AutoCloner

Multiple sequence alignment - TraesCS3D01G219400

Loading Multiple Alignment...

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	TraesCS3D01G219400	chr3D	100.000	2903	0	0	1	2903	298585549	298582647	0.000000e+00	5361.0
1	TraesCS3D01G219400	chr3A	93.893	2145	81	11	74	2203	396612199	396610090	0.000000e+00	3190.0
2	TraesCS3D01G219400	chr3A	94.737	38	2	0	44	81	396612257	396612220	3.120000e-05	60.2
3	TraesCS3D01G219400	chr3B	92.398	1447	42	25	707	2114	394089184	394087767	0.000000e+00	2001.0
4	TraesCS3D01G219400	chr3B	93.304	687	36	6	2220	2903	247563568	247562889	0.000000e+00	1005.0
5	TraesCS3D01G219400	chr3B	96.244	426	15	1	280	705	394089904	394089480	0.000000e+00	697.0
6	TraesCS3D01G219400	chr3B	88.768	276	13	12	4	274	394090249	394089987	3.610000e-84	322.0
7	TraesCS3D01G219400	chr2D	97.661	684	16	0	2220	2903	135490111	135490794	0.000000e+00	1175.0
8	TraesCS3D01G219400	chr2D	95.608	683	28	1	2221	2903	48329954	48330634	0.000000e+00	1094.0
9	TraesCS3D01G219400	chr7D	97.234	687	17	2	2217	2903	81664592	81663908	0.000000e+00	1162.0
10	TraesCS3D01G219400	chr6D	94.178	687	33	5	2221	2903	362922068	362921385	0.000000e+00	1040.0
11	TraesCS3D01G219400	chr6A	93.459	688	40	3	2221	2903	596149568	596150255	0.000000e+00	1016.0
12	TraesCS3D01G219400	chr4B	93.208	692	41	3	2217	2903	142045114	142044424	0.000000e+00	1013.0
13	TraesCS3D01G219400	chr1A	93.343	691	34	5	2217	2903	553053410	553054092	0.000000e+00	1011.0
14	TraesCS3D01G219400	chr2B	93.033	689	41	5	2220	2903	607076092	607076778	0.000000e+00	1000.0

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	TraesCS3D01G219400	chr3D	298582647	298585549	2902	True	5361.000000	5361	100.000	1	2903	1	chr3D.!!$R1	2902
1	TraesCS3D01G219400	chr3A	396610090	396612257	2167	True	1625.100000	3190	94.315	44	2203	2	chr3A.!!$R1	2159
2	TraesCS3D01G219400	chr3B	394087767	394090249	2482	True	1006.666667	2001	92.470	4	2114	3	chr3B.!!$R2	2110
3	TraesCS3D01G219400	chr3B	247562889	247563568	679	True	1005.000000	1005	93.304	2220	2903	1	chr3B.!!$R1	683
4	TraesCS3D01G219400	chr2D	135490111	135490794	683	False	1175.000000	1175	97.661	2220	2903	1	chr2D.!!$F2	683
5	TraesCS3D01G219400	chr2D	48329954	48330634	680	False	1094.000000	1094	95.608	2221	2903	1	chr2D.!!$F1	682
6	TraesCS3D01G219400	chr7D	81663908	81664592	684	True	1162.000000	1162	97.234	2217	2903	1	chr7D.!!$R1	686
7	TraesCS3D01G219400	chr6D	362921385	362922068	683	True	1040.000000	1040	94.178	2221	2903	1	chr6D.!!$R1	682
8	TraesCS3D01G219400	chr6A	596149568	596150255	687	False	1016.000000	1016	93.459	2221	2903	1	chr6A.!!$F1	682
9	TraesCS3D01G219400	chr4B	142044424	142045114	690	True	1013.000000	1013	93.208	2217	2903	1	chr4B.!!$R1	686
