AutoCloner

Multiple sequence alignment - TraesCS1D01G007600

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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	TraesCS1D01G007600	chr1D	100.000	2442	0	0	1	2442	3800823	3803264	0.000000e+00	4510.0
1	TraesCS1D01G007600	chr1D	89.419	964	88	8	15	968	3874126	3875085	0.000000e+00	1203.0
2	TraesCS1D01G007600	chr1D	92.245	245	16	2	2064	2306	3875694	3875937	6.460000e-91	344.0
3	TraesCS1D01G007600	chr1D	95.122	41	0	1	2020	2060	337997762	337997800	2.030000e-06	63.9
4	TraesCS1D01G007600	chr1A	89.495	2456	184	25	15	2442	5176182	5178591	0.000000e+00	3038.0
5	TraesCS1D01G007600	chr1A	89.697	2145	159	24	15	2143	5194282	5196380	0.000000e+00	2680.0
6	TraesCS1D01G007600	chr1A	90.059	1851	133	25	307	2143	5245940	5247753	0.000000e+00	2351.0
7	TraesCS1D01G007600	chr1A	88.350	2000	148	36	15	2000	5367012	5368940	0.000000e+00	2324.0
8	TraesCS1D01G007600	chr1A	88.144	1999	155	31	15	2000	5331646	5333575	0.000000e+00	2303.0
9	TraesCS1D01G007600	chr1A	88.627	255	27	2	15	268	5360480	5360733	2.360000e-80	309.0
10	TraesCS1D01G007600	chr1A	88.627	255	27	2	15	268	5362764	5363017	2.360000e-80	309.0
11	TraesCS1D01G007600	chr1A	84.818	303	26	12	2150	2442	5247965	5248257	1.100000e-73	287.0
12	TraesCS1D01G007600	chr1A	86.290	248	23	7	2206	2442	5196643	5196890	2.410000e-65	259.0
13	TraesCS1D01G007600	chrUn	88.106	2001	151	45	15	2000	86694	84766	0.000000e+00	2296.0
14	TraesCS1D01G007600	chrUn	89.936	1709	116	21	307	2000	281344213	281342546	0.000000e+00	2152.0
15	TraesCS1D01G007600	chrUn	89.820	1336	97	13	307	1633	231646710	231645405	0.000000e+00	1677.0
16	TraesCS1D01G007600	chr1B	89.129	1205	66	20	785	1982	6462446	6463592	0.000000e+00	1439.0
17	TraesCS1D01G007600	chr1B	91.401	721	47	6	20	739	6461740	6462446	0.000000e+00	974.0
18	TraesCS1D01G007600	chr5B	88.056	427	41	10	1644	2062	652526207	652526631	4.690000e-137	497.0
19	TraesCS1D01G007600	chr7B	84.773	440	53	14	1642	2072	213988954	213988520	1.730000e-116	429.0
20	TraesCS1D01G007600	chr2A	84.615	104	8	7	2248	2348	754180633	754180731	2.000000e-16	97.1

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	TraesCS1D01G007600	chr1D	3800823	3803264	2441	False	4510.000000	4510	100.000000	1	2442	1	chr1D.!!$F1	2441
1	TraesCS1D01G007600	chr1D	3874126	3875937	1811	False	773.500000	1203	90.832000	15	2306	2	chr1D.!!$F3	2291
