AutoCloner

Multiple sequence alignment - TraesCS1D01G233700

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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	TraesCS1D01G233700	chr1D	100.000	4026	0	0	1	4026	322129517	322133542	0.000000e+00	7435.0
1	TraesCS1D01G233700	chr1D	79.724	1376	221	28	994	2330	322031899	322033255	0.000000e+00	942.0
2	TraesCS1D01G233700	chr1A	95.121	2234	81	9	894	3109	405819225	405821448	0.000000e+00	3496.0
3	TraesCS1D01G233700	chr1A	88.654	899	65	20	22	893	304941526	304940638	0.000000e+00	1061.0
4	TraesCS1D01G233700	chr1A	80.085	703	113	13	1026	1704	405792061	405792760	7.770000e-137	497.0
5	TraesCS1D01G233700	chr1A	85.476	420	29	14	3116	3513	405821625	405822034	3.750000e-110	409.0
6	TraesCS1D01G233700	chr1A	84.810	395	60	0	1778	2172	405798142	405798536	8.110000e-107	398.0
7	TraesCS1D01G233700	chr1A	91.813	171	12	1	3645	3813	405824429	405824599	1.870000e-58	237.0
8	TraesCS1D01G233700	chr1B	97.176	956	25	1	2163	3118	434747542	434748495	0.000000e+00	1615.0
9	TraesCS1D01G233700	chr1B	94.947	752	27	3	894	1635	434746777	434747527	0.000000e+00	1168.0
10	TraesCS1D01G233700	chr1B	78.977	1251	211	28	994	2206	434659745	434660981	0.000000e+00	806.0
11	TraesCS1D01G233700	chr1B	94.531	512	27	1	3513	4024	434750667	434751177	0.000000e+00	789.0
12	TraesCS1D01G233700	chr1B	94.601	426	7	8	3117	3528	434748719	434749142	0.000000e+00	645.0
13	TraesCS1D01G233700	chr1B	77.974	454	73	24	60	502	582338743	582339180	3.990000e-65	259.0
14	TraesCS1D01G233700	chr2A	89.904	941	40	11	1	897	83710502	83709573	0.000000e+00	1160.0
15	TraesCS1D01G233700	chr2A	85.006	907	82	35	9	893	758701831	758700957	0.000000e+00	872.0
16	TraesCS1D01G233700	chr7D	88.622	958	36	16	1	894	557396952	557396004	0.000000e+00	1098.0
17	TraesCS1D01G233700	chr7D	88.187	855	75	20	1	846	555607319	555608156	0.000000e+00	996.0
18	TraesCS1D01G233700	chr7D	95.522	67	3	0	3356	3422	386719264	386719198	1.530000e-19	108.0
19	TraesCS1D01G233700	chr3D	88.865	916	48	12	22	893	558009996	558009091	0.000000e+00	1077.0
20	TraesCS1D01G233700	chr3D	94.118	68	4	0	3356	3423	400694139	400694072	1.980000e-18	104.0
21	TraesCS1D01G233700	chr3D	79.562	137	28	0	3883	4019	302925313	302925177	9.210000e-17	99.0
22	TraesCS1D01G233700	chr3D	90.909	66	6	0	3356	3421	418756840	418756775	5.540000e-14	89.8
23	TraesCS1D01G233700	chr3D	80.000	115	21	2	3885	3999	307914657	307914769	2.580000e-12	84.2
24	TraesCS1D01G233700	chr4A	87.390	912	68	20	17	893	537295291	537296190	0.000000e+00	1003.0
25	TraesCS1D01G233700	chr4B	87.208	899	71	26	22	893	525696199	525695318	0.000000e+00	983.0
26	TraesCS1D01G233700	chr4B	80.000	140	22	4	3882	4020	636241255	636241389	9.210000e-17	99.0
27	TraesCS1D01G233700	chr4B	92.647	68	5	0	3356	3423	654471069	654471136	9.210000e-17	99.0
28	TraesCS1D01G233700	chr6B	85.037	675	67	16	249	894	156649692	156649023	0.000000e+00	656.0
