Multiple sequence alignment - TraesCS5D01G241400

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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 TraesCS5D01G241400 chr5D 100.000 3473 0 0 1 3473 350321300 350324772 0.000000e+00 6414
1 TraesCS5D01G241400 chr5D 90.083 121 9 3 1355 1475 350322534 350322651 1.670000e-33 154
2 TraesCS5D01G241400 chr5B 93.505 3449 122 39 64 3441 411019894 411023311 0.000000e+00 5035
3 TraesCS5D01G241400 chr5B 90.909 121 8 3 1355 1475 411021070 411021187 3.590000e-35 159
4 TraesCS5D01G241400 chr5B 96.875 64 2 0 3 66 411019809 411019872 1.320000e-19 108
5 TraesCS5D01G241400 chr5A 94.783 2415 50 30 675 3068 450735729 450738088 0.000000e+00 3692
6 TraesCS5D01G241400 chr5A 93.521 463 23 2 3018 3473 450738077 450738539 0.000000e+00 682
7 TraesCS5D01G241400 chr5A 92.642 299 14 4 3142 3433 549019507 549019210 1.150000e-114 424
8 TraesCS5D01G241400 chr5A 90.083 121 9 3 1355 1475 450736278 450736395 1.670000e-33 154
9 TraesCS5D01G241400 chr5A 90.179 112 8 3 523 633 450735611 450735720 3.610000e-30 143
10 TraesCS5D01G241400 chr4A 91.385 650 38 8 2839 3470 592453617 592454266 0.000000e+00 874
11 TraesCS5D01G241400 chr4A 91.077 650 40 8 2839 3470 592731930 592732579 0.000000e+00 863
12 TraesCS5D01G241400 chr4A 91.077 650 40 8 2839 3470 593020473 593021122 0.000000e+00 863
13 TraesCS5D01G241400 chr4A 90.046 653 47 8 2839 3473 591589137 591588485 0.000000e+00 830
14 TraesCS5D01G241400 chr1A 93.645 299 12 3 3142 3433 591009433 591009135 1.140000e-119 440
15 TraesCS5D01G241400 chr2A 90.062 322 24 4 3142 3456 707945315 707945635 8.970000e-111 411


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 TraesCS5D01G241400 chr5D 350321300 350324772 3472 False 3284.000000 6414 95.0415 1 3473 2 chr5D.!!$F1 3472
1 TraesCS5D01G241400 chr5B 411019809 411023311 3502 False 1767.333333 5035 93.7630 3 3441 3 chr5B.!!$F1 3438
2 TraesCS5D01G241400 chr5A 450735611 450738539 2928 False 1167.750000 3692 92.1415 523 3473 4 chr5A.!!$F1 2950
3 TraesCS5D01G241400 chr4A 592453617 592454266 649 False 874.000000 874 91.3850 2839 3470 1 chr4A.!!$F1 631
4 TraesCS5D01G241400 chr4A 592731930 592732579 649 False 863.000000 863 91.0770 2839 3470 1 chr4A.!!$F2 631
5 TraesCS5D01G241400 chr4A 593020473 593021122 649 False 863.000000 863 91.0770 2839 3470 1 chr4A.!!$F3 631
6 TraesCS5D01G241400 chr4A 591588485 591589137 652 True 830.000000 830 90.0460 2839 3473 1 chr4A.!!$R1 634

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
306 333 0.106619 TTAAACCGGCCACCACACTT 60.107 50.0 0.0 0.0 0.0 3.16 F
314 341 0.798776 GCCACCACACTTCAATCGAG 59.201 55.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2021 1.688197 TCATAGATGCTGCGGTCATGA 59.312 47.619 7.11 0.0 0.0 3.07 R
2663 2722 5.221843 ACCACAAGTTAGCACCTAAGAATCA 60.222 40.000 0.00 0.0 0.0 2.57 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
