AutoCloner

Multiple sequence alignment - TraesCS1D01G000400

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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	TraesCS1D01G000400	chr1D	100.000	2210	0	0	1	2210	112958	110749	0.000000e+00	4082.0
1	TraesCS1D01G000400	chr1B	88.635	1575	82	34	145	1685	5509096	5510607	0.000000e+00	1827.0
2	TraesCS1D01G000400	chr1B	89.946	368	20	12	1821	2188	5511319	5511669	2.000000e-125	459.0
3	TraesCS1D01G000400	chr1B	79.793	579	33	30	616	1150	5505751	5506289	5.840000e-91	344.0
4	TraesCS1D01G000400	chr1B	74.828	580	105	28	59	629	5196501	5197048	7.940000e-55	224.0
5	TraesCS1D01G000400	chr1B	95.122	82	4	0	1731	1812	5511124	5511205	1.780000e-26	130.0
6	TraesCS1D01G000400	chr1B	72.195	410	87	19	28	429	607317474	607317864	1.400000e-17	100.0
7	TraesCS1D01G000400	chr1B	98.039	51	1	0	1689	1739	5510691	5510741	3.020000e-14	89.8
8	TraesCS1D01G000400	chr1A	86.014	1716	108	46	1	1662	4062231	4063868	0.000000e+00	1718.0
9	TraesCS1D01G000400	chr1A	89.822	393	25	8	1821	2207	4064218	4064601	7.090000e-135	490.0
10	TraesCS1D01G000400	chr3D	75.914	465	92	14	13	470	374036578	374036127	1.030000e-53	220.0
11	TraesCS1D01G000400	chr3D	73.134	469	109	15	9	470	481210723	481210265	3.800000e-33	152.0
12	TraesCS1D01G000400	chr6D	73.625	618	134	25	12	616	139382069	139381468	6.180000e-51	211.0
13	TraesCS1D01G000400	chr3A	75.431	464	97	11	13	470	496047728	496047276	2.220000e-50	209.0
14	TraesCS1D01G000400	chr3A	100.000	29	0	0	1215	1243	646312065	646312037	1.000000e-03	54.7
15	TraesCS1D01G000400	chr5A	75.000	456	92	18	22	470	120745015	120744575	8.050000e-45	191.0
16	TraesCS1D01G000400	chr7D	74.304	467	99	16	10	470	138494438	138494889	6.270000e-41	178.0
17	TraesCS1D01G000400	chr7D	72.273	440	95	20	15	440	422128109	422127683	6.450000e-21	111.0
18	TraesCS1D01G000400	chr4A	74.370	476	95	19	28	496	553464808	553464353	6.270000e-41	178.0
19	TraesCS1D01G000400	chr4A	73.499	483	100	19	10	482	59383873	59384337	8.170000e-35	158.0
20	TraesCS1D01G000400	chr4D	73.810	420	93	14	38	451	484063131	484062723	1.370000e-32	150.0
21	TraesCS1D01G000400	chr3B	79.433	141	27	2	331	470	792820041	792819902	5.020000e-17	99.0

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	TraesCS1D01G000400	chr1D	110749	112958	2209	True	4082.00	4082	100.000	1	2210	1	chr1D.!!$R1	2209
1	TraesCS1D01G000400	chr1B	5505751	5511669	5918	False	569.96	1827	90.307	145	2188	5	chr1B.!!$F3	2043
2	TraesCS1D01G000400	chr1B	5196501	5197048	547	False	224.00	224	74.828	59	629	1	chr1B.!!$F1	570
