Multiple sequence alignment - TraesCS6B01G164100

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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 TraesCS6B01G164100 chr6B 100.000 5479 0 0 1 5479 171443967 171449445 0.000000e+00 10118.0
1 TraesCS6B01G164100 chr6B 84.212 2711 331 54 1189 3888 129563063 129565687 0.000000e+00 2545.0
2 TraesCS6B01G164100 chr6B 86.019 1502 148 35 3128 4610 171394884 171396342 0.000000e+00 1554.0
3 TraesCS6B01G164100 chr6B 85.743 1501 152 37 3128 4610 171353585 171355041 0.000000e+00 1530.0
4 TraesCS6B01G164100 chr6B 86.689 586 54 11 1308 1888 171341564 171342130 3.600000e-176 628.0
5 TraesCS6B01G164100 chr6B 85.742 512 50 9 1308 1813 171385948 171386442 2.260000e-143 520.0
6 TraesCS6B01G164100 chr6B 86.250 480 37 13 4691 5144 171396358 171396834 1.370000e-135 494.0
7 TraesCS6B01G164100 chr6B 85.625 480 40 13 4691 5144 171355057 171355533 1.380000e-130 477.0
8 TraesCS6B01G164100 chr6B 86.337 344 37 7 5143 5476 171355693 171356036 3.120000e-97 366.0
9 TraesCS6B01G164100 chr6B 86.377 345 36 8 5143 5476 171396994 171397338 3.120000e-97 366.0
10 TraesCS6B01G164100 chr6B 86.425 221 27 2 619 836 171341347 171341567 7.090000e-59 239.0
11 TraesCS6B01G164100 chr6B 84.889 225 26 4 619 836 171385728 171385951 2.570000e-53 220.0
12 TraesCS6B01G164100 chr6B 91.935 62 3 1 4610 4669 418818349 418818410 9.780000e-13 86.1
13 TraesCS6B01G164100 chr6D 97.814 5489 101 14 1 5479 89237473 89242952 0.000000e+00 9454.0
14 TraesCS6B01G164100 chr6D 86.580 2705 272 49 1933 4610 89201592 89204232 0.000000e+00 2900.0
15 TraesCS6B01G164100 chr6D 85.766 2213 285 22 1682 3888 57582363 57584551 0.000000e+00 2314.0
16 TraesCS6B01G164100 chr6D 84.766 1733 225 31 2153 3876 57586381 57584679 0.000000e+00 1701.0
17 TraesCS6B01G164100 chr6D 87.586 580 48 12 1308 1881 89200955 89201516 0.000000e+00 651.0
18 TraesCS6B01G164100 chr6D 85.256 468 48 13 4691 5144 89204248 89204708 3.870000e-126 462.0
19 TraesCS6B01G164100 chr6D 86.603 418 51 5 1189 1605 57579432 57579845 1.800000e-124 457.0
20 TraesCS6B01G164100 chr6D 79.123 479 51 17 388 836 89200499 89200958 8.980000e-73 285.0
21 TraesCS6B01G164100 chr2D 84.225 2859 362 55 1189 4040 360991927 360989151 0.000000e+00 2699.0
22 TraesCS6B01G164100 chr2D 85.514 1850 246 16 2158 4001 360987318 360989151 0.000000e+00 1912.0
23 TraesCS6B01G164100 chr2D 84.392 1858 245 27 2150 4001 360788060 360789878 0.000000e+00 1783.0
24 TraesCS6B01G164100 chr2D 85.841 1356 156 19 1189 2542 360737699 360736378 0.000000e+00 1408.0
