AutoCloner

Multiple sequence alignment - TraesCS1B01G157200

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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	TraesCS1B01G157200	chr1B	100.000	3316	0	0	704	4019	266109246	266112561	0.000000e+00	6124.0
1	TraesCS1B01G157200	chr1B	75.857	1371	272	51	1308	2653	266258316	266259652	0.000000e+00	643.0
2	TraesCS1B01G157200	chr1B	100.000	169	0	0	1	169	266108543	266108711	3.020000e-81	313.0
3	TraesCS1B01G157200	chr1A	96.087	2351	79	11	935	3282	238671587	238673927	0.000000e+00	3819.0
4	TraesCS1B01G157200	chr1A	73.558	1456	286	64	1243	2653	238678227	238679628	7.870000e-127	464.0
5	TraesCS1B01G157200	chr1D	94.958	2241	79	13	935	3162	192566113	192568332	0.000000e+00	3482.0
6	TraesCS1B01G157200	chr1D	75.627	1436	288	54	1243	2653	192569575	192570973	0.000000e+00	656.0
7	TraesCS1B01G157200	chr1D	94.231	52	2	1	3233	3284	192568336	192568386	1.200000e-10	78.7
8	TraesCS1B01G157200	chr3B	95.811	740	30	1	3280	4019	436510644	436511382	0.000000e+00	1194.0
9	TraesCS1B01G157200	chr3B	93.249	237	13	3	704	938	82493145	82493380	2.970000e-91	346.0
10	TraesCS1B01G157200	chr3B	94.595	37	2	0	2414	2450	18775068	18775104	1.560000e-04	58.4
11	TraesCS1B01G157200	chr5B	95.412	741	32	2	3280	4019	447211446	447210707	0.000000e+00	1179.0
12	TraesCS1B01G157200	chr5B	91.983	237	17	1	704	938	50945184	50945420	8.330000e-87	331.0
13	TraesCS1B01G157200	chr2D	94.317	739	40	2	3281	4019	111160338	111161074	0.000000e+00	1131.0
14	TraesCS1B01G157200	chr7D	94.150	735	41	2	3281	4015	37923917	37924649	0.000000e+00	1118.0
15	TraesCS1B01G157200	chr7D	91.734	738	58	3	3282	4019	141231485	141230751	0.000000e+00	1022.0
16	TraesCS1B01G157200	chr7B	95.217	690	33	0	3285	3974	442361419	442362108	0.000000e+00	1092.0
17	TraesCS1B01G157200	chr7B	93.671	237	10	4	706	938	206334872	206334637	2.300000e-92	350.0
18	TraesCS1B01G157200	chr7B	97.041	169	5	0	1	169	206335196	206335028	6.570000e-73	285.0
19	TraesCS1B01G157200	chr2B	92.693	739	52	2	3281	4019	592808823	592808087	0.000000e+00	1064.0
20	TraesCS1B01G157200	chr2B	94.583	240	11	2	704	941	77492770	77492531	1.760000e-98	370.0
21	TraesCS1B01G157200	chr2B	97.633	169	4	0	1	169	77493449	77493281	1.410000e-74	291.0
22	TraesCS1B01G157200	chrUn	92.886	731	48	2	3289	4016	423674164	423674893	0.000000e+00	1059.0
23	TraesCS1B01G157200	chr2A	90.970	742	63	3	3279	4019	694757628	694758366	0.000000e+00	996.0
24	TraesCS1B01G157200	chr2A	89.540	239	21	3	704	940	394263683	394263919	2.350000e-77	300.0
25	TraesCS1B01G157200	chr2A	97.041	169	5	0	1	169	261185859	261185691	6.570000e-73	285.0
26	TraesCS1B01G157200	chr2A	97.041	169	5	0	1	169	607479066	607479234	6.570000e-73	285.0
