Multiple sequence alignment - TraesCS1B01G367000

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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 TraesCS1B01G367000 chr1B 100.000 2141 0 0 1 2141 597670678 597668538 0.000000e+00 3954
1 TraesCS1B01G367000 chr1A 92.077 1704 127 6 443 2141 537815766 537817466 0.000000e+00 2392
2 TraesCS1B01G367000 chr1A 90.611 458 38 5 2 455 537811145 537811601 8.450000e-169 603
3 TraesCS1B01G367000 chr1D 93.113 1481 96 5 666 2141 440089360 440087881 0.000000e+00 2165
4 TraesCS1B01G367000 chr1D 91.176 680 53 6 2 675 440111241 440110563 0.000000e+00 917
5 TraesCS1B01G367000 chr1D 86.427 361 39 10 2 355 91228528 91228171 9.270000e-104 387
6 TraesCS1B01G367000 chr1D 85.794 359 45 6 2 356 126438058 126437702 2.010000e-100 375
7 TraesCS1B01G367000 chr5D 85.333 900 109 12 1260 2139 561568375 561569271 0.000000e+00 909
8 TraesCS1B01G367000 chr5D 87.838 666 47 12 356 988 446885571 446884907 0.000000e+00 750
9 TraesCS1B01G367000 chr7B 85.135 888 121 7 1260 2141 63774419 63773537 0.000000e+00 898
10 TraesCS1B01G367000 chr7A 84.785 815 109 12 1259 2066 132304546 132303740 0.000000e+00 804
11 TraesCS1B01G367000 chr7A 82.701 896 117 28 1260 2120 418611324 418610432 0.000000e+00 761
12 TraesCS1B01G367000 chr7A 82.511 892 123 24 1260 2141 619288695 619289563 0.000000e+00 752
13 TraesCS1B01G367000 chr7A 87.048 664 51 14 357 987 132305226 132304565 0.000000e+00 717
14 TraesCS1B01G367000 chr3D 86.382 727 91 5 1260 1981 612607588 612606865 0.000000e+00 787
15 TraesCS1B01G367000 chr3D 85.379 766 95 11 1262 2011 80559693 80558929 0.000000e+00 778
16 TraesCS1B01G367000 chr3D 87.593 669 47 12 353 987 517477891 517478557 0.000000e+00 743
17 TraesCS1B01G367000 chr3D 87.334 679 46 17 353 992 80560387 80559710 0.000000e+00 741
18 TraesCS1B01G367000 chr3D 88.372 344 32 8 2 340 173008776 173009116 7.110000e-110 407
19 TraesCS1B01G367000 chr3B 83.790 839 113 19 1260 2086 712321639 712322466 0.000000e+00 774
20 TraesCS1B01G367000 chr3B 86.736 671 51 12 355 992 712320959 712321624 0.000000e+00 712
21 TraesCS1B01G367000 chr3B 97.778 270 6 0 992 1261 101912407 101912676 1.160000e-127 466
22 TraesCS1B01G367000 chr3B 88.926 298 22 2 355 641 704559464 704559761 7.270000e-95 357
23 TraesCS1B01G367000 chrUn 88.209 670 44 13 353 988 378803980 378803312 0.000000e+00 767
24 TraesCS1B01G367000 chrUn 88.191 669 46 8 353 988 382377306 382376638 0.000000e+00 767
