Multiple sequence alignment - TraesCS7A01G102000

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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 TraesCS7A01G102000 chr7A 100.000 3345 0 0 1 3345 62833126 62829782 0.000000e+00 6178
1 TraesCS7A01G102000 chr7A 96.718 1432 45 2 1907 3336 446620207 446618776 0.000000e+00 2383
2 TraesCS7A01G102000 chr7D 93.070 3290 193 10 4 3288 180603245 180599986 0.000000e+00 4780
3 TraesCS7A01G102000 chr7D 91.765 2635 194 15 1 2624 21977819 21980441 0.000000e+00 3642
4 TraesCS7A01G102000 chr7D 86.842 152 14 6 3197 3345 69225192 69225044 7.420000e-37 165
5 TraesCS7A01G102000 chr6D 92.861 3292 217 5 1 3288 471167191 471163914 0.000000e+00 4761
6 TraesCS7A01G102000 chr2D 92.499 3293 208 13 1 3288 112947385 112950643 0.000000e+00 4676
7 TraesCS7A01G102000 chr2D 92.024 2633 194 10 1 2624 615582021 615584646 0.000000e+00 3685
8 TraesCS7A01G102000 chr2D 91.758 2633 197 13 1 2624 643712188 643714809 0.000000e+00 3642
9 TraesCS7A01G102000 chr3B 88.796 3240 292 28 7 3219 764818585 764821780 0.000000e+00 3906
10 TraesCS7A01G102000 chr1D 92.154 2460 176 11 4 2455 212700086 212697636 0.000000e+00 3458
11 TraesCS7A01G102000 chr3D 91.781 2482 176 10 813 3288 108924885 108922426 0.000000e+00 3428
12 TraesCS7A01G102000 chr2A 96.047 1973 77 1 1 1972 25015403 25017375 0.000000e+00 3210
13 TraesCS7A01G102000 chr5A 95.743 1973 83 1 1 1972 466590269 466588297 0.000000e+00 3177
14 TraesCS7A01G102000 chr1A 96.423 1398 49 1 1892 3288 5257412 5258809 0.000000e+00 2303
15 TraesCS7A01G102000 chr1A 93.478 874 41 3 2479 3336 144579563 144580436 0.000000e+00 1284
16 TraesCS7A01G102000 chr6A 93.063 1456 79 7 1907 3345 588446513 588445063 0.000000e+00 2109


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 TraesCS7A01G102000 chr7A 62829782 62833126 3344 True 6178 6178 100.000 1 3345 1 chr7A.!!$R1 3344
1 TraesCS7A01G102000 chr7A 446618776 446620207 1431 True 2383 2383 96.718 1907 3336 1 chr7A.!!$R2 1429
2 TraesCS7A01G102000 chr7D 180599986 180603245 3259 True 4780 4780 93.070 4 3288 1 chr7D.!!$R2 3284
3 TraesCS7A01G102000 chr7D 21977819 21980441 2622 False 3642 3642 91.765 1 2624 1 chr7D.!!$F1 2623
4 TraesCS7A01G102000 chr6D 471163914 471167191 3277 True 4761 4761 92.861 1 3288 1 chr6D.!!$R1 3287
5 TraesCS7A01G102000 chr2D 112947385 112950643 3258 False 4676 4676 92.499 1 3288 1 chr2D.!!$F1 3287
6 TraesCS7A01G102000 chr2D 615582021 615584646 2625 False 3685 3685 92.024 1 2624 1 chr2D.!!$F2 2623
7 TraesCS7A01G102000 chr2D 643712188 643714809 2621 False 3642 3642 91.758 1 2624 1 chr2D.!!$F3 2623
8 TraesCS7A01G102000 chr3B 764818585 764821780 3195 False 3906 3906 88.796 7 3219 1 chr3B.!!$F1 3212
9 TraesCS7A01G102000 chr1D 212697636 212700086 2450 True 3458 3458 92.154 4 2455 1 chr1D.!!$R1 2451
