Multiple sequence alignment - TraesCS2D01G102000

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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 TraesCS2D01G102000 chr2D 100.000 2873 0 0 1 2873 55153378 55150506 0.000000e+00 5306.0
1 TraesCS2D01G102000 chr2A 96.415 2064 61 9 817 2873 55939080 55937023 0.000000e+00 3389.0
2 TraesCS2D01G102000 chr2A 94.399 607 23 4 1 605 55942954 55942357 0.000000e+00 922.0
3 TraesCS2D01G102000 chr2A 93.213 221 5 4 595 814 55941658 55941447 1.660000e-82 316.0
4 TraesCS2D01G102000 chr2B 95.504 1557 47 6 818 2364 87188555 87187012 0.000000e+00 2466.0
5 TraesCS2D01G102000 chr2B 88.610 518 39 11 2358 2862 87186038 87185528 1.890000e-171 612.0
6 TraesCS2D01G102000 chr2B 86.667 480 49 9 2321 2792 86679556 86679084 4.240000e-143 518.0
7 TraesCS2D01G102000 chr2B 86.544 379 21 13 37 414 87350531 87350182 9.650000e-105 390.0
8 TraesCS2D01G102000 chr2B 92.958 71 4 1 2120 2189 86681060 86680990 5.060000e-18 102.0
9 TraesCS2D01G102000 chr2B 94.118 51 3 0 2071 2121 86681192 86681142 8.530000e-11 78.7


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 TraesCS2D01G102000 chr2D 55150506 55153378 2872 True 5306.000000 5306 100.000000 1 2873 1 chr2D.!!$R1 2872
1 TraesCS2D01G102000 chr2A 55937023 55942954 5931 True 1542.333333 3389 94.675667 1 2873 3 chr2A.!!$R1 2872
2 TraesCS2D01G102000 chr2B 87185528 87188555 3027 True 1539.000000 2466 92.057000 818 2862 2 chr2B.!!$R3 2044
3 TraesCS2D01G102000 chr2B 86679084 86681192 2108 True 232.900000 518 91.247667 2071 2792 3 chr2B.!!$R2 721

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
146 149 1.001378 GCAGAAATCGGCAACACAACT 60.001 47.619 0.54 0.0 37.03 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 5001 0.182775 AAACAGGAAGGCACGGAACT 59.817 50.0 0.0 0.0 0.0 3.01 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
38 39 4.168088 TCCAGGAGTTTTTCTTTCCCTTCT 59.832 41.667 0.00 0.00 0.00 2.85
89 92 5.107375 GCAAAATTGTTGTAGTGCATCCAAG 60.107 40.000 0.00 0.00 32.29 3.61
145 148 1.268999 TGCAGAAATCGGCAACACAAC 60.269 47.619 5.76 0.00 43.64 3.32
146 149 1.001378 GCAGAAATCGGCAACACAACT 60.001 47.619 0.54 0.00 37.03 3.16
147 150 2.225491 GCAGAAATCGGCAACACAACTA 59.775 45.455 0.54 0.00 37.03 2.24
148 151 3.810373 CAGAAATCGGCAACACAACTAC 58.190 45.455 0.00 0.00 0.00 2.73
149 152 3.249799 CAGAAATCGGCAACACAACTACA 59.750 43.478 0.00 0.00 0.00 2.74
150 153 3.250040 AGAAATCGGCAACACAACTACAC 59.750 43.478 0.00 0.00 0.00 2.90
