AutoCloner

Multiple sequence alignment - TraesCS3D01G323300

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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	TraesCS3D01G323300	chr3D	100.000	2693	0	0	1	2693	436162683	436165375	0.000000e+00	4974.0
1	TraesCS3D01G323300	chr3D	96.068	2696	99	6	1	2693	436043469	436046160	0.000000e+00	4385.0
2	TraesCS3D01G323300	chr3D	77.642	246	49	6	250	492	526990644	526990402	7.770000e-31	145.0
3	TraesCS3D01G323300	chr3D	77.880	217	42	6	2378	2590	427443555	427443769	2.180000e-26	130.0
4	TraesCS3D01G323300	chr3A	94.807	2696	130	7	1	2693	574865213	574867901	0.000000e+00	4194.0
5	TraesCS3D01G323300	chr3A	82.174	230	36	3	250	478	501028792	501028567	2.740000e-45	193.0
6	TraesCS3D01G323300	chr3B	93.331	2699	162	13	1	2693	571810640	571813326	0.000000e+00	3971.0
7	TraesCS3D01G323300	chr5D	86.066	244	32	2	250	492	542699522	542699280	7.400000e-66	261.0
8	TraesCS3D01G323300	chr6D	84.188	234	33	3	2363	2593	114949968	114949736	9.700000e-55	224.0
9	TraesCS3D01G323300	chr2D	82.969	229	29	6	264	491	509751350	509751569	5.880000e-47	198.0
10	TraesCS3D01G323300	chr2D	78.543	247	46	6	2347	2588	628016886	628017130	3.590000e-34	156.0
11	TraesCS3D01G323300	chr1D	81.356	236	33	8	2361	2590	412513475	412513245	5.920000e-42	182.0
12	TraesCS3D01G323300	chr1D	85.542	83	12	0	268	350	308461156	308461074	1.330000e-13	87.9
13	TraesCS3D01G323300	chr1B	80.258	233	41	4	2362	2590	157897351	157897582	1.280000e-38	171.0
14	TraesCS3D01G323300	chr7B	78.656	253	46	6	238	489	662962168	662961923	7.720000e-36	161.0
15	TraesCS3D01G323300	chr7B	79.730	222	30	11	2382	2598	125379680	125379469	2.160000e-31	147.0
16	TraesCS3D01G323300	chr7D	82.171	129	19	3	48	174	611092292	611092166	1.020000e-19	108.0
17	TraesCS3D01G323300	chr2B	81.203	133	20	4	306	435	106160326	106160456	4.740000e-18	102.0

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	TraesCS3D01G323300	chr3D	436162683	436165375	2692	False	4974	4974	100.000	1	2693	1	chr3D.!!$F3	2692
1	TraesCS3D01G323300	chr3D	436043469	436046160	2691	False	4385	4385	96.068	1	2693	1	chr3D.!!$F2	2692
2	TraesCS3D01G323300	chr3A	574865213	574867901	2688	False	4194	4194	94.807	1	2693	1	chr3A.!!$F1	2692
3	TraesCS3D01G323300	chr3B	571810640	571813326	2686	False	3971	3971	93.331	1	2693	1	chr3B.!!$F1	2692

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
608	610	0.688487	ATGCTGCAAATGCCTTGGTT	59.312	45.0	6.36	0.0	41.18	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1939	1943	0.112412	ACCAACCCCAACTTAGCCAG	59.888	55.0	0.0	0.0	0.0	4.85	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
59	60	0.975556	TGATAGCCGGGAAGTCTGCA	60.976	55.000	2.18	0.00	0.00	4.41
67	68	0.737219	GGGAAGTCTGCATGCATGTC	59.263	55.000	26.79	18.98	0.00	3.06
163	164	3.332761	AATATTGCCATTGCGTACACG	57.667	42.857	0.00	0.00	41.78	4.49
197	198	0.692419	AATCTCACTGCCCCGAGGAT	60.692	55.000	0.00	0.00	33.47	3.24
210	211	4.130118	CCCCGAGGATTCAGAAATACAAG	58.870	47.826	0.00	0.00	33.47	3.16
269	270	3.322369	CAAGTGCCACACGTAAGATACA	58.678	45.455	0.00	0.00	39.64	2.29
