Multiple sequence alignment - TraesCS7D01G440800

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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 TraesCS7D01G440800 chr7D 100.000 2732 0 0 1 2732 560677624 560674893 0.000000e+00 5046.0
1 TraesCS7D01G440800 chr7D 97.593 1579 20 9 469 2045 560713284 560711722 0.000000e+00 2689.0
2 TraesCS7D01G440800 chr7D 98.427 1144 17 1 902 2045 560686912 560685770 0.000000e+00 2012.0
3 TraesCS7D01G440800 chr7D 98.013 906 18 0 1 906 560696591 560695686 0.000000e+00 1574.0
4 TraesCS7D01G440800 chr7D 98.846 693 8 0 2040 2732 560685389 560684697 0.000000e+00 1236.0
5 TraesCS7D01G440800 chr7D 98.846 693 8 0 2040 2732 560711341 560710649 0.000000e+00 1236.0
6 TraesCS7D01G440800 chr7D 100.000 74 0 0 1 74 289300392 289300465 1.320000e-28 137.0
7 TraesCS7D01G440800 chr7D 100.000 38 0 0 100 137 560677465 560677428 1.360000e-08 71.3
8 TraesCS7D01G440800 chr7D 100.000 38 0 0 160 197 560677525 560677488 1.360000e-08 71.3
9 TraesCS7D01G440800 chr7D 100.000 38 0 0 100 137 560696432 560696395 1.360000e-08 71.3
10 TraesCS7D01G440800 chr7D 100.000 38 0 0 160 197 560696492 560696455 1.360000e-08 71.3
11 TraesCS7D01G440800 chr7D 93.182 44 2 1 128 171 227283112 227283154 2.270000e-06 63.9
12 TraesCS7D01G440800 chr7A 93.202 1574 84 3 472 2045 644857991 644856441 0.000000e+00 2292.0
13 TraesCS7D01G440800 chr7A 91.272 676 47 6 2062 2732 644856021 644855353 0.000000e+00 911.0
14 TraesCS7D01G440800 chr7B 92.485 1517 102 2 472 1976 608478191 608476675 0.000000e+00 2159.0
15 TraesCS7D01G440800 chr7B 95.396 695 29 2 2040 2732 608476233 608475540 0.000000e+00 1103.0
16 TraesCS7D01G440800 chr5D 75.491 1171 231 38 598 1725 423535301 423534144 3.120000e-144 521.0
17 TraesCS7D01G440800 chr5D 95.604 273 12 0 202 474 57938076 57937804 3.230000e-119 438.0
18 TraesCS7D01G440800 chr5D 95.604 273 12 0 202 474 229203183 229202911 3.230000e-119 438.0
19 TraesCS7D01G440800 chr5D 95.604 273 12 0 202 474 331264525 331264253 3.230000e-119 438.0
20 TraesCS7D01G440800 chr5A 74.550 1167 246 35 598 1725 537124942 537123788 1.920000e-126 462.0
21 TraesCS7D01G440800 chr5A 97.436 39 1 0 133 171 273123520 273123482 1.760000e-07 67.6
22 TraesCS7D01G440800 chr3D 96.337 273 10 0 202 474 532050631 532050903 1.490000e-122 449.0
23 TraesCS7D01G440800 chr3D 95.588 272 12 0 202 473 383600380 383600109 1.160000e-118 436.0
24 TraesCS7D01G440800 chr3D 97.222 36 1 0 173 208 527875405 527875370 8.170000e-06 62.1
25 TraesCS7D01G440800 chr1D 95.971 273 11 0 202 474 427475965 427476237 6.940000e-121 444.0
26 TraesCS7D01G440800 chr1D 95.604 273 12 0 202 474 294153035 294153307 3.230000e-119 438.0
27 TraesCS7D01G440800 chr1D 75.585 897 174 35 552 1425 458875799 458876673 4.240000e-108 401.0
28 TraesCS7D01G440800 chr1D 75.615 853 161 34 545 1377 458872230 458873055 1.990000e-101 379.0
29 TraesCS7D01G440800 chr1D 98.667 75 1 0 1 75 90745397 90745471 1.710000e-27 134.0
30 TraesCS7D01G440800 chr6A 77.929 734 139 16 994 1717 616890635 616889915 1.160000e-118 436.0
31 TraesCS7D01G440800 chr6A 88.106 227 21 6 2062 2286 39149856 39149634 5.800000e-67 265.0
32 TraesCS7D01G440800 chr2D 95.588 272 12 0 202 473 562375230 562375501 1.160000e-118 436.0
