Multiple sequence alignment - TraesCS3B01G427700

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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 TraesCS3B01G427700 chr3B 100.000 3062 0 0 1 3062 666618639 666621700 0.000000e+00 5655
1 TraesCS3B01G427700 chr3B 83.160 3082 469 44 1 3057 790573729 790576785 0.000000e+00 2771
2 TraesCS3B01G427700 chr6B 93.583 3070 179 16 1 3062 46081236 46078177 0.000000e+00 4562
3 TraesCS3B01G427700 chr2B 88.356 3066 341 16 1 3057 797921240 797924298 0.000000e+00 3670
4 TraesCS3B01G427700 chr4B 86.821 3073 380 19 1 3057 46944253 46947316 0.000000e+00 3408
5 TraesCS3B01G427700 chr4B 80.081 2967 517 67 134 3056 616137430 616140366 0.000000e+00 2137
6 TraesCS3B01G427700 chr4B 88.699 292 29 4 2774 3062 593388057 593388347 1.350000e-93 353
7 TraesCS3B01G427700 chr4A 86.662 3074 385 23 1 3060 691825191 691822129 0.000000e+00 3382
8 TraesCS3B01G427700 chr7B 85.158 3079 418 32 1 3061 658458790 658461847 0.000000e+00 3118
9 TraesCS3B01G427700 chr5B 85.929 2523 340 15 1 2514 609117765 609115249 0.000000e+00 2678
10 TraesCS3B01G427700 chr5B 83.101 2947 458 29 1 2925 710458738 710461666 0.000000e+00 2647
11 TraesCS3B01G427700 chr2D 90.698 86 7 1 2975 3060 648231596 648231680 2.500000e-21 113


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 TraesCS3B01G427700 chr3B 666618639 666621700 3061 False 5655 5655 100.000 1 3062 1 chr3B.!!$F1 3061
1 TraesCS3B01G427700 chr3B 790573729 790576785 3056 False 2771 2771 83.160 1 3057 1 chr3B.!!$F2 3056
2 TraesCS3B01G427700 chr6B 46078177 46081236 3059 True 4562 4562 93.583 1 3062 1 chr6B.!!$R1 3061
3 TraesCS3B01G427700 chr2B 797921240 797924298 3058 False 3670 3670 88.356 1 3057 1 chr2B.!!$F1 3056
4 TraesCS3B01G427700 chr4B 46944253 46947316 3063 False 3408 3408 86.821 1 3057 1 chr4B.!!$F1 3056
5 TraesCS3B01G427700 chr4B 616137430 616140366 2936 False 2137 2137 80.081 134 3056 1 chr4B.!!$F3 2922
6 TraesCS3B01G427700 chr4A 691822129 691825191 3062 True 3382 3382 86.662 1 3060 1 chr4A.!!$R1 3059
7 TraesCS3B01G427700 chr7B 658458790 658461847 3057 False 3118 3118 85.158 1 3061 1 chr7B.!!$F1 3060
8 TraesCS3B01G427700 chr5B 609115249 609117765 2516 True 2678 2678 85.929 1 2514 1 chr5B.!!$R1 2513
9 TraesCS3B01G427700 chr5B 710458738 710461666 2928 False 2647 2647 83.101 1 2925 1 chr5B.!!$F1 2924

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
570 587 0.689080 GAGGGTGGCAGAGGAGATGA 60.689 60.0 0.0 0.0 0.00 2.92 F
1527 1550 0.746659 GCAAGGTGCCTGACTGTTTT 59.253 50.0 0.0 0.0 37.42 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 1730 0.191064 TCACCACCTTCTCCACCTCT 59.809 55.0 0.0 0.0 0.0 3.69 R
