Multiple sequence alignment - TraesCS3B01G459400

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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 TraesCS3B01G459400 chr3B 100.000 2306 0 0 1 2306 703008395 703006090 0 4259
1 TraesCS3B01G459400 chr3B 93.769 1300 58 7 1012 2306 201559020 201557739 0 1930
2 TraesCS3B01G459400 chr3B 94.795 999 39 6 3 993 201561616 201560623 0 1544
3 TraesCS3B01G459400 chr5B 95.542 1301 50 8 1012 2306 413609191 413610489 0 2074
4 TraesCS3B01G459400 chr5B 94.444 1296 68 4 1012 2306 432878465 432879757 0 1991
5 TraesCS3B01G459400 chr5B 94.428 987 49 5 6 992 432875893 432876873 0 1513
6 TraesCS3B01G459400 chr4D 93.832 1297 76 4 1012 2306 245650435 245651729 0 1949
7 TraesCS3B01G459400 chr1A 92.456 1299 69 11 1012 2306 371922888 371924161 0 1829
8 TraesCS3B01G459400 chr4A 91.969 1295 82 6 1014 2306 310764162 310765436 0 1796
9 TraesCS3B01G459400 chr4A 92.189 1229 73 12 1080 2306 219308174 219306967 0 1716
10 TraesCS3B01G459400 chr4A 94.422 986 50 4 7 992 310761575 310762555 0 1511
11 TraesCS3B01G459400 chr4A 93.838 990 54 6 3 992 219340703 219339721 0 1483
12 TraesCS3B01G459400 chr3D 91.371 1298 79 17 1012 2306 182097284 182098551 0 1746
13 TraesCS3B01G459400 chr5A 96.239 1037 37 2 1272 2306 482027372 482026336 0 1698
14 TraesCS3B01G459400 chr2D 95.665 992 34 5 5 992 630268391 630269377 0 1585
15 TraesCS3B01G459400 chr2D 95.573 994 34 6 3 992 272802496 272801509 0 1583
16 TraesCS3B01G459400 chr1B 95.090 998 36 6 3 992 633729707 633728715 0 1559
17 TraesCS3B01G459400 chr3A 95.152 990 42 5 3 992 672879266 672878283 0 1557
18 TraesCS3B01G459400 chr3A 94.980 737 27 7 1012 1740 672876681 672875947 0 1147
19 TraesCS3B01G459400 chr5D 94.523 986 50 4 7 992 432293550 432292569 0 1519
20 TraesCS3B01G459400 chr7A 90.366 955 75 7 1012 1963 352675707 352674767 0 1238
21 TraesCS3B01G459400 chrUn 95.816 478 14 4 1027 1499 451362693 451362217 0 767
22 TraesCS3B01G459400 chr4B 95.652 437 12 5 1012 1442 24 459 0 695


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 TraesCS3B01G459400 chr3B 703006090 703008395 2305 True 4259.0 4259 100.0000 1 2306 1 chr3B.!!$R1 2305
1 TraesCS3B01G459400 chr3B 201557739 201561616 3877 True 1737.0 1930 94.2820 3 2306 2 chr3B.!!$R2 2303
2 TraesCS3B01G459400 chr5B 413609191 413610489 1298 False 2074.0 2074 95.5420 1012 2306 1 chr5B.!!$F1 1294
3 TraesCS3B01G459400 chr5B 432875893 432879757 3864 False 1752.0 1991 94.4360 6 2306 2 chr5B.!!$F2 2300
