AutoCloner

Multiple sequence alignment - TraesCS3B01G213300

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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	TraesCS3B01G213300	chr3B	100.000	2198	0	0	1	2198	252854942	252852745	0.000000e+00	4060
1	TraesCS3B01G213300	chr3B	90.725	345	30	1	1850	2192	109065750	109066094	1.990000e-125	459
2	TraesCS3B01G213300	chr3D	95.493	1664	72	3	1	1662	174073430	174071768	0.000000e+00	2654
3	TraesCS3B01G213300	chrUn	95.614	1596	67	3	69	1662	220605610	220604016	0.000000e+00	2556
4	TraesCS3B01G213300	chrUn	95.028	543	26	1	1121	1662	220587764	220587222	0.000000e+00	852
5	TraesCS3B01G213300	chr3A	92.137	1259	89	7	405	1662	212767282	212766033	0.000000e+00	1768
6	TraesCS3B01G213300	chr3A	90.262	267	21	5	1678	1942	710951379	710951116	5.810000e-91	344
7	TraesCS3B01G213300	chr3A	89.308	159	15	1	1932	2088	708691633	708691791	4.790000e-47	198
8	TraesCS3B01G213300	chr3A	87.850	107	13	0	2086	2192	708691863	708691969	2.290000e-25	126
9	TraesCS3B01G213300	chr5B	88.395	517	48	7	1677	2188	34913296	34913805	1.440000e-171	612
10	TraesCS3B01G213300	chr1B	88.193	415	43	4	1678	2088	410330682	410331094	7.050000e-135	490
11	TraesCS3B01G213300	chr1B	86.650	412	45	5	1678	2088	658356772	658357174	4.300000e-122	448
12	TraesCS3B01G213300	chr1B	80.831	313	41	10	910	1214	662031358	662031057	6.100000e-56	228
13	TraesCS3B01G213300	chr1B	89.720	107	11	0	2086	2192	410331145	410331251	1.060000e-28	137
14	TraesCS3B01G213300	chr1B	87.850	107	13	0	2086	2192	658357246	658357352	2.290000e-25	126
15	TraesCS3B01G213300	chr4D	87.065	402	39	11	1678	2075	337135042	337134650	2.000000e-120	442
16	TraesCS3B01G213300	chr4D	86.364	110	15	0	2086	2195	337134585	337134476	1.070000e-23	121
17	TraesCS3B01G213300	chr1A	83.934	361	45	12	1677	2028	426524319	426524675	1.260000e-87	333
18	TraesCS3B01G213300	chr1A	80.645	310	43	10	910	1214	571863239	571862942	7.900000e-55	224
19	TraesCS3B01G213300	chr5D	87.814	279	29	4	1678	1954	53873794	53873519	2.720000e-84	322
20	TraesCS3B01G213300	chr5D	90.254	236	18	5	1678	1911	431899682	431899914	9.860000e-79	303
21	TraesCS3B01G213300	chr5D	90.411	146	12	1	1945	2088	53873083	53872938	8.010000e-45	191
22	TraesCS3B01G213300	chr1D	78.585	509	80	14	744	1231	475967448	475966948	2.120000e-80	309
23	TraesCS3B01G213300	chr1D	93.458	107	7	0	2086	2192	473343530	473343636	2.260000e-35	159
24	TraesCS3B01G213300	chr6B	81.694	366	50	12	1677	2028	694109704	694110066	2.760000e-74	289