25 TraesCS6B01G164100 chr2D 85.342 1228 159 17 2150 3373 360723019 360724229 0.000000e+00 1251.0
26 TraesCS6B01G164100 chr2D 84.722 720 92 10 484 1191 360930124 360929411 0.000000e+00 704.0
27 TraesCS6B01G164100 chr2D 84.254 724 95 12 482 1191 360738658 360737940 0.000000e+00 688.0
28 TraesCS6B01G164100 chr2D 85.448 591 68 8 1189 1779 360929171 360928599 2.820000e-167 599.0
29 TraesCS6B01G164100 chr2D 85.312 320 31 5 173 481 360993488 360993174 3.190000e-82 316.0
30 TraesCS6B01G164100 chr2D 84.000 325 33 8 173 486 360930835 360930519 1.490000e-75 294.0
31 TraesCS6B01G164100 chr2D 83.077 325 38 6 173 486 360739248 360738930 4.180000e-71 279.0
32 TraesCS6B01G164100 chr2D 90.625 64 4 2 4611 4673 552995124 552995062 3.520000e-12 84.2
33 TraesCS6B01G164100 chr2B 83.852 2861 361 52 1189 4040 428791873 428794641 0.000000e+00 2630.0
34 TraesCS6B01G164100 chr2B 85.068 1259 170 15 2153 3407 428796670 428795426 0.000000e+00 1267.0
35 TraesCS6B01G164100 chr2B 83.986 587 75 8 620 1191 428791050 428791632 3.730000e-151 545.0
36 TraesCS6B01G164100 chr2B 84.989 453 55 7 173 617 428785649 428786096 1.080000e-121 448.0
37 TraesCS6B01G164100 chr2B 89.855 69 4 2 4601 4669 695378455 695378390 9.780000e-13 86.1
38 TraesCS6B01G164100 chr2B 90.323 62 6 0 4608 4669 516729545 516729484 1.260000e-11 82.4
39 TraesCS6B01G164100 chr6A 86.239 654 69 15 3574 4216 107360907 107361550 0.000000e+00 689.0
40 TraesCS6B01G164100 chr6A 85.928 334 40 6 4282 4610 107361553 107361884 3.140000e-92 350.0
41 TraesCS6B01G164100 chr6A 80.913 482 34 17 4691 5144 107361900 107362351 1.470000e-85 327.0
42 TraesCS6B01G164100 chrUn 88.000 200 21 2 5143 5339 480504950 480505149 3.300000e-57 233.0
43 TraesCS6B01G164100 chr1D 88.732 71 6 2 4609 4679 37558011 37557943 9.780000e-13 86.1
44 TraesCS6B01G164100 chr1A 91.667 60 5 0 4610 4669 363454210 363454151 3.520000e-12 84.2
45 TraesCS6B01G164100 chr5B 91.803 61 2 2 4590 4650 271112791 271112848 1.260000e-11 82.4
46 TraesCS6B01G164100 chr3D 87.179 78 3 3 4603 4674 511352748 511352824 1.260000e-11 82.4


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 TraesCS6B01G164100 chr6B 171443967 171449445 5478 False 10118.000000 10118 100.000000 1 5479 1 chr6B.!!$F2 5478
1 TraesCS6B01G164100 chr6B 129563063 129565687 2624 False 2545.000000 2545 84.212000 1189 3888 1 chr6B.!!$F1 2699
2 TraesCS6B01G164100 chr6B 171394884 171397338 2454 False 804.666667 1554 86.215333 3128 5476 3 chr6B.!!$F7 2348
