Multiple sequence alignment - TraesCS6B01G202200

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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 TraesCS6B01G202200 chr6B 100.000 2771 0 0 1 2771 246802097 246799327 0.000000e+00 5118
1 TraesCS6B01G202200 chr6B 95.712 2192 71 13 596 2771 246527372 246525188 0.000000e+00 3506
2 TraesCS6B01G202200 chr6B 95.575 2192 75 12 596 2771 246377121 246374936 0.000000e+00 3491
3 TraesCS6B01G202200 chr6B 95.435 1818 78 5 957 2771 246682877 246681062 0.000000e+00 2892
4 TraesCS6B01G202200 chr6B 92.965 597 36 4 1 595 259255119 259255711 0.000000e+00 865
5 TraesCS6B01G202200 chr6B 92.593 378 13 5 596 961 246690921 246690547 1.890000e-146 529
6 TraesCS6B01G202200 chrUn 95.803 2192 70 12 596 2771 155275510 155273325 0.000000e+00 3518
7 TraesCS6B01G202200 chrUn 95.712 2192 71 13 596 2771 324095414 324093230 0.000000e+00 3506
8 TraesCS6B01G202200 chrUn 95.675 2127 70 12 596 2706 351594647 351596767 0.000000e+00 3398
9 TraesCS6B01G202200 chr2A 93.968 1459 72 9 596 2040 187816507 187817963 0.000000e+00 2193
10 TraesCS6B01G202200 chr2A 88.347 1373 131 21 596 1949 554432783 554431421 0.000000e+00 1622
11 TraesCS6B01G202200 chr2A 93.114 668 41 4 2107 2770 187817967 187818633 0.000000e+00 974
12 TraesCS6B01G202200 chr2A 88.567 656 62 8 2115 2765 311192404 311191757 0.000000e+00 784
13 TraesCS6B01G202200 chr5A 93.575 1463 80 7 596 2045 365135243 365133782 0.000000e+00 2169
14 TraesCS6B01G202200 chr5D 93.077 1459 81 8 596 2041 80812093 80813544 0.000000e+00 2117
15 TraesCS6B01G202200 chr2D 92.834 628 38 6 2146 2767 81967344 81967970 0.000000e+00 904
16 TraesCS6B01G202200 chr3B 93.289 596 36 4 1 595 334585953 334585361 0.000000e+00 876
17 TraesCS6B01G202200 chr3B 93.109 595 39 2 1 595 258029563 258028971 0.000000e+00 870
18 TraesCS6B01G202200 chr3B 92.630 597 37 6 1 596 216670155 216670745 0.000000e+00 852
19 TraesCS6B01G202200 chr5B 92.953 596 38 4 1 595 323267312 323267904 0.000000e+00 865
20 TraesCS6B01G202200 chr5B 92.761 594 41 2 3 595 226117555 226116963 0.000000e+00 857
21 TraesCS6B01G202200 chr1B 92.953 596 38 3 1 595 175742490 175743082 0.000000e+00 865
22 TraesCS6B01G202200 chr2B 92.953 596 36 5 1 595 739799403 739798813 0.000000e+00 863
23 TraesCS6B01G202200 chr2B 92.785 596 39 4 1 595 436376346 436376938 0.000000e+00 859


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 TraesCS6B01G202200 chr6B 246799327 246802097 2770 True 5118.0 5118 100.000 1 2771 1 chr6B.!!$R5 2770
