Multiple sequence alignment - TraesCS1B01G279000

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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 TraesCS1B01G279000 chr1B 100.000 3787 0 0 1 3787 487404619 487408405 0.000000e+00 6994.0
1 TraesCS1B01G279000 chr1D 96.444 2278 62 8 969 3230 363861164 363863438 0.000000e+00 3740.0
2 TraesCS1B01G279000 chr1D 94.867 565 11 5 3219 3780 363863465 363864014 0.000000e+00 867.0
3 TraesCS1B01G279000 chr1A 94.909 2200 99 5 900 3089 463218528 463220724 0.000000e+00 3430.0
4 TraesCS1B01G279000 chr1A 96.172 627 24 0 3161 3787 463220754 463221380 0.000000e+00 1026.0
5 TraesCS1B01G279000 chr4B 84.339 2503 285 47 906 3342 139572241 139569780 0.000000e+00 2351.0
6 TraesCS1B01G279000 chr4B 84.049 2307 274 49 906 3155 139549280 139547011 0.000000e+00 2135.0
7 TraesCS1B01G279000 chr4B 77.011 1318 216 45 1387 2688 535331502 535330256 0.000000e+00 675.0
8 TraesCS1B01G279000 chr4D 83.260 2485 315 58 906 3348 97962502 97960077 0.000000e+00 2191.0
9 TraesCS1B01G279000 chr4D 85.637 2040 236 23 906 2936 97970280 97968289 0.000000e+00 2091.0
10 TraesCS1B01G279000 chr4D 95.598 886 38 1 1 886 379224816 379223932 0.000000e+00 1419.0
11 TraesCS1B01G279000 chr4D 78.040 1439 244 46 1387 2793 98015418 98014020 0.000000e+00 841.0
12 TraesCS1B01G279000 chr4D 81.869 717 110 15 1611 2319 374041175 374040471 1.520000e-163 586.0
13 TraesCS1B01G279000 chr4D 78.758 918 142 31 1387 2284 435198755 435197871 1.970000e-157 566.0
14 TraesCS1B01G279000 chr4A 85.900 1383 152 18 906 2270 478209500 478210857 0.000000e+00 1434.0
15 TraesCS1B01G279000 chr4A 78.378 1443 241 46 1387 2793 478191411 478192818 0.000000e+00 870.0
16 TraesCS1B01G279000 chr4A 76.626 1322 219 54 1387 2688 36607780 36606529 0.000000e+00 647.0
17 TraesCS1B01G279000 chr4A 79.892 925 135 26 2266 3155 478216299 478217207 6.900000e-177 630.0
18 TraesCS1B01G279000 chr3D 95.578 882 34 4 1 879 448442150 448443029 0.000000e+00 1408.0
19 TraesCS1B01G279000 chr3D 78.900 1436 195 66 900 2304 134964458 134963100 0.000000e+00 874.0
20 TraesCS1B01G279000 chr7B 93.714 875 45 4 2 875 144481852 144482717 0.000000e+00 1303.0
21 TraesCS1B01G279000 chr7B 87.907 215 22 4 368 581 738906119 738906330 2.260000e-62 250.0
22 TraesCS1B01G279000 chr3B 86.344 227 26 5 357 581 723489688 723489911 3.780000e-60 243.0
23 TraesCS1B01G279000 chr3B 77.049 305 54 12 1176 1468 745203209 745202909 1.090000e-35 161.0
24 TraesCS1B01G279000 chr3B 79.688 128 21 4 82 207 622482207 622482331 1.870000e-13 87.9
25 TraesCS1B01G279000 chr6D 87.368 190 22 2 7 196 119298976 119299163 2.290000e-52 217.0
26 TraesCS1B01G279000 chr6D 76.776 366 64 17 1186 1545 143413624 143413274 6.460000e-43 185.0
