Multiple sequence alignment - TraesCS3D01G405000

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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 TraesCS3D01G405000 chr3D 100.000 4311 0 0 1 4311 519596206 519600516 0.000000e+00 7962
1 TraesCS3D01G405000 chr3D 86.221 3469 395 50 502 3943 519644709 519641297 0.000000e+00 3681
2 TraesCS3D01G405000 chr3D 89.515 1030 96 12 2232 3258 519620583 519621603 0.000000e+00 1293
3 TraesCS3D01G405000 chr3D 87.952 498 52 8 1 494 582629054 582628561 8.040000e-162 580
4 TraesCS3D01G405000 chr3A 95.890 3771 142 13 4 3765 654517491 654521257 0.000000e+00 6093
5 TraesCS3D01G405000 chr3A 95.327 2846 123 8 266 3107 654498908 654501747 0.000000e+00 4510
6 TraesCS3D01G405000 chr3A 85.573 3840 443 68 497 4298 654585148 654581382 0.000000e+00 3919
7 TraesCS3D01G405000 chr3A 95.126 1190 48 4 3129 4311 654501739 654502925 0.000000e+00 1868
8 TraesCS3D01G405000 chr3A 96.043 556 16 2 3761 4311 654541333 654541887 0.000000e+00 900
9 TraesCS3D01G405000 chr3A 90.437 481 41 5 2236 2714 654559975 654560452 2.830000e-176 628
10 TraesCS3D01G405000 chrUn 92.634 3842 250 22 497 4311 101062265 101066100 0.000000e+00 5496
11 TraesCS3D01G405000 chr3B 93.419 3723 195 25 153 3850 684137576 684133879 0.000000e+00 5472
12 TraesCS3D01G405000 chr3B 92.308 429 27 6 3888 4311 684133879 684133452 4.770000e-169 604
13 TraesCS3D01G405000 chr6A 92.678 3155 184 28 500 3612 35564038 35560889 0.000000e+00 4503
14 TraesCS3D01G405000 chr6A 87.349 498 56 6 7 500 568500578 568500084 8.090000e-157 564
15 TraesCS3D01G405000 chr7D 73.537 1931 441 54 1041 2932 612711787 612713686 0.000000e+00 671
16 TraesCS3D01G405000 chr7B 73.889 1597 353 46 1382 2943 702196546 702194979 8.040000e-162 580
17 TraesCS3D01G405000 chr5A 87.550 498 54 8 1 494 680906544 680906051 1.740000e-158 569
18 TraesCS3D01G405000 chr5A 87.550 498 52 9 1 494 613393721 613394212 6.260000e-158 568
19 TraesCS3D01G405000 chr1B 87.550 498 53 8 1 494 144924758 144925250 6.260000e-158 568
20 TraesCS3D01G405000 chr2B 87.627 493 54 7 7 495 733462335 733461846 2.250000e-157 566
21 TraesCS3D01G405000 chr6B 87.375 499 54 8 1 494 68733595 68734089 8.090000e-157 564


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 TraesCS3D01G405000 chr3D 519596206 519600516 4310 False 7962 7962 100.0000 1 4311 1 chr3D.!!$F1 4310
1 TraesCS3D01G405000 chr3D 519641297 519644709 3412 True 3681 3681 86.2210 502 3943 1 chr3D.!!$R1 3441
