AutoCloner

Multiple sequence alignment - TraesCS4A01G374400

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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	TraesCS4A01G374400	chr4A	100.000	3102	0	0	1	3102	649173843	649176944	0.000000e+00	5729
1	TraesCS4A01G374400	chr4A	93.918	2088	117	9	1	2087	657366537	657368615	0.000000e+00	3144
2	TraesCS4A01G374400	chr4A	93.726	2088	123	8	1	2087	657306842	657308922	0.000000e+00	3123
3	TraesCS4A01G374400	chr4A	93.416	2096	123	7	1	2087	649144369	649146458	0.000000e+00	3092
4	TraesCS4A01G374400	chr4A	93.164	1024	57	10	2085	3102	657309765	657310781	0.000000e+00	1491
5	TraesCS4A01G374400	chr4A	92.480	1024	65	8	2085	3102	657369456	657370473	0.000000e+00	1454
6	TraesCS4A01G374400	chr4A	90.010	1051	71	16	2085	3102	649147300	649148349	0.000000e+00	1328
7	TraesCS4A01G374400	chr4A	87.888	644	51	16	2085	2705	649059173	649059812	0.000000e+00	732
8	TraesCS4A01G374400	chr4A	90.227	440	29	5	2374	2801	649195950	649196387	2.090000e-156	562
9	TraesCS4A01G374400	chr7B	94.157	2088	117	5	1	2087	2564611	2562528	0.000000e+00	3175
10	TraesCS4A01G374400	chr7B	93.144	1021	59	7	2085	3099	2561686	2560671	0.000000e+00	1487
11	TraesCS4A01G374400	chr7D	92.949	2099	128	10	1	2087	42212192	42214282	0.000000e+00	3038
12	TraesCS4A01G374400	chr7D	92.205	2104	137	18	1	2087	42084831	42082738	0.000000e+00	2952
13	TraesCS4A01G374400	chr7D	92.187	2099	144	11	1	2087	41917441	41915351	0.000000e+00	2950
14	TraesCS4A01G374400	chr7D	92.190	1639	115	9	454	2087	567986933	567988563	0.000000e+00	2305
15	TraesCS4A01G374400	chr7D	90.625	1056	56	12	2085	3102	42248569	42249619	0.000000e+00	1362
16	TraesCS4A01G374400	chr7D	90.215	511	41	2	1	511	42245572	42246073	0.000000e+00	658
17	TraesCS4A01G374400	chr7D	90.519	443	27	7	2374	2804	42435548	42435987	3.470000e-159	571
18	TraesCS4A01G374400	chr7D	87.584	298	36	1	2805	3102	41874666	41874370	8.240000e-91	344
19	TraesCS4A01G374400	chr7A	93.368	1900	109	8	201	2087	41625898	41627793	0.000000e+00	2795
20	TraesCS4A01G374400	chr7A	92.787	1636	106	10	454	2087	655037917	655039542	0.000000e+00	2357
21	TraesCS4A01G374400	chr7A	94.141	1024	48	7	2085	3102	41628637	41629654	0.000000e+00	1548
22	TraesCS4A01G374400	chr7A	88.090	445	28	9	2374	2804	41791229	41791662	3.570000e-139	505
23	TraesCS4A01G374400	chr7A	84.350	377	37	9	2747	3102	41622328	41622703	1.770000e-92	350
24	TraesCS4A01G374400	chrUn	93.212	987	56	6	2085	3065	361890663	361891644	0.000000e+00	1441
25	TraesCS4A01G374400	chrUn	93.812	404	18	5	2085	2482	250930693	250930291	4.430000e-168	601

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	TraesCS4A01G374400	chr4A	649173843	649176944	3101	False	5729.000000	5729	100.000000	1	3102	1	chr4A.!!$F2	3101
1	TraesCS4A01G374400	chr4A	657306842	657310781	3939	False	2307.000000	3123	93.445000	1	3102	2	chr4A.!!$F5	3101
