AutoCloner

Multiple sequence alignment - TraesCS1B01G395700

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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	TraesCS1B01G395700	chr1B	100.000	2585	0	0	310	2894	627378457	627375873	0.000000e+00	4774.0
1	TraesCS1B01G395700	chr1B	93.001	2629	134	20	310	2894	600347506	600344884	0.000000e+00	3790.0
2	TraesCS1B01G395700	chr1B	100.000	39	0	0	1	39	627378766	627378728	4.000000e-09	73.1
3	TraesCS1B01G395700	chr1B	97.436	39	1	0	1	39	337579664	337579626	1.860000e-07	67.6
4	TraesCS1B01G395700	chr4A	95.506	2581	114	1	310	2888	660540879	660543459	0.000000e+00	4122.0
5	TraesCS1B01G395700	chr4A	100.000	39	0	0	1	39	677760349	677760311	4.000000e-09	73.1
6	TraesCS1B01G395700	chr4A	100.000	39	0	0	1	39	691941510	691941548	4.000000e-09	73.1
7	TraesCS1B01G395700	chr3B	94.400	2607	124	3	310	2894	751900332	751897726	0.000000e+00	3986.0
8	TraesCS1B01G395700	chr3B	94.511	2587	130	10	310	2894	557704623	557707199	0.000000e+00	3980.0
9	TraesCS1B01G395700	chr3B	94.518	2189	96	11	726	2891	766268395	766270582	0.000000e+00	3356.0
10	TraesCS1B01G395700	chr3B	100.000	39	0	0	1	39	29805165	29805203	4.000000e-09	73.1
11	TraesCS1B01G395700	chr3B	100.000	39	0	0	1	39	517883867	517883829	4.000000e-09	73.1
12	TraesCS1B01G395700	chr4B	94.095	2608	130	11	310	2894	263067335	263064729	0.000000e+00	3941.0
13	TraesCS1B01G395700	chr4B	93.636	2184	104	14	725	2886	668352630	668350460	0.000000e+00	3230.0
14	TraesCS1B01G395700	chr4B	97.436	39	1	0	1	39	263067494	263067456	1.860000e-07	67.6
15	TraesCS1B01G395700	chr4B	94.872	39	2	0	1	39	668352925	668352887	8.660000e-06	62.1
16	TraesCS1B01G395700	chr5B	93.866	2592	132	10	325	2894	492520713	492518127	0.000000e+00	3880.0
17	TraesCS1B01G395700	chrUn	93.537	2197	105	14	719	2894	290561343	290559163	0.000000e+00	3236.0
18	TraesCS1B01G395700	chrUn	94.624	1823	85	7	310	2125	236925003	236926819	0.000000e+00	2811.0
19	TraesCS1B01G395700	chrUn	95.406	1219	49	3	310	1521	35192319	35191101	0.000000e+00	1934.0
20	TraesCS1B01G395700	chrUn	100.000	39	0	0	1	39	35192464	35192426	4.000000e-09	73.1
21	TraesCS1B01G395700	chrUn	100.000	39	0	0	1	39	236924858	236924896	4.000000e-09	73.1
22	TraesCS1B01G395700	chrUn	100.000	39	0	0	1	39	264980882	264980920	4.000000e-09	73.1
23	TraesCS1B01G395700	chrUn	97.436	39	1	0	1	39	290561628	290561590	1.860000e-07	67.6
24	TraesCS1B01G395700	chr2B	93.600	1953	99	10	310	2243	700669923	700671868	0.000000e+00	2891.0
25	TraesCS1B01G395700	chr2B	92.208	154	12	0	310	463	539864964	539865117	4.860000e-53	219.0
26	TraesCS1B01G395700	chr7B	93.505	1478	75	1	1432	2888	749266896	749268373	0.000000e+00	2178.0
27	TraesCS1B01G395700	chr7B	100.000	39	0	0	1	39	715344330	715344292	4.000000e-09	73.1
28	TraesCS1B01G395700	chr6B	100.000	39	0	0	1	39	630184634	630184596	4.000000e-09	73.1

