AutoCloner

Multiple sequence alignment - TraesCS7B01G223800

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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	TraesCS7B01G223800	chr7B	100.000	3608	0	0	1	3608	423138349	423141956	0.000000e+00	6663
1	TraesCS7B01G223800	chr7A	94.231	3623	146	21	1	3603	468831087	468834666	0.000000e+00	5474
2	TraesCS7B01G223800	chr7A	87.037	108	14	0	3148	3255	222578230	222578123	4.890000e-24	122
3	TraesCS7B01G223800	chr7D	95.592	3267	117	12	290	3544	408717649	408720900	0.000000e+00	5210
4	TraesCS7B01G223800	chr7D	96.853	286	5	3	1	285	408717320	408717602	3.260000e-130	475
5	TraesCS7B01G223800	chr7D	98.333	60	1	0	3544	3603	408721018	408721077	4.930000e-19	106
6	TraesCS7B01G223800	chrUn	83.532	504	64	8	1633	2122	30346827	30346329	1.530000e-123	453
7	TraesCS7B01G223800	chrUn	81.685	546	69	27	658	1189	30347546	30347018	3.330000e-115	425
8	TraesCS7B01G223800	chrUn	80.978	368	48	11	842	1189	30342243	30341878	4.590000e-69	272
9	TraesCS7B01G223800	chrUn	87.895	190	23	0	2279	2468	30344845	30344656	1.300000e-54	224
10	TraesCS7B01G223800	chrUn	86.087	115	16	0	3141	3255	472409320	472409434	1.360000e-24	124
11	TraesCS7B01G223800	chrUn	95.522	67	3	0	1525	1591	30346900	30346834	1.370000e-19	108
12	TraesCS7B01G223800	chr5A	83.367	499	65	8	1633	2113	659186291	659186789	2.560000e-121	446
13	TraesCS7B01G223800	chr5A	82.397	534	63	18	1630	2151	659185498	659186012	1.540000e-118	436
14	TraesCS7B01G223800	chr5A	82.239	518	66	10	1605	2107	709724481	709723975	1.200000e-114	424
15	TraesCS7B01G223800	chr5A	81.481	540	71	20	658	1188	659184788	659185307	2.000000e-112	416
16	TraesCS7B01G223800	chr5A	86.010	193	27	0	2276	2468	659187093	659187285	1.310000e-49	207
17	TraesCS7B01G223800	chr5A	88.816	152	16	1	1718	1868	709732256	709732105	6.150000e-43	185
18	TraesCS7B01G223800	chr5A	92.079	101	5	2	2373	2472	709723645	709723547	4.860000e-29	139
19	TraesCS7B01G223800	chr5A	95.522	67	3	0	1525	1591	659186218	659186284	1.370000e-19	108
20	TraesCS7B01G223800	chr5A	85.714	105	12	2	1088	1189	659201296	659201400	1.370000e-19	108
21	TraesCS7B01G223800	chr4B	80.591	541	70	20	658	1189	671734187	671733673	5.650000e-103	385
22	TraesCS7B01G223800	chr4B	81.423	253	33	9	1635	1874	671733481	671733230	1.020000e-45	195
23	TraesCS7B01G223800	chr4B	85.119	168	19	5	1024	1191	671813613	671813774	2.230000e-37	167
24	TraesCS7B01G223800	chr4B	95.522	67	3	0	1525	1591	671733556	671733490	1.370000e-19	108
25	TraesCS7B01G223800	chr4A	87.963	108	13	0	3148	3255	736230834	736230727	1.050000e-25	128
26	TraesCS7B01G223800	chr3B	87.963	108	13	0	3148	3255	814646926	814646819	1.050000e-25	128

