Multiple sequence alignment - TraesCS3B01G203900

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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 TraesCS3B01G203900 chr3B 100.000 3495 0 0 1 3495 237735546 237732052 0.000000e+00 6455.0
1 TraesCS3B01G203900 chr3B 92.221 1774 90 18 1751 3495 237972968 237971214 0.000000e+00 2468.0
2 TraesCS3B01G203900 chr3B 86.469 2121 178 53 1230 3295 238113670 238111604 0.000000e+00 2226.0
3 TraesCS3B01G203900 chr3B 92.598 743 44 4 999 1730 237973767 237973025 0.000000e+00 1057.0
4 TraesCS3B01G203900 chr3B 88.554 830 70 8 1 806 237978166 237977338 0.000000e+00 983.0
5 TraesCS3B01G203900 chr3B 84.112 107 2 3 904 995 237977215 237977109 4.800000e-14 89.8
6 TraesCS3B01G203900 chr3B 97.500 40 1 0 3317 3356 238111608 238111569 6.260000e-08 69.4
7 TraesCS3B01G203900 chr3A 94.919 2539 85 13 999 3495 190094896 190092360 0.000000e+00 3934.0
8 TraesCS3B01G203900 chr3A 86.625 2056 175 53 1289 3295 190228970 190226966 0.000000e+00 2182.0
9 TraesCS3B01G203900 chr3A 86.768 2033 169 55 1289 3272 191253952 191251971 0.000000e+00 2172.0
10 TraesCS3B01G203900 chr3A 89.483 1759 128 25 1 1730 191008849 191007119 0.000000e+00 2170.0
11 TraesCS3B01G203900 chr3A 88.243 1582 114 36 1751 3293 191006604 191005056 0.000000e+00 1825.0
12 TraesCS3B01G203900 chr3A 95.221 1088 28 3 1480 2548 188112420 188113502 0.000000e+00 1700.0
13 TraesCS3B01G203900 chr3A 95.716 957 26 10 2541 3495 188113380 188114323 0.000000e+00 1526.0
14 TraesCS3B01G203900 chr3A 92.802 903 54 8 1 897 188100174 188101071 0.000000e+00 1297.0
15 TraesCS3B01G203900 chr3A 88.560 1014 79 18 1 997 190096169 190095176 0.000000e+00 1195.0
16 TraesCS3B01G203900 chr3A 92.962 611 23 7 897 1488 188101147 188101756 0.000000e+00 872.0
17 TraesCS3B01G203900 chr3A 85.374 294 40 2 1289 1582 190582899 190582609 5.670000e-78 302.0
18 TraesCS3B01G203900 chr3A 89.922 129 12 1 3367 3495 191004979 191004852 7.760000e-37 165.0
19 TraesCS3B01G203900 chr3A 89.922 129 12 1 3367 3495 191251764 191251637 7.760000e-37 165.0
20 TraesCS3B01G203900 chr3A 88.189 127 14 1 3369 3495 190226888 190226763 2.170000e-32 150.0
21 TraesCS3B01G203900 chr3A 93.651 63 3 1 1022 1084 190229119 190229058 3.710000e-15 93.5
22 TraesCS3B01G203900 chr3A 93.651 63 3 1 1022 1084 191254101 191254040 3.710000e-15 93.5
23 TraesCS3B01G203900 chr3A 89.231 65 6 1 3317 3381 191251846 191251783 2.890000e-11 80.5
24 TraesCS3B01G203900 chr3A 89.831 59 5 1 3323 3381 191005052 191004995 1.350000e-09 75.0
25 TraesCS3B01G203900 chr3D 96.749 2307 40 8 1223 3495 161401874 161399569 0.000000e+00 3812.0
26 TraesCS3B01G203900 chr3D 91.425 1761 109 19 1 1730 161499770 161498021 0.000000e+00 2377.0
27 TraesCS3B01G203900 chr3D 87.889 1866 155 36 1232 3049 161596742 161594900 0.000000e+00 2128.0
28 TraesCS3B01G203900 chr3D 88.980 1579 108 30 1751 3295 161497955 161496409 0.000000e+00 1892.0
29 TraesCS3B01G203900 chr3D 95.959 1163 37 7 1 1157 161403736 161402578 0.000000e+00 1879.0
30 TraesCS3B01G203900 chr3D 89.922 129 12 1 3367 3495 161496333 161496206 7.760000e-37 165.0
