Multiple sequence alignment - TraesCS7A01G135600

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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 TraesCS7A01G135600 chr7A 100.000 2821 0 0 1 2821 88442288 88439468 0.000000e+00 5210.0
1 TraesCS7A01G135600 chr7A 95.362 2544 85 10 1 2539 88324086 88321571 0.000000e+00 4013.0
2 TraesCS7A01G135600 chr7A 91.976 2829 170 21 10 2821 88128026 88125238 0.000000e+00 3914.0
3 TraesCS7A01G135600 chr7A 91.848 2846 164 25 10 2821 88014769 88011958 0.000000e+00 3908.0
4 TraesCS7A01G135600 chr7A 90.713 2832 184 29 10 2821 88178777 88176005 0.000000e+00 3699.0
5 TraesCS7A01G135600 chr7A 89.963 2142 167 23 700 2821 87456919 87454806 0.000000e+00 2721.0
6 TraesCS7A01G135600 chr7A 88.166 676 54 11 10 672 87457578 87456916 0.000000e+00 782.0
7 TraesCS7A01G135600 chr7D 96.464 2828 89 8 1 2821 87212857 87210034 0.000000e+00 4658.0
8 TraesCS7A01G135600 chr7D 92.509 2830 157 21 10 2821 86768902 86766110 0.000000e+00 4000.0
9 TraesCS7A01G135600 chr7D 92.053 2416 136 19 426 2821 86924515 86922136 0.000000e+00 3347.0
10 TraesCS7A01G135600 chr7D 91.511 2415 150 16 10 2407 86927673 86925297 0.000000e+00 3273.0
11 TraesCS7A01G135600 chr7D 89.100 2477 214 30 360 2821 86801001 86798566 0.000000e+00 3027.0
12 TraesCS7A01G135600 chr7D 86.749 2264 226 31 117 2344 86298583 86296358 0.000000e+00 2451.0
13 TraesCS7A01G135600 chr7B 89.406 2860 199 37 1 2821 35513671 35510877 0.000000e+00 3507.0
14 TraesCS7A01G135600 chr7B 89.206 2659 216 28 196 2817 35313792 35311168 0.000000e+00 3254.0
15 TraesCS7A01G135600 chr7B 93.333 60 4 0 124 183 35314240 35314181 3.870000e-14 89.8


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 TraesCS7A01G135600 chr7A 88439468 88442288 2820 True 5210.0 5210 100.0000 1 2821 1 chr7A.!!$R5 2820
1 TraesCS7A01G135600 chr7A 88321571 88324086 2515 True 4013.0 4013 95.3620 1 2539 1 chr7A.!!$R4 2538
2 TraesCS7A01G135600 chr7A 88125238 88128026 2788 True 3914.0 3914 91.9760 10 2821 1 chr7A.!!$R2 2811
3 TraesCS7A01G135600 chr7A 88011958 88014769 2811 True 3908.0 3908 91.8480 10 2821 1 chr7A.!!$R1 2811
4 TraesCS7A01G135600 chr7A 88176005 88178777 2772 True 3699.0 3699 90.7130 10 2821 1 chr7A.!!$R3 2811
5 TraesCS7A01G135600 chr7A 87454806 87457578 2772 True 1751.5 2721 89.0645 10 2821 2 chr7A.!!$R6 2811
6 TraesCS7A01G135600 chr7D 87210034 87212857 2823 True 4658.0 4658 96.4640 1 2821 1 chr7D.!!$R4 2820
7 TraesCS7A01G135600 chr7D 86766110 86768902 2792 True 4000.0 4000 92.5090 10 2821 1 chr7D.!!$R2 2811
8 TraesCS7A01G135600 chr7D 86922136 86927673 5537 True 3310.0 3347 91.7820 10 2821 2 chr7D.!!$R5 2811
9 TraesCS7A01G135600 chr7D 86798566 86801001 2435 True 3027.0 3027 89.1000 360 2821 1 chr7D.!!$R3 2461
10 TraesCS7A01G135600 chr7D 86296358 86298583 2225 True 2451.0 2451 86.7490 117 2344 1 chr7D.!!$R1 2227
11 TraesCS7A01G135600 chr7B 35510877 35513671 2794 True 3507.0 3507 89.4060 1 2821 1 chr7B.!!$R1 2820
12 TraesCS7A01G135600 chr7B 35311168 35314240 3072 True 1671.9 3254 91.2695 124 2817 2 chr7B.!!$R2 2693

