Multiple sequence alignment - TraesCS1B01G123300

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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 TraesCS1B01G123300 chr1B 100.000 2450 0 0 1 2450 149476215 149473766 0.000000e+00 4525
1 TraesCS1B01G123300 chr1B 93.179 2463 129 22 1 2450 556072798 556070362 0.000000e+00 3581
2 TraesCS1B01G123300 chr1B 93.139 1822 103 19 494 2308 287516947 287518753 0.000000e+00 2652
3 TraesCS1B01G123300 chr1B 89.189 111 7 4 2345 2450 200997517 200997627 1.530000e-27 134
4 TraesCS1B01G123300 chr7B 90.913 2465 175 31 1 2450 594477267 594474837 0.000000e+00 3265
5 TraesCS1B01G123300 chr7B 90.913 2465 175 31 1 2450 594481654 594479224 0.000000e+00 3265
6 TraesCS1B01G123300 chr7B 89.189 111 7 4 2345 2450 449126399 449126509 1.530000e-27 134
7 TraesCS1B01G123300 chr6B 90.810 2470 176 31 1 2450 115926522 115924084 0.000000e+00 3256
8 TraesCS1B01G123300 chr6B 85.727 2291 296 27 1 2271 314111581 314109302 0.000000e+00 2390
9 TraesCS1B01G123300 chr4B 90.068 2346 200 27 2 2338 155757745 155760066 0.000000e+00 3011
10 TraesCS1B01G123300 chr4B 90.112 1972 167 18 494 2450 534533689 534535647 0.000000e+00 2536
11 TraesCS1B01G123300 chr4B 87.292 1204 138 10 1 1201 376028093 376029284 0.000000e+00 1362
12 TraesCS1B01G123300 chr4B 89.286 112 5 5 2345 2450 350532001 350531891 1.530000e-27 134
13 TraesCS1B01G123300 chr4B 89.189 111 7 4 2345 2450 569594379 569594489 1.530000e-27 134
14 TraesCS1B01G123300 chr3B 93.297 1820 106 14 494 2308 195665854 195667662 0.000000e+00 2671
15 TraesCS1B01G123300 chr2B 89.913 1963 178 16 494 2450 388226589 388228537 0.000000e+00 2510
16 TraesCS1B01G123300 chr2B 89.189 111 7 4 2345 2450 684309331 684309221 1.530000e-27 134
17 TraesCS1B01G123300 chr2B 88.991 109 7 4 2347 2450 749456185 749456293 1.980000e-26 130
18 TraesCS1B01G123300 chr2B 87.387 111 9 4 2345 2450 637507412 637507302 3.310000e-24 122
19 TraesCS1B01G123300 chr2A 87.642 1230 133 12 1 1227 100908394 100907181 0.000000e+00 1411
20 TraesCS1B01G123300 chr2A 87.792 983 109 7 1 982 300391199 300392171 0.000000e+00 1140
21 TraesCS1B01G123300 chr6D 92.121 495 39 0 1 495 238802087 238802581 0.000000e+00 699
22 TraesCS1B01G123300 chr5B 93.750 464 29 0 1 464 373340503 373340966 0.000000e+00 697
23 TraesCS1B01G123300 chr5B 93.534 464 30 0 1 464 373348602 373349065 0.000000e+00 691


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 TraesCS1B01G123300 chr1B 149473766 149476215 2449 True 4525 4525 100.000 1 2450 1 chr1B.!!$R1 2449
1 TraesCS1B01G123300 chr1B 556070362 556072798 2436 True 3581 3581 93.179 1 2450 1 chr1B.!!$R2 2449
2 TraesCS1B01G123300 chr1B 287516947 287518753 1806 False 2652 2652 93.139 494 2308 1 chr1B.!!$F2 1814
3 TraesCS1B01G123300 chr7B 594474837 594481654 6817 True 3265 3265 90.913 1 2450 2 chr7B.!!$R1 2449
4 TraesCS1B01G123300 chr6B 115924084 115926522 2438 True 3256 3256 90.810 1 2450 1 chr6B.!!$R1 2449
5 TraesCS1B01G123300 chr6B 314109302 314111581 2279 True 2390 2390 85.727 1 2271 1 chr6B.!!$R2 2270
