Multiple sequence alignment - TraesCS7D01G317900

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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 TraesCS7D01G317900 chr7D 100.000 5074 0 0 1 5074 404747495 404752568 0.000000e+00 9371
1 TraesCS7D01G317900 chr7D 72.117 581 128 15 528 1101 95225735 95225182 1.470000e-30 145
2 TraesCS7D01G317900 chr1B 95.341 4636 165 22 474 5074 149216304 149211685 0.000000e+00 7317
3 TraesCS7D01G317900 chr1B 89.794 3204 296 22 481 3668 595418705 595415517 0.000000e+00 4076
4 TraesCS7D01G317900 chr1B 86.818 1411 146 28 3682 5074 595415445 595414057 0.000000e+00 1539
5 TraesCS7D01G317900 chr1B 87.190 484 47 5 1 478 595419293 595418819 2.080000e-148 536
6 TraesCS7D01G317900 chr1B 95.349 215 6 1 264 478 149216622 149216412 6.290000e-89 339
7 TraesCS7D01G317900 chr2A 93.422 4637 253 33 480 5074 593823708 593828334 0.000000e+00 6826
8 TraesCS7D01G317900 chr2A 91.932 471 24 8 1 463 593823178 593823642 0.000000e+00 647
9 TraesCS7D01G317900 chr5B 93.379 4637 256 32 480 5074 105970622 105975249 0.000000e+00 6815
10 TraesCS7D01G317900 chr5B 92.781 471 20 8 1 463 105970092 105970556 0.000000e+00 669
11 TraesCS7D01G317900 chr6D 95.569 3837 128 22 474 4274 208038681 208034851 0.000000e+00 6106
12 TraesCS7D01G317900 chr6D 87.943 1833 182 24 1846 3668 97954860 97953057 0.000000e+00 2124
13 TraesCS7D01G317900 chr6D 92.429 1334 92 7 481 1809 97956194 97954865 0.000000e+00 1895
14 TraesCS7D01G317900 chr6D 86.950 1410 144 27 3682 5074 97952986 97951600 0.000000e+00 1548
15 TraesCS7D01G317900 chr6D 95.926 810 25 5 4270 5074 208025738 208024932 0.000000e+00 1306
16 TraesCS7D01G317900 chr6D 97.490 478 11 1 1 478 208039265 208038789 0.000000e+00 815
17 TraesCS7D01G317900 chr6D 87.975 474 42 4 11 478 97956773 97956309 3.450000e-151 545
18 TraesCS7D01G317900 chr2D 89.751 3210 284 29 481 3676 254300572 254303750 0.000000e+00 4063
19 TraesCS7D01G317900 chr2D 86.553 1413 149 29 3679 5074 254303807 254305195 0.000000e+00 1519
20 TraesCS7D01G317900 chr2D 87.603 484 45 4 1 478 254299983 254300457 9.600000e-152 547
21 TraesCS7D01G317900 chr5D 90.760 3041 215 37 2067 5074 392333485 392330478 0.000000e+00 3999
22 TraesCS7D01G317900 chr6B 91.560 2808 193 27 2303 5074 218918794 218915995 0.000000e+00 3832
23 TraesCS7D01G317900 chr7A 87.438 2014 232 18 1398 3406 265116336 265118333 0.000000e+00 2298
24 TraesCS7D01G317900 chr7A 81.283 187 34 1 4885 5070 196681553 196681739 3.160000e-32 150
25 TraesCS7D01G317900 chr6A 72.557 747 145 46 4353 5074 142009963 142009252 6.710000e-44 189
26 TraesCS7D01G317900 chr3B 79.186 221 42 4 883 1101 632532589 632532807 3.160000e-32 150
