Multiple sequence alignment - TraesCS2A01G296200

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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 TraesCS2A01G296200 chr2A 100.000 2333 0 0 1 2333 509581590 509579258 0.000000e+00 4309.0
1 TraesCS2A01G296200 chr2A 93.292 1759 85 10 503 2240 509992468 509990722 0.000000e+00 2564.0
2 TraesCS2A01G296200 chr2D 92.567 1009 57 5 503 1494 376356647 376355640 0.000000e+00 1432.0
3 TraesCS2A01G296200 chr2D 92.588 796 41 11 1510 2298 376355656 376354872 0.000000e+00 1127.0
4 TraesCS2A01G296200 chr2D 93.083 506 31 2 1 502 292258692 292258187 0.000000e+00 737.0
5 TraesCS2A01G296200 chr2D 92.913 508 30 6 1 503 377198472 377197966 0.000000e+00 734.0
6 TraesCS2A01G296200 chr2D 86.885 61 6 2 2275 2333 128458753 128458693 1.500000e-07 67.6
7 TraesCS2A01G296200 chr2B 91.996 1012 60 6 503 1494 447825835 447824825 0.000000e+00 1400.0
8 TraesCS2A01G296200 chr2B 90.418 814 28 21 1511 2299 447824840 447824052 0.000000e+00 1026.0
9 TraesCS2A01G296200 chr2B 93.697 238 15 0 1112 1349 233078950 233079187 7.930000e-95 357.0
10 TraesCS2A01G296200 chr2B 93.878 49 2 1 2286 2333 289890596 289890644 3.220000e-09 73.1
11 TraesCS2A01G296200 chr2B 90.741 54 3 2 2282 2333 692166879 692166826 1.160000e-08 71.3
12 TraesCS2A01G296200 chr2B 92.000 50 2 2 2285 2333 578606513 578606465 4.160000e-08 69.4
13 TraesCS2A01G296200 chr6A 93.651 504 25 5 1 498 157629346 157629848 0.000000e+00 747.0
14 TraesCS2A01G296200 chr6A 92.157 51 0 4 2285 2333 107503109 107503157 4.160000e-08 69.4
15 TraesCS2A01G296200 chr1A 93.267 505 28 5 1 500 412788333 412787830 0.000000e+00 739.0
16 TraesCS2A01G296200 chr1A 92.653 245 18 0 1105 1349 36265789 36266033 1.030000e-93 353.0
17 TraesCS2A01G296200 chr4D 93.083 506 31 3 1 502 163735438 163734933 0.000000e+00 737.0
18 TraesCS2A01G296200 chr7D 92.885 506 32 3 1 502 443120619 443120114 0.000000e+00 732.0
19 TraesCS2A01G296200 chr6D 92.593 513 33 5 2 510 303579026 303578515 0.000000e+00 732.0
20 TraesCS2A01G296200 chr5D 92.427 515 34 5 1 511 120218355 120217842 0.000000e+00 730.0
21 TraesCS2A01G296200 chr3D 92.233 515 34 6 1 511 517254209 517254721 0.000000e+00 725.0
22 TraesCS2A01G296200 chr3A 77.408 872 147 36 503 1331 638016428 638015564 7.540000e-130 473.0
23 TraesCS2A01G296200 chr7B 90.968 155 14 0 1201 1355 539881581 539881427 2.350000e-50 209.0
24 TraesCS2A01G296200 chr7B 93.750 48 3 0 2283 2330 667473697 667473744 3.220000e-09 73.1
25 TraesCS2A01G296200 chr7B 82.857 70 10 2 2263 2330 595318969 595319038 6.960000e-06 62.1
26 TraesCS2A01G296200 chr5B 83.871 93 15 0 1234 1326 661863309 661863401 3.190000e-14 89.8
27 TraesCS2A01G296200 chr5B 91.071 56 1 4 2280 2333 460136226 460136173 3.220000e-09 73.1
28 TraesCS2A01G296200 chr5A 93.750 48 1 2 2283 2330 623014459 623014504 1.160000e-08 71.3


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 TraesCS2A01G296200 chr2A 509579258 509581590 2332 True 4309.0 4309 100.0000 1 2333 1 chr2A.!!$R1 2332
