Multiple sequence alignment - TraesCS2B01G323500

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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 TraesCS2B01G323500 chr2B 100.000 3221 0 0 1 3221 462300015 462303235 0.000000e+00 5949
1 TraesCS2B01G323500 chr2D 96.561 3082 58 18 156 3221 391112601 391115650 0.000000e+00 5060
2 TraesCS2B01G323500 chr2D 90.299 134 9 3 30 160 391112445 391112577 4.270000e-39 172
3 TraesCS2B01G323500 chr2A 96.491 3078 81 16 156 3221 527700416 527703478 0.000000e+00 5060
4 TraesCS2B01G323500 chr2A 86.232 138 14 4 30 163 527700260 527700396 9.310000e-31 145
5 TraesCS2B01G323500 chr3A 83.914 1119 122 28 1518 2621 57225902 57224827 0.000000e+00 1016
6 TraesCS2B01G323500 chr3A 84.971 173 20 5 2709 2877 57220352 57220182 1.540000e-38 171
7 TraesCS2B01G323500 chr3B 85.516 863 104 10 1530 2383 71327899 71327049 0.000000e+00 881
8 TraesCS2B01G323500 chr3B 85.632 522 44 14 2384 2901 71325244 71324750 1.320000e-143 520
9 TraesCS2B01G323500 chrUn 100.000 392 0 0 1407 1798 479687363 479687754 0.000000e+00 725


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 TraesCS2B01G323500 chr2B 462300015 462303235 3220 False 5949.0 5949 100.0000 1 3221 1 chr2B.!!$F1 3220
1 TraesCS2B01G323500 chr2D 391112445 391115650 3205 False 2616.0 5060 93.4300 30 3221 2 chr2D.!!$F1 3191
2 TraesCS2B01G323500 chr2A 527700260 527703478 3218 False 2602.5 5060 91.3615 30 3221 2 chr2A.!!$F1 3191
3 TraesCS2B01G323500 chr3A 57224827 57225902 1075 True 1016.0 1016 83.9140 1518 2621 1 chr3A.!!$R2 1103
4 TraesCS2B01G323500 chr3B 71324750 71327899 3149 True 700.5 881 85.5740 1530 2901 2 chr3B.!!$R1 1371

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
75 77 0.321671 ACTCACATGAACCGACAGGG 59.678 55.0 0.0 0.0 43.47 4.45 F
786 830 0.600557 CTGTCTGTCTTGCTCTCCGT 59.399 55.0 0.0 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1857 7.961325 GCTAAATGCAGAGTAAGAAAATGTC 57.039 36.0 0.00 0.0 42.31 3.06 R
2650 4523 0.250597 GGTACCACTTCCCCACACAC 60.251 60.0 7.15 0.0 0.00 3.82 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
25 26 8.658499 GAATCTCTAAAAAGCCTTATAACGGA 57.342 34.615 5.45 0.00 0.00 4.69
26 27 8.664211 AATCTCTAAAAAGCCTTATAACGGAG 57.336 34.615 5.45 0.00 0.00 4.63
27 28 6.579865 TCTCTAAAAAGCCTTATAACGGAGG 58.420 40.000 5.45 0.00 36.09 4.30
28 29 5.677567 TCTAAAAAGCCTTATAACGGAGGG 58.322 41.667 5.45 0.00 33.52 4.30
59 61 3.877508 ACTTCAGGTAAACACTTGCACTC 59.122 43.478 0.00 0.00 0.00 3.51
73 75 0.792640 GCACTCACATGAACCGACAG 59.207 55.000 0.00 0.00 0.00 3.51
75 77 0.321671 ACTCACATGAACCGACAGGG 59.678 55.000 0.00 0.00 43.47 4.45
