AutoCloner

Multiple sequence alignment - TraesCS2D01G211100

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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	TraesCS2D01G211100	chr2D	100.000	3834	0	0	1	3834	168233646	168237479	0.000000e+00	7081.0
1	TraesCS2D01G211100	chr2A	94.211	3161	105	21	1	3138	182312186	182309081	0.000000e+00	4752.0
2	TraesCS2D01G211100	chr2A	94.390	713	32	7	3127	3834	721914706	721915415	0.000000e+00	1088.0
3	TraesCS2D01G211100	chr2B	94.301	2720	69	24	309	3008	229995039	229992386	0.000000e+00	4085.0
4	TraesCS2D01G211100	chr2B	96.377	138	5	0	3001	3138	229991985	229991848	1.070000e-55	228.0
5	TraesCS2D01G211100	chr4A	89.416	1540	124	21	1100	2622	613667356	613668873	0.000000e+00	1905.0
6	TraesCS2D01G211100	chr4A	94.101	712	35	7	3125	3834	717041775	717041069	0.000000e+00	1075.0
7	TraesCS2D01G211100	chr4A	82.090	67	7	4	203	264	637225101	637225167	7.000000e-03	52.8
8	TraesCS2D01G211100	chr5D	89.727	1353	111	20	1291	2626	556154727	556153386	0.000000e+00	1703.0
9	TraesCS2D01G211100	chr5D	94.231	52	3	0	1100	1151	556154811	556154760	3.180000e-11	80.5
10	TraesCS2D01G211100	chr1B	94.053	723	30	11	3118	3834	302037529	302038244	0.000000e+00	1085.0
11	TraesCS2D01G211100	chr6B	94.610	705	28	6	3138	3834	230769398	230768696	0.000000e+00	1083.0
12	TraesCS2D01G211100	chr6B	94.350	708	31	8	3129	3834	680042983	680043683	0.000000e+00	1077.0
13	TraesCS2D01G211100	chr5B	94.242	712	33	7	3127	3834	166706366	166707073	0.000000e+00	1081.0
14	TraesCS2D01G211100	chrUn	94.150	718	26	12	3127	3834	48576205	48575494	0.000000e+00	1079.0
15	TraesCS2D01G211100	chr5A	93.767	722	31	12	3123	3834	556723509	556724226	0.000000e+00	1072.0
16	TraesCS2D01G211100	chr5A	88.696	115	12	1	81	195	374665641	374665754	5.160000e-29	139.0
17	TraesCS2D01G211100	chr3D	93.416	729	35	10	3114	3834	569061840	569062563	0.000000e+00	1068.0
18	TraesCS2D01G211100	chr3D	100.000	28	0	0	237	264	546329995	546330022	7.000000e-03	52.8
19	TraesCS2D01G211100	chr7A	87.302	126	12	3	83	205	536776116	536775992	1.440000e-29	141.0
20	TraesCS2D01G211100	chr7A	82.927	123	17	4	83	202	109434020	109433899	1.460000e-19	108.0
21	TraesCS2D01G211100	chr7A	84.545	110	14	1	83	192	454460788	454460894	5.240000e-19	106.0
22	TraesCS2D01G211100	chr4B	83.636	110	17	1	78	187	586069211	586069103	6.780000e-18	102.0
23	TraesCS2D01G211100	chr6D	82.301	113	16	2	83	195	85164604	85164712	1.130000e-15	95.3
24	TraesCS2D01G211100	chr7D	82.569	109	15	4	83	190	619292211	619292316	4.080000e-15	93.5
25	TraesCS2D01G211100	chr7D	91.111	45	4	0	220	264	558890564	558890520	1.150000e-05	62.1
26	TraesCS2D01G211100	chr7B	83.000	100	16	1	83	182	63634872	63634774	5.280000e-14	89.8
27	TraesCS2D01G211100	chr7B	100.000	32	0	0	275	306	623049765	623049796	4.140000e-05	60.2
28	TraesCS2D01G211100	chr7B	100.000	32	0	0	275	306	623099609	623099640	4.140000e-05	60.2
