Multiple sequence alignment - TraesCS6B01G173600

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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 TraesCS6B01G173600 chr6B 100.000 2729 0 0 1 2729 187844611 187847339 0.000000e+00 5040
1 TraesCS6B01G173600 chr6B 93.289 1937 120 8 298 2227 626667322 626669255 0.000000e+00 2848
2 TraesCS6B01G173600 chr6B 92.397 1631 99 11 59 1666 594959557 594961185 0.000000e+00 2302
3 TraesCS6B01G173600 chr6B 90.856 514 31 12 2228 2729 681679070 681679579 0.000000e+00 675
4 TraesCS6B01G173600 chr6B 92.754 69 5 0 1 69 594959345 594959413 1.730000e-17 100
5 TraesCS6B01G173600 chr3B 93.778 2234 127 8 1 2227 722583713 722581485 0.000000e+00 3345
6 TraesCS6B01G173600 chr3B 92.259 1912 127 11 334 2227 532747365 532745457 0.000000e+00 2691
7 TraesCS6B01G173600 chr3B 91.703 1844 115 19 420 2227 657695264 657693423 0.000000e+00 2523
8 TraesCS6B01G173600 chr3B 91.599 1845 114 25 420 2227 13988721 13986881 0.000000e+00 2510
9 TraesCS6B01G173600 chr3B 92.402 1461 85 17 79 1529 692068871 692070315 0.000000e+00 2060
10 TraesCS6B01G173600 chr4A 93.691 2219 124 13 16 2225 660870015 660867804 0.000000e+00 3308
11 TraesCS6B01G173600 chr5B 92.835 2233 119 16 1 2227 550238538 550240735 0.000000e+00 3199
12 TraesCS6B01G173600 chr5B 91.667 2196 142 20 24 2194 469494803 469496982 0.000000e+00 3003
13 TraesCS6B01G173600 chr5B 88.812 2029 157 25 1 2004 369249415 369247432 0.000000e+00 2425
14 TraesCS6B01G173600 chr5B 86.572 283 23 8 1 282 636511358 636511626 5.710000e-77 298
15 TraesCS6B01G173600 chr4B 92.530 2249 139 17 1 2227 548297771 548295530 0.000000e+00 3195
16 TraesCS6B01G173600 chr4B 92.975 2178 123 15 79 2230 212139622 212137449 0.000000e+00 3147
17 TraesCS6B01G173600 chr4B 92.499 2093 128 15 160 2230 212110389 212108304 0.000000e+00 2968
18 TraesCS6B01G173600 chr1B 91.790 2168 117 19 79 2217 604094579 604092444 0.000000e+00 2961
19 TraesCS6B01G173600 chr1B 86.792 530 40 17 2227 2729 506741917 506741391 5.100000e-157 564
20 TraesCS6B01G173600 chr7B 85.404 829 71 20 1 810 447332786 447331989 0.000000e+00 815
21 TraesCS6B01G173600 chr7B 90.329 517 34 12 2226 2729 585596117 585596630 0.000000e+00 664
22 TraesCS6B01G173600 chr2A 91.908 519 28 10 2223 2729 303686551 303687067 0.000000e+00 713
23 TraesCS6B01G173600 chr2A 91.440 514 31 10 2228 2729 575782342 575782854 0.000000e+00 693
24 TraesCS6B01G173600 chr5D 91.103 517 29 13 2228 2728 531923557 531923042 0.000000e+00 684
25 TraesCS6B01G173600 chr5D 91.951 410 17 6 2322 2729 320919055 320919450 6.600000e-156 560
26 TraesCS6B01G173600 chr7A 91.142 508 26 7 2225 2727 627187236 627186743 0.000000e+00 671
27 TraesCS6B01G173600 chr7A 90.504 516 36 10 2226 2729 595558990 595558476 0.000000e+00 669
28 TraesCS6B01G173600 chr3A 89.924 526 37 12 2218 2729 645739997 645740520 0.000000e+00 664
29 TraesCS6B01G173600 chr3A 90.254 472 25 8 2262 2729 664939626 664940080 5.030000e-167 597
30 TraesCS6B01G173600 chr3A 89.167 480 29 13 2262 2729 36855790 36856258 6.550000e-161 577
