AutoCloner

Multiple sequence alignment - TraesCS7B01G303400

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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	TraesCS7B01G303400	chr7B	100.000	2152	0	0	269	2420	542899662	542901813	0.000000e+00	3975.0
1	TraesCS7B01G303400	chr7B	98.096	893	16	1	1443	2334	543001063	543001955	0.000000e+00	1554.0
2	TraesCS7B01G303400	chr7B	90.791	771	63	5	678	1447	586090714	586091477	0.000000e+00	1024.0
3	TraesCS7B01G303400	chr7B	97.821	413	9	0	269	681	542996779	542997191	0.000000e+00	713.0
4	TraesCS7B01G303400	chr7B	94.189	413	24	0	269	681	541944332	541944744	4.390000e-177	630.0
5	TraesCS7B01G303400	chr7B	93.525	417	26	1	1747	2163	541954235	541954650	9.500000e-174	619.0
6	TraesCS7B01G303400	chr7B	93.220	413	28	0	1744	2156	541711228	541711640	2.060000e-170	608.0
7	TraesCS7B01G303400	chr7B	93.668	379	24	0	269	647	541709087	541709465	3.490000e-158	568.0
8	TraesCS7B01G303400	chr7B	89.974	379	32	4	275	649	113207429	113207053	3.620000e-133	484.0
9	TraesCS7B01G303400	chr7B	89.610	385	34	4	269	649	429270629	429271011	3.620000e-133	484.0
10	TraesCS7B01G303400	chr7B	89.351	385	35	4	269	649	742229141	742229523	1.680000e-131	479.0
11	TraesCS7B01G303400	chr7B	92.652	313	19	4	1443	1754	541953118	541953427	4.750000e-122	448.0
12	TraesCS7B01G303400	chr7B	93.413	167	11	0	2161	2327	149047170	149047004	5.170000e-62	248.0
13	TraesCS7B01G303400	chr7B	97.917	96	2	0	2325	2420	541714599	541714694	1.490000e-37	167.0
14	TraesCS7B01G303400	chr7B	97.917	96	2	0	2325	2420	541954649	541954744	1.490000e-37	167.0
15	TraesCS7B01G303400	chr7B	88.393	112	7	5	2059	2164	542889812	542889923	1.950000e-26	130.0
16	TraesCS7B01G303400	chr7B	88.393	112	7	4	2059	2164	542986922	542987033	1.950000e-26	130.0
17	TraesCS7B01G303400	chr7B	89.796	98	6	4	2325	2420	541698089	541698184	3.270000e-24	122.0
18	TraesCS7B01G303400	chr7B	88.776	98	7	4	2325	2420	542892695	542892790	1.520000e-22	117.0
19	TraesCS7B01G303400	chr7B	88.542	96	9	2	2325	2420	542889921	542890014	5.470000e-22	115.0
20	TraesCS7B01G303400	chr7B	88.542	96	9	2	2325	2420	542987031	542987124	5.470000e-22	115.0
21	TraesCS7B01G303400	chr7B	100.000	45	0	0	1	45	542899394	542899438	1.540000e-12	84.2
22	TraesCS7B01G303400	chr7B	94.000	50	2	1	2116	2164	541698042	541698091	9.280000e-10	75.0
23	TraesCS7B01G303400	chr7B	92.308	52	2	2	2115	2164	542892646	542892697	3.340000e-09	73.1
24	TraesCS7B01G303400	chr7B	92.308	52	2	2	2115	2164	542989757	542989808	3.340000e-09	73.1
25	TraesCS7B01G303400	chr2B	98.054	771	14	1	678	1447	186948079	186948849	0.000000e+00	1339.0
26	TraesCS7B01G303400	chr2B	89.870	385	33	4	269	649	695442703	695443085	7.780000e-135	490.0
27	TraesCS7B01G303400	chr2B	94.937	158	8	0	2163	2320	767379705	767379862	5.170000e-62	248.0
