AutoCloner

Multiple sequence alignment - TraesCS5B01G031300

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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	TraesCS5B01G031300	chr5B	100.000	3436	0	0	1	3436	34299652	34296217	0.000000e+00	6346
1	TraesCS5B01G031300	chr5B	96.512	3412	94	3	1	3411	123793348	123789961	0.000000e+00	5618
2	TraesCS5B01G031300	chr5B	96.278	3412	88	6	1	3411	353924449	353927822	0.000000e+00	5561
3	TraesCS5B01G031300	chr5B	96.190	3412	91	6	1	3411	18190398	18187025	0.000000e+00	5544
4	TraesCS5B01G031300	chr5B	95.076	1178	35	10	2234	3411	514054864	514053710	0.000000e+00	1832
5	TraesCS5B01G031300	chr7B	96.954	3414	79	8	1	3411	664945990	664949381	0.000000e+00	5705
6	TraesCS5B01G031300	chr7B	96.600	3412	95	5	1	3411	666622371	666618980	0.000000e+00	5638
7	TraesCS5B01G031300	chr7B	97.047	2574	73	3	1	2573	379917830	379915259	0.000000e+00	4329
8	TraesCS5B01G031300	chr3B	96.835	3412	86	4	1	3411	734220781	734224171	0.000000e+00	5683
9	TraesCS5B01G031300	chr4B	97.105	2763	75	2	1	2758	522410157	522407395	0.000000e+00	4654
10	TraesCS5B01G031300	chr3D	94.210	2677	115	11	1	2665	581478946	581476298	0.000000e+00	4048
11	TraesCS5B01G031300	chr6B	87.539	1621	115	42	1279	2858	77323085	77324659	0.000000e+00	1794
12	TraesCS5B01G031300	chr6B	94.640	541	29	0	2871	3411	77324753	77325293	0.000000e+00	839
13	TraesCS5B01G031300	chr4A	96.118	541	21	0	2871	3411	692373579	692374119	0.000000e+00	883
14	TraesCS5B01G031300	chr4A	87.438	406	21	14	2311	2710	692372915	692373296	1.130000e-119	440
15	TraesCS5B01G031300	chr4A	92.208	154	11	1	2707	2859	692373333	692373486	2.080000e-52	217

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	TraesCS5B01G031300	chr5B	34296217	34299652	3435	True	6346.000000	6346	100.000000	1	3436	1	chr5B.!!$R2	3435
1	TraesCS5B01G031300	chr5B	123789961	123793348	3387	True	5618.000000	5618	96.512000	1	3411	1	chr5B.!!$R3	3410
2	TraesCS5B01G031300	chr5B	353924449	353927822	3373	False	5561.000000	5561	96.278000	1	3411	1	chr5B.!!$F1	3410
3	TraesCS5B01G031300	chr5B	18187025	18190398	3373	True	5544.000000	5544	96.190000	1	3411	1	chr5B.!!$R1	3410
4	TraesCS5B01G031300	chr5B	514053710	514054864	1154	True	1832.000000	1832	95.076000	2234	3411	1	chr5B.!!$R4	1177
5	TraesCS5B01G031300	chr7B	664945990	664949381	3391	False	5705.000000	5705	96.954000	1	3411	1	chr7B.!!$F1	3410
6	TraesCS5B01G031300	chr7B	666618980	666622371	3391	True	5638.000000	5638	96.600000	1	3411	1	chr7B.!!$R2	3410
7	TraesCS5B01G031300	chr7B	379915259	379917830	2571	True	4329.000000	4329	97.047000	1	2573	1	chr7B.!!$R1	2572
8	TraesCS5B01G031300	chr3B	734220781	734224171	3390	False	5683.000000	5683	96.835000	1	3411	1	chr3B.!!$F1	3410
9	TraesCS5B01G031300	chr4B	522407395	522410157	2762	True	4654.000000	4654	97.105000	1	2758	1	chr4B.!!$R1	2757
10	TraesCS5B01G031300	chr3D	581476298	581478946	2648	True	4048.000000	4048	94.210000	1	2665	1	chr3D.!!$R1	2664
