Multiple sequence alignment - TraesCS6D01G115400

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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 TraesCS6D01G115400 chr6D 100.000 5177 0 0 1 5177 81936379 81931203 0.000000e+00 9561.0
1 TraesCS6D01G115400 chr6D 88.063 3795 400 30 482 4268 82139624 82135875 0.000000e+00 4449.0
2 TraesCS6D01G115400 chr6D 87.013 77 6 3 195 271 82139704 82139632 3.320000e-12 84.2
3 TraesCS6D01G115400 chr6B 94.914 5210 185 28 1 5177 156741984 156736822 0.000000e+00 8080.0
4 TraesCS6D01G115400 chr6B 87.609 3793 424 27 482 4267 157027897 157024144 0.000000e+00 4359.0
5 TraesCS6D01G115400 chr6B 81.308 3900 631 52 480 4353 157489764 157485937 0.000000e+00 3073.0
6 TraesCS6D01G115400 chr6B 80.825 3708 619 70 708 4371 157109667 157106008 0.000000e+00 2824.0
7 TraesCS6D01G115400 chr6B 82.314 3302 534 39 981 4255 156550964 156547686 0.000000e+00 2817.0
8 TraesCS6D01G115400 chr6B 85.189 2093 292 14 934 3018 157900247 157902329 0.000000e+00 2132.0
9 TraesCS6D01G115400 chr6B 87.893 1462 110 28 3755 5177 156686243 156684810 0.000000e+00 1657.0
10 TraesCS6D01G115400 chr6B 82.692 208 23 5 264 466 130964701 130964900 6.890000e-39 172.0
11 TraesCS6D01G115400 chr6A 96.817 4524 121 13 2 4518 98324839 98320332 0.000000e+00 7535.0
12 TraesCS6D01G115400 chr6A 89.335 3807 360 30 482 4281 98814098 98810331 0.000000e+00 4739.0
13 TraesCS6D01G115400 chr6A 84.345 3181 469 21 982 4146 98250013 98246846 0.000000e+00 3088.0
14 TraesCS6D01G115400 chr6A 82.647 3325 521 43 981 4282 98309991 98306700 0.000000e+00 2892.0
15 TraesCS6D01G115400 chr6A 85.062 2671 362 27 1825 4471 98916398 98913741 0.000000e+00 2687.0
16 TraesCS6D01G115400 chr6A 79.290 3718 678 58 480 4174 98982844 98979196 0.000000e+00 2516.0
17 TraesCS6D01G115400 chr6A 93.224 428 29 0 4538 4965 98320077 98319650 9.460000e-177 630.0
18 TraesCS6D01G115400 chr6A 90.135 223 10 3 4961 5177 98319162 98318946 3.950000e-71 279.0
19 TraesCS6D01G115400 chr6A 86.826 167 11 3 283 445 595488651 595488492 5.330000e-40 176.0
20 TraesCS6D01G115400 chr7D 82.674 2528 358 46 525 3019 560999783 561002263 0.000000e+00 2169.0
21 TraesCS6D01G115400 chr7A 83.049 2289 350 24 757 3019 645087615 645089891 0.000000e+00 2043.0
22 TraesCS6D01G115400 chr4D 87.222 180 18 5 291 466 509822275 509822453 3.160000e-47 200.0
23 TraesCS6D01G115400 chr2D 86.243 189 16 3 282 466 30487805 30487623 4.090000e-46 196.0
24 TraesCS6D01G115400 chr7B 85.714 189 20 4 282 464 15031621 15031434 5.290000e-45 193.0
