AutoCloner

Multiple sequence alignment - TraesCS3B01G030800

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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	TraesCS3B01G030800	chr3B	100.000	2987	0	0	1	2987	14024489	14021503	0.000000e+00	5517
1	TraesCS3B01G030800	chr3B	93.613	2928	141	18	2	2919	14066731	14063840	0.000000e+00	4329
2	TraesCS3B01G030800	chr3B	93.436	2925	151	14	70	2987	28542403	28539513	0.000000e+00	4300
3	TraesCS3B01G030800	chr3B	93.982	2825	135	15	175	2987	14106559	14103758	0.000000e+00	4242
4	TraesCS3B01G030800	chr3B	92.496	2985	186	11	7	2987	14113392	14110442	0.000000e+00	4237
5	TraesCS3B01G030800	chr3B	92.151	2994	185	23	2	2987	13995103	13992152	0.000000e+00	4181
6	TraesCS3B01G030800	chr3B	91.643	2872	174	28	127	2987	28423501	28420685	0.000000e+00	3914
7	TraesCS3B01G030800	chr3B	91.609	2872	175	27	127	2987	28410337	28407521	0.000000e+00	3908
8	TraesCS3B01G030800	chr3B	91.580	2874	173	27	127	2987	28456849	28454032	0.000000e+00	3903
9	TraesCS3B01G030800	chr3B	91.226	2872	181	19	127	2987	28530919	28528108	0.000000e+00	3842
10	TraesCS3B01G030800	chr3B	91.510	2768	173	33	232	2987	28564192	28561475	0.000000e+00	3771
11	TraesCS3B01G030800	chr3B	91.901	2272	143	13	725	2987	28492700	28490461	0.000000e+00	3138
12	TraesCS3B01G030800	chr3B	84.740	2405	278	43	2	2365	14224425	14222069	0.000000e+00	2326
13	TraesCS3B01G030800	chr3B	91.568	1352	87	9	7	1356	14134168	14132842	0.000000e+00	1840
14	TraesCS3B01G030800	chr3B	90.924	595	39	9	2401	2987	28468132	28467545	0.000000e+00	785
15	TraesCS3B01G030800	chr3B	80.814	172	30	3	329	497	12186190	12186019	6.720000e-27	132
16	TraesCS3B01G030800	chrUn	91.973	2504	150	27	495	2987	307487399	307489862	0.000000e+00	3463
17	TraesCS3B01G030800	chrUn	84.765	722	75	12	2	714	35793737	35794432	0.000000e+00	691
18	TraesCS3B01G030800	chr3D	86.458	2998	282	52	2	2964	9949312	9946404	0.000000e+00	3173
19	TraesCS3B01G030800	chr3D	83.740	738	81	15	5	734	5682637	5681931	0.000000e+00	662

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	TraesCS3B01G030800	chr3B	14021503	14024489	2986	True	5517.0	5517	100.000	1	2987	1	chr3B.!!$R3	2986
1	TraesCS3B01G030800	chr3B	14063840	14066731	2891	True	4329.0	4329	93.613	2	2919	1	chr3B.!!$R4	2917
2	TraesCS3B01G030800	chr3B	28539513	28542403	2890	True	4300.0	4300	93.436	70	2987	1	chr3B.!!$R13	2917
3	TraesCS3B01G030800	chr3B	14103758	14113392	9634	True	4239.5	4242	93.239	7	2987	2	chr3B.!!$R15	2980
4	TraesCS3B01G030800	chr3B	13992152	13995103	2951	True	4181.0	4181	92.151	2	2987	1	chr3B.!!$R2	2985