2 TraesCS3D01G405000 chr3D 519620583 519621603 1020 False 1293 1293 89.5150 2232 3258 1 chr3D.!!$F2 1026
3 TraesCS3D01G405000 chr3A 654517491 654521257 3766 False 6093 6093 95.8900 4 3765 1 chr3A.!!$F1 3761
4 TraesCS3D01G405000 chr3A 654581382 654585148 3766 True 3919 3919 85.5730 497 4298 1 chr3A.!!$R1 3801
5 TraesCS3D01G405000 chr3A 654498908 654502925 4017 False 3189 4510 95.2265 266 4311 2 chr3A.!!$F4 4045
6 TraesCS3D01G405000 chr3A 654541333 654541887 554 False 900 900 96.0430 3761 4311 1 chr3A.!!$F2 550
7 TraesCS3D01G405000 chrUn 101062265 101066100 3835 False 5496 5496 92.6340 497 4311 1 chrUn.!!$F1 3814
8 TraesCS3D01G405000 chr3B 684133452 684137576 4124 True 3038 5472 92.8635 153 4311 2 chr3B.!!$R1 4158
9 TraesCS3D01G405000 chr6A 35560889 35564038 3149 True 4503 4503 92.6780 500 3612 1 chr6A.!!$R1 3112
10 TraesCS3D01G405000 chr7D 612711787 612713686 1899 False 671 671 73.5370 1041 2932 1 chr7D.!!$F1 1891
11 TraesCS3D01G405000 chr7B 702194979 702196546 1567 True 580 580 73.8890 1382 2943 1 chr7B.!!$R1 1561

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
354 356 0.250793 CGGGGTGTGGTATTGTAGCA 59.749 55.0 0.00 0.0 0.00 3.49 F
978 1034 0.614979 CTCTCTTTGGAGGGGGACGA 60.615 60.0 0.00 0.0 39.86 4.20 F
979 1035 0.903454 TCTCTTTGGAGGGGGACGAC 60.903 60.0 0.00 0.0 39.86 4.34 F
1738 1803 0.958091 TTCGGTCTTGGCACCAATTG 59.042 50.0 1.86 0.0 36.01 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1250 0.109272 GTGCTGGTTCGATCGAGTCA 60.109 55.000 18.54 17.86 0.00 3.41 R
2406 2477 0.178950 TGAGACCTCCTGTGTGAGCT 60.179 55.000 0.00 0.00 0.00 4.09 R
2709 2788 4.278170 CACACAAATGCCGTGGGATTATAT 59.722 41.667 6.04 0.00 40.35 0.86 R
3337 3439 2.715749 TCTTGTCGATGGGCAATGAT 57.284 45.000 0.00 0.00 0.00 2.45 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
28 29 1.219393 GTCTGGGAGTAGCAGTGGC 59.781 63.158 0.00 0.00 41.61 5.01
42 43 0.604780 AGTGGCGCTCATGGCATATC 60.605 55.000 7.64 0.00 46.76 1.63
67 68 6.640518 TCAAGTCTAATGTACATGGAGGTTC 58.359 40.000 9.63 5.28 0.00 3.62
75 76 0.821517 ACATGGAGGTTCGACGCATA 59.178 50.000 0.00 0.00 0.00 3.14
132 133 5.531287 AGGTGGAGTTTGTTAGAATTGTGTC 59.469 40.000 0.00 0.00 0.00 3.67
256 257 7.147811 GGCCTCTTATATACTAATGAGAGGGTG 60.148 44.444 20.28 3.93 46.55 4.61
354 356 0.250793 CGGGGTGTGGTATTGTAGCA 59.749 55.000 0.00 0.00 0.00 3.49
365 367 3.370527 GGTATTGTAGCAGTGTCATGGGT 60.371 47.826 0.00 0.00 0.00 4.51
