AutoCloner

Multiple sequence alignment - TraesCS4D01G203200

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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	TraesCS4D01G203200	chr4D	100.000	3735	0	0	1	3735	349913335	349909601	0.000000e+00	6898.0
1	TraesCS4D01G203200	chr4B	95.569	2911	77	24	1	2889	433179926	433177046	0.000000e+00	4614.0
2	TraesCS4D01G203200	chr4B	87.336	608	60	5	3142	3735	498682780	498682176	0.000000e+00	680.0
3	TraesCS4D01G203200	chr4B	86.800	250	26	4	2900	3143	433177064	433176816	4.750000e-69	272.0
4	TraesCS4D01G203200	chr4A	94.947	2909	71	30	1	2873	114789810	114792678	0.000000e+00	4488.0
5	TraesCS4D01G203200	chr4A	86.056	251	23	8	2904	3143	114793993	114794242	3.700000e-65	259.0
6	TraesCS4D01G203200	chr4A	93.333	45	3	0	3078	3122	688476354	688476398	2.410000e-07	67.6
7	TraesCS4D01G203200	chr7D	91.500	600	39	4	3148	3735	46426614	46426015	0.000000e+00	815.0
8	TraesCS4D01G203200	chr6D	90.115	607	46	4	3143	3735	407644181	407644787	0.000000e+00	776.0
9	TraesCS4D01G203200	chr6D	89.644	618	49	7	3130	3735	260078087	260078701	0.000000e+00	773.0
10	TraesCS4D01G203200	chr6D	89.037	602	48	12	3143	3735	245276059	245276651	0.000000e+00	730.0
11	TraesCS4D01G203200	chr3D	89.268	615	51	6	3134	3735	294596650	294596038	0.000000e+00	756.0
12	TraesCS4D01G203200	chr5A	88.779	606	56	2	3142	3735	569300713	569301318	0.000000e+00	732.0
13	TraesCS4D01G203200	chr1B	88.391	603	55	5	3144	3735	206126693	206126095	0.000000e+00	712.0
14	TraesCS4D01G203200	chr1B	85.642	592	51	11	3177	3735	344573716	344573126	3.210000e-165	592.0
15	TraesCS4D01G203200	chr3B	89.184	564	49	3	3142	3693	544949822	544950385	0.000000e+00	693.0
16	TraesCS4D01G203200	chr3B	87.611	565	56	4	3148	3701	544841240	544841801	0.000000e+00	643.0
17	TraesCS4D01G203200	chr3B	86.364	66	5	2	3078	3142	564719212	564719150	6.690000e-08	69.4
18	TraesCS4D01G203200	chr6A	87.245	588	59	5	3148	3735	370154672	370154101	0.000000e+00	656.0
19	TraesCS4D01G203200	chr2B	86.777	605	51	12	3142	3735	119574011	119574597	0.000000e+00	647.0
20	TraesCS4D01G203200	chr2B	84.848	66	9	1	3078	3142	793784722	793784657	8.660000e-07	65.8
21	TraesCS4D01G203200	chr3A	84.959	605	54	16	3142	3735	733537482	733536904	2.500000e-161	579.0
22	TraesCS4D01G203200	chr7A	86.312	526	36	10	3222	3735	29906622	29907123	1.180000e-149	540.0
23	TraesCS4D01G203200	chrUn	86.567	67	8	1	3078	3143	24932840	24932774	5.170000e-09	73.1
