Multiple sequence alignment - TraesCS7A01G289800

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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 TraesCS7A01G289800 chr7A 100.000 2350 0 0 1 2350 352193859 352191510 0.000000e+00 4340.0
1 TraesCS7A01G289800 chr5D 95.374 2356 101 8 1 2350 560872633 560874986 0.000000e+00 3740.0
2 TraesCS7A01G289800 chr5D 94.688 2278 111 10 1 2272 6201116 6198843 0.000000e+00 3528.0
3 TraesCS7A01G289800 chr5D 94.667 2194 107 10 1 2189 329162342 329164530 0.000000e+00 3395.0
4 TraesCS7A01G289800 chr1D 95.204 2356 105 8 1 2350 254498162 254500515 0.000000e+00 3718.0
5 TraesCS7A01G289800 chr1D 90.811 1948 133 27 1 1942 244483884 244481977 0.000000e+00 2564.0
6 TraesCS7A01G289800 chr1A 93.968 2354 127 14 1 2349 168450402 168448059 0.000000e+00 3546.0
7 TraesCS7A01G289800 chr4D 93.628 2354 140 10 1 2349 19916660 19919008 0.000000e+00 3507.0
8 TraesCS7A01G289800 chr3B 95.800 1619 61 7 736 2350 201515580 201517195 0.000000e+00 2606.0
9 TraesCS7A01G289800 chr3B 92.208 1001 62 7 1351 2350 524777564 524776579 0.000000e+00 1402.0
10 TraesCS7A01G289800 chr3B 98.077 52 1 0 2246 2297 636817437 636817386 8.940000e-15 91.6
11 TraesCS7A01G289800 chr3B 97.368 38 1 0 2242 2279 636831910 636831947 5.420000e-07 65.8
12 TraesCS7A01G289800 chr6B 94.068 1315 76 2 1 1313 22426109 22427423 0.000000e+00 1995.0
13 TraesCS7A01G289800 chr7B 93.719 1003 44 11 1350 2350 102632114 102631129 0.000000e+00 1485.0
14 TraesCS7A01G289800 chr3D 94.742 951 47 3 1 949 21904792 21905741 0.000000e+00 1476.0
15 TraesCS7A01G289800 chr4A 92.593 216 16 0 2024 2239 76930700 76930915 6.310000e-81 311.0
16 TraesCS7A01G289800 chr2A 92.381 105 7 1 1231 1334 588453430 588453534 5.230000e-32 148.0


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 TraesCS7A01G289800 chr7A 352191510 352193859 2349 True 4340 4340 100.000 1 2350 1 chr7A.!!$R1 2349
1 TraesCS7A01G289800 chr5D 560872633 560874986 2353 False 3740 3740 95.374 1 2350 1 chr5D.!!$F2 2349
2 TraesCS7A01G289800 chr5D 6198843 6201116 2273 True 3528 3528 94.688 1 2272 1 chr5D.!!$R1 2271
3 TraesCS7A01G289800 chr5D 329162342 329164530 2188 False 3395 3395 94.667 1 2189 1 chr5D.!!$F1 2188
4 TraesCS7A01G289800 chr1D 254498162 254500515 2353 False 3718 3718 95.204 1 2350 1 chr1D.!!$F1 2349
5 TraesCS7A01G289800 chr1D 244481977 244483884 1907 True 2564 2564 90.811 1 1942 1 chr1D.!!$R1 1941
