Multiple sequence alignment - TraesCS5B01G458000

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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 TraesCS5B01G458000 chr5B 100.000 5715 0 0 1 5715 632804940 632810654 0.000000e+00 10554.0
1 TraesCS5B01G458000 chr5B 97.030 5354 96 18 387 5715 625452847 625447532 0.000000e+00 8948.0
2 TraesCS5B01G458000 chr5B 98.118 2816 39 4 2912 5715 629078445 629075632 0.000000e+00 4894.0
3 TraesCS5B01G458000 chr5B 97.051 2916 67 12 1 2902 629081468 629078558 0.000000e+00 4891.0
4 TraesCS5B01G458000 chr5B 95.682 2200 61 6 989 3174 604719190 604717011 0.000000e+00 3506.0
5 TraesCS5B01G458000 chr5B 94.245 1251 26 8 3330 4564 604717014 604715794 0.000000e+00 1869.0
6 TraesCS5B01G458000 chr5B 88.540 733 59 11 4636 5344 604715775 604715044 0.000000e+00 865.0
7 TraesCS5B01G458000 chr5B 94.754 305 16 0 5411 5715 604715046 604714742 5.180000e-130 475.0
8 TraesCS5B01G458000 chr5B 89.655 232 7 9 853 1083 604355269 604355484 4.360000e-71 279.0
9 TraesCS5B01G458000 chr5B 79.062 320 57 7 1147 1458 622977742 622977425 1.610000e-50 211.0
10 TraesCS5B01G458000 chr5B 97.222 108 1 2 853 959 604719774 604719668 1.260000e-41 182.0
11 TraesCS5B01G458000 chr5B 84.375 192 14 8 4490 4673 632809612 632809429 2.120000e-39 174.0
12 TraesCS5B01G458000 chr5B 87.671 146 6 8 4519 4662 625448616 625448751 5.930000e-35 159.0
13 TraesCS5B01G458000 chr5B 85.987 157 10 8 4519 4673 629076716 629076862 2.130000e-34 158.0
14 TraesCS5B01G458000 chr5B 75.758 330 69 10 2198 2520 626803335 626803010 7.670000e-34 156.0
15 TraesCS5B01G458000 chr5B 86.111 144 18 2 2708 2850 394253475 394253617 2.760000e-33 154.0
16 TraesCS5B01G458000 chr5B 86.111 144 18 2 2708 2850 394256133 394256275 2.760000e-33 154.0
17 TraesCS5B01G458000 chr5B 90.090 111 5 2 4565 4673 604715762 604715868 7.720000e-29 139.0
18 TraesCS5B01G458000 chr5B 77.637 237 36 12 2445 2677 627470593 627470370 1.670000e-25 128.0
19 TraesCS5B01G458000 chr5B 72.840 486 87 27 2198 2643 629281355 629281835 2.160000e-24 124.0
20 TraesCS5B01G458000 chr5B 72.840 486 87 27 2198 2643 629363649 629364129 2.160000e-24 124.0
21 TraesCS5B01G458000 chr5B 77.215 237 37 12 2445 2677 623866298 623866075 7.780000e-24 122.0
22 TraesCS5B01G458000 chr5B 83.810 105 10 3 4194 4295 633281230 633281330 6.100000e-15 93.5
23 TraesCS5B01G458000 chr5B 95.000 40 2 0 4490 4529 697609499 697609460 4.780000e-06 63.9
24 TraesCS5B01G458000 chr5D 96.301 5705 122 27 58 5715 498930411 498924749 0.000000e+00 9284.0
25 TraesCS5B01G458000 chr5D 98.529 3264 36 2 2457 5715 501709513 501706257 0.000000e+00 5751.0
26 TraesCS5B01G458000 chr5D 96.394 2191 65 10 225 2404 501711699 501709512 0.000000e+00 3596.0
