Multiple sequence alignment - TraesCS6D01G087500

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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 TraesCS6D01G087500 chr6D 100.000 2126 0 0 1 2126 52725766 52723641 0.000000e+00 3927.0
1 TraesCS6D01G087500 chr6B 89.551 2182 109 80 14 2125 119850677 119848545 0.000000e+00 2656.0
2 TraesCS6D01G087500 chr6B 88.235 136 5 4 2002 2126 712669310 712669175 3.650000e-33 152.0
3 TraesCS6D01G087500 chr6A 89.963 2142 79 70 1 2125 63611617 63609595 0.000000e+00 2639.0
4 TraesCS6D01G087500 chr6A 89.773 88 5 2 2 85 63638590 63638503 2.230000e-20 110.0
5 TraesCS6D01G087500 chr7B 89.412 170 15 1 1421 1590 547711349 547711515 5.940000e-51 211.0
6 TraesCS6D01G087500 chr7D 88.235 136 5 4 2002 2126 37275867 37276002 3.650000e-33 152.0
7 TraesCS6D01G087500 chr7D 89.333 75 2 1 1377 1451 420082382 420082450 2.910000e-14 89.8
8 TraesCS6D01G087500 chr5D 88.235 136 5 4 2002 2126 297792759 297792624 3.650000e-33 152.0
9 TraesCS6D01G087500 chr5D 88.235 136 5 4 2002 2126 384073755 384073890 3.650000e-33 152.0
10 TraesCS6D01G087500 chr5D 98.039 51 1 0 1072 1122 285247438 285247488 2.910000e-14 89.8
11 TraesCS6D01G087500 chr5D 90.000 50 5 0 1077 1126 113391895 113391846 4.900000e-07 65.8
12 TraesCS6D01G087500 chr3D 88.235 136 5 4 2002 2126 70729664 70729799 3.650000e-33 152.0
13 TraesCS6D01G087500 chr3D 87.500 136 6 4 2002 2126 443945626 443945761 1.700000e-31 147.0
14 TraesCS6D01G087500 chr3D 98.182 55 1 0 1072 1126 252334799 252334853 1.740000e-16 97.1
15 TraesCS6D01G087500 chr3B 88.235 136 5 4 2002 2126 613814562 613814427 3.650000e-33 152.0
16 TraesCS6D01G087500 chr3B 98.182 55 1 0 1072 1126 313808032 313808086 1.740000e-16 97.1
17 TraesCS6D01G087500 chr3A 87.705 122 6 2 1377 1498 531906045 531905933 1.320000e-27 134.0
18 TraesCS6D01G087500 chr3A 98.182 55 1 0 1072 1126 332220139 332220085 1.740000e-16 97.1
19 TraesCS6D01G087500 chr1D 87.705 122 6 2 1377 1498 413940966 413941078 1.320000e-27 134.0
20 TraesCS6D01G087500 chr1A 86.777 121 7 3 1378 1498 467151172 467151283 2.210000e-25 126.0
21 TraesCS6D01G087500 chr5B 98.039 51 1 0 1072 1122 322858711 322858761 2.910000e-14 89.8
22 TraesCS6D01G087500 chr5A 98.039 51 1 0 1072 1122 377119607 377119657 2.910000e-14 89.8
23 TraesCS6D01G087500 chr2B 100.000 36 0 0 1383 1418 34588163 34588128 1.360000e-07 67.6


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 TraesCS6D01G087500 chr6D 52723641 52725766 2125 True 3927 3927 100.000 1 2126 1 chr6D.!!$R1 2125
