AutoCloner

Multiple sequence alignment - TraesCS5A01G156600

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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	TraesCS5A01G156600	chr5A	100.000	2777	0	0	1	2777	335671189	335673965	0.000000e+00	5129.0
1	TraesCS5A01G156600	chr5D	97.363	1934	48	1	847	2777	253177783	253179716	0.000000e+00	3286.0
2	TraesCS5A01G156600	chr5D	89.699	864	57	14	1	834	253175195	253176056	0.000000e+00	1074.0
3	TraesCS5A01G156600	chr5D	93.970	199	11	1	1	199	389038603	389038800	1.620000e-77	300.0
4	TraesCS5A01G156600	chr5D	93.970	199	11	1	1	199	389054753	389054950	1.620000e-77	300.0
5	TraesCS5A01G156600	chr5D	79.265	381	66	11	191	567	359160858	359160487	1.280000e-63	254.0
6	TraesCS5A01G156600	chr5B	96.571	1633	46	5	836	2461	285498991	285500620	0.000000e+00	2697.0
7	TraesCS5A01G156600	chr5B	82.686	618	76	17	225	834	285498283	285498877	1.140000e-143	520.0
8	TraesCS5A01G156600	chr5B	96.029	277	11	0	2501	2777	285500618	285500894	4.220000e-123	451.0
9	TraesCS5A01G156600	chr3D	95.789	190	7	1	1	190	239343389	239343577	3.470000e-79	305.0
10	TraesCS5A01G156600	chr3D	79.683	379	71	6	192	569	90689381	90689008	4.560000e-68	268.0
11	TraesCS5A01G156600	chr3D	91.228	57	4	1	429	484	563224554	563224610	2.970000e-10	76.8
12	TraesCS5A01G156600	chr3A	95.789	190	7	1	1	190	451407228	451407040	3.470000e-79	305.0
13	TraesCS5A01G156600	chr7D	95.312	192	8	1	1	192	607071127	607071317	1.250000e-78	303.0
14	TraesCS5A01G156600	chr7D	76.883	385	73	13	191	567	365931970	365932346	1.300000e-48	204.0
15	TraesCS5A01G156600	chr7D	84.783	92	14	0	699	790	122875069	122875160	2.940000e-15	93.5
16	TraesCS5A01G156600	chr2D	93.970	199	10	2	1	199	167695723	167695919	1.620000e-77	300.0
17	TraesCS5A01G156600	chr2D	93.564	202	11	2	1	202	372200871	372201070	1.620000e-77	300.0
18	TraesCS5A01G156600	chr1D	93.970	199	10	2	1	199	410604963	410604767	1.620000e-77	300.0
19	TraesCS5A01G156600	chr1D	84.746	118	14	3	566	679	251317040	251316923	6.290000e-22	115.0
20	TraesCS5A01G156600	chr1D	88.312	77	6	2	571	644	484423206	484423282	3.810000e-14	89.8
21	TraesCS5A01G156600	chr1B	81.039	385	63	8	191	571	454599960	454600338	5.810000e-77	298.0
22	TraesCS5A01G156600	chr1B	84.058	138	18	3	699	834	317317608	317317473	2.240000e-26	130.0
23	TraesCS5A01G156600	chr2A	80.469	384	67	7	191	571	506626678	506626300	1.260000e-73	287.0
24	TraesCS5A01G156600	chr2A	88.889	99	11	0	699	797	638039282	638039380	3.760000e-24	122.0
25	TraesCS5A01G156600	chr2A	90.141	71	7	0	705	775	51373006	51372936	2.940000e-15	93.5
26	TraesCS5A01G156600	chr6B	79.003	381	72	6	190	567	450229483	450229108	1.280000e-63	254.0
27	TraesCS5A01G156600	chr6B	75.916	382	69	11	191	569	205191726	205191365	1.020000e-39	174.0
28	TraesCS5A01G156600	chr6B	81.250	112	20	1	699	810	288163711	288163601	3.810000e-14	89.8
