AutoCloner

Multiple sequence alignment - TraesCS3D01G037700

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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	TraesCS3D01G037700	chr3D	100.000	2114	0	0	1	2114	13606574	13604461	0.000000e+00	3904.0
1	TraesCS3D01G037700	chr3D	79.954	873	140	22	1249	2114	13661325	13660481	4.990000e-171	610.0
2	TraesCS3D01G037700	chr3D	73.797	374	63	20	1512	1882	13632320	13631979	4.770000e-22	115.0
3	TraesCS3D01G037700	chr3A	92.415	2083	126	13	4	2079	23314168	23316225	0.000000e+00	2942.0
4	TraesCS3D01G037700	chr3A	77.953	254	32	13	1616	1864	23375863	23376097	1.020000e-28	137.0
5	TraesCS3D01G037700	chr3A	82.796	93	10	6	1690	1781	23366282	23366369	6.250000e-11	78.7
6	TraesCS3D01G037700	chr3A	95.652	46	1	1	2070	2114	23319631	23319676	2.910000e-09	73.1
7	TraesCS3D01G037700	chr3A	97.059	34	1	0	22	55	23314142	23314175	8.150000e-05	58.4
8	TraesCS3D01G037700	chr3B	93.837	1655	85	12	463	2114	20004044	20002404	0.000000e+00	2475.0
9	TraesCS3D01G037700	chr3B	94.409	465	25	1	4	467	20019032	20018568	0.000000e+00	713.0
10	TraesCS3D01G037700	chr3B	79.954	873	155	14	1249	2114	20051590	20050731	1.780000e-175	625.0
11	TraesCS3D01G037700	chr3B	75.465	269	40	14	1616	1882	20024471	20024227	7.980000e-20	108.0
12	TraesCS3D01G037700	chr3B	81.720	93	15	1	1690	1782	19983847	19983757	2.250000e-10	76.8
13	TraesCS3D01G037700	chr1D	89.779	362	23	9	898	1247	394179514	394179873	3.200000e-123	451.0
14	TraesCS3D01G037700	chr5D	89.779	362	22	9	898	1247	554200944	554201302	1.150000e-122	449.0
15	TraesCS3D01G037700	chr5D	89.503	362	22	10	898	1247	554200401	554200044	5.350000e-121	444.0
16	TraesCS3D01G037700	chr7B	89.503	362	23	9	898	1247	262234055	262234413	5.350000e-121	444.0
17	TraesCS3D01G037700	chr7B	89.503	362	22	10	898	1247	386362872	386362515	5.350000e-121	444.0
18	TraesCS3D01G037700	chr6D	89.503	362	23	9	898	1247	431403615	431403257	5.350000e-121	444.0
19	TraesCS3D01G037700	chr2A	89.474	361	23	8	898	1247	335826881	335827237	1.930000e-120	442.0
20	TraesCS3D01G037700	chr2D	89.231	65	7	0	1800	1864	78704930	78704994	4.830000e-12	82.4

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	TraesCS3D01G037700	chr3D	13604461	13606574	2113	True	3904.0	3904	100.000	1	2114	1	chr3D.!!$R1	2113
1	TraesCS3D01G037700	chr3D	13660481	13661325	844	True	610.0	610	79.954	1249	2114	1	chr3D.!!$R3	865
