AutoCloner

Multiple sequence alignment - TraesCS5A01G067400

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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	TraesCS5A01G067400	chr5A	100.000	3077	0	0	1	3077	74862096	74865172	0.000000e+00	5683.0
1	TraesCS5A01G067400	chr5A	99.330	896	6	0	1	896	74582002	74581107	0.000000e+00	1622.0
2	TraesCS5A01G067400	chr5A	99.346	153	1	0	743	895	74581412	74581260	8.400000e-71	278.0
3	TraesCS5A01G067400	chr5A	97.826	46	1	0	2728	2773	74864778	74864823	2.540000e-11	80.5
4	TraesCS5A01G067400	chr5B	91.501	2012	111	24	1078	3072	88340258	88342226	0.000000e+00	2713.0
5	TraesCS5A01G067400	chr5B	91.339	1016	83	4	1065	2079	123437924	123436913	0.000000e+00	1384.0
6	TraesCS5A01G067400	chr5B	90.909	1012	86	5	1069	2079	123219871	123218865	0.000000e+00	1354.0
7	TraesCS5A01G067400	chr5B	90.269	668	60	4	1413	2079	123014109	123013446	0.000000e+00	869.0
8	TraesCS5A01G067400	chr5B	85.967	791	86	9	1293	2079	88211463	88212232	0.000000e+00	822.0
9	TraesCS5A01G067400	chr5B	91.404	349	30	0	1069	1417	123022480	123022132	2.150000e-131	479.0
10	TraesCS5A01G067400	chr5B	96.571	175	6	0	894	1068	123438059	123437885	1.080000e-74	291.0
11	TraesCS5A01G067400	chr5B	79.805	411	59	15	901	1306	88210910	88211301	8.400000e-71	278.0
12	TraesCS5A01G067400	chr5B	92.373	118	4	2	898	1010	88340139	88340256	2.460000e-36	163.0
13	TraesCS5A01G067400	chr6A	99.441	895	4	1	1	895	546560152	546561045	0.000000e+00	1624.0
14	TraesCS5A01G067400	chr6A	97.545	896	11	3	1	895	63059134	63058249	0.000000e+00	1522.0
15	TraesCS5A01G067400	chr6A	86.667	330	36	4	2405	2728	37834613	37834286	2.920000e-95	359.0
16	TraesCS5A01G067400	chr6A	92.647	136	10	0	2729	2864	37834330	37834195	2.420000e-46	196.0
17	TraesCS5A01G067400	chr5D	88.743	1146	93	19	1065	2182	78503961	78505098	0.000000e+00	1369.0
18	TraesCS5A01G067400	chr5D	93.552	822	37	5	901	1709	78594339	78595157	0.000000e+00	1210.0
19	TraesCS5A01G067400	chr5D	88.172	744	44	9	2334	3076	78603592	78604292	0.000000e+00	846.0
20	TraesCS5A01G067400	chr5D	86.358	777	87	11	1339	2101	78371229	78372000	0.000000e+00	830.0
21	TraesCS5A01G067400	chr5D	89.715	632	48	5	1701	2330	78602935	78603551	0.000000e+00	791.0
22	TraesCS5A01G067400	chr5D	86.833	281	34	1	1065	1342	78361836	78362116	8.290000e-81	311.0
23	TraesCS5A01G067400	chr5D	94.413	179	6	1	894	1068	78503822	78504000	3.910000e-69	272.0
24	TraesCS5A01G067400	chr5D	97.115	104	2	1	2085	2188	78603349	78603451	1.130000e-39	174.0
