AutoCloner

Multiple sequence alignment - TraesCS2A01G374900

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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	TraesCS2A01G374900	chr2A	100.000	2897	0	0	1	2897	617655512	617652616	0.000000e+00	5350
1	TraesCS2A01G374900	chr2A	85.802	162	22	1	2310	2471	731228750	731228910	1.380000e-38	171
2	TraesCS2A01G374900	chr3B	91.753	2122	149	11	777	2897	10657437	10659533	0.000000e+00	2926
3	TraesCS2A01G374900	chr3B	83.525	1912	288	19	995	2889	556880177	556882078	0.000000e+00	1760
4	TraesCS2A01G374900	chr3B	78.003	741	157	5	1000	1737	551518877	551519614	7.310000e-126	460
5	TraesCS2A01G374900	chr5A	80.687	1631	281	29	779	2393	21069718	21068106	0.000000e+00	1236
6	TraesCS2A01G374900	chr5A	89.084	513	54	2	2385	2897	21048653	21048143	1.130000e-178	636
7	TraesCS2A01G374900	chr2D	94.577	756	37	3	1	755	475093818	475093066	0.000000e+00	1166
8	TraesCS2A01G374900	chr2D	77.491	853	188	4	1031	1881	382466040	382465190	2.580000e-140	508
9	TraesCS2A01G374900	chr2B	93.378	740	35	5	24	756	556202752	556202020	0.000000e+00	1083
10	TraesCS2A01G374900	chr2B	77.114	887	197	6	1000	1883	549035863	549034980	2.580000e-140	508
11	TraesCS2A01G374900	chr2B	73.921	579	138	10	2311	2885	704323080	704323649	1.350000e-53	220
12	TraesCS2A01G374900	chr2B	77.716	359	70	10	2118	2471	646978176	646978529	8.130000e-51	211
13	TraesCS2A01G374900	chr3A	77.882	850	177	10	1037	1881	360861826	360860983	4.280000e-143	518
14	TraesCS2A01G374900	chr3A	74.601	689	173	2	1020	1707	264766749	264767436	4.690000e-78	302
15	TraesCS2A01G374900	chr1A	75.797	533	120	7	1032	1560	416679508	416678981	7.960000e-66	261
16	TraesCS2A01G374900	chr7A	86.709	158	21	0	2314	2471	126555458	126555615	2.970000e-40	176
17	TraesCS2A01G374900	chr4A	86.420	162	21	1	2310	2471	631909003	631908843	2.970000e-40	176
18	TraesCS2A01G374900	chr1B	86.709	158	21	0	2314	2471	141766104	141765947	2.970000e-40	176

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	TraesCS2A01G374900	chr2A	617652616	617655512	2896	True	5350	5350	100.000	1	2897	1	chr2A.!!$R1	2896
1	TraesCS2A01G374900	chr3B	10657437	10659533	2096	False	2926	2926	91.753	777	2897	1	chr3B.!!$F1	2120
2	TraesCS2A01G374900	chr3B	556880177	556882078	1901	False	1760	1760	83.525	995	2889	1	chr3B.!!$F3	1894
