AutoCloner

Multiple sequence alignment - TraesCS3B01G155200

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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	TraesCS3B01G155200	chr3B	100.000	2798	0	0	1	2798	147871338	147874135	0.000000e+00	5168
1	TraesCS3B01G155200	chr3B	92.412	738	55	1	1	738	808438465	808437729	0.000000e+00	1051
2	TraesCS3B01G155200	chr3B	92.647	680	50	0	1	680	808365836	808365157	0.000000e+00	979
3	TraesCS3B01G155200	chr3B	91.605	405	34	0	1	405	808402771	808402367	6.770000e-156	560
4	TraesCS3B01G155200	chr3D	91.753	2037	74	30	796	2796	96678186	96680164	0.000000e+00	2745
5	TraesCS3B01G155200	chr3A	88.302	2043	144	48	819	2796	114567054	114569066	0.000000e+00	2361
6	TraesCS3B01G155200	chr1B	93.726	797	49	1	1	797	612905451	612906246	0.000000e+00	1194
7	TraesCS3B01G155200	chr1B	92.732	798	55	1	1	798	413907317	413906523	0.000000e+00	1149
8	TraesCS3B01G155200	chr1B	92.160	625	47	2	1	625	4102671	4102049	0.000000e+00	881
9	TraesCS3B01G155200	chr1B	92.525	495	31	1	304	798	4101970	4101482	0.000000e+00	704
10	TraesCS3B01G155200	chr5B	92.365	799	60	1	1	798	166691219	166690421	0.000000e+00	1136
11	TraesCS3B01G155200	chr7B	92.394	802	49	3	1	802	713434148	713433359	0.000000e+00	1133
12	TraesCS3B01G155200	chr2B	91.615	799	53	5	1	798	368501357	368502142	0.000000e+00	1092
13	TraesCS3B01G155200	chr2D	91.364	799	49	8	1	798	623754968	623754189	0.000000e+00	1075
14	TraesCS3B01G155200	chr5A	87.109	799	61	13	1	795	590977227	590976467	0.000000e+00	867
15	TraesCS3B01G155200	chr5D	92.542	590	32	7	1	590	163815643	163816220	0.000000e+00	835
16	TraesCS3B01G155200	chrUn	83.436	163	19	3	1936	2098	381954327	381954173	8.080000e-31	145
17	TraesCS3B01G155200	chr6A	91.667	72	6	0	2027	2098	603490136	603490065	1.770000e-17	100

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	TraesCS3B01G155200	chr3B	147871338	147874135	2797	False	5168.0	5168	100.0000	1	2798	1	chr3B.!!$F1	2797
1	TraesCS3B01G155200	chr3B	808437729	808438465	736	True	1051.0	1051	92.4120	1	738	1	chr3B.!!$R3	737
2	TraesCS3B01G155200	chr3B	808365157	808365836	679	True	979.0	979	92.6470	1	680	1	chr3B.!!$R1	679
3	TraesCS3B01G155200	chr3D	96678186	96680164	1978	False	2745.0	2745	91.7530	796	2796	1	chr3D.!!$F1	2000
4	TraesCS3B01G155200	chr3A	114567054	114569066	2012	False	2361.0	2361	88.3020	819	2796	1	chr3A.!!$F1	1977
5	TraesCS3B01G155200	chr1B	612905451	612906246	795	False	1194.0	1194	93.7260	1	797	1	chr1B.!!$F1	796
6	TraesCS3B01G155200	chr1B	413906523	413907317	794	True	1149.0	1149	92.7320	1	798	1	chr1B.!!$R1	797
7	TraesCS3B01G155200	chr1B	4101482	4102671	1189	True	792.5	881	92.3425	1	798	2	chr1B.!!$R2	797
8	TraesCS3B01G155200	chr5B	166690421	166691219	798	True	1136.0	1136	92.3650	1	798	1	chr5B.!!$R1	797
9	TraesCS3B01G155200	chr7B	713433359	713434148	789	True	1133.0	1133	92.3940	1	802	1	chr7B.!!$R1	801
