Multiple sequence alignment - TraesCS7A01G290000

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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 TraesCS7A01G290000 chr7A 100.000 2453 0 0 1 2453 352194745 352192293 0 4530
1 TraesCS7A01G290000 chr1D 94.876 2459 119 6 1 2453 254497274 254499731 0 3836
2 TraesCS7A01G290000 chr1D 91.202 2455 179 20 1 2453 244484767 244482348 0 3302
3 TraesCS7A01G290000 chr5D 94.628 2457 125 7 1 2453 6202002 6199549 0 3799
4 TraesCS7A01G290000 chr5D 94.416 1773 93 6 683 2451 329162138 329163908 0 2721
5 TraesCS7A01G290000 chr5D 95.021 1647 78 4 810 2453 560872556 560874201 0 2584
6 TraesCS7A01G290000 chr4D 93.244 2457 158 8 1 2453 19915774 19918226 0 3611
7 TraesCS7A01G290000 chr6B 94.099 2203 126 4 1 2199 22425221 22427423 0 3345
8 TraesCS7A01G290000 chr1A 93.077 2210 137 10 252 2453 168451039 168448838 0 3219
9 TraesCS7A01G290000 chr1A 94.390 1123 61 2 1 1122 112776756 112775635 0 1724
10 TraesCS7A01G290000 chr3B 93.933 1978 93 4 1 1977 201512405 201514356 0 2963
11 TraesCS7A01G290000 chr3D 94.297 1841 97 5 1 1835 21903903 21905741 0 2811
12 TraesCS7A01G290000 chr3D 93.605 688 39 4 1632 2317 555757181 555757865 0 1022


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 TraesCS7A01G290000 chr7A 352192293 352194745 2452 True 4530 4530 100.000 1 2453 1 chr7A.!!$R1 2452
1 TraesCS7A01G290000 chr1D 254497274 254499731 2457 False 3836 3836 94.876 1 2453 1 chr1D.!!$F1 2452
2 TraesCS7A01G290000 chr1D 244482348 244484767 2419 True 3302 3302 91.202 1 2453 1 chr1D.!!$R1 2452
3 TraesCS7A01G290000 chr5D 6199549 6202002 2453 True 3799 3799 94.628 1 2453 1 chr5D.!!$R1 2452
4 TraesCS7A01G290000 chr5D 329162138 329163908 1770 False 2721 2721 94.416 683 2451 1 chr5D.!!$F1 1768
5 TraesCS7A01G290000 chr5D 560872556 560874201 1645 False 2584 2584 95.021 810 2453 1 chr5D.!!$F2 1643
6 TraesCS7A01G290000 chr4D 19915774 19918226 2452 False 3611 3611 93.244 1 2453 1 chr4D.!!$F1 2452
7 TraesCS7A01G290000 chr6B 22425221 22427423 2202 False 3345 3345 94.099 1 2199 1 chr6B.!!$F1 2198
8 TraesCS7A01G290000 chr1A 168448838 168451039 2201 True 3219 3219 93.077 252 2453 1 chr1A.!!$R2 2201
9 TraesCS7A01G290000 chr1A 112775635 112776756 1121 True 1724 1724 94.390 1 1122 1 chr1A.!!$R1 1121
10 TraesCS7A01G290000 chr3B 201512405 201514356 1951 False 2963 2963 93.933 1 1977 1 chr3B.!!$F1 1976
11 TraesCS7A01G290000 chr3D 21903903 21905741 1838 False 2811 2811 94.297 1 1835 1 chr3D.!!$F1 1834
12 TraesCS7A01G290000 chr3D 555757181 555757865 684 False 1022 1022 93.605 1632 2317 1 chr3D.!!$F2 685

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
259 260 0.102844 GCTTGTGTTTCTTGGCAGCA 59.897 50.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 1943 0.247736 ACTTCAGTCGCCATCTCCAC 59.752 55.0 0.0 0.0 0.0 4.02 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
