Multiple sequence alignment - TraesCS6D01G115700

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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 TraesCS6D01G115700 chr6D 100.000 4424 0 0 1 4424 82140131 82135708 0.000000e+00 8170.0
1 TraesCS6D01G115700 chr6D 88.063 3795 400 30 508 4257 81935898 81932112 0.000000e+00 4449.0
2 TraesCS6D01G115700 chr6D 83.134 3172 489 31 982 4136 81773871 81770729 0.000000e+00 2852.0
3 TraesCS6D01G115700 chr6D 100.000 505 0 0 4676 5180 82135456 82134952 0.000000e+00 933.0
4 TraesCS6D01G115700 chr6D 82.209 163 18 8 272 423 81926530 81926368 4.210000e-26 130.0
5 TraesCS6D01G115700 chr6D 81.176 170 16 11 269 430 82210483 82210322 7.040000e-24 122.0
6 TraesCS6D01G115700 chr6D 79.191 173 18 12 257 418 81764736 81764571 2.550000e-18 104.0
7 TraesCS6D01G115700 chr6D 87.013 77 6 3 428 500 81936185 81936109 3.320000e-12 84.2
8 TraesCS6D01G115700 chr6B 96.893 4442 103 12 1 4415 157028418 157023985 0.000000e+00 7406.0
9 TraesCS6D01G115700 chr6B 87.418 3799 418 27 508 4263 156741503 156737722 0.000000e+00 4313.0
10 TraesCS6D01G115700 chr6B 97.046 237 6 1 4944 5180 157023971 157023736 1.050000e-106 398.0
11 TraesCS6D01G115700 chr6B 83.230 161 17 3 272 422 156655184 156655024 6.990000e-29 139.0
12 TraesCS6D01G115700 chr6B 83.544 158 9 10 281 430 157131585 157131437 1.170000e-26 132.0
13 TraesCS6D01G115700 chr6B 80.952 168 19 12 257 418 156533984 156533824 2.530000e-23 121.0
14 TraesCS6D01G115700 chr6B 82.418 91 10 6 417 502 156741802 156741713 2.000000e-09 75.0
15 TraesCS6D01G115700 chr6A 91.352 3943 303 17 342 4263 98814263 98810338 0.000000e+00 5358.0
16 TraesCS6D01G115700 chr6A 87.395 3800 426 33 508 4263 98324367 98320577 0.000000e+00 4314.0
17 TraesCS6D01G115700 chr6A 84.710 3172 455 22 982 4135 98250013 98246854 0.000000e+00 3144.0
18 TraesCS6D01G115700 chr6A 82.930 3304 507 37 981 4255 98309991 98306716 0.000000e+00 2924.0
19 TraesCS6D01G115700 chr6A 79.733 3666 643 65 512 4136 98982837 98979231 0.000000e+00 2562.0
20 TraesCS6D01G115700 chr6A 85.176 2496 333 24 1795 4263 98916425 98913940 0.000000e+00 2525.0
21 TraesCS6D01G115700 chr6A 86.481 503 34 15 4688 5180 98810065 98809587 5.940000e-144 521.0
22 TraesCS6D01G115700 chr6A 90.681 279 23 3 67 343 98814576 98814299 8.190000e-98 368.0
23 TraesCS6D01G115700 chr6A 97.590 83 1 1 1 83 98814678 98814597 1.940000e-29 141.0
