Multiple sequence alignment - TraesCS2A01G208700

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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 TraesCS2A01G208700 chr2A 100.000 2624 0 0 1 2624 191913180 191915803 0.000000e+00 4846.0
1 TraesCS2A01G208700 chr2A 94.144 2271 63 16 219 2437 62219799 62217547 0.000000e+00 3393.0
2 TraesCS2A01G208700 chr2A 95.388 412 19 0 2193 2604 424543090 424542679 0.000000e+00 656.0
3 TraesCS2A01G208700 chr4D 95.566 2278 75 6 348 2604 215194194 215191922 0.000000e+00 3624.0
4 TraesCS2A01G208700 chr4D 95.565 1488 43 4 348 1814 417864686 417863201 0.000000e+00 2361.0
5 TraesCS2A01G208700 chr4D 94.710 794 35 3 1813 2606 417851211 417850425 0.000000e+00 1227.0
6 TraesCS2A01G208700 chr4D 88.388 732 61 14 1185 1903 465052695 465053415 0.000000e+00 859.0
7 TraesCS2A01G208700 chr4D 97.143 105 3 0 1 105 215194329 215194225 7.460000e-41 178.0
8 TraesCS2A01G208700 chr4D 94.444 108 3 2 1 105 417864824 417864717 2.090000e-36 163.0
9 TraesCS2A01G208700 chr7B 98.343 1811 26 4 816 2624 606354998 606356806 0.000000e+00 3175.0
10 TraesCS2A01G208700 chr7B 99.265 136 1 0 375 510 606354876 606355011 2.020000e-61 246.0
11 TraesCS2A01G208700 chr6B 90.564 1081 78 15 1488 2558 112884712 112883646 0.000000e+00 1410.0
12 TraesCS2A01G208700 chr6B 80.925 519 34 27 1 457 680306903 680307418 1.490000e-92 350.0
13 TraesCS2A01G208700 chr6B 100.000 34 0 0 1454 1487 112884766 112884733 2.180000e-06 63.9
14 TraesCS2A01G208700 chr1D 89.598 1019 84 15 1590 2599 164853729 164852724 0.000000e+00 1275.0
15 TraesCS2A01G208700 chr1D 87.739 628 62 11 943 1566 164855165 164854549 0.000000e+00 719.0
16 TraesCS2A01G208700 chr1D 83.263 472 51 12 3 450 164859867 164859400 2.430000e-110 409.0
17 TraesCS2A01G208700 chr1D 91.803 183 11 1 573 751 164855344 164855162 4.340000e-63 252.0
18 TraesCS2A01G208700 chr5A 94.849 563 26 2 2041 2603 60754289 60754848 0.000000e+00 876.0
19 TraesCS2A01G208700 chr5B 87.466 734 63 18 1185 1903 239331930 239331211 0.000000e+00 819.0
20 TraesCS2A01G208700 chr3B 87.022 732 70 14 1185 1903 145896503 145895784 0.000000e+00 802.0
21 TraesCS2A01G208700 chr3B 84.000 300 22 4 716 1015 516401694 516401967 5.570000e-67 265.0
22 TraesCS2A01G208700 chr3B 84.000 300 22 5 716 1015 516938641 516938914 5.570000e-67 265.0
23 TraesCS2A01G208700 chr3B 83.333 300 24 6 716 1015 515893730 515894003 1.210000e-63 254.0
24 TraesCS2A01G208700 chr3A 96.526 403 14 0 2193 2595 12569606 12569204 0.000000e+00 667.0
25 TraesCS2A01G208700 chr6A 83.648 477 44 17 1 457 594748296 594748758 4.040000e-113 418.0
26 TraesCS2A01G208700 chr6D 81.008 516 36 26 1 457 448708479 448708991 1.160000e-93 353.0
27 TraesCS2A01G208700 chr1A 80.000 480 61 25 1186 1643 99707041 99707507 3.260000e-84 322.0
28 TraesCS2A01G208700 chr1A 90.984 122 9 1 1895 2016 23230820 23230939 2.090000e-36 163.0
29 TraesCS2A01G208700 chr1A 93.396 106 7 0 458 563 48200097 48199992 9.720000e-35 158.0
30 TraesCS2A01G208700 chr1B 91.803 122 8 1 1895 2016 37620296 37620415 4.490000e-38 169.0


