Multiple sequence alignment - TraesCS7A01G106600

Loading Multiple Alignment...

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 TraesCS7A01G106600 chr7A 100.000 5435 0 0 1 5435 64697536 64692102 0 10037
1 TraesCS7A01G106600 chr7D 96.876 5442 139 10 1 5425 60416711 60411284 0 9079
2 TraesCS7A01G106600 chr7B 95.957 5441 197 18 1 5435 2915459 2910036 0 8807


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 TraesCS7A01G106600 chr7A 64692102 64697536 5434 True 10037 10037 100.000 1 5435 1 chr7A.!!$R1 5434
1 TraesCS7A01G106600 chr7D 60411284 60416711 5427 True 9079 9079 96.876 1 5425 1 chr7D.!!$R1 5424
2 TraesCS7A01G106600 chr7B 2910036 2915459 5423 True 8807 8807 95.957 1 5435 1 chr7B.!!$R1 5434

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
155 156 1.603802 CTTGTCCGCTTGTTCACACAT 59.396 47.619 0.00 0.0 31.06 3.21 F
1711 1713 0.395586 AGCTCCACACAAGCACCAAA 60.396 50.000 0.00 0.0 42.35 3.28 F
1997 1999 1.070134 ACAAGGCTTCAGCTGTTACGA 59.930 47.619 14.67 0.0 41.70 3.43 F
3639 3642 2.981859 TCAGCCCTATTTCTCGGTTC 57.018 50.000 0.00 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 1965 1.028905 CCTTGTTTCGGTTGCTCCAA 58.971 50.000 0.0 0.0 35.57 3.53 R
3243 3246 2.486191 GCCATGTTCTCCCTGTGGATAG 60.486 54.545 0.0 0.0 40.80 2.08 R
3998 4003 3.858886 TAGCCCAGCAGCTATCTCT 57.141 52.632 0.0 0.0 42.70 3.10 R
5139 5162 0.320421 CGACGAAACATGAGGGTGGT 60.320 55.000 0.0 0.0 0.00 4.16 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
61 62 6.954102 AGGTTGTTTCTTTAGCATAGGGAAAT 59.046 34.615 0.00 0.00 30.26 2.17
63 64 8.406297 GGTTGTTTCTTTAGCATAGGGAAATAG 58.594 37.037 0.00 0.00 30.26 1.73
155 156 1.603802 CTTGTCCGCTTGTTCACACAT 59.396 47.619 0.00 0.00 31.06 3.21
220 221 8.076781 TGTATCATTTAGAGTAAGCACGAGATC 58.923 37.037 0.00 0.00 0.00 2.75
320 321 1.840737 ACTAGAGCGGTGATGTGAGT 58.159 50.000 0.00 0.00 0.00 3.41
471 472 4.660789 AACAATCCAGGCATATCAAAGC 57.339 40.909 0.00 0.00 0.00 3.51
581 582 6.363088 TCATTTTTCTAGCTTTTGTCATTGCG 59.637 34.615 0.00 0.00 0.00 4.85
626 627 3.372206 CGAGCCCAGATACAGTTTTTGAG 59.628 47.826 0.00 0.00 0.00 3.02
668 669 5.011125 TGCTCTCTTTATGGGTATAGCTGTC 59.989 44.000 0.00 0.00 0.00 3.51
830 831 3.202151 TGGAGTCAAGTCTTTGGACCTTT 59.798 43.478 0.00 0.00 43.05 3.11
911 912 7.648039 TTCAACATCATCCATCATCATTCAA 57.352 32.000 0.00 0.00 0.00 2.69