24	TraesCS4D01G203200	chr5B	86.364	66	8	1	3078	3142	439458962	439459027	1.860000e-08	71.3
25	TraesCS4D01G203200	chr7B	84.000	75	9	3	3069	3142	630663488	630663560	6.690000e-08	69.4
26	TraesCS4D01G203200	chr2D	83.824	68	6	4	3078	3142	650949918	650949983	4.030000e-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	TraesCS4D01G203200	chr4D	349909601	349913335	3734	True	6898.0	6898	100.0000	1	3735	1	chr4D.!!$R1	3734
1	TraesCS4D01G203200	chr4B	433176816	433179926	3110	True	2443.0	4614	91.1845	1	3143	2	chr4B.!!$R2	3142
2	TraesCS4D01G203200	chr4B	498682176	498682780	604	True	680.0	680	87.3360	3142	3735	1	chr4B.!!$R1	593
3	TraesCS4D01G203200	chr4A	114789810	114794242	4432	False	2373.5	4488	90.5015	1	3143	2	chr4A.!!$F2	3142
4	TraesCS4D01G203200	chr7D	46426015	46426614	599	True	815.0	815	91.5000	3148	3735	1	chr7D.!!$R1	587
5	TraesCS4D01G203200	chr6D	407644181	407644787	606	False	776.0	776	90.1150	3143	3735	1	chr6D.!!$F3	592
6	TraesCS4D01G203200	chr6D	260078087	260078701	614	False	773.0	773	89.6440	3130	3735	1	chr6D.!!$F2	605
7	TraesCS4D01G203200	chr6D	245276059	245276651	592	False	730.0	730	89.0370	3143	3735	1	chr6D.!!$F1	592
8	TraesCS4D01G203200	chr3D	294596038	294596650	612	True	756.0	756	89.2680	3134	3735	1	chr3D.!!$R1	601
9	TraesCS4D01G203200	chr5A	569300713	569301318	605	False	732.0	732	88.7790	3142	3735	1	chr5A.!!$F1	593
10	TraesCS4D01G203200	chr1B	206126095	206126693	598	True	712.0	712	88.3910	3144	3735	1	chr1B.!!$R1	591
11	TraesCS4D01G203200	chr1B	344573126	344573716	590	True	592.0	592	85.6420	3177	3735	1	chr1B.!!$R2	558
12	TraesCS4D01G203200	chr3B	544949822	544950385	563	False	693.0	693	89.1840	3142	3693	1	chr3B.!!$F2	551
13	TraesCS4D01G203200	chr3B	544841240	544841801	561	False	643.0	643	87.6110	3148	3701	1	chr3B.!!$F1	553
14	TraesCS4D01G203200	chr6A	370154101	370154672	571	True	656.0	656	87.2450	3148	3735	1	chr6A.!!$R1	587
15	TraesCS4D01G203200	chr2B	119574011	119574597	586	False	647.0	647	86.7770	3142	3735	1	chr2B.!!$F1	593
16	TraesCS4D01G203200	chr3A	733536904	733537482	578	True	579.0	579	84.9590	3142	3735	1	chr3A.!!$R1	593
17	TraesCS4D01G203200	chr7A	29906622	29907123	501	False	540.0	540	86.3120	3222	3735	1	chr7A.!!$F1	513

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
