Multiple sequence alignment - TraesCS5B01G452300

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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 TraesCS5B01G452300 chr5B 100.000 5783 0 0 1 5783 625113904 625119686 0.000000e+00 10680.0
1 TraesCS5B01G452300 chr5B 99.481 5784 24 5 1 5783 628693457 628699235 0.000000e+00 10510.0
2 TraesCS5B01G452300 chr5B 92.725 2818 139 28 1 2772 629894637 629897434 0.000000e+00 4008.0
3 TraesCS5B01G452300 chr5B 95.851 2338 79 7 224 2547 626837258 626839591 0.000000e+00 3764.0
4 TraesCS5B01G452300 chr5B 95.524 2346 79 8 224 2547 623166282 623168623 0.000000e+00 3727.0
5 TraesCS5B01G452300 chr5B 92.942 2182 131 10 2874 5040 633177217 633175044 0.000000e+00 3155.0
6 TraesCS5B01G452300 chr5B 96.435 1683 58 2 3360 5041 623171482 623173163 0.000000e+00 2774.0
7 TraesCS5B01G452300 chr5B 96.376 1683 58 3 3360 5041 629897439 629899119 0.000000e+00 2767.0
8 TraesCS5B01G452300 chr5B 96.320 1685 56 5 3360 5041 626842449 626844130 0.000000e+00 2763.0
9 TraesCS5B01G452300 chr5B 91.485 1468 57 19 889 2328 633179460 633178033 0.000000e+00 1956.0
10 TraesCS5B01G452300 chr5B 98.122 213 3 1 5241 5453 625120927 625120716 2.550000e-98 370.0
11 TraesCS5B01G452300 chr5B 90.638 235 2 2 2538 2772 623171263 623171477 1.580000e-75 294.0
12 TraesCS5B01G452300 chr5B 90.583 223 20 1 5 226 626837001 626837223 1.580000e-75 294.0
13 TraesCS5B01G452300 chr5B 90.638 235 2 2 2538 2772 626842230 626842444 1.580000e-75 294.0
14 TraesCS5B01G452300 chr5B 90.551 127 10 2 5036 5161 268959422 268959547 3.580000e-37 167.0
15 TraesCS5B01G452300 chr5B 94.253 87 4 1 5156 5242 629899118 629899203 1.310000e-26 132.0
16 TraesCS5B01G452300 chr5B 97.561 41 1 0 5156 5196 626844129 626844169 2.890000e-08 71.3
17 TraesCS5B01G452300 chr5B 95.122 41 2 0 5156 5196 623173162 623173202 1.350000e-06 65.8
18 TraesCS5B01G452300 chr5A 95.374 1578 69 3 3465 5041 625733832 625732258 0.000000e+00 2507.0
19 TraesCS5B01G452300 chr5A 94.070 1602 73 7 889 2478 625738874 625737283 0.000000e+00 2412.0
20 TraesCS5B01G452300 chr5A 94.825 715 25 5 2463 3167 625737251 625736539 0.000000e+00 1105.0
21 TraesCS5B01G452300 chr5A 94.096 271 15 1 3188 3457 625735063 625734793 1.500000e-110 411.0
22 TraesCS5B01G452300 chr5A 86.861 137 17 1 92 227 683610882 683611018 1.000000e-32 152.0
23 TraesCS5B01G452300 chr5A 83.212 137 22 1 92 227 535155224 535155088 2.190000e-24 124.0
24 TraesCS5B01G452300 chr7A 99.079 543 5 0 5241 5783 487478893 487478351 0.000000e+00 976.0
25 TraesCS5B01G452300 chr7A 99.048 210 1 1 5241 5450 487477110 487477318 5.470000e-100 375.0
26 TraesCS5B01G452300 chr6A 83.626 1026 160 7 3755 4775 32898759 32897737 0.000000e+00 957.0
27 TraesCS5B01G452300 chr6A 76.436 1375 212 67 1000 2307 32900824 32899495 4.890000e-180 641.0
28 TraesCS5B01G452300 chr6B 96.558 552 17 1 5232 5783 615607165 615607714 0.000000e+00 913.0
29 TraesCS5B01G452300 chr6B 91.266 561 39 7 5230 5783 507373847 507373290 0.000000e+00 756.0
30 TraesCS5B01G452300 chr6B 83.537 164 27 0 1086 1249 714336614 714336451 2.790000e-33 154.0
31 TraesCS5B01G452300 chr6B 87.288 118 14 1 3251 3367 204946656 204946773 3.640000e-27 134.0
32 TraesCS5B01G452300 chr2D 92.922 551 29 2 5241 5782 81514788 81515337 0.000000e+00 793.0
33 TraesCS5B01G452300 chrUn 97.204 465 13 0 3360 3824 349939120 349939584 0.000000e+00 787.0
34 TraesCS5B01G452300 chrUn 97.204 465 13 0 3360 3824 349941413 349941877 0.000000e+00 787.0
35 TraesCS5B01G452300 chrUn 90.638 235 2 2 2538 2772 349938901 349939115 1.580000e-75 294.0
36 TraesCS5B01G452300 chrUn 90.638 235 2 2 2538 2772 349941194 349941408 1.580000e-75 294.0
37 TraesCS5B01G452300 chr6D 80.687 932 180 0 3806 4737 468096600 468095669 0.000000e+00 725.0
38 TraesCS5B01G452300 chr6D 77.419 1364 203 58 1000 2307 29768994 29770308 0.000000e+00 715.0
39 TraesCS5B01G452300 chr6D 79.676 989 195 6 3790 4775 468057264 468056279 0.000000e+00 708.0
40 TraesCS5B01G452300 chr7B 95.133 226 11 0 5237 5462 656195494 656195719 1.980000e-94 357.0
41 TraesCS5B01G452300 chr1B 94.017 234 12 2 5231 5462 570298558 570298791 2.560000e-93 353.0
42 TraesCS5B01G452300 chr1B 73.839 409 69 20 472 854 676897134 676896738 1.690000e-25 128.0
43 TraesCS5B01G452300 chr5D 85.928 334 35 6 4718 5041 297092971 297092640 4.290000e-91 346.0
44 TraesCS5B01G452300 chr5D 83.333 228 24 6 225 450 421546703 421546488 1.270000e-46 198.0
45 TraesCS5B01G452300 chr5D 89.855 138 12 2 92 227 421546875 421546738 5.960000e-40 176.0
46 TraesCS5B01G452300 chr5D 88.636 44 3 2 736 778 134477346 134477304 1.000000e-02 52.8
47 TraesCS5B01G452300 chr4A 90.000 200 7 3 5594 5783 489436020 489436216 4.480000e-61 246.0
48 TraesCS5B01G452300 chr4A 94.495 109 6 0 5493 5601 489434392 489434500 9.970000e-38 169.0
49 TraesCS5B01G452300 chr3A 79.381 388 46 16 92 448 19187722 19187338 5.790000e-60 243.0
50 TraesCS5B01G452300 chr3A 91.870 123 10 0 5036 5158 720229499 720229621 7.700000e-39 172.0
51 TraesCS5B01G452300 chr4D 89.000 200 9 3 5594 5783 93068223 93068027 9.690000e-58 235.0
52 TraesCS5B01G452300 chr4D 92.500 120 7 2 5039 5157 367720660 367720542 2.770000e-38 171.0
53 TraesCS5B01G452300 chr4D 96.000 100 4 0 5502 5601 93069756 93069657 4.640000e-36 163.0
54 TraesCS5B01G452300 chr4D 91.525 118 10 0 5040 5157 337412286 337412403 4.640000e-36 163.0
55 TraesCS5B01G452300 chr4B 88.500 200 10 3 5594 5783 130623450 130623254 4.510000e-56 230.0
56 TraesCS5B01G452300 chr4B 91.129 124 10 1 5035 5158 183611086 183611208 3.580000e-37 167.0
57 TraesCS5B01G452300 chr4B 94.340 106 6 0 5496 5601 130625061 130624956 4.640000e-36 163.0
58 TraesCS5B01G452300 chr3B 83.099 213 18 8 92 286 596435323 596435111 1.660000e-40 178.0
59 TraesCS5B01G452300 chr7D 75.500 400 75 15 466 854 60274117 60274504 2.140000e-39 174.0
60 TraesCS5B01G452300 chr7D 90.244 123 12 0 5036 5158 46717876 46717998 1.670000e-35 161.0
61 TraesCS5B01G452300 chr2B 91.057 123 9 2 5037 5158 239419438 239419559 1.290000e-36 165.0
62 TraesCS5B01G452300 chr1A 90.244 123 12 0 5036 5158 32469796 32469674 1.670000e-35 161.0


