AutoCloner

Multiple sequence alignment - TraesCS1B01G163800

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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	TraesCS1B01G163800	chr1B	100.000	3652	0	0	1	3652	286033601	286037252	0.000000e+00	6745
1	TraesCS1B01G163800	chr1B	95.795	3662	138	7	1	3652	338939587	338943242	0.000000e+00	5895
2	TraesCS1B01G163800	chr1B	95.464	3660	151	6	1	3652	135080129	135083781	0.000000e+00	5825
3	TraesCS1B01G163800	chr7B	96.257	3660	122	5	1	3652	716815497	716811845	0.000000e+00	5986
4	TraesCS1B01G163800	chr7B	95.027	3660	167	5	1	3652	417295164	417291512	0.000000e+00	5736
5	TraesCS1B01G163800	chr5B	96.011	3660	131	6	1	3652	127838688	127835036	0.000000e+00	5936
6	TraesCS1B01G163800	chr6B	95.082	3660	166	5	1	3652	264848874	264852527	0.000000e+00	5749
7	TraesCS1B01G163800	chr7D	94.373	3661	185	12	1	3652	306769695	306766047	0.000000e+00	5600
8	TraesCS1B01G163800	chr1D	96.061	3275	126	3	160	3432	351088205	351091478	0.000000e+00	5330
9	TraesCS1B01G163800	chr4A	92.927	3662	241	8	1	3652	281088197	281091850	0.000000e+00	5312
10	TraesCS1B01G163800	chr2B	97.015	134	4	0	1	134	357223612	357223479	3.670000e-55	226
11	TraesCS1B01G163800	chr2A	90.833	120	4	2	87	199	742178832	742178951	1.760000e-33	154
12	TraesCS1B01G163800	chr3B	88.636	88	5	1	3565	3652	798250297	798250215	6.450000e-18	102

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	TraesCS1B01G163800	chr1B	286033601	286037252	3651	False	6745	6745	100.000	1	3652	1	chr1B.!!$F2	3651
1	TraesCS1B01G163800	chr1B	338939587	338943242	3655	False	5895	5895	95.795	1	3652	1	chr1B.!!$F3	3651
2	TraesCS1B01G163800	chr1B	135080129	135083781	3652	False	5825	5825	95.464	1	3652	1	chr1B.!!$F1	3651
3	TraesCS1B01G163800	chr7B	716811845	716815497	3652	True	5986	5986	96.257	1	3652	1	chr7B.!!$R2	3651
4	TraesCS1B01G163800	chr7B	417291512	417295164	3652	True	5736	5736	95.027	1	3652	1	chr7B.!!$R1	3651
5	TraesCS1B01G163800	chr5B	127835036	127838688	3652	True	5936	5936	96.011	1	3652	1	chr5B.!!$R1	3651
6	TraesCS1B01G163800	chr6B	264848874	264852527	3653	False	5749	5749	95.082	1	3652	1	chr6B.!!$F1	3651
7	TraesCS1B01G163800	chr7D	306766047	306769695	3648	True	5600	5600	94.373	1	3652	1	chr7D.!!$R1	3651
8	TraesCS1B01G163800	chr1D	351088205	351091478	3273	False	5330	5330	96.061	160	3432	1	chr1D.!!$F1	3272
9	TraesCS1B01G163800	chr4A	281088197	281091850	3653	False	5312	5312	92.927	1	3652	1	chr4A.!!$F1	3651

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
103	104	1.686325	GCCCGGCTTGGTATCTCTCA	61.686	60.0	0.71	0.0	35.15	3.27	F
1691	1705	0.454600	GATCGCGTCCTTAGACACCA	59.545	55.0	5.77	0.0	43.73	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1780	1794	1.053424	TCTTGTGGACGGCCTAAAGT	58.947	50.0	9.82	0.0	32.47	2.66	R