877	907	0.178068	AGGGAATGGACGACGAATGG	59.822	55.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2847	2897	2.005451	GTAATGCACAGTCAGCTGAGG	58.995	52.381	18.89	15.12	45.28	3.86	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
93	98	1.493022	GTCTCCTCTCCAGCTCTCCTA	59.507	57.143	0.00	0.00	0.00	2.94
96	101	1.452145	CCTCTCCAGCTCTCCTACGC	61.452	65.000	0.00	0.00	0.00	4.42
130	135	1.712018	CTCTGGTACGTGCGGATCGA	61.712	60.000	0.00	0.00	0.00	3.59
241	253	2.512286	CGCCGATCATGTGTGCCT	60.512	61.111	0.00	0.00	0.00	4.75
331	348	4.026052	GGATTCCAACCATGTGATTCCTT	58.974	43.478	0.00	0.00	31.09	3.36
518	543	3.378112	TGGCATAGCGATCTTCCTTTTTG	59.622	43.478	0.00	0.00	0.00	2.44
524	549	4.003648	AGCGATCTTCCTTTTTGTGTAGG	58.996	43.478	0.00	0.00	0.00	3.18
607	632	1.137594	AAATTGACGGGGTGGGGAGA	61.138	55.000	0.00	0.00	0.00	3.71
732	760	7.010923	GTCTATCTCTTTTGCTGTTCCATACTG	59.989	40.741	0.00	0.00	0.00	2.74
739	767	1.745653	GCTGTTCCATACTGCCTTTCC	59.254	52.381	0.00	0.00	43.61	3.13
740	768	2.369394	CTGTTCCATACTGCCTTTCCC	58.631	52.381	0.00	0.00	0.00	3.97
741	769	1.005450	TGTTCCATACTGCCTTTCCCC	59.995	52.381	0.00	0.00	0.00	4.81
742	770	0.629058	TTCCATACTGCCTTTCCCCC	59.371	55.000	0.00	0.00	0.00	5.40
743	771	0.253630	TCCATACTGCCTTTCCCCCT	60.254	55.000	0.00	0.00	0.00	4.79
744	772	0.631212	CCATACTGCCTTTCCCCCTT	59.369	55.000	0.00	0.00	0.00	3.95
745	773	1.007118	CCATACTGCCTTTCCCCCTTT	59.993	52.381	0.00	0.00	0.00	3.11
746	774	2.559705	CCATACTGCCTTTCCCCCTTTT	60.560	50.000	0.00	0.00	0.00	2.27
747	775	2.597578	TACTGCCTTTCCCCCTTTTC	57.402	50.000	0.00	0.00	0.00	2.29
748	776	0.539669	ACTGCCTTTCCCCCTTTTCG	60.540	55.000	0.00	0.00	0.00	3.46
749	777	0.251165	CTGCCTTTCCCCCTTTTCGA	60.251	55.000	0.00	0.00	0.00	3.71
788	817	3.257935	CGCAGTTAATGGGGTGGAA	57.742	52.632	0.00	0.00	38.18	3.53
789	818	1.762708	CGCAGTTAATGGGGTGGAAT	58.237	50.000	0.00	0.00	38.18	3.01
790	819	2.099405	CGCAGTTAATGGGGTGGAATT	58.901	47.619	0.00	0.00	38.18	2.17
791	820	2.159254	CGCAGTTAATGGGGTGGAATTG	60.159	50.000	0.00	0.00	38.18	2.32
792	821	2.168313	GCAGTTAATGGGGTGGAATTGG	59.832	50.000	0.00	0.00	0.00	3.16
875	905	0.464452	GGAGGGAATGGACGACGAAT	59.536	55.000	0.00	0.00	0.00	3.34
876	906	1.571919	GAGGGAATGGACGACGAATG	58.428	55.000	0.00	0.00	0.00	2.67
877	907	0.178068	AGGGAATGGACGACGAATGG	59.822	55.000	0.00	0.00	0.00	3.16
878	908	1.436983	GGGAATGGACGACGAATGGC	61.437	60.000	0.00	0.00	0.00	4.40
1128	1165	4.498520	CTCGTCGCCGTGCAGGAT	62.499	66.667	8.24	0.00	45.00	3.24
