AutoCloner

Multiple sequence alignment - TraesCS6A01G262100

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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	TraesCS6A01G262100	chr6A	100.000	2455	0	0	1	2455	485325768	485323314	0.000000e+00	4534.0
1	TraesCS6A01G262100	chr6A	97.297	37	1	0	1272	1308	484909321	484909285	2.040000e-06	63.9
2	TraesCS6A01G262100	chr6B	91.314	1842	102	30	1	1826	520779397	520777598	0.000000e+00	2462.0
3	TraesCS6A01G262100	chr6D	92.876	1488	83	16	347	1826	344916711	344915239	0.000000e+00	2139.0
4	TraesCS6A01G262100	chr6D	94.785	326	12	2	21	342	344917283	344916959	1.010000e-138	503.0
5	TraesCS6A01G262100	chr6D	97.297	37	1	0	1272	1308	344353812	344353776	2.040000e-06	63.9
6	TraesCS6A01G262100	chr7A	97.152	632	14	2	1825	2455	114010349	114009721	0.000000e+00	1064.0
7	TraesCS6A01G262100	chr7A	96.835	632	16	2	1825	2455	114015826	114015198	0.000000e+00	1053.0
8	TraesCS6A01G262100	chr3A	97.152	632	14	2	1825	2455	8860744	8860116	0.000000e+00	1064.0
9	TraesCS6A01G262100	chr3A	96.835	632	15	3	1825	2455	101615929	101615302	0.000000e+00	1051.0
10	TraesCS6A01G262100	chr5A	96.994	632	15	2	1825	2455	573059020	573059648	0.000000e+00	1059.0
11	TraesCS6A01G262100	chr5A	96.835	632	15	3	1825	2455	523011635	523012262	0.000000e+00	1051.0
12	TraesCS6A01G262100	chr1A	96.994	632	15	2	1825	2455	556980717	556980089	0.000000e+00	1059.0
13	TraesCS6A01G262100	chrUn	96.835	632	16	2	1825	2455	336202665	336203293	0.000000e+00	1053.0
14	TraesCS6A01G262100	chr2A	96.541	636	18	2	1821	2455	749384276	749383644	0.000000e+00	1050.0

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	TraesCS6A01G262100	chr6A	485323314	485325768	2454	True	4534	4534	100.0000	1	2455	1	chr6A.!!$R2	2454
1	TraesCS6A01G262100	chr6B	520777598	520779397	1799	True	2462	2462	91.3140	1	1826	1	chr6B.!!$R1	1825
2	TraesCS6A01G262100	chr6D	344915239	344917283	2044	True	1321	2139	93.8305	21	1826	2	chr6D.!!$R2	1805
3	TraesCS6A01G262100	chr7A	114009721	114010349	628	True	1064	1064	97.1520	1825	2455	1	chr7A.!!$R1	630
4	TraesCS6A01G262100	chr7A	114015198	114015826	628	True	1053	1053	96.8350	1825	2455	1	chr7A.!!$R2	630
5	TraesCS6A01G262100	chr3A	8860116	8860744	628	True	1064	1064	97.1520	1825	2455	1	chr3A.!!$R1	630
6	TraesCS6A01G262100	chr3A	101615302	101615929	627	True	1051	1051	96.8350	1825	2455	1	chr3A.!!$R2	630
