Multiple sequence alignment - TraesCS3A01G159000

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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 TraesCS3A01G159000 chr3A 100.000 2444 0 0 1 2444 157348878 157346435 0.000000e+00 4514
1 TraesCS3A01G159000 chr3A 89.944 2496 175 23 1 2444 290707890 290710361 0.000000e+00 3149
2 TraesCS3A01G159000 chr6A 89.992 2498 175 24 1 2444 396917498 396919974 0.000000e+00 3158
3 TraesCS3A01G159000 chr6A 91.344 1421 102 7 1 1419 496085992 496084591 0.000000e+00 1923
4 TraesCS3A01G159000 chr6A 88.626 844 80 12 1614 2444 307921969 307922809 0.000000e+00 1013
5 TraesCS3A01G159000 chr1A 89.825 2457 208 19 1 2444 40279192 40281619 0.000000e+00 3114
6 TraesCS3A01G159000 chr1A 87.146 918 88 16 1554 2444 236391778 236390864 0.000000e+00 1014
7 TraesCS3A01G159000 chr1D 92.590 1282 79 6 333 1613 266178919 266177653 0.000000e+00 1827
8 TraesCS3A01G159000 chr1D 94.495 327 15 3 1 326 266181174 266180850 3.630000e-138 501
9 TraesCS3A01G159000 chr5A 90.537 1247 88 12 343 1589 1136094 1134878 0.000000e+00 1622
10 TraesCS3A01G159000 chr5A 88.721 860 78 12 1599 2444 631069580 631070434 0.000000e+00 1033
11 TraesCS3A01G159000 chr5A 95.600 250 10 1 1 249 1136338 1136089 1.360000e-107 399
12 TraesCS3A01G159000 chr3B 90.504 1032 70 13 422 1451 680396051 680395046 0.000000e+00 1338
13 TraesCS3A01G159000 chr3B 90.495 1010 72 9 442 1451 131914260 131913275 0.000000e+00 1312
14 TraesCS3A01G159000 chr3B 89.802 1010 67 6 442 1451 610990913 610991886 0.000000e+00 1262
15 TraesCS3A01G159000 chr3B 89.425 643 49 6 809 1451 731968899 731968276 0.000000e+00 793
16 TraesCS3A01G159000 chr2B 90.792 1010 69 6 442 1451 697786185 697787170 0.000000e+00 1328
17 TraesCS3A01G159000 chr2B 91.104 978 63 7 442 1419 110633116 110632163 0.000000e+00 1303
18 TraesCS3A01G159000 chr2B 89.286 868 75 11 1592 2444 318193385 318192521 0.000000e+00 1072
19 TraesCS3A01G159000 chr4B 91.631 932 60 6 442 1373 2417319 2416406 0.000000e+00 1273
20 TraesCS3A01G159000 chr4B 92.487 559 31 8 1 550 649114117 649113561 0.000000e+00 789
21 TraesCS3A01G159000 chr3D 89.107 918 71 16 1550 2444 214439219 214440130 0.000000e+00 1114
22 TraesCS3A01G159000 chr3D 96.748 123 3 1 1 123 181942704 181942825 1.150000e-48 204
23 TraesCS3A01G159000 chr7B 87.800 918 78 19 1550 2444 729438925 729438019 0.000000e+00 1044
24 TraesCS3A01G159000 chr4D 95.935 123 4 1 1 123 17107928 17108049 5.330000e-47 198
25 TraesCS3A01G159000 chr4A 88.000 100 8 4 1532 1629 158101608 158101511 5.520000e-22 115


