Multiple sequence alignment - TraesCS6D01G374100

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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 TraesCS6D01G374100 chr6D 100.000 5390 0 0 1 5390 458745720 458740331 0.000000e+00 9954.0
1 TraesCS6D01G374100 chr6D 89.149 3124 271 27 2053 5157 458716320 458713246 0.000000e+00 3829.0
2 TraesCS6D01G374100 chr6D 83.395 1614 195 35 20 1615 458717870 458716312 0.000000e+00 1428.0
3 TraesCS6D01G374100 chr6D 89.952 209 21 0 5182 5390 458691269 458691061 2.470000e-68 270.0
4 TraesCS6D01G374100 chr6B 96.979 5396 125 20 1 5390 697712413 697707050 0.000000e+00 9027.0
5 TraesCS6D01G374100 chr6B 90.522 2817 243 16 2053 4852 697674511 697671702 0.000000e+00 3701.0
6 TraesCS6D01G374100 chr6B 83.374 1636 204 43 1 1615 697676091 697674503 0.000000e+00 1452.0
7 TraesCS6D01G374100 chr6B 80.742 431 82 1 2780 3209 696854830 696855260 8.650000e-88 335.0
8 TraesCS6D01G374100 chr6B 91.866 209 17 0 5182 5390 697660758 697660550 5.280000e-75 292.0
9 TraesCS6D01G374100 chr6A 96.352 5181 162 17 1 5167 604954819 604959986 0.000000e+00 8495.0
10 TraesCS6D01G374100 chr6A 97.093 172 5 0 5219 5390 604960272 604960443 1.900000e-74 291.0
11 TraesCS6D01G374100 chr7A 75.342 803 145 41 55 818 652618678 652619466 2.410000e-88 337.0
12 TraesCS6D01G374100 chr5D 76.538 699 111 42 83 758 538155711 538156379 3.110000e-87 333.0
13 TraesCS6D01G374100 chr1D 79.873 472 72 19 354 818 479198403 479198858 1.870000e-84 324.0
14 TraesCS6D01G374100 chr5B 75.905 718 120 38 54 748 613620455 613621142 8.710000e-83 318.0
15 TraesCS6D01G374100 chr2D 76.000 700 116 41 69 745 498278086 498278756 1.130000e-81 315.0
16 TraesCS6D01G374100 chr5A 76.538 520 84 30 98 602 12149700 12149204 3.220000e-62 250.0
17 TraesCS6D01G374100 chr4D 77.515 338 48 19 75 404 17865318 17865635 1.540000e-40 178.0
18 TraesCS6D01G374100 chr4D 83.673 98 13 3 450 546 69218896 69218801 7.440000e-14 89.8
19 TraesCS6D01G374100 chr7B 75.477 367 51 30 75 419 543000367 543000018 5.630000e-30 143.0
20 TraesCS6D01G374100 chr2B 84.058 138 20 2 480 615 445248299 445248436 1.220000e-26 132.0
21 TraesCS6D01G374100 chr2B 83.784 111 13 3 445 555 785930641 785930536 3.440000e-17 100.0
22 TraesCS6D01G374100 chr4A 83.673 98 11 5 450 546 521033459 521033366 2.670000e-13 87.9


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 TraesCS6D01G374100 chr6D 458740331 458745720 5389 True 9954.0 9954 100.0000 1 5390 1 chr6D.!!$R2 5389
1 TraesCS6D01G374100 chr6D 458713246 458717870 4624 True 2628.5 3829 86.2720 20 5157 2 chr6D.!!$R3 5137
2 TraesCS6D01G374100 chr6B 697707050 697712413 5363 True 9027.0 9027 96.9790 1 5390 1 chr6B.!!$R2 5389
3 TraesCS6D01G374100 chr6B 697671702 697676091 4389 True 2576.5 3701 86.9480 1 4852 2 chr6B.!!$R3 4851
4 TraesCS6D01G374100 chr6A 604954819 604960443 5624 False 4393.0 8495 96.7225 1 5390 2 chr6A.!!$F1 5389