2	TraesCS4A01G374400	chr4A	657366537	657370473	3936	False	2299.000000	3144	93.199000	1	3102	2	chr4A.!!$F6	3101
3	TraesCS4A01G374400	chr4A	649144369	649148349	3980	False	2210.000000	3092	91.713000	1	3102	2	chr4A.!!$F4	3101
4	TraesCS4A01G374400	chr4A	649059173	649059812	639	False	732.000000	732	87.888000	2085	2705	1	chr4A.!!$F1	620
5	TraesCS4A01G374400	chr7B	2560671	2564611	3940	True	2331.000000	3175	93.650500	1	3099	2	chr7B.!!$R1	3098
6	TraesCS4A01G374400	chr7D	42212192	42214282	2090	False	3038.000000	3038	92.949000	1	2087	1	chr7D.!!$F1	2086
7	TraesCS4A01G374400	chr7D	42082738	42084831	2093	True	2952.000000	2952	92.205000	1	2087	1	chr7D.!!$R3	2086
8	TraesCS4A01G374400	chr7D	41915351	41917441	2090	True	2950.000000	2950	92.187000	1	2087	1	chr7D.!!$R2	2086
9	TraesCS4A01G374400	chr7D	567986933	567988563	1630	False	2305.000000	2305	92.190000	454	2087	1	chr7D.!!$F3	1633
10	TraesCS4A01G374400	chr7D	42245572	42249619	4047	False	1010.000000	1362	90.420000	1	3102	2	chr7D.!!$F4	3101
11	TraesCS4A01G374400	chr7A	655037917	655039542	1625	False	2357.000000	2357	92.787000	454	2087	1	chr7A.!!$F2	1633
12	TraesCS4A01G374400	chr7A	41622328	41629654	7326	False	1564.333333	2795	90.619667	201	3102	3	chr7A.!!$F3	2901
13	TraesCS4A01G374400	chrUn	361890663	361891644	981	False	1441.000000	1441	93.212000	2085	3065	1	chrUn.!!$F1	980

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
198	199	0.318869	TCAAAACATGCCTTGCTGCG	60.319	50.000	0.0	0.0	0.0	5.18	F
953	4508	2.159254	GCAAACAAGCAAACACTCCAGA	60.159	45.455	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1015	4570	0.244450	CCAGCGCCAACAATCAACAT	59.756	50.000	2.29	0.0	0.00	2.71	R
2429	6874	2.899976	ACTCGTGTGTGTTTGACATGA	58.100	42.857	0.00	0.0	36.78	3.07	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
148	149	6.575162	AAAGAACAAGCGGAACAAATCTAT	57.425	33.333	0.00	0.00	0.00	1.98
154	155	1.332028	GCGGAACAAATCTATCGTGCG	60.332	52.381	0.00	0.00	0.00	5.34
177	178	2.029666	CGGCCCGAGGAGCTTATG	59.970	66.667	0.00	0.00	0.00	1.90
197	198	1.425412	CTCAAAACATGCCTTGCTGC	58.575	50.000	0.00	0.00	0.00	5.25
198	199	0.318869	TCAAAACATGCCTTGCTGCG	60.319	50.000	0.00	0.00	0.00	5.18
222	3651	5.163301	GGATGGAGTTTCTAGATAGCCAACA	60.163	44.000	6.94	0.00	0.00	3.33
248	3677	3.364366	GGAAACTGTTCAATGCTCGACAG	60.364	47.826	0.00	0.00	43.81	3.51
314	3743	6.280643	CCATCCATGTTCGATCAGTACTTTA	58.719	40.000	2.21	0.00	0.00	1.85
317	3746	5.127194	TCCATGTTCGATCAGTACTTTAGCT	59.873	40.000	2.21	0.00	0.00	3.32
357	3786	2.299582	CCTGCAGAGTCCATCTCCATAG	59.700	54.545	17.39	0.00	43.71	2.23
358	3787	3.229293	CTGCAGAGTCCATCTCCATAGA	58.771	50.000	8.42	0.00	43.71	1.98
402	3833	7.201848	CCATGACGGGTTAGTCTACAAGTATAA	60.202	40.741	0.00	0.00	41.47	0.98
698	4246	7.335627	AGACATATCCAAAGTCGGTTGATAAA	58.664	34.615	0.00	0.00	37.36	1.40
894	4448	4.764679	TTGACACATGAAACATACCAGC	57.235	40.909	0.00	0.00	0.00	4.85