3 TraesCS6B01G164100 chr6B 171353585 171356036 2451 False 791.000000 1530 85.901667 3128 5476 3 chr6B.!!$F5 2348
4 TraesCS6B01G164100 chr6B 171341347 171342130 783 False 433.500000 628 86.557000 619 1888 2 chr6B.!!$F4 1269
5 TraesCS6B01G164100 chr6B 171385728 171386442 714 False 370.000000 520 85.315500 619 1813 2 chr6B.!!$F6 1194
6 TraesCS6B01G164100 chr6D 89237473 89242952 5479 False 9454.000000 9454 97.814000 1 5479 1 chr6D.!!$F1 5478
7 TraesCS6B01G164100 chr6D 57584679 57586381 1702 True 1701.000000 1701 84.766000 2153 3876 1 chr6D.!!$R1 1723
8 TraesCS6B01G164100 chr6D 57579432 57584551 5119 False 1385.500000 2314 86.184500 1189 3888 2 chr6D.!!$F2 2699
9 TraesCS6B01G164100 chr6D 89200499 89204708 4209 False 1074.500000 2900 84.636250 388 5144 4 chr6D.!!$F3 4756
10 TraesCS6B01G164100 chr2D 360987318 360989151 1833 False 1912.000000 1912 85.514000 2158 4001 1 chr2D.!!$F3 1843
11 TraesCS6B01G164100 chr2D 360788060 360789878 1818 False 1783.000000 1783 84.392000 2150 4001 1 chr2D.!!$F2 1851
12 TraesCS6B01G164100 chr2D 360989151 360993488 4337 True 1507.500000 2699 84.768500 173 4040 2 chr2D.!!$R4 3867
13 TraesCS6B01G164100 chr2D 360723019 360724229 1210 False 1251.000000 1251 85.342000 2150 3373 1 chr2D.!!$F1 1223
14 TraesCS6B01G164100 chr2D 360736378 360739248 2870 True 791.666667 1408 84.390667 173 2542 3 chr2D.!!$R2 2369
15 TraesCS6B01G164100 chr2D 360928599 360930835 2236 True 532.333333 704 84.723333 173 1779 3 chr2D.!!$R3 1606
16 TraesCS6B01G164100 chr2B 428791050 428794641 3591 False 1587.500000 2630 83.919000 620 4040 2 chr2B.!!$F2 3420
17 TraesCS6B01G164100 chr2B 428795426 428796670 1244 True 1267.000000 1267 85.068000 2153 3407 1 chr2B.!!$R1 1254
18 TraesCS6B01G164100 chr6A 107360907 107362351 1444 False 455.333333 689 84.360000 3574 5144 3 chr6A.!!$F1 1570

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
747 1227 0.517316 GTTCATTCCACTGTCACCGC 59.483 55.000 0.00 0.0 0.00 5.68 F
1165 1820 0.547471 TCCTGCATCTTCTCCCCACA 60.547 55.000 0.00 0.0 0.00 4.17 F
1330 2068 1.066303 CGAGAGCCGCTCAGTAAATCT 59.934 52.381 22.29 0.0 44.15 2.40 F
1654 4854 1.604604 TTCTTCAAAAGCCCCGACAG 58.395 50.000 0.00 0.0 0.00 3.51 F
2858 6122 2.542020 TGTCTGAGAATGTTGCCGAA 57.458 45.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2430 5666 1.734137 CCTCATGGCAAGCATCAGC 59.266 57.895 0.00 0.00 42.56 4.26 R
2573 5813 2.005451 GCATCATTGCTCTCAGTTCGT 58.995 47.619 0.00 0.00 45.77 3.85 R
3174 6445 4.222124 ACAACTGAAGACACCTCTTTGT 57.778 40.909 0.00 0.00 36.82 2.83 R
