Multiple sequence alignment - TraesCS7B01G305100

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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 TraesCS7B01G305100 chr7B 100.000 2802 0 0 1 2802 546884866 546887667 0.000000e+00 5175
1 TraesCS7B01G305100 chr7B 97.652 2555 53 2 1 2548 580868783 580866229 0.000000e+00 4379
2 TraesCS7B01G305100 chr7B 93.471 2818 141 8 4 2802 400951241 400948448 0.000000e+00 4145
3 TraesCS7B01G305100 chr7B 94.603 315 17 0 2488 2802 248271116 248270802 3.240000e-134 488
4 TraesCS7B01G305100 chr7B 94.603 315 17 0 2488 2802 580866254 580865940 3.240000e-134 488
5 TraesCS7B01G305100 chr5B 95.560 2815 106 3 1 2802 520578207 520575399 0.000000e+00 4488
6 TraesCS7B01G305100 chr5B 97.104 2555 64 3 1 2548 579531209 579533760 0.000000e+00 4300
7 TraesCS7B01G305100 chr5B 94.921 315 16 0 2488 2802 579533735 579534049 6.970000e-136 494
8 TraesCS7B01G305100 chr6B 97.568 2549 60 2 1 2548 474824370 474826917 0.000000e+00 4362
9 TraesCS7B01G305100 chr6B 97.295 2551 58 4 1 2548 86401657 86404199 0.000000e+00 4318
10 TraesCS7B01G305100 chr6B 94.603 315 17 0 2488 2802 663850239 663850553 3.240000e-134 488
11 TraesCS7B01G305100 chrUn 97.528 2549 56 3 1 2548 304158496 304155954 0.000000e+00 4351
12 TraesCS7B01G305100 chr1A 97.447 2546 64 1 4 2548 479208896 479206351 0.000000e+00 4340
13 TraesCS7B01G305100 chr5A 97.372 2549 60 3 1 2548 549964133 549966675 0.000000e+00 4329
14 TraesCS7B01G305100 chr5A 94.921 315 16 0 2488 2802 549966650 549966964 6.970000e-136 494
15 TraesCS7B01G305100 chr4B 97.260 2555 63 2 1 2548 468283872 468281318 0.000000e+00 4324
16 TraesCS7B01G305100 chr2A 97.058 2549 68 2 1 2548 703204509 703201967 0.000000e+00 4285
17 TraesCS7B01G305100 chr3B 93.619 2821 135 13 1 2802 708112255 708109461 0.000000e+00 4170
18 TraesCS7B01G305100 chr1B 94.937 316 14 2 2488 2802 612200698 612200384 6.970000e-136 494


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 TraesCS7B01G305100 chr7B 546884866 546887667 2801 False 5175.0 5175 100.0000 1 2802 1 chr7B.!!$F1 2801
1 TraesCS7B01G305100 chr7B 400948448 400951241 2793 True 4145.0 4145 93.4710 4 2802 1 chr7B.!!$R2 2798
2 TraesCS7B01G305100 chr7B 580865940 580868783 2843 True 2433.5 4379 96.1275 1 2802 2 chr7B.!!$R3 2801
3 TraesCS7B01G305100 chr5B 520575399 520578207 2808 True 4488.0 4488 95.5600 1 2802 1 chr5B.!!$R1 2801
4 TraesCS7B01G305100 chr5B 579531209 579534049 2840 False 2397.0 4300 96.0125 1 2802 2 chr5B.!!$F1 2801
5 TraesCS7B01G305100 chr6B 474824370 474826917 2547 False 4362.0 4362 97.5680 1 2548 1 chr6B.!!$F2 2547
6 TraesCS7B01G305100 chr6B 86401657 86404199 2542 False 4318.0 4318 97.2950 1 2548 1 chr6B.!!$F1 2547
7 TraesCS7B01G305100 chrUn 304155954 304158496 2542 True 4351.0 4351 97.5280 1 2548 1 chrUn.!!$R1 2547
8 TraesCS7B01G305100 chr1A 479206351 479208896 2545 True 4340.0 4340 97.4470 4 2548 1 chr1A.!!$R1 2544
9 TraesCS7B01G305100 chr5A 549964133 549966964 2831 False 2411.5 4329 96.1465 1 2802 2 chr5A.!!$F1 2801
10 TraesCS7B01G305100 chr4B 468281318 468283872 2554 True 4324.0 4324 97.2600 1 2548 1 chr4B.!!$R1 2547
11 TraesCS7B01G305100 chr2A 703201967 703204509 2542 True 4285.0 4285 97.0580 1 2548 1 chr2A.!!$R1 2547
12 TraesCS7B01G305100 chr3B 708109461 708112255 2794 True 4170.0 4170 93.6190 1 2802 1 chr3B.!!$R1 2801