24 TraesCS6D01G115700 chr6A 82.558 172 10 13 269 430 98917906 98917745 3.250000e-27 134.0
25 TraesCS6D01G115700 chr6A 77.844 167 20 11 263 418 98257194 98257034 2.570000e-13 87.9
26 TraesCS6D01G115700 chr6A 85.000 80 7 4 428 502 98324647 98324568 5.560000e-10 76.8
27 TraesCS6D01G115700 chr7D 82.014 2513 373 51 549 3015 560999783 561002262 0.000000e+00 2063.0
28 TraesCS6D01G115700 chr7A 82.924 2278 354 25 764 3015 645087622 645089890 0.000000e+00 2019.0


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 TraesCS6D01G115700 chr6D 82134952 82140131 5179 True 4551.5 8170 100.0000 1 5180 2 chr6D.!!$R6 5179
1 TraesCS6D01G115700 chr6D 81770729 81773871 3142 True 2852.0 2852 83.1340 982 4136 1 chr6D.!!$R2 3154
2 TraesCS6D01G115700 chr6D 81932112 81936185 4073 True 2266.6 4449 87.5380 428 4257 2 chr6D.!!$R5 3829
3 TraesCS6D01G115700 chr6B 157023736 157028418 4682 True 3902.0 7406 96.9695 1 5180 2 chr6B.!!$R5 5179
4 TraesCS6D01G115700 chr6B 156737722 156741802 4080 True 2194.0 4313 84.9180 417 4263 2 chr6B.!!$R4 3846
5 TraesCS6D01G115700 chr6A 98246854 98250013 3159 True 3144.0 3144 84.7100 982 4135 1 chr6A.!!$R1 3153
6 TraesCS6D01G115700 chr6A 98306716 98309991 3275 True 2924.0 2924 82.9300 981 4255 1 chr6A.!!$R3 3274
7 TraesCS6D01G115700 chr6A 98979231 98982837 3606 True 2562.0 2562 79.7330 512 4136 1 chr6A.!!$R4 3624
8 TraesCS6D01G115700 chr6A 98320577 98324647 4070 True 2195.4 4314 86.1975 428 4263 2 chr6A.!!$R5 3835
9 TraesCS6D01G115700 chr6A 98809587 98814678 5091 True 1597.0 5358 91.5260 1 5180 4 chr6A.!!$R6 5179
10 TraesCS6D01G115700 chr6A 98913940 98917906 3966 True 1329.5 2525 83.8670 269 4263 2 chr6A.!!$R7 3994
11 TraesCS6D01G115700 chr7D 560999783 561002262 2479 False 2063.0 2063 82.0140 549 3015 1 chr7D.!!$F1 2466
12 TraesCS6D01G115700 chr7A 645087622 645089890 2268 False 2019.0 2019 82.9240 764 3015 1 chr7A.!!$F1 2251

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
219 273 0.592247 CACTGCCAAAACTCACACGC 60.592 55.000 0.00 0.0 0.00 5.34 F
482 672 1.737793 CTGCAAATCGTTACCCACCTC 59.262 52.381 0.00 0.0 0.00 3.85 F
1720 2206 0.531311 GGCCGGGTATAACAACCTCG 60.531 60.000 2.18 0.0 39.65 4.63 F
3099 3591 1.336755 GCATTTGGTGTGTTCTTCGGT 59.663 47.619 0.00 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 2206 0.984230 TCATCTGGGAGTGTTCCACC 59.016 55.000 0.00 0.0 45.98 4.61 R
1945 2431 1.478916 GCTAAGAGAAGACGGGAGCTT 59.521 52.381 0.00 0.0 0.00 3.74 R