27 TraesCS1B01G279000 chr7D 93.103 58 3 1 417 474 131710391 131710447 2.420000e-12 84.2
28 TraesCS1B01G279000 chr7D 95.349 43 2 0 417 459 131749361 131749403 6.790000e-08 69.4


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 TraesCS1B01G279000 chr1B 487404619 487408405 3786 False 6994.0 6994 100.0000 1 3787 1 chr1B.!!$F1 3786
1 TraesCS1B01G279000 chr1D 363861164 363864014 2850 False 2303.5 3740 95.6555 969 3780 2 chr1D.!!$F1 2811
2 TraesCS1B01G279000 chr1A 463218528 463221380 2852 False 2228.0 3430 95.5405 900 3787 2 chr1A.!!$F1 2887
3 TraesCS1B01G279000 chr4B 139569780 139572241 2461 True 2351.0 2351 84.3390 906 3342 1 chr4B.!!$R2 2436
4 TraesCS1B01G279000 chr4B 139547011 139549280 2269 True 2135.0 2135 84.0490 906 3155 1 chr4B.!!$R1 2249
5 TraesCS1B01G279000 chr4B 535330256 535331502 1246 True 675.0 675 77.0110 1387 2688 1 chr4B.!!$R3 1301
6 TraesCS1B01G279000 chr4D 97960077 97962502 2425 True 2191.0 2191 83.2600 906 3348 1 chr4D.!!$R1 2442
7 TraesCS1B01G279000 chr4D 97968289 97970280 1991 True 2091.0 2091 85.6370 906 2936 1 chr4D.!!$R2 2030
8 TraesCS1B01G279000 chr4D 379223932 379224816 884 True 1419.0 1419 95.5980 1 886 1 chr4D.!!$R5 885
9 TraesCS1B01G279000 chr4D 98014020 98015418 1398 True 841.0 841 78.0400 1387 2793 1 chr4D.!!$R3 1406
10 TraesCS1B01G279000 chr4D 374040471 374041175 704 True 586.0 586 81.8690 1611 2319 1 chr4D.!!$R4 708
11 TraesCS1B01G279000 chr4D 435197871 435198755 884 True 566.0 566 78.7580 1387 2284 1 chr4D.!!$R6 897
12 TraesCS1B01G279000 chr4A 478209500 478210857 1357 False 1434.0 1434 85.9000 906 2270 1 chr4A.!!$F2 1364
13 TraesCS1B01G279000 chr4A 478191411 478192818 1407 False 870.0 870 78.3780 1387 2793 1 chr4A.!!$F1 1406
14 TraesCS1B01G279000 chr4A 36606529 36607780 1251 True 647.0 647 76.6260 1387 2688 1 chr4A.!!$R1 1301
15 TraesCS1B01G279000 chr4A 478216299 478217207 908 False 630.0 630 79.8920 2266 3155 1 chr4A.!!$F3 889
16 TraesCS1B01G279000 chr3D 448442150 448443029 879 False 1408.0 1408 95.5780 1 879 1 chr3D.!!$F1 878
17 TraesCS1B01G279000 chr3D 134963100 134964458 1358 True 874.0 874 78.9000 900 2304 1 chr3D.!!$R1 1404
18 TraesCS1B01G279000 chr7B 144481852 144482717 865 False 1303.0 1303 93.7140 2 875 1 chr7B.!!$F1 873

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
610 614 0.664767 AGCAGCGTCTTCTGTCGAAC 60.665 55.0 0.0 0.0 36.49 3.95 F
1935 1997 0.106149 GGACCAAAGACGGTGTCTGT 59.894 55.0 0.0 0.0 42.59 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2408 0.168788 AGATGGTGCAAATGAACGCG 59.831 50.0 3.53 3.53 0.00 6.01 R
3155 3314 0.681733 GGCACACTCTGAGAGACCAA 59.318 55.0 17.71 0.00 33.32 3.67 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
