Multiple sequence alignment - TraesCS7A01G477700

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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 TraesCS7A01G477700 chr7A 100.000 3312 0 0 1 3312 671188814 671192125 0.000000e+00 6117
1 TraesCS7A01G477700 chr7A 95.981 622 18 2 38 658 163373938 163373323 0.000000e+00 1003
2 TraesCS7A01G477700 chr6A 98.174 3286 47 6 28 3312 88095272 88098545 0.000000e+00 5723
3 TraesCS7A01G477700 chr6A 98.075 3273 45 4 41 3312 479403924 479407179 0.000000e+00 5679
4 TraesCS7A01G477700 chr6A 93.478 92 3 2 38 126 479403848 479403939 2.070000e-27 134
5 TraesCS7A01G477700 chr5B 98.757 3219 38 2 95 3312 522908154 522904937 0.000000e+00 5722
6 TraesCS7A01G477700 chr7D 97.670 2918 50 9 402 3312 28369167 28366261 0.000000e+00 4996
7 TraesCS7A01G477700 chr7D 93.629 361 14 7 42 401 28383197 28382845 6.290000e-147 531
8 TraesCS7A01G477700 chr7B 88.077 2340 233 26 1001 3312 133496924 133494603 0.000000e+00 2734
9 TraesCS7A01G477700 chr5D 89.136 2154 205 15 1167 3312 245298147 245300279 0.000000e+00 2654
10 TraesCS7A01G477700 chr4A 85.872 1897 211 28 1001 2860 281409988 281411864 0.000000e+00 1965
11 TraesCS7A01G477700 chr4A 93.654 457 29 0 2856 3312 281416891 281417347 0.000000e+00 684
12 TraesCS7A01G477700 chr1A 99.024 1025 10 0 2288 3312 549415506 549416530 0.000000e+00 1838
13 TraesCS7A01G477700 chr1A 97.607 794 18 1 39 831 549414714 549415507 0.000000e+00 1360
14 TraesCS7A01G477700 chr2D 80.150 932 109 43 207 1111 14462990 14463872 7.800000e-176 627
15 TraesCS7A01G477700 chr2A 79.132 714 141 8 2603 3312 751722128 751722837 1.380000e-133 486


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 TraesCS7A01G477700 chr7A 671188814 671192125 3311 False 6117.0 6117 100.0000 1 3312 1 chr7A.!!$F1 3311
1 TraesCS7A01G477700 chr7A 163373323 163373938 615 True 1003.0 1003 95.9810 38 658 1 chr7A.!!$R1 620
2 TraesCS7A01G477700 chr6A 88095272 88098545 3273 False 5723.0 5723 98.1740 28 3312 1 chr6A.!!$F1 3284
3 TraesCS7A01G477700 chr6A 479403848 479407179 3331 False 2906.5 5679 95.7765 38 3312 2 chr6A.!!$F2 3274
4 TraesCS7A01G477700 chr5B 522904937 522908154 3217 True 5722.0 5722 98.7570 95 3312 1 chr5B.!!$R1 3217
5 TraesCS7A01G477700 chr7D 28366261 28369167 2906 True 4996.0 4996 97.6700 402 3312 1 chr7D.!!$R1 2910
6 TraesCS7A01G477700 chr7B 133494603 133496924 2321 True 2734.0 2734 88.0770 1001 3312 1 chr7B.!!$R1 2311
7 TraesCS7A01G477700 chr5D 245298147 245300279 2132 False 2654.0 2654 89.1360 1167 3312 1 chr5D.!!$F1 2145
8 TraesCS7A01G477700 chr4A 281409988 281411864 1876 False 1965.0 1965 85.8720 1001 2860 1 chr4A.!!$F1 1859
9 TraesCS7A01G477700 chr1A 549414714 549416530 1816 False 1599.0 1838 98.3155 39 3312 2 chr1A.!!$F1 3273
10 TraesCS7A01G477700 chr2D 14462990 14463872 882 False 627.0 627 80.1500 207 1111 1 chr2D.!!$F1 904