24 25 4.799586 GCACACAGCTCTAGTTTCTGGTTA 60.800 45.833 11.29 0.00 41.15 2.85
27 28 4.220821 CACAGCTCTAGTTTCTGGTTAGGA 59.779 45.833 11.29 0.00 32.42 2.94
94 95 1.747355 CCTGTTCTGGATCCAATGTGC 59.253 52.381 17.00 5.31 0.00 4.57
144 145 6.338146 TCATGACTCGTTTAGGAATAACAGG 58.662 40.000 0.00 0.00 0.00 4.00
152 153 5.240121 GTTTAGGAATAACAGGTTCGTGGA 58.760 41.667 0.00 0.00 0.00 4.02
176 177 3.263425 TGGTTGGAGTATTTCAGGAGGAC 59.737 47.826 0.00 0.00 0.00 3.85
179 180 4.620086 TGGAGTATTTCAGGAGGACCTA 57.380 45.455 0.00 0.00 45.94 3.08
189 190 7.510675 TTTCAGGAGGACCTATAACAAATCT 57.489 36.000 0.00 0.00 45.94 2.40
222 223 3.523564 AGTTATGAAGGTGTGGCAGGTAT 59.476 43.478 0.00 0.00 0.00 2.73
259 260 0.102844 GCTTGTGTTTCTTGGCAGCA 59.897 50.000 0.00 0.00 0.00 4.41
279 280 5.011329 CAGCAATCTGGCATTGGGTATATTT 59.989 40.000 3.25 0.00 36.68 1.40
434 435 6.945322 ATGGTCCTAGGATATGGGTATCTA 57.055 41.667 16.27 0.00 37.46 1.98
435 436 6.342819 TGGTCCTAGGATATGGGTATCTAG 57.657 45.833 16.27 0.00 37.46 2.43
522 529 5.711698 TCCTTTTGTTTTGAGGGGAATAGT 58.288 37.500 0.00 0.00 0.00 2.12
540 547 7.446625 GGGAATAGTTTCTCATCATATTGCTGT 59.553 37.037 0.00 0.00 32.18 4.40
597 604 1.115930 AGTGTCCGTCTGCCTCAACT 61.116 55.000 0.00 0.00 0.00 3.16
615 622 9.998106 GCCTCAACTTCTATATAAAGGATTACA 57.002 33.333 0.00 0.00 0.00 2.41
657 664 8.223177 ACTGTACTTTCTAGTAATATCGCTGT 57.777 34.615 0.00 0.00 38.55 4.40
685 696 0.606096 TGCAGCTTTCGTAGTGGCTA 59.394 50.000 0.00 0.00 33.43 3.93
770 781 1.349357 GGATCAGGGATACTTCCAGCC 59.651 57.143 0.00 0.00 44.60 4.85
817 828 6.679327 ATGGTTTAGCCGAAAATCTTAGTC 57.321 37.500 0.00 0.00 41.21 2.59
837 848 8.540507 TTAGTCTATCAGAAGCTTGGTCTAAT 57.459 34.615 2.10 0.00 0.00 1.73
845 856 4.409247 AGAAGCTTGGTCTAATATTCCCGT 59.591 41.667 2.10 0.00 0.00 5.28
903 914 2.700371 GGCAAAAGGGGGATTATTCAGG 59.300 50.000 0.00 0.00 0.00 3.86
912 923 1.423161 GGATTATTCAGGGCAGGCTCT 59.577 52.381 0.00 0.00 0.00 4.09
922 933 1.699634 GGGCAGGCTCTATGGACAATA 59.300 52.381 0.00 0.00 0.00 1.90
1083 1095 4.201763 GCAGACATTCCTTTTAGAAGAGCG 60.202 45.833 0.00 0.00 34.71 5.03
1130 1166 5.404395 AGTAGGAGTAAAGGTGGAGTTCTT 58.596 41.667 0.00 0.00 0.00 2.52
1132 1168 5.648330 AGGAGTAAAGGTGGAGTTCTTTT 57.352 39.130 0.00 0.00 35.22 2.27
1172 1232 7.510685 TGGAGTAAGTTATTCTGATCCTGCTAT 59.489 37.037 5.50 0.00 0.00 2.97
1205 1266 3.266510 TGCGAGGCATTCTCAATTAGT 57.733 42.857 0.00 0.00 42.55 2.24
1233 1294 1.271856 TTGAATCAGACCGGGCTACA 58.728 50.000 11.18 5.41 0.00 2.74
1243 1304 2.872858 GACCGGGCTACATTGAAATCTC 59.127 50.000 6.32 0.00 0.00 2.75
1260 1321 2.571212 TCTCATGGTGTTTTTCGCAGT 58.429 42.857 0.00 0.00 0.00 4.40
1307 1368 1.545582 TCATGCTACCTTTGCTTTGCC 59.454 47.619 0.00 0.00 0.00 4.52
