Multiple sequence alignment - TraesCS5A01G165100

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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 TraesCS5A01G165100 chr5A 100.000 2287 0 0 1 2287 353609451 353607165 0.000000e+00 4224.0
1 TraesCS5A01G165100 chr5A 80.913 482 80 8 823 1302 487859181 487858710 9.980000e-99 370.0
2 TraesCS5A01G165100 chr5D 90.851 1563 131 10 1 1559 267071591 267073145 0.000000e+00 2084.0
3 TraesCS5A01G165100 chr5D 92.368 760 24 13 1556 2287 267074387 267075140 0.000000e+00 1051.0
4 TraesCS5A01G165100 chr5D 87.139 832 90 13 1 822 352980208 352979384 0.000000e+00 928.0
5 TraesCS5A01G165100 chr5D 86.602 821 105 5 1 820 391851923 391852739 0.000000e+00 902.0
6 TraesCS5A01G165100 chr5D 78.217 785 131 29 842 1593 82297432 82298209 1.240000e-127 466.0
7 TraesCS5A01G165100 chr5B 88.736 1669 136 26 1 1652 301193075 301194708 0.000000e+00 1993.0
8 TraesCS5A01G165100 chr5B 92.641 693 45 6 1 692 301188437 301189124 0.000000e+00 992.0
9 TraesCS5A01G165100 chr5B 92.641 693 43 7 1 692 301191529 301192214 0.000000e+00 990.0
10 TraesCS5A01G165100 chr5B 97.533 527 7 2 1767 2287 301195972 301196498 0.000000e+00 896.0
11 TraesCS5A01G165100 chr5B 81.481 81 15 0 1560 1640 429408129 429408049 1.470000e-07 67.6
12 TraesCS5A01G165100 chr3D 86.988 830 97 10 1 825 252849292 252848469 0.000000e+00 924.0
13 TraesCS5A01G165100 chr3D 86.893 824 98 9 1 820 424593681 424594498 0.000000e+00 915.0
14 TraesCS5A01G165100 chr3D 79.917 483 91 6 823 1303 352644930 352644452 1.300000e-92 350.0
15 TraesCS5A01G165100 chr2A 86.788 825 103 5 1 822 750408981 750409802 0.000000e+00 915.0
16 TraesCS5A01G165100 chr7D 78.513 861 126 29 821 1636 46960326 46961172 5.640000e-141 510.0
17 TraesCS5A01G165100 chr1A 82.574 505 76 11 862 1363 301224671 301224176 3.490000e-118 435.0
18 TraesCS5A01G165100 chr4D 84.270 445 61 6 933 1373 22045161 22045600 2.100000e-115 425.0
19 TraesCS5A01G165100 chr4D 76.293 696 127 28 862 1523 509440524 509439833 1.010000e-88 337.0
20 TraesCS5A01G165100 chr3B 79.926 538 94 9 848 1377 17556934 17557465 1.280000e-102 383.0


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 TraesCS5A01G165100 chr5A 353607165 353609451 2286 True 4224.00 4224 100.00000 1 2287 1 chr5A.!!$R1 2286
1 TraesCS5A01G165100 chr5D 267071591 267075140 3549 False 1567.50 2084 91.60950 1 2287 2 chr5D.!!$F3 2286
