Multiple sequence alignment - TraesCS7A01G340600

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 TraesCS7A01G340600 chr7A 100.000 3266 0 0 1 3266 499950718 499953983 0 6032
1 TraesCS7A01G340600 chr7A 95.693 3274 129 7 1 3266 93310871 93314140 0 5254
2 TraesCS7A01G340600 chr7A 93.464 3305 175 12 1 3266 493726512 493729814 0 4868
3 TraesCS7A01G340600 chr2A 96.026 3271 119 6 1 3266 697151050 697154314 0 5310
4 TraesCS7A01G340600 chr2A 95.873 3271 128 6 1 3266 53575674 53572406 0 5286
5 TraesCS7A01G340600 chr5A 95.963 3270 123 6 1 3266 689846372 689843108 0 5299
6 TraesCS7A01G340600 chr6A 95.874 3272 127 8 1 3266 594022897 594026166 0 5288
7 TraesCS7A01G340600 chr1A 95.503 3269 140 6 3 3266 118198333 118195067 0 5216
8 TraesCS7A01G340600 chr3A 95.964 3097 118 5 173 3266 535603338 535606430 0 5020
9 TraesCS7A01G340600 chr6D 93.489 3302 174 13 2 3266 437005274 437008571 0 4868


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 TraesCS7A01G340600 chr7A 499950718 499953983 3265 False 6032 6032 100.000 1 3266 1 chr7A.!!$F3 3265
1 TraesCS7A01G340600 chr7A 93310871 93314140 3269 False 5254 5254 95.693 1 3266 1 chr7A.!!$F1 3265
2 TraesCS7A01G340600 chr7A 493726512 493729814 3302 False 4868 4868 93.464 1 3266 1 chr7A.!!$F2 3265
3 TraesCS7A01G340600 chr2A 697151050 697154314 3264 False 5310 5310 96.026 1 3266 1 chr2A.!!$F1 3265
4 TraesCS7A01G340600 chr2A 53572406 53575674 3268 True 5286 5286 95.873 1 3266 1 chr2A.!!$R1 3265
5 TraesCS7A01G340600 chr5A 689843108 689846372 3264 True 5299 5299 95.963 1 3266 1 chr5A.!!$R1 3265
6 TraesCS7A01G340600 chr6A 594022897 594026166 3269 False 5288 5288 95.874 1 3266 1 chr6A.!!$F1 3265
7 TraesCS7A01G340600 chr1A 118195067 118198333 3266 True 5216 5216 95.503 3 3266 1 chr1A.!!$R1 3263
8 TraesCS7A01G340600 chr3A 535603338 535606430 3092 False 5020 5020 95.964 173 3266 1 chr3A.!!$F1 3093
9 TraesCS7A01G340600 chr6D 437005274 437008571 3297 False 4868 4868 93.489 2 3266 1 chr6D.!!$F1 3264

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
821 847 0.944311 AACGACGAGCGCATGTCTTT 60.944 50.000 23.71 19.39 46.04 2.52 F
1175 1205 1.004044 CACCAGCAATCCTGAGGAAGT 59.996 52.381 4.76 0.00 44.64 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 1914 0.605589 GCCGGCAAAGGTGTAGAACT 60.606 55.0 24.8 0.0 0.00 3.01 R
2803 2843 1.188219 TCCAGGTGCCTCTCTCACAC 61.188 60.0 0.0 0.0 36.22 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
58 64 2.030562 CCGGCGGTGTTGAAGTCT 59.969 61.111 19.97 0.00 0.00 3.24
69 75 3.063452 GTGTTGAAGTCTTTGCTTCGTCA 59.937 43.478 0.00 0.00 45.67 4.35
124 130 4.529109 TCGTTTGATGGTGTGTATCTCA 57.471 40.909 0.00 0.00 0.00 3.27
218 234 7.870445 GTGTAATGAACCTATGAGGAGATCTTC 59.130 40.741 0.00 0.00 37.67 2.87