21 22 0.468226 GACACAACCACCACAGAGGA 59.532 55.000 0.00 0.00 41.22 3.71
75 100 3.448660 GGCAAAGGCTTGACAATATCCTT 59.551 43.478 0.00 9.46 40.67 3.36
147 172 0.809385 TCTCGCTAACCCGACTTCAG 59.191 55.000 0.00 0.00 33.12 3.02
157 182 1.411977 CCCGACTTCAGATGAGAGCAT 59.588 52.381 0.00 0.00 37.47 3.79
210 235 1.466856 ACCAATGCGCACATCTCAAT 58.533 45.000 14.90 0.00 34.62 2.57
217 242 1.813092 GCGCACATCTCAATGGAGGAT 60.813 52.381 0.30 0.00 41.69 3.24
221 246 3.683564 GCACATCTCAATGGAGGATCACA 60.684 47.826 0.00 0.00 41.69 3.58
222 247 4.715713 CACATCTCAATGGAGGATCACAT 58.284 43.478 0.00 0.00 41.69 3.21
225 250 4.684484 TCTCAATGGAGGATCACATGAG 57.316 45.455 0.00 0.00 41.69 2.90
232 257 5.557576 TGGAGGATCACATGAGGATAAAG 57.442 43.478 0.00 0.00 36.25 1.85
254 281 5.831997 AGAAAAACTAGATGCAAACACCAC 58.168 37.500 0.00 0.00 0.00 4.16
257 284 3.222173 ACTAGATGCAAACACCACCAA 57.778 42.857 0.00 0.00 0.00 3.67
261 288 0.398381 ATGCAAACACCACCAACCCT 60.398 50.000 0.00 0.00 0.00 4.34
266 293 2.912025 CACCACCAACCCTGCACC 60.912 66.667 0.00 0.00 0.00 5.01
279 306 2.339712 GCACCGCCAAATGCAACT 59.660 55.556 0.00 0.00 41.65 3.16
282 309 1.403679 GCACCGCCAAATGCAACTATA 59.596 47.619 0.00 0.00 41.65 1.31
306 333 0.106619 TTAAACCGGCCACCACACTT 60.107 50.000 0.00 0.00 0.00 3.16
314 341 0.798776 GCCACCACACTTCAATCGAG 59.201 55.000 0.00 0.00 0.00 4.04
352 379 4.409574 AGACATGATCAGAGGCTTCAAGAT 59.590 41.667 0.00 0.82 0.00 2.40
378 405 4.699522 AAGGAGGTTGCGACGCCC 62.700 66.667 18.69 12.35 0.00 6.13
431 465 1.588403 CGAGCCTCGAGAGCACATG 60.588 63.158 22.44 3.85 43.74 3.21
453 487 3.820467 GTGGTCAATGTGTGAAAGATCCA 59.180 43.478 0.00 0.00 38.23 3.41
482 516 2.185004 CTTCGAGAAGGAAAAGGGCA 57.815 50.000 4.99 0.00 34.87 5.36
572 606 2.659291 CGAGTCAAAAGAAAACGAGGCG 60.659 50.000 0.00 0.00 0.00 5.52
573 607 2.542595 GAGTCAAAAGAAAACGAGGCGA 59.457 45.455 0.00 0.00 0.00 5.54
577 611 1.226746 AAAGAAAACGAGGCGAGGTG 58.773 50.000 0.00 0.00 0.00 4.00
643 677 2.647158 AAGGAGACGGCGAACCCTC 61.647 63.158 16.62 13.67 0.00 4.30
644 678 3.069318 GGAGACGGCGAACCCTCT 61.069 66.667 16.62 5.00 0.00 3.69
660 694 2.369394 CCTCTTGGGTCAGTAATTGGC 58.631 52.381 0.00 0.00 0.00 4.52
698 732 3.113745 CGGACAGGCATTGGCATC 58.886 61.111 13.20 9.19 43.71 3.91
810 844 1.810030 GCACCCAACGACTCGATCC 60.810 63.158 5.20 0.00 0.00 3.36
864 918 1.629353 TGCGGATACAGGTTACCCAAA 59.371 47.619 0.00 0.00 0.00 3.28
901 955 1.890510 CAGCAGAGCACAGCACACA 60.891 57.895 0.85 0.00 0.00 3.72
902 956 1.890979 AGCAGAGCACAGCACACAC 60.891 57.895 0.85 0.00 0.00 3.82
907 961 1.779025 GAGCACAGCACACACCACAG 61.779 60.000 0.00 0.00 0.00 3.66
909 963 2.516930 ACAGCACACACCACAGCC 60.517 61.111 0.00 0.00 0.00 4.85
957 1011 4.500116 GAGGGACACGAGGCGAGC 62.500 72.222 0.00 0.00 0.00 5.03
960 1014 4.838486 GGACACGAGGCGAGCGAG 62.838 72.222 4.61 0.00 0.00 5.03