29	TraesCS1D01G233700	chr7A	83.634	721	68	30	9	711	1753124	1753812	2.040000e-177	632.0
30	TraesCS1D01G233700	chr2B	80.392	459	61	27	4	450	715025796	715025355	5.020000e-84	322.0
31	TraesCS1D01G233700	chr2B	79.389	131	27	0	2668	2798	712826883	712827013	4.280000e-15	93.5
32	TraesCS1D01G233700	chr2B	89.855	69	5	2	3356	3423	11461942	11462009	1.990000e-13	87.9
33	TraesCS1D01G233700	chr5D	81.137	387	56	15	4	383	232601187	232600811	1.090000e-75	294.0
34	TraesCS1D01G233700	chr5D	92.647	68	4	1	3356	3423	582564	582630	3.310000e-16	97.1
35	TraesCS1D01G233700	chr5D	89.706	68	7	0	3356	3423	421851926	421851993	1.990000e-13	87.9
36	TraesCS1D01G233700	chr4D	80.851	141	20	5	3882	4020	496373092	496373227	1.980000e-18	104.0
37	TraesCS1D01G233700	chr3B	91.304	69	4	2	3356	3423	568427145	568427078	4.280000e-15	93.5

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	TraesCS1D01G233700	chr1D	322129517	322133542	4025	False	7435.000000	7435	100.000000	1	4026	1	chr1D.!!$F2	4025
1	TraesCS1D01G233700	chr1D	322031899	322033255	1356	False	942.000000	942	79.724000	994	2330	1	chr1D.!!$F1	1336
2	TraesCS1D01G233700	chr1A	405819225	405824599	5374	False	1380.666667	3496	90.803333	894	3813	3	chr1A.!!$F3	2919
3	TraesCS1D01G233700	chr1A	304940638	304941526	888	True	1061.000000	1061	88.654000	22	893	1	chr1A.!!$R1	871
4	TraesCS1D01G233700	chr1A	405792061	405792760	699	False	497.000000	497	80.085000	1026	1704	1	chr1A.!!$F1	678
5	TraesCS1D01G233700	chr1B	434746777	434751177	4400	False	1054.250000	1615	95.313750	894	4024	4	chr1B.!!$F3	3130
6	TraesCS1D01G233700	chr1B	434659745	434660981	1236	False	806.000000	806	78.977000	994	2206	1	chr1B.!!$F1	1212
7	TraesCS1D01G233700	chr2A	83709573	83710502	929	True	1160.000000	1160	89.904000	1	897	1	chr2A.!!$R1	896
8	TraesCS1D01G233700	chr2A	758700957	758701831	874	True	872.000000	872	85.006000	9	893	1	chr2A.!!$R2	884
9	TraesCS1D01G233700	chr7D	557396004	557396952	948	True	1098.000000	1098	88.622000	1	894	1	chr7D.!!$R2	893
10	TraesCS1D01G233700	chr7D	555607319	555608156	837	False	996.000000	996	88.187000	1	846	1	chr7D.!!$F1	845
11	TraesCS1D01G233700	chr3D	558009091	558009996	905	True	1077.000000	1077	88.865000	22	893	1	chr3D.!!$R4	871
12	TraesCS1D01G233700	chr4A	537295291	537296190	899	False	1003.000000	1003	87.390000	17	893	1	chr4A.!!$F1	876
13	TraesCS1D01G233700	chr4B	525695318	525696199	881	True	983.000000	983	87.208000	22	893	1	chr4B.!!$R1	871
14	TraesCS1D01G233700	chr6B	156649023	156649692	669	True	656.000000	656	85.037000	249	894	1	chr6B.!!$R1	645
15	TraesCS1D01G233700	chr7A	1753124	1753812	688	False	632.000000	632	83.634000	9	711	1	chr7A.!!$F1	702

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
683	905	2.029380	GGCCAAATAGCGTTGTTTCCTT	60.029	45.455	0.0	0.0	0.00	3.36	F
