Multiple sequence alignment - TraesCS1B01G141500

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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 TraesCS1B01G141500 chr1B 100.000 3904 0 0 1 3904 188907521 188903618 0.000000e+00 7210.0
1 TraesCS1B01G141500 chr1D 97.957 3231 47 6 3 3219 124905717 124902492 0.000000e+00 5583.0
2 TraesCS1B01G141500 chr1D 81.304 690 97 16 3212 3895 122237770 122238433 7.430000e-147 531.0
3 TraesCS1B01G141500 chr1A 97.468 3239 53 8 1 3219 137408678 137405449 0.000000e+00 5500.0
4 TraesCS1B01G141500 chr1A 80.939 703 96 21 3213 3904 554019708 554020383 4.470000e-144 521.0
5 TraesCS1B01G141500 chr4A 93.878 686 39 3 3220 3903 619564947 619564263 0.000000e+00 1031.0
6 TraesCS1B01G141500 chrUn 92.877 702 46 3 3204 3904 41259235 41259933 0.000000e+00 1016.0
7 TraesCS1B01G141500 chrUn 93.913 345 20 1 3560 3903 325383367 325383711 1.610000e-143 520.0
8 TraesCS1B01G141500 chrUn 85.827 127 16 1 3214 3338 217759954 217759828 2.450000e-27 134.0
9 TraesCS1B01G141500 chrUn 85.039 127 17 1 3214 3338 246301132 246301006 1.140000e-25 128.0
10 TraesCS1B01G141500 chrUn 97.959 49 1 0 2693 2741 43370833 43370785 6.950000e-13 86.1
11 TraesCS1B01G141500 chr7A 92.771 664 43 3 3242 3904 205212463 205213122 0.000000e+00 955.0
12 TraesCS1B01G141500 chr7A 81.268 347 60 4 3494 3839 470125831 470125489 3.840000e-70 276.0
13 TraesCS1B01G141500 chr2D 82.833 699 103 14 3212 3898 29304161 29304854 9.270000e-171 610.0
14 TraesCS1B01G141500 chr2A 81.935 703 90 19 3212 3904 163053228 163052553 9.470000e-156 560.0
15 TraesCS1B01G141500 chr2A 82.468 308 44 9 3214 3513 423196078 423195773 1.080000e-65 261.0
16 TraesCS1B01G141500 chr5B 80.402 398 63 9 3213 3598 633749862 633749468 4.940000e-74 289.0
17 TraesCS1B01G141500 chr5B 77.660 188 36 5 3494 3677 278428958 278428773 4.120000e-20 110.0
18 TraesCS1B01G141500 chr6B 82.623 305 43 9 3214 3510 4412027 4412329 1.080000e-65 261.0


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 TraesCS1B01G141500 chr1B 188903618 188907521 3903 True 7210 7210 100.000 1 3904 1 chr1B.!!$R1 3903
1 TraesCS1B01G141500 chr1D 124902492 124905717 3225 True 5583 5583 97.957 3 3219 1 chr1D.!!$R1 3216
2 TraesCS1B01G141500 chr1D 122237770 122238433 663 False 531 531 81.304 3212 3895 1 chr1D.!!$F1 683
3 TraesCS1B01G141500 chr1A 137405449 137408678 3229 True 5500 5500 97.468 1 3219 1 chr1A.!!$R1 3218
4 TraesCS1B01G141500 chr1A 554019708 554020383 675 False 521 521 80.939 3213 3904 1 chr1A.!!$F1 691
5 TraesCS1B01G141500 chr4A 619564263 619564947 684 True 1031 1031 93.878 3220 3903 1 chr4A.!!$R1 683
6 TraesCS1B01G141500 chrUn 41259235 41259933 698 False 1016 1016 92.877 3204 3904 1 chrUn.!!$F1 700
7 TraesCS1B01G141500 chr7A 205212463 205213122 659 False 955 955 92.771 3242 3904 1 chr7A.!!$F1 662
8 TraesCS1B01G141500 chr2D 29304161 29304854 693 False 610 610 82.833 3212 3898 1 chr2D.!!$F1 686
9 TraesCS1B01G141500 chr2A 163052553 163053228 675 True 560 560 81.935 3212 3904 1 chr2A.!!$R1 692

