AutoCloner

Multiple sequence alignment - TraesCS6D01G119900

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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	TraesCS6D01G119900	chr6D	100.000	6171	0	0	1	6171	84686800	84680630	0.000000e+00	11396.0
1	TraesCS6D01G119900	chr6D	97.658	2348	45	7	3117	5459	85543861	85546203	0.000000e+00	4023.0
2	TraesCS6D01G119900	chr6D	99.487	1949	10	0	26	1974	85503704	85505652	0.000000e+00	3544.0
3	TraesCS6D01G119900	chr6D	96.303	1055	12	12	2074	3128	85506130	85507157	0.000000e+00	1707.0
4	TraesCS6D01G119900	chr6D	89.853	749	45	10	5444	6171	85548922	85549660	0.000000e+00	933.0
5	TraesCS6D01G119900	chr6D	100.000	31	0	0	5	35	85503656	85503686	2.400000e-04	58.4
6	TraesCS6D01G119900	chr6B	92.903	3100	136	32	5	3072	161354334	161351287	0.000000e+00	4429.0
7	TraesCS6D01G119900	chr6B	95.605	1843	69	4	3140	4982	161351070	161349240	0.000000e+00	2944.0
8	TraesCS6D01G119900	chr6B	85.507	897	75	22	5296	6171	161348896	161348034	0.000000e+00	885.0
9	TraesCS6D01G119900	chr6A	90.016	2494	125	41	3	2465	101933759	101931359	0.000000e+00	3112.0
10	TraesCS6D01G119900	chr6A	92.570	1669	89	15	4510	6171	101912752	101911112	0.000000e+00	2362.0
11	TraesCS6D01G119900	chr6A	91.968	1382	90	7	3140	4518	101930423	101929060	0.000000e+00	1917.0
12	TraesCS6D01G119900	chr6A	83.725	596	51	16	2468	3051	101931223	101930662	7.090000e-144	521.0
13	TraesCS6D01G119900	chr5B	86.501	563	72	4	1176	1736	386558553	386557993	3.160000e-172	616.0
14	TraesCS6D01G119900	chr5B	77.946	662	108	25	3617	4246	386540791	386540136	4.510000e-101	379.0
15	TraesCS6D01G119900	chr5B	82.969	229	31	8	2472	2697	386542265	386542042	3.770000e-47	200.0
16	TraesCS6D01G119900	chr5D	86.910	466	59	2	1170	1634	330719392	330719856	7.090000e-144	521.0
17	TraesCS6D01G119900	chr5A	80.714	560	89	15	2472	3024	426347258	426347805	9.570000e-113	418.0
18	TraesCS6D01G119900	chr5A	81.237	469	70	11	3617	4071	426348807	426349271	4.550000e-96	363.0
19	TraesCS6D01G119900	chr5A	88.688	221	25	0	4318	4538	426349684	426349904	2.830000e-68	270.0
20	TraesCS6D01G119900	chr1B	78.489	609	101	18	1170	1766	588480795	588481385	7.550000e-99	372.0
21	TraesCS6D01G119900	chr1B	84.179	335	48	4	1373	1706	588644037	588644367	2.780000e-83	320.0
22	TraesCS6D01G119900	chr1B	83.491	212	35	0	4325	4536	588486404	588486193	1.360000e-46	198.0
23	TraesCS6D01G119900	chr1D	75.706	815	149	36	978	1772	435144763	435145548	4.550000e-96	363.0
24	TraesCS6D01G119900	chr1D	80.392	459	71	13	1337	1787	435343700	435344147	1.280000e-86	331.0
