Multiple sequence alignment - TraesCS6A01G179600

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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 TraesCS6A01G179600 chr6A 100.000 1804 0 0 1844 3647 202144275 202142472 0.000000e+00 3332.0
1 TraesCS6A01G179600 chr6A 100.000 1159 0 0 1 1159 202146118 202144960 0.000000e+00 2141.0
2 TraesCS6A01G179600 chr6A 91.711 1134 64 10 3 1134 81612509 81611404 0.000000e+00 1546.0
3 TraesCS6A01G179600 chr6A 93.501 754 46 3 1 753 344780882 344781633 0.000000e+00 1118.0
4 TraesCS6A01G179600 chr6A 92.277 751 55 3 4 753 344815652 344816400 0.000000e+00 1062.0
5 TraesCS6A01G179600 chr6A 84.557 395 57 4 1844 2235 565573908 565574301 4.420000e-104 388.0
6 TraesCS6A01G179600 chr2A 93.793 1160 62 3 1 1159 575412220 575413370 0.000000e+00 1735.0
7 TraesCS6A01G179600 chr2A 84.513 678 89 14 2972 3638 35405926 35406598 0.000000e+00 656.0
8 TraesCS6A01G179600 chr2A 90.909 66 6 0 2246 2311 35399239 35399304 5.020000e-14 89.8
9 TraesCS6A01G179600 chr4A 93.540 1161 63 4 1 1159 351895881 351897031 0.000000e+00 1718.0
10 TraesCS6A01G179600 chr4A 94.058 993 48 4 1 991 290627783 290628766 0.000000e+00 1496.0
11 TraesCS6A01G179600 chr1A 96.208 1002 36 2 1844 2843 294715057 294716058 0.000000e+00 1639.0
12 TraesCS6A01G179600 chr1A 95.609 1002 42 2 1844 2843 289022492 289023493 0.000000e+00 1605.0
13 TraesCS6A01G179600 chr1A 94.853 816 31 3 2841 3647 289024381 289025194 0.000000e+00 1264.0
14 TraesCS6A01G179600 chr1A 94.608 816 33 4 2841 3647 294716945 294717758 0.000000e+00 1253.0
15 TraesCS6A01G179600 chr6B 89.448 1033 91 9 1 1031 493698257 493699273 0.000000e+00 1288.0
16 TraesCS6A01G179600 chr6B 91.627 633 44 7 2978 3606 319512752 319512125 0.000000e+00 867.0
17 TraesCS6A01G179600 chr6B 88.025 476 49 2 1844 2311 319516776 319516301 1.140000e-154 556.0
18 TraesCS6A01G179600 chr6B 83.529 255 37 5 3392 3645 515750071 515749821 2.190000e-57 233.0
19 TraesCS6A01G179600 chr6B 73.379 586 121 24 2844 3411 174668951 174668383 6.220000e-43 185.0
20 TraesCS6A01G179600 chr6B 82.258 124 13 2 2841 2955 27609124 27609247 8.330000e-17 99.0
21 TraesCS6A01G179600 chr7D 91.691 674 39 11 2978 3647 418722369 418721709 0.000000e+00 918.0
22 TraesCS6A01G179600 chr7D 90.812 468 43 0 1844 2311 418724688 418724221 8.600000e-176 627.0
23 TraesCS6A01G179600 chr3D 89.172 471 44 4 285 750 17115733 17115265 6.790000e-162 580.0
24 TraesCS6A01G179600 chr3D 80.587 443 69 12 1877 2311 200430738 200431171 3.510000e-85 326.0
25 TraesCS6A01G179600 chr3D 83.268 257 28 8 2 252 17115974 17115727 4.740000e-54 222.0
26 TraesCS6A01G179600 chrUn 77.858 831 137 26 2841 3643 343604276 343605087 4.260000e-129 472.0
27 TraesCS6A01G179600 chrUn 77.711 830 139 25 2841 3643 343660621 343661431 1.980000e-127 466.0
28 TraesCS6A01G179600 chrUn 84.224 393 58 4 1849 2238 344366059 344365668 2.660000e-101 379.0
29 TraesCS6A01G179600 chrUn 81.890 127 14 2 2841 2958 76371221 76371095 8.330000e-17 99.0
