AutoCloner

Multiple sequence alignment - TraesCS3B01G306700

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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	TraesCS3B01G306700	chr3B	100.000	3564	0	0	1	3564	492742155	492745718	0.000000e+00	6582.0
1	TraesCS3B01G306700	chr3B	95.434	1336	44	5	3	1335	622479021	622480342	0.000000e+00	2113.0
2	TraesCS3B01G306700	chr3B	85.618	591	35	20	2900	3461	738268215	738267646	3.090000e-160	575.0
3	TraesCS3B01G306700	chr3B	85.789	570	47	15	2900	3460	502497043	502496499	1.110000e-159	573.0
4	TraesCS3B01G306700	chr3B	84.456	579	62	21	7	583	245923848	245923296	2.420000e-151	545.0
5	TraesCS3B01G306700	chr3B	89.516	372	31	5	2536	2900	622480342	622480712	6.970000e-127	464.0
6	TraesCS3B01G306700	chr3B	91.509	212	18	0	7	218	492745028	492744817	3.480000e-75	292.0
7	TraesCS3B01G306700	chr3B	90.476	210	18	1	1	210	650021397	650021190	3.500000e-70	276.0
8	TraesCS3B01G306700	chr2B	97.970	2906	43	6	1	2906	113193091	113195980	0.000000e+00	5025.0
9	TraesCS3B01G306700	chr2B	92.116	241	19	0	2663	2903	113193308	113193068	1.230000e-89	340.0
10	TraesCS3B01G306700	chr2B	91.981	212	15	2	7	218	113195949	113195740	2.690000e-76	296.0
11	TraesCS3B01G306700	chr7B	98.134	2573	34	3	1	2571	221893465	221890905	0.000000e+00	4473.0
12	TraesCS3B01G306700	chr7B	92.083	240	17	2	2663	2900	221893246	221893485	1.590000e-88	337.0
13	TraesCS3B01G306700	chr7B	90.535	243	19	4	2663	2903	246615188	246614948	5.740000e-83	318.0
14	TraesCS3B01G306700	chr7B	100.000	68	0	0	2563	2630	221888817	221888750	3.740000e-25	126.0
15	TraesCS3B01G306700	chr5B	94.214	1832	79	11	766	2584	577345620	577347437	0.000000e+00	2771.0
16	TraesCS3B01G306700	chr5B	95.082	61	3	0	706	766	577334637	577334697	2.930000e-16	97.1
17	TraesCS3B01G306700	chr5B	100.000	34	0	0	3461	3494	202862178	202862211	2.970000e-06	63.9
18	TraesCS3B01G306700	chr5A	92.625	1817	80	22	775	2581	590667761	590669533	0.000000e+00	2564.0
19	TraesCS3B01G306700	chr5A	86.824	592	45	10	2900	3462	426021505	426022092	6.490000e-177	630.0
20	TraesCS3B01G306700	chr5D	91.974	1844	81	25	766	2581	469718839	469720643	0.000000e+00	2523.0
21	TraesCS3B01G306700	chrUn	86.610	590	32	20	2900	3460	106117903	106118474	3.040000e-170	608.0
22	TraesCS3B01G306700	chr2A	87.885	520	45	9	10	514	476214473	476213957	2.370000e-166	595.0
23	TraesCS3B01G306700	chr2A	92.883	281	19	1	230	510	476212110	476212389	1.190000e-109	407.0
24	TraesCS3B01G306700	chr3D	89.126	469	28	10	127	583	284207026	284206569	2.400000e-156	562.0
25	TraesCS3B01G306700	chr3D	89.200	250	23	3	2663	2910	284204280	284204033	3.460000e-80	309.0
26	TraesCS3B01G306700	chr1A	93.889	360	12	2	230	580	444122390	444122748	5.240000e-148	534.0
27	TraesCS3B01G306700	chr1A	92.050	239	16	2	2663	2899	445887020	445886783	2.050000e-87	333.0