1325 1386 1.679153 GCCCTTCTTTTTCGGACACAA 59.321 47.619 0.00 0.00 0.00 3.33
1336 1397 1.875420 CGGACACAATTGGCATGGCA 61.875 55.000 19.43 19.43 28.57 4.92
1364 1425 5.514274 ACATTGTTCCGAGATGTTTTTGT 57.486 34.783 0.00 0.00 30.22 2.83
1445 1506 4.351111 AGATCCAACTACAAGGAAACAGGT 59.649 41.667 0.00 0.00 37.48 4.00
1624 1686 5.482908 ACCAGATCGAATATATGGAAGCAC 58.517 41.667 5.22 0.00 34.99 4.40
1645 1707 6.882678 AGCACTGGTTTATACGTTCCTTTTAT 59.117 34.615 0.00 0.00 0.00 1.40
1715 1778 3.245264 CCTAAGGTTCCACCAACTCCAAT 60.245 47.826 0.00 0.00 41.95 3.16
1785 1848 7.631007 AGGGGGACTTCTTACTTAAATTAGTG 58.369 38.462 0.00 0.00 0.00 2.74
1827 1890 6.887002 GGATCTCTTAATTGTTGAGAGGGTTT 59.113 38.462 10.41 0.00 42.03 3.27
1860 1923 6.670902 ACGGTATATAAGGCATACCCAGTAAT 59.329 38.462 6.25 0.00 43.39 1.89
1862 1925 7.364408 CGGTATATAAGGCATACCCAGTAATGT 60.364 40.741 6.25 0.00 43.39 2.71
1895 1958 0.463204 AGATGTGGAGATGGCGACTG 59.537 55.000 0.00 0.00 0.00 3.51
1902 1965 1.066858 GGAGATGGCGACTGAAGTTGA 60.067 52.381 1.68 0.00 0.00 3.18
2061 2124 5.056553 AGTTCTAAACCTAGGCCAAAACA 57.943 39.130 9.30 0.00 0.00 2.83
2067 2130 3.306472 ACCTAGGCCAAAACAAACTGA 57.694 42.857 9.30 0.00 0.00 3.41
2089 2152 4.425180 TGCAGGTAGTTTACTGAAACCA 57.575 40.909 0.00 0.00 45.21 3.67
2119 2182 2.509964 AGAATATGGAAAAGTCGCCCCT 59.490 45.455 0.00 0.00 0.00 4.79
2163 2227 1.134175 CGGGTCGCAATGGCTTTATTT 59.866 47.619 0.00 0.00 38.10 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.607490 ATAAAGCCATTGAGCCATCCT 57.393 42.857 0.00 0.00 0.00 3.24
27 28 4.085357 TCGTATAAAGCCATTGAGCCAT 57.915 40.909 0.00 0.00 0.00 4.40
94 95 5.293569 GGGAATTACGAACATACCTTGTCTG 59.706 44.000 0.00 0.00 37.68 3.51
144 145 0.106149 ACTCCAACCACTCCACGAAC 59.894 55.000 0.00 0.00 0.00 3.95
152 153 3.264450 CCTCCTGAAATACTCCAACCACT 59.736 47.826 0.00 0.00 0.00 4.00
176 177 7.998964 ACTCCAAATACCCAGATTTGTTATAGG 59.001 37.037 7.80 0.00 42.72 2.57
179 180 9.936329 ATAACTCCAAATACCCAGATTTGTTAT 57.064 29.630 7.80 0.00 42.72 1.89
189 190 5.014755 ACACCTTCATAACTCCAAATACCCA 59.985 40.000 0.00 0.00 0.00 4.51
222 223 6.016360 ACACAAGCTAGAAAACACAATATGCA 60.016 34.615 0.00 0.00 0.00 3.96
239 240 0.386838 GCTGCCAAGAAACACAAGCT 59.613 50.000 0.00 0.00 0.00 3.74
259 260 5.539955 GTCCAAATATACCCAATGCCAGATT 59.460 40.000 0.00 0.00 0.00 2.40
279 280 6.673583 TCATCAGAGACTATTTCTAGGTCCA 58.326 40.000 0.00 0.00 33.22 4.02
293 294 1.064946 CCGTCCGCTCATCAGAGAC 59.935 63.158 0.00 0.00 44.98 3.36
452 453 7.440523 CTGGATTTACAGCTTGTACTTTTCT 57.559 36.000 0.00 0.00 31.69 2.52
522 529 4.858850 ACCCACAGCAATATGATGAGAAA 58.141 39.130 2.23 0.00 35.45 2.52
540 547 4.020039 CCGCTAATATACCCAATGTACCCA 60.020 45.833 0.00 0.00 30.62 4.51
615 622 8.766994 AAGTACAGTTTCAATATTGCCCATAT 57.233 30.769 10.76 0.00 0.00 1.78
681 692 3.646637 ACCCATACCACATAGTTCTAGCC 59.353 47.826 0.00 0.00 0.00 3.93