6 TraesCS1B01G123300 chr4B 155757745 155760066 2321 False 3011 3011 90.068 2 2338 1 chr4B.!!$F1 2336
7 TraesCS1B01G123300 chr4B 534533689 534535647 1958 False 2536 2536 90.112 494 2450 1 chr4B.!!$F3 1956
8 TraesCS1B01G123300 chr4B 376028093 376029284 1191 False 1362 1362 87.292 1 1201 1 chr4B.!!$F2 1200
9 TraesCS1B01G123300 chr3B 195665854 195667662 1808 False 2671 2671 93.297 494 2308 1 chr3B.!!$F1 1814
10 TraesCS1B01G123300 chr2B 388226589 388228537 1948 False 2510 2510 89.913 494 2450 1 chr2B.!!$F1 1956
11 TraesCS1B01G123300 chr2A 100907181 100908394 1213 True 1411 1411 87.642 1 1227 1 chr2A.!!$R1 1226
12 TraesCS1B01G123300 chr2A 300391199 300392171 972 False 1140 1140 87.792 1 982 1 chr2A.!!$F1 981

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
758 5156 0.250295 CCAACACCGTCACATCCAGT 60.25 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 6320 5.070446 TGCTAATCCATAGTGGTTAGGTGAG 59.93 44.0 14.42 0.0 39.03 3.51 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
53 54 1.587613 CTCGGCAGCGAGAAGTAGC 60.588 63.158 6.54 0.00 38.18 3.58
178 179 0.981183 TCAGCGTGGTTACTCCCATT 59.019 50.000 0.00 0.00 36.74 3.16
182 183 1.207329 GCGTGGTTACTCCCATTCTCT 59.793 52.381 0.00 0.00 36.74 3.10
256 258 1.492176 ACTCATATGGGTGGCCTGAAG 59.508 52.381 7.64 0.00 0.00 3.02
324 326 8.570488 CCATTTGCTTCTAGTAATCATATGCAA 58.430 33.333 0.00 0.00 36.35 4.08
414 416 0.900421 CTCAGCACCAGGAGATGTGA 59.100 55.000 1.78 0.00 34.37 3.58
419 421 1.545428 GCACCAGGAGATGTGACCAAA 60.545 52.381 0.00 0.00 34.37 3.28
466 468 2.948979 CAACCAACAACTTCAGCACCTA 59.051 45.455 0.00 0.00 0.00 3.08
467 469 3.290948 ACCAACAACTTCAGCACCTAA 57.709 42.857 0.00 0.00 0.00 2.69
468 470 3.832527 ACCAACAACTTCAGCACCTAAT 58.167 40.909 0.00 0.00 0.00 1.73
469 471 3.569701 ACCAACAACTTCAGCACCTAATG 59.430 43.478 0.00 0.00 0.00 1.90
470 472 3.820467 CCAACAACTTCAGCACCTAATGA 59.180 43.478 0.00 0.00 0.00 2.57
471 473 4.083110 CCAACAACTTCAGCACCTAATGAG 60.083 45.833 0.00 0.00 0.00 2.90
472 474 4.357918 ACAACTTCAGCACCTAATGAGT 57.642 40.909 0.00 0.00 0.00 3.41
473 475 4.319177 ACAACTTCAGCACCTAATGAGTC 58.681 43.478 0.00 0.00 0.00 3.36
474 476 3.238108 ACTTCAGCACCTAATGAGTCG 57.762 47.619 0.00 0.00 0.00 4.18
565 576 4.162320 TGAGTCTTGAGTTCACTTGGAGTT 59.838 41.667 0.00 0.00 0.00 3.01
713 724 0.528017 CTAGAGCTGAGTGTTGCCGA 59.472 55.000 0.00 0.00 0.00 5.54
758 5156 0.250295 CCAACACCGTCACATCCAGT 60.250 55.000 0.00 0.00 0.00 4.00
781 5179 3.453717 TGAGCAAGATAGCAAGAGTCCAT 59.546 43.478 0.00 0.00 36.85 3.41
895 5293 7.526041 AGACTCATCATCTACTACTCCTGAAT 58.474 38.462 0.00 0.00 0.00 2.57
922 5320 4.841422 ACAAGAAGCTGCTGTAGATGAAT 58.159 39.130 1.35 0.00 0.00 2.57
977 5375 1.273327 ACATGAGCGTGATGTGTCAGA 59.727 47.619 0.00 0.00 34.36 3.27
1083 5482 7.967890 AGATTTGAAAAACTATTTGCTTGGG 57.032 32.000 0.00 0.00 0.00 4.12
1197 5596 5.579753 ATCATTCCCATGCTAGTCTTGAT 57.420 39.130 0.00 0.00 0.00 2.57
1351 5750 2.224079 TGCATTGTCTCTTTCGTTGAGC 59.776 45.455 0.00 0.00 0.00 4.26
1514 5921 5.449725 GGCATGAGGATAGAGAAGCAAAAAC 60.450 44.000 0.00 0.00 0.00 2.43
1807 6219 2.698855 TGAGTGCTCAAATCCCTAGC 57.301 50.000 0.00 0.00 36.53 3.42
