AutoCloner

Multiple sequence alignment - TraesCS1D01G204600

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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	TraesCS1D01G204600	chr1D	100.000	3456	0	0	1	3456	289780721	289777266	0.000000e+00	6383.0
1	TraesCS1D01G204600	chr1B	94.625	3479	130	16	1	3456	391072945	391069501	0.000000e+00	5336.0
2	TraesCS1D01G204600	chr1B	95.556	45	2	0	268	312	678449381	678449425	4.780000e-09	73.1
3	TraesCS1D01G204600	chr1B	100.000	30	0	0	665	694	85248169	85248140	4.820000e-04	56.5
4	TraesCS1D01G204600	chr1A	95.850	2771	81	9	691	3456	362196161	362193420	0.000000e+00	4449.0
5	TraesCS1D01G204600	chr1A	93.701	127	6	2	461	586	362196328	362196203	4.550000e-44	189.0
6	TraesCS1D01G204600	chr1A	91.579	95	7	1	2776	2869	362194202	362194108	2.800000e-26	130.0
7	TraesCS1D01G204600	chr2A	82.819	227	37	2	1	226	197899428	197899653	5.850000e-48	202.0
8	TraesCS1D01G204600	chr5D	82.553	235	27	12	1	226	397075385	397075156	9.790000e-46	195.0
9	TraesCS1D01G204600	chr4B	82.870	216	35	2	12	226	589027345	589027559	3.520000e-45	193.0
10	TraesCS1D01G204600	chr3D	83.105	219	30	4	12	226	480679544	480679329	3.520000e-45	193.0
11	TraesCS1D01G204600	chr2D	82.870	216	35	2	12	226	183581917	183582131	3.520000e-45	193.0
12	TraesCS1D01G204600	chr7B	81.776	214	37	2	18	230	136001087	136000875	9.860000e-41	178.0
13	TraesCS1D01G204600	chr6A	81.651	218	37	3	12	227	572131943	572132159	9.860000e-41	178.0
14	TraesCS1D01G204600	chr6B	80.973	226	40	3	1	225	10929831	10929608	3.540000e-40	176.0
15	TraesCS1D01G204600	chr6B	95.122	41	1	1	226	265	665685224	665685184	2.880000e-06	63.9
16	TraesCS1D01G204600	chr6B	96.970	33	1	0	268	300	614134879	614134847	4.820000e-04	56.5
17	TraesCS1D01G204600	chr3A	89.474	57	6	0	267	323	616368769	616368713	4.780000e-09	73.1
18	TraesCS1D01G204600	chr4A	95.122	41	1	1	226	265	66744833	66744873	2.880000e-06	63.9
19	TraesCS1D01G204600	chr5A	97.222	36	0	1	660	694	144705162	144705127	3.720000e-05	60.2
20	TraesCS1D01G204600	chrUn	100.000	30	0	0	665	694	299817561	299817590	4.820000e-04	56.5

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	TraesCS1D01G204600	chr1D	289777266	289780721	3455	True	6383.000000	6383	100.000	1	3456	1	chr1D.!!$R1	3455
1	TraesCS1D01G204600	chr1B	391069501	391072945	3444	True	5336.000000	5336	94.625	1	3456	1	chr1B.!!$R2	3455
2	TraesCS1D01G204600	chr1A	362193420	362196328	2908	True	1589.333333	4449	93.710	461	3456	3	chr1A.!!$R1	2995

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
536	544	0.307760	GCGTGGGCGAAAATGATAGG	59.692	55.0	0.0	0.0	41.33	2.57	F
2067	2086	0.391661	GCTCGATGTGGGAAAGCTCA	60.392	55.0	0.0	0.0	0.00	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2314	2333	1.369091	GATGGCGATTTCTGGCACGT	61.369	55.0	0.00	0.0	45.21	4.49	R
