Multiple sequence alignment - TraesCS4A01G351300

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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 TraesCS4A01G351300 chr4A 100.000 3322 0 0 1 3322 627291869 627288548 0.000000e+00 6135
1 TraesCS4A01G351300 chr4A 96.685 2594 73 7 1 2585 627089019 627086430 0.000000e+00 4301
2 TraesCS4A01G351300 chr4A 96.685 2594 73 7 1 2585 627168670 627166081 0.000000e+00 4301
3 TraesCS4A01G351300 chr4A 94.745 2607 110 8 1 2585 627303229 627300628 0.000000e+00 4030
4 TraesCS4A01G351300 chr4A 96.842 2248 62 5 1 2242 627005517 627003273 0.000000e+00 3749
5 TraesCS4A01G351300 chr4A 97.852 745 14 1 2580 3322 627000609 626999865 0.000000e+00 1286
6 TraesCS4A01G351300 chr4A 97.584 745 16 1 2580 3322 627086470 627085726 0.000000e+00 1275
7 TraesCS4A01G351300 chr4A 97.315 745 18 1 2580 3322 627166121 627165377 0.000000e+00 1264
8 TraesCS4A01G351300 chr4A 81.679 1370 186 34 1009 2334 626990380 626989032 0.000000e+00 1079
9 TraesCS4A01G351300 chr4A 83.333 666 82 13 1007 1648 627052559 627051899 3.690000e-164 588
10 TraesCS4A01G351300 chr4A 82.733 666 85 14 1007 1648 627255875 627255216 1.730000e-157 566
11 TraesCS4A01G351300 chr4A 95.389 347 11 3 2242 2585 627000913 627000569 6.270000e-152 547
12 TraesCS4A01G351300 chr4A 79.538 303 51 9 2033 2334 626976639 626976347 4.340000e-49 206
13 TraesCS4A01G351300 chr5B 89.134 2632 219 32 1 2585 684030966 684033577 0.000000e+00 3214
14 TraesCS4A01G351300 chr5B 88.616 2644 222 36 1 2585 684037967 684040590 0.000000e+00 3142
15 TraesCS4A01G351300 chr5B 83.750 1360 168 31 1007 2334 684049584 684050922 0.000000e+00 1238
16 TraesCS4A01G351300 chr5B 92.659 722 45 3 2607 3322 533989649 533988930 0.000000e+00 1033
17 TraesCS4A01G351300 chr5B 73.546 1255 246 52 1112 2321 684061071 684062284 1.860000e-107 399
18 TraesCS4A01G351300 chr5D 91.169 2344 156 27 12 2316 541989247 541991578 0.000000e+00 3134
19 TraesCS4A01G351300 chr5D 95.682 718 27 2 2607 3322 360997154 360996439 0.000000e+00 1151
20 TraesCS4A01G351300 chr5D 91.139 237 10 6 2351 2585 541991579 541991806 8.950000e-81 311
21 TraesCS4A01G351300 chr5D 78.832 274 42 13 2033 2302 542097422 542097683 1.580000e-38 171
22 TraesCS4A01G351300 chr7A 96.296 729 22 4 2597 3322 669696949 669696223 0.000000e+00 1192
23 TraesCS4A01G351300 chr1D 95.404 718 29 2 2607 3322 50507 51222 0.000000e+00 1140
24 TraesCS4A01G351300 chr5A 93.908 673 37 3 2654 3322 645678986 645678314 0.000000e+00 1013
25 TraesCS4A01G351300 chrUn 92.308 702 45 4 2621 3320 70992407 70991713 0.000000e+00 989
26 TraesCS4A01G351300 chrUn 99.065 107 1 0 1 107 387317346 387317240 3.380000e-45 193
27 TraesCS4A01G351300 chr3A 81.395 301 43 11 691 983 675350807 675350512 1.990000e-57 233
28 TraesCS4A01G351300 chr3D 87.363 182 22 1 802 983 540275365 540275185 1.210000e-49 207


