AutoCloner

Multiple sequence alignment - TraesCS2D01G322500

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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	TraesCS2D01G322500	chr2D	100.000	3870	0	0	1	3870	413780866	413776997	0.000000e+00	7147
1	TraesCS2D01G322500	chr2D	78.561	667	131	9	2189	2849	612438837	612438177	2.760000e-116	429
2	TraesCS2D01G322500	chr2D	78.327	263	47	8	2220	2477	43798640	43798383	1.110000e-35	161
3	TraesCS2D01G322500	chr2B	96.090	3146	80	18	738	3870	486988278	486985163	0.000000e+00	5088
4	TraesCS2D01G322500	chr2B	78.829	666	131	8	2189	2849	747310694	747310034	1.280000e-119	440
5	TraesCS2D01G322500	chr2B	78.707	263	46	8	2220	2477	68423229	68422972	2.390000e-37	167
6	TraesCS2D01G322500	chr2A	95.303	3151	88	12	751	3870	580854894	580851773	0.000000e+00	4944
7	TraesCS2D01G322500	chr2A	78.529	666	133	8	2189	2849	744530062	744529402	2.760000e-116	429
8	TraesCS2D01G322500	chr6B	92.837	726	41	5	18	741	694441855	694442571	0.000000e+00	1042
9	TraesCS2D01G322500	chr6A	92.202	731	43	8	15	741	176987535	176986815	0.000000e+00	1022
10	TraesCS2D01G322500	chr3D	94.092	677	30	4	18	693	569903119	569902452	0.000000e+00	1020
11	TraesCS2D01G322500	chr5D	91.746	739	49	6	6	741	398906691	398907420	0.000000e+00	1016
12	TraesCS2D01G322500	chr5D	75.881	539	101	25	2209	2731	332449773	332450298	8.300000e-62	248
13	TraesCS2D01G322500	chr6D	94.277	664	33	5	78	738	371535602	371534941	0.000000e+00	1011
14	TraesCS2D01G322500	chr7D	91.588	737	52	9	15	746	10720650	10719919	0.000000e+00	1009
15	TraesCS2D01G322500	chr7D	91.588	737	45	9	15	744	409486484	409485758	0.000000e+00	1002
16	TraesCS2D01G322500	chr7B	91.770	729	45	7	15	741	245662260	245662975	0.000000e+00	1000
17	TraesCS2D01G322500	chr7A	91.022	724	47	8	18	739	159552875	159552168	0.000000e+00	961
18	TraesCS2D01G322500	chr5A	76.243	543	92	26	2209	2731	433311586	433312111	1.780000e-63	254
19	TraesCS2D01G322500	chr5B	76.015	542	95	27	2209	2731	388407302	388407827	8.300000e-62	248
20	TraesCS2D01G322500	chr4D	73.665	543	119	20	2220	2750	328998312	328998842	5.100000e-44	189
21	TraesCS2D01G322500	chr4A	73.247	542	123	18	2220	2750	141130923	141130393	1.100000e-40	178

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	TraesCS2D01G322500	chr2D	413776997	413780866	3869	True	7147	7147	100.000	1	3870	1	chr2D.!!$R2	3869
1	TraesCS2D01G322500	chr2D	612438177	612438837	660	True	429	429	78.561	2189	2849	1	chr2D.!!$R3	660
