Multiple sequence alignment - TraesCS3A01G459500

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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 TraesCS3A01G459500 chr3A 100.000 1821 0 0 1 1821 696169157 696167337 0.000000e+00 3363
1 TraesCS3A01G459500 chr3A 97.352 1246 31 2 1 1244 628876108 628874863 0.000000e+00 2117
2 TraesCS3A01G459500 chr3A 100.000 589 0 0 2123 2711 696167035 696166447 0.000000e+00 1088
3 TraesCS3A01G459500 chr3A 96.599 588 15 2 1238 1821 628874576 628873990 0.000000e+00 970
4 TraesCS3A01G459500 chr3A 93.852 488 18 4 2222 2709 729297063 729296588 0.000000e+00 725
5 TraesCS3A01G459500 chr3A 93.455 275 16 2 560 833 225919827 225920100 9.040000e-110 407
6 TraesCS3A01G459500 chr3A 98.058 103 2 0 2123 2225 628873943 628873841 2.140000e-41 180
7 TraesCS3A01G459500 chr3B 92.694 917 57 6 820 1733 743814105 743813196 0.000000e+00 1314
8 TraesCS3A01G459500 chr3B 89.299 271 20 2 208 477 743814435 743814173 5.590000e-87 331
9 TraesCS3A01G459500 chr3B 77.814 311 51 9 1007 1314 779303144 779303439 2.770000e-40 176
10 TraesCS3A01G459500 chr3B 77.899 276 43 14 1042 1314 779525027 779525287 3.610000e-34 156
11 TraesCS3A01G459500 chr3D 91.736 956 62 9 820 1765 559916811 559915863 0.000000e+00 1312
12 TraesCS3A01G459500 chr3D 93.666 821 48 4 966 1786 559937464 559936648 0.000000e+00 1225
13 TraesCS3A01G459500 chr3D 87.766 564 47 6 3 564 559917352 559916809 8.180000e-180 640
14 TraesCS3A01G459500 chr3D 85.010 507 36 11 9 514 559938046 559937579 1.890000e-131 479
15 TraesCS3A01G459500 chr3D 92.720 261 18 1 563 822 170661320 170661580 2.550000e-100 375
16 TraesCS3A01G459500 chr3D 91.016 256 23 0 567 822 397800650 397800905 2.000000e-91 346
17 TraesCS3A01G459500 chr3D 80.128 312 35 14 1015 1317 582817146 582816853 9.840000e-50 207
18 TraesCS3A01G459500 chr3D 78.618 304 50 7 1011 1314 582162726 582162438 1.280000e-43 187
19 TraesCS3A01G459500 chr3D 78.261 276 42 13 1042 1314 582056815 582056555 7.770000e-36 161
20 TraesCS3A01G459500 chr3D 84.564 149 19 4 2232 2378 45364633 45364487 7.820000e-31 145
21 TraesCS3A01G459500 chr3D 76.777 211 37 9 1042 1252 582116214 582116016 1.030000e-19 108
22 TraesCS3A01G459500 chr5A 94.888 489 11 3 2226 2709 579903092 579903571 0.000000e+00 752
23 TraesCS3A01G459500 chr5A 94.845 485 14 3 2225 2709 445135452 445135925 0.000000e+00 747
24 TraesCS3A01G459500 chr5A 94.628 484 16 2 2226 2709 487637351 487636878 0.000000e+00 741
25 TraesCS3A01G459500 chr5A 94.318 264 13 2 561 822 480405323 480405060 1.170000e-108 403
26 TraesCS3A01G459500 chr2A 94.650 486 15 3 2226 2709 722079737 722080213 0.000000e+00 743
27 TraesCS3A01G459500 chr2A 91.506 518 29 7 2196 2709 70229477 70228971 0.000000e+00 699