1750	2038	0.877649	CTGTCGAATGGATCTGCCGG	60.878	60.000	0.0	0.0	40.66	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1793	2087	0.252881	ACAGAGCCTCCCATCCTTGA	60.253	55.0	0.0	0.0	0.0	3.02	R
3557	5828	0.037590	AAAGCCGCTCACCACCAATA	59.962	50.0	0.0	0.0	0.0	1.90	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
251	362	9.837525	TTTTGTTTCAAATTTGATGAACCTTTG	57.162	25.926	23.47	0.00	36.57	2.77
463	644	7.538303	AATCAATGAACGCTTTTCAACTTTT	57.462	28.000	2.11	0.00	31.55	2.27
469	650	6.329496	TGAACGCTTTTCAACTTTTCTGAAT	58.671	32.000	0.00	0.00	32.98	2.57
683	905	2.029380	GGCCAAATAGCGTTGTTTCCTT	60.029	45.455	0.00	0.00	0.00	3.36
908	1137	2.420372	GCTCCCGAAAAAGATGTCCTTC	59.580	50.000	0.00	0.00	33.02	3.46
1246	1504	1.141019	GAACCCGACATGAGCGCTA	59.859	57.895	11.50	0.00	0.00	4.26
1323	1581	3.785499	CTCCGAGACGACGACGCA	61.785	66.667	7.30	0.00	43.96	5.24
1458	1740	1.376037	CCCCAAGAAGCCTCACGAC	60.376	63.158	0.00	0.00	0.00	4.34
1685	1973	3.259902	GGTTCGTCTGTTGGTTAGATCC	58.740	50.000	0.00	0.00	0.00	3.36
1688	1976	1.470979	CGTCTGTTGGTTAGATCCGGG	60.471	57.143	0.00	0.00	0.00	5.73
1750	2038	0.877649	CTGTCGAATGGATCTGCCGG	60.878	60.000	0.00	0.00	40.66	6.13
1864	2158	2.112297	GGCTTTGGACACCCGACA	59.888	61.111	0.00	0.00	34.29	4.35
1867	2161	0.521735	GCTTTGGACACCCGACAATC	59.478	55.000	0.00	0.00	34.29	2.67
1888	2182	2.809601	GCGTCGGCAGATTCGTGT	60.810	61.111	0.00	0.00	39.62	4.49
1945	2239	1.402259	AGATCACTAAGCGTCCAGTCG	59.598	52.381	0.00	0.00	0.00	4.18
1985	2279	8.651389	TGTTGGAGATCTTATGGAGGTTATTAG	58.349	37.037	0.00	0.00	0.00	1.73
2024	2318	0.531200	GTTGTCTACTCCAGGGACCG	59.469	60.000	0.00	0.00	0.00	4.79
2034	2331	1.452108	CAGGGACCGGCAATCTTCC	60.452	63.158	0.00	0.00	0.00	3.46
2064	2361	2.422093	CCTATCCTTCTGCCTGGAAACC	60.422	54.545	0.00	0.00	35.81	3.27
2292	2597	8.791327	TGTATTTCTGTGAAAATCAGCTATCA	57.209	30.769	0.00	0.00	33.48	2.15
2308	2613	8.766000	TCAGCTATCAACTTTACGTTTTGATA	57.234	30.769	15.21	15.21	39.92	2.15
2336	2641	9.672673	AGTAGCATGTCTGATTTTATAACTGTT	57.327	29.630	0.00	0.00	0.00	3.16
2338	2643	7.253422	AGCATGTCTGATTTTATAACTGTTGC	58.747	34.615	2.69	0.00	0.00	4.17
2353	2658	5.695851	ACTGTTGCAGAGGAGTTTTATTG	57.304	39.130	2.91	0.00	35.18	1.90
2536	2841	1.341531	ACCGCTATGAGATGGCAGTAC	59.658	52.381	0.00	0.00	36.44	2.73
2815	3125	2.950673	GACGGCACCAAAATCGCA	59.049	55.556	0.00	0.00	0.00	5.10
2985	3295	2.079170	TGGTGGCAAATGTTCAAGGA	57.921	45.000	0.00	0.00	0.00	3.36
3279	3992	1.581934	TGTTGTCTTTGCTCTGGACG	58.418	50.000	0.00	0.00	33.21	4.79
3347	4067	0.734889	TCCGTCCCGAATTACTCGTC	59.265	55.000	0.00	0.00	46.65	4.20
3351	4071	0.742505	TCCCGAATTACTCGTCGCAT	59.257	50.000	0.00	0.00	46.65	4.73
3425	4155	2.954792	AGTAATTCCGGACGGAGGTAT	58.045	47.619	13.64	2.10	46.06	2.73
3557	5828	3.755378	AGAAAGCAATGCACGAGAAAGAT	59.245	39.130	8.35	0.00	0.00	2.40
3691	8067	4.081420	AGACCCTGTATGTGAAGCTTAGTG	60.081	45.833	0.00	0.00	0.00	2.74
