Multiple sequence alignment - TraesCS7A01G566400

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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 TraesCS7A01G566400 chr7A 100.000 3467 0 0 1 3467 735765807 735762341 0.000000e+00 6403
1 TraesCS7A01G566400 chr7A 83.438 1437 225 11 994 2422 642327438 642326007 0.000000e+00 1323
2 TraesCS7A01G566400 chr7A 87.963 972 94 16 2468 3426 642325888 642324927 0.000000e+00 1125
3 TraesCS7A01G566400 chr7A 85.120 914 128 7 2468 3378 625538221 625537313 0.000000e+00 928
4 TraesCS7A01G566400 chrUn 92.414 2241 106 30 211 2432 88863385 88865580 0.000000e+00 3138
5 TraesCS7A01G566400 chrUn 92.380 2244 104 31 211 2432 88842312 88844510 0.000000e+00 3134
6 TraesCS7A01G566400 chrUn 100.000 1537 0 0 1 1537 305829800 305828264 0.000000e+00 2839
7 TraesCS7A01G566400 chrUn 99.900 1001 1 0 2467 3467 365695920 365694920 0.000000e+00 1844
8 TraesCS7A01G566400 chrUn 95.464 970 43 1 2467 3435 88865688 88866657 0.000000e+00 1546
9 TraesCS7A01G566400 chrUn 100.000 672 0 0 1761 2432 365696699 365696028 0.000000e+00 1242
10 TraesCS7A01G566400 chrUn 89.735 302 20 6 519 820 88839088 88839378 3.270000e-100 375
11 TraesCS7A01G566400 chrUn 89.735 302 20 4 519 820 88858979 88859269 3.270000e-100 375
12 TraesCS7A01G566400 chrUn 81.658 398 40 11 397 782 88836386 88836010 2.020000e-77 300
13 TraesCS7A01G566400 chrUn 81.658 398 40 11 397 782 88856276 88855900 2.020000e-77 300
14 TraesCS7A01G566400 chrUn 93.382 136 9 0 3300 3435 365694952 365694817 5.870000e-48 202
15 TraesCS7A01G566400 chr7D 85.294 1462 208 2 975 2429 541966914 541965453 0.000000e+00 1502
16 TraesCS7A01G566400 chr7D 83.705 1436 223 9 994 2422 556719600 556718169 0.000000e+00 1345
17 TraesCS7A01G566400 chr7D 81.453 1445 257 10 995 2433 541502438 541500999 0.000000e+00 1173
18 TraesCS7A01G566400 chr7D 88.598 956 93 11 2468 3415 556718050 556717103 0.000000e+00 1147
19 TraesCS7A01G566400 chr7D 87.707 968 103 11 2468 3427 541965341 541964382 0.000000e+00 1114
20 TraesCS7A01G566400 chr7D 81.932 1273 209 15 1174 2429 542099621 542098353 0.000000e+00 1057
21 TraesCS7A01G566400 chr7D 85.788 971 118 13 2473 3435 542098236 542097278 0.000000e+00 1011
22 TraesCS7A01G566400 chr7B 84.615 1456 217 2 981 2429 585515177 585513722 0.000000e+00 1441
23 TraesCS7A01G566400 chr7B 84.229 1433 217 7 996 2422 604100811 604099382 0.000000e+00 1386
24 TraesCS7A01G566400 chr7B 87.320 970 104 12 2468 3426 604099263 604098302 0.000000e+00 1092
25 TraesCS7A01G566400 chr7B 87.751 898 98 10 2475 3369 585579369 585578481 0.000000e+00 1038
