Multiple sequence alignment - TraesCS1A01G269900

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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 TraesCS1A01G269900 chr1A 100.000 2288 0 0 1 2288 463969300 463971587 0 4226
1 TraesCS1A01G269900 chr2D 93.396 1696 106 5 1 1692 647091185 647089492 0 2507
2 TraesCS1A01G269900 chr2D 92.590 1714 105 8 1 1694 646800105 646798394 0 2442
3 TraesCS1A01G269900 chr2D 92.638 1698 114 7 1 1694 646863597 646861907 0 2433
4 TraesCS1A01G269900 chr2D 92.124 1714 111 8 1 1694 646883879 646882170 0 2396
5 TraesCS1A01G269900 chr2D 92.007 1714 116 7 1 1694 646961480 646959768 0 2386
6 TraesCS1A01G269900 chr2D 91.792 597 46 2 1694 2288 552010213 552010808 0 828
7 TraesCS1A01G269900 chr6D 92.765 1714 102 8 1 1694 446604640 446602929 0 2459
8 TraesCS1A01G269900 chr6D 91.833 600 43 3 1694 2288 373661515 373660917 0 832
9 TraesCS1A01G269900 chr2A 92.124 1714 109 9 1 1694 171849913 171851620 0 2394
10 TraesCS1A01G269900 chr2A 94.286 595 31 2 1694 2288 184830624 184830033 0 907
11 TraesCS1A01G269900 chr7D 90.888 1712 121 13 1 1695 568007495 568005802 0 2265
12 TraesCS1A01G269900 chr7D 92.809 598 39 2 1694 2288 490497274 490497870 0 863
13 TraesCS1A01G269900 chr7A 90.326 1716 143 9 1 1697 167800042 167798331 0 2228
14 TraesCS1A01G269900 chr2B 90.272 1727 122 18 1 1696 643125129 643126840 0 2217
15 TraesCS1A01G269900 chr2B 91.792 597 46 2 1694 2288 710218102 710217507 0 828
16 TraesCS1A01G269900 chr1B 90.173 1730 129 10 1 1700 61492747 61491029 0 2215
17 TraesCS1A01G269900 chr1B 90.430 1557 111 15 178 1698 676880460 676878906 0 2015
18 TraesCS1A01G269900 chr1B 93.155 599 36 3 1694 2288 531373350 531372753 0 874
19 TraesCS1A01G269900 chr4D 89.897 1742 131 19 1 1720 504270336 504272054 0 2200
20 TraesCS1A01G269900 chr3A 90.118 1700 145 14 2 1697 113367065 113365385 0 2187
21 TraesCS1A01G269900 chr6B 88.979 1733 140 20 1 1698 567281097 567282813 0 2095
22 TraesCS1A01G269900 chr6B 92.411 593 44 1 1694 2286 434272202 434271611 0 845
23 TraesCS1A01G269900 chr5D 93.012 601 35 2 1694 2288 85869761 85869162 0 870
24 TraesCS1A01G269900 chr1D 91.987 599 43 2 1694 2288 392639861 392639264 0 835


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 TraesCS1A01G269900 chr1A 463969300 463971587 2287 False 4226 4226 100.000 1 2288 1 chr1A.!!$F1 2287
1 TraesCS1A01G269900 chr2D 647089492 647091185 1693 True 2507 2507 93.396 1 1692 1 chr2D.!!$R5 1691
2 TraesCS1A01G269900 chr2D 646798394 646800105 1711 True 2442 2442 92.590 1 1694 1 chr2D.!!$R1 1693
