Multiple sequence alignment - TraesCS2B01G069200

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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 TraesCS2B01G069200 chr2B 100.000 2549 0 0 1 2549 36241284 36243832 0 4708
1 TraesCS2B01G069200 chr2B 96.071 1985 71 7 567 2549 543889470 543887491 0 3227
2 TraesCS2B01G069200 chr2B 95.877 1989 76 4 566 2549 596962068 596964055 0 3214
3 TraesCS2B01G069200 chr2B 95.881 1991 72 7 567 2549 602077185 602075197 0 3214
4 TraesCS2B01G069200 chr2B 95.919 1985 74 7 567 2549 544319641 544317662 0 3210
5 TraesCS2B01G069200 chr1B 96.121 1985 73 3 566 2549 498442420 498440439 0 3236
6 TraesCS2B01G069200 chr3B 95.924 1987 71 6 567 2549 703251169 703253149 0 3212
7 TraesCS2B01G069200 chr3B 95.785 1993 74 9 564 2549 722334703 722336692 0 3206
8 TraesCS2B01G069200 chr3B 93.333 570 30 3 1 566 779496439 779497004 0 835
9 TraesCS2B01G069200 chr7B 95.869 1985 77 5 567 2549 718488474 718486493 0 3206
10 TraesCS2B01G069200 chr7B 93.068 577 25 6 1 566 611290152 611290724 0 830
11 TraesCS2B01G069200 chr5B 95.825 1988 75 5 566 2548 446193255 446191271 0 3205
12 TraesCS2B01G069200 chr5B 93.728 574 24 8 1 566 447154430 447154999 0 850
13 TraesCS2B01G069200 chr5B 93.437 579 21 7 1 566 680532895 680532321 0 843
14 TraesCS2B01G069200 chr4B 93.554 574 25 5 1 566 593777201 593776632 0 845
15 TraesCS2B01G069200 chr4B 93.194 573 27 7 1 566 40591624 40592191 0 832
16 TraesCS2B01G069200 chr6B 93.380 574 25 7 1 566 28075063 28075631 0 837
17 TraesCS2B01G069200 chr4A 93.264 579 22 7 1 566 711159371 711158797 0 837
18 TraesCS2B01G069200 chr4A 93.056 576 26 7 1 566 729833517 729834088 0 830


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 TraesCS2B01G069200 chr2B 36241284 36243832 2548 False 4708 4708 100.000 1 2549 1 chr2B.!!$F1 2548
1 TraesCS2B01G069200 chr2B 543887491 543889470 1979 True 3227 3227 96.071 567 2549 1 chr2B.!!$R1 1982
2 TraesCS2B01G069200 chr2B 596962068 596964055 1987 False 3214 3214 95.877 566 2549 1 chr2B.!!$F2 1983
3 TraesCS2B01G069200 chr2B 602075197 602077185 1988 True 3214 3214 95.881 567 2549 1 chr2B.!!$R3 1982
4 TraesCS2B01G069200 chr2B 544317662 544319641 1979 True 3210 3210 95.919 567 2549 1 chr2B.!!$R2 1982
5 TraesCS2B01G069200 chr1B 498440439 498442420 1981 True 3236 3236 96.121 566 2549 1 chr1B.!!$R1 1983
6 TraesCS2B01G069200 chr3B 703251169 703253149 1980 False 3212 3212 95.924 567 2549 1 chr3B.!!$F1 1982
7 TraesCS2B01G069200 chr3B 722334703 722336692 1989 False 3206 3206 95.785 564 2549 1 chr3B.!!$F2 1985
8 TraesCS2B01G069200 chr3B 779496439 779497004 565 False 835 835 93.333 1 566 1 chr3B.!!$F3 565
9 TraesCS2B01G069200 chr7B 718486493 718488474 1981 True 3206 3206 95.869 567 2549 1 chr7B.!!$R1 1982
10 TraesCS2B01G069200 chr7B 611290152 611290724 572 False 830 830 93.068 1 566 1 chr7B.!!$F1 565
11 TraesCS2B01G069200 chr5B 446191271 446193255 1984 True 3205 3205 95.825 566 2548 1 chr5B.!!$R1 1982
12 TraesCS2B01G069200 chr5B 447154430 447154999 569 False 850 850 93.728 1 566 1 chr5B.!!$F1 565
13 TraesCS2B01G069200 chr5B 680532321 680532895 574 True 843 843 93.437 1 566 1 chr5B.!!$R2 565
14 TraesCS2B01G069200 chr4B 593776632 593777201 569 True 845 845 93.554 1 566 1 chr4B.!!$R1 565
15 TraesCS2B01G069200 chr4B 40591624 40592191 567 False 832 832 93.194 1 566 1 chr4B.!!$F1 565
16 TraesCS2B01G069200 chr6B 28075063 28075631 568 False 837 837 93.380 1 566 1 chr6B.!!$F1 565
17 TraesCS2B01G069200 chr4A 711158797 711159371 574 True 837 837 93.264 1 566 1 chr4A.!!$R1 565
18 TraesCS2B01G069200 chr4A 729833517 729834088 571 False 830 830 93.056 1 566 1 chr4A.!!$F1 565

