AutoCloner

Multiple sequence alignment - TraesCS2A01G464200

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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	TraesCS2A01G464200	chr2A	100.000	2493	0	0	1	2493	709839221	709836729	0.000000e+00	4604.0
1	TraesCS2A01G464200	chr2A	95.117	512	21	4	1	509	214741479	214741989	0.000000e+00	804.0
2	TraesCS2A01G464200	chr2B	94.129	1993	86	17	504	2493	683031312	683029348	0.000000e+00	3003.0
3	TraesCS2A01G464200	chr2D	93.684	1900	74	21	616	2493	571082514	571080639	0.000000e+00	2802.0
4	TraesCS2A01G464200	chr7A	96.844	507	14	2	1	505	162871150	162870644	0.000000e+00	846.0
5	TraesCS2A01G464200	chr4A	96.429	504	17	1	1	503	532214113	532213610	0.000000e+00	830.0
6	TraesCS2A01G464200	chr5A	95.635	504	21	1	1	503	448308367	448308870	0.000000e+00	808.0
7	TraesCS2A01G464200	chr5A	95.050	505	24	1	1	504	705763034	705762530	0.000000e+00	793.0
8	TraesCS2A01G464200	chr5A	94.152	513	16	11	1	506	657284504	657285009	0.000000e+00	769.0
9	TraesCS2A01G464200	chr4B	95.446	505	22	1	1	504	665799492	665798988	0.000000e+00	804.0
10	TraesCS2A01G464200	chr1A	95.069	507	22	3	1	505	305369902	305370407	0.000000e+00	795.0
11	TraesCS2A01G464200	chr3A	95.069	507	20	5	1	504	658057072	658057576	0.000000e+00	793.0
12	TraesCS2A01G464200	chr3B	97.959	49	1	0	527	575	68407074	68407122	4.420000e-13	86.1
13	TraesCS2A01G464200	chr3B	97.826	46	1	0	531	576	753679236	753679191	2.060000e-11	80.5
14	TraesCS2A01G464200	chr6D	93.617	47	3	0	527	573	436471686	436471640	1.240000e-08	71.3
15	TraesCS2A01G464200	chr6B	87.302	63	6	2	527	589	694429389	694429449	1.240000e-08	71.3
16	TraesCS2A01G464200	chr4D	90.566	53	4	1	528	579	297828566	297828618	4.450000e-08	69.4
17	TraesCS2A01G464200	chr1B	90.566	53	4	1	526	577	476928441	476928389	4.450000e-08	69.4
18	TraesCS2A01G464200	chr1B	86.364	66	4	5	515	576	22906909	22906973	1.600000e-07	67.6
19	TraesCS2A01G464200	chr1B	89.286	56	3	3	528	583	401443379	401443431	1.600000e-07	67.6

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	TraesCS2A01G464200	chr2A	709836729	709839221	2492	True	4604	4604	100.000	1	2493	1	chr2A.!!$R1	2492
1	TraesCS2A01G464200	chr2A	214741479	214741989	510	False	804	804	95.117	1	509	1	chr2A.!!$F1	508
2	TraesCS2A01G464200	chr2B	683029348	683031312	1964	True	3003	3003	94.129	504	2493	1	chr2B.!!$R1	1989
3	TraesCS2A01G464200	chr2D	571080639	571082514	1875	True	2802	2802	93.684	616	2493	1	chr2D.!!$R1	1877
4	TraesCS2A01G464200	chr7A	162870644	162871150	506	True	846	846	96.844	1	505	1	chr7A.!!$R1	504
5	TraesCS2A01G464200	chr4A	532213610	532214113	503	True	830	830	96.429	1	503	1	chr4A.!!$R1	502
6	TraesCS2A01G464200	chr5A	448308367	448308870	503	False	808	808	95.635	1	503	1	chr5A.!!$F1	502
7	TraesCS2A01G464200	chr5A	705762530	705763034	504	True	793	793	95.050	1	504	1	chr5A.!!$R1	503