3	TraesCS2A01G374900	chr3B	551518877	551519614	737	False	460	460	78.003	1000	1737	1	chr3B.!!$F2	737
4	TraesCS2A01G374900	chr5A	21068106	21069718	1612	True	1236	1236	80.687	779	2393	1	chr5A.!!$R2	1614
5	TraesCS2A01G374900	chr5A	21048143	21048653	510	True	636	636	89.084	2385	2897	1	chr5A.!!$R1	512
6	TraesCS2A01G374900	chr2D	475093066	475093818	752	True	1166	1166	94.577	1	755	1	chr2D.!!$R2	754
7	TraesCS2A01G374900	chr2D	382465190	382466040	850	True	508	508	77.491	1031	1881	1	chr2D.!!$R1	850
8	TraesCS2A01G374900	chr2B	556202020	556202752	732	True	1083	1083	93.378	24	756	1	chr2B.!!$R2	732
9	TraesCS2A01G374900	chr2B	549034980	549035863	883	True	508	508	77.114	1000	1883	1	chr2B.!!$R1	883
10	TraesCS2A01G374900	chr2B	704323080	704323649	569	False	220	220	73.921	2311	2885	1	chr2B.!!$F2	574
11	TraesCS2A01G374900	chr3A	360860983	360861826	843	True	518	518	77.882	1037	1881	1	chr3A.!!$R1	844
12	TraesCS2A01G374900	chr3A	264766749	264767436	687	False	302	302	74.601	1020	1707	1	chr3A.!!$F1	687
13	TraesCS2A01G374900	chr1A	416678981	416679508	527	True	261	261	75.797	1032	1560	1	chr1A.!!$R1	528

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
884	895	0.037303	TCTACCCGTCAGAACTCGGT	59.963	55.0	0.0	0.0	44.51	4.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2006	2030	0.256177	GGTGTTCCCCTCCAAGGATC	59.744	60.0	0.0	0.0	37.67	3.36	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
48	49	3.944650	TGATTAGCGGCAAAATAAGCTCA	59.055	39.130	1.45	0.00	40.73	4.26
90	91	1.550976	GAATCTGAAGGACTGACGGGT	59.449	52.381	0.00	0.00	0.00	5.28
111	112	3.349006	CTGTTTCGCGCACCTGCT	61.349	61.111	8.75	0.00	39.32	4.24
278	280	1.918467	CTGATGGGAAGGCTCTGGCA	61.918	60.000	0.00	0.00	40.87	4.92
361	363	5.416947	AGTGTACAAAGATATGTTCCGACC	58.583	41.667	0.00	0.00	34.75	4.79
362	364	4.266976	GTGTACAAAGATATGTTCCGACCG	59.733	45.833	0.00	0.00	34.75	4.79
367	369	5.646360	ACAAAGATATGTTCCGACCGAAAAT	59.354	36.000	0.00	0.00	32.80	1.82
372	377	3.612472	TGTTCCGACCGAAAATTTGAC	57.388	42.857	0.00	0.00	30.39	3.18
398	403	5.178438	TCGGCAAATTGGAAGCAAATTTTAC	59.822	36.000	0.00	0.00	35.55	2.01
559	569	4.098914	TCTGACCATGGCTTAGTTTTGT	57.901	40.909	13.04	0.00	0.00	2.83
645	655	1.123861	AGACAGAAGCAGCCAGGACA	61.124	55.000	0.00	0.00	0.00	4.02
660	670	7.433680	CAGCCAGGACAAAATTTAAACTACTT	58.566	34.615	0.00	0.00	0.00	2.24
