AutoCloner

Multiple sequence alignment - TraesCS3B01G376800

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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	TraesCS3B01G376800	chr3B	100.000	3340	0	0	1	3340	593162440	593165779	0.000000e+00	6168.0
1	TraesCS3B01G376800	chr3B	91.014	1903	70	37	822	2692	593540782	593542615	0.000000e+00	2473.0
2	TraesCS3B01G376800	chr3B	93.750	48	3	0	1222	1269	228750902	228750855	4.620000e-09	73.1
3	TraesCS3B01G376800	chr3D	90.432	3449	150	67	5	3339	451708676	451712058	0.000000e+00	4375.0
4	TraesCS3B01G376800	chr3D	86.740	2104	94	65	658	2698	451884909	451886890	0.000000e+00	2169.0
5	TraesCS3B01G376800	chr3D	83.701	589	74	7	2714	3281	595228825	595229412	1.360000e-148	536.0
6	TraesCS3B01G376800	chr3D	76.554	354	72	9	2933	3281	496685132	496685479	2.050000e-42	183.0
7	TraesCS3B01G376800	chr3D	91.667	48	4	0	1222	1269	157540740	157540693	2.150000e-07	67.6
8	TraesCS3B01G376800	chr3A	91.513	2816	93	53	5	2698	594491025	594493816	0.000000e+00	3742.0
9	TraesCS3B01G376800	chr3A	93.750	48	3	0	1222	1269	170658715	170658762	4.620000e-09	73.1
10	TraesCS3B01G376800	chr1A	83.518	631	85	12	2700	3315	491154589	491155215	3.740000e-159	571.0
11	TraesCS3B01G376800	chr1A	89.937	318	31	1	1952	2268	495192336	495192019	3.100000e-110	409.0
12	TraesCS3B01G376800	chr1A	86.728	324	41	2	1380	1702	495192933	495192611	3.170000e-95	359.0
13	TraesCS3B01G376800	chr1A	82.759	145	17	7	2918	3060	592136381	592136243	4.530000e-24	122.0
14	TraesCS3B01G376800	chr1B	90.260	308	30	0	1961	2268	533324012	533323705	1.440000e-108	403.0
15	TraesCS3B01G376800	chr1B	85.802	324	44	2	1380	1702	533324652	533324330	3.190000e-90	342.0
16	TraesCS3B01G376800	chr1B	75.332	377	78	13	2900	3270	656844234	656843867	2.060000e-37	167.0
17	TraesCS3B01G376800	chr1D	89.935	308	31	0	1961	2268	397973287	397972980	6.710000e-107	398.0
18	TraesCS3B01G376800	chr1D	85.538	325	43	4	1380	1702	397973932	397973610	1.480000e-88	337.0
19	TraesCS3B01G376800	chr2D	83.742	326	36	15	1380	1692	27837049	27837370	3.260000e-75	292.0
20	TraesCS3B01G376800	chr2A	83.962	318	33	13	1380	1684	29989773	29990085	4.220000e-74	289.0
21	TraesCS3B01G376800	chr4D	80.000	315	51	9	1380	1684	441118246	441118558	4.340000e-54	222.0
22	TraesCS3B01G376800	chr5D	74.423	563	117	16	2725	3270	464906934	464907486	2.020000e-52	217.0
23	TraesCS3B01G376800	chr5A	76.031	388	68	15	2900	3281	211460141	211460509	9.520000e-41	178.0
