Multiple sequence alignment - TraesCS4B01G194200

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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 TraesCS4B01G194200 chr4B 100.000 2558 0 0 1 2558 417374484 417371927 0.000000e+00 4724.0
1 TraesCS4B01G194200 chr3A 98.603 2362 30 3 1 2362 667661444 667663802 0.000000e+00 4176.0
2 TraesCS4B01G194200 chr3A 93.126 902 49 10 25 920 708548772 708547878 0.000000e+00 1310.0
3 TraesCS4B01G194200 chr4A 98.269 2368 38 3 1 2368 146048031 146045667 0.000000e+00 4143.0
4 TraesCS4B01G194200 chr4A 93.178 1070 62 6 1 1067 53752619 53753680 0.000000e+00 1561.0
5 TraesCS4B01G194200 chr4A 93.167 922 54 6 1 919 12668689 12667774 0.000000e+00 1345.0
6 TraesCS4B01G194200 chr4A 95.699 186 8 0 2373 2558 677895709 677895524 1.490000e-77 300.0
7 TraesCS4B01G194200 chr4A 93.506 154 6 3 1979 2131 53753677 53753827 2.560000e-55 226.0
8 TraesCS4B01G194200 chr2D 90.783 1942 124 26 1 1907 299656997 299655076 0.000000e+00 2543.0
9 TraesCS4B01G194200 chr2D 90.498 1947 127 24 1 1907 327321913 327323841 0.000000e+00 2518.0
10 TraesCS4B01G194200 chr2D 100.000 35 0 0 2209 2243 299655069 299655035 5.910000e-07 65.8
11 TraesCS4B01G194200 chr2D 95.238 42 0 2 2202 2243 327323843 327323882 5.910000e-07 65.8
12 TraesCS4B01G194200 chr2D 100.000 30 0 0 2210 2239 299655037 299655008 3.560000e-04 56.5
13 TraesCS4B01G194200 chr2D 100.000 30 0 0 2210 2239 327323880 327323909 3.560000e-04 56.5
14 TraesCS4B01G194200 chr1D 90.577 1942 129 23 1 1907 319528119 319526197 0.000000e+00 2523.0
15 TraesCS4B01G194200 chr1D 91.780 1545 79 14 1 1507 242558735 242560269 0.000000e+00 2106.0
16 TraesCS4B01G194200 chr1D 95.626 846 28 4 1506 2343 242560431 242561275 0.000000e+00 1349.0
17 TraesCS4B01G194200 chr1D 86.331 139 10 6 2251 2385 319526018 319525885 2.650000e-30 143.0
18 TraesCS4B01G194200 chr1D 100.000 35 0 0 2209 2243 319526190 319526156 5.910000e-07 65.8
19 TraesCS4B01G194200 chr1D 100.000 30 0 0 2210 2239 319526158 319526129 3.560000e-04 56.5
20 TraesCS4B01G194200 chr6A 85.256 1933 203 41 1 1869 241738171 241740085 0.000000e+00 1916.0
21 TraesCS4B01G194200 chr6A 84.086 1527 178 35 1 1480 261024732 261026240 0.000000e+00 1413.0
22 TraesCS4B01G194200 chr6A 86.683 413 27 11 1482 1867 261026800 261027211 1.410000e-117 433.0
23 TraesCS4B01G194200 chr5A 93.384 922 53 6 1 919 280765201 280766117 0.000000e+00 1358.0
24 TraesCS4B01G194200 chr7A 93.167 922 53 7 1 919 2540885 2541799 0.000000e+00 1345.0
25 TraesCS4B01G194200 chr7A 93.167 922 54 6 1 919 67563567 67564482 0.000000e+00 1345.0
26 TraesCS4B01G194200 chr1A 93.059 922 55 6 1 919 502836972 502836057 0.000000e+00 1339.0
27 TraesCS4B01G194200 chr1B 96.774 186 5 1 2373 2558 420713918 420713734 2.470000e-80 309.0
28 TraesCS4B01G194200 chr1B 92.308 39 2 1 2330 2368 633755949 633755912 1.000000e-03 54.7
29 TraesCS4B01G194200 chr7B 95.055 182 8 1 2373 2554 524876575 524876395 4.170000e-73 285.0
30 TraesCS4B01G194200 chr7B 89.583 48 1 4 2330 2377 355849412 355849455 9.890000e-05 58.4
