AutoCloner

Multiple sequence alignment - TraesCS5B01G417600

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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	TraesCS5B01G417600	chr5B	100.000	2357	0	0	1	2357	592062640	592064996	0.000000e+00	4353.0
1	TraesCS5B01G417600	chr5B	86.381	257	22	7	242	495	581760975	581761221	3.860000e-68	268.0
2	TraesCS5B01G417600	chr5B	85.603	257	24	7	242	495	420932820	420933066	8.360000e-65	257.0
3	TraesCS5B01G417600	chr4B	92.832	865	44	7	876	1739	241358205	241359052	0.000000e+00	1238.0
4	TraesCS5B01G417600	chr4B	89.420	879	72	17	876	1739	418205981	418206853	0.000000e+00	1088.0
5	TraesCS5B01G417600	chr4B	92.555	497	35	2	876	1371	623489345	623489840	0.000000e+00	712.0
6	TraesCS5B01G417600	chr4B	93.958	331	20	0	1409	1739	623489847	623490177	3.500000e-138	501.0
7	TraesCS5B01G417600	chr6B	91.908	865	52	7	876	1739	450591926	450592773	0.000000e+00	1194.0
8	TraesCS5B01G417600	chr6B	94.565	552	29	1	879	1429	658638470	658637919	0.000000e+00	852.0
9	TraesCS5B01G417600	chr6B	93.968	315	17	2	1427	1739	658625671	658625357	2.120000e-130	475.0
10	TraesCS5B01G417600	chr6B	75.660	341	80	3	977	1315	544396879	544396540	1.450000e-37	167.0
11	TraesCS5B01G417600	chr2D	89.885	870	66	13	17	875	467997057	467997915	0.000000e+00	1099.0
12	TraesCS5B01G417600	chr7D	89.064	887	70	19	1	881	93085884	93085019	0.000000e+00	1075.0
13	TraesCS5B01G417600	chr7D	83.824	340	38	12	510	846	96455054	96454729	8.180000e-80	307.0
14	TraesCS5B01G417600	chr7D	83.459	266	33	9	1476	1739	577854219	577853963	1.090000e-58	237.0
15	TraesCS5B01G417600	chr7D	82.734	278	30	11	1471	1744	158993141	158993404	5.070000e-57	231.0
16	TraesCS5B01G417600	chr7D	88.068	176	18	1	17	189	281951	282126	3.070000e-49	206.0
17	TraesCS5B01G417600	chr7D	86.857	175	20	1	17	188	124501202	124501028	2.390000e-45	193.0
18	TraesCS5B01G417600	chr7D	100.000	35	0	0	1743	1777	93085020	93084986	5.440000e-07	65.8
19	TraesCS5B01G417600	chr7A	88.343	875	77	15	15	875	367256060	367256923	0.000000e+00	1027.0
20	TraesCS5B01G417600	chr7A	83.529	340	40	11	509	846	99614560	99614235	1.060000e-78	303.0
21	TraesCS5B01G417600	chr7A	89.349	169	13	4	338	503	609388286	609388452	8.540000e-50	207.0
22	TraesCS5B01G417600	chr7A	95.238	42	2	0	1737	1778	367256922	367256963	1.510000e-07	67.6
23	TraesCS5B01G417600	chr5D	94.664	581	30	1	1778	2357	386212265	386211685	0.000000e+00	900.0
24	TraesCS5B01G417600	chr5D	94.492	581	31	1	1778	2357	393901317	393901897	0.000000e+00	894.0
25	TraesCS5B01G417600	chr5D	93.976	581	34	1	1778	2357	364248708	364249288	0.000000e+00	878.0
26	TraesCS5B01G417600	chr6D	94.492	581	31	1	1778	2357	77706740	77706160	0.000000e+00	894.0
27	TraesCS5B01G417600	chr6D	85.650	223	27	5	510	731	318564936	318564718	1.820000e-56	230.0
28	TraesCS5B01G417600	chr6D	87.500	176	19	1	17	189	108245881	108246056	1.430000e-47	200.0