29	TraesCS2D01G211100	chr1D	100.000	28	0	0	237	264	464856820	464856793	7.000000e-03	52.8
30	TraesCS2D01G211100	chr1A	100.000	28	0	0	237	264	96473379	96473352	7.000000e-03	52.8

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	TraesCS2D01G211100	chr2D	168233646	168237479	3833	False	7081.00	7081	100.000	1	3834	1	chr2D.!!$F1	3833
1	TraesCS2D01G211100	chr2A	182309081	182312186	3105	True	4752.00	4752	94.211	1	3138	1	chr2A.!!$R1	3137
2	TraesCS2D01G211100	chr2A	721914706	721915415	709	False	1088.00	1088	94.390	3127	3834	1	chr2A.!!$F1	707
3	TraesCS2D01G211100	chr2B	229991848	229995039	3191	True	2156.50	4085	95.339	309	3138	2	chr2B.!!$R1	2829
4	TraesCS2D01G211100	chr4A	613667356	613668873	1517	False	1905.00	1905	89.416	1100	2622	1	chr4A.!!$F1	1522
5	TraesCS2D01G211100	chr4A	717041069	717041775	706	True	1075.00	1075	94.101	3125	3834	1	chr4A.!!$R1	709
6	TraesCS2D01G211100	chr5D	556153386	556154811	1425	True	891.75	1703	91.979	1100	2626	2	chr5D.!!$R1	1526
7	TraesCS2D01G211100	chr1B	302037529	302038244	715	False	1085.00	1085	94.053	3118	3834	1	chr1B.!!$F1	716
8	TraesCS2D01G211100	chr6B	230768696	230769398	702	True	1083.00	1083	94.610	3138	3834	1	chr6B.!!$R1	696
9	TraesCS2D01G211100	chr6B	680042983	680043683	700	False	1077.00	1077	94.350	3129	3834	1	chr6B.!!$F1	705
10	TraesCS2D01G211100	chr5B	166706366	166707073	707	False	1081.00	1081	94.242	3127	3834	1	chr5B.!!$F1	707
11	TraesCS2D01G211100	chrUn	48575494	48576205	711	True	1079.00	1079	94.150	3127	3834	1	chrUn.!!$R1	707
12	TraesCS2D01G211100	chr5A	556723509	556724226	717	False	1072.00	1072	93.767	3123	3834	1	chr5A.!!$F2	711
13	TraesCS2D01G211100	chr3D	569061840	569062563	723	False	1068.00	1068	93.416	3114	3834	1	chr3D.!!$F2	720

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
813	819	0.034337	GTTGCTTACGTGGACCCTCA	59.966	55.000	0.00	0.0	0.0	3.86	F
2095	2120	2.202919	CTGGCGGCGATCATGACA	60.203	61.111	12.98	0.0	0.0	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2224	2249	1.105759	GGTTGATCCTGCCCATCAGC	61.106	60.000	0.0	0.0	41.5	4.26	R
3264	3724	1.069358	GTGAGAAGGAGGATAAGCGGG	59.931	57.143	0.0	0.0	0.0	6.13	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
76	77	6.199908	CGAAACAACATTGGATGCAGTTTTAA	59.800	34.615	3.63	0.00	39.24	1.52
79	80	8.449251	AACAACATTGGATGCAGTTTTAATTT	57.551	26.923	0.00	0.00	29.76	1.82
103	104	4.036262	GTGATTGCTAGATCTCAGTCGACT	59.964	45.833	13.58	13.58	0.00	4.18
218	219	2.988570	TGTTCTACTCTCTCCGTCTCC	58.011	52.381	0.00	0.00	0.00	3.71
220	221	3.773667	TGTTCTACTCTCTCCGTCTCCTA	59.226	47.826	0.00	0.00	0.00	2.94
258	259	3.014604	AGTGTAGTGTCAGAAACGCTC	57.985	47.619	0.00	0.00	45.69	5.03
264	265	6.250951	GTGTAGTGTCAGAAACGCTCTTATAC	59.749	42.308	0.00	0.00	45.69	1.47
265	266	4.745649	AGTGTCAGAAACGCTCTTATACC	58.254	43.478	0.00	0.00	45.69	2.73
