AutoCloner

Multiple sequence alignment - TraesCS7D01G298400

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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	TraesCS7D01G298400	chr7D	100.000	7968	0	0	1	7968	378163652	378155685	0.000000e+00	14715.0
1	TraesCS7D01G298400	chr7D	85.572	201	29	0	3634	3834	378173244	378173044	2.250000e-50	211.0
2	TraesCS7D01G298400	chr7B	98.761	6293	71	7	1537	7825	372825989	372819700	0.000000e+00	11182.0
3	TraesCS7D01G298400	chr7B	97.287	1548	32	2	1	1540	372827598	372826053	0.000000e+00	2617.0
4	TraesCS7D01G298400	chr7B	84.577	201	31	0	3634	3834	372832037	372831837	4.880000e-47	200.0
5	TraesCS7D01G298400	chr7A	98.252	6293	92	11	1537	7825	425779812	425773534	0.000000e+00	10996.0
6	TraesCS7D01G298400	chr7A	97.575	866	19	1	675	1540	425782283	425781420	0.000000e+00	1482.0
7	TraesCS7D01G298400	chr7A	96.070	687	18	2	1	678	425783049	425782363	0.000000e+00	1110.0
8	TraesCS7D01G298400	chr7A	95.833	144	6	0	7823	7966	425773493	425773350	4.810000e-57	233.0
9	TraesCS7D01G298400	chr7A	86.070	201	28	0	3634	3834	425790303	425790103	4.840000e-52	217.0
10	TraesCS7D01G298400	chr7A	83.516	91	13	2	4863	4952	603354839	603354928	5.120000e-12	84.2
11	TraesCS7D01G298400	chr6B	78.850	2747	471	74	4301	6968	183286651	183289366	0.000000e+00	1753.0
12	TraesCS7D01G298400	chr6B	79.580	999	141	35	2071	3033	183283886	183284857	0.000000e+00	656.0
13	TraesCS7D01G298400	chr6B	85.260	346	48	2	3054	3396	183284918	183285263	3.540000e-93	353.0
14	TraesCS7D01G298400	chr6B	85.065	308	39	7	3620	3924	183286264	183286567	2.790000e-79	307.0
15	TraesCS7D01G298400	chr6A	79.104	871	118	35	2071	2905	117061149	117061991	7.030000e-150	542.0
16	TraesCS7D01G298400	chr6A	86.788	439	56	1	4400	4838	117069839	117070275	9.290000e-134	488.0
17	TraesCS7D01G298400	chr6A	84.971	346	49	2	3054	3396	117062468	117062813	1.650000e-91	348.0
18	TraesCS7D01G298400	chr6A	86.029	272	32	6	3620	3890	117069378	117069644	3.640000e-73	287.0
19	TraesCS7D01G298400	chr6D	81.672	622	86	17	2414	3033	98035813	98036408	7.180000e-135	492.0
20	TraesCS7D01G298400	chr6D	88.060	402	46	1	4400	4801	98038256	98038655	7.240000e-130	475.0
21	TraesCS7D01G298400	chr6D	84.971	346	49	2	3054	3396	98036469	98036814	1.650000e-91	348.0
22	TraesCS7D01G298400	chr6D	85.085	295	36	8	3605	3896	98037783	98038072	2.170000e-75	294.0

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	TraesCS7D01G298400	chr7D	378155685	378163652	7967	True	14715.00	14715	100.00000	1	7968	1	chr7D.!!$R1	7967
1	TraesCS7D01G298400	chr7B	372819700	372827598	7898	True	6899.50	11182	98.02400	1	7825	2	chr7B.!!$R2	7824
2	TraesCS7D01G298400	chr7A	425773350	425783049	9699	True	3455.25	10996	96.93250	1	7966	4	chr7A.!!$R2	7965
3	TraesCS7D01G298400	chr6B	183283886	183289366	5480	False	767.25	1753	82.18875	2071	6968	4	chr6B.!!$F1	4897
4	TraesCS7D01G298400	chr6A	117061149	117062813	1664	False	445.00	542	82.03750	2071	3396	2	chr6A.!!$F1	1325
5	TraesCS7D01G298400	chr6A	117069378	117070275	897	False	387.50	488	86.40850	3620	4838	2	chr6A.!!$F2	1218
6	TraesCS7D01G298400	chr6D	98035813	98038655	2842	False	402.25	492	84.94700	2414	4801	4	chr6D.!!$F1	2387