28	TraesCS3B01G306700	chr1A	90.535	243	18	3	2660	2901	374566336	374566574	2.070000e-82	316.0
29	TraesCS3B01G306700	chr1A	88.053	226	24	3	1	224	445886802	445887026	7.590000e-67	265.0
30	TraesCS3B01G306700	chr1A	92.000	75	4	2	3458	3531	125929539	125929466	1.750000e-18	104.0
31	TraesCS3B01G306700	chr1A	79.375	160	22	6	3053	3202	244202725	244202567	6.290000e-18	102.0
32	TraesCS3B01G306700	chr1D	93.611	360	13	2	230	580	344590628	344590986	2.440000e-146	529.0
33	TraesCS3B01G306700	chr1D	95.890	73	3	0	3461	3533	209791218	209791146	6.250000e-23	119.0
34	TraesCS3B01G306700	chr1D	95.833	48	2	0	3464	3511	301354226	301354273	1.060000e-10	78.7
35	TraesCS3B01G306700	chr1B	93.388	363	14	2	230	583	466094267	466093906	2.440000e-146	529.0
36	TraesCS3B01G306700	chr1B	90.556	360	24	2	230	580	682437264	682437622	5.390000e-128	468.0
37	TraesCS3B01G306700	chr6A	90.456	241	20	3	2663	2903	352812230	352812467	7.430000e-82	315.0
38	TraesCS3B01G306700	chr4B	87.281	228	25	4	1	226	166648026	166648251	1.270000e-64	257.0

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	TraesCS3B01G306700	chr3B	492742155	492745718	3563	False	6582.0	6582	100.0000	1	3564	1	chr3B.!!$F1	3563
1	TraesCS3B01G306700	chr3B	622479021	622480712	1691	False	1288.5	2113	92.4750	3	2900	2	chr3B.!!$F2	2897
2	TraesCS3B01G306700	chr3B	738267646	738268215	569	True	575.0	575	85.6180	2900	3461	1	chr3B.!!$R5	561
3	TraesCS3B01G306700	chr3B	502496499	502497043	544	True	573.0	573	85.7890	2900	3460	1	chr3B.!!$R3	560
4	TraesCS3B01G306700	chr3B	245923296	245923848	552	True	545.0	545	84.4560	7	583	1	chr3B.!!$R1	576
5	TraesCS3B01G306700	chr2B	113193091	113195980	2889	False	5025.0	5025	97.9700	1	2906	1	chr2B.!!$F1	2905
6	TraesCS3B01G306700	chr2B	113193068	113195949	2881	True	318.0	340	92.0485	7	2903	2	chr2B.!!$R1	2896
7	TraesCS3B01G306700	chr7B	221888750	221893465	4715	True	2299.5	4473	99.0670	1	2630	2	chr7B.!!$R2	2629
8	TraesCS3B01G306700	chr5B	577345620	577347437	1817	False	2771.0	2771	94.2140	766	2584	1	chr5B.!!$F3	1818
9	TraesCS3B01G306700	chr5A	590667761	590669533	1772	False	2564.0	2564	92.6250	775	2581	1	chr5A.!!$F2	1806
10	TraesCS3B01G306700	chr5A	426021505	426022092	587	False	630.0	630	86.8240	2900	3462	1	chr5A.!!$F1	562
11	TraesCS3B01G306700	chr5D	469718839	469720643	1804	False	2523.0	2523	91.9740	766	2581	1	chr5D.!!$F1	1815
12	TraesCS3B01G306700	chrUn	106117903	106118474	571	False	608.0	608	86.6100	2900	3460	1	chrUn.!!$F1	560
13	TraesCS3B01G306700	chr2A	476213957	476214473	516	True	595.0	595	87.8850	10	514	1	chr2A.!!$R1	504
14	TraesCS3B01G306700	chr3D	284204033	284207026	2993	True	435.5	562	89.1630	127	2910	2	chr3D.!!$R1	2783

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
85	86	0.037590	TACTTGCGCAAGGGGTTCAT	59.962	50.000	43.26	27.77	42.53	2.57	F
440	519	0.802222	CATCATCGTCGACCTTGCGT	60.802	55.000	10.58	0.00	0.00	5.24	F