5	TraesCS3B01G030800	chr3B	28420685	28423501	2816	True	3914.0	3914	91.643	127	2987	1	chr3B.!!$R8	2860
6	TraesCS3B01G030800	chr3B	28407521	28410337	2816	True	3908.0	3908	91.609	127	2987	1	chr3B.!!$R7	2860
7	TraesCS3B01G030800	chr3B	28454032	28456849	2817	True	3903.0	3903	91.580	127	2987	1	chr3B.!!$R9	2860
8	TraesCS3B01G030800	chr3B	28528108	28530919	2811	True	3842.0	3842	91.226	127	2987	1	chr3B.!!$R12	2860
9	TraesCS3B01G030800	chr3B	28561475	28564192	2717	True	3771.0	3771	91.510	232	2987	1	chr3B.!!$R14	2755
10	TraesCS3B01G030800	chr3B	28490461	28492700	2239	True	3138.0	3138	91.901	725	2987	1	chr3B.!!$R11	2262
11	TraesCS3B01G030800	chr3B	14222069	14224425	2356	True	2326.0	2326	84.740	2	2365	1	chr3B.!!$R6	2363
12	TraesCS3B01G030800	chr3B	14132842	14134168	1326	True	1840.0	1840	91.568	7	1356	1	chr3B.!!$R5	1349
13	TraesCS3B01G030800	chr3B	28467545	28468132	587	True	785.0	785	90.924	2401	2987	1	chr3B.!!$R10	586
14	TraesCS3B01G030800	chrUn	307487399	307489862	2463	False	3463.0	3463	91.973	495	2987	1	chrUn.!!$F2	2492
15	TraesCS3B01G030800	chrUn	35793737	35794432	695	False	691.0	691	84.765	2	714	1	chrUn.!!$F1	712
16	TraesCS3B01G030800	chr3D	9946404	9949312	2908	True	3173.0	3173	86.458	2	2964	1	chr3D.!!$R2	2962
17	TraesCS3B01G030800	chr3D	5681931	5682637	706	True	662.0	662	83.740	5	734	1	chr3D.!!$R1	729

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
963	7652	0.249073	CTAACATGGCCGACGAGAGG	60.249	60.0	0.0	0.0	0.00	3.69	F
1590	8296	0.670162	GCAAGGTCAGCAAGCTTCAA	59.330	50.0	0.0	0.0	43.77	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1873	8582	0.250510	TACATTGGCAGCACCGTCAA	60.251	50.0	0.0	0.0	43.94	3.18	R
2727	9506	0.743345	GGTAACTCTCGCCGCCATTT	60.743	55.0	0.0	0.0	0.00	2.32	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
31	32	4.371624	TGATCTTGGTTGGTGTCATCTT	57.628	40.909	0.00	0.00	0.00	2.40
112	113	0.949105	CTAGGTGGTTGCGTGGTGTC	60.949	60.000	0.00	0.00	0.00	3.67
483	7160	6.265577	GTGTTTGATGGTGTTATAATCTGGC	58.734	40.000	0.00	0.00	0.00	4.85
484	7161	5.065859	TGTTTGATGGTGTTATAATCTGGCG	59.934	40.000	0.00	0.00	0.00	5.69
485	7162	4.681074	TGATGGTGTTATAATCTGGCGA	57.319	40.909	0.00	0.00	0.00	5.54
486	7163	5.227569	TGATGGTGTTATAATCTGGCGAT	57.772	39.130	0.00	0.00	0.00	4.58
487	7164	4.996758	TGATGGTGTTATAATCTGGCGATG	59.003	41.667	0.00	0.00	0.00	3.84
488	7165	3.738982	TGGTGTTATAATCTGGCGATGG	58.261	45.455	0.00	0.00	0.00	3.51
489	7166	3.135712	TGGTGTTATAATCTGGCGATGGT	59.864	43.478	0.00	0.00	0.00	3.55
490	7167	3.498397	GGTGTTATAATCTGGCGATGGTG	59.502	47.826	0.00	0.00	0.00	4.17
491	7168	4.127171	GTGTTATAATCTGGCGATGGTGT	58.873	43.478	0.00	0.00	0.00	4.16
