AutoCloner

Multiple sequence alignment - TraesCS6D01G157600

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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	TraesCS6D01G157600	chr6D	100.000	2573	0	0	1	2573	134278475	134281047	0.000000e+00	4752
1	TraesCS6D01G157600	chr6D	97.916	1823	34	3	754	2573	134682441	134684262	0.000000e+00	3153
2	TraesCS6D01G157600	chr6D	85.581	964	92	29	760	1706	134676303	134677236	0.000000e+00	966
3	TraesCS6D01G157600	chr6D	86.683	841	84	17	877	1701	134241134	134241962	0.000000e+00	907
4	TraesCS6D01G157600	chr6D	89.174	545	35	8	1	541	134679899	134680423	0.000000e+00	658
5	TraesCS6D01G157600	chr6D	81.006	616	85	16	982	1573	134688904	134689511	6.490000e-126	460
6	TraesCS6D01G157600	chr6D	91.139	79	7	0	623	701	134681689	134681767	9.740000e-20	108
7	TraesCS6D01G157600	chr6B	94.235	1301	30	7	754	2027	233013650	233014932	0.000000e+00	1945
8	TraesCS6D01G157600	chr6B	83.501	794	101	16	930	1706	233010435	233011215	0.000000e+00	713
9	TraesCS6D01G157600	chr6B	88.504	548	46	8	1	541	233011681	233012218	0.000000e+00	647
10	TraesCS6D01G157600	chr6B	81.366	644	80	30	982	1598	233023685	233024315	2.980000e-134	488
11	TraesCS6D01G157600	chr6B	91.875	160	13	0	2342	2501	233015249	233015408	9.260000e-55	224
12	TraesCS6D01G157600	chr6B	92.754	69	5	0	633	701	233012930	233012998	1.630000e-17	100
13	TraesCS6D01G157600	chr6A	92.976	1082	54	8	754	1814	175621691	175622771	0.000000e+00	1557
14	TraesCS6D01G157600	chr6A	84.608	1007	89	38	712	1706	175560487	175561439	0.000000e+00	941
15	TraesCS6D01G157600	chr6A	81.290	620	84	23	982	1573	175629355	175629970	8.330000e-130	473
16	TraesCS6D01G157600	chr6A	80.225	622	65	19	83	701	175596965	175597531	5.120000e-112	414
17	TraesCS6D01G157600	chr6A	88.546	227	13	3	1811	2024	175623074	175623300	1.960000e-66	263
18	TraesCS6D01G157600	chr6A	96.053	76	3	0	2426	2501	175623822	175623897	9.670000e-25	124
19	TraesCS6D01G157600	chr6A	87.500	88	11	0	2342	2429	175623430	175623517	4.530000e-18	102

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	TraesCS6D01G157600	chr6D	134278475	134281047	2572	False	4752.00	4752	100.00000	1	2573	1	chr6D.!!$F2	2572
1	TraesCS6D01G157600	chr6D	134676303	134684262	7959	False	1221.25	3153	90.95250	1	2573	4	chr6D.!!$F4	2572
2	TraesCS6D01G157600	chr6D	134241134	134241962	828	False	907.00	907	86.68300	877	1701	1	chr6D.!!$F1	824
3	TraesCS6D01G157600	chr6D	134688904	134689511	607	False	460.00	460	81.00600	982	1573	1	chr6D.!!$F3	591
4	TraesCS6D01G157600	chr6B	233010435	233015408	4973	False	725.80	1945	90.17380	1	2501	5	chr6B.!!$F2	2500