7	TraesCS6A01G262100	chr5A	573059020	573059648	628	False	1059	1059	96.9940	1825	2455	1	chr5A.!!$F2	630
8	TraesCS6A01G262100	chr5A	523011635	523012262	627	False	1051	1051	96.8350	1825	2455	1	chr5A.!!$F1	630
9	TraesCS6A01G262100	chr1A	556980089	556980717	628	True	1059	1059	96.9940	1825	2455	1	chr1A.!!$R1	630
10	TraesCS6A01G262100	chrUn	336202665	336203293	628	False	1053	1053	96.8350	1825	2455	1	chrUn.!!$F1	630
11	TraesCS6A01G262100	chr2A	749383644	749384276	632	True	1050	1050	96.5410	1821	2455	1	chr2A.!!$R1	634

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
362	610	1.182667	AATTAAACAAGGGGCGAGCC	58.817	50.0	5.37	5.37	0.0	4.7	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1584	1844	0.249868	GAAACAAACCCCAGCTTGCC	60.25	55.0	0.0	0.0	0.0	4.52	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
36	37	2.477375	TGGTTACGCGAGCAAAAAGTAG	59.523	45.455	15.93	0.00	0.00	2.57
77	82	1.383664	GGTACTACCACCCCCTCCC	60.384	68.421	0.00	0.00	38.42	4.30
190	195	3.148031	GAAGGCTAGGTACGGGGCG	62.148	68.421	0.00	0.00	35.82	6.13
275	280	5.335191	GGCCTATGCTAATTGTAATGTCAGC	60.335	44.000	0.00	0.00	37.74	4.26
361	609	4.443913	TTAAATTAAACAAGGGGCGAGC	57.556	40.909	0.00	0.00	0.00	5.03
362	610	1.182667	AATTAAACAAGGGGCGAGCC	58.817	50.000	5.37	5.37	0.00	4.70
414	662	7.408132	GCCAAAGGCTTTTCTTTAGTTTTAG	57.592	36.000	10.36	0.00	46.69	1.85
416	664	7.709182	GCCAAAGGCTTTTCTTTAGTTTTAGAA	59.291	33.333	10.36	0.00	46.69	2.10
417	665	9.249457	CCAAAGGCTTTTCTTTAGTTTTAGAAG	57.751	33.333	10.36	0.00	35.44	2.85
496	744	3.511934	ACGCTCTAATCTGAAGTGTCCTT	59.488	43.478	0.00	0.00	0.00	3.36
501	749	6.030548	TCTAATCTGAAGTGTCCTTGTCTG	57.969	41.667	0.00	0.00	0.00	3.51
551	799	2.508526	GGTGCAAGAACTCTTCACCAT	58.491	47.619	22.65	0.00	44.38	3.55
552	800	3.674997	GGTGCAAGAACTCTTCACCATA	58.325	45.455	22.65	0.00	44.38	2.74
559	807	6.071952	GCAAGAACTCTTCACCATAAAATCCA	60.072	38.462	0.00	0.00	33.11	3.41
588	838	6.592220	TGAAAAAGAAAAAGAAAAGAACCGGG	59.408	34.615	6.32	0.00	0.00	5.73
662	912	2.435059	GAGGCACGAGTTGAGGGC	60.435	66.667	0.00	0.00	0.00	5.19
777	1027	2.356553	GCCCTGCGTCGTGTACAA	60.357	61.111	0.00	0.00	0.00	2.41
778	1028	2.380410	GCCCTGCGTCGTGTACAAG	61.380	63.158	0.00	0.00	0.00	3.16
819	1072	1.698506	TGGAAATCCAGCCGTGTTTT	58.301	45.000	0.00	0.00	42.01	2.43
820	1073	1.611491	TGGAAATCCAGCCGTGTTTTC	59.389	47.619	0.00	0.00	42.01	2.29
