Multiple sequence alignment - TraesCS7D01G304100

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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 TraesCS7D01G304100 chr7D 100.000 3080 0 0 1 3080 385716975 385720054 0.000000e+00 5688
1 TraesCS7D01G304100 chr7A 93.570 2053 80 24 1 2040 433742219 433744232 0.000000e+00 3013
2 TraesCS7D01G304100 chr7A 88.722 133 14 1 2140 2271 433744938 433745070 8.840000e-36 161
3 TraesCS7D01G304100 chr7B 93.975 1776 66 14 500 2270 380079197 380080936 0.000000e+00 2649
4 TraesCS7D01G304100 chr7B 90.113 354 27 8 1 348 380076287 380076638 1.300000e-123 453
5 TraesCS7D01G304100 chr7B 89.796 147 14 1 336 482 380076657 380076802 1.460000e-43 187
6 TraesCS7D01G304100 chr1D 95.466 816 33 3 2267 3080 297519113 297519926 0.000000e+00 1299
7 TraesCS7D01G304100 chr6D 94.377 818 39 6 2267 3080 23775102 23775916 0.000000e+00 1249
8 TraesCS7D01G304100 chr6D 94.010 818 39 6 2266 3080 276128266 276127456 0.000000e+00 1230
9 TraesCS7D01G304100 chr5A 94.363 816 39 5 2269 3080 602360821 602360009 0.000000e+00 1245
10 TraesCS7D01G304100 chr3D 94.125 817 44 3 2267 3080 110280478 110279663 0.000000e+00 1240
11 TraesCS7D01G304100 chr3D 93.325 824 44 7 2264 3080 537304561 537305380 0.000000e+00 1206
12 TraesCS7D01G304100 chr5D 93.390 817 47 4 2267 3080 51856348 51855536 0.000000e+00 1203
13 TraesCS7D01G304100 chr5D 93.293 820 48 5 2264 3080 238112719 238113534 0.000000e+00 1203
14 TraesCS7D01G304100 chr2D 93.382 816 48 4 2269 3080 86069495 86068682 0.000000e+00 1203


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 TraesCS7D01G304100 chr7D 385716975 385720054 3079 False 5688.000000 5688 100.000000 1 3080 1 chr7D.!!$F1 3079
1 TraesCS7D01G304100 chr7A 433742219 433745070 2851 False 1587.000000 3013 91.146000 1 2271 2 chr7A.!!$F1 2270
2 TraesCS7D01G304100 chr7B 380076287 380080936 4649 False 1096.333333 2649 91.294667 1 2270 3 chr7B.!!$F1 2269
3 TraesCS7D01G304100 chr1D 297519113 297519926 813 False 1299.000000 1299 95.466000 2267 3080 1 chr1D.!!$F1 813
4 TraesCS7D01G304100 chr6D 23775102 23775916 814 False 1249.000000 1249 94.377000 2267 3080 1 chr6D.!!$F1 813
5 TraesCS7D01G304100 chr6D 276127456 276128266 810 True 1230.000000 1230 94.010000 2266 3080 1 chr6D.!!$R1 814
6 TraesCS7D01G304100 chr5A 602360009 602360821 812 True 1245.000000 1245 94.363000 2269 3080 1 chr5A.!!$R1 811
7 TraesCS7D01G304100 chr3D 110279663 110280478 815 True 1240.000000 1240 94.125000 2267 3080 1 chr3D.!!$R1 813
8 TraesCS7D01G304100 chr3D 537304561 537305380 819 False 1206.000000 1206 93.325000 2264 3080 1 chr3D.!!$F1 816
9 TraesCS7D01G304100 chr5D 51855536 51856348 812 True 1203.000000 1203 93.390000 2267 3080 1 chr5D.!!$R1 813
10 TraesCS7D01G304100 chr5D 238112719 238113534 815 False 1203.000000 1203 93.293000 2264 3080 1 chr5D.!!$F1 816
