Multiple sequence alignment - TraesCS7B01G380000

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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 TraesCS7B01G380000 chr7B 100.000 3077 0 0 1 3077 644531864 644528788 0.000000e+00 5683.0
1 TraesCS7B01G380000 chr7B 94.474 2280 84 20 820 3064 598469720 598467448 0.000000e+00 3474.0
2 TraesCS7B01G380000 chr7B 96.126 826 28 4 1 824 192090617 192089794 0.000000e+00 1345.0
3 TraesCS7B01G380000 chr7B 84.826 547 79 4 1391 1935 105888519 105889063 5.800000e-152 547.0
4 TraesCS7B01G380000 chr7A 91.620 2315 134 29 817 3077 638703151 638700843 0.000000e+00 3145.0
5 TraesCS7B01G380000 chr7D 93.939 1518 63 11 817 2321 552956588 552955087 0.000000e+00 2266.0
6 TraesCS7B01G380000 chr7D 89.269 643 58 5 1 639 105844846 105844211 0.000000e+00 795.0
7 TraesCS7B01G380000 chr7D 89.194 546 36 8 2384 2918 552955085 552954552 0.000000e+00 660.0
8 TraesCS7B01G380000 chr7D 83.099 71 8 2 2319 2386 221579067 221579136 9.210000e-06 62.1
9 TraesCS7B01G380000 chr6A 99.510 817 3 1 1 817 479111190 479112005 0.000000e+00 1485.0
10 TraesCS7B01G380000 chr6A 94.444 36 1 1 2354 2389 330136488 330136454 2.000000e-03 54.7
11 TraesCS7B01G380000 chr3B 97.802 819 17 1 1 818 799001843 799001025 0.000000e+00 1411.0
12 TraesCS7B01G380000 chr5B 97.433 818 12 3 1 817 680709934 680709125 0.000000e+00 1386.0
13 TraesCS7B01G380000 chr5B 95.556 180 6 1 638 817 492297715 492297538 1.400000e-73 287.0
14 TraesCS7B01G380000 chr5B 95.028 181 8 1 638 818 231022728 231022549 1.810000e-72 283.0
15 TraesCS7B01G380000 chr5B 94.737 38 2 0 2355 2392 446570060 446570097 3.310000e-05 60.2
16 TraesCS7B01G380000 chr5B 100.000 30 0 0 2319 2348 496486573 496486602 4.290000e-04 56.5
17 TraesCS7B01G380000 chr5B 94.286 35 0 1 2356 2390 602243678 602243646 6.000000e-03 52.8
18 TraesCS7B01G380000 chr2B 93.438 640 33 3 1 639 791355099 791354468 0.000000e+00 941.0
19 TraesCS7B01G380000 chr2B 93.146 642 37 4 1 639 526458607 526459244 0.000000e+00 935.0
20 TraesCS7B01G380000 chr2D 88.958 643 60 5 1 639 507436688 507436053 0.000000e+00 784.0
21 TraesCS7B01G380000 chr5D 88.025 643 64 6 1 639 17228790 17228157 0.000000e+00 749.0
22 TraesCS7B01G380000 chr3A 85.662 551 70 7 1391 1935 7158481 7159028 3.440000e-159 571.0
23 TraesCS7B01G380000 chr3D 85.118 551 73 7 1391 1935 1873002 1872455 3.470000e-154 555.0
24 TraesCS7B01G380000 chr3D 75.506 494 92 19 1434 1908 4818750 4818267 6.680000e-52 215.0
25 TraesCS7B01G380000 chr3D 100.000 30 0 0 2319 2348 44222192 44222221 4.290000e-04 56.5