448	450	3.470709	CCATCGAATAATGTCAGTGCCT	58.529	45.455	0.00	0.00	0.00	4.75
608	610	0.688487	ATGCTGCAAATGCCTTGGTT	59.312	45.000	6.36	0.00	41.18	3.67
610	612	1.690893	TGCTGCAAATGCCTTGGTTTA	59.309	42.857	0.00	0.00	41.18	2.01
815	817	5.748152	GGAACATATATGCAACGCAACAAAT	59.252	36.000	12.79	0.00	43.62	2.32
821	823	8.754096	CATATATGCAACGCAACAAATAAACAT	58.246	29.630	0.00	0.00	43.62	2.71
850	852	3.423571	GACACGTGTCTACATAGGAACG	58.576	50.000	35.51	10.72	41.65	3.95
912	914	7.761704	GTGTACATCTGTCTACATGAGAAACAT	59.238	37.037	0.00	0.00	40.17	2.71
914	916	9.239002	GTACATCTGTCTACATGAGAAACATAC	57.761	37.037	0.00	0.00	37.46	2.39
915	917	7.840931	ACATCTGTCTACATGAGAAACATACA	58.159	34.615	0.00	0.00	37.46	2.29
927	929	5.989168	TGAGAAACATACATCGTGACACTTT	59.011	36.000	3.68	0.00	0.00	2.66
947	949	1.262417	TCAATGAGCACCACCTACGA	58.738	50.000	0.00	0.00	0.00	3.43
1008	1010	3.134623	TCCCATCCATGCGCCTATATAAG	59.865	47.826	4.18	0.00	0.00	1.73
1052	1054	2.289133	ACCACACCAAAACAACACAACC	60.289	45.455	0.00	0.00	0.00	3.77
1173	1175	1.511850	TGTGACGGCTGAAGATTGTG	58.488	50.000	0.00	0.00	0.00	3.33
1174	1176	1.202639	TGTGACGGCTGAAGATTGTGT	60.203	47.619	0.00	0.00	0.00	3.72
1191	1193	1.270550	GTGTCGTCGACCTAAAAGGGA	59.729	52.381	22.05	0.00	40.58	4.20
1248	1250	1.806623	CGAGCCCAAAGATAACTCCGG	60.807	57.143	0.00	0.00	0.00	5.14
1346	1348	3.149196	GGTGGTATGCATGGATAAGGTG	58.851	50.000	10.16	0.00	0.00	4.00
1518	1520	0.256752	CATGTCCCATCTCAAGGCCA	59.743	55.000	5.01	0.00	0.00	5.36
1724	1726	5.178096	TCTCCTCAAATTACATGCTTCCA	57.822	39.130	0.00	0.00	0.00	3.53
1745	1747	8.622948	TTCCACTATTTTGTTTTTGTTTGGTT	57.377	26.923	0.00	0.00	0.00	3.67
1768	1771	7.224753	GGTTCTTTTCTGGTTTTGATTCCTTTC	59.775	37.037	0.00	0.00	0.00	2.62
1867	1871	7.120923	AGTCCTTTGTGATATTGTACGGTAT	57.879	36.000	0.00	0.00	0.00	2.73
1903	1907	6.587608	GCAAATGTTAAAATTCAGAGGTGGAG	59.412	38.462	0.00	0.00	0.00	3.86
1953	1957	5.112129	AGTAAATACTGGCTAAGTTGGGG	57.888	43.478	0.00	0.00	40.56	4.96
1955	1959	4.397919	AAATACTGGCTAAGTTGGGGTT	57.602	40.909	0.00	0.00	40.56	4.11
1957	1961	0.112412	ACTGGCTAAGTTGGGGTTGG	59.888	55.000	0.00	0.00	34.57	3.77
1958	1962	0.112412	CTGGCTAAGTTGGGGTTGGT	59.888	55.000	0.00	0.00	0.00	3.67
1977	1981	6.706270	GGTTGGTCTTCGATACACATCATAAT	59.294	38.462	0.00	0.00	0.00	1.28
2237	2243	3.161067	TGGTATGGTTGTGAATTGGTGG	58.839	45.455	0.00	0.00	0.00	4.61
2278	2284	0.036765	TTGGTACGAGCGCTCCATTT	60.037	50.000	30.66	15.23	0.00	2.32
2302	2308	1.949525	GTGTTGATGAAGTGGTGCTGT	59.050	47.619	0.00	0.00	0.00	4.40
2332	2338	3.838317	TGGTATGACCATAGGTATGAGCC	59.162	47.826	0.00	0.00	44.79	4.70
2350	2356	2.982130	GGAGCACTCGGACCATGT	59.018	61.111	0.00	0.00	0.00	3.21
2373	2379	4.457603	TGTCATATTACGCTTTGGTTGCTT	59.542	37.500	0.00	0.00	0.00	3.91
2433	2439	7.578310	ATGACTTCATTTGATAGGATGTTGG	57.422	36.000	0.00	0.00	31.37	3.77
2518	2524	8.294954	TCTCGAAGGATTAGTGTTAGAAAGAT	57.705	34.615	0.00	0.00	0.00	2.40
2627	2634	0.867746	TTTCTGTCATGCGTGTCTGC	59.132	50.000	5.68	0.00	0.00	4.26
2642	2649	1.604278	GTCTGCTTGTGTCTGGGTTTC	59.396	52.381	0.00	0.00	0.00	2.78