27	TraesCS1B01G157200	chr5A	74.942	1728	369	51	1241	2940	597688013	597686322	0.000000e+00	734.0
28	TraesCS1B01G157200	chr5A	74.017	712	162	18	2169	2867	105416184	105415483	6.620000e-68	268.0
29	TraesCS1B01G157200	chr6D	72.753	1791	413	65	1115	2869	308939454	308937703	5.910000e-148	534.0
30	TraesCS1B01G157200	chr6D	71.190	1680	380	73	1241	2859	86721579	86723215	3.870000e-85	326.0
31	TraesCS1B01G157200	chr6B	71.853	1716	374	79	1233	2885	164363166	164364835	3.770000e-105	392.0
32	TraesCS1B01G157200	chr6B	95.378	238	11	0	704	941	228970780	228970543	2.930000e-101	379.0
33	TraesCS1B01G157200	chr6B	94.894	235	12	0	704	938	548386739	548386973	6.350000e-98	368.0
34	TraesCS1B01G157200	chr6B	89.300	243	22	4	704	944	116128282	116128522	6.530000e-78	302.0
35	TraesCS1B01G157200	chr6B	97.041	169	5	0	1	169	228971515	228971347	6.570000e-73	285.0
36	TraesCS1B01G157200	chr7A	90.377	239	18	5	704	938	61799259	61799496	3.900000e-80	309.0
37	TraesCS1B01G157200	chr7A	97.590	166	4	0	4	169	26777272	26777107	6.570000e-73	285.0
38	TraesCS1B01G157200	chr7A	96.988	166	5	0	4	169	694033990	694033825	3.060000e-71	279.0
39	TraesCS1B01G157200	chr6A	72.470	1097	245	39	1241	2307	104413656	104412587	2.350000e-77	300.0
40	TraesCS1B01G157200	chr5D	73.614	830	187	24	2054	2867	98228545	98229358	1.410000e-74	291.0
41	TraesCS1B01G157200	chr3A	97.041	169	5	0	1	169	460150353	460150185	6.570000e-73	285.0
42	TraesCS1B01G157200	chr4A	97.006	167	5	0	3	169	558484858	558485024	8.500000e-72	281.0
43	TraesCS1B01G157200	chr3D	89.583	48	5	0	2414	2461	13105018	13105065	1.210000e-05	62.1

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	TraesCS1B01G157200	chr1B	266108543	266112561	4018	False	3218.500000	6124	100.0000	1	4019	2	chr1B.!!$F2	4018
1	TraesCS1B01G157200	chr1B	266258316	266259652	1336	False	643.000000	643	75.8570	1308	2653	1	chr1B.!!$F1	1345
2	TraesCS1B01G157200	chr1A	238671587	238673927	2340	False	3819.000000	3819	96.0870	935	3282	1	chr1A.!!$F1	2347
3	TraesCS1B01G157200	chr1A	238678227	238679628	1401	False	464.000000	464	73.5580	1243	2653	1	chr1A.!!$F2	1410
4	TraesCS1B01G157200	chr1D	192566113	192570973	4860	False	1405.566667	3482	88.2720	935	3284	3	chr1D.!!$F1	2349
5	TraesCS1B01G157200	chr3B	436510644	436511382	738	False	1194.000000	1194	95.8110	3280	4019	1	chr3B.!!$F3	739
6	TraesCS1B01G157200	chr5B	447210707	447211446	739	True	1179.000000	1179	95.4120	3280	4019	1	chr5B.!!$R1	739
7	TraesCS1B01G157200	chr2D	111160338	111161074	736	False	1131.000000	1131	94.3170	3281	4019	1	chr2D.!!$F1	738
8	TraesCS1B01G157200	chr7D	37923917	37924649	732	False	1118.000000	1118	94.1500	3281	4015	1	chr7D.!!$F1	734
9	TraesCS1B01G157200	chr7D	141230751	141231485	734	True	1022.000000	1022	91.7340	3282	4019	1	chr7D.!!$R1	737