25	TraesCS3B01G213300	chr6B	80.618	356	37	16	1733	2088	18125375	18125698	1.690000e-61	246
26	TraesCS3B01G213300	chr7B	79.722	360	61	9	1678	2028	91966327	91966683	1.300000e-62	250
27	TraesCS3B01G213300	chr2B	90.265	113	11	0	2086	2198	717870080	717869968	4.890000e-32	148

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	TraesCS3B01G213300	chr3B	252852745	252854942	2197	True	4060.0	4060	100.0000	1	2198	1	chr3B.!!$R1	2197
1	TraesCS3B01G213300	chr3D	174071768	174073430	1662	True	2654.0	2654	95.4930	1	1662	1	chr3D.!!$R1	1661
2	TraesCS3B01G213300	chrUn	220604016	220605610	1594	True	2556.0	2556	95.6140	69	1662	1	chrUn.!!$R2	1593
3	TraesCS3B01G213300	chrUn	220587222	220587764	542	True	852.0	852	95.0280	1121	1662	1	chrUn.!!$R1	541
4	TraesCS3B01G213300	chr3A	212766033	212767282	1249	True	1768.0	1768	92.1370	405	1662	1	chr3A.!!$R1	1257
5	TraesCS3B01G213300	chr5B	34913296	34913805	509	False	612.0	612	88.3950	1677	2188	1	chr5B.!!$F1	511
6	TraesCS3B01G213300	chr1B	410330682	410331251	569	False	313.5	490	88.9565	1678	2192	2	chr1B.!!$F1	514
7	TraesCS3B01G213300	chr1B	658356772	658357352	580	False	287.0	448	87.2500	1678	2192	2	chr1B.!!$F2	514
8	TraesCS3B01G213300	chr4D	337134476	337135042	566	True	281.5	442	86.7145	1678	2195	2	chr4D.!!$R1	517
9	TraesCS3B01G213300	chr5D	53872938	53873794	856	True	256.5	322	89.1125	1678	2088	2	chr5D.!!$R1	410
10	TraesCS3B01G213300	chr1D	475966948	475967448	500	True	309.0	309	78.5850	744	1231	1	chr1D.!!$R1	487

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
243	245	0.108585	AAACGGTCCTGCATGAGTGT	59.891	50.0	0.0	0.0	0.0	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1663	1685	0.034896	AAGAGCAACCGATCCACGTT	59.965	50.0	0.0	0.0	40.78	3.99	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
155	157	2.094762	AACACATGTTCTACCTCGGC	57.905	50.000	0.00	0.00	31.64	5.54
159	161	1.346395	ACATGTTCTACCTCGGCACAA	59.654	47.619	0.00	0.00	0.00	3.33
196	198	0.830648	CCGGATGGACCAAAGCTCTA	59.169	55.000	0.00	0.00	38.90	2.43
243	245	0.108585	AAACGGTCCTGCATGAGTGT	59.891	50.000	0.00	0.00	0.00	3.55
303	305	2.560504	CTATTGCGGGCTGTTGATACA	58.439	47.619	0.00	0.00	0.00	2.29
338	340	5.821204	ACCAGAGAAAACATTTCAACTTCG	58.179	37.500	5.71	0.00	0.00	3.79
341	343	5.909610	CAGAGAAAACATTTCAACTTCGGAC	59.090	40.000	5.71	0.00	0.00	4.79
499	501	1.531149	CTTCCCACTAGTTGCAACGTG	59.469	52.381	23.21	23.15	0.00	4.49
624	626	6.594937	TCATTTTCAAATTTTCTAGCCCATGC	59.405	34.615	0.00	0.00	37.95	4.06