953	4508	2.159254	GCAAACAAGCAAACACTCCAGA	60.159	45.455	0.00	0.00	0.00	3.86
1015	4570	7.158697	TCTCTTCGAAATGGAGAATGTTGTAA	58.841	34.615	11.88	0.00	33.82	2.41
1099	4654	5.104941	TCAATTCCCTATGTCATTGTCGAGT	60.105	40.000	0.00	0.00	0.00	4.18
1112	4667	2.351455	TGTCGAGTGTGAAAGTTGCAA	58.649	42.857	0.00	0.00	0.00	4.08
1175	4730	5.046304	AGCTACATCTTGCAAAGGAGTTCTA	60.046	40.000	0.00	0.00	46.24	2.10
1208	4763	4.716784	ACACATGTCATACCCACTAGATGT	59.283	41.667	0.00	0.00	0.00	3.06
1383	4938	2.668457	GAGCACAATAGTCAGGTTCACG	59.332	50.000	0.00	0.00	0.00	4.35
1444	4999	5.749928	GCAGAGAATATTCCAATGATCCCCA	60.750	44.000	11.92	0.00	0.00	4.96
1516	5071	1.950828	CAAGAGCTACTCTGGCATGG	58.049	55.000	0.00	0.00	40.28	3.66
1610	5165	8.773645	CAATACTTCAATCATTATACGAAGCCA	58.226	33.333	0.00	0.00	37.24	4.75
1698	5261	5.107133	CCCTACGGGCACTATATATTTTCG	58.893	45.833	0.00	0.00	35.35	3.46
1703	5266	4.561938	CGGGCACTATATATTTTCGGTGGA	60.562	45.833	0.00	0.00	0.00	4.02
1819	5392	8.709386	ACTGTTTTATAACATGCACAAACAAA	57.291	26.923	0.00	0.00	43.02	2.83
1844	5417	9.701098	AATAAACAATTAGACGAACTACACTGA	57.299	29.630	0.00	0.00	0.00	3.41
2248	6692	5.106157	GCTTTATACTCACATGGTGCAAAGT	60.106	40.000	0.00	0.00	32.98	2.66
2373	6818	7.807907	GGATTAAGTGCAATTAATACAATCCCG	59.192	37.037	28.45	0.00	36.41	5.14
2470	6916	6.812160	CGAGTAATTGTAGTAGCTTCCAAGTT	59.188	38.462	0.00	0.00	0.00	2.66
2551	6997	9.034544	GGTAATTGAAATGAATGATAACAAGGC	57.965	33.333	0.00	0.00	0.00	4.35
2616	7073	1.815003	CAAGCCAGGACAGGATTTCAC	59.185	52.381	0.00	0.00	34.48	3.18
2700	7157	2.289945	CCTTCTCAGAACCACCTTCAGG	60.290	54.545	0.00	0.00	42.17	3.86
2731	7188	4.282703	TCGCCACTTCCTTTAGAGTTTAGT	59.717	41.667	0.00	0.00	0.00	2.24
2787	7245	4.323104	GCAAGGAGAATGAAGTGTACCTCT	60.323	45.833	0.00	0.00	0.00	3.69
2819	7277	4.645863	TGTTATCATAGGCATGGCATCT	57.354	40.909	22.64	3.11	32.61	2.90
2826	7284	5.250982	TCATAGGCATGGCATCTAGATTTG	58.749	41.667	22.64	4.44	32.61	2.32
2830	7314	2.555757	GCATGGCATCTAGATTTGGTCC	59.444	50.000	1.33	0.67	0.00	4.46
2861	7345	7.558604	AGCTACCATTTATCAATGTGCAAATT	58.441	30.769	0.00	0.00	38.58	1.82
3027	7515	7.280876	CCGGTAGCGGTACAGATTATATAGTAA	59.719	40.741	24.98	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
158	159	2.499827	ATAAGCTCCTCGGGCCGTC	61.500	63.158	27.32	10.90	0.00	4.79
177	178	1.425412	CAGCAAGGCATGTTTTGAGC	58.575	50.000	13.34	3.03	0.00	4.26
197	198	3.574396	TGGCTATCTAGAAACTCCATCCG	59.426	47.826	0.00	0.00	0.00	4.18
198	199	5.163301	TGTTGGCTATCTAGAAACTCCATCC	60.163	44.000	0.00	0.00	0.00	3.51
222	3651	3.438087	CGAGCATTGAACAGTTTCCTCAT	59.562	43.478	0.00	0.00	0.00	2.90
248	3677	4.770795	AGTTGCACTTGTACCATCTATCC	58.229	43.478	0.00	0.00	0.00	2.59
270	3699	1.254026	CCTTACACTCTGGTGGTCGA	58.746	55.000	1.29	0.00	46.85	4.20
317	3746	0.033504	GTGTCTTCTGGGCTGTCGAA	59.966	55.000	0.00	0.00	0.00	3.71
357	3786	2.031258	GCCAGTTAGCCTTCCTTCTC	57.969	55.000	0.00	0.00	0.00	2.87
