AutoCloner

Multiple sequence alignment - TraesCS2B01G067800

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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	TraesCS2B01G067800	chr2B	100.000	3106	0	0	1	3106	34452977	34456082	0.000000e+00	5736
1	TraesCS2B01G067800	chr2B	94.094	2540	123	10	580	3103	34475048	34477576	0.000000e+00	3834
2	TraesCS2B01G067800	chr2B	96.334	2073	70	4	580	2651	34434357	34436424	0.000000e+00	3402
3	TraesCS2B01G067800	chr2B	93.519	864	20	6	1	841	34538494	34539344	0.000000e+00	1253
4	TraesCS2B01G067800	chr2B	95.491	377	15	1	204	580	34474637	34475011	4.430000e-168	601
5	TraesCS2B01G067800	chr2B	92.437	238	13	4	2869	3103	34441869	34442104	4.960000e-88	335
6	TraesCS2B01G067800	chr2B	94.318	176	7	2	405	580	34434148	34434320	1.840000e-67	267
7	TraesCS2B01G067800	chr2B	82.160	213	33	4	2882	3090	34418385	34418596	8.850000e-41	178
8	TraesCS2B01G067800	chrUn	89.906	1803	160	15	631	2426	210798683	210800470	0.000000e+00	2302
9	TraesCS2B01G067800	chrUn	89.739	1803	163	15	631	2426	146913923	146912136	0.000000e+00	2285
10	TraesCS2B01G067800	chrUn	89.739	1803	163	16	631	2426	154084123	154082336	0.000000e+00	2285
11	TraesCS2B01G067800	chrUn	89.773	968	88	5	2143	3106	154145128	154144168	0.000000e+00	1229
12	TraesCS2B01G067800	chr2A	89.850	1803	161	15	631	2426	22939571	22937784	0.000000e+00	2296
13	TraesCS2B01G067800	chr2A	89.795	1803	162	15	631	2426	22651377	22653164	0.000000e+00	2290
14	TraesCS2B01G067800	chr2A	89.739	1803	163	15	631	2426	22618995	22620782	0.000000e+00	2285
15	TraesCS2B01G067800	chr2A	89.739	1803	162	16	631	2426	22802482	22800696	0.000000e+00	2283
16	TraesCS2B01G067800	chr2A	77.733	247	42	8	2856	3098	22571136	22571373	4.180000e-29	139
17	TraesCS2B01G067800	chr2D	79.012	243	43	5	2859	3098	21055196	21055433	3.210000e-35	159

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	TraesCS2B01G067800	chr2B	34452977	34456082	3105	False	5736.0	5736	100.0000	1	3106	1	chr2B.!!$F3	3105
1	TraesCS2B01G067800	chr2B	34474637	34477576	2939	False	2217.5	3834	94.7925	204	3103	2	chr2B.!!$F6	2899
2	TraesCS2B01G067800	chr2B	34434148	34436424	2276	False	1834.5	3402	95.3260	405	2651	2	chr2B.!!$F5	2246
3	TraesCS2B01G067800	chr2B	34538494	34539344	850	False	1253.0	1253	93.5190	1	841	1	chr2B.!!$F4	840
4	TraesCS2B01G067800	chrUn	210798683	210800470	1787	False	2302.0	2302	89.9060	631	2426	1	chrUn.!!$F1	1795
5	TraesCS2B01G067800	chrUn	146912136	146913923	1787	True	2285.0	2285	89.7390	631	2426	1	chrUn.!!$R1	1795