625	627	4.470334	TTCAAATTTTCTAGCCCATGCC	57.530	40.909	0.00	0.00	38.69	4.40
630	632	2.530460	TTTCTAGCCCATGCCAATGT	57.470	45.000	0.00	0.00	38.69	2.71
632	634	0.625316	TCTAGCCCATGCCAATGTGT	59.375	50.000	0.00	0.00	38.69	3.72
633	635	1.005805	TCTAGCCCATGCCAATGTGTT	59.994	47.619	0.00	0.00	38.69	3.32
774	776	4.508551	TGGAAACTGCCTATCATCACAT	57.491	40.909	0.00	0.00	0.00	3.21
862	864	8.946935	CAAACATAAACATAATCTACATGCACG	58.053	33.333	0.00	0.00	0.00	5.34
954	959	3.256631	CCAGCAAGTAGGAAATTGTGCTT	59.743	43.478	0.00	0.00	40.22	3.91
979	984	2.759191	TCCATCTCGCATTATCTGTGC	58.241	47.619	0.00	0.00	39.18	4.57
1074	1092	2.730090	GCTGTTCTTGATGATGGTTGCG	60.730	50.000	0.00	0.00	0.00	4.85
1241	1262	1.687493	CACTCTCCCCTCTGTCCCC	60.687	68.421	0.00	0.00	0.00	4.81
1251	1272	1.072965	CCTCTGTCCCCATGATTAGCC	59.927	57.143	0.00	0.00	0.00	3.93
1256	1277	2.174639	TGTCCCCATGATTAGCCGAATT	59.825	45.455	0.00	0.00	0.00	2.17
1278	1299	0.179137	CGTGAGCGCTCATTCCACTA	60.179	55.000	39.91	14.61	42.18	2.74
1293	1314	1.672737	CCACTAGTTCTGCATGCGTCA	60.673	52.381	14.09	0.00	0.00	4.35
1303	1324	1.132834	TGCATGCGTCAATGTGATTCC	59.867	47.619	14.09	0.00	0.00	3.01
1393	1414	5.597182	GTGGATGAGAGTATAACTGTACCCA	59.403	44.000	0.00	0.00	0.00	4.51
1408	1429	7.691993	ACTGTACCCATGATAAGGAAGTATT	57.308	36.000	0.00	0.00	0.00	1.89
1565	1587	6.900568	TGCAAAAGAACATTTTGTAACCAG	57.099	33.333	12.99	0.00	40.47	4.00
1590	1612	1.538204	CGGTCGTCCCTATTCCACATG	60.538	57.143	0.00	0.00	0.00	3.21
1621	1643	6.870965	GGTAGGAGATATAACAGTGAGCAATG	59.129	42.308	0.00	0.00	0.00	2.82
1622	1644	6.737720	AGGAGATATAACAGTGAGCAATGA	57.262	37.500	4.83	0.00	0.00	2.57
1662	1684	5.237127	AGCCATATCACATGTGTTTGATACG	59.763	40.000	24.63	8.32	37.50	3.06
1663	1685	5.236263	GCCATATCACATGTGTTTGATACGA	59.764	40.000	24.63	3.11	37.50	3.43
1664	1686	6.238347	GCCATATCACATGTGTTTGATACGAA	60.238	38.462	24.63	2.35	37.50	3.85
1665	1687	7.125755	CCATATCACATGTGTTTGATACGAAC	58.874	38.462	24.63	0.00	37.50	3.95
1666	1688	4.639189	TCACATGTGTTTGATACGAACG	57.361	40.909	24.63	0.00	0.00	3.95
1667	1689	4.052608	TCACATGTGTTTGATACGAACGT	58.947	39.130	24.63	5.03	0.00	3.99
1668	1690	4.084797	TCACATGTGTTTGATACGAACGTG	60.085	41.667	24.63	0.00	0.00	4.49
1669	1691	3.185594	ACATGTGTTTGATACGAACGTGG	59.814	43.478	10.14	0.00	0.00	4.94
1670	1692	3.095102	TGTGTTTGATACGAACGTGGA	57.905	42.857	10.14	0.00	0.00	4.02
1671	1693	3.655486	TGTGTTTGATACGAACGTGGAT	58.345	40.909	10.14	0.00	0.00	3.41
