Multiple sequence alignment - TraesCS1D01G076000

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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 TraesCS1D01G076000 chr1D 100.000 3590 0 0 1 3590 58450558 58454147 0.000000e+00 6630.0
1 TraesCS1D01G076000 chr1A 95.979 2512 58 15 576 3049 57192068 57194574 0.000000e+00 4039.0
2 TraesCS1D01G076000 chr1A 81.883 1402 219 29 1054 2448 57392133 57390760 0.000000e+00 1149.0
3 TraesCS1D01G076000 chr1A 95.165 455 17 5 3027 3479 57194598 57195049 0.000000e+00 713.0
4 TraesCS1D01G076000 chr1A 93.627 408 18 6 105 510 57393090 57392689 1.430000e-168 603.0
5 TraesCS1D01G076000 chr1A 92.347 392 19 5 141 525 57191556 57191943 6.780000e-152 547.0
6 TraesCS1D01G076000 chr1A 82.609 253 33 6 2604 2845 57194646 57194898 2.810000e-51 213.0
7 TraesCS1D01G076000 chr1A 95.192 104 5 0 1 104 57393242 57393139 7.970000e-37 165.0
8 TraesCS1D01G076000 chr1A 93.684 95 3 2 3499 3590 57196526 57196620 4.830000e-29 139.0
9 TraesCS1D01G076000 chr1B 90.978 2782 128 57 142 2857 94185253 94182529 0.000000e+00 3633.0
10 TraesCS1D01G076000 chr1B 85.714 1477 151 36 844 2301 94200139 94198704 0.000000e+00 1504.0
11 TraesCS1D01G076000 chr1B 91.914 371 25 3 141 510 94201250 94200884 6.870000e-142 514.0
12 TraesCS1D01G076000 chr1B 89.423 104 11 0 1 104 94201432 94201329 8.090000e-27 132.0
13 TraesCS1D01G076000 chr1B 89.362 47 5 0 596 642 94200533 94200487 3.870000e-05 60.2


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 TraesCS1D01G076000 chr1D 58450558 58454147 3589 False 6630.00 6630 100.00000 1 3590 1 chr1D.!!$F1 3589
1 TraesCS1D01G076000 chr1A 57191556 57196620 5064 False 1130.20 4039 91.95680 141 3590 5 chr1A.!!$F1 3449
2 TraesCS1D01G076000 chr1A 57390760 57393242 2482 True 639.00 1149 90.23400 1 2448 3 chr1A.!!$R1 2447
3 TraesCS1D01G076000 chr1B 94182529 94185253 2724 True 3633.00 3633 90.97800 142 2857 1 chr1B.!!$R1 2715
4 TraesCS1D01G076000 chr1B 94198704 94201432 2728 True 552.55 1504 89.10325 1 2301 4 chr1B.!!$R2 2300

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
905 1515 0.674581 CGTCTCCAAGCTGGCATTCA 60.675 55.0 0.0 0.0 37.47 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2629 3255 1.729586 AGGCCCAGACAGTCAGTTTA 58.27 50.0 0.0 0.0 0.0 2.01 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 6.780031 TCCTTGAATGGTTAAGTTTCAATCCA 59.220 34.615 7.47 0.00 38.34 3.41
122 177 5.523013 GCATGCGGCTTTTATTAAAAACA 57.477 34.783 0.00 1.12 40.25 2.83
222 277 3.107601 TGAAGACTATAGCTGCCAGGTT 58.892 45.455 0.00 0.00 0.00 3.50
236 298 3.831911 TGCCAGGTTAAAGAAATTCAGGG 59.168 43.478 0.00 0.00 0.00 4.45
262 324 8.681486 ATCATGTACATCTTGCTATGCTAAAA 57.319 30.769 5.07 0.00 0.00 1.52
