AutoCloner

Multiple sequence alignment - TraesCS6B01G091900

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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	TraesCS6B01G091900	chr6B	100.000	2234	0	0	1	2234	67503687	67505920	0.000000e+00	4126.0
1	TraesCS6B01G091900	chr6B	93.756	2242	113	16	1	2234	68640528	68638306	0.000000e+00	3339.0
2	TraesCS6B01G091900	chr6B	82.270	141	20	5	1933	2071	622753098	622753235	1.400000e-22	117.0
3	TraesCS6B01G091900	chr6A	87.078	1509	123	31	197	1675	36398424	36399890	0.000000e+00	1640.0
4	TraesCS6B01G091900	chr6A	90.123	567	53	3	1669	2234	36401009	36401573	0.000000e+00	734.0
5	TraesCS6B01G091900	chr6A	90.789	152	10	2	1	152	36398278	36398425	1.350000e-47	200.0
6	TraesCS6B01G091900	chr6D	87.303	1205	94	22	197	1373	31827008	31828181	0.000000e+00	1323.0
7	TraesCS6B01G091900	chr6D	83.742	326	38	9	1403	1724	31828180	31828494	6.030000e-76	294.0
8	TraesCS6B01G091900	chr5D	82.487	394	60	8	1797	2187	441931206	441930819	9.880000e-89	337.0
9	TraesCS6B01G091900	chr5B	78.715	249	42	9	1797	2040	662606975	662606733	2.970000e-34	156.0
10	TraesCS6B01G091900	chr2B	78.829	222	41	6	1847	2065	556207872	556208090	6.430000e-31	145.0
11	TraesCS6B01G091900	chr1D	77.824	239	42	9	1813	2045	17524331	17524564	1.080000e-28	137.0
12	TraesCS6B01G091900	chr2A	81.197	117	17	1	995	1106	733583778	733583894	3.060000e-14	89.8

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	TraesCS6B01G091900	chr6B	67503687	67505920	2233	False	4126.0	4126	100.0000	1	2234	1	chr6B.!!$F1	2233
1	TraesCS6B01G091900	chr6B	68638306	68640528	2222	True	3339.0	3339	93.7560	1	2234	1	chr6B.!!$R1	2233
2	TraesCS6B01G091900	chr6A	36398278	36401573	3295	False	858.0	1640	89.3300	1	2234	3	chr6A.!!$F1	2233
3	TraesCS6B01G091900	chr6D	31827008	31828494	1486	False	808.5	1323	85.5225	197	1724	2	chr6D.!!$F1	1527

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
941	992	1.126846	CGTTTCTCGCATCACAAGGTC	59.873	52.381	0.0	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1805	2992	2.430694	TCTATAACCTCGCATGCACACT	59.569	45.455	19.57	0.0	0.0	3.55	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	Hairpin	End Stability
22	23	2.290367	TGCAATCCACAAACTCTTGTCG	59.710	45.455	0.00	44.15	4.35
23	24	2.290641	GCAATCCACAAACTCTTGTCGT	59.709	45.455	0.00	44.15	4.34
24	25	3.243068	GCAATCCACAAACTCTTGTCGTT	60.243	43.478	0.00	44.15	3.85
25	26	4.733523	GCAATCCACAAACTCTTGTCGTTT	60.734	41.667	0.00	44.15	3.60