661	671	7.595130	CAGCCAGGACAAAATTTAAACTACTTC	59.405	37.037	0.00	0.00	0.00	3.01
762	772	8.865420	TCATTAGTCTACTCAACTAACTGACT	57.135	34.615	0.00	0.00	40.86	3.41
763	773	8.731605	TCATTAGTCTACTCAACTAACTGACTG	58.268	37.037	0.00	0.00	40.86	3.51
764	774	5.968528	AGTCTACTCAACTAACTGACTGG	57.031	43.478	0.00	0.00	32.90	4.00
765	775	4.767928	AGTCTACTCAACTAACTGACTGGG	59.232	45.833	0.00	0.00	32.90	4.45
766	776	4.765856	GTCTACTCAACTAACTGACTGGGA	59.234	45.833	0.00	0.00	0.00	4.37
767	777	5.243283	GTCTACTCAACTAACTGACTGGGAA	59.757	44.000	0.00	0.00	0.00	3.97
768	778	4.338379	ACTCAACTAACTGACTGGGAAC	57.662	45.455	0.00	0.00	0.00	3.62
769	779	3.243771	ACTCAACTAACTGACTGGGAACG	60.244	47.826	0.00	0.00	0.00	3.95
770	780	2.036733	TCAACTAACTGACTGGGAACGG	59.963	50.000	0.00	0.00	44.60	4.44
808	818	1.735386	GGCGACTTTAGGGTTTCTCC	58.265	55.000	0.00	0.00	0.00	3.71
837	847	1.778334	CGATGATCGCCGGAATTGTA	58.222	50.000	5.05	0.00	31.14	2.41
848	859	2.704065	CCGGAATTGTATAGTCCCTGGT	59.296	50.000	0.00	0.00	0.00	4.00
872	883	2.593725	TCTCGCCCGATCTACCCG	60.594	66.667	0.00	0.00	0.00	5.28
884	895	0.037303	TCTACCCGTCAGAACTCGGT	59.963	55.000	0.00	0.00	44.51	4.69
885	896	0.450983	CTACCCGTCAGAACTCGGTC	59.549	60.000	0.00	0.00	44.51	4.79
886	897	0.962356	TACCCGTCAGAACTCGGTCC	60.962	60.000	0.00	0.00	44.51	4.46
887	898	2.178521	CCGTCAGAACTCGGTCCG	59.821	66.667	4.39	4.39	41.58	4.79
888	899	2.330372	CCGTCAGAACTCGGTCCGA	61.330	63.158	14.54	14.54	41.58	4.55
889	900	1.654954	CCGTCAGAACTCGGTCCGAT	61.655	60.000	15.81	0.00	41.58	4.18
890	901	0.248134	CGTCAGAACTCGGTCCGATC	60.248	60.000	15.81	10.70	34.61	3.69
936	947	2.167662	CGGCCTTGGTTTTTGATAGGT	58.832	47.619	0.00	0.00	0.00	3.08
944	955	7.496747	CCTTGGTTTTTGATAGGTTTTCTCAA	58.503	34.615	0.00	0.00	0.00	3.02
962	973	3.521727	TCAAGGAGAGAGCTAGGGTTTT	58.478	45.455	0.00	0.00	0.00	2.43
1059	1070	1.226717	GTCGCCGGAAGAGCTACTG	60.227	63.158	5.05	0.00	0.00	2.74
1536	1554	4.097286	GCAGGTTTCTTTGGTGAGTTTGTA	59.903	41.667	0.00	0.00	0.00	2.41
1578	1598	4.824479	TGTACATGCCAAGATCAAGAGA	57.176	40.909	0.00	0.00	0.00	3.10
1743	1763	1.214175	TGGGGAGACTTTGTTCTTGCA	59.786	47.619	0.00	0.00	0.00	4.08
1759	1779	1.016627	TGCAGATAATGTGCGCTTCC	58.983	50.000	9.73	0.00	44.35	3.46
1830	1850	1.227674	GAATGCAGGCGGTAGAGGG	60.228	63.158	0.00	0.00	0.00	4.30
1892	1913	0.107410	AACGCACAACCCACTGAGAA	60.107	50.000	0.00	0.00	0.00	2.87