3	TraesCS1D01G000400	chr1A	4062231	4064601	2370	False	1104.00	1718	87.918	1	2207	2	chr1A.!!$F1	2206
4	TraesCS1D01G000400	chr6D	139381468	139382069	601	True	211.00	211	73.625	12	616	1	chr6D.!!$R1	604

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
125	127	0.173708	GATCTCGGTGCCTCGACTTT	59.826	55.0	0.0	0.0	35.18	2.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1322	4565	1.069159	CAAGCAGCAAGAGCAGAACAG	60.069	52.381	0.0	0.0	45.49	3.16	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
125	127	0.173708	GATCTCGGTGCCTCGACTTT	59.826	55.000	0.00	0.00	35.18	2.66
128	130	2.742372	CGGTGCCTCGACTTTGGG	60.742	66.667	0.00	0.00	0.00	4.12
162	3365	4.456566	GGTTAGGGTTTTTGTTCTCGCATA	59.543	41.667	0.00	0.00	0.00	3.14
182	3385	0.822164	AGCGGCGTTTAGGTAGATGT	59.178	50.000	9.37	0.00	0.00	3.06
214	3418	0.824595	TCGAGTTGGTCTTCCGGACA	60.825	55.000	1.83	0.00	46.16	4.02
271	3475	1.271102	GATGGAGCTCCGGTGTAGATC	59.729	57.143	27.43	18.06	39.43	2.75
301	3509	3.260884	TCTCCTTGGTGTGATGAGGTTAC	59.739	47.826	0.00	0.00	0.00	2.50
381	3590	1.496060	AGGGTTCAGTGGCGATGATA	58.504	50.000	0.00	0.00	0.00	2.15
465	3674	0.606604	GTCAAACCGGCTCAGGTAGA	59.393	55.000	0.00	0.13	45.21	2.59
478	3687	3.896888	CTCAGGTAGAGGAGAGCATCAAT	59.103	47.826	0.00	0.00	40.84	2.57
492	3701	2.676839	GCATCAATAGCTGCGCATAGAT	59.323	45.455	12.24	0.25	0.00	1.98
498	3707	2.901292	GCTGCGCATAGATGGCCAC	61.901	63.158	12.24	1.58	0.00	5.01
505	3714	0.319040	CATAGATGGCCACTCCGACG	60.319	60.000	8.16	0.00	37.80	5.12
525	3734	2.430367	GGCAGTGGTCCTTCGGTT	59.570	61.111	0.00	0.00	0.00	4.44
537	3753	1.535462	CCTTCGGTTGTGCTCGATTTT	59.465	47.619	0.00	0.00	35.25	1.82
870	4097	2.291153	CCTCCACAATCACACCATCCTT	60.291	50.000	0.00	0.00	0.00	3.36
874	4101	3.307975	CCACAATCACACCATCCTTCTCT	60.308	47.826	0.00	0.00	0.00	3.10
875	4102	3.688185	CACAATCACACCATCCTTCTCTG	59.312	47.826	0.00	0.00	0.00	3.35
878	4105	1.552337	TCACACCATCCTTCTCTGCTC	59.448	52.381	0.00	0.00	0.00	4.26
879	4106	1.554160	CACACCATCCTTCTCTGCTCT	59.446	52.381	0.00	0.00	0.00	4.09
880	4107	2.762887	CACACCATCCTTCTCTGCTCTA	59.237	50.000	0.00	0.00	0.00	2.43
882	4109	3.030291	CACCATCCTTCTCTGCTCTACT	58.970	50.000	0.00	0.00	0.00	2.57
883	4110	3.068024	CACCATCCTTCTCTGCTCTACTC	59.932	52.174	0.00	0.00	0.00	2.59
884	4111	3.052944	ACCATCCTTCTCTGCTCTACTCT	60.053	47.826	0.00	0.00	0.00	3.24
885	4112	3.318839	CCATCCTTCTCTGCTCTACTCTG	59.681	52.174	0.00	0.00	0.00	3.35
886	4113	2.374184	TCCTTCTCTGCTCTACTCTGC	58.626	52.381	0.00	0.00	0.00	4.26
887	4114	1.065401	CCTTCTCTGCTCTACTCTGCG	59.935	57.143	0.00	0.00	0.00	5.18