28 TraesCS3A01G459500 chr2A 94.297 263 14 1 561 822 108247214 108247476 4.200000e-108 401
29 TraesCS3A01G459500 chr2A 93.680 269 15 2 559 825 477947461 477947193 4.200000e-108 401
30 TraesCS3A01G459500 chr2A 93.776 241 6 1 2220 2460 27784597 27784366 1.190000e-93 353
31 TraesCS3A01G459500 chr2A 85.350 157 18 4 2226 2378 751833686 751833531 1.000000e-34 158
32 TraesCS3A01G459500 chr4A 94.639 485 14 5 2226 2709 225972087 225971614 0.000000e+00 741
33 TraesCS3A01G459500 chr4A 88.150 481 37 10 2234 2709 719933423 719932958 3.050000e-154 555
34 TraesCS3A01G459500 chr4A 80.169 237 35 8 1054 1287 24758566 24758793 1.670000e-37 167
35 TraesCS3A01G459500 chr7A 94.792 480 14 3 2226 2705 159974010 159974478 0.000000e+00 737
36 TraesCS3A01G459500 chr7A 94.456 487 13 5 2225 2709 686188821 686188347 0.000000e+00 737
37 TraesCS3A01G459500 chr7A 94.227 485 15 5 2226 2709 630640040 630640512 0.000000e+00 728
38 TraesCS3A01G459500 chr7A 95.019 261 12 1 563 822 717747052 717746792 2.510000e-110 409
39 TraesCS3A01G459500 chr7A 93.015 272 18 1 563 833 9210710 9210439 1.960000e-106 396
40 TraesCS3A01G459500 chr7A 93.233 266 6 4 2225 2490 690382374 690382627 5.480000e-102 381
41 TraesCS3A01G459500 chr7A 90.960 177 5 4 2216 2391 614008785 614008619 7.550000e-56 228
42 TraesCS3A01G459500 chr7A 73.661 672 122 32 1010 1655 48436893 48437535 2.740000e-50 209
43 TraesCS3A01G459500 chr1A 90.164 488 18 4 2224 2709 550794346 550794805 2.310000e-170 608
44 TraesCS3A01G459500 chr1A 90.271 442 37 2 2266 2705 39182417 39181980 8.420000e-160 573
45 TraesCS3A01G459500 chr1A 94.318 264 14 1 560 822 164754554 164754291 1.170000e-108 403
46 TraesCS3A01G459500 chr1A 93.939 264 15 1 560 822 260094767 260095030 5.440000e-107 398
47 TraesCS3A01G459500 chr1A 93.939 264 15 1 560 822 489900096 489900359 5.440000e-107 398
48 TraesCS3A01G459500 chr1A 93.585 265 15 2 560 822 142959515 142959251 7.040000e-106 394
49 TraesCS3A01G459500 chr1A 93.561 264 16 1 560 822 358543556 358543293 2.530000e-105 392
50 TraesCS3A01G459500 chr1A 93.258 267 14 2 560 822 483059735 483060001 9.100000e-105 390
51 TraesCS3A01G459500 chr1A 93.182 264 17 1 560 822 107407690 107407953 1.180000e-103 387
52 TraesCS3A01G459500 chr1A 92.029 276 20 2 550 823 558301006 558301281 1.180000e-103 387
53 TraesCS3A01G459500 chr6A 93.939 264 15 1 560 822 390513829 390514092 5.440000e-107 398
54 TraesCS3A01G459500 chr6A 94.253 261 14 1 563 822 601238477 601238737 5.440000e-107 398
55 TraesCS3A01G459500 chr6A 93.609 266 16 1 559 823 287207570 287207305 1.960000e-106 396
56 TraesCS3A01G459500 chr6A 93.284 268 16 2 560 825 498952915 498952648 7.040000e-106 394
