AutoCloner

Multiple sequence alignment - TraesCS3D01G511200

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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	TraesCS3D01G511200	chr3D	100.000	2242	0	0	1	2242	596022890	596020649	0.000000e+00	4141
1	TraesCS3D01G511200	chr3D	85.864	1146	128	17	719	1836	595960884	595959745	0.000000e+00	1188
2	TraesCS3D01G511200	chr3D	84.018	901	108	16	945	1836	595999888	595999015	0.000000e+00	833
3	TraesCS3D01G511200	chr3D	92.066	542	32	9	1	536	595966864	595966328	0.000000e+00	752
4	TraesCS3D01G511200	chr3D	100.000	297	0	0	2373	2669	596020518	596020222	1.400000e-152	549
5	TraesCS3D01G511200	chr3D	93.491	169	11	0	899	1067	596037868	596037700	4.410000e-63	252
6	TraesCS3D01G511200	chr3D	94.194	155	9	0	535	689	595961037	595960883	1.240000e-58	237
7	TraesCS3D01G511200	chr3D	91.124	169	14	1	899	1067	595987382	595987215	7.430000e-56	228
8	TraesCS3D01G511200	chr3D	82.101	257	41	5	1869	2121	34772058	34772313	5.790000e-52	215
9	TraesCS3D01G511200	chr3A	93.543	1688	67	18	1	1651	726764993	726763311	0.000000e+00	2475
10	TraesCS3D01G511200	chr3A	96.974	760	15	3	900	1651	726753510	726752751	0.000000e+00	1269
11	TraesCS3D01G511200	chr3A	93.386	756	38	9	1	751	726750575	726749827	0.000000e+00	1109
12	TraesCS3D01G511200	chr3A	92.211	796	32	20	1	782	726754477	726753698	0.000000e+00	1099
13	TraesCS3D01G511200	chr3A	87.343	956	99	15	899	1840	726749705	726748758	0.000000e+00	1075
14	TraesCS3D01G511200	chr3A	92.045	352	18	4	1844	2194	726762554	726762212	1.110000e-133	486
15	TraesCS3D01G511200	chr3A	93.667	300	12	3	1844	2142	726752099	726751806	2.440000e-120	442
16	TraesCS3D01G511200	chr3A	95.477	199	8	1	1645	1843	726752341	726752144	1.540000e-82	316
17	TraesCS3D01G511200	chr3A	95.855	193	7	1	1645	1837	726762921	726762730	7.170000e-81	311
18	TraesCS3D01G511200	chr3A	94.118	153	8	1	2420	2571	726761881	726761729	5.750000e-57	231
19	TraesCS3D01G511200	chr3A	89.583	96	7	3	1874	1968	540240408	540240315	4.670000e-23	119
20	TraesCS3D01G511200	chr3B	93.128	1557	61	14	30	1546	799144492	799142942	0.000000e+00	2241
21	TraesCS3D01G511200	chr3B	86.520	957	104	13	899	1836	799113523	799112573	0.000000e+00	1029
22	TraesCS3D01G511200	chr3B	92.500	400	24	2	1844	2242	799140099	799139705	3.860000e-158	568
23	TraesCS3D01G511200	chr3B	95.333	300	12	2	1545	1843	799140442	799140144	2.400000e-130	475
24	TraesCS3D01G511200	chr3B	93.491	169	11	0	899	1067	799187016	799186848	4.410000e-63	252
