AutoCloner

Multiple sequence alignment - TraesCS2D01G158200

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	TraesCS2D01G158200	chr2D	100.000	3283	0	0	1	3283	101874227	101870945	0.000000e+00	6063
1	TraesCS2D01G158200	chr2D	91.713	724	41	10	1363	2072	101956602	101955884	0.000000e+00	987
2	TraesCS2D01G158200	chr2D	91.262	309	27	0	864	1172	101957059	101956751	3.920000e-114	422
3	TraesCS2D01G158200	chr2D	82.213	253	21	16	271	501	101958280	101958030	2.580000e-46	196
4	TraesCS2D01G158200	chr2D	86.139	101	13	1	1482	1581	211199116	211199216	1.250000e-19	108
5	TraesCS2D01G158200	chr2B	91.638	1471	57	22	1625	3056	152843901	152842458	0.000000e+00	1975
6	TraesCS2D01G158200	chr2B	88.485	1129	61	32	183	1281	152845546	152844457	0.000000e+00	1301
7	TraesCS2D01G158200	chr2B	89.506	648	46	13	1278	1909	153126896	153126255	0.000000e+00	800
8	TraesCS2D01G158200	chr2B	87.914	604	47	10	1	592	153128179	153127590	0.000000e+00	688
9	TraesCS2D01G158200	chr2B	85.612	556	40	18	733	1281	153127451	153126929	6.190000e-152	547
10	TraesCS2D01G158200	chr2B	94.611	334	10	4	1299	1632	152844394	152844069	8.130000e-141	510
11	TraesCS2D01G158200	chr2B	92.713	247	16	2	3038	3283	152840193	152839948	4.030000e-94	355
12	TraesCS2D01G158200	chr2B	80.420	143	21	6	1482	1620	266962079	266961940	5.800000e-18	102
13	TraesCS2D01G158200	chr2A	91.452	1205	59	19	2103	3283	100825284	100824100	0.000000e+00	1615
14	TraesCS2D01G158200	chr2A	90.187	1121	75	17	183	1281	100827288	100826181	0.000000e+00	1428
15	TraesCS2D01G158200	chr2A	93.705	842	32	4	1282	2108	100826144	100825309	0.000000e+00	1242
16	TraesCS2D01G158200	chr2A	90.470	724	49	11	1363	2072	100971527	100970810	0.000000e+00	937
17	TraesCS2D01G158200	chr2A	91.613	310	24	2	864	1172	100971981	100971673	8.420000e-116	427
18	TraesCS2D01G158200	chr2A	87.356	174	21	1	6	178	532046003	532045830	7.190000e-47	198
19	TraesCS2D01G158200	chr2A	84.946	186	16	8	328	501	100972760	100972575	9.360000e-41	178
20	TraesCS2D01G158200	chr2A	81.119	143	20	6	1482	1620	265274764	265274625	1.250000e-19	108
21	TraesCS2D01G158200	chr4D	92.664	259	8	4	274	521	498413835	498413577	2.410000e-96	363
22	TraesCS2D01G158200	chr4D	87.845	181	19	2	1	178	44986803	44986623	3.320000e-50	209
23	TraesCS2D01G158200	chr5B	86.592	179	21	3	3	178	703272540	703272362	9.290000e-46	195
24	TraesCS2D01G158200	chr4B	85.475	179	25	1	1	178	666298915	666299093	5.590000e-43	185
