AutoCloner

Multiple sequence alignment - TraesCS7A01G350200

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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	TraesCS7A01G350200	chr7A	100.000	1561	0	0	1	1561	512895440	512893880	0.000000e+00	2883.0
1	TraesCS7A01G350200	chr7A	84.093	1031	123	26	1	1007	422569897	422568884	0.000000e+00	957.0
2	TraesCS7A01G350200	chr7A	100.000	401	0	0	1855	2255	512893586	512893186	0.000000e+00	741.0
3	TraesCS7A01G350200	chr3A	94.182	1564	73	5	1	1560	377684316	377682767	0.000000e+00	2368.0
4	TraesCS7A01G350200	chr3A	91.607	417	19	1	1855	2255	377682713	377682297	1.510000e-156	562.0
5	TraesCS7A01G350200	chr2D	86.940	1049	75	32	1	1007	462976448	462975420	0.000000e+00	1122.0
6	TraesCS7A01G350200	chr2D	90.173	173	17	0	1388	1560	462975414	462975242	2.250000e-55	226.0
7	TraesCS7A01G350200	chr6A	84.474	1037	122	24	1	1007	435725679	435726706	0.000000e+00	987.0
8	TraesCS7A01G350200	chr6A	89.121	239	26	0	1013	1251	594515541	594515303	4.710000e-77	298.0
9	TraesCS7A01G350200	chr6A	96.000	50	2	0	1296	1345	594515305	594515256	5.160000e-12	82.4
10	TraesCS7A01G350200	chr7D	84.369	1030	122	24	1	1007	397491150	397492163	0.000000e+00	974.0
11	TraesCS7A01G350200	chr7D	83.969	1023	129	24	1	1007	554797812	554798815	0.000000e+00	948.0
12	TraesCS7A01G350200	chr5D	86.833	843	99	9	170	1007	430330925	430331760	0.000000e+00	931.0
13	TraesCS7A01G350200	chr4A	82.755	1038	131	25	1	1003	478991748	478992772	0.000000e+00	881.0
14	TraesCS7A01G350200	chr5B	85.680	845	102	10	170	1007	160518097	160518929	0.000000e+00	872.0
15	TraesCS7A01G350200	chr5B	89.011	91	10	0	1	91	160517911	160518001	1.830000e-21	113.0
16	TraesCS7A01G350200	chr4B	83.101	716	88	20	1	693	463351069	463350364	2.460000e-174	621.0
17	TraesCS7A01G350200	chr4B	83.357	691	90	17	3	676	454872411	454871729	1.140000e-172	616.0
18	TraesCS7A01G350200	chr6D	84.932	73	11	0	849	921	171060884	171060956	8.640000e-10	75.0

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	TraesCS7A01G350200	chr7A	512893186	512895440	2254	True	1812.0	2883	100.0000	1	2255	2	chr7A.!!$R2	2254
1	TraesCS7A01G350200	chr7A	422568884	422569897	1013	True	957.0	957	84.0930	1	1007	1	chr7A.!!$R1	1006
2	TraesCS7A01G350200	chr3A	377682297	377684316	2019	True	1465.0	2368	92.8945	1	2255	2	chr3A.!!$R1	2254
3	TraesCS7A01G350200	chr2D	462975242	462976448	1206	True	674.0	1122	88.5565	1	1560	2	chr2D.!!$R1	1559
4	TraesCS7A01G350200	chr6A	435725679	435726706	1027	False	987.0	987	84.4740	1	1007	1	chr6A.!!$F1	1006
5	TraesCS7A01G350200	chr7D	397491150	397492163	1013	False	974.0	974	84.3690	1	1007	1	chr7D.!!$F1	1006
6	TraesCS7A01G350200	chr7D	554797812	554798815	1003	False	948.0	948	83.9690	1	1007	1	chr7D.!!$F2	1006
7	TraesCS7A01G350200	chr5D	430330925	430331760	835	False	931.0	931	86.8330	170	1007	1	chr5D.!!$F1	837
8	TraesCS7A01G350200	chr4A	478991748	478992772	1024	False	881.0	881	82.7550	1	1003	1	chr4A.!!$F1	1002
