AutoCloner

Multiple sequence alignment - TraesCS7B01G017600

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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	TraesCS7B01G017600	chr7B	100.000	2641	0	0	1	2641	15017130	15019770	0.000000e+00	4878
1	TraesCS7B01G017600	chr7B	95.506	1335	39	11	794	2122	15298111	15299430	0.000000e+00	2113
2	TraesCS7B01G017600	chr7B	93.252	741	36	8	4	742	15069622	15070350	0.000000e+00	1079
3	TraesCS7B01G017600	chr7B	94.713	435	21	2	1044	1476	14980778	14981212	0.000000e+00	675
4	TraesCS7B01G017600	chr7B	87.815	476	41	9	2174	2641	15299438	15299904	2.310000e-150	542
5	TraesCS7B01G017600	chr7B	95.833	288	12	0	2354	2641	15071023	15071310	1.430000e-127	466
6	TraesCS7B01G017600	chr7B	91.401	314	24	3	805	1117	15070346	15070657	6.760000e-116	427
7	TraesCS7B01G017600	chr7B	85.427	199	27	2	2444	2641	15268869	15269066	3.450000e-49	206
8	TraesCS7B01G017600	chr7B	91.729	133	11	0	1993	2125	286566747	286566615	4.490000e-43	185
9	TraesCS7B01G017600	chr7B	80.769	234	32	11	2396	2623	14778716	14778490	1.260000e-38	171
10	TraesCS7B01G017600	chr7D	86.625	2243	195	72	1	2204	72215316	72217492	0.000000e+00	2383
11	TraesCS7B01G017600	chr7D	82.987	1346	153	45	767	2088	73117429	73116136	0.000000e+00	1147
12	TraesCS7B01G017600	chr7D	89.306	720	45	20	1038	1746	71864527	71863829	0.000000e+00	874
13	TraesCS7B01G017600	chr7D	93.274	446	27	2	1056	1501	58863633	58863191	0.000000e+00	654
14	TraesCS7B01G017600	chr7D	76.471	629	103	32	1761	2359	71863450	71862837	1.540000e-77	300
15	TraesCS7B01G017600	chr7A	86.441	2124	196	61	2	2088	77193858	77195926	0.000000e+00	2242
16	TraesCS7B01G017600	chr7A	88.932	768	58	9	1875	2636	77196421	77197167	0.000000e+00	922
17	TraesCS7B01G017600	chrUn	84.753	1174	136	30	1056	2206	82605062	82603909	0.000000e+00	1136
18	TraesCS7B01G017600	chrUn	84.153	1180	117	39	1056	2206	84317792	84316654	0.000000e+00	1079
19	TraesCS7B01G017600	chrUn	83.566	286	39	7	1833	2113	82602351	82602069	7.250000e-66	261
20	TraesCS7B01G017600	chrUn	86.638	232	27	4	1977	2206	82566818	82567047	1.210000e-63	254
21	TraesCS7B01G017600	chr4A	95.294	425	20	0	1043	1467	675854930	675855354	0.000000e+00	675
22	TraesCS7B01G017600	chr6B	87.097	217	25	2	1972	2185	141086151	141085935	2.630000e-60	243
23	TraesCS7B01G017600	chr3D	93.671	79	5	0	1990	2068	189780127	189780205	4.620000e-23	119