1 TraesCS6D01G087500 chr6B 119848545 119850677 2132 True 2656 2656 89.551 14 2125 1 chr6B.!!$R1 2111
2 TraesCS6D01G087500 chr6A 63609595 63611617 2022 True 2639 2639 89.963 1 2125 1 chr6A.!!$R1 2124

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
653 702 0.554865 ATTCCCATTCCCACCCTCCA 60.555 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2102 0.472471 AAAAACTCCACGGCTCTCCA 59.528 50.0 0.0 0.0 0.0 3.86 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
91 96 4.742167 CGCACCAGTCATCTTGAATACTAG 59.258 45.833 0.00 0.00 0.00 2.57
92 97 5.665459 GCACCAGTCATCTTGAATACTAGT 58.335 41.667 0.00 0.00 0.00 2.57
93 98 6.459710 CGCACCAGTCATCTTGAATACTAGTA 60.460 42.308 4.77 4.77 0.00 1.82
142 150 4.135493 GCGAAAGACGTGCGCCTC 62.135 66.667 4.18 0.00 44.55 4.70
214 222 3.999663 CAGATTCTCTCCGCTTTTGAACT 59.000 43.478 0.00 0.00 0.00 3.01
220 228 0.952010 TCCGCTTTTGAACTACCGCC 60.952 55.000 0.00 0.00 0.00 6.13
221 229 1.131826 CGCTTTTGAACTACCGCCG 59.868 57.895 0.00 0.00 0.00 6.46
223 231 1.918868 GCTTTTGAACTACCGCCGGG 61.919 60.000 8.57 0.00 40.11 5.73
225 233 3.905437 TTTGAACTACCGCCGGGCC 62.905 63.158 14.55 0.00 36.48 5.80
263 277 4.265056 ACTTTTCACCGCCCGCCT 62.265 61.111 0.00 0.00 0.00 5.52
281 302 1.364626 CTGCTTTCGGCGCATCTTCT 61.365 55.000 10.83 0.00 45.43 2.85
294 315 1.110442 ATCTTCTCGTGGCAGAGAGG 58.890 55.000 16.75 15.91 46.56 3.69
295 316 1.153667 CTTCTCGTGGCAGAGAGGC 60.154 63.158 16.75 0.00 46.56 4.70
296 317 2.880719 CTTCTCGTGGCAGAGAGGCG 62.881 65.000 16.75 3.64 46.56 5.52
335 359 1.991264 GGTAAGTTCGAGAGGTTTCGC 59.009 52.381 0.00 0.00 40.29 4.70
360 384 1.454111 GGCCTCCTCTCTAGACGCA 60.454 63.158 0.00 0.00 0.00 5.24
367 391 2.050895 CTCTAGACGCATCCGCCG 60.051 66.667 0.00 0.00 38.22 6.46
443 467 4.908687 AGTGAACGCGCCTGCACA 62.909 61.111 18.19 2.27 42.97 4.57
445 469 2.047750 TGAACGCGCCTGCACATA 60.048 55.556 5.73 0.00 42.97 2.29
450 474 2.856346 CGCGCCTGCACATACGTAC 61.856 63.158 0.00 0.00 42.97 3.67
653 702 0.554865 ATTCCCATTCCCACCCTCCA 60.555 55.000 0.00 0.00 0.00 3.86
664 714 1.850755 ACCCTCCACCCACGGAATT 60.851 57.895 0.00 0.00 33.65 2.17
686 736 2.817420 ATTCCCGTTCGTCCTCCCCT 62.817 60.000 0.00 0.00 0.00 4.79
753 803 3.039526 CCCCCTCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
754 804 2.612251 CCCCTCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
782 832 0.719015 TTCCTCCTCCTCCACTCCAT 59.281 55.000 0.00 0.00 0.00 3.41
840 903 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
843 924 5.723887 AGAGAGAGAGAGAGAGAGAGAAAGT 59.276 44.000 0.00 0.00 0.00 2.66
849 930 4.848357 AGAGAGAGAGAGAAAGTGAGGAG 58.152 47.826 0.00 0.00 0.00 3.69
