Multiple sequence alignment - TraesCS4A01G362700

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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 TraesCS4A01G362700 chr4A 100.000 4150 0 0 1 4150 636262025 636257876 0.000000e+00 7664.0
1 TraesCS4A01G362700 chr4A 96.789 2460 59 1 1691 4150 636315174 636312735 0.000000e+00 4087.0
2 TraesCS4A01G362700 chr4A 97.112 1316 30 5 2 1313 636316873 636315562 0.000000e+00 2213.0
3 TraesCS4A01G362700 chr4A 91.228 513 36 8 1 509 636317826 636317319 0.000000e+00 689.0
4 TraesCS4A01G362700 chr4A 98.039 306 4 1 1408 1713 636315213 636315516 7.900000e-147 531.0
5 TraesCS4A01G362700 chr4A 76.031 509 100 17 808 1299 636218744 636218241 1.150000e-60 244.0
6 TraesCS4A01G362700 chr5B 95.125 2769 109 9 1406 4150 676250623 676253389 0.000000e+00 4342.0
7 TraesCS4A01G362700 chr5B 95.021 1406 49 8 1 1391 676249237 676250636 0.000000e+00 2189.0
8 TraesCS4A01G362700 chr5B 78.760 984 142 37 454 1391 676240851 676241813 7.680000e-167 597.0
9 TraesCS4A01G362700 chr5B 84.912 285 40 2 1914 2198 619279732 619279451 6.790000e-73 285.0
10 TraesCS4A01G362700 chr5B 77.093 227 44 6 1862 2082 541954514 541954290 1.570000e-24 124.0
11 TraesCS4A01G362700 chr5B 97.727 44 1 0 4107 4150 376405825 376405782 4.450000e-10 76.8
12 TraesCS4A01G362700 chr5B 95.745 47 2 0 4103 4149 672106854 672106900 4.450000e-10 76.8
13 TraesCS4A01G362700 chr5D 96.209 2031 71 4 1406 3434 535643184 535645210 0.000000e+00 3319.0
14 TraesCS4A01G362700 chr5D 95.258 1413 37 11 2 1391 535641792 535643197 0.000000e+00 2211.0
15 TraesCS4A01G362700 chr5D 91.951 733 43 3 3419 4150 535645229 535645946 0.000000e+00 1013.0
16 TraesCS4A01G362700 chr5D 91.068 515 40 3 1 512 535640830 535641341 0.000000e+00 691.0
17 TraesCS4A01G362700 chr5D 87.368 285 33 1 1914 2198 499069803 499069522 1.440000e-84 324.0
18 TraesCS4A01G362700 chr5D 78.116 329 65 7 968 1293 535727702 535728026 7.030000e-48 202.0
19 TraesCS4A01G362700 chr5D 70.915 612 137 29 1902 2498 444302279 444302864 5.670000e-19 106.0
20 TraesCS4A01G362700 chr5D 100.000 42 0 0 4108 4149 557780323 557780282 1.240000e-10 78.7
21 TraesCS4A01G362700 chr5D 100.000 28 0 0 2311 2338 444532789 444532816 7.000000e-03 52.8
22 TraesCS4A01G362700 chr3A 80.154 1300 224 25 1889 3175 89667050 89668328 0.000000e+00 941.0
23 TraesCS4A01G362700 chr3A 79.677 1299 232 23 1889 3175 89578837 89580115 0.000000e+00 907.0