29	TraesCS5B01G417600	chr1D	93.976	581	33	2	1778	2357	25788344	25787765	0.000000e+00	878.0
30	TraesCS5B01G417600	chr1D	93.804	581	33	3	1778	2357	17121836	17122414	0.000000e+00	870.0
31	TraesCS5B01G417600	chr3D	93.632	581	36	1	1778	2357	570045391	570045971	0.000000e+00	867.0
32	TraesCS5B01G417600	chr3D	93.621	580	36	1	1778	2356	610135409	610135988	0.000000e+00	865.0
33	TraesCS5B01G417600	chr3D	86.381	257	22	7	242	495	15295124	15295370	3.860000e-68	268.0
34	TraesCS5B01G417600	chr3D	87.500	176	19	1	17	189	382810657	382810832	1.430000e-47	200.0
35	TraesCS5B01G417600	chr3D	88.024	167	20	0	715	881	590978266	590978100	5.140000e-47	198.0
36	TraesCS5B01G417600	chr6A	93.460	581	37	1	1778	2357	61676956	61677536	0.000000e+00	861.0
37	TraesCS5B01G417600	chrUn	92.706	425	25	4	1318	1739	88784267	88784688	2.000000e-170	608.0
38	TraesCS5B01G417600	chrUn	85.537	242	22	7	242	480	117282908	117283139	8.420000e-60	241.0
39	TraesCS5B01G417600	chr1B	83.903	497	68	10	17	512	211633467	211632982	4.590000e-127	464.0
40	TraesCS5B01G417600	chr1B	85.014	367	51	4	510	875	211632404	211632041	1.030000e-98	370.0
41	TraesCS5B01G417600	chr3B	84.239	368	40	8	510	875	573313621	573313972	2.240000e-90	342.0
42	TraesCS5B01G417600	chr2B	90.278	216	16	5	1525	1739	138254631	138254842	6.420000e-71	278.0
43	TraesCS5B01G417600	chr1A	81.366	322	47	9	561	875	167213659	167213974	1.400000e-62	250.0
44	TraesCS5B01G417600	chr1A	98.113	53	1	0	522	574	167162709	167162761	2.490000e-15	93.5
45	TraesCS5B01G417600	chr7B	89.349	169	13	4	338	503	568005730	568005896	8.540000e-50	207.0
46	TraesCS5B01G417600	chr7B	74.576	354	82	8	977	1326	634228363	634228712	5.250000e-32	148.0
47	TraesCS5B01G417600	chr4D	88.068	176	18	1	17	189	484194833	484195008	3.070000e-49	206.0
48	TraesCS5B01G417600	chr4A	74.859	354	82	5	977	1326	647282209	647281859	1.130000e-33	154.0

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	TraesCS5B01G417600	chr5B	592062640	592064996	2356	False	4353.0	4353	100.0000	1	2357	1	chr5B.!!$F3	2356
1	TraesCS5B01G417600	chr4B	241358205	241359052	847	False	1238.0	1238	92.8320	876	1739	1	chr4B.!!$F1	863
2	TraesCS5B01G417600	chr4B	418205981	418206853	872	False	1088.0	1088	89.4200	876	1739	1	chr4B.!!$F2	863
3	TraesCS5B01G417600	chr4B	623489345	623490177	832	False	606.5	712	93.2565	876	1739	2	chr4B.!!$F3	863
4	TraesCS5B01G417600	chr6B	450591926	450592773	847	False	1194.0	1194	91.9080	876	1739	1	chr6B.!!$F1	863
5	TraesCS5B01G417600	chr6B	658637919	658638470	551	True	852.0	852	94.5650	879	1429	1	chr6B.!!$R3	550
6	TraesCS5B01G417600	chr2D	467997057	467997915	858	False	1099.0	1099	89.8850	17	875	1	chr2D.!!$F1	858
7	TraesCS5B01G417600	chr7D	93084986	93085884	898	True	570.4	1075	94.5320	1	1777	2	chr7D.!!$R4	1776
8	TraesCS5B01G417600	chr7A	367256060	367256963	903	False	547.3	1027	91.7905	15	1778	2	chr7A.!!$F2	1763
