AutoCloner

Multiple sequence alignment - TraesCS1D01G298500

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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	TraesCS1D01G298500	chr1D	100.000	3419	0	0	1	3419	397082453	397079035	0.000000e+00	6314
1	TraesCS1D01G298500	chr1A	95.594	3427	112	14	1	3419	494452595	494449200	0.000000e+00	5456
2	TraesCS1D01G298500	chr1B	94.873	2789	99	14	642	3419	532174335	532171580	0.000000e+00	4318
3	TraesCS1D01G298500	chr1B	91.304	644	45	6	1	638	532175041	532174403	0.000000e+00	869
4	TraesCS1D01G298500	chr3A	80.330	788	148	5	1028	1810	595434956	595435741	1.060000e-164	590
5	TraesCS1D01G298500	chr2D	88.046	435	40	8	1622	2052	520042415	520042841	3.940000e-139	505
6	TraesCS1D01G298500	chr2D	88.506	261	19	7	1327	1579	520042158	520042415	4.290000e-79	305
7	TraesCS1D01G298500	chr2D	77.241	290	37	20	2960	3222	627184655	627184368	3.560000e-30	143
8	TraesCS1D01G298500	chr2B	87.385	436	42	7	1622	2052	612067830	612068257	3.970000e-134	488
9	TraesCS1D01G298500	chr2B	87.264	424	42	6	1634	2052	612074157	612074573	1.110000e-129	473
10	TraesCS1D01G298500	chr2B	91.031	223	19	1	1357	1579	612067609	612067830	1.990000e-77	300
11	TraesCS1D01G298500	chr7D	79.055	487	67	16	2954	3417	416245108	416245582	5.540000e-78	302
12	TraesCS1D01G298500	chr6A	78.112	466	68	22	2955	3417	452621257	452621691	7.280000e-67	265
13	TraesCS1D01G298500	chr5D	78.933	375	52	21	2959	3316	278142068	278142432	2.650000e-56	230
14	TraesCS1D01G298500	chr5D	77.346	309	49	15	3024	3316	421557631	421557934	2.730000e-36	163
15	TraesCS1D01G298500	chr6D	78.517	391	45	19	2958	3316	27117189	27116806	1.600000e-53	220
16	TraesCS1D01G298500	chr6D	77.778	378	53	22	2958	3316	88703659	88704024	1.610000e-48	204
17	TraesCS1D01G298500	chr7A	77.099	393	47	28	2958	3316	91940344	91940727	1.620000e-43	187
18	TraesCS1D01G298500	chr7A	77.143	315	46	18	3018	3314	487748453	487748147	3.530000e-35	159

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	TraesCS1D01G298500	chr1D	397079035	397082453	3418	True	6314.0	6314	100.0000	1	3419	1	chr1D.!!$R1	3418
1	TraesCS1D01G298500	chr1A	494449200	494452595	3395	True	5456.0	5456	95.5940	1	3419	1	chr1A.!!$R1	3418
2	TraesCS1D01G298500	chr1B	532171580	532175041	3461	True	2593.5	4318	93.0885	1	3419	2	chr1B.!!$R1	3418
3	TraesCS1D01G298500	chr3A	595434956	595435741	785	False	590.0	590	80.3300	1028	1810	1	chr3A.!!$F1	782
4	TraesCS1D01G298500	chr2D	520042158	520042841	683	False	405.0	505	88.2760	1327	2052	2	chr2D.!!$F1	725