30 TraesCS6A01G179600 chrUn 81.890 127 14 2 2841 2958 355649888 355649762 8.330000e-17 99.0
31 TraesCS6A01G179600 chr3B 78.142 732 127 25 2841 3548 622017820 622017098 5.590000e-118 435.0
32 TraesCS6A01G179600 chr2B 85.542 332 47 1 1844 2175 326079974 326080304 2.700000e-91 346.0
33 TraesCS6A01G179600 chr2B 89.720 107 10 1 2379 2485 326080559 326080664 6.350000e-28 135.0
34 TraesCS6A01G179600 chr7B 84.000 325 48 4 1846 2168 78280200 78279878 3.540000e-80 309.0
35 TraesCS6A01G179600 chr7B 83.529 255 37 5 3392 3645 78279495 78279245 2.190000e-57 233.0
36 TraesCS6A01G179600 chr7B 84.659 176 27 0 2310 2485 533459361 533459536 3.740000e-40 176.0
37 TraesCS6A01G179600 chr1B 83.333 324 52 2 1846 2168 572280225 572279903 7.660000e-77 298.0
38 TraesCS6A01G179600 chr1B 83.858 254 38 3 3392 3645 572279521 572279271 4.710000e-59 239.0
39 TraesCS6A01G179600 chr5D 84.967 153 17 6 2484 2635 378278892 378279039 2.270000e-32 150.0
40 TraesCS6A01G179600 chr3A 95.349 43 1 1 535 577 19774242 19774283 2.350000e-07 67.6


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 TraesCS6A01G179600 chr6A 202142472 202146118 3646 True 2736.5 3332 100.0000 1 3647 2 chr6A.!!$R2 3646
1 TraesCS6A01G179600 chr6A 81611404 81612509 1105 True 1546.0 1546 91.7110 3 1134 1 chr6A.!!$R1 1131
2 TraesCS6A01G179600 chr6A 344780882 344781633 751 False 1118.0 1118 93.5010 1 753 1 chr6A.!!$F1 752
3 TraesCS6A01G179600 chr6A 344815652 344816400 748 False 1062.0 1062 92.2770 4 753 1 chr6A.!!$F2 749
4 TraesCS6A01G179600 chr2A 575412220 575413370 1150 False 1735.0 1735 93.7930 1 1159 1 chr2A.!!$F3 1158
5 TraesCS6A01G179600 chr2A 35405926 35406598 672 False 656.0 656 84.5130 2972 3638 1 chr2A.!!$F2 666
6 TraesCS6A01G179600 chr4A 351895881 351897031 1150 False 1718.0 1718 93.5400 1 1159 1 chr4A.!!$F2 1158
7 TraesCS6A01G179600 chr4A 290627783 290628766 983 False 1496.0 1496 94.0580 1 991 1 chr4A.!!$F1 990
8 TraesCS6A01G179600 chr1A 294715057 294717758 2701 False 1446.0 1639 95.4080 1844 3647 2 chr1A.!!$F2 1803
9 TraesCS6A01G179600 chr1A 289022492 289025194 2702 False 1434.5 1605 95.2310 1844 3647 2 chr1A.!!$F1 1803
10 TraesCS6A01G179600 chr6B 493698257 493699273 1016 False 1288.0 1288 89.4480 1 1031 1 chr6B.!!$F2 1030
11 TraesCS6A01G179600 chr6B 319512125 319516776 4651 True 711.5 867 89.8260 1844 3606 2 chr6B.!!$R3 1762
12 TraesCS6A01G179600 chr7D 418721709 418724688 2979 True 772.5 918 91.2515 1844 3647 2 chr7D.!!$R1 1803
13 TraesCS6A01G179600 chr3D 17115265 17115974 709 True 401.0 580 86.2200 2 750 2 chr3D.!!$R1 748
14 TraesCS6A01G179600 chrUn 343604276 343605087 811 False 472.0 472 77.8580 2841 3643 1 chrUn.!!$F1 802
15 TraesCS6A01G179600 chrUn 343660621 343661431 810 False 466.0 466 77.7110 2841 3643 1 chrUn.!!$F2 802
16 TraesCS6A01G179600 chr3B 622017098 622017820 722 True 435.0 435 78.1420 2841 3548 1 chr3B.!!$R1 707
17 TraesCS6A01G179600 chr2B 326079974 326080664 690 False 240.5 346 87.6310 1844 2485 2 chr2B.!!$F1 641
18 TraesCS6A01G179600 chr7B 78279245 78280200 955 True 271.0 309 83.7645 1846 3645 2 chr7B.!!$R1 1799
