AutoCloner

Multiple sequence alignment - TraesCS3A01G107300

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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	TraesCS3A01G107300	chr3A	100.000	2546	0	0	1	2546	71803051	71800506	0.000000e+00	4702.0
1	TraesCS3A01G107300	chr6A	98.536	1912	28	0	635	2546	6329903	6331814	0.000000e+00	3376.0
2	TraesCS3A01G107300	chr6A	83.483	557	89	3	1870	2424	1653874	1653319	1.350000e-142	516.0
3	TraesCS3A01G107300	chr3B	96.974	1917	50	3	637	2546	60508817	60506902	0.000000e+00	3212.0
4	TraesCS3A01G107300	chr3B	85.788	584	31	24	28	574	101802533	101801965	2.840000e-159	571.0
5	TraesCS3A01G107300	chr2B	92.863	1135	73	5	636	1766	676570761	676571891	0.000000e+00	1640.0
6	TraesCS3A01G107300	chr2B	93.472	965	51	7	637	1593	300261949	300262909	0.000000e+00	1423.0
7	TraesCS3A01G107300	chr2B	94.744	704	36	1	1776	2478	676572010	676572713	0.000000e+00	1094.0
8	TraesCS3A01G107300	chr3D	92.863	1135	70	6	637	1764	14412850	14411720	0.000000e+00	1637.0
9	TraesCS3A01G107300	chr3D	94.413	698	37	2	1783	2478	14411590	14410893	0.000000e+00	1072.0
10	TraesCS3A01G107300	chr3D	81.117	609	40	18	8	576	63010120	63009547	3.920000e-113	418.0
11	TraesCS3A01G107300	chr3D	100.000	31	0	0	2516	2546	14410881	14410851	9.840000e-05	58.4
12	TraesCS3A01G107300	chr7B	91.695	1168	54	17	636	1760	186594990	186593823	0.000000e+00	1580.0
13	TraesCS3A01G107300	chr4A	94.099	966	47	6	634	1593	668446368	668447329	0.000000e+00	1459.0
14	TraesCS3A01G107300	chr4A	88.395	810	63	19	999	1806	20269808	20270588	0.000000e+00	946.0
15	TraesCS3A01G107300	chr1B	94.031	955	46	8	827	1777	529514837	529513890	0.000000e+00	1437.0
16	TraesCS3A01G107300	chr1B	95.556	225	10	0	2254	2478	529513758	529513534	6.700000e-96	361.0
17	TraesCS3A01G107300	chr5D	94.879	703	36	0	1776	2478	475822887	475822185	0.000000e+00	1099.0
18	TraesCS3A01G107300	chr5D	94.310	703	39	1	1776	2478	408255605	408254904	0.000000e+00	1075.0
19	TraesCS3A01G107300	chr5D	100.000	31	0	0	2516	2546	408254892	408254862	9.840000e-05	58.4
20	TraesCS3A01G107300	chr5D	100.000	31	0	0	2516	2546	475822173	475822143	9.840000e-05	58.4
21	TraesCS3A01G107300	chr6D	94.737	703	37	0	1776	2478	289730328	289731030	0.000000e+00	1094.0
22	TraesCS3A01G107300	chr6D	90.086	696	42	9	1001	1686	289729471	289730149	0.000000e+00	878.0
23	TraesCS3A01G107300	chr6D	100.000	31	0	0	2516	2546	289731042	289731072	9.840000e-05	58.4
24	TraesCS3A01G107300	chr1D	94.310	703	40	0	1776	2478	445368344	445369046	0.000000e+00	1077.0
25	TraesCS3A01G107300	chr1D	85.075	335	33	10	637	955	445367167	445367500	2.440000e-85	326.0
26	TraesCS3A01G107300	chr1D	100.000	31	0	0	2516	2546	445369058	445369088	9.840000e-05	58.4
27	TraesCS3A01G107300	chr2A	92.450	755	44	11	1728	2478	70036340	70037085	0.000000e+00	1066.0
28	TraesCS3A01G107300	chr2A	85.799	338	26	8	636	955	70033414	70033747	3.140000e-89	339.0
29	TraesCS3A01G107300	chr2D	83.184	559	90	2	1870	2424	119011269	119011827	2.260000e-140	508.0

