AutoCloner

Multiple sequence alignment - TraesCS1A01G426400

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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	TraesCS1A01G426400	chr1A	100.000	2201	0	0	1	2201	581205186	581207386	0.000000e+00	4065
1	TraesCS1A01G426400	chr1A	94.932	1105	47	5	293	1396	581109755	581110851	0.000000e+00	1722
2	TraesCS1A01G426400	chr1A	87.446	932	97	10	583	1514	581244896	581245807	0.000000e+00	1055
3	TraesCS1A01G426400	chr1A	95.754	471	18	1	1394	1864	581120554	581121022	0.000000e+00	758
4	TraesCS1A01G426400	chr1A	82.625	823	133	10	730	1547	581433449	581434266	0.000000e+00	719
5	TraesCS1A01G426400	chr1A	81.293	588	80	17	3	588	581215814	581216373	1.200000e-122	449
6	TraesCS1A01G426400	chr1A	93.370	181	12	0	1856	2036	581121904	581122084	3.600000e-68	268
7	TraesCS1A01G426400	chr1D	90.876	1655	96	16	1	1639	484004012	484005627	0.000000e+00	2169
8	TraesCS1A01G426400	chr1D	87.841	880	94	6	649	1526	484030160	484031028	0.000000e+00	1020
9	TraesCS1A01G426400	chr1D	81.774	1037	153	21	542	1550	484114057	484115085	0.000000e+00	835
10	TraesCS1A01G426400	chr1D	85.000	320	41	5	24	339	347051179	347050863	3.530000e-83	318
11	TraesCS1A01G426400	chr1D	95.455	66	3	0	1823	1888	484042554	484042619	2.990000e-19	106
12	TraesCS1A01G426400	chr1B	86.874	1676	137	37	560	2200	674053444	674055071	0.000000e+00	1799
13	TraesCS1A01G426400	chr1B	88.475	885	94	6	645	1526	674065474	674066353	0.000000e+00	1062
14	TraesCS1A01G426400	chr1B	81.449	1035	157	22	542	1550	674076240	674077265	0.000000e+00	815
15	TraesCS1A01G426400	chr5D	85.938	320	38	7	24	339	548259668	548259352	3.500000e-88	335
16	TraesCS1A01G426400	chr5D	84.858	317	44	3	24	337	510623659	510623974	1.270000e-82	316
17	TraesCS1A01G426400	chr7D	83.288	365	49	7	24	377	46412333	46411970	2.110000e-85	326
18	TraesCS1A01G426400	chr7D	83.288	365	49	7	24	377	638272655	638273018	2.110000e-85	326
19	TraesCS1A01G426400	chr4D	83.102	361	49	7	24	373	67337738	67338097	3.530000e-83	318
20	TraesCS1A01G426400	chr7B	83.186	339	54	3	1	337	219493397	219493060	7.630000e-80	307

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	TraesCS1A01G426400	chr1A	581205186	581207386	2200	False	4065	4065	100.000	1	2201	1	chr1A.!!$F2	2200
1	TraesCS1A01G426400	chr1A	581109755	581110851	1096	False	1722	1722	94.932	293	1396	1	chr1A.!!$F1	1103
2	TraesCS1A01G426400	chr1A	581244896	581245807	911	False	1055	1055	87.446	583	1514	1	chr1A.!!$F4	931
3	TraesCS1A01G426400	chr1A	581433449	581434266	817	False	719	719	82.625	730	1547	1	chr1A.!!$F5	817
4	TraesCS1A01G426400	chr1A	581120554	581122084	1530	False	513	758	94.562	1394	2036	2	chr1A.!!$F6	642
5	TraesCS1A01G426400	chr1A	581215814	581216373	559	False	449	449	81.293	3	588	1	chr1A.!!$F3	585