9	TraesCS5B01G417600	chr5D	386211685	386212265	580	True	900.0	900	94.6640	1778	2357	1	chr5D.!!$R1	579
10	TraesCS5B01G417600	chr5D	393901317	393901897	580	False	894.0	894	94.4920	1778	2357	1	chr5D.!!$F2	579
11	TraesCS5B01G417600	chr5D	364248708	364249288	580	False	878.0	878	93.9760	1778	2357	1	chr5D.!!$F1	579
12	TraesCS5B01G417600	chr6D	77706160	77706740	580	True	894.0	894	94.4920	1778	2357	1	chr6D.!!$R1	579
13	TraesCS5B01G417600	chr1D	25787765	25788344	579	True	878.0	878	93.9760	1778	2357	1	chr1D.!!$R1	579
14	TraesCS5B01G417600	chr1D	17121836	17122414	578	False	870.0	870	93.8040	1778	2357	1	chr1D.!!$F1	579
15	TraesCS5B01G417600	chr3D	570045391	570045971	580	False	867.0	867	93.6320	1778	2357	1	chr3D.!!$F3	579
16	TraesCS5B01G417600	chr3D	610135409	610135988	579	False	865.0	865	93.6210	1778	2356	1	chr3D.!!$F4	578
17	TraesCS5B01G417600	chr6A	61676956	61677536	580	False	861.0	861	93.4600	1778	2357	1	chr6A.!!$F1	579
18	TraesCS5B01G417600	chr1B	211632041	211633467	1426	True	417.0	464	84.4585	17	875	2	chr1B.!!$R1	858

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
51	52	1.281867	CTGTTGGTCTGATTGGCCCTA	59.718	52.381	0.0	0.0	40.46	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1375	1983	0.391661	GGCTGAGCACGAAGATGGAA	60.392	55.0	6.82	0.0	0.0	3.53	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
27	28	5.245526	AGAATGAGCAAAGCAAAGAAAGGAT	59.754	36.000	0.00	0.00	0.00	3.24
51	52	1.281867	CTGTTGGTCTGATTGGCCCTA	59.718	52.381	0.00	0.00	40.46	3.53
94	95	3.536956	TTGTGTATGGGAGGACGAATC	57.463	47.619	0.00	0.00	0.00	2.52
210	214	6.208599	ACACTATATGCTCCTCTCTTAGCTTC	59.791	42.308	0.00	0.00	39.53	3.86
223	227	7.066404	CCTCTCTTAGCTTCTTTTGGAATTACC	59.934	40.741	0.00	0.00	39.54	2.85
298	303	9.685828	GTACCTTGCATGAGTTGTAAATAAAAA	57.314	29.630	0.00	0.00	28.96	1.94
386	392	4.111255	TGACCTGGGAAATGACAATGAA	57.889	40.909	0.00	0.00	0.00	2.57
387	393	4.676109	TGACCTGGGAAATGACAATGAAT	58.324	39.130	0.00	0.00	0.00	2.57
388	394	5.825532	TGACCTGGGAAATGACAATGAATA	58.174	37.500	0.00	0.00	0.00	1.75
389	395	6.434302	TGACCTGGGAAATGACAATGAATAT	58.566	36.000	0.00	0.00	0.00	1.28
390	396	6.547141	TGACCTGGGAAATGACAATGAATATC	59.453	38.462	0.00	0.00	0.00	1.63
391	397	6.676558	ACCTGGGAAATGACAATGAATATCT	58.323	36.000	0.00	0.00	0.00	1.98
395	401	9.880157	CTGGGAAATGACAATGAATATCTTTTT	57.120	29.630	0.00	0.00	0.00	1.94
504	520	2.425143	TGTCAGAATCCCATGCTTCC	57.575	50.000	0.00	0.00	0.00	3.46
560	1156	7.024768	TGTTAGTTTTGAACTTGTTCCTTTCG	58.975	34.615	10.51	0.00	42.81	3.46
574	1170	5.065090	TGTTCCTTTCGCTCATGATGTAATG	59.935	40.000	0.00	0.00	0.00	1.90
581	1177	6.024552	TCGCTCATGATGTAATGCTATGTA	57.975	37.500	0.00	0.00	0.00	2.29
636	1234	7.272037	TCTTTTCTGTAAAACATGTCCCTTC	57.728	36.000	0.00	0.00	31.37	3.46
691	1289	2.158842	GCTTCCTCATATGACTGCCACT	60.159	50.000	0.00	0.00	0.00	4.00
692	1290	3.726607	CTTCCTCATATGACTGCCACTC	58.273	50.000	0.00	0.00	0.00	3.51
