AutoCloner

Multiple sequence alignment - TraesCS7A01G091000

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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	TraesCS7A01G091000	chr7A	100.000	3365	0	0	1	3365	55364282	55367646	0.000000e+00	6215
1	TraesCS7A01G091000	chr7A	93.283	789	49	3	2577	3365	719636200	719635416	0.000000e+00	1160
2	TraesCS7A01G091000	chr7A	86.970	944	97	17	2436	3365	596374810	596375741	0.000000e+00	1038
3	TraesCS7A01G091000	chr7D	93.045	2430	108	16	14	2404	52837148	52834741	0.000000e+00	3494
4	TraesCS7A01G091000	chr7D	92.964	1464	66	17	929	2367	53410378	53411829	0.000000e+00	2098
5	TraesCS7A01G091000	chr4A	92.739	2424	117	21	11	2405	667855096	667857489	0.000000e+00	3446
6	TraesCS7A01G091000	chr4A	93.146	963	59	5	2405	3365	428263105	428262148	0.000000e+00	1406
7	TraesCS7A01G091000	chr4A	76.695	236	40	9	1712	1939	61616145	61615917	2.120000e-22	117
8	TraesCS7A01G091000	chr4A	71.569	510	106	33	1433	1921	628485440	628485931	5.940000e-18	102
9	TraesCS7A01G091000	chr2A	92.872	982	50	14	2401	3365	114504103	114505081	0.000000e+00	1408
10	TraesCS7A01G091000	chr2A	90.983	987	37	21	2405	3365	755664227	755663267	0.000000e+00	1282
11	TraesCS7A01G091000	chr2A	88.242	876	85	14	2496	3365	38302059	38301196	0.000000e+00	1031
12	TraesCS7A01G091000	chr2A	93.225	369	23	2	2403	2769	532210068	532210436	2.950000e-150	542
13	TraesCS7A01G091000	chr2A	92.973	370	24	2	2402	2769	59005407	59005038	3.820000e-149	538
14	TraesCS7A01G091000	chr1D	91.003	967	55	12	2405	3365	349189203	349190143	0.000000e+00	1275
15	TraesCS7A01G091000	chr2B	86.997	969	108	14	2405	3365	483542782	483541824	0.000000e+00	1075
16	TraesCS7A01G091000	chr2D	91.667	708	39	13	2662	3365	624298968	624299659	0.000000e+00	963
17	TraesCS7A01G091000	chr5A	92.992	371	22	3	2402	2769	462810819	462810450	3.820000e-149	538
18	TraesCS7A01G091000	chr5A	92.453	371	25	2	2402	2769	41464736	41465106	8.270000e-146	527
19	TraesCS7A01G091000	chr3A	92.973	370	21	4	2403	2769	538021445	538021812	4.940000e-148	534
20	TraesCS7A01G091000	chr4D	76.695	236	40	11	1712	1939	404111523	404111295	2.120000e-22	117
21	TraesCS7A01G091000	chr4B	76.695	236	40	11	1712	1939	500868950	500868722	2.120000e-22	117

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	TraesCS7A01G091000	chr7A	55364282	55367646	3364	False	6215	6215	100.000	1	3365	1	chr7A.!!$F1	3364
1	TraesCS7A01G091000	chr7A	719635416	719636200	784	True	1160	1160	93.283	2577	3365	1	chr7A.!!$R1	788
2	TraesCS7A01G091000	chr7A	596374810	596375741	931	False	1038	1038	86.970	2436	3365	1	chr7A.!!$F2	929
3	TraesCS7A01G091000	chr7D	52834741	52837148	2407	True	3494	3494	93.045	14	2404	1	chr7D.!!$R1	2390
4	TraesCS7A01G091000	chr7D	53410378	53411829	1451	False	2098	2098	92.964	929	2367	1	chr7D.!!$F1	1438
