Multiple sequence alignment - TraesCS2D01G271800

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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 TraesCS2D01G271800 chr2D 100.000 2624 0 0 1 2624 335548520 335545897 0.000000e+00 4846.0
1 TraesCS2D01G271800 chr2A 96.215 1585 42 7 820 2387 446020725 446019142 0.000000e+00 2579.0
2 TraesCS2D01G271800 chr2A 89.387 848 62 5 1 821 446042977 446042131 0.000000e+00 1042.0
3 TraesCS2D01G271800 chr2A 94.857 175 7 1 2385 2557 446015108 446014934 3.330000e-69 272.0
4 TraesCS2D01G271800 chr2B 94.125 1583 81 7 433 2005 403563327 403561747 0.000000e+00 2398.0
5 TraesCS2D01G271800 chr2B 95.846 337 13 1 2019 2355 403561637 403561302 6.390000e-151 544.0
6 TraesCS2D01G271800 chr2B 92.800 250 16 2 191 438 403565315 403565066 6.900000e-96 361.0
7 TraesCS2D01G271800 chr2B 87.681 276 26 7 2354 2624 403559436 403559164 5.450000e-82 315.0
8 TraesCS2D01G271800 chr2B 90.865 208 18 1 1 207 403565601 403565394 7.150000e-71 278.0
9 TraesCS2D01G271800 chr2B 96.552 58 2 0 137 194 403565393 403565336 2.150000e-16 97.1
10 TraesCS2D01G271800 chr7A 95.918 49 2 0 2567 2615 734101414 734101366 2.160000e-11 80.5
11 TraesCS2D01G271800 chr3B 74.138 232 42 11 520 742 230946313 230946091 2.160000e-11 80.5
12 TraesCS2D01G271800 chr4A 97.674 43 1 0 2572 2614 696013810 696013768 1.010000e-09 75.0
13 TraesCS2D01G271800 chr1D 97.619 42 1 0 2571 2612 232142857 232142898 3.620000e-09 73.1
14 TraesCS2D01G271800 chr1A 97.619 42 1 0 2571 2612 316902596 316902555 3.620000e-09 73.1
15 TraesCS2D01G271800 chr7D 95.556 45 0 2 2572 2615 106367293 106367250 1.300000e-08 71.3
16 TraesCS2D01G271800 chr3D 95.556 45 0 2 2572 2615 77359467 77359424 1.300000e-08 71.3
17 TraesCS2D01G271800 chr3D 95.455 44 1 1 2566 2609 11821471 11821429 4.690000e-08 69.4
18 TraesCS2D01G271800 chr3A 90.385 52 2 3 2565 2615 428458125 428458174 6.060000e-07 65.8


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 TraesCS2D01G271800 chr2D 335545897 335548520 2623 True 4846.000000 4846 100.000000 1 2624 1 chr2D.!!$R1 2623
1 TraesCS2D01G271800 chr2A 446019142 446020725 1583 True 2579.000000 2579 96.215000 820 2387 1 chr2A.!!$R2 1567
2 TraesCS2D01G271800 chr2A 446042131 446042977 846 True 1042.000000 1042 89.387000 1 821 1 chr2A.!!$R3 820
