AutoCloner

Multiple sequence alignment - TraesCS6B01G347300

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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	TraesCS6B01G347300	chr6B	100.000	2948	0	0	1	2948	611503331	611506278	0.000000e+00	5445.0
1	TraesCS6B01G347300	chr6B	95.122	697	24	3	2262	2948	37325892	37325196	0.000000e+00	1090.0
2	TraesCS6B01G347300	chr6B	92.672	696	32	13	2265	2948	23603979	23603291	0.000000e+00	985.0
3	TraesCS6B01G347300	chr6B	96.315	597	20	2	2354	2948	37267162	37266566	0.000000e+00	979.0
4	TraesCS6B01G347300	chr6D	93.097	2289	117	23	2	2265	407526238	407528510	0.000000e+00	3314.0
5	TraesCS6B01G347300	chr6A	91.827	2239	141	26	20	2231	553058032	553060255	0.000000e+00	3083.0
6	TraesCS6B01G347300	chr6A	92.204	372	23	4	1833	2200	553064991	553065360	3.370000e-144	521.0
7	TraesCS6B01G347300	chr2B	95.833	696	18	5	2263	2948	766593784	766593090	0.000000e+00	1114.0
8	TraesCS6B01G347300	chr2B	96.812	596	15	2	2353	2948	711717571	711716980	0.000000e+00	992.0
9	TraesCS6B01G347300	chr2B	89.655	145	4	2	2266	2400	711717720	711717577	1.090000e-39	174.0
10	TraesCS6B01G347300	chr1B	95.565	699	21	1	2260	2948	49320827	49321525	0.000000e+00	1110.0
11	TraesCS6B01G347300	chr1B	94.684	696	20	7	2266	2948	551733233	551733924	0.000000e+00	1064.0
12	TraesCS6B01G347300	chr1B	92.453	53	4	0	2264	2316	565988899	565988847	3.150000e-10	76.8
13	TraesCS6B01G347300	chr3B	94.958	714	21	4	2249	2948	822864830	822865542	0.000000e+00	1105.0
14	TraesCS6B01G347300	chr3B	95.415	698	21	3	2262	2948	92126096	92126793	0.000000e+00	1101.0
15	TraesCS6B01G347300	chr4B	95.540	695	20	2	2265	2948	42015585	42014891	0.000000e+00	1101.0
16	TraesCS6B01G347300	chr5B	94.714	700	24	2	2262	2948	32130563	32131262	0.000000e+00	1075.0
17	TraesCS6B01G347300	chr5B	92.657	286	10	2	2258	2532	511710956	511710671	4.580000e-108	401.0

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	TraesCS6B01G347300	chr6B	611503331	611506278	2947	False	5445	5445	100.0000	1	2948	1	chr6B.!!$F1	2947
1	TraesCS6B01G347300	chr6B	37325196	37325892	696	True	1090	1090	95.1220	2262	2948	1	chr6B.!!$R3	686
2	TraesCS6B01G347300	chr6B	23603291	23603979	688	True	985	985	92.6720	2265	2948	1	chr6B.!!$R1	683
3	TraesCS6B01G347300	chr6B	37266566	37267162	596	True	979	979	96.3150	2354	2948	1	chr6B.!!$R2	594
4	TraesCS6B01G347300	chr6D	407526238	407528510	2272	False	3314	3314	93.0970	2	2265	1	chr6D.!!$F1	2263
5	TraesCS6B01G347300	chr6A	553058032	553060255	2223	False	3083	3083	91.8270	20	2231	1	chr6A.!!$F1	2211
6	TraesCS6B01G347300	chr2B	766593090	766593784	694	True	1114	1114	95.8330	2263	2948	1	chr2B.!!$R1	685
7	TraesCS6B01G347300	chr2B	711716980	711717720	740	True	583	992	93.2335	2266	2948	2	chr2B.!!$R2	682
