AutoCloner

Multiple sequence alignment - TraesCS7D01G404800

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	TraesCS7D01G404800	chr7D	100.000	2490	0	0	1	2490	522155686	522153197	0.000000e+00	4599.0
1	TraesCS7D01G404800	chr7D	79.583	480	59	15	1145	1586	521763944	521764422	8.650000e-80	307.0
2	TraesCS7D01G404800	chr7A	92.573	1737	73	20	706	2435	602658981	602657294	0.000000e+00	2442.0
3	TraesCS7D01G404800	chr7A	92.254	723	41	7	2	710	602659738	602659017	0.000000e+00	1011.0
4	TraesCS7D01G404800	chr7A	77.393	606	74	24	1227	1778	602099334	602099930	4.020000e-78	302.0
5	TraesCS7D01G404800	chr7A	98.980	98	1	0	2261	2358	602657189	602657286	2.550000e-40	176.0
6	TraesCS7D01G404800	chr7B	91.008	1101	45	21	706	1786	556333628	556332562	0.000000e+00	1435.0
7	TraesCS7D01G404800	chr7B	92.990	485	21	4	238	710	556334147	556333664	0.000000e+00	695.0
8	TraesCS7D01G404800	chr7B	78.488	688	84	24	1145	1778	555655994	555656671	2.320000e-105	392.0
9	TraesCS7D01G404800	chr7B	91.255	263	12	5	1	255	556335865	556335606	5.100000e-92	348.0
10	TraesCS7D01G404800	chr7B	88.768	276	27	3	2216	2490	556332229	556331957	3.970000e-88	335.0
11	TraesCS7D01G404800	chr7B	83.673	98	14	1	2395	2490	512684979	512685076	9.480000e-15	91.6
12	TraesCS7D01G404800	chr6D	88.221	416	45	3	1799	2212	123124339	123124752	6.190000e-136	494.0
13	TraesCS7D01G404800	chr6D	85.092	436	45	14	1792	2213	39568107	39567678	6.360000e-116	427.0
14	TraesCS7D01G404800	chr1D	87.844	436	34	9	1791	2212	460919094	460919524	6.190000e-136	494.0
15	TraesCS7D01G404800	chr5D	87.411	421	41	7	1799	2212	224321748	224321333	8.060000e-130	473.0
16	TraesCS7D01G404800	chr2B	87.167	413	47	5	1802	2212	170995201	170994793	4.850000e-127	464.0
17	TraesCS7D01G404800	chr4D	86.854	426	41	6	1799	2213	505256602	505256181	1.740000e-126	462.0
18	TraesCS7D01G404800	chr4D	83.834	433	54	12	1791	2212	126895970	126895543	4.990000e-107	398.0
19	TraesCS7D01G404800	chr4A	86.343	432	35	10	1799	2212	13256425	13256000	1.360000e-122	449.0
20	TraesCS7D01G404800	chr3D	86.571	417	41	8	1799	2212	360579810	360579406	1.760000e-121	446.0
21	TraesCS7D01G404800	chr2A	85.851	417	48	9	1797	2211	75050278	75050685	1.370000e-117	433.0
22	TraesCS7D01G404800	chr1A	83.841	427	51	9	1799	2212	63035244	63035665	8.350000e-105	390.0
23	TraesCS7D01G404800	chr1B	83.929	112	10	6	1029	1134	57435937	57435828	1.580000e-17	100.0

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	TraesCS7D01G404800	chr7D	522153197	522155686	2489	True	4599.00	4599	100.00000	1	2490	1	chr7D.!!$R1	2489
