Multiple sequence alignment - TraesCS6B01G246100

Loading Multiple Alignment...

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 TraesCS6B01G246100 chr6B 100.000 2462 0 0 1 2462 438633806 438631345 0.000000e+00 4547
1 TraesCS6B01G246100 chr6B 93.807 2406 137 10 4 2406 117498453 117496057 0.000000e+00 3607
2 TraesCS6B01G246100 chr3B 93.532 2412 145 11 1 2407 590297811 590295406 0.000000e+00 3579
3 TraesCS6B01G246100 chr3B 95.745 94 3 1 1 94 215100530 215100438 1.530000e-32 150
4 TraesCS6B01G246100 chr4B 92.327 2437 161 15 1 2425 650194673 650192251 0.000000e+00 3441
5 TraesCS6B01G246100 chr4B 91.916 2437 171 16 1 2425 650136310 650133888 0.000000e+00 3386
6 TraesCS6B01G246100 chr4B 91.875 2437 172 16 1 2425 650074307 650071885 0.000000e+00 3380
7 TraesCS6B01G246100 chr5B 92.802 2348 160 7 68 2411 315915171 315912829 0.000000e+00 3391
8 TraesCS6B01G246100 chr5B 92.075 2410 176 12 1 2406 184289503 184291901 0.000000e+00 3378
9 TraesCS6B01G246100 chr5B 92.040 2412 177 8 1 2409 478553213 478550814 0.000000e+00 3376
10 TraesCS6B01G246100 chr1B 92.052 2403 179 11 3 2401 535919292 535916898 0.000000e+00 3369


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 TraesCS6B01G246100 chr6B 438631345 438633806 2461 True 4547 4547 100.000 1 2462 1 chr6B.!!$R2 2461
1 TraesCS6B01G246100 chr6B 117496057 117498453 2396 True 3607 3607 93.807 4 2406 1 chr6B.!!$R1 2402
2 TraesCS6B01G246100 chr3B 590295406 590297811 2405 True 3579 3579 93.532 1 2407 1 chr3B.!!$R2 2406
3 TraesCS6B01G246100 chr4B 650192251 650194673 2422 True 3441 3441 92.327 1 2425 1 chr4B.!!$R3 2424
4 TraesCS6B01G246100 chr4B 650133888 650136310 2422 True 3386 3386 91.916 1 2425 1 chr4B.!!$R2 2424
5 TraesCS6B01G246100 chr4B 650071885 650074307 2422 True 3380 3380 91.875 1 2425 1 chr4B.!!$R1 2424
6 TraesCS6B01G246100 chr5B 315912829 315915171 2342 True 3391 3391 92.802 68 2411 1 chr5B.!!$R1 2343
7 TraesCS6B01G246100 chr5B 184289503 184291901 2398 False 3378 3378 92.075 1 2406 1 chr5B.!!$F1 2405
8 TraesCS6B01G246100 chr5B 478550814 478553213 2399 True 3376 3376 92.040 1 2409 1 chr5B.!!$R2 2408
9 TraesCS6B01G246100 chr1B 535916898 535919292 2394 True 3369 3369 92.052 3 2401 1 chr1B.!!$R1 2398

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
498 501 0.250467 GAGCCAACTCCTGCTGTTGA 60.25 55.0 8.01 0.0 45.27 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2110 0.034198 TGACGATGAACTGGGCGAAA 59.966 50.0 0.0 0.0 0.0 3.46 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