6	TraesCS2B01G067800	chrUn	154082336	154084123	1787	True	2285.0	2285	89.7390	631	2426	1	chrUn.!!$R2	1795
7	TraesCS2B01G067800	chrUn	154144168	154145128	960	True	1229.0	1229	89.7730	2143	3106	1	chrUn.!!$R3	963
8	TraesCS2B01G067800	chr2A	22937784	22939571	1787	True	2296.0	2296	89.8500	631	2426	1	chr2A.!!$R2	1795
9	TraesCS2B01G067800	chr2A	22651377	22653164	1787	False	2290.0	2290	89.7950	631	2426	1	chr2A.!!$F3	1795
10	TraesCS2B01G067800	chr2A	22618995	22620782	1787	False	2285.0	2285	89.7390	631	2426	1	chr2A.!!$F2	1795
11	TraesCS2B01G067800	chr2A	22800696	22802482	1786	True	2283.0	2283	89.7390	631	2426	1	chr2A.!!$R1	1795

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
174	198	0.114168	TTGGGCTGCCACCATAGTTT	59.886	50.0	22.05	0.0	37.93	2.66	F
175	199	0.114168	TGGGCTGCCACCATAGTTTT	59.886	50.0	22.05	0.0	31.83	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1778	1859	0.609957	CAGGCACATCCTCAAAGCCA	60.610	55.000	0.0	0.0	45.52	4.75	R
2189	2270	8.414003	ACATTATCGTACATAACTCACAGACAT	58.586	33.333	0.0	0.0	0.00	3.06	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
31	32	8.038944	TCACCAGGATATACAGTAGTGAAAAAC	58.961	37.037	4.09	0.00	30.56	2.43
35	36	8.969267	CAGGATATACAGTAGTGAAAAACGATC	58.031	37.037	4.09	0.00	0.00	3.69
36	37	8.142551	AGGATATACAGTAGTGAAAAACGATCC	58.857	37.037	4.09	6.46	0.00	3.36
48	49	3.872728	CGATCCGGTGTCGCTCGA	61.873	66.667	16.49	0.00	40.16	4.04
53	54	1.226974	CCGGTGTCGCTCGATCATT	60.227	57.895	0.00	0.00	34.56	2.57
73	74	2.055838	TGAACGTGCAATGTACGACTC	58.944	47.619	28.72	22.22	43.82	3.36
74	75	1.057285	GAACGTGCAATGTACGACTCG	59.943	52.381	28.72	3.81	43.82	4.18
84	85	0.731855	GTACGACTCGGACACCTTGC	60.732	60.000	9.04	0.00	40.85	4.01
173	197	0.611896	GTTGGGCTGCCACCATAGTT	60.612	55.000	22.05	0.00	37.93	2.24
174	198	0.114168	TTGGGCTGCCACCATAGTTT	59.886	50.000	22.05	0.00	37.93	2.66
175	199	0.114168	TGGGCTGCCACCATAGTTTT	59.886	50.000	22.05	0.00	31.83	2.43
176	200	1.266178	GGGCTGCCACCATAGTTTTT	58.734	50.000	22.05	0.00	0.00	1.94
177	201	1.204704	GGGCTGCCACCATAGTTTTTC	59.795	52.381	22.05	0.00	0.00	2.29
178	202	1.204704	GGCTGCCACCATAGTTTTTCC	59.795	52.381	15.17	0.00	0.00	3.13
189	213	5.123344	ACCATAGTTTTTCCGCAAGATGTAC	59.877	40.000	0.00	0.00	43.02	2.90
190	214	5.123186	CCATAGTTTTTCCGCAAGATGTACA	59.877	40.000	0.00	0.00	43.02	2.90
191	215	4.749245	AGTTTTTCCGCAAGATGTACAG	57.251	40.909	0.33	0.00	43.02	2.74
193	217	2.107950	TTTCCGCAAGATGTACAGGG	57.892	50.000	0.33	0.00	43.02	4.45
