AutoCloner

Multiple sequence alignment - TraesCS3D01G034800

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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	TraesCS3D01G034800	chr3D	100.000	2426	0	0	1	2426	12740308	12742733	0.000000e+00	4481.0
1	TraesCS3D01G034800	chr3D	97.030	1448	18	1	979	2426	12828830	12830252	0.000000e+00	2412.0
2	TraesCS3D01G034800	chr3D	84.608	2001	183	51	479	2426	12835224	12837152	0.000000e+00	1873.0
3	TraesCS3D01G034800	chr3D	87.785	1621	113	37	845	2426	12841094	12842668	0.000000e+00	1818.0
4	TraesCS3D01G034800	chr3D	86.476	1013	100	18	482	1471	12847971	12848969	0.000000e+00	1077.0
5	TraesCS3D01G034800	chr3D	89.578	806	61	9	1	794	12828038	12828832	0.000000e+00	1002.0
6	TraesCS3D01G034800	chr3D	81.850	573	70	15	1695	2261	12825258	12825802	3.680000e-123	451.0
7	TraesCS3D01G034800	chr3D	87.451	255	26	6	234	483	12843965	12844218	3.050000e-74	289.0
8	TraesCS3D01G034800	chr3D	87.552	241	27	3	479	718	12838903	12839141	2.380000e-70	276.0
9	TraesCS3D01G034800	chr3B	89.195	2360	169	36	1	2320	18392855	18395168	0.000000e+00	2867.0
10	TraesCS3D01G034800	chr3B	85.167	2454	207	62	19	2426	18468526	18470868	0.000000e+00	2370.0
11	TraesCS3D01G034800	chr3B	84.379	1722	161	52	85	1758	18431015	18432676	0.000000e+00	1591.0
12	TraesCS3D01G034800	chr3B	83.461	1693	182	50	775	2426	18426612	18428247	0.000000e+00	1485.0
13	TraesCS3D01G034800	chr3B	81.941	1700	213	59	763	2418	18305803	18307452	0.000000e+00	1352.0
14	TraesCS3D01G034800	chr3B	88.799	866	64	16	628	1471	18484273	18485127	0.000000e+00	1031.0
15	TraesCS3D01G034800	chr3B	82.491	811	86	30	1	804	18551437	18552198	0.000000e+00	660.0
16	TraesCS3D01G034800	chr3B	88.936	470	45	5	1959	2425	18432668	18433133	7.520000e-160	573.0
17	TraesCS3D01G034800	chr3B	88.924	316	31	4	2114	2426	18459211	18459525	1.050000e-103	387.0
18	TraesCS3D01G034800	chr3B	88.372	258	24	5	234	486	18472150	18472406	3.030000e-79	305.0
19	TraesCS3D01G034800	chr3B	84.615	260	35	5	229	484	18436811	18437069	1.110000e-63	254.0
20	TraesCS3D01G034800	chr3B	87.766	188	17	5	526	709	18452708	18452893	5.250000e-52	215.0
21	TraesCS3D01G034800	chr3A	84.141	1362	145	27	1098	2426	24529448	24528125	0.000000e+00	1253.0
22	TraesCS3D01G034800	chr3A	88.911	1019	67	19	892	1872	24559896	24558886	0.000000e+00	1214.0
23	TraesCS3D01G034800	chr3A	91.531	862	53	6	1	860	24560732	24559889	0.000000e+00	1170.0
24	TraesCS3D01G034800	chr3A	83.617	470	72	5	1959	2426	24563376	24562910	1.030000e-118	436.0
25	TraesCS3D01G034800	chr3A	93.182	44	1	2	101	142	167940480	167940523	2.010000e-06	63.9
26	TraesCS3D01G034800	chr5D	78.289	608	93	28	829	1414	23011385	23010795	2.970000e-94	355.0
27	TraesCS3D01G034800	chr6D	81.778	225	31	6	105	329	144486662	144486876	1.920000e-41	180.0
