Multiple sequence alignment - TraesCS3D01G153800

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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 TraesCS3D01G153800 chr3D 100.000 4043 0 0 1 4043 121269721 121265679 0.000000e+00 7467.0
1 TraesCS3D01G153800 chr3D 97.357 3481 80 5 567 4043 121335113 121331641 0.000000e+00 5908.0
2 TraesCS3D01G153800 chr3D 88.933 253 20 3 10 255 116075153 116074902 5.080000e-79 305.0
3 TraesCS3D01G153800 chr3D 83.333 90 10 3 3954 4038 581971658 581971569 1.200000e-10 78.7
4 TraesCS3D01G153800 chr3B 92.206 2938 189 17 522 3432 146982859 146979935 0.000000e+00 4120.0
5 TraesCS3D01G153800 chr3B 95.275 2603 103 10 833 3432 172981883 172979298 0.000000e+00 4108.0
6 TraesCS3D01G153800 chr3B 92.541 2641 185 8 797 3430 172052044 172054679 0.000000e+00 3775.0
7 TraesCS3D01G153800 chr3B 92.663 2576 178 8 862 3430 172170467 172173038 0.000000e+00 3699.0
8 TraesCS3D01G153800 chr3B 88.315 736 51 17 54 779 172091579 172092289 0.000000e+00 850.0
9 TraesCS3D01G153800 chr3B 93.186 499 31 2 54 550 172211093 172211590 0.000000e+00 730.0
10 TraesCS3D01G153800 chr3B 90.928 485 35 3 104 579 172982451 172981967 0.000000e+00 643.0
11 TraesCS3D01G153800 chr3B 90.667 375 25 6 1 375 146983303 146982939 1.310000e-134 490.0
12 TraesCS3D01G153800 chr3B 95.495 111 4 1 1 110 173000267 173000157 4.150000e-40 176.0
13 TraesCS3D01G153800 chr3B 86.765 136 8 4 645 779 172211621 172211747 4.210000e-30 143.0
14 TraesCS3D01G153800 chr3A 93.216 2609 150 20 862 3454 127858970 127856373 0.000000e+00 3812.0
15 TraesCS3D01G153800 chr3A 96.304 487 16 2 3469 3954 656200073 656200558 0.000000e+00 798.0
16 TraesCS3D01G153800 chr3A 94.054 185 11 0 4 188 127835149 127834965 8.560000e-72 281.0
17 TraesCS3D01G153800 chr3A 94.505 91 3 2 3953 4043 656200503 656200591 5.450000e-29 139.0
18 TraesCS3D01G153800 chr1B 92.654 2641 168 12 833 3468 456714315 456711696 0.000000e+00 3779.0
19 TraesCS3D01G153800 chr1B 89.527 296 13 7 304 593 456714778 456714495 3.840000e-95 359.0
20 TraesCS3D01G153800 chr1D 92.503 2641 172 12 833 3468 341030028 341027409 0.000000e+00 3757.0
21 TraesCS3D01G153800 chr1D 92.344 2547 182 8 902 3441 465903140 465900600 0.000000e+00 3611.0
22 TraesCS3D01G153800 chr1D 78.706 479 36 26 330 782 341030469 341030031 4.010000e-65 259.0
23 TraesCS3D01G153800 chr1D 90.291 103 6 3 797 897 430113581 430113681 9.120000e-27 132.0
24 TraesCS3D01G153800 chr1A 89.192 1101 82 15 833 1916 440780615 440779535 0.000000e+00 1339.0
25 TraesCS3D01G153800 chr1A 88.998 409 28 9 4 406 440781319 440780922 1.310000e-134 490.0
26 TraesCS3D01G153800 chr1A 86.207 261 22 8 3464 3710 294730876 294731136 1.850000e-68 270.0
27 TraesCS3D01G153800 chr1A 80.198 303 21 12 510 782 440780911 440780618 1.480000e-44 191.0
28 TraesCS3D01G153800 chr6D 96.718 579 16 3 3466 4043 385709568 385710144 0.000000e+00 961.0
29 TraesCS3D01G153800 chr7D 96.233 584 14 7 3464 4043 367187842 367188421 0.000000e+00 950.0