30 31 6.294176 GCAATTTATGGTAGGGCTAGATGTTG 60.294 42.308 0.00 0.00 0.00 3.33
148 150 5.519927 GGTCCATTTATAGCATGTTGTTTGC 59.480 40.000 0.00 0.00 40.45 3.68
180 182 3.610040 ATTCGTGCTCATAGGTTGTCA 57.390 42.857 0.00 0.00 0.00 3.58
181 183 3.610040 TTCGTGCTCATAGGTTGTCAT 57.390 42.857 0.00 0.00 0.00 3.06
251 254 6.653020 AGTCATGAACCATGTACATGTATGT 58.347 36.000 29.25 19.39 41.98 2.29
279 282 4.498682 GCTTTCATGGATTGTCTGGTATGC 60.499 45.833 0.00 0.00 0.00 3.14
355 358 1.550524 ACGCAAGATCTTAGTCAGGCA 59.449 47.619 7.86 0.00 43.62 4.75
388 391 0.403271 ACAGCCAGTTTGCTCCATCT 59.597 50.000 0.00 0.00 40.32 2.90
446 449 1.324736 CTGATTTAGAGGTGTTCGCGC 59.675 52.381 0.00 0.00 0.00 6.86
464 467 1.688735 CGCCTGATTCCCTCTATGTGA 59.311 52.381 0.00 0.00 0.00 3.58
498 501 0.250467 GAGCCAACTCCTGCTGTTGA 60.250 55.000 8.01 0.00 45.27 3.18
511 521 4.487412 GTTGATGCTGCTGCCGCC 62.487 66.667 13.49 0.00 38.71 6.13
641 651 6.689433 GCTCATCTCTAGTGGAGTTAGGACTA 60.689 46.154 3.16 0.00 42.40 2.59
673 684 0.839946 AGGAGGTGCACTTGAACACT 59.160 50.000 17.98 2.66 36.99 3.55
1005 1016 2.038952 ACAGAACTACAGCCAGATGCAA 59.961 45.455 0.00 0.00 44.83 4.08
1159 1170 0.603065 GCCCTTCGACAAGCCATTTT 59.397 50.000 0.00 0.00 0.00 1.82
1209 1223 0.473501 GAGGCCTGATGGAGGAGGAT 60.474 60.000 12.00 0.00 46.33 3.24
1332 1346 2.450502 ACCCAGGGTGGCTTCAGT 60.451 61.111 11.70 0.00 35.79 3.41
1540 1561 0.025898 GACGATGACGATGACGACGA 59.974 55.000 0.00 0.00 42.66 4.20
1579 1601 4.102996 AGGGCTGAAAACAATTTGATGGTT 59.897 37.500 2.79 0.00 0.00 3.67
1632 1655 2.434336 CCCTCACGATGATGGGAACTTA 59.566 50.000 12.65 0.00 37.15 2.24
1658 1681 3.655777 TGGTAGGATGACACCCTCTTTTT 59.344 43.478 0.00 0.00 35.30 1.94
1679 1702 4.919774 TGATGTGGTGGTAGGTTAACAT 57.080 40.909 8.10 2.34 0.00 2.71
1697 1720 7.325694 GTTAACATCAAGGTAGTGCTAGGTTA 58.674 38.462 0.00 0.00 0.00 2.85
1704 1727 5.820404 AGGTAGTGCTAGGTTAAACTTGT 57.180 39.130 0.00 0.00 0.00 3.16
1784 1807 3.016736 ACTTTGCTTGCTACTTGTGTGT 58.983 40.909 0.00 0.00 0.00 3.72
1805 1828 5.176223 GTGTTCCATTGATTTGTTGCTTCAG 59.824 40.000 0.00 0.00 0.00 3.02
1828 1851 3.148412 TCTTGCTCTTGTGCATTGCTAA 58.852 40.909 10.49 4.65 42.96 3.09
1923 1947 5.419542 AGTGACATCGTATAGCAACAACAT 58.580 37.500 0.00 0.00 0.00 2.71
1924 1948 5.874810 AGTGACATCGTATAGCAACAACATT 59.125 36.000 0.00 0.00 0.00 2.71
2045 2069 3.135712 TGTCAAAGTGGAAGGTGCTAAGA 59.864 43.478 0.00 0.00 0.00 2.10
2145 2169 5.612725 TGATGTGCTAGGTGTGATCATTA 57.387 39.130 0.00 0.00 0.00 1.90
2158 2182 6.000219 GTGTGATCATTATGGGTAAGCTCAT 59.000 40.000 0.00 0.00 39.53 2.90
