Multiple sequence alignment - TraesCS6A01G054700

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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 TraesCS6A01G054700 chr6A 100.000 2714 0 0 1 2714 28429242 28426529 0.000000e+00 5012.0
1 TraesCS6A01G054700 chr6D 94.980 1952 88 4 740 2683 27115508 27113559 0.000000e+00 3053.0
2 TraesCS6A01G054700 chr6D 94.993 739 23 5 2 731 27117946 27117213 0.000000e+00 1147.0
3 TraesCS6A01G054700 chr6D 97.143 35 0 1 142 176 34019687 34019654 1.050000e-04 58.4
4 TraesCS6A01G054700 chr6B 88.501 2322 208 30 395 2683 49416776 49419071 0.000000e+00 2754.0
5 TraesCS6A01G054700 chr6B 88.344 2325 202 36 393 2683 49761504 49759215 0.000000e+00 2728.0
6 TraesCS6A01G054700 chr6B 87.817 197 23 1 57 252 49761931 49761735 2.100000e-56 230.0
7 TraesCS6A01G054700 chr6B 82.812 256 38 6 3 252 49416142 49416397 9.780000e-55 224.0
8 TraesCS6A01G054700 chr6B 94.444 36 2 0 140 175 670600192 670600227 3.780000e-04 56.5
9 TraesCS6A01G054700 chr4A 100.000 38 0 0 2677 2714 57729655 57729618 1.350000e-08 71.3
10 TraesCS6A01G054700 chr5D 97.143 35 1 0 142 176 499860393 499860427 2.920000e-05 60.2
11 TraesCS6A01G054700 chr5B 97.143 35 1 0 142 176 621233783 621233817 2.920000e-05 60.2
12 TraesCS6A01G054700 chr5A 97.143 35 1 0 142 176 624201043 624201077 2.920000e-05 60.2
13 TraesCS6A01G054700 chr2B 97.143 35 0 1 142 176 709485804 709485837 1.050000e-04 58.4


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 TraesCS6A01G054700 chr6A 28426529 28429242 2713 True 5012 5012 100.0000 1 2714 1 chr6A.!!$R1 2713
1 TraesCS6A01G054700 chr6D 27113559 27117946 4387 True 2100 3053 94.9865 2 2683 2 chr6D.!!$R2 2681
2 TraesCS6A01G054700 chr6B 49416142 49419071 2929 False 1489 2754 85.6565 3 2683 2 chr6B.!!$F2 2680
3 TraesCS6A01G054700 chr6B 49759215 49761931 2716 True 1479 2728 88.0805 57 2683 2 chr6B.!!$R1 2626

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
107 119 0.671781 ATTCACTCCTCACACAGCGC 60.672 55.000 0.0 0.0 0.0 5.92 F
1066 3056 1.547223 CCCCAGCCATCTCATTCATCC 60.547 57.143 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 3244 1.558294 TCATCAAGTGCATCCTCAGCT 59.442 47.619 0.0 0.0 0.00 4.24 R
2680 4684 0.529378 CTCAGCAACCAAATGAGCCC 59.471 55.000 0.0 0.0 34.55 5.19 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