25	TraesCS2D01G158200	chr5D	85.246	183	21	5	1	180	543833148	543833327	2.010000e-42	183
26	TraesCS2D01G158200	chr3B	85.393	178	23	2	1	177	449295077	449295252	7.240000e-42	182
27	TraesCS2D01G158200	chr7D	83.957	187	28	2	3	187	178136844	178137030	9.360000e-41	178
28	TraesCS2D01G158200	chr7D	87.162	148	18	1	1352	1498	436114181	436114328	2.030000e-37	167
29	TraesCS2D01G158200	chr1A	84.831	178	26	1	2	178	561586676	561586853	9.360000e-41	178
30	TraesCS2D01G158200	chr7B	87.838	148	17	1	1352	1498	452961926	452962073	4.360000e-39	172
31	TraesCS2D01G158200	chr7A	88.652	141	15	1	1359	1498	486237288	486237148	1.570000e-38	171
32	TraesCS2D01G158200	chr3D	89.720	107	11	0	1373	1479	352367935	352367829	1.590000e-28	137

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	TraesCS2D01G158200	chr2D	101870945	101874227	3282	True	6063.000000	6063	100.000000	1	3283	1	chr2D.!!$R1	3282
1	TraesCS2D01G158200	chr2D	101955884	101958280	2396	True	535.000000	987	88.396000	271	2072	3	chr2D.!!$R2	1801
2	TraesCS2D01G158200	chr2B	152839948	152845546	5598	True	1035.250000	1975	91.861750	183	3283	4	chr2B.!!$R2	3100
3	TraesCS2D01G158200	chr2B	153126255	153128179	1924	True	678.333333	800	87.677333	1	1909	3	chr2B.!!$R3	1908
4	TraesCS2D01G158200	chr2A	100824100	100827288	3188	True	1428.333333	1615	91.781333	183	3283	3	chr2A.!!$R3	3100
5	TraesCS2D01G158200	chr2A	100970810	100972760	1950	True	514.000000	937	89.009667	328	2072	3	chr2A.!!$R4	1744

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
84	85	0.039256	CACCGGCAATGGTTGTTCTG	60.039	55.000	0.00	0.0	41.38	3.02	F
722	1512	1.005332	TGACACTGGCTAGCTCTCTCT	59.995	52.381	15.72	0.0	0.00	3.10	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1022	1872	0.671781	GCGCTTCAGCCTCTTCTTCA	60.672	55.0	0.0	0.0	37.91	3.02	R
2668	3837	2.477357	CGAAGCTGCCTGTGATTGATTG	60.477	50.0	0.0	0.0	0.00	2.67	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
21	22	4.020617	CAAGGTCAGGCCGGCTCA	62.021	66.667	28.56	7.49	43.70	4.26
28	29	1.600636	CAGGCCGGCTCAAGTTTGA	60.601	57.895	28.56	0.00	35.57	2.69
63	64	3.181967	CGTCGGCGGCTCTTTCTG	61.182	66.667	10.76	0.00	0.00	3.02
67	68	3.435186	GGCGGCTCTTTCTGGCAC	61.435	66.667	0.00	0.00	37.78	5.01
83	84	1.805428	GCACCGGCAATGGTTGTTCT	61.805	55.000	0.00	0.00	41.38	3.01
84	85	0.039256	CACCGGCAATGGTTGTTCTG	60.039	55.000	0.00	0.00	41.38	3.02
93	94	4.209703	GCAATGGTTGTTCTGTTGTTCATG	59.790	41.667	0.00	0.00	0.00	3.07
