Multiple sequence alignment - TraesCS3A01G412200

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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 TraesCS3A01G412200 chr3A 100.000 2387 0 0 1 2387 655897873 655895487 0.000000e+00 4409
1 TraesCS3A01G412200 chr3A 93.459 1437 88 2 824 2254 655628867 655630303 0.000000e+00 2128
2 TraesCS3A01G412200 chr3A 87.573 1368 150 13 898 2251 636541281 636539920 0.000000e+00 1567
3 TraesCS3A01G412200 chr3B 92.393 1722 87 25 101 1790 684761972 684763681 0.000000e+00 2414
4 TraesCS3A01G412200 chr3B 86.886 1365 151 14 898 2251 658487160 658488507 0.000000e+00 1504
5 TraesCS3A01G412200 chr3B 97.436 624 14 2 1765 2387 684763718 684764340 0.000000e+00 1062
6 TraesCS3A01G412200 chr3D 95.740 1432 59 2 824 2254 520322483 520321053 0.000000e+00 2305
7 TraesCS3A01G412200 chr3D 87.443 876 95 12 898 1764 497865434 497866303 0.000000e+00 994
8 TraesCS3A01G412200 chr3D 88.048 502 55 5 1753 2251 497866324 497866823 7.350000e-165 590
9 TraesCS3A01G412200 chr3D 81.778 675 81 23 9 653 40506252 40505590 5.840000e-146 527
10 TraesCS3A01G412200 chr3D 86.331 139 19 0 6 144 4856559 4856421 4.110000e-33 152
11 TraesCS3A01G412200 chr3D 89.516 124 7 2 2264 2387 520320846 520320729 4.110000e-33 152
12 TraesCS3A01G412200 chr4D 85.215 859 85 18 1 821 484350650 484351504 0.000000e+00 845
13 TraesCS3A01G412200 chr1D 85.985 792 72 19 72 826 124916773 124917562 0.000000e+00 811
14 TraesCS3A01G412200 chr7A 83.429 869 96 18 2 827 117352759 117353622 0.000000e+00 763
15 TraesCS3A01G412200 chr7A 82.846 752 89 23 102 820 311306949 311307693 2.590000e-179 638
16 TraesCS3A01G412200 chr5A 77.601 1317 255 28 952 2253 401317394 401316103 0.000000e+00 761
17 TraesCS3A01G412200 chr7D 83.718 823 91 19 41 827 107809280 107810095 0.000000e+00 737
18 TraesCS3A01G412200 chr7D 84.691 712 89 13 135 826 75081421 75080710 0.000000e+00 693
19 TraesCS3A01G412200 chr6A 84.924 723 68 14 120 820 256467503 256466800 0.000000e+00 693
20 TraesCS3A01G412200 chr6A 80.200 601 88 13 72 642 68943834 68943235 2.840000e-114 422
21 TraesCS3A01G412200 chr5B 92.678 478 32 1 352 826 332964590 332965067 0.000000e+00 686
22 TraesCS3A01G412200 chr5B 83.217 143 22 2 2 144 336400594 336400454 1.930000e-26 130
23 TraesCS3A01G412200 chr2A 81.412 850 130 19 5 830 30751684 30750839 0.000000e+00 669
24 TraesCS3A01G412200 chr5D 83.711 706 78 19 157 827 241956161 241956864 1.200000e-177 632
25 TraesCS3A01G412200 chr5D 77.778 666 96 35 5 643 24123968 24123328 1.740000e-96 363
26 TraesCS3A01G412200 chr5D 83.041 171 24 5 6 175 191901337 191901171 1.480000e-32 150
27 TraesCS3A01G412200 chr1B 89.641 473 45 2 351 820 645355380 645355851 1.220000e-167 599
28 TraesCS3A01G412200 chr1B 82.703 185 25 7 6 189 120042803 120042625 8.830000e-35 158
29 TraesCS3A01G412200 chr7B 81.195 686 83 21 6 648 695919199 695919881 5.890000e-141 510
30 TraesCS3A01G412200 chrUn 74.832 1041 229 25 1067 2099 287225085 287226100 7.830000e-120 440
