AutoCloner

Multiple sequence alignment - TraesCS1D01G041600

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	TraesCS1D01G041600	chr1D	100.000	2103	0	0	474	2576	20184476	20186578	0.000000e+00	3884.0
1	TraesCS1D01G041600	chr1D	83.237	1897	197	52	476	2288	20061353	20063212	0.000000e+00	1629.0
2	TraesCS1D01G041600	chr1D	100.000	161	0	0	1	161	20184003	20184163	5.390000e-77	298.0
3	TraesCS1D01G041600	chr1D	90.152	132	12	1	1	132	111267360	111267230	1.230000e-38	171.0
4	TraesCS1D01G041600	chr1D	100.000	28	0	0	1339	1366	20185368	20185341	5.000000e-03	52.8
5	TraesCS1D01G041600	chr1A	90.494	2125	152	23	476	2576	22283518	22281420	0.000000e+00	2760.0
6	TraesCS1D01G041600	chr1A	75.781	896	138	46	1000	1852	22271961	22271102	1.870000e-101	379.0
7	TraesCS1D01G041600	chr1B	89.565	1562	109	26	476	2015	33922080	33920551	0.000000e+00	1932.0
8	TraesCS1D01G041600	chr1B	81.167	1423	174	46	939	2293	33946835	33945439	0.000000e+00	1057.0
9	TraesCS1D01G041600	chr1B	96.859	573	18	0	2004	2576	33918986	33918414	0.000000e+00	959.0
10	TraesCS1D01G041600	chr1B	89.024	492	21	18	476	965	33947308	33946848	1.720000e-161	579.0
11	TraesCS1D01G041600	chr1B	75.880	937	148	54	996	1908	33857392	33856510	8.580000e-110	407.0
12	TraesCS1D01G041600	chr1B	87.500	208	15	5	654	859	33962776	33962578	1.990000e-56	230.0
13	TraesCS1D01G041600	chr1B	89.535	86	8	1	856	940	33962299	33962214	9.750000e-20	108.0
14	TraesCS1D01G041600	chr3A	91.925	161	13	0	1	161	341634628	341634468	2.580000e-55	226.0
15	TraesCS1D01G041600	chr7A	88.125	160	15	1	1	160	24752943	24753098	1.220000e-43	187.0
16	TraesCS1D01G041600	chr3B	85.714	161	10	1	1	161	76507697	76507844	9.540000e-35	158.0
17	TraesCS1D01G041600	chr3B	78.981	157	30	3	4	159	428091925	428091771	1.260000e-18	104.0
18	TraesCS1D01G041600	chr4B	97.500	80	2	0	1	80	167947727	167947648	1.240000e-28	137.0
19	TraesCS1D01G041600	chr2D	80.892	157	29	1	4	159	400514710	400514866	3.480000e-24	122.0
20	TraesCS1D01G041600	chr2B	80.892	157	29	1	4	159	45699055	45699211	3.480000e-24	122.0

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	TraesCS1D01G041600	chr1D	20184003	20186578	2575	False	2091.0	3884	100.0000	1	2576	2	chr1D.!!$F2	2575
1	TraesCS1D01G041600	chr1D	20061353	20063212	1859	False	1629.0	1629	83.2370	476	2288	1	chr1D.!!$F1	1812
2	TraesCS1D01G041600	chr1A	22281420	22283518	2098	True	2760.0	2760	90.4940	476	2576	1	chr1A.!!$R2	2100
3	TraesCS1D01G041600	chr1A	22271102	22271961	859	True	379.0	379	75.7810	1000	1852	1	chr1A.!!$R1	852
4	TraesCS1D01G041600	chr1B	33918414	33922080	3666	True	1445.5	1932	93.2120	476	2576	2	chr1B.!!$R2	2100
5	TraesCS1D01G041600	chr1B	33945439	33947308	1869	True	818.0	1057	85.0955	476	2293	2	chr1B.!!$R3	1817
