AutoCloner

Multiple sequence alignment - TraesCS6D01G110600

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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	TraesCS6D01G110600	chr6D	100.000	2764	0	0	1	2764	76063358	76066121	0.000000e+00	5105
1	TraesCS6D01G110600	chr6D	81.250	672	72	36	1001	1661	76042794	76043422	6.880000e-136	494
2	TraesCS6D01G110600	chr6D	86.444	450	38	14	1220	1661	75991672	75992106	3.220000e-129	472
3	TraesCS6D01G110600	chr6A	89.846	2019	82	54	140	2092	92053528	92055489	0.000000e+00	2479
4	TraesCS6D01G110600	chr6A	81.602	674	81	32	1001	1661	91924685	91925328	4.080000e-143	518
5	TraesCS6D01G110600	chr6A	92.361	144	10	1	1	143	92053112	92053255	1.300000e-48	204
6	TraesCS6D01G110600	chr6B	90.194	1703	90	38	434	2091	149772730	149774400	0.000000e+00	2148
7	TraesCS6D01G110600	chr6B	86.353	447	43	14	1220	1661	149611144	149611577	3.220000e-129	472
8	TraesCS6D01G110600	chr6B	86.230	443	37	14	1220	1661	149551452	149551871	2.510000e-125	459
9	TraesCS6D01G110600	chr6B	92.925	212	14	1	1451	1661	149577340	149577551	9.620000e-80	307
10	TraesCS6D01G110600	chr5D	96.329	681	21	4	2087	2764	481152619	481151940	0.000000e+00	1116
11	TraesCS6D01G110600	chr2D	96.012	677	26	1	2089	2764	521869085	521869761	0.000000e+00	1099
12	TraesCS6D01G110600	chr4D	95.748	682	20	6	2089	2764	30200191	30200869	0.000000e+00	1090
13	TraesCS6D01G110600	chr7B	94.543	678	34	3	2089	2764	25660536	25661212	0.000000e+00	1044
14	TraesCS6D01G110600	chr2B	94.527	676	36	1	2090	2764	762352349	762353024	0.000000e+00	1042
15	TraesCS6D01G110600	chr2B	94.118	680	37	3	2088	2764	677978658	677977979	0.000000e+00	1031
16	TraesCS6D01G110600	chr2B	94.126	681	35	2	2088	2764	677978679	677979358	0.000000e+00	1031
17	TraesCS6D01G110600	chr1B	93.917	674	39	2	2089	2761	408109642	408110314	0.000000e+00	1016
18	TraesCS6D01G110600	chr1B	93.962	679	29	9	2093	2764	631823899	631823226	0.000000e+00	1016
19	TraesCS6D01G110600	chrUn	86.353	447	43	14	1220	1661	78112291	78111858	3.220000e-129	472

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	TraesCS6D01G110600	chr6D	76063358	76066121	2763	False	5105.0	5105	100.0000	1	2764	1	chr6D.!!$F3	2763
1	TraesCS6D01G110600	chr6D	76042794	76043422	628	False	494.0	494	81.2500	1001	1661	1	chr6D.!!$F2	660
2	TraesCS6D01G110600	chr6A	92053112	92055489	2377	False	1341.5	2479	91.1035	1	2092	2	chr6A.!!$F2	2091
3	TraesCS6D01G110600	chr6A	91924685	91925328	643	False	518.0	518	81.6020	1001	1661	1	chr6A.!!$F1	660
