AutoCloner

Multiple sequence alignment - TraesCS3B01G075300

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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	TraesCS3B01G075300	chr3B	100.000	3248	0	0	1	3248	46280462	46283709	0.000000e+00	5999.0
1	TraesCS3B01G075300	chr3B	89.742	1394	115	11	1757	3135	47454002	47452622	0.000000e+00	1757.0
2	TraesCS3B01G075300	chr3A	93.978	2906	154	13	348	3248	38022924	38020035	0.000000e+00	4377.0
3	TraesCS3B01G075300	chr3A	90.397	2343	183	10	911	3248	38047518	38045213	0.000000e+00	3042.0
4	TraesCS3B01G075300	chr3A	90.108	1395	109	14	1757	3135	38253307	38251926	0.000000e+00	1784.0
5	TraesCS3B01G075300	chr3A	90.036	1375	128	7	1662	3036	38035822	38034457	0.000000e+00	1772.0
6	TraesCS3B01G075300	chr3A	90.864	602	31	11	271	861	38048117	38047529	0.000000e+00	785.0
7	TraesCS3B01G075300	chr3A	78.975	1132	152	53	427	1518	38037162	38036077	0.000000e+00	693.0
8	TraesCS3B01G075300	chr3A	78.033	610	105	22	933	1519	10532107	10531504	1.110000e-94	357.0
9	TraesCS3B01G075300	chr3A	91.429	70	6	0	433	502	38261946	38261877	2.670000e-16	97.1
10	TraesCS3B01G075300	chr3D	92.966	2758	153	22	235	2986	28136304	28133582	0.000000e+00	3980.0
11	TraesCS3B01G075300	chr3D	88.443	2968	285	38	16	2971	27650703	27653624	0.000000e+00	3528.0
12	TraesCS3B01G075300	chr3D	91.015	2493	200	13	636	3123	28131090	28128617	0.000000e+00	3341.0
13	TraesCS3B01G075300	chr3D	90.215	1533	132	14	1718	3248	27656714	27658230	0.000000e+00	1984.0
14	TraesCS3B01G075300	chr3D	80.318	1133	152	33	421	1519	27655417	27656512	0.000000e+00	791.0
15	TraesCS3B01G075300	chr3D	81.175	749	80	32	15	761	27758878	27759567	2.200000e-151	545.0
16	TraesCS3B01G075300	chr2B	74.099	444	93	15	1087	1518	634171876	634172309	2.590000e-36	163.0

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	TraesCS3B01G075300	chr3B	46280462	46283709	3247	False	5999.0	5999	100.000000	1	3248	1	chr3B.!!$F1	3247
1	TraesCS3B01G075300	chr3B	47452622	47454002	1380	True	1757.0	1757	89.742000	1757	3135	1	chr3B.!!$R1	1378
2	TraesCS3B01G075300	chr3A	38020035	38022924	2889	True	4377.0	4377	93.978000	348	3248	1	chr3A.!!$R2	2900
3	TraesCS3B01G075300	chr3A	38045213	38048117	2904	True	1913.5	3042	90.630500	271	3248	2	chr3A.!!$R6	2977
4	TraesCS3B01G075300	chr3A	38251926	38253307	1381	True	1784.0	1784	90.108000	1757	3135	1	chr3A.!!$R3	1378