403 467 0.968901 TATCGACACGGACAAGGCCT 60.969 55.000 0.00 0.00 0.00 5.19
435 499 3.131577 CCTGCTTGGACATATGCACAAAT 59.868 43.478 1.58 0.00 38.35 2.32
497 561 2.280103 TGGTCTATGCCCCCAAGTTTA 58.720 47.619 0.00 0.00 0.00 2.01
515 579 7.168135 CCAAGTTTAATCTGCTGTTTCTGAAAC 59.832 37.037 22.94 22.94 41.73 2.78
516 580 6.739112 AGTTTAATCTGCTGTTTCTGAAACC 58.261 36.000 25.66 14.48 40.67 3.27
518 582 4.843220 AATCTGCTGTTTCTGAAACCAG 57.157 40.909 25.66 24.01 40.67 4.00
525 589 3.030291 TGTTTCTGAAACCAGGCACATT 58.970 40.909 25.66 0.00 40.67 2.71
526 590 3.181477 TGTTTCTGAAACCAGGCACATTG 60.181 43.478 25.66 0.00 40.67 2.82
527 591 1.619654 TCTGAAACCAGGCACATTGG 58.380 50.000 0.00 0.00 41.60 3.16
746 1158 3.859961 AGTTGAATCTCGTATTGTCTGCG 59.140 43.478 0.00 0.00 0.00 5.18
905 1515 0.674581 CGTCTCCAAGCTGGCATTCA 60.675 55.000 0.00 0.00 37.47 2.57
1600 2213 2.238395 GAGAACCAGATGCCCTTCTTCT 59.762 50.000 0.00 0.00 0.00 2.85
1620 2233 2.384899 TACTCGTTGATCTCATCGCG 57.615 50.000 0.00 0.00 38.52 5.87
1622 2235 1.132453 ACTCGTTGATCTCATCGCGAA 59.868 47.619 15.24 0.00 38.26 4.70
1626 2239 1.007011 GTTGATCTCATCGCGAACACG 60.007 52.381 15.24 1.88 0.00 4.49
2172 2785 1.676635 GCTGCTGAACCTGATGGCA 60.677 57.895 0.00 0.00 36.63 4.92
2608 3230 0.951558 AAATGCACCGGAGTGTCAAC 59.048 50.000 9.46 0.00 46.35 3.18
2609 3231 1.227999 AATGCACCGGAGTGTCAACG 61.228 55.000 9.46 0.00 46.35 4.10
2614 3236 1.068417 CCGGAGTGTCAACGACCAA 59.932 57.895 0.00 0.00 0.00 3.67
2617 3239 1.871039 CGGAGTGTCAACGACCAAAAT 59.129 47.619 0.00 0.00 0.00 1.82
2620 3242 3.066203 GGAGTGTCAACGACCAAAATGTT 59.934 43.478 0.00 0.00 0.00 2.71
2787 3422 9.768662 AACTTGAGCTTGATGAATGTTTAAAAT 57.231 25.926 0.00 0.00 0.00 1.82
2845 3481 9.956797 GCAATGAATGTAAAATTTGTATGTCAC 57.043 29.630 0.00 0.00 0.00 3.67
2886 3522 6.933521 ACACATGCTTTAATATGCCACAAAAA 59.066 30.769 0.00 0.00 0.00 1.94
2887 3523 7.607223 ACACATGCTTTAATATGCCACAAAAAT 59.393 29.630 0.00 0.00 0.00 1.82
2954 3590 5.356751 CCAGGAACCGTTAATCAATGAATGA 59.643 40.000 0.00 0.00 43.67 2.57
2975 3611 2.541466 TGGTTTTCTCCTCTCCTCTCC 58.459 52.381 0.00 0.00 0.00 3.71
2976 3612 1.834896 GGTTTTCTCCTCTCCTCTCCC 59.165 57.143 0.00 0.00 0.00 4.30
2977 3613 1.834896 GTTTTCTCCTCTCCTCTCCCC 59.165 57.143 0.00 0.00 0.00 4.81
2978 3614 1.398799 TTTCTCCTCTCCTCTCCCCT 58.601 55.000 0.00 0.00 0.00 4.79
2979 3615 2.305345 TTCTCCTCTCCTCTCCCCTA 57.695 55.000 0.00 0.00 0.00 3.53
3056 3736 1.077858 CCTTCCCTCTCTGCCTTGC 60.078 63.158 0.00 0.00 0.00 4.01
3061 3741 3.123620 CTCTCTGCCTTGCCGTGC 61.124 66.667 0.00 0.00 0.00 5.34
3100 3780 7.456253 CGTCAAGTACCAGAACATTATCTTTG 58.544 38.462 0.00 0.00 0.00 2.77
3103 3783 5.815581 AGTACCAGAACATTATCTTTGGCA 58.184 37.500 0.00 0.00 0.00 4.92
3158 3838 2.363975 TAGTCCACGGGCCCATGTC 61.364 63.158 24.92 12.42 0.00 3.06