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 TraesCS5B01G452300 chr5B 625113904 625119686 5782 False 10680.000000 10680 100.000000 1 5783 1 chr5B.!!$F2 5782
1 TraesCS5B01G452300 chr5B 628693457 628699235 5778 False 10510.000000 10510 99.481000 1 5783 1 chr5B.!!$F3 5782
2 TraesCS5B01G452300 chr5B 633175044 633179460 4416 True 2555.500000 3155 92.213500 889 5040 2 chr5B.!!$R2 4151
3 TraesCS5B01G452300 chr5B 629894637 629899203 4566 False 2302.333333 4008 94.451333 1 5242 3 chr5B.!!$F6 5241
4 TraesCS5B01G452300 chr5B 623166282 623173202 6920 False 1715.200000 3727 94.429750 224 5196 4 chr5B.!!$F4 4972
5 TraesCS5B01G452300 chr5B 626837001 626844169 7168 False 1437.260000 3764 94.190600 5 5196 5 chr5B.!!$F5 5191
6 TraesCS5B01G452300 chr5A 625732258 625738874 6616 True 1608.750000 2507 94.591250 889 5041 4 chr5A.!!$R2 4152
7 TraesCS5B01G452300 chr7A 487478351 487478893 542 True 976.000000 976 99.079000 5241 5783 1 chr7A.!!$R1 542
8 TraesCS5B01G452300 chr6A 32897737 32900824 3087 True 799.000000 957 80.031000 1000 4775 2 chr6A.!!$R1 3775
9 TraesCS5B01G452300 chr6B 615607165 615607714 549 False 913.000000 913 96.558000 5232 5783 1 chr6B.!!$F2 551
10 TraesCS5B01G452300 chr6B 507373290 507373847 557 True 756.000000 756 91.266000 5230 5783 1 chr6B.!!$R1 553
11 TraesCS5B01G452300 chr2D 81514788 81515337 549 False 793.000000 793 92.922000 5241 5782 1 chr2D.!!$F1 541
12 TraesCS5B01G452300 chrUn 349938901 349941877 2976 False 540.500000 787 93.921000 2538 3824 4 chrUn.!!$F1 1286
13 TraesCS5B01G452300 chr6D 468095669 468096600 931 True 725.000000 725 80.687000 3806 4737 1 chr6D.!!$R2 931
14 TraesCS5B01G452300 chr6D 29768994 29770308 1314 False 715.000000 715 77.419000 1000 2307 1 chr6D.!!$F1 1307
15 TraesCS5B01G452300 chr6D 468056279 468057264 985 True 708.000000 708 79.676000 3790 4775 1 chr6D.!!$R1 985
16 TraesCS5B01G452300 chr4A 489434392 489436216 1824 False 207.500000 246 92.247500 5493 5783 2 chr4A.!!$F1 290

