AutoCloner

Multiple sequence alignment - TraesCS3D01G005600

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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	TraesCS3D01G005600	chr3D	100.000	2516	0	0	1	2516	2152273	2149758	0.000000e+00	4647.0
1	TraesCS3D01G005600	chr3D	88.710	62	5	2	299	359	452490576	452490516	9.650000e-10	75.0
2	TraesCS3D01G005600	chr3D	100.000	29	0	0	737	765	2151460	2151432	1.000000e-03	54.7
3	TraesCS3D01G005600	chr3D	100.000	29	0	0	814	842	2151537	2151509	1.000000e-03	54.7
4	TraesCS3D01G005600	chr3A	90.549	984	44	21	1569	2516	1919290	1920260	0.000000e+00	1256.0
5	TraesCS3D01G005600	chr3A	89.164	646	37	10	1	620	1904224	1904862	0.000000e+00	774.0
6	TraesCS3D01G005600	chr3A	90.722	291	24	1	1281	1568	1918739	1919029	3.930000e-103	385.0
7	TraesCS3D01G005600	chr3A	91.603	262	21	1	1019	1279	1909434	1909695	6.620000e-96	361.0
8	TraesCS3D01G005600	chr3A	92.727	110	7	1	616	725	1904888	1904996	9.320000e-35	158.0
9	TraesCS3D01G005600	chr3A	86.525	141	14	2	2341	2481	95843325	95843190	1.560000e-32	150.0
10	TraesCS3D01G005600	chr3B	86.165	1142	71	44	1440	2512	4332192	4331069	0.000000e+00	1153.0
11	TraesCS3D01G005600	chr3B	92.295	623	38	9	1	620	4334384	4333769	0.000000e+00	876.0
12	TraesCS3D01G005600	chr3B	90.728	604	48	2	765	1362	4332803	4332202	0.000000e+00	798.0
13	TraesCS3D01G005600	chr3B	91.484	411	28	6	4	413	4406791	4406387	2.190000e-155	558.0
14	TraesCS3D01G005600	chr2A	79.495	634	69	28	1745	2346	20809281	20809885	6.520000e-106	394.0
15	TraesCS3D01G005600	chr5B	87.671	292	30	6	1729	2017	670366538	670366250	4.010000e-88	335.0
16	TraesCS3D01G005600	chrUn	96.000	200	8	0	1	200	351353410	351353211	2.410000e-85	326.0
17	TraesCS3D01G005600	chrUn	90.574	244	18	4	378	620	351355343	351355104	4.040000e-83	318.0
18	TraesCS3D01G005600	chrUn	77.856	569	62	28	1740	2285	306110406	306110933	6.810000e-76	294.0
19	TraesCS3D01G005600	chrUn	93.458	107	6	1	619	725	351355075	351354970	9.320000e-35	158.0
20	TraesCS3D01G005600	chr2B	78.207	569	61	28	1740	2285	31678209	31677681	3.140000e-79	305.0
21	TraesCS3D01G005600	chr2B	77.719	570	61	30	1740	2285	31656948	31656421	3.170000e-74	289.0
22	TraesCS3D01G005600	chr5D	87.429	175	21	1	2106	2280	12872122	12871949	1.530000e-47	200.0
23	TraesCS3D01G005600	chr5D	88.276	145	10	4	2336	2478	227771908	227772047	1.550000e-37	167.0