33 TraesCS7D01G440800 chr6D 76.019 834 167 22 897 1717 24934296 24935109 4.240000e-108 401.0
34 TraesCS7D01G440800 chr6D 98.667 75 1 0 1 75 210783769 210783695 1.710000e-27 134.0
35 TraesCS7D01G440800 chr6D 98.667 75 1 0 1 75 309019309 309019235 1.710000e-27 134.0
36 TraesCS7D01G440800 chr6D 95.122 41 2 0 135 175 124435864 124435824 6.310000e-07 65.8
37 TraesCS7D01G440800 chr6D 93.182 44 2 1 128 171 246328540 246328582 2.270000e-06 63.9
38 TraesCS7D01G440800 chr6D 100.000 29 0 0 180 208 163681592 163681564 1.000000e-03 54.7
39 TraesCS7D01G440800 chr6D 100.000 29 0 0 180 208 271088973 271088945 1.000000e-03 54.7
40 TraesCS7D01G440800 chr6D 100.000 29 0 0 180 208 271443083 271443111 1.000000e-03 54.7
41 TraesCS7D01G440800 chr6D 100.000 29 0 0 180 208 271449907 271449935 1.000000e-03 54.7
42 TraesCS7D01G440800 chr6D 100.000 29 0 0 180 208 332047187 332047159 1.000000e-03 54.7
43 TraesCS7D01G440800 chr1A 74.861 899 182 34 545 1425 551307336 551308208 4.300000e-98 368.0
44 TraesCS7D01G440800 chr6B 80.734 327 42 14 2422 2732 72186764 72186443 4.550000e-58 235.0
45 TraesCS7D01G440800 chr6B 95.238 42 1 1 130 171 149523944 149523904 6.310000e-07 65.8
46 TraesCS7D01G440800 chr4A 100.000 75 0 0 1 75 253068647 253068573 3.670000e-29 139.0
47 TraesCS7D01G440800 chr4A 93.182 44 2 1 128 171 22488012 22487970 2.270000e-06 63.9
48 TraesCS7D01G440800 chr3A 100.000 74 0 0 1 74 207912721 207912794 1.320000e-28 137.0
49 TraesCS7D01G440800 chr4D 98.667 75 1 0 1 75 25556197 25556271 1.710000e-27 134.0
50 TraesCS7D01G440800 chr4D 98.667 75 1 0 1 75 44021178 44021252 1.710000e-27 134.0
51 TraesCS7D01G440800 chr4D 100.000 29 0 0 180 208 27367465 27367437 1.000000e-03 54.7
52 TraesCS7D01G440800 chr4B 87.719 57 3 3 135 190 617811997 617812050 2.270000e-06 63.9
53 TraesCS7D01G440800 chr2A 93.182 44 2 1 128 171 576944525 576944567 2.270000e-06 63.9
54 TraesCS7D01G440800 chrUn 100.000 28 0 0 180 207 480474209 480474236 5.000000e-03 52.8


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 TraesCS7D01G440800 chr7D 560674893 560677624 2731 True 1729.533333 5046 100.000000 1 2732 3 chr7D.!!$R1 2731
1 TraesCS7D01G440800 chr7D 560710649 560713284 2635 True 1962.500000 2689 98.219500 469 2732 2 chr7D.!!$R4 2263
2 TraesCS7D01G440800 chr7D 560684697 560686912 2215 True 1624.000000 2012 98.636500 902 2732 2 chr7D.!!$R2 1830
3 TraesCS7D01G440800 chr7D 560695686 560696591 905 True 572.200000 1574 99.337667 1 906 3 chr7D.!!$R3 905
4 TraesCS7D01G440800 chr7A 644855353 644857991 2638 True 1601.500000 2292 92.237000 472 2732 2 chr7A.!!$R1 2260
5 TraesCS7D01G440800 chr7B 608475540 608478191 2651 True 1631.000000 2159 93.940500 472 2732 2 chr7B.!!$R1 2260
6 TraesCS7D01G440800 chr5D 423534144 423535301 1157 True 521.000000 521 75.491000 598 1725 1 chr5D.!!$R4 1127
7 TraesCS7D01G440800 chr5A 537123788 537124942 1154 True 462.000000 462 74.550000 598 1725 1 chr5A.!!$R2 1127
8 TraesCS7D01G440800 chr1D 458872230 458876673 4443 False 390.000000 401 75.600000 545 1425 2 chr1D.!!$F4 880
9 TraesCS7D01G440800 chr6A 616889915 616890635 720 True 436.000000 436 77.929000 994 1717 1 chr6A.!!$R2 723
10 TraesCS7D01G440800 chr6D 24934296 24935109 813 False 401.000000 401 76.019000 897 1717 1 chr6D.!!$F1 820