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	TraesCS3A01G107300	chr3A	71800506	71803051	2545	True	4702.000000	4702	100.000000	1	2546	1	chr3A.!!$R1	2545
1	TraesCS3A01G107300	chr6A	6329903	6331814	1911	False	3376.000000	3376	98.536000	635	2546	1	chr6A.!!$F1	1911
2	TraesCS3A01G107300	chr6A	1653319	1653874	555	True	516.000000	516	83.483000	1870	2424	1	chr6A.!!$R1	554
3	TraesCS3A01G107300	chr3B	60506902	60508817	1915	True	3212.000000	3212	96.974000	637	2546	1	chr3B.!!$R1	1909
4	TraesCS3A01G107300	chr3B	101801965	101802533	568	True	571.000000	571	85.788000	28	574	1	chr3B.!!$R2	546
5	TraesCS3A01G107300	chr2B	300261949	300262909	960	False	1423.000000	1423	93.472000	637	1593	1	chr2B.!!$F1	956
6	TraesCS3A01G107300	chr2B	676570761	676572713	1952	False	1367.000000	1640	93.803500	636	2478	2	chr2B.!!$F2	1842
7	TraesCS3A01G107300	chr3D	14410851	14412850	1999	True	922.466667	1637	95.758667	637	2546	3	chr3D.!!$R2	1909
8	TraesCS3A01G107300	chr3D	63009547	63010120	573	True	418.000000	418	81.117000	8	576	1	chr3D.!!$R1	568
9	TraesCS3A01G107300	chr7B	186593823	186594990	1167	True	1580.000000	1580	91.695000	636	1760	1	chr7B.!!$R1	1124
10	TraesCS3A01G107300	chr4A	668446368	668447329	961	False	1459.000000	1459	94.099000	634	1593	1	chr4A.!!$F2	959
11	TraesCS3A01G107300	chr4A	20269808	20270588	780	False	946.000000	946	88.395000	999	1806	1	chr4A.!!$F1	807
12	TraesCS3A01G107300	chr1B	529513534	529514837	1303	True	899.000000	1437	94.793500	827	2478	2	chr1B.!!$R1	1651
13	TraesCS3A01G107300	chr5D	475822143	475822887	744	True	578.700000	1099	97.439500	1776	2546	2	chr5D.!!$R2	770
14	TraesCS3A01G107300	chr5D	408254862	408255605	743	True	566.700000	1075	97.155000	1776	2546	2	chr5D.!!$R1	770
15	TraesCS3A01G107300	chr6D	289729471	289731072	1601	False	676.800000	1094	94.941000	1001	2546	3	chr6D.!!$F1	1545
16	TraesCS3A01G107300	chr1D	445367167	445369088	1921	False	487.133333	1077	93.128333	637	2546	3	chr1D.!!$F1	1909
17	TraesCS3A01G107300	chr2A	70033414	70037085	3671	False	702.500000	1066	89.124500	636	2478	2	chr2A.!!$F1	1842
18	TraesCS3A01G107300	chr2D	119011269	119011827	558	False	508.000000	508	83.184000	1870	2424	1	chr2D.!!$F1	554

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
627	628	0.025001	CGCGCAAGAACTACCGATTG	59.975	55.0	8.75	0.0	43.02	2.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1990	3980	0.109689	GCAGCAGCAGAAGCAAAGAG	60.11	55.0	0.0	0.0	45.49	2.85	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	3.465742	TCGTCGCCATCTACTACTACT	57.534	47.619	0.00	0.00	0.00	2.57
36	37	4.928615	GTCGCCATCTACTACTACTACGAT	59.071	45.833	0.00	0.00	0.00	3.73
47	48	3.499048	ACTACTACGATGTTTGCAGTCG	58.501	45.455	10.11	10.11	40.91	4.18
51	52	2.433868	ACGATGTTTGCAGTCGTACT	57.566	45.000	14.12	0.00	45.64	2.73
128	129	2.076863	CGAAACCGAGGAATGAAAGCT	58.923	47.619	0.00	0.00	0.00	3.74
132	133	1.065854	ACCGAGGAATGAAAGCTGGAG	60.066	52.381	0.00	0.00	0.00	3.86
133	134	1.208052	CCGAGGAATGAAAGCTGGAGA	59.792	52.381	0.00	0.00	0.00	3.71
134	135	2.355108	CCGAGGAATGAAAGCTGGAGAA	60.355	50.000	0.00	0.00	0.00	2.87
135	136	2.935201	CGAGGAATGAAAGCTGGAGAAG	59.065	50.000	0.00	0.00	0.00	2.85
136	137	3.277715	GAGGAATGAAAGCTGGAGAAGG	58.722	50.000	0.00	0.00	0.00	3.46
137	138	2.915604	AGGAATGAAAGCTGGAGAAGGA	59.084	45.455	0.00	0.00	0.00	3.36
138	139	3.331889	AGGAATGAAAGCTGGAGAAGGAA	59.668	43.478	0.00	0.00	0.00	3.36
139	140	3.441922	GGAATGAAAGCTGGAGAAGGAAC	59.558	47.826	0.00	0.00	0.00	3.62
140	141	3.795688	ATGAAAGCTGGAGAAGGAACA	57.204	42.857	0.00	0.00	0.00	3.18
141	142	3.131709	TGAAAGCTGGAGAAGGAACAG	57.868	47.619	0.00	0.00	35.40	3.16
142	143	2.705658	TGAAAGCTGGAGAAGGAACAGA	59.294	45.455	0.00	0.00	34.21	3.41
143	144	3.244353	TGAAAGCTGGAGAAGGAACAGAG	60.244	47.826	0.00	0.00	34.21	3.35
144	145	1.274712	AGCTGGAGAAGGAACAGAGG	58.725	55.000	0.00	0.00	34.21	3.69
145	146	0.251634	GCTGGAGAAGGAACAGAGGG	59.748	60.000	0.00	0.00	34.21	4.30
146	147	0.908198	CTGGAGAAGGAACAGAGGGG	59.092	60.000	0.00	0.00	34.21	4.79
147	148	0.547712	TGGAGAAGGAACAGAGGGGG	60.548	60.000	0.00	0.00	0.00	5.40
148	149	1.604915	GAGAAGGAACAGAGGGGGC	59.395	63.158	0.00	0.00	0.00	5.80
149	150	2.245438	GAGAAGGAACAGAGGGGGCG	62.245	65.000	0.00	0.00	0.00	6.13
150	151	3.330720	AAGGAACAGAGGGGGCGG	61.331	66.667	0.00	0.00	0.00	6.13
151	152	3.864983	AAGGAACAGAGGGGGCGGA	62.865	63.158	0.00	0.00	0.00	5.54

