AutoCloner

Multiple sequence alignment - TraesCS3B01G379500

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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	TraesCS3B01G379500	chr3B	100.000	6099	0	0	1	6099	597449444	597455542	0.000000e+00	11263.0
1	TraesCS3B01G379500	chr3B	99.303	574	3	1	5526	6099	215588231	215587659	0.000000e+00	1037.0
2	TraesCS3B01G379500	chr3B	98.087	575	10	1	5522	6096	96845728	96846301	0.000000e+00	1000.0
3	TraesCS3B01G379500	chr3D	94.061	3755	161	24	1801	5525	454671579	454675301	0.000000e+00	5642.0
4	TraesCS3B01G379500	chr3D	88.935	723	34	16	804	1489	454670215	454670928	0.000000e+00	850.0
5	TraesCS3B01G379500	chr3D	86.047	688	75	13	1	673	454665056	454665737	0.000000e+00	719.0
6	TraesCS3B01G379500	chr3D	95.349	43	2	0	1483	1525	454671333	454671375	1.100000e-07	69.4
7	TraesCS3B01G379500	chr3A	92.650	3755	194	40	1801	5521	596741360	596745066	0.000000e+00	5330.0
8	TraesCS3B01G379500	chr3A	87.029	1087	53	36	749	1758	596740297	596741372	0.000000e+00	1146.0
9	TraesCS3B01G379500	chr3A	86.767	597	62	8	27	614	596739577	596740165	0.000000e+00	649.0
10	TraesCS3B01G379500	chr7B	99.129	574	4	1	5526	6098	443744511	443745084	0.000000e+00	1031.0
11	TraesCS3B01G379500	chr7B	99.127	573	4	1	5525	6097	361161471	361160900	0.000000e+00	1029.0
12	TraesCS3B01G379500	chr7B	99.612	516	2	0	5525	6040	361159649	361160164	0.000000e+00	942.0
13	TraesCS3B01G379500	chr4A	98.780	574	6	1	5526	6098	547192580	547193153	0.000000e+00	1020.0
14	TraesCS3B01G379500	chr4A	95.000	40	2	0	413	452	705740600	705740561	5.100000e-06	63.9
15	TraesCS3B01G379500	chr2A	98.427	572	8	1	5526	6097	182316514	182315944	0.000000e+00	1005.0
16	TraesCS3B01G379500	chr6B	98.258	574	9	1	5526	6098	203972828	203972255	0.000000e+00	1003.0
17	TraesCS3B01G379500	chr7A	97.178	567	13	2	5526	6092	688201214	688200651	0.000000e+00	955.0
18	TraesCS3B01G379500	chr7A	100.000	36	0	0	413	448	711121077	711121042	3.950000e-07	67.6
19	TraesCS3B01G379500	chr7A	100.000	28	0	0	1042	1069	118104641	118104668	1.100000e-02	52.8
20	TraesCS3B01G379500	chr2D	84.694	98	15	0	517	614	202642797	202642700	1.400000e-16	99.0
21	TraesCS3B01G379500	chr6A	95.000	40	2	0	413	452	472707998	472707959	5.100000e-06	63.9
22	TraesCS3B01G379500	chr5B	95.000	40	2	0	413	452	408357332	408357293	5.100000e-06	63.9
23	TraesCS3B01G379500	chr1A	95.000	40	2	0	413	452	291531601	291531562	5.100000e-06	63.9
24	TraesCS3B01G379500	chr1A	95.000	40	2	0	413	452	374188782	374188821	5.100000e-06	63.9
25	TraesCS3B01G379500	chr1A	95.000	40	2	0	413	452	385369735	385369774	5.100000e-06	63.9
26	TraesCS3B01G379500	chr7D	96.875	32	1	0	5095	5126	31969638	31969669	3.000000e-03	54.7

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	TraesCS3B01G379500	chr3B	597449444	597455542	6098	False	11263.000000	11263	100.000000	1	6099	1	chr3B.!!$F2	6098
1	TraesCS3B01G379500	chr3B	215587659	215588231	572	True	1037.000000	1037	99.303000	5526	6099	1	chr3B.!!$R1	573
2	TraesCS3B01G379500	chr3B	96845728	96846301	573	False	1000.000000	1000	98.087000	5522	6096	1	chr3B.!!$F1	574
3	TraesCS3B01G379500	chr3D	454670215	454675301	5086	False	2187.133333	5642	92.781667	804	5525	3	chr3D.!!$F2	4721
4	TraesCS3B01G379500	chr3D	454665056	454665737	681	False	719.000000	719	86.047000	1	673	1	chr3D.!!$F1	672
5	TraesCS3B01G379500	chr3A	596739577	596745066	5489	False	2375.000000	5330	88.815333	27	5521	3	chr3A.!!$F1	5494
6	TraesCS3B01G379500	chr7B	443744511	443745084	573	False	1031.000000	1031	99.129000	5526	6098	1	chr7B.!!$F2	572
7	TraesCS3B01G379500	chr7B	361160900	361161471	571	True	1029.000000	1029	99.127000	5525	6097	1	chr7B.!!$R1	572
8	TraesCS3B01G379500	chr7B	361159649	361160164	515	False	942.000000	942	99.612000	5525	6040	1	chr7B.!!$F1	515
9	TraesCS3B01G379500	chr4A	547192580	547193153	573	False	1020.000000	1020	98.780000	5526	6098	1	chr4A.!!$F1	572
10	TraesCS3B01G379500	chr2A	182315944	182316514	570	True	1005.000000	1005	98.427000	5526	6097	1	chr2A.!!$R1	571
11	TraesCS3B01G379500	chr6B	203972255	203972828	573	True	1003.000000	1003	98.258000	5526	6098	1	chr6B.!!$R1	572
12	TraesCS3B01G379500	chr7A	688200651	688201214	563	True	955.000000	955	97.178000	5526	6092	1	chr7A.!!$R1	566