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	TraesCS7B01G223800	chr7B	423138349	423141956	3607	False	6663.000000	6663	100.000000	1	3608	1	chr7B.!!$F1	3607
1	TraesCS7B01G223800	chr7A	468831087	468834666	3579	False	5474.000000	5474	94.231000	1	3603	1	chr7A.!!$F1	3602
2	TraesCS7B01G223800	chr7D	408717320	408721077	3757	False	1930.333333	5210	96.926000	1	3603	3	chr7D.!!$F1	3602
3	TraesCS7B01G223800	chrUn	30341878	30347546	5668	True	296.400000	453	85.922400	658	2468	5	chrUn.!!$R1	1810
4	TraesCS7B01G223800	chr5A	659184788	659187285	2497	False	322.600000	446	85.755400	658	2468	5	chr5A.!!$F2	1810
5	TraesCS7B01G223800	chr5A	709723547	709724481	934	True	281.500000	424	87.159000	1605	2472	2	chr5A.!!$R2	867
6	TraesCS7B01G223800	chr4B	671733230	671734187	957	True	229.333333	385	85.845333	658	1874	3	chr4B.!!$R1	1216

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	Hairpin	End Stability	Orientation
106	107	0.321564	TGGAAGATGCACGGGTTCAG	60.322	55.000	0.0	3.02	F
1182	1241	0.478072	TCCTGCATGTCCTTGGTTGT	59.522	50.000	0.0	3.32	F
1395	1459	2.239402	GGGAATGAAAATGCCCACCATT	59.761	45.455	45.9	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2049	2923	0.253044	TCAGGGTGCTCTTGTATGCC	59.747	55.0	0.00	0.00	4.40	R
2479	4783	0.106369	ATGTGCATGTGGATGGGGAG	60.106	55.0	0.00	0.00	4.30	R
3362	6586	0.662970	GCTGAGCCGAGATCGATGAC	60.663	60.0	0.54	43.02	3.06	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
49	50	4.644685	GCATCCAAGTTAATTAAGCCCTGA	59.355	41.667	0.00	0.0	0.00	3.86
76	77	5.789574	AGGTGGTTTGATTCCTATACCAA	57.210	39.130	0.00	0.0	40.31	3.67
106	107	0.321564	TGGAAGATGCACGGGTTCAG	60.322	55.000	0.00	0.0	0.00	3.02
165	166	5.412904	AGATGATGACATGCATGATGATCAC	59.587	40.000	32.75	23.0	37.34	3.06
253	254	5.320277	TCTCGAGGATATCATGTCACTCAT	58.680	41.667	13.56	0.0	37.22	2.90
363	407	3.066760	GGTTTAATCACTGGCCTATGCAC	59.933	47.826	3.32	0.0	40.13	4.57
418	462	9.679661	TCTCCTTGTATAATTTCTTATGCACAA	57.320	29.630	0.00	0.0	38.95	3.33
485	530	0.654683	GAGCAGCCGCAGAATAGTTG	59.345	55.000	0.00	0.0	42.27	3.16
489	534	1.398390	CAGCCGCAGAATAGTTGGTTC	59.602	52.381	0.00	0.0	0.00	3.62
573	618	8.391075	ACACAAGTTGCTATTTACATAAGTGT	57.609	30.769	1.81	0.0	42.39	3.55
1056	1112	0.898320	GCAAGTCTGAGCTGAGGGTA	59.102	55.000	0.00	0.0	0.00	3.69
1058	1114	2.175202	CAAGTCTGAGCTGAGGGTAGT	58.825	52.381	0.00	0.0	0.00	2.73
1182	1241	0.478072	TCCTGCATGTCCTTGGTTGT	59.522	50.000	0.00	0.0	0.00	3.32
1290	1354	6.873997	TGAACTGTTCTGTTGTTCTAGAGAA	58.126	36.000	20.18	0.0	40.27	2.87
1321	1385	8.173542	ACACCCTTTTTAAATACTTGTCGATT	57.826	30.769	0.00	0.0	0.00	3.34
1358	1422	4.145365	TGGGACGAATCGTGGAATATTT	57.855	40.909	14.87	0.0	41.37	1.40
1395	1459	2.239402	GGGAATGAAAATGCCCACCATT	59.761	45.455	0.00	0.0	45.90	3.16
1473	1538	3.487372	GGCTACTCTGTTTCAAACCCTT	58.513	45.455	0.00	0.0	0.00	3.95
