157 2282 8.426489 TGCCTCCGTTCTTTATAACTGTATAAT 58.574 33.333 0.00 0.00 33.22 1.28
2158 2283 9.269453 GCCTCCGTTCTTTATAACTGTATAATT 57.731 33.333 0.00 0.00 33.22 1.40
2199 2325 5.243283 TCAGAGTAAACTCCTGTAGGTTGTC 59.757 44.000 6.50 0.00 43.88 3.18
2200 2326 5.244178 CAGAGTAAACTCCTGTAGGTTGTCT 59.756 44.000 6.50 0.00 43.88 3.41
2203 2329 6.073314 AGTAAACTCCTGTAGGTTGTCTGTA 58.927 40.000 0.00 0.00 35.32 2.74
2218 2344 2.610374 GTCTGTACAGTTTTGCAACGGA 59.390 45.455 21.99 0.00 38.03 4.69
2223 2349 1.066908 ACAGTTTTGCAACGGATGTGG 59.933 47.619 0.00 0.00 38.03 4.17
2227 2353 1.164411 TTTGCAACGGATGTGGCTAG 58.836 50.000 0.00 0.00 45.85 3.42
2236 2362 3.570550 ACGGATGTGGCTAGATCTTAGTC 59.429 47.826 0.00 0.00 0.00 2.59
2240 2366 2.950309 TGTGGCTAGATCTTAGTCGACC 59.050 50.000 13.01 0.00 0.00 4.79
2243 2369 2.481185 GGCTAGATCTTAGTCGACCGAG 59.519 54.545 13.01 10.63 0.00 4.63
2280 2406 7.829706 AGTCTCAGTCAAGTGACATATACACTA 59.170 37.037 13.66 0.00 46.01 2.74
2281 2407 8.126074 GTCTCAGTCAAGTGACATATACACTAG 58.874 40.741 13.66 7.63 46.01 2.57
2282 2408 7.829706 TCTCAGTCAAGTGACATATACACTAGT 59.170 37.037 13.66 0.00 46.01 2.57
2283 2409 9.110502 CTCAGTCAAGTGACATATACACTAGTA 57.889 37.037 13.66 2.79 46.01 1.82
2284 2410 8.890718 TCAGTCAAGTGACATATACACTAGTAC 58.109 37.037 13.66 11.35 46.01 2.73
2285 2411 8.894731 CAGTCAAGTGACATATACACTAGTACT 58.105 37.037 13.66 0.00 46.01 2.73
2286 2412 9.111613 AGTCAAGTGACATATACACTAGTACTC 57.888 37.037 13.66 4.62 46.01 2.59
2287 2413 8.344098 GTCAAGTGACATATACACTAGTACTCC 58.656 40.741 0.00 0.00 46.01 3.85
2288 2414 7.501559 TCAAGTGACATATACACTAGTACTCCC 59.498 40.741 0.00 0.00 46.01 4.30
2289 2415 7.151694 AGTGACATATACACTAGTACTCCCT 57.848 40.000 0.00 0.00 45.10 4.20
2290 2416 7.225725 AGTGACATATACACTAGTACTCCCTC 58.774 42.308 0.00 0.00 45.10 4.30
2291 2417 7.072708 AGTGACATATACACTAGTACTCCCTCT 59.927 40.741 0.00 0.00 45.10 3.69
2292 2418 7.173562 GTGACATATACACTAGTACTCCCTCTG 59.826 44.444 0.00 0.00 35.66 3.35
2293 2419 7.147355 TGACATATACACTAGTACTCCCTCTGT 60.147 40.741 0.00 0.00 31.96 3.41
2294 2420 7.225725 ACATATACACTAGTACTCCCTCTGTC 58.774 42.308 0.00 0.00 31.96 3.51
2295 2421 3.369242 ACACTAGTACTCCCTCTGTCC 57.631 52.381 0.00 0.00 0.00 4.02
2296 2422 2.025131 ACACTAGTACTCCCTCTGTCCC 60.025 54.545 0.00 0.00 0.00 4.46
2297 2423 2.025226 CACTAGTACTCCCTCTGTCCCA 60.025 54.545 0.00 0.00 0.00 4.37
2298 2424 2.653366 ACTAGTACTCCCTCTGTCCCAA 59.347 50.000 0.00 0.00 0.00 4.12
2299 2425 2.239681 AGTACTCCCTCTGTCCCAAG 57.760 55.000 0.00 0.00 0.00 3.61
2300 2426 1.717077 AGTACTCCCTCTGTCCCAAGA 59.283 52.381 0.00 0.00 0.00 3.02