2	TraesCS1D01G007600	chr1A	5176182	5178591	2409	False	3038.000000	3038	89.495000	15	2442	1	chr1A.!!$F1	2427
3	TraesCS1D01G007600	chr1A	5331646	5333575	1929	False	2303.000000	2303	88.144000	15	2000	1	chr1A.!!$F2	1985
4	TraesCS1D01G007600	chr1A	5194282	5196890	2608	False	1469.500000	2680	87.993500	15	2442	2	chr1A.!!$F3	2427
5	TraesCS1D01G007600	chr1A	5245940	5248257	2317	False	1319.000000	2351	87.438500	307	2442	2	chr1A.!!$F4	2135
6	TraesCS1D01G007600	chr1A	5360480	5368940	8460	False	980.666667	2324	88.534667	15	2000	3	chr1A.!!$F5	1985
7	TraesCS1D01G007600	chrUn	84766	86694	1928	True	2296.000000	2296	88.106000	15	2000	1	chrUn.!!$R1	1985
8	TraesCS1D01G007600	chrUn	281342546	281344213	1667	True	2152.000000	2152	89.936000	307	2000	1	chrUn.!!$R3	1693
9	TraesCS1D01G007600	chrUn	231645405	231646710	1305	True	1677.000000	1677	89.820000	307	1633	1	chrUn.!!$R2	1326
10	TraesCS1D01G007600	chr1B	6461740	6463592	1852	False	1206.500000	1439	90.265000	20	1982	2	chr1B.!!$F1	1962

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
202	6735	0.179108	GGCGCCGACAGAGAAACTAT	60.179	55.0	12.58	0.0	0.0	2.12	F
501	7037	0.465824	TTACGTGGGGTTGTGGGTTG	60.466	55.0	0.00	0.0	0.0	3.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1244	7806	0.728466	AGAGTAGTCGACGCAAACGC	60.728	55.0	10.46	9.12	45.53	4.84	R
2348	9160	0.933097	ATAGCGTTCTGAGCAATGCG	59.067	50.0	0.00	0.00	42.25	4.73	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
50	51	7.320443	TCTGACATTTATGATACTTGTTGGC	57.680	36.000	0.00	0.00	0.00	4.52
53	54	4.947388	ACATTTATGATACTTGTTGGCGGT	59.053	37.500	0.00	0.00	0.00	5.68
95	6628	6.042781	GGGATGTAAGAGTGGATGTTGGTATA	59.957	42.308	0.00	0.00	0.00	1.47
109	6642	0.307760	GGTATAGTGCACGGCAATGC	59.692	55.000	12.01	0.00	46.32	3.56
202	6735	0.179108	GGCGCCGACAGAGAAACTAT	60.179	55.000	12.58	0.00	0.00	2.12
271	6804	1.152589	TGGGTGTTGCTCAATGGCA	60.153	52.632	0.00	0.00	40.74	4.92
320	6853	9.582431	GCTGAATTATATAATGCTTGCATCAAT	57.418	29.630	18.69	8.24	0.00	2.57
359	6892	6.785488	TGTACAACACATCAGAGAATGAAC	57.215	37.500	0.00	0.00	42.53	3.18
363	6896	5.468072	ACAACACATCAGAGAATGAACAGAC	59.532	40.000	0.00	0.00	42.53	3.51
368	6901	5.479724	ACATCAGAGAATGAACAGACAGAGA	59.520	40.000	0.00	0.00	42.53	3.10
394	6927	5.172934	CCTAACTAACTGCAACATACGGAA	58.827	41.667	0.00	0.00	0.00	4.30
