Multiple sequence alignment - TraesCS3B01G225900

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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 TraesCS3B01G225900 chr3B 100.000 3890 0 0 1 3890 312167822 312163933 0.000000e+00 7184.0
1 TraesCS3B01G225900 chr3B 97.105 1278 30 7 2146 3420 795970388 795971661 0.000000e+00 2148.0
2 TraesCS3B01G225900 chr3B 82.523 2346 325 51 572 2874 62881452 62879149 0.000000e+00 1982.0
3 TraesCS3B01G225900 chr3B 97.467 1066 27 0 572 1637 795969326 795970391 0.000000e+00 1820.0
4 TraesCS3B01G225900 chr1B 97.068 2865 51 5 572 3420 89441888 89439041 0.000000e+00 4795.0
5 TraesCS3B01G225900 chr1B 84.392 1275 176 17 572 1827 187184548 187185818 0.000000e+00 1230.0
6 TraesCS3B01G225900 chr6D 95.768 1465 48 1 1967 3417 229383243 229384707 0.000000e+00 2350.0
7 TraesCS3B01G225900 chr6D 96.486 1366 42 3 572 1936 229354019 229355379 0.000000e+00 2252.0
8 TraesCS3B01G225900 chr6D 94.241 573 30 3 1 571 69217488 69218059 0.000000e+00 872.0
9 TraesCS3B01G225900 chrUn 82.439 2460 359 59 572 2986 75466112 75468543 0.000000e+00 2082.0
10 TraesCS3B01G225900 chr7A 82.570 2358 356 45 572 2891 450569921 450567581 0.000000e+00 2026.0
11 TraesCS3B01G225900 chr7A 90.777 206 19 0 3215 3420 458775436 458775231 3.830000e-70 276.0
12 TraesCS3B01G225900 chr2D 82.480 2363 356 48 572 2896 121215071 121212729 0.000000e+00 2017.0
13 TraesCS3B01G225900 chr2D 94.241 573 28 4 1 571 582814636 582814067 0.000000e+00 870.0
14 TraesCS3B01G225900 chr2D 94.097 559 29 3 1 557 197862928 197863484 0.000000e+00 846.0
15 TraesCS3B01G225900 chr2D 87.910 670 55 17 2752 3417 555035344 555034697 0.000000e+00 765.0
16 TraesCS3B01G225900 chr6B 82.427 2373 353 49 572 2896 139442843 139445199 0.000000e+00 2013.0
17 TraesCS3B01G225900 chr3D 81.748 2460 365 61 572 2986 166288198 166290618 0.000000e+00 1978.0
18 TraesCS3B01G225900 chr3D 98.061 361 5 1 3421 3781 250928162 250927804 9.180000e-176 627.0
19 TraesCS3B01G225900 chr3D 100.000 115 0 0 3776 3890 250925760 250925646 3.040000e-51 213.0
20 TraesCS3B01G225900 chr7B 81.565 2441 378 56 572 2979 515067896 515070297 0.000000e+00 1949.0
21 TraesCS3B01G225900 chr5A 82.258 1798 265 42 597 2355 672817703 672815921 0.000000e+00 1504.0
22 TraesCS3B01G225900 chr1D 80.624 1507 210 58 1488 2942 122843404 122841928 0.000000e+00 1090.0
23 TraesCS3B01G225900 chr1D 90.455 220 21 0 3200 3419 121620091 121619872 1.370000e-74 291.0
24 TraesCS3B01G225900 chr7D 94.939 573 27 2 1 571 533431532 533432104 0.000000e+00 896.0
25 TraesCS3B01G225900 chr4D 94.764 573 28 2 1 571 55272717 55273289 0.000000e+00 891.0
26 TraesCS3B01G225900 chr4D 93.902 574 32 3 1 571 456282799 456283372 0.000000e+00 863.0
