Multiple sequence alignment - TraesCS7B01G200100

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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 TraesCS7B01G200100 chr7B 100.000 3512 0 0 1 3512 363001626 363005137 0.000000e+00 6486
1 TraesCS7B01G200100 chr7B 96.612 856 17 3 24 878 595538151 595538995 0.000000e+00 1410
2 TraesCS7B01G200100 chr7B 96.612 856 17 3 24 878 595542674 595543518 0.000000e+00 1410
3 TraesCS7B01G200100 chr1B 96.528 3514 114 6 1 3512 465589100 465585593 0.000000e+00 5806
4 TraesCS7B01G200100 chr1B 91.149 3028 209 40 502 3509 464914599 464917587 0.000000e+00 4052
5 TraesCS7B01G200100 chr1B 91.182 2960 231 23 565 3512 556073304 556070363 0.000000e+00 3993
6 TraesCS7B01G200100 chr1B 98.655 818 10 1 1 818 465584429 465583613 0.000000e+00 1448
7 TraesCS7B01G200100 chr6B 90.441 2992 243 35 546 3512 115927058 115924085 0.000000e+00 3901
8 TraesCS7B01G200100 chr5B 89.791 2968 241 41 551 3506 370325034 370322117 0.000000e+00 3746
9 TraesCS7B01G200100 chr4B 89.481 2966 251 42 551 3500 569591556 569594476 0.000000e+00 3692
10 TraesCS7B01G200100 chr3B 89.661 2834 266 22 679 3499 120083366 120080547 0.000000e+00 3585
11 TraesCS7B01G200100 chr3B 88.827 2855 251 49 674 3512 295072534 295069732 0.000000e+00 3443
12 TraesCS7B01G200100 chr3B 88.817 2799 275 32 582 3369 74831193 74828422 0.000000e+00 3400
13 TraesCS7B01G200100 chr3B 85.949 1701 191 30 1824 3500 393193775 393195451 0.000000e+00 1773
14 TraesCS7B01G200100 chr3B 97.613 796 17 2 24 818 133483623 133482829 0.000000e+00 1363
15 TraesCS7B01G200100 chr3B 86.678 1201 121 21 2321 3506 321734862 321733686 0.000000e+00 1295
16 TraesCS7B01G200100 chr3B 94.254 818 42 5 1 818 74827180 74826368 0.000000e+00 1245
17 TraesCS7B01G200100 chr3B 93.773 819 45 6 1 818 682847816 682847003 0.000000e+00 1225
18 TraesCS7B01G200100 chr3B 92.784 97 5 2 3406 3500 291336929 291337025 4.730000e-29 139
19 TraesCS7B01G200100 chr2A 85.472 2953 315 75 582 3509 679108955 679106092 0.000000e+00 2972
20 TraesCS7B01G200100 chr2A 84.952 2080 251 46 249 2303 100909209 100907167 0.000000e+00 2050
21 TraesCS7B01G200100 chr2B 87.270 1194 126 17 2321 3500 337501588 337502769 0.000000e+00 1339
22 TraesCS7B01G200100 chr2B 87.477 1078 111 14 2331 3404 420612815 420611758 0.000000e+00 1221
23 TraesCS7B01G200100 chr7A 82.458 781 77 36 93 821 404876318 404875546 2.300000e-176 628
24 TraesCS7B01G200100 chr7A 89.322 487 39 9 60 539 404880930 404880450 1.800000e-167 599
25 TraesCS7B01G200100 chr2D 87.879 231 25 2 249 477 276795264 276795493 5.780000e-68 268


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 TraesCS7B01G200100 chr7B 363001626 363005137 3511 False 6486.0 6486 100.0000 1 3512 1 chr7B.!!$F1 3511
1 TraesCS7B01G200100 chr7B 595538151 595543518 5367 False 1410.0 1410 96.6120 24 878 2 chr7B.!!$F2 854
2 TraesCS7B01G200100 chr1B 464914599 464917587 2988 False 4052.0 4052 91.1490 502 3509 1 chr1B.!!$F1 3007
3 TraesCS7B01G200100 chr1B 556070363 556073304 2941 True 3993.0 3993 91.1820 565 3512 1 chr1B.!!$R1 2947
4 TraesCS7B01G200100 chr1B 465583613 465589100 5487 True 3627.0 5806 97.5915 1 3512 2 chr1B.!!$R2 3511
5 TraesCS7B01G200100 chr6B 115924085 115927058 2973 True 3901.0 3901 90.4410 546 3512 1 chr6B.!!$R1 2966
6 TraesCS7B01G200100 chr5B 370322117 370325034 2917 True 3746.0 3746 89.7910 551 3506 1 chr5B.!!$R1 2955
7 TraesCS7B01G200100 chr4B 569591556 569594476 2920 False 3692.0 3692 89.4810 551 3500 1 chr4B.!!$F1 2949
8 TraesCS7B01G200100 chr3B 120080547 120083366 2819 True 3585.0 3585 89.6610 679 3499 1 chr3B.!!$R1 2820
9 TraesCS7B01G200100 chr3B 295069732 295072534 2802 True 3443.0 3443 88.8270 674 3512 1 chr3B.!!$R3 2838
10 TraesCS7B01G200100 chr3B 74826368 74831193 4825 True 2322.5 3400 91.5355 1 3369 2 chr3B.!!$R6 3368
11 TraesCS7B01G200100 chr3B 393193775 393195451 1676 False 1773.0 1773 85.9490 1824 3500 1 chr3B.!!$F2 1676
12 TraesCS7B01G200100 chr3B 133482829 133483623 794 True 1363.0 1363 97.6130 24 818 1 chr3B.!!$R2 794
13 TraesCS7B01G200100 chr3B 321733686 321734862 1176 True 1295.0 1295 86.6780 2321 3506 1 chr3B.!!$R4 1185
14 TraesCS7B01G200100 chr3B 682847003 682847816 813 True 1225.0 1225 93.7730 1 818 1 chr3B.!!$R5 817
15 TraesCS7B01G200100 chr2A 679106092 679108955 2863 True 2972.0 2972 85.4720 582 3509 1 chr2A.!!$R2 2927
16 TraesCS7B01G200100 chr2A 100907167 100909209 2042 True 2050.0 2050 84.9520 249 2303 1 chr2A.!!$R1 2054
17 TraesCS7B01G200100 chr2B 337501588 337502769 1181 False 1339.0 1339 87.2700 2321 3500 1 chr2B.!!$F1 1179
18 TraesCS7B01G200100 chr2B 420611758 420612815 1057 True 1221.0 1221 87.4770 2331 3404 1 chr2B.!!$R1 1073
19 TraesCS7B01G200100 chr7A 404875546 404876318 772 True 628.0 628 82.4580 93 821 1 chr7A.!!$R1 728

