Multiple sequence alignment - TraesCS5D01G054500

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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 TraesCS5D01G054500 chr5D 100.000 2883 0 0 390 3272 51806383 51803501 0.000000e+00 5325.0
1 TraesCS5D01G054500 chr5D 100.000 54 0 0 1 54 51806772 51806719 2.080000e-17 100.0
2 TraesCS5D01G054500 chr5D 98.039 51 1 0 1 51 498368874 498368924 4.500000e-14 89.8
3 TraesCS5D01G054500 chr2D 94.581 1993 80 8 390 2358 197523017 197521029 0.000000e+00 3057.0
4 TraesCS5D01G054500 chr5A 94.079 1993 91 12 390 2358 670476381 670474392 0.000000e+00 3001.0
5 TraesCS5D01G054500 chr5A 92.451 1987 125 14 393 2358 696328476 696326494 0.000000e+00 2815.0
6 TraesCS5D01G054500 chr1A 93.621 1991 101 11 390 2358 374208155 374210141 0.000000e+00 2950.0
7 TraesCS5D01G054500 chr1A 93.323 1992 107 14 390 2358 449450436 449452424 0.000000e+00 2918.0
8 TraesCS5D01G054500 chr1A 98.039 51 1 0 1 51 374208045 374208095 4.500000e-14 89.8
9 TraesCS5D01G054500 chr1A 96.078 51 2 0 1 51 449450326 449450376 2.090000e-12 84.2
10 TraesCS5D01G054500 chr3A 92.420 1992 99 14 390 2358 1716417 1714455 0.000000e+00 2795.0
11 TraesCS5D01G054500 chr3A 93.274 1234 81 2 390 1622 218191690 218190458 0.000000e+00 1818.0
12 TraesCS5D01G054500 chr3A 92.210 706 30 5 1675 2358 218169215 218168513 0.000000e+00 976.0
13 TraesCS5D01G054500 chr3A 95.238 63 3 0 1618 1680 218173134 218173072 2.080000e-17 100.0
14 TraesCS5D01G054500 chr3D 93.723 1641 76 7 738 2358 303482138 303480505 0.000000e+00 2435.0
15 TraesCS5D01G054500 chr3D 92.576 916 64 4 2358 3272 135590075 135590987 0.000000e+00 1312.0
16 TraesCS5D01G054500 chr3D 92.694 917 55 9 2358 3272 424338324 424337418 0.000000e+00 1312.0
17 TraesCS5D01G054500 chr3D 92.492 919 58 8 2357 3272 113619685 113620595 0.000000e+00 1304.0
18 TraesCS5D01G054500 chr3D 92.484 918 58 8 2358 3272 53999559 54000468 0.000000e+00 1303.0
19 TraesCS5D01G054500 chr3D 92.148 917 64 5 2358 3272 135634782 135635692 0.000000e+00 1288.0
20 TraesCS5D01G054500 chr7A 94.880 1211 60 2 390 1598 206573843 206575053 0.000000e+00 1892.0
21 TraesCS5D01G054500 chr7A 92.702 644 26 3 1736 2358 206575050 206575693 0.000000e+00 909.0
22 TraesCS5D01G054500 chr7A 98.039 51 1 0 1 51 206573733 206573783 4.500000e-14 89.8
23 TraesCS5D01G054500 chr5B 94.385 1211 63 4 390 1598 701465212 701466419 0.000000e+00 1855.0
24 TraesCS5D01G054500 chr5B 93.012 644 24 3 1736 2358 701466416 701467059 0.000000e+00 920.0
25 TraesCS5D01G054500 chr5B 98.039 51 1 0 1 51 701465102 701465152 4.500000e-14 89.8
26 TraesCS5D01G054500 chr1D 92.904 916 56 6 2358 3272 386959579 386960486 0.000000e+00 1323.0
