Multiple sequence alignment - TraesCS4A01G418700

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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 TraesCS4A01G418700 chr4A 100.000 5042 0 0 1 5042 688812511 688807470 0.000000e+00 9311.0
1 TraesCS4A01G418700 chr4A 99.592 4659 19 0 33 4691 688824673 688820015 0.000000e+00 8499.0
2 TraesCS4A01G418700 chr4A 96.662 4164 118 9 21 4178 688645556 688641408 0.000000e+00 6900.0
3 TraesCS4A01G418700 chr4A 81.591 2564 410 40 1603 4139 686593293 686590765 0.000000e+00 2063.0
4 TraesCS4A01G418700 chr4A 80.943 2566 423 44 1603 4139 686627350 686624822 0.000000e+00 1969.0
5 TraesCS4A01G418700 chr4A 81.055 2048 349 25 2094 4124 686572163 686570138 0.000000e+00 1596.0
6 TraesCS4A01G418700 chr4A 77.638 2142 413 45 2128 4235 689068942 689066833 0.000000e+00 1242.0
7 TraesCS4A01G418700 chr4A 77.540 2146 412 48 2128 4235 689092333 689090220 0.000000e+00 1229.0
8 TraesCS4A01G418700 chr4A 100.000 221 0 0 1 221 688824904 688824684 4.700000e-110 409.0
9 TraesCS4A01G418700 chr4A 89.855 276 13 5 4697 4959 688641399 688641126 1.740000e-89 340.0
10 TraesCS4A01G418700 chr4A 79.078 282 54 5 650 930 686594375 686594098 6.660000e-44 189.0
11 TraesCS4A01G418700 chr7A 92.052 2982 220 14 1604 4580 36317477 36314508 0.000000e+00 4178.0
12 TraesCS4A01G418700 chr7A 83.242 2924 427 40 1731 4625 36487803 36484914 0.000000e+00 2627.0
13 TraesCS4A01G418700 chr7A 81.400 2500 391 48 1671 4143 36371579 36369127 0.000000e+00 1973.0
14 TraesCS4A01G418700 chr7A 92.841 433 16 3 4576 4994 36311281 36310850 9.280000e-172 614.0
15 TraesCS4A01G418700 chr7A 92.135 356 14 4 4651 4992 36484917 36484562 1.630000e-134 490.0
16 TraesCS4A01G418700 chr7A 97.030 101 1 2 4576 4676 36314131 36314033 8.680000e-38 169.0
17 TraesCS4A01G418700 chr7A 76.923 299 54 11 634 929 36372766 36372480 6.760000e-34 156.0
18 TraesCS4A01G418700 chrUn 80.248 2906 486 55 1606 4477 90996130 90993279 0.000000e+00 2106.0
19 TraesCS4A01G418700 chrUn 80.723 2739 459 46 1606 4311 135325959 135328661 0.000000e+00 2069.0
20 TraesCS4A01G418700 chrUn 80.888 2072 334 39 2271 4311 239427387 239429427 0.000000e+00 1576.0
21 TraesCS4A01G418700 chrUn 79.558 1629 262 38 2876 4477 300832975 300831391 0.000000e+00 1098.0
22 TraesCS4A01G418700 chrUn 79.435 1629 264 38 2876 4477 91051300 91049716 0.000000e+00 1086.0
23 TraesCS4A01G418700 chrUn 73.410 346 61 19 4336 4676 135330350 135330669 3.210000e-17 100.0
24 TraesCS4A01G418700 chrUn 73.410 346 61 19 4336 4676 135363147 135363466 3.210000e-17 100.0
25 TraesCS4A01G418700 chrUn 73.410 346 61 19 4336 4676 245498699 245499018 3.210000e-17 100.0
26 TraesCS4A01G418700 chrUn 80.315 127 14 8 4553 4676 90993218 90993100 8.990000e-13 86.1
27 TraesCS4A01G418700 chrUn 80.315 127 14 8 4553 4676 91049655 91049537 8.990000e-13 86.1
28 TraesCS4A01G418700 chr7D 79.697 2177 386 40 1606 3766 36496750 36494614 0.000000e+00 1520.0
