Multiple sequence alignment - TraesCS7B01G266700

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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 TraesCS7B01G266700 chr7B 100.000 1774 0 0 938 2711 489781332 489779559 0.000000e+00 3277
1 TraesCS7B01G266700 chr7B 100.000 512 0 0 1 512 489782269 489781758 0.000000e+00 946
2 TraesCS7B01G266700 chr7B 83.014 783 87 26 941 1694 489552299 489551534 0.000000e+00 667
3 TraesCS7B01G266700 chr7D 94.196 1809 50 22 940 2711 464361423 464359633 0.000000e+00 2708
4 TraesCS7B01G266700 chr7D 92.456 517 29 6 3 512 464362030 464361517 0.000000e+00 730
5 TraesCS7B01G266700 chr7D 80.488 984 114 43 938 1870 464947884 464946928 0.000000e+00 682
6 TraesCS7B01G266700 chr7D 83.120 782 88 26 941 1694 464137814 464137049 0.000000e+00 673
7 TraesCS7B01G266700 chr7A 91.551 1586 52 21 938 2467 535272776 535274335 0.000000e+00 2111
8 TraesCS7B01G266700 chr7A 92.263 517 31 5 3 512 535272162 535272676 0.000000e+00 725
9 TraesCS7B01G266700 chr7A 83.442 767 86 22 941 1682 535590764 535591514 0.000000e+00 675
10 TraesCS7B01G266700 chr7A 78.557 998 108 61 938 1870 534766234 534767190 6.560000e-156 560
11 TraesCS7B01G266700 chr7A 92.713 247 11 2 2465 2711 535319102 535319341 1.540000e-92 350
12 TraesCS7B01G266700 chr3B 89.842 443 30 8 2264 2703 49098296 49098726 3.050000e-154 555


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 TraesCS7B01G266700 chr7B 489779559 489782269 2710 True 2111.5 3277 100.000 1 2711 2 chr7B.!!$R2 2710
1 TraesCS7B01G266700 chr7B 489551534 489552299 765 True 667.0 667 83.014 941 1694 1 chr7B.!!$R1 753
2 TraesCS7B01G266700 chr7D 464359633 464362030 2397 True 1719.0 2708 93.326 3 2711 2 chr7D.!!$R3 2708
3 TraesCS7B01G266700 chr7D 464946928 464947884 956 True 682.0 682 80.488 938 1870 1 chr7D.!!$R2 932
4 TraesCS7B01G266700 chr7D 464137049 464137814 765 True 673.0 673 83.120 941 1694 1 chr7D.!!$R1 753
5 TraesCS7B01G266700 chr7A 535272162 535274335 2173 False 1418.0 2111 91.907 3 2467 2 chr7A.!!$F4 2464
6 TraesCS7B01G266700 chr7A 535590764 535591514 750 False 675.0 675 83.442 941 1682 1 chr7A.!!$F3 741
7 TraesCS7B01G266700 chr7A 534766234 534767190 956 False 560.0 560 78.557 938 1870 1 chr7A.!!$F1 932

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
331 336 0.389296 CGACGTGTGGCACCATCTAA 60.389 55.0 16.26 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2054 0.549469 ACTGTTTTCGTTGGGAGGGT 59.451 50.0 0.0 0.0 0.0 4.34 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
33 34 2.800250 CAGAAGTTCTGCCCTTCCATT 58.200 47.619 19.55 0.00 37.72 3.16
99 100 1.779724 CGCGCTATCCTAAAGAACGTC 59.220 52.381 5.56 0.00 0.00 4.34
121 126 0.606604 TTTTCCGGAACCCTCTCTCG 59.393 55.000 18.64 0.00 0.00 4.04
148 153 5.105957 ACATTAAAATGCCGCACTAATGACA 60.106 36.000 24.71 0.00 40.04 3.58
173 178 1.153353 TCGGTCCACAAAATTCTCGC 58.847 50.000 0.00 0.00 0.00 5.03
186 191 3.634568 ATTCTCGCCGAGTTATCTCTG 57.365 47.619 14.64 0.00 38.45 3.35
197 202 5.006165 CCGAGTTATCTCTGACATCAAAAGC 59.994 44.000 0.00 0.00 38.45 3.51