492	7169	4.574828	GTGTTATAATCTGGCGATGGTGTT	59.425	41.667	0.00	0.00	0.00	3.32
636	7317	5.538053	TCTGCAATGGTCAACCTTTTTATCA	59.462	36.000	0.10	0.00	36.82	2.15
906	7595	2.357836	CCAGCCAAGATGCAGGGT	59.642	61.111	0.00	0.00	34.50	4.34
963	7652	0.249073	CTAACATGGCCGACGAGAGG	60.249	60.000	0.00	0.00	0.00	3.69
967	7656	3.663815	ATGGCCGACGAGAGGTCCT	62.664	63.158	0.00	0.00	42.99	3.85
1136	7826	2.941025	CCTCCCCTTCAAGCCCCA	60.941	66.667	0.00	0.00	0.00	4.96
1137	7827	2.547595	CCTCCCCTTCAAGCCCCAA	61.548	63.158	0.00	0.00	0.00	4.12
1199	7890	1.681486	TTGGCGCCGGTGATAGATCA	61.681	55.000	23.90	3.42	0.00	2.92
1225	7928	0.806884	TCGTGCTAATTTACGGGCCG	60.807	55.000	27.06	27.06	40.48	6.13
1328	8034	2.741985	CAAGGCATGCGTGGACGA	60.742	61.111	14.59	0.00	43.02	4.20
1590	8296	0.670162	GCAAGGTCAGCAAGCTTCAA	59.330	50.000	0.00	0.00	43.77	2.69
1597	8303	1.343142	TCAGCAAGCTTCAACTACCGA	59.657	47.619	0.00	0.00	0.00	4.69
1610	8316	2.261172	CTACCGATGTCGACCACGCA	62.261	60.000	20.53	12.20	43.02	5.24
1659	8368	1.221840	CTTCCTCATGACCGTGGGG	59.778	63.158	1.66	1.66	41.35	4.96
1826	8535	1.744798	CGTGGACATGCACATGAGGAT	60.745	52.381	17.19	0.00	41.20	3.24
2094	8833	7.342581	TGGGTGATGTTAATTAGTAGATGCAA	58.657	34.615	0.00	0.00	0.00	4.08
2147	8906	9.102757	CTGTATTCAAATCGGAGGATATTATGG	57.897	37.037	0.00	0.00	31.01	2.74
2176	8935	7.148771	CGTGTTAATCATGTTGTGAAATGCATT	60.149	33.333	5.99	5.99	40.97	3.56
2193	8952	4.233789	TGCATTTTCTTCCGTTGTTATGC	58.766	39.130	0.00	0.00	38.04	3.14
2198	8957	4.433186	TTCTTCCGTTGTTATGCCATTG	57.567	40.909	0.00	0.00	0.00	2.82
2224	8983	3.957591	TGCAAGCATTTCCTTTGCATA	57.042	38.095	7.00	0.00	42.62	3.14
2429	9194	5.940617	AGTATAACCATGCAGCAATTCCTA	58.059	37.500	0.00	0.00	0.00	2.94
2561	9327	1.644509	TCTTTGAGGGCTGCAGTCTA	58.355	50.000	19.48	2.10	0.00	2.59
2607	9377	7.769044	TCACTACACTAGCCATAATTCTTTTCC	59.231	37.037	0.00	0.00	0.00	3.13
2625	9395	7.397221	TCTTTTCCAGATGAATGAGCTTTCTA	58.603	34.615	0.00	0.00	31.67	2.10
2926	9709	2.242043	CCCCTCTTGATTTTGTGCACT	58.758	47.619	19.41	0.00	0.00	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.947652	CAACCAAGATCATCCTCGCATT	59.052	45.455	0.00	0.00	0.00	3.56
31	32	1.913419	GAGACACAGGGGGATAACCAA	59.087	52.381	0.00	0.00	42.91	3.67
112	113	3.770263	ATGAGCAATCCATTTGTCACG	57.230	42.857	0.00	0.00	37.65	4.35
295	6970	0.104855	ATACGCCATCGCTGATGTGT	59.895	50.000	14.50	14.02	38.28	3.72
483	7160	3.649073	TCGCCAGATTATAACACCATCG	58.351	45.455	0.00	0.00	0.00	3.84
484	7161	4.393062	CCATCGCCAGATTATAACACCATC	59.607	45.833	0.00	0.00	34.23	3.51