26 TraesCS7B01G380000 chr4B 97.222 180 5 0 638 817 25885968 25886147 3.850000e-79 305.0
27 TraesCS7B01G380000 chr4B 100.000 29 0 0 2320 2348 144785834 144785806 2.000000e-03 54.7
28 TraesCS7B01G380000 chr1B 95.556 180 8 0 638 817 41730094 41729915 3.880000e-74 289.0
29 TraesCS7B01G380000 chr4A 95.556 180 7 1 638 817 523046041 523045863 1.400000e-73 287.0
30 TraesCS7B01G380000 chrUn 76.068 468 86 21 1460 1908 236970910 236971370 1.440000e-53 220.0
31 TraesCS7B01G380000 chrUn 80.303 264 45 6 1651 1908 35392178 35391916 3.130000e-45 193.0
32 TraesCS7B01G380000 chr6D 100.000 30 0 0 2354 2383 9470861 9470832 4.290000e-04 56.5
33 TraesCS7B01G380000 chr6D 100.000 29 0 0 2363 2391 149721684 149721656 2.000000e-03 54.7
34 TraesCS7B01G380000 chr6D 100.000 29 0 0 2320 2348 384204080 384204052 2.000000e-03 54.7
35 TraesCS7B01G380000 chr1D 100.000 30 0 0 2319 2348 179434096 179434067 4.290000e-04 56.5
36 TraesCS7B01G380000 chr1A 96.970 33 1 0 2316 2348 481657977 481658009 4.290000e-04 56.5
37 TraesCS7B01G380000 chr5A 92.105 38 2 1 2354 2390 605589118 605589081 6.000000e-03 52.8


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 TraesCS7B01G380000 chr7B 644528788 644531864 3076 True 5683 5683 100.0000 1 3077 1 chr7B.!!$R3 3076
1 TraesCS7B01G380000 chr7B 598467448 598469720 2272 True 3474 3474 94.4740 820 3064 1 chr7B.!!$R2 2244
2 TraesCS7B01G380000 chr7B 192089794 192090617 823 True 1345 1345 96.1260 1 824 1 chr7B.!!$R1 823
3 TraesCS7B01G380000 chr7B 105888519 105889063 544 False 547 547 84.8260 1391 1935 1 chr7B.!!$F1 544
4 TraesCS7B01G380000 chr7A 638700843 638703151 2308 True 3145 3145 91.6200 817 3077 1 chr7A.!!$R1 2260
5 TraesCS7B01G380000 chr7D 552954552 552956588 2036 True 1463 2266 91.5665 817 2918 2 chr7D.!!$R2 2101
6 TraesCS7B01G380000 chr7D 105844211 105844846 635 True 795 795 89.2690 1 639 1 chr7D.!!$R1 638
7 TraesCS7B01G380000 chr6A 479111190 479112005 815 False 1485 1485 99.5100 1 817 1 chr6A.!!$F1 816
8 TraesCS7B01G380000 chr3B 799001025 799001843 818 True 1411 1411 97.8020 1 818 1 chr3B.!!$R1 817
9 TraesCS7B01G380000 chr5B 680709125 680709934 809 True 1386 1386 97.4330 1 817 1 chr5B.!!$R4 816
10 TraesCS7B01G380000 chr2B 791354468 791355099 631 True 941 941 93.4380 1 639 1 chr2B.!!$R1 638
11 TraesCS7B01G380000 chr2B 526458607 526459244 637 False 935 935 93.1460 1 639 1 chr2B.!!$F1 638
12 TraesCS7B01G380000 chr2D 507436053 507436688 635 True 784 784 88.9580 1 639 1 chr2D.!!$R1 638
13 TraesCS7B01G380000 chr5D 17228157 17228790 633 True 749 749 88.0250 1 639 1 chr5D.!!$R1 638
