AutoCloner

Multiple sequence alignment - TraesCS6B01G426400

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	TraesCS6B01G426400	chr6B	100.000	3456	0	0	1	3456	694682193	694678738	0.000000e+00	6383
1	TraesCS6B01G426400	chr7D	91.215	2732	126	47	785	3456	543731876	543729199	0.000000e+00	3611
2	TraesCS6B01G426400	chr7D	95.541	740	30	1	1	740	543732614	543731878	0.000000e+00	1181
3	TraesCS6B01G426400	chr7D	83.367	986	108	23	1026	1999	530430845	530431786	0.000000e+00	861
4	TraesCS6B01G426400	chr7D	83.197	857	119	17	1065	1911	548551106	548550265	0.000000e+00	761
5	TraesCS6B01G426400	chr7A	92.863	2256	135	14	1	2243	625643393	625641151	0.000000e+00	3251
6	TraesCS6B01G426400	chr7A	92.004	1851	100	21	1	1818	625676189	625674354	0.000000e+00	2555
7	TraesCS6B01G426400	chr7A	94.338	1148	46	9	2327	3456	625641123	625639977	0.000000e+00	1742
8	TraesCS6B01G426400	chr7A	91.560	782	36	17	2283	3041	625673853	625673079	0.000000e+00	1051
9	TraesCS6B01G426400	chr7A	84.615	1040	131	21	1026	2059	631652538	631653554	0.000000e+00	1007
10	TraesCS6B01G426400	chr7A	85.085	295	37	3	1026	1313	617552007	617552301	9.380000e-76	294
11	TraesCS6B01G426400	chr1D	90.894	1867	111	22	284	2106	110906128	110904277	0.000000e+00	2451
12	TraesCS6B01G426400	chr1D	89.030	237	17	9	2570	2802	110838640	110838409	5.650000e-73	285
13	TraesCS6B01G426400	chr7B	95.822	1149	39	5	1	1140	587480648	587479500	0.000000e+00	1847
14	TraesCS6B01G426400	chr7B	95.113	1146	36	3	1	1140	587519892	587518761	0.000000e+00	1788
15	TraesCS6B01G426400	chr7B	94.128	1141	36	6	1	1138	587102712	587101600	0.000000e+00	1707
16	TraesCS6B01G426400	chr7B	97.658	982	20	3	1	979	587441643	587440662	0.000000e+00	1683
17	TraesCS6B01G426400	chr7B	93.427	1141	35	13	1	1138	587267919	587266816	0.000000e+00	1655
18	TraesCS6B01G426400	chr7B	97.682	647	15	0	297	943	587615877	587615231	0.000000e+00	1112
19	TraesCS6B01G426400	chr7B	86.753	770	77	13	1076	1822	569439964	569440731	0.000000e+00	833
20	TraesCS6B01G426400	chr7B	99.013	304	3	0	1	304	587620876	587620573	2.350000e-151	545
21	TraesCS6B01G426400	chr1B	90.520	1076	63	20	824	1874	169025360	169024299	0.000000e+00	1386
22	TraesCS6B01G426400	chr1B	90.407	344	19	3	1869	2198	169013844	169013501	1.140000e-119	440
23	TraesCS6B01G426400	chr1B	90.857	175	10	3	2406	2574	169011430	169011256	2.680000e-56	230
24	TraesCS6B01G426400	chr2A	86.765	816	59	12	1	792	701781720	701782510	0.000000e+00	863