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
407 423 0.469892 CACCCCAAACCCTTGAAGCT 60.470 55.0 0.0 0.0 34.14 3.74 F
1018 1041 0.392193 CATGTCTTCCGCAAGCTCCT 60.392 55.0 0.0 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1385 1408 2.010497 CTAGCTCTCTGTCAGTGCGTA 58.990 52.381 0.00 0.0 44.91 4.42 R
2154 2183 2.280524 CACGCGGTCTTGGGTTCA 60.281 61.111 12.47 0.0 32.02 3.18 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
165 176 3.139770 AGGGGCGGTCGATATATATACCT 59.860 47.826 11.32 0.00 0.00 3.08
201 213 7.042335 GTGATAACTTATACCACAAGAGCACT 58.958 38.462 0.00 0.00 0.00 4.40
285 297 3.116318 GGTCTCCTACCCCCTCCA 58.884 66.667 0.00 0.00 43.16 3.86
407 423 0.469892 CACCCCAAACCCTTGAAGCT 60.470 55.000 0.00 0.00 34.14 3.74
408 424 1.154430 ACCCCAAACCCTTGAAGCTA 58.846 50.000 0.00 0.00 34.14 3.32
409 425 1.075536 ACCCCAAACCCTTGAAGCTAG 59.924 52.381 0.00 0.00 34.14 3.42
410 426 1.177401 CCCAAACCCTTGAAGCTAGC 58.823 55.000 6.62 6.62 34.14 3.42
436 452 0.477993 TAGGCCACCCCAAACCCTAA 60.478 55.000 5.01 0.00 35.39 2.69
874 897 2.986413 ACGGCGACAGAGAGCACT 60.986 61.111 16.62 0.00 34.54 4.40
930 953 1.078143 GTGGGAAGCTAGCTGTGGG 60.078 63.158 20.16 0.00 0.00 4.61
963 986 1.268283 GGAAGCTAGCTGTGGAGGGT 61.268 60.000 20.16 0.00 0.00 4.34
1018 1041 0.392193 CATGTCTTCCGCAAGCTCCT 60.392 55.000 0.00 0.00 0.00 3.69
1061 1084 3.422303 GGCGCGTGTTGAGATGCA 61.422 61.111 8.43 0.00 0.00 3.96
1324 1347 1.796151 CATGACGAATGGTTGCGCT 59.204 52.632 9.73 0.00 32.10 5.92
1326 1349 1.396648 CATGACGAATGGTTGCGCTTA 59.603 47.619 9.73 0.00 32.10 3.09
1380 1403 1.689575 CCGGAAGAAGAGATGGAGGGA 60.690 57.143 0.00 0.00 0.00 4.20
1385 1408 3.774842 AGAAGAGATGGAGGGAGAAGT 57.225 47.619 0.00 0.00 0.00 3.01
1823 1847 8.385898 AGTACACCGTGATTTAAATCAAAGAA 57.614 30.769 28.02 12.08 46.13 2.52
1844 1868 9.829507 AAAGAACAAAATGTCATGGAAAATGTA 57.170 25.926 0.00 0.00 0.00 2.29
1874 1898 5.360144 GCTCTGGTAGATGTTTACACCTAGA 59.640 44.000 0.00 0.00 32.04 2.43
1890 1914 7.158099 ACACCTAGAGCCAAAATAAATGAAC 57.842 36.000 0.00 0.00 0.00 3.18
2026 2052 3.055719 TGTTTAGGGCTGCGCTGC 61.056 61.111 28.81 28.81 0.00 5.25
2039 2065 1.364171 CGCTGCTAACCGCTAGGAT 59.636 57.895 0.00 0.00 41.02 3.24
2077 2103 2.026641 CATGGGTAGGGAAGCAATGTG 58.973 52.381 0.00 0.00 33.09 3.21
2083 2109 3.627577 GGTAGGGAAGCAATGTGTACATG 59.372 47.826 0.00 0.00 36.56 3.21
2093 2119 4.568956 CAATGTGTACATGGTGAGACTGA 58.431 43.478 0.00 0.00 36.56 3.41
2238 2267 3.559171 GGCAAGAGTTTGACATGGGTAGA 60.559 47.826 0.00 0.00 42.21 2.59