3 TraesCS2D01G271800 chr2B 403559164 403565601 6437 True 665.516667 2398 92.978167 1 2624 6 chr2B.!!$R1 2623

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
87 88 0.753262 AGTCGACAACAAGGAGCACT 59.247 50.000 19.50 0.00 0.00 4.40 F
596 2440 1.073284 TGCGTTTTAAGGAAGAGGCCT 59.927 47.619 3.86 3.86 40.93 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 3206 0.532573 GTCGCCACTTCATCTGAGGA 59.467 55.0 0.00 0.00 0.00 3.71 R
1632 3484 1.086696 ACGGAGACAAATTGATGCCG 58.913 50.0 17.77 17.77 42.64 5.69 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
87 88 0.753262 AGTCGACAACAAGGAGCACT 59.247 50.000 19.50 0.00 0.00 4.40
227 324 5.221048 CGGACTTCCTGTCTTGTCAATTTTT 60.221 40.000 0.00 0.00 44.74 1.94
318 416 2.826128 ACCAACTCTCTCAACATAGCGA 59.174 45.455 0.00 0.00 0.00 4.93
323 421 4.739195 ACTCTCTCAACATAGCGACTTTC 58.261 43.478 0.00 0.00 0.00 2.62
374 474 2.309613 TGAGCCAATGAAAAGCACAGT 58.690 42.857 0.00 0.00 0.00 3.55
379 479 4.122046 GCCAATGAAAAGCACAGTCTTTT 58.878 39.130 9.28 9.28 45.77 2.27
402 502 8.433421 TTTCTTCTTTTTATATAGGGCGTCAG 57.567 34.615 0.00 0.00 0.00 3.51
461 2305 2.567169 CGAGATTATACCTGGCCATGGA 59.433 50.000 23.24 11.74 0.00 3.41
467 2311 1.080638 TACCTGGCCATGGAAAACCT 58.919 50.000 23.24 6.62 0.00 3.50
478 2322 1.368579 GAAAACCTGACCCGGTCGA 59.631 57.895 13.02 1.73 35.89 4.20
528 2372 2.755876 GCCAAGCCTGGGCCTAAC 60.756 66.667 4.53 0.00 45.87 2.34
596 2440 1.073284 TGCGTTTTAAGGAAGAGGCCT 59.927 47.619 3.86 3.86 40.93 5.19
598 2442 2.874457 GCGTTTTAAGGAAGAGGCCTGA 60.874 50.000 12.00 0.00 38.58 3.86
599 2443 2.742589 CGTTTTAAGGAAGAGGCCTGAC 59.257 50.000 12.00 0.00 38.58 3.51
658 2502 1.384222 CGTGCCTGGGCCTAAAATCC 61.384 60.000 4.53 0.00 41.09 3.01
769 2614 9.990360 TGAGATACACTTAACAACTGACATTAA 57.010 29.630 0.00 0.00 0.00 1.40
808 2653 6.884096 TTGTCAACAACACAAAAGCAATAG 57.116 33.333 0.00 0.00 37.70 1.73
942 2794 2.717809 GAGTCGAGTTTCACGGCGC 61.718 63.158 6.90 0.00 40.37 6.53
1564 3416 3.898627 CTGCTCTCCGTGAACGCGT 62.899 63.158 5.58 5.58 38.18 6.01
1632 3484 4.637977 CAGGATTTCTTCTAAGGGTGAAGC 59.362 45.833 0.00 0.00 40.31 3.86
1863 3720 6.654793 GAAACCTAGCTGAGTTTCTATGTG 57.345 41.667 24.92 0.00 45.37 3.21
1868 3725 5.128827 CCTAGCTGAGTTTCTATGTGGGTAA 59.871 44.000 0.00 0.00 0.00 2.85
1893 3750 9.524106 AACACAAAGTAAAGCTGGTTAATTTAC 57.476 29.630 3.92 0.00 38.89 2.01
1894 3751 8.909923 ACACAAAGTAAAGCTGGTTAATTTACT 58.090 29.630 3.92 5.66 46.46 2.24
