AutoCloner

Multiple sequence alignment - TraesCS3A01G469100

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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	TraesCS3A01G469100	chr3A	100.000	2627	0	0	1	2627	701855550	701858176	0.000000e+00	4852.0
1	TraesCS3A01G469100	chr3A	94.298	2648	113	12	1	2627	700567122	700569752	0.000000e+00	4019.0
2	TraesCS3A01G469100	chr3A	81.860	215	31	7	1003	1216	697585522	697585315	9.660000e-40	174.0
3	TraesCS3A01G469100	chr3A	76.793	237	45	8	2387	2619	699250613	699250383	9.870000e-25	124.0
4	TraesCS3A01G469100	chr3A	91.803	61	5	0	1083	1143	699455084	699455024	4.660000e-13	86.1
5	TraesCS3A01G469100	chr3D	95.220	2636	96	9	1	2627	567225130	567222516	0.000000e+00	4143.0
6	TraesCS3A01G469100	chr3B	94.478	2644	126	9	1	2627	754980652	754983292	0.000000e+00	4056.0
7	TraesCS3A01G469100	chr3B	76.112	607	125	16	1702	2301	756185900	756185307	1.530000e-77	300.0
8	TraesCS3A01G469100	chr3B	79.535	215	36	7	1003	1216	749685597	749685390	2.110000e-31	147.0
9	TraesCS3A01G469100	chr3B	82.911	158	27	0	1059	1216	752920186	752920029	2.730000e-30	143.0
10	TraesCS3A01G469100	chrUn	94.487	2630	128	8	14	2627	41111960	41109332	0.000000e+00	4037.0
11	TraesCS3A01G469100	chr5D	72.655	757	167	32	1774	2505	547932579	547931838	5.690000e-52	215.0

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	TraesCS3A01G469100	chr3A	701855550	701858176	2626	False	4852	4852	100.000	1	2627	1	chr3A.!!$F2	2626
1	TraesCS3A01G469100	chr3A	700567122	700569752	2630	False	4019	4019	94.298	1	2627	1	chr3A.!!$F1	2626
2	TraesCS3A01G469100	chr3D	567222516	567225130	2614	True	4143	4143	95.220	1	2627	1	chr3D.!!$R1	2626
3	TraesCS3A01G469100	chr3B	754980652	754983292	2640	False	4056	4056	94.478	1	2627	1	chr3B.!!$F1	2626
4	TraesCS3A01G469100	chr3B	756185307	756185900	593	True	300	300	76.112	1702	2301	1	chr3B.!!$R3	599
5	TraesCS3A01G469100	chrUn	41109332	41111960	2628	True	4037	4037	94.487	14	2627	1	chrUn.!!$R1	2613
6	TraesCS3A01G469100	chr5D	547931838	547932579	741	True	215	215	72.655	1774	2505	1	chr5D.!!$R1	731

