Multiple sequence alignment - TraesCS3A01G163300

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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 TraesCS3A01G163300 chr3A 100.000 5285 0 0 1 5285 165421087 165415803 0.000000e+00 9760
1 TraesCS3A01G163300 chr3D 98.655 4386 54 5 254 4639 147817129 147821509 0.000000e+00 7768
2 TraesCS3A01G163300 chr3D 90.772 661 26 14 4638 5268 147821590 147822245 0.000000e+00 850
3 TraesCS3A01G163300 chr3D 86.700 203 12 7 1 202 147816942 147817130 1.490000e-50 211
4 TraesCS3A01G163300 chr3B 97.801 4366 66 14 1 4354 214564610 214560263 0.000000e+00 7504
5 TraesCS3A01G163300 chr3B 93.474 950 29 14 4351 5271 214560161 214559216 0.000000e+00 1380
6 TraesCS3A01G163300 chr2A 93.711 4134 204 31 555 4666 95991376 95995475 0.000000e+00 6143
7 TraesCS3A01G163300 chr2A 84.861 502 39 15 7 499 95990903 95991376 6.200000e-129 472
8 TraesCS3A01G163300 chr2D 93.534 4114 202 36 584 4666 97219730 97223810 0.000000e+00 6065
9 TraesCS3A01G163300 chr2D 85.324 586 51 16 7 580 97219081 97219643 1.650000e-159 573
10 TraesCS3A01G163300 chr2B 93.211 4154 227 34 537 4666 148237067 148241189 0.000000e+00 6058
11 TraesCS3A01G163300 chr1D 86.791 3369 427 15 940 4298 309078511 309081871 0.000000e+00 3740
12 TraesCS3A01G163300 chr1D 85.260 597 68 15 130 714 108107479 108106891 9.800000e-167 597
13 TraesCS3A01G163300 chr1B 86.574 3374 435 16 925 4287 418810313 418813679 0.000000e+00 3705
14 TraesCS3A01G163300 chr1B 85.012 427 50 8 130 543 158537238 158537663 6.330000e-114 422
15 TraesCS3A01G163300 chr1B 86.145 166 15 7 549 714 158539646 158539803 7.040000e-39 172
16 TraesCS3A01G163300 chr1A 86.526 3362 434 18 946 4298 388838782 388842133 0.000000e+00 3681
17 TraesCS3A01G163300 chr1A 85.092 597 70 15 130 714 111129736 111129147 4.560000e-165 592
18 TraesCS3A01G163300 chr5D 82.603 3219 516 33 1079 4275 46319141 46322337 0.000000e+00 2802
19 TraesCS3A01G163300 chr4B 83.019 265 31 9 458 714 329805701 329805443 1.480000e-55 228
20 TraesCS3A01G163300 chr4D 85.202 223 28 3 130 350 465774647 465774428 1.920000e-54 224
21 TraesCS3A01G163300 chr6B 88.235 85 9 1 551 634 620908267 620908183 3.370000e-17 100


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 TraesCS3A01G163300 chr3A 165415803 165421087 5284 True 9760.0 9760 100.000000 1 5285 1 chr3A.!!$R1 5284
1 TraesCS3A01G163300 chr3D 147816942 147822245 5303 False 2943.0 7768 92.042333 1 5268 3 chr3D.!!$F1 5267
2 TraesCS3A01G163300 chr3B 214559216 214564610 5394 True 4442.0 7504 95.637500 1 5271 2 chr3B.!!$R1 5270
3 TraesCS3A01G163300 chr2A 95990903 95995475 4572 False 3307.5 6143 89.286000 7 4666 2 chr2A.!!$F1 4659