2319 2351 1.367102 TGCACACGCATGAGAGTGA 59.633 52.632 26.13 11.60 46.89 3.41
2449 2481 6.325286 AGTGGCACTTGGTTTAGGATTTAAAA 59.675 34.615 15.88 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.079615 TCGGGAGGGGATATATCGATAACA 60.080 45.833 9.61 0.73 0.00 2.41
11 12 2.784095 TCTCGGGAGGGGATATATCGAT 59.216 50.000 2.16 2.16 0.00 3.59
20 21 0.178915 TTGAAGTTCTCGGGAGGGGA 60.179 55.000 4.17 0.00 0.00 4.81
53 61 1.098589 ATCGGGGAGGGGGTATATCA 58.901 55.000 0.00 0.00 0.00 2.15
165 176 2.414994 AGTTATCACGGTCGAGAGGA 57.585 50.000 0.00 0.00 0.00 3.71
222 234 1.149148 GTGTCCTCGAGAGTTTTGGC 58.851 55.000 15.71 0.00 0.00 4.52
407 423 0.837272 GGGTGGCCTAGACAATGCTA 59.163 55.000 3.32 0.00 0.00 3.49
408 424 1.609783 GGGTGGCCTAGACAATGCT 59.390 57.895 3.32 0.00 0.00 3.79
409 425 1.453928 GGGGTGGCCTAGACAATGC 60.454 63.158 3.32 0.00 0.00 3.56
410 426 0.331278 TTGGGGTGGCCTAGACAATG 59.669 55.000 3.32 0.00 0.00 2.82
436 452 2.433318 GCCTCGACGCTGCTTCTT 60.433 61.111 4.58 0.00 0.00 2.52
480 496 2.858941 GCAAACGTAGAACTAGCTAGCC 59.141 50.000 20.91 12.60 0.00 3.93
838 861 4.570663 GTCACCGCCGCTATCGCT 62.571 66.667 0.00 0.00 0.00 4.93
1053 1076 2.232208 ACAGACGAAGACATGCATCTCA 59.768 45.455 4.70 0.00 0.00 3.27
1061 1084 1.154016 CGCGGACAGACGAAGACAT 60.154 57.895 0.00 0.00 35.47 3.06
1324 1347 2.516405 TGCGGTTTGGGGCAGTAA 59.484 55.556 0.00 0.00 33.52 2.24
1380 1403 2.486203 CTCTCTGTCAGTGCGTACTTCT 59.514 50.000 2.37 0.00 34.07 2.85
1385 1408 2.010497 CTAGCTCTCTGTCAGTGCGTA 58.990 52.381 0.00 0.00 44.91 4.42
1675 1699 8.090214 TCATTGATCAAAAGTTTCTGAATTCCC 58.910 33.333 13.09 0.00 0.00 3.97
1799 1823 8.071368 TGTTCTTTGATTTAAATCACGGTGTAC 58.929 33.333 26.69 19.26 44.54 2.90
1823 1847 7.015098 TGAGGTACATTTTCCATGACATTTTGT 59.985 33.333 0.00 0.00 0.00 2.83
1844 1868 2.541233 ACATCTACCAGAGCTGAGGT 57.459 50.000 11.16 11.16 41.89 3.85
1983 2009 2.593436 CCACGCGGTCTTGGGTTT 60.593 61.111 12.47 0.00 32.02 3.27
2026 2052 2.826128 TGCCATCTATCCTAGCGGTTAG 59.174 50.000 0.00 0.00 35.00 2.34
2039 2065 4.264253 CCATGTCAAACTCTTGCCATCTA 58.736 43.478 0.00 0.00 28.75 1.98
2077 2103 8.723942 ATAAATTTCTCAGTCTCACCATGTAC 57.276 34.615 0.00 0.00 0.00 2.90
2154 2183 2.280524 CACGCGGTCTTGGGTTCA 60.281 61.111 12.47 0.00 32.02 3.18
2310 2342 6.703165 GCAAAACAAAGGAAAATCACTCTCAT 59.297 34.615 0.00 0.00 0.00 2.90
2319 2351 7.628769 ATTTCAGTGCAAAACAAAGGAAAAT 57.371 28.000 0.00 0.00 31.61 1.82
2449 2481 9.590451 CATGAACTAACATGCAAATTTATTCCT 57.410 29.630 0.00 0.00 40.54 3.36


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

AutoCloner maintained by Alex Coulton.