AutoCloner

Multiple sequence alignment - TraesCS5A01G119700

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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	TraesCS5A01G119700	chr5A	100.000	2918	0	0	1	2918	250561336	250564253	0.000000e+00	5389.0
1	TraesCS5A01G119700	chr5B	96.569	1982	66	2	1	1981	198029932	198027952	0.000000e+00	3282.0
2	TraesCS5A01G119700	chr5D	96.171	1985	71	4	1	1981	192951515	192949532	0.000000e+00	3240.0
3	TraesCS5A01G119700	chr5D	93.750	48	2	1	950	996	192950613	192950566	1.450000e-08	71.3
4	TraesCS5A01G119700	chr4A	97.655	938	21	1	1982	2918	743660266	743661203	0.000000e+00	1609.0
5	TraesCS5A01G119700	chr3B	97.548	938	22	1	1982	2918	252954131	252955068	0.000000e+00	1604.0
6	TraesCS5A01G119700	chr4B	97.441	938	23	1	1982	2918	3842579	3843516	0.000000e+00	1598.0
7	TraesCS5A01G119700	chr1D	97.228	938	25	1	1982	2918	453561107	453560170	0.000000e+00	1587.0
8	TraesCS5A01G119700	chr4D	97.122	938	25	2	1982	2918	4323765	4322829	0.000000e+00	1581.0
9	TraesCS5A01G119700	chr7D	96.912	939	27	2	1982	2918	382657201	382656263	0.000000e+00	1572.0
10	TraesCS5A01G119700	chr7D	96.695	938	29	2	1982	2918	329530022	329529086	0.000000e+00	1559.0
11	TraesCS5A01G119700	chr6D	96.588	938	30	2	1982	2918	436429924	436428988	0.000000e+00	1554.0
12	TraesCS5A01G119700	chr1A	96.060	939	35	2	1982	2918	802417	801479	0.000000e+00	1528.0

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	TraesCS5A01G119700	chr5A	250561336	250564253	2917	False	5389.00	5389	100.0000	1	2918	1	chr5A.!!$F1	2917
1	TraesCS5A01G119700	chr5B	198027952	198029932	1980	True	3282.00	3282	96.5690	1	1981	1	chr5B.!!$R1	1980
2	TraesCS5A01G119700	chr5D	192949532	192951515	1983	True	1655.65	3240	94.9605	1	1981	2	chr5D.!!$R1	1980
3	TraesCS5A01G119700	chr4A	743660266	743661203	937	False	1609.00	1609	97.6550	1982	2918	1	chr4A.!!$F1	936
4	TraesCS5A01G119700	chr3B	252954131	252955068	937	False	1604.00	1604	97.5480	1982	2918	1	chr3B.!!$F1	936
5	TraesCS5A01G119700	chr4B	3842579	3843516	937	False	1598.00	1598	97.4410	1982	2918	1	chr4B.!!$F1	936
6	TraesCS5A01G119700	chr1D	453560170	453561107	937	True	1587.00	1587	97.2280	1982	2918	1	chr1D.!!$R1	936
7	TraesCS5A01G119700	chr4D	4322829	4323765	936	True	1581.00	1581	97.1220	1982	2918	1	chr4D.!!$R1	936
8	TraesCS5A01G119700	chr7D	382656263	382657201	938	True	1572.00	1572	96.9120	1982	2918	1	chr7D.!!$R2	936
