Multiple sequence alignment - TraesCS2B01G001900

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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 TraesCS2B01G001900 chrUn 100.000 1884 0 0 999 2882 177132882 177130999 0.000000e+00 3480.0
1 TraesCS2B01G001900 chrUn 100.000 1884 0 0 999 2882 306187827 306185944 0.000000e+00 3480.0
2 TraesCS2B01G001900 chrUn 99.808 1565 0 2 3520 5084 364582435 364583996 0.000000e+00 2870.0
3 TraesCS2B01G001900 chrUn 99.870 769 1 0 1 769 177130120 177129352 0.000000e+00 1415.0
4 TraesCS2B01G001900 chrUn 97.009 769 0 1 1 769 315708434 315709179 0.000000e+00 1271.0
5 TraesCS2B01G001900 chrUn 96.296 54 2 0 3520 3573 312185285 312185232 7.010000e-14 89.8
6 TraesCS2B01G001900 chr2B 100.000 1884 0 0 999 2882 1317988 1316105 0.000000e+00 3480.0
7 TraesCS2B01G001900 chr2B 100.000 1884 0 0 999 2882 3787582 3789465 0.000000e+00 3480.0
8 TraesCS2B01G001900 chr2B 100.000 1565 0 0 3520 5084 1315467 1313903 0.000000e+00 2891.0
9 TraesCS2B01G001900 chr2B 99.490 1568 5 2 3520 5084 3789467 3791034 0.000000e+00 2848.0
10 TraesCS2B01G001900 chr2B 100.000 769 0 0 1 769 1318986 1318218 0.000000e+00 1421.0
11 TraesCS2B01G001900 chr2B 97.009 769 0 1 1 769 3784506 3785251 0.000000e+00 1271.0
12 TraesCS2B01G001900 chr2B 81.675 955 117 29 999 1918 4185215 4186146 0.000000e+00 741.0
13 TraesCS2B01G001900 chr2B 81.551 954 119 29 999 1918 3906210 3907140 0.000000e+00 734.0
14 TraesCS2B01G001900 chr2B 87.939 456 55 0 3623 4078 4186789 4187244 5.790000e-149 538.0
15 TraesCS2B01G001900 chr2B 87.500 456 57 0 3623 4078 3907783 3908238 1.250000e-145 527.0
16 TraesCS2B01G001900 chr2B 84.794 388 54 4 2015 2401 4186338 4186721 7.980000e-103 385.0
17 TraesCS2B01G001900 chr2B 84.536 388 55 4 2015 2401 3907332 3907715 3.710000e-101 379.0
18 TraesCS2B01G001900 chr2B 94.222 225 12 1 2659 2882 587934259 587934483 4.870000e-90 342.0
19 TraesCS2B01G001900 chr2B 92.188 64 4 1 3520 3582 458500284 458500221 7.010000e-14 89.8
20 TraesCS2B01G001900 chr2B 94.737 57 3 0 3520 3576 554915529 554915473 7.010000e-14 89.8
21 TraesCS2B01G001900 chr2B 79.245 106 19 3 2482 2587 356349391 356349493 2.540000e-08 71.3
22 TraesCS2B01G001900 chr5A 79.455 1358 196 63 1010 2347 599449010 599447716 0.000000e+00 885.0
23 TraesCS2B01G001900 chr5A 79.189 937 132 35 1002 1924 599390462 599389575 4.380000e-165 592.0
24 TraesCS2B01G001900 chr5A 86.580 462 59 1 3630 4088 599389089 599388628 1.630000e-139 507.0
25 TraesCS2B01G001900 chr5A 81.413 651 88 19 3630 4253 599447583 599446939 7.600000e-138 501.0
26 TraesCS2B01G001900 chr5A 85.263 380 47 4 2014 2393 599389520 599389150 2.870000e-102 383.0
27 TraesCS2B01G001900 chr5A 94.196 224 12 1 2660 2882 581492883 581492660 1.750000e-89 340.0
28 TraesCS2B01G001900 chr2A 80.709 1156 154 48 1273 2401 5785171 5784058 0.000000e+00 835.0
29 TraesCS2B01G001900 chr2A 87.476 511 53 8 3605 4106 5783825 5783317 3.410000e-161 579.0
30 TraesCS2B01G001900 chr2A 94.595 222 11 1 2662 2882 398656748 398656969 4.870000e-90 342.0
31 TraesCS2B01G001900 chr2A 89.764 254 26 0 1002 1255 5785621 5785368 4.910000e-85 326.0
32 TraesCS2B01G001900 chr5B 78.273 1413 199 58 1010 2401 588832551 588831226 0.000000e+00 809.0
33 TraesCS2B01G001900 chr5B 79.087 942 134 39 1002 1924 588778245 588777348 1.580000e-164 590.0
34 TraesCS2B01G001900 chr5B 80.530 642 93 21 3639 4253 588831143 588830507 9.970000e-127 464.0
35 TraesCS2B01G001900 chr5B 84.211 380 51 4 2014 2393 588777292 588776922 1.350000e-95 361.0
36 TraesCS2B01G001900 chr2D 81.188 505 69 13 1108 1610 7719168 7718688 2.870000e-102 383.0
37 TraesCS2B01G001900 chr4B 94.222 225 12 1 2659 2882 379892495 379892719 4.870000e-90 342.0
38 TraesCS2B01G001900 chr4B 94.595 222 11 1 2662 2882 566627627 566627406 4.870000e-90 342.0
39 TraesCS2B01G001900 chr4B 93.778 225 13 1 2659 2882 30668052 30668276 2.270000e-88 337.0
40 TraesCS2B01G001900 chr1A 96.491 57 2 0 3520 3576 566556561 566556617 1.510000e-15 95.3
41 TraesCS2B01G001900 chr3A 96.296 54 2 0 3520 3573 532344641 532344694 7.010000e-14 89.8
42 TraesCS2B01G001900 chr3A 77.982 109 18 6 2482 2587 348335524 348335629 4.250000e-06 63.9
43 TraesCS2B01G001900 chr7B 90.909 66 3 3 3524 3589 232354861 232354799 9.070000e-13 86.1
44 TraesCS2B01G001900 chr5D 93.220 59 2 2 3520 3578 410453841 410453785 9.070000e-13 86.1
45 TraesCS2B01G001900 chr1B 76.852 108 21 4 2482 2587 205200115 205200220 1.980000e-04 58.4