2	TraesCS3D01G037700	chr3A	23314142	23319676	5534	False	1024.5	2942	95.042	4	2114	3	chr3A.!!$F3	2110
3	TraesCS3D01G037700	chr3B	20002404	20004044	1640	True	2475.0	2475	93.837	463	2114	1	chr3B.!!$R2	1651
4	TraesCS3D01G037700	chr3B	20050731	20051590	859	True	625.0	625	79.954	1249	2114	1	chr3B.!!$R5	865

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
433	457	0.026803	GTGCCGAATCAAGTCGATGC	59.973	55.0	0.87	0.0	43.86	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1476	1508	1.470098	CAGACTGCATTTGTACTGCCC	59.53	52.381	3.4	0.0	38.89	5.36	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
139	163	6.265577	GCATGATAATACACAAACAAGGGAC	58.734	40.000	0.00	0.00	0.00	4.46
193	217	9.190858	TGTTTCTACACATAATTTCATTGCAAC	57.809	29.630	0.00	0.00	0.00	4.17
205	229	8.674263	AATTTCATTGCAACTATTGTTTTCCA	57.326	26.923	0.00	0.00	33.52	3.53
218	242	4.027674	TGTTTTCCATAGTAGCTTGCCA	57.972	40.909	0.00	0.00	0.00	4.92
242	266	7.390440	CCAGTTGGAATTGAGATAAGTACACAA	59.610	37.037	0.00	0.00	37.39	3.33
278	302	4.032960	TGCAGGACACATATGGTCTTTT	57.967	40.909	18.10	7.18	35.61	2.27
287	311	7.255660	GGACACATATGGTCTTTTGTTGGTTAA	60.256	37.037	18.10	0.00	35.61	2.01
354	378	7.798710	TTTTGTCCATGTTTGGGGATATTAA	57.201	32.000	0.00	0.00	43.81	1.40
364	388	6.070538	TGTTTGGGGATATTAATGTTGGTTGG	60.071	38.462	0.00	0.00	0.00	3.77
395	419	5.249163	TGGGAGTGAGATCAGAGATGAAAAA	59.751	40.000	0.00	0.00	0.00	1.94
429	453	1.078709	ATGTGTGCCGAATCAAGTCG	58.921	50.000	0.00	0.00	40.77	4.18
433	457	0.026803	GTGCCGAATCAAGTCGATGC	59.973	55.000	0.87	0.00	43.86	3.91
437	461	0.302890	CGAATCAAGTCGATGCCTGC	59.697	55.000	0.00	0.00	43.86	4.85
451	475	2.488355	CTGCATTCGCCCTTGCTG	59.512	61.111	0.00	0.00	39.60	4.41
478	502	1.342819	GGGCCTACAGACTGAGCTATG	59.657	57.143	10.08	0.00	0.00	2.23
495	519	4.832608	GGTTAGCGGGAGGGTGCG	62.833	72.222	0.00	0.00	35.87	5.34
591	615	2.031508	CCGTTGTATTTTGGTCACGCTT	60.032	45.455	0.00	0.00	0.00	4.68
594	618	5.387279	CGTTGTATTTTGGTCACGCTTATT	58.613	37.500	0.00	0.00	0.00	1.40
597	621	6.320494	TGTATTTTGGTCACGCTTATTTGT	57.680	33.333	0.00	0.00	0.00	2.83
614	638	7.094549	GCTTATTTGTGTAAGGTGGTGTTATCA	60.095	37.037	0.00	0.00	33.31	2.15
646	670	1.074872	CGTCGGTTCCCTCTTTACGC	61.075	60.000	0.00	0.00	0.00	4.42
706	730	4.827481	CGCAACTATAGTGGGCGT	57.173	55.556	29.67	6.19	43.22	5.68