3599	3628	0.682209	AAATGCATCCTCGCTGGCTT	60.682	50.0	0.00	0.0	35.26	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	9.043548	AGGTCCTGCTTAAACTAGAAATAAGTA	57.956	33.333	0.00	1.21	0.00	2.24
103	104	1.686325	GCCCGGCTTGGTATCTCTCA	61.686	60.000	0.71	0.00	35.15	3.27
187	195	5.416271	TCTCGGATAGGCTAACTTGTTTT	57.584	39.130	0.00	0.00	0.00	2.43
243	252	7.178983	TGCTGGATTTCTAGAAAATGGAATGTT	59.821	33.333	21.26	2.04	33.56	2.71
274	283	6.042552	GGAACCCTATTGATCAGATCAGAGAA	59.957	42.308	19.37	5.69	40.94	2.87
302	311	2.264455	AGTGATCTTTCTCCTGCTGGT	58.736	47.619	9.73	0.00	34.23	4.00
410	420	7.037586	TCACCCTTTTCCTCTATACATCTGTTT	60.038	37.037	0.00	0.00	0.00	2.83
449	459	5.105997	GCTATTCTCTGCAATTGAAGGTTGT	60.106	40.000	13.73	1.21	0.00	3.32
499	509	5.947663	TCAACCATCCAACCTTTCTTCTTA	58.052	37.500	0.00	0.00	0.00	2.10
539	549	6.282199	AGGTAGAATGCGTATAGTAATGGG	57.718	41.667	0.00	0.00	0.00	4.00
688	698	5.179452	TCTTCCTTAAGGGATTGTGGAAG	57.821	43.478	21.53	14.21	46.93	3.46
930	943	9.462606	CTGAGGTTAAGAAAATAATAACAGGGT	57.537	33.333	0.00	0.00	32.47	4.34
974	987	8.349568	TCTATAGCACTCTTTGAGTAAGTTCA	57.650	34.615	0.00	0.00	41.37	3.18
1262	1276	2.826128	CAGTAACTGGTAGTCTCTGGCA	59.174	50.000	0.00	0.00	30.67	4.92
1411	1425	1.005924	CAGGACAAGGCCATAAGGGTT	59.994	52.381	5.01	0.00	39.65	4.11
1531	1545	3.185880	TGCCTCCCTATCCATACCTAC	57.814	52.381	0.00	0.00	0.00	3.18
1599	1613	5.531287	GTGGATTGGCGGATTTCTAATAGTT	59.469	40.000	0.00	0.00	0.00	2.24
1633	1647	6.101332	ACACATGCAGCAATTTTTATGGTAG	58.899	36.000	0.00	0.00	0.00	3.18
1636	1650	5.991933	TGCAGCAATTTTTATGGTAGGAA	57.008	34.783	0.00	0.00	0.00	3.36
1654	1668	8.063153	TGGTAGGAAACTATGATCCAACTACTA	58.937	37.037	0.00	0.00	46.56	1.82
1691	1705	0.454600	GATCGCGTCCTTAGACACCA	59.545	55.000	5.77	0.00	43.73	4.17
1800	1814	1.270678	ACTTTAGGCCGTCCACAAGAC	60.271	52.381	0.00	0.00	42.54	3.01
1840	1854	8.588290	TGCCATACAATTACAACCTATCTTTT	57.412	30.769	0.00	0.00	0.00	2.27
1918	1932	5.371629	CAACAACAAGTACTAGCTTAACGC	58.628	41.667	0.00	0.00	39.57	4.84
2026	2043	8.688747	TCACATTCATGCATTTACCATACATA	57.311	30.769	0.00	0.00	0.00	2.29
2223	2240	7.117667	GCAATTTCGGTAGTCATTTTCCATTTT	59.882	33.333	0.00	0.00	0.00	1.82
2246	2263	2.487762	GTTGGAAAATGCAGTCGGATGA	59.512	45.455	0.00	0.00	0.00	2.92
2312	2332	2.687935	GGGAAACTTTGCACAGAGTTCA	59.312	45.455	6.92	0.00	35.08	3.18
2337	2357	2.158813	ACGATTAATGGGTGGCTTCGAT	60.159	45.455	2.36	0.00	0.00	3.59
2448	2471	2.755103	GTCTGGGCCTTCAGTTTAATGG	59.245	50.000	4.53	0.00	36.25	3.16
2464	2487	5.991933	TTAATGGTTTTATTCAGCAGCCA	57.008	34.783	0.00	0.00	0.00	4.75
2492	2515	3.009723	TCGGCAAGAACTCATTGAATCC	58.990	45.455	0.00	0.00	0.00	3.01
2537	2561	5.290493	TCAAAGTTTCTCCTGCTACTCAA	57.710	39.130	0.00	0.00	0.00	3.02
2576	2600	3.845781	ATACAAGGACATGCTGTAGGG	57.154	47.619	0.00	0.00	0.00	3.53
2696	2722	7.568366	AGGCATTATGGAATTAAGATTTCCCAA	59.432	33.333	4.28	0.28	0.00	4.12