693	1291	2.750814	TCCTCATATGACTGCCACTCA	58.249	47.619	0.00	0.00	0.00	3.41
705	1303	3.744660	CTGCCACTCAGGTTTAGTTCTT	58.255	45.455	0.00	0.00	39.15	2.52
795	1393	2.281692	TGTCGGCAGCTGCAATGT	60.282	55.556	37.63	0.00	44.36	2.71
891	1489	4.610605	TTGAAAGTATTCGGTCCTGACA	57.389	40.909	0.00	0.00	38.46	3.58
937	1535	1.602237	CTGGGTAGGCCGATGTGTT	59.398	57.895	0.00	0.00	34.97	3.32
1094	1692	2.490903	GCTACTGTTACCTTCCTGACGA	59.509	50.000	0.00	0.00	0.00	4.20
1258	1856	3.008049	AGGTTTATTGTCCGCTGAAGACT	59.992	43.478	0.00	0.00	35.21	3.24
1354	1952	0.459585	AGATGCGACGCGTAATGGTT	60.460	50.000	13.97	0.00	0.00	3.67
1367	1965	1.188863	AATGGTTGATGAAGCTGGGC	58.811	50.000	0.00	0.00	0.00	5.36
1368	1966	0.040058	ATGGTTGATGAAGCTGGGCA	59.960	50.000	0.00	0.00	0.00	5.36
1369	1967	0.609957	TGGTTGATGAAGCTGGGCAG	60.610	55.000	0.00	0.00	0.00	4.85
1372	1970	0.679002	TTGATGAAGCTGGGCAGAGC	60.679	55.000	0.00	0.00	39.46	4.09
1395	2003	1.078918	CCATCTTCGTGCTCAGCCA	60.079	57.895	0.00	0.00	0.00	4.75
1444	2057	1.873903	GCGTGGAGTGTCTGATGTGTT	60.874	52.381	0.00	0.00	0.00	3.32
1567	2182	1.808411	TCTGGAATCGTTTCAGGTGC	58.192	50.000	8.41	0.00	33.23	5.01
1701	2316	7.499321	TGAACTGTTGTTATTTCCGTTATGT	57.501	32.000	0.00	0.00	36.39	2.29
1718	2333	5.878116	CGTTATGTTGAGTAATGGAAAGGGA	59.122	40.000	0.00	0.00	0.00	4.20
1937	2553	3.432588	AGTCTGCGTCCTCGTCGG	61.433	66.667	0.00	0.00	39.49	4.79
2017	2633	4.560743	TGCTGGCCAGAACGCACA	62.561	61.111	37.21	20.18	0.00	4.57
2024	2640	2.186160	CCAGAACGCACACTGGCAA	61.186	57.895	0.00	0.00	45.30	4.52
2093	2709	1.205655	CTTCTTCGTCAGAGATGGCCA	59.794	52.381	8.56	8.56	31.12	5.36
2124	2740	1.074889	TGGTGATCGGATCTCGGGATA	59.925	52.381	18.16	0.00	39.77	2.59
2250	2867	2.995939	TCGTCGTGTAACTACTGTCGAT	59.004	45.455	0.00	0.00	29.04	3.59
2305	2922	0.458025	GGTGTTCCAGATCGGACGAC	60.458	60.000	5.89	4.30	46.36	4.34
2329	2946	1.564622	CACTGCGGTGTCGTTTCTG	59.435	57.895	17.96	0.00	38.54	3.02
2351	2968	0.179004	TTGGGAGCATCGTTTGTGGT	60.179	50.000	0.00	0.00	34.37	4.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	4.683320	GTGAATCCTTTCTTTGCTTTGCTC	59.317	41.667	0.00	0.00	32.78	4.26
27	28	2.229792	GCCAATCAGACCAACAGTGAA	58.770	47.619	0.00	0.00	0.00	3.18
74	75	2.169769	GGATTCGTCCTCCCATACACAA	59.830	50.000	0.00	0.00	0.00	3.33
94	95	3.564511	CCGTGAAAATGTGCTACTTTGG	58.435	45.455	0.00	0.00	0.00	3.28
178	182	6.651643	AGAGAGGAGCATATAGTGTTACGTAG	59.348	42.308	0.00	0.00	0.00	3.51
223	227	8.690884	TGAGAAGGAACTAGAATAACAGATCAG	58.309	37.037	0.00	0.00	38.49	2.90
238	243	6.273495	AGTTTTCCTCCTATTGAGAAGGAACT	59.727	38.462	2.29	0.00	44.42	3.01
319	325	8.517878	CACATTCAAATGTCTCCTTCAGTATTT	58.482	33.333	5.41	0.00	46.10	1.40
395	401	7.716998	AGAAGTCATACTTTCTGAAGCTTTCAA	59.283	33.333	0.00	0.00	38.80	2.69
396	402	7.172190	CAGAAGTCATACTTTCTGAAGCTTTCA	59.828	37.037	0.00	0.00	38.80	2.69
