Multiple sequence alignment - TraesCS1D01G304500

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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 TraesCS1D01G304500 chr1D 100.000 2978 0 0 1 2978 402109061 402106084 0.000000e+00 5500.0
1 TraesCS1D01G304500 chr1D 99.026 2978 28 1 1 2978 402007498 402004522 0.000000e+00 5337.0
2 TraesCS1D01G304500 chr1D 99.067 2358 18 3 47 2400 402052499 402050142 0.000000e+00 4229.0
3 TraesCS1D01G304500 chr1D 99.330 2239 14 1 1 2238 401922282 401920044 0.000000e+00 4050.0
4 TraesCS1D01G304500 chr1D 94.055 1413 70 5 830 2241 401775169 401773770 0.000000e+00 2132.0
5 TraesCS1D01G304500 chr1D 88.571 280 12 9 899 1158 401700044 401699765 3.700000e-84 322.0
6 TraesCS1D01G304500 chr1D 79.562 411 55 21 2575 2972 452115458 452115852 1.760000e-67 267.0
7 TraesCS1D01G304500 chr1D 96.939 98 3 0 2192 2289 401920052 401919955 6.600000e-37 165.0
8 TraesCS1D01G304500 chr1B 90.492 2177 137 32 11 2154 539590536 539588397 0.000000e+00 2809.0
9 TraesCS1D01G304500 chr1B 92.857 84 5 1 2495 2578 264766952 264766870 1.450000e-23 121.0
10 TraesCS1D01G304500 chr1B 86.765 68 7 2 555 621 642509309 642509375 1.140000e-09 75.0
11 TraesCS1D01G304500 chr1A 92.883 1925 93 14 605 2521 497585842 497583954 0.000000e+00 2756.0
12 TraesCS1D01G304500 chr1A 92.963 1421 65 12 830 2241 497580598 497579204 0.000000e+00 2037.0
13 TraesCS1D01G304500 chr1A 89.455 275 13 6 899 1158 497537649 497537376 1.710000e-87 333.0
14 TraesCS1D01G304500 chr1A 88.462 156 10 4 355 503 497580965 497580811 6.560000e-42 182.0
15 TraesCS1D01G304500 chr7B 87.522 1122 125 11 997 2115 535506115 535507224 0.000000e+00 1282.0
16 TraesCS1D01G304500 chr7B 82.195 410 56 14 2578 2978 601930265 601930666 1.320000e-88 337.0
17 TraesCS1D01G304500 chr7B 84.270 267 41 1 11 277 517606963 517607228 2.940000e-65 259.0
18 TraesCS1D01G304500 chr7B 80.415 337 59 5 2243 2578 526872456 526872126 1.770000e-62 250.0
19 TraesCS1D01G304500 chr7B 79.228 337 62 6 2243 2578 526880415 526880086 8.300000e-56 228.0
20 TraesCS1D01G304500 chr7D 86.968 1151 125 19 983 2127 506882674 506883805 0.000000e+00 1271.0
21 TraesCS1D01G304500 chr7D 86.090 266 36 1 11 276 94741828 94741564 4.860000e-73 285.0
22 TraesCS1D01G304500 chr4D 83.171 410 56 11 2579 2978 301503137 301502731 2.180000e-96 363.0
23 TraesCS1D01G304500 chr4D 82.558 344 50 8 2637 2973 333756504 333756164 8.070000e-76 294.0
24 TraesCS1D01G304500 chr4D 81.871 342 50 11 2645 2978 333666329 333665992 8.130000e-71 278.0
25 TraesCS1D01G304500 chr4D 79.800 401 60 18 2579 2972 101062352 101062738 3.780000e-69 272.0
26 TraesCS1D01G304500 chr5A 82.716 405 56 11 2579 2978 595157797 595158192 6.110000e-92 348.0
27 TraesCS1D01G304500 chr5A 95.652 46 2 0 552 597 47964341 47964386 1.140000e-09 75.0
28 TraesCS1D01G304500 chr7A 86.940 268 35 0 11 278 680339068 680338801 4.820000e-78 302.0
29 TraesCS1D01G304500 chr7A 83.396 265 38 5 12 275 169017981 169018240 1.070000e-59 241.0
30 TraesCS1D01G304500 chr6A 80.344 407 70 7 2579 2978 2840771 2840368 1.740000e-77 300.0
31 TraesCS1D01G304500 chr3B 81.210 314 52 6 22 334 390456168 390456475 2.290000e-61 246.0
32 TraesCS1D01G304500 chr3B 84.516 155 14 6 2430 2578 19097585 19097435 8.600000e-31 145.0
33 TraesCS1D01G304500 chr3D 79.245 318 62 4 11 328 336543370 336543683 5.000000e-53 219.0
34 TraesCS1D01G304500 chr3D 83.945 218 32 3 2363 2578 481520568 481520352 3.890000e-49 206.0
35 TraesCS1D01G304500 chr3A 91.765 85 6 1 2495 2578 700941069 700941153 1.880000e-22 117.0
36 TraesCS1D01G304500 chr3A 92.727 55 1 1 304 355 696206630 696206684 3.180000e-10 76.8
37 TraesCS1D01G304500 chr3A 90.909 55 2 1 304 355 628917675 628917729 1.480000e-08 71.3
38 TraesCS1D01G304500 chr3A 92.157 51 3 1 555 604 681348477 681348527 1.480000e-08 71.3
39 TraesCS1D01G304500 chr6B 88.095 84 10 0 2495 2578 693984486 693984403 1.890000e-17 100.0
40 TraesCS1D01G304500 chr6B 88.095 84 9 1 2495 2578 693955728 693955646 6.790000e-17 99.0
41 TraesCS1D01G304500 chr5D 95.556 45 2 0 554 598 30554223 30554179 4.120000e-09 73.1
42 TraesCS1D01G304500 chr4A 84.211 76 9 1 283 355 590653888 590653963 1.480000e-08 71.3
43 TraesCS1D01G304500 chr2B 88.889 54 4 2 555 606 67548881 67548934 6.890000e-07 65.8