266	267	3.546670	GTGTCAGAAACGCTCTTATACCG	59.453	47.826	0.00	0.00	35.42	4.02
269	270	1.202498	AGAAACGCTCTTATACCGGGC	60.202	52.381	6.32	0.00	0.00	6.13
273	274	0.387929	CGCTCTTATACCGGGCTTCA	59.612	55.000	6.32	0.00	0.00	3.02
342	343	5.234543	GGTAACTGAAACAGTCAAGAGACAC	59.765	44.000	4.88	0.00	44.62	3.67
361	362	2.028130	ACGGCTGAACATTCCAAAACA	58.972	42.857	0.00	0.00	0.00	2.83
362	363	2.223711	ACGGCTGAACATTCCAAAACAC	60.224	45.455	0.00	0.00	0.00	3.32
489	492	6.780522	TGGAAAGGGTAGCAAAGATACTTTTT	59.219	34.615	0.00	0.00	0.00	1.94
583	587	1.044231	TGATGTACCCATACGGCGGT	61.044	55.000	13.24	1.39	33.60	5.68
587	591	1.109323	GTACCCATACGGCGGTACCT	61.109	60.000	13.24	0.00	45.92	3.08
595	599	1.140375	CGGCGGTACCTACTGGAAC	59.860	63.158	10.90	0.00	37.04	3.62
597	601	1.140375	GCGGTACCTACTGGAACCG	59.860	63.158	10.90	8.32	42.86	4.44
617	623	5.429130	ACCGATCCAAGATAAGGAAGTTTC	58.571	41.667	5.81	0.00	38.93	2.78
625	631	3.199946	AGATAAGGAAGTTTCATGCCGGA	59.800	43.478	5.05	0.00	0.00	5.14
627	633	1.755179	AGGAAGTTTCATGCCGGATG	58.245	50.000	5.05	6.59	0.00	3.51
641	647	2.684881	GCCGGATGTTGTCAAATGATCT	59.315	45.455	5.05	0.00	0.00	2.75
642	648	3.488047	GCCGGATGTTGTCAAATGATCTG	60.488	47.826	5.05	0.00	0.00	2.90
643	649	3.065786	CCGGATGTTGTCAAATGATCTGG	59.934	47.826	0.00	11.37	0.00	3.86
644	650	3.940852	CGGATGTTGTCAAATGATCTGGA	59.059	43.478	0.00	0.00	0.00	3.86
645	651	4.577693	CGGATGTTGTCAAATGATCTGGAT	59.422	41.667	0.00	0.00	0.00	3.41
646	652	5.066893	CGGATGTTGTCAAATGATCTGGATT	59.933	40.000	0.00	0.00	0.00	3.01
647	653	6.501781	GGATGTTGTCAAATGATCTGGATTC	58.498	40.000	0.00	0.00	0.00	2.52
721	727	2.108075	TGACTGGGTTTCACATGATGGT	59.892	45.455	0.00	0.00	0.00	3.55
736	742	3.640407	GGTGGTGGAGCAGGAGCA	61.640	66.667	0.00	0.00	45.49	4.26
761	767	5.380651	CGTAGTACGTAGCTGATGGATTAC	58.619	45.833	14.62	0.00	36.74	1.89
813	819	0.034337	GTTGCTTACGTGGACCCTCA	59.966	55.000	0.00	0.00	0.00	3.86
836	842	6.844388	TCAGGTCATCAAGTATATTACACCCT	59.156	38.462	0.00	0.00	0.00	4.34
921	929	3.838271	GCAGCTCGTCGATCCCCA	61.838	66.667	0.00	0.00	0.00	4.96
1420	1439	2.647158	GGTGGTCTCGGAGTGGTCC	61.647	68.421	4.69	4.93	39.88	4.46
1483	1502	4.329545	TTCTTCGCCGGCTGCCTT	62.330	61.111	26.68	0.00	36.24	4.35
1576	1595	3.770040	TCCATGTCCGTCGCTGGG	61.770	66.667	0.00	0.00	0.00	4.45
1864	1883	4.863548	TCCTATTCTACTTCCTCGTCCAA	58.136	43.478	0.00	0.00	0.00	3.53
2095	2120	2.202919	CTGGCGGCGATCATGACA	60.203	61.111	12.98	0.00	0.00	3.58
2152	2177	2.251642	GCTCAACGTCGGCAACCTT	61.252	57.895	0.00	0.00	0.00	3.50
2224	2249	1.142748	GTCCATCCTCTCGTGGCTG	59.857	63.158	0.00	0.00	35.43	4.85
2700	2730	5.925397	TCGTGTAATTAAACTAAACTGCGGA	59.075	36.000	0.00	0.00	0.00	5.54
2743	2780	2.726821	TGCTCCCATTCCAATCAAGTC	58.273	47.619	0.00	0.00	0.00	3.01
2746	2783	3.703052	GCTCCCATTCCAATCAAGTCAAT	59.297	43.478	0.00	0.00	0.00	2.57