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	Hairpin	End Stability	Orientation
404	415	0.033781	CACCACCGGTCGGACTTAAA	59.966	55.0	24.32	38.96	1.52	F
616	627	0.400213	ACAAGGATGCCGTTCTTCCA	59.600	50.0	8.76	40.48	3.53	F
834	872	0.460284	AATCATCACTGGCGGACGAC	60.460	55.0	0.00	0.00	4.34	F
1888	2442	0.315568	GTTGCTCTCACGGAGTCACT	59.684	55.0	0.00	41.61	3.41	F
3278	3852	1.818959	TTGCAAGCAAGGCCATCCAC	61.819	55.0	5.01	33.74	4.02	F
4147	4727	0.462581	TGCAATCCGTGGCTCAGATC	60.463	55.0	0.00	0.00	2.75	F
4830	5421	0.616111	ACCCACCAAAAGGCAACACA	60.616	50.0	0.00	41.41	3.72	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1582	2108	0.445436	CGGAGTCAGCTGTGAAATGC	59.555	55.000	14.67	33.27	3.56	R
1597	2123	1.120530	ATACAGTGGTAAGGCCGGAG	58.879	55.000	5.05	41.21	4.63	R
2247	2804	2.112815	GGCAATCACACCGCCTACC	61.113	63.158	0.00	42.78	3.18	R
3583	4163	0.877071	CACATGGCACTCAGAACACC	59.123	55.000	0.00	0.00	4.16	R
4542	5122	0.108186	CTGCTGGGACTAATCGTGCA	60.108	55.000	0.00	35.37	4.57	R
4971	5562	0.179100	AGCATCATCACCGTTCCTCG	60.179	55.000	0.00	39.52	4.63	R
5928	6527	4.610605	TGGAAACCAGACGAATCACTTA	57.389	40.909	0.00	0.00	2.24	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	61	3.640407	GGGAGCTGGCCACACTCA	61.640	66.667	25.31	0.00	31.88	3.41
60	62	2.431683	GGAGCTGGCCACACTCAA	59.568	61.111	25.31	0.00	31.88	3.02
68	70	1.553690	GGCCACACTCAAGGGCTAGA	61.554	60.000	0.00	0.00	46.87	2.43
86	88	4.626529	GCTAGACCACTAAAAGGGCTCAAT	60.627	45.833	0.00	0.00	42.12	2.57
89	91	3.690460	ACCACTAAAAGGGCTCAATCTG	58.310	45.455	0.00	0.00	0.00	2.90
111	113	4.019321	TGGCCAGCAGTCTAATTTAGAACT	60.019	41.667	0.00	5.47	36.40	3.01
121	123	8.532819	CAGTCTAATTTAGAACTAAGTCCACCT	58.467	37.037	7.70	0.00	36.40	4.00
153	155	0.612174	CCTTGGAGAGTGTCCCTCGA	60.612	60.000	3.43	0.00	46.31	4.04
155	157	0.898789	TTGGAGAGTGTCCCTCGACC	60.899	60.000	3.43	0.00	46.31	4.79
156	158	1.000646	GGAGAGTGTCCCTCGACCT	60.001	63.158	0.00	0.00	45.44	3.85
157	159	1.316706	GGAGAGTGTCCCTCGACCTG	61.317	65.000	0.00	0.00	45.44	4.00
186	196	8.738645	TCCTTTCTATCTTAGCAAAGAAATCC	57.261	34.615	0.00	0.00	44.75	3.01
191	201	5.588958	ATCTTAGCAAAGAAATCCAAGGC	57.411	39.130	0.00	0.00	44.75	4.35
235	246	1.374947	GTCACCAGCTAGCCCACAA	59.625	57.895	12.13	0.00	0.00	3.33
237	248	0.698238	TCACCAGCTAGCCCACAATT	59.302	50.000	12.13	0.00	0.00	2.32
239	250	0.392998	ACCAGCTAGCCCACAATTCG	60.393	55.000	12.13	0.00	0.00	3.34
280	291	2.943036	AAGCCAAGGAAAACCGAGTA	57.057	45.000	0.00	0.00	0.00	2.59
282	293	3.434940	AGCCAAGGAAAACCGAGTAAT	57.565	42.857	0.00	0.00	0.00	1.89
306	317	6.824305	AGGACGATCAATTGTGAAAGATTT	57.176	33.333	5.13	0.00	37.30	2.17
310	321	9.405587	GGACGATCAATTGTGAAAGATTTAAAA	57.594	29.630	5.13	0.00	37.30	1.52
357	368	8.628882	ATTTCAAGTGCAACAAAAGTAGTTAC	57.371	30.769	0.00	0.00	41.43	2.50
398	409	4.918278	TCACCACCACCGGTCGGA	62.918	66.667	24.32	6.24	37.07	4.55
403	414	1.667151	CACCACCGGTCGGACTTAA	59.333	57.895	24.32	0.00	38.96	1.85
404	415	0.033781	CACCACCGGTCGGACTTAAA	59.966	55.000	24.32	0.00	38.96	1.52
409	420	4.002316	CCACCGGTCGGACTTAAATTAAA	58.998	43.478	16.90	0.00	38.96	1.52