25	TraesCS3D01G511200	chr5D	82.373	295	35	14	1869	2152	502182744	502182456	9.550000e-60	241
26	TraesCS3D01G511200	chr7B	82.946	258	36	7	1869	2121	174972317	174972063	2.670000e-55	226
27	TraesCS3D01G511200	chr2B	83.544	237	32	7	2437	2669	572086513	572086746	5.790000e-52	215
28	TraesCS3D01G511200	chr7A	82.039	206	32	5	1873	2076	658726047	658725845	1.270000e-38	171
29	TraesCS3D01G511200	chr2A	79.916	239	41	6	1869	2103	12969599	12969834	4.570000e-38	169

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	TraesCS3D01G511200	chr3D	596020222	596022890	2668	True	2345.000000	4141	100.000000	1	2669	2	chr3D.!!$R6	2668
1	TraesCS3D01G511200	chr3D	595999015	595999888	873	True	833.000000	833	84.018000	945	1836	1	chr3D.!!$R3	891
2	TraesCS3D01G511200	chr3D	595966328	595966864	536	True	752.000000	752	92.066000	1	536	1	chr3D.!!$R1	535
3	TraesCS3D01G511200	chr3D	595959745	595961037	1292	True	712.500000	1188	90.029000	535	1836	2	chr3D.!!$R5	1301
4	TraesCS3D01G511200	chr3A	726748758	726754477	5719	True	885.000000	1269	93.176333	1	2142	6	chr3A.!!$R2	2141
5	TraesCS3D01G511200	chr3A	726761729	726764993	3264	True	875.750000	2475	93.890250	1	2571	4	chr3A.!!$R3	2570
6	TraesCS3D01G511200	chr3B	799139705	799144492	4787	True	1094.666667	2241	93.653667	30	2242	3	chr3B.!!$R3	2212
7	TraesCS3D01G511200	chr3B	799112573	799113523	950	True	1029.000000	1029	86.520000	899	1836	1	chr3B.!!$R1	937

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
320	337	1.33802	AGAAGCAGAAAGGCAAAACCG	59.662	47.619	0.0	0.0	46.52	4.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2203	5436	1.244816	TGCATCGTATAGGAGGTCCG	58.755	55.0	8.67	0.0	42.08	4.79	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
113	115	4.773510	CAACTCCTCTTACGAAAAAGCAC	58.226	43.478	0.00	0.00	0.00	4.40
297	312	9.639601	AACTAGGAAAACAAAAGAAACAGAAAG	57.360	29.630	0.00	0.00	0.00	2.62
320	337	1.338020	AGAAGCAGAAAGGCAAAACCG	59.662	47.619	0.00	0.00	46.52	4.44
563	583	7.514127	ACGCCATCTATATATTCTATCCCCAAT	59.486	37.037	0.00	0.00	0.00	3.16
589	609	2.699846	ACTCTCGTACTACTCCGGATCT	59.300	50.000	3.57	0.00	0.00	2.75
677	703	5.738619	TCAAGGTACAGAGCTGTTCATTA	57.261	39.130	8.60	0.00	41.83	1.90
934	1045	5.793026	ATTGTTGACGTTTTTGTGCATTT	57.207	30.435	0.00	0.00	0.00	2.32
941	1052	6.142139	TGACGTTTTTGTGCATTTCTCTATG	58.858	36.000	0.00	0.00	0.00	2.23
1652	4714	3.072330	TGCACCCTTCATTTGAGTCTACA	59.928	43.478	0.00	0.00	0.00	2.74
