Multiple sequence alignment - TraesCS1B01G459000

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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 TraesCS1B01G459000 chr1B 100.000 2780 0 0 1 2780 672772599 672769820 0.000000e+00 5134
1 TraesCS1B01G459000 chr1B 99.468 188 1 0 1 188 681070245 681070432 2.650000e-90 342
2 TraesCS1B01G459000 chr7A 98.998 2596 25 1 186 2780 556118245 556115650 0.000000e+00 4649
3 TraesCS1B01G459000 chr7A 97.081 2638 37 13 183 2780 579165789 579168426 0.000000e+00 4409
4 TraesCS1B01G459000 chr7A 96.764 2596 83 1 186 2780 163921361 163918766 0.000000e+00 4327
5 TraesCS1B01G459000 chr7A 99.045 2199 20 1 183 2380 77424978 77427176 0.000000e+00 3943
6 TraesCS1B01G459000 chr7A 99.000 2199 21 1 183 2380 184628294 184630492 0.000000e+00 3938
7 TraesCS1B01G459000 chr7A 99.468 188 1 0 1 188 77423264 77423451 2.650000e-90 342
8 TraesCS1B01G459000 chr7A 99.468 188 1 0 1 188 556119850 556119663 2.650000e-90 342
9 TraesCS1B01G459000 chr7A 99.468 188 1 0 1 188 715829541 715829354 2.650000e-90 342
10 TraesCS1B01G459000 chr3A 98.960 2596 26 1 186 2780 696130478 696127883 0.000000e+00 4643
11 TraesCS1B01G459000 chr3A 97.458 2596 26 4 186 2780 645352174 645349618 0.000000e+00 4392
12 TraesCS1B01G459000 chr5A 97.419 2596 66 1 186 2780 467749431 467746836 0.000000e+00 4421
13 TraesCS1B01G459000 chr5A 99.468 188 1 0 1 188 12037424 12037611 2.650000e-90 342
14 TraesCS1B01G459000 chr5A 99.468 188 1 0 1 188 474925674 474925487 2.650000e-90 342
15 TraesCS1B01G459000 chr5B 96.361 2638 55 14 183 2780 454805671 454808307 0.000000e+00 4301
16 TraesCS1B01G459000 chr6A 98.998 2196 21 1 186 2380 41594544 41592349 0.000000e+00 3932
17 TraesCS1B01G459000 chr6A 99.468 188 1 0 1 188 564386614 564386427 2.650000e-90 342
18 TraesCS1B01G459000 chr6A 98.936 188 2 0 1 188 6910751 6910938 1.230000e-88 337
19 TraesCS1B01G459000 chr3B 96.369 1377 11 1 1404 2780 820999520 820998183 0.000000e+00 2230
20 TraesCS1B01G459000 chr3B 93.139 481 24 1 2307 2778 10097072 10097552 0.000000e+00 697
21 TraesCS1B01G459000 chr3B 96.311 244 9 0 2537 2780 59722148 59722391 4.310000e-108 401
22 TraesCS1B01G459000 chrUn 98.936 188 2 0 1 188 424947057 424946870 1.230000e-88 337


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 TraesCS1B01G459000 chr1B 672769820 672772599 2779 True 5134.0 5134 100.0000 1 2780 1 chr1B.!!$R1 2779
1 TraesCS1B01G459000 chr7A 579165789 579168426 2637 False 4409.0 4409 97.0810 183 2780 1 chr7A.!!$F2 2597
2 TraesCS1B01G459000 chr7A 163918766 163921361 2595 True 4327.0 4327 96.7640 186 2780 1 chr7A.!!$R1 2594
3 TraesCS1B01G459000 chr7A 184628294 184630492 2198 False 3938.0 3938 99.0000 183 2380 1 chr7A.!!$F1 2197
4 TraesCS1B01G459000 chr7A 556115650 556119850 4200 True 2495.5 4649 99.2330 1 2780 2 chr7A.!!$R3 2779
5 TraesCS1B01G459000 chr7A 77423264 77427176 3912 False 2142.5 3943 99.2565 1 2380 2 chr7A.!!$F3 2379
6 TraesCS1B01G459000 chr3A 696127883 696130478 2595 True 4643.0 4643 98.9600 186 2780 1 chr3A.!!$R2 2594
7 TraesCS1B01G459000 chr3A 645349618 645352174 2556 True 4392.0 4392 97.4580 186 2780 1 chr3A.!!$R1 2594
8 TraesCS1B01G459000 chr5A 467746836 467749431 2595 True 4421.0 4421 97.4190 186 2780 1 chr5A.!!$R1 2594
9 TraesCS1B01G459000 chr5B 454805671 454808307 2636 False 4301.0 4301 96.3610 183 2780 1 chr5B.!!$F1 2597
10 TraesCS1B01G459000 chr6A 41592349 41594544 2195 True 3932.0 3932 98.9980 186 2380 1 chr6A.!!$R1 2194
11 TraesCS1B01G459000 chr3B 820998183 820999520 1337 True 2230.0 2230 96.3690 1404 2780 1 chr3B.!!$R1 1376