27 TraesCS5B01G458000 chr5D 81.719 826 131 12 1138 1946 501430244 501429422 0.000000e+00 671.0
28 TraesCS5B01G458000 chr5D 87.347 245 30 1 5472 5715 275164791 275164547 4.360000e-71 279.0
29 TraesCS5B01G458000 chr5D 95.758 165 7 0 3167 3331 478161355 478161191 3.390000e-67 267.0
30 TraesCS5B01G458000 chr5D 84.375 192 14 8 4490 4673 501707299 501707482 2.120000e-39 174.0
31 TraesCS5B01G458000 chr5D 73.672 433 98 14 2101 2522 501439421 501438994 2.760000e-33 154.0
32 TraesCS5B01G458000 chr5D 82.000 150 19 5 4149 4295 501427950 501427806 2.800000e-23 121.0
33 TraesCS5B01G458000 chr5D 84.906 106 7 5 4569 4673 498925861 498925958 1.310000e-16 99.0
34 TraesCS5B01G458000 chr7D 87.343 877 77 23 1 853 434163626 434162760 0.000000e+00 974.0
35 TraesCS5B01G458000 chr7D 87.108 861 80 21 1 852 119561189 119562027 0.000000e+00 946.0
36 TraesCS5B01G458000 chr7D 95.758 165 7 0 3176 3340 174342341 174342177 3.390000e-67 267.0
37 TraesCS5B01G458000 chr2D 88.124 842 66 24 1 823 103170247 103169421 0.000000e+00 970.0
38 TraesCS5B01G458000 chr2D 87.156 872 79 21 1 850 497917480 497918340 0.000000e+00 959.0
39 TraesCS5B01G458000 chr2D 87.903 248 25 4 5469 5713 322504830 322504585 2.610000e-73 287.0
40 TraesCS5B01G458000 chr2D 98.137 161 3 0 3172 3332 519335227 519335067 1.210000e-71 281.0
41 TraesCS5B01G458000 chr2D 92.350 183 10 4 3169 3350 56541158 56540979 2.040000e-64 257.0
42 TraesCS5B01G458000 chr6D 87.086 875 81 18 1 853 428602942 428602078 0.000000e+00 961.0
43 TraesCS5B01G458000 chr3D 88.179 829 69 17 41 853 90351868 90351053 0.000000e+00 961.0
44 TraesCS5B01G458000 chr5A 87.678 844 78 16 23 853 296306782 296305952 0.000000e+00 959.0
45 TraesCS5B01G458000 chr5A 75.691 868 169 26 1118 1953 599556959 599556102 4.150000e-106 396.0
46 TraesCS5B01G458000 chr5A 75.651 768 138 29 1193 1937 629372514 629373255 2.550000e-88 337.0
47 TraesCS5B01G458000 chr5A 74.713 609 114 26 2096 2678 629249618 629249024 9.570000e-58 235.0
48 TraesCS5B01G458000 chr5A 74.465 607 113 27 2096 2678 629373396 629373984 2.070000e-54 224.0
49 TraesCS5B01G458000 chr5A 90.076 131 13 0 2720 2850 571787548 571787678 2.740000e-38 171.0
50 TraesCS5B01G458000 chr5A 86.111 144 18 2 2708 2850 311019856 311019714 2.760000e-33 154.0
51 TraesCS5B01G458000 chr5A 81.935 155 21 5 2466 2613 599555671 599555517 2.160000e-24 124.0
52 TraesCS5B01G458000 chr1D 86.483 873 87 17 1 855 470919863 470919004 0.000000e+00 929.0
53 TraesCS5B01G458000 chr1D 87.755 245 28 1 5469 5711 479896712 479896956 9.370000e-73 285.0
54 TraesCS5B01G458000 chr1D 96.894 161 5 0 3171 3331 458883508 458883668 2.620000e-68 270.0
55 TraesCS5B01G458000 chr3B 81.609 870 136 12 1111 1959 462100099 462099233 0.000000e+00 699.0
