AutoCloner

Multiple sequence alignment - TraesCS2D01G422000

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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	TraesCS2D01G422000	chr2D	100.000	4073	0	0	1	4073	535564697	535568769	0.000000e+00	7522
1	TraesCS2D01G422000	chr2A	94.255	2646	105	24	786	3406	678666772	678669395	0.000000e+00	4000
2	TraesCS2D01G422000	chr2A	75.579	475	67	29	25	479	678666082	678666527	5.370000e-44	189
3	TraesCS2D01G422000	chr2B	93.967	2652	108	18	776	3405	636770939	636773560	0.000000e+00	3964
4	TraesCS2D01G422000	chr2B	91.777	681	34	8	3396	4073	774481043	774481704	0.000000e+00	928
5	TraesCS2D01G422000	chr2B	91.667	672	34	7	3405	4073	640596741	640597393	0.000000e+00	911
6	TraesCS2D01G422000	chr2B	92.089	493	21	7	1	490	636770161	636770638	0.000000e+00	678
7	TraesCS2D01G422000	chr2B	80.124	322	47	8	2503	2810	636774444	636774762	1.470000e-54	224
8	TraesCS2D01G422000	chr2B	91.473	129	11	0	632	760	636770828	636770956	1.160000e-40	178
9	TraesCS2D01G422000	chr3D	99.100	667	6	0	3407	4073	283970270	283969604	0.000000e+00	1199
10	TraesCS2D01G422000	chr3B	95.522	670	24	4	3407	4073	193609008	193608342	0.000000e+00	1066
11	TraesCS2D01G422000	chr5A	94.196	672	31	6	3406	4073	567083988	567083321	0.000000e+00	1018
12	TraesCS2D01G422000	chr5A	93.309	553	29	6	3391	3937	406421001	406421551	0.000000e+00	809
13	TraesCS2D01G422000	chr5A	93.662	142	8	1	3932	4073	406473560	406473700	1.150000e-50	211
14	TraesCS2D01G422000	chr7A	92.431	436	23	4	3406	3833	138518774	138518341	7.480000e-172	614
15	TraesCS2D01G422000	chr7A	94.737	247	10	2	3829	4073	138512933	138512688	8.260000e-102	381
16	TraesCS2D01G422000	chr7A	86.580	231	28	2	3405	3632	138511636	138511866	6.760000e-63	252
17	TraesCS2D01G422000	chr3A	92.081	442	24	5	3640	4073	371250582	371251020	2.690000e-171	612
18	TraesCS2D01G422000	chr6B	93.496	246	11	2	3407	3647	377906093	377905848	1.080000e-95	361

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	TraesCS2D01G422000	chr2D	535564697	535568769	4072	False	7522.0	7522	100.00000	1	4073	1	chr2D.!!$F1	4072
1	TraesCS2D01G422000	chr2A	678666082	678669395	3313	False	2094.5	4000	84.91700	25	3406	2	chr2A.!!$F1	3381
2	TraesCS2D01G422000	chr2B	636770161	636774762	4601	False	1261.0	3964	89.41325	1	3405	4	chr2B.!!$F3	3404
3	TraesCS2D01G422000	chr2B	774481043	774481704	661	False	928.0	928	91.77700	3396	4073	1	chr2B.!!$F2	677
4	TraesCS2D01G422000	chr2B	640596741	640597393	652	False	911.0	911	91.66700	3405	4073	1	chr2B.!!$F1	668
5	TraesCS2D01G422000	chr3D	283969604	283970270	666	True	1199.0	1199	99.10000	3407	4073	1	chr3D.!!$R1	666
6	TraesCS2D01G422000	chr3B	193608342	193609008	666	True	1066.0	1066	95.52200	3407	4073	1	chr3B.!!$R1	666
7	TraesCS2D01G422000	chr5A	567083321	567083988	667	True	1018.0	1018	94.19600	3406	4073	1	chr5A.!!$R1	667
8	TraesCS2D01G422000	chr5A	406421001	406421551	550	False	809.0	809	93.30900	3391	3937	1	chr5A.!!$F1	546