10 TraesCS7A01G102000 chr3D 108922426 108924885 2459 True 3428 3428 91.781 813 3288 1 chr3D.!!$R1 2475
11 TraesCS7A01G102000 chr2A 25015403 25017375 1972 False 3210 3210 96.047 1 1972 1 chr2A.!!$F1 1971
12 TraesCS7A01G102000 chr5A 466588297 466590269 1972 True 3177 3177 95.743 1 1972 1 chr5A.!!$R1 1971
13 TraesCS7A01G102000 chr1A 5257412 5258809 1397 False 2303 2303 96.423 1892 3288 1 chr1A.!!$F1 1396
14 TraesCS7A01G102000 chr1A 144579563 144580436 873 False 1284 1284 93.478 2479 3336 1 chr1A.!!$F2 857
15 TraesCS7A01G102000 chr6A 588445063 588446513 1450 True 2109 2109 93.063 1907 3345 1 chr6A.!!$R1 1438

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
638 645 0.786435 AACCCTTCTTGGATGCCCTT 59.214 50.000 0.00 0.0 38.35 3.95 F
944 952 1.079621 TACACCGGGGTCATCTGGT 59.920 57.895 15.89 0.0 46.67 4.00 F
1905 1941 1.068333 CAGCAACCACAACACTATGGC 60.068 52.381 0.00 0.0 39.84 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1831 0.244450 GGACGTGGTTGATGTCGGTA 59.756 55.0 0.00 0.0 41.04 4.02 R
1924 1960 0.535780 TGCTGTGGCTGTGGAGAAAG 60.536 55.0 0.00 0.0 39.59 2.62 R
3295 3369 0.893727 ATTTCGCGCAACCCTTTCCT 60.894 50.0 8.75 0.0 0.00 3.36 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
62 63 2.093128 AGAGACCCACACGTTTCACTTT 60.093 45.455 0.00 0.00 0.00 2.66
64 65 2.011222 GACCCACACGTTTCACTTTCA 58.989 47.619 0.00 0.00 0.00 2.69
159 162 4.728102 CGTTGGACGCACCGGCTA 62.728 66.667 0.00 0.00 42.61 3.93
250 253 5.593095 AGCATCACGAACCTAAGTATGAGTA 59.407 40.000 0.00 0.00 0.00 2.59
263 266 9.167311 CCTAAGTATGAGTAGTTGCTCAATTTT 57.833 33.333 4.06 2.55 46.93 1.82
480 487 4.672587 ATCATGTCACCACTATTAGCGT 57.327 40.909 0.00 0.00 0.00 5.07
544 551 3.210227 GACGGATCAGATCAGACAGAGA 58.790 50.000 16.59 0.00 0.00 3.10
557 564 1.343465 GACAGAGAAGTTGGGGTTCGA 59.657 52.381 0.00 0.00 0.00 3.71
638 645 0.786435 AACCCTTCTTGGATGCCCTT 59.214 50.000 0.00 0.00 38.35 3.95
686 693 6.473208 AGAGGTTCTCTATAGGGCGACCAA 62.473 50.000 11.69 0.00 46.72 3.67
800 807 8.592105 GGTATGCACCGTGTTATAGTTTAATA 57.408 34.615 0.00 0.00 34.36 0.98
881 889 3.257393 CAGAGACGCTTTGCTAGTGATT 58.743 45.455 6.92 0.00 37.80 2.57
919 927 3.128589 ACACAACATTGAACGAGCAGTTT 59.871 39.130 0.00 0.00 44.35 2.66
944 952 1.079621 TACACCGGGGTCATCTGGT 59.920 57.895 15.89 0.00 46.67 4.00
1113 1122 2.727123 TTGGTCTTCTGCAGTTGGAA 57.273 45.000 14.67 0.00 0.00 3.53
1221 1251 9.528489 AATACTCCATTTGAAGCTTTAGGTAAA 57.472 29.630 0.00 0.00 0.00 2.01
1349 1379 2.010145 ACACACATCTATGGCACGAC 57.990 50.000 0.00 0.00 0.00 4.34
1364 1394 3.670055 GGCACGACAATCACAATTTTGAG 59.330 43.478 0.23 0.00 0.00 3.02
1427 1457 2.129607 ACACGGTTACACATCGTTGAC 58.870 47.619 0.00 0.00 34.73 3.18