1357	1394	2.031333	GGTACATCCATCGTCTACGTCC	60.031	54.545	0.00	0.00	37.09	4.79
1378	1415	1.217689	AGTCCCCTCTCATCCTCTCAG	59.782	57.143	0.00	0.00	0.00	3.35
1422	1462	1.665679	ACGCGCCATCTTCATGTTTAG	59.334	47.619	5.73	0.00	0.00	1.85
1444	1494	0.742990	ATGTTGCTTGCATGCATGGC	60.743	50.000	28.66	28.35	42.96	4.40
1897	1947	2.738521	CTGCCGGACACGAACCTG	60.739	66.667	5.05	0.00	44.60	4.00
2824	2874	1.535896	GGAGTAGCGATGATCGTAGCA	59.464	52.381	20.28	5.62	42.81	3.49
2847	2897	3.314357	GGGCTGACATTTTTATCCGGTAC	59.686	47.826	0.00	0.00	0.00	3.34
2857	2907	1.688772	TATCCGGTACCTCAGCTGAC	58.311	55.000	13.74	3.16	0.00	3.51
2871	2934	3.511540	TCAGCTGACTGTGCATTACTAGT	59.488	43.478	13.74	0.00	44.77	2.57
2876	2939	5.654497	CTGACTGTGCATTACTAGTGATCA	58.346	41.667	5.39	0.00	0.00	2.92
2877	2940	6.225981	TGACTGTGCATTACTAGTGATCAT	57.774	37.500	5.39	0.00	0.00	2.45
2878	2941	6.643388	TGACTGTGCATTACTAGTGATCATT	58.357	36.000	5.39	0.00	0.00	2.57
2880	2943	8.257306	TGACTGTGCATTACTAGTGATCATTTA	58.743	33.333	5.39	0.00	0.00	1.40
2881	2944	9.098355	GACTGTGCATTACTAGTGATCATTTAA	57.902	33.333	5.39	0.00	0.00	1.52
2884	2947	7.770433	TGTGCATTACTAGTGATCATTTAAGCT	59.230	33.333	5.39	0.00	0.00	3.74
2885	2948	9.261180	GTGCATTACTAGTGATCATTTAAGCTA	57.739	33.333	5.39	0.00	0.00	3.32
2886	2949	9.481340	TGCATTACTAGTGATCATTTAAGCTAG	57.519	33.333	5.39	12.07	34.00	3.42
2887	2950	9.482627	GCATTACTAGTGATCATTTAAGCTAGT	57.517	33.333	19.46	19.46	41.10	2.57
2891	2954	8.934507	ACTAGTGATCATTTAAGCTAGTTGTC	57.065	34.615	13.08	0.00	36.68	3.18
2892	2955	8.531982	ACTAGTGATCATTTAAGCTAGTTGTCA	58.468	33.333	13.08	0.00	36.68	3.58
2893	2956	9.371136	CTAGTGATCATTTAAGCTAGTTGTCAA	57.629	33.333	0.00	0.00	0.00	3.18
2894	2957	8.621532	AGTGATCATTTAAGCTAGTTGTCAAA	57.378	30.769	0.00	0.00	0.00	2.69
2895	2958	9.066892	AGTGATCATTTAAGCTAGTTGTCAAAA	57.933	29.630	0.00	0.00	0.00	2.44
2896	2959	9.677567	GTGATCATTTAAGCTAGTTGTCAAAAA	57.322	29.630	0.00	0.00	0.00	1.94
2942	4276	4.082787	ACCGTTTGCTGAATGTTGATTAGG	60.083	41.667	0.00	0.00	0.00	2.69
2985	4319	3.128764	CAGTAGCAAGGATGTCGTCAGTA	59.871	47.826	0.00	0.00	0.00	2.74
3164	4509	2.156098	GGATTTTTACGTCTGTGCCCA	58.844	47.619	0.00	0.00	0.00	5.36
3198	4543	1.067295	TACTCATCCATCCCCATGCC	58.933	55.000	0.00	0.00	0.00	4.40
3231	4577	4.588951	TGCTCACTTTTCTCCACTCTCTTA	59.411	41.667	0.00	0.00	0.00	2.10
3297	4643	3.311596	GTCAGTGCTTTGACCGTTAACTT	59.688	43.478	3.71	0.00	41.24	2.66