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
831 913 0.455972 CGATCATTTTGGCGCCGTTT 60.456 50.0 23.9 3.18 0.0 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2630 3171 0.036164 CATGAAACACCTCACCGGGA 59.964 55.0 6.32 0.0 36.97 5.14 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
64 65 0.615331 CCTGCTGCTCCTAACCTTGA 59.385 55.000 0.00 0.00 0.00 3.02
441 444 4.890158 TCTTCATATGTGTGTGGTGTCT 57.110 40.909 1.90 0.00 0.00 3.41
804 885 3.733443 GGGCATAAAAACCCTGCTATG 57.267 47.619 0.00 0.00 43.36 2.23
831 913 0.455972 CGATCATTTTGGCGCCGTTT 60.456 50.000 23.90 3.18 0.00 3.60
935 1019 6.958192 TGATATATCTCTAACCACTAACCCCC 59.042 42.308 13.79 0.00 0.00 5.40
950 1036 6.324561 CTAACCCCCGTTCTAGTTAGTATC 57.675 45.833 0.00 0.00 37.80 2.24
1233 1536 1.067706 CATTTGCCCGCTGAATGTCAA 60.068 47.619 7.67 0.00 0.00 3.18
2434 2972 4.644685 AGAGTGCTTTCAGGTTTTTGCTTA 59.355 37.500 0.00 0.00 0.00 3.09
2630 3171 5.068329 TCGAGAGAGTGCTACATCATCAAAT 59.932 40.000 0.00 0.00 34.84 2.32
2640 3181 2.224606 CATCATCAAATCCCGGTGAGG 58.775 52.381 0.00 0.00 40.63 3.86
2881 3440 3.197983 AGTGCTCAAATCCCTAGTACACC 59.802 47.826 0.00 0.00 0.00 4.16
2976 3536 2.027377 AGTGTCTTCCCATTGAGAGCAG 60.027 50.000 0.00 0.00 0.00 4.24
2977 3537 2.027745 GTGTCTTCCCATTGAGAGCAGA 60.028 50.000 0.00 0.00 0.00 4.26
3010 3570 7.105588 CCACTATGGATTAGCATGCTATGTTA 58.894 38.462 27.35 13.52 40.96 2.41
3085 3645 7.763172 TTTGTTCTTATGCGTTGTTCATTTT 57.237 28.000 0.00 0.00 0.00 1.82
3221 3798 3.135225 TGTAATTGTCGAACCAGGTGTG 58.865 45.455 0.00 0.00 0.00 3.82
3487 4091 1.754226 GGAACCTTTTGGCACAGTCAA 59.246 47.619 0.00 0.00 45.59 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 2.093021 GGGAAGAAGAGAGAAGCAGCAT 60.093 50.000 0.00 0.00 0.00 3.79
804 885 3.482110 GCGCCAAAATGATCGATTGTAAC 59.518 43.478 0.00 0.00 0.00 2.50
831 913 4.100084 TCGACGCTAGTCCCCGGA 62.100 66.667 0.73 0.00 44.28 5.14
1233 1536 3.239449 TGGAGTGTGAGAGTAACCACAT 58.761 45.455 0.00 0.00 43.99 3.21
1864 2168 7.967908 TCCTTGTCTTCTAGTTCATCTTCTTT 58.032 34.615 0.00 0.00 0.00 2.52
2348 2886 6.226052 TCCAAGTCATCAATCGAATATCCAG 58.774 40.000 0.00 0.00 0.00 3.86
2434 2972 2.551032 CAGCATGTAATGGATCGTGCAT 59.449 45.455 11.04 0.00 46.86 3.96
2630 3171 0.036164 CATGAAACACCTCACCGGGA 59.964 55.000 6.32 0.00 36.97 5.14
2640 3181 2.420022 CTCGGAATGGGTCATGAAACAC 59.580 50.000 0.00 0.00 0.00 3.32
2976 3536 5.163343 TGCTAATCCATAGTGGTTAGGTGTC 60.163 44.000 14.42 4.91 39.03 3.67
2977 3537 4.719773 TGCTAATCCATAGTGGTTAGGTGT 59.280 41.667 14.42 0.00 39.03 4.16
3221 3798 1.269621 CCGATCCCGAGAACATGGTAC 60.270 57.143 0.00 0.00 38.22 3.34
3487 4091 6.560253 ACGAAGATTAGCAAGTTCAAATGT 57.440 33.333 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.