1906 6320 1.604278 GTGTGTTCCCTTTGAGAGCAC 59.396 52.381 1.38 1.38 43.41 4.40
2128 6543 7.236847 TGGTTGGATCGGATAGGAGTAAATTAT 59.763 37.037 0.00 0.00 0.00 1.28
2129 6544 8.755977 GGTTGGATCGGATAGGAGTAAATTATA 58.244 37.037 0.00 0.00 0.00 0.98
2257 6684 4.038763 GTGTATACCATGTTCTCGGGATCA 59.961 45.833 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 3.645687 AGAGCTAGGCCTATCCTCAAAAG 59.354 47.826 28.57 13.93 43.20 2.27
178 179 3.760151 CTCATGCCAAAACAATCCAGAGA 59.240 43.478 0.00 0.00 0.00 3.10
182 183 2.250031 AGCTCATGCCAAAACAATCCA 58.750 42.857 0.00 0.00 40.80 3.41
256 258 5.127194 TGCTCCTATATGACATATTCGGGTC 59.873 44.000 13.09 9.66 34.63 4.46
324 326 6.556495 TGCTCTCCTCTTCATACATAAATCCT 59.444 38.462 0.00 0.00 0.00 3.24
332 334 4.284490 AGTTGTTGCTCTCCTCTTCATACA 59.716 41.667 0.00 0.00 0.00 2.29
414 416 4.508584 GGAGGACCATTTAACTCCTTTGGT 60.509 45.833 0.00 0.00 44.74 3.67
457 459 1.557099 ACCGACTCATTAGGTGCTGA 58.443 50.000 0.00 0.00 36.81 4.26
466 468 3.701542 TGAGATTGCTCTACCGACTCATT 59.298 43.478 0.00 0.00 41.84 2.57
467 469 3.291584 TGAGATTGCTCTACCGACTCAT 58.708 45.455 0.00 0.00 41.84 2.90
468 470 2.723273 TGAGATTGCTCTACCGACTCA 58.277 47.619 0.00 0.00 41.84 3.41
469 471 3.067461 ACATGAGATTGCTCTACCGACTC 59.933 47.826 0.00 0.00 41.84 3.36
470 472 3.027412 ACATGAGATTGCTCTACCGACT 58.973 45.455 0.00 0.00 41.84 4.18
471 473 3.119291 CACATGAGATTGCTCTACCGAC 58.881 50.000 0.00 0.00 41.84 4.79
472 474 2.481969 GCACATGAGATTGCTCTACCGA 60.482 50.000 0.00 0.00 41.84 4.69
473 475 1.863454 GCACATGAGATTGCTCTACCG 59.137 52.381 0.00 0.00 41.84 4.02
474 476 2.910199 TGCACATGAGATTGCTCTACC 58.090 47.619 0.00 0.00 41.84 3.18
509 520 4.864806 GCTTGTCTATGTCATCGAACTCAA 59.135 41.667 0.00 0.00 0.00 3.02
565 576 9.676129 AACCTTCCTAATAGGATCATCTTTAGA 57.324 33.333 10.21 0.00 45.34 2.10
595 606 9.225436 ACTTTTGATCTTCTTCATTTCCTCTAC 57.775 33.333 0.00 0.00 0.00 2.59
618 629 4.348168 TCTTCCACTAGCTCTTTTCCACTT 59.652 41.667 0.00 0.00 0.00 3.16
713 724 4.103785 CCTCACATGTATCAAGGGGAATCT 59.896 45.833 0.00 0.00 0.00 2.40
758 5156 3.261643 TGGACTCTTGCTATCTTGCTCAA 59.738 43.478 0.00 0.00 0.00 3.02
781 5179 6.726299 TCTTCAATCTGAGGTCTTTCTTCCTA 59.274 38.462 0.00 0.00 33.83 2.94
895 5293 5.977489 TCTACAGCAGCTTCTTGTACTTA 57.023 39.130 0.00 0.00 0.00 2.24
922 5320 5.824624 GCCAATGAATCTCAGGTTCTTCATA 59.175 40.000 0.00 0.00 37.35 2.15
977 5375 6.078456 TGTCATCAAGAGGATTGGGTAAAT 57.922 37.500 0.00 0.00 32.57 1.40
1083 5482 2.923121 ACAGGGTGTGTATGATCATGC 58.077 47.619 18.72 17.35 37.75 4.06
1245 5644 5.897377 AAAGCACATGTTTAGGATGGTAC 57.103 39.130 0.00 0.00 0.00 3.34
1351 5750 1.517242 AGCAAGAACCTGAAAGAGCG 58.483 50.000 0.00 0.00 34.07 5.03
1807 6219 9.334693 GCAGAAATGATTAAGTTTTCTAGTGTG 57.665 33.333 8.78 2.03 37.55 3.82
1906 6320 5.070446 TGCTAATCCATAGTGGTTAGGTGAG 59.930 44.000 14.42 0.00 39.03 3.51
2257 6684 5.836024 TCTTACCAAAGGAACATACCACT 57.164 39.130 0.00 0.00 33.22 4.00
2381 6813 6.375455 TCCTAAAGAGAGCATGATCCAAAAAC 59.625 38.462 7.49 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.