24	TraesCS3D01G005600	chr6A	87.500	144	11	4	2336	2477	31918676	31918814	2.590000e-35	159.0
25	TraesCS3D01G005600	chr6A	93.103	58	3	1	299	355	613904904	613904961	1.600000e-12	84.2
26	TraesCS3D01G005600	chr6B	86.957	138	13	2	2344	2481	22055636	22055504	1.560000e-32	150.0
27	TraesCS3D01G005600	chr1A	86.861	137	13	2	2341	2477	80620369	80620238	5.610000e-32	148.0
28	TraesCS3D01G005600	chr4B	85.417	144	14	4	2336	2477	584687386	584687524	2.610000e-30	143.0
29	TraesCS3D01G005600	chr4A	84.459	148	17	6	2336	2478	602083668	602083814	9.380000e-30	141.0
30	TraesCS3D01G005600	chr4A	90.323	62	4	2	299	359	551127079	551127019	2.070000e-11	80.5
31	TraesCS3D01G005600	chr4D	93.939	66	3	1	2220	2285	244327047	244326983	5.730000e-17	99.0
32	TraesCS3D01G005600	chr4D	90.164	61	4	2	299	357	47343951	47344011	7.460000e-11	78.7
33	TraesCS3D01G005600	chr7B	90.625	64	5	1	299	361	708439152	708439089	1.600000e-12	84.2
34	TraesCS3D01G005600	chr1D	91.379	58	4	1	299	355	352938291	352938348	7.460000e-11	78.7

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	TraesCS3D01G005600	chr3D	2149758	2152273	2515	True	1585.466667	4647	100.000000	1	2516	3	chr3D.!!$R2	2515
1	TraesCS3D01G005600	chr3A	1918739	1920260	1521	False	820.500000	1256	90.635500	1281	2516	2	chr3A.!!$F3	1235
2	TraesCS3D01G005600	chr3A	1904224	1904996	772	False	466.000000	774	90.945500	1	725	2	chr3A.!!$F2	724
3	TraesCS3D01G005600	chr3B	4331069	4334384	3315	True	942.333333	1153	89.729333	1	2512	3	chr3B.!!$R2	2511
4	TraesCS3D01G005600	chr2A	20809281	20809885	604	False	394.000000	394	79.495000	1745	2346	1	chr2A.!!$F1	601
5	TraesCS3D01G005600	chrUn	306110406	306110933	527	False	294.000000	294	77.856000	1740	2285	1	chrUn.!!$F1	545
6	TraesCS3D01G005600	chrUn	351353211	351355343	2132	True	267.333333	326	93.344000	1	725	3	chrUn.!!$R1	724
7	TraesCS3D01G005600	chr2B	31677681	31678209	528	True	305.000000	305	78.207000	1740	2285	1	chr2B.!!$R2	545
8	TraesCS3D01G005600	chr2B	31656421	31656948	527	True	289.000000	289	77.719000	1740	2285	1	chr2B.!!$R1	545

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
945	2192	2.026014	GCACCAACACAGCAACGG	59.974	61.111	0.0	0.0	0.0	4.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2495	4084	0.036388	CTGGCTCCACCGAAAGCTAA	60.036	55.0	0.0	0.0	43.94	3.09	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
93	94	3.037431	GCAGGAGATACATGCGAGAAT	57.963	47.619	0.00	0.00	45.84	2.40
