Multiple sequence alignment - TraesCS1D01G122800

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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 TraesCS1D01G122800 chr1D 100.000 4603 0 0 1 4603 123704461 123699859 0.000000e+00 8501.0
1 TraesCS1D01G122800 chr1D 100.000 29 0 0 2794 2822 245970083 245970111 2.000000e-03 54.7
2 TraesCS1D01G122800 chr1B 94.782 4638 170 33 2 4603 188266252 188261651 0.000000e+00 7158.0
3 TraesCS1D01G122800 chr1A 94.446 4663 179 34 2 4603 135972628 135967985 0.000000e+00 7103.0
4 TraesCS1D01G122800 chr1A 93.162 117 8 0 2 118 136069260 136069144 6.120000e-39 172.0
5 TraesCS1D01G122800 chr1A 92.308 117 9 0 2 118 136068836 136068720 2.850000e-37 167.0
6 TraesCS1D01G122800 chr1A 100.000 29 0 0 2794 2822 306637086 306637114 2.000000e-03 54.7
7 TraesCS1D01G122800 chr2D 82.353 408 62 6 4196 4603 43285094 43284697 3.410000e-91 346.0
8 TraesCS1D01G122800 chr6A 83.838 99 16 0 2723 2821 472520795 472520697 1.360000e-15 95.3
9 TraesCS1D01G122800 chr3D 82.692 104 16 2 2723 2825 513951647 513951749 1.760000e-14 91.6
10 TraesCS1D01G122800 chr7A 100.000 29 0 0 2796 2824 454053272 454053300 2.000000e-03 54.7
11 TraesCS1D01G122800 chr6D 100.000 29 0 0 2794 2822 302113726 302113754 2.000000e-03 54.7
12 TraesCS1D01G122800 chr4B 96.774 31 1 0 2794 2824 362839882 362839852 8.000000e-03 52.8


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 TraesCS1D01G122800 chr1D 123699859 123704461 4602 True 8501 8501 100.000 1 4603 1 chr1D.!!$R1 4602
1 TraesCS1D01G122800 chr1B 188261651 188266252 4601 True 7158 7158 94.782 2 4603 1 chr1B.!!$R1 4601
2 TraesCS1D01G122800 chr1A 135967985 135972628 4643 True 7103 7103 94.446 2 4603 1 chr1A.!!$R1 4601

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
567 580 0.905337 AGTCTTCTTCCACCTCCGGG 60.905 60.000 0.00 0.00 38.88 5.73 F
864 909 1.000274 GGCGTGCAATTAATCCCATCC 60.000 52.381 0.00 0.00 0.00 3.51 F
1973 2035 1.927174 ACTCTGCATTCGTATCGTTGC 59.073 47.619 0.00 10.74 37.49 4.17 F
2901 2968 0.740737 ATAAAACTGCAGGATGGCGC 59.259 50.000 19.93 0.00 35.86 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1797 0.253044 CAGCAACCCTGGCTAGCTTA 59.747 55.0 15.72 3.29 40.23 3.09 R
2430 2493 1.040893 AGGTATGACGATCACGCCCA 61.041 55.0 0.00 0.00 43.96 5.36 R
3496 3579 0.994247 TCCTGCATCATGGTCAAGGT 59.006 50.0 3.84 0.00 0.00 3.50 R
4209 4293 1.536943 AACTCTCCCAGCAGGACGAC 61.537 60.0 0.00 0.00 40.93 4.34 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