25	TraesCS5A01G067400	chr5D	88.372	86	10	0	2863	2948	240303161	240303076	1.510000e-18	104.0
26	TraesCS5A01G067400	chr4B	99.333	750	4	1	1	749	416490009	416490758	0.000000e+00	1356.0
27	TraesCS5A01G067400	chr4B	98.718	156	2	0	740	895	416490596	416490751	8.400000e-71	278.0
28	TraesCS5A01G067400	chr4B	83.721	129	10	6	2953	3076	141289425	141289547	9.020000e-21	111.0
29	TraesCS5A01G067400	chr2A	99.596	743	3	0	1	743	100651982	100651240	0.000000e+00	1356.0
30	TraesCS5A01G067400	chr2A	85.311	354	44	5	2380	2728	774563082	774563432	2.920000e-95	359.0
31	TraesCS5A01G067400	chr2A	98.726	157	2	0	743	899	100651392	100651236	2.340000e-71	279.0
32	TraesCS5A01G067400	chr2A	87.640	89	11	0	2862	2950	16862946	16862858	1.510000e-18	104.0
33	TraesCS5A01G067400	chr6B	99.328	744	5	0	1	744	560986021	560985278	0.000000e+00	1347.0
34	TraesCS5A01G067400	chr6B	83.881	335	46	7	2380	2707	88310217	88309884	2.300000e-81	313.0
35	TraesCS5A01G067400	chr6B	99.346	153	1	0	743	895	560985431	560985279	8.400000e-71	278.0
36	TraesCS5A01G067400	chr6B	92.453	106	8	0	2759	2864	88308392	88308287	5.310000e-33	152.0
37	TraesCS5A01G067400	chr2B	99.196	746	6	0	1	746	28082839	28083584	0.000000e+00	1345.0
38	TraesCS5A01G067400	chr2B	99.192	743	6	0	1	743	642807623	642806881	0.000000e+00	1339.0
39	TraesCS5A01G067400	chr2B	88.506	87	10	0	2862	2948	601199832	601199918	4.200000e-19	106.0
40	TraesCS5A01G067400	chr1A	99.194	744	6	0	1	744	82683597	82684340	0.000000e+00	1341.0
41	TraesCS5A01G067400	chr1A	98.718	156	2	0	740	895	82684184	82684339	8.400000e-71	278.0
42	TraesCS5A01G067400	chr3A	84.680	359	44	8	2377	2728	57617272	57617626	6.310000e-92	348.0
43	TraesCS5A01G067400	chr3A	84.591	318	43	3	2380	2691	495595421	495595104	8.290000e-81	311.0
44	TraesCS5A01G067400	chr2D	83.381	349	46	6	2388	2728	636722741	636722397	2.300000e-81	313.0
45	TraesCS5A01G067400	chr2D	88.636	88	10	0	2860	2947	636386034	636385947	1.170000e-19	108.0
46	TraesCS5A01G067400	chr4D	85.766	274	35	3	2459	2728	460486582	460486855	1.400000e-73	287.0
47	TraesCS5A01G067400	chr4D	86.458	96	11	2	2863	2956	434161698	434161603	1.510000e-18	104.0
48	TraesCS5A01G067400	chr7B	98.137	161	2	1	740	899	673689564	673689724	2.340000e-71	279.0
49	TraesCS5A01G067400	chrUn	86.207	232	29	2	2380	2608	67135293	67135524	6.590000e-62	248.0
50	TraesCS5A01G067400	chrUn	87.805	82	10	0	2647	2728	67135526	67135607	2.530000e-16	97.1
51	TraesCS5A01G067400	chr4A	88.321	137	16	0	2728	2864	716384256	716384392	6.830000e-37	165.0
