Multiple sequence alignment - TraesCS7D01G054800

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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 TraesCS7D01G054800 chr7D 100.000 4873 0 0 1 4873 29406654 29401782 0.000000e+00 8999.0
1 TraesCS7D01G054800 chr7D 90.305 3208 237 42 762 3941 4426643 4423482 0.000000e+00 4133.0
2 TraesCS7D01G054800 chr7D 89.850 867 58 14 3944 4805 4423446 4422605 0.000000e+00 1086.0
3 TraesCS7D01G054800 chr7D 83.070 951 154 7 1692 2639 4503409 4502463 0.000000e+00 857.0
4 TraesCS7D01G054800 chr7D 80.253 947 176 11 1692 2633 4291477 4290537 0.000000e+00 702.0
5 TraesCS7D01G054800 chr7D 81.957 654 110 6 3185 3831 4502166 4501514 9.220000e-152 547.0
6 TraesCS7D01G054800 chr7D 89.389 311 30 3 301 610 4427022 4426714 5.910000e-104 388.0
7 TraesCS7D01G054800 chr7D 77.537 601 124 7 3194 3784 4648310 4647711 7.760000e-93 351.0
8 TraesCS7D01G054800 chr7D 91.837 98 7 1 207 304 4427950 4427854 8.510000e-28 135.0
9 TraesCS7D01G054800 chr7D 96.341 82 3 0 1277 1358 29550330 29550411 8.510000e-28 135.0
10 TraesCS7D01G054800 chr4A 89.882 3222 237 35 762 3941 739129105 739132279 0.000000e+00 4061.0
11 TraesCS7D01G054800 chr4A 84.615 936 139 5 1692 2625 739079323 739080255 0.000000e+00 926.0
12 TraesCS7D01G054800 chr4A 79.831 947 182 9 1692 2633 739273622 739274564 0.000000e+00 682.0
13 TraesCS7D01G054800 chr4A 90.774 336 25 3 143 473 739128123 739128457 1.240000e-120 444.0
14 TraesCS7D01G054800 chr4A 88.136 354 21 8 4455 4805 739132501 739132836 7.600000e-108 401.0
15 TraesCS7D01G054800 chr4A 77.228 606 127 7 3194 3789 738963820 738964424 1.300000e-90 344.0
16 TraesCS7D01G054800 chr4A 85.804 317 31 7 272 585 739128708 739129013 1.690000e-84 324.0
17 TraesCS7D01G054800 chr4A 95.876 194 8 0 3939 4132 739132310 739132503 1.020000e-81 315.0
18 TraesCS7D01G054800 chr4A 75.231 650 143 13 3194 3831 739067401 739068044 4.770000e-75 292.0
19 TraesCS7D01G054800 chr4A 93.578 109 7 0 636 744 739129014 739129122 3.900000e-36 163.0
20 TraesCS7D01G054800 chr4A 88.776 98 11 0 1261 1358 738890283 738890186 2.380000e-23 121.0
21 TraesCS7D01G054800 chr4A 83.212 137 12 8 16 143 690186111 690186245 1.110000e-21 115.0
22 TraesCS7D01G054800 chr4A 94.286 70 4 0 4804 4873 739134028 739134097 1.850000e-19 108.0
23 TraesCS7D01G054800 chr4A 96.154 52 2 0 92 143 515856542 515856491 8.690000e-13 86.1
24 TraesCS7D01G054800 chr7A 98.242 2218 39 0 2651 4868 29663284 29661067 0.000000e+00 3880.0
25 TraesCS7D01G054800 chr7A 98.415 1767 25 1 874 2637 29665486 29663720 0.000000e+00 3105.0