194	218	1.271856	TTCCGCAAGATGTACAGGGA	58.728	50.000	0.33	0.00	43.02	4.20
195	219	1.271856	TCCGCAAGATGTACAGGGAA	58.728	50.000	0.33	0.00	43.02	3.97
196	220	1.837439	TCCGCAAGATGTACAGGGAAT	59.163	47.619	0.33	0.00	43.02	3.01
197	221	1.942657	CCGCAAGATGTACAGGGAATG	59.057	52.381	0.33	0.00	43.02	2.67
198	222	1.331756	CGCAAGATGTACAGGGAATGC	59.668	52.381	0.33	6.75	43.02	3.56
1102	1175	1.544246	ACGATGACTTGTCGATGGTGA	59.456	47.619	2.28	0.00	41.40	4.02
1173	1246	0.600255	CTGAGAAGGCACGTCGGTTT	60.600	55.000	0.00	0.00	42.91	3.27
1477	1550	6.318396	TGTGTTGCACTGCATATATGTGTTAT	59.682	34.615	14.14	0.00	38.76	1.89
1778	1859	4.704833	AGCGCCGCAACCATCACT	62.705	61.111	13.36	0.00	0.00	3.41
2150	2231	7.281774	CCTAATCATACATATGCACAATCCTCC	59.718	40.741	1.58	0.00	33.76	4.30
2189	2270	9.434275	CCCCATGTCCTATGTATAGTTCATATA	57.566	37.037	0.00	0.00	0.00	0.86
2340	2426	9.985730	TTCATGAAGCTTTCAAATGTCTAAAAT	57.014	25.926	3.38	0.00	43.95	1.82
2426	2512	9.463902	TGGGTCTTTTCGTTATTTATTGGAATA	57.536	29.630	0.00	0.00	0.00	1.75
2555	2641	5.711698	AGGAAACTCCAAGTTCCCAAAATA	58.288	37.500	0.00	0.00	34.73	1.40
2562	2648	5.837829	TCCAAGTTCCCAAAATAGCCTAAT	58.162	37.500	0.00	0.00	0.00	1.73
2566	2652	5.022787	AGTTCCCAAAATAGCCTAATGCAA	58.977	37.500	0.00	0.00	44.83	4.08
2615	2701	8.097038	GGCTATGACAAAGGAGACATCATTATA	58.903	37.037	0.00	0.00	32.42	0.98
2661	2747	7.277760	TGTGATGTTTATTGAGATCGTAGGTTG	59.722	37.037	0.00	0.00	0.00	3.77
2664	2750	9.692749	GATGTTTATTGAGATCGTAGGTTGATA	57.307	33.333	0.00	0.00	0.00	2.15
2699	2785	6.801539	TTTTCATGTATCTGGTCAACTGAC	57.198	37.500	0.98	0.98	44.04	3.51
2770	2856	7.865706	ACTTTCCGTATGAAATCAAGCTTAT	57.134	32.000	0.00	0.00	41.96	1.73
2824	2910	9.533253	AATATGTATGCAAAGCAATTTTAGGAC	57.467	29.630	0.00	0.00	43.62	3.85
2825	2911	6.338214	TGTATGCAAAGCAATTTTAGGACA	57.662	33.333	0.00	0.00	43.62	4.02
2832	2918	6.074142	GCAAAGCAATTTTAGGACAAACAGAG	60.074	38.462	0.00	0.00	0.00	3.35
2903	2989	5.218139	GGAACGGTAAGAATATACGTGGAG	58.782	45.833	0.00	0.00	37.87	3.86
3103	3193	4.253685	AGAATTGTACCACTGGAATCACG	58.746	43.478	0.71	0.00	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	6.062749	TCACTACTGTATATCCTGGTGACTC	58.937	44.000	0.00	0.00	0.00	3.36
10	11	8.142551	GGATCGTTTTTCACTACTGTATATCCT	58.857	37.037	0.00	0.00	0.00	3.24
31	32	3.182472	ATCGAGCGACACCGGATCG	62.182	63.158	22.93	22.93	42.55	3.69
35	36	1.226974	AATGATCGAGCGACACCGG	60.227	57.895	0.00	0.00	36.06	5.28
36	37	0.525455	TCAATGATCGAGCGACACCG	60.525	55.000	0.00	0.00	39.16	4.94
