Multiple sequence alignment - TraesCS4A01G070200

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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 TraesCS4A01G070200 chr4A 100.000 2284 0 0 1 2284 67596744 67599027 0.000000e+00 4218
1 TraesCS4A01G070200 chr4A 100.000 74 0 0 2521 2594 67599264 67599337 1.250000e-28 137
2 TraesCS4A01G070200 chr5A 98.425 2285 35 1 1 2284 19248877 19246593 0.000000e+00 4019
3 TraesCS4A01G070200 chr7D 98.336 2284 38 0 1 2284 381923968 381926251 0.000000e+00 4008
4 TraesCS4A01G070200 chr7D 98.249 2284 40 0 1 2284 203499966 203502249 0.000000e+00 3997
5 TraesCS4A01G070200 chr7D 98.249 2285 39 1 1 2284 382050045 382052329 0.000000e+00 3997
6 TraesCS4A01G070200 chr7D 98.249 2284 37 1 1 2284 381973800 381971520 0.000000e+00 3993
7 TraesCS4A01G070200 chr7D 97.297 74 2 0 2521 2594 203502299 203502372 2.710000e-25 126
8 TraesCS4A01G070200 chr7D 97.297 74 2 0 2521 2594 381926301 381926374 2.710000e-25 126
9 TraesCS4A01G070200 chr7D 97.297 74 2 0 2521 2594 381971465 381971392 2.710000e-25 126
10 TraesCS4A01G070200 chr7D 97.297 74 2 0 2521 2594 382052379 382052452 2.710000e-25 126
11 TraesCS4A01G070200 chr6D 98.249 2284 40 0 1 2284 124517489 124519772 0.000000e+00 3997
12 TraesCS4A01G070200 chr6D 97.297 74 2 0 2521 2594 168758190 168758263 2.710000e-25 126
13 TraesCS4A01G070200 chr1A 98.205 2284 41 0 1 2284 498691260 498688977 0.000000e+00 3991
14 TraesCS4A01G070200 chr7B 98.205 2284 40 1 1 2284 716878813 716876531 0.000000e+00 3989
15 TraesCS4A01G070200 chr7A 97.986 2284 46 0 1 2284 60279280 60281563 0.000000e+00 3964
16 TraesCS4A01G070200 chrUn 97.297 74 2 0 2521 2594 186206121 186206048 2.710000e-25 126
17 TraesCS4A01G070200 chrUn 97.297 74 2 0 2521 2594 434805875 434805948 2.710000e-25 126
18 TraesCS4A01G070200 chr4D 97.297 74 2 0 2521 2594 123337771 123337844 2.710000e-25 126
19 TraesCS4A01G070200 chr1D 97.297 74 2 0 2521 2594 269409100 269409173 2.710000e-25 126


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 TraesCS4A01G070200 chr4A 67596744 67599337 2593 False 2177.5 4218 100.0000 1 2594 2 chr4A.!!$F1 2593
1 TraesCS4A01G070200 chr5A 19246593 19248877 2284 True 4019.0 4019 98.4250 1 2284 1 chr5A.!!$R1 2283
2 TraesCS4A01G070200 chr7D 381923968 381926374 2406 False 2067.0 4008 97.8165 1 2594 2 chr7D.!!$F2 2593
3 TraesCS4A01G070200 chr7D 203499966 203502372 2406 False 2061.5 3997 97.7730 1 2594 2 chr7D.!!$F1 2593
4 TraesCS4A01G070200 chr7D 382050045 382052452 2407 False 2061.5 3997 97.7730 1 2594 2 chr7D.!!$F3 2593
5 TraesCS4A01G070200 chr7D 381971392 381973800 2408 True 2059.5 3993 97.7730 1 2594 2 chr7D.!!$R1 2593
6 TraesCS4A01G070200 chr6D 124517489 124519772 2283 False 3997.0 3997 98.2490 1 2284 1 chr6D.!!$F1 2283
7 TraesCS4A01G070200 chr1A 498688977 498691260 2283 True 3991.0 3991 98.2050 1 2284 1 chr1A.!!$R1 2283
8 TraesCS4A01G070200 chr7B 716876531 716878813 2282 True 3989.0 3989 98.2050 1 2284 1 chr7B.!!$R1 2283
9 TraesCS4A01G070200 chr7A 60279280 60281563 2283 False 3964.0 3964 97.9860 1 2284 1 chr7A.!!$F1 2283