5	TraesCS7A01G091000	chr4A	667855096	667857489	2393	False	3446	3446	92.739	11	2405	1	chr4A.!!$F2	2394
6	TraesCS7A01G091000	chr4A	428262148	428263105	957	True	1406	1406	93.146	2405	3365	1	chr4A.!!$R2	960
7	TraesCS7A01G091000	chr2A	114504103	114505081	978	False	1408	1408	92.872	2401	3365	1	chr2A.!!$F1	964
8	TraesCS7A01G091000	chr2A	755663267	755664227	960	True	1282	1282	90.983	2405	3365	1	chr2A.!!$R3	960
9	TraesCS7A01G091000	chr2A	38301196	38302059	863	True	1031	1031	88.242	2496	3365	1	chr2A.!!$R1	869
10	TraesCS7A01G091000	chr1D	349189203	349190143	940	False	1275	1275	91.003	2405	3365	1	chr1D.!!$F1	960
11	TraesCS7A01G091000	chr2B	483541824	483542782	958	True	1075	1075	86.997	2405	3365	1	chr2B.!!$R1	960
12	TraesCS7A01G091000	chr2D	624298968	624299659	691	False	963	963	91.667	2662	3365	1	chr2D.!!$F1	703

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
994	1053	0.39086	GGACGATGGTCAGGGATCAG	59.609	60.0	10.22	0.0	45.28	2.9	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2373	2459	0.320683	CTGACCCGACTGTGCATGAA	60.321	55.0	0.0	0.0	0.0	2.57	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
70	74	1.500474	ACCCTGACGGACATGATGAT	58.500	50.000	0.00	0.00	34.64	2.45
76	80	2.362077	TGACGGACATGATGATGACGAT	59.638	45.455	16.97	5.42	37.13	3.73
101	105	3.605634	CACCACCACCATTAAGATCGAA	58.394	45.455	0.00	0.00	0.00	3.71
102	106	3.623060	CACCACCACCATTAAGATCGAAG	59.377	47.826	0.00	0.00	0.00	3.79
141	147	4.619227	AACAGTGGACCGGTGCCG	62.619	66.667	24.47	14.26	39.44	5.69
262	268	4.074259	CAGTTGTCATGACTGGGAAATCA	58.926	43.478	25.55	0.00	40.58	2.57
271	277	1.339824	ACTGGGAAATCAGAGCAGCAG	60.340	52.381	0.00	0.00	38.11	4.24
354	362	7.995289	TGTGATTCATTAAACAAACAGTGACT	58.005	30.769	0.00	0.00	0.00	3.41
372	380	3.818773	TGACTTCCCTTTCATTTTCGACC	59.181	43.478	0.00	0.00	0.00	4.79
476	484	1.822371	GGTGGGCAATTTGTTATCCGT	59.178	47.619	0.00	0.00	0.00	4.69
501	509	2.154963	TCGTTTTCGCTTTGACGATCTG	59.845	45.455	0.00	0.00	42.54	2.90
507	515	1.471501	CGCTTTGACGATCTGGATCCA	60.472	52.381	15.27	15.27	34.40	3.41
517	525	3.313526	CGATCTGGATCCATTGTTTGTCC	59.686	47.826	16.63	0.00	34.40	4.02
519	527	4.387026	TCTGGATCCATTGTTTGTCCTT	57.613	40.909	16.63	0.00	0.00	3.36
520	528	4.335416	TCTGGATCCATTGTTTGTCCTTC	58.665	43.478	16.63	0.00	0.00	3.46
564	581	4.067896	GAGGAAACTGTCAATCAAGCTCA	58.932	43.478	0.00	0.00	44.43	4.26
565	582	4.660168	AGGAAACTGTCAATCAAGCTCAT	58.340	39.130	0.00	0.00	41.13	2.90
602	623	1.615392	AGTTGTTGGCTGAAGCATTCC	59.385	47.619	4.43	0.00	46.93	3.01
609	630	1.203287	GGCTGAAGCATTCCAACCTTC	59.797	52.381	4.43	0.00	46.93	3.46
610	631	1.888512	GCTGAAGCATTCCAACCTTCA	59.111	47.619	0.00	0.00	46.93	3.02
616	637	2.629617	AGCATTCCAACCTTCAGTTTGG	59.370	45.455	0.00	0.00	36.18	3.28
622	643	2.093235	CCAACCTTCAGTTTGGCCAAAA	60.093	45.455	31.92	14.82	36.18	2.44