5 TraesCS6D01G374100 chr7A 652618678 652619466 788 False 337.0 337 75.3420 55 818 1 chr7A.!!$F1 763
6 TraesCS6D01G374100 chr5D 538155711 538156379 668 False 333.0 333 76.5380 83 758 1 chr5D.!!$F1 675
7 TraesCS6D01G374100 chr5B 613620455 613621142 687 False 318.0 318 75.9050 54 748 1 chr5B.!!$F1 694
8 TraesCS6D01G374100 chr2D 498278086 498278756 670 False 315.0 315 76.0000 69 745 1 chr2D.!!$F1 676

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
936 1071 0.246635 CACACTACTTAGCACGGCCT 59.753 55.000 0.00 0.00 0.00 5.19 F
1148 1284 1.412710 TGATCCAGCGGAGAATGGTAC 59.587 52.381 3.76 0.00 37.23 3.34 F
2104 2246 3.061322 CCACCAAAGAATGCATTGTGTG 58.939 45.455 18.59 18.13 32.40 3.82 F
3285 3434 3.117738 CCATATGACTTTCTCTTGGGGCT 60.118 47.826 3.65 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2573 2722 1.436600 AGACAACATGAAGCTCTGCG 58.563 50.000 0.00 0.0 0.00 5.18 R
3191 3340 4.037446 GCAACACTTGTTATCCAGGTCAAA 59.963 41.667 0.00 0.0 36.32 2.69 R
3622 3771 1.266718 AGAAATTGTGCACGTTCGCAT 59.733 42.857 13.13 0.0 45.26 4.73 R
5035 5220 0.550914 GTACATGGCCCATCCCAAGA 59.449 55.000 0.00 0.0 38.61 3.02 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
706 837 4.095932 TCACTCGCACGTCACTTTATCTAT 59.904 41.667 0.00 0.00 0.00 1.98
936 1071 0.246635 CACACTACTTAGCACGGCCT 59.753 55.000 0.00 0.00 0.00 5.19
1107 1243 2.703798 CCTCCATGGTTGCCGCTTG 61.704 63.158 12.58 0.00 0.00 4.01
1120 1256 1.517832 CGCTTGGACCACTAGGAGG 59.482 63.158 0.00 0.00 38.69 4.30
1148 1284 1.412710 TGATCCAGCGGAGAATGGTAC 59.587 52.381 3.76 0.00 37.23 3.34
1604 1744 5.321959 TCAAGAGAGCATGACACTCTAAG 57.678 43.478 14.05 11.17 44.51 2.18
1610 1750 4.161942 AGAGCATGACACTCTAAGCATTCT 59.838 41.667 0.00 0.00 42.69 2.40
1771 1912 3.300388 TGGGTGCTTGATTTGTTAACCA 58.700 40.909 2.48 0.00 0.00 3.67
1788 1929 6.217900 TGTTAACCACCCTCCTAAAATATCCA 59.782 38.462 2.48 0.00 0.00 3.41
2104 2246 3.061322 CCACCAAAGAATGCATTGTGTG 58.939 45.455 18.59 18.13 32.40 3.82
2351 2499 7.023575 GCTTGTAAGTTGAATGTCAATACAGG 58.976 38.462 8.42 8.42 38.79 4.00
2539 2688 3.585289 TCATACCCAGCTTTTAGGTGTCA 59.415 43.478 5.03 0.00 41.84 3.58
3191 3340 3.837731 AGCCTCTACAGAAAAGCTCTTCT 59.162 43.478 0.00 0.00 36.02 2.85
3285 3434 3.117738 CCATATGACTTTCTCTTGGGGCT 60.118 47.826 3.65 0.00 0.00 5.19
3541 3690 6.421405 GTTGCAAATCTTGGTTGTTCAATTC 58.579 36.000 0.00 0.00 0.00 2.17
3562 3711 5.880054 TCTGCAAAAGCTTGGTTAGTATC 57.120 39.130 0.00 0.00 32.76 2.24
3622 3771 7.062322 ACATGGGCTACAAGATCAATATTGAA 58.938 34.615 21.50 6.19 41.13 2.69
3710 3859 7.849804 TTAGACTTCATAAGTGCATTTCCTC 57.150 36.000 0.00 0.00 43.03 3.71
3899 4048 2.923020 GTTTGCTGGTTTGACAACAGTG 59.077 45.455 7.43 0.00 34.15 3.66
3911 4060 7.225931 GGTTTGACAACAGTGATGTTAGTTCTA 59.774 37.037 7.53 0.00 34.15 2.10
4312 4467 7.281098 AGATAAGTTGCAAGATGACATGAGAT 58.719 34.615 0.00 0.00 0.00 2.75