9	TraesCS7A01G350200	chr5B	160517911	160518929	1018	False	492.5	872	87.3455	1	1007	2	chr5B.!!$F1	1006
10	TraesCS7A01G350200	chr4B	463350364	463351069	705	True	621.0	621	83.1010	1	693	1	chr4B.!!$R2	692
11	TraesCS7A01G350200	chr4B	454871729	454872411	682	True	616.0	616	83.3570	3	676	1	chr4B.!!$R1	673

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
847	970	0.871057	CACACACACACACACACACA	59.129	50.0	0.0	0.0	0.0	3.72	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2080	2208	1.148157	CCATGCTACTGCCGAACTCG	61.148	60.0	0.0	0.0	38.71	4.18	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
106	131	1.575922	GCGCACACACACACATGAT	59.424	52.632	0.30	0.00	0.00	2.45
128	153	4.835284	TGTGTGCACAGGGATTATTCTA	57.165	40.909	22.40	0.00	36.21	2.10
143	168	3.850122	ATTCTAAAGCTTTTGGACGGC	57.150	42.857	18.47	0.00	0.00	5.68
144	169	2.264005	TCTAAAGCTTTTGGACGGCA	57.736	45.000	18.47	0.00	0.00	5.69
273	377	6.073222	ACGCACATTTTTAGGAGTGAGTAAAG	60.073	38.462	0.00	0.00	41.90	1.85
290	395	5.012239	AGTAAAGGCTTGATCAATGCTTCA	58.988	37.500	21.34	9.40	0.00	3.02
440	545	9.606631	AGGCAGTATTTCTTTCAGATTTAGTAG	57.393	33.333	0.00	0.00	0.00	2.57
473	579	7.283127	TCAGTAAGGATTCATGGAATTAGCAAC	59.717	37.037	0.00	0.00	31.89	4.17
524	630	6.125327	TGTGTAGATTCAGCAAACGAAAAA	57.875	33.333	0.00	0.00	0.00	1.94
529	635	8.015087	TGTAGATTCAGCAAACGAAAAACATAG	58.985	33.333	0.00	0.00	0.00	2.23
672	778	1.523711	CCCACAAGCACACACGTCT	60.524	57.895	0.00	0.00	0.00	4.18
687	793	2.100197	ACGTCTAGTATCCAGCAGCAA	58.900	47.619	0.00	0.00	0.00	3.91
739	846	3.325135	GCATAGCCATAGTAGGACTTGGT	59.675	47.826	8.58	0.00	32.58	3.67
759	866	7.871463	ACTTGGTGTATAGTTGTTGTAGAACTC	59.129	37.037	4.21	0.00	35.30	3.01
760	867	7.292713	TGGTGTATAGTTGTTGTAGAACTCA	57.707	36.000	4.21	0.00	35.30	3.41
800	907	3.773560	TCTCAATGGTTGTAAAAGGGGG	58.226	45.455	0.00	0.00	0.00	5.40
843	966	3.320673	TTAGACACACACACACACACA	57.679	42.857	0.00	0.00	0.00	3.72
844	967	1.438651	AGACACACACACACACACAC	58.561	50.000	0.00	0.00	0.00	3.82
845	968	1.152510	GACACACACACACACACACA	58.847	50.000	0.00	0.00	0.00	3.72
846	969	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
847	970	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
851	974	1.155889	CACACACACACACACACTGT	58.844	50.000	0.00	0.00	0.00	3.55
972	1100	8.067189	CAGCTAGTTCAAAGAGAAGAAGAAAAC	58.933	37.037	0.00	0.00	36.78	2.43
984	1112	8.487028	AGAGAAGAAGAAAACCTAAACAGAGAA	58.513	33.333	0.00	0.00	0.00	2.87
1018	1146	3.770933	CTGGATGTCATTTGAAATGGGGT	59.229	43.478	17.01	4.18	0.00	4.95
1045	1173	1.277557	AGCTGATTTGCGAGGAGAAGT	59.722	47.619	0.00	0.00	38.13	3.01
1053	1181	1.203758	TGCGAGGAGAAGTTATGCGAA	59.796	47.619	0.00	0.00	0.00	4.70
1063	1191	4.745125	AGAAGTTATGCGAATACATCCACG	59.255	41.667	0.00	0.00	0.00	4.94
1092	1220	1.220749	GGCGAACATCCTGGCACTA	59.779	57.895	0.00	0.00	0.00	2.74
