AutoCloner

Multiple sequence alignment - TraesCS5A01G390700

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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	TraesCS5A01G390700	chr5A	100.000	2786	0	0	1	2786	586140030	586142815	0.000000e+00	5145
1	TraesCS5A01G390700	chr5D	94.007	2019	89	17	790	2786	465710397	465712405	0.000000e+00	3029
2	TraesCS5A01G390700	chr5B	93.520	1713	75	17	1091	2786	572943054	572944747	0.000000e+00	2516
3	TraesCS5A01G390700	chr5B	93.434	198	8	3	797	989	572942422	572942619	3.510000e-74	289
4	TraesCS5A01G390700	chr2A	89.634	820	56	10	1	798	445334933	445335745	0.000000e+00	1016
5	TraesCS5A01G390700	chr2A	80.479	292	35	11	495	766	685984663	685984952	1.310000e-48	204
6	TraesCS5A01G390700	chr6D	89.049	831	55	16	1	800	38135109	38134284	0.000000e+00	998
7	TraesCS5A01G390700	chr6D	88.835	824	60	10	1	801	325710874	325710060	0.000000e+00	983
8	TraesCS5A01G390700	chr3D	88.049	820	69	11	1	798	578355132	578355944	0.000000e+00	944
9	TraesCS5A01G390700	chr3D	87.846	831	61	15	1	800	421008560	421007739	0.000000e+00	939
10	TraesCS5A01G390700	chr3D	85.714	462	39	8	360	800	104140076	104140531	1.950000e-126	462
11	TraesCS5A01G390700	chr2D	87.470	830	65	14	1	797	448693289	448694112	0.000000e+00	920
12	TraesCS5A01G390700	chr1D	88.609	755	56	12	1	732	349804573	349805320	0.000000e+00	891
13	TraesCS5A01G390700	chr1D	85.888	822	76	17	1	800	403286906	403287709	0.000000e+00	839
14	TraesCS5A01G390700	chr4D	85.783	830	73	15	1	798	23339071	23339887	0.000000e+00	837
15	TraesCS5A01G390700	chr4D	86.066	244	12	7	584	805	498856672	498856429	2.770000e-60	243
16	TraesCS5A01G390700	chr7D	85.476	840	70	18	1	808	535567258	535566439	0.000000e+00	828
17	TraesCS5A01G390700	chr7D	82.930	826	100	24	1	798	390229743	390230555	0.000000e+00	706
18	TraesCS5A01G390700	chr7D	89.802	353	32	3	449	798	33031644	33031293	1.520000e-122	449
19	TraesCS5A01G390700	chr6A	85.759	639	61	6	1	638	616186653	616187262	0.000000e+00	649
20	TraesCS5A01G390700	chr6A	88.797	482	43	8	1	479	93937210	93936737	5.170000e-162	580
21	TraesCS5A01G390700	chrUn	86.767	529	61	4	1	524	344578228	344578752	5.170000e-162	580

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	TraesCS5A01G390700	chr5A	586140030	586142815	2785	False	5145.0	5145	100.000	1	2786	1	chr5A.!!$F1	2785
1	TraesCS5A01G390700	chr5D	465710397	465712405	2008	False	3029.0	3029	94.007	790	2786	1	chr5D.!!$F1	1996
2	TraesCS5A01G390700	chr5B	572942422	572944747	2325	False	1402.5	2516	93.477	797	2786	2	chr5B.!!$F1	1989
3	TraesCS5A01G390700	chr2A	445334933	445335745	812	False	1016.0	1016	89.634	1	798	1	chr2A.!!$F1	797