1895	1916	1.270094	CGCACAACCCACTGAGAACTA	60.270	52.381	0.00	0.00	0.00	2.24
1908	1929	0.108424	AGAACTAGAAGCAGCAGCCG	60.108	55.000	0.00	0.00	43.56	5.52
1912	1933	0.809241	CTAGAAGCAGCAGCCGGAAG	60.809	60.000	5.05	0.00	43.56	3.46
1918	1939	2.999648	AGCAGCCGGAAGAGCAGA	61.000	61.111	5.05	0.00	0.00	4.26
1929	1950	2.163211	GGAAGAGCAGAATCAGCAAACC	59.837	50.000	0.00	0.00	0.00	3.27
1943	1964	1.668751	GCAAACCAACTCGTTGTCAGA	59.331	47.619	8.77	0.00	38.85	3.27
1982	2003	2.183555	GGAGCCAAATGCAGCTGC	59.816	61.111	31.89	31.89	44.83	5.25
1994	2018	2.795175	GCAGCTGCAATGCTTGATAT	57.205	45.000	33.36	0.00	41.98	1.63
2003	2027	4.219070	TGCAATGCTTGATATTATGGCCTC	59.781	41.667	6.82	0.00	0.00	4.70
2006	2030	2.290260	TGCTTGATATTATGGCCTCGGG	60.290	50.000	3.32	0.00	0.00	5.14
2007	2031	2.027192	GCTTGATATTATGGCCTCGGGA	60.027	50.000	3.32	0.00	0.00	5.14
2078	2102	7.572861	AGATAATAATACACTCCCTGGAGGTTT	59.427	37.037	17.21	7.54	45.88	3.27
2169	2196	4.029809	GGGGTTCCACCACTCCCG	62.030	72.222	0.00	0.00	39.07	5.14
2236	2265	3.308046	GGGAGATGGCAAGAGGAATATCC	60.308	52.174	0.00	0.00	36.58	2.59
2258	2287	0.319900	TTCTCTGACGAACAGGCTGC	60.320	55.000	15.89	0.00	45.76	5.25
2396	2425	0.611714	GTCGTGGTGTGGGTAATCCT	59.388	55.000	0.00	0.00	36.20	3.24
2501	2530	0.685660	GGGTCGAGAAACTGAAGGGT	59.314	55.000	0.00	0.00	0.00	4.34
2519	2548	5.810080	AGGGTGAACTAGGTTATGATAGC	57.190	43.478	0.00	0.00	0.00	2.97
2555	2584	0.252284	GTGAGGGGAGAAGTGGAGGA	60.252	60.000	0.00	0.00	0.00	3.71
2577	2606	6.903534	AGGACTAGGTCTTTTCTGGAATGATA	59.096	38.462	0.00	0.00	32.47	2.15
2813	2842	1.351080	ATGATGGAGTGGGGCAGAGG	61.351	60.000	0.00	0.00	0.00	3.69
2846	2875	3.195610	AGATTGATGCGTTCAGGAGTGTA	59.804	43.478	0.00	0.00	35.27	2.90
2849	2878	3.086282	TGATGCGTTCAGGAGTGTAGTA	58.914	45.455	0.00	0.00	0.00	1.82
2891	2920	2.111251	GGCTATTCTGGTCCGGGC	59.889	66.667	0.00	0.00	0.00	6.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	49	3.248125	CACAATTTGAGCAATTTTGGCGT	59.752	39.130	2.79	0.00	32.24	5.68
90	91	1.005037	AGGTGCGCGAAACAGATGA	60.005	52.632	12.10	0.00	0.00	2.92
111	112	0.895100	GTGCTCCAATGACCCTGCAA	60.895	55.000	0.00	0.00	32.10	4.08
241	243	3.987547	TCAGAAGACACTCTTGCTGAAG	58.012	45.455	0.00	0.00	36.73	3.02
278	280	2.364324	TGGTCGTTGCTTTCTCAGTAGT	59.636	45.455	0.00	0.00	0.00	2.73
329	331	6.714810	ACATATCTTTGTACACTTCCTTTGCA	59.285	34.615	0.00	0.00	0.00	4.08
