AutoCloner

Multiple sequence alignment - TraesCS6D01G372400

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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	TraesCS6D01G372400	chr6D	100.000	2687	0	0	1	2687	457594175	457591489	0.000000e+00	4963
1	TraesCS6D01G372400	chr6A	94.383	1727	83	6	968	2687	604458268	604456549	0.000000e+00	2639
2	TraesCS6D01G372400	chr6A	89.590	951	69	22	1	925	604459215	604458269	0.000000e+00	1181
3	TraesCS6D01G372400	chr6A	77.273	836	94	46	409	1201	604516758	604517540	1.160000e-108	403
4	TraesCS6D01G372400	chr6B	91.377	1322	84	17	1379	2687	696023084	696021780	0.000000e+00	1783
5	TraesCS6D01G372400	chr6B	90.598	585	46	5	70	650	696023659	696023080	0.000000e+00	767
6	TraesCS6D01G372400	chr2D	77.992	1813	277	83	907	2657	21639713	21641465	0.000000e+00	1026
7	TraesCS6D01G372400	chr2D	85.022	928	119	14	910	1831	21743042	21743955	0.000000e+00	926
8	TraesCS6D01G372400	chr2D	84.565	920	122	14	910	1824	21770777	21771681	0.000000e+00	894
9	TraesCS6D01G372400	chr2D	86.111	828	108	7	1007	1831	21617462	21618285	0.000000e+00	885
10	TraesCS6D01G372400	chr2D	75.135	740	114	45	1955	2662	21618387	21619088	1.570000e-72	283
11	TraesCS6D01G372400	chr2D	76.531	392	59	17	1955	2325	21744082	21744461	1.640000e-42	183
12	TraesCS6D01G372400	chr2D	76.020	392	57	21	1955	2325	21771817	21772192	4.600000e-38	169
13	TraesCS6D01G372400	chr2B	85.565	859	114	9	978	1831	34867117	34866264	0.000000e+00	891
14	TraesCS6D01G372400	chr2A	85.681	852	111	8	988	1831	23826124	23826972	0.000000e+00	887
15	TraesCS6D01G372400	chr2A	84.307	924	128	12	910	1831	23864282	23865190	0.000000e+00	887

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	TraesCS6D01G372400	chr6D	457591489	457594175	2686	True	4963.0	4963	100.0000	1	2687	1	chr6D.!!$R1	2686
1	TraesCS6D01G372400	chr6A	604456549	604459215	2666	True	1910.0	2639	91.9865	1	2687	2	chr6A.!!$R1	2686
2	TraesCS6D01G372400	chr6A	604516758	604517540	782	False	403.0	403	77.2730	409	1201	1	chr6A.!!$F1	792
3	TraesCS6D01G372400	chr6B	696021780	696023659	1879	True	1275.0	1783	90.9875	70	2687	2	chr6B.!!$R1	2617
4	TraesCS6D01G372400	chr2D	21639713	21641465	1752	False	1026.0	1026	77.9920	907	2657	1	chr2D.!!$F1	1750
5	TraesCS6D01G372400	chr2D	21617462	21619088	1626	False	584.0	885	80.6230	1007	2662	2	chr2D.!!$F2	1655
6	TraesCS6D01G372400	chr2D	21743042	21744461	1419	False	554.5	926	80.7765	910	2325	2	chr2D.!!$F3	1415
7	TraesCS6D01G372400	chr2D	21770777	21772192	1415	False	531.5	894	80.2925	910	2325	2	chr2D.!!$F4	1415
