AutoCloner

Multiple sequence alignment - TraesCS1D01G112400

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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	TraesCS1D01G112400	chr1D	100.000	2573	0	0	1	2573	108109745	108112317	0.000000e+00	4752.0
1	TraesCS1D01G112400	chr1A	94.635	876	26	4	1	876	111132809	111133663	0.000000e+00	1338.0
2	TraesCS1D01G112400	chr1A	91.932	818	41	10	904	1704	111133662	111134471	0.000000e+00	1122.0
3	TraesCS1D01G112400	chr1A	87.654	81	6	2	1695	1772	111135172	111135251	9.800000e-15	91.6
4	TraesCS1D01G112400	chr1B	91.719	954	53	9	904	1837	158533473	158532526	0.000000e+00	1301.0
5	TraesCS1D01G112400	chr1B	93.068	880	37	10	1	876	158534331	158533472	0.000000e+00	1266.0
6	TraesCS1D01G112400	chr1B	88.330	557	65	0	1843	2399	176821281	176820725	0.000000e+00	669.0
7	TraesCS1D01G112400	chr2D	98.085	731	14	0	1843	2573	161382324	161381594	0.000000e+00	1273.0
8	TraesCS1D01G112400	chr2D	97.401	731	19	0	1843	2573	562349061	562349791	0.000000e+00	1245.0
9	TraesCS1D01G112400	chr5D	97.127	731	20	1	1843	2573	205362507	205363236	0.000000e+00	1232.0
10	TraesCS1D01G112400	chr3D	96.845	729	23	0	1845	2573	193869097	193868369	0.000000e+00	1219.0
11	TraesCS1D01G112400	chr4D	95.622	731	22	1	1843	2573	298387751	298388471	0.000000e+00	1164.0
12	TraesCS1D01G112400	chr2A	90.710	732	65	3	1843	2573	33685654	33686383	0.000000e+00	972.0
13	TraesCS1D01G112400	chr2A	86.594	731	93	3	1843	2573	535397707	535398432	0.000000e+00	802.0
14	TraesCS1D01G112400	chr5A	84.857	733	109	1	1843	2573	420242605	420241873	0.000000e+00	737.0
15	TraesCS1D01G112400	chr7D	91.495	388	32	1	2186	2573	261107956	261108342	1.360000e-147	532.0

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	TraesCS1D01G112400	chr1D	108109745	108112317	2572	False	4752.000000	4752	100.0000	1	2573	1	chr1D.!!$F1	2572
1	TraesCS1D01G112400	chr1A	111132809	111135251	2442	False	850.533333	1338	91.4070	1	1772	3	chr1A.!!$F1	1771
2	TraesCS1D01G112400	chr1B	158532526	158534331	1805	True	1283.500000	1301	92.3935	1	1837	2	chr1B.!!$R2	1836
3	TraesCS1D01G112400	chr1B	176820725	176821281	556	True	669.000000	669	88.3300	1843	2399	1	chr1B.!!$R1	556
4	TraesCS1D01G112400	chr2D	161381594	161382324	730	True	1273.000000	1273	98.0850	1843	2573	1	chr2D.!!$R1	730
5	TraesCS1D01G112400	chr2D	562349061	562349791	730	False	1245.000000	1245	97.4010	1843	2573	1	chr2D.!!$F1	730
6	TraesCS1D01G112400	chr5D	205362507	205363236	729	False	1232.000000	1232	97.1270	1843	2573	1	chr5D.!!$F1	730
7	TraesCS1D01G112400	chr3D	193868369	193869097	728	True	1219.000000	1219	96.8450	1845	2573	1	chr3D.!!$R1	728
8	TraesCS1D01G112400	chr4D	298387751	298388471	720	False	1164.000000	1164	95.6220	1843	2573	1	chr4D.!!$F1	730
9	TraesCS1D01G112400	chr2A	33685654	33686383	729	False	972.000000	972	90.7100	1843	2573	1	chr2A.!!$F1	730
