Multiple sequence alignment - TraesCS3A01G311200

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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 TraesCS3A01G311200 chr3A 100.000 2342 0 0 1 2342 550194245 550191904 0.000000e+00 4325.0
1 TraesCS3A01G311200 chr3A 90.462 2380 177 23 1 2342 424415519 424417886 0.000000e+00 3092.0
2 TraesCS3A01G311200 chr3A 90.080 2379 183 34 1 2342 424423619 424425981 0.000000e+00 3037.0
3 TraesCS3A01G311200 chr3A 93.640 456 23 5 1 454 354581957 354582408 0.000000e+00 676.0
4 TraesCS3A01G311200 chr3A 94.231 52 3 0 594 645 239006841 239006790 1.930000e-11 80.5
5 TraesCS3A01G311200 chr3A 97.778 45 1 0 594 638 238998730 238998686 6.940000e-11 78.7
6 TraesCS3A01G311200 chr4A 88.584 2365 208 36 24 2342 460302323 460304671 0.000000e+00 2815.0
7 TraesCS3A01G311200 chr4A 88.203 2365 216 35 24 2342 460310374 460312721 0.000000e+00 2763.0
8 TraesCS3A01G311200 chr4A 93.329 1724 108 7 621 2342 326154682 326152964 0.000000e+00 2540.0
9 TraesCS3A01G311200 chr4A 93.275 1725 108 8 621 2342 326146479 326144760 0.000000e+00 2536.0
10 TraesCS3A01G311200 chr4A 93.089 1722 112 6 624 2342 371964578 371966295 0.000000e+00 2514.0
11 TraesCS3A01G311200 chr6A 93.105 1726 111 7 621 2342 522305273 522306994 0.000000e+00 2521.0
12 TraesCS3A01G311200 chr6A 94.624 93 3 2 581 671 178727073 178727165 2.430000e-30 143.0
13 TraesCS3A01G311200 chr6A 93.548 93 4 2 581 671 178744179 178744271 1.130000e-28 137.0
14 TraesCS3A01G311200 chr6A 86.275 102 6 7 510 608 188126876 188126780 1.140000e-18 104.0
15 TraesCS3A01G311200 chr6A 90.909 55 3 2 591 644 138968935 138968882 3.230000e-09 73.1
16 TraesCS3A01G311200 chr1A 93.048 1726 110 10 621 2342 290860483 290858764 0.000000e+00 2514.0
17 TraesCS3A01G311200 chr1A 90.476 84 4 4 510 591 24086010 24085929 8.850000e-20 108.0
18 TraesCS3A01G311200 chr1A 84.466 103 11 5 510 609 24102734 24102634 1.920000e-16 97.1
19 TraesCS3A01G311200 chr2A 93.048 1726 109 11 621 2342 419880618 419882336 0.000000e+00 2512.0
20 TraesCS3A01G311200 chr2A 92.638 1725 117 10 621 2342 419888577 419890294 0.000000e+00 2473.0
21 TraesCS3A01G311200 chr2A 95.101 347 13 3 1 346 419887899 419888242 5.690000e-151 544.0
22 TraesCS3A01G311200 chr2A 90.476 84 4 4 510 591 145108390 145108309 8.850000e-20 108.0
23 TraesCS3A01G311200 chr2A 88.679 53 4 2 395 447 247134990 247135040 1.940000e-06 63.9
24 TraesCS3A01G311200 chr7A 92.878 1727 112 10 621 2342 68992498 68994218 0.000000e+00 2497.0
25 TraesCS3A01G311200 chr7A 92.857 462 22 7 1 459 270549983 270549530 0.000000e+00 660.0
