AutoCloner

Multiple sequence alignment - TraesCS4B01G109100

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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	TraesCS4B01G109100	chr4B	100.000	2913	0	0	1	2913	121450470	121453382	0.000000e+00	5380
1	TraesCS4B01G109100	chr4B	93.722	2915	175	7	1	2913	525795705	525792797	0.000000e+00	4362
2	TraesCS4B01G109100	chr4A	94.650	2916	151	5	1	2913	577319085	577321998	0.000000e+00	4516
3	TraesCS4B01G109100	chr4A	93.722	2915	175	6	1	2913	51976646	51979554	0.000000e+00	4362
4	TraesCS4B01G109100	chr2A	94.545	2915	154	5	1	2913	687877693	687874782	0.000000e+00	4497
5	TraesCS4B01G109100	chr2A	94.689	2730	138	6	1	2728	367831596	367828872	0.000000e+00	4231
6	TraesCS4B01G109100	chr1A	94.477	2915	154	6	1	2913	51037487	51034578	0.000000e+00	4484
7	TraesCS4B01G109100	chr3A	94.378	2917	149	11	1	2913	114345549	114342644	0.000000e+00	4464
8	TraesCS4B01G109100	chr2B	94.202	2915	160	6	1	2913	76309092	76311999	0.000000e+00	4438
9	TraesCS4B01G109100	chr2B	90.751	346	32	0	2559	2904	656567238	656567583	2.050000e-126	462
10	TraesCS4B01G109100	chr5A	94.168	2915	163	6	1	2912	370600389	370597479	0.000000e+00	4434

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	TraesCS4B01G109100	chr4B	121450470	121453382	2912	False	5380	5380	100.000	1	2913	1	chr4B.!!$F1	2912
1	TraesCS4B01G109100	chr4B	525792797	525795705	2908	True	4362	4362	93.722	1	2913	1	chr4B.!!$R1	2912
2	TraesCS4B01G109100	chr4A	577319085	577321998	2913	False	4516	4516	94.650	1	2913	1	chr4A.!!$F2	2912
3	TraesCS4B01G109100	chr4A	51976646	51979554	2908	False	4362	4362	93.722	1	2913	1	chr4A.!!$F1	2912
4	TraesCS4B01G109100	chr2A	687874782	687877693	2911	True	4497	4497	94.545	1	2913	1	chr2A.!!$R2	2912
5	TraesCS4B01G109100	chr2A	367828872	367831596	2724	True	4231	4231	94.689	1	2728	1	chr2A.!!$R1	2727
6	TraesCS4B01G109100	chr1A	51034578	51037487	2909	True	4484	4484	94.477	1	2913	1	chr1A.!!$R1	2912
7	TraesCS4B01G109100	chr3A	114342644	114345549	2905	True	4464	4464	94.378	1	2913	1	chr3A.!!$R1	2912
8	TraesCS4B01G109100	chr2B	76309092	76311999	2907	False	4438	4438	94.202	1	2913	1	chr2B.!!$F1	2912
9	TraesCS4B01G109100	chr5A	370597479	370600389	2910	True	4434	4434	94.168	1	2912	1	chr5A.!!$R1	2911

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
768	773	0.036875	AGGCAGGTGCAGTTAAGTCC	59.963	55.0	4.01	0.0	44.36	3.85	F
1166	1172	0.099968	CTCGTCCGTTCGGCTGATTA	59.900	55.0	6.35	0.0	0.00	1.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1585	1592	0.250295	CCTCCTCCACGAACAGCAAA	60.250	55.0	0.0	0.0	0.00	3.68	R
2545	2554	0.459237	ATCTCTCGTGCTTCCGCTTG	60.459	55.0	0.0	0.0	36.97	4.01	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
335	337	3.876309	AACTACAATCACCAGGGTGTT	57.124	42.857	17.46	7.26	45.55	3.32
362	366	8.999895	AGGTAGGCCAGAAGACTATTTTAATTA	58.000	33.333	5.01	0.00	37.19	1.40
427	431	6.181908	ACCCCAACGATTTTAAGCTTACATA	58.818	36.000	5.45	0.00	0.00	2.29
437	441	8.726870	ATTTTAAGCTTACATACACGGTACAT	57.273	30.769	5.45	0.00	0.00	2.29