107 119 0.671781 ATTCACTCCTCACACAGCGC 60.672 55.000 0.00 0.00 0.00 5.92
236 249 8.871686 ACTTTACAAGTTATCTTTTGGCAAAG 57.128 30.769 13.04 7.78 39.04 2.77
328 390 9.424319 CTAACACAGTTAATACTCACATGTCTT 57.576 33.333 0.00 0.00 30.26 3.01
375 439 4.577875 AGCAAAGTGAGGAAGAGATGAAG 58.422 43.478 0.00 0.00 0.00 3.02
382 446 4.453819 GTGAGGAAGAGATGAAGTTTGGTG 59.546 45.833 0.00 0.00 0.00 4.17
594 857 7.811236 TCCACGATGTTCACTTAACTAAACTAG 59.189 37.037 0.00 0.00 38.99 2.57
1066 3056 1.547223 CCCCAGCCATCTCATTCATCC 60.547 57.143 0.00 0.00 0.00 3.51
1201 3191 3.896272 TGATCATCAGGAGATCAGTGAGG 59.104 47.826 0.00 0.00 44.98 3.86
1215 3205 2.762887 CAGTGAGGAGAGCAATGGACTA 59.237 50.000 0.00 0.00 0.00 2.59
1442 3432 5.361427 GGAGGCCATAGAGAAGTTAGAAAC 58.639 45.833 5.01 0.00 0.00 2.78
1666 3656 4.767928 AGGTACCGGTTTTTGCAATAATCA 59.232 37.500 15.04 0.00 0.00 2.57
1782 3786 7.432869 TGATAATGTTTTCAGTTCAACAAGGG 58.567 34.615 0.00 0.00 36.50 3.95
1862 3866 6.050454 CAAGCATTGCAACAAATTCTCAAA 57.950 33.333 11.91 0.00 40.39 2.69
1871 3875 6.310956 TGCAACAAATTCTCAAAGACAAACTG 59.689 34.615 0.00 0.00 0.00 3.16
1873 3877 6.773976 ACAAATTCTCAAAGACAAACTGGA 57.226 33.333 0.00 0.00 0.00 3.86
1876 3880 2.833794 TCTCAAAGACAAACTGGACCG 58.166 47.619 0.00 0.00 0.00 4.79
1925 3929 9.657419 GATGATGTTTGGGAAGATAACAAAATT 57.343 29.630 0.00 0.00 36.05 1.82
1949 3953 6.371595 AGTGAATGGGAAAATTTAATGGCA 57.628 33.333 0.00 0.00 0.00 4.92
2048 4052 5.046950 AGGTGTGATGAGAAGTAGAAAGGAC 60.047 44.000 0.00 0.00 0.00 3.85
2104 4108 8.077991 TGAAAATTGTATGCTCTTCAAGAAGTG 58.922 33.333 9.44 8.34 39.38 3.16
2113 4117 4.543692 CTCTTCAAGAAGTGTGCATTTGG 58.456 43.478 9.44 0.00 39.38 3.28
2124 4128 3.494251 GTGTGCATTTGGTGGTTTGAATC 59.506 43.478 0.00 0.00 0.00 2.52
2148 4152 4.813161 CGGAAGATTATGCACATCTCTTGT 59.187 41.667 10.07 0.00 39.91 3.16
2151 4155 6.018098 GGAAGATTATGCACATCTCTTGTCAG 60.018 42.308 10.07 0.00 36.00 3.51
2195 4199 0.472471 TTCGAGGCTGTCCTTTGGTT 59.528 50.000 0.00 0.00 44.46 3.67
2221 4225 0.464373 ATTGCAGGTGGCCATCTACG 60.464 55.000 20.77 8.82 43.89 3.51
2222 4226 1.836999 TTGCAGGTGGCCATCTACGT 61.837 55.000 20.77 0.00 43.89 3.57
2233 4237 3.493503 GGCCATCTACGTAGCAATGTAAC 59.506 47.826 18.00 8.60 0.00 2.50
