Multiple sequence alignment - TraesCS4D01G263600

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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 TraesCS4D01G263600 chr4D 100.000 2546 0 0 1 2546 434465883 434468428 0.000000e+00 4702.0
1 TraesCS4D01G263600 chr4A 90.185 2588 136 52 1 2546 36100081 36102592 0.000000e+00 3264.0
2 TraesCS4D01G263600 chr4B 89.710 2138 86 56 1 2062 534326164 534328243 0.000000e+00 2606.0
3 TraesCS4D01G263600 chr4B 92.906 437 21 4 2070 2498 534328283 534328717 5.980000e-176 627.0
4 TraesCS4D01G263600 chr6D 88.506 87 10 0 2389 2475 29776446 29776360 3.460000e-19 106.0
5 TraesCS4D01G263600 chr6D 88.506 87 10 0 2389 2475 29839410 29839324 3.460000e-19 106.0
6 TraesCS4D01G263600 chr6D 92.683 41 3 0 2437 2477 106891236 106891276 2.740000e-05 60.2
7 TraesCS4D01G263600 chr5D 87.640 89 9 2 2390 2477 547927431 547927518 4.480000e-18 102.0
8 TraesCS4D01G263600 chr7A 86.667 90 8 4 2390 2477 80757213 80757126 2.080000e-16 97.1
9 TraesCS4D01G263600 chr7A 87.805 82 9 1 2390 2470 692055739 692055658 7.500000e-16 95.3
10 TraesCS4D01G263600 chr3A 84.810 79 10 2 2400 2477 718940746 718940669 7.550000e-11 78.7


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 TraesCS4D01G263600 chr4D 434465883 434468428 2545 False 4702.0 4702 100.000 1 2546 1 chr4D.!!$F1 2545
1 TraesCS4D01G263600 chr4A 36100081 36102592 2511 False 3264.0 3264 90.185 1 2546 1 chr4A.!!$F1 2545
2 TraesCS4D01G263600 chr4B 534326164 534328717 2553 False 1616.5 2606 91.308 1 2498 2 chr4B.!!$F1 2497

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
174 181 0.035458 CTTGAGAAAGTGACGGCCCT 59.965 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1937 0.322997 AGGTCCCTCACTCACTCTCG 60.323 60.0 0.0 0.0 0.0 4.04 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
174 181 0.035458 CTTGAGAAAGTGACGGCCCT 59.965 55.000 0.00 0.00 0.00 5.19
238 248 0.625351 CGTACGTACTTGCGTCGAAC 59.375 55.000 22.55 0.00 44.55 3.95
255 266 2.286184 CGAACTTTTTGTGGAGTGGTCG 60.286 50.000 0.00 0.00 0.00 4.79
258 269 2.093128 ACTTTTTGTGGAGTGGTCGTCT 60.093 45.455 0.00 0.00 0.00 4.18
259 270 3.133362 ACTTTTTGTGGAGTGGTCGTCTA 59.867 43.478 0.00 0.00 0.00 2.59
260 271 2.806608 TTTGTGGAGTGGTCGTCTAC 57.193 50.000 0.00 0.00 0.00 2.59
261 272 1.991121 TTGTGGAGTGGTCGTCTACT 58.009 50.000 0.00 0.00 38.08 2.57
262 273 1.531423 TGTGGAGTGGTCGTCTACTC 58.469 55.000 15.82 15.82 46.71 2.59
788 857 0.039074 ATCGATTTAGGGCTCGCTCG 60.039 55.000 0.00 0.00 34.94 5.03
829 898 2.428171 CCACTGCCATTATTGGTTCCTG 59.572 50.000 5.58 0.00 45.57 3.86
900 969 3.053896 GAGTCAAAACCCCGCCCG 61.054 66.667 0.00 0.00 0.00 6.13
943 1016 2.363018 CCGCCCTCTCACCTCTCA 60.363 66.667 0.00 0.00 0.00 3.27
