AutoCloner

Multiple sequence alignment - TraesCS1A01G238300

Loading Multiple Alignment...

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	TraesCS1A01G238300	chr1A	100.000	2971	0	0	1	2971	424272015	424274985	0.000000e+00	5487
1	TraesCS1A01G238300	chr1A	93.506	2972	186	7	2	2971	423164961	423161995	0.000000e+00	4412
2	TraesCS1A01G238300	chr1A	93.309	2974	191	8	1	2971	423290474	423287506	0.000000e+00	4383
3	TraesCS1A01G238300	chr1A	92.524	2983	202	15	1	2971	423228580	423225607	0.000000e+00	4253
4	TraesCS1A01G238300	chr1A	92.538	2975	203	5	1	2959	424079645	424082616	0.000000e+00	4246
5	TraesCS1A01G238300	chr1A	91.020	2784	205	20	207	2960	423551901	423549133	0.000000e+00	3714
6	TraesCS1A01G238300	chr1A	92.668	2564	179	8	397	2960	423594777	423592223	0.000000e+00	3685
7	TraesCS1A01G238300	chr1A	93.040	2227	149	4	736	2960	423515655	423513433	0.000000e+00	3249
8	TraesCS1A01G238300	chr1A	92.726	2227	154	5	736	2960	423462692	423460472	0.000000e+00	3208
9	TraesCS1A01G238300	chr1A	93.735	2059	124	4	902	2958	424392568	424394623	0.000000e+00	3083
10	TraesCS1A01G238300	chr1A	91.058	917	72	4	1	910	424390682	424391595	0.000000e+00	1230
11	TraesCS1A01G238300	chr1A	90.718	905	71	3	1	893	423144503	423143600	0.000000e+00	1194
12	TraesCS1A01G238300	chr1A	90.365	903	77	7	1	893	423085819	423084917	0.000000e+00	1177
13	TraesCS1A01G238300	chr1A	89.724	905	71	6	1	893	423270183	423269289	0.000000e+00	1136
14	TraesCS1A01G238300	chr1A	89.258	903	76	7	1	893	423208303	423207412	0.000000e+00	1110
15	TraesCS1A01G238300	chr1A	94.697	132	6	1	1	132	423552026	423551896	1.400000e-48	204
16	TraesCS1A01G238300	chr1B	88.565	2125	189	17	1	2079	435811479	435813595	0.000000e+00	2529

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	TraesCS1A01G238300	chr1A	424272015	424274985	2970	False	5487.0	5487	100.0000	1	2971	1	chr1A.!!$F2	2970
1	TraesCS1A01G238300	chr1A	423161995	423164961	2966	True	4412.0	4412	93.5060	2	2971	1	chr1A.!!$R3	2969
2	TraesCS1A01G238300	chr1A	423287506	423290474	2968	True	4383.0	4383	93.3090	1	2971	1	chr1A.!!$R7	2970
3	TraesCS1A01G238300	chr1A	423225607	423228580	2973	True	4253.0	4253	92.5240	1	2971	1	chr1A.!!$R5	2970
4	TraesCS1A01G238300	chr1A	424079645	424082616	2971	False	4246.0	4246	92.5380	1	2959	1	chr1A.!!$F1	2958
5	TraesCS1A01G238300	chr1A	423592223	423594777	2554	True	3685.0	3685	92.6680	397	2960	1	chr1A.!!$R10	2563
6	TraesCS1A01G238300	chr1A	423513433	423515655	2222	True	3249.0	3249	93.0400	736	2960	1	chr1A.!!$R9	2224
7	TraesCS1A01G238300	chr1A	423460472	423462692	2220	True	3208.0	3208	92.7260	736	2960	1	chr1A.!!$R8	2224
