Multiple sequence alignment - TraesCS1A01G324600

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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 TraesCS1A01G324600 chr1A 100.000 4227 0 0 1 4227 515151042 515146816 0.000000e+00 7806.0
1 TraesCS1A01G324600 chr1A 99.890 3651 3 1 577 4227 514894200 514890551 0.000000e+00 6719.0
2 TraesCS1A01G324600 chr1A 98.116 584 11 0 1 584 514894815 514894232 0.000000e+00 1018.0
3 TraesCS1A01G324600 chr1A 87.363 182 20 2 2829 3010 400817847 400818025 5.540000e-49 206.0
4 TraesCS1A01G324600 chr1A 97.468 79 2 0 2395 2473 95963706 95963784 7.370000e-28 135.0
5 TraesCS1A01G324600 chr6D 96.576 2687 64 5 1172 3831 300219000 300221685 0.000000e+00 4427.0
6 TraesCS1A01G324600 chr6D 89.180 610 31 19 592 1171 300217889 300218493 0.000000e+00 728.0
7 TraesCS1A01G324600 chr6D 96.629 356 11 1 3865 4220 300221686 300222040 1.310000e-164 590.0
8 TraesCS1A01G324600 chr2A 90.324 1788 103 28 592 2321 720972534 720970759 0.000000e+00 2279.0
9 TraesCS1A01G324600 chr2A 96.923 1170 34 2 3051 4219 534579795 534580963 0.000000e+00 1960.0
10 TraesCS1A01G324600 chr2A 94.371 302 16 1 1 302 1611643 1611943 2.980000e-126 462.0
11 TraesCS1A01G324600 chr2A 93.254 252 17 0 333 584 162455903 162455652 5.160000e-99 372.0
12 TraesCS1A01G324600 chr2A 89.444 180 18 1 2832 3011 260540490 260540312 4.250000e-55 226.0
13 TraesCS1A01G324600 chr2A 82.449 245 35 6 3053 3297 166782544 166782308 1.540000e-49 207.0
14 TraesCS1A01G324600 chr2A 94.937 79 4 0 2395 2473 214710773 214710851 1.600000e-24 124.0
15 TraesCS1A01G324600 chr3A 96.365 1183 35 3 3051 4227 691332690 691331510 0.000000e+00 1940.0
16 TraesCS1A01G324600 chr3A 87.007 862 94 6 1309 2159 15090745 15089891 0.000000e+00 955.0
17 TraesCS1A01G324600 chr7A 95.833 1176 39 4 3051 4219 171207007 171205835 0.000000e+00 1892.0
18 TraesCS1A01G324600 chr7A 95.253 316 14 1 3908 4223 641269750 641269436 2.270000e-137 499.0
19 TraesCS1A01G324600 chr7A 96.522 230 8 0 2602 2831 299518872 299518643 8.580000e-102 381.0
20 TraesCS1A01G324600 chr4A 95.812 1170 46 3 3051 4220 71776054 71777220 0.000000e+00 1886.0
21 TraesCS1A01G324600 chr4A 88.121 564 56 9 707 1268 733640704 733641258 0.000000e+00 660.0
22 TraesCS1A01G324600 chr4A 89.071 183 19 1 2832 3014 300289605 300289424 4.250000e-55 226.0
23 TraesCS1A01G324600 chr5D 92.028 1267 71 13 1083 2322 171684799 171683536 0.000000e+00 1753.0
24 TraesCS1A01G324600 chr5D 93.574 249 15 1 336 584 77866812 77866565 1.860000e-98 370.0
25 TraesCS1A01G324600 chr7B 91.381 1021 70 7 1306 2323 127750751 127751756 0.000000e+00 1382.0
26 TraesCS1A01G324600 chr7B 90.980 1020 81 5 1306 2322 211419201 211420212 0.000000e+00 1363.0
27 TraesCS1A01G324600 chr7B 88.475 564 54 9 707 1268 6678900 6678346 0.000000e+00 671.0
28 TraesCS1A01G324600 chr1B 93.977 880 43 5 3051 3922 15374117 15374994 0.000000e+00 1323.0