8	TraesCS2A01G464200	chr5A	657284504	657285009	505	False	769	769	94.152	1	506	1	chr5A.!!$F2	505
9	TraesCS2A01G464200	chr4B	665798988	665799492	504	True	804	804	95.446	1	504	1	chr4B.!!$R1	503
10	TraesCS2A01G464200	chr1A	305369902	305370407	505	False	795	795	95.069	1	505	1	chr1A.!!$F1	504
11	TraesCS2A01G464200	chr3A	658057072	658057576	504	False	793	793	95.069	1	504	1	chr3A.!!$F1	503

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
775	795	0.328258	AGACACCGCCAGCCTATTTT	59.672	50.0	0.0	0.0	0.0	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2082	2117	0.249741	GCTGGGTTGTACTGTGTCGT	60.25	55.0	0.0	0.0	0.0	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
436	446	2.092103	AGTTAAGGGTGCAAGTTGTCCA	60.092	45.455	16.74	1.27	0.00	4.02
532	543	9.968870	GAAAAATAGTGTAAATTGGTTACCACA	57.031	29.630	2.39	0.00	41.35	4.17
539	550	5.828328	TGTAAATTGGTTACCACATGACACA	59.172	36.000	2.39	1.20	41.35	3.72
658	672	2.767505	GCGTCCATTATTAGAGGTGGG	58.232	52.381	0.00	0.00	32.58	4.61
663	677	5.883673	CGTCCATTATTAGAGGTGGGAAAAA	59.116	40.000	0.00	0.00	32.58	1.94
670	684	2.021457	AGAGGTGGGAAAAACAACGTG	58.979	47.619	0.00	0.00	0.00	4.49
733	747	4.452733	GACGGCCGGTGAGGAAGG	62.453	72.222	31.76	0.00	45.00	3.46
760	780	2.678934	CCGGTTCCGAGGGAGACA	60.679	66.667	13.08	0.00	31.21	3.41
775	795	0.328258	AGACACCGCCAGCCTATTTT	59.672	50.000	0.00	0.00	0.00	1.82
776	796	1.173913	GACACCGCCAGCCTATTTTT	58.826	50.000	0.00	0.00	0.00	1.94
807	827	3.306595	GAACGGACGAGGTTCCCCC	62.307	68.421	0.00	0.00	38.23	5.40
811	831	4.144703	GACGAGGTTCCCCCGCTC	62.145	72.222	0.00	0.00	38.74	5.03
814	834	3.327404	GAGGTTCCCCCGCTCCAA	61.327	66.667	0.00	0.00	38.74	3.53
815	835	3.330720	AGGTTCCCCCGCTCCAAG	61.331	66.667	0.00	0.00	38.74	3.61
817	837	4.344865	GTTCCCCCGCTCCAAGCA	62.345	66.667	0.00	0.00	42.58	3.91
818	838	4.344865	TTCCCCCGCTCCAAGCAC	62.345	66.667	0.00	0.00	42.58	4.40
991	1011	3.823330	CCTTCCTACTCGCGCGGT	61.823	66.667	31.69	26.87	0.00	5.68
1047	1073	2.150611	GCGTGCACGTTATACTGTATCG	59.849	50.000	36.80	10.07	42.22	2.92
1074	1100	1.595794	CGGGCGGTACATACAATTGAC	59.404	52.381	13.59	0.00	0.00	3.18
1096	1122	0.379316	GTGGTTGACGTGGTTGGTTC	59.621	55.000	0.00	0.00	0.00	3.62
1224	1250	1.599542	GCTTCACCGTCATATTCCAGC	59.400	52.381	0.00	0.00	0.00	4.85
1441	1471	1.528076	TGCATTGACGCCACCAACT	60.528	52.632	0.00	0.00	0.00	3.16
1480	1510	3.986054	TGGTTCTCCTGCACCAGT	58.014	55.556	0.00	0.00	38.20	4.00
1567	1597	0.456312	GACCAGAAGCACGTACTCGG	60.456	60.000	0.00	0.00	41.85	4.63
1586	1616	4.754667	GGGAGGCGACGGTGGAAC	62.755	72.222	0.00	0.00	0.00	3.62
1604	1634	1.154225	CTTTTGGCGATCGTGGTGC	60.154	57.895	17.81	0.00	0.00	5.01
1607	1637	1.573829	TTTGGCGATCGTGGTGCTTC	61.574	55.000	17.81	0.00	0.00	3.86
1610	1640	1.446099	GCGATCGTGGTGCTTCTGA	60.446	57.895	17.81	0.00	0.00	3.27
