AutoCloner

Multiple sequence alignment - TraesCS3A01G228700

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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	TraesCS3A01G228700	chr3A	100.000	2249	0	0	1	2249	427758427	427760675	0.000000e+00	4154.0
1	TraesCS3A01G228700	chr3B	90.781	1779	90	29	4	1750	413043781	413042045	0.000000e+00	2309.0
2	TraesCS3A01G228700	chr3B	93.030	330	18	5	1923	2249	413041694	413041367	5.620000e-131	477.0
3	TraesCS3A01G228700	chr3B	92.000	125	6	2	1678	1798	413042041	413041917	2.970000e-39	172.0
4	TraesCS3A01G228700	chr3D	93.768	1428	44	15	854	2249	308264119	308265533	0.000000e+00	2102.0
5	TraesCS3A01G228700	chr3D	88.591	596	47	14	237	815	308263522	308264113	0.000000e+00	704.0
6	TraesCS3A01G228700	chr3D	83.553	152	14	5	1216	1363	16425344	16425200	5.040000e-27	132.0
7	TraesCS3A01G228700	chr7A	85.135	148	14	4	1216	1363	343178961	343179100	6.470000e-31	145.0
8	TraesCS3A01G228700	chr1B	84.416	154	13	9	2069	2211	655778267	655778420	8.370000e-30	141.0
9	TraesCS3A01G228700	chr1A	84.416	154	13	4	2069	2211	566006761	566006914	8.370000e-30	141.0
10	TraesCS3A01G228700	chr6B	84.459	148	16	3	1216	1363	10523181	10523041	3.010000e-29	139.0
11	TraesCS3A01G228700	chr6B	83.108	148	18	3	1216	1363	10587411	10587271	6.520000e-26	128.0
12	TraesCS3A01G228700	chr6B	82.432	148	19	3	1216	1363	10394388	10394248	3.030000e-24	122.0
13	TraesCS3A01G228700	chr4A	83.784	148	17	2	1216	1363	697959557	697959417	1.400000e-27	134.0
14	TraesCS3A01G228700	chr1D	84.106	151	9	5	2069	2211	471605935	471606078	5.040000e-27	132.0
15	TraesCS3A01G228700	chr5D	81.879	149	19	5	1216	1363	117738149	117738290	3.920000e-23	119.0
16	TraesCS3A01G228700	chr2B	100.000	28	0	0	335	362	671009074	671009101	4.000000e-03	52.8

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	TraesCS3A01G228700	chr3A	427758427	427760675	2248	False	4154	4154	100.0000	1	2249	1	chr3A.!!$F1	2248
1	TraesCS3A01G228700	chr3B	413041367	413043781	2414	True	986	2309	91.9370	4	2249	3	chr3B.!!$R1	2245
2	TraesCS3A01G228700	chr3D	308263522	308265533	2011	False	1403	2102	91.1795	237	2249	2	chr3D.!!$F1	2012

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
630	669	0.324943	CAAACCGGGATCCTGTGACT	59.675	55.0	19.51	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1711	1775	1.033746	ATGGCCTCAATGAACTGGCG	61.034	55.0	3.32	0.0	45.75	5.69	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
33	35	9.988815	TGAAATTCTTAAAATTTTCGAATCCCA	57.011	25.926	20.01	17.76	30.68	4.37
37	39	6.837992	TCTTAAAATTTTCGAATCCCAGACG	58.162	36.000	6.72	0.00	0.00	4.18