2238 4242 6.144563 CCATCTACGTAGCAATGTAACTGATG 59.855 42.308 18.00 11.01 0.00 3.07
2243 4247 4.259970 CGTAGCAATGTAACTGATGAGCAC 60.260 45.833 0.00 0.00 0.00 4.40
2250 4254 3.578282 TGTAACTGATGAGCACTGGAAGA 59.422 43.478 0.00 0.00 37.43 2.87
2255 4259 4.284490 ACTGATGAGCACTGGAAGAACTTA 59.716 41.667 0.00 0.00 37.43 2.24
2256 4260 4.825422 TGATGAGCACTGGAAGAACTTAG 58.175 43.478 0.00 0.00 37.43 2.18
2258 4262 4.527509 TGAGCACTGGAAGAACTTAGAG 57.472 45.455 0.00 0.00 37.43 2.43
2288 4292 8.514594 CAATTAGAACATTTAGAAGGAAGCACA 58.485 33.333 0.00 0.00 0.00 4.57
2322 4326 2.288213 ACAACTGTTCTTCGATCGAGCA 60.288 45.455 18.54 14.11 0.00 4.26
2339 4343 3.430790 CGAGCAACCATCATCTACCTGAA 60.431 47.826 0.00 0.00 0.00 3.02
2342 4346 3.624861 GCAACCATCATCTACCTGAACAG 59.375 47.826 0.00 0.00 0.00 3.16
2384 4388 8.494433 AGATACTGTAGCATATTTCCAAAAGGA 58.506 33.333 5.81 0.00 0.00 3.36
2387 4391 6.375455 ACTGTAGCATATTTCCAAAAGGACAG 59.625 38.462 0.00 0.00 36.39 3.51
2460 4464 0.467290 GCAAACTGAAGGTGGGACCA 60.467 55.000 0.00 0.00 41.95 4.02
2482 4486 0.252881 AGGCCAGAAGACATGGGAGA 60.253 55.000 5.01 0.00 38.33 3.71
2489 4493 5.630069 GCCAGAAGACATGGGAGAAAGATAA 60.630 44.000 0.00 0.00 38.33 1.75
2494 4498 6.705863 AGACATGGGAGAAAGATAATTTGC 57.294 37.500 0.00 0.00 0.00 3.68
2495 4499 6.189859 AGACATGGGAGAAAGATAATTTGCA 58.810 36.000 0.00 0.00 0.00 4.08
2574 4578 7.761704 CAGAAATACAGCACAGAGTACTATGTT 59.238 37.037 20.22 8.92 31.96 2.71
2575 4579 7.761704 AGAAATACAGCACAGAGTACTATGTTG 59.238 37.037 20.22 18.33 37.68 3.33
2667 4671 5.121611 TGGTTTTCTGCATCATAAGTGTACG 59.878 40.000 0.00 0.00 0.00 3.67
2683 4687 2.493278 TGTACGGTTAGACACTTAGGGC 59.507 50.000 0.00 0.00 0.00 5.19
2684 4688 1.934410 ACGGTTAGACACTTAGGGCT 58.066 50.000 0.00 0.00 0.00 5.19
2685 4689 1.823610 ACGGTTAGACACTTAGGGCTC 59.176 52.381 0.00 0.00 0.00 4.70
2686 4690 1.822990 CGGTTAGACACTTAGGGCTCA 59.177 52.381 0.00 0.00 0.00 4.26
2687 4691 2.431057 CGGTTAGACACTTAGGGCTCAT 59.569 50.000 0.00 0.00 0.00 2.90
2688 4692 3.118738 CGGTTAGACACTTAGGGCTCATT 60.119 47.826 0.00 0.00 0.00 2.57
2689 4693 4.623171 CGGTTAGACACTTAGGGCTCATTT 60.623 45.833 0.00 0.00 0.00 2.32
2690 4694 4.636206 GGTTAGACACTTAGGGCTCATTTG 59.364 45.833 0.00 0.00 0.00 2.32
2691 4695 3.356529 AGACACTTAGGGCTCATTTGG 57.643 47.619 0.00 0.00 0.00 3.28