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	Hairpin	End Stability	Orientation
551	595	0.170339	GTACCCACGCTGGATTTTGC	59.830	55.0	5.71	40.96	3.68	F
763	859	0.180406	AGTATCACGCATCAACCCCC	59.820	55.0	0.00	0.00	5.40	F
950	1049	0.249826	GCTCTATCTCCCTGCAGCAC	60.250	60.0	8.66	0.00	4.40	F
1502	1602	0.526954	ATCGACATACCCGAACACGC	60.527	55.0	0.00	39.62	5.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2134	2252	0.179029	CACGGGACTGGTTGGTTCTT	60.179	55.000	0.00	0.0	0.00	2.52	R
2751	2882	1.896220	TAGCCTGCAGTGAAAAGTGG	58.104	50.000	13.81	0.0	0.00	4.00	R
2781	2912	1.325355	CCATGATGATGGTTGCCCTC	58.675	55.000	2.51	0.0	43.98	4.30	R
3353	3504	1.742268	TGTGAGAGACTCAGCTGATCG	59.258	52.381	18.63	9.3	41.46	3.69	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
131	133	3.436243	TGTGACCCAAGAAAAACCAACT	58.564	40.909	0.00	0.00	3.16
158	160	1.589716	AAAGAGCCCAGCGAACATGC	61.590	55.000	0.00	0.00	4.06
159	161	3.869272	GAGCCCAGCGAACATGCG	61.869	66.667	0.00	40.67	4.73
160	162	4.393155	AGCCCAGCGAACATGCGA	62.393	61.111	0.00	40.67	5.10
161	163	3.204827	GCCCAGCGAACATGCGAT	61.205	61.111	0.00	40.67	4.58
162	164	1.887242	GCCCAGCGAACATGCGATA	60.887	57.895	0.00	40.67	2.92
163	165	1.934463	CCCAGCGAACATGCGATAC	59.066	57.895	0.00	40.67	2.24
164	166	0.809636	CCCAGCGAACATGCGATACA	60.810	55.000	0.00	40.67	2.29
165	167	1.220529	CCAGCGAACATGCGATACAT	58.779	50.000	0.00	40.66	2.29
203	205	1.616865	CTTCGTACAGGGAACACTGGA	59.383	52.381	8.93	42.75	3.86
305	312	1.602311	GGCAGGAATATGTCAGCCAG	58.398	55.000	0.00	44.36	4.85
327	345	1.473258	TTGACAGCTTGCACACCTTT	58.527	45.000	0.00	0.00	3.11
335	353	2.604614	GCTTGCACACCTTTTTACCTCG	60.605	50.000	0.00	0.00	4.63
368	388	0.755686	AGGCCTCTCGATGGTCAATC	59.244	55.000	0.00	0.00	2.67
369	389	0.465705	GGCCTCTCGATGGTCAATCA	59.534	55.000	0.00	34.68	2.57
370	390	1.134401	GGCCTCTCGATGGTCAATCAA	60.134	52.381	0.00	34.68	2.57
371	391	2.486191	GGCCTCTCGATGGTCAATCAAT	60.486	50.000	0.00	34.68	2.57
400	420	1.081509	CCGCACCACCGAAAACATG	60.082	57.895	0.00	0.00	3.21
421	441	2.483491	GAGCAAGCAGACTCCTGAAAAG	59.517	50.000	0.00	43.02	2.27
422	442	1.068679	GCAAGCAGACTCCTGAAAAGC	60.069	52.381	0.00	43.02	3.51
424	444	1.063183	AGCAGACTCCTGAAAAGCCT	58.937	50.000	0.00	43.02	4.58
425	445	2.260822	AGCAGACTCCTGAAAAGCCTA	58.739	47.619	0.00	43.02	3.93
427	447	2.744741	GCAGACTCCTGAAAAGCCTAAC	59.255	50.000	0.00	43.02	2.34
429	449	4.646572	CAGACTCCTGAAAAGCCTAACTT	58.353	43.478	0.00	43.02	2.66
430	450	4.453819	CAGACTCCTGAAAAGCCTAACTTG	59.546	45.833	0.00	43.02	3.16

Showing 1 to 25 of 139 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
16	17	6.488006	CCCAATCCAAAGTTGATAAGATCGAT	59.512	38.462	0.00	0.00	3.59
68	69	3.716006	CACTGACCTTGGCGCACG	61.716	66.667	10.83	0.00	5.34
102	103	6.458210	GTTTTTCTTGGGTCACAATCATCAT	58.542	36.000	0.00	38.65	2.45
131	133	1.968017	CTGGGCTCTTTTCGCTGCA	60.968	57.895	0.00	0.00	4.41
158	160	2.110990	CAAAATGCACGCCATGTATCG	58.889	47.619	0.00	31.50	2.92
159	161	2.462889	CCAAAATGCACGCCATGTATC	58.537	47.619	0.00	31.50	2.24
160	162	1.471327	GCCAAAATGCACGCCATGTAT	60.471	47.619	0.00	34.68	2.29
161	163	0.108898	GCCAAAATGCACGCCATGTA	60.109	50.000	0.00	33.49	2.29
162	164	1.374505	GCCAAAATGCACGCCATGT	60.375	52.632	0.00	33.49	3.21
163	165	2.101835	GGCCAAAATGCACGCCATG	61.102	57.895	0.00	41.25	3.66
164	166	2.265424	GGCCAAAATGCACGCCAT	59.735	55.556	0.00	41.25	4.40
165	167	4.001226	GGGCCAAAATGCACGCCA	62.001	61.111	4.39	43.50	5.69
166	168	4.758251	GGGGCCAAAATGCACGCC	62.758	66.667	4.39	40.85	5.68
203	205	1.447317	GGCGTTGGCGATGGAATGAT	61.447	55.000	0.00	41.24	2.45
238	240	0.592500	CCGAGATCACACGACATCCG	60.593	60.000	0.00	45.44	4.18
327	345	2.259204	CGACCGGTGCGAGGTAAA	59.741	61.111	14.63	43.01	2.01
350	368	0.465705	TGATTGACCATCGAGAGGCC	59.534	55.000	6.60	34.08	5.19
368	388	3.508840	GCGGGTTCGGCCAGATTG	61.509	66.667	2.24	39.65	2.67
369	389	4.028490	TGCGGGTTCGGCCAGATT	62.028	61.111	2.24	39.65	2.40
370	390	4.778143	GTGCGGGTTCGGCCAGAT	62.778	66.667	2.24	39.65	2.90
400	420	2.175878	TTTCAGGAGTCTGCTTGCTC	57.824	50.000	0.00	40.69	4.26
422	442	0.174845	TCGTCATCGGCCAAGTTAGG	59.825	55.000	2.24	37.69	2.69
424	444	0.604073	TGTCGTCATCGGCCAAGTTA	59.396	50.000	2.24	41.33	2.24
425	445	0.036388	ATGTCGTCATCGGCCAAGTT	60.036	50.000	2.24	41.33	2.66
427	447	0.374758	CAATGTCGTCATCGGCCAAG	59.625	55.000	2.24	41.33	3.61

Showing 1 to 25 of 154 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.