30 TraesCS3D01G153800 chr7D 83.853 353 30 15 3468 3805 114482174 114482514 1.090000e-80 311.0
31 TraesCS3D01G153800 chr2B 95.567 564 17 7 3484 4043 767772007 767771448 0.000000e+00 896.0
32 TraesCS3D01G153800 chr2B 77.799 536 44 41 3469 3955 470491844 470491335 1.110000e-65 261.0
33 TraesCS3D01G153800 chr5B 94.320 493 20 4 3464 3954 487458220 487458706 0.000000e+00 749.0
34 TraesCS3D01G153800 chr5B 85.294 374 37 11 3469 3826 426649457 426649828 1.770000e-98 370.0
35 TraesCS3D01G153800 chr5B 94.505 91 3 2 3953 4043 487458651 487458739 5.450000e-29 139.0
36 TraesCS3D01G153800 chr7B 84.270 356 29 13 3468 3808 73997556 73997899 5.040000e-84 322.0
37 TraesCS3D01G153800 chr7B 85.621 153 20 2 3561 3712 651144157 651144006 4.180000e-35 159.0
38 TraesCS3D01G153800 chr7B 79.104 201 28 11 3750 3943 651143995 651143802 4.240000e-25 126.0
39 TraesCS3D01G153800 chr6B 95.699 186 5 2 3861 4043 11434182 11434367 3.060000e-76 296.0
40 TraesCS3D01G153800 chr6B 91.453 117 7 3 3452 3568 11432952 11433065 1.500000e-34 158.0
41 TraesCS3D01G153800 chr2A 88.889 162 18 0 3549 3710 729669021 729668860 2.460000e-47 200.0
42 TraesCS3D01G153800 chr6A 85.870 92 6 7 3953 4038 35270437 35270527 1.550000e-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 TraesCS3D01G153800 chr3D 121265679 121269721 4042 True 7467.000000 7467 100.000000 1 4043 1 chr3D.!!$R2 4042
1 TraesCS3D01G153800 chr3D 121331641 121335113 3472 True 5908.000000 5908 97.357000 567 4043 1 chr3D.!!$R3 3476
2 TraesCS3D01G153800 chr3B 172052044 172054679 2635 False 3775.000000 3775 92.541000 797 3430 1 chr3B.!!$F1 2633
3 TraesCS3D01G153800 chr3B 172170467 172173038 2571 False 3699.000000 3699 92.663000 862 3430 1 chr3B.!!$F3 2568
4 TraesCS3D01G153800 chr3B 172979298 172982451 3153 True 2375.500000 4108 93.101500 104 3432 2 chr3B.!!$R3 3328
5 TraesCS3D01G153800 chr3B 146979935 146983303 3368 True 2305.000000 4120 91.436500 1 3432 2 chr3B.!!$R2 3431
6 TraesCS3D01G153800 chr3B 172091579 172092289 710 False 850.000000 850 88.315000 54 779 1 chr3B.!!$F2 725
7 TraesCS3D01G153800 chr3B 172211093 172211747 654 False 436.500000 730 89.975500 54 779 2 chr3B.!!$F4 725
8 TraesCS3D01G153800 chr3A 127856373 127858970 2597 True 3812.000000 3812 93.216000 862 3454 1 chr3A.!!$R2 2592
9 TraesCS3D01G153800 chr3A 656200073 656200591 518 False 468.500000 798 95.404500 3469 4043 2 chr3A.!!$F1 574
10 TraesCS3D01G153800 chr1B 456711696 456714778 3082 True 2069.000000 3779 91.090500 304 3468 2 chr1B.!!$R1 3164
11 TraesCS3D01G153800 chr1D 465900600 465903140 2540 True 3611.000000 3611 92.344000 902 3441 1 chr1D.!!$R1 2539
12 TraesCS3D01G153800 chr1D 341027409 341030469 3060 True 2008.000000 3757 85.604500 330 3468 2 chr1D.!!$R2 3138
13 TraesCS3D01G153800 chr1A 440779535 440781319 1784 True 673.333333 1339 86.129333 4 1916 3 chr1A.!!$R1 1912
14 TraesCS3D01G153800 chr6D 385709568 385710144 576 False 961.000000 961 96.718000 3466 4043 1 chr6D.!!$F1 577
15 TraesCS3D01G153800 chr7D 367187842 367188421 579 False 950.000000 950 96.233000 3464 4043 1 chr7D.!!$F2 579