3742	8118	7.224949	GCCTTAATCACAAGACTCACCTTATAC	59.775	40.741	0.00	0.00	0.00	1.47
3779	8155	2.289072	CGAGACCTTCCTGCTTGAGAAA	60.289	50.000	0.00	0.00	0.00	2.52
3808	8184	9.612620	AAAAGTCATGCGATTTCTTAAACTAAG	57.387	29.630	0.00	0.00	37.13	2.18
3815	8191	8.561738	TGCGATTTCTTAAACTAAGGAAGAAT	57.438	30.769	0.00	0.00	36.75	2.40
3834	8210	8.950210	GGAAGAATAGTGATCTGAAATGTTTCA	58.050	33.333	7.84	7.84	44.31	2.69
3877	8253	2.752903	GGTGGCAACCGTGATATTTCTT	59.247	45.455	0.00	0.00	36.51	2.52
3880	8256	5.227152	GTGGCAACCGTGATATTTCTTTTT	58.773	37.500	0.00	0.00	0.00	1.94
3881	8257	5.344933	GTGGCAACCGTGATATTTCTTTTTC	59.655	40.000	0.00	0.00	0.00	2.29
3883	8259	4.557301	GCAACCGTGATATTTCTTTTTCGG	59.443	41.667	0.00	0.00	41.95	4.30
3916	8292	3.795561	CAAGCCTTGAACTTGTAGACG	57.204	47.619	0.00	0.00	39.73	4.18
3927	8303	9.931210	CTTGAACTTGTAGACGAAAACTAAATT	57.069	29.630	0.00	0.00	0.00	1.82
3935	8311	6.954487	AGACGAAAACTAAATTGAACCCTT	57.046	33.333	0.00	0.00	0.00	3.95
3952	8328	4.371681	ACCCTTAGCTCCTAATTCCTGAA	58.628	43.478	0.00	0.00	0.00	3.02
3955	8331	6.068794	ACCCTTAGCTCCTAATTCCTGAAATT	60.069	38.462	0.00	0.00	40.67	1.82
3957	8333	7.998964	CCCTTAGCTCCTAATTCCTGAAATTAA	59.001	37.037	0.00	0.00	38.92	1.40
3969	8345	6.642707	TCCTGAAATTAACACACCGAATTT	57.357	33.333	0.00	0.00	35.90	1.82
3979	8355	5.818136	ACACACCGAATTTATTGATCCAG	57.182	39.130	0.00	0.00	0.00	3.86
3989	8365	9.929180	CGAATTTATTGATCCAGGTCTATTCTA	57.071	33.333	0.00	0.00	0.00	2.10
4004	8380	6.100668	GTCTATTCTAAACCTTGAGAGCGTT	58.899	40.000	0.00	0.00	0.00	4.84

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
443	624	6.329496	TCAGAAAAGTTGAAAAGCGTTCATT	58.671	32.000	6.69	0.00	0.00	2.57
463	644	8.640651	TCCATCAGATTTGAAAAACAATTCAGA	58.359	29.630	0.00	0.00	40.21	3.27
469	650	9.447157	AAAAAGTCCATCAGATTTGAAAAACAA	57.553	25.926	0.00	0.00	36.78	2.83
505	692	5.726729	TCGCAAAAATGGAAAAAGTTTCC	57.273	34.783	12.00	12.00	39.03	3.13
645	866	4.028993	TGGCCCTTCCTTTAGTACAAAG	57.971	45.455	0.00	3.45	35.26	2.77
683	905	8.161425	AGACAGGCTACCTTTGTTATCTTTTTA	58.839	33.333	0.00	0.00	0.00	1.52
1323	1581	3.829601	GAGAATATGTCCTCCACTCGGAT	59.170	47.826	0.00	0.00	41.79	4.18
1458	1740	1.621814	TGGAACTCAAGGTAGGGTTCG	59.378	52.381	0.00	0.00	38.94	3.95
1617	1905	1.598130	GTCGCCTTGAAGCAGTGGT	60.598	57.895	0.00	0.00	0.00	4.16
1648	1936	0.597568	AACCGATCGACAACCGTACA	59.402	50.000	18.66	0.00	39.75	2.90
1685	1973	0.745845	CAGAATGCAGTCTTCCCCCG	60.746	60.000	15.18	0.00	0.00	5.73
1688	1976	1.372087	CGCCAGAATGCAGTCTTCCC	61.372	60.000	15.18	4.75	31.97	3.97
1793	2087	0.252881	ACAGAGCCTCCCATCCTTGA	60.253	55.000	0.00	0.00	0.00	3.02
1864	2158	2.298158	AATCTGCCGACGCCGAGATT	62.298	55.000	2.87	2.87	35.70	2.40
1867	2161	2.956964	GAATCTGCCGACGCCGAG	60.957	66.667	0.00	0.00	38.22	4.63
1945	2239	7.222872	AGATCTCCAACATCAACATTATCCTC	58.777	38.462	0.00	0.00	0.00	3.71
