AutoCloner

Multiple sequence alignment - TraesCS4A01G488600

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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	TraesCS4A01G488600	chr4A	100.000	3902	0	0	1	3902	740070942	740074843	0.000000e+00	7206.0
1	TraesCS4A01G488600	chr4A	76.279	2306	410	79	622	2833	740589343	740587081	0.000000e+00	1101.0
2	TraesCS4A01G488600	chr4A	80.000	1305	210	36	473	1735	742274982	742276277	0.000000e+00	917.0
3	TraesCS4A01G488600	chr4A	81.555	1003	144	22	466	1435	740891258	740892252	0.000000e+00	789.0
4	TraesCS4A01G488600	chr4A	81.167	977	146	25	488	1434	739818440	739817472	0.000000e+00	750.0
5	TraesCS4A01G488600	chr4A	80.223	986	154	19	483	1435	741972335	741973312	0.000000e+00	702.0
6	TraesCS4A01G488600	chr4A	81.514	806	108	20	667	1457	741471841	741471062	3.310000e-175	625.0
7	TraesCS4A01G488600	chr4A	75.719	869	163	29	2008	2840	741973636	741974492	3.650000e-105	392.0
8	TraesCS4A01G488600	chr4A	82.126	414	56	15	1	411	57096368	57096766	4.830000e-89	339.0
9	TraesCS4A01G488600	chr4A	78.090	356	76	2	1918	2272	740892696	740893050	1.410000e-54	224.0
10	TraesCS4A01G488600	chr4A	80.156	257	47	4	1481	1735	739817386	739817132	5.150000e-44	189.0
11	TraesCS4A01G488600	chr4A	85.246	183	26	1	483	664	741472062	741471880	1.850000e-43	187.0
12	TraesCS4A01G488600	chr4A	82.203	118	21	0	1918	2035	742276382	742276499	6.900000e-18	102.0
13	TraesCS4A01G488600	chr4A	80.899	89	12	5	3759	3845	433273254	433273339	9.050000e-07	65.8
14	TraesCS4A01G488600	chr7D	81.341	1029	155	23	466	1457	3754360	3755388	0.000000e+00	802.0
15	TraesCS4A01G488600	chr7D	76.682	1055	190	26	1819	2821	3431339	3430289	5.740000e-148	534.0
16	TraesCS4A01G488600	chr7D	82.679	560	82	7	775	1320	3778441	3777883	2.110000e-132	483.0
17	TraesCS4A01G488600	chr7D	81.458	480	68	17	1	476	424546972	424547434	1.320000e-99	374.0
18	TraesCS4A01G488600	chr7A	81.433	991	145	27	483	1438	3573537	3572551	0.000000e+00	774.0
19	TraesCS4A01G488600	chr7A	80.830	1012	147	26	466	1435	2578615	2579621	0.000000e+00	750.0
20	TraesCS4A01G488600	chr7A	81.455	825	119	18	692	1485	3009123	3009944	0.000000e+00	645.0
21	TraesCS4A01G488600	chr7A	77.316	1058	179	30	1835	2839	3629120	3628071	5.660000e-158	568.0
22	TraesCS4A01G488600	chr7A	76.525	1082	206	29	1791	2833	2579863	2580935	7.370000e-152	547.0
23	TraesCS4A01G488600	chr7A	90.667	375	30	5	3367	3738	302054484	302054112	9.740000e-136	494.0
24	TraesCS4A01G488600	chr7A	90.642	374	29	5	3365	3734	195351706	195351335	3.500000e-135	492.0
25	TraesCS4A01G488600	chr7A	90.959	365	29	4	3375	3736	12295672	12296035	4.530000e-134	488.0
26	TraesCS4A01G488600	chr7A	90.323	372	33	3	3365	3734	645836912	645836542	5.860000e-133	484.0
27	TraesCS4A01G488600	chr7A	75.743	1010	187	28	1847	2806	3010267	3011268	4.600000e-124	455.0
28	TraesCS4A01G488600	chr7A	80.469	256	48	2	1481	1735	3629399	3629145	1.110000e-45	195.0
29	TraesCS4A01G488600	chr7A	77.043	257	55	4	1481	1735	3009973	3010227	1.130000e-30	145.0