53	54	2.055838	GAGTCGTACATTGCACGTTCA	58.944	47.619	9.13	0.00	40.27	3.18
73	74	2.738521	CTCCACGCAAGGTGTCCG	60.739	66.667	0.00	0.00	45.52	4.79
74	75	3.050275	GCTCCACGCAAGGTGTCC	61.050	66.667	0.00	0.00	45.52	4.02
91	92	1.228063	AGCAGGAAGCACTGGTGTG	60.228	57.895	6.93	0.00	46.46	3.82
169	193	4.693566	CCTGTACATCTTGCGGAAAAACTA	59.306	41.667	0.00	0.00	0.00	2.24
173	197	2.039216	TCCCTGTACATCTTGCGGAAAA	59.961	45.455	0.00	0.00	0.00	2.29
174	198	1.626321	TCCCTGTACATCTTGCGGAAA	59.374	47.619	0.00	0.00	0.00	3.13
175	199	1.271856	TCCCTGTACATCTTGCGGAA	58.728	50.000	0.00	0.00	0.00	4.30
176	200	1.271856	TTCCCTGTACATCTTGCGGA	58.728	50.000	0.00	0.00	0.00	5.54
177	201	1.942657	CATTCCCTGTACATCTTGCGG	59.057	52.381	0.00	0.00	0.00	5.69
178	202	1.331756	GCATTCCCTGTACATCTTGCG	59.668	52.381	0.00	0.00	0.00	4.85
971	1044	2.315176	AGGCACCAAACTGCAACAATA	58.685	42.857	0.00	0.00	39.08	1.90
1102	1175	3.552875	CCATCCAGTTCTCATGCTTCAT	58.447	45.455	0.00	0.00	0.00	2.57
1173	1246	5.709631	TCCGACATTGGATTTGAAAATCTCA	59.290	36.000	13.86	8.58	43.33	3.27
1332	1405	8.267620	TCATATTCTCATACCTGAATCCTGTT	57.732	34.615	0.00	0.00	35.01	3.16
1501	1582	6.624423	CAGCAGCCTAGAAATAATTGTGTTT	58.376	36.000	0.00	0.00	0.00	2.83
1778	1859	0.609957	CAGGCACATCCTCAAAGCCA	60.610	55.000	0.00	0.00	45.52	4.75
2189	2270	8.414003	ACATTATCGTACATAACTCACAGACAT	58.586	33.333	0.00	0.00	0.00	3.06
2513	2599	5.787953	TCCTCAAAATCTTGTTGCAATGA	57.212	34.783	0.59	2.12	33.94	2.57
2544	2630	5.127031	TCTTGCATTAGGCTATTTTGGGAAC	59.873	40.000	0.00	0.00	45.15	3.62
2555	2641	2.887151	AAGGTGTCTTGCATTAGGCT	57.113	45.000	0.00	0.00	45.15	4.58
2679	2765	4.283212	TGTGTCAGTTGACCAGATACATGA	59.717	41.667	9.60	0.00	44.15	3.07
2690	2776	5.473504	AGAACCCATAAATGTGTCAGTTGAC	59.526	40.000	5.33	5.33	44.97	3.18
2770	2856	7.882791	TGATTGTTGCAGAACTAGGAAATTCTA	59.117	33.333	0.00	0.00	33.35	2.10
2777	2863	6.899393	ATTTTGATTGTTGCAGAACTAGGA	57.101	33.333	0.00	0.00	32.79	2.94
2824	2910	6.250344	TGCAAGAAGATGATTCTCTGTTTG	57.750	37.500	0.00	0.00	0.00	2.93
2825	2911	7.463961	AATGCAAGAAGATGATTCTCTGTTT	57.536	32.000	0.00	0.00	0.00	2.83
2878	2964	5.302568	TCCACGTATATTCTTACCGTTCCAT	59.697	40.000	0.00	0.00	0.00	3.41
2983	3069	6.072112	AGTGTTCTTACAACATGCGATTTT	57.928	33.333	0.00	0.00	35.69	1.82
2985	3071	6.795098	TTAGTGTTCTTACAACATGCGATT	57.205	33.333	0.00	0.00	35.69	3.34
2986	3072	6.795098	TTTAGTGTTCTTACAACATGCGAT	57.205	33.333	0.00	0.00	35.69	4.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.