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 TraesCS3A01G159000 chr3A 157346435 157348878 2443 True 4514.0 4514 100.0000 1 2444 1 chr3A.!!$R1 2443
1 TraesCS3A01G159000 chr3A 290707890 290710361 2471 False 3149.0 3149 89.9440 1 2444 1 chr3A.!!$F1 2443
2 TraesCS3A01G159000 chr6A 396917498 396919974 2476 False 3158.0 3158 89.9920 1 2444 1 chr6A.!!$F2 2443
3 TraesCS3A01G159000 chr6A 496084591 496085992 1401 True 1923.0 1923 91.3440 1 1419 1 chr6A.!!$R1 1418
4 TraesCS3A01G159000 chr6A 307921969 307922809 840 False 1013.0 1013 88.6260 1614 2444 1 chr6A.!!$F1 830
5 TraesCS3A01G159000 chr1A 40279192 40281619 2427 False 3114.0 3114 89.8250 1 2444 1 chr1A.!!$F1 2443
6 TraesCS3A01G159000 chr1A 236390864 236391778 914 True 1014.0 1014 87.1460 1554 2444 1 chr1A.!!$R1 890
7 TraesCS3A01G159000 chr1D 266177653 266181174 3521 True 1164.0 1827 93.5425 1 1613 2 chr1D.!!$R1 1612
8 TraesCS3A01G159000 chr5A 631069580 631070434 854 False 1033.0 1033 88.7210 1599 2444 1 chr5A.!!$F1 845
9 TraesCS3A01G159000 chr5A 1134878 1136338 1460 True 1010.5 1622 93.0685 1 1589 2 chr5A.!!$R1 1588
10 TraesCS3A01G159000 chr3B 680395046 680396051 1005 True 1338.0 1338 90.5040 422 1451 1 chr3B.!!$R2 1029
11 TraesCS3A01G159000 chr3B 131913275 131914260 985 True 1312.0 1312 90.4950 442 1451 1 chr3B.!!$R1 1009
12 TraesCS3A01G159000 chr3B 610990913 610991886 973 False 1262.0 1262 89.8020 442 1451 1 chr3B.!!$F1 1009
13 TraesCS3A01G159000 chr3B 731968276 731968899 623 True 793.0 793 89.4250 809 1451 1 chr3B.!!$R3 642
14 TraesCS3A01G159000 chr2B 697786185 697787170 985 False 1328.0 1328 90.7920 442 1451 1 chr2B.!!$F1 1009
15 TraesCS3A01G159000 chr2B 110632163 110633116 953 True 1303.0 1303 91.1040 442 1419 1 chr2B.!!$R1 977
16 TraesCS3A01G159000 chr2B 318192521 318193385 864 True 1072.0 1072 89.2860 1592 2444 1 chr2B.!!$R2 852
17 TraesCS3A01G159000 chr4B 2416406 2417319 913 True 1273.0 1273 91.6310 442 1373 1 chr4B.!!$R1 931
18 TraesCS3A01G159000 chr4B 649113561 649114117 556 True 789.0 789 92.4870 1 550 1 chr4B.!!$R2 549
19 TraesCS3A01G159000 chr3D 214439219 214440130 911 False 1114.0 1114 89.1070 1550 2444 1 chr3D.!!$F2 894
20 TraesCS3A01G159000 chr7B 729438019 729438925 906 True 1044.0 1044 87.8000 1550 2444 1 chr7B.!!$R1 894

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
884 2819 0.6112 CCATGGTGACGTCCTGGTTA 59.389 55.0 14.12 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2348 4351 0.960364 ATGCGATCAAAACAGCGGGT 60.96 50.0 0.0 0.0 0.0 5.28 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