2684	2691	0.321564	TGTTTGCAGCACGCTAGGAT	60.322	50.000	0.00	0.00	43.06	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	60	1.215423	GGTCTTTAGGGGGACATGCAT	59.785	52.381	0.00	0.0	34.49	3.96
67	68	2.124695	GCGCTGGTCTTTAGGGGG	60.125	66.667	0.00	0.0	0.00	5.40
163	164	3.482833	GTGAGATTAGCGTTTCTCGTAGC	59.517	47.826	7.88	0.0	41.04	3.58
165	166	4.659088	CAGTGAGATTAGCGTTTCTCGTA	58.341	43.478	7.88	0.0	41.04	3.43
219	220	9.036980	AGAGTCCAATATTTACTTCTACAGTGT	57.963	33.333	0.00	0.0	35.97	3.55
269	270	1.001378	GTTCGAAGTTGGCATGTGCTT	60.001	47.619	0.00	0.0	41.70	3.91
304	305	2.159014	TGCCATCCTCGCGTAACTAAAT	60.159	45.455	5.77	0.0	0.00	1.40
653	655	1.077212	ATCCATGCACAGCCAGGTC	60.077	57.895	0.00	0.0	0.00	3.85
867	869	1.673400	ACACATGCGTTTGTTGCACTA	59.327	42.857	0.00	0.0	46.57	2.74
912	914	5.107104	GCTCATTGAAAAGTGTCACGATGTA	60.107	40.000	0.00	0.0	0.00	2.29
914	916	4.153986	GCTCATTGAAAAGTGTCACGATG	58.846	43.478	0.00	0.0	0.00	3.84
915	917	3.814842	TGCTCATTGAAAAGTGTCACGAT	59.185	39.130	0.00	0.0	0.00	3.73
927	929	1.621317	TCGTAGGTGGTGCTCATTGAA	59.379	47.619	0.00	0.0	0.00	2.69
1008	1010	1.318158	CCTCTGTTGGATGCTTGGGC	61.318	60.000	0.00	0.0	39.26	5.36
1052	1054	9.362151	ACCTCTCTCTTAGATGTTAAATCTAGG	57.638	37.037	0.00	0.0	29.64	3.02
1115	1117	4.580580	AGAACCAAGAGCAAACTAAAGTGG	59.419	41.667	0.00	0.0	0.00	4.00
1173	1175	2.955477	ATCCCTTTTAGGTCGACGAC	57.045	50.000	19.70	19.7	31.93	4.34
1174	1176	4.038402	GGATTATCCCTTTTAGGTCGACGA	59.962	45.833	9.92	0.0	31.93	4.20
1191	1193	3.627395	TGGTTTGCACTCTCGGATTAT	57.373	42.857	0.00	0.0	0.00	1.28
1248	1250	1.136252	CACACTACAACATGCACTCGC	60.136	52.381	0.00	0.0	39.24	5.03
1346	1348	2.540101	GCAGTAATCAGCGACATACACC	59.460	50.000	0.00	0.0	0.00	4.16
1533	1535	8.328758	ACATTTCTCCTTTGATTACCAGATACA	58.671	33.333	0.00	0.0	0.00	2.29
1653	1655	1.131303	ATCTTCCACCCCACAACCGA	61.131	55.000	0.00	0.0	0.00	4.69
1745	1747	7.416964	TGAAAGGAATCAAAACCAGAAAAGA	57.583	32.000	0.00	0.0	0.00	2.52
1768	1771	5.549347	TGTTTTCAATCCCCATTCACATTG	58.451	37.500	0.00	0.0	0.00	2.82
1903	1907	7.656707	ATGTTTATTTTTCACATGTCCAAGC	57.343	32.000	0.00	0.0	29.74	4.01
1939	1943	0.112412	ACCAACCCCAACTTAGCCAG	59.888	55.000	0.00	0.0	0.00	4.85
1947	1951	2.289819	TGTATCGAAGACCAACCCCAAC	60.290	50.000	0.00	0.0	42.51	3.77
1953	1957	7.715265	ATTATGATGTGTATCGAAGACCAAC	57.285	36.000	0.00	0.0	42.51	3.77
1955	1959	9.996554	ATTTATTATGATGTGTATCGAAGACCA	57.003	29.630	0.00	0.0	42.51	4.02
2278	2284	3.324846	AGCACCACTTCATCAACACTAGA	59.675	43.478	0.00	0.0	0.00	2.43
2332	2338	2.202797	CATGGTCCGAGTGCTCCG	60.203	66.667	0.00	0.0	0.00	4.63
2350	2356	4.006989	AGCAACCAAAGCGTAATATGACA	58.993	39.130	0.00	0.0	37.01	3.58
2373	2379	4.333926	CCTTTTTGGGCGAAAATTCAACAA	59.666	37.500	8.25	0.0	33.46	2.83
2433	2439	7.545615	GGAATGAACATATGGAAGAAAACCAAC	59.454	37.037	7.80	0.0	40.93	3.77
2518	2524	5.105106	TCACAGGGTTTAGATATTTCTCGCA	60.105	40.000	0.00	0.0	33.17	5.10
2627	2634	4.290155	CGAAATTGAAACCCAGACACAAG	58.710	43.478	0.00	0.0	0.00	3.16
2642	2649	4.153475	ACGTCAGATAACCAACCGAAATTG	59.847	41.667	0.00	0.0	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.