AutoCloner

Multiple sequence alignment - TraesCS1D01G128600

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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	TraesCS1D01G128600	chr1D	100.000	2288	0	0	1	2288	141896573	141898860	0.000000e+00	4226
1	TraesCS1D01G128600	chr1D	86.346	1289	159	12	1	1281	338745308	338746587	0.000000e+00	1389
2	TraesCS1D01G128600	chr1D	84.982	819	89	21	1	808	473796706	473795911	0.000000e+00	800
3	TraesCS1D01G128600	chr1D	84.821	336	41	7	1406	1736	338746587	338746917	1.690000e-86	329
4	TraesCS1D01G128600	chr1D	88.760	258	18	7	2041	2288	84806545	84806289	2.860000e-79	305
5	TraesCS1D01G128600	chr1D	79.801	302	49	10	1445	1743	114212491	114212199	2.300000e-50	209
6	TraesCS1D01G128600	chr1D	91.406	128	6	5	2016	2140	141898475	141898600	1.090000e-38	171
7	TraesCS1D01G128600	chr1D	91.406	128	6	5	1903	2028	141898588	141898712	1.090000e-38	171
8	TraesCS1D01G128600	chr1B	91.847	2036	109	27	280	2287	196058813	196060819	0.000000e+00	2787
9	TraesCS1D01G128600	chr1A	86.067	1780	176	33	1	1739	148747815	148746067	0.000000e+00	1847
10	TraesCS1D01G128600	chr4B	84.981	1598	218	14	1	1585	168575318	168573730	0.000000e+00	1602
11	TraesCS1D01G128600	chr2B	79.765	1275	209	30	1	1242	14596553	14597811	0.000000e+00	880
12	TraesCS1D01G128600	chr2B	85.059	850	105	10	1	846	449828270	449829101	0.000000e+00	846
13	TraesCS1D01G128600	chr2B	86.875	160	18	3	1445	1603	449838451	449838608	2.340000e-40	176
14	TraesCS1D01G128600	chr4D	85.837	812	101	9	781	1585	108048658	108049462	0.000000e+00	850
15	TraesCS1D01G128600	chr4D	84.899	841	98	12	1	831	108047787	108048608	0.000000e+00	822
16	TraesCS1D01G128600	chr7A	84.681	816	107	12	1	808	238871713	238870908	0.000000e+00	798
17	TraesCS1D01G128600	chr7A	88.433	268	26	5	1762	2028	38206940	38207203	3.670000e-83	318
18	TraesCS1D01G128600	chr7A	81.159	276	42	7	2	276	664693917	664694183	1.780000e-51	213
19	TraesCS1D01G128600	chr7A	84.466	103	14	2	203	304	539297027	539296926	1.450000e-17	100
20	TraesCS1D01G128600	chr3D	86.357	733	98	1	635	1367	116088060	116088790	0.000000e+00	798
21	TraesCS1D01G128600	chr3D	85.764	288	19	6	2016	2288	36572771	36573051	3.720000e-73	285
22	TraesCS1D01G128600	chr3D	89.952	209	19	1	1763	1971	461374304	461374510	3.750000e-68	268
23	TraesCS1D01G128600	chr4A	80.172	1044	165	19	709	1748	416227891	416226886	0.000000e+00	743
24	TraesCS1D01G128600	chr4A	89.179	268	26	3	1762	2028	676494333	676494598	4.710000e-87	331
25	TraesCS1D01G128600	chr4A	85.124	242	28	6	1445	1679	518856976	518857216	8.170000e-60	241
26	TraesCS1D01G128600	chr5D	88.145	523	54	7	892	1410	512389655	512390173	1.160000e-172	616
27	TraesCS1D01G128600	chr3A	84.653	606	92	1	806	1410	51696283	51696888	9.040000e-169	603
28	TraesCS1D01G128600	chr3A	77.941	272	36	17	457	727	453297913	453297665	5.090000e-32	148
