AutoCloner

Multiple sequence alignment - TraesCS3D01G348600

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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	TraesCS3D01G348600	chr3D	100.000	2620	0	0	1	2620	460260002	460257383	0.000000e+00	4839.0
1	TraesCS3D01G348600	chr3D	90.935	706	57	6	1	700	164524961	164525665	0.000000e+00	942.0
2	TraesCS3D01G348600	chr3A	93.909	1773	89	14	742	2498	602273144	602271375	0.000000e+00	2658.0
3	TraesCS3D01G348600	chr3A	95.238	84	3	1	2518	2601	602245754	602245672	5.880000e-27	132.0
4	TraesCS3D01G348600	chr3A	85.455	55	7	1	2082	2135	66912609	66912555	3.640000e-04	56.5
5	TraesCS3D01G348600	chr3B	92.926	1343	73	14	700	2030	610221724	610220392	0.000000e+00	1934.0
6	TraesCS3D01G348600	chr3B	91.142	508	26	9	2128	2620	610220387	610219884	0.000000e+00	671.0
7	TraesCS3D01G348600	chr3B	91.489	47	3	1	2043	2089	383718993	383719038	2.180000e-06	63.9
8	TraesCS3D01G348600	chr7D	94.564	699	34	4	1	698	123213898	123213203	0.000000e+00	1077.0
9	TraesCS3D01G348600	chr7D	93.608	704	38	5	1	702	83325340	83324642	0.000000e+00	1044.0
10	TraesCS3D01G348600	chr6B	93.714	700	41	2	1	699	58307640	58306943	0.000000e+00	1046.0
11	TraesCS3D01G348600	chr6B	91.441	701	45	9	1	699	519412710	519412023	0.000000e+00	948.0
12	TraesCS3D01G348600	chr7B	93.143	700	45	3	1	699	135393988	135394685	0.000000e+00	1024.0
13	TraesCS3D01G348600	chr2B	93.000	700	46	3	1	699	695894624	695895321	0.000000e+00	1018.0
14	TraesCS3D01G348600	chr2B	92.857	700	47	3	1	699	695967441	695968138	0.000000e+00	1013.0
15	TraesCS3D01G348600	chr2B	92.571	700	49	3	1	699	695931326	695932023	0.000000e+00	1002.0
16	TraesCS3D01G348600	chr1B	80.260	461	45	15	1534	1968	79980313	79980753	3.280000e-79	305.0
17	TraesCS3D01G348600	chr6A	89.831	59	5	1	2036	2093	162961253	162961195	1.010000e-09	75.0
18	TraesCS3D01G348600	chr2D	84.211	76	8	2	2044	2119	622872202	622872131	1.300000e-08	71.3
19	TraesCS3D01G348600	chr1A	96.970	33	1	0	2094	2126	25952483	25952451	3.640000e-04	56.5

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	TraesCS3D01G348600	chr3D	460257383	460260002	2619	True	4839.0	4839	100.000	1	2620	1	chr3D.!!$R1	2619
1	TraesCS3D01G348600	chr3D	164524961	164525665	704	False	942.0	942	90.935	1	700	1	chr3D.!!$F1	699
2	TraesCS3D01G348600	chr3A	602271375	602273144	1769	True	2658.0	2658	93.909	742	2498	1	chr3A.!!$R3	1756
3	TraesCS3D01G348600	chr3B	610219884	610221724	1840	True	1302.5	1934	92.034	700	2620	2	chr3B.!!$R1	1920
4	TraesCS3D01G348600	chr7D	123213203	123213898	695	True	1077.0	1077	94.564	1	698	1	chr7D.!!$R2	697
5	TraesCS3D01G348600	chr7D	83324642	83325340	698	True	1044.0	1044	93.608	1	702	1	chr7D.!!$R1	701
6	TraesCS3D01G348600	chr6B	58306943	58307640	697	True	1046.0	1046	93.714	1	699	1	chr6B.!!$R1	698