2	TraesCS2D01G322500	chr2B	486985163	486988278	3115	True	5088	5088	96.090	738	3870	1	chr2B.!!$R2	3132
3	TraesCS2D01G322500	chr2B	747310034	747310694	660	True	440	440	78.829	2189	2849	1	chr2B.!!$R3	660
4	TraesCS2D01G322500	chr2A	580851773	580854894	3121	True	4944	4944	95.303	751	3870	1	chr2A.!!$R1	3119
5	TraesCS2D01G322500	chr2A	744529402	744530062	660	True	429	429	78.529	2189	2849	1	chr2A.!!$R2	660
6	TraesCS2D01G322500	chr6B	694441855	694442571	716	False	1042	1042	92.837	18	741	1	chr6B.!!$F1	723
7	TraesCS2D01G322500	chr6A	176986815	176987535	720	True	1022	1022	92.202	15	741	1	chr6A.!!$R1	726
8	TraesCS2D01G322500	chr3D	569902452	569903119	667	True	1020	1020	94.092	18	693	1	chr3D.!!$R1	675
9	TraesCS2D01G322500	chr5D	398906691	398907420	729	False	1016	1016	91.746	6	741	1	chr5D.!!$F2	735
10	TraesCS2D01G322500	chr5D	332449773	332450298	525	False	248	248	75.881	2209	2731	1	chr5D.!!$F1	522
11	TraesCS2D01G322500	chr6D	371534941	371535602	661	True	1011	1011	94.277	78	738	1	chr6D.!!$R1	660
12	TraesCS2D01G322500	chr7D	10719919	10720650	731	True	1009	1009	91.588	15	746	1	chr7D.!!$R1	731
13	TraesCS2D01G322500	chr7D	409485758	409486484	726	True	1002	1002	91.588	15	744	1	chr7D.!!$R2	729
14	TraesCS2D01G322500	chr7B	245662260	245662975	715	False	1000	1000	91.770	15	741	1	chr7B.!!$F1	726
15	TraesCS2D01G322500	chr7A	159552168	159552875	707	True	961	961	91.022	18	739	1	chr7A.!!$R1	721
16	TraesCS2D01G322500	chr5A	433311586	433312111	525	False	254	254	76.243	2209	2731	1	chr5A.!!$F1	522
17	TraesCS2D01G322500	chr5B	388407302	388407827	525	False	248	248	76.015	2209	2731	1	chr5B.!!$F1	522

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
848	863	0.034896	GTCAGCGGGGAAGAAACAGA	59.965	55.0	0.00	0.0	0.0	3.41	F
2139	2169	0.322816	ACAGGGCAATGCAGGTAGTG	60.323	55.0	7.79	0.0	0.0	2.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2161	2191	0.458260	CAATGGCTGCAGCATAGCAA	59.542	50.0	37.63	16.94	45.13	3.91	R
3228	3273	0.389556	GTTCGGTCGGTCCCTTCTTC	60.390	60.0	0.00	0.00	0.00	2.87	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
53	54	0.392998	CCAACTTGGGATCAGTCGGG	60.393	60.000	0.00	0.00	32.67	5.14
137	144	1.411074	GGTGGTGTTCTCTGGGGTTTT	60.411	52.381	0.00	0.00	0.00	2.43
237	245	4.440127	CCTTGGCGGCCAATGTGC	62.440	66.667	32.73	0.00	43.07	4.57
247	255	4.170062	CAATGTGCTGCGGCGAGG	62.170	66.667	12.98	2.58	42.25	4.63
298	306	1.177895	TTGCTCTTTGATGGCGCCAA	61.178	50.000	36.33	16.53	0.00	4.52