186 187 2.626743 GGCTTGCAGCTAATCCATGAAT 59.373 45.455 0.00 0.0 41.99 2.57
206 207 6.946340 TGAATGGATGTAGCTAAGAAACTCA 58.054 36.000 0.00 0.0 0.00 3.41
254 255 5.183140 CCGGTTGTAACAAAATTCAGGATCT 59.817 40.000 0.00 0.0 0.00 2.75
406 410 2.432628 CAAGACCGTCGTGCTCCC 60.433 66.667 1.35 0.0 0.00 4.30
407 411 2.600769 AAGACCGTCGTGCTCCCT 60.601 61.111 0.00 0.0 0.00 4.20
408 412 1.303888 AAGACCGTCGTGCTCCCTA 60.304 57.895 0.00 0.0 0.00 3.53
610 614 0.664767 AGCAGCGTCTTCTGTCGAAC 60.665 55.000 0.00 0.0 36.49 3.95
633 637 1.489230 GACCAATAACGGGAGGTGGAT 59.511 52.381 0.00 0.0 33.77 3.41
700 704 3.458163 GGGAGATGGCGGTCACGA 61.458 66.667 0.00 0.0 44.60 4.35
810 814 1.271054 GGAGCCATGCGAGTGGATAAT 60.271 52.381 10.33 0.0 42.02 1.28
881 885 2.296190 GACCACAAGCGATTCCCTTTTT 59.704 45.455 0.00 0.0 0.00 1.94
886 890 4.681483 CACAAGCGATTCCCTTTTTCTTTC 59.319 41.667 0.00 0.0 0.00 2.62
887 891 4.584743 ACAAGCGATTCCCTTTTTCTTTCT 59.415 37.500 0.00 0.0 0.00 2.52
888 892 5.157067 CAAGCGATTCCCTTTTTCTTTCTC 58.843 41.667 0.00 0.0 0.00 2.87
889 893 4.657013 AGCGATTCCCTTTTTCTTTCTCT 58.343 39.130 0.00 0.0 0.00 3.10
890 894 4.697828 AGCGATTCCCTTTTTCTTTCTCTC 59.302 41.667 0.00 0.0 0.00 3.20
891 895 4.455877 GCGATTCCCTTTTTCTTTCTCTCA 59.544 41.667 0.00 0.0 0.00 3.27
892 896 5.048713 GCGATTCCCTTTTTCTTTCTCTCAA 60.049 40.000 0.00 0.0 0.00 3.02
893 897 6.515035 GCGATTCCCTTTTTCTTTCTCTCAAA 60.515 38.462 0.00 0.0 0.00 2.69
894 898 7.425606 CGATTCCCTTTTTCTTTCTCTCAAAA 58.574 34.615 0.00 0.0 0.00 2.44
895 899 7.920682 CGATTCCCTTTTTCTTTCTCTCAAAAA 59.079 33.333 0.00 0.0 0.00 1.94
896 900 9.770097 GATTCCCTTTTTCTTTCTCTCAAAAAT 57.230 29.630 0.00 0.0 30.61 1.82
1184 1194 1.913762 CTCACCTCCCCCACGACTT 60.914 63.158 0.00 0.0 0.00 3.01
1654 1703 1.812686 CTGGAAGTTCCCCGACACGA 61.813 60.000 19.42 0.0 35.03 4.35
1929 1991 0.108019 GAGGTTGGACCAAAGACGGT 59.892 55.000 8.94 0.0 41.95 4.83
1935 1997 0.106149 GGACCAAAGACGGTGTCTGT 59.894 55.000 0.00 0.0 42.59 3.41
1975 2037 3.365265 CCCCCAAGTTGCACTCGC 61.365 66.667 0.00 0.0 39.24 5.03
1977 2039 1.898574 CCCCAAGTTGCACTCGCTT 60.899 57.895 0.00 0.0 39.64 4.68
2150 2253 0.112995 ATTGCAGGCTGGGACAAAGA 59.887 50.000 17.64 0.0 38.70 2.52
2290 2393 3.583054 CCACATCATGGTGAAGCCT 57.417 52.632 14.29 0.0 44.46 4.58
2291 2394 1.100510 CCACATCATGGTGAAGCCTG 58.899 55.000 14.29 0.0 44.46 4.85
2292 2395 1.100510 CACATCATGGTGAAGCCTGG 58.899 55.000 14.29 0.0 41.32 4.45
2293 2396 0.700564 ACATCATGGTGAAGCCTGGT 59.299 50.000 14.29 0.0 38.35 4.00
2305 2408 1.005748 GCCTGGTGCTTCTTTTGGC 60.006 57.895 0.00 0.0 36.87 4.52
2308 2411 2.429069 GGTGCTTCTTTTGGCGCG 60.429 61.111 0.00 0.0 39.52 6.86
2337 2440 7.552458 TTTGCACCATCTTGTACTATATGTG 57.448 36.000 0.00 0.0 0.00 3.21