984	1220	1.064017	TGTGCTTTCACTTCCCTTGGT	60.064	47.619	0.00	0.00	43.49	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1585	3251	0.694771	TGAAGAGCATCAGCCCACTT	59.305	50.000	0.00	0.00	43.56	3.16	R
1727	3400	1.814394	TGCAAGAATACCTGCAGCAAG	59.186	47.619	8.66	0.00	33.06	4.01	R
2796	7349	1.512156	CGTACTTGCGCAAGGGGTTT	61.512	55.000	43.26	29.05	42.53	3.27	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
38	39	7.232941	AGTTGAGTGACACTTTAGTACCACTAT	59.767	37.037	10.01	0.00	38.82	2.12
85	86	0.037590	TACTTGCGCAAGGGGTTCAT	59.962	50.000	43.26	27.77	42.53	2.57
440	519	0.802222	CATCATCGTCGACCTTGCGT	60.802	55.000	10.58	0.00	0.00	5.24
984	1220	1.064017	TGTGCTTTCACTTCCCTTGGT	60.064	47.619	0.00	0.00	43.49	3.67
985	1221	1.609072	GTGCTTTCACTTCCCTTGGTC	59.391	52.381	0.00	0.00	40.03	4.02
986	1222	1.214175	TGCTTTCACTTCCCTTGGTCA	59.786	47.619	0.00	0.00	0.00	4.02
987	1223	2.158475	TGCTTTCACTTCCCTTGGTCAT	60.158	45.455	0.00	0.00	0.00	3.06
988	1224	2.489722	GCTTTCACTTCCCTTGGTCATC	59.510	50.000	0.00	0.00	0.00	2.92
989	1225	3.754965	CTTTCACTTCCCTTGGTCATCA	58.245	45.455	0.00	0.00	0.00	3.07
990	1226	2.859165	TCACTTCCCTTGGTCATCAC	57.141	50.000	0.00	0.00	0.00	3.06
1249	2826	5.886609	TGACATAGGAAATGTTTTCCTCCA	58.113	37.500	21.54	13.78	45.32	3.86
1585	3251	9.428097	GTGATATTCAGCATCATCAATGTACTA	57.572	33.333	0.00	0.00	37.71	1.82
1721	3394	6.037786	TCAGTATCAGTGAAAAGTAGTGGG	57.962	41.667	0.00	0.00	0.00	4.61
1727	3400	3.191371	CAGTGAAAAGTAGTGGGGCATTC	59.809	47.826	0.00	0.00	0.00	2.67
1860	3840	2.183555	GGGTCCGCAAGTACGAGG	59.816	66.667	0.00	0.00	34.06	4.63
2533	4982	1.870402	CATTACGCGGCCATGTTCATA	59.130	47.619	12.47	0.00	0.00	2.15
2541	4990	1.532868	GGCCATGTTCATATCGCTCAC	59.467	52.381	0.00	0.00	0.00	3.51
2778	7331	5.287752	GTCAGCAAATACGTAGACGAAATCA	59.712	40.000	9.41	0.00	43.02	2.57
2796	7349	6.698329	CGAAATCATACATACGGACCAAAGTA	59.302	38.462	0.00	0.00	0.00	2.24
2990	7543	3.740115	AGCACCGACTGTTAAAATGAGT	58.260	40.909	0.00	0.00	0.00	3.41
3044	7603	2.267961	CCGTCCAAGTACAGCCCC	59.732	66.667	0.00	0.00	0.00	5.80
3045	7604	2.267961	CGTCCAAGTACAGCCCCC	59.732	66.667	0.00	0.00	0.00	5.40
3046	7605	2.267961	GTCCAAGTACAGCCCCCG	59.732	66.667	0.00	0.00	0.00	5.73
3047	7606	3.006728	TCCAAGTACAGCCCCCGG	61.007	66.667	0.00	0.00	0.00	5.73
3091	7650	2.496817	CAGTAGCAGGACGCCTCC	59.503	66.667	0.00	0.00	44.04	4.30
3093	7652	0.752009	CAGTAGCAGGACGCCTCCTA	60.752	60.000	3.74	0.00	46.30	2.94
3094	7653	0.186386	AGTAGCAGGACGCCTCCTAT	59.814	55.000	3.74	0.00	46.30	2.57
3106	7665	1.203523	GCCTCCTATCATAGTCGCCAG	59.796	57.143	0.00	0.00	0.00	4.85
3137	7696	1.202132	CGTTTGTCACCCACAACACAG	60.202	52.381	0.00	0.00	45.12	3.66
3163	7744	2.041755	TCTGAGAGGAGCAGGAGTGTTA	59.958	50.000	0.00	0.00	34.20	2.41
3174	7755	4.100189	AGCAGGAGTGTTAGTATAGCTTGG	59.900	45.833	0.00	0.00	0.00	3.61
