AutoCloner

Multiple sequence alignment - TraesCS2D01G225700

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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	TraesCS2D01G225700	chr2D	100.000	2588	0	0	1	2588	193341852	193344439	0.000000e+00	4780
1	TraesCS2D01G225700	chr2B	92.938	1501	67	12	502	1994	249463466	249464935	0.000000e+00	2148
2	TraesCS2D01G225700	chr2B	97.167	353	7	1	1999	2351	249464971	249465320	6.170000e-166	593
3	TraesCS2D01G225700	chr2B	95.570	158	7	0	2431	2588	249465330	249465487	1.190000e-63	254
4	TraesCS2D01G225700	chr2A	91.896	1382	72	16	499	1876	207580123	207581468	0.000000e+00	1895
5	TraesCS2D01G225700	chr2A	96.021	578	23	0	2011	2588	207581661	207582238	0.000000e+00	941
6	TraesCS2D01G225700	chr5D	90.400	500	45	3	7	503	558036836	558036337	0.000000e+00	654
7	TraesCS2D01G225700	chr5B	90.119	506	47	3	1	505	425113094	425112591	0.000000e+00	654
8	TraesCS2D01G225700	chr5B	90.119	506	47	3	1	505	658179098	658179601	0.000000e+00	654
9	TraesCS2D01G225700	chrUn	89.723	506	49	3	1	505	53928201	53928704	0.000000e+00	643
10	TraesCS2D01G225700	chr6B	89.723	506	48	4	1	505	561640868	561641370	0.000000e+00	643
11	TraesCS2D01G225700	chr3A	89.723	506	49	3	1	505	743535643	743535140	0.000000e+00	643
12	TraesCS2D01G225700	chr4D	89.683	504	49	3	1	501	51987756	51988259	7.810000e-180	640
13	TraesCS2D01G225700	chr5A	89.526	506	50	3	1	505	99023026	99022523	2.810000e-179	638
14	TraesCS2D01G225700	chr7A	89.349	507	49	4	1	505	679315536	679315033	1.310000e-177	632

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	TraesCS2D01G225700	chr2D	193341852	193344439	2587	False	4780.000000	4780	100.0000	1	2588	1	chr2D.!!$F1	2587
1	TraesCS2D01G225700	chr2B	249463466	249465487	2021	False	998.333333	2148	95.2250	502	2588	3	chr2B.!!$F1	2086
2	TraesCS2D01G225700	chr2A	207580123	207582238	2115	False	1418.000000	1895	93.9585	499	2588	2	chr2A.!!$F1	2089
3	TraesCS2D01G225700	chr5B	425112591	425113094	503	True	654.000000	654	90.1190	1	505	1	chr5B.!!$R1	504
4	TraesCS2D01G225700	chr5B	658179098	658179601	503	False	654.000000	654	90.1190	1	505	1	chr5B.!!$F1	504
5	TraesCS2D01G225700	chrUn	53928201	53928704	503	False	643.000000	643	89.7230	1	505	1	chrUn.!!$F1	504
6	TraesCS2D01G225700	chr6B	561640868	561641370	502	False	643.000000	643	89.7230	1	505	1	chr6B.!!$F1	504
7	TraesCS2D01G225700	chr3A	743535140	743535643	503	True	643.000000	643	89.7230	1	505	1	chr3A.!!$R1	504