151 154 2.248280 ATCGGCAACACAACTACACA 57.752 45.000 0.00 0.00 0.00 3.72
152 155 2.025589 TCGGCAACACAACTACACAA 57.974 45.000 0.00 0.00 0.00 3.33
153 156 1.937223 TCGGCAACACAACTACACAAG 59.063 47.619 0.00 0.00 0.00 3.16
154 157 1.937223 CGGCAACACAACTACACAAGA 59.063 47.619 0.00 0.00 0.00 3.02
155 158 2.286184 CGGCAACACAACTACACAAGAC 60.286 50.000 0.00 0.00 0.00 3.01
156 159 2.680841 GGCAACACAACTACACAAGACA 59.319 45.455 0.00 0.00 0.00 3.41
157 160 3.486875 GGCAACACAACTACACAAGACAC 60.487 47.826 0.00 0.00 0.00 3.67
179 182 8.958119 ACACTGAACTCATGTACTTCTTTTAA 57.042 30.769 0.00 0.00 0.00 1.52
182 185 9.046296 ACTGAACTCATGTACTTCTTTTAACTG 57.954 33.333 0.00 0.00 0.00 3.16
197 200 7.867752 TCTTTTAACTGTTCCTATGTTTTCGG 58.132 34.615 0.00 0.00 0.00 4.30
206 209 5.461032 TCCTATGTTTTCGGTTTTTGCAT 57.539 34.783 0.00 0.00 0.00 3.96
277 280 8.603242 TTATCGCATAGTTTATTTTCTCTCCC 57.397 34.615 0.00 0.00 0.00 4.30
339 342 4.454728 TGGATTTAGAAGCCATTTGTGC 57.545 40.909 0.00 0.00 43.11 4.57
391 394 4.850680 TGGGTTCGTTAGGATAAGCATTT 58.149 39.130 0.00 0.00 0.00 2.32
413 416 6.656632 TTTGACCAACAATTACTATGCCAA 57.343 33.333 0.00 0.00 38.36 4.52
475 478 5.331876 AGTTACAGCTTGGCTCTACTTAG 57.668 43.478 0.00 0.00 36.40 2.18
476 479 4.160626 AGTTACAGCTTGGCTCTACTTAGG 59.839 45.833 0.00 0.00 36.40 2.69
590 593 4.505039 GGAGTTGTAGATGTCACCCAAACT 60.505 45.833 0.00 0.00 0.00 2.66
637 1349 8.881262 TGAAGAGAAAGGTCTAATTTTAGTCCT 58.119 33.333 9.47 9.47 46.53 3.85
642 1354 4.767478 AGGTCTAATTTTAGTCCTTCGGC 58.233 43.478 9.47 0.00 43.61 5.54
643 1355 3.875727 GGTCTAATTTTAGTCCTTCGGCC 59.124 47.826 0.00 0.00 36.46 6.13
701 1413 8.812513 AAGGACATGATCACAGAATTCATAAA 57.187 30.769 8.44 0.00 0.00 1.40
751 1463 9.315525 GTACCTTGATTTTATAGAACAGACTCC 57.684 37.037 0.00 0.00 0.00 3.85
766 1478 6.139679 ACAGACTCCATGATTTTTCCCTTA 57.860 37.500 0.00 0.00 0.00 2.69
1338 4423 2.513666 TTCATGGCCATCGCGTCC 60.514 61.111 17.61 4.22 35.02 4.79
1671 4756 2.172293 GGAGTCATCTGGGCTCAAGATT 59.828 50.000 0.00 0.00 0.00 2.40
1916 5001 0.680618 CATGCTTCTTTGGTTGGGCA 59.319 50.000 0.00 0.00 0.00 5.36
1919 5004 0.752658 GCTTCTTTGGTTGGGCAGTT 59.247 50.000 0.00 0.00 0.00 3.16
1923 5010 1.076632 TTTGGTTGGGCAGTTCCGT 60.077 52.632 0.00 0.00 34.94 4.69
1924 5011 1.388065 TTTGGTTGGGCAGTTCCGTG 61.388 55.000 0.00 0.00 34.94 4.94
2011 5099 8.731605 ACGGTAGATATACATGTTATCAGAGTG 58.268 37.037 20.47 12.88 0.00 3.51
2061 5149 4.424842 ACCTCTGGGAGATGATAAGATCC 58.575 47.826 0.00 0.00 36.25 3.36
