AutoCloner

Multiple sequence alignment - TraesCS3B01G242800

Loading Multiple Alignment...

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	TraesCS3B01G242800	chr3B	100.000	2336	0	0	1	2336	383485220	383487555	0.000000e+00	4314.0
1	TraesCS3B01G242800	chr1B	94.435	1689	77	7	1	1684	117380611	117378935	0.000000e+00	2582.0
2	TraesCS3B01G242800	chr6B	86.315	1688	208	13	1	1684	545251020	545252688	0.000000e+00	1816.0
3	TraesCS3B01G242800	chr6B	82.060	1165	170	31	528	1684	643939215	643938082	0.000000e+00	957.0
4	TraesCS3B01G242800	chr6B	86.186	333	44	2	92	423	643940044	643939713	2.210000e-95	359.0
5	TraesCS3B01G242800	chr7B	83.444	1655	243	21	38	1684	425399643	425398012	0.000000e+00	1509.0
6	TraesCS3B01G242800	chr3D	81.786	1691	276	27	3	1684	321922623	321924290	0.000000e+00	1387.0
7	TraesCS3B01G242800	chr3D	93.972	647	28	6	1690	2336	125053892	125054527	0.000000e+00	968.0
8	TraesCS3B01G242800	chr3D	93.663	647	32	4	1690	2336	514052916	514052279	0.000000e+00	959.0
9	TraesCS3B01G242800	chr3D	93.045	647	38	3	1690	2336	548066691	548066052	0.000000e+00	939.0
10	TraesCS3B01G242800	chr1D	79.976	1693	302	24	3	1684	97210582	97208916	0.000000e+00	1214.0
11	TraesCS3B01G242800	chr1D	93.354	647	34	3	1690	2336	272869168	272868531	0.000000e+00	948.0
12	TraesCS3B01G242800	chr4D	94.290	648	32	3	1690	2336	357944231	357944874	0.000000e+00	987.0
13	TraesCS3B01G242800	chr4D	76.471	153	21	11	1533	1684	295569705	295569843	4.170000e-08	69.4
14	TraesCS3B01G242800	chr5D	93.818	647	32	4	1690	2336	364497890	364498528	0.000000e+00	966.0
15	TraesCS3B01G242800	chr5D	95.918	49	1	1	1636	1684	547541330	547541283	6.920000e-11	78.7
16	TraesCS3B01G242800	chr2D	93.364	648	33	3	1690	2336	466475003	466474365	0.000000e+00	950.0
17	TraesCS3B01G242800	chr2D	93.199	647	36	3	1690	2336	317720709	317721347	0.000000e+00	944.0
18	TraesCS3B01G242800	chr7D	93.199	647	35	5	1690	2336	504988884	504988247	0.000000e+00	942.0
19	TraesCS3B01G242800	chr5B	79.866	1192	232	8	1	1187	557035705	557036893	0.000000e+00	865.0
20	TraesCS3B01G242800	chr7A	75.260	1152	254	31	467	1600	491261556	491262694	9.570000e-144	520.0
21	TraesCS3B01G242800	chr2A	77.057	863	151	38	842	1684	2975802	2976637	9.840000e-124	453.0
22	TraesCS3B01G242800	chr2A	77.348	181	27	8	1504	1684	436717813	436717647	6.870000e-16	95.3

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	TraesCS3B01G242800	chr3B	383485220	383487555	2335	False	4314	4314	100.000	1	2336	1	chr3B.!!$F1	2335
1	TraesCS3B01G242800	chr1B	117378935	117380611	1676	True	2582	2582	94.435	1	1684	1	chr1B.!!$R1	1683
2	TraesCS3B01G242800	chr6B	545251020	545252688	1668	False	1816	1816	86.315	1	1684	1	chr6B.!!$F1	1683