29 TraesCS1A01G324600 chr1B 93.891 622 17 2 3051 3671 660237148 660237749 0.000000e+00 918.0
30 TraesCS1A01G324600 chr1B 97.561 533 12 1 3410 3941 660237752 660238284 0.000000e+00 911.0
31 TraesCS1A01G324600 chr1B 89.431 492 46 6 788 1277 628794578 628794091 2.160000e-172 616.0
32 TraesCS1A01G324600 chr1B 95.425 306 13 1 3905 4209 15375006 15375311 1.770000e-133 486.0
33 TraesCS1A01G324600 chr1B 94.643 56 2 1 281 336 229541509 229541563 7.530000e-13 86.1
34 TraesCS1A01G324600 chr3B 91.892 888 60 5 1309 2194 143589298 143588421 0.000000e+00 1230.0
35 TraesCS1A01G324600 chr3B 95.052 768 34 2 1557 2323 458274498 458275262 0.000000e+00 1205.0
36 TraesCS1A01G324600 chr3B 87.135 754 79 7 1309 2054 7612551 7611808 0.000000e+00 839.0
37 TraesCS1A01G324600 chr3B 93.574 249 15 1 336 584 733258173 733258420 1.860000e-98 370.0
38 TraesCS1A01G324600 chr3B 84.641 306 41 3 16 315 570208664 570208359 2.470000e-77 300.0
39 TraesCS1A01G324600 chr5A 87.382 1062 73 32 592 1598 490152085 490151030 0.000000e+00 1162.0
40 TraesCS1A01G324600 chr5A 88.652 564 53 9 707 1268 115675234 115675788 0.000000e+00 676.0
41 TraesCS1A01G324600 chr5A 91.722 302 20 3 1 302 219248165 219248461 8.460000e-112 414.0
42 TraesCS1A01G324600 chr5A 96.203 79 3 0 2395 2473 220910325 220910247 3.430000e-26 130.0
43 TraesCS1A01G324600 chr3D 87.937 829 89 5 1306 2131 6011402 6012222 0.000000e+00 966.0
44 TraesCS1A01G324600 chr3D 91.061 179 15 1 2832 3010 53819503 53819326 1.520000e-59 241.0
45 TraesCS1A01G324600 chr4B 92.701 548 28 4 1306 1852 659669639 659670175 0.000000e+00 780.0
46 TraesCS1A01G324600 chr4B 93.574 249 14 2 336 584 568661891 568661645 1.860000e-98 370.0
47 TraesCS1A01G324600 chr4B 77.519 129 19 7 592 718 223343079 223343199 7.580000e-08 69.4
48 TraesCS1A01G324600 chr4B 84.000 75 9 3 592 665 349099267 349099339 7.580000e-08 69.4
49 TraesCS1A01G324600 chr2B 89.780 499 44 7 772 1268 232257867 232258360 2.140000e-177 632.0
50 TraesCS1A01G324600 chr2B 87.324 497 46 7 779 1274 699915213 699915693 1.720000e-153 553.0
51 TraesCS1A01G324600 chr7D 94.872 312 15 1 3908 4219 61444452 61444142 1.770000e-133 486.0
52 TraesCS1A01G324600 chr7D 83.871 310 37 11 10 314 588670854 588671155 2.490000e-72 283.0
53 TraesCS1A01G324600 chr7D 88.835 206 19 2 2829 3034 366755669 366755870 2.520000e-62 250.0
54 TraesCS1A01G324600 chrUn 95.695 302 12 1 1 302 337093468 337093768 6.350000e-133 484.0
55 TraesCS1A01G324600 chrUn 88.835 206 19 2 2829 3034 94057862 94058063 2.520000e-62 250.0
56 TraesCS1A01G324600 chrUn 84.058 69 10 1 595 663 40177642 40177575 9.810000e-07 65.8
57 TraesCS1A01G324600 chrUn 83.333 72 11 1 592 663 195335962 195336032 9.810000e-07 65.8
58 TraesCS1A01G324600 chr2D 93.377 302 19 1 1 302 646461115 646460815 3.000000e-121 446.0
59 TraesCS1A01G324600 chr2D 83.495 309 37 12 10 313 189668799 189668500 4.160000e-70 276.0
