Multiple sequence alignment - TraesCS7A01G513300

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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 TraesCS7A01G513300 chr7A 100.000 1696 0 0 890 2585 700256652 700258347 0.000000e+00 3133.0
1 TraesCS7A01G513300 chr7A 99.777 449 1 0 2137 2585 700266329 700266777 0.000000e+00 824.0
2 TraesCS7A01G513300 chr7A 98.710 310 4 0 2137 2446 700486582 700486273 3.760000e-153 551.0
3 TraesCS7A01G513300 chr7A 100.000 284 0 0 1 284 700255763 700256046 2.280000e-145 525.0
4 TraesCS7A01G513300 chr7A 93.380 287 19 0 1856 2142 700488727 700488441 2.380000e-115 425.0
5 TraesCS7A01G513300 chr7A 97.436 39 1 0 6 44 700488762 700488724 1.660000e-07 67.6
6 TraesCS7A01G513300 chr3D 94.530 914 40 8 954 1859 486147191 486146280 0.000000e+00 1402.0
7 TraesCS7A01G513300 chr3D 96.357 851 30 1 1012 1862 363854795 363853946 0.000000e+00 1399.0
8 TraesCS7A01G513300 chr3D 93.920 921 37 10 954 1860 124070389 124071304 0.000000e+00 1373.0
9 TraesCS7A01G513300 chr3D 93.952 248 12 2 38 284 124069443 124069688 3.140000e-99 372.0
10 TraesCS7A01G513300 chr3D 94.167 240 13 1 42 280 486147833 486147594 5.260000e-97 364.0
11 TraesCS7A01G513300 chr3A 95.039 887 38 1 974 1860 418754006 418753126 0.000000e+00 1389.0
12 TraesCS7A01G513300 chr5B 93.622 925 48 9 943 1859 56361535 56362456 0.000000e+00 1371.0
13 TraesCS7A01G513300 chr7D 93.661 915 46 4 950 1860 582089015 582089921 0.000000e+00 1358.0
14 TraesCS7A01G513300 chr7D 97.963 540 11 0 1856 2395 610519962 610519423 0.000000e+00 937.0
15 TraesCS7A01G513300 chr7D 95.993 549 16 2 1856 2399 600219680 600219133 0.000000e+00 887.0
16 TraesCS7A01G513300 chr7D 88.938 452 47 2 1947 2398 514757469 514757917 2.910000e-154 555.0
17 TraesCS7A01G513300 chr7D 96.216 185 7 0 2401 2585 610488893 610488709 1.160000e-78 303.0
18 TraesCS7A01G513300 chr7D 89.189 185 7 3 2401 2585 600219094 600218923 4.330000e-53 219.0
19 TraesCS7A01G513300 chr7D 87.245 196 13 6 2402 2585 514757958 514758153 2.010000e-51 213.0
20 TraesCS7A01G513300 chr7D 84.466 103 10 5 1912 2012 608500634 608500732 2.120000e-16 97.1
21 TraesCS7A01G513300 chr7D 100.000 44 0 0 1 44 600219720 600219677 5.930000e-12 82.4
22 TraesCS7A01G513300 chr7D 100.000 44 0 0 1 44 610520002 610519959 5.930000e-12 82.4
23 TraesCS7A01G513300 chr5D 93.189 925 51 9 954 1873 84407603 84408520 0.000000e+00 1349.0
24 TraesCS7A01G513300 chr5D 93.471 919 39 11 950 1862 432179380 432178477 0.000000e+00 1345.0
25 TraesCS7A01G513300 chr5D 92.888 928 52 10 954 1873 84452288 84453209 0.000000e+00 1336.0
26 TraesCS7A01G513300 chr5D 92.623 244 17 1 42 284 53755584 53755827 1.470000e-92 350.0
27 TraesCS7A01G513300 chr5D 92.623 244 17 1 42 284 84406848 84407091 1.470000e-92 350.0
28 TraesCS7A01G513300 chr7B 93.934 544 33 0 1856 2399 694438904 694439447 0.000000e+00 822.0
29 TraesCS7A01G513300 chr7B 91.806 537 41 1 1856 2392 685240164 685240697 0.000000e+00 745.0
30 TraesCS7A01G513300 chr7B 90.993 544 46 2 1856 2399 696190652 696191192 0.000000e+00 730.0
31 TraesCS7A01G513300 chr7B 90.809 544 47 1 1856 2399 693656084 693656624 0.000000e+00 725.0
32 TraesCS7A01G513300 chr7B 87.368 190 12 4 2402 2579 693656664 693656853 9.370000e-50 207.0
33 TraesCS7A01G513300 chr7B 87.368 190 12 4 2402 2579 696191232 696191421 9.370000e-50 207.0
34 TraesCS7A01G513300 chr7B 86.842 190 13 4 2402 2579 685240744 685240933 4.360000e-48 202.0
35 TraesCS7A01G513300 chr7B 94.355 124 7 0 2462 2585 694439527 694439650 9.440000e-45 191.0
36 TraesCS7A01G513300 chr7B 83.654 104 13 3 2484 2585 697119637 697119738 7.620000e-16 95.3
37 TraesCS7A01G513300 chr7B 82.692 104 14 3 2484 2585 685049195 685049094 3.540000e-14 89.8
38 TraesCS7A01G513300 chr7B 97.872 47 1 0 2401 2447 694439486 694439532 5.930000e-12 82.4
39 TraesCS7A01G513300 chr4B 94.215 242 13 1 44 284 577064128 577063887 4.060000e-98 368.0
40 TraesCS7A01G513300 chr4A 93.724 239 13 2 44 280 512021760 512021522 8.800000e-95 357.0
41 TraesCS7A01G513300 chr6D 93.033 244 16 1 42 284 58735218 58734975 3.160000e-94 355.0
42 TraesCS7A01G513300 chr1D 93.697 238 14 1 44 280 16966543 16966780 3.160000e-94 355.0
43 TraesCS7A01G513300 chr1B 91.968 249 16 4 39 284 144144985 144144738 1.900000e-91 346.0
44 TraesCS7A01G513300 chrUn 85.833 120 17 0 1903 2022 373724800 373724919 7.510000e-26 128.0


