Multiple sequence alignment - TraesCS6D01G274900

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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 TraesCS6D01G274900 chr6D 100.000 2996 0 0 1 2996 383746561 383743566 0.000000e+00 5533.0
1 TraesCS6D01G274900 chr6B 91.308 2278 124 35 23 2272 574022457 574020226 0.000000e+00 3042.0
2 TraesCS6D01G274900 chr6B 93.455 550 28 6 2443 2988 574020235 574019690 0.000000e+00 809.0
3 TraesCS6D01G274900 chr6A 90.303 2310 119 40 9 2272 525993613 525991363 0.000000e+00 2928.0
4 TraesCS6D01G274900 chr6A 92.730 564 28 8 2443 2996 525991372 525990812 0.000000e+00 802.0
5 TraesCS6D01G274900 chr7D 79.445 613 86 32 993 1581 165634705 165635301 6.020000e-107 398.0
6 TraesCS6D01G274900 chr7D 87.586 145 11 6 2272 2416 480049496 480049359 8.590000e-36 161.0
7 TraesCS6D01G274900 chr7D 82.707 133 19 4 1240 1370 262698821 262698691 6.790000e-22 115.0
8 TraesCS6D01G274900 chr7B 79.368 601 90 27 999 1581 128822081 128822665 2.800000e-105 392.0
9 TraesCS6D01G274900 chr7B 81.159 138 24 2 1234 1370 241107810 241107946 3.160000e-20 110.0
10 TraesCS6D01G274900 chr7A 78.734 616 90 30 992 1581 167179673 167180273 1.010000e-99 374.0
11 TraesCS6D01G274900 chr7A 82.443 131 23 0 1240 1370 285576473 285576343 6.790000e-22 115.0
12 TraesCS6D01G274900 chr3D 86.585 164 14 6 2272 2435 565410032 565410187 1.100000e-39 174.0
13 TraesCS6D01G274900 chr3D 84.906 159 19 5 2272 2426 17671031 17671188 4.000000e-34 156.0
14 TraesCS6D01G274900 chr3D 90.411 73 7 0 1235 1307 357141493 357141565 2.460000e-16 97.1
15 TraesCS6D01G274900 chr5D 89.706 136 12 2 1001 1135 319254271 319254405 3.970000e-39 172.0
16 TraesCS6D01G274900 chr5D 88.652 141 12 4 2273 2412 234820704 234820841 5.140000e-38 169.0
17 TraesCS6D01G274900 chr5B 89.706 136 12 2 1001 1135 369485439 369485573 3.970000e-39 172.0
18 TraesCS6D01G274900 chr5B 87.097 124 16 0 1458 1581 369485857 369485980 1.120000e-29 141.0
19 TraesCS6D01G274900 chr5A 89.706 136 12 2 1001 1135 414934854 414934720 3.970000e-39 172.0
20 TraesCS6D01G274900 chr5A 84.028 144 21 2 1463 1605 414934422 414934280 1.450000e-28 137.0
21 TraesCS6D01G274900 chr2A 88.112 143 13 3 2272 2410 615747590 615747448 1.850000e-37 167.0
22 TraesCS6D01G274900 chr2A 86.486 111 13 2 1471 1580 696316052 696316161 1.460000e-23 121.0
23 TraesCS6D01G274900 chr1B 85.276 163 18 5 2271 2431 87969626 87969468 2.390000e-36 163.0
24 TraesCS6D01G274900 chr1B 73.585 318 59 20 1230 1535 487951356 487951052 6.830000e-17 99.0
25 TraesCS6D01G274900 chr4A 83.425 181 18 5 2271 2445 473937360 473937534 1.110000e-34 158.0
26 TraesCS6D01G274900 chr2D 84.756 164 16 7 2273 2435 106123306 106123461 4.000000e-34 156.0
27 TraesCS6D01G274900 chr4B 82.609 184 23 6 2259 2435 406463688 406463869 1.440000e-33 154.0


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 TraesCS6D01G274900 chr6D 383743566 383746561 2995 True 5533.0 5533 100.0000 1 2996 1 chr6D.!!$R1 2995
1 TraesCS6D01G274900 chr6B 574019690 574022457 2767 True 1925.5 3042 92.3815 23 2988 2 chr6B.!!$R1 2965
2 TraesCS6D01G274900 chr6A 525990812 525993613 2801 True 1865.0 2928 91.5165 9 2996 2 chr6A.!!$R1 2987
3 TraesCS6D01G274900 chr7D 165634705 165635301 596 False 398.0 398 79.4450 993 1581 1 chr7D.!!$F1 588
4 TraesCS6D01G274900 chr7B 128822081 128822665 584 False 392.0 392 79.3680 999 1581 1 chr7B.!!$F1 582
5 TraesCS6D01G274900 chr7A 167179673 167180273 600 False 374.0 374 78.7340 992 1581 1 chr7A.!!$F1 589

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