4 TraesCS3A01G163300 chr2D 97219081 97223810 4729 False 3319.0 6065 89.429000 7 4666 2 chr2D.!!$F1 4659
5 TraesCS3A01G163300 chr2B 148237067 148241189 4122 False 6058.0 6058 93.211000 537 4666 1 chr2B.!!$F1 4129
6 TraesCS3A01G163300 chr1D 309078511 309081871 3360 False 3740.0 3740 86.791000 940 4298 1 chr1D.!!$F1 3358
7 TraesCS3A01G163300 chr1D 108106891 108107479 588 True 597.0 597 85.260000 130 714 1 chr1D.!!$R1 584
8 TraesCS3A01G163300 chr1B 418810313 418813679 3366 False 3705.0 3705 86.574000 925 4287 1 chr1B.!!$F1 3362
9 TraesCS3A01G163300 chr1B 158537238 158539803 2565 False 297.0 422 85.578500 130 714 2 chr1B.!!$F2 584
10 TraesCS3A01G163300 chr1A 388838782 388842133 3351 False 3681.0 3681 86.526000 946 4298 1 chr1A.!!$F1 3352
11 TraesCS3A01G163300 chr1A 111129147 111129736 589 True 592.0 592 85.092000 130 714 1 chr1A.!!$R1 584
12 TraesCS3A01G163300 chr5D 46319141 46322337 3196 False 2802.0 2802 82.603000 1079 4275 1 chr5D.!!$F1 3196

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
257 268 1.070445 ACTGGTCAGCACAGTCAGC 59.930 57.895 0.00 0.0 45.50 4.26 F
360 378 2.350522 AGTGAATTCAGTTAGCCAGCG 58.649 47.619 8.80 0.0 0.00 5.18 F
1598 3705 2.486191 CGCTGGCAAAGGAGGATCTTAT 60.486 50.000 0.00 0.0 33.73 1.73 F
2778 4885 1.583054 GTACTCGCATTCCATGGGAC 58.417 55.000 13.02 0.0 45.72 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 3705 1.152567 CAACCCAGGCCAAACTCCA 60.153 57.895 5.01 0.00 0.00 3.86 R
2340 4447 0.035630 GGCACACCTTCTCAGCTGAT 60.036 55.000 18.63 0.00 0.00 2.90 R
2951 5058 0.249826 GGCAGGAGAGATGCTGCTAC 60.250 60.000 19.00 2.58 44.25 3.58 R
4576 6816 3.096092 GGAAATGGTATCACAGGGCAAA 58.904 45.455 0.00 0.00 0.00 3.68 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
48 49 8.950210 AGATCGATGTTGATTCTTATGTTTTGT 58.050 29.630 0.54 0.00 0.00 2.83
50 51 9.988350 ATCGATGTTGATTCTTATGTTTTGTAC 57.012 29.630 0.00 0.00 0.00 2.90
65 66 2.717580 TGTACTATAATCTGGCGGCG 57.282 50.000 0.51 0.51 0.00 6.46
83 87 2.490991 GCGTTCTTCTAGTTTGTGGGT 58.509 47.619 0.00 0.00 0.00 4.51
170 175 4.646945 TCATAATCCGGCCTGCAAAATTTA 59.353 37.500 0.00 0.00 0.00 1.40
257 268 1.070445 ACTGGTCAGCACAGTCAGC 59.930 57.895 0.00 0.00 45.50 4.26
360 378 2.350522 AGTGAATTCAGTTAGCCAGCG 58.649 47.619 8.80 0.00 0.00 5.18
605 2693 8.763356 CATATATCTTCTTTCTCTTGTGCTGTC 58.237 37.037 0.00 0.00 0.00 3.51
708 2796 4.844349 ACATAACACCAGCTTACCTGAT 57.156 40.909 0.00 0.00 44.64 2.90
735 2828 6.062095 TCCATAATTAGCTTGTTAGAAGGCC 58.938 40.000 0.00 0.00 0.00 5.19
749 2842 7.957002 TGTTAGAAGGCCAATTTTGTTTGATA 58.043 30.769 5.01 0.00 0.00 2.15
848 2943 7.094508 TGAGTTTGTCAGCTATGTTTGAAAA 57.905 32.000 0.00 0.00 0.00 2.29