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
92 93 2.684881 CAGTTGGTCTTTGTGACTTGCT 59.315 45.455 0.00 0.0 44.74 3.91 F
847 2380 3.118542 CAAAGCTTGCTTGTTGAAGTCC 58.881 45.455 8.73 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1370 2904 4.883585 GCAAGTGTGGAATATCTGGAATCA 59.116 41.667 0.0 0.0 0.0 2.57 R
2187 3721 0.035630 CTCCCTGGCTGTGAAGAAGG 60.036 60.000 0.0 0.0 0.0 3.46 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
92 93 2.684881 CAGTTGGTCTTTGTGACTTGCT 59.315 45.455 0.00 0.00 44.74 3.91
198 1731 5.178096 TGAATTGGTCTTAGATGAGGCAA 57.822 39.130 0.00 0.00 0.00 4.52
847 2380 3.118542 CAAAGCTTGCTTGTTGAAGTCC 58.881 45.455 8.73 0.00 0.00 3.85
1370 2904 3.833732 TCGGTCTATATCAAGAGCCTGT 58.166 45.455 0.25 0.00 40.18 4.00
1926 3460 2.736890 GCTTTAATGCGGCGCTTTT 58.263 47.368 32.82 26.39 0.00 2.27
2170 3704 1.008327 TCCTTCACAGCCAGGGAGATA 59.992 52.381 0.00 0.00 0.00 1.98
2181 3715 3.069079 CAGGGAGATATTCCTGGCATG 57.931 52.381 6.80 0.00 45.98 4.06
2182 3716 2.641321 CAGGGAGATATTCCTGGCATGA 59.359 50.000 6.80 0.00 45.98 3.07
2183 3717 2.911636 AGGGAGATATTCCTGGCATGAG 59.088 50.000 0.00 0.00 45.98 2.90
2184 3718 2.617532 GGGAGATATTCCTGGCATGAGC 60.618 54.545 0.00 0.00 45.98 4.26
2195 3729 3.254629 GCATGAGCCACCTTCTTCA 57.745 52.632 0.00 0.00 33.58 3.02
2196 3730 0.807496 GCATGAGCCACCTTCTTCAC 59.193 55.000 0.00 0.00 33.58 3.18
2197 3731 1.883638 GCATGAGCCACCTTCTTCACA 60.884 52.381 0.00 0.00 33.58 3.58
2198 3732 2.082231 CATGAGCCACCTTCTTCACAG 58.918 52.381 0.00 0.00 0.00 3.66
2199 3733 0.250467 TGAGCCACCTTCTTCACAGC 60.250 55.000 0.00 0.00 0.00 4.40
2200 3734 0.957888 GAGCCACCTTCTTCACAGCC 60.958 60.000 0.00 0.00 0.00 4.85
2201 3735 1.228245 GCCACCTTCTTCACAGCCA 60.228 57.895 0.00 0.00 0.00 4.75
2202 3736 1.239968 GCCACCTTCTTCACAGCCAG 61.240 60.000 0.00 0.00 0.00 4.85
2203 3737 0.607489 CCACCTTCTTCACAGCCAGG 60.607 60.000 0.00 0.00 0.00 4.45
2204 3738 0.607489 CACCTTCTTCACAGCCAGGG 60.607 60.000 0.00 0.00 0.00 4.45
2205 3739 0.768221 ACCTTCTTCACAGCCAGGGA 60.768 55.000 0.00 0.00 0.00 4.20
2206 3740 0.035630 CCTTCTTCACAGCCAGGGAG 60.036 60.000 0.00 0.00 0.00 4.30
2207 3741 0.979665 CTTCTTCACAGCCAGGGAGA 59.020 55.000 0.00 0.00 0.00 3.71
2208 3742 1.558756 CTTCTTCACAGCCAGGGAGAT 59.441 52.381 0.00 0.00 0.00 2.75
2209 3743 1.198713 TCTTCACAGCCAGGGAGATC 58.801 55.000 0.00 0.00 0.00 2.75
2210 3744 1.202330 CTTCACAGCCAGGGAGATCT 58.798 55.000 0.00 0.00 0.00 2.75
2211 3745 1.558756 CTTCACAGCCAGGGAGATCTT 59.441 52.381 0.00 0.00 0.00 2.40
2212 3746 1.198713 TCACAGCCAGGGAGATCTTC 58.801 55.000 0.00 0.00 0.00 2.87
2213 3747 0.179936 CACAGCCAGGGAGATCTTCC 59.820 60.000 12.77 12.77 46.00 3.46
2214 3748 0.043940 ACAGCCAGGGAGATCTTCCT 59.956 55.000 17.80 17.80 45.98 3.36
2461 4190 8.826710 CACTACTCACTACATTCTTTTGAACAA 58.173 33.333 0.00 0.00 41.77 2.83