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	TraesCS1B01G395700	chr1B	627375873	627378766	2893	True	2423.55	4774	100.0000	1	2894	2	chr1B.!!$R3	2893
1	TraesCS1B01G395700	chr1B	600344884	600347506	2622	True	3790.00	3790	93.0010	310	2894	1	chr1B.!!$R2	2584
2	TraesCS1B01G395700	chr4A	660540879	660543459	2580	False	4122.00	4122	95.5060	310	2888	1	chr4A.!!$F1	2578
3	TraesCS1B01G395700	chr3B	751897726	751900332	2606	True	3986.00	3986	94.4000	310	2894	1	chr3B.!!$R2	2584
4	TraesCS1B01G395700	chr3B	557704623	557707199	2576	False	3980.00	3980	94.5110	310	2894	1	chr3B.!!$F2	2584
5	TraesCS1B01G395700	chr3B	766268395	766270582	2187	False	3356.00	3356	94.5180	726	2891	1	chr3B.!!$F3	2165
6	TraesCS1B01G395700	chr4B	263064729	263067494	2765	True	2004.30	3941	95.7655	1	2894	2	chr4B.!!$R1	2893
7	TraesCS1B01G395700	chr4B	668350460	668352925	2465	True	1646.05	3230	94.2540	1	2886	2	chr4B.!!$R2	2885
8	TraesCS1B01G395700	chr5B	492518127	492520713	2586	True	3880.00	3880	93.8660	325	2894	1	chr5B.!!$R1	2569
9	TraesCS1B01G395700	chrUn	290559163	290561628	2465	True	1651.80	3236	95.4865	1	2894	2	chrUn.!!$R2	2893
10	TraesCS1B01G395700	chrUn	236924858	236926819	1961	False	1442.05	2811	97.3120	1	2125	2	chrUn.!!$F2	2124
11	TraesCS1B01G395700	chrUn	35191101	35192464	1363	True	1003.55	1934	97.7030	1	1521	2	chrUn.!!$R1	1520
12	TraesCS1B01G395700	chr2B	700669923	700671868	1945	False	2891.00	2891	93.6000	310	2243	1	chr2B.!!$F2	1933
13	TraesCS1B01G395700	chr7B	749266896	749268373	1477	False	2178.00	2178	93.5050	1432	2888	1	chr7B.!!$F1	1456

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
651	674	2.159179	ACTTGGGCCTGTTCTGTTTT	57.841	45.0	4.53	0.0	0.00	2.43	F
1381	1413	0.605319	ACGCCATGTTCACCGTGAAT	60.605	50.0	16.80	0.0	38.79	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1508	1540	0.321830	GCCTGGCCAAATGCAACAAT	60.322	50.0	7.01	0.00	43.89	2.71	R
2453	2646	0.323629	TGCTAGTTGGTAGGCCACAC	59.676	55.0	5.01	1.37	46.01	3.82	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
339	340	5.741011	CCTAGCTTGGTTTCCATGTAGTAA	58.259	41.667	5.98	0.00	31.53	2.24
437	460	9.908152	AGGTTGTGTTTAATTAAAGTATCAAGC	57.092	29.630	21.97	21.97	0.00	4.01
511	534	4.023707	GCTACATTATGTTGATCAGTGGGC	60.024	45.833	10.69	0.00	0.00	5.36
651	674	2.159179	ACTTGGGCCTGTTCTGTTTT	57.841	45.000	4.53	0.00	0.00	2.43
748	771	3.556213	GGGCTACATTTTTGGTTGGGTTC	60.556	47.826	0.00	0.00	0.00	3.62
753	776	4.959723	ACATTTTTGGTTGGGTTCAGATG	58.040	39.130	0.00	0.00	0.00	2.90
982	1014	9.073475	AGTCCTGTTGTTTAATTTACAATGCTA	57.927	29.630	8.50	0.00	37.77	3.49
1052	1084	7.916128	TCGAGATCGTAATTGAGAAATCTTC	57.084	36.000	1.70	0.00	40.80	2.87
1071	1103	4.288626	TCTTCCAGTAGGCAGGTATGTTTT	59.711	41.667	0.00	0.00	33.74	2.43
1217	1249	2.548067	CACAAAGTGAAGCTACGGGAGT	60.548	50.000	0.00	0.00	40.76	3.85