2729	2755	2.683768	CTTAGCTCAGGACCCCACTAT	58.316	52.381	0.00	0.00	0.00	2.12
2731	2757	1.972588	AGCTCAGGACCCCACTATTT	58.027	50.000	0.00	0.00	0.00	1.40
2735	2761	2.571653	CTCAGGACCCCACTATTTGTCA	59.428	50.000	0.00	0.00	0.00	3.58
2858	2884	8.930760	GCAGTTAGCAATAATCTTTCTATCGAT	58.069	33.333	2.16	2.16	44.79	3.59
3173	3200	3.691049	TGTCTGAGTTTTTCCGCTTTG	57.309	42.857	0.00	0.00	0.00	2.77
3178	3205	1.066752	GTTTTTCCGCTTTGCCCGT	59.933	52.632	0.00	0.00	0.00	5.28
3184	3211	2.358737	CGCTTTGCCCGTTCTCCT	60.359	61.111	0.00	0.00	0.00	3.69
3273	3300	0.988063	GAGACCTCCTCCCTTTGCTT	59.012	55.000	0.00	0.00	35.87	3.91
3381	3408	8.910351	AGTAAAAGACAGAAAGCAAAGACTAT	57.090	30.769	0.00	0.00	0.00	2.12
3394	3421	7.291411	AGCAAAGACTATATTAGATGTCCGT	57.709	36.000	0.00	0.00	0.00	4.69
3548	3577	3.954200	TCAATGTGATTTCTGCTGCCTA	58.046	40.909	0.00	0.00	0.00	3.93
3562	3591	1.855360	CTGCCTAGCTTCGATTTCGTC	59.145	52.381	0.00	0.00	40.80	4.20
3568	3597	4.031878	CCTAGCTTCGATTTCGTCTGTTTC	59.968	45.833	0.00	0.00	40.80	2.78
3575	3604	3.303725	CGATTTCGTCTGTTTCAAGGCAA	60.304	43.478	0.00	0.00	34.11	4.52
3598	3627	3.774066	GTTGAGCAACCAATCATAAGCC	58.226	45.455	1.97	0.00	35.36	4.35
3599	3628	3.084536	TGAGCAACCAATCATAAGCCA	57.915	42.857	0.00	0.00	0.00	4.75
3600	3629	3.429492	TGAGCAACCAATCATAAGCCAA	58.571	40.909	0.00	0.00	0.00	4.52
3646	3675	6.820152	CGTGCCCCTATTTAGTTAGTACTTTT	59.180	38.462	0.00	0.00	35.78	2.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	6.239572	CCAAGGTGACCCAGAACAATTATTTT	60.240	38.462	0.00	0.00	0.00	1.82
103	104	5.255397	TGTGATTGGTTTTCTACAGGGAT	57.745	39.130	0.00	0.00	0.00	3.85
243	252	4.172041	TCTGATCAATAGGGTTCCCTAGGA	59.828	45.833	20.39	19.12	41.43	2.94
274	283	5.396213	GCAGGAGAAAGATCACTAGGTTCAT	60.396	44.000	0.00	0.00	0.00	2.57
302	311	3.833732	AGGAGACAGGTATCGATGCTTA	58.166	45.455	13.38	0.00	0.00	3.09
410	420	0.926293	ATAGCAAGCCCCCTTTGCTA	59.074	50.000	18.49	18.49	39.57	3.49
449	459	6.992123	CCACACAAATAAGAGATATGTAGGCA	59.008	38.462	0.00	0.00	0.00	4.75
499	509	6.290294	TCTACCTACGCTTTTATGGAAAGT	57.710	37.500	5.60	0.00	45.31	2.66
539	549	3.244009	TGCTTAGCCATACATCAGCTCTC	60.244	47.826	0.29	0.00	38.06	3.20
578	588	3.198853	AGCTGGATACTGACTTCTTTCCC	59.801	47.826	0.00	0.00	37.83	3.97
688	698	0.107410	TGTATTCCGGGATGTGTGCC	60.107	55.000	5.13	0.00	0.00	5.01
830	840	4.446889	GCCCTTCCTATCATTCCACAATCT	60.447	45.833	0.00	0.00	0.00	2.40
930	943	1.204941	GAGCCGAGTCTAAGAAAGCCA	59.795	52.381	0.00	0.00	0.00	4.75
1262	1276	2.170397	TGATGGTGCACAATATCGGTCT	59.830	45.455	20.43	0.00	0.00	3.85
1437	1451	9.712305	GCTAGGTTAAGAGATAATTGAGCATAA	57.288	33.333	0.00	0.00	30.49	1.90
1438	1452	9.094578	AGCTAGGTTAAGAGATAATTGAGCATA	57.905	33.333	0.00	0.00	31.56	3.14
1531	1545	5.916661	AGTTGTGTACCATAGTCAGTAGG	57.083	43.478	0.00	0.00	0.00	3.18
1599	1613	1.072852	TGCATGTGTAGCAGCACCA	59.927	52.632	7.96	0.00	38.52	4.17