1672	1694	3.676172	TGTGTTTGATACGAACGTGGATC	59.324	43.478	10.14	6.63	0.00	3.36
1673	1695	2.918600	TGTTTGATACGAACGTGGATCG	59.081	45.455	10.14	6.58	45.47	3.69
1674	1696	2.197792	TTGATACGAACGTGGATCGG	57.802	50.000	12.32	0.00	44.32	4.18
1675	1697	1.097232	TGATACGAACGTGGATCGGT	58.903	50.000	12.32	1.24	44.32	4.69
1682	1704	0.034896	AACGTGGATCGGTTGCTCTT	59.965	50.000	0.00	0.00	44.69	2.85
1684	1706	1.361668	CGTGGATCGGTTGCTCTTGG	61.362	60.000	0.00	0.00	35.71	3.61
1760	1785	1.004891	ACCATCCTTCTCCTCCCCC	59.995	63.158	0.00	0.00	0.00	5.40
1838	1865	1.918800	CTTCCCCCTTCCGTCCAGT	60.919	63.158	0.00	0.00	0.00	4.00
2097	2647	2.752358	CTGGAGGCTGGAGTTGCA	59.248	61.111	0.00	0.00	0.00	4.08
2156	2706	4.443934	CGAGAGGTGGAGGAAGGT	57.556	61.111	0.00	0.00	0.00	3.50
2167	2717	2.116983	GAGGAAGGTGTGGAGCTGCA	62.117	60.000	2.72	2.72	0.00	4.41
2195	2745	2.107750	CAGATCTGGCGCGGATGT	59.892	61.111	15.38	11.49	28.51	3.06
2196	2746	1.953138	CAGATCTGGCGCGGATGTC	60.953	63.158	15.38	6.81	28.51	3.06
2197	2747	3.032609	GATCTGGCGCGGATGTCG	61.033	66.667	17.07	0.00	42.76	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	54	9.226606	CAGAATACCCTTTGTTACTGTTATGAA	57.773	33.333	0.00	0.00	0.00	2.57
55	56	8.561738	ACAGAATACCCTTTGTTACTGTTATG	57.438	34.615	0.00	0.00	33.15	1.90
58	59	7.891498	AAACAGAATACCCTTTGTTACTGTT	57.109	32.000	0.00	0.00	40.97	3.16
136	138	1.346395	TGCCGAGGTAGAACATGTGTT	59.654	47.619	0.00	0.00	41.64	3.32
155	157	6.146898	CGGGTTAACAAATAAGAACCTTGTG	58.853	40.000	8.10	0.00	41.00	3.33
159	161	5.245584	TCCGGGTTAACAAATAAGAACCT	57.754	39.130	8.10	0.00	41.00	3.50
243	245	3.922171	ACATTGGGGCACTTTTCAAAA	57.078	38.095	0.00	0.00	0.00	2.44
303	305	7.027874	TGTTTTCTCTGGTTATCACCCTAAT	57.972	36.000	0.00	0.00	43.49	1.73
338	340	2.361438	CACTTGGACCTAGTATCCGTCC	59.639	54.545	8.34	7.88	45.30	4.79
341	343	1.687123	CCCACTTGGACCTAGTATCCG	59.313	57.143	8.34	0.00	39.30	4.18
379	381	6.745116	ACGAACGATTGACATATATCTTGGA	58.255	36.000	0.14	0.00	0.00	3.53
481	483	0.882927	GCACGTTGCAACTAGTGGGA	60.883	55.000	27.81	0.00	44.26	4.37
499	501	1.290203	CACATGATCCAGGTACACGC	58.710	55.000	0.00	0.00	0.00	5.34
624	626	4.545823	AGTCGTAAACACAACACATTGG	57.454	40.909	0.00	0.00	40.42	3.16
625	627	6.281848	ACTAGTCGTAAACACAACACATTG	57.718	37.500	0.00	0.00	41.98	2.82
633	635	8.137437	GCCCTATAATAACTAGTCGTAAACACA	58.863	37.037	0.00	0.00	0.00	3.72
862	864	6.746104	CTCTATATATAGAGCAATGCACGC	57.254	41.667	28.53	1.65	46.80	5.34
