AutoCloner

Multiple sequence alignment - TraesCS6D01G035800

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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	TraesCS6D01G035800	chr6D	100.000	3524	0	0	1	3524	14657589	14654066	0.000000e+00	6508
1	TraesCS6D01G035800	chr6D	85.833	2040	226	32	601	2605	14681181	14679170	0.000000e+00	2108
2	TraesCS6D01G035800	chr6D	90.362	1546	147	2	1001	2544	14632985	14631440	0.000000e+00	2028
3	TraesCS6D01G035800	chr6D	89.937	1580	143	8	955	2525	14664582	14663010	0.000000e+00	2023
4	TraesCS6D01G035800	chr6B	93.776	3551	152	19	1	3524	26627915	26624407	0.000000e+00	5269
5	TraesCS6D01G035800	chr6B	89.364	1683	154	17	858	2525	26634940	26633268	0.000000e+00	2093
6	TraesCS6D01G035800	chr6B	85.572	2003	239	29	601	2588	26646017	26644050	0.000000e+00	2052
7	TraesCS6D01G035800	chr6B	89.845	1546	155	2	1001	2544	26618399	26616854	0.000000e+00	1984
8	TraesCS6D01G035800	chr6B	79.654	231	24	15	82	299	26639908	26639688	1.020000e-30	145
9	TraesCS6D01G035800	chr6A	91.772	3075	209	12	1	3057	15746620	15749668	0.000000e+00	4237
10	TraesCS6D01G035800	chr6A	89.909	1536	155	0	1001	2536	15756654	15758189	0.000000e+00	1978
11	TraesCS6D01G035800	chr6A	86.373	477	25	17	3059	3523	15750073	15750521	5.290000e-133	484
12	TraesCS6D01G035800	chr6A	84.516	155	13	7	116	264	15726849	15726998	3.670000e-30	143

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	TraesCS6D01G035800	chr6D	14654066	14657589	3523	True	6508.0	6508	100.0000	1	3524	1	chr6D.!!$R2	3523
1	TraesCS6D01G035800	chr6D	14679170	14681181	2011	True	2108.0	2108	85.8330	601	2605	1	chr6D.!!$R4	2004
2	TraesCS6D01G035800	chr6D	14631440	14632985	1545	True	2028.0	2028	90.3620	1001	2544	1	chr6D.!!$R1	1543
3	TraesCS6D01G035800	chr6D	14663010	14664582	1572	True	2023.0	2023	89.9370	955	2525	1	chr6D.!!$R3	1570
4	TraesCS6D01G035800	chr6B	26624407	26627915	3508	True	5269.0	5269	93.7760	1	3524	1	chr6B.!!$R2	3523
5	TraesCS6D01G035800	chr6B	26633268	26634940	1672	True	2093.0	2093	89.3640	858	2525	1	chr6B.!!$R3	1667
6	TraesCS6D01G035800	chr6B	26644050	26646017	1967	True	2052.0	2052	85.5720	601	2588	1	chr6B.!!$R5	1987
7	TraesCS6D01G035800	chr6B	26616854	26618399	1545	True	1984.0	1984	89.8450	1001	2544	1	chr6B.!!$R1	1543
8	TraesCS6D01G035800	chr6A	15746620	15750521	3901	False	2360.5	4237	89.0725	1	3523	2	chr6A.!!$F3	3522
9	TraesCS6D01G035800	chr6A	15756654	15758189	1535	False	1978.0	1978	89.9090	1001	2536	1	chr6A.!!$F2	1535

