AutoCloner

Multiple sequence alignment - TraesCS3A01G229400

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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	TraesCS3A01G229400	chr3A	100.000	3546	0	0	561	4106	429462234	429465779	0.000000e+00	6549.0
1	TraesCS3A01G229400	chr3A	86.713	2032	150	50	1120	3082	489566759	489568739	0.000000e+00	2146.0
2	TraesCS3A01G229400	chr3A	100.000	226	0	0	1	226	429461674	429461899	6.350000e-113	418.0
3	TraesCS3A01G229400	chr3A	90.043	231	8	6	11	226	489565799	489566029	6.720000e-73	285.0
4	TraesCS3A01G229400	chr3D	97.366	2012	40	11	915	2913	309689114	309691125	0.000000e+00	3410.0
5	TraesCS3A01G229400	chr3D	88.470	1804	131	32	1120	2889	367358545	367360305	0.000000e+00	2108.0
6	TraesCS3A01G229400	chr3D	92.107	1229	66	6	2898	4105	309692907	309694125	0.000000e+00	1703.0
7	TraesCS3A01G229400	chr3D	97.177	248	5	2	667	912	309688823	309689070	6.350000e-113	418.0
8	TraesCS3A01G229400	chr3D	98.913	184	2	0	40	223	309688329	309688512	3.060000e-86	329.0
9	TraesCS3A01G229400	chr3D	88.346	266	21	7	2874	3137	367360324	367360581	1.110000e-80	311.0
10	TraesCS3A01G229400	chr3D	89.806	206	6	6	36	226	367357134	367357339	2.450000e-62	250.0
11	TraesCS3A01G229400	chr3D	94.872	78	4	0	562	639	309688599	309688676	5.570000e-24	122.0
12	TraesCS3A01G229400	chr3D	100.000	31	0	0	639	669	309688756	309688786	1.590000e-04	58.4
13	TraesCS3A01G229400	chr3B	96.701	2031	49	8	915	2932	411506859	411504834	0.000000e+00	3363.0
14	TraesCS3A01G229400	chr3B	85.960	2037	136	51	1120	3082	479495685	479497645	0.000000e+00	2039.0
15	TraesCS3A01G229400	chr3B	92.868	659	34	3	3451	4105	411504648	411503999	0.000000e+00	944.0
16	TraesCS3A01G229400	chr3B	83.718	823	100	18	3289	4089	479500903	479501713	0.000000e+00	747.0
17	TraesCS3A01G229400	chr3B	99.115	226	2	0	1	226	411507846	411507621	1.370000e-109	407.0
18	TraesCS3A01G229400	chr3B	88.745	231	11	3	11	226	479494749	479494979	6.770000e-68	268.0
19	TraesCS3A01G229400	chr3B	100.000	95	0	0	673	767	411507417	411507323	4.220000e-40	176.0
20	TraesCS3A01G229400	chr3B	98.824	85	1	0	827	911	411506997	411506913	7.110000e-33	152.0
21	TraesCS3A01G229400	chr1D	87.023	131	13	2	94	221	460789475	460789604	1.190000e-30	145.0
22	TraesCS3A01G229400	chr2A	81.395	129	24	0	3320	3448	39945332	39945460	5.610000e-19	106.0

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	TraesCS3A01G229400	chr3A	429461674	429465779	4105	False	3483.500000	6549	100.000000	1	4106	2	chr3A.!!$F1	4105
1	TraesCS3A01G229400	chr3A	489565799	489568739	2940	False	1215.500000	2146	88.378000	11	3082	2	chr3A.!!$F2	3071
