Multiple sequence alignment - TraesCS4A01G435100

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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 TraesCS4A01G435100 chr4A 100.000 2548 0 0 1 2548 705529820 705527273 0 4706
1 TraesCS4A01G435100 chr2B 94.318 2552 125 14 1 2548 458656866 458659401 0 3892
2 TraesCS4A01G435100 chr2B 96.183 1991 70 6 562 2548 692955888 692957876 0 3251
3 TraesCS4A01G435100 chr2B 95.986 1993 69 8 565 2548 492636660 492638650 0 3227
4 TraesCS4A01G435100 chr2B 95.951 568 20 1 1 568 176331689 176332253 0 918
5 TraesCS4A01G435100 chr2B 95.775 568 21 2 1 568 681305724 681305160 0 913
6 TraesCS4A01G435100 chr1B 96.382 1990 64 6 566 2548 581717565 581715577 0 3269
7 TraesCS4A01G435100 chr1B 96.165 1982 72 4 568 2548 520844120 520842142 0 3236
8 TraesCS4A01G435100 chr1B 96.127 568 21 1 1 568 563161048 563160482 0 926
9 TraesCS4A01G435100 chr1B 95.775 568 22 2 1 568 115887812 115888377 0 915
10 TraesCS4A01G435100 chr1B 95.775 568 21 1 1 568 585992760 585992196 0 913
11 TraesCS4A01G435100 chr7B 96.369 1983 68 4 569 2548 720989190 720987209 0 3260
12 TraesCS4A01G435100 chr7B 96.024 1987 71 6 568 2548 677862791 677860807 0 3225
13 TraesCS4A01G435100 chr7B 96.020 1985 72 6 569 2548 602142437 602144419 0 3221
14 TraesCS4A01G435100 chr5B 95.838 1994 78 4 559 2548 497276154 497278146 0 3217
15 TraesCS4A01G435100 chr3B 95.951 568 21 1 1 568 416838794 416838229 0 920
16 TraesCS4A01G435100 chr4B 95.775 568 22 1 1 568 469488193 469488758 0 915
17 TraesCS4A01G435100 chr6B 95.775 568 20 2 1 568 444822669 444822106 0 913


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 TraesCS4A01G435100 chr4A 705527273 705529820 2547 True 4706 4706 100.000 1 2548 1 chr4A.!!$R1 2547
1 TraesCS4A01G435100 chr2B 458656866 458659401 2535 False 3892 3892 94.318 1 2548 1 chr2B.!!$F2 2547
2 TraesCS4A01G435100 chr2B 692955888 692957876 1988 False 3251 3251 96.183 562 2548 1 chr2B.!!$F4 1986
3 TraesCS4A01G435100 chr2B 492636660 492638650 1990 False 3227 3227 95.986 565 2548 1 chr2B.!!$F3 1983
4 TraesCS4A01G435100 chr2B 176331689 176332253 564 False 918 918 95.951 1 568 1 chr2B.!!$F1 567
5 TraesCS4A01G435100 chr2B 681305160 681305724 564 True 913 913 95.775 1 568 1 chr2B.!!$R1 567
6 TraesCS4A01G435100 chr1B 581715577 581717565 1988 True 3269 3269 96.382 566 2548 1 chr1B.!!$R3 1982
7 TraesCS4A01G435100 chr1B 520842142 520844120 1978 True 3236 3236 96.165 568 2548 1 chr1B.!!$R1 1980
8 TraesCS4A01G435100 chr1B 563160482 563161048 566 True 926 926 96.127 1 568 1 chr1B.!!$R2 567
9 TraesCS4A01G435100 chr1B 115887812 115888377 565 False 915 915 95.775 1 568 1 chr1B.!!$F1 567
10 TraesCS4A01G435100 chr1B 585992196 585992760 564 True 913 913 95.775 1 568 1 chr1B.!!$R4 567
11 TraesCS4A01G435100 chr7B 720987209 720989190 1981 True 3260 3260 96.369 569 2548 1 chr7B.!!$R2 1979
12 TraesCS4A01G435100 chr7B 677860807 677862791 1984 True 3225 3225 96.024 568 2548 1 chr7B.!!$R1 1980
13 TraesCS4A01G435100 chr7B 602142437 602144419 1982 False 3221 3221 96.020 569 2548 1 chr7B.!!$F1 1979
14 TraesCS4A01G435100 chr5B 497276154 497278146 1992 False 3217 3217 95.838 559 2548 1 chr5B.!!$F1 1989
15 TraesCS4A01G435100 chr3B 416838229 416838794 565 True 920 920 95.951 1 568 1 chr3B.!!$R1 567
16 TraesCS4A01G435100 chr4B 469488193 469488758 565 False 915 915 95.775 1 568 1 chr4B.!!$F1 567
17 TraesCS4A01G435100 chr6B 444822106 444822669 563 True 913 913 95.775 1 568 1 chr6B.!!$R1 567