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
584	604	0.107643	TGAACACGCATCTTGTGGGA	59.892	50.0	0.0	0.0	43.02	4.37	F
1836	1919	0.105224	TCACCACCGACAACGTCATT	59.895	50.0	0.0	0.0	37.88	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2281	2364	2.013807	CGACGGGTAATGTGCATGG	58.986	57.895	0.0	0.0	0.0	3.66	R
2967	3056	0.729116	CGCATCGACCAATTCAAGCT	59.271	50.000	0.0	0.0	0.0	3.74	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
114	115	3.288092	ACTTGTCCCCTTGAGTTTGAAC	58.712	45.455	0.00	0.00	0.00	3.18
125	126	2.729360	TGAGTTTGAACGTATGCTGTCG	59.271	45.455	0.00	0.00	0.00	4.35
147	148	4.809426	CGGTGTCAGGGTTGATATAGTTTC	59.191	45.833	0.00	0.00	35.39	2.78
316	320	1.153289	AGCTGCTGCAGGTAATCCG	60.153	57.895	30.72	4.70	40.59	4.18
320	324	0.179121	TGCTGCAGGTAATCCGTACG	60.179	55.000	17.12	8.69	39.05	3.67
402	421	2.750350	CTGGCCGACAGGAACCTT	59.250	61.111	0.00	0.00	43.70	3.50
434	453	4.482386	CTGTCCAAGTTGCATCAATTCAG	58.518	43.478	0.00	0.00	0.00	3.02
486	506	4.206375	TGAAGCTCAAACTGTTCATGGAA	58.794	39.130	0.00	0.00	0.00	3.53
487	507	4.644234	TGAAGCTCAAACTGTTCATGGAAA	59.356	37.500	0.00	0.00	0.00	3.13
488	508	5.126869	TGAAGCTCAAACTGTTCATGGAAAA	59.873	36.000	0.00	0.00	0.00	2.29
489	509	5.796424	AGCTCAAACTGTTCATGGAAAAT	57.204	34.783	0.00	0.00	0.00	1.82
490	510	5.535333	AGCTCAAACTGTTCATGGAAAATG	58.465	37.500	0.00	0.00	0.00	2.32
491	511	4.687483	GCTCAAACTGTTCATGGAAAATGG	59.313	41.667	0.00	0.00	0.00	3.16
492	512	5.212532	TCAAACTGTTCATGGAAAATGGG	57.787	39.130	0.00	0.00	0.00	4.00
493	513	4.898265	TCAAACTGTTCATGGAAAATGGGA	59.102	37.500	0.00	0.00	0.00	4.37
564	584	3.069586	TGTCCAGTTCAGACACTCGATTT	59.930	43.478	0.00	0.00	39.29	2.17
584	604	0.107643	TGAACACGCATCTTGTGGGA	59.892	50.000	0.00	0.00	43.02	4.37
734	759	6.149973	ACCGCTGTTTAAACCTTTACTAATCC	59.850	38.462	15.59	0.00	0.00	3.01
770	796	5.678132	TGATTCCGTCAGATGCAATAATG	57.322	39.130	0.00	0.00	31.80	1.90
789	815	0.723981	GCATTCTTCTGTCCGTCTGC	59.276	55.000	0.00	0.00	0.00	4.26
974	1029	0.612229	TCCAAGGAGCAAGCAGAGAG	59.388	55.000	0.00	0.00	0.00	3.20
1488	1564	4.323417	TCAACAGTAAAATCATCGGCACT	58.677	39.130	0.00	0.00	0.00	4.40
1500	1576	1.973281	CGGCACTGTGAATGGCCTT	60.973	57.895	12.86	0.00	44.23	4.35
1836	1919	0.105224	TCACCACCGACAACGTCATT	59.895	50.000	0.00	0.00	37.88	2.57
2205	2288	2.906897	AACGTTGGTGCAGGGCTG	60.907	61.111	0.00	0.00	0.00	4.85
2558	2642	3.745799	TGTCACCAATGAATTGTACGGT	58.254	40.909	2.55	0.00	36.31	4.83
2741	2827	6.572519	ACTACATGCACAGTTTTGATGTTTT	58.427	32.000	0.00	0.00	0.00	2.43