6	TraesCS1D01G041600	chr1B	33856510	33857392	882	True	407.0	407	75.8800	996	1908	1	chr1B.!!$R1	912

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
128	129	1.142748	GCCATCTCGACCTCCACTG	59.857	63.158	0.0	0.0	0.0	3.66	F
129	130	1.142748	CCATCTCGACCTCCACTGC	59.857	63.158	0.0	0.0	0.0	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1515	1610	0.109723	GGTGGAAAGTGTACCCAGCA	59.890	55.0	11.1	0.0	45.08	4.41	R
1582	1679	0.179097	GCAACGGAGTGGGAGAGATC	60.179	60.0	0.0	0.0	45.00	2.75	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
47	48	4.478371	CAGATCTGGGCGCCTGCA	62.478	66.667	28.56	16.20	45.35	4.41
48	49	4.172512	AGATCTGGGCGCCTGCAG	62.173	66.667	28.56	25.07	45.35	4.41
93	94	3.426568	GTCGCCAGGCAGCTTCAC	61.427	66.667	13.30	0.00	0.00	3.18
94	95	4.704833	TCGCCAGGCAGCTTCACC	62.705	66.667	13.30	0.00	0.00	4.02
123	124	4.933064	CCGCGCCATCTCGACCTC	62.933	72.222	0.00	0.00	0.00	3.85
124	125	4.933064	CGCGCCATCTCGACCTCC	62.933	72.222	0.00	0.00	0.00	4.30
125	126	3.838271	GCGCCATCTCGACCTCCA	61.838	66.667	0.00	0.00	0.00	3.86
126	127	2.105128	CGCCATCTCGACCTCCAC	59.895	66.667	0.00	0.00	0.00	4.02
127	128	2.418910	CGCCATCTCGACCTCCACT	61.419	63.158	0.00	0.00	0.00	4.00
128	129	1.142748	GCCATCTCGACCTCCACTG	59.857	63.158	0.00	0.00	0.00	3.66
129	130	1.142748	CCATCTCGACCTCCACTGC	59.857	63.158	0.00	0.00	0.00	4.40
130	131	1.226802	CATCTCGACCTCCACTGCG	60.227	63.158	0.00	0.00	0.00	5.18
131	132	3.069980	ATCTCGACCTCCACTGCGC	62.070	63.158	0.00	0.00	0.00	6.09
497	498	4.607293	AATTTTCAGCCTCTCCAAAACC	57.393	40.909	0.00	0.00	0.00	3.27
522	523	6.768834	AGACAGGTCTCTAGAGGAGGAAACT	61.769	48.000	19.67	5.03	42.10	2.66
551	554	7.737607	TGACCTTGAGAATATATAAAGGCCCTA	59.262	37.037	0.00	0.00	40.93	3.53
590	593	3.381590	GGTCAAACCTGAATAAGCCCATC	59.618	47.826	0.00	0.00	34.73	3.51
690	701	1.548357	AAGGGATGCACTGAGCTCGT	61.548	55.000	9.64	7.31	45.94	4.18
698	709	2.872001	CTGAGCTCGTGACGCGTC	60.872	66.667	31.66	31.66	42.13	5.19
740	751	1.325640	CGATCTCGAACCACTTGCATG	59.674	52.381	0.00	0.00	43.02	4.06
774	796	1.570475	CGGCGTCGAGGAGATACTC	59.430	63.158	1.44	0.00	39.00	2.59
898	921	8.086143	AGCTACTACTGGGTGATTTGTTTATA	57.914	34.615	0.00	0.00	0.00	0.98
921	944	8.704849	ATAGTGCAAATGGCCTATAAATACAA	57.295	30.769	3.32	0.00	43.89	2.41
922	945	7.042797	AGTGCAAATGGCCTATAAATACAAG	57.957	36.000	3.32	0.00	43.89	3.16
972	1034	6.294473	TCAGCTTCTTCATCTTCAGAGTTTT	58.706	36.000	0.00	0.00	0.00	2.43
980	1042	9.029368	TCTTCATCTTCAGAGTTTTAGAGATCA	57.971	33.333	0.00	0.00	0.00	2.92
982	1044	9.650539	TTCATCTTCAGAGTTTTAGAGATCAAG	57.349	33.333	0.00	0.00	0.00	3.02
985	1047	7.095910	TCTTCAGAGTTTTAGAGATCAAGCAG	58.904	38.462	0.00	0.00	0.00	4.24
998	1060	1.202806	TCAAGCAGTTGGGTTCAGAGG	60.203	52.381	0.00	0.00	34.30	3.69
