Multiple sequence alignment - TraesCS3D01G181700

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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 TraesCS3D01G181700 chr3D 100.000 2405 0 0 1 2405 164401404 164399000 0.000000e+00 4442
1 TraesCS3D01G181700 chr3A 91.518 2358 97 36 1 2299 196421625 196419312 0.000000e+00 3151
2 TraesCS3D01G181700 chr3A 93.182 88 5 1 2298 2385 196417235 196417149 6.980000e-26 128
3 TraesCS3D01G181700 chr3B 90.550 2402 96 48 1 2345 240409155 240406828 0.000000e+00 3057


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 TraesCS3D01G181700 chr3D 164399000 164401404 2404 True 4442.0 4442 100.00 1 2405 1 chr3D.!!$R1 2404
1 TraesCS3D01G181700 chr3A 196417149 196421625 4476 True 1639.5 3151 92.35 1 2385 2 chr3A.!!$R1 2384
2 TraesCS3D01G181700 chr3B 240406828 240409155 2327 True 3057.0 3057 90.55 1 2345 1 chr3B.!!$R1 2344

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
810 845 0.178992 CGCCATCTCTCCTCTCCTCT 60.179 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 1886 0.169672 CAGGCTCACAGGCAATTTCG 59.83 55.0 0.0 0.0 44.19 3.46 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
155 172 4.894114 GGACAGGACCATTTAGTAGCTAGA 59.106 45.833 0.00 0.00 0.00 2.43
254 281 1.635281 GCATCGAAAGCGCTCTCTG 59.365 57.895 12.06 2.40 37.46 3.35
282 310 2.550978 CATCTGACACCCCATAACGTC 58.449 52.381 0.00 0.00 0.00 4.34
284 312 1.548719 TCTGACACCCCATAACGTCTG 59.451 52.381 0.00 0.00 0.00 3.51
356 384 4.261072 CGTCGTACTACTAGCCATTGATGT 60.261 45.833 0.00 0.00 0.00 3.06
383 411 3.508762 AGTAAATACAGCCGAACACTCG 58.491 45.455 0.00 0.00 45.02 4.18
399 427 6.771188 AACACTCGAAATGACACTAGAAAG 57.229 37.500 0.00 0.00 0.00 2.62
400 428 5.844004 ACACTCGAAATGACACTAGAAAGT 58.156 37.500 0.00 0.00 35.91 2.66
401 429 6.978338 ACACTCGAAATGACACTAGAAAGTA 58.022 36.000 0.00 0.00 33.48 2.24
402 430 6.862090 ACACTCGAAATGACACTAGAAAGTAC 59.138 38.462 0.00 0.00 33.48 2.73
404 432 7.542477 CACTCGAAATGACACTAGAAAGTACAT 59.458 37.037 0.00 0.00 35.11 2.29
405 433 8.737175 ACTCGAAATGACACTAGAAAGTACATA 58.263 33.333 0.00 0.00 33.63 2.29
413 442 9.676861 TGACACTAGAAAGTACATAAGCTAGTA 57.323 33.333 0.00 0.00 37.15 1.82
421 450 9.573133 GAAAGTACATAAGCTAGTAACGGTTTA 57.427 33.333 0.00 0.00 0.00 2.01
425 454 7.161773 ACATAAGCTAGTAACGGTTTACTGA 57.838 36.000 8.32 0.00 46.23 3.41
427 456 8.090214 ACATAAGCTAGTAACGGTTTACTGAAA 58.910 33.333 8.32 0.00 46.23 2.69
429 458 6.775939 AGCTAGTAACGGTTTACTGAAAAC 57.224 37.500 8.32 0.00 46.23 2.43
446 475 4.805192 TGAAAACAAAAGCAGATGCAAGTC 59.195 37.500 7.68 0.00 45.16 3.01