1655	2508	4.056092	TCTGCATTGCATTTGTTCACAA	57.944	36.364	12.53	0.0	38.13	3.33
1692	2549	3.679502	GCATGCCAAATCCTTGTGTTAAC	59.320	43.478	6.36	0.0	0.00	2.01
2049	2923	3.871485	CCTGAAAGAGATGGTGGAAGAG	58.129	50.000	0.00	0.0	34.07	2.85
2277	4581	2.481952	GAGTTGCAGTCATCAGTTGGTC	59.518	50.000	0.00	0.0	0.00	4.02
2479	4783	2.070783	CAATGCCATTTTGGTCAGTGC	58.929	47.619	0.00	0.0	40.46	4.40
2508	4812	5.823209	TCCACATGCACATCTTCTTAATG	57.177	39.130	0.00	0.0	0.00	1.90
2578	4882	7.094975	CGTTCATGGTTAATCTACAGGTCAAAA	60.095	37.037	0.00	0.0	0.00	2.44
2687	4991	5.981174	AGCTAATTAACCTACCTTGCGTTA	58.019	37.500	0.00	0.0	0.00	3.18
2721	5025	3.382083	AAGGACTTCTTTGTTGGTGGT	57.618	42.857	0.00	0.0	29.99	4.16
2722	5026	3.382083	AGGACTTCTTTGTTGGTGGTT	57.618	42.857	0.00	0.0	0.00	3.67
2726	5030	4.868171	GGACTTCTTTGTTGGTGGTTTTTC	59.132	41.667	0.00	0.0	0.00	2.29
2736	5040	6.410540	TGTTGGTGGTTTTTCTTTAAGCAAT	58.589	32.000	0.00	0.0	35.09	3.56
3033	6207	9.294614	AGAAGTTCAGAGATCTTTAAGCAATTT	57.705	29.630	5.50	0.0	0.00	1.82
3052	6226	6.071952	GCAATTTACTGAAGTTTCATCCCAGA	60.072	38.462	0.00	0.0	36.46	3.86
3362	6586	4.436332	TGAGATGAAGATGACATTGACGG	58.564	43.478	0.00	0.0	0.00	4.79
3406	6630	4.461405	CTTGCGATTTCACAGCTATATGC	58.539	43.478	0.00	0.0	43.29	3.14
3603	7511	1.072806	ACATATGACGCATCCAGCCAT	59.927	47.619	10.38	0.0	41.38	4.40
3604	7512	2.302733	ACATATGACGCATCCAGCCATA	59.697	45.455	10.38	0.0	41.38	2.74
3605	7513	3.054875	ACATATGACGCATCCAGCCATAT	60.055	43.478	10.38	0.0	38.09	1.78
3606	7514	2.574006	ATGACGCATCCAGCCATATT	57.426	45.000	0.00	0.0	41.38	1.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
49	50	9.177927	TGGTATAGGAATCAAACCACCTATTAT	57.822	33.333	0.00	0.00	41.21	1.28
106	107	1.292992	TCAGCATGTCACATCATCGC	58.707	50.000	0.00	0.00	37.40	4.58
231	232	5.641783	ATGAGTGACATGATATCCTCGAG	57.358	43.478	5.13	5.13	37.87	4.04
253	254	4.264487	TGTCATTGGTAGTACTCACCCCTA	60.264	45.833	0.00	0.00	34.99	3.53
363	407	1.236616	TGGGTGCGTGCATCTTCTTG	61.237	55.000	4.93	0.00	0.00	3.02
485	530	5.791336	AAGTTTGAAAAGGATGGAGAACC	57.209	39.130	0.00	0.00	0.00	3.62
489	534	6.820335	AGGAAAAAGTTTGAAAAGGATGGAG	58.180	36.000	0.00	0.00	0.00	3.86
870	921	5.047377	GGGTCAACTTCTTGATGCCATTTTA	60.047	40.000	0.00	0.00	38.69	1.52
1056	1112	0.325484	AGCAGAGCTCCTCCATGACT	60.325	55.000	10.93	0.99	30.62	3.41
1058	1114	0.540454	CAAGCAGAGCTCCTCCATGA	59.460	55.000	10.93	0.00	38.25	3.07
1230	1289	8.202745	ACTTCTTACTGAACAAAAGAGTGAAG	57.797	34.615	0.00	0.00	31.30	3.02
1358	1422	4.080186	TCATTCCCATGCTTCATGAGAGAA	60.080	41.667	8.26	8.29	43.81	2.87
1395	1459	9.996554	TTCAGTTTCAGTTTCATATCAGTCTAA	57.003	29.630	0.00	0.00	0.00	2.10
1446	1511	3.402628	TGAAACAGAGTAGCCCTGAAC	57.597	47.619	0.00	0.00	35.69	3.18
