Multiple sequence alignment - TraesCS1D01G347500

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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 TraesCS1D01G347500 chr1D 100.000 4374 0 0 1 4374 434384916 434389289 0 8078
1 TraesCS1D01G347500 chr1D 96.827 2427 64 7 1957 4374 434776279 434773857 0 4043
2 TraesCS1D01G347500 chr1D 96.637 1695 51 4 2683 4374 465558595 465560286 0 2809
3 TraesCS1D01G347500 chr1D 92.899 1718 87 17 1 1712 20609123 20607435 0 2464
4 TraesCS1D01G347500 chr1D 92.666 1718 94 13 1 1712 467744524 467746215 0 2446
5 TraesCS1D01G347500 chr1D 96.371 1185 42 1 77 1260 434778188 434777004 0 1949
6 TraesCS1D01G347500 chr1D 94.518 912 50 0 290 1201 477595135 477594224 0 1408
7 TraesCS1D01G347500 chr1D 96.479 426 11 3 2339 2762 477593229 477592806 0 701
8 TraesCS1D01G347500 chr5D 97.352 2039 48 5 2339 4374 72457534 72455499 0 3461
9 TraesCS1D01G347500 chr5D 93.101 1667 86 12 50 1712 319464173 319462532 0 2414
10 TraesCS1D01G347500 chr5D 94.504 1401 69 7 315 1712 72459262 72457867 0 2154
11 TraesCS1D01G347500 chr2A 92.764 2073 110 13 289 2340 735537415 735535362 0 2961
12 TraesCS1D01G347500 chr2A 92.487 1717 101 14 1 1712 710032542 710030849 0 2431
13 TraesCS1D01G347500 chr6D 96.932 1695 45 5 2683 4374 449931537 449933227 0 2835
14 TraesCS1D01G347500 chr6D 92.669 1214 64 12 1 1211 448299834 448298643 0 1725
15 TraesCS1D01G347500 chr3D 96.932 1695 45 5 2683 4374 591937646 591935956 0 2835
16 TraesCS1D01G347500 chr3D 91.482 2078 130 16 290 2337 517375411 517377471 0 2813
17 TraesCS1D01G347500 chr3D 96.169 1044 40 0 1 1044 520570578 520569535 0 1707
18 TraesCS1D01G347500 chr3D 93.494 538 28 3 1 531 596306216 596306753 0 793
19 TraesCS1D01G347500 chr7D 96.868 1692 47 4 2683 4371 120550240 120551928 0 2826
20 TraesCS1D01G347500 chr7D 96.755 1695 49 4 2683 4374 1440713 1442404 0 2820
21 TraesCS1D01G347500 chr7D 92.782 1427 76 12 290 1712 580162035 580160632 0 2039
22 TraesCS1D01G347500 chr7D 92.346 1215 64 15 501 1712 520310863 520309675 0 1701
23 TraesCS1D01G347500 chr7D 91.716 1014 57 11 700 1712 597377099 597376112 0 1382
24 TraesCS1D01G347500 chr7D 92.429 951 64 4 290 1235 60011919 60010972 0 1351
25 TraesCS1D01G347500 chr2D 96.755 1695 47 6 2683 4374 20254936 20253247 0 2819
26 TraesCS1D01G347500 chr2D 93.858 1791 87 15 290 2062 524241106 524242891 0 2676
27 TraesCS1D01G347500 chr2D 92.205 1719 98 12 1 1712 20257591 20255902 0 2399
28 TraesCS1D01G347500 chr2D 94.860 1070 34 6 1287 2335 618507932 618506863 0 1652
29 TraesCS1D01G347500 chr2D 93.257 1053 50 8 1308 2340 7376592 7375541 0 1531
30 TraesCS1D01G347500 chr2D 90.196 765 45 6 1600 2340 648736619 648737377 0 970
31 TraesCS1D01G347500 chr2D 96.244 426 14 2 2339 2762 618506787 618506362 0 697
32 TraesCS1D01G347500 chr2D 95.794 428 13 4 2339 2762 7375470 7375044 0 686
