AutoCloner

Multiple sequence alignment - TraesCS7D01G228400

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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	TraesCS7D01G228400	chr7D	100.000	2322	0	0	1	2322	188550652	188548331	0.000000e+00	4289
1	TraesCS7D01G228400	chr7D	97.405	1002	20	1	1327	2322	101765406	101766407	0.000000e+00	1701
2	TraesCS7D01G228400	chr7D	81.967	244	30	10	487	718	585666129	585666370	6.550000e-46	195
3	TraesCS7D01G228400	chr7A	94.473	1339	50	12	1	1331	195485632	195486954	0.000000e+00	2041
4	TraesCS7D01G228400	chr4D	98.695	996	13	0	1327	2322	486781502	486780507	0.000000e+00	1768
5	TraesCS7D01G228400	chr5D	98.394	996	16	0	1327	2322	482801300	482802295	0.000000e+00	1751
6	TraesCS7D01G228400	chr5D	82.579	442	60	8	1	426	282379216	282379656	7.830000e-100	374
7	TraesCS7D01G228400	chr6D	98.293	996	16	1	1327	2322	464278638	464277644	0.000000e+00	1744
8	TraesCS7D01G228400	chr6D	98.094	997	18	1	1327	2322	296680358	296681354	0.000000e+00	1735
9	TraesCS7D01G228400	chr6D	81.275	251	35	9	481	720	382617303	382617552	2.350000e-45	193
10	TraesCS7D01G228400	chr5B	95.766	992	39	1	1331	2322	444757456	444758444	0.000000e+00	1596
11	TraesCS7D01G228400	chr6B	95.665	992	40	1	1331	2322	276766470	276767458	0.000000e+00	1591
12	TraesCS7D01G228400	chr3B	94.790	998	48	3	1327	2322	485404737	485403742	0.000000e+00	1552
13	TraesCS7D01G228400	chr6A	91.376	974	70	7	1350	2322	586031188	586030228	0.000000e+00	1321
14	TraesCS7D01G228400	chr7B	90.959	365	16	9	717	1073	332340517	332340162	2.090000e-130	475
15	TraesCS7D01G228400	chr7B	96.198	263	10	0	1069	1331	332340006	332339744	4.580000e-117	431
16	TraesCS7D01G228400	chr7B	87.069	232	16	8	275	494	332340741	332340512	1.380000e-62	250
17	TraesCS7D01G228400	chr7B	81.690	213	29	8	517	719	133529950	133530162	3.970000e-38	169
18	TraesCS7D01G228400	chr7B	80.841	214	28	10	484	685	133529717	133529929	3.090000e-34	156
19	TraesCS7D01G228400	chr4B	85.356	239	26	5	489	718	183525224	183524986	2.980000e-59	239
20	TraesCS7D01G228400	chr2B	82.427	239	33	7	489	718	449826847	449827085	1.410000e-47	200
21	TraesCS7D01G228400	chr3A	82.008	239	34	6	489	718	701176862	701177100	6.550000e-46	195
22	TraesCS7D01G228400	chr1A	78.947	247	38	8	482	717	362190245	362190488	3.090000e-34	156

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	TraesCS7D01G228400	chr7D	188548331	188550652	2321	True	4289.000000	4289	100.000000	1	2322	1	chr7D.!!$R1	2321
1	TraesCS7D01G228400	chr7D	101765406	101766407	1001	False	1701.000000	1701	97.405000	1327	2322	1	chr7D.!!$F1	995
