Multiple sequence alignment - TraesCS7B01G017800

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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 TraesCS7B01G017800 chr7B 100.000 2453 0 0 1 2453 15037518 15035066 0.000000e+00 4530
1 TraesCS7B01G017800 chr2B 96.556 2468 69 3 1 2453 640105627 640108093 0.000000e+00 4072
2 TraesCS7B01G017800 chr2B 96.104 2464 81 3 4 2453 683669689 683672151 0.000000e+00 4004
3 TraesCS7B01G017800 chr1B 96.471 2465 67 6 3 2453 277433932 277436390 0.000000e+00 4052
4 TraesCS7B01G017800 chr1B 96.522 2358 67 3 110 2453 313093410 313091054 0.000000e+00 3886
5 TraesCS7B01G017800 chr3B 96.347 2464 72 4 4 2453 312175442 312172983 0.000000e+00 4036
6 TraesCS7B01G017800 chr3B 96.436 2273 67 2 5 2264 752283804 752281533 0.000000e+00 3736
7 TraesCS7B01G017800 chr3B 99.065 107 1 0 5 111 172982450 172982556 2.490000e-45 193
8 TraesCS7B01G017800 chr3B 96.774 93 3 0 2361 2453 752281174 752281082 3.270000e-34 156
9 TraesCS7B01G017800 chr6B 96.346 2463 73 4 5 2453 646622797 646625256 0.000000e+00 4034
10 TraesCS7B01G017800 chr6B 96.756 2312 58 4 4 2302 440785322 440783015 0.000000e+00 3838
11 TraesCS7B01G017800 chr4B 95.695 2462 90 4 5 2451 66092794 66095254 0.000000e+00 3945
12 TraesCS7B01G017800 chr4A 96.304 2408 69 4 65 2453 647219057 647216651 0.000000e+00 3936
13 TraesCS7B01G017800 chr4A 92.274 453 35 0 65 517 631704341 631703889 0.000000e+00 643


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 TraesCS7B01G017800 chr7B 15035066 15037518 2452 True 4530 4530 100.000 1 2453 1 chr7B.!!$R1 2452
1 TraesCS7B01G017800 chr2B 640105627 640108093 2466 False 4072 4072 96.556 1 2453 1 chr2B.!!$F1 2452
2 TraesCS7B01G017800 chr2B 683669689 683672151 2462 False 4004 4004 96.104 4 2453 1 chr2B.!!$F2 2449
3 TraesCS7B01G017800 chr1B 277433932 277436390 2458 False 4052 4052 96.471 3 2453 1 chr1B.!!$F1 2450
4 TraesCS7B01G017800 chr1B 313091054 313093410 2356 True 3886 3886 96.522 110 2453 1 chr1B.!!$R1 2343
5 TraesCS7B01G017800 chr3B 312172983 312175442 2459 True 4036 4036 96.347 4 2453 1 chr3B.!!$R1 2449
6 TraesCS7B01G017800 chr3B 752281082 752283804 2722 True 1946 3736 96.605 5 2453 2 chr3B.!!$R2 2448
7 TraesCS7B01G017800 chr6B 646622797 646625256 2459 False 4034 4034 96.346 5 2453 1 chr6B.!!$F1 2448
8 TraesCS7B01G017800 chr6B 440783015 440785322 2307 True 3838 3838 96.756 4 2302 1 chr6B.!!$R1 2298
9 TraesCS7B01G017800 chr4B 66092794 66095254 2460 False 3945 3945 95.695 5 2451 1 chr4B.!!$F1 2446
10 TraesCS7B01G017800 chr4A 647216651 647219057 2406 True 3936 3936 96.304 65 2453 1 chr4A.!!$R2 2388