2 TraesCS5A01G165100 chr5D 352979384 352980208 824 True 928.00 928 87.13900 1 822 1 chr5D.!!$R1 821
3 TraesCS5A01G165100 chr5D 391851923 391852739 816 False 902.00 902 86.60200 1 820 1 chr5D.!!$F2 819
4 TraesCS5A01G165100 chr5D 82297432 82298209 777 False 466.00 466 78.21700 842 1593 1 chr5D.!!$F1 751
5 TraesCS5A01G165100 chr5B 301188437 301196498 8061 False 1217.75 1993 92.88775 1 2287 4 chr5B.!!$F1 2286
6 TraesCS5A01G165100 chr3D 252848469 252849292 823 True 924.00 924 86.98800 1 825 1 chr3D.!!$R1 824
7 TraesCS5A01G165100 chr3D 424593681 424594498 817 False 915.00 915 86.89300 1 820 1 chr3D.!!$F1 819
8 TraesCS5A01G165100 chr2A 750408981 750409802 821 False 915.00 915 86.78800 1 822 1 chr2A.!!$F1 821
9 TraesCS5A01G165100 chr7D 46960326 46961172 846 False 510.00 510 78.51300 821 1636 1 chr7D.!!$F1 815
10 TraesCS5A01G165100 chr4D 509439833 509440524 691 True 337.00 337 76.29300 862 1523 1 chr4D.!!$R1 661
11 TraesCS5A01G165100 chr3B 17556934 17557465 531 False 383.00 383 79.92600 848 1377 1 chr3B.!!$F1 529

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
858 5509 1.073923 GTCTTGGAGAAGGGCAAGGAA 59.926 52.381 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
1699 8841 1.601903 GCATGGTGTTTCGTTGTCTCA 59.398 47.619 0.0 0.0 0.0 3.27 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
87 88 4.693566 CCCTTTGCTTCACGATACTTTACA 59.306 41.667 0.00 0.00 0.00 2.41
110 111 6.014584 ACAAAAACCCAAGGTGAGATTTATCC 60.015 38.462 0.00 0.00 35.34 2.59
167 169 3.302699 CGGTCTTCTCGTTATCGGTTTTC 59.697 47.826 0.00 0.00 37.69 2.29
207 209 2.220586 TTCCGGCATCCCTGTGACA 61.221 57.895 0.00 0.00 0.00 3.58
275 277 3.407888 AGAGGGCCCTAAGAATATCTCCT 59.592 47.826 28.78 10.19 0.00 3.69
282 284 5.623368 GCCCTAAGAATATCTCCTCATCGTG 60.623 48.000 0.00 0.00 0.00 4.35
296 298 3.176552 CATCGTGAGAGGAGCAAATCT 57.823 47.619 0.00 0.00 46.52 2.40
364 366 5.301555 TGAAAGTTGTCGTTATGATCACCA 58.698 37.500 0.00 0.00 0.00 4.17
401 1947 3.228188 TGAGCAACTCCAAAGTCCATT 57.772 42.857 0.00 0.00 33.48 3.16
404 1950 3.299503 AGCAACTCCAAAGTCCATTGTT 58.700 40.909 0.00 0.00 33.48 2.83
422 3515 9.253832 TCCATTGTTTGGTATGAAATGACTATT 57.746 29.630 0.00 0.00 46.52 1.73
727 5375 6.774656 GGTTTCCTCTGAATCACATATTCCAT 59.225 38.462 0.00 0.00 0.00 3.41
729 5377 9.512588 GTTTCCTCTGAATCACATATTCCATAT 57.487 33.333 0.00 0.00 0.00 1.78
830 5480 3.514645 CATAATTGCAACACAAGGAGGC 58.485 45.455 0.00 0.00 42.87 4.70