372 374 0.904649 CAGTGTCATGGGTAGGAGCA 59.095 55.000 0.00 0.00 0.00 4.26
420 424 9.498176 GTATCCATATTGGGTAAACTCGTTAAT 57.502 33.333 0.00 0.00 34.34 1.40
449 453 3.125658 CGATGTCATGCTTGTGTGATTGA 59.874 43.478 0.00 0.00 0.00 2.57
925 974 2.284699 CCTCTCCCCGGTGTCCTT 60.285 66.667 0.00 0.00 0.00 3.36
933 982 1.109609 CCCGGTGTCCTTACCTCTAC 58.890 60.000 0.00 0.00 38.62 2.59
978 1034 0.614979 CTCTCTTTGGAGGGGGACGA 60.615 60.000 0.00 0.00 39.86 4.20
979 1035 0.903454 TCTCTTTGGAGGGGGACGAC 60.903 60.000 0.00 0.00 39.86 4.34
1227 1283 2.107953 GCACTCCGCCAGATCTCC 59.892 66.667 0.00 0.00 32.94 3.71
1692 1754 7.147776 CCCATGCTTAAGAAATTGGAGATTCTT 60.148 37.037 6.67 6.10 45.29 2.52
1738 1803 0.958091 TTCGGTCTTGGCACCAATTG 59.042 50.000 1.86 0.00 36.01 2.32
1826 1892 2.197324 GTTGGGGTTGCAGGTGGA 59.803 61.111 0.00 0.00 0.00 4.02
1832 1898 1.682087 GGGGTTGCAGGTGGAAGATAC 60.682 57.143 0.00 0.00 0.00 2.24
2136 2205 3.866651 TCACTGCAGAAGCTTAAGATCC 58.133 45.455 23.35 0.00 42.74 3.36
2263 2334 2.291153 CCCAACAGATTGTCCCTGTGAT 60.291 50.000 0.00 0.00 43.42 3.06
2314 2385 4.588951 TCCTTGACTGCTCTTGAAGAAGTA 59.411 41.667 0.00 0.00 44.65 2.24
2315 2386 4.688413 CCTTGACTGCTCTTGAAGAAGTAC 59.312 45.833 0.00 0.00 44.65 2.73
2370 2441 8.617809 TGAGTTTGATTTACTGAAACAACTACC 58.382 33.333 0.00 0.00 32.96 3.18
2688 2767 5.938322 AGTTTACTTGTGCATGTATTTCCG 58.062 37.500 0.00 0.00 0.00 4.30
2874 2964 0.465460 TCAAGCCCTCGTGTTTTGCT 60.465 50.000 0.00 0.00 0.00 3.91
3319 3421 4.290711 ACCATCGGCATGATTATCATCA 57.709 40.909 4.51 0.00 43.85 3.07
3337 3439 9.571816 TTATCATCATCTTGCATATGTGGTTTA 57.428 29.630 4.29 0.00 0.00 2.01
3378 3480 6.051717 AGATCGTCCTTTCCATGTCAATTAG 58.948 40.000 0.00 0.00 0.00 1.73
3489 3592 7.133891 AGTTAATGTGTCAACTTATGTCAGC 57.866 36.000 0.00 0.00 30.89 4.26
3524 3627 5.247564 AGCTAGTTACTACATGTTTCCACCA 59.752 40.000 2.30 0.00 0.00 4.17
3675 3783 8.930760 GCATCTTCTGTTACTTAGCTAATATGG 58.069 37.037 6.64 0.00 0.00 2.74
3899 4022 1.916181 CCACCCTGACCAACTAGGATT 59.084 52.381 0.00 0.00 41.22 3.01
3901 4024 1.831736 ACCCTGACCAACTAGGATTCG 59.168 52.381 0.00 0.00 41.22 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.270907 ACTCCCAGACTCCACATGAC 58.729 55.000 0.00 0.00 0.00 3.06
1 2 2.739943 CTACTCCCAGACTCCACATGA 58.260 52.381 0.00 0.00 0.00 3.07
2 3 1.137872 GCTACTCCCAGACTCCACATG 59.862 57.143 0.00 0.00 0.00 3.21
8 9 0.820871 CCACTGCTACTCCCAGACTC 59.179 60.000 0.00 0.00 34.47 3.36