851 932 3.591527 AGAGAGAGAGAAAGTGAGGAGGA 59.408 47.826 0.00 0.00 0.00 3.71
858 939 2.975489 AGAAAGTGAGGAGGAGAAGCAA 59.025 45.455 0.00 0.00 0.00 3.91
864 945 1.827969 GAGGAGGAGAAGCAAGCAGTA 59.172 52.381 0.00 0.00 0.00 2.74
865 946 1.552792 AGGAGGAGAAGCAAGCAGTAC 59.447 52.381 0.00 0.00 0.00 2.73
867 948 1.202582 GAGGAGAAGCAAGCAGTACGA 59.797 52.381 0.00 0.00 0.00 3.43
868 949 1.203523 AGGAGAAGCAAGCAGTACGAG 59.796 52.381 0.00 0.00 0.00 4.18
869 950 1.202582 GGAGAAGCAAGCAGTACGAGA 59.797 52.381 0.00 0.00 0.00 4.04
870 951 2.525055 GAGAAGCAAGCAGTACGAGAG 58.475 52.381 0.00 0.00 0.00 3.20
871 952 0.995728 GAAGCAAGCAGTACGAGAGC 59.004 55.000 0.00 0.00 0.00 4.09
872 953 0.605589 AAGCAAGCAGTACGAGAGCT 59.394 50.000 0.00 0.00 41.03 4.09
873 954 1.464734 AGCAAGCAGTACGAGAGCTA 58.535 50.000 5.77 0.00 37.70 3.32
874 955 1.403679 AGCAAGCAGTACGAGAGCTAG 59.596 52.381 5.77 0.00 37.70 3.42
875 956 1.535015 GCAAGCAGTACGAGAGCTAGG 60.535 57.143 5.77 3.84 37.70 3.02
876 957 2.017782 CAAGCAGTACGAGAGCTAGGA 58.982 52.381 5.77 0.00 37.70 2.94
877 958 2.421751 AGCAGTACGAGAGCTAGGAA 57.578 50.000 0.00 0.00 36.73 3.36
878 959 2.294074 AGCAGTACGAGAGCTAGGAAG 58.706 52.381 0.00 0.00 36.73 3.46
879 960 2.092861 AGCAGTACGAGAGCTAGGAAGA 60.093 50.000 0.00 0.00 36.73 2.87
880 961 2.683867 GCAGTACGAGAGCTAGGAAGAA 59.316 50.000 0.00 0.00 0.00 2.52
892 973 2.312424 AGGAAGAAAGAGGTCGGTCT 57.688 50.000 0.00 0.00 0.00 3.85
893 974 2.172679 AGGAAGAAAGAGGTCGGTCTC 58.827 52.381 0.00 0.00 0.00 3.36
894 975 1.893801 GGAAGAAAGAGGTCGGTCTCA 59.106 52.381 8.26 0.00 36.30 3.27
936 1017 1.248486 GGTTGGTTGCTTCTCTTCCC 58.752 55.000 0.00 0.00 0.00 3.97
1184 1269 1.057275 CCTCCTCCTCCTTTAGCCCC 61.057 65.000 0.00 0.00 0.00 5.80
1341 1434 1.020333 CAGAGAGTGCTTGCCTGCTC 61.020 60.000 0.00 0.00 0.00 4.26
1352 1445 3.052082 CCTGCTCGCTTGGTGGTG 61.052 66.667 0.00 0.00 0.00 4.17
1353 1446 2.031012 CTGCTCGCTTGGTGGTGA 59.969 61.111 0.00 0.00 0.00 4.02
1354 1447 2.031012 TGCTCGCTTGGTGGTGAG 59.969 61.111 0.00 0.00 44.06 3.51
1355 1448 2.743928 GCTCGCTTGGTGGTGAGG 60.744 66.667 7.08 0.00 42.22 3.86
1983 2087 8.842358 TTCTGGTGTTTCAGGTTAATTACTAG 57.158 34.615 0.00 0.00 35.58 2.57
2088 2194 4.776349 TGTGTAATCTGAACTGGTGTGTT 58.224 39.130 0.00 0.00 0.00 3.32
2125 2231 4.336433 TGGTTCTTAAGCTTAGCATGCATC 59.664 41.667 21.98 5.43 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.399181 TCTAGCAACGGGCCAGGG 61.399 66.667 8.08 0.00 46.50 4.45
70 75 7.147897 TGGTACTAGTATTCAAGATGACTGGTG 60.148 40.741 5.75 0.00 34.87 4.17
71 76 6.895756 TGGTACTAGTATTCAAGATGACTGGT 59.104 38.462 5.75 0.00 37.40 4.00
