Multiple sequence alignment - TraesCS7A01G234200

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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 TraesCS7A01G234200 chr7A 100.000 3159 0 0 1 3159 206573456 206576614 0.000000e+00 5834.0
1 TraesCS7A01G234200 chr5B 98.486 2245 30 3 1 2244 701464824 701467065 0.000000e+00 3954.0
2 TraesCS7A01G234200 chr5B 98.237 397 6 1 2761 3156 701467258 701467654 0.000000e+00 693.0
3 TraesCS7A01G234200 chr5B 88.060 67 5 3 2383 2448 231093189 231093253 3.380000e-10 76.8
4 TraesCS7A01G234200 chr1B 97.820 2248 45 1 1 2244 23815840 23818087 0.000000e+00 3877.0
5 TraesCS7A01G234200 chr1B 95.904 2246 67 3 1 2244 48529649 48531871 0.000000e+00 3615.0
6 TraesCS7A01G234200 chr1B 97.008 869 22 4 2294 3159 666991854 666990987 0.000000e+00 1458.0
7 TraesCS7A01G234200 chr1B 100.000 46 0 0 2252 2297 388031953 388031998 5.610000e-13 86.1
8 TraesCS7A01G234200 chr2B 96.745 2243 59 4 1 2243 142887186 142889414 0.000000e+00 3725.0
9 TraesCS7A01G234200 chr2B 95.600 500 19 2 2661 3159 573751698 573752195 0.000000e+00 798.0
10 TraesCS7A01G234200 chr2B 96.063 381 9 3 2294 2673 573736318 573736693 1.610000e-172 616.0
11 TraesCS7A01G234200 chr5A 96.585 1640 48 7 1 1634 670476770 670475133 0.000000e+00 2712.0
12 TraesCS7A01G234200 chr5A 95.870 1598 61 5 4 1598 696328865 696327270 0.000000e+00 2580.0
13 TraesCS7A01G234200 chr5A 95.840 649 24 2 1595 2243 670475032 670474387 0.000000e+00 1046.0
14 TraesCS7A01G234200 chr3B 96.912 1619 42 2 1 1612 607523082 607521465 0.000000e+00 2706.0
15 TraesCS7A01G234200 chr3B 95.727 866 36 1 2294 3159 487853433 487852569 0.000000e+00 1393.0
16 TraesCS7A01G234200 chr3B 97.802 637 14 0 1608 2244 607501966 607501330 0.000000e+00 1099.0
17 TraesCS7A01G234200 chr2D 96.188 1600 59 2 1 1598 197523406 197521807 0.000000e+00 2615.0
18 TraesCS7A01G234200 chr2D 95.846 650 22 3 1595 2243 197521669 197521024 0.000000e+00 1046.0
19 TraesCS7A01G234200 chr1A 96.190 1601 57 4 1 1598 449450047 449451646 0.000000e+00 2615.0
20 TraesCS7A01G234200 chr1A 95.617 867 33 4 2294 3159 387225818 387224956 0.000000e+00 1386.0
21 TraesCS7A01G234200 chr1A 95.652 644 25 3 1595 2238 374209501 374210141 0.000000e+00 1031.0
22 TraesCS7A01G234200 chr3A 95.000 1600 56 4 1 1598 1716806 1715229 0.000000e+00 2490.0
23 TraesCS7A01G234200 chr3A 94.434 1599 84 5 1 1598 218192076 218190482 0.000000e+00 2455.0