830	1083	1.721926	GCCGTGTTTTCTCTCTTCTCG	59.278	52.381	0.00	0.00	0.00	4.04
838	1091	3.743091	CTCTCTTCTCGCGCGTCCC	62.743	68.421	30.98	0.00	0.00	4.46
860	1113	2.680805	GCACCTATAGCTCAGCAACCAA	60.681	50.000	0.00	0.00	0.00	3.67
870	1123	4.081476	AGCTCAGCAACCAAATATTTTCCC	60.081	41.667	0.00	0.00	0.00	3.97
948	1204	2.026822	AGACCTCAGCACCGAAATCAAT	60.027	45.455	0.00	0.00	0.00	2.57
1054	1310	2.438434	CCATTGTGCCCCTCGACC	60.438	66.667	0.00	0.00	0.00	4.79
1137	1393	3.794028	CCAGAGATTTCGACGTCTTCATC	59.206	47.826	14.70	11.17	0.00	2.92
1160	1416	9.590451	CATCTACAGGTAGTTTAATTTTACGGA	57.410	33.333	6.37	0.00	34.84	4.69
1176	1432	3.643159	ACGGATTTGTTTGCTCCTTTC	57.357	42.857	0.00	0.00	0.00	2.62
1212	1468	3.808466	TCTCAGATCGCCCATATATGC	57.192	47.619	7.24	0.00	0.00	3.14
1225	1481	5.351465	GCCCATATATGCACACACTGTATAC	59.649	44.000	7.24	0.00	30.99	1.47
1249	1505	3.070734	AGTGCTATTCTGATCCAGCGATT	59.929	43.478	0.00	0.00	36.81	3.34
1254	1510	2.209838	TCTGATCCAGCGATTCGTTC	57.790	50.000	8.03	0.00	0.00	3.95
1314	1570	2.527624	AGGAGTGCAGGGCTGTGA	60.528	61.111	0.00	0.00	0.00	3.58
1509	1766	5.942826	CCTCCTTCATCAGAAATAATAGGGC	59.057	44.000	0.00	0.00	32.35	5.19
1517	1774	2.781174	AGAAATAATAGGGCCACGGGAA	59.219	45.455	6.18	0.00	0.00	3.97
1535	1795	2.158813	GGAAAACTAGCCATCCGATCCA	60.159	50.000	0.00	0.00	0.00	3.41
1538	1798	4.974645	AAACTAGCCATCCGATCCAATA	57.025	40.909	0.00	0.00	0.00	1.90
1541	1801	4.357325	ACTAGCCATCCGATCCAATAGAT	58.643	43.478	0.00	0.00	38.17	1.98
1553	1813	7.505923	TCCGATCCAATAGATAAACTCTTCTGA	59.494	37.037	0.00	0.00	34.42	3.27
1584	1844	3.606595	TCTTCCAGTTGAGATGAGCAG	57.393	47.619	0.00	0.00	0.00	4.24
1599	1859	3.053828	CAGGCAAGCTGGGGTTTG	58.946	61.111	0.00	0.00	36.85	2.93
1626	1886	3.521560	CTTATTAGGTGCTCGCACTTCA	58.478	45.455	20.05	6.27	45.52	3.02
1634	1894	0.366871	GCTCGCACTTCACGTGTATG	59.633	55.000	16.51	13.02	45.57	2.39
1638	1898	1.999735	CGCACTTCACGTGTATGGAAT	59.000	47.619	16.51	0.00	45.57	3.01
1680	1940	0.528901	TTACTGTGCGTGTGAGCGTT	60.529	50.000	0.00	0.00	40.67	4.84
1804	2071	1.332375	GTAGCAGCGGAGTCTGAGTAG	59.668	57.143	2.16	0.00	34.49	2.57
1807	2074	1.950909	GCAGCGGAGTCTGAGTAGTAT	59.049	52.381	2.16	0.00	34.49	2.12
1818	2085	5.307196	AGTCTGAGTAGTATGTGTTTGGGTT	59.693	40.000	0.00	0.00	0.00	4.11
1823	2090	6.182507	AGTAGTATGTGTTTGGGTTCTTGA	57.817	37.500	0.00	0.00	0.00	3.02
1873	2140	9.158233	ACGAGATTTAATCCGAATAAACAGAAA	57.842	29.630	17.75	0.00	0.00	2.52