52	TraesCS5A01G067400	chr3B	87.591	137	17	0	2728	2864	151178559	151178695	3.180000e-35	159.0
53	TraesCS5A01G067400	chr3D	89.412	85	9	0	2863	2947	320635164	320635248	1.170000e-19	108.0
54	TraesCS5A01G067400	chr7A	87.097	93	11	1	2862	2953	136806191	136806099	1.510000e-18	104.0

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	TraesCS5A01G067400	chr5A	74862096	74865172	3076	False	2881.750000	5683	98.913000	1	3077	2	chr5A.!!$F1	3076
1	TraesCS5A01G067400	chr5A	74581107	74582002	895	True	950.000000	1622	99.338000	1	896	2	chr5A.!!$R1	895
2	TraesCS5A01G067400	chr5B	88340139	88342226	2087	False	1438.000000	2713	91.937000	898	3072	2	chr5B.!!$F2	2174
3	TraesCS5A01G067400	chr5B	123218865	123219871	1006	True	1354.000000	1354	90.909000	1069	2079	1	chr5B.!!$R3	1010
4	TraesCS5A01G067400	chr5B	123013446	123014109	663	True	869.000000	869	90.269000	1413	2079	1	chr5B.!!$R1	666
5	TraesCS5A01G067400	chr5B	123436913	123438059	1146	True	837.500000	1384	93.955000	894	2079	2	chr5B.!!$R4	1185
6	TraesCS5A01G067400	chr5B	88210910	88212232	1322	False	550.000000	822	82.886000	901	2079	2	chr5B.!!$F1	1178
7	TraesCS5A01G067400	chr6A	546560152	546561045	893	False	1624.000000	1624	99.441000	1	895	1	chr6A.!!$F1	894
8	TraesCS5A01G067400	chr6A	63058249	63059134	885	True	1522.000000	1522	97.545000	1	895	1	chr6A.!!$R1	894
9	TraesCS5A01G067400	chr5D	78594339	78595157	818	False	1210.000000	1210	93.552000	901	1709	1	chr5D.!!$F3	808
10	TraesCS5A01G067400	chr5D	78371229	78372000	771	False	830.000000	830	86.358000	1339	2101	1	chr5D.!!$F2	762
11	TraesCS5A01G067400	chr5D	78503822	78505098	1276	False	820.500000	1369	91.578000	894	2182	2	chr5D.!!$F4	1288
12	TraesCS5A01G067400	chr5D	78602935	78604292	1357	False	603.666667	846	91.667333	1701	3076	3	chr5D.!!$F5	1375
13	TraesCS5A01G067400	chr4B	416490009	416490758	749	False	817.000000	1356	99.025500	1	895	2	chr4B.!!$F2	894
14	TraesCS5A01G067400	chr2A	100651236	100651982	746	True	817.500000	1356	99.161000	1	899	2	chr2A.!!$R2	898
15	TraesCS5A01G067400	chr6B	560985278	560986021	743	True	812.500000	1347	99.337000	1	895	2	chr6B.!!$R2	894
16	TraesCS5A01G067400	chr6B	88308287	88310217	1930	True	232.500000	313	88.167000	2380	2864	2	chr6B.!!$R1	484
17	TraesCS5A01G067400	chr2B	28082839	28083584	745	False	1345.000000	1345	99.196000	1	746	1	chr2B.!!$F1	745
18	TraesCS5A01G067400	chr2B	642806881	642807623	742	True	1339.000000	1339	99.192000	1	743	1	chr2B.!!$R1	742
19	TraesCS5A01G067400	chr1A	82683597	82684340	743	False	809.500000	1341	98.956000	1	895	2	chr1A.!!$F1	894