2166 2190 6.808321 TTATGGGTAAGCTCATCAACTAGT 57.192 37.500 0.00 0.00 37.03 2.57
2205 2230 5.239359 ACATGTATGTTGTATGCAAGCAG 57.761 39.130 0.00 0.00 37.90 4.24
2221 2246 1.011968 GCAGACGCCGTGTTCATGTA 61.012 55.000 0.00 0.00 0.00 2.29
2229 2254 1.133598 CCGTGTTCATGTACCGCTAGA 59.866 52.381 0.00 0.00 0.00 2.43
2239 2264 0.758734 TACCGCTAGAGCCAATGCAT 59.241 50.000 0.00 0.00 41.13 3.96
2261 2287 3.056536 TGCAACCAAACAAAGTGCACTTA 60.057 39.130 31.31 9.28 34.61 2.24
2269 2295 7.040961 ACCAAACAAAGTGCACTTACGTATTAT 60.041 33.333 31.31 11.33 34.61 1.28
2279 2305 7.169308 GTGCACTTACGTATTATCTAATGCAGT 59.831 37.037 10.32 0.00 0.00 4.40
2312 2338 1.277557 AGGCAACCAAACAACTTGCAA 59.722 42.857 0.00 0.00 41.77 4.08
2347 2373 3.319122 GGTCTGTTTTTGCTCAATCAGGT 59.681 43.478 6.66 0.00 0.00 4.00
2353 2379 1.909700 TTGCTCAATCAGGTTGGGTC 58.090 50.000 0.00 0.00 40.60 4.46
2411 2437 1.815757 ACCAAACACACCCTAGGAGT 58.184 50.000 11.48 5.60 0.00 3.85
2412 2438 2.980548 ACCAAACACACCCTAGGAGTA 58.019 47.619 11.48 0.00 0.00 2.59
2413 2439 2.904434 ACCAAACACACCCTAGGAGTAG 59.096 50.000 11.48 5.55 0.00 2.57
2414 2440 3.170717 CCAAACACACCCTAGGAGTAGA 58.829 50.000 11.48 0.00 0.00 2.59
2415 2441 3.195825 CCAAACACACCCTAGGAGTAGAG 59.804 52.174 11.48 0.00 0.00 2.43
2416 2442 4.087182 CAAACACACCCTAGGAGTAGAGA 58.913 47.826 11.48 0.00 0.00 3.10
2417 2443 4.611564 AACACACCCTAGGAGTAGAGAT 57.388 45.455 11.48 0.00 0.00 2.75
2418 2444 5.728937 AACACACCCTAGGAGTAGAGATA 57.271 43.478 11.48 0.00 0.00 1.98
2425 2451 5.134679 ACCCTAGGAGTAGAGATAAAGCAGA 59.865 44.000 11.48 0.00 0.00 4.26
2426 2452 5.710099 CCCTAGGAGTAGAGATAAAGCAGAG 59.290 48.000 11.48 0.00 0.00 3.35
2427 2453 5.183140 CCTAGGAGTAGAGATAAAGCAGAGC 59.817 48.000 1.05 0.00 0.00 4.09
2428 2454 3.568007 AGGAGTAGAGATAAAGCAGAGCG 59.432 47.826 0.00 0.00 0.00 5.03
2429 2455 3.316868 GGAGTAGAGATAAAGCAGAGCGT 59.683 47.826 0.00 0.00 0.00 5.07
2430 2456 4.533222 GAGTAGAGATAAAGCAGAGCGTC 58.467 47.826 0.00 0.00 0.00 5.19
2431 2457 2.880963 AGAGATAAAGCAGAGCGTCC 57.119 50.000 0.00 0.00 0.00 4.79
2432 2458 1.410882 AGAGATAAAGCAGAGCGTCCC 59.589 52.381 0.00 0.00 0.00 4.46
2433 2459 0.103208 AGATAAAGCAGAGCGTCCCG 59.897 55.000 0.00 0.00 0.00 5.14
2434 2460 0.102481 GATAAAGCAGAGCGTCCCGA 59.898 55.000 0.00 0.00 0.00 5.14
2435 2461 0.103208 ATAAAGCAGAGCGTCCCGAG 59.897 55.000 0.00 0.00 0.00 4.63
2436 2462 1.248785 TAAAGCAGAGCGTCCCGAGT 61.249 55.000 0.00 0.00 0.00 4.18
2437 2463 2.771763 AAAGCAGAGCGTCCCGAGTG 62.772 60.000 0.00 0.00 0.00 3.51
2438 2464 4.057428 GCAGAGCGTCCCGAGTGT 62.057 66.667 0.00 0.00 0.00 3.55
