AutoCloner

Multiple sequence alignment - TraesCS3D01G133500

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	TraesCS3D01G133500	chr3D	100.000	2690	0	0	1	2690	92863814	92866503	0.000000e+00	4968.0
1	TraesCS3D01G133500	chr3D	86.536	869	83	17	887	1748	92877463	92876622	0.000000e+00	926.0
2	TraesCS3D01G133500	chr3D	78.924	688	93	31	958	1614	92870813	92871479	1.150000e-113	420.0
3	TraesCS3D01G133500	chr3D	88.000	100	12	0	1183	1282	92891127	92891226	4.700000e-23	119.0
4	TraesCS3D01G133500	chr3B	92.036	1984	83	27	745	2690	143585929	143583983	0.000000e+00	2719.0
5	TraesCS3D01G133500	chr3B	80.144	695	91	29	946	1614	143571062	143570389	2.420000e-130	475.0
6	TraesCS3D01G133500	chr3B	79.213	712	105	24	897	1581	143556729	143557424	3.160000e-124	455.0
7	TraesCS3D01G133500	chr3B	79.630	432	65	13	1171	1591	143506063	143506482	3.390000e-74	289.0
8	TraesCS3D01G133500	chr6D	94.110	747	18	2	1	747	472885477	472886197	0.000000e+00	1112.0
9	TraesCS3D01G133500	chr6D	90.678	118	9	2	2157	2272	337846792	337846675	3.590000e-34	156.0
10	TraesCS3D01G133500	chr6D	89.524	105	11	0	2165	2269	458509496	458509392	1.680000e-27	134.0
11	TraesCS3D01G133500	chr6D	87.069	116	10	2	2157	2272	34190110	34190220	2.810000e-25	126.0
12	TraesCS3D01G133500	chr3A	87.772	965	82	17	799	1748	547193777	547194720	0.000000e+00	1096.0
13	TraesCS3D01G133500	chr3A	90.435	230	19	3	518	745	698898599	698898827	1.570000e-77	300.0
14	TraesCS3D01G133500	chr3A	89.474	76	4	3	730	805	547193693	547193764	2.850000e-15	93.5
15	TraesCS3D01G133500	chr3A	85.393	89	8	5	1	88	701898994	701898910	1.330000e-13	87.9
16	TraesCS3D01G133500	chr3A	81.633	98	7	7	1	94	208648156	208648246	1.340000e-08	71.3
17	TraesCS3D01G133500	chr5D	90.850	765	39	11	1	747	275607237	275606486	0.000000e+00	996.0
18	TraesCS3D01G133500	chr5D	85.593	118	14	3	2158	2274	408743586	408743701	1.310000e-23	121.0
19	TraesCS3D01G133500	chr5D	86.792	106	14	0	2163	2268	486291543	486291438	4.700000e-23	119.0
20	TraesCS3D01G133500	chr5D	93.651	63	2	1	1	63	393844173	393844233	2.850000e-15	93.5
21	TraesCS3D01G133500	chr2A	86.478	318	35	8	429	744	751192468	751192779	2.560000e-90	342.0
22	TraesCS3D01G133500	chr7D	82.398	392	53	13	366	745	513135953	513136340	7.180000e-86	327.0
23	TraesCS3D01G133500	chr6B	91.739	230	16	3	517	744	567404991	567405219	1.550000e-82	316.0
