AutoCloner

Multiple sequence alignment - TraesCS2A01G404300

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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	TraesCS2A01G404300	chr2A	100.000	2549	0	0	1	2549	659814012	659816560	0.000000e+00	4708
1	TraesCS2A01G404300	chr2A	92.699	452	32	1	118	569	162018588	162019038	0.000000e+00	651
2	TraesCS2A01G404300	chr1A	95.370	1987	81	8	569	2549	71245441	71243460	0.000000e+00	3149
3	TraesCS2A01G404300	chr1A	88.433	536	55	6	1	532	443732537	443732005	7.690000e-180	640
4	TraesCS2A01G404300	chr1A	90.980	255	11	3	2298	2548	556203463	556203709	1.460000e-87	333
5	TraesCS2A01G404300	chr1A	85.787	197	19	4	1	195	352609373	352609184	1.550000e-47	200
6	TraesCS2A01G404300	chr3A	95.140	1996	88	9	562	2549	696312550	696310556	0.000000e+00	3140
7	TraesCS2A01G404300	chr3A	92.747	455	32	1	116	569	611491458	611491004	0.000000e+00	656
8	TraesCS2A01G404300	chr3A	92.715	453	31	2	118	570	453089285	453088835	0.000000e+00	652
9	TraesCS2A01G404300	chr6B	94.414	2023	76	11	558	2549	660437755	660435739	0.000000e+00	3075
10	TraesCS2A01G404300	chr6B	87.826	575	53	15	6	570	181929358	181928791	0.000000e+00	658
11	TraesCS2A01G404300	chr2B	94.286	2030	81	11	551	2549	4739857	4741882	0.000000e+00	3073
12	TraesCS2A01G404300	chr1B	94.920	1949	85	8	571	2510	554735924	554733981	0.000000e+00	3038
13	TraesCS2A01G404300	chr6A	94.599	1981	72	9	561	2510	617222879	617220903	0.000000e+00	3033
14	TraesCS2A01G404300	chr5A	94.327	1992	92	13	566	2549	30204983	30206961	0.000000e+00	3033
15	TraesCS2A01G404300	chr5A	93.096	449	28	3	123	571	109995080	109995525	0.000000e+00	654
16	TraesCS2A01G404300	chr5A	92.699	452	32	1	118	569	374401495	374401045	0.000000e+00	651
17	TraesCS2A01G404300	chr5A	92.218	257	8	5	2298	2549	553436179	553435930	1.120000e-93	353
18	TraesCS2A01G404300	chrUn	94.589	1959	92	9	561	2510	87140318	87142271	0.000000e+00	3018
19	TraesCS2A01G404300	chrUn	94.108	1188	43	4	1389	2549	353552995	353551808	0.000000e+00	1781
20	TraesCS2A01G404300	chrUn	86.296	270	18	11	2298	2549	20575002	20575270	2.500000e-70	276
21	TraesCS2A01G404300	chr3D	93.383	1995	113	14	568	2549	410899591	410901579	0.000000e+00	2935
22	TraesCS2A01G404300	chr3D	92.188	256	8	3	2298	2549	527511338	527511585	4.030000e-93	351
23	TraesCS2A01G404300	chr7D	87.835	559	53	9	6	560	629352504	629353051	2.140000e-180	641
24	TraesCS2A01G404300	chr5B	85.589	569	69	9	6	565	519972294	519971730	3.650000e-163	584
25	TraesCS2A01G404300	chr3B	85.490	572	70	10	6	570	90232797	90233362	3.650000e-163	584
26	TraesCS2A01G404300	chr6D	91.732	254	12	3	2298	2549	448519203	448519449	6.750000e-91	344
27	TraesCS2A01G404300	chr6D	90.980	255	12	3	2298	2549	312542600	312542354	1.460000e-87	333
28	TraesCS2A01G404300	chr1D	91.051	257	9	3	2298	2548	464039268	464039516	4.060000e-88	335
29	TraesCS2A01G404300	chr4A	86.735	196	21	4	1	195	572417203	572417012	1.990000e-51	213

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	TraesCS2A01G404300	chr2A	659814012	659816560	2548	False	4708	4708	100.000	1	2549	1	chr2A.!!$F2	2548