25	TraesCS6D01G119900	chr1D	82.547	212	37	0	4325	4536	435150843	435150632	2.940000e-43	187.0
26	TraesCS6D01G119900	chr4B	85.537	242	28	5	5182	5420	312160173	312160410	4.780000e-61	246.0
27	TraesCS6D01G119900	chr7D	92.683	41	3	0	4657	4697	575596889	575596929	6.680000e-05	60.2

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	TraesCS6D01G119900	chr6D	84680630	84686800	6170	True	11396.000000	11396	100.000000	1	6171	1	chr6D.!!$R1	6170
1	TraesCS6D01G119900	chr6D	85543861	85549660	5799	False	2478.000000	4023	93.755500	3117	6171	2	chr6D.!!$F2	3054
2	TraesCS6D01G119900	chr6D	85503656	85507157	3501	False	1769.800000	3544	98.596667	5	3128	3	chr6D.!!$F1	3123
3	TraesCS6D01G119900	chr6B	161348034	161354334	6300	True	2752.666667	4429	91.338333	5	6171	3	chr6B.!!$R1	6166
4	TraesCS6D01G119900	chr6A	101911112	101912752	1640	True	2362.000000	2362	92.570000	4510	6171	1	chr6A.!!$R1	1661
5	TraesCS6D01G119900	chr6A	101929060	101933759	4699	True	1850.000000	3112	88.569667	3	4518	3	chr6A.!!$R2	4515
6	TraesCS6D01G119900	chr5B	386557993	386558553	560	True	616.000000	616	86.501000	1176	1736	1	chr5B.!!$R1	560
7	TraesCS6D01G119900	chr5B	386540136	386542265	2129	True	289.500000	379	80.457500	2472	4246	2	chr5B.!!$R2	1774
8	TraesCS6D01G119900	chr5A	426347258	426349904	2646	False	350.333333	418	83.546333	2472	4538	3	chr5A.!!$F1	2066
9	TraesCS6D01G119900	chr1B	588480795	588481385	590	False	372.000000	372	78.489000	1170	1766	1	chr1B.!!$F1	596
10	TraesCS6D01G119900	chr1D	435144763	435145548	785	False	363.000000	363	75.706000	978	1772	1	chr1D.!!$F1	794

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	Hairpin	End Stability	Orientation
1865	1936	2.202623	GCTCTACGACGTGCCCTG	60.203	66.667	11.56	0.00	4.45	F
2167	2620	0.463474	GCCTGTTCCTCATCAGCCTC	60.463	60.000	0.00	0.00	4.70	F
4014	5391	0.623723	TTGCAAGGATGGGGAGTACC	59.376	55.000	0.00	39.11	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
4014	5391	7.187824	ACATATACTCATATACAAGGGCCAG	57.812	40.000	6.18	0.00	4.85	R
4125	5534	1.546323	CCCTGCAGAACATGGTGAGTT	60.546	52.381	17.39	29.86	3.01	R
5497	9879	0.106819	GGATCACAGAGGGCTGCAAT	60.107	55.000	0.50	46.26	3.56	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
1865	1936	2.202623	GCTCTACGACGTGCCCTG	60.203	66.667	11.56	0.00	0.00	4.45
2048	2423	1.069636	GCGACTTCAGTTTCAGCCAAG	60.070	52.381	0.00	0.00	0.00	3.61
2076	2529	6.324561	TGCATTTGAGTAGTAATTTGCACA	57.675	33.333	0.00	0.00	0.00	4.57
2161	2614	2.892425	CGGCGCCTGTTCCTCATC	60.892	66.667	26.68	0.00	0.00	2.92
2162	2615	2.268920	GGCGCCTGTTCCTCATCA	59.731	61.111	22.15	0.00	0.00	3.07