836 5486 3.120086 AACACAAGGAGGCGGTGCT 62.120 57.895 0.00 0.00 36.00 4.40
839 5489 4.335647 CAAGGAGGCGGTGCTGGT 62.336 66.667 0.00 0.00 0.00 4.00
858 5509 1.073923 GTCTTGGAGAAGGGCAAGGAA 59.926 52.381 0.00 0.00 0.00 3.36
882 5533 3.744719 TCGCCCTTGGACGACGAG 61.745 66.667 0.00 0.00 32.45 4.18
1067 5727 1.939934 CAAGCTGAAGACAAACACCGA 59.060 47.619 0.00 0.00 0.00 4.69
1093 5754 3.308705 GGAGGGTGACGGTTCGGT 61.309 66.667 0.00 0.00 0.00 4.69
1207 5874 2.352805 CCCTGACACCCAGAAGGC 59.647 66.667 0.00 0.00 45.78 4.35
1340 6017 7.148523 GGTTTAGTTTAAGACTGTCGTATTGGG 60.149 40.741 4.34 0.00 39.48 4.12
1486 6214 2.389998 GTTGCATGTAACCAAACACCG 58.610 47.619 15.06 0.00 30.75 4.94
1539 6280 1.751924 CCAACTTTCGTTTCACCCCAA 59.248 47.619 0.00 0.00 0.00 4.12
1545 6286 4.202430 ACTTTCGTTTCACCCCAAGATAGT 60.202 41.667 0.00 0.00 0.00 2.12
1548 6289 2.027561 CGTTTCACCCCAAGATAGTGGA 60.028 50.000 0.00 0.00 41.65 4.02
1581 7567 6.183360 ACAACCAAACAAAGTGCAGATATTGA 60.183 34.615 7.46 0.00 0.00 2.57
1684 8826 1.398692 AAGATGCAACCAAACACCGT 58.601 45.000 0.00 0.00 0.00 4.83
1685 8827 0.667993 AGATGCAACCAAACACCGTG 59.332 50.000 0.00 0.00 0.00 4.94
1686 8828 0.939106 GATGCAACCAAACACCGTGC 60.939 55.000 0.00 0.00 0.00 5.34
1687 8829 1.391157 ATGCAACCAAACACCGTGCT 61.391 50.000 0.00 0.00 0.00 4.40
1688 8830 1.140804 GCAACCAAACACCGTGCTT 59.859 52.632 0.00 0.00 0.00 3.91
1689 8831 1.145162 GCAACCAAACACCGTGCTTG 61.145 55.000 7.56 7.56 0.00 4.01
1699 8841 1.200716 CACCGTGCTTGCATTTCTGAT 59.799 47.619 0.00 0.00 0.00 2.90
1717 8859 3.738982 TGATGAGACAACGAAACACCAT 58.261 40.909 0.00 0.00 0.00 3.55
1731 8873 1.274167 ACACCATGCTTGCATTTCTGG 59.726 47.619 5.24 8.24 0.00 3.86
1732 8874 1.274167 CACCATGCTTGCATTTCTGGT 59.726 47.619 11.48 11.48 37.47 4.00
1752 8894 3.291585 GTGAGAAACAACACGATGCAAG 58.708 45.455 0.00 0.00 0.00 4.01
1756 8898 4.601019 AGAAACAACACGATGCAAGAAAG 58.399 39.130 0.00 0.00 0.00 2.62
1757 8899 4.096382 AGAAACAACACGATGCAAGAAAGT 59.904 37.500 0.00 0.00 0.00 2.66
1758 8900 5.295787 AGAAACAACACGATGCAAGAAAGTA 59.704 36.000 0.00 0.00 0.00 2.24
1759 8901 5.689383 AACAACACGATGCAAGAAAGTAT 57.311 34.783 0.00 0.00 0.00 2.12
1763 8905 4.827692 ACACGATGCAAGAAAGTATACCA 58.172 39.130 0.00 0.00 0.00 3.25
1803 8968 3.499737 GCGTGTCCGGAATGGCAG 61.500 66.667 5.23 0.00 37.80 4.85
2014 9184 2.689034 CCTCGCTTTCCCCTCCCT 60.689 66.667 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 5.185056 CGGATAAATCTCACCTTGGGTTTTT 59.815 40.000 0.00 0.00 31.02 1.94