19 TraesCS6A01G179600 chr1B 572279271 572280225 954 True 268.5 298 83.5955 1846 3645 2 chr1B.!!$R1 1799

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
841 863 0.390340 GTCAGACGCTGCCATTCTCA 60.390 55.0 0.00 0.0 0.00 3.27 F
1062 1085 0.878416 GCGATGGTGGCAACTTGTTA 59.122 50.0 3.27 0.0 37.61 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2364 5858 0.110509 GAACACTAGCGACGTCGACA 60.111 55.0 39.74 24.35 43.02 4.35 R
2878 7263 2.026822 GGATCTGTTTCCCTGCTGAAGA 60.027 50.0 0.00 0.00 0.00 2.87 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
50 52 3.113260 AGGAAAGACTTCAACACTCCG 57.887 47.619 0.00 0.00 32.75 4.63
102 106 7.444629 TGAAAATGCAGGCTGAGATATATTC 57.555 36.000 20.86 12.21 0.00 1.75
103 107 7.229308 TGAAAATGCAGGCTGAGATATATTCT 58.771 34.615 20.86 0.00 37.41 2.40
228 244 5.211973 AGGATGGAATCTACTGCTTACTCA 58.788 41.667 0.00 0.00 44.71 3.41
262 279 2.708216 TTCAGCCACAAAGAGTCACA 57.292 45.000 0.00 0.00 0.00 3.58
318 335 2.423538 ACCAGTCAGAAAGCAACAACAC 59.576 45.455 0.00 0.00 0.00 3.32
325 345 4.159321 TCAGAAAGCAACAACACCATTTCA 59.841 37.500 0.00 0.00 0.00 2.69
477 497 1.968493 ACGACTAGGAAGGTGCTTTGA 59.032 47.619 0.00 0.00 0.00 2.69
747 769 3.112263 ACTTTGGCCCACTATGTAGCTA 58.888 45.455 0.00 0.00 0.00 3.32
825 847 1.738346 CGATCTGGCGGAGATGGTCA 61.738 60.000 1.04 0.00 41.91 4.02
841 863 0.390340 GTCAGACGCTGCCATTCTCA 60.390 55.000 0.00 0.00 0.00 3.27
1062 1085 0.878416 GCGATGGTGGCAACTTGTTA 59.122 50.000 3.27 0.00 37.61 2.41
1121 1145 2.204090 GGAGGGAGGTGGGGACAA 60.204 66.667 0.00 0.00 46.06 3.18
1131 1155 2.903350 GGGGACAACGGCGTGTTT 60.903 61.111 15.70 0.00 39.29 2.83
1960 1986 1.131638 CCCTGTATGGAAGCCTAGCA 58.868 55.000 0.00 0.00 38.35 3.49
1992 2018 1.210478 AGTGCATTTGAGGGCGATAGT 59.790 47.619 0.00 0.00 39.35 2.12
2021 2047 1.550976 CTTTCTTCTACGGCAGAGGGT 59.449 52.381 0.00 0.00 33.83 4.34
2171 2205 2.181521 GGTTCGGCACCGTTTGACA 61.182 57.895 9.23 0.00 40.74 3.58
2180 2214 2.668250 CACCGTTTGACACGATGACTA 58.332 47.619 0.00 0.00 46.71 2.59
2212 2246 2.484264 GACGGCTCTTTTATGTTGCAGT 59.516 45.455 0.00 0.00 35.06 4.40
2279 2317 1.174712 ATTGCCTATGATGCACGGCC 61.175 55.000 0.00 0.00 41.80 6.13
2364 5858 0.473326 GAGCCATCATCCCTGCTTCT 59.527 55.000 0.00 0.00 33.41 2.85
2436 5930 1.338200 ACCTTGCATCTGTCGGTCTTC 60.338 52.381 0.00 0.00 0.00 2.87
2588 6082 2.061848 TCTTGGGAGGATGTTGAACCA 58.938 47.619 0.00 0.00 0.00 3.67
2779 6273 1.339055 GGAGTACATGCTGGACTTGCA 60.339 52.381 0.00 0.00 42.76 4.08
2878 7263 5.475220 TCTTCTTCGTCTGATTCTGACTCTT 59.525 40.000 18.05 0.00 31.62 2.85
2881 7275 5.475220 TCTTCGTCTGATTCTGACTCTTCTT 59.525 40.000 18.05 0.00 31.62 2.52
2912 7306 3.213160 ACAGATCCCCTCCTCTTCTTT 57.787 47.619 0.00 0.00 0.00 2.52
2988 7382 3.514151 ATCCCATAGCCATCCATCCTA 57.486 47.619 0.00 0.00 0.00 2.94
3227 7634 8.457261 GTCATTGCTCAGATTAAGAAAGTGAAT 58.543 33.333 0.00 0.00 0.00 2.57
3362 7781 9.905713 AAATTCATACCTTAGATCTGCTTTGTA 57.094 29.630 5.18 0.56 0.00 2.41