11	TraesCS5B01G031300	chr6B	77323085	77325293	2208	False	1316.500000	1794	91.089500	1279	3411	2	chr6B.!!$F1	2132
12	TraesCS5B01G031300	chr4A	692372915	692374119	1204	False	513.333333	883	91.921333	2311	3411	3	chr4A.!!$F1	1100

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
503	508	0.106708	GGCGATGATCAGTGGCCTTA	59.893	55.000	21.06	40.59	2.69	F
1010	1016	0.251297	CAGGTTTGGATGTGGGAGCA	60.251	55.000	0.00	0.00	4.26	F
1072	1078	1.078497	GGATGGGTCGCACATGACA	60.078	57.895	0.00	40.72	3.58	F
1752	1759	1.144913	ACTGGTTGAAGCTAAAGCCCA	59.855	47.619	8.34	43.38	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1734	1741	1.144913	ACTGGGCTTTAGCTTCAACCA	59.855	47.619	0.00	0.00	41.70	3.67	R
2138	2147	3.588955	CATCTTGTGGAATCGACTCACA	58.411	45.455	11.64	11.64	39.31	3.58	R
2313	2349	5.518128	CGTCTTGATTGTACTCCTCTTCATG	59.482	44.000	0.00	0.00	0.00	3.07	R
3416	3672	0.250338	AGAGGAAACCGTGAAGTGCC	60.250	55.000	0.00	0.00	0.00	5.01	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
79	80	9.138062	GTTATGTATGTTTGATTTGTTCATGCA	57.862	29.630	0.00	0.00	36.13	3.96
193	194	6.821665	CGGGGTAAGACTCAATCTATTTGAAA	59.178	38.462	0.00	0.00	43.64	2.69
279	284	1.337384	ACACCTATGCGCATGAGGGA	61.337	55.000	31.50	16.73	34.41	4.20
416	421	2.540515	CGATGACCGCACTTATTGACT	58.459	47.619	0.00	0.00	0.00	3.41
483	488	1.293498	CCGTGACCTTGGAGGACAG	59.707	63.158	0.07	0.00	40.51	3.51
503	508	0.106708	GGCGATGATCAGTGGCCTTA	59.893	55.000	21.06	0.00	40.59	2.69
557	562	3.555956	CGTAAGTGCTAATTGGCGAGATT	59.444	43.478	9.40	3.96	34.52	2.40
609	614	1.593787	CTCCTGAAGAAGGCGAGCA	59.406	57.895	0.00	0.00	46.92	4.26
683	688	2.579201	CTCCGGACGCCAATGAGT	59.421	61.111	0.00	0.00	0.00	3.41
695	700	2.223782	GCCAATGAGTTTGTTGTGCAGA	60.224	45.455	0.00	0.00	33.15	4.26
754	759	5.342866	AGGGTAGTGTTTCCAGATTCTACT	58.657	41.667	0.00	0.00	0.00	2.57
845	850	7.782897	TCAGGAGCACTAGCATACTTATATT	57.217	36.000	0.00	0.00	45.49	1.28
846	851	8.879427	TCAGGAGCACTAGCATACTTATATTA	57.121	34.615	0.00	0.00	45.49	0.98
945	950	2.181777	GCTCGACGAGGCATGTCA	59.818	61.111	25.31	0.00	36.11	3.58
967	972	0.620556	GGAAGAAGGGCACATCTGGA	59.379	55.000	0.00	0.00	0.00	3.86
968	973	1.213926	GGAAGAAGGGCACATCTGGAT	59.786	52.381	0.00	0.00	0.00	3.41
969	974	2.439507	GGAAGAAGGGCACATCTGGATA	59.560	50.000	0.00	0.00	0.00	2.59
1010	1016	0.251297	CAGGTTTGGATGTGGGAGCA	60.251	55.000	0.00	0.00	0.00	4.26
1051	1057	6.465321	CCCTAAGAAAAACAAGACACCTCCTA	60.465	42.308	0.00	0.00	0.00	2.94
1072	1078	1.078497	GGATGGGTCGCACATGACA	60.078	57.895	0.00	0.00	40.72	3.58
1290	1296	5.989168	TCATCTTGTGTTGTAAGTCGATTGT	59.011	36.000	0.00	0.00	0.00	2.71
1358	1365	2.746904	CACGTGACAGGAATATTTGGCA	59.253	45.455	10.90	0.00	0.00	4.92
1361	1368	3.620488	GTGACAGGAATATTTGGCAGGA	58.380	45.455	0.00	0.00	31.82	3.86
1626	1633	2.079088	TTGGGCCATCAAGCACTCCA	62.079	55.000	7.26	0.00	36.97	3.86