890	4117	2.105930	CTGCTCTACTCTGCGCCC	59.894	66.667	4.18	0.00	0.00	6.13
892	4119	4.228567	GCTCTACTCTGCGCCCCC	62.229	72.222	4.18	0.00	0.00	5.40
934	4161	0.606401	TTGCCTTCCTTTCTCTGCCG	60.606	55.000	0.00	0.00	0.00	5.69
951	4182	1.866237	CGCGAGGAGCTAGCTAGAG	59.134	63.158	25.15	10.69	45.59	2.43
955	4186	2.808933	GCGAGGAGCTAGCTAGAGAGAA	60.809	54.545	25.15	0.00	44.04	2.87
964	4195	7.100458	AGCTAGCTAGAGAGAAAGAAAGAAG	57.900	40.000	25.15	0.00	0.00	2.85
967	4202	6.358974	AGCTAGAGAGAAAGAAAGAAGCTT	57.641	37.500	0.00	0.00	34.26	3.74
973	4208	1.880027	GAAAGAAAGAAGCTTGCCGGA	59.120	47.619	5.05	0.00	0.00	5.14
1274	4515	0.107945	CTGCTCTTCCCCTTCTTCCG	60.108	60.000	0.00	0.00	0.00	4.30
1312	4553	2.603021	GATCCATCTGACTCCTGCCTA	58.397	52.381	0.00	0.00	0.00	3.93
1316	4557	2.971330	CCATCTGACTCCTGCCTATCTT	59.029	50.000	0.00	0.00	0.00	2.40
1317	4558	3.006752	CCATCTGACTCCTGCCTATCTTC	59.993	52.174	0.00	0.00	0.00	2.87
1322	4565	3.449018	TGACTCCTGCCTATCTTCTGTTC	59.551	47.826	0.00	0.00	0.00	3.18
1330	4573	3.620821	GCCTATCTTCTGTTCTGTTCTGC	59.379	47.826	0.00	0.00	0.00	4.26
1451	4713	3.880040	CCATGGAGTGGCACATACA	57.120	52.632	21.41	15.23	44.52	2.29
1516	4780	9.273016	GATGTGTACATATAGTAAGGTTTGCAT	57.727	33.333	4.95	0.00	36.57	3.96
1517	4781	9.627123	ATGTGTACATATAGTAAGGTTTGCATT	57.373	29.630	2.87	0.00	34.26	3.56
1578	4855	1.626825	AGCGCTTTTCAACTACCCCTA	59.373	47.619	2.64	0.00	0.00	3.53
1581	4858	3.404899	CGCTTTTCAACTACCCCTACAA	58.595	45.455	0.00	0.00	0.00	2.41
1583	4860	3.504906	GCTTTTCAACTACCCCTACAACC	59.495	47.826	0.00	0.00	0.00	3.77
1584	4861	3.793819	TTTCAACTACCCCTACAACCC	57.206	47.619	0.00	0.00	0.00	4.11
1591	4868	0.845102	ACCCCTACAACCCTCCCTTG	60.845	60.000	0.00	0.00	0.00	3.61
1685	4962	8.206867	TCTGCTGATACAATGAATTAGCTACTT	58.793	33.333	0.00	0.00	37.00	2.24
1686	4963	8.146479	TGCTGATACAATGAATTAGCTACTTG	57.854	34.615	0.37	0.31	37.00	3.16
1687	4964	7.986889	TGCTGATACAATGAATTAGCTACTTGA	59.013	33.333	0.37	0.00	37.00	3.02
1742	5490	8.485591	GCAATACTCCATCAATTAAGTACGTAC	58.514	37.037	18.10	18.10	0.00	3.67
1760	5508	5.912528	ACGTACGTTGATCAATGAGAAAAC	58.087	37.500	29.89	17.95	0.00	2.43
1807	5555	6.827762	TCCATCACACATAATACATGCTTGAA	59.172	34.615	6.60	0.00	0.00	2.69
1812	5560	9.394767	TCACACATAATACATGCTTGAATACTT	57.605	29.630	6.60	0.00	0.00	2.24
1862	5798	4.080129	TCCAATCAAAGAGGAAGATGAGGG	60.080	45.833	0.00	0.00	0.00	4.30
1912	5848	1.199327	CTCTTGTGCTGTTGATGCCTG	59.801	52.381	0.00	0.00	0.00	4.85
1913	5849	0.388134	CTTGTGCTGTTGATGCCTGC	60.388	55.000	0.00	0.00	0.00	4.85