5	TraesCS6D01G157600	chr6B	233023685	233024315	630	False	488.00	488	81.36600	982	1598	1	chr6B.!!$F1	616
6	TraesCS6D01G157600	chr6A	175560487	175561439	952	False	941.00	941	84.60800	712	1706	1	chr6A.!!$F1	994
7	TraesCS6D01G157600	chr6A	175621691	175623897	2206	False	511.50	1557	91.26875	754	2501	4	chr6A.!!$F4	1747
8	TraesCS6D01G157600	chr6A	175629355	175629970	615	False	473.00	473	81.29000	982	1573	1	chr6A.!!$F3	591
9	TraesCS6D01G157600	chr6A	175596965	175597531	566	False	414.00	414	80.22500	83	701	1	chr6A.!!$F2	618

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
635	5938	0.464452	CGGGTGAAGGGGATGACTAC	59.536	60.0	0.0	0.0	0.0	2.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2309	8838	1.003839	CTAACAAGCACGCCCTCCA	60.004	57.895	0.0	0.0	0.0	3.86	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
49	3672	2.159366	CCACAGTACTGTCATCTCGTCC	60.159	54.545	25.63	0.00	42.83	4.79
77	3700	2.860293	CTTTCACGCGCGGAACAT	59.140	55.556	35.22	9.87	0.00	2.71
78	3701	1.206578	CTTTCACGCGCGGAACATT	59.793	52.632	35.22	8.98	0.00	2.71
79	3702	0.789383	CTTTCACGCGCGGAACATTC	60.789	55.000	35.22	0.00	0.00	2.67
80	3703	1.225376	TTTCACGCGCGGAACATTCT	61.225	50.000	35.22	7.19	0.00	2.40
81	3704	1.623081	TTCACGCGCGGAACATTCTC	61.623	55.000	35.22	0.00	0.00	2.87
96	3719	3.243234	ACATTCTCTTCTCCTATCGCGTG	60.243	47.826	5.77	0.00	0.00	5.34
151	3774	2.165301	CGAAAGGTCCGTGGCGATC	61.165	63.158	0.00	0.00	0.00	3.69
161	3784	4.028490	TGGCGATCGTTTGGGGCT	62.028	61.111	17.81	0.00	0.00	5.19
181	3804	4.812476	CGGTTGGCGCTCGATGGA	62.812	66.667	7.64	0.00	0.00	3.41
239	3862	4.166888	GATGCGCAGGAGCCAGGA	62.167	66.667	18.32	0.00	37.52	3.86
240	3863	4.172512	ATGCGCAGGAGCCAGGAG	62.173	66.667	18.32	0.00	37.52	3.69
369	3998	3.693578	CAGAGGAATGAGCTCCTTTTTCC	59.306	47.826	19.43	19.43	46.33	3.13
396	4025	5.533903	TGGGAATAGTCATAGTAGTCGGTTC	59.466	44.000	0.00	0.00	0.00	3.62
397	4026	5.533903	GGGAATAGTCATAGTAGTCGGTTCA	59.466	44.000	0.00	0.00	0.00	3.18
399	4028	6.039047	GGAATAGTCATAGTAGTCGGTTCACA	59.961	42.308	0.00	0.00	0.00	3.58
400	4029	7.255520	GGAATAGTCATAGTAGTCGGTTCACAT	60.256	40.741	0.00	0.00	0.00	3.21
401	4030	5.250235	AGTCATAGTAGTCGGTTCACATG	57.750	43.478	0.00	0.00	0.00	3.21
402	4031	3.797256	GTCATAGTAGTCGGTTCACATGC	59.203	47.826	0.00	0.00	0.00	4.06
404	4033	1.267121	AGTAGTCGGTTCACATGCCT	58.733	50.000	0.00	0.00	0.00	4.75
438	4067	1.448540	ACGGCAGCTTTCCTCATCG	60.449	57.895	0.00	0.00	0.00	3.84
449	4078	2.961526	TCCTCATCGTGGCTTCTTAC	57.038	50.000	0.00	0.00	0.00	2.34