11 TraesCS7D01G304100 chr2D 86068682 86069495 813 True 1203.000000 1203 93.382000 2269 3080 1 chr2D.!!$R1 811


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
979 3406 0.106149 CGAACCCTATAAAGCGGCCT 59.894 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2230 5304 0.472471 AGATTGGTTGTGACACCGGT 59.528 50.0 0.0 0.0 40.09 5.28 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
91 98 5.416947 ACAAATATACTCGAGTGTTCCACC 58.583 41.667 28.12 0.00 34.49 4.61
94 101 0.963962 TACTCGAGTGTTCCACCCAC 59.036 55.000 28.12 0.00 34.49 4.61
106 113 2.379972 TCCACCCACGTGTGAAATTTT 58.620 42.857 15.65 0.00 38.55 1.82
108 115 4.145807 TCCACCCACGTGTGAAATTTTAT 58.854 39.130 15.65 0.00 38.55 1.40
159 166 4.077822 CAGAGAAGAGAAAATTGGTGCCT 58.922 43.478 0.00 0.00 0.00 4.75
234 243 6.610075 AAACACTAGGAATGCCATTTCATT 57.390 33.333 0.00 0.00 39.20 2.57
312 321 9.715121 ATTCAGAAATGTTTGATGTTTTGCTAT 57.285 25.926 0.00 0.00 0.00 2.97
348 388 3.247411 CACTGTTCATTCAAGTGCGTGTA 59.753 43.478 0.00 0.00 0.00 2.90
354 394 4.234574 TCATTCAAGTGCGTGTACTACTG 58.765 43.478 0.00 0.00 0.00 2.74
358 398 0.601558 AGTGCGTGTACTACTGTGGG 59.398 55.000 0.00 0.00 0.00 4.61
375 415 1.669999 GGGCCCATGTTCACTGATGC 61.670 60.000 19.95 0.00 0.00 3.91
380 420 3.618019 GCCCATGTTCACTGATGCAATTT 60.618 43.478 0.00 0.00 0.00 1.82
427 474 4.339247 CGGAGTTCTATCCATTTTGCCAAT 59.661 41.667 0.00 0.00 39.53 3.16
431 478 8.084684 GGAGTTCTATCCATTTTGCCAATATTC 58.915 37.037 0.00 0.00 39.34 1.75
436 483 9.866655 TCTATCCATTTTGCCAATATTCTAAGT 57.133 29.630 0.00 0.00 0.00 2.24
455 502 9.899661 TTCTAAGTGGCAGAAAGCTTATATAAA 57.100 29.630 0.00 0.00 44.79 1.40
534 2958 2.363680 CCTGATGGAGTCTCGCATAACT 59.636 50.000 4.40 0.00 34.57 2.24
535 2959 3.570125 CCTGATGGAGTCTCGCATAACTA 59.430 47.826 4.40 0.00 34.57 2.24
536 2960 4.038042 CCTGATGGAGTCTCGCATAACTAA 59.962 45.833 4.40 0.00 34.57 2.24
545 2969 4.740695 GTCTCGCATAACTAATCACTCACC 59.259 45.833 0.00 0.00 0.00 4.02
574 2998 1.631898 TGCTACTTGGTTTACCCCCTC 59.368 52.381 0.00 0.00 34.29 4.30
678 3102 1.064654 GGTCGCCGTACGTATTCTCTT 59.935 52.381 15.21 0.00 44.19 2.85
679 3103 2.478539 GGTCGCCGTACGTATTCTCTTT 60.479 50.000 15.21 0.00 44.19 2.52
893 3319 4.021719 CACTGAAAAATGGCAATCTCCACT 60.022 41.667 0.00 0.00 39.25 4.00
909 3335 0.535797 CACTTTCCCGAGACTACCCC 59.464 60.000 0.00 0.00 0.00 4.95
979 3406 0.106149 CGAACCCTATAAAGCGGCCT 59.894 55.000 0.00 0.00 0.00 5.19
1035 3462 1.251527 CCGAGTGGTGGTCAGCTAGT 61.252 60.000 1.84 0.00 0.00 2.57
1162 3589 5.738619 TTGTTAGCTGTGTATCAGGAGAA 57.261 39.130 0.00 0.00 43.78 2.87
1185 3612 1.330155 TTAGAGACAGGGGAGGGGAT 58.670 55.000 0.00 0.00 0.00 3.85
1551 3987 2.041966 GACGAATACAGGTACGCGATG 58.958 52.381 15.93 8.53 0.00 3.84