944 1017 2.716017 CCGCCCTCTCACCTCTCAC 61.716 68.421 0.00 0.00 0.00 3.51
945 1018 2.716017 CGCCCTCTCACCTCTCACC 61.716 68.421 0.00 0.00 0.00 4.02
946 1019 1.305718 GCCCTCTCACCTCTCACCT 60.306 63.158 0.00 0.00 0.00 4.00
947 1020 1.326951 GCCCTCTCACCTCTCACCTC 61.327 65.000 0.00 0.00 0.00 3.85
948 1021 0.334676 CCCTCTCACCTCTCACCTCT 59.665 60.000 0.00 0.00 0.00 3.69
949 1022 1.684869 CCCTCTCACCTCTCACCTCTC 60.685 61.905 0.00 0.00 0.00 3.20
1470 1558 4.944069 CTAGGAGGCGGGGGAGGG 62.944 77.778 0.00 0.00 0.00 4.30
1521 1609 1.515304 GTCGTCGCTGCTCTTCCTC 60.515 63.158 0.00 0.00 0.00 3.71
1530 1618 2.105466 GCTCTTCCTCTGCAAGCCG 61.105 63.158 0.00 0.00 0.00 5.52
1552 1640 2.672961 GGACGTGTCCTGATCAATGA 57.327 50.000 11.81 0.00 46.16 2.57
1553 1641 2.544685 GGACGTGTCCTGATCAATGAG 58.455 52.381 11.81 0.00 46.16 2.90
1554 1642 1.929836 GACGTGTCCTGATCAATGAGC 59.070 52.381 0.00 0.00 0.00 4.26
1555 1643 0.926155 CGTGTCCTGATCAATGAGCG 59.074 55.000 0.00 1.34 0.00 5.03
1556 1644 0.654683 GTGTCCTGATCAATGAGCGC 59.345 55.000 0.00 0.00 0.00 5.92
1557 1645 0.807275 TGTCCTGATCAATGAGCGCG 60.807 55.000 0.00 0.00 0.00 6.86
1558 1646 1.884464 TCCTGATCAATGAGCGCGC 60.884 57.895 26.66 26.66 0.00 6.86
1559 1647 2.630317 CTGATCAATGAGCGCGCC 59.370 61.111 30.33 19.97 0.00 6.53
1560 1648 3.219513 CTGATCAATGAGCGCGCCG 62.220 63.158 30.33 11.69 0.00 6.46
1561 1649 2.961721 GATCAATGAGCGCGCCGA 60.962 61.111 30.33 15.73 0.00 5.54
1562 1650 3.215606 GATCAATGAGCGCGCCGAC 62.216 63.158 30.33 19.93 0.00 4.79
1644 1784 3.370978 GGTTGACAATGACATAGTGGTCG 59.629 47.826 0.00 0.00 40.72 4.79
1765 1908 9.462174 GCATTGAATATGGAAATAAACGAATGA 57.538 29.630 0.00 0.00 0.00 2.57
1793 1937 7.387397 TCATTCTTTCTTTCTTTCTCAGAGAGC 59.613 37.037 0.00 0.00 34.30 4.09
1972 2119 1.293763 TGTGACCCCTCCATCCATCTA 59.706 52.381 0.00 0.00 0.00 1.98
1978 2125 2.383683 CCCCTCCATCCATCTACTCCTA 59.616 54.545 0.00 0.00 0.00 2.94
1979 2126 3.565449 CCCCTCCATCCATCTACTCCTAG 60.565 56.522 0.00 0.00 0.00 3.02
2036 2183 3.518998 CTCTCGCGACCGGGTGAT 61.519 66.667 3.71 0.00 36.05 3.06
2050 2197 1.770658 GGGTGATGGATGGATGAGTGA 59.229 52.381 0.00 0.00 0.00 3.41
2053 2200 1.770658 TGATGGATGGATGAGTGACCC 59.229 52.381 0.00 0.00 0.00 4.46
2062 2209 2.544685 GATGAGTGACCCGTGAATGAG 58.455 52.381 0.00 0.00 0.00 2.90
2064 2211 1.000843 TGAGTGACCCGTGAATGAGTG 59.999 52.381 0.00 0.00 0.00 3.51
2068 2215 2.350895 CCCGTGAATGAGTGGGCA 59.649 61.111 0.00 0.00 34.25 5.36
2156 2335 2.660258 ATACGGCTAGCCCCAAAGCG 62.660 60.000 28.09 16.20 39.71 4.68
2213 2400 0.886563 ACTGGCTGCTTTGATTGCTC 59.113 50.000 0.00 0.00 0.00 4.26
2235 2422 3.246226 CGATGTTTCTTTGGATAGCTCCG 59.754 47.826 0.00 0.00 45.37 4.63