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
444 461 0.324943 GTGCCTTCCCTGCTCTACAA 59.675 55.0 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 1865 1.040646 GATGTGGATCCTCTACGGCA 58.959 55.0 14.23 1.31 29.68 5.69 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
148 149 7.005296 TGTAACCTTGTATATCTCTCTCTCCC 58.995 42.308 0.00 0.00 0.00 4.30
160 164 2.091055 TCTCTCTCCCCCTCAATACAGG 60.091 54.545 0.00 0.00 0.00 4.00
190 194 2.493675 CGGTCATTCTCTCTTCCTCACA 59.506 50.000 0.00 0.00 0.00 3.58
209 213 8.106462 TCCTCACATTTTCTAACATGGTATCAA 58.894 33.333 0.00 0.00 0.00 2.57
257 261 2.051518 GCCGCCACCCATGAAATCA 61.052 57.895 0.00 0.00 0.00 2.57
258 262 1.394266 GCCGCCACCCATGAAATCAT 61.394 55.000 0.00 0.00 36.96 2.45
444 461 0.324943 GTGCCTTCCCTGCTCTACAA 59.675 55.000 0.00 0.00 0.00 2.41
457 474 1.002430 CTCTACAACAAGCTCCAGGCA 59.998 52.381 0.00 0.00 44.79 4.75
460 477 1.708341 ACAACAAGCTCCAGGCATTT 58.292 45.000 0.00 0.00 44.79 2.32
589 606 2.679059 GCTCATCTCTTGTTGCTGCCTA 60.679 50.000 0.00 0.00 0.00 3.93
614 631 4.284234 AGCTGCTATCAAATTGGGTGTTTT 59.716 37.500 0.00 0.00 0.00 2.43
751 768 1.133915 TCTTGAGGACGGCTGGTTTTT 60.134 47.619 0.00 0.00 0.00 1.94
796 813 4.825634 CACCTAGTCCAAATGATGATGCAT 59.174 41.667 0.00 0.00 0.00 3.96
823 840 4.201861 GGAAGTCTTGGCAAAAGATCGATC 60.202 45.833 17.91 17.91 0.00 3.69
826 843 4.946157 AGTCTTGGCAAAAGATCGATCATT 59.054 37.500 26.47 18.47 0.00 2.57
967 984 4.036734 GTGCACTTCATTTCTCCTTGTTGA 59.963 41.667 10.32 0.00 0.00 3.18
997 1014 1.414919 ACAACACTCGGTAGCCAGAAA 59.585 47.619 0.00 0.00 0.00 2.52
1175 1192 3.438087 CCAGACTTTGAGAACATTCGCAT 59.562 43.478 0.00 0.00 36.88 4.73
1182 1200 6.925165 ACTTTGAGAACATTCGCATTCAATTT 59.075 30.769 0.00 0.00 36.88 1.82
1289 1307 0.523519 TCTGCGCAGACTCTACACAG 59.476 55.000 35.30 7.31 31.41 3.66
1361 1379 0.664767 GCTGTCGTCTGCTCGTTCTT 60.665 55.000 4.40 0.00 35.98 2.52
1370 1388 2.072298 CTGCTCGTTCTTCAAGAAGGG 58.928 52.381 17.69 10.69 39.73 3.95
1450 1468 0.325296 TAGACGGGCCCTCAATCAGT 60.325 55.000 22.43 8.29 0.00 3.41
1454 1472 1.915228 GGGCCCTCAATCAGTAGCA 59.085 57.895 17.04 0.00 0.00 3.49
1471 1489 3.650950 ATCGTGCACCCCAGGCTT 61.651 61.111 12.15 0.00 0.00 4.35
1585 1604 4.916041 TCTTTCCATGTGACCTCTGATT 57.084 40.909 0.00 0.00 0.00 2.57
1652 1671 1.202348 TCAGACTGCTGATGGTACACG 59.798 52.381 0.00 0.00 45.88 4.49
1753 1772 4.885907 CCATGAATCTTATGTCTGTTGGCT 59.114 41.667 0.00 0.00 0.00 4.75
1846 1865 1.560505 GGTCATTGGAACTGGCCATT 58.439 50.000 5.51 0.00 38.31 3.16
1901 1920 2.372172 ACACCTTACACCTTCCTTCAGG 59.628 50.000 0.00 0.00 40.23 3.86
1953 1972 4.397103 GCATCAACATCAAGATCCACTTCA 59.603 41.667 0.00 0.00 36.61 3.02
2059 2080 4.411869 TGGGTCATGTTTCCATAGATGCTA 59.588 41.667 0.00 0.00 0.00 3.49
2115 2136 6.951971 ACAAATACAGCTTCCATACTCTTCT 58.048 36.000 0.00 0.00 0.00 2.85
2127 2148 6.058833 TCCATACTCTTCTAGCACTACTCAG 58.941 44.000 0.00 0.00 0.00 3.35
2156 2177 6.491403 AGTCATCCTTTTGATTTAGTGCACTT 59.509 34.615 27.06 7.02 0.00 3.16