24 TraesCS4A01G362700 chr3A 79.314 933 136 36 448 1356 89665737 89666636 5.940000e-168 601.0
25 TraesCS4A01G362700 chr3A 79.259 945 124 43 457 1356 89577506 89578423 9.930000e-166 593.0
26 TraesCS4A01G362700 chr3D 80.077 1300 223 27 1889 3175 75545141 75546417 0.000000e+00 933.0
27 TraesCS4A01G362700 chr3D 81.322 696 106 16 619 1299 75543994 75544680 1.010000e-150 544.0
28 TraesCS4A01G362700 chr3B 79.292 1299 237 22 1889 3175 121642747 121644025 0.000000e+00 880.0
29 TraesCS4A01G362700 chr3B 75.309 243 43 12 1596 1834 121642406 121642635 2.640000e-17 100.0
30 TraesCS4A01G362700 chr5A 78.142 183 37 1 1905 2084 561978650 561978468 3.390000e-21 113.0
31 TraesCS4A01G362700 chr5A 78.873 142 26 2 1902 2039 561168269 561168410 4.420000e-15 93.5
32 TraesCS4A01G362700 chr6D 70.732 615 133 36 1902 2498 28852452 28853037 1.230000e-15 95.3
33 TraesCS4A01G362700 chr2B 100.000 43 0 0 4107 4149 195058404 195058362 3.440000e-11 80.5
34 TraesCS4A01G362700 chr4B 97.778 45 1 0 4106 4150 168567517 168567561 1.240000e-10 78.7
35 TraesCS4A01G362700 chr2D 97.674 43 1 0 4108 4150 99959427 99959385 1.600000e-09 75.0


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 TraesCS4A01G362700 chr4A 636257876 636262025 4149 True 7664.000000 7664 100.0000 1 4150 1 chr4A.!!$R2 4149
1 TraesCS4A01G362700 chr4A 636312735 636317826 5091 True 2329.666667 4087 95.0430 1 4150 3 chr4A.!!$R3 4149
2 TraesCS4A01G362700 chr4A 636218241 636218744 503 True 244.000000 244 76.0310 808 1299 1 chr4A.!!$R1 491
3 TraesCS4A01G362700 chr5B 676249237 676253389 4152 False 3265.500000 4342 95.0730 1 4150 2 chr5B.!!$F3 4149
4 TraesCS4A01G362700 chr5B 676240851 676241813 962 False 597.000000 597 78.7600 454 1391 1 chr5B.!!$F2 937
5 TraesCS4A01G362700 chr5D 535640830 535645946 5116 False 1808.500000 3319 93.6215 1 4150 4 chr5D.!!$F4 4149
6 TraesCS4A01G362700 chr3A 89665737 89668328 2591 False 771.000000 941 79.7340 448 3175 2 chr3A.!!$F2 2727
7 TraesCS4A01G362700 chr3A 89577506 89580115 2609 False 750.000000 907 79.4680 457 3175 2 chr3A.!!$F1 2718
8 TraesCS4A01G362700 chr3D 75543994 75546417 2423 False 738.500000 933 80.6995 619 3175 2 chr3D.!!$F1 2556
9 TraesCS4A01G362700 chr3B 121642406 121644025 1619 False 490.000000 880 77.3005 1596 3175 2 chr3B.!!$F1 1579

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
163 1137 2.672651 TCCACTGCCATGTTGCCG 60.673 61.111 0.00 0.0 0.0 5.69 F