8	TraesCS6B01G347300	chr1B	49320827	49321525	698	False	1110	1110	95.5650	2260	2948	1	chr1B.!!$F1	688
9	TraesCS6B01G347300	chr1B	551733233	551733924	691	False	1064	1064	94.6840	2266	2948	1	chr1B.!!$F2	682
10	TraesCS6B01G347300	chr3B	822864830	822865542	712	False	1105	1105	94.9580	2249	2948	1	chr3B.!!$F2	699
11	TraesCS6B01G347300	chr3B	92126096	92126793	697	False	1101	1101	95.4150	2262	2948	1	chr3B.!!$F1	686
12	TraesCS6B01G347300	chr4B	42014891	42015585	694	True	1101	1101	95.5400	2265	2948	1	chr4B.!!$R1	683
13	TraesCS6B01G347300	chr5B	32130563	32131262	699	False	1075	1075	94.7140	2262	2948	1	chr5B.!!$F1	686

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
176	179	0.328258	GGCCATCACAAGTGGGTAGT	59.672	55.0	0.0	0.0	37.22	2.73	F
1006	1042	0.179073	CCTGTCCTCTGTAATGGCCG	60.179	60.0	0.0	0.0	0.00	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1337	1373	0.109226	GAGAAGGACACGGGTCTTCG	60.109	60.0	18.98	0.00	43.77	3.79	R
2794	2907	2.674852	CACCTGATCGATGTTTCCACAG	59.325	50.0	0.54	1.48	35.94	3.66	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
24	26	5.512404	CCAACCCTACTAATCAGACACACAA	60.512	44.000	0.00	0.00	0.00	3.33
108	110	4.133078	CAAAAGAGCTCTGAAGTTCCACT	58.867	43.478	19.06	0.00	33.49	4.00
176	179	0.328258	GGCCATCACAAGTGGGTAGT	59.672	55.000	0.00	0.00	37.22	2.73
181	184	0.396435	TCACAAGTGGGTAGTGCCTG	59.604	55.000	0.00	0.00	37.43	4.85
190	193	0.889306	GGTAGTGCCTGACGAGAAGT	59.111	55.000	0.00	0.00	0.00	3.01
351	359	2.444895	CGAGGGAGGGAGGAAGGG	60.445	72.222	0.00	0.00	0.00	3.95
361	369	1.566298	GGAGGAAGGGTGGCAGTGAT	61.566	60.000	0.00	0.00	0.00	3.06
446	454	4.790861	GTCGAAGCCCCGTCCGTC	62.791	72.222	0.00	0.00	0.00	4.79
556	570	2.231964	ACTGTAAACCGGATCGCTTGTA	59.768	45.455	9.46	0.00	0.00	2.41
627	641	3.570125	GGAAGGCAAAACTAGCTCTTGTT	59.430	43.478	0.00	0.00	0.00	2.83
629	643	4.574599	AGGCAAAACTAGCTCTTGTTTG	57.425	40.909	9.49	9.39	38.24	2.93
651	665	1.750399	CCCATCTCCGGCTGTTTGG	60.750	63.158	0.00	4.55	0.00	3.28
732	747	2.917971	CGAGGCTAGAGTTTTCAAGACG	59.082	50.000	0.00	0.00	0.00	4.18
770	789	3.296709	CGGCGGACAGCTGTACCTT	62.297	63.158	23.55	0.00	46.91	3.50
783	802	3.431346	GCTGTACCTTGAGATCTGCATGA	60.431	47.826	0.00	0.00	0.00	3.07
784	803	4.118410	CTGTACCTTGAGATCTGCATGAC	58.882	47.826	0.00	0.00	0.00	3.06
785	804	2.306341	ACCTTGAGATCTGCATGACG	57.694	50.000	0.00	0.00	0.00	4.35
786	805	0.935898	CCTTGAGATCTGCATGACGC	59.064	55.000	0.00	0.00	42.89	5.19
787	806	1.472904	CCTTGAGATCTGCATGACGCT	60.473	52.381	0.00	0.00	43.06	5.07
788	807	1.593469	CTTGAGATCTGCATGACGCTG	59.407	52.381	0.00	0.00	43.06	5.18
795	817	2.887568	GCATGACGCTGACCCGAG	60.888	66.667	0.00	0.00	37.77	4.63
802	824	3.394836	GCTGACCCGAGGGAAGCT	61.395	66.667	23.61	1.71	41.64	3.74
