Multiple sequence alignment - TraesCS3A01G219700

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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 TraesCS3A01G219700 chr3A 100.000 2225 0 0 1 2225 404469313 404467089 0.000000e+00 4109
1 TraesCS3A01G219700 chr3A 97.593 1454 33 1 1 1454 404460933 404459482 0.000000e+00 2490
2 TraesCS3A01G219700 chr3A 96.129 775 22 6 1455 2225 537116532 537115762 0.000000e+00 1258
3 TraesCS3A01G219700 chr3A 96.680 482 12 3 1455 1935 404459452 404458974 0.000000e+00 798
4 TraesCS3A01G219700 chr3A 83.678 484 73 6 1742 2222 263247125 263247605 3.370000e-123 451
5 TraesCS3A01G219700 chr4A 94.407 1484 52 5 1 1454 147976668 147978150 0.000000e+00 2252
6 TraesCS3A01G219700 chr4A 94.081 1301 66 6 164 1454 147990133 147991432 0.000000e+00 1965
7 TraesCS3A01G219700 chr4A 92.109 697 45 7 1455 2147 147978180 147978870 0.000000e+00 974
8 TraesCS3A01G219700 chr6D 91.703 1145 60 20 827 1937 17866752 17865609 0.000000e+00 1555
9 TraesCS3A01G219700 chr6D 86.306 314 16 15 491 794 136743223 136743519 1.280000e-82 316
10 TraesCS3A01G219700 chr5A 96.645 775 19 5 1455 2225 119193605 119192834 0.000000e+00 1280
11 TraesCS3A01G219700 chr5A 93.040 819 31 4 1 794 396288151 396287334 0.000000e+00 1173
12 TraesCS3A01G219700 chr5A 90.504 516 24 9 303 794 396270714 396270200 0.000000e+00 658
13 TraesCS3A01G219700 chr5A 87.821 468 41 13 1 464 373021286 373020831 3.250000e-148 534
14 TraesCS3A01G219700 chr7A 96.707 577 19 0 878 1454 66124548 66123972 0.000000e+00 961
15 TraesCS3A01G219700 chr7A 96.888 482 12 2 1455 1935 66123942 66123463 0.000000e+00 804
16 TraesCS3A01G219700 chr7A 91.627 418 22 10 89 498 391787472 391787884 1.150000e-157 566
17 TraesCS3A01G219700 chr7A 85.078 449 63 4 1776 2222 402027804 402027358 2.600000e-124 455
18 TraesCS3A01G219700 chrUn 96.888 482 12 2 1455 1935 257350081 257350560 0.000000e+00 804
19 TraesCS3A01G219700 chrUn 96.888 482 12 2 1455 1935 332695715 332695236 0.000000e+00 804
20 TraesCS3A01G219700 chrUn 96.032 252 10 0 1203 1454 257349800 257350051 5.720000e-111 411
21 TraesCS3A01G219700 chrUn 96.032 252 10 0 1203 1454 332695996 332695745 5.720000e-111 411
22 TraesCS3A01G219700 chr6A 84.605 760 97 18 1473 2225 456040482 456041228 0.000000e+00 737
23 TraesCS3A01G219700 chr6A 85.841 678 83 13 1491 2163 401341251 401340582 0.000000e+00 708
24 TraesCS3A01G219700 chr6A 83.285 688 96 18 1545 2225 477456269 477456944 1.130000e-172 616
25 TraesCS3A01G219700 chr6A 88.009 467 41 11 1 464 171351242 171351696 2.510000e-149 538
26 TraesCS3A01G219700 chr6A 88.009 467 41 11 1 464 171359021 171359475 2.510000e-149 538
27 TraesCS3A01G219700 chr2A 82.438 689 102 17 1545 2225 582621812 582621135 3.180000e-163 584
28 TraesCS3A01G219700 chr2A 97.525 202 5 0 275 476 59640837 59641038 1.640000e-91 346
29 TraesCS3A01G219700 chr1A 95.556 360 16 0 3 362 149244614 149244255 5.330000e-161 577
30 TraesCS3A01G219700 chr1A 87.425 334 27 9 474 794 371408374 371408705 9.700000e-99 370
31 TraesCS3A01G219700 chr3D 93.770 305 19 0 859 1163 123146918 123146614 2.010000e-125 459
32 TraesCS3A01G219700 chr3D 93.770 305 19 0 859 1163 123152860 123152556 2.010000e-125 459
33 TraesCS3A01G219700 chr3D 90.635 299 21 3 502 794 77601172 77601469 7.450000e-105 390
34 TraesCS3A01G219700 chr3D 89.865 296 28 2 1155 1448 77989402 77989697 1.610000e-101 379
35 TraesCS3A01G219700 chr2D 93.770 305 19 0 859 1163 198616134 198615830 2.010000e-125 459
36 TraesCS3A01G219700 chr2D 92.787 305 22 0 859 1163 198601208 198600904 2.030000e-120 442
37 TraesCS3A01G219700 chr2D 89.241 316 22 6 491 794 435625602 435625287 3.470000e-103 385
38 TraesCS3A01G219700 chr2D 89.116 294 21 5 502 785 435633590 435633298 2.720000e-94 355
39 TraesCS3A01G219700 chr1D 89.899 297 28 2 1154 1448 79294342 79294046 4.480000e-102 381