5	TraesCS3B01G075300	chr3A	38034457	38037162	2705	True	1232.5	1772	84.505500	427	3036	2	chr3A.!!$R5	2609
6	TraesCS3B01G075300	chr3A	10531504	10532107	603	True	357.0	357	78.033000	933	1519	1	chr3A.!!$R1	586
7	TraesCS3B01G075300	chr3D	28128617	28136304	7687	True	3660.5	3980	91.990500	235	3123	2	chr3D.!!$R1	2888
8	TraesCS3B01G075300	chr3D	27650703	27658230	7527	False	2101.0	3528	86.325333	16	3248	3	chr3D.!!$F2	3232
9	TraesCS3B01G075300	chr3D	27758878	27759567	689	False	545.0	545	81.175000	15	761	1	chr3D.!!$F1	746

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	Hairpin	End Stability	Orientation
218	235	0.327924	TTCAATCCTGTCCACGGCAT	59.672	50.0	0.00	0.00	4.40	F
871	922	0.472471	TTCCACACAAGGACCCTGTC	59.528	55.0	0.00	37.42	3.51	F
1313	1416	0.669077	GTCAGTACTCGATCGCCCAT	59.331	55.0	11.09	0.00	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1521	1624	0.317160	TTGTCGTGCTCCCAGTACAG	59.683	55.000	29.68	2.74	R
1694	1908	1.000396	GCAGGCAGGGGACTTTCAT	60.000	57.895	40.21	2.57	R
2532	11930	1.069159	ACGCCGAAGCTGTAGATATCG	60.069	52.381	36.60	2.92	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
30	31	9.443283	CTGCAAAATATTCACTGCTTAGTAATC	57.557	33.333	14.60	0.00	35.78	1.75
205	222	0.811616	ACCAGCCGCGAGATTCAATC	60.812	55.000	8.23	0.00	0.00	2.67
218	235	0.327924	TTCAATCCTGTCCACGGCAT	59.672	50.000	0.00	0.00	0.00	4.40
230	247	4.523173	TGTCCACGGCATAACCAAAATAAA	59.477	37.500	0.00	0.00	39.03	1.40
294	318	8.494016	AAACAGCTATACCAATAAACAGAGAC	57.506	34.615	0.00	0.00	0.00	3.36
318	342	4.647424	TCGCAAAGATCACAAGGTTTTT	57.353	36.364	0.00	0.00	0.00	1.94
322	346	4.440880	CAAAGATCACAAGGTTTTTGCCA	58.559	39.130	0.00	0.00	0.00	4.92
366	394	2.164624	AGAGTTATGGCGAGTGAGACAC	59.835	50.000	0.00	0.00	34.10	3.67
372	400	4.868195	CGAGTGAGACACGCATGA	57.132	55.556	0.00	0.00	39.64	3.07
379	411	5.776955	AGTGAGACACGCATGACTCCATG	62.777	52.174	9.62	0.00	44.17	3.66
419	451	0.605589	ATGATAGCTAGGCCAGTCGC	59.394	55.000	5.01	0.80	0.00	5.19
560	605	5.384063	AATGCCGTGACAAATCATAACAA	57.616	34.783	0.00	0.00	37.14	2.83
648	693	6.717997	CACAGTTAGGGTTTATGGTTTAGGTT	59.282	38.462	0.00	0.00	0.00	3.50
661	706	7.865706	ATGGTTTAGGTTTACATCAGCTTAG	57.134	36.000	0.00	0.00	0.00	2.18
747	793	9.672086	CATTATTTTTCTTTGGAAGACGTACAA	57.328	29.630	0.00	0.00	37.23	2.41
819	870	5.419542	TCAAACAGTCATGGCTATAGACAC	58.580	41.667	11.42	0.00	34.80	3.67