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 TraesCS2B01G001900 chr2B 1313903 1318986 5083 True 2597.333333 3480 100.000000 1 5084 3 chr2B.!!$R3 5083
1 TraesCS2B01G001900 chrUn 306185944 306187827 1883 True 3480.000000 3480 100.000000 999 2882 1 chrUn.!!$R1 1883
2 TraesCS2B01G001900 chrUn 364582435 364583996 1561 False 2870.000000 2870 99.808000 3520 5084 1 chrUn.!!$F2 1564
3 TraesCS2B01G001900 chrUn 177129352 177132882 3530 True 2447.500000 3480 99.935000 1 2882 2 chrUn.!!$R3 2881
4 TraesCS2B01G001900 chrUn 315708434 315709179 745 False 1271.000000 1271 97.009000 1 769 1 chrUn.!!$F1 768
5 TraesCS2B01G001900 chr2B 3784506 3791034 6528 False 2533.000000 3480 98.833000 1 5084 3 chr2B.!!$F3 5083
6 TraesCS2B01G001900 chr2B 4185215 4187244 2029 False 554.666667 741 84.802667 999 4078 3 chr2B.!!$F5 3079
7 TraesCS2B01G001900 chr2B 3906210 3908238 2028 False 546.666667 734 84.529000 999 4078 3 chr2B.!!$F4 3079
8 TraesCS2B01G001900 chr5A 599446939 599449010 2071 True 693.000000 885 80.434000 1010 4253 2 chr5A.!!$R3 3243
9 TraesCS2B01G001900 chr5A 599388628 599390462 1834 True 494.000000 592 83.677333 1002 4088 3 chr5A.!!$R2 3086
10 TraesCS2B01G001900 chr2A 5783317 5785621 2304 True 580.000000 835 85.983000 1002 4106 3 chr2A.!!$R1 3104
11 TraesCS2B01G001900 chr5B 588830507 588832551 2044 True 636.500000 809 79.401500 1010 4253 2 chr5B.!!$R2 3243
12 TraesCS2B01G001900 chr5B 588776922 588778245 1323 True 475.500000 590 81.649000 1002 2393 2 chr5B.!!$R1 1391

