AutoCloner

Multiple sequence alignment - TraesCS7B01G304000

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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	TraesCS7B01G304000	chr7B	100.000	4257	0	0	1	4257	544483803	544479547	0.000000e+00	7862.0
1	TraesCS7B01G304000	chr7B	90.761	368	33	1	2751	3117	193310835	193311202	1.380000e-134	490.0
2	TraesCS7B01G304000	chr7A	94.890	2407	79	19	1889	4257	585357767	585355367	0.000000e+00	3723.0
3	TraesCS7B01G304000	chr7A	95.595	1067	41	2	806	1872	585358810	585357750	0.000000e+00	1705.0
4	TraesCS7B01G304000	chr7A	95.294	425	16	3	290	712	585359749	585359327	0.000000e+00	671.0
5	TraesCS7B01G304000	chr7A	89.973	369	36	1	2751	3118	221267308	221266940	3.850000e-130	475.0
6	TraesCS7B01G304000	chr7A	90.378	291	25	3	1	289	585360180	585359891	3.110000e-101	379.0
7	TraesCS7B01G304000	chr7A	88.636	44	5	0	32	75	723161178	723161135	2.000000e-03	54.7
8	TraesCS7B01G304000	chr7D	94.454	2416	75	25	1	2375	512750016	512747619	0.000000e+00	3664.0
9	TraesCS7B01G304000	chr7D	97.897	1617	33	1	2641	4257	512747182	512745567	0.000000e+00	2796.0
10	TraesCS7B01G304000	chr7D	89.973	369	36	1	2751	3118	208223488	208223120	3.850000e-130	475.0
11	TraesCS7B01G304000	chr7D	100.000	154	0	0	2443	2596	512747334	512747181	6.970000e-73	285.0
12	TraesCS7B01G304000	chr5D	87.731	432	45	5	2752	3182	374391716	374392140	8.220000e-137	497.0
13	TraesCS7B01G304000	chr5B	88.889	405	40	3	2752	3155	446996505	446996905	1.060000e-135	494.0
14	TraesCS7B01G304000	chr5A	89.867	375	36	2	2752	3125	476225335	476225708	8.280000e-132	481.0
15	TraesCS7B01G304000	chr3B	85.974	385	50	4	2752	3134	638357251	638356869	3.960000e-110	409.0
16	TraesCS7B01G304000	chr1A	87.736	106	12	1	3685	3789	481924517	481924412	5.780000e-24	122.0
17	TraesCS7B01G304000	chr1A	88.235	102	9	3	3682	3781	481924418	481924518	7.480000e-23	119.0
18	TraesCS7B01G304000	chr1D	88.776	98	8	3	3685	3780	313208276	313208372	2.690000e-22	117.0
19	TraesCS7B01G304000	chr1D	86.111	108	11	4	3678	3783	446426968	446426863	3.480000e-21	113.0
20	TraesCS7B01G304000	chr1D	85.849	106	14	1	3685	3789	381307088	381306983	1.250000e-20	111.0
21	TraesCS7B01G304000	chr1D	87.129	101	10	3	3683	3781	381306990	381307089	1.250000e-20	111.0
22	TraesCS7B01G304000	chr1B	86.869	99	10	3	3685	3781	511444551	511444648	1.620000e-19	108.0
23	TraesCS7B01G304000	chr6B	85.366	82	8	4	291	370	705509324	705509245	9.810000e-12	82.4
24	TraesCS7B01G304000	chr6B	88.636	44	5	0	32	75	300964323	300964366	2.000000e-03	54.7
25	TraesCS7B01G304000	chr4A	95.122	41	2	0	330	370	710200521	710200561	9.880000e-07	65.8
26	TraesCS7B01G304000	chr6D	100.000	29	0	0	31	59	110157900	110157928	2.000000e-03	54.7
27	TraesCS7B01G304000	chr2A	88.636	44	5	0	32	75	42481258	42481301	2.000000e-03	54.7