28	TraesCS7B01G303400	chr5D	97.147	771	22	0	678	1448	213479453	213480223	0.000000e+00	1303.0
29	TraesCS7B01G303400	chr5D	96.507	773	25	2	678	1449	417730112	417729341	0.000000e+00	1277.0
30	TraesCS7B01G303400	chr5D	93.373	166	11	0	2162	2327	61057926	61058091	1.860000e-61	246.0
31	TraesCS7B01G303400	chr2D	96.104	770	29	1	678	1446	1625401	1626170	0.000000e+00	1254.0
32	TraesCS7B01G303400	chr1A	94.812	771	40	0	678	1448	54108756	54107986	0.000000e+00	1203.0
33	TraesCS7B01G303400	chr1A	95.598	727	27	1	678	1399	121537814	121538540	0.000000e+00	1160.0
34	TraesCS7B01G303400	chr3D	96.537	722	24	1	678	1399	71369721	71369001	0.000000e+00	1194.0
35	TraesCS7B01G303400	chr3D	92.398	171	13	0	2157	2327	550509427	550509597	6.680000e-61	244.0
36	TraesCS7B01G303400	chr1D	92.727	770	55	1	678	1447	331563469	331564237	0.000000e+00	1110.0
37	TraesCS7B01G303400	chr4D	89.487	390	34	5	269	655	464529528	464529913	1.010000e-133	486.0
38	TraesCS7B01G303400	chr4D	86.644	292	26	10	1443	1729	445379815	445380098	6.500000e-81	311.0
39	TraesCS7B01G303400	chr3B	89.034	383	35	5	272	649	640077538	640077158	3.640000e-128	468.0
40	TraesCS7B01G303400	chr6B	90.402	323	23	6	1443	1764	54099850	54099535	3.720000e-113	418.0
41	TraesCS7B01G303400	chr6B	93.413	167	10	1	2162	2327	566615886	566616052	1.860000e-61	246.0
42	TraesCS7B01G303400	chr2A	89.474	323	24	5	1443	1764	199579555	199579242	1.350000e-107	399.0
43	TraesCS7B01G303400	chr4B	89.028	319	27	6	1443	1760	455028509	455028198	2.920000e-104	388.0
44	TraesCS7B01G303400	chr4B	85.321	327	42	6	1443	1767	554566721	554566399	1.390000e-87	333.0
45	TraesCS7B01G303400	chr7D	83.557	298	33	13	1466	1760	633938544	633938828	5.130000e-67	265.0
46	TraesCS7B01G303400	chr7A	83.165	297	42	8	1468	1760	514711204	514711496	5.130000e-67	265.0
47	TraesCS7B01G303400	chr7A	93.333	165	11	0	2162	2326	443397632	443397796	6.680000e-61	244.0
48	TraesCS7B01G303400	chr1B	93.939	165	10	0	2162	2326	54997226	54997390	1.440000e-62	250.0
49	TraesCS7B01G303400	chrUn	92.000	175	13	1	2162	2336	112299381	112299208	6.680000e-61	244.0

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	TraesCS7B01G303400	chr7B	542899394	542901813	2419	False	2029.600000	3975	100.0000	1	2420	2	chr7B.!!$F9	2419
1	TraesCS7B01G303400	chr7B	542996779	543001955	5176	False	1133.500000	1554	97.9585	269	2334	2	chr7B.!!$F11	2065
2	TraesCS7B01G303400	chr7B	586090714	586091477	763	False	1024.000000	1024	90.7910	678	1447	1	chr7B.!!$F3	769
3	TraesCS7B01G303400	chr7B	541709087	541714694	5607	False	447.666667	608	94.9350	269	2420	3	chr7B.!!$F6	2151
4	TraesCS7B01G303400	chr7B	541953118	541954744	1626	False	411.333333	619	94.6980	1443	2420	3	chr7B.!!$F7	977
5	TraesCS7B01G303400	chr2B	186948079	186948849	770	False	1339.000000	1339	98.0540	678	1447	1	chr2B.!!$F1	769
6	TraesCS7B01G303400	chr5D	213479453	213480223	770	False	1303.000000	1303	97.1470	678	1448	1	chr5D.!!$F2	770