6 TraesCS7A01G289800 chr1A 168448059 168450402 2343 True 3546 3546 93.968 1 2349 1 chr1A.!!$R1 2348
7 TraesCS7A01G289800 chr4D 19916660 19919008 2348 False 3507 3507 93.628 1 2349 1 chr4D.!!$F1 2348
8 TraesCS7A01G289800 chr3B 201515580 201517195 1615 False 2606 2606 95.800 736 2350 1 chr3B.!!$F1 1614
9 TraesCS7A01G289800 chr3B 524776579 524777564 985 True 1402 1402 92.208 1351 2350 1 chr3B.!!$R1 999
10 TraesCS7A01G289800 chr6B 22426109 22427423 1314 False 1995 1995 94.068 1 1313 1 chr6B.!!$F1 1312
11 TraesCS7A01G289800 chr7B 102631129 102632114 985 True 1485 1485 93.719 1350 2350 1 chr7B.!!$R1 1000
12 TraesCS7A01G289800 chr3D 21904792 21905741 949 False 1476 1476 94.742 1 949 1 chr3D.!!$F1 948

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
347 350 1.271856 TTGAATCAGACCGGGCTACA 58.728 50.0 11.18 5.41 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2166 1.144969 CGTACGGCTCAAGCAGAAAA 58.855 50.0 7.57 0.0 44.36 2.29 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
26 27 1.423161 GGATTATTCAGGGCAGGCTCT 59.577 52.381 0.00 0.00 0.00 4.09
36 37 1.699634 GGGCAGGCTCTATGGACAATA 59.300 52.381 0.00 0.00 0.00 1.90
197 199 4.201763 GCAGACATTCCTTTTAGAAGAGCG 60.202 45.833 0.00 0.00 34.71 5.03
244 246 5.404395 AGTAGGAGTAAAGGTGGAGTTCTT 58.596 41.667 0.00 0.00 0.00 2.52
246 248 5.648330 AGGAGTAAAGGTGGAGTTCTTTT 57.352 39.130 0.00 0.00 35.22 2.27
286 288 7.510685 TGGAGTAAGTTATTCTGATCCTGCTAT 59.489 37.037 5.50 0.00 0.00 2.97
319 322 3.266510 TGCGAGGCATTCTCAATTAGT 57.733 42.857 0.00 0.00 42.55 2.24
347 350 1.271856 TTGAATCAGACCGGGCTACA 58.728 50.000 11.18 5.41 0.00 2.74
357 360 2.872858 GACCGGGCTACATTGAAATCTC 59.127 50.000 6.32 0.00 0.00 2.75
374 377 2.571212 TCTCATGGTGTTTTTCGCAGT 58.429 42.857 0.00 0.00 0.00 4.40
421 424 1.545582 TCATGCTACCTTTGCTTTGCC 59.454 47.619 0.00 0.00 0.00 4.52
439 442 1.679153 GCCCTTCTTTTTCGGACACAA 59.321 47.619 0.00 0.00 0.00 3.33
450 453 1.875420 CGGACACAATTGGCATGGCA 61.875 55.000 19.43 19.43 28.57 4.92
478 481 5.514274 ACATTGTTCCGAGATGTTTTTGT 57.486 34.783 0.00 0.00 30.22 2.83
559 562 4.351111 AGATCCAACTACAAGGAAACAGGT 59.649 41.667 0.00 0.00 37.48 4.00
738 742 5.482908 ACCAGATCGAATATATGGAAGCAC 58.517 41.667 5.22 0.00 34.99 4.40
759 763 6.882678 AGCACTGGTTTATACGTTCCTTTTAT 59.117 34.615 0.00 0.00 0.00 1.40
829 834 3.245264 CCTAAGGTTCCACCAACTCCAAT 60.245 47.826 0.00 0.00 41.95 3.16
899 904 7.631007 AGGGGGACTTCTTACTTAAATTAGTG 58.369 38.462 0.00 0.00 0.00 2.74