2	TraesCS3A01G229400	chr3D	309688329	309694125	5796	False	1006.733333	3410	96.739167	40	4105	6	chr3D.!!$F1	4065
3	TraesCS3A01G229400	chr3D	367357134	367360581	3447	False	889.666667	2108	88.874000	36	3137	3	chr3D.!!$F2	3101
4	TraesCS3A01G229400	chr3B	479494749	479501713	6964	False	1018.000000	2039	86.141000	11	4089	3	chr3B.!!$F1	4078
5	TraesCS3A01G229400	chr3B	411503999	411507846	3847	True	1008.400000	3363	97.501600	1	4105	5	chr3B.!!$R1	4104

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
595	611	0.177141	TTCCGTTTATGGCCTCTCCG	59.823	55.0	3.32	0.0	37.8	4.63	F
1480	2336	0.322816	CTGGGTCATGGTGTTCAGGG	60.323	60.0	0.00	0.0	0.0	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2177	3104	1.082756	CGCCGTGACAGCAAAAGAC	60.083	57.895	0.0	0.0	0.0	3.01	R
3289	7906	0.686789	ATTGTTTGCTTGGAAGGGCC	59.313	50.000	0.0	0.0	37.1	5.80	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
585	601	4.699637	TCCGCATATTCAGTTCCGTTTAT	58.300	39.130	0.00	0.00	0.00	1.40
591	607	2.396590	TCAGTTCCGTTTATGGCCTC	57.603	50.000	3.32	0.00	0.00	4.70
592	608	1.906574	TCAGTTCCGTTTATGGCCTCT	59.093	47.619	3.32	0.00	0.00	3.69
593	609	2.093658	TCAGTTCCGTTTATGGCCTCTC	60.094	50.000	3.32	0.00	0.00	3.20
594	610	1.209747	AGTTCCGTTTATGGCCTCTCC	59.790	52.381	3.32	0.00	0.00	3.71
595	611	0.177141	TTCCGTTTATGGCCTCTCCG	59.823	55.000	3.32	0.00	37.80	4.63
802	979	3.266513	ACTTTAGAGTACTCCCTCCGTCT	59.733	47.826	19.38	0.74	33.32	4.18
926	1733	4.056050	ACTAGTATTTTATTCCGCAGCCG	58.944	43.478	0.00	0.00	0.00	5.52
946	1760	3.499048	CGTCAAAGTACGTAGCAGTCAT	58.501	45.455	0.00	0.00	38.07	3.06
1072	1893	9.396022	TGGAAGAAGAAATTAGGTTCATATGAC	57.604	33.333	4.48	0.93	0.00	3.06
1073	1894	9.620259	GGAAGAAGAAATTAGGTTCATATGACT	57.380	33.333	4.48	2.92	0.00	3.41
1079	1900	9.499479	AGAAATTAGGTTCATATGACTATGCTG	57.501	33.333	4.48	0.00	35.64	4.41
1080	1901	9.494271	GAAATTAGGTTCATATGACTATGCTGA	57.506	33.333	4.48	0.00	35.64	4.26
1081	1902	9.851686	AAATTAGGTTCATATGACTATGCTGAA	57.148	29.630	4.48	0.00	35.64	3.02
1433	2289	3.681835	GCTCCTGTCGTCCGTGGT	61.682	66.667	0.00	0.00	0.00	4.16
1480	2336	0.322816	CTGGGTCATGGTGTTCAGGG	60.323	60.000	0.00	0.00	0.00	4.45
1562	2418	1.097547	ATGCTCGTGGCCTACATTGC	61.098	55.000	3.32	5.88	40.92	3.56
1720	2603	6.033341	TGGAATTAACTTCGCATTTATGTGC	58.967	36.000	0.00	0.00	41.65	4.57
1850	2752	5.589855	TGCTCTCAATATGGTACCAAATGTG	59.410	40.000	20.76	17.29	0.00	3.21
1912	2816	8.465273	AGAAGGCTGAACTTACATTTTTACTT	57.535	30.769	0.00	0.00	0.00	2.24
1994	2898	1.134670	GCTGCTGGAAGGTACGATCTT	60.135	52.381	0.00	0.00	0.00	2.40
2177	3104	1.372997	CGGTGGTCGTCAGTGGAAG	60.373	63.158	0.00	0.00	0.00	3.46