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
626 627 1.944024 GGATTCACGTGTGTGTGGAAA 59.056 47.619 16.51 0.0 46.49 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4839 8412 3.087031 AGGCAATGTGAAGTGAGGATTG 58.913 45.455 0.0 0.0 0.0 2.67 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
626 627 1.944024 GGATTCACGTGTGTGTGGAAA 59.056 47.619 16.51 0.0 46.49 3.13
627 628 2.356382 GGATTCACGTGTGTGTGGAAAA 59.644 45.455 16.51 0.0 46.49 2.29
628 629 3.004315 GGATTCACGTGTGTGTGGAAAAT 59.996 43.478 16.51 4.2 46.49 1.82
629 630 3.412981 TTCACGTGTGTGTGGAAAATG 57.587 42.857 16.51 0.0 46.49 2.32
630 631 2.360844 TCACGTGTGTGTGGAAAATGT 58.639 42.857 16.51 0.0 46.49 2.71
631 632 2.750166 TCACGTGTGTGTGGAAAATGTT 59.250 40.909 16.51 0.0 46.49 2.71
632 633 3.105203 CACGTGTGTGTGGAAAATGTTC 58.895 45.455 7.58 0.0 41.34 3.18
633 634 2.750166 ACGTGTGTGTGGAAAATGTTCA 59.250 40.909 0.00 0.0 35.25 3.18
634 635 3.181501 ACGTGTGTGTGGAAAATGTTCAG 60.182 43.478 0.00 0.0 35.25 3.02
635 636 3.181501 CGTGTGTGTGGAAAATGTTCAGT 60.182 43.478 0.00 0.0 35.25 3.41
636 637 4.104776 GTGTGTGTGGAAAATGTTCAGTG 58.895 43.478 0.00 0.0 35.25 3.66
637 638 3.130164 TGTGTGTGGAAAATGTTCAGTGG 59.870 43.478 0.00 0.0 35.25 4.00
638 639 2.692557 TGTGTGGAAAATGTTCAGTGGG 59.307 45.455 0.00 0.0 35.25 4.61
639 640 2.693074 GTGTGGAAAATGTTCAGTGGGT 59.307 45.455 0.00 0.0 35.25 4.51
640 641 3.886505 GTGTGGAAAATGTTCAGTGGGTA 59.113 43.478 0.00 0.0 35.25 3.69
641 642 4.522789 GTGTGGAAAATGTTCAGTGGGTAT 59.477 41.667 0.00 0.0 35.25 2.73
642 643 5.010617 GTGTGGAAAATGTTCAGTGGGTATT 59.989 40.000 0.00 0.0 35.25 1.89
643 644 6.207810 GTGTGGAAAATGTTCAGTGGGTATTA 59.792 38.462 0.00 0.0 35.25 0.98
644 645 6.432783 TGTGGAAAATGTTCAGTGGGTATTAG 59.567 38.462 0.00 0.0 35.25 1.73
645 646 6.657541 GTGGAAAATGTTCAGTGGGTATTAGA 59.342 38.462 0.00 0.0 35.25 2.10
646 647 6.884295 TGGAAAATGTTCAGTGGGTATTAGAG 59.116 38.462 0.00 0.0 35.25 2.43
647 648 7.110155 GGAAAATGTTCAGTGGGTATTAGAGA 58.890 38.462 0.00 0.0 35.25 3.10
648 649 7.610305 GGAAAATGTTCAGTGGGTATTAGAGAA 59.390 37.037 0.00 0.0 35.25 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
626 627 7.496346 TCTTCTCTAATACCCACTGAACATT 57.504 36.000 0.0 0.0 0.0 2.71
627 628 7.682787 ATCTTCTCTAATACCCACTGAACAT 57.317 36.000 0.0 0.0 0.0 2.71
628 629 8.783660 ATATCTTCTCTAATACCCACTGAACA 57.216 34.615 0.0 0.0 0.0 3.18
629 630 9.482627 CAATATCTTCTCTAATACCCACTGAAC 57.517 37.037 0.0 0.0 0.0 3.18
630 631 9.434275 TCAATATCTTCTCTAATACCCACTGAA 57.566 33.333 0.0 0.0 0.0 3.02
631 632 8.861086 GTCAATATCTTCTCTAATACCCACTGA 58.139 37.037 0.0 0.0 0.0 3.41
632 633 8.091449 GGTCAATATCTTCTCTAATACCCACTG 58.909 40.741 0.0 0.0 0.0 3.66
633 634 7.789831 TGGTCAATATCTTCTCTAATACCCACT 59.210 37.037 0.0 0.0 0.0 4.00
634 635 7.963532 TGGTCAATATCTTCTCTAATACCCAC 58.036 38.462 0.0 0.0 0.0 4.61
635 636 8.742125 ATGGTCAATATCTTCTCTAATACCCA 57.258 34.615 0.0 0.0 0.0 4.51
4839 8412 3.087031 AGGCAATGTGAAGTGAGGATTG 58.913 45.455 0.0 0.0 0.0 2.67


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

AutoCloner maintained by Alex Coulton.