414 424 0.174389 AGTGTCAGCTATGCCTCGTG 59.826 55.0 0.00 0.0 0.00 4.35 F
1155 1199 0.096628 AGCGACGCTTACACTCGTAG 59.903 55.0 18.46 0.0 39.22 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1457 1543 0.179100 CGCGATCTTGGACCATCTGT 60.179 55.0 0.0 0.0 0.0 3.41 R
2664 2783 0.034059 AAGCACTCCTCACACTTCCG 59.966 55.0 0.0 0.0 0.0 4.30 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
77 81 2.355481 ACGGCTCGTTTGGTCGAC 60.355 61.111 7.13 7.13 36.35 4.20
84 88 2.305127 CGTTTGGTCGACGGTCACC 61.305 63.158 9.92 17.46 36.90 4.02
141 145 0.518636 GCAAGAAAGAGTGCATCGCA 59.481 50.000 0.00 0.00 40.58 5.10
287 296 2.099431 GTGCGAGGCAGCTTCTCTG 61.099 63.158 2.62 6.74 45.62 3.35
314 323 1.529152 GGTGGCCCGGAAAATTTCGT 61.529 55.000 0.73 0.00 0.00 3.85
316 325 1.540707 GTGGCCCGGAAAATTTCGTTA 59.459 47.619 0.73 0.00 0.00 3.18
361 370 2.434336 ACTCCTGTGCAAACTACAGTCA 59.566 45.455 0.00 0.00 43.05 3.41
362 371 2.802816 CTCCTGTGCAAACTACAGTCAC 59.197 50.000 0.00 0.00 43.05 3.67
365 374 1.137282 TGTGCAAACTACAGTCACCGA 59.863 47.619 0.00 0.00 0.00 4.69
414 424 0.174389 AGTGTCAGCTATGCCTCGTG 59.826 55.000 0.00 0.00 0.00 4.35
427 437 1.878102 GCCTCGTGAACATCAGTGGTT 60.878 52.381 0.00 0.00 0.00 3.67
437 447 6.586844 GTGAACATCAGTGGTTACTTCTCTAC 59.413 42.308 0.00 0.00 34.07 2.59
439 449 6.274157 ACATCAGTGGTTACTTCTCTACAG 57.726 41.667 0.00 0.00 34.07 2.74
443 453 7.120923 TCAGTGGTTACTTCTCTACAGTTTT 57.879 36.000 0.00 0.00 34.07 2.43
444 454 7.208080 TCAGTGGTTACTTCTCTACAGTTTTC 58.792 38.462 0.00 0.00 34.07 2.29
445 455 6.984474 CAGTGGTTACTTCTCTACAGTTTTCA 59.016 38.462 0.00 0.00 34.07 2.69
446 456 7.657761 CAGTGGTTACTTCTCTACAGTTTTCAT 59.342 37.037 0.00 0.00 34.07 2.57
447 457 8.211629 AGTGGTTACTTCTCTACAGTTTTCATT 58.788 33.333 0.00 0.00 31.66 2.57
448 458 8.837389 GTGGTTACTTCTCTACAGTTTTCATTT 58.163 33.333 0.00 0.00 0.00 2.32
449 459 9.403583 TGGTTACTTCTCTACAGTTTTCATTTT 57.596 29.630 0.00 0.00 0.00 1.82
469 479 1.488390 TCAACAGTATACCCCGGGTC 58.512 55.000 21.85 0.00 37.09 4.46
790 834 3.760035 ACGTACTGGGGCTCTGCG 61.760 66.667 0.00 0.00 0.00 5.18
982 1026 3.680786 CACTGGTGCTCGTCCGGA 61.681 66.667 0.00 0.00 35.49 5.14
1032 1076 3.241530 TGCTGCGAGAAGGTGGGT 61.242 61.111 0.00 0.00 0.00 4.51
1035 1079 1.216710 CTGCGAGAAGGTGGGTCTC 59.783 63.158 0.00 0.00 38.54 3.36
1150 1194 1.080705 GGTCAGCGACGCTTACACT 60.081 57.895 29.31 3.86 36.40 3.55
1155 1199 0.096628 AGCGACGCTTACACTCGTAG 59.903 55.000 18.46 0.00 39.22 3.51
1156 1200 1.462094 GCGACGCTTACACTCGTAGC 61.462 60.000 13.73 4.39 46.21 3.58
1157 1201 0.179207 CGACGCTTACACTCGTAGCA 60.179 55.000 0.00 0.00 39.22 3.49
1199 1251 4.645921 GCCACCCTGCAAACGCAC 62.646 66.667 0.00 0.00 35.03 5.34
1202 1254 2.439338 ACCCTGCAAACGCACACA 60.439 55.556 0.00 0.00 35.03 3.72
1203 1255 2.332514 CCCTGCAAACGCACACAG 59.667 61.111 0.00 0.00 35.03 3.66
1211 1263 2.719046 GCAAACGCACACAGTACATTTC 59.281 45.455 0.00 0.00 0.00 2.17
1218 1270 4.149221 CGCACACAGTACATTTCGTCTTAA 59.851 41.667 0.00 0.00 0.00 1.85
1378 1440 1.604604 GGCAACAGGTGTGTGTGTAT 58.395 50.000 0.00 0.00 36.84 2.29
1379 1441 1.535462 GGCAACAGGTGTGTGTGTATC 59.465 52.381 0.00 0.00 36.84 2.24
1380 1442 1.535462 GCAACAGGTGTGTGTGTATCC 59.465 52.381 0.00 0.00 36.84 2.59
1381 1443 2.844946 CAACAGGTGTGTGTGTATCCA 58.155 47.619 0.00 0.00 36.84 3.41
1455 1541 1.597742 ATTCTGTTCTTGTGCTGCGT 58.402 45.000 0.00 0.00 0.00 5.24
1457 1543 0.179086 TCTGTTCTTGTGCTGCGTCA 60.179 50.000 0.00 0.00 0.00 4.35
1790 1876 4.200283 CTGCTCCTCCTCGTCCGC 62.200 72.222 0.00 0.00 0.00 5.54
