AutoCloner

Multiple sequence alignment - TraesCS1B01G214700

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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	TraesCS1B01G214700	chr1B	100.000	3277	0	0	1	3277	389734074	389737350	0.000000e+00	6052
1	TraesCS1B01G214700	chr1D	94.320	2500	124	8	782	3276	288147213	288149699	0.000000e+00	3814
2	TraesCS1B01G214700	chr1A	93.463	2570	118	21	725	3277	359689170	359691706	0.000000e+00	3770
3	TraesCS1B01G214700	chr1A	74.038	728	172	15	15	732	171042325	171043045	6.920000e-72	281
4	TraesCS1B01G214700	chr1A	93.258	89	6	0	1958	2046	525837409	525837497	7.380000e-27	132
5	TraesCS1B01G214700	chr7B	96.190	735	27	1	1	734	465958584	465959318	0.000000e+00	1201
6	TraesCS1B01G214700	chr7B	75.042	597	137	10	142	731	248504990	248504399	1.940000e-67	267
7	TraesCS1B01G214700	chr7B	93.258	89	6	0	1958	2046	684164031	684164119	7.380000e-27	132
8	TraesCS1B01G214700	chr4B	95.225	733	35	0	1	733	407569854	407569122	0.000000e+00	1160
9	TraesCS1B01G214700	chr4B	72.565	729	179	16	15	732	72165302	72164584	5.510000e-53	219
10	TraesCS1B01G214700	chr6A	93.469	735	46	2	1	734	206903045	206903778	0.000000e+00	1090
11	TraesCS1B01G214700	chr6D	75.853	733	156	17	14	733	293330105	293329381	1.450000e-93	353
12	TraesCS1B01G214700	chr2D	74.966	731	167	15	14	734	607521333	607520609	4.080000e-84	322
13	TraesCS1B01G214700	chr2D	91.549	142	7	1	592	733	634143624	634143488	1.200000e-44	191
14	TraesCS1B01G214700	chr5A	92.391	92	7	0	1958	2049	146515870	146515779	7.380000e-27	132
15	TraesCS1B01G214700	chr4A	93.258	89	6	0	1958	2046	196784980	196785068	7.380000e-27	132
16	TraesCS1B01G214700	chr2A	92.391	92	7	0	1958	2049	484993959	484993868	7.380000e-27	132
17	TraesCS1B01G214700	chr2A	91.304	92	8	0	1958	2049	101128038	101127947	3.430000e-25	126

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	TraesCS1B01G214700	chr1B	389734074	389737350	3276	False	6052	6052	100.000	1	3277	1	chr1B.!!$F1	3276
1	TraesCS1B01G214700	chr1D	288147213	288149699	2486	False	3814	3814	94.320	782	3276	1	chr1D.!!$F1	2494
2	TraesCS1B01G214700	chr1A	359689170	359691706	2536	False	3770	3770	93.463	725	3277	1	chr1A.!!$F2	2552
3	TraesCS1B01G214700	chr1A	171042325	171043045	720	False	281	281	74.038	15	732	1	chr1A.!!$F1	717
4	TraesCS1B01G214700	chr7B	465958584	465959318	734	False	1201	1201	96.190	1	734	1	chr7B.!!$F1	733
5	TraesCS1B01G214700	chr7B	248504399	248504990	591	True	267	267	75.042	142	731	1	chr7B.!!$R1	589
6	TraesCS1B01G214700	chr4B	407569122	407569854	732	True	1160	1160	95.225	1	733	1	chr4B.!!$R2	732
7	TraesCS1B01G214700	chr4B	72164584	72165302	718	True	219	219	72.565	15	732	1	chr4B.!!$R1	717
8	TraesCS1B01G214700	chr6A	206903045	206903778	733	False	1090	1090	93.469	1	734	1	chr6A.!!$F1	733
