AutoCloner

Multiple sequence alignment - TraesCS7B01G043000

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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	TraesCS7B01G043000	chr7B	100.000	3113	0	0	1	3113	42178607	42175495	0.000000e+00	5749.0
1	TraesCS7B01G043000	chr7B	82.918	2365	325	40	324	2641	42139948	42137616	0.000000e+00	2056.0
2	TraesCS7B01G043000	chr7A	94.583	3120	152	11	1	3113	94130567	94133676	0.000000e+00	4809.0
3	TraesCS7B01G043000	chr7A	94.366	2840	131	15	1	2814	93897719	93900555	0.000000e+00	4331.0
4	TraesCS7B01G043000	chr7A	82.892	2268	318	37	324	2562	94186025	94188251	0.000000e+00	1975.0
5	TraesCS7B01G043000	chr7A	82.023	2353	336	40	324	2631	94217234	94219544	0.000000e+00	1921.0
6	TraesCS7B01G043000	chr7A	75.835	1887	386	41	272	2113	63759735	63757874	0.000000e+00	894.0
7	TraesCS7B01G043000	chr7A	92.529	174	12	1	2870	3043	93900554	93900726	6.670000e-62	248.0
8	TraesCS7B01G043000	chr7D	94.631	2980	136	13	143	3113	91990592	91993556	0.000000e+00	4595.0
9	TraesCS7B01G043000	chr7D	75.648	1889	386	47	272	2113	59163136	59161275	0.000000e+00	872.0
10	TraesCS7B01G043000	chr4A	90.323	62	6	0	2645	2706	655050943	655050882	7.160000e-12	82.4

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	TraesCS7B01G043000	chr7B	42175495	42178607	3112	True	5749.0	5749	100.0000	1	3113	1	chr7B.!!$R2	3112
1	TraesCS7B01G043000	chr7B	42137616	42139948	2332	True	2056.0	2056	82.9180	324	2641	1	chr7B.!!$R1	2317
2	TraesCS7B01G043000	chr7A	94130567	94133676	3109	False	4809.0	4809	94.5830	1	3113	1	chr7A.!!$F1	3112
3	TraesCS7B01G043000	chr7A	93897719	93900726	3007	False	2289.5	4331	93.4475	1	3043	2	chr7A.!!$F4	3042
4	TraesCS7B01G043000	chr7A	94186025	94188251	2226	False	1975.0	1975	82.8920	324	2562	1	chr7A.!!$F2	2238
5	TraesCS7B01G043000	chr7A	94217234	94219544	2310	False	1921.0	1921	82.0230	324	2631	1	chr7A.!!$F3	2307
6	TraesCS7B01G043000	chr7A	63757874	63759735	1861	True	894.0	894	75.8350	272	2113	1	chr7A.!!$R1	1841
7	TraesCS7B01G043000	chr7D	91990592	91993556	2964	False	4595.0	4595	94.6310	143	3113	1	chr7D.!!$F1	2970
8	TraesCS7B01G043000	chr7D	59161275	59163136	1861	True	872.0	872	75.6480	272	2113	1	chr7D.!!$R1	1841

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
82	83	1.053424	AGAACCTTGGCACGAGGTAA	58.947	50.0	11.17	0.0	46.6	2.85	F
1040	1081	3.046390	GCTCAGCTATCACGTACATCAC	58.954	50.0	0.00	0.0	0.0	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1363	1404	0.328258	GTACCAGGGTGTTGCTCCAT	59.672	55.0	0.06	0.0	0.0	3.41	R
3022	3189	0.391661	GAGAAGATGAAGCGGGCACA	60.392	55.0	0.00	0.0	0.0	4.57	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
41	42	2.713828	AGGCCAATTTTGTAACCCCT	57.286	45.000	5.01	0.00	0.00	4.79
51	52	4.345859	TTTGTAACCCCTATATGAGCCG	57.654	45.455	0.00	0.00	0.00	5.52
77	78	1.080093	CGCTAGAACCTTGGCACGA	60.080	57.895	0.00	0.00	0.00	4.35
82	83	1.053424	AGAACCTTGGCACGAGGTAA	58.947	50.000	11.17	0.00	46.60	2.85
97	98	6.797995	GCACGAGGTAATTTAAAATTCGAACA	59.202	34.615	0.00	0.00	0.00	3.18
