Multiple sequence alignment - TraesCS3A01G163800

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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 TraesCS3A01G163800 chr3A 100.000 2723 0 0 1 2723 167875543 167872821 0.000000e+00 5029
1 TraesCS3A01G163800 chr4D 91.909 2756 180 15 2 2719 497396782 497394032 0.000000e+00 3814
2 TraesCS3A01G163800 chr4D 81.719 640 72 22 202 803 43274800 43274168 2.440000e-135 492
3 TraesCS3A01G163800 chr4D 88.822 331 31 4 2 330 43275043 43274717 4.220000e-108 401
4 TraesCS3A01G163800 chr6B 88.467 2792 207 36 2 2719 592965656 592968406 0.000000e+00 3265
5 TraesCS3A01G163800 chr2B 86.370 2722 262 47 48 2722 77579520 77576861 0.000000e+00 2870
6 TraesCS3A01G163800 chr2D 89.362 2256 183 22 475 2719 343541892 343544101 0.000000e+00 2784
7 TraesCS3A01G163800 chr2D 87.755 1960 161 20 475 2425 296535040 296533151 0.000000e+00 2217
8 TraesCS3A01G163800 chr5D 89.848 2167 168 23 564 2722 472515364 472513242 0.000000e+00 2736
9 TraesCS3A01G163800 chr5D 89.322 2051 169 23 2 2036 57136993 57139009 0.000000e+00 2529
10 TraesCS3A01G163800 chr1D 88.889 2259 189 27 475 2719 61384073 61386283 0.000000e+00 2724
11 TraesCS3A01G163800 chr7B 86.464 2571 233 50 205 2719 731851391 731848880 0.000000e+00 2713
12 TraesCS3A01G163800 chr7B 87.732 2266 207 38 475 2719 92648267 92650482 0.000000e+00 2579
13 TraesCS3A01G163800 chr3D 88.054 2277 201 36 475 2722 64821894 64819660 0.000000e+00 2632
14 TraesCS3A01G163800 chr4B 89.540 1998 165 13 2 1962 167413099 167415089 0.000000e+00 2492
15 TraesCS3A01G163800 chr4A 86.983 2274 208 37 475 2722 660869553 660867342 0.000000e+00 2479
16 TraesCS3A01G163800 chr4A 86.519 586 69 8 835 1412 703507306 703507889 1.060000e-178 636
17 TraesCS3A01G163800 chr5A 91.471 1407 84 8 68 1438 693363262 693364668 0.000000e+00 1901
18 TraesCS3A01G163800 chr1B 84.900 1702 209 29 335 2016 339142653 339140980 0.000000e+00 1676
19 TraesCS3A01G163800 chr2A 88.801 1393 114 13 198 1552 320185383 320183995 0.000000e+00 1670
20 TraesCS3A01G163800 chr2A 87.231 1441 132 22 2 1402 666129038 666127610 0.000000e+00 1594
21 TraesCS3A01G163800 chr2A 89.024 328 32 4 2 327 320185648 320185323 1.170000e-108 403
22 TraesCS3A01G163800 chr3B 81.271 1212 162 41 337 1536 230927917 230926759 0.000000e+00 920
23 TraesCS3A01G163800 chr3B 81.387 1182 153 39 372 1536 231982689 231981558 0.000000e+00 902
24 TraesCS3A01G163800 chr3B 86.626 329 29 8 2 318 689530093 689530418 1.550000e-92 350


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 TraesCS3A01G163800 chr3A 167872821 167875543 2722 True 5029.0 5029 100.0000 1 2723 1 chr3A.!!$R1 2722