16 TraesCS3D01G153800 chr2B 767771448 767772007 559 True 896.000000 896 95.567000 3484 4043 1 chr2B.!!$R2 559
17 TraesCS3D01G153800 chr2B 470491335 470491844 509 True 261.000000 261 77.799000 3469 3955 1 chr2B.!!$R1 486
18 TraesCS3D01G153800 chr5B 487458220 487458739 519 False 444.000000 749 94.412500 3464 4043 2 chr5B.!!$F2 579
19 TraesCS3D01G153800 chr6B 11432952 11434367 1415 False 227.000000 296 93.576000 3452 4043 2 chr6B.!!$F1 591

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
779 870 0.531200 GAACGGTCTCCACTCGGAAT 59.469 55.0 0.0 0.0 42.21 3.01 F
1855 2024 1.595993 CGAGGAGGCCGAGAAGAACA 61.596 60.0 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2554 0.668535 CGATATCGGTCCAGCTGACA 59.331 55.0 17.39 0.0 46.38 3.58 R
3694 3894 0.033601 TGGCAAGTGTGAGTGGGTTT 60.034 50.0 0.00 0.0 0.00 3.27 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
28 29 3.259064 CAGCCTGAAAAATCAGCATTGG 58.741 45.455 0.28 0.00 36.46 3.16
220 230 4.100498 GGATAACGGATCTTACAGTTGGGA 59.900 45.833 0.00 0.00 34.66 4.37
273 284 3.157252 TCGGCCAGGCTCCATCTC 61.157 66.667 12.43 0.00 0.00 2.75
295 306 1.606668 CCACTGCCACAACACGTAAAT 59.393 47.619 0.00 0.00 0.00 1.40
296 307 2.604373 CCACTGCCACAACACGTAAATG 60.604 50.000 0.00 0.00 0.00 2.32
344 357 1.938585 AGACAGACGGATTGGGAGAA 58.061 50.000 0.00 0.00 0.00 2.87
499 518 1.139853 AGGCGGAGATGAATTGAGGAC 59.860 52.381 0.00 0.00 0.00 3.85
502 521 2.196749 CGGAGATGAATTGAGGACACG 58.803 52.381 0.00 0.00 0.00 4.49
546 574 5.449553 AGGGAAAAGAAAAGAAGAAGCTCA 58.550 37.500 0.00 0.00 0.00 4.26
555 583 2.493907 GAAGAAGCTCAGGTCGCCGT 62.494 60.000 0.00 0.00 0.00 5.68
606 671 4.097361 GAGCACCTCCCCGTTCCC 62.097 72.222 0.00 0.00 0.00 3.97
725 804 1.434622 CGTGCACATCCATCTCAGCC 61.435 60.000 18.64 0.00 0.00 4.85
754 845 2.182825 CAGCTACACGTGGACGAATAC 58.817 52.381 21.57 0.12 43.02 1.89
765 856 0.903187 GACGAATACGACGTGAACGG 59.097 55.000 11.56 0.00 43.97 4.44
779 870 0.531200 GAACGGTCTCCACTCGGAAT 59.469 55.000 0.00 0.00 42.21 3.01
1096 1258 3.249189 TGTGCACCCTCCACCCTC 61.249 66.667 15.69 0.00 32.30 4.30
1293 1462 2.741985 CTGTGCCACGATGCCGAA 60.742 61.111 0.00 0.00 39.50 4.30
1614 1783 1.734465 GGAAAACCGCTGACTCTGATG 59.266 52.381 0.00 0.00 0.00 3.07
1709 1878 2.768344 CCTGTATGGCCCTCCCGT 60.768 66.667 0.00 0.00 35.87 5.28
1855 2024 1.595993 CGAGGAGGCCGAGAAGAACA 61.596 60.000 0.00 0.00 0.00 3.18
1970 2139 1.927895 CTGACTCTAATGGACGGCAC 58.072 55.000 0.00 0.00 0.00 5.01
2012 2181 3.255423 TAATGGGCGCCACGAACCA 62.255 57.895 30.85 16.51 39.05 3.67
2372 2541 2.576317 GCTACGTGAGACCGTCGC 60.576 66.667 0.00 0.00 41.29 5.19
2841 3010 1.523711 CATCGGCGCCACCAATAGT 60.524 57.895 28.98 0.00 39.03 2.12
3172 3352 3.582647 TGAGATAAAGGTGGCTCACTTCA 59.417 43.478 5.48 0.00 32.85 3.02
3228 3408 1.153449 CGCCGCCATCAGGAAGTAA 60.153 57.895 0.00 0.00 36.89 2.24
3457 3638 3.506455 TCCTCTCGTCGATCACTTCTTTT 59.494 43.478 0.00 0.00 0.00 2.27
3462 3643 3.367932 TCGTCGATCACTTCTTTTCATGC 59.632 43.478 0.00 0.00 0.00 4.06