99	100	3.476552	TGTTCTGTTGTTCATGGACCTC	58.523	45.455	0.46	0.00	0.00	3.85
220	227	3.010027	TGACAGGAATTGAATGGGCTACA	59.990	43.478	0.00	0.00	0.00	2.74
221	228	3.356290	ACAGGAATTGAATGGGCTACAC	58.644	45.455	0.00	0.00	0.00	2.90
246	253	4.436852	CGTAACTGTTGTGGTTCATATGCC	60.437	45.833	2.69	0.00	0.00	4.40
269	276	4.188462	TGGTGGAGAATAGTTGCATTACG	58.812	43.478	0.00	0.00	0.00	3.18
273	280	5.523916	GTGGAGAATAGTTGCATTACGTGAT	59.476	40.000	0.00	0.00	0.00	3.06
297	308	2.228822	ACGATGGACAGGAAATGTTTGC	59.771	45.455	0.00	0.00	44.17	3.68
317	342	2.202388	CCGTGCTGCTCAATTGCG	60.202	61.111	0.00	0.00	35.36	4.85
377	405	1.421485	GCAAAGTGAGCGTCATCCG	59.579	57.895	0.00	0.00	40.40	4.18
475	526	5.846203	AGGTGTCAAGGTGAAAAATGATTG	58.154	37.500	0.00	0.00	0.00	2.67
478	529	5.922544	GTGTCAAGGTGAAAAATGATTGAGG	59.077	40.000	0.00	0.00	0.00	3.86
481	532	6.207417	GTCAAGGTGAAAAATGATTGAGGAGA	59.793	38.462	0.00	0.00	0.00	3.71
718	1508	2.096248	GTACTGACACTGGCTAGCTCT	58.904	52.381	15.72	0.00	0.00	4.09
722	1512	1.005332	TGACACTGGCTAGCTCTCTCT	59.995	52.381	15.72	0.00	0.00	3.10
723	1513	1.676006	GACACTGGCTAGCTCTCTCTC	59.324	57.143	15.72	0.00	0.00	3.20
724	1514	1.284785	ACACTGGCTAGCTCTCTCTCT	59.715	52.381	15.72	0.00	0.00	3.10
725	1515	1.949525	CACTGGCTAGCTCTCTCTCTC	59.050	57.143	15.72	0.00	0.00	3.20
726	1516	1.846439	ACTGGCTAGCTCTCTCTCTCT	59.154	52.381	15.72	0.00	0.00	3.10
727	1517	2.224606	CTGGCTAGCTCTCTCTCTCTG	58.775	57.143	15.72	0.00	0.00	3.35
728	1518	1.563879	TGGCTAGCTCTCTCTCTCTGT	59.436	52.381	15.72	0.00	0.00	3.41
899	1739	3.818787	CTCTGCCATTGCCGCCAC	61.819	66.667	0.00	0.00	36.33	5.01
971	1811	1.427020	GCAACGCCATTGAGCTCTC	59.573	57.895	16.19	0.00	41.23	3.20
1074	1924	1.813192	GGAGGAGGACGAGAAGCTG	59.187	63.158	0.00	0.00	0.00	4.24
1164	2014	1.208293	GCCTATAGCCACATCCCTAGC	59.792	57.143	0.00	0.00	34.35	3.42
1233	2085	1.404391	GCAGTAGCTTACTCGCCAGTA	59.596	52.381	0.00	0.00	36.76	2.74
1249	2105	3.458189	CCAGTAATGCTAGTGCCACTAC	58.542	50.000	0.00	0.00	38.71	2.73
1260	2116	4.836125	AGTGCCACTACAACATTTTCTG	57.164	40.909	0.00	0.00	0.00	3.02
1269	2125	9.612620	CCACTACAACATTTTCTGTCTAAATTC	57.387	33.333	0.00	0.00	36.98	2.17
1307	2218	9.179909	TGTGGAGAACTAGTTAACAATTTTGAA	57.820	29.630	8.42	0.00	0.00	2.69
1308	2219	9.665264	GTGGAGAACTAGTTAACAATTTTGAAG	57.335	33.333	8.42	0.00	0.00	3.02
1309	2220	9.403583	TGGAGAACTAGTTAACAATTTTGAAGT	57.596	29.630	8.42	0.00	0.00	3.01