31 TraesCS4B01G194200 chr3B 93.158 190 9 2 2373 2558 237161845 237161656 2.510000e-70 276.0
32 TraesCS4B01G194200 chr3B 94.444 36 2 0 2330 2365 824185252 824185287 3.560000e-04 56.5
33 TraesCS4B01G194200 chr3B 96.970 33 0 1 2330 2362 762387066 762387097 1.000000e-03 54.7
34 TraesCS4B01G194200 chrUn 82.353 119 14 7 2373 2489 67066201 67066088 2.090000e-16 97.1
35 TraesCS4B01G194200 chr6B 81.967 122 15 7 2370 2489 126251710 126251594 2.090000e-16 97.1
36 TraesCS4B01G194200 chr5B 82.353 119 14 7 2373 2489 507034118 507034005 2.090000e-16 97.1
37 TraesCS4B01G194200 chr5B 79.832 119 17 7 2373 2489 507053937 507053824 2.110000e-11 80.5
38 TraesCS4B01G194200 chr5B 92.308 39 2 1 2330 2368 697961108 697961071 1.000000e-03 54.7
39 TraesCS4B01G194200 chr2B 92.308 39 2 1 2330 2368 792770397 792770360 1.000000e-03 54.7


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 TraesCS4B01G194200 chr4B 417371927 417374484 2557 True 4724.000000 4724 100.000000 1 2558 1 chr4B.!!$R1 2557
1 TraesCS4B01G194200 chr3A 667661444 667663802 2358 False 4176.000000 4176 98.603000 1 2362 1 chr3A.!!$F1 2361
2 TraesCS4B01G194200 chr3A 708547878 708548772 894 True 1310.000000 1310 93.126000 25 920 1 chr3A.!!$R1 895
3 TraesCS4B01G194200 chr4A 146045667 146048031 2364 True 4143.000000 4143 98.269000 1 2368 1 chr4A.!!$R2 2367
4 TraesCS4B01G194200 chr4A 12667774 12668689 915 True 1345.000000 1345 93.167000 1 919 1 chr4A.!!$R1 918
5 TraesCS4B01G194200 chr4A 53752619 53753827 1208 False 893.500000 1561 93.342000 1 2131 2 chr4A.!!$F1 2130
6 TraesCS4B01G194200 chr2D 299655008 299656997 1989 True 888.433333 2543 96.927667 1 2243 3 chr2D.!!$R1 2242
7 TraesCS4B01G194200 chr2D 327321913 327323909 1996 False 880.100000 2518 95.245333 1 2243 3 chr2D.!!$F1 2242
8 TraesCS4B01G194200 chr1D 242558735 242561275 2540 False 1727.500000 2106 93.703000 1 2343 2 chr1D.!!$F1 2342
9 TraesCS4B01G194200 chr1D 319525885 319528119 2234 True 697.075000 2523 94.227000 1 2385 4 chr1D.!!$R1 2384
10 TraesCS4B01G194200 chr6A 241738171 241740085 1914 False 1916.000000 1916 85.256000 1 1869 1 chr6A.!!$F1 1868
11 TraesCS4B01G194200 chr6A 261024732 261027211 2479 False 923.000000 1413 85.384500 1 1867 2 chr6A.!!$F2 1866
12 TraesCS4B01G194200 chr5A 280765201 280766117 916 False 1358.000000 1358 93.384000 1 919 1 chr5A.!!$F1 918
13 TraesCS4B01G194200 chr7A 2540885 2541799 914 False 1345.000000 1345 93.167000 1 919 1 chr7A.!!$F1 918
14 TraesCS4B01G194200 chr7A 67563567 67564482 915 False 1345.000000 1345 93.167000 1 919 1 chr7A.!!$F2 918
15 TraesCS4B01G194200 chr1A 502836057 502836972 915 True 1339.000000 1339 93.059000 1 919 1 chr1A.!!$R1 918


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
142 144 1.884579 GTGAGGTTACTGAGTCGACCA 59.115 52.381 13.01 9.18 34.6 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 2366 1.745141 GCTCGACAAATCAGCAGGGAT 60.745 52.381 0.0 0.0 32.45 3.85 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