24	TraesCS3B01G376800	chr2B	75.711	387	71	13	2900	3281	531162597	531162229	4.430000e-39	172.0
25	TraesCS3B01G376800	chr7B	74.801	377	80	13	2900	3270	60063292	60062925	4.460000e-34	156.0

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	TraesCS3B01G376800	chr3B	593162440	593165779	3339	False	6168.0	6168	100.0000	1	3340	1	chr3B.!!$F1	3339
1	TraesCS3B01G376800	chr3B	593540782	593542615	1833	False	2473.0	2473	91.0140	822	2692	1	chr3B.!!$F2	1870
2	TraesCS3B01G376800	chr3D	451708676	451712058	3382	False	4375.0	4375	90.4320	5	3339	1	chr3D.!!$F1	3334
3	TraesCS3B01G376800	chr3D	451884909	451886890	1981	False	2169.0	2169	86.7400	658	2698	1	chr3D.!!$F2	2040
4	TraesCS3B01G376800	chr3D	595228825	595229412	587	False	536.0	536	83.7010	2714	3281	1	chr3D.!!$F4	567
5	TraesCS3B01G376800	chr3A	594491025	594493816	2791	False	3742.0	3742	91.5130	5	2698	1	chr3A.!!$F2	2693
6	TraesCS3B01G376800	chr1A	491154589	491155215	626	False	571.0	571	83.5180	2700	3315	1	chr1A.!!$F1	615
7	TraesCS3B01G376800	chr1A	495192019	495192933	914	True	384.0	409	88.3325	1380	2268	2	chr1A.!!$R2	888
8	TraesCS3B01G376800	chr1B	533323705	533324652	947	True	372.5	403	88.0310	1380	2268	2	chr1B.!!$R2	888
9	TraesCS3B01G376800	chr1D	397972980	397973932	952	True	367.5	398	87.7365	1380	2268	2	chr1D.!!$R1	888
10	TraesCS3B01G376800	chr5D	464906934	464907486	552	False	217.0	217	74.4230	2725	3270	1	chr5D.!!$F1	545

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
331	350	0.037697	TCTGGGACGATTGGTTGTCG	60.038	55.0	0.0	0.0	44.26	4.35	F
2009	2286	0.036164	TCAGGTTCACCATCAACGGG	59.964	55.0	0.0	0.0	38.89	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2279	2572	1.066002	CAATGCAATCCATCCGTCCAC	59.934	52.381	0.0	0.00	31.43	4.02	R
3137	3494	0.039798	CTTCGACGTCGTTCCTCCAA	60.040	55.000	34.4	19.63	40.80	3.53	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
46	47	0.749091	TAGTGCTGGGCATGCATGTC	60.749	55.000	26.79	25.10	41.91	3.06
49	50	2.827190	CTGGGCATGCATGTCGCT	60.827	61.111	26.79	0.00	43.06	4.93
113	124	1.179152	TAACTCCCTGATTCGCGTGA	58.821	50.000	5.77	0.00	0.00	4.35
331	350	0.037697	TCTGGGACGATTGGTTGTCG	60.038	55.000	0.00	0.00	44.26	4.35
377	396	8.764287	TCATATTAATCTACGTGCAACTTGATG	58.236	33.333	0.00	0.00	31.75	3.07
421	440	2.095212	GGGTTTGCTTTAGGCTTTCGAG	60.095	50.000	0.00	0.00	42.39	4.04
481	500	1.077930	CATCCTGTCCCTGCCACAG	60.078	63.158	0.00	0.00	40.96	3.66
590	613	3.118000	AGCAGCATCTTGATCCTGATTGA	60.118	43.478	5.79	0.00	0.00	2.57
616	639	4.184629	GTGATATATGCCGATCAGGTTCC	58.815	47.826	0.00	0.00	43.70	3.62