26 TraesCS7D01G054800 chr7A 89.947 1900 140 29 762 2644 4255254 4253389 0.000000e+00 2403.0
27 TraesCS7D01G054800 chr7A 95.804 858 30 3 1 858 29668241 29667390 0.000000e+00 1380.0
28 TraesCS7D01G054800 chr7A 85.858 1294 145 17 2658 3941 4253322 4252057 0.000000e+00 1341.0
29 TraesCS7D01G054800 chr7A 83.333 936 151 5 1692 2625 4329855 4328923 0.000000e+00 859.0
30 TraesCS7D01G054800 chr7A 79.449 944 185 9 1692 2630 4069965 4069026 0.000000e+00 660.0
31 TraesCS7D01G054800 chr7A 76.248 661 147 8 3184 3836 4015214 4014556 4.670000e-90 342.0
32 TraesCS7D01G054800 chr7A 93.636 110 7 0 638 747 4255343 4255234 1.090000e-36 165.0
33 TraesCS7D01G054800 chr7A 86.957 138 12 4 9 143 124404319 124404453 3.040000e-32 150.0
34 TraesCS7D01G054800 chr7A 95.122 82 4 0 1277 1358 4016872 4016791 3.960000e-26 130.0
35 TraesCS7D01G054800 chr7A 95.122 82 4 0 1277 1358 29784412 29784493 3.960000e-26 130.0
36 TraesCS7D01G054800 chr7A 88.776 98 11 0 1261 1358 4625654 4625751 2.380000e-23 121.0
37 TraesCS7D01G054800 chr2D 89.437 142 11 3 2 142 576424267 576424405 5.010000e-40 176.0
38 TraesCS7D01G054800 chr5B 81.169 154 23 5 2698 2846 476927806 476927654 8.570000e-23 119.0
39 TraesCS7D01G054800 chr5B 92.857 56 4 0 88 143 112556682 112556627 1.120000e-11 82.4
40 TraesCS7D01G054800 chr5B 92.982 57 3 1 88 143 639124800 639124744 1.120000e-11 82.4
41 TraesCS7D01G054800 chr1A 92.982 57 3 1 88 143 232098724 232098780 1.120000e-11 82.4
42 TraesCS7D01G054800 chr1A 92.857 56 4 0 88 143 528550066 528550121 1.120000e-11 82.4
43 TraesCS7D01G054800 chr3D 93.333 45 3 0 2741 2785 504268171 504268215 3.150000e-07 67.6


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 TraesCS7D01G054800 chr7D 29401782 29406654 4872 True 8999.000000 8999 100.000000 1 4873 1 chr7D.!!$R3 4872
1 TraesCS7D01G054800 chr7D 4422605 4427950 5345 True 1435.500000 4133 90.345250 207 4805 4 chr7D.!!$R4 4598
2 TraesCS7D01G054800 chr7D 4290537 4291477 940 True 702.000000 702 80.253000 1692 2633 1 chr7D.!!$R1 941
3 TraesCS7D01G054800 chr7D 4501514 4503409 1895 True 702.000000 857 82.513500 1692 3831 2 chr7D.!!$R5 2139
4 TraesCS7D01G054800 chr7D 4647711 4648310 599 True 351.000000 351 77.537000 3194 3784 1 chr7D.!!$R2 590
5 TraesCS7D01G054800 chr4A 739079323 739080255 932 False 926.000000 926 84.615000 1692 2625 1 chr4A.!!$F4 933
6 TraesCS7D01G054800 chr4A 739128123 739134097 5974 False 830.857143 4061 91.190857 143 4873 7 chr4A.!!$F6 4730
