Multiple sequence alignment - TraesCS5B01G537500

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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 TraesCS5B01G537500 chr5B 100.000 2549 0 0 1 2549 693448943 693446395 0.000000e+00 4708
1 TraesCS5B01G537500 chr5B 94.377 1885 92 9 670 2549 508124428 508122553 0.000000e+00 2881
2 TraesCS5B01G537500 chr5B 94.261 1882 101 7 671 2549 680230521 680228644 0.000000e+00 2870
3 TraesCS5B01G537500 chr5B 93.333 675 36 8 1 671 494320265 494320934 0.000000e+00 989
4 TraesCS5B01G537500 chr4D 94.779 1877 91 6 676 2549 43272661 43270789 0.000000e+00 2916
5 TraesCS5B01G537500 chr3B 94.327 1886 95 6 671 2549 548772371 548774251 0.000000e+00 2880
6 TraesCS5B01G537500 chr3B 93.614 1879 117 3 671 2549 548243033 548244908 0.000000e+00 2802
7 TraesCS5B01G537500 chr3B 91.342 231 11 4 2319 2549 763483862 763483641 8.860000e-80 307
8 TraesCS5B01G537500 chr7B 93.886 1881 105 9 671 2549 523524979 523523107 0.000000e+00 2828
9 TraesCS5B01G537500 chr7B 93.780 1881 106 8 671 2549 523399757 523397886 0.000000e+00 2815
10 TraesCS5B01G537500 chr7B 93.452 672 40 4 1 671 45975547 45974879 0.000000e+00 994
11 TraesCS5B01G537500 chr7B 93.304 672 43 2 1 671 264038038 264037368 0.000000e+00 990
12 TraesCS5B01G537500 chr2D 93.904 1788 100 8 671 2455 632386701 632388482 0.000000e+00 2689
13 TraesCS5B01G537500 chr2D 93.778 675 32 10 1 671 610503116 610502448 0.000000e+00 1005
14 TraesCS5B01G537500 chr2D 93.314 673 40 4 2 671 78790694 78790024 0.000000e+00 989
15 TraesCS5B01G537500 chr2B 92.455 1882 132 9 671 2549 710554387 710552513 0.000000e+00 2680
16 TraesCS5B01G537500 chr6B 93.926 675 32 8 1 671 185054846 185054177 0.000000e+00 1011
17 TraesCS5B01G537500 chr4B 93.304 672 43 2 1 671 145489704 145490374 0.000000e+00 990
18 TraesCS5B01G537500 chr5D 93.323 674 38 7 1 671 300541024 300540355 0.000000e+00 989
19 TraesCS5B01G537500 chr1B 93.155 672 45 1 1 671 231536250 231535579 0.000000e+00 985


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 TraesCS5B01G537500 chr5B 693446395 693448943 2548 True 4708 4708 100.000 1 2549 1 chr5B.!!$R3 2548
1 TraesCS5B01G537500 chr5B 508122553 508124428 1875 True 2881 2881 94.377 670 2549 1 chr5B.!!$R1 1879
2 TraesCS5B01G537500 chr5B 680228644 680230521 1877 True 2870 2870 94.261 671 2549 1 chr5B.!!$R2 1878
3 TraesCS5B01G537500 chr5B 494320265 494320934 669 False 989 989 93.333 1 671 1 chr5B.!!$F1 670
4 TraesCS5B01G537500 chr4D 43270789 43272661 1872 True 2916 2916 94.779 676 2549 1 chr4D.!!$R1 1873
5 TraesCS5B01G537500 chr3B 548772371 548774251 1880 False 2880 2880 94.327 671 2549 1 chr3B.!!$F2 1878
6 TraesCS5B01G537500 chr3B 548243033 548244908 1875 False 2802 2802 93.614 671 2549 1 chr3B.!!$F1 1878
7 TraesCS5B01G537500 chr7B 523523107 523524979 1872 True 2828 2828 93.886 671 2549 1 chr7B.!!$R4 1878
8 TraesCS5B01G537500 chr7B 523397886 523399757 1871 True 2815 2815 93.780 671 2549 1 chr7B.!!$R3 1878
9 TraesCS5B01G537500 chr7B 45974879 45975547 668 True 994 994 93.452 1 671 1 chr7B.!!$R1 670
10 TraesCS5B01G537500 chr7B 264037368 264038038 670 True 990 990 93.304 1 671 1 chr7B.!!$R2 670