27 TraesCS7D01G317900 chr3D 81.714 175 31 1 4900 5074 31586884 31587057 1.470000e-30 145


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 TraesCS7D01G317900 chr7D 404747495 404752568 5073 False 9371.000000 9371 100.00000 1 5074 1 chr7D.!!$F1 5073
1 TraesCS7D01G317900 chr1B 149211685 149216622 4937 True 3828.000000 7317 95.34500 264 5074 2 chr1B.!!$R1 4810
2 TraesCS7D01G317900 chr1B 595414057 595419293 5236 True 2050.333333 4076 87.93400 1 5074 3 chr1B.!!$R2 5073
3 TraesCS7D01G317900 chr2A 593823178 593828334 5156 False 3736.500000 6826 92.67700 1 5074 2 chr2A.!!$F1 5073
4 TraesCS7D01G317900 chr5B 105970092 105975249 5157 False 3742.000000 6815 93.08000 1 5074 2 chr5B.!!$F1 5073
5 TraesCS7D01G317900 chr6D 208034851 208039265 4414 True 3460.500000 6106 96.52950 1 4274 2 chr6D.!!$R3 4273
6 TraesCS7D01G317900 chr6D 97951600 97956773 5173 True 1528.000000 2124 88.82425 11 5074 4 chr6D.!!$R2 5063
7 TraesCS7D01G317900 chr6D 208024932 208025738 806 True 1306.000000 1306 95.92600 4270 5074 1 chr6D.!!$R1 804
8 TraesCS7D01G317900 chr2D 254299983 254305195 5212 False 2043.000000 4063 87.96900 1 5074 3 chr2D.!!$F1 5073
9 TraesCS7D01G317900 chr5D 392330478 392333485 3007 True 3999.000000 3999 90.76000 2067 5074 1 chr5D.!!$R1 3007
10 TraesCS7D01G317900 chr6B 218915995 218918794 2799 True 3832.000000 3832 91.56000 2303 5074 1 chr6B.!!$R1 2771
11 TraesCS7D01G317900 chr7A 265116336 265118333 1997 False 2298.000000 2298 87.43800 1398 3406 1 chr7A.!!$F2 2008

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
313 325 0.179059 TGGTGTGTAGTGTGGCTGTG 60.179 55.000 0.00 0.00 0.00 3.66 F
319 335 0.969894 GTAGTGTGGCTGTGAGGACT 59.030 55.000 0.00 0.00 0.00 3.85 F
478 498 1.742831 TGCATTGCCGTAAGATTCACC 59.257 47.619 6.12 0.00 43.02 4.02 F
864 1005 3.120991 GCTTTACGTGGCGCTATCATAAG 60.121 47.826 7.64 5.86 0.00 1.73 F
2605 2763 1.726853 ACAACAGATACTCCTTGCGC 58.273 50.000 0.00 0.00 0.00 6.09 F
2969 3144 0.249031 GTTGGGCCGCAGAATAATGC 60.249 55.000 0.00 0.00 42.95 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 1418 2.724977 TCTCGTAAACTGACCAGCTG 57.275 50.000 6.78 6.78 0.00 4.24 R
1926 2069 6.049955 TGATCCAAAGAACCCTGTAACTAG 57.950 41.667 0.00 0.00 0.00 2.57 R
2417 2573 3.614092 TCCTGGATGAAAGACTCATTGC 58.386 45.455 0.00 0.00 45.23 3.56 R
2753 2923 1.609208 CTCACCCAAAGAACCCTGTG 58.391 55.000 0.00 0.00 0.00 3.66 R
3753 4002 0.746063 TCTAACCCGTTGACACGTGT 59.254 50.000 23.64 23.64 45.62 4.49 R
4207 4461 1.352156 GGAGCGTACCAAGAGCAACG 61.352 60.000 0.00 0.00 38.34 4.10 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
73 74 1.752498 TGAACATGAGAATGCCATGCC 59.248 47.619 0.00 0.00 43.76 4.40