708	732	2.212869	CGCAACTATAGTGGGCGTAA	57.787	50.000	29.67	0.00	43.22	3.18
710	734	2.283351	CGCAACTATAGTGGGCGTAAAC	59.717	50.000	29.67	6.43	43.22	2.01
735	759	4.024809	GCGCCTTACCATCTAGTTCAATTC	60.025	45.833	0.00	0.00	0.00	2.17
770	794	8.165397	TCAATGATGAGATGAGAGATCTCTAGT	58.835	37.037	25.18	16.17	43.62	2.57
798	822	7.977789	TTTCATACTGCAGAACACATTTCTA	57.022	32.000	23.35	0.00	0.00	2.10
806	830	5.091431	GCAGAACACATTTCTAGCACAATC	58.909	41.667	0.00	0.00	0.00	2.67
826	850	6.601613	ACAATCAGTGTTAGTTTCTCCACAAA	59.398	34.615	0.00	0.00	37.01	2.83
830	854	6.984474	TCAGTGTTAGTTTCTCCACAAACTAG	59.016	38.462	6.05	0.00	45.34	2.57
876	900	1.268896	GGAATCATGGTGCATGCTTCG	60.269	52.381	20.33	3.10	43.55	3.79
896	920	2.215587	CGTGGTGATGTTTATCGTAGCG	59.784	50.000	0.00	0.00	36.04	4.26
930	954	5.336770	GGAATTCTTTCTTGGTCATTGGGAC	60.337	44.000	5.23	0.00	37.62	4.46
945	969	3.564053	TGGGACCCGTGGATAATTTAC	57.436	47.619	5.91	0.00	0.00	2.01
1016	1040	9.617523	ACAAATGGAAATGATTGAAGTTTTTCT	57.382	25.926	0.00	0.00	34.31	2.52
1042	1066	6.773976	TTGGAATTGTCTTAGGCCTAATTG	57.226	37.500	25.37	14.90	0.00	2.32
1070	1094	7.925043	TTACTTTAGCGGGATTATTTGTGAA	57.075	32.000	0.00	0.00	0.00	3.18
1211	1235	5.864628	AAGTTATTTTCCTCTGCTTCGAC	57.135	39.130	0.00	0.00	0.00	4.20
1212	1236	4.894784	AGTTATTTTCCTCTGCTTCGACA	58.105	39.130	0.00	0.00	0.00	4.35
1257	1281	7.824779	GCTCTTAGGATTTGAAAGAAAGGTAGA	59.175	37.037	0.00	0.00	0.00	2.59
1324	1348	6.208599	GGTCATGAATTGGGTGAAAACTCTTA	59.791	38.462	0.00	0.00	0.00	2.10
1504	1536	2.906389	ACAAATGCAGTCTGTAGGAGGA	59.094	45.455	0.93	0.00	0.00	3.71
1536	1568	5.520288	CCGACAAACTCGTAGAATTCATCAT	59.480	40.000	8.44	0.00	41.18	2.45
1592	1624	0.532573	GCTCCACTTGTCGATCCTCA	59.467	55.000	0.00	0.00	0.00	3.86
1614	1646	3.384789	AGCCTCTTCTATACGATTGCACA	59.615	43.478	0.00	0.00	0.00	4.57
1671	1703	2.148768	GGTACTTGTTTCTTCCCCACG	58.851	52.381	0.00	0.00	0.00	4.94
1672	1704	2.224354	GGTACTTGTTTCTTCCCCACGA	60.224	50.000	0.00	0.00	0.00	4.35
1673	1705	2.951229	ACTTGTTTCTTCCCCACGAT	57.049	45.000	0.00	0.00	0.00	3.73
1674	1706	3.223674	ACTTGTTTCTTCCCCACGATT	57.776	42.857	0.00	0.00	0.00	3.34
1676	1708	4.721132	ACTTGTTTCTTCCCCACGATTTA	58.279	39.130	0.00	0.00	0.00	1.40
1678	1710	5.183140	ACTTGTTTCTTCCCCACGATTTATG	59.817	40.000	0.00	0.00	0.00	1.90
1842	1881	4.525912	ATTCAATGCTTGGTTGGTCTTC	57.474	40.909	0.00	0.00	0.00	2.87