447	451	5.715279	ACATACACGGTACATGCTATCCTAT	59.285	40.000	0.00	0.00	0.00	2.57
481	486	1.772063	GAAACTGCCACACGAGCGTT	61.772	55.000	0.00	0.00	0.00	4.84
515	520	0.461961	CTCTTCGCCTCTTCGGGAAT	59.538	55.000	0.00	0.00	0.00	3.01
522	527	1.674817	GCCTCTTCGGGAATTCGAACA	60.675	52.381	0.00	0.00	43.12	3.18
599	604	2.009051	CACCGATTGAACTGCTGCATA	58.991	47.619	1.31	0.00	0.00	3.14
701	706	1.152963	ACTCCTGCCTTTGCGTGTT	60.153	52.632	0.00	0.00	41.78	3.32
768	773	0.036875	AGGCAGGTGCAGTTAAGTCC	59.963	55.000	4.01	0.00	44.36	3.85
788	793	3.219052	CGCGAGGGAGAGGATAATAAC	57.781	52.381	0.00	0.00	0.00	1.89
993	999	0.257616	TGTAATACCCCAGCCCAAGC	59.742	55.000	0.00	0.00	40.32	4.01
1020	1026	2.741092	GTTGTGCACGAGGAGGGA	59.259	61.111	13.13	0.00	0.00	4.20
1034	1040	1.619827	GGAGGGAGAGATCATGCAGAG	59.380	57.143	0.00	0.00	0.00	3.35
1049	1055	1.682684	AGAGCGAACAGGACCCGAT	60.683	57.895	0.00	0.00	0.00	4.18
1058	1064	2.143419	AGGACCCGATGATGGAGCC	61.143	63.158	0.00	0.00	0.00	4.70
1070	1076	2.293184	TGATGGAGCCCTCTAAGGTCTT	60.293	50.000	0.00	0.00	31.93	3.01
1086	1092	0.895530	TCTTGATGGACCTCACCGTC	59.104	55.000	0.00	0.00	43.84	4.79
1166	1172	0.099968	CTCGTCCGTTCGGCTGATTA	59.900	55.000	6.35	0.00	0.00	1.75
1301	1307	2.125912	AGAAGTGCGAGCGCGATT	60.126	55.556	15.92	4.40	45.51	3.34
1340	1346	3.770040	CGGCGGTGGACTCCATCA	61.770	66.667	9.12	0.00	33.50	3.07
1427	1434	3.217242	GATCACCAGAGCGTGTGTT	57.783	52.632	0.00	0.00	35.18	3.32
1570	1577	2.198287	CCAGCTGCAAGTGCCACTT	61.198	57.895	8.66	3.74	39.39	3.16
1580	1587	1.675641	GTGCCACTTTCGGAGCCAT	60.676	57.895	0.00	0.00	0.00	4.40
1610	1617	3.881019	TTCGTGGAGGAGGACCGCT	62.881	63.158	0.00	0.00	41.83	5.52
1612	1619	2.997897	GTGGAGGAGGACCGCTGT	60.998	66.667	0.00	0.00	41.83	4.40
1651	1658	2.432456	GTGCTCGACATCGGTGCA	60.432	61.111	15.17	15.17	42.78	4.57
1841	1848	1.346068	AGGAGCTGACCTTCTTGACAC	59.654	52.381	0.00	0.00	36.86	3.67
1870	1877	4.424711	CTGCTGGCCGGGGCTAAA	62.425	66.667	22.12	5.87	41.60	1.85
1901	1908	4.330250	CCTCCACATTCAGATTGACAAGT	58.670	43.478	0.00	0.00	0.00	3.16
1932	1939	5.123979	CCTAAATGTTTCTACAGTGCCTTCC	59.876	44.000	0.00	0.00	37.77	3.46
2009	2016	4.293648	GGTGGGTTTTGGTGGCGC	62.294	66.667	0.00	0.00	0.00	6.53
2084	2092	4.824289	ACATGCATTGGTCAATTTTCTCC	58.176	39.130	0.00	0.00	0.00	3.71
2098	2106	8.462016	GTCAATTTTCTCCTAATACTTGCATGT	58.538	33.333	10.40	10.40	0.00	3.21
2122	2130	8.538701	TGTAATGATTTAATGCACCTTGGAATT	58.461	29.630	0.00	0.00	0.00	2.17
2316	2325	4.454161	CGTCACATTCCAAATTACTCCACA	59.546	41.667	0.00	0.00	0.00	4.17
2432	2441	0.529337	AGATGACTGCGCATTCCTCG	60.529	55.000	23.06	7.89	0.00	4.63
2545	2554	3.859414	AGGGAGAGGCGAGCATGC	61.859	66.667	10.51	10.51	0.00	4.06
2806	2815	1.177256	AGGCGACGACTGTTACAGGT	61.177	55.000	17.21	5.65	35.51	4.00
2808	2817	1.007336	GCGACGACTGTTACAGGTGG	61.007	60.000	17.21	8.14	35.51	4.61
2830	2839	0.668706	GCATGCGATCGTCCATAGCT	60.669	55.000	17.81	0.00	34.33	3.32
2868	2877	3.329889	TGGGCGAGGTTGCAGGAT	61.330	61.111	0.00	0.00	36.28	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