2482 2512 0.918983 TGCAATAGGGAGGGGTTGAG 59.081 55.0 0.0 0.0 0.0 3.02 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
66 69 6.432472 AGAAGATGAGGTTGATTTTGGAGAAC 59.568 38.462 0.00 0.00 0.00 3.01
124 127 1.081092 CAACAGAGGAGGAGGGGGA 59.919 63.158 0.00 0.00 0.00 4.81
127 130 1.156322 ACAGAGGAGGAGGGGGAGAA 61.156 60.000 0.00 0.00 0.00 2.87
164 167 4.597507 AGAACTTGTGAGACCCCTGATTAA 59.402 41.667 0.00 0.00 0.00 1.40
308 312 4.026357 GGGTGAGAGGGAGGGGGT 62.026 72.222 0.00 0.00 0.00 4.95
521 538 3.703556 TGACAGATTTGGCAGTTTTGGAA 59.296 39.130 0.00 0.00 37.44 3.53
527 544 2.276732 TGGCAGTTTTGGAAGAGGAG 57.723 50.000 0.00 0.00 0.00 3.69
552 569 2.905415 AGATTTGGTGCTGGGAATGA 57.095 45.000 0.00 0.00 0.00 2.57
570 587 0.689080 GAGGGTGGCAGAGGAGATGA 60.689 60.000 0.00 0.00 0.00 2.92
589 606 2.930040 TGAAGATGAAGACGAATTCGCC 59.070 45.455 27.03 17.29 44.43 5.54
655 672 4.331108 GAAAGAAAGAGGCAGTGGAAGAT 58.669 43.478 0.00 0.00 0.00 2.40
657 674 5.707066 AAGAAAGAGGCAGTGGAAGATAT 57.293 39.130 0.00 0.00 0.00 1.63
661 678 4.620589 AGAGGCAGTGGAAGATATGATG 57.379 45.455 0.00 0.00 0.00 3.07
663 680 2.374504 AGGCAGTGGAAGATATGATGGG 59.625 50.000 0.00 0.00 0.00 4.00
685 702 1.280421 AGAGCAAATGGTGAGGGAGAC 59.720 52.381 0.00 0.00 0.00 3.36
706 723 2.026449 CAGCTCTGGAATGGAGAAAGGT 60.026 50.000 0.00 0.00 33.03 3.50
885 906 3.938334 GGCATGAGGAGAGAAGAGAAAAC 59.062 47.826 0.00 0.00 0.00 2.43
915 936 2.555325 CCATGCAGAAAGCTGACAAGAA 59.445 45.455 0.00 0.00 45.17 2.52
917 938 4.500205 CCATGCAGAAAGCTGACAAGAAAA 60.500 41.667 0.00 0.00 45.17 2.29
1059 1082 2.110188 AGACCCAAGACACTCTACCAGA 59.890 50.000 0.00 0.00 0.00 3.86
1254 1277 2.771943 TCCCTTAGGTGTGGTGATCATC 59.228 50.000 0.00 0.00 0.00 2.92
1298 1321 3.327757 ACTGAACTCACAAAGGCTATGGA 59.672 43.478 0.00 0.00 0.00 3.41
1309 1332 6.012745 ACAAAGGCTATGGAAGAGATGTTTT 58.987 36.000 0.00 0.00 0.00 2.43
1393 1416 5.253330 CCAATAAGGCAAAACTGGTAGAGA 58.747 41.667 0.00 0.00 0.00 3.10
1527 1550 0.746659 GCAAGGTGCCTGACTGTTTT 59.253 50.000 0.00 0.00 37.42 2.43
1646 1672 5.183530 TGTGGAATCAGAGATGTGGAAAT 57.816 39.130 0.00 0.00 0.00 2.17
1704 1730 7.239763 TCTACTCATGTTCAGAATTGGTGTA 57.760 36.000 0.00 0.00 0.00 2.90
1723 1749 0.191064 AGAGGTGGAGAAGGTGGTGA 59.809 55.000 0.00 0.00 0.00 4.02
1798 1824 5.768980 AGAAGATGGAGATGGAGAAACAA 57.231 39.130 0.00 0.00 0.00 2.83
1801 1827 6.658391 AGAAGATGGAGATGGAGAAACAAAAG 59.342 38.462 0.00 0.00 0.00 2.27
1821 1847 8.826765 ACAAAAGATAGAAAGAGATTCAGGGTA 58.173 33.333 0.00 0.00 40.72 3.69
1865 1891 2.568623 ACACTGGGATGTTTGTCTCC 57.431 50.000 0.00 0.00 0.00 3.71
2001 2028 6.498304 AGAAAGTGACATCATGTTCAACAAC 58.502 36.000 0.00 0.00 0.00 3.32