24 TraesCS7A01G234200 chr3A 95.686 649 20 4 1595 2243 1715090 1714450 0.000000e+00 1037.0
25 TraesCS7A01G234200 chr4A 96.408 863 23 5 2294 3154 324710175 324709319 0.000000e+00 1415.0
26 TraesCS7A01G234200 chr4A 95.848 867 33 3 2294 3159 706561452 706560588 0.000000e+00 1399.0
27 TraesCS7A01G234200 chr4A 95.161 868 34 5 2294 3159 551274808 551275669 0.000000e+00 1363.0
28 TraesCS7A01G234200 chr5D 96.386 581 19 1 2579 3159 498378766 498379344 0.000000e+00 955.0
29 TraesCS7A01G234200 chr7B 79.789 1044 172 21 1 1035 612640469 612641482 0.000000e+00 723.0
30 TraesCS7A01G234200 chr7B 97.674 43 1 0 2300 2342 208148143 208148101 1.220000e-09 75.0
31 TraesCS7A01G234200 chr7D 81.818 308 45 7 2360 2663 115864704 115864404 6.770000e-62 248.0


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 TraesCS7A01G234200 chr7A 206573456 206576614 3158 False 5834.0 5834 100.0000 1 3159 1 chr7A.!!$F1 3158
1 TraesCS7A01G234200 chr5B 701464824 701467654 2830 False 2323.5 3954 98.3615 1 3156 2 chr5B.!!$F2 3155
2 TraesCS7A01G234200 chr1B 23815840 23818087 2247 False 3877.0 3877 97.8200 1 2244 1 chr1B.!!$F1 2243
3 TraesCS7A01G234200 chr1B 48529649 48531871 2222 False 3615.0 3615 95.9040 1 2244 1 chr1B.!!$F2 2243
4 TraesCS7A01G234200 chr1B 666990987 666991854 867 True 1458.0 1458 97.0080 2294 3159 1 chr1B.!!$R1 865
5 TraesCS7A01G234200 chr2B 142887186 142889414 2228 False 3725.0 3725 96.7450 1 2243 1 chr2B.!!$F1 2242
6 TraesCS7A01G234200 chr5A 696327270 696328865 1595 True 2580.0 2580 95.8700 4 1598 1 chr5A.!!$R1 1594
7 TraesCS7A01G234200 chr5A 670474387 670476770 2383 True 1879.0 2712 96.2125 1 2243 2 chr5A.!!$R2 2242
8 TraesCS7A01G234200 chr3B 607521465 607523082 1617 True 2706.0 2706 96.9120 1 1612 1 chr3B.!!$R3 1611
9 TraesCS7A01G234200 chr3B 487852569 487853433 864 True 1393.0 1393 95.7270 2294 3159 1 chr3B.!!$R1 865
10 TraesCS7A01G234200 chr3B 607501330 607501966 636 True 1099.0 1099 97.8020 1608 2244 1 chr3B.!!$R2 636
11 TraesCS7A01G234200 chr2D 197521024 197523406 2382 True 1830.5 2615 96.0170 1 2243 2 chr2D.!!$R1 2242
12 TraesCS7A01G234200 chr1A 449450047 449451646 1599 False 2615.0 2615 96.1900 1 1598 1 chr1A.!!$F2 1597
13 TraesCS7A01G234200 chr1A 387224956 387225818 862 True 1386.0 1386 95.6170 2294 3159 1 chr1A.!!$R1 865
14 TraesCS7A01G234200 chr1A 374209501 374210141 640 False 1031.0 1031 95.6520 1595 2238 1 chr1A.!!$F1 643