2301 2427 2.316372 AGTACTCCCTCTGTCCCAAGAT 59.684 50.000 0.00 0.00 0.00 2.40
2302 2428 3.532232 AGTACTCCCTCTGTCCCAAGATA 59.468 47.826 0.00 0.00 0.00 1.98
2303 2429 3.715648 ACTCCCTCTGTCCCAAGATAT 57.284 47.619 0.00 0.00 0.00 1.63
2304 2430 4.834406 ACTCCCTCTGTCCCAAGATATA 57.166 45.455 0.00 0.00 0.00 0.86
2305 2431 5.157770 ACTCCCTCTGTCCCAAGATATAA 57.842 43.478 0.00 0.00 0.00 0.98
2306 2432 5.151454 ACTCCCTCTGTCCCAAGATATAAG 58.849 45.833 0.00 0.00 0.00 1.73
2307 2433 5.103043 ACTCCCTCTGTCCCAAGATATAAGA 60.103 44.000 0.00 0.00 0.00 2.10
2308 2434 5.788430 TCCCTCTGTCCCAAGATATAAGAA 58.212 41.667 0.00 0.00 0.00 2.52
2309 2435 5.841237 TCCCTCTGTCCCAAGATATAAGAAG 59.159 44.000 0.00 0.00 0.00 2.85
2310 2436 5.012561 CCCTCTGTCCCAAGATATAAGAAGG 59.987 48.000 0.00 0.00 0.00 3.46
2311 2437 5.604650 CCTCTGTCCCAAGATATAAGAAGGT 59.395 44.000 0.00 0.00 0.00 3.50
2312 2438 6.100424 CCTCTGTCCCAAGATATAAGAAGGTT 59.900 42.308 0.00 0.00 0.00 3.50
2313 2439 7.366011 CCTCTGTCCCAAGATATAAGAAGGTTT 60.366 40.741 0.00 0.00 0.00 3.27
2314 2440 7.928873 TCTGTCCCAAGATATAAGAAGGTTTT 58.071 34.615 0.00 0.00 0.00 2.43
2315 2441 8.390921 TCTGTCCCAAGATATAAGAAGGTTTTT 58.609 33.333 0.00 0.00 0.00 1.94
2316 2442 9.681062 CTGTCCCAAGATATAAGAAGGTTTTTA 57.319 33.333 0.00 0.00 0.00 1.52
2342 2468 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
2343 2469 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
2344 2470 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
2345 2471 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
2346 2472 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
2347 2473 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
2348 2474 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
2358 2484 9.632969 CAAAAACGTTCTTATATTATGAGACGG 57.367 33.333 0.00 8.31 0.00 4.79
2359 2485 9.590451 AAAAACGTTCTTATATTATGAGACGGA 57.410 29.630 0.00 0.00 0.00 4.69
2360 2486 8.798748 AAACGTTCTTATATTATGAGACGGAG 57.201 34.615 0.00 6.40 0.00 4.63
2361 2487 6.910995 ACGTTCTTATATTATGAGACGGAGG 58.089 40.000 16.71 6.29 0.00 4.30
2362 2488 6.072064 ACGTTCTTATATTATGAGACGGAGGG 60.072 42.308 16.71 2.79 0.00 4.30
2363 2489 6.625300 CGTTCTTATATTATGAGACGGAGGGG 60.625 46.154 0.00 0.00 0.00 4.79
2364 2490 5.269991 TCTTATATTATGAGACGGAGGGGG 58.730 45.833 0.00 0.00 0.00 5.40
2365 2491 3.562108 ATATTATGAGACGGAGGGGGT 57.438 47.619 0.00 0.00 0.00 4.95
2366 2492 4.687262 ATATTATGAGACGGAGGGGGTA 57.313 45.455 0.00 0.00 0.00 3.69
2367 2493 2.852714 TTATGAGACGGAGGGGGTAA 57.147 50.000 0.00 0.00 0.00 2.85
2368 2494 2.852714 TATGAGACGGAGGGGGTAAA 57.147 50.000 0.00 0.00 0.00 2.01
2369 2495 1.961133 ATGAGACGGAGGGGGTAAAA 58.039 50.000 0.00 0.00 0.00 1.52
