AutoCloner

Multiple sequence alignment - TraesCS7A01G289900

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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	TraesCS7A01G289900	chr7A	100.000	2117	0	0	1	2117	352194130	352192014	0.000000e+00	3910
1	TraesCS7A01G289900	chr1D	94.854	2118	100	9	2	2112	254497890	254500005	0.000000e+00	3299
2	TraesCS7A01G289900	chr1D	91.051	2112	146	24	4	2112	244484152	244482081	0.000000e+00	2813
3	TraesCS7A01G289900	chr5D	94.518	2116	107	9	2	2112	6201386	6199275	0.000000e+00	3256
4	TraesCS7A01G289900	chr5D	94.388	2049	106	9	68	2112	329162138	329164181	0.000000e+00	3138
5	TraesCS7A01G289900	chr5D	95.057	1922	89	6	195	2112	560872556	560874475	0.000000e+00	3018
6	TraesCS7A01G289900	chr1A	93.381	2115	125	13	2	2112	168450669	168448566	0.000000e+00	3116
7	TraesCS7A01G289900	chr4D	93.283	2114	132	10	2	2110	19916389	19918497	0.000000e+00	3109
8	TraesCS7A01G289900	chr6B	94.014	1587	91	4	2	1584	22425837	22427423	0.000000e+00	2401
9	TraesCS7A01G289900	chr3D	94.204	1225	64	4	2	1220	21904518	21905741	0.000000e+00	1862
10	TraesCS7A01G289900	chr3B	95.672	1109	43	5	1007	2112	201515580	201516686	0.000000e+00	1777
11	TraesCS7A01G289900	chr3B	94.297	491	25	3	1622	2112	524777564	524777077	0.000000e+00	749
12	TraesCS7A01G289900	chr7B	94.118	493	27	2	1621	2112	102632114	102631623	0.000000e+00	749
13	TraesCS7A01G289900	chr7D	97.043	372	10	1	1588	1959	231542485	231542115	1.780000e-175	625
14	TraesCS7A01G289900	chr2A	96.053	304	11	1	1492	1794	677892867	677893170	5.250000e-136	494

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	TraesCS7A01G289900	chr7A	352192014	352194130	2116	True	3910	3910	100.000	1	2117	1	chr7A.!!$R1	2116
1	TraesCS7A01G289900	chr1D	254497890	254500005	2115	False	3299	3299	94.854	2	2112	1	chr1D.!!$F1	2110
2	TraesCS7A01G289900	chr1D	244482081	244484152	2071	True	2813	2813	91.051	4	2112	1	chr1D.!!$R1	2108
3	TraesCS7A01G289900	chr5D	6199275	6201386	2111	True	3256	3256	94.518	2	2112	1	chr5D.!!$R1	2110
4	TraesCS7A01G289900	chr5D	329162138	329164181	2043	False	3138	3138	94.388	68	2112	1	chr5D.!!$F1	2044
5	TraesCS7A01G289900	chr5D	560872556	560874475	1919	False	3018	3018	95.057	195	2112	1	chr5D.!!$F2	1917
6	TraesCS7A01G289900	chr1A	168448566	168450669	2103	True	3116	3116	93.381	2	2112	1	chr1A.!!$R1	2110
7	TraesCS7A01G289900	chr4D	19916389	19918497	2108	False	3109	3109	93.283	2	2110	1	chr4D.!!$F1	2108
8	TraesCS7A01G289900	chr6B	22425837	22427423	1586	False	2401	2401	94.014	2	1584	1	chr6B.!!$F1	1582