Showing 1 to 25 of 183 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	3.005791	GCCACTAAGTTCATTGCAACCTT	59.994	43.478	0.00	4.56	0.00	3.50
9	10	2.558359	AGCCACTAAGTTCATTGCAACC	59.442	45.455	0.00	0.00	0.00	3.77
10	11	3.923017	AGCCACTAAGTTCATTGCAAC	57.077	42.857	0.00	0.00	0.00	4.17
11	12	3.888323	TGAAGCCACTAAGTTCATTGCAA	59.112	39.130	0.00	0.00	0.00	4.08
13	14	4.156556	TGATGAAGCCACTAAGTTCATTGC	59.843	41.667	0.00	0.00	40.27	3.56
14	15	5.181811	TGTGATGAAGCCACTAAGTTCATTG	59.818	40.000	0.00	0.00	40.27	2.82
15	16	5.182001	GTGTGATGAAGCCACTAAGTTCATT	59.818	40.000	0.00	0.00	40.27	2.57
55	57	2.921834	TAGTGGTCTAGCCCTTGAGT	57.078	50.000	0.00	0.00	36.04	3.41
59	61	2.576648	CCCTTTTAGTGGTCTAGCCCTT	59.423	50.000	0.00	0.00	36.04	3.95
60	62	2.197465	CCCTTTTAGTGGTCTAGCCCT	58.803	52.381	0.00	0.00	36.04	5.19
68	70	3.562176	CCAGATTGAGCCCTTTTAGTGGT	60.562	47.826	0.00	0.00	0.00	4.16
86	88	3.774766	TCTAAATTAGACTGCTGGCCAGA	59.225	43.478	37.21	19.62	44.64	3.86
89	91	4.518249	AGTTCTAAATTAGACTGCTGGCC	58.482	43.478	1.61	0.00	33.84	5.36
94	96	7.278203	GGTGGACTTAGTTCTAAATTAGACTGC	59.722	40.741	1.61	0.00	33.84	4.40
121	123	2.708861	TCTCCAAGGAGTGCAACCTAAA	59.291	45.455	15.36	3.11	42.49	1.85
153	155	5.721960	TGCTAAGATAGAAAGGAGAACAGGT	59.278	40.000	0.00	0.00	0.00	4.00
155	157	8.037758	TCTTTGCTAAGATAGAAAGGAGAACAG	58.962	37.037	6.50	0.00	35.49	3.16
156	158	7.907389	TCTTTGCTAAGATAGAAAGGAGAACA	58.093	34.615	6.50	0.00	35.49	3.18
157	159	8.779354	TTCTTTGCTAAGATAGAAAGGAGAAC	57.221	34.615	11.41	0.00	40.01	3.01
186	196	1.151668	CAGTCTTCCGAGTTGCCTTG	58.848	55.000	0.00	0.00	0.00	3.61
191	201	2.609737	GGTACCACAGTCTTCCGAGTTG	60.610	54.545	7.15	0.00	0.00	3.16
257	268	3.123050	CTCGGTTTTCCTTGGCTTTTTG	58.877	45.455	0.00	0.00	37.95	2.44
265	276	4.565564	CGTCCTATTACTCGGTTTTCCTTG	59.434	45.833	0.00	0.00	37.95	3.61
280	291	8.511604	AATCTTTCACAATTGATCGTCCTATT	57.488	30.769	13.59	0.00	0.00	1.73
282	293	7.921786	AAATCTTTCACAATTGATCGTCCTA	57.078	32.000	13.59	0.00	0.00	2.94

Showing 1 to 25 of 186 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.