1896 3753 8.287503 ACAAAGTAAAGCTGGTTAATTTACTCG 58.712 33.333 10.20 8.16 44.74 4.18
1897 3754 6.980051 AGTAAAGCTGGTTAATTTACTCGG 57.020 37.500 5.66 0.00 42.99 4.63
1898 3755 6.704310 AGTAAAGCTGGTTAATTTACTCGGA 58.296 36.000 5.66 0.00 42.99 4.55
2180 4136 3.620488 TCATATTCCTTGGGTTGTCAGC 58.380 45.455 0.00 0.00 0.00 4.26
2192 4148 4.644234 TGGGTTGTCAGCATATATGGTTTG 59.356 41.667 14.68 5.40 36.17 2.93
2201 4157 7.335422 GTCAGCATATATGGTTTGGAAGATAGG 59.665 40.741 14.68 0.09 36.17 2.57
2222 4178 3.083997 GCCTCTCCCGACCATGGT 61.084 66.667 19.89 19.89 0.00 3.55
2224 4180 1.991230 CCTCTCCCGACCATGGTTT 59.009 57.895 20.85 0.00 0.00 3.27
2230 4186 1.134220 TCCCGACCATGGTTTATCTGC 60.134 52.381 20.85 2.83 0.00 4.26
2251 4207 2.057137 TGGCTTGGTATGGATTGCTC 57.943 50.000 0.00 0.00 0.00 4.26
2331 4287 8.736244 GTGTTATTCCTGTATGTTTTGGTATGT 58.264 33.333 0.00 0.00 0.00 2.29
2407 6231 8.061237 ATGCAAGCATTTCATAGCAAGAATTGT 61.061 33.333 0.86 0.00 40.23 2.71
2428 6252 6.114221 TGTGCTAACAACAGTTACACTTTC 57.886 37.500 15.26 0.00 34.52 2.62
2446 6270 5.180868 CACTTTCTGAAGTTCTCTGGAATGG 59.819 44.000 4.17 3.64 43.48 3.16
2526 6350 1.226717 GACGCTACTCCGAGCTTGG 60.227 63.158 14.59 14.59 40.51 3.61
2527 6351 1.935327 GACGCTACTCCGAGCTTGGT 61.935 60.000 19.96 4.02 40.51 3.67
2528 6352 1.215647 CGCTACTCCGAGCTTGGTT 59.784 57.895 19.96 10.62 40.51 3.67
2529 6353 1.078759 CGCTACTCCGAGCTTGGTTG 61.079 60.000 19.96 15.48 40.51 3.77
2530 6354 0.246635 GCTACTCCGAGCTTGGTTGA 59.753 55.000 19.96 5.22 39.50 3.18
2531 6355 1.337823 GCTACTCCGAGCTTGGTTGAA 60.338 52.381 19.96 0.00 39.50 2.69
2532 6356 2.870435 GCTACTCCGAGCTTGGTTGAAA 60.870 50.000 19.96 0.00 39.50 2.69
2550 6374 6.416514 GTTGAAAGTTGAAACGTACTACCTG 58.583 40.000 0.00 0.00 0.00 4.00
2552 6376 6.804677 TGAAAGTTGAAACGTACTACCTGTA 58.195 36.000 0.00 0.00 0.00 2.74
2553 6377 7.264221 TGAAAGTTGAAACGTACTACCTGTAA 58.736 34.615 0.00 0.00 32.25 2.41
2554 6378 7.436080 TGAAAGTTGAAACGTACTACCTGTAAG 59.564 37.037 0.00 0.00 36.82 2.34
2555 6379 5.225642 AGTTGAAACGTACTACCTGTAAGC 58.774 41.667 0.00 0.00 34.66 3.09
2556 6380 5.010415 AGTTGAAACGTACTACCTGTAAGCT 59.990 40.000 0.00 0.00 34.66 3.74
2557 6381 6.207417 AGTTGAAACGTACTACCTGTAAGCTA 59.793 38.462 0.00 0.00 34.66 3.32
2558 6382 6.573664 TGAAACGTACTACCTGTAAGCTAA 57.426 37.500 0.00 0.00 34.66 3.09