2361	3298	2.157738	GCATGACCTTGCAAGTTCTCT	58.842	47.619	22.58	9.21	42.31	3.10
2429	3397	1.218875	TGCCTGTGCGTACGTTCTTG	61.219	55.000	17.90	4.60	41.78	3.02
2565	3533	1.656587	GGGAAAAGGGGCTTTGGATT	58.343	50.000	0.00	0.00	33.64	3.01
2649	3617	0.449388	GGCAGAAGATGGTTTGCTCG	59.551	55.000	0.00	0.00	36.79	5.03
2720	3690	6.656693	CAGTCCAAAGAATTATTCAGGAGTGT	59.343	38.462	24.55	10.19	40.30	3.55
2722	3692	7.175641	AGTCCAAAGAATTATTCAGGAGTGTTG	59.824	37.037	15.56	6.02	33.02	3.33
2738	3708	3.630312	AGTGTTGCACAATCTTACGGTTT	59.370	39.130	2.01	0.00	36.74	3.27
2931	5761	1.897802	GGAGGAAGAGGACGTAAACCA	59.102	52.381	0.00	0.00	0.00	3.67
2932	5762	2.094130	GGAGGAAGAGGACGTAAACCAG	60.094	54.545	0.00	0.00	0.00	4.00
2933	5763	2.824341	GAGGAAGAGGACGTAAACCAGA	59.176	50.000	0.00	0.00	0.00	3.86
2934	5764	2.826725	AGGAAGAGGACGTAAACCAGAG	59.173	50.000	0.00	0.00	0.00	3.35
2935	5765	2.608268	GAAGAGGACGTAAACCAGAGC	58.392	52.381	0.00	0.00	0.00	4.09
2936	5766	0.896226	AGAGGACGTAAACCAGAGCC	59.104	55.000	0.00	0.00	0.00	4.70
3075	5921	3.002583	TCCATGCCGGACAGCTCA	61.003	61.111	5.05	0.00	39.64	4.26
3095	7711	2.549754	CAAGACTTGACGGTTGCATCTT	59.450	45.455	9.76	0.00	0.00	2.40
3097	7713	0.593128	ACTTGACGGTTGCATCTTGC	59.407	50.000	0.00	0.00	45.29	4.01
3110	7726	6.542370	GGTTGCATCTTGCCTCTACTATTAAA	59.458	38.462	0.00	0.00	44.23	1.52
3111	7727	7.067008	GGTTGCATCTTGCCTCTACTATTAAAA	59.933	37.037	0.00	0.00	44.23	1.52
3139	7755	9.360093	CTCTACTAATACAAAGAGTTGGTGAAG	57.640	37.037	0.00	0.00	39.22	3.02
3145	7761	0.402121	AAGAGTTGGTGAAGCCTCCC	59.598	55.000	0.00	0.00	38.35	4.30
3149	7765	2.231380	TTGGTGAAGCCTCCCTCCC	61.231	63.158	0.00	0.00	38.35	4.30
3150	7766	2.610859	GGTGAAGCCTCCCTCCCA	60.611	66.667	0.00	0.00	0.00	4.37
3167	7783	3.941483	CTCCCATCTATTCTTTGTTGCGT	59.059	43.478	0.00	0.00	0.00	5.24
3183	7799	1.006832	GCGTAGTTGATGGTCGCATT	58.993	50.000	0.00	0.00	45.01	3.56
3193	7809	5.131594	TGATGGTCGCATTTTTGATGAAA	57.868	34.783	0.00	0.00	0.00	2.69
3204	7820	7.358683	CGCATTTTTGATGAAACCTTTTCTCTC	60.359	37.037	0.68	0.00	0.00	3.20
3239	7855	7.313951	TGTTGCTTTTTATTCTTGGTTTTGG	57.686	32.000	0.00	0.00	0.00	3.28
3337	9276	3.072184	CCAGGTAGGGAGGAATGAATGAG	59.928	52.174	0.00	0.00	0.00	2.90
3411	9350	6.348132	GCCATGTAAAAACTGGTAAAATTGCC	60.348	38.462	0.00	0.00	32.42	4.52
3455	9411	4.283978	TCATGTTCTAAAGTAACACCCCGA	59.716	41.667	0.00	0.00	39.51	5.14
3515	9472	0.106918	TGTTGTGGCCTTTCGTCCTT	60.107	50.000	3.32	0.00	0.00	3.36
3580	9541	3.370840	TTTATCACCCTTGCATCTGCT	57.629	42.857	3.53	0.00	42.66	4.24
3609	9570	1.072489	TGTCCTTGTTAACGGCATCCA	59.928	47.619	0.26	0.00	0.00	3.41