89 91 3.070446 CCGACAGGGGTAATGTATGCTAA 59.930 47.826 0.00 0.00 0.00 3.09
131 134 8.408601 CCTGAAGAATATGAAAAACCTGGTATG 58.591 37.037 0.00 0.00 0.00 2.39
145 148 4.264623 ACCTGGTATGGCCCTCAAAAATAA 60.265 41.667 0.00 0.00 36.04 1.40
154 157 4.988540 GGCCCTCAAAAATAAAAGTGACAC 59.011 41.667 0.00 0.00 0.00 3.67
181 214 2.213310 TCCCTGAAATATTGGGGCTGA 58.787 47.619 13.53 0.00 41.22 4.26
184 217 2.590821 CTGAAATATTGGGGCTGAGGG 58.409 52.381 0.00 0.00 0.00 4.30
186 219 2.584965 TGAAATATTGGGGCTGAGGGAA 59.415 45.455 0.00 0.00 0.00 3.97
187 220 2.755952 AATATTGGGGCTGAGGGAAC 57.244 50.000 0.00 0.00 0.00 3.62
188 221 1.607225 ATATTGGGGCTGAGGGAACA 58.393 50.000 0.00 0.00 0.00 3.18
189 222 1.607225 TATTGGGGCTGAGGGAACAT 58.393 50.000 0.00 0.00 0.00 2.71
190 223 1.607225 ATTGGGGCTGAGGGAACATA 58.393 50.000 0.00 0.00 0.00 2.29
191 224 1.607225 TTGGGGCTGAGGGAACATAT 58.393 50.000 0.00 0.00 0.00 1.78
210 243 6.333416 ACATATATAGTATGCACTTCGGCTG 58.667 40.000 0.00 0.00 36.14 4.85
340 373 6.976088 ACACGATATCCAACAAACATCAAAA 58.024 32.000 0.00 0.00 0.00 2.44
396 429 8.259411 TCAGCACAATAATTTAATGGCAAGATT 58.741 29.630 0.00 0.00 0.00 2.40
489 533 5.016031 TCTCCTGATCTCAGATATGGATGGA 59.984 44.000 8.78 2.33 46.59 3.41
496 540 6.803366 TCTCAGATATGGATGGACATATGG 57.197 41.667 7.80 0.00 42.48 2.74
604 648 3.822735 AGTAGCACACAAGCATCATGTTT 59.177 39.130 0.00 0.00 36.85 2.83
657 701 7.392766 ACTTTGGATGGATGAGATGGTTATA 57.607 36.000 0.00 0.00 0.00 0.98
688 732 2.811317 CCAAGCGGAGTCAGCGAC 60.811 66.667 9.69 1.15 40.04 5.19
712 756 2.165437 TCAAATACATCCGCAAAAGGCC 59.835 45.455 0.00 0.00 40.31 5.19
786 830 0.600557 CTGTCTGTCTTGCTCTCCGT 59.399 55.000 0.00 0.00 0.00 4.69
951 1003 4.385447 CCAAATCCAACATTAGTGTTTGCG 59.615 41.667 0.08 0.00 46.07 4.85
976 1028 5.283763 AGCATCATTAGCTCCCTCCATATA 58.716 41.667 0.00 0.00 38.01 0.86
1798 1857 4.668431 GCTGCATACATGTTATCGCATCTG 60.668 45.833 2.30 0.00 0.00 2.90
2187 2255 6.271159 ACCAGAGATGTAATTATTCTCCTCCC 59.729 42.308 17.96 2.41 37.24 4.30
2613 4486 7.814264 ATGAGATAAGCTCCAAAAGGTAATG 57.186 36.000 0.00 0.00 43.26 1.90
2650 4523 1.581934 TTCCAGACAGAAAGTGTGCG 58.418 50.000 0.00 0.00 40.56 5.34
2800 4673 8.753133 TCGCTTTAGATCACTAATCATGGATAT 58.247 33.333 0.00 0.00 38.23 1.63
2905 4781 5.477291 TGTCTGTCCTAAGAGAAGTTGGTAG 59.523 44.000 0.00 0.00 0.00 3.18
2906 4782 5.477637 GTCTGTCCTAAGAGAAGTTGGTAGT 59.522 44.000 0.00 0.00 0.00 2.73
2907 4783 5.477291 TCTGTCCTAAGAGAAGTTGGTAGTG 59.523 44.000 0.00 0.00 0.00 2.74
2908 4784 5.145564 TGTCCTAAGAGAAGTTGGTAGTGT 58.854 41.667 0.00 0.00 0.00 3.55
2909 4785 6.309357 TGTCCTAAGAGAAGTTGGTAGTGTA 58.691 40.000 0.00 0.00 0.00 2.90