361	363	2.025544	TTGCCGACGTCAAATTTTCG	57.974	45.000	17.16	9.91	0.00	3.46
362	364	4.375908	CCAATTTGCCGACGTCAAATTTTC	60.376	41.667	22.75	1.25	46.15	2.29
367	369	1.309950	TCCAATTTGCCGACGTCAAA	58.690	45.000	17.16	6.51	37.75	2.69
372	377	0.039617	TTGCTTCCAATTTGCCGACG	60.040	50.000	0.00	0.00	0.00	5.12
398	403	5.678583	TCTTCAGATATCTTCAGGCCTTTG	58.321	41.667	0.00	0.00	0.00	2.77
513	522	8.491045	AAAATCCTAAGAAAAAGGAACCATGA	57.509	30.769	0.00	0.00	46.06	3.07
660	670	3.578282	TCAGAGCTTCTGTATGTGTTGGA	59.422	43.478	11.37	0.00	44.58	3.53
661	671	3.930336	TCAGAGCTTCTGTATGTGTTGG	58.070	45.455	11.37	0.00	44.58	3.77
690	700	3.489738	CCTTGGTTGCTGTCTCAAAACTG	60.490	47.826	0.00	0.00	0.00	3.16
736	746	9.469097	AGTCAGTTAGTTGAGTAGACTAATGAT	57.531	33.333	0.00	0.00	40.53	2.45
756	766	1.489230	AGAAAACCGTTCCCAGTCAGT	59.511	47.619	0.00	0.00	0.00	3.41
757	767	2.256117	AGAAAACCGTTCCCAGTCAG	57.744	50.000	0.00	0.00	0.00	3.51
758	768	2.721425	AAGAAAACCGTTCCCAGTCA	57.279	45.000	0.00	0.00	0.00	3.41
759	769	2.292569	GGAAAGAAAACCGTTCCCAGTC	59.707	50.000	0.00	0.00	44.43	3.51
760	770	2.304092	GGAAAGAAAACCGTTCCCAGT	58.696	47.619	0.00	0.00	44.43	4.00
765	775	3.504906	CCTTAGGGGAAAGAAAACCGTTC	59.495	47.826	0.00	0.00	37.23	3.95
766	776	3.493334	CCTTAGGGGAAAGAAAACCGTT	58.507	45.455	0.00	0.00	37.23	4.44
767	777	2.816712	GCCTTAGGGGAAAGAAAACCGT	60.817	50.000	0.00	0.00	37.23	4.83
768	778	1.816835	GCCTTAGGGGAAAGAAAACCG	59.183	52.381	0.00	0.00	37.23	4.44
769	779	1.816835	CGCCTTAGGGGAAAGAAAACC	59.183	52.381	9.98	0.00	37.91	3.27
808	818	2.349843	CGATCATCGCCGGAATACG	58.650	57.895	5.05	0.00	43.80	3.06
820	830	4.495422	GACTATACAATTCCGGCGATCAT	58.505	43.478	9.30	0.00	0.00	2.45
837	847	3.639094	CGAGAGAATCAACCAGGGACTAT	59.361	47.826	0.00	0.00	33.92	2.12
848	859	1.403814	AGATCGGGCGAGAGAATCAA	58.596	50.000	0.00	0.00	37.82	2.57
872	883	0.809385	TGATCGGACCGAGTTCTGAC	59.191	55.000	22.99	7.75	39.91	3.51
884	895	1.632164	AGGATCCCCCTTGATCGGA	59.368	57.895	8.55	0.00	44.85	4.55
885	896	4.320844	AGGATCCCCCTTGATCGG	57.679	61.111	8.55	0.00	44.85	4.18
984	995	2.093447	CGCCATCCTCTTCTAGTTTGGT	60.093	50.000	0.00	0.00	31.16	3.67
988	999	0.466124	GCCGCCATCCTCTTCTAGTT	59.534	55.000	0.00	0.00	0.00	2.24
990	1001	1.006805	CGCCGCCATCCTCTTCTAG	60.007	63.158	0.00	0.00	0.00	2.43
1059	1070	1.168714	CTTGCAGGTTAAGTCTGGCC	58.831	55.000	0.00	0.00	33.16	5.36
