Multiple sequence alignment - TraesCS7B01G338500

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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 TraesCS7B01G338500 chr7B 100.000 2873 0 0 1 2873 592866726 592869598 0.000000e+00 5306.0
1 TraesCS7B01G338500 chr7B 98.572 2871 38 3 1 2870 592806935 592809803 0.000000e+00 5072.0
2 TraesCS7B01G338500 chr7B 92.407 1778 100 24 782 2549 592718270 592720022 0.000000e+00 2503.0
3 TraesCS7B01G338500 chr7B 92.308 585 30 6 218 790 592716559 592717140 0.000000e+00 817.0
4 TraesCS7B01G338500 chr7B 85.624 793 85 17 1009 1776 592534840 592534052 0.000000e+00 806.0
5 TraesCS7B01G338500 chr7B 95.381 433 16 3 2117 2549 592912364 592912792 0.000000e+00 686.0
6 TraesCS7B01G338500 chr7A 91.715 1738 78 33 693 2394 634476617 634478324 0.000000e+00 2351.0
7 TraesCS7B01G338500 chr7A 91.821 1675 85 31 427 2076 634463419 634465066 0.000000e+00 2287.0
8 TraesCS7B01G338500 chr7A 90.701 1312 71 22 745 2029 634605253 634606540 0.000000e+00 1700.0
9 TraesCS7B01G338500 chr7A 87.918 687 71 11 52 732 634604254 634604934 0.000000e+00 798.0
10 TraesCS7B01G338500 chr7A 89.817 383 36 3 49 429 634462446 634462827 3.330000e-134 488.0
11 TraesCS7B01G338500 chr7A 83.244 561 54 18 52 607 634475718 634476243 2.000000e-131 479.0
12 TraesCS7B01G338500 chr7D 89.842 1841 114 28 693 2496 549134480 549136284 0.000000e+00 2296.0
13 TraesCS7B01G338500 chr7D 93.031 1277 62 11 815 2085 549274160 549275415 0.000000e+00 1840.0
14 TraesCS7B01G338500 chr7D 84.678 855 97 26 948 1776 548916136 548915290 0.000000e+00 822.0
15 TraesCS7B01G338500 chr7D 90.000 640 52 10 49 682 549133861 549134494 0.000000e+00 817.0
16 TraesCS7B01G338500 chr7D 92.923 325 22 1 2548 2871 544371422 544371746 3.350000e-129 472.0
17 TraesCS7B01G338500 chr7D 86.250 160 16 4 1009 1164 614535605 614535762 4.920000e-38 169.0
18 TraesCS7B01G338500 chr3A 92.308 325 24 1 2548 2871 24682216 24681892 7.250000e-126 460.0
19 TraesCS7B01G338500 chr4B 91.385 325 27 1 2548 2871 107849876 107849552 7.300000e-121 444.0
20 TraesCS7B01G338500 chr5A 91.077 325 28 1 2548 2871 23431699 23432023 3.400000e-119 438.0
21 TraesCS7B01G338500 chr5A 77.857 280 57 5 2597 2873 635563907 635563630 4.920000e-38 169.0
22 TraesCS7B01G338500 chr6B 90.244 328 27 3 2549 2871 116461244 116461571 9.520000e-115 424.0
23 TraesCS7B01G338500 chr2A 90.594 202 17 2 2548 2747 740253457 740253256 1.700000e-67 267.0
24 TraesCS7B01G338500 chr2A 88.732 142 15 1 2730 2870 740251942 740251801 3.810000e-39 172.0
25 TraesCS7B01G338500 chr1B 74.699 332 68 14 2548 2870 288442898 288443222 1.800000e-27 134.0
26 TraesCS7B01G338500 chr1B 97.778 45 1 0 3 47 676720069 676720025 8.530000e-11 78.7


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 TraesCS7B01G338500 chr7B 592866726 592869598 2872 False 5306.0 5306 100.0000 1 2873 1 chr7B.!!$F2 2872
1 TraesCS7B01G338500 chr7B 592806935 592809803 2868 False 5072.0 5072 98.5720 1 2870 1 chr7B.!!$F1 2869
2 TraesCS7B01G338500 chr7B 592716559 592720022 3463 False 1660.0 2503 92.3575 218 2549 2 chr7B.!!$F4 2331
3 TraesCS7B01G338500 chr7B 592534052 592534840 788 True 806.0 806 85.6240 1009 1776 1 chr7B.!!$R1 767
4 TraesCS7B01G338500 chr7A 634475718 634478324 2606 False 1415.0 2351 87.4795 52 2394 2 chr7A.!!$F2 2342
5 TraesCS7B01G338500 chr7A 634462446 634465066 2620 False 1387.5 2287 90.8190 49 2076 2 chr7A.!!$F1 2027
6 TraesCS7B01G338500 chr7A 634604254 634606540 2286 False 1249.0 1700 89.3095 52 2029 2 chr7A.!!$F3 1977
7 TraesCS7B01G338500 chr7D 549274160 549275415 1255 False 1840.0 1840 93.0310 815 2085 1 chr7D.!!$F2 1270
8 TraesCS7B01G338500 chr7D 549133861 549136284 2423 False 1556.5 2296 89.9210 49 2496 2 chr7D.!!$F4 2447
9 TraesCS7B01G338500 chr7D 548915290 548916136 846 True 822.0 822 84.6780 948 1776 1 chr7D.!!$R1 828
10 TraesCS7B01G338500 chr2A 740251801 740253457 1656 True 219.5 267 89.6630 2548 2870 2 chr2A.!!$R1 322