29	TraesCS1D01G128600	chr7D	91.418	268	21	2	1762	2028	58994541	58994807	1.290000e-97	366
30	TraesCS1D01G128600	chr7D	87.037	270	31	4	1760	2028	165487036	165487302	3.690000e-78	302
31	TraesCS1D01G128600	chr7D	85.714	126	12	6	2035	2159	85204544	85204664	6.630000e-26	128
32	TraesCS1D01G128600	chr7B	91.204	216	17	2	1763	1978	691041627	691041414	2.220000e-75	292
33	TraesCS1D01G128600	chr5B	81.148	366	53	7	1285	1636	44768994	44769357	1.730000e-71	279
34	TraesCS1D01G128600	chr5B	84.387	269	37	4	1762	2028	490235434	490235699	2.250000e-65	259
35	TraesCS1D01G128600	chr2D	85.556	270	20	5	1762	2028	645179273	645179526	4.850000e-67	265
36	TraesCS1D01G128600	chr2D	79.225	284	34	11	2022	2283	84744717	84744997	8.400000e-40	174
37	TraesCS1D01G128600	chrUn	82.946	258	14	6	2051	2278	93046266	93046523	2.980000e-49	206
38	TraesCS1D01G128600	chrUn	88.298	94	9	2	1936	2028	93046263	93046355	6.680000e-21	111
39	TraesCS1D01G128600	chr3B	93.130	131	8	1	2029	2159	41349072	41348943	8.340000e-45	191
40	TraesCS1D01G128600	chr3B	87.755	98	9	1	2191	2288	41336305	41336211	6.680000e-21	111
41	TraesCS1D01G128600	chr2A	78.477	302	27	18	2016	2283	74956866	74956569	1.820000e-36	163

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	TraesCS1D01G128600	chr1D	141896573	141898860	2287	False	1522.666667	4226	94.270667	1	2288	3	chr1D.!!$F1	2287
1	TraesCS1D01G128600	chr1D	338745308	338746917	1609	False	859.000000	1389	85.583500	1	1736	2	chr1D.!!$F2	1735
2	TraesCS1D01G128600	chr1D	473795911	473796706	795	True	800.000000	800	84.982000	1	808	1	chr1D.!!$R3	807
3	TraesCS1D01G128600	chr1B	196058813	196060819	2006	False	2787.000000	2787	91.847000	280	2287	1	chr1B.!!$F1	2007
4	TraesCS1D01G128600	chr1A	148746067	148747815	1748	True	1847.000000	1847	86.067000	1	1739	1	chr1A.!!$R1	1738
5	TraesCS1D01G128600	chr4B	168573730	168575318	1588	True	1602.000000	1602	84.981000	1	1585	1	chr4B.!!$R1	1584
6	TraesCS1D01G128600	chr2B	14596553	14597811	1258	False	880.000000	880	79.765000	1	1242	1	chr2B.!!$F1	1241
7	TraesCS1D01G128600	chr2B	449828270	449829101	831	False	846.000000	846	85.059000	1	846	1	chr2B.!!$F2	845
8	TraesCS1D01G128600	chr4D	108047787	108049462	1675	False	836.000000	850	85.368000	1	1585	2	chr4D.!!$F1	1584
9	TraesCS1D01G128600	chr7A	238870908	238871713	805	True	798.000000	798	84.681000	1	808	1	chr7A.!!$R1	807
10	TraesCS1D01G128600	chr3D	116088060	116088790	730	False	798.000000	798	86.357000	635	1367	1	chr3D.!!$F2	732
11	TraesCS1D01G128600	chr4A	416226886	416227891	1005	True	743.000000	743	80.172000	709	1748	1	chr4A.!!$R1	1039
12	TraesCS1D01G128600	chr5D	512389655	512390173	518	False	616.000000	616	88.145000	892	1410	1	chr5D.!!$F1	518
13	TraesCS1D01G128600	chr3A	51696283	51696888	605	False	603.000000	603	84.653000	806	1410	1	chr3A.!!$F1	604

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