2887	2911	1.660167	GCATGCAGCACAGTCATAGA	58.340	50.0	14.21	0.0	44.79	1.98	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
55	56	1.139947	GGGCTCCGACGAGAAAGAG	59.860	63.158	0.00	0.00	38.52	2.85
71	72	0.757188	AGAGTAGGGCATGGGAGACG	60.757	60.000	0.00	0.00	0.00	4.18
106	107	4.357947	GTGAGCCGGCTCGTGACA	62.358	66.667	42.48	28.03	45.48	3.58
110	111	2.742372	GCCGGCTCGTGACAATGT	60.742	61.111	22.15	0.00	0.00	2.71
117	118	2.531206	GCTCGTGACAATGTCCTACTC	58.469	52.381	11.24	0.00	0.00	2.59
126	127	3.197983	ACAATGTCCTACTCTACCTTGCC	59.802	47.826	0.00	0.00	0.00	4.52
127	128	1.471119	TGTCCTACTCTACCTTGCCG	58.529	55.000	0.00	0.00	0.00	5.69
132	133	1.381928	TACTCTACCTTGCCGGCGAG	61.382	60.000	33.44	33.44	38.75	5.03
145	146	3.112709	GCGAGCGGACCAACACTC	61.113	66.667	0.00	0.00	0.00	3.51
160	161	2.811101	CTCTAGGGAGTGCAGCCG	59.189	66.667	0.00	0.00	35.03	5.52
161	162	3.438017	CTCTAGGGAGTGCAGCCGC	62.438	68.421	0.00	0.00	35.03	6.53
184	185	2.801699	CGCTAGACATGGATACGGCAAA	60.802	50.000	0.00	0.00	42.51	3.68
209	210	3.471680	GGATGAGCTCCGCTTAAAGATT	58.528	45.455	12.15	0.00	39.88	2.40
225	226	7.331687	GCTTAAAGATTGGTTTATGTTGCATGT	59.668	33.333	0.00	0.00	0.00	3.21
360	362	4.612412	TTGCGCGTCGGGAAGGTT	62.612	61.111	14.18	0.00	0.00	3.50
361	363	4.612412	TGCGCGTCGGGAAGGTTT	62.612	61.111	14.18	0.00	0.00	3.27
362	364	4.084888	GCGCGTCGGGAAGGTTTG	62.085	66.667	14.18	0.00	0.00	2.93
363	365	2.356553	CGCGTCGGGAAGGTTTGA	60.357	61.111	2.62	0.00	0.00	2.69
364	366	1.957186	CGCGTCGGGAAGGTTTGAA	60.957	57.895	2.62	0.00	0.00	2.69
365	367	1.866925	GCGTCGGGAAGGTTTGAAG	59.133	57.895	0.00	0.00	0.00	3.02
366	368	0.601841	GCGTCGGGAAGGTTTGAAGA	60.602	55.000	0.00	0.00	0.00	2.87
378	380	4.410099	AGGTTTGAAGATCAGATTTGCCA	58.590	39.130	0.00	0.00	0.00	4.92
381	383	5.990996	GGTTTGAAGATCAGATTTGCCAAAA	59.009	36.000	0.00	0.00	0.00	2.44
430	438	4.733887	GGTTACGACACGATCTAACATCTG	59.266	45.833	0.00	0.00	0.00	2.90
484	492	0.798776	CCACTTGAGGTTGACATCGC	59.201	55.000	0.00	0.00	0.00	4.58
521	529	4.051922	GGTATCACTCCTAATCAAGCGTG	58.948	47.826	0.00	0.00	0.00	5.34
536	544	0.307760	GCGTGGGCGAAAATGATAGG	59.692	55.000	0.00	0.00	41.33	2.57
611	620	3.896272	GAGTACCACCCGGAGAAGATTAT	59.104	47.826	0.73	0.00	35.59	1.28
614	623	2.700897	ACCACCCGGAGAAGATTATCAG	59.299	50.000	0.73	0.00	35.59	2.90
660	669	7.147794	TGGTTAACATACATCGAAGAGTACCAT	60.148	37.037	8.10	0.00	43.63	3.55
756	769	6.655078	AGCACACTGGAAAATAACATTCTT	57.345	33.333	0.00	0.00	0.00	2.52
759	772	8.806146	AGCACACTGGAAAATAACATTCTTTAT	58.194	29.630	0.00	0.00	0.00	1.40
760	773	9.423061	GCACACTGGAAAATAACATTCTTTATT	57.577	29.630	0.00	0.00	33.84	1.40
962	977	3.636231	CTTCCCACCTCGCACCCA	61.636	66.667	0.00	0.00	0.00	4.51
