Multiple sequence alignment - TraesCS2A01G580600

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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 TraesCS2A01G580600 chr2A 100.000 5627 0 0 1 5627 772960818 772966444 0.000000e+00 10392.0
1 TraesCS2A01G580600 chr2A 97.842 695 14 1 1 695 700233300 700232607 0.000000e+00 1199.0
2 TraesCS2A01G580600 chr2A 96.186 472 16 2 222 693 22594855 22595324 0.000000e+00 771.0
3 TraesCS2A01G580600 chr2A 95.595 227 4 4 1 224 22594561 22594784 5.360000e-95 359.0
4 TraesCS2A01G580600 chr2A 78.970 233 32 9 1782 2002 772859167 772859394 5.880000e-30 143.0
5 TraesCS2A01G580600 chr2A 87.500 72 6 3 1644 1713 772789602 772789672 4.670000e-11 80.5
6 TraesCS2A01G580600 chr2D 99.445 4868 18 3 766 5627 647515670 647510806 0.000000e+00 8831.0
7 TraesCS2A01G580600 chr2D 98.450 774 8 2 1 773 647519784 647519014 0.000000e+00 1360.0
8 TraesCS2A01G580600 chr2B 88.421 2254 168 35 1519 3728 788520029 788522233 0.000000e+00 2630.0
9 TraesCS2A01G580600 chr2B 91.110 1451 80 26 3716 5137 788523935 788525365 0.000000e+00 1919.0
10 TraesCS2A01G580600 chr2B 91.465 703 51 8 827 1523 788519276 788519975 0.000000e+00 957.0
11 TraesCS2A01G580600 chr2B 91.222 581 36 12 4417 4989 788533539 788534112 0.000000e+00 776.0
12 TraesCS2A01G580600 chr2B 80.143 559 91 17 821 1377 788228273 788228813 3.160000e-107 399.0
13 TraesCS2A01G580600 chr2B 84.248 419 48 12 781 1194 788296561 788296966 5.280000e-105 392.0
14 TraesCS2A01G580600 chr2B 85.379 383 41 10 822 1200 788419727 788419356 3.180000e-102 383.0
15 TraesCS2A01G580600 chr2B 83.532 419 51 12 781 1194 788278955 788279360 5.320000e-100 375.0
16 TraesCS2A01G580600 chr2B 92.414 145 11 0 5219 5363 788525383 788525527 2.050000e-49 207.0
17 TraesCS2A01G580600 chr2B 77.089 371 51 11 1791 2128 788136474 788136843 3.460000e-42 183.0
18 TraesCS2A01G580600 chr2B 85.542 166 18 3 5463 5627 788534528 788534688 9.700000e-38 169.0
19 TraesCS2A01G580600 chr2B 84.536 97 4 1 5219 5315 788534248 788534333 1.000000e-12 86.1
20 TraesCS2A01G580600 chr2B 95.122 41 2 0 5353 5393 788531156 788531196 1.310000e-06 65.8
21 TraesCS2A01G580600 chr3A 96.788 467 13 2 228 694 136522978 136522514 0.000000e+00 778.0
22 TraesCS2A01G580600 chr3A 95.556 225 6 3 1 224 136523276 136523055 1.930000e-94 357.0
23 TraesCS2A01G580600 chr5A 95.570 474 17 3 222 694 383833944 383834414 0.000000e+00 756.0
24 TraesCS2A01G580600 chr5A 94.690 226 7 4 1 224 383833651 383833873 4.170000e-91 346.0
25 TraesCS2A01G580600 chr1A 95.940 468 16 3 228 694 97157278 97156813 0.000000e+00 756.0
26 TraesCS2A01G580600 chr1A 79.199 899 129 36 2465 3320 537830964 537830081 6.320000e-159 571.0
27 TraesCS2A01G580600 chr1A 86.914 405 41 10 3756 4155 537829674 537829277 1.440000e-120 444.0
28 TraesCS2A01G580600 chr1A 95.575 226 5 3 1 224 97157577 97157355 1.930000e-94 357.0
29 TraesCS2A01G580600 chr1A 89.243 251 20 3 914 1158 537831713 537831464 1.970000e-79 307.0
30 TraesCS2A01G580600 chr1A 91.176 68 6 0 157 224 22365876 22365809 6.000000e-15 93.5
31 TraesCS2A01G580600 chrUn 100.000 403 0 0 3504 3906 478363535 478363937 0.000000e+00 745.0
32 TraesCS2A01G580600 chrUn 84.000 425 50 12 781 1200 275724272 275723861 5.280000e-105 392.0
33 TraesCS2A01G580600 chr7D 94.515 474 21 4 222 694 11122730 11122261 0.000000e+00 726.0
34 TraesCS2A01G580600 chr7D 88.000 75 9 0 147 221 400867551 400867477 7.760000e-14 89.8
35 TraesCS2A01G580600 chr4B 92.671 423 24 5 233 652 223391115 223391533 2.240000e-168 603.0
36 TraesCS2A01G580600 chr4B 91.962 423 27 6 233 652 223400223 223400641 2.260000e-163 586.0
37 TraesCS2A01G580600 chr4B 86.192 239 15 4 1 224 223390802 223391037 5.630000e-60 243.0
38 TraesCS2A01G580600 chr4B 84.583 240 18 5 1 224 223399909 223400145 2.640000e-53 220.0
39 TraesCS2A01G580600 chr1D 78.881 947 150 31 2415 3320 440040077 440041014 3.750000e-166 595.0
40 TraesCS2A01G580600 chr1D 81.421 549 78 21 3617 4155 440041435 440041969 1.450000e-115 427.0
41 TraesCS2A01G580600 chr1D 88.511 235 19 6 914 1144 440039367 440039597 1.540000e-70 278.0
42 TraesCS2A01G580600 chr1B 79.852 809 120 28 2540 3318 597548350 597549145 8.240000e-153 551.0
43 TraesCS2A01G580600 chr1B 87.160 405 40 10 3756 4155 597549554 597549951 3.090000e-122 449.0
44 TraesCS2A01G580600 chr1B 85.549 173 9 9 1 160 212648454 212648285 3.490000e-37 167.0
45 TraesCS2A01G580600 chr1B 89.706 68 7 0 154 221 659571922 659571989 2.790000e-13 87.9
46 TraesCS2A01G580600 chr7B 81.548 168 14 4 1 154 519233252 519233416 7.660000e-24 122.0


