Multiple sequence alignment - TraesCS1D01G348700

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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 TraesCS1D01G348700 chr1D 100.000 2174 0 0 1 2174 435293434 435295607 0.000000e+00 4015
1 TraesCS1D01G348700 chr1D 90.873 252 22 1 637 887 472906401 472906150 9.610000e-89 337
2 TraesCS1D01G348700 chr1D 86.066 122 15 1 1215 1336 472906148 472906029 1.750000e-26 130
3 TraesCS1D01G348700 chr1B 96.076 1988 69 5 1 1980 588515964 588517950 0.000000e+00 3230
4 TraesCS1D01G348700 chr1B 88.427 337 36 1 1 334 657406903 657406567 9.350000e-109 403
5 TraesCS1D01G348700 chr1B 95.477 199 7 1 1976 2174 588526300 588526496 1.250000e-82 316
6 TraesCS1D01G348700 chr1B 86.066 122 15 2 1215 1336 657406296 657406177 1.750000e-26 130
7 TraesCS1D01G348700 chr1A 94.006 1368 54 11 1 1358 532796652 532798001 0.000000e+00 2047
8 TraesCS1D01G348700 chr1A 94.545 495 16 2 1352 1836 532806763 532807256 0.000000e+00 754
9 TraesCS1D01G348700 chr1A 95.640 344 14 1 1831 2174 532807382 532807724 3.150000e-153 551
10 TraesCS1D01G348700 chr1A 89.021 337 34 1 1 334 566636832 566636496 4.320000e-112 414
11 TraesCS1D01G348700 chr7D 88.048 912 84 9 1 887 279741311 279740400 0.000000e+00 1057
12 TraesCS1D01G348700 chr7D 87.224 861 69 17 63 887 621644866 621644011 0.000000e+00 942
13 TraesCS1D01G348700 chr7D 85.446 213 24 5 1627 1836 279738693 279738485 4.700000e-52 215
14 TraesCS1D01G348700 chr7D 93.243 74 5 0 1836 1909 632655170 632655243 2.280000e-20 110
15 TraesCS1D01G348700 chr7B 88.048 912 84 10 1 887 253698738 253699649 0.000000e+00 1057
16 TraesCS1D01G348700 chr7B 90.780 564 46 4 326 887 718361506 718362065 0.000000e+00 749
17 TraesCS1D01G348700 chr7B 85.060 502 50 8 1336 1836 746275076 746274599 2.510000e-134 488
18 TraesCS1D01G348700 chr7B 85.060 502 50 11 1336 1836 746489893 746489416 2.510000e-134 488
19 TraesCS1D01G348700 chr7B 83.235 507 54 15 1333 1836 744662785 744663263 9.210000e-119 436
20 TraesCS1D01G348700 chr7B 85.915 213 23 5 1627 1836 253701796 253702004 1.010000e-53 220
21 TraesCS1D01G348700 chr7A 87.829 912 86 10 1 887 316021019 316021930 0.000000e+00 1046
22 TraesCS1D01G348700 chr7A 86.790 863 72 20 63 887 717086789 717085931 0.000000e+00 924
23 TraesCS1D01G348700 chr7A 79.890 363 42 16 1832 2169 717082916 717082560 1.000000e-58 237
24 TraesCS1D01G348700 chr5D 84.211 494 52 11 81 549 557181735 557182227 7.070000e-125 457
25 TraesCS1D01G348700 chr5D 89.726 146 14 1 1692 1836 557182827 557182972 3.690000e-43 185
26 TraesCS1D01G348700 chr5D 89.167 120 8 3 1836 1950 557183101 557183220 6.250000e-31 145
27 TraesCS1D01G348700 chrUn 90.634 331 23 4 893 1217 363863617 363863289 1.190000e-117 433
28 TraesCS1D01G348700 chrUn 89.021 337 20 5 893 1214 430358292 430358626 3.360000e-108 401
29 TraesCS1D01G348700 chrUn 87.647 340 25 7 893 1217 354743903 354743566 1.580000e-101 379
30 TraesCS1D01G348700 chr2D 90.663 332 21 5 893 1217 196967420 196967092 1.190000e-117 433
31 TraesCS1D01G348700 chr2D 90.634 331 23 4 893 1217 272805340 272805012 1.190000e-117 433
32 TraesCS1D01G348700 chr3D 88.529 340 22 5 893 1217 589253259 589252922 1.560000e-106 396
33 TraesCS1D01G348700 chr5B 88.415 328 29 5 893 1214 432873059 432873383 9.410000e-104 387
34 TraesCS1D01G348700 chr5B 88.933 253 26 2 1576 1826 709422560 709422308 5.830000e-81 311
35 TraesCS1D01G348700 chr5B 87.912 91 6 1 1368 1453 709422712 709422622 3.820000e-18 102
36 TraesCS1D01G348700 chr4A 90.043 231 22 1 1607 1836 605666452 605666682 4.540000e-77 298
37 TraesCS1D01G348700 chr4A 91.005 189 15 2 1360 1547 605666268 605666455 9.960000e-64 254
38 TraesCS1D01G348700 chr4A 82.143 252 24 7 1 252 605665451 605665681 1.700000e-46 196
39 TraesCS1D01G348700 chr4A 90.647 139 8 3 1836 1969 605666811 605666949 1.710000e-41 180