225 230 1.377366 TTTTTGCGTCCGTCCAAGCA 61.377 50.000 0.00 0.00 37.89 3.91
245 250 3.789459 GCACTTCTCGTCGAGTTATCTCC 60.789 52.174 21.15 2.92 37.40 3.71
257 262 6.369065 GTCGAGTTATCTCCAACATCAAAAGT 59.631 38.462 0.00 0.00 37.40 2.66
296 301 1.265905 GTCCAAACGCCGAAAGAACAT 59.734 47.619 0.00 0.00 0.00 2.71
299 304 3.564644 TCCAAACGCCGAAAGAACATTTA 59.435 39.130 0.00 0.00 0.00 1.40
309 314 5.523916 CCGAAAGAACATTTACTGGATCGAT 59.476 40.000 0.00 0.00 0.00 3.59
313 318 7.875316 AAGAACATTTACTGGATCGATATCG 57.125 36.000 19.14 19.14 41.45 2.92
329 334 1.888436 ATCGACGTGTGGCACCATCT 61.888 55.000 16.26 0.00 0.00 2.90
331 336 0.389296 CGACGTGTGGCACCATCTAA 60.389 55.000 16.26 0.00 0.00 2.10
350 355 9.045223 CCATCTAATCGATGTTTGTAGAAATCA 57.955 33.333 0.00 0.00 46.56 2.57
979 989 2.281208 CAAACCCCACTCGGCGAA 60.281 61.111 12.13 0.00 0.00 4.70
980 990 2.032071 AAACCCCACTCGGCGAAG 59.968 61.111 12.13 6.54 0.00 3.79
981 991 2.513259 AAACCCCACTCGGCGAAGA 61.513 57.895 12.13 0.00 0.00 2.87
1093 1106 1.286260 GTGCTCAACCTCGTCGTCT 59.714 57.895 0.00 0.00 0.00 4.18
1383 1429 3.670637 GAGCATGTCTGAGGCGGCA 62.671 63.158 13.08 0.00 36.12 5.69
1386 1432 2.104859 CATGTCTGAGGCGGCAGTG 61.105 63.158 13.08 0.00 37.20 3.66
1532 1596 3.146828 GCCCCCTGGTGGTCAAAGT 62.147 63.158 0.00 0.00 0.00 2.66
1539 1603 1.142870 CTGGTGGTCAAAGTGGAGGAA 59.857 52.381 0.00 0.00 0.00 3.36
1777 1841 3.121019 CTTCCCGCGCTAGTAGCT 58.879 61.111 19.66 0.00 39.60 3.32
1972 2054 2.016604 GCACCTTTCTGTCACCACACA 61.017 52.381 0.00 0.00 0.00 3.72
1973 2055 1.670811 CACCTTTCTGTCACCACACAC 59.329 52.381 0.00 0.00 0.00 3.82
1979 2079 2.397413 CTGTCACCACACACCCTCCC 62.397 65.000 0.00 0.00 0.00 4.30
1983 2083 2.281484 CCACACACCCTCCCAACG 60.281 66.667 0.00 0.00 0.00 4.10
2125 2225 4.735985 CAAAGTAAGCACATGCAGCAATA 58.264 39.130 12.59 3.56 45.16 1.90
2193 2293 3.873062 TGGTTACAGGGGTAGGTAGTTT 58.127 45.455 0.00 0.00 0.00 2.66
2198 2298 6.841229 GGTTACAGGGGTAGGTAGTTTAGTAT 59.159 42.308 0.00 0.00 0.00 2.12
2199 2299 7.345653 GGTTACAGGGGTAGGTAGTTTAGTATT 59.654 40.741 0.00 0.00 0.00 1.89
2227 2327 5.922053 TCAGTTCACTAGATCATTGATGGG 58.078 41.667 3.32 0.00 0.00 4.00
2231 2331 1.271054 ACTAGATCATTGATGGGGCGC 60.271 52.381 3.32 0.00 0.00 6.53
2232 2332 0.320683 TAGATCATTGATGGGGCGCG 60.321 55.000 0.00 0.00 0.00 6.86
2358 2481 4.351874 TCTAGTCTTGGTCAAAGTTGGG 57.648 45.455 0.00 0.00 37.18 4.12
2424 2547 8.806146 ACAAGGACAATTAGCATTTACAGAATT 58.194 29.630 0.00 0.00 0.00 2.17
2524 2647 8.870879 GCGAGTTAGAAACAAAGTAGATTGTAT 58.129 33.333 0.00 0.00 42.49 2.29
2605 2744 4.462483 TGACTTCACTGGTTCAAAAGCTTT 59.538 37.500 5.69 5.69 0.00 3.51
2610 2749 3.062504 CACTGGTTCAAAAGCTTTTGTGC 59.937 43.478 37.79 31.09 45.77 4.57
2690 2829 0.968405 GCATGGTTGAAGGCTTGGAA 59.032 50.000 3.46 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.595716 GGCAGAACTTCTGTTGTGAGTTATAT 59.404 38.462 18.16 0.00 46.46 0.86
1 2 5.932303 GGCAGAACTTCTGTTGTGAGTTATA 59.068 40.000 18.16 0.00 46.46 0.98
15 16 1.740025 CGAATGGAAGGGCAGAACTTC 59.260 52.381 0.00 0.00 42.73 3.01