1655	2508	1.808945	GCATGCTCAGTTGCTTAGTGT	59.191	47.619	11.37	0.00	35.95	3.55
1730	2600	4.370917	GAGTCTCTTGCATGGAGATCTTC	58.629	47.826	18.55	13.91	41.13	2.87
1863	2733	2.162408	GAGCAGAAAGGCCATGTACAAC	59.838	50.000	5.01	0.00	0.00	3.32
1934	2808	5.463061	CGTTTTCCGACACTTAAGGACTAAA	59.537	40.000	7.53	0.00	39.56	1.85
1940	2814	1.136446	CGCGTTTTCCGACACTTAAGG	60.136	52.381	7.53	0.00	39.56	2.69
2049	2923	0.253044	TCAGGGTGCTCTTGTATGCC	59.747	55.000	0.00	0.00	0.00	4.40
2179	4370	9.844257	AATCTTCAGATAATTGCTAGTAGCTTT	57.156	29.630	22.34	17.12	36.78	3.51
2277	4581	3.199880	AGGTCAGTGGAAACAACTCAG	57.800	47.619	0.00	0.00	46.06	3.35
2479	4783	0.106369	ATGTGCATGTGGATGGGGAG	60.106	55.000	0.00	0.00	0.00	4.30
2508	4812	4.678622	TCATGCAATGCAATGACTGATTC	58.321	39.130	13.45	0.00	46.21	2.52
2578	4882	1.708993	TTGAGCCTGTCCAGCTGGTT	61.709	55.000	31.58	11.81	41.75	3.67
2736	5040	2.270352	CTGGAACCAACTACCAGCAA	57.730	50.000	0.00	0.00	43.32	3.91
2938	6112	5.491635	TGTTCACGTCATTTTGTTGATGA	57.508	34.783	0.95	0.00	36.37	2.92
2946	6120	7.190871	ACGTTTTCTATTGTTCACGTCATTTT	58.809	30.769	0.00	0.00	36.13	1.82
3033	6207	6.373005	TCAATCTGGGATGAAACTTCAGTA	57.627	37.500	0.00	0.00	41.08	2.74
3362	6586	0.662970	GCTGAGCCGAGATCGATGAC	60.663	60.000	0.54	0.00	43.02	3.06
3406	6630	7.473366	CCAAACATCTTCATCTTCATCTCAAG	58.527	38.462	0.00	0.00	0.00	3.02
3407	6631	6.127814	GCCAAACATCTTCATCTTCATCTCAA	60.128	38.462	0.00	0.00	0.00	3.02
3408	6632	5.356190	GCCAAACATCTTCATCTTCATCTCA	59.644	40.000	0.00	0.00	0.00	3.27
3409	6633	5.221009	GGCCAAACATCTTCATCTTCATCTC	60.221	44.000	0.00	0.00	0.00	2.75
3410	6634	4.643784	GGCCAAACATCTTCATCTTCATCT	59.356	41.667	0.00	0.00	0.00	2.90
3411	6635	4.400251	TGGCCAAACATCTTCATCTTCATC	59.600	41.667	0.61	0.00	0.00	2.92
3412	6636	4.346730	TGGCCAAACATCTTCATCTTCAT	58.653	39.130	0.61	0.00	0.00	2.57
3413	6637	3.760151	CTGGCCAAACATCTTCATCTTCA	59.240	43.478	7.01	0.00	0.00	3.02
3414	6638	3.760684	ACTGGCCAAACATCTTCATCTTC	59.239	43.478	7.01	0.00	0.00	2.87
3415	6639	3.771216	ACTGGCCAAACATCTTCATCTT	58.229	40.909	7.01	0.00	0.00	2.40
3416	6640	3.446442	ACTGGCCAAACATCTTCATCT	57.554	42.857	7.01	0.00	0.00	2.90
3417	6641	4.525912	AAACTGGCCAAACATCTTCATC	57.474	40.909	7.01	0.00	0.00	2.92
3418	6642	4.101430	ACAAAACTGGCCAAACATCTTCAT	59.899	37.500	7.01	0.00	0.00	2.57
3419	6643	3.450457	ACAAAACTGGCCAAACATCTTCA	59.550	39.130	7.01	0.00	0.00	3.02
3420	6644	4.058721	ACAAAACTGGCCAAACATCTTC	57.941	40.909	7.01	0.00	0.00	2.87
3537	6764	9.185680	TCATGTAGAGCTTAAGATGTAGTACAA	57.814	33.333	7.16	0.00	0.00	2.41
3541	7449	7.507277	TGGATCATGTAGAGCTTAAGATGTAGT	59.493	37.037	6.67	0.00	31.91	2.73
3542	7450	7.890515	TGGATCATGTAGAGCTTAAGATGTAG	58.109	38.462	6.67	0.00	31.91	2.74

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.