Multiple sequence alignment - TraesCS5A01G333300

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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 TraesCS5A01G333300 chr5A 100.000 3778 0 0 1 3778 542027511 542023734 0.000000e+00 6977
1 TraesCS5A01G333300 chr5A 98.566 837 12 0 2942 3778 542017610 542016774 0.000000e+00 1480
2 TraesCS5A01G333300 chr1A 96.400 2583 64 8 377 2939 394418058 394420631 0.000000e+00 4228
3 TraesCS5A01G333300 chr1A 96.888 1928 37 8 1033 2939 394506632 394508557 0.000000e+00 3206
4 TraesCS5A01G333300 chr1A 98.571 840 11 1 2939 3778 11926950 11927788 0.000000e+00 1483
5 TraesCS5A01G333300 chr1A 98.456 842 13 0 2937 3778 327297433 327298274 0.000000e+00 1483
6 TraesCS5A01G333300 chr1A 96.380 663 21 3 377 1039 394488212 394488871 0.000000e+00 1088
7 TraesCS5A01G333300 chr1A 98.153 379 7 0 1 379 394417034 394417412 0.000000e+00 662
8 TraesCS5A01G333300 chr1A 97.889 379 8 0 1 379 394487188 394487566 0.000000e+00 656
9 TraesCS5A01G333300 chr4B 95.581 2580 86 9 380 2938 77616327 77613755 0.000000e+00 4108
10 TraesCS5A01G333300 chr2B 95.395 2584 82 10 377 2939 238550302 238552869 0.000000e+00 4078
11 TraesCS5A01G333300 chr2B 81.210 777 111 13 377 1128 37447935 37447169 9.040000e-166 593
12 TraesCS5A01G333300 chr2B 94.987 379 18 1 1 379 622494355 622493978 9.040000e-166 593
13 TraesCS5A01G333300 chr3B 95.085 2584 100 7 377 2939 678822928 678825505 0.000000e+00 4043
14 TraesCS5A01G333300 chr3B 94.987 379 19 0 1 379 728853934 728854312 2.510000e-166 595
15 TraesCS5A01G333300 chr2A 92.103 2520 117 33 460 2939 27757429 27759906 0.000000e+00 3476
16 TraesCS5A01G333300 chr2A 98.452 840 12 1 2940 3778 546690403 546689564 0.000000e+00 1478
17 TraesCS5A01G333300 chr2D 94.706 1530 75 4 1412 2939 607122446 607123971 0.000000e+00 2372
18 TraesCS5A01G333300 chr2D 94.023 1489 85 4 1412 2897 486367036 486368523 0.000000e+00 2254
19 TraesCS5A01G333300 chr2D 89.035 1067 68 14 377 1407 607121350 607122403 0.000000e+00 1277
20 TraesCS5A01G333300 chr2D 96.042 379 15 0 1 379 82247978 82247600 5.360000e-173 617
21 TraesCS5A01G333300 chr5D 94.157 1489 83 4 1412 2897 324730282 324728795 0.000000e+00 2265
22 TraesCS5A01G333300 chr5D 94.023 1489 85 4 1412 2897 46635327 46636814 0.000000e+00 2254
23 TraesCS5A01G333300 chr5D 86.680 1006 76 15 448 1407 324731318 324730325 0.000000e+00 1062
24 TraesCS5A01G333300 chr5D 86.238 1010 76 15 445 1407 133266529 133267522 0.000000e+00 1037
25 TraesCS5A01G333300 chr4D 93.620 1489 91 4 1412 2897 129500064 129498577 0.000000e+00 2220
26 TraesCS5A01G333300 chr4D 88.075 1065 77 15 379 1407 129501157 129500107 0.000000e+00 1218
27 TraesCS5A01G333300 chr4D 96.042 379 15 0 1 379 502621391 502621769 5.360000e-173 617
28 TraesCS5A01G333300 chrUn 94.132 1227 68 4 1412 2636 388007592 388008816 0.000000e+00 1864