27 TraesCS5D01G054500 chr1D 92.686 916 50 8 2358 3272 240427170 240428069 0.000000e+00 1304.0
28 TraesCS5D01G054500 chr4D 92.375 918 53 11 2358 3272 488190448 488189545 0.000000e+00 1291.0
29 TraesCS5D01G054500 chr7D 92.191 922 53 13 2354 3272 205030662 205031567 0.000000e+00 1286.0
30 TraesCS5D01G054500 chr2A 92.083 720 52 5 919 1636 648155166 648155882 0.000000e+00 1009.0
31 TraesCS5D01G054500 chr2A 87.599 758 51 16 1630 2358 648156005 648156748 0.000000e+00 839.0
32 TraesCS5D01G054500 chr2B 93.002 643 24 3 1736 2358 142888768 142889409 0.000000e+00 918.0
33 TraesCS5D01G054500 chr2B 98.039 51 1 0 1 51 142887462 142887512 4.500000e-14 89.8
34 TraesCS5D01G054500 chr1B 92.702 644 26 3 1736 2358 23817438 23818081 0.000000e+00 909.0
35 TraesCS5D01G054500 chr1B 92.081 644 30 3 1736 2358 48531222 48531865 0.000000e+00 887.0
36 TraesCS5D01G054500 chr1B 93.878 245 10 1 2119 2358 388031636 388031880 6.670000e-97 364.0
37 TraesCS5D01G054500 chr1B 98.039 51 1 0 1 51 388030728 388030778 4.500000e-14 89.8
38 TraesCS5D01G054500 chr1B 96.078 51 2 0 1 51 23816121 23816171 2.090000e-12 84.2
39 TraesCS5D01G054500 chr1B 96.078 51 2 0 1 51 48529927 48529977 2.090000e-12 84.2
40 TraesCS5D01G054500 chr3B 92.552 631 26 3 1749 2358 607501966 607501336 0.000000e+00 885.0


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 TraesCS5D01G054500 chr5D 51803501 51806772 3271 True 2712.500000 5325 100.000000 1 3272 2 chr5D.!!$R1 3271
1 TraesCS5D01G054500 chr2D 197521029 197523017 1988 True 3057.000000 3057 94.581000 390 2358 1 chr2D.!!$R1 1968
2 TraesCS5D01G054500 chr5A 670474392 670476381 1989 True 3001.000000 3001 94.079000 390 2358 1 chr5A.!!$R1 1968
3 TraesCS5D01G054500 chr5A 696326494 696328476 1982 True 2815.000000 2815 92.451000 393 2358 1 chr5A.!!$R2 1965
4 TraesCS5D01G054500 chr1A 374208045 374210141 2096 False 1519.900000 2950 95.830000 1 2358 2 chr1A.!!$F1 2357
5 TraesCS5D01G054500 chr1A 449450326 449452424 2098 False 1501.100000 2918 94.700500 1 2358 2 chr1A.!!$F2 2357
6 TraesCS5D01G054500 chr3A 1714455 1716417 1962 True 2795.000000 2795 92.420000 390 2358 1 chr3A.!!$R1 1968
7 TraesCS5D01G054500 chr3A 218190458 218191690 1232 True 1818.000000 1818 93.274000 390 1622 1 chr3A.!!$R2 1232
8 TraesCS5D01G054500 chr3A 218168513 218173134 4621 True 538.000000 976 93.724000 1618 2358 2 chr3A.!!$R3 740
9 TraesCS5D01G054500 chr3D 303480505 303482138 1633 True 2435.000000 2435 93.723000 738 2358 1 chr3D.!!$R1 1620
10 TraesCS5D01G054500 chr3D 135590075 135590987 912 False 1312.000000 1312 92.576000 2358 3272 1 chr3D.!!$F3 914
11 TraesCS5D01G054500 chr3D 424337418 424338324 906 True 1312.000000 1312 92.694000 2358 3272 1 chr3D.!!$R2 914