8	TraesCS2D01G225700	chr4D	51987756	51988259	503	False	640.000000	640	89.6830	1	501	1	chr4D.!!$F1	500
9	TraesCS2D01G225700	chr5A	99022523	99023026	503	True	638.000000	638	89.5260	1	505	1	chr5A.!!$R1	504
10	TraesCS2D01G225700	chr7A	679315033	679315536	503	True	632.000000	632	89.3490	1	505	1	chr7A.!!$R1	504

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
589	593	0.250252	TGATGACAGTTGCGCAAGGA	60.25	50.0	25.78	0.0	38.28	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2522	2655	0.612732	CCTGCCACAATGTCCACCAT	60.613	55.0	0.0	0.0	34.36	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
47	48	4.235762	ACGCCAGACAACGCCACT	62.236	61.111	0.00	0.00	0.00	4.00
70	71	4.521062	GCGCTCGTCCATCCAGCT	62.521	66.667	0.00	0.00	0.00	4.24
75	76	0.463295	CTCGTCCATCCAGCTGCATT	60.463	55.000	8.66	0.00	0.00	3.56
76	77	0.462581	TCGTCCATCCAGCTGCATTC	60.463	55.000	8.66	0.00	0.00	2.67
85	86	1.801913	AGCTGCATTCGTCGTCGAC	60.802	57.895	15.51	15.51	46.03	4.20
91	92	1.624487	CATTCGTCGTCGACATCCAA	58.376	50.000	24.13	11.41	46.03	3.53
111	112	1.037493	CTGCACCATGCTGCCAATAT	58.963	50.000	10.45	0.00	45.31	1.28
136	137	1.002366	GTCATCGACGCAGCAGAAAT	58.998	50.000	0.00	0.00	0.00	2.17
152	153	0.322187	AAATAACGCCGCACCTCCTT	60.322	50.000	0.00	0.00	0.00	3.36
188	189	1.450312	GCCGCTGTTGGAGCTACAT	60.450	57.895	0.00	0.00	46.64	2.29
215	216	2.238144	CCATCACCCACAACATCTCTCT	59.762	50.000	0.00	0.00	0.00	3.10
274	275	4.465512	GTACGGCGCGAAGGACGA	62.466	66.667	12.10	0.00	45.77	4.20
310	312	9.007901	CAATCTAGACTGAATTTTGGACTTTCT	57.992	33.333	0.00	0.00	0.00	2.52
314	316	6.129179	AGACTGAATTTTGGACTTTCTTCCA	58.871	36.000	0.00	0.00	44.39	3.53
324	326	2.108425	GACTTTCTTCCAGGAGGGGTTT	59.892	50.000	0.00	0.00	37.22	3.27
360	362	1.739338	GACCTCGACATCGCCTCCAT	61.739	60.000	0.00	0.00	39.60	3.41
362	364	1.735973	CTCGACATCGCCTCCATGA	59.264	57.895	0.00	0.00	39.60	3.07
421	423	3.550030	CCGAACAAGCCGATCAAAGTTTT	60.550	43.478	0.00	0.00	0.00	2.43
428	430	1.130561	CCGATCAAAGTTTTCTCCGGC	59.869	52.381	0.00	0.00	0.00	6.13
456	459	2.237893	CCTATACCACCAAACCTCCGTT	59.762	50.000	0.00	0.00	0.00	4.44
471	474	4.467084	GTTGGCTCCGGATCCGCA	62.467	66.667	29.12	17.90	38.24	5.69
473	476	3.969250	TTGGCTCCGGATCCGCAAC	62.969	63.158	29.12	18.06	38.24	4.17
589	593	0.250252	TGATGACAGTTGCGCAAGGA	60.250	50.000	25.78	0.00	38.28	3.36
645	649	5.473504	AGTTTCCCAGAAATCACACATGTAC	59.526	40.000	0.00	0.00	0.00	2.90
646	650	3.595173	TCCCAGAAATCACACATGTACG	58.405	45.455	0.00	0.00	0.00	3.67