4	TraesCS6D01G110600	chr6B	149772730	149774400	1670	False	2148.0	2148	90.1940	434	2091	1	chr6B.!!$F4	1657
5	TraesCS6D01G110600	chr5D	481151940	481152619	679	True	1116.0	1116	96.3290	2087	2764	1	chr5D.!!$R1	677
6	TraesCS6D01G110600	chr2D	521869085	521869761	676	False	1099.0	1099	96.0120	2089	2764	1	chr2D.!!$F1	675
7	TraesCS6D01G110600	chr4D	30200191	30200869	678	False	1090.0	1090	95.7480	2089	2764	1	chr4D.!!$F1	675
8	TraesCS6D01G110600	chr7B	25660536	25661212	676	False	1044.0	1044	94.5430	2089	2764	1	chr7B.!!$F1	675
9	TraesCS6D01G110600	chr2B	762352349	762353024	675	False	1042.0	1042	94.5270	2090	2764	1	chr2B.!!$F2	674
10	TraesCS6D01G110600	chr2B	677977979	677978658	679	True	1031.0	1031	94.1180	2088	2764	1	chr2B.!!$R1	676
11	TraesCS6D01G110600	chr2B	677978679	677979358	679	False	1031.0	1031	94.1260	2088	2764	1	chr2B.!!$F1	676
12	TraesCS6D01G110600	chr1B	408109642	408110314	672	False	1016.0	1016	93.9170	2089	2761	1	chr1B.!!$F1	672
13	TraesCS6D01G110600	chr1B	631823226	631823899	673	True	1016.0	1016	93.9620	2093	2764	1	chr1B.!!$R1	671

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
933	1247	0.107945	GCAGGCAACCTTCGATCTCT	60.108	55.0	0.0	0.0	37.17	3.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2012	2388	0.107703	TGGCTGGAACATTCGCTAGG	60.108	55.0	0.0	0.0	38.2	3.02	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
72	74	2.167219	CGCACCTACATGTGAGCCG	61.167	63.158	9.11	1.05	38.55	5.52
111	113	0.447801	GTAGTTGCATGTTCGCCAGG	59.552	55.000	0.00	0.00	0.00	4.45
118	120	1.359848	CATGTTCGCCAGGTGTACTC	58.640	55.000	10.79	0.00	0.00	2.59
136	138	4.284550	AACTGCATGCCCACCGGT	62.285	61.111	16.68	0.00	0.00	5.28
207	485	0.323302	TCAGCCCGCACACTATCAAA	59.677	50.000	0.00	0.00	0.00	2.69
329	608	6.657541	TCAGTGGGATGGTGTTTAGTTAATTC	59.342	38.462	0.00	0.00	0.00	2.17
332	611	5.878116	TGGGATGGTGTTTAGTTAATTCTCG	59.122	40.000	0.00	0.00	0.00	4.04
375	654	9.745018	TCATACCTCAAATCAGAAGAAGAAAAT	57.255	29.630	0.00	0.00	0.00	1.82
586	870	4.916870	AGTAAAAGCAGTTTTTGACCGTC	58.083	39.130	5.29	0.00	39.29	4.79
596	884	6.640907	GCAGTTTTTGACCGTCTTGATATTTT	59.359	34.615	0.00	0.00	0.00	1.82
597	885	7.169140	GCAGTTTTTGACCGTCTTGATATTTTT	59.831	33.333	0.00	0.00	0.00	1.94
600	888	9.191995	GTTTTTGACCGTCTTGATATTTTTGAT	57.808	29.630	0.00	0.00	0.00	2.57
612	900	5.879777	TGATATTTTTGATCGAGCCTGACAA	59.120	36.000	0.00	0.00	0.00	3.18
613	901	4.691860	ATTTTTGATCGAGCCTGACAAG	57.308	40.909	0.00	0.00	0.00	3.16