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
95 99 4.264614 GCTCATTGATGCTGACAAATTTCG 59.735 41.667 0.0 0.0 0.0 3.46 F
858 863 5.192927 TGTTATGCTTTATTCACAGGAGGG 58.807 41.667 0.0 0.0 0.0 4.30 F
1328 1333 0.815615 GTGGCGGGACTCAATGGATC 60.816 60.000 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 1306 3.775654 GTCCCGCCACCAGAGAGG 61.776 72.222 0.0 0.0 45.67 3.69 R
2417 2428 3.944055 TCTCTCACTTCACTAAGCACC 57.056 47.619 0.0 0.0 36.05 5.01 R
3186 3207 0.033504 ATATTCGGGGCACAGCTACG 59.966 55.000 0.0 0.0 0.00 3.51 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
45 49 5.191727 ACCTGTACCAATCAATCCAATCA 57.808 39.130 0.00 0.0 0.00 2.57
95 99 4.264614 GCTCATTGATGCTGACAAATTTCG 59.735 41.667 0.00 0.0 0.00 3.46
322 327 6.150140 CCTTTCTGTTTCTTATTCACAGGGAG 59.850 42.308 0.00 0.0 38.80 4.30
540 545 5.957842 TTTCGTAAATTTCAGTGGCAGAT 57.042 34.783 0.00 0.0 0.00 2.90
563 568 9.981114 AGATGTGGTTTCTTTATTTGTAAAAGG 57.019 29.630 0.00 0.0 35.18 3.11
858 863 5.192927 TGTTATGCTTTATTCACAGGAGGG 58.807 41.667 0.00 0.0 0.00 4.30
1328 1333 0.815615 GTGGCGGGACTCAATGGATC 60.816 60.000 0.00 0.0 0.00 3.36
1464 1469 4.016444 CCCACACAATAGTTATGGCACTT 58.984 43.478 0.00 0.0 0.00 3.16
1466 1471 5.393027 CCCACACAATAGTTATGGCACTTTC 60.393 44.000 0.00 0.0 0.00 2.62
1738 1743 5.570205 TGACACCTAAAACCACCTTGATA 57.430 39.130 0.00 0.0 0.00 2.15
1757 1762 8.363390 CCTTGATATAGCTGACTCAGTTTGATA 58.637 37.037 7.89 0.0 33.43 2.15
2429 2440 6.245408 ACATGATTTAAGGGTGCTTAGTGAA 58.755 36.000 0.00 0.0 0.00 3.18
2929 2950 5.872963 AGATAGCATATGGAATGCAGTTCA 58.127 37.500 12.12 0.0 46.77 3.18
3094 3115 0.925558 TGCCTTGCTATGGGGAATGA 59.074 50.000 0.00 0.0 0.00 2.57
3186 3207 3.577415 ACCCCTATGTAATCTAACTCCGC 59.423 47.826 0.00 0.0 0.00 5.54
3259 3280 4.651778 ACGGGCTACAATGCATATACATT 58.348 39.130 0.00 0.0 40.90 2.71
3307 3334 3.983044 AGGTTGACGCTTATTTCTCCT 57.017 42.857 0.00 0.0 0.00 3.69
3317 3344 4.127171 GCTTATTTCTCCTTCATACGCCA 58.873 43.478 0.00 0.0 0.00 5.69
3318 3345 4.574828 GCTTATTTCTCCTTCATACGCCAA 59.425 41.667 0.00 0.0 0.00 4.52
3320 3347 3.973206 TTTCTCCTTCATACGCCAAGA 57.027 42.857 0.00 0.0 0.00 3.02
3347 3374 1.683790 GGACATCAAACGAGCGTCCG 61.684 60.000 0.00 0.0 37.04 4.79
3422 3449 7.083197 CCAACACATATGTGGGGAGAAATGTA 61.083 42.308 33.32 0.0 45.39 2.29
3426 3453 6.260936 CACATATGTGGGGAGAAATGTAGTTC 59.739 42.308 25.41 0.0 42.10 3.01
3533 3563 3.322466 CCCACCTCACCTTCGCCT 61.322 66.667 0.00 0.0 0.00 5.52
3574 3604 2.926242 GGACTTCCCCACGGACCA 60.926 66.667 0.00 0.0 38.14 4.02
