Multiple sequence alignment - TraesCS2D01G216700

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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 TraesCS2D01G216700 chr2D 100.000 4469 0 0 1 4469 179660334 179664802 0.000000e+00 8253.0
1 TraesCS2D01G216700 chr2B 97.084 2881 70 6 813 3685 236456237 236459111 0.000000e+00 4843.0
2 TraesCS2D01G216700 chr2B 91.854 712 28 6 3684 4372 236459193 236459897 0.000000e+00 966.0
3 TraesCS2D01G216700 chr2B 92.695 397 17 7 334 723 236455392 236455783 3.020000e-156 562.0
4 TraesCS2D01G216700 chr2B 83.099 355 10 13 1 314 236454761 236455106 1.220000e-70 278.0
5 TraesCS2D01G216700 chr2B 94.286 105 5 1 4358 4462 236459917 236460020 4.630000e-35 159.0
6 TraesCS2D01G216700 chr2B 90.090 111 4 2 4001 4110 72417266 72417370 2.170000e-28 137.0
7 TraesCS2D01G216700 chr2B 94.118 51 3 0 721 771 236456162 236456212 1.330000e-10 78.7
8 TraesCS2D01G216700 chr2A 96.011 2532 76 8 1961 4469 194122871 194125400 0.000000e+00 4093.0
9 TraesCS2D01G216700 chr2A 91.047 1843 92 26 2 1789 194121037 194122861 0.000000e+00 2422.0
10 TraesCS2D01G216700 chr2A 95.000 40 1 1 563 601 194122649 194122688 1.340000e-05 62.1
11 TraesCS2D01G216700 chr1B 84.086 1439 208 12 997 2426 123967921 123966495 0.000000e+00 1369.0
12 TraesCS2D01G216700 chr1A 82.039 1481 235 20 997 2464 96462663 96464125 0.000000e+00 1232.0
13 TraesCS2D01G216700 chr1A 79.341 1486 240 32 997 2465 96470479 96471914 0.000000e+00 981.0
14 TraesCS2D01G216700 chr1A 98.039 51 1 0 4001 4051 22569856 22569806 6.160000e-14 89.8
15 TraesCS2D01G216700 chr1A 98.039 51 1 0 4001 4051 498684715 498684665 6.160000e-14 89.8
16 TraesCS2D01G216700 chr1A 96.078 51 2 0 4205 4255 548453472 548453422 2.860000e-12 84.2
17 TraesCS2D01G216700 chr1D 82.515 1304 203 13 1181 2464 78983060 78981762 0.000000e+00 1122.0
18 TraesCS2D01G216700 chr1D 94.118 51 3 0 4205 4255 453571678 453571628 1.330000e-10 78.7
19 TraesCS2D01G216700 chr6A 80.868 1359 219 22 972 2303 574709 573365 0.000000e+00 1031.0
20 TraesCS2D01G216700 chr5B 79.042 1503 254 35 997 2461 610664610 610663131 0.000000e+00 974.0
21 TraesCS2D01G216700 chrUn 80.639 1064 180 16 1246 2303 217766738 217765695 0.000000e+00 800.0
22 TraesCS2D01G216700 chrUn 80.639 1064 180 16 1246 2303 246307916 246306873 0.000000e+00 800.0
23 TraesCS2D01G216700 chrUn 98.039 51 1 0 4001 4051 186201906 186201856 6.160000e-14 89.8
24 TraesCS2D01G216700 chr4D 96.380 221 8 0 2327 2547 466320135 466320355 9.140000e-97 364.0
25 TraesCS2D01G216700 chr4D 96.380 221 8 0 2327 2547 471173436 471173216 9.140000e-97 364.0
26 TraesCS2D01G216700 chr7A 72.571 525 137 7 2549 3069 617703895 617703374 9.950000e-37 165.0