614	902	1.442769	TTTGATCGAGCCTGACAAGC	58.557	50.000	0.00	0.00	0.00	4.01
615	903	0.321346	TTGATCGAGCCTGACAAGCA	59.679	50.000	0.00	0.00	0.00	3.91
616	904	0.108472	TGATCGAGCCTGACAAGCAG	60.108	55.000	0.00	0.00	44.49	4.24
715	1011	6.237384	CGTAGCGTTTGTTCACGACTAATTAT	60.237	38.462	0.00	0.00	43.15	1.28
721	1017	9.405083	CGTTTGTTCACGACTAATTATGAATAC	57.595	33.333	3.27	2.83	43.15	1.89
873	1169	4.042062	TCTGTAGTAGGTAAGCCGCCTATA	59.958	45.833	2.47	0.00	40.33	1.31
931	1245	1.078143	GGCAGGCAACCTTCGATCT	60.078	57.895	0.00	0.00	37.17	2.75
932	1246	1.092345	GGCAGGCAACCTTCGATCTC	61.092	60.000	0.00	0.00	37.17	2.75
933	1247	0.107945	GCAGGCAACCTTCGATCTCT	60.108	55.000	0.00	0.00	37.17	3.10
934	1248	1.933247	CAGGCAACCTTCGATCTCTC	58.067	55.000	0.00	0.00	37.17	3.20
935	1249	1.480137	CAGGCAACCTTCGATCTCTCT	59.520	52.381	0.00	0.00	37.17	3.10
936	1250	1.754226	AGGCAACCTTCGATCTCTCTC	59.246	52.381	0.00	0.00	37.17	3.20
937	1251	1.535015	GGCAACCTTCGATCTCTCTCG	60.535	57.143	0.00	0.00	39.99	4.04
938	1252	1.402259	GCAACCTTCGATCTCTCTCGA	59.598	52.381	0.00	0.00	45.32	4.04
939	1253	2.034053	GCAACCTTCGATCTCTCTCGAT	59.966	50.000	0.00	0.00	46.16	3.59
940	1254	3.851838	GCAACCTTCGATCTCTCTCGATC	60.852	52.174	0.00	0.00	46.16	3.69
964	1280	2.408704	GTCTCGATCAACACAAGAACCG	59.591	50.000	0.00	0.00	0.00	4.44
984	1300	2.092323	GGCAAATTAGCTTCGGGTTCT	58.908	47.619	0.00	0.00	34.17	3.01
1218	1549	3.248171	GGCGTCGCTGCTACTTCG	61.248	66.667	18.11	0.00	34.52	3.79
1272	1603	4.738345	AGCAGCGACGTCGACGAC	62.738	66.667	41.52	33.70	43.02	4.34
1405	1736	3.196463	CTCTCTCACGTACGTCCATACT	58.804	50.000	19.94	0.00	0.00	2.12
1406	1737	2.934553	TCTCTCACGTACGTCCATACTG	59.065	50.000	19.94	5.64	0.00	2.74
1407	1738	2.676839	CTCTCACGTACGTCCATACTGT	59.323	50.000	19.94	0.00	0.00	3.55
1408	1739	3.860641	TCTCACGTACGTCCATACTGTA	58.139	45.455	19.94	0.00	0.00	2.74
1409	1740	3.618594	TCTCACGTACGTCCATACTGTAC	59.381	47.826	19.94	0.00	34.81	2.90
1709	2052	2.740714	GCTCACGATGGCCAACGAC	61.741	63.158	37.90	20.98	0.00	4.34
1739	2082	0.040958	GTTCGTCCTGCAACAAGCTG	60.041	55.000	0.00	0.00	45.94	4.24
1769	2112	1.148273	GATGCCGGCATAAGGGACA	59.852	57.895	40.56	11.35	36.70	4.02
1773	2116	2.499205	CGGCATAAGGGACAGCGA	59.501	61.111	0.00	0.00	0.00	4.93
1775	2118	1.823295	GGCATAAGGGACAGCGAGA	59.177	57.895	0.00	0.00	0.00	4.04
1776	2119	0.394565	GGCATAAGGGACAGCGAGAT	59.605	55.000	0.00	0.00	0.00	2.75
1777	2120	1.202698	GGCATAAGGGACAGCGAGATT	60.203	52.381	0.00	0.00	0.00	2.40
