AutoCloner

Multiple sequence alignment - TraesCS7B01G203300

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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	TraesCS7B01G203300	chr7B	100.000	8035	0	0	1	8035	372827592	372819558	0.000000e+00	14838.0
1	TraesCS7B01G203300	chr7B	84.577	201	31	0	3701	3901	372832037	372831837	4.920000e-47	200.0
2	TraesCS7B01G203300	chr7A	97.941	6509	116	10	1532	8035	425779885	425773390	0.000000e+00	11261.0
3	TraesCS7B01G203300	chr7A	97.578	867	17	3	675	1540	425782283	425781420	0.000000e+00	1482.0
4	TraesCS7B01G203300	chr7A	97.357	681	15	2	1	678	425783043	425782363	0.000000e+00	1155.0
5	TraesCS7B01G203300	chr7A	86.070	201	28	0	3701	3901	425790303	425790103	4.880000e-52	217.0
6	TraesCS7B01G203300	chr7A	83.516	91	13	2	4930	5019	603354839	603354928	5.170000e-12	84.2
7	TraesCS7B01G203300	chr7D	98.761	6293	71	7	1604	7893	378162116	378155828	0.000000e+00	11182.0
8	TraesCS7B01G203300	chr7D	97.276	1542	32	2	1	1540	378163646	378162113	0.000000e+00	2606.0
9	TraesCS7B01G203300	chr7D	85.572	201	29	0	3701	3901	378173244	378173044	2.270000e-50	211.0
10	TraesCS7B01G203300	chr6B	78.566	2748	477	76	4368	7035	183286651	183289366	0.000000e+00	1709.0
11	TraesCS7B01G203300	chr6B	79.520	1001	138	37	2138	3100	183283886	183284857	0.000000e+00	651.0
12	TraesCS7B01G203300	chr6B	85.065	308	39	7	3687	3991	183286264	183286567	2.820000e-79	307.0
13	TraesCS7B01G203300	chr6A	79.104	871	118	35	2138	2972	117061149	117061991	7.090000e-150	542.0
14	TraesCS7B01G203300	chr6A	86.105	439	59	1	4467	4905	117069839	117070275	9.440000e-129	472.0
15	TraesCS7B01G203300	chr6A	85.662	272	33	6	3687	3957	117069378	117069644	1.710000e-71	281.0
16	TraesCS7B01G203300	chr6D	81.090	624	86	19	2481	3100	98035813	98036408	3.390000e-128	470.0
17	TraesCS7B01G203300	chr6D	85.748	428	59	1	4467	4894	98038256	98038681	1.230000e-122	451.0
18	TraesCS7B01G203300	chr6D	84.746	295	37	8	3672	3963	98037783	98038072	1.020000e-73	289.0

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	TraesCS7B01G203300	chr7B	372819558	372827592	8034	True	14838.000000	14838	100.000000	1	8035	1	chr7B.!!$R1	8034
1	TraesCS7B01G203300	chr7A	425773390	425783043	9653	True	4632.666667	11261	97.625333	1	8035	3	chr7A.!!$R2	8034
2	TraesCS7B01G203300	chr7D	378155828	378163646	7818	True	6894.000000	11182	98.018500	1	7893	2	chr7D.!!$R2	7892