7	TraesCS7B01G303400	chr5D	417729341	417730112	771	True	1277.000000	1277	96.5070	678	1449	1	chr5D.!!$R1	771
8	TraesCS7B01G303400	chr2D	1625401	1626170	769	False	1254.000000	1254	96.1040	678	1446	1	chr2D.!!$F1	768
9	TraesCS7B01G303400	chr1A	54107986	54108756	770	True	1203.000000	1203	94.8120	678	1448	1	chr1A.!!$R1	770
10	TraesCS7B01G303400	chr1A	121537814	121538540	726	False	1160.000000	1160	95.5980	678	1399	1	chr1A.!!$F1	721
11	TraesCS7B01G303400	chr3D	71369001	71369721	720	True	1194.000000	1194	96.5370	678	1399	1	chr3D.!!$R1	721
12	TraesCS7B01G303400	chr1D	331563469	331564237	768	False	1110.000000	1110	92.7270	678	1447	1	chr1D.!!$F1	769

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
571	572	2.202987	CCAGGAGCGGATGCAGAC	60.203	66.667	0.0	0.0	46.23	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1680	7412	0.035439	AATCCCGGTCGATTGCACTT	60.035	50.0	0.0	0.0	31.19	3.16	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
17	18	2.896443	CTTCCGACAGCTCCCCTC	59.104	66.667	0.00	0.00	0.00	4.30
18	19	2.683933	TTCCGACAGCTCCCCTCC	60.684	66.667	0.00	0.00	0.00	4.30
43	44	3.048602	ACCTCTTGGTCGTCGGTG	58.951	61.111	0.00	0.00	44.78	4.94
44	45	2.261671	CCTCTTGGTCGTCGGTGG	59.738	66.667	0.00	0.00	0.00	4.61
532	533	3.295273	ACGTCTGCTCCAGCGTCA	61.295	61.111	8.22	0.00	45.83	4.35
571	572	2.202987	CCAGGAGCGGATGCAGAC	60.203	66.667	0.00	0.00	46.23	3.51
729	1189	3.951775	TTGCTAAATTTTCCGGCACAT	57.048	38.095	0.00	0.00	32.47	3.21
1342	6733	6.442952	AGTGTAGCTAGATCTAAATTCTGCG	58.557	40.000	3.57	0.00	0.00	5.18
1471	7202	2.571757	CGCCTCACCGTGAGCTTA	59.428	61.111	21.26	0.00	42.98	3.09
1510	7241	1.605165	AAAAATGAAGCGGGCCGGA	60.605	52.632	29.48	0.00	0.00	5.14
1675	7407	4.020573	TCGATTTAGACCGGGATTGCATAT	60.021	41.667	6.32	0.00	0.00	1.78
1680	7412	7.883391	TTTAGACCGGGATTGCATATTTTAA	57.117	32.000	6.32	0.00	0.00	1.52
1681	7413	7.883391	TTAGACCGGGATTGCATATTTTAAA	57.117	32.000	6.32	0.00	0.00	1.52
1710	7442	2.084546	GACCGGGATTTTGACTTGAGG	58.915	52.381	6.32	0.00	0.00	3.86
1714	7446	2.890945	CGGGATTTTGACTTGAGGGTTT	59.109	45.455	0.00	0.00	0.00	3.27
1723	7455	2.081462	ACTTGAGGGTTTATTTCGCCG	58.919	47.619	0.00	0.00	0.00	6.46
1732	7464	3.934579	GGTTTATTTCGCCGAACCTCTAA	59.065	43.478	0.00	0.00	38.74	2.10
1740	7472	2.352421	CGCCGAACCTCTAAGAGTTCAA	60.352	50.000	4.03	0.00	0.00	2.69
1741	7473	3.254892	GCCGAACCTCTAAGAGTTCAAG	58.745	50.000	4.03	0.00	0.00	3.02
1799	8885	4.340381	TCCTCCGCTTTTGTATACTAGTCC	59.660	45.833	0.00	0.00	0.00	3.85
1807	8893	6.979238	GCTTTTGTATACTAGTCCATCTCGTT	59.021	38.462	0.00	0.00	0.00	3.85
1812	8898	5.831702	ATACTAGTCCATCTCGTTCGTTT	57.168	39.130	0.00	0.00	0.00	3.60
1827	8913	4.302509	TTTGCGGAGGCGGTCGAA	62.303	61.111	0.00	0.00	44.10	3.71
1842	8928	0.747255	TCGAAGAGCACCCAGATAGC	59.253	55.000	0.00	0.00	0.00	2.97