26 TraesCS3A01G311200 chr5A 93.952 463 21 6 1 459 398148871 398148412 0.000000e+00 693.0
27 TraesCS3A01G311200 chr5A 95.652 391 17 0 65 455 398164717 398164327 1.530000e-176 628.0
28 TraesCS3A01G311200 chr5A 92.920 113 7 1 434 545 159352990 159352878 1.860000e-36 163.0
29 TraesCS3A01G311200 chr5A 89.091 110 12 0 453 562 493983830 493983721 1.130000e-28 137.0
30 TraesCS3A01G311200 chr5A 89.873 79 4 4 515 591 645955020 645954944 5.330000e-17 99.0
31 TraesCS3A01G311200 chr5A 97.222 36 0 1 557 591 493983699 493983664 2.510000e-05 60.2
32 TraesCS3A01G311200 chr4B 92.308 78 6 0 336 413 226557470 226557547 6.840000e-21 111.0


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 TraesCS3A01G311200 chr3A 550191904 550194245 2341 True 4325.0 4325 100.0000 1 2342 1 chr3A.!!$R3 2341
1 TraesCS3A01G311200 chr3A 424415519 424417886 2367 False 3092.0 3092 90.4620 1 2342 1 chr3A.!!$F2 2341
2 TraesCS3A01G311200 chr3A 424423619 424425981 2362 False 3037.0 3037 90.0800 1 2342 1 chr3A.!!$F3 2341
3 TraesCS3A01G311200 chr4A 460302323 460304671 2348 False 2815.0 2815 88.5840 24 2342 1 chr4A.!!$F2 2318
4 TraesCS3A01G311200 chr4A 460310374 460312721 2347 False 2763.0 2763 88.2030 24 2342 1 chr4A.!!$F3 2318
5 TraesCS3A01G311200 chr4A 326152964 326154682 1718 True 2540.0 2540 93.3290 621 2342 1 chr4A.!!$R2 1721
6 TraesCS3A01G311200 chr4A 326144760 326146479 1719 True 2536.0 2536 93.2750 621 2342 1 chr4A.!!$R1 1721
7 TraesCS3A01G311200 chr4A 371964578 371966295 1717 False 2514.0 2514 93.0890 624 2342 1 chr4A.!!$F1 1718
8 TraesCS3A01G311200 chr6A 522305273 522306994 1721 False 2521.0 2521 93.1050 621 2342 1 chr6A.!!$F3 1721
9 TraesCS3A01G311200 chr1A 290858764 290860483 1719 True 2514.0 2514 93.0480 621 2342 1 chr1A.!!$R3 1721
10 TraesCS3A01G311200 chr2A 419880618 419882336 1718 False 2512.0 2512 93.0480 621 2342 1 chr2A.!!$F2 1721
11 TraesCS3A01G311200 chr2A 419887899 419890294 2395 False 1508.5 2473 93.8695 1 2342 2 chr2A.!!$F3 2341
12 TraesCS3A01G311200 chr7A 68992498 68994218 1720 False 2497.0 2497 92.8780 621 2342 1 chr7A.!!$F1 1721

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
455 650 0.546267 CCATCGATCCCCATCTCCCT 60.546 60.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 2589 0.106918 AACCCGAAGAAGCAACACCA 60.107 50.0 0.0 0.0 0.0 4.17 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
28 30 6.697641 TTTTGGACACCTCTAATTCCTAGT 57.302 37.500 0.00 0.00 0.00 2.57
104 106 6.704289 CAATCATGCCTCTCCTATTTTTCA 57.296 37.500 0.00 0.00 0.00 2.69
191 194 9.042450 ACCTTTCTTTTCTTCCCTTTTTCTTTA 57.958 29.630 0.00 0.00 0.00 1.85