2917	2967	6.072783	GCTTATTCTAACTCTGCATGGAATCC	60.073	42.308	0.49	0.00	0.00	3.01
2949	2999	2.946990	TGCTGATAGATTCGTCGTACCA	59.053	45.455	0.00	0.00	0.00	3.25
2950	3000	3.568430	TGCTGATAGATTCGTCGTACCAT	59.432	43.478	0.00	0.00	0.00	3.55
3059	3517	2.672996	GTGTTGCACCCTGCCGAT	60.673	61.111	0.00	0.00	44.23	4.18
3091	3549	6.844097	GGAATACTGTTTCCACCCATTTTA	57.156	37.500	13.39	0.00	43.92	1.52
3099	3557	8.100164	ACTGTTTCCACCCATTTTAATTTATGG	58.900	33.333	0.00	0.00	40.82	2.74
3178	3637	1.305201	TGCAACGGGAGAGAAAACAC	58.695	50.000	0.00	0.00	0.00	3.32
3264	3724	3.065233	TGCGAGGCATCATATTTGTGTTC	59.935	43.478	0.00	0.00	31.71	3.18
3285	3745	1.757118	CCGCTTATCCTCCTTCTCACA	59.243	52.381	0.00	0.00	0.00	3.58
3457	3938	5.947663	TGAGAAATCTGTTGTTTTCCCCTA	58.052	37.500	0.00	0.00	34.25	3.53
3467	3948	5.217393	GTTGTTTTCCCCTACGACATTTTC	58.783	41.667	0.00	0.00	0.00	2.29
3559	4040	2.280592	GGATCGCCGCCGGTATTT	60.281	61.111	4.45	0.00	34.56	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	52	3.287312	ACTGCATCCAATGTTGTTTCG	57.713	42.857	0.00	0.00	0.00	3.46
57	58	7.714377	TCACAAATTAAAACTGCATCCAATGTT	59.286	29.630	0.00	0.00	0.00	2.71
76	77	5.752472	CGACTGAGATCTAGCAATCACAAAT	59.248	40.000	0.00	0.00	0.00	2.32
79	80	3.947834	TCGACTGAGATCTAGCAATCACA	59.052	43.478	0.00	0.00	0.00	3.58
149	150	8.970691	AAGAAAATTTTACACGGATCTTCATG	57.029	30.769	2.75	0.00	0.00	3.07
150	151	9.981114	AAAAGAAAATTTTACACGGATCTTCAT	57.019	25.926	2.75	0.00	0.00	2.57
209	210	3.712091	AAACGCTATTAGGAGACGGAG	57.288	47.619	0.00	0.00	0.00	4.63
234	235	3.855895	GCGTTTCTGACACTACACTAGCA	60.856	47.826	0.00	0.00	0.00	3.49
243	244	4.674623	CGGTATAAGAGCGTTTCTGACACT	60.675	45.833	0.00	0.00	44.09	3.55
258	259	5.855045	AGACTTAATGAAGCCCGGTATAAG	58.145	41.667	0.00	1.12	35.97	1.73
264	265	2.691409	TGAGACTTAATGAAGCCCGG	57.309	50.000	0.00	0.00	35.97	5.73
265	266	4.191544	TGATTGAGACTTAATGAAGCCCG	58.808	43.478	0.00	0.00	35.97	6.13
266	267	5.649831	AGTTGATTGAGACTTAATGAAGCCC	59.350	40.000	0.00	0.00	35.97	5.19
269	270	8.768957	TCTCAGTTGATTGAGACTTAATGAAG	57.231	34.615	0.00	0.00	46.42	3.02
342	343	2.223688	TGTGTTTTGGAATGTTCAGCCG	60.224	45.455	0.00	0.00	0.00	5.52
361	362	1.234821	CGGTGCCATGTGTTTACTGT	58.765	50.000	0.00	0.00	0.00	3.55
362	363	1.234821	ACGGTGCCATGTGTTTACTG	58.765	50.000	0.00	0.00	0.00	2.74
489	492	3.349022	CCGTTGCTATTGTTTTAGGGGA	58.651	45.455	0.00	0.00	0.00	4.81
551	555	7.595819	ATGGGTACATCAAAAGTTTCTTTGA	57.404	32.000	0.00	1.58	46.45	2.69
559	563	3.275999	GCCGTATGGGTACATCAAAAGT	58.724	45.455	2.41	0.00	38.53	2.66
595	599	5.428253	TGAAACTTCCTTATCTTGGATCGG	58.572	41.667	0.00	0.00	33.09	4.18
597	601	6.238869	GGCATGAAACTTCCTTATCTTGGATC	60.239	42.308	0.00	0.00	33.09	3.36
617	623	2.164017	TCATTTGACAACATCCGGCATG	59.836	45.455	0.00	4.32	38.64	4.06
625	631	6.096423	CCAGAATCCAGATCATTTGACAACAT	59.904	38.462	0.00	0.00	0.00	2.71
