Multiple sequence alignment - TraesCS2B01G329200

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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 TraesCS2B01G329200 chr2B 100.000 3392 0 0 1 3392 472903048 472899657 0.000000e+00 6264
1 TraesCS2B01G329200 chr2B 91.811 635 39 3 1 622 780018969 780018335 0.000000e+00 872
2 TraesCS2B01G329200 chr2B 91.814 623 38 3 1 610 49897534 49898156 0.000000e+00 856
3 TraesCS2B01G329200 chr2B 89.760 625 39 4 1 613 41825684 41825073 0.000000e+00 776
4 TraesCS2B01G329200 chr2B 89.181 342 24 3 1 330 256325597 256325257 6.770000e-112 414
5 TraesCS2B01G329200 chr2D 96.652 2808 58 16 614 3392 398783998 398781198 0.000000e+00 4632
6 TraesCS2B01G329200 chr2D 96.212 264 10 0 1185 1448 642836772 642837035 1.870000e-117 433
7 TraesCS2B01G329200 chr2D 95.833 264 11 0 1185 1448 585381610 585381873 8.700000e-116 427
8 TraesCS2B01G329200 chr2D 93.827 162 3 2 937 1098 585381458 585381612 1.570000e-58 237
9 TraesCS2B01G329200 chr2D 92.121 165 5 2 936 1098 642836616 642836774 3.410000e-55 226
10 TraesCS2B01G329200 chr2A 95.535 1814 66 4 630 2437 536627626 536625822 0.000000e+00 2887
11 TraesCS2B01G329200 chr2A 83.246 949 103 45 2477 3392 536625738 536624813 0.000000e+00 821
12 TraesCS2B01G329200 chr3B 91.969 635 36 5 1 621 383691154 383690521 0.000000e+00 876
13 TraesCS2B01G329200 chr3B 91.746 630 38 7 1 616 792120181 792119552 0.000000e+00 863
14 TraesCS2B01G329200 chr3B 91.746 630 37 8 1 616 792159464 792158836 0.000000e+00 861
15 TraesCS2B01G329200 chr6B 91.811 635 39 3 1 622 715186655 715187289 0.000000e+00 872
16 TraesCS2B01G329200 chr6B 91.069 627 43 3 1 614 703296868 703296242 0.000000e+00 835
17 TraesCS2B01G329200 chr6B 74.018 866 201 23 1531 2384 518035158 518034305 7.020000e-87 331
18 TraesCS2B01G329200 chr6B 73.819 783 181 21 1618 2388 518032666 518031896 4.280000e-74 289
19 TraesCS2B01G329200 chr6B 92.105 76 4 1 1 74 169100102 169100027 4.630000e-19 106
20 TraesCS2B01G329200 chr4A 91.653 623 39 3 4 613 702648378 702647756 0.000000e+00 850
21 TraesCS2B01G329200 chr4A 87.312 465 25 5 1 452 674525497 674525940 5.050000e-138 501
22 TraesCS2B01G329200 chr4A 89.697 165 9 2 936 1098 347399516 347399674 1.600000e-48 204
23 TraesCS2B01G329200 chr4A 93.860 114 6 1 1341 1453 347399738 347399851 1.620000e-38 171
24 TraesCS2B01G329200 chr4A 96.000 75 3 0 1185 1259 347399672 347399746 4.600000e-24 122
25 TraesCS2B01G329200 chr1B 91.181 635 42 7 1 621 402040448 402041082 0.000000e+00 850
26 TraesCS2B01G329200 chr1B 88.889 387 29 5 1 375 562633814 562633430 6.630000e-127 464
27 TraesCS2B01G329200 chr1B 93.939 264 16 0 1185 1448 642618914 642618651 1.900000e-107 399