108 109 4.261698 GCTAGCAGCCTAGTTAGTTCCTAC 60.262 50.000 10.63 0.00 42.51 3.18
177 182 4.720046 AGAGGTGAATAGAGATGACGCTA 58.280 43.478 0.00 0.00 33.42 4.26
299 310 7.994425 TTTTCATATGTGCTAGGTTTTCTCA 57.006 32.000 1.90 0.00 0.00 3.27
331 343 5.482878 CCTTGTAGGGTTAGTGAAAGAGGTA 59.517 44.000 0.00 0.00 0.00 3.08
341 353 1.435563 TGAAAGAGGTAGAGGGGTGGA 59.564 52.381 0.00 0.00 0.00 4.02
352 364 1.215423 GAGGGGTGGAGGCAAACATAT 59.785 52.381 0.00 0.00 0.00 1.78
405 417 2.001076 AGCTGGCTAAAAACTGGCTT 57.999 45.000 0.00 0.00 0.00 4.35
446 458 3.895232 ACAAGTCGAATATGAGCCACT 57.105 42.857 0.00 0.00 0.00 4.00
475 488 6.293135 GCAATTTTCTTTTGCGGGAATAAACA 60.293 34.615 0.00 0.00 39.98 2.83
510 523 1.837439 CAACTCCAGCATACACCCCTA 59.163 52.381 0.00 0.00 0.00 3.53
539 552 5.163612 GGAATGAAATTGCAAGTAGGTCCTC 60.164 44.000 4.94 0.00 44.83 3.71
567 580 0.905337 AGTCTTCTTCCACCTCCGGG 60.905 60.000 0.00 0.00 38.88 5.73
584 597 2.098117 CCGGGATCTCAAGTCAATTTGC 59.902 50.000 0.00 0.00 0.00 3.68
586 599 2.749621 GGGATCTCAAGTCAATTTGCGT 59.250 45.455 0.00 0.00 0.00 5.24
864 909 1.000274 GGCGTGCAATTAATCCCATCC 60.000 52.381 0.00 0.00 0.00 3.51
1075 1126 2.433838 CCTGCGCTGTGGTCAGAG 60.434 66.667 9.73 0.00 43.76 3.35
1179 1230 3.334054 AAGGAGCAGTCCCAGGGC 61.334 66.667 0.00 0.00 45.26 5.19
1442 1495 7.295930 TGCAATTACATCGATACGACTAGTAG 58.704 38.462 0.00 0.00 39.18 2.57
1443 1496 6.741811 GCAATTACATCGATACGACTAGTAGG 59.258 42.308 7.94 0.00 39.18 3.18
1444 1497 7.360691 GCAATTACATCGATACGACTAGTAGGA 60.361 40.741 7.94 0.00 39.18 2.94
1445 1498 7.830940 ATTACATCGATACGACTAGTAGGAG 57.169 40.000 7.94 0.00 39.18 3.69
1446 1499 5.212532 ACATCGATACGACTAGTAGGAGT 57.787 43.478 7.94 3.77 39.18 3.85
1447 1500 6.338214 ACATCGATACGACTAGTAGGAGTA 57.662 41.667 7.94 5.87 39.18 2.59
1556 1609 3.425193 GCTACCTGTGTTTGCATTTTTCG 59.575 43.478 0.00 0.00 0.00 3.46
1683 1736 9.487790 CATTAAAACCCAAACTATGACATGTTT 57.512 29.630 0.00 4.46 36.91 2.83
1964 2026 5.582550 TGTCATAAGAGTACTCTGCATTCG 58.417 41.667 25.83 11.44 40.36 3.34
1973 2035 1.927174 ACTCTGCATTCGTATCGTTGC 59.073 47.619 0.00 10.74 37.49 4.17
2016 2079 7.602265 TCAATGTCATTTCTTCTTCATACGACA 59.398 33.333 0.00 0.00 35.54 4.35
2053 2116 7.110155 GGTTCCATTACCTCAAGATAACAGAA 58.890 38.462 0.00 0.00 35.23 3.02
2571 2634 1.346068 TGGCTACAGTGTGCACATACA 59.654 47.619 24.69 11.25 0.00 2.29
2594 2657 3.806949 TTTCCTCTACTTGCCACCAAT 57.193 42.857 0.00 0.00 0.00 3.16