25 TraesCS6D01G115400 chr7B 85.638 188 16 4 283 466 680910914 680911094 2.460000e-43 187.0
26 TraesCS6D01G115400 chr2A 82.192 219 27 4 252 466 569281635 569281845 1.480000e-40 178.0
27 TraesCS6D01G115400 chr4B 83.684 190 25 4 282 466 643784363 643784551 1.920000e-39 174.0
28 TraesCS6D01G115400 chr1D 83.246 191 22 5 283 467 394464362 394464548 3.210000e-37 167.0


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 TraesCS6D01G115400 chr6D 81931203 81936379 5176 True 9561.000000 9561 100.000 1 5177 1 chr6D.!!$R1 5176
1 TraesCS6D01G115400 chr6D 82135875 82139704 3829 True 2266.600000 4449 87.538 195 4268 2 chr6D.!!$R2 4073
2 TraesCS6D01G115400 chr6B 156736822 156741984 5162 True 8080.000000 8080 94.914 1 5177 1 chr6B.!!$R3 5176
3 TraesCS6D01G115400 chr6B 157024144 157027897 3753 True 4359.000000 4359 87.609 482 4267 1 chr6B.!!$R4 3785
4 TraesCS6D01G115400 chr6B 157485937 157489764 3827 True 3073.000000 3073 81.308 480 4353 1 chr6B.!!$R6 3873
5 TraesCS6D01G115400 chr6B 157106008 157109667 3659 True 2824.000000 2824 80.825 708 4371 1 chr6B.!!$R5 3663
6 TraesCS6D01G115400 chr6B 156547686 156550964 3278 True 2817.000000 2817 82.314 981 4255 1 chr6B.!!$R1 3274
7 TraesCS6D01G115400 chr6B 157900247 157902329 2082 False 2132.000000 2132 85.189 934 3018 1 chr6B.!!$F2 2084
8 TraesCS6D01G115400 chr6B 156684810 156686243 1433 True 1657.000000 1657 87.893 3755 5177 1 chr6B.!!$R2 1422
9 TraesCS6D01G115400 chr6A 98810331 98814098 3767 True 4739.000000 4739 89.335 482 4281 1 chr6A.!!$R3 3799
10 TraesCS6D01G115400 chr6A 98246846 98250013 3167 True 3088.000000 3088 84.345 982 4146 1 chr6A.!!$R1 3164
11 TraesCS6D01G115400 chr6A 98306700 98309991 3291 True 2892.000000 2892 82.647 981 4282 1 chr6A.!!$R2 3301
12 TraesCS6D01G115400 chr6A 98318946 98324839 5893 True 2814.666667 7535 93.392 2 5177 3 chr6A.!!$R7 5175
13 TraesCS6D01G115400 chr6A 98913741 98916398 2657 True 2687.000000 2687 85.062 1825 4471 1 chr6A.!!$R4 2646
14 TraesCS6D01G115400 chr6A 98979196 98982844 3648 True 2516.000000 2516 79.290 480 4174 1 chr6A.!!$R5 3694
15 TraesCS6D01G115400 chr7D 560999783 561002263 2480 False 2169.000000 2169 82.674 525 3019 1 chr7D.!!$F1 2494
16 TraesCS6D01G115400 chr7A 645087615 645089891 2276 False 2043.000000 2043 83.049 757 3019 1 chr7A.!!$F1 2262


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
413 421 0.034477 ATAGGCCCAAAGTTGTCGGG 60.034 55.000 0.00 1.61 43.42 5.14 F
1238 1293 3.118261 GGGATCACCTGCAGTCAAGATAA 60.118 47.826 13.81 0.00 35.85 1.75 F