1793 1879 3.213402 CTCCTCCTCGTCCGCCTC 61.213 72.222 0.00 0.00 0.00 4.70
1794 1880 3.997400 CTCCTCCTCGTCCGCCTCA 62.997 68.421 0.00 0.00 0.00 3.86
1795 1881 3.522731 CCTCCTCGTCCGCCTCAG 61.523 72.222 0.00 0.00 0.00 3.35
2061 2155 4.779993 ACACCTCACTTCTTTCCTTCTT 57.220 40.909 0.00 0.00 0.00 2.52
2062 2156 4.709250 ACACCTCACTTCTTTCCTTCTTC 58.291 43.478 0.00 0.00 0.00 2.87
2063 2157 4.410555 ACACCTCACTTCTTTCCTTCTTCT 59.589 41.667 0.00 0.00 0.00 2.85
2066 2160 5.841783 ACCTCACTTCTTTCCTTCTTCTAGT 59.158 40.000 0.00 0.00 0.00 2.57
2071 2165 7.711339 TCACTTCTTTCCTTCTTCTAGTTGTTC 59.289 37.037 0.00 0.00 0.00 3.18
2080 2174 6.350110 CCTTCTTCTAGTTGTTCTCCTCTCAG 60.350 46.154 0.00 0.00 0.00 3.35
2083 2177 4.986783 TCTAGTTGTTCTCCTCTCAGTCA 58.013 43.478 0.00 0.00 0.00 3.41
2093 2187 0.732571 CTCTCAGTCACTCGCTCTCC 59.267 60.000 0.00 0.00 0.00 3.71
2094 2188 0.036875 TCTCAGTCACTCGCTCTCCA 59.963 55.000 0.00 0.00 0.00 3.86
2127 2231 3.914426 TCTTTGGTATCTTGGGAGAGC 57.086 47.619 0.00 0.00 34.85 4.09
2145 2255 4.084287 AGAGCATTTGTCCATGTTCATGT 58.916 39.130 11.13 0.00 36.97 3.21
2146 2256 4.157289 AGAGCATTTGTCCATGTTCATGTC 59.843 41.667 11.13 5.51 36.97 3.06
2266 2377 3.153919 TGGATCATCGATCACGGTATGA 58.846 45.455 0.00 0.00 40.50 2.15
2278 2389 6.668541 ATCACGGTATGATCTTTCAGTTTG 57.331 37.500 0.00 0.00 45.52 2.93
2279 2390 5.547465 TCACGGTATGATCTTTCAGTTTGT 58.453 37.500 0.00 0.00 34.73 2.83
2280 2391 5.637810 TCACGGTATGATCTTTCAGTTTGTC 59.362 40.000 0.00 0.00 34.73 3.18
2281 2392 5.639506 CACGGTATGATCTTTCAGTTTGTCT 59.360 40.000 0.00 0.00 34.73 3.41
2282 2393 6.811665 CACGGTATGATCTTTCAGTTTGTCTA 59.188 38.462 0.00 0.00 34.73 2.59
2283 2394 7.330946 CACGGTATGATCTTTCAGTTTGTCTAA 59.669 37.037 0.00 0.00 34.73 2.10
2284 2395 8.041323 ACGGTATGATCTTTCAGTTTGTCTAAT 58.959 33.333 0.00 0.00 34.73 1.73
2285 2396 8.883731 CGGTATGATCTTTCAGTTTGTCTAATT 58.116 33.333 0.00 0.00 34.73 1.40
2289 2400 7.796838 TGATCTTTCAGTTTGTCTAATTCACG 58.203 34.615 0.00 0.00 0.00 4.35
2290 2401 7.441157 TGATCTTTCAGTTTGTCTAATTCACGT 59.559 33.333 0.00 0.00 0.00 4.49
2291 2402 7.173863 TCTTTCAGTTTGTCTAATTCACGTC 57.826 36.000 0.00 0.00 0.00 4.34
2292 2403 6.984474 TCTTTCAGTTTGTCTAATTCACGTCT 59.016 34.615 0.00 0.00 0.00 4.18
2293 2404 8.139350 TCTTTCAGTTTGTCTAATTCACGTCTA 58.861 33.333 0.00 0.00 0.00 2.59
2294 2405 7.869016 TTCAGTTTGTCTAATTCACGTCTAG 57.131 36.000 0.00 0.00 0.00 2.43
2295 2406 7.210718 TCAGTTTGTCTAATTCACGTCTAGA 57.789 36.000 0.00 0.00 0.00 2.43
2296 2407 7.827701 TCAGTTTGTCTAATTCACGTCTAGAT 58.172 34.615 0.00 0.00 0.00 1.98
2297 2408 7.755373 TCAGTTTGTCTAATTCACGTCTAGATG 59.245 37.037 10.54 10.54 0.00 2.90
2298 2409 7.542477 CAGTTTGTCTAATTCACGTCTAGATGT 59.458 37.037 11.99 11.99 0.00 3.06
2299 2410 8.088981 AGTTTGTCTAATTCACGTCTAGATGTT 58.911 33.333 15.12 3.67 0.00 2.71
2300 2411 8.709646 GTTTGTCTAATTCACGTCTAGATGTTT 58.290 33.333 15.12 9.87 0.00 2.83
2301 2412 8.827177 TTGTCTAATTCACGTCTAGATGTTTT 57.173 30.769 15.12 11.28 0.00 2.43
2302 2413 8.827177 TGTCTAATTCACGTCTAGATGTTTTT 57.173 30.769 15.12 10.96 0.00 1.94
2323 2434 7.667043 TTTTTATGAATGTCACGTCTAAGCT 57.333 32.000 0.00 0.00 0.00 3.74
2324 2435 6.887376 TTTATGAATGTCACGTCTAAGCTC 57.113 37.500 0.00 0.00 0.00 4.09
2325 2436 3.232213 TGAATGTCACGTCTAAGCTCC 57.768 47.619 0.00 0.00 0.00 4.70
2326 2437 2.094182 TGAATGTCACGTCTAAGCTCCC 60.094 50.000 0.00 0.00 0.00 4.30
2327 2438 1.557099 ATGTCACGTCTAAGCTCCCA 58.443 50.000 0.00 0.00 0.00 4.37
2328 2439 0.601558 TGTCACGTCTAAGCTCCCAC 59.398 55.000 0.00 0.00 0.00 4.61