2559 6383 7.161773 TGAAACGTACTACCTGTAAGCTAAT 57.838 36.000 0.00 0.00 34.66 1.73
2561 6385 8.184192 TGAAACGTACTACCTGTAAGCTAATAC 58.816 37.037 0.00 0.00 34.66 1.89
2562 6386 7.872113 AACGTACTACCTGTAAGCTAATACT 57.128 36.000 0.00 0.00 34.66 2.12
2563 6387 7.872113 ACGTACTACCTGTAAGCTAATACTT 57.128 36.000 0.00 0.00 34.66 2.24
2565 6389 8.743714 ACGTACTACCTGTAAGCTAATACTTTT 58.256 33.333 0.00 0.00 34.66 2.27
2586 6419 9.034544 ACTTTTAAACGTAGTGATCTAAAACGT 57.965 29.630 9.30 9.30 45.00 3.99
2587 6420 9.508495 CTTTTAAACGTAGTGATCTAAAACGTC 57.492 33.333 13.60 0.00 45.00 4.34
2588 6421 8.801715 TTTAAACGTAGTGATCTAAAACGTCT 57.198 30.769 13.60 5.89 45.00 4.18
2620 6453 8.682936 AATTTACAGAGGGAGTAATTGCTATG 57.317 34.615 0.00 0.00 32.07 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 2.034001 CCTTGTTGTCGACTCGTTGTTC 60.034 50.000 17.92 0.00 0.00 3.18
87 88 1.462432 TGGTTGGTCTGGGTGCCTA 60.462 57.895 0.00 0.00 0.00 3.93
124 125 3.253061 TGAACCATGGGTGCCCGA 61.253 61.111 18.09 0.00 35.34 5.14
318 416 7.556275 TGGTTTAATTTGAGTCACTGAGAAAGT 59.444 33.333 0.00 0.00 40.93 2.66
323 421 8.925161 TTTTTGGTTTAATTTGAGTCACTGAG 57.075 30.769 0.00 0.00 0.00 3.35
374 474 9.106070 GACGCCCTATATAAAAAGAAGAAAAGA 57.894 33.333 0.00 0.00 0.00 2.52
379 479 6.984474 CACTGACGCCCTATATAAAAAGAAGA 59.016 38.462 0.00 0.00 0.00 2.87
382 482 6.474140 TCACTGACGCCCTATATAAAAAGA 57.526 37.500 0.00 0.00 0.00 2.52
461 2305 1.070275 GTCGACCGGGTCAGGTTTT 59.930 57.895 25.80 0.00 46.09 2.43
467 2311 2.361610 GTAGGGTCGACCGGGTCA 60.362 66.667 27.68 11.07 46.96 4.02
515 2359 0.777446 TCAAAAGTTAGGCCCAGGCT 59.223 50.000 8.89 0.35 42.39 4.58
559 2403 1.532868 CGCAGATATGCTAAGCCCAAC 59.467 52.381 11.09 0.00 0.00 3.77
626 2470 4.211502 GCACGGCCCATCAATGGC 62.212 66.667 0.00 0.00 46.70 4.40
678 2522 1.299976 CGGCAGAAAACCTAGGCCT 59.700 57.895 11.78 11.78 42.43 5.19
769 2614 7.451731 TGTTGACAATAGGATTAGGGAGATT 57.548 36.000 0.00 0.00 0.00 2.40
1323 3175 2.070639 AGGTGTTTCCTCCTCTGCC 58.929 57.895 0.00 0.00 44.42 4.85
1344 3196 4.103153 ACTTCATCTGAGGACTTTTCACCA 59.897 41.667 0.00 0.00 0.00 4.17
1354 3206 0.532573 GTCGCCACTTCATCTGAGGA 59.467 55.000 0.00 0.00 0.00 3.71
1564 3416 3.141488 GGAGAGCTCGGCGAGGAA 61.141 66.667 35.03 1.92 0.00 3.36
1605 3457 5.785423 TCACCCTTAGAAGAAATCCTGAAGA 59.215 40.000 0.00 0.00 0.00 2.87