7 TraesCS7D01G054800 chr4A 739273622 739274564 942 False 682.000000 682 79.831000 1692 2633 1 chr4A.!!$F5 941
8 TraesCS7D01G054800 chr4A 738963820 738964424 604 False 344.000000 344 77.228000 3194 3789 1 chr4A.!!$F2 595
9 TraesCS7D01G054800 chr4A 739067401 739068044 643 False 292.000000 292 75.231000 3194 3831 1 chr4A.!!$F3 637
10 TraesCS7D01G054800 chr7A 29661067 29668241 7174 True 2788.333333 3880 97.487000 1 4868 3 chr7A.!!$R5 4867
11 TraesCS7D01G054800 chr7A 4252057 4255343 3286 True 1303.000000 2403 89.813667 638 3941 3 chr7A.!!$R4 3303
12 TraesCS7D01G054800 chr7A 4328923 4329855 932 True 859.000000 859 83.333000 1692 2625 1 chr7A.!!$R2 933
13 TraesCS7D01G054800 chr7A 4069026 4069965 939 True 660.000000 660 79.449000 1692 2630 1 chr7A.!!$R1 938
14 TraesCS7D01G054800 chr7A 4014556 4016872 2316 True 236.000000 342 85.685000 1277 3836 2 chr7A.!!$R3 2559

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
90 91 0.179045 AGTGGGCTGTATTCGGATGC 60.179 55.000 0.00 0.0 0.00 3.91 F
1338 4539 1.092348 GTTACCATTTCCAGCCGGAC 58.908 55.000 5.05 0.0 42.67 4.79 F
2257 5765 1.470098 GCGTCGACTTCTACCCTGTTA 59.530 52.381 14.70 0.0 0.00 2.41 F
2502 6034 2.418746 GGCGTATGTTGGTGAGACAGAT 60.419 50.000 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 4743 1.495951 CCGGAGCACGTAAGCAAAC 59.504 57.895 0.0 0.00 42.24 2.93 R
3030 7029 0.622136 TGCCTGCTCATGGATTCAGT 59.378 50.000 0.0 0.00 0.00 3.41 R
3120 7119 4.136796 GGAAATTCCGGTGATCATGATGA 58.863 43.478 14.3 0.44 0.00 2.92 R
4361 8413 2.949177 TCTGGGCTGCAAGTTTCTAA 57.051 45.000 0.5 0.00 35.30 2.10 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
38 39 2.127980 GCTTAGCTATTGCGCGCG 60.128 61.111 28.44 28.44 45.42 6.86
85 86 1.732259 GACACAAGTGGGCTGTATTCG 59.268 52.381 5.08 0.00 34.19 3.34
90 91 0.179045 AGTGGGCTGTATTCGGATGC 60.179 55.000 0.00 0.00 0.00 3.91
102 103 5.466728 TGTATTCGGATGCTTTCATTCTAGC 59.533 40.000 0.00 0.00 37.89 3.42
103 104 3.827008 TCGGATGCTTTCATTCTAGCT 57.173 42.857 0.00 0.00 38.22 3.32
104 105 4.937201 TCGGATGCTTTCATTCTAGCTA 57.063 40.909 0.00 0.00 38.22 3.32
178 179 1.254026 GACCCCTTTTACCACAAGGC 58.746 55.000 0.00 0.00 39.78 4.35
210 216 2.363038 TGCAGATCAACTTGCAGCTTTT 59.637 40.909 3.41 0.00 32.29 2.27
323 1164 8.425237 AATTGCCATTTATCATACCATCATCA 57.575 30.769 0.00 0.00 0.00 3.07
509 1794 9.684448 CGTCATGACATGTCTAGTCTATTTAAT 57.316 33.333 25.55 4.39 36.94 1.40
530 1815 9.639563 TTTAATGGTTGATGCATCTTATTCCTA 57.360 29.630 26.32 8.18 0.00 2.94
631 1916 6.757478 GGCTAGTACTCTGTATTGTTTCCTTC 59.243 42.308 0.00 0.00 0.00 3.46