33 TraesCS1D01G347500 chrUn 96.696 1695 50 4 2683 4374 110737140 110735449 0 2815
34 TraesCS1D01G347500 chrUn 91.780 1180 66 14 536 1712 67730611 67729460 0 1613
35 TraesCS1D01G347500 chrUn 95.016 923 44 2 290 1211 101654505 101655426 0 1448
36 TraesCS1D01G347500 chrUn 92.340 966 46 12 751 1712 110739052 110738111 0 1349
37 TraesCS1D01G347500 chr4B 91.256 1967 127 17 410 2340 669367620 669369577 0 2638
38 TraesCS1D01G347500 chr4B 91.209 1968 128 19 410 2340 669174405 669176364 0 2634
39 TraesCS1D01G347500 chr4B 91.057 1968 128 24 410 2340 669529702 669527746 0 2615
40 TraesCS1D01G347500 chr4B 90.955 1968 129 21 410 2340 668567224 668565269 0 2603
41 TraesCS1D01G347500 chr4B 90.604 1969 135 23 410 2340 668500074 668498118 0 2566
42 TraesCS1D01G347500 chr4B 90.041 1958 131 28 420 2340 668943406 668941476 0 2477
43 TraesCS1D01G347500 chr4B 95.316 427 16 4 2339 2762 668941405 668940980 0 675
44 TraesCS1D01G347500 chr4B 95.316 427 16 4 2339 2762 669527675 669527250 0 675
45 TraesCS1D01G347500 chr4B 95.305 426 17 3 2339 2762 668498047 668497623 0 673
46 TraesCS1D01G347500 chr5A 91.269 1970 119 23 410 2340 707964864 707962909 0 2636
47 TraesCS1D01G347500 chr2B 92.864 1079 56 6 1282 2340 774451924 774450847 0 1546
48 TraesCS1D01G347500 chr4A 91.256 995 77 6 721 1712 638512503 638513490 0 1347
49 TraesCS1D01G347500 chr4A 96.714 426 9 4 2339 2762 638513843 638514265 0 704


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 TraesCS1D01G347500 chr1D 434384916 434389289 4373 False 8078.0 8078 100.0000 1 4374 1 chr1D.!!$F1 4373
1 TraesCS1D01G347500 chr1D 434773857 434778188 4331 True 2996.0 4043 96.5990 77 4374 2 chr1D.!!$R2 4297
2 TraesCS1D01G347500 chr1D 465558595 465560286 1691 False 2809.0 2809 96.6370 2683 4374 1 chr1D.!!$F2 1691
3 TraesCS1D01G347500 chr1D 20607435 20609123 1688 True 2464.0 2464 92.8990 1 1712 1 chr1D.!!$R1 1711
4 TraesCS1D01G347500 chr1D 467744524 467746215 1691 False 2446.0 2446 92.6660 1 1712 1 chr1D.!!$F3 1711
5 TraesCS1D01G347500 chr1D 477592806 477595135 2329 True 1054.5 1408 95.4985 290 2762 2 chr1D.!!$R3 2472
6 TraesCS1D01G347500 chr5D 72455499 72459262 3763 True 2807.5 3461 95.9280 315 4374 2 chr5D.!!$R2 4059
7 TraesCS1D01G347500 chr5D 319462532 319464173 1641 True 2414.0 2414 93.1010 50 1712 1 chr5D.!!$R1 1662
8 TraesCS1D01G347500 chr2A 735535362 735537415 2053 True 2961.0 2961 92.7640 289 2340 1 chr2A.!!$R2 2051
9 TraesCS1D01G347500 chr2A 710030849 710032542 1693 True 2431.0 2431 92.4870 1 1712 1 chr2A.!!$R1 1711
10 TraesCS1D01G347500 chr6D 449931537 449933227 1690 False 2835.0 2835 96.9320 2683 4374 1 chr6D.!!$F1 1691
11 TraesCS1D01G347500 chr6D 448298643 448299834 1191 True 1725.0 1725 92.6690 1 1211 1 chr6D.!!$R1 1210