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	TraesCS7B01G017600	chr7B	15017130	15019770	2640	False	4878.000000	4878	100.000000	1	2641	1	chr7B.!!$F2	2640
1	TraesCS7B01G017600	chr7B	15298111	15299904	1793	False	1327.500000	2113	91.660500	794	2641	2	chr7B.!!$F5	1847
2	TraesCS7B01G017600	chr7B	15069622	15071310	1688	False	657.333333	1079	93.495333	4	2641	3	chr7B.!!$F4	2637
3	TraesCS7B01G017600	chr7D	72215316	72217492	2176	False	2383.000000	2383	86.625000	1	2204	1	chr7D.!!$F1	2203
4	TraesCS7B01G017600	chr7D	73116136	73117429	1293	True	1147.000000	1147	82.987000	767	2088	1	chr7D.!!$R2	1321
5	TraesCS7B01G017600	chr7D	71862837	71864527	1690	True	587.000000	874	82.888500	1038	2359	2	chr7D.!!$R3	1321
6	TraesCS7B01G017600	chr7A	77193858	77197167	3309	False	1582.000000	2242	87.686500	2	2636	2	chr7A.!!$F1	2634
7	TraesCS7B01G017600	chrUn	84316654	84317792	1138	True	1079.000000	1079	84.153000	1056	2206	1	chrUn.!!$R1	1150
8	TraesCS7B01G017600	chrUn	82602069	82605062	2993	True	698.500000	1136	84.159500	1056	2206	2	chrUn.!!$R2	1150

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
138	141	0.179020	CACTTCCTTGGTGCTGGACA	60.179	55.0	0.77	0.0	31.24	4.02	F
860	876	0.533755	CTGATCCAACGGCTCATCCC	60.534	60.0	0.00	0.0	27.07	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1405	1439	0.033796	CCTTGGGCATGATGGTGACT	60.034	55.0	0.00	0.00	0.0	3.41	R
2613	4412	0.532573	AGATCTGTACTGTGGCACCG	59.467	55.0	16.26	11.76	0.0	4.94	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
39	40	2.461300	TCGGAGAAGGTCATGATCCT	57.539	50.000	1.24	6.68	36.81	3.24
83	86	1.003233	GTCTCAACGTCATTTCCCCCT	59.997	52.381	0.00	0.00	0.00	4.79
116	119	3.121944	CGTCTTGAAGTTCTTGATCCACG	59.878	47.826	4.17	0.03	0.00	4.94
138	141	0.179020	CACTTCCTTGGTGCTGGACA	60.179	55.000	0.77	0.00	31.24	4.02
172	176	1.304464	TGTGGTTGGTGGTGTTGCA	60.304	52.632	0.00	0.00	0.00	4.08
251	255	2.251893	GTCGACCGATTGACTTGTCTC	58.748	52.381	3.51	0.00	36.42	3.36
305	310	2.358125	CCGGTGGCAACGATGACA	60.358	61.111	29.07	0.00	44.25	3.58
367	372	6.693113	GCTTCTTTCTCCTACAAAACTTGTTG	59.307	38.462	0.00	0.00	42.22	3.33
387	393	3.151022	GTCAGAGCCGCCTAGCCT	61.151	66.667	0.00	0.00	0.00	4.58
491	499	3.192844	CCTGGTGAAGTTAGAGTCGCTTA	59.807	47.826	0.00	0.00	0.00	3.09
504	512	0.818296	TCGCTTACTCAGGGAGAAGC	59.182	55.000	14.73	14.73	39.52	3.86
507	516	1.204941	GCTTACTCAGGGAGAAGCGAA	59.795	52.381	0.00	0.00	35.23	4.70