10	TraesCS3B01G155200	chr2B	368501357	368502142	785	False	1092.0	1092	91.6150	1	798	1	chr2B.!!$F1	797
11	TraesCS3B01G155200	chr2D	623754189	623754968	779	True	1075.0	1075	91.3640	1	798	1	chr2D.!!$R1	797
12	TraesCS3B01G155200	chr5A	590976467	590977227	760	True	867.0	867	87.1090	1	795	1	chr5A.!!$R1	794
13	TraesCS3B01G155200	chr5D	163815643	163816220	577	False	835.0	835	92.5420	1	590	1	chr5D.!!$F1	589

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
388	398	1.214367	ATGTCGGTCGTGTGTGAAAC	58.786	50.0	0.0	0.0	37.35	2.78	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2130	2588	0.179192	CAACCATGCGACCATGTTCG	60.179	55.0	8.47	8.47	45.9	3.95	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
90	91	4.430765	GACGGCGACCCATGACGT	62.431	66.667	16.62	0.00	40.85	4.34
257	258	4.666532	GTCTGCGTTGCACGGTGC	62.667	66.667	25.55	25.55	42.82	5.01
331	333	2.510411	CCCCTCGCATGTGGCATA	59.490	61.111	6.39	0.00	45.17	3.14
365	375	2.191908	GCGCCATGGTGGTATCCA	59.808	61.111	26.23	0.00	40.46	3.41
388	398	1.214367	ATGTCGGTCGTGTGTGAAAC	58.786	50.000	0.00	0.00	37.35	2.78
438	840	2.432628	GAACGGGAGCCACGACAG	60.433	66.667	3.78	0.00	34.93	3.51
467	869	1.670811	GTGGTGATTTGCGATGTAGGG	59.329	52.381	0.00	0.00	0.00	3.53
497	901	5.884792	AGGAAAGTTCTGATTCCATCATGAC	59.115	40.000	0.00	0.00	46.14	3.06
612	1019	5.818857	TGATGAGATTGATCGCTTGATTTGA	59.181	36.000	0.00	0.00	30.70	2.69
635	1042	8.575649	TGAATAAGTTGGGAAAGTTAGAATCC	57.424	34.615	0.00	0.00	0.00	3.01
649	1056	9.503399	AAAGTTAGAATCCGTCTCTTTTTGTAT	57.497	29.630	0.00	0.00	37.84	2.29
802	1212	9.462174	CTCATTCATTAGAAGTAGAGATCACAC	57.538	37.037	0.00	0.00	37.14	3.82
817	1227	2.009051	TCACACGGATCATGTTGATGC	58.991	47.619	0.00	0.00	41.12	3.91
876	1287	7.362142	GCCTATGATCATCAGTAGACACGATAA	60.362	40.741	12.53	0.00	0.00	1.75
942	1353	3.309961	TCAAGCGATCCTCATATCTGC	57.690	47.619	0.00	0.00	0.00	4.26
967	1378	5.973565	CAGAATAATTCCTTTCCAATCACGC	59.026	40.000	0.00	0.00	0.00	5.34
1714	2151	3.591254	GACACACGCCCTCTGGTCC	62.591	68.421	0.00	0.00	0.00	4.46
1715	2152	3.314331	CACACGCCCTCTGGTCCT	61.314	66.667	0.00	0.00	0.00	3.85
1716	2153	2.526873	ACACGCCCTCTGGTCCTT	60.527	61.111	0.00	0.00	0.00	3.36
1717	2154	2.266055	CACGCCCTCTGGTCCTTC	59.734	66.667	0.00	0.00	0.00	3.46
1718	2155	3.003763	ACGCCCTCTGGTCCTTCC	61.004	66.667	0.00	0.00	0.00	3.46
1719	2156	3.787001	CGCCCTCTGGTCCTTCCC	61.787	72.222	0.00	0.00	34.77	3.97
1720	2157	3.787001	GCCCTCTGGTCCTTCCCG	61.787	72.222	0.00	0.00	34.77	5.14
1721	2158	2.038975	CCCTCTGGTCCTTCCCGA	59.961	66.667	0.00	0.00	34.77	5.14
1876	2322	1.203287	GCTGGAAGGGACAATCTTTGC	59.797	52.381	0.00	0.00	0.00	3.68
1882	2328	4.221482	GGAAGGGACAATCTTTGCTGAAAT	59.779	41.667	0.00	0.00	0.00	2.17
1887	2334	5.178067	GGGACAATCTTTGCTGAAATGTTTG	59.822	40.000	4.40	4.40	32.68	2.93
1927	2375	3.423645	GCTTAATCGAGCTCACAACACAC	60.424	47.826	15.40	0.00	39.57	3.82
