Multiple sequence alignment - TraesCS1B01G210200

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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 TraesCS1B01G210200 chr1B 100.000 3665 0 0 1 3665 381507064 381503400 0.000000e+00 6769.0
1 TraesCS1B01G210200 chr1B 97.538 2640 54 2 1035 3665 198412778 198410141 0.000000e+00 4505.0
2 TraesCS1B01G210200 chr1D 93.055 2635 171 6 1035 3665 361107370 361104744 0.000000e+00 3842.0
3 TraesCS1B01G210200 chr1D 96.637 1011 11 10 31 1027 280718792 280717791 0.000000e+00 1657.0
4 TraesCS1B01G210200 chr1D 72.840 405 94 15 2318 2712 45478349 45478747 1.380000e-24 124.0
5 TraesCS1B01G210200 chr1A 98.164 2179 39 1 1487 3665 562123363 562121186 0.000000e+00 3801.0
6 TraesCS1B01G210200 chr1A 96.928 1009 16 7 31 1027 352872247 352871242 0.000000e+00 1677.0
7 TraesCS1B01G210200 chr1A 89.130 46 5 0 3005 3050 392522100 392522055 1.420000e-04 58.4
8 TraesCS1B01G210200 chr7A 87.297 2645 298 16 1035 3665 538978891 538981511 0.000000e+00 2988.0
9 TraesCS1B01G210200 chr3B 86.277 2638 337 15 1035 3660 112900111 112902735 0.000000e+00 2843.0
10 TraesCS1B01G210200 chr6A 92.141 1107 78 7 2563 3665 443349204 443350305 0.000000e+00 1554.0
11 TraesCS1B01G210200 chr6A 100.000 31 0 0 3005 3035 129347749 129347779 1.420000e-04 58.4
12 TraesCS1B01G210200 chr2A 81.142 753 137 4 1035 1785 371711012 371711761 1.880000e-167 599.0
13 TraesCS1B01G210200 chr4B 79.743 622 126 0 1035 1656 392105439 392104818 5.580000e-123 451.0
14 TraesCS1B01G210200 chr6B 90.476 315 28 2 3352 3665 163950151 163949838 7.320000e-112 414.0
15 TraesCS1B01G210200 chr5A 87.356 261 27 5 698 953 374628992 374628733 9.950000e-76 294.0
16 TraesCS1B01G210200 chr7D 73.134 402 92 15 2324 2715 21284052 21283657 2.970000e-26 130.0
17 TraesCS1B01G210200 chr2D 83.333 138 21 2 3529 3665 647882602 647882738 3.840000e-25 126.0
18 TraesCS1B01G210200 chr2D 77.381 168 36 2 1067 1233 60118566 60118400 8.380000e-17 99.0
19 TraesCS1B01G210200 chr7B 77.895 190 38 2 1046 1233 61057689 61057876 8.320000e-22 115.0
20 TraesCS1B01G210200 chr4A 77.222 180 39 2 1055 1233 595057566 595057744 1.800000e-18 104.0
21 TraesCS1B01G210200 chr5D 79.518 83 17 0 2999 3081 555482437 555482519 3.950000e-05 60.2


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 TraesCS1B01G210200 chr1B 381503400 381507064 3664 True 6769 6769 100.000 1 3665 1 chr1B.!!$R2 3664
1 TraesCS1B01G210200 chr1B 198410141 198412778 2637 True 4505 4505 97.538 1035 3665 1 chr1B.!!$R1 2630