12 TraesCS1D01G347500 chr3D 591935956 591937646 1690 True 2835.0 2835 96.9320 2683 4374 1 chr3D.!!$R2 1691
13 TraesCS1D01G347500 chr3D 517375411 517377471 2060 False 2813.0 2813 91.4820 290 2337 1 chr3D.!!$F1 2047
14 TraesCS1D01G347500 chr3D 520569535 520570578 1043 True 1707.0 1707 96.1690 1 1044 1 chr3D.!!$R1 1043
15 TraesCS1D01G347500 chr3D 596306216 596306753 537 False 793.0 793 93.4940 1 531 1 chr3D.!!$F2 530
16 TraesCS1D01G347500 chr7D 120550240 120551928 1688 False 2826.0 2826 96.8680 2683 4371 1 chr7D.!!$F2 1688
17 TraesCS1D01G347500 chr7D 1440713 1442404 1691 False 2820.0 2820 96.7550 2683 4374 1 chr7D.!!$F1 1691
18 TraesCS1D01G347500 chr7D 580160632 580162035 1403 True 2039.0 2039 92.7820 290 1712 1 chr7D.!!$R3 1422
19 TraesCS1D01G347500 chr7D 520309675 520310863 1188 True 1701.0 1701 92.3460 501 1712 1 chr7D.!!$R2 1211
20 TraesCS1D01G347500 chr7D 597376112 597377099 987 True 1382.0 1382 91.7160 700 1712 1 chr7D.!!$R4 1012
21 TraesCS1D01G347500 chr7D 60010972 60011919 947 True 1351.0 1351 92.4290 290 1235 1 chr7D.!!$R1 945
22 TraesCS1D01G347500 chr2D 524241106 524242891 1785 False 2676.0 2676 93.8580 290 2062 1 chr2D.!!$F1 1772
23 TraesCS1D01G347500 chr2D 20253247 20257591 4344 True 2609.0 2819 94.4800 1 4374 2 chr2D.!!$R2 4373
24 TraesCS1D01G347500 chr2D 618506362 618507932 1570 True 1174.5 1652 95.5520 1287 2762 2 chr2D.!!$R3 1475
25 TraesCS1D01G347500 chr2D 7375044 7376592 1548 True 1108.5 1531 94.5255 1308 2762 2 chr2D.!!$R1 1454
26 TraesCS1D01G347500 chr2D 648736619 648737377 758 False 970.0 970 90.1960 1600 2340 1 chr2D.!!$F2 740
27 TraesCS1D01G347500 chrUn 110735449 110739052 3603 True 2082.0 2815 94.5180 751 4374 2 chrUn.!!$R2 3623
28 TraesCS1D01G347500 chrUn 67729460 67730611 1151 True 1613.0 1613 91.7800 536 1712 1 chrUn.!!$R1 1176
29 TraesCS1D01G347500 chrUn 101654505 101655426 921 False 1448.0 1448 95.0160 290 1211 1 chrUn.!!$F1 921
30 TraesCS1D01G347500 chr4B 669367620 669369577 1957 False 2638.0 2638 91.2560 410 2340 1 chr4B.!!$F2 1930
31 TraesCS1D01G347500 chr4B 669174405 669176364 1959 False 2634.0 2634 91.2090 410 2340 1 chr4B.!!$F1 1930
32 TraesCS1D01G347500 chr4B 668565269 668567224 1955 True 2603.0 2603 90.9550 410 2340 1 chr4B.!!$R1 1930
33 TraesCS1D01G347500 chr4B 669527250 669529702 2452 True 1645.0 2615 93.1865 410 2762 2 chr4B.!!$R4 2352
34 TraesCS1D01G347500 chr4B 668497623 668500074 2451 True 1619.5 2566 92.9545 410 2762 2 chr4B.!!$R2 2352
35 TraesCS1D01G347500 chr4B 668940980 668943406 2426 True 1576.0 2477 92.6785 420 2762 2 chr4B.!!$R3 2342
36 TraesCS1D01G347500 chr5A 707962909 707964864 1955 True 2636.0 2636 91.2690 410 2340 1 chr5A.!!$R1 1930
37 TraesCS1D01G347500 chr2B 774450847 774451924 1077 True 1546.0 1546 92.8640 1282 2340 1 chr2B.!!$R1 1058
38 TraesCS1D01G347500 chr4A 638512503 638514265 1762 False 1025.5 1347 93.9850 721 2762 2 chr4A.!!$F1 2041