14 TraesCS7B01G380000 chr3A 7158481 7159028 547 False 571 571 85.6620 1391 1935 1 chr3A.!!$F1 544
15 TraesCS7B01G380000 chr3D 1872455 1873002 547 True 555 555 85.1180 1391 1935 1 chr3D.!!$R1 544

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
818 824 2.28797 CGCACGGGCATTATACTAGTCA 60.288 50.0 11.77 0.0 41.24 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2360 2415 0.035458 CTCCCTCCGTCCCATAATGC 59.965 60.0 0.0 0.0 0.0 3.56 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
818 824 2.287970 CGCACGGGCATTATACTAGTCA 60.288 50.000 11.77 0.00 41.24 3.41
819 825 3.057734 GCACGGGCATTATACTAGTCAC 58.942 50.000 3.77 0.00 40.72 3.67
820 826 3.243771 GCACGGGCATTATACTAGTCACT 60.244 47.826 3.77 0.00 40.72 3.41
849 862 6.152492 AGTTTCCTGTTAGCAGTAGTAGTACC 59.848 42.308 5.81 0.00 41.02 3.34
1216 1241 2.125106 GGAAGATCTTGGCCGCGT 60.125 61.111 14.00 0.00 0.00 6.01
1343 1377 4.657824 CGACGGCGTGTTCTGGGT 62.658 66.667 21.19 0.00 0.00 4.51
1854 1888 2.202932 GGGCTCGTCGTCATGCAT 60.203 61.111 0.00 0.00 0.00 3.96
1909 1946 1.763655 ATCGCAGAGATCCTGGCCA 60.764 57.895 4.71 4.71 43.63 5.36
1913 1950 2.039624 AGAGATCCTGGCCACCGT 59.960 61.111 0.00 0.00 0.00 4.83
2240 2292 4.456911 GTGAACATTCCATCACAGACACAT 59.543 41.667 1.30 0.00 44.19 3.21
2382 2437 3.173965 CATTATGGGACGGAGGGAGTAT 58.826 50.000 0.00 0.00 0.00 2.12
2402 2457 6.032094 AGTATGATTTTTGAAATCAGCAGCG 58.968 36.000 17.79 0.00 39.69 5.18
2594 2658 2.924290 GTCTATGACAGCAACTTCGTCC 59.076 50.000 0.00 0.00 32.09 4.79
2750 2824 7.569639 TTGTATGTAGCAGTAGTAGGAAGAG 57.430 40.000 0.00 0.00 0.00 2.85
2781 2855 1.204941 GGAAGTACGCAGACAGACCAT 59.795 52.381 0.00 0.00 0.00 3.55
2800 2875 4.083110 ACCATTGAGAAGTTTCAGCGATTG 60.083 41.667 0.00 0.00 0.00 2.67
2820 2895 2.022129 CACGAACCCGAGACAGCAC 61.022 63.158 0.00 0.00 39.50 4.40
2841 2916 5.038683 CACGCATTATCGTACTAGTCCAAA 58.961 41.667 0.00 0.00 41.21 3.28
2852 2928 6.041296 TCGTACTAGTCCAAAAAGAGGTTCTT 59.959 38.462 0.00 0.00 38.59 2.52
2876 2952 7.172868 TGCATAAATGTGAATCAAGAATGGT 57.827 32.000 0.00 0.00 0.00 3.55
2879 2955 9.754382 GCATAAATGTGAATCAAGAATGGTAAT 57.246 29.630 0.00 0.00 0.00 1.89
2900 2976 3.551496 TTGGGCAAGACAGGAGCGG 62.551 63.158 0.00 0.00 0.00 5.52
2908 2988 4.148825 ACAGGAGCGGCCGATGTC 62.149 66.667 33.48 21.26 43.43 3.06
2918 2998 3.069980 GCCGATGTCGAGACAGGCT 62.070 63.158 21.83 3.89 44.53 4.58
2941 3027 7.065283 GCTTTTTCATCTTTGTGCAATTGTAC 58.935 34.615 18.59 18.59 0.00 2.90
2957 3053 9.606631 TGCAATTGTACACTATACAATGTATCA 57.393 29.630 9.43 0.00 44.57 2.15
2963 3059 8.789762 TGTACACTATACAATGTATCATACGCT 58.210 33.333 9.43 0.00 34.00 5.07