2 TraesCS1B01G210200 chr1D 361104744 361107370 2626 True 3842 3842 93.055 1035 3665 1 chr1D.!!$R2 2630
3 TraesCS1B01G210200 chr1D 280717791 280718792 1001 True 1657 1657 96.637 31 1027 1 chr1D.!!$R1 996
4 TraesCS1B01G210200 chr1A 562121186 562123363 2177 True 3801 3801 98.164 1487 3665 1 chr1A.!!$R3 2178
5 TraesCS1B01G210200 chr1A 352871242 352872247 1005 True 1677 1677 96.928 31 1027 1 chr1A.!!$R1 996
6 TraesCS1B01G210200 chr7A 538978891 538981511 2620 False 2988 2988 87.297 1035 3665 1 chr7A.!!$F1 2630
7 TraesCS1B01G210200 chr3B 112900111 112902735 2624 False 2843 2843 86.277 1035 3660 1 chr3B.!!$F1 2625
8 TraesCS1B01G210200 chr6A 443349204 443350305 1101 False 1554 1554 92.141 2563 3665 1 chr6A.!!$F2 1102
9 TraesCS1B01G210200 chr2A 371711012 371711761 749 False 599 599 81.142 1035 1785 1 chr2A.!!$F1 750
10 TraesCS1B01G210200 chr4B 392104818 392105439 621 True 451 451 79.743 1035 1656 1 chr4B.!!$R1 621

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
19 20 0.865111 CGTGGCACGATGTCTCAAAA 59.135 50.000 34.85 0.0 46.05 2.44 F
20 21 1.262950 CGTGGCACGATGTCTCAAAAA 59.737 47.619 34.85 0.0 46.05 1.94 F
1027 1050 1.682854 ACCAAGCACACAACAATGGAG 59.317 47.619 0.00 0.0 0.00 3.86 F
2381 2426 2.357517 CAGCCCGCGTCTTCAAGT 60.358 61.111 4.92 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1055 0.322816 AGTACGCCTCCACCGAGTTA 60.323 55.000 0.00 0.0 33.93 2.24 R
1795 1828 0.824109 CCACTATCTTCAGGGCGACA 59.176 55.000 0.00 0.0 0.00 4.35 R
2618 2663 0.530744 ATTCGCGGTCTGCAGTTCTA 59.469 50.000 14.67 0.0 46.97 2.10 R
3371 3422 1.075226 AGGGGATGGCTTCTCGCTA 60.075 57.895 0.07 0.0 39.13 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
17 18 4.260194 CGTGGCACGATGTCTCAA 57.740 55.556 34.85 0.0 46.05 3.02
18 19 2.527671 CGTGGCACGATGTCTCAAA 58.472 52.632 34.85 0.0 46.05 2.69
19 20 0.865111 CGTGGCACGATGTCTCAAAA 59.135 50.000 34.85 0.0 46.05 2.44
20 21 1.262950 CGTGGCACGATGTCTCAAAAA 59.737 47.619 34.85 0.0 46.05 1.94
21 22 2.095768 CGTGGCACGATGTCTCAAAAAT 60.096 45.455 34.85 0.0 46.05 1.82
22 23 3.492313 GTGGCACGATGTCTCAAAAATC 58.508 45.455 0.00 0.0 0.00 2.17
23 24 2.487762 TGGCACGATGTCTCAAAAATCC 59.512 45.455 0.00 0.0 0.00 3.01
24 25 2.749621 GGCACGATGTCTCAAAAATCCT 59.250 45.455 0.00 0.0 0.00 3.24
25 26 3.181506 GGCACGATGTCTCAAAAATCCTC 60.182 47.826 0.00 0.0 0.00 3.71
26 27 3.484229 GCACGATGTCTCAAAAATCCTCG 60.484 47.826 0.00 0.0 0.00 4.63
27 28 3.062639 CACGATGTCTCAAAAATCCTCGG 59.937 47.826 0.00 0.0 0.00 4.63