7	TraesCS3D01G348600	chr6B	519412023	519412710	687	True	948.0	948	91.441	1	699	1	chr6B.!!$R2	698
8	TraesCS3D01G348600	chr7B	135393988	135394685	697	False	1024.0	1024	93.143	1	699	1	chr7B.!!$F1	698
9	TraesCS3D01G348600	chr2B	695894624	695895321	697	False	1018.0	1018	93.000	1	699	1	chr2B.!!$F1	698
10	TraesCS3D01G348600	chr2B	695967441	695968138	697	False	1013.0	1013	92.857	1	699	1	chr2B.!!$F3	698
11	TraesCS3D01G348600	chr2B	695931326	695932023	697	False	1002.0	1002	92.571	1	699	1	chr2B.!!$F2	698

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
914	930	0.033991	CCTCGTCCTCCTCTTCTCCA	60.034	60.0	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2030	2064	1.997606	GTAATTCGGACCGAGGTTGTG	59.002	52.381	17.51	0.0	37.14	3.33	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
66	67	6.018262	TCGGAATATCACGAAATGTTCCATTC	60.018	38.462	20.85	7.73	43.44	2.67
69	70	8.190784	GGAATATCACGAAATGTTCCATTCTTT	58.809	33.333	18.23	0.00	43.03	2.52
116	118	3.112580	AGTTCGCGGTTTCAAATTTGTG	58.887	40.909	17.47	5.63	0.00	3.33
212	216	7.678947	TGTTCACATGGTTTCAAATTTGTTT	57.321	28.000	17.47	0.00	0.00	2.83
215	219	5.587844	TCACATGGTTTCAAATTTGTTTGGG	59.412	36.000	17.47	8.74	32.99	4.12
234	238	7.659390	TGTTTGGGATTTCATAATTTGTTCACC	59.341	33.333	0.00	0.00	0.00	4.02
448	457	3.153919	TGCAGTAATTGGTTCCTGTTCC	58.846	45.455	0.00	0.00	0.00	3.62
471	480	2.446435	ACAGTGCACAAGTCAGGTTTT	58.554	42.857	21.04	0.00	0.00	2.43
537	547	2.590291	TGTTGGCGATGTGTGCGT	60.590	55.556	0.00	0.00	0.00	5.24
708	723	1.872773	AGGAGCTCTCGGATTTTCCT	58.127	50.000	14.64	0.00	33.30	3.36
710	725	2.696187	AGGAGCTCTCGGATTTTCCTAC	59.304	50.000	14.64	0.00	33.47	3.18
711	726	2.696187	GGAGCTCTCGGATTTTCCTACT	59.304	50.000	14.64	0.00	33.30	2.57
712	727	3.890147	GGAGCTCTCGGATTTTCCTACTA	59.110	47.826	14.64	0.00	33.30	1.82
714	729	3.319689	AGCTCTCGGATTTTCCTACTAGC	59.680	47.826	0.00	0.00	33.30	3.42
715	730	3.553302	GCTCTCGGATTTTCCTACTAGCC	60.553	52.174	0.00	0.00	33.30	3.93
716	731	3.637229	CTCTCGGATTTTCCTACTAGCCA	59.363	47.826	0.00	0.00	33.30	4.75
717	732	4.028131	TCTCGGATTTTCCTACTAGCCAA	58.972	43.478	0.00	0.00	33.30	4.52
718	733	4.468510	TCTCGGATTTTCCTACTAGCCAAA	59.531	41.667	0.00	0.00	33.30	3.28
719	734	5.130477	TCTCGGATTTTCCTACTAGCCAAAT	59.870	40.000	0.00	0.00	33.30	2.32
720	735	5.751586	TCGGATTTTCCTACTAGCCAAATT	58.248	37.500	0.00	0.00	33.30	1.82
721	736	5.820947	TCGGATTTTCCTACTAGCCAAATTC	59.179	40.000	0.00	0.00	33.30	2.17
722	737	5.277345	CGGATTTTCCTACTAGCCAAATTCG	60.277	44.000	0.00	5.24	33.30	3.34
822	837	1.946768	CATCTCTCTCACGGTCCTCTC	59.053	57.143	0.00	0.00	0.00	3.20
883	899	1.341581	GGCAAGCAAGGTAATACCCCA	60.342	52.381	5.71	0.00	39.75	4.96
890	906	1.147600	GGTAATACCCCAGCACCCG	59.852	63.158	0.00	0.00	30.04	5.28