1	TraesCS7D01G404800	chr7A	602657294	602659738	2444	True	1726.50	2442	92.41350	2	2435	2	chr7A.!!$R1	2433
2	TraesCS7D01G404800	chr7A	602099334	602099930	596	False	302.00	302	77.39300	1227	1778	1	chr7A.!!$F1	551
3	TraesCS7D01G404800	chr7B	556331957	556335865	3908	True	703.25	1435	91.00525	1	2490	4	chr7B.!!$R1	2489
4	TraesCS7D01G404800	chr7B	555655994	555656671	677	False	392.00	392	78.48800	1145	1778	1	chr7B.!!$F2	633

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
945	2487	0.108804	TAAAAGACGAGCCTCCGCAG	60.109	55.0	0.0	0.0	37.52	5.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2380	4020	1.042559	CCAACAGTTTGGTGCACCCT	61.043	55.0	32.62	19.73	46.63	4.34	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
57	58	6.831976	AGGAAAATATGACACCAGACTATCC	58.168	40.000	0.00	0.00	0.00	2.59
75	76	9.349713	AGACTATCCAAACTAACAAATTGACAA	57.650	29.630	0.00	0.00	0.00	3.18
76	77	9.612620	GACTATCCAAACTAACAAATTGACAAG	57.387	33.333	0.00	0.00	0.00	3.16
83	84	9.743057	CAAACTAACAAATTGACAAGACCAATA	57.257	29.630	0.00	0.00	33.51	1.90
138	143	7.001674	TGCAACAGGAAAAGAAATACTCCTAA	58.998	34.615	0.00	0.00	36.10	2.69
229	240	0.987294	CTGCCCTGAAAAGAGGAGGA	59.013	55.000	0.00	0.00	34.69	3.71
232	243	1.073923	GCCCTGAAAAGAGGAGGACAA	59.926	52.381	0.00	0.00	34.69	3.18
326	1817	8.703604	TTTGTACTGATATACTGTTCTTCTGC	57.296	34.615	0.00	0.00	33.04	4.26
592	2091	4.286032	TCATGTACTCCTAGGCAACAGTTT	59.714	41.667	2.96	0.00	41.41	2.66
603	2102	3.132824	AGGCAACAGTTTCCTCCAAAAAG	59.867	43.478	0.00	0.00	41.41	2.27
643	2142	1.888512	TGGCAAATCTTGAAGGAGCAC	59.111	47.619	0.00	0.00	0.00	4.40
657	2156	0.463474	GAGCACCAGGGAATCTCTGC	60.463	60.000	4.21	0.00	0.00	4.26
776	2316	2.368221	ACCAGCAGGATTATCAGAGAGC	59.632	50.000	0.35	0.00	38.69	4.09
789	2329	9.316730	GATTATCAGAGAGCATTAATCCTGATC	57.683	37.037	0.00	2.24	40.53	2.92
812	2353	7.244886	TCTTGTGAGATATCAAAGGAGTGAA	57.755	36.000	5.32	0.00	0.00	3.18
819	2360	3.923017	ATCAAAGGAGTGAAAAAGGCG	57.077	42.857	0.00	0.00	0.00	5.52
942	2484	1.993370	CAGTTAAAAGACGAGCCTCCG	59.007	52.381	0.00	0.00	0.00	4.63
943	2485	0.720027	GTTAAAAGACGAGCCTCCGC	59.280	55.000	0.00	0.00	0.00	5.54
944	2486	0.319083	TTAAAAGACGAGCCTCCGCA	59.681	50.000	0.00	0.00	37.52	5.69
945	2487	0.108804	TAAAAGACGAGCCTCCGCAG	60.109	55.000	0.00	0.00	37.52	5.18
946	2488	2.100879	AAAAGACGAGCCTCCGCAGT	62.101	55.000	0.00	0.00	37.52	4.40
947	2489	2.493907	AAAGACGAGCCTCCGCAGTC	62.494	60.000	0.00	0.00	42.01	3.51