861	912	3.218453	ACCGTTGAATGATTCCACACAA	58.782	40.909	9.63	0.00	0.00	3.33
862	913	3.253188	ACCGTTGAATGATTCCACACAAG	59.747	43.478	9.63	0.00	0.00	3.16
863	914	3.366273	CCGTTGAATGATTCCACACAAGG	60.366	47.826	9.63	0.00	32.17	3.61
864	915	3.501828	CGTTGAATGATTCCACACAAGGA	59.498	43.478	9.63	0.00	33.11	3.36
865	916	4.613622	CGTTGAATGATTCCACACAAGGAC	60.614	45.833	9.63	0.00	37.42	3.85
866	917	3.420893	TGAATGATTCCACACAAGGACC	58.579	45.455	2.26	0.00	37.42	4.46
867	918	2.514458	ATGATTCCACACAAGGACCC	57.486	50.000	0.00	0.00	37.42	4.46
868	919	1.444933	TGATTCCACACAAGGACCCT	58.555	50.000	0.00	0.00	37.42	4.34
869	920	1.073763	TGATTCCACACAAGGACCCTG	59.926	52.381	0.00	0.00	37.42	4.45
870	921	1.073923	GATTCCACACAAGGACCCTGT	59.926	52.381	0.00	0.00	37.42	4.00
871	922	0.472471	TTCCACACAAGGACCCTGTC	59.528	55.000	0.00	0.00	37.42	3.51
907	974	4.030913	TCTACAATCCCCTACCACTCTTG	58.969	47.826	0.00	0.00	0.00	3.02
908	975	2.632537	ACAATCCCCTACCACTCTTGT	58.367	47.619	0.00	0.00	0.00	3.16
959	1043	7.981102	ATTGTAAGTTTCCAACTAAGACTCC	57.019	36.000	0.00	0.00	41.91	3.85
1052	1137	3.535962	CCTGCCTCTCCTCCTCGC	61.536	72.222	0.00	0.00	0.00	5.03
1134	1231	4.082523	GTGTGGCCAGCCGCTCTA	62.083	66.667	21.94	0.11	46.12	2.43
1300	1403	1.651240	GCTCGCCTGTACGGTCAGTA	61.651	60.000	0.00	0.00	34.02	2.74
1313	1416	0.669077	GTCAGTACTCGATCGCCCAT	59.331	55.000	11.09	0.00	0.00	4.00
1337	1440	1.294659	CTGGGCGAGTTCAGTCTTGC	61.295	60.000	0.00	0.00	42.34	4.01
1437	1540	1.192146	CGGTTCAGGGAAGGTCAGGA	61.192	60.000	0.00	0.00	0.00	3.86
1521	1624	1.064685	CCAGGAGGGTGTAACAATCCC	60.065	57.143	0.00	0.00	42.21	3.85
1563	1696	2.353269	CCGTTGCAACACAAGTTACTCA	59.647	45.455	28.01	0.00	39.50	3.41
1694	1908	5.808366	AATCAAACACTCTCACCTACAGA	57.192	39.130	0.00	0.00	0.00	3.41
1785	6341	0.681175	GGCCAACAAGCATGAAACCT	59.319	50.000	0.00	0.00	0.00	3.50
1839	6395	0.106369	TAGCTCCTGTAGGCGGCTTA	60.106	55.000	19.76	6.09	41.49	3.09
1939	6504	2.169561	GAGGAAGAGTTTGGGGAGCTAG	59.830	54.545	0.00	0.00	0.00	3.42
2022	6587	1.051556	AGCTCGGGGAAGGAGGATTC	61.052	60.000	0.00	0.00	32.10	2.52
2245	6810	5.429762	TCCTTGGACAGATGGATCTATTGTT	59.570	40.000	0.00	0.00	34.85	2.83
2322	6890	5.576128	ACTCATATAGCTAAGGGACTCTCC	58.424	45.833	0.00	0.00	38.49	3.71
2365	6933	6.585702	CACAAAACGAATTGCTCATTTGGATA	59.414	34.615	0.00	0.00	35.94	2.59
2532	11930	0.804989	CACAGATCACGGAAAAGGCC	59.195	55.000	0.00	0.00	0.00	5.19
