AutoCloner

Multiple sequence alignment - TraesCS7A01G392000

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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	TraesCS7A01G392000	chr7A	100.000	2336	0	0	1	2336	567791293	567793628	0.000000e+00	4314
1	TraesCS7A01G392000	chr7A	97.267	439	10	2	1632	2068	567798083	567797645	0.000000e+00	743
2	TraesCS7A01G392000	chr7A	94.265	279	13	3	1006	1284	569112478	569112203	7.720000e-115	424
3	TraesCS7A01G392000	chr7A	88.385	353	33	5	1012	1361	568695653	568695306	3.590000e-113	418
4	TraesCS7A01G392000	chr7A	97.177	248	6	1	2068	2314	675467243	675466996	3.590000e-113	418
5	TraesCS7A01G392000	chr7A	86.494	385	33	13	1003	1386	568579867	568580233	2.800000e-109	405
6	TraesCS7A01G392000	chr7A	86.340	388	32	15	1003	1386	568129884	568130254	1.010000e-108	403
7	TraesCS7A01G392000	chr7A	97.333	225	6	0	1639	1863	675467493	675467269	1.310000e-102	383
8	TraesCS7A01G392000	chr7A	94.805	231	12	0	1635	1865	675462348	675462578	6.140000e-96	361
9	TraesCS7A01G392000	chr7A	96.078	204	6	1	1866	2067	675462758	675462961	4.810000e-87	331
10	TraesCS7A01G392000	chr7D	87.032	1681	118	51	28	1634	501507937	501509591	0.000000e+00	1805
11	TraesCS7A01G392000	chr7D	81.994	672	56	28	1007	1632	501609973	501609321	5.760000e-141	510
12	TraesCS7A01G392000	chr7D	89.724	399	31	7	1639	2029	585191040	585190644	3.470000e-138	501
13	TraesCS7A01G392000	chr7D	96.283	269	10	0	2068	2336	585187597	585187865	2.130000e-120	442
14	TraesCS7A01G392000	chr7B	84.688	1600	113	54	143	1631	530869022	530870600	0.000000e+00	1476
15	TraesCS7A01G392000	chr7B	82.440	672	56	28	1006	1638	531222312	531221664	4.420000e-147	531
16	TraesCS7A01G392000	chr7B	78.442	719	86	43	692	1381	531179858	531180536	2.800000e-109	405
17	TraesCS7A01G392000	chr4A	97.541	610	15	0	1636	2245	186476582	186477191	0.000000e+00	1044
18	TraesCS7A01G392000	chr4A	97.454	432	11	0	1637	2068	186482051	186481620	0.000000e+00	737
19	TraesCS7A01G392000	chr4A	96.599	294	10	0	1638	1931	488542280	488541987	2.700000e-134	488
20	TraesCS7A01G392000	chr4A	100.000	79	0	0	2258	2336	186477499	186477577	1.870000e-31	147
21	TraesCS7A01G392000	chr6A	96.811	439	12	2	1632	2068	569966883	569967321	0.000000e+00	732
22	TraesCS7A01G392000	chr3D	88.000	225	25	2	1639	1863	370046	369824	4.950000e-67	265

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	TraesCS7A01G392000	chr7A	567791293	567793628	2335	False	4314.0	4314	100.0000	1	2336	1	chr7A.!!$F1	2335