2687 2750 3.377172 ACAACTAAACACACAAGCTCCAC 59.623 43.478 0.00 0.00 0.00 4.02
2747 2813 7.504403 ACTCCCTCAGATTCATATTACTTGTG 58.496 38.462 0.00 0.00 0.00 3.33
2766 2832 4.952460 TGTGACCCACTTAGTACAACTTC 58.048 43.478 0.00 0.00 35.11 3.01
2788 2854 9.609346 ACTTCAGTACAAAGTTGTATTAAGTGT 57.391 29.630 18.22 8.87 44.59 3.55
2790 2856 8.951787 TCAGTACAAAGTTGTATTAAGTGTGT 57.048 30.769 7.14 0.00 44.59 3.72
2792 2858 8.067784 CAGTACAAAGTTGTATTAAGTGTGTGG 58.932 37.037 7.14 0.00 44.59 4.17
2829 2895 8.373220 GGATCGGAGGGAGTATTAAATTCTAAA 58.627 37.037 0.00 0.00 0.00 1.85
2838 2905 9.628500 GGAGTATTAAATTCTAAAGTGACCCAT 57.372 33.333 0.00 0.00 0.00 4.00
2901 2968 0.740737 ATAAAACTGCAGGATGGCGC 59.259 50.000 19.93 0.00 35.86 6.53
3021 3094 8.519526 TGTTATGGTTCTGCCTAAATTTGTAAG 58.480 33.333 0.00 0.00 38.35 2.34
3119 3192 2.106511 CTCTGGAAAAACCTGTCCTGGA 59.893 50.000 0.00 0.00 39.86 3.86
3164 3237 7.386059 AGAAATTGTTGAAAGGTGTCAAAAGT 58.614 30.769 0.00 0.00 39.18 2.66
3251 3324 7.636150 AAGACTGGTCAATTGATTTCTATGG 57.364 36.000 12.12 0.00 0.00 2.74
3267 3340 9.979578 GATTTCTATGGATCTCGAGCATATTAT 57.020 33.333 7.81 0.00 0.00 1.28
3288 3361 2.371841 TGTCCACATGACTTTAGCACCT 59.628 45.455 0.00 0.00 44.75 4.00
3344 3417 6.533730 AGACTCACTGTTCCATGTTTTATGA 58.466 36.000 0.00 0.00 0.00 2.15
3378 3451 2.858344 CTCTTAGTTGACATTACCGCGG 59.142 50.000 26.86 26.86 0.00 6.46
3436 3519 6.912203 TTTGCAATTCATTATGCTGGATTG 57.088 33.333 0.00 1.22 42.63 2.67
3496 3579 4.055360 CGACAACACAATGACCTTCTACA 58.945 43.478 0.00 0.00 0.00 2.74
3505 3588 2.684943 TGACCTTCTACACCTTGACCA 58.315 47.619 0.00 0.00 0.00 4.02
3578 3661 0.739813 CACGAGACCCGGATGGAAAC 60.740 60.000 0.73 0.00 43.93 2.78
3616 3699 5.580691 CACAAGTGTAACAAGTGAGAGTCAA 59.419 40.000 0.00 0.00 43.60 3.18
4006 4090 2.158957 TCCCATCCGAAAGCTGTATGTC 60.159 50.000 0.00 0.00 0.00 3.06
4049 4133 4.194640 TGCTTTCATGGAAGATCAGTAGC 58.805 43.478 18.45 0.16 0.00 3.58
4238 4322 0.178944 TGGGAGAGTTCGGACTGGAA 60.179 55.000 0.00 0.00 35.88 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.003859 TGAAAAACACTGGAGTTAGGGTAA 57.996 37.500 0.00 0.00 31.86 2.85
108 109 0.685458 CTTCCCAATGCCCTTCCTGG 60.685 60.000 0.00 0.00 0.00 4.45
204 209 1.000771 CTCTCTCTCCCGACCCACA 60.001 63.158 0.00 0.00 0.00 4.17
331 343 1.142688 ATGTTTGCCTCCACCCCTCT 61.143 55.000 0.00 0.00 0.00 3.69
341 353 4.603131 AGTTGGTCATCATATGTTTGCCT 58.397 39.130 1.90 0.00 0.00 4.75