15 TraesCS7A01G234200 chr3A 218190482 218192076 1594 True 2455.0 2455 94.4340 1 1598 1 chr3A.!!$R1 1597
16 TraesCS7A01G234200 chr3A 1714450 1716806 2356 True 1763.5 2490 95.3430 1 2243 2 chr3A.!!$R2 2242
17 TraesCS7A01G234200 chr4A 324709319 324710175 856 True 1415.0 1415 96.4080 2294 3154 1 chr4A.!!$R1 860
18 TraesCS7A01G234200 chr4A 706560588 706561452 864 True 1399.0 1399 95.8480 2294 3159 1 chr4A.!!$R2 865
19 TraesCS7A01G234200 chr4A 551274808 551275669 861 False 1363.0 1363 95.1610 2294 3159 1 chr4A.!!$F1 865
20 TraesCS7A01G234200 chr5D 498378766 498379344 578 False 955.0 955 96.3860 2579 3159 1 chr5D.!!$F1 580
21 TraesCS7A01G234200 chr7B 612640469 612641482 1013 False 723.0 723 79.7890 1 1035 1 chr7B.!!$F1 1034

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 3.641436 TGAACCACTACACACACATCTCT 59.359 43.478 0.0 0.0 0.0 3.10 F
899 914 4.989168 GGCTGATTATAACAACTAGTCGGG 59.011 45.833 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 1269 1.270358 GCCACTCTGTTTCCGAGAGTT 60.270 52.381 1.21 0.0 46.57 3.01 R
2245 2438 0.326264 ATCCAGAACAGAGGTGCCAC 59.674 55.000 0.00 0.0 0.00 5.01 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
127 128 3.641436 TGAACCACTACACACACATCTCT 59.359 43.478 0.00 0.00 0.00 3.10
899 914 4.989168 GGCTGATTATAACAACTAGTCGGG 59.011 45.833 0.00 0.00 0.00 5.14
1132 1153 6.884295 TGAAGGGTGGACTAGAATTACAAATG 59.116 38.462 0.00 0.00 0.00 2.32
1225 1269 8.650143 AAAAGGAAATTATAAGGCAGTGAGAA 57.350 30.769 0.00 0.00 0.00 2.87
1729 1917 6.500049 CCATTTCTCCTATGGATTCCTCTACT 59.500 42.308 3.95 0.00 44.36 2.57
1742 1930 8.772250 TGGATTCCTCTACTAATGATTTGAACT 58.228 33.333 3.95 0.00 0.00 3.01
2122 2311 5.677319 ATACCAAGGACTCAAATCTTCGA 57.323 39.130 0.00 0.00 0.00 3.71
2201 2393 3.509575 AGTTCACCTTCTTGTTTTGCACA 59.490 39.130 0.00 0.00 0.00 4.57
2202 2394 4.160252 AGTTCACCTTCTTGTTTTGCACAT 59.840 37.500 0.00 0.00 34.43 3.21
2245 2438 8.586570 TTTACTTTGTGGCATTATTGACTTTG 57.413 30.769 0.00 0.00 0.00 2.77
2246 2439 6.160576 ACTTTGTGGCATTATTGACTTTGT 57.839 33.333 0.00 0.00 0.00 2.83
2247 2440 5.984926 ACTTTGTGGCATTATTGACTTTGTG 59.015 36.000 0.00 0.00 0.00 3.33
2248 2441 4.517952 TGTGGCATTATTGACTTTGTGG 57.482 40.909 0.00 0.00 0.00 4.17
2249 2442 3.253230 GTGGCATTATTGACTTTGTGGC 58.747 45.455 0.00 0.00 0.00 5.01
2250 2443 2.896044 TGGCATTATTGACTTTGTGGCA 59.104 40.909 0.00 0.00 39.38 4.92
