AutoCloner

Multiple sequence alignment - TraesCS3A01G026200

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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	TraesCS3A01G026200	chr3A	100.000	2465	0	0	1	2465	13817102	13819566	0.000000e+00	4553.0
1	TraesCS3A01G026200	chr3A	97.129	1045	27	2	952	1993	13811586	13812630	0.000000e+00	1760.0
2	TraesCS3A01G026200	chr3A	98.039	306	6	0	2009	2314	13812616	13812921	1.300000e-147	532.0
3	TraesCS3A01G026200	chr3A	79.084	655	86	34	941	1550	13832494	13833142	1.060000e-108	403.0
4	TraesCS3A01G026200	chr3D	88.100	1605	94	38	7	1563	6466877	6465322	0.000000e+00	1816.0
5	TraesCS3A01G026200	chr3D	80.905	597	72	26	997	1556	6460845	6460254	1.350000e-117	433.0
6	TraesCS3A01G026200	chr3B	89.106	1074	54	26	485	1529	6944900	6945939	0.000000e+00	1277.0
7	TraesCS3A01G026200	chr3B	94.545	275	13	2	2192	2465	6947781	6948054	8.150000e-115	424.0
8	TraesCS3A01G026200	chr3B	86.053	380	44	7	1134	1508	6951710	6952085	1.370000e-107	399.0
9	TraesCS3A01G026200	chr3B	89.046	283	26	4	1	281	6944204	6944483	1.810000e-91	346.0
10	TraesCS3A01G026200	chr3B	92.271	207	7	5	294	491	6944666	6944872	4.010000e-73	285.0
11	TraesCS3A01G026200	chr3B	89.583	96	9	1	1515	1609	6945952	6946047	1.200000e-23	121.0
12	TraesCS3A01G026200	chr2D	88.525	183	20	1	1623	1804	592290043	592290225	1.150000e-53	220.0
13	TraesCS3A01G026200	chr2D	87.151	179	21	2	1625	1802	193345628	193345805	4.160000e-48	202.0
14	TraesCS3A01G026200	chr6B	86.631	187	22	3	1625	1810	586652101	586651917	1.160000e-48	204.0
15	TraesCS3A01G026200	chr6B	86.813	182	23	1	1625	1805	620698811	620698992	4.160000e-48	202.0
16	TraesCS3A01G026200	chr2B	87.222	180	22	1	1625	1803	723426030	723426209	1.160000e-48	204.0
17	TraesCS3A01G026200	chr2B	86.885	183	21	3	1625	1805	571836696	571836877	4.160000e-48	202.0
18	TraesCS3A01G026200	chr2B	86.885	183	21	3	1623	1803	571997473	571997654	4.160000e-48	202.0
19	TraesCS3A01G026200	chr2B	85.638	188	25	2	1623	1809	269864812	269864626	1.930000e-46	196.0
20	TraesCS3A01G026200	chr5A	96.774	31	1	0	550	580	41356490	41356520	4.000000e-03	52.8

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	TraesCS3A01G026200	chr3A	13817102	13819566	2464	False	4553.000000	4553	100.000000	1	2465	1	chr3A.!!$F1	2464
1	TraesCS3A01G026200	chr3A	13811586	13812921	1335	False	1146.000000	1760	97.584000	952	2314	2	chr3A.!!$F3	1362
2	TraesCS3A01G026200	chr3A	13832494	13833142	648	False	403.000000	403	79.084000	941	1550	1	chr3A.!!$F2	609
3	TraesCS3A01G026200	chr3D	6465322	6466877	1555	True	1816.000000	1816	88.100000	7	1563	1	chr3D.!!$R2	1556
4	TraesCS3A01G026200	chr3D	6460254	6460845	591	True	433.000000	433	80.905000	997	1556	1	chr3D.!!$R1	559
5	TraesCS3A01G026200	chr3B	6944204	6952085	7881	False	475.333333	1277	90.100667	1	2465	6	chr3B.!!$F1	2464

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