1466	1484	0.105964	TTCCCCAATACGAGATGCCG	59.894	55.000	0.00	0.00	0.00	5.69
1536	1554	4.223032	ACATCAATCTTCACCCGTACTCTT	59.777	41.667	0.00	0.00	0.00	2.85
1578	1598	4.104738	TCTCCCTTCTTTCCAGTCACAAAT	59.895	41.667	0.00	0.00	0.00	2.32
1743	1763	1.134818	TGTCGGAAGCGCACATTATCT	60.135	47.619	11.47	0.00	0.00	1.98
1759	1779	1.961180	CTACCCCTCCCTGCTTGTCG	61.961	65.000	0.00	0.00	0.00	4.35
1892	1913	1.544825	TTCCGGCTGCTGCTTCTAGT	61.545	55.000	15.64	0.00	39.59	2.57
1895	1916	2.046507	CTTCCGGCTGCTGCTTCT	60.047	61.111	15.64	0.00	39.59	2.85
1908	1929	2.163211	GGTTTGCTGATTCTGCTCTTCC	59.837	50.000	15.38	9.39	0.00	3.46
1912	1933	2.555757	AGTTGGTTTGCTGATTCTGCTC	59.444	45.455	15.38	7.08	0.00	4.26
1918	1939	2.687935	ACAACGAGTTGGTTTGCTGATT	59.312	40.909	18.66	0.00	44.45	2.57
1929	1950	3.124128	CACCATCATCTGACAACGAGTTG	59.876	47.826	13.76	13.76	45.58	3.16
1943	1964	1.361204	TGGTCCTGTCACACCATCAT	58.639	50.000	0.00	0.00	37.78	2.45
1984	2005	3.614092	CCGAGGCCATAATATCAAGCAT	58.386	45.455	5.01	0.00	0.00	3.79
1985	2006	2.290260	CCCGAGGCCATAATATCAAGCA	60.290	50.000	5.01	0.00	0.00	3.91
1990	2011	3.041946	AGGATCCCGAGGCCATAATATC	58.958	50.000	8.55	1.93	0.00	1.63
1994	2018	0.764890	CAAGGATCCCGAGGCCATAA	59.235	55.000	8.55	0.00	0.00	1.90
2003	2027	1.692749	TTCCCCTCCAAGGATCCCG	60.693	63.158	8.55	0.00	37.67	5.14
2006	2030	0.256177	GGTGTTCCCCTCCAAGGATC	59.744	60.000	0.00	0.00	37.67	3.36
2007	2031	0.477597	TGGTGTTCCCCTCCAAGGAT	60.478	55.000	0.00	0.00	37.67	3.24
2055	2079	6.445786	ACAAACCTCCAGGGAGTGTATTATTA	59.554	38.462	14.00	0.00	40.44	0.98
2169	2196	1.002087	CTTGGGGATACATAGACCGGC	59.998	57.143	0.00	0.00	39.74	6.13
2258	2287	2.037251	TCCTTGTCCTCTTTCCGTTCAG	59.963	50.000	0.00	0.00	0.00	3.02
2431	2460	7.716799	ATACATAATACGGTCGGGGTAAATA	57.283	36.000	0.00	0.00	0.00	1.40
2483	2512	1.343465	TCACCCTTCAGTTTCTCGACC	59.657	52.381	0.00	0.00	0.00	4.79
2501	2530	6.294010	CGTAGCTGCTATCATAACCTAGTTCA	60.294	42.308	13.20	0.00	0.00	3.18
2555	2584	9.981460	ATTTTATCATTCCAGAAAAGACCTAGT	57.019	29.630	0.00	0.00	0.00	2.57
2813	2842	1.674962	GCATCAATCTGTCCTTGGCTC	59.325	52.381	0.00	0.00	0.00	4.70
2846	2875	1.340991	ACCAGGGCGCAATCATTTACT	60.341	47.619	10.83	0.00	0.00	2.24
2849	2878	1.656818	CGACCAGGGCGCAATCATTT	61.657	55.000	10.83	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.