1758	4820	4.552355	CGGTGTGTTGTGACTTATGAGTA	58.448	43.478	0.00	0.00	35.88	2.59
1829	4892	7.012515	TGTTGTTTTCAAGTACGGATGTGTTAT	59.987	33.333	0.00	0.00	40.74	1.89
1855	5087	2.679082	ACAATAGTGCGGAGACCCTAT	58.321	47.619	0.00	0.00	0.00	2.57
1858	5090	4.838986	ACAATAGTGCGGAGACCCTATATT	59.161	41.667	0.00	0.00	0.00	1.28
1891	5123	6.873997	ACAACGTTGAGGATATCACTTATCA	58.126	36.000	33.66	0.00	38.82	2.15
2142	5375	7.698836	ACATAACAAGATCTGCAAACAAAAC	57.301	32.000	0.00	0.00	0.00	2.43
2425	6449	2.851824	CGTGAAAAACAGGAGTTTGTGC	59.148	45.455	0.00	0.00	46.79	4.57
2496	6521	5.326200	ACACGATACTCAAGACCTAAAGG	57.674	43.478	0.00	0.00	42.17	3.11
2529	6813	9.687717	CAAAACATAACACTTGAAAACAATCAC	57.312	29.630	0.00	0.00	0.00	3.06
2571	6855	3.314080	TGGAGCAAAAGTTTGTACTTCCG	59.686	43.478	5.71	0.00	43.74	4.30
2572	6856	3.562557	GGAGCAAAAGTTTGTACTTCCGA	59.437	43.478	5.71	0.00	43.74	4.55
2573	6857	4.035909	GGAGCAAAAGTTTGTACTTCCGAA	59.964	41.667	5.71	0.00	43.74	4.30
2574	6858	4.916870	AGCAAAAGTTTGTACTTCCGAAC	58.083	39.130	5.71	0.00	43.74	3.95
2575	6859	4.396790	AGCAAAAGTTTGTACTTCCGAACA	59.603	37.500	5.71	0.00	43.74	3.18
2576	6860	5.096849	GCAAAAGTTTGTACTTCCGAACAA	58.903	37.500	5.71	0.00	43.74	2.83
2577	6861	5.746721	GCAAAAGTTTGTACTTCCGAACAAT	59.253	36.000	5.71	0.00	43.74	2.71
2578	6862	6.075046	GCAAAAGTTTGTACTTCCGAACAATC	60.075	38.462	5.71	0.00	43.74	2.67
2579	6863	5.684550	AAGTTTGTACTTCCGAACAATCC	57.315	39.130	0.00	0.00	40.60	3.01
2580	6864	4.969484	AGTTTGTACTTCCGAACAATCCT	58.031	39.130	0.00	0.00	35.64	3.24
2581	6865	5.374071	AGTTTGTACTTCCGAACAATCCTT	58.626	37.500	0.00	0.00	35.64	3.36
2582	6866	5.238650	AGTTTGTACTTCCGAACAATCCTTG	59.761	40.000	0.00	0.00	35.64	3.61
2583	6867	4.610605	TGTACTTCCGAACAATCCTTGA	57.389	40.909	0.00	0.00	0.00	3.02
2584	6868	4.312443	TGTACTTCCGAACAATCCTTGAC	58.688	43.478	0.00	0.00	0.00	3.18
2585	6869	3.485463	ACTTCCGAACAATCCTTGACA	57.515	42.857	0.00	0.00	0.00	3.58
2586	6870	3.815809	ACTTCCGAACAATCCTTGACAA	58.184	40.909	0.00	0.00	0.00	3.18
2587	6871	4.204012	ACTTCCGAACAATCCTTGACAAA	58.796	39.130	0.00	0.00	0.00	2.83
2588	6872	4.036380	ACTTCCGAACAATCCTTGACAAAC	59.964	41.667	0.00	0.00	0.00	2.93
2589	6873	2.546368	TCCGAACAATCCTTGACAAACG	59.454	45.455	0.00	0.00	0.00	3.60
2590	6874	2.307049	CGAACAATCCTTGACAAACGC	58.693	47.619	0.00	0.00	0.00	4.84
2591	6875	2.307049	GAACAATCCTTGACAAACGCG	58.693	47.619	3.53	3.53	0.00	6.01