115	116	2.733227	GCATTCAAGGCGATCCACAAAG	60.733	50.000	0.00	0.00	33.74	2.77
116	117	2.270352	TTCAAGGCGATCCACAAAGT	57.730	45.000	0.00	0.00	33.74	2.66
134	135	3.998672	GTCTCCCGTGGCCGACAA	61.999	66.667	0.00	0.00	35.63	3.18
206	207	4.125703	CTGCTCCTCACCAAATGATCTAC	58.874	47.826	0.00	0.00	36.48	2.59
250	251	7.575414	TGTCTGTTCCTCTCAGTAATAGATC	57.425	40.000	0.00	0.00	34.86	2.75
251	252	6.261158	TGTCTGTTCCTCTCAGTAATAGATCG	59.739	42.308	0.00	0.00	34.86	3.69
253	254	6.261158	TCTGTTCCTCTCAGTAATAGATCGTG	59.739	42.308	0.00	0.00	34.86	4.35
258	259	7.258441	TCCTCTCAGTAATAGATCGTGTTTTG	58.742	38.462	0.00	0.00	0.00	2.44
260	261	7.221067	CCTCTCAGTAATAGATCGTGTTTTGTC	59.779	40.741	0.00	0.00	0.00	3.18
261	262	7.827701	TCTCAGTAATAGATCGTGTTTTGTCT	58.172	34.615	0.00	0.00	0.00	3.41
262	263	7.755373	TCTCAGTAATAGATCGTGTTTTGTCTG	59.245	37.037	0.00	0.00	0.00	3.51
263	264	7.375834	TCAGTAATAGATCGTGTTTTGTCTGT	58.624	34.615	0.00	0.00	0.00	3.41
264	265	7.541091	TCAGTAATAGATCGTGTTTTGTCTGTC	59.459	37.037	0.00	0.00	0.00	3.51
267	269	3.309388	AGATCGTGTTTTGTCTGTCGAG	58.691	45.455	0.00	0.00	0.00	4.04
486	511	4.838486	GGTCCAGTCTCGCGCTCG	62.838	72.222	5.56	0.00	0.00	5.03
531	556	3.624305	GCACGAAGCGAGACATAGA	57.376	52.632	0.00	0.00	0.00	1.98
561	586	6.213600	CCCTAGGGCATACAAGACATATTACT	59.786	42.308	16.90	0.00	0.00	2.24
576	601	8.107095	AGACATATTACTGTTTGGTACCACATT	58.893	33.333	16.04	7.34	0.00	2.71
615	640	5.504665	CCCAGAAGCAAATCATAACTTAGCG	60.505	44.000	0.00	0.00	0.00	4.26
645	700	2.094494	TCTTTCCTAGCAAGCTGTCGAG	60.094	50.000	4.53	0.00	0.00	4.04
928	2175	6.971602	AGATATGTAGAGTCACCGTGTATTG	58.028	40.000	0.00	0.00	0.00	1.90
945	2192	2.026014	GCACCAACACAGCAACGG	59.974	61.111	0.00	0.00	0.00	4.44
1014	2261	3.364062	CTTAGCTATGGTTCTCGTCGTG	58.636	50.000	0.00	0.00	0.00	4.35
1041	2288	0.419459	CCCTATCCTATGGCCTCCCT	59.581	60.000	3.32	0.00	0.00	4.20
1125	2372	1.592669	CGTGGCTATGCTAAGCGCT	60.593	57.895	2.64	2.64	43.74	5.92
1173	2420	3.190849	CATGACCTCGCCAGCGTG	61.191	66.667	12.32	9.56	40.74	5.34
1216	2463	2.736995	CCAAGAAGAACGCCGCGA	60.737	61.111	21.79	0.00	0.00	5.87
1224	2471	3.215606	GAACGCCGCGATCATCTGC	62.216	63.158	21.79	0.00	0.00	4.26
1302	2549	2.577644	GCACATGTCATTGCCGCG	60.578	61.111	0.00	0.00	32.21	6.46
1476	2723	3.774959	GACGATGGAGCGATGCGGT	62.775	63.158	0.00	0.00	41.33	5.68
