Multiple sequence alignment - TraesCS1A01G357000

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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 TraesCS1A01G357000 chr1A 100.000 2333 0 0 1 2333 539843255 539840923 0.000000e+00 4309
1 TraesCS1A01G357000 chr1A 93.560 1646 69 23 1 1622 7955960 7957592 0.000000e+00 2418
2 TraesCS1A01G357000 chr1A 97.127 905 23 3 1369 2273 7957384 7958285 0.000000e+00 1524
3 TraesCS1A01G357000 chr1A 100.000 61 0 0 2273 2333 539834211 539834151 1.890000e-21 113
4 TraesCS1A01G357000 chr5A 93.682 1646 65 26 1 1622 345653536 345651906 0.000000e+00 2427
5 TraesCS1A01G357000 chr5A 93.260 1647 71 25 1 1622 634752626 634754257 0.000000e+00 2390
6 TraesCS1A01G357000 chr5A 97.332 1387 34 2 1 1386 133827293 133828677 0.000000e+00 2353
7 TraesCS1A01G357000 chr5A 97.192 1389 38 1 1 1388 501877002 501878390 0.000000e+00 2348
8 TraesCS1A01G357000 chr5A 96.162 912 29 6 1369 2280 345652114 345651209 0.000000e+00 1485
9 TraesCS1A01G357000 chr5A 96.026 906 30 4 1369 2274 634754049 634754948 0.000000e+00 1469
10 TraesCS1A01G357000 chr5A 96.923 65 1 1 2270 2333 180814197 180814261 8.820000e-20 108
11 TraesCS1A01G357000 chr2A 93.378 1646 71 23 1 1622 55069647 55068016 0.000000e+00 2401
12 TraesCS1A01G357000 chr2A 93.135 1646 76 22 1 1622 599672284 599670652 0.000000e+00 2379
13 TraesCS1A01G357000 chr2A 97.566 904 19 3 1369 2272 55068224 55067324 0.000000e+00 1544
14 TraesCS1A01G357000 chr2A 100.000 59 0 0 2273 2331 655592304 655592246 2.450000e-20 110
15 TraesCS1A01G357000 chr7A 93.256 1646 74 23 1 1622 578424342 578422710 0.000000e+00 2390
16 TraesCS1A01G357000 chr7A 96.692 907 28 2 1369 2275 639851683 639850779 0.000000e+00 1507
17 TraesCS1A01G357000 chr7A 96.571 904 27 4 1369 2272 578422918 578422019 0.000000e+00 1495
18 TraesCS1A01G357000 chr7A 94.919 925 24 5 1369 2293 493525451 493526352 0.000000e+00 1426
19 TraesCS1A01G357000 chr7A 100.000 61 0 0 2273 2333 239839728 239839788 1.890000e-21 113
20 TraesCS1A01G357000 chr7A 96.923 65 1 1 2270 2333 213205150 213205086 8.820000e-20 108
21 TraesCS1A01G357000 chr3A 97.332 1387 36 1 1 1386 513304547 513305933 0.000000e+00 2355
22 TraesCS1A01G357000 chr3A 96.875 64 1 1 2270 2333 616994801 616994739 3.170000e-19 106
23 TraesCS1A01G357000 chr6A 97.566 904 17 4 1369 2272 436400068 436400966 0.000000e+00 1543
24 TraesCS1A01G357000 chr6A 93.855 830 46 4 1443 2272 136675464 136676288 0.000000e+00 1245
25 TraesCS1A01G357000 chr2B 91.128 913 51 8 1369 2272 750617804 750618695 0.000000e+00 1210