402	411	0.819259	GTTGCTCCTGAGTTGTGCCA	60.819	55.000	0.00	0.00	0.00	4.92
426	435	1.705337	GCTCGGTATGCACGCAATGT	61.705	55.000	0.00	0.00	0.00	2.71
455	464	3.983044	AGGTTCCTCGCAAAGTCTAAT	57.017	42.857	0.00	0.00	0.00	1.73
521	530	3.344515	GTGGTGATGGTCCTTTTAGTCC	58.655	50.000	0.00	0.00	0.00	3.85
538	547	3.217017	CGCTAGCTAGGTCCCGCA	61.217	66.667	22.10	0.00	0.00	5.69
629	641	9.737844	TCCTTATAAACGGGTTAACTTGTTTAT	57.262	29.630	29.64	29.64	44.89	1.40
725	740	4.716977	GGACTCCTCCCCCGGTGT	62.717	72.222	0.00	0.00	33.75	4.16
841	856	1.903877	ATGACCAGTCAGCGGGGAAG	61.904	60.000	6.63	0.00	43.61	3.46
842	857	2.203788	ACCAGTCAGCGGGGAAGA	60.204	61.111	0.00	0.00	34.09	2.87
843	858	1.827399	GACCAGTCAGCGGGGAAGAA	61.827	60.000	0.00	0.00	34.09	2.52
844	859	1.374947	CCAGTCAGCGGGGAAGAAA	59.625	57.895	0.00	0.00	0.00	2.52
845	860	0.955919	CCAGTCAGCGGGGAAGAAAC	60.956	60.000	0.00	0.00	0.00	2.78
846	861	0.250295	CAGTCAGCGGGGAAGAAACA	60.250	55.000	0.00	0.00	0.00	2.83
847	862	0.035458	AGTCAGCGGGGAAGAAACAG	59.965	55.000	0.00	0.00	0.00	3.16
848	863	0.034896	GTCAGCGGGGAAGAAACAGA	59.965	55.000	0.00	0.00	0.00	3.41
849	864	0.984230	TCAGCGGGGAAGAAACAGAT	59.016	50.000	0.00	0.00	0.00	2.90
850	865	2.093658	GTCAGCGGGGAAGAAACAGATA	60.094	50.000	0.00	0.00	0.00	1.98
851	866	2.569853	TCAGCGGGGAAGAAACAGATAA	59.430	45.455	0.00	0.00	0.00	1.75
990	1016	2.541762	CGCTCGAATCAAGAATTCCCTC	59.458	50.000	0.65	0.00	40.69	4.30
1452	1478	1.221213	AGGAGCTCCTGGAGGACTCT	61.221	60.000	34.74	12.99	46.55	3.24
1572	1598	1.631072	CTTTATCGACACCTGCGCG	59.369	57.895	0.00	0.00	0.00	6.86
1776	1802	3.474570	GCGTGGATGAGGGCTCCT	61.475	66.667	0.00	0.00	36.03	3.69
1797	1823	1.279271	GAAAGGAAGCTACTGGCCTCA	59.721	52.381	3.32	0.00	43.05	3.86
1878	1904	2.651361	CAGGACGCCGTGAACTCT	59.349	61.111	0.00	0.00	0.00	3.24
1969	1995	0.889186	CCCCAAGGACAAGGTGAACG	60.889	60.000	0.00	0.00	33.47	3.95
2052	2078	1.614051	GGCATCACCACCATGAAGACA	60.614	52.381	0.00	0.00	38.86	3.41
2139	2169	0.322816	ACAGGGCAATGCAGGTAGTG	60.323	55.000	7.79	0.00	0.00	2.74
2146	2176	3.694072	GGCAATGCAGGTAGTGATTAACA	59.306	43.478	7.79	0.00	0.00	2.41
2159	2189	9.230932	GGTAGTGATTAACAAGTACGTATCTTC	57.769	37.037	0.00	0.00	0.00	2.87
2323	2355	0.108804	CGTTCCAGGACACGCTGTAT	60.109	55.000	10.12	0.00	0.00	2.29
2871	2906	2.910977	ACCTCGGGTTCAAGGTCTAAAT	59.089	45.455	0.00	0.00	42.28	1.40
2970	3005	2.068519	GAACGTGTGATGACTGATGCA	58.931	47.619	0.00	0.00	0.00	3.96
3194	3239	9.219603	CACATCTCAACTTCTTATTTTGGACTA	57.780	33.333	0.00	0.00	0.00	2.59
