AutoCloner

Multiple sequence alignment - TraesCS7A01G460300

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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	TraesCS7A01G460300	chr7A	100.000	2564	0	0	1	2564	656981419	656983982	0.000000e+00	4735
1	TraesCS7A01G460300	chr7A	96.283	565	10	4	1	562	76929676	76930232	0.000000e+00	917
2	TraesCS7A01G460300	chr7A	80.134	1047	141	25	608	1615	655452253	655451235	0.000000e+00	719
3	TraesCS7A01G460300	chr7A	78.059	752	103	24	669	1384	654503690	654502965	3.950000e-113	418
4	TraesCS7A01G460300	chr7D	95.179	2012	81	7	562	2564	568324214	568322210	0.000000e+00	3164
5	TraesCS7A01G460300	chr7D	84.589	1434	178	31	583	1985	568463873	568462452	0.000000e+00	1384
6	TraesCS7A01G460300	chr7D	80.763	1232	172	33	608	1796	568185799	568184590	0.000000e+00	902
7	TraesCS7A01G460300	chr7B	94.326	1974	99	6	602	2564	623934255	623932284	0.000000e+00	3013
8	TraesCS7A01G460300	chr7B	82.955	528	56	14	608	1102	622838241	622837715	1.810000e-121	446
9	TraesCS7A01G460300	chr7B	79.258	458	66	11	1144	1595	622832902	622832468	2.500000e-75	292
10	TraesCS7A01G460300	chr3A	95.390	564	15	4	1	561	69332312	69331757	0.000000e+00	887
11	TraesCS7A01G460300	chr1A	94.681	564	19	4	1	561	541652272	541651717	0.000000e+00	865
12	TraesCS7A01G460300	chr3B	91.711	567	26	8	1	561	780361434	780361985	0.000000e+00	767
13	TraesCS7A01G460300	chr4B	91.489	564	36	5	1	561	530174250	530174804	0.000000e+00	765
14	TraesCS7A01G460300	chr4D	82.781	453	44	19	115	561	5233713	5234137	8.660000e-100	374
15	TraesCS7A01G460300	chr5B	81.387	274	36	9	308	566	641337872	641338145	2.590000e-50	209

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	TraesCS7A01G460300	chr7A	656981419	656983982	2563	False	4735	4735	100.000	1	2564	1	chr7A.!!$F2	2563
1	TraesCS7A01G460300	chr7A	76929676	76930232	556	False	917	917	96.283	1	562	1	chr7A.!!$F1	561
2	TraesCS7A01G460300	chr7A	655451235	655452253	1018	True	719	719	80.134	608	1615	1	chr7A.!!$R2	1007
3	TraesCS7A01G460300	chr7A	654502965	654503690	725	True	418	418	78.059	669	1384	1	chr7A.!!$R1	715
4	TraesCS7A01G460300	chr7D	568322210	568324214	2004	True	3164	3164	95.179	562	2564	1	chr7D.!!$R2	2002
5	TraesCS7A01G460300	chr7D	568462452	568463873	1421	True	1384	1384	84.589	583	1985	1	chr7D.!!$R3	1402
6	TraesCS7A01G460300	chr7D	568184590	568185799	1209	True	902	902	80.763	608	1796	1	chr7D.!!$R1	1188
7	TraesCS7A01G460300	chr7B	623932284	623934255	1971	True	3013	3013	94.326	602	2564	1	chr7B.!!$R3	1962