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
305 306 0.466372 GTAATCCCTGCAGCTTCCCC 60.466 60.0 8.66 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1618 0.89327 TCCGGTGCATGGAAAACTGG 60.893 55.0 8.09 0.0 41.03 4.0 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
81 82 1.533625 CCAACGAAATGAAGGCCTCA 58.466 50.000 5.23 6.53 38.81 3.86
118 119 3.650409 CCGATCCTGAAGTTCTCGG 57.350 57.895 14.60 14.60 42.40 4.63
135 136 3.371102 TCGGGAAGAGAATAAGATGCG 57.629 47.619 0.00 0.00 0.00 4.73
226 227 2.353406 CGCGGGAGGAAGAAAGAAAGTA 60.353 50.000 0.00 0.00 0.00 2.24
249 250 1.964223 AGAGCGTCTTCTCCTTTGTCA 59.036 47.619 0.00 0.00 33.66 3.58
305 306 0.466372 GTAATCCCTGCAGCTTCCCC 60.466 60.000 8.66 0.00 0.00 4.81
462 465 2.572104 ACCACTAAAGGAAAGGCTCGAT 59.428 45.455 0.00 0.00 0.00 3.59
495 499 6.362248 GGATATTAGCTGGGTAAGGAAAACA 58.638 40.000 0.00 0.00 0.00 2.83
666 670 2.513204 CATGTAGCTGCTGCGCCT 60.513 61.111 13.43 0.00 45.42 5.52
740 744 2.211250 TAACCACGTCTCTGCTAGGT 57.789 50.000 0.00 0.00 0.00 3.08
1132 1136 5.457633 GCTTCCTATGGGGGTACATTACAAT 60.458 44.000 0.00 0.00 35.33 2.71
1471 1475 0.395312 CGCAGGAATACCCCCGTTAT 59.605 55.000 0.00 0.00 36.73 1.89
1558 1562 1.751924 CAGTGGGAGTAGTGACTAGCC 59.248 57.143 0.00 0.00 35.45 3.93
1624 1628 0.472471 AGACCGAAGCCAGTTTTCCA 59.528 50.000 0.00 0.00 0.00 3.53
1681 1685 3.154710 CACAGATGGGAATGCATGCTAT 58.845 45.455 20.33 7.43 0.00 2.97
1711 1715 4.038522 CAGGGTCGAGTCTGATACATCAAT 59.961 45.833 8.75 0.00 36.18 2.57
1854 1858 2.208619 TGCTCCCCGTCGGTTGTTA 61.209 57.895 11.06 0.00 0.00 2.41
1946 1950 0.965439 CTCATTTGGGGCGGAAAACA 59.035 50.000 0.00 0.00 0.00 2.83
2065 2069 3.737172 GCCAATGGCGCACGAAGT 61.737 61.111 9.14 0.00 40.21 3.01
2116 2120 3.650950 GTGGGGGAGAAGCAGCCA 61.651 66.667 0.00 0.00 0.00 4.75
2539 2543 2.146920 GGCAGAGGGTCTGTAGTACT 57.853 55.000 0.00 0.00 45.94 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 3.063485 GAGCCGCATCTTATTCTCTTCC 58.937 50.000 0.00 0.00 0.00 3.46
135 136 4.423209 ACAGAGGGAGGGGGAGCC 62.423 72.222 0.00 0.00 0.00 4.70
266 267 4.178956 ACAAAAAGAGGGTGCTTTCCTA 57.821 40.909 0.00 0.00 37.12 2.94
495 499 3.444034 TCGACATCTCAATCTCCGAAAGT 59.556 43.478 0.00 0.00 0.00 2.66
666 670 4.340246 CCTGCTGCTCACTGGGCA 62.340 66.667 2.91 2.91 38.10 5.36
672 676 3.426568 GCCGAACCTGCTGCTCAC 61.427 66.667 0.00 0.00 0.00 3.51
740 744 0.179048 CTCGGCCATTCCACATGCTA 60.179 55.000 2.24 0.00 34.01 3.49
744 748 1.153086 GCTCTCGGCCATTCCACAT 60.153 57.895 2.24 0.00 34.27 3.21
790 794 3.799232 GCTGTTCACGTAACTCCACTCTT 60.799 47.826 0.00 0.00 38.99 2.85
861 865 5.843019 AAGGGAAGGACTTATTCTCAACA 57.157 39.130 0.00 0.00 28.99 3.33
1045 1049 3.004752 AGGCGCAATAGAAAGGAATGT 57.995 42.857 10.83 0.00 0.00 2.71
1132 1136 7.878477 CAATGCTGCAGAAAAAGAAGATTTA 57.122 32.000 20.43 0.00 0.00 1.40
1160 1164 3.262915 GGCCAGTGCTCCTAAGATCATAT 59.737 47.826 0.00 0.00 37.74 1.78
1614 1618 0.893270 TCCGGTGCATGGAAAACTGG 60.893 55.000 8.09 0.00 41.03 4.00
1624 1628 2.125673 GCTACGTGTCCGGTGCAT 60.126 61.111 0.00 0.00 38.78 3.96
1681 1685 1.613925 CAGACTCGACCCTGTCTTTCA 59.386 52.381 2.51 0.00 41.06 2.69
1711 1715 2.651455 ACAAGGATATGGAGTCGACGA 58.349 47.619 10.46 0.00 0.00 4.20
2059 2063 1.019278 CCCTTACGCATGCACTTCGT 61.019 55.000 19.57 9.46 39.88 3.85
2065 2069 2.749839 GTGCCCCTTACGCATGCA 60.750 61.111 19.57 0.00 38.76 3.96
2073 2077 3.520317 TCTTTATTTCTCCGTGCCCCTTA 59.480 43.478 0.00 0.00 0.00 2.69
2116 2120 3.965888 AAGCGAAGGGAATGAGCTT 57.034 47.368 0.00 0.00 42.51 3.74
2531 2535 2.747989 CTCCAGTGCTTCGAGTACTACA 59.252 50.000 0.00 0.00 39.17 2.74
2539 2543 0.532573 GGATCACTCCAGTGCTTCGA 59.467 55.000 1.49 0.00 45.25 3.71


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

AutoCloner maintained by Alex Coulton.