Multiple sequence alignment - TraesCS5D01G417100

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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 TraesCS5D01G417100 chr5D 100.000 3014 0 0 1 3014 479193483 479196496 0.000000e+00 5566
1 TraesCS5D01G417100 chr5D 91.419 606 36 13 2415 3014 486893859 486893264 0.000000e+00 817
2 TraesCS5D01G417100 chr5D 79.112 608 92 25 1096 1691 355676984 355677568 1.310000e-103 387
3 TraesCS5D01G417100 chr5D 96.476 227 8 0 2788 3014 526477834 526478060 2.840000e-100 375
4 TraesCS5D01G417100 chr5D 89.655 145 9 6 2657 2798 53010437 53010578 2.390000e-41 180
5 TraesCS5D01G417100 chr5B 92.134 2301 83 33 4 2258 586915196 586917444 0.000000e+00 3157
6 TraesCS5D01G417100 chr5B 79.180 610 88 29 1096 1691 420386235 420386819 1.310000e-103 387
7 TraesCS5D01G417100 chr5B 94.714 227 12 0 2788 3014 278452513 278452739 1.330000e-93 353
8 TraesCS5D01G417100 chr5B 95.556 90 2 2 2320 2409 586917464 586917551 3.130000e-30 143
9 TraesCS5D01G417100 chr5A 90.672 2412 91 34 41 2400 597940045 597942374 0.000000e+00 3085
10 TraesCS5D01G417100 chr5A 91.875 160 11 2 2568 2725 706030180 706030339 3.910000e-54 222
11 TraesCS5D01G417100 chr4D 89.314 627 30 21 2417 3014 500313968 500314586 0.000000e+00 752
12 TraesCS5D01G417100 chr4D 90.093 323 14 12 2414 2725 12629189 12628874 1.300000e-108 403
13 TraesCS5D01G417100 chr3B 89.195 435 24 6 9 432 542129285 542129707 3.440000e-144 521
14 TraesCS5D01G417100 chr3B 94.330 194 11 0 1086 1279 613754270 613754077 6.320000e-77 298
15 TraesCS5D01G417100 chr3B 93.860 114 7 0 1739 1852 613753713 613753600 3.990000e-39 172
16 TraesCS5D01G417100 chr7D 91.040 346 14 11 2395 2728 159007719 159008059 4.580000e-123 451
17 TraesCS5D01G417100 chr7D 91.235 251 16 5 2413 2659 106994950 106994702 1.340000e-88 337
18 TraesCS5D01G417100 chr2D 93.729 303 14 5 2407 2704 189688898 189688596 1.650000e-122 449
19 TraesCS5D01G417100 chr2D 87.195 328 12 12 2415 2716 454959160 454958837 2.220000e-91 346
20 TraesCS5D01G417100 chrUn 84.009 444 39 19 2581 3014 399210312 399209891 6.050000e-107 398
21 TraesCS5D01G417100 chrUn 84.009 444 39 19 2581 3014 474516958 474517379 6.050000e-107 398
22 TraesCS5D01G417100 chrUn 94.714 227 12 0 2788 3014 422669879 422670105 1.330000e-93 353
23 TraesCS5D01G417100 chrUn 94.714 227 12 0 2788 3014 461622609 461622835 1.330000e-93 353
24 TraesCS5D01G417100 chr2A 95.154 227 11 0 2788 3014 579838135 579838361 2.860000e-95 359
25 TraesCS5D01G417100 chr1D 92.460 252 13 5 2414 2659 16702865 16703116 3.700000e-94 355
26 TraesCS5D01G417100 chr6D 93.151 146 9 1 2423 2567 43144870 43145015 2.350000e-51 213
27 TraesCS5D01G417100 chr7A 90.625 160 13 2 2568 2725 629782668 629782827 8.470000e-51 211
28 TraesCS5D01G417100 chr3D 86.294 197 16 10 2627 2814 389189831 389189637 1.420000e-48 204