2329 2440 0.601558 GTCACGTCTAAGCTCCCACA 59.398 55.000 0.00 0.00 0.00 4.17
2330 2441 1.000506 GTCACGTCTAAGCTCCCACAA 59.999 52.381 0.00 0.00 0.00 3.33
2331 2442 1.689813 TCACGTCTAAGCTCCCACAAA 59.310 47.619 0.00 0.00 0.00 2.83
2332 2443 2.301870 TCACGTCTAAGCTCCCACAAAT 59.698 45.455 0.00 0.00 0.00 2.32
2333 2444 3.512329 TCACGTCTAAGCTCCCACAAATA 59.488 43.478 0.00 0.00 0.00 1.40
2334 2445 4.161565 TCACGTCTAAGCTCCCACAAATAT 59.838 41.667 0.00 0.00 0.00 1.28
2335 2446 5.361571 TCACGTCTAAGCTCCCACAAATATA 59.638 40.000 0.00 0.00 0.00 0.86
2336 2447 6.041637 TCACGTCTAAGCTCCCACAAATATAT 59.958 38.462 0.00 0.00 0.00 0.86
2337 2448 7.231925 TCACGTCTAAGCTCCCACAAATATATA 59.768 37.037 0.00 0.00 0.00 0.86
2338 2449 7.870954 CACGTCTAAGCTCCCACAAATATATAA 59.129 37.037 0.00 0.00 0.00 0.98
2339 2450 8.594550 ACGTCTAAGCTCCCACAAATATATAAT 58.405 33.333 0.00 0.00 0.00 1.28
2340 2451 8.873830 CGTCTAAGCTCCCACAAATATATAATG 58.126 37.037 0.00 0.00 0.00 1.90
2341 2452 8.669243 GTCTAAGCTCCCACAAATATATAATGC 58.331 37.037 0.00 0.00 0.00 3.56
2342 2453 8.382405 TCTAAGCTCCCACAAATATATAATGCA 58.618 33.333 0.00 0.00 0.00 3.96
2343 2454 7.458409 AAGCTCCCACAAATATATAATGCAG 57.542 36.000 0.00 0.00 0.00 4.41
2344 2455 5.416952 AGCTCCCACAAATATATAATGCAGC 59.583 40.000 0.00 0.00 0.00 5.25
2345 2456 5.183713 GCTCCCACAAATATATAATGCAGCA 59.816 40.000 0.00 0.00 0.00 4.41
2346 2457 6.294675 GCTCCCACAAATATATAATGCAGCAA 60.295 38.462 0.00 0.00 0.00 3.91
2347 2458 6.980593 TCCCACAAATATATAATGCAGCAAC 58.019 36.000 0.00 0.00 0.00 4.17
2348 2459 6.548993 TCCCACAAATATATAATGCAGCAACA 59.451 34.615 0.00 0.00 0.00 3.33
2349 2460 7.069208 TCCCACAAATATATAATGCAGCAACAA 59.931 33.333 0.00 0.00 0.00 2.83
2350 2461 7.383029 CCCACAAATATATAATGCAGCAACAAG 59.617 37.037 0.00 0.00 0.00 3.16
2351 2462 8.136800 CCACAAATATATAATGCAGCAACAAGA 58.863 33.333 0.00 0.00 0.00 3.02
2352 2463 9.518906 CACAAATATATAATGCAGCAACAAGAA 57.481 29.630 0.00 0.00 0.00 2.52
2406 2517 9.739276 ACAGAATGGAAATTAGTTTAGATGTGA 57.261 29.630 0.00 0.00 43.62 3.58
2407 2518 9.994432 CAGAATGGAAATTAGTTTAGATGTGAC 57.006 33.333 0.00 0.00 0.00 3.67
2408 2519 9.739276 AGAATGGAAATTAGTTTAGATGTGACA 57.261 29.630 0.00 0.00 0.00 3.58
2424 2535 7.665690 AGATGTGACATAATCTAGATGTGTCC 58.334 38.462 29.89 24.42 37.65 4.02
2425 2536 7.508636 AGATGTGACATAATCTAGATGTGTCCT 59.491 37.037 29.89 22.36 37.65 3.85
2426 2537 8.712228 ATGTGACATAATCTAGATGTGTCCTA 57.288 34.615 29.89 23.51 37.65 2.94
2427 2538 8.533569 TGTGACATAATCTAGATGTGTCCTAA 57.466 34.615 29.89 20.21 37.65 2.69
2428 2539 8.977412 TGTGACATAATCTAGATGTGTCCTAAA 58.023 33.333 29.89 18.52 37.65 1.85
2429 2540 9.250624 GTGACATAATCTAGATGTGTCCTAAAC 57.749 37.037 29.89 22.79 37.65 2.01
2430 2541 8.977412 TGACATAATCTAGATGTGTCCTAAACA 58.023 33.333 29.89 18.21 37.65 2.83
2431 2542 9.469807 GACATAATCTAGATGTGTCCTAAACAG 57.530 37.037 26.33 5.80 38.97 3.16
2432 2543 9.201989 ACATAATCTAGATGTGTCCTAAACAGA 57.798 33.333 5.86 0.00 38.97 3.41
2433 2544 9.469807 CATAATCTAGATGTGTCCTAAACAGAC 57.530 37.037 5.86 0.00 38.97 3.51
2434 2545 5.916661 TCTAGATGTGTCCTAAACAGACC 57.083 43.478 0.00 0.00 38.97 3.85
2435 2546 5.580998 TCTAGATGTGTCCTAAACAGACCT 58.419 41.667 0.00 0.00 38.97 3.85
2436 2547 6.728411 TCTAGATGTGTCCTAAACAGACCTA 58.272 40.000 0.00 0.00 38.97 3.08
2437 2548 7.355101 TCTAGATGTGTCCTAAACAGACCTAT 58.645 38.462 0.00 0.00 38.97 2.57
2438 2549 6.227298 AGATGTGTCCTAAACAGACCTATG 57.773 41.667 0.00 0.00 38.97 2.23
2439 2550 5.958380 AGATGTGTCCTAAACAGACCTATGA 59.042 40.000 0.00 0.00 38.97 2.15
2440 2551 6.613271 AGATGTGTCCTAAACAGACCTATGAT 59.387 38.462 0.00 0.00 38.97 2.45