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
271 272 0.107017 CGGACCCTTACCTCCTACGA 60.107 60.0 0.00 0.00 0.00 3.43 F
280 281 0.679321 ACCTCCTACGAGAACGACCC 60.679 60.0 0.00 0.00 42.66 4.46 F
1342 1632 0.590230 CAGCGACTTCGACGAGGATC 60.590 60.0 14.47 6.72 43.02 3.36 F
3252 3956 0.394762 ATGCAACATGCCGTCTCCAT 60.395 50.0 0.00 0.00 44.23 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1342 1632 1.459209 CTCCGAGAGATCGTCGATGAG 59.541 57.143 13.54 7.95 39.92 2.90 R
2071 2379 1.817099 CCTGCTTGATGGAGTCGGC 60.817 63.158 0.00 0.00 31.70 5.54 R
3267 3971 2.907458 ACTGGCCTTTTGCTTCCTAT 57.093 45.000 3.32 0.00 40.92 2.57 R
4147 4855 8.918202 ATACATGTTCACTTCTTACCAGAAAA 57.082 30.769 2.30 0.00 38.63 2.29 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
84 85 1.689582 GATCGGAGGGAAGGGTGGT 60.690 63.158 0.00 0.00 0.00 4.16
194 195 3.441572 ATGCTTCTCATGTTGGTACAAGC 59.558 43.478 0.00 0.00 37.53 4.01
271 272 0.107017 CGGACCCTTACCTCCTACGA 60.107 60.000 0.00 0.00 0.00 3.43
280 281 0.679321 ACCTCCTACGAGAACGACCC 60.679 60.000 0.00 0.00 42.66 4.46
900 921 2.045242 TCGTCCTCTCCCACTCCG 60.045 66.667 0.00 0.00 0.00 4.63
975 996 1.376037 CTCCTCCCTTCCAACACGC 60.376 63.158 0.00 0.00 0.00 5.34
1342 1632 0.590230 CAGCGACTTCGACGAGGATC 60.590 60.000 14.47 6.72 43.02 3.36
1624 1922 6.084738 TGTAGGATTGTAGGGATCTAGCATT 58.915 40.000 0.00 0.00 0.00 3.56
1626 1924 4.910304 AGGATTGTAGGGATCTAGCATTGT 59.090 41.667 0.00 0.00 0.00 2.71
1880 2188 1.303236 CGACACCATTGGCTTCCCA 60.303 57.895 1.54 0.00 40.06 4.37
1899 2207 2.886523 CCAAGGACAGTGAGAAAATGCA 59.113 45.455 0.00 0.00 0.00 3.96
2071 2379 1.750193 TAGGCCTTCTTTCATTGCCG 58.250 50.000 12.58 0.00 46.67 5.69
2187 2495 1.332375 CCGTCGACTCATCTCCTTCTC 59.668 57.143 14.70 0.00 0.00 2.87
2266 2575 7.284261 TGACCACTTGATTATTTCTTTGACACA 59.716 33.333 0.00 0.00 0.00 3.72
2309 2636 1.236616 TGCCTTGTTGCATGAGGACG 61.237 55.000 13.08 0.00 36.04 4.79
2991 3695 9.618890 AGCAAATAGATAGTTGTCATGTTACAT 57.381 29.630 0.00 0.00 34.12 2.29
3252 3956 0.394762 ATGCAACATGCCGTCTCCAT 60.395 50.000 0.00 0.00 44.23 3.41
3267 3971 2.642311 TCTCCATTGGCAACTCCTACAA 59.358 45.455 0.00 0.00 35.26 2.41
3416 4120 1.218585 CTAGACTGCTGCTGCTGCT 59.781 57.895 27.67 18.48 41.07 4.24
3417 4121 1.079336 TAGACTGCTGCTGCTGCTG 60.079 57.895 27.75 27.75 41.07 4.41
3672 4378 6.075315 AGGGTGGTGCTTAGAAAAATAAACT 58.925 36.000 0.00 0.00 0.00 2.66
3674 4380 6.239204 GGGTGGTGCTTAGAAAAATAAACTGT 60.239 38.462 0.00 0.00 0.00 3.55
3712 4419 5.192927 CCATTGCCTATTTCTACAGGACAA 58.807 41.667 0.00 0.00 34.62 3.18
3720 4427 7.054124 CCTATTTCTACAGGACAAATGCCTAA 58.946 38.462 0.00 0.00 33.51 2.69
3828 4535 4.561500 TTGTACAAGGCCATAGCAACTA 57.438 40.909 5.01 0.00 42.56 2.24
3844 4551 3.000376 GCAACTAAAGTATCGTACGGTGC 60.000 47.826 16.52 12.60 0.00 5.01