33 34 4.794278 TGTTATTTCAGTGGCTAGACGA 57.206 40.909 0.00 0.00 0.00 4.20
105 106 1.677966 CACGAGAGAGGGTTCCGGA 60.678 63.158 0.00 0.00 0.00 5.14
121 126 3.216147 AGTGCGGCATTTTAATGTCAC 57.784 42.857 5.72 10.52 40.97 3.67
148 153 5.983720 CGAGAATTTTGTGGACCGATATAGT 59.016 40.000 0.00 0.00 0.00 2.12
173 178 5.006165 GCTTTTGATGTCAGAGATAACTCGG 59.994 44.000 0.00 0.00 46.64 4.63
186 191 4.489679 AAGAGAAACGGCTTTTGATGTC 57.510 40.909 0.00 0.00 0.00 3.06
197 202 1.659211 CGGACGCAAAAAGAGAAACGG 60.659 52.381 0.00 0.00 0.00 4.44
225 230 3.607741 TGGAGATAACTCGACGAGAAGT 58.392 45.455 30.56 16.80 43.44 3.01
282 287 2.482721 CCAGTAAATGTTCTTTCGGCGT 59.517 45.455 6.85 0.00 0.00 5.68
309 314 0.179121 GATGGTGCCACACGTCGATA 60.179 55.000 0.00 0.00 34.83 2.92
313 318 1.933853 GATTAGATGGTGCCACACGTC 59.066 52.381 0.00 0.00 34.83 4.34
331 336 9.965824 AAAGTTTTGATTTCTACAAACATCGAT 57.034 25.926 0.00 0.00 37.05 3.59
979 989 1.216710 CGCCGCTTCTTCTCCTTCT 59.783 57.895 0.00 0.00 0.00 2.85
980 990 2.456948 GCGCCGCTTCTTCTCCTTC 61.457 63.158 0.00 0.00 0.00 3.46
981 991 2.435059 GCGCCGCTTCTTCTCCTT 60.435 61.111 0.00 0.00 0.00 3.36
1093 1106 0.242825 GAGGTGACGACGATGGTGAA 59.757 55.000 0.00 0.00 0.00 3.18
1165 1178 1.984570 CCAGGTTCCTCCTCTCGCA 60.985 63.158 0.00 0.00 46.24 5.10
1526 1590 1.072505 GCCGGTTCCTCCACTTTGA 59.927 57.895 1.90 0.00 35.57 2.69
1527 1591 2.325082 CGCCGGTTCCTCCACTTTG 61.325 63.158 1.90 0.00 35.57 2.77
1972 2054 0.549469 ACTGTTTTCGTTGGGAGGGT 59.451 50.000 0.00 0.00 0.00 4.34
1973 2055 1.687563 AACTGTTTTCGTTGGGAGGG 58.312 50.000 0.00 0.00 0.00 4.30
1979 2079 5.623673 CGGGAAAGAATAACTGTTTTCGTTG 59.376 40.000 15.24 4.79 31.89 4.10
1983 2083 5.849604 CGAACGGGAAAGAATAACTGTTTTC 59.150 40.000 0.00 3.20 32.95 2.29
2125 2225 4.942761 ATGACTGAAACAGTGGCAAATT 57.057 36.364 9.15 0.00 45.44 1.82
2231 2331 3.720949 TTATAGATGGACCCGACAACG 57.279 47.619 0.00 0.00 39.43 4.10
2358 2481 6.470235 GCAGTGTCAATTTATGCAGTTACATC 59.530 38.462 0.00 0.00 36.88 3.06
2524 2647 7.233757 GGGCTCCTATTCTAACAAGATAGAAGA 59.766 40.741 6.09 1.39 43.21 2.87
2526 2649 6.844388 TGGGCTCCTATTCTAACAAGATAGAA 59.156 38.462 2.85 2.85 43.87 2.10
2528 2651 6.672266 TGGGCTCCTATTCTAACAAGATAG 57.328 41.667 0.00 0.00 0.00 2.08
2529 2652 7.633018 ATTGGGCTCCTATTCTAACAAGATA 57.367 36.000 0.00 0.00 0.00 1.98
2530 2653 5.975988 TTGGGCTCCTATTCTAACAAGAT 57.024 39.130 0.00 0.00 0.00 2.40
2531 2654 5.975988 ATTGGGCTCCTATTCTAACAAGA 57.024 39.130 0.00 0.00 0.00 3.02
2532 2655 8.160106 AGATTATTGGGCTCCTATTCTAACAAG 58.840 37.037 0.00 0.00 0.00 3.16
2533 2656 8.045720 AGATTATTGGGCTCCTATTCTAACAA 57.954 34.615 0.00 0.00 0.00 2.83
2536 2659 8.322091 GCTTAGATTATTGGGCTCCTATTCTAA 58.678 37.037 7.12 7.12 0.00 2.10
2537 2660 7.457852 TGCTTAGATTATTGGGCTCCTATTCTA 59.542 37.037 0.00 0.00 0.00 2.10
2545 2683 2.816672 GCCTGCTTAGATTATTGGGCTC 59.183 50.000 0.00 0.00 35.92 4.70
2605 2744 2.951269 CTGCCCTTGATCAGCACAA 58.049 52.632 4.13 0.00 32.06 3.33
2610 2749 4.823442 TGTATATTTGCTGCCCTTGATCAG 59.177 41.667 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.