57 TraesCS3A01G459500 chr5B 94.253 261 14 1 563 822 44237433 44237173 5.440000e-107 398
58 TraesCS3A01G459500 chr5B 93.939 264 15 1 560 822 445601248 445600985 5.440000e-107 398
59 TraesCS3A01G459500 chr5B 93.939 264 15 1 560 822 470519198 470519461 5.440000e-107 398
60 TraesCS3A01G459500 chr4B 93.561 264 16 1 560 822 382819782 382819519 2.530000e-105 392
61 TraesCS3A01G459500 chr4B 92.674 273 19 1 553 824 400363439 400363167 2.530000e-105 392
62 TraesCS3A01G459500 chr4B 93.130 262 17 1 562 822 28324219 28324480 1.520000e-102 383
63 TraesCS3A01G459500 chr4B 92.366 262 19 1 562 822 516973795 516974056 3.300000e-99 372
64 TraesCS3A01G459500 chr4B 93.103 203 13 1 563 764 180940310 180940512 2.040000e-76 296
65 TraesCS3A01G459500 chr2D 91.571 261 20 2 563 822 84746755 84746496 2.570000e-95 359
66 TraesCS3A01G459500 chr2D 85.430 151 16 6 2232 2378 543057759 543057611 4.680000e-33 152
67 TraesCS3A01G459500 chrUn 73.375 646 115 34 1037 1655 346091644 346091029 1.280000e-43 187
68 TraesCS3A01G459500 chr1D 84.516 155 19 5 2225 2378 443543780 443543930 6.050000e-32 148


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 TraesCS3A01G459500 chr3A 696166447 696169157 2710 True 2225.5 3363 100.000000 1 2711 2 chr3A.!!$R3 2710
1 TraesCS3A01G459500 chr3A 628873841 628876108 2267 True 1089.0 2117 97.336333 1 2225 3 chr3A.!!$R2 2224
2 TraesCS3A01G459500 chr3B 743813196 743814435 1239 True 822.5 1314 90.996500 208 1733 2 chr3B.!!$R1 1525
3 TraesCS3A01G459500 chr3D 559915863 559917352 1489 True 976.0 1312 89.751000 3 1765 2 chr3D.!!$R6 1762
4 TraesCS3A01G459500 chr3D 559936648 559938046 1398 True 852.0 1225 89.338000 9 1786 2 chr3D.!!$R7 1777
5 TraesCS3A01G459500 chr2A 70228971 70229477 506 True 699.0 699 91.506000 2196 2709 1 chr2A.!!$R2 513
6 TraesCS3A01G459500 chr7A 48436893 48437535 642 False 209.0 209 73.661000 1010 1655 1 chr7A.!!$F1 645

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
277 279 1.523938 GTCTTCATAGCACGCCCCC 60.524 63.158 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2643 1.137697 CCGGGACTAAAGGCCCTTAT 58.862 55.0 18.97 0.0 42.4 1.73 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
18 19 3.390280 CTCCCTCACCTCCTGTCTT 57.610 57.895 0.00 0.00 0.00 3.01
178 180 6.701400 GGTTTCTGCAACATGAGTTTTACAAT 59.299 34.615 0.00 0.00 37.07 2.71
277 279 1.523938 GTCTTCATAGCACGCCCCC 60.524 63.158 0.00 0.00 0.00 5.40
568 598 1.903860 TGCCCAACGTAATGTACTCCT 59.096 47.619 0.00 0.00 0.00 3.69
571 601 3.184541 CCCAACGTAATGTACTCCTTCG 58.815 50.000 0.00 0.00 0.00 3.79
616 647 5.049129 TGGTTTTGCCAAAAGTCAAACTTTG 60.049 36.000 2.15 0.00 43.56 2.77
732 763 7.732222 ATATTGGGGTTGTTATGTGAATGTT 57.268 32.000 0.00 0.00 0.00 2.71