2163	2616	1.817099	GGCGCCTGTTCCTCATCAG	60.817	63.158	22.15	0.00	0.00	2.90
2164	2617	2.467826	GCGCCTGTTCCTCATCAGC	61.468	63.158	0.00	0.00	0.00	4.26
2165	2618	1.817099	CGCCTGTTCCTCATCAGCC	60.817	63.158	0.00	0.00	0.00	4.85
2166	2619	1.606531	GCCTGTTCCTCATCAGCCT	59.393	57.895	0.00	0.00	0.00	4.58
2167	2620	0.463474	GCCTGTTCCTCATCAGCCTC	60.463	60.000	0.00	0.00	0.00	4.70
2168	2621	0.907486	CCTGTTCCTCATCAGCCTCA	59.093	55.000	0.00	0.00	0.00	3.86
2169	2622	1.280133	CCTGTTCCTCATCAGCCTCAA	59.720	52.381	0.00	0.00	0.00	3.02
2170	2623	2.630158	CTGTTCCTCATCAGCCTCAAG	58.370	52.381	0.00	0.00	0.00	3.02
2171	2624	1.339438	TGTTCCTCATCAGCCTCAAGC	60.339	52.381	0.00	0.00	44.25	4.01
2223	2676	2.125350	CTCCTCTGCTTCGTGGCC	60.125	66.667	0.00	0.00	0.00	5.36
3154	4361	8.684386	TGTCCTTTCAATTGTTGATACTTACA	57.316	30.769	5.13	0.00	39.84	2.41
4014	5391	0.623723	TTGCAAGGATGGGGAGTACC	59.376	55.000	0.00	0.00	39.11	3.34
4125	5534	1.040893	TCGAGCTCCCCGATGCTAAA	61.041	55.000	8.47	0.00	39.91	1.85
4155	5565	0.820226	TTCTGCAGGGAGAGATCACG	59.180	55.000	15.13	0.00	0.00	4.35
4625	6197	7.936496	ACACAAATCCATCACATATGTGTAA	57.064	32.000	30.03	16.20	45.59	2.41
4850	6423	1.737236	GCAACTATGATGTCAACGGCA	59.263	47.619	0.00	0.00	0.00	5.69
4898	6471	3.667087	GCATGACGCAAACTCCCA	58.333	55.556	0.00	0.00	41.79	4.37
4954	6527	0.183492	TGCTGGAGTGCCTTGAACTT	59.817	50.000	0.00	0.00	34.31	2.66
4998	6571	2.433145	CAGCGTCAGTGGCGACAT	60.433	61.111	23.55	2.26	46.14	3.06
5002	6575	1.361668	GCGTCAGTGGCGACATGAAT	61.362	55.000	23.55	0.00	46.14	2.57
5137	6710	1.448069	GCCTAACTCTAGCAGGGCC	59.552	63.158	0.00	0.00	34.19	5.80
5216	6800	1.608801	CCTTTGTGCATCAAAAGGGCC	60.609	52.381	21.90	0.00	44.08	5.80
5240	6824	4.607557	CGGAGGCTTTAATTATGTAACGCG	60.608	45.833	3.53	3.53	30.96	6.01
5380	7025	4.551671	ACTCATGCTATCCTACTGAGGTT	58.448	43.478	0.00	0.00	44.19	3.50
5420	7068	3.921104	TCCTAGCTCTGAATCCACAGAT	58.079	45.455	0.00	0.00	44.32	2.90
5486	9868	4.293648	GTGGGTTTTGCCGCCACC	62.294	66.667	0.00	0.00	38.44	4.61
5529	9912	2.615447	CTGTGATCCCGAAATGATGTGG	59.385	50.000	0.00	0.00	0.00	4.17
5587	9970	1.432514	GCGTTCAGATCAACAGCAGA	58.567	50.000	0.00	0.00	0.00	4.26
5602	9985	1.381928	GCAGACATGGATGCTGTGGG	61.382	60.000	15.03	0.00	39.38	4.61
5629	10013	0.901124	TCTGAAGGAGAGCAAGCCTC	59.099	55.000	0.00	3.02	41.07	4.70
5664	10048	5.628797	TGCCACCAGATCTACATCATTTA	57.371	39.130	0.00	0.00	0.00	1.40
5694	10078	0.393808	GGGAGGCAACGGCATAGAAA	60.394	55.000	0.00	0.00	43.71	2.52
5696	10080	2.486548	GGGAGGCAACGGCATAGAAATA	60.487	50.000	0.00	0.00	43.71	1.40