2916 4792 3.646637 AGAAGTTGGTAGTGTAGTGCCTT 59.353 43.478 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.658499 TCCGTTATAAGGCTTTTTAGAGATTC 57.342 34.615 4.45 0.00 0.00 2.52
1 2 7.715686 CCTCCGTTATAAGGCTTTTTAGAGATT 59.284 37.037 4.45 0.00 0.00 2.40
2 3 7.217906 CCTCCGTTATAAGGCTTTTTAGAGAT 58.782 38.462 4.45 0.00 0.00 2.75
3 4 6.407752 CCCTCCGTTATAAGGCTTTTTAGAGA 60.408 42.308 4.45 0.00 0.00 3.10
4 5 5.758784 CCCTCCGTTATAAGGCTTTTTAGAG 59.241 44.000 4.45 5.03 0.00 2.43
5 6 5.426185 TCCCTCCGTTATAAGGCTTTTTAGA 59.574 40.000 4.45 0.00 0.00 2.10
6 7 5.677567 TCCCTCCGTTATAAGGCTTTTTAG 58.322 41.667 4.45 0.00 0.00 1.85
7 8 5.190330 ACTCCCTCCGTTATAAGGCTTTTTA 59.810 40.000 4.45 0.00 0.00 1.52
8 9 4.018688 ACTCCCTCCGTTATAAGGCTTTTT 60.019 41.667 4.45 0.00 0.00 1.94
9 10 3.522343 ACTCCCTCCGTTATAAGGCTTTT 59.478 43.478 4.45 0.00 0.00 2.27
10 11 3.113043 ACTCCCTCCGTTATAAGGCTTT 58.887 45.455 4.45 0.00 0.00 3.51
11 12 2.760581 ACTCCCTCCGTTATAAGGCTT 58.239 47.619 4.58 4.58 0.00 4.35
12 13 2.473576 ACTCCCTCCGTTATAAGGCT 57.526 50.000 0.00 0.00 0.00 4.58
13 14 3.229293 ACTACTCCCTCCGTTATAAGGC 58.771 50.000 0.00 0.00 0.00 4.35
14 15 4.891756 TGAACTACTCCCTCCGTTATAAGG 59.108 45.833 0.00 0.00 0.00 2.69
15 16 5.593502 AGTGAACTACTCCCTCCGTTATAAG 59.406 44.000 0.00 0.00 33.17 1.73
16 17 5.513233 AGTGAACTACTCCCTCCGTTATAA 58.487 41.667 0.00 0.00 33.17 0.98
17 18 5.121380 AGTGAACTACTCCCTCCGTTATA 57.879 43.478 0.00 0.00 33.17 0.98
18 19 3.978610 AGTGAACTACTCCCTCCGTTAT 58.021 45.455 0.00 0.00 33.17 1.89
19 20 3.446442 AGTGAACTACTCCCTCCGTTA 57.554 47.619 0.00 0.00 33.17 3.18
20 21 2.305858 AGTGAACTACTCCCTCCGTT 57.694 50.000 0.00 0.00 33.17 4.44
21 22 2.169330 GAAGTGAACTACTCCCTCCGT 58.831 52.381 0.00 0.00 39.18 4.69
22 23 2.164624 CTGAAGTGAACTACTCCCTCCG 59.835 54.545 0.00 0.00 39.18 4.63
23 24 2.498078 CCTGAAGTGAACTACTCCCTCC 59.502 54.545 0.00 0.00 39.18 4.30
24 25 3.166679 ACCTGAAGTGAACTACTCCCTC 58.833 50.000 0.00 0.00 39.18 4.30
25 26 3.261818 ACCTGAAGTGAACTACTCCCT 57.738 47.619 0.00 0.00 39.18 4.20
26 27 5.221581 TGTTTACCTGAAGTGAACTACTCCC 60.222 44.000 2.77 0.00 43.54 4.30
27 28 5.695363 GTGTTTACCTGAAGTGAACTACTCC 59.305 44.000 2.77 0.00 43.54 3.85
28 29 6.514063 AGTGTTTACCTGAAGTGAACTACTC 58.486 40.000 2.77 0.00 43.54 2.59
59 61 0.611200 TACCCCTGTCGGTTCATGTG 59.389 55.000 0.00 0.00 37.34 3.21
121 124 1.080638 TTTGAGGGCCATACCAGGTT 58.919 50.000 6.18 0.00 42.05 3.50
123 126 2.230130 TTTTTGAGGGCCATACCAGG 57.770 50.000 6.18 0.00 42.05 4.45
131 134 4.988540 GTGTCACTTTTATTTTTGAGGGCC 59.011 41.667 0.00 0.00 0.00 5.80
145 148 7.595819 TTTCAGGGATATTTTGTGTCACTTT 57.404 32.000 4.27 0.00 27.76 2.66