8	TraesCS6D01G372400	chr2B	34866264	34867117	853	True	891.0	891	85.5650	978	1831	1	chr2B.!!$R1	853
9	TraesCS6D01G372400	chr2A	23826124	23826972	848	False	887.0	887	85.6810	988	1831	1	chr2A.!!$F1	843
10	TraesCS6D01G372400	chr2A	23864282	23865190	908	False	887.0	887	84.3070	910	1831	1	chr2A.!!$F2	921

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
961	1049	0.659427	TTCCTATCTACGACACGCCG	59.341	55.0	0.0	0.0	0.0	6.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1859	1953	2.935849	CACACACACACACACACTACAT	59.064	45.455	0.0	0.0	0.0	2.29	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
45	47	2.597578	ATACCCCAAACAACACCCTC	57.402	50.000	0.00	0.00	0.00	4.30
65	67	7.173907	CACCCTCCTACATGCTCTAAATTAATG	59.826	40.741	0.00	0.00	0.00	1.90
73	75	8.681486	ACATGCTCTAAATTAATGTCTATGCA	57.319	30.769	0.00	0.00	0.00	3.96
206	212	8.890472	TGTTATCTGACTGGGGCTATATTATTT	58.110	33.333	0.00	0.00	0.00	1.40
207	213	9.384764	GTTATCTGACTGGGGCTATATTATTTC	57.615	37.037	0.00	0.00	0.00	2.17
330	336	3.120649	GGCACGCCGAATATTTCTATGAC	60.121	47.826	0.00	0.00	0.00	3.06
436	454	7.094975	GGTGTATGTTAATGCTTCGCCATATAA	60.095	37.037	0.00	0.00	0.00	0.98
514	543	9.689976	CACATTTTACATGGTAGAAAAATCACA	57.310	29.630	0.00	0.00	31.05	3.58
545	577	0.891373	GAGGCTCCCCTTCTTTTTGC	59.109	55.000	2.15	0.00	43.12	3.68
550	582	1.000171	CTCCCCTTCTTTTTGCTGCAC	60.000	52.381	0.00	0.00	0.00	4.57
551	583	0.752054	CCCCTTCTTTTTGCTGCACA	59.248	50.000	0.00	0.00	0.00	4.57
614	653	5.830912	TGCTTCATCGTTTTCAGAAATGTT	58.169	33.333	0.00	0.00	34.18	2.71
645	684	1.210204	AAGCAGGCTGGGGAGATCAA	61.210	55.000	17.64	0.00	0.00	2.57
715	755	7.492669	TGATGATTAGCTAGTTTTCTTTCCTCG	59.507	37.037	0.00	0.00	0.00	4.63
758	798	8.887036	TTCCATAGCATGTAGTAGTAACAATG	57.113	34.615	0.00	0.00	0.00	2.82
811	884	7.957002	ACTATTCATGTCATCCTAGTTGGTAG	58.043	38.462	0.00	0.00	37.07	3.18
842	915	6.241207	TCAATTACAGCTTGCACTAACTTC	57.759	37.500	0.00	0.00	0.00	3.01
843	916	5.762711	TCAATTACAGCTTGCACTAACTTCA	59.237	36.000	0.00	0.00	0.00	3.02
952	1040	5.005779	CAGCAACGTGAACATTCCTATCTAC	59.994	44.000	0.00	0.00	0.00	2.59
959	1047	3.351020	ACATTCCTATCTACGACACGC	57.649	47.619	0.00	0.00	0.00	5.34
960	1048	2.034305	ACATTCCTATCTACGACACGCC	59.966	50.000	0.00	0.00	0.00	5.68
961	1049	0.659427	TTCCTATCTACGACACGCCG	59.341	55.000	0.00	0.00	0.00	6.46
986	1074	3.489229	GCTCCCAAATTAAATCGAGCACC	60.489	47.826	0.00	0.00	41.80	5.01
1005	1093	3.244345	CACCGTACATACTTACAATGGCG	59.756	47.826	0.00	0.00	0.00	5.69
1074	1168	5.937540	ACCAATCAACAACGATGATAGTGAA	59.062	36.000	0.00	0.00	36.53	3.18