5697	10081	2.808543	GGAGGCAACGGCATAGAAATAG	59.191	50.000	0.00	0.00	43.71	1.73
5698	10082	3.494398	GGAGGCAACGGCATAGAAATAGA	60.494	47.826	0.00	0.00	43.71	1.98
5699	10083	4.127171	GAGGCAACGGCATAGAAATAGAA	58.873	43.478	0.00	0.00	43.71	2.10
5700	10084	4.718961	AGGCAACGGCATAGAAATAGAAT	58.281	39.130	0.00	0.00	43.71	2.40
5701	10085	4.757149	AGGCAACGGCATAGAAATAGAATC	59.243	41.667	0.00	0.00	43.71	2.52
5805	10206	0.533032	AACTAGAGCTTCTCCGGCAC	59.467	55.000	0.00	0.00	0.00	5.01
6090	10502	1.367840	GCCGAATAGGAGCGACCAT	59.632	57.895	5.84	0.00	45.00	3.55
6104	10520	0.470341	GACCATAGGGACTCAAGCCC	59.530	60.000	0.00	0.00	46.40	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.098982	TGTTGGTCTTAAATCATGTGGGTTTT	59.901	34.615	0.00	0.00	0.00	2.43
1	2	5.600484	TGTTGGTCTTAAATCATGTGGGTTT	59.400	36.000	0.00	0.00	0.00	3.27
1865	1936	2.042831	GCAGTCTGCATCACCACCC	61.043	63.158	20.16	0.00	44.26	4.61
2010	2134	5.842907	AGTCGCAATTCATACTATGCTGTA	58.157	37.500	0.00	0.00	36.67	2.74
2048	2423	7.970061	TGCAAATTACTACTCAAATGCAAGATC	59.030	33.333	0.00	0.00	39.36	2.75
2076	2529	0.184451	CAGGAGCCTGCAATGGGTAT	59.816	55.000	3.18	0.00	38.02	2.73
2150	2603	2.630158	CTTGAGGCTGATGAGGAACAG	58.370	52.381	0.00	0.00	37.22	3.16
2151	2604	1.339438	GCTTGAGGCTGATGAGGAACA	60.339	52.381	0.00	0.00	38.06	3.18
2152	2605	1.377536	GCTTGAGGCTGATGAGGAAC	58.622	55.000	0.00	0.00	38.06	3.62
2153	2606	0.107993	CGCTTGAGGCTGATGAGGAA	60.108	55.000	0.00	0.00	39.13	3.36
2154	2607	1.519246	CGCTTGAGGCTGATGAGGA	59.481	57.895	0.00	0.00	39.13	3.71
2155	2608	1.523258	CCGCTTGAGGCTGATGAGG	60.523	63.158	0.00	0.00	39.13	3.86
2156	2609	4.121691	CCGCTTGAGGCTGATGAG	57.878	61.111	0.00	0.00	39.13	2.90
2165	2618	3.793144	GAACAGGCGCCGCTTGAG	61.793	66.667	28.32	10.50	37.87	3.02
2171	2624	2.892425	GATGAGGAACAGGCGCCG	60.892	66.667	23.20	18.60	0.00	6.46
2172	2625	1.817099	CTGATGAGGAACAGGCGCC	60.817	63.158	21.89	21.89	0.00	6.53
2173	2626	2.467826	GCTGATGAGGAACAGGCGC	61.468	63.158	0.00	0.00	35.05	6.53
2174	2627	1.817099	GGCTGATGAGGAACAGGCG	60.817	63.158	0.00	0.00	46.23	5.52
2176	2629	0.907486	TGAGGCTGATGAGGAACAGG	59.093	55.000	0.00	0.00	35.05	4.00
2223	2676	4.073293	AGGTAATCAAAGTCGCCTATGG	57.927	45.455	0.00	0.00	0.00	2.74
2283	2736	3.280938	TTGGGGCTGATGAACGGGG	62.281	63.158	0.00	0.00	0.00	5.73
4014	5391	7.187824	ACATATACTCATATACAAGGGCCAG	57.812	40.000	6.18	0.00	0.00	4.85
4125	5534	1.546323	CCCTGCAGAACATGGTGAGTT	60.546	52.381	17.39	0.00	29.86	3.01
4155	5565	5.529060	GTCTCCAGGTTAAACATCCATCATC	59.471	44.000	0.00	0.00	0.00	2.92
4625	6197	1.299541	GCGTACCTGCAGTGCATATT	58.700	50.000	20.10	8.35	38.13	1.28