74 75 5.873712 CACAGATAGAGCATCAGTCAACTTT 59.126 40.000 0.00 0.00 37.82 2.66
84 86 6.770785 AGCATCAGTCAACTTTAGGTTTACAA 59.229 34.615 0.00 0.00 35.25 2.41
151 153 8.005466 GCAACATTCAAATTCAAACATACACAG 58.995 33.333 0.00 0.00 0.00 3.66
200 202 3.423539 AAGCATACACTTCAGGCAAGA 57.576 42.857 0.00 0.00 35.82 3.02
232 234 4.853743 CAGCGGATTTGAAGAGCTAAAAAC 59.146 41.667 0.00 0.00 36.28 2.43
233 235 4.518970 AGCGGATTTGAAGAGCTAAAAACA 59.481 37.500 0.00 0.00 36.28 2.83
235 237 5.343325 GCGGATTTGAAGAGCTAAAAACAAG 59.657 40.000 0.00 0.00 0.00 3.16
236 238 5.343325 CGGATTTGAAGAGCTAAAAACAAGC 59.657 40.000 0.00 0.00 40.40 4.01
237 239 6.215845 GGATTTGAAGAGCTAAAAACAAGCA 58.784 36.000 0.00 0.00 42.62 3.91
483 2409 3.815809 TCTCTGTTTTGACCGTCCAATT 58.184 40.909 0.00 0.00 0.00 2.32
497 2423 3.303725 CGTCCAATTGTCAAACACGACAT 60.304 43.478 4.43 0.00 45.03 3.06
498 2424 3.974401 GTCCAATTGTCAAACACGACATG 59.026 43.478 4.43 0.00 45.03 3.21
531 2465 8.256605 GCAGGTAGACAACATCATATATGAGAT 58.743 37.037 19.73 8.37 40.64 2.75
583 2517 4.558226 ACAACACCTATCAATGCTCAGA 57.442 40.909 0.00 0.00 0.00 3.27
586 2520 4.833478 ACACCTATCAATGCTCAGAAGT 57.167 40.909 0.00 0.00 0.00 3.01
588 2522 5.564550 ACACCTATCAATGCTCAGAAGTTT 58.435 37.500 0.00 0.00 0.00 2.66
608 2543 3.961480 TCACCTTGATACACAGAGTGG 57.039 47.619 1.93 0.00 37.94 4.00
623 2558 7.514721 ACACAGAGTGGAAAAAGAGGTAAATA 58.485 34.615 1.93 0.00 37.94 1.40
681 2616 4.420522 ACAAGGAATTGTGCCAAAACAT 57.579 36.364 0.00 0.00 33.23 2.71
686 2621 6.849085 AGGAATTGTGCCAAAACATGTATA 57.151 33.333 0.00 0.00 0.00 1.47
884 2819 0.611200 CCATGGTGACGTCCTGGTTA 59.389 55.000 14.12 0.00 0.00 2.85
939 2874 2.029290 CGGAAGAAGAAAAGACGAGGGA 60.029 50.000 0.00 0.00 0.00 4.20
970 2908 3.373110 GGGATTCATACCTTTGAGCCCTT 60.373 47.826 0.00 0.00 38.26 3.95
1061 2999 4.853050 GAGCTGCTCCATGGCGCT 62.853 66.667 26.18 19.89 41.66 5.92
1123 3061 1.804396 CTCGAGCGAGGATGGCATCT 61.804 60.000 25.48 12.59 44.88 2.90
1137 3075 1.135094 GCATCTTGGATCTGGGAGGA 58.865 55.000 0.00 0.00 0.00 3.71
1151 3089 1.137282 GGGAGGAAGAGACGATGAACC 59.863 57.143 0.00 0.00 0.00 3.62
1171 3109 2.698797 CCGAGGAAGTTAGGAATGGCTA 59.301 50.000 0.00 0.00 0.00 3.93
1214 3161 1.532604 ATGCACCTGAGTCGTCGGAA 61.533 55.000 0.00 0.00 0.00 4.30
1232 3179 1.847890 AACCACGCCGATCAAAACCG 61.848 55.000 0.00 0.00 0.00 4.44
1240 3187 2.734670 CCGATCAAAACCGTAGCGATA 58.265 47.619 0.00 0.00 0.00 2.92
1245 3192 2.756760 TCAAAACCGTAGCGATAGGAGT 59.243 45.455 1.27 0.00 0.00 3.85