31 TraesCS3A01G412200 chrUn 74.832 1041 229 25 1067 2099 287476983 287477998 7.830000e-120 440
32 TraesCS3A01G412200 chr4A 79.935 618 84 23 72 649 210204530 210203913 3.670000e-113 418
33 TraesCS3A01G412200 chr1A 87.791 172 17 4 5 175 208907113 208906945 5.200000e-47 198
34 TraesCS3A01G412200 chr4B 83.041 171 27 2 2 172 347388656 347388488 1.140000e-33 154
35 TraesCS3A01G412200 chr2D 83.140 172 22 6 6 175 195729579 195729745 1.480000e-32 150


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 TraesCS3A01G412200 chr3A 655895487 655897873 2386 True 4409.0 4409 100.0000 1 2387 1 chr3A.!!$R2 2386
1 TraesCS3A01G412200 chr3A 655628867 655630303 1436 False 2128.0 2128 93.4590 824 2254 1 chr3A.!!$F1 1430
2 TraesCS3A01G412200 chr3A 636539920 636541281 1361 True 1567.0 1567 87.5730 898 2251 1 chr3A.!!$R1 1353
3 TraesCS3A01G412200 chr3B 684761972 684764340 2368 False 1738.0 2414 94.9145 101 2387 2 chr3B.!!$F2 2286
4 TraesCS3A01G412200 chr3B 658487160 658488507 1347 False 1504.0 1504 86.8860 898 2251 1 chr3B.!!$F1 1353
5 TraesCS3A01G412200 chr3D 520320729 520322483 1754 True 1228.5 2305 92.6280 824 2387 2 chr3D.!!$R3 1563
6 TraesCS3A01G412200 chr3D 497865434 497866823 1389 False 792.0 994 87.7455 898 2251 2 chr3D.!!$F1 1353
7 TraesCS3A01G412200 chr3D 40505590 40506252 662 True 527.0 527 81.7780 9 653 1 chr3D.!!$R2 644
8 TraesCS3A01G412200 chr4D 484350650 484351504 854 False 845.0 845 85.2150 1 821 1 chr4D.!!$F1 820
9 TraesCS3A01G412200 chr1D 124916773 124917562 789 False 811.0 811 85.9850 72 826 1 chr1D.!!$F1 754
10 TraesCS3A01G412200 chr7A 117352759 117353622 863 False 763.0 763 83.4290 2 827 1 chr7A.!!$F1 825
11 TraesCS3A01G412200 chr7A 311306949 311307693 744 False 638.0 638 82.8460 102 820 1 chr7A.!!$F2 718
12 TraesCS3A01G412200 chr5A 401316103 401317394 1291 True 761.0 761 77.6010 952 2253 1 chr5A.!!$R1 1301
13 TraesCS3A01G412200 chr7D 107809280 107810095 815 False 737.0 737 83.7180 41 827 1 chr7D.!!$F1 786
14 TraesCS3A01G412200 chr7D 75080710 75081421 711 True 693.0 693 84.6910 135 826 1 chr7D.!!$R1 691
15 TraesCS3A01G412200 chr6A 256466800 256467503 703 True 693.0 693 84.9240 120 820 1 chr6A.!!$R2 700
16 TraesCS3A01G412200 chr6A 68943235 68943834 599 True 422.0 422 80.2000 72 642 1 chr6A.!!$R1 570
17 TraesCS3A01G412200 chr2A 30750839 30751684 845 True 669.0 669 81.4120 5 830 1 chr2A.!!$R1 825
18 TraesCS3A01G412200 chr5D 241956161 241956864 703 False 632.0 632 83.7110 157 827 1 chr5D.!!$F1 670
19 TraesCS3A01G412200 chr5D 24123328 24123968 640 True 363.0 363 77.7780 5 643 1 chr5D.!!$R1 638
20 TraesCS3A01G412200 chr7B 695919199 695919881 682 False 510.0 510 81.1950 6 648 1 chr7B.!!$F1 642
21 TraesCS3A01G412200 chrUn 287225085 287226100 1015 False 440.0 440 74.8320 1067 2099 1 chrUn.!!$F1 1032
22 TraesCS3A01G412200 chrUn 287476983 287477998 1015 False 440.0 440 74.8320 1067 2099 1 chrUn.!!$F2 1032
23 TraesCS3A01G412200 chr4A 210203913 210204530 617 True 418.0 418 79.9350 72 649 1 chr4A.!!$R1 577