8	TraesCS7A01G460300	chr7B	622837715	622838241	526	True	446	446	82.955	608	1102	1	chr7B.!!$R2	494
9	TraesCS7A01G460300	chr3A	69331757	69332312	555	True	887	887	95.390	1	561	1	chr3A.!!$R1	560
10	TraesCS7A01G460300	chr1A	541651717	541652272	555	True	865	865	94.681	1	561	1	chr1A.!!$R1	560
11	TraesCS7A01G460300	chr3B	780361434	780361985	551	False	767	767	91.711	1	561	1	chr3B.!!$F1	560
12	TraesCS7A01G460300	chr4B	530174250	530174804	554	False	765	765	91.489	1	561	1	chr4B.!!$F1	560

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
266	275	0.172578	CTGGTGAGACGACGGCAATA	59.827	55.000	2.19	0.0	0.00	1.90	F
1228	1286	1.005037	GTGACGGACATCCACTGCA	60.005	57.895	0.00	0.0	35.14	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1243	1301	0.317436	CTAGTCAGATCGTGAGCGGC	60.317	60.000	0.0	0.0	35.13	6.53	R
2388	2501	1.003696	ACTAGCAGAAAGGGAGTTGCC	59.996	52.381	0.0	0.0	37.26	4.52	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
79	80	1.450848	ATGATGAGCGGCAGGTGTG	60.451	57.895	1.45	0.00	0.00	3.82
87	88	2.269241	GGCAGGTGTGGCTAGGAC	59.731	66.667	0.00	0.00	45.85	3.85
88	89	2.125512	GCAGGTGTGGCTAGGACG	60.126	66.667	0.00	0.00	0.00	4.79
89	90	2.579201	CAGGTGTGGCTAGGACGG	59.421	66.667	0.00	0.00	0.00	4.79
90	91	1.982395	CAGGTGTGGCTAGGACGGA	60.982	63.158	0.00	0.00	0.00	4.69
132	139	4.728772	TGAGGAAAAAGAAGAAGCCATGA	58.271	39.130	0.00	0.00	0.00	3.07
163	170	2.597510	GTTGGGTGTGGCTGGGAC	60.598	66.667	0.00	0.00	0.00	4.46
266	275	0.172578	CTGGTGAGACGACGGCAATA	59.827	55.000	2.19	0.00	0.00	1.90
411	421	4.504864	GGTGTGCCTGCTATTATACATGGA	60.505	45.833	0.00	0.00	0.00	3.41
534	547	3.071837	TGATACCGGCCTGCACGA	61.072	61.111	0.00	0.00	0.00	4.35
569	582	6.071463	CCAAAGCGCATTTTCGTATAGATAC	58.929	40.000	11.47	0.00	0.00	2.24
574	587	6.259167	AGCGCATTTTCGTATAGATACCAAAA	59.741	34.615	11.47	7.39	37.60	2.44
575	588	7.041372	AGCGCATTTTCGTATAGATACCAAAAT	60.041	33.333	11.47	10.42	41.46	1.82
576	589	8.225107	GCGCATTTTCGTATAGATACCAAAATA	58.775	33.333	13.95	0.00	39.97	1.40
836	867	5.999205	TTGCCAACCATTTGATACAAGAT	57.001	34.783	0.00	0.00	34.24	2.40
1078	1136	1.205485	TTGTTCGCGCAATGCACAAC	61.205	50.000	8.75	5.07	46.97	3.32
1125	1183	7.224949	TGCACCATCGATAAAAATAACGTGATA	59.775	33.333	0.00	0.00	0.00	2.15
1126	1184	7.740346	GCACCATCGATAAAAATAACGTGATAG	59.260	37.037	0.00	0.00	0.00	2.08
1161	1219	5.278022	GGGTATCATCGAAAAGAATCTTGGC	60.278	44.000	0.00	0.00	0.00	4.52
1228	1286	1.005037	GTGACGGACATCCACTGCA	60.005	57.895	0.00	0.00	35.14	4.41