395	6928	5.640357	CCTAACTAACTGCAACATACGGAAA	59.360	40.000	0.00	0.00	0.00	3.13
405	6940	0.520412	CATACGGAAAAAGGCACGCG	60.520	55.000	3.53	3.53	0.00	6.01
407	6942	4.025401	CGGAAAAAGGCACGCGCT	62.025	61.111	5.73	0.00	38.60	5.92
435	6970	5.472137	GCACGAGAGATCTTAGATCCTAACT	59.528	44.000	17.61	12.07	0.00	2.24
475	7010	2.233922	ACACGAGCTTTGCTACACCTAT	59.766	45.455	0.00	0.00	39.88	2.57
492	7028	0.549658	TATGGGGGTTTACGTGGGGT	60.550	55.000	0.00	0.00	0.00	4.95
493	7029	1.437013	ATGGGGGTTTACGTGGGGTT	61.437	55.000	0.00	0.00	0.00	4.11
495	7031	1.151221	GGGGTTTACGTGGGGTTGT	59.849	57.895	0.00	0.00	0.00	3.32
501	7037	0.465824	TTACGTGGGGTTGTGGGTTG	60.466	55.000	0.00	0.00	0.00	3.77
507	7043	1.343069	GGGGTTGTGGGTTGCATAAA	58.657	50.000	0.00	0.00	0.00	1.40
542	7078	2.963599	AATTGTTCGTTAGTGGGGGT	57.036	45.000	0.00	0.00	0.00	4.95
545	7085	1.714541	TGTTCGTTAGTGGGGGTGTA	58.285	50.000	0.00	0.00	0.00	2.90
610	7155	9.613957	CAGAATGAAGTTACGTAGGATACATAG	57.386	37.037	0.00	0.00	39.55	2.23
632	7177	3.669122	GGATGCATTACGTAGTTCTAGCG	59.331	47.826	0.00	0.00	37.78	4.26
745	7290	6.701145	TGGCAAAGACTAACAATACACAAA	57.299	33.333	0.00	0.00	0.00	2.83
749	7294	5.352643	AAGACTAACAATACACAAACCGC	57.647	39.130	0.00	0.00	0.00	5.68
756	7301	0.663688	ATACACAAACCGCGCAAACA	59.336	45.000	8.75	0.00	0.00	2.83
758	7303	0.663688	ACACAAACCGCGCAAACATA	59.336	45.000	8.75	0.00	0.00	2.29
760	7305	1.648191	CACAAACCGCGCAAACATATG	59.352	47.619	8.75	0.00	0.00	1.78
770	7315	3.500982	CGCAAACATATGGGTCACTTTG	58.499	45.455	7.80	8.50	0.00	2.77
771	7316	3.253230	GCAAACATATGGGTCACTTTGC	58.747	45.455	17.93	17.93	37.43	3.68
776	7321	4.261801	ACATATGGGTCACTTTGCTGTAC	58.738	43.478	7.80	0.00	0.00	2.90
797	7342	8.492673	TGTACATAATCCTTCTCATGTCAAAC	57.507	34.615	0.00	0.00	33.78	2.93
926	7474	9.677567	CAGATCAGTAAATTAGCTAGTTCTCTC	57.322	37.037	1.53	0.00	0.00	3.20
968	7520	6.235664	GTGGAGATAGAGTACTAGCTAGCTT	58.764	44.000	24.88	8.55	44.01	3.74
969	7521	6.148811	GTGGAGATAGAGTACTAGCTAGCTTG	59.851	46.154	24.88	23.43	44.01	4.01
970	7522	5.123344	GGAGATAGAGTACTAGCTAGCTTGC	59.877	48.000	24.88	12.54	44.01	4.01
971	7523	5.876357	AGATAGAGTACTAGCTAGCTTGCT	58.124	41.667	24.88	25.51	42.50	3.91
1244	7806	2.022129	GTCTCGCCGACTGTGTTGG	61.022	63.158	0.00	0.00	39.96	3.77
1427	7989	0.584876	GTGTGTTGGTACCTCGTTGC	59.415	55.000	14.36	0.00	0.00	4.17
1450	8012	5.066505	GCTGCTAAGCCATGTAATTAAGTGT	59.933	40.000	0.00	0.00	44.22	3.55