1	TraesCS2A01G404300	chr1A	71243460	71245441	1981	True	3149	3149	95.370	569	2549	1	chr1A.!!$R1	1980
2	TraesCS2A01G404300	chr1A	443732005	443732537	532	True	640	640	88.433	1	532	1	chr1A.!!$R3	531
3	TraesCS2A01G404300	chr3A	696310556	696312550	1994	True	3140	3140	95.140	562	2549	1	chr3A.!!$R3	1987
4	TraesCS2A01G404300	chr6B	660435739	660437755	2016	True	3075	3075	94.414	558	2549	1	chr6B.!!$R2	1991
5	TraesCS2A01G404300	chr6B	181928791	181929358	567	True	658	658	87.826	6	570	1	chr6B.!!$R1	564
6	TraesCS2A01G404300	chr2B	4739857	4741882	2025	False	3073	3073	94.286	551	2549	1	chr2B.!!$F1	1998
7	TraesCS2A01G404300	chr1B	554733981	554735924	1943	True	3038	3038	94.920	571	2510	1	chr1B.!!$R1	1939
8	TraesCS2A01G404300	chr6A	617220903	617222879	1976	True	3033	3033	94.599	561	2510	1	chr6A.!!$R1	1949
9	TraesCS2A01G404300	chr5A	30204983	30206961	1978	False	3033	3033	94.327	566	2549	1	chr5A.!!$F1	1983
10	TraesCS2A01G404300	chrUn	87140318	87142271	1953	False	3018	3018	94.589	561	2510	1	chrUn.!!$F2	1949
11	TraesCS2A01G404300	chrUn	353551808	353552995	1187	True	1781	1781	94.108	1389	2549	1	chrUn.!!$R1	1160
12	TraesCS2A01G404300	chr3D	410899591	410901579	1988	False	2935	2935	93.383	568	2549	1	chr3D.!!$F1	1981
13	TraesCS2A01G404300	chr7D	629352504	629353051	547	False	641	641	87.835	6	560	1	chr7D.!!$F1	554
14	TraesCS2A01G404300	chr5B	519971730	519972294	564	True	584	584	85.589	6	565	1	chr5B.!!$R1	559
15	TraesCS2A01G404300	chr3B	90232797	90233362	565	False	584	584	85.490	6	570	1	chr3B.!!$F1	564

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
806	823	0.03601	CCCAACAGAGAGCCGTTGAT	60.036	55.0	3.93	0.0	44.2	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2323	2366	0.468226	AGGAAAACCACTCTCACGCA	59.532	50.0	0.0	0.0	0.0	5.24	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
56	57	6.993902	TCAAAAACTGAGGGAAATACTTACGT	59.006	34.615	0.00	0.00	0.00	3.57
58	59	6.796705	AAACTGAGGGAAATACTTACGTTG	57.203	37.500	0.00	0.00	0.00	4.10
95	97	4.474394	CCTTTCCTCTTCAAGGGAAAACT	58.526	43.478	16.45	0.00	42.49	2.66
121	124	0.252239	TGCTCAAGAGGTAGCAGGGA	60.252	55.000	0.00	0.00	43.56	4.20
173	183	1.625228	CCCCCTCTGGTACATCCTTCA	60.625	57.143	0.00	0.00	38.20	3.02
268	279	7.866870	AGGTCTCTAATATTTGCTCCTTTTCT	58.133	34.615	0.00	0.00	0.00	2.52
269	280	7.772757	AGGTCTCTAATATTTGCTCCTTTTCTG	59.227	37.037	0.00	0.00	0.00	3.02
287	298	2.912956	TCTGGCCCAGAATTCTAGTTGT	59.087	45.455	12.03	0.00	37.57	3.32
289	300	2.026262	TGGCCCAGAATTCTAGTTGTCC	60.026	50.000	7.86	4.79	0.00	4.02
294	305	3.557595	CCAGAATTCTAGTTGTCCGCATC	59.442	47.826	7.86	0.00	0.00	3.91
296	307	2.622064	ATTCTAGTTGTCCGCATCCC	57.378	50.000	0.00	0.00	0.00	3.85
388	399	8.426569	AACAGCCCATAATGCAATAAATATCT	57.573	30.769	0.00	0.00	0.00	1.98
391	402	9.961265	CAGCCCATAATGCAATAAATATCTATG	57.039	33.333	0.00	0.00	0.00	2.23
446	461	1.339151	CCCAAGCTTAGACCTCGCTTT	60.339	52.381	0.00	0.00	41.65	3.51
449	464	3.067106	CAAGCTTAGACCTCGCTTTTCA	58.933	45.455	0.00	0.00	41.65	2.69