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
103	104	1.069978	TGGACAGCGTCTCATTGAACA	59.930	47.619	8.26	0.0	32.47	3.18	F
345	353	1.447643	GCATCGGACAGCCCATAGT	59.552	57.895	0.00	0.0	34.14	2.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1343	1357	0.040425	GGTGTCGGTCATGTTGTTGC	60.040	55.0	0.00	0.0	0.00	4.17	R
1723	1753	0.527113	CACGCATTGGCCAGAATGAA	59.473	50.0	19.62	0.0	39.69	2.57	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
103	104	1.069978	TGGACAGCGTCTCATTGAACA	59.930	47.619	8.26	0.00	32.47	3.18
152	153	1.586042	ACAACAGCTTTGCGTTGCG	60.586	52.632	13.05	0.00	42.16	4.85
170	171	2.202623	GGTCTTCGAGCGACGCAT	60.203	61.111	23.70	7.08	42.26	4.73
242	247	7.998964	AGGGAAGTTCTAAGAGAGATAAGAGAG	59.001	40.741	2.25	0.00	32.88	3.20
288	296	1.673033	CCACGTCAACTCCTGGTGATC	60.673	57.143	2.23	0.00	0.00	2.92
343	351	2.421314	CGCATCGGACAGCCCATA	59.579	61.111	0.00	0.00	34.14	2.74
345	353	1.447643	GCATCGGACAGCCCATAGT	59.552	57.895	0.00	0.00	34.14	2.12
602	612	5.654650	TCAGAAAGCTTGAACTTGGGTAAAA	59.345	36.000	0.00	0.00	0.00	1.52
630	640	6.070995	TGTCTTTGTTACCGTCATTCCTAGAT	60.071	38.462	0.00	0.00	0.00	1.98
692	702	4.002906	AGCTCCGTCAATAAGTGTTTCA	57.997	40.909	0.00	0.00	0.00	2.69
767	778	6.015350	TGGAAACGTCAAATAGGGCATAAAAA	60.015	34.615	0.00	0.00	0.00	1.94
814	826	7.476540	AAGAAAATATTGTTTAGGGTCCCAC	57.523	36.000	11.55	0.00	0.00	4.61
845	857	9.317936	GAAATATATTTTTCAGAAGGGCCAAAG	57.682	33.333	11.92	0.00	35.98	2.77
1245	1259	3.194968	ACGAAGAATACATCCTCACCGTT	59.805	43.478	0.00	0.00	0.00	4.44
1330	1344	1.552799	TTCCTGCGATGGCCTTCTCA	61.553	55.000	16.03	13.26	38.85	3.27
1343	1357	1.761784	CCTTCTCATCCTCTCCAGGTG	59.238	57.143	0.00	0.00	41.28	4.00
1356	1370	0.314935	CCAGGTGCAACAACATGACC	59.685	55.000	3.64	0.00	39.98	4.02
1386	1400	7.942341	ACCATTGATTTCTCAGTTTGTAACCTA	59.058	33.333	0.00	0.00	31.68	3.08
1459	1473	2.260844	ATTGGGGATGTACTCGCATG	57.739	50.000	0.00	0.00	38.54	4.06
1495	1509	1.355971	TCGATTGCTACTTGAACGCC	58.644	50.000	0.00	0.00	0.00	5.68
1545	1559	3.262420	ACTTGGCTACTATGTCTTTGCG	58.738	45.455	0.00	0.00	0.00	4.85
1610	1629	5.182001	AGTCAACATCACAATGCTTTACCTC	59.818	40.000	0.00	0.00	36.26	3.85
1700	1730	6.293626	GCTTCAGAGTGAAAGCAAAGTGATAA	60.294	38.462	2.41	0.00	35.73	1.75
1712	1742	7.948278	AGCAAAGTGATAATAGTATTCGACC	57.052	36.000	0.00	0.00	0.00	4.79
1723	1753	3.511477	AGTATTCGACCCCATAGCTGAT	58.489	45.455	0.00	0.00	0.00	2.90
1992	2022	2.893489	TGCTCTTGCTAGTCAGTTCTGA	59.107	45.455	0.00	0.00	40.48	3.27
2002	2032	3.687125	AGTCAGTTCTGATCGGTGTCTA	58.313	45.455	5.80	0.00	0.00	2.59
2083	2113	8.336801	ACTTCTTTTTGTCTAAATATCGGCTT	57.663	30.769	0.00	0.00	0.00	4.35
2084	2114	8.793592	ACTTCTTTTTGTCTAAATATCGGCTTT	58.206	29.630	0.00	0.00	0.00	3.51
2530	2593	9.995003	TTGTTAGAAATTTTTATGGCTCATGTT	57.005	25.926	0.00	0.00	0.00	2.71
2619	2682	2.015587	GTGTGTTTCCGGTTTGTACCA	58.984	47.619	0.00	0.00	45.31	3.25