2795 2911 2.124903 GCGAACGACTGAAGTCAAAGA 58.875 47.619 10.88 0.0 44.99 2.52
2851 2967 6.899393 AATTGTTGTGTTCTGTGGTCATAT 57.101 33.333 0.00 0.0 0.00 1.78
2943 3064 6.424207 GCTTAAGTGTTGAAGTTAGTGCTACT 59.576 38.462 4.02 0.0 0.00 2.57
2944 3065 7.597743 GCTTAAGTGTTGAAGTTAGTGCTACTA 59.402 37.037 4.02 0.0 0.00 1.82
3155 3314 7.715249 TGCTTACTGTCTTGACAATTTACTCTT 59.285 33.333 4.95 0.0 0.00 2.85
3157 3316 9.869844 CTTACTGTCTTGACAATTTACTCTTTG 57.130 33.333 4.95 0.0 0.00 2.77
3158 3317 7.264373 ACTGTCTTGACAATTTACTCTTTGG 57.736 36.000 4.95 0.0 0.00 3.28
3159 3318 6.828785 ACTGTCTTGACAATTTACTCTTTGGT 59.171 34.615 4.95 0.0 0.00 3.67
3260 3486 3.686726 CCTATCTGGTTCTTCAGTTGTGC 59.313 47.826 0.00 0.0 36.25 4.57
3278 3505 9.643693 CAGTTGTGCTATTTGAATCCTTATTTT 57.356 29.630 0.00 0.0 0.00 1.82
3473 3703 4.127171 GGTAAACAGAAGTGAGCAACTCA 58.873 43.478 0.00 0.0 38.56 3.41
3490 3720 3.233507 ACTCATGGTTCATTGCTTGGTT 58.766 40.909 0.00 0.0 0.00 3.67
3675 3905 4.326826 CCACCAGAGTCATTTTCTGCTAA 58.673 43.478 0.00 0.0 40.54 3.09
3751 3981 5.724328 TCAGAACTATTGCTTAGGACACAG 58.276 41.667 0.00 0.0 31.68 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 4.913924 GCGATGATTTTTGCTACATCCATC 59.086 41.667 0.00 0.00 36.71 3.51
186 187 4.081087 GGGTGAGTTTCTTAGCTACATCCA 60.081 45.833 0.00 0.00 0.00 3.41
254 255 1.929806 CTTCGACGGACATGGACGGA 61.930 60.000 14.40 2.21 0.00 4.69
304 306 6.198966 GTCTTGAATTTGTTACAACTGGCAAG 59.801 38.462 17.11 17.11 0.00 4.01
393 397 0.106819 ATACTAGGGAGCACGACGGT 60.107 55.000 0.00 0.00 0.00 4.83
397 401 2.953284 AGCTATACTAGGGAGCACGA 57.047 50.000 13.32 0.00 38.73 4.35
406 410 9.851043 GCTAAATCGAAAACAAAGCTATACTAG 57.149 33.333 0.00 0.00 0.00 2.57
407 411 8.823818 GGCTAAATCGAAAACAAAGCTATACTA 58.176 33.333 0.00 0.00 0.00 1.82
408 412 7.465513 CGGCTAAATCGAAAACAAAGCTATACT 60.466 37.037 0.00 0.00 0.00 2.12
610 614 1.881252 CCTCCCGTTATTGGTCGCG 60.881 63.158 0.00 0.00 0.00 5.87
633 637 3.043713 CGACCGCAAGCTGCTTCA 61.044 61.111 12.82 0.00 42.25 3.02
861 865 1.995376 AAAAGGGAATCGCTTGTGGT 58.005 45.000 13.35 0.00 36.76 4.16
881 885 9.421399 GGGGGAATTATATTTTTGAGAGAAAGA 57.579 33.333 0.00 0.00 0.00 2.52
887 891 9.782900 AGAAAAGGGGGAATTATATTTTTGAGA 57.217 29.630 0.00 0.00 0.00 3.27
890 894 9.613428 GGAAGAAAAGGGGGAATTATATTTTTG 57.387 33.333 0.00 0.00 0.00 2.44
891 895 8.482943 CGGAAGAAAAGGGGGAATTATATTTTT 58.517 33.333 0.00 0.00 0.00 1.94
892 896 7.418597 GCGGAAGAAAAGGGGGAATTATATTTT 60.419 37.037 0.00 0.00 0.00 1.82
893 897 6.041637 GCGGAAGAAAAGGGGGAATTATATTT 59.958 38.462 0.00 0.00 0.00 1.40
894 898 5.538813 GCGGAAGAAAAGGGGGAATTATATT 59.461 40.000 0.00 0.00 0.00 1.28
895 899 5.077564 GCGGAAGAAAAGGGGGAATTATAT 58.922 41.667 0.00 0.00 0.00 0.86
