AutoCloner

Multiple sequence alignment - TraesCS6D01G045100

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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	TraesCS6D01G045100	chr6D	100.000	3080	0	0	1	3080	20313155	20310076	0.000000e+00	5688
1	TraesCS6D01G045100	chr6D	79.792	1539	287	18	669	2198	20602858	20601335	0.000000e+00	1098
2	TraesCS6D01G045100	chr6D	79.878	1471	267	20	678	2139	16242667	16244117	0.000000e+00	1050
3	TraesCS6D01G045100	chr6D	95.593	295	13	0	185	479	20312664	20312370	1.000000e-129	473
4	TraesCS6D01G045100	chr6D	95.593	295	13	0	492	786	20312971	20312677	1.000000e-129	473
5	TraesCS6D01G045100	chrUn	94.617	2935	97	18	184	3080	273854065	273856976	0.000000e+00	4488
6	TraesCS6D01G045100	chrUn	88.794	821	24	26	1	786	273853560	273854347	0.000000e+00	944
7	TraesCS6D01G045100	chrUn	96.141	311	12	0	169	479	273854352	273854662	2.740000e-140	508
8	TraesCS6D01G045100	chrUn	91.531	307	12	4	484	786	273853767	273854063	7.950000e-111	411
9	TraesCS6D01G045100	chrUn	93.617	235	9	4	165	393	476350643	476350877	2.270000e-91	346
10	TraesCS6D01G045100	chrUn	92.825	223	10	2	484	700	476350655	476350877	4.960000e-83	318
11	TraesCS6D01G045100	chr6B	94.412	2935	102	12	184	3080	34342176	34339266	0.000000e+00	4455
12	TraesCS6D01G045100	chr6B	81.077	1337	217	21	881	2201	34685399	34684083	0.000000e+00	1035
13	TraesCS6D01G045100	chr6B	88.794	821	24	26	1	786	34342681	34341894	0.000000e+00	944
14	TraesCS6D01G045100	chr6B	96.753	308	10	0	172	479	34341886	34341579	5.890000e-142	514
15	TraesCS6D01G045100	chr6B	91.776	304	11	4	487	786	34342471	34342178	7.950000e-111	411
16	TraesCS6D01G045100	chr6A	94.654	1908	89	5	965	2868	20310456	20308558	0.000000e+00	2946
17	TraesCS6D01G045100	chr6A	79.663	1544	276	27	669	2198	20522594	20521075	0.000000e+00	1077
18	TraesCS6D01G045100	chr6A	99.078	217	2	0	2864	3080	20303469	20303253	1.040000e-104	390
19	TraesCS6D01G045100	chr6A	98.214	56	1	0	3025	3080	20303204	20303149	7.030000e-17	99
20	TraesCS6D01G045100	chr7D	79.937	1271	228	20	844	2099	632406579	632405321	0.000000e+00	909
21	TraesCS6D01G045100	chr7B	79.250	1147	218	16	964	2098	744570684	744569546	0.000000e+00	782
22	TraesCS6D01G045100	chr1B	81.395	387	60	7	2652	3028	401344416	401344032	3.860000e-79	305
23	TraesCS6D01G045100	chr1A	81.167	377	59	4	2652	3022	372029278	372028908	3.000000e-75	292

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	TraesCS6D01G045100	chr6D	20310076	20313155	3079	True	2211.333333	5688	97.06200	1	3080	3	chr6D.!!$R2	3079