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 TraesCS1D01G348700 chr1D 435293434 435295607 2173 False 4015.000000 4015 100.000000 1 2174 1 chr1D.!!$F1 2173
1 TraesCS1D01G348700 chr1B 588515964 588517950 1986 False 3230.000000 3230 96.076000 1 1980 1 chr1B.!!$F1 1979
2 TraesCS1D01G348700 chr1B 657406177 657406903 726 True 266.500000 403 87.246500 1 1336 2 chr1B.!!$R1 1335
3 TraesCS1D01G348700 chr1A 532796652 532798001 1349 False 2047.000000 2047 94.006000 1 1358 1 chr1A.!!$F1 1357
4 TraesCS1D01G348700 chr1A 532806763 532807724 961 False 652.500000 754 95.092500 1352 2174 2 chr1A.!!$F2 822
5 TraesCS1D01G348700 chr7D 621644011 621644866 855 True 942.000000 942 87.224000 63 887 1 chr7D.!!$R1 824
6 TraesCS1D01G348700 chr7D 279738485 279741311 2826 True 636.000000 1057 86.747000 1 1836 2 chr7D.!!$R2 1835
7 TraesCS1D01G348700 chr7B 718361506 718362065 559 False 749.000000 749 90.780000 326 887 1 chr7B.!!$F1 561
8 TraesCS1D01G348700 chr7B 253698738 253702004 3266 False 638.500000 1057 86.981500 1 1836 2 chr7B.!!$F3 1835
9 TraesCS1D01G348700 chr7A 316021019 316021930 911 False 1046.000000 1046 87.829000 1 887 1 chr7A.!!$F1 886
10 TraesCS1D01G348700 chr7A 717082560 717086789 4229 True 580.500000 924 83.340000 63 2169 2 chr7A.!!$R1 2106
11 TraesCS1D01G348700 chr5D 557181735 557183220 1485 False 262.333333 457 87.701333 81 1950 3 chr5D.!!$F1 1869
12 TraesCS1D01G348700 chr4A 605665451 605666949 1498 False 232.000000 298 88.459500 1 1969 4 chr4A.!!$F1 1968