4675	6248	0.506932	CGACACCAAAGCTGTACACG	59.493	55.000	0.00	0.00	0.00	4.49
4832	6405	3.374988	CACATGCCGTTGACATCATAGTT	59.625	43.478	0.00	0.00	0.00	2.24
4850	6423	2.264794	GTCGGCGACCTTCCACAT	59.735	61.111	28.72	0.00	0.00	3.21
4886	6459	2.251642	GCTTCGTGGGAGTTTGCGT	61.252	57.895	0.00	0.00	0.00	5.24
4898	6471	2.202440	CATCGTCGGTCGCTTCGT	60.202	61.111	0.00	0.00	39.67	3.85
4973	6546	0.388649	CCACTGACGCTGGTGTAGAC	60.389	60.000	0.00	0.00	0.00	2.59
4998	6571	1.164411	GGTGTTGACGATGCCATTCA	58.836	50.000	0.00	0.00	0.00	2.57
5002	6575	2.161078	TAGCGGTGTTGACGATGCCA	62.161	55.000	0.00	0.00	0.00	4.92
5216	6800	4.319261	GCGTTACATAATTAAAGCCTCCGG	60.319	45.833	0.00	0.00	32.26	5.14
5240	6824	9.525409	CATGATCAATCCCTCAAAAATAGAAAC	57.475	33.333	0.00	0.00	0.00	2.78
5380	7025	2.498167	GAAGAAGCAGTGAAGGAAGCA	58.502	47.619	0.00	0.00	0.00	3.91
5420	7068	2.749600	ACAGCATCCATGGCCATTTTA	58.250	42.857	17.92	4.49	0.00	1.52
5486	9868	4.799473	CTGCAATGACCACGCGCG	62.799	66.667	30.96	30.96	0.00	6.86
5488	9870	4.465512	GGCTGCAATGACCACGCG	62.466	66.667	3.53	3.53	0.00	6.01
5489	9871	4.120331	GGGCTGCAATGACCACGC	62.120	66.667	0.50	0.00	34.56	5.34
5497	9879	0.106819	GGATCACAGAGGGCTGCAAT	60.107	55.000	0.50	0.00	46.26	3.56
5529	9912	0.657840	GGTGCCATCAGTACGAATGC	59.342	55.000	0.00	5.42	30.59	3.56
5570	9953	3.126514	CCATGTCTGCTGTTGATCTGAAC	59.873	47.826	0.00	0.00	0.00	3.18
5626	10010	1.272092	TGGCAAAGGATGGTTCTGAGG	60.272	52.381	0.00	0.00	0.00	3.86
5629	10013	0.890683	GGTGGCAAAGGATGGTTCTG	59.109	55.000	0.00	0.00	0.00	3.02
5664	10048	1.215423	GTTGCCTCCCATACCTTCCAT	59.785	52.381	0.00	0.00	0.00	3.41
5674	10058	1.558167	TTCTATGCCGTTGCCTCCCA	61.558	55.000	0.00	0.00	36.33	4.37
5694	10078	1.668419	GCGTGCACCCTTGATTCTAT	58.332	50.000	12.15	0.00	0.00	1.98
5696	10080	1.675641	GGCGTGCACCCTTGATTCT	60.676	57.895	12.15	0.00	0.00	2.40
5697	10081	2.877691	GGCGTGCACCCTTGATTC	59.122	61.111	12.15	0.00	0.00	2.52
5698	10082	3.055719	CGGCGTGCACCCTTGATT	61.056	61.111	12.15	0.00	0.00	2.57
5805	10206	2.531927	TACCGCGTTGTCTGTAGGCG	62.532	60.000	4.92	0.00	46.08	5.52
5807	10208	0.806868	TCTACCGCGTTGTCTGTAGG	59.193	55.000	14.99	0.00	33.22	3.18
5817	10218	2.757099	AATCCCCGTCTACCGCGT	60.757	61.111	4.92	0.00	34.38	6.01
5821	10222	1.335132	TGCCAGAATCCCCGTCTACC	61.335	60.000	0.00	0.00	0.00	3.18
5866	10267	4.154347	CCAGAGGTGAGGCCGCTC	62.154	72.222	8.34	3.59	44.40	5.03
6078	10490	0.851469	AGTCCCTATGGTCGCTCCTA	59.149	55.000	0.00	0.00	37.07	2.94
6104	10520	2.587194	CCAGGATCTTCAGCGCGG	60.587	66.667	8.83	0.00	0.00	6.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.