440 1414 2.878406 TGGCAGTGCTGTTAACTTCTTC 59.122 45.455 16.11 0.0 0.0 2.87 F
2084 3338 1.586422 CGGCCTATGACCACAGAATG 58.414 55.000 0.00 0.0 46.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1409 2587 1.067142 ACGTGTGTGTGAAGTCTGTGT 60.067 47.619 0.00 0.0 0.00 3.72 R
2096 3350 1.130054 GGAGCATGGATGGCCTAGGA 61.130 60.000 14.75 0.0 34.31 2.94 R
3649 4983 0.803768 CATCGACCTCGCTTCCACAG 60.804 60.000 0.00 0.0 39.60 3.66 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
33 34 3.641437 TTTGAATTTGGAACGCTGGAG 57.359 42.857 0.00 0.00 0.00 3.86
37 38 3.634448 TGAATTTGGAACGCTGGAGAAAA 59.366 39.130 0.00 0.00 0.00 2.29
163 1137 2.672651 TCCACTGCCATGTTGCCG 60.673 61.111 0.00 0.00 0.00 5.69
265 1239 6.509418 TGCATAGATTGTAAGTTTTCACCC 57.491 37.500 0.00 0.00 0.00 4.61
277 1251 3.581332 AGTTTTCACCCGAGGTCTTATCA 59.419 43.478 0.00 0.00 31.02 2.15
284 1258 3.521937 ACCCGAGGTCTTATCATGGAAAA 59.478 43.478 0.00 0.00 0.00 2.29
320 1294 2.890311 ACAATGAAATTTGGGCTCGACA 59.110 40.909 0.00 0.00 31.22 4.35
440 1414 2.878406 TGGCAGTGCTGTTAACTTCTTC 59.122 45.455 16.11 0.00 0.00 2.87
445 1419 6.036470 GCAGTGCTGTTAACTTCTTCTTTTT 58.964 36.000 8.18 0.00 0.00 1.94
798 1827 3.487544 GCAGTAAATGGCCGTTCAATCTC 60.488 47.826 11.51 0.00 0.00 2.75
1391 2569 7.338957 ACTTATAGGACTAGTTACGCAGACTTT 59.661 37.037 0.00 0.00 0.00 2.66
1464 2645 7.114247 GCATGTTCGCACTTTCTTAAAATTACA 59.886 33.333 0.00 0.00 0.00 2.41
1664 2846 9.838339 ATTCGTGGATTAATTAACTCTCTCAAT 57.162 29.630 0.00 0.00 0.00 2.57
1752 2934 5.541845 TGGATCTGATTGTATCGAATGGTC 58.458 41.667 0.00 0.00 0.00 4.02
1939 3193 7.557719 CAGAAGAAAATTCCCTTATGGAGCTTA 59.442 37.037 0.00 0.00 46.24 3.09
2084 3338 1.586422 CGGCCTATGACCACAGAATG 58.414 55.000 0.00 0.00 46.00 2.67
2635 3895 2.507407 TACCCAAACCAGATGGAAGC 57.493 50.000 5.72 0.00 40.56 3.86
2709 3972 4.112634 CGACTTCAAACTTGTGAGAGTGA 58.887 43.478 0.00 0.00 0.00 3.41
3183 4457 4.849111 CTCAGCAGAGTTAATTTCGTCC 57.151 45.455 0.00 0.00 37.11 4.79
3190 4464 5.867716 GCAGAGTTAATTTCGTCCTGTCTTA 59.132 40.000 0.00 0.00 0.00 2.10
3224 4498 1.270094 ACGCTTCAGTCGTGGATTTCA 60.270 47.619 0.00 0.00 38.88 2.69
3273 4567 0.973496 TAGCTGATGTACGTGGGCCA 60.973 55.000 0.00 0.00 0.00 5.36
3354 4652 6.093357 TGTCGTTGTTGCATGTTGTATCATAT 59.907 34.615 0.00 0.00 0.00 1.78
3427 4759 3.018856 TGTTGGATCCATGATGCAGTTC 58.981 45.455 17.06 0.00 41.08 3.01