3383 7802 3.083349 CCGCACTGGGAGGGATCA 61.083 66.667 0.00 0.00 31.91 2.92
3388 7807 1.118838 CACTGGGAGGGATCAGAGTC 58.881 60.000 0.00 0.00 35.20 3.36
3390 7809 0.031716 CTGGGAGGGATCAGAGTCCA 60.032 60.000 0.00 0.00 40.17 4.02
3537 7959 2.166664 GTCAGCCTGACTACCTACAAGG 59.833 54.545 17.57 0.00 43.73 3.61
3614 8038 2.400269 ATACGTTGGTTGGGCGGTGT 62.400 55.000 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.732443 TCTTTCCTATCACTCTCCCCTCTA 59.268 45.833 0.00 0.00 0.00 2.43
228 244 5.244402 TGTGGCTGAAATTCTGAATGAACAT 59.756 36.000 3.22 0.00 37.52 2.71
270 287 2.876550 GGTGACTGTTTGTGTTCCCTAC 59.123 50.000 0.00 0.00 0.00 3.18
271 288 2.775384 AGGTGACTGTTTGTGTTCCCTA 59.225 45.455 0.00 0.00 41.13 3.53
318 335 5.297776 AGAGCGATACCTCAAAATGAAATGG 59.702 40.000 0.00 0.00 34.26 3.16
325 345 2.171448 AGGCAGAGCGATACCTCAAAAT 59.829 45.455 0.00 0.00 34.26 1.82
511 533 1.165270 GTCACTTTTGATCGGGGGTG 58.835 55.000 0.00 0.00 33.11 4.61
747 769 5.297776 CGGTCTAAATGATTCAGCAAAGGAT 59.702 40.000 0.00 0.00 0.00 3.24
814 836 1.226802 CAGCGTCTGACCATCTCCG 60.227 63.158 1.55 0.00 32.44 4.63
825 847 1.376543 CAATGAGAATGGCAGCGTCT 58.623 50.000 0.00 0.00 0.00 4.18
841 863 0.543277 TTCCTCCTCGATGCAGCAAT 59.457 50.000 1.53 0.00 0.00 3.56
889 911 2.435805 ACACTGTCTGGTGTCATTCAGT 59.564 45.455 0.00 0.00 45.94 3.41
1062 1085 0.032813 CAAACCATCCTCCCCAGCAT 60.033 55.000 0.00 0.00 0.00 3.79
1992 2018 1.747355 CGTAGAAGAAAGGGGTCGCTA 59.253 52.381 0.00 0.00 0.00 4.26
1999 2025 1.134670 CCTCTGCCGTAGAAGAAAGGG 60.135 57.143 0.00 0.00 34.32 3.95
2021 2047 2.649531 ACCGAAAATGGTTCCTGTCA 57.350 45.000 0.00 0.00 39.99 3.58
2106 2140 3.302365 AAATGGCAGGTTTCAACATCG 57.698 42.857 0.00 0.00 0.00 3.84
2171 2205 4.184629 GTCCAAAAGCATCTAGTCATCGT 58.815 43.478 0.00 0.00 0.00 3.73
2180 2214 0.326264 AGAGCCGTCCAAAAGCATCT 59.674 50.000 0.00 0.00 0.00 2.90
2248 2283 6.422701 GCATCATAGGCAATTACTAACGTACA 59.577 38.462 0.00 0.00 0.00 2.90
2318 5806 0.591170 CACGCTTTCAACCGGAACAT 59.409 50.000 9.46 0.00 34.56 2.71
2364 5858 0.110509 GAACACTAGCGACGTCGACA 60.111 55.000 39.74 24.35 43.02 4.35
2588 6082 4.890499 ATCTCCTCGGACATATCCCTAT 57.110 45.455 0.00 0.00 42.83 2.57
2651 6145 4.288626 GGGGCCTGAATAAGTACCATATCA 59.711 45.833 0.84 0.00 0.00 2.15
2779 6273 4.095334 GCAAACGGAATTACCTAACCGAAT 59.905 41.667 11.27 0.00 46.94 3.34
2878 7263 2.026822 GGATCTGTTTCCCTGCTGAAGA 60.027 50.000 0.00 0.00 0.00 2.87
3147 7550 2.762887 TCTAAGCATGCACACTAGCTCT 59.237 45.455 21.98 0.00 36.07 4.09
3286 7698 1.306141 AGGATTCCAGTCCGAGCCA 60.306 57.895 5.29 0.00 43.27 4.75
3383 7802 1.133513 AGCTGGAGATCGATGGACTCT 60.134 52.381 0.54 0.00 0.00 3.24
3388 7807 0.964700 TAGCAGCTGGAGATCGATGG 59.035 55.000 17.12 0.00 0.00 3.51
3390 7809 2.492881 CAGATAGCAGCTGGAGATCGAT 59.507 50.000 17.12 0.00 0.00 3.59
3537 7959 1.477014 GGGATTTCTTGTCGGGATCCC 60.477 57.143 22.12 22.12 46.52 3.85
3554 7976 1.354368 GGGTTCAGATGTTTCCTGGGA 59.646 52.381 0.00 0.00 32.73 4.37


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

AutoCloner maintained by Alex Coulton.