1017 1018 6.572167 TTTGTGATGCATCAAATGTCACTA 57.428 33.333 30.24 12.17 37.25 2.74
1347 1348 4.343239 GGGCTAAGGTAAGAAGGAACGATA 59.657 45.833 0.00 0.00 0.00 2.92
1419 1420 3.596214 ACACAATATCTCCGTGTTCCAC 58.404 45.455 0.00 0.00 40.91 4.02
1652 1653 6.831769 ACAAAGTTACATCTTATGCTTCACG 58.168 36.000 0.00 0.00 0.00 4.35
1711 1713 0.395586 AGCTCCACACAAGCACCAAA 60.396 50.000 0.00 0.00 42.35 3.28
1754 1756 5.232610 AGACAATCTTTAGAGTACGACGG 57.767 43.478 0.00 0.00 0.00 4.79
1895 1897 9.747898 TCCCTTGTATGTCAATTTTATGTTAGT 57.252 29.630 0.00 0.00 35.35 2.24
1997 1999 1.070134 ACAAGGCTTCAGCTGTTACGA 59.930 47.619 14.67 0.00 41.70 3.43
2099 2101 3.867857 TGTTTTGGCAGGAAGAAAAACC 58.132 40.909 6.32 0.00 40.25 3.27
2336 2338 5.410355 AAAACTAGCACCATGATTTGCAT 57.590 34.783 14.07 4.73 41.48 3.96
2637 2639 4.517952 TTGCACAATTCATCAACCGAAT 57.482 36.364 0.00 0.00 34.56 3.34
2729 2731 7.811282 AGAATGACAACCACACCCAATATATA 58.189 34.615 0.00 0.00 0.00 0.86
2756 2758 4.909284 AGGGATGTCTCTTTTATAGGGGT 58.091 43.478 0.00 0.00 0.00 4.95
2762 2764 7.229506 GGATGTCTCTTTTATAGGGGTTCATTG 59.770 40.741 0.00 0.00 0.00 2.82
2902 2905 6.069331 ACTCATTTATAGCGGTTCTCTAGGA 58.931 40.000 0.00 0.00 0.00 2.94
3011 3014 4.606210 TGGCCTCTTTTTAGGTTATTCCC 58.394 43.478 3.32 0.00 39.02 3.97
3013 3016 3.066342 GCCTCTTTTTAGGTTATTCCCGC 59.934 47.826 0.00 0.00 39.02 6.13
3116 3119 6.938507 TGGAGTGGACTACGTACAAATTTAT 58.061 36.000 0.00 0.00 0.00 1.40
3117 3120 6.814644 TGGAGTGGACTACGTACAAATTTATG 59.185 38.462 0.00 0.00 0.00 1.90
3243 3246 6.985188 TTGTATTTCTCTGGCTTGTGTATC 57.015 37.500 0.00 0.00 0.00 2.24
3639 3642 2.981859 TCAGCCCTATTTCTCGGTTC 57.018 50.000 0.00 0.00 0.00 3.62
3748 3751 3.075884 GGCGTTTGTAATTGGTCAGGTA 58.924 45.455 0.00 0.00 0.00 3.08
3758 3761 5.982890 AATTGGTCAGGTAAGTCAATTGG 57.017 39.130 5.42 0.00 36.88 3.16
4347 4353 4.938575 TGAAAATGGCTACTTTCCCCTA 57.061 40.909 1.41 0.00 31.75 3.53
4365 4371 3.007398 CCCTAGTCACAGCTCTTCACTTT 59.993 47.826 0.00 0.00 0.00 2.66
4487 4493 7.417612 GGGCATCATTAAAAGTGTATGTACTG 58.582 38.462 0.00 0.00 0.00 2.74
4645 4652 8.477419 TTGAAGAACTAAAGAAATGGTTGGAT 57.523 30.769 0.00 0.00 0.00 3.41
4646 4653 8.477419 TGAAGAACTAAAGAAATGGTTGGATT 57.523 30.769 0.00 0.00 0.00 3.01
4832 4839 9.229784 GTCAATCAAACATGCATGTATTTAGAG 57.770 33.333 31.55 18.30 40.80 2.43