224 240 4.892934 ACCTATGAGGAGATCTTCTGTGAC 59.107 45.833 8.74 0.00 37.67 3.67
327 343 4.212004 CCGTATGTAATCTTCGACGGTCTA 59.788 45.833 6.57 0.00 43.69 2.59
396 422 2.747989 TCTTAGTAGACGTGTGAGGCAG 59.252 50.000 0.00 0.00 0.00 4.85
430 456 2.159099 TCTACAGGCATCGATGTTGGAC 60.159 50.000 25.47 9.15 0.00 4.02
503 529 3.282021 GGGCATGCATCTGAAGACTTAA 58.718 45.455 21.36 0.00 0.00 1.85
506 532 5.279384 GGCATGCATCTGAAGACTTAATTG 58.721 41.667 21.36 0.00 0.00 2.32
801 827 2.539338 GGTTGCCTCGACGCACAAA 61.539 57.895 8.67 0.00 38.83 2.83
821 847 0.944311 AACGACGAGCGCATGTCTTT 60.944 50.000 23.71 19.39 46.04 2.52
1096 1126 2.338620 CCGGTCAGAAGCACGACA 59.661 61.111 0.00 0.00 33.66 4.35
1175 1205 1.004044 CACCAGCAATCCTGAGGAAGT 59.996 52.381 4.76 0.00 44.64 3.01
1238 1268 1.731433 TACCCTCACTACATCGGCGC 61.731 60.000 0.00 0.00 0.00 6.53
1374 1404 4.351111 ACCATCCTACAGTTTCAACCTCTT 59.649 41.667 0.00 0.00 0.00 2.85
1500 1530 4.687901 TGAACTTGACTCACCAGATCAA 57.312 40.909 0.00 0.00 0.00 2.57
1600 1630 8.645487 CGTACTTTCTGTTCTAGTGTATTTTCC 58.355 37.037 0.00 0.00 0.00 3.13
1904 1938 0.179015 TACACCTTTGCCGGCTTCAA 60.179 50.000 29.70 16.43 0.00 2.69
1982 2016 2.860690 TACGTCGACATCCAGCGCAC 62.861 60.000 17.16 0.00 0.00 5.34
2082 2117 9.823647 TTCTACAAACAGATGAAGGATAAGATC 57.176 33.333 0.00 0.00 0.00 2.75
2115 2150 2.926329 AGACCATAAACTGTGGGGGATT 59.074 45.455 0.00 0.00 41.14 3.01
2388 2423 8.083828 AGGAGTTTGTAATGTCATCTGTATCT 57.916 34.615 0.00 0.00 0.00 1.98
2704 2739 1.906105 GAGGCACGTGGATGGGGTAA 61.906 60.000 18.88 0.00 0.00 2.85
2803 2843 1.800805 AAGAGTCATGGCAAGTGTCG 58.199 50.000 0.00 0.00 0.00 4.35
3003 3044 2.694829 AAGTGTCTCGTGGCGTGACC 62.695 60.000 17.14 10.70 45.65 4.02
3038 3079 1.373748 GCAGTTACGGAAGGCACGA 60.374 57.895 3.38 0.00 34.93 4.35
3054 3095 0.396811 ACGAAGGTGAAGACCCAAGG 59.603 55.000 0.00 0.00 44.40 3.61
3069 3110 1.048160 CAAGGGGCACAAAAGTGGGT 61.048 55.000 0.00 0.00 0.00 4.51
3141 3201 5.345702 CGAATACGAATTTAGGGAGTCACA 58.654 41.667 0.00 0.00 42.66 3.58
3242 3302 3.686691 GCTCTTAACCCTCTGGATGCATT 60.687 47.826 0.00 0.00 34.81 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 45 4.555709 ACTTCAACACCGCCGGCA 62.556 61.111 28.98 0.53 0.00 5.69
58 64 1.338674 ACCCGATGATGACGAAGCAAA 60.339 47.619 0.00 0.00 0.00 3.68
69 75 1.913419 ACAAAGTACCCACCCGATGAT 59.087 47.619 0.00 0.00 0.00 2.45
124 130 1.541672 CCAACCACCCTCCCACTTT 59.458 57.895 0.00 0.00 0.00 2.66
218 234 3.130633 TCGAAACATTCCACAGTCACAG 58.869 45.455 0.00 0.00 0.00 3.66
224 240 4.618489 GCAAAATCTCGAAACATTCCACAG 59.382 41.667 0.00 0.00 0.00 3.66
327 343 7.968405 GGCGACACAAATCTTGATACTAAAATT 59.032 33.333 0.00 0.00 0.00 1.82
396 422 1.139853 CCTGTAGAGCCTGATGTTCCC 59.860 57.143 0.00 0.00 0.00 3.97