650	671	1.877637	TCACCAACCACGAATGACAG	58.122	50.000	0.00	0.00	0.00	3.51
727	749	7.576750	TGCTCATCTACTTAACAACTTAACG	57.423	36.000	0.00	0.00	0.00	3.18
729	751	7.327761	TGCTCATCTACTTAACAACTTAACGAC	59.672	37.037	0.00	0.00	0.00	4.34
736	758	6.712549	ACTTAACAACTTAACGACTGAAAGC	58.287	36.000	0.00	0.00	37.60	3.51
738	760	3.192466	ACAACTTAACGACTGAAAGCGT	58.808	40.909	0.00	0.00	45.69	5.07
876	910	3.748645	AGAGAGACCAGAGGAAAGCTA	57.251	47.619	0.00	0.00	0.00	3.32
881	915	5.555966	AGAGACCAGAGGAAAGCTAAAAAG	58.444	41.667	0.00	0.00	0.00	2.27
904	945	7.962964	AGATTTCAAGTTGAGAATGTCGTTA	57.037	32.000	5.56	0.00	0.00	3.18
908	949	4.326278	TCAAGTTGAGAATGTCGTTATCGC	59.674	41.667	0.08	0.00	36.96	4.58
915	956	6.327154	TGAGAATGTCGTTATCGCTCTTTAA	58.673	36.000	0.00	0.00	36.96	1.52
921	962	8.867112	ATGTCGTTATCGCTCTTTAAGATTTA	57.133	30.769	0.00	0.00	36.96	1.40
922	963	8.336498	TGTCGTTATCGCTCTTTAAGATTTAG	57.664	34.615	0.00	0.00	36.96	1.85
936	979	9.109393	CTTTAAGATTTAGGGATCGACATTCAA	57.891	33.333	0.00	0.00	0.00	2.69
956	1003	5.690865	TCAACAAGTCAAAACTGGGAGTAT	58.309	37.500	0.00	0.00	35.36	2.12
960	1007	4.974645	AGTCAAAACTGGGAGTATGACA	57.025	40.909	17.80	0.00	42.67	3.58
962	1009	5.063880	AGTCAAAACTGGGAGTATGACAAC	58.936	41.667	17.80	1.29	42.67	3.32
968	1015	3.254060	CTGGGAGTATGACAACGTGAAG	58.746	50.000	0.00	0.00	0.00	3.02
989	1039	2.808315	CTCGGACGATGGTCAGGG	59.192	66.667	10.22	1.52	45.28	4.45
991	1050	1.076265	TCGGACGATGGTCAGGGAT	60.076	57.895	10.22	0.00	45.28	3.85
994	1053	0.390860	GGACGATGGTCAGGGATCAG	59.609	60.000	10.22	0.00	45.28	2.90
995	1054	0.390860	GACGATGGTCAGGGATCAGG	59.609	60.000	2.59	0.00	42.91	3.86
996	1055	1.070445	CGATGGTCAGGGATCAGGC	59.930	63.158	0.00	0.00	0.00	4.85
997	1056	1.070445	GATGGTCAGGGATCAGGCG	59.930	63.158	0.00	0.00	0.00	5.52
1013	1075	2.107141	CGGGATGGCGAGGAGAAC	59.893	66.667	0.00	0.00	0.00	3.01
1023	1085	1.376037	GAGGAGAACGGCCAAGGTG	60.376	63.158	2.24	0.00	0.00	4.00
1153	1218	4.056125	CGGTCCTGACGCTGCTGA	62.056	66.667	0.00	0.00	0.00	4.26
1170	1235	1.451028	GATCCTGCTCCACTGCACC	60.451	63.158	0.00	0.00	38.12	5.01
1564	1632	4.988716	ACCACGGCTCCCTCGACA	62.989	66.667	0.00	0.00	0.00	4.35
1578	1646	0.324738	TCGACAGCTGGATCTTCCCT	60.325	55.000	19.93	0.00	35.03	4.20
1579	1647	0.539051	CGACAGCTGGATCTTCCCTT	59.461	55.000	19.93	0.00	35.03	3.95
2373	2459	1.215673	TCAGGGAGATAGCGTTCCTCT	59.784	52.381	0.00	0.00	33.85	3.69
2387	2473	0.247460	TCCTCTTCATGCACAGTCGG	59.753	55.000	0.00	0.00	0.00	4.79
2399	2485	2.418197	GCACAGTCGGGTCAGCTATTAA	60.418	50.000	0.00	0.00	0.00	1.40
2454	2540	4.114997	CGCGCCGCAAAATTCCCT	62.115	61.111	10.75	0.00	0.00	4.20
2531	2619	1.299926	GGCATACGTAGTCCAGCGG	60.300	63.158	0.08	0.00	43.93	5.52
2996	3134	0.037139	CACGGTGGTTCGGTTATGGA	60.037	55.000	0.00	0.00	0.00	3.41