38	40	6.428771	TCTTAAAATTTTCGAATCCCAGACGT	59.571	34.615	6.72	0.00	0.00	4.34
66	68	4.626042	TCCAATGGTGAACAATTTTTCGG	58.374	39.130	0.00	0.00	0.00	4.30
67	69	4.342378	TCCAATGGTGAACAATTTTTCGGA	59.658	37.500	0.00	0.00	0.00	4.55
72	74	4.339530	TGGTGAACAATTTTTCGGACATGA	59.660	37.500	0.00	0.00	0.00	3.07
140	144	9.737427	TTTCTATAAACGTGAGCAAATTTCAAA	57.263	25.926	0.00	0.00	0.00	2.69
214	218	3.401033	GGAACCCCCTGAACAATTTTG	57.599	47.619	0.00	0.00	0.00	2.44
215	219	2.969262	GGAACCCCCTGAACAATTTTGA	59.031	45.455	0.00	0.00	0.00	2.69
216	220	3.006859	GGAACCCCCTGAACAATTTTGAG	59.993	47.826	0.00	0.00	0.00	3.02
217	221	3.611025	ACCCCCTGAACAATTTTGAGA	57.389	42.857	0.00	0.00	0.00	3.27
282	286	8.840321	TGTGAACAAATTTTGAAAAACAGGAAA	58.160	25.926	15.81	0.00	0.00	3.13
283	287	9.670719	GTGAACAAATTTTGAAAAACAGGAAAA	57.329	25.926	15.81	0.00	0.00	2.29
628	667	1.131303	ACCAAACCGGGATCCTGTGA	61.131	55.000	19.51	0.00	40.22	3.58
630	669	0.324943	CAAACCGGGATCCTGTGACT	59.675	55.000	19.51	0.00	0.00	3.41
642	681	3.021695	TCCTGTGACTCGGTAAATCGAT	58.978	45.455	0.00	0.00	38.55	3.59
646	685	3.692593	TGTGACTCGGTAAATCGATCAGA	59.307	43.478	0.00	0.00	38.55	3.27
688	747	1.669115	CTCGCACCTGTTCCCTGTG	60.669	63.158	0.00	0.00	0.00	3.66
697	756	1.608590	CTGTTCCCTGTGCGTTTCAAT	59.391	47.619	0.00	0.00	0.00	2.57
735	794	7.502339	CAGTTAGCGTCAAATAGAATATTCGG	58.498	38.462	9.78	0.00	0.00	4.30
752	811	1.978617	GGTGTCCACAATGCCCAGG	60.979	63.158	0.00	0.00	0.00	4.45
753	812	1.228552	GTGTCCACAATGCCCAGGT	60.229	57.895	0.00	0.00	0.00	4.00
952	1012	2.035626	ACATCCCCAAAGGCCACG	59.964	61.111	5.01	0.00	34.51	4.94
1225	1285	0.321653	CGAGCCCAAACCTAGCTTGT	60.322	55.000	0.00	0.00	36.87	3.16
1252	1312	2.365105	TGTCCCCCGTCTGATCCC	60.365	66.667	0.00	0.00	0.00	3.85
1369	1431	1.141858	GATCCCTGGGTGGTGATCTTC	59.858	57.143	13.56	0.00	38.44	2.87
1385	1447	6.142139	GTGATCTTCTATCTGATCTGTGTCG	58.858	44.000	0.00	0.00	39.63	4.35
1399	1461	8.352752	TGATCTGTGTCGAATAATGTTATGTC	57.647	34.615	0.00	0.00	0.00	3.06
1401	1463	5.746721	TCTGTGTCGAATAATGTTATGTCGG	59.253	40.000	0.00	0.00	31.20	4.79
1402	1464	5.412640	TGTGTCGAATAATGTTATGTCGGT	58.587	37.500	0.00	0.00	31.20	4.69
1506	1569	6.876789	TGAACTTTCAGTGTTAGTTGTCTGAA	59.123	34.615	14.43	0.00	42.57	3.02
1719	1783	1.237285	ACCAGAATGCACGCCAGTTC	61.237	55.000	0.00	0.00	31.97	3.01
1761	1901	7.675962	TTAGTTAGTTGTGTTGTTGTTGAGT	57.324	32.000	0.00	0.00	0.00	3.41
1862	2084	5.640357	CACTTCCAAATAGTAAGCCGTGTTA	59.360	40.000	0.00	0.00	0.00	2.41
1917	2139	4.890088	ACTAGATAGACAACGTTTTGCCA	58.110	39.130	0.00	0.00	36.00	4.92
1918	2140	4.929808	ACTAGATAGACAACGTTTTGCCAG	59.070	41.667	0.00	0.00	36.00	4.85