142 144 1.884579 GTGAGGTTACTGAGTCGACCA 59.115 52.381 13.01 9.18 34.60 4.02
183 185 4.214971 GTGTGGATCTATTCATGTGCATCC 59.785 45.833 0.00 0.00 0.00 3.51
333 338 7.945033 TTTAGCTGACAATTCCAACAATTTC 57.055 32.000 0.00 0.00 0.00 2.17
639 657 5.006746 GCTAGACCATCCTTGTTGTAAATCG 59.993 44.000 0.00 0.00 0.00 3.34
1089 1131 4.790962 AGCTGGCGGTGCATGAGG 62.791 66.667 0.00 0.00 0.00 3.86
1127 1185 1.522580 GGCATCGTCTCCAAGCTCC 60.523 63.158 0.00 0.00 0.00 4.70
1246 1321 0.535335 GGAGGAGCATAACGACACCA 59.465 55.000 0.00 0.00 0.00 4.17
1563 2366 1.555075 GGTTGGCATCACTAGGTGAGA 59.445 52.381 6.53 0.00 46.04 3.27
2324 3291 8.777865 TCAAAATTCACCACATGTTTTTGTTA 57.222 26.923 21.64 8.70 40.05 2.41
2326 3293 9.831737 CAAAATTCACCACATGTTTTTGTTAAA 57.168 25.926 17.29 3.72 37.52 1.52
2357 3324 0.955905 ACGCACGGGCATTTTTACTT 59.044 45.000 11.77 0.00 41.24 2.24
2358 3325 2.152830 ACGCACGGGCATTTTTACTTA 58.847 42.857 11.77 0.00 41.24 2.24
2359 3326 2.160813 ACGCACGGGCATTTTTACTTAG 59.839 45.455 11.77 0.00 41.24 2.18
2362 3329 4.493545 CGCACGGGCATTTTTACTTAGTAG 60.494 45.833 11.77 0.00 41.24 2.57
2365 3332 6.238022 GCACGGGCATTTTTACTTAGTAGTAG 60.238 42.308 3.77 0.00 37.81 2.57
2366 3333 6.815142 CACGGGCATTTTTACTTAGTAGTAGT 59.185 38.462 0.00 0.00 38.09 2.73
2367 3334 7.975616 CACGGGCATTTTTACTTAGTAGTAGTA 59.024 37.037 0.00 0.00 38.09 1.82
2368 3335 8.193438 ACGGGCATTTTTACTTAGTAGTAGTAG 58.807 37.037 0.00 0.00 38.09 2.57
2400 3367 9.988350 ATAATAAAGCAAATAGTGTTTCTGTCG 57.012 29.630 0.00 0.00 29.15 4.35
2401 3368 5.751243 AAAGCAAATAGTGTTTCTGTCGT 57.249 34.783 0.00 0.00 29.15 4.34
2402 3369 4.992381 AGCAAATAGTGTTTCTGTCGTC 57.008 40.909 0.00 0.00 0.00 4.20
2403 3370 3.746492 AGCAAATAGTGTTTCTGTCGTCC 59.254 43.478 0.00 0.00 0.00 4.79
2404 3371 3.423123 GCAAATAGTGTTTCTGTCGTCCG 60.423 47.826 0.00 0.00 0.00 4.79
2405 3372 3.655276 AATAGTGTTTCTGTCGTCCGT 57.345 42.857 0.00 0.00 0.00 4.69
2406 3373 2.693797 TAGTGTTTCTGTCGTCCGTC 57.306 50.000 0.00 0.00 0.00 4.79
2407 3374 0.742505 AGTGTTTCTGTCGTCCGTCA 59.257 50.000 0.00 0.00 0.00 4.35
2408 3375 1.340248 AGTGTTTCTGTCGTCCGTCAT 59.660 47.619 0.00 0.00 0.00 3.06
2409 3376 1.719780 GTGTTTCTGTCGTCCGTCATC 59.280 52.381 0.00 0.00 0.00 2.92
2410 3377 1.611977 TGTTTCTGTCGTCCGTCATCT 59.388 47.619 0.00 0.00 0.00 2.90
2411 3378 2.815503 TGTTTCTGTCGTCCGTCATCTA 59.184 45.455 0.00 0.00 0.00 1.98
2412 3379 3.253921 TGTTTCTGTCGTCCGTCATCTAA 59.746 43.478 0.00 0.00 0.00 2.10
2413 3380 4.232221 GTTTCTGTCGTCCGTCATCTAAA 58.768 43.478 0.00 0.00 0.00 1.85
2414 3381 4.713824 TTCTGTCGTCCGTCATCTAAAT 57.286 40.909 0.00 0.00 0.00 1.40
2415 3382 4.713824 TCTGTCGTCCGTCATCTAAATT 57.286 40.909 0.00 0.00 0.00 1.82
2416 3383 5.823209 TCTGTCGTCCGTCATCTAAATTA 57.177 39.130 0.00 0.00 0.00 1.40
2417 3384 5.575957 TCTGTCGTCCGTCATCTAAATTAC 58.424 41.667 0.00 0.00 0.00 1.89
2418 3385 4.675510 TGTCGTCCGTCATCTAAATTACC 58.324 43.478 0.00 0.00 0.00 2.85
2419 3386 4.400251 TGTCGTCCGTCATCTAAATTACCT 59.600 41.667 0.00 0.00 0.00 3.08