27	28	3.601435	TCCACAAACTCTTGTCGTTTCA	58.399	40.909	0.00	44.15	2.69
28	29	3.621268	TCCACAAACTCTTGTCGTTTCAG	59.379	43.478	0.00	44.15	3.02
30	31	4.494199	CCACAAACTCTTGTCGTTTCAGTC	60.494	45.833	0.00	44.15	3.51
31	32	3.621715	ACAAACTCTTGTCGTTTCAGTCC	59.378	43.478	0.00	42.25	3.85
32	33	3.821421	AACTCTTGTCGTTTCAGTCCT	57.179	42.857	0.00	0.00	3.85
33	34	3.099267	ACTCTTGTCGTTTCAGTCCTG	57.901	47.619	0.00	0.00	3.86
75	76	4.097741	TCCACAAACCAACACAAATCAGAG	59.902	41.667	0.00	0.00	3.35
82	83	8.755018	CAAACCAACACAAATCAGAGAATAAAC	58.245	33.333	0.00	0.00	2.01
152	153	6.145535	CGAGCAATATTTAGCAAATCCCTTC	58.854	40.000	1.12	32.38	3.46
167	168	7.521585	GCAAATCCCTTCGGTACCATTATTTAG	60.522	40.741	13.54	0.00	1.85
171	172	7.221450	TCCCTTCGGTACCATTATTTAGATTG	58.779	38.462	13.54	0.00	2.67
183	184	9.305925	CCATTATTTAGATTGGAGCTTTTCAAC	57.694	33.333	0.00	0.00	3.18
422	429	4.764679	TCCAACCACAAAATGATTCTCG	57.235	40.909	0.00	0.00	4.04
494	501	6.530120	TGCTCTACCTTTGTCTAATCAAACA	58.470	36.000	0.00	34.30	2.83
516	523	2.542411	GCTCGCCAGCCAAATAAATCTG	60.542	50.000	0.00	40.14	2.90
536	543	2.092646	TGGAATGGAGGGATAACAACGG	60.093	50.000	0.00	0.00	4.44
595	623	6.049790	CCTGATGATGATATAGAGCATGTGG	58.950	44.000	0.00	29.84	4.17
896	944	4.547671	TCAGGACTACAAATAGGAGGGAG	58.452	47.826	0.00	32.08	4.30
898	946	2.036089	GGACTACAAATAGGAGGGAGCG	59.964	54.545	0.00	32.08	5.03
899	947	2.957006	GACTACAAATAGGAGGGAGCGA	59.043	50.000	0.00	32.08	4.93
900	948	2.959707	ACTACAAATAGGAGGGAGCGAG	59.040	50.000	0.00	32.08	5.03
941	992	1.126846	CGTTTCTCGCATCACAAGGTC	59.873	52.381	0.00	0.00	3.85
961	1012	4.715523	TGGCCCCGTAGCACAAGC	62.716	66.667	0.00	42.56	4.01
1052	1103	4.399395	CCTCCTGCTGGCGCTCAA	62.399	66.667	7.64	36.97	3.02
1296	1350	7.080473	TATGATTCCATTGCAAGTGTGCTACT	61.080	38.462	4.94	41.54	2.57
1424	1481	9.442047	GTAGCATTCCAATTCTACAGCTATAAT	57.558	33.333	4.74	35.89	1.28
1451	1508	4.457257	TGTGCAATGATAAACCATGTTCGA	59.543	37.500	0.00	0.00	3.71
1464	1521	7.867445	AACCATGTTCGAAACACAAATAATC	57.133	32.000	0.00	45.50	1.75
1467	1524	6.307800	CCATGTTCGAAACACAAATAATCCAC	59.692	38.462	0.00	45.50	4.02
1490	1547	3.681897	CCATCCTTCAGAAGAACAGAACG	59.318	47.826	12.14	0.00	3.95
1556	1613	2.243478	TGCTCTAGTCTGGATCAGTCCT	59.757	50.000	0.00	45.32	3.85
1644	1703	6.795590	TCCCTTTAGGTGGACAAAATTCATA	58.204	36.000	0.00	36.75	2.15
1645	1704	7.242359	TCCCTTTAGGTGGACAAAATTCATAA	58.758	34.615	0.00	36.75	1.90
1751	2938	2.681976	GCCTCAGTGCTCATACAACCAT	60.682	50.000	0.00	0.00	3.55