93	100	0.321653	GGCTGGACCACGATCTTGTT	60.322	55.0	0.0	0.0	38.86	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1570	1814	0.671796	GGTTGGCCGCTTGTTTAAGT	59.328	50.0	0.0	0.0	36.27	2.24	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	100	0.321653	GGCTGGACCACGATCTTGTT	60.322	55.000	0.00	0.00	38.86	2.83
115	122	3.517296	TCCTCGCTGGAATCTAGATCT	57.483	47.619	5.51	0.00	42.94	2.75
124	131	6.529829	CGCTGGAATCTAGATCTATTAGCAAC	59.470	42.308	5.51	0.00	0.00	4.17
129	136	8.732531	GGAATCTAGATCTATTAGCAACGTACT	58.267	37.037	5.51	0.00	0.00	2.73
184	191	1.190643	CCGCTTCTTCTTCCTCCTCT	58.809	55.000	0.00	0.00	0.00	3.69
185	192	1.552792	CCGCTTCTTCTTCCTCCTCTT	59.447	52.381	0.00	0.00	0.00	2.85
186	193	2.027653	CCGCTTCTTCTTCCTCCTCTTT	60.028	50.000	0.00	0.00	0.00	2.52
190	197	4.222810	GCTTCTTCTTCCTCCTCTTTCTCT	59.777	45.833	0.00	0.00	0.00	3.10
227	234	2.554344	GGTGCCACCAAAGTCCTATTCA	60.554	50.000	9.55	0.00	38.42	2.57
228	235	2.749621	GTGCCACCAAAGTCCTATTCAG	59.250	50.000	0.00	0.00	0.00	3.02
268	275	0.324738	CCTGAGGAGCCCTGTACTCA	60.325	60.000	0.00	0.00	37.61	3.41
305	312	1.117994	TGCCCTCTGTCTAGCATCAG	58.882	55.000	0.00	0.00	0.00	2.90
421	448	0.546122	TTCACCACAGTGTCTGCCTT	59.454	50.000	0.00	0.00	44.83	4.35
475	502	1.956477	GCACACTTCCATGGTGTTCTT	59.044	47.619	12.58	0.00	44.25	2.52
504	532	4.357947	GGTCACCGAGCGAGCACA	62.358	66.667	0.00	0.00	0.00	4.57
629	669	3.055891	GGAGGGTTAACTTAGTGCGGTTA	60.056	47.826	5.42	0.00	0.00	2.85
655	695	5.280317	GGTTAAGTAGTGATCTTTGGGGTGA	60.280	44.000	0.00	0.00	0.00	4.02
775	871	6.091034	CACAGATCAAGACAGAGAACAATGAG	59.909	42.308	0.00	0.00	0.00	2.90
776	872	6.014755	ACAGATCAAGACAGAGAACAATGAGA	60.015	38.462	0.00	0.00	0.00	3.27
777	873	6.872547	CAGATCAAGACAGAGAACAATGAGAA	59.127	38.462	0.00	0.00	0.00	2.87
778	874	7.063662	CAGATCAAGACAGAGAACAATGAGAAG	59.936	40.741	0.00	0.00	0.00	2.85
779	875	5.545588	TCAAGACAGAGAACAATGAGAAGG	58.454	41.667	0.00	0.00	0.00	3.46
780	876	4.550076	AGACAGAGAACAATGAGAAGGG	57.450	45.455	0.00	0.00	0.00	3.95
797	893	3.050275	GCAAGGAGGTGGTGCGTC	61.050	66.667	0.00	0.00	0.00	5.19
798	894	2.738521	CAAGGAGGTGGTGCGTCG	60.739	66.667	0.00	0.00	33.10	5.12
954	1191	3.256960	GAGGAGGGTGGGCCAACA	61.257	66.667	25.48	0.00	36.17	3.33
1097	1336	1.004440	GGGTCACTGTGAGGCTGAC	60.004	63.158	11.41	0.00	34.68	3.51
1410	1653	8.190122	TGCTTGCTATGGTTTAGAATTATGTTG	58.810	33.333	0.00	0.00	0.00	3.33
1411	1654	7.649306	GCTTGCTATGGTTTAGAATTATGTTGG	59.351	37.037	0.00	0.00	0.00	3.77
1437	1680	7.611213	AGTGTGGTAGTATGTTAAATTGCTC	57.389	36.000	0.00	0.00	0.00	4.26
1468	1712	3.733443	ATCTTTTGTGTGTCTTTGGGC	57.267	42.857	0.00	0.00	0.00	5.36
1530	1774	2.817844	GCCGAAAAGGTTACCAGACAAT	59.182	45.455	3.51	0.00	43.70	2.71
1570	1814	3.883830	ACACCATGCTTTGTGTTTTCA	57.116	38.095	3.86	0.00	42.82	2.69
1636	1880	3.381949	GTTGTAGGCTAGAAGGTATGCG	58.618	50.000	4.08	0.00	0.00	4.73
