AutoCloner

Multiple sequence alignment - TraesCS6D01G135300

Loading Multiple Alignment...

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	TraesCS6D01G135300	chr6D	100.000	3126	0	0	1	3126	103034277	103037402	0.000000e+00	5773
1	TraesCS6D01G135300	chr6A	92.874	2175	98	21	39	2194	124310551	124312687	0.000000e+00	3105
2	TraesCS6D01G135300	chr6A	82.945	1372	169	35	818	2182	1062162	1063475	0.000000e+00	1177
3	TraesCS6D01G135300	chr6A	88.912	974	59	13	2196	3126	124914607	124913640	0.000000e+00	1155
4	TraesCS6D01G135300	chr6A	91.761	704	42	6	2437	3126	124426347	124427048	0.000000e+00	965
5	TraesCS6D01G135300	chr6A	93.367	603	27	7	2532	3126	124313260	124313857	0.000000e+00	880
6	TraesCS6D01G135300	chr6A	93.878	245	8	2	2197	2440	124312811	124313049	2.290000e-96	363
7	TraesCS6D01G135300	chr6A	92.070	227	13	4	2196	2421	124426064	124426286	6.510000e-82	315
8	TraesCS6D01G135300	chr6A	100.000	40	0	0	1	40	124310485	124310524	1.200000e-09	75
9	TraesCS6D01G135300	chr6B	93.401	1091	45	12	274	1358	188695352	188696421	0.000000e+00	1591
10	TraesCS6D01G135300	chr6B	95.433	832	29	3	1358	2185	188696457	188697283	0.000000e+00	1317
11	TraesCS6D01G135300	chr6B	83.504	1370	167	29	818	2182	5101111	5102426	0.000000e+00	1223
12	TraesCS6D01G135300	chr6B	92.373	118	9	0	39	156	188695226	188695343	5.360000e-38	169
13	TraesCS6D01G135300	chr7D	90.819	708	42	6	2437	3126	169428195	169427493	0.000000e+00	926
14	TraesCS6D01G135300	chr7D	88.494	704	46	18	2437	3126	169539024	169538342	0.000000e+00	819
15	TraesCS6D01G135300	chr7D	92.070	227	13	4	2196	2421	169428478	169428256	6.510000e-82	315
16	TraesCS6D01G135300	chr7D	91.189	227	12	5	2196	2421	169418468	169418249	5.070000e-78	302
17	TraesCS6D01G135300	chr7D	86.404	228	15	11	2196	2421	169539297	169539084	5.210000e-58	235
18	TraesCS6D01G135300	chr7D	93.204	103	6	1	2320	2421	169481186	169481084	1.940000e-32	150
19	TraesCS6D01G135300	chrUn	88.920	713	45	13	2437	3126	82710840	82710139	0.000000e+00	848
20	TraesCS6D01G135300	chrUn	89.748	556	51	3	2438	2988	293554866	293555420	0.000000e+00	706
21	TraesCS6D01G135300	chrUn	89.748	556	51	3	2438	2988	314487628	314488182	0.000000e+00	706
22	TraesCS6D01G135300	chrUn	89.624	559	52	3	2438	2991	325382106	325381549	0.000000e+00	706
23	TraesCS6D01G135300	chr7A	89.624	559	52	3	2438	2991	171944454	171943897	0.000000e+00	706
24	TraesCS6D01G135300	chr7A	89.674	184	11	5	2243	2421	171436329	171436149	8.720000e-56	228
25	TraesCS6D01G135300	chr4B	78.092	671	123	16	1478	2127	6061083	6061750	1.350000e-108	403