2370 2496 1.732117 TGAGACGGAGGGGGTAAAAA 58.268 50.000 0.00 0.00 0.00 1.94
2390 2516 5.921962 AAAATAGGGCTTTGATTGAGGTC 57.078 39.130 0.00 0.00 0.00 3.85
2391 2517 4.591321 AATAGGGCTTTGATTGAGGTCA 57.409 40.909 0.00 0.00 0.00 4.02
2392 2518 2.503895 AGGGCTTTGATTGAGGTCAG 57.496 50.000 0.00 0.00 0.00 3.51
2393 2519 1.988107 AGGGCTTTGATTGAGGTCAGA 59.012 47.619 0.00 0.00 0.00 3.27
2394 2520 2.579860 AGGGCTTTGATTGAGGTCAGAT 59.420 45.455 0.00 0.00 0.00 2.90
2395 2521 3.782523 AGGGCTTTGATTGAGGTCAGATA 59.217 43.478 0.00 0.00 0.00 1.98
2396 2522 4.228210 AGGGCTTTGATTGAGGTCAGATAA 59.772 41.667 0.00 0.00 0.00 1.75
2397 2523 4.578105 GGGCTTTGATTGAGGTCAGATAAG 59.422 45.833 0.00 0.00 0.00 1.73
2398 2524 4.578105 GGCTTTGATTGAGGTCAGATAAGG 59.422 45.833 0.00 0.00 0.00 2.69
2399 2525 4.578105 GCTTTGATTGAGGTCAGATAAGGG 59.422 45.833 0.00 0.00 0.00 3.95
2400 2526 3.845781 TGATTGAGGTCAGATAAGGGC 57.154 47.619 0.00 0.00 0.00 5.19
2401 2527 3.114606 TGATTGAGGTCAGATAAGGGCA 58.885 45.455 0.00 0.00 0.00 5.36
2402 2528 3.118261 TGATTGAGGTCAGATAAGGGCAC 60.118 47.826 0.00 0.00 0.00 5.01
2403 2529 2.254152 TGAGGTCAGATAAGGGCACT 57.746 50.000 0.00 0.00 0.00 4.40
2404 2530 3.398318 TGAGGTCAGATAAGGGCACTA 57.602 47.619 0.00 0.00 0.00 2.74
2405 2531 3.719871 TGAGGTCAGATAAGGGCACTAA 58.280 45.455 0.00 0.00 0.00 2.24
2406 2532 4.298626 TGAGGTCAGATAAGGGCACTAAT 58.701 43.478 0.00 0.00 0.00 1.73
2407 2533 4.345257 TGAGGTCAGATAAGGGCACTAATC 59.655 45.833 0.00 0.00 0.00 1.75
2408 2534 3.648545 AGGTCAGATAAGGGCACTAATCC 59.351 47.826 0.00 0.00 0.00 3.01
2409 2535 3.648545 GGTCAGATAAGGGCACTAATCCT 59.351 47.826 0.00 0.00 34.29 3.24
2410 2536 4.503991 GGTCAGATAAGGGCACTAATCCTG 60.504 50.000 0.00 0.00 32.95 3.86
2411 2537 3.648067 TCAGATAAGGGCACTAATCCTGG 59.352 47.826 0.00 0.00 32.95 4.45
2412 2538 3.392616 CAGATAAGGGCACTAATCCTGGT 59.607 47.826 0.00 0.00 32.95 4.00
2413 2539 4.047883 AGATAAGGGCACTAATCCTGGTT 58.952 43.478 0.00 0.00 32.95 3.67
2414 2540 2.808906 AAGGGCACTAATCCTGGTTC 57.191 50.000 0.00 0.00 32.95 3.62
2415 2541 1.668826 AGGGCACTAATCCTGGTTCA 58.331 50.000 0.00 0.00 31.11 3.18
2416 2542 1.282157 AGGGCACTAATCCTGGTTCAC 59.718 52.381 0.00 0.00 31.11 3.18
2417 2543 1.282157 GGGCACTAATCCTGGTTCACT 59.718 52.381 0.00 0.00 0.00 3.41
2418 2544 2.633488 GGCACTAATCCTGGTTCACTC 58.367 52.381 0.00 0.00 0.00 3.51
2419 2545 2.027192 GGCACTAATCCTGGTTCACTCA 60.027 50.000 0.00 0.00 0.00 3.41
2420 2546 3.003480 GCACTAATCCTGGTTCACTCAC 58.997 50.000 0.00 0.00 0.00 3.51
2421 2547 3.254060 CACTAATCCTGGTTCACTCACG 58.746 50.000 0.00 0.00 0.00 4.35
2422 2548 3.056821 CACTAATCCTGGTTCACTCACGA 60.057 47.826 0.00 0.00 0.00 4.35