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
885	1041	6.630413	GCAATCCTACCAACTCAGTCATTAGA	60.63	42.308	0.0	0.0	0.0	2.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2377	2850	1.075542	GCACGTGCACACTTATAGCA	58.924	50.0	34.52	0.0	41.59	3.49	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
885	1041	6.630413	GCAATCCTACCAACTCAGTCATTAGA	60.630	42.308	0.00	0.00	0.00	2.10
899	1055	8.144155	TCAGTCATTAGAAGTAGAGATACGTG	57.856	38.462	0.00	0.00	0.00	4.49
1242	1425	2.185867	GTATCCTTGCCGACGCCA	59.814	61.111	0.00	0.00	0.00	5.69
1274	1457	3.151022	GGTCCTGAGCTCCTCCGG	61.151	72.222	12.15	6.69	36.42	5.14
1283	1466	2.647158	GCTCCTCCGGTTCCTCGTT	61.647	63.158	0.00	0.00	0.00	3.85
1328	1685	3.112263	TGAACCCTAAGGACGGATCAAT	58.888	45.455	0.00	0.00	36.73	2.57
1350	1707	1.464734	TCGAGCTTCCGACTCTCAAT	58.535	50.000	0.00	0.00	33.14	2.57
1367	1724	1.530013	AATGACGACGAGGTCCCGTT	61.530	55.000	0.00	0.00	43.49	4.44
1586	1963	4.657013	GTCAATGGGAGGTTCTTCTTCTT	58.343	43.478	0.00	0.00	0.00	2.52
1588	1965	4.013050	CAATGGGAGGTTCTTCTTCTTCC	58.987	47.826	0.00	0.00	0.00	3.46
1596	1979	3.815962	GGTTCTTCTTCTTCCAGTCCAAC	59.184	47.826	0.00	0.00	0.00	3.77
1597	1980	3.386768	TCTTCTTCTTCCAGTCCAACG	57.613	47.619	0.00	0.00	0.00	4.10
1598	1981	2.698797	TCTTCTTCTTCCAGTCCAACGT	59.301	45.455	0.00	0.00	0.00	3.99
1626	2009	2.357034	GGCACGCTCGACTTCCAA	60.357	61.111	0.00	0.00	0.00	3.53
1787	2170	2.279918	GTGCGTCGACCAACCAGT	60.280	61.111	10.58	0.00	0.00	4.00
2164	2600	5.878669	ACTTTGTAAAACTCTCGGTTGAAGT	59.121	36.000	0.00	0.00	38.29	3.01
2165	2601	7.043565	ACTTTGTAAAACTCTCGGTTGAAGTA	58.956	34.615	0.00	0.00	38.29	2.24
2166	2602	7.224167	ACTTTGTAAAACTCTCGGTTGAAGTAG	59.776	37.037	0.00	0.00	38.29	2.57
2167	2603	6.395426	TGTAAAACTCTCGGTTGAAGTAGA	57.605	37.500	0.00	0.00	38.29	2.59
2168	2604	6.808829	TGTAAAACTCTCGGTTGAAGTAGAA	58.191	36.000	0.00	0.00	38.29	2.10
2169	2605	7.439381	TGTAAAACTCTCGGTTGAAGTAGAAT	58.561	34.615	0.00	0.00	38.29	2.40
2170	2606	6.787085	AAAACTCTCGGTTGAAGTAGAATG	57.213	37.500	0.00	0.00	38.29	2.67
2171	2607	5.470047	AACTCTCGGTTGAAGTAGAATGT	57.530	39.130	0.00	0.00	36.70	2.71
2172	2608	5.470047	ACTCTCGGTTGAAGTAGAATGTT	57.530	39.130	0.00	0.00	0.00	2.71
2178	2614	4.675114	CGGTTGAAGTAGAATGTTTTGTGC	59.325	41.667	0.00	0.00	0.00	4.57
2223	2659	9.016623	GGTTGAAGTAGAATGTTTTGTGTTTAC	57.983	33.333	0.00	0.00	0.00	2.01
2233	2669	5.710984	TGTTTTGTGTTTACCGTGTGATTT	58.289	33.333	0.00	0.00	0.00	2.17
