Multiple sequence alignment - TraesCS7D01G303000

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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 TraesCS7D01G303000 chr7D 100.000 3491 0 0 1 3491 383269097 383272587 0.000000e+00 6447.0
1 TraesCS7D01G303000 chr7A 93.618 3353 139 27 4 3340 432137663 432140956 0.000000e+00 4937.0
2 TraesCS7D01G303000 chr7B 95.195 2560 85 20 4 2556 377812560 377815088 0.000000e+00 4012.0
3 TraesCS7D01G303000 chr7B 94.241 955 43 5 2549 3491 377815517 377816471 0.000000e+00 1448.0
4 TraesCS7D01G303000 chr2A 88.889 81 9 0 3411 3491 76520566 76520646 2.220000e-17 100.0
5 TraesCS7D01G303000 chr2A 89.610 77 8 0 3415 3491 391841470 391841394 7.970000e-17 99.0
6 TraesCS7D01G303000 chr1B 88.750 80 9 0 3412 3491 624606758 624606837 7.970000e-17 99.0
7 TraesCS7D01G303000 chr1A 89.610 77 8 0 3415 3491 347943307 347943231 7.970000e-17 99.0
8 TraesCS7D01G303000 chr5B 86.905 84 11 0 3408 3491 679149147 679149230 1.030000e-15 95.3
9 TraesCS7D01G303000 chr6D 88.312 77 9 0 3415 3491 472581343 472581267 3.710000e-15 93.5
10 TraesCS7D01G303000 chr3D 85.714 84 12 0 3408 3491 548714248 548714165 4.800000e-14 89.8
11 TraesCS7D01G303000 chr4A 87.013 77 9 1 3415 3491 646254134 646254059 6.210000e-13 86.1


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 TraesCS7D01G303000 chr7D 383269097 383272587 3490 False 6447 6447 100.000 1 3491 1 chr7D.!!$F1 3490
1 TraesCS7D01G303000 chr7A 432137663 432140956 3293 False 4937 4937 93.618 4 3340 1 chr7A.!!$F1 3336
2 TraesCS7D01G303000 chr7B 377812560 377816471 3911 False 2730 4012 94.718 4 3491 2 chr7B.!!$F1 3487