896 900 4.466827 GCGGAAGAAAAGGGGGAATTATA 58.533 43.478 0.00 0.00 0.00 0.98
897 901 3.296854 GCGGAAGAAAAGGGGGAATTAT 58.703 45.455 0.00 0.00 0.00 1.28
898 902 2.622190 GGCGGAAGAAAAGGGGGAATTA 60.622 50.000 0.00 0.00 0.00 1.40
903 907 2.750237 CGGCGGAAGAAAAGGGGG 60.750 66.667 0.00 0.00 0.00 5.40
1169 1179 2.995574 CGAAGTCGTGGGGGAGGT 60.996 66.667 0.00 0.00 34.11 3.85
1184 1194 2.181777 GGCTGATGCAGTCGACGA 59.818 61.111 10.46 0.00 41.91 4.20
1431 1477 4.357947 GTGAGGTGGACGCAGCGA 62.358 66.667 24.65 0.00 0.00 4.93
1670 1719 2.039348 CGGAGGTTAGGGAAAAAGGTGA 59.961 50.000 0.00 0.00 0.00 4.02
1929 1991 3.056821 CGATCTTCACCTTGGTACAGACA 60.057 47.826 0.00 0.00 42.39 3.41
1935 1997 0.539986 GGCCGATCTTCACCTTGGTA 59.460 55.000 0.00 0.00 0.00 3.25
1975 2037 8.284945 TGATTTTCTGAATCCAAGTATCCAAG 57.715 34.615 0.00 0.00 0.00 3.61
1977 2039 7.835682 ACATGATTTTCTGAATCCAAGTATCCA 59.164 33.333 0.00 0.00 0.00 3.41
2150 2253 2.360350 CATGGTGCTTGGGCTCGT 60.360 61.111 0.00 0.00 39.59 4.18
2290 2393 2.727544 GCGCCAAAAGAAGCACCA 59.272 55.556 0.00 0.00 0.00 4.17
2291 2394 2.429069 CGCGCCAAAAGAAGCACC 60.429 61.111 0.00 0.00 0.00 5.01
2292 2395 1.268778 GAACGCGCCAAAAGAAGCAC 61.269 55.000 5.73 0.00 0.00 4.40
2293 2396 1.008995 GAACGCGCCAAAAGAAGCA 60.009 52.632 5.73 0.00 0.00 3.91
2296 2399 2.123342 CAAATGAACGCGCCAAAAGAA 58.877 42.857 5.73 0.00 0.00 2.52
2300 2403 1.066422 TGCAAATGAACGCGCCAAA 59.934 47.368 5.73 0.00 0.00 3.28
2304 2407 1.405469 GATGGTGCAAATGAACGCGC 61.405 55.000 5.73 0.00 37.92 6.86
2305 2408 0.168788 AGATGGTGCAAATGAACGCG 59.831 50.000 3.53 3.53 0.00 6.01
2308 2411 5.376854 AGTACAAGATGGTGCAAATGAAC 57.623 39.130 0.00 0.00 0.00 3.18
2337 2440 6.237648 GCAACAGCAGCAATTGACAATAATAC 60.238 38.462 10.34 0.00 0.00 1.89
2795 2911 6.534475 AGTGACCATGAAATAAACATGCAT 57.466 33.333 0.00 0.00 42.31 3.96
2851 2967 3.220940 TGAAAACAGTGCATGTCCATGA 58.779 40.909 11.35 0.00 43.00 3.07
2943 3064 9.563748 TGATAGTCATTTGCATCATTGAAGATA 57.436 29.630 0.00 0.00 0.00 1.98
2944 3065 8.459911 TGATAGTCATTTGCATCATTGAAGAT 57.540 30.769 0.00 0.00 0.00 2.40
3040 3184 3.682377 TGTGCAATGTAACACCATACTCG 59.318 43.478 0.00 0.00 35.90 4.18
3155 3314 0.681733 GGCACACTCTGAGAGACCAA 59.318 55.000 17.71 0.00 33.32 3.67
3157 3316 2.355946 TGGCACACTCTGAGAGACC 58.644 57.895 17.71 11.83 33.32 3.85
3278 3505 6.810911 TGCAAAAGTAACCAAATTAGCTTGA 58.189 32.000 0.00 0.00 0.00 3.02
3473 3703 4.895668 AATGAACCAAGCAATGAACCAT 57.104 36.364 0.00 0.00 0.00 3.55
3606 3836 3.060479 ACCATAAGGGACTATGGCAGA 57.940 47.619 9.13 0.00 40.65 4.26
3724 3954 6.989169 GTGTCCTAAGCAATAGTTCTGATCAT 59.011 38.462 0.00 0.00 0.00 2.45
3727 3957 6.070538 ACTGTGTCCTAAGCAATAGTTCTGAT 60.071 38.462 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.