26	TraesCS6D01G135300	chr7B	88.976	127	9	4	2196	2320	134632140	134632017	5.400000e-33	152

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	TraesCS6D01G135300	chr6D	103034277	103037402	3125	False	5773.000000	5773	100.000000	1	3126	1	chr6D.!!$F1	3125
1	TraesCS6D01G135300	chr6A	1062162	1063475	1313	False	1177.000000	1177	82.945000	818	2182	1	chr6A.!!$F1	1364
2	TraesCS6D01G135300	chr6A	124913640	124914607	967	True	1155.000000	1155	88.912000	2196	3126	1	chr6A.!!$R1	930
3	TraesCS6D01G135300	chr6A	124310485	124313857	3372	False	1105.750000	3105	95.029750	1	3126	4	chr6A.!!$F2	3125
4	TraesCS6D01G135300	chr6A	124426064	124427048	984	False	640.000000	965	91.915500	2196	3126	2	chr6A.!!$F3	930
5	TraesCS6D01G135300	chr6B	5101111	5102426	1315	False	1223.000000	1223	83.504000	818	2182	1	chr6B.!!$F1	1364
6	TraesCS6D01G135300	chr6B	188695226	188697283	2057	False	1025.666667	1591	93.735667	39	2185	3	chr6B.!!$F2	2146
7	TraesCS6D01G135300	chr7D	169427493	169428478	985	True	620.500000	926	91.444500	2196	3126	2	chr7D.!!$R3	930
8	TraesCS6D01G135300	chr7D	169538342	169539297	955	True	527.000000	819	87.449000	2196	3126	2	chr7D.!!$R4	930
9	TraesCS6D01G135300	chrUn	82710139	82710840	701	True	848.000000	848	88.920000	2437	3126	1	chrUn.!!$R1	689
10	TraesCS6D01G135300	chrUn	293554866	293555420	554	False	706.000000	706	89.748000	2438	2988	1	chrUn.!!$F1	550
11	TraesCS6D01G135300	chrUn	314487628	314488182	554	False	706.000000	706	89.748000	2438	2988	1	chrUn.!!$F2	550
12	TraesCS6D01G135300	chrUn	325381549	325382106	557	True	706.000000	706	89.624000	2438	2991	1	chrUn.!!$R2	553
13	TraesCS6D01G135300	chr7A	171943897	171944454	557	True	706.000000	706	89.624000	2438	2991	1	chr7A.!!$R2	553
14	TraesCS6D01G135300	chr4B	6061083	6061750	667	False	403.000000	403	78.092000	1478	2127	1	chr4B.!!$F1	649

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
209	244	0.518195	TGAACGCACATCAGCACATG	59.482	50.0	0.0	0.0	0.00	3.21	F
1041	1087	0.389948	AGACGATGAACAAGTCCGCC	60.390	55.0	0.0	0.0	35.65	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1399	1493	0.467804	TCACCACAAGCTAGCACACA	59.532	50.0	18.83	0.0	0.0	3.72	R
2376	2616	0.325933	TGGGATCAGAACTGCACCTG	59.674	55.0	0.00	0.0	0.0	4.00	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
79	108	2.125106	GGAGTGACCGGGACATGC	60.125	66.667	6.32	2.21	0.00	4.06
112	141	5.928264	ACACATAAAAAGCTCAAGCAATTCC	59.072	36.000	4.59	0.00	45.16	3.01
186	221	0.814010	GCCTATTCATTCACGGGCGT	60.814	55.000	0.00	0.00	0.00	5.68
201	236	2.476051	CGTGGCTGAACGCACATC	59.524	61.111	0.00	0.00	41.67	3.06