141	142	6.947464	AGTAGCTTATTTTCTAGTGAAGGCA	58.053	36.000	0.00	0.00	33.28	4.75
237	238	8.149647	AGATTTTGGATGTAACAAATTTGCTCA	58.850	29.630	18.12	14.01	37.62	4.26
615	621	7.275183	CCTACTACAAATTCACATGATCCAGA	58.725	38.462	0.00	0.00	0.00	3.86
1040	1081	3.046390	GCTCAGCTATCACGTACATCAC	58.954	50.000	0.00	0.00	0.00	3.06
1197	1238	4.457496	ACGCCATCTGCTGACCCG	62.457	66.667	0.00	1.87	38.05	5.28
1363	1404	7.339976	TCTCCATCAAGCATATGAAACAAATCA	59.660	33.333	6.97	0.00	32.06	2.57
1377	1418	2.173519	CAAATCATGGAGCAACACCCT	58.826	47.619	0.00	0.00	0.00	4.34
1438	1479	5.074584	ACTCAGTCCCGAAGATCTAAAAC	57.925	43.478	0.00	0.00	0.00	2.43
1513	1554	2.431419	CCATTGCATTATGGCCACAAGA	59.569	45.455	8.16	0.00	38.75	3.02
1618	1659	2.034532	TGCACTCACCATGGGCTG	59.965	61.111	18.09	6.33	0.00	4.85
1642	1683	2.127271	TCTGCCACAACACCATATGG	57.873	50.000	20.68	20.68	42.17	2.74
1754	1804	1.304381	TGCCACAGATTGCTTCCCC	60.304	57.895	0.00	0.00	0.00	4.81
1815	1865	4.831155	CCCCCACTAGATATAAGTGTCGAA	59.169	45.833	13.79	0.00	42.30	3.71
2043	2093	4.655963	CTTACATGGGCTATAATGGTGCT	58.344	43.478	0.00	0.00	0.00	4.40
2088	2138	0.335705	ATGGTGGATGGGTTGATGCA	59.664	50.000	0.00	0.00	0.00	3.96
2238	2288	8.083462	TCGAGGCAATAATATACATGTTCAAC	57.917	34.615	2.30	0.00	0.00	3.18
2256	2306	2.641783	CGTTCGACGTGTTGGACCG	61.642	63.158	0.00	0.00	36.74	4.79
2260	2310	1.372499	CGACGTGTTGGACCGTGAT	60.372	57.895	0.00	0.00	37.44	3.06
2402	2475	7.061566	TCTAGGTATTATGTGTTGCATAGCA	57.938	36.000	0.00	0.00	40.74	3.49
2414	2487	8.774890	TGTGTTGCATAGCATTTTCATTATTT	57.225	26.923	0.00	0.00	38.76	1.40
2688	2777	7.293299	TCATCCCACTACCATATTTCTCTTGAT	59.707	37.037	0.00	0.00	0.00	2.57
2691	2780	9.170890	TCCCACTACCATATTTCTCTTGATATT	57.829	33.333	0.00	0.00	0.00	1.28
2785	2892	3.637911	ATTTAGTACGCAACCATCCCA	57.362	42.857	0.00	0.00	0.00	4.37
2814	2922	8.074370	TCGTTTGATCTTCTGACTATATAACCG	58.926	37.037	0.00	0.00	0.00	4.44
2825	2933	1.339097	ATATAACCGCCGAGGAAGCT	58.661	50.000	3.89	0.00	45.00	3.74
2831	2939	0.806492	CCGCCGAGGAAGCTAAAGAC	60.806	60.000	0.00	0.00	45.00	3.01
2849	2957	8.230486	GCTAAAGACGCTTAATGCATATAACAT	58.770	33.333	0.00	0.00	43.06	2.71
2859	2967	8.939201	TTAATGCATATAACATGGTTGTTTGG	57.061	30.769	0.00	0.00	43.57	3.28
2867	2975	3.892284	ACATGGTTGTTTGGTCTACACA	58.108	40.909	0.00	0.00	29.55	3.72
2880	3045	4.231195	TGGTCTACACACCCTCCTATTCTA	59.769	45.833	0.00	0.00	35.26	2.10
2883	3048	6.183360	GGTCTACACACCCTCCTATTCTAAAG	60.183	46.154	0.00	0.00	0.00	1.85
2903	3068	1.269448	GCGAGCCATCACTTCCAAAAA	59.731	47.619	0.00	0.00	0.00	1.94
2934	3101	2.546899	TGTGGGCCACTCATTACTAGT	58.453	47.619	34.69	0.00	35.11	2.57
2969	3136	0.961857	AGCTCGATGTTGCATGCCAA	60.962	50.000	16.68	6.85	0.00	4.52
2984	3151	1.106351	GCCAACACCACCACACATCA	61.106	55.000	0.00	0.00	0.00	3.07
2990	3157	0.984230	ACCACCACACATCACCTAGG	59.016	55.000	7.41	7.41	0.00	3.02
3022	3189	2.040544	CGCCGACAATGCTTCCCTT	61.041	57.895	0.00	0.00	0.00	3.95
3054	3221	1.452651	CTTCTCATGGCCATGGCGT	60.453	57.895	38.81	18.52	43.06	5.68
