Multiple sequence alignment - TraesCS7D01G334500

Loading Multiple Alignment...

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 TraesCS7D01G334500 chr7D 100.000 2565 0 0 1 2565 426546747 426549311 0.000000e+00 4737.0
1 TraesCS7D01G334500 chr7D 96.109 1208 28 5 1360 2565 38024321 38023131 0.000000e+00 1953.0
2 TraesCS7D01G334500 chr7D 96.410 780 21 5 593 1368 426632101 426632877 0.000000e+00 1279.0
3 TraesCS7D01G334500 chr7D 94.268 785 19 4 610 1368 426495977 426496761 0.000000e+00 1177.0
4 TraesCS7D01G334500 chr7D 98.316 594 9 1 1 593 153661797 153662390 0.000000e+00 1040.0
5 TraesCS7D01G334500 chr7D 79.022 634 84 36 721 1338 426643794 426644394 3.090000e-104 388.0
6 TraesCS7D01G334500 chr7D 87.135 342 31 7 1035 1363 426450361 426450702 2.410000e-100 375.0
7 TraesCS7D01G334500 chr7D 89.384 292 26 4 1077 1364 426517875 426518165 1.880000e-96 363.0
8 TraesCS7D01G334500 chr7D 85.484 62 3 4 721 781 426453995 426454051 2.760000e-05 60.2
9 TraesCS7D01G334500 chr2D 96.437 1207 26 3 1361 2565 643059169 643060360 0.000000e+00 1975.0
10 TraesCS7D01G334500 chr2D 98.316 594 9 1 1 593 422562699 422563292 0.000000e+00 1040.0
11 TraesCS7D01G334500 chr2D 98.475 590 8 1 1 589 78071245 78071834 0.000000e+00 1038.0
12 TraesCS7D01G334500 chr5D 96.262 1204 28 5 1365 2565 447258515 447257326 0.000000e+00 1958.0
13 TraesCS7D01G334500 chr5D 94.886 1232 26 4 1355 2565 175961924 175960709 0.000000e+00 1892.0
14 TraesCS7D01G334500 chr5D 97.997 599 10 2 1 598 151927642 151928239 0.000000e+00 1038.0
15 TraesCS7D01G334500 chr5B 96.262 1204 26 7 1365 2565 689115428 689114241 0.000000e+00 1956.0
16 TraesCS7D01G334500 chr7B 96.096 1204 29 4 1365 2565 133522048 133523236 0.000000e+00 1947.0
17 TraesCS7D01G334500 chr7B 95.918 784 24 2 593 1368 443701765 443702548 0.000000e+00 1264.0
18 TraesCS7D01G334500 chr7B 89.899 297 22 7 1077 1368 443696498 443696791 2.410000e-100 375.0
19 TraesCS7D01G334500 chr7B 86.957 69 5 4 721 786 443730464 443730531 9.840000e-10 75.0
20 TraesCS7D01G334500 chr3D 96.144 1193 28 5 1376 2565 144291112 144289935 0.000000e+00 1932.0
21 TraesCS7D01G334500 chr3D 95.690 1137 25 7 1437 2565 438456522 438457642 0.000000e+00 1807.0
22 TraesCS7D01G334500 chr3D 96.415 809 15 1 1362 2170 229473350 229474144 0.000000e+00 1321.0
23 TraesCS7D01G334500 chr3D 98.651 593 7 1 1 592 364981045 364981637 0.000000e+00 1050.0
24 TraesCS7D01G334500 chr6D 95.631 1213 33 6 1358 2565 19898723 19897526 0.000000e+00 1929.0
25 TraesCS7D01G334500 chr6D 98.319 595 8 2 1 594 436857382 436857975 0.000000e+00 1042.0
26 TraesCS7D01G334500 chr6D 98.316 594 9 1 1 593 162223882 162223289 0.000000e+00 1040.0
27 TraesCS7D01G334500 chr3A 95.768 1205 32 7 1365 2565 572457233 572458422 0.000000e+00 1925.0