1359 1418 1.104630 CCTACAACTCCGAGGACTCC 58.895 60.000 0.00 0.00 31.45 3.85
1881 1940 2.029666 ACCACGCAGCTCAGTGAC 59.970 61.111 17.08 0.00 40.56 3.67
1914 1973 3.306780 GCCTCAAGCAGAAGTACCAGTTA 60.307 47.826 0.00 0.00 42.97 2.24
1947 2006 3.248043 CAAGAATGGACGGGAGCAA 57.752 52.632 0.00 0.00 0.00 3.91
2912 2991 7.976175 AGTGTCTTCTTTTTGGTTTCTTGATTC 59.024 33.333 0.00 0.00 0.00 2.52
3084 3203 5.493133 TTGTAAAGTTTGCGAGATGTTGT 57.507 34.783 0.00 0.00 0.00 3.32
3138 3261 7.664552 ATTTGGCTTGAATTGAATAGGATGA 57.335 32.000 0.00 0.00 0.00 2.92
3171 3294 6.834451 TGGTTGTTATAGTTGAGGGTCAAAAA 59.166 34.615 0.00 0.00 38.22 1.94
3196 3320 5.826643 AGGGGTTAGCTTTAACATGATTCA 58.173 37.500 0.00 0.00 0.00 2.57
3260 3384 3.942130 TCTGAAGTCGATGCTTTCTCA 57.058 42.857 0.00 0.00 0.00 3.27
3338 3470 6.539826 TCTCTGCACATGTTTAATGTCTATGG 59.460 38.462 0.00 0.00 0.00 2.74
3384 3516 1.860676 TGTCGGTGAGCTTGTGTTAC 58.139 50.000 0.00 0.00 0.00 2.50
3385 3517 1.137282 TGTCGGTGAGCTTGTGTTACA 59.863 47.619 0.00 0.00 0.00 2.41
3441 3578 6.382282 TCTCTCATCTCACTGGTGTTTGATAT 59.618 38.462 0.53 0.00 0.00 1.63
3457 3600 3.459828 TGATATGGGTCTTGGTCCTTGA 58.540 45.455 0.00 0.00 0.00 3.02
3460 3603 1.741028 TGGGTCTTGGTCCTTGATGA 58.259 50.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.104120 CTCTGTGGTGGTTGTGTCGA 59.896 55.000 0.00 0.00 0.00 4.20
1 2 0.880278 CCTCTGTGGTGGTTGTGTCG 60.880 60.000 0.00 0.00 0.00 4.35
16 17 6.179906 TGAAGATGAAAGTTGAAGTCCTCT 57.820 37.500 0.00 0.00 0.00 3.69
21 22 6.429385 GGTGAGATGAAGATGAAAGTTGAAGT 59.571 38.462 0.00 0.00 0.00 3.01
75 100 2.158219 TGAACACACCTCCTCCTCCTTA 60.158 50.000 0.00 0.00 0.00 2.69
87 112 2.550978 CCTCGTCCATATGAACACACC 58.449 52.381 3.65 0.00 0.00 4.16
88 113 2.550978 CCCTCGTCCATATGAACACAC 58.449 52.381 3.65 0.00 0.00 3.82
89 114 1.484653 CCCCTCGTCCATATGAACACA 59.515 52.381 3.65 0.00 0.00 3.72
126 151 2.617308 CTGAAGTCGGGTTAGCGAGATA 59.383 50.000 0.00 0.00 0.00 1.98
157 182 1.512926 GAGTTTGCGAAAGAGCCTGA 58.487 50.000 0.00 0.00 36.02 3.86
160 185 1.061276 GATCGAGTTTGCGAAAGAGCC 59.939 52.381 0.00 0.00 44.22 4.70
162 187 2.251040 TCGATCGAGTTTGCGAAAGAG 58.749 47.619 15.15 0.00 44.22 2.85
210 235 5.218959 TCTTTATCCTCATGTGATCCTCCA 58.781 41.667 4.18 0.00 0.00 3.86
221 246 9.466497 TTGCATCTAGTTTTTCTTTATCCTCAT 57.534 29.630 0.00 0.00 0.00 2.90
222 247 8.862325 TTGCATCTAGTTTTTCTTTATCCTCA 57.138 30.769 0.00 0.00 0.00 3.86
225 250 9.129209 GTGTTTGCATCTAGTTTTTCTTTATCC 57.871 33.333 0.00 0.00 0.00 2.59
232 257 4.982295 GGTGGTGTTTGCATCTAGTTTTTC 59.018 41.667 0.00 0.00 0.00 2.29
243 270 1.000993 AGGGTTGGTGGTGTTTGCA 59.999 52.632 0.00 0.00 0.00 4.08
257 284 2.990967 CATTTGGCGGTGCAGGGT 60.991 61.111 0.00 0.00 0.00 4.34
268 295 7.480810 GGTTTAAGGTCTATAGTTGCATTTGG 58.519 38.462 0.00 0.00 0.00 3.28
279 306 2.435437 GGTGGCCGGTTTAAGGTCTATA 59.565 50.000 1.90 0.00 33.78 1.31
