AutoCloner

Multiple sequence alignment - TraesCS3D01G081800

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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	TraesCS3D01G081800	chr3D	100.000	2468	0	0	1	2468	40998164	41000631	0.000000e+00	4558
1	TraesCS3D01G081800	chr3D	98.811	1009	12	0	1460	2468	580302772	580303780	0.000000e+00	1797
2	TraesCS3D01G081800	chr3D	88.585	622	51	6	846	1463	41050507	41051112	0.000000e+00	737
3	TraesCS3D01G081800	chr2D	99.105	1006	9	0	1463	2468	646518733	646519738	0.000000e+00	1808
4	TraesCS3D01G081800	chr2D	97.313	856	21	2	1	855	112884966	112885820	0.000000e+00	1452
5	TraesCS3D01G081800	chr1D	99.007	1007	10	0	1462	2468	361855153	361856159	0.000000e+00	1805
6	TraesCS3D01G081800	chr6D	98.909	1008	11	0	1461	2468	26748997	26747990	0.000000e+00	1801
7	TraesCS3D01G081800	chr6D	94.262	122	5	2	734	855	19672520	19672401	4.190000e-43	185
8	TraesCS3D01G081800	chr5D	98.908	1007	11	0	1462	2468	24098152	24097146	0.000000e+00	1799
9	TraesCS3D01G081800	chr5D	98.714	1011	11	2	1458	2468	492305649	492304641	0.000000e+00	1794
10	TraesCS3D01G081800	chr7D	98.907	1006	11	0	1463	2468	572001135	572000130	0.000000e+00	1797
11	TraesCS3D01G081800	chr7D	90.712	786	64	2	1	785	500980039	500979262	0.000000e+00	1038
12	TraesCS3D01G081800	chr4D	98.907	1006	11	0	1463	2468	504546406	504545401	0.000000e+00	1797
13	TraesCS3D01G081800	chrUn	98.810	1008	12	0	1461	2468	95578540	95579547	0.000000e+00	1796
14	TraesCS3D01G081800	chr3B	92.982	855	46	3	1	841	607481806	607482660	0.000000e+00	1234
15	TraesCS3D01G081800	chr7A	87.239	862	59	17	1	842	610687606	610686776	0.000000e+00	935
16	TraesCS3D01G081800	chr3A	88.764	623	54	12	845	1463	52963029	52963639	0.000000e+00	749
17	TraesCS3D01G081800	chr4B	80.796	854	155	8	1	849	294770693	294771542	0.000000e+00	660
18	TraesCS3D01G081800	chr2B	86.723	354	46	1	503	856	682175260	682174908	2.300000e-105	392

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	TraesCS3D01G081800	chr3D	40998164	41000631	2467	False	4558	4558	100.000	1	2468	1	chr3D.!!$F1	2467
1	TraesCS3D01G081800	chr3D	580302772	580303780	1008	False	1797	1797	98.811	1460	2468	1	chr3D.!!$F3	1008
2	TraesCS3D01G081800	chr3D	41050507	41051112	605	False	737	737	88.585	846	1463	1	chr3D.!!$F2	617
3	TraesCS3D01G081800	chr2D	646518733	646519738	1005	False	1808	1808	99.105	1463	2468	1	chr2D.!!$F2	1005
4	TraesCS3D01G081800	chr2D	112884966	112885820	854	False	1452	1452	97.313	1	855	1	chr2D.!!$F1	854
5	TraesCS3D01G081800	chr1D	361855153	361856159	1006	False	1805	1805	99.007	1462	2468	1	chr1D.!!$F1	1006
6	TraesCS3D01G081800	chr6D	26747990	26748997	1007	True	1801	1801	98.909	1461	2468	1	chr6D.!!$R2	1007
7	TraesCS3D01G081800	chr5D	24097146	24098152	1006	True	1799	1799	98.908	1462	2468	1	chr5D.!!$R1	1006
8	TraesCS3D01G081800	chr5D	492304641	492305649	1008	True	1794	1794	98.714	1458	2468	1	chr5D.!!$R2	1010