10	TraesCS1B01G157200	chr7B	442361419	442362108	689	False	1092.000000	1092	95.2170	3285	3974	1	chr7B.!!$F1	689
11	TraesCS1B01G157200	chr7B	206334637	206335196	559	True	317.500000	350	95.3560	1	938	2	chr7B.!!$R1	937
12	TraesCS1B01G157200	chr2B	592808087	592808823	736	True	1064.000000	1064	92.6930	3281	4019	1	chr2B.!!$R1	738
13	TraesCS1B01G157200	chr2B	77492531	77493449	918	True	330.500000	370	96.1080	1	941	2	chr2B.!!$R2	940
14	TraesCS1B01G157200	chrUn	423674164	423674893	729	False	1059.000000	1059	92.8860	3289	4016	1	chrUn.!!$F1	727
15	TraesCS1B01G157200	chr2A	694757628	694758366	738	False	996.000000	996	90.9700	3279	4019	1	chr2A.!!$F3	740
16	TraesCS1B01G157200	chr5A	597686322	597688013	1691	True	734.000000	734	74.9420	1241	2940	1	chr5A.!!$R2	1699
17	TraesCS1B01G157200	chr5A	105415483	105416184	701	True	268.000000	268	74.0170	2169	2867	1	chr5A.!!$R1	698
18	TraesCS1B01G157200	chr6D	308937703	308939454	1751	True	534.000000	534	72.7530	1115	2869	1	chr6D.!!$R1	1754
19	TraesCS1B01G157200	chr6D	86721579	86723215	1636	False	326.000000	326	71.1900	1241	2859	1	chr6D.!!$F1	1618
20	TraesCS1B01G157200	chr6B	164363166	164364835	1669	False	392.000000	392	71.8530	1233	2885	1	chr6B.!!$F2	1652
21	TraesCS1B01G157200	chr6B	228970543	228971515	972	True	332.000000	379	96.2095	1	941	2	chr6B.!!$R1	940
22	TraesCS1B01G157200	chr6A	104412587	104413656	1069	True	300.000000	300	72.4700	1241	2307	1	chr6A.!!$R1	1066
23	TraesCS1B01G157200	chr5D	98228545	98229358	813	False	291.000000	291	73.6140	2054	2867	1	chr5D.!!$F1	813

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	Hairpin	End Stability	Orientation
991	1068	2.174363	TGTGCAGGAGACACAGAATG	57.826	50.0	42.88	2.67	F
1040	1117	0.168568	GTCGTCTCCTTCCTCGTGTC	59.831	60.0	0.00	3.67	F
2391	5674	0.458716	GCTTGCTCTACCTCCACGAC	60.459	60.0	0.00	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2391	5674	0.320771	CCACCACTTTCTCCCAGTCG	60.321	60.0	0.00	0.00	4.18	R
3001	6305	0.461961	CATCACCTCCCGGAGAGAAC	59.538	60.0	16.69	46.50	3.01	R
3412	6717	0.609131	CAACCTTTGGGTCATCGCCT	60.609	55.0	0.00	46.67	5.52	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
891	960	2.883730	CGTGCGCGCTAAAGGCTA	60.884	61.111	33.29	5.92	39.13	3.93
991	1068	2.174363	TGTGCAGGAGACACAGAATG	57.826	50.000	0.00	0.00	42.88	2.67
1040	1117	0.168568	GTCGTCTCCTTCCTCGTGTC	59.831	60.000	0.00	0.00	0.00	3.67
1105	1182	1.896660	AACGGCTTTGATGGTGCGT	60.897	52.632	0.00	0.00	0.00	5.24
1113	1190	2.434185	GATGGTGCGTGGCTCGAA	60.434	61.111	13.77	0.00	42.86	3.71
1251	1334	2.258591	GTCGCACGCTCCTTCTCA	59.741	61.111	0.00	0.00	0.00	3.27
1569	1668	2.830923	CAGGAACCTGACTCTCATCAGT	59.169	50.000	14.94	0.00	46.30	3.41