4	TraesCS5A01G390700	chr6D	38134284	38135109	825	True	998.0	998	89.049	1	800	1	chr6D.!!$R1	799
5	TraesCS5A01G390700	chr6D	325710060	325710874	814	True	983.0	983	88.835	1	801	1	chr6D.!!$R2	800
6	TraesCS5A01G390700	chr3D	578355132	578355944	812	False	944.0	944	88.049	1	798	1	chr3D.!!$F2	797
7	TraesCS5A01G390700	chr3D	421007739	421008560	821	True	939.0	939	87.846	1	800	1	chr3D.!!$R1	799
8	TraesCS5A01G390700	chr2D	448693289	448694112	823	False	920.0	920	87.470	1	797	1	chr2D.!!$F1	796
9	TraesCS5A01G390700	chr1D	349804573	349805320	747	False	891.0	891	88.609	1	732	1	chr1D.!!$F1	731
10	TraesCS5A01G390700	chr1D	403286906	403287709	803	False	839.0	839	85.888	1	800	1	chr1D.!!$F2	799
11	TraesCS5A01G390700	chr4D	23339071	23339887	816	False	837.0	837	85.783	1	798	1	chr4D.!!$F1	797
12	TraesCS5A01G390700	chr7D	535566439	535567258	819	True	828.0	828	85.476	1	808	1	chr7D.!!$R2	807
13	TraesCS5A01G390700	chr7D	390229743	390230555	812	False	706.0	706	82.930	1	798	1	chr7D.!!$F1	797
14	TraesCS5A01G390700	chr6A	616186653	616187262	609	False	649.0	649	85.759	1	638	1	chr6A.!!$F1	637
15	TraesCS5A01G390700	chrUn	344578228	344578752	524	False	580.0	580	86.767	1	524	1	chrUn.!!$F1	523

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
627	668	0.179134	ACCGCTTCACTGAGATACGC	60.179	55.0	0.0	0.0	0.0	4.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2072	2503	0.037975	GACCATGTTTGCAAGGCCAG	60.038	55.0	5.01	0.0	36.99	4.85	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
54	55	5.411831	AGTAGTCTTGCATCAACATCTCA	57.588	39.130	0.00	0.00	0.00	3.27
418	449	4.353437	GGCGACAACGACGAGGGT	62.353	66.667	0.00	0.00	42.66	4.34
439	471	1.066587	GCTCTTCTCACCGGATCCG	59.933	63.158	27.65	27.65	39.44	4.18
475	513	1.090052	GTATCGGTGCTGAAGGGTGC	61.090	60.000	0.00	0.00	0.00	5.01
525	563	2.044451	ATTTGGCCGGAATCGCCA	60.044	55.556	5.05	0.53	39.48	5.69
598	638	3.127533	GCGCGGGCTGAAATGTCT	61.128	61.111	18.33	0.00	35.83	3.41
627	668	0.179134	ACCGCTTCACTGAGATACGC	60.179	55.000	0.00	0.00	0.00	4.42
651	692	2.962569	GCAGGGGCGAAGGAAAAC	59.037	61.111	0.00	0.00	0.00	2.43
782	845	2.673687	CGGGCTTTTTGCGGGGTA	60.674	61.111	0.00	0.00	44.05	3.69
788	851	1.474879	GCTTTTTGCGGGGTATGCTAA	59.525	47.619	0.00	0.00	0.00	3.09
908	972	1.007387	GCAAAACGCCAACTCCCTG	60.007	57.895	0.00	0.00	32.94	4.45
938	1002	1.831652	AACCACCAGCGGAGAAGGAG	61.832	60.000	1.50	0.00	0.00	3.69
947	1015	1.222113	GGAGAAGGAGGGAAAGCGG	59.778	63.158	0.00	0.00	0.00	5.52
1120	1530	4.363990	CCGCACTCTGACGGCTGT	62.364	66.667	0.00	0.00	43.44	4.40
1134	1544	0.240945	GGCTGTGTGAAATTGGTCGG	59.759	55.000	0.00	0.00	0.00	4.79