29	TraesCS5A01G156600	chr7B	77.439	328	68	5	191	514	26898553	26898228	1.020000e-44	191.0
30	TraesCS5A01G156600	chr2B	85.586	111	15	1	566	675	372090838	372090728	6.290000e-22	115.0
31	TraesCS5A01G156600	chr6D	81.343	134	24	1	699	832	158585169	158585301	1.050000e-19	108.0
32	TraesCS5A01G156600	chr7A	84.946	93	13	1	699	790	125769493	125769585	2.940000e-15	93.5
33	TraesCS5A01G156600	chr6A	94.737	38	2	0	584	621	109377011	109377048	2.990000e-05	60.2

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	TraesCS5A01G156600	chr5A	335671189	335673965	2776	False	5129.000000	5129	100.000	1	2777	1	chr5A.!!$F1	2776
1	TraesCS5A01G156600	chr5D	253175195	253179716	4521	False	2180.000000	3286	93.531	1	2777	2	chr5D.!!$F3	2776
2	TraesCS5A01G156600	chr5B	285498283	285500894	2611	False	1222.666667	2697	91.762	225	2777	3	chr5B.!!$F1	2552

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
75	76	0.174845	TTCATTCTACGCCTCCCACG	59.825	55.0	0.0	0.0	0.0	4.94	F
76	77	0.681887	TCATTCTACGCCTCCCACGA	60.682	55.0	0.0	0.0	0.0	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1311	3065	0.601576	CATCGGGGTTGTCGTTGACA	60.602	55.0	0.0	0.0	41.09	3.58	R
1969	3726	5.179742	ACGAACATAAGCACGGTTAAAATCA	59.820	36.0	0.0	0.0	0.00	2.57	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
50	51	1.202806	TGCAGGGTTGTTTGAGAGAGG	60.203	52.381	0.00	0.00	0.00	3.69
61	62	4.263639	TGTTTGAGAGAGGCCATCTTCATT	60.264	41.667	5.01	0.00	38.84	2.57
66	67	3.320541	AGAGAGGCCATCTTCATTCTACG	59.679	47.826	5.01	0.00	38.84	3.51
75	76	0.174845	TTCATTCTACGCCTCCCACG	59.825	55.000	0.00	0.00	0.00	4.94
76	77	0.681887	TCATTCTACGCCTCCCACGA	60.682	55.000	0.00	0.00	0.00	4.35
97	98	8.499162	CCACGAATTGATAAATCTTAGGTCATC	58.501	37.037	0.00	0.00	0.00	2.92
120	121	4.082571	CCACTTGAGGGAAATTTGCTACTG	60.083	45.833	9.70	0.26	0.00	2.74
142	143	2.143122	CCTACAAAACTCTGCGCTTGA	58.857	47.619	9.73	6.21	0.00	3.02
167	168	3.318017	CCCAACACGAGTCTACAAGAAG	58.682	50.000	0.00	0.00	0.00	2.85
176	177	6.255887	CACGAGTCTACAAGAAGAAAAGTTGT	59.744	38.462	0.00	0.00	38.04	3.32
222	223	1.202855	AGAAGCCATGTCAGCAACTGT	60.203	47.619	0.00	0.00	32.61	3.55
267	268	1.079612	CGGTCAAACCTACGGGTCC	60.080	63.158	0.00	0.00	46.67	4.46
362	363	1.133025	GTCATCACCGAAAATGGCCAG	59.867	52.381	13.05	0.00	0.00	4.85
365	366	3.747976	ACCGAAAATGGCCAGCGC	61.748	61.111	13.05	0.00	0.00	5.92
382	383	2.159627	AGCGCTGACATTTTTAGGTTCG	59.840	45.455	10.39	0.00	0.00	3.95
456	459	5.803020	ATTTTCTATGAGGACGTTTCAGC	57.197	39.130	9.19	0.00	0.00	4.26
467	471	2.046285	GTTTCAGCGATGGTGGGGG	61.046	63.158	0.00	0.00	0.00	5.40
482	486	2.360726	GGGTGACGGCCGGAAAAT	60.361	61.111	31.76	7.71	0.00	1.82
505	509	2.357637	CCGCCAACGTATTTTCCATGAT	59.642	45.455	0.00	0.00	37.70	2.45
536	540	4.705023	GGTTATACAGGGCACAAGTGAAAT	59.295	41.667	4.04	0.00	0.00	2.17