1857	8943	2.901051	ATAGCGGGCGGTTGAGAACG	62.901	60.000	0.00	0.00	0.00	3.95
1928	9014	3.691049	ATCCGGCATGAAAATAACGTG	57.309	42.857	0.00	0.00	0.00	4.49
1965	9051	6.704937	TGACAAAAGCATGCATGAATGTTTTA	59.295	30.769	30.64	9.76	39.24	1.52
1966	9052	7.095565	TGACAAAAGCATGCATGAATGTTTTAG	60.096	33.333	30.64	20.10	39.24	1.85
2003	9089	1.153628	CGGTAGCCACGGAAGGAAG	60.154	63.158	0.00	0.00	0.00	3.46
2010	9096	0.320073	CCACGGAAGGAAGTACGCAA	60.320	55.000	0.00	0.00	0.00	4.85
2072	9158	2.562912	GTTGGTGTGCGCCATCAG	59.437	61.111	4.18	0.00	35.07	2.90
2077	9163	4.019312	TGTGCGCCATCAGCCAGA	62.019	61.111	4.18	0.00	38.78	3.86
2095	9181	5.127194	AGCCAGATGACGATAAGTGTTTCTA	59.873	40.000	0.00	0.00	0.00	2.10
2161	9406	3.557686	GCCTCAGTTTGCCATTCCAATTT	60.558	43.478	0.00	0.00	0.00	1.82
2162	9407	4.322650	GCCTCAGTTTGCCATTCCAATTTA	60.323	41.667	0.00	0.00	0.00	1.40
2163	9408	5.170748	CCTCAGTTTGCCATTCCAATTTAC	58.829	41.667	0.00	0.00	0.00	2.01
2164	9409	5.047092	CCTCAGTTTGCCATTCCAATTTACT	60.047	40.000	0.00	0.00	0.00	2.24
2165	9410	6.024552	TCAGTTTGCCATTCCAATTTACTC	57.975	37.500	0.00	0.00	0.00	2.59
2166	9411	5.047377	TCAGTTTGCCATTCCAATTTACTCC	60.047	40.000	0.00	0.00	0.00	3.85
2167	9412	4.222810	AGTTTGCCATTCCAATTTACTCCC	59.777	41.667	0.00	0.00	0.00	4.30
2168	9413	3.756082	TGCCATTCCAATTTACTCCCT	57.244	42.857	0.00	0.00	0.00	4.20
2169	9414	3.631250	TGCCATTCCAATTTACTCCCTC	58.369	45.455	0.00	0.00	0.00	4.30
2170	9415	3.269381	TGCCATTCCAATTTACTCCCTCT	59.731	43.478	0.00	0.00	0.00	3.69
2171	9416	3.633986	GCCATTCCAATTTACTCCCTCTG	59.366	47.826	0.00	0.00	0.00	3.35
2172	9417	4.860022	CCATTCCAATTTACTCCCTCTGT	58.140	43.478	0.00	0.00	0.00	3.41
2173	9418	5.264395	CCATTCCAATTTACTCCCTCTGTT	58.736	41.667	0.00	0.00	0.00	3.16
2174	9419	5.358160	CCATTCCAATTTACTCCCTCTGTTC	59.642	44.000	0.00	0.00	0.00	3.18
2175	9420	4.569719	TCCAATTTACTCCCTCTGTTCC	57.430	45.455	0.00	0.00	0.00	3.62
2176	9421	4.175962	TCCAATTTACTCCCTCTGTTCCT	58.824	43.478	0.00	0.00	0.00	3.36
2177	9422	5.347124	TCCAATTTACTCCCTCTGTTCCTA	58.653	41.667	0.00	0.00	0.00	2.94
2178	9423	5.788533	TCCAATTTACTCCCTCTGTTCCTAA	59.211	40.000	0.00	0.00	0.00	2.69
2179	9424	6.273730	TCCAATTTACTCCCTCTGTTCCTAAA	59.726	38.462	0.00	0.00	0.00	1.85
2180	9425	7.036863	TCCAATTTACTCCCTCTGTTCCTAAAT	60.037	37.037	0.00	0.00	0.00	1.40
2181	9426	8.272173	CCAATTTACTCCCTCTGTTCCTAAATA	58.728	37.037	0.00	0.00	0.00	1.40
2182	9427	9.853177	CAATTTACTCCCTCTGTTCCTAAATAT	57.147	33.333	0.00	0.00	0.00	1.28
2219	9464	9.950496	AGACATTTCAAATAGACTACAACAGAT	57.050	29.630	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.726351	GGAGGGGAGCTGTCGGAAG	61.726	68.421	0.00	0.00	0.00	3.46
1	2	2.683933	GGAGGGGAGCTGTCGGAA	60.684	66.667	0.00	0.00	0.00	4.30
27	28	2.261671	CCACCGACGACCAAGAGG	59.738	66.667	0.00	0.00	42.21	3.69
571	572	1.073216	GTCGTCGATGCAGACCACAG	61.073	60.000	0.00	0.00	37.85	3.66
