Multiple sequence alignment - TraesCS6D01G156200

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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 TraesCS6D01G156200 chr6D 100.000 6222 0 0 1 6222 132314569 132308348 0.000000e+00 11490.0
1 TraesCS6D01G156200 chr6D 98.169 2950 31 5 2358 5285 132413291 132410343 0.000000e+00 5127.0
2 TraesCS6D01G156200 chr6D 98.108 2061 29 3 1 2061 132415343 132413293 0.000000e+00 3581.0
3 TraesCS6D01G156200 chr6D 86.905 336 30 9 5644 5973 87083312 87083639 1.270000e-96 364.0
4 TraesCS6D01G156200 chr6D 87.227 321 34 4 5317 5634 87082946 87083262 5.930000e-95 359.0
5 TraesCS6D01G156200 chr6A 97.458 5310 98 12 1 5285 171461696 171456399 0.000000e+00 9023.0
6 TraesCS6D01G156200 chr6B 94.785 3030 115 14 606 3611 229729812 229726802 0.000000e+00 4680.0
7 TraesCS6D01G156200 chr6B 90.248 1610 99 26 3701 5272 229726803 229725214 0.000000e+00 2050.0
8 TraesCS6D01G156200 chr6B 93.475 613 27 7 1 608 229730438 229729834 0.000000e+00 898.0
9 TraesCS6D01G156200 chr2A 94.073 793 21 2 5285 6051 734964136 734964928 0.000000e+00 1181.0
10 TraesCS6D01G156200 chr2A 95.954 173 7 0 6047 6219 734966534 734966706 1.320000e-71 281.0
11 TraesCS6D01G156200 chr2A 81.273 267 30 14 2167 2423 386294347 386294603 1.370000e-46 198.0
12 TraesCS6D01G156200 chr5D 81.888 519 53 16 5644 6127 548285101 548284589 3.490000e-107 399.0
13 TraesCS6D01G156200 chr5D 85.890 326 32 6 5320 5634 548285473 548285151 9.990000e-88 335.0
14 TraesCS6D01G156200 chr5D 78.058 515 96 15 1156 1658 74090878 74090369 6.060000e-80 309.0
15 TraesCS6D01G156200 chr5D 80.385 260 44 7 2167 2420 315936231 315935973 2.290000e-44 191.0
16 TraesCS6D01G156200 chr5D 87.500 64 5 1 5660 5720 444310011 444309948 3.110000e-08 71.3
17 TraesCS6D01G156200 chr5B 81.801 522 49 20 5644 6127 594278964 594279477 4.520000e-106 396.0
18 TraesCS6D01G156200 chr5B 86.018 329 33 5 5317 5634 594278588 594278914 2.150000e-89 340.0
19 TraesCS6D01G156200 chr5B 78.860 421 79 8 1154 1571 78420696 78421109 6.140000e-70 276.0
20 TraesCS6D01G156200 chr1B 88.024 334 32 6 5645 5973 470894632 470894302 7.560000e-104 388.0
21 TraesCS6D01G156200 chr1B 86.025 322 39 5 5317 5634 470895008 470894689 2.150000e-89 340.0
22 TraesCS6D01G156200 chr1B 80.303 264 43 7 2169 2426 104349882 104349622 2.290000e-44 191.0
23 TraesCS6D01G156200 chr7A 87.574 338 31 8 5645 5973 672011539 672011874 1.270000e-101 381.0
24 TraesCS6D01G156200 chr7A 84.161 322 45 4 5317 5634 672011163 672011482 2.180000e-79 307.0
25 TraesCS6D01G156200 chr7A 84.112 107 15 2 2167 2271 700824169 700824063 1.100000e-17 102.0
26 TraesCS6D01G156200 chr4A 85.119 336 40 7 5644 5973 352129989 352129658 9.990000e-88 335.0
27 TraesCS6D01G156200 chr4A 89.205 176 16 2 5462 5634 352130214 352130039 3.780000e-52 217.0
28 TraesCS6D01G156200 chr4A 77.703 296 55 11 213 505 516487625 516487912 2.980000e-38 171.0