9	TraesCS5A01G119700	chr7D	329529086	329530022	936	True	1559.00	1559	96.6950	1982	2918	1	chr7D.!!$R1	936
10	TraesCS5A01G119700	chr6D	436428988	436429924	936	True	1554.00	1554	96.5880	1982	2918	1	chr6D.!!$R1	936
11	TraesCS5A01G119700	chr1A	801479	802417	938	True	1528.00	1528	96.0600	1982	2918	1	chr1A.!!$R1	936

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	Hairpin	End Stability	Orientation
341	343	0.254178	GGATCATGTCACTGCCACCT	59.746	55.0	0.00	4.00	F
521	523	0.681564	TGGTCGGGTTGTTGCACTTT	60.682	50.0	0.00	2.66	F
544	546	1.047801	GGGTGCCAAGGTGAAATTGT	58.952	50.0	0.00	2.71	F
1417	1421	0.165295	CGACGACTACGACAAGCAGA	59.835	55.0	42.66	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1397	1401	0.110328	CTGCTTGTCGTAGTCGTCGT	60.110	55.000	0.00	38.33	4.34	R
1403	1407	0.456221	CCGGATCTGCTTGTCGTAGT	59.544	55.000	0.00	0.00	2.73	R
1745	1749	1.067142	TCATTGTCGTCTCCCTTTCCG	60.067	52.381	0.00	0.00	4.30	R
2579	2585	0.173481	TCGCTTTCTCGAGGTCATGG	59.827	55.000	13.56	34.09	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
169	171	7.934665	TGTGAATTAGTTACTTAAGTTGCCAGA	59.065	33.333	14.49	0.00	0.00	3.86
218	220	4.156477	CCTTCTCCCCATTGGTTTGTTTA	58.844	43.478	1.20	0.00	34.77	2.01
219	221	4.021456	CCTTCTCCCCATTGGTTTGTTTAC	60.021	45.833	1.20	0.00	34.77	2.01
341	343	0.254178	GGATCATGTCACTGCCACCT	59.746	55.000	0.00	0.00	0.00	4.00
465	467	3.713248	ACCTGAGCATATCAATCTCACCA	59.287	43.478	0.00	0.00	37.52	4.17
478	480	5.241506	TCAATCTCACCAAAAAGATGTGACC	59.758	40.000	0.00	0.00	35.34	4.02
521	523	0.681564	TGGTCGGGTTGTTGCACTTT	60.682	50.000	0.00	0.00	0.00	2.66
544	546	1.047801	GGGTGCCAAGGTGAAATTGT	58.952	50.000	0.00	0.00	0.00	2.71
560	562	9.617975	GGTGAAATTGTTTAAGAAGAATCAGAG	57.382	33.333	0.00	0.00	29.36	3.35
641	643	1.614317	CCATGAGTTCTCCCAACCACC	60.614	57.143	0.00	0.00	0.00	4.61
660	662	2.031870	CCCTCATCACACCATAGTCGA	58.968	52.381	0.00	0.00	0.00	4.20
931	935	1.308216	ATAGCCTGGTGGGAAGCCT	60.308	57.895	0.00	0.00	37.23	4.58
946	950	1.962822	GCCTTTGCCTGCAAAAGCC	60.963	57.895	21.75	9.13	43.60	4.35
1071	1075	1.371558	GTCTGTCAAGGAGGCGGTT	59.628	57.895	0.00	0.00	0.00	4.44
1167	1171	1.545706	GGGAGAGGAGTTCTTGGCGT	61.546	60.000	0.00	0.00	35.87	5.68
1255	1259	1.922135	CTCCACCAATCCAAACGCCG	61.922	60.000	0.00	0.00	0.00	6.46
1287	1291	1.172180	TTGCCAAGCACGAGGGAAAG	61.172	55.000	0.00	0.00	38.71	2.62
1360	1364	1.553690	CCTGGTCCCGTTGTCTCCAT	61.554	60.000	0.00	0.00	0.00	3.41
