Multiple sequence alignment - TraesCS1B01G111100

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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 TraesCS1B01G111100 chr1B 100.000 2351 0 0 1 2351 127295899 127293549 0.000000e+00 4342
1 TraesCS1B01G111100 chr3A 92.654 2355 126 18 21 2351 33835487 33837818 0.000000e+00 3347
2 TraesCS1B01G111100 chr3A 92.295 2336 121 30 21 2351 120238222 120240503 0.000000e+00 3262
3 TraesCS1B01G111100 chr3A 93.042 618 31 5 25 642 40153699 40153094 0.000000e+00 893
4 TraesCS1B01G111100 chr6A 92.539 2359 121 22 21 2351 85543471 85545802 0.000000e+00 3330
5 TraesCS1B01G111100 chr6A 80.085 236 26 8 996 1212 61397019 61396786 3.130000e-34 156
6 TraesCS1B01G111100 chr4A 91.348 1988 110 23 21 1985 374574352 374576300 0.000000e+00 2662
7 TraesCS1B01G111100 chr4A 97.019 369 9 2 1984 2351 374585039 374585406 9.230000e-174 619
8 TraesCS1B01G111100 chr3D 91.623 1719 86 17 21 1714 592964832 592966517 0.000000e+00 2324
9 TraesCS1B01G111100 chr3D 95.478 774 21 7 1580 2351 592966490 592967251 0.000000e+00 1223
10 TraesCS1B01G111100 chr2B 92.898 1577 80 11 796 2351 190041773 190040208 0.000000e+00 2263
11 TraesCS1B01G111100 chr2B 91.831 759 45 10 26 784 190042566 190041825 0.000000e+00 1042
12 TraesCS1B01G111100 chr4D 92.103 1355 70 12 21 1353 450210926 450212265 0.000000e+00 1875
13 TraesCS1B01G111100 chr4D 94.758 248 13 0 1524 1771 198583939 198584186 1.020000e-103 387
14 TraesCS1B01G111100 chr1A 83.778 1313 160 24 483 1771 218980588 218981871 0.000000e+00 1195
15 TraesCS1B01G111100 chr1A 91.522 460 33 5 24 481 218979312 218979767 1.530000e-176 628
16 TraesCS1B01G111100 chr1A 80.838 334 29 15 1774 2106 540722568 540722867 1.820000e-56 230
17 TraesCS1B01G111100 chr2D 89.388 556 51 6 1141 1692 72151144 72150593 0.000000e+00 693
18 TraesCS1B01G111100 chr3B 83.309 689 101 7 1065 1746 161126129 161126810 7.130000e-175 623
19 TraesCS1B01G111100 chr4B 89.189 481 45 6 1774 2250 211584576 211585053 5.590000e-166 593
20 TraesCS1B01G111100 chr4B 80.465 215 14 14 611 806 211582890 211583095 3.150000e-29 139
21 TraesCS1B01G111100 chr1D 81.928 415 37 14 1774 2185 460528426 460528047 1.360000e-82 316
22 TraesCS1B01G111100 chr1D 84.677 248 12 12 492 733 452545217 452545444 8.460000e-55 224
23 TraesCS1B01G111100 chr2A 88.966 145 14 2 2120 2263 95223171 95223314 6.680000e-41 178
24 TraesCS1B01G111100 chr7B 88.276 145 15 2 2120 2263 633744286 633744429 3.110000e-39 172
25 TraesCS1B01G111100 chrUn 94.624 93 5 0 1774 1866 68534395 68534487 6.770000e-31 145