29 TraesCS6D01G156200 chr5A 76.693 502 104 11 1154 1648 69103998 69103503 3.700000e-67 267.0
30 TraesCS6D01G156200 chr4D 84.351 262 35 4 2167 2422 301756303 301756564 1.040000e-62 252.0
31 TraesCS6D01G156200 chr4D 75.974 308 58 15 212 512 67358128 67357830 1.810000e-30 145.0
32 TraesCS6D01G156200 chr4B 82.061 262 41 4 2167 2422 376157709 376157970 1.050000e-52 219.0
33 TraesCS6D01G156200 chr4B 77.104 297 53 14 213 501 99430382 99430671 2.320000e-34 158.0
34 TraesCS6D01G156200 chr4B 84.892 139 13 6 2168 2301 93286449 93286314 3.910000e-27 134.0
35 TraesCS6D01G156200 chr7B 91.262 103 9 0 5524 5626 641101276 641101174 2.340000e-29 141.0
36 TraesCS6D01G156200 chr7B 91.398 93 7 1 6130 6222 503117734 503117825 6.550000e-25 126.0
37 TraesCS6D01G156200 chr2D 92.000 100 8 0 5524 5623 191027678 191027777 2.340000e-29 141.0
38 TraesCS6D01G156200 chr2D 85.000 120 11 4 4877 4995 166197115 166197228 1.420000e-21 115.0
39 TraesCS6D01G156200 chr3D 84.286 140 20 2 2284 2422 159794640 159794502 1.090000e-27 135.0
40 TraesCS6D01G156200 chr1D 80.645 155 25 4 2258 2408 404253054 404253207 1.420000e-21 115.0
41 TraesCS6D01G156200 chr1D 76.437 174 33 7 2255 2422 478140149 478140320 3.090000e-13 87.9


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 TraesCS6D01G156200 chr6D 132308348 132314569 6221 True 11490.000000 11490 100.0000 1 6222 1 chr6D.!!$R1 6221
1 TraesCS6D01G156200 chr6D 132410343 132415343 5000 True 4354.000000 5127 98.1385 1 5285 2 chr6D.!!$R2 5284
2 TraesCS6D01G156200 chr6D 87082946 87083639 693 False 361.500000 364 87.0660 5317 5973 2 chr6D.!!$F1 656
3 TraesCS6D01G156200 chr6A 171456399 171461696 5297 True 9023.000000 9023 97.4580 1 5285 1 chr6A.!!$R1 5284
4 TraesCS6D01G156200 chr6B 229725214 229730438 5224 True 2542.666667 4680 92.8360 1 5272 3 chr6B.!!$R1 5271
5 TraesCS6D01G156200 chr2A 734964136 734966706 2570 False 731.000000 1181 95.0135 5285 6219 2 chr2A.!!$F2 934
6 TraesCS6D01G156200 chr5D 548284589 548285473 884 True 367.000000 399 83.8890 5320 6127 2 chr5D.!!$R4 807
7 TraesCS6D01G156200 chr5D 74090369 74090878 509 True 309.000000 309 78.0580 1156 1658 1 chr5D.!!$R1 502
8 TraesCS6D01G156200 chr5B 594278588 594279477 889 False 368.000000 396 83.9095 5317 6127 2 chr5B.!!$F2 810
9 TraesCS6D01G156200 chr1B 470894302 470895008 706 True 364.000000 388 87.0245 5317 5973 2 chr1B.!!$R2 656
10 TraesCS6D01G156200 chr7A 672011163 672011874 711 False 344.000000 381 85.8675 5317 5973 2 chr7A.!!$F1 656
11 TraesCS6D01G156200 chr4A 352129658 352130214 556 True 276.000000 335 87.1620 5462 5973 2 chr4A.!!$R1 511


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
258 264 2.698797 TCAAAGGAGTTTGACCTCGTCT 59.301 45.455 0.00 0.0 45.82 4.18 F
449 455 6.771267 TCGTATCTCCACACTACAATCTGTAT 59.229 38.462 0.00 0.0 31.66 2.29 F
1538 1578 4.074970 AGGACTTGCTACAAGATTGTTGG 58.925 43.478 13.94 0.0 42.35 3.77 F