56 TraesCS5B01G458000 chr3B 83.240 179 23 7 3003 3180 462097574 462097402 2.130000e-34 158.0
57 TraesCS5B01G458000 chr2B 85.056 629 78 10 1142 1754 667422783 667422155 1.350000e-175 627.0
58 TraesCS5B01G458000 chr2B 77.551 539 81 17 2011 2524 667421976 667421453 7.250000e-74 289.0
59 TraesCS5B01G458000 chr2B 83.389 301 46 3 5172 5471 179147159 179147456 5.640000e-70 276.0
60 TraesCS5B01G458000 chr2B 82.909 275 44 3 5198 5471 390610965 390610693 1.590000e-60 244.0
61 TraesCS5B01G458000 chr2A 88.250 400 35 8 1145 1533 699529840 699529442 8.670000e-128 468.0
62 TraesCS5B01G458000 chr2A 77.909 593 91 13 1955 2523 699527576 699527000 3.300000e-87 333.0
63 TraesCS5B01G458000 chr2A 87.654 243 26 3 5469 5709 487998041 487998281 4.360000e-71 279.0
64 TraesCS5B01G458000 chr3A 87.552 241 28 1 5233 5471 172628229 172627989 1.570000e-70 278.0
65 TraesCS5B01G458000 chr3A 82.759 319 48 4 5145 5457 746561016 746561333 1.570000e-70 278.0
66 TraesCS5B01G458000 chr4D 81.858 226 38 2 5243 5467 5796433 5796656 2.720000e-43 187.0
67 TraesCS5B01G458000 chr7B 95.000 40 2 0 4490 4529 403298302 403298341 4.780000e-06 63.9


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 TraesCS5B01G458000 chr5B 632804940 632810654 5714 False 10554.0 10554 100.0000 1 5715 1 chr5B.!!$F7 5714
1 TraesCS5B01G458000 chr5B 625447532 625452847 5315 True 8948.0 8948 97.0300 387 5715 1 chr5B.!!$R3 5328
2 TraesCS5B01G458000 chr5B 629075632 629081468 5836 True 4892.5 4894 97.5845 1 5715 2 chr5B.!!$R9 5714
3 TraesCS5B01G458000 chr5B 604714742 604719774 5032 True 1379.4 3506 94.0886 853 5715 5 chr5B.!!$R8 4862
4 TraesCS5B01G458000 chr5D 498924749 498930411 5662 True 9284.0 9284 96.3010 58 5715 1 chr5D.!!$R3 5657
5 TraesCS5B01G458000 chr5D 501706257 501711699 5442 True 4673.5 5751 97.4615 225 5715 2 chr5D.!!$R6 5490
6 TraesCS5B01G458000 chr5D 501427806 501430244 2438 True 396.0 671 81.8595 1138 4295 2 chr5D.!!$R5 3157
7 TraesCS5B01G458000 chr7D 434162760 434163626 866 True 974.0 974 87.3430 1 853 1 chr7D.!!$R2 852
8 TraesCS5B01G458000 chr7D 119561189 119562027 838 False 946.0 946 87.1080 1 852 1 chr7D.!!$F1 851
9 TraesCS5B01G458000 chr2D 103169421 103170247 826 True 970.0 970 88.1240 1 823 1 chr2D.!!$R2 822
10 TraesCS5B01G458000 chr2D 497917480 497918340 860 False 959.0 959 87.1560 1 850 1 chr2D.!!$F1 849
11 TraesCS5B01G458000 chr6D 428602078 428602942 864 True 961.0 961 87.0860 1 853 1 chr6D.!!$R1 852
12 TraesCS5B01G458000 chr3D 90351053 90351868 815 True 961.0 961 88.1790 41 853 1 chr3D.!!$R1 812
13 TraesCS5B01G458000 chr5A 296305952 296306782 830 True 959.0 959 87.6780 23 853 1 chr5A.!!$R1 830
