Multiple sequence alignment - TraesCS3A01G165200

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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 TraesCS3A01G165200 chr3A 100.000 3197 0 0 1 3197 170387409 170390605 0.000000e+00 5904.0
1 TraesCS3A01G165200 chr3A 98.051 1180 23 0 1 1180 170314399 170315578 0.000000e+00 2052.0
2 TraesCS3A01G165200 chr3A 95.885 972 16 1 1 948 170311884 170310913 0.000000e+00 1552.0
3 TraesCS3A01G165200 chr3A 98.421 380 4 1 2793 3172 170310910 170310533 0.000000e+00 667.0
4 TraesCS3A01G165200 chr3A 100.000 263 0 0 1182 1444 170310274 170310536 1.330000e-133 486.0
5 TraesCS3A01G165200 chr3A 82.143 196 25 8 2996 3186 170485820 170486010 3.300000e-35 159.0
6 TraesCS3A01G165200 chr3D 89.756 2294 147 51 251 2522 157753425 157751198 0.000000e+00 2854.0
7 TraesCS3A01G165200 chr3D 89.624 559 21 15 2630 3160 157751080 157750531 0.000000e+00 676.0
8 TraesCS3A01G165200 chrUn 98.269 1444 24 1 1 1444 293322895 293324337 0.000000e+00 2527.0
9 TraesCS3A01G165200 chrUn 96.805 1471 23 1 1 1447 287218551 287217081 0.000000e+00 2435.0
10 TraesCS3A01G165200 chrUn 95.791 974 17 1 1 950 287215736 287216709 0.000000e+00 1550.0
11 TraesCS3A01G165200 chrUn 95.791 974 17 1 1 950 300437132 300436159 0.000000e+00 1550.0
12 TraesCS3A01G165200 chrUn 95.679 972 18 1 1 948 293325685 293324714 0.000000e+00 1541.0
13 TraesCS3A01G165200 chrUn 95.733 914 15 1 59 948 389792198 389791285 0.000000e+00 1450.0
14 TraesCS3A01G165200 chrUn 98.421 380 4 1 2793 3172 293324711 293324334 0.000000e+00 667.0
15 TraesCS3A01G165200 chrUn 98.421 380 4 1 2793 3172 389791282 389790905 0.000000e+00 667.0
16 TraesCS3A01G165200 chrUn 97.403 385 8 1 2788 3172 287216705 287217087 0.000000e+00 654.0
17 TraesCS3A01G165200 chrUn 97.403 385 8 1 2788 3172 300436163 300435781 0.000000e+00 654.0
18 TraesCS3A01G165200 chrUn 100.000 263 0 0 1182 1444 389790646 389790908 1.330000e-133 486.0
19 TraesCS3A01G165200 chrUn 99.612 258 1 0 1187 1444 300435527 300435784 3.730000e-129 472.0
20 TraesCS3A01G165200 chr3B 90.747 1513 75 26 1035 2522 229008960 229007488 0.000000e+00 1958.0
21 TraesCS3A01G165200 chr3B 89.313 655 36 17 2566 3197 229007378 229006735 0.000000e+00 791.0
22 TraesCS3A01G165200 chr3B 82.234 197 27 6 2996 3191 228983687 228983498 2.550000e-36 163.0
23 TraesCS3A01G165200 chr3B 97.917 48 1 0 2519 2566 229007463 229007416 2.040000e-12 84.2
24 TraesCS3A01G165200 chr6D 86.130 1651 119 54 707 2342 438531348 438532903 0.000000e+00 1679.0
25 TraesCS3A01G165200 chr6D 86.253 1353 87 38 707 2022 438524970 438523680 0.000000e+00 1376.0
