Multiple sequence alignment - TraesCS7A01G275200

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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 TraesCS7A01G275200 chr7A 100.000 2447 0 0 1 2447 287847811 287850257 0.000000e+00 4519.0
1 TraesCS7A01G275200 chr7B 91.171 2016 106 36 312 2305 244635176 244637141 0.000000e+00 2671.0
2 TraesCS7A01G275200 chr7B 92.923 325 9 3 1 323 244633232 244633544 6.170000e-126 460.0
3 TraesCS7A01G275200 chr7B 94.667 75 4 0 2336 2410 244637141 244637215 1.540000e-22 117.0
4 TraesCS7A01G275200 chr7D 95.597 1431 53 3 1000 2421 264319942 264321371 0.000000e+00 2285.0
5 TraesCS7A01G275200 chr7D 94.729 645 24 5 361 999 264318024 264318664 0.000000e+00 994.0
6 TraesCS7A01G275200 chr7D 95.149 268 12 1 1 267 264317159 264317426 2.910000e-114 422.0
7 TraesCS7A01G275200 chr6A 84.020 1383 198 20 676 2040 34282374 34280997 0.000000e+00 1308.0
8 TraesCS7A01G275200 chr6A 83.688 1269 188 12 788 2040 34284284 34283019 0.000000e+00 1179.0
9 TraesCS7A01G275200 chr6A 84.112 107 12 2 2044 2150 34280948 34280847 5.570000e-17 99.0
10 TraesCS7A01G275200 chr6A 84.043 94 10 2 2057 2150 34393522 34393434 4.340000e-13 86.1
11 TraesCS7A01G275200 chr6B 83.452 1263 186 13 788 2040 62636138 62634889 0.000000e+00 1153.0
12 TraesCS7A01G275200 chr3B 84.731 1133 156 11 922 2038 780301925 780300794 0.000000e+00 1118.0
13 TraesCS7A01G275200 chr3B 78.539 219 40 4 2056 2272 780354286 780354073 1.180000e-28 137.0
14 TraesCS7A01G275200 chr3D 84.568 1134 157 12 922 2038 583284347 583283215 0.000000e+00 1109.0
15 TraesCS7A01G275200 chr3D 84.439 1131 159 11 924 2038 583181478 583180349 0.000000e+00 1098.0
16 TraesCS7A01G275200 chr3D 84.879 1078 150 10 972 2038 583187412 583186337 0.000000e+00 1075.0
17 TraesCS7A01G275200 chr3D 78.539 219 40 6 2056 2272 583288642 583288429 1.180000e-28 137.0
18 TraesCS7A01G275200 chr3D 84.375 96 12 1 2056 2151 583276891 583276799 9.320000e-15 91.6
19 TraesCS7A01G275200 chr3D 83.333 96 13 2 2056 2151 583168758 583168666 4.340000e-13 86.1
20 TraesCS7A01G275200 chr3D 100.000 33 0 0 2046 2078 583180301 583180269 7.310000e-06 62.1


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 TraesCS7A01G275200 chr7A 287847811 287850257 2446 False 4519.000000 4519 100.000000 1 2447 1 chr7A.!!$F1 2446
1 TraesCS7A01G275200 chr7B 244633232 244637215 3983 False 1082.666667 2671 92.920333 1 2410 3 chr7B.!!$F1 2409
2 TraesCS7A01G275200 chr7D 264317159 264321371 4212 False 1233.666667 2285 95.158333 1 2421 3 chr7D.!!$F1 2420
