Multiple sequence alignment - TraesCS4A01G425800

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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 TraesCS4A01G425800 chr4A 100.000 3050 0 0 1 3050 697734823 697731774 0.000000e+00 5633
1 TraesCS4A01G425800 chr4A 97.134 1012 28 1 2039 3050 697747925 697746915 0.000000e+00 1707
2 TraesCS4A01G425800 chr7B 94.716 2309 113 7 1 2306 143198464 143196162 0.000000e+00 3579
3 TraesCS4A01G425800 chr7B 97.038 709 21 0 2342 3050 679983480 679984188 0.000000e+00 1194
4 TraesCS4A01G425800 chr7B 96.186 708 27 0 2342 3049 143192277 143191570 0.000000e+00 1158
5 TraesCS4A01G425800 chr5B 94.637 2312 117 7 1 2306 42677503 42679813 0.000000e+00 3576
6 TraesCS4A01G425800 chr5B 94.678 2311 102 13 1 2306 239173166 239175460 0.000000e+00 3567
7 TraesCS4A01G425800 chr5B 92.553 2323 150 21 2 2312 419832931 419835242 0.000000e+00 3310
8 TraesCS4A01G425800 chr5B 95.910 709 29 0 2342 3050 538729887 538729179 0.000000e+00 1149
9 TraesCS4A01G425800 chr5B 95.904 708 28 1 2343 3050 42681631 42682337 0.000000e+00 1146
10 TraesCS4A01G425800 chr4B 93.382 2312 141 11 1 2306 474332838 474330533 0.000000e+00 3411
11 TraesCS4A01G425800 chr4B 93.339 2312 136 10 1 2306 609363068 609365367 0.000000e+00 3400
12 TraesCS4A01G425800 chr4B 91.871 2325 162 23 2 2314 581846545 581848854 0.000000e+00 3221
13 TraesCS4A01G425800 chr3B 93.262 2330 133 19 1 2312 786519590 786521913 0.000000e+00 3411
14 TraesCS4A01G425800 chr3B 90.163 2328 191 26 1 2306 44333980 44336291 0.000000e+00 2996
15 TraesCS4A01G425800 chr3B 97.368 76 2 0 2231 2306 636433623 636433548 2.470000e-26 130
16 TraesCS4A01G425800 chr2B 93.011 2318 143 16 2 2306 22543096 22540785 0.000000e+00 3365
17 TraesCS4A01G425800 chr2B 96.615 709 24 0 2342 3050 215485536 215484828 0.000000e+00 1177
18 TraesCS4A01G425800 chr2B 95.628 709 31 0 2342 3050 119785626 119784918 0.000000e+00 1138
19 TraesCS4A01G425800 chr2D 95.910 709 29 0 2342 3050 192144332 192145040 0.000000e+00 1149
20 TraesCS4A01G425800 chr5D 95.769 709 30 0 2342 3050 13780413 13781121 0.000000e+00 1144


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 TraesCS4A01G425800 chr4A 697731774 697734823 3049 True 5633.0 5633 100.0000 1 3050 1 chr4A.!!$R1 3049
1 TraesCS4A01G425800 chr4A 697746915 697747925 1010 True 1707.0 1707 97.1340 2039 3050 1 chr4A.!!$R2 1011
2 TraesCS4A01G425800 chr7B 143191570 143198464 6894 True 2368.5 3579 95.4510 1 3049 2 chr7B.!!$R1 3048
3 TraesCS4A01G425800 chr7B 679983480 679984188 708 False 1194.0 1194 97.0380 2342 3050 1 chr7B.!!$F1 708
4 TraesCS4A01G425800 chr5B 239173166 239175460 2294 False 3567.0 3567 94.6780 1 2306 1 chr5B.!!$F1 2305
5 TraesCS4A01G425800 chr5B 419832931 419835242 2311 False 3310.0 3310 92.5530 2 2312 1 chr5B.!!$F2 2310
6 TraesCS4A01G425800 chr5B 42677503 42682337 4834 False 2361.0 3576 95.2705 1 3050 2 chr5B.!!$F3 3049
7 TraesCS4A01G425800 chr5B 538729179 538729887 708 True 1149.0 1149 95.9100 2342 3050 1 chr5B.!!$R1 708