1891	2158	7.765695	ACAGAAAATAAATCATGACCACAGT	57.234	32.000	0.00	0.00	0.00	3.55
1918	2185	7.579726	GCAGAGATTAAACTAATCATGCGAAT	58.420	34.615	15.10	0.00	45.41	3.34
2062	2329	2.126228	GTCGCCCATGTCGTCGAA	60.126	61.111	0.00	0.00	32.49	3.71
2189	2456	2.240162	GATCACGAGAGGCGGGGTTT	62.240	60.000	0.00	0.00	45.52	3.27
2392	2659	2.259618	CGAGTCGTCACGATCCAAAAT	58.740	47.619	1.61	0.00	38.42	1.82
2420	2688	4.494410	GGAAACGTTCAGTAATTAATGCGC	59.506	41.667	8.04	0.00	0.00	6.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
190	195	9.489084	GGAAAAGAATATGGTTATTATTTGCCC	57.511	33.333	10.03	6.65	43.28	5.36
275	280	4.527564	GGTGAACAGTGAAAGATTTGTCG	58.472	43.478	0.00	0.00	0.00	4.35
342	347	1.548719	GGCTCGCCCCTTGTTTAATTT	59.451	47.619	0.00	0.00	0.00	1.82
343	348	1.182667	GGCTCGCCCCTTGTTTAATT	58.817	50.000	0.00	0.00	0.00	1.40
427	675	7.575720	GCACTGAATATACTTTGAACCTTTGCT	60.576	37.037	0.00	0.00	0.00	3.91
430	678	7.448469	ACAGCACTGAATATACTTTGAACCTTT	59.552	33.333	4.31	0.00	0.00	3.11
496	744	4.600576	TGTTGAGCGCGCCAGACA	62.601	61.111	30.33	25.27	0.00	3.41
584	834	1.014352	CTAAGAAAATGGACGCCCGG	58.986	55.000	0.00	0.00	34.29	5.73
588	838	6.140737	CGAAATATTGCTAAGAAAATGGACGC	59.859	38.462	0.00	0.00	0.00	5.19
650	900	1.536943	GGTCTCAGCCCTCAACTCGT	61.537	60.000	0.00	0.00	0.00	4.18
662	912	1.018148	ACTCTGCGTATCGGTCTCAG	58.982	55.000	0.00	0.00	0.00	3.35
776	1026	4.268359	GAACCATCATGGCTTCTCTTCTT	58.732	43.478	2.52	0.00	42.67	2.52
777	1027	3.371380	GGAACCATCATGGCTTCTCTTCT	60.371	47.826	2.52	0.00	42.67	2.85
778	1028	2.948315	GGAACCATCATGGCTTCTCTTC	59.052	50.000	2.52	0.00	42.67	2.87
819	1072	2.751913	GGACGCGCGAGAAGAGAGA	61.752	63.158	39.36	0.00	0.00	3.10
820	1073	2.277628	GGACGCGCGAGAAGAGAG	60.278	66.667	39.36	3.76	0.00	3.20
838	1091	1.212616	GTTGCTGAGCTATAGGTGCG	58.787	55.000	9.66	1.03	35.28	5.34
844	1097	7.014230	GGGAAAATATTTGGTTGCTGAGCTATA	59.986	37.037	5.83	0.00	0.00	1.31
860	1113	3.330998	GGAGGGAGATCGGGGAAAATATT	59.669	47.826	0.00	0.00	0.00	1.28
948	1204	7.148035	GGTTGGTTTAACTTAACAGGTCTTTGA	60.148	37.037	14.02	0.00	39.31	2.69
1160	1416	6.161381	CAGCTAATGAAAGGAGCAAACAAAT	58.839	36.000	0.00	0.00	38.73	2.32
1162	1418	4.559300	GCAGCTAATGAAAGGAGCAAACAA	60.559	41.667	0.00	0.00	38.73	2.83
1191	1447	3.515104	TGCATATATGGGCGATCTGAGAA	59.485	43.478	14.51	0.00	0.00	2.87
1212	1468	7.645735	CAGAATAGCACTAGTATACAGTGTGTG	59.354	40.741	24.04	16.71	44.30	3.82