29 TraesCS5A01G333300 chrUn 96.042 379 15 0 1 379 134331118 134330740 5.360000e-173 617
30 TraesCS5A01G333300 chrUn 83.766 616 74 15 535 1128 71017183 71016572 9.160000e-156 560
31 TraesCS5A01G333300 chrUn 92.199 282 16 2 1126 1407 388007274 388007549 9.840000e-106 394
32 TraesCS5A01G333300 chr7A 98.571 840 11 1 2939 3778 733469145 733469983 0.000000e+00 1483
33 TraesCS5A01G333300 chr6A 98.570 839 11 1 2940 3778 67384287 67385124 0.000000e+00 1482
34 TraesCS5A01G333300 chr3A 98.451 839 13 0 2940 3778 23332257 23331419 0.000000e+00 1478
35 TraesCS5A01G333300 chr3A 98.451 839 13 0 2940 3778 23339233 23338395 0.000000e+00 1478
36 TraesCS5A01G333300 chr4A 98.451 839 12 1 2940 3778 18165291 18166128 0.000000e+00 1476
37 TraesCS5A01G333300 chr3D 96.042 379 15 0 1 379 579347256 579347634 5.360000e-173 617
38 TraesCS5A01G333300 chr6B 94.444 378 21 0 1 378 55637239 55636862 1.960000e-162 582
39 TraesCS5A01G333300 chr1B 84.988 413 39 9 377 772 62478422 62478016 7.600000e-107 398


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 TraesCS5A01G333300 chr5A 542023734 542027511 3777 True 6977.0 6977 100.0000 1 3778 1 chr5A.!!$R2 3777
1 TraesCS5A01G333300 chr5A 542016774 542017610 836 True 1480.0 1480 98.5660 2942 3778 1 chr5A.!!$R1 836
2 TraesCS5A01G333300 chr1A 394506632 394508557 1925 False 3206.0 3206 96.8880 1033 2939 1 chr1A.!!$F3 1906
3 TraesCS5A01G333300 chr1A 394417034 394420631 3597 False 2445.0 4228 97.2765 1 2939 2 chr1A.!!$F4 2938
4 TraesCS5A01G333300 chr1A 11926950 11927788 838 False 1483.0 1483 98.5710 2939 3778 1 chr1A.!!$F1 839
5 TraesCS5A01G333300 chr1A 327297433 327298274 841 False 1483.0 1483 98.4560 2937 3778 1 chr1A.!!$F2 841
6 TraesCS5A01G333300 chr1A 394487188 394488871 1683 False 872.0 1088 97.1345 1 1039 2 chr1A.!!$F5 1038
7 TraesCS5A01G333300 chr4B 77613755 77616327 2572 True 4108.0 4108 95.5810 380 2938 1 chr4B.!!$R1 2558
8 TraesCS5A01G333300 chr2B 238550302 238552869 2567 False 4078.0 4078 95.3950 377 2939 1 chr2B.!!$F1 2562
9 TraesCS5A01G333300 chr2B 37447169 37447935 766 True 593.0 593 81.2100 377 1128 1 chr2B.!!$R1 751
10 TraesCS5A01G333300 chr3B 678822928 678825505 2577 False 4043.0 4043 95.0850 377 2939 1 chr3B.!!$F1 2562
11 TraesCS5A01G333300 chr2A 27757429 27759906 2477 False 3476.0 3476 92.1030 460 2939 1 chr2A.!!$F1 2479
12 TraesCS5A01G333300 chr2A 546689564 546690403 839 True 1478.0 1478 98.4520 2940 3778 1 chr2A.!!$R1 838
13 TraesCS5A01G333300 chr2D 486367036 486368523 1487 False 2254.0 2254 94.0230 1412 2897 1 chr2D.!!$F1 1485
14 TraesCS5A01G333300 chr2D 607121350 607123971 2621 False 1824.5 2372 91.8705 377 2939 2 chr2D.!!$F2 2562
15 TraesCS5A01G333300 chr5D 46635327 46636814 1487 False 2254.0 2254 94.0230 1412 2897 1 chr5D.!!$F1 1485
16 TraesCS5A01G333300 chr5D 324728795 324731318 2523 True 1663.5 2265 90.4185 448 2897 2 chr5D.!!$R1 2449