1119	1247	2.359602	CACTGCTGTGAGGGCCTG	60.360	66.667	12.95	0.00	46.55	4.85
1163	1291	1.541147	TGCTGCTCCGGAAAATTTGAG	59.459	47.619	5.23	0.00	0.00	3.02
1205	1333	0.321346	TTCCAGCATCTGAGCGTGAA	59.679	50.000	0.00	0.00	40.15	3.18
1206	1334	0.390340	TCCAGCATCTGAGCGTGAAC	60.390	55.000	0.00	0.00	40.15	3.18
1208	1336	1.436600	CAGCATCTGAGCGTGAACTT	58.563	50.000	0.00	0.00	40.15	2.66
1224	1352	5.561679	GTGAACTTCCCTTCTCTTATGGTT	58.438	41.667	0.00	0.00	0.00	3.67
1231	1359	3.198635	CCCTTCTCTTATGGTTGAGCTCA	59.801	47.826	13.74	13.74	0.00	4.26
1257	1385	0.906066	TGTTCCCCGTGCATTAGCTA	59.094	50.000	0.00	0.00	42.74	3.32
1287	1415	7.379059	TGGATGATACTTATCAGTGTTCCAT	57.621	36.000	12.40	0.00	45.01	3.41
1299	1427	5.316167	TCAGTGTTCCATTGTTCTAGCAAT	58.684	37.500	0.00	0.00	39.42	3.56
1354	1482	4.018490	TCAGGTAGCCGTCTTTGTGTATA	58.982	43.478	0.00	0.00	0.00	1.47
1386	1514	5.723672	ATCTGAGTTAACAACCGAGAAGA	57.276	39.130	8.61	1.25	0.00	2.87
1428	1556	1.203137	AGGGGAGCACTACACACACTA	60.203	52.381	0.00	0.00	0.00	2.74
1430	1558	3.028850	GGGGAGCACTACACACACTATA	58.971	50.000	0.00	0.00	0.00	1.31
1484	1612	2.601666	ACGGCAGCAGAGGAGACA	60.602	61.111	0.00	0.00	0.00	3.41
1511	1639	3.261897	GGGAAGGTCAAAGAGAGATGACA	59.738	47.826	8.04	0.00	46.07	3.58
1533	1661	3.103742	GGGAAGGTCAGAGAGAGTTGAT	58.896	50.000	0.00	0.00	0.00	2.57
1880	2008	1.909700	TCCAACTTGGATCTTGGTGC	58.090	50.000	6.39	0.00	42.67	5.01
1882	2010	2.642311	TCCAACTTGGATCTTGGTGCTA	59.358	45.455	6.39	0.00	42.67	3.49
1925	2053	1.505353	CGACGGTGTACAGGGAGAC	59.495	63.158	0.00	0.00	0.00	3.36
1927	2055	1.930908	GACGGTGTACAGGGAGACGG	61.931	65.000	0.00	0.00	0.00	4.79
2129	2257	1.672356	GCGTGAGATGTTGGTGGCT	60.672	57.895	0.00	0.00	0.00	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
106	131	4.032960	AGAATAATCCCTGTGCACACAA	57.967	40.909	17.42	4.35	41.33	3.33
128	153	1.327303	TGATGCCGTCCAAAAGCTTT	58.673	45.000	5.69	5.69	0.00	3.51
143	168	7.760131	ACTGTGAAATCAGTTTTGTTTGATG	57.240	32.000	0.00	0.00	44.92	3.07
144	169	8.465999	TGTACTGTGAAATCAGTTTTGTTTGAT	58.534	29.630	4.72	0.00	44.92	2.57
243	309	2.413796	CTCCTAAAAATGTGCGTGCGTA	59.586	45.455	0.00	0.00	0.00	4.42
273	377	2.751259	TCTGTGAAGCATTGATCAAGCC	59.249	45.455	14.54	7.12	0.00	4.35
440	545	6.644347	TCCATGAATCCTTACTGAGTCTTTC	58.356	40.000	0.00	0.00	30.95	2.62
473	579	6.427974	CATGCTGAGTATTCTTGCTACAATG	58.572	40.000	5.70	0.00	0.00	2.82
524	630	8.784994	CGTTAGTTCATAGTCCTACATCTATGT	58.215	37.037	10.55	0.63	42.12	2.29
529	635	8.375608	TCTACGTTAGTTCATAGTCCTACATC	57.624	38.462	0.00	0.00	0.00	3.06
672	778	2.837591	TCCTTGTTGCTGCTGGATACTA	59.162	45.455	0.00	0.00	37.61	1.82
687	793	2.375146	GAGGTGGTTTGTGTTCCTTGT	58.625	47.619	0.00	0.00	0.00	3.16
739	846	7.875554	TGCATTGAGTTCTACAACAACTATACA	59.124	33.333	0.00	0.00	34.10	2.29
759	866	3.434641	AGATGTTCAGAGACGTTGCATTG	59.565	43.478	0.00	0.00	0.00	2.82
760	867	3.668447	AGATGTTCAGAGACGTTGCATT	58.332	40.909	0.00	0.00	0.00	3.56