627	633	5.649395	TCCAGAATCCAGATCATTTGACAAC	59.351	40.000	0.00	0.00	0.00	3.32
641	647	3.256879	CGATTAGCTAGCTCCAGAATCCA	59.743	47.826	23.26	0.00	0.00	3.41
642	648	3.843999	CGATTAGCTAGCTCCAGAATCC	58.156	50.000	23.26	8.51	0.00	3.01
643	649	3.249917	GCGATTAGCTAGCTCCAGAATC	58.750	50.000	23.26	21.72	44.04	2.52
644	650	3.311486	GCGATTAGCTAGCTCCAGAAT	57.689	47.619	23.26	15.39	44.04	2.40
645	651	2.802787	GCGATTAGCTAGCTCCAGAA	57.197	50.000	23.26	10.60	44.04	3.02
678	684	3.742882	ACGATATTGATCCGCATGTTCTG	59.257	43.478	0.00	0.00	0.00	3.02
761	767	2.789399	AGGGGTATCAAGGGTAAATGGG	59.211	50.000	0.00	0.00	0.00	4.00
764	770	4.667858	TGCATAGGGGTATCAAGGGTAAAT	59.332	41.667	0.00	0.00	0.00	1.40
766	772	3.671079	TGCATAGGGGTATCAAGGGTAA	58.329	45.455	0.00	0.00	0.00	2.85
767	773	3.354233	TGCATAGGGGTATCAAGGGTA	57.646	47.619	0.00	0.00	0.00	3.69
768	774	2.206322	TGCATAGGGGTATCAAGGGT	57.794	50.000	0.00	0.00	0.00	4.34
769	775	2.291153	CCATGCATAGGGGTATCAAGGG	60.291	54.545	0.00	0.00	0.00	3.95
770	776	2.881403	GCCATGCATAGGGGTATCAAGG	60.881	54.545	14.50	2.82	0.00	3.61
771	777	2.040813	AGCCATGCATAGGGGTATCAAG	59.959	50.000	6.00	0.00	36.59	3.02
772	778	2.040278	GAGCCATGCATAGGGGTATCAA	59.960	50.000	7.68	0.00	38.81	2.57
773	779	1.630369	GAGCCATGCATAGGGGTATCA	59.370	52.381	7.68	0.00	38.81	2.15
774	780	1.406069	CGAGCCATGCATAGGGGTATC	60.406	57.143	7.68	3.96	38.81	2.24
813	819	7.076446	AGAGGGTGTAATATACTTGATGACCT	58.924	38.462	0.00	0.00	0.00	3.85
828	834	6.206787	TGTTAGAATATGGGAGAGGGTGTAA	58.793	40.000	0.00	0.00	0.00	2.41
836	842	7.670140	AGTCACGATATGTTAGAATATGGGAGA	59.330	37.037	0.00	0.00	0.00	3.71
921	929	1.001268	ACGCACAAGATCGATCGCTAT	60.001	47.619	19.33	0.00	0.00	2.97
1047	1055	1.231296	GCCGCTAGCTTATCTTGGCC	61.231	60.000	13.93	0.00	38.99	5.36
2152	2177	2.752030	CTCAGGTAGAGGTTGGATCCA	58.248	52.381	11.44	11.44	40.84	3.41
2224	2249	1.105759	GGTTGATCCTGCCCATCAGC	61.106	60.000	0.00	0.00	41.50	4.26
2435	2460	2.359850	CAGCGCCTGCCTTACCAA	60.360	61.111	2.29	0.00	44.31	3.67
2700	2730	9.189156	AGCATGGTATTAACTTTGTACATCAAT	57.811	29.630	0.00	0.00	35.84	2.57
2743	2780	2.180017	GCGACCTGGCAGCAATTG	59.820	61.111	9.56	0.00	0.00	2.32
2917	2967	3.103447	TCTATCAGCATCTTCCAAGCG	57.897	47.619	0.00	0.00	0.00	4.68
3091	3549	9.605951	AGCAATTCAATATAGGTCCCATAAATT	57.394	29.630	0.00	0.00	0.00	1.82
3099	3557	7.573968	AGACAAAGCAATTCAATATAGGTCC	57.426	36.000	0.00	0.00	0.00	4.46
3178	3637	3.308595	TGTTGAGTTAAGAGCGTGTGTTG	59.691	43.478	0.00	0.00	0.00	3.33
3264	3724	1.069358	GTGAGAAGGAGGATAAGCGGG	59.931	57.143	0.00	0.00	0.00	6.13
3457	3938	3.270877	GCATACCTCTGGAAAATGTCGT	58.729	45.455	0.00	0.00	0.00	4.34
3467	3948	3.827008	ACTACACATGCATACCTCTGG	57.173	47.619	0.00	0.00	0.00	3.86
3513	3994	6.010850	TGCAAATAAACACCCCACTATAACA	58.989	36.000	0.00	0.00	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.