10	TraesCS1D01G112400	chr2A	535397707	535398432	725	False	802.000000	802	86.5940	1843	2573	1	chr2A.!!$F2	730
11	TraesCS1D01G112400	chr5A	420241873	420242605	732	True	737.000000	737	84.8570	1843	2573	1	chr5A.!!$R1	730

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
852	859	0.243365	TGCTGGCATTAAAACGCAGG	59.757	50.0	0.0	0.0	0.0	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1777	2515	3.140325	TCAGGAATGAACCAGGAACAC	57.86	47.619	0.0	0.0	0.0	3.32	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
143	144	0.307760	CACAACAGCAAGTTCCGGAC	59.692	55.000	1.83	0.00	38.74	4.79
150	151	2.032681	AAGTTCCGGACTGGCTGC	59.967	61.111	1.83	0.00	39.00	5.25
286	287	6.413018	AAATATTCGACCGAAAACACCTAC	57.587	37.500	8.97	0.00	37.69	3.18
293	294	2.370849	ACCGAAAACACCTACTGGTCAT	59.629	45.455	0.00	0.00	46.60	3.06
391	394	7.122501	TGCTGGTAATGATAAGAAAAATGCAGA	59.877	33.333	0.00	0.00	0.00	4.26
428	431	3.230976	ACAAGTCAAAGGATTGTTCCCC	58.769	45.455	0.00	0.00	43.76	4.81
581	588	3.564455	GTGAGGACACGAGACGTTT	57.436	52.632	0.00	0.00	38.32	3.60
582	589	1.406447	GTGAGGACACGAGACGTTTC	58.594	55.000	0.00	0.00	38.32	2.78
583	590	1.026584	TGAGGACACGAGACGTTTCA	58.973	50.000	6.91	4.03	38.15	2.69
584	591	1.268896	TGAGGACACGAGACGTTTCAC	60.269	52.381	6.91	6.43	38.15	3.18
732	739	2.527442	GCCACAAGTTGCGAATAGTC	57.473	50.000	1.81	0.00	0.00	2.59
733	740	2.076863	GCCACAAGTTGCGAATAGTCT	58.923	47.619	1.81	0.00	0.00	3.24
734	741	2.094417	GCCACAAGTTGCGAATAGTCTC	59.906	50.000	1.81	0.00	0.00	3.36
767	774	3.878778	CAGAAAGGTATGTAGGCAAGCT	58.121	45.455	0.00	0.00	0.00	3.74
812	819	2.096406	CATTTGACGTCGCTGGCG	59.904	61.111	11.62	8.80	41.35	5.69
843	850	0.922626	TGTGGGGTATGCTGGCATTA	59.077	50.000	13.39	0.00	37.82	1.90
852	859	0.243365	TGCTGGCATTAAAACGCAGG	59.757	50.000	0.00	0.00	0.00	4.85
882	889	5.592708	CGAGTTCGTTAAAGATCGAGAAG	57.407	43.478	8.20	0.00	37.38	2.85
883	890	5.322310	CGAGTTCGTTAAAGATCGAGAAGA	58.678	41.667	8.20	0.00	37.38	2.87
884	891	5.966503	CGAGTTCGTTAAAGATCGAGAAGAT	59.033	40.000	8.20	0.00	37.38	2.40
885	892	6.469595	CGAGTTCGTTAAAGATCGAGAAGATT	59.530	38.462	8.20	0.00	37.38	2.40
886	893	7.512272	CGAGTTCGTTAAAGATCGAGAAGATTG	60.512	40.741	8.20	0.00	37.38	2.67
887	894	7.313646	AGTTCGTTAAAGATCGAGAAGATTGA	58.686	34.615	0.00	0.00	40.26	2.57
888	895	7.486551	AGTTCGTTAAAGATCGAGAAGATTGAG	59.513	37.037	0.00	0.00	40.26	3.02
889	896	7.085052	TCGTTAAAGATCGAGAAGATTGAGA	57.915	36.000	0.00	0.00	40.26	3.27
890	897	7.190191	TCGTTAAAGATCGAGAAGATTGAGAG	58.810	38.462	0.00	0.00	40.26	3.20
891	898	6.416455	CGTTAAAGATCGAGAAGATTGAGAGG	59.584	42.308	0.00	0.00	40.26	3.69
892	899	4.320608	AAGATCGAGAAGATTGAGAGGC	57.679	45.455	0.00	0.00	40.26	4.70
893	900	3.295093	AGATCGAGAAGATTGAGAGGCA	58.705	45.455	0.00	0.00	40.26	4.75
894	901	2.949451	TCGAGAAGATTGAGAGGCAC	57.051	50.000	0.00	0.00	0.00	5.01
895	902	3.030291	ATCGAGAAGATTGAGAGGCACT	58.970	45.455	0.00	0.00	37.73	4.40