1752	1759	1.144913	ACTGGTTGAAGCTAAAGCCCA	59.855	47.619	8.34	0.00	43.38	5.36
2021	2028	2.432146	TGAAGATGAGGGAAGTGGATCG	59.568	50.000	0.00	0.00	0.00	3.69
2138	2147	8.629158	TGCATCTTTGTTATGTTGTAGAGTTTT	58.371	29.630	0.00	0.00	0.00	2.43
2390	2426	2.747460	GCGCCTGAGCCATCACAA	60.747	61.111	0.00	0.00	34.57	3.33
2443	2479	7.164803	AGAGGAAGGAAGAAGTGAATTAGTTG	58.835	38.462	0.00	0.00	0.00	3.16
2459	2495	8.630037	TGAATTAGTTGATACTAGATTCTCGCA	58.370	33.333	0.00	0.00	38.09	5.10
2719	2872	3.011818	TGCTGTTATGCTGTCATCCTTG	58.988	45.455	0.00	0.00	34.22	3.61
2721	2874	3.011818	CTGTTATGCTGTCATCCTTGCA	58.988	45.455	0.00	0.00	39.83	4.08
2744	2918	7.708322	TGCATTTTGCTGTTATGTTGAAGTTTA	59.292	29.630	0.75	0.00	45.31	2.01
2988	3243	8.830580	GCATTACATAGTTCAACTGACATACAT	58.169	33.333	0.00	0.00	0.00	2.29
3218	3473	3.368427	GCTTGGGTCGATATATAGCAGCA	60.368	47.826	0.00	0.00	0.00	4.41
3365	3621	3.885297	CGGGGACATAGCTTCATTGATTT	59.115	43.478	0.00	0.00	0.00	2.17
3407	3663	3.782523	AGGCCTATTCAAGTCCATCTGAA	59.217	43.478	1.29	0.00	0.00	3.02
3417	3673	4.469883	CATCTGAAGATGGGCGGG	57.530	61.111	11.76	0.00	46.09	6.13
3418	3674	1.895707	CATCTGAAGATGGGCGGGC	60.896	63.158	11.76	0.00	46.09	6.13
3419	3675	2.377810	ATCTGAAGATGGGCGGGCA	61.378	57.895	3.27	0.00	32.68	5.36
3420	3676	2.615227	ATCTGAAGATGGGCGGGCAC	62.615	60.000	3.27	0.00	32.68	5.01
3421	3677	3.329889	TGAAGATGGGCGGGCACT	61.330	61.111	3.27	0.00	0.00	4.40
3422	3678	2.044946	GAAGATGGGCGGGCACTT	60.045	61.111	3.27	5.79	0.00	3.16
3423	3679	2.044946	AAGATGGGCGGGCACTTC	60.045	61.111	3.27	0.86	0.00	3.01
3424	3680	2.819984	GAAGATGGGCGGGCACTTCA	62.820	60.000	20.78	5.82	37.48	3.02
3425	3681	3.134127	GATGGGCGGGCACTTCAC	61.134	66.667	3.27	0.00	0.00	3.18
3430	3686	3.284449	GCGGGCACTTCACGGTTT	61.284	61.111	0.00	0.00	0.00	3.27
3431	3687	2.943653	CGGGCACTTCACGGTTTC	59.056	61.111	0.00	0.00	0.00	2.78
3432	3688	2.613506	CGGGCACTTCACGGTTTCC	61.614	63.158	0.00	0.00	0.00	3.13
3433	3689	1.228154	GGGCACTTCACGGTTTCCT	60.228	57.895	0.00	0.00	0.00	3.36
3434	3690	1.235281	GGGCACTTCACGGTTTCCTC	61.235	60.000	0.00	0.00	0.00	3.71
3435	3691	0.250338	GGCACTTCACGGTTTCCTCT	60.250	55.000	0.00	0.00	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	67	7.259882	TCCTACAAATCATGCATGAACAAATC	58.740	34.615	31.79	0.00	40.69	2.17
79	80	1.202927	CCCCGCCATCCTACAAATCAT	60.203	52.381	0.00	0.00	0.00	2.45
155	156	4.272748	GTCTTACCCCGTTATTCTCAATGC	59.727	45.833	0.00	0.00	0.00	3.56
193	194	8.082242	GCAAAACTGACAAGTAATAACCAAGAT	58.918	33.333	0.00	0.00	34.77	2.40
279	284	0.465705	CCAGTCGTGGGCACTATGAT	59.534	55.000	0.00	0.00	40.67	2.45
416	421	1.053835	TGTGTCTCTGGCCTCCAACA	61.054	55.000	3.32	0.38	30.80	3.33
483	488	2.592861	GGCCACTGATCATCGCCC	60.593	66.667	14.12	2.60	33.30	6.13
503	508	4.219288	GGTCAAAGCTTCTCCATTGATTGT	59.781	41.667	0.00	0.00	34.62	2.71
557	562	1.039068	CCTGTCAATTGGCCAACACA	58.961	50.000	23.27	21.37	0.00	3.72
