Multiple sequence alignment - TraesCS5A01G273700

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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 TraesCS5A01G273700 chr5A 100.000 2492 0 0 1 2492 482755238 482752747 0 4602
1 TraesCS5A01G273700 chr5A 94.064 1213 46 10 1306 2492 591751020 591752232 0 1818
2 TraesCS5A01G273700 chr7A 94.996 2518 97 5 1 2492 595120014 595122528 0 3925
3 TraesCS5A01G273700 chr7A 94.920 1437 48 3 1080 2491 67308817 67307381 0 2226
4 TraesCS5A01G273700 chr7A 94.784 1438 46 9 1080 2492 67045118 67043685 0 2213
5 TraesCS5A01G273700 chr2A 94.897 2528 93 6 1 2492 206090092 206092619 0 3921
6 TraesCS5A01G273700 chr2A 94.758 2518 105 5 1 2492 458999267 458996751 0 3893
7 TraesCS5A01G273700 chr2A 94.557 2517 106 10 1 2492 515493920 515491410 0 3860
8 TraesCS5A01G273700 chr2A 93.383 2267 118 13 1 2236 749465061 749467326 0 3326
9 TraesCS5A01G273700 chr2A 93.998 1283 48 12 1235 2490 560659045 560657765 0 1916
10 TraesCS5A01G273700 chr6A 94.559 2518 109 5 1 2492 54961580 54959065 0 3866
11 TraesCS5A01G273700 chr1A 94.270 2426 108 14 96 2492 399798851 399796428 0 3681
12 TraesCS5A01G273700 chr5B 91.792 2522 169 19 1 2492 658937410 658934897 0 3476
13 TraesCS5A01G273700 chr2B 91.829 2264 148 17 1 2233 676182514 676180257 0 3121
14 TraesCS5A01G273700 chr3A 94.977 1553 55 6 1 1531 692596076 692594525 0 2414


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 TraesCS5A01G273700 chr5A 482752747 482755238 2491 True 4602 4602 100.000 1 2492 1 chr5A.!!$R1 2491
1 TraesCS5A01G273700 chr5A 591751020 591752232 1212 False 1818 1818 94.064 1306 2492 1 chr5A.!!$F1 1186
2 TraesCS5A01G273700 chr7A 595120014 595122528 2514 False 3925 3925 94.996 1 2492 1 chr7A.!!$F1 2491
3 TraesCS5A01G273700 chr7A 67307381 67308817 1436 True 2226 2226 94.920 1080 2491 1 chr7A.!!$R2 1411
4 TraesCS5A01G273700 chr7A 67043685 67045118 1433 True 2213 2213 94.784 1080 2492 1 chr7A.!!$R1 1412
5 TraesCS5A01G273700 chr2A 206090092 206092619 2527 False 3921 3921 94.897 1 2492 1 chr2A.!!$F1 2491
6 TraesCS5A01G273700 chr2A 458996751 458999267 2516 True 3893 3893 94.758 1 2492 1 chr2A.!!$R1 2491
7 TraesCS5A01G273700 chr2A 515491410 515493920 2510 True 3860 3860 94.557 1 2492 1 chr2A.!!$R2 2491
8 TraesCS5A01G273700 chr2A 749465061 749467326 2265 False 3326 3326 93.383 1 2236 1 chr2A.!!$F2 2235
9 TraesCS5A01G273700 chr2A 560657765 560659045 1280 True 1916 1916 93.998 1235 2490 1 chr2A.!!$R3 1255
10 TraesCS5A01G273700 chr6A 54959065 54961580 2515 True 3866 3866 94.559 1 2492 1 chr6A.!!$R1 2491
11 TraesCS5A01G273700 chr1A 399796428 399798851 2423 True 3681 3681 94.270 96 2492 1 chr1A.!!$R1 2396
12 TraesCS5A01G273700 chr5B 658934897 658937410 2513 True 3476 3476 91.792 1 2492 1 chr5B.!!$R1 2491
13 TraesCS5A01G273700 chr2B 676180257 676182514 2257 True 3121 3121 91.829 1 2233 1 chr2B.!!$R1 2232
14 TraesCS5A01G273700 chr3A 692594525 692596076 1551 True 2414 2414 94.977 1 1531 1 chr3A.!!$R1 1530