8 TraesCS4A01G425800 chr4B 474330533 474332838 2305 True 3411.0 3411 93.3820 1 2306 1 chr4B.!!$R1 2305
9 TraesCS4A01G425800 chr4B 609363068 609365367 2299 False 3400.0 3400 93.3390 1 2306 1 chr4B.!!$F2 2305
10 TraesCS4A01G425800 chr4B 581846545 581848854 2309 False 3221.0 3221 91.8710 2 2314 1 chr4B.!!$F1 2312
11 TraesCS4A01G425800 chr3B 786519590 786521913 2323 False 3411.0 3411 93.2620 1 2312 1 chr3B.!!$F2 2311
12 TraesCS4A01G425800 chr3B 44333980 44336291 2311 False 2996.0 2996 90.1630 1 2306 1 chr3B.!!$F1 2305
13 TraesCS4A01G425800 chr2B 22540785 22543096 2311 True 3365.0 3365 93.0110 2 2306 1 chr2B.!!$R1 2304
14 TraesCS4A01G425800 chr2B 215484828 215485536 708 True 1177.0 1177 96.6150 2342 3050 1 chr2B.!!$R3 708
15 TraesCS4A01G425800 chr2B 119784918 119785626 708 True 1138.0 1138 95.6280 2342 3050 1 chr2B.!!$R2 708
16 TraesCS4A01G425800 chr2D 192144332 192145040 708 False 1149.0 1149 95.9100 2342 3050 1 chr2D.!!$F1 708
17 TraesCS4A01G425800 chr5D 13780413 13781121 708 False 1144.0 1144 95.7690 2342 3050 1 chr5D.!!$F1 708

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
430 442 0.338467 TCCTCCGATCCCCTTCTTCA 59.662 55.0 0.0 0.0 0.0 3.02 F
1315 1347 0.884704 GCCTCGTGAACCAGAAGCAA 60.885 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 1885 0.245539 ACTTGTACATGACCGACGGG 59.754 55.0 20.00 2.2 40.11 5.28 R
2615 6552 0.033781 ACCCGCGCAAGTACAAGTAA 59.966 50.0 8.75 0.0 41.68 2.24 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
66 68 2.512476 ACCCCTGACCTTTTTGTGTAGT 59.488 45.455 0.00 0.00 0.00 2.73
292 304 2.036217 CCATTGCAGCAGTTCCAGAAAA 59.964 45.455 0.00 0.00 0.00 2.29
401 413 3.536956 TTCGTCACCAATCCATCCTAC 57.463 47.619 0.00 0.00 0.00 3.18
429 441 1.044611 CTCCTCCGATCCCCTTCTTC 58.955 60.000 0.00 0.00 0.00 2.87
430 442 0.338467 TCCTCCGATCCCCTTCTTCA 59.662 55.000 0.00 0.00 0.00 3.02
431 443 1.204146 CCTCCGATCCCCTTCTTCAA 58.796 55.000 0.00 0.00 0.00 2.69
718 738 6.696583 TGGATACATATGCTTTGAATTTTGCG 59.303 34.615 1.58 0.00 46.17 4.85
730 750 3.181524 TGAATTTTGCGTCTAGTAAGCGC 60.182 43.478 0.00 0.00 43.74 5.92
776 796 9.398170 CGAAAGATAATTGTGTTGACAAGAATT 57.602 29.630 0.00 0.00 45.29 2.17
833 860 3.213506 TGATCACTGGGACAAACAACAG 58.786 45.455 0.00 0.00 38.70 3.16
901 928 4.104776 GCCGGTGTTATGAATTTCATGTG 58.895 43.478 19.81 5.21 37.70 3.21
936 968 8.266473 ACACAAATGCCCATATGTAATGATTTT 58.734 29.630 1.24 0.00 0.00 1.82
937 969 8.767085 CACAAATGCCCATATGTAATGATTTTC 58.233 33.333 1.24 0.00 0.00 2.29
971 1003 1.538950 GGAGCTTGCACCTTTGAAGAG 59.461 52.381 1.88 0.00 0.00 2.85
1315 1347 0.884704 GCCTCGTGAACCAGAAGCAA 60.885 55.000 0.00 0.00 0.00 3.91
1320 1352 3.476552 TCGTGAACCAGAAGCAAAAGAT 58.523 40.909 0.00 0.00 0.00 2.40
1387 1419 6.552859 TTCAATCGAACTTTGATACTTGCA 57.447 33.333 1.02 0.00 33.37 4.08
1467 1499 4.757149 GTGATATCCAGGACTATGTTTGCC 59.243 45.833 0.00 0.00 0.00 4.52
1472 1504 2.632377 CAGGACTATGTTTGCCGATGT 58.368 47.619 0.00 0.00 0.00 3.06