740	977	0.037326	TCGATGAGACCAACAGGCAC	60.037	55.0	0.0	0.0	0.0	5.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1636	1969	1.131315	GCAGCCACCGAAGAAAAGATC	59.869	52.381	0.0	0.0	0.0	2.75	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
60	61	8.517878	CCTCAACTGTAATGATTTTGAGTGATT	58.482	33.333	13.32	0.00	40.99	2.57
95	96	7.939039	TCCAATGATAAAGAGCGGAGAAAATAT	59.061	33.333	0.00	0.00	0.00	1.28
125	127	2.392613	AAACAAAGTGCTGCGCTCGG	62.393	55.000	17.01	13.56	0.00	4.63
141	143	3.729698	GGCCGGCGCTAAACGTTT	61.730	61.111	22.54	18.90	46.11	3.60
204	206	4.698304	TCGTCGGCCAAAAGAAGAATATTT	59.302	37.500	2.24	0.00	0.00	1.40
273	275	2.098443	GCGTTCCTTCCAACAGAAAACA	59.902	45.455	0.00	0.00	32.88	2.83
404	576	1.002033	CAGAGAACCTGTTGCTTGCAC	60.002	52.381	0.00	0.00	38.10	4.57
734	971	7.482654	TGATCAATTAATCGATGAGACCAAC	57.517	36.000	0.00	0.00	0.00	3.77
735	972	7.047271	TGATCAATTAATCGATGAGACCAACA	58.953	34.615	0.00	0.00	0.00	3.33
739	976	0.904649	ATCGATGAGACCAACAGGCA	59.095	50.000	0.00	0.00	0.00	4.75
740	977	0.037326	TCGATGAGACCAACAGGCAC	60.037	55.000	0.00	0.00	0.00	5.01
741	978	1.354337	CGATGAGACCAACAGGCACG	61.354	60.000	0.00	0.00	0.00	5.34
742	979	1.639298	GATGAGACCAACAGGCACGC	61.639	60.000	0.00	0.00	0.00	5.34
743	980	2.280797	GAGACCAACAGGCACGCA	60.281	61.111	0.00	0.00	0.00	5.24
859	1100	6.203723	CCAGTGCCTATAAGAATAAGAAGCAC	59.796	42.308	0.00	0.00	46.34	4.40
868	1109	3.327757	AGAATAAGAAGCACACCCACTCA	59.672	43.478	0.00	0.00	0.00	3.41
884	1125	2.355132	CACTCAAGCTGCATCTTCCATC	59.645	50.000	0.00	0.00	0.00	3.51
922	1163	0.592637	CATCGCTTCCTTGTTGTGCA	59.407	50.000	0.00	0.00	0.00	4.57
923	1164	0.593128	ATCGCTTCCTTGTTGTGCAC	59.407	50.000	10.75	10.75	0.00	4.57
924	1165	0.463654	TCGCTTCCTTGTTGTGCACT	60.464	50.000	19.41	0.00	0.00	4.40
925	1166	0.317269	CGCTTCCTTGTTGTGCACTG	60.317	55.000	19.41	3.15	0.00	3.66
926	1167	0.595825	GCTTCCTTGTTGTGCACTGC	60.596	55.000	19.41	11.12	0.00	4.40
937	1178	3.179443	TGTGCACTGCTAGCTATTACC	57.821	47.619	19.41	0.80	0.00	2.85
1487	1791	2.102420	TGACTATCATTCATTCGCCGGT	59.898	45.455	1.90	0.00	0.00	5.28
1633	1966	1.153823	AACGAGCGAAGGTGATCCG	60.154	57.895	0.00	0.00	39.88	4.18
1667	2000	2.045045	TGGCTGCTATGGTGGTGC	60.045	61.111	0.00	0.00	0.00	5.01
1692	2025	5.878116	CGGAGGTAAATGACAGAAATTGGTA	59.122	40.000	0.00	0.00	0.00	3.25
1700	2033	6.690194	ATGACAGAAATTGGTATCAAGCTC	57.310	37.500	0.00	0.00	36.19	4.09
1745	2079	2.550606	GTTTTGTCATGTCGGCCTTACA	59.449	45.455	9.92	9.92	0.00	2.41
1843	2179	1.244019	ATTGCTGGCTTCAACGACCC	61.244	55.000	0.00	0.00	0.00	4.46
1978	2352	6.869695	ACGACACCAGTTACATTACATCATA	58.130	36.000	0.00	0.00	0.00	2.15
1979	2353	7.324935	ACGACACCAGTTACATTACATCATAA	58.675	34.615	0.00	0.00	0.00	1.90
1980	2354	7.491372	ACGACACCAGTTACATTACATCATAAG	59.509	37.037	0.00	0.00	0.00	1.73
1981	2355	7.704899	CGACACCAGTTACATTACATCATAAGA	59.295	37.037	0.00	0.00	0.00	2.10
1982	2356	9.547753	GACACCAGTTACATTACATCATAAGAT	57.452	33.333	0.00	0.00	33.87	2.40
