Multiple sequence alignment - TraesCS7A01G226100

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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 TraesCS7A01G226100 chr7A 100.000 2322 0 0 1 2322 195485624 195487945 0.000000e+00 4289
1 TraesCS7A01G226100 chr7D 94.506 1347 50 12 1 1331 188550660 188549322 0.000000e+00 2056
2 TraesCS7A01G226100 chr7D 93.849 1008 43 7 1321 2322 188544300 188543306 0.000000e+00 1500
3 TraesCS7A01G226100 chr7B 92.004 1013 46 9 1070 2075 332340005 332339021 0.000000e+00 1389
4 TraesCS7A01G226100 chr7B 92.500 360 15 8 722 1073 332340517 332340162 2.660000e-139 505
5 TraesCS7A01G226100 chr7B 91.538 260 14 2 2071 2322 332315595 332315336 3.670000e-93 351
6 TraesCS7A01G226100 chr7B 82.222 405 48 15 39 428 556498177 556498572 6.190000e-86 327
7 TraesCS7A01G226100 chr7B 84.914 232 21 9 273 492 332340741 332340512 3.000000e-54 222
8 TraesCS7A01G226100 chr5D 81.514 449 58 11 1 424 282379208 282379656 1.710000e-91 346
9 TraesCS7A01G226100 chr5D 88.333 240 25 3 486 723 4029902 4030140 3.780000e-73 285
10 TraesCS7A01G226100 chr4B 90.377 239 21 2 487 723 183525224 183524986 1.730000e-81 313
11 TraesCS7A01G226100 chr2D 87.866 239 27 2 487 723 428709914 428710152 1.760000e-71 279
12 TraesCS7A01G226100 chr2B 87.866 239 27 2 487 723 273870008 273869770 1.760000e-71 279
13 TraesCS7A01G226100 chr5A 87.500 240 28 2 487 724 589296932 589296693 2.270000e-70 276
14 TraesCS7A01G226100 chr6B 86.220 254 32 3 475 725 454030303 454030556 2.940000e-69 272
15 TraesCS7A01G226100 chr1D 87.029 239 29 2 487 723 366857639 366857401 3.800000e-68 268
16 TraesCS7A01G226100 chr5B 86.531 245 26 6 487 726 529963621 529963863 1.770000e-66 263
17 TraesCS7A01G226100 chr6D 84.024 169 25 2 1716 1884 17131425 17131591 6.640000e-36 161


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 TraesCS7A01G226100 chr7A 195485624 195487945 2321 False 4289.000000 4289 100.000 1 2322 1 chr7A.!!$F1 2321
1 TraesCS7A01G226100 chr7D 188549322 188550660 1338 True 2056.000000 2056 94.506 1 1331 1 chr7D.!!$R2 1330
2 TraesCS7A01G226100 chr7D 188543306 188544300 994 True 1500.000000 1500 93.849 1321 2322 1 chr7D.!!$R1 1001
3 TraesCS7A01G226100 chr7B 332339021 332340741 1720 True 705.333333 1389 89.806 273 2075 3 chr7B.!!$R2 1802