3192	7773	1.188219	GGCAGGATCGAGGGATAGCA	61.188	60.000	0.00	0.00	31.51	3.49
3256	7837	2.815647	GCCGGACTTCAGAAGCGG	60.816	66.667	19.64	19.64	37.26	5.52
3257	7838	2.657237	CCGGACTTCAGAAGCGGT	59.343	61.111	16.98	0.00	31.91	5.68
3258	7839	1.446272	CCGGACTTCAGAAGCGGTC	60.446	63.158	16.98	6.74	31.91	4.79
3259	7840	1.289066	CGGACTTCAGAAGCGGTCA	59.711	57.895	10.33	0.00	0.00	4.02
3260	7841	1.009389	CGGACTTCAGAAGCGGTCAC	61.009	60.000	10.33	0.00	0.00	3.67
3261	7842	0.033504	GGACTTCAGAAGCGGTCACA	59.966	55.000	10.33	0.00	0.00	3.58
3262	7843	1.423395	GACTTCAGAAGCGGTCACAG	58.577	55.000	10.33	0.00	0.00	3.66
3263	7844	0.034059	ACTTCAGAAGCGGTCACAGG	59.966	55.000	10.33	0.00	0.00	4.00
3264	7845	1.294659	CTTCAGAAGCGGTCACAGGC	61.295	60.000	0.00	0.00	0.00	4.85
3265	7846	3.114616	CAGAAGCGGTCACAGGCG	61.115	66.667	0.00	0.00	0.00	5.52
3266	7847	4.379243	AGAAGCGGTCACAGGCGG	62.379	66.667	0.00	0.00	0.00	6.13
3302	7898	1.068083	CGCTACACCCGCATGATCT	59.932	57.895	0.00	0.00	0.00	2.75
3339	7935	0.253044	TAGCAAAGTAGCAGCAGGGG	59.747	55.000	0.00	0.00	36.85	4.79
3340	7936	1.002134	GCAAAGTAGCAGCAGGGGA	60.002	57.895	0.00	0.00	0.00	4.81
3385	7981	3.112075	CGCACGACGGCAGAACAT	61.112	61.111	0.00	0.00	38.44	2.71
3420	8016	2.367202	GGATCCCGTGGCAGAGGAA	61.367	63.158	9.33	0.00	32.26	3.36
3434	8030	1.480954	AGAGGAAACGCGTGTGGATAT	59.519	47.619	14.98	0.00	34.13	1.63
3469	8066	2.892425	CGCTTGACGGCTGGGATC	60.892	66.667	0.00	0.00	38.44	3.36
3470	8067	2.514824	GCTTGACGGCTGGGATCC	60.515	66.667	1.92	1.92	0.00	3.36
3471	8068	2.989639	CTTGACGGCTGGGATCCA	59.010	61.111	15.23	0.00	0.00	3.41
3498	8095	4.881440	GCGGCATGCTGGGATCCA	62.881	66.667	27.34	0.00	41.73	3.41
3527	8124	4.176752	GCGTGGGGATCCAGGGTC	62.177	72.222	15.23	0.00	46.08	4.46
3528	8125	3.849951	CGTGGGGATCCAGGGTCG	61.850	72.222	15.23	6.85	45.05	4.79
3529	8126	3.480133	GTGGGGATCCAGGGTCGG	61.480	72.222	15.23	0.00	45.05	4.79
3530	8127	4.815973	TGGGGATCCAGGGTCGGG	62.816	72.222	15.23	0.00	38.32	5.14
3551	8148	4.813526	CGACGACGAGGCCGAGTG	62.814	72.222	10.85	6.28	42.66	3.51
3552	8149	4.477975	GACGACGAGGCCGAGTGG	62.478	72.222	10.85	11.78	39.50	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
103	104	7.360861	CCAAGTCAGCAAATACGTAGATGAAAA	60.361	37.037	13.00	0.00	0.00	2.29
211	214	2.321263	CATTGTTCCGGCGTTTTTACC	58.679	47.619	6.01	0.00	0.00	2.85
440	519	2.086869	CTGGAGGTACTTAACGACGGA	58.913	52.381	0.00	0.00	41.55	4.69
699	899	3.179265	CGCTACCGGACTTGTGCG	61.179	66.667	9.46	10.64	37.57	5.34
700	900	3.488090	GCGCTACCGGACTTGTGC	61.488	66.667	9.46	9.48	34.32	4.57
702	902	1.019278	CAATGCGCTACCGGACTTGT	61.019	55.000	9.46	0.00	37.72	3.16
703	903	1.715585	CAATGCGCTACCGGACTTG	59.284	57.895	9.46	0.00	37.72	3.16
984	1220	4.679905	GCAGTCATGTCTGATGAGTGATGA	60.680	45.833	21.91	0.00	46.88	2.92
985	1221	3.556365	GCAGTCATGTCTGATGAGTGATG	59.444	47.826	21.91	3.74	46.88	3.07