17 TraesCS5A01G333300 chr5D 133266529 133267522 993 False 1037.0 1037 86.2380 445 1407 1 chr5D.!!$F2 962
18 TraesCS5A01G333300 chr4D 129498577 129501157 2580 True 1719.0 2220 90.8475 379 2897 2 chr4D.!!$R1 2518
19 TraesCS5A01G333300 chrUn 388007274 388008816 1542 False 1129.0 1864 93.1655 1126 2636 2 chrUn.!!$F1 1510
20 TraesCS5A01G333300 chrUn 71016572 71017183 611 True 560.0 560 83.7660 535 1128 1 chrUn.!!$R1 593
21 TraesCS5A01G333300 chr7A 733469145 733469983 838 False 1483.0 1483 98.5710 2939 3778 1 chr7A.!!$F1 839
22 TraesCS5A01G333300 chr6A 67384287 67385124 837 False 1482.0 1482 98.5700 2940 3778 1 chr6A.!!$F1 838
23 TraesCS5A01G333300 chr3A 23331419 23332257 838 True 1478.0 1478 98.4510 2940 3778 1 chr3A.!!$R1 838
24 TraesCS5A01G333300 chr3A 23338395 23339233 838 True 1478.0 1478 98.4510 2940 3778 1 chr3A.!!$R2 838
25 TraesCS5A01G333300 chr4A 18165291 18166128 837 False 1476.0 1476 98.4510 2940 3778 1 chr4A.!!$F1 838

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
441 1090 0.455410 CTAGCGACTCTGCTGAGCTT 59.545 55.0 19.49 1.97 46.70 3.74 F
889 1581 0.690762 GGGTGCACCTTCCTAACTGA 59.309 55.0 33.91 0.00 35.85 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 2690 1.228063 CAACAGAGCTGGTGCCTGT 60.228 57.895 2.16 0.0 45.62 4.00 R
2843 3623 0.244450 CAGCACGGGCATTGAAACAT 59.756 50.000 14.57 0.0 44.61 2.71 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
46 47 5.954752 TGCCATTTATAATCCAACCACTTCA 59.045 36.000 0.00 0.00 0.00 3.02
48 49 6.096846 GCCATTTATAATCCAACCACTTCAGT 59.903 38.462 0.00 0.00 0.00 3.41
65 66 6.757947 CACTTCAGTGTTTCATGGTGAATTTT 59.242 34.615 0.00 0.00 40.96 1.82
183 184 0.539986 GATTACGGTGGCCTTGAGGA 59.460 55.000 3.32 0.00 37.39 3.71
357 358 6.312672 AGTTGGTTTTGCTGTTATGTTTGTTC 59.687 34.615 0.00 0.00 0.00 3.18
413 1062 0.814010 GCACCTGAGTTTGTGGACGT 60.814 55.000 0.00 0.00 33.08 4.34
441 1090 0.455410 CTAGCGACTCTGCTGAGCTT 59.545 55.000 19.49 1.97 46.70 3.74
461 1110 5.416013 AGCTTTCTGGTTAATGGTAAGCTTC 59.584 40.000 0.00 0.00 42.86 3.86
536 1185 1.549203 CCCCACAGTTGAAATCAGGG 58.451 55.000 0.00 0.00 34.58 4.45
537 1186 1.549203 CCCACAGTTGAAATCAGGGG 58.451 55.000 0.00 0.00 0.00 4.79
574 1228 4.669768 TGATAGGGAAATAAATCAGGGCCT 59.330 41.667 0.00 0.00 0.00 5.19
616 1271 3.326880 TCGGAGATTTATTTAGAGGGGGC 59.673 47.826 0.00 0.00 0.00 5.80
623 1294 4.405756 TTATTTAGAGGGGGCCAAACAA 57.594 40.909 4.39 0.00 0.00 2.83
783 1457 6.327279 GGCAACTTTTAATCTGTTACTGGT 57.673 37.500 0.00 0.00 0.00 4.00
836 1523 7.624360 ATCTTGCCGATTTTGTTGATAGTAA 57.376 32.000 0.00 0.00 0.00 2.24
889 1581 0.690762 GGGTGCACCTTCCTAACTGA 59.309 55.000 33.91 0.00 35.85 3.41
932 1627 9.959721 ACGGCCTCATATATACTCAATAAAATT 57.040 29.630 0.00 0.00 0.00 1.82
1572 2345 7.316544 ACTACGAAAACACTTCAATCTGTTT 57.683 32.000 0.00 0.00 41.36 2.83