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 TraesCS7A01G513300 chr7A 700255763 700258347 2584 False 1829.000000 3133 100.000000 1 2585 2 chr7A.!!$F2 2584
1 TraesCS7A01G513300 chr7A 700486273 700488762 2489 True 347.866667 551 96.508667 6 2446 3 chr7A.!!$R1 2440
2 TraesCS7A01G513300 chr3D 363853946 363854795 849 True 1399.000000 1399 96.357000 1012 1862 1 chr3D.!!$R1 850
3 TraesCS7A01G513300 chr3D 486146280 486147833 1553 True 883.000000 1402 94.348500 42 1859 2 chr3D.!!$R2 1817
4 TraesCS7A01G513300 chr3D 124069443 124071304 1861 False 872.500000 1373 93.936000 38 1860 2 chr3D.!!$F1 1822
5 TraesCS7A01G513300 chr3A 418753126 418754006 880 True 1389.000000 1389 95.039000 974 1860 1 chr3A.!!$R1 886
6 TraesCS7A01G513300 chr5B 56361535 56362456 921 False 1371.000000 1371 93.622000 943 1859 1 chr5B.!!$F1 916
7 TraesCS7A01G513300 chr7D 582089015 582089921 906 False 1358.000000 1358 93.661000 950 1860 1 chr7D.!!$F1 910
8 TraesCS7A01G513300 chr7D 610519423 610520002 579 True 509.700000 937 98.981500 1 2395 2 chr7D.!!$R3 2394
9 TraesCS7A01G513300 chr7D 600218923 600219720 797 True 396.133333 887 95.060667 1 2585 3 chr7D.!!$R2 2584
10 TraesCS7A01G513300 chr7D 514757469 514758153 684 False 384.000000 555 88.091500 1947 2585 2 chr7D.!!$F3 638
11 TraesCS7A01G513300 chr5D 432178477 432179380 903 True 1345.000000 1345 93.471000 950 1862 1 chr5D.!!$R1 912
12 TraesCS7A01G513300 chr5D 84452288 84453209 921 False 1336.000000 1336 92.888000 954 1873 1 chr5D.!!$F2 919
13 TraesCS7A01G513300 chr5D 84406848 84408520 1672 False 849.500000 1349 92.906000 42 1873 2 chr5D.!!$F3 1831
14 TraesCS7A01G513300 chr7B 685240164 685240933 769 False 473.500000 745 89.324000 1856 2579 2 chr7B.!!$F2 723
15 TraesCS7A01G513300 chr7B 696190652 696191421 769 False 468.500000 730 89.180500 1856 2579 2 chr7B.!!$F5 723
16 TraesCS7A01G513300 chr7B 693656084 693656853 769 False 466.000000 725 89.088500 1856 2579 2 chr7B.!!$F3 723
17 TraesCS7A01G513300 chr7B 694438904 694439650 746 False 365.133333 822 95.387000 1856 2585 3 chr7B.!!$F4 729