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 TraesCS1D01G304500 chr1D 402106084 402109061 2977 True 5500.000000 5500 100.0000 1 2978 1 chr1D.!!$R5 2977
1 TraesCS1D01G304500 chr1D 402004522 402007498 2976 True 5337.000000 5337 99.0260 1 2978 1 chr1D.!!$R3 2977
2 TraesCS1D01G304500 chr1D 402050142 402052499 2357 True 4229.000000 4229 99.0670 47 2400 1 chr1D.!!$R4 2353
3 TraesCS1D01G304500 chr1D 401773770 401775169 1399 True 2132.000000 2132 94.0550 830 2241 1 chr1D.!!$R2 1411
4 TraesCS1D01G304500 chr1D 401919955 401922282 2327 True 2107.500000 4050 98.1345 1 2289 2 chr1D.!!$R6 2288
5 TraesCS1D01G304500 chr1B 539588397 539590536 2139 True 2809.000000 2809 90.4920 11 2154 1 chr1B.!!$R2 2143
6 TraesCS1D01G304500 chr1A 497579204 497585842 6638 True 1658.333333 2756 91.4360 355 2521 3 chr1A.!!$R2 2166
7 TraesCS1D01G304500 chr7B 535506115 535507224 1109 False 1282.000000 1282 87.5220 997 2115 1 chr7B.!!$F2 1118
8 TraesCS1D01G304500 chr7D 506882674 506883805 1131 False 1271.000000 1271 86.9680 983 2127 1 chr7D.!!$F1 1144

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
368 375 2.310779 TGCTCTTAGGTCCTCACACT 57.689 50.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2543 2944 2.076184 GGTTCCATCCCCCGATCCA 61.076 63.158 0.0 0.0 0.0 3.41 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
51 52 4.667935 TTCCTCCGCCCTTCCCCA 62.668 66.667 0.00 0.00 0.0 4.96
368 375 2.310779 TGCTCTTAGGTCCTCACACT 57.689 50.000 0.00 0.00 0.0 3.55
775 808 6.992715 ACACATCCATCTAACTAACTATTGGC 59.007 38.462 0.00 0.00 0.0 4.52
2580 2981 2.288579 ACCTTCAAACACATGCATGCAG 60.289 45.455 26.69 20.59 0.0 4.41
2688 3089 8.669571 AGCTAACTCAAAATATACCCCATACAT 58.330 33.333 0.00 0.00 0.0 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.978617 CACCATTTCCTTGCCGCCT 60.979 57.895 0.00 0.00 0.00 5.52
97 98 4.559300 CGGATCACCAAAAGATGCAGTTTT 60.559 41.667 4.17 4.17 33.97 2.43
415 422 4.772624 ACTTATGTAGAGCCAACTCACTCA 59.227 41.667 0.00 0.00 46.09 3.41
2543 2944 2.076184 GGTTCCATCCCCCGATCCA 61.076 63.158 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.