9	TraesCS1B01G214700	chr6D	293329381	293330105	724	True	353	353	75.853	14	733	1	chr6D.!!$R1	719
10	TraesCS1B01G214700	chr2D	607520609	607521333	724	True	322	322	74.966	14	734	1	chr2D.!!$R1	720

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
567	569	0.470833	GAGAGAGGCTGGCATAGGGA	60.471	60.0	3.38	0.0	0.0	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2396	2423	0.035036	TGCCCAACCGACAATTACGA	59.965	50.0	5.91	0.0	0.0	3.43	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
154	155	6.347110	CGCTTAAGTGCAAAATCTTTGTTTC	58.653	36.000	2.51	0.00	0.00	2.78
207	208	2.760385	GGAGAGCTAGGCACGGGT	60.760	66.667	0.00	0.00	0.00	5.28
345	346	3.641434	ATTTGGATGTGGAGAGACCTG	57.359	47.619	0.00	0.00	39.86	4.00
448	449	4.047125	CATCGGGGTGGCTTGGGT	62.047	66.667	0.00	0.00	0.00	4.51
468	469	0.749818	TTTGTGGAAGCAGCGGAACA	60.750	50.000	0.00	0.00	0.00	3.18
567	569	0.470833	GAGAGAGGCTGGCATAGGGA	60.471	60.000	3.38	0.00	0.00	4.20
620	625	2.165641	GGCTTTAGTTTATGTGGGGTGC	59.834	50.000	0.00	0.00	0.00	5.01
662	669	1.380302	GTGTGCATCCTCCCTTGGT	59.620	57.895	0.00	0.00	0.00	3.67
748	757	1.895231	AAAAACAGTCGTCGGGGCC	60.895	57.895	0.00	0.00	0.00	5.80
750	759	2.726822	AAAACAGTCGTCGGGGCCTC	62.727	60.000	0.84	0.00	0.00	4.70
798	807	4.312443	GACGATAAACACCAGAAACTCCA	58.688	43.478	0.00	0.00	0.00	3.86
921	931	0.726827	TTTATCTTTGCGCGCCTGAG	59.273	50.000	30.77	22.35	0.00	3.35
1043	1053	0.892358	AGGCGTACACTGACCGAAGA	60.892	55.000	0.00	0.00	0.00	2.87
1071	1081	4.175337	CATGGCCCCGACCGTCAT	62.175	66.667	0.00	0.00	0.00	3.06
1374	1388	3.612004	CGAGCTTACCGAGTTCTTCAACT	60.612	47.826	0.00	0.00	46.21	3.16
1397	1411	4.341806	TCCTTGAAACAAGAGGTACGTACA	59.658	41.667	26.02	0.00	32.33	2.90
1398	1412	5.011329	TCCTTGAAACAAGAGGTACGTACAT	59.989	40.000	26.02	20.48	32.33	2.29
1399	1413	6.209192	TCCTTGAAACAAGAGGTACGTACATA	59.791	38.462	26.02	0.00	32.33	2.29
1400	1414	7.039882	CCTTGAAACAAGAGGTACGTACATAT	58.960	38.462	26.02	14.94	0.00	1.78
1408	1422	2.761767	AGGTACGTACATATGTGGCACA	59.238	45.455	24.36	24.36	0.00	4.57
1421	1435	2.296752	TGTGGCACATTGGAGTTCATTG	59.703	45.455	17.96	0.00	44.52	2.82
1639	1661	3.068590	AGCTGAAGGTGATTTTGGTGTTG	59.931	43.478	0.00	0.00	0.00	3.33
1804	1826	6.128007	CGTGCCTAAGATTGATTTTACTGGTT	60.128	38.462	0.00	0.00	0.00	3.67
1808	1830	9.736023	GCCTAAGATTGATTTTACTGGTTAATG	57.264	33.333	0.00	0.00	0.00	1.90
1816	1838	8.050778	TGATTTTACTGGTTAATGTGGTCATC	57.949	34.615	0.00	0.00	32.56	2.92
1868	1890	1.838112	TCCATCGCTGCCAATTTTCT	58.162	45.000	0.00	0.00	0.00	2.52
1869	1891	2.997980	TCCATCGCTGCCAATTTTCTA	58.002	42.857	0.00	0.00	0.00	2.10
1870	1892	3.351740	TCCATCGCTGCCAATTTTCTAA	58.648	40.909	0.00	0.00	0.00	2.10
1871	1893	3.378112	TCCATCGCTGCCAATTTTCTAAG	59.622	43.478	0.00	0.00	0.00	2.18