1641	1671	2.125952	CCGCATCTCACGTGCAGA	60.126	61.111	11.67	14.70	42.62	4.26
1650	1680	1.662629	CTCACGTGCAGAACATCATCC	59.337	52.381	11.67	0.00	0.00	3.51
1693	1723	9.722056	GTTGATCTGTATGAATAATTTGTGTCC	57.278	33.333	0.00	0.00	0.00	4.02
1856	1890	4.927425	CCTGGCAGACATTTGATTTGAAAG	59.073	41.667	17.94	0.00	0.00	2.62
1933	1968	8.468399	ACTTAGAAAAACAAAAACGGTATCCAA	58.532	29.630	0.00	0.00	0.00	3.53
1970	2005	9.710900	ATTGTGCATACGAGAATAATAATCTGA	57.289	29.630	0.00	0.00	0.00	3.27
2082	2117	7.281324	CACCAATAATCAGTTATTTACCGGACA	59.719	37.037	9.46	0.00	38.21	4.02
2099	2134	0.825410	ACACGACACAGTACAACCCA	59.175	50.000	0.00	0.00	0.00	4.51
2120	2155	1.470098	GCACCGTGATTGCAGAAAGAT	59.530	47.619	1.65	0.00	39.93	2.40
2124	2159	4.813161	CACCGTGATTGCAGAAAGATAGAT	59.187	41.667	0.00	0.00	0.00	1.98
2159	2194	2.987547	ATGCTGCGCCATATGCCC	60.988	61.111	4.18	0.00	36.24	5.36
2176	2211	1.214589	CCCCAACAGACCGAGTACG	59.785	63.158	0.00	0.00	39.43	3.67
2205	2240	5.068460	CACCATAACAACAGACCTCCAAAAA	59.932	40.000	0.00	0.00	0.00	1.94
2400	2435	0.607217	CTGCACTGCACCTCCATGAA	60.607	55.000	0.00	0.00	33.79	2.57
2447	2482	2.172505	ACCATGGTGAACAGAACTGTGA	59.827	45.455	18.99	0.00	44.13	3.58
2454	2489	6.764379	TGGTGAACAGAACTGTGAATATACA	58.236	36.000	8.25	0.38	44.13	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
436	446	3.662759	TTGGTCCCTCAACTTCAAACT	57.337	42.857	0.00	0.00	0.00	2.66
521	532	3.567585	CACATGTGTCATGTGGTAACCAA	59.432	43.478	25.74	0.00	44.04	3.67
532	543	3.696051	GGATTGCTTACCACATGTGTCAT	59.304	43.478	23.79	11.74	0.00	3.06
658	672	3.175152	TGCATGTGACACGTTGTTTTTC	58.825	40.909	0.00	0.00	0.00	2.29
663	677	1.378531	AACTGCATGTGACACGTTGT	58.621	45.000	0.00	0.00	0.00	3.32
775	795	1.448922	CCGTTCCTTTCCCACGCAAA	61.449	55.000	0.00	0.00	32.43	3.68
776	796	1.894756	CCGTTCCTTTCCCACGCAA	60.895	57.895	0.00	0.00	32.43	4.85
781	801	1.669440	CTCGTCCGTTCCTTTCCCA	59.331	57.895	0.00	0.00	0.00	4.37
811	831	2.916502	TATACTGCGGCCGTGCTTGG	62.917	60.000	28.70	12.62	35.36	3.61
812	832	1.087202	TTATACTGCGGCCGTGCTTG	61.087	55.000	28.70	14.45	35.36	4.01
813	833	0.391927	TTTATACTGCGGCCGTGCTT	60.392	50.000	28.70	11.42	35.36	3.91
814	834	0.391927	TTTTATACTGCGGCCGTGCT	60.392	50.000	28.70	11.43	35.36	4.40
815	835	0.247934	GTTTTATACTGCGGCCGTGC	60.248	55.000	28.70	11.88	0.00	5.34
816	836	0.025770	CGTTTTATACTGCGGCCGTG	59.974	55.000	28.70	21.79	0.00	4.94
817	837	0.108709	TCGTTTTATACTGCGGCCGT	60.109	50.000	28.70	9.89	0.00	5.68
818	838	0.575390	CTCGTTTTATACTGCGGCCG	59.425	55.000	24.05	24.05	0.00	6.13
819	839	0.935196	CCTCGTTTTATACTGCGGCC	59.065	55.000	0.00	0.00	0.00	6.13
820	840	0.935196	CCCTCGTTTTATACTGCGGC	59.065	55.000	0.00	0.00	0.00	6.53
821	841	1.578583	CCCCTCGTTTTATACTGCGG	58.421	55.000	0.00	0.00	0.00	5.69
822	842	0.935196	GCCCCTCGTTTTATACTGCG	59.065	55.000	0.00	0.00	0.00	5.18