28 TraesCS2B01G329200 chr1B 89.759 166 9 5 935 1098 642619071 642618912 4.440000e-49 206
29 TraesCS2B01G329200 chr7B 90.952 641 42 6 1 626 125641528 125642167 0.000000e+00 848
30 TraesCS2B01G329200 chr4B 90.302 629 45 6 1 615 659615038 659614412 0.000000e+00 809
31 TraesCS2B01G329200 chr4B 79.915 234 38 6 3167 3392 646658290 646658522 2.710000e-36 163
32 TraesCS2B01G329200 chr6A 73.387 868 207 23 1529 2384 483741755 483740900 5.500000e-78 302
33 TraesCS2B01G329200 chr6A 72.819 791 191 21 1610 2388 483739188 483738410 7.270000e-62 248
34 TraesCS2B01G329200 chr5B 89.024 246 16 1 1 235 584322997 584323242 9.200000e-76 294
35 TraesCS2B01G329200 chr6D 72.970 788 189 21 1610 2384 343305798 343305022 1.560000e-63 254
36 TraesCS2B01G329200 chr4D 77.778 306 46 18 3100 3392 502411362 502411658 5.820000e-38 169
37 TraesCS2B01G329200 chr5A 77.617 277 45 13 3125 3392 685537253 685537521 5.860000e-33 152


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 TraesCS2B01G329200 chr2B 472899657 472903048 3391 True 6264 6264 100.0000 1 3392 1 chr2B.!!$R3 3391
1 TraesCS2B01G329200 chr2B 780018335 780018969 634 True 872 872 91.8110 1 622 1 chr2B.!!$R4 621
2 TraesCS2B01G329200 chr2B 49897534 49898156 622 False 856 856 91.8140 1 610 1 chr2B.!!$F1 609
3 TraesCS2B01G329200 chr2B 41825073 41825684 611 True 776 776 89.7600 1 613 1 chr2B.!!$R1 612
4 TraesCS2B01G329200 chr2D 398781198 398783998 2800 True 4632 4632 96.6520 614 3392 1 chr2D.!!$R1 2778
5 TraesCS2B01G329200 chr2A 536624813 536627626 2813 True 1854 2887 89.3905 630 3392 2 chr2A.!!$R1 2762
6 TraesCS2B01G329200 chr3B 383690521 383691154 633 True 876 876 91.9690 1 621 1 chr3B.!!$R1 620
7 TraesCS2B01G329200 chr3B 792119552 792120181 629 True 863 863 91.7460 1 616 1 chr3B.!!$R2 615
8 TraesCS2B01G329200 chr3B 792158836 792159464 628 True 861 861 91.7460 1 616 1 chr3B.!!$R3 615
9 TraesCS2B01G329200 chr6B 715186655 715187289 634 False 872 872 91.8110 1 622 1 chr6B.!!$F1 621
10 TraesCS2B01G329200 chr6B 703296242 703296868 626 True 835 835 91.0690 1 614 1 chr6B.!!$R2 613
11 TraesCS2B01G329200 chr6B 518031896 518035158 3262 True 310 331 73.9185 1531 2388 2 chr6B.!!$R3 857
12 TraesCS2B01G329200 chr4A 702647756 702648378 622 True 850 850 91.6530 4 613 1 chr4A.!!$R1 609
13 TraesCS2B01G329200 chr1B 402040448 402041082 634 False 850 850 91.1810 1 621 1 chr1B.!!$F1 620
14 TraesCS2B01G329200 chr7B 125641528 125642167 639 False 848 848 90.9520 1 626 1 chr7B.!!$F1 625
15 TraesCS2B01G329200 chr4B 659614412 659615038 626 True 809 809 90.3020 1 615 1 chr4B.!!$R1 614
16 TraesCS2B01G329200 chr6A 483738410 483741755 3345 True 275 302 73.1030 1529 2388 2 chr6A.!!$R1 859