27 TraesCS3B01G225900 chr4D 81.651 109 16 2 3509 3614 323554901 323555008 1.930000e-13 87.9
28 TraesCS3B01G225900 chr4A 94.590 573 29 2 1 571 722419599 722420171 0.000000e+00 885.0
29 TraesCS3B01G225900 chr5D 94.241 573 30 3 1 571 51642828 51642257 0.000000e+00 872.0
30 TraesCS3B01G225900 chr5D 85.597 486 61 6 2458 2942 535527126 535526649 5.800000e-138 501.0
31 TraesCS3B01G225900 chr2A 93.531 572 35 2 2 571 764778578 764779149 0.000000e+00 850.0
32 TraesCS3B01G225900 chr3A 98.936 470 5 0 3421 3890 333318259 333318728 0.000000e+00 841.0
33 TraesCS3B01G225900 chr2B 80.903 864 142 18 2126 2985 212061665 212060821 0.000000e+00 660.0
34 TraesCS3B01G225900 chr2B 91.469 211 18 0 3215 3425 128365011 128364801 1.370000e-74 291.0
35 TraesCS3B01G225900 chr1A 80.987 689 106 21 2307 2986 42898329 42899001 1.240000e-144 523.0
36 TraesCS3B01G225900 chr5B 90.411 219 19 2 3199 3416 554656134 554655917 1.770000e-73 287.0
37 TraesCS3B01G225900 chr5B 89.954 219 22 0 3199 3417 33544552 33544770 2.290000e-72 283.0


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 TraesCS3B01G225900 chr3B 312163933 312167822 3889 True 7184 7184 100.0000 1 3890 1 chr3B.!!$R2 3889
1 TraesCS3B01G225900 chr3B 795969326 795971661 2335 False 1984 2148 97.2860 572 3420 2 chr3B.!!$F1 2848
2 TraesCS3B01G225900 chr3B 62879149 62881452 2303 True 1982 1982 82.5230 572 2874 1 chr3B.!!$R1 2302
3 TraesCS3B01G225900 chr1B 89439041 89441888 2847 True 4795 4795 97.0680 572 3420 1 chr1B.!!$R1 2848
4 TraesCS3B01G225900 chr1B 187184548 187185818 1270 False 1230 1230 84.3920 572 1827 1 chr1B.!!$F1 1255
5 TraesCS3B01G225900 chr6D 229383243 229384707 1464 False 2350 2350 95.7680 1967 3417 1 chr6D.!!$F3 1450
6 TraesCS3B01G225900 chr6D 229354019 229355379 1360 False 2252 2252 96.4860 572 1936 1 chr6D.!!$F2 1364
7 TraesCS3B01G225900 chr6D 69217488 69218059 571 False 872 872 94.2410 1 571 1 chr6D.!!$F1 570
8 TraesCS3B01G225900 chrUn 75466112 75468543 2431 False 2082 2082 82.4390 572 2986 1 chrUn.!!$F1 2414
9 TraesCS3B01G225900 chr7A 450567581 450569921 2340 True 2026 2026 82.5700 572 2891 1 chr7A.!!$R1 2319
10 TraesCS3B01G225900 chr2D 121212729 121215071 2342 True 2017 2017 82.4800 572 2896 1 chr2D.!!$R1 2324
11 TraesCS3B01G225900 chr2D 582814067 582814636 569 True 870 870 94.2410 1 571 1 chr2D.!!$R3 570
12 TraesCS3B01G225900 chr2D 197862928 197863484 556 False 846 846 94.0970 1 557 1 chr2D.!!$F1 556
13 TraesCS3B01G225900 chr2D 555034697 555035344 647 True 765 765 87.9100 2752 3417 1 chr2D.!!$R2 665
14 TraesCS3B01G225900 chr6B 139442843 139445199 2356 False 2013 2013 82.4270 572 2896 1 chr6B.!!$F1 2324
15 TraesCS3B01G225900 chr3D 166288198 166290618 2420 False 1978 1978 81.7480 572 2986 1 chr3D.!!$F1 2414