2218 2239 7.548780 GTGGCCACAAACATTATGTCATATTTT 59.451 33.333 31.23 0.00 0.00 1.82
2245 2266 4.270008 TGATCACTCTCGACATACTTGGA 58.730 43.478 0.00 0.00 0.00 3.53
2269 2290 9.424319 GGATCTATTTTATGAAGCATCGTTCTA 57.576 33.333 0.00 0.00 0.00 2.10
2278 2299 9.554724 TTATGAAGCATCGTTCTAAATTGTTTC 57.445 29.630 0.00 0.00 0.00 2.78
2399 2682 2.488153 TCGCGAGTTTCTCTCATCTGAA 59.512 45.455 3.71 0.00 42.88 3.02
2441 2724 2.036098 CCTGGTGCCCATGCTCAA 59.964 61.111 0.00 0.00 38.71 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 164 4.561105 AGAGAGAATGACCGAACAGTTTC 58.439 43.478 0.00 0.00 0.00 2.78
209 213 1.703513 GACTAGGGTTTGGTCCTGGTT 59.296 52.381 0.90 0.00 44.48 3.67
257 261 1.144057 GAATCACCTCACCGGCGAT 59.856 57.895 9.30 0.00 36.10 4.58
258 262 2.225791 CTGAATCACCTCACCGGCGA 62.226 60.000 9.30 0.00 35.61 5.54
444 461 0.613012 GGGAAATGCCTGGAGCTTGT 60.613 55.000 0.00 0.00 44.23 3.16
457 474 4.832492 TCTTGCTAGATAGGAGGGGAAAT 58.168 43.478 0.00 0.00 0.00 2.17
460 477 3.245803 GGATCTTGCTAGATAGGAGGGGA 60.246 52.174 10.76 0.00 41.23 4.81
535 552 0.185901 AAAGAGGAGCAGCAACCCAA 59.814 50.000 0.00 0.00 0.00 4.12
589 606 2.756760 CACCCAATTTGATAGCAGCTGT 59.243 45.455 16.64 0.00 0.00 4.40
823 840 7.543172 CAGAATTAAAACTCCCATCACACAATG 59.457 37.037 0.00 0.00 0.00 2.82
826 843 5.476599 CCAGAATTAAAACTCCCATCACACA 59.523 40.000 0.00 0.00 0.00 3.72
967 984 5.178809 GCTACCGAGTGTTGTGTAAATTCTT 59.821 40.000 0.00 0.00 0.00 2.52
1175 1192 4.624015 AGTCGTACGACCAAGAAATTGAA 58.376 39.130 37.43 2.01 45.59 2.69
1182 1200 1.446907 GAGGAGTCGTACGACCAAGA 58.553 55.000 37.43 6.38 45.59 3.02
1289 1307 2.737252 CGAGGAAAAGCCAGAACACTAC 59.263 50.000 0.00 0.00 40.02 2.73
1361 1379 2.044793 ATGGTGTCCTCCCTTCTTGA 57.955 50.000 0.00 0.00 0.00 3.02
1450 1468 2.584064 CTGGGGTGCACGATGCTA 59.416 61.111 11.45 0.00 45.31 3.49
1454 1472 3.628646 GAAGCCTGGGGTGCACGAT 62.629 63.158 11.45 0.00 0.00 3.73
1471 1489 2.621338 CCTCGCTTGCTGTTGATAAGA 58.379 47.619 0.00 0.00 0.00 2.10
1585 1604 1.875009 CAAGACACAAGCTGAGAGCA 58.125 50.000 0.00 0.00 45.56 4.26
1652 1671 7.331791 AGAACCCTGATGAGTAATAGAACAAC 58.668 38.462 0.00 0.00 0.00 3.32
1753 1772 7.331026 ACAAAGTAGTTCATATCAGCAAGCTA 58.669 34.615 0.00 0.00 0.00 3.32
1846 1865 1.040646 GATGTGGATCCTCTACGGCA 58.959 55.000 14.23 1.31 29.68 5.69
1901 1920 3.894547 AACGCGGATGTGGTGGGAC 62.895 63.158 12.47 0.00 0.00 4.46
1953 1972 2.035832 CCACTGGGCAAAAGAAAACGAT 59.964 45.455 0.00 0.00 0.00 3.73
2059 2080 5.298527 GCTTACAACCCTTACAGTGAAAACT 59.701 40.000 0.00 0.00 0.00 2.66
2115 2136 5.131308 AGGATGACTAGACTGAGTAGTGCTA 59.869 44.000 0.00 0.00 37.25 3.49
2127 2148 7.334421 TGCACTAAATCAAAAGGATGACTAGAC 59.666 37.037 0.00 0.00 36.02 2.59
2218 2239 6.456795 AGTATGTCGAGAGTGATCATCAAA 57.543 37.500 0.00 0.00 0.00 2.69
2399 2682 2.225394 TGAAAGCTGAGGGAGAGTACCT 60.225 50.000 0.00 0.00 42.18 3.08


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

AutoCloner maintained by Alex Coulton.