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
127 128 0.53578 CTGGTTCTGTGAGGCAGCAA 60.536 55.0 0.0 0.0 44.66 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1746 0.756294 TGTCACTCACGAACCACCAT 59.244 50.0 0.0 0.0 0.0 3.55 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
53 54 1.274703 ACGAGGTCAGGGGCAATCAT 61.275 55.000 0.00 0.00 0.00 2.45
127 128 0.535780 CTGGTTCTGTGAGGCAGCAA 60.536 55.000 0.00 0.00 44.66 3.91
257 258 1.817357 CAGCAAGCACATGAAGGAGA 58.183 50.000 0.00 0.00 0.00 3.71
586 593 3.415457 TCATGCATTACAGTGTGACCA 57.585 42.857 5.88 0.00 0.00 4.02
643 650 4.763793 TCCAGAGGAAGAATTTTGCTCAAG 59.236 41.667 17.43 11.98 39.03 3.02
768 779 0.608856 TGGCAGATGTTTCATGCGGT 60.609 50.000 0.00 0.00 40.90 5.68
782 793 4.590487 CGGTATCAACTGCCGTGT 57.410 55.556 0.00 0.00 46.81 4.49
813 824 3.742433 TTTGATTTTTGCATCCCGTGT 57.258 38.095 0.00 0.00 0.00 4.49
848 859 7.151976 GGCAACTTCAAAGTAAAATACATGGT 58.848 34.615 0.00 0.00 38.57 3.55
872 883 5.975693 AATTTTGTTCATACATGGACGGT 57.024 34.783 0.00 0.00 39.20 4.83
1161 1175 5.468409 TGCTGAATTCTTCATCAACAACGTA 59.532 36.000 7.05 0.00 39.30 3.57
1218 1232 2.239654 GGTCCAGATCAGACATTTCCCA 59.760 50.000 15.39 0.00 35.89 4.37
1398 1422 2.523168 TGCAGGACGGACTGTGGA 60.523 61.111 9.83 0.00 40.59 4.02
1607 1651 3.050619 CGGACGCATACCTTACATTCTC 58.949 50.000 0.00 0.00 0.00 2.87
1671 1719 2.365293 TGTCCGTGTGCTATGCTATGAT 59.635 45.455 0.00 0.00 0.00 2.45
1698 1746 1.019673 CCGAGTAGCCTAGTACGCAA 58.980 55.000 0.00 0.00 0.00 4.85
1923 1978 7.627585 AAGTCATTGTCATTTTCATTTGACG 57.372 32.000 0.00 0.00 44.11 4.35
1946 2002 6.255670 ACGGTTTTGCTTCTTCTTTTTCATTC 59.744 34.615 0.00 0.00 0.00 2.67
1992 2049 6.482308 GGTAGTTTTGATCATGTAGCCGTAAT 59.518 38.462 0.00 0.00 0.00 1.89
2092 2150 4.778842 AAGCGTGTCGAATTATCATGAC 57.221 40.909 0.00 0.00 0.00 3.06
2251 2355 5.989168 TGAGTATAATTAACATGGCAGACCG 59.011 40.000 0.00 0.00 39.70 4.79
2359 2487 3.058914 GGCAGATCAAGTACACACAACAC 60.059 47.826 0.00 0.00 0.00 3.32
2385 2513 3.766545 ACTGCAGTTACCCATTCAATGT 58.233 40.909 15.25 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 0.178995 TCTGCAGGCACATTGGAACA 60.179 50.000 15.13 0.00 0.00 3.18
202 203 5.499139 TTCCAAATCGCTTGACAATATCC 57.501 39.130 0.00 0.00 37.17 2.59
257 258 5.643379 AAATGTGGTCATTACGCTTTCAT 57.357 34.783 0.00 0.00 42.60 2.57
401 403 3.576078 TGGTTCTGTCCAAACATGAGT 57.424 42.857 0.00 0.00 34.13 3.41
586 593 4.255510 AGTCACCATCCCATATTTTGCT 57.744 40.909 0.00 0.00 0.00 3.91
643 650 2.096218 GTGTGAGCTTGAATTGACCGTC 60.096 50.000 0.00 0.00 0.00 4.79
740 751 5.781210 TGAAACATCTGCCACATAAACAA 57.219 34.783 0.00 0.00 0.00 2.83
768 779 3.991773 GTCAGTTTACACGGCAGTTGATA 59.008 43.478 0.00 0.00 0.00 2.15
782 793 8.825745 GGATGCAAAAATCAAAAAGTCAGTTTA 58.174 29.630 0.00 0.00 0.00 2.01
813 824 6.952773 ACTTTGAAGTTGCCACATAGTTTA 57.047 33.333 0.00 0.00 35.21 2.01
848 859 7.455641 ACCGTCCATGTATGAACAAAATTTA 57.544 32.000 0.00 0.00 39.58 1.40
1056 1070 4.838423 TGGTTCTTCAGGTCAAGACAGATA 59.162 41.667 2.29 0.00 31.88 1.98
1161 1175 3.139077 GTGACGGTTCCATGTCTCTTTT 58.861 45.455 0.00 0.00 36.10 2.27
1218 1232 2.730090 CGTAGTCGCCACGTACTCAATT 60.730 50.000 0.00 0.00 34.74 2.32
1398 1422 4.320935 GCAAGGTATTCCAACGTGTGAAAT 60.321 41.667 4.36 0.00 35.89 2.17
1607 1651 2.280628 GACCTTACATTCCTCGGCAAG 58.719 52.381 0.00 0.00 0.00 4.01
1671 1719 0.905809 TAGGCTACTCGGGGTTGCAA 60.906 55.000 15.96 0.00 45.79 4.08
1698 1746 0.756294 TGTCACTCACGAACCACCAT 59.244 50.000 0.00 0.00 0.00 3.55
1921 1976 5.066968 TGAAAAAGAAGAAGCAAAACCGT 57.933 34.783 0.00 0.00 0.00 4.83
1923 1978 6.763135 AGGAATGAAAAAGAAGAAGCAAAACC 59.237 34.615 0.00 0.00 0.00 3.27
1946 2002 1.153429 GGTAGCCGGTGCAGTTAGG 60.153 63.158 1.90 0.00 41.13 2.69
1992 2049 1.266718 GTGCATCAACCGCAGAAAAGA 59.733 47.619 0.00 0.00 40.78 2.52
2092 2150 7.749126 TGTAATGACTCTACATCGCGTATATTG 59.251 37.037 5.77 0.04 0.00 1.90
2385 2513 4.158394 GGCATCAGAAGTTGCAGGAAAATA 59.842 41.667 0.00 0.00 41.24 1.40


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

AutoCloner maintained by Alex Coulton.