3866 4573 5.122239 TGCTCTATGTTATGTTTGCTGTGTC 59.878 40.000 0.00 0.00 0.00 3.67
4147 4855 1.548582 CCCAGAAGTGCCTGTTTCCAT 60.549 52.381 0.00 0.00 32.43 3.41
4161 4869 6.681777 CCTGTTTCCATTTTCTGGTAAGAAG 58.318 40.000 0.00 0.00 46.08 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 4.264623 ACCCTAAAATATTTCCCACCAGCA 60.265 41.667 0.10 0.00 0.00 4.41
194 195 8.338259 CAAATGGACCTATATTCTTTCTTCACG 58.662 37.037 0.00 0.00 0.00 4.35
271 272 2.524887 TTCACCGGGGGTCGTTCT 60.525 61.111 2.42 0.00 37.11 3.01
280 281 0.739813 GTTGTCGATCCTTCACCGGG 60.740 60.000 6.32 0.00 0.00 5.73
678 690 4.261801 GTGGACACCAGCAGTAATTACAT 58.738 43.478 17.65 0.61 32.34 2.29
764 776 3.680786 CAGTGAGGACGCGTGGGA 61.681 66.667 20.70 0.00 0.00 4.37
900 921 2.029307 GAGGACGAGGTGGTATGGCC 62.029 65.000 0.00 0.00 37.90 5.36
975 996 1.000486 TCGACAAGAGGAGGAGGGG 60.000 63.158 0.00 0.00 0.00 4.79
1157 1178 4.208686 GTAGCTCGACGGCTGGGG 62.209 72.222 17.58 0.00 43.01 4.96
1277 1324 1.595003 CGAACTCTATCTCGTCCACGC 60.595 57.143 0.00 0.00 39.60 5.34
1342 1632 1.459209 CTCCGAGAGATCGTCGATGAG 59.541 57.143 13.54 7.95 39.92 2.90
1624 1922 3.772025 ACCACCATCCAACAAGAAAAACA 59.228 39.130 0.00 0.00 0.00 2.83
1626 1924 5.428184 AAACCACCATCCAACAAGAAAAA 57.572 34.783 0.00 0.00 0.00 1.94
1880 2188 2.555757 GCTGCATTTTCTCACTGTCCTT 59.444 45.455 0.00 0.00 0.00 3.36
1899 2207 3.718723 AGTTCTGGAGATAGGAACTGCT 58.281 45.455 6.75 0.00 45.06 4.24
2071 2379 1.817099 CCTGCTTGATGGAGTCGGC 60.817 63.158 0.00 0.00 31.70 5.54
2266 2575 4.790937 ACCAATTGCCAAAACAGGAAATT 58.209 34.783 0.00 0.00 45.87 1.82
2309 2636 3.713826 TCAGGTCAAGGTATTGGTTCC 57.286 47.619 0.00 0.00 37.02 3.62
2794 3498 8.438676 AATGATACTTGATACTTGTTACAGGC 57.561 34.615 0.00 0.00 0.00 4.85
3267 3971 2.907458 ACTGGCCTTTTGCTTCCTAT 57.093 45.000 3.32 0.00 40.92 2.57
3416 4120 1.228769 ACACGACAGTCCTAGGGCA 60.229 57.895 17.52 0.00 0.00 5.36
3417 4121 1.511768 GACACGACAGTCCTAGGGC 59.488 63.158 4.79 4.79 32.36 5.19
3630 4336 5.221925 CCACCCTTAGCATCTACCATTGTAT 60.222 44.000 0.00 0.00 0.00 2.29
3672 4378 4.431809 CAATGGTGCTTCAGAAAAACACA 58.568 39.130 11.01 2.58 32.89 3.72
3712 4419 4.102681 AGGGTAGACGCTTAATTAGGCATT 59.897 41.667 18.43 5.51 35.46 3.56
3720 4427 5.410355 TTTGTACAGGGTAGACGCTTAAT 57.590 39.130 0.00 0.00 37.00 1.40
3828 4535 4.337555 ACATAGAGCACCGTACGATACTTT 59.662 41.667 18.76 8.11 0.00 2.66
3844 4551 6.726258 TGACACAGCAAACATAACATAGAG 57.274 37.500 0.00 0.00 0.00 2.43
3866 4573 5.395778 CGTACGATTCTAGAACGGAAGAATG 59.604 44.000 22.52 10.35 41.40 2.67
4022 4729 5.465532 TCATTGCATGCTTTACTTTTGGA 57.534 34.783 20.33 0.00 0.00 3.53
4147 4855 8.918202 ATACATGTTCACTTCTTACCAGAAAA 57.082 30.769 2.30 0.00 38.63 2.29


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

AutoCloner maintained by Alex Coulton.