3	TraesCS3B01G242800	chr6B	643938082	643940044	1962	True	658	957	84.123	92	1684	2	chr6B.!!$R1	1592
4	TraesCS3B01G242800	chr7B	425398012	425399643	1631	True	1509	1509	83.444	38	1684	1	chr7B.!!$R1	1646
5	TraesCS3B01G242800	chr3D	321922623	321924290	1667	False	1387	1387	81.786	3	1684	1	chr3D.!!$F2	1681
6	TraesCS3B01G242800	chr3D	125053892	125054527	635	False	968	968	93.972	1690	2336	1	chr3D.!!$F1	646
7	TraesCS3B01G242800	chr3D	514052279	514052916	637	True	959	959	93.663	1690	2336	1	chr3D.!!$R1	646
8	TraesCS3B01G242800	chr3D	548066052	548066691	639	True	939	939	93.045	1690	2336	1	chr3D.!!$R2	646
9	TraesCS3B01G242800	chr1D	97208916	97210582	1666	True	1214	1214	79.976	3	1684	1	chr1D.!!$R1	1681
10	TraesCS3B01G242800	chr1D	272868531	272869168	637	True	948	948	93.354	1690	2336	1	chr1D.!!$R2	646
11	TraesCS3B01G242800	chr4D	357944231	357944874	643	False	987	987	94.290	1690	2336	1	chr4D.!!$F2	646
12	TraesCS3B01G242800	chr5D	364497890	364498528	638	False	966	966	93.818	1690	2336	1	chr5D.!!$F1	646
13	TraesCS3B01G242800	chr2D	466474365	466475003	638	True	950	950	93.364	1690	2336	1	chr2D.!!$R1	646
14	TraesCS3B01G242800	chr2D	317720709	317721347	638	False	944	944	93.199	1690	2336	1	chr2D.!!$F1	646
15	TraesCS3B01G242800	chr7D	504988247	504988884	637	True	942	942	93.199	1690	2336	1	chr7D.!!$R1	646
16	TraesCS3B01G242800	chr5B	557035705	557036893	1188	False	865	865	79.866	1	1187	1	chr5B.!!$F1	1186
17	TraesCS3B01G242800	chr7A	491261556	491262694	1138	False	520	520	75.260	467	1600	1	chr7A.!!$F1	1133
18	TraesCS3B01G242800	chr2A	2975802	2976637	835	False	453	453	77.057	842	1684	1	chr2A.!!$F1	842

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
890	1287	0.327924	AGGGATGTGATGAAACGCCA	59.672	50.0	0.0	0.0	0.0	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2123	2557	0.596083	GGGAGACGTGCTCATCATCG	60.596	60.0	14.26	0.0	45.81	3.84	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
204	207	0.988832	TGGGGAAGAAACGCTACCAT	59.011	50.000	0.00	0.00	0.00	3.55
273	276	2.423947	GGGCATCAAGGATCTCCACAAT	60.424	50.000	0.00	0.00	38.89	2.71
327	330	3.563512	CTGGATACGGGGAAGGGG	58.436	66.667	0.00	0.00	40.24	4.79
396	399	1.995376	CCACTGTTAAGCCCAAGGTT	58.005	50.000	0.00	0.00	37.50	3.50
441	444	5.494724	TCTCTCCTGAAAATCAAGGATGTG	58.505	41.667	0.00	0.00	0.00	3.21
644	1040	1.696336	ACTGAATGCTGACCTGACTGT	59.304	47.619	0.00	0.00	0.00	3.55
651	1047	1.606737	GCTGACCTGACTGTCCAGTTC	60.607	57.143	5.17	2.21	42.66	3.01
669	1065	4.081309	CAGTTCGAGGGATTACAAAGGGTA	60.081	45.833	0.00	0.00	0.00	3.69
704	1100	3.469008	AACCTCTGACGATTGTGACAA	57.531	42.857	0.00	0.00	0.00	3.18
810	1207	6.642430	CAATTTTAAATGGATCTGGAAGGCA	58.358	36.000	0.00	0.00	0.00	4.75