282 309 1.377612 GGTGGCCGGTTTAAGGTCT 59.622 57.895 1.90 0.00 33.78 3.85
306 333 2.475111 GCTTGTTTGACGTCTCGATTGA 59.525 45.455 17.92 0.00 0.00 2.57
314 341 3.002246 TCATGTCTTGCTTGTTTGACGTC 59.998 43.478 9.11 9.11 32.64 4.34
413 440 1.588403 CATGTGCTCTCGAGGCTCG 60.588 63.158 30.10 30.10 42.10 5.03
431 465 3.820467 TGGATCTTTCACACATTGACCAC 59.180 43.478 0.00 0.00 32.26 4.16
453 487 1.714794 CTTCTCGAAGGCATTGTCGT 58.285 50.000 0.00 0.00 38.41 4.34
478 512 4.525100 TGTGAATTAAAGTTTAGGGTGCCC 59.475 41.667 0.00 0.00 0.00 5.36
480 514 6.919721 TGATGTGAATTAAAGTTTAGGGTGC 58.080 36.000 0.00 0.00 0.00 5.01
482 516 7.397192 AGCATGATGTGAATTAAAGTTTAGGGT 59.603 33.333 0.00 0.00 0.00 4.34
492 526 5.047872 AGTGCAACAGCATGATGTGAATTAA 60.048 36.000 18.80 0.00 41.42 1.40
493 527 4.460034 AGTGCAACAGCATGATGTGAATTA 59.540 37.500 18.80 0.05 41.42 1.40
496 530 2.227149 GAGTGCAACAGCATGATGTGAA 59.773 45.455 18.80 3.70 41.42 3.18
515 549 5.175859 TCAAGTTTGGCTAGGTTTATCGAG 58.824 41.667 0.00 0.00 0.00 4.04
516 550 5.155278 TCAAGTTTGGCTAGGTTTATCGA 57.845 39.130 0.00 0.00 0.00 3.59
517 551 5.391629 GGTTCAAGTTTGGCTAGGTTTATCG 60.392 44.000 0.00 0.00 0.00 2.92
518 552 5.475564 TGGTTCAAGTTTGGCTAGGTTTATC 59.524 40.000 0.00 0.00 0.00 1.75
519 553 5.390387 TGGTTCAAGTTTGGCTAGGTTTAT 58.610 37.500 0.00 0.00 0.00 1.40
520 554 4.794334 TGGTTCAAGTTTGGCTAGGTTTA 58.206 39.130 0.00 0.00 0.00 2.01
521 555 3.636764 CTGGTTCAAGTTTGGCTAGGTTT 59.363 43.478 0.00 0.00 0.00 3.27
643 677 1.468520 CACGCCAATTACTGACCCAAG 59.531 52.381 0.00 0.00 0.00 3.61
644 678 1.529226 CACGCCAATTACTGACCCAA 58.471 50.000 0.00 0.00 0.00 4.12
1107 1166 2.122769 TTGGAGGGGTCGGTGTCA 60.123 61.111 0.00 0.00 0.00 3.58
1575 1634 1.959282 GGTTTGATGATGGATGCCTCC 59.041 52.381 0.22 0.22 42.45 4.30
1881 1940 4.697756 TTGAGGCGCCGGACCTTG 62.698 66.667 23.20 0.00 37.77 3.61
1947 2006 3.341823 GTCATGAGGAGTGTGCAATTCT 58.658 45.455 0.00 0.00 0.00 2.40
1962 2021 1.688197 TCATAGATGCTGCGGTCATGA 59.312 47.619 7.11 0.00 0.00 3.07
2663 2722 5.221843 ACCACAAGTTAGCACCTAAGAATCA 60.222 40.000 0.00 0.00 0.00 2.57
2912 2991 6.149308 TGAGTACACAACTAGAAATGCCAATG 59.851 38.462 0.00 0.00 39.07 2.82
2963 3042 2.926200 CACAGTAGCAGATTGTTCCTCG 59.074 50.000 0.00 0.00 0.00 4.63
3084 3203 5.371176 TGCCTTACATAATGGATGGTAGGAA 59.629 40.000 9.91 0.00 40.28 3.36
3138 3261 5.312895 TCAACTATAACAACCACAGCACAT 58.687 37.500 0.00 0.00 0.00 3.21
3171 3294 7.502561 GTGAATCATGTTAAAGCTAACCCCTAT 59.497 37.037 0.00 0.00 37.24 2.57
3260 3384 8.643324 GTGTATTTCAGACTACTATTCCATCCT 58.357 37.037 0.00 0.00 0.00 3.24
3338 3470 0.729140 GCATAACAGCCGCACAACAC 60.729 55.000 0.00 0.00 0.00 3.32
3384 3516 1.132262 ACACCAAAACGCAGAAGTGTG 59.868 47.619 0.00 0.00 38.75 3.82
3385 3517 1.400494 GACACCAAAACGCAGAAGTGT 59.600 47.619 1.31 1.31 40.91 3.55
3441 3578 1.741028 TCATCAAGGACCAAGACCCA 58.259 50.000 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.