415	421	3.931578	AGGTACAGATGTTGCAGAAGTC	58.068	45.455	0.00	0.00	0.00	3.01
458	464	6.599638	GGACATACTGTTTCCAGAAGCTAATT	59.400	38.462	0.00	0.00	41.50	1.40
560	1156	6.091849	CCTGTACATAGCATTACATCATGAGC	59.908	42.308	0.09	0.00	0.00	4.26
574	1170	5.218139	GGTATCAACGTACCTGTACATAGC	58.782	45.833	8.09	4.31	40.79	2.97
581	1177	4.525487	TCTTCTTGGTATCAACGTACCTGT	59.475	41.667	6.77	0.00	43.68	4.00
636	1234	4.939509	AGTAACGAACCCAAATCAATCG	57.060	40.909	0.00	0.00	39.30	3.34
691	1289	8.746052	TGAATCAAAAGAAGAACTAAACCTGA	57.254	30.769	0.00	0.00	0.00	3.86
692	1290	8.624776	ACTGAATCAAAAGAAGAACTAAACCTG	58.375	33.333	0.00	0.00	0.00	4.00
693	1291	8.753497	ACTGAATCAAAAGAAGAACTAAACCT	57.247	30.769	0.00	0.00	0.00	3.50
694	1292	9.452065	GAACTGAATCAAAAGAAGAACTAAACC	57.548	33.333	0.00	0.00	0.00	3.27
698	1296	8.964476	ACAGAACTGAATCAAAAGAAGAACTA	57.036	30.769	8.87	0.00	0.00	2.24
795	1393	4.519350	CCTTACACCACTCGATATGCTCTA	59.481	45.833	0.00	0.00	0.00	2.43
891	1489	0.106819	GCCTGCTCATGACATCCCTT	60.107	55.000	0.00	0.00	0.00	3.95
972	1570	4.373156	AGCAACTGGACAGGTAAAGAAT	57.627	40.909	4.14	0.00	0.00	2.40
1068	1666	2.302157	AGGAAGGTAACAGTAGCACCAC	59.698	50.000	0.00	0.00	41.41	4.16
1094	1692	5.147767	AGCCAAAGGTGTAAAATCTTTCCT	58.852	37.500	0.00	0.00	0.00	3.36
1258	1856	1.834378	CTCGCTCCATAGCCTCCCA	60.834	63.158	0.00	0.00	46.68	4.37
1280	1878	5.045012	AGCATTCATCCTCAGCATCTTTA	57.955	39.130	0.00	0.00	0.00	1.85
1354	1952	1.077930	GCTCTGCCCAGCTTCATCA	60.078	57.895	0.00	0.00	36.38	3.07
1367	1965	2.159599	GCACGAAGATGGAAAAGCTCTG	60.160	50.000	0.00	0.00	0.00	3.35
1368	1966	2.079925	GCACGAAGATGGAAAAGCTCT	58.920	47.619	0.00	0.00	0.00	4.09
1369	1967	2.079925	AGCACGAAGATGGAAAAGCTC	58.920	47.619	0.00	0.00	0.00	4.09
1372	1970	2.159599	GCTGAGCACGAAGATGGAAAAG	60.160	50.000	0.00	0.00	0.00	2.27
1375	1983	0.391661	GGCTGAGCACGAAGATGGAA	60.392	55.000	6.82	0.00	0.00	3.53
1407	2019	0.465097	CGCATCCAGAGAAAGGCCAT	60.465	55.000	5.01	0.00	0.00	4.40
1444	2057	2.374184	CCAACAACCAACCAGTTCAGA	58.626	47.619	0.00	0.00	0.00	3.27
1495	2109	2.540265	CCTGATCAGATAGGCCACAC	57.460	55.000	24.62	0.00	0.00	3.82
1701	2316	5.833131	GGCATTATCCCTTTCCATTACTCAA	59.167	40.000	0.00	0.00	0.00	3.02
1862	2478	3.213402	CACCACCAACCGCCGTTT	61.213	61.111	0.00	0.00	0.00	3.60
1870	2486	2.573083	CCACATGGCCACCACCAAC	61.573	63.158	8.16	0.00	44.65	3.77
1897	2513	2.365635	CCCAGATCCGGTCCACCT	60.366	66.667	0.00	0.00	0.00	4.00
1903	2519	2.285368	TGGAAGCCCAGATCCGGT	60.285	61.111	0.00	0.00	37.58	5.28
2010	2626	4.250431	GCGTTGCCAGTGTGCGTT	62.250	61.111	0.00	0.00	0.00	4.84
2024	2640	1.437986	GCGAGATGAAGTAGGGCGT	59.562	57.895	0.00	0.00	0.00	5.68
2124	2740	1.043816	CAGCCGGGACTAGATGATGT	58.956	55.000	2.18	0.00	0.00	3.06
2250	2867	1.600638	CCAGAGCAGCATGAGTGGA	59.399	57.895	0.00	0.00	39.69	4.02
2329	2946	1.197721	CACAAACGATGCTCCCAAGAC	59.802	52.381	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.