1778	2121	2.037251	GGCATAAGGGACAGCGAGATTA	59.963	50.000	0.00	0.00	0.00	1.75
1779	2122	3.307059	GGCATAAGGGACAGCGAGATTAT	60.307	47.826	0.00	0.00	0.00	1.28
1780	2123	4.319177	GCATAAGGGACAGCGAGATTATT	58.681	43.478	0.00	0.00	0.00	1.40
1781	2124	5.479306	GCATAAGGGACAGCGAGATTATTA	58.521	41.667	0.00	0.00	0.00	0.98
1885	2239	3.119919	GCATGAGCTTCAGGAAACAAGAG	60.120	47.826	0.00	0.00	37.91	2.85
1980	2354	6.795144	TGTTTATAGAATACCAAGGACGGA	57.205	37.500	0.00	0.00	0.00	4.69
2006	2382	2.147150	CTATCTGACGATCGCTCAGGA	58.853	52.381	30.00	22.34	36.55	3.86
2008	2384	1.098129	TCTGACGATCGCTCAGGAGG	61.098	60.000	30.00	16.65	36.55	4.30
2012	2388	3.934962	GATCGCTCAGGAGGCCCC	61.935	72.222	0.00	0.00	0.00	5.80
2021	2397	2.849646	GGAGGCCCCCTAGCGAAT	60.850	66.667	0.00	0.00	31.76	3.34
2043	2419	2.409870	CCAGCCAGGATCGTTTGCC	61.410	63.158	0.00	0.00	41.22	4.52
2159	2545	4.445453	CTCCATCGTTTCATCAAGATCCA	58.555	43.478	0.00	0.00	0.00	3.41
2182	2568	9.474313	TCCATGCAGGTTTTATACTCTATTTTT	57.526	29.630	0.00	0.00	39.02	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	0.613260	GTGCCTGATACCTGGACACA	59.387	55.000	0.00	0.00	37.81	3.72
55	57	1.815421	CCGGCTCACATGTAGGTGC	60.815	63.158	0.00	0.00	38.66	5.01
111	113	0.804989	GGGCATGCAGTTGAGTACAC	59.195	55.000	21.36	0.00	0.00	2.90
118	120	3.751246	CCGGTGGGCATGCAGTTG	61.751	66.667	21.36	4.61	0.00	3.16
136	138	6.839124	AGTGTGGAATTGCAATTCTAATGA	57.161	33.333	37.77	23.08	43.33	2.57
329	608	8.875803	GGTATGACTATCTACAATCTAGACGAG	58.124	40.741	0.00	0.00	0.00	4.18
332	611	9.727859	TGAGGTATGACTATCTACAATCTAGAC	57.272	37.037	0.00	0.00	0.00	2.59
375	654	9.860650	AGATTTTGTGTGTATATATTAGGGCAA	57.139	29.630	0.00	0.00	0.00	4.52
520	801	2.003443	CAACAGCGTTGGCGTTTCG	61.003	57.895	3.74	0.00	46.35	3.46
532	813	3.626028	ACGTGGAAGAAATTCAACAGC	57.374	42.857	0.00	0.00	0.00	4.40
586	870	6.037500	TGTCAGGCTCGATCAAAAATATCAAG	59.962	38.462	0.00	0.00	0.00	3.02
596	884	0.321346	TGCTTGTCAGGCTCGATCAA	59.679	50.000	8.55	0.00	0.00	2.57
597	885	0.108472	CTGCTTGTCAGGCTCGATCA	60.108	55.000	8.55	0.00	39.15	2.92
600	888	1.588597	CTCTGCTTGTCAGGCTCGA	59.411	57.895	8.55	4.25	43.06	4.04
612	900	3.203263	TCACTGGTAGACTATCCTCTGCT	59.797	47.826	0.00	0.00	0.00	4.24
613	901	3.556999	TCACTGGTAGACTATCCTCTGC	58.443	50.000	0.00	0.00	0.00	4.26
614	902	5.197451	ACTTCACTGGTAGACTATCCTCTG	58.803	45.833	0.00	0.00	0.00	3.35
615	903	5.459982	ACTTCACTGGTAGACTATCCTCT	57.540	43.478	0.00	0.00	0.00	3.69
616	904	7.826918	ATTACTTCACTGGTAGACTATCCTC	57.173	40.000	0.00	0.00	0.00	3.71
