AutoCloner

Multiple sequence alignment - TraesCS1B01G260700

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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	TraesCS1B01G260700	chr1B	100.000	3014	0	0	1	3014	458262012	458265025	0.000000e+00	5566.0
1	TraesCS1B01G260700	chr1B	92.899	2718	137	21	343	3014	458128971	458131678	0.000000e+00	3899.0
2	TraesCS1B01G260700	chr1B	93.882	2419	93	23	367	2740	458080818	458083226	0.000000e+00	3596.0
3	TraesCS1B01G260700	chr1B	92.571	1225	68	6	853	2076	458172230	458173432	0.000000e+00	1736.0
4	TraesCS1B01G260700	chr1B	94.151	701	32	5	1	693	458127392	458128091	0.000000e+00	1059.0
5	TraesCS1B01G260700	chr1D	91.046	1854	95	27	367	2183	342169599	342171418	0.000000e+00	2438.0
6	TraesCS1B01G260700	chr1A	93.217	1607	79	14	598	2183	441841567	441843164	0.000000e+00	2337.0
7	TraesCS1B01G260700	chr5B	85.285	999	120	14	998	1984	585495922	585494939	0.000000e+00	1005.0
8	TraesCS1B01G260700	chr5D	84.870	998	126	12	998	1984	478001037	478000054	0.000000e+00	983.0
9	TraesCS1B01G260700	chr5D	83.525	261	37	4	3	261	57175640	57175384	3.880000e-59	239.0
10	TraesCS1B01G260700	chr5D	78.988	257	37	11	457	696	33047244	33047500	3.110000e-35	159.0
11	TraesCS1B01G260700	chr5D	78.409	264	38	13	457	701	37048573	37048310	1.450000e-33	154.0
12	TraesCS1B01G260700	chr5A	84.839	996	130	10	998	1984	597280073	597279090	0.000000e+00	983.0
13	TraesCS1B01G260700	chr5A	84.835	877	108	11	998	1863	597265620	597264758	0.000000e+00	859.0
14	TraesCS1B01G260700	chr5A	82.375	261	40	6	3	261	488304687	488304431	3.910000e-54	222.0
15	TraesCS1B01G260700	chr2D	82.460	935	127	21	1064	1978	637802161	637803078	0.000000e+00	784.0
16	TraesCS1B01G260700	chr2A	83.705	718	97	13	1265	1978	761541977	761541276	0.000000e+00	660.0
17	TraesCS1B01G260700	chr2A	83.938	579	68	17	1041	1609	14997665	14998228	5.720000e-147	531.0
18	TraesCS1B01G260700	chr2A	83.077	260	37	4	3	261	49810267	49810520	2.340000e-56	230.0
19	TraesCS1B01G260700	chr2A	78.161	261	47	7	3	261	488018400	488018652	1.120000e-34	158.0
20	TraesCS1B01G260700	chr7D	82.443	262	39	5	3	261	59942257	59942514	3.910000e-54	222.0
21	TraesCS1B01G260700	chr3A	79.365	315	52	7	9	314	743856979	743856669	3.040000e-50	209.0
22	TraesCS1B01G260700	chr3A	79.615	260	48	5	3	261	73931851	73931596	6.640000e-42	182.0
23	TraesCS1B01G260700	chr4D	83.568	213	31	2	9	220	93351034	93350825	2.370000e-46	196.0
24	TraesCS1B01G260700	chr3D	75.117	213	37	14	457	662	604603797	604603594	5.350000e-13	86.1

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	TraesCS1B01G260700	chr1B	458262012	458265025	3013	False	5566	5566	100.000	1	3014	1	chr1B.!!$F3	3013