1662	1676	6.092396	GTCTAAGGACGCGATCTAATAGATCA	59.908	42.308	24.84	6.75	40.56	2.92
1691	1705	2.373169	AGGTGGGATATGATTGCATCGT	59.627	45.455	0.00	0.00	35.94	3.73
1780	1794	1.053424	TCTTGTGGACGGCCTAAAGT	58.947	50.000	9.82	0.00	32.47	2.66
1800	1814	4.574421	TGTATGGCAGTATCCGAAAACATG	59.426	41.667	0.00	0.00	0.00	3.21
1840	1854	6.265196	GCATGGATATTTTGTACCCATTGAGA	59.735	38.462	0.00	0.00	35.60	3.27
2085	2102	6.374333	AGCGAAAACCTAGATTTGCTTTATCA	59.626	34.615	10.22	0.00	0.00	2.15
2223	2240	3.410631	TCCGACTGCATTTTCCAACTA	57.589	42.857	0.00	0.00	0.00	2.24
2246	2263	6.044404	CCCTTGATCACTTATAGTACCCCAAT	59.956	42.308	0.00	0.00	0.00	3.16
2312	2332	4.274950	CGAAGCCACCCATTAATCGTAATT	59.725	41.667	0.00	0.00	0.00	1.40
2337	2357	2.523245	TGCATGTGCCCACAAGAAATA	58.477	42.857	5.08	0.00	45.41	1.40
2464	2487	3.266510	TGAGTTCTTGCCGATAAGCAT	57.733	42.857	0.00	0.00	43.64	3.79
2467	2490	5.801350	TTCAATGAGTTCTTGCCGATAAG	57.199	39.130	0.00	0.00	0.00	1.73
2472	2495	2.749076	TGGATTCAATGAGTTCTTGCCG	59.251	45.455	0.00	0.00	0.00	5.69
2492	2515	4.433186	TTTGTTATGAGCCCAAACGATG	57.567	40.909	0.00	0.00	0.00	3.84
2537	2561	4.901849	TGTATAATGCTCAAGGCTCTAGGT	59.098	41.667	0.00	0.00	42.39	3.08
2729	2755	7.675062	AGCAATACCAAACCAAATATGACAAA	58.325	30.769	0.00	0.00	0.00	2.83
2731	2757	6.849085	AGCAATACCAAACCAAATATGACA	57.151	33.333	0.00	0.00	0.00	3.58
2735	2761	5.221165	GCGGTAGCAATACCAAACCAAATAT	60.221	40.000	5.37	0.00	44.35	1.28
2818	2844	3.807209	GCTAACTGCCCAAAGTGAGAAGA	60.807	47.826	0.00	0.00	30.95	2.87
2855	2881	3.000041	TGAAACAGATTTCCGGACATCG	59.000	45.455	21.81	18.56	43.18	3.84
2858	2884	3.750371	ACATGAAACAGATTTCCGGACA	58.250	40.909	1.83	0.00	43.18	4.02
2895	2921	7.140048	GTCTTACGTGTAAAGGATCCTCTATG	58.860	42.308	16.52	9.58	0.00	2.23
2899	2925	4.401837	AGGTCTTACGTGTAAAGGATCCTC	59.598	45.833	16.52	2.97	0.00	3.71
3173	3200	1.079057	GAAGTGGAGGAGAACGGGC	60.079	63.158	0.00	0.00	0.00	6.13
3178	3205	1.938585	ACGGATGAAGTGGAGGAGAA	58.061	50.000	0.00	0.00	0.00	2.87
3273	3300	8.982091	AGTCACTCTTCTAAGTGCTATATACA	57.018	34.615	0.00	0.00	45.12	2.29
3410	3437	9.748708	CAAGTCCAATCAATCTTTGAAAAACTA	57.251	29.630	0.00	0.00	43.95	2.24
3548	3577	3.390135	TGAAACAGACGAAATCGAAGCT	58.610	40.909	10.16	1.23	43.02	3.74
3562	3591	2.544486	GCTCAACCTTGCCTTGAAACAG	60.544	50.000	0.00	0.00	0.00	3.16
3568	3597	3.575399	GTTGCTCAACCTTGCCTTG	57.425	52.632	1.45	0.00	35.36	3.61
3596	3625	3.207669	CATCCTCGCTGGCTTGGC	61.208	66.667	0.00	0.00	35.26	4.52
3597	3626	3.207669	GCATCCTCGCTGGCTTGG	61.208	66.667	0.00	0.00	35.26	3.61
3598	3627	1.381928	AATGCATCCTCGCTGGCTTG	61.382	55.000	0.00	0.00	35.26	4.01
3599	3628	0.682209	AAATGCATCCTCGCTGGCTT	60.682	50.000	0.00	0.00	35.26	4.35
3600	3629	1.077212	AAATGCATCCTCGCTGGCT	60.077	52.632	0.00	0.00	35.26	4.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.