167 169 5.914085 ACATGTCAACGAGAAAGAAGAAG 57.086 39.130 0.00 0.00 0.00 2.85
207 209 3.374208 TCTGGCCAGACATAGGTGACTAT 60.374 47.826 32.00 0.00 42.63 2.12
275 277 2.762887 AGATTTGCTCCTCTCACGATGA 59.237 45.455 0.00 0.00 0.00 2.92
282 284 4.081752 TCAAGAGTGAGATTTGCTCCTCTC 60.082 45.833 0.00 0.00 43.97 3.20
364 366 4.450976 TGCTCAAACGCCATCTATAACAT 58.549 39.130 0.00 0.00 0.00 2.71
816 5466 2.594592 ACCGCCTCCTTGTGTTGC 60.595 61.111 0.00 0.00 0.00 4.17
830 5480 0.671781 CTTCTCCAAGACCAGCACCG 60.672 60.000 0.00 0.00 0.00 4.94
836 5486 0.401738 CTTGCCCTTCTCCAAGACCA 59.598 55.000 0.00 0.00 40.59 4.02
839 5489 1.352352 CTTCCTTGCCCTTCTCCAAGA 59.648 52.381 2.22 0.00 40.59 3.02
858 5509 2.847234 TCCAAGGGCGACACCACT 60.847 61.111 0.00 0.00 42.05 4.00
908 5563 0.250597 GTTGTAGTTCCCCCGCTTGT 60.251 55.000 0.00 0.00 0.00 3.16
1067 5727 1.750399 GTCACCCTCCATGCGCAAT 60.750 57.895 17.11 0.00 0.00 3.56
1093 5754 3.009033 AGGATGACCCTTTCGTTCATCAA 59.991 43.478 11.75 0.00 44.85 2.57
1161 5828 5.237815 CAACTTGAAGGTGACTATGTAGCA 58.762 41.667 3.67 0.00 42.68 3.49
1444 6165 2.479275 GCTTGTTGTCGAGTAACTTCCC 59.521 50.000 12.19 0.00 0.00 3.97
1486 6214 3.307339 TTACGCGAAAACACAAGACAC 57.693 42.857 15.93 0.00 0.00 3.67
1539 6280 6.686484 TGGTTGTATGCATATCCACTATCT 57.314 37.500 10.16 0.00 0.00 1.98
1545 6286 6.210385 ACTTTGTTTGGTTGTATGCATATCCA 59.790 34.615 10.16 15.18 0.00 3.41
1548 6289 5.868801 GCACTTTGTTTGGTTGTATGCATAT 59.131 36.000 10.16 0.00 0.00 1.78
1684 8826 3.414269 TGTCTCATCAGAAATGCAAGCA 58.586 40.909 0.00 0.00 0.00 3.91
1685 8827 4.164294 GTTGTCTCATCAGAAATGCAAGC 58.836 43.478 0.00 0.00 0.00 4.01
1686 8828 4.152938 TCGTTGTCTCATCAGAAATGCAAG 59.847 41.667 0.00 0.00 0.00 4.01
1687 8829 4.064388 TCGTTGTCTCATCAGAAATGCAA 58.936 39.130 0.00 0.00 0.00 4.08
1688 8830 3.663025 TCGTTGTCTCATCAGAAATGCA 58.337 40.909 0.00 0.00 0.00 3.96
1689 8831 4.668576 TTCGTTGTCTCATCAGAAATGC 57.331 40.909 0.00 0.00 0.00 3.56
1699 8841 1.601903 GCATGGTGTTTCGTTGTCTCA 59.398 47.619 0.00 0.00 0.00 3.27
1717 8859 2.275134 TCTCACCAGAAATGCAAGCA 57.725 45.000 0.00 0.00 0.00 3.91
1731 8873 3.002246 TCTTGCATCGTGTTGTTTCTCAC 59.998 43.478 0.00 0.00 0.00 3.51
1732 8874 3.202097 TCTTGCATCGTGTTGTTTCTCA 58.798 40.909 0.00 0.00 0.00 3.27
2014 9184 2.039624 GGGGAGTGGAGCAGGAGA 59.960 66.667 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.