Multiple sequence alignment - TraesCS7D01G393000

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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 TraesCS7D01G393000 chr7D 100.000 2972 0 0 1 2972 508318322 508321293 0.000000e+00 5489.0
1 TraesCS7D01G393000 chr7D 78.529 503 103 5 824 1325 508300937 508300439 2.860000e-85 326.0
2 TraesCS7D01G393000 chr7D 88.158 76 9 0 797 872 508275851 508275776 1.130000e-14 91.6
3 TraesCS7D01G393000 chr7D 88.158 76 9 0 797 872 508301012 508300937 1.130000e-14 91.6
4 TraesCS7D01G393000 chr7D 86.486 74 9 1 154 226 256282078 256282151 2.460000e-11 80.5
5 TraesCS7D01G393000 chr7B 95.368 2979 128 9 1 2972 536560125 536563100 0.000000e+00 4728.0
6 TraesCS7D01G393000 chr7A 93.952 2976 164 12 1 2972 578573518 578576481 0.000000e+00 4484.0
7 TraesCS7D01G393000 chr7A 93.403 1637 102 5 1059 2692 578325710 578327343 0.000000e+00 2420.0
8 TraesCS7D01G393000 chr7A 94.700 283 15 0 2690 2972 578338167 578338449 9.780000e-120 440.0
9 TraesCS7D01G393000 chr7A 79.298 570 112 6 779 1347 578237908 578237344 7.720000e-106 394.0
10 TraesCS7D01G393000 chr7A 78.641 206 39 3 15 219 252709859 252709658 6.680000e-27 132.0
11 TraesCS7D01G393000 chr1D 86.512 1987 209 26 291 2268 79172282 79174218 0.000000e+00 2130.0
12 TraesCS7D01G393000 chr1D 88.999 709 76 2 2266 2972 79309779 79310487 0.000000e+00 876.0
13 TraesCS7D01G393000 chr1D 77.333 150 23 5 79 226 478027655 478027515 8.830000e-11 78.7
14 TraesCS7D01G393000 chr1B 84.516 2099 233 52 174 2252 10127819 10125793 0.000000e+00 1991.0
15 TraesCS7D01G393000 chr1B 86.010 1451 186 13 1529 2972 130425115 130426555 0.000000e+00 1539.0
16 TraesCS7D01G393000 chr1B 85.458 949 123 9 590 1533 130422443 130423381 0.000000e+00 974.0
17 TraesCS7D01G393000 chr1B 87.860 659 73 7 2316 2972 10125792 10125139 0.000000e+00 767.0
18 TraesCS7D01G393000 chr1B 88.852 305 29 4 293 596 130366688 130366988 1.300000e-98 370.0
19 TraesCS7D01G393000 chr1B 82.796 93 15 1 60 151 47628974 47629066 6.830000e-12 82.4
20 TraesCS7D01G393000 chr2A 89.005 1055 108 5 1444 2492 103506051 103504999 0.000000e+00 1299.0
21 TraesCS7D01G393000 chr2A 90.144 416 38 3 2557 2972 103504999 103504587 3.370000e-149 538.0
22 TraesCS7D01G393000 chr1A 87.904 835 79 12 291 1119 98024758 98025576 0.000000e+00 963.0
23 TraesCS7D01G393000 chr1A 87.353 680 77 8 2297 2972 98222883 98223557 0.000000e+00 771.0
24 TraesCS7D01G393000 chr1A 85.051 689 99 4 1167 1855 98025852 98026536 0.000000e+00 699.0
25 TraesCS7D01G393000 chr1A 86.304 460 54 6 1845 2299 98182752 98183207 2.660000e-135 492.0
26 TraesCS7D01G393000 chr3D 75.701 321 54 15 419 718 103821982 103821665 3.990000e-29 139.0
27 TraesCS7D01G393000 chr3B 75.466 322 54 17 419 718 154452585 154452267 1.860000e-27 134.0
