Multiple sequence alignment - TraesCS1A01G159900

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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 TraesCS1A01G159900 chr1A 100.000 2246 0 0 1 2246 287039075 287041320 0.000000e+00 4148
1 TraesCS1A01G159900 chr7A 95.811 2268 71 6 1 2246 647417620 647415355 0.000000e+00 3640
2 TraesCS1A01G159900 chr7A 95.526 1341 40 3 1 1321 106589979 106588639 0.000000e+00 2126
3 TraesCS1A01G159900 chr7A 94.535 860 28 3 1 841 617961193 617960334 0.000000e+00 1310
4 TraesCS1A01G159900 chr7A 93.282 387 16 5 1302 1678 617959357 617958971 1.510000e-156 562
5 TraesCS1A01G159900 chr3A 96.043 2249 66 12 1 2246 122543419 122541191 0.000000e+00 3639
6 TraesCS1A01G159900 chr3A 95.776 2249 75 11 1 2246 49521445 49519214 0.000000e+00 3609
7 TraesCS1A01G159900 chr3A 96.586 1318 38 3 3 1318 41657037 41658349 0.000000e+00 2178
8 TraesCS1A01G159900 chr3A 95.078 1341 42 5 1 1321 743242961 743241625 0.000000e+00 2089
9 TraesCS1A01G159900 chr3A 91.275 149 10 2 2098 2246 743489639 743489784 1.360000e-47 200
10 TraesCS1A01G159900 chr5A 95.408 2243 93 10 10 2246 388937759 388935521 0.000000e+00 3563
11 TraesCS1A01G159900 chr5A 96.226 106 4 0 1573 1678 422094863 422094758 8.250000e-40 174
12 TraesCS1A01G159900 chr2A 95.522 1340 40 4 1 1321 708688386 708689724 0.000000e+00 2124
13 TraesCS1A01G159900 chr2A 95.302 1341 43 4 1 1321 88834914 88836254 0.000000e+00 2109
14 TraesCS1A01G159900 chr2A 94.412 859 27 5 1 838 3340861 3341719 0.000000e+00 1301
15 TraesCS1A01G159900 chr2A 95.515 379 14 3 1302 1678 3342255 3342632 8.870000e-169 603
16 TraesCS1A01G159900 chr4B 93.107 885 33 9 1 857 239619997 239620881 0.000000e+00 1271
17 TraesCS1A01G159900 chr4B 85.535 318 33 6 1702 2009 413339759 413339445 1.000000e-83 320
18 TraesCS1A01G159900 chr7D 96.278 403 14 1 1692 2093 621937393 621937795 0.000000e+00 660
19 TraesCS1A01G159900 chr7D 96.040 404 14 2 1692 2093 85521033 85520630 0.000000e+00 656
20 TraesCS1A01G159900 chr6D 94.815 405 18 2 1692 2093 65146849 65146445 1.460000e-176 628
21 TraesCS1A01G159900 chr6D 92.079 404 19 3 1692 2093 32520618 32521010 7.010000e-155 556
22 TraesCS1A01G159900 chr3B 93.830 389 14 4 1300 1678 782860583 782860195 5.380000e-161 577
23 TraesCS1A01G159900 chr1B 93.229 384 16 4 1305 1678 627843719 627843336 7.010000e-155 556
24 TraesCS1A01G159900 chr1D 92.701 274 19 1 1302 1575 15314038 15313766 5.810000e-106 394
25 TraesCS1A01G159900 chrUn 94.836 213 10 1 1692 1903 31511154 31511366 4.620000e-87 331
26 TraesCS1A01G159900 chrUn 92.727 110 8 0 1984 2093 31511374 31511483 2.310000e-35 159
27 TraesCS1A01G159900 chr7B 96.226 106 4 0 1573 1678 670113506 670113611 8.250000e-40 174
28 TraesCS1A01G159900 chr7B 96.190 105 4 0 1574 1678 490139270 490139166 2.970000e-39 172
29 TraesCS1A01G159900 chr2B 96.226 106 4 0 1573 1678 8262131 8262026 8.250000e-40 174