6	TraesCS1A01G426400	chr1D	484004012	484005627	1615	False	2169	2169	90.876	1	1639	1	chr1D.!!$F1	1638
7	TraesCS1A01G426400	chr1D	484030160	484031028	868	False	1020	1020	87.841	649	1526	1	chr1D.!!$F2	877
8	TraesCS1A01G426400	chr1D	484114057	484115085	1028	False	835	835	81.774	542	1550	1	chr1D.!!$F4	1008
9	TraesCS1A01G426400	chr1B	674053444	674055071	1627	False	1799	1799	86.874	560	2200	1	chr1B.!!$F1	1640
10	TraesCS1A01G426400	chr1B	674065474	674066353	879	False	1062	1062	88.475	645	1526	1	chr1B.!!$F2	881
11	TraesCS1A01G426400	chr1B	674076240	674077265	1025	False	815	815	81.449	542	1550	1	chr1B.!!$F3	1008

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
417	435	0.316937	TGCGCTTGCGCTTATTATGC	60.317	50.0	33.96	8.65	43.34	3.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1738	1843	0.39113	GCATGACGCCTTGACCACTA	60.391	55.0	0.0	0.0	32.94	2.74	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
32	33	2.365582	GAATGGTCGTACCTGGCAATT	58.634	47.619	0.00	0.00	39.58	2.32
71	72	7.995289	TGTTGTTATCTTGTTGAAGACATTGT	58.005	30.769	0.00	0.00	41.12	2.71
81	82	5.937540	TGTTGAAGACATTGTTCGGATATGT	59.062	36.000	0.00	0.00	35.33	2.29
151	157	4.988598	CTGGTGACGGTGGCGCTT	62.989	66.667	7.64	0.00	0.00	4.68
153	159	4.980805	GGTGACGGTGGCGCTTGA	62.981	66.667	7.64	0.00	0.00	3.02
154	160	3.414700	GTGACGGTGGCGCTTGAG	61.415	66.667	7.64	0.00	0.00	3.02
155	161	3.923864	TGACGGTGGCGCTTGAGT	61.924	61.111	7.64	2.73	0.00	3.41
156	162	3.414700	GACGGTGGCGCTTGAGTG	61.415	66.667	7.64	0.00	0.00	3.51
157	163	4.235762	ACGGTGGCGCTTGAGTGT	62.236	61.111	7.64	0.00	0.00	3.55
158	164	2.972505	CGGTGGCGCTTGAGTGTT	60.973	61.111	7.64	0.00	0.00	3.32
164	170	1.963338	GCGCTTGAGTGTTGCTCCT	60.963	57.895	0.00	0.00	43.48	3.69
219	225	3.181476	CGTCCATGTGGTGTCATGAGATA	60.181	47.826	0.00	0.00	45.41	1.98
241	247	4.202441	AGTTGGTGCAGATATGGTCATTC	58.798	43.478	0.00	0.00	0.00	2.67
252	258	7.412853	CAGATATGGTCATTCTTGTAGTTTGC	58.587	38.462	0.00	0.00	0.00	3.68
276	282	4.324669	CGATCGCATATCTAATCGCTTTGT	59.675	41.667	0.26	0.00	35.19	2.83
381	399	4.747108	GTGCATTCTAGCTATACAGGTGTG	59.253	45.833	0.00	0.00	33.61	3.82
384	402	5.682471	GCATTCTAGCTATACAGGTGTGTGT	60.682	44.000	0.00	0.00	37.52	3.72
388	406	1.732259	GCTATACAGGTGTGTGTGTGC	59.268	52.381	0.00	0.00	37.52	4.57
390	408	1.227999	ATACAGGTGTGTGTGTGCGC	61.228	55.000	0.00	0.00	37.52	6.09
391	409	2.304901	TACAGGTGTGTGTGTGCGCT	62.305	55.000	9.73	0.00	37.52	5.92
417	435	0.316937	TGCGCTTGCGCTTATTATGC	60.317	50.000	33.96	8.65	43.34	3.14
951	1011	4.098807	GGACCAAACACAAACATACCAGTT	59.901	41.667	0.00	0.00	0.00	3.16
956	1016	7.036220	CCAAACACAAACATACCAGTTACAAA	58.964	34.615	0.00	0.00	0.00	2.83