4402 4557 8.914011 TCCATATTATATGACCTATTCACTCCG 58.086 37.037 13.29 0.00 36.92 4.63
4875 5058 7.054124 AGGTCATACACTCAAAGTCTGAAAAA 58.946 34.615 0.00 0.00 32.17 1.94
5035 5220 4.523943 TGGCACATTGATTTAGCAAGTCTT 59.476 37.500 0.00 0.00 0.00 3.01
5054 5239 0.550914 TCTTGGGATGGGCCATGTAC 59.449 55.000 26.77 13.97 38.95 2.90
5166 5351 1.381872 TCTAGGCAGCACCCCTCTC 60.382 63.158 0.00 0.00 40.58 3.20
5216 5401 6.459923 GCCTGTTTTAATTGGATGGTGTAAA 58.540 36.000 0.00 0.00 0.00 2.01
5305 5725 8.458573 TGTAACTAATGAAATGAAACTGTGGT 57.541 30.769 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 67 9.382275 AGCAAAAGAAGCAGAAAAGAAAAATTA 57.618 25.926 0.00 0.00 0.00 1.40
67 69 7.854557 AGCAAAAGAAGCAGAAAAGAAAAAT 57.145 28.000 0.00 0.00 0.00 1.82
936 1071 3.780850 GAGAGGGGATTAGGGTTCTTTCA 59.219 47.826 0.00 0.00 0.00 2.69
1107 1243 4.377263 GACCCCTCCTAGTGGTCC 57.623 66.667 0.00 0.00 42.21 4.46
1120 1256 2.187946 CGCTGGATCAGTGGACCC 59.812 66.667 0.00 0.00 38.21 4.46
1171 1307 0.906756 CTCTTCCCCTCTGCCACAGA 60.907 60.000 0.00 0.00 38.25 3.41
1175 1311 0.252881 ACATCTCTTCCCCTCTGCCA 60.253 55.000 0.00 0.00 0.00 4.92
1313 1449 9.702253 AGTATCAGACTGACTAGAATTTCCTTA 57.298 33.333 7.47 0.00 36.87 2.69
1482 1621 6.385033 CAAGAAGATTGAGTGGATGGAAAAC 58.615 40.000 0.00 0.00 0.00 2.43
1698 1839 7.881912 TCTTAACTCATATATTTGGCCCCTA 57.118 36.000 0.00 0.00 0.00 3.53
1751 1892 3.649073 GTGGTTAACAAATCAAGCACCC 58.351 45.455 8.10 0.00 43.78 4.61
1771 1912 5.224441 TGTAGCTGGATATTTTAGGAGGGT 58.776 41.667 0.00 0.00 0.00 4.34
2104 2246 1.466856 TGTTGCTCTTCATCATGCCC 58.533 50.000 0.00 0.00 0.00 5.36
2351 2499 5.065988 TCCTTGCCGCATTAAATTTCTCTAC 59.934 40.000 0.00 0.00 0.00 2.59
2497 2645 8.682710 GGTATGATTTAGAATTTGGCACTAACA 58.317 33.333 0.00 0.00 0.00 2.41
2573 2722 1.436600 AGACAACATGAAGCTCTGCG 58.563 50.000 0.00 0.00 0.00 5.18
3191 3340 4.037446 GCAACACTTGTTATCCAGGTCAAA 59.963 41.667 0.00 0.00 36.32 2.69
3562 3711 2.688507 AGGTTGTCAGCACGAATACAG 58.311 47.619 0.00 0.00 0.00 2.74
3622 3771 1.266718 AGAAATTGTGCACGTTCGCAT 59.733 42.857 13.13 0.00 45.26 4.73
3899 4048 8.561738 TCCAAGGTTTCATTAGAACTAACATC 57.438 34.615 0.00 0.00 32.39 3.06
3911 4060 3.966665 TGCCTTCTTTCCAAGGTTTCATT 59.033 39.130 1.33 0.00 44.50 2.57
4312 4467 3.785486 CCATCTCTCTTGCATAACGACA 58.215 45.455 0.00 0.00 0.00 4.35
4429 4585 5.552870 AGTTCAACATAGGTCTGTTCACT 57.447 39.130 0.00 0.00 37.25 3.41
4542 4698 5.911378 TGTAAACATGCATAGCCAAATCA 57.089 34.783 0.00 0.00 0.00 2.57
4957 5140 1.154169 CGTCGTCGGATCCGTTTCA 60.154 57.895 32.15 11.81 40.74 2.69
5035 5220 0.550914 GTACATGGCCCATCCCAAGA 59.449 55.000 0.00 0.00 38.61 3.02
5216 5401 3.581770 GTGTACTAGGAGGGGTTTCAAGT 59.418 47.826 0.00 0.00 0.00 3.16
5287 5707 7.068103 TGTTACTCACCACAGTTTCATTTCATT 59.932 33.333 0.00 0.00 0.00 2.57
5305 5725 0.838608 ACCCCAAACCGTGTTACTCA 59.161 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.