202	237	2.316867	CGTGGCTGAACGCACATCA	61.317	57.895	0.00	0.00	41.67	3.07
203	238	1.499056	GTGGCTGAACGCACATCAG	59.501	57.895	6.13	6.13	45.65	2.90
207	242	2.237416	CTGAACGCACATCAGCACA	58.763	52.632	0.00	0.00	38.03	4.57
208	243	0.800631	CTGAACGCACATCAGCACAT	59.199	50.000	0.00	0.00	38.03	3.21
209	244	0.518195	TGAACGCACATCAGCACATG	59.482	50.000	0.00	0.00	0.00	3.21
231	266	3.861840	CCTCGGTTGCTCTATTTTCAGA	58.138	45.455	0.00	0.00	0.00	3.27
232	267	4.253685	CCTCGGTTGCTCTATTTTCAGAA	58.746	43.478	0.00	0.00	0.00	3.02
261	296	6.204075	TGTCAAAAACAAAACAACGAACAG	57.796	33.333	0.00	0.00	34.03	3.16
268	303	3.119280	ACAAAACAACGAACAGAAAGGGG	60.119	43.478	0.00	0.00	0.00	4.79
271	306	2.572290	ACAACGAACAGAAAGGGGAAG	58.428	47.619	0.00	0.00	0.00	3.46
275	310	1.282157	CGAACAGAAAGGGGAAGGGAT	59.718	52.381	0.00	0.00	0.00	3.85
320	357	3.296854	TCCTATGTCCGTGATGCTAACT	58.703	45.455	0.00	0.00	0.00	2.24
340	377	3.126831	CTGGTTCGCTTATAGCCTTCTG	58.873	50.000	0.00	0.00	38.18	3.02
413	450	5.248087	CACTATGAAATTCTTGTACGCGTG	58.752	41.667	24.59	4.70	0.00	5.34
556	596	8.977505	GTACATACAAAATCTTGTTGCACAATT	58.022	29.630	0.00	0.00	43.45	2.32
655	698	8.638685	AATCATGCATACAGAAATTAACAAGC	57.361	30.769	0.00	0.00	0.00	4.01
711	754	5.485620	CCATGATCCCATCTATACTGTGTG	58.514	45.833	0.00	0.00	0.00	3.82
744	787	1.207488	TGGGATGGGGGACAGTTCAG	61.207	60.000	0.00	0.00	0.00	3.02
839	882	4.881850	ACATTTCTCCAACACGTTCTTCTT	59.118	37.500	0.00	0.00	0.00	2.52
878	924	4.082245	TGCTTTTAGACTAATGCCCAAAGC	60.082	41.667	15.51	15.51	43.16	3.51
900	946	1.134175	GCCACAATTAACATCCACCCG	59.866	52.381	0.00	0.00	0.00	5.28
901	947	1.748493	CCACAATTAACATCCACCCGG	59.252	52.381	0.00	0.00	0.00	5.73
902	948	1.134175	CACAATTAACATCCACCCGGC	59.866	52.381	0.00	0.00	0.00	6.13
903	949	0.744281	CAATTAACATCCACCCGGCC	59.256	55.000	0.00	0.00	0.00	6.13
938	984	2.101582	CCACCTTGGTCCTCTCTTATCG	59.898	54.545	0.00	0.00	31.35	2.92
945	991	2.226912	GGTCCTCTCTTATCGTCATCGG	59.773	54.545	0.00	0.00	37.69	4.18
1040	1086	0.992802	GAGACGATGAACAAGTCCGC	59.007	55.000	0.00	0.00	35.65	5.54
1041	1087	0.389948	AGACGATGAACAAGTCCGCC	60.390	55.000	0.00	0.00	35.65	6.13
1042	1088	1.683790	GACGATGAACAAGTCCGCCG	61.684	60.000	0.00	0.00	0.00	6.46
1043	1089	2.785258	GATGAACAAGTCCGCCGC	59.215	61.111	0.00	0.00	0.00	6.53
1044	1090	2.746277	ATGAACAAGTCCGCCGCC	60.746	61.111	0.00	0.00	0.00	6.13
1071	1117	2.029964	GTTCCCGAGGCGTTCACA	59.970	61.111	0.00	0.00	0.00	3.58
1191	1237	1.910580	ATGCAGGAACCTACCCCGTG	61.911	60.000	0.00	0.00	0.00	4.94
1346	1397	2.407090	CTCAACAATGACGCAGAGACA	58.593	47.619	0.00	0.00	0.00	3.41