12 TraesCS5D01G054500 chr3D 113619685 113620595 910 False 1304.000000 1304 92.492000 2357 3272 1 chr3D.!!$F2 915
13 TraesCS5D01G054500 chr3D 53999559 54000468 909 False 1303.000000 1303 92.484000 2358 3272 1 chr3D.!!$F1 914
14 TraesCS5D01G054500 chr3D 135634782 135635692 910 False 1288.000000 1288 92.148000 2358 3272 1 chr3D.!!$F4 914
15 TraesCS5D01G054500 chr7A 206573733 206575693 1960 False 963.600000 1892 95.207000 1 2358 3 chr7A.!!$F1 2357
16 TraesCS5D01G054500 chr5B 701465102 701467059 1957 False 954.933333 1855 95.145333 1 2358 3 chr5B.!!$F1 2357
17 TraesCS5D01G054500 chr1D 386959579 386960486 907 False 1323.000000 1323 92.904000 2358 3272 1 chr1D.!!$F2 914
18 TraesCS5D01G054500 chr1D 240427170 240428069 899 False 1304.000000 1304 92.686000 2358 3272 1 chr1D.!!$F1 914
19 TraesCS5D01G054500 chr4D 488189545 488190448 903 True 1291.000000 1291 92.375000 2358 3272 1 chr4D.!!$R1 914
20 TraesCS5D01G054500 chr7D 205030662 205031567 905 False 1286.000000 1286 92.191000 2354 3272 1 chr7D.!!$F1 918
21 TraesCS5D01G054500 chr2A 648155166 648156748 1582 False 924.000000 1009 89.841000 919 2358 2 chr2A.!!$F1 1439
22 TraesCS5D01G054500 chr2B 142887462 142889409 1947 False 503.900000 918 95.520500 1 2358 2 chr2B.!!$F1 2357
23 TraesCS5D01G054500 chr1B 23816121 23818081 1960 False 496.600000 909 94.390000 1 2358 2 chr1B.!!$F1 2357
24 TraesCS5D01G054500 chr1B 48529927 48531865 1938 False 485.600000 887 94.079500 1 2358 2 chr1B.!!$F2 2357
25 TraesCS5D01G054500 chr1B 388030728 388031880 1152 False 226.900000 364 95.958500 1 2358 2 chr1B.!!$F3 2357
26 TraesCS5D01G054500 chr3B 607501336 607501966 630 True 885.000000 885 92.552000 1749 2358 1 chr3B.!!$R1 609

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
424 425 0.615544 ATGGGGTTTCATGTGCCAGG 60.616 55.0 0.00 0.00 0.00 4.45 F
1233 1260 0.037590 AGGCAGTGAGAGACTCTCGT 59.962 55.0 24.09 13.38 46.25 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 5881 0.171903 AGAAATGGCATCGCTTGTGC 59.828 50.0 0.0 0.0 41.78 4.57 R
2470 6548 0.034337 ACCTAACGCTTCCGCTTTCA 59.966 50.0 0.0 0.0 38.22 2.69 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
51 52 6.015603 TGTCATGGTTGCTTGTGATTTTGATA 60.016 34.615 0.00 0.00 0.00 2.15
424 425 0.615544 ATGGGGTTTCATGTGCCAGG 60.616 55.000 0.00 0.00 0.00 4.45
463 464 6.545567 TCATAGATGGTGGATATGCAAACAT 58.454 36.000 13.23 13.23 40.49 2.71
600 624 2.487762 GCAATTCTTCGGAACCACATCA 59.512 45.455 0.00 0.00 36.72 3.07
611 635 3.119352 GGAACCACATCAAAAGGAGCATC 60.119 47.826 0.00 0.00 0.00 3.91
618 642 2.582052 TCAAAAGGAGCATCGGTGTTT 58.418 42.857 0.00 0.00 34.37 2.83
682 707 7.296628 ACCCTATAGAGTCACAAATCAGATC 57.703 40.000 0.00 0.00 0.00 2.75
724 749 9.149225 GTATTCCATAACATCATTAGAGCTCAG 57.851 37.037 17.77 2.74 0.00 3.35