28 TraesCS7D01G334500 chr6A 95.195 1207 35 9 1365 2565 534788574 534787385 0.000000e+00 1886.0
29 TraesCS7D01G334500 chr3B 95.460 771 19 3 1365 2134 695580992 695581747 0.000000e+00 1216.0
30 TraesCS7D01G334500 chr1D 98.644 590 7 1 1 589 442082189 442082778 0.000000e+00 1044.0
31 TraesCS7D01G334500 chr1D 98.148 594 10 1 1 593 201297032 201296439 0.000000e+00 1035.0
32 TraesCS7D01G334500 chr7A 88.520 331 32 3 1035 1362 507022926 507022599 1.850000e-106 396.0
33 TraesCS7D01G334500 chr7A 85.976 328 37 5 1045 1364 507014425 507014099 2.440000e-90 342.0
34 TraesCS7D01G334500 chr7A 85.714 91 9 4 721 811 507018913 507018827 2.720000e-15 93.5
35 TraesCS7D01G334500 chr7A 80.508 118 18 4 721 834 506873927 506873811 4.550000e-13 86.1
36 TraesCS7D01G334500 chr2B 89.130 322 28 5 1053 1368 753834742 753835062 6.650000e-106 394.0
37 TraesCS7D01G334500 chr2A 89.370 254 13 2 1367 1620 732235798 732236037 8.910000e-80 307.0


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 TraesCS7D01G334500 chr7D 426546747 426549311 2564 False 4737.00 4737 100.0000 1 2565 1 chr7D.!!$F4 2564
1 TraesCS7D01G334500 chr7D 38023131 38024321 1190 True 1953.00 1953 96.1090 1360 2565 1 chr7D.!!$R1 1205
2 TraesCS7D01G334500 chr7D 426632101 426632877 776 False 1279.00 1279 96.4100 593 1368 1 chr7D.!!$F5 775
3 TraesCS7D01G334500 chr7D 426495977 426496761 784 False 1177.00 1177 94.2680 610 1368 1 chr7D.!!$F2 758
4 TraesCS7D01G334500 chr7D 153661797 153662390 593 False 1040.00 1040 98.3160 1 593 1 chr7D.!!$F1 592
5 TraesCS7D01G334500 chr7D 426643794 426644394 600 False 388.00 388 79.0220 721 1338 1 chr7D.!!$F6 617
6 TraesCS7D01G334500 chr7D 426450361 426454051 3690 False 217.60 375 86.3095 721 1363 2 chr7D.!!$F7 642
7 TraesCS7D01G334500 chr2D 643059169 643060360 1191 False 1975.00 1975 96.4370 1361 2565 1 chr2D.!!$F3 1204
8 TraesCS7D01G334500 chr2D 422562699 422563292 593 False 1040.00 1040 98.3160 1 593 1 chr2D.!!$F2 592
9 TraesCS7D01G334500 chr2D 78071245 78071834 589 False 1038.00 1038 98.4750 1 589 1 chr2D.!!$F1 588
10 TraesCS7D01G334500 chr5D 447257326 447258515 1189 True 1958.00 1958 96.2620 1365 2565 1 chr5D.!!$R2 1200
11 TraesCS7D01G334500 chr5D 175960709 175961924 1215 True 1892.00 1892 94.8860 1355 2565 1 chr5D.!!$R1 1210
12 TraesCS7D01G334500 chr5D 151927642 151928239 597 False 1038.00 1038 97.9970 1 598 1 chr5D.!!$F1 597
13 TraesCS7D01G334500 chr5B 689114241 689115428 1187 True 1956.00 1956 96.2620 1365 2565 1 chr5B.!!$R1 1200
14 TraesCS7D01G334500 chr7B 133522048 133523236 1188 False 1947.00 1947 96.0960 1365 2565 1 chr7B.!!$F1 1200
15 TraesCS7D01G334500 chr7B 443701765 443702548 783 False 1264.00 1264 95.9180 593 1368 1 chr7B.!!$F3 775
16 TraesCS7D01G334500 chr3D 144289935 144291112 1177 True 1932.00 1932 96.1440 1376 2565 1 chr3D.!!$R1 1189