2243 2433 1.621992 TGGATAGCTCCGACTGGATC 58.378 55.000 0.00 0.00 45.33 3.36
2348 2538 5.437060 GGCCTCCTTTAGTTCACATGATTA 58.563 41.667 0.00 0.00 0.00 1.75
2350 2540 7.224297 GGCCTCCTTTAGTTCACATGATTATA 58.776 38.462 0.00 0.00 0.00 0.98
2383 2573 3.065371 GGAAATGAATAGGGCTTGTCACG 59.935 47.826 0.00 0.00 0.00 4.35
2391 2581 0.818040 GGGCTTGTCACGGTGAAAGT 60.818 55.000 13.23 0.00 0.00 2.66
2397 2587 4.436050 GCTTGTCACGGTGAAAGTATCATG 60.436 45.833 13.23 8.67 40.97 3.07
2402 2592 3.374988 CACGGTGAAAGTATCATGCATGT 59.625 43.478 25.43 15.34 40.97 3.21
2409 2599 7.148255 GGTGAAAGTATCATGCATGTCAACTAA 60.148 37.037 25.43 5.50 40.97 2.24
2503 2693 1.680735 CTGCGATCTTCTACTGCCTCT 59.319 52.381 0.00 0.00 0.00 3.69
2514 2704 1.221021 CTGCCTCTACGTTTCCCCC 59.779 63.158 0.00 0.00 0.00 5.40
2537 2727 0.815615 CTTTCCCGGAGCCTATGTGC 60.816 60.000 0.73 0.00 0.00 4.57
2538 2728 2.587322 TTTCCCGGAGCCTATGTGCG 62.587 60.000 0.73 0.00 36.02 5.34
2539 2729 3.536917 CCCGGAGCCTATGTGCGA 61.537 66.667 0.73 0.00 36.02 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 140 2.559922 AAAATATGGGGGCGCCGTCA 62.560 55.000 22.54 21.09 0.00 4.35
174 181 8.545472 AGGTAGGCACACTGTTTAAATATAGAA 58.455 33.333 0.00 0.00 0.00 2.10
238 248 2.561569 AGACGACCACTCCACAAAAAG 58.438 47.619 0.00 0.00 0.00 2.27
255 266 4.320348 GGCGTACAGTGGATATGAGTAGAC 60.320 50.000 0.00 0.00 0.00 2.59
258 269 2.551032 CGGCGTACAGTGGATATGAGTA 59.449 50.000 0.00 0.00 0.00 2.59
259 270 1.337071 CGGCGTACAGTGGATATGAGT 59.663 52.381 0.00 0.00 0.00 3.41
260 271 1.607148 TCGGCGTACAGTGGATATGAG 59.393 52.381 6.85 0.00 0.00 2.90
261 272 1.335810 GTCGGCGTACAGTGGATATGA 59.664 52.381 6.85 0.00 0.00 2.15
262 273 1.767289 GTCGGCGTACAGTGGATATG 58.233 55.000 6.85 0.00 0.00 1.78
263 274 0.309922 CGTCGGCGTACAGTGGATAT 59.690 55.000 6.85 0.00 0.00 1.63
264 275 1.723273 CGTCGGCGTACAGTGGATA 59.277 57.895 6.85 0.00 0.00 2.59
265 276 2.488355 CGTCGGCGTACAGTGGAT 59.512 61.111 6.85 0.00 0.00 3.41
943 1016 3.547787 AAGGGAGGTGGCGAGAGGT 62.548 63.158 0.00 0.00 0.00 3.85
944 1017 2.685380 AAGGGAGGTGGCGAGAGG 60.685 66.667 0.00 0.00 0.00 3.69
945 1018 2.726351 GGAAGGGAGGTGGCGAGAG 61.726 68.421 0.00 0.00 0.00 3.20
946 1019 2.683933 GGAAGGGAGGTGGCGAGA 60.684 66.667 0.00 0.00 0.00 4.04
947 1020 3.787001 GGGAAGGGAGGTGGCGAG 61.787 72.222 0.00 0.00 0.00 5.03
948 1021 4.332543 AGGGAAGGGAGGTGGCGA 62.333 66.667 0.00 0.00 0.00 5.54
949 1022 2.873557 TAGAGGGAAGGGAGGTGGCG 62.874 65.000 0.00 0.00 0.00 5.69
1401 1489 1.747367 CGAGAGGGAGAGCGACAGT 60.747 63.158 0.00 0.00 0.00 3.55
1521 1609 4.988598 ACGTCCACCGGCTTGCAG 62.989 66.667 0.00 0.00 42.24 4.41
1564 1652 3.036084 GATCATACGGCCGGCGTG 61.036 66.667 31.76 23.40 0.00 5.34