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
502 525 0.107017 CCCTACTACCTTCGTCCGGA 60.107 60.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2140 2343 1.200519 ATAACCACTTAGGCCGAGCA 58.799 50.0 8.86 0.0 43.14 4.26 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
38 39 5.591877 AGCTAGCATTGGAGTAAATGGAAAG 59.408 40.000 18.83 0.00 37.89 2.62
41 42 6.272822 AGCATTGGAGTAAATGGAAAGAAC 57.727 37.500 0.00 0.00 37.89 3.01
45 46 5.223449 TGGAGTAAATGGAAAGAACGAGT 57.777 39.130 0.00 0.00 0.00 4.18
85 86 7.509318 ACTGGCCTATAAGTGACTGTTATATCA 59.491 37.037 3.32 0.00 0.00 2.15
111 112 7.359595 TCAATTTCATCGTTTTACTGTGGAAG 58.640 34.615 0.00 0.00 0.00 3.46
133 134 1.276421 GTAGCTTCCAAGAGGCTCACA 59.724 52.381 18.26 0.00 41.02 3.58
147 148 2.338500 GCTCACACTACTAACACTGGC 58.662 52.381 0.00 0.00 0.00 4.85
169 170 4.439974 GCTGACACCAAGTTCAAAACATGA 60.440 41.667 0.00 0.00 32.12 3.07
224 226 7.611855 CCACTCTCCTCTTAAAACAAATACCAT 59.388 37.037 0.00 0.00 0.00 3.55
226 228 8.383175 ACTCTCCTCTTAAAACAAATACCATCA 58.617 33.333 0.00 0.00 0.00 3.07
227 229 8.792830 TCTCCTCTTAAAACAAATACCATCAG 57.207 34.615 0.00 0.00 0.00 2.90
297 308 5.352569 AGATGATAAAAGAACGCCAGAACAG 59.647 40.000 0.00 0.00 0.00 3.16
327 338 4.542697 ACCCAAACCAACACAGATAAACT 58.457 39.130 0.00 0.00 0.00 2.66
438 460 9.148879 ACAGCCTCTAGTACTAATTGACATTAT 57.851 33.333 3.76 0.00 0.00 1.28
450 472 9.772973 ACTAATTGACATTATAAACGAGGCATA 57.227 29.630 0.00 0.00 0.00 3.14
502 525 0.107017 CCCTACTACCTTCGTCCGGA 60.107 60.000 0.00 0.00 0.00 5.14
528 551 0.815095 GGCCCCCTTCGTATTTTGTG 59.185 55.000 0.00 0.00 0.00 3.33
534 557 2.495669 CCCTTCGTATTTTGTGCCCAAT 59.504 45.455 0.00 0.00 0.00 3.16
541 564 5.866633 TCGTATTTTGTGCCCAATTTTCATC 59.133 36.000 0.00 0.00 0.00 2.92
594 617 9.567848 GGTATGTCACAAAACTTATATTGTTGG 57.432 33.333 0.00 0.00 37.66 3.77
616 639 9.358872 GTTGGATTCATATTTGAAAGAGGTTTC 57.641 33.333 2.59 0.00 44.70 2.78
621 644 9.880157 ATTCATATTTGAAAGAGGTTTCCAATG 57.120 29.630 2.59 2.14 44.70 2.82
970 1003 0.612229 AGCAGACACCTCACCTGATG 59.388 55.000 0.00 0.00 0.00 3.07
1016 1053 4.024556 CACAAGGATGAAGACTGTCAACAC 60.025 45.833 10.88 4.94 0.00 3.32
1068 1265 6.116126 GCTATCCTCAGGTAATCAACAGTTT 58.884 40.000 0.00 0.00 0.00 2.66
1120 1317 9.987272 CTTTTCTGTTGATTTTTCCTAATCCTT 57.013 29.630 0.00 0.00 34.34 3.36
1416 1613 2.203907 AGCCAGCCCTGAGTCACT 60.204 61.111 0.00 0.00 0.00 3.41
1454 1651 9.390795 CACTGCAGAATGTATTGATTTATAAGC 57.609 33.333 23.35 0.00 33.36 3.09
1587 1784 8.300286 TGAGCGGAATTAGATAAACTAGATGAG 58.700 37.037 0.00 0.00 32.30 2.90
1627 1824 4.091800 CGGAAACCTTGCTAAAAATGCATG 59.908 41.667 0.00 0.00 40.34 4.06
1640 1837 8.909671 GCTAAAAATGCATGAATAGTTGCTATC 58.090 33.333 0.00 0.00 39.60 2.08
1700 1902 8.246871 AGCTTAAAAGATAAAATGAGAAGTGCC 58.753 33.333 0.00 0.00 0.00 5.01
1712 1914 4.899502 TGAGAAGTGCCTAAAAAGAGAGG 58.100 43.478 0.00 0.00 35.78 3.69
1713 1915 4.257731 GAGAAGTGCCTAAAAAGAGAGGG 58.742 47.826 0.00 0.00 33.04 4.30
1801 2003 3.076079 TGCATGAAGTGATGATGTGGT 57.924 42.857 0.00 0.00 0.00 4.16
2009 2211 7.680730 TCACTTCTCAAGCTTATCTAAAAGGT 58.319 34.615 0.00 0.00 38.80 3.50
2117 2320 1.717077 AGGGTCACACCTCCTTCTCTA 59.283 52.381 0.00 0.00 38.64 2.43