1582 2355 7.491682 ACACTTCAATCTGTTTGTTTATTGCT 58.508 30.769 0.00 0.00 36.65 3.91
1755 2530 9.872684 ATCATTGGTATGAACCTTGATCTTAAT 57.127 29.630 0.00 0.00 46.91 1.40
1913 2690 2.993840 ACGCAGCAGAGAGGAGCA 60.994 61.111 0.00 0.00 0.00 4.26
2335 3112 5.583854 TGAAGCAAGAATTCAGCTCTGTATC 59.416 40.000 21.06 15.83 37.70 2.24
2341 3118 1.629013 TTCAGCTCTGTATCGCAACG 58.371 50.000 0.00 0.00 0.00 4.10
2756 3535 1.338484 CCAGAGCAAGTTAGAGCAGCA 60.338 52.381 0.00 0.00 0.00 4.41
3149 3929 3.191371 CCTAACCATGGACAAAGAGTTGC 59.809 47.826 21.47 0.00 38.39 4.17
3159 3939 5.538053 TGGACAAAGAGTTGCCATTTGATTA 59.462 36.000 4.08 0.00 38.39 1.75
3332 4114 4.351192 GAACACTTTGTGTGCTACCAAAG 58.649 43.478 16.00 16.00 46.79 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 173 2.956132 TGTTCAAAATCCTCAAGGCCA 58.044 42.857 5.01 0.0 34.44 5.36
357 358 8.542132 CACATGACAAACAGAAATTACCAAAAG 58.458 33.333 0.00 0.0 0.00 2.27
413 1062 2.159366 GCAGAGTCGCTAGCTACAAGAA 60.159 50.000 20.27 0.0 0.00 2.52
441 1090 6.377146 GGAATGAAGCTTACCATTAACCAGAA 59.623 38.462 12.06 0.0 33.57 3.02
461 1110 2.810439 TTTCTTTTGTGGCGGGAATG 57.190 45.000 0.00 0.0 0.00 2.67
574 1228 1.715931 ACCCCCTGATTTGAATGGTGA 59.284 47.619 0.00 0.0 0.00 4.02
616 1271 1.414061 TTGTGGGGCCCATTGTTTGG 61.414 55.000 31.48 0.0 46.00 3.28
623 1294 2.206536 CGTGTTTTGTGGGGCCCAT 61.207 57.895 31.48 0.0 35.28 4.00
664 1335 0.534877 AAGTGCAACACTCGATGCCA 60.535 50.000 6.29 0.0 44.62 4.92
889 1581 1.305219 CGTGGGGAATTGTGCGACAT 61.305 55.000 0.00 0.0 0.00 3.06
932 1627 0.106619 GAGAGGAAGGAGCCCGTAGA 60.107 60.000 0.00 0.0 0.00 2.59
1045 1757 5.352569 CGTCTGAGGAAAGTGCTATGAAATT 59.647 40.000 0.00 0.0 0.00 1.82
1200 1934 9.900112 ACCAGGGTATATCTTCTAATCTAAACT 57.100 33.333 0.00 0.0 0.00 2.66
1418 2190 6.783892 TTTGGACCACAGTTTTATACGTAC 57.216 37.500 0.00 0.0 0.00 3.67
1426 2198 4.343814 CCCATAGTTTTGGACCACAGTTTT 59.656 41.667 0.00 0.0 39.25 2.43
1681 2456 5.994887 AACGATAAAACTGTGTTGCTGTA 57.005 34.783 0.00 0.0 0.00 2.74
1764 2541 2.173569 GGGCTCCTAATCCAGATTGTGT 59.826 50.000 3.10 0.0 32.50 3.72
1913 2690 1.228063 CAACAGAGCTGGTGCCTGT 60.228 57.895 2.16 0.0 45.62 4.00
2103 2880 9.930693 TGTCAAACAAAGTAACCAACTAATTTT 57.069 25.926 0.00 0.0 37.50 1.82
2756 3535 6.672593 TCCTTAGCCACCAATAAATCTCAAT 58.327 36.000 0.00 0.0 0.00 2.57
2843 3623 0.244450 CAGCACGGGCATTGAAACAT 59.756 50.000 14.57 0.0 44.61 2.71
3149 3929 5.574891 TGTGATCCCGTTTAATCAAATGG 57.425 39.130 0.00 0.0 46.47 3.16
3159 3939 5.496556 TCAACTAATGATGTGATCCCGTTT 58.503 37.500 0.00 0.0 31.50 3.60
3275 4057 7.005296 ACGGGAGTTACATAATCTCATAGTCT 58.995 38.462 0.00 0.0 43.33 3.24
3332 4114 1.202557 TCACCCAGTTACGTTGTGACC 60.203 52.381 0.00 0.0 31.45 4.02
3680 4462 1.425066 GACCTGGATGCCCATATTGGA 59.575 52.381 0.00 0.0 40.96 3.53


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

AutoCloner maintained by Alex Coulton.