1	TraesCS6D01G045100	chr6D	20601335	20602858	1523	True	1098.000000	1098	79.79200	669	2198	1	chr6D.!!$R1	1529
2	TraesCS6D01G045100	chr6D	16242667	16244117	1450	False	1050.000000	1050	79.87800	678	2139	1	chr6D.!!$F1	1461
3	TraesCS6D01G045100	chrUn	273853560	273856976	3416	False	1587.750000	4488	92.77075	1	3080	4	chrUn.!!$F1	3079
4	TraesCS6D01G045100	chr6B	34339266	34342681	3415	True	1581.000000	4455	92.93375	1	3080	4	chr6B.!!$R2	3079
5	TraesCS6D01G045100	chr6B	34684083	34685399	1316	True	1035.000000	1035	81.07700	881	2201	1	chr6B.!!$R1	1320
6	TraesCS6D01G045100	chr6A	20308558	20310456	1898	True	2946.000000	2946	94.65400	965	2868	1	chr6A.!!$R1	1903
7	TraesCS6D01G045100	chr6A	20521075	20522594	1519	True	1077.000000	1077	79.66300	669	2198	1	chr6A.!!$R2	1529
8	TraesCS6D01G045100	chr7D	632405321	632406579	1258	True	909.000000	909	79.93700	844	2099	1	chr7D.!!$R1	1255
9	TraesCS6D01G045100	chr7B	744569546	744570684	1138	True	782.000000	782	79.25000	964	2098	1	chr7B.!!$R1	1134

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
634	952	0.384309	TGCCTACACGATCGATCCAC	59.616	55.000	24.34	6.97	0.0	4.02	F
1457	1798	1.003866	GGCAGTGACAAACGTGAAGAC	60.004	52.381	0.00	0.00	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1735	2076	1.999648	TTCAGCACCCATTTGAAGCT	58.00	45.0	0.0	0.0	35.63	3.74	R
2940	3311	0.469917	ACTGATATCCCTGCCAACCG	59.53	55.0	0.0	0.0	0.00	4.44	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
22	23	2.101750	TGAAGTGACACTCGGCTTACAA	59.898	45.455	8.93	0.00	0.00	2.41
44	46	2.159379	GCTTAAGCCGGTCCAAATGAAG	60.159	50.000	17.00	0.00	34.31	3.02
88	90	2.240279	ACACTCGGCTTACTCTTCACT	58.760	47.619	0.00	0.00	0.00	3.41
90	92	2.229062	CACTCGGCTTACTCTTCACTGA	59.771	50.000	0.00	0.00	0.00	3.41
91	93	2.490115	ACTCGGCTTACTCTTCACTGAG	59.510	50.000	0.00	0.00	39.23	3.35
235	267	8.192743	AGAGATAGACAGATTTGATATGTGCT	57.807	34.615	0.00	0.00	34.37	4.40
286	318	0.678048	CCAGCTTCACCTTGTAGCCC	60.678	60.000	1.60	0.00	40.99	5.19
320	352	0.606604	ACGACCTTGCCTACACGATT	59.393	50.000	0.00	0.00	0.00	3.34
371	403	9.456147	AATTCAGAGTATACGCAGATAGATAGT	57.544	33.333	9.39	0.00	0.00	2.12
613	931	4.215613	GCCCAAAATTTTCTAGTGACGACT	59.784	41.667	0.00	0.00	36.07	4.18
629	947	1.466866	CGACTTTGCCTACACGATCGA	60.467	52.381	24.34	0.00	0.00	3.59
634	952	0.384309	TGCCTACACGATCGATCCAC	59.616	55.000	24.34	6.97	0.00	4.02