3 TraesCS7A01G275200 chr6A 34280847 34284284 3437 True 862.000000 1308 83.940000 676 2150 3 chr6A.!!$R2 1474
4 TraesCS7A01G275200 chr6B 62634889 62636138 1249 True 1153.000000 1153 83.452000 788 2040 1 chr6B.!!$R1 1252
5 TraesCS7A01G275200 chr3B 780300794 780301925 1131 True 1118.000000 1118 84.731000 922 2038 1 chr3B.!!$R1 1116
6 TraesCS7A01G275200 chr3D 583283215 583284347 1132 True 1109.000000 1109 84.568000 922 2038 1 chr3D.!!$R4 1116
7 TraesCS7A01G275200 chr3D 583186337 583187412 1075 True 1075.000000 1075 84.879000 972 2038 1 chr3D.!!$R2 1066
8 TraesCS7A01G275200 chr3D 583180269 583181478 1209 True 580.050000 1098 92.219500 924 2078 2 chr3D.!!$R6 1154

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
439 2393 1.608590 ACACACCAAAGGCTCATTTCG 59.391 47.619 0.00 0.0 0.00 3.46 F
489 2444 2.585557 ACTCACACGGTGGGTGGTTTA 61.586 52.381 15.98 0.0 46.35 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1444 6720 0.248289 GCCAAGCGGGTGTAAGACTA 59.752 55.0 0.00 0.0 39.65 2.59 R
1659 6938 0.822164 GCAATTGCTCCTCCTTGCAT 59.178 50.0 23.21 0.0 42.66 3.96 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
18 20 2.436646 CTTCGCTGGCCCACGAAT 60.437 61.111 24.79 0.0 46.15 3.34
249 263 5.924825 TCGAGATCTGACTATGCATCAAATG 59.075 40.000 0.19 0.0 0.00 2.32
286 300 4.941657 AGAAGCAAAAGCCAGAAGAAAAG 58.058 39.130 0.00 0.0 0.00 2.27
350 2299 5.957842 AAATAAAGACGGCTGATGTTTGA 57.042 34.783 0.00 0.0 0.00 2.69
439 2393 1.608590 ACACACCAAAGGCTCATTTCG 59.391 47.619 0.00 0.0 0.00 3.46
460 2415 9.874205 ATTTCGACAATGGTTTGATATGAAATT 57.126 25.926 0.00 0.0 33.91 1.82
489 2444 2.585557 ACTCACACGGTGGGTGGTTTA 61.586 52.381 15.98 0.0 46.35 2.01
655 2611 2.915659 AGAACGGACGACAGGGCA 60.916 61.111 0.00 0.0 0.00 5.36
911 2874 5.221682 CCAGATCTCAAGCCATAGAAGACAT 60.222 44.000 0.00 0.0 0.00 3.06
1024 4273 4.819630 TGGTACATCAAACCAGAAGTTGTC 59.180 41.667 0.00 0.0 42.10 3.18
1261 6537 6.547510 GGGTGTTGAAGAGATTATTTGCCTAT 59.452 38.462 0.00 0.0 0.00 2.57
1307 6583 2.842496 AGCAGAGGAAGATGTTGGATGA 59.158 45.455 0.00 0.0 0.00 2.92
1659 6938 5.906113 TTCACAAAAAGAAGGCAGTTGTA 57.094 34.783 0.00 0.0 31.44 2.41
1688 6967 1.307097 GAGCAATTGCAGGAGCTAGG 58.693 55.000 30.89 0.0 45.16 3.02
1697 6976 0.461961 CAGGAGCTAGGGTGCAGTAC 59.538 60.000 0.00 0.0 34.99 2.73
1744 7023 6.214412 AGGACATCTGTTCAGGAAATTACTCT 59.786 38.462 0.00 0.0 0.00 3.24
2011 7299 4.142227 TGGTTAGTCGATCTTGCTCCTTAC 60.142 45.833 0.00 0.0 0.00 2.34
