Multiple sequence alignment - TraesCS1B01G286400

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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 TraesCS1B01G286400 chr1B 100.000 2549 0 0 1 2549 498442987 498440439 0 4708
1 TraesCS1B01G286400 chr1B 94.542 568 31 0 1 568 415019381 415018814 0 878
2 TraesCS1B01G286400 chr5B 96.429 1988 63 4 567 2548 446193256 446191271 0 3271
3 TraesCS1B01G286400 chr5B 95.926 1988 72 5 569 2549 269389473 269391458 0 3214
4 TraesCS1B01G286400 chr5B 94.190 568 33 0 1 568 48894651 48895218 0 867
5 TraesCS1B01G286400 chr5B 93.673 569 33 3 1 568 493412759 493412193 0 848
6 TraesCS1B01G286400 chr5B 93.486 568 37 0 1 568 502679548 502678981 0 845
7 TraesCS1B01G286400 chr2B 96.121 1985 73 3 568 2549 36241849 36243832 0 3236
8 TraesCS1B01G286400 chr2B 96.028 1989 73 3 567 2549 596962067 596964055 0 3230
9 TraesCS1B01G286400 chr2B 95.980 1990 70 6 569 2549 602077185 602075197 0 3223
10 TraesCS1B01G286400 chr2B 95.917 1984 74 6 569 2549 544319641 544317662 0 3208
11 TraesCS1B01G286400 chr2B 95.867 1984 75 6 569 2549 543889470 543887491 0 3203
12 TraesCS1B01G286400 chr3B 95.980 1990 70 8 568 2549 722334705 722336692 0 3223
13 TraesCS1B01G286400 chr3B 94.014 568 34 0 1 568 158348440 158349007 0 861
14 TraesCS1B01G286400 chr7B 95.968 1984 75 4 569 2549 718488474 718486493 0 3216
15 TraesCS1B01G286400 chr7B 94.014 568 32 2 1 568 655016152 655015587 0 859
16 TraesCS1B01G286400 chr7B 93.310 568 38 0 1 568 529571643 529571076 0 839
17 TraesCS1B01G286400 chr4B 94.366 568 32 0 1 568 77778927 77779494 0 872
18 TraesCS1B01G286400 chr6B 94.190 568 32 1 1 568 632148647 632148081 0 865


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 TraesCS1B01G286400 chr1B 498440439 498442987 2548 True 4708 4708 100.000 1 2549 1 chr1B.!!$R2 2548
1 TraesCS1B01G286400 chr1B 415018814 415019381 567 True 878 878 94.542 1 568 1 chr1B.!!$R1 567
2 TraesCS1B01G286400 chr5B 446191271 446193256 1985 True 3271 3271 96.429 567 2548 1 chr5B.!!$R1 1981
3 TraesCS1B01G286400 chr5B 269389473 269391458 1985 False 3214 3214 95.926 569 2549 1 chr5B.!!$F2 1980
4 TraesCS1B01G286400 chr5B 48894651 48895218 567 False 867 867 94.190 1 568 1 chr5B.!!$F1 567
5 TraesCS1B01G286400 chr5B 493412193 493412759 566 True 848 848 93.673 1 568 1 chr5B.!!$R2 567
6 TraesCS1B01G286400 chr5B 502678981 502679548 567 True 845 845 93.486 1 568 1 chr5B.!!$R3 567
7 TraesCS1B01G286400 chr2B 36241849 36243832 1983 False 3236 3236 96.121 568 2549 1 chr2B.!!$F1 1981