977 3077 3.457234 CTTGCCCTTTTGACACCTTTTC 58.543 45.455 0.00 0.00 0.00 2.29
1317 3418 3.548770 CATCAAGGCCTCAGCTGATAAA 58.451 45.455 18.63 0.00 33.44 1.40
1598 3705 2.486191 CGCTGGCAAAGGAGGATCTTAT 60.486 50.000 0.00 0.00 33.73 1.73
2340 4447 5.789574 ACATACCTGAGTTTGGGGATAAA 57.210 39.130 0.00 0.00 29.99 1.40
2778 4885 1.583054 GTACTCGCATTCCATGGGAC 58.417 55.000 13.02 0.00 45.72 4.46
2951 5058 1.377725 GTGATGGTCCAGCACCCAG 60.378 63.158 26.72 0.00 43.80 4.45
4329 6450 7.012421 ACAGAACTTTGTTGAGGTACTTGATTC 59.988 37.037 0.00 0.00 41.55 2.52
4453 6688 4.167319 AGTTTTTGTGCCTGGGGAAATAT 58.833 39.130 0.00 0.00 0.00 1.28
4574 6814 2.543641 GCCTATGAAATGTTTGCAGCC 58.456 47.619 0.00 0.00 0.00 4.85
4575 6815 2.167075 GCCTATGAAATGTTTGCAGCCT 59.833 45.455 0.00 0.00 0.00 4.58
4576 6816 3.368739 GCCTATGAAATGTTTGCAGCCTT 60.369 43.478 0.00 0.00 0.00 4.35
4859 7187 8.905660 AGATGATTCTGATTTTGACATCCTAG 57.094 34.615 0.00 0.00 34.96 3.02
4908 7236 2.092103 TCCTACAGGTGTTTTGCAAGGT 60.092 45.455 0.00 0.00 36.34 3.50
4942 7270 3.117701 TGGTTGTTCCTCCTGTTGATTCA 60.118 43.478 0.00 0.00 37.07 2.57
5017 7345 4.260170 ACTGCAGATGATTGAGAAGGAAC 58.740 43.478 23.35 0.00 0.00 3.62
5046 7374 7.406553 GTTTCCAAGCTTTTACCAATTTTGTC 58.593 34.615 0.00 0.00 0.00 3.18
5065 7393 8.463930 TTTTGTCTCTTTTTAGATGTGGATGT 57.536 30.769 0.00 0.00 0.00 3.06
5160 7507 2.092968 TGGCACTTGATCACATACTCCC 60.093 50.000 0.00 0.00 0.00 4.30
5161 7508 2.092968 GGCACTTGATCACATACTCCCA 60.093 50.000 0.00 0.00 0.00 4.37
5162 7509 3.434167 GGCACTTGATCACATACTCCCAT 60.434 47.826 0.00 0.00 0.00 4.00
5163 7510 3.562973 GCACTTGATCACATACTCCCATG 59.437 47.826 0.00 0.00 0.00 3.66
5164 7511 4.684214 GCACTTGATCACATACTCCCATGA 60.684 45.833 0.00 0.00 0.00 3.07
5165 7512 5.618236 CACTTGATCACATACTCCCATGAT 58.382 41.667 0.00 0.00 34.50 2.45
5166 7513 6.742363 GCACTTGATCACATACTCCCATGATA 60.742 42.308 0.00 0.00 31.96 2.15
5167 7514 7.392418 CACTTGATCACATACTCCCATGATAT 58.608 38.462 0.00 0.00 31.96 1.63
5168 7515 8.534496 CACTTGATCACATACTCCCATGATATA 58.466 37.037 0.00 0.00 31.96 0.86
5214 7566 4.836825 AGTAATGCTGTTATGCTGTCAGT 58.163 39.130 0.93 0.00 0.00 3.41
5215 7567 5.248640 AGTAATGCTGTTATGCTGTCAGTT 58.751 37.500 0.93 0.00 0.00 3.16
5240 7594 5.469373 TTTAGATGTGTCATTGTCGATGC 57.531 39.130 0.00 0.00 35.64 3.91
5272 7626 4.487714 TCTCAGTTATGTCATGTTCCCC 57.512 45.455 0.00 0.00 0.00 4.81
5273 7627 3.199946 TCTCAGTTATGTCATGTTCCCCC 59.800 47.826 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.889045 AGAACGCCGCCAGATTATAGTA 59.111 45.455 0.00 0.00 0.00 1.82
49 50 1.687123 AGAACGCCGCCAGATTATAGT 59.313 47.619 0.00 0.00 0.00 2.12