2129 7462 8.081633 CAGAATGCAACAAAGTCCAAATTAGTA 58.918 33.333 0.00 0.0 0.00 1.82
2230 7564 1.338020 CCACAACTCTGCTTTTGTCCC 59.662 52.381 0.00 0.0 33.59 4.46
2253 7587 6.382570 CCCACAGGATTAACAATAATTTGGGA 59.617 38.462 0.00 0.0 38.43 4.37
2306 7649 8.957466 GCAAAGTTTGTTCCTTTCCTATAGTAT 58.043 33.333 16.70 0.0 29.89 2.12
2334 7677 4.267452 CAGTACACAAACAACAACCAATGC 59.733 41.667 0.00 0.0 0.00 3.56
2395 7738 6.155221 TCTGTACATGCTTACCAGAGATCTTT 59.845 38.462 0.00 0.0 0.00 2.52
2414 7757 8.497745 AGATCTTTAGAATGGAGCAGGAAATTA 58.502 33.333 0.00 0.0 0.00 1.40
2415 7758 9.125026 GATCTTTAGAATGGAGCAGGAAATTAA 57.875 33.333 0.00 0.0 0.00 1.40
2417 7760 9.479549 TCTTTAGAATGGAGCAGGAAATTAATT 57.520 29.630 0.00 0.0 0.00 1.40
2418 7761 9.741647 CTTTAGAATGGAGCAGGAAATTAATTC 57.258 33.333 0.10 0.0 37.31 2.17
2419 7762 8.821686 TTAGAATGGAGCAGGAAATTAATTCA 57.178 30.769 0.10 0.0 39.98 2.57
2420 7763 7.344095 AGAATGGAGCAGGAAATTAATTCAG 57.656 36.000 0.10 0.0 39.98 3.02
2421 7764 7.121382 AGAATGGAGCAGGAAATTAATTCAGA 58.879 34.615 0.10 0.0 39.98 3.27
2422 7765 7.616935 AGAATGGAGCAGGAAATTAATTCAGAA 59.383 33.333 0.10 0.0 39.98 3.02
2423 7766 7.909485 ATGGAGCAGGAAATTAATTCAGAAT 57.091 32.000 0.10 0.0 39.98 2.40
2424 7767 9.425248 AATGGAGCAGGAAATTAATTCAGAATA 57.575 29.630 0.10 0.0 39.98 1.75
2425 7768 8.455903 TGGAGCAGGAAATTAATTCAGAATAG 57.544 34.615 0.10 0.0 39.98 1.73
2426 7769 8.274322 TGGAGCAGGAAATTAATTCAGAATAGA 58.726 33.333 0.10 0.0 39.98 1.98
2427 7770 8.782144 GGAGCAGGAAATTAATTCAGAATAGAG 58.218 37.037 0.10 0.0 39.98 2.43
2428 7771 9.336171 GAGCAGGAAATTAATTCAGAATAGAGT 57.664 33.333 0.10 0.0 39.98 3.24
2429 7772 9.692325 AGCAGGAAATTAATTCAGAATAGAGTT 57.308 29.630 0.10 0.0 39.98 3.01
2442 7785 8.651589 TCAGAATAGAGTTTCTCTCCTAAACA 57.348 34.615 2.41 0.0 43.71 2.83
2443 7786 9.261035 TCAGAATAGAGTTTCTCTCCTAAACAT 57.739 33.333 2.41 0.0 43.71 2.71
2444 7787 9.883142 CAGAATAGAGTTTCTCTCCTAAACATT 57.117 33.333 2.41 0.0 43.71 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 20 3.865446 CATGCTGTCAGTCTGGTTGATA 58.135 45.455 0.93 0.00 0.00 2.15
64 78 9.034800 AGGTTCATTTTTGGCTAAATAGATGAA 57.965 29.630 17.52 17.52 33.04 2.57
65 79 8.469200 CAGGTTCATTTTTGGCTAAATAGATGA 58.531 33.333 10.57 10.57 0.00 2.92
66 80 8.253113 ACAGGTTCATTTTTGGCTAAATAGATG 58.747 33.333 0.00 2.41 0.00 2.90
67 81 8.366359 ACAGGTTCATTTTTGGCTAAATAGAT 57.634 30.769 0.00 0.00 0.00 1.98
68 82 7.775053 ACAGGTTCATTTTTGGCTAAATAGA 57.225 32.000 0.00 0.00 0.00 1.98