660 1945 1.993701 TTGGTTGTGCCTGCTCTCCA 61.994 55.000 0.00 0.00 38.35 3.86
738 2023 8.827677 GTTATGCCTAAAATTGGTACTCACTAG 58.172 37.037 0.00 0.00 0.00 2.57
790 2075 5.606505 TCACTAAAGTCTGTTGTATGCACA 58.393 37.500 0.00 0.00 0.00 4.57
866 4047 9.783425 GTCTAAATTCATTCGCAAAAAGAAAAG 57.217 29.630 0.00 0.00 0.00 2.27
937 4134 3.363772 GCAGCTATAAATTGCGCTCTCTG 60.364 47.826 9.73 4.29 33.76 3.35
956 4157 2.634940 CTGAGACTCAAGAAAGACCCCA 59.365 50.000 6.61 0.00 0.00 4.96
1188 4389 4.382320 GGCGACGTGGTTAGCCCA 62.382 66.667 0.00 0.00 43.54 5.36
1338 4539 1.092348 GTTACCATTTCCAGCCGGAC 58.908 55.000 5.05 0.00 42.67 4.79
1523 4743 2.143925 GGAGAAAGAAACTGACCACCG 58.856 52.381 0.00 0.00 0.00 4.94
1953 5458 2.943978 GCTCGCCCAGGTACAGTGT 61.944 63.158 0.00 0.00 0.00 3.55
2257 5765 1.470098 GCGTCGACTTCTACCCTGTTA 59.530 52.381 14.70 0.00 0.00 2.41
2502 6034 2.418746 GGCGTATGTTGGTGAGACAGAT 60.419 50.000 0.00 0.00 0.00 2.90
2925 6892 6.707440 TTTCACTATTAGGCTCTCTGAGAG 57.293 41.667 26.58 26.58 45.04 3.20
3030 7029 8.161425 ACATAAGAGAACCTTTTAAGTTGCCTA 58.839 33.333 0.00 0.00 36.34 3.93
3063 7062 4.347292 TGAGCAGGCAAGAGATAATCTGAT 59.653 41.667 0.00 0.00 38.67 2.90
3091 7090 9.606631 AACAGAAACATCTTATTAGCTAGAAGG 57.393 33.333 14.31 5.44 0.00 3.46
3120 7119 6.879458 GGTAGTGGTTCTTGATATCAAAGTGT 59.121 38.462 18.47 3.73 35.15 3.55
3140 7139 4.336433 GTGTCATCATGATCACCGGAATTT 59.664 41.667 9.46 0.00 0.00 1.82
4259 8310 5.447548 GCTTTTCTGCAAGATCTCTGTGATC 60.448 44.000 10.86 10.86 46.36 2.92
4410 8462 6.494893 TCGGAATTTCTGATTTTAGGTGTG 57.505 37.500 3.74 0.00 0.00 3.82
4452 8504 6.128929 CGCGGAAATATCGATCACTGAAATTA 60.129 38.462 0.00 0.00 0.00 1.40
4618 8670 6.428159 GTGTCTATTTTGTTCTGTGATGACCT 59.572 38.462 0.00 0.00 0.00 3.85
4822 10070 9.116067 TGTATATATAAAAAGCCAAGTGGTGAC 57.884 33.333 0.00 0.00 37.57 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.008019 GCAATAGCTAAGCTGATGCTAAACA 59.992 40.000 16.07 0.69 43.28 2.83
43 44 1.401905 GAGGGTTCCTTATTGCAAGCG 59.598 52.381 4.94 0.00 31.76 4.68
48 49 3.010420 GTGTCTGAGGGTTCCTTATTGC 58.990 50.000 0.00 0.00 31.76 3.56
49 50 4.286297 TGTGTCTGAGGGTTCCTTATTG 57.714 45.455 0.00 0.00 31.76 1.90
85 86 6.000219 TCCATTAGCTAGAATGAAAGCATCC 59.000 40.000 10.26 0.00 41.32 3.51
90 91 5.237344 CCGGTTCCATTAGCTAGAATGAAAG 59.763 44.000 10.26 3.69 38.83 2.62
102 103 0.759346 CCTCTCCCCGGTTCCATTAG 59.241 60.000 0.00 0.00 0.00 1.73
103 104 1.342672 GCCTCTCCCCGGTTCCATTA 61.343 60.000 0.00 0.00 0.00 1.90
104 105 2.680370 GCCTCTCCCCGGTTCCATT 61.680 63.158 0.00 0.00 0.00 3.16