485	7162	4.041567	TCCATCGCCAGATTATAACACCAT	59.958	41.667	0.00	0.00	34.23	3.55
486	7163	3.389656	TCCATCGCCAGATTATAACACCA	59.610	43.478	0.00	0.00	34.23	4.17
487	7164	3.997021	CTCCATCGCCAGATTATAACACC	59.003	47.826	0.00	0.00	34.23	4.16
488	7165	4.632153	ACTCCATCGCCAGATTATAACAC	58.368	43.478	0.00	0.00	34.23	3.32
489	7166	4.343814	TGACTCCATCGCCAGATTATAACA	59.656	41.667	0.00	0.00	34.23	2.41
490	7167	4.883083	TGACTCCATCGCCAGATTATAAC	58.117	43.478	0.00	0.00	34.23	1.89
491	7168	5.545063	TTGACTCCATCGCCAGATTATAA	57.455	39.130	0.00	0.00	34.23	0.98
492	7169	5.545063	TTTGACTCCATCGCCAGATTATA	57.455	39.130	0.00	0.00	34.23	0.98
636	7317	9.106070	CTTTCTTTTAAGTACCTACAAGTGTGT	57.894	33.333	0.00	0.00	42.09	3.72
946	7635	2.227089	GACCTCTCGTCGGCCATGTT	62.227	60.000	2.24	0.00	0.00	2.71
950	7639	2.888464	CTAGGACCTCTCGTCGGCCA	62.888	65.000	2.24	0.00	42.99	5.36
963	7652	1.439644	CAGCCGCTCCTTCTAGGAC	59.560	63.158	0.00	0.00	40.06	3.85
967	7656	2.058595	GGTCCAGCCGCTCCTTCTA	61.059	63.158	0.00	0.00	0.00	2.10
1050	7739	0.108804	CCACTCGCTGGATGTACGTT	60.109	55.000	0.00	0.00	43.95	3.99
1107	7797	4.741239	GGGAGGGTGCAGAGGGGA	62.741	72.222	0.00	0.00	0.00	4.81
1136	7826	3.268034	AGAGAGGAACCTGGAAGACTT	57.732	47.619	0.00	0.00	34.07	3.01
1137	7827	3.268034	AAGAGAGGAACCTGGAAGACT	57.732	47.619	0.00	0.00	34.07	3.24
1199	7890	5.675323	GCCCGTAAATTAGCACGAAAGAATT	60.675	40.000	8.30	0.00	40.56	2.17
1225	7928	1.400242	GCAAGCACACAAATCGGAGAC	60.400	52.381	0.00	0.00	42.51	3.36
1328	8034	4.736896	GGTCGAAGAAGCCGCCGT	62.737	66.667	0.00	0.00	39.69	5.68
1590	8296	1.798735	CGTGGTCGACATCGGTAGT	59.201	57.895	18.91	0.00	40.29	2.73
1597	8303	2.433145	CAGCTGCGTGGTCGACAT	60.433	61.111	18.91	0.00	39.71	3.06
1641	8350	1.221840	CCCCACGGTCATGAGGAAG	59.778	63.158	0.00	0.00	0.00	3.46
1873	8582	0.250510	TACATTGGCAGCACCGTCAA	60.251	50.000	0.00	0.00	43.94	3.18
1883	8592	0.988063	TGGCACTAGGTACATTGGCA	59.012	50.000	4.55	4.55	41.76	4.92
2094	8833	8.137745	ACCCAACAATGACATTAAAGATGAAT	57.862	30.769	0.00	0.00	0.00	2.57
2147	8906	7.617122	GCATTTCACAACATGATTAACACGAAC	60.617	37.037	0.00	0.00	37.11	3.95
2176	8935	4.804108	CAATGGCATAACAACGGAAGAAA	58.196	39.130	0.00	0.00	0.00	2.52
2198	8957	2.159327	AGGAAATGCTTGCAAGTTGC	57.841	45.000	26.55	21.17	45.29	4.17
2429	9194	5.704978	GGAAGACTTTGAGAGAAGCTTCATT	59.295	40.000	27.57	15.16	39.19	2.57
2727	9506	0.743345	GGTAACTCTCGCCGCCATTT	60.743	55.000	0.00	0.00	0.00	2.32
2787	9567	5.130350	TCTAAAAGTTGGGAGTTGTCCAAG	58.870	41.667	0.00	0.00	46.07	3.61
2926	9709	6.787225	GGTTTTAAATACACCGACATGCATA	58.213	36.000	0.00	0.00	0.00	3.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.