280	282	9.814899	CATCTGGTCAAGACAGGAATATATATC	57.185	37.037	2.29	0.00	37.88	1.63
335	337	7.983166	TTAAAATAGTCTTCTGGCCTACCTA	57.017	36.000	3.32	0.00	36.63	3.08
384	388	1.146930	CGGCTCCATGCTATGTGGT	59.853	57.895	0.00	0.00	42.39	4.16
427	431	5.322754	AGTATAGGATAGCATGTACCGTGT	58.677	41.667	0.00	0.00	0.00	4.49
437	441	8.603304	TCATGTGTAGAGTAGTATAGGATAGCA	58.397	37.037	0.00	0.00	0.00	3.49
447	451	5.479027	TGGCAGTTTCATGTGTAGAGTAGTA	59.521	40.000	0.00	0.00	0.00	1.82
515	520	6.811665	CAGTAGTACTCCATCATTTGTTCGAA	59.188	38.462	0.00	0.00	0.00	3.71
522	527	5.423015	CAGTGCAGTAGTACTCCATCATTT	58.577	41.667	0.00	0.00	38.75	2.32
701	706	1.613928	TATCGGGCCCACCTGTCAA	60.614	57.895	24.92	0.00	43.58	3.18
768	773	2.557056	TGTTATTATCCTCTCCCTCGCG	59.443	50.000	0.00	0.00	0.00	5.87
786	791	4.233123	TCGTACATCAACGAGAAGTGTT	57.767	40.909	0.00	0.00	46.29	3.32
993	999	1.354337	CGTGCACAACCATCTCTCGG	61.354	60.000	18.64	0.00	0.00	4.63
1020	1026	1.479730	TGTTCGCTCTGCATGATCTCT	59.520	47.619	0.00	0.00	0.00	3.10
1034	1040	1.144057	ATCATCGGGTCCTGTTCGC	59.856	57.895	0.00	0.00	0.00	4.70
1049	1055	1.794714	GACCTTAGAGGGCTCCATCA	58.205	55.000	3.28	0.00	41.45	3.07
1086	1092	2.034687	CACAAGGGGCAGTGGAGG	59.965	66.667	0.00	0.00	32.24	4.30
1166	1172	2.760092	TCAAGAAAACTGCACCTTGCTT	59.240	40.909	0.00	0.00	45.31	3.91
1179	1185	5.008514	TCGAACAGCACATCAATCAAGAAAA	59.991	36.000	0.00	0.00	0.00	2.29
1299	1305	1.647545	CCGCACATCGAAGCCACAAT	61.648	55.000	0.00	0.00	41.67	2.71
1301	1307	2.723586	TTCCGCACATCGAAGCCACA	62.724	55.000	0.00	0.00	41.67	4.17
1340	1346	1.189524	TCCACCCTCACCGACGAAAT	61.190	55.000	0.00	0.00	0.00	2.17
1580	1587	0.749818	TCCACGAACAGCAAAAGCCA	60.750	50.000	0.00	0.00	0.00	4.75
1585	1592	0.250295	CCTCCTCCACGAACAGCAAA	60.250	55.000	0.00	0.00	0.00	3.68
1610	1617	0.378962	CCGACCAAGAAAAACGCACA	59.621	50.000	0.00	0.00	0.00	4.57
1612	1619	1.357334	GCCGACCAAGAAAAACGCA	59.643	52.632	0.00	0.00	0.00	5.24
1651	1658	1.699656	CGACCGACACGACGATAGGT	61.700	60.000	0.00	5.07	43.77	3.08
1841	1848	3.437795	CAGCAGCTTGGGCGGAAG	61.438	66.667	0.00	0.00	44.37	3.46
1901	1908	6.422701	CACTGTAGAAACATTTAGGACGTGAA	59.577	38.462	0.00	0.00	34.37	3.18
2055	2062	8.761575	AAAATTGACCAATGCATGTACTTTAG	57.238	30.769	0.00	0.00	0.00	1.85
2098	2106	9.381033	CAAATTCCAAGGTGCATTAAATCATTA	57.619	29.630	0.00	0.00	0.00	1.90
2122	2130	2.739943	TGTTCCCCAACACATGTTCAA	58.260	42.857	0.00	0.00	37.61	2.69
2316	2325	8.028938	GTGAACAGGTTTGCAATTCAATATAGT	58.971	33.333	12.67	0.00	34.12	2.12
2432	2441	4.338118	TGTTTTTGTGGATGAGGAGTTGAC	59.662	41.667	0.00	0.00	0.00	3.18
2545	2554	0.459237	ATCTCTCGTGCTTCCGCTTG	60.459	55.000	0.00	0.00	36.97	4.01
2607	2616	1.548269	GACCTCTGTGCTGCTACTTCT	59.452	52.381	0.00	0.00	0.00	2.85
2711	2720	2.970379	ATGGCACGGCAGGACATCA	61.970	57.895	0.00	0.00	0.00	3.07
2806	2815	1.595109	GGACGATCGCATGCATCCA	60.595	57.895	19.57	0.00	0.00	3.41
2808	2817	1.657594	CTATGGACGATCGCATGCATC	59.342	52.381	19.57	17.28	0.00	3.91
2868	2877	2.844946	TCAAACGAGGCTTTCATGTCA	58.155	42.857	0.00	0.00	0.00	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.