1326	2237	4.406456	TGAAGTAGTGCCAATTTGATGGT	58.594	39.130	0.00	0.00	42.75	3.55
1327	2238	4.218200	TGAAGTAGTGCCAATTTGATGGTG	59.782	41.667	0.00	0.00	42.75	4.17
1376	2287	4.744867	GCTGCATTATTAGGCCTTGAGAGA	60.745	45.833	12.58	0.00	0.00	3.10
1445	2356	3.403558	AAGAGGGGCGCCTTCTCC	61.404	66.667	31.66	23.63	39.09	3.71
2069	3189	1.829533	CAGCAGCAACCACCACCTT	60.830	57.895	0.00	0.00	0.00	3.50
2144	3294	1.112916	TGGACGAGCTCAAGTGGTCA	61.113	55.000	15.40	1.41	34.46	4.02
2367	3521	3.002042	CACGACATGCAAAGATCCAGATC	59.998	47.826	0.00	0.00	38.09	2.75
2398	3552	8.595533	CGTATACGCGAGTTTATAATACTCCTA	58.404	37.037	15.93	0.00	46.40	2.94
2399	3553	9.913451	GTATACGCGAGTTTATAATACTCCTAG	57.087	37.037	15.93	11.89	46.40	3.02
2400	3554	6.874288	ACGCGAGTTTATAATACTCCTAGT	57.126	37.500	15.93	12.28	46.40	2.57
2441	3600	4.038642	TGGTGAGGTTTTGGCTTGTAAATC	59.961	41.667	0.00	0.00	0.00	2.17
2517	3680	8.712285	ATTTGGTGATTGATTGATTGATTGAC	57.288	30.769	0.00	0.00	0.00	3.18
2519	3682	5.127519	TGGTGATTGATTGATTGATTGACCC	59.872	40.000	0.00	0.00	0.00	4.46
2568	3731	2.492088	TGACGAACACAGAAGGATCGAT	59.508	45.455	0.00	0.00	37.27	3.59
2668	3837	1.271325	TGGTGTGGTGTGGTGATGATC	60.271	52.381	0.00	0.00	0.00	2.92
2939	4117	1.594331	GATGGACCGGCTTAATCACC	58.406	55.000	0.00	0.00	0.00	4.02
2978	4157	7.518731	TGAAATGAAGTTTGGAAACGAAAAG	57.481	32.000	0.00	0.00	43.51	2.27
3022	4202	4.905429	TGTTAGAAGGTGCAGCTTTCATA	58.095	39.130	30.17	20.05	35.86	2.15
3023	4203	5.500234	TGTTAGAAGGTGCAGCTTTCATAT	58.500	37.500	30.17	16.62	35.86	1.78
3057	4237	6.601613	TGCCTAGGTAGGTTGATTTTGTATTG	59.398	38.462	11.31	0.00	45.42	1.90
3101	6563	6.938507	TGTTTCTTAGGCGACCTAGAAATAA	58.061	36.000	15.91	7.49	37.42	1.40
3168	6632	4.287067	TCACCTCAAGAGTAGCCTGATTTT	59.713	41.667	0.00	0.00	0.00	1.82
3172	6636	4.433615	TCAAGAGTAGCCTGATTTTAGCG	58.566	43.478	0.00	0.00	0.00	4.26
3173	6637	2.827652	AGAGTAGCCTGATTTTAGCGC	58.172	47.619	0.00	0.00	0.00	5.92
3206	6670	0.169672	CTGCAAAAGAGGTGCGATGG	59.830	55.000	0.00	0.00	45.27	3.51
3234	6698	1.772182	GGACGGCTATCAATGTCGAG	58.228	55.000	0.00	0.00	32.17	4.04

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	0.946221	CTGTCGCCGCTCTCAAACTT	60.946	55.000	0.00	0.00	0.00	2.66
50	51	3.435186	GTGCCAGAAAGAGCCGCC	61.435	66.667	0.00	0.00	0.00	6.13
58	59	2.274645	CCATTGCCGGTGCCAGAAA	61.275	57.895	1.90	0.00	36.33	2.52
63	64	2.763627	GAACAACCATTGCCGGTGCC	62.764	60.000	1.90	0.00	39.95	5.01