28	TraesCS7B01G304000	chr2A	88.636	44	5	0	32	75	757962687	757962644	2.000000e-03	54.7
29	TraesCS7B01G304000	chr6A	88.372	43	5	0	32	74	103848638	103848596	8.000000e-03	52.8

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	TraesCS7B01G304000	chr7B	544479547	544483803	4256	True	7862.000000	7862	100.000000	1	4257	1	chr7B.!!$R1	4256
1	TraesCS7B01G304000	chr7A	585355367	585360180	4813	True	1619.500000	3723	94.039250	1	4257	4	chr7A.!!$R3	4256
2	TraesCS7B01G304000	chr7D	512745567	512750016	4449	True	2248.333333	3664	97.450333	1	4257	3	chr7D.!!$R2	4256

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
204	223	0.465460	GCATTGATGGCCCTAACCGA	60.465	55.0	0.0	0.0	0.0	4.69	F
1894	2493	0.529773	TCTCTCTCTCTCGCTCGCTC	60.530	60.0	0.0	0.0	0.0	5.03	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1896	2495	0.028242	AAGATACGTCAGCGAGCGAG	59.972	55.000	0.00	0.0	42.00	5.03	R
3648	4492	2.832661	GCCCGTGGCCATTGCATA	60.833	61.111	9.72	0.0	44.06	3.14	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
102	103	1.450134	TTGCATGCACTAGAGGCGG	60.450	57.895	22.58	0.00	0.00	6.13
145	164	3.437795	GCGCTGGCAGCTCAACAT	61.438	61.111	34.17	0.00	39.60	2.71
167	186	4.487714	TGTGATGTTCCTATTCTGGTCC	57.512	45.455	0.00	0.00	0.00	4.46
172	191	3.516586	TGTTCCTATTCTGGTCCAGTCA	58.483	45.455	18.65	7.34	32.61	3.41
192	211	2.922162	ACTCCTCGGAGGCATTGAT	58.078	52.632	19.48	0.00	45.88	2.57
204	223	0.465460	GCATTGATGGCCCTAACCGA	60.465	55.000	0.00	0.00	0.00	4.69
218	237	2.930826	AACCGATGACAACTTGTCCT	57.069	45.000	17.51	9.14	46.40	3.85
224	243	3.243035	CGATGACAACTTGTCCTGCAAAA	60.243	43.478	17.51	0.00	46.40	2.44
263	283	6.499172	CACGAGAAAATAGAGTAGCAGATCA	58.501	40.000	0.00	0.00	0.00	2.92
281	301	6.108687	CAGATCAGTTGGCTTTGTATAGTCA	58.891	40.000	0.00	0.00	0.00	3.41
286	306	5.234329	CAGTTGGCTTTGTATAGTCATACCG	59.766	44.000	0.00	0.00	36.90	4.02
303	464	3.510531	ACCGAGAGTATGGCTAGATCA	57.489	47.619	0.00	0.00	0.00	2.92
340	502	0.892063	AGGAACTCTTGCCTCTCGAC	59.108	55.000	0.00	0.00	0.00	4.20
476	639	5.335661	GCTGGGTGACATAAATTTTCGTCTT	60.336	40.000	16.25	0.00	0.00	3.01
561	724	5.190357	AGGAGAGAATTCAAGCTTCCAAT	57.810	39.130	8.44	0.00	0.00	3.16
884	1481	3.954258	CTCTCCCTCTCTTCTTCTTCTCC	59.046	52.174	0.00	0.00	0.00	3.71
885	1482	3.596046	TCTCCCTCTCTTCTTCTTCTCCT	59.404	47.826	0.00	0.00	0.00	3.69
886	1483	3.954258	CTCCCTCTCTTCTTCTTCTCCTC	59.046	52.174	0.00	0.00	0.00	3.71
953	1550	0.734889	GCCATTTCTCATCCACACCG	59.265	55.000	0.00	0.00	0.00	4.94
978	1575	1.856259	TCTCCTATCTCCAGCTCCACT	59.144	52.381	0.00	0.00	0.00	4.00
1039	1636	1.362224	TTTCTTGAGGGGCTACAGCT	58.638	50.000	0.54	0.00	41.70	4.24
1096	1693	0.909610	CTTCCCCAGCTACACCTCCA	60.910	60.000	0.00	0.00	0.00	3.86
1178	1775	2.993853	GCCCTCCTCCTCAACCTG	59.006	66.667	0.00	0.00	0.00	4.00
1431	2028	1.857638	AAGAAGGGCAGGAGGAAGGC	61.858	60.000	0.00	0.00	0.00	4.35