3191 3871 7.907045 GTGTGCATATACAAGAGAAGTGATTTG 59.093 37.037 0.00 0.00 31.36 2.32
3254 3935 9.692325 ATATAAGAAACTTGAGCTTGAGGAATT 57.308 29.630 0.00 0.00 0.00 2.17
3256 3937 7.823745 AAGAAACTTGAGCTTGAGGAATTTA 57.176 32.000 0.00 0.00 0.00 1.40
3522 5672 2.969628 TTTTTGCGGCAAGGAAAGAA 57.030 40.000 15.78 3.34 41.17 2.52
3523 5673 2.507339 TTTTGCGGCAAGGAAAGAAG 57.493 45.000 15.78 0.00 41.17 2.85
3533 5683 4.056050 GCAAGGAAAGAAGTACGAACTCA 58.944 43.478 0.00 0.00 33.75 3.41
3546 5696 1.673168 GAACTCATGATCCTGCACCC 58.327 55.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.118496 ACAATTTTGGGTGAGAACAATGTTA 57.882 32.000 0.00 0.00 0.00 2.41
34 35 4.537751 TGGTACAATTTTGGGTGAGAACA 58.462 39.130 0.00 0.00 31.92 3.18
35 36 4.825085 TCTGGTACAATTTTGGGTGAGAAC 59.175 41.667 0.00 0.00 38.70 3.01
222 277 9.342308 GATGTACATGATCCCTGAATTTCTTTA 57.658 33.333 14.43 0.00 0.00 1.85
236 298 7.895975 TTAGCATAGCAAGATGTACATGATC 57.104 36.000 14.43 0.00 0.00 2.92
262 324 5.618236 TGAGCATAGCTATGAGATTTTGCT 58.382 37.500 33.10 22.84 39.88 3.91
291 354 5.240403 GCATTTGGTTGCAAAAAGGGATAAA 59.760 36.000 0.00 0.00 42.31 1.40
292 355 4.759183 GCATTTGGTTGCAAAAAGGGATAA 59.241 37.500 0.00 0.00 42.31 1.75
293 356 4.322567 GCATTTGGTTGCAAAAAGGGATA 58.677 39.130 0.00 0.00 42.31 2.59
403 467 0.850100 TCCAAGCAGGGTTCCTTCAA 59.150 50.000 0.00 0.00 38.24 2.69
497 561 3.571401 CCTGGTTTCAGAAACAGCAGATT 59.429 43.478 24.37 0.00 46.95 2.40
515 579 3.289836 TGAATCATACCAATGTGCCTGG 58.710 45.455 0.00 0.00 40.05 4.45
516 580 3.243301 GCTGAATCATACCAATGTGCCTG 60.243 47.826 0.00 0.00 34.50 4.85
518 582 2.689471 TGCTGAATCATACCAATGTGCC 59.311 45.455 0.00 0.00 34.50 5.01
525 589 2.689471 GCACCATTGCTGAATCATACCA 59.311 45.455 0.00 0.00 46.17 3.25
526 590 3.360249 GCACCATTGCTGAATCATACC 57.640 47.619 0.00 0.00 46.17 2.73
552 907 0.327095 TATAGCCCCAGGTGAAGCCA 60.327 55.000 0.00 0.00 40.61 4.75
553 908 0.108774 GTATAGCCCCAGGTGAAGCC 59.891 60.000 0.00 0.00 37.58 4.35
746 1158 5.050837 CCAATTCTTTGCTTTGCTTGTACAC 60.051 40.000 0.00 0.00 0.00 2.90
905 1515 1.213926 GGAATGGAATCTGAGCCCAGT 59.786 52.381 0.00 4.34 41.16 4.00
1338 1951 4.451150 TGGATGACGGCGAGGTGC 62.451 66.667 16.62 4.19 45.38 5.01
1600 2213 2.353579 TCGCGATGAGATCAACGAGTAA 59.646 45.455 15.50 0.00 43.47 2.24
1620 2233 2.357034 TCCGGCAGCTTCGTGTTC 60.357 61.111 0.00 0.00 0.00 3.18
1622 2235 3.165160 AACTCCGGCAGCTTCGTGT 62.165 57.895 0.00 2.14 0.00 4.49
1626 2239 1.807573 CTCGAACTCCGGCAGCTTC 60.808 63.158 0.00 2.12 39.14 3.86
2172 2785 2.202623 GACGCCGACTGCTCGAAT 60.203 61.111 0.00 0.00 43.06 3.34
2614 3236 9.131791 ACAGTCAGTTTACCAAAGATAACATTT 57.868 29.630 0.00 0.00 0.00 2.32