352 364 7.496346 ACTATTAAAGAGGAGTTGGTCATCA 57.504 36.000 0.00 0.00 38.52 3.07
384 396 2.437413 AGCCAGTTTTTAGCCAGCTAC 58.563 47.619 0.00 0.00 0.00 3.58
398 410 6.209986 TGATTTTGATTCAATCTCAAGCCAGT 59.790 34.615 0.00 0.00 34.33 4.00
431 443 2.279741 GCACAAGTGGCTCATATTCGA 58.720 47.619 2.00 0.00 0.00 3.71
475 488 4.746466 TGGAGTTGGTTTAATGGATTGGT 58.254 39.130 0.00 0.00 0.00 3.67
510 523 6.041979 ACCTACTTGCAATTTCATTCCTTGTT 59.958 34.615 0.00 0.00 0.00 2.83
539 552 0.955919 GGAAGAAGACTTGTGCCCCG 60.956 60.000 0.00 0.00 36.39 5.73
567 580 4.084507 CGAACGCAAATTGACTTGAGATC 58.915 43.478 0.00 0.00 31.37 2.75
584 597 0.456312 AACTCGGCTTAGAGCGAACG 60.456 55.000 0.00 0.00 43.62 3.95
586 599 2.490903 ACTAAACTCGGCTTAGAGCGAA 59.509 45.455 0.00 0.00 43.62 4.70
763 808 9.807649 GCAAATAGTAGGACAATGATCATTTTT 57.192 29.630 18.41 10.07 0.00 1.94
864 909 3.157932 TCTGGTTTTCTTTTTGGTGCG 57.842 42.857 0.00 0.00 0.00 5.34
891 936 5.828328 CCTTTTACTGTCTCTTTCAGGGTTT 59.172 40.000 0.00 0.00 37.25 3.27
979 1024 3.437642 TGGCCTTCCCAAGAACAAG 57.562 52.632 3.32 0.00 41.82 3.16
1075 1126 1.812922 CAGAGGGAGTGTGATGCGC 60.813 63.158 0.00 0.00 0.00 6.09
1218 1269 7.287810 TGTGCTATCAGTACTAGATAGGAACA 58.712 38.462 26.41 22.53 44.44 3.18
1409 1462 4.313277 TCGATGTAATTGCAGAGAGAGG 57.687 45.455 1.90 0.00 0.00 3.69
1442 1495 7.175293 CCATGGTACTGATCTAACTAGTACTCC 59.825 44.444 15.84 5.52 43.79 3.85
1443 1496 7.720515 ACCATGGTACTGATCTAACTAGTACTC 59.279 40.741 18.10 9.44 43.79 2.59
1444 1497 7.584532 ACCATGGTACTGATCTAACTAGTACT 58.415 38.462 18.10 0.00 43.79 2.73
1445 1498 7.720515 AGACCATGGTACTGATCTAACTAGTAC 59.279 40.741 19.80 10.42 43.66 2.73
1446 1499 7.813331 AGACCATGGTACTGATCTAACTAGTA 58.187 38.462 19.80 0.00 0.00 1.82
1447 1500 6.674573 AGACCATGGTACTGATCTAACTAGT 58.325 40.000 19.80 0.00 0.00 2.57
1556 1609 1.138661 CTGCTCCTCAGAACCTCCATC 59.861 57.143 0.00 0.00 45.72 3.51
1683 1736 6.209986 TGCTACTTCAGTACCAGCTACTAAAA 59.790 38.462 0.00 0.00 33.53 1.52
1744 1797 0.253044 CAGCAACCCTGGCTAGCTTA 59.747 55.000 15.72 3.29 40.23 3.09
1781 1834 4.457257 TGAACACCGTGAATGCAAATATCA 59.543 37.500 5.28 0.00 0.00 2.15
1964 2026 5.912955 ACAAAAACTTGCTTAGCAACGATAC 59.087 36.000 16.30 0.00 43.99 2.24
1973 2035 6.751425 TGACATTGACACAAAAACTTGCTTAG 59.249 34.615 0.00 0.00 0.00 2.18
2016 2079 4.386424 GGTAATGGAACCCAGCCTTTCTAT 60.386 45.833 0.00 0.00 36.75 1.98
2053 2116 4.817318 ACTTTGACCCAAAATGTGTTGT 57.183 36.364 0.00 0.00 32.75 3.32