29 TraesCS4A01G418700 chr7D 78.684 2219 406 43 2128 4311 37217020 37214834 0.000000e+00 1415.0
30 TraesCS4A01G418700 chr7D 81.990 1005 144 23 3231 4213 36493368 36492379 0.000000e+00 819.0
31 TraesCS4A01G418700 chr4D 100.000 29 0 0 380 408 487053485 487053513 3.000000e-03 54.7


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 TraesCS4A01G418700 chr4A 688807470 688812511 5041 True 9311.000000 9311 100.000000 1 5042 1 chr4A.!!$R3 5041
1 TraesCS4A01G418700 chr4A 688820015 688824904 4889 True 4454.000000 8499 99.796000 1 4691 2 chr4A.!!$R8 4690
2 TraesCS4A01G418700 chr4A 688641126 688645556 4430 True 3620.000000 6900 93.258500 21 4959 2 chr4A.!!$R7 4938
3 TraesCS4A01G418700 chr4A 686624822 686627350 2528 True 1969.000000 1969 80.943000 1603 4139 1 chr4A.!!$R2 2536
4 TraesCS4A01G418700 chr4A 686570138 686572163 2025 True 1596.000000 1596 81.055000 2094 4124 1 chr4A.!!$R1 2030
5 TraesCS4A01G418700 chr4A 689066833 689068942 2109 True 1242.000000 1242 77.638000 2128 4235 1 chr4A.!!$R4 2107
6 TraesCS4A01G418700 chr4A 689090220 689092333 2113 True 1229.000000 1229 77.540000 2128 4235 1 chr4A.!!$R5 2107
7 TraesCS4A01G418700 chr4A 686590765 686594375 3610 True 1126.000000 2063 80.334500 650 4139 2 chr4A.!!$R6 3489
8 TraesCS4A01G418700 chr7A 36310850 36317477 6627 True 1653.666667 4178 93.974333 1604 4994 3 chr7A.!!$R1 3390
9 TraesCS4A01G418700 chr7A 36484562 36487803 3241 True 1558.500000 2627 87.688500 1731 4992 2 chr7A.!!$R3 3261
10 TraesCS4A01G418700 chr7A 36369127 36372766 3639 True 1064.500000 1973 79.161500 634 4143 2 chr7A.!!$R2 3509
11 TraesCS4A01G418700 chrUn 239427387 239429427 2040 False 1576.000000 1576 80.888000 2271 4311 1 chrUn.!!$F2 2040
12 TraesCS4A01G418700 chrUn 300831391 300832975 1584 True 1098.000000 1098 79.558000 2876 4477 1 chrUn.!!$R1 1601
13 TraesCS4A01G418700 chrUn 90993100 90996130 3030 True 1096.050000 2106 80.281500 1606 4676 2 chrUn.!!$R2 3070
14 TraesCS4A01G418700 chrUn 135325959 135330669 4710 False 1084.500000 2069 77.066500 1606 4676 2 chrUn.!!$F4 3070
15 TraesCS4A01G418700 chrUn 91049537 91051300 1763 True 586.050000 1086 79.875000 2876 4676 2 chrUn.!!$R3 1800
16 TraesCS4A01G418700 chr7D 37214834 37217020 2186 True 1415.000000 1415 78.684000 2128 4311 1 chr7D.!!$R1 2183
17 TraesCS4A01G418700 chr7D 36492379 36496750 4371 True 1169.500000 1520 80.843500 1606 4213 2 chr7D.!!$R2 2607

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
296 496 1.936767 ATCATTGGTGACGGCCCCAT 61.937 55.0 0.0 0.0 37.14 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4370 6604 2.242965 AGACATCCCAATCCATGAGCAA 59.757 45.455 0.0 0.0 0.0 3.91 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
162 362 3.433031 CGGTATTGCCCACCTTAATCTCA 60.433 47.826 0.00 0.00 33.62 3.27
296 496 1.936767 ATCATTGGTGACGGCCCCAT 61.937 55.000 0.00 0.00 37.14 4.00