455 485 3.106738 GATGCAAGTCATCCCCAGG 57.893 57.895 0.00 0.00 44.54 4.45
473 503 3.037249 GTCGCACGCGGTTAACCA 61.037 61.111 24.14 0.00 40.25 3.67
649 684 4.202315 ACGAATCGAACCATCCAATCCATA 60.202 41.667 10.55 0.00 0.00 2.74
652 687 2.105821 TCGAACCATCCAATCCATACCC 59.894 50.000 0.00 0.00 0.00 3.69
662 697 2.436542 CAATCCATACCCAGTTACCGGA 59.563 50.000 9.46 0.00 0.00 5.14
803 838 3.893763 CGACGCGCCATCTCTCCT 61.894 66.667 5.73 0.00 0.00 3.69
804 839 2.026879 GACGCGCCATCTCTCCTC 59.973 66.667 5.73 0.00 0.00 3.71
805 840 2.441164 ACGCGCCATCTCTCCTCT 60.441 61.111 5.73 0.00 0.00 3.69
810 845 0.178992 CGCCATCTCTCCTCTCCTCT 60.179 60.000 0.00 0.00 0.00 3.69
813 848 1.203050 CCATCTCTCCTCTCCTCTCCC 60.203 61.905 0.00 0.00 0.00 4.30
814 849 0.771127 ATCTCTCCTCTCCTCTCCCG 59.229 60.000 0.00 0.00 0.00 5.14
815 850 1.150536 CTCTCCTCTCCTCTCCCGG 59.849 68.421 0.00 0.00 0.00 5.73
816 851 1.619975 TCTCCTCTCCTCTCCCGGT 60.620 63.158 0.00 0.00 0.00 5.28
817 852 1.152839 CTCCTCTCCTCTCCCGGTC 60.153 68.421 0.00 0.00 0.00 4.79
818 853 1.619975 TCCTCTCCTCTCCCGGTCT 60.620 63.158 0.00 0.00 0.00 3.85
819 854 1.152839 CCTCTCCTCTCCCGGTCTC 60.153 68.421 0.00 0.00 0.00 3.36
820 855 1.152839 CTCTCCTCTCCCGGTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
821 856 2.123640 CTCCTCTCCCGGTCTCCC 60.124 72.222 0.00 0.00 0.00 4.30
822 857 2.617538 TCCTCTCCCGGTCTCCCT 60.618 66.667 0.00 0.00 0.00 4.20
823 858 2.123640 CCTCTCCCGGTCTCCCTC 60.124 72.222 0.00 0.00 0.00 4.30
824 859 2.123640 CTCTCCCGGTCTCCCTCC 60.124 72.222 0.00 0.00 0.00 4.30
825 860 2.944954 TCTCCCGGTCTCCCTCCA 60.945 66.667 0.00 0.00 0.00 3.86
826 861 2.283809 CTCCCGGTCTCCCTCCAT 59.716 66.667 0.00 0.00 0.00 3.41
827 862 1.834822 CTCCCGGTCTCCCTCCATC 60.835 68.421 0.00 0.00 0.00 3.51
828 863 2.283809 CCCGGTCTCCCTCCATCT 59.716 66.667 0.00 0.00 0.00 2.90
829 864 1.834822 CCCGGTCTCCCTCCATCTC 60.835 68.421 0.00 0.00 0.00 2.75
830 865 1.834822 CCGGTCTCCCTCCATCTCC 60.835 68.421 0.00 0.00 0.00 3.71
857 892 2.201921 TCTCTTCTCACCTACTGCGT 57.798 50.000 0.00 0.00 0.00 5.24
958 995 0.320771 CTTGGTTCCTCCGTCCACAG 60.321 60.000 0.00 0.00 39.52 3.66
1092 1129 3.717294 GCCTCGGCCTTGAAGGGA 61.717 66.667 13.99 1.55 35.37 4.20
1342 1379 1.482593 CCTCCTACTACAACTGCCAGG 59.517 57.143 0.00 0.00 0.00 4.45
1418 1460 3.012844 AGGGGCTGATTCATTAAACCCTT 59.987 43.478 0.00 0.00 44.56 3.95
1460 1505 4.818546 GCATGCCTCATCAATTAGTACTGT 59.181 41.667 6.36 0.00 0.00 3.55
1536 1585 7.856398 CACTTCTTATGATGCTTGATCAATCAC 59.144 37.037 13.87 8.92 44.50 3.06
1541 1590 4.338012 TGATGCTTGATCAATCACCACTT 58.662 39.130 13.87 0.00 38.19 3.16
1543 1592 2.229543 TGCTTGATCAATCACCACTTGC 59.770 45.455 8.96 6.11 36.36 4.01