17 TraesCS2B01G329200 chr6D 343305022 343305798 776 True 254 254 72.9700 1610 2384 1 chr6D.!!$R1 774

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
362 388 0.309612 GTGTCGTGTGGGCGAAAATT 59.690 50.0 0.00 0.0 42.82 1.82 F
810 841 0.673437 ATTGTCAGCCACCGTTTTGG 59.327 50.0 0.00 0.0 46.41 3.28 F
2184 2227 0.596600 TGCTCGAGTTCGCGTTCTTT 60.597 50.0 15.13 0.0 39.60 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 2227 1.629043 GGAGCACCCGGTAGATATCA 58.371 55.000 5.32 0.00 0.00 2.15 R
2260 4801 2.574929 GATGGGCACGTACGTGGA 59.425 61.111 40.17 13.47 45.49 4.02 R
3272 5933 2.945008 CGGCTAAGATCATGGCTTGAAA 59.055 45.455 7.20 0.00 38.03 2.69 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
152 165 2.293122 TCAAACAGTAGTTGCCATGTGC 59.707 45.455 0.00 0.00 38.17 4.57
169 182 2.081462 GTGCGTTTACCTAGTTGCCAT 58.919 47.619 0.00 0.00 0.00 4.40
213 226 4.201812 CCATGTACAGTTAATCGCAGTTGG 60.202 45.833 0.33 0.00 0.00 3.77
241 254 5.125417 GTGTGTTTATCTGGTTGCCACATAT 59.875 40.000 0.00 0.00 34.31 1.78
362 388 0.309612 GTGTCGTGTGGGCGAAAATT 59.690 50.000 0.00 0.00 42.82 1.82
469 498 1.166531 GGGCGTGTGAGCAAACTCTT 61.167 55.000 0.00 0.00 43.85 2.85
542 573 6.533819 TTCGTGTCAAGATTCGTGTAAAAT 57.466 33.333 0.00 0.00 0.00 1.82
693 724 2.753296 TGCCTTTCGAAGCAAAATTGG 58.247 42.857 9.42 0.33 35.69 3.16
810 841 0.673437 ATTGTCAGCCACCGTTTTGG 59.327 50.000 0.00 0.00 46.41 3.28
934 965 1.655329 GTCGCCGATCTCGAGGAAT 59.345 57.895 13.56 0.00 43.02 3.01
1037 1074 2.662596 GATCACCACCACCTCGCA 59.337 61.111 0.00 0.00 0.00 5.10
1038 1075 1.741770 GATCACCACCACCTCGCAC 60.742 63.158 0.00 0.00 0.00 5.34
1039 1076 2.172483 GATCACCACCACCTCGCACT 62.172 60.000 0.00 0.00 0.00 4.40
1040 1077 2.172483 ATCACCACCACCTCGCACTC 62.172 60.000 0.00 0.00 0.00 3.51
1041 1078 3.991051 ACCACCACCTCGCACTCG 61.991 66.667 0.00 0.00 0.00 4.18
1158 1198 2.497092 CTTCGTCGTCATCGCCACG 61.497 63.158 0.00 0.00 38.18 4.94
2046 2089 2.322830 GCCCTTCAACCGGTTCGTC 61.323 63.158 19.24 0.00 0.00 4.20
2184 2227 0.596600 TGCTCGAGTTCGCGTTCTTT 60.597 50.000 15.13 0.00 39.60 2.52
2475 5061 6.709846 GTGCTTATAATTGAGAAGAGATGCCT 59.290 38.462 0.00 0.00 0.00 4.75
2554 5140 6.970043 GCGCAATTGTTGGATAATAACACTTA 59.030 34.615 0.30 0.00 37.73 2.24
2670 5262 9.444600 TGTATCTACTGTCTGCGACATATATAA 57.555 33.333 10.93 2.11 41.94 0.98
2671 5263 9.923786 GTATCTACTGTCTGCGACATATATAAG 57.076 37.037 10.93 2.38 41.94 1.73
2714 5333 1.270147 ACCTACTGGCTTCGTTGTGAC 60.270 52.381 0.00 0.00 36.63 3.67
2717 5336 1.299541 ACTGGCTTCGTTGTGACTTG 58.700 50.000 0.00 0.00 0.00 3.16
2851 5470 3.549299 CTTGTTCATCAGTCACAAGCC 57.451 47.619 0.00 0.00 40.63 4.35