644	651	3.845259	GATGTGGCGAGGGCGGTA	61.845	66.667	0.00	0.00	41.24	4.02
691	699	5.599359	TGATGCAAGCAAAACAAATCATG	57.401	34.783	0.00	0.00	0.00	3.07
703	738	7.095144	GCAAAACAAATCATGGAATCAATGTCA	60.095	33.333	0.00	0.00	0.00	3.58
748	783	7.030165	TGTTTTGCTTTCTCGTATTTGTTTCA	58.970	30.769	0.00	0.00	0.00	2.69
797	832	4.603985	TGTATAATCGACGTGTGTGGATC	58.396	43.478	0.00	0.00	41.97	3.36
798	833	3.793797	ATAATCGACGTGTGTGGATCA	57.206	42.857	0.00	0.00	41.97	2.92
799	834	2.672961	AATCGACGTGTGTGGATCAT	57.327	45.000	0.00	0.00	41.97	2.45
802	837	5.447624	AATCGACGTGTGTGGATCATATA	57.552	39.130	0.00	0.00	41.97	0.86
804	839	3.252458	TCGACGTGTGTGGATCATATAGG	59.748	47.826	0.00	0.00	0.00	2.57
814	849	6.315393	GTGTGGATCATATAGGTTTGACGTTT	59.685	38.462	0.00	0.00	0.00	3.60
874	2624	4.782019	AACCGCAATTCATTAGCTTTCA	57.218	36.364	0.00	0.00	0.00	2.69
1260	3014	3.834799	GACCCGGAATCCGTCGCT	61.835	66.667	21.12	0.00	46.80	4.93
1311	3065	3.351885	AGCCTCGTCCTCCTCCCT	61.352	66.667	0.00	0.00	0.00	4.20
1329	3083	0.320421	CTGTCAACGACAACCCCGAT	60.320	55.000	0.00	0.00	42.26	4.18
1598	3352	2.504175	GGGCTATCTGTAACTGGTGGAA	59.496	50.000	0.00	0.00	0.00	3.53
1969	3726	9.733556	TCAAATGTGGTCAATACTTAATACTGT	57.266	29.630	0.00	0.00	0.00	3.55
2148	3905	6.017109	CCATGCACAAGTTCTTTTACTACTGT	60.017	38.462	0.00	0.00	0.00	3.55
2313	4070	6.305693	AGAACAAAGCTATGACAGTTGAAC	57.694	37.500	0.00	0.00	0.00	3.18
2315	4072	3.058914	ACAAAGCTATGACAGTTGAACGC	60.059	43.478	0.00	0.00	0.00	4.84
2464	4221	7.337938	TGAAGATGCATATACTTCCTTTCACA	58.662	34.615	18.78	2.45	39.14	3.58
2465	4222	7.828717	TGAAGATGCATATACTTCCTTTCACAA	59.171	33.333	18.78	1.38	39.14	3.33
2493	4250	7.653311	GGACATTTTCAGTGCTGTAAATTTCTT	59.347	33.333	19.72	7.01	38.11	2.52
2604	4361	7.231115	TGTTCATTTTGATCATTGAGGTGAAGA	59.769	33.333	0.00	0.00	0.00	2.87
2750	4507	4.339247	ACAATGAATACAATGGGCTACTGC	59.661	41.667	0.00	0.00	31.86	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	2.139118	GAGGCGTAGAATGAAGATGGC	58.861	52.381	0.00	0.00	0.00	4.40
61	62	0.174845	CAATTCGTGGGAGGCGTAGA	59.825	55.000	0.00	0.00	0.00	2.59
66	67	4.137543	AGATTTATCAATTCGTGGGAGGC	58.862	43.478	0.00	0.00	0.00	4.70
75	76	9.566432	AGTGGATGACCTAAGATTTATCAATTC	57.434	33.333	0.00	0.00	37.04	2.17
76	77	9.927081	AAGTGGATGACCTAAGATTTATCAATT	57.073	29.630	0.00	0.00	37.04	2.32
97	98	4.082125	AGTAGCAAATTTCCCTCAAGTGG	58.918	43.478	0.00	0.00	0.00	4.00
120	121	1.797025	AGCGCAGAGTTTTGTAGGAC	58.203	50.000	11.47	0.00	0.00	3.85
142	143	0.320697	GTAGACTCGTGTTGGGCCTT	59.679	55.000	4.53	0.00	0.00	4.35
167	168	7.116519	GGTCTGATGTCTACTACACAACTTTTC	59.883	40.741	0.00	0.00	42.09	2.29
176	177	4.042271	TGTGGGTCTGATGTCTACTACA	57.958	45.455	0.00	0.00	43.86	2.74
210	211	1.827789	GGGCCAACAGTTGCTGACA	60.828	57.895	4.39	0.00	35.18	3.58
212	213	2.203480	GGGGCCAACAGTTGCTGA	60.203	61.111	4.39	0.00	35.18	4.26