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 TraesCS5D01G417100 chr5D 479193483 479196496 3013 False 5566 5566 100.000 1 3014 1 chr5D.!!$F3 3013
1 TraesCS5D01G417100 chr5D 486893264 486893859 595 True 817 817 91.419 2415 3014 1 chr5D.!!$R1 599
2 TraesCS5D01G417100 chr5D 355676984 355677568 584 False 387 387 79.112 1096 1691 1 chr5D.!!$F2 595
3 TraesCS5D01G417100 chr5B 586915196 586917551 2355 False 1650 3157 93.845 4 2409 2 chr5B.!!$F3 2405
4 TraesCS5D01G417100 chr5B 420386235 420386819 584 False 387 387 79.180 1096 1691 1 chr5B.!!$F2 595
5 TraesCS5D01G417100 chr5A 597940045 597942374 2329 False 3085 3085 90.672 41 2400 1 chr5A.!!$F1 2359
6 TraesCS5D01G417100 chr4D 500313968 500314586 618 False 752 752 89.314 2417 3014 1 chr4D.!!$F1 597
7 TraesCS5D01G417100 chr3B 613753600 613754270 670 True 235 298 94.095 1086 1852 2 chr3B.!!$R1 766

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
297 309 0.032952 GTGACACGCTGGGTCTACAA 59.967 55.0 11.28 0.0 36.26 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2327 0.031178 CTGCTGTCACAAACAAGCCC 59.969 55.0 0.0 0.0 37.45 5.19 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
37 38 2.813908 CCAGCGTTCGTGCTACCC 60.814 66.667 0.00 0.00 45.23 3.69
137 139 2.769376 CAACGGCGCAATTAGTAAGTG 58.231 47.619 10.83 5.98 0.00 3.16
256 268 2.397413 CTTCGCCCAGGGTCACAACT 62.397 60.000 7.55 0.00 0.00 3.16
297 309 0.032952 GTGACACGCTGGGTCTACAA 59.967 55.000 11.28 0.00 36.26 2.41
317 329 4.933064 GCCGATCTCCGTCCGCAG 62.933 72.222 0.00 0.00 36.31 5.18
355 367 2.949106 CGTCCGTCCACACGTACT 59.051 61.111 0.00 0.00 45.17 2.73
356 368 1.154338 CGTCCGTCCACACGTACTC 60.154 63.158 0.00 0.00 45.17 2.59
357 369 1.211190 GTCCGTCCACACGTACTCC 59.789 63.158 0.00 0.00 45.17 3.85
358 370 2.177531 CCGTCCACACGTACTCCG 59.822 66.667 0.00 0.00 45.17 4.63
359 371 2.177531 CGTCCACACGTACTCCGG 59.822 66.667 0.00 0.00 41.42 5.14
361 373 1.505353 GTCCACACGTACTCCGGAG 59.495 63.158 30.11 30.11 42.24 4.63
705 747 3.161450 GAGCCGCCCCACTATGGA 61.161 66.667 0.00 0.00 40.96 3.41
706 748 3.164269 AGCCGCCCCACTATGGAG 61.164 66.667 0.00 0.00 40.96 3.86
714 760 1.330655 CCCACTATGGAGACGGCACT 61.331 60.000 0.00 0.00 40.96 4.40
782 828 4.090057 GTCGCTTCCCGCACAAGC 62.090 66.667 1.94 1.94 42.51 4.01
784 830 4.389576 CGCTTCCCGCACAAGCAC 62.390 66.667 10.82 0.00 45.66 4.40
2003 2160 2.870161 CGTCGCGGAGTTCGTCAG 60.870 66.667 6.13 0.00 41.72 3.51
2026 2183 7.038231 TCAGTCACTCCTAGCTAGCTACATATA 60.038 40.741 20.67 1.02 0.00 0.86
2027 2184 7.065324 CAGTCACTCCTAGCTAGCTACATATAC 59.935 44.444 20.67 13.57 0.00 1.47
2076 2240 2.108168 GTGATCAGGCCAGTGGTAGTA 58.892 52.381 11.74 0.00 0.00 1.82
2111 2280 7.488322 AGAGAATAAGTGTAGAGTGAGAATGC 58.512 38.462 0.00 0.00 0.00 3.56
2136 2308 3.462483 TGCTGTTACCTCTGTTTTCGA 57.538 42.857 0.00 0.00 0.00 3.71
2155 2327 4.186926 TCGATTCTTCTTGGAAGCAGATG 58.813 43.478 2.74 0.00 31.94 2.90