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 TraesCS2A01G208700 chr2A 191913180 191915803 2623 False 4846.000000 4846 100.000000 1 2624 1 chr2A.!!$F1 2623
1 TraesCS2A01G208700 chr2A 62217547 62219799 2252 True 3393.000000 3393 94.144000 219 2437 1 chr2A.!!$R1 2218
2 TraesCS2A01G208700 chr4D 215191922 215194329 2407 True 1901.000000 3624 96.354500 1 2604 2 chr4D.!!$R2 2603
3 TraesCS2A01G208700 chr4D 417863201 417864824 1623 True 1262.000000 2361 95.004500 1 1814 2 chr4D.!!$R3 1813
4 TraesCS2A01G208700 chr4D 417850425 417851211 786 True 1227.000000 1227 94.710000 1813 2606 1 chr4D.!!$R1 793
5 TraesCS2A01G208700 chr4D 465052695 465053415 720 False 859.000000 859 88.388000 1185 1903 1 chr4D.!!$F1 718
6 TraesCS2A01G208700 chr7B 606354876 606356806 1930 False 1710.500000 3175 98.804000 375 2624 2 chr7B.!!$F1 2249
7 TraesCS2A01G208700 chr6B 112883646 112884766 1120 True 736.950000 1410 95.282000 1454 2558 2 chr6B.!!$R1 1104
8 TraesCS2A01G208700 chr6B 680306903 680307418 515 False 350.000000 350 80.925000 1 457 1 chr6B.!!$F1 456
9 TraesCS2A01G208700 chr1D 164852724 164855344 2620 True 748.666667 1275 89.713333 573 2599 3 chr1D.!!$R2 2026
10 TraesCS2A01G208700 chr5A 60754289 60754848 559 False 876.000000 876 94.849000 2041 2603 1 chr5A.!!$F1 562
11 TraesCS2A01G208700 chr5B 239331211 239331930 719 True 819.000000 819 87.466000 1185 1903 1 chr5B.!!$R1 718
12 TraesCS2A01G208700 chr3B 145895784 145896503 719 True 802.000000 802 87.022000 1185 1903 1 chr3B.!!$R1 718
13 TraesCS2A01G208700 chr6D 448708479 448708991 512 False 353.000000 353 81.008000 1 457 1 chr6D.!!$F1 456