14 TraesCS5B01G458000 chr5A 629372514 629373984 1470 False 280.5 337 75.0580 1193 2678 2 chr5A.!!$F2 1485
15 TraesCS5B01G458000 chr5A 599555517 599556959 1442 True 260.0 396 78.8130 1118 2613 2 chr5A.!!$R4 1495
16 TraesCS5B01G458000 chr5A 629249024 629249618 594 True 235.0 235 74.7130 2096 2678 1 chr5A.!!$R3 582
17 TraesCS5B01G458000 chr1D 470919004 470919863 859 True 929.0 929 86.4830 1 855 1 chr1D.!!$R1 854
18 TraesCS5B01G458000 chr3B 462097402 462100099 2697 True 428.5 699 82.4245 1111 3180 2 chr3B.!!$R1 2069
19 TraesCS5B01G458000 chr2B 667421453 667422783 1330 True 458.0 627 81.3035 1142 2524 2 chr2B.!!$R2 1382
20 TraesCS5B01G458000 chr2A 699527000 699529840 2840 True 400.5 468 83.0795 1145 2523 2 chr2A.!!$R1 1378

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
968 1179 0.466124 GAGACGCTGCCCTATTTCCT 59.534 55.000 0.00 0.00 0.00 3.36 F
1221 1910 1.596477 GGGTGATGCTGGATCGCTC 60.596 63.158 19.73 13.97 40.85 5.03 F
2788 5184 7.063074 ACAGATGTATCTAACACTAAAACGTGC 59.937 37.037 0.00 0.00 42.09 5.34 F
3489 6011 2.094417 CGCAGCCTTCTTTTGCTACTAC 59.906 50.000 0.00 0.00 35.69 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2907 5303 2.157738 GTCCTTGTGCTGAGAATTGCT 58.842 47.619 0.0 0.0 0.0 3.91 R
2908 5304 2.157738 AGTCCTTGTGCTGAGAATTGC 58.842 47.619 0.0 0.0 0.0 3.56 R
3667 6226 4.746466 TGATTGACCCAAACTAACCCAAT 58.254 39.130 0.0 0.0 0.0 3.16 R
5422 8318 1.442769 GGCAGAAAGAGATGTTCGCA 58.557 50.000 0.0 0.0 0.0 5.10 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
75 80 4.149598 AGAGCACGGTATTTTTCCCTTTT 58.850 39.130 0.00 0.00 0.00 2.27
625 797 6.944867 AAAACAAATATTTTTCGCGCAAAC 57.055 29.167 8.75 0.00 0.00 2.93
768 961 2.119611 TCCAGAGGGAGCGTCCAA 59.880 61.111 6.41 0.00 38.64 3.53
800 993 1.807165 GCGAATGACTGAGAGCGCA 60.807 57.895 11.47 0.00 43.45 6.09
862 1073 1.728074 TTGCTCTCGTACGTGTGCG 60.728 57.895 28.21 15.50 44.93 5.34
932 1143 1.302949 GCTGGCCCATTACCTCACA 59.697 57.895 0.00 0.00 0.00 3.58
968 1179 0.466124 GAGACGCTGCCCTATTTCCT 59.534 55.000 0.00 0.00 0.00 3.36
1083 1757 2.212811 AGATCCGATCGCCATGCCT 61.213 57.895 10.32 0.00 0.00 4.75
1221 1910 1.596477 GGGTGATGCTGGATCGCTC 60.596 63.158 19.73 13.97 40.85 5.03
2788 5184 7.063074 ACAGATGTATCTAACACTAAAACGTGC 59.937 37.037 0.00 0.00 42.09 5.34
3489 6011 2.094417 CGCAGCCTTCTTTTGCTACTAC 59.906 50.000 0.00 0.00 35.69 2.73
4674 7486 1.492764 TTTGGGACGGAGGGAGTATC 58.507 55.000 0.00 0.00 0.00 2.24
4677 7489 1.041437 GGGACGGAGGGAGTATCAAG 58.959 60.000 0.00 0.00 36.25 3.02
4742 7554 8.331931 TCCTGTAATCATATGTTTAAGACCCT 57.668 34.615 7.63 0.00 0.00 4.34
4744 7556 8.210946 CCTGTAATCATATGTTTAAGACCCTGA 58.789 37.037 7.63 0.00 0.00 3.86
4771 7583 6.219417 TCAAAAGTTTGAGATTGAAAGCCA 57.781 33.333 2.32 0.00 41.88 4.75