1511	8073	5.130292	TCGTTCTATTGTTCCTCTTCGTT	57.870	39.130	0.00	0.00	0.00	3.85
1512	8074	5.535333	TCGTTCTATTGTTCCTCTTCGTTT	58.465	37.500	0.00	0.00	0.00	3.60
1513	8075	5.987347	TCGTTCTATTGTTCCTCTTCGTTTT	59.013	36.000	0.00	0.00	0.00	2.43
1514	8076	7.147312	TCGTTCTATTGTTCCTCTTCGTTTTA	58.853	34.615	0.00	0.00	0.00	1.52
1536	8098	8.819643	TTTATTAATTGTTCCCCTTTGTTTCG	57.180	30.769	0.00	0.00	0.00	3.46
1578	8146	4.332186	CATGTGTGCAAGTCATGTACTC	57.668	45.455	14.73	0.00	44.16	2.59
1579	8147	2.766313	TGTGTGCAAGTCATGTACTCC	58.234	47.619	0.00	0.00	44.16	3.85
1580	8148	2.368548	TGTGTGCAAGTCATGTACTCCT	59.631	45.455	0.00	0.00	44.16	3.69
1581	8149	3.576550	TGTGTGCAAGTCATGTACTCCTA	59.423	43.478	0.00	0.00	44.16	2.94
1588	8156	8.523658	GTGCAAGTCATGTACTCCTATATATGA	58.476	37.037	0.00	0.00	41.01	2.15
1639	8210	0.183492	GCTCATGCTGGGGTGGATAA	59.817	55.000	0.00	0.00	36.03	1.75
1640	8211	1.972872	CTCATGCTGGGGTGGATAAC	58.027	55.000	0.00	0.00	0.00	1.89
1641	8212	1.492176	CTCATGCTGGGGTGGATAACT	59.508	52.381	0.00	0.00	0.00	2.24
1642	8213	1.212688	TCATGCTGGGGTGGATAACTG	59.787	52.381	0.00	0.00	0.00	3.16
1855	8432	5.239306	TCATTCCTGACACTGTTCATGTTTC	59.761	40.000	0.00	0.00	0.00	2.78
1856	8433	4.422073	TCCTGACACTGTTCATGTTTCT	57.578	40.909	0.00	0.00	0.00	2.52
2096	8680	9.226606	CGGTGCTTATAAAATAGGGATAAATCA	57.773	33.333	0.00	0.00	0.00	2.57
2159	8952	0.753111	CATGCTAGGGGTTTGCCTCC	60.753	60.000	0.00	0.00	35.21	4.30
2241	9038	5.514500	TCTGGGCTAAAACTTCAGGTATT	57.486	39.130	0.00	0.00	0.00	1.89
2286	9088	4.391830	CGTGCTATGACAAAATAGTGTGGT	59.608	41.667	0.00	0.00	33.42	4.16
2291	9093	6.183360	GCTATGACAAAATAGTGTGGTCCTTC	60.183	42.308	0.00	0.00	33.42	3.46
2348	9160	5.442909	CGTTGTACACTGAGATTTTAGCGAC	60.443	44.000	0.00	0.00	0.00	5.19
2360	9172	0.108851	TTAGCGACGCATTGCTCAGA	60.109	50.000	23.70	0.00	42.40	3.27
2371	9183	2.959507	TTGCTCAGAACGCTATAGCA	57.040	45.000	23.99	0.92	42.21	3.49
2374	9186	2.362077	TGCTCAGAACGCTATAGCATGA	59.638	45.455	23.99	18.47	42.21	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	8.408601	GCCAACAAGTATCATAAATGTCAGAAT	58.591	33.333	0.00	0.00	0.00	2.40
25	26	7.413988	CGCCAACAAGTATCATAAATGTCAGAA	60.414	37.037	0.00	0.00	0.00	3.02
42	43	2.903547	CGACCCAACCGCCAACAAG	61.904	63.158	0.00	0.00	0.00	3.16
50	51	1.263217	CTTTCAAACTCGACCCAACCG	59.737	52.381	0.00	0.00	0.00	4.44