25	TraesCS6B01G426400	chr2A	81.693	437	44	14	790	1197	701782672	701783101	7.150000e-87	331
26	TraesCS6B01G426400	chr6A	80.790	557	107	0	2898	3454	93814881	93814325	1.470000e-118	436

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	TraesCS6B01G426400	chr6B	694678738	694682193	3455	True	6383.0	6383	100.0000	1	3456	1	chr6B.!!$R1	3455
1	TraesCS6B01G426400	chr7D	543729199	543732614	3415	True	2396.0	3611	93.3780	1	3456	2	chr7D.!!$R2	3455
2	TraesCS6B01G426400	chr7D	530430845	530431786	941	False	861.0	861	83.3670	1026	1999	1	chr7D.!!$F1	973
3	TraesCS6B01G426400	chr7D	548550265	548551106	841	True	761.0	761	83.1970	1065	1911	1	chr7D.!!$R1	846
4	TraesCS6B01G426400	chr7A	625639977	625643393	3416	True	2496.5	3251	93.6005	1	3456	2	chr7A.!!$R1	3455
5	TraesCS6B01G426400	chr7A	625673079	625676189	3110	True	1803.0	2555	91.7820	1	3041	2	chr7A.!!$R2	3040
6	TraesCS6B01G426400	chr7A	631652538	631653554	1016	False	1007.0	1007	84.6150	1026	2059	1	chr7A.!!$F2	1033
7	TraesCS6B01G426400	chr1D	110904277	110906128	1851	True	2451.0	2451	90.8940	284	2106	1	chr1D.!!$R2	1822
8	TraesCS6B01G426400	chr7B	587479500	587480648	1148	True	1847.0	1847	95.8220	1	1140	1	chr7B.!!$R4	1139
9	TraesCS6B01G426400	chr7B	587518761	587519892	1131	True	1788.0	1788	95.1130	1	1140	1	chr7B.!!$R5	1139
10	TraesCS6B01G426400	chr7B	587101600	587102712	1112	True	1707.0	1707	94.1280	1	1138	1	chr7B.!!$R1	1137
11	TraesCS6B01G426400	chr7B	587440662	587441643	981	True	1683.0	1683	97.6580	1	979	1	chr7B.!!$R3	978
12	TraesCS6B01G426400	chr7B	587266816	587267919	1103	True	1655.0	1655	93.4270	1	1138	1	chr7B.!!$R2	1137
13	TraesCS6B01G426400	chr7B	587615231	587615877	646	True	1112.0	1112	97.6820	297	943	1	chr7B.!!$R6	646
14	TraesCS6B01G426400	chr7B	569439964	569440731	767	False	833.0	833	86.7530	1076	1822	1	chr7B.!!$F1	746
15	TraesCS6B01G426400	chr1B	169024299	169025360	1061	True	1386.0	1386	90.5200	824	1874	1	chr1B.!!$R1	1050
16	TraesCS6B01G426400	chr1B	169011256	169013844	2588	True	335.0	440	90.6320	1869	2574	2	chr1B.!!$R2	705
17	TraesCS6B01G426400	chr2A	701781720	701783101	1381	False	597.0	863	84.2290	1	1197	2	chr2A.!!$F1	1196
18	TraesCS6B01G426400	chr6A	93814325	93814881	556	True	436.0	436	80.7900	2898	3454	1	chr6A.!!$R1	556

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