2271	2707	0.037590	TACGCTTCAAACCTGCCCAT	59.962	50.000	0.00	0.00	0.00	4.00
2291	2727	4.878397	CCATCACTGGGTTCTGACTTTATC	59.122	45.833	0.00	0.00	39.04	1.75
2314	2750	3.251245	TGTTGGTTAACATTAGTGGCACG	59.749	43.478	12.71	0.00	41.66	5.34
2330	2766	1.740380	GCACGTGCCTGTCATACATCT	60.740	52.381	30.12	0.00	34.31	2.90
2347	2820	1.139734	CTGGTCACCTCATCGGTCG	59.860	63.158	0.00	0.00	44.93	4.79
2351	2824	2.058001	TCACCTCATCGGTCGCCAT	61.058	57.895	0.00	0.00	44.93	4.40
2353	2826	2.058001	ACCTCATCGGTCGCCATGA	61.058	57.895	0.00	9.06	44.93	3.07
2377	2850	2.094338	GTCGTTGGATTAGACCCTTCGT	60.094	50.000	0.00	0.00	0.00	3.85
2381	2854	2.742348	TGGATTAGACCCTTCGTGCTA	58.258	47.619	0.00	0.00	0.00	3.49
2503	2978	9.679661	TGTATCAACATAAGAGAGGCAATAAAA	57.320	29.630	0.00	0.00	0.00	1.52
2554	3031	9.688091	AGATTACTCAGACTAACACTCTATTGA	57.312	33.333	0.00	0.00	0.00	2.57
2557	3034	7.526142	ACTCAGACTAACACTCTATTGAACA	57.474	36.000	0.00	0.00	0.00	3.18
2656	3146	2.799978	CGGAAAATTGGCAAAGAACACC	59.200	45.455	3.01	2.95	0.00	4.16
2670	3172	5.930837	AAGAACACCTGAAACATTTTCCA	57.069	34.783	0.00	0.00	0.00	3.53
2700	3203	5.694816	ACGCATCATTCATCGTAAACAAAA	58.305	33.333	0.00	0.00	33.02	2.44
2872	4817	4.897076	TGAACTTAACTGGTACTCTGTCCA	59.103	41.667	0.00	0.00	0.00	4.02
2878	4823	3.093057	ACTGGTACTCTGTCCATCTCAC	58.907	50.000	0.00	0.00	33.01	3.51
2948	4893	9.898576	CTTATATTATGGGATGGAGGGAGTATA	57.101	37.037	0.00	0.00	0.00	1.47
2951	4896	9.764776	ATATTATGGGATGGAGGGAGTATAAAT	57.235	33.333	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
885	1041	2.030213	GTCGCGTCACGTATCTCTACTT	59.970	50.000	5.77	0.00	44.19	2.24
899	1055	4.719369	AGAACAGGGCGTCGCGTC	62.719	66.667	11.75	6.11	0.00	5.19
1274	1457	2.251893	CTGCGTCTTCTAACGAGGAAC	58.748	52.381	0.00	0.00	45.37	3.62
1283	1466	0.325296	ATGGGTCCCTGCGTCTTCTA	60.325	55.000	10.00	0.00	0.00	2.10
1328	1685	2.640184	TGAGAGTCGGAAGCTCGATTA	58.360	47.619	0.45	0.00	41.40	1.75
1350	1707	2.595463	AACGGGACCTCGTCGTCA	60.595	61.111	8.23	0.00	43.07	4.35
1586	1963	0.536687	AGAGTCGACGTTGGACTGGA	60.537	55.000	22.85	0.00	44.41	3.86
1588	1965	0.875728	AGAGAGTCGACGTTGGACTG	59.124	55.000	22.85	0.00	44.41	3.51
1917	2300	2.828868	ACGCAGTTGGGCTTGAGA	59.171	55.556	0.00	0.00	37.78	3.27
2167	2603	9.816354	AGTTTTACAAGATAAGCACAAAACATT	57.184	25.926	9.03	0.00	37.04	2.71
2168	2604	9.463443	GAGTTTTACAAGATAAGCACAAAACAT	57.537	29.630	9.03	0.00	37.04	2.71
2169	2605	8.682710	AGAGTTTTACAAGATAAGCACAAAACA	58.317	29.630	9.03	0.00	37.04	2.83