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 TraesCS4A01G351300 chr4A 627288548 627291869 3321 True 6135.000000 6135 100.000000 1 3322 1 chr4A.!!$R5 3321
1 TraesCS4A01G351300 chr4A 627300628 627303229 2601 True 4030.000000 4030 94.745000 1 2585 1 chr4A.!!$R6 2584
2 TraesCS4A01G351300 chr4A 627085726 627089019 3293 True 2788.000000 4301 97.134500 1 3322 2 chr4A.!!$R8 3321
3 TraesCS4A01G351300 chr4A 627165377 627168670 3293 True 2782.500000 4301 97.000000 1 3322 2 chr4A.!!$R9 3321
4 TraesCS4A01G351300 chr4A 626999865 627005517 5652 True 1860.666667 3749 96.694333 1 3322 3 chr4A.!!$R7 3321
5 TraesCS4A01G351300 chr4A 626989032 626990380 1348 True 1079.000000 1079 81.679000 1009 2334 1 chr4A.!!$R2 1325
6 TraesCS4A01G351300 chr4A 627051899 627052559 660 True 588.000000 588 83.333000 1007 1648 1 chr4A.!!$R3 641
7 TraesCS4A01G351300 chr4A 627255216 627255875 659 True 566.000000 566 82.733000 1007 1648 1 chr4A.!!$R4 641
8 TraesCS4A01G351300 chr5B 684030966 684033577 2611 False 3214.000000 3214 89.134000 1 2585 1 chr5B.!!$F1 2584
9 TraesCS4A01G351300 chr5B 684037967 684040590 2623 False 3142.000000 3142 88.616000 1 2585 1 chr5B.!!$F2 2584
10 TraesCS4A01G351300 chr5B 684049584 684050922 1338 False 1238.000000 1238 83.750000 1007 2334 1 chr5B.!!$F3 1327
11 TraesCS4A01G351300 chr5B 533988930 533989649 719 True 1033.000000 1033 92.659000 2607 3322 1 chr5B.!!$R1 715
12 TraesCS4A01G351300 chr5B 684061071 684062284 1213 False 399.000000 399 73.546000 1112 2321 1 chr5B.!!$F4 1209
13 TraesCS4A01G351300 chr5D 541989247 541991806 2559 False 1722.500000 3134 91.154000 12 2585 2 chr5D.!!$F2 2573
14 TraesCS4A01G351300 chr5D 360996439 360997154 715 True 1151.000000 1151 95.682000 2607 3322 1 chr5D.!!$R1 715
15 TraesCS4A01G351300 chr7A 669696223 669696949 726 True 1192.000000 1192 96.296000 2597 3322 1 chr7A.!!$R1 725
16 TraesCS4A01G351300 chr1D 50507 51222 715 False 1140.000000 1140 95.404000 2607 3322 1 chr1D.!!$F1 715
17 TraesCS4A01G351300 chr5A 645678314 645678986 672 True 1013.000000 1013 93.908000 2654 3322 1 chr5A.!!$R1 668
18 TraesCS4A01G351300 chrUn 70991713 70992407 694 True 989.000000 989 92.308000 2621 3320 1 chrUn.!!$R1 699