24	TraesCS3D01G133500	chr2D	90.830	229	18	3	518	744	604244783	604244556	1.210000e-78	303.0
25	TraesCS3D01G133500	chr2D	86.842	114	15	0	2157	2270	317879135	317879248	7.820000e-26	128.0
26	TraesCS3D01G133500	chr4B	90.435	230	21	1	516	744	25280872	25281101	4.350000e-78	302.0
27	TraesCS3D01G133500	chr7B	89.744	234	23	1	515	747	624712495	624712262	5.630000e-77	298.0
28	TraesCS3D01G133500	chr1B	82.822	163	6	16	1	143	658415359	658415519	2.810000e-25	126.0
29	TraesCS3D01G133500	chr6A	85.470	117	16	1	2157	2272	608899774	608899658	1.310000e-23	121.0
30	TraesCS3D01G133500	chr4D	85.965	114	12	4	2157	2268	445482484	445482373	4.700000e-23	119.0
31	TraesCS3D01G133500	chr1D	98.077	52	1	0	1	52	326162741	326162690	1.030000e-14	91.6
32	TraesCS3D01G133500	chr2B	88.406	69	4	4	1	67	242984544	242984610	2.220000e-11	80.5
33	TraesCS3D01G133500	chr5A	82.955	88	10	4	1	88	9507014	9507096	1.030000e-09	75.0

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	TraesCS3D01G133500	chr3D	92863814	92866503	2689	False	4968.00	4968	100.000	1	2690	1	chr3D.!!$F1	2689
1	TraesCS3D01G133500	chr3D	92876622	92877463	841	True	926.00	926	86.536	887	1748	1	chr3D.!!$R1	861
2	TraesCS3D01G133500	chr3D	92870813	92871479	666	False	420.00	420	78.924	958	1614	1	chr3D.!!$F2	656
3	TraesCS3D01G133500	chr3B	143583983	143585929	1946	True	2719.00	2719	92.036	745	2690	1	chr3B.!!$R2	1945
4	TraesCS3D01G133500	chr3B	143570389	143571062	673	True	475.00	475	80.144	946	1614	1	chr3B.!!$R1	668
5	TraesCS3D01G133500	chr3B	143556729	143557424	695	False	455.00	455	79.213	897	1581	1	chr3B.!!$F2	684
6	TraesCS3D01G133500	chr6D	472885477	472886197	720	False	1112.00	1112	94.110	1	747	1	chr6D.!!$F2	746
7	TraesCS3D01G133500	chr3A	547193693	547194720	1027	False	594.75	1096	88.623	730	1748	2	chr3A.!!$F3	1018
8	TraesCS3D01G133500	chr5D	275606486	275607237	751	True	996.00	996	90.850	1	747	1	chr5D.!!$R1	746

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
660	677	0.037734	CTTTACCGAGGGCCAAAGGT	59.962	55.0	18.95	18.95	40.52	3.5	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1767	1864	0.179081	GGAACTCGGTCATGGGCTAC	60.179	60.0	0.0	0.0	0.0	3.58	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	46	4.169856	ACTGAGATATCCCTCCTTCTGTCT	59.830	45.833	0.00	0.00	32.32	3.41
58	59	6.339587	TCCTTCTGTCTTTCTTTCTCTCTC	57.660	41.667	0.00	0.00	0.00	3.20
156	157	2.185608	GAGACGGGCAGAAGCTCC	59.814	66.667	0.00	0.00	38.29	4.70