1851 4289 5.141182 TGGCGGGCTGGATTAATTAATTAA 58.859 37.500 20.11 20.11 36.75 1.40
1852 4290 5.777732 TGGCGGGCTGGATTAATTAATTAAT 59.222 36.000 26.27 26.27 43.54 1.40
1853 4291 6.268847 TGGCGGGCTGGATTAATTAATTAATT 59.731 34.615 26.54 23.28 41.59 1.40
1854 4292 7.451877 TGGCGGGCTGGATTAATTAATTAATTA 59.548 33.333 26.54 21.49 41.59 1.40
1961 4399 2.514592 CCCTGCCCTGTACATGCG 60.515 66.667 11.54 7.38 0.00 4.73
2090 5163 7.643569 TCAAAGTATACGGTACATCTTACCA 57.356 36.000 0.00 0.00 37.44 3.25
2196 5269 1.145119 GTTTTCCTCCTCCCCACAAGT 59.855 52.381 0.00 0.00 0.00 3.16
2197 5270 2.374170 GTTTTCCTCCTCCCCACAAGTA 59.626 50.000 0.00 0.00 0.00 2.24
2200 5274 1.132657 TCCTCCTCCCCACAAGTAACA 60.133 52.381 0.00 0.00 0.00 2.41
2230 5304 3.518303 GACTAGGGTCTTTTTGCCTCCTA 59.482 47.826 0.00 0.00 39.24 2.94
2303 5380 3.996621 CCCCCAACAGGCCACCAT 61.997 66.667 5.01 0.00 0.00 3.55
2346 5425 2.961768 AAAAATGCCCCAGTCGCG 59.038 55.556 0.00 0.00 0.00 5.87
2590 5675 0.977395 GCTAGATAGCCATTCCCCGT 59.023 55.000 0.09 0.00 43.39 5.28
2950 6036 1.950216 TGCATGCTCTACTCCGACTAG 59.050 52.381 20.33 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 98 7.922505 TTTCTTCATAAAATTTCACACGTGG 57.077 32.000 21.57 9.11 0.00 4.94
94 101 9.179552 TGTCATTTCTTCATAAAATTTCACACG 57.820 29.630 0.00 0.00 0.00 4.49
106 113 9.599866 AAATACGACTCATGTCATTTCTTCATA 57.400 29.630 0.00 0.00 43.06 2.15
108 115 7.905604 AAATACGACTCATGTCATTTCTTCA 57.094 32.000 0.00 0.00 43.06 3.02
126 133 9.884465 AATTTTCTCTTCTCTGTTCAAAATACG 57.116 29.630 0.00 0.00 0.00 3.06
139 146 4.074970 TGAGGCACCAATTTTCTCTTCTC 58.925 43.478 0.00 0.00 0.00 2.87
153 160 4.898829 AAAAATTGCTTTTTGAGGCACC 57.101 36.364 0.00 0.00 41.77 5.01
326 335 2.032054 ACACGCACTTGAATGAACAGTG 59.968 45.455 0.00 0.00 0.00 3.66
348 388 0.328258 GAACATGGGCCCACAGTAGT 59.672 55.000 31.51 17.93 0.00 2.73
354 394 0.323725 ATCAGTGAACATGGGCCCAC 60.324 55.000 31.51 15.89 0.00 4.61
358 398 0.889994 TTGCATCAGTGAACATGGGC 59.110 50.000 0.00 0.00 0.00 5.36
375 415 3.426191 TCGTAACCGACTTGACGAAATTG 59.574 43.478 0.00 0.00 41.04 2.32
380 420 1.334960 GGTTCGTAACCGACTTGACGA 60.335 52.381 0.00 0.00 44.13 4.20
431 478 9.109393 TGTTTATATAAGCTTTCTGCCACTTAG 57.891 33.333 3.20 0.00 44.23 2.18
436 483 8.116651 TGTTTGTTTATATAAGCTTTCTGCCA 57.883 30.769 3.20 0.00 44.23 4.92
452 499 9.319143 CCAATTTGTTGGTAGATTGTTTGTTTA 57.681 29.630 0.00 0.00 37.32 2.01
455 502 5.757808 GCCAATTTGTTGGTAGATTGTTTGT 59.242 36.000 8.79 0.00 43.90 2.83
498 1196 3.420893 CATCAGGTTTGAGCCCAACTAA 58.579 45.455 0.00 0.00 36.61 2.24
534 2958 3.932710 GCAGAATGAACGGTGAGTGATTA 59.067 43.478 0.00 0.00 39.69 1.75
535 2959 2.744202 GCAGAATGAACGGTGAGTGATT 59.256 45.455 0.00 0.00 39.69 2.57
536 2960 2.027745 AGCAGAATGAACGGTGAGTGAT 60.028 45.455 0.00 0.00 39.69 3.06
545 2969 4.749245 AAACCAAGTAGCAGAATGAACG 57.251 40.909 0.00 0.00 39.69 3.95