1334	1353	1.304952	CCACCTCCTCGTCTCCTCT	59.695	63.158	0.00	0.00	0.00	3.69
1544	1563	3.687321	CTCCTGGGTCATGGTGGCG	62.687	68.421	0.00	0.00	0.00	5.69
1720	1739	0.539051	CCCTTCGAGAGCAACCTCAT	59.461	55.000	0.00	0.00	40.68	2.90
2067	2086	0.391661	GCTCGATGTGGGAAAGCTCA	60.392	55.000	0.00	0.00	0.00	4.26
2685	2704	3.453717	TCAGGCTGATGCTAAGATGACTT	59.546	43.478	14.43	0.00	39.59	3.01
2803	2822	9.836864	TGATGCTAAGATGACTGTAAATTGTAT	57.163	29.630	0.00	0.00	0.00	2.29
2934	2958	5.679601	TGCATAGCATGAGGTTACACATTA	58.320	37.500	0.00	0.00	31.71	1.90
3006	3030	8.616076	ACGAGAAAAAGGATGATCACATTATTC	58.384	33.333	0.00	0.00	36.82	1.75
3063	3088	2.507484	TCTGCCCATGAAGAAACACAG	58.493	47.619	0.00	0.00	0.00	3.66
3073	3098	6.692681	CCATGAAGAAACACAGTAGTTGTTTG	59.307	38.462	5.24	0.00	38.16	2.93
3333	3359	6.488344	TCATGGTGTGTGAGATCTCTACTATC	59.512	42.308	22.95	14.53	0.00	2.08
3341	3367	8.511321	GTGTGAGATCTCTACTATCATGGTTAG	58.489	40.741	22.95	0.00	0.00	2.34
3438	3464	8.928270	AAACTAACTAACTAGATGGTCAATCG	57.072	34.615	0.00	0.00	40.54	3.34
3450	3476	6.469410	AGATGGTCAATCGTTGTAAAGGTAA	58.531	36.000	0.00	0.00	40.54	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	4.487412	GGACGGTGCCGGTAGACG	62.487	72.222	15.44	13.67	44.69	4.18
55	56	2.822399	CCGTCTCCCATGCCCTAC	59.178	66.667	0.00	0.00	0.00	3.18
101	102	5.411781	CAAGGTAGAGTAGGACATTGTCAC	58.588	45.833	18.09	8.86	33.75	3.67
104	105	3.197983	GGCAAGGTAGAGTAGGACATTGT	59.802	47.826	0.00	0.00	39.06	2.71
106	107	2.431057	CGGCAAGGTAGAGTAGGACATT	59.569	50.000	0.00	0.00	0.00	2.71
110	111	1.041447	GCCGGCAAGGTAGAGTAGGA	61.041	60.000	24.80	0.00	43.70	2.94
127	128	4.681978	AGTGTTGGTCCGCTCGCC	62.682	66.667	0.00	0.00	0.00	5.54
132	133	1.218316	CCCTAGAGTGTTGGTCCGC	59.782	63.158	0.00	0.00	0.00	5.54
145	146	4.537433	GGCGGCTGCACTCCCTAG	62.537	72.222	21.31	0.00	45.35	3.02
160	161	0.388649	CGTATCCATGTCTAGCGGGC	60.389	60.000	0.00	0.00	0.00	6.13
161	162	0.243907	CCGTATCCATGTCTAGCGGG	59.756	60.000	0.00	0.00	34.77	6.13
354	356	5.047802	TGGCAAATCTGATCTTCAAACCTTC	60.048	40.000	0.00	0.00	0.00	3.46
355	357	4.834496	TGGCAAATCTGATCTTCAAACCTT	59.166	37.500	0.00	0.00	0.00	3.50
356	358	4.410099	TGGCAAATCTGATCTTCAAACCT	58.590	39.130	0.00	0.00	0.00	3.50
357	359	4.789012	TGGCAAATCTGATCTTCAAACC	57.211	40.909	0.00	0.00	0.00	3.27
358	360	7.148523	GGATTTTGGCAAATCTGATCTTCAAAC	60.149	37.037	14.29	0.00	45.45	2.93
359	361	6.875195	GGATTTTGGCAAATCTGATCTTCAAA	59.125	34.615	14.29	0.00	45.45	2.69
360	362	6.400568	GGATTTTGGCAAATCTGATCTTCAA	58.599	36.000	14.29	0.00	45.45	2.69
361	363	5.969423	GGATTTTGGCAAATCTGATCTTCA	58.031	37.500	14.29	0.00	45.45	3.02
430	438	2.705154	GCAACGAATTAATGTCTCGCC	58.295	47.619	7.72	0.00	36.03	5.54
484	492	1.956629	ATACCAGAAGCCCACGACCG	61.957	60.000	0.00	0.00	0.00	4.79