3680	9641	2.614520	TCACCGATGCTTTTCGTTTTGA	59.385	40.909	4.15	1.88	37.42	2.69
3754	9715	1.917955	CAACGACTAATGACGCGACAT	59.082	47.619	18.14	18.14	34.96	3.06
3794	9755	4.221342	GTTATACGCCGACGACATTATCA	58.779	43.478	0.00	0.00	43.93	2.15
3808	9769	6.538742	ACGACATTATCATTTTCTACCACCAG	59.461	38.462	0.00	0.00	0.00	4.00
3921	9884	3.748048	CACCTATCAAGTGTTGTGGTGAG	59.252	47.826	16.52	1.07	43.19	3.51
4032	9995	0.317479	CCGACGTTGACCTTCTCCTT	59.683	55.000	3.74	0.00	0.00	3.36
4105	10068	3.209812	TCCATCGTCGGAGGAGCG	61.210	66.667	6.55	0.50	0.00	5.03

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
574	590	1.209747	GGAGAGGCCATAAACGGAACT	59.790	52.381	5.01	0.00	36.34	3.01
575	591	1.664873	GGAGAGGCCATAAACGGAAC	58.335	55.000	5.01	0.00	36.34	3.62
585	601	1.327690	ATAAACGAGCGGAGAGGCCA	61.328	55.000	5.01	0.00	35.94	5.36
591	607	0.464452	AGGGGAATAAACGAGCGGAG	59.536	55.000	0.00	0.00	0.00	4.63
592	608	0.906775	AAGGGGAATAAACGAGCGGA	59.093	50.000	0.00	0.00	0.00	5.54
593	609	1.296727	GAAGGGGAATAAACGAGCGG	58.703	55.000	0.00	0.00	0.00	5.52
594	610	1.933853	CTGAAGGGGAATAAACGAGCG	59.066	52.381	0.00	0.00	0.00	5.03
595	611	2.987232	ACTGAAGGGGAATAAACGAGC	58.013	47.619	0.00	0.00	0.00	5.03
802	979	7.546667	ACTTAGAAAAACACAAAGTCACTACGA	59.453	33.333	0.00	0.00	0.00	3.43
926	1733	5.634020	AGAAATGACTGCTACGTACTTTGAC	59.366	40.000	0.00	0.00	0.00	3.18
946	1760	6.990349	AGATAGTTTGAACGGTTCTTCAGAAA	59.010	34.615	20.53	10.13	35.58	2.52
1077	1898	9.844790	TTTATGTTGATTACTTGCTGAATTCAG	57.155	29.630	27.82	27.82	46.40	3.02
1078	1899	9.624697	GTTTATGTTGATTACTTGCTGAATTCA	57.375	29.630	8.12	8.12	0.00	2.57
1079	1900	9.846248	AGTTTATGTTGATTACTTGCTGAATTC	57.154	29.630	0.00	0.00	0.00	2.17
1362	2218	4.131376	GTGATGGGCTGGATCACG	57.869	61.111	8.40	0.00	40.16	4.35
1480	2336	4.185286	GGTGTACCCCATCCCGGC	62.185	72.222	0.00	0.00	0.00	6.13
1518	2374	1.893137	ACGTTGAGCCAGTATGAGACA	59.107	47.619	0.00	0.00	39.69	3.41
1562	2418	1.144565	CTTGCAGGAGCTCGACATCG	61.145	60.000	7.83	0.00	42.74	3.84
1850	2752	3.641437	TTAAGCCACATCAAACAGTGC	57.359	42.857	0.00	0.00	34.48	4.40
1912	2816	5.543714	TCGTGAGGCTGTGAAAATAGTAAA	58.456	37.500	0.00	0.00	0.00	2.01
1994	2898	2.745281	GCCGTGTATTAACTGCCTTGAA	59.255	45.455	0.00	0.00	0.00	2.69
2177	3104	1.082756	CGCCGTGACAGCAAAAGAC	60.083	57.895	0.00	0.00	0.00	3.01
2565	3533	2.571757	GATCCACAGACGACGCCA	59.428	61.111	0.00	0.00	0.00	5.69
2649	3617	4.868314	AGGTGTAACAGTAGGTTCAGAC	57.132	45.455	0.00	0.00	40.96	3.51
2720	3690	3.303461	CGACAAACCGTAAGATTGTGCAA	60.303	43.478	0.00	0.00	43.77	4.08
2722	3692	2.834689	CGACAAACCGTAAGATTGTGC	58.165	47.619	4.96	0.00	43.77	4.57