427	428	1.380112	GGAGGCCGGACAGAGTAGT	60.380	63.158	11.69	0.00	0.00	2.73
647	664	7.859325	TGGATAATTAGCAACTGACTTTACC	57.141	36.000	2.72	0.00	0.00	2.85
660	677	0.037734	CTTTACCGAGGGCCAAAGGT	59.962	55.000	18.95	18.95	40.52	3.50
679	696	9.554395	CCAAAGGTCAATACATATACATGTGTA	57.446	33.333	9.11	6.70	45.17	2.90
751	769	6.338146	ACTATACACATCTAACAACACGCAT	58.662	36.000	0.00	0.00	0.00	4.73
837	878	1.483004	TGTTGTCGGTTCAGACTTCCA	59.517	47.619	4.95	0.00	41.47	3.53
856	897	7.661040	ACTTCCAACTCGAATTTGAATCAATT	58.339	30.769	7.80	0.00	0.00	2.32
923	964	4.153117	CGGACACAGAAAAATCTCTCAAGG	59.847	45.833	0.00	0.00	0.00	3.61
1177	1274	0.391661	CTACATGTGGCGCCTCACTT	60.392	55.000	31.72	22.76	38.40	3.16
1194	1291	2.237143	CACTTATGTTCTGGAGCCTGGA	59.763	50.000	0.00	0.00	0.00	3.86
1310	1407	4.785950	GCACATGCGACGAGTCTA	57.214	55.556	0.00	0.00	0.00	2.59
1311	1408	3.258225	GCACATGCGACGAGTCTAT	57.742	52.632	0.00	0.00	0.00	1.98
1431	1528	2.595463	TGGTCGACGACGGACCTT	60.595	61.111	20.92	0.00	39.01	3.50
1533	1630	7.191551	CACAAATTCATATCAGCGTTGAGATT	58.808	34.615	6.65	0.27	33.12	2.40
1584	1681	0.538057	CATGCCTCACCTTGTGTGGT	60.538	55.000	14.65	0.00	45.53	4.16
1616	1713	2.900106	GCCAGTCCTTCCCAGCACT	61.900	63.158	0.00	0.00	0.00	4.40
1637	1734	4.305479	AGCGATGCCGATGCCGAT	62.305	61.111	0.00	0.00	38.22	4.18
1638	1735	4.081030	GCGATGCCGATGCCGATG	62.081	66.667	0.00	0.00	38.22	3.84
1639	1736	4.081030	CGATGCCGATGCCGATGC	62.081	66.667	0.00	0.00	38.22	3.91
1680	1777	3.554324	TGTGTGCGACAGAAAGAAAGTAC	59.446	43.478	0.00	0.00	0.00	2.73
1689	1786	8.706035	GCGACAGAAAGAAAGTACATTTACTAA	58.294	33.333	0.00	0.00	37.59	2.24
1740	1837	3.081804	CCAAAGCTATTTCCCACTCGTT	58.918	45.455	0.00	0.00	0.00	3.85
1748	1845	5.063564	GCTATTTCCCACTCGTTTTCTAGTG	59.936	44.000	0.00	0.00	41.41	2.74
1767	1864	3.195698	GTTCGCGCTTAGGGCCTG	61.196	66.667	18.53	0.23	38.28	4.85
1771	1868	2.589159	GCGCTTAGGGCCTGTAGC	60.589	66.667	24.60	24.60	42.60	3.58
1787	1888	0.616395	TAGCCCATGACCGAGTTCCA	60.616	55.000	0.00	0.00	0.00	3.53
1802	1910	4.273480	CGAGTTCCATTGTGTTTCTTCACT	59.727	41.667	0.00	0.00	38.90	3.41
1917	2035	3.243839	GCTTGGAGATTTGCTTGACCAAA	60.244	43.478	0.00	0.00	38.87	3.28
2029	2149	7.714703	TCATTGTCAACTTGATTTGTGATTCA	58.285	30.769	0.00	0.00	0.00	2.57
2046	2166	7.067116	TGTGATTCATCGTTCTTTTCGTAAAC	58.933	34.615	0.00	0.00	0.00	2.01
2093	2213	3.840468	AGTTCGTGTTTCCACCAAAAAC	58.160	40.909	0.00	0.00	38.41	2.43
