Multiple sequence alignment - TraesCS4A01G156000

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 TraesCS4A01G156000 chr4A 100.000 2305 0 0 1 2305 310785484 310783180 0 4257
1 TraesCS4A01G156000 chr7B 95.844 2310 84 6 1 2305 663100878 663098576 0 3723
2 TraesCS4A01G156000 chr7B 95.498 2310 92 6 1 2305 662724951 662727253 0 3679
3 TraesCS4A01G156000 chr6D 95.844 2310 84 6 1 2305 389247275 389244973 0 3723
4 TraesCS4A01G156000 chr5D 95.758 2310 86 6 1 2305 503243819 503246121 0 3712
5 TraesCS4A01G156000 chr3D 95.711 2308 88 7 1 2305 589264976 589262677 0 3703
6 TraesCS4A01G156000 chr2A 95.671 2310 88 6 1 2305 726907908 726905606 0 3701
7 TraesCS4A01G156000 chr3A 95.669 2309 89 6 1 2305 66006585 66004284 0 3699
8 TraesCS4A01G156000 chr3B 95.413 2311 93 6 1 2305 201538068 201540371 0 3668
9 TraesCS4A01G156000 chr2B 95.327 2311 94 6 1 2305 474919477 474921779 0 3657


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 TraesCS4A01G156000 chr4A 310783180 310785484 2304 True 4257 4257 100.000 1 2305 1 chr4A.!!$R1 2304
1 TraesCS4A01G156000 chr7B 663098576 663100878 2302 True 3723 3723 95.844 1 2305 1 chr7B.!!$R1 2304
2 TraesCS4A01G156000 chr7B 662724951 662727253 2302 False 3679 3679 95.498 1 2305 1 chr7B.!!$F1 2304
3 TraesCS4A01G156000 chr6D 389244973 389247275 2302 True 3723 3723 95.844 1 2305 1 chr6D.!!$R1 2304
4 TraesCS4A01G156000 chr5D 503243819 503246121 2302 False 3712 3712 95.758 1 2305 1 chr5D.!!$F1 2304
5 TraesCS4A01G156000 chr3D 589262677 589264976 2299 True 3703 3703 95.711 1 2305 1 chr3D.!!$R1 2304
6 TraesCS4A01G156000 chr2A 726905606 726907908 2302 True 3701 3701 95.671 1 2305 1 chr2A.!!$R1 2304
7 TraesCS4A01G156000 chr3A 66004284 66006585 2301 True 3699 3699 95.669 1 2305 1 chr3A.!!$R1 2304
8 TraesCS4A01G156000 chr3B 201538068 201540371 2303 False 3668 3668 95.413 1 2305 1 chr3B.!!$F1 2304
9 TraesCS4A01G156000 chr2B 474919477 474921779 2302 False 3657 3657 95.327 1 2305 1 chr2B.!!$F1 2304

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
98 99 0.038892 TCGTGTCGTAAGGTCTTGGC 60.039 55.0 0.0 0.0 38.47 4.52 F
307 308 0.250166 ACTCCAAAAACCCGTCCTCG 60.250 55.0 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 1208 0.249911 AACCTCAACCTGTGCTCGAC 60.250 55.0 0.0 0.0 0.00 4.20 R
2215 2223 0.115745 AGTTCCTACGGGGTGGAGAA 59.884 55.0 0.0 0.0 36.25 2.87 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