3588 4922 2.480759 GGTGCCTGAATGTGAATGATGC 60.481 50.000 0.00 0.00 0.00 3.91
3613 4947 2.854963 AGATTGCACTTGTTCAGCTGA 58.145 42.857 13.74 13.74 0.00 4.26
3649 4983 2.439156 AGCTTCCTGGCCATTCGC 60.439 61.111 5.51 7.15 0.00 4.70
4088 5429 6.603201 TCCATCCACTAGAAATGAATGAAACC 59.397 38.462 0.00 0.00 0.00 3.27
4126 5467 3.130164 GTCTACTCCCTCCGTTCCTAAAC 59.870 52.174 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.871933 ATTTTCTCCAGCGTTCCAAATT 57.128 36.364 0.00 0.00 0.00 1.82
33 34 9.651718 AGAATTATGAAGTCGCGAAATATTTTC 57.348 29.630 12.06 12.06 0.00 2.29
163 1137 0.316204 ATGCTTGAACAGGCAAGTGC 59.684 50.000 14.80 0.00 46.46 4.40
265 1239 7.169982 GTCATACTTTTCCATGATAAGACCTCG 59.830 40.741 0.00 0.00 33.92 4.63
277 1251 7.523293 TGTCATTTGTGTCATACTTTTCCAT 57.477 32.000 0.00 0.00 0.00 3.41
284 1258 9.985730 AAATTTCATTGTCATTTGTGTCATACT 57.014 25.926 0.00 0.00 0.00 2.12
402 1376 2.288091 TGCCACATCAAAATGTTGGACG 60.288 45.455 0.00 0.00 43.74 4.79
445 1419 3.410631 TTGCAGGGACGAGTATTGAAA 57.589 42.857 0.00 0.00 0.00 2.69
446 1420 3.071479 GTTTGCAGGGACGAGTATTGAA 58.929 45.455 0.00 0.00 0.00 2.69
447 1421 2.695359 GTTTGCAGGGACGAGTATTGA 58.305 47.619 0.00 0.00 0.00 2.57
448 1422 1.393539 CGTTTGCAGGGACGAGTATTG 59.606 52.381 12.25 0.00 41.53 1.90
450 1424 0.606604 ACGTTTGCAGGGACGAGTAT 59.393 50.000 21.04 1.68 41.53 2.12
452 1426 0.390124 TTACGTTTGCAGGGACGAGT 59.610 50.000 21.04 6.92 41.53 4.18
455 1429 2.981400 ATTTTACGTTTGCAGGGACG 57.019 45.000 14.99 14.99 44.34 4.79
834 1865 5.483811 TGGTGCAGATTCGTTTAGTCAATA 58.516 37.500 0.00 0.00 0.00 1.90
1354 2411 8.291191 ACTAGTCCTATAAGTGGTAGAAACAC 57.709 38.462 0.00 0.00 39.10 3.32
1355 2412 8.890410 AACTAGTCCTATAAGTGGTAGAAACA 57.110 34.615 0.00 0.00 0.00 2.83
1394 2572 8.788806 TGAAGTCTGTGTAACTTTCTTTCAAAA 58.211 29.630 0.00 0.00 37.10 2.44
1395 2573 8.234546 GTGAAGTCTGTGTAACTTTCTTTCAAA 58.765 33.333 0.00 0.00 37.10 2.69
1398 2576 7.148474 TGTGTGAAGTCTGTGTAACTTTCTTTC 60.148 37.037 0.00 0.00 37.10 2.62
1399 2577 6.653320 TGTGTGAAGTCTGTGTAACTTTCTTT 59.347 34.615 0.00 0.00 37.10 2.52
1400 2578 6.092259 GTGTGTGAAGTCTGTGTAACTTTCTT 59.908 38.462 0.00 0.00 37.10 2.52
1402 2580 5.350365 TGTGTGTGAAGTCTGTGTAACTTTC 59.650 40.000 0.00 0.00 37.10 2.62
1403 2581 5.121768 GTGTGTGTGAAGTCTGTGTAACTTT 59.878 40.000 0.00 0.00 37.10 2.66
1404 2582 4.630069 GTGTGTGTGAAGTCTGTGTAACTT 59.370 41.667 0.00 0.00 39.61 2.66
1405 2583 4.181578 GTGTGTGTGAAGTCTGTGTAACT 58.818 43.478 0.00 0.00 38.04 2.24