487	4119	2.907696	TCCCCGTGAGAATGGAGTTTTA	59.092	45.455	0.00	0.00	0.00	1.52
492	4124	5.183140	CCCGTGAGAATGGAGTTTTACAAAT	59.817	40.000	0.00	0.00	0.00	2.32
513	4145	7.669722	ACAAATGAGTAGGAAATTGGAGCTTTA	59.330	33.333	0.00	0.00	0.00	1.85
514	4146	8.689972	CAAATGAGTAGGAAATTGGAGCTTTAT	58.310	33.333	0.00	0.00	0.00	1.40
535	4167	3.950397	TCCCACTACAATGTGATTGGTC	58.050	45.455	0.00	0.00	44.42	4.02
541	4173	5.062183	CACTACAATGTGATTGGTCTACACG	59.938	44.000	0.00	0.00	44.42	4.49
544	4177	5.543714	ACAATGTGATTGGTCTACACGTAA	58.456	37.500	0.00	0.00	44.42	3.18
545	4178	5.992829	ACAATGTGATTGGTCTACACGTAAA	59.007	36.000	0.00	0.00	44.42	2.01
599	5442	7.992754	AGTATAGTACACTATTAAGGGGACG	57.007	40.000	7.18	0.00	45.64	4.79
600	5443	7.749666	AGTATAGTACACTATTAAGGGGACGA	58.250	38.462	7.18	0.00	45.64	4.20
601	5444	8.389366	AGTATAGTACACTATTAAGGGGACGAT	58.611	37.037	7.18	0.00	45.64	3.73
602	5445	9.018582	GTATAGTACACTATTAAGGGGACGATT	57.981	37.037	7.18	0.00	45.64	3.34
604	5447	7.902920	AGTACACTATTAAGGGGACGATTAA	57.097	36.000	0.00	0.00	45.64	1.40
605	5448	8.488308	AGTACACTATTAAGGGGACGATTAAT	57.512	34.615	0.00	0.00	45.64	1.40
606	5449	8.931568	AGTACACTATTAAGGGGACGATTAATT	58.068	33.333	0.00	0.00	45.64	1.40
607	5450	9.551734	GTACACTATTAAGGGGACGATTAATTT	57.448	33.333	0.00	0.00	27.65	1.82
609	5452	9.470399	ACACTATTAAGGGGACGATTAATTTTT	57.530	29.630	0.00	0.00	34.35	1.94
630	5473	2.779742	TTTGGCGGGTGAAGGGGATG	62.780	60.000	0.00	0.00	0.00	3.51
635	5938	0.464452	CGGGTGAAGGGGATGACTAC	59.536	60.000	0.00	0.00	0.00	2.73
838	6781	4.313282	TGAGAAGTGCTGTCTCATTTCTG	58.687	43.478	9.58	0.00	45.11	3.02
921	6869	0.839946	ATCACCTCCTTTCCATCCCG	59.160	55.000	0.00	0.00	0.00	5.14
977	6931	4.511454	CAGAAAAATCTCACACTTCCACGA	59.489	41.667	0.00	0.00	0.00	4.35
1037	6991	2.283529	GCTCTTCCACCCACCGAGA	61.284	63.158	0.00	0.00	0.00	4.04
1744	7759	8.840200	AAAGAGACTGTAAATATCTCCCAGTA	57.160	34.615	0.00	0.00	39.84	2.74
1746	7761	9.440761	AAGAGACTGTAAATATCTCCCAGTATT	57.559	33.333	0.00	0.00	39.84	1.89
1776	7791	4.394920	ACAATACTGGATGCAAAACTACCG	59.605	41.667	0.00	0.00	0.00	4.02
1862	8183	6.685527	TTTGCGCAAAATCTGTATGGTATA	57.314	33.333	31.98	4.40	0.00	1.47
2057	8395	4.471904	TTCAACCAGTCAGCGATAGAAT	57.528	40.909	0.00	0.00	39.76	2.40
2247	8775	6.074463	CGCAGACGGAGGAAGTATAAAATTAC	60.074	42.308	0.00	0.00	34.97	1.89
2324	8853	0.037590	TTTATGGAGGGCGTGCTTGT	59.962	50.000	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	2.892334	CGTTCCCAATATGGCGGCG	61.892	63.158	0.51	0.51	35.79	6.46
3	4	3.030652	CGTTCCCAATATGGCGGC	58.969	61.111	0.00	0.00	35.79	6.53