42 43 6.227298 ACCTCCATGTACATTAGACTTGAG 57.773 41.667 5.37 4.04 0.00 3.02
67 68 2.733552 CCTTGGATTCATCTATGCGTCG 59.266 50.000 0.00 0.00 0.00 5.12
75 76 2.776536 CTCCACCTCCTTGGATTCATCT 59.223 50.000 0.00 0.00 44.97 2.90
148 149 4.897076 TCAGAGTCCAACTGTAACCTAACA 59.103 41.667 0.00 0.00 36.81 2.41
154 155 2.689646 GGCTCAGAGTCCAACTGTAAC 58.310 52.381 0.00 0.00 36.81 2.50
256 257 2.124903 CATAGGTTACATCGTGCGTCC 58.875 52.381 0.00 0.00 0.00 4.79
329 331 4.966274 TACCACACCCCGGCCACT 62.966 66.667 2.24 0.00 0.00 4.00
331 333 2.936584 AATACCACACCCCGGCCA 60.937 61.111 2.24 0.00 0.00 5.36
354 356 0.905357 GTGCTCCTACCCATGACACT 59.095 55.000 0.00 0.00 0.00 3.55
365 367 0.395311 CCTGACTACGGGTGCTCCTA 60.395 60.000 4.53 0.00 37.74 2.94
404 408 6.543465 TCGAGATCTATTAACGAGTTTACCCA 59.457 38.462 0.00 0.00 0.00 4.51
420 424 4.098501 ACACAAGCATGACATCGAGATCTA 59.901 41.667 0.00 0.00 0.00 1.98
449 453 1.955080 GTCGATCTACCGAGGACCAAT 59.045 52.381 0.00 0.00 39.43 3.16
722 733 3.154827 TGACCCTGGAGATTTCAAACC 57.845 47.619 0.00 0.00 0.00 3.27
925 974 5.134725 AGGGACGGAATAAAGTAGAGGTA 57.865 43.478 0.00 0.00 0.00 3.08
933 982 1.134189 GGGTGGAGGGACGGAATAAAG 60.134 57.143 0.00 0.00 0.00 1.85
1194 1250 0.109272 GTGCTGGTTCGATCGAGTCA 60.109 55.000 18.54 17.86 0.00 3.41
1227 1283 0.322008 GGGAAACTGCAGGAGGACAG 60.322 60.000 19.93 0.00 39.86 3.51
1692 1754 3.495434 ACCTCCAACATCACGGTAAAA 57.505 42.857 0.00 0.00 0.00 1.52
1738 1803 2.567615 AGTACCACCAGACATTCTCCAC 59.432 50.000 0.00 0.00 0.00 4.02
1826 1892 3.910627 AGGGAGTTGTCCTTGTGTATCTT 59.089 43.478 0.00 0.00 43.36 2.40
1832 1898 2.654863 ACAAAGGGAGTTGTCCTTGTG 58.345 47.619 0.00 0.00 43.24 3.33
2370 2441 7.475771 TTTTTAAGCTTTGGTGCAAATACAG 57.524 32.000 3.20 0.00 32.70 2.74
2406 2477 0.178950 TGAGACCTCCTGTGTGAGCT 60.179 55.000 0.00 0.00 0.00 4.09
2620 2698 6.229733 CCACATTTCAACCACCATAAACATT 58.770 36.000 0.00 0.00 0.00 2.71
2709 2788 4.278170 CACACAAATGCCGTGGGATTATAT 59.722 41.667 6.04 0.00 40.35 0.86
3319 3421 7.149973 GCAATGATAAACCACATATGCAAGAT 58.850 34.615 1.58 0.00 34.32 2.40
3337 3439 2.715749 TCTTGTCGATGGGCAATGAT 57.284 45.000 0.00 0.00 0.00 2.45
3378 3480 9.559958 CTAGTAAAACAACATGTTGAATGGATC 57.440 33.333 38.30 22.19 40.14 3.36
3489 3592 9.847706 CATGTAGTAACTAGCTATAGTGATTGG 57.152 37.037 0.84 0.00 41.54 3.16
3899 4022 3.818787 GCGTCTAGGGTTCGCCGA 61.819 66.667 9.89 0.00 43.41 5.54


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

AutoCloner maintained by Alex Coulton.