1077	1171	7.430211	CCAATCAACAACGATGATAGTGAAATG	59.570	37.037	0.00	2.42	36.53	2.32
1085	1179	6.112734	ACGATGATAGTGAAATGGCAGTTAA	58.887	36.000	0.00	0.00	0.00	2.01
1086	1180	6.258727	ACGATGATAGTGAAATGGCAGTTAAG	59.741	38.462	0.00	0.00	0.00	1.85
1089	1183	3.525800	AGTGAAATGGCAGTTAAGGGT	57.474	42.857	0.00	0.00	0.00	4.34
1114	1208	1.375523	GTGCCAACTCCTACCACGG	60.376	63.158	0.00	0.00	0.00	4.94
1212	1306	1.147600	GTCCTTCACCAACCACGGT	59.852	57.895	0.00	0.00	41.07	4.83
1292	1386	2.673610	CGTGCCTCTTCTTCTCCTTCAG	60.674	54.545	0.00	0.00	0.00	3.02
1639	1733	1.025041	GAAGGGCATCGGATTCAACC	58.975	55.000	0.00	0.00	0.00	3.77
1644	1738	0.451783	GCATCGGATTCAACCACACC	59.548	55.000	0.00	0.00	0.00	4.16
1795	1889	4.140947	AGCATGTAAATATGATGGGGTGGT	60.141	41.667	0.00	0.00	0.00	4.16
1804	1898	2.588620	TGATGGGGTGGTTGTTGTTAC	58.411	47.619	0.00	0.00	0.00	2.50
1811	1905	2.223548	GGTGGTTGTTGTTACCGTTTCC	60.224	50.000	0.00	0.00	38.55	3.13
1827	1921	3.129638	CGTTTCCTTTTTGTTCTGGTGGA	59.870	43.478	0.00	0.00	0.00	4.02
1938	2038	1.131218	CTGACACTGCGTGCATTCG	59.869	57.895	8.31	0.00	36.98	3.34
2109	2244	4.438797	CAGAGAAACACATGAAGTTTTGCG	59.561	41.667	17.52	7.58	39.15	4.85
2668	2864	5.024555	GCTTTGATTTCTCATTAGTGCGAC	58.975	41.667	0.00	0.00	0.00	5.19
2684	2880	3.684788	GTGCGACTATTCTTCACATGGTT	59.315	43.478	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	4.090819	GGTGTTGTTTGGGGTATTATGGT	58.909	43.478	0.00	0.00	0.00	3.55
65	67	8.807948	ATTTGGGGTATTATATGTGCATAGAC	57.192	34.615	0.00	0.00	0.00	2.59
73	75	6.272792	TCCGGTGTATTTGGGGTATTATATGT	59.727	38.462	0.00	0.00	0.00	2.29
134	136	4.908601	TGGAAGAATGTTAGCTCCTGAA	57.091	40.909	0.00	0.00	0.00	3.02
206	212	5.106442	CACGTACTATATGTTGTGCCAAGA	58.894	41.667	0.00	0.00	30.84	3.02
207	213	4.868171	ACACGTACTATATGTTGTGCCAAG	59.132	41.667	0.00	0.00	37.34	3.61
296	302	1.650912	GCGTGCCTGATATTGCCTG	59.349	57.895	0.00	0.00	0.00	4.85
394	407	3.620427	ACACCTTGTTCGTATATGGCA	57.380	42.857	0.00	0.00	0.00	4.92
436	454	5.437289	TTCGTGCATTCAGATTTTGTTCT	57.563	34.783	0.00	0.00	0.00	3.01
514	543	0.988063	GGAGCCTCTTGGGAAAGAGT	59.012	55.000	13.02	0.00	43.62	3.24
550	582	3.607439	CCAATAGTTATTCGCGTGCTTG	58.393	45.455	5.77	0.45	0.00	4.01
551	583	2.031683	GCCAATAGTTATTCGCGTGCTT	59.968	45.455	5.77	0.00	0.00	3.91
614	653	1.299648	CCTGCTTGATTCCCCGTGA	59.700	57.895	0.00	0.00	0.00	4.35
645	684	5.427036	TTTTAACTCGCGTCAATTTCCTT	57.573	34.783	5.77	0.00	0.00	3.36
676	716	5.210715	GCTAATCATCAGCTTGTGCATAAC	58.789	41.667	0.00	0.00	42.74	1.89
715	755	2.705730	GAAGTCTTCTTCCAGGAAGGC	58.294	52.381	26.42	15.06	45.19	4.35