1243	1301	0.926155	CTGCATCTGTGATCGGTTCG	59.074	55.000	0.00	0.00	0.00	3.95
1291	1349	1.750193	ACCCAAGTTCGCATGTATGG	58.250	50.000	0.00	0.00	0.00	2.74
1294	1352	1.677576	CCAAGTTCGCATGTATGGCAT	59.322	47.619	4.88	4.88	38.60	4.40
1378	1472	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1379	1473	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1380	1474	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1381	1475	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1491	1585	2.081462	GGTTACCTTGTTCCGGTCATG	58.919	52.381	0.00	4.94	35.98	3.07
1495	1589	1.271379	ACCTTGTTCCGGTCATGAAGG	60.271	52.381	11.24	11.24	36.76	3.46
1578	1682	9.651913	GGGAATAATTGAATAAAGCAAAGAACA	57.348	29.630	0.00	0.00	0.00	3.18
1926	2038	4.703897	TGGTTTGGAGACAGTTCTAACAG	58.296	43.478	0.00	0.00	44.54	3.16
1944	2056	1.194547	CAGAAATTGGACCACGACACG	59.805	52.381	0.00	0.00	0.00	4.49
1958	2070	3.846896	CACGACACGACAACTTCTATCTC	59.153	47.826	0.00	0.00	0.00	2.75
2106	2219	3.315191	ACGGTGTGGAATCTTCTTTGTTG	59.685	43.478	0.00	0.00	0.00	3.33
2125	2238	2.209273	TGGTGGAAATCATACGCATCG	58.791	47.619	0.00	0.00	0.00	3.84
2132	2245	4.688879	GGAAATCATACGCATCGGATGTTA	59.311	41.667	18.54	10.94	46.91	2.41
2134	2247	4.521130	ATCATACGCATCGGATGTTAGT	57.479	40.909	18.54	16.95	46.91	2.24
2181	2294	4.502105	TCTATTGGGCTTAACTGATGCA	57.498	40.909	0.00	0.00	0.00	3.96
2192	2305	5.991606	GCTTAACTGATGCATGATACACCTA	59.008	40.000	2.46	0.00	0.00	3.08
2266	2379	0.610174	ATCACTGTGTCCATGAGCGT	59.390	50.000	7.79	0.00	0.00	5.07
2274	2387	3.568430	TGTGTCCATGAGCGTATAGGTAG	59.432	47.826	0.00	0.00	0.00	3.18
2279	2392	4.022242	TCCATGAGCGTATAGGTAGAAAGC	60.022	45.833	0.00	0.00	0.00	3.51
2308	2421	1.372997	GACGCGAAGAAGCTGGTGA	60.373	57.895	15.93	0.00	34.40	4.02
2328	2441	1.810030	GTTCGAGGGACCATGTCGC	60.810	63.158	3.35	3.35	44.21	5.19
2361	2474	0.106918	AACCTTCACCGCTTTCACCA	60.107	50.000	0.00	0.00	0.00	4.17
2388	2501	0.317479	CGGCCTATAGGAAGGGTTCG	59.683	60.000	23.61	9.34	37.11	3.95
2405	2518	1.302832	CGGCAACTCCCTTTCTGCT	60.303	57.895	0.00	0.00	35.13	4.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
79	80	3.155167	CCAGGGTCCGTCCTAGCC	61.155	72.222	0.00	0.00	34.92	3.93
81	82	3.155167	GGCCAGGGTCCGTCCTAG	61.155	72.222	0.00	0.00	34.92	3.02
82	83	4.791069	GGGCCAGGGTCCGTCCTA	62.791	72.222	4.39	0.00	34.92	2.94
88	89	3.493303	GATCCAGGGCCAGGGTCC	61.493	72.222	17.14	0.00	40.91	4.46
89	90	3.866582	CGATCCAGGGCCAGGGTC	61.867	72.222	17.91	17.91	32.77	4.46
90	91	3.943137	TTCGATCCAGGGCCAGGGT	62.943	63.158	15.80	8.07	0.00	4.34