69	3692	2.682155	AGGAGAAGAGAATGTTCCGC	57.318	50.000	0.00	0.00	39.56	5.54
77	3700	1.065701	GCACGCGATAGGAGAAGAGAA	59.934	52.381	15.93	0.00	0.00	2.87
78	3701	0.663688	GCACGCGATAGGAGAAGAGA	59.336	55.000	15.93	0.00	0.00	3.10
79	3702	0.658829	CGCACGCGATAGGAGAAGAG	60.659	60.000	15.93	0.00	42.83	2.85
80	3703	1.093496	TCGCACGCGATAGGAGAAGA	61.093	55.000	15.93	0.00	44.01	2.87
81	3704	1.355563	TCGCACGCGATAGGAGAAG	59.644	57.895	15.93	0.00	44.01	2.85
96	3719	4.090057	GCTTCACCCGTGCTTCGC	62.090	66.667	0.00	0.00	38.35	4.70
108	3731	2.951475	AAGCGTTTCCGGTGGCTTCA	62.951	55.000	14.88	0.00	45.47	3.02
151	3774	2.593436	AACCGTGAGCCCCAAACG	60.593	61.111	0.00	0.00	37.07	3.60
161	3784	4.063967	ATCGAGCGCCAACCGTGA	62.064	61.111	2.29	0.00	39.71	4.35
238	3861	0.390860	CGTGTCCCCATCATCTCCTC	59.609	60.000	0.00	0.00	0.00	3.71
239	3862	1.690219	GCGTGTCCCCATCATCTCCT	61.690	60.000	0.00	0.00	0.00	3.69
240	3863	1.227674	GCGTGTCCCCATCATCTCC	60.228	63.158	0.00	0.00	0.00	3.71
270	3893	2.353958	CCAGCATGTCAGCCACCT	59.646	61.111	0.00	0.00	34.23	4.00
369	3998	5.048643	CCGACTACTATGACTATTCCCACAG	60.049	48.000	0.00	0.00	0.00	3.66
396	4025	0.311790	ACTGACGCAAAAGGCATGTG	59.688	50.000	0.00	0.00	45.17	3.21
397	4026	0.311790	CACTGACGCAAAAGGCATGT	59.688	50.000	0.00	0.00	45.17	3.21
399	4028	1.286880	GCACTGACGCAAAAGGCAT	59.713	52.632	0.00	0.00	45.17	4.40
400	4029	2.117779	TGCACTGACGCAAAAGGCA	61.118	52.632	0.00	0.00	45.17	4.75
401	4030	1.658409	GTGCACTGACGCAAAAGGC	60.658	57.895	10.32	0.00	45.14	4.35
402	4031	0.592247	GTGTGCACTGACGCAAAAGG	60.592	55.000	19.41	0.00	45.14	3.11
404	4033	1.061729	CGTGTGCACTGACGCAAAA	59.938	52.632	19.41	0.00	45.14	2.44
438	4067	8.549338	AGAATACAAAAGTAGTAAGAAGCCAC	57.451	34.615	0.00	0.00	0.00	5.01
449	4078	7.270047	TCACGGGGATTAGAATACAAAAGTAG	58.730	38.462	0.00	0.00	0.00	2.57
470	4102	6.898041	TCATTTGTAAAACTCCATTCTCACG	58.102	36.000	0.00	0.00	0.00	4.35
487	4119	5.574188	AGCTCCAATTTCCTACTCATTTGT	58.426	37.500	0.00	0.00	0.00	2.83
492	4124	6.357367	GGATAAAGCTCCAATTTCCTACTCA	58.643	40.000	0.00	0.00	35.24	3.41
513	4145	4.228210	AGACCAATCACATTGTAGTGGGAT	59.772	41.667	13.95	0.64	43.88	3.85
514	4146	3.587061	AGACCAATCACATTGTAGTGGGA	59.413	43.478	13.95	0.00	39.93	4.37
573	5416	9.507329	CGTCCCCTTAATAGTGTACTATACTAA	57.493	37.037	5.06	1.75	38.15	2.24
609	5452	1.834822	CCCCTTCACCCGCCAAAAA	60.835	57.895	0.00	0.00	0.00	1.94
610	5453	2.087857	ATCCCCTTCACCCGCCAAAA	62.088	55.000	0.00	0.00	0.00	2.44
611	5454	2.543797	ATCCCCTTCACCCGCCAAA	61.544	57.895	0.00	0.00	0.00	3.28