31 TraesCS6B01G173600 chrUn 91.268 481 28 11 2262 2729 74794262 74793783 0.000000e+00 643
32 TraesCS6B01G173600 chr3D 90.039 512 25 10 2224 2729 418849217 418848726 8.240000e-180 640


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 TraesCS6B01G173600 chr6B 187844611 187847339 2728 False 5040 5040 100.0000 1 2729 1 chr6B.!!$F1 2728
1 TraesCS6B01G173600 chr6B 626667322 626669255 1933 False 2848 2848 93.2890 298 2227 1 chr6B.!!$F2 1929
2 TraesCS6B01G173600 chr6B 594959345 594961185 1840 False 1201 2302 92.5755 1 1666 2 chr6B.!!$F4 1665
3 TraesCS6B01G173600 chr6B 681679070 681679579 509 False 675 675 90.8560 2228 2729 1 chr6B.!!$F3 501
4 TraesCS6B01G173600 chr3B 722581485 722583713 2228 True 3345 3345 93.7780 1 2227 1 chr3B.!!$R4 2226
5 TraesCS6B01G173600 chr3B 532745457 532747365 1908 True 2691 2691 92.2590 334 2227 1 chr3B.!!$R2 1893
6 TraesCS6B01G173600 chr3B 657693423 657695264 1841 True 2523 2523 91.7030 420 2227 1 chr3B.!!$R3 1807
7 TraesCS6B01G173600 chr3B 13986881 13988721 1840 True 2510 2510 91.5990 420 2227 1 chr3B.!!$R1 1807
8 TraesCS6B01G173600 chr3B 692068871 692070315 1444 False 2060 2060 92.4020 79 1529 1 chr3B.!!$F1 1450
9 TraesCS6B01G173600 chr4A 660867804 660870015 2211 True 3308 3308 93.6910 16 2225 1 chr4A.!!$R1 2209
10 TraesCS6B01G173600 chr5B 550238538 550240735 2197 False 3199 3199 92.8350 1 2227 1 chr5B.!!$F2 2226
11 TraesCS6B01G173600 chr5B 469494803 469496982 2179 False 3003 3003 91.6670 24 2194 1 chr5B.!!$F1 2170
12 TraesCS6B01G173600 chr5B 369247432 369249415 1983 True 2425 2425 88.8120 1 2004 1 chr5B.!!$R1 2003
13 TraesCS6B01G173600 chr4B 548295530 548297771 2241 True 3195 3195 92.5300 1 2227 1 chr4B.!!$R3 2226
14 TraesCS6B01G173600 chr4B 212137449 212139622 2173 True 3147 3147 92.9750 79 2230 1 chr4B.!!$R2 2151
15 TraesCS6B01G173600 chr4B 212108304 212110389 2085 True 2968 2968 92.4990 160 2230 1 chr4B.!!$R1 2070
16 TraesCS6B01G173600 chr1B 604092444 604094579 2135 True 2961 2961 91.7900 79 2217 1 chr1B.!!$R2 2138
17 TraesCS6B01G173600 chr1B 506741391 506741917 526 True 564 564 86.7920 2227 2729 1 chr1B.!!$R1 502
18 TraesCS6B01G173600 chr7B 447331989 447332786 797 True 815 815 85.4040 1 810 1 chr7B.!!$R1 809
19 TraesCS6B01G173600 chr7B 585596117 585596630 513 False 664 664 90.3290 2226 2729 1 chr7B.!!$F1 503
20 TraesCS6B01G173600 chr2A 303686551 303687067 516 False 713 713 91.9080 2223 2729 1 chr2A.!!$F1 506
21 TraesCS6B01G173600 chr2A 575782342 575782854 512 False 693 693 91.4400 2228 2729 1 chr2A.!!$F2 501
22 TraesCS6B01G173600 chr5D 531923042 531923557 515 True 684 684 91.1030 2228 2728 1 chr5D.!!$R1 500
23 TraesCS6B01G173600 chr7A 595558476 595558990 514 True 669 669 90.5040 2226 2729 1 chr7A.!!$R1 503
24 TraesCS6B01G173600 chr3A 645739997 645740520 523 False 664 664 89.9240 2218 2729 1 chr3A.!!$F2 511

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
353 608 0.106819 GCATCCTGGCCAACTGAGAT 60.107 55.0 7.01 1.29 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 2264 0.472044 TTGCACACTGGACTGCCTAA 59.528 50.0 0.0 0.0 31.97 2.69 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