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
945 1902 1.595382 CCCGGCTCCATTCGTCATC 60.595 63.158 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 3409 0.46546 AAGTGCGTTTTGGAGCTCCA 60.465 50.0 32.0 32.0 45.94 3.86 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
205 543 5.925969 TCACGATGCAAATATACATCACGAT 59.074 36.000 11.63 0.00 42.28 3.73
209 731 7.545615 ACGATGCAAATATACATCACGATATGT 59.454 33.333 11.15 11.15 42.28 2.29
218 740 7.703058 ATACATCACGATATGTATCTGGTCA 57.297 36.000 16.45 0.00 45.61 4.02
259 781 2.260869 CGCCCAACCACCACTTCAG 61.261 63.158 0.00 0.00 0.00 3.02
944 1901 2.505982 CCCGGCTCCATTCGTCAT 59.494 61.111 0.00 0.00 0.00 3.06
945 1902 1.595382 CCCGGCTCCATTCGTCATC 60.595 63.158 0.00 0.00 0.00 2.92
946 1903 1.951130 CCGGCTCCATTCGTCATCG 60.951 63.158 0.00 0.00 38.55 3.84
948 1905 2.247437 GGCTCCATTCGTCATCGCC 61.247 63.158 0.00 0.00 36.96 5.54
952 1909 3.640000 CATTCGTCATCGCCCCGC 61.640 66.667 0.00 0.00 36.96 6.13
1198 2665 2.561569 CTCGGTCACACCTCAACTTTT 58.438 47.619 0.00 0.00 35.66 2.27
1219 2686 1.888172 GAGATCGAGAGTCGGGCGA 60.888 63.158 7.94 7.94 40.88 5.54
1238 2705 0.471617 AAAGCGGAGATGCCTATGCT 59.528 50.000 0.00 0.00 38.71 3.79
1245 2712 1.058428 AGATGCCTATGCTGCAGGGA 61.058 55.000 22.79 14.94 42.92 4.20
1335 2811 0.757188 AGACCGATGAGGAGGCGATT 60.757 55.000 0.00 0.00 45.00 3.34
1495 3038 3.003173 CCGAGGAGGACTGGGCAA 61.003 66.667 0.00 0.00 45.00 4.52
1752 3394 4.463539 CCATCAATTTGGACCATCTGTTGA 59.536 41.667 0.00 4.55 39.25 3.18
1814 3596 3.486875 CGGTCCAAATTTTACATCTCCGC 60.487 47.826 0.00 0.00 0.00 5.54
2095 3882 3.256631 GCATTGTCCTGACATCCAGTTTT 59.743 43.478 0.03 0.00 41.52 2.43
2157 3944 9.292195 GTACTTCTGAGCTTCTATCCTTAGTAT 57.708 37.037 0.00 0.00 0.00 2.12
2399 4260 1.452833 GGGAGGTCAGCAATGGAGC 60.453 63.158 0.00 0.00 0.00 4.70
2471 4332 2.691011 TGATAAAATACAAAGGCGCCCC 59.309 45.455 26.15 0.00 0.00 5.80
2538 4411 3.066342 TCGAAGAGAAGACAAACACGACT 59.934 43.478 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 451 1.552792 TGCATATGGACCGTCTGTTGA 59.447 47.619 4.56 0.00 0.00 3.18
250 772 0.108019 GGGAACGGAACTGAAGTGGT 59.892 55.000 0.00 0.00 0.00 4.16
928 1885 1.951130 CGATGACGAATGGAGCCGG 60.951 63.158 0.00 0.00 42.66 6.13
936 1893 4.910585 GGCGGGGCGATGACGAAT 62.911 66.667 0.00 0.00 42.66 3.34
1198 2665 0.816018 GCCCGACTCTCGATCTCTGA 60.816 60.000 0.00 0.00 43.74 3.27
1219 2686 0.471617 AGCATAGGCATCTCCGCTTT 59.528 50.000 0.67 0.00 44.61 3.51
1232 2699 2.646930 TGTTGATTCCCTGCAGCATAG 58.353 47.619 8.66 0.00 0.00 2.23
1234 2701 1.754803 CATGTTGATTCCCTGCAGCAT 59.245 47.619 8.66 0.37 36.57 3.79
1238 2705 2.041485 TCCTTCATGTTGATTCCCTGCA 59.959 45.455 0.00 0.00 0.00 4.41
1245 2712 4.872691 GTCGTGATCTCCTTCATGTTGATT 59.127 41.667 0.00 0.00 34.79 2.57
1335 2811 1.371183 CTCCCGAGCAAACCTCACA 59.629 57.895 0.00 0.00 40.78 3.58
1495 3038 0.705253 TCCTCCTCCTCCGAGAAGTT 59.295 55.000 0.00 0.00 38.52 2.66
1666 3307 9.393512 AGATGTTAAACGACATACTACTAGTCT 57.606 33.333 0.00 0.00 40.21 3.24
1686 3327 8.472413 CAATAGATGGTCCAAAATGAAGATGTT 58.528 33.333 0.00 0.00 0.00 2.71
1767 3409 0.465460 AAGTGCGTTTTGGAGCTCCA 60.465 50.000 32.00 32.00 45.94 3.86
2095 3882 3.577848 CCCCACCAATCACTGAATTTTGA 59.422 43.478 0.00 0.00 0.00 2.69
2157 3944 5.763204 GGTGGAACAGAAAACTACTTGATCA 59.237 40.000 0.00 0.00 41.80 2.92
2399 4260 2.222027 GGGTCTTGCCGATGAATAAGG 58.778 52.381 0.00 0.00 38.44 2.69


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

AutoCloner maintained by Alex Coulton.