17 TraesCS7D01G334500 chr3D 438456522 438457642 1120 False 1807.00 1807 95.6900 1437 2565 1 chr3D.!!$F3 1128
18 TraesCS7D01G334500 chr3D 229473350 229474144 794 False 1321.00 1321 96.4150 1362 2170 1 chr3D.!!$F1 808
19 TraesCS7D01G334500 chr3D 364981045 364981637 592 False 1050.00 1050 98.6510 1 592 1 chr3D.!!$F2 591
20 TraesCS7D01G334500 chr6D 19897526 19898723 1197 True 1929.00 1929 95.6310 1358 2565 1 chr6D.!!$R1 1207
21 TraesCS7D01G334500 chr6D 436857382 436857975 593 False 1042.00 1042 98.3190 1 594 1 chr6D.!!$F1 593
22 TraesCS7D01G334500 chr6D 162223289 162223882 593 True 1040.00 1040 98.3160 1 593 1 chr6D.!!$R2 592
23 TraesCS7D01G334500 chr3A 572457233 572458422 1189 False 1925.00 1925 95.7680 1365 2565 1 chr3A.!!$F1 1200
24 TraesCS7D01G334500 chr6A 534787385 534788574 1189 True 1886.00 1886 95.1950 1365 2565 1 chr6A.!!$R1 1200
25 TraesCS7D01G334500 chr3B 695580992 695581747 755 False 1216.00 1216 95.4600 1365 2134 1 chr3B.!!$F1 769
26 TraesCS7D01G334500 chr1D 442082189 442082778 589 False 1044.00 1044 98.6440 1 589 1 chr1D.!!$F1 588
27 TraesCS7D01G334500 chr1D 201296439 201297032 593 True 1035.00 1035 98.1480 1 593 1 chr1D.!!$R1 592
28 TraesCS7D01G334500 chr7A 507018827 507022926 4099 True 244.75 396 87.1170 721 1362 2 chr7A.!!$R3 641


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
169 170 0.665835 GGTGAACAAATGCACGGACA 59.334 50.0 0.00 0.0 35.91 4.02 F
759 790 0.873312 CATGTCGACGGGAGCATCTG 60.873 60.0 11.62 0.0 33.73 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1130 1204 0.108615 GAAGAGGAGCAGCGCAAGTA 60.109 55.0 11.47 0.0 41.68 2.24 R
1988 3001 5.531287 ACCGCTCAAACAAACTAGAAGAAAT 59.469 36.0 0.00 0.0 0.00 2.17 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
169 170 0.665835 GGTGAACAAATGCACGGACA 59.334 50.000 0.00 0.00 35.91 4.02
177 178 3.049206 CAAATGCACGGACAAAATCGTT 58.951 40.909 0.00 0.00 37.53 3.85
510 512 2.640421 GCGGGCGCTACACAAAAA 59.360 55.556 7.64 0.00 38.26 1.94
638 640 1.816224 AGTGGACAACAAGCGTGTTTT 59.184 42.857 15.65 9.70 46.01 2.43
639 641 2.230266 AGTGGACAACAAGCGTGTTTTT 59.770 40.909 15.65 5.71 46.01 1.94
661 663 3.066621 TGATTCCATAGCATTTCAACGGC 59.933 43.478 0.00 0.00 0.00 5.68
708 710 3.306780 CGTACCCTTTCATTCCAGTGAGT 60.307 47.826 0.00 0.00 0.00 3.41
759 790 0.873312 CATGTCGACGGGAGCATCTG 60.873 60.000 11.62 0.00 33.73 2.90
1031 1082 5.704515 AGATTATGCTTCCATTCATCTTCCG 59.295 40.000 0.00 0.00 31.27 4.30
1130 1204 0.107165 GGGAGCGCTTCTTGGGTTAT 60.107 55.000 16.97 0.00 0.00 1.89
1412 1663 4.399978 CGGGCTTCGTAAAATTTGTACTG 58.600 43.478 0.00 0.00 0.00 2.74
1423 1676 5.528043 AAATTTGTACTGGTTGCATGTCA 57.472 34.783 0.00 0.00 0.00 3.58
1481 1825 8.217111 ACACACAAAAATGATTTAAAATCCCCT 58.783 29.630 0.00 0.00 0.00 4.79
1482 1826 9.065798 CACACAAAAATGATTTAAAATCCCCTT 57.934 29.630 0.00 0.00 0.00 3.95