3 TraesCS1A01G269900 chr2D 646861907 646863597 1690 True 2433 2433 92.638 1 1694 1 chr2D.!!$R2 1693
4 TraesCS1A01G269900 chr2D 646882170 646883879 1709 True 2396 2396 92.124 1 1694 1 chr2D.!!$R3 1693
5 TraesCS1A01G269900 chr2D 646959768 646961480 1712 True 2386 2386 92.007 1 1694 1 chr2D.!!$R4 1693
6 TraesCS1A01G269900 chr2D 552010213 552010808 595 False 828 828 91.792 1694 2288 1 chr2D.!!$F1 594
7 TraesCS1A01G269900 chr6D 446602929 446604640 1711 True 2459 2459 92.765 1 1694 1 chr6D.!!$R2 1693
8 TraesCS1A01G269900 chr6D 373660917 373661515 598 True 832 832 91.833 1694 2288 1 chr6D.!!$R1 594
9 TraesCS1A01G269900 chr2A 171849913 171851620 1707 False 2394 2394 92.124 1 1694 1 chr2A.!!$F1 1693
10 TraesCS1A01G269900 chr2A 184830033 184830624 591 True 907 907 94.286 1694 2288 1 chr2A.!!$R1 594
11 TraesCS1A01G269900 chr7D 568005802 568007495 1693 True 2265 2265 90.888 1 1695 1 chr7D.!!$R1 1694
12 TraesCS1A01G269900 chr7D 490497274 490497870 596 False 863 863 92.809 1694 2288 1 chr7D.!!$F1 594
13 TraesCS1A01G269900 chr7A 167798331 167800042 1711 True 2228 2228 90.326 1 1697 1 chr7A.!!$R1 1696
14 TraesCS1A01G269900 chr2B 643125129 643126840 1711 False 2217 2217 90.272 1 1696 1 chr2B.!!$F1 1695
15 TraesCS1A01G269900 chr2B 710217507 710218102 595 True 828 828 91.792 1694 2288 1 chr2B.!!$R1 594
16 TraesCS1A01G269900 chr1B 61491029 61492747 1718 True 2215 2215 90.173 1 1700 1 chr1B.!!$R1 1699
17 TraesCS1A01G269900 chr1B 676878906 676880460 1554 True 2015 2015 90.430 178 1698 1 chr1B.!!$R3 1520
18 TraesCS1A01G269900 chr1B 531372753 531373350 597 True 874 874 93.155 1694 2288 1 chr1B.!!$R2 594
19 TraesCS1A01G269900 chr4D 504270336 504272054 1718 False 2200 2200 89.897 1 1720 1 chr4D.!!$F1 1719
20 TraesCS1A01G269900 chr3A 113365385 113367065 1680 True 2187 2187 90.118 2 1697 1 chr3A.!!$R1 1695
21 TraesCS1A01G269900 chr6B 567281097 567282813 1716 False 2095 2095 88.979 1 1698 1 chr6B.!!$F1 1697
22 TraesCS1A01G269900 chr6B 434271611 434272202 591 True 845 845 92.411 1694 2286 1 chr6B.!!$R1 592
23 TraesCS1A01G269900 chr5D 85869162 85869761 599 True 870 870 93.012 1694 2288 1 chr5D.!!$R1 594
24 TraesCS1A01G269900 chr1D 392639264 392639861 597 True 835 835 91.987 1694 2288 1 chr1D.!!$R1 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
116 117 0.103208 GTCGATCTGCCAGGAACGAT 59.897 55.0 10.56 0.0 41.14 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1759 0.181824 ACTAGGGCGTGTTTGGTTGT 59.818 50.0 0.0 0.0 0.0 3.32 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
34 35 3.064945 TCGAGCCTCTGCGCTTCT 61.065 61.111 9.73 0.00 44.33 2.85