2254 2462 4.737054 CATTATTGACTTTGTGGCACCTC 58.263 43.478 16.26 5.06 30.21 3.85
2262 2470 0.179020 TTGTGGCACCTCTGTTCTGG 60.179 55.000 16.26 0.00 0.00 3.86
2264 2472 0.326264 GTGGCACCTCTGTTCTGGAT 59.674 55.000 6.29 0.00 0.00 3.41
2267 2475 2.846206 TGGCACCTCTGTTCTGGATTAT 59.154 45.455 0.00 0.00 0.00 1.28
2270 2478 5.843969 TGGCACCTCTGTTCTGGATTATATA 59.156 40.000 0.00 0.00 0.00 0.86
2271 2479 6.166982 GGCACCTCTGTTCTGGATTATATAC 58.833 44.000 0.00 0.00 0.00 1.47
2272 2480 6.166982 GCACCTCTGTTCTGGATTATATACC 58.833 44.000 0.00 0.00 0.00 2.73
2273 2481 6.239600 GCACCTCTGTTCTGGATTATATACCA 60.240 42.308 0.00 0.00 34.81 3.25
2285 2493 7.907389 TGGATTATATACCAGATCTTGTGACC 58.093 38.462 9.65 3.73 0.00 4.02
2286 2494 7.734865 TGGATTATATACCAGATCTTGTGACCT 59.265 37.037 9.65 0.00 0.00 3.85
2287 2495 8.598041 GGATTATATACCAGATCTTGTGACCTT 58.402 37.037 9.65 0.00 0.00 3.50
2290 2498 3.425162 ACCAGATCTTGTGACCTTTCC 57.575 47.619 0.00 0.00 0.00 3.13
2291 2499 2.040412 ACCAGATCTTGTGACCTTTCCC 59.960 50.000 0.00 0.00 0.00 3.97
2292 2500 2.619074 CCAGATCTTGTGACCTTTCCCC 60.619 54.545 0.00 0.00 0.00 4.81
2322 2530 3.222173 TGCTAGTTGGTCCATGTGTTT 57.778 42.857 0.00 0.00 0.00 2.83
2342 2550 7.148306 TGTGTTTCTTGGTTAGTTCTCTGAAAC 60.148 37.037 0.00 0.00 41.03 2.78
2347 2555 8.190326 TCTTGGTTAGTTCTCTGAAACTATGA 57.810 34.615 10.87 2.15 40.46 2.15
2675 2887 6.967199 GCTTTGGATTTAAACTCTATGAACCG 59.033 38.462 0.00 0.00 0.00 4.44
2762 3029 5.428253 TCTGTTGTTGTCTTAGCTTCAAGT 58.572 37.500 0.00 0.00 0.00 3.16
2797 3064 5.338614 ACGTGTATTAGTGACAAAGCAAC 57.661 39.130 0.00 0.00 0.00 4.17
3038 3305 6.154363 TCAAAGAAGTTGATGGTGGAAGTTTT 59.846 34.615 0.00 0.00 41.47 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1132 1153 6.474751 GCTAGTGGAAATTTCTGATTGAATGC 59.525 38.462 17.42 7.44 34.24 3.56
1225 1269 1.270358 GCCACTCTGTTTCCGAGAGTT 60.270 52.381 1.21 0.00 46.57 3.01
1346 1390 2.291089 TGCCTTGAAGAGCATGAATGGA 60.291 45.455 0.00 0.00 33.08 3.41
1742 1930 8.956446 TCATCAACATTGGTAGAGGAGATATA 57.044 34.615 0.00 0.00 0.00 0.86
1936 2125 1.668751 TCGTCAACCAGTTTTGCAGAC 59.331 47.619 0.00 0.00 0.00 3.51
2122 2311 5.843019 TCTCCTCCTTCAACCAATAAAGT 57.157 39.130 0.00 0.00 0.00 2.66
2244 2437 1.053835 TCCAGAACAGAGGTGCCACA 61.054 55.000 0.00 0.00 0.00 4.17
2245 2438 0.326264 ATCCAGAACAGAGGTGCCAC 59.674 55.000 0.00 0.00 0.00 5.01
2246 2439 1.067295 AATCCAGAACAGAGGTGCCA 58.933 50.000 0.00 0.00 0.00 4.92