5	TraesCS1D01G298500	chr2B	612067609	612068257	648	False	394.0	488	89.2080	1357	2052	2	chr2B.!!$F2	695

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
24	25	0.106419	AACCGAGGGCAAAAACAGGA	60.106	50.000	0.00	0.00	0.00	3.86	F
465	473	0.329596	AATCTTGCAGAGGACACCCC	59.670	55.000	0.00	0.00	0.00	4.95	F
494	502	0.389426	GAGCTTTGGCCATGCTGTTG	60.389	55.000	30.46	8.62	39.73	3.33	F
906	978	1.068541	CCGATATCCGAAGCGTGATGA	60.069	52.381	0.00	0.00	41.76	2.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1316	1392	2.285668	TCCTTGCCCCCTCCTCAG	60.286	66.667	0.00	0.00	0.0	3.35	R
2097	2186	0.984995	CCTTCTTTCCTTCCCTCGGT	59.015	55.000	0.00	0.00	0.0	4.69	R
2321	2410	3.292936	GTTGCTGTGCCTGCTGCT	61.293	61.111	0.00	0.00	42.0	4.24	R
2778	2867	1.131883	GCCACAGAGCATGCTAACAAG	59.868	52.381	22.74	11.06	0.0	3.16	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
24	25	0.106419	AACCGAGGGCAAAAACAGGA	60.106	50.000	0.00	0.00	0.00	3.86
103	104	1.080025	GCTCCACCACACGTAGGAC	60.080	63.158	12.70	0.00	0.00	3.85
126	131	3.077556	GAGCCGGAGAAGCCCAGA	61.078	66.667	5.05	0.00	0.00	3.86
136	141	1.846712	GAAGCCCAGACAGCCTCCTT	61.847	60.000	0.00	0.00	0.00	3.36
263	268	1.986631	TGGGACTTGGGAATTCCGTTA	59.013	47.619	18.30	4.58	38.76	3.18
264	269	2.578940	TGGGACTTGGGAATTCCGTTAT	59.421	45.455	18.30	4.08	38.76	1.89
282	287	4.505922	CGTTATTCTTCAGATCAGGTGAGC	59.494	45.833	0.00	0.00	0.00	4.26
393	398	3.619038	GTCGCCTCAATTCTAGGAGTTTG	59.381	47.826	7.44	0.00	36.08	2.93
405	410	0.868406	GGAGTTTGACGCTCCTGTTG	59.132	55.000	4.26	0.00	46.71	3.33
419	424	0.457035	CTGTTGGGCAATCCGATTGG	59.543	55.000	20.26	0.00	40.57	3.16
442	450	5.761234	GGACAATGTTGGAGTTACACTTGTA	59.239	40.000	0.00	0.00	32.56	2.41
444	452	5.238650	ACAATGTTGGAGTTACACTTGTAGC	59.761	40.000	0.00	0.00	31.63	3.58
465	473	0.329596	AATCTTGCAGAGGACACCCC	59.670	55.000	0.00	0.00	0.00	4.95
466	474	0.842030	ATCTTGCAGAGGACACCCCA	60.842	55.000	0.00	0.00	37.41	4.96
494	502	0.389426	GAGCTTTGGCCATGCTGTTG	60.389	55.000	30.46	8.62	39.73	3.33
512	520	5.127693	TGTTGAATGTCCCAATTTTACCG	57.872	39.130	0.00	0.00	0.00	4.02
592	600	4.574892	TGCGTTCTTCTCATGGAAATGTA	58.425	39.130	0.00	0.00	33.07	2.29
594	602	4.870426	GCGTTCTTCTCATGGAAATGTAGA	59.130	41.667	0.00	0.00	33.07	2.59
601	609	8.277197	TCTTCTCATGGAAATGTAGATTGGATT	58.723	33.333	0.00	0.00	33.07	3.01
610	618	7.587757	GGAAATGTAGATTGGATTTTCGATTCG	59.412	37.037	0.00	0.00	0.00	3.34
618	626	5.029650	TGGATTTTCGATTCGTCACAAAG	57.970	39.130	5.89	0.00	0.00	2.77