57 212 4.873827 TCGTGAACATATAACCTGCTTTCC 59.126 41.667 0.00 0.00 0.00 3.13
85 240 6.199342 GCGAACACTTTAGATAGGCTTTAGAG 59.801 42.308 0.00 0.00 0.00 2.43
132 289 4.853924 ACATGTTTTCTGGCCAACTAAG 57.146 40.909 7.01 0.00 0.00 2.18
192 350 4.679197 GCAACTGAGACATCTATTCTAGCG 59.321 45.833 0.00 0.00 0.00 4.26
353 608 0.106819 GCATCCTGGCCAACTGAGAT 60.107 55.000 7.01 1.29 0.00 2.75
646 935 9.590451 AATTATGTCCAAATTATGTGCAGAAAG 57.410 29.630 0.00 0.00 0.00 2.62
698 989 3.511146 ACCTGCGGATCATTTCAACAAAT 59.489 39.130 0.00 0.00 31.91 2.32
918 1223 8.896320 AAGTTTTTAGGTTGTTTGAAACACTT 57.104 26.923 10.72 4.78 41.97 3.16
941 1251 6.627395 TTTTCGTGGTTAACAACTGATGAT 57.373 33.333 11.34 0.00 0.00 2.45
945 1255 6.873997 TCGTGGTTAACAACTGATGATATCT 58.126 36.000 11.34 0.00 0.00 1.98
948 1258 8.135529 CGTGGTTAACAACTGATGATATCTCTA 58.864 37.037 11.34 0.00 0.00 2.43
1024 1345 3.442977 GCTTGATCTCAATGAGTTGCCTT 59.557 43.478 10.36 0.00 35.02 4.35
1088 1409 3.515104 CCCAGCATACCACAAGGAAATTT 59.485 43.478 0.00 0.00 38.69 1.82
1114 1459 3.374058 AGAAAATGGGCGATCTGTTTACG 59.626 43.478 0.00 0.00 0.00 3.18
1358 1703 3.391296 TCTCAACCTATGGAACCCTATGC 59.609 47.826 0.00 0.00 0.00 3.14
1472 1817 1.577328 CGGACACCTCACACCAATGC 61.577 60.000 0.00 0.00 0.00 3.56
1513 1858 2.754552 TGCTGCAACAAGTTCAAGAAGT 59.245 40.909 0.00 0.00 0.00 3.01
1532 1877 2.842496 AGTCCAAAGCTGATGATGGAGA 59.158 45.455 1.41 0.00 42.35 3.71
1594 1940 7.167535 TCCAAAACATGTTGATAGTGATGAGA 58.832 34.615 12.82 0.00 0.00 3.27
1659 2005 7.095144 GCTGGTCCTAGTAAGAAAAAGAAGAAC 60.095 40.741 0.00 0.00 0.00 3.01
1726 2073 2.481441 TGGTGAAGCTGATAGATGGGT 58.519 47.619 0.00 0.00 0.00 4.51
1859 2206 7.372451 AGTTTTTGCGCATCTTGTATAACTA 57.628 32.000 12.75 0.00 0.00 2.24
1891 2244 5.962031 ACTACAGGTGTGTTTCTATATCCCA 59.038 40.000 0.00 0.00 38.19 4.37
1911 2264 7.039722 TCCCATACAGAATTAAGTTTCCCTT 57.960 36.000 0.00 0.00 37.17 3.95
1953 2306 6.308015 ACTGTTATGGTACTCCTATGCAAA 57.692 37.500 0.00 0.00 34.23 3.68
1962 2315 6.663093 TGGTACTCCTATGCAAATGAAATGTT 59.337 34.615 0.00 0.00 34.23 2.71
1990 2343 3.118408 TGTGCAACTAGTGTCCAACTTCT 60.118 43.478 0.00 0.00 34.00 2.85
2005 2358 7.041167 TGTCCAACTTCTCATGTTGTTTCTATG 60.041 37.037 0.00 0.00 42.09 2.23
2197 2558 9.465494 CATTCGTGCGACTAAAAATGATATATC 57.535 33.333 5.73 5.73 0.00 1.63
2287 2648 1.445716 CTACTAGCAGCGCGGGTACT 61.446 60.000 15.43 9.42 0.00 2.73
2326 2691 7.095271 GCGCTACAGCTAATAGTTAGTAGTAGT 60.095 40.741 19.54 9.64 40.61 2.73
2430 2815 2.117910 CGCTTCTAGTAAACTAGGCGC 58.882 52.381 20.18 17.77 44.08 6.53
2431 2816 2.223525 CGCTTCTAGTAAACTAGGCGCT 60.224 50.000 20.18 0.00 44.08 5.92
2432 2817 3.003068 CGCTTCTAGTAAACTAGGCGCTA 59.997 47.826 20.18 0.00 44.08 4.26
2433 2818 4.289342 GCTTCTAGTAAACTAGGCGCTAC 58.711 47.826 15.39 0.00 44.60 3.58
2434 2819 4.036616 GCTTCTAGTAAACTAGGCGCTACT 59.963 45.833 15.39 8.72 44.60 2.57
2435 2820 5.238214 GCTTCTAGTAAACTAGGCGCTACTA 59.762 44.000 15.39 9.46 44.60 1.82