3095	3262	1.604604	CACACCCGGAATGTTTCACT	58.395	50.000	0.73	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
97	98	4.561752	ACTCCCTCCAGCTGAGTTTATAT	58.438	43.478	17.39	0.00	39.65	0.86
141	142	6.279513	TGTTGTGAAAGAATGGACTTTTGT	57.720	33.333	0.00	0.00	39.71	2.83
356	358	4.165950	ACACATCCTCACCCATTAGCATTA	59.834	41.667	0.00	0.00	0.00	1.90
599	605	6.550938	TGAGTAGTCTGGATCATGTGAATT	57.449	37.500	0.00	0.00	0.00	2.17
603	609	5.482006	TGTTTGAGTAGTCTGGATCATGTG	58.518	41.667	0.00	0.00	0.00	3.21
1040	1081	4.152938	TGAAATCACGCTCTTTGTCATCAG	59.847	41.667	0.00	0.00	0.00	2.90
1363	1404	0.328258	GTACCAGGGTGTTGCTCCAT	59.672	55.000	0.06	0.00	0.00	3.41
1414	1455	4.720649	TTAGATCTTCGGGACTGAGTTG	57.279	45.455	0.00	0.00	0.00	3.16
1438	1479	8.768957	ACACGATAGATTTCATTGGATAGATG	57.231	34.615	0.00	0.00	41.38	2.90
1618	1659	0.537143	TGGTGTTGTGGCAGATGGTC	60.537	55.000	0.00	0.00	0.00	4.02
1642	1683	1.342174	TGGTGGTAGTGGAGACGAAAC	59.658	52.381	0.00	0.00	0.00	2.78
1643	1684	1.342174	GTGGTGGTAGTGGAGACGAAA	59.658	52.381	0.00	0.00	0.00	3.46
1754	1804	4.271049	CCTGATTAGATGTGGTTTGTAGCG	59.729	45.833	0.00	0.00	0.00	4.26
1815	1865	5.546499	TGGGTTGGAAGAACTTACATAGTCT	59.454	40.000	0.07	0.00	35.54	3.24
2009	2059	2.569059	CCATGTAAGCACCCATCTCTG	58.431	52.381	0.00	0.00	0.00	3.35
2043	2093	4.080919	CCCACAGAAGATTGTCCTACATCA	60.081	45.833	0.00	0.00	0.00	3.07
2088	2138	1.409427	CTAGAAGAAGATTCCGGCGGT	59.591	52.381	27.32	7.44	0.00	5.68
2269	2319	6.735678	AACACAATGTGACGCATAGATAAA	57.264	33.333	21.34	0.00	36.67	1.40
2311	2362	8.080417	CAGAACATGTCAACAAGAAGAATCAAT	58.920	33.333	0.00	0.00	0.00	2.57
2318	2369	4.556942	TGCAGAACATGTCAACAAGAAG	57.443	40.909	0.00	0.00	0.00	2.85
2375	2426	8.836413	GCTATGCAACACATAATACCTAGAAAA	58.164	33.333	0.00	0.00	40.75	2.29
2492	2566	9.898152	TGGTTGAATCACAATATACTAACATGA	57.102	29.630	0.00	0.00	40.76	3.07
2572	2646	3.904800	TGATCGTAGCAGGAATTGGAA	57.095	42.857	0.00	0.00	0.00	3.53
2752	2859	9.821662	GTTGCGTACTAAATTCAAGTTTTATCT	57.178	29.630	0.00	0.00	0.00	1.98
2764	2871	3.945285	CTGGGATGGTTGCGTACTAAATT	59.055	43.478	0.00	0.00	0.00	1.82
2785	2892	5.923733	ATAGTCAGAAGATCAAACGACCT	57.076	39.130	0.00	0.00	0.00	3.85
2814	2922	1.422179	GCGTCTTTAGCTTCCTCGGC	61.422	60.000	0.00	0.00	0.00	5.54
2831	2939	6.437928	ACAACCATGTTATATGCATTAAGCG	58.562	36.000	3.54	0.00	41.38	4.68
2849	2957	2.645802	GGTGTGTAGACCAAACAACCA	58.354	47.619	0.00	0.00	35.88	3.67
2859	2967	6.683360	GCTTTAGAATAGGAGGGTGTGTAGAC	60.683	46.154	0.00	0.00	0.00	2.59
2867	2975	2.365941	GCTCGCTTTAGAATAGGAGGGT	59.634	50.000	0.00	0.00	0.00	4.34
2883	3048	0.881118	TTTTGGAAGTGATGGCTCGC	59.119	50.000	0.00	0.00	0.00	5.03
2903	3068	1.675641	GGCCCACATCGAAGCTTGT	60.676	57.895	2.10	0.00	0.00	3.16
2934	3101	1.141657	GAGCTCCATCTTGGCATGGTA	59.858	52.381	0.87	0.00	43.62	3.25
2969	3136	1.347707	CTAGGTGATGTGTGGTGGTGT	59.652	52.381	0.00	0.00	0.00	4.16
3009	3176	1.187567	GGGCACAAGGGAAGCATTGT	61.188	55.000	0.00	0.00	40.18	2.71
3022	3189	0.391661	GAGAAGATGAAGCGGGCACA	60.392	55.000	0.00	0.00	0.00	4.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.