11 TraesCS7A01G477700 chr2A 751722128 751722837 709 False 486.0 486 79.1320 2603 3312 1 chr2A.!!$F1 709

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
21 22 0.106918 AAAACTGCCACTCGGTTGGA 60.107 50.000 7.35 0.0 43.21 3.53 F
22 23 0.110486 AAACTGCCACTCGGTTGGAT 59.890 50.000 7.35 0.0 43.21 3.41 F
23 24 0.321653 AACTGCCACTCGGTTGGATC 60.322 55.000 7.35 0.0 42.45 3.36 F
34 35 0.321653 GGTTGGATCCGACAGCAACT 60.322 55.000 29.59 0.0 32.12 3.16 F
35 36 1.066430 GGTTGGATCCGACAGCAACTA 60.066 52.381 29.59 0.0 32.12 2.24 F
36 37 2.000447 GTTGGATCCGACAGCAACTAC 59.000 52.381 25.05 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 1842 7.718314 TCAGCATAACGACCTAGAGAATAGTTA 59.282 37.037 0.00 0.0 0.00 2.24 R
2081 2209 3.167485 TCTCCTCAATGGCAGCAAATTT 58.833 40.909 0.00 0.0 35.26 1.82 R
2082 2210 2.811410 TCTCCTCAATGGCAGCAAATT 58.189 42.857 0.00 0.0 35.26 1.82 R
2108 2236 2.023404 TGATGCTGTAGGGGTCCTCTAA 60.023 50.000 0.00 0.0 34.61 2.10 R
2148 2276 2.038557 TGTAGACCTTCCAAGCCTTCAC 59.961 50.000 0.00 0.0 0.00 3.18 R
2459 2587 2.819608 GCATGCCTAACCAAAAGTCTCA 59.180 45.455 6.36 0.0 0.00 3.27 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
19 20 2.119671 GAAAAACTGCCACTCGGTTG 57.880 50.000 0.00 0.00 43.21 3.77
20 21 0.744281 AAAAACTGCCACTCGGTTGG 59.256 50.000 0.00 0.00 43.21 3.77
21 22 0.106918 AAAACTGCCACTCGGTTGGA 60.107 50.000 7.35 0.00 43.21 3.53
22 23 0.110486 AAACTGCCACTCGGTTGGAT 59.890 50.000 7.35 0.00 43.21 3.41
23 24 0.321653 AACTGCCACTCGGTTGGATC 60.322 55.000 7.35 0.00 42.45 3.36
24 25 1.450312 CTGCCACTCGGTTGGATCC 60.450 63.158 4.20 4.20 39.24 3.36
32 33 4.713946 GGTTGGATCCGACAGCAA 57.286 55.556 29.59 5.17 32.12 3.91
33 34 2.171635 GGTTGGATCCGACAGCAAC 58.828 57.895 29.59 16.34 32.12 4.17
34 35 0.321653 GGTTGGATCCGACAGCAACT 60.322 55.000 29.59 0.00 32.12 3.16
35 36 1.066430 GGTTGGATCCGACAGCAACTA 60.066 52.381 29.59 0.00 32.12 2.24
36 37 2.000447 GTTGGATCCGACAGCAACTAC 59.000 52.381 25.05 0.00 0.00 2.73
473 558 2.706190 GGCCTCCTTGCTTCTATTCCTA 59.294 50.000 0.00 0.00 0.00 2.94
726 815 8.601546 AGAGGTCTCAGATTTGACTAAATTCTT 58.398 33.333 0.55 0.00 36.66 2.52
886 975 5.243730 TCATAGCTATTGGATCATCACGTGA 59.756 40.000 22.48 22.48 42.06 4.35
1427 1555 5.247110 AGTCAAACAGAAGGAGCAAGATCTA 59.753 40.000 0.00 0.00 0.00 1.98
1714 1842 6.942532 TGATTGTTCTAAGCAAGTCTTTGT 57.057 33.333 0.00 0.00 36.65 2.83
2043 2171 2.949451 AGTGCTACTGATGACTTCCG 57.051 50.000 0.00 0.00 0.00 4.30
2108 2236 2.617532 GCTGCCATTGAGGAGAAGAAGT 60.618 50.000 0.00 0.00 41.22 3.01
2148 2276 5.388111 CATCAACAAGTGTATCACAGCAAG 58.612 41.667 2.80 0.00 36.74 4.01
2456 2584 9.563748 TGGTTTAGTATATTTTGGTAGGTATGC 57.436 33.333 0.00 0.00 0.00 3.14
3136 3271 1.483827 TCTTGCATCTGAAGCCGATCT 59.516 47.619 2.09 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.269051 CCAACCGAGTGGCAGTTTTTC 60.269 52.381 0.00 0.00 39.70 2.29
2 3 0.106918 TCCAACCGAGTGGCAGTTTT 60.107 50.000 0.00 0.00 38.68 2.43
