Multiple sequence alignment - TraesCS7A01G288600

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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 TraesCS7A01G288600 chr7A 100.000 2475 0 0 1 2475 347383184 347385658 0.000000e+00 4571
1 TraesCS7A01G288600 chr7A 96.222 2488 77 4 1 2475 401494982 401497465 0.000000e+00 4058
2 TraesCS7A01G288600 chr7A 90.047 422 38 3 1463 1883 458555683 458555265 6.020000e-151 544
3 TraesCS7A01G288600 chr7A 87.316 339 33 6 1 329 458556519 458556181 1.800000e-101 379
4 TraesCS7A01G288600 chr7A 77.393 491 86 19 461 936 657352834 657353314 4.060000e-68 268
5 TraesCS7A01G288600 chr6A 96.262 2488 77 7 1 2475 242010628 242008144 0.000000e+00 4065
6 TraesCS7A01G288600 chr6A 94.384 463 22 4 2013 2475 180952684 180952226 0.000000e+00 708
7 TraesCS7A01G288600 chr2A 96.141 2488 80 3 1 2475 284782265 284784749 0.000000e+00 4048
8 TraesCS7A01G288600 chr2A 94.397 464 22 4 2013 2475 528783399 528782939 0.000000e+00 710
9 TraesCS7A01G288600 chr2A 93.548 465 26 4 2012 2475 482546045 482546506 0.000000e+00 689
10 TraesCS7A01G288600 chr2D 93.037 876 44 6 1025 1887 64941660 64940789 0.000000e+00 1264
11 TraesCS7A01G288600 chr2D 91.622 740 35 6 28 767 64942371 64941659 0.000000e+00 998
12 TraesCS7A01G288600 chr1B 92.848 769 47 5 1 764 226904477 226905242 0.000000e+00 1109
13 TraesCS7A01G288600 chr1B 91.061 716 39 4 52 767 227793153 227793843 0.000000e+00 944
14 TraesCS7A01G288600 chr1B 88.995 418 41 4 1467 1883 310676592 310676179 1.700000e-141 512
15 TraesCS7A01G288600 chr1B 88.201 339 30 6 1 329 390092032 390091694 1.780000e-106 396
16 TraesCS7A01G288600 chr1B 87.611 339 32 4 1 329 412240626 412240288 3.860000e-103 385
17 TraesCS7A01G288600 chr1B 88.136 236 26 2 1873 2108 606148584 606148817 1.870000e-71 279
18 TraesCS7A01G288600 chr1B 87.045 247 28 4 1873 2118 412239684 412239441 2.420000e-70 276
19 TraesCS7A01G288600 chr5D 95.676 555 18 6 909 1462 534638075 534638624 0.000000e+00 887
20 TraesCS7A01G288600 chr5D 95.676 555 18 6 909 1462 534857968 534858517 0.000000e+00 887
21 TraesCS7A01G288600 chr5D 95.161 558 21 6 909 1465 534866092 534866644 0.000000e+00 876
22 TraesCS7A01G288600 chr5D 87.440 621 47 16 317 936 534856425 534857015 0.000000e+00 686
23 TraesCS7A01G288600 chr5D 93.514 370 19 4 1463 1831 198493533 198493168 1.670000e-151 545
24 TraesCS7A01G288600 chr5D 93.633 267 17 0 1 267 198494340 198494074 1.380000e-107 399
25 TraesCS7A01G288600 chr5D 77.264 497 81 25 460 936 534864655 534865139 1.890000e-66 263
26 TraesCS7A01G288600 chr5D 88.263 213 23 1 317 527 228445898 228445686 1.140000e-63 254
27 TraesCS7A01G288600 chr5D 92.079 101 8 0 836 936 534637022 534637122 2.570000e-30 143
28 TraesCS7A01G288600 chr5B 95.818 550 19 4 917 1465 675081267 675081813 0.000000e+00 885
29 TraesCS7A01G288600 chr5B 95.495 555 19 6 909 1462 674893292 674893841 0.000000e+00 881
30 TraesCS7A01G288600 chr5B 87.770 417 34 11 317 732 675079413 675079813 2.880000e-129 472
31 TraesCS7A01G288600 chr5B 91.626 203 12 4 735 936 675080110 675080308 2.420000e-70 276
32 TraesCS7A01G288600 chr5B 83.654 208 32 1 322 527 251567447 251567240 6.980000e-46 195
33 TraesCS7A01G288600 chr5B 90.000 150 15 0 787 936 675423345 675423494 6.980000e-46 195
34 TraesCS7A01G288600 chr5B 90.526 95 8 1 673 767 280176329 280176422 9.290000e-25 124
35 TraesCS7A01G288600 chr4A 94.803 558 23 6 909 1465 636963854 636963302 0.000000e+00 865
36 TraesCS7A01G288600 chr4A 94.600 463 21 4 2013 2474 123476644 123477103 0.000000e+00 713
37 TraesCS7A01G288600 chr4A 87.456 287 23 2 317 602 636687636 636687362 3.970000e-83 318
38 TraesCS7A01G288600 chr4A 86.689 293 29 6 646 936 636687360 636687076 1.430000e-82 316
39 TraesCS7A01G288600 chr4A 77.246 501 79 24 462 936 636965290 636964799 6.790000e-66 261
40 TraesCS7A01G288600 chr4A 76.983 517 71 40 452 936 636680485 636679985 4.090000e-63 252
41 TraesCS7A01G288600 chr1A 94.397 464 21 5 2013 2475 534671675 534672134 0.000000e+00 708
42 TraesCS7A01G288600 chr1A 93.534 464 27 2 2012 2475 288306435 288306895 0.000000e+00 688
43 TraesCS7A01G288600 chr2B 91.003 389 32 2 1495 1883 51451679 51451294 2.820000e-144 521
44 TraesCS7A01G288600 chr2B 88.942 208 23 0 52 259 501131949 501131742 8.780000e-65 257
45 TraesCS7A01G288600 chr2B 85.714 238 29 5 1873 2108 51451373 51451139 1.900000e-61 246
46 TraesCS7A01G288600 chr3B 90.674 386 34 1 1498 1883 410849772 410849389 1.700000e-141 512
47 TraesCS7A01G288600 chr3B 89.431 246 24 2 1873 2118 410849468 410849225 2.390000e-80 309
48 TraesCS7A01G288600 chr7D 77.888 502 73 20 457 936 568598107 568598592 6.740000e-71 278
49 TraesCS7A01G288600 chr4B 87.793 213 24 1 317 527 426877414 426877626 5.290000e-62 248
50 TraesCS7A01G288600 chr7B 86.574 216 25 4 1904 2118 579440462 579440674 4.120000e-58 235
51 TraesCS7A01G288600 chr7B 79.006 362 56 16 580 935 624350868 624351215 1.910000e-56 230
52 TraesCS7A01G288600 chr7B 81.250 224 39 2 1881 2103 714749801 714750022 7.030000e-41 178
53 TraesCS7A01G288600 chr4D 83.893 149 22 2 317 464 280924958 280925105 9.230000e-30 141
54 TraesCS7A01G288600 chr4D 89.157 83 8 1 379 460 148512885 148512803 4.350000e-18 102