1	TraesCS7A01G392000	chr7A	675462348	675462961	613	False	346.0	361	95.4415	1635	2067	2	chr7A.!!$F4	432
2	TraesCS7A01G392000	chr7D	501507937	501509591	1654	False	1805.0	1805	87.0320	28	1634	1	chr7D.!!$F1	1606
3	TraesCS7A01G392000	chr7D	501609321	501609973	652	True	510.0	510	81.9940	1007	1632	1	chr7D.!!$R1	625
4	TraesCS7A01G392000	chr7B	530869022	530870600	1578	False	1476.0	1476	84.6880	143	1631	1	chr7B.!!$F1	1488
5	TraesCS7A01G392000	chr7B	531221664	531222312	648	True	531.0	531	82.4400	1006	1638	1	chr7B.!!$R1	632
6	TraesCS7A01G392000	chr7B	531179858	531180536	678	False	405.0	405	78.4420	692	1381	1	chr7B.!!$F2	689
7	TraesCS7A01G392000	chr4A	186476582	186477577	995	False	595.5	1044	98.7705	1636	2336	2	chr4A.!!$F1	700

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
577	611	0.39086	GATCTCGCCACCTATGCTGT	59.609	55.0	0.0	0.0	0.0	4.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1570	1737	0.610174	AATCGAACTGGAGAGCAGCA	59.39	50.0	0.0	0.0	0.0	4.41	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
42	43	4.983671	AAAAATAATCTCCGTTGCCCTC	57.016	40.909	0.00	0.00	0.00	4.30
71	72	5.047377	GGGGTAGTGCTTGAAATGAATGAAA	60.047	40.000	0.00	0.00	0.00	2.69
73	74	6.928492	GGGTAGTGCTTGAAATGAATGAAAAA	59.072	34.615	0.00	0.00	0.00	1.94
153	156	8.441312	TCTTAAACTTGTACTACAAAGTTGGG	57.559	34.615	9.16	4.55	37.69	4.12
154	157	8.048514	TCTTAAACTTGTACTACAAAGTTGGGT	58.951	33.333	9.16	0.00	37.69	4.51
158	161	6.161381	ACTTGTACTACAAAGTTGGGTATCG	58.839	40.000	3.26	0.00	37.69	2.92
183	187	3.410516	CAATGCGCGGTCGTCACA	61.411	61.111	8.83	0.00	38.14	3.58
238	250	3.106986	AAGGCGTGGATCATCCCGG	62.107	63.158	14.25	0.00	35.03	5.73
282	304	2.223572	CCGGGCAAGCATACATTTCTTC	60.224	50.000	0.00	0.00	0.00	2.87
284	306	2.223572	GGGCAAGCATACATTTCTTCCG	60.224	50.000	0.00	0.00	0.00	4.30
320	342	2.063156	TGCGTTTGATTTCCACATGC	57.937	45.000	0.00	0.00	37.83	4.06
322	344	1.994916	CGTTTGATTTCCACATGCCC	58.005	50.000	0.00	0.00	0.00	5.36
358	380	3.461214	TCCACCCGGAGTTCTACAA	57.539	52.632	0.73	0.00	35.91	2.41
388	410	4.454948	GTGCCAGCACAGTGTACA	57.545	55.556	17.61	0.00	45.53	2.90
389	411	2.238353	GTGCCAGCACAGTGTACAG	58.762	57.895	17.61	0.00	45.53	2.74
432	454	2.026879	GAGCATCCGCCTCTCGTC	59.973	66.667	0.00	0.00	39.83	4.20
453	475	1.207089	TCACCCCGTATCTTTGCAGAG	59.793	52.381	0.00	0.00	30.36	3.35
479	507	2.232452	CCAGAACCTACTCACTGAGGTG	59.768	54.545	10.86	0.00	45.64	4.00
548	582	7.088905	GGATGTTCTTTAATCATGATGGCATC	58.911	38.462	20.52	20.52	30.68	3.91
552	586	4.756642	TCTTTAATCATGATGGCATCGGAC	59.243	41.667	21.65	0.00	30.68	4.79