1504	2751	3.781770	GACCTCATCGGCCTGCTCG	62.782	68.421	0.00	0.00	35.61	5.03
1507	2754	4.193334	TCATCGGCCTGCTCGTCG	62.193	66.667	0.00	0.00	0.00	5.12
1537	2784	7.926555	AGTGACCGATAATAAATCATTTCTCGT	59.073	33.333	0.00	0.00	32.71	4.18
1688	3200	2.034999	GGCATTCCGTTGTCCCCA	59.965	61.111	0.00	0.00	0.00	4.96
1689	3201	1.379843	GGCATTCCGTTGTCCCCAT	60.380	57.895	0.00	0.00	0.00	4.00
1690	3202	0.970427	GGCATTCCGTTGTCCCCATT	60.970	55.000	0.00	0.00	0.00	3.16
1692	3204	1.955208	GCATTCCGTTGTCCCCATTCT	60.955	52.381	0.00	0.00	0.00	2.40
1693	3205	2.682563	GCATTCCGTTGTCCCCATTCTA	60.683	50.000	0.00	0.00	0.00	2.10
1694	3206	3.616219	CATTCCGTTGTCCCCATTCTAA	58.384	45.455	0.00	0.00	0.00	2.10
1695	3207	2.773993	TCCGTTGTCCCCATTCTAAC	57.226	50.000	0.00	0.00	0.00	2.34
1698	3210	1.066716	CGTTGTCCCCATTCTAACCGA	60.067	52.381	0.00	0.00	0.00	4.69
1699	3211	2.419574	CGTTGTCCCCATTCTAACCGAT	60.420	50.000	0.00	0.00	0.00	4.18
1700	3212	3.203716	GTTGTCCCCATTCTAACCGATC	58.796	50.000	0.00	0.00	0.00	3.69
1701	3213	2.473070	TGTCCCCATTCTAACCGATCA	58.527	47.619	0.00	0.00	0.00	2.92
1702	3214	2.434336	TGTCCCCATTCTAACCGATCAG	59.566	50.000	0.00	0.00	0.00	2.90
1703	3215	2.698797	GTCCCCATTCTAACCGATCAGA	59.301	50.000	0.00	0.00	0.00	3.27
1736	3274	3.827898	CTGCCGTCCCCGTCTCTC	61.828	72.222	0.00	0.00	0.00	3.20
1737	3275	4.361971	TGCCGTCCCCGTCTCTCT	62.362	66.667	0.00	0.00	0.00	3.10
1740	3278	1.820481	CCGTCCCCGTCTCTCTCTC	60.820	68.421	0.00	0.00	0.00	3.20
1741	3279	1.222387	CGTCCCCGTCTCTCTCTCT	59.778	63.158	0.00	0.00	0.00	3.10
1742	3280	0.812412	CGTCCCCGTCTCTCTCTCTC	60.812	65.000	0.00	0.00	0.00	3.20
1743	3281	0.544697	GTCCCCGTCTCTCTCTCTCT	59.455	60.000	0.00	0.00	0.00	3.10
2090	3669	2.088674	CTCCGCCCTCTTACATCCGG	62.089	65.000	0.00	0.00	37.21	5.14
2266	3845	2.803133	CGTCAACAAAGTCTGCTCCTCA	60.803	50.000	0.00	0.00	0.00	3.86
2289	3876	3.652869	GGGATGAAGGGTAATCCATCTCA	59.347	47.826	4.22	0.00	43.63	3.27
2290	3877	4.505742	GGGATGAAGGGTAATCCATCTCAC	60.506	50.000	4.22	0.00	43.63	3.51
2298	3885	3.243771	GGTAATCCATCTCACCACCTACG	60.244	52.174	0.00	0.00	0.00	3.51
2337	3926	3.111098	GTCACTGCTGCTCAAAAACTTG	58.889	45.455	0.00	0.00	0.00	3.16
2356	3945	1.109323	GTGTTGTTGGCCTGCTCCTT	61.109	55.000	3.32	0.00	0.00	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
93	94	0.322366	TGTGGATCGCCTTGAATGCA	60.322	50.000	0.00	0.00	34.31	3.96
115	116	4.736896	GTCGGCCACGGGAGACAC	62.737	72.222	2.24	0.00	41.39	3.67