3	TraesCS7B01G203300	chr6B	183283886	183289366	5480	False	889.000000	1709	81.050333	2138	7035	3	chr6B.!!$F1	4897
4	TraesCS7B01G203300	chr6A	117061149	117061991	842	False	542.000000	542	79.104000	2138	2972	1	chr6A.!!$F1	834
5	TraesCS7B01G203300	chr6A	117069378	117070275	897	False	376.500000	472	85.883500	3687	4905	2	chr6A.!!$F2	1218
6	TraesCS7B01G203300	chr6D	98035813	98038681	2868	False	403.333333	470	83.861333	2481	4894	3	chr6D.!!$F1	2413

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
793	880	1.098050	GTTCATGCCAGCAACCTAGG	58.902	55.000	7.41	7.41	0.00	3.02	F
2162	3795	0.548031	AGAACACCGCATGATGGGAT	59.452	50.000	11.37	0.00	31.21	3.85	F
3068	4736	1.135046	CTCTCCGCTGCGATGTAATG	58.865	55.000	25.45	4.61	0.00	1.90	F
4355	6850	0.525311	TACGCATGCACCACCAAATG	59.475	50.000	19.57	0.00	0.00	2.32	F
6005	8558	1.353022	GGTGTGGTACAGGGGATTTCA	59.647	52.381	0.00	0.00	41.80	2.69	F
6249	8802	3.241701	CCGGATGAACCAAAATTGAACG	58.758	45.455	0.00	0.00	38.90	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2225	3860	1.825285	CGATTTCTGCGGCAGGATCG	61.825	60.000	33.19	33.19	39.42	3.69	R
3484	5195	4.768968	CCTCAGGAAATATTTATGCAGGGG	59.231	45.833	0.00	0.00	0.00	4.79	R
4487	6984	0.603975	GACCTCCTGACAGTTGCACC	60.604	60.000	0.93	0.00	0.00	5.01	R
6249	8802	3.983044	ACCTACAATTCTGTCCTCACC	57.017	47.619	0.00	0.00	36.96	4.02	R
6923	9491	1.202927	ACCACCTCACCTTTGTCCATG	60.203	52.381	0.00	0.00	0.00	3.66	R
8011	10582	1.361204	TCTGGAGAACTGCATCCCAA	58.639	50.000	1.64	0.00	34.47	4.12	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
142	146	4.819630	TGACTTGGTATCTTTTGTGGACAC	59.180	41.667	0.00	0.00	0.00	3.67
226	230	1.204941	GCGAATGGACAGACTACCACT	59.795	52.381	3.17	0.00	39.06	4.00
235	239	4.551388	GACAGACTACCACTCAAGTTCAG	58.449	47.826	0.00	0.00	0.00	3.02
483	487	7.141363	CCTGCAAAGTAATATCAAAGTATGCC	58.859	38.462	0.00	0.00	0.00	4.40
488	492	9.113838	CAAAGTAATATCAAAGTATGCCAGAGT	57.886	33.333	0.00	0.00	0.00	3.24
638	642	8.868916	GTTACAACAACAACAAAAGATTCATGT	58.131	29.630	0.00	0.00	0.00	3.21
793	880	1.098050	GTTCATGCCAGCAACCTAGG	58.902	55.000	7.41	7.41	0.00	3.02
1044	1131	1.771565	TCCCCGTCGAATCATGTACT	58.228	50.000	0.00	0.00	0.00	2.73
1239	1326	6.456501	GCCTTCGATGTCCTATTACATACTT	58.543	40.000	0.00	0.00	40.17	2.24
1729	3361	6.647067	AGAAATGAGAACAACAGCACTAGTAC	59.353	38.462	0.00	0.00	0.00	2.73