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
612 619 0.034059 AAGAATCTGATAGGCCGCCG 59.966 55.0 3.05 0.00 0.0 6.46 F
1852 1860 0.605319 CCTTTACAAGACAGCCGGCA 60.605 55.0 31.54 0.76 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 2270 2.475466 GCCGTCGACGAGGTGGATA 61.475 63.158 37.65 0.00 43.02 2.59 R
3203 3685 2.741517 GTGGCATACAACAAATTTGGCC 59.258 45.455 21.74 21.07 40.51 5.36 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
99 100 1.142474 GCAGCCTCAAAACAACATGC 58.858 50.000 0.00 0.00 0.00 4.06
183 184 7.549488 GCTTATCAAACCGCCTATATACATCTT 59.451 37.037 0.00 0.00 0.00 2.40
214 215 5.826208 ACGGTTCAGACAATTTTAGACCTTT 59.174 36.000 0.00 0.00 0.00 3.11
217 218 8.347035 CGGTTCAGACAATTTTAGACCTTTAAA 58.653 33.333 0.00 0.00 0.00 1.52
275 276 0.753262 CGAAATCCCCTGATCCGTCT 59.247 55.000 0.00 0.00 0.00 4.18
355 359 4.731313 AAGGATCATTCTAACCCCATCC 57.269 45.455 0.00 0.00 0.00 3.51
410 417 8.937835 TCCTCTCATATATTCATTGGACAAAGA 58.062 33.333 0.00 0.00 0.00 2.52
412 419 9.217278 CTCTCATATATTCATTGGACAAAGAGG 57.783 37.037 0.00 0.00 0.00 3.69
421 428 3.644966 TGGACAAAGAGGCGGATAATT 57.355 42.857 0.00 0.00 0.00 1.40
553 560 1.201880 ACCGACTCGAAAACTAGAGCC 59.798 52.381 0.00 0.00 37.99 4.70
566 573 1.139853 CTAGAGCCGGAAGCCTGAAAT 59.860 52.381 5.05 0.00 45.47 2.17
599 606 4.187694 ACTCCTTCATCTCGCAAAGAATC 58.812 43.478 0.00 0.00 37.61 2.52
612 619 0.034059 AAGAATCTGATAGGCCGCCG 59.966 55.000 3.05 0.00 0.00 6.46
637 644 5.773239 TTCTCGGACGATTCATGTTAAAC 57.227 39.130 0.00 0.00 0.00 2.01
683 690 1.599518 TGACCGGTTTCGCAGCAAT 60.600 52.632 9.42 0.00 34.56 3.56
687 694 2.082366 CGGTTTCGCAGCAATGCAC 61.082 57.895 8.35 0.00 34.41 4.57
701 708 5.049612 CAGCAATGCACAAGGTATCATCTAG 60.050 44.000 8.35 0.00 0.00 2.43
932 940 2.124942 CTTCCTCCTGGCTTCCGC 60.125 66.667 0.00 0.00 0.00 5.54
1470 1478 2.981350 GGCGCGTTCCTTTCCCAA 60.981 61.111 8.43 0.00 0.00 4.12
1743 1751 2.602267 TGGGCCGAGAACTTCCGA 60.602 61.111 0.00 0.00 0.00 4.55
1815 1823 2.668550 GCCTCCGACGCAAAGGTT 60.669 61.111 9.87 0.00 32.49 3.50
1852 1860 0.605319 CCTTTACAAGACAGCCGGCA 60.605 55.000 31.54 0.76 0.00 5.69
2034 2042 0.818040 AGCCAGTGACGGTGTTTTCC 60.818 55.000 0.00 0.00 0.00 3.13
2262 2270 1.515954 CCACGACCTGGAAGCGTAT 59.484 57.895 0.00 0.00 43.95 3.06
2556 3003 2.031683 CCGTGTTTGGTCTCTTGTTCAC 59.968 50.000 0.00 0.00 0.00 3.18
2747 3197 7.507733 TGGTATTTATGTACAAAAACGGTGT 57.492 32.000 0.00 0.00 0.00 4.16
2802 3252 2.107953 GAGATCCCGCTGTCAGCC 59.892 66.667 19.14 4.62 38.18 4.85
2838 3297 7.504403 ACTACTCCAGATACATTCATTTCAGG 58.496 38.462 0.00 0.00 0.00 3.86
2928 3403 8.732746 AAACATTGGTACTTGTCCTATATGAC 57.267 34.615 1.49 1.49 35.77 3.06
2929 3404 7.676683 ACATTGGTACTTGTCCTATATGACT 57.323 36.000 9.23 0.00 36.21 3.41
2930 3405 8.090788 ACATTGGTACTTGTCCTATATGACTT 57.909 34.615 9.23 0.00 36.21 3.01
2931 3406 8.204836 ACATTGGTACTTGTCCTATATGACTTC 58.795 37.037 9.23 0.00 36.21 3.01
2932 3407 7.727578 TTGGTACTTGTCCTATATGACTTCA 57.272 36.000 9.23 0.00 36.21 3.02
2933 3408 7.914427 TGGTACTTGTCCTATATGACTTCAT 57.086 36.000 9.23 0.00 40.22 2.57
2934 3409 9.429109 TTGGTACTTGTCCTATATGACTTCATA 57.571 33.333 9.23 1.43 42.38 2.15