8	TraesCS1A01G238300	chr1A	424390682	424394623	3941	False	2156.5	3083	92.3965	1	2958	2	chr1A.!!$F3	2957
9	TraesCS1A01G238300	chr1A	423549133	423552026	2893	True	1959.0	3714	92.8585	1	2960	2	chr1A.!!$R11	2959
10	TraesCS1A01G238300	chr1A	423143600	423144503	903	True	1194.0	1194	90.7180	1	893	1	chr1A.!!$R2	892
11	TraesCS1A01G238300	chr1A	423084917	423085819	902	True	1177.0	1177	90.3650	1	893	1	chr1A.!!$R1	892
12	TraesCS1A01G238300	chr1A	423269289	423270183	894	True	1136.0	1136	89.7240	1	893	1	chr1A.!!$R6	892
13	TraesCS1A01G238300	chr1A	423207412	423208303	891	True	1110.0	1110	89.2580	1	893	1	chr1A.!!$R4	892
14	TraesCS1A01G238300	chr1B	435811479	435813595	2116	False	2529.0	2529	88.5650	1	2079	1	chr1B.!!$F1	2078

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
408	448	0.929244	ATGAAATGCCCCCTGCTAGT	59.071	50.0	0.0	0.0	42.0	2.57	F
557	599	4.889409	TCTTGTTCAGAAATCAAAGGTGCT	59.111	37.5	0.0	0.0	0.0	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1478	2550	0.981183	ATAAGGGGACAAGCGTGACA	59.019	50.0	6.65	0.0	0.00	3.58	R
2543	3621	0.610174	CCACAAGCACTGGAGCTAGA	59.390	55.0	0.00	0.0	45.89	2.43	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
28	29	4.192317	ACTATCGTCATTTTCCAAGAGGC	58.808	43.478	0.00	0.00	33.74	4.70
120	121	3.819245	CCTGTTTCAGGTTGGGACA	57.181	52.632	7.55	0.00	45.82	4.02
121	122	2.292828	CCTGTTTCAGGTTGGGACAT	57.707	50.000	7.55	0.00	45.82	3.06
143	144	2.840038	ACTGTGCCAAGATCATCACCTA	59.160	45.455	0.00	0.00	0.00	3.08
172	173	4.664677	GGCCGGGTGATCGATCCG	62.665	72.222	22.31	18.47	43.05	4.18
190	192	5.007234	CGATCCGAAAATATGCACCAAGTTA	59.993	40.000	0.00	0.00	0.00	2.24
402	420	3.635591	CTTGAGTAATGAAATGCCCCCT	58.364	45.455	0.00	0.00	0.00	4.79
405	423	1.288932	AGTAATGAAATGCCCCCTGCT	59.711	47.619	0.00	0.00	42.00	4.24
408	448	0.929244	ATGAAATGCCCCCTGCTAGT	59.071	50.000	0.00	0.00	42.00	2.57
550	592	7.011950	ACGTATTGTGTCTTGTTCAGAAATCAA	59.988	33.333	0.00	0.00	31.28	2.57
557	599	4.889409	TCTTGTTCAGAAATCAAAGGTGCT	59.111	37.500	0.00	0.00	0.00	4.40
561	603	6.503524	TGTTCAGAAATCAAAGGTGCTAAAC	58.496	36.000	0.00	0.00	0.00	2.01
602	645	6.111768	ACTATCAAGATGACACATTTTCGC	57.888	37.500	0.00	0.00	0.00	4.70
811	864	6.440965	AGGAGGTAGTATATGCCCTAATTGTC	59.559	42.308	0.00	0.00	33.23	3.18
1065	2113	5.892348	ACAACCAAAAGGACATAGGAGAAT	58.108	37.500	0.00	0.00	0.00	2.40
1144	2192	5.048083	TGCTTGATGGTACTTTTGATGGTTC	60.048	40.000	0.00	0.00	0.00	3.62
1305	2353	6.798482	TCTGTTGCCAATGATATGAATGTTC	58.202	36.000	0.00	0.00	0.00	3.18
1478	2550	3.107642	CCTCGTAGTGGAAACTTGTGT	57.892	47.619	0.00	0.00	45.27	3.72
1487	2560	1.400494	GGAAACTTGTGTGTCACGCTT	59.600	47.619	17.06	3.48	37.14	4.68
1711	2784	8.148351	TCCACTATTGTCCTACTATTTGCATAC	58.852	37.037	0.00	0.00	0.00	2.39