647	651	3.007506	TCCCAGAAATCACACATGTACGT	59.992	43.478	0.00	0.00	0.00	3.57
689	693	0.386113	GCAAACCAAACCAGCCGTTA	59.614	50.000	0.00	0.00	33.05	3.18
738	745	8.172159	CGTACTTCTATACGTACATCCTCTAG	57.828	42.308	0.00	0.00	42.37	2.43
791	798	0.741915	TTTTCCAGACGCACCCAAAC	59.258	50.000	0.00	0.00	0.00	2.93
889	896	6.122277	TCCATCTGTAATCCCAATGAAACTC	58.878	40.000	0.00	0.00	0.00	3.01
920	927	1.953559	TATGGCCGTCTCATTTGCTC	58.046	50.000	0.00	0.00	0.00	4.26
946	953	2.159382	ACGTCCCATTGACATCCAAAC	58.841	47.619	0.00	0.00	44.71	2.93
973	980	7.490402	CCAAAGATATTCATCAAAGGCTTCAAC	59.510	37.037	0.00	0.00	33.21	3.18
1143	1150	1.733399	GGTGGTGAGCTCGACGTTC	60.733	63.158	9.64	0.00	0.00	3.95
1155	1162	2.977829	CTCGACGTTCACTCAATTCGAA	59.022	45.455	0.00	0.00	33.36	3.71
1158	1165	3.910170	CGACGTTCACTCAATTCGAAGTA	59.090	43.478	3.35	0.00	0.00	2.24
1173	1180	0.838987	AAGTAACCTCCTTCCCGCCA	60.839	55.000	0.00	0.00	0.00	5.69
1332	1339	4.059459	GCGCGAACCACACAGACG	62.059	66.667	12.10	0.00	0.00	4.18
1689	1700	4.311816	CTTGCAAGCTTTTCTCTTGGAA	57.688	40.909	14.65	8.84	45.28	3.53
1748	1762	8.798748	AGTATATGCTACGTAGTCAACATTTC	57.201	34.615	22.98	11.05	43.93	2.17
1864	1881	1.815003	CTTCACAAGATCCACAAGGCC	59.185	52.381	0.00	0.00	33.74	5.19
1872	1889	1.467342	GATCCACAAGGCCGTTACAAC	59.533	52.381	0.00	0.00	33.74	3.32
1881	1898	1.953772	CCGTTACAACCAGGCAACC	59.046	57.895	0.00	0.00	37.17	3.77
1883	1900	0.820074	CGTTACAACCAGGCAACCCA	60.820	55.000	0.00	0.00	37.17	4.51
1900	1917	1.403679	CCCACGTTGCTTGTTCTTGAA	59.596	47.619	0.00	0.00	0.00	2.69
1932	1949	5.645624	TCTTGAAAAACAAACAGCGAATCA	58.354	33.333	0.00	0.00	38.08	2.57
1946	1963	7.470289	ACAGCGAATCATTCTCAAATACTAC	57.530	36.000	0.00	0.00	0.00	2.73
1962	1979	5.687166	ATACTACCCCACAAATTCGAGAA	57.313	39.130	0.00	0.00	0.00	2.87
1966	1983	2.292292	ACCCCACAAATTCGAGAAAACG	59.708	45.455	0.00	0.00	0.00	3.60
1994	2011	2.589407	CACTGTTATTTCAATGCGCACG	59.411	45.455	14.90	7.41	0.00	5.34
1995	2012	2.176369	CTGTTATTTCAATGCGCACGG	58.824	47.619	14.90	8.27	0.00	4.94
1996	2013	0.913876	GTTATTTCAATGCGCACGGC	59.086	50.000	14.90	0.00	43.96	5.68
2079	2212	0.041312	CAAGAAACGCCACAACCGAG	60.041	55.000	0.00	0.00	0.00	4.63
2353	2486	2.515057	GTCACCGTGCACAACCCA	60.515	61.111	18.64	0.00	0.00	4.51
2389	2522	3.740397	TACGGCGAGGTGGTCACG	61.740	66.667	16.62	0.00	0.00	4.35
2531	2664	0.324614	CAGGCACTACATGGTGGACA	59.675	55.000	0.00	0.00	36.02	4.02