1920	2142	4.134563	AGATAGACAACGTTTTGCCAGTT	58.865	39.130	0.00	0.00	36.00	3.16
2003	2249	8.922676	TGTTATGATCTTAAGAAGTTGACGTTC	58.077	33.333	9.71	0.00	0.00	3.95
2025	2271	6.060028	TCAACTTTAACTTGCTGTGATCAC	57.940	37.500	19.27	19.27	0.00	3.06
2137	2388	5.305644	ACAGGTATCCATCTATTCTCACCAC	59.694	44.000	0.00	0.00	0.00	4.16
2138	2389	5.305386	CAGGTATCCATCTATTCTCACCACA	59.695	44.000	0.00	0.00	0.00	4.17
2139	2390	6.013898	CAGGTATCCATCTATTCTCACCACAT	60.014	42.308	0.00	0.00	0.00	3.21
2140	2391	6.212388	AGGTATCCATCTATTCTCACCACATC	59.788	42.308	0.00	0.00	0.00	3.06
2142	2393	5.955961	TCCATCTATTCTCACCACATCAA	57.044	39.130	0.00	0.00	0.00	2.57
2143	2394	5.674525	TCCATCTATTCTCACCACATCAAC	58.325	41.667	0.00	0.00	0.00	3.18
2144	2395	4.509230	CCATCTATTCTCACCACATCAACG	59.491	45.833	0.00	0.00	0.00	4.10
2154	2406	3.938334	CACCACATCAACGGAATCATGTA	59.062	43.478	0.00	0.00	0.00	2.29
2203	2455	4.913784	TCTAAACCACCATAACCCTGAAC	58.086	43.478	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	6.608610	ACGTCTGGGATTCGAAAATTTTAAG	58.391	36.000	0.00	1.58	0.00	1.85
19	20	5.447624	AAAACGTCTGGGATTCGAAAATT	57.552	34.783	0.00	0.00	0.00	1.82
21	22	4.904253	AAAAACGTCTGGGATTCGAAAA	57.096	36.364	0.00	0.00	0.00	2.29
64	66	9.061610	GTTGTTAAATAAATGTTCTCATGTCCG	57.938	33.333	0.00	0.00	34.19	4.79
66	68	9.607285	ACGTTGTTAAATAAATGTTCTCATGTC	57.393	29.630	0.00	0.00	34.19	3.06
67	69	9.393249	CACGTTGTTAAATAAATGTTCTCATGT	57.607	29.630	0.00	0.00	34.19	3.21
72	74	9.790389	TTGTTCACGTTGTTAAATAAATGTTCT	57.210	25.926	0.00	0.00	0.00	3.01
140	144	8.693625	TCAAAATTTCAAGAAATGGCCAATTTT	58.306	25.926	10.96	11.28	40.57	1.82
144	148	6.600822	TGTTCAAAATTTCAAGAAATGGCCAA	59.399	30.769	10.96	0.00	40.57	4.52
200	204	4.144297	TCAGGTCTCAAAATTGTTCAGGG	58.856	43.478	0.00	0.00	0.00	4.45
201	205	5.067674	TGTTCAGGTCTCAAAATTGTTCAGG	59.932	40.000	0.00	0.00	0.00	3.86
202	206	6.135290	TGTTCAGGTCTCAAAATTGTTCAG	57.865	37.500	0.00	0.00	0.00	3.02
203	207	6.713762	ATGTTCAGGTCTCAAAATTGTTCA	57.286	33.333	0.00	0.00	0.00	3.18
204	208	8.424274	AAAATGTTCAGGTCTCAAAATTGTTC	57.576	30.769	0.00	0.00	0.00	3.18
205	209	8.791327	AAAAATGTTCAGGTCTCAAAATTGTT	57.209	26.923	0.00	0.00	0.00	2.83
250	254	9.753669	GTTTTTCAAAATTTGTTCACAGGTTAG	57.246	29.630	5.56	0.00	0.00	2.34
595	634	1.110518	TTTGGTTCCCAAGGCGGTTC	61.111	55.000	0.00	0.00	44.84	3.62
628	667	4.440250	CCACTTCTGATCGATTTACCGAGT	60.440	45.833	0.00	0.00	42.21	4.18
630	669	3.181479	CCCACTTCTGATCGATTTACCGA	60.181	47.826	0.00	0.00	43.16	4.69
664	723	1.664965	GAACAGGTGCGAGCGAACT	60.665	57.895	0.51	0.00	0.00	3.01
688	747	3.360669	GCGACAAACTTTCATTGAAACGC	60.361	43.478	19.70	19.70	39.08	4.84