28 TraesCS7D01G393000 chr3B 92.453 53 3 1 175 226 662553115 662553167 1.140000e-09 75.0
29 TraesCS7D01G393000 chr3B 86.567 67 5 3 162 226 38868885 38868821 1.480000e-08 71.3
30 TraesCS7D01G393000 chr3B 88.000 50 5 1 68 117 59901555 59901507 1.150000e-04 58.4
31 TraesCS7D01G393000 chr4D 82.171 129 18 5 15 140 62711469 62711343 4.050000e-19 106.0
32 TraesCS7D01G393000 chr4D 80.882 136 18 4 94 227 505996745 505996874 1.880000e-17 100.0
33 TraesCS7D01G393000 chr2D 72.455 334 73 19 903 1224 94138182 94138508 4.080000e-14 89.8


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 TraesCS7D01G393000 chr7D 508318322 508321293 2971 False 5489.0 5489 100.0000 1 2972 1 chr7D.!!$F2 2971
1 TraesCS7D01G393000 chr7D 508300439 508301012 573 True 208.8 326 83.3435 797 1325 2 chr7D.!!$R2 528
2 TraesCS7D01G393000 chr7B 536560125 536563100 2975 False 4728.0 4728 95.3680 1 2972 1 chr7B.!!$F1 2971
3 TraesCS7D01G393000 chr7A 578573518 578576481 2963 False 4484.0 4484 93.9520 1 2972 1 chr7A.!!$F3 2971
4 TraesCS7D01G393000 chr7A 578325710 578327343 1633 False 2420.0 2420 93.4030 1059 2692 1 chr7A.!!$F1 1633
5 TraesCS7D01G393000 chr7A 578237344 578237908 564 True 394.0 394 79.2980 779 1347 1 chr7A.!!$R2 568
6 TraesCS7D01G393000 chr1D 79172282 79174218 1936 False 2130.0 2130 86.5120 291 2268 1 chr1D.!!$F1 1977
7 TraesCS7D01G393000 chr1D 79309779 79310487 708 False 876.0 876 88.9990 2266 2972 1 chr1D.!!$F2 706
8 TraesCS7D01G393000 chr1B 10125139 10127819 2680 True 1379.0 1991 86.1880 174 2972 2 chr1B.!!$R1 2798
9 TraesCS7D01G393000 chr1B 130422443 130426555 4112 False 1256.5 1539 85.7340 590 2972 2 chr1B.!!$F3 2382
10 TraesCS7D01G393000 chr2A 103504587 103506051 1464 True 918.5 1299 89.5745 1444 2972 2 chr2A.!!$R1 1528
11 TraesCS7D01G393000 chr1A 98024758 98026536 1778 False 831.0 963 86.4775 291 1855 2 chr1A.!!$F3 1564
12 TraesCS7D01G393000 chr1A 98222883 98223557 674 False 771.0 771 87.3530 2297 2972 1 chr1A.!!$F2 675

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
37 38 2.032634 GGCCTTTCGACGATGTGCA 61.033 57.895 0.00 0.0 0.0 4.57 F
1119 1201 0.892755 AGTTGGCCATCATGTGCAAG 59.107 50.000 16.12 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 1657 0.111061 TTCTGAGCATGGCCTTGTGT 59.889 50.0 19.05 7.79 0.00 3.72 R
2263 4358 0.931005 GGTTGTGCGCATCTAGCTAC 59.069 55.0 15.91 7.21 42.61 3.58 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
37 38 2.032634 GGCCTTTCGACGATGTGCA 61.033 57.895 0.00 0.00 0.00 4.57
45 46 3.157932 TCGACGATGTGCATTATGTGA 57.842 42.857 0.00 0.00 0.00 3.58
47 48 2.219445 CGACGATGTGCATTATGTGAGG 59.781 50.000 0.00 0.00 0.00 3.86
145 147 3.157881 CGAGGTGCTCATAGGGATAGAA 58.842 50.000 0.00 0.00 0.00 2.10
146 148 3.057174 CGAGGTGCTCATAGGGATAGAAC 60.057 52.174 0.00 0.00 0.00 3.01