2536	2669	2.162208	GCACTACATGGTGGACATTGTG	59.838	50.000	0.00	0.00	37.84	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	0.038892	GGCGTCGACAACTGACCTAA	60.039	55.000	17.16	0.00	32.68	2.69
13	14	1.666553	GTCATGGTGGCGTCGACAA	60.667	57.895	17.16	0.00	0.00	3.18
75	76	0.109919	CAGTTGGATGTCGACGACGA	60.110	55.000	22.06	5.75	46.56	4.20
76	77	1.674611	GCAGTTGGATGTCGACGACG	61.675	60.000	22.06	0.00	34.95	5.12
128	129	1.644786	GGTGCGGCGTTATTTCTGCT	61.645	55.000	9.37	0.00	35.69	4.24
130	131	0.373716	GAGGTGCGGCGTTATTTCTG	59.626	55.000	9.37	0.00	0.00	3.02
136	137	2.047655	CAAGGAGGTGCGGCGTTA	60.048	61.111	9.37	0.00	0.00	3.18
152	153	4.314440	GACGGTGTGGAGGCTGCA	62.314	66.667	3.93	3.93	0.00	4.41
177	178	1.951209	TGGACTCCATGTAGCTCCAA	58.049	50.000	7.00	0.00	0.00	3.53
188	189	0.400213	GTTGTGGGTGATGGACTCCA	59.600	55.000	0.00	0.00	38.19	3.86
215	216	1.301716	GAGGTTCTGCTGTTCGGCA	60.302	57.895	6.16	6.16	40.15	5.69
274	275	4.891727	CTAGATTGGGCGCGGCGT	62.892	66.667	27.12	15.05	0.00	5.68
289	291	7.287061	TGGAAGAAAGTCCAAAATTCAGTCTA	58.713	34.615	0.00	0.00	44.91	2.59
310	312	1.140134	CCTCCAAACCCCTCCTGGAA	61.140	60.000	0.00	0.00	38.75	3.53
314	316	1.852626	CCACCTCCAAACCCCTCCT	60.853	63.158	0.00	0.00	0.00	3.69
324	326	1.218196	GGTCTCTCCTATCCACCTCCA	59.782	57.143	0.00	0.00	0.00	3.86
360	362	1.955778	TCTCGACGTTGTTACCCTTCA	59.044	47.619	1.96	0.00	0.00	3.02
362	364	2.030451	GTCTCTCGACGTTGTTACCCTT	60.030	50.000	1.96	0.00	0.00	3.95
421	423	1.448814	TATAGGATGGGGGCCGGAGA	61.449	60.000	5.05	0.00	0.00	3.71
428	430	1.827792	TTGGTGGTATAGGATGGGGG	58.172	55.000	0.00	0.00	0.00	5.40
456	459	4.467084	GTTGCGGATCCGGAGCCA	62.467	66.667	36.24	20.85	41.44	4.75
470	473	1.152989	TTTCGGTTCGTGGTCCGTTG	61.153	55.000	3.64	0.00	45.88	4.10
471	474	1.143620	TTTCGGTTCGTGGTCCGTT	59.856	52.632	3.64	0.00	45.88	4.44
473	476	2.312436	GGTTTCGGTTCGTGGTCCG	61.312	63.158	0.00	0.00	46.93	4.79
487	491	5.948162	ACATATGTTTCATCTCTGCAGGTTT	59.052	36.000	15.13	0.00	0.00	3.27
553	557	7.882791	ACTGTCATCATGTACATAACTTTTCCA	59.117	33.333	8.32	0.00	0.00	3.53
589	593	7.346751	TGAAACTAAAAACCAAGAGAGCAAT	57.653	32.000	0.00	0.00	0.00	3.56
664	668	1.341209	GCTGGTTTGGTTTGCTTAGCT	59.659	47.619	5.60	0.00	0.00	3.32
689	693	5.581085	GTCTCGCATGTTATACCTCAAACTT	59.419	40.000	0.00	0.00	0.00	2.66
735	742	3.094572	TCTGGGGAGAACGGTAAACTAG	58.905	50.000	0.00	0.00	0.00	2.57
736	743	2.827921	GTCTGGGGAGAACGGTAAACTA	59.172	50.000	0.00	0.00	0.00	2.24