25 TraesCS1B01G367000 chrUn 97.778 270 6 0 992 1261 93408400 93408131 1.160000e-127 466
26 TraesCS1B01G367000 chrUn 97.778 270 6 0 992 1261 444245200 444244931 1.160000e-127 466
27 TraesCS1B01G367000 chrUn 81.852 540 75 8 1622 2141 299823039 299822503 1.170000e-117 433
28 TraesCS1B01G367000 chrUn 81.852 540 75 8 1622 2141 309591665 309591129 1.170000e-117 433
29 TraesCS1B01G367000 chr2A 88.191 669 46 8 353 988 398618266 398617598 0.000000e+00 767
30 TraesCS1B01G367000 chr2A 87.892 669 47 9 353 988 398712178 398712845 0.000000e+00 756
31 TraesCS1B01G367000 chr2D 87.910 670 47 12 356 992 6477853 6477185 0.000000e+00 758
32 TraesCS1B01G367000 chr2D 97.778 270 6 0 992 1261 272792681 272792412 1.160000e-127 466
33 TraesCS1B01G367000 chr2D 85.950 363 41 9 2 356 375832497 375832137 1.550000e-101 379
34 TraesCS1B01G367000 chr5A 87.761 670 47 12 353 988 632144720 632144052 0.000000e+00 750
35 TraesCS1B01G367000 chr5A 92.962 341 22 2 649 988 577766585 577766246 1.480000e-136 496
36 TraesCS1B01G367000 chr5B 87.688 666 48 13 355 987 544425000 544425664 0.000000e+00 745
37 TraesCS1B01G367000 chr5B 87.237 666 52 11 355 988 429750723 429750059 0.000000e+00 728
38 TraesCS1B01G367000 chr3A 87.389 674 50 16 353 992 143949543 143948871 0.000000e+00 741
39 TraesCS1B01G367000 chr3A 97.778 270 6 0 992 1261 594898392 594898123 1.160000e-127 466
40 TraesCS1B01G367000 chr6D 86.418 670 56 14 353 988 2000053 1999385 0.000000e+00 701
41 TraesCS1B01G367000 chr6D 85.714 672 56 22 353 988 73628596 73627929 0.000000e+00 673
42 TraesCS1B01G367000 chr4D 97.778 270 6 0 992 1261 30386766 30386497 1.160000e-127 466
43 TraesCS1B01G367000 chr4A 97.778 270 6 0 992 1261 73811703 73811972 1.160000e-127 466
44 TraesCS1B01G367000 chr4A 86.351 359 44 5 3 356 118603024 118603382 9.270000e-104 387
45 TraesCS1B01G367000 chr7D 86.313 358 45 4 2 355 506169972 506169615 9.270000e-104 387
46 TraesCS1B01G367000 chr4B 84.807 362 48 6 2 356 168561043 168561404 7.270000e-95 357


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 TraesCS1B01G367000 chr1B 597668538 597670678 2140 True 3954.0 3954 100.0000 1 2141 1 chr1B.!!$R1 2140
1 TraesCS1B01G367000 chr1A 537815766 537817466 1700 False 2392.0 2392 92.0770 443 2141 1 chr1A.!!$F2 1698
2 TraesCS1B01G367000 chr1D 440087881 440089360 1479 True 2165.0 2165 93.1130 666 2141 1 chr1D.!!$R3 1475
3 TraesCS1B01G367000 chr1D 440110563 440111241 678 True 917.0 917 91.1760 2 675 1 chr1D.!!$R4 673