1533	2130	1.307517	GTACTGGATCCCCACCCCA	60.308	63.158	9.90	0.00	37.58	4.96
1637	2234	2.945008	GGTGATCCATCTTCGAATTGCA	59.055	45.455	0.00	0.00	0.00	4.08
1690	2287	4.099633	TCTGATCCTGTCTGGTCTTGATT	58.900	43.478	0.00	0.00	37.07	2.57
1746	2343	8.592155	GTTTGTGTTGTGAACTTCTTTTTATCC	58.408	33.333	0.00	0.00	0.00	2.59
1750	2347	8.188139	GTGTTGTGAACTTCTTTTTATCCTTCA	58.812	33.333	0.00	0.00	0.00	3.02
1880	2479	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1890	2489	2.362397	TCTCTCTCTCTCTCTCTCGCTC	59.638	54.545	0.00	0.00	0.00	5.03
1891	2490	1.067060	TCTCTCTCTCTCTCTCGCTCG	59.933	57.143	0.00	0.00	0.00	5.03
1893	2492	0.530650	CTCTCTCTCTCTCGCTCGCT	60.531	60.000	0.00	0.00	0.00	4.93
1894	2493	0.529773	TCTCTCTCTCTCGCTCGCTC	60.530	60.000	0.00	0.00	0.00	5.03
1895	2494	1.821241	CTCTCTCTCTCGCTCGCTCG	61.821	65.000	0.00	0.00	0.00	5.03
1896	2495	3.506312	CTCTCTCTCGCTCGCTCGC	62.506	68.421	0.00	0.00	0.00	5.03
1897	2496	3.572539	CTCTCTCGCTCGCTCGCT	61.573	66.667	0.00	0.00	0.00	4.93
1898	2497	3.506312	CTCTCTCGCTCGCTCGCTC	62.506	68.421	0.00	0.00	0.00	5.03
1899	2498	4.936248	CTCTCGCTCGCTCGCTCG	62.936	72.222	0.00	0.00	0.00	5.03
1932	2531	6.706270	ACGTATCTTGTTGATTTGACTGAACT	59.294	34.615	0.00	0.00	36.65	3.01
1953	2552	1.571936	GGGAGGGAAGTAGAGAGAGGT	59.428	57.143	0.00	0.00	0.00	3.85
2093	2700	0.683973	CTCCTATGCTGGCTACTGGG	59.316	60.000	0.00	0.00	0.00	4.45
2146	2754	4.273274	CGCTTGTTTTGCCTTTTCAATTG	58.727	39.130	0.00	0.00	0.00	2.32
2610	3452	2.515290	TCCGATCGAGCCGCTGTA	60.515	61.111	18.66	0.00	0.00	2.74
2636	3478	1.660575	AACGAACACTCTGCGGTCG	60.661	57.895	1.31	1.31	0.00	4.79
3196	4038	2.587753	CACACCGTCAACACCGCT	60.588	61.111	0.00	0.00	0.00	5.52
3536	4378	8.329203	AGAGGTGAGTGAATTTCTAATTGTTC	57.671	34.615	0.00	0.00	0.00	3.18
3712	4560	1.129811	CCGTCCCAAAATAAGTGTCGC	59.870	52.381	0.00	0.00	0.00	5.19
3973	4828	7.759886	TCCAAGAAGTGATTTACTATCGTTCTG	59.240	37.037	0.00	0.00	39.18	3.02
4070	4925	9.930158	AGTTTAAGGCCCATGTTATCTATTAAA	57.070	29.630	0.00	0.00	0.00	1.52
4185	5040	9.440773	GAAATTTCCTCAATAGAAAAATGGCTT	57.559	29.630	6.95	0.00	36.83	4.35
4203	5058	3.843426	CTTCAAAGCTAGTATTCGCCG	57.157	47.619	0.00	0.00	0.00	6.46
4225	5080	2.472861	CGTCGATGCATGTACCAAGATC	59.527	50.000	2.46	0.00	0.00	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
145	164	4.288366	TGGACCAGAATAGGAACATCACAA	59.712	41.667	0.00	0.00	0.00	3.33
167	186	1.662438	GCCTCCGAGGAGTCTGACTG	61.662	65.000	19.33	0.03	37.67	3.51
172	191	0.324738	TCAATGCCTCCGAGGAGTCT	60.325	55.000	19.33	0.00	37.67	3.24
192	211	0.035820	GTTGTCATCGGTTAGGGCCA	60.036	55.000	6.18	0.00	0.00	5.36
218	237	6.754209	TCGTGCTTAATCTTTTTCTTTTTGCA	59.246	30.769	0.00	0.00	0.00	4.08
263	283	5.128171	TCGGTATGACTATACAAAGCCAACT	59.872	40.000	0.00	0.00	40.77	3.16
281	301	5.180810	TGATCTAGCCATACTCTCGGTAT	57.819	43.478	0.00	0.00	41.38	2.73