557	591	3.643978	GATGGCATCGGACGCAGC	61.644	66.667	12.40	0.70	0.00	5.25
574	608	4.251760	CGATCTCGCCACCTATGC	57.748	61.111	0.00	0.00	0.00	3.14
577	611	0.390860	GATCTCGCCACCTATGCTGT	59.609	55.000	0.00	0.00	0.00	4.40
580	614	3.566853	CGCCACCTATGCTGTGCG	61.567	66.667	0.00	0.00	32.30	5.34
598	632	4.209866	GGCCCCCACCTATGCTGG	62.210	72.222	0.00	0.00	0.00	4.85
600	634	4.209866	CCCCCACCTATGCTGGGC	62.210	72.222	2.34	0.00	46.58	5.36
602	636	4.569180	CCCACCTATGCTGGGCGG	62.569	72.222	0.00	0.00	42.22	6.13
603	637	4.569180	CCACCTATGCTGGGCGGG	62.569	72.222	0.00	0.00	0.00	6.13
815	884	2.540145	GGCGGGCCGACTATAAATG	58.460	57.895	33.44	0.00	0.00	2.32
852	922	4.271816	CCCGATCGCAGTCTCCCG	62.272	72.222	10.32	0.00	0.00	5.14
881	954	0.976641	TACAGCCACCCACAGAGAAG	59.023	55.000	0.00	0.00	0.00	2.85
990	1080	1.664017	CATGAGGCCGATCAGAGCG	60.664	63.158	0.00	0.00	31.44	5.03
1366	1491	3.001406	ACCCGTGTACCCTCTGCC	61.001	66.667	0.00	0.00	0.00	4.85
1462	1595	6.729690	ATTAGCAGAGAAGATAGAGCTGTT	57.270	37.500	0.00	0.00	33.83	3.16
1523	1686	1.418373	CGTTGAGATCTGTGAACGCA	58.582	50.000	14.77	0.00	35.29	5.24
1570	1737	0.523072	AAATGCATGACGCTCGCTTT	59.477	45.000	0.00	0.00	43.06	3.51
1665	1837	2.360350	CACGGCAGACCCAGCAAT	60.360	61.111	0.00	0.00	0.00	3.56
1826	1998	0.471780	CCCTTTTGCAGAAACCCCCT	60.472	55.000	0.00	0.00	0.00	4.79
1916	2267	4.519213	ACTGGCTGTACTAACACAAAACA	58.481	39.130	0.00	0.00	0.00	2.83
1950	2301	3.441572	CAGTTGGCAAAGGACAATAGAGG	59.558	47.826	0.00	0.00	45.61	3.69
1958	2309	2.537143	AGGACAATAGAGGACAACGGT	58.463	47.619	0.00	0.00	0.00	4.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	4.600062	AGAGGGCAACGGAGATTATTTTT	58.400	39.130	0.00	0.00	37.60	1.94
22	23	4.080299	AGAGAGGGCAACGGAGATTATTTT	60.080	41.667	0.00	0.00	37.60	1.82
23	24	3.456277	AGAGAGGGCAACGGAGATTATTT	59.544	43.478	0.00	0.00	37.60	1.40
24	25	3.041946	AGAGAGGGCAACGGAGATTATT	58.958	45.455	0.00	0.00	37.60	1.40
25	26	2.683768	AGAGAGGGCAACGGAGATTAT	58.316	47.619	0.00	0.00	37.60	1.28
26	27	2.160721	AGAGAGGGCAACGGAGATTA	57.839	50.000	0.00	0.00	37.60	1.75
42	43	4.162320	TCATTTCAAGCACTACCCCTAGAG	59.838	45.833	0.00	0.00	0.00	2.43
71	72	8.436046	AACAAAGACATGCATTAATGTGTTTT	57.564	26.923	16.61	11.89	46.20	2.43
73	74	7.208777	TGAACAAAGACATGCATTAATGTGTT	58.791	30.769	16.61	14.83	43.63	3.32
129	132	8.217131	ACCCAACTTTGTAGTACAAGTTTAAG	57.783	34.615	19.51	14.93	39.53	1.85
133	136	6.647895	CGATACCCAACTTTGTAGTACAAGTT	59.352	38.462	15.06	16.67	39.53	2.66
135	138	6.090358	CACGATACCCAACTTTGTAGTACAAG	59.910	42.308	15.06	11.89	39.53	3.16