1	TraesCS1B01G260700	chr1B	458080818	458083226	2408	False	3596	3596	93.882	367	2740	1	chr1B.!!$F1	2373
2	TraesCS1B01G260700	chr1B	458127392	458131678	4286	False	2479	3899	93.525	1	3014	2	chr1B.!!$F4	3013
3	TraesCS1B01G260700	chr1B	458172230	458173432	1202	False	1736	1736	92.571	853	2076	1	chr1B.!!$F2	1223
4	TraesCS1B01G260700	chr1D	342169599	342171418	1819	False	2438	2438	91.046	367	2183	1	chr1D.!!$F1	1816
5	TraesCS1B01G260700	chr1A	441841567	441843164	1597	False	2337	2337	93.217	598	2183	1	chr1A.!!$F1	1585
6	TraesCS1B01G260700	chr5B	585494939	585495922	983	True	1005	1005	85.285	998	1984	1	chr5B.!!$R1	986
7	TraesCS1B01G260700	chr5D	478000054	478001037	983	True	983	983	84.870	998	1984	1	chr5D.!!$R3	986
8	TraesCS1B01G260700	chr5A	597279090	597280073	983	True	983	983	84.839	998	1984	1	chr5A.!!$R3	986
9	TraesCS1B01G260700	chr5A	597264758	597265620	862	True	859	859	84.835	998	1863	1	chr5A.!!$R2	865
10	TraesCS1B01G260700	chr2D	637802161	637803078	917	False	784	784	82.460	1064	1978	1	chr2D.!!$F1	914
11	TraesCS1B01G260700	chr2A	761541276	761541977	701	True	660	660	83.705	1265	1978	1	chr2A.!!$R1	713
12	TraesCS1B01G260700	chr2A	14997665	14998228	563	False	531	531	83.938	1041	1609	1	chr2A.!!$F1	568

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
793	2075	0.244994	ATATCAGGCTGCGGATCGAC	59.755	55.0	10.34	0.0	0.0	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2394	3737	1.61785	CAGAGTCCAGAGAGCAACTGT	59.382	52.381	0.0	0.0	34.04	3.55	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
51	52	1.444383	GCGACGACACATGAGAGCA	60.444	57.895	0.00	0.00	0.00	4.26
54	55	1.678269	GACGACACATGAGAGCACGC	61.678	60.000	0.00	0.00	0.00	5.34
56	57	2.433145	ACACATGAGAGCACGCCG	60.433	61.111	0.00	0.00	0.00	6.46
72	73	1.087771	GCCGGATCAGTTTGTACCCG	61.088	60.000	5.05	0.00	36.98	5.28
93	94	5.395324	CCCGAAACCTAGTATGTGACTTGAT	60.395	44.000	0.00	0.00	39.81	2.57
136	137	5.523552	CGATGTTAGGCTTTGATGTGATGTA	59.476	40.000	0.00	0.00	0.00	2.29
181	182	2.009774	CGGCACTCCTTTATCAAGTGG	58.990	52.381	4.14	0.00	40.57	4.00
193	194	3.241530	AAGTGGCCAGGAGTCGCA	61.242	61.111	5.11	0.00	0.00	5.10
194	195	2.818169	AAGTGGCCAGGAGTCGCAA	61.818	57.895	5.11	0.00	0.00	4.85
235	236	4.317488	TGACTTCCAATTACCCGTTGTAC	58.683	43.478	0.00	0.00	0.00	2.90
251	252	6.594159	CCCGTTGTACTATTTTCTGATGTCTT	59.406	38.462	0.00	0.00	0.00	3.01
277	286	5.660460	TGAATAAGTGACTGTATGCATCGT	58.340	37.500	0.19	0.00	0.00	3.73
292	301	2.866762	GCATCGTCCAAATGTAGAGACC	59.133	50.000	0.00	0.00	0.00	3.85
296	305	1.829222	GTCCAAATGTAGAGACCGGGA	59.171	52.381	6.32	0.00	0.00	5.14