402	3833	3.642848	TGCAAGCATTTCTTTCCTTTCCT	59.357	39.130	0.00	0.00	31.27	3.36
555	4098	7.466185	CGTCCCAAATTACTTGTCGCATAATTA	60.466	37.037	0.00	0.00	32.65	1.40
575	4118	2.991713	AGTATATACTCCCTCCGTCCCA	59.008	50.000	9.71	0.00	0.00	4.37
625	4171	9.554395	TTCTTTCAGTTACTGTTGTCATCAATA	57.446	29.630	12.41	0.00	35.92	1.90
674	4222	7.548196	TTTATCAACCGACTTTGGATATGTC	57.452	36.000	0.00	0.00	0.00	3.06
709	4258	3.265791	GCACTCTTGATCGATTGGTCTT	58.734	45.455	0.00	0.00	0.00	3.01
710	4259	2.736719	CGCACTCTTGATCGATTGGTCT	60.737	50.000	0.00	0.00	0.00	3.85
711	4260	1.590238	CGCACTCTTGATCGATTGGTC	59.410	52.381	0.00	0.00	0.00	4.02
953	4508	1.357420	TGGGATGGGTGCAATTGTAGT	59.643	47.619	7.40	0.00	0.00	2.73
1015	4570	0.244450	CCAGCGCCAACAATCAACAT	59.756	50.000	2.29	0.00	0.00	2.71
1099	4654	1.596709	CGATGCGTTGCAACTTTCACA	60.597	47.619	26.09	16.03	43.62	3.58
1143	4698	1.293924	CAAGATGTAGCTTGAGGCGG	58.706	55.000	3.93	0.00	46.31	6.13
1175	4730	2.275134	TGACATGTGTGGCAACTCAT	57.725	45.000	1.15	2.85	41.45	2.90
1230	4785	6.039616	GTCATCCAAGTACTTTGCAAACAAA	58.960	36.000	8.05	0.00	43.45	2.83
1238	4793	7.413438	GCTCAACATAGTCATCCAAGTACTTTG	60.413	40.741	5.07	2.38	36.50	2.77
1239	4794	6.595716	GCTCAACATAGTCATCCAAGTACTTT	59.404	38.462	5.07	0.00	0.00	2.66
1317	4872	8.187913	TGATGGACCAACATTTTTCTTCATTA	57.812	30.769	0.00	0.00	0.00	1.90
1383	4938	1.864029	GCCACGACAAGAAACTTTGCC	60.864	52.381	0.00	0.00	0.00	4.52
1444	4999	1.215423	ACCCAGGAAACTTTGCAGTCT	59.785	47.619	0.00	0.00	40.21	3.24
1516	5071	3.809832	CCAGATCCAACGACCAATACATC	59.190	47.826	0.00	0.00	0.00	3.06
1698	5261	6.715347	ATAAGAAATTGCCTTGTATCCACC	57.285	37.500	4.21	0.00	0.00	4.61
1819	5392	9.701098	TTCAGTGTAGTTCGTCTAATTGTTTAT	57.299	29.630	0.00	0.00	0.00	1.40
1898	5471	4.649692	ACATGTCACATCTCTTTGAAGCT	58.350	39.130	0.00	0.00	0.00	3.74
1951	5525	3.461831	TCATCCCCAACCGGATTAATTCT	59.538	43.478	9.46	0.00	40.88	2.40
2132	6556	9.647918	TCTATCAAAGATAGATAGACAAGTGGT	57.352	33.333	11.60	0.00	45.40	4.16
2168	6608	4.220382	CCTGGCACATATGAACCTTGAAAA	59.780	41.667	10.38	0.00	38.20	2.29
2297	6741	5.512788	CGGATGACTTTTGCATGTGTAAATC	59.487	40.000	0.00	0.00	30.13	2.17
2429	6874	2.899976	ACTCGTGTGTGTTTGACATGA	58.100	42.857	0.00	0.00	36.78	3.07
2551	6997	6.906157	ACATATCAAGCAAATATTGGGAGG	57.094	37.500	0.00	0.00	0.00	4.30
2645	7102	4.463539	TGTGCTCGGTGGTAGATTAAACTA	59.536	41.667	0.00	0.00	0.00	2.24
2731	7188	3.267812	AGGGAAGAAATGCCAGAGAATGA	59.732	43.478	0.00	0.00	43.29	2.57
2787	7245	4.674101	GCCTATGATAACAAAGCGCAAACA	60.674	41.667	11.47	0.00	0.00	2.83
2819	7277	7.865530	TGGTAGCTATAATGGACCAAATCTA	57.134	36.000	0.00	0.00	37.24	1.98
2826	7284	9.686683	ATTGATAAATGGTAGCTATAATGGACC	57.313	33.333	0.00	0.00	0.00	4.46
2830	7314	9.778993	GCACATTGATAAATGGTAGCTATAATG	57.221	33.333	7.72	0.00	34.56	1.90
2861	7345	3.733988	CGCCGACTAGTTCTAGCAATTCA	60.734	47.826	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.