2896 5515 5.491982 ACCATAAAAGAACAGAGTAGCCAG 58.508 41.667 0.00 0.00 0.00 4.85
3117 5774 7.331026 TCCACCACATAAAAACAACAAATTGA 58.669 30.769 0.00 0.00 39.30 2.57
3213 5870 9.851686 ATATGCAGGATTACATGTCTTAAAGAA 57.148 29.630 0.00 0.00 0.00 2.52
3272 5933 3.118112 AGCCTATCACATGCTTAGCAACT 60.118 43.478 12.08 0.00 43.62 3.16
3316 5977 3.646162 ACCTCATGTAAAGACTGTCCACA 59.354 43.478 3.76 7.03 0.00 4.17
3382 6043 1.066908 GCCTCTGTCTTCTGATCCTCG 59.933 57.143 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 89 3.029320 ACTACGGTTTGATTACACGCA 57.971 42.857 0.00 0.00 0.00 5.24
152 165 3.071479 ACACATGGCAACTAGGTAAACG 58.929 45.455 0.00 0.00 37.61 3.60
213 226 3.244976 GCAACCAGATAAACACACATGC 58.755 45.455 0.00 0.00 0.00 4.06
337 363 0.319211 CGCCCACACGACACTCTTAA 60.319 55.000 0.00 0.00 34.06 1.85
362 388 1.739929 CATGCGGTGTGGCGAACTA 60.740 57.895 0.00 0.00 35.06 2.24
459 488 0.465460 TGGGCGTTGAAGAGTTTGCT 60.465 50.000 0.00 0.00 0.00 3.91
469 498 2.203139 CTGGTGTGTGGGCGTTGA 60.203 61.111 0.00 0.00 0.00 3.18
542 573 5.346551 CACGTTTAGATGGTCGTTGATTGTA 59.653 40.000 0.00 0.00 34.30 2.41
711 742 2.362077 GGATGTGTGACTGGTTGCTTTT 59.638 45.455 0.00 0.00 0.00 2.27
916 947 0.873054 TATTCCTCGAGATCGGCGAC 59.127 55.000 13.76 6.55 40.29 5.19
934 965 6.982160 ACTAGCTCTAGCAGTCTAGTAGTA 57.018 41.667 4.54 0.00 45.16 1.82
1037 1074 3.352222 GCTGTTGCTGCTGCGAGT 61.352 61.111 11.21 0.00 43.34 4.18
1114 1154 4.093952 CAGCTTGGCGTGCCGAAG 62.094 66.667 6.37 11.58 39.42 3.79
1158 1198 0.169894 GGTACACCGAGACGAGGTTC 59.830 60.000 0.00 0.00 40.59 3.62
2184 2227 1.629043 GGAGCACCCGGTAGATATCA 58.371 55.000 5.32 0.00 0.00 2.15
2260 4801 2.574929 GATGGGCACGTACGTGGA 59.425 61.111 40.17 13.47 45.49 4.02
2475 5061 6.821388 ACCATGTAAAATTTGCCACAGTTTA 58.179 32.000 0.00 0.00 0.00 2.01
2686 5305 5.927281 ACGAAGCCAGTAGGTATCTTAAA 57.073 39.130 0.00 0.00 37.19 1.52
2689 5308 3.514309 ACAACGAAGCCAGTAGGTATCTT 59.486 43.478 0.00 0.00 37.19 2.40
2714 5333 6.495706 TGATGATGCTTAGTACTCGTACAAG 58.504 40.000 0.00 0.00 38.48 3.16
2717 5336 6.496571 AGTTGATGATGCTTAGTACTCGTAC 58.503 40.000 0.00 0.00 36.35 3.67
2851 5470 4.665833 TCTGGGTCGTATGTTCTATTGG 57.334 45.455 0.00 0.00 0.00 3.16
2896 5515 2.213499 CTGTCTTGTGTGGTTCCTGTC 58.787 52.381 0.00 0.00 0.00 3.51
3117 5774 3.201487 TCCATCTTGCTCATGAACTGGAT 59.799 43.478 0.00 0.00 0.00 3.41
3213 5870 3.033909 AGCCTTTTCAGTTCCTTTGCTT 58.966 40.909 0.00 0.00 0.00 3.91
3272 5933 2.945008 CGGCTAAGATCATGGCTTGAAA 59.055 45.455 7.20 0.00 38.03 2.69
3316 5977 4.343814 ACCATTTCAAATGTCGGAAAGGTT 59.656 37.500 9.31 0.00 36.55 3.50


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

AutoCloner maintained by Alex Coulton.