9	TraesCS7A01G289900	chr3D	21904518	21905741	1223	False	1862	1862	94.204	2	1220	1	chr3D.!!$F1	1218
10	TraesCS7A01G289900	chr3B	201515580	201516686	1106	False	1777	1777	95.672	1007	2112	1	chr3B.!!$F1	1105

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
70	76	0.606096	TGCAGCTTTCGTAGTGGCTA	59.394	50.0	0.0	0.0	33.43	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1265	1275	0.247736	ACTTCAGTCGCCATCTCCAC	59.752	55.0	0.0	0.0	0.0	4.02	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
28	29	6.719370	TGGGCAATATTGAAACTGTACTTTCT	59.281	34.615	19.73	0.00	32.25	2.52
70	76	0.606096	TGCAGCTTTCGTAGTGGCTA	59.394	50.000	0.00	0.00	33.43	3.93
155	161	1.349357	GGATCAGGGATACTTCCAGCC	59.651	57.143	0.00	0.00	44.60	4.85
202	208	6.679327	ATGGTTTAGCCGAAAATCTTAGTC	57.321	37.500	0.00	0.00	41.21	2.59
222	228	8.540507	TTAGTCTATCAGAAGCTTGGTCTAAT	57.459	34.615	2.10	0.00	0.00	1.73
230	236	4.409247	AGAAGCTTGGTCTAATATTCCCGT	59.591	41.667	2.10	0.00	0.00	5.28
288	294	2.700371	GGCAAAAGGGGGATTATTCAGG	59.300	50.000	0.00	0.00	0.00	3.86
297	303	1.423161	GGATTATTCAGGGCAGGCTCT	59.577	52.381	0.00	0.00	0.00	4.09
307	313	1.699634	GGGCAGGCTCTATGGACAATA	59.300	52.381	0.00	0.00	0.00	1.90
468	475	4.201763	GCAGACATTCCTTTTAGAAGAGCG	60.202	45.833	0.00	0.00	34.71	5.03
515	522	5.404395	AGTAGGAGTAAAGGTGGAGTTCTT	58.596	41.667	0.00	0.00	0.00	2.52
517	524	5.648330	AGGAGTAAAGGTGGAGTTCTTTT	57.352	39.130	0.00	0.00	35.22	2.27
557	564	7.510685	TGGAGTAAGTTATTCTGATCCTGCTAT	59.489	37.037	5.50	0.00	0.00	2.97
590	598	3.266510	TGCGAGGCATTCTCAATTAGT	57.733	42.857	0.00	0.00	42.55	2.24
618	626	1.271856	TTGAATCAGACCGGGCTACA	58.728	50.000	11.18	5.41	0.00	2.74
628	636	2.872858	GACCGGGCTACATTGAAATCTC	59.127	50.000	6.32	0.00	0.00	2.75
645	653	2.571212	TCTCATGGTGTTTTTCGCAGT	58.429	42.857	0.00	0.00	0.00	4.40
692	700	1.545582	TCATGCTACCTTTGCTTTGCC	59.454	47.619	0.00	0.00	0.00	4.52
710	718	1.679153	GCCCTTCTTTTTCGGACACAA	59.321	47.619	0.00	0.00	0.00	3.33
721	729	1.875420	CGGACACAATTGGCATGGCA	61.875	55.000	19.43	19.43	28.57	4.92
749	757	5.514274	ACATTGTTCCGAGATGTTTTTGT	57.486	34.783	0.00	0.00	30.22	2.83
830	838	4.351111	AGATCCAACTACAAGGAAACAGGT	59.649	41.667	0.00	0.00	37.48	4.00
1009	1018	5.482908	ACCAGATCGAATATATGGAAGCAC	58.517	41.667	5.22	0.00	34.99	4.40
1030	1039	6.882678	AGCACTGGTTTATACGTTCCTTTTAT	59.117	34.615	0.00	0.00	0.00	1.40
1100	1110	3.245264	CCTAAGGTTCCACCAACTCCAAT	60.245	47.826	0.00	0.00	41.95	3.16
1170	1180	7.631007	AGGGGGACTTCTTACTTAAATTAGTG	58.369	38.462	0.00	0.00	0.00	2.74