843	966	8.677148	ATAATCTTGACAAAACTACAGTGTGT	57.323	30.769	5.88	0.00	32.01	3.72
882	1005	4.609947	TGTGTTGCTCATGTGAAAATGTC	58.390	39.130	0.00	0.00	0.00	3.06
972	1100	5.575995	GCTACTACGGTTTTCTCTGTTTAGG	59.424	44.000	0.00	0.00	0.00	2.69
984	1112	2.829720	TGACATCCAGCTACTACGGTTT	59.170	45.455	0.00	0.00	0.00	3.27
1018	1146	0.606130	TCGCAAATCAGCTTCAGCCA	60.606	50.000	0.00	0.00	43.38	4.75
1045	1173	3.047093	CGACGTGGATGTATTCGCATAA	58.953	45.455	0.00	0.00	0.00	1.90
1053	1181	1.226859	CGTGCCGACGTGGATGTAT	60.227	57.895	0.00	0.00	42.00	2.29
1083	1211	0.737715	GTTGCTCGACTAGTGCCAGG	60.738	60.000	0.00	0.00	38.49	4.45
1084	1212	0.038251	TGTTGCTCGACTAGTGCCAG	60.038	55.000	0.00	0.00	38.49	4.85
1119	1247	3.772060	AAATCGAAGCATGCCTTCTTC	57.228	42.857	15.66	10.65	46.29	2.87
1143	1271	1.541147	CTCAAATTTTCCGGAGCAGCA	59.459	47.619	3.34	0.00	0.00	4.41
1152	1280	0.170339	CGACGGCCCTCAAATTTTCC	59.830	55.000	0.00	0.00	0.00	3.13
1205	1333	4.323868	GCTCAACCATAAGAGAAGGGAAGT	60.324	45.833	0.00	0.00	33.74	3.01
1206	1334	4.080638	AGCTCAACCATAAGAGAAGGGAAG	60.081	45.833	0.00	0.00	33.74	3.46
1208	1336	3.452627	GAGCTCAACCATAAGAGAAGGGA	59.547	47.826	9.40	0.00	33.74	4.20
1224	1352	0.394762	GGAACATGGCCATGAGCTCA	60.395	55.000	44.72	20.79	41.20	4.26
1231	1359	2.044053	CACGGGGAACATGGCCAT	60.044	61.111	14.09	14.09	0.00	4.40
1257	1385	8.027524	ACACTGATAAGTATCATCCATCACTT	57.972	34.615	1.56	0.00	41.46	3.16
1287	1415	5.125900	CCATGATTCACCATTGCTAGAACAA	59.874	40.000	0.00	0.00	0.00	2.83
1299	1427	5.762179	AGTCTAGAAACCATGATTCACCA	57.238	39.130	12.02	0.00	0.00	4.17
1300	1428	7.770897	ACATTAGTCTAGAAACCATGATTCACC	59.229	37.037	12.02	0.39	0.00	4.02
1354	1482	5.604758	TGTTAACTCAGATAGATGCAGCT	57.395	39.130	10.44	10.44	0.00	4.24
1386	1514	4.769688	TGAAAATCCTCTCACGTATGCAT	58.230	39.130	3.79	3.79	0.00	3.96
1428	1556	1.143813	CCCAGGTGCCTCTCCAATAT	58.856	55.000	0.00	0.00	0.00	1.28
1430	1558	0.625683	ATCCCAGGTGCCTCTCCAAT	60.626	55.000	0.00	0.00	0.00	3.16
1484	1612	0.035056	CTCTTTGACCTTCCCCGCAT	60.035	55.000	0.00	0.00	0.00	4.73
1511	1639	2.110899	TCAACTCTCTCTGACCTTCCCT	59.889	50.000	0.00	0.00	0.00	4.20
1533	1661	3.376078	GGTGAGCGACCGTACCCA	61.376	66.667	0.00	0.00	34.02	4.51
1890	2018	2.594592	GGCCTTGACCAGTTGCGT	60.595	61.111	0.00	0.00	0.00	5.24
1961	2089	2.359850	GATCCTTGTGCACCGCCA	60.360	61.111	15.69	0.00	0.00	5.69
1970	2098	4.115199	GCCGGCCTGGATCCTTGT	62.115	66.667	18.11	0.00	42.00	3.16
2049	2177	4.169696	CAACCGCCGCCCCTATCA	62.170	66.667	0.00	0.00	0.00	2.15
2077	2205	2.571757	CTACTGCCGAACTCGCCA	59.428	61.111	0.00	0.00	38.18	5.69
2080	2208	1.148157	CCATGCTACTGCCGAACTCG	61.148	60.000	0.00	0.00	38.71	4.18
2114	2242	1.303561	GCCAGCCACCAACATCTCA	60.304	57.895	0.00	0.00	0.00	3.27
2136	2264	4.415150	CCACCAGCATCCCACGCT	62.415	66.667	0.00	0.00	41.47	5.07
2226	2370	1.151450	CCACCTCCAGTTGCCACTT	59.849	57.895	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.