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 TraesCS1A01G159900 chr1A 287039075 287041320 2245 False 4148 4148 100.0000 1 2246 1 chr1A.!!$F1 2245
1 TraesCS1A01G159900 chr7A 647415355 647417620 2265 True 3640 3640 95.8110 1 2246 1 chr7A.!!$R2 2245
2 TraesCS1A01G159900 chr7A 106588639 106589979 1340 True 2126 2126 95.5260 1 1321 1 chr7A.!!$R1 1320
3 TraesCS1A01G159900 chr7A 617958971 617961193 2222 True 936 1310 93.9085 1 1678 2 chr7A.!!$R3 1677
4 TraesCS1A01G159900 chr3A 122541191 122543419 2228 True 3639 3639 96.0430 1 2246 1 chr3A.!!$R2 2245
5 TraesCS1A01G159900 chr3A 49519214 49521445 2231 True 3609 3609 95.7760 1 2246 1 chr3A.!!$R1 2245
6 TraesCS1A01G159900 chr3A 41657037 41658349 1312 False 2178 2178 96.5860 3 1318 1 chr3A.!!$F1 1315
7 TraesCS1A01G159900 chr3A 743241625 743242961 1336 True 2089 2089 95.0780 1 1321 1 chr3A.!!$R3 1320
8 TraesCS1A01G159900 chr5A 388935521 388937759 2238 True 3563 3563 95.4080 10 2246 1 chr5A.!!$R1 2236
9 TraesCS1A01G159900 chr2A 708688386 708689724 1338 False 2124 2124 95.5220 1 1321 1 chr2A.!!$F2 1320
10 TraesCS1A01G159900 chr2A 88834914 88836254 1340 False 2109 2109 95.3020 1 1321 1 chr2A.!!$F1 1320
11 TraesCS1A01G159900 chr2A 3340861 3342632 1771 False 952 1301 94.9635 1 1678 2 chr2A.!!$F3 1677
12 TraesCS1A01G159900 chr4B 239619997 239620881 884 False 1271 1271 93.1070 1 857 1 chr4B.!!$F1 856