4 TraesCS1B01G367000 chr5D 561568375 561569271 896 False 909.0 909 85.3330 1260 2139 1 chr5D.!!$F1 879
5 TraesCS1B01G367000 chr5D 446884907 446885571 664 True 750.0 750 87.8380 356 988 1 chr5D.!!$R1 632
6 TraesCS1B01G367000 chr7B 63773537 63774419 882 True 898.0 898 85.1350 1260 2141 1 chr7B.!!$R1 881
7 TraesCS1B01G367000 chr7A 418610432 418611324 892 True 761.0 761 82.7010 1260 2120 1 chr7A.!!$R1 860
8 TraesCS1B01G367000 chr7A 132303740 132305226 1486 True 760.5 804 85.9165 357 2066 2 chr7A.!!$R2 1709
9 TraesCS1B01G367000 chr7A 619288695 619289563 868 False 752.0 752 82.5110 1260 2141 1 chr7A.!!$F1 881
10 TraesCS1B01G367000 chr3D 612606865 612607588 723 True 787.0 787 86.3820 1260 1981 1 chr3D.!!$R1 721
11 TraesCS1B01G367000 chr3D 80558929 80560387 1458 True 759.5 778 86.3565 353 2011 2 chr3D.!!$R2 1658
12 TraesCS1B01G367000 chr3D 517477891 517478557 666 False 743.0 743 87.5930 353 987 1 chr3D.!!$F2 634
13 TraesCS1B01G367000 chr3B 712320959 712322466 1507 False 743.0 774 85.2630 355 2086 2 chr3B.!!$F3 1731
14 TraesCS1B01G367000 chrUn 378803312 378803980 668 True 767.0 767 88.2090 353 988 1 chrUn.!!$R4 635
15 TraesCS1B01G367000 chrUn 382376638 382377306 668 True 767.0 767 88.1910 353 988 1 chrUn.!!$R5 635
16 TraesCS1B01G367000 chrUn 299822503 299823039 536 True 433.0 433 81.8520 1622 2141 1 chrUn.!!$R2 519
17 TraesCS1B01G367000 chrUn 309591129 309591665 536 True 433.0 433 81.8520 1622 2141 1 chrUn.!!$R3 519
18 TraesCS1B01G367000 chr2A 398617598 398618266 668 True 767.0 767 88.1910 353 988 1 chr2A.!!$R1 635
19 TraesCS1B01G367000 chr2A 398712178 398712845 667 False 756.0 756 87.8920 353 988 1 chr2A.!!$F1 635
20 TraesCS1B01G367000 chr2D 6477185 6477853 668 True 758.0 758 87.9100 356 992 1 chr2D.!!$R1 636
21 TraesCS1B01G367000 chr5A 632144052 632144720 668 True 750.0 750 87.7610 353 988 1 chr5A.!!$R2 635
22 TraesCS1B01G367000 chr5B 544425000 544425664 664 False 745.0 745 87.6880 355 987 1 chr5B.!!$F1 632
23 TraesCS1B01G367000 chr5B 429750059 429750723 664 True 728.0 728 87.2370 355 988 1 chr5B.!!$R1 633
24 TraesCS1B01G367000 chr3A 143948871 143949543 672 True 741.0 741 87.3890 353 992 1 chr3A.!!$R1 639
25 TraesCS1B01G367000 chr6D 1999385 2000053 668 True 701.0 701 86.4180 353 988 1 chr6D.!!$R1 635
26 TraesCS1B01G367000 chr6D 73627929 73628596 667 True 673.0 673 85.7140 353 988 1 chr6D.!!$R2 635

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