975	1035	9.834628	GTTACAAAAGTATTGCATAGTGCTTTA	57.165	29.630	9.52	0.00	45.31	1.85
1020	1080	4.082571	GCGATGGCAAATAATAGCATCCTT	60.083	41.667	0.00	0.00	39.62	3.36
1377	1445	0.174389	TGTTGTTTGCAATGTGCCGT	59.826	45.000	0.00	0.00	44.23	5.68
1461	1529	7.731882	TTCATGGTTAAACTCATGTTACGAA	57.268	32.000	11.81	0.00	40.94	3.85
1473	1541	7.956558	ACTCATGTTACGAAAATAAAGGTACG	58.043	34.615	0.00	0.00	0.00	3.67
1618	1722	8.498054	TCAATCAAGCTTCTAAAACTAGATGG	57.502	34.615	0.00	0.00	0.00	3.51
1671	1776	7.601130	CCATTTTGCTTCATCTCTTTTTCATCA	59.399	33.333	0.00	0.00	0.00	3.07
1698	1803	6.951198	TCTTCTTATTCCCAATGCCTAAAACA	59.049	34.615	0.00	0.00	0.00	2.83
1738	1843	2.158900	CGACCCAACTTAGATGAGGCAT	60.159	50.000	0.00	0.00	0.00	4.40
1784	1889	4.562347	CCTGCTCATGTACTTGAACACTCT	60.562	45.833	12.09	0.00	30.75	3.24
1786	1891	4.202253	TGCTCATGTACTTGAACACTCTGT	60.202	41.667	12.09	0.00	30.75	3.41
1787	1892	4.387256	GCTCATGTACTTGAACACTCTGTC	59.613	45.833	12.09	0.00	30.75	3.51
1821	1929	4.687215	GCGGCACTGAGGAGCACA	62.687	66.667	0.00	0.00	0.00	4.57
1939	2945	2.037381	AGATCGAGCATGCACATCAGAT	59.963	45.455	21.98	14.57	0.00	2.90
1969	2975	2.763710	TGCTCGGCATCTAGGGCA	60.764	61.111	9.10	0.00	31.71	5.36
2073	3087	1.449601	CGTGTATGGTCCCCAGTGC	60.450	63.158	0.00	0.00	36.75	4.40
2074	3088	1.077716	GTGTATGGTCCCCAGTGCC	60.078	63.158	0.00	0.00	36.75	5.01
2081	3096	3.691342	TCCCCAGTGCCGTTCGAG	61.691	66.667	0.00	0.00	0.00	4.04
2102	3117	2.280321	GCGTGGTGTGGTACGGTT	60.280	61.111	0.00	0.00	40.43	4.44
2126	3141	1.067295	TGAAGGTCTGGATGTGCCTT	58.933	50.000	0.00	0.00	43.30	4.35
2135	3150	2.749621	CTGGATGTGCCTTGGTTAAGAC	59.250	50.000	0.00	0.00	35.92	3.01
2139	3154	4.636206	GGATGTGCCTTGGTTAAGACTAAG	59.364	45.833	0.00	0.00	42.23	2.18
2140	3155	3.408634	TGTGCCTTGGTTAAGACTAAGC	58.591	45.455	0.00	0.00	41.51	3.09
2151	3166	1.726853	AGACTAAGCATGTCAACGGC	58.273	50.000	0.00	0.00	36.94	5.68
2160	3175	1.546589	ATGTCAACGGCGGACCCTTA	61.547	55.000	13.24	0.00	34.36	2.69
2163	3178	0.320946	TCAACGGCGGACCCTTAAAG	60.321	55.000	13.24	0.00	0.00	1.85
2165	3180	0.109153	AACGGCGGACCCTTAAAGTT	59.891	50.000	13.24	0.00	0.00	2.66
2166	3181	0.109153	ACGGCGGACCCTTAAAGTTT	59.891	50.000	13.24	0.00	0.00	2.66
2188	3203	7.719633	AGTTTACACAATATTTGTCTGTGGACT	59.280	33.333	8.85	6.89	43.23	3.85
2189	3204	8.995220	GTTTACACAATATTTGTCTGTGGACTA	58.005	33.333	8.85	0.00	43.23	2.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	1.094785	ACATCGCAATTGCCAGGTAC	58.905	50.000	24.24	0.00	37.91	3.34
32	33	7.609760	AGATAACAACATAAGAAACATCGCA	57.390	32.000	0.00	0.00	0.00	5.10
101	102	3.041946	AGGTCGGAATCTAGGCTTTCAT	58.958	45.455	0.00	0.00	0.00	2.57
130	131	2.662596	GCCACCGTCACCAGATCA	59.337	61.111	0.00	0.00	0.00	2.92
152	158	2.550830	TCAGGAAAGGAGCAACACTC	57.449	50.000	0.00	0.00	45.45	3.51