877	1146	1.263217	GCAAACCGAGTGACATTCGTT	59.737	47.619	17.65	10.0	36.37	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2685	5121	0.400975	TAAACCGGGGTTGCTTGCTA	59.599	50.0	7.79	0.0	38.47	3.49	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
856	1112	4.760047	CTTCCGGTGAGGCGGTGG	62.760	72.222	0.00	0.00	40.77	4.61
877	1146	1.263217	GCAAACCGAGTGACATTCGTT	59.737	47.619	17.65	10.00	36.37	3.85
950	1224	1.429148	ATCTTCGAACGGCAATCGGC	61.429	55.000	8.76	0.00	44.45	5.54
1112	1410	4.069232	CGGCTCCCGCAAGAGACA	62.069	66.667	6.64	0.00	42.54	3.41
1140	1438	1.174783	GGAGCACAGAGGACTACGAA	58.825	55.000	0.00	0.00	0.00	3.85
1142	1440	0.889306	AGCACAGAGGACTACGAACC	59.111	55.000	0.00	0.00	0.00	3.62
1491	1835	2.894387	GTCATGCGGCAGCTCCTC	60.894	66.667	10.92	0.00	45.42	3.71
1545	1894	2.350895	CACCGGGACATCAAGCCA	59.649	61.111	6.32	0.00	0.00	4.75
1771	2120	2.742372	CGCTGTTCCCGGGACAAG	60.742	66.667	26.87	24.08	0.00	3.16
1838	2193	2.078849	TGTGTAGGATTCACGCACAG	57.921	50.000	0.00	0.00	38.48	3.66
2021	2377	2.203280	CCCGTGGTTCACTGGCAA	60.203	61.111	0.00	0.00	32.51	4.52
2035	2391	3.423154	GCAACGCCGACTTCCCTG	61.423	66.667	0.00	0.00	0.00	4.45
2036	2392	3.423154	CAACGCCGACTTCCCTGC	61.423	66.667	0.00	0.00	0.00	4.85
2037	2393	4.699522	AACGCCGACTTCCCTGCC	62.700	66.667	0.00	0.00	0.00	4.85
2039	2395	4.821589	CGCCGACTTCCCTGCCTC	62.822	72.222	0.00	0.00	0.00	4.70
2040	2396	3.394836	GCCGACTTCCCTGCCTCT	61.395	66.667	0.00	0.00	0.00	3.69
2049	2415	2.510238	CCTGCCTCTGCTGCGTAC	60.510	66.667	0.00	0.00	38.71	3.67
2059	2425	3.913573	CTGCGTACGATGCGTGCC	61.914	66.667	21.65	0.00	41.39	5.01
2189	2603	9.683069	CTGTAATGGAATTGTAATTTAGGATGC	57.317	33.333	0.00	0.00	36.99	3.91
2194	2608	6.096705	TGGAATTGTAATTTAGGATGCTGTGG	59.903	38.462	0.00	0.00	0.00	4.17
2200	2614	0.543277	TTAGGATGCTGTGGAGGCTG	59.457	55.000	0.00	0.00	0.00	4.85
2224	2638	4.080863	GGATCTCCCTCTCTGCAACTAAAA	60.081	45.833	0.00	0.00	0.00	1.52
2258	2759	6.015519	AGCTATTTCCTATCAGTGCTAGAGTG	60.016	42.308	2.50	0.00	0.00	3.51
2261	2762	4.439253	TCCTATCAGTGCTAGAGTGCTA	57.561	45.455	2.50	0.00	0.00	3.49
2269	2770	3.066064	AGTGCTAGAGTGCTACAATCTCG	59.934	47.826	0.22	0.00	38.15	4.04
2279	4078	5.864474	AGTGCTACAATCTCGTAGTTTCAAG	59.136	40.000	0.00	0.00	40.87	3.02
2303	4710	7.896811	AGATAATAGCGATTAGACCATGACAA	58.103	34.615	5.49	0.00	31.02	3.18
2304	4711	8.031864	AGATAATAGCGATTAGACCATGACAAG	58.968	37.037	5.49	0.00	31.02	3.16
2306	4713	4.207891	AGCGATTAGACCATGACAAGTT	57.792	40.909	0.00	0.00	0.00	2.66