733 758 3.445450 TCATTAGAGCTCAGAGTGGTGAC 59.555 47.826 17.77 0.00 0.00 3.67
742 767 0.900182 AGAGTGGTGACGAGGCATGA 60.900 55.000 0.00 0.00 0.00 3.07
771 796 2.158579 ACCAACCACCGTTAATTCCACT 60.159 45.455 0.00 0.00 0.00 4.00
951 977 8.253867 TCACCTTTTCTTAGGTAAAGTAGTGA 57.746 34.615 9.93 9.93 46.80 3.41
1003 1029 8.574251 TTGTTGGTTCAATAATGTAGCTATGT 57.426 30.769 0.00 0.00 0.00 2.29
1051 1077 6.127535 CCATGCATATGAGAAAGGTCTTGTTT 60.128 38.462 6.97 0.00 36.36 2.83
1083 1109 3.950397 TGACCACAACAATCCCATCTAC 58.050 45.455 0.00 0.00 0.00 2.59
1108 1134 2.554344 GGTCAAAATGGGTGGACTGCTA 60.554 50.000 0.00 0.00 0.00 3.49
1233 1260 0.037590 AGGCAGTGAGAGACTCTCGT 59.962 55.000 24.09 13.38 46.25 4.18
1239 1266 4.468643 CAGTGAGAGACTCTCGTAAACAC 58.531 47.826 24.09 16.89 46.25 3.32
1242 1269 3.502595 TGAGAGACTCTCGTAAACACAGG 59.497 47.826 24.09 0.00 46.25 4.00
1247 1274 0.981183 TCTCGTAAACACAGGGGCAT 59.019 50.000 0.00 0.00 0.00 4.40
1307 1334 9.841295 TGAACCTGTAATATGGGATAAACTTAC 57.159 33.333 0.00 0.00 0.00 2.34
1401 1428 6.726379 TGATCCCAACCATACAATGTTTCTA 58.274 36.000 0.00 0.00 0.00 2.10
1532 1559 5.013079 TCCATCGACCCTGCATATTAAATCT 59.987 40.000 0.00 0.00 0.00 2.40
1824 5873 5.295431 TGAACTTTGTATCAATTCCGCAG 57.705 39.130 0.00 0.00 0.00 5.18
2132 6198 1.956477 GCAAGATGGAAACTGTGTGGT 59.044 47.619 0.00 0.00 0.00 4.16
2202 6275 3.004862 GGCTTTTCAAATGCCCAATGAG 58.995 45.455 14.87 0.00 40.71 2.90
2217 6290 5.049818 GCCCAATGAGTCGAGAAATATTCAG 60.050 44.000 0.00 0.00 0.00 3.02
2444 6522 0.105039 CATAGCAACGAGAGGGGGAC 59.895 60.000 0.00 0.00 0.00 4.46
2470 6548 2.341101 CCACGCACCCTCGTAGACT 61.341 63.158 0.00 0.00 41.21 3.24
2508 6586 2.738314 GGTTAACGCGGTTGATGTAGTT 59.262 45.455 12.47 0.00 0.00 2.24
2538 6616 0.462047 ACGATCCAACCGATCCAAGC 60.462 55.000 0.00 0.00 44.07 4.01
2606 6684 2.525368 TGTCCCTCGAACTCTTGATCA 58.475 47.619 0.00 0.00 0.00 2.92
2607 6685 3.099905 TGTCCCTCGAACTCTTGATCAT 58.900 45.455 0.00 0.00 0.00 2.45
2671 6749 1.211743 CGGTGATGGTGATGTGATCG 58.788 55.000 0.00 0.00 0.00 3.69
2937 7028 1.484653 GAAAGAGGGAGAGGGAGAAGC 59.515 57.143 0.00 0.00 0.00 3.86
2943 7034 1.352687 GGGAGAGGGAGAAGCAAAAGT 59.647 52.381 0.00 0.00 0.00 2.66
3025 7119 3.775654 GTGGCCGTCCTCCCTCTG 61.776 72.222 0.00 0.00 0.00 3.35
3224 7319 4.150359 TCTAGGACTCCGAACAAACTTCT 58.850 43.478 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
396 397 4.889409 CACATGAAACCCCATGCTAATAGT 59.111 41.667 0.00 0.0 45.79 2.12
406 407 1.228831 CCTGGCACATGAAACCCCA 60.229 57.895 0.00 0.0 38.20 4.96
463 464 1.774110 TGGTGCAAGAAAAGAAGGCA 58.226 45.000 0.00 0.0 0.00 4.75
600 624 5.523438 TTTAAAACACCGATGCTCCTTTT 57.477 34.783 0.00 0.0 0.00 2.27
611 635 4.037021 GGAACCGTCTTTTTAAAACACCG 58.963 43.478 0.00 3.1 0.00 4.94