952	1003	1.738099	CCCTGTTCTCTGCCGTTCG	60.738	63.158	0.00	0.00	0.00	3.95
1166	1229	2.720134	GCTCCTGCTCTTCTCGGCT	61.720	63.158	0.00	0.00	36.03	5.52
1176	1239	2.518973	CTTCTCGGCTGCCTTCTGCT	62.519	60.000	17.92	0.00	42.00	4.24
1299	1371	6.911250	TCAGGAGTATTACACTGTTGAAGA	57.089	37.500	14.36	0.00	37.72	2.87
1333	1421	4.231426	ACCTACCTACCTACCTGTATGTGT	59.769	45.833	0.00	0.00	0.00	3.72
1544	1651	2.440796	CCGGGCAGCATCACCATT	60.441	61.111	0.00	0.00	0.00	3.16
1873	2081	1.227556	ACGCTCACTTGACCACCAC	60.228	57.895	0.00	0.00	0.00	4.16
1902	2114	2.557924	TGTTCCAAGTTGCATGATCCAC	59.442	45.455	0.00	0.00	0.00	4.02
1903	2115	2.821969	GTTCCAAGTTGCATGATCCACT	59.178	45.455	0.00	0.00	0.00	4.00
1904	2116	3.998913	TCCAAGTTGCATGATCCACTA	57.001	42.857	0.00	0.00	0.00	2.74
1905	2117	3.877559	TCCAAGTTGCATGATCCACTAG	58.122	45.455	0.00	0.00	0.00	2.57
1906	2118	3.264193	TCCAAGTTGCATGATCCACTAGT	59.736	43.478	0.00	0.00	0.00	2.57
1907	2119	4.469586	TCCAAGTTGCATGATCCACTAGTA	59.530	41.667	0.00	0.00	0.00	1.82
1908	2120	4.813161	CCAAGTTGCATGATCCACTAGTAG	59.187	45.833	0.00	0.00	0.00	2.57
1909	2121	5.395657	CCAAGTTGCATGATCCACTAGTAGA	60.396	44.000	3.59	0.00	0.00	2.59
1910	2122	5.939764	AGTTGCATGATCCACTAGTAGAA	57.060	39.130	3.59	0.00	0.00	2.10
1912	2124	6.109359	AGTTGCATGATCCACTAGTAGAAAC	58.891	40.000	3.59	0.00	0.00	2.78
1916	2128	6.109359	GCATGATCCACTAGTAGAAACTGTT	58.891	40.000	3.59	0.00	36.36	3.16
1954	2166	3.120338	TGAAGATTTGTGTTTCGCCGATC	60.120	43.478	0.00	0.00	0.00	3.69
2009	2286	0.036164	TCAGGTTCACCATCAACGGG	59.964	55.000	0.00	0.00	38.89	5.28
2279	2572	1.062206	GTTCTAGCGAGGTCGTCCG	59.938	63.158	0.69	0.00	42.22	4.79
2538	2845	8.406297	GGTGATTTATTTAAGGGTGCTTTAGAG	58.594	37.037	0.00	0.00	0.00	2.43
2544	2851	3.697619	AAGGGTGCTTTAGAGGTACAC	57.302	47.619	0.00	0.00	0.00	2.90
2545	2852	2.616524	AGGGTGCTTTAGAGGTACACA	58.383	47.619	0.00	0.00	32.89	3.72
2682	3017	6.901265	TGCTAGTTTATGGTTTAACCGTTTC	58.099	36.000	14.53	5.73	42.58	2.78
2692	3029	6.344500	TGGTTTAACCGTTTCAAGTAGTACA	58.656	36.000	9.77	0.00	42.58	2.90
2723	3061	5.565723	TTTTTCGTTTGAGAGTACGCTAC	57.434	39.130	0.00	0.00	37.66	3.58
2806	3146	2.159156	ACAACGAGTGTAGCACAACTCA	60.159	45.455	11.66	0.00	39.29	3.41
2845	3186	1.669115	CGGCCACCAGAGACAACAG	60.669	63.158	2.24	0.00	0.00	3.16
2875	3216	3.185455	AGGAGAAGTGCCTATCCAAAGT	58.815	45.455	0.00	0.00	32.92	2.66
2876	3217	4.362677	AGGAGAAGTGCCTATCCAAAGTA	58.637	43.478	0.00	0.00	32.92	2.24
2962	3317	0.323633	CACCATCCACCCTTGATGCA	60.324	55.000	0.00	0.00	38.61	3.96