1 TraesCS6B01G202200 chr6B 246525188 246527372 2184 True 3506.0 3506 95.712 596 2771 1 chr6B.!!$R2 2175
2 TraesCS6B01G202200 chr6B 246374936 246377121 2185 True 3491.0 3491 95.575 596 2771 1 chr6B.!!$R1 2175
3 TraesCS6B01G202200 chr6B 246681062 246682877 1815 True 2892.0 2892 95.435 957 2771 1 chr6B.!!$R3 1814
4 TraesCS6B01G202200 chr6B 259255119 259255711 592 False 865.0 865 92.965 1 595 1 chr6B.!!$F1 594
5 TraesCS6B01G202200 chrUn 155273325 155275510 2185 True 3518.0 3518 95.803 596 2771 1 chrUn.!!$R1 2175
6 TraesCS6B01G202200 chrUn 324093230 324095414 2184 True 3506.0 3506 95.712 596 2771 1 chrUn.!!$R2 2175
7 TraesCS6B01G202200 chrUn 351594647 351596767 2120 False 3398.0 3398 95.675 596 2706 1 chrUn.!!$F1 2110
8 TraesCS6B01G202200 chr2A 554431421 554432783 1362 True 1622.0 1622 88.347 596 1949 1 chr2A.!!$R2 1353
9 TraesCS6B01G202200 chr2A 187816507 187818633 2126 False 1583.5 2193 93.541 596 2770 2 chr2A.!!$F1 2174
10 TraesCS6B01G202200 chr2A 311191757 311192404 647 True 784.0 784 88.567 2115 2765 1 chr2A.!!$R1 650
11 TraesCS6B01G202200 chr5A 365133782 365135243 1461 True 2169.0 2169 93.575 596 2045 1 chr5A.!!$R1 1449
12 TraesCS6B01G202200 chr5D 80812093 80813544 1451 False 2117.0 2117 93.077 596 2041 1 chr5D.!!$F1 1445
13 TraesCS6B01G202200 chr2D 81967344 81967970 626 False 904.0 904 92.834 2146 2767 1 chr2D.!!$F1 621
14 TraesCS6B01G202200 chr3B 334585361 334585953 592 True 876.0 876 93.289 1 595 1 chr3B.!!$R2 594
15 TraesCS6B01G202200 chr3B 258028971 258029563 592 True 870.0 870 93.109 1 595 1 chr3B.!!$R1 594
16 TraesCS6B01G202200 chr3B 216670155 216670745 590 False 852.0 852 92.630 1 596 1 chr3B.!!$F1 595
17 TraesCS6B01G202200 chr5B 323267312 323267904 592 False 865.0 865 92.953 1 595 1 chr5B.!!$F1 594
18 TraesCS6B01G202200 chr5B 226116963 226117555 592 True 857.0 857 92.761 3 595 1 chr5B.!!$R1 592
19 TraesCS6B01G202200 chr1B 175742490 175743082 592 False 865.0 865 92.953 1 595 1 chr1B.!!$F1 594
20 TraesCS6B01G202200 chr2B 739798813 739799403 590 True 863.0 863 92.953 1 595 1 chr2B.!!$R1 594
21 TraesCS6B01G202200 chr2B 436376346 436376938 592 False 859.0 859 92.785 1 595 1 chr2B.!!$F1 594

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
95 96 0.617935 TGAAGATGGCCATCGGTGAA 59.382 50.0 34.48 19.55 42.48 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2112 3.006323 AGGCGCAAAACATTTGACCAATA 59.994 39.13 10.83 0.0 0.0 1.9 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