612	613	1.993956	TCCATCAACCACAAACCCAG	58.006	50.000	0.00	0.00	0.00	4.45
729	1189	2.707849	GCCTAGAACGACCGCCTCA	61.708	63.158	0.00	0.00	0.00	3.86
868	3017	6.297694	TGCAATAACAAAATTTTCTGCCAC	57.702	33.333	0.00	0.00	0.00	5.01
1342	6733	2.424956	GAGCCATTTCAATCCACTCACC	59.575	50.000	0.00	0.00	0.00	4.02
1510	7241	2.237392	GCTACACCTTCTCCCTGTTGAT	59.763	50.000	0.00	0.00	0.00	2.57
1675	7407	2.226912	CCCGGTCGATTGCACTTTAAAA	59.773	45.455	0.00	0.00	0.00	1.52
1680	7412	0.035439	AATCCCGGTCGATTGCACTT	60.035	50.000	0.00	0.00	31.19	3.16
1681	7413	0.035439	AAATCCCGGTCGATTGCACT	60.035	50.000	6.70	0.00	32.75	4.40
1710	7442	2.353323	AGAGGTTCGGCGAAATAAACC	58.647	47.619	25.48	21.07	41.20	3.27
1714	7446	3.698040	ACTCTTAGAGGTTCGGCGAAATA	59.302	43.478	25.48	11.91	33.35	1.40
1723	7455	8.148999	TCTTAAACCTTGAACTCTTAGAGGTTC	58.851	37.037	14.24	13.88	46.88	3.62
1760	8846	4.698780	GCGGAGGAAGTGTTAAATTTAGGT	59.301	41.667	0.00	0.00	0.00	3.08
1780	8866	5.844004	AGATGGACTAGTATACAAAAGCGG	58.156	41.667	5.50	0.00	0.00	5.52
1799	8885	0.366871	CTCCGCAAACGAACGAGATG	59.633	55.000	0.14	0.00	43.93	2.90
1827	8913	2.136878	CCCGCTATCTGGGTGCTCT	61.137	63.158	0.00	0.00	42.07	4.09
1838	8924	1.153429	GTTCTCAACCGCCCGCTAT	60.153	57.895	0.00	0.00	0.00	2.97
1842	8928	2.809601	CTCGTTCTCAACCGCCCG	60.810	66.667	0.00	0.00	0.00	6.13
1857	8943	6.421377	TGATGTTGTGTGCATATTACACTC	57.579	37.500	16.70	9.83	46.49	3.51
1907	8993	3.442273	ACACGTTATTTTCATGCCGGATT	59.558	39.130	5.05	0.00	0.00	3.01
1928	9014	4.297510	TGCTTTTGTCATGTGTTGCATAC	58.702	39.130	0.00	0.00	35.74	2.39
1939	9025	4.827692	ACATTCATGCATGCTTTTGTCAT	58.172	34.783	22.25	0.00	0.00	3.06
1965	9051	4.205587	CCGGTCTACCACTACATTACTCT	58.794	47.826	0.00	0.00	35.14	3.24
1966	9052	3.950395	ACCGGTCTACCACTACATTACTC	59.050	47.826	0.00	0.00	35.14	2.59
2027	9113	0.531974	TTCTGAGCCCAACACGTGTC	60.532	55.000	23.61	9.49	0.00	3.67
2061	9147	2.515523	ATCTGGCTGATGGCGCAC	60.516	61.111	10.83	0.00	42.94	5.34
2062	9148	2.515290	CATCTGGCTGATGGCGCA	60.515	61.111	22.47	0.00	46.55	6.09
2072	9158	4.184629	AGAAACACTTATCGTCATCTGGC	58.815	43.478	0.00	0.00	0.00	4.85
2077	9163	9.035607	GTCAATCATAGAAACACTTATCGTCAT	57.964	33.333	0.00	0.00	0.00	3.06
2095	9181	3.639672	TGCATCAGGAGTGTCAATCAT	57.360	42.857	2.27	0.00	0.00	2.45
2161	9406	9.364653	GACTTATATTTAGGAACAGAGGGAGTA	57.635	37.037	0.00	0.00	0.00	2.59
2162	9407	8.068733	AGACTTATATTTAGGAACAGAGGGAGT	58.931	37.037	0.00	0.00	0.00	3.85
2163	9408	8.485578	AGACTTATATTTAGGAACAGAGGGAG	57.514	38.462	0.00	0.00	0.00	4.30
2164	9409	8.855804	AAGACTTATATTTAGGAACAGAGGGA	57.144	34.615	0.00	0.00	0.00	4.20
2165	9410	9.907229	AAAAGACTTATATTTAGGAACAGAGGG	57.093	33.333	0.00	0.00	0.00	4.30
2207	9452	9.239002	GTCTACATACATTCATCTGTTGTAGTC	57.761	37.037	16.69	12.09	39.12	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.