2423 2549 3.576982 ACTAATCCTGGTTCACTCACGAA 59.423 43.478 0.00 0.00 0.00 3.85
2424 2550 3.703001 AATCCTGGTTCACTCACGAAT 57.297 42.857 0.00 0.00 0.00 3.34
2425 2551 2.743636 TCCTGGTTCACTCACGAATC 57.256 50.000 0.00 0.00 0.00 2.52
2426 2552 1.067846 TCCTGGTTCACTCACGAATCG 60.068 52.381 0.00 0.00 0.00 3.34
2427 2553 1.336887 CCTGGTTCACTCACGAATCGT 60.337 52.381 0.96 0.96 42.36 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.517453 TCCAAATTCGTGGTGGAAAAGTAG 59.483 41.667 0.00 0.00 38.50 2.57
95 97 8.327271 AGATATATCCCATTTCCATGAGTTCTG 58.673 37.037 9.18 0.00 31.07 3.02
100 105 7.228906 GCATCAGATATATCCCATTTCCATGAG 59.771 40.741 9.18 0.52 31.07 2.90
102 107 6.264744 GGCATCAGATATATCCCATTTCCATG 59.735 42.308 9.18 0.00 0.00 3.66
103 108 6.161705 AGGCATCAGATATATCCCATTTCCAT 59.838 38.462 9.18 0.00 0.00 3.41
104 109 5.493613 AGGCATCAGATATATCCCATTTCCA 59.506 40.000 9.18 0.00 0.00 3.53
106 111 6.656902 TCAGGCATCAGATATATCCCATTTC 58.343 40.000 9.18 0.00 0.00 2.17
107 112 6.647461 TCAGGCATCAGATATATCCCATTT 57.353 37.500 9.18 0.00 0.00 2.32
109 114 5.397672 GCTTCAGGCATCAGATATATCCCAT 60.398 44.000 9.18 0.00 41.35 4.00
110 115 4.080695 GCTTCAGGCATCAGATATATCCCA 60.081 45.833 9.18 0.00 41.35 4.37
111 116 4.450053 GCTTCAGGCATCAGATATATCCC 58.550 47.826 9.18 3.24 41.35 3.85
392 406 1.141858 GAAGGATGGATGTCTCCCACC 59.858 57.143 0.00 0.00 41.29 4.61
394 408 1.511613 GGAAGGATGGATGTCTCCCA 58.488 55.000 0.00 0.00 41.29 4.37
402 417 2.694397 TCTCGAATGGGAAGGATGGAT 58.306 47.619 0.00 0.00 0.00 3.41
405 420 3.624861 CAGTTTCTCGAATGGGAAGGATG 59.375 47.826 0.00 0.00 0.00 3.51
418 433 1.066573 ACATCCTGGAGCAGTTTCTCG 60.067 52.381 1.52 0.00 33.98 4.04
428 443 1.763770 GGGGGCATACATCCTGGAG 59.236 63.158 1.52 0.00 0.00 3.86
432 447 3.941188 CGCGGGGGCATACATCCT 61.941 66.667 0.00 0.00 0.00 3.24
605 638 4.483243 CCGGGCACTTGGCGGTAT 62.483 66.667 9.11 0.00 46.16 2.73
709 763 0.107361 TCTCGCCGTCTCTGTCCATA 60.107 55.000 0.00 0.00 0.00 2.74
724 778 3.843426 AAGATAAATTTCGCGCTCTCG 57.157 42.857 5.56 0.00 39.07 4.04
778 832 3.169733 GCGTTCGATCGGGTATATCTTC 58.830 50.000 16.41 0.00 0.00 2.87
788 842 3.884350 TCTCCGGCGTTCGATCGG 61.884 66.667 16.41 12.98 44.59 4.18
843 899 3.046087 CACAGGACACAGCGGCAG 61.046 66.667 1.45 0.00 0.00 4.85
844 900 3.860605 ACACAGGACACAGCGGCA 61.861 61.111 1.45 0.00 0.00 5.69
845 901 3.349006 CACACAGGACACAGCGGC 61.349 66.667 0.00 0.00 0.00 6.53
846 902 2.666190 CCACACAGGACACAGCGG 60.666 66.667 0.00 0.00 41.22 5.52
847 903 3.349006 GCCACACAGGACACAGCG 61.349 66.667 0.00 0.00 41.22 5.18
853 909 2.668550 GGTTCGGCCACACAGGAC 60.669 66.667 2.24 0.00 44.64 3.85