228 242 7.437748 TGTTTTGGAAAGAGTAAGAGAGAGAG 58.562 38.462 0.00 0.00 0.00 3.20
229 243 7.287927 TGTTTTGGAAAGAGTAAGAGAGAGAGA 59.712 37.037 0.00 0.00 0.00 3.10
276 290 2.578021 CTGATCTTTTCCCTCTCCCCAA 59.422 50.000 0.00 0.00 0.00 4.12
384 527 1.285078 TCAACTCTCTCGATCCCCTCA 59.715 52.381 0.00 0.00 0.00 3.86
455 650 0.546267 CCATCGATCCCCATCTCCCT 60.546 60.000 0.00 0.00 0.00 4.20
470 665 2.294078 CCCTGTTCTTCCCTCGCCT 61.294 63.158 0.00 0.00 0.00 5.52
500 695 2.179547 CACACGCACACTTCCAGCA 61.180 57.895 0.00 0.00 0.00 4.41
671 974 1.115467 CTCTTCCACATCGTAGCCCT 58.885 55.000 0.00 0.00 0.00 5.19
751 1054 0.955919 CCTTCTCCTGTTCGTTGCCC 60.956 60.000 0.00 0.00 0.00 5.36
1059 1368 0.247814 CGAGACCATCATTGCAACGC 60.248 55.000 0.00 0.00 0.00 4.84
1061 1370 1.139520 GACCATCATTGCAACGCCC 59.860 57.895 0.00 0.00 0.00 6.13
1096 1405 3.626670 CGGAGTACCTCAAGTTCGTCTAT 59.373 47.826 0.00 0.00 31.08 1.98
1106 1415 7.093902 ACCTCAAGTTCGTCTATATGAAACTGA 60.094 37.037 0.00 0.00 32.46 3.41
1161 1470 3.307906 ACCGGCAAGGCTACACGA 61.308 61.111 0.00 0.00 46.52 4.35
1279 1588 1.028330 ACATCTACCGCCGTCTTCGA 61.028 55.000 0.00 0.00 39.71 3.71
1511 1822 1.177256 ACGACTACACCGCTTGACCT 61.177 55.000 0.00 0.00 0.00 3.85
2040 2358 2.097825 GCTCCATCTCTTGCCATGTTT 58.902 47.619 0.00 0.00 0.00 2.83
2043 2361 4.158394 GCTCCATCTCTTGCCATGTTTAAA 59.842 41.667 0.00 0.00 0.00 1.52
2076 2395 6.834168 ATTTTGTTGGGTTCATAACGAGAT 57.166 33.333 0.00 0.00 0.00 2.75
2077 2396 5.873179 TTTGTTGGGTTCATAACGAGATC 57.127 39.130 0.00 0.00 0.00 2.75
2091 2410 9.661187 TCATAACGAGATCGAACTAAATAAGTC 57.339 33.333 9.58 0.00 43.02 3.01
2104 2423 9.394477 GAACTAAATAAGTCATGTGGTGTTTTC 57.606 33.333 0.00 0.00 37.50 2.29
2105 2424 8.691661 ACTAAATAAGTCATGTGGTGTTTTCT 57.308 30.769 0.00 0.00 30.33 2.52
2118 2437 6.183360 TGTGGTGTTTTCTTCAATATGCAACT 60.183 34.615 0.00 0.00 0.00 3.16
2139 2459 2.016318 CCGTTGCATAATGAGCTCCAA 58.984 47.619 12.15 3.91 0.00 3.53
2192 2513 2.166829 TGCCATGCTTCATTAAACCGT 58.833 42.857 0.00 0.00 0.00 4.83
2220 2541 4.665212 CATCATACTTGGTTGTGCATCAC 58.335 43.478 0.00 0.00 34.56 3.06
2221 2542 3.749226 TCATACTTGGTTGTGCATCACA 58.251 40.909 0.00 0.00 43.02 3.58
2235 2557 2.229543 GCATCACACCATGTTCATGTGT 59.770 45.455 11.13 11.57 43.42 3.72
2249 2571 7.022055 TGTTCATGTGTTGGTTGTTTACTAG 57.978 36.000 0.00 0.00 0.00 2.57
2266 2589 7.338449 TGTTTACTAGGTTGTTTGCTTCTTTCT 59.662 33.333 0.00 0.00 0.00 2.52
2293 2616 1.337541 GCTTCTTCGGGTTAGTTCCGT 60.338 52.381 2.42 0.00 46.82 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 106 3.761218 TCATAAAAATGTGCACGGTCCAT 59.239 39.130 13.13 0.00 0.00 3.41