609	614	3.544684	TGCAACACTTTCTCACTGTCAT	58.455	40.909	0.00	0.00	0.00	3.06
695	700	0.107017	AGATATGCTTGGGCGTGCTT	60.107	50.000	0.00	0.00	42.25	3.91
705	710	6.701841	CGTTAACAGATACCACAGATATGCTT	59.298	38.462	6.39	0.00	0.00	3.91
754	759	5.922960	ATATCCACTGGGCTTTATTACCA	57.077	39.130	0.00	0.00	0.00	3.25
846	851	9.747898	TGACAATTTGGTTACTAATTACCTGAT	57.252	29.630	0.78	0.00	35.41	2.90
945	950	2.441001	CCAGATGTGCCCTTCTTCCTAT	59.559	50.000	0.00	0.00	0.00	2.57
967	972	1.618343	GCACCAAACAAAGCCACCTAT	59.382	47.619	0.00	0.00	0.00	2.57
968	973	1.036707	GCACCAAACAAAGCCACCTA	58.963	50.000	0.00	0.00	0.00	3.08
969	974	1.685355	GGCACCAAACAAAGCCACCT	61.685	55.000	0.00	0.00	46.26	4.00
1010	1016	4.778143	GGCGTCCAACGGGCATCT	62.778	66.667	1.33	0.00	42.82	2.90
1029	1035	7.501225	CCTTTAGGAGGTGTCTTGTTTTTCTTA	59.499	37.037	0.00	0.00	40.95	2.10
1030	1036	6.321435	CCTTTAGGAGGTGTCTTGTTTTTCTT	59.679	38.462	0.00	0.00	40.95	2.52
1051	1057	0.327924	TCATGTGCGACCCATCCTTT	59.672	50.000	0.00	0.00	0.00	3.11
1281	1287	4.633126	GCATCATATGGCATACAATCGACT	59.367	41.667	9.83	0.00	0.00	4.18
1358	1365	3.749954	GCATATCAGTGGGCATCTTTCCT	60.750	47.826	0.00	0.00	0.00	3.36
1361	1368	3.589951	AGCATATCAGTGGGCATCTTT	57.410	42.857	0.00	0.00	0.00	2.52
1626	1633	7.890127	TCTTTGATTCCACAAATCTATCCACTT	59.110	33.333	0.00	0.00	43.61	3.16
1734	1741	1.144913	ACTGGGCTTTAGCTTCAACCA	59.855	47.619	0.00	0.00	41.70	3.67
1752	1759	1.877443	CAATTCCGAACGGTTCCAACT	59.123	47.619	14.83	0.00	36.47	3.16
2021	2028	8.608844	TTGTTTTCCTAAGAGATTTCTCAGAC	57.391	34.615	10.07	0.00	45.21	3.51
2138	2147	3.588955	CATCTTGTGGAATCGACTCACA	58.411	45.455	11.64	11.64	39.31	3.58
2313	2349	5.518128	CGTCTTGATTGTACTCCTCTTCATG	59.482	44.000	0.00	0.00	0.00	3.07
2443	2479	7.527084	ACAAAGTTTGCGAGAATCTAGTATC	57.473	36.000	15.59	0.00	0.00	2.24
2479	2515	7.430793	CACGAATCAAACATAACAAAGTTCACA	59.569	33.333	0.00	0.00	0.00	3.58
2719	2872	6.529463	AACTTCAACATAACAGCAAAATGC	57.471	33.333	0.00	0.00	45.46	3.56
2721	2874	9.762933	ACATAAACTTCAACATAACAGCAAAAT	57.237	25.926	0.00	0.00	0.00	1.82
2988	3243	9.410556	GAACTATGTCCGTTAAAGTTTGTACTA	57.589	33.333	0.00	0.00	33.17	1.82
3218	3473	5.622460	CGCTAGATTATGAGCCCGACTTATT	60.622	44.000	0.00	0.00	35.13	1.40
3365	3621	0.830648	GGACGGATCATTGACTGGGA	59.169	55.000	0.00	0.00	0.00	4.37
3380	3636	1.941325	GACTTGAATAGGCCTGGACG	58.059	55.000	17.99	1.02	0.00	4.79
3407	3663	3.329889	TGAAGTGCCCGCCCATCT	61.330	61.111	0.00	0.00	0.00	2.90
3413	3669	3.249973	GAAACCGTGAAGTGCCCGC	62.250	63.158	0.00	0.00	0.00	6.13
3414	3670	2.613506	GGAAACCGTGAAGTGCCCG	61.614	63.158	0.00	0.00	0.00	6.13
3415	3671	1.228154	AGGAAACCGTGAAGTGCCC	60.228	57.895	0.00	0.00	0.00	5.36
3416	3672	0.250338	AGAGGAAACCGTGAAGTGCC	60.250	55.000	0.00	0.00	0.00	5.01
3417	3673	3.307379	AGAGGAAACCGTGAAGTGC	57.693	52.632	0.00	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.