1602 1632 4.379813 CGTCATGAAAATTTGCAGGCTACT 60.380 41.667 5.92 0.00 0.00 2.57
1695 1725 1.274167 CGTCCAGTGCTACAACCCTTA 59.726 52.381 0.00 0.00 0.00 2.69
1785 1815 3.292159 CAGCACCAGCAGCAGCAA 61.292 61.111 3.17 0.00 45.49 3.91
1801 1831 1.667830 CAACCGCGTCACTCCATGT 60.668 57.895 4.92 0.00 0.00 3.21
1840 1870 1.139734 CGTCTAGCACATCAGCCGT 59.860 57.895 0.00 0.00 34.23 5.68
1905 1941 1.068333 CAGCAACCACAACACTATGGC 60.068 52.381 0.00 0.00 39.84 4.40
1944 1980 0.106769 TTTCTCCACAGCCACAGCAA 60.107 50.000 0.00 0.00 43.56 3.91
1953 1989 2.111043 CCACAGCAACACGGTCCT 59.889 61.111 0.00 0.00 0.00 3.85
1978 2014 0.944386 GAGCTTCGTGTTTGAGCCAA 59.056 50.000 0.00 0.00 0.00 4.52
2068 2104 6.710744 ACCTCATTCTTCATGACTAAACGTTT 59.289 34.615 18.90 18.90 36.94 3.60
2121 2157 6.098017 CGTCTATGTCAGCATCACATGATAT 58.902 40.000 0.00 0.00 35.95 1.63
2149 2185 2.168521 GAGTGATCAACATCCCGAGGAA 59.831 50.000 0.00 0.00 34.34 3.36
2306 2342 3.561120 TTGGGATGGTCGCCGCTTT 62.561 57.895 0.00 0.00 0.00 3.51
2394 2436 8.171164 TGACCATCTACTTATGTATGAGACTG 57.829 38.462 0.00 0.00 0.00 3.51
2653 2696 0.473755 TGCAGAACTCTTGCCCTTCA 59.526 50.000 0.00 0.00 0.00 3.02
2694 2737 3.368427 CCTTGGACGATGCAGAACTCTTA 60.368 47.826 0.00 0.00 0.00 2.10
2838 2882 2.574006 TGGATGCTTTTCTGCAGTCT 57.426 45.000 14.67 0.00 46.71 3.24
2841 2885 3.638160 TGGATGCTTTTCTGCAGTCTTTT 59.362 39.130 14.67 0.00 46.71 2.27
2869 2913 0.259065 TCACTCTCCGGCTCCACTAT 59.741 55.000 0.00 0.00 0.00 2.12
3146 3191 4.541705 CTTATCCTCCTCTGTCTGAAGGA 58.458 47.826 3.40 3.40 0.00 3.36
3230 3275 1.896660 GCGGGAAAGAGTTGGCACA 60.897 57.895 0.00 0.00 0.00 4.57
3267 3313 1.072505 GGTGGCGGGAAAGAGTTGA 59.927 57.895 0.00 0.00 0.00 3.18
3293 3367 5.106475 GCGAACATATGGCGGGAAAATATTA 60.106 40.000 17.96 0.00 0.00 0.98
3294 3368 6.568844 GCGAACATATGGCGGGAAAATATTAA 60.569 38.462 17.96 0.00 0.00 1.40
3295 3369 7.364200 CGAACATATGGCGGGAAAATATTAAA 58.636 34.615 7.80 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 1.135094 GAGCCATCTCTCCCCATTGA 58.865 55.000 0.00 0.00 36.42 2.57
64 65 2.549580 GGAGCCATCTCTCCCCATT 58.450 57.895 0.00 0.00 45.40 3.16
134 137 0.457035 GTGCGTCCAACGGTCCTATA 59.543 55.000 1.33 0.00 42.82 1.31
250 253 5.722021 AATTACCCGAAAATTGAGCAACT 57.278 34.783 0.00 0.00 0.00 3.16
396 403 1.743321 CTCCAGGCTCCGAGTGATCC 61.743 65.000 0.00 0.00 0.00 3.36
460 467 3.780902 CACGCTAATAGTGGTGACATGA 58.219 45.455 0.00 0.00 46.14 3.07
480 487 1.694150 GTGCCATAGGGATGTAGAGCA 59.306 52.381 0.00 0.00 35.59 4.26
524 531 3.289407 TCTCTGTCTGATCTGATCCGT 57.711 47.619 14.71 0.00 0.00 4.69
544 551 1.070275 GACCGTCGAACCCCAACTT 59.930 57.895 0.00 0.00 0.00 2.66
557 564 1.336125 GTATGTAGCCGCTAAGACCGT 59.664 52.381 0.46 0.00 0.00 4.83
638 645 5.163385 CCCACGACCATAGTTGTAGGAATAA 60.163 44.000 0.00 0.00 40.59 1.40