114 117 0.560688 TGGCCTCCTCCCAAAGTTTT 59.439 50.0 3.32 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1196 1244 2.59575 TGGATCCCGGTTGTTCAATT 57.404 45.0 9.9 0.0 0.0 2.32 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
21 22 2.036089 CGAGATTAGGGTTAGAGGTGCC 59.964 54.545 0.00 0.00 0.00 5.01
23 24 3.648545 GAGATTAGGGTTAGAGGTGCCAT 59.351 47.826 0.00 0.00 0.00 4.40
47 48 4.567318 CCCACAAGCTCATAGGGC 57.433 61.111 0.00 0.00 31.81 5.19
78 81 2.431683 GCCTGGTGAGCTTGTGGA 59.568 61.111 0.00 0.00 0.00 4.02
83 86 2.619849 CCTGGTGAGCTTGTGGATCATT 60.620 50.000 0.00 0.00 42.56 2.57
93 96 1.134699 TGTGGATCATTCGTGGCTCTC 60.135 52.381 0.00 0.00 0.00 3.20
94 97 1.137872 GTGGATCATTCGTGGCTCTCT 59.862 52.381 0.00 0.00 0.00 3.10
107 110 1.306482 CTCTCTTGGCCTCCTCCCA 60.306 63.158 3.32 0.00 0.00 4.37
111 114 0.772124 TCTTGGCCTCCTCCCAAAGT 60.772 55.000 3.32 0.00 41.49 2.66
114 117 0.560688 TGGCCTCCTCCCAAAGTTTT 59.439 50.000 3.32 0.00 0.00 2.43
122 125 2.820197 CCTCCCAAAGTTTTCTAGGTGC 59.180 50.000 0.00 0.00 0.00 5.01
126 129 3.255888 CCCAAAGTTTTCTAGGTGCCTTC 59.744 47.826 0.00 0.00 0.00 3.46
160 164 8.159709 AGAAAAATCGTCAAAAGTTTTGTTTCG 58.840 29.630 24.00 23.44 0.00 3.46
166 170 5.117287 CGTCAAAAGTTTTGTTTCGTTTGGA 59.883 36.000 24.00 2.22 35.17 3.53
175 180 3.001414 TGTTTCGTTTGGACTCGTTTGA 58.999 40.909 0.00 0.00 0.00 2.69
189 194 7.390440 TGGACTCGTTTGATATTGATTTTCTGT 59.610 33.333 0.00 0.00 0.00 3.41
190 195 7.693951 GGACTCGTTTGATATTGATTTTCTGTG 59.306 37.037 0.00 0.00 0.00 3.66
248 254 5.727766 ACTGGGCACTAGGTTAATAGGTTAA 59.272 40.000 0.00 0.00 43.06 2.01
257 263 9.690913 ACTAGGTTAATAGGTTAATCCCAAAAC 57.309 33.333 0.00 0.00 32.41 2.43
359 366 2.838202 ACACCGGAGACATATCAAAGGT 59.162 45.455 9.46 0.00 0.00 3.50
794 839 8.752005 TGCAGTAAATTTATTGGCTAGATTCT 57.248 30.769 18.91 0.00 0.00 2.40
820 865 2.942804 TCACCAACAAAGAGGCATTGA 58.057 42.857 4.96 0.00 0.00 2.57
940 987 5.781818 TGATGCTGGATACTTATCTGATCCA 59.218 40.000 0.00 3.00 45.45 3.41
941 988 6.270695 TGATGCTGGATACTTATCTGATCCAA 59.729 38.462 4.51 0.00 46.54 3.53
1007 1055 9.788960 GAGGTACAACCATAGAAAAATGAAATC 57.211 33.333 0.00 0.00 41.95 2.17
1035 1083 8.408043 AAATATTCCGAGATGGCAAATATTCA 57.592 30.769 11.12 0.00 36.68 2.57
1059 1107 8.316946 TCAGAGATGACTATGAAAACACATCTT 58.683 33.333 0.00 0.00 42.51 2.40
1196 1244 7.523709 GCAAAGAATGACCTTGGTTATCAAAGA 60.524 37.037 0.00 0.00 34.56 2.52
1279 1327 3.426615 TGACAAAACAAACTCTGGTGGT 58.573 40.909 0.00 0.00 0.00 4.16