53	54	1.491332	TCCCTTTCAAACTCGACCCAA	59.509	47.619	0.00	0.00	0.00	4.12
109	6642	8.487176	CAATTAATTTTTCAAACTTCAGGTCCG	58.513	33.333	0.00	0.00	0.00	4.79
112	6645	8.490311	TCCCAATTAATTTTTCAAACTTCAGGT	58.510	29.630	0.00	0.00	0.00	4.00
202	6735	2.260844	CAAACCTTGCAGACCTCTCA	57.739	50.000	0.00	0.00	0.00	3.27
226	6759	1.153349	CTAGCGCCACCTCCCTTTC	60.153	63.158	2.29	0.00	0.00	2.62
320	6853	5.811100	TGTTGTACATCGACACTTGTAAACA	59.189	36.000	0.00	14.04	35.71	2.83
359	6892	4.020543	AGTTAGTTAGGGCTCTCTGTCTG	58.979	47.826	0.00	0.00	0.00	3.51
363	6896	2.497675	TGCAGTTAGTTAGGGCTCTCTG	59.502	50.000	0.00	0.00	0.00	3.35
368	6901	3.721087	ATGTTGCAGTTAGTTAGGGCT	57.279	42.857	0.00	0.00	0.00	5.19
394	6927	3.964875	CACCAGCGCGTGCCTTTT	61.965	61.111	19.02	0.00	44.31	2.27
405	6940	0.108424	AAGATCTCTCGTGCACCAGC	60.108	55.000	12.15	0.00	42.57	4.85
407	6942	2.723273	TCTAAGATCTCTCGTGCACCA	58.277	47.619	12.15	0.00	0.00	4.17
435	6970	5.711506	TCGTGTTGTACCATAGTCCTTAGAA	59.288	40.000	0.00	0.00	0.00	2.10
475	7010	2.083670	AACCCCACGTAAACCCCCA	61.084	57.895	0.00	0.00	0.00	4.96
481	7017	0.258194	AACCCACAACCCCACGTAAA	59.742	50.000	0.00	0.00	0.00	2.01
492	7028	5.069648	TGACAAATCTTTATGCAACCCACAA	59.930	36.000	0.00	0.00	0.00	3.33
493	7029	4.586421	TGACAAATCTTTATGCAACCCACA	59.414	37.500	0.00	0.00	0.00	4.17
495	7031	5.798125	TTGACAAATCTTTATGCAACCCA	57.202	34.783	0.00	0.00	0.00	4.51
507	7043	9.965824	AACGAACAATTAGAAATTGACAAATCT	57.034	25.926	16.94	10.60	33.51	2.40
531	7067	1.605992	GCCCTACACCCCCACTAAC	59.394	63.158	0.00	0.00	0.00	2.34
542	7078	3.529734	TGAATTTTAGGATGGGCCCTACA	59.470	43.478	25.70	2.00	38.45	2.74
545	7085	2.091111	CCTGAATTTTAGGATGGGCCCT	60.091	50.000	25.70	8.64	37.52	5.19
610	7155	3.669122	CGCTAGAACTACGTAATGCATCC	59.331	47.826	0.00	0.00	0.00	3.51
632	7177	3.658757	TGTACCCGTACTACCAAACAC	57.341	47.619	6.56	0.00	37.00	3.32
698	7243	2.691526	TGCTAACCCTCGTAGTACATGG	59.308	50.000	0.00	1.60	0.00	3.66
745	7290	1.373590	GACCCATATGTTTGCGCGGT	61.374	55.000	8.83	0.00	0.00	5.68
749	7294	3.500982	CAAAGTGACCCATATGTTTGCG	58.499	45.455	1.24	0.00	0.00	4.85
756	7301	4.568072	TGTACAGCAAAGTGACCCATAT	57.432	40.909	0.00	0.00	0.00	1.78
758	7303	2.949177	TGTACAGCAAAGTGACCCAT	57.051	45.000	0.00	0.00	0.00	4.00
760	7305	4.335594	GGATTATGTACAGCAAAGTGACCC	59.664	45.833	0.33	0.00	0.00	4.46