1898	1938	8.422577	ACACTAGTACTGATGCATATATCCAA	57.577	34.615	5.39	0.00	0.00	3.53
1926	1966	5.324784	ACTTACACATCATCTAACGCTGA	57.675	39.130	0.00	0.00	0.00	4.26
2024	2064	3.056393	TGAAATCTTGAGCAATTGGCCTG	60.056	43.478	3.32	0.00	46.50	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	6.708054	CACCTTTTAGCAGGATAATGGTAGAG	59.292	42.308	0.00	0.00	37.39	2.43
4	5	6.591935	TCACCTTTTAGCAGGATAATGGTAG	58.408	40.000	0.00	0.00	37.39	3.18
6	7	5.450818	TCACCTTTTAGCAGGATAATGGT	57.549	39.130	0.00	0.00	37.39	3.55
7	8	5.278660	GCATCACCTTTTAGCAGGATAATGG	60.279	44.000	0.00	0.00	37.39	3.16
94	118	9.147732	TCATGCCTCTAATGTCTTCTTATCTTA	57.852	33.333	0.00	0.00	0.00	2.10
107	131	8.839343	TGTTTGTGTATTATCATGCCTCTAATG	58.161	33.333	0.00	0.00	0.00	1.90
164	188	8.863049	GCAATGAAATTATGTGTAGAAACAAGG	58.137	33.333	0.00	0.00	33.40	3.61
193	217	6.318648	TGGCAAGCTACTATGGAAAACAATAG	59.681	38.462	0.00	0.00	0.00	1.73
196	220	4.402829	TGGCAAGCTACTATGGAAAACAA	58.597	39.130	0.00	0.00	0.00	2.83
199	223	4.301072	ACTGGCAAGCTACTATGGAAAA	57.699	40.909	0.00	0.00	0.00	2.29
203	227	2.092968	TCCAACTGGCAAGCTACTATGG	60.093	50.000	0.00	0.00	34.44	2.74
205	229	4.510167	ATTCCAACTGGCAAGCTACTAT	57.490	40.909	0.00	0.00	34.44	2.12
218	242	8.950210	CATTGTGTACTTATCTCAATTCCAACT	58.050	33.333	0.00	0.00	30.19	3.16
261	285	4.522789	ACCAACAAAAGACCATATGTGTCC	59.477	41.667	16.22	4.32	33.09	4.02
291	315	9.539194	AGAATGAGAAGGGATTTGTCTTAATTT	57.461	29.630	0.00	0.00	30.68	1.82
354	378	2.652348	TCCCAATACCTCCAACCAACAT	59.348	45.455	0.00	0.00	0.00	2.71
364	388	4.219115	TCTGATCTCACTCCCAATACCTC	58.781	47.826	0.00	0.00	0.00	3.85
395	419	4.641989	GGCACACATACATTTGAAGAGGAT	59.358	41.667	0.00	0.00	0.00	3.24
429	453	2.123428	AAGGGCGAATGCAGGCATC	61.123	57.895	7.29	1.00	45.35	3.91
478	502	4.832608	CGCACCCTCCCGCTAACC	62.833	72.222	0.00	0.00	0.00	2.85
502	526	4.894896	CCCAATAGGCACCGGGGC	62.895	72.222	24.13	24.13	43.80	5.80
525	549	2.203280	CCACACCTCAACCCGCAA	60.203	61.111	0.00	0.00	0.00	4.85
591	615	7.675962	GTGATAACACCACCTTACACAAATA	57.324	36.000	0.00	0.00	40.74	1.40
614	638	1.481871	ACCGACGACCATAATCAGGT	58.518	50.000	0.00	0.00	43.46	4.00
646	670	2.296752	TGGACTTGAACCATGTTGCATG	59.703	45.455	2.38	2.38	32.03	4.06
706	730	0.538118	AGATGGTAAGGCGCGGTTTA	59.462	50.000	8.83	0.00	0.00	2.01
708	732	0.104304	CTAGATGGTAAGGCGCGGTT	59.896	55.000	8.83	0.00	0.00	4.44