11 TraesCS5B01G537500 chr2D 632386701 632388482 1781 False 2689 2689 93.904 671 2455 1 chr2D.!!$F1 1784
12 TraesCS5B01G537500 chr2D 610502448 610503116 668 True 1005 1005 93.778 1 671 1 chr2D.!!$R2 670
13 TraesCS5B01G537500 chr2D 78790024 78790694 670 True 989 989 93.314 2 671 1 chr2D.!!$R1 669
14 TraesCS5B01G537500 chr2B 710552513 710554387 1874 True 2680 2680 92.455 671 2549 1 chr2B.!!$R1 1878
15 TraesCS5B01G537500 chr6B 185054177 185054846 669 True 1011 1011 93.926 1 671 1 chr6B.!!$R1 670
16 TraesCS5B01G537500 chr4B 145489704 145490374 670 False 990 990 93.304 1 671 1 chr4B.!!$F1 670
17 TraesCS5B01G537500 chr5D 300540355 300541024 669 True 989 989 93.323 1 671 1 chr5D.!!$R1 670
18 TraesCS5B01G537500 chr1B 231535579 231536250 671 True 985 985 93.155 1 671 1 chr1B.!!$R1 670

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
240 243 0.515564 CAAAGGTAACAAGCGTCGGG 59.484 55.0 0.0 0.0 41.41 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 1814 1.139058 AGTTGGCCCATTAGTCTAGCG 59.861 52.381 0.0 0.0 0.0 4.26 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
77 78 3.632604 TCACCGTATTCTCCTTGAGCTAG 59.367 47.826 0.00 0.00 0.00 3.42
163 165 1.613317 TTGGTCACTCGGCGATCCAT 61.613 55.000 11.27 0.00 0.00 3.41
183 186 5.103982 TCCATAATTCCTCTTGGATGCTCAA 60.104 40.000 0.00 0.00 42.81 3.02
202 205 0.896923 AACCATGACGCCTAACCGTA 59.103 50.000 0.00 0.00 42.24 4.02
240 243 0.515564 CAAAGGTAACAAGCGTCGGG 59.484 55.000 0.00 0.00 41.41 5.14
264 267 6.373005 TCCACACAGGAATAATCTCTTCAA 57.627 37.500 0.00 0.00 45.65 2.69
268 271 7.201679 CCACACAGGAATAATCTCTTCAATGAC 60.202 40.741 0.00 0.00 41.22 3.06
400 406 0.615331 TTTCTCTCGGAGCAGCCAAT 59.385 50.000 0.00 0.00 35.94 3.16
616 625 2.084546 GCACTGGCGAATTCCTAACTT 58.915 47.619 0.00 0.00 0.00 2.66
660 669 2.416162 GCGACCAGAAGATCTTCGTCTT 60.416 50.000 26.99 16.70 43.97 3.01
666 675 5.174395 CCAGAAGATCTTCGTCTTTGTCAT 58.826 41.667 25.88 5.41 43.97 3.06
710 719 1.542492 GTCTCCGTCAGGTCAACCTA 58.458 55.000 0.33 0.00 46.65 3.08
740 749 0.840722 CCTTACAGGTGGGACCAGGT 60.841 60.000 0.00 0.00 41.95 4.00
794 803 3.953775 CGTGGCTTGTGGGACCCT 61.954 66.667 13.00 0.00 0.00 4.34
818 827 2.026636 AGAGAGCCGTTGAGTAGAGAGT 60.027 50.000 0.00 0.00 0.00 3.24
820 829 2.085320 GAGCCGTTGAGTAGAGAGTCA 58.915 52.381 0.00 0.00 32.95 3.41
843 852 2.432874 TGCGGGTGTGCTATATAAGTGT 59.567 45.455 0.00 0.00 35.36 3.55
901 910 3.062466 TGACCACGGCGAGAGAGG 61.062 66.667 16.62 9.67 0.00 3.69
902 911 3.063084 GACCACGGCGAGAGAGGT 61.063 66.667 16.62 13.03 34.76 3.85
928 943 1.296715 CGGTGGGAAGCTAGCTGTT 59.703 57.895 20.16 2.53 0.00 3.16
987 1002 1.141645 CGACGTTGAAATCCCGTTCA 58.858 50.000 0.00 0.00 35.72 3.18
1228 1243 3.499338 AGCAATGGGTTGATCTGTTTCA 58.501 40.909 0.00 0.00 37.53 2.69
1411 1426 3.441922 CACTGACAGAGAGCTAGCTGTTA 59.558 47.826 24.99 10.46 44.77 2.41
1431 1446 8.678199 GCTGTTAAGCTTAGGATGTTTAAGAAT 58.322 33.333 6.24 0.00 46.60 2.40
1559 1574 3.006217 GGAAAGGCATGAATTATGGAGGC 59.994 47.826 0.00 0.00 37.26 4.70
1561 1576 2.590821 AGGCATGAATTATGGAGGCAC 58.409 47.619 0.00 0.00 37.26 5.01