28	TraesCS3D01G034800	chr1B	78.995	219	35	7	110	327	308336512	308336720	3.250000e-29	139.0
29	TraesCS3D01G034800	chr4B	95.238	42	0	2	102	141	70967216	70967175	5.600000e-07	65.8
30	TraesCS3D01G034800	chr2D	95.000	40	2	0	103	142	272736686	272736725	2.010000e-06	63.9
31	TraesCS3D01G034800	chr2B	83.824	68	9	2	76	142	221139695	221139761	2.010000e-06	63.9
32	TraesCS3D01G034800	chr1A	83.824	68	9	2	76	142	324770479	324770545	2.010000e-06	63.9
33	TraesCS3D01G034800	chr5A	94.872	39	2	0	2008	2046	329239099	329239137	7.240000e-06	62.1

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	TraesCS3D01G034800	chr3D	12740308	12742733	2425	False	4481.000000	4481	100.000000	1	2426	1	chr3D.!!$F1	2425
1	TraesCS3D01G034800	chr3D	12825258	12830252	4994	False	1288.333333	2412	89.486000	1	2426	3	chr3D.!!$F2	2425
2	TraesCS3D01G034800	chr3D	12835224	12848969	13745	False	1066.600000	1873	86.774400	234	2426	5	chr3D.!!$F3	2192
3	TraesCS3D01G034800	chr3B	18392855	18395168	2313	False	2867.000000	2867	89.195000	1	2320	1	chr3B.!!$F2	2319
4	TraesCS3D01G034800	chr3B	18305803	18307452	1649	False	1352.000000	1352	81.941000	763	2418	1	chr3B.!!$F1	1655
5	TraesCS3D01G034800	chr3B	18468526	18472406	3880	False	1337.500000	2370	86.769500	19	2426	2	chr3B.!!$F8	2407
6	TraesCS3D01G034800	chr3B	18484273	18485127	854	False	1031.000000	1031	88.799000	628	1471	1	chr3B.!!$F5	843
7	TraesCS3D01G034800	chr3B	18426612	18437069	10457	False	975.750000	1591	85.347750	85	2426	4	chr3B.!!$F7	2341
8	TraesCS3D01G034800	chr3B	18551437	18552198	761	False	660.000000	660	82.491000	1	804	1	chr3B.!!$F6	803
9	TraesCS3D01G034800	chr3A	24528125	24529448	1323	True	1253.000000	1253	84.141000	1098	2426	1	chr3A.!!$R1	1328
10	TraesCS3D01G034800	chr3A	24558886	24563376	4490	True	940.000000	1214	88.019667	1	2426	3	chr3A.!!$R2	2425
11	TraesCS3D01G034800	chr5D	23010795	23011385	590	True	355.000000	355	78.289000	829	1414	1	chr5D.!!$R1	585

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
709	7021	0.766131	TCCGCTTGGAACCCTTACAA	59.234	50.0	0.0	0.0	39.4	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1884	10221	0.326595	TGCATTAGGTCTGCGGGAAA	59.673	50.0	0.0	0.0	42.62	3.13	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
201	6121	7.830217	TGATAATGTTTCGTGAAAGTTTTCG	57.170	32.000	0.00	7.50	40.01	3.46
229	6149	2.749621	CTGCTTACAAACAGGACCATCC	59.250	50.000	0.00	0.00	36.58	3.51
231	6151	2.356135	CTTACAAACAGGACCATCCCG	58.644	52.381	0.00	0.00	37.19	5.14
418	6372	3.323115	TGCACCAAGTTTTGCCATAATGA	59.677	39.130	4.18	0.00	38.00	2.57
450	6405	6.367374	TTTTACCACACTCTACATGGATCA	57.633	37.500	0.00	0.00	36.94	2.92
461	6416	7.813627	CACTCTACATGGATCATATGAAGACAG	59.186	40.741	9.99	3.13	0.00	3.51
