Multiple sequence alignment - TraesCS7A01G455100

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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 TraesCS7A01G455100 chr7A 100.000 1528 0 0 767 2294 650260775 650259248 0.000000e+00 2822
1 TraesCS7A01G455100 chr7A 97.820 1514 31 2 783 2294 650324575 650323062 0.000000e+00 2612
2 TraesCS7A01G455100 chr7A 96.667 1500 48 2 797 2294 707844389 707845888 0.000000e+00 2492
3 TraesCS7A01G455100 chr7A 100.000 447 0 0 1 447 650261541 650261095 0.000000e+00 826
4 TraesCS7A01G455100 chr7A 94.607 445 22 2 1 445 707843565 707844007 0.000000e+00 688
5 TraesCS7A01G455100 chr7A 95.442 373 16 1 1 372 650325217 650324845 5.460000e-166 593
6 TraesCS7A01G455100 chr2A 96.706 1518 42 5 784 2294 600113448 600111932 0.000000e+00 2519
7 TraesCS7A01G455100 chr2A 96.542 1475 50 1 821 2294 23796207 23797681 0.000000e+00 2440
8 TraesCS7A01G455100 chr2A 96.444 1434 47 4 863 2294 571019198 571020629 0.000000e+00 2362
9 TraesCS7A01G455100 chr2A 95.592 431 17 2 1 431 571018480 571018908 0.000000e+00 689
10 TraesCS7A01G455100 chr2A 93.080 448 29 2 1 447 23795475 23795921 0.000000e+00 654
11 TraesCS7A01G455100 chr2A 98.319 119 2 0 1 119 734856596 734856714 2.310000e-50 209
12 TraesCS7A01G455100 chr1A 96.207 1529 56 2 767 2293 380400781 380402309 0.000000e+00 2501
13 TraesCS7A01G455100 chr1A 95.092 1528 72 3 769 2294 531840080 531838554 0.000000e+00 2403
14 TraesCS7A01G455100 chr1A 95.536 448 18 2 1 447 11026976 11026530 0.000000e+00 715
15 TraesCS7A01G455100 chr1B 95.299 1489 67 3 808 2294 658504122 658502635 0.000000e+00 2359
16 TraesCS7A01G455100 chr1B 93.994 333 19 1 115 447 235897031 235897362 9.460000e-139 503
17 TraesCS7A01G455100 chr4A 93.876 1486 85 6 812 2294 382145490 382146972 0.000000e+00 2235
18 TraesCS7A01G455100 chr5A 95.312 448 17 3 1 447 603018544 603018988 0.000000e+00 708
19 TraesCS7A01G455100 chr5A 95.078 447 21 1 1 447 507566376 507565931 0.000000e+00 702
20 TraesCS7A01G455100 chrUn 93.909 394 24 0 1 394 248381265 248380872 1.520000e-166 595


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 TraesCS7A01G455100 chr7A 650259248 650261541 2293 True 1824.0 2822 100.000 1 2294 2 chr7A.!!$R1 2293
1 TraesCS7A01G455100 chr7A 650323062 650325217 2155 True 1602.5 2612 96.631 1 2294 2 chr7A.!!$R2 2293
2 TraesCS7A01G455100 chr7A 707843565 707845888 2323 False 1590.0 2492 95.637 1 2294 2 chr7A.!!$F1 2293
3 TraesCS7A01G455100 chr2A 600111932 600113448 1516 True 2519.0 2519 96.706 784 2294 1 chr2A.!!$R1 1510
4 TraesCS7A01G455100 chr2A 23795475 23797681 2206 False 1547.0 2440 94.811 1 2294 2 chr2A.!!$F2 2293
5 TraesCS7A01G455100 chr2A 571018480 571020629 2149 False 1525.5 2362 96.018 1 2294 2 chr2A.!!$F3 2293
6 TraesCS7A01G455100 chr1A 380400781 380402309 1528 False 2501.0 2501 96.207 767 2293 1 chr1A.!!$F1 1526
7 TraesCS7A01G455100 chr1A 531838554 531840080 1526 True 2403.0 2403 95.092 769 2294 1 chr1A.!!$R2 1525
8 TraesCS7A01G455100 chr1B 658502635 658504122 1487 True 2359.0 2359 95.299 808 2294 1 chr1B.!!$R1 1486
9 TraesCS7A01G455100 chr4A 382145490 382146972 1482 False 2235.0 2235 93.876 812 2294 1 chr4A.!!$F1 1482