941 946 6.887002 GGATCTCTTAATTGTTGAGAGGGTTT 59.113 38.462 10.41 0.00 42.03 3.27
974 979 6.670902 ACGGTATATAAGGCATACCCAGTAAT 59.329 38.462 6.25 0.00 43.39 1.89
976 981 7.364408 CGGTATATAAGGCATACCCAGTAATGT 60.364 40.741 6.25 0.00 43.39 2.71
1009 1014 0.463204 AGATGTGGAGATGGCGACTG 59.537 55.000 0.00 0.00 0.00 3.51
1016 1021 1.066858 GGAGATGGCGACTGAAGTTGA 60.067 52.381 1.68 0.00 0.00 3.18
1175 1180 5.056553 AGTTCTAAACCTAGGCCAAAACA 57.943 39.130 9.30 0.00 0.00 2.83
1181 1186 3.306472 ACCTAGGCCAAAACAAACTGA 57.694 42.857 9.30 0.00 0.00 3.41
1203 1208 4.425180 TGCAGGTAGTTTACTGAAACCA 57.575 40.909 0.00 0.00 45.21 3.67
1233 1238 2.509964 AGAATATGGAAAAGTCGCCCCT 59.490 45.455 0.00 0.00 0.00 4.79
1604 1612 7.526142 AGTATCTGGAGCACGAAATAGATAA 57.474 36.000 0.00 0.00 31.28 1.75
1612 1620 6.146347 GGAGCACGAAATAGATAAAGTGGATC 59.854 42.308 0.00 0.00 0.00 3.36
1617 1625 9.490663 CACGAAATAGATAAAGTGGATCAAAAC 57.509 33.333 0.00 0.00 0.00 2.43
1657 1665 6.504398 TCATACTCACTATTAAGACCTTGCG 58.496 40.000 0.00 0.00 0.00 4.85
1841 1852 5.184671 CCTTGCCTTTTCTTTAGCTTGAGAT 59.815 40.000 0.00 0.00 0.00 2.75
1842 1853 5.633830 TGCCTTTTCTTTAGCTTGAGATG 57.366 39.130 0.00 0.00 0.00 2.90
2009 2020 5.388599 AGGGAAAGGAAGAAAGAAAGACA 57.611 39.130 0.00 0.00 0.00 3.41
2045 2057 9.153721 GAGATTTTTGGCATTATCATCACAAAA 57.846 29.630 0.00 0.00 36.41 2.44
2210 2223 0.185416 CGGCTCTTAGAGGGGGACTA 59.815 60.000 11.54 0.00 0.00 2.59
2331 2345 9.520204 CTTCCCATGTCAACATATTTTATTGTC 57.480 33.333 0.00 0.00 34.26 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.289945 CCTATTGTCCATAGAGCCTGCC 60.290 54.545 0.00 0.00 37.65 4.85
26 27 6.032039 AGCTATTCCATCCCTATTGTCCATA 58.968 40.000 0.00 0.00 0.00 2.74
36 37 2.492025 TCCAACAGCTATTCCATCCCT 58.508 47.619 0.00 0.00 0.00 4.20
140 142 4.641989 CCCTCCTCATCTACCAAAACAATG 59.358 45.833 0.00 0.00 0.00 2.82
141 143 4.540099 TCCCTCCTCATCTACCAAAACAAT 59.460 41.667 0.00 0.00 0.00 2.71
197 199 8.739972 ACTTGTTCAACACTATATTTGGATTCC 58.260 33.333 0.00 0.00 0.00 3.01
232 234 1.692411 GCCACAAAAGAACTCCACCT 58.308 50.000 0.00 0.00 0.00 4.00
244 246 3.482436 ACTCCATTAAGTTCGCCACAAA 58.518 40.909 0.00 0.00 0.00 2.83
246 248 2.851263 ACTCCATTAAGTTCGCCACA 57.149 45.000 0.00 0.00 0.00 4.17
319 322 4.021544 CCCGGTCTGATTCAAAAATTTCCA 60.022 41.667 0.00 0.00 0.00 3.53
334 337 2.107950 TTTCAATGTAGCCCGGTCTG 57.892 50.000 0.00 0.00 0.00 3.51
347 350 5.634859 GCGAAAAACACCATGAGATTTCAAT 59.365 36.000 0.00 0.00 36.78 2.57