647	965	4.386867	TCGATCCACTACTTCACCATTC	57.613	45.455	0.00	0.00	0.00	2.67
657	975	7.393234	CCACTACTTCACCATTCCTTAAATTCA	59.607	37.037	0.00	0.00	0.00	2.57
806	1135	4.123497	TCCAGATTCATTGTGTACCTCG	57.877	45.455	0.00	0.00	0.00	4.63
853	1183	2.589720	TGGTCGGTTCACTACTTCAGA	58.410	47.619	0.00	0.00	0.00	3.27
1097	1435	5.896106	TGGACATCACTGATAGAGACTTGAT	59.104	40.000	0.00	0.00	0.00	2.57
1232	1570	5.567224	GCATGATCCACAAATTCAACCAAGA	60.567	40.000	0.00	0.00	0.00	3.02
1293	1634	5.163374	TGACATGACCGATGAAGAGATTGAT	60.163	40.000	0.00	0.00	35.80	2.57
1361	1702	3.353836	CCAAGGCCGGTTCACACG	61.354	66.667	1.90	0.00	0.00	4.49
1413	1754	2.218953	TGTTCGTAGATTGGCGGATC	57.781	50.000	0.00	0.00	35.04	3.36
1457	1798	1.003866	GGCAGTGACAAACGTGAAGAC	60.004	52.381	0.00	0.00	0.00	3.01
1532	1873	2.945668	GCATCAACTCCATAAGGACCAC	59.054	50.000	0.00	0.00	39.61	4.16
1751	2092	1.251251	GACAGCTTCAAATGGGTGCT	58.749	50.000	0.00	0.00	34.75	4.40
1778	2119	3.557903	ATGAGGTGGCGTTGCTGCT	62.558	57.895	0.00	0.00	34.52	4.24
1944	2285	5.048846	ACCCCAAGAAACGCATAGATTAT	57.951	39.130	0.00	0.00	0.00	1.28
2205	2553	9.819267	AAGCTAGACTTACTATTGATTTGTACC	57.181	33.333	0.00	0.00	36.62	3.34
2328	2676	9.185192	CAGAGAACACATAAATTTCTCCAAAAC	57.815	33.333	0.00	0.00	44.29	2.43
2329	2677	8.912988	AGAGAACACATAAATTTCTCCAAAACA	58.087	29.630	0.00	0.00	44.29	2.83
2330	2678	9.528018	GAGAACACATAAATTTCTCCAAAACAA	57.472	29.630	0.00	0.00	39.51	2.83
2331	2679	9.883142	AGAACACATAAATTTCTCCAAAACAAA	57.117	25.926	0.00	0.00	0.00	2.83
2333	2681	9.883142	AACACATAAATTTCTCCAAAACAAAGA	57.117	25.926	0.00	0.00	0.00	2.52
2408	2756	4.111375	ACAAACGCGATTAGAGTCAGAT	57.889	40.909	15.93	0.00	30.72	2.90
2518	2866	1.153958	GCACCGCTTCAATGCCTTC	60.154	57.895	0.00	0.00	33.06	3.46
2643	3014	0.953727	ACATGTGTCTTTGCGTGCAT	59.046	45.000	0.00	0.00	0.00	3.96
2650	3021	2.009774	GTCTTTGCGTGCATAGTCCAT	58.990	47.619	11.21	0.00	0.00	3.41
2666	3037	1.480545	TCCATTTCTCGATTCGGAGCA	59.519	47.619	6.18	0.00	33.98	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	1.004277	TCATTTGGACCGGCTTAAGCT	59.996	47.619	25.88	7.44	41.70	3.74
44	46	5.007385	ACACTCATAATACGGTCCTCAAC	57.993	43.478	0.00	0.00	0.00	3.18
88	90	3.613030	GGCGAAACCCTATTTAACCTCA	58.387	45.455	0.00	0.00	0.00	3.86
90	92	2.236893	TCGGCGAAACCCTATTTAACCT	59.763	45.455	7.35	0.00	33.26	3.50
91	93	2.610833	CTCGGCGAAACCCTATTTAACC	59.389	50.000	12.13	0.00	33.26	2.85
247	279	8.429237	AGCTGGTAGTAATTGCTAGAGATATT	57.571	34.615	3.22	0.00	31.71	1.28