1225	1481	3.254411	TCGCTGGATCAGAATAGCACTAG	59.746	47.826	0.00	0.00	35.98	2.57
1249	1505	2.880268	TGGTTCGTAGTGAGAAGAACGA	59.120	45.455	0.00	0.00	42.61	3.85
1254	1510	3.366476	CCTCTGTGGTTCGTAGTGAGAAG	60.366	52.174	0.00	0.00	0.00	2.85
1314	1570	1.602851	CACCTCGTCGGTATCGATCTT	59.397	52.381	0.00	0.00	46.94	2.40
1334	1590	2.380084	TGGTGTTAATCCTCTCACGC	57.620	50.000	0.00	0.00	0.00	5.34
1509	1766	1.379527	GATGGCTAGTTTTCCCGTGG	58.620	55.000	0.00	0.00	0.00	4.94
1517	1774	3.864789	ATTGGATCGGATGGCTAGTTT	57.135	42.857	0.00	0.00	0.00	2.66
1562	1822	4.121317	CTGCTCATCTCAACTGGAAGATC	58.879	47.826	0.00	0.00	37.43	2.75
1570	1830	1.949547	GCTTGCCTGCTCATCTCAACT	60.950	52.381	0.00	0.00	0.00	3.16
1584	1844	0.249868	GAAACAAACCCCAGCTTGCC	60.250	55.000	0.00	0.00	0.00	4.52
1599	1859	2.285660	GCGAGCACCTAATAAGCGAAAC	60.286	50.000	0.00	0.00	0.00	2.78
1626	1886	7.659799	TGCATTTTATAGCTATTCCATACACGT	59.340	33.333	12.39	0.00	0.00	4.49
1634	1894	9.801873	TTTTCTTGTGCATTTTATAGCTATTCC	57.198	29.630	12.39	0.00	0.00	3.01
1680	1940	4.398358	CACCTGAGGTAGACGAAGTTATCA	59.602	45.833	2.59	0.00	35.04	2.15
1785	2051	1.065345	ACTACTCAGACTCCGCTGCTA	60.065	52.381	0.00	0.00	35.86	3.49
1786	2052	0.322997	ACTACTCAGACTCCGCTGCT	60.323	55.000	0.00	0.00	35.86	4.24
1787	2053	1.380524	TACTACTCAGACTCCGCTGC	58.619	55.000	0.00	0.00	35.86	5.25
1804	2071	5.507315	CCAACTCAAGAACCCAAACACATAC	60.507	44.000	0.00	0.00	0.00	2.39
1807	2074	2.757868	CCAACTCAAGAACCCAAACACA	59.242	45.455	0.00	0.00	0.00	3.72
1818	2085	7.707624	ATTTGCTCATATTTCCAACTCAAGA	57.292	32.000	0.00	0.00	0.00	3.02
1823	2090	8.612619	CGTAGTAATTTGCTCATATTTCCAACT	58.387	33.333	0.00	0.00	0.00	3.16
1873	2140	6.653020	TCTGCTACTGTGGTCATGATTTATT	58.347	36.000	0.00	0.00	0.00	1.40
1891	2158	7.433680	TCGCATGATTAGTTTAATCTCTGCTA	58.566	34.615	20.98	14.36	43.84	3.49
1918	2185	7.444299	TGTGATATGTTCATCTGCTATGCTAA	58.556	34.615	0.00	0.00	36.54	3.09
2062	2329	2.600769	ACCTCGGCAACCTCGTCT	60.601	61.111	0.00	0.00	0.00	4.18
2231	2498	2.290514	CCAAGCAAGTCTTCTCCATCCA	60.291	50.000	0.00	0.00	31.27	3.41
2309	2576	1.511768	GTCAGGCAGACGTCTACCC	59.488	63.158	27.82	24.14	37.53	3.69
2392	2659	8.117988	GCATTAATTACTGAACGTTTCCGATTA	58.882	33.333	0.46	2.08	37.88	1.75
2416	2684	7.804129	GTCATTAATTAATAATTAACGGGCGCA	59.196	33.333	17.40	0.00	43.78	6.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.