1565 1653 4.295119 GGATCATACGGCCGGCGT 62.295 66.667 31.76 24.22 0.00 5.68
1583 1699 3.554692 CGCGACGGCATTGAGGAC 61.555 66.667 0.00 0.00 39.92 3.85
1618 1758 1.327460 CTATGTCATTGTCAACCGCGG 59.673 52.381 26.86 26.86 0.00 6.46
1765 1908 9.790344 TCTCTGAGAAAGAAAGAAAGAATGAAT 57.210 29.630 4.57 0.00 33.37 2.57
1766 1909 9.270640 CTCTCTGAGAAAGAAAGAAAGAATGAA 57.729 33.333 8.95 0.00 33.37 2.57
1767 1910 7.387397 GCTCTCTGAGAAAGAAAGAAAGAATGA 59.613 37.037 8.95 0.00 33.37 2.57
1768 1911 7.520686 GCTCTCTGAGAAAGAAAGAAAGAATG 58.479 38.462 8.95 0.00 33.37 2.67
1793 1937 0.322997 AGGTCCCTCACTCACTCTCG 60.323 60.000 0.00 0.00 0.00 4.04
1960 2106 6.134535 AGTACTAGGAGTAGATGGATGGAG 57.865 45.833 0.00 0.00 30.12 3.86
1972 2119 8.672815 CGTAAGTTAAGCTTAAGTACTAGGAGT 58.327 37.037 23.55 10.43 40.94 3.85
2036 2183 0.617535 ACGGGTCACTCATCCATCCA 60.618 55.000 0.00 0.00 0.00 3.41
2050 2197 2.063015 TTGCCCACTCATTCACGGGT 62.063 55.000 0.00 0.00 41.11 5.28
2053 2200 0.518636 CACTTGCCCACTCATTCACG 59.481 55.000 0.00 0.00 0.00 4.35
2062 2209 0.811281 GGTGATTAGCACTTGCCCAC 59.189 55.000 0.00 1.93 46.86 4.61
2064 2211 1.839424 AAGGTGATTAGCACTTGCCC 58.161 50.000 0.00 0.00 46.86 5.36
2068 2215 5.600696 CAAACCAAAAGGTGATTAGCACTT 58.399 37.500 0.00 0.00 46.86 3.16
2093 2272 1.326951 AAACAACTTGCCCCTTGCGT 61.327 50.000 0.00 0.00 45.60 5.24
2156 2335 0.745468 CCCGGAGTAGTAGCAAGACC 59.255 60.000 0.73 0.00 0.00 3.85
2213 2400 4.802876 GGAGCTATCCAAAGAAACATCG 57.197 45.455 0.00 0.00 45.87 3.84
2235 2422 2.159282 TCTTTCGGCGTAAGATCCAGTC 60.159 50.000 22.46 0.00 43.02 3.51
2243 2433 2.556806 CGTTGTTTCTTTCGGCGTAAG 58.443 47.619 18.62 18.62 43.44 2.34
2368 2558 0.981183 TCACCGTGACAAGCCCTATT 59.019 50.000 0.00 0.00 0.00 1.73
2374 2564 3.064207 TGATACTTTCACCGTGACAAGC 58.936 45.455 16.74 7.43 0.00 4.01
2383 2573 5.124457 AGTTGACATGCATGATACTTTCACC 59.876 40.000 32.75 16.44 37.11 4.02
2391 2581 5.430886 ACTGCTTAGTTGACATGCATGATA 58.569 37.500 32.75 17.43 33.02 2.15
2397 2587 5.862924 TCTAAACTGCTTAGTTGACATGC 57.137 39.130 0.00 0.00 38.57 4.06
2402 2592 5.178797 GCCTCATCTAAACTGCTTAGTTGA 58.821 41.667 9.84 9.84 41.17 3.18
2409 2599 0.462759 GCCGCCTCATCTAAACTGCT 60.463 55.000 0.00 0.00 0.00 4.24
2515 2705 0.249489 CATAGGCTCCGGGAAAGTCG 60.249 60.000 0.00 0.00 0.00 4.18
2516 2706 0.831307 ACATAGGCTCCGGGAAAGTC 59.169 55.000 0.00 0.00 0.00 3.01
2517 2707 0.541863 CACATAGGCTCCGGGAAAGT 59.458 55.000 0.00 0.00 0.00 2.66
2518 2708 0.815615 GCACATAGGCTCCGGGAAAG 60.816 60.000 0.00 0.00 0.00 2.62
2519 2709 1.223487 GCACATAGGCTCCGGGAAA 59.777 57.895 0.00 0.00 0.00 3.13
2522 2712 3.506059 CTCGCACATAGGCTCCGGG 62.506 68.421 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.