222	223	2.916934	AGATACTAACAGTTGGGGCCAA	59.083	45.455	4.39	0.00	0.00	4.52
267	268	0.462375	TATTCCCGTCACCCGTGATG	59.538	55.000	9.65	9.65	44.14	3.07
300	301	4.108501	ACCCAATCGGTTTCCTAAGTTT	57.891	40.909	0.00	0.00	45.36	2.66
321	322	9.671279	GATGACCCATAATGTCACATATGATAA	57.329	33.333	10.38	0.00	44.85	1.75
329	330	3.681313	CGGTGATGACCCATAATGTCACA	60.681	47.826	0.00	0.00	44.85	3.58
362	363	2.095919	ACGAACCTAAAAATGTCAGCGC	60.096	45.455	0.00	0.00	0.00	5.92
365	366	5.030874	GGTGACGAACCTAAAAATGTCAG	57.969	43.478	5.01	0.00	46.55	3.51
382	383	2.094894	CACAGATCGCATTTCAGGTGAC	59.905	50.000	0.00	0.00	0.00	3.67
456	459	4.467084	CCGTCACCCCCACCATCG	62.467	72.222	0.00	0.00	0.00	3.84
467	471	2.178273	GCATTTTCCGGCCGTCAC	59.822	61.111	26.12	1.86	0.00	3.67
482	486	0.889638	TGGAAAATACGTTGGCGGCA	60.890	50.000	7.97	7.97	43.45	5.69
505	509	4.083565	GTGCCCTGTATAACCCTTTTTCA	58.916	43.478	0.00	0.00	0.00	2.69
621	628	1.515954	CCCTCGCCACATCGTACTT	59.484	57.895	0.00	0.00	0.00	2.24
629	636	4.155733	CATACCGCCCTCGCCACA	62.156	66.667	0.00	0.00	0.00	4.17
643	650	0.533531	CATTCTCCGCTGCTGCCATA	60.534	55.000	10.24	0.00	35.36	2.74
644	651	1.822613	CATTCTCCGCTGCTGCCAT	60.823	57.895	10.24	0.00	35.36	4.40
676	684	6.938030	ACATTGATTCCATGATTTGTTTTGCT	59.062	30.769	4.84	0.00	0.00	3.91
691	699	5.902613	TCAACAATCCTGACATTGATTCC	57.097	39.130	0.25	0.00	37.24	3.01
703	738	9.480053	CAAAACAAATCATAGTTCAACAATCCT	57.520	29.630	0.00	0.00	0.00	3.24
790	825	5.607939	ACGTCAAACCTATATGATCCACA	57.392	39.130	0.00	0.00	0.00	4.17
797	832	8.233868	TCAAATGTGAAACGTCAAACCTATATG	58.766	33.333	0.00	0.00	42.39	1.78
798	833	8.330466	TCAAATGTGAAACGTCAAACCTATAT	57.670	30.769	0.00	0.00	42.39	0.86
799	834	7.094975	CCTCAAATGTGAAACGTCAAACCTATA	60.095	37.037	0.00	0.00	42.39	1.31
802	837	4.202010	CCTCAAATGTGAAACGTCAAACCT	60.202	41.667	0.00	0.00	42.39	3.50
804	839	4.668289	ACCTCAAATGTGAAACGTCAAAC	58.332	39.130	0.00	0.00	42.39	2.93
874	2624	4.256110	GCAGGGGTGTAGTTTTAATACGT	58.744	43.478	0.00	0.00	0.00	3.57
1311	3065	0.601576	CATCGGGGTTGTCGTTGACA	60.602	55.000	0.00	0.00	41.09	3.58
1969	3726	5.179742	ACGAACATAAGCACGGTTAAAATCA	59.820	36.000	0.00	0.00	0.00	2.57
2148	3905	9.973450	TGCTTATTGTAACATTTTAGCAAAGAA	57.027	25.926	0.00	0.00	34.76	2.52
2244	4001	3.254470	TCGTCAGTTCTGTTTCCAACA	57.746	42.857	0.00	0.00	39.52	3.33
2246	4003	4.497340	GCATTTCGTCAGTTCTGTTTCCAA	60.497	41.667	0.00	0.00	0.00	3.53
2464	4221	2.949447	ACAGCACTGAAAATGTCCCTT	58.051	42.857	4.31	0.00	0.00	3.95
2465	4222	2.664402	ACAGCACTGAAAATGTCCCT	57.336	45.000	4.31	0.00	0.00	4.20
2468	4225	8.579682	AAGAAATTTACAGCACTGAAAATGTC	57.420	30.769	4.31	0.00	0.00	3.06
2604	4361	5.758296	ACATCACAGTGTTTGTTTATCGTCT	59.242	36.000	0.00	0.00	38.16	4.18
2750	4507	0.872388	GTAAGGGAAACTGCACACCG	59.128	55.000	0.00	0.00	0.00	4.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.