2178	2298	3.930012	CGAGATTCCCCTCCCCGC	61.930	72.222	0.00	0.00	0.00	6.13
2226	2346	4.162690	AGGCGAATCCACGGGCTC	62.163	66.667	0.00	0.00	37.29	4.70
2262	2382	0.393132	GTGGAGAGTTTGCCCTAGCC	60.393	60.000	0.00	0.00	38.69	3.93
2277	2397	2.829592	GCCGCCTAGGGTAGCAAT	59.170	61.111	11.72	0.00	41.48	3.56
2285	2405	3.879892	GCCTAGGGTAGCAATTTCTCTTG	59.120	47.826	11.72	0.00	0.00	3.02
2294	2414	7.244192	GGTAGCAATTTCTCTTGAACATGTAC	58.756	38.462	0.00	0.00	31.02	2.90
2295	2415	7.119846	GGTAGCAATTTCTCTTGAACATGTACT	59.880	37.037	0.00	0.00	31.02	2.73
2296	2416	9.151471	GTAGCAATTTCTCTTGAACATGTACTA	57.849	33.333	0.00	0.00	31.02	1.82
2297	2417	8.261492	AGCAATTTCTCTTGAACATGTACTAG	57.739	34.615	0.00	0.00	31.02	2.57
2298	2418	7.880195	AGCAATTTCTCTTGAACATGTACTAGT	59.120	33.333	0.00	0.00	31.02	2.57
2299	2419	8.507249	GCAATTTCTCTTGAACATGTACTAGTT	58.493	33.333	0.00	3.65	31.02	2.24
2302	2422	8.958119	TTTCTCTTGAACATGTACTAGTTTGT	57.042	30.769	0.00	0.04	31.02	2.83
2303	2423	8.958119	TTCTCTTGAACATGTACTAGTTTGTT	57.042	30.769	14.67	14.67	35.14	2.83
2304	2424	8.958119	TCTCTTGAACATGTACTAGTTTGTTT	57.042	30.769	15.46	0.00	32.73	2.83
2305	2425	9.042008	TCTCTTGAACATGTACTAGTTTGTTTC	57.958	33.333	15.46	7.90	32.73	2.78
2306	2426	8.958119	TCTTGAACATGTACTAGTTTGTTTCT	57.042	30.769	15.46	0.19	32.73	2.52
2307	2427	8.826710	TCTTGAACATGTACTAGTTTGTTTCTG	58.173	33.333	15.46	10.54	32.73	3.02
2308	2428	8.500753	TTGAACATGTACTAGTTTGTTTCTGT	57.499	30.769	15.46	3.70	32.73	3.41
2309	2429	9.602568	TTGAACATGTACTAGTTTGTTTCTGTA	57.397	29.630	15.46	3.72	32.73	2.74
2310	2430	9.772973	TGAACATGTACTAGTTTGTTTCTGTAT	57.227	29.630	15.46	0.00	32.73	2.29
2343	2463	8.449251	TGCATGAGATGTGCTTTATTTATGTA	57.551	30.769	0.00	0.00	42.92	2.29
2394	2514	6.787085	ATGCTTTCTTATATAGCCGTTGAC	57.213	37.500	0.00	0.00	34.03	3.18
2488	2609	2.446435	TGTTTTCCCAGAGCATTAGGC	58.554	47.619	0.00	0.00	45.30	3.93
2514	2639	5.447478	TTCGTCACAAAAATTTGCAAGTG	57.553	34.783	0.00	3.48	41.79	3.16
2547	2672	5.731599	TCATCAATGTTTGTTGCCAAAAC	57.268	34.783	0.00	0.00	41.99	2.43
2629	2754	0.249238	GCCTGTGAGCAGATACTCCG	60.249	60.000	0.00	0.00	45.28	4.63
2655	2780	7.447430	CGTCCAAATTTGCATCATTTTTCTAC	58.553	34.615	12.92	0.02	0.00	2.59
2666	2791	9.806203	TGCATCATTTTTCTACCATCTATTTTG	57.194	29.630	0.00	0.00	0.00	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