854 910 4.308458 CGGTTCGGCCACACAGGA 62.308 66.667 2.24 0.00 41.22 3.86
928 990 1.075482 ATAAGCATCCGCCCATGGG 59.925 57.895 27.87 27.87 39.83 4.00
954 1016 2.285977 CTGGTTAATTAGGTGGCGGTC 58.714 52.381 0.00 0.00 0.00 4.79
975 1037 1.195115 CGTCTTTCTGGGATCAGGGA 58.805 55.000 0.00 0.00 41.23 4.20
989 1051 0.827368 GGAGGCCATCTCTTCGTCTT 59.173 55.000 5.01 0.00 42.10 3.01
994 1056 1.416030 GGAGAAGGAGGCCATCTCTTC 59.584 57.143 20.35 17.81 44.75 2.87
1106 1176 2.922740 ACGTACCTGTGATTGTTGGT 57.077 45.000 0.00 0.00 36.66 3.67
1111 1181 4.860907 GGTTACTGTACGTACCTGTGATTG 59.139 45.833 22.43 5.63 0.00 2.67
1133 1203 8.589335 AAGTATATACACGTTAGATTGCTTGG 57.411 34.615 15.18 0.00 0.00 3.61
1176 1246 0.454600 ACGAGACGTACGATTGCCAT 59.545 50.000 24.41 0.00 38.73 4.40
1198 1268 8.120465 CGAGCGTTATAAAGTGACCAAATAAAT 58.880 33.333 0.35 0.00 0.00 1.40
1199 1269 7.413219 CCGAGCGTTATAAAGTGACCAAATAAA 60.413 37.037 0.35 0.00 0.00 1.40
1202 1272 4.331717 CCGAGCGTTATAAAGTGACCAAAT 59.668 41.667 0.35 0.00 0.00 2.32
1226 1296 4.154015 CCTGCAGATCATTAACACAACGAA 59.846 41.667 17.39 0.00 0.00 3.85
1432 1502 1.000938 GGTTTCAGGCTTTCAGCACAG 60.001 52.381 0.00 0.00 44.75 3.66
1467 1545 0.679505 CCTTCAGTTCACGGAGTCCA 59.320 55.000 10.49 0.00 41.61 4.02
1601 1679 2.774687 ACGCGGAAAATACAAAGAGGT 58.225 42.857 12.47 0.00 0.00 3.85
1606 1687 3.605743 ACGAAACGCGGAAAATACAAA 57.394 38.095 12.47 0.00 46.49 2.83
1618 1699 2.106418 GACCTGAAAACAACGAAACGC 58.894 47.619 0.00 0.00 0.00 4.84
1619 1700 3.392769 TGACCTGAAAACAACGAAACG 57.607 42.857 0.00 0.00 0.00 3.60
1625 1706 6.560253 ACAGATACATGACCTGAAAACAAC 57.440 37.500 16.34 0.00 0.00 3.32
1722 1803 9.901724 CAATCACGAAGAACAGTATAACATTAC 57.098 33.333 0.00 0.00 0.00 1.89
1803 1912 3.101437 TCCTTTCCGTGTAGGCATCTTA 58.899 45.455 0.00 0.00 40.77 2.10
1804 1913 1.906574 TCCTTTCCGTGTAGGCATCTT 59.093 47.619 0.00 0.00 40.77 2.40
1942 2051 7.793902 AGTACGACAAACAATGATGAAGTAAC 58.206 34.615 0.00 0.00 0.00 2.50
2112 2237 4.889409 AGGCATGTTCTCTGTGAAGAAAAA 59.111 37.500 0.00 0.00 37.04 1.94
2117 2242 2.354259 GGAGGCATGTTCTCTGTGAAG 58.646 52.381 14.67 0.00 35.01 3.02
2118 2243 1.338105 CGGAGGCATGTTCTCTGTGAA 60.338 52.381 14.80 0.00 34.01 3.18
2120 2245 0.036952 ACGGAGGCATGTTCTCTGTG 60.037 55.000 22.87 13.57 45.86 3.66
2121 2246 2.366469 ACGGAGGCATGTTCTCTGT 58.634 52.632 19.90 19.90 43.68 3.41
2122 2247 1.363744 GAACGGAGGCATGTTCTCTG 58.636 55.000 18.93 18.93 40.94 3.35
2156 2281 4.831155 TCTGATCGAAGGTATCCCGTTAAT 59.169 41.667 0.00 0.00 35.12 1.40
2157 2282 4.209538 TCTGATCGAAGGTATCCCGTTAA 58.790 43.478 0.00 0.00 35.12 2.01