1884	1906	7.176865	GCCAATTTTCTAAGTAAGAGTTTCCCT	59.823	37.037	0.00	0.00	35.05	4.20
1913	1935	8.201554	TGATCCGTTCTTCTGAATTTCTAATG	57.798	34.615	0.00	0.00	34.40	1.90
2001	2023	1.539388	CCGAACCTGCAAAATGCTACA	59.461	47.619	3.78	0.00	45.31	2.74
2046	2069	3.716601	CTCCAGGCGTTCAAACAATTTT	58.283	40.909	0.00	0.00	0.00	1.82
2138	2161	2.430465	GATGAAGCACTTGAAGAGGCA	58.570	47.619	13.92	0.07	0.00	4.75
2197	2220	6.692232	GGAGACGTGCAATTACTGTATATC	57.308	41.667	0.00	0.00	0.00	1.63
2198	2221	6.213677	GGAGACGTGCAATTACTGTATATCA	58.786	40.000	0.00	0.00	0.00	2.15
2308	2332	5.047802	ACTTTTGATGTCTTTAGCCACCATG	60.048	40.000	0.00	0.00	0.00	3.66
2310	2334	3.346315	TGATGTCTTTAGCCACCATGTG	58.654	45.455	0.00	0.00	0.00	3.21
2318	2342	0.968901	AGCCACCATGTGCCAGAATG	60.969	55.000	0.00	0.00	31.34	2.67
2344	2369	2.334023	AGGTAATTTTGCCCTTGCCAA	58.666	42.857	0.00	0.00	36.33	4.52
2348	2373	4.634004	GGTAATTTTGCCCTTGCCAATAAC	59.366	41.667	0.00	0.00	36.33	1.89
2396	2423	4.069304	TCCGTTCCGAAAGATGATTGTTT	58.931	39.130	0.00	0.00	0.00	2.83
2410	2437	5.676532	TGATTGTTTCGTAATTGTCGGTT	57.323	34.783	5.34	0.00	0.00	4.44
2430	2457	1.202758	TGGGCATAGGGTTCTATTGCG	60.203	52.381	0.00	0.00	34.16	4.85
2451	2478	4.400961	AGCGCACCCTGCTCCTTC	62.401	66.667	11.47	0.00	42.25	3.46
2463	2490	4.590647	CCCTGCTCCTTCATCTATGTCTAA	59.409	45.833	0.00	0.00	0.00	2.10
2470	2497	5.363868	TCCTTCATCTATGTCTAAGGTGTGG	59.636	44.000	8.13	0.00	38.29	4.17
2495	2522	0.324614	TCCTGTTGATCACGCCATGT	59.675	50.000	0.00	0.00	0.00	3.21
2561	2588	1.822990	GTACACTAGCTAGGGCACACA	59.177	52.381	23.24	0.41	41.70	3.72
2604	2631	2.514803	CTAGGGTTTTTGTGAGGGGTG	58.485	52.381	0.00	0.00	0.00	4.61
2667	2694	2.370189	AGGGGCTCATGTTATCAGCTAC	59.630	50.000	3.65	0.00	0.00	3.58
2686	2713	0.397816	CGGAGAGGAGGGGAGTGAAT	60.398	60.000	0.00	0.00	0.00	2.57
2765	2792	2.159382	GGGCAAACTTTTCTCGGATCA	58.841	47.619	0.00	0.00	0.00	2.92
2795	2822	0.323087	GGTTCGGTGGTAGGGCAAAT	60.323	55.000	0.00	0.00	0.00	2.32
2878	2905	1.071471	CTTCACGGCAGGAGTTGGT	59.929	57.895	0.00	0.00	0.00	3.67
2916	2943	1.685765	GAAGGGCCATGGGGGTTTC	60.686	63.158	15.13	0.00	39.65	2.78
3008	3035	3.112263	TCCGATGTGGATTAGGGTCTTT	58.888	45.455	0.00	0.00	43.74	2.52
3010	3037	3.118408	CCGATGTGGATTAGGGTCTTTGA	60.118	47.826	0.00	0.00	42.00	2.69
3016	3043	3.134458	GGATTAGGGTCTTTGATCTGCG	58.866	50.000	0.00	0.00	0.00	5.18
3085	3112	2.748058	GATGAGTTGGTGGGTGCGGT	62.748	60.000	0.00	0.00	0.00	5.68
3089	3116	2.517402	TTGGTGGGTGCGGTTGTC	60.517	61.111	0.00	0.00	0.00	3.18
3097	3124	1.577328	GGTGCGGTTGTCTGACCATG	61.577	60.000	5.17	0.00	39.78	3.66
3136	3163	8.820831	AGATAAAGTATATGAGGATGAAGGTGG	58.179	37.037	0.00	0.00	0.00	4.61
3171	3198	4.286297	TGAATCGTTGGTGAGGAGATTT	57.714	40.909	0.00	0.00	32.42	2.17