2692 4696 2.644798 AGACACTTAGGGCTCATTTGGT 59.355 45.455 0.00 0.00 0.00 3.67
2693 4697 3.074538 AGACACTTAGGGCTCATTTGGTT 59.925 43.478 0.00 0.00 0.00 3.67
2694 4698 3.157087 ACACTTAGGGCTCATTTGGTTG 58.843 45.455 0.00 0.00 0.00 3.77
2695 4699 2.094545 CACTTAGGGCTCATTTGGTTGC 60.095 50.000 0.00 0.00 0.00 4.17
2696 4700 2.225117 ACTTAGGGCTCATTTGGTTGCT 60.225 45.455 0.00 0.00 0.00 3.91
2697 4701 1.838112 TAGGGCTCATTTGGTTGCTG 58.162 50.000 0.00 0.00 0.00 4.41
2698 4702 0.112995 AGGGCTCATTTGGTTGCTGA 59.887 50.000 0.00 0.00 0.00 4.26
2699 4703 0.529378 GGGCTCATTTGGTTGCTGAG 59.471 55.000 0.00 0.00 39.50 3.35
2700 4704 0.529378 GGCTCATTTGGTTGCTGAGG 59.471 55.000 0.00 0.00 37.47 3.86
2701 4705 1.538047 GCTCATTTGGTTGCTGAGGA 58.462 50.000 0.00 0.00 37.47 3.71
2702 4706 1.471684 GCTCATTTGGTTGCTGAGGAG 59.528 52.381 0.00 0.00 37.47 3.69
2703 4707 2.089980 CTCATTTGGTTGCTGAGGAGG 58.910 52.381 0.00 0.00 34.17 4.30
2704 4708 1.180029 CATTTGGTTGCTGAGGAGGG 58.820 55.000 0.00 0.00 0.00 4.30
2705 4709 1.075601 ATTTGGTTGCTGAGGAGGGA 58.924 50.000 0.00 0.00 0.00 4.20
2706 4710 0.850100 TTTGGTTGCTGAGGAGGGAA 59.150 50.000 0.00 0.00 0.00 3.97
2707 4711 0.850100 TTGGTTGCTGAGGAGGGAAA 59.150 50.000 0.00 0.00 0.00 3.13
2708 4712 0.850100 TGGTTGCTGAGGAGGGAAAA 59.150 50.000 0.00 0.00 0.00 2.29
2709 4713 1.248486 GGTTGCTGAGGAGGGAAAAC 58.752 55.000 0.00 0.00 0.00 2.43
2710 4714 1.248486 GTTGCTGAGGAGGGAAAACC 58.752 55.000 0.00 0.00 40.67 3.27
2711 4715 0.112412 TTGCTGAGGAGGGAAAACCC 59.888 55.000 0.00 0.00 41.63 4.11
2712 4716 1.065410 TGCTGAGGAGGGAAAACCCA 61.065 55.000 8.05 0.00 41.63 4.51
2713 4717 0.322906 GCTGAGGAGGGAAAACCCAG 60.323 60.000 8.05 0.00 41.63 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.070786 AGCAACGAAAAGGAGGCGA 59.929 52.632 0.00 0.00 0.00 5.54
51 63 1.134367 TGATGCGAGGCTGTACTGTAC 59.866 52.381 10.98 10.98 0.00 2.90
52 64 1.405463 CTGATGCGAGGCTGTACTGTA 59.595 52.381 0.00 0.00 0.00 2.74
53 65 0.174389 CTGATGCGAGGCTGTACTGT 59.826 55.000 0.00 0.00 0.00 3.55
54 66 0.529337 CCTGATGCGAGGCTGTACTG 60.529 60.000 0.00 0.00 0.00 2.74
55 67 0.684479 TCCTGATGCGAGGCTGTACT 60.684 55.000 0.00 0.00 32.51 2.73
107 119 2.284417 GCGTACCTCAAATTAAGAGCCG 59.716 50.000 3.00 5.75 0.00 5.52