1374	1464	5.221661	GGGTTTAACCTCAAGTCTCTCTCAA	60.222	44.000	14.27	0.00	38.64	3.02
1399	1493	9.950496	AAAAGATGATCTGTTGTAACTCTGTAT	57.050	29.630	0.00	0.00	0.00	2.29
1400	1494	8.939201	AAGATGATCTGTTGTAACTCTGTATG	57.061	34.615	0.00	0.00	0.00	2.39
1401	1495	8.072321	AGATGATCTGTTGTAACTCTGTATGT	57.928	34.615	0.00	0.00	0.00	2.29
1402	1496	7.978414	AGATGATCTGTTGTAACTCTGTATGTG	59.022	37.037	0.00	0.00	0.00	3.21
1439	1533	7.446931	TGGTGATCAACTAACTAATTCTGCAAA	59.553	33.333	12.94	0.00	0.00	3.68
2023	2139	2.292389	TGGGATCATGGTGGCATTTCTT	60.292	45.455	0.00	0.00	0.00	2.52
2049	2165	0.813821	GCCTTGGGTGAGAAAGATGC	59.186	55.000	0.00	0.00	0.00	3.91
2190	2306	7.827729	GGTTGGTCCACTAAATAAAGTACAGAT	59.172	37.037	0.00	0.00	35.97	2.90
2266	2503	2.154462	TGCTTTACTTCTTGCTCCTGC	58.846	47.619	0.00	0.00	40.20	4.85
2376	2616	1.541233	CCGTCTGATCCCAAGCATACC	60.541	57.143	0.00	0.00	0.00	2.73
2585	3005	3.069016	ACTCGAGTGATACACAACACCAA	59.931	43.478	19.30	0.00	36.74	3.67
2596	3016	3.317993	ACACAACACCAATTTCTGTAGCC	59.682	43.478	0.00	0.00	0.00	3.93
2955	3407	6.035005	GGCTGAAAAGAAAAACAAGAGTCAAC	59.965	38.462	0.00	0.00	0.00	3.18
2970	3422	0.389817	TCAACATTCTCGCCGTGGAG	60.390	55.000	0.00	0.00	35.32	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
79	108	9.132521	CTTGAGCTTTTTATGTGTTTGGAATAG	57.867	33.333	0.00	0.00	0.00	1.73
201	236	2.872557	CAACCGAGGCATGTGCTG	59.127	61.111	4.84	0.00	41.70	4.41
202	237	3.058160	GCAACCGAGGCATGTGCT	61.058	61.111	4.84	0.00	41.70	4.40
203	238	3.044059	GAGCAACCGAGGCATGTGC	62.044	63.158	0.00	0.00	41.14	4.57
204	239	0.108186	TAGAGCAACCGAGGCATGTG	60.108	55.000	0.00	0.00	0.00	3.21
205	240	0.833287	ATAGAGCAACCGAGGCATGT	59.167	50.000	0.00	0.00	0.00	3.21
206	241	1.959042	AATAGAGCAACCGAGGCATG	58.041	50.000	0.00	0.00	0.00	4.06
207	242	2.717639	AAATAGAGCAACCGAGGCAT	57.282	45.000	0.00	0.00	0.00	4.40
208	243	2.290008	TGAAAATAGAGCAACCGAGGCA	60.290	45.455	0.00	0.00	0.00	4.75
209	244	2.352960	CTGAAAATAGAGCAACCGAGGC	59.647	50.000	0.00	0.00	0.00	4.70
243	278	5.407084	CCCTTTCTGTTCGTTGTTTTGTTTT	59.593	36.000	0.00	0.00	0.00	2.43
258	293	1.918957	CTGATCCCTTCCCCTTTCTGT	59.081	52.381	0.00	0.00	0.00	3.41
261	296	2.780010	TCATCTGATCCCTTCCCCTTTC	59.220	50.000	0.00	0.00	0.00	2.62
268	303	4.754114	GTGCAGTAATCATCTGATCCCTTC	59.246	45.833	0.00	0.00	35.20	3.46
271	306	4.348863	AGTGCAGTAATCATCTGATCCC	57.651	45.455	0.00	0.00	35.20	3.85
275	310	4.952262	GCAAAGTGCAGTAATCATCTGA	57.048	40.909	0.00	0.00	44.26	3.27
320	357	2.741878	GCAGAAGGCTATAAGCGAACCA	60.742	50.000	0.00	0.00	43.62	3.67