1212	1222	6.887002	GGATCTCTTAATTGTTGAGAGGGTTT	59.113	38.462	10.41	0.00	42.03	3.27
1245	1255	6.670902	ACGGTATATAAGGCATACCCAGTAAT	59.329	38.462	6.25	0.00	43.39	1.89
1247	1257	7.364408	CGGTATATAAGGCATACCCAGTAATGT	60.364	40.741	6.25	0.00	43.39	2.71
1280	1290	0.463204	AGATGTGGAGATGGCGACTG	59.537	55.000	0.00	0.00	0.00	3.51
1287	1297	1.066858	GGAGATGGCGACTGAAGTTGA	60.067	52.381	1.68	0.00	0.00	3.18
1446	1456	5.056553	AGTTCTAAACCTAGGCCAAAACA	57.943	39.130	9.30	0.00	0.00	2.83
1452	1462	3.306472	ACCTAGGCCAAAACAAACTGA	57.694	42.857	9.30	0.00	0.00	3.41
1474	1484	4.425180	TGCAGGTAGTTTACTGAAACCA	57.575	40.909	0.00	0.00	45.21	3.67
1504	1514	2.509964	AGAATATGGAAAAGTCGCCCCT	59.490	45.455	0.00	0.00	0.00	4.79
1875	1887	7.526142	AGTATCTGGAGCACGAAATAGATAA	57.474	36.000	0.00	0.00	31.28	1.75
1884	1896	6.582636	AGCACGAAATAGATAAAGTGGATCA	58.417	36.000	0.00	0.00	0.00	2.92
1888	1900	9.490663	CACGAAATAGATAAAGTGGATCAAAAC	57.509	33.333	0.00	0.00	0.00	2.43
1928	1940	6.504398	TCATACTCACTATTAAGACCTTGCG	58.496	40.000	0.00	0.00	0.00	4.85
2099	2113	2.227194	TCGAAGAACCCTTGCCTTTTC	58.773	47.619	0.00	0.00	31.62	2.29
2112	2126	5.184671	CCTTGCCTTTTCTTTAGCTTGAGAT	59.815	40.000	0.00	0.00	0.00	2.75
2113	2127	5.633830	TGCCTTTTCTTTAGCTTGAGATG	57.366	39.130	0.00	0.00	0.00	2.90
2114	2128	5.316167	TGCCTTTTCTTTAGCTTGAGATGA	58.684	37.500	0.00	0.00	0.00	2.92
2115	2129	5.769662	TGCCTTTTCTTTAGCTTGAGATGAA	59.230	36.000	0.00	0.00	0.00	2.57
2116	2130	6.265196	TGCCTTTTCTTTAGCTTGAGATGAAA	59.735	34.615	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	8.766994	AAGTACAGTTTCAATATTGCCCATAT	57.233	30.769	10.76	0.00	0.00	1.78
66	72	3.646637	ACCCATACCACATAGTTCTAGCC	59.353	47.826	0.00	0.00	0.00	3.93
70	76	3.134804	GCTGACCCATACCACATAGTTCT	59.865	47.826	0.00	0.00	0.00	3.01
102	108	3.463944	AGTAGGCCCAAATAATTCGACG	58.536	45.455	0.00	0.00	0.00	5.12
103	109	3.493503	CGAGTAGGCCCAAATAATTCGAC	59.506	47.826	0.00	0.00	0.00	4.20
202	208	7.821846	GGGAATATTAGACCAAGCTTCTGATAG	59.178	40.741	0.00	0.00	28.31	2.08
266	272	2.700371	CTGAATAATCCCCCTTTTGCCC	59.300	50.000	0.00	0.00	0.00	5.36
288	294	2.289945	CCTATTGTCCATAGAGCCTGCC	60.290	54.545	0.00	0.00	37.65	4.85
297	303	6.032039	AGCTATTCCATCCCTATTGTCCATA	58.968	40.000	0.00	0.00	0.00	2.74
307	313	2.492025	TCCAACAGCTATTCCATCCCT	58.508	47.619	0.00	0.00	0.00	4.20
411	418	4.641989	CCCTCCTCATCTACCAAAACAATG	59.358	45.833	0.00	0.00	0.00	2.82
412	419	4.540099	TCCCTCCTCATCTACCAAAACAAT	59.460	41.667	0.00	0.00	0.00	2.71