50 51 2.440539 AGAACGCCGCCAGATTATAG 57.559 50.000 0.00 0.00 0.00 1.31
65 66 4.124970 ACGAACCCACAAACTAGAAGAAC 58.875 43.478 0.00 0.00 0.00 3.01
83 87 0.759959 TCACTTGGGCCAACTACGAA 59.240 50.000 16.66 0.00 0.00 3.85
195 203 1.195115 TCGCCCTGTGCTAGAAAGAT 58.805 50.000 0.00 0.00 38.05 2.40
257 268 6.636850 ACGTAAGCTTAAAATTCAGCAAAGTG 59.363 34.615 7.99 0.00 45.62 3.16
605 2693 6.455360 AGGTTGGTATATTTGATGCAACAG 57.545 37.500 0.00 0.00 0.00 3.16
708 2796 7.509546 CCTTCTAACAAGCTAATTATGGAGGA 58.490 38.462 0.00 0.00 0.00 3.71
749 2842 5.839621 GCCATAAGCAAACATCATCAAGAT 58.160 37.500 0.00 0.00 42.97 2.40
848 2943 6.497624 AGTGCAATCTCCTTGAATATCTCT 57.502 37.500 0.00 0.00 36.97 3.10
977 3077 9.048446 ACATTTTCCTGAATGATCAACAAAAAG 57.952 29.630 0.00 2.01 38.93 2.27
1317 3418 3.584848 ACTGTTGAATCTCCCTAGCAAGT 59.415 43.478 0.00 0.00 0.00 3.16
1590 3697 3.217626 CAGGCCAAACTCCATAAGATCC 58.782 50.000 5.01 0.00 0.00 3.36
1598 3705 1.152567 CAACCCAGGCCAAACTCCA 60.153 57.895 5.01 0.00 0.00 3.86
2340 4447 0.035630 GGCACACCTTCTCAGCTGAT 60.036 55.000 18.63 0.00 0.00 2.90
2951 5058 0.249826 GGCAGGAGAGATGCTGCTAC 60.250 60.000 19.00 2.58 44.25 3.58
3054 5161 5.121105 TGATTGTAGATGCTGAATGTCAGG 58.879 41.667 7.34 0.00 44.43 3.86
3180 5287 7.826918 TCTTAGAATAGCCTCCTTAAGAGTC 57.173 40.000 3.36 0.00 41.47 3.36
4329 6450 5.960113 ACTATGCAGTGAGAAGTAGACAAG 58.040 41.667 0.00 0.00 32.25 3.16
4574 6814 4.381932 GGAAATGGTATCACAGGGCAAAAG 60.382 45.833 0.00 0.00 0.00 2.27
4575 6815 3.513515 GGAAATGGTATCACAGGGCAAAA 59.486 43.478 0.00 0.00 0.00 2.44
4576 6816 3.096092 GGAAATGGTATCACAGGGCAAA 58.904 45.455 0.00 0.00 0.00 3.68
4739 7066 8.229253 ACCTCGGGTTTAACATAATATTTTCC 57.771 34.615 0.00 0.00 27.29 3.13
4840 7168 7.855375 AGATCACTAGGATGTCAAAATCAGAA 58.145 34.615 0.00 0.00 36.00 3.02
4846 7174 4.466370 ACCGAGATCACTAGGATGTCAAAA 59.534 41.667 14.46 0.00 44.43 2.44
4859 7187 2.159170 CCAAGAGAGGAACCGAGATCAC 60.159 54.545 0.00 0.00 0.00 3.06
4908 7236 4.084287 AGGAACAACCAGTCGATACTACA 58.916 43.478 0.00 0.00 42.04 2.74
4942 7270 3.008813 CCTGATATAGGTGCCTCATGCTT 59.991 47.826 0.00 0.00 42.00 3.91
4961 7289 2.504367 ACGTTCCTTTCCATGTTCCTG 58.496 47.619 0.00 0.00 0.00 3.86
4962 7290 2.951229 ACGTTCCTTTCCATGTTCCT 57.049 45.000 0.00 0.00 0.00 3.36
4978 7306 2.213499 CAGTCAAGCTGGAGAAAACGT 58.787 47.619 0.00 0.00 41.42 3.99
5035 7363 8.143835 CCACATCTAAAAAGAGACAAAATTGGT 58.856 33.333 0.00 0.00 0.00 3.67
5046 7374 9.258826 CATCTCTACATCCACATCTAAAAAGAG 57.741 37.037 0.00 0.00 0.00 2.85
5240 7594 8.706936 CATGACATAACTGAGAAATAGATTCCG 58.293 37.037 0.00 0.00 38.94 4.30


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

AutoCloner maintained by Alex Coulton.