1299 1347 6.046593 GTGGTTACATCCACGAATCATTCTA 58.953 40.000 0.00 0.00 46.38 2.10
1329 1377 9.755804 TTATTGCTTTGTTTGAAACATGATGTA 57.244 25.926 11.97 0.00 41.79 2.29
1352 1400 5.574891 AATGTGTATGGCTTCGCAAAATA 57.425 34.783 0.00 0.00 0.00 1.40
1356 1404 7.270757 TGTGTATGGCTTCGCAAAATAATAT 57.729 32.000 0.00 0.00 0.00 1.28
1357 1405 7.711846 TGTGTATGGCTTCGCAAAATAATATT 58.288 30.769 0.00 0.00 0.00 1.28
1398 1446 4.650588 GTGGGATTGGATCATTGGAATCAA 59.349 41.667 0.00 0.00 37.28 2.57
1448 1497 8.806429 ATGGATGTATTACACAGATGAAACAA 57.194 30.769 0.00 0.00 41.51 2.83
1696 1748 5.887598 TGATAATCTGTTTGTGATCCTTGGG 59.112 40.000 0.00 0.00 0.00 4.12
1717 1769 5.415701 TGGGTCTTTGATATTGCACTCTTTC 59.584 40.000 0.00 0.00 0.00 2.62
1734 1787 8.577296 GCACTCTTTCCCTTTATAAGTTTTTCT 58.423 33.333 0.00 0.00 0.00 2.52
1767 1822 8.803235 GTTTCTTATGGAAGGTTTTAATGAGGT 58.197 33.333 0.00 0.00 35.16 3.85
1820 1877 8.367156 CCATTTTCTCCTTATTTTTCCAGTGAA 58.633 33.333 0.00 0.00 0.00 3.18
1844 1901 5.930837 TTTTTGAAGGTGTTCTTGATGGT 57.069 34.783 0.00 0.00 35.50 3.55
1891 1950 4.316025 TTCCTACAGGATTTTTGGAGGG 57.684 45.455 3.79 0.00 45.25 4.30
1929 2036 8.500837 TGTTGATGACGATGTTTACAAAAATC 57.499 30.769 0.00 0.00 30.78 2.17
1955 2063 4.949856 TGAAACAGGGATTAGGAAGAATGC 59.050 41.667 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 81 1.745141 GCCAAGAGAGCCACGAATGAT 60.745 52.381 0.00 0.00 0.00 2.45
93 96 0.113190 AACTTTGGGAGGAGGCCAAG 59.887 55.000 5.01 0.00 0.00 3.61
94 97 0.560688 AAACTTTGGGAGGAGGCCAA 59.439 50.000 5.01 0.00 0.00 4.52
107 110 4.145052 CCAGAAGGCACCTAGAAAACTTT 58.855 43.478 0.00 0.00 0.00 2.66
122 125 2.094545 CGATTTTTCTTGGGCCAGAAGG 60.095 50.000 6.23 0.00 34.22 3.46
126 129 1.885887 TGACGATTTTTCTTGGGCCAG 59.114 47.619 6.23 0.96 0.00 4.85
160 164 8.742554 AAAATCAATATCAAACGAGTCCAAAC 57.257 30.769 0.00 0.00 0.00 2.93
166 170 8.322906 TCACAGAAAATCAATATCAAACGAGT 57.677 30.769 0.00 0.00 0.00 4.18
213 218 1.526686 TGCCCAGTGTCAGTTGCTG 60.527 57.895 0.00 0.00 0.00 4.41
214 219 1.526917 GTGCCCAGTGTCAGTTGCT 60.527 57.895 0.00 0.00 0.00 3.91
215 220 0.250295 TAGTGCCCAGTGTCAGTTGC 60.250 55.000 0.00 0.00 0.00 4.17
221 227 3.629142 ATTAACCTAGTGCCCAGTGTC 57.371 47.619 0.00 0.00 0.00 3.67
222 228 3.454812 CCTATTAACCTAGTGCCCAGTGT 59.545 47.826 0.00 0.00 0.00 3.55
335 342 5.130477 ACCTTTGATATGTCTCCGGTGTATT 59.870 40.000 0.00 0.00 0.00 1.89
340 347 4.569719 AAACCTTTGATATGTCTCCGGT 57.430 40.909 0.00 0.00 0.00 5.28