2059 2086 2.733227 GCATTGTGCGCTAAAGCTGAAT 60.733 45.455 9.73 0.00 39.32 2.57
2097 2124 3.429492 TGAGGGCAATCAACAAGCAATA 58.571 40.909 0.00 0.00 0.00 1.90
2118 2145 8.857216 GCAATACAGAAAAAGATCAATCAACAG 58.143 33.333 0.00 0.00 0.00 3.16
2150 2178 7.126421 AGAGATCCAAAAGCTAATACAAGAGGA 59.874 37.037 0.00 0.00 0.00 3.71
2155 2183 7.121168 TCCAAAAGCTAATACAAGAGGATGTTG 59.879 37.037 0.00 0.00 46.09 3.33
2169 2198 6.735556 AGAGGATGTTGACAGGGAAAATATT 58.264 36.000 0.00 0.00 0.00 1.28
2277 2306 2.910688 ACCCACTGACTATAATGCCG 57.089 50.000 0.00 0.00 0.00 5.69
2281 2310 2.394708 CACTGACTATAATGCCGGTCG 58.605 52.381 1.90 0.00 0.00 4.79
2305 2334 0.774096 TCAATTGGGACCCTGGGTGA 60.774 55.000 26.16 9.65 35.25 4.02
2343 2372 2.499289 ACATGGAGCTGAGGTTACAGAG 59.501 50.000 0.00 0.00 39.94 3.35
2386 2416 4.508662 AGTGGAGATAAAAAGAAGCCTCG 58.491 43.478 0.00 0.00 0.00 4.63
2406 2436 3.881089 TCGGGAACAAAGGAAAAGAAGAC 59.119 43.478 0.00 0.00 0.00 3.01
2484 2514 9.833182 GGTAAGAATTCTGTTTCTGAATTTCTC 57.167 33.333 9.17 4.69 40.36 2.87
2537 2567 8.917088 CATGGTAGGAATTGATTTAGGATGTTT 58.083 33.333 0.00 0.00 0.00 2.83
2686 2718 2.749280 TGCAGAGACACACCAGTATG 57.251 50.000 0.00 0.00 0.00 2.39
2803 2837 5.073428 GGAATGTTCTCTGGAAAGAAAGGT 58.927 41.667 0.00 0.00 37.04 3.50
3011 3054 4.574674 TTTGGAATGTGAGAGGCATAGT 57.425 40.909 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 21 2.307686 TCAAACCAAGGTGGGATAGGAC 59.692 50.000 0.00 0.00 43.37 3.85
66 69 6.543831 CCAATGGGAGTTTCCTGAATTACTAG 59.456 42.308 0.00 0.00 36.57 2.57
131 134 4.039852 GTCTCACAAGTTCTTCCTCCTCTT 59.960 45.833 0.00 0.00 0.00 2.85
133 136 3.306433 GGTCTCACAAGTTCTTCCTCCTC 60.306 52.174 0.00 0.00 0.00 3.71
164 167 1.005924 CACCTACTGAGCCCCCAAAAT 59.994 52.381 0.00 0.00 0.00 1.82
308 312 3.069586 CCCTACACGATGGAATTGCTCTA 59.930 47.826 0.00 0.00 0.00 2.43
517 534 3.491766 AATCTACCACCTCCTCTTCCA 57.508 47.619 0.00 0.00 0.00 3.53
521 538 2.840651 CACCAAATCTACCACCTCCTCT 59.159 50.000 0.00 0.00 0.00 3.69
527 544 1.463674 CCAGCACCAAATCTACCACC 58.536 55.000 0.00 0.00 0.00 4.61
552 569 0.252881 TTCATCTCCTCTGCCACCCT 60.253 55.000 0.00 0.00 0.00 4.34
570 587 1.927174 CGGCGAATTCGTCTTCATCTT 59.073 47.619 27.91 0.00 42.59 2.40
589 606 2.185004 TTTCTTCCCTTCCTTCTGCG 57.815 50.000 0.00 0.00 0.00 5.18
655 672 2.785269 ACCATTTGCTCTCCCCATCATA 59.215 45.455 0.00 0.00 0.00 2.15
657 674 1.002069 ACCATTTGCTCTCCCCATCA 58.998 50.000 0.00 0.00 0.00 3.07
661 678 0.394899 CCTCACCATTTGCTCTCCCC 60.395 60.000 0.00 0.00 0.00 4.81
663 680 0.620556 TCCCTCACCATTTGCTCTCC 59.379 55.000 0.00 0.00 0.00 3.71
685 702 2.026449 ACCTTTCTCCATTCCAGAGCTG 60.026 50.000 0.00 0.00 0.00 4.24