236 249 0.318275 CGAGCCGTAGATGCCTCTTC 60.318 60.000 0.00 0.00 32.66 2.87
354 418 4.322567 ACTTCATCTCTTCCTCACTTTGC 58.677 43.478 0.00 0.00 0.00 3.68
358 422 4.349342 ACCAAACTTCATCTCTTCCTCACT 59.651 41.667 0.00 0.00 0.00 3.41
375 439 4.261197 CCTGAGTCTTTAGTTGCACCAAAC 60.261 45.833 0.00 0.00 0.00 2.93
382 446 3.753272 TGAATGCCTGAGTCTTTAGTTGC 59.247 43.478 0.00 0.00 0.00 4.17
680 967 4.608269 TCATTAATTTCCATGGAGGCACA 58.392 39.130 15.53 0.00 37.29 4.57
1066 3056 3.941483 AGATAACCGAATGCCTTGTTCAG 59.059 43.478 0.00 0.00 0.00 3.02
1201 3191 2.430332 ACTCAGCTAGTCCATTGCTCTC 59.570 50.000 0.00 0.00 37.96 3.20
1254 3244 1.558294 TCATCAAGTGCATCCTCAGCT 59.442 47.619 0.00 0.00 0.00 4.24
1442 3432 2.489329 CCACCCACATCTTTAGCAACAG 59.511 50.000 0.00 0.00 0.00 3.16
1512 3502 4.563184 GTCTGGTATACACTTCTTTCAGCG 59.437 45.833 5.01 0.00 0.00 5.18
1640 3630 2.054232 TGCAAAAACCGGTACCTGAA 57.946 45.000 8.00 0.00 0.00 3.02
1666 3656 4.731313 AGGGTTGTCTTTCTCCAATTCT 57.269 40.909 0.00 0.00 0.00 2.40
1782 3786 6.151817 ACTGCCTCCAAGATCTTTTTCATTAC 59.848 38.462 4.86 0.00 0.00 1.89
1839 3843 5.660629 TTGAGAATTTGTTGCAATGCTTG 57.339 34.783 6.82 0.00 0.00 4.01
1853 3857 4.275936 CGGTCCAGTTTGTCTTTGAGAATT 59.724 41.667 0.00 0.00 0.00 2.17
1862 3866 4.141779 ACTTTCTTACGGTCCAGTTTGTCT 60.142 41.667 0.00 0.00 0.00 3.41
1871 3875 3.041508 AGCAGAACTTTCTTACGGTCC 57.958 47.619 0.00 0.00 34.74 4.46
1873 3877 6.369065 CAGAATAAGCAGAACTTTCTTACGGT 59.631 38.462 0.00 0.00 39.97 4.83
1876 3880 7.907214 TCCAGAATAAGCAGAACTTTCTTAC 57.093 36.000 0.00 0.00 39.97 2.34
1925 3929 7.327214 GTGCCATTAAATTTTCCCATTCACTA 58.673 34.615 0.00 0.00 0.00 2.74
1949 3953 2.224670 TGTTTGGATACTCCGCAAAGGT 60.225 45.455 0.00 0.00 40.17 3.50
2086 4090 3.748048 TGCACACTTCTTGAAGAGCATAC 59.252 43.478 16.21 2.78 0.00 2.39
2104 4108 3.066380 GGATTCAAACCACCAAATGCAC 58.934 45.455 0.00 0.00 0.00 4.57
2113 4117 5.733373 GCATAATCTTCCGGATTCAAACCAC 60.733 44.000 4.15 0.00 42.96 4.16
2124 4128 4.000331 AGAGATGTGCATAATCTTCCGG 58.000 45.455 14.12 0.00 34.50 5.14
2179 4183 2.561478 TGTAACCAAAGGACAGCCTC 57.439 50.000 0.00 0.00 46.28 4.70
2195 4199 1.202989 TGGCCACCTGCAATCTTTGTA 60.203 47.619 0.00 0.00 43.89 2.41
2221 4225 4.872691 AGTGCTCATCAGTTACATTGCTAC 59.127 41.667 0.00 0.00 0.00 3.58