27 TraesCS2D01G216700 chr4B 100.000 51 0 0 4001 4051 88872237 88872287 1.320000e-15 95.3
28 TraesCS2D01G216700 chr4B 98.039 51 1 0 4001 4051 209306176 209306226 6.160000e-14 89.8
29 TraesCS2D01G216700 chr7B 98.039 51 1 0 4001 4051 716872267 716872217 6.160000e-14 89.8
30 TraesCS2D01G216700 chr3D 92.727 55 4 0 4205 4259 8506769 8506715 3.710000e-11 80.5


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 TraesCS2D01G216700 chr2D 179660334 179664802 4468 False 8253.000000 8253 100.000000 1 4469 1 chr2D.!!$F1 4468
1 TraesCS2D01G216700 chr2B 236454761 236460020 5259 False 1147.783333 4843 92.189333 1 4462 6 chr2B.!!$F2 4461
2 TraesCS2D01G216700 chr2A 194121037 194125400 4363 False 2192.366667 4093 94.019333 2 4469 3 chr2A.!!$F1 4467
3 TraesCS2D01G216700 chr1B 123966495 123967921 1426 True 1369.000000 1369 84.086000 997 2426 1 chr1B.!!$R1 1429
4 TraesCS2D01G216700 chr1A 96462663 96464125 1462 False 1232.000000 1232 82.039000 997 2464 1 chr1A.!!$F1 1467
5 TraesCS2D01G216700 chr1A 96470479 96471914 1435 False 981.000000 981 79.341000 997 2465 1 chr1A.!!$F2 1468
6 TraesCS2D01G216700 chr1D 78981762 78983060 1298 True 1122.000000 1122 82.515000 1181 2464 1 chr1D.!!$R1 1283
7 TraesCS2D01G216700 chr6A 573365 574709 1344 True 1031.000000 1031 80.868000 972 2303 1 chr6A.!!$R1 1331
8 TraesCS2D01G216700 chr5B 610663131 610664610 1479 True 974.000000 974 79.042000 997 2461 1 chr5B.!!$R1 1464
9 TraesCS2D01G216700 chrUn 217765695 217766738 1043 True 800.000000 800 80.639000 1246 2303 1 chrUn.!!$R2 1057
10 TraesCS2D01G216700 chrUn 246306873 246307916 1043 True 800.000000 800 80.639000 1246 2303 1 chrUn.!!$R3 1057

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
282 326 0.252881 TGGCCATCTTCCAGAGGAGT 60.253 55.0 0.00 0.00 31.21 3.85 F
1164 1888 0.317160 CGCAGAGTAACACCACCTCA 59.683 55.0 0.00 0.00 0.00 3.86 F
1395 2128 1.192146 TCAAGGACAGCGGTAGCCTT 61.192 55.0 12.77 12.77 46.67 4.35 F
2743 3521 0.322008 GCAACTCTTCCCTGGTGAGG 60.322 60.0 11.45 0.00 39.42 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1285 2018 1.228154 GGAGGACAAGGTTGCCGTT 60.228 57.895 0.0 0.0 32.17 4.44 R
2743 3521 1.214589 CCCAGCTCAATGCAGTTGC 59.785 57.895 0.0 0.0 45.94 4.17 R
3294 4072 2.050144 ACGGGAGGCATATTCACATCT 58.950 47.619 0.0 0.0 0.00 2.90 R
3741 4608 0.661020 CGCCTTTTTCCAAGACACGT 59.339 50.000 0.0 0.0 0.00 4.49 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
100 126 0.799917 CAGTGGAGACTGCGATCACG 60.800 60.000 0.00 0.00 43.24 4.35
184 224 7.306167 CGAACAAGACAATTCAAAATTCTGGTG 60.306 37.037 0.00 0.00 0.00 4.17
192 232 3.636679 TCAAAATTCTGGTGTTCACCCA 58.363 40.909 17.78 6.71 0.00 4.51
272 313 0.924823 AAGATCTGCCTGGCCATCTT 59.075 50.000 26.04 26.04 34.46 2.40