1756 1802 0.673644 AACTCGCAATCTGGGGTTCG 60.674 55.000 0.00 0.0 0.00 3.95 F
3086 3137 0.811281 GTGCTGTAACCCATGCTTCC 59.189 55.000 0.00 0.0 0.00 3.46 F
3207 3258 1.202879 AGACTCGATGGCCACCAAAAA 60.203 47.619 8.16 0.0 36.95 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1578 0.107017 ACATACCATGTGAGCAGGCC 60.107 55.000 0.0 0.0 43.01 5.19 R
1756 1802 4.781934 ACCCAGAAATACTATGGCAACTC 58.218 43.478 0.0 0.0 32.46 3.01 R
3344 3395 0.177373 GTACAAGGCCCTAACCTCCG 59.823 60.000 0.0 0.0 39.93 4.63 R
3417 3484 2.158460 TCACACCAGACCTTCTCTCTGA 60.158 50.000 0.0 0.0 37.90 3.27 R
4658 4727 2.400399 CTGCTGCACACATTTTCCAAG 58.600 47.619 0.0 0.0 0.00 3.61 R
5238 5350 9.495754 GCTATCAATTCACTGACATTTTTCTAC 57.504 33.333 0.0 0.0 0.00 2.59 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
166 168 7.413328 GGGCATTGAAGTTAAAATGAATTGAGC 60.413 37.037 12.71 0.00 36.13 4.26
258 264 2.698797 TCAAAGGAGTTTGACCTCGTCT 59.301 45.455 0.00 0.00 45.82 4.18
449 455 6.771267 TCGTATCTCCACACTACAATCTGTAT 59.229 38.462 0.00 0.00 31.66 2.29
1498 1538 8.665643 TCACTTGAAAATTGCAGATGATTTTT 57.334 26.923 7.95 0.49 36.04 1.94
1538 1578 4.074970 AGGACTTGCTACAAGATTGTTGG 58.925 43.478 13.94 0.00 42.35 3.77
1756 1802 0.673644 AACTCGCAATCTGGGGTTCG 60.674 55.000 0.00 0.00 0.00 3.95
2067 2115 4.840911 CATGACAATACACATGTAGCTGC 58.159 43.478 0.00 0.00 38.98 5.25
3086 3137 0.811281 GTGCTGTAACCCATGCTTCC 59.189 55.000 0.00 0.00 0.00 3.46
3199 3250 1.604185 GCATACTGAGACTCGATGGCC 60.604 57.143 0.00 0.00 0.00 5.36
3207 3258 1.202879 AGACTCGATGGCCACCAAAAA 60.203 47.619 8.16 0.00 36.95 1.94
3414 3481 1.694150 TCTGCTGGATCGATAAAGGGG 59.306 52.381 0.00 0.00 0.00 4.79
3417 3484 1.630878 GCTGGATCGATAAAGGGGGAT 59.369 52.381 0.00 0.00 0.00 3.85
3743 3810 2.617274 GCAGTGTCCGCACCCTTTC 61.617 63.158 0.00 0.00 46.35 2.62
3778 3845 4.640201 TCTTTCACAACTTCTTGGTCTTGG 59.360 41.667 0.00 0.00 0.00 3.61
4182 4251 9.230122 TCAGTCAAAATATAAGCATCTGTTTCA 57.770 29.630 0.00 0.00 0.00 2.69
4658 4727 5.277857 TGAGCCTACTATTAAGGAAGCAC 57.722 43.478 0.00 0.00 36.08 4.40
5088 5183 7.844482 TGTCGTTAGTAGAAAAGCAAACTAAC 58.156 34.615 12.12 12.12 45.49 2.34
5238 5350 5.739752 TCAGAGTCATTGAGTGTTTGTTG 57.260 39.130 0.00 0.00 0.00 3.33
5287 5399 5.065346 GCAACTAAAGCATTCTCCTCTTACC 59.935 44.000 0.00 0.00 0.00 2.85
5292 5404 5.559148 AAGCATTCTCCTCTTACCCATAG 57.441 43.478 0.00 0.00 0.00 2.23
5298 5410 7.256332 GCATTCTCCTCTTACCCATAGTGAATA 60.256 40.741 0.00 0.00 0.00 1.75
5300 5412 7.841282 TCTCCTCTTACCCATAGTGAATAAG 57.159 40.000 0.00 0.00 0.00 1.73
5402 5523 4.171005 CAATGTTTCTGCTGCATGTAAGG 58.829 43.478 1.31 0.00 0.00 2.69
5441 5562 7.213178 ACTAACCCTTGTTTGGAGATGATAT 57.787 36.000 0.00 0.00 35.87 1.63
5726 5900 7.338710 AGTAATGGTATGATGCAGTTAACACT 58.661 34.615 8.61 0.00 0.00 3.55
5761 5937 3.330766 GTACAGGCGTACAGCTCAG 57.669 57.895 12.54 3.54 46.18 3.35