2617 3239 7.441157 CAGACAGTCAGTTTACCAAAGATAACA 59.559 37.037 2.66 0.00 0.00 2.41
2620 3242 6.464222 CCAGACAGTCAGTTTACCAAAGATA 58.536 40.000 2.66 0.00 0.00 1.98
2629 3255 1.729586 AGGCCCAGACAGTCAGTTTA 58.270 50.000 0.00 0.00 0.00 2.01
2886 3522 8.985315 ATAATCCGGCAACATAATGATCATAT 57.015 30.769 9.04 2.30 0.00 1.78
2887 3523 9.546428 CTATAATCCGGCAACATAATGATCATA 57.454 33.333 9.04 0.00 0.00 2.15
2954 3590 3.111484 GGAGAGGAGAGGAGAAAACCAT 58.889 50.000 0.00 0.00 0.00 3.55
2975 3611 1.380280 TGAGGGGGAGGAGGATAGGG 61.380 65.000 0.00 0.00 0.00 3.53
2976 3612 0.178918 GTGAGGGGGAGGAGGATAGG 60.179 65.000 0.00 0.00 0.00 2.57
2977 3613 0.178918 GGTGAGGGGGAGGAGGATAG 60.179 65.000 0.00 0.00 0.00 2.08
2978 3614 1.675936 GGGTGAGGGGGAGGAGGATA 61.676 65.000 0.00 0.00 0.00 2.59
2979 3615 2.706071 GGTGAGGGGGAGGAGGAT 59.294 66.667 0.00 0.00 0.00 3.24
3021 3657 1.686110 GGAAGAAGGAGGGGCGAGA 60.686 63.158 0.00 0.00 0.00 4.04
3115 3795 1.003839 CGCTAGAACACAAGGCCCA 60.004 57.895 0.00 0.00 0.00 5.36
3304 3985 6.276611 TGACGTACACATTTTACAAGACAC 57.723 37.500 0.00 0.00 0.00 3.67
3503 5653 2.167487 ACTTCTTTCCTTGCCGCAAAAA 59.833 40.909 7.33 5.14 0.00 1.94
3504 5654 1.754226 ACTTCTTTCCTTGCCGCAAAA 59.246 42.857 7.33 0.00 0.00 2.44
3505 5655 1.398692 ACTTCTTTCCTTGCCGCAAA 58.601 45.000 7.33 0.00 0.00 3.68
3506 5656 1.877443 GTACTTCTTTCCTTGCCGCAA 59.123 47.619 5.52 5.52 0.00 4.85
3507 5657 1.519408 GTACTTCTTTCCTTGCCGCA 58.481 50.000 0.00 0.00 0.00 5.69
3508 5658 0.442699 CGTACTTCTTTCCTTGCCGC 59.557 55.000 0.00 0.00 0.00 6.53
3509 5659 2.074547 TCGTACTTCTTTCCTTGCCG 57.925 50.000 0.00 0.00 0.00 5.69
3510 5660 3.400255 AGTTCGTACTTCTTTCCTTGCC 58.600 45.455 0.00 0.00 0.00 4.52
3511 5661 4.056050 TGAGTTCGTACTTCTTTCCTTGC 58.944 43.478 0.00 0.00 33.84 4.01
3512 5662 5.926542 TCATGAGTTCGTACTTCTTTCCTTG 59.073 40.000 0.00 0.00 33.84 3.61
3513 5663 6.097915 TCATGAGTTCGTACTTCTTTCCTT 57.902 37.500 0.00 0.00 33.84 3.36
3515 5665 5.520649 GGATCATGAGTTCGTACTTCTTTCC 59.479 44.000 0.09 0.00 33.84 3.13
3516 5666 6.254589 CAGGATCATGAGTTCGTACTTCTTTC 59.745 42.308 0.00 0.00 33.84 2.62
3517 5667 6.102663 CAGGATCATGAGTTCGTACTTCTTT 58.897 40.000 0.00 0.00 33.84 2.52
3518 5668 5.655488 CAGGATCATGAGTTCGTACTTCTT 58.345 41.667 0.00 0.00 33.84 2.52
3519 5669 4.440802 GCAGGATCATGAGTTCGTACTTCT 60.441 45.833 12.39 0.00 33.84 2.85
3520 5670 3.799420 GCAGGATCATGAGTTCGTACTTC 59.201 47.826 12.39 0.00 33.84 3.01
3521 5671 3.195610 TGCAGGATCATGAGTTCGTACTT 59.804 43.478 12.39 0.00 33.84 2.24
3522 5672 2.760650 TGCAGGATCATGAGTTCGTACT 59.239 45.455 12.39 0.00 37.31 2.73
3523 5673 2.860735 GTGCAGGATCATGAGTTCGTAC 59.139 50.000 12.39 0.00 0.00 3.67
3533 5683 2.053244 CTAGAAGGGGTGCAGGATCAT 58.947 52.381 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.