2592	6876	1.588674	ACAATCCTTGACAAACGCGA	58.411	45.000	15.93	0.00	0.00	5.87
2593	6877	1.263217	ACAATCCTTGACAAACGCGAC	59.737	47.619	15.93	0.00	0.00	5.19
2594	6878	0.872388	AATCCTTGACAAACGCGACC	59.128	50.000	15.93	0.00	0.00	4.79
2595	6879	0.250124	ATCCTTGACAAACGCGACCA	60.250	50.000	15.93	0.00	0.00	4.02
2596	6880	0.462225	TCCTTGACAAACGCGACCAA	60.462	50.000	15.93	8.08	0.00	3.67
2597	6881	0.378962	CCTTGACAAACGCGACCAAA	59.621	50.000	15.93	0.00	0.00	3.28
2598	6882	1.001815	CCTTGACAAACGCGACCAAAT	60.002	47.619	15.93	0.00	0.00	2.32
2599	6883	2.542824	CCTTGACAAACGCGACCAAATT	60.543	45.455	15.93	0.00	0.00	1.82
2600	6884	2.853731	TGACAAACGCGACCAAATTT	57.146	40.000	15.93	0.00	0.00	1.82
2601	6885	3.152261	TGACAAACGCGACCAAATTTT	57.848	38.095	15.93	0.00	0.00	1.82
2602	6886	3.109619	TGACAAACGCGACCAAATTTTC	58.890	40.909	15.93	3.40	0.00	2.29
2603	6887	3.109619	GACAAACGCGACCAAATTTTCA	58.890	40.909	15.93	0.00	0.00	2.69
2604	6888	3.512680	ACAAACGCGACCAAATTTTCAA	58.487	36.364	15.93	0.00	0.00	2.69
2605	6889	3.927142	ACAAACGCGACCAAATTTTCAAA	59.073	34.783	15.93	0.00	0.00	2.69
2606	6890	4.389077	ACAAACGCGACCAAATTTTCAAAA	59.611	33.333	15.93	0.00	0.00	2.44
2607	6891	5.064071	ACAAACGCGACCAAATTTTCAAAAT	59.936	32.000	15.93	0.00	0.00	1.82
2608	6892	5.726729	AACGCGACCAAATTTTCAAAATT	57.273	30.435	15.93	1.98	0.00	1.82
2609	6893	6.830114	AACGCGACCAAATTTTCAAAATTA	57.170	29.167	15.93	0.00	0.00	1.40
2610	6894	7.414814	AACGCGACCAAATTTTCAAAATTAT	57.585	28.000	15.93	0.00	0.00	1.28
2611	6895	6.816377	ACGCGACCAAATTTTCAAAATTATG	58.184	32.000	15.93	8.96	0.00	1.90
2614	6898	8.167985	CGCGACCAAATTTTCAAAATTATGAAT	58.832	29.630	8.55	2.71	38.98	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
297	312	3.804325	GGTTTTGCCTTTCTGCTTCTTTC	59.196	43.478	0.00	0.00	0.00	2.62
320	337	1.639298	ATGCTGCTTCTTTCGTCGGC	61.639	55.000	0.00	0.00	0.00	5.54
404	421	0.111446	TCCCACTCATTTTGGCCGAA	59.889	50.000	0.00	0.00	32.13	4.30
563	583	3.181471	CCGGAGTAGTACGAGAGTTAGGA	60.181	52.174	2.98	0.00	46.40	2.94
589	609	1.460305	GCAGGCAGGGAGGGAGATA	60.460	63.158	0.00	0.00	0.00	1.98
677	703	4.023291	AGAATGGATACGCCCAAAACAAT	58.977	39.130	0.00	0.00	40.04	2.71
871	954	9.658799	GGACAATGTTGAGCAGTACATATATAT	57.341	33.333	0.00	0.00	34.04	0.86
872	955	8.646900	TGGACAATGTTGAGCAGTACATATATA	58.353	33.333	0.00	0.00	34.04	0.86
873	956	7.442364	GTGGACAATGTTGAGCAGTACATATAT	59.558	37.037	0.00	0.00	34.04	0.86
891	975	0.036388	CCAGCAGGTACGTGGACAAT	60.036	55.000	16.75	0.00	32.60	2.71