10	TraesCS3D01G219400	chr1A	553053410	553054092	682	False	1011.000000	1011	93.343	2217	2903	1	chr1A.!!$F1	686
11	TraesCS3D01G219400	chr2B	607076092	607076778	686	False	1000.000000	1000	93.033	2220	2903	1	chr2B.!!$F1	683

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
487	598	0.251165	ACCTTTACCCGCAGCAACAT	60.251	50.0	0.0	0.0	0.0	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2178	2625	0.044092	TGGCTACAAGGATCCCTGGA	59.956	55.0	14.94	5.11	32.13	3.86	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
97	131	3.060895	GCTGTCTAAGTGTTGCGTGATAC	59.939	47.826	0.00	0.00	0.00	2.24
98	132	4.486090	CTGTCTAAGTGTTGCGTGATACT	58.514	43.478	0.00	0.00	0.00	2.12
100	134	4.022676	TGTCTAAGTGTTGCGTGATACTCA	60.023	41.667	0.00	0.00	0.00	3.41
114	148	2.665649	TACTCAGCAACGTATGGGTG	57.334	50.000	10.26	8.83	31.14	4.61
136	170	2.685388	GAGGGCAAGGTAGCTTTGATTC	59.315	50.000	3.96	0.00	34.17	2.52
202	236	1.579698	CCGATGCATCAACTGGAGAG	58.420	55.000	25.70	6.49	0.00	3.20
203	237	1.134580	CCGATGCATCAACTGGAGAGT	60.135	52.381	25.70	0.00	0.00	3.24
204	238	2.101415	CCGATGCATCAACTGGAGAGTA	59.899	50.000	25.70	0.00	0.00	2.59
210	244	4.711846	TGCATCAACTGGAGAGTAGTATGT	59.288	41.667	0.00	0.00	0.00	2.29
212	246	5.737635	GCATCAACTGGAGAGTAGTATGTCC	60.738	48.000	0.00	0.00	33.24	4.02
221	255	1.135199	AGTAGTATGTCCAACGCACGG	60.135	52.381	0.00	0.00	0.00	4.94
294	405	1.271707	GGGGCTAGTAGTTTTGGTGCA	60.272	52.381	0.00	0.00	0.00	4.57
487	598	0.251165	ACCTTTACCCGCAGCAACAT	60.251	50.000	0.00	0.00	0.00	2.71
511	622	0.721483	CGCAAAACCTCGAACTTCGC	60.721	55.000	6.29	0.00	40.21	4.70
701	812	2.901338	ACTGGCTAGTCTGGTACTCA	57.099	50.000	6.17	0.00	39.80	3.41
831	1237	0.946221	GAGACCAATCATAGCCCGCG	60.946	60.000	0.00	0.00	0.00	6.46
897	1303	4.998672	CGTCCTTGTATAAAACCAACCTGA	59.001	41.667	0.00	0.00	0.00	3.86
966	1380	1.806568	GCTGAGACTAGTCGCTGCT	59.193	57.895	34.82	14.59	45.53	4.24
983	1397	1.134128	TGCTGTTCTGTTCTGCTTCCA	60.134	47.619	0.00	0.00	0.00	3.53
1223	1649	2.683933	GAGGAGGGGACGGAAGCA	60.684	66.667	0.00	0.00	0.00	3.91
1233	1659	0.884704	GACGGAAGCACAAGAAGCCA	60.885	55.000	0.00	0.00	0.00	4.75
1503	1929	1.338890	TGTCCTGGGTGACGGTTGAA	61.339	55.000	0.00	0.00	38.11	2.69
1983	2417	5.920840	GTGTTAGTCTGCGCTATGATTATGA	59.079	40.000	9.73	0.00	0.00	2.15
2129	2575	2.767644	TCCCGAGGACTCATATGGAA	57.232	50.000	2.13	0.00	0.00	3.53
2130	2576	2.598565	TCCCGAGGACTCATATGGAAG	58.401	52.381	2.13	0.00	0.00	3.46
2133	2579	2.301296	CCGAGGACTCATATGGAAGCAT	59.699	50.000	2.13	0.00	0.00	3.79
2144	2590	5.310331	TCATATGGAAGCATATCCCTTGACA	59.690	40.000	2.13	0.00	38.82	3.58
2149	2595	4.999950	GGAAGCATATCCCTTGACATACTG	59.000	45.833	0.00	0.00	33.05	2.74
2150	2596	4.013267	AGCATATCCCTTGACATACTGC	57.987	45.455	0.00	0.00	0.00	4.40