4854 4861 8.628630 AGAGAAATAATAGCAGAAAATAGGCC 57.371 34.615 0.00 0.00 0.00 5.19
4908 4915 4.634883 GCAGATCGATATGAGGCATTCATT 59.365 41.667 23.60 0.00 44.14 2.57
5075 5098 6.496565 TGGTTCAACCCATTATTCACATCTTT 59.503 34.615 3.42 0.00 37.50 2.52
5088 5111 4.676546 TCACATCTTTGCTCTCATACTCG 58.323 43.478 0.00 0.00 0.00 4.18
5109 5132 1.574428 GGCAGTGCACCGTTGTTAG 59.426 57.895 18.61 0.00 0.00 2.34
5139 5162 2.824546 GGCATCCATCGCTCTCCA 59.175 61.111 0.00 0.00 0.00 3.86
5158 5181 0.320421 ACCACCCTCATGTTTCGTCG 60.320 55.000 0.00 0.00 0.00 5.12
5183 5206 3.045634 TCTGGGATGTATACACCAAGGG 58.954 50.000 20.14 9.82 31.63 3.95
5197 5220 2.110721 ACCAAGGGCAAGAGGAAGAAAT 59.889 45.455 0.00 0.00 0.00 2.17
5299 5322 7.344095 AGTATACTGTTAGCTTATTGACCGT 57.656 36.000 4.10 0.00 0.00 4.83
5305 5328 1.904287 AGCTTATTGACCGTTTGGCA 58.096 45.000 0.00 0.00 39.70 4.92
5306 5329 2.235016 AGCTTATTGACCGTTTGGCAA 58.765 42.857 0.00 0.00 39.70 4.52
5365 5388 2.764010 TGTTAGCTTATTGGCCTCGAGA 59.236 45.455 15.71 0.00 0.00 4.04
5425 5448 9.727627 GATCTGTTTGAGGCTTTAATCTAATTG 57.272 33.333 0.00 0.00 0.00 2.32
5430 5453 8.435430 GTTTGAGGCTTTAATCTAATTGCAAAC 58.565 33.333 1.71 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 7.587629 CAAGACTTCTTGTGCATTAGAATTCA 58.412 34.615 21.88 0.90 46.11 2.57
155 156 6.889177 TGCTTTACTATTGATTCCAATCACCA 59.111 34.615 1.28 0.00 44.54 4.17
190 191 9.678941 TCGTGCTTACTCTAAATGATACATTAG 57.321 33.333 0.00 0.00 0.00 1.73
220 221 7.439157 TCATGTTGAGTAGTTGGAGAAATTG 57.561 36.000 0.00 0.00 0.00 2.32
304 305 0.969149 TTCACTCACATCACCGCTCT 59.031 50.000 0.00 0.00 0.00 4.09
471 472 2.589014 GCAAGCTCTGAAAACATTCCG 58.411 47.619 0.00 0.00 0.00 4.30
626 627 2.305052 AGCACCCAAGTACTTTACTCCC 59.695 50.000 5.07 0.00 38.26 4.30
668 669 6.110543 TCGATCATGCTGTTGAAGTTTATG 57.889 37.500 0.00 0.00 0.00 1.90
830 831 3.897239 CCAATTGCATAGTAGGTTGGGA 58.103 45.455 0.00 0.00 34.05 4.37
898 899 6.584185 TGGATAGCATTTGAATGATGATGG 57.416 37.500 7.86 0.00 38.70 3.51
946 947 1.344114 GCCACAAAATTGAAGGCCTCA 59.656 47.619 5.23 2.73 42.60 3.86
998 999 4.847198 ACCTAGTGACATTTGATGCATCA 58.153 39.130 25.42 25.42 34.44 3.07
1146 1147 3.715618 TTACGTTGTTGCGCTATTCAG 57.284 42.857 9.73 0.00 34.88 3.02
1347 1348 8.638873 TGTTGTAGTGTTATATGCTGCTAGTAT 58.361 33.333 0.00 0.00 0.00 2.12
1711 1713 6.440647 TGTCTCCCTTGTGACTTGATATTACT 59.559 38.462 0.00 0.00 36.26 2.24