948	2490	4.500116	GACGAGCCTCCGCAGTCC	62.500	72.222	0.00	0.00	38.32	3.85
979	2521	3.071023	TCCACATCGGAGTTTCTCTGTTT	59.929	43.478	5.65	0.00	39.64	2.83
1016	2558	3.415212	CCAAGATGAAGAAAGGTGCTCA	58.585	45.455	0.00	0.00	0.00	4.26
1030	2572	1.140804	GCTCACGCTCTCTTCCTCC	59.859	63.158	0.00	0.00	0.00	4.30
1031	2573	1.319614	GCTCACGCTCTCTTCCTCCT	61.320	60.000	0.00	0.00	0.00	3.69
1032	2574	0.738389	CTCACGCTCTCTTCCTCCTC	59.262	60.000	0.00	0.00	0.00	3.71
1033	2575	0.681564	TCACGCTCTCTTCCTCCTCC	60.682	60.000	0.00	0.00	0.00	4.30
1086	2628	2.973899	GAAGCAGCTCGGACAGGA	59.026	61.111	0.00	0.00	0.00	3.86
1166	2708	4.084013	GCATGGTCAGTAGTTTGTGTACAC	60.084	45.833	19.36	19.36	0.00	2.90
1175	2718	4.008074	AGTTTGTGTACACCATCTCCTG	57.992	45.455	22.91	0.00	0.00	3.86
1205	2748	9.780413	GCTCTCAACTTTCTTGATATTTAAAGG	57.220	33.333	0.00	0.00	34.07	3.11
1221	2767	2.163454	AGGTCACCCTTGCCATGAA	58.837	52.632	0.00	0.00	38.13	2.57
1262	2808	0.326595	TCCTGGAATTGCCGCTTACA	59.673	50.000	0.00	0.00	40.66	2.41
1263	2809	1.173043	CCTGGAATTGCCGCTTACAA	58.827	50.000	0.00	0.00	40.66	2.41
1300	2862	2.690510	AGGCTCCTGGGGAAGCTC	60.691	66.667	0.00	0.00	0.00	4.09
1447	3015	1.000506	GTGACCTTCGTTCTGGCACTA	59.999	52.381	0.00	0.00	32.07	2.74
1457	3025	0.528017	TCTGGCACTAGTCTTCAGCG	59.472	55.000	0.00	0.00	0.00	5.18
1508	3086	1.652947	AAGTACTTGATCCGGGTGGT	58.347	50.000	7.48	0.00	36.30	4.16
1509	3087	2.537633	AGTACTTGATCCGGGTGGTA	57.462	50.000	0.00	0.00	36.30	3.25
1530	3108	6.430308	TGGTATACTGCTAGTATCTGTGTAGC	59.570	42.308	10.76	8.84	40.37	3.58
1736	3342	6.978343	AAAATGGAATTCAGACATTGCATG	57.022	33.333	7.93	0.00	42.54	4.06
1943	3549	7.770897	ACATGTGTGTAAAATTTTAGGGCAAAA	59.229	29.630	10.92	4.05	37.37	2.44
1961	3567	4.618227	GCAAAATACGTTGAAATGAGGGCT	60.618	41.667	0.00	0.00	0.00	5.19
1999	3605	7.054491	ACAAATCTGAGGCTTTTTAACACAT	57.946	32.000	0.00	0.00	0.00	3.21
2002	3608	7.472334	AATCTGAGGCTTTTTAACACATGAT	57.528	32.000	0.00	0.00	0.00	2.45
2069	3675	8.086522	CAGGTCTCATTTCAATGTTTTTCATCT	58.913	33.333	0.00	0.00	37.65	2.90
2109	3715	9.988350	CATACACATAACATCCTTGTTTACTTC	57.012	33.333	0.00	0.00	43.57	3.01
2112	3718	7.669722	ACACATAACATCCTTGTTTACTTCCAT	59.330	33.333	0.00	0.00	43.57	3.41
2114	3720	9.920946	ACATAACATCCTTGTTTACTTCCATAT	57.079	29.630	0.00	0.00	43.57	1.78
2457	4097	6.884280	ATTCATCGAAAAATCCCATAGTCC	57.116	37.500	0.00	0.00	0.00	3.85
2468	4108	1.559219	CCCATAGTCCCATGTGTCACA	59.441	52.381	8.40	8.40	0.00	3.58
2469	4109	2.026356	CCCATAGTCCCATGTGTCACAA	60.026	50.000	10.28	0.00	0.00	3.33