2625	12023	5.243507	GTCAGAAGAGAGCATCCATCTCATA	59.756	44.000	5.81	0.00	44.68	2.15
2787	12185	2.339769	AGGCCTAAACTGTCTGAGGTT	58.660	47.619	1.29	0.00	35.11	3.50
2814	12212	2.936498	CGTATTGGAAGGTGTCATGACC	59.064	50.000	22.85	13.66	36.09	4.02
2838	12236	5.303971	GCAGACCTCAACATAGAGCATAAT	58.696	41.667	0.00	0.00	34.26	1.28
2940	12338	0.329596	GCCCCAGGTGAAACAGAGAT	59.670	55.000	0.00	0.00	39.98	2.75
2972	12371	3.961849	TGGTAGGCAATTAGATTGTGCA	58.038	40.909	2.97	0.00	42.20	4.57
3096	12505	3.191371	GCAAACCTTCTTCGATCCACAAT	59.809	43.478	0.00	0.00	0.00	2.71
3099	12508	4.408182	ACCTTCTTCGATCCACAATAGG	57.592	45.455	0.00	0.00	0.00	2.57
3229	12639	5.782047	TGTTGTAAAATTCTCATTGCCCAG	58.218	37.500	0.00	0.00	0.00	4.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.588719	AAGCAGTGAATATTTTGCAGGTTA	57.411	33.333	17.35	0.00	38.97	2.85
1	2	5.473066	AAGCAGTGAATATTTTGCAGGTT	57.527	34.783	17.35	6.26	38.97	3.50
2	3	5.711976	ACTAAGCAGTGAATATTTTGCAGGT	59.288	36.000	17.35	11.71	38.97	4.00
3	4	6.199937	ACTAAGCAGTGAATATTTTGCAGG	57.800	37.500	17.35	11.30	38.97	4.85
4	5	9.443283	GATTACTAAGCAGTGAATATTTTGCAG	57.557	33.333	17.35	11.68	38.97	4.41
5	6	8.405531	GGATTACTAAGCAGTGAATATTTTGCA	58.594	33.333	17.35	0.00	38.97	4.08
6	7	8.405531	TGGATTACTAAGCAGTGAATATTTTGC	58.594	33.333	10.72	10.72	36.14	3.68
11	12	9.905713	TCTTTTGGATTACTAAGCAGTGAATAT	57.094	29.630	0.00	0.00	36.14	1.28
12	13	9.905713	ATCTTTTGGATTACTAAGCAGTGAATA	57.094	29.630	0.00	0.00	36.14	1.75
13	14	8.814038	ATCTTTTGGATTACTAAGCAGTGAAT	57.186	30.769	0.00	0.00	36.14	2.57
111	114	9.712305	CTCTCTTCCAAACTAATTGAAGTTCTA	57.288	33.333	4.17	0.00	41.85	2.10
112	115	8.432805	TCTCTCTTCCAAACTAATTGAAGTTCT	58.567	33.333	4.17	0.00	41.85	3.01
113	116	8.608844	TCTCTCTTCCAAACTAATTGAAGTTC	57.391	34.615	0.00	0.00	41.85	3.01
114	117	8.980481	TTCTCTCTTCCAAACTAATTGAAGTT	57.020	30.769	0.00	0.00	41.85	2.66
115	118	9.579932	AATTCTCTCTTCCAAACTAATTGAAGT	57.420	29.630	0.00	0.00	41.85	3.01
192	209	1.212616	GGACAGGATTGAATCTCGCG	58.787	55.000	0.00	0.00	0.00	5.87
205	222	0.322098	TTGGTTATGCCGTGGACAGG	60.322	55.000	0.00	0.00	41.21	4.00
218	235	6.465948	TCTGAGGTACGCTTTATTTTGGTTA	58.534	36.000	0.00	0.00	0.00	2.85
230	247	2.279582	CGTTGAATCTGAGGTACGCT	57.720	50.000	0.00	0.00	0.00	5.07
272	296	6.273825	ACGTCTCTGTTTATTGGTATAGCTG	58.726	40.000	0.00	0.00	0.00	4.24
294	318	1.531149	ACCTTGTGATCTTTGCGAACG	59.469	47.619	0.00	0.00	0.00	3.95