4 TraesCS3B01G459400 chr4D 245650435 245651729 1294 False 1949.0 1949 93.8320 1012 2306 1 chr4D.!!$F1 1294
5 TraesCS3B01G459400 chr1A 371922888 371924161 1273 False 1829.0 1829 92.4560 1012 2306 1 chr1A.!!$F1 1294
6 TraesCS3B01G459400 chr4A 219306967 219308174 1207 True 1716.0 1716 92.1890 1080 2306 1 chr4A.!!$R1 1226
7 TraesCS3B01G459400 chr4A 310761575 310765436 3861 False 1653.5 1796 93.1955 7 2306 2 chr4A.!!$F1 2299
8 TraesCS3B01G459400 chr4A 219339721 219340703 982 True 1483.0 1483 93.8380 3 992 1 chr4A.!!$R2 989
9 TraesCS3B01G459400 chr3D 182097284 182098551 1267 False 1746.0 1746 91.3710 1012 2306 1 chr3D.!!$F1 1294
10 TraesCS3B01G459400 chr5A 482026336 482027372 1036 True 1698.0 1698 96.2390 1272 2306 1 chr5A.!!$R1 1034
11 TraesCS3B01G459400 chr2D 630268391 630269377 986 False 1585.0 1585 95.6650 5 992 1 chr2D.!!$F1 987
12 TraesCS3B01G459400 chr2D 272801509 272802496 987 True 1583.0 1583 95.5730 3 992 1 chr2D.!!$R1 989
13 TraesCS3B01G459400 chr1B 633728715 633729707 992 True 1559.0 1559 95.0900 3 992 1 chr1B.!!$R1 989
14 TraesCS3B01G459400 chr3A 672875947 672879266 3319 True 1352.0 1557 95.0660 3 1740 2 chr3A.!!$R1 1737
15 TraesCS3B01G459400 chr5D 432292569 432293550 981 True 1519.0 1519 94.5230 7 992 1 chr5D.!!$R1 985
16 TraesCS3B01G459400 chr7A 352674767 352675707 940 True 1238.0 1238 90.3660 1012 1963 1 chr7A.!!$R1 951

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
280 293 1.010602 TCTATCTAGGCCCCAGGGGT 61.011 60.0 27.04 9.89 46.51 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 3251 2.079925 GAAAGCGTGAAGAGAGCCAAT 58.92 47.619 0.0 0.0 0.0 3.16 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
39 47 6.273026 TCCTTCCTCTATCCATATTCATGCAA 59.727 38.462 0.00 0.00 0.00 4.08
43 51 8.571461 TCCTCTATCCATATTCATGCAAAATC 57.429 34.615 0.00 0.00 0.00 2.17
66 74 5.361571 TCGCTCATGAACTAATACCCAACTA 59.638 40.000 0.00 0.00 0.00 2.24
187 196 2.672961 TGAGATCAATTCGGAAGCGT 57.327 45.000 0.00 0.00 0.00 5.07
207 216 6.398918 AGCGTCTTTTCTTATTCTAGCAGAA 58.601 36.000 1.85 1.85 38.78 3.02
280 293 1.010602 TCTATCTAGGCCCCAGGGGT 61.011 60.000 27.04 9.89 46.51 4.95
295 308 2.296190 CAGGGGTTAGGAACAAAACAGC 59.704 50.000 0.00 0.00 0.00 4.40
365 378 2.160022 TGTACGGTTTTGAAATAGCGGC 59.840 45.455 13.14 0.00 39.38 6.53
449 463 6.092259 AGTTGAAGCATAGTCAAAATACGGTC 59.908 38.462 0.00 0.00 36.77 4.79
475 489 3.625853 TGGATGGAATATTTGGCGTCAA 58.374 40.909 0.00 0.00 0.00 3.18