3203 3685 6.424812 TCATGTTAGTGCCTAATCATTCATCG 59.575 38.462 0.00 0.00 0.00 3.84
3371 3858 9.614792 ACTTAGAATAAGTTTTGTGACAGACTT 57.385 29.630 16.75 16.75 36.42 3.01
3471 3958 6.930068 ACTACCTCTGGTACAAAGTTGTAT 57.070 37.500 7.14 0.00 44.59 2.29
3480 3967 6.870971 GGTACAAAGTTGTATCAAGGTTGA 57.129 37.500 9.16 0.00 44.59 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.492764 TACGCTTAGGCTTAGGGCTT 58.507 50.000 16.27 2.25 46.62 4.35
2 3 1.540580 CCTTACGCTTAGGCTTAGGGC 60.541 57.143 16.27 4.40 33.97 5.19
5 6 5.228665 GGATTACCTTACGCTTAGGCTTAG 58.771 45.833 0.00 0.00 36.17 2.18
99 100 0.647410 CAATAACACGAGAGCAGCCG 59.353 55.000 0.00 0.00 0.00 5.52
183 184 2.900716 TTGTCTGAACCGTCATGTCA 57.099 45.000 0.00 0.00 31.85 3.58
214 215 6.757947 CCGTGAATAAACGAGGGACTATTTTA 59.242 38.462 0.00 0.00 46.49 1.52
217 218 4.403432 TCCGTGAATAAACGAGGGACTATT 59.597 41.667 0.00 0.00 46.49 1.73
221 222 2.094338 AGTCCGTGAATAAACGAGGGAC 60.094 50.000 0.00 0.00 46.49 4.46
382 389 9.565090 TTTGTCCAATGAATATATGAGAGGAAG 57.435 33.333 0.00 0.00 0.00 3.46
410 417 3.327757 TGCTATTCCTCAATTATCCGCCT 59.672 43.478 0.00 0.00 0.00 5.52
412 419 5.392380 CCAATGCTATTCCTCAATTATCCGC 60.392 44.000 0.00 0.00 0.00 5.54
421 428 3.494924 CGGTCATCCAATGCTATTCCTCA 60.495 47.826 0.00 0.00 0.00 3.86
566 573 5.394224 CGAGATGAAGGAGTTAAGTAGCCAA 60.394 44.000 0.00 0.00 0.00 4.52
599 606 0.034059 AGAAATCGGCGGCCTATCAG 59.966 55.000 18.34 0.39 0.00 2.90
612 619 6.583912 TTAACATGAATCGTCCGAGAAATC 57.416 37.500 0.00 0.00 0.00 2.17
652 659 6.675971 GCGAAACCGGTCACAATATATTTCAA 60.676 38.462 8.04 0.00 0.00 2.69
932 940 1.532505 CGGGTACGTACGTCCAAGATG 60.533 57.143 26.53 5.86 34.81 2.90
1815 1823 3.235481 TTCCGGAACCCGCACTCA 61.235 61.111 14.35 0.00 46.86 3.41
2262 2270 2.475466 GCCGTCGACGAGGTGGATA 61.475 63.158 37.65 0.00 43.02 2.59
2556 3003 2.746277 AGCTGCTTTTACCCGCCG 60.746 61.111 0.00 0.00 0.00 6.46
2599 3047 3.116079 TGGTAAAACTTGAGGACCGAC 57.884 47.619 0.00 0.00 32.55 4.79
2600 3048 3.135167 ACTTGGTAAAACTTGAGGACCGA 59.865 43.478 0.00 0.00 32.55 4.69
2660 3110 4.826733 ACTTTGATGTGCACACCAATTCTA 59.173 37.500 26.95 11.47 0.00 2.10
2743 3193 3.619929 ACGTAAGACAAGACAACAACACC 59.380 43.478 0.00 0.00 43.62 4.16
2747 3197 4.496360 TCACACGTAAGACAAGACAACAA 58.504 39.130 0.00 0.00 43.62 2.83
2838 3297 3.181485 CCTCTGTCCAGAATTACTCGACC 60.181 52.174 0.00 0.00 36.22 4.79
2897 3356 9.747898 ATAGGACAAGTACCAATGTTTTATCAA 57.252 29.630 0.00 0.00 0.00 2.57
2955 3430 6.399639 ACAAATAGTGGAACCGACAATTTT 57.600 33.333 0.00 0.00 37.80 1.82
3203 3685 2.741517 GTGGCATACAACAAATTTGGCC 59.258 45.455 21.74 21.07 40.51 5.36
3356 3843 6.954944 TGCACTTATAAGTCTGTCACAAAAC 58.045 36.000 15.35 0.00 37.08 2.43
3397 3884 7.668492 ACGGAGGGACTAATATCATAACTTTC 58.332 38.462 0.00 0.00 41.55 2.62
3404 3891 4.405756 AGGACGGAGGGACTAATATCAT 57.594 45.455 0.00 0.00 41.55 2.45
3413 3900 5.434408 ACATTTATTTTAGGACGGAGGGAC 58.566 41.667 0.00 0.00 0.00 4.46
3452 3939 5.643777 CCTTGATACAACTTTGTACCAGAGG 59.356 44.000 3.95 7.02 45.47 3.69


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

AutoCloner maintained by Alex Coulton.