2	TraesCS7D01G228400	chr7A	195485632	195486954	1322	False	2041.000000	2041	94.473000	1	1331	1	chr7A.!!$F1	1330
3	TraesCS7D01G228400	chr4D	486780507	486781502	995	True	1768.000000	1768	98.695000	1327	2322	1	chr4D.!!$R1	995
4	TraesCS7D01G228400	chr5D	482801300	482802295	995	False	1751.000000	1751	98.394000	1327	2322	1	chr5D.!!$F2	995
5	TraesCS7D01G228400	chr6D	464277644	464278638	994	True	1744.000000	1744	98.293000	1327	2322	1	chr6D.!!$R1	995
6	TraesCS7D01G228400	chr6D	296680358	296681354	996	False	1735.000000	1735	98.094000	1327	2322	1	chr6D.!!$F1	995
7	TraesCS7D01G228400	chr5B	444757456	444758444	988	False	1596.000000	1596	95.766000	1331	2322	1	chr5B.!!$F1	991
8	TraesCS7D01G228400	chr6B	276766470	276767458	988	False	1591.000000	1591	95.665000	1331	2322	1	chr6B.!!$F1	991
9	TraesCS7D01G228400	chr3B	485403742	485404737	995	True	1552.000000	1552	94.790000	1327	2322	1	chr3B.!!$R1	995
10	TraesCS7D01G228400	chr6A	586030228	586031188	960	True	1321.000000	1321	91.376000	1350	2322	1	chr6A.!!$R1	972
11	TraesCS7D01G228400	chr7B	332339744	332340741	997	True	385.333333	475	91.408667	275	1331	3	chr7B.!!$R1	1056

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
883	912	0.248907	ATCAGCGTTACCGACCATCG	60.249	55.0	0.0	0.0	40.07	3.84	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1695	1891	2.672478	CGCCTGGTTTGAACAACAACAA	60.672	45.455	0.0	0.0	38.29	2.83	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
30	31	5.951747	AGCTAGCATTGGAGTAAATGGAAAA	59.048	36.000	18.83	0.00	37.89	2.29
77	78	6.920817	TGGCCTATAAGTGACTGTTATATCG	58.079	40.000	3.32	0.00	0.00	2.92
103	104	5.890424	ATTTCATCGTTTTACCGTGGAAT	57.110	34.783	0.00	0.00	0.00	3.01
125	126	0.532573	TAGCTTCCAAGAGGCTCACG	59.467	55.000	18.26	6.75	41.02	4.35
139	140	1.201647	GCTCACGCTACTAACACTGGA	59.798	52.381	0.00	0.00	0.00	3.86
161	162	5.451798	GGATGACACCAAGTTCAAAACATGT	60.452	40.000	0.00	0.00	0.00	3.21
166	167	5.163457	ACACCAAGTTCAAAACATGTAAGGG	60.163	40.000	0.00	0.00	0.00	3.95
192	193	2.465299	CCACGCACGAACAACACCA	61.465	57.895	0.00	0.00	0.00	4.17
217	218	7.981102	ACTCTCCTCTTAAAACAAATACCAC	57.019	36.000	0.00	0.00	0.00	4.16
219	220	7.086685	TCTCCTCTTAAAACAAATACCACCT	57.913	36.000	0.00	0.00	0.00	4.00
220	221	7.523415	TCTCCTCTTAAAACAAATACCACCTT	58.477	34.615	0.00	0.00	0.00	3.50
221	222	7.664318	TCTCCTCTTAAAACAAATACCACCTTC	59.336	37.037	0.00	0.00	0.00	3.46
222	223	6.428771	TCCTCTTAAAACAAATACCACCTTCG	59.571	38.462	0.00	0.00	0.00	3.79
223	224	6.428771	CCTCTTAAAACAAATACCACCTTCGA	59.571	38.462	0.00	0.00	0.00	3.71
224	225	7.120726	CCTCTTAAAACAAATACCACCTTCGAT	59.879	37.037	0.00	0.00	0.00	3.59
225	226	7.812648	TCTTAAAACAAATACCACCTTCGATG	58.187	34.615	0.00	0.00	0.00	3.84