813	1210	5.659440	TTAAATGGATCTGGAAGGCAAAC	57.341	39.130	0.00	0.00	0.00	2.93
890	1287	0.327924	AGGGATGTGATGAAACGCCA	59.672	50.000	0.00	0.00	0.00	5.69
899	1296	0.678950	ATGAAACGCCAAAACTGGGG	59.321	50.000	6.67	6.67	46.01	4.96
1147	1545	3.002791	CGCAGAAATCAGGCTACTTTCA	58.997	45.455	17.95	0.00	32.55	2.69
1191	1589	2.542020	TTGAGATTGTCTTCACGGCA	57.458	45.000	0.00	0.00	0.00	5.69
1237	1635	0.034896	GCTGTTGAAGGACGAGGGAA	59.965	55.000	0.00	0.00	0.00	3.97
1241	1639	1.619332	GTTGAAGGACGAGGGAAGAGT	59.381	52.381	0.00	0.00	0.00	3.24
1329	1727	1.771565	CATACACGAGGTCCACCCTA	58.228	55.000	0.00	0.00	46.51	3.53
1343	1741	2.620234	CCCTAGGGTGATCAAGGCA	58.380	57.895	20.88	0.00	0.00	4.75
1396	1796	1.354337	GCTGATCGTGCTTCTTCGCA	61.354	55.000	3.62	0.00	37.62	5.10
1409	1812	0.109272	CTTCGCAGACCTCGTTAGCA	60.109	55.000	0.00	0.00	34.32	3.49
1421	1824	0.167908	CGTTAGCATTTTGGCGCTCA	59.832	50.000	7.64	0.00	39.70	4.26
1448	1872	4.689612	TTATTCTGCTATTCCGCCTCTT	57.310	40.909	0.00	0.00	0.00	2.85
1599	2030	1.145119	ACTCGCTTTTTCCCTTTCCCT	59.855	47.619	0.00	0.00	0.00	4.20
1600	2031	2.239400	CTCGCTTTTTCCCTTTCCCTT	58.761	47.619	0.00	0.00	0.00	3.95
1601	2032	2.628178	CTCGCTTTTTCCCTTTCCCTTT	59.372	45.455	0.00	0.00	0.00	3.11
1602	2033	2.626266	TCGCTTTTTCCCTTTCCCTTTC	59.374	45.455	0.00	0.00	0.00	2.62
1603	2034	2.288825	CGCTTTTTCCCTTTCCCTTTCC	60.289	50.000	0.00	0.00	0.00	3.13
1604	2035	2.038557	GCTTTTTCCCTTTCCCTTTCCC	59.961	50.000	0.00	0.00	0.00	3.97
1605	2036	3.587498	CTTTTTCCCTTTCCCTTTCCCT	58.413	45.455	0.00	0.00	0.00	4.20
1606	2037	3.717507	TTTTCCCTTTCCCTTTCCCTT	57.282	42.857	0.00	0.00	0.00	3.95
1607	2038	3.717507	TTTCCCTTTCCCTTTCCCTTT	57.282	42.857	0.00	0.00	0.00	3.11
1608	2039	2.992847	TCCCTTTCCCTTTCCCTTTC	57.007	50.000	0.00	0.00	0.00	2.62
1609	2040	1.431633	TCCCTTTCCCTTTCCCTTTCC	59.568	52.381	0.00	0.00	0.00	3.13
1610	2041	1.552486	CCCTTTCCCTTTCCCTTTCCC	60.552	57.143	0.00	0.00	0.00	3.97
1633	2065	6.472887	CCTTTTTACATACTCCTGGACTTGA	58.527	40.000	0.00	0.00	0.00	3.02
1644	2076	5.251700	ACTCCTGGACTTGATTGTATTTCCT	59.748	40.000	0.00	0.00	0.00	3.36
1764	2196	3.505680	GGTTGCATCTTTCATGTGGTGTA	59.494	43.478	0.00	0.00	0.00	2.90
1839	2271	4.334552	ACAGTTGTGAATATGCCATGTCA	58.665	39.130	0.00	0.00	0.00	3.58
1869	2301	3.678056	TCGTACATATTCCATCCTGGC	57.322	47.619	0.00	0.00	37.47	4.85
1881	2313	2.498481	CCATCCTGGCATCATGTGTTTT	59.502	45.455	0.00	0.00	0.00	2.43
1995	2427	8.776376	ACAATTCAAAATCAATAAAGCGGAAT	57.224	26.923	0.00	0.00	0.00	3.01
1996	2428	9.868277	ACAATTCAAAATCAATAAAGCGGAATA	57.132	25.926	0.00	0.00	0.00	1.75
2058	2490	3.961408	GGAGGGCTTCTACAGATTCTACA	59.039	47.826	0.00	0.00	0.00	2.74