2420 3387 4.974888 GTCGTCCGTCATCTAAATTACCTC 59.025 45.833 0.00 0.00 0.00 3.85
2421 3388 4.037208 TCGTCCGTCATCTAAATTACCTCC 59.963 45.833 0.00 0.00 0.00 4.30
2422 3389 4.296690 GTCCGTCATCTAAATTACCTCCG 58.703 47.826 0.00 0.00 0.00 4.63
2423 3390 4.037208 GTCCGTCATCTAAATTACCTCCGA 59.963 45.833 0.00 0.00 0.00 4.55
2424 3391 4.646040 TCCGTCATCTAAATTACCTCCGAA 59.354 41.667 0.00 0.00 0.00 4.30
2425 3392 5.127519 TCCGTCATCTAAATTACCTCCGAAA 59.872 40.000 0.00 0.00 0.00 3.46
2426 3393 5.989777 CCGTCATCTAAATTACCTCCGAAAT 59.010 40.000 0.00 0.00 0.00 2.17
2427 3394 6.482308 CCGTCATCTAAATTACCTCCGAAATT 59.518 38.462 0.00 0.00 0.00 1.82
2428 3395 7.345192 CGTCATCTAAATTACCTCCGAAATTG 58.655 38.462 0.00 0.00 0.00 2.32
2429 3396 7.011109 CGTCATCTAAATTACCTCCGAAATTGT 59.989 37.037 0.00 0.00 0.00 2.71
2430 3397 8.122952 GTCATCTAAATTACCTCCGAAATTGTG 58.877 37.037 0.00 0.00 0.00 3.33
2431 3398 8.044309 TCATCTAAATTACCTCCGAAATTGTGA 58.956 33.333 0.00 0.00 0.00 3.58
2432 3399 8.673711 CATCTAAATTACCTCCGAAATTGTGAA 58.326 33.333 0.00 0.00 0.00 3.18
2433 3400 8.801882 TCTAAATTACCTCCGAAATTGTGAAT 57.198 30.769 0.00 0.00 0.00 2.57
2434 3401 9.893634 TCTAAATTACCTCCGAAATTGTGAATA 57.106 29.630 0.00 0.00 0.00 1.75
2440 3407 7.329588 ACCTCCGAAATTGTGAATATTTACC 57.670 36.000 7.81 0.00 0.00 2.85
2441 3408 6.320418 ACCTCCGAAATTGTGAATATTTACCC 59.680 38.462 7.81 0.00 0.00 3.69
2442 3409 6.366315 TCCGAAATTGTGAATATTTACCCG 57.634 37.500 7.81 4.33 0.00 5.28
2443 3410 4.973663 CCGAAATTGTGAATATTTACCCGC 59.026 41.667 7.81 0.00 0.00 6.13
2444 3411 4.973663 CGAAATTGTGAATATTTACCCGCC 59.026 41.667 7.81 0.00 0.00 6.13
2445 3412 5.449314 CGAAATTGTGAATATTTACCCGCCA 60.449 40.000 7.81 0.00 0.00 5.69
2446 3413 6.478512 AAATTGTGAATATTTACCCGCCAT 57.521 33.333 7.81 0.00 0.00 4.40
2447 3414 4.909696 TTGTGAATATTTACCCGCCATG 57.090 40.909 7.81 0.00 0.00 3.66
2448 3415 2.621055 TGTGAATATTTACCCGCCATGC 59.379 45.455 7.81 0.00 0.00 4.06
2449 3416 2.030274 GTGAATATTTACCCGCCATGCC 60.030 50.000 0.00 0.00 0.00 4.40
2450 3417 2.235016 GAATATTTACCCGCCATGCCA 58.765 47.619 0.00 0.00 0.00 4.92
2451 3418 1.616159 ATATTTACCCGCCATGCCAC 58.384 50.000 0.00 0.00 0.00 5.01
2452 3419 0.466555 TATTTACCCGCCATGCCACC 60.467 55.000 0.00 0.00 0.00 4.61
2453 3420 2.506884 ATTTACCCGCCATGCCACCA 62.507 55.000 0.00 0.00 0.00 4.17
2454 3421 3.636929 TTACCCGCCATGCCACCAG 62.637 63.158 0.00 0.00 0.00 4.00
2456 3423 4.108299 CCCGCCATGCCACCAGTA 62.108 66.667 0.00 0.00 0.00 2.74
2457 3424 2.045438 CCGCCATGCCACCAGTAA 60.045 61.111 0.00 0.00 0.00 2.24
2458 3425 2.114670 CCGCCATGCCACCAGTAAG 61.115 63.158 0.00 0.00 0.00 2.34
2459 3426 1.377202 CGCCATGCCACCAGTAAGT 60.377 57.895 0.00 0.00 0.00 2.24
2460 3427 0.107897 CGCCATGCCACCAGTAAGTA 60.108 55.000 0.00 0.00 0.00 2.24
2461 3428 1.668419 GCCATGCCACCAGTAAGTAG 58.332 55.000 0.00 0.00 0.00 2.57
2462 3429 1.209504 GCCATGCCACCAGTAAGTAGA 59.790 52.381 0.00 0.00 0.00 2.59
2463 3430 2.355716 GCCATGCCACCAGTAAGTAGAA 60.356 50.000 0.00 0.00 0.00 2.10
2464 3431 3.872240 GCCATGCCACCAGTAAGTAGAAA 60.872 47.826 0.00 0.00 0.00 2.52