3227	3272	0.887836	TACGTGACAGCACCGAGACT	60.888	55.000	0.00	0.00	42.09	3.24
3228	3273	1.730902	CGTGACAGCACCGAGACTG	60.731	63.158	0.00	0.00	42.09	3.51
3229	3274	1.660355	GTGACAGCACCGAGACTGA	59.340	57.895	5.68	0.00	39.14	3.41
3274	3322	3.184379	CCAATAATCTCCACGTACGCATG	59.816	47.826	16.72	7.07	0.00	4.06
3497	3551	3.852536	GTCACTTCTCACTATGCACGTAC	59.147	47.826	0.00	0.00	0.00	3.67
3521	3575	1.913762	CCTCCCCACCGTCTCACTT	60.914	63.158	0.00	0.00	0.00	3.16
3630	3684	2.106511	TCTCCCAAACTTCCCAAGTGAG	59.893	50.000	0.00	0.00	41.91	3.51
3790	3850	7.281774	ACATGAACCTATGCTCAATTTCAGTAG	59.718	37.037	0.00	0.00	0.00	2.57
3802	3862	8.713271	GCTCAATTTCAGTAGCCACTTATATAC	58.287	37.037	0.00	0.00	30.46	1.47
3863	3923	2.724358	CGGTTTCGCGCGCTTTTT	60.724	55.556	30.48	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	3.595758	ACCACCAGCAGCAAACGC	61.596	61.111	0.00	0.00	0.00	4.84
4	5	2.332514	CACCACCAGCAGCAAACG	59.667	61.111	0.00	0.00	0.00	3.60
5	6	2.127232	ACCACCACCAGCAGCAAAC	61.127	57.895	0.00	0.00	0.00	2.93
6	7	2.126596	CACCACCACCAGCAGCAAA	61.127	57.895	0.00	0.00	0.00	3.68
7	8	2.519063	CACCACCACCAGCAGCAA	60.519	61.111	0.00	0.00	0.00	3.91
8	9	4.584518	CCACCACCACCAGCAGCA	62.585	66.667	0.00	0.00	0.00	4.41
10	11	2.595463	CACCACCACCACCAGCAG	60.595	66.667	0.00	0.00	0.00	4.24
11	12	4.202574	CCACCACCACCACCAGCA	62.203	66.667	0.00	0.00	0.00	4.41
12	13	4.204028	ACCACCACCACCACCAGC	62.204	66.667	0.00	0.00	0.00	4.85
13	14	2.203337	CACCACCACCACCACCAG	60.203	66.667	0.00	0.00	0.00	4.00
247	255	2.125512	ATCACCAAGAGCGCGACC	60.126	61.111	12.10	0.00	0.00	4.79
252	260	1.081892	CCAAGACATCACCAAGAGCG	58.918	55.000	0.00	0.00	0.00	5.03
298	306	4.141959	CGATTAACAATTTGGGGAGGCATT	60.142	41.667	0.78	0.00	0.00	3.56
402	411	2.510906	GTGCATACCGAGCCCCAT	59.489	61.111	0.00	0.00	0.00	4.00
426	435	1.290955	CGAGGAACCTAACGCACCA	59.709	57.895	0.00	0.00	0.00	4.17
455	464	2.756207	TGTCGTCGAGGGATCACAATAA	59.244	45.455	5.12	0.00	0.00	1.40
521	530	3.217017	TGCGGGACCTAGCTAGCG	61.217	66.667	15.74	13.85	0.00	4.26
538	547	3.366052	AGAACAAGACACCCAACAAGT	57.634	42.857	0.00	0.00	0.00	3.16
599	608	8.911965	ACAAGTTAACCCGTTTATAAGGAAAAA	58.088	29.630	0.88	0.00	0.00	1.94
618	627	6.427547	ACCGGATCGAAAACATAAACAAGTTA	59.572	34.615	9.46	0.00	0.00	2.24
629	641	1.525941	GGGAAACCGGATCGAAAACA	58.474	50.000	9.46	0.00	43.64	2.83
841	856	6.622549	TCTTCGGAGAGTTCTTATCTGTTTC	58.377	40.000	0.00	0.00	38.43	2.78