8 TraesCS1B01G286400 chr2B 596962067 596964055 1988 False 3230 3230 96.028 567 2549 1 chr2B.!!$F2 1982
9 TraesCS1B01G286400 chr2B 602075197 602077185 1988 True 3223 3223 95.980 569 2549 1 chr2B.!!$R3 1980
10 TraesCS1B01G286400 chr2B 544317662 544319641 1979 True 3208 3208 95.917 569 2549 1 chr2B.!!$R2 1980
11 TraesCS1B01G286400 chr2B 543887491 543889470 1979 True 3203 3203 95.867 569 2549 1 chr2B.!!$R1 1980
12 TraesCS1B01G286400 chr3B 722334705 722336692 1987 False 3223 3223 95.980 568 2549 1 chr3B.!!$F2 1981
13 TraesCS1B01G286400 chr3B 158348440 158349007 567 False 861 861 94.014 1 568 1 chr3B.!!$F1 567
14 TraesCS1B01G286400 chr7B 718486493 718488474 1981 True 3216 3216 95.968 569 2549 1 chr7B.!!$R3 1980
15 TraesCS1B01G286400 chr7B 655015587 655016152 565 True 859 859 94.014 1 568 1 chr7B.!!$R2 567
16 TraesCS1B01G286400 chr7B 529571076 529571643 567 True 839 839 93.310 1 568 1 chr7B.!!$R1 567
17 TraesCS1B01G286400 chr4B 77778927 77779494 567 False 872 872 94.366 1 568 1 chr4B.!!$F1 567
18 TraesCS1B01G286400 chr6B 632148081 632148647 566 True 865 865 94.190 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
221 222 1.077716 GTGACCCCAGCCGCTATTT 60.078 57.895 0.0 0.0 0.0 1.40 F
788 789 1.221840 CGCATGGCTTGTAGGACCT 59.778 57.895 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1190 1194 0.036388 GCTCAAAGATCCCGACCACA 60.036 55.000 0.0 0.0 0.0 4.17 R
2386 2399 2.890945 GTGCCACTCTAACCAAAACCAT 59.109 45.455 0.0 0.0 0.0 3.55 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
21 22 2.284405 GGACGAACTGGAGGGGGA 60.284 66.667 0.00 0.00 0.00 4.81
45 46 4.003648 GTGAATGGGTCGAAAGTGAATCT 58.996 43.478 0.00 0.00 0.00 2.40
84 85 1.414919 GTGGTCCTGTCCTTGTGTGTA 59.585 52.381 0.00 0.00 0.00 2.90
221 222 1.077716 GTGACCCCAGCCGCTATTT 60.078 57.895 0.00 0.00 0.00 1.40
381 382 2.758009 GTGAGTGTTTTACCGGTGCTA 58.242 47.619 19.93 0.00 0.00 3.49
781 782 2.336088 GTTGCACGCATGGCTTGT 59.664 55.556 2.12 0.00 30.33 3.16
788 789 1.221840 CGCATGGCTTGTAGGACCT 59.778 57.895 0.00 0.00 0.00 3.85
807 809 3.801129 GCAGAGAGCCGTTAAGCC 58.199 61.111 0.00 0.00 37.23 4.35
965 969 3.775654 GCTAGCTGTGGAGGGCGT 61.776 66.667 7.70 0.00 0.00 5.68
1215 1219 1.480545 TCGGGATCTTTGAGCAATCGA 59.519 47.619 0.00 0.00 0.00 3.59
1284 1288 1.759445 GATGCTCTGGCCAAGACTCTA 59.241 52.381 7.01 0.00 37.74 2.43
1397 1401 2.546321 CGAAGCACGCACTGACAC 59.454 61.111 0.00 0.00 34.51 3.67
1408 1412 1.474478 GCACTGACACAGAGCTAGCTA 59.526 52.381 19.38 0.00 42.94 3.32
1709 1715 7.929785 AGAAACTTTTGATCAATGAAATGCAGT 59.070 29.630 9.40 0.00 0.00 4.40