1612 1627 8.650143 ATTCACCTAGTTTAAATGTTGGTCAT 57.350 30.769 0.00 0.00 38.57 3.06
1791 1814 3.169198 GCGTAGAGCCAAGTGCAC 58.831 61.111 9.40 9.40 44.83 4.57
1957 1980 9.528489 AGAGCCAAACAATTAAGGTTAGAAATA 57.472 29.630 0.00 0.00 0.00 1.40
2251 2277 2.029623 GGTAACCGCTAGGACAGATGA 58.970 52.381 0.00 0.00 41.02 2.92
2313 2339 7.484035 AGTGAGACTATGAAAGTTGTCAAAC 57.516 36.000 0.00 0.00 39.07 2.93
2317 2343 8.902806 TGAGACTATGAAAGTTGTCAAACAAAT 58.097 29.630 0.00 0.00 40.15 2.32
2375 2405 5.046950 AGTGGTTTTCCTTTGTTTTGCACTA 60.047 36.000 0.00 0.00 41.38 2.74
2396 2426 6.041523 CACTAAAATTTTGGAGGGTTGGAAGA 59.958 38.462 19.79 0.00 0.00 2.87
2480 2510 3.010420 GAGTGGCACTTGGTTTAGGATC 58.990 50.000 22.98 0.10 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 0.386113 GGGCGAGGTCTATGTGACTC 59.614 60.000 0.00 0.00 44.74 3.36
183 186 0.896923 TACGGTTAGGCGTCATGGTT 59.103 50.000 0.00 0.00 0.00 3.67
240 243 5.734720 TGAAGAGATTATTCCTGTGTGGAC 58.265 41.667 0.00 0.00 46.14 4.02
253 256 6.256539 GTGATTGAGCGTCATTGAAGAGATTA 59.743 38.462 3.64 0.00 0.00 1.75
264 267 2.086869 CCCAAAGTGATTGAGCGTCAT 58.913 47.619 0.00 0.00 41.85 3.06
268 271 2.034558 ACAAACCCAAAGTGATTGAGCG 59.965 45.455 0.00 0.00 41.85 5.03
440 446 2.035961 GTCTTATCATGTCGGGCTGCTA 59.964 50.000 0.00 0.00 0.00 3.49
616 625 5.545588 CTGAGGAATTTGTTCTGACTGAGA 58.454 41.667 0.00 0.00 0.00 3.27
660 669 4.384940 TCACGGAATGAGTTCAATGACAA 58.615 39.130 0.00 0.00 36.01 3.18
666 675 4.058124 CAGAGTTCACGGAATGAGTTCAA 58.942 43.478 0.00 0.00 38.99 2.69
794 803 0.528017 CTACTCAACGGCTCTCTGCA 59.472 55.000 0.00 0.00 45.15 4.41
818 827 2.928801 ATATAGCACACCCGCAATGA 57.071 45.000 0.00 0.00 0.00 2.57
820 829 4.065088 CACTTATATAGCACACCCGCAAT 58.935 43.478 0.00 0.00 0.00 3.56
901 910 1.819632 CTTCCCACCGCCATGCTAC 60.820 63.158 0.00 0.00 0.00 3.58
902 911 2.589540 CTTCCCACCGCCATGCTA 59.410 61.111 0.00 0.00 0.00 3.49
977 992 1.517832 CTCGGAGCTGAACGGGATT 59.482 57.895 0.00 0.00 30.70 3.01
1056 1071 2.101415 CGGACAGATGAAGACAGGCATA 59.899 50.000 0.00 0.00 0.00 3.14
1228 1243 1.475280 GCATGTCACCTGCATGAACAT 59.525 47.619 9.17 2.84 44.60 2.71
1411 1426 9.755122 AACCTTATTCTTAAACATCCTAAGCTT 57.245 29.630 3.48 3.48 0.00 3.74
1425 1440 8.822805 TCTTCAAGCTTCCTAACCTTATTCTTA 58.177 33.333 0.00 0.00 0.00 2.10
1431 1446 6.620877 TGATCTTCAAGCTTCCTAACCTTA 57.379 37.500 0.00 0.00 0.00 2.69
1791 1814 1.139058 AGTTGGCCCATTAGTCTAGCG 59.861 52.381 0.00 0.00 0.00 4.26
1908 1931 9.075678 CTCTGGAATAATTCAATTAGCTTCCAT 57.924 33.333 19.18 0.00 40.42 3.41
2251 2277 3.244911 CCCTACCCATGTCAAAGTCTTGT 60.245 47.826 0.00 0.00 33.94 3.16
2304 2330 5.907391 CGGTCTCACTAATTTGTTTGACAAC 59.093 40.000 17.22 6.50 37.90 3.32
2313 2339 5.862924 ACATTCACGGTCTCACTAATTTG 57.137 39.130 0.00 0.00 0.00 2.32
2317 2343 3.496884 GCAAACATTCACGGTCTCACTAA 59.503 43.478 0.00 0.00 0.00 2.24
2375 2405 6.101005 TCAATCTTCCAACCCTCCAAAATTTT 59.899 34.615 0.00 0.00 0.00 1.82
2396 2426 3.978217 CGGTGCAAACATACGTTTTCAAT 59.022 39.130 0.00 0.00 42.82 2.57
2427 2457 2.293399 CCAAGTGCCACTCTAACCAAAC 59.707 50.000 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.