565	574	2.202824	CGTCGGTGGTGTGTGTGT	60.203	61.111	0.00	0.00	0.00	3.72
567	576	2.177580	GTCGGTGGTGTGTGTGTGG	61.178	63.158	0.00	0.00	0.00	4.17
568	577	2.899838	CGGTGGTGTGTGTGTGGG	60.900	66.667	0.00	0.00	0.00	4.61
569	578	2.274104	GGTGGTGTGTGTGTGGGT	59.726	61.111	0.00	0.00	0.00	4.51
570	579	1.822186	GGTGGTGTGTGTGTGGGTC	60.822	63.158	0.00	0.00	0.00	4.46
613	622	2.774234	CAGGGTTCCCTATCATGTGAGT	59.226	50.000	10.33	0.00	34.60	3.41
635	644	9.047371	TGAGTGTGTTCTAATTATTTTCGTCAA	57.953	29.630	0.00	0.00	0.00	3.18
636	645	9.872757	GAGTGTGTTCTAATTATTTTCGTCAAA	57.127	29.630	0.00	0.00	0.00	2.69
764	779	3.064324	GGCCCGCTCAAAGCACAT	61.064	61.111	0.00	0.00	42.58	3.21
809	824	0.548031	ATCATGATCCGTGGCCAACT	59.452	50.000	7.24	0.00	0.00	3.16
825	840	2.602933	CCAACTCGCACAAACACATCTG	60.603	50.000	0.00	0.00	0.00	2.90
829	844	1.608109	TCGCACAAACACATCTGCAAT	59.392	42.857	0.00	0.00	0.00	3.56
860	876	0.533755	CTGATCCAACGGCTCATCCC	60.534	60.000	0.00	0.00	27.07	3.85
1222	1256	0.539986	GGGAGATCCGCAAGTACCAA	59.460	55.000	0.00	0.00	36.71	3.67
1502	1545	1.539712	GCCGGTAATACTGCTGGGTAC	60.540	57.143	1.90	0.00	34.35	3.34
1576	1628	4.700268	TGTTGGTGTTGATATGATGTGC	57.300	40.909	0.00	0.00	0.00	4.57
1623	1675	4.797800	TCGAATGAAATGGCAATGGAAA	57.202	36.364	0.00	0.00	0.00	3.13
1624	1676	5.144692	TCGAATGAAATGGCAATGGAAAA	57.855	34.783	0.00	0.00	0.00	2.29
1667	1736	5.626142	TGCTAATTTTGTCTTCCAGTACCA	58.374	37.500	0.00	0.00	0.00	3.25
1864	2672	4.283212	GGGATTTGGTGAACTCATTTTGGA	59.717	41.667	0.00	0.00	0.00	3.53
1964	3138	7.423199	ACATGTGATGTGATTCTGAATTATGC	58.577	34.615	4.11	0.00	43.01	3.14
2142	3346	5.971792	GTCTTCATGATGATTCTTGTGCATG	59.028	40.000	13.82	0.00	35.63	4.06
2180	3384	9.453325	GTTGATAATTACTGTAGAGACTACAGC	57.547	37.037	27.77	15.93	46.46	4.40
2229	3968	7.118496	AGATATAGTGGGCATTATAGCAGAC	57.882	40.000	0.00	0.00	35.83	3.51
2253	3998	5.934625	CACAAGTCTATAGCAGGACAAACTT	59.065	40.000	0.00	0.00	35.18	2.66
2254	3999	7.097192	CACAAGTCTATAGCAGGACAAACTTA	58.903	38.462	0.00	0.00	35.18	2.24
2255	4000	7.063544	CACAAGTCTATAGCAGGACAAACTTAC	59.936	40.741	0.00	0.00	35.18	2.34
2256	4001	7.038941	ACAAGTCTATAGCAGGACAAACTTACT	60.039	37.037	0.00	0.00	35.18	2.24
2257	4002	8.467598	CAAGTCTATAGCAGGACAAACTTACTA	58.532	37.037	0.00	0.00	35.18	1.82
2258	4003	7.998580	AGTCTATAGCAGGACAAACTTACTAC	58.001	38.462	0.00	0.00	35.18	2.73