31 TraesCS3B01G203900 chr3D 88.372 129 13 2 3367 3495 161594605 161594479 1.680000e-33 154.0
32 TraesCS3B01G203900 chr3D 94.681 94 5 0 1 94 161438936 161438843 2.810000e-31 147.0
33 TraesCS3B01G203900 chr3D 90.476 63 5 1 1022 1084 161596819 161596758 8.040000e-12 82.4
34 TraesCS3B01G203900 chr3D 93.750 48 3 0 3317 3364 161496413 161496366 4.840000e-09 73.1
35 TraesCS3B01G203900 chr3D 97.500 40 1 0 3317 3356 161594684 161594645 6.260000e-08 69.4
36 TraesCS3B01G203900 chr6D 88.344 163 14 3 550 707 281926087 281926249 1.280000e-44 191.0
37 TraesCS3B01G203900 chr6D 100.000 34 0 0 864 897 452414539 452414572 2.910000e-06 63.9
38 TraesCS3B01G203900 chr7D 80.214 187 25 10 714 897 579794562 579794385 2.830000e-26 130.0
39 TraesCS3B01G203900 chr2D 80.588 170 21 10 730 897 124318470 124318311 1.700000e-23 121.0


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 TraesCS3B01G203900 chr3B 237732052 237735546 3494 True 6455.000 6455 100.000000 1 3495 1 chr3B.!!$R1 3494
1 TraesCS3B01G203900 chr3B 237971214 237978166 6952 True 1149.450 2468 89.371250 1 3495 4 chr3B.!!$R2 3494
2 TraesCS3B01G203900 chr3B 238111569 238113670 2101 True 1147.700 2226 91.984500 1230 3356 2 chr3B.!!$R3 2126
3 TraesCS3B01G203900 chr3A 190092360 190096169 3809 True 2564.500 3934 91.739500 1 3495 2 chr3A.!!$R2 3494
4 TraesCS3B01G203900 chr3A 188112420 188114323 1903 False 1613.000 1700 95.468500 1480 3495 2 chr3A.!!$F2 2015
5 TraesCS3B01G203900 chr3A 188100174 188101756 1582 False 1084.500 1297 92.882000 1 1488 2 chr3A.!!$F1 1487
6 TraesCS3B01G203900 chr3A 191004852 191008849 3997 True 1058.750 2170 89.369750 1 3495 4 chr3A.!!$R4 3494
7 TraesCS3B01G203900 chr3A 190226763 190229119 2356 True 808.500 2182 89.488333 1022 3495 3 chr3A.!!$R3 2473
8 TraesCS3B01G203900 chr3A 191251637 191254101 2464 True 627.750 2172 89.893000 1022 3495 4 chr3A.!!$R5 2473
9 TraesCS3B01G203900 chr3D 161399569 161403736 4167 True 2845.500 3812 96.354000 1 3495 2 chr3D.!!$R2 3494
10 TraesCS3B01G203900 chr3D 161496206 161499770 3564 True 1126.775 2377 91.019250 1 3495 4 chr3D.!!$R3 3494
11 TraesCS3B01G203900 chr3D 161594479 161596819 2340 True 608.450 2128 91.059250 1022 3495 4 chr3D.!!$R4 2473

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
286 307 0.321564 CTCGATGGTTGGTGCCTTCA 60.322 55.000 0.00 0.0 33.71 3.02 F
1140 4993 1.613925 TCGATATCTTCCTCCGCCTTG 59.386 52.381 0.34 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 5900 0.460311 CGATCCAGTTAGCTTCCGGT 59.540 55.000 0.00 0.0 0.0 5.28 R
2804 7895 2.810650 GGTACTTCTACAGATGTGCCG 58.189 52.381 13.86 0.0 42.0 5.69 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
154 173 8.723942 AATCTGATCTATTTGGTCTACAACAC 57.276 34.615 0.00 0.0 39.19 3.32
173 192 3.254060 CACGACGAGTGGAGAATGAAAT 58.746 45.455 0.00 0.0 46.77 2.17
286 307 0.321564 CTCGATGGTTGGTGCCTTCA 60.322 55.000 0.00 0.0 33.71 3.02
434 455 2.746277 CTTTCCCAACGCCCTCGG 60.746 66.667 0.00 0.0 40.69 4.63
632 666 7.711846 TGTATTGTAATGTGCAATGAATACCC 58.288 34.615 0.00 0.0 37.18 3.69
687 722 1.950909 CCAAAACTACAGGGCGTTTGA 59.049 47.619 0.00 0.0 33.93 2.69