1296 3243 2.412323 CGGATCTCGACGGGGAACA 61.412 63.158 0.00 0.00 42.43 3.18
1362 3309 4.348495 GGAGGGAGTGGGGGTGGA 62.348 72.222 0.00 0.00 0.00 4.02
1420 3367 2.700540 GGAGGTGGGAAGGAGGGATTAT 60.701 54.545 0.00 0.00 0.00 1.28
1447 3394 3.068064 TGGCCACGAGATGAGCGA 61.068 61.111 0.00 0.00 0.00 4.93
1484 3431 1.995626 GAGAGGTAAGGGGCAGCCA 60.996 63.158 15.19 0.00 0.00 4.75
1487 3434 2.137177 GAGGTAAGGGGCAGCCAACA 62.137 60.000 15.19 0.00 0.00 3.33
1545 3492 2.046023 CGGGTGAATCCTGCTGCA 60.046 61.111 0.88 0.88 35.61 4.41
1640 3628 2.159240 CGACGGTGGATTCAGATCAGAA 60.159 50.000 2.74 2.74 33.77 3.02
1700 3688 1.979693 GGTGCGAGAGGAGGAGTGT 60.980 63.158 0.00 0.00 0.00 3.55
1719 3707 2.987547 GGACGTGGGTGAGACCGA 60.988 66.667 0.00 0.00 39.83 4.69
1733 3721 4.386951 CCGACGACATGTGGGCCA 62.387 66.667 12.78 0.00 39.78 5.36
1866 3854 7.599998 GGTCGTAACTGACTAAAATTAAGGTGA 59.400 37.037 0.00 0.00 38.91 4.02
2077 4078 8.096621 TGAAGGACCTACCATATATTTGTTGA 57.903 34.615 0.00 0.00 42.04 3.18
2095 4096 8.517062 TTTGTTGAAAATTTGGACCAAATCAT 57.483 26.923 28.49 20.84 42.32 2.45
2348 4351 2.232941 CCACTAGCTAGGAACGGTCAAA 59.767 50.000 24.35 0.00 0.00 2.69
2362 4365 1.339929 GGTCAAACCCGCTGTTTTGAT 59.660 47.619 4.28 0.00 44.80 2.57
2370 4373 1.913403 CCGCTGTTTTGATCGCATTTC 59.087 47.619 0.00 0.00 0.00 2.17
2387 4390 5.798910 GCATTTCGAAATGGGCATAAAAAG 58.201 37.500 38.24 18.37 44.54 2.27
2432 4446 6.734137 TGTAAAACCTTCACATTGTGTCATC 58.266 36.000 16.06 1.17 34.79 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 111 4.235939 TGTTGCAATGCGTTTCAGTTAT 57.764 36.364 0.59 0.00 0.00 1.89
151 153 1.004679 TAGCGGGTCAAACGTTCCC 60.005 57.895 12.50 12.50 37.98 3.97
200 202 1.839994 TCAAATCCGCTGGAAGGATCT 59.160 47.619 1.44 0.00 46.99 2.75
249 252 1.329256 GCCTAATCCTGAGGTCGCTA 58.671 55.000 0.00 0.00 36.37 4.26
338 2264 6.466812 CATGGTTCATCAGTGTATATGCCTA 58.533 40.000 0.00 0.00 0.00 3.93
497 2423 2.105649 TGTTGTCTACCTGCCATGTTCA 59.894 45.455 0.00 0.00 0.00 3.18
498 2424 2.778299 TGTTGTCTACCTGCCATGTTC 58.222 47.619 0.00 0.00 0.00 3.18
531 2465 8.040727 TGTACGTGTGTATCCTCTAGTAGTTTA 58.959 37.037 0.00 0.00 32.11 2.01
583 2517 5.760253 CACTCTGTGTATCAAGGTGAAACTT 59.240 40.000 0.00 0.00 36.74 2.66
586 2520 4.346709 TCCACTCTGTGTATCAAGGTGAAA 59.653 41.667 0.00 0.00 33.61 2.69
588 2522 3.506398 TCCACTCTGTGTATCAAGGTGA 58.494 45.455 0.00 0.00 33.61 4.02
623 2558 1.822371 GTGTTGGTGTTTGTGGAGGTT 59.178 47.619 0.00 0.00 0.00 3.50
884 2819 2.452505 CCCCTTCTCGTCTCTCTTTCT 58.547 52.381 0.00 0.00 0.00 2.52