136	139	5.927689	CACGATACCCAACTTTGTAGTACAA	59.072	40.000	11.75	11.75	36.11	2.41
137	140	5.472148	CACGATACCCAACTTTGTAGTACA	58.528	41.667	0.00	0.00	33.17	2.90
138	141	4.328169	GCACGATACCCAACTTTGTAGTAC	59.672	45.833	0.00	0.00	33.17	2.73
140	143	3.244284	TGCACGATACCCAACTTTGTAGT	60.244	43.478	0.00	0.00	35.68	2.73
141	144	3.331150	TGCACGATACCCAACTTTGTAG	58.669	45.455	0.00	0.00	0.00	2.74
153	156	1.187553	CGCATTGCGTTGCACGATAC	61.188	55.000	22.42	0.00	46.05	2.24
154	157	1.060151	CGCATTGCGTTGCACGATA	59.940	52.632	22.42	0.67	46.05	2.92
183	187	1.606903	TTGAAAATACCAACGGCGGT	58.393	45.000	13.24	0.00	43.46	5.68
238	250	1.609320	GCTGAACTTGGTCCAGGAGAC	60.609	57.143	8.21	0.00	45.51	3.36
284	306	1.620413	GCATGCTCTGCCGCAAAAAC	61.620	55.000	11.37	0.00	45.66	2.43
294	316	2.095110	TGGAAATCAAACGCATGCTCTG	60.095	45.455	17.13	9.96	0.00	3.35
320	342	1.912043	AGGAGATTCAGTGAACCTGGG	59.088	52.381	5.96	0.00	41.83	4.45
322	344	2.568956	TGGAGGAGATTCAGTGAACCTG	59.431	50.000	16.14	0.00	42.97	4.00
355	377	1.237285	GCACTGGCGGAGTTCATTGT	61.237	55.000	0.00	0.00	29.75	2.71
358	380	2.045926	GGCACTGGCGGAGTTCAT	60.046	61.111	0.00	0.00	42.47	2.57
383	405	1.663739	GCCGAGGTGTGACTGTACA	59.336	57.895	0.00	0.00	0.00	2.90
384	406	1.443872	CGCCGAGGTGTGACTGTAC	60.444	63.158	0.00	0.00	0.00	2.90
385	407	1.457823	AACGCCGAGGTGTGACTGTA	61.458	55.000	9.28	0.00	38.98	2.74
386	408	2.694829	GAACGCCGAGGTGTGACTGT	62.695	60.000	9.28	0.00	38.98	3.55
387	409	2.022129	GAACGCCGAGGTGTGACTG	61.022	63.158	9.28	0.00	38.98	3.51
388	410	2.338984	GAACGCCGAGGTGTGACT	59.661	61.111	9.28	0.00	38.98	3.41
389	411	2.737376	GGAACGCCGAGGTGTGAC	60.737	66.667	9.28	6.87	38.98	3.67
432	454	1.207089	TCTGCAAAGATACGGGGTGAG	59.793	52.381	0.00	0.00	0.00	3.51
453	475	3.827302	TCAGTGAGTAGGTTCTGGAAGTC	59.173	47.826	0.00	0.00	33.76	3.01
479	507	9.508567	GTGCCAGTAGAAGAATTATTTGAATTC	57.491	33.333	0.00	0.00	37.01	2.17
488	516	5.738619	TGAGTGTGCCAGTAGAAGAATTA	57.261	39.130	0.00	0.00	0.00	1.40
489	517	4.623932	TGAGTGTGCCAGTAGAAGAATT	57.376	40.909	0.00	0.00	0.00	2.17
490	518	4.623932	TTGAGTGTGCCAGTAGAAGAAT	57.376	40.909	0.00	0.00	0.00	2.40
530	563	4.377738	CGTCCGATGCCATCATGATTAAAG	60.378	45.833	5.16	0.00	31.96	1.85
557	591	0.665670	CAGCATAGGTGGCGAGATCG	60.666	60.000	0.00	0.00	43.27	3.69
580	614	4.209866	CAGCATAGGTGGGGGCCC	62.210	72.222	15.76	15.76	0.00	5.80
608	642	2.029288	CTGCGTGTGCCAGTAGGTG	61.029	63.158	0.00	0.00	41.78	4.00
610	644	3.121030	GCTGCGTGTGCCAGTAGG	61.121	66.667	0.00	0.00	41.78	3.18