787 818 5.179368 TGAATGAGATTGACTTCGGACAAAC 59.821 40.000 0.00 0.00 33.90 2.93
796 827 8.658499 ATTGACTTCGGACAAACCTAATATAC 57.342 34.615 0.00 0.00 33.90 1.47
798 829 7.262772 TGACTTCGGACAAACCTAATATACAG 58.737 38.462 0.00 0.00 36.31 2.74
799 830 7.123098 TGACTTCGGACAAACCTAATATACAGA 59.877 37.037 0.00 0.00 36.31 3.41
812 843 9.760077 ACCTAATATACAGAGTAAAAATGACCG 57.240 33.333 0.00 0.00 0.00 4.79
1176 1241 3.265601 AAGAAGGTGCCCCTGCTT 58.734 55.556 1.89 1.89 45.49 3.91
1641 2020 3.589654 CTTGCCGAGCAGGGACGAA 62.590 63.158 0.00 0.00 41.35 3.85
1718 2097 6.922957 TCAATGCACAAGAAATAAGACCAAAC 59.077 34.615 0.00 0.00 0.00 2.93
1744 2127 1.261885 CCGAACATTGTTGCGTGTGTA 59.738 47.619 6.80 0.00 0.00 2.90
1770 2153 5.300792 TGAGTTATGACCCAAAACTTTCCAC 59.699 40.000 0.00 0.00 33.72 4.02
2151 2534 3.311596 ACTTTGACCAACGCTCAGTTTAC 59.688 43.478 0.00 0.00 42.02 2.01
2220 2605 6.774354 TTGTCACTGATTTTACGTTAGGAC 57.226 37.500 0.00 0.00 0.00 3.85
2230 2615 1.933021 ACGTTAGGACCATCCACTGA 58.067 50.000 0.00 0.00 39.61 3.41
2245 2630 4.108570 TCCACTGATAGAAAAAGGGCCTA 58.891 43.478 6.41 0.00 0.00 3.93
2247 2632 5.908831 TCCACTGATAGAAAAAGGGCCTATA 59.091 40.000 6.41 0.00 0.00 1.31
2258 2643 0.761702 GGGCCTATAGTCCCGGTTCA 60.762 60.000 2.38 0.00 32.00 3.18
2280 2665 1.077930 GGGCCTTTAGTCCCGGTTC 60.078 63.158 0.84 0.00 32.00 3.62
2318 2703 2.428171 GTGTCGGTACTAATGCCCTGTA 59.572 50.000 0.00 0.00 0.00 2.74
2341 2726 3.270877 CTTTAGTCCCGGTTCAATCCAG 58.729 50.000 0.00 0.00 0.00 3.86
2342 2727 2.241281 TAGTCCCGGTTCAATCCAGA 57.759 50.000 0.00 0.00 0.00 3.86
2343 2728 1.358152 AGTCCCGGTTCAATCCAGAA 58.642 50.000 0.00 0.00 0.00 3.02
2344 2729 1.003233 AGTCCCGGTTCAATCCAGAAC 59.997 52.381 0.00 0.00 45.50 3.01
2345 2730 0.036765 TCCCGGTTCAATCCAGAACG 60.037 55.000 0.00 0.00 46.81 3.95
2346 2731 1.024579 CCCGGTTCAATCCAGAACGG 61.025 60.000 0.00 0.00 46.81 4.44
2411 2796 1.001641 CAGGCAGGAGACCCTTTGG 60.002 63.158 0.00 0.00 42.02 3.28
2448 2833 2.301346 CAACCAGGACCAATAGGCATC 58.699 52.381 0.00 0.00 39.06 3.91
2469 2854 0.599991 ACGCGTCAGCATTTCTGTGA 60.600 50.000 5.58 0.00 45.49 3.58
2519 2904 1.074395 GGGTTTGGGGGTTTTGGGA 60.074 57.895 0.00 0.00 0.00 4.37
2606 2991 1.374125 CATCCGTGCTTGGTCGACA 60.374 57.895 18.91 0.27 0.00 4.35
2610 2995 1.007336 CCGTGCTTGGTCGACACTAC 61.007 60.000 18.91 7.63 32.07 2.73
2643 3028 7.153985 ACATACGTATAGAGAGGACTAGACAC 58.846 42.308 7.96 0.00 35.23 3.67
2703 3088 9.828039 AAGATCGTCATGAACATATATGCATAT 57.172 29.630 22.31 22.31 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.056125 CCTGGCTGAGCACGACGA 62.056 66.667 6.82 0.00 0.00 4.20
84 85 0.034337 GTTGTAGGAGGTTGCGGTGA 59.966 55.000 0.00 0.00 0.00 4.02