273 314 0.473326 AGATCTGCCTGGCCATCTTC 59.527 55.000 19.53 9.38 0.00 2.87
274 315 0.536915 GATCTGCCTGGCCATCTTCC 60.537 60.000 17.53 0.00 0.00 3.46
282 326 0.252881 TGGCCATCTTCCAGAGGAGT 60.253 55.000 0.00 0.00 31.21 3.85
286 330 1.135915 CCATCTTCCAGAGGAGTCGTG 59.864 57.143 0.00 0.00 31.21 4.35
314 362 6.713450 GGTTGTTGAATTCTGGAAGTAACCTA 59.287 38.462 7.05 0.00 33.06 3.08
315 363 7.229907 GGTTGTTGAATTCTGGAAGTAACCTAA 59.770 37.037 7.05 0.00 33.06 2.69
316 364 8.626526 GTTGTTGAATTCTGGAAGTAACCTAAA 58.373 33.333 7.05 0.00 33.76 1.85
317 365 8.754991 TGTTGAATTCTGGAAGTAACCTAAAA 57.245 30.769 7.05 0.00 33.76 1.52
385 699 5.343307 AAAATATTTGCGGCCAAAGATCT 57.657 34.783 2.24 0.00 40.81 2.75
421 735 1.314730 TCCAAGTCAAAGCCGGAAAC 58.685 50.000 5.05 0.00 0.00 2.78
438 752 1.704641 AACCCACTTTTCTGGCTTCC 58.295 50.000 0.00 0.00 0.00 3.46
600 914 7.200434 ACAGTACTTCATCCAGTGGAATAAT 57.800 36.000 17.71 3.79 34.34 1.28
629 948 8.934023 AATTAAAGAAGGGAAAGTGACATACA 57.066 30.769 0.00 0.00 0.00 2.29
630 949 9.533831 AATTAAAGAAGGGAAAGTGACATACAT 57.466 29.630 0.00 0.00 0.00 2.29
631 950 8.561738 TTAAAGAAGGGAAAGTGACATACATC 57.438 34.615 0.00 0.00 0.00 3.06
632 951 4.759782 AGAAGGGAAAGTGACATACATCG 58.240 43.478 0.00 0.00 0.00 3.84
633 952 2.906354 AGGGAAAGTGACATACATCGC 58.094 47.619 0.00 0.00 33.46 4.58
634 953 2.501723 AGGGAAAGTGACATACATCGCT 59.498 45.455 0.00 0.00 41.24 4.93
635 954 3.704566 AGGGAAAGTGACATACATCGCTA 59.295 43.478 0.00 0.00 38.51 4.26
636 955 3.802685 GGGAAAGTGACATACATCGCTAC 59.197 47.826 0.00 0.00 38.51 3.58
719 1039 4.420168 TCAAGCAAGGAAAAGAAAACACG 58.580 39.130 0.00 0.00 0.00 4.49
731 1433 3.959943 AGAAAACACGTTAACCATGTGC 58.040 40.909 10.15 4.83 45.32 4.57
740 1442 5.514914 CACGTTAACCATGTGCCATAAATTC 59.485 40.000 0.00 0.00 35.57 2.17
741 1443 5.417580 ACGTTAACCATGTGCCATAAATTCT 59.582 36.000 0.00 0.00 0.00 2.40
806 1508 0.456824 CAATTCAGCAGCAGCAGCAG 60.457 55.000 12.92 3.97 45.49 4.24
900 1607 1.519719 CCTGTAGCTCACCAGGCTC 59.480 63.158 12.51 0.00 41.65 4.70
1037 1755 1.475213 CCTCCTCCTATTCGGCCAAAC 60.475 57.143 2.24 0.00 0.00 2.93
1109 1827 0.895530 TCACAGAAGATCGTGTCCCC 59.104 55.000 0.00 0.00 34.66 4.81
1164 1888 0.317160 CGCAGAGTAACACCACCTCA 59.683 55.000 0.00 0.00 0.00 3.86
1285 2018 2.749839 CCTTGGAAATCGCCCGCA 60.750 61.111 0.00 0.00 0.00 5.69
1395 2128 1.192146 TCAAGGACAGCGGTAGCCTT 61.192 55.000 12.77 12.77 46.67 4.35
1414 2147 1.519455 GAACTCACCGATGCCTCCG 60.519 63.158 0.00 0.00 0.00 4.63
1471 2204 2.193536 ACAAACACCTGGCTTCCGC 61.194 57.895 0.00 0.00 0.00 5.54
1537 2270 3.129462 GCTTATTCCTTGGAAGAACAGCC 59.871 47.826 8.16 0.00 31.22 4.85
2256 3028 2.107378 TGGAAATGGAGTTGGCACACTA 59.893 45.455 0.00 0.00 39.29 2.74
2743 3521 0.322008 GCAACTCTTCCCTGGTGAGG 60.322 60.000 11.45 0.00 39.42 3.86