3252 3747 0.827507 TTTCTTCACCCTGGCCTTGC 60.828 55.000 3.32 0.0 0.00 4.01 R
4398 4952 1.549170 AGTGGGCCGAGTACAACTAAG 59.451 52.381 0.00 0.0 0.00 2.18 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
93 130 4.881019 AAGATAATCTCGATGAGGGTGG 57.119 45.455 0.00 0.00 0.00 4.61
121 158 7.427318 CGTTCCGCTACCAACTTAAAATATTTC 59.573 37.037 0.10 0.00 0.00 2.17
219 273 0.592247 CACTGCCAAAACTCACACGC 60.592 55.000 0.00 0.00 0.00 5.34
268 322 5.464057 CCGAACCACAATATAATAAGTGCGA 59.536 40.000 0.00 0.00 0.00 5.10
482 672 1.737793 CTGCAAATCGTTACCCACCTC 59.262 52.381 0.00 0.00 0.00 3.85
486 676 3.007635 CAAATCGTTACCCACCTCTTCC 58.992 50.000 0.00 0.00 0.00 3.46
562 963 8.966868 TCAAGAAGTAAATTTTCTGGTCAAGTT 58.033 29.630 0.00 0.00 35.20 2.66
1112 1586 2.971330 CCTCTCCTATCAGTTCCTGCAT 59.029 50.000 0.00 0.00 0.00 3.96
1720 2206 0.531311 GGCCGGGTATAACAACCTCG 60.531 60.000 2.18 0.00 39.65 4.63
1945 2431 1.680735 GCAACAACAACATGTCAGGGA 59.319 47.619 0.00 0.00 31.81 4.20
2506 2992 4.080638 ACTCCCTAAGCCATCTCTTCTTTG 60.081 45.833 0.00 0.00 0.00 2.77
3099 3591 1.336755 GCATTTGGTGTGTTCTTCGGT 59.663 47.619 0.00 0.00 0.00 4.69
3242 3737 4.065088 TCAGAGCAAACATTAGTGGTGAC 58.935 43.478 0.00 0.00 0.00 3.67
3405 3900 4.526262 TCCAAGCTGGCAATTAAAAAGCTA 59.474 37.500 0.00 0.00 43.22 3.32
3986 4484 1.472376 GCAGATGAGGTCCGAGGAAAG 60.472 57.143 0.00 0.00 0.00 2.62
4385 4939 2.641815 AGTGTTCAGCCAGGAGATTCTT 59.358 45.455 0.00 0.00 0.00 2.52
4398 4952 4.219288 AGGAGATTCTTGTGGCATGTTTTC 59.781 41.667 0.00 0.00 0.00 2.29
4415 4969 3.323751 TTTCTTAGTTGTACTCGGCCC 57.676 47.619 0.00 0.00 0.00 5.80
4702 5256 6.724263 TCTGTACACATTTGAACAATGACAC 58.276 36.000 0.00 0.00 0.00 3.67
4718 5272 6.151985 ACAATGACACAAACAAGAACTGGTAA 59.848 34.615 0.00 0.00 0.00 2.85
4772 5327 3.694566 AGAAAAACGCCAGGGATGTTATC 59.305 43.478 0.00 0.00 0.00 1.75
4773 5328 2.799126 AAACGCCAGGGATGTTATCA 57.201 45.000 0.00 0.00 0.00 2.15
4774 5329 3.297134 AAACGCCAGGGATGTTATCAT 57.703 42.857 0.00 0.00 36.95 2.45
4775 5330 2.260844 ACGCCAGGGATGTTATCATG 57.739 50.000 0.00 0.00 34.06 3.07
4776 5331 1.768275 ACGCCAGGGATGTTATCATGA 59.232 47.619 0.00 0.00 34.06 3.07
4777 5332 2.373169 ACGCCAGGGATGTTATCATGAT 59.627 45.455 13.81 13.81 34.06 2.45
4778 5333 3.582647 ACGCCAGGGATGTTATCATGATA 59.417 43.478 11.49 11.49 34.06 2.15
4779 5334 4.225942 ACGCCAGGGATGTTATCATGATAT 59.774 41.667 16.06 2.63 34.06 1.63