461	476	2.997485	GCTTTTCATCAAGCGGAAGT	57.003	45.000	0.00	0.00	39.92	3.01
549	565	5.311265	TGAGGGCATCATGATCATTCTTAC	58.689	41.667	5.16	0.00	31.12	2.34
601	617	2.243736	TCCTTTTTCCCTCAGTGGTGTT	59.756	45.455	0.00	0.00	0.00	3.32
624	640	2.846193	TGTACTCAGTTTTGCCCTCAC	58.154	47.619	0.00	0.00	0.00	3.51
653	669	0.881796	GTGCTCAGTTTTGCCCCTAC	59.118	55.000	0.00	0.00	0.00	3.18
657	673	1.351017	CTCAGTTTTGCCCCTACTCCA	59.649	52.381	0.00	0.00	0.00	3.86
665	681	2.735772	CCCCTACTCCATGCGCACT	61.736	63.158	14.90	0.00	0.00	4.40
688	704	1.267261	CTCGTTCCGTGAACTCTGTCT	59.733	52.381	12.80	0.00	40.05	3.41
712	728	2.092861	TCCGTCAGGTCAACCTTTTGAA	60.093	45.455	0.00	0.00	46.09	2.69
738	754	1.462432	TTACAGGTGGGACCAGGCA	60.462	57.895	0.00	0.00	41.95	4.75
773	790	2.442212	TTTATCAGACCGTTGCACGA	57.558	45.000	9.75	0.00	46.05	4.35
806	823	0.036010	CCCAACAGAGAGCCGTTGAT	60.036	55.000	3.93	0.00	44.20	2.57
814	831	1.748493	GAGAGCCGTTGATCAGAGAGT	59.252	52.381	0.00	0.00	0.00	3.24
868	891	4.953868	CGGTGACCACGGCGACAA	62.954	66.667	16.62	0.00	0.00	3.18
904	931	0.461163	CACGGCGAGAGAGAGAGAGA	60.461	60.000	16.62	0.00	0.00	3.10
905	932	0.179084	ACGGCGAGAGAGAGAGAGAG	60.179	60.000	16.62	0.00	0.00	3.20
909	936	2.011548	GCGAGAGAGAGAGAGAGCACA	61.012	57.143	0.00	0.00	0.00	4.57
1118	1146	0.969894	CGGAGGGTTTCTCAGACACT	59.030	55.000	0.00	0.00	44.19	3.55
1135	1163	2.368875	ACACTGAGGAACCAGAATCGTT	59.631	45.455	0.00	0.00	37.59	3.85
1251	1281	1.170442	TCATGCAGGTGACATGCTTG	58.830	50.000	25.65	25.65	45.33	4.01
1321	1351	4.660168	AGAAGAGCATGAAGAATGGTTGT	58.340	39.130	0.00	0.00	46.95	3.32
1594	1624	8.256605	TCTTGAAATTGTTTGAGAAATTCACCA	58.743	29.630	0.00	0.00	34.94	4.17
1660	1690	8.697507	AAAGAGAAGAAGTGACCAACATTTAT	57.302	30.769	0.00	0.00	0.00	1.40
1727	1758	5.677567	TGATCAATGAAATGCAGCTCTCTA	58.322	37.500	0.00	0.00	0.00	2.43
1833	1865	1.620323	GCATCCAATTAGGCCCATTCC	59.380	52.381	0.00	0.00	37.29	3.01
1836	1868	0.184933	CCAATTAGGCCCATTCCGGA	59.815	55.000	0.00	0.00	36.56	5.14
1936	1969	6.710744	GGAAGCTAATTGAATTATTCCGGAGA	59.289	38.462	3.34	0.00	29.32	3.71
1948	1981	9.849166	GAATTATTCCGGAGACAAACAATTAAA	57.151	29.630	3.34	0.00	0.00	1.52
1950	1983	8.624367	TTATTCCGGAGACAAACAATTAAAGA	57.376	30.769	3.34	0.00	0.00	2.52
2144	2180	3.967332	AATGAAGGGTGGAAAATGCAG	57.033	42.857	0.00	0.00	0.00	4.41
2181	2217	1.609794	GGGACTCGAACCCAGGACT	60.610	63.158	18.78	0.00	46.05	3.85
2195	2231	1.822186	GGACTGCGTGGGTTTGTGT	60.822	57.895	0.00	0.00	0.00	3.72
2215	2251	2.046314	TTTAGGGCTGCGCTGGTC	60.046	61.111	27.01	6.71	0.00	4.02
2323	2366	2.226437	GAGACCGTGAATGTTTGCACAT	59.774	45.455	0.00	0.00	46.34	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	59	0.319405	AAAGGGTGATGCAGCAAAGC	59.681	50.000	6.05	0.00	33.07	3.51
95	97	2.738643	GCTACCTCTTGAGCATGCGTTA	60.739	50.000	13.01	0.00	38.62	3.18
209	220	5.449553	ACTCCAAAAGTCCTGAAACTTCAT	58.550	37.500	0.00	0.00	38.52	2.57
268	279	2.026262	GGACAACTAGAATTCTGGGCCA	60.026	50.000	21.34	5.85	0.00	5.36