1 TraesCS3A01G163800 chr4D 497394032 497396782 2750 True 3814.0 3814 91.9090 2 2719 1 chr4D.!!$R1 2717
2 TraesCS3A01G163800 chr4D 43274168 43275043 875 True 446.5 492 85.2705 2 803 2 chr4D.!!$R2 801
3 TraesCS3A01G163800 chr6B 592965656 592968406 2750 False 3265.0 3265 88.4670 2 2719 1 chr6B.!!$F1 2717
4 TraesCS3A01G163800 chr2B 77576861 77579520 2659 True 2870.0 2870 86.3700 48 2722 1 chr2B.!!$R1 2674
5 TraesCS3A01G163800 chr2D 343541892 343544101 2209 False 2784.0 2784 89.3620 475 2719 1 chr2D.!!$F1 2244
6 TraesCS3A01G163800 chr2D 296533151 296535040 1889 True 2217.0 2217 87.7550 475 2425 1 chr2D.!!$R1 1950
7 TraesCS3A01G163800 chr5D 472513242 472515364 2122 True 2736.0 2736 89.8480 564 2722 1 chr5D.!!$R1 2158
8 TraesCS3A01G163800 chr5D 57136993 57139009 2016 False 2529.0 2529 89.3220 2 2036 1 chr5D.!!$F1 2034
9 TraesCS3A01G163800 chr1D 61384073 61386283 2210 False 2724.0 2724 88.8890 475 2719 1 chr1D.!!$F1 2244
10 TraesCS3A01G163800 chr7B 731848880 731851391 2511 True 2713.0 2713 86.4640 205 2719 1 chr7B.!!$R1 2514
11 TraesCS3A01G163800 chr7B 92648267 92650482 2215 False 2579.0 2579 87.7320 475 2719 1 chr7B.!!$F1 2244
12 TraesCS3A01G163800 chr3D 64819660 64821894 2234 True 2632.0 2632 88.0540 475 2722 1 chr3D.!!$R1 2247
13 TraesCS3A01G163800 chr4B 167413099 167415089 1990 False 2492.0 2492 89.5400 2 1962 1 chr4B.!!$F1 1960
14 TraesCS3A01G163800 chr4A 660867342 660869553 2211 True 2479.0 2479 86.9830 475 2722 1 chr4A.!!$R1 2247
15 TraesCS3A01G163800 chr4A 703507306 703507889 583 False 636.0 636 86.5190 835 1412 1 chr4A.!!$F1 577
16 TraesCS3A01G163800 chr5A 693363262 693364668 1406 False 1901.0 1901 91.4710 68 1438 1 chr5A.!!$F1 1370
17 TraesCS3A01G163800 chr1B 339140980 339142653 1673 True 1676.0 1676 84.9000 335 2016 1 chr1B.!!$R1 1681
18 TraesCS3A01G163800 chr2A 666127610 666129038 1428 True 1594.0 1594 87.2310 2 1402 1 chr2A.!!$R1 1400
19 TraesCS3A01G163800 chr2A 320183995 320185648 1653 True 1036.5 1670 88.9125 2 1552 2 chr2A.!!$R2 1550
20 TraesCS3A01G163800 chr3B 230926759 230927917 1158 True 920.0 920 81.2710 337 1536 1 chr3B.!!$R1 1199
21 TraesCS3A01G163800 chr3B 231981558 231982689 1131 True 902.0 902 81.3870 372 1536 1 chr3B.!!$R2 1164

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
324 444 2.416431 GCCAACTGAAACATGCATCCTC 60.416 50.0 0.0 0.0 0.0 3.71 F
1280 1609 0.036952 ACTCTTGATGACACGGGCAG 60.037 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1655 0.603707 CATCACCGTCAACAGCACCT 60.604 55.0 0.0 0.0 0.00 4.00 R