2742	2828	7.041107	ACTACATGCACAGTTTTGATGTTTTT	58.959	30.769	0.00	0.00	0.00	1.94
2777	2863	5.449553	ACACCTTCCTTCAAGTCAATTTCT	58.550	37.500	0.00	0.00	0.00	2.52
2931	3020	5.227908	CAAAGACTCATGAGCTGCAAAATT	58.772	37.500	22.83	7.87	0.00	1.82
3046	3135	1.410517	GCTGATCCTAGCTACAGTGCA	59.589	52.381	9.95	0.00	40.52	4.57
3057	3146	5.567138	AGCTACAGTGCAAATAACCATTC	57.433	39.130	0.00	0.00	34.99	2.67
3178	3672	7.118680	ACACTGTTTGGATACGGTTTTACATAG	59.881	37.037	0.00	0.00	35.48	2.23
3198	3693	7.312899	ACATAGAAATTTTGTCGGAATGGAAC	58.687	34.615	0.00	0.00	0.00	3.62
3207	3702	6.785337	TTGTCGGAATGGAACTCTATAAGA	57.215	37.500	0.00	0.00	0.00	2.10
3241	3736	7.754924	TGATCAAAGCATTTTCGTAGGAATTTC	59.245	33.333	0.00	0.00	35.03	2.17
3362	3857	5.410067	ACATTCCATAGGCATTTTCGTTTG	58.590	37.500	0.00	0.00	0.00	2.93
3374	3869	5.702865	CATTTTCGTTTGACATCCACTCAT	58.297	37.500	0.00	0.00	0.00	2.90
3375	3870	5.766150	TTTTCGTTTGACATCCACTCATT	57.234	34.783	0.00	0.00	0.00	2.57
3504	4010	6.425417	TGCGGTTTTTGGAATTCTAAAAATCC	59.575	34.615	32.04	29.67	44.22	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
114	115	0.802222	CCTGACACCGACAGCATACG	60.802	60.000	0.00	0.00	34.47	3.06
125	126	5.990668	AGAAACTATATCAACCCTGACACC	58.009	41.667	0.00	0.00	33.30	4.16
147	148	2.937469	TGCAACACAAACACTTGGAG	57.063	45.000	0.00	0.00	36.82	3.86
299	303	0.179084	TACGGATTACCTGCAGCAGC	60.179	55.000	17.81	2.48	42.57	5.25
308	312	1.591619	GAAGCAAGCGTACGGATTACC	59.408	52.381	18.39	0.00	0.00	2.85
313	317	0.459585	GGATGAAGCAAGCGTACGGA	60.460	55.000	18.39	0.00	0.00	4.69
316	320	1.726853	ACTGGATGAAGCAAGCGTAC	58.273	50.000	0.00	0.00	0.00	3.67
320	324	1.726853	ACGTACTGGATGAAGCAAGC	58.273	50.000	0.00	0.00	0.00	4.01
434	453	0.247814	CTGCGATGCAACAATCCGTC	60.248	55.000	0.00	0.00	38.41	4.79
486	506	0.321653	GCGGTGTCAGTCTCCCATTT	60.322	55.000	0.00	0.00	0.00	2.32
487	507	1.296715	GCGGTGTCAGTCTCCCATT	59.703	57.895	0.00	0.00	0.00	3.16
488	508	1.892819	CTGCGGTGTCAGTCTCCCAT	61.893	60.000	0.00	0.00	0.00	4.00
489	509	2.523168	TGCGGTGTCAGTCTCCCA	60.523	61.111	0.00	0.00	0.00	4.37
490	510	2.262915	CTGCGGTGTCAGTCTCCC	59.737	66.667	0.00	0.00	0.00	4.30
491	511	1.248785	TACCTGCGGTGTCAGTCTCC	61.249	60.000	10.01	0.00	36.19	3.71
492	512	0.601558	TTACCTGCGGTGTCAGTCTC	59.398	55.000	10.01	0.00	36.19	3.36
493	513	0.317479	GTTACCTGCGGTGTCAGTCT	59.683	55.000	10.01	0.00	36.19	3.24
519	539	1.867233	CAGTGACAGGGTTTCTGAACG	59.133	52.381	0.00	0.00	46.18	3.95