1325	1357	2.109799	CCCGTGCCCATGAGCTAG	59.890	66.667	0.00	0.00	0.00	3.42
1327	1359	1.522092	CCGTGCCCATGAGCTAGAA	59.478	57.895	0.00	0.00	0.00	2.10
1381	1413	0.605319	ACGCCATGTTCACCGTGAAT	60.605	50.000	16.80	0.00	38.79	2.57
1389	1421	3.655486	TGTTCACCGTGAATATGTTCGT	58.345	40.909	16.80	0.00	38.79	3.85
1463	1495	1.898472	CTGCCTCTCTTCTTCCTGTCA	59.102	52.381	0.00	0.00	0.00	3.58
1508	1540	1.668237	CGACAACACCATGTTCACACA	59.332	47.619	0.00	0.00	38.77	3.72
1529	1561	1.071128	GTTGCATTTGGCCAGGCAA	59.929	52.632	27.49	27.49	43.32	4.52
1558	1611	3.917760	GCGGGGATGACGAGGAGG	61.918	72.222	0.00	0.00	0.00	4.30
1584	1637	0.244994	GGCAAGAAGACGAGCAGAGA	59.755	55.000	0.00	0.00	0.00	3.10
1593	1646	0.105760	ACGAGCAGAGAGGGGATGAT	60.106	55.000	0.00	0.00	0.00	2.45
1645	1752	1.299648	GCTATGGTGGTGGCTGACA	59.700	57.895	0.00	0.00	0.00	3.58
1648	1755	0.767998	TATGGTGGTGGCTGACAACA	59.232	50.000	0.00	0.00	46.67	3.33
1671	1778	0.182061	CTGCTATGGTGGTGGCTGAT	59.818	55.000	0.00	0.00	0.00	2.90
1681	1788	1.131638	GGTGGCTGATGATGACCCTA	58.868	55.000	0.00	0.00	0.00	3.53
1701	1862	0.465705	CTATGGTGGTGGCTGACGAT	59.534	55.000	0.00	0.00	0.00	3.73
1778	1939	4.873129	CGCGATGGTAGTGGCGCT	62.873	66.667	7.64	5.62	46.54	5.92
1811	1972	4.408821	GGGCGACAGGACCATGCA	62.409	66.667	0.00	0.00	46.58	3.96
1883	2044	5.768980	ATCAGGTTGATGAAGGAGAAGAA	57.231	39.130	0.00	0.00	35.43	2.52
1884	2045	5.157940	TCAGGTTGATGAAGGAGAAGAAG	57.842	43.478	0.00	0.00	0.00	2.85
1885	2046	4.019860	TCAGGTTGATGAAGGAGAAGAAGG	60.020	45.833	0.00	0.00	0.00	3.46
1946	2132	3.387699	AGCATGTTGGGTTTAAGCTTGTT	59.612	39.130	9.86	0.00	0.00	2.83
2193	2381	3.066190	CCTAGCCACGGACGACCA	61.066	66.667	4.48	0.00	35.59	4.02
2317	2508	4.603131	ACAAGGTAGGCATTTCATCACAT	58.397	39.130	0.00	0.00	0.00	3.21
2390	2581	3.498082	GATGAAATCGACCGGTTTTTGG	58.502	45.455	9.42	0.00	31.13	3.28
2453	2646	3.882444	ACCTCCATGTCACATCATCAAG	58.118	45.455	0.00	0.00	0.00	3.02
2774	2968	2.124901	CCCTAACGGCGCCATTCA	60.125	61.111	28.98	7.07	0.00	2.57
2840	3034	1.031571	GCATGCATTTCCGACCCTCA	61.032	55.000	14.21	0.00	0.00	3.86
2863	3057	1.808133	GCTACTCCCGGCAATTCAGAG	60.808	57.143	0.00	0.00	0.00	3.35
2883	3077	2.125147	CCTTCGGCCGATTCAGCA	60.125	61.111	31.56	12.27	0.00	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
314	315	1.355720	ACATGGAAACCAAGCTAGGCT	59.644	47.619	0.00	0.00	42.56	4.58
339	340	6.014647	TCAAACCTACACTCCAGTAGTACAT	58.985	40.000	2.52	0.00	39.84	2.29
347	348	2.808543	GCAAGTCAAACCTACACTCCAG	59.191	50.000	0.00	0.00	0.00	3.86
383	384	6.043243	TGCATCTAACCCCAACCAAAAATAAA	59.957	34.615	0.00	0.00	0.00	1.40
437	460	4.634443	TCATCAAATCTGTCACTGAGCATG	59.366	41.667	0.00	0.00	0.00	4.06
587	610	6.826231	TGAAACTTATCAAGACAGACACCAAA	59.174	34.615	0.00	0.00	0.00	3.28
701	724	6.223852	CGACATATACCCTGCTCAAATAAGT	58.776	40.000	0.00	0.00	0.00	2.24