1406 2584 3.000078 CGTGTGTGTGAAGTCTGTGTAAC 60.000 47.826 0.00 0.00 37.35 2.50
1407 2585 3.183754 CGTGTGTGTGAAGTCTGTGTAA 58.816 45.455 0.00 0.00 0.00 2.41
1408 2586 2.164827 ACGTGTGTGTGAAGTCTGTGTA 59.835 45.455 0.00 0.00 0.00 2.90
1409 2587 1.067142 ACGTGTGTGTGAAGTCTGTGT 60.067 47.619 0.00 0.00 0.00 3.72
1410 2588 1.640428 ACGTGTGTGTGAAGTCTGTG 58.360 50.000 0.00 0.00 0.00 3.66
1413 2591 3.247006 AGAAACGTGTGTGTGAAGTCT 57.753 42.857 0.00 0.00 0.00 3.24
1414 2592 4.565564 ACTTAGAAACGTGTGTGTGAAGTC 59.434 41.667 0.00 0.00 0.00 3.01
1415 2593 4.328983 CACTTAGAAACGTGTGTGTGAAGT 59.671 41.667 0.00 0.00 0.00 3.01
1416 2594 4.782195 GCACTTAGAAACGTGTGTGTGAAG 60.782 45.833 0.00 0.00 33.78 3.02
1752 2934 1.618861 GCGGAATCCAGACGATATCG 58.381 55.000 23.18 23.18 46.33 2.92
1761 2943 2.213499 GTATGAGTTGGCGGAATCCAG 58.787 52.381 0.00 0.00 37.44 3.86
1819 3003 3.192633 CCACCTTGGATTAACCTTTTCCG 59.807 47.826 0.00 0.00 40.96 4.30
1939 3193 7.281774 CAGCTTTCCACTGTACATGAATCTTAT 59.718 37.037 0.00 0.00 0.00 1.73
2048 3302 2.474816 GCCGGCTTATGAGTAACTGAG 58.525 52.381 22.15 0.00 0.00 3.35
2084 3338 1.587547 GCCTAGGAATAGCAGTGCAC 58.412 55.000 19.20 9.40 0.00 4.57
2096 3350 1.130054 GGAGCATGGATGGCCTAGGA 61.130 60.000 14.75 0.00 34.31 2.94
2237 3493 5.766150 ATGTCAACATTTTCTCCGAAACA 57.234 34.783 0.00 0.00 31.37 2.83
2653 3913 2.223845 GCAAATTGCCAACATGTTGTCC 59.776 45.455 31.20 22.99 37.42 4.02
2709 3972 3.055167 GGGCAGGGTTGATTAAAAGCAAT 60.055 43.478 0.00 0.00 36.62 3.56
3178 4452 1.893137 ACTGCACATAAGACAGGACGA 59.107 47.619 0.00 0.00 35.70 4.20
3179 4453 2.370281 ACTGCACATAAGACAGGACG 57.630 50.000 0.00 0.00 35.70 4.79
3183 4457 4.737279 CGTCTGATACTGCACATAAGACAG 59.263 45.833 16.35 8.82 33.75 3.51
3190 4464 2.094026 TGAAGCGTCTGATACTGCACAT 60.094 45.455 0.31 0.00 32.36 3.21
3273 4567 7.275920 ATTACTAAGTAAATGCAGTAGCAGCT 58.724 34.615 0.00 0.00 40.95 4.24
3306 4604 3.701241 ACAAAGGCAACACATAAACACG 58.299 40.909 0.00 0.00 41.41 4.49
3427 4759 5.530915 TCCCATTGAACTTTGTGACACTTAG 59.469 40.000 7.20 6.57 0.00 2.18
3613 4947 1.026182 TCATCGCGCTCCAATGCTTT 61.026 50.000 5.56 0.00 0.00 3.51
3649 4983 0.803768 CATCGACCTCGCTTCCACAG 60.804 60.000 0.00 0.00 39.60 3.66
4088 5429 0.039074 AGACGAGTCTTGGTGCTTCG 60.039 55.000 0.00 0.00 36.31 3.79


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

AutoCloner maintained by Alex Coulton.