686 693 1.000506 AGGCTCACGAACACGTACATT 59.999 47.619 0.00 0.00 38.51 2.71
741 748 0.038526 ACACAGACCGAAAGTAGGCG 60.039 55.000 0.00 0.00 0.00 5.52
881 889 5.020795 TGTTGTGTATGCCTTCCTAGTCTA 58.979 41.667 0.00 0.00 0.00 2.59
919 927 2.998480 ACCCCGGTGTACGCATCA 60.998 61.111 8.97 0.00 42.52 3.07
944 952 1.956629 GCTGCTTCCGTGTAGGGCTA 61.957 60.000 0.00 0.00 41.52 3.93
1113 1122 3.437344 GGTTCTCTATAGGGAGAGGCAGT 60.437 52.174 1.80 0.00 42.84 4.40
1121 1130 1.756690 GCACCGGGTTCTCTATAGGGA 60.757 57.143 6.32 0.00 0.00 4.20
1196 1208 9.700831 ATTTACCTAAAGCTTCAAATGGAGTAT 57.299 29.630 0.00 0.00 0.00 2.12
1221 1251 4.734398 AATTGTGGTGTGTGTTCAACAT 57.266 36.364 0.00 0.00 41.97 2.71
1349 1379 7.646446 TTCATTGAGCTCAAAATTGTGATTG 57.354 32.000 31.55 20.95 39.55 2.67
1364 1394 7.113124 CGCAAATAGAGATTGAATTCATTGAGC 59.887 37.037 9.40 6.23 0.00 4.26
1417 1447 0.034896 GTGGGAGTGGTCAACGATGT 59.965 55.000 0.00 0.00 0.00 3.06
1427 1457 1.992277 CTCCTCTGGGTGGGAGTGG 60.992 68.421 0.00 0.00 42.86 4.00
1465 1495 3.762288 GTCATAGCTCGGGTACATATCCA 59.238 47.826 0.00 0.00 0.00 3.41
1602 1632 3.696281 TCGTAGAGTTCGTGTGTCAAA 57.304 42.857 0.00 0.00 0.00 2.69
1695 1725 6.824305 ATCTTGTTCTGAATTCGTTCCAAT 57.176 33.333 0.04 0.00 0.00 3.16
1785 1815 1.214589 GTACATGGAGTGACGCGGT 59.785 57.895 12.47 0.00 0.00 5.68
1801 1831 0.244450 GGACGTGGTTGATGTCGGTA 59.756 55.000 0.00 0.00 41.04 4.02
1905 1941 4.052229 ACGAAGCTCGACGTGGGG 62.052 66.667 11.57 0.00 43.74 4.96
1924 1960 0.535780 TGCTGTGGCTGTGGAGAAAG 60.536 55.000 0.00 0.00 39.59 2.62
1944 1980 2.952245 CTCGACGAAGGACCGTGT 59.048 61.111 0.00 0.00 43.49 4.49
1953 1989 0.850217 CAAACACGAAGCTCGACGAA 59.150 50.000 13.25 0.00 43.74 3.85
1978 2014 1.893808 CTGGTTGTGACGGCTGCTT 60.894 57.895 0.00 0.00 0.00 3.91
2068 2104 1.306148 CGTAGGCTCCTACACGATGA 58.694 55.000 21.93 0.00 46.69 2.92
2121 2157 1.281867 GATGTTGATCACTCCCCCACA 59.718 52.381 0.00 0.00 0.00 4.17
2149 2185 3.310774 GCGACATCTGAGCATGTATGTTT 59.689 43.478 0.00 0.00 37.11 2.83
2653 2696 3.185455 AGGGTAAGAGTTCTGCATCCTT 58.815 45.455 0.00 0.00 0.00 3.36
2694 2737 0.824759 GTACTGCATCCTCGAAGGGT 59.175 55.000 0.00 0.00 35.59 4.34
2869 2913 1.202915 TGCATGCAAGGTGGAAGAAGA 60.203 47.619 20.30 0.00 0.00 2.87
3146 3191 8.401955 TTTTCTCATCCCTACCTATAAAACCT 57.598 34.615 0.00 0.00 0.00 3.50
3230 3275 1.099689 CCGTTTCCCGCCATATGTTT 58.900 50.000 1.24 0.00 34.38 2.83
3267 3313 2.581208 TTCCCGCCATATGTTCGCGT 62.581 55.000 19.06 0.00 44.29 6.01
3293 3367 1.104577 TTCGCGCAACCCTTTCCTTT 61.105 50.000 8.75 0.00 0.00 3.11
3294 3368 1.104577 TTTCGCGCAACCCTTTCCTT 61.105 50.000 8.75 0.00 0.00 3.36
3295 3369 0.893727 ATTTCGCGCAACCCTTTCCT 60.894 50.000 8.75 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.