171	172	2.685017	AGCAGGCGGATGAGGTCA	60.685	61.111	0.00	0.00	0.00	4.02
206	207	5.757320	AGACAAGCCGAGAAATGATCTATTG	59.243	40.000	0.00	0.00	38.96	1.90
250	251	3.918258	TTTCTCGACAGACAAAACACG	57.082	42.857	0.00	0.00	0.00	4.49
421	446	2.414161	GCGCTCGCTATTTCTGGTTTTT	60.414	45.455	0.00	0.00	38.26	1.94
422	447	1.130561	GCGCTCGCTATTTCTGGTTTT	59.869	47.619	0.00	0.00	38.26	2.43
486	511	0.174617	AAGCTAGTCTCGCCTGAAGC	59.825	55.000	0.00	0.00	38.52	3.86
487	512	1.748493	AGAAGCTAGTCTCGCCTGAAG	59.252	52.381	0.00	0.00	0.00	3.02
561	586	1.333177	GGGCAATGTGGTACCAAACA	58.667	50.000	18.31	12.24	0.00	2.83
615	640	2.514803	TGCTAGGAAAGAAAAGCCCAC	58.485	47.619	0.00	0.00	33.99	4.61
662	721	4.539726	TGATGATCTGGGAAAATTCAGGG	58.460	43.478	0.00	0.00	0.00	4.45
928	2175	2.026014	CCGTTGCTGTGTTGGTGC	59.974	61.111	0.00	0.00	0.00	5.01
945	2192	7.787725	AGTTTGCACTTTGTATATACCTAGC	57.212	36.000	10.38	7.87	0.00	3.42
1024	2271	0.908198	GCAGGGAGGCCATAGGATAG	59.092	60.000	5.01	0.00	0.00	2.08
1026	2273	3.913107	GCAGGGAGGCCATAGGAT	58.087	61.111	5.01	0.00	0.00	3.24
1125	2372	3.565214	TGGCCGCTCTTTGGGTCA	61.565	61.111	0.00	0.00	35.08	4.02
1152	2399	2.580815	CTGGCGAGGTCATGCTCA	59.419	61.111	0.00	0.00	0.00	4.26
1216	2463	1.043816	CCACCTAGGTCGCAGATGAT	58.956	55.000	12.84	0.00	40.67	2.45
1302	2549	1.810030	GTCGACCATGAGTTCGGCC	60.810	63.158	3.51	0.00	0.00	6.13
1438	2685	2.281070	GCGATCCATGTCGGCCAT	60.281	61.111	2.24	0.00	41.72	4.40
1476	2723	2.994995	ATGAGGTCACCGGCGACA	60.995	61.111	23.31	4.34	37.66	4.35
1504	2751	1.935933	ATTATCGGTCACTTGGCGAC	58.064	50.000	0.00	0.00	0.00	5.19
1507	2754	6.560253	ATGATTTATTATCGGTCACTTGGC	57.440	37.500	0.00	0.00	0.00	4.52
1567	3066	2.802247	GCCAGCATTTTGTTTTCTCCAC	59.198	45.455	0.00	0.00	0.00	4.02
1568	3067	2.699846	AGCCAGCATTTTGTTTTCTCCA	59.300	40.909	0.00	0.00	0.00	3.86
1569	3068	3.391506	AGCCAGCATTTTGTTTTCTCC	57.608	42.857	0.00	0.00	0.00	3.71
1570	3069	5.739752	AAAAGCCAGCATTTTGTTTTCTC	57.260	34.783	0.00	0.00	0.00	2.87
1598	3108	5.237048	GCCCAGCATTTGTTTTATTCTCAA	58.763	37.500	0.00	0.00	0.00	3.02
1599	3109	4.322650	GGCCCAGCATTTGTTTTATTCTCA	60.323	41.667	0.00	0.00	0.00	3.27
1602	3112	3.934579	CTGGCCCAGCATTTGTTTTATTC	59.065	43.478	0.00	0.00	0.00	1.75
1603	3113	3.327464	ACTGGCCCAGCATTTGTTTTATT	59.673	39.130	11.63	0.00	34.37	1.40
1605	3115	2.298729	GACTGGCCCAGCATTTGTTTTA	59.701	45.455	11.63	0.00	34.37	1.52
