Multiple sequence alignment - TraesCS4A01G024900

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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 TraesCS4A01G024900 chr4A 100.000 2633 0 0 1 2633 17244817 17247449 0.000000e+00 4863
1 TraesCS4A01G024900 chr7A 97.153 2634 67 5 1 2633 672599454 672596828 0.000000e+00 4442
2 TraesCS4A01G024900 chr7A 96.925 2634 73 3 1 2633 113794948 113797574 0.000000e+00 4409
3 TraesCS4A01G024900 chr7A 96.831 2114 40 3 521 2633 674116095 674114008 0.000000e+00 3507
4 TraesCS4A01G024900 chr7A 97.732 529 12 0 1 529 674121703 674121175 0.000000e+00 911
5 TraesCS4A01G024900 chr7A 100.000 74 0 0 2241 2314 113797235 113797308 1.270000e-28 137
6 TraesCS4A01G024900 chr7A 97.260 73 2 0 2120 2192 613713189 613713117 9.900000e-25 124
7 TraesCS4A01G024900 chr5A 97.882 2314 43 1 1 2314 609823842 609821535 0.000000e+00 3997
8 TraesCS4A01G024900 chr5A 91.949 857 54 5 415 1271 688243208 688244049 0.000000e+00 1186
9 TraesCS4A01G024900 chr5A 97.647 340 7 1 2295 2633 609821608 609821269 1.360000e-162 582
10 TraesCS4A01G024900 chr5A 87.067 433 44 6 1356 1784 688244181 688244605 1.830000e-131 479
11 TraesCS4A01G024900 chr5A 88.379 327 32 3 1356 1682 680364945 680365265 3.180000e-104 388
12 TraesCS4A01G024900 chr5A 89.157 249 20 4 1117 1359 680364641 680364888 1.180000e-78 303
13 TraesCS4A01G024900 chr5A 92.920 113 8 0 1706 1818 680365260 680365372 5.830000e-37 165
14 TraesCS4A01G024900 chr5A 98.630 73 1 0 2120 2192 605038938 605038866 2.130000e-26 130
15 TraesCS4A01G024900 chr3A 97.276 2313 46 4 2 2314 697520140 697522435 0.000000e+00 3906
16 TraesCS4A01G024900 chr3A 96.481 341 10 2 2295 2633 697522362 697522702 1.770000e-156 562
17 TraesCS4A01G024900 chr4B 89.608 943 75 9 415 1350 649491307 649492233 0.000000e+00 1177
18 TraesCS4A01G024900 chr4B 89.394 462 28 4 1356 1817 649492303 649492743 1.770000e-156 562
19 TraesCS4A01G024900 chr4D 86.645 936 65 26 415 1344 503669221 503670102 0.000000e+00 981
20 TraesCS4A01G024900 chr4D 88.300 641 41 14 721 1359 503639662 503640270 0.000000e+00 737
21 TraesCS4A01G024900 chr4D 86.866 434 44 5 1356 1784 503670177 503670602 8.530000e-130 473
22 TraesCS4A01G024900 chr4D 85.468 406 23 15 1412 1817 503641746 503642115 8.840000e-105 390
23 TraesCS4A01G024900 chr4D 92.920 113 8 0 1990 2102 198583169 198583281 5.830000e-37 165
24 TraesCS4A01G024900 chr4D 98.630 73 1 0 2120 2192 198584148 198584076 2.130000e-26 130
25 TraesCS4A01G024900 chr1B 93.311 598 24 5 415 1005 117290240 117289652 0.000000e+00 869
26 TraesCS4A01G024900 chr1B 94.330 388 22 0 2 389 117290917 117290530 1.740000e-166 595
27 TraesCS4A01G024900 chr1B 94.602 352 17 2 2284 2633 117289647 117289296 6.410000e-151 544
28 TraesCS4A01G024900 chr5D 93.750 352 19 3 2284 2633 358667904 358667554 2.320000e-145 525
29 TraesCS4A01G024900 chr5D 93.238 281 18 1 56 335 358669211 358668931 1.890000e-111 412
30 TraesCS4A01G024900 chr5D 91.538 130 11 0 1836 1965 548028003 548027874 2.080000e-41 180
31 TraesCS4A01G024900 chr5D 95.050 101 5 0 1833 1933 358668096 358667996 2.710000e-35 159
32 TraesCS4A01G024900 chr5D 95.604 91 1 2 2226 2314 358667910 358667821 2.730000e-30 143
33 TraesCS4A01G024900 chr7D 95.092 326 15 1 11 335 32582890 32582565 1.810000e-141 512
34 TraesCS4A01G024900 chr2A 91.738 351 19 4 2291 2631 207108769 207109119 1.830000e-131 479
35 TraesCS4A01G024900 chr2A 90.517 116 8 2 2201 2314 207108732 207108846 1.630000e-32 150
36 TraesCS4A01G024900 chr3B 90.909 352 29 2 2285 2633 742768166 742767815 1.100000e-128 470
37 TraesCS4A01G024900 chr5B 90.909 132 12 0 1834 1965 692215151 692215020 7.490000e-41 178
38 TraesCS4A01G024900 chr5B 98.630 73 1 0 2120 2192 386155100 386155028 2.130000e-26 130
39 TraesCS4A01G024900 chr2D 93.103 116 5 2 2201 2314 107761085 107761199 1.620000e-37 167
40 TraesCS4A01G024900 chr6A 91.150 113 10 0 1990 2102 36692100 36692212 1.260000e-33 154
41 TraesCS4A01G024900 chr6B 92.473 93 7 0 2010 2102 67995842 67995934 1.640000e-27 134