26 TraesCS7A01G566400 chr1A 77.500 400 67 15 1 392 534447899 534448283 5.830000e-53 219
27 TraesCS7A01G566400 chr2D 75.806 372 78 12 35 399 3989828 3990194 9.890000e-41 178
28 TraesCS7A01G566400 chr2D 79.747 158 28 3 233 387 637583769 637583613 1.020000e-20 111
29 TraesCS7A01G566400 chr5A 76.852 324 45 15 78 390 365654047 365653743 4.630000e-34 156
30 TraesCS7A01G566400 chr2A 78.027 223 43 6 91 310 194717322 194717541 6.040000e-28 135


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 TraesCS7A01G566400 chr7A 735762341 735765807 3466 True 6403.0 6403 100.000000 1 3467 1 chr7A.!!$R2 3466
1 TraesCS7A01G566400 chr7A 642324927 642327438 2511 True 1224.0 1323 85.700500 994 3426 2 chr7A.!!$R3 2432
2 TraesCS7A01G566400 chr7A 625537313 625538221 908 True 928.0 928 85.120000 2468 3378 1 chr7A.!!$R1 910
3 TraesCS7A01G566400 chrUn 305828264 305829800 1536 True 2839.0 2839 100.000000 1 1537 1 chrUn.!!$R3 1536
4 TraesCS7A01G566400 chrUn 88863385 88866657 3272 False 2342.0 3138 93.939000 211 3435 2 chrUn.!!$F3 3224
5 TraesCS7A01G566400 chrUn 88839088 88844510 5422 False 1754.5 3134 91.057500 211 2432 2 chrUn.!!$F2 2221
6 TraesCS7A01G566400 chrUn 365694817 365696699 1882 True 1096.0 1844 97.760667 1761 3467 3 chrUn.!!$R4 1706
7 TraesCS7A01G566400 chr7D 541964382 541966914 2532 True 1308.0 1502 86.500500 975 3427 2 chr7D.!!$R2 2452
8 TraesCS7A01G566400 chr7D 556717103 556719600 2497 True 1246.0 1345 86.151500 994 3415 2 chr7D.!!$R4 2421
9 TraesCS7A01G566400 chr7D 541500999 541502438 1439 True 1173.0 1173 81.453000 995 2433 1 chr7D.!!$R1 1438
10 TraesCS7A01G566400 chr7D 542097278 542099621 2343 True 1034.0 1057 83.860000 1174 3435 2 chr7D.!!$R3 2261
11 TraesCS7A01G566400 chr7B 585513722 585515177 1455 True 1441.0 1441 84.615000 981 2429 1 chr7B.!!$R1 1448
12 TraesCS7A01G566400 chr7B 604098302 604100811 2509 True 1239.0 1386 85.774500 996 3426 2 chr7B.!!$R3 2430
13 TraesCS7A01G566400 chr7B 585578481 585579369 888 True 1038.0 1038 87.751000 2475 3369 1 chr7B.!!$R2 894

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
2434 5494 7.827236 TCCAGAGAAACAAAAAGAAGAACTACA 59.173 33.333 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3438 6715 0.107897 TTATGTGCGCTTCCGACCAT 60.108 50.0 9.73 2.13 36.29 3.55 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
2434 5494 7.827236 TCCAGAGAAACAAAAAGAAGAACTACA 59.173 33.333 0.00 0.00 0.00 2.74
2437 5497 8.669243 AGAGAAACAAAAAGAAGAACTACAGTG 58.331 33.333 0.00 0.00 0.00 3.66
2440 5500 9.278734 GAAACAAAAAGAAGAACTACAGTGAAG 57.721 33.333 0.00 0.00 0.00 3.02