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 TraesCS7A01G288600 chr7A 347383184 347385658 2474 False 4571.000000 4571 100.0000 1 2475 1 chr7A.!!$F1 2474
1 TraesCS7A01G288600 chr7A 401494982 401497465 2483 False 4058.000000 4058 96.2220 1 2475 1 chr7A.!!$F2 2474
2 TraesCS7A01G288600 chr7A 458555265 458556519 1254 True 461.500000 544 88.6815 1 1883 2 chr7A.!!$R1 1882
3 TraesCS7A01G288600 chr6A 242008144 242010628 2484 True 4065.000000 4065 96.2620 1 2475 1 chr6A.!!$R2 2474
4 TraesCS7A01G288600 chr2A 284782265 284784749 2484 False 4048.000000 4048 96.1410 1 2475 1 chr2A.!!$F1 2474
5 TraesCS7A01G288600 chr2D 64940789 64942371 1582 True 1131.000000 1264 92.3295 28 1887 2 chr2D.!!$R1 1859
6 TraesCS7A01G288600 chr1B 226904477 226905242 765 False 1109.000000 1109 92.8480 1 764 1 chr1B.!!$F1 763
7 TraesCS7A01G288600 chr1B 227793153 227793843 690 False 944.000000 944 91.0610 52 767 1 chr1B.!!$F2 715
8 TraesCS7A01G288600 chr1B 412239441 412240626 1185 True 330.500000 385 87.3280 1 2118 2 chr1B.!!$R3 2117
9 TraesCS7A01G288600 chr5D 534856425 534858517 2092 False 786.500000 887 91.5580 317 1462 2 chr5D.!!$F2 1145
10 TraesCS7A01G288600 chr5D 534864655 534866644 1989 False 569.500000 876 86.2125 460 1465 2 chr5D.!!$F3 1005
11 TraesCS7A01G288600 chr5D 534637022 534638624 1602 False 515.000000 887 93.8775 836 1462 2 chr5D.!!$F1 626
12 TraesCS7A01G288600 chr5D 198493168 198494340 1172 True 472.000000 545 93.5735 1 1831 2 chr5D.!!$R2 1830
13 TraesCS7A01G288600 chr5B 674893292 674893841 549 False 881.000000 881 95.4950 909 1462 1 chr5B.!!$F2 553
14 TraesCS7A01G288600 chr5B 675079413 675081813 2400 False 544.333333 885 91.7380 317 1465 3 chr5B.!!$F4 1148
15 TraesCS7A01G288600 chr4A 636963302 636965290 1988 True 563.000000 865 86.0245 462 1465 2 chr4A.!!$R3 1003
16 TraesCS7A01G288600 chr4A 636687076 636687636 560 True 317.000000 318 87.0725 317 936 2 chr4A.!!$R2 619
17 TraesCS7A01G288600 chr4A 636679985 636680485 500 True 252.000000 252 76.9830 452 936 1 chr4A.!!$R1 484
18 TraesCS7A01G288600 chr2B 51451139 51451679 540 True 383.500000 521 88.3585 1495 2108 2 chr2B.!!$R2 613
19 TraesCS7A01G288600 chr3B 410849225 410849772 547 True 410.500000 512 90.0525 1498 2118 2 chr3B.!!$R1 620