2796 3574 1.761449 TTGCACTTGGAACAGCAAGA 58.239 45.000 0.00 0.00 41.06 3.02
2844 3622 2.579873 AGGGATTGCATCATACACTGC 58.420 47.619 0.00 0.00 38.87 4.40
2868 3646 5.985530 CGATGTCAAGCCAGATAACATTCTA 59.014 40.000 0.00 0.00 31.04 2.10
3261 4039 1.000506 GAAAGCACTAGACCCACGACA 59.999 52.381 0.00 0.00 0.00 4.35
3270 4048 2.759985 ACCCACGACAGGTCAGATT 58.240 52.632 0.00 0.00 28.99 2.40
3294 4072 4.720273 GTCCAAATCCTAGAGGGGTTTCTA 59.280 45.833 0.00 0.00 44.52 2.10
3360 4138 4.646492 GGTGAAAGCCCTGATGTCATAAAT 59.354 41.667 0.00 0.00 0.00 1.40
3399 4177 0.397941 CAAGCCAGACTTCCCAGACA 59.602 55.000 0.00 0.00 36.04 3.41
3525 4303 9.237846 GCCTTTATATGTTTGAAAAGTGCTATC 57.762 33.333 0.00 0.00 0.00 2.08
3586 4369 6.755141 TCAGCTTTTTATGTCGTCCTATGTAC 59.245 38.462 0.00 0.00 0.00 2.90
3590 4373 7.012044 GCTTTTTATGTCGTCCTATGTACCAAT 59.988 37.037 0.00 0.00 0.00 3.16
3591 4374 8.795842 TTTTTATGTCGTCCTATGTACCAATT 57.204 30.769 0.00 0.00 0.00 2.32
3621 4404 2.110901 AGGCTCACAGCAGAATTGAG 57.889 50.000 0.00 0.00 44.75 3.02
3669 4452 1.875514 TGCATGCTATCTTGCGGAATC 59.124 47.619 20.33 0.00 43.81 2.52
3741 4608 3.088532 AGTGTCTGCCTTTTCACAAACA 58.911 40.909 0.00 0.00 33.84 2.83
3802 4669 2.237643 TGCTATTTGGCAGAAGCACAA 58.762 42.857 14.15 0.00 44.61 3.33
3935 4805 3.181506 GGACAGAAGAAATCAATGGACGC 60.182 47.826 0.00 0.00 0.00 5.19
3948 4818 2.125512 GACGCGTTGCCTCTCCAT 60.126 61.111 15.53 0.00 0.00 3.41
4031 4917 2.885135 TGGCTGGATTGACATGAACT 57.115 45.000 0.00 0.00 0.00 3.01
4102 4989 4.096532 GGCTAACCCTCTATTGCTTTCAAC 59.903 45.833 0.00 0.00 34.60 3.18
4435 5358 3.628942 TGGCAGAATTCGATCAGGATTTG 59.371 43.478 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 224 1.640917 TCTACCTGGTCTGGGTGAAC 58.359 55.000 0.63 0.00 37.65 3.18
272 313 1.979155 CCTGCACGACTCCTCTGGA 60.979 63.158 0.00 0.00 0.00 3.86
273 314 1.821061 AACCTGCACGACTCCTCTGG 61.821 60.000 0.00 0.00 0.00 3.86
274 315 0.668706 CAACCTGCACGACTCCTCTG 60.669 60.000 0.00 0.00 0.00 3.35
282 326 2.290367 CAGAATTCAACAACCTGCACGA 59.710 45.455 8.44 0.00 0.00 4.35
286 330 3.319122 ACTTCCAGAATTCAACAACCTGC 59.681 43.478 8.44 0.00 0.00 4.85
320 368 4.083802 GCGAATACTCAAAGTTGCAGAACT 60.084 41.667 0.00 0.00 44.79 3.01
321 369 4.151798 GCGAATACTCAAAGTTGCAGAAC 58.848 43.478 0.00 0.00 0.00 3.01
324 372 3.811722 TGCGAATACTCAAAGTTGCAG 57.188 42.857 0.00 0.00 0.00 4.41
325 373 3.812609 TCTTGCGAATACTCAAAGTTGCA 59.187 39.130 0.00 0.00 0.00 4.08
327 375 6.017933 GTCATCTTGCGAATACTCAAAGTTG 58.982 40.000 0.00 0.00 0.00 3.16
328 376 5.700832 TGTCATCTTGCGAATACTCAAAGTT 59.299 36.000 0.00 0.00 0.00 2.66
385 699 6.375736 TGACTTGGAATATTTAAACGATGGCA 59.624 34.615 0.00 0.00 0.00 4.92