318	342	2.780094	CGTGCAAACAAGGGTGGCA	61.780	57.895	0.00	0.00	36.25	4.92
322	346	1.893786	TTTGCGTGCAAACAAGGGT	59.106	47.368	15.51	0.00	40.51	4.34
379	411	2.830285	GCCGTCAACCACACCACAC	61.830	63.158	0.00	0.00	0.00	3.82
380	412	2.515057	GCCGTCAACCACACCACA	60.515	61.111	0.00	0.00	0.00	4.17
381	413	0.604243	TATGCCGTCAACCACACCAC	60.604	55.000	0.00	0.00	0.00	4.16
382	414	0.326595	ATATGCCGTCAACCACACCA	59.673	50.000	0.00	0.00	0.00	4.17
383	415	0.732571	CATATGCCGTCAACCACACC	59.267	55.000	0.00	0.00	0.00	4.16
384	416	1.732941	TCATATGCCGTCAACCACAC	58.267	50.000	0.00	0.00	0.00	3.82
385	417	2.708216	ATCATATGCCGTCAACCACA	57.292	45.000	0.00	0.00	0.00	4.17
419	451	2.266055	GCCTCCTTCACCAGTCGG	59.734	66.667	0.00	0.00	38.77	4.79
560	605	9.965902	ATCTTAGTTTGTTCATTCCTAATCTGT	57.034	29.630	0.00	0.00	0.00	3.41
589	634	5.221441	GCCTTTCAGGAAATTGTTAGGTTGT	60.221	40.000	0.00	0.00	37.67	3.32
674	720	8.296713	ACGTATTGTGTGATTAATTTTTCTGCT	58.703	29.630	0.00	0.00	0.00	4.24
747	793	6.527423	TGTTTAGTCCCTTTCGAATTGTAGT	58.473	36.000	0.00	0.00	0.00	2.73
819	870	2.483877	TCAGCATGAAAACAGCCTAACG	59.516	45.455	0.00	0.00	45.97	3.18
861	912	3.461773	CCGCATCGACAGGGTCCT	61.462	66.667	0.00	0.00	0.00	3.85
862	913	3.718210	GACCGCATCGACAGGGTCC	62.718	68.421	16.01	3.13	42.45	4.46
863	914	2.202756	GACCGCATCGACAGGGTC	60.203	66.667	12.99	12.99	41.84	4.46
864	915	3.771160	GGACCGCATCGACAGGGT	61.771	66.667	3.00	3.00	34.94	4.34
865	916	4.530857	GGGACCGCATCGACAGGG	62.531	72.222	7.44	2.27	0.00	4.45
866	917	3.461773	AGGGACCGCATCGACAGG	61.462	66.667	0.00	0.00	0.00	4.00
867	918	2.202797	CAGGGACCGCATCGACAG	60.203	66.667	0.00	0.00	0.00	3.51
868	919	2.994995	ACAGGGACCGCATCGACA	60.995	61.111	0.00	0.00	0.00	4.35
869	920	1.381928	TAGACAGGGACCGCATCGAC	61.382	60.000	0.00	0.00	0.00	4.20
870	921	1.077285	TAGACAGGGACCGCATCGA	60.077	57.895	0.00	0.00	0.00	3.59
871	922	1.065928	GTAGACAGGGACCGCATCG	59.934	63.158	0.00	0.00	0.00	3.84
907	974	3.270877	CTTGTGATGGCTAACAGGGTAC	58.729	50.000	0.00	0.00	0.00	3.34
908	975	2.238646	CCTTGTGATGGCTAACAGGGTA	59.761	50.000	7.46	0.00	38.41	3.69
959	1043	1.136474	TGCACGCGTTAACTTGAATCG	60.136	47.619	10.22	0.00	0.00	3.34
1052	1137	1.153745	GTGGCAGCGAGTAGGAGTG	60.154	63.158	0.00	0.00	0.00	3.51
1155	1255	2.758327	CACGTCTCCCCCGGATCA	60.758	66.667	0.73	0.00	0.00	2.92
1248	1348	4.517663	CCAGTTTGGCATGACCCA	57.482	55.556	0.00	0.00	37.83	4.51