2465 3432 4.331968 CCATGCCACCAGTAAGTAGAAAA 58.668 43.478 0.00 0.00 0.00 2.29
2466 3433 4.764823 CCATGCCACCAGTAAGTAGAAAAA 59.235 41.667 0.00 0.00 0.00 1.94
2505 3472 2.904866 TTTTTGCCGCGGTCAGCT 60.905 55.556 28.70 0.00 45.59 4.24
2506 3473 2.485795 TTTTTGCCGCGGTCAGCTT 61.486 52.632 28.70 0.00 45.59 3.74
2507 3474 1.167155 TTTTTGCCGCGGTCAGCTTA 61.167 50.000 28.70 7.28 45.59 3.09
2508 3475 1.573829 TTTTGCCGCGGTCAGCTTAG 61.574 55.000 28.70 0.00 45.59 2.18
2509 3476 3.950794 TTGCCGCGGTCAGCTTAGG 62.951 63.158 28.70 0.00 45.59 2.69
2510 3477 4.452733 GCCGCGGTCAGCTTAGGT 62.453 66.667 28.70 0.00 45.59 3.08
2511 3478 2.202756 CCGCGGTCAGCTTAGGTC 60.203 66.667 19.50 0.00 45.59 3.85
2512 3479 2.571757 CGCGGTCAGCTTAGGTCA 59.428 61.111 0.00 0.00 45.59 4.02
2513 3480 1.080093 CGCGGTCAGCTTAGGTCAA 60.080 57.895 0.00 0.00 45.59 3.18
2514 3481 0.460284 CGCGGTCAGCTTAGGTCAAT 60.460 55.000 0.00 0.00 45.59 2.57
2515 3482 1.202371 CGCGGTCAGCTTAGGTCAATA 60.202 52.381 0.00 0.00 45.59 1.90
2516 3483 2.474816 GCGGTCAGCTTAGGTCAATAG 58.525 52.381 0.00 0.00 44.04 1.73
2517 3484 2.803492 GCGGTCAGCTTAGGTCAATAGG 60.803 54.545 0.00 0.00 44.04 2.57
2518 3485 2.431057 CGGTCAGCTTAGGTCAATAGGT 59.569 50.000 0.00 0.00 0.00 3.08
2519 3486 3.491104 CGGTCAGCTTAGGTCAATAGGTC 60.491 52.174 0.00 0.00 0.00 3.85
2520 3487 3.491104 GGTCAGCTTAGGTCAATAGGTCG 60.491 52.174 0.00 0.00 0.00 4.79
2521 3488 2.693591 TCAGCTTAGGTCAATAGGTCGG 59.306 50.000 0.00 0.00 0.00 4.79
2522 3489 2.693591 CAGCTTAGGTCAATAGGTCGGA 59.306 50.000 0.00 0.00 0.00 4.55
2523 3490 3.132289 CAGCTTAGGTCAATAGGTCGGAA 59.868 47.826 0.00 0.00 0.00 4.30
2524 3491 3.967987 AGCTTAGGTCAATAGGTCGGAAT 59.032 43.478 0.00 0.00 0.00 3.01
2525 3492 4.039366 AGCTTAGGTCAATAGGTCGGAATC 59.961 45.833 0.00 0.00 0.00 2.52
2526 3493 4.799917 GCTTAGGTCAATAGGTCGGAATCC 60.800 50.000 0.00 0.00 0.00 3.01
2527 3494 2.047830 AGGTCAATAGGTCGGAATCCC 58.952 52.381 0.00 0.00 0.00 3.85
2528 3495 1.766496 GGTCAATAGGTCGGAATCCCA 59.234 52.381 0.00 0.00 0.00 4.37
2529 3496 2.372172 GGTCAATAGGTCGGAATCCCAT 59.628 50.000 0.00 0.00 0.00 4.00
2530 3497 3.557264 GGTCAATAGGTCGGAATCCCATC 60.557 52.174 0.00 0.00 0.00 3.51
2531 3498 2.637872 TCAATAGGTCGGAATCCCATCC 59.362 50.000 0.00 0.00 36.05 3.51
2532 3499 2.371841 CAATAGGTCGGAATCCCATCCA 59.628 50.000 0.00 0.00 39.61 3.41
2533 3500 1.717032 TAGGTCGGAATCCCATCCAG 58.283 55.000 0.00 0.00 39.61 3.86
2534 3501 0.326618 AGGTCGGAATCCCATCCAGT 60.327 55.000 0.00 0.00 39.61 4.00
2535 3502 1.062428 AGGTCGGAATCCCATCCAGTA 60.062 52.381 0.00 0.00 39.61 2.74
2536 3503 1.344763 GGTCGGAATCCCATCCAGTAG 59.655 57.143 0.00 0.00 39.61 2.57
2537 3504 2.317040 GTCGGAATCCCATCCAGTAGA 58.683 52.381 0.00 0.00 39.61 2.59
2538 3505 2.698797 GTCGGAATCCCATCCAGTAGAA 59.301 50.000 0.00 0.00 39.61 2.10
2539 3506 3.134081 GTCGGAATCCCATCCAGTAGAAA 59.866 47.826 0.00 0.00 39.61 2.52
2540 3507 3.778075 TCGGAATCCCATCCAGTAGAAAA 59.222 43.478 0.00 0.00 39.61 2.29