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 TraesCS1B01G111100 chr1B 127293549 127295899 2350 True 4342.0 4342 100.0000 1 2351 1 chr1B.!!$R1 2350
1 TraesCS1B01G111100 chr3A 33835487 33837818 2331 False 3347.0 3347 92.6540 21 2351 1 chr3A.!!$F1 2330
2 TraesCS1B01G111100 chr3A 120238222 120240503 2281 False 3262.0 3262 92.2950 21 2351 1 chr3A.!!$F2 2330
3 TraesCS1B01G111100 chr3A 40153094 40153699 605 True 893.0 893 93.0420 25 642 1 chr3A.!!$R1 617
4 TraesCS1B01G111100 chr6A 85543471 85545802 2331 False 3330.0 3330 92.5390 21 2351 1 chr6A.!!$F1 2330
5 TraesCS1B01G111100 chr4A 374574352 374576300 1948 False 2662.0 2662 91.3480 21 1985 1 chr4A.!!$F1 1964
6 TraesCS1B01G111100 chr3D 592964832 592967251 2419 False 1773.5 2324 93.5505 21 2351 2 chr3D.!!$F1 2330
7 TraesCS1B01G111100 chr2B 190040208 190042566 2358 True 1652.5 2263 92.3645 26 2351 2 chr2B.!!$R1 2325
8 TraesCS1B01G111100 chr4D 450210926 450212265 1339 False 1875.0 1875 92.1030 21 1353 1 chr4D.!!$F2 1332
9 TraesCS1B01G111100 chr1A 218979312 218981871 2559 False 911.5 1195 87.6500 24 1771 2 chr1A.!!$F2 1747
10 TraesCS1B01G111100 chr2D 72150593 72151144 551 True 693.0 693 89.3880 1141 1692 1 chr2D.!!$R1 551
11 TraesCS1B01G111100 chr3B 161126129 161126810 681 False 623.0 623 83.3090 1065 1746 1 chr3B.!!$F1 681
12 TraesCS1B01G111100 chr4B 211582890 211585053 2163 False 366.0 593 84.8270 611 2250 2 chr4B.!!$F1 1639

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
800 1690 0.817634 CCCTTTCCACTGACGCACAA 60.818 55.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 3882 2.972713 AGGCTGAATTAGAGCGGGATTA 59.027 45.455 0.0 0.0 37.32 1.75 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
184 186 4.066646 TCTTCAATGTCCACGAACTTGA 57.933 40.909 0.00 0.00 0.00 3.02
196 199 2.890945 ACGAACTTGATTTTCTTGGGGG 59.109 45.455 0.00 0.00 0.00 5.40
238 241 9.567776 CGATGACTGTAATATCTCTAGGGATAT 57.432 37.037 17.96 17.96 39.67 1.63
388 392 7.647318 TGTGCGATAACATTTAAATTGGCATAG 59.353 33.333 9.54 0.00 0.00 2.23
447 451 8.420222 TCCACATCATTATGTTGTGAAAAACTT 58.580 29.630 27.96 0.00 45.87 2.66
463 467 1.995376 ACTTGGTGAATTTTCGGCCT 58.005 45.000 0.00 0.00 0.00 5.19
527 1352 8.306761 ACTTTGTTTCTTCTCTCAAAATTGTGT 58.693 29.630 0.00 0.00 31.07 3.72
686 1521 9.436957 TTTTTAGGCATTTGTTTTCTTACAACA 57.563 25.926 0.00 0.00 37.72 3.33
753 1601 4.702274 GGGCCAACCAGCACCCAT 62.702 66.667 4.39 0.00 42.33 4.00
754 1602 2.358619 GGCCAACCAGCACCCATA 59.641 61.111 0.00 0.00 35.26 2.74
800 1690 0.817634 CCCTTTCCACTGACGCACAA 60.818 55.000 0.00 0.00 0.00 3.33