47 48 2.612746 GGGGTGCCCTAGGGAACA 60.613 66.667 35.94 21.13 45.77 3.18
93 94 0.520404 TCAGCTCGTGTCGTAAGGTC 59.480 55.000 0.00 0.00 38.47 3.85
98 99 0.038892 TCGTGTCGTAAGGTCTTGGC 60.039 55.000 0.00 0.00 38.47 4.52
150 151 6.371389 GTGTTTAGTTGCCACTATGAGTTTC 58.629 40.000 0.00 0.00 35.32 2.78
158 159 3.118884 GCCACTATGAGTTTCGAACCCTA 60.119 47.826 0.00 0.00 0.00 3.53
226 227 0.901580 CATCATGCCCCTTATGCCCC 60.902 60.000 0.00 0.00 0.00 5.80
239 240 3.884774 GCCCCTGGGTGACACACA 61.885 66.667 10.75 10.75 35.86 3.72
265 266 2.380571 AATGGGCGGGACAAAGGGTT 62.381 55.000 0.00 0.00 0.00 4.11
307 308 0.250166 ACTCCAAAAACCCGTCCTCG 60.250 55.000 0.00 0.00 0.00 4.63
318 319 1.214589 CGTCCTCGGTTCGGATTGT 59.785 57.895 0.00 0.00 32.25 2.71
367 368 0.672342 ATCGCTAGTAATCGCCGGTT 59.328 50.000 1.90 0.00 0.00 4.44
409 411 1.063070 TCCTGGGCCTTTACACACCA 61.063 55.000 4.53 0.00 0.00 4.17
496 498 1.544825 AAGGCTAGGCTTGCGACTGA 61.545 55.000 29.03 0.00 0.00 3.41
648 650 4.745649 ACGTCTGAGCTAAACTTGGATAC 58.254 43.478 0.00 0.00 0.00 2.24
799 801 2.539302 CATGGGGGTGTCAAAAGGAAT 58.461 47.619 0.00 0.00 0.00 3.01
960 962 6.892485 TGGATAGTTCAATGTGATCATCAGT 58.108 36.000 0.00 0.00 32.56 3.41
965 967 3.538591 TCAATGTGATCATCAGTGCCTC 58.461 45.455 16.00 0.00 32.56 4.70
1054 1056 4.095782 TGAAACCAAACAAACTTCTCCTCG 59.904 41.667 0.00 0.00 0.00 4.63
1058 1060 3.412386 CAAACAAACTTCTCCTCGGGAT 58.588 45.455 0.00 0.00 0.00 3.85
1123 1125 3.026707 TCTATTCACTCGTGGGATCCA 57.973 47.619 15.23 0.00 0.00 3.41
1165 1172 2.031508 CGGCTCCTCTATTCTCGAGAAC 60.032 54.545 29.24 13.93 36.80 3.01
1201 1208 5.981088 ATCAGTGTATGGAGAGCTATCTG 57.019 43.478 8.50 0.00 35.30 2.90
1222 1229 0.249868 CGAGCACAGGTTGAGGTTCA 60.250 55.000 0.00 0.00 0.00 3.18
1276 1283 3.434984 GCATCTTCACAGACCAAGAACTC 59.565 47.826 0.00 0.00 32.40 3.01
1298 1305 3.388024 CCGAGATCACCCCTTTCATTCTA 59.612 47.826 0.00 0.00 0.00 2.10
1327 1334 2.228059 GAGGGATCGTACCATTCGAGA 58.772 52.381 0.00 0.00 40.57 4.04
1329 1336 1.000496 GGGATCGTACCATTCGAGACC 60.000 57.143 0.00 0.00 40.57 3.85
1346 1354 4.022849 CGAGACCTTTTTCATGCTTTTCCT 60.023 41.667 0.00 0.00 0.00 3.36
1365 1373 1.302511 GGCGGTCTGGAGAAAGCAA 60.303 57.895 6.85 0.00 32.63 3.91
1438 1446 8.933653 TGAAATTCTTTTTCCTTAAATGGGAGT 58.066 29.630 0.00 0.00 34.06 3.85
1479 1487 5.044030 AGGATCTTAGAGTGTCTAGGGTTGA 60.044 44.000 0.00 0.00 29.56 3.18