150 152 3.999663 GTGCTCATAGGGATAGAACATGC 59.000 47.826 0.00 0.00 0.00 4.06
269 273 9.498307 ACGCAAATATTTACAACTATAGCAAAC 57.502 29.630 0.00 0.00 0.00 2.93
270 274 9.716507 CGCAAATATTTACAACTATAGCAAACT 57.283 29.630 0.00 0.00 0.00 2.66
410 415 5.127194 TGAATCACTGGTGGTCATCTAGTAC 59.873 44.000 0.70 0.00 0.00 2.73
519 525 4.732923 CCAATCGGTTTAATTGCGTACATG 59.267 41.667 0.00 0.00 33.65 3.21
789 812 5.605534 ACTACTATGAGCATTCCATGTGTC 58.394 41.667 0.00 0.00 0.00 3.67
1084 1166 2.180159 GAAGCGGTGTGAGGGCCTAA 62.180 60.000 5.73 0.00 0.00 2.69
1119 1201 0.892755 AGTTGGCCATCATGTGCAAG 59.107 50.000 16.12 0.00 0.00 4.01
1281 1591 5.070847 AGGCTTTCTCAACCAACATTTTGAT 59.929 36.000 0.00 0.00 34.24 2.57
1289 1599 4.701956 ACCAACATTTTGATAAGCTCCG 57.298 40.909 0.00 0.00 34.24 4.63
1297 1607 1.271840 TGATAAGCTCCGGGCCAAGT 61.272 55.000 4.39 0.00 43.05 3.16
1347 1657 3.024547 CAACGAGACCAGAATCCTCCTA 58.975 50.000 0.00 0.00 0.00 2.94
1600 3648 1.618837 ACTACATGCACACGGAGTCTT 59.381 47.619 0.00 0.00 41.61 3.01
1614 3662 3.682921 GGAGTCTTCGTCGACTTATCAC 58.317 50.000 14.70 3.88 43.91 3.06
1617 3665 0.832030 CTTCGTCGACTTATCACGCG 59.168 55.000 14.70 3.53 32.69 6.01
1684 3771 1.436600 GATGATGTATCCGGCAGCAG 58.563 55.000 0.00 0.00 35.66 4.24
1687 3774 0.815213 GATGTATCCGGCAGCAGCAA 60.815 55.000 2.65 0.00 44.61 3.91
1797 3884 3.051803 TGATGAGGTATGGAGGAGACCTT 60.052 47.826 0.00 0.00 46.94 3.50
1857 3944 1.761449 ATGACACCAACACAAGCACA 58.239 45.000 0.00 0.00 0.00 4.57
1870 3957 1.002430 CAAGCACAGTCTTCCCTAGCA 59.998 52.381 0.00 0.00 0.00 3.49
1893 3980 3.132289 GTGATATTCACCCGAAGAGGTCA 59.868 47.826 0.00 0.00 41.37 4.02
2030 4125 5.869579 AGAGACATGTAATCTTGGTTGTGT 58.130 37.500 0.00 0.00 0.00 3.72
2119 4214 7.390440 TCTGTTTGTTTGATCTCCGTGATTTAT 59.610 33.333 0.00 0.00 35.14 1.40
2263 4358 0.868406 GTTCACTCCTGGTTTCTGCG 59.132 55.000 0.00 0.00 0.00 5.18
2323 4419 6.263168 AGTTCTAGGAAAGTGAAAACACATGG 59.737 38.462 0.00 0.00 0.00 3.66
2427 4523 9.063615 GTAAAGAACTCCTTAAAAATCACCTCA 57.936 33.333 0.00 0.00 34.00 3.86
2614 4713 2.944129 CCAAAAAGTGGGAGTCCTCAA 58.056 47.619 9.58 0.00 44.64 3.02
2785 4884 6.986231 GGCCTAATACCTTTGGAAATGAAATG 59.014 38.462 0.00 0.00 29.71 2.32
2799 4898 6.127535 GGAAATGAAATGAATGAGCTCCTTCA 60.128 38.462 29.07 29.07 35.95 3.02
2859 4958 5.713025 ACTAAATGGCACTTTAGCACATTG 58.287 37.500 19.96 5.74 40.72 2.82
2866 4965 2.483877 CACTTTAGCACATTGCCGAAGA 59.516 45.455 14.50 0.00 46.52 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.115554 CTCACATAATGCACATCGTCGA 58.884 45.455 0.00 0.00 0.00 4.20
37 38 4.713792 GGAATGTCTCCCCTCACATAAT 57.286 45.455 0.00 0.00 38.44 1.28
150 152 2.268491 TATAAACGCACGCGCACACG 62.268 55.000 12.02 10.02 44.19 4.49