153	159	2.856222	CTTCAGGAAAGGAGCAACACT	58.144	47.619	0.00	0.00	0.00	3.55
164	170	2.435372	ACAGCAACACCTTCAGGAAA	57.565	45.000	0.00	0.00	38.94	3.13
175	181	4.272504	CGAAGAGGTTCTTAAACAGCAACA	59.727	41.667	0.00	0.00	36.73	3.33
219	225	3.939740	ATGACCATATCTGCACCAACT	57.060	42.857	0.00	0.00	0.00	3.16
241	247	3.877801	GCGATCGGCAAACTACAAG	57.122	52.632	18.30	0.00	42.87	3.16
252	258	3.071786	AGCGATTAGATATGCGATCGG	57.928	47.619	18.30	0.00	41.08	4.18
402	420	7.531280	AGATACATAGCATAATAAGCGCAAG	57.469	36.000	11.47	0.00	37.01	4.01
449	467	9.773328	TCTGTTCGACAAATGATGAATTTTATC	57.227	29.630	0.00	0.00	36.28	1.75
452	470	8.137437	AGTTCTGTTCGACAAATGATGAATTTT	58.863	29.630	0.00	0.00	36.28	1.82
925	985	4.822896	TGGTATGTTTGTGTTTGGTCCTAC	59.177	41.667	0.00	0.00	0.00	3.18
975	1035	5.065218	CGCCTAAGTTCACAAAGAGCAATAT	59.935	40.000	0.00	0.00	0.00	1.28
1020	1080	4.509616	TGAGAAAAACAACGAAGACCTGA	58.490	39.130	0.00	0.00	0.00	3.86
1119	1179	1.378762	GTCCCTAGGGCAGCAAACA	59.621	57.895	24.42	0.00	34.68	2.83
1461	1529	6.866480	TCAACTACGGATCGTACCTTTATTT	58.134	36.000	0.00	0.00	41.54	1.40
1473	1541	7.787725	AATAAACTGGAATCAACTACGGATC	57.212	36.000	0.00	0.00	0.00	3.36
1671	1776	8.478066	GTTTTAGGCATTGGGAATAAGAAGAAT	58.522	33.333	0.00	0.00	0.00	2.40
1698	1803	1.544724	GGTACACATGCATGGTTGGT	58.455	50.000	29.41	21.81	0.00	3.67
1738	1843	0.391130	GCATGACGCCTTGACCACTA	60.391	55.000	0.00	0.00	32.94	2.74
1784	1889	0.672401	GAAACAATCGGCCGGAGACA	60.672	55.000	27.83	5.39	0.00	3.41
1786	1891	4.609995	GAAACAATCGGCCGGAGA	57.390	55.556	27.83	6.34	0.00	3.71
1821	1929	1.213537	GTGGCACATGCGCAAGAAT	59.786	52.632	20.91	0.00	44.52	2.40
1939	2945	2.360483	TGCCGAGCATTTTTCTCAAACA	59.640	40.909	0.00	0.00	31.71	2.83
2011	3017	1.078759	GAACCTCGATGAGCACACCG	61.079	60.000	0.00	0.00	0.00	4.94
2081	3096	3.047877	GTACCACACCACGCCAGC	61.048	66.667	0.00	0.00	0.00	4.85
2102	3117	3.609853	GCACATCCAGACCTTCATGTAA	58.390	45.455	0.00	0.00	0.00	2.41
2126	3141	4.688879	CGTTGACATGCTTAGTCTTAACCA	59.311	41.667	0.00	0.00	36.94	3.67
2135	3150	0.739462	TCCGCCGTTGACATGCTTAG	60.739	55.000	0.00	0.00	0.00	2.18
2139	3154	3.799755	GGTCCGCCGTTGACATGC	61.800	66.667	0.00	0.00	34.36	4.06
2140	3155	3.124921	GGGTCCGCCGTTGACATG	61.125	66.667	0.00	0.00	34.36	3.21
2151	3166	5.952526	ATTGTGTAAACTTTAAGGGTCCG	57.047	39.130	0.00	0.00	0.00	4.79
2160	3175	8.908903	TCCACAGACAAATATTGTGTAAACTTT	58.091	29.630	0.00	0.00	45.52	2.66
2163	3178	7.871853	AGTCCACAGACAAATATTGTGTAAAC	58.128	34.615	0.00	0.96	45.52	2.01
2165	3180	9.733556	ATTAGTCCACAGACAAATATTGTGTAA	57.266	29.630	0.00	0.00	45.52	2.41
2166	3181	9.378551	GATTAGTCCACAGACAAATATTGTGTA	57.621	33.333	0.00	0.00	45.52	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.