1543 1551 4.079253 GAGTTATTTCCCAAGGACTTGCA 58.921 43.478 6.54 0.00 39.16 4.08
1548 1556 0.482446 TCCCAAGGACTTGCAATGGT 59.518 50.000 13.57 3.32 39.16 3.55
1549 1557 1.707989 TCCCAAGGACTTGCAATGGTA 59.292 47.619 13.57 0.00 39.16 3.25
1588 1596 1.202580 AGAAGCACACTTGAAGAGCGT 60.203 47.619 0.00 0.00 35.82 5.07
1615 1623 1.220749 GGGGAGTTGTATGCTGCGA 59.779 57.895 0.00 0.00 0.00 5.10
1617 1625 1.668419 GGGAGTTGTATGCTGCGATT 58.332 50.000 0.00 0.00 0.00 3.34
1685 1693 1.202099 TTGGTTGGATCGTAGGGGCA 61.202 55.000 0.00 0.00 0.00 5.36
1704 1712 2.163412 GCAATGATTTACTTCACGGGCA 59.837 45.455 0.00 0.00 0.00 5.36
1709 1717 3.008157 TGATTTACTTCACGGGCAAGGTA 59.992 43.478 2.66 0.00 0.00 3.08
1711 1719 3.706600 TTACTTCACGGGCAAGGTATT 57.293 42.857 2.66 0.00 0.00 1.89
1723 1731 3.826729 GGCAAGGTATTTGGTTCAAGTCT 59.173 43.478 0.00 0.00 37.26 3.24
1740 1748 2.691996 TAGGATGGCCCAGCTGCA 60.692 61.111 8.66 0.81 37.41 4.41
1866 1874 0.038435 TCGTTGCGATTACGGGTTGA 60.038 50.000 0.00 0.00 39.38 3.18
1913 1921 7.914427 ATGATAGTATCTTGTACCTGAACCA 57.086 36.000 11.40 0.00 0.00 3.67
1959 1967 2.553028 GGGAAGAGGACTGAAACATGCA 60.553 50.000 0.00 0.00 0.00 3.96
1962 1970 2.508526 AGAGGACTGAAACATGCAACC 58.491 47.619 0.00 0.00 0.00 3.77
1967 1975 3.490078 GGACTGAAACATGCAACCGAAAA 60.490 43.478 0.00 0.00 0.00 2.29
2001 2009 5.070847 AGACAAAAAGATGGGCTGTCAAAAT 59.929 36.000 3.61 0.00 39.08 1.82
2020 2028 4.561254 AATGGTAGAGGAGGTAGGATGT 57.439 45.455 0.00 0.00 0.00 3.06
2028 2036 1.279271 GGAGGTAGGATGTGCAGTTGT 59.721 52.381 0.00 0.00 0.00 3.32
2032 2040 3.009473 AGGTAGGATGTGCAGTTGTTCAT 59.991 43.478 0.00 0.00 0.00 2.57
2054 2062 7.931275 TCATATCTAGTATGGATCGTACATGC 58.069 38.462 8.91 1.28 40.52 4.06
2123 2131 3.115390 CCCTGGGGAAGAAGATCAAGTA 58.885 50.000 4.27 0.00 37.50 2.24
2126 2134 4.033709 CTGGGGAAGAAGATCAAGTAGGA 58.966 47.826 0.00 0.00 0.00 2.94
2171 2179 2.701551 TCTCCCTTCAACCCTTTGAGA 58.298 47.619 0.00 0.00 42.79 3.27
2206 2214 2.654385 AGGAAGGAAAATCCATGGACCA 59.346 45.455 18.99 0.00 39.61 4.02
2208 2216 3.448660 GGAAGGAAAATCCATGGACCAAG 59.551 47.826 18.99 0.00 39.61 3.61
2215 2223 0.413037 TCCATGGACCAAGCCCATTT 59.587 50.000 11.44 0.00 42.18 2.32
2277 2285 3.681835 GGCGTCCAGGAGTCACGT 61.682 66.667 0.00 0.00 35.91 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.401738 CACCTGTGTCCATGTTCCCT 59.598 55.000 0.00 0.00 0.00 4.20