1968	2426	4.035017	CACTAACGGTTTCTTTTGCTGTG	58.965	43.478	0.00	0.00	0.00	3.66
2015	2473	2.940514	TGATCCAGGACTGAAGGGTA	57.059	50.000	0.00	0.00	0.00	3.69
2037	2495	8.788325	GGTACCACACTAATTAAACATCTCTT	57.212	34.615	7.15	0.00	0.00	2.85
2099	2557	5.240891	CAACCTGAAGATCACACATACACT	58.759	41.667	0.00	0.00	0.00	3.55
2102	2560	4.093998	CCTGAAGATCACACATACACTTGC	59.906	45.833	0.00	0.00	0.00	4.01
2108	2566	3.392882	TCACACATACACTTGCTGTCAG	58.607	45.455	0.00	0.00	33.91	3.51
2110	2568	1.466167	CACATACACTTGCTGTCAGCC	59.534	52.381	21.99	4.93	41.51	4.85
2111	2569	1.349026	ACATACACTTGCTGTCAGCCT	59.651	47.619	21.99	1.67	41.51	4.58
2112	2570	1.736126	CATACACTTGCTGTCAGCCTG	59.264	52.381	21.99	15.95	41.51	4.85
2113	2571	0.758734	TACACTTGCTGTCAGCCTGT	59.241	50.000	21.99	19.96	41.51	4.00
2114	2572	0.533755	ACACTTGCTGTCAGCCTGTC	60.534	55.000	21.99	0.00	41.51	3.51
2115	2573	1.301244	ACTTGCTGTCAGCCTGTCG	60.301	57.895	21.99	8.13	41.51	4.35
2116	2574	1.301244	CTTGCTGTCAGCCTGTCGT	60.301	57.895	21.99	0.00	41.51	4.34
2151	2611	1.876497	AACATGGTCGCATGGTTGCC	61.876	55.000	7.75	0.00	46.57	4.52
2174	2634	8.289618	TGCCGACTGAATATATAAATTTCAAGC	58.710	33.333	0.00	2.31	0.00	4.01
2189	2649	2.151202	TCAAGCAATCGGACTGAAACC	58.849	47.619	0.00	0.00	0.00	3.27
2205	2665	6.119536	ACTGAAACCACTCAAATCAACTGTA	58.880	36.000	0.00	0.00	0.00	2.74
2206	2666	6.260936	ACTGAAACCACTCAAATCAACTGTAG	59.739	38.462	0.00	0.00	0.00	2.74
2207	2667	6.353323	TGAAACCACTCAAATCAACTGTAGA	58.647	36.000	0.00	0.00	0.00	2.59
2208	2668	6.260050	TGAAACCACTCAAATCAACTGTAGAC	59.740	38.462	0.00	0.00	0.00	2.59
2211	2680	4.452455	CCACTCAAATCAACTGTAGACACC	59.548	45.833	0.00	0.00	0.00	4.16
2221	2690	5.934043	TCAACTGTAGACACCATGATGAAAG	59.066	40.000	0.00	0.00	0.00	2.62
2256	2725	4.397417	GCAGAATATGTCAAGAAACCAGCT	59.603	41.667	0.00	0.00	0.00	4.24
2308	2777	2.202395	GCTGCCTTGGTTTGCCTGA	61.202	57.895	0.00	0.00	35.27	3.86
2314	2783	2.031120	CCTTGGTTTGCCTGACAGAAA	58.969	47.619	3.32	0.00	35.27	2.52
2319	2788	1.098869	TTTGCCTGACAGAAAACGCA	58.901	45.000	3.32	1.31	0.00	5.24
2320	2789	0.662619	TTGCCTGACAGAAAACGCAG	59.337	50.000	3.32	0.00	0.00	5.18
2321	2790	0.179059	TGCCTGACAGAAAACGCAGA	60.179	50.000	3.32	0.00	0.00	4.26
2475	2956	2.124570	CATCAACCTGAGGGGGCG	60.125	66.667	2.38	0.00	40.03	6.13
2679	3160	5.476599	TGAAAATCAACCCATAACTGTCCTG	59.523	40.000	0.00	0.00	0.00	3.86
2695	3176	7.693969	ACTGTCCTGAGAAAATAAAATGAGG	57.306	36.000	0.00	0.00	0.00	3.86
2739	3220	8.942338	TGAATAACGGATATACATATTGGCTC	57.058	34.615	0.00	0.00	0.00	4.70

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
322	324	1.962822	CATCGCCGCTATGCCACAT	60.963	57.895	0.00	0.00	0.00	3.21
369	379	1.214367	GTTTCACACACGACCGACAT	58.786	50.000	0.00	0.00	0.00	3.06
388	398	2.578163	TTCCCAGCAGCTTCGATCCG	62.578	60.000	0.00	0.00	0.00	4.18
438	840	3.376859	TCGCAAATCACCACATATTCACC	59.623	43.478	0.00	0.00	0.00	4.02