66	67	0.467290	ACAGAACAACCATTGCCGGT	60.467	50.000	1.90	0.00	42.71	5.28
67	68	0.673437	AACAGAACAACCATTGCCGG	59.327	50.000	0.00	0.00	0.00	6.13
83	84	2.038426	ACATCGAGGTCCATGAACAACA	59.962	45.455	0.00	0.00	0.00	3.33
84	85	2.699954	ACATCGAGGTCCATGAACAAC	58.300	47.619	0.00	0.00	0.00	3.32
121	122	1.072331	CAGTGGAGTACAAAGCACCCT	59.928	52.381	0.00	0.00	0.00	4.34
192	193	4.640201	CCCATTCAATTCCTGTCAATACGT	59.360	41.667	0.00	0.00	0.00	3.57
194	196	4.646492	AGCCCATTCAATTCCTGTCAATAC	59.354	41.667	0.00	0.00	0.00	1.89
220	227	2.975266	TGAACCACAACAGTTACGTGT	58.025	42.857	0.00	0.00	0.00	4.49
221	228	5.617609	CATATGAACCACAACAGTTACGTG	58.382	41.667	0.00	0.00	0.00	4.49
246	253	4.271049	CGTAATGCAACTATTCTCCACCAG	59.729	45.833	0.00	0.00	0.00	4.00
269	276	4.386867	TTTCCTGTCCATCGTCTATCAC	57.613	45.455	0.00	0.00	0.00	3.06
273	280	4.819105	AACATTTCCTGTCCATCGTCTA	57.181	40.909	0.00	0.00	36.98	2.59
289	300	1.007038	CAGCACGGCAGCAAACATT	60.007	52.632	0.00	0.00	36.85	2.71
297	308	1.154093	CAATTGAGCAGCACGGCAG	60.154	57.895	0.00	0.00	35.83	4.85
317	342	1.804151	TGCAAGTTATCTGGAACGCAC	59.196	47.619	0.00	0.00	34.36	5.34
475	526	2.202810	CGCGCCTTTCCTCTCCTC	60.203	66.667	0.00	0.00	0.00	3.71
478	529	0.953960	TTTTCCGCGCCTTTCCTCTC	60.954	55.000	0.00	0.00	0.00	3.20
481	532	2.626780	GCTTTTCCGCGCCTTTCCT	61.627	57.895	0.00	0.00	0.00	3.36
604	1314	7.745620	AGTTGGTCGTGAAATCTTTTATCTT	57.254	32.000	0.00	0.00	0.00	2.40
718	1508	2.379005	ACACACACACACAGAGAGAGA	58.621	47.619	0.00	0.00	0.00	3.10
722	1512	2.758423	ACAGTACACACACACACAGAGA	59.242	45.455	0.00	0.00	0.00	3.10
723	1513	3.116300	GACAGTACACACACACACAGAG	58.884	50.000	0.00	0.00	0.00	3.35
724	1514	2.758423	AGACAGTACACACACACACAGA	59.242	45.455	0.00	0.00	0.00	3.41
725	1515	3.165058	AGACAGTACACACACACACAG	57.835	47.619	0.00	0.00	0.00	3.66
726	1516	3.444388	TGTAGACAGTACACACACACACA	59.556	43.478	0.00	0.00	0.00	3.72
727	1517	4.036567	TGTAGACAGTACACACACACAC	57.963	45.455	0.00	0.00	0.00	3.82
728	1518	4.722361	TTGTAGACAGTACACACACACA	57.278	40.909	0.00	0.00	0.00	3.72
969	1809	1.859564	CTGAGACGACGCGAACGAG	60.860	63.158	28.40	15.92	43.93	4.18
1022	1872	0.671781	GCGCTTCAGCCTCTTCTTCA	60.672	55.000	0.00	0.00	37.91	3.02
1074	1924	3.426159	CGTACTTGGCAATGTGGTTCATC	60.426	47.826	0.00	0.00	35.48	2.92
1164	2014	4.196193	AGAGCTAGTGCAGTAGTAGTGAG	58.804	47.826	25.71	5.73	42.74	3.51