1984 2045 1.532437 TGAGCAACTGCACAAATCTCG 59.468 47.619 4.22 0.00 45.16 4.04 F
2160 2221 3.171277 GCGGCTAGCTAACAACAAATTG 58.829 45.455 15.72 0.00 44.04 2.32 F
2317 2378 4.351874 TCGTTCAATTTCAAGGGAGAGT 57.648 40.909 0.00 0.00 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 1567 1.203052 CATGTGGTGGATGGAAACTGC 59.797 52.381 0.00 0.00 0.00 4.40 R
2317 2378 2.190538 TCTGTCATCCTCTGGCATGAA 58.809 47.619 0.00 0.00 39.17 2.57 R
3984 4064 1.988107 AGGACCTCAATCTGCTTTCCA 59.012 47.619 0.00 0.00 0.00 3.53 R
4101 4181 5.770663 GCAGGAGACTACTTCCATGATAGTA 59.229 44.000 0.00 0.45 40.21 1.82 R
4283 4404 1.065854 GGCAGTCTGTCAGGCTATGTT 60.066 52.381 6.65 0.00 0.00 2.71 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
56 62 0.575859 CAGATGAAGCTCGCGTGATG 59.424 55.000 13.13 0.00 0.00 3.07
92 98 3.030873 AGAGGATGGAAGAGAGGACAG 57.969 52.381 0.00 0.00 0.00 3.51
103 109 0.252421 AGAGGACAGATCACCCAGCA 60.252 55.000 0.00 0.00 0.00 4.41
104 110 0.615331 GAGGACAGATCACCCAGCAA 59.385 55.000 0.00 0.00 0.00 3.91
105 111 0.326264 AGGACAGATCACCCAGCAAC 59.674 55.000 0.00 0.00 0.00 4.17
106 112 0.036732 GGACAGATCACCCAGCAACA 59.963 55.000 0.00 0.00 0.00 3.33
107 113 1.446907 GACAGATCACCCAGCAACAG 58.553 55.000 0.00 0.00 0.00 3.16
108 114 0.767375 ACAGATCACCCAGCAACAGT 59.233 50.000 0.00 0.00 0.00 3.55
351 357 1.156736 CATGAGGTCACGGGTTGTTC 58.843 55.000 0.00 0.00 0.00 3.18
388 396 4.729868 ACAGAAATGTAGGAAAAGGCTGT 58.270 39.130 0.00 0.00 0.00 4.40
413 421 0.034477 ATAGGCCCAAAGTTGTCGGG 60.034 55.000 0.00 1.61 43.42 5.14
518 527 3.252974 AGGCAAAGGATACGTCAAGAG 57.747 47.619 0.00 0.00 46.39 2.85
522 531 4.443034 GGCAAAGGATACGTCAAGAGGTAT 60.443 45.833 13.45 13.45 42.84 2.73
676 690 5.122512 GACTACACAGTCTACAAAGCAGA 57.877 43.478 0.00 0.00 46.56 4.26
1238 1293 3.118261 GGGATCACCTGCAGTCAAGATAA 60.118 47.826 13.81 0.00 35.85 1.75
1984 2045 1.532437 TGAGCAACTGCACAAATCTCG 59.468 47.619 4.22 0.00 45.16 4.04
2046 2107 6.917533 ACTTAGCAATGTCAATTTCTCCAAG 58.082 36.000 0.00 0.00 0.00 3.61
2160 2221 3.171277 GCGGCTAGCTAACAACAAATTG 58.829 45.455 15.72 0.00 44.04 2.32
2317 2378 4.351874 TCGTTCAATTTCAAGGGAGAGT 57.648 40.909 0.00 0.00 0.00 3.24
2592 2653 6.639632 ATGCTAAAATCAACTGACAACACT 57.360 33.333 0.00 0.00 0.00 3.55
3945 4025 5.533528 ACCTGTTTCAGTATTTTGTACACCC 59.466 40.000 0.00 0.00 0.00 4.61
4101 4181 2.441001 CCATAATCAGTTCAGGAGGCCT 59.559 50.000 3.86 3.86 0.00 5.19
4214 4301 8.856103 TGATAGATAATCCTGTATTTGTCGTGA 58.144 33.333 0.00 0.00 33.22 4.35