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
103	104	1.078848	GAAGAGGCGCATGTCAGGT	60.079	57.895	10.83	0.00	0.00	4.00
152	153	3.701604	ATGCGTCGCTCGAAGACCC	62.702	63.158	19.50	6.73	42.86	4.46
343	351	5.426689	TCTGAATCTTCCTTGTATGCACT	57.573	39.130	0.00	0.00	0.00	4.40
345	353	5.877012	GTCTTCTGAATCTTCCTTGTATGCA	59.123	40.000	0.00	0.00	0.00	3.96
389	397	1.879575	AGATCCCTCCACGAATCCAA	58.120	50.000	0.00	0.00	0.00	3.53
517	526	4.586306	TGGACTATGGACAGAGTACAGA	57.414	45.455	7.86	0.00	38.46	3.41
602	612	4.454504	GGAATGACGGTAACAAAGACACAT	59.545	41.667	0.00	0.00	0.00	3.21
646	656	0.116342	TGGCAGACTTCCTGGTAGGA	59.884	55.000	5.28	0.00	44.10	2.94
657	667	1.703411	GGAGCTAGATCTGGCAGACT	58.297	55.000	29.91	19.78	39.73	3.24
716	726	5.505654	CCATTTCGTTGTTGAGTGCTACTTT	60.506	40.000	0.00	0.00	0.00	2.66
798	809	4.180723	TCCTTAGTGGGACCCTAAACAAT	58.819	43.478	13.00	0.00	36.20	2.71
845	857	4.141756	TGCAGGAGATGAGAGAATTCCTTC	60.142	45.833	0.65	0.83	36.15	3.46
981	995	1.691196	TCTTGGTTGTTGCTCCCTTG	58.309	50.000	0.00	0.00	0.00	3.61
1077	1091	1.564818	ACTAGGATCTCCCAGACGACA	59.435	52.381	0.00	0.00	37.41	4.35
1330	1344	1.067295	TTGTTGCACCTGGAGAGGAT	58.933	50.000	0.00	0.00	42.93	3.24
1343	1357	0.040425	GGTGTCGGTCATGTTGTTGC	60.040	55.000	0.00	0.00	0.00	4.17
1356	1370	5.149273	CAAACTGAGAAATCAATGGTGTCG	58.851	41.667	0.00	0.00	0.00	4.35
1386	1400	1.160137	GAGCAAATTGACGAGTGGCT	58.840	50.000	0.00	0.00	0.00	4.75
1459	1473	1.945394	TCGATACTCGCCAGTAGGTTC	59.055	52.381	0.00	0.00	38.56	3.62
1483	1497	4.041740	TGTAGCTATGGCGTTCAAGTAG	57.958	45.455	0.00	0.00	44.37	2.57
1495	1509	3.871006	TCAGGCGTTTCATTGTAGCTATG	59.129	43.478	0.00	0.00	0.00	2.23
1545	1559	1.374758	CGACTGGTGAGAGCCCAAC	60.375	63.158	0.00	0.00	0.00	3.77
1610	1629	2.681706	CAGGCTATCGCATACCAAGAG	58.318	52.381	0.00	0.00	38.10	2.85
1700	1730	4.673968	TCAGCTATGGGGTCGAATACTAT	58.326	43.478	0.00	0.00	0.00	2.12
1712	1742	2.818432	GCCAGAATGAATCAGCTATGGG	59.182	50.000	9.81	0.63	39.69	4.00
1723	1753	0.527113	CACGCATTGGCCAGAATGAA	59.473	50.000	19.62	0.00	39.69	2.57
1992	2022	4.397103	TGTCAACGTAAGATAGACACCGAT	59.603	41.667	0.00	0.00	39.49	4.18
2002	2032	6.037172	GCTTACCATCATTGTCAACGTAAGAT	59.963	38.462	15.51	3.23	43.62	2.40
2083	2113	3.207265	TGCTGGACAAGACTTTGCTAA	57.793	42.857	0.00	0.00	37.85	3.09
2084	2114	2.928801	TGCTGGACAAGACTTTGCTA	57.071	45.000	0.00	0.00	37.85	3.49
2194	2244	4.878397	GCAGCTCATAAGGATACAACAGTT	59.122	41.667	0.00	0.00	41.41	3.16
2195	2245	4.080919	TGCAGCTCATAAGGATACAACAGT	60.081	41.667	0.00	0.00	41.41	3.55
2196	2246	4.445453	TGCAGCTCATAAGGATACAACAG	58.555	43.478	0.00	0.00	41.41	3.16
2197	2247	4.486125	TGCAGCTCATAAGGATACAACA	57.514	40.909	0.00	0.00	41.41	3.33
2198	2248	4.635765	TGTTGCAGCTCATAAGGATACAAC	59.364	41.667	1.17	0.00	41.41	3.32
2199	2249	4.842574	TGTTGCAGCTCATAAGGATACAA	58.157	39.130	1.17	0.00	41.41	2.41
2200	2250	4.486125	TGTTGCAGCTCATAAGGATACA	57.514	40.909	1.17	0.00	41.41	2.29
2201	2251	5.303971	AGATGTTGCAGCTCATAAGGATAC	58.696	41.667	1.17	0.00	0.00	2.24
2202	2252	5.557576	AGATGTTGCAGCTCATAAGGATA	57.442	39.130	1.17	0.00	0.00	2.59
2203	2253	4.434545	AGATGTTGCAGCTCATAAGGAT	57.565	40.909	1.17	0.00	0.00	3.24
2204	2254	3.920231	AGATGTTGCAGCTCATAAGGA	57.080	42.857	1.17	0.00	0.00	3.36
2205	2255	5.303165	TCATAGATGTTGCAGCTCATAAGG	58.697	41.667	1.17	0.00	30.76	2.69
2206	2256	6.856135	TTCATAGATGTTGCAGCTCATAAG	57.144	37.500	1.17	0.00	30.76	1.73
2207	2257	7.255346	CCAATTCATAGATGTTGCAGCTCATAA	60.255	37.037	1.17	0.00	30.76	1.90
2250	2300	4.811969	TGCAAAATGAAGAAGATGCCAT	57.188	36.364	0.00	0.00	33.01	4.40
2530	2593	4.227197	ACTCTTTGACTCAAGGAAGAGGA	58.773	43.478	17.59	0.00	45.81	3.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.