2982 3078 3.127030 CGCTCATCAGTTAAACCCCTTTC 59.873 47.826 0.00 0.00 0.00 2.62
3031 3127 3.318839 TGGTTTTCATCAAGACTTGCCAG 59.681 43.478 10.50 3.05 0.00 4.85
3038 3134 5.559770 TCATCAAGACTTGCCAGATTGTTA 58.440 37.500 10.50 0.00 0.00 2.41
3065 3161 6.655003 CCTATTTCTGCAACTAAAACCTCTGA 59.345 38.462 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
833 839 4.444022 CCTCTCCGGTACTACTACTGCTAA 60.444 50.000 0.00 0.00 0.00 3.09
1046 1068 3.399181 CGGGTGGAGGCTTAGGCA 61.399 66.667 8.84 0.00 40.87 4.75
1202 1227 2.298158 CTGGTACGCGGCCAAGATCT 62.298 60.000 21.77 0.00 35.32 2.75
1854 1888 3.766691 GCGTCTCCCTGGCGGTAA 61.767 66.667 0.00 0.00 45.03 2.85
1896 1930 2.039624 ACGGTGGCCAGGATCTCT 59.960 61.111 5.11 0.00 0.00 3.10
1909 1946 2.651361 CGCTCTGTTCCTGACGGT 59.349 61.111 0.00 0.00 36.00 4.83
1913 1950 2.351244 ATCGCCGCTCTGTTCCTGA 61.351 57.895 0.00 0.00 0.00 3.86
2240 2292 6.656632 TTTGTGCCTGTAATGGAATGTTTA 57.343 33.333 0.00 0.00 0.00 2.01
2312 2364 1.387539 GACCGAGGGAGTAGGTGTAC 58.612 60.000 0.00 0.00 38.57 2.90
2360 2415 0.035458 CTCCCTCCGTCCCATAATGC 59.965 60.000 0.00 0.00 0.00 3.56
2382 2437 4.241590 ACGCTGCTGATTTCAAAAATCA 57.758 36.364 12.97 12.97 35.56 2.57
2704 2772 4.686191 TTGACCATTGTTTGATGCCTTT 57.314 36.364 0.00 0.00 0.00 3.11
2781 2855 2.226437 GGCAATCGCTGAAACTTCTCAA 59.774 45.455 0.00 0.00 38.60 3.02
2800 2875 2.432628 CTGTCTCGGGTTCGTGGC 60.433 66.667 0.00 0.00 37.69 5.01
2820 2895 6.474427 TCTTTTTGGACTAGTACGATAATGCG 59.526 38.462 0.00 0.00 37.29 4.73
2841 2916 6.899393 TCACATTTATGCAAGAACCTCTTT 57.101 33.333 0.00 0.00 33.78 2.52
2852 2928 7.172868 ACCATTCTTGATTCACATTTATGCA 57.827 32.000 0.00 0.00 0.00 3.96
2876 2952 3.420893 CTCCTGTCTTGCCCAACAATTA 58.579 45.455 0.00 0.00 37.72 1.40
2879 2955 0.823356 GCTCCTGTCTTGCCCAACAA 60.823 55.000 0.00 0.00 36.62 2.83
2900 2976 2.564553 AAGCCTGTCTCGACATCGGC 62.565 60.000 17.72 17.72 46.81 5.54
2908 2988 4.023707 ACAAAGATGAAAAAGCCTGTCTCG 60.024 41.667 0.00 0.00 0.00 4.04
2918 2998 7.763528 AGTGTACAATTGCACAAAGATGAAAAA 59.236 29.630 13.07 0.00 40.61 1.94
2941 3027 8.917415 ATGAGCGTATGATACATTGTATAGTG 57.083 34.615 9.27 0.73 0.00 2.74
2957 3053 3.454812 AGGGGTTTAACTGATGAGCGTAT 59.545 43.478 0.00 0.00 0.00 3.06
2959 3055 1.628846 AGGGGTTTAACTGATGAGCGT 59.371 47.619 0.00 0.00 0.00 5.07
2961 3057 4.079253 TGAAAGGGGTTTAACTGATGAGC 58.921 43.478 0.00 0.00 0.00 4.26
2963 3059 5.576563 TCTGAAAGGGGTTTAACTGATGA 57.423 39.130 0.00 0.00 0.00 2.92
3038 3134 7.004691 AGAGGTTTTAGTTGCAGAAATAGGTT 58.995 34.615 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.