685 696 3.134804 GCTGACCCATACCACATAGTTCT 59.865 47.826 0.00 0.00 0.00 3.01
717 728 3.463944 AGTAGGCCCAAATAATTCGACG 58.536 45.455 0.00 0.00 0.00 5.12
817 828 7.821846 GGGAATATTAGACCAAGCTTCTGATAG 59.178 40.741 0.00 0.00 28.31 2.08
881 892 2.700371 CTGAATAATCCCCCTTTTGCCC 59.300 50.000 0.00 0.00 0.00 5.36
903 914 2.289945 CCTATTGTCCATAGAGCCTGCC 60.290 54.545 0.00 0.00 37.65 4.85
912 923 6.032039 AGCTATTCCATCCCTATTGTCCATA 58.968 40.000 0.00 0.00 0.00 2.74
922 933 2.492025 TCCAACAGCTATTCCATCCCT 58.508 47.619 0.00 0.00 0.00 4.20
1026 1038 4.641989 CCCTCCTCATCTACCAAAACAATG 59.358 45.833 0.00 0.00 0.00 2.82
1027 1039 4.540099 TCCCTCCTCATCTACCAAAACAAT 59.460 41.667 0.00 0.00 0.00 2.71
1083 1095 8.739972 ACTTGTTCAACACTATATTTGGATTCC 58.260 33.333 0.00 0.00 0.00 3.01
1118 1154 1.692411 GCCACAAAAGAACTCCACCT 58.308 50.000 0.00 0.00 0.00 4.00
1130 1166 3.482436 ACTCCATTAAGTTCGCCACAAA 58.518 40.909 0.00 0.00 0.00 2.83
1132 1168 2.851263 ACTCCATTAAGTTCGCCACA 57.149 45.000 0.00 0.00 0.00 4.17
1205 1266 4.021544 CCCGGTCTGATTCAAAAATTTCCA 60.022 41.667 0.00 0.00 0.00 3.53
1220 1281 2.107950 TTTCAATGTAGCCCGGTCTG 57.892 50.000 0.00 0.00 0.00 3.51
1233 1294 5.634859 GCGAAAAACACCATGAGATTTCAAT 59.365 36.000 0.00 0.00 36.78 2.57
1243 1304 3.364964 GGACTACTGCGAAAAACACCATG 60.365 47.826 0.00 0.00 0.00 3.66
1307 1368 4.298332 CCAATTGTGTCCGAAAAAGAAGG 58.702 43.478 4.43 0.00 0.00 3.46
1325 1386 2.512692 TGTTCTAGTGCCATGCCAAT 57.487 45.000 0.00 0.00 0.00 3.16
1336 1397 5.407407 ACATCTCGGAACAATGTTCTAGT 57.593 39.130 23.30 11.36 0.00 2.57
1559 1620 7.888021 ACTTCCACACCTATTCATTTGTCATTA 59.112 33.333 0.00 0.00 0.00 1.90
1613 1675 5.925509 ACGTATAAACCAGTGCTTCCATAT 58.074 37.500 0.00 0.00 0.00 1.78
1624 1686 9.269415 CGAAAATAAAAGGAACGTATAAACCAG 57.731 33.333 0.00 0.00 0.00 4.00
1681 1744 2.249309 ACCTTAGGTGGTTCTCGGAT 57.751 50.000 1.74 0.00 36.89 4.18
1785 1848 4.499183 AGATCCATTCGAAGAACACAGAC 58.501 43.478 3.35 0.00 45.90 3.51
1827 1890 3.455177 TGCCTTATATACCGTGTTTGGGA 59.545 43.478 0.00 0.00 0.00 4.37
1860 1923 6.358178 TCCACATCTGGTTTACTTGTAAACA 58.642 36.000 27.08 16.98 40.63 2.83
1862 1925 6.833041 TCTCCACATCTGGTTTACTTGTAAA 58.167 36.000 2.22 2.22 38.90 2.01
1880 1943 0.247736 ACTTCAGTCGCCATCTCCAC 59.752 55.000 0.00 0.00 0.00 4.02
2061 2124 5.865085 TCAGTAAACTACCTGCATCAGTTT 58.135 37.500 18.65 18.65 43.16 2.66
2067 2130 4.980573 TGGTTTCAGTAAACTACCTGCAT 58.019 39.130 0.00 0.00 43.76 3.96
2089 2152 7.917505 GCGACTTTTCCATATTCTGAATTCAAT 59.082 33.333 9.88 3.76 0.00 2.57
2119 2182 2.127651 AAAGGAGTAGTCCCCAACCA 57.872 50.000 13.30 0.00 45.26 3.67
2255 2319 4.515191 TGGATGGAAAAACTCTGACTTTCG 59.485 41.667 0.00 0.00 31.21 3.46
2257 2321 6.790232 TTTGGATGGAAAAACTCTGACTTT 57.210 33.333 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.