91 96 3.099267 AGCGCAGAATGTAGATGGTAC 57.901 47.619 11.47 0.00 39.31 3.34
92 97 3.457234 CAAGCGCAGAATGTAGATGGTA 58.543 45.455 11.47 0.00 39.31 3.25
93 98 2.283298 CAAGCGCAGAATGTAGATGGT 58.717 47.619 11.47 0.00 39.31 3.55
142 150 4.154347 GCCTCTGTCTGGGCTCCG 62.154 72.222 0.00 0.00 44.48 4.63
229 237 5.538053 TGAAAAGTGAAAATCATGCTACCCA 59.462 36.000 0.00 0.00 0.00 4.51
395 419 2.882777 CGCCACTGCTGTAGCTCG 60.883 66.667 11.87 2.94 42.66 5.03
396 420 3.191539 GCGCCACTGCTGTAGCTC 61.192 66.667 11.87 0.64 42.66 4.09
443 467 2.028484 CCATGCCGCCGTACGTAT 59.972 61.111 15.21 0.00 41.42 3.06
562 594 4.200283 GAGTGAGAGCGCGGGGAG 62.200 72.222 8.83 0.00 0.00 4.30
564 596 4.504916 CTGAGTGAGAGCGCGGGG 62.505 72.222 8.83 0.00 0.00 5.73
567 599 3.713205 ATGGCTGAGTGAGAGCGCG 62.713 63.158 0.00 0.00 37.32 6.86
568 600 1.427592 GAATGGCTGAGTGAGAGCGC 61.428 60.000 0.00 0.00 37.32 5.92
569 601 0.809241 GGAATGGCTGAGTGAGAGCG 60.809 60.000 0.00 0.00 37.32 5.03
570 602 0.540923 AGGAATGGCTGAGTGAGAGC 59.459 55.000 0.00 0.00 35.57 4.09
571 603 1.743091 GCAGGAATGGCTGAGTGAGAG 60.743 57.143 0.00 0.00 0.00 3.20
572 604 0.251354 GCAGGAATGGCTGAGTGAGA 59.749 55.000 0.00 0.00 0.00 3.27
573 605 0.035725 TGCAGGAATGGCTGAGTGAG 60.036 55.000 0.00 0.00 0.00 3.51
574 606 0.622136 ATGCAGGAATGGCTGAGTGA 59.378 50.000 0.00 0.00 0.00 3.41
575 607 0.738975 CATGCAGGAATGGCTGAGTG 59.261 55.000 0.00 0.00 0.00 3.51
576 608 1.035932 GCATGCAGGAATGGCTGAGT 61.036 55.000 14.21 0.00 0.00 3.41
577 609 1.734137 GCATGCAGGAATGGCTGAG 59.266 57.895 14.21 0.00 0.00 3.35
623 661 2.370189 GGAATGGGAATCCGATCTGAGT 59.630 50.000 0.00 0.00 35.24 3.41
624 662 2.289945 GGGAATGGGAATCCGATCTGAG 60.290 54.545 0.00 0.00 37.87 3.35
625 663 1.699634 GGGAATGGGAATCCGATCTGA 59.300 52.381 0.00 0.00 37.87 3.27
626 664 1.421268 TGGGAATGGGAATCCGATCTG 59.579 52.381 0.00 0.00 37.87 2.90
627 665 1.421646 GTGGGAATGGGAATCCGATCT 59.578 52.381 0.00 0.00 37.87 2.75
664 714 1.079405 GAGGACGAACGGGAATGCA 60.079 57.895 0.00 0.00 0.00 3.96
753 803 1.719378 AGGAGGAGGAAGAAGAGTGGA 59.281 52.381 0.00 0.00 0.00 4.02
754 804 2.107366 GAGGAGGAGGAAGAAGAGTGG 58.893 57.143 0.00 0.00 0.00 4.00
840 903 1.003003 GCTTGCTTCTCCTCCTCACTT 59.997 52.381 0.00 0.00 0.00 3.16
843 924 0.612229 CTGCTTGCTTCTCCTCCTCA 59.388 55.000 0.00 0.00 0.00 3.86
849 930 1.202582 TCTCGTACTGCTTGCTTCTCC 59.797 52.381 0.00 0.00 0.00 3.71
851 932 1.403514 GCTCTCGTACTGCTTGCTTCT 60.404 52.381 0.00 0.00 0.00 2.85
858 939 2.092861 TCTTCCTAGCTCTCGTACTGCT 60.093 50.000 0.00 0.00 40.43 4.24