1397	1401	3.138798	GCCGTCTCTAGCCCACGA	61.139	66.667	8.89	0.00	35.49	4.35
1403	1407	2.046988	TCTAGCCCACGACGACGA	60.047	61.111	15.32	0.00	42.66	4.20
1417	1421	0.165295	CGACGACTACGACAAGCAGA	59.835	55.000	0.00	0.00	42.66	4.26
1418	1422	1.202043	CGACGACTACGACAAGCAGAT	60.202	52.381	0.00	0.00	42.66	2.90
1420	1424	1.132643	ACGACTACGACAAGCAGATCC	59.867	52.381	0.00	0.00	42.66	3.36
1590	1594	1.889170	CTCTCGAGGCTGGCATACATA	59.111	52.381	13.56	0.00	0.00	2.29
1745	1749	2.440980	GGAGGTGAAGCATGGCCC	60.441	66.667	0.00	0.00	0.00	5.80
1761	1765	3.373226	CCGGAAAGGGAGACGACA	58.627	61.111	0.00	0.00	35.97	4.35
1763	1767	0.249398	CCGGAAAGGGAGACGACAAT	59.751	55.000	0.00	0.00	35.97	2.71
1772	1776	2.607187	GGAGACGACAATGACAACGAT	58.393	47.619	0.00	0.00	0.00	3.73
1833	1837	2.289631	TGTTGTTCCGCTCATCAGTGAT	60.290	45.455	0.00	0.00	32.98	3.06
1975	1979	6.762702	TGTGTATGATTGTTTGATCTGCAT	57.237	33.333	0.00	0.00	0.00	3.96
2018	2022	5.887754	ACCTAAGGTTAATGAGGCTGAAAA	58.112	37.500	0.00	0.00	27.29	2.29
2129	2134	2.217750	CATGTGGTTCGTCCTTCACAA	58.782	47.619	0.00	0.00	42.35	3.33
2163	2168	3.181474	GCAAGGTAGACACATCCTAGACC	60.181	52.174	0.00	0.00	0.00	3.85
2280	2286	4.162651	AGTCAAATGGCCCTTTCTTCAAT	58.837	39.130	2.61	0.00	0.00	2.57
2337	2343	3.250762	GCGTGCAATGATCCATAGCTTTA	59.749	43.478	0.00	0.00	0.00	1.85
2415	2421	1.804151	CGAAGAAGGGATTGCGACAAA	59.196	47.619	0.00	0.00	0.00	2.83
2579	2585	5.174035	CGACGATACAATTCTCTTCATGGAC	59.826	44.000	0.00	0.00	0.00	4.02
2599	2605	1.404181	CCATGACCTCGAGAAAGCGAA	60.404	52.381	15.71	0.00	40.13	4.70
2651	2657	5.623368	CGAGCAACTCTCAGGTCTTAAGATT	60.623	44.000	8.75	0.00	41.98	2.40
2745	2752	0.399806	ATGTGGGTTGGGCCAGTTTT	60.400	50.000	6.23	0.00	39.65	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	2.603173	GGACAGAGTTTGCAGAAAAGCG	60.603	50.000	0.00	0.00	37.31	4.68
169	171	6.311735	ACAAGGTTACCTGATACCAACAAAT	58.688	36.000	3.99	0.00	36.87	2.32
198	200	3.898741	GGTAAACAAACCAATGGGGAGAA	59.101	43.478	3.55	0.00	39.50	2.87
240	242	3.713248	TCATGCCTGACACCTATCTGAAT	59.287	43.478	0.00	0.00	0.00	2.57
444	446	4.347360	TGGTGAGATTGATATGCTCAGG	57.653	45.455	0.00	0.00	39.15	3.86
465	467	1.702957	TCTCCCGGGTCACATCTTTTT	59.297	47.619	22.86	0.00	0.00	1.94
478	480	1.136305	TCGCTATTTCTTGTCTCCCGG	59.864	52.381	0.00	0.00	0.00	5.73
521	523	0.260230	TTTCACCTTGGCACCCTTGA	59.740	50.000	0.00	0.00	0.00	3.02
544	546	8.138928	TCACTCATCCTCTGATTCTTCTTAAA	57.861	34.615	0.00	0.00	32.10	1.52