4780 5335 4.813161 CGCCAGGGATGTTATCATGATATC 59.187 45.833 16.06 15.14 34.06 1.63
4872 5427 5.543507 TGGTTGTTTTCTAACATTGGCAT 57.456 34.783 0.00 0.00 43.43 4.40
4873 5428 6.656632 TGGTTGTTTTCTAACATTGGCATA 57.343 33.333 0.00 0.00 43.43 3.14
4886 5446 4.702131 ACATTGGCATACAGAAAACTCCTC 59.298 41.667 0.00 0.00 0.00 3.71
4891 5451 4.142881 GGCATACAGAAAACTCCTCGTTTC 60.143 45.833 0.00 0.00 44.77 2.78
4895 5455 3.118371 ACAGAAAACTCCTCGTTTCTGGT 60.118 43.478 22.97 11.04 44.77 4.00
4896 5456 3.248602 CAGAAAACTCCTCGTTTCTGGTG 59.751 47.826 15.22 0.88 44.77 4.17
4900 5460 1.070289 ACTCCTCGTTTCTGGTGAACC 59.930 52.381 0.00 0.00 31.02 3.62
4903 5463 0.878523 CTCGTTTCTGGTGAACCGCA 60.879 55.000 0.00 0.00 37.87 5.69
4912 5472 2.673368 CTGGTGAACCGCAAGAGATTAC 59.327 50.000 0.00 0.00 39.43 1.89
5004 5566 1.374758 CGAAGGCAACGAGGAAGCT 60.375 57.895 0.00 0.00 46.39 3.74
5055 5618 2.700773 GGCAAATCCAGTCGGCACC 61.701 63.158 0.00 0.00 34.01 5.01
5130 5693 2.361757 TGCTTGGTGATTGGTGAACAAG 59.638 45.455 0.00 0.00 43.48 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 112 2.558795 CGTCCACCCTCATCGAGATTAT 59.441 50.000 0.00 0.00 0.00 1.28
219 273 4.741342 ACGATTCGAAGTAAACTGGGTAG 58.259 43.478 13.95 0.00 0.00 3.18
268 322 1.821061 CGTTCTCCTGGCTCCACTGT 61.821 60.000 0.00 0.00 0.00 3.55
350 445 2.900546 TCTTCCTTCCTCTTGACCTGAC 59.099 50.000 0.00 0.00 0.00 3.51
482 672 4.371786 GCCTGTTTTGAAAGGAAAGGAAG 58.628 43.478 0.00 0.00 35.40 3.46
486 676 4.406648 AAGGCCTGTTTTGAAAGGAAAG 57.593 40.909 5.69 0.00 35.40 2.62
562 963 2.092321 ACTCTAAGCTCTTCCCGCTAGA 60.092 50.000 0.00 0.00 36.56 2.43
1112 1586 3.393970 CGCCCTTCTCCTGCTCCA 61.394 66.667 0.00 0.00 0.00 3.86
1720 2206 0.984230 TCATCTGGGAGTGTTCCACC 59.016 55.000 0.00 0.00 45.98 4.61
1945 2431 1.478916 GCTAAGAGAAGACGGGAGCTT 59.521 52.381 0.00 0.00 0.00 3.74
2506 2992 9.378551 TGTAAGACTATTATTTGACACATCCAC 57.621 33.333 0.00 0.00 0.00 4.02
2540 3026 3.951563 TCTCCATCAAGGTTAATGGGG 57.048 47.619 1.80 0.00 43.73 4.96
2864 3356 6.721208 TGAAAGGAAGTTCAGGCTATTCAATT 59.279 34.615 5.01 0.00 32.56 2.32
3099 3591 5.474532 CAGAAACAGAAGAATTGTGATCCCA 59.525 40.000 0.00 0.00 42.84 4.37
3252 3747 0.827507 TTTCTTCACCCTGGCCTTGC 60.828 55.000 3.32 0.00 0.00 4.01
3405 3900 5.003160 TCCATCAGACACATTTCATCGTTT 58.997 37.500 0.00 0.00 0.00 3.60
3986 4484 2.087646 GATCCAAGACCTCAACTTGCC 58.912 52.381 0.00 0.00 42.03 4.52