1714 1792 7.758076 TCGTCTCATATTAGTTGTCGTTCAAAT 59.242 33.333 2.53 2.53 37.81 2.32
1747 1825 3.195661 GCCTCGGTTTAACTATGGTGAG 58.804 50.000 0.00 0.00 0.00 3.51
2291 2378 5.291178 CACAAGCTCAAGAGAGGATATCTG 58.709 45.833 2.05 0.00 42.33 2.90
2355 4520 4.100808 GTCTCTAAGACTCAATCAGGGCAT 59.899 45.833 0.00 0.00 41.88 4.40
2364 4529 4.263905 ACTCAATCAGGGCATTTCTAACCA 60.264 41.667 0.00 0.00 0.00 3.67
2366 4531 5.271598 TCAATCAGGGCATTTCTAACCAAT 58.728 37.500 0.00 0.00 0.00 3.16
2369 4534 3.011144 TCAGGGCATTTCTAACCAATCCA 59.989 43.478 0.00 0.00 0.00 3.41
2375 4540 5.106157 GGCATTTCTAACCAATCCATATCCG 60.106 44.000 0.00 0.00 0.00 4.18
2381 4546 7.127012 TCTAACCAATCCATATCCGTTGTTA 57.873 36.000 0.00 0.00 0.00 2.41
2382 4547 7.214381 TCTAACCAATCCATATCCGTTGTTAG 58.786 38.462 0.00 0.00 0.00 2.34
2384 4549 5.751586 ACCAATCCATATCCGTTGTTAGTT 58.248 37.500 0.00 0.00 0.00 2.24
2385 4550 5.588648 ACCAATCCATATCCGTTGTTAGTTG 59.411 40.000 0.00 0.00 0.00 3.16
2386 4551 5.820423 CCAATCCATATCCGTTGTTAGTTGA 59.180 40.000 0.00 0.00 0.00 3.18
2387 4552 6.017934 CCAATCCATATCCGTTGTTAGTTGAG 60.018 42.308 0.00 0.00 0.00 3.02
2388 4553 4.439057 TCCATATCCGTTGTTAGTTGAGC 58.561 43.478 0.00 0.00 0.00 4.26
2389 4554 4.081365 TCCATATCCGTTGTTAGTTGAGCA 60.081 41.667 0.00 0.00 0.00 4.26
2390 4555 4.634004 CCATATCCGTTGTTAGTTGAGCAA 59.366 41.667 0.00 0.00 0.00 3.91
2391 4556 5.123186 CCATATCCGTTGTTAGTTGAGCAAA 59.877 40.000 0.00 0.00 0.00 3.68
2392 4557 6.348950 CCATATCCGTTGTTAGTTGAGCAAAA 60.349 38.462 0.00 0.00 0.00 2.44
2393 4558 4.966965 TCCGTTGTTAGTTGAGCAAAAA 57.033 36.364 0.00 0.00 0.00 1.94
2394 4559 4.915704 TCCGTTGTTAGTTGAGCAAAAAG 58.084 39.130 0.00 0.00 0.00 2.27
2395 4560 4.396790 TCCGTTGTTAGTTGAGCAAAAAGT 59.603 37.500 0.00 0.00 0.00 2.66
2396 4561 4.733405 CCGTTGTTAGTTGAGCAAAAAGTC 59.267 41.667 0.00 0.00 0.00 3.01
2397 4562 4.433304 CGTTGTTAGTTGAGCAAAAAGTCG 59.567 41.667 0.00 0.00 0.00 4.18
2398 4563 4.545823 TGTTAGTTGAGCAAAAAGTCGG 57.454 40.909 0.00 0.00 0.00 4.79
2399 4564 3.942748 TGTTAGTTGAGCAAAAAGTCGGT 59.057 39.130 0.00 0.00 0.00 4.69
2400 4565 4.396790 TGTTAGTTGAGCAAAAAGTCGGTT 59.603 37.500 0.00 0.00 0.00 4.44
2401 4566 5.106078 TGTTAGTTGAGCAAAAAGTCGGTTT 60.106 36.000 0.00 0.00 0.00 3.27
2402 4567 4.450082 AGTTGAGCAAAAAGTCGGTTTT 57.550 36.364 0.00 0.00 40.26 2.43
2403 4568 5.570234 AGTTGAGCAAAAAGTCGGTTTTA 57.430 34.783 0.00 0.00 37.37 1.52
2404 4569 5.337554 AGTTGAGCAAAAAGTCGGTTTTAC 58.662 37.500 0.00 0.00 37.37 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 140 1.529713 GGTCCTGTCCCCGCAAAAA 60.530 57.895 0.00 0.00 0.00 1.94