468	475	8.739972	ACTTGTTCAACACTATATTTGGATTCC	58.260	33.333	0.00	0.00	0.00	3.01
503	510	1.692411	GCCACAAAAGAACTCCACCT	58.308	50.000	0.00	0.00	0.00	4.00
515	522	3.482436	ACTCCATTAAGTTCGCCACAAA	58.518	40.909	0.00	0.00	0.00	2.83
517	524	2.851263	ACTCCATTAAGTTCGCCACA	57.149	45.000	0.00	0.00	0.00	4.17
590	598	4.021544	CCCGGTCTGATTCAAAAATTTCCA	60.022	41.667	0.00	0.00	0.00	3.53
605	613	2.107950	TTTCAATGTAGCCCGGTCTG	57.892	50.000	0.00	0.00	0.00	3.51
618	626	5.634859	GCGAAAAACACCATGAGATTTCAAT	59.365	36.000	0.00	0.00	36.78	2.57
628	636	3.364964	GGACTACTGCGAAAAACACCATG	60.365	47.826	0.00	0.00	0.00	3.66
692	700	4.298332	CCAATTGTGTCCGAAAAAGAAGG	58.702	43.478	4.43	0.00	0.00	3.46
710	718	2.512692	TGTTCTAGTGCCATGCCAAT	57.487	45.000	0.00	0.00	0.00	3.16
721	729	5.407407	ACATCTCGGAACAATGTTCTAGT	57.593	39.130	23.30	11.36	0.00	2.57
944	952	7.888021	ACTTCCACACCTATTCATTTGTCATTA	59.112	33.333	0.00	0.00	0.00	1.90
998	1007	5.925509	ACGTATAAACCAGTGCTTCCATAT	58.074	37.500	0.00	0.00	0.00	1.78
1009	1018	9.269415	CGAAAATAAAAGGAACGTATAAACCAG	57.731	33.333	0.00	0.00	0.00	4.00
1066	1076	2.249309	ACCTTAGGTGGTTCTCGGAT	57.751	50.000	1.74	0.00	36.89	4.18
1170	1180	4.499183	AGATCCATTCGAAGAACACAGAC	58.501	43.478	3.35	0.00	45.90	3.51
1212	1222	3.455177	TGCCTTATATACCGTGTTTGGGA	59.545	43.478	0.00	0.00	0.00	4.37
1245	1255	6.358178	TCCACATCTGGTTTACTTGTAAACA	58.642	36.000	27.08	16.98	40.63	2.83
1247	1257	6.833041	TCTCCACATCTGGTTTACTTGTAAA	58.167	36.000	2.22	2.22	38.90	2.01
1265	1275	0.247736	ACTTCAGTCGCCATCTCCAC	59.752	55.000	0.00	0.00	0.00	4.02
1446	1456	5.865085	TCAGTAAACTACCTGCATCAGTTT	58.135	37.500	18.65	18.65	43.16	2.66
1452	1462	4.980573	TGGTTTCAGTAAACTACCTGCAT	58.019	39.130	0.00	0.00	43.76	3.96
1474	1484	7.917505	GCGACTTTTCCATATTCTGAATTCAAT	59.082	33.333	9.88	3.76	0.00	2.57
1504	1514	2.127651	AAAGGAGTAGTCCCCAACCA	57.872	50.000	13.30	0.00	45.26	3.67
1640	1651	4.515191	TGGATGGAAAAACTCTGACTTTCG	59.485	41.667	0.00	0.00	31.21	3.46
1642	1653	6.790232	TTTGGATGGAAAAACTCTGACTTT	57.210	33.333	0.00	0.00	0.00	2.66
1861	1873	6.844696	TGATCCACTTTATCTATTTCGTGC	57.155	37.500	0.00	0.00	0.00	5.34
1875	1887	6.484364	AGTTCCATTTGTTTTGATCCACTT	57.516	33.333	0.00	0.00	0.00	3.16
1888	1900	9.334947	AGTGAGTATGAATCATAGTTCCATTTG	57.665	33.333	11.49	0.00	31.06	2.32
1928	1940	7.497925	ACTACTTGAATTTTTCAGTCTGGTC	57.502	36.000	0.00	0.00	41.38	4.02
2025	2038	8.771920	AATCAGTGTAATGACTCGACAAAATA	57.228	30.769	0.00	0.00	30.46	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.