1983	2357	9.905713	ACACCAGTTACATTACATCATAAGATT	57.094	29.630	0.00	0.00	30.20	2.40
1985	2359	8.840321	ACCAGTTACATTACATCATAAGATTGC	58.160	33.333	0.00	0.00	30.20	3.56
1986	2360	8.292448	CCAGTTACATTACATCATAAGATTGCC	58.708	37.037	0.00	0.00	30.20	4.52
1987	2361	9.060347	CAGTTACATTACATCATAAGATTGCCT	57.940	33.333	0.00	0.00	30.20	4.75
1988	2362	9.632638	AGTTACATTACATCATAAGATTGCCTT	57.367	29.630	0.00	0.00	38.87	4.35
1989	2363	9.669353	GTTACATTACATCATAAGATTGCCTTG	57.331	33.333	0.00	0.00	36.34	3.61
1990	2364	7.886629	ACATTACATCATAAGATTGCCTTGT	57.113	32.000	0.00	0.00	36.34	3.16
1991	2365	7.709947	ACATTACATCATAAGATTGCCTTGTG	58.290	34.615	0.00	0.00	43.00	3.33
1992	2366	7.340232	ACATTACATCATAAGATTGCCTTGTGT	59.660	33.333	0.00	0.00	42.46	3.72
1993	2367	8.839343	CATTACATCATAAGATTGCCTTGTGTA	58.161	33.333	0.00	0.00	42.46	2.90
1994	2368	6.683974	ACATCATAAGATTGCCTTGTGTAC	57.316	37.500	0.00	0.00	42.46	2.90
1995	2369	5.590259	ACATCATAAGATTGCCTTGTGTACC	59.410	40.000	0.00	0.00	42.46	3.34
1996	2370	4.523083	TCATAAGATTGCCTTGTGTACCC	58.477	43.478	0.00	0.00	42.46	3.69
1997	2371	4.227300	TCATAAGATTGCCTTGTGTACCCT	59.773	41.667	0.00	0.00	42.46	4.34
1998	2372	3.525800	AAGATTGCCTTGTGTACCCTT	57.474	42.857	0.00	0.00	32.92	3.95
1999	2373	3.073274	AGATTGCCTTGTGTACCCTTC	57.927	47.619	0.00	0.00	0.00	3.46
2000	2374	2.375174	AGATTGCCTTGTGTACCCTTCA	59.625	45.455	0.00	0.00	0.00	3.02
2001	2375	2.738587	TTGCCTTGTGTACCCTTCAA	57.261	45.000	0.00	0.00	0.00	2.69
2002	2376	2.738587	TGCCTTGTGTACCCTTCAAA	57.261	45.000	0.00	0.00	0.00	2.69
2003	2377	3.019799	TGCCTTGTGTACCCTTCAAAA	57.980	42.857	0.00	0.00	0.00	2.44
2004	2378	3.366396	TGCCTTGTGTACCCTTCAAAAA	58.634	40.909	0.00	0.00	0.00	1.94
2189	2563	0.037605	AGTTAGGTCCGGCTTGAACG	60.038	55.000	0.00	0.00	0.00	3.95
2284	3979	9.513906	TTCATAGATTGAAATACCAACTTCACA	57.486	29.630	0.00	0.00	41.38	3.58
2290	3985	7.475771	TTGAAATACCAACTTCACAAATTGC	57.524	32.000	0.00	0.00	31.41	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
60	61	6.929049	CGCTCTTTATCATTGGACAAGGTATA	59.071	38.462	0.00	0.00	0.00	1.47
61	62	5.760253	CGCTCTTTATCATTGGACAAGGTAT	59.240	40.000	0.00	0.00	0.00	2.73
67	68	3.450817	TCTCCGCTCTTTATCATTGGACA	59.549	43.478	0.00	0.00	0.00	4.02
95	96	6.362016	CGCAGCACTTTGTTTTGTCATATTAA	59.638	34.615	0.00	0.00	0.00	1.40
99	100	3.626977	CGCAGCACTTTGTTTTGTCATA	58.373	40.909	0.00	0.00	0.00	2.15
125	127	2.501008	CAAACGTTTAGCGCCGGC	60.501	61.111	19.07	19.07	46.11	6.13
141	143	1.355005	CGCATTGGTCATACGTCACA	58.645	50.000	0.00	0.00	0.00	3.58
153	155	4.626604	AGAAAATAAACATGTGCGCATTGG	59.373	37.500	15.91	8.62	31.99	3.16
154	156	5.766702	AGAAAATAAACATGTGCGCATTG	57.233	34.783	15.91	17.50	31.99	2.82
289	377	5.966636	TCGACGATGGTTCTTCATATTTG	57.033	39.130	0.00	0.00	0.00	2.32
292	464	4.280929	TGGATCGACGATGGTTCTTCATAT	59.719	41.667	16.49	0.00	0.00	1.78