647	664	1.339631	TGTATTGACCTTTGGCCCTCG	60.340	52.381	0.00	0.00	0.00	4.63
679	696	1.780919	AGGGGTTTCCTGCACTTTACT	59.219	47.619	0.00	0.00	46.07	2.24
751	769	0.803380	TCGACTCGTATCGTCTCGCA	60.803	55.000	10.11	0.00	42.80	5.10
837	878	6.624423	CAGGGAATTGATTCAAATTCGAGTT	58.376	36.000	2.68	0.00	44.20	3.01
856	897	3.536917	CGATACGGGCAGCAGGGA	61.537	66.667	0.00	0.00	0.00	4.20
923	964	7.371936	CGGCTTTACATCTATATATAGGAGGC	58.628	42.308	17.81	15.33	0.00	4.70
1169	1266	2.284190	GCTCCAGAACATAAGTGAGGC	58.716	52.381	0.00	0.00	0.00	4.70
1177	1274	3.898123	GAGTATCCAGGCTCCAGAACATA	59.102	47.826	0.00	0.00	0.00	2.29
1194	1291	2.099756	GCCAGTAAACCGTACCGAGTAT	59.900	50.000	0.00	0.00	0.00	2.12
1209	1306	2.606519	AGCCCTTGGACGCCAGTA	60.607	61.111	0.00	0.00	33.81	2.74
1249	1346	2.125106	GTTGAAGGCCGGCGAGAT	60.125	61.111	22.54	5.90	0.00	2.75
1310	1407	0.898320	CACGGTGTTCTCCTCCTGAT	59.102	55.000	0.00	0.00	0.00	2.90
1311	1408	0.178973	TCACGGTGTTCTCCTCCTGA	60.179	55.000	8.17	0.00	0.00	3.86
1431	1528	2.492088	CTGATTAGACAGGGACACGTCA	59.508	50.000	0.00	0.00	34.48	4.35
1475	1572	2.419198	CCTCCATCTTCTCCCGCG	59.581	66.667	0.00	0.00	0.00	6.46
1533	1630	1.348008	CCTCTGGATGGGCTGGCTTA	61.348	60.000	0.00	0.00	0.00	3.09
1562	1659	1.303888	CACAAGGTGAGGCATGGCT	60.304	57.895	23.58	23.58	35.23	4.75
1634	1731	2.741985	TGCACTTGGACGGCATCG	60.742	61.111	0.00	0.00	43.02	3.84
1635	1732	3.044059	GCTGCACTTGGACGGCATC	62.044	63.158	0.00	0.00	38.10	3.91
1636	1733	3.058160	GCTGCACTTGGACGGCAT	61.058	61.111	0.00	0.00	38.10	4.40
1637	1734	4.560743	TGCTGCACTTGGACGGCA	62.561	61.111	0.00	0.00	45.62	5.69
1638	1735	4.030452	GTGCTGCACTTGGACGGC	62.030	66.667	24.68	0.00	38.70	5.68
1639	1736	2.591429	TGTGCTGCACTTGGACGG	60.591	61.111	30.43	0.00	35.11	4.79
1680	1777	6.912591	GCCGTTGATGATCCTTTTAGTAAATG	59.087	38.462	0.00	0.00	0.00	2.32
1689	1786	1.376609	GCCGCCGTTGATGATCCTTT	61.377	55.000	0.00	0.00	0.00	3.11
1767	1864	0.179081	GGAACTCGGTCATGGGCTAC	60.179	60.000	0.00	0.00	0.00	3.58
1771	1868	1.340017	ACAATGGAACTCGGTCATGGG	60.340	52.381	0.00	0.00	0.00	4.00
1897	2015	3.960102	AGTTTGGTCAAGCAAATCTCCAA	59.040	39.130	10.23	0.00	33.90	3.53
1917	2035	7.461182	TCCAATGGATTTAATGACGAAAAGT	57.539	32.000	0.00	0.00	0.00	2.66
2046	2166	9.949174	TCATTGTTATAAATTGATGGTGATTCG	57.051	29.630	0.00	0.00	0.00	3.34
2093	2213	1.532868	CTTGAGCTTCAACCAACCGAG	59.467	52.381	0.00	0.00	32.21	4.63