2684 3039 0.630673 AGGTTTGCCATCCATAGCCA 59.369 50.0 0.0 0.0 37.19 4.75 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
54 56 6.171213 CAGATATCAAGCATCATAGCCAGAA 58.829 40.000 5.32 0.00 34.23 3.02
73 75 6.763610 GCCAGAATGAAACTTGTATACTAGCT 59.236 38.462 13.36 0.00 39.69 3.32
83 85 8.684973 AACTTGTATACTAGCTAAACTCAACG 57.315 34.615 13.36 0.00 0.00 4.10
94 96 4.151689 GCTAAACTCAACGTGCATTGTAGA 59.848 41.667 0.00 0.00 0.00 2.59
149 152 5.120519 ACTTGTTGTTTGCAAATGAACACAG 59.879 36.000 26.80 25.47 35.66 3.66
195 202 7.646314 CAACCAAAAATCCATAAATGTGCAAA 58.354 30.769 0.00 0.00 0.00 3.68
196 203 7.437793 ACCAAAAATCCATAAATGTGCAAAG 57.562 32.000 0.00 0.00 0.00 2.77
207 216 7.041235 CCATAAATGTGCAAAGGAAAAACATGT 60.041 33.333 0.00 0.00 32.04 3.21
236 245 3.877559 CCAGCTGAAACATGTATCCTGA 58.122 45.455 17.39 0.00 0.00 3.86
255 331 2.957680 TGACCAAACTGAACATGCATGT 59.042 40.909 26.61 26.61 44.20 3.21
324 444 2.416431 GCCAACTGAAACATGCATCCTC 60.416 50.000 0.00 0.00 0.00 3.71
722 950 7.278646 GCAAACAGAGGAAAAAGTCAGAAAAAT 59.721 33.333 0.00 0.00 0.00 1.82
803 1046 6.912591 GCAACTAACATAACCATTCTATGCAC 59.087 38.462 0.00 0.00 31.12 4.57
1053 1352 2.092753 TGATCTCATTGAGTTGCCTCCC 60.093 50.000 13.23 0.00 36.86 4.30
1096 1395 0.179048 TATGGATCAGCAGCAACCCG 60.179 55.000 0.00 0.00 0.00 5.28
1115 1414 0.953003 GGCGTACCACTAGGAGCTAG 59.047 60.000 0.00 0.00 39.72 3.42
1139 1438 5.824624 GTGCTGATTATGGGAGAGAAAATGA 59.175 40.000 0.00 0.00 0.00 2.57
1280 1609 0.036952 ACTCTTGATGACACGGGCAG 60.037 55.000 0.00 0.00 0.00 4.85
1281 1610 0.036952 CTCTTGATGACACGGGCAGT 60.037 55.000 0.00 0.00 0.00 4.40
1323 1655 3.954904 CAACTAGGACTAAGCTAGGAGCA 59.045 47.826 0.64 0.00 45.56 4.26
1502 1836 0.039911 ACCTCTAGGCGGACAACTCT 59.960 55.000 6.07 0.00 39.32 3.24
1599 1934 0.178918 CTCCTCCTATCCTGGACCCC 60.179 65.000 0.00 0.00 31.94 4.95
1698 2033 9.397280 GCTGGTCCTAGTAAGAAAAATAAGAAT 57.603 33.333 0.00 0.00 0.00 2.40
1739 2074 3.077359 AGTAGACTCAATGCAAGGCAAC 58.923 45.455 0.00 0.00 43.62 4.17
1840 2175 6.538945 AACCTTTGTTGTCCAAATACTTGT 57.461 33.333 0.00 0.00 42.02 3.16
1864 2199 1.833630 CACACCAAGGCATCTCTCCTA 59.166 52.381 0.00 0.00 32.65 2.94
1867 2202 4.101585 CACACCAAGGCATCTCTCCTAATA 59.898 45.833 0.00 0.00 32.65 0.98
1874 2209 6.582929 AGGCATCTCTCCTAATAAAAAGGT 57.417 37.500 0.00 0.00 35.48 3.50
1926 2266 8.818622 ACTTGACTACAGGTGTGTTCTATATA 57.181 34.615 0.00 0.00 38.19 0.86
1933 2273 7.035840 ACAGGTGTGTTCTATATACCTTACG 57.964 40.000 0.00 0.00 39.63 3.18
1934 2274 6.604795 ACAGGTGTGTTCTATATACCTTACGT 59.395 38.462 0.00 0.00 39.63 3.57