2158 2283 3.819337 CTCTGATCGAAGGTATCCCGTTA 59.181 47.826 0.00 0.00 35.12 3.18
2159 2284 2.623889 CTCTGATCGAAGGTATCCCGTT 59.376 50.000 0.00 0.00 35.12 4.44
2160 2285 2.231529 CTCTGATCGAAGGTATCCCGT 58.768 52.381 0.00 0.00 35.12 5.28
2161 2286 2.231529 ACTCTGATCGAAGGTATCCCG 58.768 52.381 0.00 0.00 35.12 5.14
2162 2287 5.302313 AGTTTACTCTGATCGAAGGTATCCC 59.698 44.000 0.00 0.00 0.00 3.85
2172 2298 4.641094 ACCTACAGGAGTTTACTCTGATCG 59.359 45.833 9.56 0.00 42.48 3.69
2177 2303 5.244178 CAGACAACCTACAGGAGTTTACTCT 59.756 44.000 9.56 0.00 42.48 3.24
2178 2304 5.010820 ACAGACAACCTACAGGAGTTTACTC 59.989 44.000 1.29 1.18 42.14 2.59
2199 2325 3.003275 ACATCCGTTGCAAAACTGTACAG 59.997 43.478 21.44 21.44 0.00 2.74
2200 2326 2.946329 ACATCCGTTGCAAAACTGTACA 59.054 40.909 0.00 0.00 0.00 2.90
2203 2329 1.066908 CCACATCCGTTGCAAAACTGT 59.933 47.619 0.00 0.00 0.00 3.55
2218 2344 3.570550 GGTCGACTAAGATCTAGCCACAT 59.429 47.826 16.46 0.00 0.00 3.21
2223 2349 3.184986 GTCTCGGTCGACTAAGATCTAGC 59.815 52.174 16.46 3.10 0.00 3.42
2227 2353 5.731599 TTAAGTCTCGGTCGACTAAGATC 57.268 43.478 16.46 12.03 43.14 2.75
2248 2374 6.222038 TGTCACTTGACTGAGACTTAGTTT 57.778 37.500 10.63 0.00 44.99 2.66
2256 2382 7.829706 ACTAGTGTATATGTCACTTGACTGAGA 59.170 37.037 20.93 0.00 42.50 3.27
2259 2385 8.894731 AGTACTAGTGTATATGTCACTTGACTG 58.105 37.037 20.93 11.02 42.50 3.51
2264 2390 7.584532 AGGGAGTACTAGTGTATATGTCACTT 58.415 38.462 16.54 6.54 42.50 3.16
2267 2393 7.147355 ACAGAGGGAGTACTAGTGTATATGTCA 60.147 40.741 5.39 0.00 0.00 3.58
2276 2402 2.025226 TGGGACAGAGGGAGTACTAGTG 60.025 54.545 5.39 0.00 0.00 2.74
2277 2403 2.285707 TGGGACAGAGGGAGTACTAGT 58.714 52.381 0.00 0.00 0.00 2.57
2278 2404 3.053544 TCTTGGGACAGAGGGAGTACTAG 60.054 52.174 0.00 0.00 42.39 2.57
2279 2405 2.924302 TCTTGGGACAGAGGGAGTACTA 59.076 50.000 0.00 0.00 42.39 1.82
2280 2406 1.717077 TCTTGGGACAGAGGGAGTACT 59.283 52.381 0.00 0.00 42.39 2.73
2281 2407 2.233305 TCTTGGGACAGAGGGAGTAC 57.767 55.000 0.00 0.00 42.39 2.73
2282 2408 4.834406 ATATCTTGGGACAGAGGGAGTA 57.166 45.455 0.00 0.00 42.39 2.59
2283 2409 3.715648 ATATCTTGGGACAGAGGGAGT 57.284 47.619 0.00 0.00 42.39 3.85
2284 2410 5.398236 TCTTATATCTTGGGACAGAGGGAG 58.602 45.833 0.00 0.00 42.39 4.30
2285 2411 5.418692 TCTTATATCTTGGGACAGAGGGA 57.581 43.478 0.00 0.00 42.39 4.20
2286 2412 5.012561 CCTTCTTATATCTTGGGACAGAGGG 59.987 48.000 0.00 0.00 42.39 4.30
2287 2413 5.604650 ACCTTCTTATATCTTGGGACAGAGG 59.395 44.000 0.00 0.00 42.39 3.69
2288 2414 6.739331 ACCTTCTTATATCTTGGGACAGAG 57.261 41.667 0.00 0.00 42.39 3.35
2289 2415 7.510675 AAACCTTCTTATATCTTGGGACAGA 57.489 36.000 0.00 0.00 42.39 3.41