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 TraesCS4A01G024900 chr4A 17244817 17247449 2632 False 4863.000000 4863 100.0000 1 2633 1 chr4A.!!$F1 2632
1 TraesCS4A01G024900 chr7A 672596828 672599454 2626 True 4442.000000 4442 97.1530 1 2633 1 chr7A.!!$R2 2632
2 TraesCS4A01G024900 chr7A 674114008 674116095 2087 True 3507.000000 3507 96.8310 521 2633 1 chr7A.!!$R3 2112
3 TraesCS4A01G024900 chr7A 113794948 113797574 2626 False 2273.000000 4409 98.4625 1 2633 2 chr7A.!!$F1 2632
4 TraesCS4A01G024900 chr7A 674121175 674121703 528 True 911.000000 911 97.7320 1 529 1 chr7A.!!$R4 528
5 TraesCS4A01G024900 chr5A 609821269 609823842 2573 True 2289.500000 3997 97.7645 1 2633 2 chr5A.!!$R2 2632
6 TraesCS4A01G024900 chr5A 688243208 688244605 1397 False 832.500000 1186 89.5080 415 1784 2 chr5A.!!$F2 1369
7 TraesCS4A01G024900 chr5A 680364641 680365372 731 False 285.333333 388 90.1520 1117 1818 3 chr5A.!!$F1 701
8 TraesCS4A01G024900 chr3A 697520140 697522702 2562 False 2234.000000 3906 96.8785 2 2633 2 chr3A.!!$F1 2631
9 TraesCS4A01G024900 chr4B 649491307 649492743 1436 False 869.500000 1177 89.5010 415 1817 2 chr4B.!!$F1 1402
10 TraesCS4A01G024900 chr4D 503669221 503670602 1381 False 727.000000 981 86.7555 415 1784 2 chr4D.!!$F3 1369
11 TraesCS4A01G024900 chr4D 503639662 503642115 2453 False 563.500000 737 86.8840 721 1817 2 chr4D.!!$F2 1096
12 TraesCS4A01G024900 chr1B 117289296 117290917 1621 True 669.333333 869 94.0810 2 2633 3 chr1B.!!$R1 2631
13 TraesCS4A01G024900 chr5D 358667554 358669211 1657 True 309.750000 525 94.4105 56 2633 4 chr5D.!!$R2 2577