5086 7907 1.132834 CTTGTTCGGCTGCATGCAATA 59.867 47.619 22.88 1.28 45.15 1.90
5091 7912 3.523606 TCGGCTGCATGCAATATTTTT 57.476 38.095 22.88 0.00 45.15 1.94
5154 7975 3.058160 GCGGCTGTGGTTCATGCT 61.058 61.111 0.00 0.00 0.00 3.79
5164 7985 1.315257 GGTTCATGCTGGTCGGCAAT 61.315 55.000 8.64 0.00 45.68 3.56
5422 8318 0.608640 CCTAGTTCAGGCCGTCTTGT 59.391 55.000 0.00 0.00 37.70 3.16
5551 8447 0.515564 GGACAATACGTGTTGCGCTT 59.484 50.000 23.00 5.32 41.96 4.68
5631 8527 2.650322 TGGTATGGGGCAAACTTCCTTA 59.350 45.455 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 80 0.599558 CACGGGTGTACCTCTTTCGA 59.400 55.000 0.44 0.00 36.97 3.71
189 197 0.892358 AGTCACGACCGTGCCTCTTA 60.892 55.000 16.76 0.00 45.04 2.10
394 521 7.161404 GCCTCTCATAAAGGGAAAAACAAAAT 58.839 34.615 0.00 0.00 34.26 1.82
427 554 1.275471 TTGTGCTTTCGCGAGAGTCG 61.275 55.000 25.34 4.35 43.69 4.18
455 582 1.335182 TCATGGTTTTGCTTTCGCGAA 59.665 42.857 19.38 19.38 39.65 4.70
461 588 2.030805 GCGAGAGTCATGGTTTTGCTTT 60.031 45.455 0.00 0.00 0.00 3.51
667 847 1.481363 GACGTTTTGGTTTTCCCCCAA 59.519 47.619 0.00 0.00 40.15 4.12
835 1042 4.787083 CACGTACGAGAGCAACTAGTTAAG 59.213 45.833 24.41 0.00 36.06 1.85
862 1073 0.954452 CTCACTGCTGTTTGGTTCCC 59.046 55.000 0.00 0.00 0.00 3.97
1083 1757 2.705487 ATCTCCTCCTCCAGCCCGA 61.705 63.158 0.00 0.00 0.00 5.14
2902 5298 3.770263 TGTGCTGAGAATTGCTAATGC 57.230 42.857 0.00 0.00 40.20 3.56
2903 5299 4.397103 TCCTTGTGCTGAGAATTGCTAATG 59.603 41.667 0.00 0.00 0.00 1.90
2904 5300 4.397417 GTCCTTGTGCTGAGAATTGCTAAT 59.603 41.667 0.00 0.00 0.00 1.73
2905 5301 3.753272 GTCCTTGTGCTGAGAATTGCTAA 59.247 43.478 0.00 0.00 0.00 3.09
2906 5302 3.008375 AGTCCTTGTGCTGAGAATTGCTA 59.992 43.478 0.00 0.00 0.00 3.49
2907 5303 2.157738 GTCCTTGTGCTGAGAATTGCT 58.842 47.619 0.00 0.00 0.00 3.91
2908 5304 2.157738 AGTCCTTGTGCTGAGAATTGC 58.842 47.619 0.00 0.00 0.00 3.56
3489 6011 3.503363 TGCTTCAGAATAGCACACCAAAG 59.497 43.478 0.00 0.00 43.30 2.77
3667 6226 4.746466 TGATTGACCCAAACTAACCCAAT 58.254 39.130 0.00 0.00 0.00 3.16
4674 7486 6.821031 ACTCTTACTGACAGTAGGTACTTG 57.179 41.667 20.52 11.36 41.75 3.16
4677 7489 7.118390 TCGTTTACTCTTACTGACAGTAGGTAC 59.882 40.741 20.52 12.90 31.47 3.34
5091 7912 9.177608 AGCATTATCTACATCTTTGTTGCTTTA 57.822 29.630 0.00 0.00 38.61 1.85
5164 7985 4.941263 CCATTTTATAGGCCGCTAGCATTA 59.059 41.667 16.45 1.32 46.50 1.90
5422 8318 1.442769 GGCAGAAAGAGATGTTCGCA 58.557 50.000 0.00 0.00 0.00 5.10
5551 8447 3.831911 GAGATGGGGGTTCATTCAACAAA 59.168 43.478 0.00 0.00 36.61 2.83
5631 8527 6.212888 AGTTCACAAAACTTTTCATGAGCT 57.787 33.333 0.00 7.87 0.00 4.09


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

AutoCloner maintained by Alex Coulton.