2541 3508 4.226394 TCGGAATCCCATCCAGTAGAAAAA 59.774 41.667 0.00 0.00 39.61 1.94
2542 3509 5.104109 TCGGAATCCCATCCAGTAGAAAAAT 60.104 40.000 0.00 0.00 39.61 1.82
2543 3510 5.239525 CGGAATCCCATCCAGTAGAAAAATC 59.760 44.000 0.00 0.00 39.61 2.17
2544 3511 6.129179 GGAATCCCATCCAGTAGAAAAATCA 58.871 40.000 0.00 0.00 39.42 2.57
2545 3512 6.779539 GGAATCCCATCCAGTAGAAAAATCAT 59.220 38.462 0.00 0.00 39.42 2.45
2546 3513 7.944554 GGAATCCCATCCAGTAGAAAAATCATA 59.055 37.037 0.00 0.00 39.42 2.15
2547 3514 8.697507 AATCCCATCCAGTAGAAAAATCATAC 57.302 34.615 0.00 0.00 0.00 2.39
2548 3515 7.206789 TCCCATCCAGTAGAAAAATCATACA 57.793 36.000 0.00 0.00 0.00 2.29
2549 3516 7.815383 TCCCATCCAGTAGAAAAATCATACAT 58.185 34.615 0.00 0.00 0.00 2.29
2550 3517 7.720957 TCCCATCCAGTAGAAAAATCATACATG 59.279 37.037 0.00 0.00 0.00 3.21
2551 3518 7.503566 CCCATCCAGTAGAAAAATCATACATGT 59.496 37.037 2.69 2.69 0.00 3.21
2552 3519 9.559732 CCATCCAGTAGAAAAATCATACATGTA 57.440 33.333 8.27 8.27 0.00 2.29
2555 3522 9.599866 TCCAGTAGAAAAATCATACATGTAGTG 57.400 33.333 11.91 9.73 0.00 2.74
2556 3523 8.338259 CCAGTAGAAAAATCATACATGTAGTGC 58.662 37.037 11.91 0.00 0.00 4.40
2557 3524 8.882736 CAGTAGAAAAATCATACATGTAGTGCA 58.117 33.333 11.91 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 144 4.336433 CCACACGAATAGAGCCAAATGAAT 59.664 41.667 0.00 0.00 0.00 2.57
250 255 8.613922 AAACCCCAATTTAATGAGATCAAGAT 57.386 30.769 0.00 0.00 0.00 2.40
333 338 7.010697 TCCGTACATGCAAATACAATACAAG 57.989 36.000 10.38 0.00 0.00 3.16
639 657 4.654724 AGACCCTAGCTAGAACCCAATAAC 59.345 45.833 22.70 2.03 0.00 1.89
1084 1126 2.519377 TTTGTCGTCGTTGTCCTCAT 57.481 45.000 0.00 0.00 0.00 2.90
1089 1131 3.541711 CCAGAATTTTGTCGTCGTTGTC 58.458 45.455 0.00 0.00 0.00 3.18
1127 1185 4.724697 CCTGCGTTGCTTGCGACG 62.725 66.667 25.61 25.61 41.89 5.12
1563 2366 1.745141 GCTCGACAAATCAGCAGGGAT 60.745 52.381 0.00 0.00 32.45 3.85
2385 3352 3.005050 TGACGGACGACAGAAACACTATT 59.995 43.478 0.00 0.00 0.00 1.73
2386 3353 2.555325 TGACGGACGACAGAAACACTAT 59.445 45.455 0.00 0.00 0.00 2.12
2387 3354 1.948834 TGACGGACGACAGAAACACTA 59.051 47.619 0.00 0.00 0.00 2.74
2388 3355 0.742505 TGACGGACGACAGAAACACT 59.257 50.000 0.00 0.00 0.00 3.55
2389 3356 1.719780 GATGACGGACGACAGAAACAC 59.280 52.381 0.00 0.00 0.00 3.32
2390 3357 1.611977 AGATGACGGACGACAGAAACA 59.388 47.619 0.00 0.00 0.00 2.83
2391 3358 2.349297 AGATGACGGACGACAGAAAC 57.651 50.000 0.00 0.00 0.00 2.78
2392 3359 4.508461 TTTAGATGACGGACGACAGAAA 57.492 40.909 0.00 0.00 0.00 2.52
2393 3360 4.713824 ATTTAGATGACGGACGACAGAA 57.286 40.909 0.00 0.00 0.00 3.02
2394 3361 4.713824 AATTTAGATGACGGACGACAGA 57.286 40.909 0.00 0.00 0.00 3.41
2395 3362 4.738740 GGTAATTTAGATGACGGACGACAG 59.261 45.833 0.00 0.00 0.00 3.51
2396 3363 4.400251 AGGTAATTTAGATGACGGACGACA 59.600 41.667 0.00 0.00 0.00 4.35
2397 3364 4.929781 AGGTAATTTAGATGACGGACGAC 58.070 43.478 0.00 0.00 0.00 4.34
2398 3365 4.037208 GGAGGTAATTTAGATGACGGACGA 59.963 45.833 0.00 0.00 0.00 4.20
2399 3366 4.296690 GGAGGTAATTTAGATGACGGACG 58.703 47.826 0.00 0.00 0.00 4.79