30	TraesCS4A01G488600	chrUn	79.175	994	163	30	466	1435	23780948	23781921	0.000000e+00	649.0
31	TraesCS4A01G488600	chrUn	79.175	994	163	30	466	1435	291095405	291096378	0.000000e+00	649.0
32	TraesCS4A01G488600	chrUn	82.909	275	43	4	1463	1735	23781982	23782254	1.080000e-60	244.0
33	TraesCS4A01G488600	chrUn	82.909	275	43	4	1463	1735	291096439	291096711	1.080000e-60	244.0
34	TraesCS4A01G488600	chrUn	71.062	546	136	15	2049	2580	90316726	90316189	3.190000e-21	113.0
35	TraesCS4A01G488600	chr1A	91.281	367	28	3	3365	3728	273077181	273076816	7.530000e-137	497.0
36	TraesCS4A01G488600	chr1A	90.107	374	34	3	3365	3736	379137117	379136745	2.110000e-132	483.0
37	TraesCS4A01G488600	chr1A	85.185	81	8	4	3758	3836	291919501	291919579	3.230000e-11	80.5
38	TraesCS4A01G488600	chr5A	90.786	369	29	5	3375	3740	482289490	482289856	4.530000e-134	488.0
39	TraesCS4A01G488600	chr5A	90.566	371	29	5	3365	3731	365049151	365049519	1.630000e-133	486.0
40	TraesCS4A01G488600	chr2A	90.349	373	31	5	3365	3734	383249349	383248979	5.860000e-133	484.0
41	TraesCS4A01G488600	chr2A	83.229	477	68	6	1	476	719549510	719549975	1.000000e-115	427.0
42	TraesCS4A01G488600	chr6A	82.737	475	64	9	4	476	500499381	500498923	1.310000e-109	407.0
43	TraesCS4A01G488600	chr5B	82.316	475	68	8	1	470	621403852	621404315	7.860000e-107	398.0
44	TraesCS4A01G488600	chr5B	78.033	478	91	8	1	476	77928493	77928958	4.930000e-74	289.0
45	TraesCS4A01G488600	chr5B	77.941	476	81	19	7	476	388164884	388165341	3.840000e-70	276.0
46	TraesCS4A01G488600	chr5B	80.142	282	45	8	197	476	622748070	622748342	2.380000e-47	200.0
47	TraesCS4A01G488600	chr2B	85.304	313	44	2	1	312	706419046	706419357	4.860000e-84	322.0
48	TraesCS4A01G488600	chr2B	79.096	177	27	5	301	476	466033917	466034084	3.190000e-21	113.0
49	TraesCS4A01G488600	chr2B	96.000	50	2	0	3758	3807	519318984	519318935	8.990000e-12	82.4
50	TraesCS4A01G488600	chr5D	82.371	329	54	4	8	334	74413414	74413088	2.300000e-72	283.0
51	TraesCS4A01G488600	chr6D	77.662	479	81	20	1	476	159986853	159987308	6.430000e-68	268.0
52	TraesCS4A01G488600	chr6D	82.011	189	21	8	290	476	338399112	338399289	8.740000e-32	148.0
53	TraesCS4A01G488600	chr6D	87.324	71	4	5	3758	3826	164163808	164163741	4.180000e-10	76.8
54	TraesCS4A01G488600	chr6B	78.320	369	61	13	113	476	585713414	585713060	1.830000e-53	220.0
55	TraesCS4A01G488600	chr6B	88.889	63	5	1	3758	3820	174753113	174753053	4.180000e-10	76.8
56	TraesCS4A01G488600	chr6B	89.831	59	4	2	3758	3816	389762325	389762381	1.500000e-09	75.0
57	TraesCS4A01G488600	chr4D	77.492	311	39	22	152	455	258743742	258744028	1.450000e-34	158.0
58	TraesCS4A01G488600	chr3D	89.062	64	6	1	3758	3821	231179515	231179453	1.160000e-10	78.7
59	TraesCS4A01G488600	chr1B	87.302	63	7	1	3758	3820	234819716	234819655	1.950000e-08	71.3
60	TraesCS4A01G488600	chr4B	80.220	91	15	3	3759	3848	285400023	285399935	9.050000e-07	65.8