896	903	3.621558	TCGAGAAGATTGAGAGGCACTA	58.378	45.455	0.00	0.00	41.55	2.74
897	904	4.017126	TCGAGAAGATTGAGAGGCACTAA	58.983	43.478	0.00	0.00	41.55	2.24
898	905	4.646945	TCGAGAAGATTGAGAGGCACTAAT	59.353	41.667	0.00	0.00	41.55	1.73
899	906	5.828328	TCGAGAAGATTGAGAGGCACTAATA	59.172	40.000	0.00	0.00	41.55	0.98
900	907	6.321435	TCGAGAAGATTGAGAGGCACTAATAA	59.679	38.462	0.00	0.00	41.55	1.40
901	908	7.014711	TCGAGAAGATTGAGAGGCACTAATAAT	59.985	37.037	0.00	0.00	41.55	1.28
902	909	8.300286	CGAGAAGATTGAGAGGCACTAATAATA	58.700	37.037	0.00	0.00	41.55	0.98
903	910	9.988815	GAGAAGATTGAGAGGCACTAATAATAA	57.011	33.333	0.00	0.00	41.55	1.40
932	939	8.897872	AAAATCTGCAATTTGTGAGAAGAAAT	57.102	26.923	7.36	0.00	0.00	2.17
936	943	5.451908	TGCAATTTGTGAGAAGAAATCGAC	58.548	37.500	0.00	0.00	0.00	4.20
1192	1207	3.958147	ATCAGCGTGGGGAGCAACG	62.958	63.158	0.00	0.00	42.61	4.10
1535	1550	0.684805	GTGAGGACGGAGGAGGATGT	60.685	60.000	0.00	0.00	0.00	3.06
1636	1654	1.270550	CTGGCATGGTGTTTCTGTTCC	59.729	52.381	0.00	0.00	0.00	3.62
1648	1671	6.128661	GGTGTTTCTGTTCCTTTTGTTTTGTC	60.129	38.462	0.00	0.00	0.00	3.18
1737	2472	6.242396	TCGAATAAATCTCCCAGGAAAAACA	58.758	36.000	0.00	0.00	0.00	2.83
1777	2515	5.754406	CACTCAGATCCTAGAAGAAATGCAG	59.246	44.000	0.00	0.00	0.00	4.41
1810	2548	8.160765	TGGTTCATTCCTGAATAAACTTACTGA	58.839	33.333	6.00	0.00	43.08	3.41
1832	2570	7.068348	ACTGATTCTTGAGCTTCATTATGCAAT	59.932	33.333	0.00	0.00	0.00	3.56
1837	2575	8.284945	TCTTGAGCTTCATTATGCAATAAACT	57.715	30.769	0.00	0.00	42.96	2.66
1838	2576	8.186163	TCTTGAGCTTCATTATGCAATAAACTG	58.814	33.333	0.00	0.00	42.96	3.16
1839	2577	6.267817	TGAGCTTCATTATGCAATAAACTGC	58.732	36.000	0.00	0.00	42.96	4.40
1840	2578	5.276270	AGCTTCATTATGCAATAAACTGCG	58.724	37.500	0.00	0.00	42.96	5.18
1841	2579	4.442073	GCTTCATTATGCAATAAACTGCGG	59.558	41.667	0.00	0.00	42.96	5.69
1935	2673	1.674057	CAGGACCTCCTTGACGCTT	59.326	57.895	0.00	0.00	46.09	4.68
1946	2684	5.048713	CCTCCTTGACGCTTTAAATCAGTTT	60.049	40.000	0.00	0.00	0.00	2.66
2272	3012	2.611518	CAAGGCTTTCGACTCGATCTT	58.388	47.619	1.07	2.22	35.23	2.40
2367	3107	3.053849	GCCTCGTCGTCCTCTGTCC	62.054	68.421	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	3.136626	GGTATGGAGTGGCATCTAAGGTT	59.863	47.826	0.00	0.00	0.00	3.50
150	151	5.127845	ACTGTCTGTATGGTTGTATCTGGAG	59.872	44.000	0.00	0.00	0.00	3.86
310	313	7.012799	ACAGTTCCTTATTAGCGGTACTAGTAC	59.987	40.741	22.53	22.53	30.91	2.73
311	314	7.056635	ACAGTTCCTTATTAGCGGTACTAGTA	58.943	38.462	0.00	0.00	30.91	1.82
312	315	5.890419	ACAGTTCCTTATTAGCGGTACTAGT	59.110	40.000	0.00	0.00	30.91	2.57
313	316	6.388435	ACAGTTCCTTATTAGCGGTACTAG	57.612	41.667	0.00	0.00	30.91	2.57
314	317	7.880160	TTACAGTTCCTTATTAGCGGTACTA	57.120	36.000	0.00	0.00	30.91	1.82
315	318	6.780457	TTACAGTTCCTTATTAGCGGTACT	57.220	37.500	0.00	0.00	32.02	2.73
391	394	6.126863	TGACTTGTTACTTCCCAGATGAAT	57.873	37.500	0.00	0.00	0.00	2.57