1812	2887	1.545582	GCAAGGAAGCTAACATTGGCA	59.454	47.619	16.01	0.00	37.10	4.92
1989	3064	8.314021	GTTTGGAAATAAAGATTCACTTGGGAT	58.686	33.333	0.00	0.00	38.98	3.85
2145	3222	3.462982	GGACGACTTTTGGGCAAAATTT	58.537	40.909	0.00	0.00	39.29	1.82
2236	3313	4.412843	TGGAACTACACACCAGATAGTGA	58.587	43.478	0.00	0.00	40.34	3.41
2329	3407	7.856145	ACAATCATCTTTGATACCAAGAGTC	57.144	36.000	0.00	0.00	41.83	3.36
2388	3466	5.596836	TTGGGACCAAATAGATTCATTGC	57.403	39.130	0.32	0.00	32.44	3.56
2435	3513	9.076781	CATACCAATGGTCCATCAAACATATTA	57.923	33.333	8.82	0.00	37.09	0.98
2497	3575	5.772672	TGGCTATCTACCACAACAATGTTTT	59.227	36.000	0.00	0.00	37.82	2.43
2509	3587	4.034285	ACAATGTTTTCCCTTCTCCGAT	57.966	40.909	0.00	0.00	0.00	4.18
2561	3639	1.001293	TGTCTAGCTCCAGTGCTTGTG	59.999	52.381	0.00	0.00	43.74	3.33
2582	3660	2.286891	GGTCGTCGCTAAGTGGTCTATC	60.287	54.545	0.00	0.00	0.00	2.08
2627	3705	8.035984	ACTTCTAGTATTCTTTGAACTACCTGC	58.964	37.037	0.00	0.00	0.00	4.85
2650	3728	0.392461	TTGGTGAATACTGCCTCGGC	60.392	55.000	0.00	0.00	42.35	5.54
2765	3843	2.355986	AAGTCCGATGCGCCAGGTA	61.356	57.895	4.18	0.00	0.00	3.08
2783	3861	6.679843	CCAGGTATCTTCTAGTTATTCGTCC	58.320	44.000	0.00	0.00	0.00	4.79
2797	3875	1.434555	TCGTCCTTGTTGCCATTACG	58.565	50.000	0.00	0.00	0.00	3.18
2860	3939	9.944663	GCATTGCATCATCATATTTTTCAAAAT	57.055	25.926	3.15	3.13	41.24	1.82
2917	3996	0.105778	TCCGACACTCACACATGCAA	59.894	50.000	0.00	0.00	0.00	4.08
2943	4022	1.947456	GCACCTTCCAGTTCTCGTTTT	59.053	47.619	0.00	0.00	0.00	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	4.679654	GCAACCTGAATTACTTCAAAACCG	59.320	41.667	0.00	0.00	40.78	4.44
120	121	3.457380	AGGTGATGATCTTGGCACAGTAT	59.543	43.478	0.00	0.00	42.39	2.12
121	122	2.840038	AGGTGATGATCTTGGCACAGTA	59.160	45.455	0.00	0.00	42.39	2.74
143	144	0.113580	ACCCGGCCCAACTTTTACAT	59.886	50.000	0.00	0.00	0.00	2.29
172	173	7.377766	TCTCTGTAACTTGGTGCATATTTTC	57.622	36.000	0.00	0.00	0.00	2.29
190	192	5.220951	CGTTGAGCAGATGTACTATCTCTGT	60.221	44.000	13.19	4.78	38.88	3.41
253	255	5.069516	CCATTACATGCCCAGCTTTATTCTT	59.930	40.000	0.00	0.00	0.00	2.52
280	282	0.179032	TGCTGTCCGTGACCAATTGT	60.179	50.000	4.43	0.00	0.00	2.71
316	328	0.833287	AGGGAGCGAGCATGTGTAAT	59.167	50.000	0.00	0.00	0.00	1.89
376	394	5.278660	GGGGCATTTCATTACTCAAGCTATG	60.279	44.000	0.00	0.00	0.00	2.23
402	420	3.006940	CGCACTTTTTATCCCACTAGCA	58.993	45.455	0.00	0.00	0.00	3.49
405	423	2.290387	TGGCGCACTTTTTATCCCACTA	60.290	45.455	10.83	0.00	0.00	2.74
408	448	0.885196	GTGGCGCACTTTTTATCCCA	59.115	50.000	10.83	0.00	0.00	4.37
413	453	2.640421	GCGGTGGCGCACTTTTTA	59.360	55.556	10.83	0.00	34.40	1.52