1300	1403	2.413351	CGTGATGGGCGATCGAGT	59.587	61.111	21.57	0.00	33.17	4.18
1301	1404	3.032609	GCGTGATGGGCGATCGAG	61.033	66.667	21.57	2.75	33.17	4.04
1337	1440	1.479323	CATCATCACTTTGGCCTTGGG	59.521	52.381	3.32	0.00	0.00	4.12
1521	1624	0.317160	TTGTCGTGCTCCCAGTACAG	59.683	55.000	0.00	0.00	29.68	2.74
1563	1696	2.751806	GCACATCTGCTTAAAGAAGGCT	59.248	45.455	0.00	0.00	40.63	4.58
1694	1908	1.000396	GCAGGCAGGGGACTTTCAT	60.000	57.895	0.00	0.00	40.21	2.57
1735	6291	1.255667	GGCAGAGTACTTGGGGTCGA	61.256	60.000	0.00	0.00	0.00	4.20
1785	6341	4.040755	CTCTTCTTCCAGAGGGGGATTTA	58.959	47.826	0.00	0.00	37.28	1.40
1839	6395	4.590222	AGGAACAAGATGGTGAGCAAAATT	59.410	37.500	0.00	0.00	0.00	1.82
1898	6454	5.013495	TCCTCTTCTTCCATCTCATGTTGTT	59.987	40.000	0.00	0.00	0.00	2.83
2022	6587	1.235724	GTCCCTTGAAAACAGACCCG	58.764	55.000	0.00	0.00	0.00	5.28
2245	6810	3.943381	GGAGAAGCATCATTGTCATGTCA	59.057	43.478	0.00	0.00	0.00	3.58
2322	6890	4.397481	TGTGCACTCCTCATGAAGATAG	57.603	45.455	19.41	0.00	0.00	2.08
2365	6933	7.004086	TCTAAGAGGATGTTTTGTGGTTTGAT	58.996	34.615	0.00	0.00	0.00	2.57
2532	11930	1.069159	ACGCCGAAGCTGTAGATATCG	60.069	52.381	0.00	0.00	36.60	2.92
2625	12023	5.530176	TTACCTTTTCCTCCAATAGGCTT	57.470	39.130	0.00	0.00	46.10	4.35
2776	12174	5.120208	CCAATACGTTTACAACCTCAGACAG	59.880	44.000	0.00	0.00	0.00	3.51
2787	12185	4.958509	TGACACCTTCCAATACGTTTACA	58.041	39.130	0.00	0.00	0.00	2.41
2793	12191	2.936498	GGTCATGACACCTTCCAATACG	59.064	50.000	26.47	0.00	33.08	3.06
2814	12212	1.134995	TGCTCTATGTTGAGGTCTGCG	60.135	52.381	0.00	0.00	34.82	5.18
2900	12298	4.222588	GGCCTGATACATCTGAAGCTAGAT	59.777	45.833	0.00	0.00	37.90	1.98
2907	12305	1.770658	CTGGGGCCTGATACATCTGAA	59.229	52.381	0.84	0.00	0.00	3.02
2940	12338	7.801104	TCTAATTGCCTACCATGTCAGAATTA	58.199	34.615	0.00	0.00	0.00	1.40
3067	12476	5.815740	GGATCGAAGAAGGTTTGCAATACTA	59.184	40.000	0.00	0.00	43.58	1.82
3096	12505	5.762179	AGGAACACAAATGATCTCACCTA	57.238	39.130	0.00	0.00	0.00	3.08
3099	12508	6.317789	TCAAAGGAACACAAATGATCTCAC	57.682	37.500	0.00	0.00	0.00	3.51
3103	12512	5.382618	AGCTCAAAGGAACACAAATGATC	57.617	39.130	0.00	0.00	0.00	2.92
3154	12563	7.710907	TCATAACTCAAACTAGATTTGCGCTAT	59.289	33.333	9.73	1.37	46.32	2.97
3201	12610	7.148590	GGGCAATGAGAATTTTACAACATGTTC	60.149	37.037	8.48	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.