2290 2416 8.581253 AAAAACCTTCTTATATCTTGGGACAG 57.419 34.615 0.00 0.00 42.39 3.51
2319 2445 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
2320 2446 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
2321 2447 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
2332 2458 9.632969 CCGTCTCATAATATAAGAACGTTTTTG 57.367 33.333 13.87 0.00 0.00 2.44
2333 2459 9.590451 TCCGTCTCATAATATAAGAACGTTTTT 57.410 29.630 9.22 9.22 0.00 1.94
2334 2460 9.245962 CTCCGTCTCATAATATAAGAACGTTTT 57.754 33.333 0.46 0.00 0.00 2.43
2335 2461 7.866393 CCTCCGTCTCATAATATAAGAACGTTT 59.134 37.037 0.46 0.00 0.00 3.60
2336 2462 7.368833 CCTCCGTCTCATAATATAAGAACGTT 58.631 38.462 0.00 0.00 0.00 3.99
2337 2463 6.072064 CCCTCCGTCTCATAATATAAGAACGT 60.072 42.308 0.00 0.00 0.00 3.99
2338 2464 6.323266 CCCTCCGTCTCATAATATAAGAACG 58.677 44.000 0.00 0.00 0.00 3.95
2339 2465 6.351117 CCCCCTCCGTCTCATAATATAAGAAC 60.351 46.154 0.00 0.00 0.00 3.01
2340 2466 5.720041 CCCCCTCCGTCTCATAATATAAGAA 59.280 44.000 0.00 0.00 0.00 2.52
2341 2467 5.222484 ACCCCCTCCGTCTCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2342 2468 5.024118 ACCCCCTCCGTCTCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2343 2469 5.019657 ACCCCCTCCGTCTCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2344 2470 4.687262 ACCCCCTCCGTCTCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2345 2471 3.562108 ACCCCCTCCGTCTCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2346 2472 4.474303 TTACCCCCTCCGTCTCATAATA 57.526 45.455 0.00 0.00 0.00 0.98
2347 2473 3.339713 TTACCCCCTCCGTCTCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
2348 2474 2.852714 TTACCCCCTCCGTCTCATAA 57.147 50.000 0.00 0.00 0.00 1.90
2349 2475 2.852714 TTTACCCCCTCCGTCTCATA 57.147 50.000 0.00 0.00 0.00 2.15
2350 2476 1.961133 TTTTACCCCCTCCGTCTCAT 58.039 50.000 0.00 0.00 0.00 2.90
2351 2477 1.732117 TTTTTACCCCCTCCGTCTCA 58.268 50.000 0.00 0.00 0.00 3.27
2367 2493 5.779771 TGACCTCAATCAAAGCCCTATTTTT 59.220 36.000 0.00 0.00 0.00 1.94
2368 2494 5.332743 TGACCTCAATCAAAGCCCTATTTT 58.667 37.500 0.00 0.00 0.00 1.82
2369 2495 4.934356 TGACCTCAATCAAAGCCCTATTT 58.066 39.130 0.00 0.00 0.00 1.40
2370 2496 4.228210 TCTGACCTCAATCAAAGCCCTATT 59.772 41.667 0.00 0.00 0.00 1.73
2371 2497 3.782523 TCTGACCTCAATCAAAGCCCTAT 59.217 43.478 0.00 0.00 0.00 2.57
2372 2498 3.181329 TCTGACCTCAATCAAAGCCCTA 58.819 45.455 0.00 0.00 0.00 3.53
2373 2499 1.988107 TCTGACCTCAATCAAAGCCCT 59.012 47.619 0.00 0.00 0.00 5.19
2374 2500 2.496899 TCTGACCTCAATCAAAGCCC 57.503 50.000 0.00 0.00 0.00 5.19
2375 2501 4.578105 CCTTATCTGACCTCAATCAAAGCC 59.422 45.833 0.00 0.00 0.00 4.35
2376 2502 4.578105 CCCTTATCTGACCTCAATCAAAGC 59.422 45.833 0.00 0.00 0.00 3.51