2441 5501 8.561738 AACAAAAAGAAGAACTACAGTGAAGA 57.438 30.769 0.00 0.00 0.00 2.87
2442 5502 8.738645 ACAAAAAGAAGAACTACAGTGAAGAT 57.261 30.769 0.00 0.00 0.00 2.40
2443 5503 8.616076 ACAAAAAGAAGAACTACAGTGAAGATG 58.384 33.333 0.00 0.00 0.00 2.90
2444 5504 6.793492 AAAGAAGAACTACAGTGAAGATGC 57.207 37.500 0.00 0.00 0.00 3.91
2445 5505 5.736951 AGAAGAACTACAGTGAAGATGCT 57.263 39.130 0.00 0.00 0.00 3.79
2446 5506 5.719173 AGAAGAACTACAGTGAAGATGCTC 58.281 41.667 0.00 0.00 0.00 4.26
2448 5508 3.759086 AGAACTACAGTGAAGATGCTCGA 59.241 43.478 0.00 0.00 0.00 4.04
2449 5509 4.400884 AGAACTACAGTGAAGATGCTCGAT 59.599 41.667 0.00 0.00 0.00 3.59
2450 5510 4.039151 ACTACAGTGAAGATGCTCGATG 57.961 45.455 0.00 0.00 0.00 3.84
2453 5513 1.931841 CAGTGAAGATGCTCGATGGTG 59.068 52.381 0.00 0.00 0.00 4.17
2455 5515 0.538584 TGAAGATGCTCGATGGTGCT 59.461 50.000 3.45 0.00 33.89 4.40
2456 5516 1.065926 TGAAGATGCTCGATGGTGCTT 60.066 47.619 3.45 0.00 33.89 3.91
2458 5518 3.181462 TGAAGATGCTCGATGGTGCTTAT 60.181 43.478 3.45 0.00 33.89 1.73
2459 5519 3.037431 AGATGCTCGATGGTGCTTATC 57.963 47.619 3.45 0.00 33.89 1.75
2460 5520 2.072298 GATGCTCGATGGTGCTTATCC 58.928 52.381 3.45 0.00 33.89 2.59
2462 5522 1.069204 TGCTCGATGGTGCTTATCCTC 59.931 52.381 3.45 0.00 33.89 3.71
2464 5524 2.224161 GCTCGATGGTGCTTATCCTCTT 60.224 50.000 0.00 0.00 0.00 2.85
2822 5956 5.948162 ACACTGTGATATCAAGCCAGAAAAT 59.052 36.000 22.12 3.77 0.00 1.82
3445 6722 8.771920 TTGTAATTATTATGAGCTATGGTCGG 57.228 34.615 0.00 0.00 32.15 4.79
3446 6723 8.129496 TGTAATTATTATGAGCTATGGTCGGA 57.871 34.615 0.00 0.00 32.15 4.55
3447 6724 8.590204 TGTAATTATTATGAGCTATGGTCGGAA 58.410 33.333 0.00 0.00 32.15 4.30
3448 6725 9.088512 GTAATTATTATGAGCTATGGTCGGAAG 57.911 37.037 0.00 0.00 32.15 3.46
3449 6726 3.386768 TTATGAGCTATGGTCGGAAGC 57.613 47.619 0.00 0.00 36.48 3.86
3450 6727 0.032678 ATGAGCTATGGTCGGAAGCG 59.967 55.000 0.00 0.00 41.19 4.68
3451 6728 1.951631 GAGCTATGGTCGGAAGCGC 60.952 63.158 0.00 0.00 41.19 5.92
3452 6729 2.202878 GCTATGGTCGGAAGCGCA 60.203 61.111 11.47 0.00 0.00 6.09
3453 6730 2.526120 GCTATGGTCGGAAGCGCAC 61.526 63.158 11.47 2.54 0.00 5.34
3454 6731 1.153647 CTATGGTCGGAAGCGCACA 60.154 57.895 11.47 0.00 0.00 4.57
3455 6732 0.530650 CTATGGTCGGAAGCGCACAT 60.531 55.000 11.47 4.75 0.00 3.21
3456 6733 0.747852 TATGGTCGGAAGCGCACATA 59.252 50.000 11.47 3.77 0.00 2.29
3457 6734 0.107897 ATGGTCGGAAGCGCACATAA 60.108 50.000 11.47 0.00 0.00 1.90
3458 6735 0.320858 TGGTCGGAAGCGCACATAAA 60.321 50.000 11.47 0.00 0.00 1.40