2307	4714	5.339008	AGCGATTAGACCATGACAAGTTA	57.661	39.130	0.00	0.00	0.00	2.24
2381	4798	6.311723	AGAAAACAGACAAAGTTAACACACG	58.688	36.000	8.61	0.00	0.00	4.49
2533	4962	7.159322	TCATCTGTACAGAGTAGTCCTTTTC	57.841	40.000	28.29	0.00	41.33	2.29
2561	4992	6.352516	ACCTAACAGAATGGATGTCAGAATC	58.647	40.000	0.00	0.00	43.62	2.52
2685	5121	9.494055	ACATATCACTACCCATTAGCTACATAT	57.506	33.333	0.00	0.00	0.00	1.78
2723	5160	8.663025	CCGGTTTAAGAGGTTTAATCTTACTTC	58.337	37.037	0.00	0.00	38.62	3.01
2736	5173	4.993705	TCTTACTTCAGACCCAACCATT	57.006	40.909	0.00	0.00	0.00	3.16
2741	5178	3.395941	ACTTCAGACCCAACCATTTCTCT	59.604	43.478	0.00	0.00	0.00	3.10
2750	5187	4.507335	CCCAACCATTTCTCTCTTCCAAGA	60.507	45.833	0.00	0.00	0.00	3.02
2765	5202	7.557719	TCTCTTCCAAGAAAATACATCCATTCC	59.442	37.037	0.00	0.00	34.03	3.01
2766	5203	6.318648	TCTTCCAAGAAAATACATCCATTCCG	59.681	38.462	0.00	0.00	30.73	4.30
2767	5204	5.750524	TCCAAGAAAATACATCCATTCCGA	58.249	37.500	0.00	0.00	0.00	4.55
2780	5217	0.887933	ATTCCGAGCGCCAAACATTT	59.112	45.000	2.29	0.00	0.00	2.32
2781	5218	0.039617	TTCCGAGCGCCAAACATTTG	60.040	50.000	2.29	0.00	37.90	2.32
2794	5231	1.304713	CATTTGGTGCTCTGGCCCT	60.305	57.895	0.00	0.00	37.74	5.19
2809	5246	1.172812	GCCCTGGTGGTGAAGACAAC	61.173	60.000	0.00	0.00	36.04	3.32
2819	5256	4.278419	GTGGTGAAGACAACCAAGCTTAAT	59.722	41.667	0.00	0.00	35.05	1.40
2825	5262	2.295909	GACAACCAAGCTTAATGCCACA	59.704	45.455	0.00	0.00	44.23	4.17
2835	5272	3.429410	GCTTAATGCCACATGAAAGGTCC	60.429	47.826	0.00	0.00	35.15	4.46
2860	5298	4.320608	TTGTTTTCATGGAAGCTTGGTC	57.679	40.909	2.10	0.00	0.00	4.02
2914	5355	1.000060	CTAGCCAGAGAGAGCTCATGC	60.000	57.143	17.77	8.59	43.81	4.06
3031	5472	3.131478	GGTCGCCCGGGAACATTG	61.131	66.667	29.31	5.75	0.00	2.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
856	1112	0.165944	CGAATGTCACTCGGTTTGCC	59.834	55.000	0.00	0.00	32.62	4.52
877	1146	0.967380	TCCGACTGCTGCTCTGATCA	60.967	55.000	0.00	0.00	0.00	2.92
950	1224	2.749044	AGGAGCGGCACATGCAAG	60.749	61.111	6.15	0.00	44.36	4.01
1112	1410	4.827087	CTGTGCTCCCGATGCGCT	62.827	66.667	9.73	0.00	41.05	5.92
1128	1426	1.642952	GCGTCGGTTCGTAGTCCTCT	61.643	60.000	0.00	0.00	0.00	3.69
1771	2120	2.583593	GAGCTGGTCGACCGCATC	60.584	66.667	35.60	28.08	39.43	3.91
2035	2391	2.105128	ATCGTACGCAGCAGAGGC	59.895	61.111	11.24	0.00	41.61	4.70
2036	2392	2.233654	GCATCGTACGCAGCAGAGG	61.234	63.158	21.49	3.68	0.00	3.69