855	875	2.758327	CGGGAGGGTGGTGATCGA	60.758	66.667	0.00	0.00	0.00	3.59
991	1011	2.052779	CCATGGCCATCGAGCTAGA	58.947	57.895	17.61	0.00	0.00	2.43
1047	1073	2.300850	TATGTACCGCCCGAACCAGC	62.301	60.000	0.00	0.00	0.00	4.85
1074	1100	1.444119	CCAACCACGTCAACCACAGG	61.444	60.000	0.00	0.00	0.00	4.00
1096	1122	2.280797	CCACACACACGACAGGGG	60.281	66.667	0.00	0.00	0.00	4.79
1302	1328	0.943835	GTTTTGATGGTGCCGTTGCC	60.944	55.000	0.00	0.00	36.33	4.52
1305	1331	1.657556	CGGTTTTGATGGTGCCGTT	59.342	52.632	0.00	0.00	37.87	4.44
1409	1439	2.159585	TCAATGCACGCGATAAACCAAG	60.160	45.455	15.93	0.00	0.00	3.61
1441	1471	2.290641	GCTCTTCTTCTGCGGACAAAAA	59.709	45.455	0.00	0.00	0.00	1.94
1480	1510	0.176910	TACGGCATCAGAATCGGCAA	59.823	50.000	0.00	0.00	0.00	4.52
1586	1616	1.154225	GCACCACGATCGCCAAAAG	60.154	57.895	16.60	1.68	0.00	2.27
1604	1634	3.382111	ACCGAGCAGGGTCAGAAG	58.618	61.111	3.26	0.00	46.96	2.85
1630	1660	1.662629	GGATGATGTTCTGCACGTGAG	59.337	52.381	22.23	13.81	0.00	3.51
1632	1662	1.441738	TGGATGATGTTCTGCACGTG	58.558	50.000	12.28	12.28	0.00	4.49
1650	1680	2.094026	TCAACGGGAGACATCACTCATG	60.094	50.000	0.00	0.00	38.51	3.07
1707	1741	5.640783	GGTCGTTTTACATAACTAGCCACTT	59.359	40.000	0.00	0.00	0.00	3.16
1712	1746	5.865552	TCACAGGTCGTTTTACATAACTAGC	59.134	40.000	0.00	0.00	0.00	3.42
1718	1752	5.603596	ACAAGTCACAGGTCGTTTTACATA	58.396	37.500	0.00	0.00	0.00	2.29
1720	1754	3.864243	ACAAGTCACAGGTCGTTTTACA	58.136	40.909	0.00	0.00	0.00	2.41
1887	1921	2.544267	GTGCTTTTTACTCGCTGTGTCT	59.456	45.455	0.00	0.00	0.00	3.41
1924	1959	8.227791	GCACAATATGTAATACTTTGGATACCG	58.772	37.037	0.00	0.00	0.00	4.02
1933	1968	9.758651	TTCTCGTATGCACAATATGTAATACTT	57.241	29.630	0.00	0.00	31.84	2.24
1970	2005	9.918630	CTAAAATTTTGACTGGAATTCAGACAT	57.081	29.630	13.76	0.00	44.79	3.06
2006	2041	8.506196	TTATTCCTCTAGGTGGTGCTATTATT	57.494	34.615	0.00	0.00	36.34	1.40
2007	2042	8.543774	CATTATTCCTCTAGGTGGTGCTATTAT	58.456	37.037	0.00	0.00	36.34	1.28
2082	2117	0.249741	GCTGGGTTGTACTGTGTCGT	60.250	55.000	0.00	0.00	0.00	4.34
2099	2134	0.877071	CTTTCTGCAATCACGGTGCT	59.123	50.000	2.51	0.00	42.69	4.40
2124	2159	6.200854	CGCAGCATGTTGATAAAGTAGACATA	59.799	38.462	14.38	0.00	39.31	2.29
2159	2194	4.883026	CGTACTCGGTCTGTTGGG	57.117	61.111	0.00	0.00	0.00	4.12
2176	2211	2.812011	GGTCTGTTGTTATGGTGTCACC	59.188	50.000	15.64	15.64	39.22	4.02
2205	2240	4.932200	CGAGCTTGTCTTACCTCAGAATTT	59.068	41.667	0.00	0.00	0.00	1.82
2400	2435	4.664062	CCGGGATGGCTTGTGATT	57.336	55.556	0.00	0.00	0.00	2.57
2439	2474	5.298347	GGGGTAGCTGTATATTCACAGTTC	58.702	45.833	0.00	0.27	46.31	3.01
2447	2482	2.708037	TCCGGGGGTAGCTGTATATT	57.292	50.000	0.00	0.00	0.00	1.28
2454	2489	2.446036	GTGGATCCGGGGGTAGCT	60.446	66.667	7.39	0.00	0.00	3.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.