2400 2463 1.608717 GGCGTCCTGTCAGTGGATCT 61.609 60.000 0.00 0.00 35.87 2.75
2430 2493 1.040893 AGGTATGACGATCACGCCCA 61.041 55.000 0.00 0.00 43.96 5.36
2571 2634 4.112634 TGGTGGCAAGTAGAGGAAAAAT 57.887 40.909 0.00 0.00 0.00 1.82
2687 2750 8.183104 TCCATGAGTAAGTATACAGATCCTTG 57.817 38.462 5.50 0.75 34.29 3.61
2730 2796 7.200434 AGTGGGTCACAAGTAATATGAATCT 57.800 36.000 0.78 0.00 36.74 2.40
2747 2813 5.211174 ACTGAAGTTGTACTAAGTGGGTC 57.789 43.478 0.00 0.00 0.00 4.46
2766 2832 8.067784 CCACACACTTAATACAACTTTGTACTG 58.932 37.037 3.95 0.00 45.47 2.74
2788 2854 3.389656 TCCGATCCATATTACTTGCCACA 59.610 43.478 0.00 0.00 0.00 4.17
2790 2856 3.007940 CCTCCGATCCATATTACTTGCCA 59.992 47.826 0.00 0.00 0.00 4.92
2792 2858 3.260884 TCCCTCCGATCCATATTACTTGC 59.739 47.826 0.00 0.00 0.00 4.01
2829 2895 2.528564 CATGGGTTTTCATGGGTCACT 58.471 47.619 0.00 0.00 40.43 3.41
2901 2968 3.316308 GCAACCATATCTACCAAGGCAAG 59.684 47.826 0.00 0.00 0.00 4.01
3021 3094 3.562635 GCCTGACTACGGCAACAC 58.437 61.111 0.00 0.00 46.77 3.32
3150 3223 1.404035 GACCGCACTTTTGACACCTTT 59.596 47.619 0.00 0.00 0.00 3.11
3164 3237 4.729227 TCAACTATAACATCAGACCGCA 57.271 40.909 0.00 0.00 0.00 5.69
3249 3322 4.772100 TGGACATAATATGCTCGAGATCCA 59.228 41.667 18.75 4.98 0.00 3.41
3251 3324 5.714047 TGTGGACATAATATGCTCGAGATC 58.286 41.667 18.75 0.00 0.00 2.75
3288 3361 6.156775 TCTCATGTCAAAGAGATGGGAATGTA 59.843 38.462 4.44 0.00 39.37 2.29
3378 3451 8.283291 GCAACATTATAAAGTCATAGTAGGTGC 58.717 37.037 0.00 0.00 0.00 5.01
3463 3546 1.134371 TGTGTTGTCGGACAATGGACA 60.134 47.619 24.81 22.14 40.59 4.02
3496 3579 0.994247 TCCTGCATCATGGTCAAGGT 59.006 50.000 3.84 0.00 0.00 3.50
3505 3588 3.474600 GTGTAGCTGATTCCTGCATCAT 58.525 45.455 0.00 0.00 39.38 2.45
3578 3661 2.970609 CACTTGTGTAAATTCCAACGCG 59.029 45.455 3.53 3.53 0.00 6.01
3602 3685 5.888161 AGTTGGAAATTTGACTCTCACTTGT 59.112 36.000 0.00 0.00 0.00 3.16
3616 3699 5.531287 GTGAGGTGTGTTCTAGTTGGAAATT 59.469 40.000 0.00 0.00 0.00 1.82
3783 3866 6.107901 TGGCTAACATTTTAAATGCCAGTT 57.892 33.333 16.57 6.97 43.09 3.16
3791 3874 8.207545 ACAGACCAAATTGGCTAACATTTTAAA 58.792 29.630 12.67 0.00 42.67 1.52
3978 4062 2.982488 AGCTTTCGGATGGGATTAGGAT 59.018 45.455 0.00 0.00 0.00 3.24
4049 4133 2.868583 CGGGCTTCTGTAATGTGATGAG 59.131 50.000 0.00 0.00 0.00 2.90
4209 4293 1.536943 AACTCTCCCAGCAGGACGAC 61.537 60.000 0.00 0.00 40.93 4.34


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

AutoCloner maintained by Alex Coulton.