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
331 334 0.687757 CCGAACCAGATCTCCCTCCA 60.688 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 2412 0.598158 GCAAGTTGGCACCACACATG 60.598 55.0 4.75 0.0 0.0 3.21 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
163 165 1.779061 GCAGAACCTCCCTTCCCACA 61.779 60.000 0.00 0.00 0.00 4.17
255 258 0.981183 ACCAAACCCTAGCATCGTGA 59.019 50.000 0.00 0.00 0.00 4.35
316 319 3.712907 CGCCTCCCTTTCCCCGAA 61.713 66.667 0.00 0.00 0.00 4.30
331 334 0.687757 CCGAACCAGATCTCCCTCCA 60.688 60.000 0.00 0.00 0.00 3.86
841 1055 1.201429 AGACCACATCCTCCCACCAC 61.201 60.000 0.00 0.00 0.00 4.16
881 1095 1.152567 CTCCCCTCCTCGCAGATCT 60.153 63.158 0.00 0.00 33.89 2.75
1412 1628 2.938354 GTGCATGCACAGTCCTTCT 58.062 52.632 39.12 0.00 45.53 2.85
1502 1719 6.845758 TTCTACCTTGTTAGGAGAATTCGA 57.154 37.500 0.00 0.00 45.05 3.71
1733 1950 7.055378 CTACTGAGTAGACAGGTTACATACCT 58.945 42.308 14.31 0.00 46.95 3.08
1939 2158 9.595823 GTGTTGATCTATACTTTAAAGCACCTA 57.404 33.333 15.24 0.59 0.00 3.08
2186 2412 1.862201 TGTTTCATGTGGTCGTTCGAC 59.138 47.619 15.66 15.66 34.65 4.20
2204 2430 0.746063 ACATGTGTGGTGCCAACTTG 59.254 50.000 0.00 5.48 0.00 3.16
2248 2474 8.862325 TGTCAATAGTCTTTTGGTTCATACAT 57.138 30.769 3.57 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
255 258 1.306568 GAGGGAGGGGAGTCTGCTT 60.307 63.158 0.00 0.00 0.00 3.91
316 319 0.684805 GTCGTGGAGGGAGATCTGGT 60.685 60.000 0.00 0.00 0.00 4.00
331 334 2.037527 GAGGGAGGTCTGGGTCGT 59.962 66.667 0.00 0.00 0.00 4.34
881 1095 3.253188 GTGCTGTTTGGATTTGTGCTCTA 59.747 43.478 0.00 0.00 0.00 2.43
1005 1221 2.994995 ACCATGGAGTCGACGGCA 60.995 61.111 21.47 0.00 0.00 5.69
1502 1719 4.018960 ACAGCTGATTACCCTTGACTCATT 60.019 41.667 23.35 0.00 0.00 2.57
1733 1950 2.486203 GCACGAACCATGGACAAACATA 59.514 45.455 21.47 0.00 0.00 2.29
1932 2151 1.372582 CATGCGTGAACATAGGTGCT 58.627 50.000 0.00 0.00 0.00 4.40
1939 2158 2.703798 GCTGGCCATGCGTGAACAT 61.704 57.895 5.51 0.00 0.00 2.71
2186 2412 0.598158 GCAAGTTGGCACCACACATG 60.598 55.000 4.75 0.00 0.00 3.21
2204 2430 6.127810 TGACATCAGCTATCAAAGAAATGC 57.872 37.500 0.00 0.00 0.00 3.56
2248 2474 7.179872 AGAGCATTCATATATGAGGCACTAAGA 59.820 37.037 28.53 10.77 41.55 2.10


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

AutoCloner maintained by Alex Coulton.