2288	4033	7.849804	TGAAGCTCTTATTTTCTGGTATCAC	57.150	36.000	0.00	0.00	0.00	3.06
2328	4073	5.182001	ACTGACAGAATGAGTAATTTGGTGC	59.818	40.000	10.08	0.00	39.69	5.01
2417	4209	6.346477	ACAGCATCTCTGAGTAAACTTGTA	57.654	37.500	4.32	0.00	45.72	2.41
2424	4223	6.736123	TCTCTGAGTAAACTTGTACTGTGAC	58.264	40.000	4.32	0.00	34.40	3.67
2434	4233	1.207089	TGTACTGTGACCAGGCTATGC	59.793	52.381	0.00	0.00	43.36	3.14
2436	4235	1.257750	ACTGTGACCAGGCTATGCGA	61.258	55.000	0.00	0.00	43.36	5.10
2440	4239	0.104855	TGACCAGGCTATGCGATCAC	59.895	55.000	0.00	0.00	0.00	3.06
2613	4412	0.968405	TTGCCCTTCACAATCTTGCC	59.032	50.000	0.00	0.00	0.00	4.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	2.706190	CCGAAGAGATTAATCCAGGGGT	59.294	50.000	11.92	0.00	0.00	4.95
28	29	2.969238	CCGCGCAGGATCATGACC	60.969	66.667	12.39	1.52	45.00	4.02
83	86	2.294074	CTTCAAGACGACACCCCAAAA	58.706	47.619	0.00	0.00	0.00	2.44
138	141	0.674581	CACACCACACGATCAGGCAT	60.675	55.000	0.00	0.00	0.00	4.40
204	208	1.200519	GACATGCCACTACCCCACTA	58.799	55.000	0.00	0.00	0.00	2.74
241	245	4.823442	TGACTTTACCGTAGAGACAAGTCA	59.177	41.667	14.60	14.60	44.86	3.41
251	255	3.851976	ACAGCTCTGACTTTACCGTAG	57.148	47.619	3.60	0.00	0.00	3.51
288	293	1.745115	ATGTCATCGTTGCCACCGG	60.745	57.895	0.00	0.00	0.00	5.28
367	372	2.409651	CTAGGCGGCTCTGACGAC	59.590	66.667	17.67	0.00	46.15	4.34
491	499	0.892063	GTCTTCGCTTCTCCCTGAGT	59.108	55.000	0.00	0.00	0.00	3.41
504	512	0.388134	ACGGGTTGTCATCGTCTTCG	60.388	55.000	0.00	0.00	38.55	3.79
507	516	0.815734	CCTACGGGTTGTCATCGTCT	59.184	55.000	0.00	0.00	38.19	4.18
535	544	2.087009	CCGACGAGAGGAACAACGC	61.087	63.158	0.00	0.00	0.00	4.84
565	574	1.456705	GGCAACCCACAAAGACCCA	60.457	57.895	0.00	0.00	0.00	4.51
567	576	4.268720	TGGCAACCCACAAAGACC	57.731	55.556	0.00	0.00	35.79	3.85
764	779	5.479306	GTGGAGTAGCATTTCTCACTTGTA	58.521	41.667	0.00	0.00	32.93	2.41
809	824	1.020437	TTGCAGATGTGTTTGTGCGA	58.980	45.000	0.00	0.00	38.84	5.10
825	840	1.031571	TCAGCCGGAATGGACATTGC	61.032	55.000	5.05	4.36	42.00	3.56
829	844	1.271127	TGGATCAGCCGGAATGGACA	61.271	55.000	5.05	0.50	42.00	4.02
1405	1439	0.033796	CCTTGGGCATGATGGTGACT	60.034	55.000	0.00	0.00	0.00	3.41
1502	1545	1.000955	AGACAAGAACAGCCACTACGG	59.999	52.381	0.00	0.00	38.11	4.02
1503	1546	2.329379	GAGACAAGAACAGCCACTACG	58.671	52.381	0.00	0.00	0.00	3.51
1504	1547	2.288273	ACGAGACAAGAACAGCCACTAC	60.288	50.000	0.00	0.00	0.00	2.73