2441 2552 6.222038 TGTGTCCTAAACAGACCTATGATC 57.778 41.667 0.00 0.00 38.97 2.92
2442 2553 5.958380 TGTGTCCTAAACAGACCTATGATCT 59.042 40.000 0.00 0.00 38.97 2.75
2443 2554 7.123383 TGTGTCCTAAACAGACCTATGATCTA 58.877 38.462 0.00 0.00 38.97 1.98
2444 2555 7.785028 TGTGTCCTAAACAGACCTATGATCTAT 59.215 37.037 0.00 0.00 38.97 1.98
2445 2556 8.085296 GTGTCCTAAACAGACCTATGATCTATG 58.915 40.741 0.00 0.00 38.97 2.23
2494 2605 4.325741 CACGCACAAAAGAACAAACATTCA 59.674 37.500 0.00 0.00 0.00 2.57
2497 2608 5.164012 CGCACAAAAGAACAAACATTCACAA 60.164 36.000 0.00 0.00 0.00 3.33
2500 2611 5.347364 ACAAAAGAACAAACATTCACAACCG 59.653 36.000 0.00 0.00 0.00 4.44
2554 2673 4.762251 AGCTAAGCCTTTCGTCAAAGAAAT 59.238 37.500 0.00 0.00 41.60 2.17
2579 2698 7.656707 ATGTTTTGTTTTATGAACATGGCTC 57.343 32.000 0.00 0.00 40.21 4.70
2636 2755 1.599576 GGCAGAGACTCCCTGGAAC 59.400 63.158 0.00 0.00 32.51 3.62
2648 2767 1.151668 CCTGGAACGAAAGCTCAGTG 58.848 55.000 0.00 0.00 0.00 3.66
2664 2783 1.671379 GTGCTTCCGGGACCAGTTC 60.671 63.158 0.00 0.00 0.00 3.01
2687 2806 3.006967 GGAAGTGTGAGGAGTGCTTTAGA 59.993 47.826 0.00 0.00 0.00 2.10
2688 2807 4.503296 GGAAGTGTGAGGAGTGCTTTAGAA 60.503 45.833 0.00 0.00 0.00 2.10
2878 2999 2.309528 TTATGGTCGCAGCCTTGTAG 57.690 50.000 0.00 0.00 0.00 2.74
2880 3001 0.833287 ATGGTCGCAGCCTTGTAGAT 59.167 50.000 0.00 0.00 0.00 1.98
2913 3034 1.480137 AGGTCTCGAGAAGCATCCTTG 59.520 52.381 18.55 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.521451 TACCGCCAACTCCAGCCAA 61.521 57.895 0.00 0.00 0.00 4.52
1 2 2.925706 TACCGCCAACTCCAGCCA 60.926 61.111 0.00 0.00 0.00 4.75
4 5 3.065306 TGGTACCGCCAACTCCAG 58.935 61.111 7.57 0.00 45.94 3.86
141 145 0.675633 GTGACAAACCCTGCAAGCAT 59.324 50.000 0.00 0.00 0.00 3.79
150 154 1.966451 CCTGCTCCGTGACAAACCC 60.966 63.158 0.00 0.00 0.00 4.11
314 323 5.064962 CGGGCTATGTTAACGTGGAAAATAA 59.935 40.000 14.76 0.00 0.00 1.40
316 325 3.375922 CGGGCTATGTTAACGTGGAAAAT 59.624 43.478 14.76 0.00 0.00 1.82
361 370 0.108804 CGGTCAGCAGTACAATCGGT 60.109 55.000 0.00 0.00 0.00 4.69
362 371 2.665777 CGGTCAGCAGTACAATCGG 58.334 57.895 0.00 0.00 0.00 4.18
383 393 0.886490 CTGACACTGGTGGACTTGCC 60.886 60.000 5.70 0.00 34.19 4.52
390 400 0.745845 GGCATAGCTGACACTGGTGG 60.746 60.000 0.00 0.00 34.19 4.61
414 424 6.688578 TGTAGAGAAGTAACCACTGATGTTC 58.311 40.000 0.00 0.00 34.36 3.18
437 447 9.191995 GGGTATACTGTTGAAAAATGAAAACTG 57.808 33.333 2.25 0.00 0.00 3.16
439 449 7.327518 CGGGGTATACTGTTGAAAAATGAAAAC 59.672 37.037 2.25 0.00 0.00 2.43
443 453 4.944930 CCGGGGTATACTGTTGAAAAATGA 59.055 41.667 2.25 0.00 0.00 2.57
444 454 4.097286 CCCGGGGTATACTGTTGAAAAATG 59.903 45.833 14.71 0.00 0.00 2.32
445 455 4.264038 ACCCGGGGTATACTGTTGAAAAAT 60.264 41.667 27.92 0.00 32.11 1.82
446 456 3.074242 ACCCGGGGTATACTGTTGAAAAA 59.926 43.478 27.92 0.00 32.11 1.94
447 457 2.643801 ACCCGGGGTATACTGTTGAAAA 59.356 45.455 27.92 0.00 32.11 2.29
448 458 2.236893 GACCCGGGGTATACTGTTGAAA 59.763 50.000 27.92 0.00 35.25 2.69
449 459 1.832998 GACCCGGGGTATACTGTTGAA 59.167 52.381 27.92 0.00 35.25 2.69
450 460 1.488390 GACCCGGGGTATACTGTTGA 58.512 55.000 27.92 0.00 35.25 3.18
469 479 3.343617 ACACGTGAACATAGGGATTTGG 58.656 45.455 25.01 0.00 0.00 3.28
575 604 0.179119 AATCACCGCGGCAGTAGTAC 60.179 55.000 28.58 0.00 0.00 2.73
578 607 1.215655 GCTAATCACCGCGGCAGTAG 61.216 60.000 28.58 24.32 0.00 2.57
582 611 2.046796 TTGCTAATCACCGCGGCA 60.047 55.556 28.58 13.44 0.00 5.69
859 903 1.937191 AGTTTGGCCTTAATGTGGGG 58.063 50.000 3.32 0.00 0.00 4.96