419 445 3.007506 TGCCTCTAAAAGTCCAACATCGA 59.992 43.478 0.00 0.00 0.00 3.59
423 449 3.476552 CAGTGCCTCTAAAAGTCCAACA 58.523 45.455 0.00 0.00 0.00 3.33
430 456 5.491982 AGTTGATACCAGTGCCTCTAAAAG 58.508 41.667 0.00 0.00 0.00 2.27
503 529 2.169832 CACAACCGTGACTCTCCAAT 57.830 50.000 0.00 0.00 46.80 3.16
560 586 1.212751 CCGACGCATCACTCTCACA 59.787 57.895 0.00 0.00 0.00 3.58
801 827 0.944311 AAGACATGCGCTCGTCGTTT 60.944 50.000 19.42 10.04 41.07 3.60
821 847 1.748122 GTCGTGGTAGAGAGGGCGA 60.748 63.158 0.00 0.00 0.00 5.54
910 936 6.877611 ACAATAGTGTTTTCGGAATTGAGT 57.122 33.333 5.32 0.00 32.58 3.41
997 1027 4.096190 CAGATGGTTCCTCTGCCATTAT 57.904 45.455 0.00 0.00 44.73 1.28
1005 1035 0.034670 GCTTGGCAGATGGTTCCTCT 60.035 55.000 0.00 0.00 0.00 3.69
1096 1126 2.301346 CTCCTTGAGGTGCACTTTGTT 58.699 47.619 17.98 0.00 36.34 2.83
1175 1205 4.743057 ATCCTGTTGATCATCTTGTCGA 57.257 40.909 0.00 0.00 0.00 4.20
1198 1228 1.140312 AAGCCACAGACCCTCTTCAA 58.860 50.000 0.00 0.00 0.00 2.69
1238 1268 3.487372 TCCCTGGTATACTCGACATCAG 58.513 50.000 2.25 0.00 0.00 2.90
1374 1404 8.779303 TGAAAAGATAATTAAACAGAAGCACGA 58.221 29.630 0.00 0.00 0.00 4.35
1789 1820 7.940850 TCATCAAGTATCGATCAAGTACATGA 58.059 34.615 0.00 2.84 32.69 3.07
1880 1914 0.605589 GCCGGCAAAGGTGTAGAACT 60.606 55.000 24.80 0.00 0.00 3.01
1904 1938 6.318144 CAGCATCTCTTTGTCACCTTCAATAT 59.682 38.462 0.00 0.00 0.00 1.28
2052 2087 6.373005 TCCTTCATCTGTTTGTAGAATGGA 57.627 37.500 0.00 0.00 0.00 3.41
2082 2117 7.009631 CACAGTTTATGGTCTTCAACTCTATCG 59.990 40.741 0.00 0.00 0.00 2.92
2115 2150 1.638589 AGGTAATTTGGCAGTGGGCTA 59.361 47.619 0.00 0.00 44.01 3.93
2512 2547 7.761704 TGCTTTGCATTTTGTTGTTTTAGAGTA 59.238 29.630 0.00 0.00 31.71 2.59
2513 2548 6.593382 TGCTTTGCATTTTGTTGTTTTAGAGT 59.407 30.769 0.00 0.00 31.71 3.24
2514 2549 7.002816 TGCTTTGCATTTTGTTGTTTTAGAG 57.997 32.000 0.00 0.00 31.71 2.43
2515 2550 6.593382 ACTGCTTTGCATTTTGTTGTTTTAGA 59.407 30.769 0.00 0.00 38.13 2.10
2516 2551 6.774084 ACTGCTTTGCATTTTGTTGTTTTAG 58.226 32.000 0.00 0.00 38.13 1.85
2517 2552 6.593382 AGACTGCTTTGCATTTTGTTGTTTTA 59.407 30.769 0.00 0.00 38.13 1.52
2704 2739 6.836527 ACTATGTATTAGGAGCTCAACTCTGT 59.163 38.462 17.19 0.06 45.48 3.41
2803 2843 1.188219 TCCAGGTGCCTCTCTCACAC 61.188 60.000 0.00 0.00 36.22 3.82
2987 3027 3.986006 GGGTCACGCCACGAGACA 61.986 66.667 16.97 0.00 46.03 3.41
3003 3044 2.138320 CTGCATCTACGTGCCTAATGG 58.862 52.381 0.00 0.00 44.43 3.16
3038 3079 2.081585 GCCCCTTGGGTCTTCACCTT 62.082 60.000 4.84 0.00 46.51 3.50
3141 3201 4.345257 TGACTTTCTAGAGGCTTCACAACT 59.655 41.667 0.00 0.00 0.00 3.16
3159 3219 2.661866 GCCAGACACGCGTGACTT 60.662 61.111 42.94 23.47 33.60 3.01
3242 3302 2.207229 CCTCTCCGACCACACCACA 61.207 63.158 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.