9	TraesCS3D01G081800	chr7D	572000130	572001135	1005	True	1797	1797	98.907	1463	2468	1	chr7D.!!$R2	1005
10	TraesCS3D01G081800	chr7D	500979262	500980039	777	True	1038	1038	90.712	1	785	1	chr7D.!!$R1	784
11	TraesCS3D01G081800	chr4D	504545401	504546406	1005	True	1797	1797	98.907	1463	2468	1	chr4D.!!$R1	1005
12	TraesCS3D01G081800	chrUn	95578540	95579547	1007	False	1796	1796	98.810	1461	2468	1	chrUn.!!$F1	1007
13	TraesCS3D01G081800	chr3B	607481806	607482660	854	False	1234	1234	92.982	1	841	1	chr3B.!!$F1	840
14	TraesCS3D01G081800	chr7A	610686776	610687606	830	True	935	935	87.239	1	842	1	chr7A.!!$R1	841
15	TraesCS3D01G081800	chr3A	52963029	52963639	610	False	749	749	88.764	845	1463	1	chr3A.!!$F1	618
16	TraesCS3D01G081800	chr4B	294770693	294771542	849	False	660	660	80.796	1	849	1	chr4B.!!$F1	848

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
86	91	0.249531	TTCGACTACGGCTTTGTGCA	60.250	50.0	0.0	0.0	45.15	4.57	F
790	841	0.401738	ATGTAAGTGTGCTGGTGGCT	59.598	50.0	0.0	0.0	42.39	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1265	1324	0.680061	GTCGCCATAGGGGTCTAAGG	59.320	60.0	0.0	0.0	39.65	2.69	R
2220	2279	1.851021	CTTCGCATGAAACCGTGCCA	61.851	55.0	0.0	0.0	42.13	4.92	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
86	91	0.249531	TTCGACTACGGCTTTGTGCA	60.250	50.000	0.00	0.00	45.15	4.57
182	190	4.806892	TGCTATGGAAATGGTGGAATCAT	58.193	39.130	0.00	0.00	0.00	2.45
353	381	8.550280	TGATGGGGATCAATTGAAAATCAATA	57.450	30.769	13.09	1.19	45.57	1.90
423	461	1.112113	ATCCGCGATAACACTGGAGT	58.888	50.000	8.23	0.00	31.10	3.85
501	539	2.959484	CGGAGGCTTGCCTTCAGGA	61.959	63.158	18.95	0.00	37.39	3.86
641	692	7.921041	TTCAGAGATATCCACCAGTTTATCT	57.079	36.000	0.00	0.00	34.84	1.98
698	749	6.208007	TGTTCCTCGAGACTGTAATAAAGTCA	59.792	38.462	15.71	0.00	45.38	3.41
790	841	0.401738	ATGTAAGTGTGCTGGTGGCT	59.598	50.000	0.00	0.00	42.39	4.75
903	954	2.942710	GCAGCATGGCAGCTTATAATG	58.057	47.619	8.43	0.00	43.70	1.90
904	955	2.352421	GCAGCATGGCAGCTTATAATGG	60.352	50.000	8.43	0.00	43.70	3.16
905	956	2.889045	CAGCATGGCAGCTTATAATGGT	59.111	45.455	8.43	0.00	43.70	3.55
906	957	3.319972	CAGCATGGCAGCTTATAATGGTT	59.680	43.478	8.43	0.00	43.70	3.67
907	958	3.571401	AGCATGGCAGCTTATAATGGTTC	59.429	43.478	5.75	0.00	43.70	3.62
908	959	3.318839	GCATGGCAGCTTATAATGGTTCA	59.681	43.478	0.00	0.00	0.00	3.18
909	960	4.021719	GCATGGCAGCTTATAATGGTTCAT	60.022	41.667	0.00	0.00	0.00	2.57
910	961	5.706916	CATGGCAGCTTATAATGGTTCATC	58.293	41.667	0.00	0.00	0.00	2.92
911	962	5.052693	TGGCAGCTTATAATGGTTCATCT	57.947	39.130	0.00	0.00	0.00	2.90
912	963	4.823442	TGGCAGCTTATAATGGTTCATCTG	59.177	41.667	0.00	0.00	0.00	2.90
913	964	4.320788	GGCAGCTTATAATGGTTCATCTGC	60.321	45.833	0.00	0.00	42.40	4.26
914	965	4.276678	GCAGCTTATAATGGTTCATCTGCA	59.723	41.667	0.00	0.00	42.59	4.41