2161	2607	2.238395	TGACATACTGCAGGTGCCATTA	59.762	45.455	19.93	0.00	41.18	1.90
2170	2617	3.780624	GGTGCCATTAGTCACCGAT	57.219	52.632	0.00	0.00	42.67	4.18
2190	2637	0.326618	ATGTCGGTCCAGGGATCCTT	60.327	55.000	12.58	0.00	0.00	3.36
2196	2643	0.470341	GTCCAGGGATCCTTGTAGCC	59.530	60.000	21.40	3.75	0.00	3.93
2211	2658	2.969628	TAGCCAAGCTACAAGAGAGC	57.030	50.000	0.00	0.00	40.44	4.09
2212	2659	0.979665	AGCCAAGCTACAAGAGAGCA	59.020	50.000	0.00	0.00	42.69	4.26
2213	2660	1.558756	AGCCAAGCTACAAGAGAGCAT	59.441	47.619	0.00	0.00	42.69	3.79
2214	2661	1.669779	GCCAAGCTACAAGAGAGCATG	59.330	52.381	0.00	0.00	42.69	4.06
2241	2688	8.807581	GTTTCTGTTTTGAATCGAAAGTGATTT	58.192	29.630	0.00	0.00	38.65	2.17
2303	2752	2.202518	GACGCGACGATCCCGAAA	60.203	61.111	15.93	0.00	39.50	3.46
2368	2817	2.126189	GACACAGGCGTCCGTACC	60.126	66.667	0.00	0.00	0.00	3.34
2743	3202	3.304659	GGTTGTCGCATGATTTGACTTGT	60.305	43.478	0.00	0.00	33.81	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	9.453830	AATATTACTTCTCTATCAAGGGGAGTT	57.546	33.333	0.00	0.00	0.00	3.01
2	3	9.453830	AAATATTACTTCTCTATCAAGGGGAGT	57.546	33.333	0.00	0.00	0.00	3.85
50	56	8.484799	GCCTTAATTTTTACTCGGTTTTTCTTG	58.515	33.333	0.00	0.00	0.00	3.02
97	131	0.249120	TCCACCCATACGTTGCTGAG	59.751	55.000	0.00	0.00	0.00	3.35
98	132	0.249120	CTCCACCCATACGTTGCTGA	59.751	55.000	0.00	0.00	0.00	4.26
100	134	1.602237	CCTCCACCCATACGTTGCT	59.398	57.895	0.00	0.00	0.00	3.91
114	148	0.328258	TCAAAGCTACCTTGCCCTCC	59.672	55.000	0.00	0.00	0.00	4.30
136	170	1.731720	GACTTCCTACTTGCCAGCAG	58.268	55.000	0.00	0.00	0.00	4.24
202	236	1.135315	TCCGTGCGTTGGACATACTAC	60.135	52.381	0.00	0.00	0.00	2.73
203	237	1.175654	TCCGTGCGTTGGACATACTA	58.824	50.000	0.00	0.00	0.00	1.82
204	238	1.969085	TCCGTGCGTTGGACATACT	59.031	52.632	0.00	0.00	0.00	2.12
210	244	3.293714	TACCGTCCGTGCGTTGGA	61.294	61.111	2.01	0.00	0.00	3.53
212	246	1.950130	TTGTACCGTCCGTGCGTTG	60.950	57.895	0.00	0.00	0.00	4.10
221	255	4.330620	TGAAAGTGAAGTTGTTGTACCGTC	59.669	41.667	0.00	0.00	0.00	4.79
294	405	5.742063	CTTTATCTTAGGGAAAGGAACCGT	58.258	41.667	0.00	0.00	35.75	4.83
487	598	0.653636	GTTCGAGGTTTTGCGTGTGA	59.346	50.000	0.00	0.00	0.00	3.58
623	734	4.764771	TGCTTGCTGCCCCATCCC	62.765	66.667	0.00	0.00	42.00	3.85
763	1169	2.972505	CAGCACGTGAAAGGCCGT	60.973	61.111	22.23	0.00	37.90	5.68
897	1303	2.125269	GTAGACCACGGCGGCAAT	60.125	61.111	13.24	0.00	39.03	3.56
966	1380	1.810031	CGGTGGAAGCAGAACAGAACA	60.810	52.381	0.00	0.00	0.00	3.18
1223	1649	0.820891	CACAGTGGCTGGCTTCTTGT	60.821	55.000	2.00	0.00	35.51	3.16
1471	1897	0.179020	CAGGACACCACTTGCCTCAA	60.179	55.000	0.00	0.00	31.51	3.02
1474	1900	2.833913	CCCAGGACACCACTTGCCT	61.834	63.158	0.00	0.00	33.44	4.75