546 560 8.749354 GTGAAAGATTACCCTTTGATTTACCAT 58.251 33.333 0.00 0.00 36.58 3.55
589 603 7.888546 AGTAGCAGGTTACCAAACTGAATATTT 59.111 33.333 8.11 0.00 35.81 1.40
591 605 6.719370 AGCAGGTTACCAAACTGAATATTTCA 59.281 34.615 8.11 0.00 38.17 2.69
918 932 5.885912 GGGCAATCTCTTATTAACAACCTCA 59.114 40.000 0.00 0.00 0.00 3.86
992 1006 4.882671 TCAACACAAAAGCTCTCTCAAC 57.117 40.909 0.00 0.00 0.00 3.18
993 1007 4.517285 TCAACACAAAAGCTCTCTCAACT 58.483 39.130 0.00 0.00 0.00 3.16
994 1008 4.943705 TCAACACAAAAGCTCTCTCAACTT 59.056 37.500 0.00 0.00 0.00 2.66
995 1009 4.889832 ACACAAAAGCTCTCTCAACTTG 57.110 40.909 0.00 0.00 0.00 3.16
996 1010 4.517285 ACACAAAAGCTCTCTCAACTTGA 58.483 39.130 0.00 0.00 0.00 3.02
997 1011 4.333926 ACACAAAAGCTCTCTCAACTTGAC 59.666 41.667 0.00 0.00 0.00 3.18
998 1012 3.879892 ACAAAAGCTCTCTCAACTTGACC 59.120 43.478 0.00 0.00 0.00 4.02
999 1013 4.133078 CAAAAGCTCTCTCAACTTGACCT 58.867 43.478 0.00 0.00 0.00 3.85
1001 1015 5.753721 AAAGCTCTCTCAACTTGACCTAT 57.246 39.130 0.00 0.00 0.00 2.57
1084 2689 1.336440 TCACAAGCCGAAACATGGTTG 59.664 47.619 0.00 0.00 43.62 3.77
1090 2695 1.948611 GCCGAAACATGGTTGGAGCTA 60.949 52.381 7.12 0.00 0.00 3.32
1096 2701 6.147821 CCGAAACATGGTTGGAGCTATAATAG 59.852 42.308 7.12 0.00 0.00 1.73
1185 2790 8.749354 AGTCGCCAATTAAAAGGAGATATTTTT 58.251 29.630 6.33 0.00 36.14 1.94
1254 2859 6.360618 ACTATCCATTCTTTCTTCCATCCAC 58.639 40.000 0.00 0.00 0.00 4.02
1546 3188 9.904647 CAATTTATTGGCTAATTCAAATTCGTG 57.095 29.630 11.31 2.04 34.22 4.35
1639 3285 3.970610 CACGCTTTCTCACAAACAGATTG 59.029 43.478 0.00 0.00 44.95 2.67
1704 3350 4.993905 TCGTCTGGTGTCTACAATACATG 58.006 43.478 0.00 0.00 0.00 3.21
1862 3511 9.109393 GCTTGTCCAACAGATGTATTAGAAATA 57.891 33.333 0.00 0.00 0.00 1.40
1897 3546 4.040217 TGGATGTAAAGCCAAGCAAATTGT 59.960 37.500 0.00 0.00 37.17 2.71
1957 3606 1.153086 GTGAATCTGCCTGCCCGAT 60.153 57.895 0.00 0.00 0.00 4.18
2242 3892 5.823570 TCACAAGGGAAACAAAATCGTTAGA 59.176 36.000 0.00 0.00 0.00 2.10
2246 3896 4.157840 AGGGAAACAAAATCGTTAGATGGC 59.842 41.667 0.00 0.00 37.14 4.40
2302 3952 7.751047 TCTAATGACTTATGCGTTCTGTTAC 57.249 36.000 0.00 0.00 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 47 5.680619 TGGGTATTAGTTCATGAGCGATTT 58.319 37.500 3.72 0.00 0.00 2.17
43 51 4.442706 AGTTGGGTATTAGTTCATGAGCG 58.557 43.478 3.72 0.00 0.00 5.03
187 196 9.965902 AATTCCTTCTGCTAGAATAAGAAAAGA 57.034 29.630 0.00 0.00 33.13 2.52