582 3006 4.762251 GGTGGAGTAGCAGAATGAACTTTT 59.238 41.667 0.00 0.00 39.69 2.27
583 3007 4.327680 GGTGGAGTAGCAGAATGAACTTT 58.672 43.478 0.00 0.00 39.69 2.66
584 3008 3.617531 CGGTGGAGTAGCAGAATGAACTT 60.618 47.826 0.00 0.00 39.69 2.66
585 3009 2.093973 CGGTGGAGTAGCAGAATGAACT 60.094 50.000 0.00 0.00 39.69 3.01
678 3102 2.190161 GTGCGTACGTATCTGATGCAA 58.810 47.619 17.90 0.00 32.04 4.08
679 3103 1.835121 GTGCGTACGTATCTGATGCA 58.165 50.000 17.90 0.00 0.00 3.96
887 3313 1.477295 GGTAGTCTCGGGAAAGTGGAG 59.523 57.143 0.00 0.00 0.00 3.86
893 3319 0.616679 CCAGGGGTAGTCTCGGGAAA 60.617 60.000 0.00 0.00 0.00 3.13
922 3348 4.699522 AAACACCTCCGCTCCGCC 62.700 66.667 0.00 0.00 0.00 6.13
979 3406 0.174617 TCTGCAGTGTCACGTGTTGA 59.825 50.000 16.51 0.00 0.00 3.18
1035 3462 1.304134 TACGAGTGGCCTCAGCTCA 60.304 57.895 3.32 0.00 37.59 4.26
1162 3589 2.360854 CCCCTCCCCTGTCTCTAATCTT 60.361 54.545 0.00 0.00 0.00 2.40
1185 3612 1.986631 CCCGACCCCTCTCTCTAGATA 59.013 57.143 0.00 0.00 0.00 1.98
1416 3852 0.681733 CACCCTCATAGATGTCCCCG 59.318 60.000 0.00 0.00 0.00 5.73
1551 3987 0.941542 AGAGAGAGACGCGTATCTGC 59.058 55.000 38.07 27.77 30.29 4.26
1851 4289 9.884814 ATAGACTAGTAGGAGTGGTTGATTAAT 57.115 33.333 0.00 0.00 0.00 1.40
1854 4292 9.303116 CATATAGACTAGTAGGAGTGGTTGATT 57.697 37.037 0.00 0.00 0.00 2.57
1861 4299 4.201734 CGCGCATATAGACTAGTAGGAGTG 60.202 50.000 8.75 0.00 0.00 3.51
1873 4311 3.179433 GCACTGACGCGCATATAGA 57.821 52.632 5.73 0.00 0.00 1.98
1950 4388 3.706287 TACGTGACGCATGTACAGG 57.294 52.632 4.25 2.43 35.12 4.00
1961 4399 1.016627 ATGCATGCATGGTACGTGAC 58.983 50.000 31.74 9.08 35.03 3.67
2107 5180 9.747898 TTGAGGAAATTAGGCAGTATTTCTAAA 57.252 29.630 14.40 7.53 39.53 1.85
2126 5199 2.093181 CCCACGGATACATGTTGAGGAA 60.093 50.000 2.30 0.00 0.00 3.36
2196 5269 1.509463 CCTAGTCGCGCTGGTGTTA 59.491 57.895 5.56 0.00 0.00 2.41
2197 5270 2.261671 CCTAGTCGCGCTGGTGTT 59.738 61.111 5.56 0.00 0.00 3.32
2200 5274 3.450115 GACCCTAGTCGCGCTGGT 61.450 66.667 5.56 6.75 32.18 4.00
2230 5304 0.472471 AGATTGGTTGTGACACCGGT 59.528 50.000 0.00 0.00 40.09 5.28
2346 5425 2.677979 GCTTTTCGTCGTCCTGGGC 61.678 63.158 0.00 0.00 0.00 5.36
2590 5675 3.660865 GAACCTCTGCTACTTTTTCCGA 58.339 45.455 0.00 0.00 0.00 4.55
2599 5684 1.226717 CTCGGCGAACCTCTGCTAC 60.227 63.158 12.13 0.00 0.00 3.58
2624 5709 1.228245 GCCCAGCTGTTGTTGGAGA 60.228 57.895 13.81 0.00 45.89 3.71
2666 5751 2.669240 GCTAAACTGCCCCTCCGT 59.331 61.111 0.00 0.00 0.00 4.69
2915 6001 1.134995 CATGCAGTAGCCTTCGAGACA 60.135 52.381 0.00 0.00 41.13 3.41
2956 6042 1.375908 GCCGTGAAGTGGAGCATCA 60.376 57.895 0.00 0.00 36.25 3.07
3009 6095 5.380043 TCACAATTCTGAGGAAGAGCTTTT 58.620 37.500 0.00 0.00 35.91 2.27



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

AutoCloner maintained by Alex Coulton.