16 TraesCS3B01G225900 chr3D 250925646 250928162 2516 True 420 627 99.0305 3421 3890 2 chr3D.!!$R1 469
17 TraesCS3B01G225900 chr7B 515067896 515070297 2401 False 1949 1949 81.5650 572 2979 1 chr7B.!!$F1 2407
18 TraesCS3B01G225900 chr5A 672815921 672817703 1782 True 1504 1504 82.2580 597 2355 1 chr5A.!!$R1 1758
19 TraesCS3B01G225900 chr1D 122841928 122843404 1476 True 1090 1090 80.6240 1488 2942 1 chr1D.!!$R2 1454
20 TraesCS3B01G225900 chr7D 533431532 533432104 572 False 896 896 94.9390 1 571 1 chr7D.!!$F1 570
21 TraesCS3B01G225900 chr4D 55272717 55273289 572 False 891 891 94.7640 1 571 1 chr4D.!!$F1 570
22 TraesCS3B01G225900 chr4D 456282799 456283372 573 False 863 863 93.9020 1 571 1 chr4D.!!$F3 570
23 TraesCS3B01G225900 chr4A 722419599 722420171 572 False 885 885 94.5900 1 571 1 chr4A.!!$F1 570
24 TraesCS3B01G225900 chr5D 51642257 51642828 571 True 872 872 94.2410 1 571 1 chr5D.!!$R1 570
25 TraesCS3B01G225900 chr2A 764778578 764779149 571 False 850 850 93.5310 2 571 1 chr2A.!!$F1 569
26 TraesCS3B01G225900 chr2B 212060821 212061665 844 True 660 660 80.9030 2126 2985 1 chr2B.!!$R2 859
27 TraesCS3B01G225900 chr1A 42898329 42899001 672 False 523 523 80.9870 2307 2986 1 chr1A.!!$F1 679

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
254 256 1.342076 TGTAGACGCCCTCCAGATCTT 60.342 52.381 0.00 0.00 0.00 2.40 F
595 599 4.208047 GCTATGATGAGTTGCGACTAACAG 59.792 45.833 6.58 0.42 35.88 3.16 F
2507 2620 1.168714 GTGAAGCATTGGGAGTCCAC 58.831 55.000 12.30 0.78 43.94 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 2279 3.152341 CCTTGTTGCACTTCTCCTTCAT 58.848 45.455 0.00 0.0 0.00 2.57 R
2772 2921 0.959372 GCAACATGTCTGGCTCTGCT 60.959 55.000 0.00 0.0 0.00 4.24 R
3308 3465 1.484227 TTCACGTGTTCGGTTGCTCG 61.484 55.000 16.51 0.0 41.85 5.03 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
254 256 1.342076 TGTAGACGCCCTCCAGATCTT 60.342 52.381 0.00 0.00 0.00 2.40
595 599 4.208047 GCTATGATGAGTTGCGACTAACAG 59.792 45.833 6.58 0.42 35.88 3.16
616 620 5.009410 ACAGAAAGAAACTTTCATGCTCTGG 59.991 40.000 20.97 7.06 32.33 3.86
1165 1180 8.718102 TCTCCATGTAATTGTTAGCTAACTTC 57.282 34.615 31.14 18.61 37.12 3.01
1320 1336 8.073467 ACTTCTAAAGAGCTCTATAACTTGCT 57.927 34.615 18.59 0.00 38.59 3.91
1331 1347 6.256757 GCTCTATAACTTGCTTCATTCTCGTT 59.743 38.462 0.00 0.00 0.00 3.85
1395 1411 7.611213 AAAAATGGGTCATACTAAGAGTTCG 57.389 36.000 0.00 0.00 0.00 3.95
2173 2279 5.530915 GTGTATTGTGCAGCCATAAGGAATA 59.469 40.000 0.00 0.00 36.89 1.75
2507 2620 1.168714 GTGAAGCATTGGGAGTCCAC 58.831 55.000 12.30 0.78 43.94 4.02
2772 2921 5.011635 TGCACTTCAGTTGATACCAGACTTA 59.988 40.000 0.00 0.00 0.00 2.24
2933 3083 6.844696 TCAGCTTGTCTTGTTTAACTACTG 57.155 37.500 0.00 0.00 0.00 2.74
3069 3224 3.536158 TTTGCACTCTGTTCGCATAAC 57.464 42.857 0.00 0.00 35.19 1.89