3012	3368	2.668144	TTGGACGGTCCCAAGAAAAT	57.332	45.000	23.81	0.00	40.99	1.82
3016	3372	2.552373	GGACGGTCCCAAGAAAATCACT	60.552	50.000	16.55	0.00	0.00	3.41
3037	3393	1.006102	CTTGAACTCACCGGCGACT	60.006	57.895	9.30	0.00	0.00	4.18
3039	3395	0.892755	TTGAACTCACCGGCGACTAT	59.107	50.000	9.30	0.00	0.00	2.12
3124	3481	3.314693	ACCTCAGGTAGTGTCTCCAAAA	58.685	45.455	0.00	0.00	32.11	2.44
3128	3485	4.651778	TCAGGTAGTGTCTCCAAAAATGG	58.348	43.478	0.00	0.00	0.00	3.16
3231	3594	1.136329	ACCAACCCCATGTGAGAGCT	61.136	55.000	0.00	0.00	0.00	4.09
3239	3602	2.102252	CCCATGTGAGAGCTAGGAAGAC	59.898	54.545	0.00	0.00	0.00	3.01
3287	3654	2.888998	GAAAAACGACACGGGCGCT	61.889	57.895	7.64	0.00	0.00	5.92
3339	3706	5.665916	AATCAATTGACCTTTGTCCCATC	57.334	39.130	11.07	0.00	41.01	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.040062	CCAGTCCAACACCAAATGATAAGTTTA	60.040	37.037	0.00	0.00	0.00	2.01
1	2	6.239289	CCAGTCCAACACCAAATGATAAGTTT	60.239	38.462	0.00	0.00	0.00	2.66
2	3	5.243730	CCAGTCCAACACCAAATGATAAGTT	59.756	40.000	0.00	0.00	0.00	2.66
3	4	4.766891	CCAGTCCAACACCAAATGATAAGT	59.233	41.667	0.00	0.00	0.00	2.24
49	50	1.879575	ATGCCACTTCCCTAGCACTA	58.120	50.000	0.00	0.00	38.21	2.74
60	61	5.310451	TCTAACGAGGTTAAAATGCCACTT	58.690	37.500	0.00	0.00	0.00	3.16
93	94	1.546923	TCACGCGAATCAGGGAGTTAA	59.453	47.619	15.93	0.00	0.00	2.01
113	124	5.661759	ACTAGGGAAGAAACATCGGATTAGT	59.338	40.000	0.00	0.00	0.00	2.24
278	293	1.261238	CCTCCTCTGGACGCCTTTCT	61.261	60.000	0.00	0.00	0.00	2.52
377	396	4.184629	ACTTGTTTAGTGATGCTCGATCC	58.815	43.478	0.00	0.00	35.19	3.36
481	500	4.990426	TGCCAAACTTTTACTACTACGACC	59.010	41.667	0.00	0.00	0.00	4.79
482	501	6.401796	CCATGCCAAACTTTTACTACTACGAC	60.402	42.308	0.00	0.00	0.00	4.34
483	502	5.640357	CCATGCCAAACTTTTACTACTACGA	59.360	40.000	0.00	0.00	0.00	3.43
487	506	4.148838	TGCCATGCCAAACTTTTACTACT	58.851	39.130	0.00	0.00	0.00	2.57
520	539	3.869246	CGCCGTCTGGTAATTCAGTTATT	59.131	43.478	0.00	0.00	37.67	1.40
590	613	4.160439	ACCTGATCGGCATATATCACGATT	59.840	41.667	17.39	4.49	44.99	3.34
894	930	0.249911	GTGGGGACTGCGTATCCATC	60.250	60.000	3.41	0.00	38.06	3.51
952	1003	2.096819	TGGAATCGTTAATCGCTTTGCC	59.903	45.455	0.00	0.00	39.67	4.52
1308	1380	5.068723	CACATACAGGTAGGTAGGTAGGTTG	59.931	48.000	0.00	0.00	36.24	3.77
1333	1421	3.344892	TACACTCATGTCGGGAACCACA	61.345	50.000	0.00	0.00	45.37	4.17
1544	1651	2.428187	CACAGGTTGGTGGCGGTA	59.572	61.111	0.00	0.00	35.13	4.02