210 222 6.183360 GCTCCTTCTCTCTCTCTTACTCTTTC 60.183 46.154 0.00 0.00 0.00 2.62
228 242 1.676967 CTGGCTGTTGGGCTCCTTC 60.677 63.158 0.00 0.00 41.48 3.46
229 243 2.437897 CTGGCTGTTGGGCTCCTT 59.562 61.111 0.00 0.00 41.48 3.36
250 264 2.437651 GAGAGGGAAAAGATCAGGAGGG 59.562 54.545 0.00 0.00 0.00 4.30
400 595 1.974343 AGCGAGCGAGAAGAGTGGT 60.974 57.895 0.00 0.00 0.00 4.16
455 650 2.347490 GCAGGCGAGGGAAGAACA 59.653 61.111 0.00 0.00 0.00 3.18
751 1054 2.046892 CTGCTGGTCTTGGACGGG 60.047 66.667 0.00 0.00 32.65 5.28
1015 1324 2.978156 TCCAGATCAAAACAAGGCCT 57.022 45.000 0.00 0.00 0.00 5.19
1026 1335 0.382158 GTCTCGACGCATCCAGATCA 59.618 55.000 0.00 0.00 0.00 2.92
1096 1405 6.624423 GCGTAGAGGTACTTGTCAGTTTCATA 60.624 42.308 0.00 0.00 41.55 2.15
1106 1415 0.524862 CCGTGCGTAGAGGTACTTGT 59.475 55.000 0.00 0.00 41.55 3.16
1132 1441 0.322322 TTGCCGGTGTAGGTACTTGG 59.678 55.000 1.90 0.00 41.75 3.61
1161 1470 2.604462 GTGTTGTAGTGGAACGAACGTT 59.396 45.455 12.30 12.30 45.86 3.99
1373 1684 1.033746 GTCATCGTGGTACTCGGGGA 61.034 60.000 10.03 6.39 45.95 4.81
1411 1722 1.916000 CGACGGTATTCGAACTTGACC 59.084 52.381 0.00 5.16 41.78 4.02
1511 1822 1.517694 GCGTTATCGGAGCGGTTCA 60.518 57.895 0.00 0.00 37.56 3.18
1673 1990 2.320781 CGATAGAAGGTGGGGTGATCT 58.679 52.381 0.00 0.00 39.76 2.75
2026 2344 5.843673 TGTTGTTTAAACATGGCAAGAGA 57.156 34.783 21.17 1.01 38.95 3.10
2062 2380 7.695869 ATTTAGTTCGATCTCGTTATGAACC 57.304 36.000 0.00 0.00 39.71 3.62
2065 2383 9.661187 GACTTATTTAGTTCGATCTCGTTATGA 57.339 33.333 0.00 0.00 37.17 2.15
2076 2395 6.460781 ACACCACATGACTTATTTAGTTCGA 58.539 36.000 0.00 0.00 37.17 3.71
2077 2396 6.721571 ACACCACATGACTTATTTAGTTCG 57.278 37.500 0.00 0.00 37.17 3.95
2089 2408 6.308766 GCATATTGAAGAAAACACCACATGAC 59.691 38.462 0.00 0.00 0.00 3.06
2091 2410 6.157904 TGCATATTGAAGAAAACACCACATG 58.842 36.000 0.00 0.00 0.00 3.21
2118 2437 1.209261 TGGAGCTCATTATGCAACGGA 59.791 47.619 17.19 0.00 0.00 4.69
2139 2459 8.367156 AGTGCACAAACAATCCTACAAATTAAT 58.633 29.630 21.04 0.00 0.00 1.40
2192 2513 4.096231 GCACAACCAAGTATGATGCATGTA 59.904 41.667 2.46 0.00 0.00 2.29
2220 2541 3.181477 ACAACCAACACATGAACATGGTG 60.181 43.478 17.25 14.38 43.34 4.17
2221 2542 3.030291 ACAACCAACACATGAACATGGT 58.970 40.909 17.25 5.56 45.97 3.55
2229 2551 6.183360 ACAACCTAGTAAACAACCAACACATG 60.183 38.462 0.00 0.00 0.00 3.21
2235 2557 5.419471 AGCAAACAACCTAGTAAACAACCAA 59.581 36.000 0.00 0.00 0.00 3.67
2249 2571 3.119137 ACACCAGAAAGAAGCAAACAACC 60.119 43.478 0.00 0.00 0.00 3.77
2266 2589 0.106918 AACCCGAAGAAGCAACACCA 60.107 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.