3348	4694	0.883833	CCATTGGACCTGACAAGTGC	59.116	55.000	0.00	0.00	0.00	4.40
3351	4697	2.358737	GGACCTGACAAGTGCGGG	60.359	66.667	0.00	0.00	37.80	6.13
3660	5045	1.489824	CACCCGTTTTGCTACGACG	59.510	57.895	7.91	0.00	43.99	5.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
93	98	2.587194	GCAGAGCGGATGATGCGT	60.587	61.111	8.38	0.00	37.44	5.24
96	101	0.600518	CAGAGGCAGAGCGGATGATG	60.601	60.000	0.00	0.00	0.00	3.07
143	153	4.247781	CATGTGAGCCATGGGACC	57.752	61.111	15.13	0.00	46.03	4.46
224	235	2.512286	AGGCACACATGATCGGCG	60.512	61.111	0.00	0.00	0.00	6.46
225	236	1.026182	TTGAGGCACACATGATCGGC	61.026	55.000	0.00	0.00	0.00	5.54
226	237	1.600957	GATTGAGGCACACATGATCGG	59.399	52.381	0.00	0.00	0.00	4.18
241	253	0.616371	ACGAACGGGGATTGGATTGA	59.384	50.000	0.00	0.00	0.00	2.57
331	348	0.925720	AAAGGGGATCCATCAGCCCA	60.926	55.000	15.23	0.00	43.89	5.36
474	492	3.842007	ATGCCCATTCTCTCTCTCTTG	57.158	47.619	0.00	0.00	0.00	3.02
475	493	4.525024	CAAATGCCCATTCTCTCTCTCTT	58.475	43.478	0.00	0.00	0.00	2.85
502	520	4.003648	CCTACACAAAAAGGAAGATCGCT	58.996	43.478	0.00	0.00	34.58	4.93
518	543	5.593679	TCAAACTAGGCATCTACCTACAC	57.406	43.478	0.00	0.00	41.50	2.90
524	549	6.961554	CGTTGAAAATCAAACTAGGCATCTAC	59.038	38.462	0.00	0.00	38.22	2.59
732	760	1.583495	CGTCGAAAAGGGGGAAAGGC	61.583	60.000	0.00	0.00	0.00	4.35
738	766	2.685850	AATCTACGTCGAAAAGGGGG	57.314	50.000	0.00	0.00	0.00	5.40
739	767	6.673154	AATAAAATCTACGTCGAAAAGGGG	57.327	37.500	0.00	0.00	0.00	4.79
740	768	7.483691	CCAAAATAAAATCTACGTCGAAAAGGG	59.516	37.037	0.00	0.00	0.00	3.95
741	769	7.007995	GCCAAAATAAAATCTACGTCGAAAAGG	59.992	37.037	0.00	0.00	0.00	3.11
742	770	7.749126	AGCCAAAATAAAATCTACGTCGAAAAG	59.251	33.333	0.00	0.00	0.00	2.27
743	771	7.586747	AGCCAAAATAAAATCTACGTCGAAAA	58.413	30.769	0.00	0.00	0.00	2.29
744	772	7.136289	AGCCAAAATAAAATCTACGTCGAAA	57.864	32.000	0.00	0.00	0.00	3.46
745	773	6.183360	GGAGCCAAAATAAAATCTACGTCGAA	60.183	38.462	0.00	0.00	0.00	3.71
746	774	5.292589	GGAGCCAAAATAAAATCTACGTCGA	59.707	40.000	0.00	0.00	0.00	4.20
747	775	5.499047	GGAGCCAAAATAAAATCTACGTCG	58.501	41.667	0.00	0.00	0.00	5.12
748	776	5.499047	CGGAGCCAAAATAAAATCTACGTC	58.501	41.667	0.00	0.00	0.00	4.34
749	777	5.479716	CGGAGCCAAAATAAAATCTACGT	57.520	39.130	0.00	0.00	0.00	3.57
787	816	6.503560	TTACGTACCCTATCATTCCCAATT	57.496	37.500	0.00	0.00	0.00	2.32
788	817	6.697641	ATTACGTACCCTATCATTCCCAAT	57.302	37.500	0.00	0.00	0.00	3.16