1503	1929	0.108138	GCCAGATGCCTGTAACGTCT	60.108	55.000	0.00	0.00	38.74	4.18
1568	1994	3.708734	CGGACACGAACGTTGGGC	61.709	66.667	15.01	1.92	44.60	5.36
1605	2031	1.021202	TGAAAGCCACGTTTGTCCAG	58.979	50.000	0.00	0.00	0.00	3.86
2086	2532	7.878644	GGACCCTACCATTGTTAGAAAGATATC	59.121	40.741	0.00	0.00	0.00	1.63
2087	2533	7.202195	GGGACCCTACCATTGTTAGAAAGATAT	60.202	40.741	2.09	0.00	0.00	1.63
2089	2535	5.104067	GGGACCCTACCATTGTTAGAAAGAT	60.104	44.000	2.09	0.00	0.00	2.40
2129	2575	3.392285	TGCAGTATGTCAAGGGATATGCT	59.608	43.478	0.00	0.00	37.92	3.79
2130	2576	3.743521	TGCAGTATGTCAAGGGATATGC	58.256	45.455	0.00	0.00	39.31	3.14
2133	2579	3.134623	CACCTGCAGTATGTCAAGGGATA	59.865	47.826	13.81	0.00	39.31	2.59
2144	2590	2.505407	TGACTAATGGCACCTGCAGTAT	59.495	45.455	13.81	0.00	44.36	2.12
2170	2617	0.561184	AGGATCCCTGGACCGACATA	59.439	55.000	8.55	0.00	29.57	2.29
2178	2625	0.044092	TGGCTACAAGGATCCCTGGA	59.956	55.000	14.94	5.11	32.13	3.86
2196	2643	2.983229	ACCATGCTCTCTTGTAGCTTG	58.017	47.619	0.00	0.00	42.02	4.01
2203	2650	4.843220	AAACAGAAACCATGCTCTCTTG	57.157	40.909	0.00	0.00	0.00	3.02
2204	2651	4.889409	TCAAAACAGAAACCATGCTCTCTT	59.111	37.500	0.00	0.00	0.00	2.85
2205	2652	4.464008	TCAAAACAGAAACCATGCTCTCT	58.536	39.130	0.00	0.00	0.00	3.10
2206	2653	4.836125	TCAAAACAGAAACCATGCTCTC	57.164	40.909	0.00	0.00	0.00	3.20
2207	2654	5.563475	CGATTCAAAACAGAAACCATGCTCT	60.563	40.000	0.00	0.00	0.00	4.09
2208	2655	4.618489	CGATTCAAAACAGAAACCATGCTC	59.382	41.667	0.00	0.00	0.00	4.26
2209	2656	4.278170	TCGATTCAAAACAGAAACCATGCT	59.722	37.500	0.00	0.00	0.00	3.79
2210	2657	4.545610	TCGATTCAAAACAGAAACCATGC	58.454	39.130	0.00	0.00	0.00	4.06
2211	2658	6.697019	ACTTTCGATTCAAAACAGAAACCATG	59.303	34.615	0.00	0.00	0.00	3.66
2212	2659	6.697019	CACTTTCGATTCAAAACAGAAACCAT	59.303	34.615	0.00	0.00	0.00	3.55
2213	2660	6.033341	CACTTTCGATTCAAAACAGAAACCA	58.967	36.000	0.00	0.00	0.00	3.67
2214	2661	6.262601	TCACTTTCGATTCAAAACAGAAACC	58.737	36.000	0.00	0.00	0.00	3.27
2215	2662	7.914537	ATCACTTTCGATTCAAAACAGAAAC	57.085	32.000	0.00	0.00	0.00	2.78
2241	2688	7.038302	ACTCTCTGTAACCATTGACAAAGGATA	60.038	37.037	16.13	5.93	0.00	2.59
2276	2725	2.687805	CGTCGCGTCTCTCCAGGAA	61.688	63.158	5.77	0.00	0.00	3.36
2277	2726	2.871216	ATCGTCGCGTCTCTCCAGGA	62.871	60.000	5.77	0.00	0.00	3.86
2303	2752	0.911769	TCCTGGAACCGATGCATCTT	59.088	50.000	23.73	12.68	0.00	2.40
2368	2817	1.416049	CATCGAACGAGTTGCACCG	59.584	57.895	2.94	0.00	0.00	4.94
2437	2892	2.572556	TGGTCAAGCGTAAATTAGGGGA	59.427	45.455	0.00	0.00	0.00	4.81
2715	3174	2.401583	ATCATGCGACAACCTTGCTA	57.598	45.000	0.00	0.00	0.00	3.49
2743	3202	3.857157	AGCGGGGAAATAAGCATTCTA	57.143	42.857	0.00	0.00	0.00	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.