915	966	5.562307	GCAGCTTATAATGGTTCATCTGCAG	60.562	44.000	7.63	7.63	42.59	4.41
916	967	5.761726	CAGCTTATAATGGTTCATCTGCAGA	59.238	40.000	20.79	20.79	0.00	4.26
941	996	4.398358	TCTCGATGCCGGGAATATTAGTAG	59.602	45.833	0.00	0.00	43.21	2.57
942	997	3.446161	TCGATGCCGGGAATATTAGTAGG	59.554	47.826	0.00	0.00	36.24	3.18
960	1019	5.988287	AGTAGGAGTACTATATACGAGCCC	58.012	45.833	0.00	0.00	37.76	5.19
979	1038	2.598589	CCAAGCGACAATCACATTTGG	58.401	47.619	0.00	0.00	0.00	3.28
1008	1067	3.065095	CACAAAACAAAACAATGGGCCAG	59.935	43.478	13.78	0.82	0.00	4.85
1128	1187	2.513204	CCCGTCATGCTGCTCCAG	60.513	66.667	0.00	0.00	34.12	3.86
1201	1260	2.227089	GATGAGGACCCACGACGCTT	62.227	60.000	0.00	0.00	0.00	4.68
1227	1286	3.005539	ACACGGCCCATGAGCTCT	61.006	61.111	16.19	0.00	0.00	4.09
1228	1287	2.513204	CACGGCCCATGAGCTCTG	60.513	66.667	16.19	10.42	0.00	3.35
1294	1353	3.365291	TATGGCGACCACTGGCGAC	62.365	63.158	13.90	11.97	35.80	5.19
1308	1367	2.335011	CGACAGATGCGCCGGATA	59.665	61.111	5.05	0.00	0.00	2.59
1329	1388	2.574399	GTCACCGAGCTCCTCACC	59.426	66.667	8.47	0.00	0.00	4.02
1356	1415	1.228894	AGTCCTCTCCTTCCGTGCA	60.229	57.895	0.00	0.00	0.00	4.57
1414	1473	3.393970	CTGCCAGCGGGGAAGAGA	61.394	66.667	4.64	0.00	46.79	3.10
1426	1485	0.528466	GGAAGAGATCGACATGCGCA	60.528	55.000	14.96	14.96	40.61	6.09
1449	1508	2.821366	CTGTCTGCGATGGTGGCC	60.821	66.667	0.00	0.00	0.00	5.36
1518	1577	6.546034	CCATTAGTCCCCAAAATAATCGAACT	59.454	38.462	0.00	0.00	0.00	3.01
1542	1601	3.736720	GACAAAAGGGGTCTTTAGTCGT	58.263	45.455	0.00	0.00	41.92	4.34
1825	1884	2.489329	CAAGGTGTTCGATGAAATGCCT	59.511	45.455	0.00	0.00	0.00	4.75
2220	2279	0.311790	CGTTCACATGCACCTGCTTT	59.688	50.000	0.00	0.00	42.66	3.51
2289	2348	5.860648	AAGAGGGGTTAGAATGGAAGAAA	57.139	39.130	0.00	0.00	0.00	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	36	6.294473	TGCATTTCTCTTCAGAGTTTCTTCT	58.706	36.000	3.73	0.00	42.60	2.85
86	91	0.899720	CTTCCCTGGCATTTGCACAT	59.100	50.000	4.74	0.00	44.36	3.21
353	381	1.494721	ACTATGGAACGCCCCATCAAT	59.505	47.619	11.85	0.00	43.07	2.57
397	425	4.093703	CCAGTGTTATCGCGGATTACAAAA	59.906	41.667	6.13	0.00	34.22	2.44
513	551	1.140312	GGAGATCCCCCATACTGCAA	58.860	55.000	0.00	0.00	0.00	4.08
790	841	2.121538	AGGCACAGCTCGATCGCTA	61.122	57.895	11.09	0.00	38.41	4.26
898	949	5.609423	GAGACTCTGCAGATGAACCATTAT	58.391	41.667	18.63	0.00	0.00	1.28
899	950	4.440663	CGAGACTCTGCAGATGAACCATTA	60.441	45.833	18.63	0.00	0.00	1.90
900	951	3.678252	CGAGACTCTGCAGATGAACCATT	60.678	47.826	18.63	0.00	0.00	3.16
901	952	2.159128	CGAGACTCTGCAGATGAACCAT	60.159	50.000	18.63	0.00	0.00	3.55
902	953	1.203287	CGAGACTCTGCAGATGAACCA	59.797	52.381	18.63	0.00	0.00	3.67
903	954	1.474478	TCGAGACTCTGCAGATGAACC	59.526	52.381	18.63	5.13	0.00	3.62
904	955	2.929531	TCGAGACTCTGCAGATGAAC	57.070	50.000	18.63	8.96	0.00	3.18
905	956	2.480932	GCATCGAGACTCTGCAGATGAA	60.481	50.000	18.63	0.33	40.62	2.57