872	897	4.185467	TCAACAACAACAGCAACAACAT	57.815	36.364	0.00	0.00	0.00	2.71
982	1014	4.041444	AGCCATCTCACTTCTCTGAAAAGT	59.959	41.667	0.00	0.00	37.44	2.66
1052	1084	4.331968	TGAAAAACATACCTGCCTACTGG	58.668	43.478	0.00	0.00	40.61	4.00
1071	1103	9.676861	AGTGATGATAAAGAAATGAGTGATGAA	57.323	29.630	0.00	0.00	0.00	2.57
1325	1357	2.561858	AGACAAGGAAGTACCCGAGTTC	59.438	50.000	0.00	0.00	40.05	3.01
1327	1359	2.305858	AGACAAGGAAGTACCCGAGT	57.694	50.000	0.00	0.00	40.05	4.18
1381	1413	2.482336	GCACATGGTGTTGACGAACATA	59.518	45.455	0.00	0.00	43.95	2.29
1389	1421	1.603171	ATGCGGCACATGGTGTTGA	60.603	52.632	4.03	0.00	37.70	3.18
1463	1495	2.041620	TGCTGGTAGAGGAAGCCAAAAT	59.958	45.455	0.00	0.00	36.05	1.82
1508	1540	0.321830	GCCTGGCCAAATGCAACAAT	60.322	50.000	7.01	0.00	43.89	2.71
1558	1611	0.603569	TCGTCTTCTTGCCCACTCTC	59.396	55.000	0.00	0.00	0.00	3.20
1584	1637	2.196742	TAGCAAGGTCATCATCCCCT	57.803	50.000	0.00	0.00	0.00	4.79
1593	1646	0.327924	CCACCACCATAGCAAGGTCA	59.672	55.000	0.00	0.00	37.23	4.02
1645	1752	0.777446	ACCACCATAGCAGGGTTGTT	59.223	50.000	0.00	0.00	36.19	2.83
1648	1755	1.691219	CCACCACCATAGCAGGGTT	59.309	57.895	0.00	0.00	36.19	4.11
1671	1778	3.038280	CACCACCATAGTAGGGTCATCA	58.962	50.000	2.82	0.00	36.19	3.07
1681	1788	0.902984	TCGTCAGCCACCACCATAGT	60.903	55.000	0.00	0.00	0.00	2.12
1701	1862	1.374125	CACCACAATCGCGAGGTCA	60.374	57.895	16.66	0.00	30.44	4.02
1811	1972	5.395324	CGGATGTACTCCTCTACCACAATTT	60.395	44.000	8.96	0.00	42.47	1.82
1883	2044	6.688073	TTTCTTAACATCTTCACTCCTCCT	57.312	37.500	0.00	0.00	0.00	3.69
1884	2045	7.607991	TCATTTTCTTAACATCTTCACTCCTCC	59.392	37.037	0.00	0.00	0.00	4.30
1885	2046	8.553459	TCATTTTCTTAACATCTTCACTCCTC	57.447	34.615	0.00	0.00	0.00	3.71
1963	2149	5.640357	CCATGAGCATGCACAAAATTAAACT	59.360	36.000	21.69	0.00	37.49	2.66
2151	2339	6.922957	GGTTTGAGTCATGTTTTTAGCATTCA	59.077	34.615	0.00	0.00	0.00	2.57
2193	2381	0.389426	CCGTCGGATTTCTTCACGGT	60.389	55.000	4.91	0.00	44.08	4.83
2200	2388	4.904253	TTTCAAAAACCGTCGGATTTCT	57.096	36.364	20.51	7.03	27.63	2.52
2256	2447	4.083581	ACGCATGTCTTTAGCATTCAAC	57.916	40.909	0.00	0.00	0.00	3.18
2291	2482	3.712016	TGAAATGCCTACCTTGTAGCA	57.288	42.857	0.00	0.00	40.00	3.49
2317	2508	4.025229	GCCGTGCAAATCTATTGTCGATTA	60.025	41.667	0.00	0.00	31.27	1.75
2379	2570	0.456628	CCGTGTTTCCAAAAACCGGT	59.543	50.000	0.00	0.00	44.87	5.28
2431	2624	4.263639	ACTTGATGATGTGACATGGAGGTT	60.264	41.667	1.23	0.00	0.00	3.50
2453	2646	0.323629	TGCTAGTTGGTAGGCCACAC	59.676	55.000	5.01	1.37	46.01	3.82
2568	2761	0.813184	GGATGCGGCCATATCATTGG	59.187	55.000	15.76	0.00	39.94	3.16
2774	2968	9.440761	AATAGGGTCTACTTTGAGATAGACATT	57.559	33.333	12.18	2.93	46.14	2.71
2840	3034	2.037772	CTGAATTGCCGGGAGTAGCTAT	59.962	50.000	2.18	0.00	0.00	2.97

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.