226	227	5.385509	AAAACAAATACCACCTTCGATGG	57.614	39.130	15.45	15.45	43.43	3.51
227	228	2.365582	ACAAATACCACCTTCGATGGC	58.634	47.619	16.84	0.00	41.31	4.40
228	229	2.290641	ACAAATACCACCTTCGATGGCA	60.291	45.455	16.84	0.00	41.31	4.92
229	230	2.752354	CAAATACCACCTTCGATGGCAA	59.248	45.455	16.84	0.00	41.31	4.52
486	499	4.272489	CTTCCCTGTCTGGCAATTAATCA	58.728	43.478	0.00	0.00	0.00	2.57
504	517	0.737219	CACTACTACCTTCGTCCGGG	59.263	60.000	0.00	0.00	0.00	5.73
535	549	2.490509	CCCCTTCGTATTTTGTCCCAAC	59.509	50.000	0.00	0.00	0.00	3.77
542	556	7.094549	CCTTCGTATTTTGTCCCAACTTTCATA	60.095	37.037	0.00	0.00	0.00	2.15
736	757	0.620556	ACCACAGAAGCCCCACTATG	59.379	55.000	0.00	0.00	0.00	2.23
883	912	0.248907	ATCAGCGTTACCGACCATCG	60.249	55.000	0.00	0.00	40.07	3.84
888	917	0.526739	CGTTACCGACCATCGATGCA	60.527	55.000	20.25	0.00	43.74	3.96
965	994	1.067495	GTAGCAGACACCTCACCTGAC	60.067	57.143	0.00	0.00	0.00	3.51
1058	1087	4.162320	TCTTTTGGTGCTATCCTCAGGTAG	59.838	45.833	0.00	0.00	0.00	3.18
1112	1301	6.687105	CGACGTTCTTTTCTGTTGATTTTTCT	59.313	34.615	0.00	0.00	0.00	2.52
1168	1357	1.136147	GTTGATGCAGGCTTCAGCG	59.864	57.895	9.39	0.00	43.26	5.18
1273	1462	2.639286	GGCAAGGTCACTGCAACG	59.361	61.111	0.00	0.00	0.00	4.10
1300	1489	1.761174	CCAGGGGTGTAAGTGCACT	59.239	57.895	15.25	15.25	39.21	4.40
1528	1724	3.636231	TGCTAAGCACGGCCAGGT	61.636	61.111	2.24	0.00	31.71	4.00
1594	1790	1.021390	GCTCTGGTGCATGCTAACGT	61.021	55.000	20.33	0.00	0.00	3.99
1709	1905	3.256879	TGCAGGACTTGTTGTTGTTCAAA	59.743	39.130	0.00	0.00	37.81	2.69
1840	2036	4.261783	GCAGGGTCAGAAAAAGAAGAAAGG	60.262	45.833	0.00	0.00	0.00	3.11
2013	2209	4.155462	GTCTGTTGTATGGTGAGACGAGTA	59.845	45.833	0.00	0.00	0.00	2.59
2162	2358	2.677003	GGACGATGTTGTGGGCACG	61.677	63.158	0.00	0.00	0.00	5.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	4.826274	TTTACTCCAATGCTAGCTCAGT	57.174	40.909	17.23	12.04	0.00	3.41
30	31	3.686726	GTCCATCAAACTCTCGCTCATTT	59.313	43.478	0.00	0.00	0.00	2.32
33	34	1.895798	AGTCCATCAAACTCTCGCTCA	59.104	47.619	0.00	0.00	0.00	4.26
37	38	1.363744	GCCAGTCCATCAAACTCTCG	58.636	55.000	0.00	0.00	0.00	4.04
77	78	4.849383	CCACGGTAAAACGATGAAATTGAC	59.151	41.667	0.00	0.00	37.61	3.18
103	104	2.761208	GTGAGCCTCTTGGAAGCTACTA	59.239	50.000	0.00	0.00	36.87	1.82
125	126	3.056107	TGGTGTCATCCAGTGTTAGTAGC	60.056	47.826	0.00	0.00	33.19	3.58
139	140	5.596836	ACATGTTTTGAACTTGGTGTCAT	57.403	34.783	0.00	0.00	39.93	3.06
161	162	2.994699	CGTGGATGGGTGCCCTTA	59.005	61.111	8.91	0.00	36.94	2.69
192	193	7.447545	GGTGGTATTTGTTTTAAGAGGAGAGTT	59.552	37.037	0.00	0.00	0.00	3.01