326	498	7.715265	TTTTTATATGAAGCTCTGATCGACC	57.285	36.000	0.00	0.00	0.00	4.79
523	745	2.082231	CATCTCCCACTGCAGAAACTG	58.918	52.381	23.35	8.00	34.12	3.16
534	756	0.896923	TGCAATTTGCCATCTCCCAC	59.103	50.000	18.27	0.00	44.23	4.61
623	858	4.364409	GTGAACGTTCGCCGCCAC	62.364	66.667	27.45	14.16	41.42	5.01
672	909	0.736325	GGTACGTAGCACAGTGCCAG	60.736	60.000	22.41	15.38	46.52	4.85
734	971	4.034258	CACCTGCTTGCGTGCCTG	62.034	66.667	0.00	0.00	0.00	4.85
735	972	2.674563	TAACACCTGCTTGCGTGCCT	62.675	55.000	0.00	0.00	33.09	4.75
739	976	0.944386	CAACTAACACCTGCTTGCGT	59.056	50.000	0.00	0.00	0.00	5.24
740	977	0.238289	CCAACTAACACCTGCTTGCG	59.762	55.000	0.00	0.00	0.00	4.85
741	978	1.604604	TCCAACTAACACCTGCTTGC	58.395	50.000	0.00	0.00	0.00	4.01
742	979	3.191371	GGATTCCAACTAACACCTGCTTG	59.809	47.826	0.00	0.00	0.00	4.01
743	980	3.181434	TGGATTCCAACTAACACCTGCTT	60.181	43.478	1.94	0.00	0.00	3.91
767	1004	4.000325	TGATCTGACGTTGTTTATGTGGG	59.000	43.478	0.00	0.00	0.00	4.61
829	1069	1.879575	TCTTATAGGCACTGGCACCT	58.120	50.000	5.25	0.45	43.71	4.00
859	1100	0.322277	AGATGCAGCTTGAGTGGGTG	60.322	55.000	0.00	0.00	35.58	4.61
868	1109	0.107312	AGCGATGGAAGATGCAGCTT	60.107	50.000	18.77	18.77	0.00	3.74
922	1163	8.310382	CAAGAAGATATGGTAATAGCTAGCAGT	58.690	37.037	18.83	4.94	41.20	4.40
923	1164	8.526978	TCAAGAAGATATGGTAATAGCTAGCAG	58.473	37.037	18.83	0.00	41.20	4.24
924	1165	8.307483	GTCAAGAAGATATGGTAATAGCTAGCA	58.693	37.037	18.83	3.19	42.07	3.49
925	1166	8.527810	AGTCAAGAAGATATGGTAATAGCTAGC	58.472	37.037	6.62	6.62	33.87	3.42
937	1178	7.147312	GTGATCTCCTGAGTCAAGAAGATATG	58.853	42.308	10.13	0.00	0.00	1.78
1609	1942	1.202486	TCACCTTCGCTCGTTGAAACT	60.202	47.619	0.00	0.00	0.00	2.66
1633	1966	1.393883	GCCACCGAAGAAAAGATCGAC	59.606	52.381	0.00	0.00	41.43	4.20
1636	1969	1.131315	GCAGCCACCGAAGAAAAGATC	59.869	52.381	0.00	0.00	0.00	2.75
1667	2000	4.096382	CCAATTTCTGTCATTTACCTCCGG	59.904	45.833	0.00	0.00	0.00	5.14
1692	2025	4.333690	AGCAAAACATCTCTGAGCTTGAT	58.666	39.130	12.47	0.89	0.00	2.57
1700	2033	7.814642	ACTGAAAAGATAGCAAAACATCTCTG	58.185	34.615	0.00	0.00	31.10	3.35
1978	2352	3.181434	TGAAGGGTACACAAGGCAATCTT	60.181	43.478	0.00	0.00	35.79	2.40
1979	2353	2.375174	TGAAGGGTACACAAGGCAATCT	59.625	45.455	0.00	0.00	0.00	2.40
1980	2354	2.790433	TGAAGGGTACACAAGGCAATC	58.210	47.619	0.00	0.00	0.00	2.67
1981	2355	2.969821	TGAAGGGTACACAAGGCAAT	57.030	45.000	0.00	0.00	0.00	3.56
1982	2356	2.738587	TTGAAGGGTACACAAGGCAA	57.261	45.000	0.00	0.00	0.00	4.52
1983	2357	2.738587	TTTGAAGGGTACACAAGGCA	57.261	45.000	0.00	0.00	0.00	4.75
2005	2379	6.038492	CCAAAATGACACAAGGCAATCTTTTT	59.962	34.615	0.00	0.00	32.41	1.94
2006	2380	5.528320	CCAAAATGACACAAGGCAATCTTTT	59.472	36.000	0.00	0.00	32.41	2.27
2007	2381	5.058490	CCAAAATGACACAAGGCAATCTTT	58.942	37.500	0.00	0.00	32.41	2.52
2330	4025	8.651389	TGGAATTGGTTATTACAATTGGTGAAA	58.349	29.630	10.83	0.00	45.60	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.