2014	3647	2.991250	TGGTTCAAGCTGGCTAGAATC	58.009	47.619	0.00	0.00	0.00	2.52
2104	3737	7.667635	TGGTGACAGATTTCATAATAACACCAA	59.332	33.333	0.00	0.00	46.64	3.67
2162	3795	0.548031	AGAACACCGCATGATGGGAT	59.452	50.000	11.37	0.00	31.21	3.85
2225	3860	5.585047	ACAGTCTTACCTTTCTTGTCACAAC	59.415	40.000	0.00	0.00	0.00	3.32
2315	3951	2.312722	ATCTGACATCAGTGCTCAGC	57.687	50.000	8.70	0.00	44.12	4.26
2619	4286	1.450312	GATGCTCCTCGTGGTTGGG	60.450	63.158	2.99	0.00	34.23	4.12
2741	4409	4.593634	ACCTTGTTAGAACTAAGCCTCTGT	59.406	41.667	0.00	0.00	0.00	3.41
2847	4515	6.294176	CCGTCTTCTCATTTGTTGGAGAAAAT	60.294	38.462	5.70	0.00	46.28	1.82
3068	4736	1.135046	CTCTCCGCTGCGATGTAATG	58.865	55.000	25.45	4.61	0.00	1.90
3422	5133	1.555075	GGATGTGGGAAGAGCACTGTA	59.445	52.381	0.00	0.00	0.00	2.74
3484	5195	3.379057	AGGCTTCTAGAAGAGAACGCTAC	59.621	47.826	32.16	13.19	39.36	3.58
4018	6513	9.084533	ACAGATAGGTCTAAATAGCCTTAAGAG	57.915	37.037	3.36	0.00	33.76	2.85
4049	6544	2.325583	ACTTTTGAGTTCGGCACTGA	57.674	45.000	0.00	0.00	35.01	3.41
4126	6621	2.426024	CTCCCTCCGTTTGACTATTCGA	59.574	50.000	0.00	0.00	0.00	3.71
4210	6705	4.671377	TGTTGCAATGTTTTCACTCTGTC	58.329	39.130	0.59	0.00	0.00	3.51
4340	6835	1.135257	AGTGAGACAGAGCATGTACGC	60.135	52.381	0.00	0.69	44.17	4.42
4355	6850	0.525311	TACGCATGCACCACCAAATG	59.475	50.000	19.57	0.00	0.00	2.32
4416	6913	8.517878	AGCTAGTTGTACAGAATTTAGTTACGA	58.482	33.333	0.00	0.00	0.00	3.43
4487	6984	4.162509	CCACTTAAGGTAGGAGAAAGAGGG	59.837	50.000	7.53	0.00	0.00	4.30
4496	6993	1.528129	GAGAAAGAGGGGTGCAACTG	58.472	55.000	0.00	0.00	36.74	3.16
4646	7143	2.768527	CAGAGCTATGAAAGGGAGGACA	59.231	50.000	0.88	0.00	0.00	4.02
4816	7313	7.227156	AGTCTAGAAAAGAAATCCAGCAAGAA	58.773	34.615	0.00	0.00	35.47	2.52
4861	7358	6.094742	TCAATTGCACACTTCTTTTCACACTA	59.905	34.615	0.00	0.00	0.00	2.74
5067	7596	5.568685	TTACTGATCAGGTCGAAGAAGAG	57.431	43.478	26.08	0.00	39.69	2.85
6005	8558	1.353022	GGTGTGGTACAGGGGATTTCA	59.647	52.381	0.00	0.00	41.80	2.69
6249	8802	3.241701	CCGGATGAACCAAAATTGAACG	58.758	45.455	0.00	0.00	38.90	3.95
6923	9491	3.991605	AACGCAGATGTAATTGTCGTC	57.008	42.857	0.00	0.00	0.00	4.20
7482	10050	3.262151	TCCAACACATACATTTCTCCGGA	59.738	43.478	2.93	2.93	0.00	5.14
7557	10125	4.722194	CCATTTGGTAAGTCAATGACGTG	58.278	43.478	11.92	1.39	37.67	4.49
7560	10128	1.803334	GGTAAGTCAATGACGTGCCA	58.197	50.000	25.40	0.00	43.38	4.92