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
490 530 1.06909 GGCTGTGTCTGTGGAACGA 59.931 57.895 0.0 0.0 42.39 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1868 1.868713 TTCGGTGGCTTATACTCCCA 58.131 50.0 0.0 0.0 0.0 4.37 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
86 87 2.033299 GCTGCTGTTGACTTTGTTGCTA 59.967 45.455 0.00 0.00 0.00 3.49
97 98 4.310769 ACTTTGTTGCTACTGCTGTAGAG 58.689 43.478 28.86 19.29 46.76 2.43
260 264 4.832266 AGCACCATTCTGTTGACCAATTAA 59.168 37.500 0.00 0.00 0.00 1.40
301 305 1.446907 CTGCTGTCCCATCAACTGTC 58.553 55.000 0.00 0.00 0.00 3.51
440 480 7.475015 ACGGAACTCAATTGATTATGTTGATG 58.525 34.615 8.96 4.54 32.05 3.07
490 530 1.069090 GGCTGTGTCTGTGGAACGA 59.931 57.895 0.00 0.00 42.39 3.85
910 956 7.543947 TTGCAATGTGTGTATGAGATTAGAG 57.456 36.000 0.00 0.00 0.00 2.43
1021 1067 9.639601 GATTTATGGTTAAAGAAGAAAACAGGG 57.360 33.333 0.00 0.00 31.07 4.45
1083 1129 4.002906 ACGGAGACTTGCTTCACATTTA 57.997 40.909 0.00 0.00 0.00 1.40
1145 1194 4.128643 ACTTTTGGGAAAACGTCGACATA 58.871 39.130 17.16 0.00 0.00 2.29
1340 1645 6.681777 ACAAAATACATCTTGTGGAAAGCTC 58.318 36.000 0.00 0.00 34.52 4.09
1438 1749 5.990386 TGTTACTGTAACTTAATGGTCGCAA 59.010 36.000 25.91 3.91 39.38 4.85
1461 1772 4.102367 ACATTGCAAACTAACCCCAACATT 59.898 37.500 1.71 0.00 0.00 2.71
1551 1862 1.202879 CCATAAGCCGGCTAATGGGAA 60.203 52.381 33.07 9.74 36.12 3.97
1557 1868 1.474330 CCGGCTAATGGGAAAAGCTT 58.526 50.000 0.00 0.00 36.48 3.74
1593 1904 2.423538 CCGAAAGAACTGGCCCTTAATG 59.576 50.000 0.00 0.00 0.00 1.90
1688 4930 8.370266 TCAGTTTACTGTATATGGTACCTTGT 57.630 34.615 14.36 7.90 44.12 3.16
1857 5231 5.998454 AGCGATATGAACAGAAAATCCAG 57.002 39.130 0.00 0.00 0.00 3.86
2022 5402 2.130426 TGGCACACCGCAACCAAAT 61.130 52.632 0.00 0.00 45.17 2.32
2170 5571 5.105187 GGACTTGGGGTAGTACTATCGTTTT 60.105 44.000 5.75 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 2.163509 ACATGTCGACTCTACAGCAGT 58.836 47.619 17.92 0.00 0.00 4.40
97 98 1.728971 CTCTCAGGCAAACATGTCGAC 59.271 52.381 9.11 9.11 0.00 4.20
199 203 2.330216 ACAGAGGCTACCAGTCAAGTT 58.670 47.619 0.00 0.00 0.00 2.66
203 207 0.321671 GCAACAGAGGCTACCAGTCA 59.678 55.000 0.00 0.00 0.00 3.41
204 208 0.610687 AGCAACAGAGGCTACCAGTC 59.389 55.000 0.00 0.00 40.47 3.51
260 264 8.096414 AGCAGCCAAATTTACAATAAAATCAGT 58.904 29.630 0.00 0.00 0.00 3.41
269 273 3.055891 GGGACAGCAGCCAAATTTACAAT 60.056 43.478 0.00 0.00 0.00 2.71
301 305 5.728049 CGAATATTCTACAACAGCAACAACG 59.272 40.000 13.45 0.00 0.00 4.10
440 480 3.246619 CAGTCGGCTACTCAGAGTTTTC 58.753 50.000 8.80 0.00 35.76 2.29
490 530 1.852157 TTCACCCTGGGCAGTCCAT 60.852 57.895 14.08 0.00 46.01 3.41
806 846 3.679980 CACTAACATCGGACAGAACTTGG 59.320 47.826 0.00 0.00 0.00 3.61
1021 1067 8.352942 ACTGAATACTTGAAATTCAACAGAACC 58.647 33.333 21.96 6.39 41.50 3.62
1098 1144 3.937706 CGCAGACCTCTTTCTGATGATTT 59.062 43.478 4.29 0.00 45.19 2.17
1100 1146 2.762887 TCGCAGACCTCTTTCTGATGAT 59.237 45.455 4.29 0.00 45.19 2.45
1106 1155 1.917872 AGTCTCGCAGACCTCTTTCT 58.082 50.000 11.24 0.00 46.18 2.52
1145 1194 2.833338 TCTTTGCCAAATAAGCCAGCAT 59.167 40.909 0.00 0.00 32.67 3.79
1197 1246 9.023967 CAATTTCCTTCCGAATATTCAATTGAC 57.976 33.333 20.11 0.00 28.81 3.18
1263 1313 5.122554 GCTACCTTTTCTAAAACAGCTCCTC 59.877 44.000 0.00 0.00 0.00 3.71
1340 1645 3.607741 ACTCAAATGTGATCTGCCTCTG 58.392 45.455 0.00 0.00 31.85 3.35
1438 1749 3.034635 TGTTGGGGTTAGTTTGCAATGT 58.965 40.909 0.00 0.00 0.00 2.71
1461 1772 9.563748 AACAGTGCCTAAATGTAACTTAGTTTA 57.436 29.630 1.94 0.00 0.00 2.01
1482 1793 2.294074 TGTAAGCCGCAAAAGAACAGT 58.706 42.857 0.00 0.00 0.00 3.55
1551 1862 3.621558 GTGGCTTATACTCCCAAGCTTT 58.378 45.455 0.00 0.00 45.20 3.51
1557 1868 1.868713 TTCGGTGGCTTATACTCCCA 58.131 50.000 0.00 0.00 0.00 4.37
1688 4930 5.300539 TGATTCCAAATCAAAACAACTCCGA 59.699 36.000 0.00 0.00 0.00 4.55
1826 5069 6.060028 TCTGTTCATATCGCTAATTTTGCC 57.940 37.500 0.00 0.00 0.00 4.52
1829 5072 9.736023 GGATTTTCTGTTCATATCGCTAATTTT 57.264 29.630 0.00 0.00 0.00 1.82
1857 5231 4.142600 GGGCACACTGTCACTATTTTGATC 60.143 45.833 0.00 0.00 0.00 2.92
1909 5284 7.394016 TCATCATTTTGCCTAACTCAGTTCTA 58.606 34.615 0.00 0.00 0.00 2.10
2044 5424 4.322198 GGTTGAACGGTCTTCAGTATGGTA 60.322 45.833 0.33 0.00 36.16 3.25


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

AutoCloner maintained by Alex Coulton.