1 TraesCS2A01G296200 chr2A 509990722 509992468 1746 True 2564.0 2564 93.2920 503 2240 1 chr2A.!!$R2 1737
2 TraesCS2A01G296200 chr2D 376354872 376356647 1775 True 1279.5 1432 92.5775 503 2298 2 chr2D.!!$R4 1795
3 TraesCS2A01G296200 chr2D 292258187 292258692 505 True 737.0 737 93.0830 1 502 1 chr2D.!!$R2 501
4 TraesCS2A01G296200 chr2D 377197966 377198472 506 True 734.0 734 92.9130 1 503 1 chr2D.!!$R3 502
5 TraesCS2A01G296200 chr2B 447824052 447825835 1783 True 1213.0 1400 91.2070 503 2299 2 chr2B.!!$R3 1796
6 TraesCS2A01G296200 chr6A 157629346 157629848 502 False 747.0 747 93.6510 1 498 1 chr6A.!!$F2 497
7 TraesCS2A01G296200 chr1A 412787830 412788333 503 True 739.0 739 93.2670 1 500 1 chr1A.!!$R1 499
8 TraesCS2A01G296200 chr4D 163734933 163735438 505 True 737.0 737 93.0830 1 502 1 chr4D.!!$R1 501
9 TraesCS2A01G296200 chr7D 443120114 443120619 505 True 732.0 732 92.8850 1 502 1 chr7D.!!$R1 501
10 TraesCS2A01G296200 chr6D 303578515 303579026 511 True 732.0 732 92.5930 2 510 1 chr6D.!!$R1 508
11 TraesCS2A01G296200 chr5D 120217842 120218355 513 True 730.0 730 92.4270 1 511 1 chr5D.!!$R1 510
12 TraesCS2A01G296200 chr3D 517254209 517254721 512 False 725.0 725 92.2330 1 511 1 chr3D.!!$F1 510
13 TraesCS2A01G296200 chr3A 638015564 638016428 864 True 473.0 473 77.4080 503 1331 1 chr3A.!!$R1 828

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
514 521 1.509463 GTATCACGCCACCTCGACA 59.491 57.895 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1664 1741 0.314302 AAGGACGGAGAACTGTGTCG 59.686 55.0 0.0 0.0 35.56 4.35 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
328 334 5.565439 GCTTGTTTGGAGTTGTGCAGAATAT 60.565 40.000 0.00 0.0 0.00 1.28
354 360 2.163818 TGACGTAGCCTTTTCAGGTG 57.836 50.000 0.00 0.0 43.18 4.00
514 521 1.509463 GTATCACGCCACCTCGACA 59.491 57.895 0.00 0.0 0.00 4.35
687 706 4.065281 CGACGCGTCCCCTTTCCT 62.065 66.667 31.84 0.0 0.00 3.36
688 707 2.703798 CGACGCGTCCCCTTTCCTA 61.704 63.158 31.84 0.0 0.00 2.94
841 888 2.421877 CGAGGTCGTGGACTGCAAGT 62.422 60.000 0.00 0.0 42.48 3.16
852 899 1.591703 CTGCAAGTAGTCGGCTCCA 59.408 57.895 0.00 0.0 0.00 3.86
872 919 4.443266 GGCAGCGGCGTTCTCTCT 62.443 66.667 9.37 0.0 42.47 3.10
943 990 4.351938 TGAACGTGTCGAGCCGGG 62.352 66.667 2.18 0.0 0.00 5.73
974 1021 4.109675 GGGCCGGCACTGGTACAT 62.110 66.667 30.85 0.0 38.20 2.29
1024 1071 4.196778 TGGGCGGGTGCAACTTCA 62.197 61.111 0.00 0.0 45.35 3.02
1261 1308 2.568612 CGCGAAGAGAGGTGCTCA 59.431 61.111 0.00 0.0 46.45 4.26
1263 1310 0.382158 CGCGAAGAGAGGTGCTCATA 59.618 55.000 0.00 0.0 46.45 2.15
1356 1403 0.464013 TTCTTTTTGCCACCGACGGA 60.464 50.000 23.38 0.0 0.00 4.69
1375 1426 2.359900 GACGGATCCAGCAATGAGTTT 58.640 47.619 13.41 0.0 0.00 2.66
1426 1480 2.582728 TCATGCGGGAAATGAATTGC 57.417 45.000 0.00 0.0 31.17 3.56
1664 1741 4.150980 CCATGCAATGTGTGACATTCAAAC 59.849 41.667 0.00 0.0 44.91 2.93
1678 1755 1.847818 TCAAACGACACAGTTCTCCG 58.152 50.000 0.00 0.0 32.43 4.63