864 945 3.020984 CCTCTTTCTTCCTAGCTCTCGT 58.979 50.000 0.00 0.00 0.00 4.18
865 946 3.020984 ACCTCTTTCTTCCTAGCTCTCG 58.979 50.000 0.00 0.00 0.00 4.04
867 948 3.020984 CGACCTCTTTCTTCCTAGCTCT 58.979 50.000 0.00 0.00 0.00 4.09
868 949 2.100087 CCGACCTCTTTCTTCCTAGCTC 59.900 54.545 0.00 0.00 0.00 4.09
869 950 2.104170 CCGACCTCTTTCTTCCTAGCT 58.896 52.381 0.00 0.00 0.00 3.32
870 951 1.826096 ACCGACCTCTTTCTTCCTAGC 59.174 52.381 0.00 0.00 0.00 3.42
871 952 3.358118 AGACCGACCTCTTTCTTCCTAG 58.642 50.000 0.00 0.00 0.00 3.02
872 953 3.245158 TGAGACCGACCTCTTTCTTCCTA 60.245 47.826 5.79 0.00 34.38 2.94
873 954 2.172679 GAGACCGACCTCTTTCTTCCT 58.827 52.381 0.00 0.00 0.00 3.36
874 955 1.893801 TGAGACCGACCTCTTTCTTCC 59.106 52.381 5.79 0.00 34.38 3.46
875 956 2.559231 AGTGAGACCGACCTCTTTCTTC 59.441 50.000 5.79 0.00 34.38 2.87
876 957 2.559231 GAGTGAGACCGACCTCTTTCTT 59.441 50.000 5.79 0.00 34.38 2.52
877 958 2.164338 GAGTGAGACCGACCTCTTTCT 58.836 52.381 5.79 2.75 34.38 2.52
878 959 1.887198 TGAGTGAGACCGACCTCTTTC 59.113 52.381 5.79 4.45 34.38 2.62
879 960 1.996798 TGAGTGAGACCGACCTCTTT 58.003 50.000 5.79 0.00 34.38 2.52
880 961 2.096248 GATGAGTGAGACCGACCTCTT 58.904 52.381 5.79 0.00 34.38 2.85
892 973 1.451927 GGCGGCAATGGATGAGTGA 60.452 57.895 3.07 0.00 0.00 3.41
893 974 0.179048 TAGGCGGCAATGGATGAGTG 60.179 55.000 13.08 0.00 0.00 3.51
894 975 0.107456 CTAGGCGGCAATGGATGAGT 59.893 55.000 13.08 0.00 0.00 3.41
936 1017 4.740822 CTTGGGTTGCCTCCGGGG 62.741 72.222 0.00 0.00 38.36 5.73
1184 1269 0.750911 GCTTGAAGGGATGAGCAGGG 60.751 60.000 0.00 0.00 35.29 4.45
1332 1425 2.979676 CACCAAGCGAGCAGGCAA 60.980 61.111 6.51 0.00 34.64 4.52
1341 1434 1.003355 ATCACCTCACCACCAAGCG 60.003 57.895 0.00 0.00 0.00 4.68
1351 1444 3.298958 GAGGACGCCATCACCTCA 58.701 61.111 0.00 0.00 46.42 3.86
1352 1445 2.303549 CTGGAGGACGCCATCACCTC 62.304 65.000 0.00 0.00 46.44 3.85
1353 1446 2.284625 TGGAGGACGCCATCACCT 60.285 61.111 0.00 0.00 36.68 4.00
1354 1447 2.187946 CTGGAGGACGCCATCACC 59.812 66.667 0.00 0.00 37.30 4.02
1355 1448 2.512515 GCTGGAGGACGCCATCAC 60.513 66.667 0.00 0.00 37.30 3.06
1983 2087 3.678548 CGGCTCTCCAGTTTTTGTAGTAC 59.321 47.826 0.00 0.00 0.00 2.73
1993 2099 1.122019 AACTCCACGGCTCTCCAGTT 61.122 55.000 0.00 0.00 0.00 3.16
1994 2100 1.122019 AAACTCCACGGCTCTCCAGT 61.122 55.000 0.00 0.00 0.00 4.00
1996 2102 0.472471 AAAAACTCCACGGCTCTCCA 59.528 50.000 0.00 0.00 0.00 3.86
2088 2194 6.374333 GCTTAAGAACCATCATCACTTGGTAA 59.626 38.462 6.67 0.00 45.44 2.85


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

AutoCloner maintained by Alex Coulton.