1008	1070	2.370519	TGGGTTCAGAGGAATGACGAAA	59.629	45.455	0.00	0.00	35.05	3.46
1056	1118	3.031964	GCGCATGCTTCTGCTCGTT	62.032	57.895	17.13	0.00	40.06	3.85
1170	1250	2.920912	TTCCCGTCGTTCCAGGCT	60.921	61.111	0.00	0.00	0.00	4.58
1373	1453	4.664677	GACGCCACCGACAGCAGT	62.665	66.667	0.00	0.00	38.29	4.40
1392	1472	1.800586	GTGATCAAGAAGCACAGCGAA	59.199	47.619	0.00	0.00	32.96	4.70
1470	1565	1.968017	ACCTTGCGACGAGTACGGA	60.968	57.895	0.00	0.00	44.46	4.69
1479	1574	3.450115	GAGTACGGAGCCGGCAGT	61.450	66.667	31.54	26.03	44.69	4.40
1527	1622	2.348998	GCTGCTGCTGGGTACACT	59.651	61.111	8.53	0.00	36.03	3.55
1663	1767	6.775594	ACTTTGGCAGTAACTTCTCTTTTT	57.224	33.333	0.00	0.00	31.97	1.94
1751	1870	1.966451	CCAGTGAAAGGCGTCCCAC	60.966	63.158	0.00	3.75	0.00	4.61
1791	1917	8.761575	TTCTTTGAGATGATTAATTTTGTGCC	57.238	30.769	0.00	0.00	0.00	5.01
1897	2049	1.610522	CCTTTGGTCAAGTGGCTCAAG	59.389	52.381	0.00	0.00	0.00	3.02
1912	2064	6.543831	AGTGGCTCAAGATGTAATTATCCAAC	59.456	38.462	0.00	0.00	0.00	3.77
2060	3791	9.801873	ATTAATTATTGTTCGGTCCAAATTGAG	57.198	29.630	0.00	0.00	0.00	3.02
2081	3812	1.390123	CCGTGAACTATGCAACTGTCG	59.610	52.381	0.00	0.00	0.00	4.35
2267	4026	8.618677	ACTATTTATGTCATGTGAAGCAATCAG	58.381	33.333	0.00	0.00	39.19	2.90
2354	4114	7.840489	AGTTGCTTGATTTTTCATGTTTTACG	58.160	30.769	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	4.478371	TGCAGGCGCCCAGATCTG	62.478	66.667	26.15	16.24	37.32	2.90
31	32	4.172512	CTGCAGGCGCCCAGATCT	62.173	66.667	26.15	0.00	37.32	2.75
76	77	3.426568	GTGAAGCTGCCTGGCGAC	61.427	66.667	14.98	8.48	37.29	5.19
77	78	4.704833	GGTGAAGCTGCCTGGCGA	62.705	66.667	14.98	2.35	37.29	5.54
106	107	4.933064	GAGGTCGAGATGGCGCGG	62.933	72.222	8.83	0.00	37.92	6.46
107	108	4.933064	GGAGGTCGAGATGGCGCG	62.933	72.222	0.00	0.00	38.75	6.86
108	109	3.838271	TGGAGGTCGAGATGGCGC	61.838	66.667	0.00	0.00	0.00	6.53
109	110	2.105128	GTGGAGGTCGAGATGGCG	59.895	66.667	0.00	0.00	0.00	5.69
110	111	1.142748	CAGTGGAGGTCGAGATGGC	59.857	63.158	0.00	0.00	0.00	4.40
111	112	1.142748	GCAGTGGAGGTCGAGATGG	59.857	63.158	0.00	0.00	0.00	3.51
112	113	1.226802	CGCAGTGGAGGTCGAGATG	60.227	63.158	0.00	0.00	0.00	2.90
113	114	3.069980	GCGCAGTGGAGGTCGAGAT	62.070	63.158	0.30	0.00	0.00	2.75
114	115	3.749064	GCGCAGTGGAGGTCGAGA	61.749	66.667	0.30	0.00	0.00	4.04
473	474	5.466728	GGTTTTGGAGAGGCTGAAAATTTTC	59.533	40.000	21.60	21.60	37.69	2.29
474	475	5.104569	TGGTTTTGGAGAGGCTGAAAATTTT	60.105	36.000	2.28	2.28	0.00	1.82
485	486	2.191128	CCTGTCTGGTTTTGGAGAGG	57.809	55.000	0.00	0.00	36.82	3.69
497	498	2.507886	TCCTCCTCTAGAGACCTGTCTG	59.492	54.545	21.76	1.70	46.50	3.51
522	523	7.719633	GGCCTTTATATATTCTCAAGGTCAACA	59.280	37.037	9.07	0.00	38.81	3.33
551	554	2.224597	TGACCTGTGCACATGACTCATT	60.225	45.455	26.20	4.85	0.00	2.57