913	929	0.256464	TCCTCGTCCTCCTCTTCTCC	59.744	60.000	0.00	0.00	0.00	3.71
914	930	0.033991	CCTCGTCCTCCTCTTCTCCA	60.034	60.000	0.00	0.00	0.00	3.86
918	934	0.978667	GTCCTCCTCTTCTCCACCCC	60.979	65.000	0.00	0.00	0.00	4.95
922	938	2.428484	CCTCCTCTTCTCCACCCCATAT	60.428	54.545	0.00	0.00	0.00	1.78
927	943	3.318313	TCTTCTCCACCCCATATTCCTC	58.682	50.000	0.00	0.00	0.00	3.71
928	944	3.051032	TCTTCTCCACCCCATATTCCTCT	60.051	47.826	0.00	0.00	0.00	3.69
937	954	5.934625	CACCCCATATTCCTCTAAGAATTCG	59.065	44.000	0.00	0.00	37.62	3.34
942	959	7.600752	CCCATATTCCTCTAAGAATTCGTCTTC	59.399	40.741	0.00	0.00	43.49	2.87
944	961	9.405587	CATATTCCTCTAAGAATTCGTCTTCTC	57.594	37.037	0.00	0.00	43.49	2.87
946	963	7.469537	TTCCTCTAAGAATTCGTCTTCTCTT	57.530	36.000	0.00	0.00	43.49	2.85
959	976	4.442612	CGTCTTCTCTTGACATGGATCCAT	60.443	45.833	22.15	22.15	37.08	3.41
970	987	0.988063	TGGATCCATGGAAACCACGA	59.012	50.000	28.76	14.51	35.80	4.35
1021	1038	2.888212	CCCCTTTTCTTGGACCAATCA	58.112	47.619	7.54	0.00	0.00	2.57
1026	1043	4.298332	CTTTTCTTGGACCAATCAAACCG	58.702	43.478	7.54	0.00	0.00	4.44
1034	1051	0.609131	CCAATCAAACCGCCTGACCT	60.609	55.000	0.00	0.00	0.00	3.85
1049	1067	0.818938	GACCTCGTCCTCTCCTTTCC	59.181	60.000	0.00	0.00	0.00	3.13
1204	1222	3.998672	GCGGGGTTGTCCTCACGA	61.999	66.667	0.00	0.00	32.73	4.35
1239	1257	1.550869	CCCAACTGGCCCTTCTTCAAT	60.551	52.381	0.00	0.00	0.00	2.57
1314	1332	4.710167	ATCAGCAGCGCACCAGCA	62.710	61.111	11.47	0.00	42.27	4.41
1448	1472	4.518590	TGGATGTTGTGTTACCTGAATGTG	59.481	41.667	0.00	0.00	0.00	3.21
1455	1481	7.283354	TGTTGTGTTACCTGAATGTGTTATGAA	59.717	33.333	0.00	0.00	0.00	2.57
1498	1529	6.932356	TTTGTCTGGATATCTGCTTTCATC	57.068	37.500	2.05	0.00	0.00	2.92
1499	1530	4.965814	TGTCTGGATATCTGCTTTCATCC	58.034	43.478	2.05	0.00	37.95	3.51
1599	1631	7.039574	TGTTCAGTCCATTCATGTGATTTTGAT	60.040	33.333	0.00	0.00	0.00	2.57
1601	1633	8.217131	TCAGTCCATTCATGTGATTTTGATAG	57.783	34.615	0.00	0.00	0.00	2.08
1619	1651	9.995003	TTTTGATAGTAAATGCTTTGTTTCCAT	57.005	25.926	0.00	0.00	0.00	3.41
1625	1657	3.967332	ATGCTTTGTTTCCATTCTGGG	57.033	42.857	0.00	0.00	38.32	4.45
1627	1659	2.247358	GCTTTGTTTCCATTCTGGGGA	58.753	47.619	0.00	0.00	38.32	4.81
1640	1672	3.214694	TCTGGGGAATGGAAAGGACTA	57.785	47.619	0.00	0.00	0.00	2.59
1708	1740	6.238184	GCCATTGCAAAATTAAGATACCTTGC	60.238	38.462	1.71	1.22	39.62	4.01
1709	1741	7.043565	CCATTGCAAAATTAAGATACCTTGCT	58.956	34.615	1.71	0.00	39.82	3.91
1848	1880	2.543031	GCTGGTCGTTAGATGCGTGATA	60.543	50.000	0.00	0.00	0.00	2.15
2001	2035	5.918011	TCAACGTTGCAACTGGAAAATATTC	59.082	36.000	26.09	0.00	34.66	1.75
2030	2064	9.152595	CATCCCTAGTTAGTTTCTTTGTCTAAC	57.847	37.037	0.00	0.00	41.86	2.34
2066	2100	8.381387	GTCCGAATTACTTGTCTTAGATTTGTC	58.619	37.037	0.00	0.00	0.00	3.18