155 172 2.544267 GTGACAGCTTCGTTTAGTGCTT 59.456 45.455 0.00 0.00 33.03 3.91
277 304 2.747446 GGGCACATCAATAACAGACGTT 59.253 45.455 0.00 0.00 39.24 3.99
282 310 4.022068 ACAACTTGGGCACATCAATAACAG 60.022 41.667 0.00 0.00 0.00 3.16
284 312 4.519540 ACAACTTGGGCACATCAATAAC 57.480 40.909 0.00 0.00 0.00 1.89
356 384 1.202817 TCGGCTGTATTTACTCGTGCA 59.797 47.619 0.00 0.00 0.00 4.57
383 411 9.372369 AGCTTATGTACTTTCTAGTGTCATTTC 57.628 33.333 0.00 0.00 35.78 2.17
395 423 8.471361 AAACCGTTACTAGCTTATGTACTTTC 57.529 34.615 0.00 0.00 0.00 2.62
396 424 9.358872 GTAAACCGTTACTAGCTTATGTACTTT 57.641 33.333 0.00 0.00 37.27 2.66
399 427 8.184192 TCAGTAAACCGTTACTAGCTTATGTAC 58.816 37.037 0.00 0.00 46.71 2.90
400 428 8.279970 TCAGTAAACCGTTACTAGCTTATGTA 57.720 34.615 0.00 0.00 46.71 2.29
401 429 7.161773 TCAGTAAACCGTTACTAGCTTATGT 57.838 36.000 0.00 0.00 46.71 2.29
402 430 8.470040 TTTCAGTAAACCGTTACTAGCTTATG 57.530 34.615 0.00 0.00 46.71 1.90
404 432 7.925483 TGTTTTCAGTAAACCGTTACTAGCTTA 59.075 33.333 0.00 0.00 46.71 3.09
405 433 6.762661 TGTTTTCAGTAAACCGTTACTAGCTT 59.237 34.615 0.00 0.00 46.71 3.74
413 442 5.471257 TGCTTTTGTTTTCAGTAAACCGTT 58.529 33.333 0.60 0.00 44.49 4.44
421 450 4.389890 TGCATCTGCTTTTGTTTTCAGT 57.610 36.364 3.53 0.00 42.66 3.41
423 452 4.757594 ACTTGCATCTGCTTTTGTTTTCA 58.242 34.783 3.53 0.00 42.66 2.69
425 454 4.757594 TGACTTGCATCTGCTTTTGTTTT 58.242 34.783 3.53 0.00 42.66 2.43
427 456 4.595762 ATGACTTGCATCTGCTTTTGTT 57.404 36.364 3.53 0.00 42.66 2.83
438 467 1.217057 ACCCTGGGGATGACTTGCAT 61.217 55.000 18.88 0.00 40.77 3.96
446 475 4.838152 CGTGCGACCCTGGGGATG 62.838 72.222 18.88 7.23 38.96 3.51
453 483 3.993584 TTAACCGCGTGCGACCCT 61.994 61.111 16.91 0.00 42.83 4.34
455 485 3.781162 GGTTAACCGCGTGCGACC 61.781 66.667 16.91 11.33 42.83 4.79
473 503 3.821033 GACAAGTTGCTACATCTTTGGGT 59.179 43.478 1.81 0.00 0.00 4.51
573 608 2.517875 AGCCGATGCATCTTGGGC 60.518 61.111 27.36 27.36 44.07 5.36
649 684 0.252197 GAGCATTCCGGTAACTGGGT 59.748 55.000 0.00 0.00 0.00 4.51
803 838 2.691779 GGGAGACCGGGAGAGGAGA 61.692 68.421 6.32 0.00 43.64 3.71
804 839 2.123640 GGGAGACCGGGAGAGGAG 60.124 72.222 6.32 0.00 43.64 3.69
815 850 1.765904 GAAAGGGAGATGGAGGGAGAC 59.234 57.143 0.00 0.00 0.00 3.36
816 851 1.653918 AGAAAGGGAGATGGAGGGAGA 59.346 52.381 0.00 0.00 0.00 3.71
817 852 2.188818 AGAAAGGGAGATGGAGGGAG 57.811 55.000 0.00 0.00 0.00 4.30
818 853 2.668850 AAGAAAGGGAGATGGAGGGA 57.331 50.000 0.00 0.00 0.00 4.20
819 854 2.849318 AGAAAGAAAGGGAGATGGAGGG 59.151 50.000 0.00 0.00 0.00 4.30
820 855 3.779738 AGAGAAAGAAAGGGAGATGGAGG 59.220 47.826 0.00 0.00 0.00 4.30