590	593	5.636965	CAGTAGTTCAGTTCAGATCAACCAG	59.363	44.000	0.00	0.00	0.00	4.00
740	751	1.723870	CCGCTGCTTAGATGCAACC	59.276	57.895	0.00	0.00	42.83	3.77
763	774	1.570475	CGGCGTCGAGTATCTCCTC	59.430	63.158	1.44	0.00	39.00	3.71
767	778	3.950254	CGGCGGCGTCGAGTATCT	61.950	66.667	32.11	0.00	39.00	1.98
898	921	6.607198	ACTTGTATTTATAGGCCATTTGCACT	59.393	34.615	5.01	0.00	43.89	4.40
921	944	2.187599	GAAACGCATCAAGCCGCACT	62.188	55.000	0.00	0.00	41.38	4.40
922	945	1.797537	GAAACGCATCAAGCCGCAC	60.798	57.895	0.00	0.00	41.38	5.34
972	1034	3.582647	TGAACCCAACTGCTTGATCTCTA	59.417	43.478	0.00	0.00	0.00	2.43
980	1042	1.140312	TCCTCTGAACCCAACTGCTT	58.860	50.000	0.00	0.00	0.00	3.91
982	1044	1.815003	CATTCCTCTGAACCCAACTGC	59.185	52.381	0.00	0.00	32.13	4.40
985	1047	2.076863	CGTCATTCCTCTGAACCCAAC	58.923	52.381	0.00	0.00	32.13	3.77
998	1060	5.851177	TCGAAAGCAAATCTTTTCGTCATTC	59.149	36.000	15.97	0.00	44.58	2.67
1008	1070	4.006319	CCTTCTCCTCGAAAGCAAATCTT	58.994	43.478	0.00	0.00	36.34	2.40
1149	1229	1.068417	CTGGAACGACGGGAACACA	59.932	57.895	0.00	0.00	0.00	3.72
1373	1453	2.168326	TTCGCTGTGCTTCTTGATCA	57.832	45.000	0.00	0.00	0.00	2.92
1435	1530	1.697432	AGGTGGATGGTTCAAGTCGAA	59.303	47.619	0.00	0.00	0.00	3.71
1479	1574	2.861006	CACTCGTCGTCGCTCTCA	59.139	61.111	0.00	0.00	36.96	3.27
1515	1610	0.109723	GGTGGAAAGTGTACCCAGCA	59.890	55.000	11.10	0.00	45.08	4.41
1577	1674	1.187087	GGAGTGGGAGAGATCGTGTT	58.813	55.000	0.00	0.00	0.00	3.32
1580	1677	0.323542	AACGGAGTGGGAGAGATCGT	60.324	55.000	0.00	0.00	45.00	3.73
1582	1679	0.179097	GCAACGGAGTGGGAGAGATC	60.179	60.000	0.00	0.00	45.00	2.75
1584	1681	2.283529	GGCAACGGAGTGGGAGAGA	61.284	63.158	0.00	0.00	45.00	3.10
1585	1682	2.266055	GGCAACGGAGTGGGAGAG	59.734	66.667	0.00	0.00	45.00	3.20
1711	1824	3.868077	GGCACTCATCTACTGCTACAAAG	59.132	47.826	0.00	0.00	0.00	2.77
1745	1864	1.745232	TGATTTATGTGCCGTGGGAC	58.255	50.000	3.27	3.27	36.97	4.46
1747	1866	3.381272	AGAAATGATTTATGTGCCGTGGG	59.619	43.478	0.00	0.00	0.00	4.61
1751	1870	6.554419	TCTCAAAGAAATGATTTATGTGCCG	58.446	36.000	0.00	0.00	0.00	5.69
1791	1917	2.094026	GCCTCCAAAGCCACCAAATTAG	60.094	50.000	0.00	0.00	0.00	1.73
1869	1996	4.682787	CCACTTGACCAAAGGTTTCTTTC	58.317	43.478	0.00	0.00	40.92	2.62
1873	2005	2.031870	AGCCACTTGACCAAAGGTTTC	58.968	47.619	0.00	0.00	40.51	2.78
2036	3765	7.254852	GCTCAATTTGGACCGAACAATAATTA	58.745	34.615	0.00	0.00	0.00	1.40
2046	3777	0.953471	CACGGCTCAATTTGGACCGA	60.953	55.000	26.86	0.00	46.71	4.69
2060	3791	1.128692	GACAGTTGCATAGTTCACGGC	59.871	52.381	0.00	0.00	0.00	5.68
2081	3812	6.993079	AGAATTTTCTGGGTTTAATGTGGTC	58.007	36.000	0.00	0.00	35.89	4.02
2352	4112	8.512138	GGGCATATAGAATTAATGCTAAAACGT	58.488	33.333	7.27	0.00	44.29	3.99

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.