70 71 1.835483 CTTGTCATGGATAGCGCCGC 61.835 60.000 2.29 0.00 0.00 6.53
88 89 1.531423 GCGATGATGAAGATGGCCAT 58.469 50.000 20.96 20.96 0.00 4.40
95 96 0.617935 TGAAGATGGCCATCGGTGAA 59.382 50.000 34.48 19.55 42.48 3.18
164 166 4.577246 GCTACAGAGGCTCGCGGG 62.577 72.222 6.13 2.60 0.00 6.13
655 663 6.753913 ATGCTATCCAGACTATTTTCCTCA 57.246 37.500 0.00 0.00 0.00 3.86
656 664 6.753913 TGCTATCCAGACTATTTTCCTCAT 57.246 37.500 0.00 0.00 0.00 2.90
657 665 6.528321 TGCTATCCAGACTATTTTCCTCATG 58.472 40.000 0.00 0.00 0.00 3.07
658 666 6.327365 TGCTATCCAGACTATTTTCCTCATGA 59.673 38.462 0.00 0.00 0.00 3.07
660 668 7.882271 GCTATCCAGACTATTTTCCTCATGATT 59.118 37.037 0.00 0.00 0.00 2.57
661 669 9.790344 CTATCCAGACTATTTTCCTCATGATTT 57.210 33.333 0.00 0.00 0.00 2.17
809 820 2.549926 GGGTTGTTGGCTGTTTTTCAG 58.450 47.619 0.00 0.00 46.12 3.02
872 883 4.335594 GCCTCCTACGAAACAGCAAAATAT 59.664 41.667 0.00 0.00 0.00 1.28
1068 1091 6.775629 TCTTACAGGAAAGTAATGTTGGCTTT 59.224 34.615 0.00 0.00 33.82 3.51
1093 1116 7.396540 AGTTTATTGAATGCTTCCTTGGTAG 57.603 36.000 0.00 0.00 0.00 3.18
1188 1213 3.713826 TCCACAATTCCCTAGGTCAAC 57.286 47.619 8.29 0.00 0.00 3.18
1203 1228 2.687935 GGTCAACATGCCCGTATTCAAT 59.312 45.455 0.00 0.00 0.00 2.57
1405 1431 2.644798 AGATTTGTACCAGCTCCCAAGT 59.355 45.455 0.00 0.00 0.00 3.16
1557 1584 5.812642 CCTAAGTATGGAACTAACTGTGCTG 59.187 44.000 0.00 0.00 37.50 4.41
1654 1681 4.080526 TGGAGGGTTTCTCTAATGTAAGCC 60.081 45.833 0.00 0.00 42.10 4.35
1805 1832 6.070656 TCCAAGGACAATGAAATTCAACTCT 58.929 36.000 0.00 0.00 31.22 3.24
1835 1862 5.489792 AACTTCTTTCCTGCAGAGACATA 57.510 39.130 17.39 0.00 0.00 2.29
1865 1893 8.624776 GTTCTCTATTTATTTGTCTCCCAATGG 58.375 37.037 0.00 0.00 31.81 3.16
1886 1914 9.211485 CAATGGCAGAAAAGAGATGTTATTTTT 57.789 29.630 0.00 0.00 0.00 1.94
1887 1915 8.767478 ATGGCAGAAAAGAGATGTTATTTTTG 57.233 30.769 0.00 0.00 0.00 2.44
2132 2160 9.716531 TGCATTTCCAATTAACATGTTTATTCA 57.283 25.926 17.78 8.63 0.00 2.57
2214 2242 8.827832 AAGAATCCCAATGATGAAATGTTCTA 57.172 30.769 0.00 0.00 32.68 2.10
2218 2246 6.484288 TCCCAATGATGAAATGTTCTACACT 58.516 36.000 0.00 0.00 0.00 3.55
2275 2303 5.431765 TCTCAAGGGTCTCATTAATTCTGC 58.568 41.667 0.00 0.00 0.00 4.26
2284 2312 5.591877 GTCTCATTAATTCTGCCACCTTCAT 59.408 40.000 0.00 0.00 0.00 2.57
2408 2436 7.448161 TGATAATTTCTTTGCAAGACCTTCAGA 59.552 33.333 0.00 0.00 37.23 3.27
2423 2451 5.630121 ACCTTCAGATGTAAACAATGTCCA 58.370 37.500 0.00 0.00 0.00 4.02