803	825	2.896443	CTGACCCGAGGGAAGCTC	59.104	66.667	16.26	2.24	38.96	4.09
824	846	2.879462	GGAACGGACGTAGCTGCG	60.879	66.667	23.12	23.12	37.94	5.18
826	848	3.966026	GAACGGACGTAGCTGCGCT	62.966	63.158	24.60	11.42	43.41	5.92
827	849	3.966026	AACGGACGTAGCTGCGCTC	62.966	63.158	24.60	18.80	40.44	5.03
828	850	4.180946	CGGACGTAGCTGCGCTCT	62.181	66.667	24.60	4.60	40.44	4.09
829	851	2.580867	GGACGTAGCTGCGCTCTG	60.581	66.667	24.60	0.00	40.44	3.35
830	852	3.251043	GACGTAGCTGCGCTCTGC	61.251	66.667	24.60	10.81	46.70	4.26
832	854	4.801624	CGTAGCTGCGCTCTGCCA	62.802	66.667	12.24	0.00	45.60	4.92
833	855	2.202987	GTAGCTGCGCTCTGCCAT	60.203	61.111	9.73	0.00	45.60	4.40
867	895	4.557205	AGCCTCTATAAATAAGCGGTTCG	58.443	43.478	1.59	0.00	0.00	3.95
868	896	4.038883	AGCCTCTATAAATAAGCGGTTCGT	59.961	41.667	1.59	0.00	0.00	3.85
871	899	6.157211	CCTCTATAAATAAGCGGTTCGTCAT	58.843	40.000	1.59	0.00	0.00	3.06
880	908	2.616842	AGCGGTTCGTCATTTCACTTTT	59.383	40.909	0.00	0.00	0.00	2.27
946	981	2.607635	CTCTCTCGTCAGTCTCTGTAGC	59.392	54.545	0.00	0.00	32.61	3.58
988	1024	0.942252	GTTCTTCGACCACAACCACC	59.058	55.000	0.00	0.00	0.00	4.61
989	1025	0.834612	TTCTTCGACCACAACCACCT	59.165	50.000	0.00	0.00	0.00	4.00
998	1034	0.469917	CACAACCACCTGTCCTCTGT	59.530	55.000	0.00	0.00	0.00	3.41
1005	1041	0.912486	ACCTGTCCTCTGTAATGGCC	59.088	55.000	0.00	0.00	0.00	5.36
1006	1042	0.179073	CCTGTCCTCTGTAATGGCCG	60.179	60.000	0.00	0.00	0.00	6.13
1353	1389	2.342648	GCGAAGACCCGTGTCCTT	59.657	61.111	0.00	0.00	42.81	3.36
1981	2017	5.411977	TGCATTCCAGCATTATTTTTGTTGG	59.588	36.000	0.66	0.66	44.26	3.77
2104	2143	7.376866	CGAAATGAAATCGGGTTATTCTCAATG	59.623	37.037	0.00	0.00	36.68	2.82
2184	2224	4.747810	AGTTTTGTGGAAGAGCTTTTGTG	58.252	39.130	0.00	0.00	0.00	3.33
2211	2251	3.620488	AGGCTCATTTGCTATTTTCCGA	58.380	40.909	0.00	0.00	0.00	4.55
2483	2593	7.716998	CAGTATTAGAAATCTACCAGCAACCAT	59.283	37.037	0.00	0.00	0.00	3.55
2564	2674	4.663334	TGAGGCAGACTCTTCTACTACAA	58.337	43.478	4.45	0.00	46.72	2.41
2572	2682	7.600752	GCAGACTCTTCTACTACAAATCTGTTT	59.399	37.037	0.00	0.00	36.96	2.83
2788	2901	9.733556	TCACCACAACTTTGATAACTTATGTAT	57.266	29.630	0.00	0.00	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.020573	TGTGTGTCTGATTAGTAGGGTTGG	60.021	45.833	0.00	0.00	0.00	3.77
4	5	8.786826	TTTAATTGTGTGTCTGATTAGTAGGG	57.213	34.615	0.00	0.00	0.00	3.53
39	41	8.919777	AATTTAGAAGATTTATACCCTTCCGG	57.080	34.615	0.00	0.00	37.58	5.14
176	179	1.000955	GAGGAAACTTCTCGTCAGGCA	59.999	52.381	0.00	0.00	44.43	4.75
190	193	3.018856	TCCGTATAACTGAGCGAGGAAA	58.981	45.455	0.00	0.00	0.00	3.13
361	369	2.343758	GTGGTGCAGAGAAGCGGA	59.656	61.111	0.00	0.00	37.31	5.54
446	454	7.706281	ATACACTAATCTTTGCTTCAGATCG	57.294	36.000	0.00	0.00	30.19	3.69