399	402	5.535030	ACAATCCTTTGACTTGTTACTTCCC	59.465	40.000	0.00	0.00	36.64	3.97
401	404	7.139392	GGAACAATCCTTTGACTTGTTACTTC	58.861	38.462	3.05	0.00	41.72	3.01
578	585	3.546218	GCAAGAGACTGAAACCGTGAAAC	60.546	47.826	0.00	0.00	0.00	2.78
579	586	2.612212	GCAAGAGACTGAAACCGTGAAA	59.388	45.455	0.00	0.00	0.00	2.69
580	587	2.158957	AGCAAGAGACTGAAACCGTGAA	60.159	45.455	0.00	0.00	0.00	3.18
581	588	1.412710	AGCAAGAGACTGAAACCGTGA	59.587	47.619	0.00	0.00	0.00	4.35
582	589	1.795286	GAGCAAGAGACTGAAACCGTG	59.205	52.381	0.00	0.00	0.00	4.94
583	590	1.270358	GGAGCAAGAGACTGAAACCGT	60.270	52.381	0.00	0.00	0.00	4.83
584	591	1.270305	TGGAGCAAGAGACTGAAACCG	60.270	52.381	0.00	0.00	0.00	4.44
585	592	2.037772	TCTGGAGCAAGAGACTGAAACC	59.962	50.000	0.00	0.00	0.00	3.27
725	732	7.891183	TCTGCACAAAAACTAGAGACTATTC	57.109	36.000	0.00	0.00	0.00	1.75
728	735	6.706270	CCTTTCTGCACAAAAACTAGAGACTA	59.294	38.462	0.00	0.00	0.00	2.59
729	736	5.529060	CCTTTCTGCACAAAAACTAGAGACT	59.471	40.000	0.00	0.00	0.00	3.24
730	737	5.297029	ACCTTTCTGCACAAAAACTAGAGAC	59.703	40.000	0.00	0.00	0.00	3.36
731	738	5.437060	ACCTTTCTGCACAAAAACTAGAGA	58.563	37.500	0.00	0.00	0.00	3.10
732	739	5.757850	ACCTTTCTGCACAAAAACTAGAG	57.242	39.130	0.00	0.00	0.00	2.43
733	740	6.770785	ACATACCTTTCTGCACAAAAACTAGA	59.229	34.615	0.00	0.00	0.00	2.43
734	741	6.970484	ACATACCTTTCTGCACAAAAACTAG	58.030	36.000	0.00	0.00	0.00	2.57
767	774	5.295787	CCTTTTGCTCGCCACATAAACTATA	59.704	40.000	0.00	0.00	0.00	1.31
812	819	2.114670	CCCCACATGTCATGGACGC	61.115	63.158	17.08	0.00	39.87	5.19
843	850	2.542907	CGTGTCTGCCCTGCGTTTT	61.543	57.895	0.00	0.00	0.00	2.43
876	883	2.957491	AGTGCCTCTCAATCTTCTCG	57.043	50.000	0.00	0.00	0.00	4.04
877	884	9.988815	TTATTATTAGTGCCTCTCAATCTTCTC	57.011	33.333	0.00	0.00	0.00	2.87
906	913	8.721019	TTTCTTCTCACAAATTGCAGATTTTT	57.279	26.923	0.00	0.00	0.00	1.94
918	925	3.059868	GCGTGTCGATTTCTTCTCACAAA	60.060	43.478	0.00	0.00	31.60	2.83
1174	1189	2.045926	GTTGCTCCCCACGCTGAT	60.046	61.111	0.00	0.00	0.00	2.90
1175	1190	4.680237	CGTTGCTCCCCACGCTGA	62.680	66.667	0.00	0.00	0.00	4.26
1326	1341	0.536687	ACGAAGACTCCCACACGAGA	60.537	55.000	0.00	0.00	33.83	4.04
1386	1401	3.083997	ATCTCCCCGAGGCACACC	61.084	66.667	0.00	0.00	0.00	4.16
1525	1540	4.899239	CGCCGCCACATCCTCCTC	62.899	72.222	0.00	0.00	0.00	3.71
1648	1671	9.401058	AGAACTCAGATGGAATTAATAACCTTG	57.599	33.333	11.27	8.15	0.00	3.61
1777	2515	3.140325	TCAGGAATGAACCAGGAACAC	57.860	47.619	0.00	0.00	0.00	3.32
1810	2548	9.525409	GTTTATTGCATAATGAAGCTCAAGAAT	57.475	29.630	0.00	0.00	0.00	2.40
1815	2553	6.267817	GCAGTTTATTGCATAATGAAGCTCA	58.732	36.000	0.00	0.00	43.53	4.26
1967	2705	5.755409	TTGCAGAGTTCAGGATACCTAAA	57.245	39.130	0.00	0.00	29.64	1.85
2272	3012	3.484953	ACTCCAGTAGGTATTCCCACA	57.515	47.619	0.00	0.00	35.89	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.