3689 3726 1.206371 TGACGCCCCTAAGCTAAGAAC 59.794 52.381 0.00 0.0 0.00 3.01
3698 3735 0.535335 AAGCTAAGAACGCGGATCCA 59.465 50.000 12.47 0.0 0.00 3.41
3734 3771 6.765989 AGCCATTGTCACGTTGTAACATATAT 59.234 34.615 0.00 0.0 0.00 0.86
3884 3921 8.705048 TTAACCCAAAAATTGTACAACTTGAC 57.295 30.769 20.49 0.0 0.00 3.18
3885 3922 6.287589 ACCCAAAAATTGTACAACTTGACA 57.712 33.333 20.49 0.0 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 49 3.066900 AGCTACGACACTCGAATGCTATT 59.933 43.478 0.00 0.0 43.74 1.73
81 85 3.252944 TGAAGCATCGAAATTTGTCAGCA 59.747 39.130 0.00 0.0 0.00 4.41
95 99 5.467705 ACAGCTGAATTTTCTTGAAGCATC 58.532 37.500 23.35 0.0 33.08 3.91
315 320 3.857157 TCAACAGCTAAAACTCCCTGT 57.143 42.857 0.00 0.0 40.02 4.00
422 427 6.201044 CGATGAGCGTTTAATGTAAGGAGAAT 59.799 38.462 0.00 0.0 34.64 2.40
1301 1306 3.775654 GTCCCGCCACCAGAGAGG 61.776 72.222 0.00 0.0 45.67 3.69
1328 1333 8.652810 AAATTTTGAAACAGAATGAGTGAAGG 57.347 30.769 0.00 0.0 39.69 3.46
1435 1440 7.397476 TGCCATAACTATTGTGTGGGAAAATAA 59.603 33.333 11.85 0.0 34.95 1.40
1738 1743 8.043113 TGTCAAATATCAAACTGAGTCAGCTAT 58.957 33.333 20.31 10.5 34.37 2.97
2417 2428 3.944055 TCTCTCACTTCACTAAGCACC 57.056 47.619 0.00 0.0 36.05 5.01
2429 2440 9.817809 TTTGCTAATAATATTCGTTCTCTCACT 57.182 29.630 0.00 0.0 0.00 3.41
2929 2950 1.354705 GCTGGTCCCTTAGTTCCCTTT 59.645 52.381 0.00 0.0 0.00 3.11
3094 3115 9.965902 AAAGAAAGGAGTTAGATTACATCATGT 57.034 29.630 0.00 0.0 0.00 3.21
3144 3165 1.141645 GGTACAACACGTGATTCGCA 58.858 50.000 25.01 0.0 44.19 5.10
3186 3207 0.033504 ATATTCGGGGCACAGCTACG 59.966 55.000 0.00 0.0 0.00 3.51
3307 3334 2.670905 CGAACATGTCTTGGCGTATGAA 59.329 45.455 0.00 0.0 0.00 2.57
3317 3344 3.186409 CGTTTGATGTCCGAACATGTCTT 59.814 43.478 0.00 0.0 46.20 3.01
3318 3345 2.736721 CGTTTGATGTCCGAACATGTCT 59.263 45.455 0.00 0.0 46.20 3.41
3320 3347 2.736721 CTCGTTTGATGTCCGAACATGT 59.263 45.455 0.00 0.0 46.20 3.21
3347 3374 3.653344 GTTGGATTTTCAAGAGCCCAAC 58.347 45.455 0.00 0.0 44.19 3.77
3533 3563 2.203938 AAGGGGAGAGGGCGACAA 60.204 61.111 0.00 0.0 0.00 3.18
3574 3604 2.125225 GGGGGACTCCTCCTTGGT 59.875 66.667 6.76 0.0 36.68 3.67
3664 3700 2.742116 GCTTAGGGGCGTCATGGGA 61.742 63.158 0.00 0.0 0.00 4.37
3689 3726 0.933097 CAAGAGACATTGGATCCGCG 59.067 55.000 7.39 0.0 0.00 6.46
3734 3771 4.390603 GTGGTAATGCACATCGTTCAACTA 59.609 41.667 0.00 0.0 0.00 2.24
3826 3863 2.172851 ATGCATTGGTTGGTTGCTTG 57.827 45.000 0.00 0.0 37.28 4.01


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

AutoCloner maintained by Alex Coulton.