3245 3402 6.469139 TTGATGCATAAAACACAAAGCATG 57.531 33.333 0.00 0.00 42.18 4.06
3267 3424 7.654568 CATGTGCAATTCCATAGTATGTCATT 58.345 34.615 9.28 4.23 0.00 2.57
3308 3465 1.413812 GATTCCATGGCCCAATTCCAC 59.586 52.381 6.96 0.00 36.26 4.02
3355 3512 7.171653 TGTATTCATGTCCATTACAGTTTCCA 58.828 34.615 0.00 0.00 42.70 3.53
3359 3516 4.974645 TGTCCATTACAGTTTCCACTCT 57.025 40.909 0.00 0.00 33.01 3.24
3431 3589 3.681705 CACAGCGCAAGTGTTATGG 57.318 52.632 20.69 0.00 41.68 2.74
3571 3729 5.840243 ATGCCAGTATACTTACACGTACA 57.160 39.130 1.56 0.00 0.00 2.90
3619 3777 5.279156 CCCTTATACAACGGGGATACTACAC 60.279 48.000 0.00 0.00 41.25 2.90
3620 3778 5.302568 CCTTATACAACGGGGATACTACACA 59.697 44.000 0.00 0.00 0.00 3.72
3631 3789 7.725397 ACGGGGATACTACACAACTAATATACA 59.275 37.037 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 4.546570 GTGAAAACTTGCTTTCGGCTTAT 58.453 39.130 0.00 0.00 42.39 1.73
230 232 3.075005 GGAGGGCGTCTACAGGCA 61.075 66.667 7.19 0.00 34.92 4.75
409 412 1.215647 GGTGGCGATCTCTTGTCGT 59.784 57.895 0.00 0.00 40.98 4.34
595 599 4.802999 CCCAGAGCATGAAAGTTTCTTTC 58.197 43.478 16.33 13.28 0.00 2.62
616 620 3.499737 CTCCCGCAACATCGTGCC 61.500 66.667 0.00 0.00 41.73 5.01
1320 1336 7.095229 CCACAACATTTCTAGAACGAGAATGAA 60.095 37.037 17.15 0.00 35.41 2.57
1331 1347 6.672266 AGTTCTCTCCACAACATTTCTAGA 57.328 37.500 0.00 0.00 0.00 2.43
1380 1396 9.574458 CAAAGAAAGATCGAACTCTTAGTATGA 57.426 33.333 1.82 0.00 34.40 2.15
1395 1411 9.061435 CCTGGTCCTTTATATCAAAGAAAGATC 57.939 37.037 0.00 0.00 32.94 2.75
1447 1468 5.300411 TCAGCATGTCATCACTATCCATT 57.700 39.130 0.00 0.00 37.40 3.16
2173 2279 3.152341 CCTTGTTGCACTTCTCCTTCAT 58.848 45.455 0.00 0.00 0.00 2.57
2772 2921 0.959372 GCAACATGTCTGGCTCTGCT 60.959 55.000 0.00 0.00 0.00 4.24
2933 3083 3.621715 CCGCACTAGTTCAAATAGGTTCC 59.378 47.826 0.00 0.00 0.00 3.62
3215 3371 9.932699 CTTTGTGTTTTATGCATCAAATCAAAA 57.067 25.926 23.46 14.88 0.00 2.44
3245 3402 6.202762 TCGAATGACATACTATGGAATTGCAC 59.797 38.462 0.12 0.00 33.60 4.57
3267 3424 7.012327 GGAATCTCAATACCAAATCATGTTCGA 59.988 37.037 0.00 0.00 0.00 3.71
3308 3465 1.484227 TTCACGTGTTCGGTTGCTCG 61.484 55.000 16.51 0.00 41.85 5.03
3355 3512 6.729690 TTGGTTTCATTTCCAATTCAGAGT 57.270 33.333 0.00 0.00 38.57 3.24
3381 3539 7.123383 TGTCTGTATTGGAGACCTCTGTATTA 58.877 38.462 0.00 0.00 39.36 0.98
3431 3589 7.600375 TCTCAATCGATCAAATATCCTGTTAGC 59.400 37.037 0.00 0.00 0.00 3.09
3571 3729 6.406849 GGGTTTCATGCATATTTACCACACAT 60.407 38.462 16.55 0.00 0.00 3.21
3697 3855 7.905265 TGTGGATATGTTTTTGTCATGGAAAT 58.095 30.769 0.00 0.00 0.00 2.17
3742 3900 2.965572 TGCCCATGCTTTTGATAAGC 57.034 45.000 0.47 0.47 43.29 3.09


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

AutoCloner maintained by Alex Coulton.