611	645	2.047844	AGCTGCGTGTGCCAGTAG	60.048	61.111	0.00	0.00	41.78	2.57
612	646	2.357396	CAGCTGCGTGTGCCAGTA	60.357	61.111	0.00	0.00	41.78	2.74
636	691	1.792301	CTGCATGCACACGAAGGAG	59.208	57.895	18.46	0.00	0.00	3.69
806	875	1.348036	GAGGGAGGCGGCATTTATAGT	59.652	52.381	13.08	0.00	0.00	2.12
829	899	2.835431	ACTGCGATCGGGAGGAGG	60.835	66.667	18.30	0.00	38.63	4.30
852	922	2.047274	TGGCTGTAACGGCTGAGC	60.047	61.111	0.00	0.00	35.82	4.26
858	928	1.671054	CTGTGGGTGGCTGTAACGG	60.671	63.158	0.00	0.00	0.00	4.44
881	954	2.171489	GAGTGGTGGTTTCGCGCTTC	62.171	60.000	5.56	0.00	0.00	3.86
1032	1146	2.182030	GTCGGCGTCCTCCAGAAG	59.818	66.667	6.85	0.00	0.00	2.85
1318	1435	3.885521	CTACGACGCGTCCTCCCC	61.886	72.222	31.84	8.55	41.54	4.81
1319	1436	3.885521	CCTACGACGCGTCCTCCC	61.886	72.222	31.84	9.34	41.54	4.30
1392	1518	5.141182	GGGGAAAATCCTAGGAGAAAATCC	58.859	45.833	18.34	17.74	41.91	3.01
1462	1595	1.021202	CCTCACCAAGAACGCAAACA	58.979	50.000	0.00	0.00	0.00	2.83
1523	1686	3.724732	ATGCAGGCCAAAATTCCATTT	57.275	38.095	5.01	0.00	0.00	2.32
1570	1737	0.610174	AATCGAACTGGAGAGCAGCA	59.390	50.000	0.00	0.00	0.00	4.41
1662	1834	1.312371	ATCACGGGCCGGACAAATTG	61.312	55.000	31.78	17.35	0.00	2.32
1665	1837	2.359354	CATCACGGGCCGGACAAA	60.359	61.111	31.78	10.65	0.00	2.83
1826	1998	5.310451	GGGTTCAGTACTGGTAAATGTCAA	58.690	41.667	22.48	3.51	0.00	3.18
1916	2267	4.530710	TTGCCAACTGAATACGAGTAGT	57.469	40.909	0.00	0.00	0.00	2.73
1950	2301	1.192428	ACCCAGGATCTACCGTTGTC	58.808	55.000	0.00	0.00	44.74	3.18
2137	2490	1.203928	GATGACGTCATCTTGGAGCG	58.796	55.000	38.94	0.00	46.88	5.03
2245	2598	4.003648	GCATAACAGGGCATACCATAGTC	58.996	47.826	0.00	0.00	43.89	2.59
2246	2599	3.652869	AGCATAACAGGGCATACCATAGT	59.347	43.478	0.00	0.00	43.89	2.12
2248	2601	3.909995	AGAGCATAACAGGGCATACCATA	59.090	43.478	0.00	0.00	43.89	2.74
2249	2602	2.713167	AGAGCATAACAGGGCATACCAT	59.287	45.455	0.00	0.00	43.89	3.55
2250	2603	2.126882	AGAGCATAACAGGGCATACCA	58.873	47.619	0.00	0.00	43.89	3.25
2251	2604	2.158755	ACAGAGCATAACAGGGCATACC	60.159	50.000	0.00	0.00	40.67	2.73
2252	2605	3.199880	ACAGAGCATAACAGGGCATAC	57.800	47.619	0.00	0.00	0.00	2.39
2253	2606	3.455910	AGAACAGAGCATAACAGGGCATA	59.544	43.478	0.00	0.00	0.00	3.14
2254	2607	2.240667	AGAACAGAGCATAACAGGGCAT	59.759	45.455	0.00	0.00	0.00	4.40
2255	2608	1.630369	AGAACAGAGCATAACAGGGCA	59.370	47.619	0.00	0.00	0.00	5.36
2256	2609	2.012673	CAGAACAGAGCATAACAGGGC	58.987	52.381	0.00	0.00	0.00	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.