132	139	3.117888	ACACCCAACTCAAACAGACTCAT	60.118	43.478	0.00	0.00	0.00	2.90
163	170	0.038159	ACAGGAGAGCTCGTTTTCCG	60.038	55.000	8.37	8.66	34.87	4.30
266	275	3.713764	AGTTGATAGTTGGGCATCTAGCT	59.286	43.478	0.00	0.00	44.79	3.32
411	421	3.503748	GCTAGAAATTGAACAGTGGCAGT	59.496	43.478	0.00	0.00	0.00	4.40
534	547	3.064324	GCTTTGGTGGCCGAGCAT	61.064	61.111	0.00	0.00	36.02	3.79
580	593	7.936847	CGGATAAGCCTATCTCTATCTATCTGT	59.063	40.741	2.43	0.00	35.23	3.41
581	594	7.094805	GCGGATAAGCCTATCTCTATCTATCTG	60.095	44.444	2.43	0.00	35.23	2.90
1125	1183	4.588951	TCGATGATACCCTTGCAGTATTCT	59.411	41.667	0.00	0.00	30.57	2.40
1126	1184	4.883083	TCGATGATACCCTTGCAGTATTC	58.117	43.478	0.00	0.00	30.57	1.75
1135	1193	6.543831	CCAAGATTCTTTTCGATGATACCCTT	59.456	38.462	0.00	0.00	0.00	3.95
1136	1194	6.058183	CCAAGATTCTTTTCGATGATACCCT	58.942	40.000	0.00	0.00	0.00	4.34
1228	1286	4.835927	GGCGAACCGATCACAGAT	57.164	55.556	0.00	0.00	0.00	2.90
1243	1301	0.317436	CTAGTCAGATCGTGAGCGGC	60.317	60.000	0.00	0.00	35.13	6.53
1391	1485	3.250521	TGCACATATATCAACACATGCGG	59.749	43.478	0.00	0.00	34.56	5.69
1519	1619	2.832129	TCTTACACTGAAGGCCTAGGTG	59.168	50.000	22.79	22.79	0.00	4.00
1578	1682	4.585581	TGCATATGCCATTCAGCTAACATT	59.414	37.500	24.54	0.00	41.18	2.71
1583	1687	5.947566	ACATTATGCATATGCCATTCAGCTA	59.052	36.000	24.54	3.07	41.18	3.32
1926	2038	1.193874	GTCGTGTCGTGGTCCAATTTC	59.806	52.381	0.00	0.00	0.00	2.17
1944	2056	9.646427	AGTAGAACAAATGAGATAGAAGTTGTC	57.354	33.333	0.00	0.00	0.00	3.18
1958	2070	8.783093	TGTTATGGAAGTGAAGTAGAACAAATG	58.217	33.333	0.00	0.00	0.00	2.32
2106	2219	1.531149	CCGATGCGTATGATTTCCACC	59.469	52.381	0.00	0.00	0.00	4.61
2125	2238	6.763135	TGAGCAATGATCTACAACTAACATCC	59.237	38.462	0.00	0.00	0.00	3.51
2132	2245	5.555017	ACAACTGAGCAATGATCTACAACT	58.445	37.500	0.00	0.00	0.00	3.16
2134	2247	4.627035	CGACAACTGAGCAATGATCTACAA	59.373	41.667	0.00	0.00	0.00	2.41
2181	2294	7.448469	ACTTTGTGCTTCTTTTAGGTGTATCAT	59.552	33.333	0.00	0.00	0.00	2.45
2266	2379	4.357142	CGCAAGTTCGCTTTCTACCTATA	58.643	43.478	0.00	0.00	34.74	1.31
2274	2387	1.206831	GTCCCGCAAGTTCGCTTTC	59.793	57.895	0.00	0.00	34.74	2.62
2308	2421	1.605058	CGACATGGTCCCTCGAACCT	61.605	60.000	6.34	0.00	37.69	3.50
2361	2474	2.642171	TCCTATAGGCCGATGGGAAT	57.358	50.000	25.55	0.00	33.82	3.01
2388	2501	1.003696	ACTAGCAGAAAGGGAGTTGCC	59.996	52.381	0.00	0.00	37.26	4.52
2405	2518	4.202357	ACACAGGAGAAGATTGCAACACTA	60.202	41.667	0.00	0.00	0.00	2.74

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.