2439 2465 2.179517 CAGAGCGTCCCGAGTGTC 59.820 66.667 0.00 0.00 0.00 3.67
2440 2466 2.034376 AGAGCGTCCCGAGTGTCT 59.966 61.111 0.00 0.00 0.00 3.41
2441 2467 1.604023 AGAGCGTCCCGAGTGTCTT 60.604 57.895 0.00 0.00 0.00 3.01
2442 2468 1.179814 AGAGCGTCCCGAGTGTCTTT 61.180 55.000 0.00 0.00 0.00 2.52
2443 2469 0.319641 GAGCGTCCCGAGTGTCTTTT 60.320 55.000 0.00 0.00 0.00 2.27
2444 2470 0.319641 AGCGTCCCGAGTGTCTTTTC 60.320 55.000 0.00 0.00 0.00 2.29
2445 2471 0.319641 GCGTCCCGAGTGTCTTTTCT 60.320 55.000 0.00 0.00 0.00 2.52
2446 2472 1.699343 CGTCCCGAGTGTCTTTTCTC 58.301 55.000 0.00 0.00 0.00 2.87
2447 2473 1.269998 CGTCCCGAGTGTCTTTTCTCT 59.730 52.381 0.00 0.00 0.00 3.10
2448 2474 2.486982 CGTCCCGAGTGTCTTTTCTCTA 59.513 50.000 0.00 0.00 0.00 2.43
2449 2475 3.057736 CGTCCCGAGTGTCTTTTCTCTAA 60.058 47.826 0.00 0.00 0.00 2.10
2450 2476 4.558095 CGTCCCGAGTGTCTTTTCTCTAAA 60.558 45.833 0.00 0.00 0.00 1.85
2451 2477 4.924462 GTCCCGAGTGTCTTTTCTCTAAAG 59.076 45.833 0.00 0.00 43.82 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.760580 ATCTAGCCTACCACATGCTTC 57.239 47.619 0.00 0.00 36.57 3.86
148 150 7.912773 CCTATGAGCACGAATATACATCTACAG 59.087 40.741 0.00 0.00 0.00 2.74
180 182 9.948964 TTCATTGCTATCATACTAAGCATACAT 57.051 29.630 0.00 0.00 45.09 2.29
181 183 9.208022 GTTCATTGCTATCATACTAAGCATACA 57.792 33.333 0.00 0.00 45.09 2.29
251 254 3.057104 CAGACAATCCATGAAAGCAGCAA 60.057 43.478 0.00 0.00 0.00 3.91
279 282 5.878332 TTGATGGTAAGCATAACACACAG 57.122 39.130 0.00 0.00 29.75 3.66
355 358 1.367840 GCTGTCGGACAGGACAAGT 59.632 57.895 32.63 0.00 46.01 3.16
388 391 0.944386 GCTGCGAGTCCTTGACAAAA 59.056 50.000 0.00 0.00 34.60 2.44
446 449 3.708631 ACTGTCACATAGAGGGAATCAGG 59.291 47.826 0.00 0.00 0.00 3.86
511 521 1.073216 CTGCTACCTTGAGTGCGACG 61.073 60.000 0.00 0.00 0.00 5.12
512 522 1.355066 GCTGCTACCTTGAGTGCGAC 61.355 60.000 0.00 0.00 0.00 5.19
513 523 1.079819 GCTGCTACCTTGAGTGCGA 60.080 57.895 0.00 0.00 0.00 5.10
514 524 1.357258 CTGCTGCTACCTTGAGTGCG 61.357 60.000 0.00 0.00 0.00 5.34
607 617 4.361420 CACTAGAGATGAGCTCACACATG 58.639 47.826 20.97 10.42 46.45 3.21
641 651 0.853530 ACCTCCTTGAAGCCCTTGTT 59.146 50.000 0.00 0.00 0.00 2.83
673 684 1.771073 CGAACACCTGCTTCGCAACA 61.771 55.000 0.00 0.00 38.41 3.33
1159 1170 2.178325 TCTTCCTATCATGGACGGGGTA 59.822 50.000 0.00 0.00 35.58 3.69
1209 1223 5.416639 AGTCATGCTGCAAAAGACATTGATA 59.583 36.000 24.81 0.00 31.84 2.15
1239 1253 1.972872 CTGTTGCAACCTCCTTCACT 58.027 50.000 26.14 0.00 0.00 3.41
1332 1346 1.953231 CTGCCATGAGAGCCTCGTCA 61.953 60.000 0.00 0.00 32.35 4.35