5922 6108 7.915293 ACAAATCGGACATACTTGTTGAATA 57.085 32.000 0.00 0.00 35.79 1.75
5944 6130 0.317020 TGTGATCTATCTGCGTCGCG 60.317 55.000 13.38 0.00 0.00 5.87
5999 6210 2.747460 GCGATGCTTGTGGCTGGA 60.747 61.111 0.00 0.00 42.39 3.86
6139 7968 9.232473 GTAGAAAGAAACCATCATTTCCTACTT 57.768 33.333 0.00 0.00 39.05 2.24
6179 8008 6.335777 TGACAGTCATCATCATGTCTTACAG 58.664 40.000 0.00 0.00 42.02 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 91 7.812191 TGTTCACTATAATTTCAATGCACCAAC 59.188 33.333 0.00 0.00 0.00 3.77
166 168 6.634837 CAGTTCAGTACATACGCATCTTCTAG 59.365 42.308 0.00 0.00 0.00 2.43
258 264 8.271458 TGATACAAATATGAAAGCCTCCACTAA 58.729 33.333 0.00 0.00 0.00 2.24
562 568 1.132500 AAGCACTGATAGCTACCCCC 58.868 55.000 0.00 0.00 42.53 5.40
637 667 5.405935 AGGGCTTAAATCAAACCATTGTC 57.594 39.130 0.00 0.00 37.79 3.18
797 827 8.636213 CATTTTCCATATAAGCAGATCCACTTT 58.364 33.333 3.39 0.00 0.00 2.66
1376 1416 6.137794 AGATTAGATTCTTGTCGACGTGAT 57.862 37.500 11.62 2.17 0.00 3.06
1498 1538 2.170166 CCTGGCCTTGAACATGCTAAA 58.830 47.619 3.32 0.00 0.00 1.85
1538 1578 0.107017 ACATACCATGTGAGCAGGCC 60.107 55.000 0.00 0.00 43.01 5.19
1756 1802 4.781934 ACCCAGAAATACTATGGCAACTC 58.218 43.478 0.00 0.00 32.46 3.01
3086 3137 2.352805 GACTGCAGACCCCCTTGG 59.647 66.667 23.35 0.00 41.37 3.61
3207 3258 7.231467 TCCAGAACTGTCTATAAAGCCTTTTT 58.769 34.615 0.00 0.00 30.85 1.94
3288 3339 3.000727 GGTACTCAAAGGGTTGACATCG 58.999 50.000 0.00 0.00 38.88 3.84
3289 3340 3.344515 GGGTACTCAAAGGGTTGACATC 58.655 50.000 0.00 0.00 38.88 3.06
3344 3395 0.177373 GTACAAGGCCCTAACCTCCG 59.823 60.000 0.00 0.00 39.93 4.63
3414 3481 2.430332 CACCAGACCTTCTCTCTGATCC 59.570 54.545 0.00 0.00 37.90 3.36
3417 3484 2.158460 TCACACCAGACCTTCTCTCTGA 60.158 50.000 0.00 0.00 37.90 3.27
4658 4727 2.400399 CTGCTGCACACATTTTCCAAG 58.600 47.619 0.00 0.00 0.00 3.61
5238 5350 9.495754 GCTATCAATTCACTGACATTTTTCTAC 57.504 33.333 0.00 0.00 0.00 2.59
5287 5399 8.774586 GTGTGTTATTAGCCTTATTCACTATGG 58.225 37.037 0.00 0.00 0.00 2.74
5292 5404 9.326413 ACTATGTGTGTTATTAGCCTTATTCAC 57.674 33.333 0.00 0.00 0.00 3.18
5298 5410 6.062258 ACCACTATGTGTGTTATTAGCCTT 57.938 37.500 0.00 0.00 44.81 4.35
5300 5412 6.579865 ACTACCACTATGTGTGTTATTAGCC 58.420 40.000 0.00 0.00 44.81 3.93
5441 5562 8.733458 TGTTGTTTCGCTAATAGTTCTACTCTA 58.267 33.333 0.00 0.00 0.00 2.43
5459 5580 3.246619 TGCAGTTTTTCCGTGTTGTTTC 58.753 40.909 0.00 0.00 0.00 2.78
5638 5764 0.534412 CTGTAGGCTGGTGAGGTCTG 59.466 60.000 0.00 0.00 0.00 3.51
5726 5900 8.472413 ACGCCTGTACTTTAGAATGTAATCTTA 58.528 33.333 0.00 0.00 0.00 2.10
5922 6108 2.796383 GCGACGCAGATAGATCACACTT 60.796 50.000 16.42 0.00 0.00 3.16
5999 6210 3.309436 TATGTTCAGCACGCCGCCT 62.309 57.895 0.00 0.00 44.04 5.52
6179 8008 9.968743 GTACCTAATATGTTCGCTTAAATATGC 57.031 33.333 0.00 0.00 0.00 3.14



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

AutoCloner maintained by Alex Coulton.