Showing 1 to 25 of 314 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.875908	TGGCGACGATTCATAGCAGC	60.876	55.000	0.00	0.00	0.00	5.25
2	3	1.341209	AGATGGCGACGATTCATAGCA	59.659	47.619	0.00	0.00	0.00	3.49
3	4	2.071688	AGATGGCGACGATTCATAGC	57.928	50.000	0.00	0.00	0.00	2.97
4	5	4.427096	AGTAGATGGCGACGATTCATAG	57.573	45.455	0.00	0.00	0.00	2.23
5	6	5.001874	AGTAGTAGATGGCGACGATTCATA	58.998	41.667	0.00	0.00	0.00	2.15
6	7	3.821600	AGTAGTAGATGGCGACGATTCAT	59.178	43.478	0.00	0.00	0.00	2.57
31	32	3.058085	TCAGTACGACTGCAAACATCGTA	60.058	43.478	14.58	14.58	46.63	3.43
36	37	1.497991	GCTCAGTACGACTGCAAACA	58.502	50.000	9.34	0.00	45.54	2.83
47	48	1.153745	CACCAGCCTCGCTCAGTAC	60.154	63.158	0.00	0.00	36.40	2.73
71	72	1.154543	AAAAATCGTTCCGTCGCGC	60.155	52.632	0.00	0.00	0.00	6.86
91	92	4.083749	GGTTTCGAGCTCCTTCTTTTTCTC	60.084	45.833	8.47	0.00	0.00	2.87
128	129	0.547712	CCCCCTCTGTTCCTTCTCCA	60.548	60.000	0.00	0.00	0.00	3.86
132	133	2.269241	CGCCCCCTCTGTTCCTTC	59.731	66.667	0.00	0.00	0.00	3.46
133	134	3.330720	CCGCCCCCTCTGTTCCTT	61.331	66.667	0.00	0.00	0.00	3.36
134	135	3.864983	TTCCGCCCCCTCTGTTCCT	62.865	63.158	0.00	0.00	0.00	3.36
135	136	3.327404	TTCCGCCCCCTCTGTTCC	61.327	66.667	0.00	0.00	0.00	3.62
136	137	2.269241	CTTCCGCCCCCTCTGTTC	59.731	66.667	0.00	0.00	0.00	3.18
137	138	3.330720	CCTTCCGCCCCCTCTGTT	61.331	66.667	0.00	0.00	0.00	3.16
138	139	3.864983	TTCCTTCCGCCCCCTCTGT	62.865	63.158	0.00	0.00	0.00	3.41
139	140	2.137177	TTTTCCTTCCGCCCCCTCTG	62.137	60.000	0.00	0.00	0.00	3.35
140	141	1.850755	TTTTCCTTCCGCCCCCTCT	60.851	57.895	0.00	0.00	0.00	3.69
141	142	1.378646	CTTTTCCTTCCGCCCCCTC	60.379	63.158	0.00	0.00	0.00	4.30
142	143	1.432023	TTCTTTTCCTTCCGCCCCCT	61.432	55.000	0.00	0.00	0.00	4.79
143	144	0.965866	CTTCTTTTCCTTCCGCCCCC	60.966	60.000	0.00	0.00	0.00	5.40
144	145	0.037734	TCTTCTTTTCCTTCCGCCCC	59.962	55.000	0.00	0.00	0.00	5.80

Showing 1 to 25 of 308 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.