286	318	5.625311	GCAAGGTCGTCACTAGAAAATTTTG	59.375	40.000	8.47	0.00	0.00	2.44
320	352	3.650942	AGAAATGGTGAAGTAGTGGACCA	59.349	43.478	0.00	0.00	42.60	4.02
559	877	6.284459	GTGAAGCTGGTAGTAATTGCTAGAT	58.716	40.000	3.22	0.00	33.28	1.98
613	931	1.478916	TGGATCGATCGTGTAGGCAAA	59.521	47.619	18.81	0.00	0.00	3.68
629	947	6.636454	TTAAGGAATGGTGAAGTAGTGGAT	57.364	37.500	0.00	0.00	0.00	3.41
634	952	8.792830	TCTGAATTTAAGGAATGGTGAAGTAG	57.207	34.615	0.00	0.00	0.00	2.57
647	965	9.347934	CTATCTGCGTATACTCTGAATTTAAGG	57.652	37.037	6.54	0.00	0.00	2.69
730	1048	8.367156	TGCATATGTAGCACATATCAAAGTAGA	58.633	33.333	14.86	0.00	45.83	2.59
806	1135	8.056407	AGGCAAGGTTATCACTAGAAAATTTC	57.944	34.615	0.00	0.00	0.00	2.17
1097	1435	2.461300	CCATAGGGACTCCTCTGACA	57.539	55.000	0.00	0.00	43.66	3.58
1232	1570	0.254178	CAGCTTGTAGGGTGCATCCT	59.746	55.000	24.88	24.88	40.79	3.24
1293	1634	2.738139	CAGCGACCGTGCATGTGA	60.738	61.111	4.96	0.00	37.31	3.58
1413	1754	1.024579	GGCGTTGGTCATACCCTGTG	61.025	60.000	0.00	0.00	37.50	3.66
1532	1873	2.287069	ACAGACAACGACTTCAGACTCG	60.287	50.000	0.00	0.00	35.96	4.18
1735	2076	1.999648	TTCAGCACCCATTTGAAGCT	58.000	45.000	0.00	0.00	35.63	3.74
1751	2092	3.558931	ACGCCACCTCATCATTATTCA	57.441	42.857	0.00	0.00	0.00	2.57
2118	2463	5.530915	CACCAGTTTCCTTTTCAGATACACA	59.469	40.000	0.00	0.00	0.00	3.72
2179	2527	9.819267	GGTACAAATCAATAGTAAGTCTAGCTT	57.181	33.333	0.00	5.06	41.05	3.74
2205	2553	8.438676	AGACGGGTAAAGAGAAATGAAATATG	57.561	34.615	0.00	0.00	0.00	1.78
2212	2560	6.426937	TGAGAAAAGACGGGTAAAGAGAAATG	59.573	38.462	0.00	0.00	0.00	2.32
2221	2569	6.712998	TGAATCAAATGAGAAAAGACGGGTAA	59.287	34.615	0.00	0.00	0.00	2.85
2286	2634	6.876257	GTGTTCTCTGAGAATTAATGTGAGGT	59.124	38.462	21.86	0.00	36.50	3.85
2288	2636	7.895975	TGTGTTCTCTGAGAATTAATGTGAG	57.104	36.000	21.86	0.00	36.50	3.51
2408	2756	4.649674	GGAGACTCCATTGGTCTATGTACA	59.350	45.833	17.10	0.00	43.13	2.90
2434	2782	6.375736	TGTCCCGCAAATTTCTGTGAATTATA	59.624	34.615	0.00	0.00	0.00	0.98
2518	2866	2.294512	GGAAAGCCAACCACAAGAAGAG	59.705	50.000	0.00	0.00	0.00	2.85
2643	3014	3.243434	GCTCCGAATCGAGAAATGGACTA	60.243	47.826	3.36	0.00	30.97	2.59
2650	3021	2.736721	CAAAGTGCTCCGAATCGAGAAA	59.263	45.455	3.36	0.00	30.97	2.52
2666	3037	1.311059	GCCCATGATCCCCCAAAGT	59.689	57.895	0.00	0.00	0.00	2.66
2940	3311	0.469917	ACTGATATCCCTGCCAACCG	59.530	55.000	0.00	0.00	0.00	4.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.