2064	2496	2.029623	TCTACAGATTCTACACCGCCC	58.970	52.381	0.00	0.00	0.00	6.13
2065	2497	1.068741	CTACAGATTCTACACCGCCCC	59.931	57.143	0.00	0.00	0.00	5.80
2095	2529	5.350633	CCAAGAAGATTTGCAAGACAACAA	58.649	37.500	0.00	0.00	38.23	2.83
2123	2557	2.052157	GACACTCAACGTAGCTGTGTC	58.948	52.381	20.08	20.08	46.50	3.67
2178	2612	0.984995	GGTGCTCCCTCTAACTTGGT	59.015	55.000	0.00	0.00	0.00	3.67
2183	2617	2.418884	GCTCCCTCTAACTTGGTACTGC	60.419	54.545	0.00	0.00	0.00	4.40
2213	2647	6.152492	TGTGGTTGCATGTTATGTATGATGTT	59.848	34.615	0.00	0.00	0.00	2.71
2215	2649	8.187480	GTGGTTGCATGTTATGTATGATGTTTA	58.813	33.333	0.00	0.00	0.00	2.01
2216	2650	8.404765	TGGTTGCATGTTATGTATGATGTTTAG	58.595	33.333	0.00	0.00	0.00	1.85
2217	2651	8.620416	GGTTGCATGTTATGTATGATGTTTAGA	58.380	33.333	0.00	0.00	0.00	2.10
2295	2731	9.655769	CATTATACTTGTGAATAAGACATGTGC	57.344	33.333	1.15	0.00	34.54	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	0.839277	TGCCGATCCAGGAATCACAT	59.161	50.000	0.00	0.00	0.00	3.21
204	207	4.021104	CACACTCTAGTCCATTTGACCAGA	60.021	45.833	0.00	0.00	45.68	3.86
327	330	2.608752	CCTCACAACATCTTGCCAAAGC	60.609	50.000	0.00	0.00	40.48	3.51
366	369	1.764571	TAACAGTGGCCACCGAGCTT	61.765	55.000	32.29	14.79	0.00	3.74
396	399	5.433051	AGATTTCCAGACAGGGGAATCATTA	59.567	40.000	14.06	0.00	43.57	1.90
441	444	1.697982	ACTTTCCTCCCGGCCATATAC	59.302	52.381	2.24	0.00	0.00	1.47
644	1040	3.055385	CCTTTGTAATCCCTCGAACTGGA	60.055	47.826	0.94	0.94	34.54	3.86
651	1047	4.081309	TCAACTACCCTTTGTAATCCCTCG	60.081	45.833	0.00	0.00	0.00	4.63
704	1100	2.305635	GGTCCAAAGCCCCATTCAAAAT	59.694	45.455	0.00	0.00	0.00	1.82
810	1207	5.975988	TCTGGATCTTAATAGGCAGGTTT	57.024	39.130	0.00	0.00	0.00	3.27
890	1287	3.964108	GGTTGCCACCCCAGTTTT	58.036	55.556	0.00	0.00	37.03	2.43
899	1296	0.755327	AGAACACCTTGGGTTGCCAC	60.755	55.000	0.00	0.00	31.02	5.01
1147	1545	8.753497	AAAGGAGATGACAACTTCTTAAACTT	57.247	30.769	6.69	0.00	32.71	2.66
1191	1589	3.555795	CCCAGTAAGATAGATGCGTGCAT	60.556	47.826	7.12	7.12	39.69	3.96
1237	1635	1.412079	CCATGCTCTAGCTCCACTCT	58.588	55.000	3.26	0.00	42.66	3.24
1241	1639	2.817424	CGCCATGCTCTAGCTCCA	59.183	61.111	3.26	0.00	42.66	3.86
1329	1727	1.211457	GAGACATGCCTTGATCACCCT	59.789	52.381	0.00	0.00	0.00	4.34
1396	1796	2.084546	GCCAAAATGCTAACGAGGTCT	58.915	47.619	0.00	0.00	0.00	3.85
1409	1812	7.042523	GCAGAATAATAAAATGAGCGCCAAAAT	60.043	33.333	2.29	0.00	0.00	1.82
1421	1824	7.885399	AGAGGCGGAATAGCAGAATAATAAAAT	59.115	33.333	0.00	0.00	39.27	1.82
1448	1872	3.937814	ACATCAACATCAAAGCCTACGA	58.062	40.909	0.00	0.00	0.00	3.43
1529	1954	1.209128	CTCGCAATCGAAACGCCTAT	58.791	50.000	0.00	0.00	44.98	2.57
1599	2030	6.722590	GGAGTATGTAAAAAGGGAAAGGGAAA	59.277	38.462	0.00	0.00	0.00	3.13