2051 2392 7.801104 TCCCATGCTGTTTCTATATCACTTTA 58.199 34.615 0.00 0.00 0.00 1.85
2081 2423 6.237901 TGTTGTGCAACTAGATTACCTTCAT 58.762 36.000 14.97 0.00 41.67 2.57
2131 2479 5.455201 GCAAAATGCAAGTGTTTTTAAAGGC 59.545 36.000 0.00 0.00 44.26 4.35
2132 2480 6.549952 CAAAATGCAAGTGTTTTTAAAGGCA 58.450 32.000 0.00 0.00 0.00 4.75
2151 2499 3.077359 GCACAGCTACTTGTCCATTTCT 58.923 45.455 0.00 0.00 0.00 2.52
2172 2520 1.339055 TGCAACTATCCTCTGTGCCAC 60.339 52.381 0.00 0.00 0.00 5.01
2187 2535 4.790937 TGTGCCACCACATGTCATATTAT 58.209 39.130 0.00 0.00 46.51 1.28
2274 2629 6.872920 TGCAGGACGTATGATGCATATAATA 58.127 36.000 0.00 0.00 43.34 0.98
2276 2631 6.980978 GCAGGACGTATGATGCATATAATAGT 59.019 38.462 0.00 0.00 38.54 2.12
2281 2636 9.388346 GACGTATGATGCATATAATAGTAGAGC 57.612 37.037 0.00 0.00 0.00 4.09
2322 2677 3.419759 CCGTTCGGACCAAAGGCG 61.420 66.667 5.19 0.00 0.00 5.52
2400 2755 2.286950 TGAGACAATTGCGCACTTCAAC 60.287 45.455 11.12 4.81 0.00 3.18
2413 2768 5.718246 CGCACTTCAACGATATACAGAAAG 58.282 41.667 0.00 0.00 0.00 2.62
2482 2837 6.478512 AAGTTGTCAACATATTTTGGGTGT 57.521 33.333 17.78 0.00 0.00 4.16
2525 2880 1.729276 CGGAGGCGTACCACGATTA 59.271 57.895 2.35 0.00 46.05 1.75
2532 2887 3.570975 AGGCGTACCACGATTACATATCA 59.429 43.478 2.35 0.00 46.05 2.15
2543 2898 7.201688 CCACGATTACATATCATTTGACACCAA 60.202 37.037 0.00 0.00 0.00 3.67
2667 3022 1.474077 GCATCGAGCTTTGATTGGGTT 59.526 47.619 0.01 0.00 41.15 4.11
2684 3039 2.355818 GGGTTTTCCGAGCATTCCTAGT 60.356 50.000 0.00 0.00 41.82 2.57
2719 3074 5.297029 GGCAAACCTCCTGATAACTTCATAC 59.703 44.000 0.00 0.00 32.72 2.39
2722 3077 4.631234 ACCTCCTGATAACTTCATACCCA 58.369 43.478 0.00 0.00 32.72 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 75 5.051153 TGTCTACAATGCACGTTGAGTTTA 58.949 37.500 9.50 0.00 33.37 2.01
83 85 7.358352 GCATGTTTAGTTTTGTCTACAATGCAC 60.358 37.037 0.00 0.00 35.55 4.57
94 96 8.076178 GTCAGTAGAATGCATGTTTAGTTTTGT 58.924 33.333 0.00 0.00 0.00 2.83
149 152 6.856426 GGTTGCACAGATTCTACAGTTTTTAC 59.144 38.462 0.00 0.00 0.00 2.01
195 202 5.440610 CTGGCTAGGATACATGTTTTTCCT 58.559 41.667 21.42 21.42 41.43 3.36
196 203 4.036852 GCTGGCTAGGATACATGTTTTTCC 59.963 45.833 2.30 8.81 41.41 3.13
207 216 3.455910 ACATGTTTCAGCTGGCTAGGATA 59.544 43.478 15.13 0.00 0.00 2.59
255 331 1.761784 ACATGTTTTTCAGCTGGCCAA 59.238 42.857 15.13 1.64 0.00 4.52
583 783 7.201857 CCAGGTGAAAGAAGAAAGAAGATTTGT 60.202 37.037 0.00 0.00 0.00 2.83
882 1143 5.165676 CAACACAATCATAAGCACTTGCAT 58.834 37.500 3.62 0.00 45.16 3.96
1096 1395 0.953003 CTAGCTCCTAGTGGTACGCC 59.047 60.000 0.00 0.00 41.54 5.68
1115 1414 5.824624 TCATTTTCTCTCCCATAATCAGCAC 59.175 40.000 0.00 0.00 0.00 4.40