1505	1548	1.961394	ACGAGACAAGAACAGCCACTA	59.039	47.619	0.00	0.00	0.00	2.74
1506	1549	0.753262	ACGAGACAAGAACAGCCACT	59.247	50.000	0.00	0.00	0.00	4.00
1509	1552	1.996191	GATCACGAGACAAGAACAGCC	59.004	52.381	0.00	0.00	0.00	4.85
1576	1628	1.681793	ACGATCCATAGGAACAGACGG	59.318	52.381	0.00	0.00	34.34	4.79
1623	1675	7.458409	AGCATCACATGATAACTGAACTTTT	57.542	32.000	0.00	0.00	32.63	2.27
1624	1676	8.565896	TTAGCATCACATGATAACTGAACTTT	57.434	30.769	0.00	0.00	36.34	2.66
1667	1736	3.562973	CCGCAGAATAACAGAGCAATGAT	59.437	43.478	0.00	0.00	0.00	2.45
1828	2288	3.181448	ACCAAATCCCTGTACAAACGTCT	60.181	43.478	0.00	0.00	0.00	4.18
1829	2289	3.058501	CACCAAATCCCTGTACAAACGTC	60.059	47.826	0.00	0.00	0.00	4.34
1864	2672	3.930336	TCACATCGAACAGAGCAGAAAT	58.070	40.909	0.00	0.00	0.00	2.17
1964	3138	1.154908	CAAGTTTCGAACGACGGCG	60.155	57.895	10.39	10.39	42.82	6.46
2142	3346	9.846248	ACAGTAATTATCAACTGCAAATTTCTC	57.154	29.630	6.09	0.00	45.65	2.87
2206	3928	6.758886	GTGTCTGCTATAATGCCCACTATATC	59.241	42.308	0.00	0.00	0.00	1.63
2209	3931	4.347876	TGTGTCTGCTATAATGCCCACTAT	59.652	41.667	0.00	0.00	0.00	2.12
2229	3968	5.482908	AGTTTGTCCTGCTATAGACTTGTG	58.517	41.667	3.21	0.00	34.02	3.33
2241	3986	7.769220	TCATAGTAGTAGTAAGTTTGTCCTGC	58.231	38.462	0.00	0.00	0.00	4.85
2257	4002	8.763601	ACCAGAAAATAAGAGCTTCATAGTAGT	58.236	33.333	0.00	0.00	0.00	2.73
2282	4027	7.813148	TCAGTTAAAAGCTGTGTAGAGTGATAC	59.187	37.037	0.00	0.00	35.60	2.24
2288	4033	6.216569	TCTGTCAGTTAAAAGCTGTGTAGAG	58.783	40.000	0.00	0.00	35.60	2.43
2328	4073	0.946221	GTCAGAGACAGTGTTGCCGG	60.946	60.000	0.00	0.00	32.09	6.13
2398	4190	7.327275	GTCACAGTACAAGTTTACTCAGAGATG	59.673	40.741	3.79	0.00	29.30	2.90
2417	4209	1.219124	CGCATAGCCTGGTCACAGT	59.781	57.895	0.00	0.00	43.36	3.55
2424	4223	1.665916	CCGTGATCGCATAGCCTGG	60.666	63.158	7.12	0.00	35.54	4.45
2434	4233	1.577328	AACTTTGCCAGCCGTGATCG	61.577	55.000	0.00	0.00	0.00	3.69
2436	4235	1.039856	AAAACTTTGCCAGCCGTGAT	58.960	45.000	0.00	0.00	0.00	3.06
2440	4239	1.860326	CTTTCAAAACTTTGCCAGCCG	59.140	47.619	0.00	0.00	38.05	5.52
2482	4281	1.073964	CTGCAGTGATGAGTGGTTCG	58.926	55.000	5.25	0.00	0.00	3.95
2591	4390	2.224018	GCAAGATTGTGAAGGGCAACAA	60.224	45.455	0.00	0.00	39.74	2.83
2613	4412	0.532573	AGATCTGTACTGTGGCACCG	59.467	55.000	16.26	11.76	0.00	4.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.