84 85 3.830755 AGACTTAAGCCAAGACCTTACGA 59.169 43.478 1.29 0.00 37.71 3.43
93 94 1.126846 CGTTGCGAGACTTAAGCCAAG 59.873 52.381 1.29 0.00 40.38 3.61
150 151 1.017701 GGCGGTCTGTTTAGGGTTCG 61.018 60.000 0.00 0.00 0.00 3.95
158 159 0.179051 TTAACACCGGCGGTCTGTTT 60.179 50.000 31.32 22.61 31.02 2.83
226 227 1.270785 TGTAGCATGTGTGTCACCCAG 60.271 52.381 0.00 0.00 32.73 4.45
239 240 1.152963 GTCCCGCCCATTGTAGCAT 60.153 57.895 0.00 0.00 0.00 3.79
307 308 0.392461 TGCAGCCTACAATCCGAACC 60.392 55.000 0.00 0.00 0.00 3.62
393 394 1.151908 GGTGGTGTGTAAAGGCCCA 59.848 57.895 0.00 0.00 0.00 5.36
409 411 1.063867 AGCTCCTATAGTGTGACGGGT 60.064 52.381 0.00 0.00 0.00 5.28
496 498 4.304939 GCTACCTTGTTACGACTTCACTT 58.695 43.478 0.00 0.00 0.00 3.16
648 650 5.122396 CACCCTAAATGAAAGAAGACTTCCG 59.878 44.000 11.67 0.00 35.05 4.30
786 788 3.430453 TCCATCCCATTCCTTTTGACAC 58.570 45.455 0.00 0.00 0.00 3.67
799 801 3.644966 AGCGATAAAAACTCCATCCCA 57.355 42.857 0.00 0.00 0.00 4.37
952 954 0.977627 TCGGGTGAGGCACTGATGAT 60.978 55.000 0.00 0.00 41.55 2.45
960 962 1.296392 CACATCTTCGGGTGAGGCA 59.704 57.895 0.00 0.00 37.18 4.75
965 967 2.627515 ATGATCCACATCTTCGGGTG 57.372 50.000 0.00 0.00 33.46 4.61
1054 1056 1.207791 ATCGCCCCATCTATCATCCC 58.792 55.000 0.00 0.00 0.00 3.85
1058 1060 1.625315 CCTGAATCGCCCCATCTATCA 59.375 52.381 0.00 0.00 0.00 2.15
1154 1161 3.325135 GGGATGTATGGGTTCTCGAGAAT 59.675 47.826 29.29 16.55 36.33 2.40
1165 1172 4.982241 ACACTGATAAGGGATGTATGGG 57.018 45.455 0.00 0.00 0.00 4.00
1201 1208 0.249911 AACCTCAACCTGTGCTCGAC 60.250 55.000 0.00 0.00 0.00 4.20
1222 1229 3.303049 GCTCCATTTTCCCATTGAGGAT 58.697 45.455 0.00 0.00 41.22 3.24
1276 1283 2.171448 AGAATGAAAGGGGTGATCTCGG 59.829 50.000 0.00 0.00 0.00 4.63
1298 1305 0.561184 TACGATCCCTCCATCACCCT 59.439 55.000 0.00 0.00 0.00 4.34
1305 1312 1.037493 CGAATGGTACGATCCCTCCA 58.963 55.000 0.00 0.93 0.00 3.86
1327 1334 3.494924 GCCAGGAAAAGCATGAAAAAGGT 60.495 43.478 0.00 0.00 0.00 3.50
1329 1336 2.733026 CGCCAGGAAAAGCATGAAAAAG 59.267 45.455 0.00 0.00 0.00 2.27
1346 1354 2.050836 TTGCTTTCTCCAGACCGCCA 62.051 55.000 0.00 0.00 0.00 5.69
1438 1446 5.880901 AGATCCTTTTTCAAACCTGCTCTA 58.119 37.500 0.00 0.00 0.00 2.43
1479 1487 1.574263 GTTAAGAGACCCTCCTGGCT 58.426 55.000 0.00 0.00 37.83 4.75
1543 1551 4.243643 CCCCTTCTCCCTCTTATACCATT 58.756 47.826 0.00 0.00 0.00 3.16