117 118 9.112725 CTCATGTTCAACCATCATCTTGTAATA 57.887 33.333 0.00 0.00 0.00 0.98
313 325 0.179059 TGGTGTGTAGTGTGGCTGTG 60.179 55.000 0.00 0.00 0.00 3.66
319 335 0.969894 GTAGTGTGGCTGTGAGGACT 59.030 55.000 0.00 0.00 0.00 3.85
478 498 1.742831 TGCATTGCCGTAAGATTCACC 59.257 47.619 6.12 0.00 43.02 4.02
493 627 3.972950 TTCACCGTTGTTTATGTGTGG 57.027 42.857 0.00 0.00 0.00 4.17
536 670 9.511272 TGGTAATTTATCCATGATCAGATGAAG 57.489 33.333 0.09 0.00 0.00 3.02
645 779 4.038642 TGAACTAAACCAGCCAATTGGAAC 59.961 41.667 29.02 11.36 40.87 3.62
777 914 7.386059 AGACCAATGAACAAAGAAACAAAAGT 58.614 30.769 0.00 0.00 0.00 2.66
864 1005 3.120991 GCTTTACGTGGCGCTATCATAAG 60.121 47.826 7.64 5.86 0.00 1.73
1070 1212 7.987458 TCAGTGGATTACTCTGGTCAATAATTC 59.013 37.037 0.00 0.00 37.60 2.17
1275 1418 5.530712 AGAGTTTTCCACGAGTTAGAGAAC 58.469 41.667 0.00 0.00 35.64 3.01
2280 2427 3.181510 GCAACCATCATACAAACGTCCTC 60.182 47.826 0.00 0.00 0.00 3.71
2281 2428 4.253685 CAACCATCATACAAACGTCCTCT 58.746 43.478 0.00 0.00 0.00 3.69
2436 2592 4.333095 CAGAGCAATGAGTCTTTCATCCAG 59.667 45.833 0.00 0.00 45.82 3.86
2605 2763 1.726853 ACAACAGATACTCCTTGCGC 58.273 50.000 0.00 0.00 0.00 6.09
2753 2923 7.758528 ACATGTACTAATTGTTAGGTTCTCGTC 59.241 37.037 0.00 0.00 37.57 4.20
2823 2993 5.350914 TGTTGGCAAGACAAATTCAAAACAG 59.649 36.000 0.00 0.00 31.17 3.16
2969 3144 0.249031 GTTGGGCCGCAGAATAATGC 60.249 55.000 0.00 0.00 42.95 3.56
3167 3351 9.165035 CCAATATGGTTGAGCAACAATTAATTT 57.835 29.630 14.55 0.67 42.85 1.82
3400 3589 4.717233 ATTTATTGCACATTTCCAGCGA 57.283 36.364 0.00 0.00 0.00 4.93
3526 3715 6.480981 CCAAGTTGAAAAATCTCTGCACATTT 59.519 34.615 3.87 0.00 0.00 2.32
3758 4007 5.120399 TGATCTCCAACTTAACAAACACGT 58.880 37.500 0.00 0.00 0.00 4.49
3806 4058 4.091075 CGTATGGCAGATTCTGATTCATCG 59.909 45.833 17.87 15.35 32.44 3.84
4541 4800 1.598701 GCAAGGTGGACAATGGGCTC 61.599 60.000 0.00 0.00 0.00 4.70
4650 4909 3.396260 TTGAAACGTCCAGACTTAGGG 57.604 47.619 0.00 0.00 0.00 3.53
4915 5180 5.772825 ACACAAATGAACTGTTGCTATGT 57.227 34.783 0.00 0.00 0.00 2.29
4958 5224 2.111756 CTGCAACGCTTTTTCACACTC 58.888 47.619 0.00 0.00 0.00 3.51
5041 5307 2.027003 TAATCCGTTGGTAAAGCCCG 57.973 50.000 0.00 0.00 36.04 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 0.681733 TCAGTCAAGCCTTCTTCGCT 59.318 50.000 0.00 0.00 38.53 4.93
313 325 6.815089 AGTTGTTCTGATGATCATAGTCCTC 58.185 40.000 8.54 0.00 0.00 3.71
478 498 6.946165 TGTAGTTAACCACACATAAACAACG 58.054 36.000 2.51 0.00 0.00 4.10
536 670 1.880027 ACGCTTGGTTGTTTCTCCATC 59.120 47.619 0.00 0.00 33.50 3.51
645 779 1.621301 CGCAAGACGTCCAGCTTCTG 61.621 60.000 22.41 7.80 43.02 3.02