475	6430	4.973396	TGAAGACAGCATGCTAATTTTCG	58.027	39.130	22.19	8.74	42.53	3.46
490	6798	4.766404	ATTTTCGTCAATTTCGGAGCTT	57.234	36.364	0.00	0.00	0.00	3.74
504	6812	5.592104	TCGGAGCTTGTTTGAGTGATATA	57.408	39.130	0.00	0.00	0.00	0.86
510	6818	8.677300	GGAGCTTGTTTGAGTGATATATTGAAA	58.323	33.333	0.00	0.00	0.00	2.69
537	6845	8.642908	AAATTGTGTTCTTACCTTTTTAGTGC	57.357	30.769	0.00	0.00	0.00	4.40
538	6846	7.582667	ATTGTGTTCTTACCTTTTTAGTGCT	57.417	32.000	0.00	0.00	0.00	4.40
709	7021	0.766131	TCCGCTTGGAACCCTTACAA	59.234	50.000	0.00	0.00	39.40	2.41
719	7031	7.228507	GCTTGGAACCCTTACAATTCAATTTTT	59.771	33.333	0.00	0.00	0.00	1.94
761	7500	3.476295	TGTACGTAACAGCCTTCGTAG	57.524	47.619	0.00	0.00	38.97	3.51
765	7504	2.257034	CGTAACAGCCTTCGTAGGAAC	58.743	52.381	12.94	0.00	45.05	3.62
881	9037	4.025401	GTGTTGTTGCCCCTCGCG	62.025	66.667	0.00	0.00	42.08	5.87
966	9134	3.495543	GCACAGAGCAGGCTTAGC	58.504	61.111	0.00	0.00	44.79	3.09
1776	10112	2.083774	CTCGTGCCTTAAAATGCCTGA	58.916	47.619	0.00	0.00	0.00	3.86
1793	10129	4.994471	AAAACGTCCGGGCCGACC	62.994	66.667	30.79	16.23	0.00	4.79
1873	10210	0.404040	TCCAATTTCCCGCAGACCTT	59.596	50.000	0.00	0.00	0.00	3.50
1874	10211	0.811281	CCAATTTCCCGCAGACCTTC	59.189	55.000	0.00	0.00	0.00	3.46
1875	10212	0.447801	CAATTTCCCGCAGACCTTCG	59.552	55.000	0.00	0.00	0.00	3.79
1876	10213	0.676782	AATTTCCCGCAGACCTTCGG	60.677	55.000	1.13	1.13	44.89	4.30
1889	10226	1.182667	CCTTCGGGTTCCAATTTCCC	58.817	55.000	0.00	0.00	37.98	3.97
1892	10229	4.105388	GGGTTCCAATTTCCCGCA	57.895	55.556	0.00	0.00	0.00	5.69
1893	10230	1.890174	GGGTTCCAATTTCCCGCAG	59.110	57.895	0.00	0.00	0.00	5.18
1894	10231	0.610785	GGGTTCCAATTTCCCGCAGA	60.611	55.000	0.00	0.00	0.00	4.26
1895	10232	0.526211	GGTTCCAATTTCCCGCAGAC	59.474	55.000	0.00	0.00	0.00	3.51
1896	10233	0.526211	GTTCCAATTTCCCGCAGACC	59.474	55.000	0.00	0.00	0.00	3.85
1897	10234	0.404040	TTCCAATTTCCCGCAGACCT	59.596	50.000	0.00	0.00	0.00	3.85
2054	10398	2.514592	CATCTTCATGGCGGCGGT	60.515	61.111	9.78	0.00	0.00	5.68
2396	10745	5.824904	AGCTAATGAACATCCATTGTGTC	57.175	39.130	0.00	0.00	38.99	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
142	6059	1.771255	GCCTCTAGGGGTCATGTCAAT	59.229	52.381	11.24	0.00	35.18	2.57
143	6060	1.204146	GCCTCTAGGGGTCATGTCAA	58.796	55.000	11.24	0.00	35.18	3.18
144	6061	0.339859	AGCCTCTAGGGGTCATGTCA	59.660	55.000	11.24	0.00	43.10	3.58
145	6062	0.755686	CAGCCTCTAGGGGTCATGTC	59.244	60.000	11.24	0.00	45.10	3.06
146	6063	0.043334	ACAGCCTCTAGGGGTCATGT	59.957	55.000	11.24	10.31	45.10	3.21
147	6064	0.467384	CACAGCCTCTAGGGGTCATG	59.533	60.000	11.24	9.65	45.10	3.07
148	6065	0.692419	CCACAGCCTCTAGGGGTCAT	60.692	60.000	11.24	0.00	45.10	3.06
149	6066	1.306141	CCACAGCCTCTAGGGGTCA	60.306	63.158	11.24	0.00	45.10	4.02