60 TraesCS1A01G324600 chr2D 89.163 203 18 2 2832 3034 532459284 532459086 2.520000e-62 250.0
61 TraesCS1A01G324600 chr2D 86.667 120 16 0 2489 2608 625762509 625762628 2.650000e-27 134.0
62 TraesCS1A01G324600 chr2D 85.950 121 15 2 2489 2608 625778877 625778996 1.230000e-25 128.0
63 TraesCS1A01G324600 chr2D 91.935 62 4 1 275 336 648666980 648667040 7.530000e-13 86.1
64 TraesCS1A01G324600 chr6B 97.391 230 6 0 2602 2831 25744104 25744333 3.960000e-105 392.0
65 TraesCS1A01G324600 chr6B 94.422 251 14 0 334 584 578559457 578559207 1.840000e-103 387.0
66 TraesCS1A01G324600 chr6B 93.023 258 16 1 329 584 65064674 65064931 3.990000e-100 375.0
67 TraesCS1A01G324600 chr6B 95.876 97 2 2 2970 3065 25744582 25744677 5.660000e-34 156.0
68 TraesCS1A01G324600 chr5B 93.574 249 15 1 336 584 671039799 671039552 1.860000e-98 370.0
69 TraesCS1A01G324600 chr5B 91.923 260 20 1 325 584 492534933 492534675 3.110000e-96 363.0
70 TraesCS1A01G324600 chr6A 82.704 318 45 7 7 316 391862837 391862522 1.500000e-69 274.0
71 TraesCS1A01G324600 chr6A 97.458 118 3 0 2714 2831 80106985 80107102 7.170000e-48 202.0
72 TraesCS1A01G324600 chr6A 93.976 83 5 0 2602 2684 80106901 80106983 4.440000e-25 126.0
73 TraesCS1A01G324600 chr6A 86.567 67 5 3 600 664 8333943 8333879 2.110000e-08 71.3
74 TraesCS1A01G324600 chr1D 93.333 105 7 0 2395 2499 120811698 120811802 5.660000e-34 156.0


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 TraesCS1A01G324600 chr1A 515146816 515151042 4226 True 7806.0 7806 100.000000 1 4227 1 chr1A.!!$R1 4226
1 TraesCS1A01G324600 chr1A 514890551 514894815 4264 True 3868.5 6719 99.003000 1 4227 2 chr1A.!!$R2 4226
2 TraesCS1A01G324600 chr6D 300217889 300222040 4151 False 1915.0 4427 94.128333 592 4220 3 chr6D.!!$F1 3628
3 TraesCS1A01G324600 chr2A 720970759 720972534 1775 True 2279.0 2279 90.324000 592 2321 1 chr2A.!!$R4 1729
4 TraesCS1A01G324600 chr2A 534579795 534580963 1168 False 1960.0 1960 96.923000 3051 4219 1 chr2A.!!$F3 1168
5 TraesCS1A01G324600 chr3A 691331510 691332690 1180 True 1940.0 1940 96.365000 3051 4227 1 chr3A.!!$R2 1176
6 TraesCS1A01G324600 chr3A 15089891 15090745 854 True 955.0 955 87.007000 1309 2159 1 chr3A.!!$R1 850
7 TraesCS1A01G324600 chr7A 171205835 171207007 1172 True 1892.0 1892 95.833000 3051 4219 1 chr7A.!!$R1 1168
8 TraesCS1A01G324600 chr4A 71776054 71777220 1166 False 1886.0 1886 95.812000 3051 4220 1 chr4A.!!$F1 1169
9 TraesCS1A01G324600 chr4A 733640704 733641258 554 False 660.0 660 88.121000 707 1268 1 chr4A.!!$F2 561
10 TraesCS1A01G324600 chr5D 171683536 171684799 1263 True 1753.0 1753 92.028000 1083 2322 1 chr5D.!!$R2 1239
11 TraesCS1A01G324600 chr7B 127750751 127751756 1005 False 1382.0 1382 91.381000 1306 2323 1 chr7B.!!$F1 1017
12 TraesCS1A01G324600 chr7B 211419201 211420212 1011 False 1363.0 1363 90.980000 1306 2322 1 chr7B.!!$F2 1016