433	473	6.259550	AGTCAACTATGCAGGTTTCATTTC	57.740	37.500	5.29	0.00	0.00	2.17
527	569	8.352201	CCTTTGATTTCTGAACAAGACACAATA	58.648	33.333	0.00	0.00	33.46	1.90
529	571	6.152661	ACCTTTGATTTCTGAACAAGACACAA	59.847	34.615	0.00	0.00	33.46	3.33
1011	2059	3.391296	ACTACTTTGCTGGTTCCTTCTGA	59.609	43.478	0.00	0.00	0.00	3.27
1144	2192	4.062293	TCACTCGACAATAAAGTGGTTGG	58.938	43.478	2.26	0.00	40.60	3.77
1305	2353	7.133891	ACTTGAACGATCAAACTTCATAAGG	57.866	36.000	9.52	0.00	44.64	2.69
1367	2439	3.118738	CCTCACTCTATTAGGCACGGTTT	60.119	47.826	0.00	0.00	0.00	3.27
1468	2540	2.159572	ACAAGCGTGACACACAAGTTTC	60.160	45.455	6.65	0.00	33.40	2.78
1478	2550	0.981183	ATAAGGGGACAAGCGTGACA	59.019	50.000	6.65	0.00	0.00	3.58
1487	2560	7.147915	GCATGATAACTTTCAAATAAGGGGACA	60.148	37.037	0.00	0.00	0.00	4.02
1651	2724	4.411256	ACACGGGAAGAAAAACTACTGA	57.589	40.909	0.00	0.00	0.00	3.41
1660	2733	5.049267	GTGCTAATACAAACACGGGAAGAAA	60.049	40.000	0.00	0.00	0.00	2.52
1711	2784	8.954950	ACTAGGATTCTGTGAAATCAATGTAG	57.045	34.615	0.00	0.00	37.38	2.74
1744	2817	4.441356	GCCATGAGAACCTTTTGTTGTTCA	60.441	41.667	0.00	0.00	42.57	3.18
1788	2863	4.210331	CCAATGTTAGCTTCCTTGCCTAT	58.790	43.478	0.00	0.00	0.00	2.57
1812	2887	1.224592	GTTCATGGTGCCCCTCGAT	59.775	57.895	0.00	0.00	0.00	3.59
1825	2900	4.101114	TGTACATGGAGTGTAGGGTTCAT	58.899	43.478	0.00	0.00	43.70	2.57
1989	3064	9.241919	TCCAGCTAGAAAAACAATTCATAATGA	57.758	29.630	0.00	0.00	0.00	2.57
2302	3380	9.739276	ACTCTTGGTATCAAAGATGATTGTTTA	57.261	29.630	0.00	0.00	43.89	2.01
2329	3407	6.238842	CCATAATATGTTTTCCAGCTGTCCTG	60.239	42.308	13.81	0.00	41.41	3.86
2388	3466	2.658325	GCGCTTATTTTGTGTGCAAGAG	59.342	45.455	0.00	0.00	37.20	2.85
2435	3513	2.294512	GCAGCTTGTTAGTTTCCAGCTT	59.705	45.455	0.00	0.00	0.00	3.74
2509	3587	1.207089	GTCGTCATCACCCATCCTTCA	59.793	52.381	0.00	0.00	0.00	3.02
2543	3621	0.610174	CCACAAGCACTGGAGCTAGA	59.390	55.000	0.00	0.00	45.89	2.43
2561	3639	1.089920	TAGACCACTTAGCGACGACC	58.910	55.000	0.00	0.00	0.00	4.79
2627	3705	3.448686	CGAGGCAGTATTCACCAACTAG	58.551	50.000	0.00	0.00	0.00	2.57
2694	3772	9.480861	TCATGAGAGAGATACTTTCCTTTTCTA	57.519	33.333	0.00	0.00	0.00	2.10
2731	3809	2.633481	GGACTTGGGGCGTTATAGAGAT	59.367	50.000	0.00	0.00	0.00	2.75
2737	3815	0.179056	CATCGGACTTGGGGCGTTAT	60.179	55.000	0.00	0.00	0.00	1.89
2765	3843	6.535508	GCAACAAGGACGAATAACTAGAAGAT	59.464	38.462	0.00	0.00	0.00	2.40
2797	3875	4.339439	AAAATGCAACACACAAGCAAAC	57.661	36.364	0.00	0.00	42.15	2.93
2860	3939	2.151202	GAGAAAGTGACCGGATGCAAA	58.849	47.619	9.46	0.00	0.00	3.68
2917	3996	0.818040	GAACTGGAAGGTGCAACGGT	60.818	55.000	0.00	0.00	39.30	4.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.