450	6405	7.012704	ACGAAAATTAGCATGCTGTCTTCATAT	59.987	33.333	30.42	11.68	0.00	1.78
461	6416	5.275881	CCGAAATTGACGAAAATTAGCATGC	60.276	40.000	10.51	10.51	0.00	4.06
475	6430	4.222114	CTCAAACAAGCTCCGAAATTGAC	58.778	43.478	0.00	0.00	0.00	3.18
589	6899	2.178580	TGAAGCCCCATGGTCAAATTC	58.821	47.619	11.73	8.04	0.00	2.17
669	6981	4.624364	CGCCACCTGCCACACTGA	62.624	66.667	0.00	0.00	36.24	3.41
761	7500	3.441572	CCTGATGTCACCAATTCTGTTCC	59.558	47.826	0.00	0.00	0.00	3.62
765	7504	3.688185	CACTCCTGATGTCACCAATTCTG	59.312	47.826	0.00	0.00	0.00	3.02
1776	10112	4.994471	GGTCGGCCCGGACGTTTT	62.994	66.667	13.68	0.00	37.82	2.43
1875	10212	0.610785	TCTGCGGGAAATTGGAACCC	60.611	55.000	0.00	0.00	40.17	4.11
1876	10213	0.526211	GTCTGCGGGAAATTGGAACC	59.474	55.000	0.00	0.00	0.00	3.62
1877	10214	0.526211	GGTCTGCGGGAAATTGGAAC	59.474	55.000	0.00	0.00	0.00	3.62
1878	10215	0.404040	AGGTCTGCGGGAAATTGGAA	59.596	50.000	0.00	0.00	0.00	3.53
1879	10216	1.281419	TAGGTCTGCGGGAAATTGGA	58.719	50.000	0.00	0.00	0.00	3.53
1880	10217	2.122783	TTAGGTCTGCGGGAAATTGG	57.877	50.000	0.00	0.00	0.00	3.16
1881	10218	2.223572	GCATTAGGTCTGCGGGAAATTG	60.224	50.000	0.00	0.00	0.00	2.32
1882	10219	2.024414	GCATTAGGTCTGCGGGAAATT	58.976	47.619	0.00	0.00	0.00	1.82
1883	10220	1.064758	TGCATTAGGTCTGCGGGAAAT	60.065	47.619	0.00	0.00	42.62	2.17
1884	10221	0.326595	TGCATTAGGTCTGCGGGAAA	59.673	50.000	0.00	0.00	42.62	3.13
1885	10222	0.326595	TTGCATTAGGTCTGCGGGAA	59.673	50.000	0.00	0.00	42.62	3.97
1886	10223	0.326595	TTTGCATTAGGTCTGCGGGA	59.673	50.000	0.00	0.00	42.62	5.14
1887	10224	1.334869	GATTTGCATTAGGTCTGCGGG	59.665	52.381	0.00	0.00	42.62	6.13
1888	10225	1.334869	GGATTTGCATTAGGTCTGCGG	59.665	52.381	0.00	0.00	42.62	5.69
1889	10226	1.003545	CGGATTTGCATTAGGTCTGCG	60.004	52.381	0.00	0.00	42.62	5.18
1890	10227	1.334869	CCGGATTTGCATTAGGTCTGC	59.665	52.381	0.00	0.00	40.10	4.26
1891	10228	1.949525	CCCGGATTTGCATTAGGTCTG	59.050	52.381	0.73	0.00	0.00	3.51
1892	10229	1.843851	TCCCGGATTTGCATTAGGTCT	59.156	47.619	0.73	0.00	0.00	3.85
1893	10230	2.158813	TCTCCCGGATTTGCATTAGGTC	60.159	50.000	0.73	0.00	0.00	3.85
1894	10231	1.843851	TCTCCCGGATTTGCATTAGGT	59.156	47.619	0.73	0.00	0.00	3.08
1895	10232	2.498167	CTCTCCCGGATTTGCATTAGG	58.502	52.381	0.73	0.00	0.00	2.69
1896	10233	2.158755	ACCTCTCCCGGATTTGCATTAG	60.159	50.000	0.73	0.00	0.00	1.73
1897	10234	1.843851	ACCTCTCCCGGATTTGCATTA	59.156	47.619	0.73	0.00	0.00	1.90
2054	10398	7.880160	TTTTCAAGGTTGATCTCTTTCTTCA	57.120	32.000	0.00	0.00	37.00	3.02
2280	10629	2.659063	CCTCATCACCCTGTCGCCA	61.659	63.158	0.00	0.00	0.00	5.69
2396	10745	5.123186	TCCGTATGCAATCTTTACAACCAAG	59.877	40.000	0.00	0.00	0.00	3.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.