534	548	1.393539	CAAGCGATCCGGTTTACAGTG	59.606	52.381	0.00	0.00	45.20	3.66
617	631	0.394938	TGGGCGACAAACAAGAGCTA	59.605	50.000	0.00	0.00	0.00	3.32
627	641	4.467084	GCCGGAGATGGGCGACAA	62.467	66.667	5.05	0.00	41.39	3.18
651	665	1.383523	GTAGGTCAATGGCTTGGCTC	58.616	55.000	2.28	0.00	37.16	4.70
766	781	1.741732	GCGTCATGCAGATCTCAAGGT	60.742	52.381	0.00	0.00	45.45	3.50
783	802	3.382832	CTTCCCTCGGGTCAGCGT	61.383	66.667	1.18	0.00	36.47	5.07
784	803	4.821589	GCTTCCCTCGGGTCAGCG	62.822	72.222	11.46	0.00	34.67	5.18
785	804	3.378399	GAGCTTCCCTCGGGTCAGC	62.378	68.421	16.48	16.48	40.51	4.26
786	805	2.726351	GGAGCTTCCCTCGGGTCAG	61.726	68.421	1.18	1.10	41.71	3.51
787	806	2.683933	GGAGCTTCCCTCGGGTCA	60.684	66.667	1.18	0.00	41.71	4.02
823	845	3.592814	CATGGGCATGGCAGAGCG	61.593	66.667	22.06	0.28	35.24	5.03
867	895	7.194607	TGAGATGTGAGAAAAGTGAAATGAC	57.805	36.000	0.00	0.00	0.00	3.06
868	896	6.072838	GCTGAGATGTGAGAAAAGTGAAATGA	60.073	38.462	0.00	0.00	0.00	2.57
871	899	5.125356	TGCTGAGATGTGAGAAAAGTGAAA	58.875	37.500	0.00	0.00	0.00	2.69
880	908	2.954318	TGATCGATGCTGAGATGTGAGA	59.046	45.455	0.54	0.00	0.00	3.27
988	1024	0.537188	ACGGCCATTACAGAGGACAG	59.463	55.000	2.24	0.00	29.93	3.51
989	1025	0.535335	GACGGCCATTACAGAGGACA	59.465	55.000	2.24	0.00	29.93	4.02
998	1034	1.870383	GCACAAACGACGGCCATTA	59.130	52.632	2.24	0.00	0.00	1.90
1005	1041	2.127758	GCCTTCGCACAAACGACG	60.128	61.111	0.00	0.00	42.78	5.12
1006	1042	1.082756	CTGCCTTCGCACAAACGAC	60.083	57.895	0.00	0.00	42.78	4.34
1055	1091	2.575893	CCCATGCAAAGCTGTGCCA	61.576	57.895	26.04	14.28	44.26	4.92
1113	1149	1.937191	TGTGGTAGGAGAGCATGTCA	58.063	50.000	0.00	0.00	37.99	3.58
1213	1249	1.027792	AGCGAGAGGAGGAAGTCGAC	61.028	60.000	7.70	7.70	34.28	4.20
1337	1373	0.109226	GAGAAGGACACGGGTCTTCG	60.109	60.000	18.98	0.00	43.77	3.79
1353	1389	3.134792	GAGAGCTGGTCCGCGAGA	61.135	66.667	8.23	0.00	34.40	4.04
2104	2143	5.964758	TCAGAAATAAATGGACATTGCACC	58.035	37.500	0.00	0.00	0.00	5.01
2184	2224	5.511234	AAATAGCAAATGAGCCTCATGTC	57.489	39.130	8.21	0.72	37.15	3.06
2211	2251	7.972277	GTGAAAGTGAAGTCATGCATTAATGAT	59.028	33.333	19.73	7.05	38.76	2.45
2373	2479	9.661563	TTAAAAATAAGAGGTGCGAGAATTCTA	57.338	29.630	8.25	0.00	0.00	2.10
2456	2566	7.048512	GGTTGCTGGTAGATTTCTAATACTGT	58.951	38.462	0.00	0.00	0.00	3.55
2564	2674	9.209175	GACAGTAGAATAACACTCAAACAGATT	57.791	33.333	0.00	0.00	0.00	2.40
2572	2682	6.978338	AGAAACGACAGTAGAATAACACTCA	58.022	36.000	0.00	0.00	0.00	3.41
2788	2901	6.761242	CCTGATCGATGTTTCCACAGTATTTA	59.239	38.462	0.54	0.00	35.94	1.40
2794	2907	2.674852	CACCTGATCGATGTTTCCACAG	59.325	50.000	0.54	1.48	35.94	3.66
2804	2917	7.925483	TCAAAAATTGTTTTTCACCTGATCGAT	59.075	29.630	0.00	0.00	40.65	3.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.