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 TraesCS2A01G580600 chr2A 772960818 772966444 5626 False 10392.000000 10392 100.000000 1 5627 1 chr2A.!!$F3 5626
1 TraesCS2A01G580600 chr2A 700232607 700233300 693 True 1199.000000 1199 97.842000 1 695 1 chr2A.!!$R1 694
2 TraesCS2A01G580600 chr2A 22594561 22595324 763 False 565.000000 771 95.890500 1 693 2 chr2A.!!$F4 692
3 TraesCS2A01G580600 chr2D 647510806 647519784 8978 True 5095.500000 8831 98.947500 1 5627 2 chr2D.!!$R1 5626
4 TraesCS2A01G580600 chr2B 788519276 788525527 6251 False 1428.250000 2630 90.852500 827 5363 4 chr2B.!!$F5 4536
5 TraesCS2A01G580600 chr2B 788228273 788228813 540 False 399.000000 399 80.143000 821 1377 1 chr2B.!!$F2 556
6 TraesCS2A01G580600 chr2B 788531156 788534688 3532 False 274.225000 776 89.105500 4417 5627 4 chr2B.!!$F6 1210
7 TraesCS2A01G580600 chr3A 136522514 136523276 762 True 567.500000 778 96.172000 1 694 2 chr3A.!!$R1 693
8 TraesCS2A01G580600 chr5A 383833651 383834414 763 False 551.000000 756 95.130000 1 694 2 chr5A.!!$F1 693
9 TraesCS2A01G580600 chr1A 97156813 97157577 764 True 556.500000 756 95.757500 1 694 2 chr1A.!!$R2 693
10 TraesCS2A01G580600 chr1A 537829277 537831713 2436 True 440.666667 571 85.118667 914 4155 3 chr1A.!!$R3 3241
11 TraesCS2A01G580600 chr4B 223390802 223391533 731 False 423.000000 603 89.431500 1 652 2 chr4B.!!$F1 651
12 TraesCS2A01G580600 chr4B 223399909 223400641 732 False 403.000000 586 88.272500 1 652 2 chr4B.!!$F2 651
13 TraesCS2A01G580600 chr1D 440039367 440041969 2602 False 433.333333 595 82.937667 914 4155 3 chr1D.!!$F1 3241
14 TraesCS2A01G580600 chr1B 597548350 597549951 1601 False 500.000000 551 83.506000 2540 4155 2 chr1B.!!$F2 1615