26 TraesCS3A01G165200 chr6D 91.260 492 25 12 2033 2522 438523700 438523225 0.000000e+00 654.0
27 TraesCS3A01G165200 chr6D 87.040 625 23 23 2566 3160 438519614 438519018 0.000000e+00 652.0
28 TraesCS3A01G165200 chr6D 85.067 375 33 15 307 678 438525327 438524973 8.430000e-96 361.0
29 TraesCS3A01G165200 chr6D 92.369 249 15 4 1 246 438530708 438530955 5.070000e-93 351.0
30 TraesCS3A01G165200 chr6D 91.270 252 16 5 1 249 438525612 438525364 3.950000e-89 339.0
31 TraesCS3A01G165200 chr7B 91.860 86 5 2 2752 2835 750378817 750378902 5.600000e-23 119.0
32 TraesCS3A01G165200 chr7A 92.593 81 6 0 2752 2832 732845103 732845023 2.010000e-22 117.0
33 TraesCS3A01G165200 chr7D 87.805 82 6 2 1483 1564 327491085 327491008 3.400000e-15 93.5
34 TraesCS3A01G165200 chr5A 94.828 58 3 0 1508 1565 1710949 1710892 1.220000e-14 91.6


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 TraesCS3A01G165200 chr3A 170387409 170390605 3196 False 5904.0 5904 100.0000 1 3197 1 chr3A.!!$F1 3196
1 TraesCS3A01G165200 chr3A 170310274 170315578 5304 False 1269.0 2052 99.0255 1 1444 2 chr3A.!!$F3 1443
2 TraesCS3A01G165200 chr3A 170310533 170311884 1351 True 1109.5 1552 97.1530 1 3172 2 chr3A.!!$R1 3171
3 TraesCS3A01G165200 chr3D 157750531 157753425 2894 True 1765.0 2854 89.6900 251 3160 2 chr3D.!!$R1 2909
4 TraesCS3A01G165200 chrUn 293322895 293324337 1442 False 2527.0 2527 98.2690 1 1444 1 chrUn.!!$F1 1443
5 TraesCS3A01G165200 chrUn 287217081 287218551 1470 True 2435.0 2435 96.8050 1 1447 1 chrUn.!!$R1 1446
6 TraesCS3A01G165200 chrUn 293324334 293325685 1351 True 1104.0 1541 97.0500 1 3172 2 chrUn.!!$R2 3171
7 TraesCS3A01G165200 chrUn 287215736 287217087 1351 False 1102.0 1550 96.5970 1 3172 2 chrUn.!!$F4 3171
8 TraesCS3A01G165200 chrUn 300435781 300437132 1351 True 1102.0 1550 96.5970 1 3172 2 chrUn.!!$R3 3171
9 TraesCS3A01G165200 chrUn 389790905 389792198 1293 True 1058.5 1450 97.0770 59 3172 2 chrUn.!!$R4 3113
10 TraesCS3A01G165200 chr3B 229006735 229008960 2225 True 944.4 1958 92.6590 1035 3197 3 chr3B.!!$R2 2162
11 TraesCS3A01G165200 chr6D 438530708 438532903 2195 False 1015.0 1679 89.2495 1 2342 2 chr6D.!!$F1 2341
12 TraesCS3A01G165200 chr6D 438519018 438525612 6594 True 676.4 1376 88.1780 1 3160 5 chr6D.!!$R1 3159

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
406 4559 1.242665 CCTACCGGCCGTAGAGGATC 61.243 65.0 25.46 0.0 46.53 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 6594 0.676782 ACATGCAACTAAGCGACCCC 60.677 55.0 0.0 0.0 37.31 4.95 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