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
489 927 3.694043 TGTGTCACTAGCAGCCAAATA 57.306 42.857 4.27 0.0 0.00 1.40 F
1413 4628 2.414559 CGAGGCAACAATCATGGACAAC 60.415 50.000 0.00 0.0 41.41 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 4775 1.345089 TCCTCGTCGATCCAAAAACCA 59.655 47.619 0.0 0.0 0.00 3.67 R
2696 5969 2.188817 GACAGGGGTCTTAGTGGTGAT 58.811 52.381 0.0 0.0 40.99 3.06 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
304 725 5.309020 AGCCAAGAAATCTGCCTATAGATGA 59.691 40.000 0.00 0.00 37.48 2.92
370 796 6.814954 AGAGAAAGGATATGCTTACCTTCA 57.185 37.500 10.15 0.00 42.25 3.02
489 927 3.694043 TGTGTCACTAGCAGCCAAATA 57.306 42.857 4.27 0.00 0.00 1.40
909 1355 7.438459 CACACAAGAGGGCTATAAATACACTAC 59.562 40.741 0.00 0.00 0.00 2.73
1005 1458 3.983044 ACTACCCACTTTCTCATGGAC 57.017 47.619 0.00 0.00 38.34 4.02
1101 1554 5.856126 ACAAAATCATGTACGACGACAAT 57.144 34.783 0.00 0.00 31.83 2.71
1125 1581 7.692460 TGATGACAAGAACAAGAAGCATAAT 57.308 32.000 0.00 0.00 0.00 1.28
1174 1630 6.147864 TGTTTCCTTCAAAGACCATGAAAG 57.852 37.500 0.00 0.00 36.43 2.62
1413 4628 2.414559 CGAGGCAACAATCATGGACAAC 60.415 50.000 0.00 0.00 41.41 3.32
1557 4775 1.344114 GTTGTTGCCCCACATCAATGT 59.656 47.619 0.00 0.00 39.51 2.71
1624 4843 4.589908 ACCCTCCATTGTCATGTAGTTTC 58.410 43.478 0.00 0.00 0.00 2.78
1831 5054 6.966751 AGGATAGACCATGATTGATAATGGG 58.033 40.000 11.29 0.00 46.45 4.00
1948 5171 3.138283 AGATGGTGGTCTTGGAGAACAAA 59.862 43.478 0.00 0.00 44.64 2.83
2062 5285 8.283291 CCTTGTCATGTAGTTTTAGTTGTTCTC 58.717 37.037 0.00 0.00 0.00 2.87
2363 5634 9.516314 TGTAATGATTGTCGTTTCACTATAGAG 57.484 33.333 6.78 0.00 0.00 2.43
2529 5802 2.526304 TCGAACCTGTCAAACTGGAG 57.474 50.000 9.65 2.13 39.29 3.86
2696 5969 5.538053 TGGAAAAACATATCCAAGCACTTCA 59.462 36.000 0.00 0.00 42.61 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.574013 GCATTGTCTAGCTATCATATGGGC 59.426 45.833 2.13 5.60 0.00 5.36
304 725 2.606795 CCACATCCAACGCACGAAATTT 60.607 45.455 0.00 0.00 0.00 1.82
370 796 4.574674 ATGATCCACACACATTACCAGT 57.425 40.909 0.00 0.00 0.00 4.00
434 863 8.694540 TGGAGTTTTATTGCATACATATTTGCT 58.305 29.630 0.00 0.00 39.60 3.91
489 927 1.406069 GCACACAGGATCTCCATTCGT 60.406 52.381 0.00 0.00 38.89 3.85
585 1027 4.352039 AGATAGAACACGTATCTTGTGCG 58.648 43.478 8.19 0.00 41.03 5.34
586 1028 7.364200 AGATAGATAGAACACGTATCTTGTGC 58.636 38.462 8.19 0.00 41.03 4.57
909 1355 2.043227 GATGGAGACTGGGGAGTAAGG 58.957 57.143 0.00 0.00 0.00 2.69
1005 1458 0.999712 ACCCCTGGTTGACTATTGGG 59.000 55.000 0.00 0.00 37.58 4.12
1101 1554 7.692460 ATTATGCTTCTTGTTCTTGTCATCA 57.308 32.000 0.00 0.00 0.00 3.07
1125 1581 6.358991 TGCATGGAGAGAATTCATGATGTAA 58.641 36.000 8.44 0.00 40.28 2.41
1343 4551 1.414919 GGTCGCCCATGGTGTAGATAA 59.585 52.381 11.73 0.00 34.40 1.75
1413 4628 4.202243 ACACAACCAAAGGACAATCCATTG 60.202 41.667 5.96 5.96 42.95 2.82
1557 4775 1.345089 TCCTCGTCGATCCAAAAACCA 59.655 47.619 0.00 0.00 0.00 3.67
1624 4843 7.571026 TGTTCACTGAAAACAAACAACAATTG 58.429 30.769 3.24 3.24 33.86 2.32
1831 5054 2.097925 CAGTGCGCAACGAAATGAAAAC 60.098 45.455 14.00 0.00 31.66 2.43
1948 5171 1.971357 ACTGGTCGATCAGTGGAAGTT 59.029 47.619 29.92 3.52 45.27 2.66
2203 5435 9.336171 GCCAGAAAGAAAGTTCATCTATATCTT 57.664 33.333 0.00 0.00 0.00 2.40
2210 5442 7.823745 TTTAAGCCAGAAAGAAAGTTCATCT 57.176 32.000 0.00 0.00 0.00 2.90
2304 5565 4.033932 TCTGTTTGATTGTGACAAGACGTG 59.966 41.667 3.74 0.00 0.00 4.49
2460 5733 3.692101 TGTTTATTTACGGGCACTGGATG 59.308 43.478 0.00 0.00 40.47 3.51
2529 5802 8.348507 AGCAACTAATATAGATTGAAGCAAAGC 58.651 33.333 0.00 0.00 0.00 3.51
2598 5871 7.433719 CACAATGTTCAAAAGAATTGTTCGGTA 59.566 33.333 0.00 0.00 40.36 4.02
2602 5875 7.277539 TGGACACAATGTTCAAAAGAATTGTTC 59.722 33.333 0.00 0.00 40.36 3.18
2696 5969 2.188817 GACAGGGGTCTTAGTGGTGAT 58.811 52.381 0.00 0.00 40.99 3.06


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

AutoCloner maintained by Alex Coulton.