1216	1626	5.840081	ACCCTAGATACAAAGAGGTACACT	58.160	41.667	0.00	0.00	0.00	3.55
1287	1697	0.255890	CCCGTCCCTCCAAATCATGT	59.744	55.000	0.00	0.00	0.00	3.21
1288	1698	1.488812	CCCGTCCCTCCAAATCATGTA	59.511	52.381	0.00	0.00	0.00	2.29
1289	1699	2.485479	CCCGTCCCTCCAAATCATGTAG	60.485	54.545	0.00	0.00	0.00	2.74
1312	1722	3.325870	TCAATCTGCGTCTTACAGTTGG	58.674	45.455	0.00	0.00	36.50	3.77
1316	1726	1.122632	TGCGTCTTACAGTTGGGGGA	61.123	55.000	0.00	0.00	0.00	4.81
1318	1728	1.339727	GCGTCTTACAGTTGGGGGATT	60.340	52.381	0.00	0.00	0.00	3.01
1321	1731	3.439129	CGTCTTACAGTTGGGGGATTTTC	59.561	47.826	0.00	0.00	0.00	2.29
1419	1833	3.499737	CGCCCCAACATCGTCAGC	61.500	66.667	0.00	0.00	0.00	4.26
1421	1835	1.750399	GCCCCAACATCGTCAGCAT	60.750	57.895	0.00	0.00	0.00	3.79
1426	1840	2.746904	CCCAACATCGTCAGCATTAACA	59.253	45.455	0.00	0.00	0.00	2.41
1435	1849	0.381801	CAGCATTAACACCCGCATCC	59.618	55.000	0.00	0.00	0.00	3.51
1436	1850	0.255890	AGCATTAACACCCGCATCCT	59.744	50.000	0.00	0.00	0.00	3.24
1442	1856	0.827507	AACACCCGCATCCTGCTTTT	60.828	50.000	0.00	0.00	42.25	2.27
1568	1987	6.535811	CGTAAGTGTGTGTGTTTGTCTTTAA	58.464	36.000	0.00	0.00	0.00	1.52
1570	1989	7.006742	CGTAAGTGTGTGTGTTTGTCTTTAAAC	59.993	37.037	0.00	0.00	40.18	2.01
1582	2001	5.229921	TGTCTTTAAACTGCACTGTGAAC	57.770	39.130	12.86	0.00	0.00	3.18
1587	2006	5.888691	TTAAACTGCACTGTGAACTTTCA	57.111	34.783	12.86	0.00	34.20	2.69
1605	2024	7.243604	ACTTTCATGGGATGCAAAGAAAATA	57.756	32.000	8.76	0.00	34.48	1.40
1822	2253	4.460948	TCGGGTGAAAACTATGTCTACC	57.539	45.455	0.00	0.00	0.00	3.18
1845	2276	5.473504	CCTTACACAAGGCTTTGTATCAGTT	59.526	40.000	14.45	0.00	45.53	3.16
1866	2297	5.762218	AGTTGCTCTATTAGGTCATGATTGC	59.238	40.000	0.00	0.00	0.00	3.56
1894	2325	0.798776	GGCACACATCTTTCTCGTGG	59.201	55.000	0.00	0.00	34.91	4.94
1896	2327	0.798776	CACACATCTTTCTCGTGGCC	59.201	55.000	0.00	0.00	34.91	5.36
1898	2329	1.072331	ACACATCTTTCTCGTGGCCTT	59.928	47.619	3.32	0.00	34.91	4.35
1899	2330	2.154462	CACATCTTTCTCGTGGCCTTT	58.846	47.619	3.32	0.00	0.00	3.11
1900	2331	3.244422	ACACATCTTTCTCGTGGCCTTTA	60.244	43.478	3.32	0.00	34.91	1.85
1905	2336	5.871396	TCTTTCTCGTGGCCTTTATAGAT	57.129	39.130	3.32	0.00	0.00	1.98
1913	2344	9.653287	TCTCGTGGCCTTTATAGATAATAATTG	57.347	33.333	3.32	0.00	30.11	2.32
1945	2376	4.023707	CAGTTCCCTTGATGTTTCACACTC	60.024	45.833	0.00	0.00	0.00	3.51
2055	2486	8.405531	CAATACTTTTTCCATGATAATCACGGT	58.594	33.333	0.00	0.00	30.56	4.83
2072	2503	0.530870	GGTATCTTGGCTCTCGTGGC	60.531	60.000	0.00	0.00	0.00	5.01
2075	2506	2.249413	ATCTTGGCTCTCGTGGCTGG	62.249	60.000	0.00	0.00	0.00	4.85