501 701 4.709604 ACCTTTGCGGATGGTACAGGTAT 61.710 47.826 0.47 0.00 37.95 2.73
591 791 4.619336 GCTTACGAAGACAGTGAAGAAGAG 59.381 45.833 0.00 0.00 0.00 2.85
669 869 3.759086 TGCAGTCTAGTACACCAGAAGAG 59.241 47.826 0.00 0.00 0.00 2.85
952 1154 2.423373 CCCACCGAATCCAATCCAGAAT 60.423 50.000 0.00 0.00 0.00 2.40
4370 6604 6.112058 AGCAAATGTAATGGTGTGTTGTTTT 58.888 32.000 0.00 0.00 0.00 2.43
4692 10989 3.646715 CGGGTTCCTTCTGGGCCA 61.647 66.667 5.85 5.85 32.90 5.36
4782 11079 4.202377 CCTGAAATCCTGCATCTCTGATCT 60.202 45.833 0.00 0.00 0.00 2.75
4994 11305 6.128472 CGTACCCGGCCTATAAATTTGTATTC 60.128 42.308 0.00 0.00 0.00 1.75
4995 11306 5.697067 ACCCGGCCTATAAATTTGTATTCA 58.303 37.500 0.00 0.00 0.00 2.57
4996 11307 5.533528 ACCCGGCCTATAAATTTGTATTCAC 59.466 40.000 0.00 0.00 0.00 3.18
4997 11308 5.048294 CCCGGCCTATAAATTTGTATTCACC 60.048 44.000 0.00 0.00 0.00 4.02
4998 11309 5.768164 CCGGCCTATAAATTTGTATTCACCT 59.232 40.000 0.00 0.00 0.00 4.00
4999 11310 6.072673 CCGGCCTATAAATTTGTATTCACCTC 60.073 42.308 0.00 0.00 0.00 3.85
5000 11311 6.347402 CGGCCTATAAATTTGTATTCACCTCG 60.347 42.308 0.00 0.00 0.00 4.63
5001 11312 6.708949 GGCCTATAAATTTGTATTCACCTCGA 59.291 38.462 0.00 0.00 0.00 4.04
5002 11313 7.307811 GGCCTATAAATTTGTATTCACCTCGAC 60.308 40.741 0.00 0.00 0.00 4.20
5003 11314 7.225931 GCCTATAAATTTGTATTCACCTCGACA 59.774 37.037 0.00 0.00 0.00 4.35
5004 11315 9.104965 CCTATAAATTTGTATTCACCTCGACAA 57.895 33.333 0.00 0.00 0.00 3.18
5014 11325 9.619316 TGTATTCACCTCGACAAAAATAATTTG 57.381 29.630 0.00 0.00 35.64 2.32
5015 11326 9.834628 GTATTCACCTCGACAAAAATAATTTGA 57.165 29.630 7.83 0.00 33.83 2.69
5017 11328 9.927668 ATTCACCTCGACAAAAATAATTTGATT 57.072 25.926 7.83 0.00 33.83 2.57
5018 11329 9.757227 TTCACCTCGACAAAAATAATTTGATTT 57.243 25.926 7.83 0.00 33.83 2.17
5019 11330 9.405587 TCACCTCGACAAAAATAATTTGATTTC 57.594 29.630 7.83 0.00 33.83 2.17
5020 11331 9.410556 CACCTCGACAAAAATAATTTGATTTCT 57.589 29.630 7.83 0.00 33.83 2.52
5021 11332 9.626045 ACCTCGACAAAAATAATTTGATTTCTC 57.374 29.630 7.83 0.00 33.83 2.87
5022 11333 9.624697 CCTCGACAAAAATAATTTGATTTCTCA 57.375 29.630 7.83 0.00 33.83 3.27
5025 11336 9.679596 CGACAAAAATAATTTGATTTCTCATGC 57.320 29.630 7.83 0.00 33.83 4.06
5026 11337 9.977762 GACAAAAATAATTTGATTTCTCATGCC 57.022 29.630 7.83 0.00 33.83 4.40
5027 11338 9.729281 ACAAAAATAATTTGATTTCTCATGCCT 57.271 25.926 7.83 0.00 33.83 4.75
5032 11343 9.538508 AATAATTTGATTTCTCATGCCTAAAGC 57.461 29.630 0.00 0.00 44.14 3.51
5033 11344 6.786967 ATTTGATTTCTCATGCCTAAAGCT 57.213 33.333 0.00 0.00 44.23 3.74
5034 11345 5.824904 TTGATTTCTCATGCCTAAAGCTC 57.175 39.130 0.00 0.00 44.23 4.09
5035 11346 5.108187 TGATTTCTCATGCCTAAAGCTCT 57.892 39.130 0.00 0.00 44.23 4.09
5036 11347 4.880120 TGATTTCTCATGCCTAAAGCTCTG 59.120 41.667 0.00 0.00 44.23 3.35
5037 11348 4.558226 TTTCTCATGCCTAAAGCTCTGA 57.442 40.909 0.00 0.00 44.23 3.27