7629	10197	7.390718	ACCTATAATCCATAGCCACGAAAATTC	59.609	37.037	0.00	0.00	36.09	2.17
7631	10199	2.285083	TCCATAGCCACGAAAATTCCG	58.715	47.619	0.00	0.00	0.00	4.30
7645	10214	3.678056	AATTCCGCCCCTTTTCTTTTC	57.322	42.857	0.00	0.00	0.00	2.29
7728	10297	1.065709	ACTACGGCCAGTGGGTTATTG	60.066	52.381	12.15	0.00	35.43	1.90
7874	10443	1.160329	GGCGAGGCGAAATGTAGCAT	61.160	55.000	0.00	0.00	34.54	3.79
7965	10536	4.116238	GCTCGAATTAGAAGTCCTTGAGG	58.884	47.826	0.00	0.00	0.00	3.86
7994	10565	1.286553	GTATGTCCACCCCCAATTCCA	59.713	52.381	0.00	0.00	0.00	3.53
7995	10566	1.018031	ATGTCCACCCCCAATTCCAT	58.982	50.000	0.00	0.00	0.00	3.41
8011	10582	1.697432	TCCATGACGAAAACCCTGTCT	59.303	47.619	0.00	0.00	33.81	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
226	230	5.359194	ACTTGAAGAAGACCTGAACTTGA	57.641	39.130	0.00	0.00	32.98	3.02
235	239	5.509670	CCCCAAATTCAACTTGAAGAAGACC	60.510	44.000	9.97	0.00	40.05	3.85
488	492	4.561530	CACTTGGTGAAAGCTACTCTAGCA	60.562	45.833	4.16	0.00	44.39	3.49
638	642	4.972514	TGTTGTTGTGTCAAATGCTACA	57.027	36.364	0.00	0.00	0.00	2.74
696	783	5.967674	GCGTGGAACTCAATTATTCATTCAG	59.032	40.000	0.00	0.00	31.75	3.02
697	784	5.447144	CGCGTGGAACTCAATTATTCATTCA	60.447	40.000	0.00	0.00	31.75	2.57
698	785	4.963953	CGCGTGGAACTCAATTATTCATTC	59.036	41.667	0.00	0.00	31.75	2.67
701	788	3.331150	ACGCGTGGAACTCAATTATTCA	58.669	40.909	12.93	0.00	31.75	2.57
793	880	6.736807	AGCGGTTGACGTTTTAAATTAAAC	57.263	33.333	0.00	0.00	46.52	2.01
1044	1131	1.069090	GTCAACAGCACTGTCGGGA	59.931	57.895	3.32	0.13	44.13	5.14
1239	1326	1.686355	ACGCATCAACAGTTTTCCCA	58.314	45.000	0.00	0.00	0.00	4.37
1729	3361	4.256110	TCTGAATGTATGCTGTCAGGTTG	58.744	43.478	1.14	0.00	38.42	3.77
2014	3647	9.556030	GGTTAAGGAATTCGACAAAAAGATAAG	57.444	33.333	0.00	0.00	0.00	1.73
2104	3737	3.011708	AGGGCAAGTAACCAAATGAGGAT	59.988	43.478	0.00	0.00	0.00	3.24
2162	3795	9.428097	CACTAATGCTATTCATATTGCTAGTGA	57.572	33.333	11.67	0.00	40.05	3.41
2225	3860	1.825285	CGATTTCTGCGGCAGGATCG	61.825	60.000	33.19	33.19	39.42	3.69
2315	3951	4.034510	GTGTCAAAAGCTCCGATATCTTGG	59.965	45.833	0.34	0.00	0.00	3.61
2493	4160	3.209410	CATAAAGTGACCCATCTGAGGC	58.791	50.000	0.00	0.00	0.00	4.70
2847	4515	2.394930	TGAAGGATTTCATCGCCGAA	57.605	45.000	0.00	0.00	38.37	4.30
3068	4736	8.558973	AGATTGCTGGAAATATAATACTCAGC	57.441	34.615	0.00	0.00	44.24	4.26