301	310	6.014840	GTCCAAATGTAGAGACCGGGATAATA	60.015	42.308	6.32	0.00	0.00	0.98
314	323	5.472820	ACCGGGATAATACTCGTTCTCTAAG	59.527	44.000	6.32	0.00	31.23	2.18
347	356	4.162096	TGAGCTCTTTACTCACGAGAAC	57.838	45.455	16.19	0.00	39.21	3.01
356	365	2.438411	ACTCACGAGAACCACCTCTAG	58.562	52.381	0.00	0.00	0.00	2.43
502	519	7.282224	AGCCTGCATATAAATTTTGTTCGAGTA	59.718	33.333	0.00	0.00	0.00	2.59
711	1972	4.548991	CGGAGGATACACAGTACACTAC	57.451	50.000	0.00	0.00	41.41	2.73
723	1990	6.127703	ACACAGTACACTACATAGATCACCAC	60.128	42.308	0.00	0.00	0.00	4.16
732	1999	3.386078	ACATAGATCACCACTTCGCTCAT	59.614	43.478	0.00	0.00	0.00	2.90
776	2058	9.778741	CTTTTGTCCTGCCATTATACTAAGATA	57.221	33.333	0.00	0.00	0.00	1.98
787	2069	4.727507	ATACTAAGATATCAGGCTGCGG	57.272	45.455	10.34	0.00	0.00	5.69
793	2075	0.244994	ATATCAGGCTGCGGATCGAC	59.755	55.000	10.34	0.00	0.00	4.20
822	2104	6.037098	AGTCATCTAATCGAAGTAAGCACAC	58.963	40.000	0.00	0.00	0.00	3.82
825	2107	5.244785	TCTAATCGAAGTAAGCACACGAT	57.755	39.130	0.00	0.00	43.17	3.73
826	2108	6.367686	TCTAATCGAAGTAAGCACACGATA	57.632	37.500	0.00	0.00	41.75	2.92
896	2179	5.965922	AGCTCACATGCCCTAAATAAAAAC	58.034	37.500	0.00	0.00	0.00	2.43
897	2180	5.716703	AGCTCACATGCCCTAAATAAAAACT	59.283	36.000	0.00	0.00	0.00	2.66
2085	3406	3.611970	TCCAGGAGTTCTCTTCTCTACG	58.388	50.000	0.00	0.00	33.06	3.51
2394	3737	3.800531	GGAAATCTTCCGAACCCGATTA	58.199	45.455	0.00	0.00	40.59	1.75
2727	4073	8.055279	ACACATGAAAAATGAGATAAACGGAT	57.945	30.769	0.00	0.00	0.00	4.18
2826	4172	7.831691	TGAACAAAATAATCTGACAAAGGGA	57.168	32.000	0.00	0.00	0.00	4.20
2910	4256	3.548668	CACGTAACAAGACTGAACGTCAA	59.451	43.478	0.00	0.00	45.32	3.18
2950	4297	3.044235	AGCTCATGTTCGTTCATGTCA	57.956	42.857	16.93	4.25	43.70	3.58
2974	4321	2.329379	GACTTAGTGAACACGGCAGAG	58.671	52.381	0.00	0.00	36.20	3.35
3005	4352	2.594303	CAACCTCGCTGGCACCAA	60.594	61.111	0.00	0.00	40.22	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	2.939103	CGTCTTCCACCAATCCATCTTC	59.061	50.000	0.00	0.00	0.00	2.87
51	52	0.390735	GGTACAAACTGATCCGGCGT	60.391	55.000	6.01	0.00	0.00	5.68
54	55	0.533491	TCGGGTACAAACTGATCCGG	59.467	55.000	0.00	0.00	38.21	5.14
56	57	2.745821	GGTTTCGGGTACAAACTGATCC	59.254	50.000	7.10	0.00	34.66	3.36
72	73	5.817816	CCCATCAAGTCACATACTAGGTTTC	59.182	44.000	0.00	0.00	37.50	2.78
93	94	1.079621	TCTAAAGTCGGAGGCCCCA	59.920	57.895	0.00	0.00	34.14	4.96
136	137	5.934402	AGTCCGAGTCTAATACCAAACAT	57.066	39.130	0.00	0.00	0.00	2.71
181	182	0.109597	CAATTGTTGCGACTCCTGGC	60.110	55.000	5.50	0.00	0.00	4.85
182	183	1.238439	ACAATTGTTGCGACTCCTGG	58.762	50.000	4.92	0.00	0.00	4.45
193	194	7.458409	AGTCATCATCTTAGCAACAATTGTT	57.542	32.000	18.13	18.13	39.12	2.83