1572	1671	2.317371	ACCTGACTCTCATCAGTGGT	57.683	50.000	2.35	0.00	43.99	4.16
1686	1788	0.746923	TCATCTCCGTCACCGTCGAT	60.747	55.000	0.00	0.00	0.00	3.59
2023	5279	4.513442	GTTGGCATACAAGGATCTGTACA	58.487	43.478	0.00	0.00	40.38	2.90
2024	5280	5.126067	GTTGGCATACAAGGATCTGTACAT	58.874	41.667	0.00	0.00	40.38	2.29
2124	5383	1.376037	CAAGAAGGAGGTGGCCGTC	60.376	63.158	0.00	0.00	36.79	4.79
2140	5399	2.050714	TCAAGGTCGTCGTGTCGC	60.051	61.111	0.00	0.00	0.00	5.19
2391	5674	0.458716	GCTTGCTCTACCTCCACGAC	60.459	60.000	0.00	0.00	0.00	4.34
2935	6239	2.334946	GCCTTGATGCAGAACGCCA	61.335	57.895	0.00	0.00	41.33	5.69
2984	6288	0.797249	CCGTTGTCTTCGGCGACTAG	60.797	60.000	10.16	5.50	41.48	2.57
3066	6370	1.664151	GGCAACAACATAGGAGTACGC	59.336	52.381	0.00	0.00	0.00	4.42
3067	6371	2.618053	GCAACAACATAGGAGTACGCT	58.382	47.619	0.00	0.00	0.00	5.07
3084	6388	0.895100	GCTTGCCAGGGATCACAACA	60.895	55.000	0.00	0.00	0.00	3.33
3095	6399	4.720773	AGGGATCACAACATCTTCTGATCT	59.279	41.667	0.00	0.00	39.27	2.75
3210	6515	1.445410	CGTCAATCGAACCGGCAGA	60.445	57.895	0.00	0.00	42.86	4.26
3226	6531	2.943690	GGCAGACAGTACGTGAGATAGA	59.056	50.000	0.00	0.00	0.00	1.98
3269	6574	5.917541	TTTCGGTAGACAATTTGTGAGTC	57.082	39.130	6.80	0.00	0.00	3.36
3270	6575	3.921677	TCGGTAGACAATTTGTGAGTCC	58.078	45.455	6.80	3.64	32.82	3.85
3271	6576	3.000727	CGGTAGACAATTTGTGAGTCCC	58.999	50.000	6.80	0.00	32.82	4.46
3272	6577	3.344515	GGTAGACAATTTGTGAGTCCCC	58.655	50.000	6.80	0.00	32.82	4.81
3273	6578	3.244770	GGTAGACAATTTGTGAGTCCCCA	60.245	47.826	6.80	0.00	32.82	4.96
3274	6579	3.593442	AGACAATTTGTGAGTCCCCAA	57.407	42.857	6.80	0.00	32.82	4.12
3275	6580	3.909732	AGACAATTTGTGAGTCCCCAAA	58.090	40.909	6.80	7.33	35.25	3.28
3276	6581	4.482990	AGACAATTTGTGAGTCCCCAAAT	58.517	39.130	6.80	10.51	41.69	2.32
3277	6582	4.281688	AGACAATTTGTGAGTCCCCAAATG	59.718	41.667	6.80	12.18	39.65	2.32
3278	6583	3.966665	ACAATTTGTGAGTCCCCAAATGT	59.033	39.130	14.94	12.61	39.65	2.71
3304	6609	3.878160	TTTTGAAACGGAGGCAAAAGT	57.122	38.095	0.00	0.00	36.80	2.66
3412	6717	0.673644	GACCCTAGCTTCTTTGCGCA	60.674	55.000	5.66	5.66	38.13	6.09
3474	6779	1.033746	CAAGATTGGCGGTGGAGCAT	61.034	55.000	0.00	0.00	39.27	3.79
3637	6942	0.886490	CAAGCGGAAGTGTCAAGCCT	60.886	55.000	0.00	0.00	31.57	4.58
3772	7078	4.514585	TGGCCACCCACGCTTTGT	62.515	61.111	0.00	0.00	35.79	2.83
3804	7110	2.408050	CCGTCCAAACTCTGTCTTGAG	58.592	52.381	0.00	0.00	39.78	3.02
3978	7290	1.716581	CTTCGTTGAGCTCGTCAAGAC	59.283	52.381	9.64	0.16	46.18	3.01
3993	7305	3.927142	GTCAAGACGGACCTCATTTAGTG	59.073	47.826	0.00	0.00	0.00	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
933	1006	7.331791	AGCAGTAGTTTTATGGACTTTAGAGG	58.668	38.462	0.00	0.00	0.00	3.69