3000	3138	1.137479	GGTGGTTCGGTTATGGATCGA	59.863	52.381	0.00	0.00	0.00	3.59
3195	3333	4.101448	AATGCCGCCGGAGAGCTT	62.101	61.111	7.68	3.24	0.00	3.74
3233	3371	2.965716	AAGGTGACAGCCGCTTTGCT	62.966	55.000	0.00	0.00	44.00	3.91
3349	3487	2.548875	GAATTGTGCAAGTGTTTGGCA	58.451	42.857	0.00	0.00	34.79	4.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.327032	GCTGCAGAAATAAAGTTAGTTCCAAAG	59.673	37.037	20.43	4.75	38.20	2.77
1	2	7.014230	AGCTGCAGAAATAAAGTTAGTTCCAAA	59.986	33.333	20.43	0.00	38.20	3.28
2	3	6.490040	AGCTGCAGAAATAAAGTTAGTTCCAA	59.510	34.615	20.43	0.00	38.20	3.53
3	4	6.003950	AGCTGCAGAAATAAAGTTAGTTCCA	58.996	36.000	20.43	0.72	38.20	3.53
4	5	6.502136	AGCTGCAGAAATAAAGTTAGTTCC	57.498	37.500	20.43	0.00	38.20	3.62
5	6	7.584987	TCAAGCTGCAGAAATAAAGTTAGTTC	58.415	34.615	20.43	3.63	37.84	3.01
6	7	7.308830	CCTCAAGCTGCAGAAATAAAGTTAGTT	60.309	37.037	20.43	0.00	0.00	2.24
7	8	6.150140	CCTCAAGCTGCAGAAATAAAGTTAGT	59.850	38.462	20.43	0.00	0.00	2.24
8	9	6.150140	ACCTCAAGCTGCAGAAATAAAGTTAG	59.850	38.462	20.43	0.00	0.00	2.34
9	10	6.003950	ACCTCAAGCTGCAGAAATAAAGTTA	58.996	36.000	20.43	0.00	0.00	2.24
21	22	1.354031	TCCCAATAACCTCAAGCTGCA	59.646	47.619	1.02	0.00	0.00	4.41
70	74	1.369692	GTGGTGGTGGTCATCGTCA	59.630	57.895	0.00	0.00	0.00	4.35
76	80	2.058705	TCTTAATGGTGGTGGTGGTCA	58.941	47.619	0.00	0.00	0.00	4.02
101	105	2.836636	TCAGTAGACATGCCCTCTCT	57.163	50.000	0.00	0.00	0.00	3.10
102	106	2.961741	TCATCAGTAGACATGCCCTCTC	59.038	50.000	0.00	0.00	0.00	3.20
141	147	7.823149	AAGCATCTCAGCAACAAAAATAATC	57.177	32.000	0.00	0.00	36.85	1.75
262	268	4.737476	AGGGCCCTCTGCTGCTCT	62.737	66.667	22.28	0.00	40.92	4.09
271	277	0.919710	ACTATGTTTCCAGGGCCCTC	59.080	55.000	25.77	11.55	0.00	4.30
308	314	0.730265	TATTCGTGTGCGGCAATTCC	59.270	50.000	3.23	0.00	38.89	3.01
354	362	2.156098	CGGGTCGAAAATGAAAGGGAA	58.844	47.619	0.00	0.00	0.00	3.97
372	380	4.752101	CCTTATTGACTAGATGAAAGGCGG	59.248	45.833	0.00	0.00	0.00	6.13
476	484	1.658931	CGTCAAAGCGAAAACGATGCA	60.659	47.619	0.00	0.00	37.31	3.96
501	509	4.335416	TCAGAAGGACAAACAATGGATCC	58.665	43.478	4.20	4.20	0.00	3.36
507	515	4.641396	TCGTCATCAGAAGGACAAACAAT	58.359	39.130	6.45	0.00	35.96	2.71
517	525	5.347342	AGCTCTGTTTATCGTCATCAGAAG	58.653	41.667	0.00	0.00	35.26	2.85
519	527	4.991153	AGCTCTGTTTATCGTCATCAGA	57.009	40.909	0.00	0.00	34.62	3.27
520	528	5.105063	TCAAGCTCTGTTTATCGTCATCAG	58.895	41.667	0.00	0.00	0.00	2.90
596	617	2.867647	GCCAAACTGAAGGTTGGAATGC	60.868	50.000	27.59	10.64	38.29	3.56
602	623	2.977772	TTTGGCCAAACTGAAGGTTG	57.022	45.000	27.13	0.88	38.29	3.77
609	630	1.515081	CCTGCATTTTGGCCAAACTG	58.485	50.000	33.15	33.15	35.07	3.16
610	631	0.250424	GCCTGCATTTTGGCCAAACT	60.250	50.000	30.43	22.51	43.11	2.66
611	632	2.246841	GCCTGCATTTTGGCCAAAC	58.753	52.632	30.43	19.18	43.11	2.93