770	7315	6.283694	TGACATGAGAAGGATTATGTACAGC	58.716	40.000	0.00	0.00	34.18	4.40
771	7316	8.607459	GTTTGACATGAGAAGGATTATGTACAG	58.393	37.037	0.00	0.00	34.18	2.74
776	7321	6.094464	TGCAGTTTGACATGAGAAGGATTATG	59.906	38.462	0.00	0.00	0.00	1.90
797	7342	3.616821	CACCAATGATTGAATGCTTGCAG	59.383	43.478	6.76	0.00	0.00	4.41
968	7520	3.958798	GTGAGGATTACCCAGTACTAGCA	59.041	47.826	0.00	0.00	37.41	3.49
969	7521	3.004524	CGTGAGGATTACCCAGTACTAGC	59.995	52.174	0.00	0.00	37.41	3.42
970	7522	4.205587	ACGTGAGGATTACCCAGTACTAG	58.794	47.826	0.00	0.00	37.41	2.57
971	7523	4.240881	ACGTGAGGATTACCCAGTACTA	57.759	45.455	0.00	0.00	37.41	1.82
1244	7806	0.728466	AGAGTAGTCGACGCAAACGC	60.728	55.000	10.46	9.12	45.53	4.84
1290	7852	2.277591	GCATGCAGGAGGTTTGGCA	61.278	57.895	14.21	0.00	41.00	4.92
1404	7966	1.414919	ACGAGGTACCAACACACACAT	59.585	47.619	15.94	0.00	0.00	3.21
1427	7989	6.683974	ACACTTAATTACATGGCTTAGCAG	57.316	37.500	6.53	0.00	0.00	4.24
1450	8012	4.621068	GCACAGAGCAATAGCATTTGTA	57.379	40.909	0.00	0.00	45.49	2.41
1511	8073	8.639761	TCGAAACAAAGGGGAACAATTAATAAA	58.360	29.630	0.00	0.00	0.00	1.40
1512	8074	8.083462	GTCGAAACAAAGGGGAACAATTAATAA	58.917	33.333	0.00	0.00	0.00	1.40
1513	8075	7.309316	GGTCGAAACAAAGGGGAACAATTAATA	60.309	37.037	0.00	0.00	0.00	0.98
1514	8076	6.452242	GTCGAAACAAAGGGGAACAATTAAT	58.548	36.000	0.00	0.00	0.00	1.40
1517	8079	3.069016	GGTCGAAACAAAGGGGAACAATT	59.931	43.478	0.00	0.00	0.00	2.32
1594	8162	6.096036	CGTCAGACACATGATAGAAAGAAGT	58.904	40.000	0.00	0.00	0.00	3.01
1939	8517	7.766278	GGATGTTCACAAGAGATATGTGTAAGT	59.234	37.037	6.56	0.00	46.42	2.24
1941	8519	7.549134	GTGGATGTTCACAAGAGATATGTGTAA	59.451	37.037	6.56	0.00	46.42	2.41
2018	8600	6.823689	CCACCCTTTATATGCTACCATGATAC	59.176	42.308	0.00	0.00	32.85	2.24
2062	8646	6.874134	CCTATTTTATAAGCACCGTATGAGCT	59.126	38.462	0.00	0.00	41.03	4.09
2159	8952	1.067749	CAGATCAGCCGCTGAGAGG	59.932	63.158	26.35	14.66	44.08	3.69
2286	9088	5.179368	GCACGCTAATAGCATATTTGAAGGA	59.821	40.000	13.15	0.00	42.58	3.36
2324	9136	4.619760	TCGCTAAAATCTCAGTGTACAACG	59.380	41.667	0.00	0.00	0.00	4.10
2325	9137	5.442909	CGTCGCTAAAATCTCAGTGTACAAC	60.443	44.000	0.00	0.00	0.00	3.32
2348	9160	0.933097	ATAGCGTTCTGAGCAATGCG	59.067	50.000	0.00	0.00	42.25	4.73
2360	9172	6.035005	CGTTGCTAATATCATGCTATAGCGTT	59.965	38.462	16.97	6.54	45.83	4.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.