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
225 245 7.997803 GGTAGGTAGGTAAGAGTTAATCAGAGA 59.002 40.741 0.00 0.00 0.00 3.10 F
1613 5173 7.645340 GCATGACTTGTAATTATGCCACTTTAG 59.355 37.037 0.00 0.00 38.48 1.85 F
1631 5191 8.201464 CCACTTTAGGTTACAAATTGTTCCTTT 58.799 33.333 20.88 7.18 35.92 3.11 F
2558 6173 3.716601 GGTGGTTCTTCAATTGGTTGTG 58.283 45.455 5.42 0.00 36.69 3.33 F
3393 7039 7.852945 CGAGAGGAAAAATTTATAGCATGTCAC 59.147 37.037 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 5191 5.019470 TGTCCCAACAATAATGCATGGTAA 58.981 37.500 0.00 0.0 35.89 2.85 R
2528 6129 1.140052 TGAAGAACCACCGAAGCTTCA 59.860 47.619 25.47 0.0 41.67 3.02 R
2582 6197 3.679083 GCTGTTCGCAGGGTACTTAAGAT 60.679 47.826 10.09 0.0 45.10 2.40 R
3502 7149 4.522405 TGATGGTAGGTGGTTCATGTTTTG 59.478 41.667 0.00 0.0 0.00 2.44 R
5503 11180 2.613223 GCTTGACCACAGAGTTCCCTAC 60.613 54.545 0.00 0.0 0.00 3.18 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
225 245 7.997803 GGTAGGTAGGTAAGAGTTAATCAGAGA 59.002 40.741 0.00 0.00 0.00 3.10
1613 5173 7.645340 GCATGACTTGTAATTATGCCACTTTAG 59.355 37.037 0.00 0.00 38.48 1.85
1631 5191 8.201464 CCACTTTAGGTTACAAATTGTTCCTTT 58.799 33.333 20.88 7.18 35.92 3.11
2558 6173 3.716601 GGTGGTTCTTCAATTGGTTGTG 58.283 45.455 5.42 0.00 36.69 3.33
2582 6197 8.569641 GTGGGTTTATGTACATTCTGTTTTGTA 58.430 33.333 14.77 0.00 0.00 2.41
3393 7039 7.852945 CGAGAGGAAAAATTTATAGCATGTCAC 59.147 37.037 0.00 0.00 0.00 3.67
3502 7149 6.844696 TCGCTATCACAATTTCCACTATTC 57.155 37.500 0.00 0.00 0.00 1.75
3906 9463 2.094545 GCCCAAGGTACATTCTTGCTTG 60.095 50.000 5.17 0.00 40.00 4.01
5197 10788 2.928801 TGCTGAGCTAAAAGGTGACA 57.071 45.000 5.83 0.00 0.00 3.58
5208 10799 7.210174 AGCTAAAAGGTGACAAAAATCCTTTC 58.790 34.615 7.32 0.00 45.69 2.62
5209 10800 6.983890 GCTAAAAGGTGACAAAAATCCTTTCA 59.016 34.615 7.32 0.00 45.69 2.69
5210 10801 7.494298 GCTAAAAGGTGACAAAAATCCTTTCAA 59.506 33.333 7.32 0.66 45.69 2.69
5503 11180 4.635223 TGAGCTCCTGAATCAATTATCCG 58.365 43.478 12.15 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 245 9.800572 TGATATAGAGTAGTCTTAACATGCTCT 57.199 33.333 5.16 0.0 35.59 4.09
597 696 7.149569 GAGAATTCTCACATGGAAACATTCA 57.850 36.000 27.08 0.0 45.09 2.57
1591 5151 7.625828 ACCTAAAGTGGCATAATTACAAGTC 57.374 36.000 0.00 0.0 0.00 3.01
1613 5173 7.095397 GCATGGTAAAAGGAACAATTTGTAACC 60.095 37.037 14.10 14.1 0.00 2.85
1631 5191 5.019470 TGTCCCAACAATAATGCATGGTAA 58.981 37.500 0.00 0.0 35.89 2.85
2528 6129 1.140052 TGAAGAACCACCGAAGCTTCA 59.860 47.619 25.47 0.0 41.67 3.02
2582 6197 3.679083 GCTGTTCGCAGGGTACTTAAGAT 60.679 47.826 10.09 0.0 45.10 2.40
3502 7149 4.522405 TGATGGTAGGTGGTTCATGTTTTG 59.478 41.667 0.00 0.0 0.00 2.44
5503 11180 2.613223 GCTTGACCACAGAGTTCCCTAC 60.613 54.545 0.00 0.0 0.00 3.18
5516 11193 0.035534 ATACACGCCATGCTTGACCA 60.036 50.000 0.22 0.0 32.11 4.02


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

AutoCloner maintained by Alex Coulton.