4139 4647 6.772360 TGTATTTTGGCTGATCTTTGCATA 57.228 33.333 0.00 0.00 0.00 3.14
4249 4771 6.858478 TCTCGTTGATTGCTCTAAGATTATCG 59.142 38.462 0.00 0.00 0.00 2.92
4385 4939 5.825679 AGTACAACTAAGAAAACATGCCACA 59.174 36.000 0.00 0.00 0.00 4.17
4398 4952 1.549170 AGTGGGCCGAGTACAACTAAG 59.451 52.381 0.00 0.00 0.00 2.18
4675 5229 8.075574 TGTCATTGTTCAAATGTGTACAGATTC 58.924 33.333 17.68 6.91 36.53 2.52
4676 5230 7.862372 GTGTCATTGTTCAAATGTGTACAGATT 59.138 33.333 12.23 12.23 36.53 2.40
4677 5231 7.013178 TGTGTCATTGTTCAAATGTGTACAGAT 59.987 33.333 0.00 0.00 36.53 2.90
4678 5232 6.317391 TGTGTCATTGTTCAAATGTGTACAGA 59.683 34.615 0.00 0.00 36.53 3.41
4679 5233 6.493978 TGTGTCATTGTTCAAATGTGTACAG 58.506 36.000 0.00 0.00 36.53 2.74
4680 5234 6.442513 TGTGTCATTGTTCAAATGTGTACA 57.557 33.333 0.00 0.00 33.67 2.90
4681 5235 7.274468 TGTTTGTGTCATTGTTCAAATGTGTAC 59.726 33.333 0.00 0.00 33.46 2.90
4682 5236 7.315890 TGTTTGTGTCATTGTTCAAATGTGTA 58.684 30.769 0.00 0.00 33.46 2.90
4683 5237 6.162079 TGTTTGTGTCATTGTTCAAATGTGT 58.838 32.000 0.00 0.00 33.46 3.72
4686 5240 7.522901 TCTTGTTTGTGTCATTGTTCAAATG 57.477 32.000 0.00 0.00 33.46 2.32
4722 5276 8.718734 GTTCACCTCTAAACAACTTTTATCGAT 58.281 33.333 2.16 2.16 0.00 3.59
4723 5277 7.711772 TGTTCACCTCTAAACAACTTTTATCGA 59.288 33.333 0.00 0.00 32.69 3.59
4724 5278 7.857569 TGTTCACCTCTAAACAACTTTTATCG 58.142 34.615 0.00 0.00 32.69 2.92
4725 5279 9.665264 CTTGTTCACCTCTAAACAACTTTTATC 57.335 33.333 0.00 0.00 39.70 1.75
4726 5280 9.403583 TCTTGTTCACCTCTAAACAACTTTTAT 57.596 29.630 0.00 0.00 39.70 1.40
4727 5281 8.795842 TCTTGTTCACCTCTAAACAACTTTTA 57.204 30.769 0.00 0.00 39.70 1.52
4728 5282 7.696992 TCTTGTTCACCTCTAAACAACTTTT 57.303 32.000 0.00 0.00 39.70 2.27
4729 5283 7.696992 TTCTTGTTCACCTCTAAACAACTTT 57.303 32.000 0.00 0.00 39.70 2.66
4730 5284 7.696992 TTTCTTGTTCACCTCTAAACAACTT 57.303 32.000 0.00 0.00 39.70 2.66
4891 5451 1.813513 AATCTCTTGCGGTTCACCAG 58.186 50.000 0.00 0.00 35.14 4.00
4895 5455 2.289382 TGCTGTAATCTCTTGCGGTTCA 60.289 45.455 0.00 0.00 0.00 3.18
4896 5456 2.094417 GTGCTGTAATCTCTTGCGGTTC 59.906 50.000 0.00 0.00 0.00 3.62
4900 5460 3.677601 CATTGTGCTGTAATCTCTTGCG 58.322 45.455 0.00 0.00 0.00 4.85
5055 5618 5.863898 TGGACATGACATTTCGAATTAACG 58.136 37.500 0.00 0.00 0.00 3.18
5130 5693 4.236935 CTGAATTGTTGTTGTGTATGGCC 58.763 43.478 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.