178 179 7.329438 CAAGTTGATCTGCATACAAAACTTG 57.671 36.000 19.09 19.09 43.54 3.16
210 216 4.098044 TGCAAAACCAAAACTTACCGATCA 59.902 37.500 0.00 0.00 0.00 2.92
323 1164 7.500559 GTCACTTATTTCTGATATGAAGGGCTT 59.499 37.037 0.00 0.00 0.00 4.35
509 1794 6.318648 GTGTTAGGAATAAGATGCATCAACCA 59.681 38.462 27.81 10.33 0.00 3.67
530 1815 8.557450 AGGGTAACAATCCTTATCATAAGTGTT 58.443 33.333 13.56 13.56 39.74 3.32
631 1916 4.050553 CAGGCACAACCAAAATACAGTTG 58.949 43.478 0.00 0.00 45.02 3.16
660 1945 7.285401 AGACAGATCCAAACAAAATACAGTTGT 59.715 33.333 0.00 0.00 40.92 3.32
761 2046 5.864418 ACAACAGACTTTAGTGAGTACCA 57.136 39.130 0.00 0.00 0.00 3.25
829 2122 8.352942 GCGAATGAATTTAGACCCATCTTAATT 58.647 33.333 1.95 1.95 43.51 1.40
866 4047 7.775561 ACTGAATCATTAATTTAGACCCACCTC 59.224 37.037 0.00 0.00 35.18 3.85
937 4134 2.635427 ACTGGGGTCTTTCTTGAGTCTC 59.365 50.000 0.00 0.00 0.00 3.36
956 4157 5.024785 ACTGAAGAGGAAAGTTTTCGACT 57.975 39.130 0.00 0.00 41.47 4.18
1338 4539 5.416083 TCCATACCGTTCATGTAGTTCTTG 58.584 41.667 0.00 0.00 0.00 3.02
1523 4743 1.495951 CCGGAGCACGTAAGCAAAC 59.504 57.895 0.00 0.00 42.24 2.93
1556 4801 2.555325 CCGTTTGGATCTGCATGCATAT 59.445 45.455 22.97 20.02 37.49 1.78
1953 5458 1.891919 GTCTGCAGGTTCGGCAACA 60.892 57.895 15.13 0.00 41.39 3.33
2257 5765 1.565759 TGATGAGTTGCTATTGCCCCT 59.434 47.619 0.00 0.00 38.71 4.79
2752 6715 8.898761 AGTGAATAAACACAGTAAAACATGTCA 58.101 29.630 0.00 0.00 42.45 3.58
2815 6778 8.540492 CCTGTGTTCACTATTATACGATGTTTC 58.460 37.037 4.59 0.00 0.00 2.78
2925 6892 6.986904 ACCTTTTTGAGTTAGATTCGATCC 57.013 37.500 0.00 0.00 0.00 3.36
3030 7029 0.622136 TGCCTGCTCATGGATTCAGT 59.378 50.000 0.00 0.00 0.00 3.41
3091 7090 8.561738 TTTGATATCAAGAACCACTACCTTTC 57.438 34.615 17.28 0.00 37.15 2.62
3120 7119 4.136796 GGAAATTCCGGTGATCATGATGA 58.863 43.478 14.30 0.44 0.00 2.92
3140 7139 9.167311 GAGAGTTCATTTTAATTCAAGCTAGGA 57.833 33.333 0.00 0.00 0.00 2.94
4259 8310 4.323417 TGCAGGTTGTAGGTAGTGAAATG 58.677 43.478 0.00 0.00 0.00 2.32
4361 8413 2.949177 TCTGGGCTGCAAGTTTCTAA 57.051 45.000 0.50 0.00 35.30 2.10
4410 8462 2.969306 CCGCGTGTCTCGTATAATGTAC 59.031 50.000 4.92 0.00 42.13 2.90
4452 8504 7.363268 GCAAGTTGTATCATTCTTTTGGAGGAT 60.363 37.037 4.48 0.00 0.00 3.24
4502 8554 6.435591 TGGGTTGCATACATAAGTTTTGATGA 59.564 34.615 0.00 0.00 0.00 2.92
4618 8670 2.867624 AGGCAAGTCTGAATTCAGCAA 58.132 42.857 27.45 11.31 43.46 3.91
4822 10070 4.870123 TTTGTGGTGAAATGGAGAATGG 57.130 40.909 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.