1638	1882	1.962100	GTAGGCTAGAAGGTATGCGGT	59.038	52.381	0.00	0.00	0.00	5.68
1713	1965	5.454187	CCGGATTTGGAAGTGTAGGCTATTA	60.454	44.000	0.00	0.00	0.00	0.98
1757	2009	8.073768	AGAACCAAACACGTTCTTATGTATTTG	58.926	33.333	0.00	0.00	46.01	2.32
1770	2022	9.840427	TTCTTATGTATTTGCTTTCAGTTTAGC	57.160	29.630	0.00	0.00	37.89	3.09
1815	2067	4.202377	TGAAATAGGGTCAGTCGGTTTTCA	60.202	41.667	0.00	0.00	31.50	2.69
1825	2077	1.468914	GTCGGTTTTCAAGAGATGGCC	59.531	52.381	0.00	0.00	0.00	5.36
1858	2110	3.452990	GGAGGTAAGGAAGGAGAAGGAAG	59.547	52.174	0.00	0.00	0.00	3.46
1867	2119	3.724914	GAGAAGGAAGGGGCTCGCG	62.725	68.421	0.00	0.00	0.00	5.87
1901	2153	5.427481	CCCCAGTATCTAACTTAGGGTTCAA	59.573	44.000	0.00	0.00	41.56	2.69
1908	2160	1.073098	ACTTAGGGTTCAAGGTGGGG	58.927	55.000	0.00	0.00	0.00	4.96
1955	2207	3.041940	GGTGGTGCACTTCGTCGG	61.042	66.667	17.98	0.00	34.40	4.79
1993	2245	1.834822	GCGGGCCTAGAGAGATGGT	60.835	63.158	0.84	0.00	0.00	3.55
1998	2251	1.182385	GCCTAGAGAGATGGTCGGGG	61.182	65.000	0.00	0.00	0.00	5.73
2020	2273	2.435410	GGCTAAACCGTCGGTGGG	60.435	66.667	19.67	12.01	35.34	4.61
2070	2323	4.373116	GGTGCACTTCGCCGGAGA	62.373	66.667	17.98	3.81	41.33	3.71
2071	2324	2.357034	GTGCACTTCGCCGGAGAA	60.357	61.111	19.99	19.99	41.33	2.87
2105	2358	3.631046	CGGGCCTAGAGGGATGGC	61.631	72.222	0.84	0.00	45.42	4.40
2191	2451	3.195698	GATGGTCGCAGGCGGTTC	61.196	66.667	14.24	5.04	40.25	3.62
2220	2492	3.634448	CGGCTGGAGAAGAAGAAGAGATA	59.366	47.826	0.00	0.00	0.00	1.98
2236	2508	7.648770	AGAAGAGATAGAGGTAGAAGAAAGGT	58.351	38.462	0.00	0.00	0.00	3.50
2241	2513	0.903236	AGGTAGAAGAAAGGTCGGGC	59.097	55.000	0.00	0.00	0.00	6.13
2261	2533	0.026285	GCCGTTGGATTTCGATCGTG	59.974	55.000	15.94	0.00	0.00	4.35
2283	2555	3.303791	GCGTTTGAAAAATCGACTGACCT	60.304	43.478	0.00	0.00	0.00	3.85
2287	2559	6.438763	GTTTGAAAAATCGACTGACCTGATT	58.561	36.000	0.00	0.00	33.94	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
85	92	1.066858	TCCAGCGAGGACAACAAGATC	60.067	52.381	0.00	0.00	43.07	2.75
115	122	2.498481	AGGCCACAGTACGTTGCTAATA	59.502	45.455	5.01	0.00	36.51	0.98
124	131	2.125512	GAGCCAGGCCACAGTACG	60.126	66.667	8.22	0.00	0.00	3.67
184	191	5.422331	ACCGGAGATCATCAGTTTAGAGAAA	59.578	40.000	9.46	0.00	0.00	2.52
185	192	4.956700	ACCGGAGATCATCAGTTTAGAGAA	59.043	41.667	9.46	0.00	0.00	2.87
186	193	4.339530	CACCGGAGATCATCAGTTTAGAGA	59.660	45.833	9.46	0.00	0.00	3.10
190	197	2.158957	GGCACCGGAGATCATCAGTTTA	60.159	50.000	9.46	0.00	0.00	2.01
250	257	0.820871	GTGAGTACAGGGCTCCTCAG	59.179	60.000	0.00	0.00	34.80	3.35
268	275	0.110486	CAAGGTGGGCCAAGTACAGT	59.890	55.000	8.40	0.00	37.19	3.55
305	312	0.179062	ATGAATCAGGCTGACTCCGC	60.179	55.000	21.89	9.63	0.00	5.54
421	448	3.044235	ACATCGAAGACATGCACAAGA	57.956	42.857	0.00	0.00	42.51	3.02
475	502	0.948623	CGGTGACCGCATCAAGTTCA	60.949	55.000	12.53	0.00	41.17	3.18
629	669	5.253096	ACCCCAAAGATCACTACTTAACCAT	59.747	40.000	0.00	0.00	0.00	3.55