1985	2279	4.281898	ACAGATAGGTACACAAACCCAC	57.718	45.455	0.00	0.00	40.71	4.61
2024	2318	1.087501	GAACCACTCGGAAGATTGCC	58.912	55.000	0.00	0.00	39.22	4.52
2034	2331	2.482142	GCAGAAGGATAGGAACCACTCG	60.482	54.545	0.00	0.00	0.00	4.18
2064	2361	0.320247	AGAGCAAGTTCACCTCTGCG	60.320	55.000	0.00	0.00	34.82	5.18
2292	2597	7.718272	TGCTACTGTATCAAAACGTAAAGTT	57.282	32.000	0.00	0.00	46.76	2.66
2308	2613	9.102757	CAGTTATAAAATCAGACATGCTACTGT	57.897	33.333	12.55	0.00	35.84	3.55
2336	2641	4.144297	ACTTGCAATAAAACTCCTCTGCA	58.856	39.130	0.00	0.00	37.98	4.41
2338	2643	4.919754	GCAACTTGCAATAAAACTCCTCTG	59.080	41.667	8.97	0.00	44.26	3.35
2353	2658	5.047847	TCCTCGTACTAATATGCAACTTGC	58.952	41.667	6.82	6.82	45.29	4.01
2371	2676	2.679355	TTGAAAACATTGCGTCCTCG	57.321	45.000	0.00	0.00	40.37	4.63
2536	2841	1.067846	TGCAGTAGGACGCTGTTACAG	60.068	52.381	8.18	8.18	36.42	2.74
2728	3038	1.882623	GGAGAAGCTTCTTTGGTGTGG	59.117	52.381	29.02	0.00	37.73	4.17
2815	3125	3.413105	AGTAAGAAGGCCTCCATCTCT	57.587	47.619	5.23	0.66	29.65	3.10
2985	3295	1.428869	AGAAGCTCTCCACAACACCT	58.571	50.000	0.00	0.00	0.00	4.00
3279	3992	2.029844	GCAGACCGCAGAACCAGTC	61.030	63.158	0.00	0.00	41.79	3.51
3557	5828	0.037590	AAAGCCGCTCACCACCAATA	59.962	50.000	0.00	0.00	0.00	1.90
3593	5864	2.852495	TTCGCTCCCTGTGAATCGGC	62.852	60.000	0.00	0.00	39.91	5.54
3691	8067	5.221126	GGATCCAAGGTAAAAGACATCATGC	60.221	44.000	6.95	0.00	0.00	4.06
3759	8135	3.409026	TTTCTCAAGCAGGAAGGTCTC	57.591	47.619	0.00	0.00	0.00	3.36
3779	8155	8.352942	AGTTTAAGAAATCGCATGACTTTTCTT	58.647	29.630	22.40	22.40	45.45	2.52
3808	8184	8.950210	TGAAACATTTCAGATCACTATTCTTCC	58.050	33.333	2.89	0.00	41.88	3.46
3877	8253	6.037726	GGCTTGTTTTAGACTTTTCCGAAAA	58.962	36.000	6.16	6.16	0.00	2.29
3880	8256	4.457466	AGGCTTGTTTTAGACTTTTCCGA	58.543	39.130	0.00	0.00	24.99	4.55
3881	8257	4.830826	AGGCTTGTTTTAGACTTTTCCG	57.169	40.909	0.00	0.00	24.99	4.30
3883	8259	7.258441	AGTTCAAGGCTTGTTTTAGACTTTTC	58.742	34.615	25.39	4.18	40.65	2.29
3910	8286	7.430992	AGGGTTCAATTTAGTTTTCGTCTAC	57.569	36.000	0.00	0.00	0.00	2.59
3916	8292	7.176865	AGGAGCTAAGGGTTCAATTTAGTTTTC	59.823	37.037	0.00	0.00	0.00	2.29
3927	8303	4.164221	CAGGAATTAGGAGCTAAGGGTTCA	59.836	45.833	0.00	0.00	29.02	3.18
3935	8311	8.325787	TGTGTTAATTTCAGGAATTAGGAGCTA	58.674	33.333	0.00	0.00	40.36	3.32
3952	8328	8.744652	TGGATCAATAAATTCGGTGTGTTAATT	58.255	29.630	0.00	0.00	0.00	1.40
3955	8331	6.317642	CCTGGATCAATAAATTCGGTGTGTTA	59.682	38.462	0.00	0.00	0.00	2.41
3957	8333	4.640201	CCTGGATCAATAAATTCGGTGTGT	59.360	41.667	0.00	0.00	0.00	3.72
3979	8355	5.044558	CGCTCTCAAGGTTTAGAATAGACC	58.955	45.833	0.00	0.00	45.66	3.85
3989	8365	0.472471	TGGGAACGCTCTCAAGGTTT	59.528	50.000	0.00	0.00	0.00	3.27
4004	8380	2.817258	CGTTAGCAATCCTTGTTTGGGA	59.183	45.455	0.00	0.00	37.26	4.37

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.