26 TraesCS1A01G357000 chr4A 93.017 802 47 7 1471 2272 29672660 29671868 0.000000e+00 1162
27 TraesCS1A01G357000 chr7B 91.447 760 61 4 1515 2272 46781506 46782263 0.000000e+00 1040
28 TraesCS1A01G357000 chr7B 85.497 724 78 13 1390 2093 724302481 724301765 0.000000e+00 730
29 TraesCS1A01G357000 chr6B 87.093 829 79 18 1445 2264 621035358 621036167 0.000000e+00 913
30 TraesCS1A01G357000 chr7D 94.595 74 2 2 2261 2333 411131627 411131555 1.890000e-21 113
31 TraesCS1A01G357000 chr2D 93.333 75 3 2 2261 2333 565607712 565607638 2.450000e-20 110
32 TraesCS1A01G357000 chr5B 96.875 64 1 1 2270 2333 285881104 285881166 3.170000e-19 106


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 TraesCS1A01G357000 chr1A 539840923 539843255 2332 True 4309.0 4309 100.0000 1 2333 1 chr1A.!!$R2 2332
1 TraesCS1A01G357000 chr1A 7955960 7958285 2325 False 1971.0 2418 95.3435 1 2273 2 chr1A.!!$F1 2272
2 TraesCS1A01G357000 chr5A 133827293 133828677 1384 False 2353.0 2353 97.3320 1 1386 1 chr5A.!!$F1 1385
3 TraesCS1A01G357000 chr5A 501877002 501878390 1388 False 2348.0 2348 97.1920 1 1388 1 chr5A.!!$F3 1387
4 TraesCS1A01G357000 chr5A 345651209 345653536 2327 True 1956.0 2427 94.9220 1 2280 2 chr5A.!!$R1 2279
5 TraesCS1A01G357000 chr5A 634752626 634754948 2322 False 1929.5 2390 94.6430 1 2274 2 chr5A.!!$F4 2273
6 TraesCS1A01G357000 chr2A 599670652 599672284 1632 True 2379.0 2379 93.1350 1 1622 1 chr2A.!!$R1 1621
7 TraesCS1A01G357000 chr2A 55067324 55069647 2323 True 1972.5 2401 95.4720 1 2272 2 chr2A.!!$R3 2271
8 TraesCS1A01G357000 chr7A 578422019 578424342 2323 True 1942.5 2390 94.9135 1 2272 2 chr7A.!!$R3 2271
9 TraesCS1A01G357000 chr7A 639850779 639851683 904 True 1507.0 1507 96.6920 1369 2275 1 chr7A.!!$R2 906
10 TraesCS1A01G357000 chr7A 493525451 493526352 901 False 1426.0 1426 94.9190 1369 2293 1 chr7A.!!$F2 924
11 TraesCS1A01G357000 chr3A 513304547 513305933 1386 False 2355.0 2355 97.3320 1 1386 1 chr3A.!!$F1 1385
12 TraesCS1A01G357000 chr6A 436400068 436400966 898 False 1543.0 1543 97.5660 1369 2272 1 chr6A.!!$F2 903
13 TraesCS1A01G357000 chr6A 136675464 136676288 824 False 1245.0 1245 93.8550 1443 2272 1 chr6A.!!$F1 829
14 TraesCS1A01G357000 chr2B 750617804 750618695 891 False 1210.0 1210 91.1280 1369 2272 1 chr2B.!!$F1 903
15 TraesCS1A01G357000 chr4A 29671868 29672660 792 True 1162.0 1162 93.0170 1471 2272 1 chr4A.!!$R1 801
16 TraesCS1A01G357000 chr7B 46781506 46782263 757 False 1040.0 1040 91.4470 1515 2272 1 chr7B.!!$F1 757
17 TraesCS1A01G357000 chr7B 724301765 724302481 716 True 730.0 730 85.4970 1390 2093 1 chr7B.!!$R1 703