269	280	2.644676	GGACAACTAGAATTCTGGGCC	58.355	52.381	21.34	13.86	0.00	5.80
296	307	4.034285	ACAAGGTTTACATGAAGAGGGG	57.966	45.455	0.00	0.00	0.00	4.79
352	363	6.642131	GCATTATGGGCTGTTATTACACATTG	59.358	38.462	0.00	0.00	0.00	2.82
388	399	7.554211	TCCATTTTGCATCATGCTTTTACATA	58.446	30.769	11.84	0.00	45.31	2.29
391	402	6.314400	ACATCCATTTTGCATCATGCTTTTAC	59.686	34.615	11.84	0.00	45.31	2.01
414	425	1.668826	AGCTTGGGGGAGTTGATACA	58.331	50.000	0.00	0.00	0.00	2.29
446	461	2.672961	ATCGACTTCCGCTTGATGAA	57.327	45.000	0.00	0.00	38.37	2.57
449	464	2.552743	TCGATATCGACTTCCGCTTGAT	59.447	45.455	23.48	0.00	44.22	2.57
461	476	7.655732	ACATGTGGTCATATTTTTCGATATCGA	59.344	33.333	23.48	23.48	38.46	3.59
479	494	5.163195	ACACCTCTTTCTCTAAACATGTGGT	60.163	40.000	0.00	0.00	0.00	4.16
587	603	1.434188	ACATGAACACCACTGAGGGA	58.566	50.000	0.00	0.00	43.89	4.20
601	617	3.072330	TGAGGGCAAAACTGAGTACATGA	59.928	43.478	0.00	0.00	0.00	3.07
624	640	2.624316	AACTGAGCACAATTCGCATG	57.376	45.000	0.00	0.00	0.00	4.06
653	669	2.163390	CGAGTCAGTGCGCATGGAG	61.163	63.158	15.91	3.97	0.00	3.86
657	673	1.738099	GGAACGAGTCAGTGCGCAT	60.738	57.895	15.91	0.00	0.00	4.73
688	704	3.143010	AGGTTGACCTGACGGAGAA	57.857	52.632	0.97	0.00	46.55	2.87
738	754	2.489938	TAAAATTGGCCGTCTCTGCT	57.510	45.000	0.00	0.00	0.00	4.24
773	790	2.391130	TTGGGTCCCACAAGCCACT	61.391	57.895	11.24	0.00	46.05	4.00
806	823	2.636412	CCCGCCAACGACTCTCTGA	61.636	63.158	0.00	0.00	43.93	3.27
814	831	1.605971	TATAGCACACCCGCCAACGA	61.606	55.000	0.00	0.00	43.93	3.85
843	860	2.898343	GTGGTCACCGCCGTTGTT	60.898	61.111	0.00	0.00	0.00	2.83
868	891	4.681978	GGTCACCGCCGTGCTCTT	62.682	66.667	0.00	0.00	40.04	2.85
905	932	3.605749	TAGCTTCCCACCGCTGTGC	62.606	63.158	2.22	0.00	41.35	4.57
909	936	2.685380	AGCTAGCTTCCCACCGCT	60.685	61.111	12.68	0.00	40.15	5.52
941	969	0.835941	CTCCACTGCTAGCTTCCCAT	59.164	55.000	17.23	0.00	0.00	4.00
1118	1146	1.616865	ACGAACGATTCTGGTTCCTCA	59.383	47.619	0.14	0.00	40.46	3.86
1135	1163	1.728074	CGCTGCACACGTAGAACGA	60.728	57.895	6.44	0.00	46.05	3.85
1197	1227	3.094572	CAACCCATTGCTCAAAGATCCT	58.905	45.455	0.00	0.00	0.00	3.24
1251	1281	2.160417	CAGAGCATCGACCCAAAGAAAC	59.840	50.000	0.00	0.00	42.67	2.78
1614	1644	9.693157	CTCTTTTTGTTTCAACATTTAAGCAAG	57.307	29.630	0.00	0.00	38.95	4.01
1727	1758	3.297134	TTTTGGACAGAAAGGCAGAGT	57.703	42.857	0.00	0.00	0.00	3.24
1833	1865	4.389077	AGAAAAATACGCAAGAGAACTCCG	59.611	41.667	0.00	0.00	43.62	4.63
1836	1868	6.619801	AACAGAAAAATACGCAAGAGAACT	57.380	33.333	0.00	0.00	43.62	3.01
2162	2198	1.609794	GTCCTGGGTTCGAGTCCCT	60.610	63.158	22.42	0.00	44.84	4.20
2181	2217	0.603569	AAACAACACAAACCCACGCA	59.396	45.000	0.00	0.00	0.00	5.24
2215	2251	0.538584	TGCCATCTGTCCTAGCAGTG	59.461	55.000	0.00	0.00	37.70	3.66
2218	2254	1.208052	GTCTTGCCATCTGTCCTAGCA	59.792	52.381	0.00	0.00	0.00	3.49
2323	2366	0.468226	AGGAAAACCACTCTCACGCA	59.532	50.000	0.00	0.00	0.00	5.24
2493	2588	1.596496	AAATCGGAGGGGGTGAGAAT	58.404	50.000	0.00	0.00	0.00	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.