2222 4226 4.872124 CAGTGCTCATCAGTTACATTGCTA 59.128 41.667 0.00 0.00 0.00 3.49
2233 4237 3.331478 AGTTCTTCCAGTGCTCATCAG 57.669 47.619 0.00 0.00 0.00 2.90
2238 4242 4.461081 TCTCTCTAAGTTCTTCCAGTGCTC 59.539 45.833 0.00 0.00 0.00 4.26
2243 4247 8.744652 TCTAATTGTCTCTCTAAGTTCTTCCAG 58.255 37.037 0.00 0.00 0.00 3.86
2255 4259 9.883142 CCTTCTAAATGTTCTAATTGTCTCTCT 57.117 33.333 0.00 0.00 0.00 3.10
2256 4260 9.877178 TCCTTCTAAATGTTCTAATTGTCTCTC 57.123 33.333 0.00 0.00 0.00 3.20
2288 4292 5.784177 AGAACAGTTGTGACGATAACATCT 58.216 37.500 0.00 0.00 0.00 2.90
2322 4326 5.248640 CAACTGTTCAGGTAGATGATGGTT 58.751 41.667 4.82 0.00 0.00 3.67
2339 4343 4.981806 TCTAAAACAAAGCTGCAACTGT 57.018 36.364 1.02 0.00 0.00 3.55
2342 4346 6.438763 ACAGTATCTAAAACAAAGCTGCAAC 58.561 36.000 1.02 0.00 0.00 4.17
2384 4388 8.652290 ACTATGTCTTCCTTCTTAAACTTCTGT 58.348 33.333 0.00 0.00 0.00 3.41
2387 4391 9.490379 TTCACTATGTCTTCCTTCTTAAACTTC 57.510 33.333 0.00 0.00 0.00 3.01
2460 4464 1.428912 TCCCATGTCTTCTGGCCTTTT 59.571 47.619 3.32 0.00 32.08 2.27
2482 4486 4.248058 GCCAACTGCTGCAAATTATCTTT 58.752 39.130 3.02 0.00 36.87 2.52
2489 4493 1.042229 TCTTGCCAACTGCTGCAAAT 58.958 45.000 3.02 0.00 45.94 2.32
2494 4498 1.677576 TGACTTTCTTGCCAACTGCTG 59.322 47.619 0.00 0.00 42.00 4.41
2495 4499 2.057137 TGACTTTCTTGCCAACTGCT 57.943 45.000 0.00 0.00 42.00 4.24
2667 4671 4.489306 AATGAGCCCTAAGTGTCTAACC 57.511 45.455 0.00 0.00 0.00 2.85
2680 4684 0.529378 CTCAGCAACCAAATGAGCCC 59.471 55.000 0.00 0.00 34.55 5.19
2683 4687 2.089980 CCTCCTCAGCAACCAAATGAG 58.910 52.381 0.00 0.00 40.13 2.90
2684 4688 1.272092 CCCTCCTCAGCAACCAAATGA 60.272 52.381 0.00 0.00 0.00 2.57
2685 4689 1.180029 CCCTCCTCAGCAACCAAATG 58.820 55.000 0.00 0.00 0.00 2.32
2686 4690 1.075601 TCCCTCCTCAGCAACCAAAT 58.924 50.000 0.00 0.00 0.00 2.32
2687 4691 0.850100 TTCCCTCCTCAGCAACCAAA 59.150 50.000 0.00 0.00 0.00 3.28
2688 4692 0.850100 TTTCCCTCCTCAGCAACCAA 59.150 50.000 0.00 0.00 0.00 3.67
2689 4693 0.850100 TTTTCCCTCCTCAGCAACCA 59.150 50.000 0.00 0.00 0.00 3.67
2690 4694 1.248486 GTTTTCCCTCCTCAGCAACC 58.752 55.000 0.00 0.00 0.00 3.77
2691 4695 1.248486 GGTTTTCCCTCCTCAGCAAC 58.752 55.000 0.00 0.00 0.00 4.17
2692 4696 3.745723 GGTTTTCCCTCCTCAGCAA 57.254 52.632 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.