982 1026 0.891449 ATCTCTGCCGGTCGATCGAT 60.891 55.000 21.90 0.00 0.00 3.59
1032 1076 2.592993 CCACGGGCCCTTCTTGAGA 61.593 63.158 22.43 0.00 0.00 3.27
1035 1079 2.359975 GTCCACGGGCCCTTCTTG 60.360 66.667 22.43 11.30 0.00 3.02
1150 1194 0.316841 TCGCCATGCATATGCTACGA 59.683 50.000 27.13 24.10 42.66 3.43
1155 1199 1.785041 AACCGTCGCCATGCATATGC 61.785 55.000 21.09 21.09 42.50 3.14
1156 1200 0.235665 GAACCGTCGCCATGCATATG 59.764 55.000 0.00 0.00 0.00 1.78
1157 1201 1.221466 CGAACCGTCGCCATGCATAT 61.221 55.000 0.00 0.00 41.08 1.78
1178 1230 2.909965 GTTTGCAGGGTGGCCGAA 60.910 61.111 0.00 0.00 0.00 4.30
1199 1251 8.332464 TGAAACTTTAAGACGAAATGTACTGTG 58.668 33.333 0.00 0.00 0.00 3.66
1203 1255 9.037417 CGATTGAAACTTTAAGACGAAATGTAC 57.963 33.333 0.00 0.00 0.00 2.90
1211 1263 3.833061 CACGCGATTGAAACTTTAAGACG 59.167 43.478 15.93 0.00 0.00 4.18
1218 1270 0.238289 CCTGCACGCGATTGAAACTT 59.762 50.000 15.93 0.00 0.00 2.66
1378 1440 2.043852 GGGAGGAGTCGAGCTGGA 60.044 66.667 0.00 0.00 0.00 3.86
1379 1441 3.151022 GGGGAGGAGTCGAGCTGG 61.151 72.222 0.00 0.00 0.00 4.85
1380 1442 2.043450 AGGGGAGGAGTCGAGCTG 60.043 66.667 0.00 0.00 0.00 4.24
1381 1443 2.277404 GAGGGGAGGAGTCGAGCT 59.723 66.667 0.00 0.00 0.00 4.09
1455 1541 1.134699 GCGATCTTGGACCATCTGTGA 60.135 52.381 0.00 0.00 0.00 3.58
1457 1543 0.179100 CGCGATCTTGGACCATCTGT 60.179 55.000 0.00 0.00 0.00 3.41
1607 1693 4.463879 CCTGCTGCGGGTCCTCAG 62.464 72.222 19.55 2.82 0.00 3.35
1930 2016 2.271800 GAAGAGATCGACGCCAATGTT 58.728 47.619 0.00 0.00 0.00 2.71
2010 2096 5.583495 CACAATCTAACTCTAACCCTCGAG 58.417 45.833 5.13 5.13 0.00 4.04
2061 2155 4.762765 GTGACTGAGAGGAGAACAACTAGA 59.237 45.833 0.00 0.00 0.00 2.43
2062 2156 4.764823 AGTGACTGAGAGGAGAACAACTAG 59.235 45.833 0.00 0.00 0.00 2.57
2063 2157 4.730966 AGTGACTGAGAGGAGAACAACTA 58.269 43.478 0.00 0.00 0.00 2.24
2066 2160 2.554462 CGAGTGACTGAGAGGAGAACAA 59.446 50.000 0.00 0.00 0.00 2.83
2071 2165 0.732571 GAGCGAGTGACTGAGAGGAG 59.267 60.000 0.00 0.00 0.00 3.69
2080 2174 0.527385 GCAGATGGAGAGCGAGTGAC 60.527 60.000 0.00 0.00 0.00 3.67
2083 2177 0.395586 AGAGCAGATGGAGAGCGAGT 60.396 55.000 0.00 0.00 0.00 4.18
2093 2187 4.843220 ACCAAAGAAAACAGAGCAGATG 57.157 40.909 0.00 0.00 0.00 2.90
2094 2188 6.479884 AGATACCAAAGAAAACAGAGCAGAT 58.520 36.000 0.00 0.00 0.00 2.90
2127 2231 4.787260 TGGACATGAACATGGACAAATG 57.213 40.909 17.25 0.00 42.91 2.32
2266 2377 7.657761 AGACGTGAATTAGACAAACTGAAAGAT 59.342 33.333 0.00 0.00 37.43 2.40
2267 2378 6.984474 AGACGTGAATTAGACAAACTGAAAGA 59.016 34.615 0.00 0.00 37.43 2.52
2268 2379 7.178712 AGACGTGAATTAGACAAACTGAAAG 57.821 36.000 0.00 0.00 42.29 2.62
2269 2380 8.139350 TCTAGACGTGAATTAGACAAACTGAAA 58.861 33.333 0.00 0.00 0.00 2.69
2270 2381 7.654568 TCTAGACGTGAATTAGACAAACTGAA 58.345 34.615 0.00 0.00 0.00 3.02
2271 2382 7.210718 TCTAGACGTGAATTAGACAAACTGA 57.789 36.000 0.00 0.00 0.00 3.41
2272 2383 7.542477 ACATCTAGACGTGAATTAGACAAACTG 59.458 37.037 0.00 0.00 0.00 3.16
2273 2384 7.603651 ACATCTAGACGTGAATTAGACAAACT 58.396 34.615 0.00 0.00 0.00 2.66
2274 2385 7.813852 ACATCTAGACGTGAATTAGACAAAC 57.186 36.000 0.00 0.00 0.00 2.93
2275 2386 8.827177 AAACATCTAGACGTGAATTAGACAAA 57.173 30.769 0.00 0.00 0.00 2.83
2276 2387 8.827177 AAAACATCTAGACGTGAATTAGACAA 57.173 30.769 0.00 0.00 0.00 3.18
2277 2388 8.827177 AAAAACATCTAGACGTGAATTAGACA 57.173 30.769 0.00 0.00 0.00 3.41
2299 2410 7.148474 GGAGCTTAGACGTGACATTCATAAAAA 60.148 37.037 0.00 0.00 0.00 1.94
2300 2411 6.312918 GGAGCTTAGACGTGACATTCATAAAA 59.687 38.462 0.00 0.00 0.00 1.52