1825 1903 3.120165 GCTAAGTAGGAACAGCAAAGCAC 60.120 47.826 0.00 0.0 34.13 4.40
1908 1987 3.099362 CGATGTCGACGAGGTTAAAGAG 58.901 50.000 11.62 0.0 43.02 2.85
1938 2017 8.789825 AACATTATCTGATATGCTCTTGGATC 57.210 34.615 0.00 0.0 0.00 3.36
2077 2158 8.077836 AGAGCATCGCAATCTACTTTATTTAC 57.922 34.615 0.00 0.0 42.67 2.01
2299 2385 6.359480 AGCGGCAAAAATACAGATTACTAC 57.641 37.500 1.45 0.0 0.00 2.73
2300 2386 6.113411 AGCGGCAAAAATACAGATTACTACT 58.887 36.000 1.45 0.0 0.00 2.57
2301 2387 6.258068 AGCGGCAAAAATACAGATTACTACTC 59.742 38.462 1.45 0.0 0.00 2.59
2302 2388 6.511282 GCGGCAAAAATACAGATTACTACTCC 60.511 42.308 0.00 0.0 0.00 3.85
2303 2389 6.018180 CGGCAAAAATACAGATTACTACTCCC 60.018 42.308 0.00 0.0 0.00 4.30
2304 2390 7.054751 GGCAAAAATACAGATTACTACTCCCT 58.945 38.462 0.00 0.0 0.00 4.20
2305 2391 7.226918 GGCAAAAATACAGATTACTACTCCCTC 59.773 40.741 0.00 0.0 0.00 4.30
2306 2392 7.226918 GCAAAAATACAGATTACTACTCCCTCC 59.773 40.741 0.00 0.0 0.00 4.30
2307 2393 6.651975 AAATACAGATTACTACTCCCTCCG 57.348 41.667 0.00 0.0 0.00 4.63
2308 2394 3.666345 ACAGATTACTACTCCCTCCGT 57.334 47.619 0.00 0.0 0.00 4.69
2309 2395 3.553904 ACAGATTACTACTCCCTCCGTC 58.446 50.000 0.00 0.0 0.00 4.79
2310 2396 2.885894 CAGATTACTACTCCCTCCGTCC 59.114 54.545 0.00 0.0 0.00 4.79
2311 2397 1.878734 GATTACTACTCCCTCCGTCCG 59.121 57.143 0.00 0.0 0.00 4.79
2312 2398 0.911769 TTACTACTCCCTCCGTCCGA 59.088 55.000 0.00 0.0 0.00 4.55
2313 2399 0.911769 TACTACTCCCTCCGTCCGAA 59.088 55.000 0.00 0.0 0.00 4.30
2314 2400 0.038744 ACTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.0 0.00 3.46
2315 2401 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.0 0.00 2.29
2316 2402 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.0 0.00 1.82
2317 2403 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.0 0.00 1.40
2318 2404 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.0 0.00 1.89
2319 2405 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.0 0.00 2.12
2320 2406 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.0 0.00 2.24
2321 2407 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.0 0.00 3.16
2322 2408 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.0 0.00 3.16
2323 2409 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.0 0.00 3.18
2324 2410 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.0 0.00 3.58
2325 2411 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.0 0.00 3.06
2326 2412 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.0 0.00 2.92
2327 2413 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.0 0.00 3.07
2328 2414 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.0 0.00 2.57
2329 2415 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.0 32.87 2.69
2330 2416 6.403200 CCGTCCGAAAATACTTGTCATCAAAT 60.403 38.462 0.00 0.0 32.87 2.32
2331 2417 6.465781 CGTCCGAAAATACTTGTCATCAAATG 59.534 38.462 0.00 0.0 32.87 2.32