1139 1438 4.341235 TCTGTGTGTAGTAAACAGAGTGCT 59.659 41.667 15.37 0.00 44.01 4.40
1280 1609 1.080569 CCAGGAACATTTGCCGCAC 60.081 57.895 0.00 0.00 0.00 5.34
1281 1610 1.523154 GACCAGGAACATTTGCCGCA 61.523 55.000 0.00 0.00 0.00 5.69
1323 1655 0.603707 CATCACCGTCAACAGCACCT 60.604 55.000 0.00 0.00 0.00 4.00
1599 1934 5.009631 TCAACAGGTTTTGGATCTGGTATG 58.990 41.667 0.00 0.00 33.19 2.39
1698 2033 7.170320 GTCTACTTTATTGTCTCGTGTTTCCAA 59.830 37.037 0.00 0.00 0.00 3.53
1739 2074 5.396484 CATCTAGCAACTTCACCAACATTG 58.604 41.667 0.00 0.00 0.00 2.82
1798 2133 1.737838 TTGTTCACCAGCGGATGATC 58.262 50.000 0.00 0.00 0.00 2.92
1840 2175 1.911357 AGAGATGCCTTGGTGTGATCA 59.089 47.619 0.00 0.00 0.00 2.92
1867 2202 9.777297 ATACAAGATGCATAAAAACACCTTTTT 57.223 25.926 0.00 0.00 41.52 1.94
1874 2209 8.518702 TGCAGTTATACAAGATGCATAAAAACA 58.481 29.630 0.00 0.00 41.65 2.83
1926 2266 7.250032 AGAGGGAAACTTAATTACGTAAGGT 57.750 36.000 14.25 6.83 46.39 3.50
1933 2273 6.651086 ACTGCCTAGAGGGAAACTTAATTAC 58.349 40.000 0.00 0.00 34.22 1.89
1934 2274 6.126854 GGACTGCCTAGAGGGAAACTTAATTA 60.127 42.308 0.00 0.00 34.22 1.40
2051 2392 2.917933 TCTAGTTGCACAACAAGCACT 58.082 42.857 15.40 0.00 42.54 4.40
2131 2479 4.614535 GCAAGAAATGGACAAGTAGCTGTG 60.615 45.833 0.00 0.00 0.00 3.66
2132 2480 3.503748 GCAAGAAATGGACAAGTAGCTGT 59.496 43.478 0.00 0.00 0.00 4.40
2151 2499 1.350684 TGGCACAGAGGATAGTTGCAA 59.649 47.619 0.00 0.00 0.00 4.08
2172 2520 7.308169 CCAGCTACACAATAATATGACATGTGG 60.308 40.741 1.15 0.00 44.24 4.17
2187 2535 1.202746 TGCACACATCCAGCTACACAA 60.203 47.619 0.00 0.00 0.00 3.33
2274 2629 7.009550 TCATCTCAGATCCATAAAGCTCTACT 58.990 38.462 0.00 0.00 0.00 2.57
2276 2631 7.093421 CCATCATCTCAGATCCATAAAGCTCTA 60.093 40.741 0.00 0.00 0.00 2.43
2281 2636 5.411977 GCACCATCATCTCAGATCCATAAAG 59.588 44.000 0.00 0.00 0.00 1.85
2322 2677 9.916397 CGGAAACTTGTACATAGATTTGTTATC 57.084 33.333 0.00 0.00 0.00 1.75
2400 2755 4.174411 TGGATCGGCTTTCTGTATATCG 57.826 45.455 0.00 0.00 0.00 2.92
2413 2768 5.467063 CCTTATAGAAGAAGTTTGGATCGGC 59.533 44.000 0.00 0.00 34.25 5.54
2525 2880 7.828717 TCATGTAGTTGGTGTCAAATGATATGT 59.171 33.333 0.00 0.00 34.28 2.29
2532 2887 4.724399 TGGTCATGTAGTTGGTGTCAAAT 58.276 39.130 0.00 0.00 34.28 2.32
2570 2925 2.813474 CGATGAAGGGCGCGAACA 60.813 61.111 12.10 1.52 0.00 3.18
2667 3022 1.406887 GCCACTAGGAATGCTCGGAAA 60.407 52.381 0.00 0.00 36.89 3.13
2684 3039 0.630673 AGGTTTGCCATCCATAGCCA 59.369 50.000 0.00 0.00 37.19 4.75


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

AutoCloner maintained by Alex Coulton.