1548 1556 3.803644 TCTTCCCCCTTCTCCCTCTTATA 59.196 47.826 0.00 0.00 0.00 0.98
1549 1557 2.597304 TCTTCCCCCTTCTCCCTCTTAT 59.403 50.000 0.00 0.00 0.00 1.73
1615 1623 3.117360 GGGAGTGATTCATCCTTCCCAAT 60.117 47.826 15.85 0.00 42.99 3.16
1617 1625 1.846439 GGGAGTGATTCATCCTTCCCA 59.154 52.381 15.85 0.00 42.99 4.37
1685 1693 3.443681 CCTTGCCCGTGAAGTAAATCATT 59.556 43.478 0.00 0.00 0.00 2.57
1704 1712 6.697641 TCCTAGACTTGAACCAAATACCTT 57.302 37.500 0.00 0.00 0.00 3.50
1709 1717 4.273318 GCCATCCTAGACTTGAACCAAAT 58.727 43.478 0.00 0.00 0.00 2.32
1711 1719 2.026262 GGCCATCCTAGACTTGAACCAA 60.026 50.000 0.00 0.00 0.00 3.67
1723 1731 2.691996 TGCAGCTGGGCCATCCTA 60.692 61.111 17.12 0.00 36.20 2.94
1740 1748 5.222130 TGCTTCTTCTATTCTTTTCCCTGGT 60.222 40.000 0.00 0.00 0.00 4.00
1804 1812 1.508256 ACCAACTGAGCTATACCCCC 58.492 55.000 0.00 0.00 0.00 5.40
1805 1813 3.573695 TCTACCAACTGAGCTATACCCC 58.426 50.000 0.00 0.00 0.00 4.95
1806 1814 4.857509 CTCTACCAACTGAGCTATACCC 57.142 50.000 0.00 0.00 0.00 3.69
1866 1874 1.066143 CCGCCTGGACAATTAGACAGT 60.066 52.381 0.00 0.00 37.49 3.55
1959 1967 5.272283 TGTCTCAGTAGAGTTTTTCGGTT 57.728 39.130 0.00 0.00 42.66 4.44
1962 1970 7.906160 TCTTTTTGTCTCAGTAGAGTTTTTCG 58.094 34.615 0.00 0.00 42.66 3.46
1967 1975 6.234177 CCCATCTTTTTGTCTCAGTAGAGTT 58.766 40.000 0.00 0.00 42.66 3.01
2001 2009 2.690026 GCACATCCTACCTCCTCTACCA 60.690 54.545 0.00 0.00 0.00 3.25
2020 2028 7.360113 TCCATACTAGATATGAACAACTGCA 57.640 36.000 0.00 0.00 43.12 4.41
2028 2036 8.406297 GCATGTACGATCCATACTAGATATGAA 58.594 37.037 0.00 0.00 43.12 2.57
2032 2040 6.183360 CGTGCATGTACGATCCATACTAGATA 60.183 42.308 29.28 0.00 46.46 1.98
2054 2062 0.866061 CGCCGACTCCAACTATCGTG 60.866 60.000 0.00 0.00 34.02 4.35
2123 2131 3.695830 TCAAGTTATTCGCAAGGTCCT 57.304 42.857 0.00 0.00 38.47 3.85
2126 2134 3.081061 TGCATCAAGTTATTCGCAAGGT 58.919 40.909 0.00 0.00 38.47 3.50
2171 2179 6.976934 TTTCCTTCCTTTTGCTACATTTCT 57.023 33.333 0.00 0.00 0.00 2.52
2206 2214 0.252239 GGGGTGGAGAAAATGGGCTT 60.252 55.000 0.00 0.00 0.00 4.35
2208 2216 2.052104 CGGGGTGGAGAAAATGGGC 61.052 63.158 0.00 0.00 0.00 5.36
2215 2223 0.115745 AGTTCCTACGGGGTGGAGAA 59.884 55.000 0.00 0.00 36.25 2.87
2277 2285 2.291735 TGAACAGGGTCTATGGTCGGTA 60.292 50.000 0.00 0.00 37.18 4.02


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

AutoCloner maintained by Alex Coulton.