560	562	1.474077	GGTGCCACATTTCACTCATCC	59.526	52.381	0.00	0.00	33.91	3.51
641	643	2.544694	GCTCGACTATGGTGTGATGAGG	60.545	54.545	0.00	0.00	0.00	3.86
660	662	8.798859	ACAACAAGACAAAATATCAGATAGCT	57.201	30.769	0.00	0.00	0.00	3.32
946	950	4.624882	CAGGCTATAGAAATAGAAGCAGCG	59.375	45.833	3.21	0.00	37.84	5.18
1100	1104	1.073897	GGCCTGAACTGTGCTTCCT	59.926	57.895	0.00	0.00	0.00	3.36
1125	1129	0.109179	CAACACGATGGTTGGCATGG	60.109	55.000	10.16	0.00	43.39	3.66
1255	1259	4.776647	GGCAATGGCAACCGCGAC	62.777	66.667	8.23	0.00	43.71	5.19
1260	1264	1.668793	GTGCTTGGCAATGGCAACC	60.669	57.895	18.49	12.76	42.98	3.77
1360	1364	1.971505	GACGATGATGCCTGGGACCA	61.972	60.000	0.00	0.00	0.00	4.02
1397	1401	0.110328	CTGCTTGTCGTAGTCGTCGT	60.110	55.000	0.00	0.00	38.33	4.34
1403	1407	0.456221	CCGGATCTGCTTGTCGTAGT	59.544	55.000	0.00	0.00	0.00	2.73
1442	1446	2.092538	ACCTTCTTGATGGAGCTCATGG	60.093	50.000	17.19	7.16	35.97	3.66
1745	1749	1.067142	TCATTGTCGTCTCCCTTTCCG	60.067	52.381	0.00	0.00	0.00	4.30
1757	1761	4.862574	TCCTCTTTATCGTTGTCATTGTCG	59.137	41.667	0.00	0.00	0.00	4.35
1761	1765	6.037610	GCATCTTCCTCTTTATCGTTGTCATT	59.962	38.462	0.00	0.00	0.00	2.57
1763	1767	4.870426	GCATCTTCCTCTTTATCGTTGTCA	59.130	41.667	0.00	0.00	0.00	3.58
1772	1776	4.558226	TGCTTCTGCATCTTCCTCTTTA	57.442	40.909	0.00	0.00	45.31	1.85
1833	1837	4.780815	TCTTCTTCTTGGAGAAAAGCACA	58.219	39.130	0.00	0.00	35.38	4.57
2018	2022	9.726438	GGCAAATAGGTCTATATTGTTGTATCT	57.274	33.333	0.00	0.00	0.00	1.98
2129	2134	6.320164	TGTGTCTACCTTGCATAAAAGTTGTT	59.680	34.615	0.00	0.00	0.00	2.83
2163	2168	6.147821	ACAGTTTCATGAAGGATAACAACTCG	59.852	38.462	8.41	4.90	0.00	4.18
2212	2217	6.199719	GTCTATTTTAAGTACGACCCCATTCG	59.800	42.308	0.00	0.00	44.87	3.34
2248	2253	4.220602	AGGGCCATTTGACTTTGTCATAAC	59.779	41.667	6.18	0.00	42.40	1.89
2280	2286	8.820831	AGAAAATCCTTTCATTCTGAGAGTCTA	58.179	33.333	0.00	0.00	42.99	2.59
2337	2343	1.251251	GCAACACTGCCTCCTGAAAT	58.749	50.000	0.00	0.00	43.26	2.17
2415	2421	1.270826	CATGGGCGATATCGAGTCACT	59.729	52.381	28.63	4.57	43.02	3.41
2579	2585	0.173481	TCGCTTTCTCGAGGTCATGG	59.827	55.000	13.56	0.00	34.09	3.66
2714	2721	2.556189	CAACCCACATCCGAACAATTCA	59.444	45.455	0.00	0.00	0.00	2.57
2745	2752	4.322424	CGGTATCCCCAAATATGTGATCGA	60.322	45.833	0.00	0.00	0.00	3.59
2808	2815	0.615331	TTTTGCAGCCTCTCCTCGAT	59.385	50.000	0.00	0.00	0.00	3.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.