885 1791 2.681778 CCTCGTCTCCCACTGCCT 60.682 66.667 0.00 0.00 0.00 4.75
1062 1968 2.137528 TGACAACAGCTCCCCGACA 61.138 57.895 0.00 0.00 0.00 4.35
1076 2001 2.643272 GACACCGACGACAGCTCA 59.357 61.111 0.00 0.00 0.00 4.26
1089 2014 4.393693 GCTCAAAGCTCTGTGGCT 57.606 55.556 0.00 0.00 45.30 4.75
1174 2118 2.043752 TCCACGTCCCCATCGCTA 60.044 61.111 0.00 0.00 0.00 4.26
1452 3191 4.402155 TCTTTCTTCAGCAAGCCAAGAAAA 59.598 37.500 20.82 13.63 42.65 2.29
1463 3202 1.703411 CCAAGAAAAAGGGAGTGCCA 58.297 50.000 2.50 0.00 35.15 4.92
1465 3204 1.615392 CAAGAAAAAGGGAGTGCCAGG 59.385 52.381 2.50 0.00 35.15 4.45
1486 3225 5.049060 CAGGAGTAGTACTCTGAATCCATCG 60.049 48.000 25.70 2.99 44.46 3.84
1493 3232 3.877559 ACTCTGAATCCATCGATGCAAA 58.122 40.909 20.25 7.79 33.34 3.68
1522 3262 6.041511 CCAAACATGTGAATCAAGTTGTGAA 58.958 36.000 0.00 0.00 40.50 3.18
1804 3750 5.879237 TGATTTGCAACTAAATTCTAGCCG 58.121 37.500 0.00 0.00 30.78 5.52
1847 3793 8.461222 TGAATGCACATCAAGGAGTATTTTTAG 58.539 33.333 1.68 0.00 0.00 1.85
1907 3854 3.548587 CAATTCAGCTCGTTTCTGTGTG 58.451 45.455 0.00 0.00 33.48 3.82
1908 3855 2.309528 TTCAGCTCGTTTCTGTGTGT 57.690 45.000 0.00 0.00 33.48 3.72
1909 3856 3.446310 TTCAGCTCGTTTCTGTGTGTA 57.554 42.857 0.00 0.00 33.48 2.90
1910 3857 3.660501 TCAGCTCGTTTCTGTGTGTAT 57.339 42.857 0.00 0.00 33.48 2.29
1911 3858 3.575630 TCAGCTCGTTTCTGTGTGTATC 58.424 45.455 0.00 0.00 33.48 2.24
1912 3859 2.668457 CAGCTCGTTTCTGTGTGTATCC 59.332 50.000 0.00 0.00 0.00 2.59
1913 3860 2.299013 AGCTCGTTTCTGTGTGTATCCA 59.701 45.455 0.00 0.00 0.00 3.41
1927 3882 5.046304 GTGTGTATCCAGTATCCATATGCCT 60.046 44.000 0.00 0.00 0.00 4.75
1961 3917 2.856760 TCAGCCTACTCCCATCTCTT 57.143 50.000 0.00 0.00 0.00 2.85
1971 3927 8.325046 GCCTACTCCCATCTCTTGATAAATAAT 58.675 37.037 0.00 0.00 0.00 1.28
2039 3998 3.518634 TTCAGCACCAAACCAGAAAAC 57.481 42.857 0.00 0.00 0.00 2.43
2121 4080 4.755266 AGGTTCAGTGTTTCACTACTGT 57.245 40.909 2.03 0.00 43.43 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 146 7.857734 TGAAGATGCCTTATTATCAAACGAA 57.142 32.000 0.00 0.00 31.62 3.85
184 186 2.181975 CATGTCTGCCCCCAAGAAAAT 58.818 47.619 0.00 0.00 0.00 1.82
196 199 4.510711 AGTCATCGAATCAATCATGTCTGC 59.489 41.667 0.00 0.00 0.00 4.26
289 292 9.927668 CCTTTTGTATTCAACCAATTTGTCTAT 57.072 29.630 0.00 0.00 36.49 1.98
290 293 7.870445 GCCTTTTGTATTCAACCAATTTGTCTA 59.130 33.333 0.00 0.00 36.49 2.59
357 361 7.385650 CAATTTAAATGTTATCGCACAAGCTG 58.614 34.615 0.39 0.00 39.10 4.24
359 363 6.695245 CCAATTTAAATGTTATCGCACAAGC 58.305 36.000 0.39 0.00 37.42 4.01
405 409 2.158519 TGTGGAGGCGGTGATATCTCTA 60.159 50.000 3.98 0.00 0.00 2.43