2073	2107	5.992217	ACTTGTCTTAGATTTGTCCAGACAC	59.008	40.000	0.00	0.00	42.73	3.67
2096	2130	6.691818	CACGGATGTATCTAGACAAGTGTAAC	59.308	42.308	0.00	0.00	32.96	2.50
2122	2156	4.360951	AGACAAGTAATTTGGGACGGAA	57.639	40.909	0.00	0.00	41.25	4.30
2338	2383	8.936864	GGCCATATCTTAGTCATGTTGTAATAC	58.063	37.037	0.00	0.00	0.00	1.89
2369	2415	6.593268	ACTAAGAGAGAACCTTCAACTACC	57.407	41.667	0.00	0.00	0.00	3.18
2473	2524	2.301346	CTTGAGCCACCACAGAAACTT	58.699	47.619	0.00	0.00	0.00	2.66
2537	2588	7.394923	TCTTGGTTAAAGAAAAACAGGAAGTGA	59.605	33.333	0.00	0.00	42.09	3.41
2540	2591	7.978975	TGGTTAAAGAAAAACAGGAAGTGAATG	59.021	33.333	0.00	0.00	0.00	2.67
2559	2610	9.638176	AGTGAATGATTAAATAATCTGAGCCTT	57.362	29.630	12.89	0.61	41.93	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
212	216	6.924913	TGGTGAACAAATTATGAAATCCCA	57.075	33.333	0.00	0.00	0.00	4.37
448	457	1.070758	ACCTGACTTGTGCACTGTAGG	59.929	52.381	19.41	20.95	0.00	3.18
471	480	3.689161	AGCAGCGCATGTATTAAAGAACA	59.311	39.130	11.47	0.00	0.00	3.18
537	547	1.891919	GACCAAGTGCTTGCGACCA	60.892	57.895	6.42	0.00	39.16	4.02
563	573	3.449227	AGGCGCGACGAGGATTCA	61.449	61.111	12.10	0.00	0.00	2.57
708	723	2.433239	GAGGGGACGAATTTGGCTAGTA	59.567	50.000	0.00	0.00	0.00	1.82
710	725	1.486726	AGAGGGGACGAATTTGGCTAG	59.513	52.381	0.00	0.00	0.00	3.42
711	726	1.209504	CAGAGGGGACGAATTTGGCTA	59.790	52.381	0.00	0.00	0.00	3.93
712	727	0.035056	CAGAGGGGACGAATTTGGCT	60.035	55.000	0.00	0.00	0.00	4.75
714	729	0.322456	TGCAGAGGGGACGAATTTGG	60.322	55.000	0.00	0.00	0.00	3.28
715	730	0.804989	GTGCAGAGGGGACGAATTTG	59.195	55.000	0.00	0.00	0.00	2.32
716	731	0.322546	GGTGCAGAGGGGACGAATTT	60.323	55.000	0.00	0.00	39.01	1.82
717	732	1.201429	AGGTGCAGAGGGGACGAATT	61.201	55.000	0.00	0.00	39.01	2.17
718	733	0.325296	TAGGTGCAGAGGGGACGAAT	60.325	55.000	0.00	0.00	39.01	3.34
719	734	0.970937	CTAGGTGCAGAGGGGACGAA	60.971	60.000	0.00	0.00	39.01	3.85
720	735	1.379977	CTAGGTGCAGAGGGGACGA	60.380	63.158	0.00	0.00	39.01	4.20
721	736	1.379977	TCTAGGTGCAGAGGGGACG	60.380	63.158	0.00	0.00	39.01	4.79
722	737	1.668101	CGTCTAGGTGCAGAGGGGAC	61.668	65.000	0.00	0.00	37.06	4.46
883	899	4.680537	ACGAGGAGGACGGGTGCT	62.681	66.667	0.00	0.00	34.93	4.40
890	906	0.033894	AAGAGGAGGACGAGGAGGAC	60.034	60.000	0.00	0.00	0.00	3.85
895	911	0.033991	TGGAGAAGAGGAGGACGAGG	60.034	60.000	0.00	0.00	0.00	4.63
913	929	5.934625	CGAATTCTTAGAGGAATATGGGGTG	59.065	44.000	3.52	0.00	35.19	4.61
914	930	5.607171	ACGAATTCTTAGAGGAATATGGGGT	59.393	40.000	3.52	0.00	35.19	4.95
918	934	9.405587	GAGAAGACGAATTCTTAGAGGAATATG	57.594	37.037	3.52	0.00	45.24	1.78
922	938	7.176865	TCAAGAGAAGACGAATTCTTAGAGGAA	59.823	37.037	3.52	0.00	45.24	3.36
927	943	7.009999	CCATGTCAAGAGAAGACGAATTCTTAG	59.990	40.741	3.52	0.00	45.24	2.18
928	944	6.813649	CCATGTCAAGAGAAGACGAATTCTTA	59.186	38.462	3.52	0.00	45.24	2.10