286	306	4.159506	GGTCCATGATCTAGCCATACTCTC	59.840	50.000	0.00	0.00	0.00	3.20
303	464	0.830648	CTCCATACACGGTGGTCCAT	59.169	55.000	13.48	0.00	37.96	3.41
476	639	5.186797	CCCCTGCAATACTTTAATTGACCAA	59.813	40.000	0.91	0.00	38.84	3.67
953	1550	2.884639	GAGCTGGAGATAGGAGAGACAC	59.115	54.545	0.00	0.00	0.00	3.67
978	1575	1.754803	GATGGATCGACTGGTGGTACA	59.245	52.381	0.00	0.00	0.00	2.90
1039	1636	1.080093	CTGCGTTGGAGTAGCGGAA	60.080	57.895	0.00	0.00	39.46	4.30
1096	1693	2.038762	AGGTGGGTGGTGGAGGTT	60.039	61.111	0.00	0.00	0.00	3.50
1178	1775	1.532794	TGTTGATGGGGGTTGTGGC	60.533	57.895	0.00	0.00	0.00	5.01
1431	2028	1.327303	CATCCTCCTCCTCTCCTTCG	58.673	60.000	0.00	0.00	0.00	3.79
1533	2130	2.061061	GGACCAATGAGGATCTGGGAT	58.939	52.381	3.26	0.00	41.22	3.85
1637	2234	2.427812	TGAAATCCGATGCATGCACAAT	59.572	40.909	25.37	7.40	0.00	2.71
1690	2287	6.755542	AACAAAATCAACTAAAATCCCCCA	57.244	33.333	0.00	0.00	0.00	4.96
1746	2343	2.730090	GCTCCAATTCACGCACATGAAG	60.730	50.000	0.00	0.00	41.76	3.02
1750	2347	0.806868	CTGCTCCAATTCACGCACAT	59.193	50.000	0.00	0.00	0.00	3.21
1880	2479	3.506312	GAGCGAGCGAGCGAGAGAG	62.506	68.421	1.41	0.00	43.00	3.20
1894	2493	3.791928	ATACGTCAGCGAGCGAGCG	62.792	63.158	0.00	6.65	43.00	5.03
1895	2494	2.006587	GATACGTCAGCGAGCGAGC	61.007	63.158	0.00	0.00	42.00	5.03
1896	2495	0.028242	AAGATACGTCAGCGAGCGAG	59.972	55.000	0.00	0.00	42.00	5.03
1897	2496	0.248094	CAAGATACGTCAGCGAGCGA	60.248	55.000	0.00	0.00	42.00	4.93
1898	2497	0.523546	ACAAGATACGTCAGCGAGCG	60.524	55.000	0.00	0.00	42.00	5.03
1899	2498	1.321743	CAACAAGATACGTCAGCGAGC	59.678	52.381	0.00	0.00	42.00	5.03
1900	2499	2.863739	TCAACAAGATACGTCAGCGAG	58.136	47.619	0.00	0.00	42.00	5.03
1932	2531	1.571457	CCTCTCTCTACTTCCCTCCCA	59.429	57.143	0.00	0.00	0.00	4.37
1953	2552	1.079612	CGGCAGACAGAGTGCATGA	60.080	57.895	0.00	0.00	43.12	3.07
2069	2676	1.622811	GTAGCCAGCATAGGAGCTCAT	59.377	52.381	17.19	11.85	44.54	2.90
2099	2706	3.698289	ACTCCAAGATCGGTCAGTCTAA	58.302	45.455	0.00	0.00	0.00	2.10
2172	2780	4.342092	CCAGATCTCTCTCCTTTTCTCTCC	59.658	50.000	0.00	0.00	0.00	3.71
2268	2876	4.430423	CGTTGGCTTGAGACGCGC	62.430	66.667	5.73	0.00	0.00	6.86
2417	3042	7.014449	TCTCTCTCTAGCTACCAGTATCTAGT	58.986	42.308	12.89	0.00	34.92	2.57
2610	3452	0.459585	AGAGTGTTCGTTGCGTGTGT	60.460	50.000	0.00	0.00	0.00	3.72
2636	3478	3.982241	GTGGTGCTTGCTGGTGCC	61.982	66.667	0.00	0.00	38.71	5.01
3648	4492	2.832661	GCCCGTGGCCATTGCATA	60.833	61.111	9.72	0.00	44.06	3.14
3936	4790	8.655935	AAATCACTTCTTGGATGTAAGGAAAT	57.344	30.769	0.00	0.00	0.00	2.17
4070	4925	4.228210	TCAAGAAGCTGGAAATATCCCACT	59.772	41.667	0.00	0.00	45.95	4.00
4185	5040	1.567504	GCGGCGAATACTAGCTTTGA	58.432	50.000	12.98	0.00	0.00	2.69
4203	5058	0.301687	CTTGGTACATGCATCGACGC	59.698	55.000	0.00	0.00	39.30	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.