1223	2075	1.471676	GCACTAGCATTACTGGCGAGT	60.472	52.381	6.61	6.61	46.05	4.18
1233	2085	3.417069	TGTTGTAGTGGCACTAGCATT	57.583	42.857	26.87	3.68	44.61	3.56
1249	2105	9.270576	CATCTCGAATTTAGACAGAAAATGTTG	57.729	33.333	0.00	0.00	44.17	3.33
1260	2116	6.183360	CCACAGAAACCATCTCGAATTTAGAC	60.183	42.308	0.00	0.00	35.73	2.59
1269	2125	2.996621	GTTCTCCACAGAAACCATCTCG	59.003	50.000	0.00	0.00	40.49	4.04
1307	2218	3.766545	ACACCATCAAATTGGCACTACT	58.233	40.909	0.00	0.00	40.68	2.57
1308	2219	4.519540	AACACCATCAAATTGGCACTAC	57.480	40.909	0.00	0.00	40.68	2.73
1309	2220	6.404184	CGATTAACACCATCAAATTGGCACTA	60.404	38.462	0.00	0.00	40.68	2.74
1376	2287	2.124819	CTGCAGCTCTTCCCGCAT	60.125	61.111	0.00	0.00	33.15	4.73
1445	2356	3.114390	AGGTCCTCCTCCTCCTGG	58.886	66.667	0.00	0.00	40.58	4.45
1526	2437	4.657824	ACCTCGTTGTCGGTGCGG	62.658	66.667	0.00	0.00	37.69	5.69
2367	3521	6.872710	TTATAAACTCGCGTATACGTTACG	57.127	37.500	25.04	19.58	43.13	3.18
2398	3552	7.676947	TCACCAAACATTTCTTAGTAGCTACT	58.323	34.615	28.50	28.50	40.24	2.57
2399	3553	7.064728	CCTCACCAAACATTTCTTAGTAGCTAC	59.935	40.741	16.43	16.43	0.00	3.58
2400	3554	7.103641	CCTCACCAAACATTTCTTAGTAGCTA	58.896	38.462	0.00	0.00	0.00	3.32
2441	3600	3.190953	AGAGAGAACGTAAGGGAGAAACG	59.809	47.826	0.00	0.00	46.39	3.60
2517	3680	4.925061	TTTACACGCAAAGTTATACGGG	57.075	40.909	0.00	0.00	34.45	5.28
2519	3682	5.279751	GCACTTTTACACGCAAAGTTATACG	59.720	40.000	0.00	0.00	41.58	3.06
2611	3775	6.910536	ATTAACCACGCAAAAATCAAACAA	57.089	29.167	0.00	0.00	0.00	2.83
2668	3837	2.477357	CGAAGCTGCCTGTGATTGATTG	60.477	50.000	0.00	0.00	0.00	2.67
2939	4117	0.604243	TTTCATGGAACCGTGACCCG	60.604	55.000	14.35	0.00	41.12	5.28
2941	4119	2.432444	TCATTTCATGGAACCGTGACC	58.568	47.619	14.35	0.00	41.12	4.02
2978	4157	5.006941	ACAAAATTCAAAAGCACAGTGATGC	59.993	36.000	4.15	3.18	46.50	3.91
3022	4202	3.707316	CCTACCTAGGCAGCTAGATGAT	58.293	50.000	13.26	1.47	36.53	2.45
3023	4203	3.162147	CCTACCTAGGCAGCTAGATGA	57.838	52.381	13.26	0.00	36.53	2.92
3172	6636	3.414700	CAGTTGCACGACCTCGGC	61.415	66.667	0.00	0.94	44.95	5.54
3173	6637	3.414700	GCAGTTGCACGACCTCGG	61.415	66.667	0.00	0.00	44.95	4.63
3196	6660	3.768633	GATGAAGACCATCGCACCT	57.231	52.632	0.00	0.00	41.88	4.00
3206	6670	1.337071	TGATAGCCGTCCGATGAAGAC	59.663	52.381	0.00	0.00	0.00	3.01
3234	6698	9.855021	AAAACCATAGCAATAGTTATTTGTCAC	57.145	29.630	0.00	0.00	0.00	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.