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 TraesCS3A01G219700 chr3A 404467089 404469313 2224 True 4109.0 4109 100.0000 1 2225 1 chr3A.!!$R1 2224
1 TraesCS3A01G219700 chr3A 404458974 404460933 1959 True 1644.0 2490 97.1365 1 1935 2 chr3A.!!$R3 1934
2 TraesCS3A01G219700 chr3A 537115762 537116532 770 True 1258.0 1258 96.1290 1455 2225 1 chr3A.!!$R2 770
3 TraesCS3A01G219700 chr4A 147990133 147991432 1299 False 1965.0 1965 94.0810 164 1454 1 chr4A.!!$F1 1290
4 TraesCS3A01G219700 chr4A 147976668 147978870 2202 False 1613.0 2252 93.2580 1 2147 2 chr4A.!!$F2 2146
5 TraesCS3A01G219700 chr6D 17865609 17866752 1143 True 1555.0 1555 91.7030 827 1937 1 chr6D.!!$R1 1110
6 TraesCS3A01G219700 chr5A 119192834 119193605 771 True 1280.0 1280 96.6450 1455 2225 1 chr5A.!!$R1 770
7 TraesCS3A01G219700 chr5A 396287334 396288151 817 True 1173.0 1173 93.0400 1 794 1 chr5A.!!$R4 793
8 TraesCS3A01G219700 chr5A 396270200 396270714 514 True 658.0 658 90.5040 303 794 1 chr5A.!!$R3 491
9 TraesCS3A01G219700 chr7A 66123463 66124548 1085 True 882.5 961 96.7975 878 1935 2 chr7A.!!$R2 1057
10 TraesCS3A01G219700 chrUn 257349800 257350560 760 False 607.5 804 96.4600 1203 1935 2 chrUn.!!$F1 732
11 TraesCS3A01G219700 chrUn 332695236 332695996 760 True 607.5 804 96.4600 1203 1935 2 chrUn.!!$R1 732
12 TraesCS3A01G219700 chr6A 456040482 456041228 746 False 737.0 737 84.6050 1473 2225 1 chr6A.!!$F3 752
13 TraesCS3A01G219700 chr6A 401340582 401341251 669 True 708.0 708 85.8410 1491 2163 1 chr6A.!!$R1 672
14 TraesCS3A01G219700 chr6A 477456269 477456944 675 False 616.0 616 83.2850 1545 2225 1 chr6A.!!$F4 680
15 TraesCS3A01G219700 chr2A 582621135 582621812 677 True 584.0 584 82.4380 1545 2225 1 chr2A.!!$R1 680