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
905 914 0.450184 GACGAGAGAGTGAGAGCACC 59.55 60.0 0.0 0.0 46.32 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2058 1.761784 CTCTTGCCATCTGTCCTAGCT 59.238 52.381 0.0 0.0 0.0 3.32 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
210 211 2.949644 CACTTTCCGAGGAAACAACCTT 59.050 45.455 12.85 0.0 40.73 3.50
293 294 3.432378 TCCTCTCCCTACTGTCAAGAAC 58.568 50.000 0.00 0.0 0.00 3.01
439 440 8.463930 TTGTTAGTGGATTCTTTTTGATGAGT 57.536 30.769 0.00 0.0 0.00 3.41
448 449 9.334947 GGATTCTTTTTGATGAGTATGAGATGA 57.665 33.333 0.00 0.0 0.00 2.92
887 896 4.994201 GCACGACGCTGACCACGA 62.994 66.667 0.00 0.0 37.77 4.35
896 905 1.579084 GCTGACCACGACGAGAGAGT 61.579 60.000 0.00 0.0 0.00 3.24
905 914 0.450184 GACGAGAGAGTGAGAGCACC 59.550 60.000 0.00 0.0 46.32 5.01
1138 1147 1.076332 GAGGAACCACAATCGTTCGG 58.924 55.000 0.00 0.0 40.46 4.30
1176 1185 0.697854 ATGGGGTAAGAATCGGGGCT 60.698 55.000 0.00 0.0 0.00 5.19
1206 1215 3.681593 TTTTCGTGGTCGGGATCTTTA 57.318 42.857 0.00 0.0 37.69 1.85
1213 1222 3.694566 GTGGTCGGGATCTTTAAGCAATT 59.305 43.478 0.00 0.0 0.00 2.32
1239 1248 4.512484 TGATCTATTCCGTGTTCATGCAA 58.488 39.130 0.00 0.0 0.00 4.08
1270 1279 3.140325 TCTTTCTTTGGGTCGATGCTT 57.860 42.857 0.00 0.0 0.00 3.91
1273 1282 2.559698 TCTTTGGGTCGATGCTTTGA 57.440 45.000 0.00 0.0 0.00 2.69
1405 1415 0.808125 CGCACTGACAGAGAGCTAGT 59.192 55.000 10.08 0.0 36.21 2.57
1554 1564 8.481492 AATGTATGGAAAGGCATGAATTATGA 57.519 30.769 0.00 0.0 39.21 2.15
1627 1639 8.608844 TGTTGGTCAAAGTTGTTTAAATGTTT 57.391 26.923 0.00 0.0 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 7.443259 AAATAGTAACGTTTGCAACTACCAT 57.557 32.000 5.91 0.0 0.00 3.55
20 21 9.106286 GTTAAAATAGTAACGTTTGCAACTACC 57.894 33.333 5.91 0.0 0.00 3.18
365 366 3.613494 TTCCGATTAACATGGAACCGA 57.387 42.857 0.00 0.0 36.87 4.69
439 440 9.942850 TGTGTTTCTAGTTTCATTCATCTCATA 57.057 29.630 0.00 0.0 0.00 2.15
448 449 7.339466 ACAGAAGGTTGTGTTTCTAGTTTCATT 59.661 33.333 0.00 0.0 29.44 2.57
461 463 2.690840 AGAGGGTACAGAAGGTTGTGT 58.309 47.619 0.00 0.0 38.34 3.72
529 531 6.326583 ACGGGTGAATCAGGAAATAGATAGAA 59.673 38.462 0.00 0.0 0.00 2.10
548 552 4.142049 ACCCATTTTTATATTGCACGGGTG 60.142 41.667 0.00 0.0 42.76 4.61
887 896 0.250945 TGGTGCTCTCACTCTCTCGT 60.251 55.000 0.00 0.0 42.72 4.18
905 914 4.077184 TAGCTTCCCACCGCCGTG 62.077 66.667 0.00 0.0 39.91 4.94
998 1007 0.391661 GGAGCTTGCGGAAGACATGA 60.392 55.000 21.87 0.0 0.00 3.07
1061 1070 1.371267 CGCGGACAGACGAAGACAA 60.371 57.895 0.00 0.0 35.47 3.18
1086 1095 2.103143 CTCCGATCAACGCTCGCT 59.897 61.111 0.00 0.0 41.07 4.93
1138 1147 0.386858 TTCTCGCTGCACACGTAGAC 60.387 55.000 0.00 0.0 0.00 2.59
1206 1215 4.949856 ACGGAATAGATCAACCAATTGCTT 59.050 37.500 0.00 0.0 35.63 3.91
1213 1222 4.545208 TGAACACGGAATAGATCAACCA 57.455 40.909 0.00 0.0 0.00 3.67
1239 1248 3.571401 CCCAAAGAAAGAAGCATGTCACT 59.429 43.478 0.00 0.0 0.00 3.41
1270 1279 7.388776 CAGTTCATTTATCAGAGTCTTGGTCAA 59.611 37.037 0.00 0.0 0.00 3.18
1273 1282 5.645497 GCAGTTCATTTATCAGAGTCTTGGT 59.355 40.000 0.00 0.0 0.00 3.67
1405 1415 5.620206 TCTTCAACATCCTAAGCTCAACAA 58.380 37.500 0.00 0.0 0.00 2.83
1669 1684 8.482852 TGAATTCCTCATTTCTTCTCCTTTTT 57.517 30.769 2.27 0.0 0.00 1.94
1670 1685 7.946776 TCTGAATTCCTCATTTCTTCTCCTTTT 59.053 33.333 2.27 0.0 32.14 2.27
1980 1997 3.319198 GGTTCGAGTCCCCAGCCA 61.319 66.667 0.00 0.0 0.00 4.75
2003 2020 2.030490 AACACCACTAACCCACGCGA 62.030 55.000 15.93 0.0 0.00 5.87
2041 2058 1.761784 CTCTTGCCATCTGTCCTAGCT 59.238 52.381 0.00 0.0 0.00 3.32


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

AutoCloner maintained by Alex Coulton.