734 777 5.511729 GTGAGTGTTTCTCGGTTTGAAAAAG 59.488 40.000 0.00 0.0 45.46 2.27
742 785 3.622630 TCGGTTTGAAAAAGAAGGTCCA 58.377 40.909 0.00 0.0 0.00 4.02
1005 4840 4.384940 GGCTCATTTCCTTCTATCAGACC 58.615 47.826 0.00 0.0 0.00 3.85
1028 4881 4.011517 GGTTGGTTCGGCGAGGGA 62.012 66.667 10.46 0.0 0.00 4.20
1140 4993 1.613925 TCGATATCTTCCTCCGCCTTG 59.386 52.381 0.34 0.0 0.00 3.61
1246 5737 3.075005 CATCGACCTCCACCCGGT 61.075 66.667 0.00 0.0 37.50 5.28
1730 6242 1.077501 ATGGTTGGATGTCCCGCAG 60.078 57.895 0.00 0.0 37.93 5.18
2531 7611 6.133356 ACCATTTACATTCGGGGTGAATTAT 58.867 36.000 0.00 0.0 45.06 1.28
2534 7614 7.651704 CCATTTACATTCGGGGTGAATTATTTC 59.348 37.037 0.00 0.0 45.06 2.17
2564 7644 6.173339 GTTCCTTGACATTCAGGATTCAGTA 58.827 40.000 0.00 0.0 0.00 2.74
2610 7692 6.334102 TGGTTTATGGTAATTGTGTTGTCC 57.666 37.500 0.00 0.0 0.00 4.02
3216 8339 1.865970 GAGAGATGCTCAATTGCTCGG 59.134 52.381 0.00 0.0 43.38 4.63
3431 8719 1.989706 TTAAACTGGCACCCTGAACC 58.010 50.000 0.00 0.0 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 173 3.487574 GCTATTTCATTCTCCACTCGTCG 59.512 47.826 0.00 0.00 0.00 5.12
173 192 6.372659 GTCAGGTGAGATGAATTCTTTTGCTA 59.627 38.462 7.05 0.00 33.74 3.49
241 262 1.030457 CTGGCCTGCAATGAAGATCC 58.970 55.000 3.32 0.00 0.00 3.36
286 307 1.908793 CGTCCAGGGGATCGGCTAT 60.909 63.158 0.00 0.00 32.73 2.97
409 430 2.361230 GTTGGGAAAGGAGGCGGG 60.361 66.667 0.00 0.00 0.00 6.13
434 455 3.541713 TTTGGTTTGGTGGCCGGC 61.542 61.111 21.18 21.18 0.00 6.13
619 649 4.046286 AGAAACTGGGGTATTCATTGCA 57.954 40.909 0.00 0.00 0.00 4.08
667 702 1.950909 TCAAACGCCCTGTAGTTTTGG 59.049 47.619 0.00 0.00 38.37 3.28
742 785 5.514500 TTGCAGTATCTAAAAAGGGGTCT 57.486 39.130 0.00 0.00 0.00 3.85
862 992 8.575649 TTTAGGAGAATACCATGGTTTTCTTC 57.424 34.615 36.11 34.68 43.07 2.87
1005 4840 2.943653 GCCGAACCAACCAACTCG 59.056 61.111 0.00 0.00 0.00 4.18
1028 4881 4.960866 GCGGTTGGACGGGGGTTT 62.961 66.667 0.00 0.00 0.00 3.27
1394 5900 0.460311 CGATCCAGTTAGCTTCCGGT 59.540 55.000 0.00 0.00 0.00 5.28
2427 7497 8.217131 TGACTTGTCATTGAATCCTGAATATG 57.783 34.615 0.00 0.00 0.00 1.78
2531 7611 5.384336 TGAATGTCAAGGAACAGATGGAAA 58.616 37.500 0.00 0.00 31.50 3.13
2534 7614 3.693085 CCTGAATGTCAAGGAACAGATGG 59.307 47.826 0.00 0.00 31.50 3.51
2564 7644 7.233348 ACCATCAAAATACTGGATTGACTTGTT 59.767 33.333 0.00 0.00 36.03 2.83
2788 7879 3.190327 TGTGCCGAAAATAACACAGATGG 59.810 43.478 0.00 0.00 38.07 3.51
2804 7895 2.810650 GGTACTTCTACAGATGTGCCG 58.189 52.381 13.86 0.00 42.00 5.69
2860 7953 9.524106 CATGCAAACAAATCATATAGAACACAT 57.476 29.630 0.00 0.00 0.00 3.21
3001 8099 5.702670 TGACACAAATTCCTGAAGAGATGTC 59.297 40.000 0.00 0.00 34.66 3.06
3124 8245 4.462834 TGAGCCCTATGTTATACTCCATCG 59.537 45.833 0.00 0.00 0.00 3.84
3200 8323 1.202222 CCAACCGAGCAATTGAGCATC 60.202 52.381 10.34 0.13 36.85 3.91
3216 8339 7.383300 CAGAAAAAGGAAATCAGATTGACCAAC 59.617 37.037 16.99 7.39 0.00 3.77
3413 8701 0.111639 GGGTTCAGGGTGCCAGTTTA 59.888 55.000 0.00 0.00 0.00 2.01
3431 8719 3.505680 TGGCAGCTACACAAATAACAAGG 59.494 43.478 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.