2474	4114	7.223584	CCATAGTCCCATGTGTCACAATAATA	58.776	38.462	10.28	0.42	0.00	0.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	8.647143	ATTGGTCTTGTCAATTTGTTAGTTTG	57.353	30.769	0.00	0.00	31.49	2.93
75	76	0.328258	GGCACCACTGGTATTGGTCT	59.672	55.000	0.00	0.00	44.54	3.85
76	77	0.328258	AGGCACCACTGGTATTGGTC	59.672	55.000	0.00	0.00	44.54	4.02
83	84	1.004745	CTATGGAAAGGCACCACTGGT	59.995	52.381	0.00	0.00	40.36	4.00
138	143	6.653740	GTGCTACAAAACCACCTTCTATTACT	59.346	38.462	0.00	0.00	0.00	2.24
275	1762	3.441572	GCAAGGACAACAGCTGTATCAAT	59.558	43.478	22.01	10.46	38.84	2.57
326	1817	3.318839	TGAGCCCAAGTTGACATTTTCTG	59.681	43.478	3.87	0.00	0.00	3.02
531	2030	4.321899	GCAGGCTGTAATGTGGAAAATCAA	60.322	41.667	17.16	0.00	0.00	2.57
532	2031	3.193267	GCAGGCTGTAATGTGGAAAATCA	59.807	43.478	17.16	0.00	0.00	2.57
539	2038	2.114670	CGGGCAGGCTGTAATGTGG	61.115	63.158	17.16	0.00	0.00	4.17
561	2060	5.059833	GCCTAGGAGTACATGATTTTGAGG	58.940	45.833	14.75	0.00	0.00	3.86
592	2091	5.421374	GCCTAGTACTAGACTTTTTGGAGGA	59.579	44.000	28.07	0.00	39.81	3.71
603	2102	3.759618	CCAGCTATGGCCTAGTACTAGAC	59.240	52.174	28.07	18.46	40.52	2.59
643	2142	1.817099	GCACGCAGAGATTCCCTGG	60.817	63.158	0.00	0.00	32.51	4.45
760	2300	7.846644	GGATTAATGCTCTCTGATAATCCTG	57.153	40.000	14.13	0.00	44.31	3.86
762	2302	7.619050	TCAGGATTAATGCTCTCTGATAATCC	58.381	38.462	6.49	13.77	46.42	3.01
776	2316	9.939802	TGATATCTCACAAGATCAGGATTAATG	57.060	33.333	3.98	0.00	41.46	1.90
789	2329	7.912056	TTTCACTCCTTTGATATCTCACAAG	57.088	36.000	3.98	1.67	0.00	3.16
812	2353	2.912624	GCTCTGTGCTGCGCCTTTT	61.913	57.895	11.12	0.00	38.95	2.27
819	2360	3.873883	GGATGCGCTCTGTGCTGC	61.874	66.667	9.73	10.14	40.03	5.25
833	2375	0.987294	CACTCTGTTGGGAGGTGGAT	59.013	55.000	0.00	0.00	37.63	3.41
942	2484	3.044305	GGAGTGTGTGCGGACTGC	61.044	66.667	8.99	0.00	46.70	4.40
943	2485	1.956170	GTGGAGTGTGTGCGGACTG	60.956	63.158	8.99	0.00	0.00	3.51
944	2486	1.758440	ATGTGGAGTGTGTGCGGACT	61.758	55.000	8.99	0.00	0.00	3.85
945	2487	1.291877	GATGTGGAGTGTGTGCGGAC	61.292	60.000	0.00	0.00	0.00	4.79
946	2488	1.005037	GATGTGGAGTGTGTGCGGA	60.005	57.895	0.00	0.00	0.00	5.54
947	2489	2.382746	CGATGTGGAGTGTGTGCGG	61.383	63.158	0.00	0.00	0.00	5.69
948	2490	2.382746	CCGATGTGGAGTGTGTGCG	61.383	63.158	0.00	0.00	42.00	5.34
979	2521	4.966787	GGGGCGGACTTGGTTGCA	62.967	66.667	0.00	0.00	0.00	4.08
1016	2558	0.395173	GAGGAGGAGGAAGAGAGCGT	60.395	60.000	0.00	0.00	0.00	5.07
1030	2572	0.251634	GCAAAGGTGAGGAGGAGGAG	59.748	60.000	0.00	0.00	0.00	3.69