2105	2536	2.490903	ACATGGTCAGCTTGATTTCTGC	59.509	45.455	0.00	0.00	0.00	4.26
2129	2564	3.043465	TCTCTCTGCTTCCATCCATCT	57.957	47.619	0.00	0.00	0.00	2.90
2272	2713	6.805271	GCAATGATTTCATCTATTTGCGCTAT	59.195	34.615	9.73	4.77	35.10	2.97
2325	2766	6.619446	GCGCTTGATTATATCCTAGCTGTTTG	60.619	42.308	0.00	0.00	35.22	2.93
2359	2800	6.438108	ACCCCTTTACACACCATATAAAAACC	59.562	38.462	0.00	0.00	0.00	3.27
2360	2801	6.127281	CCCCTTTACACACCATATAAAAACCC	60.127	42.308	0.00	0.00	0.00	4.11
2389	2830	7.870445	TCAACTTTTATTGATACAAAACCAGGC	59.130	33.333	0.00	0.00	33.62	4.85
2433	2874	7.619050	AGAGTCTGATTACAAATGAGACACAT	58.381	34.615	17.55	1.95	41.45	3.21
2464	2905	7.538575	ACACATTTTGAAGTATGGAGCAATAC	58.461	34.615	0.00	0.00	33.90	1.89
2597	3038	0.877071	CATGCGTCTTCCAGTGCTTT	59.123	50.000	0.00	0.00	0.00	3.51
2599	3040	0.179059	TGCGTCTTCCAGTGCTTTGA	60.179	50.000	0.00	0.00	0.00	2.69
2614	3055	4.393680	GTGCTTTGACCACCGTTATATCAA	59.606	41.667	0.00	0.00	0.00	2.57
2616	3057	4.873827	GCTTTGACCACCGTTATATCAAGA	59.126	41.667	0.00	0.00	31.34	3.02
2753	3194	3.008704	AGCCTAGACCATTTACACGGTTT	59.991	43.478	0.00	0.00	34.99	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	4.386088	CCTCAGAATCACCATCTTGGGAAT	60.386	45.833	0.00	0.00	43.37	3.01
67	68	3.686241	CGTCTTTGCATTCCTCAGAATCA	59.314	43.478	0.00	0.00	40.89	2.57
279	308	4.051922	CGGTATGCCTAGTTGATTGACTC	58.948	47.826	0.00	0.00	0.00	3.36
280	309	3.741388	GCGGTATGCCTAGTTGATTGACT	60.741	47.826	0.00	0.00	37.76	3.41
281	310	2.544267	GCGGTATGCCTAGTTGATTGAC	59.456	50.000	0.00	0.00	37.76	3.18
282	311	2.833794	GCGGTATGCCTAGTTGATTGA	58.166	47.619	0.00	0.00	37.76	2.57
598	638	2.204461	TGAAGCGGTTGACGGGAGA	61.204	57.895	3.70	0.00	44.51	3.71
644	685	1.539827	CAAAATCTCGGCCGTTTTCCT	59.460	47.619	27.15	7.13	0.00	3.36
647	688	0.038618	GGCAAAATCTCGGCCGTTTT	60.039	50.000	27.15	21.03	38.04	2.43
648	689	1.584495	GGCAAAATCTCGGCCGTTT	59.416	52.632	27.15	15.94	38.04	3.60
938	1002	1.927608	GCTTCTGCTTCCGCTTTCCC	61.928	60.000	0.00	0.00	36.97	3.97
947	1015	1.499502	GCTCGGTTGCTTCTGCTTC	59.500	57.895	0.00	0.00	40.48	3.86
1073	1141	4.890306	GAGGAGGAGGGGGAGGGC	62.890	77.778	0.00	0.00	0.00	5.19
1074	1142	4.179599	GGAGGAGGAGGGGGAGGG	62.180	77.778	0.00	0.00	0.00	4.30
1075	1143	3.039526	AGGAGGAGGAGGGGGAGG	61.040	72.222	0.00	0.00	0.00	4.30
1077	1145	3.036959	GGAGGAGGAGGAGGGGGA	61.037	72.222	0.00	0.00	0.00	4.81
1120	1530	0.893270	CCTGCCCGACCAATTTCACA	60.893	55.000	0.00	0.00	0.00	3.58
1188	1598	4.717280	ACCTCTTTGTATCTAGGGTTCTGG	59.283	45.833	0.00	0.00	33.16	3.86
1257	1667	2.993264	GGACGGGTCGGAAGTGGA	60.993	66.667	0.00	0.00	0.00	4.02