622	643	1.153524	TGGTTGGTGAAGCCTGCAT	59.846	52.632	0.00	0.00	38.35	3.96
650	671	0.739813	GGATAGTGCGGTGTCACCAC	60.740	60.000	21.91	12.94	38.47	4.16
661	682	3.118992	TCAGTGACATCAGTGGATAGTGC	60.119	47.826	15.12	0.00	45.06	4.40
727	749	4.154918	AGAATTCCATTCACGCTTTCAGTC	59.845	41.667	0.65	0.00	41.71	3.51
729	751	4.656041	GAGAATTCCATTCACGCTTTCAG	58.344	43.478	0.65	0.00	41.71	3.02
738	760	5.064707	GGAATTTCGTCGAGAATTCCATTCA	59.935	40.000	31.12	4.59	41.23	2.57
876	910	8.190784	ACGACATTCTCAACTTGAAATCTTTTT	58.809	29.630	0.00	0.00	0.00	1.94
881	915	7.632515	CGATAACGACATTCTCAACTTGAAATC	59.367	37.037	0.00	0.00	42.66	2.17
904	945	6.015350	TCGATCCCTAAATCTTAAAGAGCGAT	60.015	38.462	0.00	0.00	35.99	4.58
908	949	8.894768	AATGTCGATCCCTAAATCTTAAAGAG	57.105	34.615	0.00	0.00	0.00	2.85
915	956	5.989477	TGTTGAATGTCGATCCCTAAATCT	58.011	37.500	0.00	0.00	0.00	2.40
921	962	3.007940	TGACTTGTTGAATGTCGATCCCT	59.992	43.478	0.00	0.00	33.81	4.20
922	963	3.334691	TGACTTGTTGAATGTCGATCCC	58.665	45.455	0.00	0.00	33.81	3.85
936	979	5.063880	GTCATACTCCCAGTTTTGACTTGT	58.936	41.667	10.15	0.00	37.27	3.16
956	1003	0.318699	CGAGCTCCTTCACGTTGTCA	60.319	55.000	8.47	0.00	0.00	3.58
960	1007	1.289380	GTCCGAGCTCCTTCACGTT	59.711	57.895	8.47	0.00	0.00	3.99
962	1009	1.994507	ATCGTCCGAGCTCCTTCACG	61.995	60.000	8.47	11.14	0.00	4.35
968	1015	2.343163	CTGACCATCGTCCGAGCTCC	62.343	65.000	8.47	0.00	38.32	4.70
989	1039	3.873026	CTCGCCATCCCGCCTGATC	62.873	68.421	0.00	0.00	0.00	2.92
995	1054	3.849951	TTCTCCTCGCCATCCCGC	61.850	66.667	0.00	0.00	0.00	6.13
996	1055	2.107141	GTTCTCCTCGCCATCCCG	59.893	66.667	0.00	0.00	0.00	5.14
997	1056	2.107141	CGTTCTCCTCGCCATCCC	59.893	66.667	0.00	0.00	0.00	3.85
1008	1067	2.032681	AGCACCTTGGCCGTTCTC	59.967	61.111	0.00	0.00	0.00	2.87
1101	1166	1.516423	GGCCGTGGAGAGGTAGAAC	59.484	63.158	0.00	0.00	0.00	3.01
1153	1218	2.673523	GGTGCAGTGGAGCAGGAT	59.326	61.111	9.14	0.00	46.69	3.24
1232	1297	0.731417	GCGGAAGTAGCTGTACTCGA	59.269	55.000	0.00	0.00	38.66	4.04
1564	1632	0.990818	GGGGAAGGGAAGATCCAGCT	60.991	60.000	0.00	0.00	38.64	4.24
1839	1925	4.814294	CACTCGGGCGCCAGGTAC	62.814	72.222	30.85	9.46	0.00	3.34
2373	2459	0.320683	CTGACCCGACTGTGCATGAA	60.321	55.000	0.00	0.00	0.00	2.57
2387	2473	5.277857	TGCTCTAAGGTTAATAGCTGACC	57.722	43.478	0.00	0.00	34.28	4.02
2399	2485	3.683847	GCATGTTGGAGATGCTCTAAGGT	60.684	47.826	3.13	0.00	42.52	3.50
2551	2639	2.484662	CAGCAAATAAGCGGCGCA	59.515	55.556	35.02	15.48	40.15	6.09
2769	2907	1.862827	GCGTTTTGTCGAACACCTAGT	59.137	47.619	0.00	0.00	0.00	2.57
2869	3007	7.486802	TCATACGACGAACTCATCTACAATA	57.513	36.000	0.00	0.00	0.00	1.90
3008	3146	2.503356	GCATCGATCCTATCCCTCCAAT	59.497	50.000	0.00	0.00	0.00	3.16
3195	3333	0.991146	TCTGAAAGGTGCTATGCCCA	59.009	50.000	0.00	0.00	0.00	5.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.