2226	2346	0.391661	CACTCAAGACATCACCGGGG	60.392	60.000	6.32	0.00	0.00	5.73
2230	2350	2.564947	ACTCTCCACTCAAGACATCACC	59.435	50.000	0.00	0.00	0.00	4.02
2262	2382	2.103263	AGAGAAATTGCTACCCTAGGCG	59.897	50.000	2.05	0.00	0.00	5.52
2277	2397	8.958119	ACAAACTAGTACATGTTCAAGAGAAA	57.042	30.769	2.30	0.00	35.08	2.52
2299	2419	9.791820	CTCATGCATTTGATAATACAGAAACAA	57.208	29.630	0.00	0.00	0.00	2.83
2300	2420	9.176460	TCTCATGCATTTGATAATACAGAAACA	57.824	29.630	0.00	0.00	0.00	2.83
2303	2423	9.346005	ACATCTCATGCATTTGATAATACAGAA	57.654	29.630	0.00	0.00	0.00	3.02
2304	2424	8.780249	CACATCTCATGCATTTGATAATACAGA	58.220	33.333	0.00	0.00	0.00	3.41
2305	2425	7.537649	GCACATCTCATGCATTTGATAATACAG	59.462	37.037	0.00	0.00	42.88	2.74
2306	2426	7.229907	AGCACATCTCATGCATTTGATAATACA	59.770	33.333	0.00	0.00	45.92	2.29
2307	2427	7.591165	AGCACATCTCATGCATTTGATAATAC	58.409	34.615	0.00	0.00	45.92	1.89
2308	2428	7.754851	AGCACATCTCATGCATTTGATAATA	57.245	32.000	0.00	0.00	45.92	0.98
2309	2429	6.650427	AGCACATCTCATGCATTTGATAAT	57.350	33.333	0.00	0.00	45.92	1.28
2310	2430	6.459670	AAGCACATCTCATGCATTTGATAA	57.540	33.333	0.00	0.00	45.92	1.75
2311	2431	6.459670	AAAGCACATCTCATGCATTTGATA	57.540	33.333	0.00	0.00	45.92	2.15
2312	2432	5.339008	AAAGCACATCTCATGCATTTGAT	57.661	34.783	0.00	0.43	45.92	2.57
2313	2433	4.794278	AAAGCACATCTCATGCATTTGA	57.206	36.364	0.00	0.00	45.92	2.69
2368	2488	7.599245	GTCAACGGCTATATAAGAAAGCATACT	59.401	37.037	0.00	0.00	38.01	2.12
2394	2514	8.936864	AGAAATAGTTTATCCAGTGAAGAAACG	58.063	33.333	0.00	0.00	36.36	3.60
2488	2609	7.006387	CACTTGCAAATTTTTGTGACGAAAAAG	59.994	33.333	14.13	8.71	38.02	2.27
2581	2706	5.811190	TGCTCCCTAACAAGCAGTAAATTA	58.189	37.500	0.00	0.00	43.30	1.40
2582	2707	4.662278	TGCTCCCTAACAAGCAGTAAATT	58.338	39.130	0.00	0.00	43.30	1.82
2591	2716	2.424956	GGCTCAAATGCTCCCTAACAAG	59.575	50.000	0.00	0.00	0.00	3.16
2593	2718	1.635487	AGGCTCAAATGCTCCCTAACA	59.365	47.619	0.00	0.00	0.00	2.41
2595	2720	1.635487	ACAGGCTCAAATGCTCCCTAA	59.365	47.619	0.00	0.00	0.00	2.69
2629	2754	4.666928	AAAATGATGCAAATTTGGACGC	57.333	36.364	19.47	12.74	0.00	5.19
2655	2780	7.338800	AGGCAGTAACATTCAAAATAGATGG	57.661	36.000	0.00	0.00	0.00	3.51
2664	2789	6.533367	GTGAAACAAAAGGCAGTAACATTCAA	59.467	34.615	0.00	0.00	36.32	2.69
2666	2791	6.510746	GTGAAACAAAAGGCAGTAACATTC	57.489	37.500	0.00	0.00	36.32	2.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.