906	957	1.066757	GCATCGAGACTCTGCAGATGA	59.933	52.381	18.63	10.64	40.62	2.92
907	958	1.489574	GCATCGAGACTCTGCAGATG	58.510	55.000	18.63	11.82	40.97	2.90
908	959	0.388659	GGCATCGAGACTCTGCAGAT	59.611	55.000	18.63	7.64	37.64	2.90
909	960	1.812525	GGCATCGAGACTCTGCAGA	59.187	57.895	17.19	17.19	37.64	4.26
910	961	1.588403	CGGCATCGAGACTCTGCAG	60.588	63.158	16.09	7.63	37.64	4.41
911	962	2.491621	CGGCATCGAGACTCTGCA	59.508	61.111	16.09	0.00	37.64	4.41
912	963	2.279120	CCGGCATCGAGACTCTGC	60.279	66.667	7.92	7.92	39.00	4.26
913	964	1.667154	TTCCCGGCATCGAGACTCTG	61.667	60.000	0.00	0.00	39.00	3.35
914	965	0.757188	ATTCCCGGCATCGAGACTCT	60.757	55.000	0.00	0.00	39.00	3.24
915	966	0.959553	TATTCCCGGCATCGAGACTC	59.040	55.000	0.00	0.00	39.00	3.36
916	967	1.633774	ATATTCCCGGCATCGAGACT	58.366	50.000	0.00	0.00	39.00	3.24
937	992	5.486775	TGGGCTCGTATATAGTACTCCTACT	59.513	44.000	0.00	0.00	37.04	2.57
941	996	4.142425	GCTTGGGCTCGTATATAGTACTCC	60.142	50.000	0.00	0.00	35.22	3.85
942	997	4.437121	CGCTTGGGCTCGTATATAGTACTC	60.437	50.000	0.00	0.00	36.09	2.59
960	1019	3.495193	CTCCAAATGTGATTGTCGCTTG	58.505	45.455	0.00	0.00	0.00	4.01
979	1038	5.050837	CCATTGTTTTGTTTTGTGCTAGCTC	60.051	40.000	17.23	13.38	0.00	4.09
1102	1161	2.829914	CATGACGGGCCACCCATG	60.830	66.667	4.39	10.49	45.83	3.66
1170	1229	2.226896	CCTCATCACTTCGCGAGCG	61.227	63.158	9.59	11.64	41.35	5.03
1173	1232	1.511305	GGTCCTCATCACTTCGCGA	59.489	57.895	3.71	3.71	0.00	5.87
1210	1269	3.005539	AGAGCTCATGGGCCGTGT	61.006	61.111	24.48	6.33	0.00	4.49
1265	1324	0.680061	GTCGCCATAGGGGTCTAAGG	59.320	60.000	0.00	0.00	39.65	2.69
1269	1328	2.064581	GTGGTCGCCATAGGGGTCT	61.065	63.158	0.00	0.00	39.65	3.85
1271	1330	2.040606	AGTGGTCGCCATAGGGGT	59.959	61.111	0.00	0.00	39.65	4.95
1294	1353	2.740055	GGCTATCCGGCGCATCTG	60.740	66.667	10.83	0.00	0.00	2.90
1314	1373	4.803426	GCGGTGAGGAGCTCGGTG	62.803	72.222	7.83	0.00	32.35	4.94
1356	1415	1.043673	CGACTTCCTCCTCCCGGATT	61.044	60.000	0.73	0.00	39.01	3.01
1366	1425	2.892425	CATGGCGGCGACTTCCTC	60.892	66.667	16.45	0.00	0.00	3.71
1402	1461	0.757188	ATGTCGATCTCTTCCCCGCT	60.757	55.000	0.00	0.00	0.00	5.52
1437	1496	4.758251	CTGTCGGCCACCATCGCA	62.758	66.667	2.24	0.00	0.00	5.10
1440	1499	3.127533	GTGCTGTCGGCCACCATC	61.128	66.667	2.24	0.00	40.92	3.51
1449	1508	2.049526	TAGTGCACGGTGCTGTCG	60.050	61.111	30.81	0.00	45.31	4.35
1458	1517	3.368236	GCCTCTTTTTCTACTAGTGCACG	59.632	47.826	12.01	0.00	0.00	5.34
1518	1577	2.158726	ACTAAAGACCCCTTTTGTCGCA	60.159	45.455	0.00	0.00	41.96	5.10
1542	1601	2.284405	GGGTCTCCTCCCGAACCA	60.284	66.667	0.00	0.00	38.17	3.67
1825	1884	3.819368	TCATGTTTGTTTCAGGCTCTCA	58.181	40.909	0.00	0.00	0.00	3.27
2220	2279	1.851021	CTTCGCATGAAACCGTGCCA	61.851	55.000	0.00	0.00	42.13	4.92
2289	2348	6.214208	TCATCGATATCATCCCCTTCTTCATT	59.786	38.462	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.