2247 2440 3.567478 ATAATCCAGAACAGAGGTGCC 57.433 47.619 0.00 0.00 0.00 5.01
2248 2441 6.166982 GGTATATAATCCAGAACAGAGGTGC 58.833 44.000 0.00 0.00 0.00 5.01
2249 2442 7.303182 TGGTATATAATCCAGAACAGAGGTG 57.697 40.000 0.00 0.00 0.00 4.00
2264 2472 8.429641 GGAAAGGTCACAAGATCTGGTATATAA 58.570 37.037 1.34 0.00 34.77 0.98
2267 2475 5.130477 GGGAAAGGTCACAAGATCTGGTATA 59.870 44.000 1.34 0.00 34.77 1.47
2270 2478 2.040412 GGGAAAGGTCACAAGATCTGGT 59.960 50.000 0.00 0.00 34.77 4.00
2271 2479 2.619074 GGGGAAAGGTCACAAGATCTGG 60.619 54.545 0.00 0.00 34.77 3.86
2272 2480 2.307098 AGGGGAAAGGTCACAAGATCTG 59.693 50.000 0.00 0.00 34.77 2.90
2273 2481 2.637165 AGGGGAAAGGTCACAAGATCT 58.363 47.619 0.00 0.00 36.57 2.75
2274 2482 3.084786 CAAGGGGAAAGGTCACAAGATC 58.915 50.000 0.00 0.00 0.00 2.75
2275 2483 2.447047 ACAAGGGGAAAGGTCACAAGAT 59.553 45.455 0.00 0.00 0.00 2.40
2276 2484 1.850345 ACAAGGGGAAAGGTCACAAGA 59.150 47.619 0.00 0.00 0.00 3.02
2277 2485 2.364972 ACAAGGGGAAAGGTCACAAG 57.635 50.000 0.00 0.00 0.00 3.16
2278 2486 3.050089 TCTACAAGGGGAAAGGTCACAA 58.950 45.455 0.00 0.00 0.00 3.33
2280 2488 3.782656 TTCTACAAGGGGAAAGGTCAC 57.217 47.619 0.00 0.00 0.00 3.67
2281 2489 4.662278 CAATTCTACAAGGGGAAAGGTCA 58.338 43.478 0.00 0.00 0.00 4.02
2282 2490 3.444034 GCAATTCTACAAGGGGAAAGGTC 59.556 47.826 0.00 0.00 0.00 3.85
2283 2491 3.076032 AGCAATTCTACAAGGGGAAAGGT 59.924 43.478 0.00 0.00 0.00 3.50
2284 2492 3.701664 AGCAATTCTACAAGGGGAAAGG 58.298 45.455 0.00 0.00 0.00 3.11
2285 2493 5.501156 ACTAGCAATTCTACAAGGGGAAAG 58.499 41.667 0.00 0.00 0.00 2.62
2286 2494 5.514500 ACTAGCAATTCTACAAGGGGAAA 57.486 39.130 0.00 0.00 0.00 3.13
2287 2495 5.253330 CAACTAGCAATTCTACAAGGGGAA 58.747 41.667 0.00 0.00 0.00 3.97
2288 2496 4.324254 CCAACTAGCAATTCTACAAGGGGA 60.324 45.833 0.00 0.00 0.00 4.81
2289 2497 3.947834 CCAACTAGCAATTCTACAAGGGG 59.052 47.826 0.00 0.00 0.00 4.79
2290 2498 4.589908 ACCAACTAGCAATTCTACAAGGG 58.410 43.478 0.00 0.00 0.00 3.95
2291 2499 4.636206 GGACCAACTAGCAATTCTACAAGG 59.364 45.833 0.00 0.00 0.00 3.61
2292 2500 5.245531 TGGACCAACTAGCAATTCTACAAG 58.754 41.667 0.00 0.00 0.00 3.16
2322 2530 8.088981 GTCATAGTTTCAGAGAACTAACCAAGA 58.911 37.037 2.07 0.00 43.24 3.02
2347 2555 9.686683 ACTGACAGAAGCAAATTATATTAAGGT 57.313 29.630 10.08 0.00 0.00 3.50
2657 2869 8.617290 AACACTTCGGTTCATAGAGTTTAAAT 57.383 30.769 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.