937	954	4.478206	TGGATCCATGTCAAGAGAAGAC	57.522	45.455	11.44	0.00	36.55	3.01
959	976	1.002624	GCTGGGATCGTGGTTTCCA	60.003	57.895	0.00	0.00	33.43	3.53
970	987	3.564218	GATCTGGGGCGCTGGGAT	61.564	66.667	7.64	6.38	0.00	3.85
1021	1038	2.342648	GACGAGGTCAGGCGGTTT	59.657	61.111	0.00	0.00	32.09	3.27
1026	1043	2.419739	GGAGAGGACGAGGTCAGGC	61.420	68.421	0.00	0.00	33.68	4.85
1034	1051	0.114560	ACCAGGAAAGGAGAGGACGA	59.885	55.000	0.00	0.00	0.00	4.20
1049	1067	1.586422	CCAATCCATCTACGCACCAG	58.414	55.000	0.00	0.00	0.00	4.00
1314	1332	0.542702	TCTTCTTACCCCCGGTCGTT	60.543	55.000	0.00	0.00	37.09	3.85
1399	1420	6.015434	TGTCATACTCAGAAGTTCAGCAACTA	60.015	38.462	5.50	0.00	42.45	2.24
1406	1427	6.070596	ACATCCATGTCATACTCAGAAGTTCA	60.071	38.462	5.50	0.00	35.87	3.18
1462	1488	5.505181	TCCAGACAAAAGAAGGAAGCTAT	57.495	39.130	0.00	0.00	0.00	2.97
1476	1506	5.131642	AGGATGAAAGCAGATATCCAGACAA	59.868	40.000	0.00	0.00	41.19	3.18
1498	1529	2.280628	GTGATACGGCTTTCCAAGAGG	58.719	52.381	0.00	0.00	0.00	3.69
1499	1530	2.093447	AGGTGATACGGCTTTCCAAGAG	60.093	50.000	0.00	0.00	0.00	2.85
1575	1607	6.897706	TCAAAATCACATGAATGGACTGAA	57.102	33.333	0.00	0.00	0.00	3.02
1619	1651	2.358258	AGTCCTTTCCATTCCCCAGAA	58.642	47.619	0.00	0.00	36.15	3.02
1625	1657	4.828072	ACTCACTAGTCCTTTCCATTCC	57.172	45.455	0.00	0.00	0.00	3.01
1627	1659	6.441088	AAGAACTCACTAGTCCTTTCCATT	57.559	37.500	0.00	0.00	33.75	3.16
1708	1740	2.165030	CAGGGCAAATCAAGGCAGTTAG	59.835	50.000	0.00	0.00	0.00	2.34
1709	1741	2.170166	CAGGGCAAATCAAGGCAGTTA	58.830	47.619	0.00	0.00	0.00	2.24
1848	1880	5.643777	AGAAAATGCTACAACGCAGTCTATT	59.356	36.000	0.00	0.00	45.00	1.73
2001	2035	6.164176	ACAAAGAAACTAACTAGGGATGACG	58.836	40.000	0.00	0.00	0.00	4.35
2030	2064	1.997606	GTAATTCGGACCGAGGTTGTG	59.002	52.381	17.51	0.00	37.14	3.33
2066	2100	3.883489	TGTCTAGATACATCCGTGTCTGG	59.117	47.826	0.00	0.04	42.88	3.86
2073	2107	7.012515	AGAGTTACACTTGTCTAGATACATCCG	59.987	40.741	0.00	0.00	0.00	4.18
2096	2130	5.581085	CCGTCCCAAATTACTTGTCTTAGAG	59.419	44.000	0.00	0.00	32.65	2.43
2098	2132	5.484715	TCCGTCCCAAATTACTTGTCTTAG	58.515	41.667	0.00	0.00	32.65	2.18
2104	2138	3.681593	TCCTTCCGTCCCAAATTACTTG	58.318	45.455	0.00	0.00	34.52	3.16
2122	2156	3.266772	TGCCACCTCAATCAAATACTCCT	59.733	43.478	0.00	0.00	0.00	3.69
2369	2415	2.559668	ACAGCCCAAATGTTGAGACATG	59.440	45.455	0.00	0.00	45.58	3.21
2512	2563	7.543756	TCACTTCCTGTTTTTCTTTAACCAAG	58.456	34.615	0.00	0.00	0.00	3.61
2559	2610	9.551734	CATCTGGTTTGATGATAACTATGAGAA	57.448	33.333	0.00	0.00	44.71	2.87
2564	2615	8.896744	CACAACATCTGGTTTGATGATAACTAT	58.103	33.333	10.89	0.00	44.71	2.12
2565	2616	7.148255	GCACAACATCTGGTTTGATGATAACTA	60.148	37.037	10.89	0.00	44.71	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.