1754 1756 4.941873 CCTTCCCACCAACTATTACTTGAC 59.058 45.833 0.00 0.00 0.00 3.18
1963 1965 1.028905 CCTTGTTTCGGTTGCTCCAA 58.971 50.000 0.00 0.00 35.57 3.53
1997 1999 4.383552 GGTCTGAATGAGCCACTAACATCT 60.384 45.833 0.00 0.00 37.22 2.90
2099 2101 2.686915 AGTACCTTCGATGTAACCTCCG 59.313 50.000 0.00 0.00 0.00 4.63
2463 2465 4.446857 TGTAAGTCTTTTTCGTTGCTCG 57.553 40.909 0.00 0.00 41.41 5.03
2729 2731 7.013834 CCCTATAAAAGAGACATCCCTACTCT 58.986 42.308 0.00 0.00 41.86 3.24
2750 2752 4.186077 TGTTTTGTCCAATGAACCCCTA 57.814 40.909 0.00 0.00 0.00 3.53
3011 3014 3.526931 TCCTTGATTCTAGGAACAGCG 57.473 47.619 13.55 0.00 38.83 5.18
3013 3016 5.104776 TGACCATCCTTGATTCTAGGAACAG 60.105 44.000 18.71 13.04 44.59 3.16
3243 3246 2.486191 GCCATGTTCTCCCTGTGGATAG 60.486 54.545 0.00 0.00 40.80 2.08
3998 4003 3.858886 TAGCCCAGCAGCTATCTCT 57.141 52.632 0.00 0.00 42.70 3.10
4347 4353 3.201290 CACAAAGTGAAGAGCTGTGACT 58.799 45.455 0.00 0.00 39.80 3.41
4365 4371 3.743521 ACAGAAGAACATGCTTAGCACA 58.256 40.909 9.82 0.00 43.04 4.57
4631 4638 6.328934 ACCCAAGTTAAATCCAACCATTTCTT 59.671 34.615 0.00 0.00 0.00 2.52
4645 4652 4.383173 GTTTCTCCGAGACCCAAGTTAAA 58.617 43.478 0.00 0.00 0.00 1.52
4646 4653 3.553508 CGTTTCTCCGAGACCCAAGTTAA 60.554 47.826 0.00 0.00 0.00 2.01
4685 4692 7.606456 TGTTCTTCCTACTTTGGTATGATGTTC 59.394 37.037 0.00 0.00 0.00 3.18
4832 4839 7.667635 AGGAGGCCTATTTTCTGCTATTATTTC 59.332 37.037 4.42 0.00 28.47 2.17
4841 4848 4.423625 TTCTAGGAGGCCTATTTTCTGC 57.576 45.455 4.42 0.00 35.36 4.26
4883 4890 3.523606 ATGCCTCATATCGATCTGCTC 57.476 47.619 0.00 0.00 0.00 4.26
4908 4915 0.324738 AGGTTCCTCGGATCAGCTCA 60.325 55.000 0.00 0.00 0.00 4.26
5027 5050 1.525197 CACTTGCTCGCGTTCAAACTA 59.475 47.619 5.77 0.00 0.00 2.24
5063 5086 6.920210 CGAGTATGAGAGCAAAGATGTGAATA 59.080 38.462 0.00 0.00 0.00 1.75
5075 5098 2.134287 GCCCCCGAGTATGAGAGCA 61.134 63.158 0.00 0.00 0.00 4.26
5139 5162 0.320421 CGACGAAACATGAGGGTGGT 60.320 55.000 0.00 0.00 0.00 4.16
5158 5181 5.357032 CCTTGGTGTATACATCCCAGAAAAC 59.643 44.000 13.58 0.00 0.00 2.43
5183 5206 3.126686 GTGCTCTCATTTCTTCCTCTTGC 59.873 47.826 0.00 0.00 0.00 4.01
5197 5220 7.169645 GCAATTTGTTTTTATGAAGTGCTCTCA 59.830 33.333 0.00 0.00 39.26 3.27


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

AutoCloner maintained by Alex Coulton.