340	377	5.682943	TGTTAACTCACAGTTACCATTGC	57.317	39.130	7.22	0.00	40.12	3.56
451	488	3.850752	TCCTCTCTGAAACAGGAGAAGT	58.149	45.455	14.18	0.00	33.66	3.01
556	596	4.475381	TCTGGGAGAGAGCTAAGAAGTAGA	59.525	45.833	0.00	0.00	30.50	2.59
655	698	2.268280	CTGGCCAGCTCACTCCAG	59.732	66.667	22.33	5.89	39.95	3.86
744	787	5.627499	TCCATCTAACTGCATTTGTTCAC	57.373	39.130	0.00	0.00	0.00	3.18
878	924	2.166254	GGGTGGATGTTAATTGTGGCTG	59.834	50.000	0.00	0.00	0.00	4.85
900	946	2.628178	GGTGGCAAATTTATAGGAGGCC	59.372	50.000	0.00	0.00	40.29	5.19
901	947	3.566351	AGGTGGCAAATTTATAGGAGGC	58.434	45.455	0.00	0.00	0.00	4.70
902	948	4.342092	CCAAGGTGGCAAATTTATAGGAGG	59.658	45.833	0.00	0.00	0.00	4.30
903	949	4.956075	ACCAAGGTGGCAAATTTATAGGAG	59.044	41.667	0.00	0.00	42.67	3.69
938	984	2.003301	GAGCTTTGAGGTTCCGATGAC	58.997	52.381	0.00	0.00	0.00	3.06
945	991	5.527582	TGTCTTAACAAGAGCTTTGAGGTTC	59.472	40.000	13.35	0.00	38.41	3.62
1058	1104	2.885644	CCGATGTGAACGCCTCGG	60.886	66.667	14.95	14.95	43.98	4.63
1066	1112	0.605319	GGCTGGAACACCGATGTGAA	60.605	55.000	0.00	0.00	45.76	3.18
1337	1388	2.737252	GTTAAACCCTCTTGTCTCTGCG	59.263	50.000	0.00	0.00	0.00	5.18
1374	1464	9.376075	CATACAGAGTTACAACAGATCATCTTT	57.624	33.333	0.00	0.00	0.00	2.52
1399	1493	0.467804	TCACCACAAGCTAGCACACA	59.532	50.000	18.83	0.00	0.00	3.72
1400	1494	1.734465	GATCACCACAAGCTAGCACAC	59.266	52.381	18.83	0.00	0.00	3.82
1401	1495	1.347378	TGATCACCACAAGCTAGCACA	59.653	47.619	18.83	0.00	0.00	4.57
1402	1496	2.099141	TGATCACCACAAGCTAGCAC	57.901	50.000	18.83	0.00	0.00	4.40
1439	1533	4.916983	TGCTGAACTGCACTACAAAATT	57.083	36.364	2.46	0.00	38.12	1.82
2023	2139	0.991146	TCTCACCCAAGGCAGCATTA	59.009	50.000	0.00	0.00	0.00	1.90
2049	2165	3.640498	TCTCAGTATGGCCTCAAGATCTG	59.360	47.826	3.32	3.51	36.16	2.90
2089	2205	1.671054	AACCGGATCAAGCGTGGTG	60.671	57.895	9.46	0.00	32.14	4.17
2117	2233	4.395583	GCTGCTGCTTCACGCCAC	62.396	66.667	8.53	0.00	38.05	5.01
2146	2262	0.958822	CCTGCGGCTGGTTAACTTTT	59.041	50.000	16.91	0.00	0.00	2.27
2190	2306	5.237815	CAAATTGCTCAGAGGTACAGTACA	58.762	41.667	12.89	0.00	0.00	2.90
2194	2310	3.754188	GCAAATTGCTCAGAGGTACAG	57.246	47.619	11.19	0.00	40.96	2.74
2266	2503	1.009829	GAAGTACCATTGCAGGCTCG	58.990	55.000	0.00	0.00	0.00	5.03
2376	2616	0.325933	TGGGATCAGAACTGCACCTG	59.674	55.000	0.00	0.00	0.00	4.00
2585	3005	2.301870	TGGAGAACACGGCTACAGAAAT	59.698	45.455	0.00	0.00	0.00	2.17
2955	3407	0.738975	TAGTCTCCACGGCGAGAATG	59.261	55.000	16.62	0.00	40.53	2.67
2970	3422	4.079844	ACCTTACTACAGGAGGGAGTAGTC	60.080	50.000	8.35	0.00	45.69	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.