1754	2941	4.813161	CCTCAGTGCTCATACAACCATAAG	59.187	45.833	0.00	0.00	1.73
1776	2963	2.671070	GCGTTTGAATGTGGTCAATCCC	60.671	50.000	0.00	37.36	3.85
1788	2975	1.162505	TCAATCCCAAGGTTTCCCCA	58.837	50.000	0.00	34.66	4.96
1791	2978	2.708325	CAATCCCAAGGTTTCCCCAAAA	59.292	45.455	0.00	34.66	2.44
1846	3033	9.967451	TTATAGATTGTTTTGTCCCTAATGTGA	57.033	29.630	0.00	0.00	3.58
1905	3092	3.547649	GGTACGAAACAAAGGCGAATT	57.452	42.857	0.00	0.00	2.17
1963	3150	8.628882	ACACTTAAAAATGTTTCACAGCTAAC	57.371	30.769	0.00	0.00	2.34
1975	3162	5.375417	TCACAGCTAACCAACATCATTTG	57.625	39.130	0.00	0.00	2.32
1976	3163	5.069318	TCACAGCTAACCAACATCATTTGA	58.931	37.500	0.00	0.00	2.69
1978	3165	6.040278	TCACAGCTAACCAACATCATTTGAAA	59.960	34.615	0.00	0.00	2.69
2041	3228	6.687081	TGTCAAAATTGAAGTTACGGTTCT	57.313	33.333	0.00	39.21	3.01
2042	3229	7.090953	TGTCAAAATTGAAGTTACGGTTCTT	57.909	32.000	0.00	39.21	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	2.866762	GACAGTGTGACAGGACTGAAAC	59.133	50.000	17.61	4.52	41.90	2.78
23	24	2.158957	GGACAGTGTGACAGGACTGAAA	60.159	50.000	17.61	0.00	41.90	2.69
24	25	1.412710	GGACAGTGTGACAGGACTGAA	59.587	52.381	17.61	0.00	41.90	3.02
25	26	1.040646	GGACAGTGTGACAGGACTGA	58.959	55.000	17.61	0.00	41.90	3.41
27	28	1.043816	CAGGACAGTGTGACAGGACT	58.956	55.000	0.00	0.00	0.00	3.85
28	29	1.040646	TCAGGACAGTGTGACAGGAC	58.959	55.000	0.00	0.00	0.00	3.85
30	31	2.224378	ACAATCAGGACAGTGTGACAGG	60.224	50.000	0.00	0.00	0.00	4.00
31	32	3.117491	ACAATCAGGACAGTGTGACAG	57.883	47.619	0.00	0.00	0.00	3.51
32	33	3.466836	GAACAATCAGGACAGTGTGACA	58.533	45.455	0.00	0.00	0.00	3.58
33	34	2.808543	GGAACAATCAGGACAGTGTGAC	59.191	50.000	0.00	0.00	0.00	3.67
152	153	6.231211	AGCTCCAATCTAAATAATGGTACCG	58.769	40.000	7.57	0.00	34.50	4.02
183	184	5.909621	ATGTGGTCAATCTCAAAATGGAG	57.090	39.130	0.00	0.00	36.21	3.86
247	248	2.950975	TCTGCATTGTGTTTCTCAAGCA	59.049	40.909	0.00	0.00	32.65	3.91
248	249	3.243168	TGTCTGCATTGTGTTTCTCAAGC	60.243	43.478	0.00	0.00	0.00	4.01
422	429	4.466015	CCCACCCATAATTATGCCAATACC	59.534	45.833	18.40	0.00	32.40	2.73
466	473	4.826274	TTAGACAAAGGTAGAGCATGCT	57.174	40.909	22.92	22.92	0.00	3.79
494	501	1.678101	GATTTATTTGGCTGGCGAGCT	59.322	47.619	20.62	2.93	45.44	4.09
516	523	2.092592	ACCGTTGTTATCCCTCCATTCC	60.093	50.000	0.00	0.00	0.00	3.01
536	543	6.531503	TGGATAAAGATGGATAGGATCGAC	57.468	41.667	0.00	0.00	0.00	4.20
883	931	0.465705	TGCTCGCTCCCTCCTATTTG	59.534	55.000	0.00	0.00	0.00	2.32
896	944	1.221414	GGTATGGATGTCTTGCTCGC	58.779	55.000	0.00	0.00	0.00	5.03