789	818	6.503560	AATTACGTACCCTATCATTCCCAA	57.496	37.500	0.00	0.00	0.00	4.12
790	819	6.292923	CAAATTACGTACCCTATCATTCCCA	58.707	40.000	0.00	0.00	0.00	4.37
791	820	5.704053	CCAAATTACGTACCCTATCATTCCC	59.296	44.000	0.00	0.00	0.00	3.97
792	821	6.527423	TCCAAATTACGTACCCTATCATTCC	58.473	40.000	0.00	0.00	0.00	3.01
877	907	0.677731	TAACACCATCAGCAGCCAGC	60.678	55.000	0.00	0.00	46.19	4.85
878	908	1.674441	CATAACACCATCAGCAGCCAG	59.326	52.381	0.00	0.00	0.00	4.85
949	986	2.544267	GCGTCACTCAAAACTTGCTAGT	59.456	45.455	0.00	0.00	35.68	2.57
1305	1342	1.973281	CTTGGCGGCAATGTGGAGT	60.973	57.895	25.71	0.00	0.00	3.85
1357	1394	1.063341	TGAGAGGATGAGAGGGGACTG	60.063	57.143	0.00	0.00	44.43	3.51
1378	1415	0.999228	CGTGCGTGTGAGAGTGAGAC	60.999	60.000	0.00	0.00	0.00	3.36
1422	1462	3.500455	TGCATGCAAGCAACATGAC	57.500	47.368	20.30	8.60	46.33	3.06
1444	1494	1.079543	CTCCTTCACCACCTCTGCG	60.080	63.158	0.00	0.00	0.00	5.18
1897	1947	3.202706	GCCCGGTTGATCGCCTTC	61.203	66.667	0.00	0.00	0.00	3.46
2665	2715	2.283966	AGTCCAGACCCCGAGTGG	60.284	66.667	0.00	0.00	0.00	4.00
2824	2874	2.025321	ACCGGATAAAAATGTCAGCCCT	60.025	45.455	9.46	0.00	0.00	5.19
2847	2897	2.005451	GTAATGCACAGTCAGCTGAGG	58.995	52.381	18.89	15.12	45.28	3.86
2857	2907	8.066595	GCTTAAATGATCACTAGTAATGCACAG	58.933	37.037	0.00	0.00	0.00	3.66
2895	2958	7.653311	GGTGAACAGCTTAAATGATCACTTTTT	59.347	33.333	20.55	0.00	44.97	1.94
2896	2959	7.147976	GGTGAACAGCTTAAATGATCACTTTT	58.852	34.615	20.55	0.00	44.97	2.27
2897	2960	6.568462	CGGTGAACAGCTTAAATGATCACTTT	60.568	38.462	20.55	3.09	44.97	2.66
2898	2961	5.106555	CGGTGAACAGCTTAAATGATCACTT	60.107	40.000	20.55	0.00	44.97	3.16
2899	2962	4.393062	CGGTGAACAGCTTAAATGATCACT	59.607	41.667	20.55	0.00	44.97	3.41
2900	2963	4.154195	ACGGTGAACAGCTTAAATGATCAC	59.846	41.667	16.34	16.34	44.92	3.06
2901	2964	4.323417	ACGGTGAACAGCTTAAATGATCA	58.677	39.130	0.00	0.00	0.00	2.92
2958	4292	3.128938	ACGACATCCTTGCTACTGTACTC	59.871	47.826	0.00	0.00	0.00	2.59
3154	4499	0.251341	AAGGAACCATGGGCACAGAC	60.251	55.000	18.09	0.00	0.00	3.51
3198	4543	5.169836	AGAAAAGTGAGCAAACGTTAAGG	57.830	39.130	0.00	0.00	0.00	2.69
3297	4643	4.308458	CGTGGCCCCACTCGTCAA	62.308	66.667	14.93	0.00	44.16	3.18
3465	4827	2.053244	AGCAGGCTAGCTGGATATGTT	58.947	47.619	15.72	0.00	44.66	2.71
3468	4830	2.170187	GCATAGCAGGCTAGCTGGATAT	59.830	50.000	15.72	12.24	46.11	1.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.