655	695	4.202430	CCGTCCAAAGCCCCTATATTTACT	60.202	45.833	0.00	0.00	0.00	2.24
775	871	1.303643	CACCACCTCCTTGCCCTTC	60.304	63.158	0.00	0.00	0.00	3.46
776	872	2.846532	CACCACCTCCTTGCCCTT	59.153	61.111	0.00	0.00	0.00	3.95
777	873	3.971702	GCACCACCTCCTTGCCCT	61.972	66.667	0.00	0.00	0.00	5.19
779	875	4.643387	ACGCACCACCTCCTTGCC	62.643	66.667	0.00	0.00	32.31	4.52
780	876	3.050275	GACGCACCACCTCCTTGC	61.050	66.667	0.00	0.00	0.00	4.01
795	891	2.190578	CCCTTCTCCATGGGCGAC	59.809	66.667	13.02	0.00	36.61	5.19
804	900	1.301293	CACCTCCTTGCCCTTCTCC	59.699	63.158	0.00	0.00	0.00	3.71
872	1105	0.935831	CGTTACTGCGTCGTTGTCCA	60.936	55.000	0.00	0.00	0.00	4.02
877	1110	0.311790	TCTTCCGTTACTGCGTCGTT	59.688	50.000	0.00	0.00	0.00	3.85
889	1122	1.686110	CACTAGGGGGCTCTTCCGT	60.686	63.158	0.00	0.00	34.94	4.69
954	1191	1.701847	AGGATGACCTTGCAGAAGTGT	59.298	47.619	0.00	0.00	45.36	3.55
1097	1336	2.267961	GGGTGGCCCTACTGTTCG	59.732	66.667	0.00	0.00	41.34	3.95
1141	1380	2.035193	CGATCTTGATCTGATGGACGGT	59.965	50.000	8.70	0.00	0.00	4.83
1410	1653	7.120726	AGCAATTTAACATACTACCACACTTCC	59.879	37.037	0.00	0.00	0.00	3.46
1411	1654	8.040716	AGCAATTTAACATACTACCACACTTC	57.959	34.615	0.00	0.00	0.00	3.01
1437	1680	4.516698	ACACACAAAAGATAGCAAGGAGTG	59.483	41.667	0.00	0.00	0.00	3.51
1468	1712	2.866156	CACATATGGGCGTGTAGAACAG	59.134	50.000	7.80	0.00	0.00	3.16
1530	1774	5.508825	GGTGTTTGGTTTCATGCAATGTCTA	60.509	40.000	0.00	0.00	46.80	2.59
1570	1814	0.671796	GGTTGGCCGCTTGTTTAAGT	59.328	50.000	0.00	0.00	36.27	2.24
1636	1880	5.587844	ACATCTGCATCTAGTTTGATTGACC	59.412	40.000	0.00	0.00	0.00	4.02
1638	1882	7.692460	AAACATCTGCATCTAGTTTGATTGA	57.308	32.000	6.07	0.00	31.81	2.57
1757	2009	7.217070	CGATTGACATTTAGCTAAACTGAAAGC	59.783	37.037	20.85	17.47	37.60	3.51
1815	2067	1.965754	GCTCACTCCGGCCATCTCTT	61.966	60.000	2.24	0.00	0.00	2.85
1836	2088	3.117552	TCCTTCTCCTTCCTTACCTCC	57.882	52.381	0.00	0.00	0.00	4.30
1867	2119	1.504221	AGATACTGGGGTAGTCCTCCC	59.496	57.143	0.00	0.00	43.90	4.30
1873	2125	5.713807	CCCTAAGTTAGATACTGGGGTAGT	58.286	45.833	11.66	0.00	41.80	2.73
1978	2230	1.182385	CCCGACCATCTCTCTAGGCC	61.182	65.000	0.00	0.00	0.00	5.19
1993	2245	4.770874	GTTTAGCCGCTGCCCCGA	62.771	66.667	2.16	0.00	38.69	5.14
2071	2324	1.610038	CCCGCCCTCGTTTAAGTTTTT	59.390	47.619	0.00	0.00	0.00	1.94
2202	2462	6.086011	ACCTCTATCTCTTCTTCTTCTCCA	57.914	41.667	0.00	0.00	0.00	3.86
2203	2463	7.514721	TCTACCTCTATCTCTTCTTCTTCTCC	58.485	42.308	0.00	0.00	0.00	3.71
2220	2492	2.458620	CCCGACCTTTCTTCTACCTCT	58.541	52.381	0.00	0.00	0.00	3.69
2241	2513	1.272715	CGATCGAAATCCAACGGCG	59.727	57.895	10.26	4.80	0.00	6.46
2248	2520	1.392168	TCAAACGCACGATCGAAATCC	59.608	47.619	24.34	3.79	0.00	3.01
2261	2533	2.971261	GGTCAGTCGATTTTTCAAACGC	59.029	45.455	0.00	0.00	0.00	4.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.