2430 2458 8.253810 TCAGATGTAAACAATGTCCAAAAACAA 58.746 29.630 0.00 0.00 31.81 2.83
2545 2575 2.106338 TCAAAGGAACAGCACCATGAGA 59.894 45.455 0.00 0.00 0.00 3.27
2577 2607 7.759489 TCTGCTATTTGTTTAACATGGTTCT 57.241 32.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 1.730612 CGATGGCCATCTTCATCATCG 59.269 52.381 36.51 22.04 46.69 3.84
164 166 1.619332 GATAGATCGGGAGTTCCACCC 59.381 57.143 0.00 0.00 43.57 4.61
310 317 0.179034 GGAAGCATCGAGGAAGCCAT 60.179 55.000 0.00 0.00 0.00 4.40
475 482 8.496534 TTACTTTTGGGACTAACCTACTAACT 57.503 34.615 0.00 0.00 38.98 2.24
669 679 6.091437 GCAGAAGAACATCATGAAGAAAAGG 58.909 40.000 4.68 0.00 0.00 3.11
809 820 5.278022 CCAGCTGGTCTTTGTTCTTTAGTTC 60.278 44.000 25.53 0.00 0.00 3.01
872 883 3.669536 TGACCATGTCGTCAATGCTAAA 58.330 40.909 2.68 0.00 39.78 1.85
1093 1116 5.273944 CAGCTTGTACAAAAGAACTTGTCC 58.726 41.667 10.03 0.00 40.08 4.02
1155 1180 6.209391 AGGGAATTGTGGAAAGTTACAATCTG 59.791 38.462 3.55 0.00 44.32 2.90
1188 1213 5.167121 TGTTTTTCATTGAATACGGGCATG 58.833 37.500 0.00 0.00 0.00 4.06
1265 1290 7.476540 AGAAATGTATCACCACTGTAGTACA 57.523 36.000 2.36 2.36 31.89 2.90
1325 1350 5.973899 TCCATATGTAGCAGCAAACAAAA 57.026 34.783 1.24 0.00 0.00 2.44
1329 1354 6.799512 AGAATTTCCATATGTAGCAGCAAAC 58.200 36.000 1.24 0.00 0.00 2.93
1405 1431 4.033709 TGGAAAACCCACCTGAAATTGAA 58.966 39.130 0.00 0.00 40.82 2.69
1548 1575 7.767261 TGTGAAAGTAAAATAACAGCACAGTT 58.233 30.769 0.00 0.00 35.55 3.16
1550 1577 6.857964 CCTGTGAAAGTAAAATAACAGCACAG 59.142 38.462 0.00 0.00 46.05 3.66
1782 1809 6.336842 AGAGTTGAATTTCATTGTCCTTGG 57.663 37.500 0.00 0.00 0.00 3.61
1805 1832 5.010314 TCTGCAGGAAAGAAGTTACTAACGA 59.990 40.000 15.13 0.00 36.23 3.85
1886 1914 5.464069 TGGTATGGAAGAATAGGCTCTACA 58.536 41.667 0.00 0.00 0.00 2.74
1887 1915 6.420913 TTGGTATGGAAGAATAGGCTCTAC 57.579 41.667 0.00 0.00 0.00 2.59
2041 2069 7.331193 CCCTGTTACACTAACTAACATGAACTC 59.669 40.741 0.00 0.00 39.38 3.01
2047 2075 6.932960 GTGAACCCTGTTACACTAACTAACAT 59.067 38.462 0.00 0.00 39.38 2.71
2084 2112 3.006323 AGGCGCAAAACATTTGACCAATA 59.994 39.130 10.83 0.00 0.00 1.90
2408 2436 8.037758 TCAGTTGTTTTTGGACATTGTTTACAT 58.962 29.630 0.00 0.00 0.00 2.29
2536 2566 7.798596 ATAGCAGATTAGTTTTCTCATGGTG 57.201 36.000 0.00 0.00 0.00 4.17
2577 2607 6.533723 ACGTAATGCAAGAAAATATCACTCGA 59.466 34.615 0.00 0.00 0.00 4.04
2626 2656 7.940850 AGCTTCTTTACAAACTTATTCTGCAA 58.059 30.769 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.