357 360 3.364964 GGACTACTGCGAAAAACACCATG 60.365 47.826 0.00 0.00 0.00 3.66
421 424 4.298332 CCAATTGTGTCCGAAAAAGAAGG 58.702 43.478 4.43 0.00 0.00 3.46
439 442 2.512692 TGTTCTAGTGCCATGCCAAT 57.487 45.000 0.00 0.00 0.00 3.16
450 453 5.407407 ACATCTCGGAACAATGTTCTAGT 57.593 39.130 23.30 11.36 0.00 2.57
673 676 7.888021 ACTTCCACACCTATTCATTTGTCATTA 59.112 33.333 0.00 0.00 0.00 1.90
727 731 5.925509 ACGTATAAACCAGTGCTTCCATAT 58.074 37.500 0.00 0.00 0.00 1.78
738 742 9.269415 CGAAAATAAAAGGAACGTATAAACCAG 57.731 33.333 0.00 0.00 0.00 4.00
795 800 2.249309 ACCTTAGGTGGTTCTCGGAT 57.751 50.000 1.74 0.00 36.89 4.18
899 904 4.499183 AGATCCATTCGAAGAACACAGAC 58.501 43.478 3.35 0.00 45.90 3.51
941 946 3.455177 TGCCTTATATACCGTGTTTGGGA 59.545 43.478 0.00 0.00 0.00 4.37
974 979 6.358178 TCCACATCTGGTTTACTTGTAAACA 58.642 36.000 27.08 16.98 40.63 2.83
976 981 6.833041 TCTCCACATCTGGTTTACTTGTAAA 58.167 36.000 2.22 2.22 38.90 2.01
994 999 0.247736 ACTTCAGTCGCCATCTCCAC 59.752 55.000 0.00 0.00 0.00 4.02
1175 1180 5.865085 TCAGTAAACTACCTGCATCAGTTT 58.135 37.500 18.65 18.65 43.16 2.66
1181 1186 4.980573 TGGTTTCAGTAAACTACCTGCAT 58.019 39.130 0.00 0.00 43.76 3.96
1203 1208 7.917505 GCGACTTTTCCATATTCTGAATTCAAT 59.082 33.333 9.88 3.76 0.00 2.57
1233 1238 2.127651 AAAGGAGTAGTCCCCAACCA 57.872 50.000 13.30 0.00 45.26 3.67
1369 1375 4.515191 TGGATGGAAAAACTCTGACTTTCG 59.485 41.667 0.00 0.00 31.21 3.46
1371 1377 6.790232 TTTGGATGGAAAAACTCTGACTTT 57.210 33.333 0.00 0.00 0.00 2.66
1590 1598 6.844696 TGATCCACTTTATCTATTTCGTGC 57.155 37.500 0.00 0.00 0.00 5.34
1604 1612 6.484364 AGTTCCATTTGTTTTGATCCACTT 57.516 33.333 0.00 0.00 0.00 3.16
1617 1625 9.334947 AGTGAGTATGAATCATAGTTCCATTTG 57.665 33.333 11.49 0.00 31.06 2.32
1657 1665 7.497925 ACTACTTGAATTTTTCAGTCTGGTC 57.502 36.000 0.00 0.00 41.38 4.02
1747 1756 8.184848 TGTAATGACTCGACAAAATAGAGAGAG 58.815 37.037 0.00 0.00 34.34 3.20
1754 1764 8.771920 AATCAGTGTAATGACTCGACAAAATA 57.228 30.769 0.00 0.00 30.46 1.40
1841 1852 5.301805 TCATACTAGAGCCACGATGATTTCA 59.698 40.000 0.00 0.00 0.00 2.69
1842 1853 5.773575 TCATACTAGAGCCACGATGATTTC 58.226 41.667 0.00 0.00 0.00 2.17
2084 2096 2.231235 GCCACTGAATTGGGTCGATTTT 59.769 45.455 0.00 0.00 37.10 1.82
2153 2166 1.144969 CGTACGGCTCAAGCAGAAAA 58.855 50.000 7.57 0.00 44.36 2.29
2307 2321 8.821686 AGACAATAAAATATGTTGACATGGGA 57.178 30.769 6.87 0.00 37.15 4.37


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

AutoCloner maintained by Alex Coulton.