2377 2503 4.578105 GCCCTTATCTGACCTCAATCAAAG 59.422 45.833 0.00 0.00 0.00 2.77
2378 2504 4.018506 TGCCCTTATCTGACCTCAATCAAA 60.019 41.667 0.00 0.00 0.00 2.69
2379 2505 3.523157 TGCCCTTATCTGACCTCAATCAA 59.477 43.478 0.00 0.00 0.00 2.57
2380 2506 3.114606 TGCCCTTATCTGACCTCAATCA 58.885 45.455 0.00 0.00 0.00 2.57
2381 2507 3.135530 AGTGCCCTTATCTGACCTCAATC 59.864 47.826 0.00 0.00 0.00 2.67
2382 2508 3.118531 AGTGCCCTTATCTGACCTCAAT 58.881 45.455 0.00 0.00 0.00 2.57
2383 2509 2.551270 AGTGCCCTTATCTGACCTCAA 58.449 47.619 0.00 0.00 0.00 3.02
2384 2510 2.254152 AGTGCCCTTATCTGACCTCA 57.746 50.000 0.00 0.00 0.00 3.86
2385 2511 4.262678 GGATTAGTGCCCTTATCTGACCTC 60.263 50.000 0.00 0.00 29.53 3.85
2386 2512 3.648545 GGATTAGTGCCCTTATCTGACCT 59.351 47.826 0.00 0.00 29.53 3.85
2387 2513 3.648545 AGGATTAGTGCCCTTATCTGACC 59.351 47.826 0.00 0.00 29.53 4.02
2388 2514 4.503991 CCAGGATTAGTGCCCTTATCTGAC 60.504 50.000 0.00 0.00 29.53 3.51
2389 2515 3.648067 CCAGGATTAGTGCCCTTATCTGA 59.352 47.826 0.00 0.00 29.53 3.27
2390 2516 3.392616 ACCAGGATTAGTGCCCTTATCTG 59.607 47.826 0.00 0.00 29.53 2.90
2391 2517 3.669949 ACCAGGATTAGTGCCCTTATCT 58.330 45.455 0.00 0.00 29.53 1.98
2392 2518 4.141482 TGAACCAGGATTAGTGCCCTTATC 60.141 45.833 0.00 0.00 0.00 1.75
2393 2519 3.785887 TGAACCAGGATTAGTGCCCTTAT 59.214 43.478 0.00 0.00 0.00 1.73
2394 2520 3.054655 GTGAACCAGGATTAGTGCCCTTA 60.055 47.826 0.00 0.00 0.00 2.69
2395 2521 1.992557 TGAACCAGGATTAGTGCCCTT 59.007 47.619 0.00 0.00 0.00 3.95
2396 2522 1.282157 GTGAACCAGGATTAGTGCCCT 59.718 52.381 0.00 0.00 0.00 5.19
2397 2523 1.282157 AGTGAACCAGGATTAGTGCCC 59.718 52.381 0.00 0.00 0.00 5.36
2398 2524 2.027192 TGAGTGAACCAGGATTAGTGCC 60.027 50.000 0.00 0.00 0.00 5.01
2399 2525 3.003480 GTGAGTGAACCAGGATTAGTGC 58.997 50.000 0.00 0.00 0.00 4.40
2400 2526 3.056821 TCGTGAGTGAACCAGGATTAGTG 60.057 47.826 0.00 0.00 0.00 2.74
2401 2527 3.162666 TCGTGAGTGAACCAGGATTAGT 58.837 45.455 0.00 0.00 0.00 2.24
2402 2528 3.868757 TCGTGAGTGAACCAGGATTAG 57.131 47.619 0.00 0.00 0.00 1.73
2403 2529 4.676986 CGATTCGTGAGTGAACCAGGATTA 60.677 45.833 0.00 0.00 0.00 1.75
2404 2530 3.600388 GATTCGTGAGTGAACCAGGATT 58.400 45.455 0.00 0.00 0.00 3.01
2405 2531 2.417379 CGATTCGTGAGTGAACCAGGAT 60.417 50.000 0.00 0.00 0.00 3.24
2406 2532 1.067846 CGATTCGTGAGTGAACCAGGA 60.068 52.381 0.00 0.00 0.00 3.86
2407 2533 1.336887 ACGATTCGTGAGTGAACCAGG 60.337 52.381 11.56 0.00 39.18 4.45
2408 2534 2.065993 ACGATTCGTGAGTGAACCAG 57.934 50.000 11.56 0.00 39.18 4.00


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

AutoCloner maintained by Alex Coulton.