3172	3199	4.002982	TGAATCGTTGGTGAGGAGATTTG	58.997	43.478	0.00	0.00	32.42	2.32
3188	3215	3.525199	AGATTTGTGTTGGCTAGGGAGAT	59.475	43.478	0.00	0.00	0.00	2.75
3202	3229	3.184628	AGGGAGATGAACAAGGACATGA	58.815	45.455	0.00	0.00	0.00	3.07
3256	3283	7.315890	CAAGAAGAAGAAACTTTTCTGGTGTT	58.684	34.615	4.99	0.00	46.22	3.32
3264	3291	5.576447	AACTTTTCTGGTGTTGTTTCGAT	57.424	34.783	0.00	0.00	0.00	3.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
154	155	2.330041	GGTGTTGAACCGCCAACG	59.670	61.111	0.00	0.00	46.89	4.10
265	266	0.250901	ACCACACTGGACCAAGATGC	60.251	55.000	0.00	0.00	40.96	3.91
296	297	1.327303	GGAGACAACCATGCCAAACA	58.673	50.000	0.00	0.00	0.00	2.83
345	346	3.135348	TCCAACAGATCATCATCCACCTC	59.865	47.826	0.00	0.00	0.00	3.85
448	449	0.383949	GTTCCGCTGCTTCCACAAAA	59.616	50.000	0.00	0.00	0.00	2.44
468	469	2.288030	CCGTCCTGTTAAAGACACGAGT	60.288	50.000	0.00	0.00	35.23	4.18
567	569	2.552315	CAAAGCGTGACAACCCAACTAT	59.448	45.455	0.00	0.00	0.00	2.12
620	625	2.751436	CCTCGGCCACACCCATTG	60.751	66.667	2.24	0.00	33.26	2.82
662	669	5.548056	AGGGAGAAACCAATTACAAGAGAGA	59.452	40.000	0.00	0.00	41.20	3.10
748	757	1.447643	CCGATGTGGGCTTAGGGAG	59.552	63.158	0.00	0.00	0.00	4.30
773	782	1.717194	TTCTGGTGTTTATCGTCCGC	58.283	50.000	0.00	0.00	0.00	5.54
986	996	3.236322	CGTTAAGCGCGTTGGTCA	58.764	55.556	8.43	0.00	0.00	4.02
1043	1053	0.620556	GGGGCCATGGATATCGATGT	59.379	55.000	18.40	0.00	31.27	3.06
1210	1220	2.682856	GTTCTCAAAGCCACACTCACAA	59.317	45.455	0.00	0.00	0.00	3.33
1374	1388	4.341806	TGTACGTACCTCTTGTTTCAAGGA	59.658	41.667	22.43	0.00	34.16	3.36
1375	1389	4.624015	TGTACGTACCTCTTGTTTCAAGG	58.376	43.478	22.43	0.00	36.21	3.61
1397	1411	3.966979	TGAACTCCAATGTGCCACATAT	58.033	40.909	11.38	0.00	37.97	1.78
1398	1412	3.431673	TGAACTCCAATGTGCCACATA	57.568	42.857	11.38	0.00	37.97	2.29
1399	1413	2.291209	TGAACTCCAATGTGCCACAT	57.709	45.000	4.03	4.03	41.31	3.21
1400	1414	2.291209	ATGAACTCCAATGTGCCACA	57.709	45.000	0.00	0.00	0.00	4.17
1408	1422	2.299867	GCCACAACCAATGAACTCCAAT	59.700	45.455	0.00	0.00	0.00	3.16
1421	1435	3.712881	GTCACTCGCGCCACAACC	61.713	66.667	0.00	0.00	0.00	3.77
1457	1471	4.704833	CCACCCTGTCCCACTGCG	62.705	72.222	0.00	0.00	0.00	5.18
1804	1826	7.068962	AGCATGATCAAATTGATGACCACATTA	59.931	33.333	13.82	0.00	37.20	1.90
1808	1830	5.041287	CAGCATGATCAAATTGATGACCAC	58.959	41.667	13.82	0.00	37.20	4.16
1816	1838	6.745907	CAGACTTGTACAGCATGATCAAATTG	59.254	38.462	0.00	0.65	39.69	2.32
1868	1890	7.389607	CGGATCAAAAAGGGAAACTCTTACTTA	59.610	37.037	0.00	0.00	0.00	2.24
1869	1891	6.206829	CGGATCAAAAAGGGAAACTCTTACTT	59.793	38.462	0.00	0.00	0.00	2.24
1870	1892	5.705905	CGGATCAAAAAGGGAAACTCTTACT	59.294	40.000	0.00	0.00	0.00	2.24