13 TraesCS1A01G324600 chr7B 6678346 6678900 554 True 671.0 671 88.475000 707 1268 1 chr7B.!!$R1 561
14 TraesCS1A01G324600 chr1B 660237148 660238284 1136 False 914.5 918 95.726000 3051 3941 2 chr1B.!!$F3 890
15 TraesCS1A01G324600 chr1B 15374117 15375311 1194 False 904.5 1323 94.701000 3051 4209 2 chr1B.!!$F2 1158
16 TraesCS1A01G324600 chr3B 143588421 143589298 877 True 1230.0 1230 91.892000 1309 2194 1 chr3B.!!$R2 885
17 TraesCS1A01G324600 chr3B 458274498 458275262 764 False 1205.0 1205 95.052000 1557 2323 1 chr3B.!!$F1 766
18 TraesCS1A01G324600 chr3B 7611808 7612551 743 True 839.0 839 87.135000 1309 2054 1 chr3B.!!$R1 745
19 TraesCS1A01G324600 chr5A 490151030 490152085 1055 True 1162.0 1162 87.382000 592 1598 1 chr5A.!!$R2 1006
20 TraesCS1A01G324600 chr5A 115675234 115675788 554 False 676.0 676 88.652000 707 1268 1 chr5A.!!$F1 561
21 TraesCS1A01G324600 chr3D 6011402 6012222 820 False 966.0 966 87.937000 1306 2131 1 chr3D.!!$F1 825
22 TraesCS1A01G324600 chr4B 659669639 659670175 536 False 780.0 780 92.701000 1306 1852 1 chr4B.!!$F3 546
23 TraesCS1A01G324600 chr6B 25744104 25744677 573 False 274.0 392 96.633500 2602 3065 2 chr6B.!!$F2 463

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
255 256 0.035739 AACGATACCACAAAGCCGGT 59.964 50.0 1.90 0.00 39.41 5.28 F
299 300 1.771073 TTCTCCAGTTGCAACGCACG 61.771 55.0 23.21 13.53 38.71 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 2879 1.140852 CTTGGGTGGGAATCGATAGCA 59.859 52.381 0.0 0.0 0.00 3.49 R
3236 4120 5.409214 CCATTTTCAATCTTGCAAAACCGAT 59.591 36.000 0.0 0.0 27.94 4.18 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
141 142 1.450312 GTGCCATTGACCTCCCTCG 60.450 63.158 0.00 0.00 0.00 4.63
239 240 4.412207 GCCTTCCATAAAAGCACTAAACG 58.588 43.478 0.00 0.00 0.00 3.60
240 241 4.155280 GCCTTCCATAAAAGCACTAAACGA 59.845 41.667 0.00 0.00 0.00 3.85
255 256 0.035739 AACGATACCACAAAGCCGGT 59.964 50.000 1.90 0.00 39.41 5.28
299 300 1.771073 TTCTCCAGTTGCAACGCACG 61.771 55.000 23.21 13.53 38.71 5.34
528 529 7.093684 GGTCTTATAGGGGCTTATAAGTCTCAG 60.094 44.444 18.97 7.60 41.32 3.35
2218 2879 4.778143 GAACATCGCCGCCACCCT 62.778 66.667 0.00 0.00 0.00 4.34
3236 4120 2.158957 GGTCTGACATGAATAAGGCCGA 60.159 50.000 10.38 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 3.594775 CGGTTGCAAGCAGTGGCA 61.595 61.111 26.71 0.00 44.61 4.92
204 205 0.533755 GGAAGGCCACCATCGAGATG 60.534 60.000 5.01 6.12 38.51 2.90
239 240 1.737793 CAGAACCGGCTTTGTGGTATC 59.262 52.381 0.00 0.00 37.54 2.24
240 241 1.073284 ACAGAACCGGCTTTGTGGTAT 59.927 47.619 0.00 0.00 37.54 2.73
382 383 7.947782 TGGTTTAGATGGAACTTATAGGGAT 57.052 36.000 0.00 0.00 0.00 3.85
2218 2879 1.140852 CTTGGGTGGGAATCGATAGCA 59.859 52.381 0.00 0.00 0.00 3.49
3236 4120 5.409214 CCATTTTCAATCTTGCAAAACCGAT 59.591 36.000 0.00 0.00 27.94 4.18


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

AutoCloner maintained by Alex Coulton.