521	529	2.341846	TCCACCTATCATTTTCGCCC	57.658	50.000	0.00	0.00	0.00	6.13
587	596	0.613853	CTTCTCCGGGTGGTACTCCA	60.614	60.000	0.00	0.00	45.05	3.86
611	620	2.153645	AGCATCACATGTTTTCGCTGA	58.846	42.857	0.00	0.00	0.00	4.26
614	623	1.470098	AGGAGCATCACATGTTTTCGC	59.530	47.619	0.00	0.00	36.25	4.70
660	669	9.241919	TCCACAAAGAAATATAAGAGCATTTGA	57.758	29.630	0.00	0.00	32.28	2.69
682	695	4.816925	GCAAGTCAAATATACTCCCTCCAC	59.183	45.833	0.00	0.00	0.00	4.02
683	696	4.721776	AGCAAGTCAAATATACTCCCTCCA	59.278	41.667	0.00	0.00	0.00	3.86
761	774	6.438259	TTTCTGTGTGTCGGTTATGAAAAA	57.562	33.333	0.00	0.00	0.00	1.94
932	947	1.694525	GGGAAGGAGGAAGGGGAGG	60.695	68.421	0.00	0.00	0.00	4.30
933	948	1.082954	TGGGAAGGAGGAAGGGGAG	59.917	63.158	0.00	0.00	0.00	4.30
934	949	1.229853	GTGGGAAGGAGGAAGGGGA	60.230	63.158	0.00	0.00	0.00	4.81
935	950	2.309504	GGTGGGAAGGAGGAAGGGG	61.310	68.421	0.00	0.00	0.00	4.79
936	951	1.229984	AGGTGGGAAGGAGGAAGGG	60.230	63.158	0.00	0.00	0.00	3.95
937	952	1.617947	CGAGGTGGGAAGGAGGAAGG	61.618	65.000	0.00	0.00	0.00	3.46
938	953	1.901085	CGAGGTGGGAAGGAGGAAG	59.099	63.158	0.00	0.00	0.00	3.46
939	954	2.291043	GCGAGGTGGGAAGGAGGAA	61.291	63.158	0.00	0.00	0.00	3.36
940	955	2.683933	GCGAGGTGGGAAGGAGGA	60.684	66.667	0.00	0.00	0.00	3.71
941	956	3.003173	TGCGAGGTGGGAAGGAGG	61.003	66.667	0.00	0.00	0.00	4.30
942	957	2.266055	GTGCGAGGTGGGAAGGAG	59.734	66.667	0.00	0.00	0.00	3.69
943	958	3.319198	GGTGCGAGGTGGGAAGGA	61.319	66.667	0.00	0.00	0.00	3.36
962	977	3.840132	GGTGGTGGGGTTGGGGTT	61.840	66.667	0.00	0.00	0.00	4.11
1061	1080	2.444706	CCAGATCTGGGCCGAGGA	60.445	66.667	31.14	4.10	46.81	3.71
1334	1353	4.055227	GGGCGGATGGGGTGGAAA	62.055	66.667	0.00	0.00	0.00	3.13
2067	2086	3.402681	CTGCTCACATCCCCGGGT	61.403	66.667	21.85	0.00	0.00	5.28
2314	2333	1.369091	GATGGCGATTTCTGGCACGT	61.369	55.000	0.00	0.00	45.21	4.49
2704	2723	7.567458	ACTACTGGTGGTAAGTACAAGAAAAA	58.433	34.615	0.00	0.00	0.00	1.94
2803	2822	5.779529	AAGTACAAGAGAAGACGGTGTAA	57.220	39.130	0.00	0.00	0.00	2.41
2807	2826	5.105837	GGTGATAAGTACAAGAGAAGACGGT	60.106	44.000	0.00	0.00	0.00	4.83
2887	2911	1.660167	GCATGCAGCACAGTCATAGA	58.340	50.000	14.21	0.00	44.79	1.98
2934	2958	4.157289	CCAAAATAGTCACTGCATTCTGCT	59.843	41.667	0.34	0.00	45.31	4.24
3063	3088	6.359480	AGACTACACAAAGCAAACAACTAC	57.641	37.500	0.00	0.00	0.00	2.73
3073	3098	4.023963	GGAAGACCAAAGACTACACAAAGC	60.024	45.833	0.00	0.00	35.97	3.51
3310	3336	6.368805	TGATAGTAGAGATCTCACACACCAT	58.631	40.000	24.39	14.38	0.00	3.55
3333	3359	2.592102	ATATGCCCAGGCTAACCATG	57.408	50.000	10.58	0.00	42.51	3.66
3341	3367	2.371510	AGAAGAGAGAATATGCCCAGGC	59.628	50.000	0.38	0.38	42.35	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.