612	5455	2.938798	ATCCCCTTCACCCGCCAA	60.939	61.111	0.00	0.00	0.00	4.52
613	5456	3.727258	CATCCCCTTCACCCGCCA	61.727	66.667	0.00	0.00	0.00	5.69
614	5457	3.407967	TCATCCCCTTCACCCGCC	61.408	66.667	0.00	0.00	0.00	6.13
615	5458	1.335132	TAGTCATCCCCTTCACCCGC	61.335	60.000	0.00	0.00	0.00	6.13
616	5459	0.464452	GTAGTCATCCCCTTCACCCG	59.536	60.000	0.00	0.00	0.00	5.28
617	5460	1.880941	AGTAGTCATCCCCTTCACCC	58.119	55.000	0.00	0.00	0.00	4.61
618	5461	2.838202	TGAAGTAGTCATCCCCTTCACC	59.162	50.000	0.00	0.00	38.61	4.02
620	5463	3.769844	GAGTGAAGTAGTCATCCCCTTCA	59.230	47.826	0.00	0.00	40.57	3.02
621	5464	4.027437	AGAGTGAAGTAGTCATCCCCTTC	58.973	47.826	0.00	0.00	38.90	3.46
625	5468	4.538738	ACCTAGAGTGAAGTAGTCATCCC	58.461	47.826	0.00	0.00	38.90	3.85
697	6002	8.090788	TGCTGGAGAAGTAAAATCCTACTATT	57.909	34.615	0.00	0.00	31.72	1.73
701	6006	6.174049	ACTTGCTGGAGAAGTAAAATCCTAC	58.826	40.000	0.00	0.00	31.72	3.18
702	6007	6.013725	TGACTTGCTGGAGAAGTAAAATCCTA	60.014	38.462	0.00	0.00	33.71	2.94
703	6008	5.221925	TGACTTGCTGGAGAAGTAAAATCCT	60.222	40.000	0.00	0.00	33.71	3.24
704	6009	5.003804	TGACTTGCTGGAGAAGTAAAATCC	58.996	41.667	0.00	0.00	33.71	3.01
705	6010	6.560253	TTGACTTGCTGGAGAAGTAAAATC	57.440	37.500	0.00	0.00	33.71	2.17
706	6011	6.959639	TTTGACTTGCTGGAGAAGTAAAAT	57.040	33.333	0.00	0.00	31.45	1.82
708	6013	6.767524	TTTTTGACTTGCTGGAGAAGTAAA	57.232	33.333	0.00	0.00	33.71	2.01
748	6690	8.616076	GCACTGCTTGAAAATTCATATACTACT	58.384	33.333	0.00	0.00	37.00	2.57
749	6691	8.397906	TGCACTGCTTGAAAATTCATATACTAC	58.602	33.333	1.98	0.00	37.00	2.73
750	6692	8.504812	TGCACTGCTTGAAAATTCATATACTA	57.495	30.769	1.98	0.00	37.00	1.82
751	6693	7.395190	TGCACTGCTTGAAAATTCATATACT	57.605	32.000	1.98	0.00	37.00	2.12
752	6694	7.703621	ACATGCACTGCTTGAAAATTCATATAC	59.296	33.333	20.62	0.00	37.20	1.47
921	6869	2.424956	GGAGCTTTGGATGTTGGATGTC	59.575	50.000	0.00	0.00	0.00	3.06
1037	6991	2.359230	GCTGCTGCGAGAGGGTTT	60.359	61.111	0.00	0.00	0.00	3.27
1746	7761	9.899661	AGTTTTGCATCCAGTATTGTACTATAA	57.100	29.630	0.00	0.00	37.23	0.98
1776	7791	7.607607	ACTCAAGAATTAATTTTTGGCATTCCC	59.392	33.333	23.76	0.64	33.96	3.97
1836	8157	6.147864	ACCATACAGATTTTGCGCAAATAT	57.852	33.333	33.94	27.00	35.02	1.28
1862	8183	5.880332	TCGTAGCAGATAAAGCAGGAAAAAT	59.120	36.000	0.00	0.00	0.00	1.82
2057	8395	1.643868	CGCTTGGCATCCACGCTTTA	61.644	55.000	11.64	0.00	44.99	1.85
2247	8775	6.687081	AGTAGAGTAAGAGTTTGATCCTCG	57.313	41.667	0.00	0.00	34.08	4.63
2309	8838	1.003839	CTAACAAGCACGCCCTCCA	60.004	57.895	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.