939 2874 6.011628 TCAAAGGTATGAATCCCTTTCTCCTT 60.012 38.462 0.82 0.00 45.67 3.36
970 2908 0.524862 GAACGAGTAGCTCCAACCGA 59.475 55.000 0.00 0.00 0.00 4.69
1006 2944 0.640495 TTCTCGGGATTCCTACCCCT 59.360 55.000 2.01 0.00 44.09 4.79
1061 2999 3.011517 GCTTCCTCCCCTGCCTCA 61.012 66.667 0.00 0.00 0.00 3.86
1123 3061 2.472029 GTCTCTTCCTCCCAGATCCAA 58.528 52.381 0.00 0.00 0.00 3.53
1137 3075 1.835494 TCCTCGGTTCATCGTCTCTT 58.165 50.000 0.00 0.00 0.00 2.85
1151 3089 2.990066 AGCCATTCCTAACTTCCTCG 57.010 50.000 0.00 0.00 0.00 4.63
1171 3109 4.510748 CCATCTACTCCATCTCCTCCTCAT 60.511 50.000 0.00 0.00 0.00 2.90
1214 3161 2.322081 CGGTTTTGATCGGCGTGGT 61.322 57.895 6.85 0.00 0.00 4.16
1226 3173 2.223433 CGACTCCTATCGCTACGGTTTT 60.223 50.000 0.00 0.00 34.90 2.43
1232 3179 1.263752 GTGACCGACTCCTATCGCTAC 59.736 57.143 0.00 0.00 40.87 3.58
1240 3187 2.571216 CCAACCGTGACCGACTCCT 61.571 63.158 0.00 0.00 35.63 3.69
1374 3321 3.855352 CTGGATAGAGCAGGCGCCG 62.855 68.421 23.20 17.35 39.83 6.46
1375 3322 2.030262 CTGGATAGAGCAGGCGCC 59.970 66.667 21.89 21.89 39.83 6.53
1386 3333 0.399091 CACCTCCCTGCCTCTGGATA 60.399 60.000 0.00 0.00 0.00 2.59
1420 3367 2.046023 CGTGGCCAGATCCAGCAA 60.046 61.111 5.11 0.00 36.67 3.91
1447 3394 1.360551 CGCCCAGATCGACTCGATT 59.639 57.895 15.02 3.35 47.00 3.34
1484 3431 0.401395 TCTCCCCCAACCTCACTGTT 60.401 55.000 0.00 0.00 0.00 3.16
1487 3434 0.790993 TACTCTCCCCCAACCTCACT 59.209 55.000 0.00 0.00 0.00 3.41
1621 3604 3.452264 TCATTCTGATCTGAATCCACCGT 59.548 43.478 21.18 1.48 34.77 4.83
1640 3628 0.859760 CCCTCTCTCCTCTCCCTCAT 59.140 60.000 0.00 0.00 0.00 2.90
1700 3688 2.920912 GGTCTCACCCACGTCCCA 60.921 66.667 0.00 0.00 30.04 4.37
1719 3707 1.678635 CCAATGGCCCACATGTCGT 60.679 57.895 0.00 0.00 40.44 4.34
1733 3721 1.212688 TCGGATGTTGCTGGATCCAAT 59.787 47.619 17.00 5.66 38.50 3.16
1915 3909 9.248291 CTAAAGTCAAATTTGCTAACACAATGT 57.752 29.630 13.54 0.00 0.00 2.71
2017 4014 3.712187 TGGGCACTCGAAAATGAAAAAC 58.288 40.909 0.00 0.00 0.00 2.43
2119 4120 5.075858 CCATTTGGTCAAGTGTGCATTAT 57.924 39.130 0.00 0.00 0.00 1.28
2297 4298 9.495572 AATCTTGGAAAACTTTTTGTGTTTGTA 57.504 25.926 0.00 0.00 37.64 2.41
2348 4351 0.960364 ATGCGATCAAAACAGCGGGT 60.960 50.000 0.00 0.00 0.00 5.28
2370 4373 6.777526 TTTGAACTTTTTATGCCCATTTCG 57.222 33.333 0.00 0.00 0.00 3.46
2410 4413 6.951062 TGATGACACAATGTGAAGGTTTTA 57.049 33.333 21.34 0.00 36.96 1.52
2420 4434 5.499313 TGGTCACATATGATGACACAATGT 58.501 37.500 25.90 0.00 46.89 2.71


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

AutoCloner maintained by Alex Coulton.