2195 2367 2.880890 GTGACAGATGGCTTTGTTCACT 59.119 45.455 0.00 0.00 0.00 3.41
2196 2368 2.880268 TGACAGATGGCTTTGTTCACTG 59.120 45.455 0.00 0.00 0.00 3.66
2265 2438 7.335627 TGAACTTTGGAACGGATAAGTATGAT 58.664 34.615 0.00 0.00 31.06 2.45
2266 2439 7.279981 TGAACTTTGGAACGGATAAGTATGATG 59.720 37.037 0.00 0.00 31.06 3.07
2267 2440 6.884832 ACTTTGGAACGGATAAGTATGATGA 58.115 36.000 0.00 0.00 0.00 2.92
2273 2446 7.106239 GGAACGGATAAGTATGATGAATGGAT 58.894 38.462 0.00 0.00 0.00 3.41
2275 2448 7.244886 ACGGATAAGTATGATGAATGGATGA 57.755 36.000 0.00 0.00 0.00 2.92
2288 2461 0.617535 TGGATGAAAGAGGGGCTCGA 60.618 55.000 0.00 0.00 35.36 4.04
2386 2560 0.098728 GTGACCATGCAACCATACGC 59.901 55.000 0.00 0.00 0.00 4.42
2404 2578 2.746904 ACGCCATGTCATCAATCGAAAA 59.253 40.909 0.00 0.00 0.00 2.29
2405 2579 3.181507 ACGCCATGTCATCAATCGAAAAG 60.182 43.478 0.00 0.00 0.00 2.27
2408 2582 5.401550 GCCATGTCATCAATCGAAAAGAAA 58.598 37.500 0.00 0.00 0.00 2.52
2409 2583 5.863397 GCCATGTCATCAATCGAAAAGAAAA 59.137 36.000 0.00 0.00 0.00 2.29
2410 2584 6.365789 GCCATGTCATCAATCGAAAAGAAAAA 59.634 34.615 0.00 0.00 0.00 1.94
2411 2585 7.411157 GCCATGTCATCAATCGAAAAGAAAAAG 60.411 37.037 0.00 0.00 0.00 2.27
2412 2586 7.809331 CCATGTCATCAATCGAAAAGAAAAAGA 59.191 33.333 0.00 0.00 0.00 2.52
2413 2587 9.184062 CATGTCATCAATCGAAAAGAAAAAGAA 57.816 29.630 0.00 0.00 0.00 2.52
2512 2687 5.997746 CCACCTCATATTATACAGTTGTGGG 59.002 44.000 0.00 0.00 36.70 4.61
2515 2690 5.997746 CCTCATATTATACAGTTGTGGGTGG 59.002 44.000 0.00 0.00 0.00 4.61
2831 3052 4.477975 GCCGTCCGACTCCGTCAG 62.478 72.222 0.00 0.00 32.09 3.51
2832 3053 2.745100 CCGTCCGACTCCGTCAGA 60.745 66.667 0.00 0.00 32.09 3.27
2833 3054 2.479650 CGTCCGACTCCGTCAGAC 59.520 66.667 0.00 1.30 36.83 3.51
2834 3055 2.479650 GTCCGACTCCGTCAGACG 59.520 66.667 16.50 16.50 42.11 4.18
2835 3056 3.429141 TCCGACTCCGTCAGACGC 61.429 66.667 18.02 2.80 40.91 5.19
2836 3057 4.477975 CCGACTCCGTCAGACGCC 62.478 72.222 18.02 5.28 40.91 5.68
2837 3058 4.813526 CGACTCCGTCAGACGCCG 62.814 72.222 18.02 12.20 40.91 6.46
2883 3104 1.439228 CCGCATCTCACCGTCATCT 59.561 57.895 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 125 3.120477 TGGCGTTTCACTTACTAATTGCG 60.120 43.478 0.00 0.00 0.00 4.85
256 268 1.454847 GGTGCCTTGTGGGTTGTGA 60.455 57.895 0.00 0.00 37.43 3.58
317 329 3.435186 GGCGCTCCAGTTGGCTTC 61.435 66.667 7.64 0.00 34.44 3.86
359 371 1.154197 GGGTTTTGGAGCACGTACTC 58.846 55.000 7.29 7.29 35.86 2.59
361 373 1.154197 GAGGGTTTTGGAGCACGTAC 58.846 55.000 0.00 0.00 0.00 3.67
689 731 3.164269 CTCCATAGTGGGGCGGCT 61.164 66.667 9.56 0.00 38.32 5.52
702 744 4.056125 CGCTGAGTGCCGTCTCCA 62.056 66.667 0.00 0.00 38.78 3.86
705 747 4.074526 ATGCGCTGAGTGCCGTCT 62.075 61.111 16.16 0.00 38.39 4.18
706 748 3.857854 CATGCGCTGAGTGCCGTC 61.858 66.667 16.16 0.00 38.39 4.79