1031	2573	0.178891	AGCAAAGGTGAGGAGGAGGA	60.179	55.000	0.00	0.00	0.00	3.71
1032	2574	0.695347	AAGCAAAGGTGAGGAGGAGG	59.305	55.000	0.00	0.00	0.00	4.30
1033	2575	1.339535	GGAAGCAAAGGTGAGGAGGAG	60.340	57.143	0.00	0.00	0.00	3.69
1068	2610	2.492449	TTCCTGTCCGAGCTGCTTCG	62.492	60.000	2.53	8.96	40.18	3.79
1082	2624	0.681887	TGCATCAGCCATGGTTCCTG	60.682	55.000	14.67	12.36	41.13	3.86
1106	2648	2.633967	AGATGAGGCCTCAGATGATGAC	59.366	50.000	37.03	20.01	43.61	3.06
1166	2708	2.746362	GTTGAGAGCAAACAGGAGATGG	59.254	50.000	0.00	0.00	35.42	3.51
1205	2748	1.598701	GGCTTCATGGCAAGGGTGAC	61.599	60.000	0.00	0.00	41.37	3.67
1221	2767	7.337942	CAGGAATACTTTTGTAAGAGATTGGCT	59.662	37.037	0.00	0.00	38.54	4.75
1262	2808	1.550869	CCTGCCTTGGGTTTCTGGATT	60.551	52.381	0.00	0.00	0.00	3.01
1263	2809	0.040204	CCTGCCTTGGGTTTCTGGAT	59.960	55.000	0.00	0.00	0.00	3.41
1434	3002	2.229062	CTGAAGACTAGTGCCAGAACGA	59.771	50.000	0.00	0.00	0.00	3.85
1447	3015	1.827969	AGAATGGTAGCGCTGAAGACT	59.172	47.619	22.90	9.48	0.00	3.24
1457	3025	2.815478	CACCGAGAGAAGAATGGTAGC	58.185	52.381	0.00	0.00	0.00	3.58
1508	3086	6.228995	ACGCTACACAGATACTAGCAGTATA	58.771	40.000	8.27	0.00	41.21	1.47
1509	3087	5.064558	ACGCTACACAGATACTAGCAGTAT	58.935	41.667	8.09	8.09	43.64	2.12
1530	3108	5.483213	CAAACAATTTCTGAAACTGCAACG	58.517	37.500	11.13	0.00	0.00	4.10
1631	3236	1.985159	TCTGGTACCTGCTGACCAAAT	59.015	47.619	14.36	0.00	45.03	2.32
1736	3342	3.377172	AGGAACATACGGCATTTTAGTGC	59.623	43.478	0.00	0.00	44.31	4.40
1798	3404	3.625764	TCGGCCTCCAAAGAAAATATTCG	59.374	43.478	0.00	0.00	40.63	3.34
1890	3496	3.931907	TGCCTGCAGGTATATCTTTGT	57.068	42.857	32.81	0.00	37.57	2.83
1902	3508	1.814394	ACATGTGTGTTATGCCTGCAG	59.186	47.619	6.78	6.78	34.01	4.41
1934	3540	5.124776	CCTCATTTCAACGTATTTTGCCCTA	59.875	40.000	0.00	0.00	0.00	3.53
1943	3549	3.009723	CACAGCCCTCATTTCAACGTAT	58.990	45.455	0.00	0.00	0.00	3.06
1972	3578	7.821846	TGTGTTAAAAAGCCTCAGATTTGTTTT	59.178	29.630	0.00	0.00	30.45	2.43
1973	3579	7.327214	TGTGTTAAAAAGCCTCAGATTTGTTT	58.673	30.769	0.00	0.00	30.45	2.83
1974	3580	6.872920	TGTGTTAAAAAGCCTCAGATTTGTT	58.127	32.000	0.00	0.00	30.45	2.83
1999	3605	7.103745	TGGTCTAGGAGGATGAATAGTATCA	57.896	40.000	0.00	0.00	0.00	2.15
2002	3608	7.103745	TCATGGTCTAGGAGGATGAATAGTA	57.896	40.000	0.00	0.00	0.00	1.82
2380	4020	1.042559	CCAACAGTTTGGTGCACCCT	61.043	55.000	32.62	19.73	46.63	4.34
2440	4080	4.036734	CACATGGGACTATGGGATTTTTCG	59.963	45.833	0.00	0.00	33.20	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.