467	869	8.384607	GATGGAATCAGAACTTTCCTAATACC	57.615	38.462	3.44	0.00	44.70	2.73
497	901	7.730364	AATCCAATTTACTAATACTCCTGCG	57.270	36.000	0.00	0.00	0.00	5.18
612	1019	7.173032	ACGGATTCTAACTTTCCCAACTTATT	58.827	34.615	0.00	0.00	0.00	1.40
812	1222	0.608856	AACGTTCAGCCCATGCATCA	60.609	50.000	0.00	0.00	41.13	3.07
814	1224	0.895100	ACAACGTTCAGCCCATGCAT	60.895	50.000	0.00	0.00	41.13	3.96
815	1225	1.528076	ACAACGTTCAGCCCATGCA	60.528	52.632	0.00	0.00	41.13	3.96
816	1226	1.081242	CACAACGTTCAGCCCATGC	60.081	57.895	0.00	0.00	37.95	4.06
817	1227	0.667993	AACACAACGTTCAGCCCATG	59.332	50.000	0.00	0.00	29.27	3.66
893	1304	2.793232	CCGGTTAATGCGTAGTTAGCTC	59.207	50.000	0.00	0.00	35.28	4.09
942	1353	6.498304	CGTGATTGGAAAGGAATTATTCTGG	58.502	40.000	4.87	0.00	0.00	3.86
967	1378	0.822532	GGAGGGATTGCTGCCATCAG	60.823	60.000	14.68	0.00	43.16	2.90
1887	2334	1.002468	AGCTGTGTGAATTTGACGTGC	60.002	47.619	0.00	0.00	0.00	5.34
2037	2495	5.544176	ACAGAAGGAACTGACCATCTTCTAA	59.456	40.000	0.00	0.00	41.25	2.10
2099	2557	0.880278	GAACGACAGGCTGACAGCAA	60.880	55.000	27.87	0.00	44.75	3.91
2102	2560	1.073964	CATGAACGACAGGCTGACAG	58.926	55.000	23.66	13.73	0.00	3.51
2108	2566	0.438830	GTTCGACATGAACGACAGGC	59.561	55.000	16.10	6.74	46.85	4.85
2130	2588	0.179192	CAACCATGCGACCATGTTCG	60.179	55.000	8.47	8.47	45.90	3.95
2174	2634	2.766313	TGAGTGGTTTCAGTCCGATTG	58.234	47.619	0.00	0.00	41.46	2.67
2189	2649	5.056480	TGGTGTCTACAGTTGATTTGAGTG	58.944	41.667	0.00	0.00	0.00	3.51
2205	2665	3.755378	GCAACTCTTTCATCATGGTGTCT	59.245	43.478	5.73	0.00	0.00	3.41
2206	2666	3.755378	AGCAACTCTTTCATCATGGTGTC	59.245	43.478	5.73	0.00	0.00	3.67
2207	2667	3.759581	AGCAACTCTTTCATCATGGTGT	58.240	40.909	5.73	0.00	0.00	4.16
2208	2668	4.778534	AAGCAACTCTTTCATCATGGTG	57.221	40.909	0.00	0.00	0.00	4.17
2211	2680	5.330295	GCAGTAAGCAACTCTTTCATCATG	58.670	41.667	0.00	0.00	44.79	3.07
2245	2714	4.104383	TCCATTCAAGAGCTGGTTTCTT	57.896	40.909	0.00	0.00	35.34	2.52
2256	2725	6.149973	CAGAGCACAAACTAATCCATTCAAGA	59.850	38.462	0.00	0.00	0.00	3.02
2308	2777	2.542595	CGGTTTACTCTGCGTTTTCTGT	59.457	45.455	0.00	0.00	0.00	3.41
2314	2783	2.472488	CGTTTACGGTTTACTCTGCGTT	59.528	45.455	0.00	0.00	35.37	4.84
2319	2788	1.269448	TCGGCGTTTACGGTTTACTCT	59.731	47.619	6.85	0.00	40.23	3.24
2320	2789	1.696988	TCGGCGTTTACGGTTTACTC	58.303	50.000	6.85	0.00	40.23	2.59
2321	2790	2.262211	GATCGGCGTTTACGGTTTACT	58.738	47.619	6.85	0.00	40.23	2.24
2366	2847	6.647334	TTCTCCATTGTTGCATCTTGTAAA	57.353	33.333	0.00	0.00	0.00	2.01
2475	2956	0.250338	GTGAGGTTGTGTCCTGTCCC	60.250	60.000	0.00	0.00	38.02	4.46
2516	2997	3.295093	TGTTTTGGTGACATCATGTGGT	58.705	40.909	0.00	0.00	42.32	4.16
2629	3110	6.094186	GCTTCGATTTTTCTGATCCCTAAACT	59.906	38.462	0.00	0.00	0.00	2.66
2739	3220	6.596888	AGATCATGAATACATATTGCCTTCCG	59.403	38.462	0.00	0.00	35.09	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.