85 86 1.280746 GTCGTCGTTGTCGTCCTCA 59.719 57.895 0.00 0.00 38.33 3.86
116 117 0.103208 GTCGATCTGCCAGGAACGAT 59.897 55.000 10.56 0.00 41.14 3.73
128 129 3.329542 GAACGATGGCCTGGCTCCA 62.330 63.158 19.68 9.49 38.09 3.86
176 177 3.983821 TCTTCTTCCTCCTCCTTAGACC 58.016 50.000 0.00 0.00 0.00 3.85
227 228 1.583495 CGTCTCCCAGTACACTGCGA 61.583 60.000 3.75 0.38 42.47 5.10
247 248 0.172578 CACGACGGTCATTAGGAGCA 59.827 55.000 9.10 0.00 44.30 4.26
250 251 1.403647 CGACGGTCATTAGGAGCACAA 60.404 52.381 9.10 0.00 44.30 3.33
454 455 1.664965 GCCGAAGTTCGAGCACACT 60.665 57.895 26.37 0.00 43.74 3.55
628 635 1.355112 GTGGGTAAGTAGTGGTGGGT 58.645 55.000 0.00 0.00 0.00 4.51
700 718 3.256383 TGCCGTTGTAACTACAAGCTCTA 59.744 43.478 12.39 0.00 45.82 2.43
710 728 5.024785 ACTACAAGCTCTACAATTAGCCC 57.975 43.478 0.00 0.00 39.64 5.19
778 811 0.462581 GAGCAATGAGATGGGCACGA 60.463 55.000 0.00 0.00 0.00 4.35
801 846 1.134848 GTTGACAACAAGGGCAAGCAA 60.135 47.619 13.52 0.00 36.64 3.91
863 908 0.324460 ACCGAGGAAGACCCGAAGAT 60.324 55.000 0.00 0.00 40.87 2.40
1023 1071 0.178992 CCCTGGACTTCACCAAGCAA 60.179 55.000 0.00 0.00 39.59 3.91
1108 1156 4.708177 GGTTAAGCTGATGAATAGCAGGA 58.292 43.478 0.00 0.00 43.53 3.86
1296 1344 4.416601 AAGGAGTAGGGCGGGGCT 62.417 66.667 0.00 0.00 0.00 5.19
1330 1378 3.731264 GCGTACTATCGAGTCTGCTTTGT 60.731 47.826 0.00 0.00 37.10 2.83
1394 1442 9.929180 GTGGTACTGCTTATATCTGAATTATGA 57.071 33.333 0.00 0.00 0.00 2.15
1677 1758 2.569657 CGGGTACTGTAGCGCACA 59.430 61.111 11.47 11.35 35.30 4.57
1678 1759 1.080366 CGGGTACTGTAGCGCACAA 60.080 57.895 11.47 0.00 36.48 3.33
1806 1887 5.188434 CCCTCTGATCTTGAGCATGTTTAA 58.812 41.667 9.74 0.00 0.00 1.52
1809 1890 6.292757 CCTCTGATCTTGAGCATGTTTAATCG 60.293 42.308 9.74 0.00 0.00 3.34
1942 2024 2.325583 AGTGGTGTCATGTGAACGTT 57.674 45.000 0.00 0.00 0.00 3.99
1949 2031 3.183775 GTGTCATGTGAACGTTGACTACC 59.816 47.826 18.62 5.21 0.00 3.18
1951 2033 4.278919 TGTCATGTGAACGTTGACTACCTA 59.721 41.667 18.62 0.00 0.00 3.08
1966 2048 7.108841 TGACTACCTAACACTTCACCATATC 57.891 40.000 0.00 0.00 0.00 1.63
2191 2283 2.589157 CCTAAGCACCGGTCCACCA 61.589 63.158 2.59 0.00 35.14 4.17
2244 2337 5.745294 CGAATTAAGCCAACATGATGAAAGG 59.255 40.000 4.25 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.243873 TGAAGAAGAAGAAGAAGCGCAGA 60.244 43.478 11.47 0.0 0.00 4.26
34 35 2.987149 GCACGACGATGAAGAAGAAGAA 59.013 45.455 0.00 0.0 0.00 2.52
67 68 0.725118 CTGAGGACGACAACGACGAC 60.725 60.000 0.00 0.0 42.66 4.34
75 76 2.282251 ACTCCGCTGAGGACGACA 60.282 61.111 10.11 0.0 45.98 4.35
227 228 0.172803 GCTCCTAATGACCGTCGTGT 59.827 55.000 0.00 0.0 0.00 4.49