625	633	6.403333	TTCGATTCGTCACAAAGAAATAGG	57.597	37.500	5.89	0.00	0.00	2.57
641	649	2.535836	TAGGGGGTGTAAAAATGCCC	57.464	50.000	0.00	0.00	40.35	5.36
724	796	5.764131	TGTTTATTTTGTTTCGCAGGTAGG	58.236	37.500	0.00	0.00	0.00	3.18
872	944	2.350772	GGTTGCAGACTGGTTTCATTCG	60.351	50.000	4.26	0.00	0.00	3.34
891	963	1.386533	GACTCCTCCGTGTTCCGATA	58.613	55.000	0.00	0.00	39.56	2.92
906	978	1.068541	CCGATATCCGAAGCGTGATGA	60.069	52.381	0.00	0.00	41.76	2.92
940	1012	6.723977	ACTCTGTCTTCTCTAACATTCCTCTT	59.276	38.462	0.00	0.00	0.00	2.85
960	1033	3.735237	TTGAGTCTGAACCAGTCTGTC	57.265	47.619	0.00	0.00	30.81	3.51
1316	1392	2.801077	TTAGCCAAGGGGAAGCTTAC	57.199	50.000	0.00	0.00	38.06	2.34
1845	1931	5.542779	AGAAAAGACAAGACTTATGCGAGT	58.457	37.500	0.00	0.00	0.00	4.18
1870	1956	3.730761	CTGCGTCTGGCCTTGCAC	61.731	66.667	3.32	0.00	42.61	4.57
2097	2186	2.489285	GCGATGAAATTGGCCGCA	59.511	55.556	0.00	0.00	44.55	5.69
2152	2241	5.349061	TGAAGCAGAAATCTATGAGCTCA	57.651	39.130	20.79	20.79	0.00	4.26
2468	2557	4.336433	CACATATTTCATGGTGAGACCCAC	59.664	45.833	0.00	0.00	44.95	4.61
2515	2604	1.242076	ATGTGCTTGCAGTTCTCACC	58.758	50.000	0.00	0.00	0.00	4.02
2547	2636	1.613437	CATTGTTGGGAACGAAGGCTT	59.387	47.619	0.00	0.00	0.00	4.35
2550	2639	0.822121	GTTGGGAACGAAGGCTTGGT	60.822	55.000	9.25	9.25	0.00	3.67
2778	2867	6.697892	ACTGATACTTAAGAAACTATCAGCGC	59.302	38.462	25.92	0.00	39.58	5.92
3155	3253	3.109592	TTCTTGGTGGCGTCGGGTT	62.110	57.895	0.00	0.00	0.00	4.11
3180	3278	3.009115	CTCCGGCCCTTTCCCTCA	61.009	66.667	0.00	0.00	0.00	3.86
3235	3333	2.829003	CTCCCTCCAGCGCGTCTA	60.829	66.667	8.43	0.00	0.00	2.59
3409	3508	2.031919	GTGGTGGTGGTGATGCGA	59.968	61.111	0.00	0.00	0.00	5.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
103	104	2.496817	CTTCTCCGGCTCCCTTCG	59.503	66.667	0.00	0.00	0.00	3.79
263	268	4.840716	AAGCTCACCTGATCTGAAGAAT	57.159	40.909	0.38	0.00	0.00	2.40
264	269	5.745312	TTAAGCTCACCTGATCTGAAGAA	57.255	39.130	0.38	0.00	0.00	2.52
282	287	3.648545	AGTTCAGGGGCTAGGCTATTAAG	59.351	47.826	16.80	1.29	0.00	1.85
293	298	1.903877	CGGATCACAGTTCAGGGGCT	61.904	60.000	0.00	0.00	0.00	5.19
393	398	1.648467	GATTGCCCAACAGGAGCGTC	61.648	60.000	0.00	0.00	38.24	5.19
405	410	1.067516	CATTGTCCAATCGGATTGCCC	59.932	52.381	22.35	15.31	45.33	5.36
444	452	1.815003	GGGTGTCCTCTGCAAGATTTG	59.185	52.381	0.00	0.00	45.62	2.32
465	473	0.785979	GCCAAAGCTCGCACAAAATG	59.214	50.000	0.00	0.00	35.50	2.32
466	474	0.319813	GGCCAAAGCTCGCACAAAAT	60.320	50.000	0.00	0.00	39.73	1.82