154 157 6.270695 AGCCCCAATATTTCAGGGATATTTTG 59.729 38.462 16.08 0.00 45.80 2.44
181 214 7.363880 CCGAAGTGCATACTATATATGTTCCCT 60.364 40.741 0.00 0.00 35.69 4.20
184 217 7.009631 CAGCCGAAGTGCATACTATATATGTTC 59.990 40.741 0.00 0.00 35.69 3.18
186 219 6.071334 ACAGCCGAAGTGCATACTATATATGT 60.071 38.462 0.00 0.00 35.69 2.29
187 220 6.333416 ACAGCCGAAGTGCATACTATATATG 58.667 40.000 0.00 0.00 35.69 1.78
188 221 6.531503 ACAGCCGAAGTGCATACTATATAT 57.468 37.500 0.00 0.00 35.69 0.86
189 222 5.977489 ACAGCCGAAGTGCATACTATATA 57.023 39.130 0.00 0.00 35.69 0.86
190 223 4.873746 ACAGCCGAAGTGCATACTATAT 57.126 40.909 0.00 0.00 35.69 0.86
191 224 5.777850 TTACAGCCGAAGTGCATACTATA 57.222 39.130 0.00 0.00 35.69 1.31
210 243 6.962686 TGATATGCATGCTTGTGATCTTTAC 58.037 36.000 20.33 0.00 0.00 2.01
354 387 5.486526 TGTGCTGATTTGACCAAAGTTTTT 58.513 33.333 1.57 0.00 33.32 1.94
362 395 9.368674 CATTAAATTATTGTGCTGATTTGACCA 57.631 29.630 0.00 0.00 0.00 4.02
367 400 8.789825 TTGCCATTAAATTATTGTGCTGATTT 57.210 26.923 8.59 0.00 0.00 2.17
396 429 4.546829 ACCAGAAGTAATGCGAAACCTA 57.453 40.909 0.00 0.00 0.00 3.08
489 533 6.332976 AGTTTTCTCAATCCTCCCATATGT 57.667 37.500 1.24 0.00 0.00 2.29
604 648 5.032327 AGCAGACTCTTGCATCATAATCA 57.968 39.130 0.52 0.00 46.47 2.57
657 701 4.776349 TCCGCTTGGATATGTTACATTGT 58.224 39.130 2.23 0.00 36.65 2.71
684 728 1.136611 GCGGATGTATTTGATCGTCGC 60.137 52.381 0.00 0.00 0.00 5.19
688 732 4.282068 CCTTTTGCGGATGTATTTGATCG 58.718 43.478 0.00 0.00 0.00 3.69
891 941 9.887629 CTCCTATATATTTGATGTTCAGAGCAT 57.112 33.333 0.00 0.00 0.00 3.79
951 1003 2.634940 TGGAGGGAGCTAATGATGCTAC 59.365 50.000 0.00 0.00 41.30 3.58
1798 1857 7.961325 GCTAAATGCAGAGTAAGAAAATGTC 57.039 36.000 0.00 0.00 42.31 3.06
2187 2255 7.712264 TTAAATTTGTTTCATGCACCTTCTG 57.288 32.000 0.00 0.00 0.00 3.02
2268 2336 5.883661 TCAAATGCTTGAGTAATTGCTAGC 58.116 37.500 8.10 8.10 36.62 3.42
2613 4486 6.425114 GTCTGGAATGGACACACATATACATC 59.575 42.308 0.00 0.00 34.23 3.06
2650 4523 0.250597 GGTACCACTTCCCCACACAC 60.251 60.000 7.15 0.00 0.00 3.82
2835 4708 5.770162 AGGGTTGGATTAAGAAGTCAACAAG 59.230 40.000 0.00 0.00 39.33 3.16
2905 4781 6.743575 AAACTATTGATGAAGGCACTACAC 57.256 37.500 0.00 0.00 38.49 2.90
2906 4782 7.065803 GCTAAAACTATTGATGAAGGCACTACA 59.934 37.037 0.00 0.00 38.49 2.74
2907 4783 7.065803 TGCTAAAACTATTGATGAAGGCACTAC 59.934 37.037 0.00 0.00 38.49 2.73
2908 4784 7.109501 TGCTAAAACTATTGATGAAGGCACTA 58.890 34.615 0.00 0.00 38.49 2.74
2916 4792 7.395190 ACAAGCATGCTAAAACTATTGATGA 57.605 32.000 23.00 0.00 0.00 2.92
3084 4960 5.297547 TCCAGTATCGCATCAATAGGAAAC 58.702 41.667 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.