18 TraesCS1A01G357000 chr6B 621035358 621036167 809 False 913.0 913 87.0930 1445 2264 1 chr6B.!!$F1 819

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
634 637 0.178068 AGCCAGTCAAGAACACACGT 59.822 50.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1970 3.545366 TTTGGGCCACAACCTTTTTAC 57.455 42.857 5.23 0.0 39.19 2.01 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
31 32 6.515272 AATATTCAAAGAACAGACGCCATT 57.485 33.333 0.00 0.00 0.00 3.16
148 151 1.009552 TGGAGATGTGGTCTACCCCAT 59.990 52.381 0.00 0.00 36.93 4.00
293 296 6.508880 CGAGAAAAAGTCGTGTACAATCACAA 60.509 38.462 0.00 0.00 38.12 3.33
466 469 0.472734 AAGGGTGAGGAGCTGTCTGT 60.473 55.000 0.00 0.00 0.00 3.41
485 488 5.239525 GTCTGTGATTGACTTGTTTAAGGCT 59.760 40.000 0.00 0.00 42.73 4.58
573 576 3.740764 GCTTTGCCCTGTTTGATTCACAA 60.741 43.478 0.00 0.00 36.65 3.33
634 637 0.178068 AGCCAGTCAAGAACACACGT 59.822 50.000 0.00 0.00 0.00 4.49
791 795 8.449423 AGCCATCTTATATAGAACCACCATTA 57.551 34.615 0.00 0.00 36.22 1.90
1130 1134 1.747355 GAATGTTGGGCTCCAGTCATG 59.253 52.381 11.51 0.00 33.81 3.07
1195 1199 1.328279 TCGTGACCTTGAGCAGAAGA 58.672 50.000 0.00 0.00 0.00 2.87
1330 1334 2.888212 AGTCTCAAGAGCAGGAAGAGT 58.112 47.619 0.00 0.00 0.00 3.24
1495 1644 5.818678 ACCTGTGAAGTTATGTGAACCTA 57.181 39.130 0.00 0.00 0.00 3.08
1513 1662 9.167311 GTGAACCTATGAAGTTATGTGATCTTT 57.833 33.333 0.00 0.00 0.00 2.52
1766 1951 7.446625 TGCATAACACAAAATAAAAAGGCCAAT 59.553 29.630 5.01 0.00 0.00 3.16
1785 1970 4.752101 CCAATGCCCTAATTCGAACTAGAG 59.248 45.833 14.92 2.89 0.00 2.43
2285 2478 7.718334 TTCTTGTAGTGATAAGTCATGGAGA 57.282 36.000 0.00 0.00 36.60 3.71
2288 2481 8.253810 TCTTGTAGTGATAAGTCATGGAGAAAG 58.746 37.037 0.00 0.00 36.60 2.62
2289 2482 6.341316 TGTAGTGATAAGTCATGGAGAAAGC 58.659 40.000 0.00 0.00 36.60 3.51
2290 2483 5.426689 AGTGATAAGTCATGGAGAAAGCA 57.573 39.130 0.00 0.00 36.60 3.91
2291 2484 5.809001 AGTGATAAGTCATGGAGAAAGCAA 58.191 37.500 0.00 0.00 36.60 3.91
2292 2485 6.421485 AGTGATAAGTCATGGAGAAAGCAAT 58.579 36.000 0.00 0.00 36.60 3.56
2293 2486 7.568349 AGTGATAAGTCATGGAGAAAGCAATA 58.432 34.615 0.00 0.00 36.60 1.90
2294 2487 7.714377 AGTGATAAGTCATGGAGAAAGCAATAG 59.286 37.037 0.00 0.00 36.60 1.73
2295 2488 6.484643 TGATAAGTCATGGAGAAAGCAATAGC 59.515 38.462 0.00 0.00 42.56 2.97
2296 2489 4.226427 AGTCATGGAGAAAGCAATAGCA 57.774 40.909 0.00 0.00 45.49 3.49
2297 2490 4.592942 AGTCATGGAGAAAGCAATAGCAA 58.407 39.130 0.00 0.00 45.49 3.91
2298 2491 5.198965 AGTCATGGAGAAAGCAATAGCAAT 58.801 37.500 0.00 0.00 45.49 3.56