2066 5154 4.306391 TGGGAGATGATAAGATCCAACCA 58.694 43.478 0.00 0.00 33.24 3.67
2124 5297 7.940137 TGTTTTTCCTACATTGCCTCTTAGTTA 59.060 33.333 0.00 0.00 0.00 2.24
2125 5298 8.957466 GTTTTTCCTACATTGCCTCTTAGTTAT 58.043 33.333 0.00 0.00 0.00 1.89
2175 5348 9.675464 TGGTAATACCAGTTTCTTTTACATAGG 57.325 33.333 8.27 0.00 44.79 2.57
2833 8348 9.237846 GCTTAAATAAACAGGAGACATTTATGC 57.762 33.333 0.00 0.00 35.36 3.14
2863 8378 4.454678 GCTCCATGTGATTTCTGACCATA 58.545 43.478 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.613925 GAAAAACTCCTGGACTTGCCC 59.386 52.381 0.00 0.00 34.97 5.36
19 20 4.730966 AGGAGAAGGGAAAGAAAAACTCC 58.269 43.478 0.00 0.00 41.74 3.85
38 39 5.779241 AATGGTTTCTTACATGGAGAGGA 57.221 39.130 0.00 0.00 0.00 3.71
92 95 4.956075 ACTCTGGGAATTCAACAAAGTTGT 59.044 37.500 7.93 0.00 44.72 3.32
145 148 5.292765 ACATGAGTTCAGTGTCTTGTGTAG 58.707 41.667 0.00 0.00 31.73 2.74
146 149 5.276461 ACATGAGTTCAGTGTCTTGTGTA 57.724 39.130 0.00 0.00 31.73 2.90
147 150 4.142609 ACATGAGTTCAGTGTCTTGTGT 57.857 40.909 0.00 0.00 31.73 3.72
148 151 5.292765 AGTACATGAGTTCAGTGTCTTGTG 58.707 41.667 0.00 6.58 34.12 3.33
149 152 5.537300 AGTACATGAGTTCAGTGTCTTGT 57.463 39.130 0.00 6.17 35.76 3.16
150 153 6.219473 AGAAGTACATGAGTTCAGTGTCTTG 58.781 40.000 0.00 0.00 39.63 3.02
151 154 6.412362 AGAAGTACATGAGTTCAGTGTCTT 57.588 37.500 0.00 0.00 39.63 3.01
152 155 6.412362 AAGAAGTACATGAGTTCAGTGTCT 57.588 37.500 0.00 0.00 39.63 3.41
153 156 7.484035 AAAAGAAGTACATGAGTTCAGTGTC 57.516 36.000 0.00 0.00 39.63 3.67
154 157 8.827677 GTTAAAAGAAGTACATGAGTTCAGTGT 58.172 33.333 0.00 0.00 39.63 3.55
155 158 9.046296 AGTTAAAAGAAGTACATGAGTTCAGTG 57.954 33.333 0.00 0.00 39.63 3.66
156 159 9.046296 CAGTTAAAAGAAGTACATGAGTTCAGT 57.954 33.333 0.00 0.00 39.63 3.41
157 160 9.046296 ACAGTTAAAAGAAGTACATGAGTTCAG 57.954 33.333 0.00 0.00 39.63 3.02
179 182 6.270064 CAAAAACCGAAAACATAGGAACAGT 58.730 36.000 0.00 0.00 0.00 3.55
182 185 5.044558 TGCAAAAACCGAAAACATAGGAAC 58.955 37.500 0.00 0.00 0.00 3.62
197 200 1.936547 TGCCGTTTGGAATGCAAAAAC 59.063 42.857 0.51 0.00 37.49 2.43
206 209 2.851263 ACTCAGTATGCCGTTTGGAA 57.149 45.000 0.00 0.00 36.79 3.53
256 259 5.817816 ACAGGGAGAGAAAATAAACTATGCG 59.182 40.000 0.00 0.00 0.00 4.73
276 279 3.056821 TGATGACCGACAACTTCTACAGG 60.057 47.826 0.00 0.00 0.00 4.00
277 280 4.169508 CTGATGACCGACAACTTCTACAG 58.830 47.826 0.00 0.00 0.00 2.74
339 342 4.258457 TGTATTTTGGAAGGTATGGGGG 57.742 45.455 0.00 0.00 0.00 5.40