2301 2412 5.810587 GGAGCTTAGACGTGACATTCATAAA 59.189 40.000 0.00 0.00 0.00 1.40
2302 2413 5.348986 GGAGCTTAGACGTGACATTCATAA 58.651 41.667 0.00 0.00 0.00 1.90
2303 2414 4.202121 GGGAGCTTAGACGTGACATTCATA 60.202 45.833 0.00 0.00 0.00 2.15
2304 2415 3.430929 GGGAGCTTAGACGTGACATTCAT 60.431 47.826 0.00 0.00 0.00 2.57
2305 2416 2.094182 GGGAGCTTAGACGTGACATTCA 60.094 50.000 0.00 0.00 0.00 2.57
2306 2417 2.094182 TGGGAGCTTAGACGTGACATTC 60.094 50.000 0.00 0.00 0.00 2.67
2307 2418 1.899814 TGGGAGCTTAGACGTGACATT 59.100 47.619 0.00 0.00 0.00 2.71
2308 2419 1.204941 GTGGGAGCTTAGACGTGACAT 59.795 52.381 0.00 0.00 0.00 3.06
2309 2420 0.601558 GTGGGAGCTTAGACGTGACA 59.398 55.000 0.00 0.00 0.00 3.58
2310 2421 0.601558 TGTGGGAGCTTAGACGTGAC 59.398 55.000 0.00 0.00 0.00 3.67
2311 2422 1.334160 TTGTGGGAGCTTAGACGTGA 58.666 50.000 0.00 0.00 0.00 4.35
2312 2423 2.163818 TTTGTGGGAGCTTAGACGTG 57.836 50.000 0.00 0.00 0.00 4.49
2313 2424 4.755266 ATATTTGTGGGAGCTTAGACGT 57.245 40.909 0.00 0.00 0.00 4.34
2314 2425 8.873830 CATTATATATTTGTGGGAGCTTAGACG 58.126 37.037 0.00 0.00 0.00 4.18
2315 2426 8.669243 GCATTATATATTTGTGGGAGCTTAGAC 58.331 37.037 0.00 0.00 0.00 2.59
2316 2427 8.382405 TGCATTATATATTTGTGGGAGCTTAGA 58.618 33.333 0.00 0.00 0.00 2.10
2317 2428 8.565896 TGCATTATATATTTGTGGGAGCTTAG 57.434 34.615 0.00 0.00 0.00 2.18
2318 2429 7.121168 GCTGCATTATATATTTGTGGGAGCTTA 59.879 37.037 0.00 0.00 0.00 3.09
2319 2430 6.071728 GCTGCATTATATATTTGTGGGAGCTT 60.072 38.462 0.00 0.00 0.00 3.74
2320 2431 5.416952 GCTGCATTATATATTTGTGGGAGCT 59.583 40.000 0.00 0.00 0.00 4.09
2321 2432 5.183713 TGCTGCATTATATATTTGTGGGAGC 59.816 40.000 0.00 0.00 0.00 4.70
2322 2433 6.822667 TGCTGCATTATATATTTGTGGGAG 57.177 37.500 0.00 0.00 0.00 4.30
2323 2434 6.548993 TGTTGCTGCATTATATATTTGTGGGA 59.451 34.615 1.84 0.00 0.00 4.37
2324 2435 6.747125 TGTTGCTGCATTATATATTTGTGGG 58.253 36.000 1.84 0.00 0.00 4.61
2325 2436 8.136800 TCTTGTTGCTGCATTATATATTTGTGG 58.863 33.333 1.84 0.00 0.00 4.17
2326 2437 9.518906 TTCTTGTTGCTGCATTATATATTTGTG 57.481 29.630 1.84 0.00 0.00 3.33
2380 2491 9.739276 TCACATCTAAACTAATTTCCATTCTGT 57.261 29.630 0.00 0.00 0.00 3.41
2381 2492 9.994432 GTCACATCTAAACTAATTTCCATTCTG 57.006 33.333 0.00 0.00 0.00 3.02
2382 2493 9.739276 TGTCACATCTAAACTAATTTCCATTCT 57.261 29.630 0.00 0.00 0.00 2.40
2398 2509 8.797438 GGACACATCTAGATTATGTCACATCTA 58.203 37.037 30.42 0.00 41.18 1.98
2399 2510 7.508636 AGGACACATCTAGATTATGTCACATCT 59.491 37.037 30.42 21.64 41.18 2.90
2400 2511 7.665690 AGGACACATCTAGATTATGTCACATC 58.334 38.462 30.42 20.45 41.18 3.06
2401 2512 7.609097 AGGACACATCTAGATTATGTCACAT 57.391 36.000 30.42 20.36 41.18 3.21
2402 2513 8.533569 TTAGGACACATCTAGATTATGTCACA 57.466 34.615 30.42 21.25 41.18 3.58
2403 2514 9.250624 GTTTAGGACACATCTAGATTATGTCAC 57.749 37.037 30.42 23.64 41.18 3.67
2404 2515 8.977412 TGTTTAGGACACATCTAGATTATGTCA 58.023 33.333 30.42 18.32 41.18 3.58
2405 2516 9.469807 CTGTTTAGGACACATCTAGATTATGTC 57.530 37.037 25.85 25.85 35.39 3.06
2406 2517 9.201989 TCTGTTTAGGACACATCTAGATTATGT 57.798 33.333 16.08 16.08 38.08 2.29
2407 2518 9.469807 GTCTGTTTAGGACACATCTAGATTATG 57.530 37.037 1.33 7.32 33.82 1.90
2408 2519 8.643324 GGTCTGTTTAGGACACATCTAGATTAT 58.357 37.037 1.33 0.00 35.61 1.28
2409 2520 7.839705 AGGTCTGTTTAGGACACATCTAGATTA 59.160 37.037 1.33 0.00 35.61 1.75
2410 2521 6.670027 AGGTCTGTTTAGGACACATCTAGATT 59.330 38.462 1.33 0.00 35.61 2.40
2411 2522 6.198639 AGGTCTGTTTAGGACACATCTAGAT 58.801 40.000 0.00 0.00 35.61 1.98
2412 2523 5.580998 AGGTCTGTTTAGGACACATCTAGA 58.419 41.667 0.00 0.00 35.61 2.43