3617 3810 3.136443 TCCCGCCTTCATCAACTATGATT 59.864 43.478 0.00 0.00 43.89 2.57
3694 3894 2.992164 GCCACCGCCTAAACCCTA 59.008 61.111 0.00 0.00 0.00 3.53
3695 3895 1.300634 GCCACCGCCTAAACCCTAA 59.699 57.895 0.00 0.00 0.00 2.69
3696 3896 0.322726 GCCACCGCCTAAACCCTAAA 60.323 55.000 0.00 0.00 0.00 1.85
3697 3897 1.456296 CCACCGCCTAAACCCTAAAC 58.544 55.000 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.004733 GCCAATGCTGATTTTTCAGGC 58.995 47.619 5.24 0.00 38.14 4.85
28 29 2.376915 TTGATGTCGTGTTTGTTCGC 57.623 45.000 0.00 0.00 0.00 4.70
220 230 3.160679 AGGATGCTGCTAAAGTGGTTT 57.839 42.857 0.00 0.00 0.00 3.27
273 284 2.668185 TACGTGTTGTGGCAGTGGGG 62.668 60.000 0.00 0.00 0.00 4.96
295 306 5.869649 TCTGCCTAAATGCTATCTACACA 57.130 39.130 0.00 0.00 0.00 3.72
296 307 7.553881 TTTTCTGCCTAAATGCTATCTACAC 57.446 36.000 0.00 0.00 0.00 2.90
412 431 1.077930 CCTCAGGCACCCATCACTG 60.078 63.158 0.00 0.00 0.00 3.66
499 518 2.730090 GCCAAATTGATGTGAGCTCGTG 60.730 50.000 9.64 0.00 0.00 4.35
502 521 2.751259 TCTGCCAAATTGATGTGAGCTC 59.249 45.455 6.82 6.82 0.00 4.09
606 671 2.105649 GGCAGGAGATAGAAGAAAGGGG 59.894 54.545 0.00 0.00 0.00 4.79
725 804 3.435327 TCCACGTGTAGCTGCAAATTAAG 59.565 43.478 15.65 0.00 0.00 1.85
754 845 1.728426 GTGGAGACCGTTCACGTCG 60.728 63.158 0.00 0.00 37.74 5.12
831 978 3.646715 CTCCGGTTGGAAGGCCCA 61.647 66.667 0.00 0.00 45.87 5.36
1019 1181 2.358247 GGTTCGCCGCCTTCTTCA 60.358 61.111 0.00 0.00 0.00 3.02
1096 1258 2.021355 GAGAGCTTCTCCATGGTGTG 57.979 55.000 12.58 8.23 37.55 3.82
1291 1460 2.395690 CACGCGTCTGCCGAATTC 59.604 61.111 9.86 0.00 39.56 2.17
1416 1585 3.059982 CCACGCACCAGGAAGAGA 58.940 61.111 0.00 0.00 0.00 3.10
1747 1916 1.134438 AAGAAGAAGGCCCCGGTCTT 61.134 55.000 0.00 0.00 43.40 3.01
1855 2024 1.135094 ATGAAGATGATGGAGGGCGT 58.865 50.000 0.00 0.00 0.00 5.68
2012 2181 1.224592 GGGTCGATGCTGTTGGGAT 59.775 57.895 0.00 0.00 0.00 3.85
2385 2554 0.668535 CGATATCGGTCCAGCTGACA 59.331 55.000 17.39 0.00 46.38 3.58
2841 3010 3.776969 AGGCAGAGTCAATAATGTCAGGA 59.223 43.478 0.00 0.00 0.00 3.86
3040 3209 1.509463 CGTACTTGCACGCCCTCTA 59.491 57.895 0.00 0.00 34.78 2.43
3172 3352 1.202154 CGCGTACTTCATCGACTCCTT 60.202 52.381 0.00 0.00 0.00 3.36
3228 3408 2.980233 GTCTGCGCAAAGGCCTGT 60.980 61.111 13.05 0.00 36.38 4.00
3457 3638 6.671190 GCATGTTTGCTAGTTATATGCATGA 58.329 36.000 10.16 0.00 45.77 3.07
3617 3810 1.977129 TGTGATCAGATGGACACCACA 59.023 47.619 0.00 0.00 35.80 4.17
3691 3891 1.880027 GCAAGTGTGAGTGGGTTTAGG 59.120 52.381 0.00 0.00 0.00 2.69
3692 3892 1.880027 GGCAAGTGTGAGTGGGTTTAG 59.120 52.381 0.00 0.00 0.00 1.85
3693 3893 1.213182 TGGCAAGTGTGAGTGGGTTTA 59.787 47.619 0.00 0.00 0.00 2.01
3694 3894 0.033601 TGGCAAGTGTGAGTGGGTTT 60.034 50.000 0.00 0.00 0.00 3.27
3695 3895 0.751643 GTGGCAAGTGTGAGTGGGTT 60.752 55.000 0.00 0.00 0.00 4.11
3696 3896 1.152963 GTGGCAAGTGTGAGTGGGT 60.153 57.895 0.00 0.00 0.00 4.51
3697 3897 1.149174 AGTGGCAAGTGTGAGTGGG 59.851 57.895 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.