1600	2031	6.046286	AGGAGTATGTAAAAAGGGAAAGGGAA	59.954	38.462	0.00	0.00	0.00	3.97
1601	2032	5.554350	AGGAGTATGTAAAAAGGGAAAGGGA	59.446	40.000	0.00	0.00	0.00	4.20
1602	2033	5.652452	CAGGAGTATGTAAAAAGGGAAAGGG	59.348	44.000	0.00	0.00	0.00	3.95
1603	2034	5.652452	CCAGGAGTATGTAAAAAGGGAAAGG	59.348	44.000	0.00	0.00	0.00	3.11
1604	2035	6.374613	GTCCAGGAGTATGTAAAAAGGGAAAG	59.625	42.308	0.00	0.00	0.00	2.62
1605	2036	6.045106	AGTCCAGGAGTATGTAAAAAGGGAAA	59.955	38.462	0.00	0.00	0.00	3.13
1606	2037	5.550403	AGTCCAGGAGTATGTAAAAAGGGAA	59.450	40.000	0.00	0.00	0.00	3.97
1607	2038	5.098663	AGTCCAGGAGTATGTAAAAAGGGA	58.901	41.667	0.00	0.00	0.00	4.20
1608	2039	5.437191	AGTCCAGGAGTATGTAAAAAGGG	57.563	43.478	0.00	0.00	0.00	3.95
1609	2040	6.472887	TCAAGTCCAGGAGTATGTAAAAAGG	58.527	40.000	0.00	0.00	0.00	3.11
1610	2041	8.454106	CAATCAAGTCCAGGAGTATGTAAAAAG	58.546	37.037	0.00	0.00	0.00	2.27
1644	2076	7.401060	TCCCCTTTCCATTATAGAGCATAAA	57.599	36.000	0.00	0.00	32.84	1.40
1687	2119	8.512956	CCATCATAAATGGCATTTCAACAAAAA	58.487	29.630	27.42	9.30	33.82	1.94
1688	2120	7.120873	CCCATCATAAATGGCATTTCAACAAAA	59.879	33.333	27.42	10.03	37.85	2.44
1764	2196	6.870769	ACAAATAAGAAGCAATGCAAGCTAT	58.129	32.000	16.20	9.23	42.53	2.97
1839	2271	7.228706	GGATGGAATATGTACGAAAAACAGGAT	59.771	37.037	0.00	0.00	0.00	3.24
1869	2301	8.084073	ACTTTGATGTAAGGAAAACACATGATG	58.916	33.333	0.00	0.00	33.16	3.07
1903	2335	7.173390	CAGAACTCATTCATGCATGATACTGAT	59.827	37.037	29.13	16.61	37.29	2.90
1995	2427	7.147915	CCTTTATCCACTGCCTTGCTAATTTTA	60.148	37.037	0.00	0.00	0.00	1.52
1996	2428	6.351286	CCTTTATCCACTGCCTTGCTAATTTT	60.351	38.462	0.00	0.00	0.00	1.82
2043	2475	2.429610	GGGCGGTGTAGAATCTGTAGAA	59.570	50.000	0.00	0.00	0.00	2.10
2095	2529	3.865745	GCTACGTTGAGTGTCTATGCATT	59.134	43.478	3.54	0.00	0.00	3.56
2123	2557	0.596083	GGGAGACGTGCTCATCATCG	60.596	60.000	14.26	0.00	45.81	3.84
2178	2612	5.034852	ACATGCAACCACATATAGCAGTA	57.965	39.130	0.00	0.00	38.75	2.74
2183	2617	9.218440	TCATACATAACATGCAACCACATATAG	57.782	33.333	0.00	0.00	0.00	1.31
2213	2647	9.618890	ATTAGAAGCAATACAAGCTCAATCTAA	57.381	29.630	9.09	9.09	42.53	2.10
2215	2649	8.517062	AATTAGAAGCAATACAAGCTCAATCT	57.483	30.769	0.00	0.00	42.53	2.40
2216	2650	9.578439	AAAATTAGAAGCAATACAAGCTCAATC	57.422	29.630	0.00	0.00	42.53	2.67
2217	2651	9.362539	CAAAATTAGAAGCAATACAAGCTCAAT	57.637	29.630	0.00	0.00	42.53	2.57
2218	2652	8.359642	ACAAAATTAGAAGCAATACAAGCTCAA	58.640	29.630	0.00	0.00	42.53	3.02
2219	2653	7.885297	ACAAAATTAGAAGCAATACAAGCTCA	58.115	30.769	0.00	0.00	42.53	4.26
2220	2654	8.642020	CAACAAAATTAGAAGCAATACAAGCTC	58.358	33.333	0.00	0.00	42.53	4.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.