7 8 2.668632 GGATCCAACCGAGTGGCA 59.331 61.111 6.95 0.00 38.68 4.92
15 16 0.321653 AGTTGCTGTCGGATCCAACC 60.322 55.000 13.41 0.00 38.58 3.77
16 17 2.000447 GTAGTTGCTGTCGGATCCAAC 59.000 52.381 13.41 3.67 38.20 3.77
17 18 1.899814 AGTAGTTGCTGTCGGATCCAA 59.100 47.619 13.41 0.00 0.00 3.53
18 19 1.476891 GAGTAGTTGCTGTCGGATCCA 59.523 52.381 13.41 0.00 0.00 3.41
19 20 1.751924 AGAGTAGTTGCTGTCGGATCC 59.248 52.381 0.00 0.00 0.00 3.36
20 21 3.512033 AAGAGTAGTTGCTGTCGGATC 57.488 47.619 0.00 0.00 0.00 3.36
21 22 4.270834 TCTAAGAGTAGTTGCTGTCGGAT 58.729 43.478 0.00 0.00 0.00 4.18
22 23 3.682696 TCTAAGAGTAGTTGCTGTCGGA 58.317 45.455 0.00 0.00 0.00 4.55
23 24 3.732471 GCTCTAAGAGTAGTTGCTGTCGG 60.732 52.174 0.00 0.00 31.39 4.79
24 25 3.127895 AGCTCTAAGAGTAGTTGCTGTCG 59.872 47.826 1.90 0.00 37.09 4.35
25 26 4.439563 GGAGCTCTAAGAGTAGTTGCTGTC 60.440 50.000 14.64 0.00 37.89 3.51
26 27 3.445805 GGAGCTCTAAGAGTAGTTGCTGT 59.554 47.826 14.64 0.00 37.89 4.40
27 28 3.699038 AGGAGCTCTAAGAGTAGTTGCTG 59.301 47.826 14.64 0.00 37.89 4.41
28 29 3.976015 AGGAGCTCTAAGAGTAGTTGCT 58.024 45.455 14.64 2.09 39.27 3.91
29 30 4.729227 AAGGAGCTCTAAGAGTAGTTGC 57.271 45.455 14.64 0.00 31.39 4.17
30 31 6.274157 TCAAAGGAGCTCTAAGAGTAGTTG 57.726 41.667 14.64 5.35 31.39 3.16
31 32 7.179338 TGAATCAAAGGAGCTCTAAGAGTAGTT 59.821 37.037 14.64 0.00 31.39 2.24
32 33 6.665680 TGAATCAAAGGAGCTCTAAGAGTAGT 59.334 38.462 14.64 0.00 31.39 2.73
33 34 7.106439 TGAATCAAAGGAGCTCTAAGAGTAG 57.894 40.000 14.64 0.00 31.39 2.57
34 35 7.418368 CCATGAATCAAAGGAGCTCTAAGAGTA 60.418 40.741 14.64 0.00 31.39 2.59
35 36 6.347696 CATGAATCAAAGGAGCTCTAAGAGT 58.652 40.000 14.64 6.20 31.39 3.24
36 37 5.759273 CCATGAATCAAAGGAGCTCTAAGAG 59.241 44.000 14.64 0.62 0.00 2.85
161 236 5.492524 TCCTGTGAAATAGAGAAGGGGAAAT 59.507 40.000 0.00 0.00 0.00 2.17
210 285 1.710244 TTCCTGCCAGGATTCTTTCCA 59.290 47.619 15.62 0.00 45.34 3.53
262 344 4.636975 GCGTTTATTTACCGCGAAAACTA 58.363 39.130 8.23 0.00 37.89 2.24
473 558 5.431765 CTTGTTGCTGGACTTCCTATACAT 58.568 41.667 0.00 0.00 36.82 2.29
902 1000 4.479158 AGGGAAATTTTAGTGCCTTGTGA 58.521 39.130 0.00 0.00 30.11 3.58
1714 1842 7.718314 TCAGCATAACGACCTAGAGAATAGTTA 59.282 37.037 0.00 0.00 0.00 2.24
2081 2209 3.167485 TCTCCTCAATGGCAGCAAATTT 58.833 40.909 0.00 0.00 35.26 1.82
2082 2210 2.811410 TCTCCTCAATGGCAGCAAATT 58.189 42.857 0.00 0.00 35.26 1.82
2108 2236 2.023404 TGATGCTGTAGGGGTCCTCTAA 60.023 50.000 0.00 0.00 34.61 2.10
2148 2276 2.038557 TGTAGACCTTCCAAGCCTTCAC 59.961 50.000 0.00 0.00 0.00 3.18
2456 2584 3.486383 TGCCTAACCAAAAGTCTCAAGG 58.514 45.455 0.00 0.00 0.00 3.61
2458 2586 3.255642 GCATGCCTAACCAAAAGTCTCAA 59.744 43.478 6.36 0.00 0.00 3.02
2459 2587 2.819608 GCATGCCTAACCAAAAGTCTCA 59.180 45.455 6.36 0.00 0.00 3.27
3136 3271 1.303561 GTGCATGCTGGTTGGGAGA 60.304 57.895 20.33 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.