954	959	5.525012	CACAGATAATGCGAGATGGAAAGAA	59.475	40.000	0.00	0.00	0.00	2.52
979	984	0.872388	GGTCGGTTGTTGTTGGCTAG	59.128	55.000	0.00	0.00	0.00	3.42
1241	1262	3.740832	TCACGCTAATTCGGCTAATCATG	59.259	43.478	0.00	0.00	0.00	3.07
1278	1299	1.198408	CACATTGACGCATGCAGAACT	59.802	47.619	19.57	0.00	0.00	3.01
1293	1314	2.557924	TGAAAAGCAGCGGAATCACATT	59.442	40.909	0.00	0.00	0.00	2.71
1303	1324	6.865726	AGTATATAGAGACATGAAAAGCAGCG	59.134	38.462	0.00	0.00	0.00	5.18
1433	1454	8.791327	TGTAGCAATTGAAGATAAATCTGTGA	57.209	30.769	10.34	0.00	37.19	3.58
1565	1587	2.973180	GAATAGGGACGACCGCCTGC	62.973	65.000	0.00	0.00	46.96	4.85
1590	1612	6.097839	TCACTGTTATATCTCCTACCACCAAC	59.902	42.308	0.00	0.00	0.00	3.77
1621	1643	5.897377	ATGGCTACACAATTACCAAGTTC	57.103	39.130	0.00	0.00	33.30	3.01
1622	1644	7.067008	GTGATATGGCTACACAATTACCAAGTT	59.933	37.037	0.00	0.00	33.30	2.66
1662	1684	0.389948	AGAGCAACCGATCCACGTTC	60.390	55.000	0.00	0.00	40.78	3.95
1663	1685	0.034896	AAGAGCAACCGATCCACGTT	59.965	50.000	0.00	0.00	40.78	3.99
1664	1686	0.670546	CAAGAGCAACCGATCCACGT	60.671	55.000	0.00	0.00	40.78	4.49
1665	1687	1.361668	CCAAGAGCAACCGATCCACG	61.362	60.000	0.00	0.00	42.18	4.94
1666	1688	1.026718	CCCAAGAGCAACCGATCCAC	61.027	60.000	0.00	0.00	0.00	4.02
1667	1689	1.299648	CCCAAGAGCAACCGATCCA	59.700	57.895	0.00	0.00	0.00	3.41
1668	1690	0.744771	GACCCAAGAGCAACCGATCC	60.745	60.000	0.00	0.00	0.00	3.36
1669	1691	1.084370	CGACCCAAGAGCAACCGATC	61.084	60.000	0.00	0.00	0.00	3.69
1670	1692	1.079127	CGACCCAAGAGCAACCGAT	60.079	57.895	0.00	0.00	0.00	4.18
1671	1693	2.342279	CGACCCAAGAGCAACCGA	59.658	61.111	0.00	0.00	0.00	4.69
1672	1694	3.423154	GCGACCCAAGAGCAACCG	61.423	66.667	0.00	0.00	0.00	4.44
1673	1695	2.032681	AGCGACCCAAGAGCAACC	59.967	61.111	0.00	0.00	0.00	3.77
1674	1696	2.035442	GGAGCGACCCAAGAGCAAC	61.035	63.158	0.00	0.00	0.00	4.17
1675	1697	2.347490	GGAGCGACCCAAGAGCAA	59.653	61.111	0.00	0.00	0.00	3.91
1726	1749	2.123468	GTGGGTGGGTTGTTGGCT	60.123	61.111	0.00	0.00	0.00	4.75
1731	1756	1.368268	AAGGATGGTGGGTGGGTTGT	61.368	55.000	0.00	0.00	0.00	3.32
1734	1759	1.151587	AGAAGGATGGTGGGTGGGT	60.152	57.895	0.00	0.00	0.00	4.51
1915	1942	4.643387	GCCTTCGTGCACCACCCT	62.643	66.667	12.15	0.00	0.00	4.34
2001	2477	4.828925	GCAGAGGAGCTCCACCGC	62.829	72.222	33.90	26.94	38.89	5.68
2138	2688	1.305381	ACCTTCCTCCACCTCTCGG	60.305	63.158	0.00	0.00	0.00	4.63
2152	2702	2.281070	CGTGCAGCTCCACACCTT	60.281	61.111	8.83	0.00	35.47	3.50

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.