941	1052	9.351570	GTCGTTAGACACTTATATATTTAGGCC	57.648	37.037	0.00	0.00	46.32	5.19
1095	1218	0.673985	TGAAGATGAGGCGATACCGG	59.326	55.000	0.00	0.00	46.52	5.28
1829	4892	3.119245	GGTCTCCGCACTATTGTAACAGA	60.119	47.826	0.00	0.00	0.00	3.41
1855	5087	7.643569	TCCTCAACGTTGTATACTACCAATA	57.356	36.000	26.47	2.91	0.00	1.90
1858	5090	7.503230	TGATATCCTCAACGTTGTATACTACCA	59.497	37.037	26.47	14.16	0.00	3.25
1891	5123	4.104086	TCCCCAGCCGATTGAGATATAAT	58.896	43.478	0.00	0.00	0.00	1.28
1901	5133	3.593442	TCATTTAATCCCCAGCCGATT	57.407	42.857	0.00	0.00	34.40	3.34
2110	5342	9.448438	TTTGCAGATCTTGTTATGTAATACAGT	57.552	29.630	0.00	0.00	0.00	3.55
2111	5343	9.708222	GTTTGCAGATCTTGTTATGTAATACAG	57.292	33.333	0.00	0.00	0.00	2.74
2112	5344	9.225436	TGTTTGCAGATCTTGTTATGTAATACA	57.775	29.630	0.00	0.00	0.00	2.29
2142	5375	6.281405	GGGTCTATTCCTAACACTATGTGTG	58.719	44.000	4.01	1.20	46.79	3.82
2163	5396	4.502604	CGGGAACATACTGATAAATCGGGT	60.503	45.833	3.92	0.00	37.50	5.28
2203	5436	1.244816	TGCATCGTATAGGAGGTCCG	58.755	55.000	8.67	0.00	42.08	4.79
2425	6449	1.364626	CCTTTGGCTAGCAGCACTCG	61.365	60.000	18.24	0.00	44.75	4.18
2454	6478	7.470079	TCGTGTTGTACTTCTGACAGTATATC	58.530	38.462	1.59	0.00	31.82	1.63
2496	6521	1.059942	GTGTTATGTTTTGCGGCTGC	58.940	50.000	11.65	11.65	43.20	5.25
2575	6859	0.872388	GGTCGCGTTTGTCAAGGATT	59.128	50.000	5.77	0.00	0.00	3.01
2576	6860	0.250124	TGGTCGCGTTTGTCAAGGAT	60.250	50.000	5.77	0.00	0.00	3.24
2577	6861	0.462225	TTGGTCGCGTTTGTCAAGGA	60.462	50.000	5.77	0.00	0.00	3.36
2578	6862	0.378962	TTTGGTCGCGTTTGTCAAGG	59.621	50.000	5.77	0.00	0.00	3.61
2579	6863	2.399396	ATTTGGTCGCGTTTGTCAAG	57.601	45.000	5.77	0.00	0.00	3.02
2580	6864	2.853731	AATTTGGTCGCGTTTGTCAA	57.146	40.000	5.77	2.23	0.00	3.18
2581	6865	2.853731	AAATTTGGTCGCGTTTGTCA	57.146	40.000	5.77	0.00	0.00	3.58
2582	6866	3.109619	TGAAAATTTGGTCGCGTTTGTC	58.890	40.909	5.77	0.33	0.00	3.18
2583	6867	3.152261	TGAAAATTTGGTCGCGTTTGT	57.848	38.095	5.77	0.00	0.00	2.83
2584	6868	4.506838	TTTGAAAATTTGGTCGCGTTTG	57.493	36.364	5.77	0.00	0.00	2.93
2585	6869	5.726729	ATTTTGAAAATTTGGTCGCGTTT	57.273	30.435	5.77	0.00	0.00	3.60
2586	6870	5.726729	AATTTTGAAAATTTGGTCGCGTT	57.273	30.435	9.92	0.00	0.00	4.84
2587	6871	6.642950	TCATAATTTTGAAAATTTGGTCGCGT	59.357	30.769	19.57	0.00	0.00	6.01
2588	6872	7.043454	TCATAATTTTGAAAATTTGGTCGCG	57.957	32.000	19.57	0.00	0.00	5.87

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.