2413 2524 5.923733 AGGTCTGTTTAGGACACATCTAG 57.076 43.478 0.00 0.00 35.61 2.43
2414 2525 7.123383 TCATAGGTCTGTTTAGGACACATCTA 58.877 38.462 0.00 0.00 35.61 1.98
2415 2526 5.958380 TCATAGGTCTGTTTAGGACACATCT 59.042 40.000 0.00 0.00 35.61 2.90
2416 2527 6.222038 TCATAGGTCTGTTTAGGACACATC 57.778 41.667 0.00 0.00 35.61 3.06
2417 2528 6.613271 AGATCATAGGTCTGTTTAGGACACAT 59.387 38.462 0.00 0.00 35.61 3.21
2418 2529 5.958380 AGATCATAGGTCTGTTTAGGACACA 59.042 40.000 0.00 0.00 35.61 3.72
2419 2530 6.472686 AGATCATAGGTCTGTTTAGGACAC 57.527 41.667 0.00 0.00 35.61 3.67
2420 2531 8.004801 TCATAGATCATAGGTCTGTTTAGGACA 58.995 37.037 0.00 0.00 35.61 4.02
2421 2532 8.410673 TCATAGATCATAGGTCTGTTTAGGAC 57.589 38.462 0.00 0.00 0.00 3.85
2422 2533 9.249053 GATCATAGATCATAGGTCTGTTTAGGA 57.751 37.037 0.00 0.00 0.00 2.94
2423 2534 9.253832 AGATCATAGATCATAGGTCTGTTTAGG 57.746 37.037 9.43 0.00 0.00 2.69
2426 2537 9.775854 CAAAGATCATAGATCATAGGTCTGTTT 57.224 33.333 9.43 0.00 0.00 2.83
2427 2538 8.373981 CCAAAGATCATAGATCATAGGTCTGTT 58.626 37.037 9.43 0.00 0.00 3.16
2428 2539 7.512058 ACCAAAGATCATAGATCATAGGTCTGT 59.488 37.037 9.43 0.00 0.00 3.41
2429 2540 7.905265 ACCAAAGATCATAGATCATAGGTCTG 58.095 38.462 9.43 0.00 0.00 3.51
2430 2541 8.503428 AACCAAAGATCATAGATCATAGGTCT 57.497 34.615 9.43 0.00 0.00 3.85
2431 2542 8.370940 TGAACCAAAGATCATAGATCATAGGTC 58.629 37.037 9.43 4.31 0.00 3.85
2432 2543 8.267620 TGAACCAAAGATCATAGATCATAGGT 57.732 34.615 9.43 9.65 0.00 3.08
2433 2544 8.997323 GTTGAACCAAAGATCATAGATCATAGG 58.003 37.037 9.43 9.12 0.00 2.57
2434 2545 9.551734 TGTTGAACCAAAGATCATAGATCATAG 57.448 33.333 9.43 0.00 0.00 2.23
2435 2546 9.330063 GTGTTGAACCAAAGATCATAGATCATA 57.670 33.333 9.43 0.00 0.00 2.15
2436 2547 7.011763 CGTGTTGAACCAAAGATCATAGATCAT 59.988 37.037 9.43 0.00 0.00 2.45
2437 2548 6.313658 CGTGTTGAACCAAAGATCATAGATCA 59.686 38.462 9.43 0.00 0.00 2.92
2438 2549 6.709643 CGTGTTGAACCAAAGATCATAGATC 58.290 40.000 0.00 0.00 0.00 2.75
2439 2550 5.065218 GCGTGTTGAACCAAAGATCATAGAT 59.935 40.000 0.00 0.00 0.00 1.98
2440 2551 4.391830 GCGTGTTGAACCAAAGATCATAGA 59.608 41.667 0.00 0.00 0.00 1.98
2441 2552 4.393062 AGCGTGTTGAACCAAAGATCATAG 59.607 41.667 0.00 0.00 0.00 2.23
2442 2553 4.323417 AGCGTGTTGAACCAAAGATCATA 58.677 39.130 0.00 0.00 0.00 2.15
2443 2554 3.149196 AGCGTGTTGAACCAAAGATCAT 58.851 40.909 0.00 0.00 0.00 2.45
2444 2555 2.548057 GAGCGTGTTGAACCAAAGATCA 59.452 45.455 0.00 0.00 0.00 2.92
2445 2556 2.548057 TGAGCGTGTTGAACCAAAGATC 59.452 45.455 0.00 0.00 0.00 2.75
2494 2605 9.120538 AGAATTGAATATGTTTATAGCGGTTGT 57.879 29.630 0.00 0.00 0.00 3.32
2497 2608 8.902540 TCAGAATTGAATATGTTTATAGCGGT 57.097 30.769 0.00 0.00 0.00 5.68
2554 2673 8.363390 TGAGCCATGTTCATAAAACAAAACATA 58.637 29.630 0.00 0.00 39.62 2.29
2579 2698 3.483196 GCGTGCATGCACAAATACTATTG 59.517 43.478 40.95 25.32 46.47 1.90
2648 2767 2.434359 CGAACTGGTCCCGGAAGC 60.434 66.667 0.73 0.00 0.00 3.86
2664 2783 0.034059 AAGCACTCCTCACACTTCCG 59.966 55.000 0.00 0.00 0.00 4.30
2813 2934 9.996554 TTTGAGTACTGTTTTCTGAATGATCTA 57.003 29.630 0.00 0.00 0.00 1.98
2814 2935 8.908786 TTTGAGTACTGTTTTCTGAATGATCT 57.091 30.769 0.00 0.00 0.00 2.75
2824 2945 7.730364 TGATCCTTCTTTGAGTACTGTTTTC 57.270 36.000 0.00 0.00 0.00 2.29
2878 2999 3.530535 GAGACCTGGCAAAGAGAAGATC 58.469 50.000 0.00 0.00 0.00 2.75
2880 3001 1.273606 CGAGACCTGGCAAAGAGAAGA 59.726 52.381 0.00 0.00 0.00 2.87
2913 3034 3.632145 AGAATTATGTTCCCGGTGATTGC 59.368 43.478 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.