2172	2608	8.999431	CCTAGAGTTTTACAAGATAAGCACAAA	58.001	33.333	0.00	0.00	0.00	2.83
2196	2632	7.404671	AACACAAAACATTCTACTTCAACCT	57.595	32.000	0.00	0.00	0.00	3.50
2197	2633	9.016623	GTAAACACAAAACATTCTACTTCAACC	57.983	33.333	0.00	0.00	0.00	3.77
2271	2707	4.593206	ACAGATAAAGTCAGAACCCAGTGA	59.407	41.667	0.00	0.00	0.00	3.41
2314	2750	2.093500	TGACCAGATGTATGACAGGCAC	60.093	50.000	0.00	0.00	0.00	5.01
2347	2820	1.453155	AATCCAACGACACTCATGGC	58.547	50.000	0.00	0.00	32.87	4.40
2351	2824	2.232941	GGGTCTAATCCAACGACACTCA	59.767	50.000	0.00	0.00	0.00	3.41
2353	2826	2.537143	AGGGTCTAATCCAACGACACT	58.463	47.619	0.00	0.00	36.64	3.55
2377	2850	1.075542	GCACGTGCACACTTATAGCA	58.924	50.000	34.52	0.00	41.59	3.49
2414	2887	8.464404	CCTAGAATGAATGTTGATTGTGTTCAT	58.536	33.333	0.00	0.00	40.22	2.57
2537	3014	8.353684	CCGATATGTTCAATAGAGTGTTAGTCT	58.646	37.037	0.00	0.00	0.00	3.24
2547	3024	5.839063	AGGGTTCTCCGATATGTTCAATAGA	59.161	40.000	0.00	0.00	41.52	1.98
2548	3025	5.928839	CAGGGTTCTCCGATATGTTCAATAG	59.071	44.000	0.00	0.00	41.52	1.73
2549	3026	5.221641	CCAGGGTTCTCCGATATGTTCAATA	60.222	44.000	0.00	0.00	41.52	1.90
2550	3027	4.444876	CCAGGGTTCTCCGATATGTTCAAT	60.445	45.833	0.00	0.00	41.52	2.57
2551	3028	3.118408	CCAGGGTTCTCCGATATGTTCAA	60.118	47.826	0.00	0.00	41.52	2.69
2552	3029	2.434336	CCAGGGTTCTCCGATATGTTCA	59.566	50.000	0.00	0.00	41.52	3.18
2553	3030	2.434702	ACCAGGGTTCTCCGATATGTTC	59.565	50.000	0.00	0.00	41.52	3.18
2554	3031	2.478292	ACCAGGGTTCTCCGATATGTT	58.522	47.619	0.00	0.00	41.52	2.71
2555	3032	2.176247	ACCAGGGTTCTCCGATATGT	57.824	50.000	0.00	0.00	41.52	2.29
2556	3033	4.283467	TGAATACCAGGGTTCTCCGATATG	59.717	45.833	0.00	0.00	41.52	1.78
2557	3034	4.489737	TGAATACCAGGGTTCTCCGATAT	58.510	43.478	0.00	0.00	41.52	1.63
2670	3172	2.352651	CGATGAATGATGCGTTCCACTT	59.647	45.455	0.00	0.00	0.00	3.16
2677	3179	4.937696	TTGTTTACGATGAATGATGCGT	57.062	36.364	0.00	0.00	40.42	5.24
2867	4812	5.069119	ACGCTCTTATATTGTGAGATGGACA	59.931	40.000	0.00	0.00	0.00	4.02
2872	4817	8.391106	GTCAAAAACGCTCTTATATTGTGAGAT	58.609	33.333	0.00	0.00	0.00	2.75
2878	4823	6.249260	GCAGTGTCAAAAACGCTCTTATATTG	59.751	38.462	0.00	0.00	45.69	1.90
2949	4894	8.936864	GCGCAACCTATATCATAGTTCTTTATT	58.063	33.333	0.30	0.00	0.00	1.40
2950	4895	8.314751	AGCGCAACCTATATCATAGTTCTTTAT	58.685	33.333	11.47	0.00	0.00	1.40
2951	4896	7.667557	AGCGCAACCTATATCATAGTTCTTTA	58.332	34.615	11.47	0.00	0.00	1.85
2962	4907	5.941948	ACCATTTAAGCGCAACCTATATC	57.058	39.130	11.47	0.00	0.00	1.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.