2777	3747	1.747924	CTCACTGAGCGATCTCTCCAA	59.252	52.381	10.15	0.00	40.03	3.53
2778	3748	1.065126	TCTCACTGAGCGATCTCTCCA	60.065	52.381	10.15	0.00	40.03	3.86
2931	5761	2.774809	GAGGGATAAAAGGAGTGGCTCT	59.225	50.000	0.00	0.00	0.00	4.09
2932	5762	2.774809	AGAGGGATAAAAGGAGTGGCTC	59.225	50.000	0.00	0.00	0.00	4.70
2933	5763	2.852130	AGAGGGATAAAAGGAGTGGCT	58.148	47.619	0.00	0.00	0.00	4.75
2934	5764	3.653835	AAGAGGGATAAAAGGAGTGGC	57.346	47.619	0.00	0.00	0.00	5.01
2935	5765	6.314899	AGTAAAGAGGGATAAAAGGAGTGG	57.685	41.667	0.00	0.00	0.00	4.00
2936	5766	7.168905	ACAAGTAAAGAGGGATAAAAGGAGTG	58.831	38.462	0.00	0.00	0.00	3.51
2977	5809	4.425577	AATCGAGCTTCACCAAACATTC	57.574	40.909	0.00	0.00	0.00	2.67
3075	5921	2.549754	CAAGATGCAACCGTCAAGTCTT	59.450	45.455	0.00	0.00	0.00	3.01
3110	7726	9.877178	CACCAACTCTTTGTATTAGTAGAGATT	57.123	33.333	0.00	0.00	37.99	2.40
3111	7727	9.256228	TCACCAACTCTTTGTATTAGTAGAGAT	57.744	33.333	0.00	0.00	37.99	2.75
3121	7737	4.327680	GAGGCTTCACCAACTCTTTGTAT	58.672	43.478	0.00	0.00	43.14	2.29
3124	7740	1.882623	GGAGGCTTCACCAACTCTTTG	59.117	52.381	0.00	0.00	43.14	2.77
3139	7755	2.037385	AGAATAGATGGGAGGGAGGC	57.963	55.000	0.00	0.00	0.00	4.70
3145	7761	3.941483	ACGCAACAAAGAATAGATGGGAG	59.059	43.478	0.00	0.00	0.00	4.30
3149	7765	7.060600	TCAACTACGCAACAAAGAATAGATG	57.939	36.000	0.00	0.00	0.00	2.90
3150	7766	7.201644	CCATCAACTACGCAACAAAGAATAGAT	60.202	37.037	0.00	0.00	0.00	1.98
3167	7783	5.414144	TCATCAAAAATGCGACCATCAACTA	59.586	36.000	0.00	0.00	0.00	2.24
3183	7799	8.469309	AGATGAGAGAAAAGGTTTCATCAAAA	57.531	30.769	13.36	0.00	44.02	2.44
3239	7855	0.949397	GTCCCCAAAAGTCGGTTGTC	59.051	55.000	0.00	0.00	0.00	3.18
3289	7906	0.686789	ATTGTTTGCTTGGAAGGGCC	59.313	50.000	0.00	0.00	37.10	5.80
3294	9233	2.035321	GGGACGAATTGTTTGCTTGGAA	59.965	45.455	0.00	0.00	0.00	3.53
3411	9350	3.694734	ACAAATCTTTCACAACACTGCG	58.305	40.909	0.00	0.00	0.00	5.18
3555	9516	5.394443	GCAGATGCAAGGGTGATAAAAATCA	60.394	40.000	0.00	0.00	41.59	2.57
3580	9541	3.562141	CGTTAACAAGGACATGTGTGGAA	59.438	43.478	1.15	0.00	32.81	3.53
3609	9570	1.935400	TGGAAGATGGGTGGGCCAT	60.935	57.895	10.70	0.00	36.17	4.40
3661	9622	3.252215	TGATCAAAACGAAAAGCATCGGT	59.748	39.130	10.61	1.80	46.48	4.69
3680	9641	2.370349	AGAGTTCAGGACGTCGATGAT	58.630	47.619	19.12	8.55	0.00	2.45
3754	9715	3.688694	AACGAAACACTATAGGCCACA	57.311	42.857	5.01	0.00	0.00	4.17
3794	9755	2.301870	TGCTCGTCTGGTGGTAGAAAAT	59.698	45.455	0.00	0.00	0.00	1.82
3808	9769	1.651138	CACTGAAGATTCGTGCTCGTC	59.349	52.381	8.17	0.00	38.33	4.20
3944	9907	4.854924	CGATGGGGCACGCCATGA	62.855	66.667	22.45	0.00	39.01	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.