710	734	0.104304	AACTAGATGGTAAGGCGCGG	59.896	55.000	8.83	0.00	0.00	6.46
786	810	6.082338	CACTGATTGTGCTAGAAATGTGTTC	58.918	40.000	0.00	0.00	40.06	3.18
806	830	6.761714	ACTAGTTTGTGGAGAAACTAACACTG	59.238	38.462	9.62	2.43	44.15	3.66
851	875	2.934887	CATGCACCATGATTCCTGGTA	58.065	47.619	12.58	0.37	45.23	3.25
853	877	0.387929	GCATGCACCATGATTCCTGG	59.612	55.000	14.21	6.45	43.81	4.45
870	894	2.670905	CGATAAACATCACCACGAAGCA	59.329	45.455	0.00	0.00	0.00	3.91
876	900	2.538449	CCGCTACGATAAACATCACCAC	59.462	50.000	0.00	0.00	0.00	4.16
896	920	7.896811	ACCAAGAAAGAATTCCTAATTTGTCC	58.103	34.615	0.65	0.00	36.12	4.02
930	954	8.897872	AAATAGTACTGTAAATTATCCACGGG	57.102	34.615	5.39	0.00	0.00	5.28
977	1001	4.577988	TCCATTTGTTCGAGGGGATAAA	57.422	40.909	0.00	0.00	0.00	1.40
1016	1040	8.912988	CAATTAGGCCTAAGACAATTCCAAATA	58.087	33.333	28.35	1.72	0.00	1.40
1026	1050	7.374975	AGTAATAGCAATTAGGCCTAAGACA	57.625	36.000	28.35	13.09	0.00	3.41
1042	1066	8.015658	CACAAATAATCCCGCTAAAGTAATAGC	58.984	37.037	0.00	0.00	43.88	2.97
1070	1094	3.181501	ACGCTTGTATTGCAAATACGCAT	60.182	39.130	1.71	0.00	42.62	4.73
1211	1235	6.686630	AGAGCGTGATTCCTTCTATCTTATG	58.313	40.000	0.00	0.00	0.00	1.90
1212	1236	6.909550	AGAGCGTGATTCCTTCTATCTTAT	57.090	37.500	0.00	0.00	0.00	1.73
1284	1308	5.423704	TCATGACCGGGTAAATTGTCTTA	57.576	39.130	6.32	0.00	0.00	2.10
1298	1322	3.255642	AGTTTTCACCCAATTCATGACCG	59.744	43.478	0.00	0.00	0.00	4.79
1324	1348	1.677576	CGTGCTATGTGCCCAAATGAT	59.322	47.619	0.00	0.00	42.00	2.45
1476	1508	1.470098	CAGACTGCATTTGTACTGCCC	59.530	52.381	3.40	0.00	38.89	5.36
1562	1594	2.290641	ACAAGTGGAGCAAACTTAAGCG	59.709	45.455	1.29	0.00	35.70	4.68
1592	1624	3.384789	TGTGCAATCGTATAGAAGAGGCT	59.615	43.478	0.00	0.00	0.00	4.58
1614	1646	8.718656	AGAGGTATCAGGTTAGATATTGCTTTT	58.281	33.333	0.00	0.00	33.42	2.27
1628	1660	4.271807	TGAGGATTGAGAGGTATCAGGT	57.728	45.455	0.00	0.00	0.00	4.00
1669	1701	8.186163	TCGTAAGACAACACTATCATAAATCGT	58.814	33.333	0.00	0.00	45.01	3.73
1865	1905	4.096532	GCATCAGTACTAGTGTAGCACTCA	59.903	45.833	5.39	0.00	41.21	3.41
1898	1938	8.630917	AGCGTTAGATGATGTGTAAGTAAGTAT	58.369	33.333	0.00	0.00	0.00	2.12
1926	1966	3.009026	TGCATGCGTTGTAATCTGACAT	58.991	40.909	14.09	0.00	0.00	3.06
2055	2095	7.243487	AGTAAATTAATGTGTGCTTCATGACG	58.757	34.615	0.00	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.