3243 6514 7.667557 AGCAGTTTGTGAGTATACTTACTTGA 58.332 34.615 23.63 10.71 38.81 3.02 R
4647 7960 2.946785 ACTCCCTCCGTCCTACATTAG 58.053 52.381 0.00 0.00 0.00 1.73 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
40 41 4.342862 ACTGCTGGTGGTGATGTATATC 57.657 45.455 0.00 0.00 0.00 1.63
68 69 4.769488 TCAGTTGTAGCAATATTTTGGGCA 59.231 37.500 0.00 0.00 33.22 5.36
113 114 7.071321 GCACCATATACCTATAGGGCTTCTATT 59.929 40.741 22.91 1.68 42.30 1.73
114 115 8.424918 CACCATATACCTATAGGGCTTCTATTG 58.575 40.741 22.91 7.11 42.30 1.90
120 121 1.048601 TAGGGCTTCTATTGGAGGCG 58.951 55.000 3.00 0.00 46.30 5.52
144 147 1.989706 TTGCCCCAAGTGACCTAAAC 58.010 50.000 0.00 0.00 0.00 2.01
192 195 4.640771 TTTAGGACTGCTGTTGGAGATT 57.359 40.909 0.00 0.00 35.49 2.40
232 239 3.067106 ACCACAACATAAGAAGCACGAG 58.933 45.455 0.00 0.00 0.00 4.18
235 242 3.123621 CACAACATAAGAAGCACGAGACC 59.876 47.826 0.00 0.00 0.00 3.85
299 306 6.176183 CCACTCTGGTTCTGAATACTGAAAT 58.824 40.000 0.00 0.00 36.16 2.17
747 1227 0.517316 GTTCATTCCACTGTCACCGC 59.483 55.000 0.00 0.00 0.00 5.68
1165 1820 0.547471 TCCTGCATCTTCTCCCCACA 60.547 55.000 0.00 0.00 0.00 4.17
1330 2068 1.066303 CGAGAGCCGCTCAGTAAATCT 59.934 52.381 22.29 0.00 44.15 2.40
1377 2115 4.034163 GCCTAGGTATTTCTCTTCAAACGC 59.966 45.833 11.31 0.00 0.00 4.84
1654 4854 1.604604 TTCTTCAAAAGCCCCGACAG 58.395 50.000 0.00 0.00 0.00 3.51
2032 5262 2.958355 TCCTTTTCCTTTCCTGCTTGTG 59.042 45.455 0.00 0.00 0.00 3.33
2858 6122 2.542020 TGTCTGAGAATGTTGCCGAA 57.458 45.000 0.00 0.00 0.00 4.30
2861 6125 3.006430 TGTCTGAGAATGTTGCCGAACTA 59.994 43.478 0.00 0.00 32.79 2.24
3017 6287 5.182950 TCTGGCACCAAACTTGTTATATGTG 59.817 40.000 0.00 0.00 0.00 3.21
3174 6445 5.854010 ACTCTCAGACACTTAACTCAACA 57.146 39.130 0.00 0.00 0.00 3.33
3242 6513 6.012658 TGTCTGTCATAGAAAATGGCAAAC 57.987 37.500 0.00 0.00 37.12 2.93
3243 6514 5.769662 TGTCTGTCATAGAAAATGGCAAACT 59.230 36.000 0.00 0.00 37.12 2.66
3244 6515 6.072508 TGTCTGTCATAGAAAATGGCAAACTC 60.073 38.462 0.00 0.00 37.12 3.01
3807 7094 6.422776 ACGATGACATGACTAAAACAATCC 57.577 37.500 0.00 0.00 0.00 3.01
4203 7509 8.378172 TCTTCTAAAATGTTTCGATTGAGTGT 57.622 30.769 0.00 0.00 0.00 3.55
4647 7960 2.766970 TGTAAGACGCTTTTTGGCAC 57.233 45.000 0.00 0.00 0.00 5.01
4698 8011 1.942776 AGGGGGAGCAAAATGAAAGG 58.057 50.000 0.00 0.00 0.00 3.11
4849 8188 5.467705 GCATATCTCCAAATTCTGAATGGC 58.532 41.667 3.22 0.00 34.13 4.40
4922 8263 3.009916 GCATCCCAGGACAATCTCCATAT 59.990 47.826 0.00 0.00 42.46 1.78