2037	2393	2.571562	CGCATCGTACGCAGCAGAG	61.572	63.158	24.34	10.25	0.00	3.35
2038	2394	2.579518	CGCATCGTACGCAGCAGA	60.580	61.111	24.34	3.85	0.00	4.26
2039	2395	2.880879	ACGCATCGTACGCAGCAG	60.881	61.111	24.34	19.64	38.73	4.24
2040	2396	3.178592	CACGCATCGTACGCAGCA	61.179	61.111	24.34	4.89	38.32	4.41
2059	2425	3.006859	TGATGATGTAGAATGGCGGTAGG	59.993	47.826	0.00	0.00	0.00	3.18
2189	2603	1.694133	GGAGATCCCAGCCTCCACAG	61.694	65.000	0.00	0.00	46.28	3.66
2224	2638	5.133941	TGATAGGAAATAGCTGTCGACTCT	58.866	41.667	17.92	15.45	0.00	3.24
2258	2759	8.630278	TTATCTTGAAACTACGAGATTGTAGC	57.370	34.615	7.09	0.00	44.55	3.58
2261	2762	9.250624	GCTATTATCTTGAAACTACGAGATTGT	57.749	33.333	0.00	0.00	40.32	2.71
2279	4078	7.815068	ACTTGTCATGGTCTAATCGCTATTATC	59.185	37.037	0.00	0.00	0.00	1.75
2285	4092	3.895232	ACTTGTCATGGTCTAATCGCT	57.105	42.857	0.00	0.00	0.00	4.93
2295	4702	6.582295	GTGTAACAATGCTTAACTTGTCATGG	59.418	38.462	0.00	0.00	34.61	3.66
2381	4798	4.253685	TCAGGTGAGCTTATTAGTTGTGC	58.746	43.478	0.00	0.00	0.00	4.57
2533	4962	7.331026	TCTGACATCCATTCTGTTAGGTTAAG	58.669	38.462	0.00	0.00	32.67	1.85
2561	4992	9.737427	AGTATCAGTTTTATGTATTCTCAGACG	57.263	33.333	0.00	0.00	0.00	4.18
2591	5022	9.593134	GTATAATTCATAAGCTACTCTCATGGG	57.407	37.037	0.00	0.00	0.00	4.00
2685	5121	0.400975	TAAACCGGGGTTGCTTGCTA	59.599	50.000	7.79	0.00	38.47	3.49
2689	5125	1.546998	CCTCTTAAACCGGGGTTGCTT	60.547	52.381	7.79	0.00	38.47	3.91
2723	5160	3.710209	AGAGAGAAATGGTTGGGTCTG	57.290	47.619	0.00	0.00	0.00	3.51
2736	5173	7.689299	TGGATGTATTTTCTTGGAAGAGAGAA	58.311	34.615	0.00	0.00	36.22	2.87
2741	5178	6.318648	CGGAATGGATGTATTTTCTTGGAAGA	59.681	38.462	0.00	0.00	0.00	2.87
2750	5187	2.290641	GCGCTCGGAATGGATGTATTTT	59.709	45.455	0.00	0.00	0.00	1.82
2781	5218	4.729918	CACCAGGGCCAGAGCACC	62.730	72.222	6.18	0.00	46.94	5.01
2794	5231	2.021723	GCTTGGTTGTCTTCACCACCA	61.022	52.381	0.00	0.00	44.71	4.17
2809	5246	3.872511	TTCATGTGGCATTAAGCTTGG	57.127	42.857	9.86	0.00	44.79	3.61
2819	5256	0.409092	ATGGGACCTTTCATGTGGCA	59.591	50.000	0.00	0.00	0.00	4.92
2825	5262	5.885449	TGAAAACAAATGGGACCTTTCAT	57.115	34.783	0.00	0.00	30.13	2.57
2835	5272	4.453136	CCAAGCTTCCATGAAAACAAATGG	59.547	41.667	0.00	0.00	44.06	3.16
2860	5298	7.011109	TCTGTTTGAAGTCTTAAAGGTCTTTCG	59.989	37.037	0.00	0.00	34.23	3.46
2914	5355	0.036952	AGTGGATGCTCACCGAAGTG	60.037	55.000	0.00	0.00	46.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.