1902	2114	5.265407	GAAACCGCAACAGTTTCTACTAG	57.735	43.478	8.70	0.00	46.18	2.57
1909	2121	2.088423	TCAGTGAAACCGCAACAGTTT	58.912	42.857	0.00	0.00	40.07	2.66
1910	2122	1.745232	TCAGTGAAACCGCAACAGTT	58.255	45.000	0.00	0.00	37.80	3.16
1912	2124	1.670811	AGTTCAGTGAAACCGCAACAG	59.329	47.619	7.25	0.00	37.80	3.16
1916	2128	1.939934	CTTCAGTTCAGTGAAACCGCA	59.060	47.619	7.25	0.00	37.80	5.69
2009	2286	1.348036	ACCAGGTTGAAGTAGGAGTGC	59.652	52.381	0.00	0.00	0.00	4.40
2279	2572	1.066002	CAATGCAATCCATCCGTCCAC	59.934	52.381	0.00	0.00	31.43	4.02
2289	2582	1.551883	AGCTCCAAACCAATGCAATCC	59.448	47.619	0.00	0.00	0.00	3.01
2291	2584	2.633967	TCAAGCTCCAAACCAATGCAAT	59.366	40.909	0.00	0.00	0.00	3.56
2538	2845	1.340017	ACCACTCCATGCATGTGTACC	60.340	52.381	24.58	0.00	0.00	3.34
2544	2851	0.524414	CACACACCACTCCATGCATG	59.476	55.000	20.19	20.19	0.00	4.06
2545	2852	0.401356	TCACACACCACTCCATGCAT	59.599	50.000	0.00	0.00	0.00	3.96
2771	3110	7.960880	ACACTCGTTGTTCGCAATAAGTTGC	62.961	44.000	3.18	3.18	46.08	4.17
2778	3117	1.459592	GCTACACTCGTTGTTCGCAAT	59.540	47.619	0.00	0.00	39.91	3.56
2806	3146	1.002087	CCTTCGGACTAGCTTGGTGTT	59.998	52.381	0.00	0.00	0.00	3.32
2826	3167	3.050275	GTTGTCTCTGGTGGCCGC	61.050	66.667	8.12	8.12	0.00	6.53
2828	3169	0.108585	TTCTGTTGTCTCTGGTGGCC	59.891	55.000	0.00	0.00	0.00	5.36
2836	3177	7.442666	ACTTCTCCTTTGTATTTCTGTTGTCTC	59.557	37.037	0.00	0.00	0.00	3.36
2845	3186	6.261158	GGATAGGCACTTCTCCTTTGTATTTC	59.739	42.308	0.00	0.00	41.75	2.17
2875	3216	0.942410	GACGCGGTGTTGTTGCTCTA	60.942	55.000	12.47	0.00	0.00	2.43
2876	3217	2.203015	ACGCGGTGTTGTTGCTCT	60.203	55.556	12.47	0.00	0.00	4.09
2962	3317	5.440610	CATCTACTTGCCACCTCCTTTTAT	58.559	41.667	0.00	0.00	0.00	1.40
3012	3368	1.068588	CCGGTGAGTTCAAGACAGTGA	59.931	52.381	0.00	0.00	0.00	3.41
3016	3372	1.300620	CGCCGGTGAGTTCAAGACA	60.301	57.895	10.20	0.00	0.00	3.41
3037	3393	3.807622	GCTTTAGGAGCGCAATGTACATA	59.192	43.478	11.47	0.00	42.46	2.29
3039	3395	2.006888	GCTTTAGGAGCGCAATGTACA	58.993	47.619	11.47	0.00	42.46	2.90
3137	3494	0.039798	CTTCGACGTCGTTCCTCCAA	60.040	55.000	34.40	19.63	40.80	3.53
3138	3495	0.886043	TCTTCGACGTCGTTCCTCCA	60.886	55.000	34.40	13.39	40.80	3.86
3165	3522	1.635663	CGGAGTTGGATTGGCACGAC	61.636	60.000	0.00	0.00	0.00	4.34
3169	3526	0.608035	GGTTCGGAGTTGGATTGGCA	60.608	55.000	0.00	0.00	0.00	4.92
3231	3594	0.892358	AGTGTGTCGGCGTCTTCCTA	60.892	55.000	6.85	0.00	0.00	2.94
3287	3654	2.598099	TCGGTGTAGGTGGCGACA	60.598	61.111	0.00	0.00	38.70	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.