782 828 4.794439 TCGATGGTGCGCGAGGTG 62.794 66.667 12.10 0.00 32.13 4.00
847 926 4.143742 CGCTCATATATATACATGCACGCG 60.144 45.833 3.53 3.53 31.84 6.01
992 1073 2.108514 CGCGTGGCCATGATGACTT 61.109 57.895 29.54 0.00 0.00 3.01
1287 1384 0.173708 CGTGGAAGTAGAGGAGCACC 59.826 60.000 0.00 0.00 0.00 5.01
1560 1695 3.778360 GATGTTACCGCCGGCGCTA 62.778 63.158 42.39 31.06 38.24 4.26
1572 1707 1.348538 CGAGGTTGTGCGCGATGTTA 61.349 55.000 12.10 0.00 0.00 2.41
1620 1755 2.342279 CCTTTGCCGTCGTCCTGA 59.658 61.111 0.00 0.00 0.00 3.86
2003 2160 6.316890 GGTATATGTAGCTAGCTAGGAGTGAC 59.683 46.154 24.78 14.10 0.00 3.67
2026 2183 2.301296 CAGACCAGACAATGAGTGAGGT 59.699 50.000 0.00 0.00 34.61 3.85
2027 2184 2.354503 CCAGACCAGACAATGAGTGAGG 60.355 54.545 0.00 0.00 0.00 3.86
2064 2228 6.239396 TCTAGTATCTCATACTACCACTGGC 58.761 44.000 0.00 0.00 43.93 4.85
2111 2280 1.865865 ACAGAGGTAACAGCAACACG 58.134 50.000 0.00 0.00 41.41 4.49
2136 2308 3.629087 CCCATCTGCTTCCAAGAAGAAT 58.371 45.455 8.50 0.00 43.77 2.40
2155 2327 0.031178 CTGCTGTCACAAACAAGCCC 59.969 55.000 0.00 0.00 37.45 5.19
2164 2336 1.270465 CCATCTGTCACTGCTGTCACA 60.270 52.381 0.00 0.00 0.00 3.58
2265 2438 1.925255 AGCCCCTCTTTCATCCATTCA 59.075 47.619 0.00 0.00 0.00 2.57
2266 2439 2.580962 GAGCCCCTCTTTCATCCATTC 58.419 52.381 0.00 0.00 0.00 2.67
2267 2440 1.133976 CGAGCCCCTCTTTCATCCATT 60.134 52.381 0.00 0.00 0.00 3.16
2273 2446 0.683179 TCGATCGAGCCCCTCTTTCA 60.683 55.000 15.15 0.00 0.00 2.69
2275 2448 0.676736 GATCGATCGAGCCCCTCTTT 59.323 55.000 22.32 1.52 0.00 2.52
2304 2477 2.540101 CTGCGCCTTTATAAACCTCGAG 59.460 50.000 4.18 5.13 0.00 4.04
2359 2533 0.749818 TTGCATGGTCACCACACGTT 60.750 50.000 0.00 0.00 35.80 3.99
2386 2560 7.809331 TCTTTTTCTTTTCGATTGATGACATGG 59.191 33.333 0.00 0.00 0.00 3.66
2404 2578 2.682594 AGCAAGCCCCTTTCTTTTTCT 58.317 42.857 0.00 0.00 0.00 2.52
2405 2579 3.393800 GAAGCAAGCCCCTTTCTTTTTC 58.606 45.455 0.00 0.00 28.16 2.29
2408 2582 0.961753 CGAAGCAAGCCCCTTTCTTT 59.038 50.000 0.00 0.00 28.16 2.52
2409 2583 0.895559 CCGAAGCAAGCCCCTTTCTT 60.896 55.000 0.00 0.00 30.42 2.52
2410 2584 1.303643 CCGAAGCAAGCCCCTTTCT 60.304 57.895 0.00 0.00 0.00 2.52
2411 2585 0.322187 TACCGAAGCAAGCCCCTTTC 60.322 55.000 0.00 0.00 0.00 2.62
2412 2586 0.322546 CTACCGAAGCAAGCCCCTTT 60.323 55.000 0.00 0.00 0.00 3.11
2413 2587 1.198759 TCTACCGAAGCAAGCCCCTT 61.199 55.000 0.00 0.00 0.00 3.95
2439 2613 1.944709 GCCCTTCTACGTTTTGTGTGT 59.055 47.619 0.00 0.00 0.00 3.72
2440 2614 1.944024 TGCCCTTCTACGTTTTGTGTG 59.056 47.619 0.00 0.00 0.00 3.82
2441 2615 2.158871 TCTGCCCTTCTACGTTTTGTGT 60.159 45.455 0.00 0.00 0.00 3.72
2442 2616 2.489971 TCTGCCCTTCTACGTTTTGTG 58.510 47.619 0.00 0.00 0.00 3.33
2545 2721 1.064803 CGTGCTGGCAGTTTGTTTGTA 59.935 47.619 17.16 0.00 0.00 2.41
2928 3149 2.529389 GGGTGGGGAGAGTGGTGT 60.529 66.667 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.