1610	3120	1.065199	TCTAGACTGGCCCAGCATTTG	60.065	52.381	11.63	0.00	34.37	2.32
1612	3122	1.211457	CTTCTAGACTGGCCCAGCATT	59.789	52.381	11.63	0.00	34.37	3.56
1686	3198	2.100916	ACGGTCTGATCGGTTAGAATGG	59.899	50.000	15.53	0.00	0.00	3.16
1688	3200	2.361438	GGACGGTCTGATCGGTTAGAAT	59.639	50.000	15.53	0.00	0.00	2.40
1689	3201	1.747355	GGACGGTCTGATCGGTTAGAA	59.253	52.381	15.53	0.00	0.00	2.10
1690	3202	1.386533	GGACGGTCTGATCGGTTAGA	58.613	55.000	15.53	0.00	0.00	2.10
1692	3204	0.033796	AGGGACGGTCTGATCGGTTA	60.034	55.000	15.53	0.00	0.00	2.85
1693	3205	1.305046	AGGGACGGTCTGATCGGTT	60.305	57.895	15.53	0.00	0.00	4.44
1694	3206	1.753463	GAGGGACGGTCTGATCGGT	60.753	63.158	15.53	0.07	0.00	4.69
1695	3207	1.448922	GAGAGGGACGGTCTGATCGG	61.449	65.000	15.53	0.00	0.00	4.18
1698	3210	2.122167	GCGAGAGGGACGGTCTGAT	61.122	63.158	8.23	0.00	0.00	2.90
1699	3211	2.750637	GCGAGAGGGACGGTCTGA	60.751	66.667	8.23	0.00	0.00	3.27
1700	3212	3.827898	GGCGAGAGGGACGGTCTG	61.828	72.222	8.23	0.00	0.00	3.51
1736	3274	2.838736	CCGGAGAGAGAGAAGAGAGAG	58.161	57.143	0.00	0.00	0.00	3.20
1737	3275	1.134220	GCCGGAGAGAGAGAAGAGAGA	60.134	57.143	5.05	0.00	0.00	3.10
1740	3278	0.395036	TGGCCGGAGAGAGAGAAGAG	60.395	60.000	5.05	0.00	0.00	2.85
1741	3279	0.039764	TTGGCCGGAGAGAGAGAAGA	59.960	55.000	5.05	0.00	0.00	2.87
1742	3280	0.898320	TTTGGCCGGAGAGAGAGAAG	59.102	55.000	5.05	0.00	0.00	2.85
1743	3281	1.482593	GATTTGGCCGGAGAGAGAGAA	59.517	52.381	5.05	0.00	0.00	2.87
1788	3331	0.260523	GCTCCTACCCCTCTGTCTCT	59.739	60.000	0.00	0.00	0.00	3.10
1999	3555	2.168728	CGGGGGAGTAAGAAAGAAGAGG	59.831	54.545	0.00	0.00	0.00	3.69
2078	3657	5.359756	TGATCAATCAACCGGATGTAAGAG	58.640	41.667	9.46	0.00	36.02	2.85
2090	3669	1.596727	GAGAGCGCCTGATCAATCAAC	59.403	52.381	2.29	0.00	36.18	3.18
2266	3845	3.913163	GAGATGGATTACCCTTCATCCCT	59.087	47.826	0.00	0.00	40.54	4.20
2290	3877	2.218603	ACAAGCAACTTTCGTAGGTGG	58.781	47.619	7.31	0.00	42.15	4.61
2298	3885	4.098416	GTGACAACTGACAAGCAACTTTC	58.902	43.478	0.00	0.00	0.00	2.62
2337	3926	1.109323	AAGGAGCAGGCCAACAACAC	61.109	55.000	5.01	0.00	0.00	3.32
2356	3945	2.959372	GCAAGCATGACAGCTGCA	59.041	55.556	15.27	13.46	45.89	4.41
2377	3966	0.904865	TCCCCAGCTGAATCGACTGT	60.905	55.000	17.39	0.00	0.00	3.55
2495	4084	0.036388	CTGGCTCCACCGAAAGCTAA	60.036	55.000	0.00	0.00	43.94	3.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.