174 4303 2.094675 GTAAACATGGCTGGACTGCAT 58.905 47.619 0.00 0.00 34.04 3.96
406 4559 1.242665 CCTACCGGCCGTAGAGGATC 61.243 65.000 25.46 0.00 46.53 3.36
680 4837 1.663702 CGACGTCACGCTTCCCTTT 60.664 57.895 17.16 0.00 0.00 3.11
796 4977 2.839098 CCAGCTGGGTCCAGTGTT 59.161 61.111 26.14 2.62 45.24 3.32
869 5050 3.926616 TCTCCGCTCGAGAAAAGAAAAT 58.073 40.909 18.75 0.00 44.94 1.82
1605 5821 2.264794 GACGACATCAACCCCGCT 59.735 61.111 0.00 0.00 0.00 5.52
1607 5823 3.499737 CGACATCAACCCCGCTGC 61.500 66.667 0.00 0.00 0.00 5.25
1735 5975 1.296715 CGTGGTGGAAGGAAGAGGG 59.703 63.158 0.00 0.00 0.00 4.30
1858 6098 1.589716 GGTGATTGCACAGCCACCTC 61.590 60.000 14.97 0.00 46.96 3.85
1860 6100 2.360350 ATTGCACAGCCACCTCCG 60.360 61.111 0.00 0.00 0.00 4.63
1890 6130 0.179020 CGCCATTGCCTCCTTATCCA 60.179 55.000 0.00 0.00 0.00 3.41
1891 6131 1.613836 GCCATTGCCTCCTTATCCAG 58.386 55.000 0.00 0.00 0.00 3.86
1947 6187 1.812922 CATCCTGTCACCGCTGCTC 60.813 63.158 0.00 0.00 0.00 4.26
2012 6255 1.381599 GATTGGGCTTGGGCATGGA 60.382 57.895 0.00 0.00 40.87 3.41
2106 6349 1.818785 GTGGAGGCAGCAGCAGATC 60.819 63.158 2.65 0.00 44.61 2.75
2165 6408 2.512515 GGAGCAGGTCATGACGGC 60.513 66.667 25.29 25.29 34.04 5.68
2208 6451 6.106648 TCAGGAAGCTGATTACCTCATATG 57.893 41.667 0.00 0.00 32.10 1.78
2316 6559 5.880332 TGGAAAAGGCATACATACAGAGTTC 59.120 40.000 0.00 0.00 0.00 3.01
2324 6567 3.026630 ACATACAGAGTTCGTGGTGTG 57.973 47.619 0.00 0.00 0.00 3.82
2334 6577 2.254546 TCGTGGTGTGCTTCTCATTT 57.745 45.000 0.00 0.00 0.00 2.32
2342 6585 4.513318 GGTGTGCTTCTCATTTATAGGCTC 59.487 45.833 0.00 0.00 0.00 4.70
2374 6620 3.429822 GGGTCGCTTAGTTGCATGTAGTA 60.430 47.826 0.00 0.00 0.00 1.82
2376 6622 4.421948 GTCGCTTAGTTGCATGTAGTAGT 58.578 43.478 0.00 0.00 0.00 2.73
2377 6623 4.499758 GTCGCTTAGTTGCATGTAGTAGTC 59.500 45.833 0.00 0.00 0.00 2.59
2378 6624 4.157105 TCGCTTAGTTGCATGTAGTAGTCA 59.843 41.667 0.00 0.00 0.00 3.41
2441 6687 6.501781 GGATGATGATCAAAGTTTGTCATCC 58.498 40.000 30.58 30.58 44.83 3.51
2470 6716 3.247173 GCTCACTTTATTCTCTGATGCGG 59.753 47.826 0.00 0.00 0.00 5.69
2488 6734 3.004002 TGCGGTCAGTCGTATAATTCGAT 59.996 43.478 0.00 0.00 39.45 3.59
2499 6745 7.652105 AGTCGTATAATTCGATAAATGCAGTGT 59.348 33.333 0.00 0.00 39.45 3.55
2581 10397 7.719193 TGAAAACAGTATGATCCTTCAAACTCA 59.281 33.333 0.00 0.00 39.69 3.41
2600 10416 6.241207 ACTCATGTGATTTCGTTTTACCAG 57.759 37.500 0.94 0.00 0.00 4.00
2642 10458 3.077359 GTTCTCCTGTCATCCAGTTTGG 58.923 50.000 0.00 0.00 39.74 3.28
2654 10470 3.486383 TCCAGTTTGGGTCAATTCTGTC 58.514 45.455 0.00 0.00 38.32 3.51