1483 1827 9.283768 ACACAAAAATGATTTAAAATCCCCTTC 57.716 29.630 0.00 0.00 0.00 3.46
1484 1828 9.282569 CACAAAAATGATTTAAAATCCCCTTCA 57.717 29.630 0.00 0.00 0.00 3.02
1485 1829 9.283768 ACAAAAATGATTTAAAATCCCCTTCAC 57.716 29.630 0.00 0.00 0.00 3.18
1486 1830 8.729756 CAAAAATGATTTAAAATCCCCTTCACC 58.270 33.333 0.00 0.00 0.00 4.02
1487 1831 7.813087 AAATGATTTAAAATCCCCTTCACCT 57.187 32.000 0.00 0.00 0.00 4.00
1488 1832 6.796785 ATGATTTAAAATCCCCTTCACCTG 57.203 37.500 0.00 0.00 0.00 4.00
1489 1833 5.650283 TGATTTAAAATCCCCTTCACCTGT 58.350 37.500 0.00 0.00 0.00 4.00
1490 1834 6.795590 TGATTTAAAATCCCCTTCACCTGTA 58.204 36.000 0.00 0.00 0.00 2.74
1491 1835 7.242359 TGATTTAAAATCCCCTTCACCTGTAA 58.758 34.615 0.00 0.00 0.00 2.41
1492 1836 7.730784 TGATTTAAAATCCCCTTCACCTGTAAA 59.269 33.333 0.00 0.00 0.00 2.01
1493 1837 7.916077 TTTAAAATCCCCTTCACCTGTAAAA 57.084 32.000 0.00 0.00 0.00 1.52
1494 1838 7.916077 TTAAAATCCCCTTCACCTGTAAAAA 57.084 32.000 0.00 0.00 0.00 1.94
2174 3597 2.645838 AAGTGTGAATCACAGGCAGT 57.354 45.000 17.28 0.00 45.43 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 3.343941 TCCTTCCGATCCAACGATTTT 57.656 42.857 0.00 0.00 35.09 1.82
177 178 1.490490 CTCCCAAATCCTTCCGATCCA 59.510 52.381 0.00 0.00 0.00 3.41
510 512 2.632537 ACTATTTCACACCCCTGACCT 58.367 47.619 0.00 0.00 0.00 3.85
638 640 4.439974 GCCGTTGAAATGCTATGGAATCAA 60.440 41.667 0.00 0.00 30.96 2.57
639 641 3.066621 GCCGTTGAAATGCTATGGAATCA 59.933 43.478 0.00 0.00 30.96 2.57
661 663 0.537371 AGAAAACGGGCTGGGACAAG 60.537 55.000 0.00 0.00 38.70 3.16
708 710 1.133699 GGATGGTGCTGGATCCAATCA 60.134 52.381 17.00 13.67 38.46 2.57
1009 1060 4.217118 GCGGAAGATGAATGGAAGCATAAT 59.783 41.667 0.00 0.00 0.00 1.28
1031 1082 1.069364 GCAAGCAAGAAGAGAGTGTGC 60.069 52.381 0.00 0.00 35.41 4.57
1130 1204 0.108615 GAAGAGGAGCAGCGCAAGTA 60.109 55.000 11.47 0.00 41.68 2.24
1412 1663 7.763528 TGTCCATATTAAATTTGACATGCAACC 59.236 33.333 0.00 0.00 35.91 3.77
1481 1825 6.214191 TGCAAGTGAATTTTTACAGGTGAA 57.786 33.333 0.00 0.00 0.00 3.18
1482 1826 5.843673 TGCAAGTGAATTTTTACAGGTGA 57.156 34.783 0.00 0.00 0.00 4.02
1483 1827 6.479660 ACATTGCAAGTGAATTTTTACAGGTG 59.520 34.615 4.94 0.00 0.00 4.00
1484 1828 6.581712 ACATTGCAAGTGAATTTTTACAGGT 58.418 32.000 4.94 0.00 0.00 4.00
1485 1829 8.761575 ATACATTGCAAGTGAATTTTTACAGG 57.238 30.769 4.94 0.00 0.00 4.00
1561 2318 8.925338 TGTTTTTGTAGCCCCTTCTTTATTTTA 58.075 29.630 0.00 0.00 0.00 1.52
1986 2999 6.918022 CCGCTCAAACAAACTAGAAGAAATTT 59.082 34.615 0.00 0.00 0.00 1.82
1988 3001 5.531287 ACCGCTCAAACAAACTAGAAGAAAT 59.469 36.000 0.00 0.00 0.00 2.17
2174 3597 7.517614 TTAGCCTTGTTGTTCACAATTGATA 57.482 32.000 13.59 0.00 44.72 2.15



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

AutoCloner maintained by Alex Coulton.