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
695 705 0.179000 GCTGATCTTCACCCGGTCAT 59.821 55.0 0.00 0.0 0.00 3.06 F
1633 1702 0.879765 GTCTTCTTGTCCGAGACCGA 59.120 55.0 2.23 0.0 38.22 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1740 1.812571 CGGCTTTGGCAGAACTAATGT 59.187 47.619 0.00 0.0 40.87 2.71 R
3226 5727 0.249676 CAGCAGTCCAGAGCTCATGT 59.750 55.000 17.77 0.0 39.50 3.21 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
90 91 6.624352 TTTCTGTGAAGTGGAAGATCAAAG 57.376 37.500 0.00 0.00 31.03 2.77
241 242 2.005451 GCACTTAGCCATGAGTGTCTG 58.995 52.381 12.37 0.00 43.24 3.51
307 308 0.260230 TGAGCCTGAGGTCCTAGGAG 59.740 60.000 13.15 0.00 39.89 3.69
470 474 6.874278 TGTTGAGAGAGGATTAATGAAGGA 57.126 37.500 0.00 0.00 0.00 3.36
505 509 1.004560 ACACCACTCACATCTGCCG 60.005 57.895 0.00 0.00 0.00 5.69
592 596 3.819368 TGTGTTCTCAATGTGATGGTGT 58.181 40.909 0.00 0.00 0.00 4.16
671 680 4.892965 AACGCTTGTGCCTGGCCA 62.893 61.111 17.53 4.71 35.36 5.36
695 705 0.179000 GCTGATCTTCACCCGGTCAT 59.821 55.000 0.00 0.00 0.00 3.06
819 842 2.828520 TCTTTCTCTCTCAACCGCATCT 59.171 45.455 0.00 0.00 0.00 2.90
1314 1368 1.065410 TCAACCAGAAAGGGCCCTCA 61.065 55.000 28.84 0.00 43.89 3.86
1621 1690 1.448540 CCTCCGCATGCGTCTTCTT 60.449 57.895 35.55 0.00 37.81 2.52
1633 1702 0.879765 GTCTTCTTGTCCGAGACCGA 59.120 55.000 2.23 0.00 38.22 4.69
1671 1740 9.078990 AGATCACTTCGATTGTTATACCAGATA 57.921 33.333 0.00 0.00 33.17 1.98
2581 5073 2.105649 TGTTCAGTTGGGCTACACATCA 59.894 45.455 0.00 0.00 0.00 3.07
2757 5252 7.761704 TCTTTCTTCTTCTCCAAGATGTATTCG 59.238 37.037 0.00 0.00 38.50 3.34
2777 5273 2.095008 CGATCTCCTGTATGCGCTACAT 60.095 50.000 9.73 0.00 39.58 2.29
2930 5430 2.632544 ATGTCGTCTTCCGCCGTCA 61.633 57.895 0.00 0.00 36.19 4.35
3108 5608 3.126453 AGGATAAAGATGGCAAGGAGGT 58.874 45.455 0.00 0.00 0.00 3.85
3155 5655 4.624913 AGTCTGGGTAATGGAAGATCAGA 58.375 43.478 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 1.739466 TGCGATTGTTGGAGAGAATGC 59.261 47.619 0.00 0.0 0.00 3.56
170 171 5.873179 TTAAGGTCAGCATAAGAAAACGG 57.127 39.130 0.00 0.0 0.00 4.44
241 242 7.660208 CACACTATACAAACCCATATACCTTCC 59.340 40.741 0.00 0.0 0.00 3.46
272 273 5.185442 TCAGGCTCAATCACATTGCATAAAA 59.815 36.000 0.00 0.0 40.05 1.52
307 308 7.048512 AGGCTAACAACTGGTTAATCATACTC 58.951 38.462 0.00 0.0 41.27 2.59
470 474 2.356535 GGTGTCATCCTTTCCTCAGCAT 60.357 50.000 0.00 0.0 0.00 3.79
505 509 5.803020 ATGAAATCGACTCTAAAGTTGGC 57.197 39.130 0.00 0.0 37.48 4.52
592 596 9.562408 AAAGAAAACCTAAAAACACTTCCAAAA 57.438 25.926 0.00 0.0 0.00 2.44
1188 1232 2.126463 CAGACGAAAGAGGCGCGA 60.126 61.111 12.10 0.0 0.00 5.87
1621 1690 2.362503 AGGCATCGGTCTCGGACA 60.363 61.111 6.41 0.0 33.68 4.02
1633 1702 1.918253 GTGATCTCACCCCAGGCAT 59.082 57.895 0.00 0.0 40.85 4.40
1671 1740 1.812571 CGGCTTTGGCAGAACTAATGT 59.187 47.619 0.00 0.0 40.87 2.71
1855 1939 9.237846 GATTAAGATTGAAATTGAATCGTTCCC 57.762 33.333 0.00 0.0 35.36 3.97
1980 2064 3.728845 CTCCAATACCTCCAACCATACG 58.271 50.000 0.00 0.0 0.00 3.06
2757 5252 3.249091 CATGTAGCGCATACAGGAGATC 58.751 50.000 19.79 0.0 46.71 2.75
3119 5619 1.550976 CCAGACTTGGTGTAGAGGGTC 59.449 57.143 0.00 0.0 39.79 4.46
3155 5655 2.375174 TCAACAGATGGCCAAGTACCTT 59.625 45.455 10.96 0.0 0.00 3.50
3226 5727 0.249676 CAGCAGTCCAGAGCTCATGT 59.750 55.000 17.77 0.0 39.50 3.21


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

AutoCloner maintained by Alex Coulton.