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
156 178 0.404040 GTGGGTCCCAATGGTCAGAA 59.596 55.000 13.78 0.0 34.18 3.02 F
1022 1250 4.736126 TGGCATCGAATAGAAGAGTTGA 57.264 40.909 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1111 1339 0.324738 TCGACATCTTCTCCAGGGCT 60.325 55.0 0.00 0.00 0.0 5.19 R
1951 2532 0.746204 TGTGCGCTTGGACTGTCAAA 60.746 50.0 9.73 3.55 34.6 2.69 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
156 178 0.404040 GTGGGTCCCAATGGTCAGAA 59.596 55.000 13.78 0.0 34.18 3.02
444 492 8.032451 TGAAACACGAATGAAGTACATCATCTA 58.968 33.333 13.61 0.0 39.08 1.98
477 525 7.957002 TCAAACAATATGGTAAGGAGCAAAAA 58.043 30.769 0.00 0.0 36.46 1.94
777 828 7.255346 CCGGTTTAAATTAACTCCTTTGACACT 60.255 37.037 0.00 0.0 0.00 3.55
890 1118 6.817184 TCCTGATATACAAAGGTAAGCTCAC 58.183 40.000 0.00 0.0 32.19 3.51
892 1120 7.783119 TCCTGATATACAAAGGTAAGCTCACTA 59.217 37.037 0.00 0.0 32.19 2.74
952 1180 6.635030 AAGTAACCACCAAAATCTCTCAAC 57.365 37.500 0.00 0.0 0.00 3.18
1022 1250 4.736126 TGGCATCGAATAGAAGAGTTGA 57.264 40.909 0.00 0.0 0.00 3.18
1153 1381 2.753043 CCCTTGAGCTGCCGCATT 60.753 61.111 2.05 0.0 39.10 3.56
1221 1449 1.134189 CATGAAGAGGATGAGGCTGCA 60.134 52.381 0.50 0.0 0.00 4.41
1227 1455 0.979709 AGGATGAGGCTGCACTGCTA 60.980 55.000 0.50 0.0 0.00 3.49
1296 1524 8.721478 CAACAAGACAGTGTAATAGTAGCAAAT 58.279 33.333 0.00 0.0 0.00 2.32
1361 1928 2.180946 TCCACTCCATACTCCATGCT 57.819 50.000 0.00 0.0 32.84 3.79
1559 2127 3.319137 TCTTCAGCTGCATAAACGACT 57.681 42.857 9.47 0.0 0.00 4.18
1628 2207 2.900546 AGAAGACGGAAACAGGACTCAT 59.099 45.455 0.00 0.0 0.00 2.90
1670 2249 2.276309 GAGGACCTTCCATGGCCCTG 62.276 65.000 6.96 0.0 40.19 4.45
1828 2409 7.716560 TCCCCAAACTGAACTTACTAGTTAAAC 59.283 37.037 0.00 0.0 44.51 2.01
1850 2431 3.129287 CCAAAGCTATCGGCACAAGATTT 59.871 43.478 0.00 0.0 44.79 2.17
1948 2529 6.944862 AGATTCAGTTTCAGTTGAGCCTAAAT 59.055 34.615 0.00 0.0 0.00 1.40
1949 2530 8.103305 AGATTCAGTTTCAGTTGAGCCTAAATA 58.897 33.333 0.00 0.0 0.00 1.40
1951 2532 8.635765 TTCAGTTTCAGTTGAGCCTAAATAAT 57.364 30.769 0.00 0.0 0.00 1.28
2054 2636 1.141053 CCAATAGTACTGCCCCCAGAC 59.859 57.143 5.39 0.0 41.77 3.51
2063 2645 3.710722 CCCCCAGACGAGCTGCTT 61.711 66.667 2.53 0.0 43.50 3.91
2069 2651 2.464865 CCAGACGAGCTGCTTATACAC 58.535 52.381 2.53 0.0 43.50 2.90
2139 2721 5.668558 TGATCATTTTCAGCATCATCTCG 57.331 39.130 0.00 0.0 0.00 4.04
2165 2747 6.073981 AGAGGAAGAAAAATTCAAAGAGGCT 58.926 36.000 0.00 0.0 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 146 1.075536 GGACCCACTCAAACCCATCTT 59.924 52.381 0.00 0.00 0.00 2.40
444 492 9.747898 TCCTTACCATATTGTTTGATAACTTGT 57.252 29.630 0.00 0.00 35.24 3.16
477 525 7.670364 AGTTAATGTGCTTTTAGATTGCCTTT 58.330 30.769 0.00 0.00 0.00 3.11
480 528 6.868339 ACAAGTTAATGTGCTTTTAGATTGCC 59.132 34.615 0.00 0.00 30.82 4.52
482 530 9.559958 CCTACAAGTTAATGTGCTTTTAGATTG 57.440 33.333 0.00 0.00 34.75 2.67
642 693 9.851686 TTTGTCCTTCTATGCTTACATGATAAT 57.148 29.630 0.00 0.00 37.04 1.28
829 880 5.465724 CGGTTACTGGTATTTGGCTTCTATC 59.534 44.000 0.00 0.00 0.00 2.08
892 1120 9.491675 TGTATCACATTGAAAAAGAAAATGCAT 57.508 25.926 0.00 0.00 35.20 3.96
952 1180 5.278561 GGAGGTCTCTAGTTAATGATCGGTG 60.279 48.000 0.00 0.00 0.00 4.94
1022 1250 3.715628 AGTCGCTTTTTCTTTGCACAT 57.284 38.095 0.00 0.00 0.00 3.21
1111 1339 0.324738 TCGACATCTTCTCCAGGGCT 60.325 55.000 0.00 0.00 0.00 5.19
1153 1381 1.969200 TTTGCTGCCTTGCCTTGCAA 61.969 50.000 0.00 0.00 46.80 4.08
1221 1449 6.317391 GCTAAAATCTTCTTGTCCATAGCAGT 59.683 38.462 0.00 0.00 34.78 4.40
1227 1455 6.963322 ACCTAGCTAAAATCTTCTTGTCCAT 58.037 36.000 0.00 0.00 0.00 3.41
1296 1524 6.554982 ACTGGGTAATGATGCTCTGAATACTA 59.445 38.462 0.00 0.00 0.00 1.82
1361 1928 3.244387 TGCTGTTGCTGGAGTGTATGTAA 60.244 43.478 0.00 0.00 40.48 2.41
1628 2207 2.355716 CCTTTCCCCTATCTTGTTCGCA 60.356 50.000 0.00 0.00 0.00 5.10
1670 2249 7.761249 AGTTGCCAAAAATATGTAATCAAGAGC 59.239 33.333 0.00 0.00 0.00 4.09
1697 2276 6.720112 AAATATGTAATCAAGGCAGTGCAT 57.280 33.333 18.61 7.05 0.00 3.96
1752 2333 7.066163 CCATTTAGTATGCTTGATTGTGAGTCA 59.934 37.037 0.00 0.00 0.00 3.41
1828 2409 1.737838 TCTTGTGCCGATAGCTTTGG 58.262 50.000 0.00 0.00 44.23 3.28
1850 2431 2.238521 GGAGTGGCCATTTTCTGTCAA 58.761 47.619 9.72 0.00 36.34 3.18
1917 2498 5.227908 TCAACTGAAACTGAATCTCGGTAC 58.772 41.667 0.00 0.00 34.28 3.34
1948 2529 2.225491 GTGCGCTTGGACTGTCAAATTA 59.775 45.455 9.73 0.00 0.00 1.40
1949 2530 1.001378 GTGCGCTTGGACTGTCAAATT 60.001 47.619 9.73 0.00 0.00 1.82
1951 2532 0.746204 TGTGCGCTTGGACTGTCAAA 60.746 50.000 9.73 3.55 34.60 2.69
2054 2636 2.526077 TCGTTGTGTATAAGCAGCTCG 58.474 47.619 0.00 0.00 0.00 5.03
2063 2645 9.563898 CTGTTAGTTGACTTATCGTTGTGTATA 57.436 33.333 0.00 0.00 0.00 1.47
2069 2651 7.576750 TTAGCTGTTAGTTGACTTATCGTTG 57.423 36.000 0.00 0.00 0.00 4.10
2139 2721 6.865726 GCCTCTTTGAATTTTTCTTCCTCTTC 59.134 38.462 0.00 0.00 0.00 2.87
2165 2747 8.888716 CCAGTGTGTTTATTTGTACATATAGCA 58.111 33.333 0.00 2.94 0.00 3.49


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

AutoCloner maintained by Alex Coulton.