2400 3367 4.037208 TCGGAGGTAATTTAGATGACGGAC 59.963 45.833 0.00 0.00 0.00 4.79
2401 3368 4.209538 TCGGAGGTAATTTAGATGACGGA 58.790 43.478 0.00 0.00 0.00 4.69
2402 3369 4.579454 TCGGAGGTAATTTAGATGACGG 57.421 45.455 0.00 0.00 0.00 4.79
2403 3370 7.011109 ACAATTTCGGAGGTAATTTAGATGACG 59.989 37.037 0.00 0.00 0.00 4.35
2404 3371 8.122952 CACAATTTCGGAGGTAATTTAGATGAC 58.877 37.037 0.00 0.00 0.00 3.06
2405 3372 8.044309 TCACAATTTCGGAGGTAATTTAGATGA 58.956 33.333 0.00 0.00 0.00 2.92
2406 3373 8.208718 TCACAATTTCGGAGGTAATTTAGATG 57.791 34.615 0.00 0.00 0.00 2.90
2407 3374 8.801882 TTCACAATTTCGGAGGTAATTTAGAT 57.198 30.769 0.00 0.00 0.00 1.98
2408 3375 8.801882 ATTCACAATTTCGGAGGTAATTTAGA 57.198 30.769 0.00 0.00 0.00 2.10
2414 3381 8.895737 GGTAAATATTCACAATTTCGGAGGTAA 58.104 33.333 0.00 0.00 0.00 2.85
2415 3382 7.499895 GGGTAAATATTCACAATTTCGGAGGTA 59.500 37.037 0.00 0.00 0.00 3.08
2416 3383 6.320418 GGGTAAATATTCACAATTTCGGAGGT 59.680 38.462 0.00 0.00 0.00 3.85
2417 3384 6.512741 CGGGTAAATATTCACAATTTCGGAGG 60.513 42.308 0.00 0.00 0.00 4.30
2418 3385 6.427150 CGGGTAAATATTCACAATTTCGGAG 58.573 40.000 0.00 0.00 0.00 4.63
2419 3386 5.220892 GCGGGTAAATATTCACAATTTCGGA 60.221 40.000 0.00 0.00 0.00 4.55
2420 3387 4.973663 GCGGGTAAATATTCACAATTTCGG 59.026 41.667 0.00 0.00 0.00 4.30
2421 3388 4.973663 GGCGGGTAAATATTCACAATTTCG 59.026 41.667 0.00 0.00 0.00 3.46
2422 3389 5.897050 TGGCGGGTAAATATTCACAATTTC 58.103 37.500 0.00 0.00 0.00 2.17
2423 3390 5.923733 TGGCGGGTAAATATTCACAATTT 57.076 34.783 0.00 0.00 0.00 1.82
2424 3391 5.738783 GCATGGCGGGTAAATATTCACAATT 60.739 40.000 0.00 0.00 0.00 2.32
2425 3392 4.261994 GCATGGCGGGTAAATATTCACAAT 60.262 41.667 0.00 0.00 0.00 2.71
2426 3393 3.067461 GCATGGCGGGTAAATATTCACAA 59.933 43.478 0.00 0.00 0.00 3.33
2427 3394 2.621055 GCATGGCGGGTAAATATTCACA 59.379 45.455 0.00 0.00 0.00 3.58
2428 3395 2.030274 GGCATGGCGGGTAAATATTCAC 60.030 50.000 2.41 0.00 0.00 3.18
2429 3396 2.235016 GGCATGGCGGGTAAATATTCA 58.765 47.619 2.41 0.00 0.00 2.57
2430 3397 2.030274 GTGGCATGGCGGGTAAATATTC 60.030 50.000 15.27 0.00 0.00 1.75
2431 3398 1.960689 GTGGCATGGCGGGTAAATATT 59.039 47.619 15.27 0.00 0.00 1.28
2432 3399 1.616159 GTGGCATGGCGGGTAAATAT 58.384 50.000 15.27 0.00 0.00 1.28
2433 3400 0.466555 GGTGGCATGGCGGGTAAATA 60.467 55.000 15.27 0.00 0.00 1.40
2434 3401 1.756561 GGTGGCATGGCGGGTAAAT 60.757 57.895 15.27 0.00 0.00 1.40
2435 3402 2.361865 GGTGGCATGGCGGGTAAA 60.362 61.111 15.27 0.00 0.00 2.01
2436 3403 3.636929 CTGGTGGCATGGCGGGTAA 62.637 63.158 15.27 0.00 0.00 2.85
2437 3404 4.108299 CTGGTGGCATGGCGGGTA 62.108 66.667 15.27 0.08 0.00 3.69
2439 3406 3.636929 TTACTGGTGGCATGGCGGG 62.637 63.158 15.27 6.88 0.00 6.13
2440 3407 2.045438 TTACTGGTGGCATGGCGG 60.045 61.111 15.27 7.23 0.00 6.13
2441 3408 0.107897 TACTTACTGGTGGCATGGCG 60.108 55.000 15.27 2.39 0.00 5.69
2442 3409 1.209504 TCTACTTACTGGTGGCATGGC 59.790 52.381 13.29 13.29 0.00 4.40
2443 3410 3.627395 TTCTACTTACTGGTGGCATGG 57.373 47.619 0.00 0.00 0.00 3.66