706 723 7.004691 TCTGGATCATCGTATCTTTCTCCTTA 58.995 38.462 0.00 0.00 0.00 2.69
885 906 2.573369 CTTTCTGCATGGGATCTCTGG 58.427 52.381 0.00 0.00 0.00 3.86
915 936 4.330250 CATCACTGGATCTTGGTCACTTT 58.670 43.478 0.00 0.00 0.00 2.66
917 938 2.238144 CCATCACTGGATCTTGGTCACT 59.762 50.000 0.00 0.00 46.37 3.41
1254 1277 9.170734 TCAGTTTCATTGATATTTCCTTCTCTG 57.829 33.333 0.00 0.00 0.00 3.35
1298 1321 4.651045 GCCATCCCCAATAAAACATCTCTT 59.349 41.667 0.00 0.00 0.00 2.85
1309 1332 0.846015 CTCCACTGCCATCCCCAATA 59.154 55.000 0.00 0.00 0.00 1.90
1422 1445 0.917333 TAATGACCACCCCTGTCCCC 60.917 60.000 0.00 0.00 31.60 4.81
1527 1550 3.820467 CACAAATGCCCAAGAAGTGTCTA 59.180 43.478 0.00 0.00 32.16 2.59
1669 1695 1.055040 ATGAGTAGATCAGGGGCAGC 58.945 55.000 0.00 0.00 42.53 5.25
1704 1730 0.191064 TCACCACCTTCTCCACCTCT 59.809 55.000 0.00 0.00 0.00 3.69
1723 1749 9.136323 CTTATCCTCTTTATACCAGCCAATTTT 57.864 33.333 0.00 0.00 0.00 1.82
1798 1824 8.846423 TCTACCCTGAATCTCTTTCTATCTTT 57.154 34.615 0.00 0.00 35.23 2.52
1801 1827 8.472007 TCTTCTACCCTGAATCTCTTTCTATC 57.528 38.462 0.00 0.00 35.23 2.08
1821 1847 9.331282 GTAATGCCTTTATGTTCAGTATCTTCT 57.669 33.333 0.00 0.00 0.00 2.85
1865 1891 5.182001 CCATCTACTTCCTCACTTTGTTTGG 59.818 44.000 0.00 0.00 0.00 3.28
2001 2028 7.360776 GCTTTGTCTTCTTCTAAGGTCTTGATG 60.361 40.741 0.00 0.00 0.00 3.07
2059 2086 6.969043 TGCCCTCAAGATCCTTAATTCTTTA 58.031 36.000 0.00 0.00 29.85 1.85
2097 2124 6.395426 TGCTGTTGATTGATCTTTTTCTGT 57.605 33.333 0.00 0.00 0.00 3.41
2118 2145 2.720915 AGCTTTTGGATCTCTTCCTGC 58.279 47.619 0.00 0.00 45.68 4.85
2150 2178 9.265862 TCCATTTAATATTTTCCCTGTCAACAT 57.734 29.630 0.00 0.00 0.00 2.71
2155 2183 7.428826 CAGCTCCATTTAATATTTTCCCTGTC 58.571 38.462 0.00 0.00 0.00 3.51
2169 2198 5.841267 TCCATATTAGCCAGCTCCATTTA 57.159 39.130 0.00 0.00 0.00 1.40
2277 2306 1.389555 GTCCCAATTGATTCCCGACC 58.610 55.000 7.12 0.00 0.00 4.79
2281 2310 1.689258 CCAGGGTCCCAATTGATTCCC 60.689 57.143 11.55 17.89 35.56 3.97
2343 2372 3.108847 TCTTTCTCCTCTCCCTCCTTC 57.891 52.381 0.00 0.00 0.00 3.46
2386 2416 3.958147 TGGTCTTCTTTTCCTTTGTTCCC 59.042 43.478 0.00 0.00 0.00 3.97
2406 2436 6.764308 TTTGCCATCTCTTCTATTTTCTGG 57.236 37.500 0.00 0.00 0.00 3.86
2482 2512 0.918983 TGCAATAGGGAGGGGTTGAG 59.081 55.000 0.00 0.00 0.00 3.02
2484 2514 2.230130 TTTGCAATAGGGAGGGGTTG 57.770 50.000 0.00 0.00 0.00 3.77
2645 2677 5.010012 GCATTCTTCCACTTTTTCTCCTGAA 59.990 40.000 0.00 0.00 0.00 3.02
2686 2718 8.671921 CAATATCCACATCTCCAGTATTTATGC 58.328 37.037 0.00 0.00 0.00 3.14
2803 2837 1.321474 CTGGTGAGCTTTTTCTGCCA 58.679 50.000 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.