2584 4313 1.665448 CGCAACCGTTCATGCATTCAA 60.665 47.619 0.00 0.00 42.68 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 7.787904 TCTTAGTATTAGGAGGGTCAATTGCTA 59.212 37.037 0.00 0.00 0.00 3.49
198 1731 3.550820 TGTGTAACTGCAATGGTTCACT 58.449 40.909 14.66 0.00 38.04 3.41
447 1980 1.200484 GTCTATAGCCCTAGCAGTCGC 59.800 57.143 0.00 0.00 43.56 5.19
847 2380 7.148340 GGACATCCAACAAGACTAGATTTTCTG 60.148 40.741 0.00 0.00 35.64 3.02
1370 2904 4.883585 GCAAGTGTGGAATATCTGGAATCA 59.116 41.667 0.00 0.00 0.00 2.57
2177 3711 0.807496 GTGAAGAAGGTGGCTCATGC 59.193 55.000 0.00 0.00 38.76 4.06
2178 3712 2.082231 CTGTGAAGAAGGTGGCTCATG 58.918 52.381 0.00 0.00 0.00 3.07
2179 3713 1.612726 GCTGTGAAGAAGGTGGCTCAT 60.613 52.381 0.00 0.00 0.00 2.90
2180 3714 0.250467 GCTGTGAAGAAGGTGGCTCA 60.250 55.000 0.00 0.00 0.00 4.26
2181 3715 0.957888 GGCTGTGAAGAAGGTGGCTC 60.958 60.000 0.00 0.00 0.00 4.70
2182 3716 1.073897 GGCTGTGAAGAAGGTGGCT 59.926 57.895 0.00 0.00 0.00 4.75
2183 3717 1.228245 TGGCTGTGAAGAAGGTGGC 60.228 57.895 0.00 0.00 0.00 5.01
2184 3718 0.607489 CCTGGCTGTGAAGAAGGTGG 60.607 60.000 0.00 0.00 0.00 4.61
2185 3719 0.607489 CCCTGGCTGTGAAGAAGGTG 60.607 60.000 0.00 0.00 0.00 4.00
2186 3720 0.768221 TCCCTGGCTGTGAAGAAGGT 60.768 55.000 0.00 0.00 0.00 3.50
2187 3721 0.035630 CTCCCTGGCTGTGAAGAAGG 60.036 60.000 0.00 0.00 0.00 3.46
2188 3722 0.979665 TCTCCCTGGCTGTGAAGAAG 59.020 55.000 0.00 0.00 0.00 2.85
2189 3723 1.556911 GATCTCCCTGGCTGTGAAGAA 59.443 52.381 0.00 0.00 0.00 2.52
2190 3724 1.198713 GATCTCCCTGGCTGTGAAGA 58.801 55.000 0.00 0.00 0.00 2.87
2191 3725 1.202330 AGATCTCCCTGGCTGTGAAG 58.798 55.000 0.00 0.00 0.00 3.02
2192 3726 1.556911 GAAGATCTCCCTGGCTGTGAA 59.443 52.381 0.00 0.00 0.00 3.18
2193 3727 1.198713 GAAGATCTCCCTGGCTGTGA 58.801 55.000 0.00 0.00 0.00 3.58
2194 3728 0.179936 GGAAGATCTCCCTGGCTGTG 59.820 60.000 0.00 0.00 38.44 3.66
2195 3729 0.043940 AGGAAGATCTCCCTGGCTGT 59.956 55.000 0.00 0.00 46.81 4.40
2196 3730 0.469070 CAGGAAGATCTCCCTGGCTG 59.531 60.000 19.98 0.00 46.81 4.85
2197 3731 2.928002 CAGGAAGATCTCCCTGGCT 58.072 57.895 19.98 0.00 46.81 4.75
2200 3734 1.138568 ATGCCAGGAAGATCTCCCTG 58.861 55.000 20.73 20.73 46.81 4.45
2201 3735 1.138568 CATGCCAGGAAGATCTCCCT 58.861 55.000 0.00 0.00 46.81 4.20
2202 3736 1.072015 CTCATGCCAGGAAGATCTCCC 59.928 57.143 0.00 0.00 46.81 4.30
2203 3737 1.542987 GCTCATGCCAGGAAGATCTCC 60.543 57.143 0.00 0.00 45.81 3.71
2204 3738 1.881591 GCTCATGCCAGGAAGATCTC 58.118 55.000 0.00 0.00 0.00 2.75
2461 4190 7.041721 TGAGAATGCAAGAACGATTACTACAT 58.958 34.615 0.00 0.00 0.00 2.29
2553 4282 2.594592 GGTTGCGACTGGTTGCCT 60.595 61.111 3.59 0.00 39.22 4.75
2584 4313 2.093973 CACTAAGGATCGGTGACTGCTT 60.094 50.000 0.00 0.00 33.32 3.91


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

AutoCloner maintained by Alex Coulton.