406 410 1.333177 GTGGAGGCGGTGATATCTCT 58.667 55.000 3.98 0.00 0.00 3.10
447 451 3.133003 TGAAAAAGGCCGAAAATTCACCA 59.867 39.130 0.00 0.00 0.00 4.17
463 467 0.534203 AGAAGGGCGACGCTGAAAAA 60.534 50.000 20.77 0.00 0.00 1.94
686 1521 1.620323 GCCTTGGATCAGCAACCTTTT 59.380 47.619 0.00 0.00 0.00 2.27
753 1601 3.077695 AGAGAGTGAGGGGAAGGAGTTTA 59.922 47.826 0.00 0.00 0.00 2.01
754 1602 2.158081 AGAGAGTGAGGGGAAGGAGTTT 60.158 50.000 0.00 0.00 0.00 2.66
800 1690 0.179073 CTCCGCCGTGATCTGGATTT 60.179 55.000 8.54 0.00 0.00 2.17
828 1734 3.844090 GGCGAGAGTGGAGGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
971 1877 1.238439 CAACGACTGAGCCAACCAAT 58.762 50.000 0.00 0.00 0.00 3.16
974 1880 1.557443 CGACAACGACTGAGCCAACC 61.557 60.000 0.00 0.00 42.66 3.77
1062 1968 1.664965 GCTTTGAGCTGTCGTCGGT 60.665 57.895 0.00 0.00 38.45 4.69
1076 2001 2.359230 GCCGAGCCACAGAGCTTT 60.359 61.111 0.00 0.00 45.15 3.51
1452 3191 0.117340 ACTACTCCTGGCACTCCCTT 59.883 55.000 0.00 0.00 0.00 3.95
1463 3202 5.067273 CGATGGATTCAGAGTACTACTCCT 58.933 45.833 11.94 0.00 46.18 3.69
1465 3204 6.607689 CATCGATGGATTCAGAGTACTACTC 58.392 44.000 17.96 8.02 45.38 2.59
1486 3225 5.412640 TCACATGTTTGGATCATTTGCATC 58.587 37.500 0.00 0.00 0.00 3.91
1493 3232 6.845758 ACTTGATTCACATGTTTGGATCAT 57.154 33.333 7.85 0.00 33.99 2.45
1522 3262 6.261826 GTGAATTAAGCATGCAGAGATACCTT 59.738 38.462 21.98 4.30 0.00 3.50
1560 3301 5.916661 TTTCTAGCAACTACTCCTACTGG 57.083 43.478 0.00 0.00 0.00 4.00
1804 3750 4.034279 GCATTCAGACTCAGAATTCAGAGC 59.966 45.833 23.49 16.99 33.64 4.09
1847 3793 3.926616 TGCTACTCCTTGCTGTACTTTC 58.073 45.455 0.00 0.00 0.00 2.62
1907 3854 7.445945 GGATTAGGCATATGGATACTGGATAC 58.554 42.308 4.56 0.00 37.61 2.24
1908 3855 6.558775 GGGATTAGGCATATGGATACTGGATA 59.441 42.308 4.56 0.00 37.61 2.59
1909 3856 5.370880 GGGATTAGGCATATGGATACTGGAT 59.629 44.000 4.56 0.00 37.61 3.41
1910 3857 4.721776 GGGATTAGGCATATGGATACTGGA 59.278 45.833 4.56 0.00 37.61 3.86
1911 3858 4.443457 CGGGATTAGGCATATGGATACTGG 60.443 50.000 4.56 0.00 37.61 4.00
1912 3859 4.697514 CGGGATTAGGCATATGGATACTG 58.302 47.826 4.56 0.00 37.61 2.74
1913 3860 3.134804 GCGGGATTAGGCATATGGATACT 59.865 47.826 4.56 0.00 37.61 2.12
1927 3882 2.972713 AGGCTGAATTAGAGCGGGATTA 59.027 45.455 0.00 0.00 37.32 1.75
2039 3998 5.527214 TCAGGCCATAATCGTTTGACATAAG 59.473 40.000 5.01 0.00 0.00 1.73
2121 4080 8.934023 AAACAACTGAATCTTTAATCCCAGTA 57.066 30.769 0.00 0.00 34.22 2.74


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

AutoCloner maintained by Alex Coulton.