3459 6736 0.800012 GGTCGGAAGCGCACATAAAA 59.200 50.000 11.47 0.00 0.00 1.52
3460 6737 1.198178 GGTCGGAAGCGCACATAAAAA 59.802 47.619 11.47 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2434 5494 1.741732 GCACCATCGAGCATCTTCACT 60.742 52.381 0.00 0.00 0.00 3.41
2437 5497 1.661341 AAGCACCATCGAGCATCTTC 58.339 50.000 0.00 0.00 0.00 2.87
2440 5500 2.072298 GGATAAGCACCATCGAGCATC 58.928 52.381 0.00 0.00 0.00 3.91
2441 5501 1.696336 AGGATAAGCACCATCGAGCAT 59.304 47.619 0.00 0.00 0.00 3.79
2442 5502 1.069204 GAGGATAAGCACCATCGAGCA 59.931 52.381 0.00 0.00 0.00 4.26
2443 5503 1.342819 AGAGGATAAGCACCATCGAGC 59.657 52.381 0.00 0.00 0.00 5.03
2444 5504 3.742433 AAGAGGATAAGCACCATCGAG 57.258 47.619 0.00 0.00 0.00 4.04
2445 5505 3.574396 CCTAAGAGGATAAGCACCATCGA 59.426 47.826 0.00 0.00 37.67 3.59
2446 5506 3.322254 ACCTAAGAGGATAAGCACCATCG 59.678 47.826 0.00 0.00 37.67 3.84
2448 5508 5.717119 AAACCTAAGAGGATAAGCACCAT 57.283 39.130 0.00 0.00 37.67 3.55
2449 5509 5.253330 CAAAACCTAAGAGGATAAGCACCA 58.747 41.667 0.00 0.00 37.67 4.17
2450 5510 4.640647 CCAAAACCTAAGAGGATAAGCACC 59.359 45.833 0.00 0.00 37.67 5.01
2453 5513 6.094186 CAGAACCAAAACCTAAGAGGATAAGC 59.906 42.308 0.00 0.00 37.67 3.09
2455 5515 7.086685 ACAGAACCAAAACCTAAGAGGATAA 57.913 36.000 0.00 0.00 37.67 1.75
2456 5516 6.697641 ACAGAACCAAAACCTAAGAGGATA 57.302 37.500 0.00 0.00 37.67 2.59
2458 5518 6.697641 ATACAGAACCAAAACCTAAGAGGA 57.302 37.500 0.00 0.00 37.67 3.71
2459 5519 6.940298 TGAATACAGAACCAAAACCTAAGAGG 59.060 38.462 0.00 0.00 42.49 3.69
2460 5520 7.979444 TGAATACAGAACCAAAACCTAAGAG 57.021 36.000 0.00 0.00 0.00 2.85
2462 5522 7.309194 CCCTTGAATACAGAACCAAAACCTAAG 60.309 40.741 0.00 0.00 0.00 2.18
2464 5524 6.007703 CCCTTGAATACAGAACCAAAACCTA 58.992 40.000 0.00 0.00 0.00 3.08
2822 5956 8.478877 GGAAGGAGTGAAGAATCAAGAAGTATA 58.521 37.037 0.00 0.00 37.30 1.47
3427 6704 4.380550 CGCTTCCGACCATAGCTCATAATA 60.381 45.833 0.00 0.00 36.29 0.98
3435 6712 2.202878 TGCGCTTCCGACCATAGC 60.203 61.111 9.73 0.00 36.29 2.97
3436 6713 0.530650 ATGTGCGCTTCCGACCATAG 60.531 55.000 9.73 0.00 36.29 2.23
3437 6714 0.747852 TATGTGCGCTTCCGACCATA 59.252 50.000 9.73 1.19 36.29 2.74
3438 6715 0.107897 TTATGTGCGCTTCCGACCAT 60.108 50.000 9.73 2.13 36.29 3.55
3439 6716 0.320858 TTTATGTGCGCTTCCGACCA 60.321 50.000 9.73 0.00 36.29 4.02
3440 6717 0.800012 TTTTATGTGCGCTTCCGACC 59.200 50.000 9.73 0.00 36.29 4.79
3441 6718 2.604969 TTTTTATGTGCGCTTCCGAC 57.395 45.000 9.73 0.00 36.29 4.79


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

AutoCloner maintained by Alex Coulton.