1871	1893	5.472478	ACGGATCAAAAAGGGAAACTCTTAC	59.528	40.000	0.00	0.00	0.00	2.34
1884	1906	7.940850	AGAAATTCAGAAGAACGGATCAAAAA	58.059	30.769	0.00	0.00	36.39	1.94
1913	1935	0.729140	GTACGCAAACCACTGCATGC	60.729	55.000	11.82	11.82	42.77	4.06
2001	2023	8.749696	AGCCCTCCTTATCTAAGAATCTTATT	57.250	34.615	2.87	0.00	35.33	1.40
2046	2069	3.509575	ACGCTTTCCTGCAAAATCCATTA	59.490	39.130	0.00	0.00	0.00	1.90
2138	2161	3.245016	TGTGCTTCTCTCAATTGGGATGT	60.245	43.478	8.85	0.00	0.00	3.06
2308	2332	4.846779	TTACCTTTGAACATTCTGGCAC	57.153	40.909	0.00	0.00	0.00	5.01
2310	2334	6.347644	GCAAAATTACCTTTGAACATTCTGGC	60.348	38.462	0.39	0.00	38.35	4.85
2318	2342	4.213270	GCAAGGGCAAAATTACCTTTGAAC	59.787	41.667	16.43	2.00	43.68	3.18
2348	2373	6.417635	CCGTGCTATTAATTTTATGCAACCAG	59.582	38.462	0.00	0.00	32.10	4.00
2396	2423	0.035036	TGCCCAACCGACAATTACGA	59.965	50.000	5.91	0.00	0.00	3.43
2410	2437	1.202758	CGCAATAGAACCCTATGCCCA	60.203	52.381	0.00	0.00	35.84	5.36
2449	2476	4.408921	CCCCACACCTTAGACATAGATGAA	59.591	45.833	0.00	0.00	0.00	2.57
2451	2478	3.495100	GCCCCACACCTTAGACATAGATG	60.495	52.174	0.00	0.00	0.00	2.90
2463	2490	3.953775	CAGGAACGCCCCACACCT	61.954	66.667	0.00	0.00	34.66	4.00
2470	2497	1.635663	CGTGATCAACAGGAACGCCC	61.636	60.000	0.00	0.00	36.62	6.13
2495	2522	2.600790	TGAACGGGTGAAAGAGAGGTA	58.399	47.619	0.00	0.00	0.00	3.08
2561	2588	4.504858	GGAAGAGTCGGTGTTGTATGATT	58.495	43.478	0.00	0.00	0.00	2.57
2667	2694	0.397816	ATTCACTCCCCTCCTCTCCG	60.398	60.000	0.00	0.00	0.00	4.63
2686	2713	1.551430	CCCGTGTATGTTGTCCCTACA	59.449	52.381	0.00	0.00	0.00	2.74
2750	2777	2.814336	GTTGGCTGATCCGAGAAAAGTT	59.186	45.455	0.00	0.00	37.80	2.66
2777	2804	2.011947	GTATTTGCCCTACCACCGAAC	58.988	52.381	0.00	0.00	0.00	3.95
2863	2890	2.111043	ACACCAACTCCTGCCGTG	59.889	61.111	0.00	0.00	0.00	4.94
2864	2891	1.978455	TTCACACCAACTCCTGCCGT	61.978	55.000	0.00	0.00	0.00	5.68
2878	2905	4.680237	CCGGTGCGCTCCTTCACA	62.680	66.667	24.75	0.00	35.04	3.58
2893	2920	2.124151	CCCATGGCCCTTCTTCCG	60.124	66.667	6.09	0.00	0.00	4.30
2916	2943	6.122277	TCTCCATTACCAAAAGCTCCTTATG	58.878	40.000	0.00	0.00	0.00	1.90
3008	3035	0.751643	TGGATCCGAGACGCAGATCA	60.752	55.000	7.39	0.00	38.52	2.92
3010	3037	0.316522	CATGGATCCGAGACGCAGAT	59.683	55.000	7.39	0.00	0.00	2.90
3016	3043	1.869767	GCATGTTCATGGATCCGAGAC	59.130	52.381	7.39	3.95	0.00	3.36
3065	3092	1.302431	CGCACCCACCAACTCATCA	60.302	57.895	0.00	0.00	0.00	3.07
3171	3198	1.951209	TCATCTCCCTAGCCAACACA	58.049	50.000	0.00	0.00	0.00	3.72
3172	3199	2.027192	TGTTCATCTCCCTAGCCAACAC	60.027	50.000	0.00	0.00	0.00	3.32
3188	3215	1.881973	GCTTGCTCATGTCCTTGTTCA	59.118	47.619	0.00	0.00	0.00	3.18
3202	3229	0.397941	TCTACAGTTGCCTGCTTGCT	59.602	50.000	0.00	0.00	42.81	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.