2299 2492 6.359804 AGTCATGGAGAAAGCAATAGCAATA 58.640 36.000 0.00 0.00 45.49 1.90
2300 2493 6.830324 AGTCATGGAGAAAGCAATAGCAATAA 59.170 34.615 0.00 0.00 45.49 1.40
2301 2494 7.340232 AGTCATGGAGAAAGCAATAGCAATAAA 59.660 33.333 0.00 0.00 45.49 1.40
2302 2495 7.433425 GTCATGGAGAAAGCAATAGCAATAAAC 59.567 37.037 0.00 0.00 45.49 2.01
2303 2496 7.340232 TCATGGAGAAAGCAATAGCAATAAACT 59.660 33.333 0.00 0.00 45.49 2.66
2304 2497 8.623903 CATGGAGAAAGCAATAGCAATAAACTA 58.376 33.333 0.00 0.00 45.49 2.24
2305 2498 8.574251 TGGAGAAAGCAATAGCAATAAACTAA 57.426 30.769 0.00 0.00 45.49 2.24
2306 2499 9.019656 TGGAGAAAGCAATAGCAATAAACTAAA 57.980 29.630 0.00 0.00 45.49 1.85
2307 2500 9.290483 GGAGAAAGCAATAGCAATAAACTAAAC 57.710 33.333 0.00 0.00 45.49 2.01
2308 2501 8.895932 AGAAAGCAATAGCAATAAACTAAACG 57.104 30.769 0.00 0.00 45.49 3.60
2309 2502 8.726988 AGAAAGCAATAGCAATAAACTAAACGA 58.273 29.630 0.00 0.00 45.49 3.85
2310 2503 9.503427 GAAAGCAATAGCAATAAACTAAACGAT 57.497 29.630 0.00 0.00 45.49 3.73
2311 2504 9.503427 AAAGCAATAGCAATAAACTAAACGATC 57.497 29.630 0.00 0.00 45.49 3.69
2312 2505 8.208718 AGCAATAGCAATAAACTAAACGATCA 57.791 30.769 0.00 0.00 45.49 2.92
2313 2506 8.840321 AGCAATAGCAATAAACTAAACGATCAT 58.160 29.630 0.00 0.00 45.49 2.45
2318 2511 7.630924 AGCAATAAACTAAACGATCATAGTGC 58.369 34.615 0.00 0.00 32.84 4.40
2319 2512 7.495934 AGCAATAAACTAAACGATCATAGTGCT 59.504 33.333 0.00 0.00 32.84 4.40
2320 2513 8.761497 GCAATAAACTAAACGATCATAGTGCTA 58.239 33.333 0.00 1.50 32.84 3.49
2323 2516 6.830114 AACTAAACGATCATAGTGCTAAGC 57.170 37.500 0.00 0.00 32.84 3.09
2324 2517 6.150396 ACTAAACGATCATAGTGCTAAGCT 57.850 37.500 0.00 0.00 31.35 3.74
2325 2518 7.273320 ACTAAACGATCATAGTGCTAAGCTA 57.727 36.000 0.00 0.00 31.35 3.32
2326 2519 7.713750 ACTAAACGATCATAGTGCTAAGCTAA 58.286 34.615 0.00 0.00 31.35 3.09
2327 2520 6.830114 AAACGATCATAGTGCTAAGCTAAC 57.170 37.500 0.00 0.00 0.00 2.34
2328 2521 4.537965 ACGATCATAGTGCTAAGCTAACG 58.462 43.478 0.00 0.00 0.00 3.18
2329 2522 4.275196 ACGATCATAGTGCTAAGCTAACGA 59.725 41.667 0.00 0.00 0.00 3.85
2330 2523 5.212934 CGATCATAGTGCTAAGCTAACGAA 58.787 41.667 0.00 0.00 0.00 3.85
2331 2524 5.859114 CGATCATAGTGCTAAGCTAACGAAT 59.141 40.000 0.00 0.00 0.00 3.34
2332 2525 6.183359 CGATCATAGTGCTAAGCTAACGAATG 60.183 42.308 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 251 4.303282 TCGATTCATCTTGTTCGACACAA 58.697 39.130 11.07 11.07 43.55 3.33
293 296 1.493022 TGTAGTGCCTGGAACCAGTTT 59.507 47.619 17.92 4.96 42.15 2.66
466 469 5.007682 GGGTAGCCTTAAACAAGTCAATCA 58.992 41.667 2.95 0.00 0.00 2.57
485 488 1.133945 TGCTTCTTGCTGTTGTGGGTA 60.134 47.619 0.00 0.00 43.37 3.69