1429 1444 1.792757 TTGCCCAACCAGCTCCTGAT 61.793 55.000 0.00 0.00 32.44 2.90
1658 1681 4.287326 TGATGTTAACCTACCACCACATCA 59.713 41.667 8.37 8.37 45.11 3.07
1679 1702 6.183361 ACAAGTTTAACCTAGCACTACCTTGA 60.183 38.462 0.00 0.00 0.00 3.02
1697 1720 6.728200 CATGATCATACGGCATAACAAGTTT 58.272 36.000 8.15 0.00 0.00 2.66
1704 1727 3.127376 GCATGCATGATCATACGGCATAA 59.873 43.478 30.64 5.02 42.81 1.90
1784 1807 4.039488 AGCTGAAGCAACAAATCAATGGAA 59.961 37.500 4.90 0.00 45.16 3.53
1858 1882 4.919774 TGAACTATAAACCCCTGAAGCA 57.080 40.909 0.00 0.00 0.00 3.91
1923 1947 5.962031 TGCCTAGTCTTGAACCCTCTATAAA 59.038 40.000 0.00 0.00 0.00 1.40
1924 1948 5.525484 TGCCTAGTCTTGAACCCTCTATAA 58.475 41.667 0.00 0.00 0.00 0.98
2045 2069 0.620556 AGCCCAAACTGACGATCCAT 59.379 50.000 0.00 0.00 0.00 3.41
2086 2110 0.034198 TGACGATGAACTGGGCGAAA 59.966 50.000 0.00 0.00 0.00 3.46
2145 2169 4.471386 ACACTAGTTGATGAGCTTACCCAT 59.529 41.667 0.00 0.00 0.00 4.00
2158 2182 5.069383 TGTGCTTACCTTGTACACTAGTTGA 59.931 40.000 0.00 0.00 32.49 3.18
2166 2190 4.456535 ACATGTTGTGCTTACCTTGTACA 58.543 39.130 0.00 0.00 0.00 2.90
2202 2227 1.011968 TACATGAACACGGCGTCTGC 61.012 55.000 10.85 0.00 41.71 4.26
2205 2230 1.680105 CGGTACATGAACACGGCGTC 61.680 60.000 10.85 0.00 0.00 5.19
2221 2246 0.816825 CATGCATTGGCTCTAGCGGT 60.817 55.000 0.00 0.00 43.26 5.68
2229 2254 0.397187 TTTGGTTGCATGCATTGGCT 59.603 45.000 23.37 0.00 41.91 4.75
2239 2264 1.274728 AGTGCACTTTGTTTGGTTGCA 59.725 42.857 15.25 0.00 0.00 4.08
2261 2287 6.806751 AGTGTCACTGCATTAGATAATACGT 58.193 36.000 4.21 0.00 0.00 3.57
2269 2295 4.160252 TGCATCTAGTGTCACTGCATTAGA 59.840 41.667 16.03 10.03 40.35 2.10
2279 2305 1.339055 GGTTGCCTGCATCTAGTGTCA 60.339 52.381 0.00 0.00 0.00 3.58
2312 2338 3.350219 AACAGACCCTAATGCGTCATT 57.650 42.857 9.46 9.46 37.80 2.57
2347 2373 1.403647 CGCATACACTTCTCGACCCAA 60.404 52.381 0.00 0.00 0.00 4.12
2353 2379 1.520174 CTGCATCGCATACACTTCTCG 59.480 52.381 0.00 0.00 38.13 4.04
2411 2437 2.623889 GGGACGCTCTGCTTTATCTCTA 59.376 50.000 0.00 0.00 0.00 2.43
2412 2438 1.410882 GGGACGCTCTGCTTTATCTCT 59.589 52.381 0.00 0.00 0.00 3.10
2413 2439 1.859383 GGGACGCTCTGCTTTATCTC 58.141 55.000 0.00 0.00 0.00 2.75
2428 2454 4.516365 TTAGAGAAAAGACACTCGGGAC 57.484 45.455 0.00 0.00 38.08 4.46
2429 2455 4.831155 TCTTTAGAGAAAAGACACTCGGGA 59.169 41.667 0.00 0.00 46.88 5.14
2430 2456 5.135508 TCTTTAGAGAAAAGACACTCGGG 57.864 43.478 0.00 0.00 46.88 5.14


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

AutoCloner maintained by Alex Coulton.