986	1222	3.197116	TGCAGTCATGTCTGATGAGTGAT	59.803	43.478	21.91	0.00	46.88	3.06
987	1223	2.564062	TGCAGTCATGTCTGATGAGTGA	59.436	45.455	21.91	5.89	46.88	3.41
988	1224	2.968675	TGCAGTCATGTCTGATGAGTG	58.031	47.619	21.91	13.05	46.73	3.51
989	1225	3.908643	ATGCAGTCATGTCTGATGAGT	57.091	42.857	21.91	1.67	37.61	3.41
990	1226	4.211584	GCTAATGCAGTCATGTCTGATGAG	59.788	45.833	21.91	14.76	37.61	2.90
1585	3251	0.694771	TGAAGAGCATCAGCCCACTT	59.305	50.000	0.00	0.00	43.56	3.16
1727	3400	1.814394	TGCAAGAATACCTGCAGCAAG	59.186	47.619	8.66	0.00	33.06	4.01
2677	7230	6.388619	AGGGTGAATACTAGTTCATTTGGT	57.611	37.500	0.00	0.00	39.99	3.67
2678	7231	6.992715	CCTAGGGTGAATACTAGTTCATTTGG	59.007	42.308	0.00	0.00	39.99	3.28
2680	7233	6.157994	TGCCTAGGGTGAATACTAGTTCATTT	59.842	38.462	11.72	0.00	39.99	2.32
2778	7331	5.430886	GGGTTTACTTTGGTCCGTATGTAT	58.569	41.667	0.00	0.00	0.00	2.29
2796	7349	1.512156	CGTACTTGCGCAAGGGGTTT	61.512	55.000	43.26	29.05	42.53	3.27
2916	7469	5.680619	TGTTGCTACTTGGTGGATATAAGG	58.319	41.667	0.00	0.00	0.00	2.69
2990	7543	2.202905	ACGTCCGTGTTTTGGCGA	60.203	55.556	0.00	0.00	32.72	5.54
3047	7606	0.601558	TCTACAGGACGGCTGTTGTC	59.398	55.000	6.27	0.00	36.37	3.18
3091	7650	2.163412	GGAGAGCTGGCGACTATGATAG	59.837	54.545	0.00	0.00	0.00	2.08
3092	7651	2.163509	GGAGAGCTGGCGACTATGATA	58.836	52.381	0.00	0.00	0.00	2.15
3093	7652	0.965439	GGAGAGCTGGCGACTATGAT	59.035	55.000	0.00	0.00	0.00	2.45
3094	7653	0.395724	TGGAGAGCTGGCGACTATGA	60.396	55.000	0.00	0.00	0.00	2.15
3106	7665	1.996191	GTGACAAACGAGATGGAGAGC	59.004	52.381	0.00	0.00	0.00	4.09
3137	7696	0.108233	CCTGCTCCTCTCAGACTTGC	60.108	60.000	0.00	0.00	33.54	4.01
3163	7744	2.560542	CTCGATCCTGCCAAGCTATACT	59.439	50.000	0.00	0.00	0.00	2.12
3174	7755	0.681733	TTGCTATCCCTCGATCCTGC	59.318	55.000	0.00	0.00	0.00	4.85
3192	7773	2.591715	GTGCTCGCTGTGTGGGTT	60.592	61.111	0.00	0.00	0.00	4.11
3198	7779	1.501337	ATGTGTGTGTGCTCGCTGTG	61.501	55.000	0.56	0.00	0.00	3.66
3302	7898	0.186630	TACACTATGGGGCGCCTCTA	59.813	55.000	29.93	15.79	0.00	2.43
3377	7973	2.185004	ACCACACCACTATGTTCTGC	57.815	50.000	0.00	0.00	0.00	4.26
3420	8016	0.810031	GGCTCATATCCACACGCGTT	60.810	55.000	10.22	0.00	0.00	4.84
3481	8078	4.881440	TGGATCCCAGCATGCCGC	62.881	66.667	15.66	0.00	42.91	6.53
3482	8079	2.593725	CTGGATCCCAGCATGCCG	60.594	66.667	15.66	3.33	45.13	5.69
3510	8107	4.176752	GACCCTGGATCCCCACGC	62.177	72.222	9.90	0.00	37.58	5.34
3511	8108	3.849951	CGACCCTGGATCCCCACG	61.850	72.222	9.90	4.51	37.58	4.94
3512	8109	3.480133	CCGACCCTGGATCCCCAC	61.480	72.222	9.90	0.00	37.58	4.61
3513	8110	4.815973	CCCGACCCTGGATCCCCA	62.816	72.222	9.90	0.00	40.95	4.96
3534	8131	4.813526	CACTCGGCCTCGTCGTCG	62.814	72.222	0.00	0.00	37.69	5.12
3535	8132	4.477975	CCACTCGGCCTCGTCGTC	62.478	72.222	0.00	0.00	37.69	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.