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
275 420 0.034896 GCTCGTCTCTTTGGTTGGGA 59.965 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2165 3.092301 CCTGATTGAAAAGGAACCCTCC 58.908 50.0 0.0 0.0 42.81 4.3 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
54 55 3.134792 ATCACTCGTCTCGCGCCT 61.135 61.111 0.00 0.00 41.07 5.52
137 205 1.078848 GCAGGACCGTGCTCATCTT 60.079 57.895 7.37 0.00 40.54 2.40
196 324 1.031571 TTGCAGGACGGATTGATGGC 61.032 55.000 0.00 0.00 0.00 4.40
221 349 1.074889 AGTTTTGGCCGGTCTATTGGT 59.925 47.619 7.97 0.00 0.00 3.67
275 420 0.034896 GCTCGTCTCTTTGGTTGGGA 59.965 55.000 0.00 0.00 0.00 4.37
304 449 1.385347 TCCTGGGTGAGGTGGTGTT 60.385 57.895 0.00 0.00 43.37 3.32
505 672 0.103390 TTCTTGAAGGTGTCGTCGCA 59.897 50.000 0.00 0.00 0.00 5.10
667 839 0.375803 GCGTGTTCACGGTTGAAGTT 59.624 50.000 23.27 0.00 42.60 2.66
687 859 0.034896 CCCGGTTGCTCTTGTAGTGT 59.965 55.000 0.00 0.00 0.00 3.55
778 957 1.297664 CGTTTGTACCGGGTTGTTGA 58.702 50.000 4.31 0.00 0.00 3.18
904 1086 2.325761 GTGTTGTAGTGACTACTGGCG 58.674 52.381 21.95 0.00 37.78 5.69
917 1099 4.959723 ACTACTGGCGTTTAAACTAACCA 58.040 39.130 16.01 17.26 0.00 3.67
1137 1327 4.261322 GCATTGGTATCGATTGCTGTCAAT 60.261 41.667 1.71 2.94 45.04 2.57
1645 1844 1.330655 TTTCTCTGCTAGGGAGGCGG 61.331 60.000 0.00 0.00 37.41 6.13
1720 1919 6.382282 AGATTCTATGTGTCATGGTCTCAGAA 59.618 38.462 0.00 0.00 0.00 3.02
1902 2165 3.893200 AGCTGAGAGAGATCATCCAAGAG 59.107 47.826 0.00 0.00 0.00 2.85
2107 2371 0.037447 GGGAAGCTTGCAAGAGGAGT 59.963 55.000 30.39 8.93 0.00 3.85
2137 2401 1.202806 GCCCTTATGCTATGCTGGTCA 60.203 52.381 0.00 0.00 0.00 4.02
2269 2732 6.727824 AACTACACATTGTGATGTTAGCTC 57.272 37.500 23.12 0.00 43.92 4.09
2338 2801 8.920174 TCAAATTCAATCATATTTGCTGGAGAT 58.080 29.630 0.00 0.00 40.09 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.580815 CTCGATCCTGCTGCACCA 59.419 61.111 0.00 0.00 0.00 4.17
289 434 0.768622 CCTTAACACCACCTCACCCA 59.231 55.000 0.00 0.00 0.00 4.51
304 449 1.632018 CCCCGGCATCCAAGACCTTA 61.632 60.000 0.00 0.00 0.00 2.69
427 594 2.203422 CAGGTTTTCACCCCGGCA 60.203 61.111 0.00 0.00 45.63 5.69
505 672 0.456221 CACGACGGGTAATGAGAGCT 59.544 55.000 0.00 0.00 0.00 4.09
667 839 0.320374 CACTACAAGAGCAACCGGGA 59.680 55.000 6.32 0.00 0.00 5.14
687 859 1.169661 CGCAGCAACACCAACCCTAA 61.170 55.000 0.00 0.00 0.00 2.69
821 1003 3.596214 ACGCCTCAAAATCGTGATTACT 58.404 40.909 0.00 0.00 34.92 2.24
859 1041 4.464069 TGTTGAAAGAAGGTGTTTTGGG 57.536 40.909 0.00 0.00 0.00 4.12
1605 1804 8.650835 AGAAATAATCATTCGGCCTCCTGAGG 62.651 46.154 8.91 8.91 40.36 3.86
1645 1844 7.040409 GGGAATTTGGTGGTGATTATATCAGAC 60.040 40.741 0.00 0.00 40.53 3.51
1765 2024 5.221048 GGTCAAATATAATGCTCGCACCTTT 60.221 40.000 0.00 0.00 0.00 3.11
1902 2165 3.092301 CCTGATTGAAAAGGAACCCTCC 58.908 50.000 0.00 0.00 42.81 4.30
2197 2462 5.360714 TGACCTCAAAGAAAGCATCAGTTTT 59.639 36.000 0.00 0.00 0.00 2.43
2269 2732 4.510711 GTCATGCCATGTTGAGAGATACAG 59.489 45.833 4.31 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.