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
205 206 1.153628 GTTGGTCATAGCGAGCGGT 60.154 57.895 0.00 0.00 45.52 5.68 F
1029 1100 1.144716 CTCGCAATCCAGCCTGCTA 59.855 57.895 0.00 0.00 36.38 3.49 F
1107 1181 0.907486 AACTAGATGAGCAGCTGCCA 59.093 50.000 34.39 29.29 43.38 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1038 1109 1.836802 AGAATGAGGAGAAGCTGGACC 59.163 52.381 0.0 0.0 0.00 4.46 R
4755 12986 4.439837 GGTCTACGGGACTTGTTCAGTATC 60.440 50.000 9.9 0.0 43.97 2.24 R
5070 13305 6.357367 AGATACATCCATTTAAGGGACACAC 58.643 40.000 0.0 0.0 37.23 3.82 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
205 206 1.153628 GTTGGTCATAGCGAGCGGT 60.154 57.895 0.00 0.00 45.52 5.68
974 1035 4.331108 AGCTAGCCAAGAAGAAAAAGGAG 58.669 43.478 12.13 0.00 0.00 3.69
979 1040 5.449553 AGCCAAGAAGAAAAAGGAGAGAAA 58.550 37.500 0.00 0.00 0.00 2.52
980 1041 5.893824 AGCCAAGAAGAAAAAGGAGAGAAAA 59.106 36.000 0.00 0.00 0.00 2.29
981 1042 6.040278 AGCCAAGAAGAAAAAGGAGAGAAAAG 59.960 38.462 0.00 0.00 0.00 2.27
982 1043 6.212235 CCAAGAAGAAAAAGGAGAGAAAAGC 58.788 40.000 0.00 0.00 0.00 3.51
987 1052 8.160106 AGAAGAAAAAGGAGAGAAAAGCAGATA 58.840 33.333 0.00 0.00 0.00 1.98
1029 1100 1.144716 CTCGCAATCCAGCCTGCTA 59.855 57.895 0.00 0.00 36.38 3.49
1038 1109 4.087892 AGCCTGCTACCACTGCCG 62.088 66.667 0.00 0.00 0.00 5.69
1107 1181 0.907486 AACTAGATGAGCAGCTGCCA 59.093 50.000 34.39 29.29 43.38 4.92
4755 12986 2.036475 AGATATAGCACACCGGCTTCTG 59.964 50.000 0.00 0.00 42.71 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 206 4.812476 CGTCGCGCCTCCAATCCA 62.812 66.667 0.00 0.00 0.00 3.41
974 1035 0.042621 GCGCGCTATCTGCTTTTCTC 60.043 55.000 26.67 0.00 40.11 2.87
979 1040 2.578163 TTCCTGCGCGCTATCTGCTT 62.578 55.000 33.29 0.00 40.11 3.91
980 1041 3.081311 TTCCTGCGCGCTATCTGCT 62.081 57.895 33.29 0.00 40.11 4.24
981 1042 2.586079 TTCCTGCGCGCTATCTGC 60.586 61.111 33.29 0.55 38.57 4.26
982 1043 0.877649 ATGTTCCTGCGCGCTATCTG 60.878 55.000 33.29 15.37 0.00 2.90
1038 1109 1.836802 AGAATGAGGAGAAGCTGGACC 59.163 52.381 0.00 0.00 0.00 4.46
1107 1181 2.047274 CAGCCCGGACGTGTGATT 60.047 61.111 0.73 0.00 0.00 2.57
4755 12986 4.439837 GGTCTACGGGACTTGTTCAGTATC 60.440 50.000 9.90 0.00 43.97 2.24
5070 13305 6.357367 AGATACATCCATTTAAGGGACACAC 58.643 40.000 0.00 0.00 37.23 3.82


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

AutoCloner maintained by Alex Coulton.