532 535 6.538742 GCAAAGCATGGAGTGACTTACTATAA 59.461 38.462 0.00 0.00 40.53 0.98
573 576 3.159472 TCATCAAAGCATCAAAGCTGGT 58.841 40.909 0.00 0.00 45.89 4.00
679 682 6.258727 GCATCAAATAGCTACAGCAAGTTCTA 59.741 38.462 3.70 0.00 45.16 2.10
1130 1134 1.804748 CTTTGCCGGAGTTGTTCCTAC 59.195 52.381 5.05 0.00 44.41 3.18
1195 1199 2.244486 TGAAGCTCAGACCTCTCCAT 57.756 50.000 0.00 0.00 0.00 3.41
1495 1644 8.641498 AGGTTCAAAAGATCACATAACTTCAT 57.359 30.769 0.00 0.00 0.00 2.57
1513 1662 7.873719 TCACAGAAAATAAACAGAGGTTCAA 57.126 32.000 0.00 0.00 35.82 2.69
1766 1951 6.534475 TTTACTCTAGTTCGAATTAGGGCA 57.466 37.500 23.28 11.30 0.00 5.36
1771 1956 9.768662 ACAACCTTTTTACTCTAGTTCGAATTA 57.231 29.630 0.00 0.00 0.00 1.40
1785 1970 3.545366 TTTGGGCCACAACCTTTTTAC 57.455 42.857 5.23 0.00 39.19 2.01
2102 2294 4.973663 GTCACAAACGTTTATGACCAAAGG 59.026 41.667 32.36 12.40 36.31 3.11
2276 2469 4.970662 TTGCTATTGCTTTCTCCATGAC 57.029 40.909 0.00 0.00 40.48 3.06
2278 2471 7.486647 AGTTTATTGCTATTGCTTTCTCCATG 58.513 34.615 0.00 0.00 40.48 3.66
2280 2473 8.574251 TTAGTTTATTGCTATTGCTTTCTCCA 57.426 30.769 0.00 0.00 40.48 3.86
2282 2475 9.000018 CGTTTAGTTTATTGCTATTGCTTTCTC 58.000 33.333 0.00 0.00 40.48 2.87
2285 2478 9.503427 GATCGTTTAGTTTATTGCTATTGCTTT 57.497 29.630 0.00 0.00 40.48 3.51
2292 2485 8.761497 GCACTATGATCGTTTAGTTTATTGCTA 58.239 33.333 0.00 0.00 0.00 3.49
2293 2486 7.495934 AGCACTATGATCGTTTAGTTTATTGCT 59.504 33.333 0.00 0.52 0.00 3.91
2294 2487 7.630924 AGCACTATGATCGTTTAGTTTATTGC 58.369 34.615 0.00 0.00 0.00 3.56
2297 2490 8.979574 GCTTAGCACTATGATCGTTTAGTTTAT 58.020 33.333 0.00 0.00 0.00 1.40
2298 2491 8.195436 AGCTTAGCACTATGATCGTTTAGTTTA 58.805 33.333 7.07 0.00 0.00 2.01
2299 2492 7.042335 AGCTTAGCACTATGATCGTTTAGTTT 58.958 34.615 7.07 0.00 0.00 2.66
2300 2493 6.574350 AGCTTAGCACTATGATCGTTTAGTT 58.426 36.000 7.07 0.00 0.00 2.24
2301 2494 6.150396 AGCTTAGCACTATGATCGTTTAGT 57.850 37.500 7.07 0.00 0.00 2.24
2302 2495 7.149112 CGTTAGCTTAGCACTATGATCGTTTAG 60.149 40.741 7.07 0.00 0.00 1.85
2303 2496 6.635641 CGTTAGCTTAGCACTATGATCGTTTA 59.364 38.462 7.07 0.00 0.00 2.01
2304 2497 5.459107 CGTTAGCTTAGCACTATGATCGTTT 59.541 40.000 7.07 0.00 0.00 3.60
2305 2498 4.976731 CGTTAGCTTAGCACTATGATCGTT 59.023 41.667 7.07 0.00 0.00 3.85
2306 2499 4.275196 TCGTTAGCTTAGCACTATGATCGT 59.725 41.667 7.07 0.00 0.00 3.73
2307 2500 4.784329 TCGTTAGCTTAGCACTATGATCG 58.216 43.478 7.07 0.19 0.00 3.69
2308 2501 7.043454 CATTCGTTAGCTTAGCACTATGATC 57.957 40.000 7.07 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.