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
749 1999 1.203052 CTACTCCGCAAAACGTCCCTA 59.797 52.381 0.0 0.0 41.42 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2748 6552 3.69046 ACTTGAAATTGGAGGGCTACTG 58.31 45.455 0.0 0.0 0.0 2.74 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
42 43 3.061697 CGAACGGTAGCCATGTTTTCTAC 59.938 47.826 0.00 0.00 33.72 2.59
682 1625 2.271800 CACGGTAGGCTCATCAAGTTC 58.728 52.381 0.00 0.00 0.00 3.01
725 1669 3.118542 GTTGGTGAAACGTCGTCTTAGT 58.881 45.455 0.00 0.00 38.12 2.24
749 1999 1.203052 CTACTCCGCAAAACGTCCCTA 59.797 52.381 0.00 0.00 41.42 3.53
755 2005 2.140717 CGCAAAACGTCCCTAAGAACT 58.859 47.619 0.00 0.00 36.87 3.01
1003 3408 3.444034 TCTCTAGTCAATACGCTGCACTT 59.556 43.478 0.00 0.00 0.00 3.16
1673 4109 2.032681 GGTGCTCCTCGGCAACTT 59.967 61.111 0.00 0.00 45.46 2.66
1681 4117 0.603707 CCTCGGCAACTTGCTCTTCA 60.604 55.000 13.43 0.00 44.28 3.02
1766 4202 0.539438 ATCAAGGCAAACTTCCGGCA 60.539 50.000 0.00 0.00 37.29 5.69
2510 4981 8.627208 AGATTATTATGTGGTGCCAGAATTAG 57.373 34.615 0.00 0.00 29.70 1.73
2728 5199 7.152645 AGCCGAACGATTTATATGAAGTACAT 58.847 34.615 0.00 0.00 42.39 2.29
2775 6579 5.196695 AGCCCTCCAATTTCAAGTAAGATC 58.803 41.667 0.00 0.00 0.00 2.75
2824 6629 2.868583 CGAGTATTCCTGATTGCACCAG 59.131 50.000 8.03 8.03 0.00 4.00
2870 6675 0.803768 CATGCGTGAGTCCTCGAAGG 60.804 60.000 0.00 0.00 36.46 3.46
2871 6676 1.251527 ATGCGTGAGTCCTCGAAGGT 61.252 55.000 8.62 0.00 36.53 3.50
2872 6677 1.289380 GCGTGAGTCCTCGAAGGTT 59.711 57.895 8.62 0.00 36.53 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 4.537965 GGTGCGTATGTCACTATCACTAG 58.462 47.826 8.68 0.00 34.97 2.57
546 1158 1.981256 AGCACGGTTGTTCTTCCAAT 58.019 45.000 0.00 0.00 0.00 3.16
618 1559 2.998279 GCATGGGCTCTTGTGGTGC 61.998 63.158 0.92 0.00 36.96 5.01
682 1625 5.388654 ACTTGATGGGCCCATATTAGAAAG 58.611 41.667 37.57 29.00 36.70 2.62
725 1669 1.669760 CGTTTTGCGGAGTAGGCCA 60.670 57.895 5.01 0.00 36.85 5.36
749 1999 7.323656 CGATTGCAAGTCGAATTTTAAGTTCTT 59.676 33.333 19.81 0.00 41.40 2.52
755 2005 8.783999 TTTTACGATTGCAAGTCGAATTTTAA 57.216 26.923 26.77 16.32 41.40 1.52
2097 4545 8.926715 ACTCCTTTTTAGAAATTCACACAAAC 57.073 30.769 0.00 0.00 0.00 2.93
2269 4738 9.941325 ATAAAATGGTAATGAATTTCACTGCAA 57.059 25.926 0.15 0.00 0.00 4.08
2748 6552 3.690460 ACTTGAAATTGGAGGGCTACTG 58.310 45.455 0.00 0.00 0.00 2.74
2750 6554 5.497474 TCTTACTTGAAATTGGAGGGCTAC 58.503 41.667 0.00 0.00 0.00 3.58
2775 6579 0.443869 CTCGTTCAATTGTGCCTCCG 59.556 55.000 5.13 0.84 0.00 4.63
2824 6629 1.441311 GAGCTAGACTGCCTGGAGC 59.559 63.158 0.00 0.00 44.14 4.70


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

AutoCloner maintained by Alex Coulton.