2132 2335 6.569780 TCCTTCTCTAAACAAAAACAAAGGC 58.430 36.000 0.00 0.00 32.61 4.35
2153 2356 3.733337 CAATAGATTGCTCGGCCTAAGT 58.267 45.455 0.00 0.00 0.00 2.24
2155 2358 0.179000 AGATTGCTCGGCCTAAGTGG 59.821 55.000 0.00 0.00 39.35 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.675698 GTCCATCAAACTCTCACTCGTTC 59.324 47.826 0.00 0.00 0.00 3.95
41 42 3.249091 CAGTCCATCAAACTCTCACTCG 58.751 50.000 0.00 0.00 0.00 4.18
45 46 1.003580 GGCCAGTCCATCAAACTCTCA 59.996 52.381 0.00 0.00 34.01 3.27
85 86 7.447374 TCCACAGTAAAACGATGAAATTGAT 57.553 32.000 0.00 0.00 0.00 2.57
111 112 1.827969 TGAGCCTCTTGGAAGCTACTC 59.172 52.381 0.00 0.00 36.87 2.59
133 134 2.299297 GGTGTCAGCCAGTGTTAGTAGT 59.701 50.000 0.00 0.00 0.00 2.73
147 148 5.247507 TCATGTTTTGAACTTGGTGTCAG 57.752 39.130 0.00 0.00 37.22 3.51
169 170 1.303317 GCGTGGATGGGTGTCCTTT 60.303 57.895 0.00 0.00 39.12 3.11
174 175 3.171828 TTCGTGCGTGGATGGGTGT 62.172 57.895 0.00 0.00 0.00 4.16
224 226 4.138290 TCTTACGAATTTTGTTGGCCTGA 58.862 39.130 3.32 0.00 0.00 3.86
226 228 5.523438 TTTCTTACGAATTTTGTTGGCCT 57.477 34.783 3.32 0.00 0.00 5.19
227 229 6.415702 GTTTTTCTTACGAATTTTGTTGGCC 58.584 36.000 0.00 0.00 0.00 5.36
284 295 4.524749 GTTTTAGTTCTGTTCTGGCGTTC 58.475 43.478 0.00 0.00 0.00 3.95
297 308 5.074584 TGTGTTGGTTTGGGTTTTAGTTC 57.925 39.130 0.00 0.00 0.00 3.01
341 357 6.654582 TCTTCTTTAGCATGTTATTGCAGTCA 59.345 34.615 0.00 0.00 45.23 3.41
383 405 1.092921 TGCTGCGTCGTTTTTCACCT 61.093 50.000 0.00 0.00 0.00 4.00
412 434 7.425224 AATGTCAATTAGTACTAGAGGCTGT 57.575 36.000 2.23 0.00 0.00 4.40
438 460 2.029200 TGGTTGACGTATGCCTCGTTTA 60.029 45.455 0.00 0.00 41.64 2.01
484 507 1.978454 ATCCGGACGAAGGTAGTAGG 58.022 55.000 6.12 0.00 0.00 3.18
502 525 0.406361 TACGAAGGGGGCCAACAAAT 59.594 50.000 4.39 0.00 0.00 2.32
528 551 5.743872 GTCAAATCTACGATGAAAATTGGGC 59.256 40.000 0.00 0.00 0.00 5.36
565 588 9.515226 ACAATATAAGTTTTGTGACATACCACT 57.485 29.630 0.00 0.00 37.89 4.00
588 611 8.421249 ACCTCTTTCAAATATGAATCCAACAA 57.579 30.769 0.00 0.00 44.70 2.83
590 613 9.358872 GAAACCTCTTTCAAATATGAATCCAAC 57.641 33.333 0.00 0.00 44.70 3.77
681 705 9.070179 GTTTATTAGTCACCCTTTTAGTTTGGA 57.930 33.333 0.00 0.00 0.00 3.53
970 1003 9.965824 TGTGAATGAAAGATAAAAAGGAAACTC 57.034 29.630 0.00 0.00 42.68 3.01
983 1016 7.120873 CAGTCTTCATCCTTGTGAATGAAAGAT 59.879 37.037 0.00 0.00 37.47 2.40
1016 1053 0.316204 AGTAAGACCCACGAACACCG 59.684 55.000 0.00 0.00 45.44 4.94
1033 1070 3.054802 CCTGAGGATAGCACCAAAAGAGT 60.055 47.826 0.00 0.00 0.00 3.24
1068 1265 6.916440 ACGTCGGATTACATGCATAATACTA 58.084 36.000 0.00 0.00 0.00 1.82
1120 1317 4.449068 GCAGATCTCAGAAAGAAACGAACA 59.551 41.667 0.00 0.00 37.61 3.18
1168 1365 1.513800 CGAGTCACTGCAGAGCTCG 60.514 63.158 28.06 28.06 42.01 5.03
1416 1613 6.230472 ACATTCTGCAGTGACAAGTAATGTA 58.770 36.000 19.00 0.00 44.12 2.29
1841 2043 9.701098 AAATATGTGATAAATGCAAGCCATAAG 57.299 29.630 0.00 0.00 32.67 1.73
2132 2335 3.496130 CACTTAGGCCGAGCAATCTATTG 59.504 47.826 8.86 0.00 40.66 1.90
2140 2343 1.200519 ATAACCACTTAGGCCGAGCA 58.799 50.000 8.86 0.00 43.14 4.26


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

AutoCloner maintained by Alex Coulton.