194	195	7.362401	GGAAGTCATCATCTTAGCAACAATTGT	60.362	37.037	4.92	4.92	0.00	2.71
251	252	7.926018	ACGATGCATACAGTCACTTATTCATAA	59.074	33.333	0.00	0.00	0.00	1.90
277	286	2.241281	TCCCGGTCTCTACATTTGGA	57.759	50.000	0.00	0.00	0.00	3.53
292	301	6.798315	TCTTAGAGAACGAGTATTATCCCG	57.202	41.667	0.00	0.00	0.00	5.14
296	305	7.167801	GCGCTTTTCTTAGAGAACGAGTATTAT	59.832	37.037	0.00	0.00	33.26	1.28
301	310	2.987821	GCGCTTTTCTTAGAGAACGAGT	59.012	45.455	0.00	0.00	33.26	4.18
347	356	2.558795	CCGATGTACCATCTAGAGGTGG	59.441	54.545	18.68	15.02	40.26	4.61
356	365	8.718734	GGATTTTTATAGAACCGATGTACCATC	58.281	37.037	0.00	0.00	0.00	3.51
502	519	7.707104	AGTTTGATCAAAGTCGAGACATTTTT	58.293	30.769	21.05	0.00	28.36	1.94
685	707	0.040646	ACTGTGTATCCTCCGGTCCA	59.959	55.000	0.00	0.00	0.00	4.02
711	1972	3.443099	TGAGCGAAGTGGTGATCTATG	57.557	47.619	0.00	0.00	0.00	2.23
723	1990	3.197790	CCGGCCACATGAGCGAAG	61.198	66.667	2.24	0.00	0.00	3.79
732	1999	3.947459	TGTTAGCAGCCGGCCACA	61.947	61.111	26.15	15.57	46.50	4.17
776	2058	2.419198	GTCGATCCGCAGCCTGAT	59.581	61.111	0.00	0.00	0.00	2.90
787	2069	5.907945	TCGATTAGATGACTTTTCGTCGATC	59.092	40.000	0.00	0.00	45.87	3.69
793	2075	7.009265	TGCTTACTTCGATTAGATGACTTTTCG	59.991	37.037	0.00	0.00	33.63	3.46
802	2084	5.244785	TCGTGTGCTTACTTCGATTAGAT	57.755	39.130	0.00	0.00	0.00	1.98
804	2086	6.856426	TCATATCGTGTGCTTACTTCGATTAG	59.144	38.462	12.79	0.00	40.72	1.73
805	2087	6.731164	TCATATCGTGTGCTTACTTCGATTA	58.269	36.000	12.79	0.00	40.72	1.75
810	2092	6.414079	CAACATCATATCGTGTGCTTACTTC	58.586	40.000	0.00	0.00	0.00	3.01
822	2104	4.713854	TCGAACATGCAACATCATATCG	57.286	40.909	0.00	0.00	36.83	2.92
825	2107	5.502220	CGTTCATCGAACATGCAACATCATA	60.502	40.000	7.56	0.00	42.05	2.15
826	2108	4.665212	GTTCATCGAACATGCAACATCAT	58.335	39.130	0.00	0.00	41.62	2.45
868	2150	0.390492	TAGGGCATGTGAGCTCGATG	59.610	55.000	17.35	17.35	40.85	3.84
896	2179	3.368236	GTCGGCTGCTAGAGTTTTTACAG	59.632	47.826	0.00	0.00	0.00	2.74
897	2180	3.323243	GTCGGCTGCTAGAGTTTTTACA	58.677	45.455	0.00	0.00	0.00	2.41
1662	2979	1.756024	CACCAGGTCCGGGTTGTTA	59.244	57.895	11.53	0.00	36.19	2.41
2059	3377	4.711355	AGAGAAGAGAACTCCTGGAATCAG	59.289	45.833	10.70	0.00	40.59	2.90
2085	3406	2.346803	ACACGCTCATCACATTACACC	58.653	47.619	0.00	0.00	0.00	4.16
2394	3737	1.617850	CAGAGTCCAGAGAGCAACTGT	59.382	52.381	0.00	0.00	34.04	3.55
2826	4172	7.145932	TCGATCAATAGACGATGTACATCAT	57.854	36.000	30.15	19.63	37.69	2.45
2950	4297	2.224426	TGCCGTGTTCACTAAGTCCATT	60.224	45.455	1.53	0.00	0.00	3.16
2974	4321	0.321653	AGGTTGACGAAGCCATGGAC	60.322	55.000	18.40	7.03	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.