976	1053	2.693069	GTGTCCATTCTGTGTCTCCTG	58.307	52.381	0.00	0.00	0.00	3.86
991	1068	2.583593	GAGCCGCATCTCGTGTCC	60.584	66.667	0.00	0.00	36.19	4.02
1040	1117	0.174617	GAGGAACTGGAAGAGGAGCG	59.825	60.000	0.00	0.00	41.55	5.03
1251	1334	3.044305	GCGAACACGAAGGCTGCT	61.044	61.111	0.00	0.00	0.00	4.24
1572	1671	1.252215	CCCACACTTGCATGGCATCA	61.252	55.000	0.00	0.00	38.76	3.07
2007	5263	3.641436	TGGCGATGTACAGATCCTTGTAT	59.359	43.478	0.33	0.00	36.08	2.29
2124	5383	2.354188	TGCGACACGACGACCTTG	60.354	61.111	0.00	0.00	35.09	3.61
2351	5631	1.944676	GACGCGACGCCTCTAATGG	60.945	63.158	15.93	0.00	0.00	3.16
2391	5674	0.320771	CCACCACTTTCTCCCAGTCG	60.321	60.000	0.00	0.00	0.00	4.18
2663	5967	4.351938	CCAGCCGGTTGTCGTCGA	62.352	66.667	17.69	0.00	37.11	4.20
2935	6239	1.183676	ACGTAGGAGTCGTTGCCCTT	61.184	55.000	0.00	0.00	38.38	3.95
2958	6262	2.373540	CCGAAGACAACGGGTATGAA	57.626	50.000	0.00	0.00	45.65	2.57
3001	6305	0.461961	CATCACCTCCCGGAGAGAAC	59.538	60.000	16.69	0.00	46.50	3.01
3043	6347	2.496899	ACTCCTATGTTGTTGCCAGG	57.503	50.000	0.00	0.00	0.00	4.45
3056	6360	1.327690	CCCTGGCAAGCGTACTCCTA	61.328	60.000	0.00	0.00	0.00	2.94
3057	6361	2.660064	CCCTGGCAAGCGTACTCCT	61.660	63.158	0.00	0.00	0.00	3.69
3059	6363	0.530870	GATCCCTGGCAAGCGTACTC	60.531	60.000	0.00	0.00	0.00	2.59
3060	6364	1.264749	TGATCCCTGGCAAGCGTACT	61.265	55.000	0.00	0.00	0.00	2.73
3061	6365	1.090052	GTGATCCCTGGCAAGCGTAC	61.090	60.000	0.00	0.00	0.00	3.67
3062	6366	1.220749	GTGATCCCTGGCAAGCGTA	59.779	57.895	0.00	0.00	0.00	4.42
3063	6367	2.045926	GTGATCCCTGGCAAGCGT	60.046	61.111	0.00	0.00	0.00	5.07
3064	6368	1.675310	TTGTGATCCCTGGCAAGCG	60.675	57.895	0.00	0.00	0.00	4.68
3065	6369	0.895100	TGTTGTGATCCCTGGCAAGC	60.895	55.000	0.00	0.00	0.00	4.01
3066	6370	1.747355	GATGTTGTGATCCCTGGCAAG	59.253	52.381	0.00	0.00	0.00	4.01
3067	6371	1.355381	AGATGTTGTGATCCCTGGCAA	59.645	47.619	0.00	0.00	0.00	4.52
3118	6423	3.967332	AAAAATGTTGCAGGGATCAGG	57.033	42.857	0.00	0.00	0.00	3.86
3210	6515	5.998363	TCATGCTATCTATCTCACGTACTGT	59.002	40.000	0.00	0.00	0.00	3.55
3226	6531	7.132213	CGAAAATCCGTTAACAATCATGCTAT	58.868	34.615	6.39	0.00	0.00	2.97
3412	6717	0.609131	CAACCTTTGGGTCATCGCCT	60.609	55.000	0.00	0.00	46.67	5.52
3474	6779	5.468746	ACGCAAGAGTGTTTAAGCATAAGAA	59.531	36.000	0.00	0.00	43.62	2.52
3637	6942	5.011586	TCATTGAGAAATTCCTCATGCACA	58.988	37.500	0.00	0.00	42.18	4.57
3772	7078	1.116308	TTGGACGGCGGATAGATTGA	58.884	50.000	13.24	0.00	0.00	2.57
3942	7254	6.283694	TCAACGAAGATGATATCCTTTGGAG	58.716	40.000	11.50	5.74	33.37	3.86
3978	7290	3.118775	TGGATGACACTAAATGAGGTCCG	60.119	47.826	0.00	0.00	32.00	4.79
3993	7305	4.084118	GCAATTCTTCGCTCTATGGATGAC	60.084	45.833	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.