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
367 462 1.604147 GGGGAATTTTGTCAGGGGCG 61.604 60.000 0.00 0.0 0.00 6.13 F
1096 1507 1.384502 AGGGATCTTCATGCCCCGA 60.385 57.895 1.98 0.0 41.59 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 3498 1.625818 GCCAGAACCCAGAGAAAGAGA 59.374 52.381 0.0 0.0 0.0 3.10 R
2337 4365 4.884164 AGACAAGCAGTTTTTAGAGCAAGT 59.116 37.500 0.0 0.0 0.0 3.16 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
367 462 1.604147 GGGGAATTTTGTCAGGGGCG 61.604 60.000 0.00 0.00 0.00 6.13
491 881 4.759693 TGTCAGTGTCAAAACTCTTGTTGT 59.240 37.500 0.00 0.00 36.39 3.32
627 1022 4.242811 AGGCCATCCTATCAATTGACCTA 58.757 43.478 11.07 0.00 42.06 3.08
661 1056 6.431198 TTTTTCGAGTTAAGCTTCACTTGT 57.569 33.333 21.98 0.06 39.58 3.16
673 1074 3.120060 GCTTCACTTGTTGCCATCTAGTG 60.120 47.826 10.02 10.02 38.98 2.74
859 1270 7.596248 GCGCCAATGATGTATCTTTTTCATATT 59.404 33.333 0.00 0.00 0.00 1.28
1018 1429 6.982724 CAGCTACATGAATCTAGTGTTGATCA 59.017 38.462 0.00 0.00 0.00 2.92
1096 1507 1.384502 AGGGATCTTCATGCCCCGA 60.385 57.895 1.98 0.00 41.59 5.14
1328 1741 3.306364 CCTCCCTGTATGAGAATAAGGCG 60.306 52.174 0.00 0.00 31.26 5.52
1584 3490 2.586425 ACATGGTTGTTGCAAGCTACT 58.414 42.857 0.00 0.00 29.55 2.57
1588 3494 3.287222 TGGTTGTTGCAAGCTACTTCTT 58.713 40.909 0.00 0.00 0.00 2.52
1589 3495 3.315191 TGGTTGTTGCAAGCTACTTCTTC 59.685 43.478 0.00 0.00 0.00 2.87
1590 3496 3.565902 GGTTGTTGCAAGCTACTTCTTCT 59.434 43.478 0.00 0.00 0.00 2.85
1592 3498 5.450550 GGTTGTTGCAAGCTACTTCTTCTTT 60.451 40.000 0.00 0.00 0.00 2.52
2040 3978 8.262601 AGGAATAATTGAAAAGAACCTGGTTT 57.737 30.769 14.28 0.00 0.00 3.27
2149 4087 3.435327 TGCAAATACTCCTACTGCAAACG 59.565 43.478 0.00 0.00 39.91 3.60
2326 4266 6.755206 TGTCTACTGCTTGCTCTAAAAACTA 58.245 36.000 0.00 0.00 0.00 2.24
2337 4365 7.058023 TGCTCTAAAAACTACTTGTCTACCA 57.942 36.000 0.00 0.00 0.00 3.25
2385 4413 9.683069 CTACTGCTTTGACATGTTTTAGATTTT 57.317 29.630 0.00 0.00 0.00 1.82
2418 4446 1.948834 CATGTGTGTGGTGAGCTTCAA 59.051 47.619 0.00 0.00 0.00 2.69
2423 4451 2.698274 TGTGTGGTGAGCTTCAAGACTA 59.302 45.455 0.00 0.00 0.00 2.59
2597 4628 2.867647 GCCCAAGGATGAGTTTTTGTGC 60.868 50.000 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 280 1.374252 CGGCGAAGTGGTAAGCTGT 60.374 57.895 0.00 0.0 0.00 4.40
367 462 9.899226 ACAAGTTTGCTAGAAACTTAATGATTC 57.101 29.630 21.90 0.0 45.57 2.52
642 1037 3.247648 GCAACAAGTGAAGCTTAACTCGA 59.752 43.478 17.16 0.0 35.27 4.04
661 1056 1.204146 GGTCCCTCACTAGATGGCAA 58.796 55.000 0.00 0.0 30.36 4.52
673 1074 3.376082 TGGTACAGACTGGTCCCTC 57.624 57.895 7.51 0.0 0.00 4.30
1018 1429 2.431782 ACAAACTCCACAAAAGCTGCAT 59.568 40.909 1.02 0.0 0.00 3.96
1328 1741 6.238759 CCATAACAGCAAGTCTATTTAAGGCC 60.239 42.308 0.00 0.0 0.00 5.19
1584 3490 5.896073 ACCCAGAGAAAGAGAAAGAAGAA 57.104 39.130 0.00 0.0 0.00 2.52
1588 3494 4.040952 CCAGAACCCAGAGAAAGAGAAAGA 59.959 45.833 0.00 0.0 0.00 2.52
1589 3495 4.322567 CCAGAACCCAGAGAAAGAGAAAG 58.677 47.826 0.00 0.0 0.00 2.62
1590 3496 3.496870 GCCAGAACCCAGAGAAAGAGAAA 60.497 47.826 0.00 0.0 0.00 2.52
1592 3498 1.625818 GCCAGAACCCAGAGAAAGAGA 59.374 52.381 0.00 0.0 0.00 3.10
2326 4266 5.546621 TTTAGAGCAAGTGGTAGACAAGT 57.453 39.130 0.00 0.0 0.00 3.16
2337 4365 4.884164 AGACAAGCAGTTTTTAGAGCAAGT 59.116 37.500 0.00 0.0 0.00 3.16


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

AutoCloner maintained by Alex Coulton.