11 TraesCS7D01G440800 chr1A 551307336 551308208 872 False 368.000000 368 74.861000 545 1425 1 chr1A.!!$F1 880

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
433 434 0.436913 CATCGAACGTTAAGCGCACA 59.563 50.0 11.47 0.0 46.11 4.57 F
1385 1430 0.924823 ATGGAGAAGGAAGGCATGCT 59.075 50.0 18.92 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1566 0.107017 ATAAGCCTCGCAGCCATTGT 60.107 50.000 0.0 0.0 0.0 2.71 R
2501 4631 3.004752 AGGTTGGATCAGGTATTGTGC 57.995 47.619 0.0 0.0 0.0 4.57 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 29 2.100584 GCCAACTCAACAAACACCATCA 59.899 45.455 0.00 0.0 0.00 3.07
31 32 4.261322 CCAACTCAACAAACACCATCAGAG 60.261 45.833 0.00 0.0 0.00 3.35
306 307 7.595502 GTCCGAATATAGCCTTCCAATATATCG 59.404 40.741 0.00 0.0 0.00 2.92
431 432 0.711670 GTCATCGAACGTTAAGCGCA 59.288 50.000 11.47 0.0 46.11 6.09
433 434 0.436913 CATCGAACGTTAAGCGCACA 59.563 50.000 11.47 0.0 46.11 4.57
441 442 1.470979 CGTTAAGCGCACAGACCCTAT 60.471 52.381 11.47 0.0 0.00 2.57
693 696 3.702048 GACTGCGGCCACCACCTA 61.702 66.667 2.24 0.0 0.00 3.08
1385 1430 0.924823 ATGGAGAAGGAAGGCATGCT 59.075 50.000 18.92 0.0 0.00 3.79
1437 1566 2.435805 AGAAGAGGATGAAATGCGGCTA 59.564 45.455 0.00 0.0 40.91 3.93
1500 1629 3.650942 ACCTCCAACACCTCAAGTTCATA 59.349 43.478 0.00 0.0 0.00 2.15
1605 1734 1.825090 TGAAGATGGCGTGCTTCAAT 58.175 45.000 14.89 0.0 45.26 2.57
1840 2023 4.435425 CCAACATATGGGCAAATTGTCTG 58.565 43.478 7.80 0.0 46.27 3.51
1992 3201 5.045942 TGTGCCTTCTTTATGATGTACTCCA 60.046 40.000 0.00 0.0 0.00 3.86
2037 3246 2.721425 TGAACCGGGATTTATGGGAC 57.279 50.000 6.32 0.0 0.00 4.46
2106 3723 0.772124 TTCCTCCCCTCTTGCAAGGT 60.772 55.000 25.73 0.0 34.34 3.50
2191 3808 6.235231 TGAACTTCAGGTAGATAATGGGAC 57.765 41.667 0.00 0.0 0.00 4.46
2501 4631 4.691685 TGCAATAGATTTGGCAAGCAAAAG 59.308 37.500 5.70 0.0 32.54 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.380471 AGATGCTCTACAGGTGTCTCT 57.620 47.619 0.00 0.00 0.00 3.10
31 32 8.144478 TGATTATAAAGATGCTCTACAGGTGTC 58.856 37.037 0.00 0.00 0.00 3.67
60 61 9.471084 CATCCGTGTATAATCACAATGTAACTA 57.529 33.333 0.00 0.00 38.12 2.24
306 307 4.612943 GAAATGGTCGAGAGGTACAGATC 58.387 47.826 0.00 0.00 0.00 2.75
338 339 3.988517 CAGATGAGATCACGGACATGATG 59.011 47.826 0.00 0.00 39.48 3.07
406 407 7.432559 GCGCTTAACGTTCGATGACGATTTA 62.433 44.000 16.02 3.16 45.47 1.40
441 442 6.212589 TCATGTCTACATAGTTCTCAAACCCA 59.787 38.462 0.00 0.00 33.29 4.51
449 450 5.297278 GTCTCGGTCATGTCTACATAGTTCT 59.703 44.000 0.00 0.00 34.26 3.01
693 696 1.982938 GTAGCCCTGGACCACGAGT 60.983 63.158 0.00 0.00 0.00 4.18
1385 1430 1.271543 CCACATCTTGTGCTTCCTCCA 60.272 52.381 2.09 0.00 46.51 3.86
1437 1566 0.107017 ATAAGCCTCGCAGCCATTGT 60.107 50.000 0.00 0.00 0.00 2.71
1500 1629 2.549754 CTCAGACAACCGCTTTTCACAT 59.450 45.455 0.00 0.00 0.00 3.21
1605 1734 7.121759 CAGGAGGAAGATTGAGCTTGAATAAAA 59.878 37.037 0.00 0.00 0.00 1.52
1840 2023 4.210331 AGCAGACCATCCATTCCATAAAC 58.790 43.478 0.00 0.00 0.00 2.01
2106 3723 7.283127 GCTGAATATTTCCCTGTAGTGAATCAA 59.717 37.037 0.00 0.00 0.00 2.57
2501 4631 3.004752 AGGTTGGATCAGGTATTGTGC 57.995 47.619 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.