5038 11349 3.533606 TCTCATGCCTAAAGCTCTGAC 57.466 47.619 0.00 0.00 44.23 3.51
5039 11350 2.169352 TCTCATGCCTAAAGCTCTGACC 59.831 50.000 0.00 0.00 44.23 4.02
5040 11351 2.170187 CTCATGCCTAAAGCTCTGACCT 59.830 50.000 0.00 0.00 44.23 3.85
5041 11352 2.573462 TCATGCCTAAAGCTCTGACCTT 59.427 45.455 0.00 0.00 44.23 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 362 1.898574 CGCCTTGGCCAGTTTCAGT 60.899 57.895 5.11 0.0 0.00 3.41
296 496 4.028490 GGACCACGTGCCCATCCA 62.028 66.667 10.91 0.0 0.00 3.41
591 791 1.154205 CCACGCCTTGATCGTCATCC 61.154 60.000 0.00 0.0 38.19 3.51
669 869 1.943340 GCTAGCTGCACCCTAATGTTC 59.057 52.381 7.70 0.0 42.31 3.18
952 1154 3.136443 AGGCCGAATTGATCATCCTGTTA 59.864 43.478 0.00 0.0 30.69 2.41
4370 6604 2.242965 AGACATCCCAATCCATGAGCAA 59.757 45.455 0.00 0.0 0.00 3.91
4692 10989 2.838637 AGGATCTCGAGGAAGGAGTT 57.161 50.000 13.56 0.0 33.26 3.01
4782 11079 0.818296 GCTCCTCTCGACCTAAAGCA 59.182 55.000 0.00 0.0 0.00 3.91
4974 11285 5.768164 AGGTGAATACAAATTTATAGGCCGG 59.232 40.000 0.00 0.0 0.00 6.13
4994 11305 9.410556 AGAAATCAAATTATTTTTGTCGAGGTG 57.589 29.630 0.00 0.0 0.00 4.00
4995 11306 9.626045 GAGAAATCAAATTATTTTTGTCGAGGT 57.374 29.630 0.00 0.0 0.00 3.85
4996 11307 9.624697 TGAGAAATCAAATTATTTTTGTCGAGG 57.375 29.630 0.00 0.0 0.00 4.63
4999 11310 9.679596 GCATGAGAAATCAAATTATTTTTGTCG 57.320 29.630 0.00 0.0 0.00 4.35
5000 11311 9.977762 GGCATGAGAAATCAAATTATTTTTGTC 57.022 29.630 0.00 0.0 0.00 3.18
5001 11312 9.729281 AGGCATGAGAAATCAAATTATTTTTGT 57.271 25.926 0.00 0.0 0.00 2.83
5006 11317 9.538508 GCTTTAGGCATGAGAAATCAAATTATT 57.461 29.630 0.00 0.0 41.35 1.40
5007 11318 8.921205 AGCTTTAGGCATGAGAAATCAAATTAT 58.079 29.630 0.00 0.0 44.79 1.28
5008 11319 8.297470 AGCTTTAGGCATGAGAAATCAAATTA 57.703 30.769 0.00 0.0 44.79 1.40
5009 11320 7.123847 AGAGCTTTAGGCATGAGAAATCAAATT 59.876 33.333 0.00 0.0 44.79 1.82
5010 11321 6.606395 AGAGCTTTAGGCATGAGAAATCAAAT 59.394 34.615 0.00 0.0 44.79 2.32
5011 11322 5.948162 AGAGCTTTAGGCATGAGAAATCAAA 59.052 36.000 0.00 0.0 44.79 2.69
5012 11323 5.356190 CAGAGCTTTAGGCATGAGAAATCAA 59.644 40.000 0.00 0.0 44.79 2.57
5013 11324 4.880120 CAGAGCTTTAGGCATGAGAAATCA 59.120 41.667 0.00 0.0 44.79 2.57
5014 11325 5.007528 GTCAGAGCTTTAGGCATGAGAAATC 59.992 44.000 0.00 0.0 44.79 2.17
5015 11326 4.880696 GTCAGAGCTTTAGGCATGAGAAAT 59.119 41.667 0.00 0.0 44.79 2.17
5016 11327 4.256920 GTCAGAGCTTTAGGCATGAGAAA 58.743 43.478 0.00 0.0 44.79 2.52
5017 11328 3.369892 GGTCAGAGCTTTAGGCATGAGAA 60.370 47.826 0.00 0.0 44.79 2.87
5018 11329 2.169352 GGTCAGAGCTTTAGGCATGAGA 59.831 50.000 0.00 0.0 44.79 3.27
5019 11330 2.170187 AGGTCAGAGCTTTAGGCATGAG 59.830 50.000 0.00 0.0 44.79 2.90
5020 11331 2.191400 AGGTCAGAGCTTTAGGCATGA 58.809 47.619 0.00 0.0 44.79 3.07
5021 11332 2.706339 AGGTCAGAGCTTTAGGCATG 57.294 50.000 0.00 0.0 44.79 4.06


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

AutoCloner maintained by Alex Coulton.