391 394 6.266558 ACTTTGGCATAGTAATTGTTGGTCAA 59.733 34.615 8.93 0.00 40.53 3.18
475 478 4.932146 AGTGCATTGTGTTTTTCTGTACC 58.068 39.130 0.00 0.00 0.00 3.34
476 479 6.636850 CCTTAGTGCATTGTGTTTTTCTGTAC 59.363 38.462 0.00 0.00 0.00 2.90
590 593 9.923143 TCTTCATCGAGAACATACTTTAGAAAA 57.077 29.630 0.00 0.00 31.61 2.29
643 1355 4.755123 ACCATAATTTCCGATTAGCCGAAG 59.245 41.667 0.00 0.00 0.00 3.79
656 1368 5.418840 TCCTTCCAAGAAGCACCATAATTTC 59.581 40.000 0.00 0.00 0.00 2.17
701 1413 6.486657 ACTGAGCAGTTGTGTATAACATTTGT 59.513 34.615 0.00 0.00 38.83 2.83
711 1423 3.639561 TCAAGGTACTGAGCAGTTGTGTA 59.360 43.478 8.60 0.00 40.86 2.90
717 1429 8.079211 TCTATAAAATCAAGGTACTGAGCAGT 57.921 34.615 8.35 8.35 40.86 4.40
807 1519 6.841229 TCTCACTATCCCATTTGTATCTCTGT 59.159 38.462 0.00 0.00 0.00 3.41
808 1520 7.295322 TCTCACTATCCCATTTGTATCTCTG 57.705 40.000 0.00 0.00 0.00 3.35
809 1521 8.503428 AATCTCACTATCCCATTTGTATCTCT 57.497 34.615 0.00 0.00 0.00 3.10
810 1522 9.566432 AAAATCTCACTATCCCATTTGTATCTC 57.434 33.333 0.00 0.00 0.00 2.75
889 3966 2.427753 GATGAGGGTGGGGATCGC 59.572 66.667 0.06 0.06 0.00 4.58
1242 4327 1.380650 GAAGGAGGAGGCGAGGTCT 60.381 63.158 0.00 0.00 0.00 3.85
1307 4392 4.722700 TGAAGGCGGGCTTGAGGC 62.723 66.667 22.39 7.63 40.90 4.70
1422 4507 4.778415 CCGAGCTCCACCACGTCG 62.778 72.222 8.47 0.00 0.00 5.12
1576 4661 4.416533 GAGCCTCACATCAGCTCG 57.583 61.111 0.00 0.00 43.18 5.03
1671 4756 4.293648 CGTGACAGGACCGGCACA 62.294 66.667 18.37 5.77 0.00 4.57
1916 5001 0.182775 AAACAGGAAGGCACGGAACT 59.817 50.000 0.00 0.00 0.00 3.01
1919 5004 0.759959 TACAAACAGGAAGGCACGGA 59.240 50.000 0.00 0.00 0.00 4.69
1923 5010 7.669722 AGAAATTCTAATACAAACAGGAAGGCA 59.330 33.333 0.00 0.00 0.00 4.75
1924 5011 7.970614 CAGAAATTCTAATACAAACAGGAAGGC 59.029 37.037 0.00 0.00 0.00 4.35
1966 5053 5.467705 ACCGTATCTTGTGTTGAGAAGTAC 58.532 41.667 0.00 0.00 0.00 2.73
2011 5099 1.000274 AGCGGAAATGGAGCAAAACAC 60.000 47.619 0.00 0.00 0.00 3.32
2061 5149 2.703798 CGCAGCCCCTTGATGGTTG 61.704 63.158 0.00 0.00 37.18 3.77
2066 5154 0.328258 AAACTACGCAGCCCCTTGAT 59.672 50.000 0.00 0.00 0.00 2.57
2124 5297 9.003658 CAGAGTAACAAAAACCATCTACAGAAT 57.996 33.333 0.00 0.00 0.00 2.40
2125 5298 7.444183 CCAGAGTAACAAAAACCATCTACAGAA 59.556 37.037 0.00 0.00 0.00 3.02
2175 5348 4.598062 CTTTGTCAAGGGAGAAAAACGTC 58.402 43.478 0.00 0.00 36.05 4.34
2833 8348 3.784511 AATCACATGGAGCCTATGAGG 57.215 47.619 0.00 0.00 38.80 3.86


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

AutoCloner maintained by Alex Coulton.