738	745	1.338484	GGTCTGGGGAGAACGGTAAAC	60.338	57.143	0.00	0.00	0.00	2.01
784	791	1.484653	GGTTTCTTTGCAGGTTTGGGT	59.515	47.619	0.00	0.00	0.00	4.51
791	798	4.453819	TGTTTTGTTTGGTTTCTTTGCAGG	59.546	37.500	0.00	0.00	0.00	4.85
889	896	1.677552	GGCCATATGTAGGACGGGG	59.322	63.158	0.00	0.00	0.00	5.73
920	927	2.925578	TGTCAATGGGACGTAGTACG	57.074	50.000	20.82	20.82	46.96	3.67
946	953	6.097270	TGAAGCCTTTGATGAATATCTTTGGG	59.903	38.462	0.00	0.00	34.31	4.12
1135	1142	2.691984	TCGAATTGAGTGAACGTCGA	57.308	45.000	0.00	0.00	33.27	4.20
1143	1150	4.822026	AGGAGGTTACTTCGAATTGAGTG	58.178	43.478	0.00	0.00	0.00	3.51
1155	1162	0.838987	TTGGCGGGAAGGAGGTTACT	60.839	55.000	0.00	0.00	0.00	2.24
1158	1165	1.074951	CTTTGGCGGGAAGGAGGTT	59.925	57.895	0.00	0.00	0.00	3.50
1173	1180	2.242043	CCCAAGCTCATGTTGACCTTT	58.758	47.619	0.00	0.00	0.00	3.11
1351	1358	1.375523	CCACCTTGTCCGCCTGTAC	60.376	63.158	0.00	0.00	0.00	2.90
1353	1360	3.168528	ACCACCTTGTCCGCCTGT	61.169	61.111	0.00	0.00	0.00	4.00
1668	1679	3.996150	TCCAAGAGAAAAGCTTGCAAG	57.004	42.857	22.44	22.44	41.00	4.01
1671	1682	5.163673	CCTCTATTCCAAGAGAAAAGCTTGC	60.164	44.000	0.00	0.00	44.93	4.01
1748	1762	8.654230	AATACTGATTGTATGAGTGCACTTAG	57.346	34.615	22.65	4.76	40.69	2.18
1822	1836	9.784531	TGAAGAACATCTCTTATTTTTCTCTGT	57.215	29.630	0.00	0.00	44.82	3.41
1864	1881	0.820074	TGGGTTGCCTGGTTGTAACG	60.820	55.000	0.00	0.00	0.00	3.18
1881	1898	2.842208	TTCAAGAACAAGCAACGTGG	57.158	45.000	0.00	0.00	0.00	4.94
1883	1900	5.493133	TGTATTTCAAGAACAAGCAACGT	57.507	34.783	0.00	0.00	0.00	3.99
1900	1917	9.986833	GCTGTTTGTTTTTCAAGAATTTGTATT	57.013	25.926	0.00	0.00	37.35	1.89
1932	1949	7.067008	CGAATTTGTGGGGTAGTATTTGAGAAT	59.933	37.037	0.00	0.00	0.00	2.40
1946	1963	2.550606	TCGTTTTCTCGAATTTGTGGGG	59.449	45.455	0.00	0.00	36.89	4.96
1962	1979	8.967218	CATTGAAATAACAGTGACAATTCGTTT	58.033	29.630	0.00	0.00	30.82	3.60
1966	1983	6.452872	GCGCATTGAAATAACAGTGACAATTC	60.453	38.462	0.30	0.00	30.82	2.17
1970	1987	3.251972	TGCGCATTGAAATAACAGTGACA	59.748	39.130	5.66	0.00	30.82	3.58
1994	2011	1.406898	GCTGGAATTGAAGCTTAGGCC	59.593	52.381	0.00	0.00	39.73	5.19
1995	2012	2.094675	TGCTGGAATTGAAGCTTAGGC	58.905	47.619	0.00	0.00	40.21	3.93
1996	2013	3.350833	AGTGCTGGAATTGAAGCTTAGG	58.649	45.455	0.00	0.00	40.21	2.69
2079	2212	2.125633	GAGGGACGGCGGAACTTC	60.126	66.667	13.24	2.82	0.00	3.01
2522	2655	0.612732	CCTGCCACAATGTCCACCAT	60.613	55.000	0.00	0.00	34.36	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.