777 914 6.401047 ACCTTTACTTGCGCTAGTATATCA 57.599 37.500 27.84 13.53 31.09 2.15
864 1005 8.763356 TCATCTACATTTCAAACAAAACAATGC 58.237 29.630 0.00 0.00 0.00 3.56
892 1033 3.263425 TCCAAGCGAGAAGGGTAAGAAAT 59.737 43.478 0.00 0.00 0.00 2.17
1070 1212 1.303236 TGTGCCTTTGGGGTCATCG 60.303 57.895 0.00 0.00 37.43 3.84
1275 1418 2.724977 TCTCGTAAACTGACCAGCTG 57.275 50.000 6.78 6.78 0.00 4.24
1926 2069 6.049955 TGATCCAAAGAACCCTGTAACTAG 57.950 41.667 0.00 0.00 0.00 2.57
2038 2184 7.701539 AGAACATACTTGTAAAATGGCATCA 57.298 32.000 0.00 0.00 34.06 3.07
2280 2427 9.896645 ATATAAATGAGCATACCTATCCACAAG 57.103 33.333 0.00 0.00 0.00 3.16
2417 2573 3.614092 TCCTGGATGAAAGACTCATTGC 58.386 45.455 0.00 0.00 45.23 3.56
2436 2592 5.125100 TCTCTTGTTGCACATTTTCATCC 57.875 39.130 0.00 0.00 0.00 3.51
2605 2763 7.805071 CCTAATGAAAAGAAGTAACAACAGCTG 59.195 37.037 13.48 13.48 0.00 4.24
2616 2774 8.870075 AAGATAAGCACCTAATGAAAAGAAGT 57.130 30.769 0.00 0.00 0.00 3.01
2753 2923 1.609208 CTCACCCAAAGAACCCTGTG 58.391 55.000 0.00 0.00 0.00 3.66
2888 3063 5.523552 GTCTGTTGATTGAAACCAAAAAGGG 59.476 40.000 0.00 0.00 43.89 3.95
2969 3144 3.385193 TGCATCCATACACTACCATCG 57.615 47.619 0.00 0.00 0.00 3.84
3167 3351 6.261435 TCCTACCATGAGAAGAGGAAGTAAA 58.739 40.000 0.00 0.00 33.33 2.01
3285 3470 6.874134 ACTAACCTTATCTGCACTAGTGTTTG 59.126 38.462 23.44 13.67 0.00 2.93
3400 3589 8.481314 TCAGACTTCATTTCTAGCATGAGTATT 58.519 33.333 0.00 0.00 32.20 1.89
3526 3715 5.950758 TGCAAACGAAAGGCTAAAATAGA 57.049 34.783 0.00 0.00 0.00 1.98
3679 3912 1.619332 TGGCATGTCATGTTGTGCAAT 59.381 42.857 14.26 0.00 39.27 3.56
3753 4002 0.746063 TCTAACCCGTTGACACGTGT 59.254 50.000 23.64 23.64 45.62 4.49
3758 4007 5.320549 GAGTATTCTCTAACCCGTTGACA 57.679 43.478 0.00 0.00 37.68 3.58
4149 4401 3.418047 ACAGTGCCAACCTATTTGTACC 58.582 45.455 0.00 0.00 32.71 3.34
4207 4461 1.352156 GGAGCGTACCAAGAGCAACG 61.352 60.000 0.00 0.00 38.34 4.10
4234 4488 5.104067 ACCCTCAACTTTATATTCTGGGTCC 60.104 44.000 0.00 0.00 41.05 4.46
4493 4751 4.202641 ACATCTGGGCCATACATCATCAAT 60.203 41.667 6.72 0.00 0.00 2.57
4541 4800 8.603242 AACACTACACAAGACTAACAAATAGG 57.397 34.615 0.00 0.00 35.81 2.57
4871 5133 2.549329 TGCTGCACACTGTACAAATGAG 59.451 45.455 12.56 6.78 0.00 2.90
4898 5163 7.880195 AGAACTAGAACATAGCAACAGTTCATT 59.120 33.333 12.52 5.31 43.00 2.57
4915 5180 7.861372 GCAGATTAGCAACGTATAGAACTAGAA 59.139 37.037 0.00 0.00 0.00 2.10
4958 5224 9.944663 ACAACATATATAAATGCGTTGGTAAAG 57.055 29.630 13.07 0.00 38.39 1.85
5041 5307 8.612619 GTTATATGCCCATATATGTGTTGCTAC 58.387 37.037 11.73 0.00 36.47 3.58


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

AutoCloner maintained by Alex Coulton.