744	784	9.469239	GCACGTTAATTTCATTGTTACTACTAC	57.531	33.333	0.00	0.00	0.00	2.73
745	785	9.426837	AGCACGTTAATTTCATTGTTACTACTA	57.573	29.630	0.00	0.00	0.00	1.82
747	787	7.480542	CCAGCACGTTAATTTCATTGTTACTAC	59.519	37.037	0.00	0.00	0.00	2.73
811	884	7.752695	AGTGCAAGCTGTAATTGAATTAGTAC	58.247	34.615	0.00	0.00	0.00	2.73
842	915	7.261325	TCAACTCTCTAGCTAGCTGTATTTTG	58.739	38.462	27.68	20.07	0.00	2.44
843	916	7.411486	TCAACTCTCTAGCTAGCTGTATTTT	57.589	36.000	27.68	10.09	0.00	1.82
959	1047	0.744281	ATTTAATTTGGGAGCGCCGG	59.256	50.000	2.29	0.00	33.83	6.13
960	1048	1.596954	CGATTTAATTTGGGAGCGCCG	60.597	52.381	2.29	0.00	33.83	6.46
961	1049	1.673920	TCGATTTAATTTGGGAGCGCC	59.326	47.619	2.29	0.00	0.00	6.53
966	1054	2.680841	CGGTGCTCGATTTAATTTGGGA	59.319	45.455	0.00	0.00	42.43	4.37
986	1074	4.357142	AGACGCCATTGTAAGTATGTACG	58.643	43.478	0.00	0.00	0.00	3.67
1005	1093	5.066968	ACGATGGAGAAGAAGAAGAAGAC	57.933	43.478	0.00	0.00	0.00	3.01
1074	1168	1.680860	GCCGTACCCTTAACTGCCATT	60.681	52.381	0.00	0.00	0.00	3.16
1077	1171	0.743345	CTGCCGTACCCTTAACTGCC	60.743	60.000	0.00	0.00	0.00	4.85
1114	1208	2.329379	GACACTCGACATGACCTTGTC	58.671	52.381	0.00	1.33	42.10	3.18
1212	1306	0.606604	GGTTGGAGGTCTCGCACTTA	59.393	55.000	0.00	0.00	0.00	2.24
1264	1358	3.760035	GAAGAGGCACGCGGAGGA	61.760	66.667	12.47	0.00	0.00	3.71
1292	1386	1.272781	GTGACTGACTATGCTGTCGC	58.727	55.000	0.00	0.00	38.94	5.19
1639	1733	1.127567	TTCTGGGGAGGAGTGGTGTG	61.128	60.000	0.00	0.00	0.00	3.82
1644	1738	0.326264	CAACCTTCTGGGGAGGAGTG	59.674	60.000	0.00	0.00	40.03	3.51
1716	1810	5.163864	TGCGTGTCAACTATCTATGCTTTTG	60.164	40.000	0.00	0.00	0.00	2.44
1717	1811	4.935205	TGCGTGTCAACTATCTATGCTTTT	59.065	37.500	0.00	0.00	0.00	2.27
1767	1861	5.124457	CCCCATCATATTTACATGCTAGCAC	59.876	44.000	22.07	0.00	0.00	4.40
1795	1889	5.780984	ACAAAAAGGAAACGGTAACAACAA	58.219	33.333	0.00	0.00	0.00	2.83
1804	1898	3.443976	CACCAGAACAAAAAGGAAACGG	58.556	45.455	0.00	0.00	0.00	4.44
1811	1905	8.166422	ACTACTAAATCCACCAGAACAAAAAG	57.834	34.615	0.00	0.00	0.00	2.27
1859	1953	2.935849	CACACACACACACACACTACAT	59.064	45.455	0.00	0.00	0.00	2.29
1938	2038	5.118642	ACAAGATGCAAGAAGAAAAGAGC	57.881	39.130	0.00	0.00	0.00	4.09
1979	2105	6.961359	TCACTACTTTGACATAATGGAACG	57.039	37.500	0.00	0.00	0.00	3.95
2158	2295	3.953612	ACTTGTGCAGTTGATTTCTTGGA	59.046	39.130	0.00	0.00	27.32	3.53
2171	2310	4.194640	AGGATGCTTACATACTTGTGCAG	58.805	43.478	0.00	0.00	45.89	4.41
2550	2742	9.342308	CTTGGTGGTTGATTCTTACATATGTAT	57.658	33.333	16.16	2.43	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.