697	756	3.602390	GCTAACTGCGACAAACTTTCA	57.398	42.857	0.00	0.00	0.00	2.69
735	794	1.228552	ACCTGGGCATTGTGGACAC	60.229	57.895	0.00	0.00	0.00	3.67
752	811	2.861147	ACTTTCCAAGTAGCCAGGAC	57.139	50.000	0.00	0.00	40.69	3.85
753	812	3.486383	CAAACTTTCCAAGTAGCCAGGA	58.514	45.455	0.00	0.00	41.91	3.86
759	818	2.593026	TGGGCCAAACTTTCCAAGTAG	58.407	47.619	2.13	0.00	41.91	2.57
952	1012	2.674462	GCTGGACGAAAACCCTAGAGAC	60.674	54.545	0.00	0.00	0.00	3.36
1225	1285	2.592993	CGGGGGACAGAAGCTGGAA	61.593	63.158	0.00	0.00	35.51	3.53
1369	1431	8.809159	AACATTATTCGACACAGATCAGATAG	57.191	34.615	0.00	0.00	0.00	2.08
1385	1447	5.924254	TCGATCCACCGACATAACATTATTC	59.076	40.000	0.00	0.00	33.14	1.75
1506	1569	3.562973	CGCATCAGGCAGAGAAATACAAT	59.437	43.478	0.00	0.00	45.17	2.71
1568	1631	8.756864	GCAATAATGAGTAGTACTGCTTACTTC	58.243	37.037	15.09	2.77	41.60	3.01
1583	1646	5.621197	TTACGCAACAAGCAATAATGAGT	57.379	34.783	0.00	0.00	46.13	3.41
1672	1736	3.488778	AAATCCATCTAGGCTGCTGAG	57.511	47.619	0.00	0.00	37.29	3.35
1711	1775	1.033746	ATGGCCTCAATGAACTGGCG	61.034	55.000	3.32	0.00	45.75	5.69
1719	1783	4.147321	ACTAATTAGCCATGGCCTCAATG	58.853	43.478	33.14	20.60	43.17	2.82
1759	1899	9.435570	ACCTTATATCAGGTATAAACTGTGACT	57.564	33.333	6.82	0.00	46.14	3.41
1843	2065	5.318349	CGTTTAACACGGCTTACTATTTGG	58.682	41.667	0.00	0.00	45.89	3.28
1862	2084	6.928492	ACAAAATTTCTATGTGGCAATCGTTT	59.072	30.769	0.00	0.00	0.00	3.60
1917	2139	8.255206	TGTAGACAAATCGTACCATAATCAACT	58.745	33.333	0.00	0.00	0.00	3.16
1918	2140	8.415192	TGTAGACAAATCGTACCATAATCAAC	57.585	34.615	0.00	0.00	0.00	3.18
1920	2142	8.417884	TGATGTAGACAAATCGTACCATAATCA	58.582	33.333	0.00	0.00	0.00	2.57
2003	2249	5.215160	GGTGATCACAGCAAGTTAAAGTTG	58.785	41.667	26.47	0.00	43.08	3.16
2134	2385	3.938334	TGTACATGATTCCGTTGATGTGG	59.062	43.478	0.00	0.00	31.56	4.17
2137	2388	4.271049	GGACTGTACATGATTCCGTTGATG	59.729	45.833	0.00	0.00	0.00	3.07
2138	2389	4.081142	TGGACTGTACATGATTCCGTTGAT	60.081	41.667	0.00	0.00	0.00	2.57
2139	2390	3.259625	TGGACTGTACATGATTCCGTTGA	59.740	43.478	0.00	0.00	0.00	3.18
2140	2391	3.595173	TGGACTGTACATGATTCCGTTG	58.405	45.455	0.00	0.00	0.00	4.10
2142	2393	2.832129	ACTGGACTGTACATGATTCCGT	59.168	45.455	0.00	1.32	0.00	4.69
2143	2394	3.526931	ACTGGACTGTACATGATTCCG	57.473	47.619	0.00	0.77	0.00	4.30
2144	2395	5.730550	TGTTACTGGACTGTACATGATTCC	58.269	41.667	0.00	1.05	0.00	3.01
2154	2406	4.162698	TGTGTAACCTTGTTACTGGACTGT	59.837	41.667	15.74	0.00	34.36	3.55
2203	2455	3.829886	TCTTGTGAAGCGGCTAATTTG	57.170	42.857	1.35	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.