178 180 7.126573 TCCCATGTTGTAACAGAGGTCATATTA 59.873 37.037 14.19 0.00 43.04 0.98
277 279 8.824781 CATCAATAGTCATGACCAAAGTTCTAG 58.175 37.037 22.21 2.37 0.00 2.43
568 598 3.135994 GTGCAGAGTAAAAAGGACCGAA 58.864 45.455 0.00 0.00 0.00 4.30
571 601 4.321230 CCAATGTGCAGAGTAAAAAGGACC 60.321 45.833 0.00 0.00 0.00 4.46
691 722 9.759473 ACCCCAATATTATTAGATTCATCTTGG 57.241 33.333 0.00 0.00 38.32 3.61
765 796 4.455877 GGTTTGTCCGAAGTCAATCTCATT 59.544 41.667 0.00 0.00 0.00 2.57
770 801 7.787725 ATATTAGGTTTGTCCGAAGTCAATC 57.212 36.000 0.00 0.00 41.99 2.67
787 818 9.204570 CCGGTCATTTTTACTCTGTATATTAGG 57.795 37.037 0.00 0.00 0.00 2.69
796 827 3.055385 TCCCTCCGGTCATTTTTACTCTG 60.055 47.826 0.00 0.00 0.00 3.35
798 829 3.055312 ACTCCCTCCGGTCATTTTTACTC 60.055 47.826 0.00 0.00 0.00 2.59
799 830 2.910977 ACTCCCTCCGGTCATTTTTACT 59.089 45.455 0.00 0.00 0.00 2.24
807 838 1.492764 GGAATTACTCCCTCCGGTCA 58.507 55.000 0.00 0.00 38.44 4.02
808 839 0.388294 CGGAATTACTCCCTCCGGTC 59.612 60.000 0.00 0.00 46.66 4.79
812 843 1.884235 CATGCGGAATTACTCCCTCC 58.116 55.000 0.00 0.00 41.87 4.30
1718 2097 2.032377 ACGCAACAATGTTCGGTACAAG 60.032 45.455 17.25 0.00 40.89 3.16
1744 2127 5.535030 GGAAAGTTTTGGGTCATAACTCACT 59.465 40.000 4.70 0.00 34.93 3.41
2220 2605 3.633986 GCCCTTTTTCTATCAGTGGATGG 59.366 47.826 0.00 0.00 34.89 3.51
2230 2615 4.286291 CGGGACTATAGGCCCTTTTTCTAT 59.714 45.833 36.19 0.00 42.40 1.98
2245 2630 1.697982 GCCCTTATGAACCGGGACTAT 59.302 52.381 6.32 0.00 40.55 2.12
2247 2632 1.632965 GGCCCTTATGAACCGGGACT 61.633 60.000 6.32 0.00 43.05 3.85
2258 2643 1.137697 CCGGGACTAAAGGCCCTTAT 58.862 55.000 18.97 0.00 42.40 1.73
2280 2665 1.346722 ACACTTTAGTCCCGGTTCAGG 59.653 52.381 0.00 0.00 0.00 3.86
2318 2703 2.026542 GGATTGAACCGGGACTAAAGGT 60.027 50.000 6.32 0.00 40.50 3.50
2345 2730 1.668419 CATCAGTCCCGGTTCAATCC 58.332 55.000 0.00 0.00 0.00 3.01
2346 2731 1.668419 CCATCAGTCCCGGTTCAATC 58.332 55.000 0.00 0.00 0.00 2.67
2347 2732 0.255890 CCCATCAGTCCCGGTTCAAT 59.744 55.000 0.00 0.00 0.00 2.57
2348 2733 1.682849 CCCATCAGTCCCGGTTCAA 59.317 57.895 0.00 0.00 0.00 2.69
2349 2734 2.966732 GCCCATCAGTCCCGGTTCA 61.967 63.158 0.00 0.00 0.00 3.18
2392 2777 1.001641 CAAAGGGTCTCCTGCCTGG 60.002 63.158 0.00 0.00 44.07 4.45
2411 2796 2.750237 GGTGCCACCAATCGGGAC 60.750 66.667 9.55 0.00 43.66 4.46
2434 2819 1.166531 GCGTGGATGCCTATTGGTCC 61.167 60.000 0.00 0.00 35.27 4.46
2448 2833 3.566261 AGAAATGCTGACGCGTGG 58.434 55.556 20.70 10.85 39.65 4.94
2588 2973 1.374125 TGTCGACCAAGCACGGATG 60.374 57.895 14.12 0.00 0.00 3.51
2589 2974 1.374252 GTGTCGACCAAGCACGGAT 60.374 57.895 14.12 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.