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
85 90 1.00176 TTCTTCCTCCTCTCCCCGG 59.998 63.158 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 3455 0.87439 TACGAGCGTAGACCAAACGT 59.126 50.0 0.0 0.0 42.26 3.99 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
85 90 1.001760 TTCTTCCTCCTCTCCCCGG 59.998 63.158 0.00 0.00 0.00 5.73
122 127 1.765314 GGTCTAGTGCATGTCCATCCT 59.235 52.381 0.00 0.00 0.00 3.24
467 503 8.962111 GCTTATTCTTACTGCTTTTATGAATGC 58.038 33.333 1.58 1.58 36.69 3.56
688 749 2.429250 ACCCGGTTTGTCCTTTTTGAAG 59.571 45.455 0.00 0.00 0.00 3.02
834 1202 2.022764 TGCACCGTCCTCACATATTG 57.977 50.000 0.00 0.00 0.00 1.90
1684 3324 3.016031 TGATTTGAAGCAGTGTGTGTGT 58.984 40.909 0.00 0.00 0.00 3.72
1685 3325 2.917701 TTTGAAGCAGTGTGTGTGTG 57.082 45.000 0.00 0.00 0.00 3.82
1737 3377 4.641989 GCAATGTGATTCACTTACTCCCAT 59.358 41.667 17.26 0.00 35.11 4.00
1979 3619 2.253154 GCGGCGCGGTTTAGTTTT 59.747 55.556 19.09 0.00 0.00 2.43
2006 3646 1.122632 TTGAGGTCCACTTACGCCCA 61.123 55.000 0.00 0.00 0.00 5.36
2015 3655 2.151202 CACTTACGCCCAATGTGAAGT 58.849 47.619 0.00 0.00 0.00 3.01
2135 3776 1.160137 GCGGTTTTCTGTCTGATGCT 58.840 50.000 0.00 0.00 0.00 3.79
2360 4001 7.615582 TGTTTGAACAAAATAAACCATGCAA 57.384 28.000 0.00 0.00 35.67 4.08
2380 4021 6.589135 TGCAATTCTCTATCATGTCTGATGT 58.411 36.000 0.00 0.00 42.19 3.06
2414 4055 1.285641 CCGATGCAGTGCGGTTTTT 59.714 52.632 11.20 0.00 42.49 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 55 0.544223 GAAGGAAAGGAGAGAGGGGC 59.456 60.000 0.00 0.00 0.00 5.80
431 467 5.221621 GCAGTAAGAATAAGCTCCAGGAGAT 60.222 44.000 21.89 11.93 0.00 2.75
834 1202 3.716601 AGTTGCCTGCAAACATGTAAAC 58.283 40.909 6.07 0.00 37.70 2.01
902 1270 2.146342 CGAACATCACCAGCAACTTCT 58.854 47.619 0.00 0.00 0.00 2.85
944 2297 2.728007 AGGCAAAGAATCTACCCTTGC 58.272 47.619 8.45 8.45 0.00 4.01
1339 2958 5.559770 TCACCAGAATCTTCAATGCTACAA 58.440 37.500 0.00 0.00 0.00 2.41
1737 3377 7.548780 GCATTAATTTTTCTGCCCTTTCACATA 59.451 33.333 0.00 0.00 0.00 2.29
1815 3455 0.874390 TACGAGCGTAGACCAAACGT 59.126 50.000 0.00 0.00 42.26 3.99
1979 3619 1.507140 AGTGGACCTCAACACTTCCA 58.493 50.000 0.00 0.00 45.03 3.53
2015 3655 1.334160 TAGACGGAAAGTGGAGTGCA 58.666 50.000 0.00 0.00 0.00 4.57
2360 4001 7.377398 GCACTACATCAGACATGATAGAGAAT 58.623 38.462 0.00 0.00 44.58 2.40
2371 4012 2.831685 AAACCGCACTACATCAGACA 57.168 45.000 0.00 0.00 0.00 3.41
2380 4021 2.519826 CGGACGAAAAACCGCACTA 58.480 52.632 0.00 0.00 42.55 2.74
2414 4055 2.028476 CGTGGGTACTTCATCCAACTGA 60.028 50.000 0.00 0.00 31.73 3.41


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

AutoCloner maintained by Alex Coulton.