69 83 8.831715 AAACAGGTTCATTTTTGGCTAAATAG 57.168 30.769 0.00 0.00 0.00 1.73
71 85 9.791801 AATAAACAGGTTCATTTTTGGCTAAAT 57.208 25.926 0.00 0.00 0.00 1.40
72 86 9.267084 GAATAAACAGGTTCATTTTTGGCTAAA 57.733 29.630 0.00 0.00 0.00 1.85
73 87 8.424918 TGAATAAACAGGTTCATTTTTGGCTAA 58.575 29.630 0.00 0.00 0.00 3.09
74 88 7.957002 TGAATAAACAGGTTCATTTTTGGCTA 58.043 30.769 0.00 0.00 0.00 3.93
75 89 6.825610 TGAATAAACAGGTTCATTTTTGGCT 58.174 32.000 0.00 0.00 0.00 4.75
76 90 7.603784 AGATGAATAAACAGGTTCATTTTTGGC 59.396 33.333 2.55 0.00 34.62 4.52
130 144 4.735985 TGCACTTACTTGCTGCAATAATG 58.264 39.130 16.38 10.88 43.41 1.90
249 263 7.585210 GCTTTTGCTTCTCATTTGAATTTGTTC 59.415 33.333 0.00 0.00 43.35 3.18
439 2393 8.984891 TGACAATTTCATATCAAACCATTGTC 57.015 30.769 12.94 12.94 43.07 3.18
460 2415 0.966179 ACCGTGTGAGTAGCATGACA 59.034 50.000 0.00 0.00 0.00 3.58
655 2611 0.037303 AGTGTGTAATGCTGGCTGCT 59.963 50.000 17.45 0.58 43.37 4.24
1024 4273 3.447229 GTGAAAGAGAGGAGAAGAGGAGG 59.553 52.174 0.00 0.00 0.00 4.30
1236 4492 4.706962 AGGCAAATAATCTCTTCAACACCC 59.293 41.667 0.00 0.00 0.00 4.61
1261 6537 4.019860 AGAGGAGCTAACTTGATTGCTTGA 60.020 41.667 0.00 0.00 35.76 3.02
1444 6720 0.248289 GCCAAGCGGGTGTAAGACTA 59.752 55.000 0.00 0.00 39.65 2.59
1659 6938 0.822164 GCAATTGCTCCTCCTTGCAT 59.178 50.000 23.21 0.00 42.66 3.96
1688 6967 0.824759 AAGATCTCCGGTACTGCACC 59.175 55.000 0.00 0.00 44.75 5.01
1697 6976 1.680735 CTCCACTCTCAAGATCTCCGG 59.319 57.143 0.00 0.00 0.00 5.14
1985 7272 3.119101 GGAGCAAGATCGACTAACCAAGA 60.119 47.826 0.00 0.00 0.00 3.02
2011 7299 1.402613 TGATCTGGCATGTTTCATGCG 59.597 47.619 22.48 13.35 45.41 4.73
2155 7488 6.702723 TGGCTAAAATGCTTAAATGATGCATC 59.297 34.615 20.14 20.14 45.60 3.91
2230 7564 9.369904 CTTTCCCAAATTATTGTTAATCCTGTG 57.630 33.333 0.00 0.00 34.60 3.66
2253 7587 4.394729 TCGCAAGTTTGGATTAGGTCTTT 58.605 39.130 0.00 0.00 39.48 2.52
2306 7649 5.473846 TGGTTGTTGTTTGTGTACTGAGAAA 59.526 36.000 0.00 0.00 0.00 2.52
2334 7677 7.650890 TGATGTGTGCCAATAAGCATATAAAG 58.349 34.615 0.00 0.00 46.24 1.85
2384 7727 5.287674 TGCTCCATTCTAAAGATCTCTGG 57.712 43.478 0.00 0.00 0.00 3.86
2395 7738 8.274322 TCTGAATTAATTTCCTGCTCCATTCTA 58.726 33.333 1.43 0.00 33.04 2.10
2417 7760 8.651589 TGTTTAGGAGAGAAACTCTATTCTGA 57.348 34.615 1.12 0.00 41.35 3.27
2418 7761 9.883142 AATGTTTAGGAGAGAAACTCTATTCTG 57.117 33.333 1.12 0.00 41.35 3.02


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

AutoCloner maintained by Alex Coulton.