689	981	0.160182	GTCGTGAACAAACGCTACGG	59.840	55.000	0.00	0.00	43.26	4.02
873	1169	1.408127	GGTTTGTTGGCCAAGGCTTTT	60.408	47.619	21.21	0.00	41.60	2.27
940	1254	3.203161	TCTTGTGTTGATCGAGACTCG	57.797	47.619	18.91	18.91	42.10	4.18
964	1280	2.092323	AGAACCCGAAGCTAATTTGCC	58.908	47.619	8.30	0.00	0.00	4.52
984	1300	6.294010	GGCTAGACATGATGACAGTATACGAA	60.294	42.308	0.00	0.00	0.00	3.85
1218	1549	0.534652	CCCTCTTGCTATGCTGCCTC	60.535	60.000	0.00	0.00	0.00	4.70
1272	1603	4.495939	CCTCCGTCGTCGTCGTCG	62.496	72.222	13.54	13.54	44.85	5.12
1303	1634	3.441290	CTTCCTCGTCCCGTCGCT	61.441	66.667	0.00	0.00	0.00	4.93
1408	1739	9.397280	GCTAATTAAGGACAGAAATTAGAAGGT	57.603	33.333	14.91	0.00	42.11	3.50
1409	1740	9.396022	TGCTAATTAAGGACAGAAATTAGAAGG	57.604	33.333	14.91	0.00	42.11	3.46
1709	2052	0.532862	AGGACGAACACACAGCCTTG	60.533	55.000	0.00	0.00	0.00	3.61
1764	2107	3.060602	GCAGTAATAATCTCGCTGTCCC	58.939	50.000	0.00	0.00	0.00	4.46
1769	2112	1.605712	GGCGGCAGTAATAATCTCGCT	60.606	52.381	3.07	0.00	41.18	4.93
1773	2116	2.047061	TCAGGGCGGCAGTAATAATCT	58.953	47.619	12.47	0.00	0.00	2.40
1775	2118	3.290948	TTTCAGGGCGGCAGTAATAAT	57.709	42.857	12.47	0.00	0.00	1.28
1776	2119	2.791347	TTTCAGGGCGGCAGTAATAA	57.209	45.000	12.47	0.00	0.00	1.40
1777	2120	2.571212	CATTTCAGGGCGGCAGTAATA	58.429	47.619	12.47	0.00	0.00	0.98
1778	2121	1.392589	CATTTCAGGGCGGCAGTAAT	58.607	50.000	12.47	5.53	0.00	1.89
1779	2122	1.312371	GCATTTCAGGGCGGCAGTAA	61.312	55.000	12.47	3.13	0.00	2.24
1780	2123	1.748879	GCATTTCAGGGCGGCAGTA	60.749	57.895	12.47	0.00	0.00	2.74
1781	2124	3.064324	GCATTTCAGGGCGGCAGT	61.064	61.111	12.47	0.00	0.00	4.40
1824	2178	4.707448	AGCTAACTGACTATAGTGCACTGT	59.293	41.667	29.57	24.89	0.00	3.55
1825	2179	5.255710	AGCTAACTGACTATAGTGCACTG	57.744	43.478	29.57	15.20	0.00	3.66
1980	2354	4.998033	TGAGCGATCGTCAGATAGTTATCT	59.002	41.667	17.81	0.00	43.51	1.98
2006	2382	1.984288	GAACATTCGCTAGGGGGCCT	61.984	60.000	0.84	0.00	37.71	5.19
2008	2384	1.526225	GGAACATTCGCTAGGGGGC	60.526	63.158	6.99	0.00	0.00	5.80
2012	2388	0.107703	TGGCTGGAACATTCGCTAGG	60.108	55.000	0.00	0.00	38.20	3.02
2014	2390	0.107703	CCTGGCTGGAACATTCGCTA	60.108	55.000	4.05	0.00	38.20	4.26
2117	2499	3.748370	TGGATTGCCCACCGGTAT	58.252	55.556	6.87	0.00	40.82	2.73
2245	2639	6.592607	CGTTGTCTCTACTCTAACTCTCTCTT	59.407	42.308	0.00	0.00	0.00	2.85
2536	2934	5.288232	CAGTTTGTGAAAATGAGCGAAACAA	59.712	36.000	0.00	0.00	38.65	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.