217	218	1.243342	TGTTGGCTTGCCATCGAAGG	61.243	55.000	15.58	1.31	0.00	3.46
219	220	1.035923	TTTGTTGGCTTGCCATCGAA	58.964	45.000	15.58	16.44	0.00	3.71
220	221	1.035923	TTTTGTTGGCTTGCCATCGA	58.964	45.000	15.58	11.45	0.00	3.59
221	222	2.083167	ATTTTGTTGGCTTGCCATCG	57.917	45.000	15.58	0.00	0.00	3.84
222	223	2.412770	CGAATTTTGTTGGCTTGCCATC	59.587	45.455	15.58	14.67	0.00	3.51
223	224	2.224257	ACGAATTTTGTTGGCTTGCCAT	60.224	40.909	15.58	0.00	0.00	4.40
224	225	1.137872	ACGAATTTTGTTGGCTTGCCA	59.862	42.857	10.65	10.65	0.00	4.92
225	226	1.864565	ACGAATTTTGTTGGCTTGCC	58.135	45.000	4.43	4.43	0.00	4.52
226	227	4.295051	TCTTACGAATTTTGTTGGCTTGC	58.705	39.130	0.00	0.00	0.00	4.01
227	228	6.820470	TTTCTTACGAATTTTGTTGGCTTG	57.180	33.333	0.00	0.00	0.00	4.01
228	229	7.201574	GGTTTTTCTTACGAATTTTGTTGGCTT	60.202	33.333	0.00	0.00	0.00	4.35
229	230	6.256975	GGTTTTTCTTACGAATTTTGTTGGCT	59.743	34.615	0.00	0.00	0.00	4.75
388	400	0.764226	CTTTGCTGCGTCGTTTTTCG	59.236	50.000	0.00	0.00	41.41	3.46
466	479	3.266772	AGTGATTAATTGCCAGACAGGGA	59.733	43.478	0.00	0.00	38.09	4.20
486	499	0.329596	ACCCGGACGAAGGTAGTAGT	59.670	55.000	0.73	0.00	33.52	2.73
504	517	0.537828	TACGAAGGGGGCCAACAAAC	60.538	55.000	4.39	0.00	0.00	2.93
676	697	8.301720	GTTTATTAGTCACCCTTTTAGTTTGGG	58.698	37.037	0.00	0.00	46.07	4.12
736	757	0.940126	CGCTGATCAACTACATGCCC	59.060	55.000	0.00	0.00	0.00	5.36
888	917	7.448469	GGTTGGAAGGATATTTATAGTGCACAT	59.552	37.037	21.04	12.77	0.00	3.21
929	958	1.610624	GCTACTGGTGTTGCAAGCCTA	60.611	52.381	17.67	2.14	42.80	3.93
980	1009	8.694540	TCTTCATCCTTGTGAATGAAAGAAAAA	58.305	29.630	0.00	0.00	37.47	1.94
981	1010	8.137437	GTCTTCATCCTTGTGAATGAAAGAAAA	58.863	33.333	0.00	0.00	37.47	2.29
982	1011	7.503566	AGTCTTCATCCTTGTGAATGAAAGAAA	59.496	33.333	0.00	0.00	37.47	2.52
983	1012	7.000472	AGTCTTCATCCTTGTGAATGAAAGAA	59.000	34.615	0.00	0.00	37.47	2.52
1058	1087	7.076842	ACATGCATAATACTCAACTGTTGAC	57.923	36.000	18.69	7.69	35.46	3.18
1112	1301	6.218019	TCAGAAAGAAACGAACGAGGATTAA	58.782	36.000	0.14	0.00	0.00	1.40
1168	1357	1.153862	CGAGTCACTGCAGAGCTCC	60.154	63.158	23.35	5.45	0.00	4.70
1300	1489	4.576053	GCTTAATCATGTGGTATGCAGACA	59.424	41.667	14.36	3.49	0.00	3.41
1528	1724	4.783621	GCTCGAGCACATGGCCCA	62.784	66.667	31.91	0.00	46.50	5.36
1594	1790	2.809174	CCGCGTCGAACATGCTGA	60.809	61.111	4.92	0.00	34.45	4.26
1695	1891	2.672478	CGCCTGGTTTGAACAACAACAA	60.672	45.455	0.00	0.00	38.29	2.83
1840	2036	5.163248	CCTCCCTTCTTTCTATCCTTTCTCC	60.163	48.000	0.00	0.00	0.00	3.71
2013	2209	6.660949	CCCATACAAACTCTCTTTGAGGAAAT	59.339	38.462	0.00	0.00	46.72	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.