375 380 6.547141 ACCACCAGTGATTCATATGGTAAATG 59.453 38.462 20.08 13.68 44.16 2.32
376 381 6.672593 ACCACCAGTGATTCATATGGTAAAT 58.327 36.000 20.08 10.20 44.16 1.40
379 384 4.719273 TGACCACCAGTGATTCATATGGTA 59.281 41.667 20.08 7.70 44.16 3.25
380 385 3.523157 TGACCACCAGTGATTCATATGGT 59.477 43.478 16.64 16.64 46.91 3.55
382 387 5.618236 AGATGACCACCAGTGATTCATATG 58.382 41.667 12.26 0.00 35.01 1.78
383 388 5.901413 AGATGACCACCAGTGATTCATAT 57.099 39.130 12.26 8.44 35.01 1.78
384 389 5.899547 ACTAGATGACCACCAGTGATTCATA 59.100 40.000 12.26 1.96 35.01 2.15
410 415 7.233632 TCCATATATTCAGGATTGACCAAAGG 58.766 38.462 0.00 0.00 42.04 3.11
478 483 1.881324 TGGTCATGCATGTTGTGTGAG 59.119 47.619 25.43 0.00 0.00 3.51
700 720 7.341805 AGAGCCACATGAATCTTATTAACAGT 58.658 34.615 0.00 0.00 0.00 3.55
1084 1166 0.545548 AACTCCTCCGCCTTCTTCCT 60.546 55.000 0.00 0.00 0.00 3.36
1119 1201 3.567579 TAGCACACAGGCCTTGGCC 62.568 63.158 22.29 22.29 0.00 5.36
1226 1536 1.610886 CCGTCTTCTTGAAGTTCCCCC 60.611 57.143 9.80 0.00 0.00 5.40
1281 1591 2.668632 CACTTGGCCCGGAGCTTA 59.331 61.111 0.73 0.00 43.05 3.09
1297 1607 2.203480 GCCCTGGAGTTTGTGGCA 60.203 61.111 0.00 0.00 41.76 4.92
1347 1657 0.111061 TTCTGAGCATGGCCTTGTGT 59.889 50.000 19.05 7.79 0.00 3.72
1600 3648 1.581912 GCGCGTGATAAGTCGACGA 60.582 57.895 10.46 2.41 33.61 4.20
1617 3665 1.452108 GTATGGAGCTGGTGGTGGC 60.452 63.158 0.00 0.00 0.00 5.01
1684 3771 3.059352 AGTGACATAGGGAACTGTTGC 57.941 47.619 3.17 3.17 43.88 4.17
1687 3774 3.769844 CCACTAGTGACATAGGGAACTGT 59.230 47.826 24.68 0.00 43.88 3.55
1754 3841 5.240891 TCATGTCAAGTGAATCCTCTTGTC 58.759 41.667 12.37 9.09 41.86 3.18
1797 3884 2.313317 CCACTATAGACCAGGGCGTTA 58.687 52.381 6.78 0.00 0.00 3.18
1857 3944 5.069781 GTGAATATCACTGCTAGGGAAGACT 59.930 44.000 3.31 0.00 43.73 3.24
1870 3957 3.375699 ACCTCTTCGGGTGAATATCACT 58.624 45.455 10.06 0.00 46.19 3.41
1893 3980 0.481128 AACCGAACCCCACCTCAAAT 59.519 50.000 0.00 0.00 0.00 2.32
2030 4125 4.082841 TGAAATATGCTTGCGCTCAAAGAA 60.083 37.500 9.73 0.00 36.97 2.52
2082 4177 6.713762 TCAAACAAACAGACCATTGAAGAT 57.286 33.333 0.00 0.00 0.00 2.40
2119 4214 4.072131 GCAACATAGAAGTTGGAACCAGA 58.928 43.478 8.66 0.00 46.81 3.86
2190 4285 7.084486 GTCAAGGGTCAACAAAAACTATCATC 58.916 38.462 0.00 0.00 0.00 2.92
2263 4358 0.931005 GGTTGTGCGCATCTAGCTAC 59.069 55.000 15.91 7.21 42.61 3.58
2427 4523 4.060900 CGCTTAGGCATGTCACAATAGAT 58.939 43.478 0.00 0.00 38.60 1.98
2614 4713 7.468752 TTCTATCCTAGGTCTAGAGGAAACT 57.531 40.000 9.08 0.00 44.98 2.66
2775 4874 6.860080 TGAAGGAGCTCATTCATTTCATTTC 58.140 36.000 33.47 10.57 41.05 2.17
2785 4884 5.047802 TGGAACATTTTGAAGGAGCTCATTC 60.048 40.000 29.39 29.39 37.19 2.67
2859 4958 1.706287 GCCTCACGGATTTCTTCGGC 61.706 60.000 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.