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
328 397 0.323269 TTCGATTTGGGCATGGCAGA 60.323 50.0 22.06 5.61 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 2871 0.105593 ATGACCTAGACGCATGCCAG 59.894 55.0 13.15 0.85 0.0 4.85 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
35 36 3.680338 GACGACGACGAGCCCTTCC 62.680 68.421 15.32 0.00 42.66 3.46
36 37 3.441290 CGACGACGAGCCCTTCCT 61.441 66.667 0.00 0.00 42.66 3.36
40 44 2.646175 CGACGAGCCCTTCCTGGAA 61.646 63.158 9.14 9.14 38.35 3.53
111 115 2.611518 CAAGAACGTCCTCATCCTCAC 58.388 52.381 0.00 0.00 0.00 3.51
185 201 1.063166 GGCGACGACTACCGGTAAG 59.937 63.158 16.65 12.26 43.93 2.34
186 202 1.584742 GCGACGACTACCGGTAAGC 60.585 63.158 16.65 9.40 43.93 3.09
187 203 1.297158 CGACGACTACCGGTAAGCG 60.297 63.158 25.47 25.47 43.93 4.68
191 215 1.064654 ACGACTACCGGTAAGCGAATC 59.935 52.381 30.77 15.34 43.93 2.52
215 245 2.040213 CTCTGCGCCGCGAATCATTT 62.040 55.000 18.91 0.00 0.00 2.32
217 247 2.040213 CTGCGCCGCGAATCATTTCT 62.040 55.000 18.91 0.00 0.00 2.52
229 271 4.099266 CGAATCATTTCTCTCCCTCTGTCT 59.901 45.833 0.00 0.00 0.00 3.41
290 336 1.699083 TCTGTCAATCCAAGTGGCTGA 59.301 47.619 0.00 0.00 34.44 4.26
328 397 0.323269 TTCGATTTGGGCATGGCAGA 60.323 50.000 22.06 5.61 0.00 4.26
571 651 2.769663 ACGGTAAATCTGTATCCAGGCA 59.230 45.455 0.00 0.00 39.31 4.75
700 805 5.363562 TTCCACTACTTCATGATGATGCT 57.636 39.130 15.03 0.00 0.00 3.79
767 872 2.196776 GATCCCCGACTCCCCGTA 59.803 66.667 0.00 0.00 0.00 4.02
1008 1113 1.457643 CAGAGTAGGGATGGCGGGA 60.458 63.158 0.00 0.00 0.00 5.14
1395 1502 6.467047 CGACATGTTAGTGTAACGGTACTAAG 59.533 42.308 12.67 0.00 45.86 2.18
1599 2543 2.238646 ACCTTCTGGACAAGACACACAA 59.761 45.455 0.00 0.00 33.46 3.33
1643 2589 6.880529 ACTTAATGCCTTTGGGAATTTTGATG 59.119 34.615 0.00 0.00 37.59 3.07
1906 2871 6.790285 AAGAACATTCATTTTCACATTGCC 57.210 33.333 0.00 0.00 0.00 4.52
1992 2957 6.642950 CCGATAGTTTCATTCGAATAGCTCTT 59.357 38.462 10.97 0.00 34.92 2.85
2146 3113 6.491714 ACTAATTGATCCATGTAGCAGACT 57.508 37.500 0.00 0.00 0.00 3.24
2325 3294 2.177734 ACGTTAGGAAGAAGGGGAGAC 58.822 52.381 0.00 0.00 0.00 3.36
2393 3362 6.313519 AGGTGAGCATTACTATTCAAAGGA 57.686 37.500 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.398381 CCCTCCTCCTCCTCTTCCAG 60.398 65.000 0.00 0.00 0.00 3.86
36 37 1.706575 CCCTCCTCCTCCTCTTCCA 59.293 63.158 0.00 0.00 0.00 3.53
40 44 2.366570 GTGCCCTCCTCCTCCTCT 59.633 66.667 0.00 0.00 0.00 3.69
143 147 1.218047 CGTCCTTGATGGCTTCGGA 59.782 57.895 0.00 0.00 35.26 4.55
182 198 2.473816 CGCAGAGGAATGATTCGCTTA 58.526 47.619 0.00 0.00 0.00 3.09
183 199 1.293924 CGCAGAGGAATGATTCGCTT 58.706 50.000 0.00 0.00 0.00 4.68
185 201 1.278038 GCGCAGAGGAATGATTCGC 59.722 57.895 0.30 0.00 0.00 4.70
186 202 1.825285 CGGCGCAGAGGAATGATTCG 61.825 60.000 10.83 0.00 0.00 3.34
187 203 1.937391 CGGCGCAGAGGAATGATTC 59.063 57.895 10.83 0.00 0.00 2.52
215 245 6.328782 TCTATTAACAGACAGAGGGAGAGA 57.671 41.667 0.00 0.00 0.00 3.10
217 247 8.915036 GTTTATCTATTAACAGACAGAGGGAGA 58.085 37.037 0.00 0.00 0.00 3.71
328 397 2.762887 TGCAGAGATCCTTGACGAAGAT 59.237 45.455 0.00 0.00 0.00 2.40
571 651 2.569404 GGTGAAGAGGTGGACTGAATCT 59.431 50.000 0.00 0.00 0.00 2.40
700 805 0.322098 CCATCCAAGTACGCACCCAA 60.322 55.000 0.00 0.00 0.00 4.12
767 872 6.434028 AGCTTTGTATGGTGAACAATGTATGT 59.566 34.615 0.00 0.00 46.82 2.29
1008 1113 1.226746 GCCAGTACAACTCAAACGCT 58.773 50.000 0.00 0.00 0.00 5.07
1906 2871 0.105593 ATGACCTAGACGCATGCCAG 59.894 55.000 13.15 0.85 0.00 4.85
2177 3144 6.602009 TGTCCTCACTCGTTAATAATCTCAGA 59.398 38.462 0.00 0.00 0.00 3.27
2325 3294 3.491267 GTGAACTTCAGAAACTCACCTCG 59.509 47.826 11.11 0.00 32.10 4.63


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

AutoCloner maintained by Alex Coulton.