4270 4384 6.868622 AGAACTACTGCTTCTGATAATCGTT 58.131 36.000 0.00 0.00 0.00 3.85
4283 4404 8.148807 TCTGATAATCGTTCAGTTTGTTTTGA 57.851 30.769 1.07 0.00 41.13 2.69
4502 4629 7.478520 GCTTCGTATAAGCAGATTTTAGGAA 57.521 36.000 4.91 4.62 42.56 3.36
4507 4634 6.257193 CGTATAAGCAGATTTTAGGAACCGTT 59.743 38.462 0.00 0.00 0.00 4.44
4510 4637 2.163613 GCAGATTTTAGGAACCGTTGGG 59.836 50.000 0.00 0.00 40.11 4.12
4512 4639 1.475280 GATTTTAGGAACCGTTGGGGC 59.525 52.381 0.00 0.00 40.62 5.80
4513 4640 0.479378 TTTTAGGAACCGTTGGGGCT 59.521 50.000 0.00 0.00 40.62 5.19
4514 4641 0.250989 TTTAGGAACCGTTGGGGCTG 60.251 55.000 0.00 0.00 40.62 4.85
4515 4642 2.132089 TTAGGAACCGTTGGGGCTGG 62.132 60.000 0.00 0.00 40.62 4.85
4516 4643 3.961414 GGAACCGTTGGGGCTGGA 61.961 66.667 0.00 0.00 40.62 3.86
4517 4644 2.359975 GAACCGTTGGGGCTGGAG 60.360 66.667 0.00 0.00 40.62 3.86
4518 4645 4.660938 AACCGTTGGGGCTGGAGC 62.661 66.667 0.00 0.00 40.62 4.70
4636 5008 5.061064 GCACGCACAGCAGTATTATATACTC 59.939 44.000 0.00 0.00 0.00 2.59
4710 5082 5.477291 TGGTTGTGTTGTTTTCCTAGTGAAA 59.523 36.000 3.19 3.19 41.18 2.69
4758 5130 1.480137 AGAGACTATGTGCTGCCACTC 59.520 52.381 0.00 0.00 42.54 3.51
4776 5148 2.028112 ACTCTTTGCTTCGTATCAGCCA 60.028 45.455 0.00 0.00 36.33 4.75
4780 5152 1.474330 TGCTTCGTATCAGCCAGAGA 58.526 50.000 0.00 0.00 36.33 3.10
4781 5153 1.135139 TGCTTCGTATCAGCCAGAGAC 59.865 52.381 0.00 0.00 36.33 3.36
4832 5206 1.579429 GTTGGTCGTGGTCCATTGC 59.421 57.895 0.00 0.00 34.75 3.56
4877 5251 5.653769 TGGAATGGAATGAGAATTGGAGAAC 59.346 40.000 0.00 0.00 0.00 3.01
5069 5941 1.141881 ATACGCCCACGCTTCAGAG 59.858 57.895 0.00 0.00 45.53 3.35
5114 6043 0.036010 CAGTCCAAGAACCGGCATCT 60.036 55.000 0.00 2.13 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.151883 TCTGATGCTTACCTTTGCCTTTT 58.848 39.130 0.00 0.00 0.00 2.27
56 62 6.099845 TCCATCCTCTTGATTTACTAACCCTC 59.900 42.308 0.00 0.00 0.00 4.30
92 98 3.003480 GACTTACTGTTGCTGGGTGATC 58.997 50.000 0.00 0.00 0.00 2.92
103 109 3.394606 AGGTGGATGGTTGACTTACTGTT 59.605 43.478 0.00 0.00 0.00 3.16
104 110 2.979678 AGGTGGATGGTTGACTTACTGT 59.020 45.455 0.00 0.00 0.00 3.55
105 111 3.703001 AGGTGGATGGTTGACTTACTG 57.297 47.619 0.00 0.00 0.00 2.74
106 112 3.394606 ACAAGGTGGATGGTTGACTTACT 59.605 43.478 0.00 0.00 0.00 2.24
107 113 3.751518 ACAAGGTGGATGGTTGACTTAC 58.248 45.455 0.00 0.00 0.00 2.34
108 114 3.244770 GGACAAGGTGGATGGTTGACTTA 60.245 47.826 0.00 0.00 0.00 2.24
143 149 3.084039 CCAGGCAAGAAGAAGTGCAATA 58.916 45.455 0.00 0.00 42.74 1.90