3234	4945	7.011950	TCCGTTTGATTCATAATTTATCGCTGT	59.988	33.333	0.00	0.00	0.00	4.40
3422	5133	9.745018	TCATAGAATCTTTGAACCAGAGAAATT	57.255	29.630	0.91	0.00	28.70	1.82
3484	5195	4.768968	CCTCAGGAAATATTTATGCAGGGG	59.231	45.833	0.00	0.00	0.00	4.79
3933	6424	7.653311	ACAAAATAGAGAAATTTGTGAGGTTGC	59.347	33.333	0.00	0.00	43.50	4.17
4018	6513	6.255887	CCGAACTCAAAAGTATAGACCACATC	59.744	42.308	0.00	0.00	33.48	3.06
4139	6634	7.990886	TGGACGGATATATTAAAACAGAGCTTT	59.009	33.333	0.00	0.00	0.00	3.51
4210	6705	7.675161	ATTCCTGAAACAATTTAATAGGGGG	57.325	36.000	0.00	0.00	0.00	5.40
4340	6835	3.119388	CCTAAGTCATTTGGTGGTGCATG	60.119	47.826	0.00	0.00	0.00	4.06
4487	6984	0.603975	GACCTCCTGACAGTTGCACC	60.604	60.000	0.93	0.00	0.00	5.01
4496	6993	2.894126	TCTCTGTTTCTGACCTCCTGAC	59.106	50.000	0.00	0.00	0.00	3.51
4646	7143	4.574674	TCTGTGGGCAATCAAGATAACT	57.425	40.909	0.00	0.00	0.00	2.24
4816	7313	6.839124	TTGATTGCATTTACCTGTCTTCAT	57.161	33.333	0.00	0.00	0.00	2.57
5067	7596	4.151689	TCTTTATACGTTGCACTGTCTTGC	59.848	41.667	0.00	0.00	43.31	4.01
6249	8802	3.983044	ACCTACAATTCTGTCCTCACC	57.017	47.619	0.00	0.00	36.96	4.02
6923	9491	1.202927	ACCACCTCACCTTTGTCCATG	60.203	52.381	0.00	0.00	0.00	3.66
7097	9665	7.920738	ACTGTCAAACTCTGTCTTTACATTTC	58.079	34.615	0.00	0.00	34.37	2.17
7433	10001	3.178046	GGGGGTTACACATTCCCAAAAT	58.822	45.455	0.00	0.00	42.71	1.82
7554	10122	3.003378	TCTCTATCGATAGTTGTGGCACG	59.997	47.826	27.34	3.84	37.40	5.34
7557	10125	5.593010	AGTTTCTCTATCGATAGTTGTGGC	58.407	41.667	27.34	16.03	37.40	5.01
7585	10153	4.946160	AGGTTTGGATTTCCTGGTGATA	57.054	40.909	0.00	0.00	36.82	2.15
7629	10197	1.616159	TCAGAAAAGAAAAGGGGCGG	58.384	50.000	0.00	0.00	0.00	6.13
7631	10199	5.470098	GGAATTTTCAGAAAAGAAAAGGGGC	59.530	40.000	13.71	0.00	46.88	5.80
7645	10214	7.664758	AGGAGAAATCTTTGTGGAATTTTCAG	58.335	34.615	0.00	0.00	0.00	3.02
7728	10297	4.793216	GTCGTGAATGCAATTATGGACAAC	59.207	41.667	0.00	0.00	36.07	3.32
7874	10443	4.808077	TTGTTTGTTTATAACGCACCGA	57.192	36.364	0.00	0.00	0.00	4.69
7913	10484	8.092521	ACGAATTTAAGATGCTAGGATTGATG	57.907	34.615	0.00	0.00	0.00	3.07
7994	10565	2.504367	CCAAGACAGGGTTTTCGTCAT	58.496	47.619	0.00	0.00	31.92	3.06
7995	10566	1.476110	CCCAAGACAGGGTTTTCGTCA	60.476	52.381	0.00	0.00	44.24	4.35
8011	10582	1.361204	TCTGGAGAACTGCATCCCAA	58.639	50.000	1.64	0.00	34.47	4.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.