341 348 5.671493 AGTAAACCTTTGATATGTCTCCGG 58.329 41.667 0.00 0.00 0.00 5.14
342 349 8.712285 TTTAGTAAACCTTTGATATGTCTCCG 57.288 34.615 0.00 0.00 0.00 4.63
472 483 9.679661 TTTAAGATGATTACTTGCCTCATGTAA 57.320 29.630 7.45 7.45 38.00 2.41
656 678 7.509546 TCATCATCACCCTTAGGTCTAAATTC 58.490 38.462 0.00 0.00 46.45 2.17
731 776 3.334691 TGGTGCAGTTTGCTAGATACAC 58.665 45.455 0.00 0.00 45.31 2.90
794 839 1.955778 CCTCTTTGTTGGTGATGCACA 59.044 47.619 0.00 0.00 35.86 4.57
820 865 7.639113 TCTAAAAATGTTCTTCACACCAACT 57.361 32.000 0.00 0.00 38.61 3.16
940 987 9.911788 AAACCAGTCTGTGATCTATCATTATTT 57.088 29.630 0.00 0.00 39.30 1.40
941 988 9.911788 AAAACCAGTCTGTGATCTATCATTATT 57.088 29.630 0.00 0.00 39.30 1.40
949 996 5.808366 AGACAAAACCAGTCTGTGATCTA 57.192 39.130 0.00 0.00 44.23 1.98
1007 1055 4.811555 TTGCCATCTCGGAATATTTTCG 57.188 40.909 5.99 5.99 36.56 3.46
1035 1083 8.944029 CAAAGATGTGTTTTCATAGTCATCTCT 58.056 33.333 0.00 0.00 38.27 3.10
1055 1103 6.418101 TCTTTCAATTCGAGGATCCAAAGAT 58.582 36.000 15.82 0.00 34.57 2.40
1059 1107 5.187772 TCTCTCTTTCAATTCGAGGATCCAA 59.812 40.000 15.82 0.00 0.00 3.53
1105 1153 5.840693 GGATCCATTCCAAATACCCAGAATT 59.159 40.000 6.95 0.00 44.74 2.17
1196 1244 2.595750 TGGATCCCGGTTGTTCAATT 57.404 45.000 9.90 0.00 0.00 2.32
1320 1368 6.238456 CGAAGCCATACACATTTACATCATGT 60.238 38.462 0.00 0.00 35.10 3.21
1528 1580 7.928908 TCACATGACTTCTTTTGCAAAATAC 57.071 32.000 24.06 13.76 0.00 1.89
1577 1629 8.601845 TCTCAAATAAAGAACTTGACGATGAA 57.398 30.769 0.00 0.00 0.00 2.57
1696 1748 5.649831 AGGGAAAGAGTGCAATATCAAAGAC 59.350 40.000 0.00 0.00 0.00 3.01
1717 1769 9.996554 AACCATTCAAGAAAAACTTATAAAGGG 57.003 29.630 0.00 0.00 37.03 3.95
1734 1787 7.610580 AAACCTTCCATAAGAAACCATTCAA 57.389 32.000 0.00 0.00 38.06 2.69
1787 1842 9.185192 GAAAAATAAGGAGAAAATGGCATATCG 57.815 33.333 0.00 0.00 0.00 2.92
1826 1883 7.402054 ACAATATACCATCAAGAACACCTTCA 58.598 34.615 0.00 0.00 31.42 3.02
1832 1889 9.772973 GGTATGTACAATATACCATCAAGAACA 57.227 33.333 16.11 0.00 46.03 3.18
1891 1950 3.314635 GTCATCAACATCTTGATCAGCCC 59.685 47.826 0.00 0.00 44.04 5.19
1913 2020 9.782028 CTGTTTCAATGATTTTTGTAAACATCG 57.218 29.630 0.00 0.00 36.79 3.84
1915 2022 9.054922 CCCTGTTTCAATGATTTTTGTAAACAT 57.945 29.630 0.00 0.00 36.79 2.71
1929 2036 7.486647 CATTCTTCCTAATCCCTGTTTCAATG 58.513 38.462 0.00 0.00 0.00 2.82


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

AutoCloner maintained by Alex Coulton.