1890 1896 7.296628 ACACCTAGTGCCAAAATAAATGAAA 57.703 32.000 0.00 0.00 36.98 2.69
1891 1897 7.906327 ACACCTAGTGCCAAAATAAATGAAAT 58.094 30.769 0.00 0.00 36.98 2.17
2212 2222 0.464452 GCTGGTAACCGCTAGGACAT 59.536 55.000 0.00 0.00 41.02 3.06
2355 2368 3.069443 GCACTGAAATTTTGGAGGGTTGA 59.931 43.478 0.00 0.00 0.00 3.18
2386 2399 1.685148 TGTATGTTTGCACTGCCACA 58.315 45.000 5.77 5.77 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.285962 CATTCACATCCCCCTCCAGTT 59.714 52.381 0.00 0.00 0.00 3.16
21 22 3.417069 TCACTTTCGACCCATTCACAT 57.583 42.857 0.00 0.00 0.00 3.21
45 46 1.292223 GCAGGTAGACGGCAGTTCA 59.708 57.895 0.00 0.00 40.25 3.18
158 159 0.179029 CCAACCACAGGAGGACGTTT 60.179 55.000 0.00 0.00 0.00 3.60
221 222 1.758514 GAGTCCGGGATGCCTCTCA 60.759 63.158 0.00 0.00 0.00 3.27
338 339 3.128375 CGTGCAAAGCCAAACCCT 58.872 55.556 0.00 0.00 0.00 4.34
369 370 1.134521 CATCAGGCTAGCACCGGTAAA 60.135 52.381 18.24 0.00 33.69 2.01
381 382 2.632377 CACGTGGTAAATCATCAGGCT 58.368 47.619 7.95 0.00 0.00 4.58
637 638 0.769247 ACGGACTAGGGGCAAAACTT 59.231 50.000 0.00 0.00 0.00 2.66
669 670 2.808543 GAGACGCCAAAGTTCACAGAAT 59.191 45.455 0.00 0.00 0.00 2.40
781 782 0.179015 CGGCTCTCTGCTAGGTCCTA 60.179 60.000 0.00 0.00 42.39 2.94
788 789 0.460311 GGCTTAACGGCTCTCTGCTA 59.540 55.000 0.00 0.00 42.39 3.49
803 804 2.125512 CGCAACGGCTCTAGGCTT 60.126 61.111 0.00 0.00 41.46 4.35
807 809 2.509336 CACCCGCAACGGCTCTAG 60.509 66.667 0.00 0.00 46.86 2.43
862 864 2.182791 CGCCATGCTCTCTGTCGT 59.817 61.111 0.00 0.00 0.00 4.34
882 884 1.974265 CTCTCTCTCTCGCCATGGTA 58.026 55.000 14.67 0.74 0.00 3.25
965 969 4.467084 GGGATCTCAACGCCGCCA 62.467 66.667 0.00 0.00 0.00 5.69
1099 1103 0.472471 GGTGTGTGAGAAACCCTCCA 59.528 55.000 0.00 0.00 41.25 3.86
1190 1194 0.036388 GCTCAAAGATCCCGACCACA 60.036 55.000 0.00 0.00 0.00 4.17
1215 1219 4.216042 TGCATGAACACGAAACAGATCAAT 59.784 37.500 0.00 0.00 0.00 2.57
1284 1288 6.579666 TGCTCTTCTTGCAGTTCATTTATT 57.420 33.333 0.00 0.00 35.31 1.40
1408 1412 6.715280 TCTTCTTCAACATCCTAAGCTCAAT 58.285 36.000 0.00 0.00 0.00 2.57
1723 1729 8.927675 TTTCTAACCTTAATTGTTTGGCTCTA 57.072 30.769 0.00 0.00 0.00 2.43
2212 2222 3.245229 ACCCATGTCAAACTCTTGCCATA 60.245 43.478 0.00 0.00 29.52 2.74
2355 2368 7.011295 CAGTGCAAACATACATTTTCAACCTTT 59.989 33.333 0.00 0.00 0.00 3.11
2386 2399 2.890945 GTGCCACTCTAACCAAAACCAT 59.109 45.455 0.00 0.00 0.00 3.55



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

AutoCloner maintained by Alex Coulton.