28 29 3.056107 ACGATGTCTCAAAAATCCTCGGA 60.056 43.478 0.00 0.0 0.00 4.55
29 30 3.307242 CGATGTCTCAAAAATCCTCGGAC 59.693 47.826 0.00 0.0 0.00 4.79
789 812 4.431416 TGTACAACCCAGAACATGACTT 57.569 40.909 0.00 0.0 0.00 3.01
1027 1050 1.682854 ACCAAGCACACAACAATGGAG 59.317 47.619 0.00 0.0 0.00 3.86
1028 1051 1.682854 CCAAGCACACAACAATGGAGT 59.317 47.619 0.00 0.0 0.00 3.85
1029 1052 2.884012 CCAAGCACACAACAATGGAGTA 59.116 45.455 0.00 0.0 0.00 2.59
1030 1053 3.304659 CCAAGCACACAACAATGGAGTAC 60.305 47.826 0.00 0.0 0.00 2.73
1031 1054 3.207265 AGCACACAACAATGGAGTACA 57.793 42.857 0.00 0.0 0.00 2.90
1032 1055 3.754965 AGCACACAACAATGGAGTACAT 58.245 40.909 0.00 0.0 43.07 2.29
1033 1056 4.905429 AGCACACAACAATGGAGTACATA 58.095 39.130 0.00 0.0 39.40 2.29
1547 1579 4.088351 TCGGGGCTGGGAGGATCA 62.088 66.667 0.00 0.0 36.25 2.92
2381 2426 2.357517 CAGCCCGCGTCTTCAAGT 60.358 61.111 4.92 0.0 0.00 3.16
2909 2960 9.154847 TGATGTTCTATGGATTTTGCTATATCG 57.845 33.333 0.00 0.0 0.00 2.92
3103 3154 4.761739 CCATTTAGTCTGTTTGCAGGAGAA 59.238 41.667 0.00 0.0 42.78 2.87
3591 3644 5.581085 CCAACGCTAAGCAAACTAGACTATT 59.419 40.000 0.00 0.0 0.00 1.73
3592 3645 6.092259 CCAACGCTAAGCAAACTAGACTATTT 59.908 38.462 0.00 0.0 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.865111 TTTTGAGACATCGTGCCACG 59.135 50.000 11.80 11.80 44.19 4.94
1 2 3.492313 GATTTTTGAGACATCGTGCCAC 58.508 45.455 0.00 0.00 0.00 5.01
2 3 2.487762 GGATTTTTGAGACATCGTGCCA 59.512 45.455 0.00 0.00 0.00 4.92
3 4 2.749621 AGGATTTTTGAGACATCGTGCC 59.250 45.455 0.00 0.00 0.00 5.01
4 5 3.484229 CGAGGATTTTTGAGACATCGTGC 60.484 47.826 0.00 0.00 33.16 5.34
5 6 3.062639 CCGAGGATTTTTGAGACATCGTG 59.937 47.826 0.00 0.00 35.37 4.35
6 7 3.056107 TCCGAGGATTTTTGAGACATCGT 60.056 43.478 0.00 0.00 35.37 3.73
7 8 3.307242 GTCCGAGGATTTTTGAGACATCG 59.693 47.826 0.00 0.00 36.56 3.84
8 9 4.508662 AGTCCGAGGATTTTTGAGACATC 58.491 43.478 0.00 0.00 0.00 3.06
9 10 4.559862 AGTCCGAGGATTTTTGAGACAT 57.440 40.909 0.00 0.00 0.00 3.06
10 11 4.322499 GGTAGTCCGAGGATTTTTGAGACA 60.322 45.833 0.00 0.00 0.00 3.41
11 12 4.182339 GGTAGTCCGAGGATTTTTGAGAC 58.818 47.826 0.00 0.00 0.00 3.36
12 13 3.835978 TGGTAGTCCGAGGATTTTTGAGA 59.164 43.478 0.00 0.00 36.30 3.27
13 14 4.202245 TGGTAGTCCGAGGATTTTTGAG 57.798 45.455 0.00 0.00 36.30 3.02
14 15 4.837093 ATGGTAGTCCGAGGATTTTTGA 57.163 40.909 0.00 0.00 36.30 2.69
15 16 5.878116 TGTTATGGTAGTCCGAGGATTTTTG 59.122 40.000 0.00 0.00 36.30 2.44
16 17 6.057321 TGTTATGGTAGTCCGAGGATTTTT 57.943 37.500 0.00 0.00 36.30 1.94