1914	5850	1.808531	TTGTGCTGTTGATGCCTGCC	61.809	55.000	0.00	0.00	0.00	4.85
1964	5900	1.735376	CGTATGGCACGCCCTAGTCT	61.735	60.000	5.42	0.00	45.03	3.24
1976	5912	2.419297	GCCCTAGTCTCACACCAATCAG	60.419	54.545	0.00	0.00	0.00	2.90
2060	5996	0.521242	GCCTTAACGTTGATGCTGCG	60.521	55.000	11.99	0.00	0.00	5.18
2066	6002	0.723414	ACGTTGATGCTGCGAGAATG	59.277	50.000	0.00	0.00	0.00	2.67
2146	6086	4.819105	TTCTTTCTGGCGATTAAGGAGA	57.181	40.909	0.00	0.00	0.00	3.71
2151	6091	6.316390	TCTTTCTGGCGATTAAGGAGATTTTC	59.684	38.462	0.00	0.00	0.00	2.29
2188	6128	8.524870	ACTGAAATGTTTTCATAATCAAGCAC	57.475	30.769	3.36	0.00	39.94	4.40
2189	6129	8.143193	ACTGAAATGTTTTCATAATCAAGCACA	58.857	29.630	3.36	0.00	39.94	4.57
2197	6142	4.314961	TCATAATCAAGCACACACGACTT	58.685	39.130	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
94	95	1.462238	CGAGATCCCCCTTCCCCAT	60.462	63.158	0.00	0.00	0.00	4.00
100	102	3.090532	GGCACCGAGATCCCCCTT	61.091	66.667	0.00	0.00	0.00	3.95
125	127	5.289652	ACCCTAACCTAAACTACTACCCA	57.710	43.478	0.00	0.00	0.00	4.51
128	130	8.908786	ACAAAAACCCTAACCTAAACTACTAC	57.091	34.615	0.00	0.00	0.00	2.73
162	3365	1.206371	ACATCTACCTAAACGCCGCTT	59.794	47.619	0.00	0.00	0.00	4.68
182	3385	2.139917	CAACTCGAAATGAACCACCGA	58.860	47.619	0.00	0.00	0.00	4.69
271	3475	2.026915	TCACACCAAGGAGACATCATGG	60.027	50.000	0.00	0.00	38.98	3.66
301	3509	2.845967	GCACACAAACAACGAGAAACTG	59.154	45.455	0.00	0.00	0.00	3.16
381	3590	1.101635	TGCGGCGTACTAGAGCTGAT	61.102	55.000	9.37	0.00	42.01	2.90
498	3707	4.742201	CCACTGCCACCGTCGGAG	62.742	72.222	20.51	10.53	0.00	4.63
505	3714	2.358737	CGAAGGACCACTGCCACC	60.359	66.667	0.00	0.00	0.00	4.61
643	3862	2.901249	GCAGCTCCATGCATGAATTTT	58.099	42.857	28.31	6.56	45.77	1.82
870	4097	1.380403	GGCGCAGAGTAGAGCAGAGA	61.380	60.000	10.83	0.00	35.93	3.10
874	4101	3.461773	GGGGCGCAGAGTAGAGCA	61.462	66.667	10.83	0.00	35.93	4.26
875	4102	4.228567	GGGGGCGCAGAGTAGAGC	62.229	72.222	10.83	0.00	0.00	4.09
887	4114	4.785453	CAGAACAGGAGCGGGGGC	62.785	72.222	0.00	0.00	0.00	5.80
890	4117	2.125350	GAGCAGAACAGGAGCGGG	60.125	66.667	0.00	0.00	0.00	6.13
892	4119	2.099431	GCAGAGCAGAACAGGAGCG	61.099	63.158	0.00	0.00	0.00	5.03
900	4127	0.679002	GGCAATGGAGCAGAGCAGAA	60.679	55.000	0.00	0.00	35.83	3.02
934	4161	1.156736	CTCTCTAGCTAGCTCCTCGC	58.843	60.000	23.26	0.00	39.57	5.03
951	4182	2.095516	CCGGCAAGCTTCTTTCTTTCTC	60.096	50.000	0.00	0.00	0.00	2.87
955	4186	1.202818	ACTCCGGCAAGCTTCTTTCTT	60.203	47.619	0.00	0.00	0.00	2.52
973	4208	2.231540	CTCCCTCCCCTTCTCCGACT	62.232	65.000	0.00	0.00	0.00	4.18