2952 10785 1.079681 TCCAACGACACGGCCATAC 60.080 57.895 2.24 0.00 0.00 2.39
2953 10786 1.374885 CCAACGACACGGCCATACA 60.375 57.895 2.24 0.00 0.00 2.29
3188 11055 4.675029 CGACGGCGTCCCCTTGTT 62.675 66.667 31.86 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 4133 4.991776 TCCAAAATCCACTCCAATGTACA 58.008 39.130 0.00 0.00 0.00 2.90
680 4837 8.868916 CAATCCTCAAAAGAAAAAGAAAAACGA 58.131 29.630 0.00 0.00 0.00 3.85
869 5050 1.086696 GAGTGGCTGCATCGCTTTTA 58.913 50.000 0.50 0.00 0.00 1.52
1735 5975 2.705826 CTCAATCTCTTGCGCCGC 59.294 61.111 4.18 0.00 32.11 6.53
1743 5983 1.053264 AGATGGGCGCCTCAATCTCT 61.053 55.000 28.56 18.01 0.00 3.10
1809 6049 1.944676 CTCGAACGCCGTGATAGCC 60.945 63.158 0.00 0.00 39.75 3.93
2012 6255 2.443255 AGAATATCAGCACCCCCGAATT 59.557 45.455 0.00 0.00 0.00 2.17
2072 6315 1.811266 CACTTCTCATCACCGGGCG 60.811 63.158 6.32 0.00 0.00 6.13
2106 6349 0.827368 GGTAGACCTCCAGCTCAAGG 59.173 60.000 9.02 9.02 38.70 3.61
2165 6408 2.724977 TGACCTGAGTTCTTGTAGCG 57.275 50.000 0.00 0.00 0.00 4.26
2208 6451 2.750948 TCGGAGAGTTTTACAGCACAC 58.249 47.619 0.00 0.00 0.00 3.82
2316 6559 4.271049 CCTATAAATGAGAAGCACACCACG 59.729 45.833 0.00 0.00 0.00 4.94
2324 6567 2.739379 GCCGAGCCTATAAATGAGAAGC 59.261 50.000 0.00 0.00 0.00 3.86
2351 6594 0.676782 ACATGCAACTAAGCGACCCC 60.677 55.000 0.00 0.00 37.31 4.95
2374 6620 8.718158 TCATCTCTAACCTTATGATGATGACT 57.282 34.615 0.00 0.00 38.67 3.41
2376 6622 9.152327 AGTTCATCTCTAACCTTATGATGATGA 57.848 33.333 0.00 0.00 41.73 2.92
2377 6623 9.775854 AAGTTCATCTCTAACCTTATGATGATG 57.224 33.333 0.00 0.00 41.73 3.07
2441 6687 6.634805 TCAGAGAATAAAGTGAGCTACAAGG 58.365 40.000 0.00 0.00 0.00 3.61
2470 6716 8.003508 TGCATTTATCGAATTATACGACTGAC 57.996 34.615 0.00 0.00 42.37 3.51
2488 6734 6.719370 AGATTCAAAACCCTACACTGCATTTA 59.281 34.615 0.00 0.00 0.00 1.40
2499 6745 6.552008 ACAAATCTCCAGATTCAAAACCCTA 58.448 36.000 2.24 0.00 43.41 3.53
2581 10397 4.277174 TGCACTGGTAAAACGAAATCACAT 59.723 37.500 0.00 0.00 0.00 3.21
2600 10416 2.119801 ACCACAGAAGATGGATGCAC 57.880 50.000 0.00 0.00 39.87 4.57
2642 10458 4.336713 GGCTTAATCCAGACAGAATTGACC 59.663 45.833 0.00 0.00 0.00 4.02
2654 10470 1.009829 GTGCAGACGGCTTAATCCAG 58.990 55.000 0.00 0.00 45.15 3.86
2784 10607 9.277783 GCATTTCTATTTGTAGATACTGATGGT 57.722 33.333 0.00 0.00 0.00 3.55
2952 10785 1.373497 GTCGTCCTGCAGGAGTGTG 60.373 63.158 35.92 23.78 46.49 3.82
2953 10786 2.920645 CGTCGTCCTGCAGGAGTGT 61.921 63.158 35.92 0.00 46.49 3.55


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

AutoCloner maintained by Alex Coulton.