494	502	5.774630	TGAAACGGTAAAATTGGGACATTC	58.225	37.500	0.00	0.00	39.30	2.67
512	520	3.438434	GGGCAAACTCTGAGATCTGAAAC	59.562	47.826	12.44	0.00	0.00	2.78
581	589	7.706159	TCGAAAATCCAATCTACATTTCCATG	58.294	34.615	0.00	0.00	36.34	3.66
592	600	4.935205	TGTGACGAATCGAAAATCCAATCT	59.065	37.500	10.55	0.00	0.00	2.40
594	602	5.621197	TTGTGACGAATCGAAAATCCAAT	57.379	34.783	10.55	0.00	0.00	3.16
601	609	6.128391	CCCTATTTCTTTGTGACGAATCGAAA	60.128	38.462	10.55	0.00	0.00	3.46
610	618	3.763057	ACACCCCCTATTTCTTTGTGAC	58.237	45.455	0.00	0.00	0.00	3.67
618	626	4.141801	GGGCATTTTTACACCCCCTATTTC	60.142	45.833	0.00	0.00	36.24	2.17
641	649	2.689983	CAAATCTTCGGGGAATGAAGGG	59.310	50.000	3.19	0.00	42.43	3.95
709	781	3.482436	ACAAATCCTACCTGCGAAACAA	58.518	40.909	0.00	0.00	0.00	2.83
724	796	0.798776	CGTCACCAGCCTGACAAATC	59.201	55.000	0.00	0.00	40.67	2.17
872	944	1.386533	TATCGGAACACGGAGGAGTC	58.613	55.000	0.00	0.00	44.45	3.36
891	963	1.751351	TCTCTTCATCACGCTTCGGAT	59.249	47.619	0.00	0.00	0.00	4.18
940	1012	2.034685	CGACAGACTGGTTCAGACTCAA	59.965	50.000	7.51	0.00	34.66	3.02
960	1033	7.173907	AGCCTGAATTTTTATGATGGTCTATCG	59.826	37.037	0.00	0.00	38.71	2.92
1316	1392	2.285668	TCCTTGCCCCCTCCTCAG	60.286	66.667	0.00	0.00	0.00	3.35
1845	1931	2.357881	CCAGACGCAGCAGCTTCA	60.358	61.111	10.19	0.00	41.15	3.02
2097	2186	0.984995	CCTTCTTTCCTTCCCTCGGT	59.015	55.000	0.00	0.00	0.00	4.69
2152	2241	3.496130	TCGACTAAGAGAAAAGACGACGT	59.504	43.478	0.00	0.00	35.57	4.34
2321	2410	3.292936	GTTGCTGTGCCTGCTGCT	61.293	61.111	0.00	0.00	42.00	4.24
2468	2557	8.682936	ACTAATCTAAGAGGCAAATATGGTTG	57.317	34.615	0.00	0.00	0.00	3.77
2515	2604	5.614324	TCCCAACAATGGTAGACATCTAG	57.386	43.478	0.00	0.00	46.01	2.43
2536	2625	2.545113	GGGAAAAACCAAGCCTTCGTTC	60.545	50.000	0.00	0.00	41.20	3.95
2547	2636	6.561519	TTTTACAGAAATGGGGAAAAACCA	57.438	33.333	0.00	0.00	43.22	3.67
2550	2639	9.467796	AAACAATTTTACAGAAATGGGGAAAAA	57.532	25.926	0.00	0.00	0.00	1.94
2778	2867	1.131883	GCCACAGAGCATGCTAACAAG	59.868	52.381	22.74	11.06	0.00	3.16
2989	3081	0.988678	CTAGGGTTTCCTCCTGGGGG	60.989	65.000	6.15	6.15	43.66	5.40
3136	3228	2.742372	CCCGACGCCACCAAGAAG	60.742	66.667	0.00	0.00	0.00	2.85
3173	3271	2.428925	GGACGCCGGTATGAGGGAA	61.429	63.158	1.90	0.00	0.00	3.97
3180	3278	4.157120	GCCACAGGACGCCGGTAT	62.157	66.667	1.90	0.00	29.37	2.73
3351	3450	1.146041	GCCATCGCCTACCATCACA	59.854	57.895	0.00	0.00	0.00	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.