1632 3484 1.086696 ACGGAGACAAATTGATGCCG 58.913 50.000 17.77 17.77 42.64 5.69
1863 3720 3.887110 ACCAGCTTTACTTTGTGTTACCC 59.113 43.478 0.00 0.00 0.00 3.69
1868 3725 8.909923 AGTAAATTAACCAGCTTTACTTTGTGT 58.090 29.630 5.66 0.00 40.84 3.72
1893 3750 7.534239 GCAAGTAAGTTTATCAGTTTTTCCGAG 59.466 37.037 0.00 0.00 0.00 4.63
1894 3751 7.012515 TGCAAGTAAGTTTATCAGTTTTTCCGA 59.987 33.333 0.00 0.00 0.00 4.55
1896 3753 8.135529 AGTGCAAGTAAGTTTATCAGTTTTTCC 58.864 33.333 0.00 0.00 0.00 3.13
1897 3754 9.516314 AAGTGCAAGTAAGTTTATCAGTTTTTC 57.484 29.630 0.00 0.00 0.00 2.29
1898 3755 9.301153 CAAGTGCAAGTAAGTTTATCAGTTTTT 57.699 29.630 0.00 0.00 0.00 1.94
2180 4136 7.225538 GCGATCCTATCTTCCAAACCATATATG 59.774 40.741 5.68 5.68 0.00 1.78
2201 4157 2.203771 ATGGTCGGGAGAGGCGATC 61.204 63.158 0.00 0.00 41.26 3.69
2222 4178 3.890756 CCATACCAAGCCATGCAGATAAA 59.109 43.478 0.00 0.00 0.00 1.40
2224 4180 2.710471 TCCATACCAAGCCATGCAGATA 59.290 45.455 0.00 0.00 0.00 1.98
2230 4186 2.295349 GAGCAATCCATACCAAGCCATG 59.705 50.000 0.00 0.00 0.00 3.66
2251 4207 6.017275 GTCATGATCATAGAAAAAGAGCAGGG 60.017 42.308 8.15 0.00 31.32 4.45
2331 4287 5.361571 TCACGACCAATAGCTGAACCTATAA 59.638 40.000 0.00 0.00 0.00 0.98
2387 6211 5.385396 GCACAATTCTTGCTATGAAATGC 57.615 39.130 1.90 0.00 37.00 3.56
2421 6245 5.359194 TTCCAGAGAACTTCAGAAAGTGT 57.641 39.130 0.00 0.00 45.07 3.55
2428 6252 3.063510 TGCCATTCCAGAGAACTTCAG 57.936 47.619 0.00 0.00 33.97 3.02
2526 6350 6.036408 ACAGGTAGTACGTTTCAACTTTCAAC 59.964 38.462 0.00 0.00 0.00 3.18
2527 6351 6.108015 ACAGGTAGTACGTTTCAACTTTCAA 58.892 36.000 0.00 0.00 0.00 2.69
2528 6352 5.663456 ACAGGTAGTACGTTTCAACTTTCA 58.337 37.500 0.00 0.00 0.00 2.69
2529 6353 7.568315 GCTTACAGGTAGTACGTTTCAACTTTC 60.568 40.741 0.00 0.00 30.91 2.62
2530 6354 6.201615 GCTTACAGGTAGTACGTTTCAACTTT 59.798 38.462 0.00 0.00 30.91 2.66
2531 6355 5.693555 GCTTACAGGTAGTACGTTTCAACTT 59.306 40.000 0.00 0.00 30.91 2.66
2532 6356 5.010415 AGCTTACAGGTAGTACGTTTCAACT 59.990 40.000 0.00 0.00 30.91 3.16
2561 6385 9.508495 GACGTTTTAGATCACTACGTTTAAAAG 57.492 33.333 13.78 0.00 32.06 2.27
2562 6386 9.248291 AGACGTTTTAGATCACTACGTTTAAAA 57.752 29.630 13.78 3.47 32.06 1.52
2563 6387 8.801715 AGACGTTTTAGATCACTACGTTTAAA 57.198 30.769 13.78 0.00 32.06 1.52


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

AutoCloner maintained by Alex Coulton.