4983 8324 8.910944 TGTATCTTCATAACCAGAAGTACCTAC 58.089 37.037 0.00 0.00 42.35 3.18
5197 8701 6.291377 TGCTTGAGTCTACAAACAATCTTCT 58.709 36.000 0.00 0.00 0.00 2.85
5319 8825 6.878317 TGTCCTTACTATTCTGATCAACCAG 58.122 40.000 0.00 0.00 35.55 4.00
5469 8983 4.889409 ACTCAAGGAATTTCTGAAGCAACA 59.111 37.500 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.474427 CCAAAATATTGCTACAACTGATGCAG 59.526 38.462 0.00 0.00 36.75 4.41
217 224 1.736032 GCGGTCTCGTGCTTCTTATGT 60.736 52.381 0.00 0.00 38.89 2.29
235 242 3.713205 ATCAGACCTGAGCAGCGCG 62.713 63.158 0.00 0.00 43.61 6.86
299 306 4.866508 GGACATTCCCGATGAGTATGTA 57.133 45.455 0.00 0.00 39.15 2.29
747 1227 1.004918 GTGGTCTCCTGTTGTCGGG 60.005 63.158 0.00 0.00 41.27 5.14
1193 1930 3.655777 AGTTCCCTCAAGTTCCCATAACA 59.344 43.478 0.00 0.00 0.00 2.41
1330 2068 7.147915 GGCAATACTCCAACCTATCAATGAAAA 60.148 37.037 0.00 0.00 0.00 2.29
1349 2087 8.613482 GTTTGAAGAGAAATACCTAGGCAATAC 58.387 37.037 9.30 0.00 0.00 1.89
1377 2115 0.320374 TCCACACTAGGAAAGGTGCG 59.680 55.000 0.00 0.00 36.99 5.34
1654 4854 6.864360 ATCAGCTTCTTTTAGCAGATGATC 57.136 37.500 2.09 0.00 43.21 2.92
2430 5666 1.734137 CCTCATGGCAAGCATCAGC 59.266 57.895 0.00 0.00 42.56 4.26
2573 5813 2.005451 GCATCATTGCTCTCAGTTCGT 58.995 47.619 0.00 0.00 45.77 3.85
3174 6445 4.222124 ACAACTGAAGACACCTCTTTGT 57.778 40.909 0.00 0.00 36.82 2.83
3242 6513 7.815068 AGCAGTTTGTGAGTATACTTACTTGAG 59.185 37.037 23.63 13.30 38.81 3.02
3243 6514 7.667557 AGCAGTTTGTGAGTATACTTACTTGA 58.332 34.615 23.63 10.71 38.81 3.02
3244 6515 7.891183 AGCAGTTTGTGAGTATACTTACTTG 57.109 36.000 23.63 17.55 38.81 3.16
3807 7094 5.344743 TTGTTAGCAGTATCTCCTCCTTG 57.655 43.478 0.00 0.00 0.00 3.61
4168 7474 7.432252 CGAAACATTTTAGAAGATATTGGTGGC 59.568 37.037 0.00 0.00 0.00 5.01
4647 7960 2.946785 ACTCCCTCCGTCCTACATTAG 58.053 52.381 0.00 0.00 0.00 1.73
4698 8011 7.916914 TTATCAGTAGGCCTTTTGTAGTTTC 57.083 36.000 12.58 0.00 0.00 2.78
4849 8188 6.232581 AGATATTCAGAAACTCCAGTCCAG 57.767 41.667 0.00 0.00 0.00 3.86
4922 8263 8.713971 TCTTGAGGATCTACCAAATGCTATTAA 58.286 33.333 0.00 0.00 42.04 1.40
4983 8324 5.312079 ACACTCTCATTCCTGGAAGAAAAG 58.688 41.667 15.34 11.60 34.07 2.27
5319 8825 7.074653 TCATAAGTCCCAAGTATAATCCCAC 57.925 40.000 0.00 0.00 0.00 4.61
5439 8953 8.730680 GCTTCAGAAATTCCTTGAGTTACATTA 58.269 33.333 0.00 0.00 0.00 1.90
5451 8965 3.225104 TGCTGTTGCTTCAGAAATTCCT 58.775 40.909 11.67 0.00 40.48 3.36


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

AutoCloner maintained by Alex Coulton.