2332 2418 6.747280 GTCCGAAAATACTTGTCATCAAATGG 59.253 38.462 0.00 0.0 32.87 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.439245 GCCGGGGGAACTTTCCTT 59.561 61.111 2.18 0.00 46.72 3.36
12 13 3.572222 TTCCGCCGGGGGAACTTT 61.572 61.111 40.65 0.00 41.08 2.66
131 134 3.519510 TGCCCATCTTCTGGTATATAGGC 59.480 47.826 0.00 0.00 44.30 3.93
344 350 3.613432 GCTGGAAATCTGCACCTGAAAAG 60.613 47.826 1.92 0.00 39.69 2.27
354 360 0.391661 TCCGACAGCTGGAAATCTGC 60.392 55.000 19.93 0.00 40.14 4.26
470 477 8.649841 CGTCAATTTTGCATCATGTTTTCTTAT 58.350 29.630 0.00 0.00 0.00 1.73
728 775 1.183030 CCTGTAGTCCACGTCCACCA 61.183 60.000 0.00 0.00 0.00 4.17
827 874 0.240145 CGACTACTTGCAGTCCACGA 59.760 55.000 0.00 0.00 41.65 4.35
841 888 2.283604 TGCCACTGGAGCCGACTA 60.284 61.111 0.00 0.00 0.00 2.59
919 966 4.953868 CGACACGTTCACCGCCCA 62.954 66.667 0.00 0.00 41.42 5.36
955 1002 4.338710 GTACCAGTGCCGGCCCAA 62.339 66.667 26.77 1.08 0.00 4.12
986 1033 3.853330 CCATCGCGAACTGCACCG 61.853 66.667 15.24 0.00 46.97 4.94
992 1039 2.434884 CCAGCACCATCGCGAACT 60.435 61.111 15.24 2.73 36.85 3.01
1052 1099 2.338620 CCTCGCTGACGTGTCCAA 59.661 61.111 0.00 0.00 41.18 3.53
1053 1100 2.910479 ACCTCGCTGACGTGTCCA 60.910 61.111 0.00 0.00 41.18 4.02
1155 1202 2.042435 CTCTCGCCTCCCCTCCTT 60.042 66.667 0.00 0.00 0.00 3.36
1261 1308 1.819229 CGGAGCAGCACAGGTCTAT 59.181 57.895 0.00 0.00 36.33 1.98
1356 1403 2.496899 AAACTCATTGCTGGATCCGT 57.503 45.000 7.39 0.00 0.00 4.69
1375 1426 4.716794 TGCACCTACATCATGCATGAATA 58.283 39.130 31.79 23.87 44.17 1.75
1510 1564 7.718272 TGTAAATACACGTTAGTTCTTGCTT 57.282 32.000 0.00 0.00 0.00 3.91
1664 1741 0.314302 AAGGACGGAGAACTGTGTCG 59.686 55.000 0.00 0.00 35.56 4.35
1836 1914 1.624813 CAATGTTTTCCCCATGGCTGT 59.375 47.619 6.09 0.00 0.00 4.40
1908 1987 6.171921 AGAGCATATCAGATAATGTTCCTGC 58.828 40.000 0.00 0.00 0.00 4.85
1966 2045 5.036090 TGTAATCGACGCGTAATATTGTGT 58.964 37.500 13.97 0.00 0.00 3.72
2002 2083 8.380743 TGCTGAATTTTATGTTTTGCAAGAAT 57.619 26.923 0.00 0.00 0.00 2.40
2087 2168 2.228925 TGTGCTGATGCTTGTTGCTTA 58.771 42.857 0.00 0.00 43.37 3.09
2092 2173 1.268692 CGTGTTGTGCTGATGCTTGTT 60.269 47.619 0.00 0.00 40.48 2.83
2181 2262 2.299867 ACATTGCAAAGGCTAAACAGGG 59.700 45.455 1.71 0.00 41.91 4.45
2299 2385 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2300 2386 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2301 2387 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2302 2388 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2303 2389 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2304 2390 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2305 2391 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2306 2392 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2307 2393 6.747280 CCATTTGATGACAAGTATTTTCGGAC 59.253 38.462 0.00 0.00 37.32 4.79
2308 2394 6.851609 CCATTTGATGACAAGTATTTTCGGA 58.148 36.000 0.00 0.00 37.32 4.55


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

AutoCloner maintained by Alex Coulton.