564	584	0.950836	CCCACAAGATGCGTGTTCAA	59.049	50.000	0.00	0.00	32.26	2.69
584	604	3.550431	ACAGCTCAGCACGTGGGT	61.550	61.111	18.88	2.75	0.00	4.51
685	705	2.438411	ACAACGGAGTCGAGAGAGAAT	58.562	47.619	0.00	0.00	45.00	2.40
734	759	1.134907	GGAATCATGGCTGCAACTTGG	60.135	52.381	0.50	0.00	0.00	3.61
770	796	0.723981	GCAGACGGACAGAAGAATGC	59.276	55.000	0.00	0.00	0.00	3.56
783	809	2.034812	GGGTAAGATAGACAGGCAGACG	59.965	54.545	0.00	0.00	0.00	4.18
789	815	3.964031	AGCTGAAGGGTAAGATAGACAGG	59.036	47.826	0.00	0.00	0.00	4.00
948	1002	0.251077	CTTGCTCCTTGGAGGCTTGT	60.251	55.000	17.33	0.00	34.61	3.16
974	1029	1.377536	CTTGCTTGAGCTAGGCTTCC	58.622	55.000	4.44	0.00	39.88	3.46
1836	1919	2.947652	GTGGTCATAGTAGTACTCGGCA	59.052	50.000	5.96	0.00	0.00	5.69
2205	2288	4.537936	AGTGAAGAAAAGAAGTTGCGTC	57.462	40.909	0.00	0.00	0.00	5.19
2281	2364	2.013807	CGACGGGTAATGTGCATGG	58.986	57.895	0.00	0.00	0.00	3.66
2544	2628	3.423907	GCGACGAAACCGTACAATTCATT	60.424	43.478	0.00	0.00	40.80	2.57
2558	2642	5.339348	CGGTTTGTATATATACGCGACGAAA	59.661	40.000	15.93	8.49	36.06	3.46
2594	2680	1.632018	TTATTACGCTGGGGCTGCCT	61.632	55.000	19.68	0.00	36.09	4.75
2741	2827	3.146066	GGAAGGTGTATGAAGCACACAA	58.854	45.455	7.80	0.00	46.53	3.33
2742	2828	2.371841	AGGAAGGTGTATGAAGCACACA	59.628	45.455	7.80	0.00	46.53	3.72
2777	2863	9.734620	GATAATACATTGAAAGTGCAAGCATTA	57.265	29.630	0.00	0.00	0.00	1.90
2870	2959	5.820423	CAGAACAAATAATATGTGGGACGGA	59.180	40.000	0.00	0.00	0.00	4.69
2967	3056	0.729116	CGCATCGACCAATTCAAGCT	59.271	50.000	0.00	0.00	0.00	3.74
3046	3135	5.067283	GTCCCACTTATGCGAATGGTTATTT	59.933	40.000	0.00	0.00	0.00	1.40
3112	3606	8.499162	CATTGGGATGAATTATCGTAAGAAGAC	58.501	37.037	0.00	0.00	42.71	3.01
3113	3607	7.173218	GCATTGGGATGAATTATCGTAAGAAGA	59.827	37.037	0.00	0.00	42.71	2.87
3166	3660	7.299586	TCCGACAAAATTTCTATGTAAAACCG	58.700	34.615	0.00	0.00	0.00	4.44
3178	3672	6.013842	AGAGTTCCATTCCGACAAAATTTC	57.986	37.500	0.00	0.00	0.00	2.17
3188	3683	4.282195	AGGCTCTTATAGAGTTCCATTCCG	59.718	45.833	5.67	0.00	44.12	4.30
3198	3693	7.523293	TTTGATCAGAGAGGCTCTTATAGAG	57.477	40.000	19.80	5.58	45.04	2.43
3207	3702	3.648507	AATGCTTTGATCAGAGAGGCT	57.351	42.857	17.06	0.00	0.00	4.58
3241	3736	5.680594	TTCCAAATGATTCCAATCCCTTG	57.319	39.130	0.00	1.44	34.50	3.61
3327	3822	7.398829	TGCCTATGGAATGTAGTACAGAAAAA	58.601	34.615	9.25	0.00	0.00	1.94
3344	3839	4.433186	TGTCAAACGAAAATGCCTATGG	57.567	40.909	0.00	0.00	0.00	2.74

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.