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	TraesCS4A01G488600	chr4A	740070942	740074843	3901	False	7206.0	7206	100.000000	1	3902	1	chr4A.!!$F3	3901
1	TraesCS4A01G488600	chr4A	740587081	740589343	2262	True	1101.0	1101	76.279000	622	2833	1	chr4A.!!$R1	2211
2	TraesCS4A01G488600	chr4A	741972335	741974492	2157	False	547.0	702	77.971000	483	2840	2	chr4A.!!$F5	2357
3	TraesCS4A01G488600	chr4A	742274982	742276499	1517	False	509.5	917	81.101500	473	2035	2	chr4A.!!$F6	1562
4	TraesCS4A01G488600	chr4A	740891258	740893050	1792	False	506.5	789	79.822500	466	2272	2	chr4A.!!$F4	1806
5	TraesCS4A01G488600	chr4A	739817132	739818440	1308	True	469.5	750	80.661500	488	1735	2	chr4A.!!$R2	1247
6	TraesCS4A01G488600	chr4A	741471062	741472062	1000	True	406.0	625	83.380000	483	1457	2	chr4A.!!$R3	974
7	TraesCS4A01G488600	chr7D	3754360	3755388	1028	False	802.0	802	81.341000	466	1457	1	chr7D.!!$F1	991
8	TraesCS4A01G488600	chr7D	3430289	3431339	1050	True	534.0	534	76.682000	1819	2821	1	chr7D.!!$R1	1002
9	TraesCS4A01G488600	chr7D	3777883	3778441	558	True	483.0	483	82.679000	775	1320	1	chr7D.!!$R2	545
10	TraesCS4A01G488600	chr7A	3572551	3573537	986	True	774.0	774	81.433000	483	1438	1	chr7A.!!$R1	955
11	TraesCS4A01G488600	chr7A	2578615	2580935	2320	False	648.5	750	78.677500	466	2833	2	chr7A.!!$F2	2367
12	TraesCS4A01G488600	chr7A	3009123	3011268	2145	False	415.0	645	78.080333	692	2806	3	chr7A.!!$F3	2114
13	TraesCS4A01G488600	chr7A	3628071	3629399	1328	True	381.5	568	78.892500	1481	2839	2	chr7A.!!$R5	1358
14	TraesCS4A01G488600	chrUn	23780948	23782254	1306	False	446.5	649	81.042000	466	1735	2	chrUn.!!$F1	1269
15	TraesCS4A01G488600	chrUn	291095405	291096711	1306	False	446.5	649	81.042000	466	1735	2	chrUn.!!$F2	1269

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	0.107831	TAGCAGCAACGTGTTTCCCT	59.892	50.0	0.00	0.0	0.00	4.20	F
1786	2089	0.036577	CTGGGAGATCATCGGGATGC	60.037	60.0	3.77	0.0	38.65	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1909	2212	0.029474	TTCCCAATCTCCCCCGGTAT	60.029	55.0	0.0	0.0	0.0	2.73	R
3014	3407	0.033405	AGATGGCTGCTGATTGGCTT	60.033	50.0	0.0	0.0	0.0	4.35	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	1.532078	GGTTTCCCCCAAAGCGGAA	60.532	57.895	0.00	0.00	36.35	4.30
19	20	1.532604	GGTTTCCCCCAAAGCGGAAG	61.533	60.000	0.00	0.00	39.29	3.46
20	21	1.228737	TTTCCCCCAAAGCGGAAGG	60.229	57.895	0.00	0.00	39.29	3.46
21	22	2.723464	TTTCCCCCAAAGCGGAAGGG	62.723	60.000	0.00	0.00	39.29	3.95
22	23	3.979497	CCCCCAAAGCGGAAGGGT	61.979	66.667	0.00	0.00	41.16	4.34
23	24	2.676471	CCCCAAAGCGGAAGGGTG	60.676	66.667	0.00	0.00	41.16	4.61
24	25	2.434331	CCCAAAGCGGAAGGGTGA	59.566	61.111	0.00	0.00	37.81	4.02
26	27	0.825840	CCCAAAGCGGAAGGGTGAAA	60.826	55.000	0.00	0.00	37.81	2.69
27	28	1.256812	CCAAAGCGGAAGGGTGAAAT	58.743	50.000	0.00	0.00	36.56	2.17
28	29	2.442413	CCAAAGCGGAAGGGTGAAATA	58.558	47.619	0.00	0.00	36.56	1.40
29	30	2.423538	CCAAAGCGGAAGGGTGAAATAG	59.576	50.000	0.00	0.00	36.56	1.73
30	31	3.343617	CAAAGCGGAAGGGTGAAATAGA	58.656	45.455	0.00	0.00	0.00	1.98