724 749 0.176680 ATCATGCCTCGTCACCACTC 59.823 55.000 0.00 0.0 0.00 3.51
733 758 1.233019 GGTGATCCAATCATGCCTCG 58.767 55.000 0.00 0.0 42.04 4.63
951 977 9.725206 TGGGGTACTAGTTAAATTTCTCTCTAT 57.275 33.333 0.00 0.0 0.00 1.98
1051 1077 7.230510 GGGATTGTTGTGGTCAAGCATTATATA 59.769 37.037 0.00 0.0 33.61 0.86
1083 1109 0.037590 TCCACCCATTTTGACCTCGG 59.962 55.000 0.00 0.0 0.00 4.63
1108 1134 4.650972 TTGTAATGCTAGTCCACCCTTT 57.349 40.909 0.00 0.0 0.00 3.11
1153 1180 3.888323 TGTTGCTTGGTGAAATGAGCTAA 59.112 39.130 0.00 0.0 36.16 3.09
1233 1260 1.006813 ATCCCATGCCCCTGTGTTTA 58.993 50.000 0.00 0.0 0.00 2.01
1239 1266 2.476078 ATCCCATCCCATGCCCCTG 61.476 63.158 0.00 0.0 0.00 4.45
1242 1269 1.002069 TATCATCCCATCCCATGCCC 58.998 55.000 0.00 0.0 0.00 5.36
1247 1274 3.688126 GCAAAGTGTATCATCCCATCCCA 60.688 47.826 0.00 0.0 0.00 4.37
1401 1428 6.520021 TCCTTGGATGATCCTATTGAATGT 57.480 37.500 13.44 0.0 37.46 2.71
1730 5750 3.320626 TGTTCGCTCAGAAACATCAGAG 58.679 45.455 0.00 0.0 41.10 3.35
1832 5881 0.171903 AGAAATGGCATCGCTTGTGC 59.828 50.000 0.00 0.0 41.78 4.57
2013 6064 3.679917 CGATCTGGCTTTGCTTCCTCTTA 60.680 47.826 0.00 0.0 0.00 2.10
2086 6137 5.491070 TGATTCCTTCAACTCGTCAATCAT 58.509 37.500 0.00 0.0 0.00 2.45
2132 6198 2.083774 CTTCCATTGGTTCTAGCGCAA 58.916 47.619 11.47 0.0 0.00 4.85
2202 6275 6.844696 TGGTATTGCTGAATATTTCTCGAC 57.155 37.500 0.00 0.0 0.00 4.20
2217 6290 5.904362 AAGATTTGAGTCCTTGGTATTGC 57.096 39.130 0.00 0.0 0.00 3.56
2444 6522 2.972505 GGGTGCGTGGACACACTG 60.973 66.667 3.12 0.0 45.50 3.66
2457 6535 1.732732 CGCTTTCAGTCTACGAGGGTG 60.733 57.143 0.00 0.0 0.00 4.61
2470 6548 0.034337 ACCTAACGCTTCCGCTTTCA 59.966 50.000 0.00 0.0 38.22 2.69
2508 6586 2.400399 GTTGGATCGTGAAGACGTTCA 58.600 47.619 0.00 0.0 46.20 3.18
2538 6616 0.727122 GAGGTGTCGTACGTTCGGTG 60.727 60.000 16.05 0.0 0.00 4.94
2572 6650 1.833630 AGGGACATCATCGAGCTGAAA 59.166 47.619 0.00 0.0 0.00 2.69
2606 6684 1.144093 CTCTCCCTCGACCCTCTACAT 59.856 57.143 0.00 0.0 0.00 2.29
2607 6685 0.547075 CTCTCCCTCGACCCTCTACA 59.453 60.000 0.00 0.0 0.00 2.74
2781 6863 2.836372 CCCTCCTTTATATACGGGGGTC 59.164 54.545 12.94 0.0 36.68 4.46
2991 7083 2.437180 CAAGAGGAGGCGCATGCA 60.437 61.111 17.59 0.0 45.35 3.96
2994 7088 2.270205 CCACAAGAGGAGGCGCAT 59.730 61.111 10.83 0.0 0.00 4.73
2995 7089 4.704833 GCCACAAGAGGAGGCGCA 62.705 66.667 10.83 0.0 38.86 6.09
3014 7108 2.035632 CATAGTGGACAGAGGGAGGAC 58.964 57.143 0.00 0.0 0.00 3.85
3184 7278 4.279420 CCTAGATGAGATCACGGACATGAA 59.721 45.833 0.00 0.0 30.82 2.57
3224 7319 3.149981 TGAGTTGTGTGTTTTGGTGACA 58.850 40.909 0.00 0.0 39.83 3.58


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

AutoCloner maintained by Alex Coulton.