898	946	2.939103	GTGTGGTATGGATGTCTTGCTC	59.061	50.000	0.00	0.00	0.00	4.26
899	947	2.573462	AGTGTGGTATGGATGTCTTGCT	59.427	45.455	0.00	0.00	0.00	3.91
900	948	2.939103	GAGTGTGGTATGGATGTCTTGC	59.061	50.000	0.00	0.00	0.00	4.01
941	992	4.690719	TGTGCTACGGGGCCAACG	62.691	66.667	16.38	16.38	37.36	4.10
961	1012	2.549754	AGCTGGTTTTGTGATGAACTCG	59.450	45.455	0.00	0.00	0.00	4.18
1080	1131	1.975407	CTTGAGGTTGCAGCAGGGG	60.975	63.158	2.05	0.00	0.00	4.79
1143	1194	0.748005	CGGAGAATGGCGAAATGGGT	60.748	55.000	0.00	0.00	0.00	4.51
1208	1262	3.702048	CGGGGAAGACCTTGCGGA	61.702	66.667	0.00	0.00	40.03	5.54
1268	1322	4.009675	ACACTTGCAATGGAATCATACGT	58.990	39.130	0.00	0.00	32.44	3.57
1296	1350	0.108329	GCGAAACTAGCTAGGTGCCA	60.108	55.000	24.35	0.00	44.23	4.92
1424	1481	4.280425	ACATGGTTTATCATTGCACACACA	59.720	37.500	0.00	0.00	0.00	3.72
1451	1508	5.341169	AGGATGGGTGGATTATTTGTGTTT	58.659	37.500	0.00	0.00	0.00	2.83
1464	1521	2.040278	TGTTCTTCTGAAGGATGGGTGG	59.960	50.000	16.83	0.00	32.15	4.61
1467	1524	3.988976	TCTGTTCTTCTGAAGGATGGG	57.011	47.619	16.83	3.88	32.15	4.00
1490	1547	6.393171	GGCAGATTTAATTGGAGGATTATGC	58.607	40.000	0.00	0.00	0.00	3.14
1556	1613	0.176680	GAGAAGGCAGCCGAGATGAA	59.823	55.000	5.55	0.00	0.00	2.57
1644	1703	1.946267	CGCAGTTGCTAAACCGGTT	59.054	52.632	15.86	15.86	36.94	4.44
1645	1704	2.613506	GCGCAGTTGCTAAACCGGT	61.614	57.895	0.00	0.00	36.94	5.28
1714	2898	6.405731	GCACTGAGGCCACATTCAAAAATATA	60.406	38.462	5.01	0.00	0.00	0.86
1719	2903	1.340889	GCACTGAGGCCACATTCAAAA	59.659	47.619	5.01	0.00	0.00	2.44
1751	2938	2.852449	TGACCACATTCAAACGCCTTA	58.148	42.857	0.00	0.00	0.00	2.69
1754	2941	2.595386	GATTGACCACATTCAAACGCC	58.405	47.619	0.00	0.00	38.95	5.68
1791	2978	4.167554	TGCACACTTCGACAAAAACTTT	57.832	36.364	0.00	0.00	0.00	2.66
1805	2992	2.430694	TCTATAACCTCGCATGCACACT	59.569	45.455	19.57	0.00	0.00	3.55
1846	3033	8.680039	ATTGGAAATCAACACATCAACAAAAT	57.320	26.923	0.00	0.00	38.31	1.82
1899	3086	6.138761	CCTTAATCAATAGCTCACAATTCGC	58.861	40.000	0.00	0.00	0.00	4.70
1905	3092	5.252547	TGCAACCTTAATCAATAGCTCACA	58.747	37.500	0.00	0.00	0.00	3.58
1956	3143	7.894376	ATTTTCAAATGATGTTGGTTAGCTG	57.106	32.000	0.00	0.00	0.00	4.24
1963	3150	8.815141	TGTGTAGAATTTTCAAATGATGTTGG	57.185	30.769	0.00	0.00	0.00	3.77
2055	3242	8.935844	GGGGCAGATTCAAATACTTTTTAAAAG	58.064	33.333	15.03	15.03	0.00	2.27
2160	3347	6.697019	CCTGTTTTAAGTGACACCAGAAAATG	59.303	38.462	0.84	4.72	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.