842	857	6.591750	TCTTCGGAGAGTTCTTATCTGTTT	57.408	37.500	0.00	0.00	38.43	2.83
843	858	6.591750	TTCTTCGGAGAGTTCTTATCTGTT	57.408	37.500	0.00	0.00	38.43	3.16
844	859	6.153680	ACATTCTTCGGAGAGTTCTTATCTGT	59.846	38.462	0.00	0.00	38.43	3.41
845	860	6.568869	ACATTCTTCGGAGAGTTCTTATCTG	58.431	40.000	0.00	0.00	38.43	2.90
846	861	6.378564	TGACATTCTTCGGAGAGTTCTTATCT	59.621	38.462	0.00	0.00	38.43	1.98
847	862	6.474102	GTGACATTCTTCGGAGAGTTCTTATC	59.526	42.308	0.00	0.00	38.43	1.75
848	863	6.334202	GTGACATTCTTCGGAGAGTTCTTAT	58.666	40.000	0.00	0.00	38.43	1.73
849	864	5.336531	GGTGACATTCTTCGGAGAGTTCTTA	60.337	44.000	0.00	0.00	38.43	2.10
850	865	4.561105	GTGACATTCTTCGGAGAGTTCTT	58.439	43.478	0.00	0.00	38.43	2.52
851	866	3.056465	GGTGACATTCTTCGGAGAGTTCT	60.056	47.826	0.00	0.00	38.43	3.01
990	1016	3.896133	GGATGCATGGCAGTGGCG	61.896	66.667	2.46	0.00	43.65	5.69
1452	1478	2.879233	GCCCTTGAGGTCGTCCACA	61.879	63.158	0.51	0.00	38.26	4.17
1776	1802	1.279271	GAGGCCAGTAGCTTCCTTTCA	59.721	52.381	5.01	0.00	41.63	2.69
1878	1904	0.846015	CAGGGTGATCCTTGGGCATA	59.154	55.000	0.00	0.00	45.47	3.14
1969	1995	1.126079	CCGTCGCCGTACATGAATAC	58.874	55.000	0.00	0.00	0.00	1.89
2139	2169	8.870879	AGCAAAGAAGATACGTACTTGTTAATC	58.129	33.333	15.41	2.71	32.14	1.75
2146	2176	6.477033	CAGCATAGCAAAGAAGATACGTACTT	59.523	38.462	0.00	3.72	0.00	2.24
2159	2189	0.744874	ATGGCTGCAGCATAGCAAAG	59.255	50.000	37.63	0.00	45.13	2.77
2161	2191	0.458260	CAATGGCTGCAGCATAGCAA	59.542	50.000	37.63	16.94	45.13	3.91
2898	2933	2.514592	CATGTACAGGGCGCAGGG	60.515	66.667	10.83	0.00	0.00	4.45
2904	2939	1.961394	TCGGTATCTCATGTACAGGGC	59.039	52.381	7.81	0.00	0.00	5.19
2970	3005	3.624861	CGAAGGTTTAGCTGATCTTGCAT	59.375	43.478	12.40	2.72	0.00	3.96
3227	3272	0.828762	TTCGGTCGGTCCCTTCTTCA	60.829	55.000	0.00	0.00	0.00	3.02
3228	3273	0.389556	GTTCGGTCGGTCCCTTCTTC	60.390	60.000	0.00	0.00	0.00	2.87
3229	3274	1.670015	GTTCGGTCGGTCCCTTCTT	59.330	57.895	0.00	0.00	0.00	2.52
3274	3322	0.879090	CCCGGGTTAAACACAAGCTC	59.121	55.000	14.18	0.00	0.00	4.09
3405	3459	3.071874	TGCAGTTTGTAATCTCCCTGG	57.928	47.619	0.00	0.00	0.00	4.45
3584	3638	2.261729	GGAAAGGGGATAGCTAGGGAG	58.738	57.143	0.00	0.00	0.00	4.30
3645	3699	1.786937	ACTCCTGCCTCTTGATCGAT	58.213	50.000	0.00	0.00	0.00	3.59
3790	3850	6.128902	CGATTCAAGAACCGTATATAAGTGGC	60.129	42.308	0.00	0.00	0.00	5.01
3802	3862	1.340465	CGACGCGATTCAAGAACCG	59.660	57.895	15.93	0.00	0.00	4.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.