1497 1529 1.700955 GCAGGAATGCTCCATGGATT 58.299 50.000 16.63 6.87 45.24 3.01
1842 1874 4.766891 ACAAGTGGGATGTGTTAAATGAGG 59.233 41.667 0.00 0.00 0.00 3.86
1846 1878 3.214328 GGGATGTGTTAAATGAGGCGAT 58.786 45.455 0.00 0.00 0.00 4.58
1853 1885 3.876914 TGTTAAATGAGGCGATGGATGAC 59.123 43.478 0.00 0.00 0.00 3.06
1971 2004 5.958428 TCGTAACTCGATATCAATTTTGCG 58.042 37.500 3.12 5.69 44.01 4.85
1986 2019 7.158021 TCAATTTTGCGTTCTATCCCATTTTT 58.842 30.769 0.00 0.00 0.00 1.94
2210 2244 1.669440 GGACAAGGTGCTACACGGA 59.331 57.895 0.00 0.00 34.83 4.69
2615 6552 1.289530 TCAACCTTGGGTGGGAACTTT 59.710 47.619 4.73 0.00 35.34 2.66
2931 6869 0.593128 AGTGGTGAAATGCTTGTCGC 59.407 50.000 0.00 0.00 39.77 5.19
2932 6870 0.725784 GTGGTGAAATGCTTGTCGCG 60.726 55.000 0.00 0.00 43.27 5.87
2957 6895 6.428385 AAAGCGAGACAATAATCTTGAAGG 57.572 37.500 0.00 0.00 32.45 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 91 3.064987 CTAGGCGCTGCACCGTAGT 62.065 63.158 7.64 0.00 0.00 2.73
264 271 2.601067 TGCTGCAATGGGTGGGTG 60.601 61.111 0.00 0.00 0.00 4.61
323 335 1.004891 AGGGGATTGAGAGGGGGAC 59.995 63.158 0.00 0.00 0.00 4.46
401 413 1.957877 GGATCGGAGGAGAGTACCTTG 59.042 57.143 0.00 0.00 40.73 3.61
544 560 9.610104 AAATAAACTAAACTAGGGTTCCCAAAT 57.390 29.630 10.73 0.00 34.14 2.32
547 563 9.081204 GAAAAATAAACTAAACTAGGGTTCCCA 57.919 33.333 10.73 0.00 34.14 4.37
718 738 7.752557 ATAAACTAAACTGCGCTTACTAGAC 57.247 36.000 9.73 0.00 0.00 2.59
833 860 1.002250 CCGACATAGCATACGACCGC 61.002 60.000 0.00 0.00 0.00 5.68
901 928 7.548780 ACATATGGGCATTTGTGTTTGAAATAC 59.451 33.333 7.80 0.00 32.95 1.89
936 968 4.202010 GCAAGCTCCTACAAACAAACAAGA 60.202 41.667 0.00 0.00 0.00 3.02
937 969 4.044426 GCAAGCTCCTACAAACAAACAAG 58.956 43.478 0.00 0.00 0.00 3.16
971 1003 2.987547 TGACCCCGTGAGACCGAC 60.988 66.667 0.00 0.00 0.00 4.79
1106 1138 2.802247 CTCCAATGATCAATAAGCGCGA 59.198 45.455 12.10 0.00 0.00 5.87
1315 1347 8.432805 TGTGACTCTTTCCTTCTTCTTATCTTT 58.567 33.333 0.00 0.00 0.00 2.52
1320 1352 5.511545 GGCTGTGACTCTTTCCTTCTTCTTA 60.512 44.000 0.00 0.00 0.00 2.10
1387 1419 3.378512 TGTCCTCATTAGCATCCTCAGT 58.621 45.455 0.00 0.00 0.00 3.41
1467 1499 1.012086 CATTCCTGCCTGTGACATCG 58.988 55.000 0.00 0.00 0.00 3.84
1481 1513 1.069668 GCCAAATCCATGGAGCATTCC 59.930 52.381 21.33 3.09 43.54 3.01
1497 1529 1.896660 GGTCAACGCCTTCAGCCAA 60.897 57.895 0.00 0.00 38.78 4.52
1842 1874 2.658593 CGACGGGTCATCCATCGC 60.659 66.667 0.00 0.00 37.17 4.58
1853 1885 0.245539 ACTTGTACATGACCGACGGG 59.754 55.000 20.00 2.20 40.11 5.28
1971 2004 5.261216 TCCACCTGAAAAATGGGATAGAAC 58.739 41.667 0.00 0.00 34.03 3.01
1986 2019 2.669133 CGGCTCCCATTCCACCTGA 61.669 63.158 0.00 0.00 0.00 3.86
2615 6552 0.033781 ACCCGCGCAAGTACAAGTAA 59.966 50.000 8.75 0.00 41.68 2.24
2931 6869 4.566759 TCAAGATTATTGTCTCGCTTTCCG 59.433 41.667 0.00 0.00 38.61 4.30
2932 6870 6.422776 TTCAAGATTATTGTCTCGCTTTCC 57.577 37.500 0.00 0.00 0.00 3.13
2957 6895 2.280628 CTTAAGGAGTTGGCCGATGAC 58.719 52.381 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.