1287	1697	5.836821	ACTGTAAGACGCAGATTGATCTA	57.163	39.130	0.00	0.00	37.43	1.98
1288	1698	4.727507	ACTGTAAGACGCAGATTGATCT	57.272	40.909	0.00	0.00	37.43	2.75
1289	1699	4.033358	CCAACTGTAAGACGCAGATTGATC	59.967	45.833	0.00	0.00	37.43	2.92
1568	1987	3.067180	CCATGAAAGTTCACAGTGCAGTT	59.933	43.478	0.00	0.00	40.49	3.16
1570	1989	2.030540	CCCATGAAAGTTCACAGTGCAG	60.031	50.000	0.00	0.00	40.49	4.41
1582	2001	7.279313	CCTTATTTTCTTTGCATCCCATGAAAG	59.721	37.037	0.00	0.00	32.15	2.62
1587	2006	5.129320	GGTCCTTATTTTCTTTGCATCCCAT	59.871	40.000	0.00	0.00	0.00	4.00
1626	2045	1.520590	CATTCCAAACAACGCAAACGG	59.479	47.619	0.00	0.00	46.04	4.44
1822	2253	6.373779	CAACTGATACAAAGCCTTGTGTAAG	58.626	40.000	11.02	9.13	45.53	2.34
1845	2276	5.059161	GTGCAATCATGACCTAATAGAGCA	58.941	41.667	0.00	0.00	0.00	4.26
1913	2344	8.887036	AAACATCAAGGGAACTGTTTTATTTC	57.113	30.769	0.00	0.00	42.68	2.17
1945	2376	3.287867	AGCAGGATGTACAAATGAGGG	57.712	47.619	0.00	0.00	39.31	4.30
2046	2477	3.004419	CGAGAGCCAAGATACCGTGATTA	59.996	47.826	0.00	0.00	0.00	1.75
2055	2486	0.461548	CAGCCACGAGAGCCAAGATA	59.538	55.000	0.00	0.00	0.00	1.98
2072	2503	0.037975	GACCATGTTTGCAAGGCCAG	60.038	55.000	5.01	0.00	36.99	4.85
2075	2506	0.668401	GCTGACCATGTTTGCAAGGC	60.668	55.000	0.00	0.00	36.99	4.35
2105	2536	2.172082	TGGATGGAAGCAGAGAGATTGG	59.828	50.000	0.00	0.00	0.00	3.16
2257	2698	6.642540	TCTGACACTTATAGCGCAAATAGATG	59.357	38.462	11.47	11.09	0.00	2.90
2359	2800	7.061789	GGTTTTGTATCAATAAAAGTTGAGCGG	59.938	37.037	0.00	0.00	41.05	5.52
2360	2801	7.593273	TGGTTTTGTATCAATAAAAGTTGAGCG	59.407	33.333	0.00	0.00	41.05	5.03
2389	2830	9.390795	CAGACTCTTTTCAATTTTAGTCATGTG	57.609	33.333	0.00	0.00	36.63	3.21
2422	2863	7.750229	AAATGTGTCAACTATGTGTCTCATT	57.250	32.000	0.00	0.00	37.91	2.57
2433	2874	7.094805	GCTCCATACTTCAAAATGTGTCAACTA	60.095	37.037	0.00	0.00	0.00	2.24
2464	2905	3.209410	GAATCAGGTGGGCAATGTCTAG	58.791	50.000	0.00	0.00	0.00	2.43
2477	2918	3.495100	GGATGCCATTACTCGAATCAGGT	60.495	47.826	0.00	0.00	0.00	4.00
2597	3038	4.464951	AGTGTCTTGATATAACGGTGGTCA	59.535	41.667	0.00	0.00	0.00	4.02
2599	3040	5.655532	AGTAGTGTCTTGATATAACGGTGGT	59.344	40.000	0.00	0.00	0.00	4.16
2614	3055	7.727181	ACTCATGTAACTTTGAAGTAGTGTCT	58.273	34.615	0.00	0.00	38.57	3.41
2616	3057	9.257651	GTAACTCATGTAACTTTGAAGTAGTGT	57.742	33.333	0.00	0.00	38.57	3.55
2660	3101	4.099881	AGCCATGTCATTCACTTTGTGTTT	59.900	37.500	0.00	0.00	34.79	2.83
2662	3103	3.005050	CAGCCATGTCATTCACTTTGTGT	59.995	43.478	0.00	0.00	34.79	3.72
2666	3107	4.025040	TCTCAGCCATGTCATTCACTTT	57.975	40.909	0.00	0.00	0.00	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.