421 735 0.178964 TGGGAAGCCAGAAAAGTGGG 60.179 55.000 0.00 0.00 38.14 4.61
466 780 1.434622 GCCATGATGCTGACTGTCGG 61.435 60.000 12.29 12.29 0.00 4.79
632 951 4.688021 GGTAGCATAGCTATGATGGTAGC 58.312 47.826 33.10 23.87 43.30 3.58
740 1442 9.398538 AGTAGGAGTACTAGAATCTTGTGTTAG 57.601 37.037 7.58 0.00 37.76 2.34
788 1490 1.883732 CTGCTGCTGCTGCTGAATT 59.116 52.632 27.67 0.00 40.01 2.17
810 1512 2.809861 ATTGAGAGCCACACGCCCTG 62.810 60.000 0.00 0.00 38.78 4.45
811 1513 2.527951 GATTGAGAGCCACACGCCCT 62.528 60.000 0.00 0.00 38.78 5.19
900 1607 1.676006 GTGGTTGGACACAGGTTTCTG 59.324 52.381 0.00 0.00 46.10 3.02
932 1647 0.962855 GGGAGCCTGAACTTTGGAGC 60.963 60.000 0.00 0.00 0.00 4.70
980 1695 2.705148 TGGATCATGGATGGGAGCTTA 58.295 47.619 0.00 0.00 0.00 3.09
1008 1723 4.591072 CCGAATAGGAGGAGGAAGAAGAAT 59.409 45.833 0.00 0.00 45.00 2.40
1109 1827 2.184167 ACGGTGAACTTGTTGCCCG 61.184 57.895 14.74 14.74 41.09 6.13
1164 1888 3.780294 TGTAGTAATTGCTGGAGGTGGAT 59.220 43.478 6.28 0.00 0.00 3.41
1285 2018 1.228154 GGAGGACAAGGTTGCCGTT 60.228 57.895 0.00 0.00 32.17 4.44
1395 2128 1.596934 GGAGGCATCGGTGAGTTCA 59.403 57.895 0.00 0.00 0.00 3.18
1414 2147 4.388773 TCGCCAATAAACTATCGATGCATC 59.611 41.667 17.10 17.10 0.00 3.91
2743 3521 1.214589 CCCAGCTCAATGCAGTTGC 59.785 57.895 0.00 0.00 45.94 4.17
2796 3574 2.196595 TCATGCAGGTAGTTTAGGCCT 58.803 47.619 11.78 11.78 0.00 5.19
2844 3622 4.813161 AGAATGTTATCTGGCTTGACATCG 59.187 41.667 0.00 0.00 31.10 3.84
3261 4039 5.032846 TCTAGGATTTGGACAATCTGACCT 58.967 41.667 0.00 0.00 33.37 3.85
3270 4048 2.661176 ACCCCTCTAGGATTTGGACA 57.339 50.000 0.00 0.00 38.24 4.02
3294 4072 2.050144 ACGGGAGGCATATTCACATCT 58.950 47.619 0.00 0.00 0.00 2.90
3360 4138 5.931146 GCTTGAAGACAGATCTGAGAAGAAA 59.069 40.000 29.27 13.75 34.48 2.52
3399 4177 4.022416 TGAGAAGTTGTTGTGCTGTTTTGT 60.022 37.500 0.00 0.00 0.00 2.83
3565 4347 7.837202 TTGGTACATAGGACGACATAAAAAG 57.163 36.000 0.00 0.00 39.30 2.27
3586 4369 5.240623 TGTGAGCCTACAGTGTTTAAATTGG 59.759 40.000 0.00 0.00 0.00 3.16
3621 4404 8.850452 CAGAAATCTCGTTTTTATTTTGGCTAC 58.150 33.333 0.00 0.00 0.00 3.58
3741 4608 0.661020 CGCCTTTTTCCAAGACACGT 59.339 50.000 0.00 0.00 0.00 4.49
3802 4669 6.553100 TGGACTTTCCTTTGTGAAATTATGGT 59.447 34.615 0.00 0.00 37.46 3.55
3917 4787 2.699954 ACGCGTCCATTGATTTCTTCT 58.300 42.857 5.58 0.00 0.00 2.85
3935 4805 0.758734 TATCCCATGGAGAGGCAACG 59.241 55.000 15.22 0.00 36.93 4.10
3948 4818 3.389983 CGTTACCTCCTGGAAATATCCCA 59.610 47.826 0.00 0.00 45.95 4.37
4031 4917 3.873910 GCCAGTTGCTGTCCTAATAGAA 58.126 45.455 0.00 0.00 36.87 2.10
4296 5185 8.749841 ATATATGAGTAGAAACTGATGAACGC 57.250 34.615 0.00 0.00 35.56 4.84


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

AutoCloner maintained by Alex Coulton.