247 248 4.202419 TGGTGCAAGTACAAGACCTATTGT 60.202 41.667 0.00 0.0 45.19 2.71
250 251 3.583086 AGTGGTGCAAGTACAAGACCTAT 59.417 43.478 0.00 0.0 0.00 2.57
303 304 1.153107 CGCTGGGCCATGAATCAGA 60.153 57.895 6.72 0.0 0.00 3.27
454 455 3.138304 CAAGTTCGAGAACACCATGGAA 58.862 45.455 21.47 0.0 43.47 3.53
499 500 1.857638 GCTGGAGGGCCTTCTTCCTT 61.858 60.000 14.33 0.0 32.74 3.36
570 572 0.423544 AACCTTCCTCCTCCCCATCT 59.576 55.000 0.00 0.0 0.00 2.90
628 635 5.972557 TCCCCCTATATTTACTCACCCTA 57.027 43.478 0.00 0.0 0.00 3.53
700 718 3.073062 ACACAGAGTTCAGGGCTAATTGT 59.927 43.478 0.00 0.0 0.00 2.71
710 728 1.004610 CACGCACAACACAGAGTTCAG 60.005 52.381 0.00 0.0 38.74 3.02
778 811 1.756538 CTTGCCCTTGTTGTCAACCTT 59.243 47.619 13.13 0.0 0.00 3.50
801 846 2.445155 GGCATTGGGTGAAGGGGT 59.555 61.111 0.00 0.0 0.00 4.95
905 951 0.659123 GTAGTTGCGGCGTTTGTTGG 60.659 55.000 9.37 0.0 0.00 3.77
980 1028 1.144708 TGGGGATGCACTCAAGTTTCA 59.855 47.619 0.00 0.0 0.00 2.69
1089 1137 5.512060 GGTCATCCTGCTATTCATCAGCTTA 60.512 44.000 0.00 0.0 39.83 3.09
1130 1178 1.884075 ATGAACGGCTGCGTAGGTGA 61.884 55.000 1.76 0.0 0.00 4.02
1152 1200 3.134623 TCACCATGTAGCCGATCTTGATT 59.865 43.478 0.00 0.0 0.00 2.57
1291 1339 1.224870 GCTGGAAAGAGGTAGCCCC 59.775 63.158 0.00 0.0 0.00 5.80
1296 1344 3.562973 CGATAGTACGCTGGAAAGAGGTA 59.437 47.826 0.00 0.0 0.00 3.08
1330 1378 6.342111 TCAACGCATAAACCATAGACATGTA 58.658 36.000 0.00 0.0 0.00 2.29
1394 1442 8.700051 ACAGAGTATAAACAGAGCATCAACTAT 58.300 33.333 0.00 0.0 37.82 2.12
1677 1758 1.314730 CTAGGGCGTGTTTGGTTGTT 58.685 50.000 0.00 0.0 0.00 2.83
1678 1759 0.181824 ACTAGGGCGTGTTTGGTTGT 59.818 50.000 0.00 0.0 0.00 3.32
1806 1887 7.781548 ACAAAAGTAACTACTCACAAACGAT 57.218 32.000 0.00 0.0 34.99 3.73
1809 1890 9.274065 CAAGAACAAAAGTAACTACTCACAAAC 57.726 33.333 0.00 0.0 34.99 2.93
1942 2024 6.895756 AGATATGGTGAAGTGTTAGGTAGTCA 59.104 38.462 0.00 0.0 0.00 3.41
1949 2031 4.130118 GCCCAGATATGGTGAAGTGTTAG 58.870 47.826 5.49 0.0 0.00 2.34
1951 2033 2.357154 GGCCCAGATATGGTGAAGTGTT 60.357 50.000 5.49 0.0 0.00 3.32
1966 2048 0.186873 ATGCATTCCCTTAGGCCCAG 59.813 55.000 0.00 0.0 0.00 4.45
2103 2195 4.142730 GCAAGCATCCTCAACTACAAGAAG 60.143 45.833 0.00 0.0 0.00 2.85
2116 2208 3.801997 CCCTCCCGCAAGCATCCT 61.802 66.667 0.00 0.0 0.00 3.24
2215 2307 5.957842 TCATGTTGGCTTAATTCGTCTTT 57.042 34.783 0.00 0.0 0.00 2.52
2218 2310 5.484173 TCATCATGTTGGCTTAATTCGTC 57.516 39.130 3.98 0.0 0.00 4.20
2244 2337 4.138487 ACACGGGAATTTCATCTAGTCC 57.862 45.455 0.00 0.0 0.00 3.85


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

AutoCloner maintained by Alex Coulton.