33	34	5.367945	AAGCGGAAGGGTGAAATAGAATA	57.632	39.130	0.00	0.00	0.00	1.75
35	36	3.498777	GCGGAAGGGTGAAATAGAATAGC	59.501	47.826	0.00	0.00	0.00	2.97
36	37	4.703897	CGGAAGGGTGAAATAGAATAGCA	58.296	43.478	0.00	0.00	0.00	3.49
38	39	4.517075	GGAAGGGTGAAATAGAATAGCAGC	59.483	45.833	0.00	0.00	0.00	5.25
39	40	4.778213	AGGGTGAAATAGAATAGCAGCA	57.222	40.909	0.00	0.00	0.00	4.41
40	41	5.116084	AGGGTGAAATAGAATAGCAGCAA	57.884	39.130	0.00	0.00	0.00	3.91
41	42	4.884164	AGGGTGAAATAGAATAGCAGCAAC	59.116	41.667	0.00	0.00	0.00	4.17
43	44	4.332819	GGTGAAATAGAATAGCAGCAACGT	59.667	41.667	0.00	0.00	0.00	3.99
44	45	5.258622	GTGAAATAGAATAGCAGCAACGTG	58.741	41.667	0.00	0.00	0.00	4.49
45	46	4.935205	TGAAATAGAATAGCAGCAACGTGT	59.065	37.500	0.00	0.00	0.00	4.49
46	47	5.411361	TGAAATAGAATAGCAGCAACGTGTT	59.589	36.000	0.00	0.00	0.00	3.32
47	48	5.880054	AATAGAATAGCAGCAACGTGTTT	57.120	34.783	0.00	0.00	0.00	2.83
48	49	3.813529	AGAATAGCAGCAACGTGTTTC	57.186	42.857	0.00	0.00	0.00	2.78

Showing 1 to 25 of 1,052 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.979497	ACCCTTCCGCTTTGGGGG	61.979	66.667	0.00	0.00	44.97	5.40
6	7	2.676471	CACCCTTCCGCTTTGGGG	60.676	66.667	0.00	0.00	44.97	4.96
7	8	0.825840	TTTCACCCTTCCGCTTTGGG	60.826	55.000	0.00	0.00	46.07	4.12
8	9	1.256812	ATTTCACCCTTCCGCTTTGG	58.743	50.000	0.00	0.00	40.09	3.28
9	10	3.343617	TCTATTTCACCCTTCCGCTTTG	58.656	45.455	0.00	0.00	0.00	2.77
10	11	3.713826	TCTATTTCACCCTTCCGCTTT	57.286	42.857	0.00	0.00	0.00	3.51
11	12	3.713826	TTCTATTTCACCCTTCCGCTT	57.286	42.857	0.00	0.00	0.00	4.68
12	13	3.933861	ATTCTATTTCACCCTTCCGCT	57.066	42.857	0.00	0.00	0.00	5.52
13	14	3.498777	GCTATTCTATTTCACCCTTCCGC	59.501	47.826	0.00	0.00	0.00	5.54
14	15	4.703897	TGCTATTCTATTTCACCCTTCCG	58.296	43.478	0.00	0.00	0.00	4.30
18	19	4.778213	TGCTGCTATTCTATTTCACCCT	57.222	40.909	0.00	0.00	0.00	4.34
19	20	4.260784	CGTTGCTGCTATTCTATTTCACCC	60.261	45.833	0.00	0.00	0.00	4.61
20	21	4.332819	ACGTTGCTGCTATTCTATTTCACC	59.667	41.667	0.00	0.00	0.00	4.02
21	22	5.163854	ACACGTTGCTGCTATTCTATTTCAC	60.164	40.000	0.00	0.00	0.00	3.18
22	23	4.935205	ACACGTTGCTGCTATTCTATTTCA	59.065	37.500	0.00	0.00	0.00	2.69
23	24	5.470845	ACACGTTGCTGCTATTCTATTTC	57.529	39.130	0.00	0.00	0.00	2.17
24	25	5.880054	AACACGTTGCTGCTATTCTATTT	57.120	34.783	0.00	0.00	0.00	1.40
26	27	4.332819	GGAAACACGTTGCTGCTATTCTAT	59.667	41.667	0.00	0.00	0.00	1.98
27	28	3.682858	GGAAACACGTTGCTGCTATTCTA	59.317	43.478	0.00	0.00	0.00	2.10
28	29	2.484264	GGAAACACGTTGCTGCTATTCT	59.516	45.455	0.00	0.00	0.00	2.40
29	30	2.414161	GGGAAACACGTTGCTGCTATTC	60.414	50.000	0.00	0.00	0.00	1.75
30	31	1.539827	GGGAAACACGTTGCTGCTATT	59.460	47.619	0.00	0.00	0.00	1.73
33	34	0.751643	AAGGGAAACACGTTGCTGCT	60.752	50.000	0.00	0.00	0.00	4.24
35	36	0.030638	CCAAGGGAAACACGTTGCTG	59.969	55.000	0.00	0.00	35.52	4.41
36	37	0.395173	ACCAAGGGAAACACGTTGCT	60.395	50.000	0.00	0.00	35.52	3.91

Showing 1 to 25 of 1,066 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.