2436 2821 6.610741 TTCTAGTAAACTAGGCGCTACTAC 57.389 41.667 15.39 1.10 44.60 2.73
2437 2822 5.923204 TCTAGTAAACTAGGCGCTACTACT 58.077 41.667 15.39 8.60 44.60 2.57
2438 2823 7.055667 TCTAGTAAACTAGGCGCTACTACTA 57.944 40.000 15.39 9.25 44.60 1.82
2439 2824 7.675062 TCTAGTAAACTAGGCGCTACTACTAT 58.325 38.462 15.39 0.00 44.60 2.12
2482 2867 2.369532 AGTAGCGTGTAGTTTTCCCCAA 59.630 45.455 0.00 0.00 0.00 4.12
2557 2947 7.675161 TTCATAGATAGAAATCAGGGACACA 57.325 36.000 0.00 0.00 34.28 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 212 2.789893 GCCTATCTAAAGTGTTCGCTCG 59.210 50.000 0.00 0.00 0.00 5.03
61 216 7.481642 TCTCTAAAGCCTATCTAAAGTGTTCG 58.518 38.462 0.00 0.00 0.00 3.95
132 289 2.094597 TCAGTTTAGCCAACATGCATGC 60.095 45.455 26.53 11.82 37.93 4.06
192 350 2.618241 TGGTCAGCAATGTGTTCAGTTC 59.382 45.455 0.00 0.00 0.00 3.01
542 809 7.834068 TGACAGATTATAGCTGTTTCTGTTC 57.166 36.000 21.50 16.63 45.94 3.18
606 891 9.941325 TTTGGACATAATTTGATGCTACATTTT 57.059 25.926 0.00 0.00 0.00 1.82
646 935 2.220313 GGCAAGGAGCTGATTCAGATC 58.780 52.381 20.98 20.98 44.92 2.75
698 989 7.138054 AGAGTTTTCTGACTTTTTCCCTCTA 57.862 36.000 0.00 0.00 30.72 2.43
918 1223 6.627395 ATCATCAGTTGTTAACCACGAAAA 57.373 33.333 2.48 0.00 0.00 2.29
1000 1321 3.380637 GGCAACTCATTGAGATCAAGCAT 59.619 43.478 20.33 0.00 39.47 3.79
1024 1345 5.169992 TGAGGAAGCTCATTGAGATCAAA 57.830 39.130 17.87 2.18 39.55 2.69
1088 1409 2.290260 ACAGATCGCCCATTTTCTGTCA 60.290 45.455 0.00 0.00 44.00 3.58
1114 1459 0.792640 CCATGACTTGTCTGCGTGTC 59.207 55.000 0.00 0.00 0.00 3.67
1358 1703 0.524862 GCTGTCAAACCTCATGCCAG 59.475 55.000 0.00 0.00 0.00 4.85
1513 1858 3.520721 TCTTCTCCATCATCAGCTTTGGA 59.479 43.478 0.00 0.00 36.81 3.53
1532 1877 1.494960 GACAGGAGGAGCCTCATCTT 58.505 55.000 17.68 0.00 46.97 2.40
1659 2005 1.352114 TTATTGTCTCGCGTTTCCGG 58.648 50.000 5.77 0.00 33.68 5.14
1726 2073 1.480212 AAGTGCGTCACCTCCCATCA 61.480 55.000 6.39 0.00 34.49 3.07
1859 2206 3.906720 ACACACCTGTAGTCAAGTTGT 57.093 42.857 2.11 0.00 0.00 3.32
1891 2244 8.113462 TGCCTAAAGGGAAACTTAATTCTGTAT 58.887 33.333 0.00 0.00 38.85 2.29
1911 2264 0.472044 TTGCACACTGGACTGCCTAA 59.528 50.000 0.00 0.00 31.97 2.69
1953 2306 9.762933 ACTAGTTGCACAAATAAAACATTTCAT 57.237 25.926 0.00 0.00 0.00 2.57
1962 2315 6.320164 AGTTGGACACTAGTTGCACAAATAAA 59.680 34.615 0.00 0.00 31.97 1.40
1966 2319 3.616219 AGTTGGACACTAGTTGCACAAA 58.384 40.909 0.00 0.00 31.97 2.83
1990 2343 6.545666 ACCAAAGTGACATAGAAACAACATGA 59.454 34.615 0.00 0.00 0.00 3.07
2140 2497 4.202253 CCAGCTGCACAGTAATAGGACATA 60.202 45.833 8.66 0.00 0.00 2.29
2197 2558 7.480542 CGTCCTCCATAATACAAAAAGAAAACG 59.519 37.037 0.00 0.00 0.00 3.60
2217 2578 6.690194 TTTTCCTAGTAGTGATACGTCCTC 57.310 41.667 0.00 0.00 0.00 3.71
2287 2648 3.303593 GCTGTAGCGCGATACTAGTACAA 60.304 47.826 31.61 11.65 0.00 2.41
2421 2806 3.488363 AGCATAGTAGTAGCGCCTAGTT 58.512 45.455 2.29 0.00 0.00 2.24
2429 2814 7.852971 AGCATAGTAGTAGCATAGTAGTAGC 57.147 40.000 0.00 0.00 36.22 3.58
2689 3090 0.981277 TTTCGGGGTGAGGGAGGATC 60.981 60.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.