280 293 3.639561 GGAAAGGGCTGTTTTGTTCCTAA 59.360 43.478 0.00 0.00 33.28 2.69
295 308 7.341805 TCTCTATGATCAGAAAAAGGAAAGGG 58.658 38.462 0.09 0.00 0.00 3.95
434 447 7.094549 CCATCCAAAAAGACCGTATTTTGACTA 60.095 37.037 17.47 7.98 45.09 2.59
449 463 5.418676 ACGCCAAATATTCCATCCAAAAAG 58.581 37.500 0.00 0.00 0.00 2.27
546 560 4.647853 TGCTACTAATTCTTCCTCCGCTTA 59.352 41.667 0.00 0.00 0.00 3.09
666 680 0.898326 AAATTCCACCCGCCCAAGTC 60.898 55.000 0.00 0.00 0.00 3.01
723 737 9.558396 AAAATTCCAACTGCTTTATTCATTTGA 57.442 25.926 0.00 0.00 0.00 2.69
882 896 1.133356 AGATTGCCCAGGGAAATAGGC 60.133 52.381 12.45 0.00 45.96 3.93
992 1006 7.671302 ACATGCTATAAGGTACATAGGTCAAG 58.329 38.462 0.00 0.00 0.00 3.02
993 1007 7.612065 ACATGCTATAAGGTACATAGGTCAA 57.388 36.000 0.00 0.00 0.00 3.18
994 1008 7.948447 AGTACATGCTATAAGGTACATAGGTCA 59.052 37.037 0.00 0.00 38.78 4.02
995 1009 8.350852 AGTACATGCTATAAGGTACATAGGTC 57.649 38.462 0.00 0.00 38.78 3.85
996 1010 8.722622 AAGTACATGCTATAAGGTACATAGGT 57.277 34.615 0.00 0.00 38.78 3.08
997 1011 9.998106 AAAAGTACATGCTATAAGGTACATAGG 57.002 33.333 0.00 0.00 38.78 2.57
1044 2649 9.293404 CTTGTGATCAATCCATAGATACCAATT 57.707 33.333 0.00 0.00 32.82 2.32
1145 2750 9.554395 TTAATTGGCGACTATCAAATAGATCAA 57.446 29.630 0.00 0.00 38.19 2.57
1185 2790 5.406780 CGCAAGGGTTATAACAAAAATTGCA 59.593 36.000 25.19 0.00 40.27 4.08
1254 2859 4.317671 ACGAGTGGATTTCCTATTACGG 57.682 45.455 0.00 0.00 36.82 4.02
1319 2940 8.204836 GCCTTTGTTTAGAGGATTCTATGTCTA 58.795 37.037 0.00 0.00 35.88 2.59
1320 2941 7.051000 GCCTTTGTTTAGAGGATTCTATGTCT 58.949 38.462 0.00 0.00 35.88 3.41
1321 2942 6.823689 TGCCTTTGTTTAGAGGATTCTATGTC 59.176 38.462 0.00 0.00 35.88 3.06
1538 3180 9.453325 AATTTTACGAATTGTACACACGAATTT 57.547 25.926 17.93 6.79 31.20 1.82
1605 3251 2.079925 GAAAGCGTGAAGAGAGCCAAT 58.920 47.619 0.00 0.00 0.00 3.16
1833 3482 2.936919 ACATCTGTTGGACAAGCTCA 57.063 45.000 0.00 0.00 0.00 4.26
1862 3511 4.447762 GCTTTACATCCATCCCAGGGTATT 60.448 45.833 5.01 0.00 0.00 1.89
1897 3546 2.702751 TTCGGTTCTCAGCGCGGAAA 62.703 55.000 12.27 6.40 43.85 3.13
2101 3751 2.375146 ACGTTTTGACCAGAAAAGCCT 58.625 42.857 0.00 0.00 0.00 4.58
2183 3833 9.301153 GAAAATTAATGAACCTGCAAATATCGT 57.699 29.630 0.00 0.00 0.00 3.73
2214 3864 4.202111 CGATTTTGTTTCCCTTGTGAGGTT 60.202 41.667 0.00 0.00 41.85 3.50
2221 3871 6.092748 CCATCTAACGATTTTGTTTCCCTTG 58.907 40.000 0.00 0.00 33.32 3.61


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

AutoCloner maintained by Alex Coulton.