17 18 5.687166 TGTTATGGTAGTCCGAGGATTTT 57.313 39.130 0.00 0.00 36.30 1.82
18 19 5.365605 TGATGTTATGGTAGTCCGAGGATTT 59.634 40.000 0.00 0.00 36.30 2.17
19 20 4.899457 TGATGTTATGGTAGTCCGAGGATT 59.101 41.667 0.00 0.00 36.30 3.01
20 21 4.480115 TGATGTTATGGTAGTCCGAGGAT 58.520 43.478 0.00 0.00 36.30 3.24
21 22 3.889538 CTGATGTTATGGTAGTCCGAGGA 59.110 47.826 0.00 0.00 36.30 3.71
22 23 3.637229 ACTGATGTTATGGTAGTCCGAGG 59.363 47.826 0.00 0.00 36.30 4.63
23 24 4.920640 ACTGATGTTATGGTAGTCCGAG 57.079 45.455 0.00 0.00 36.30 4.63
24 25 6.124340 TCTTACTGATGTTATGGTAGTCCGA 58.876 40.000 0.00 0.00 36.30 4.55
25 26 6.387041 TCTTACTGATGTTATGGTAGTCCG 57.613 41.667 0.00 0.00 36.30 4.79
26 27 9.614792 ATTTTCTTACTGATGTTATGGTAGTCC 57.385 33.333 0.00 0.00 0.00 3.85
588 607 4.909880 GCACACGGTGAACTTCTTTTAATC 59.090 41.667 16.29 0.00 35.23 1.75
789 812 4.006780 TCTTGTTAGCTTCTGTGCATGA 57.993 40.909 0.00 0.00 34.99 3.07
825 848 6.238648 GCCAAGAGTTGTTAGCTAAAAGTTCA 60.239 38.462 7.99 0.00 0.00 3.18
963 986 6.072175 GCCATGTTCAAATCAAAGTGTACCTA 60.072 38.462 0.00 0.00 0.00 3.08
1027 1050 1.535437 CGCCTCCACCGAGTTATGTAC 60.535 57.143 0.00 0.00 33.93 2.90
1028 1051 0.742505 CGCCTCCACCGAGTTATGTA 59.257 55.000 0.00 0.00 33.93 2.29
1029 1052 1.255667 ACGCCTCCACCGAGTTATGT 61.256 55.000 0.00 0.00 33.93 2.29
1030 1053 0.742505 TACGCCTCCACCGAGTTATG 59.257 55.000 0.00 0.00 33.93 1.90
1031 1054 0.743097 GTACGCCTCCACCGAGTTAT 59.257 55.000 0.00 0.00 33.93 1.89
1032 1055 0.322816 AGTACGCCTCCACCGAGTTA 60.323 55.000 0.00 0.00 33.93 2.24
1033 1056 0.322816 TAGTACGCCTCCACCGAGTT 60.323 55.000 0.00 0.00 33.93 3.01
1470 1493 4.043310 TCTTGGTCATCATCCCTTCTTTGT 59.957 41.667 0.00 0.00 0.00 2.83
1547 1579 0.832135 TTCACGCCAAGAGGAGGAGT 60.832 55.000 0.00 0.00 39.91 3.85
1603 1635 4.415332 GCGGTCTTCGTCCTCGCA 62.415 66.667 0.00 0.00 44.87 5.10
1708 1741 4.379243 CTTGCGAGCGTCAGGGGT 62.379 66.667 0.00 0.00 0.00 4.95
1795 1828 0.824109 CCACTATCTTCAGGGCGACA 59.176 55.000 0.00 0.00 0.00 4.35
2031 2064 1.663379 CCAGCACCGATGTACGAGGA 61.663 60.000 7.89 0.00 45.77 3.71
2381 2426 4.162320 CCACTGGCATAGTCCTCTTCTTTA 59.838 45.833 0.00 0.00 37.60 1.85
2618 2663 0.530744 ATTCGCGGTCTGCAGTTCTA 59.469 50.000 14.67 0.00 46.97 2.10
2909 2960 4.106925 CAGAGGCTGCCTGGGACC 62.107 72.222 28.82 11.37 31.76 4.46
3371 3422 1.075226 AGGGGATGGCTTCTCGCTA 60.075 57.895 0.07 0.00 39.13 4.26
3592 3645 4.037923 GTCCCACTCTTCATTGCAGAAAAA 59.962 41.667 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.