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
159 160 0.807496 GGAGCTGCTTTCACATGGAC 59.193 55.0 2.53 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 1899 2.752354 CGAAACAATATGGTGAAGGCCA 59.248 45.455 5.01 0.0 43.48 5.36 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
159 160 0.807496 GGAGCTGCTTTCACATGGAC 59.193 55.000 2.53 0.00 0.00 4.02
174 175 7.581213 TCACATGGACTCAAAATAACTTTGT 57.419 32.000 0.00 0.00 44.18 2.83
464 467 4.933330 TCTTTCATATGTAGCTGGACGAC 58.067 43.478 1.90 0.00 0.00 4.34
546 549 3.461773 GCTGGGAGCGTCTGCCTA 61.462 66.667 15.91 4.84 42.66 3.93
876 879 2.031919 AACCCGATGTGCTTGCGA 59.968 55.556 0.00 0.00 0.00 5.10
877 880 1.377202 AACCCGATGTGCTTGCGAT 60.377 52.632 0.00 0.00 0.00 4.58
973 976 5.465724 GTGTATCGTCAGTTTGGTCTTTTCT 59.534 40.000 0.00 0.00 0.00 2.52
1001 1004 2.275418 GCCGGATTGGGTGGACAT 59.725 61.111 5.05 0.00 38.63 3.06
1009 1012 4.482990 GGATTGGGTGGACATGGATAAAT 58.517 43.478 0.00 0.00 0.00 1.40
1250 1253 7.175293 ACCCAATTGCTTTTGATAACTACGTAA 59.825 33.333 0.00 0.00 0.00 3.18
1309 1312 3.742882 CGCCGGCATATAATGAGGATATG 59.257 47.826 28.98 0.00 39.36 1.78
1387 1390 3.170362 CAAGGGCAAGGAGTCCCA 58.830 61.111 5.25 0.00 45.84 4.37
1445 1448 4.202472 CCCCTCTTTACTTTCCTGTTGACT 60.202 45.833 0.00 0.00 0.00 3.41
1469 1472 6.619744 TGTATTACACATGTTTGAATGGCTG 58.380 36.000 0.00 0.00 30.04 4.85
1518 1523 2.932622 GCACCGAGATCAAGAAAGCAGA 60.933 50.000 0.00 0.00 0.00 4.26
1701 1706 3.442625 GCCAAGAAGTTAAGGCGGTTATT 59.557 43.478 0.00 0.00 37.41 1.40
1752 1758 3.378512 TGATGAACCATCTGCCTCTAGT 58.621 45.455 8.22 0.00 41.06 2.57
1893 1899 5.864474 GTGATTCTCACTTGATTACGACACT 59.136 40.000 0.00 0.00 43.73 3.55
2348 2381 6.149633 GCGAACCTGAAGTAATGTTGAATTT 58.850 36.000 0.00 0.00 0.00 1.82
2531 2576 2.813726 TACTGTGTGGCGCCCAACT 61.814 57.895 26.77 9.64 34.18 3.16
2700 2786 8.330466 TCAAAAATTACTACGACATGGTTCAT 57.670 30.769 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
464 467 2.316867 TGTGATCCTGCAACACGCG 61.317 57.895 3.53 3.53 46.97 6.01
546 549 2.125106 GCTCTTCGGGCGTCCAAT 60.125 61.111 6.96 0.00 0.00 3.16
876 879 5.163364 CCGCATAAGCCAGAGATCCTTATAT 60.163 44.000 0.00 0.00 37.52 0.86
877 880 4.160439 CCGCATAAGCCAGAGATCCTTATA 59.840 45.833 0.00 0.00 37.52 0.98
973 976 4.853142 ATCCGGCGGGTGAGGCTA 62.853 66.667 27.98 3.68 33.83 3.93
1001 1004 9.434275 TCTCTTACCTATGAAGTGATTTATCCA 57.566 33.333 0.00 0.00 0.00 3.41
1009 1012 5.658634 ACATGCTCTCTTACCTATGAAGTGA 59.341 40.000 0.00 0.00 0.00 3.41
1229 1232 8.612619 CCATCTTACGTAGTTATCAAAAGCAAT 58.387 33.333 0.00 0.00 37.78 3.56
1250 1253 6.154706 ACTCGAGTAGTTCCAATAAACCATCT 59.845 38.462 18.46 0.00 33.35 2.90
1309 1312 4.035909 TCAAAGTTTACGGGTTCTTCAAGC 59.964 41.667 0.00 0.00 0.00 4.01
1387 1390 4.081087 ACATAGTTAATCACCGGAACAGCT 60.081 41.667 9.46 0.00 0.00 4.24
1445 1448 6.432472 TCAGCCATTCAAACATGTGTAATACA 59.568 34.615 0.00 0.00 44.87 2.29
1469 1472 4.551603 CGGATGAGAAAGAATGAATGCGTC 60.552 45.833 0.00 0.00 0.00 5.19
1518 1523 5.471556 CAGAATAGACTGGCTCTCATCAT 57.528 43.478 0.00 0.00 34.64 2.45
1893 1899 2.752354 CGAAACAATATGGTGAAGGCCA 59.248 45.455 5.01 0.00 43.48 5.36
2304 2337 4.024725 TCGCAAACACAAATACCACACTAC 60.025 41.667 0.00 0.00 0.00 2.73
2531 2576 2.047274 GTAGTGCAGCGCCCAAGA 60.047 61.111 2.29 0.00 0.00 3.02
2680 2766 6.312918 GTGTCATGAACCATGTCGTAGTAATT 59.687 38.462 0.00 0.00 41.98 1.40
2700 2786 9.194271 CATTTGTCATTTGTAATGAATGTGTCA 57.806 29.630 3.83 0.00 41.67 3.58
2743 2829 5.817296 GCATGTGAGATGTTGGTGAACTATA 59.183 40.000 0.00 0.00 32.79 1.31


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

AutoCloner maintained by Alex Coulton.