302 308 1.680735 CACAAGGCAACAGCTTTACCA 59.319 47.619 0.00 0.00 41.41 3.25
388 396 4.076394 GACAACTTTGGGCCTATTGTACA 58.924 43.478 4.53 0.00 33.76 2.90
454 462 4.373156 AGATGTGTTTAAAGGGCAGTCT 57.627 40.909 0.00 0.00 0.00 3.24
676 690 8.706492 TGAATAGTCGACCGTACAAATAAAAT 57.294 30.769 13.01 0.00 0.00 1.82
1238 1293 2.027745 AGCAAGACATTGATGACCGTCT 60.028 45.455 0.00 0.00 40.38 4.18
1506 1567 1.203052 CATGTGGTGGATGGAAACTGC 59.797 52.381 0.00 0.00 0.00 4.40
1815 1876 3.953712 TTTCTGAGGTTGACTATGCGA 57.046 42.857 0.00 0.00 0.00 5.10
1984 2045 5.008613 TGTTGCTCTTGAGGTCAATTGTTAC 59.991 40.000 5.13 0.00 35.02 2.50
2046 2107 5.186198 TCTAAAGTTCTTAGATTGGGCAGC 58.814 41.667 0.00 0.00 0.00 5.25
2317 2378 2.190538 TCTGTCATCCTCTGGCATGAA 58.809 47.619 0.00 0.00 39.17 2.57
2592 2653 2.307686 GACCCTTGGGTCCAAATGAGTA 59.692 50.000 24.48 0.00 35.33 2.59
3984 4064 1.988107 AGGACCTCAATCTGCTTTCCA 59.012 47.619 0.00 0.00 0.00 3.53
4101 4181 5.770663 GCAGGAGACTACTTCCATGATAGTA 59.229 44.000 0.00 0.45 40.21 1.82
4208 4295 3.870723 TGCAACTACATTGTTCACGAC 57.129 42.857 0.00 0.00 40.77 4.34
4270 4384 5.592282 TCAGGCTATGTTCAAAACAAACTGA 59.408 36.000 11.53 11.53 45.86 3.41
4283 4404 1.065854 GGCAGTCTGTCAGGCTATGTT 60.066 52.381 6.65 0.00 0.00 2.71
4512 4639 1.197430 AACTCACCTCCAGGCTCCAG 61.197 60.000 0.00 0.00 39.32 3.86
4513 4640 0.116342 TAACTCACCTCCAGGCTCCA 59.884 55.000 0.00 0.00 39.32 3.86
4514 4641 0.537653 GTAACTCACCTCCAGGCTCC 59.462 60.000 0.00 0.00 39.32 4.70
4515 4642 0.537653 GGTAACTCACCTCCAGGCTC 59.462 60.000 0.00 0.00 44.79 4.70
4516 4643 2.685202 GGTAACTCACCTCCAGGCT 58.315 57.895 0.00 0.00 44.79 4.58
4636 5008 8.916654 CATGCTCGTCAAACTTAAGTATATAGG 58.083 37.037 8.92 1.63 0.00 2.57
4643 5015 3.074412 CCCATGCTCGTCAAACTTAAGT 58.926 45.455 1.12 1.12 0.00 2.24
4682 5054 6.816140 CACTAGGAAAACAACACAACCATTTT 59.184 34.615 0.00 0.00 0.00 1.82
4758 5130 2.606725 CTCTGGCTGATACGAAGCAAAG 59.393 50.000 0.00 0.00 42.69 2.77
4776 5148 4.699257 ACAGTAATTCGGTAACTCGTCTCT 59.301 41.667 0.00 0.00 0.00 3.10
4780 5152 4.154195 ACGTACAGTAATTCGGTAACTCGT 59.846 41.667 0.00 0.00 0.00 4.18
4781 5153 4.651994 ACGTACAGTAATTCGGTAACTCG 58.348 43.478 0.00 0.00 0.00 4.18
4832 5206 4.202182 CCATATTTCCATTCTGTGCTTGGG 60.202 45.833 0.00 0.00 0.00 4.12
4841 5215 8.229605 TCTCATTCCATTCCATATTTCCATTCT 58.770 33.333 0.00 0.00 0.00 2.40
4877 5251 1.710013 AAGATGGCAGTCGTGTTACG 58.290 50.000 0.00 0.00 44.19 3.18



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

AutoCloner maintained by Alex Coulton.