1312	4553	4.888326	AGAGCAGAACAGAACAGAAGAT	57.112	40.909	0.00	0.00	0.00	2.40
1316	4557	2.103771	AGCAAGAGCAGAACAGAACAGA	59.896	45.455	0.00	0.00	45.49	3.41
1317	4558	2.223611	CAGCAAGAGCAGAACAGAACAG	59.776	50.000	0.00	0.00	45.49	3.16
1322	4565	1.069159	CAAGCAGCAAGAGCAGAACAG	60.069	52.381	0.00	0.00	45.49	3.16
1578	4855	2.509964	GGATATCACAAGGGAGGGTTGT	59.490	50.000	4.83	0.00	38.71	3.32
1581	4858	2.022035	TCTGGATATCACAAGGGAGGGT	60.022	50.000	4.83	0.00	0.00	4.34
1583	4860	3.312890	ACTCTGGATATCACAAGGGAGG	58.687	50.000	4.83	0.00	0.00	4.30
1584	4861	6.035368	CATACTCTGGATATCACAAGGGAG	57.965	45.833	4.83	6.31	0.00	4.30
1641	4918	5.591472	CAGCAGAATCATGAACCCAAGAATA	59.409	40.000	0.00	0.00	0.00	1.75
1685	4962	9.679661	TTACTTGGTTAAATTCAGCTATCATCA	57.320	29.630	0.00	0.00	0.00	3.07
1742	5490	6.414408	AGCTAGTTTTCTCATTGATCAACG	57.586	37.500	11.07	1.83	0.00	4.10
1760	5508	1.681793	AGCGTATGTGTGGGTAGCTAG	59.318	52.381	0.00	0.00	0.00	3.42
1812	5560	9.606631	ATGCACAGGACTAACAAAATTTTAAAA	57.393	25.926	2.44	2.51	0.00	1.52
1813	5561	9.606631	AATGCACAGGACTAACAAAATTTTAAA	57.393	25.926	2.44	0.00	0.00	1.52
1814	5562	9.255304	GAATGCACAGGACTAACAAAATTTTAA	57.745	29.630	2.44	0.00	0.00	1.52
1815	5563	7.870445	GGAATGCACAGGACTAACAAAATTTTA	59.130	33.333	2.44	0.00	0.00	1.52
1816	5564	6.705825	GGAATGCACAGGACTAACAAAATTTT	59.294	34.615	0.00	0.00	0.00	1.82
1817	5565	6.183360	TGGAATGCACAGGACTAACAAAATTT	60.183	34.615	0.00	0.00	0.00	1.82
1818	5566	5.304101	TGGAATGCACAGGACTAACAAAATT	59.696	36.000	0.00	0.00	0.00	1.82
1819	5567	4.832266	TGGAATGCACAGGACTAACAAAAT	59.168	37.500	0.00	0.00	0.00	1.82
1862	5798	4.641954	CAGTACGACTGCACAATGATTTC	58.358	43.478	0.00	0.00	39.62	2.17
1964	5900	2.562738	ACTGATCGACTGATTGGTGTGA	59.437	45.455	0.00	0.00	34.09	3.58
2060	5996	5.674820	GCTTTTGTAGCTAGGCAACATTCTC	60.675	44.000	0.00	0.00	46.77	2.87
2110	6046	6.644181	GCCAGAAAGAAAATGAAAGGAGAAAG	59.356	38.462	0.00	0.00	0.00	2.62
2116	6052	4.503741	TCGCCAGAAAGAAAATGAAAGG	57.496	40.909	0.00	0.00	0.00	3.11
2119	6055	6.432783	TCCTTAATCGCCAGAAAGAAAATGAA	59.567	34.615	0.00	0.00	0.00	2.57
2122	6062	6.180472	TCTCCTTAATCGCCAGAAAGAAAAT	58.820	36.000	0.00	0.00	0.00	1.82
2127	6067	6.317391	AGAAAATCTCCTTAATCGCCAGAAAG	59.683	38.462	0.00	0.00	0.00	2.62
2161	6101	9.545105	TGCTTGATTATGAAAACATTTCAGTTT	57.455	25.926	10.82	0.00	43.13	2.66
2173	6113	4.754618	AGTCGTGTGTGCTTGATTATGAAA	59.245	37.500	0.00	0.00	0.00	2.69
2176	6116	4.152223	TCAAGTCGTGTGTGCTTGATTATG	59.848	41.667	0.00	0.00	42.24	1.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.