2444 3411 5.957842 TTTTTCTACTTACTGGTGGCATG 57.042 39.130 0.00 0.00 0.00 4.06
2494 3461 2.202756 GACCTAAGCTGACCGCGG 60.203 66.667 26.86 26.86 45.59 6.46
2495 3462 0.460284 ATTGACCTAAGCTGACCGCG 60.460 55.000 0.00 0.00 45.59 6.46
2496 3463 2.474816 CTATTGACCTAAGCTGACCGC 58.525 52.381 0.00 0.00 39.57 5.68
2497 3464 2.431057 ACCTATTGACCTAAGCTGACCG 59.569 50.000 0.00 0.00 0.00 4.79
2498 3465 3.491104 CGACCTATTGACCTAAGCTGACC 60.491 52.174 0.00 0.00 0.00 4.02
2499 3466 3.491104 CCGACCTATTGACCTAAGCTGAC 60.491 52.174 0.00 0.00 0.00 3.51
2500 3467 2.693591 CCGACCTATTGACCTAAGCTGA 59.306 50.000 0.00 0.00 0.00 4.26
2501 3468 2.693591 TCCGACCTATTGACCTAAGCTG 59.306 50.000 0.00 0.00 0.00 4.24
2502 3469 3.028094 TCCGACCTATTGACCTAAGCT 57.972 47.619 0.00 0.00 0.00 3.74
2503 3470 3.814005 TTCCGACCTATTGACCTAAGC 57.186 47.619 0.00 0.00 0.00 3.09
2504 3471 4.262506 GGGATTCCGACCTATTGACCTAAG 60.263 50.000 0.00 0.00 0.00 2.18
2505 3472 3.644738 GGGATTCCGACCTATTGACCTAA 59.355 47.826 0.00 0.00 0.00 2.69
2506 3473 3.236896 GGGATTCCGACCTATTGACCTA 58.763 50.000 0.00 0.00 0.00 3.08
2507 3474 2.047830 GGGATTCCGACCTATTGACCT 58.952 52.381 0.00 0.00 0.00 3.85
2508 3475 1.766496 TGGGATTCCGACCTATTGACC 59.234 52.381 0.00 0.00 35.24 4.02
2509 3476 3.557264 GGATGGGATTCCGACCTATTGAC 60.557 52.174 0.00 0.00 35.24 3.18
2510 3477 2.637872 GGATGGGATTCCGACCTATTGA 59.362 50.000 0.00 0.00 35.24 2.57
2511 3478 2.371841 TGGATGGGATTCCGACCTATTG 59.628 50.000 6.83 0.00 38.74 1.90
2512 3479 2.639839 CTGGATGGGATTCCGACCTATT 59.360 50.000 6.83 0.00 38.74 1.73
2513 3480 2.260822 CTGGATGGGATTCCGACCTAT 58.739 52.381 6.83 0.00 38.74 2.57
2514 3481 1.062428 ACTGGATGGGATTCCGACCTA 60.062 52.381 6.83 0.00 38.74 3.08
2515 3482 0.326618 ACTGGATGGGATTCCGACCT 60.327 55.000 6.83 0.00 38.74 3.85
2516 3483 1.344763 CTACTGGATGGGATTCCGACC 59.655 57.143 0.00 0.96 38.74 4.79
2517 3484 2.317040 TCTACTGGATGGGATTCCGAC 58.683 52.381 0.00 0.00 38.74 4.79
2518 3485 2.767644 TCTACTGGATGGGATTCCGA 57.232 50.000 0.00 0.00 38.74 4.55
2519 3486 3.838244 TTTCTACTGGATGGGATTCCG 57.162 47.619 0.00 0.00 38.74 4.30
2520 3487 6.129179 TGATTTTTCTACTGGATGGGATTCC 58.871 40.000 0.00 0.00 36.24 3.01
2521 3488 7.830099 ATGATTTTTCTACTGGATGGGATTC 57.170 36.000 0.00 0.00 0.00 2.52
2522 3489 8.281531 TGTATGATTTTTCTACTGGATGGGATT 58.718 33.333 0.00 0.00 0.00 3.01
2523 3490 7.815383 TGTATGATTTTTCTACTGGATGGGAT 58.185 34.615 0.00 0.00 0.00 3.85
2524 3491 7.206789 TGTATGATTTTTCTACTGGATGGGA 57.793 36.000 0.00 0.00 0.00 4.37
2525 3492 7.503566 ACATGTATGATTTTTCTACTGGATGGG 59.496 37.037 0.00 0.00 0.00 4.00
2526 3493 8.455903 ACATGTATGATTTTTCTACTGGATGG 57.544 34.615 0.00 0.00 0.00 3.51
2529 3496 9.599866 CACTACATGTATGATTTTTCTACTGGA 57.400 33.333 5.91 0.00 0.00 3.86
2530 3497 8.338259 GCACTACATGTATGATTTTTCTACTGG 58.662 37.037 5.91 0.00 0.00 4.00
2531 3498 8.882736 TGCACTACATGTATGATTTTTCTACTG 58.117 33.333 5.91 0.00 0.00 2.74



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

AutoCloner maintained by Alex Coulton.