821 856 5.189539 AGAAGAGAAAGAAAGGGAGATGGAG 59.810 44.000 0.00 0.00 0.00 3.86
822 857 5.097234 AGAAGAGAAAGAAAGGGAGATGGA 58.903 41.667 0.00 0.00 0.00 3.41
823 858 5.046014 TGAGAAGAGAAAGAAAGGGAGATGG 60.046 44.000 0.00 0.00 0.00 3.51
824 859 5.874261 GTGAGAAGAGAAAGAAAGGGAGATG 59.126 44.000 0.00 0.00 0.00 2.90
825 860 5.045942 GGTGAGAAGAGAAAGAAAGGGAGAT 60.046 44.000 0.00 0.00 0.00 2.75
826 861 4.284746 GGTGAGAAGAGAAAGAAAGGGAGA 59.715 45.833 0.00 0.00 0.00 3.71
827 862 4.285775 AGGTGAGAAGAGAAAGAAAGGGAG 59.714 45.833 0.00 0.00 0.00 4.30
828 863 4.235372 AGGTGAGAAGAGAAAGAAAGGGA 58.765 43.478 0.00 0.00 0.00 4.20
829 864 4.632327 AGGTGAGAAGAGAAAGAAAGGG 57.368 45.455 0.00 0.00 0.00 3.95
830 865 6.162777 CAGTAGGTGAGAAGAGAAAGAAAGG 58.837 44.000 0.00 0.00 0.00 3.11
985 1022 2.263540 CATTTGGCTGCAGGTGGC 59.736 61.111 17.12 3.06 45.13 5.01
1320 1357 0.178301 GGCAGTTGTAGTAGGAGGCC 59.822 60.000 0.00 0.00 0.00 5.19
1418 1460 4.908601 TGCAGGTAAGAAGGAATGAAGA 57.091 40.909 0.00 0.00 0.00 2.87
1506 1554 7.755591 TGATCAAGCATCATAAGAAGTGTTTC 58.244 34.615 0.00 0.00 36.51 2.78
1519 1567 3.959293 AGTGGTGATTGATCAAGCATCA 58.041 40.909 30.51 30.51 44.44 3.07
1541 1590 2.616960 GTACGATTGATCACACCAGCA 58.383 47.619 0.00 0.00 0.00 4.41
1570 1631 1.856539 AACCATGCCTCCTCCAGTGG 61.857 60.000 1.40 1.40 0.00 4.00
1714 1792 2.684001 ACCGAGGCAAATGTTATCGA 57.316 45.000 0.00 0.00 35.47 3.59
1720 1798 4.398044 CCATAGTTAAACCGAGGCAAATGT 59.602 41.667 0.00 0.00 0.00 2.71
1721 1799 4.398044 ACCATAGTTAAACCGAGGCAAATG 59.602 41.667 0.00 0.00 0.00 2.32
1747 1825 1.881973 TGGCAGAGAAGCACATTCAAC 59.118 47.619 0.00 0.00 40.67 3.18
1808 1886 0.169672 CAGGCTCACAGGCAATTTCG 59.830 55.000 0.00 0.00 44.19 3.46
2109 2196 9.445786 ACAAATGAATCGTTTTAAAGTGTACAG 57.554 29.630 0.00 0.00 0.00 2.74
2233 2320 3.197766 TCCTTGCGACTGTAAGATTCCAT 59.802 43.478 0.00 0.00 39.89 3.41
2246 2333 3.984633 GCACTTCTAGATATCCTTGCGAC 59.015 47.826 0.00 0.00 0.00 5.19
2355 4520 6.419791 ACAACGGATATGGATTGGTTAGAAA 58.580 36.000 0.00 0.00 0.00 2.52
2364 4529 5.527582 GCTCAACTAACAACGGATATGGATT 59.472 40.000 0.00 0.00 0.00 3.01
2366 4531 4.081365 TGCTCAACTAACAACGGATATGGA 60.081 41.667 0.00 0.00 0.00 3.41
2369 4534 6.811253 TTTTGCTCAACTAACAACGGATAT 57.189 33.333 0.00 0.00 0.00 1.63
2375 4540 4.733405 CCGACTTTTTGCTCAACTAACAAC 59.267 41.667 0.00 0.00 0.00 3.32
2381 4546 4.450082 AAAACCGACTTTTTGCTCAACT 57.550 36.364 0.00 0.00 0.00 3.16
2382 4547 5.615495 GTAAAACCGACTTTTTGCTCAAC 57.385 39.130 0.00 0.00 33.84 3.18


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

AutoCloner maintained by Alex Coulton.