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
538 542 0.594028 ACACAGTACGCACACACGAG 60.594 55.0 0.0 0.0 36.7 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2016 1.066858 GGAGGAGAATTGTGACGCTCA 60.067 52.381 0.0 0.0 0.0 4.26 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
538 542 0.594028 ACACAGTACGCACACACGAG 60.594 55.000 0.00 0.00 36.70 4.18
619 623 2.292569 GGCATCGACGAATAGTAGTGGA 59.707 50.000 0.00 0.00 0.00 4.02
706 710 3.634448 AGAGCATCAGCAATACGTAGAGT 59.366 43.478 0.08 0.00 45.49 3.24
838 884 1.609210 TGGTCAGTCGAGCATGGGA 60.609 57.895 0.00 0.00 44.51 4.37
842 888 1.078918 CAGTCGAGCATGGGAAGCA 60.079 57.895 0.00 0.00 0.00 3.91
1016 1074 1.741770 GAATGGACGCGGCTCACTT 60.742 57.895 13.91 4.99 0.00 3.16
1350 1408 0.179100 GCTCTTATCCAGCACGCAGA 60.179 55.000 0.00 0.00 36.82 4.26
1426 1484 1.368641 CCACGCCTTGATCGATGAAA 58.631 50.000 0.54 0.00 0.00 2.69
1475 1562 4.003648 GAGTGTGCATAGTGTAGGCTTTT 58.996 43.478 0.00 0.00 36.27 2.27
1476 1563 4.398319 AGTGTGCATAGTGTAGGCTTTTT 58.602 39.130 0.00 0.00 36.27 1.94
1985 2077 3.372954 CGAGATTTAGGAGCGGTTACAG 58.627 50.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 201 9.554395 TGCTTCAGATAATTCACGGATTAAATA 57.446 29.630 0.00 0.0 0.00 1.40
210 211 4.517285 TGGACCTGCTTCAGATAATTCAC 58.483 43.478 0.00 0.0 32.44 3.18
213 214 4.891756 CCATTGGACCTGCTTCAGATAATT 59.108 41.667 0.00 0.0 32.44 1.40
538 542 2.534019 CGGTGTGTGAGTGTGTGCC 61.534 63.158 0.00 0.0 0.00 5.01
610 614 2.680805 GCTTGCCTGCAATCCACTACTA 60.681 50.000 4.84 0.0 35.20 1.82
619 623 4.430765 GCTGCGCTTGCCTGCAAT 62.431 61.111 9.73 0.0 41.22 3.56
678 682 0.255033 ATTGCTGATGCTCTGCTCCA 59.745 50.000 13.26 0.0 41.21 3.86
833 879 1.741770 GTTCGTCGCTGCTTCCCAT 60.742 57.895 0.00 0.0 0.00 4.00
838 884 2.027024 TCACGTTCGTCGCTGCTT 59.973 55.556 0.00 0.0 44.19 3.91
1016 1074 2.360852 GTCCACGACCTCCCTCGA 60.361 66.667 0.00 0.0 37.11 4.04
1475 1562 8.840833 AAAAACAGAAAGGAGCAAAACTAAAA 57.159 26.923 0.00 0.0 0.00 1.52
1476 1563 8.311109 AGAAAAACAGAAAGGAGCAAAACTAAA 58.689 29.630 0.00 0.0 0.00 1.85
1477 1564 7.836842 AGAAAAACAGAAAGGAGCAAAACTAA 58.163 30.769 0.00 0.0 0.00 2.24
1734 1823 7.872061 TCCATATCCAATTATGGTACTGACT 57.128 36.000 9.64 0.0 45.93 3.41
1924 2016 1.066858 GGAGGAGAATTGTGACGCTCA 60.067 52.381 0.00 0.0 0.00 4.26
2149 2244 1.278127 GTTGTAGAGCTGCCCCTTACA 59.722 52.381 0.00 0.0 0.00 2.41


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

AutoCloner maintained by Alex Coulton.