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
273	277	1.341080	AGTTGAATTTGGGGTGCCTG	58.659	50.000	0.00	0.00	0.00	4.85	F
735	830	2.285756	TCCACGCGTCACTAAAAACAAG	59.714	45.455	9.86	0.00	0.00	3.16	F
1083	1178	1.686355	AGAAAAACACATCACCGCCA	58.314	45.000	0.00	0.00	0.00	5.69	F
2278	3990	2.032549	CGGAGCTTTTGACACTGACTTG	60.033	50.000	0.00	0.00	0.00	3.16	F
2960	4991	0.031994	CTGCAAAAGGGGGTGAAACG	59.968	55.000	0.00	0.00	38.12	3.60	F
4143	7001	4.422840	TGTTGCAATGTTTTCACTCTGTG	58.577	39.130	0.59	0.00	34.45	3.66	F
4246	7104	7.057894	AGGTTTAGTGTTTCCTTTGTCACATA	58.942	34.615	0.00	0.00	33.84	2.29	F
6397	9319	1.538950	GGCCGAGTACTTATAGACGGG	59.461	57.143	17.21	3.16	40.55	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1083	1178	0.537143	TTTCTGGCGTTGATGGTGCT	60.537	50.000	0.00	0.00	0.00	4.40	R
2278	3990	0.597637	CCATGATAGTCGCGGTGGTC	60.598	60.000	6.13	0.56	0.00	4.02	R
2322	4034	5.195940	TCTCTCCAATTGCCTCTTTTATGG	58.804	41.667	0.00	0.00	0.00	2.74	R
4246	7104	2.174360	TGCTCTGTCTCACTATGCACT	58.826	47.619	0.00	0.00	0.00	4.40	R
4808	7668	5.381174	ACAATGCGATTATGGATTCCATG	57.619	39.130	25.47	11.60	44.84	3.66	R
6397	9319	3.526534	GTTGTAGCCTCTGATGTCCTTC	58.473	50.000	0.00	0.00	0.00	3.46	R
6634	9556	3.341823	CACAGCTATCCTCTGCTTTTGT	58.658	45.455	0.00	0.00	37.44	2.83	R
7887	10863	0.179001	CCCAGGACAGGGTTTTCGTT	60.179	55.000	0.00	0.00	44.24	3.85	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
123	125	2.621055	GCCACAAGAACATGGTTGTACA	59.379	45.455	9.29	0.00	38.34	2.90
124	126	3.067461	GCCACAAGAACATGGTTGTACAA	59.933	43.478	3.59	3.59	38.34	2.41
130	134	7.652909	CACAAGAACATGGTTGTACAAAATGAT	59.347	33.333	27.19	20.15	35.10	2.45
162	166	7.103641	TCTTTTGTGGACATATCACCTAAGAC	58.896	38.462	0.00	0.00	33.13	3.01
163	167	6.367374	TTTGTGGACATATCACCTAAGACA	57.633	37.500	0.00	0.00	34.46	3.41
209	213	7.041916	CCGCCTATTACTAGAACTATAGGATCG	60.042	44.444	19.16	15.26	41.31	3.69
229	233	1.363744	GGAAGCGAATGGACAGACTG	58.636	55.000	0.00	0.00	0.00	3.51
273	277	1.341080	AGTTGAATTTGGGGTGCCTG	58.659	50.000	0.00	0.00	0.00	4.85
317	321	5.289510	ACTAGTTCCTCCAAGGTATCCATT	58.710	41.667	0.00	0.00	36.53	3.16
583	595	4.183865	TCTATGCAAGTCGTGGATGAAAG	58.816	43.478	3.08	0.00	38.95	2.62
708	803	7.750458	ACAATGATGTGACATCAAACGAATAAC	59.250	33.333	29.42	0.00	38.69	1.89
735	830	2.285756	TCCACGCGTCACTAAAAACAAG	59.714	45.455	9.86	0.00	0.00	3.16
983	1078	5.363101	TGCTACTCTCCTGCAAATTATCTG	58.637	41.667	0.00	0.00	33.48	2.90
1083	1178	1.686355	AGAAAAACACATCACCGCCA	58.314	45.000	0.00	0.00	0.00	5.69
1396	1491	8.552083	AATGCTTTTCTTCCATTTTATTGGAC	57.448	30.769	0.00	0.00	45.42	4.02
1481	1576	7.094634	CCATATATGTGGTTCTTGGCACTTATC	60.095	40.741	10.25	0.00	34.46	1.75
2114	3823	5.543790	TGGGAGCACTAGCAATATGAATAGA	59.456	40.000	0.00	0.00	45.49	1.98
2278	3990	2.032549	CGGAGCTTTTGACACTGACTTG	60.033	50.000	0.00	0.00	0.00	3.16
2322	4034	2.484264	GAGCAACCAACCACATGAGTAC	59.516	50.000	0.00	0.00	0.00	2.73
2960	4991	0.031994	CTGCAAAAGGGGGTGAAACG	59.968	55.000	0.00	0.00	38.12	3.60
3047	5078	6.916360	TCTAGCATATACCATGTGATGTCA	57.084	37.500	0.00	0.00	0.00	3.58
3094	5168	6.238320	GCAATTTCAGATATCTCTCAAACGCT	60.238	38.462	1.03	0.00	0.00	5.07
3908	6766	9.778993	CTCTATTTTGTATGGTTGTGAATCAAG	57.221	33.333	0.00	0.00	36.66	3.02
4143	7001	4.422840	TGTTGCAATGTTTTCACTCTGTG	58.577	39.130	0.59	0.00	34.45	3.66
4246	7104	7.057894	AGGTTTAGTGTTTCCTTTGTCACATA	58.942	34.615	0.00	0.00	33.84	2.29
5297	8189	8.299570	AGCAAGTACTCAATTATTTTGTTCCTG	58.700	33.333	0.00	0.00	0.00	3.86
6397	9319	1.538950	GGCCGAGTACTTATAGACGGG	59.461	57.143	17.21	3.16	40.55	5.28
7053	9984	7.013369	GGGAAAATGTAAAGACAGAGTTTGACT	59.987	37.037	0.00	0.00	39.50	3.41
7526	10458	7.759886	CGATAGAGAAACTAAAACATCACCAGA	59.240	37.037	0.00	0.00	34.56	3.86
7559	10491	6.597562	ACCTATAATCCATAGCCACGAAAAA	58.402	36.000	0.00	0.00	36.09	1.94
7602	10534	6.975196	TGAAAATTCCACCAAGATTTCTCA	57.025	33.333	0.00	0.00	30.39	3.27
7648	10580	0.963962	AGTTTGCGAGGAACTACGGA	59.036	50.000	0.00	0.00	41.55	4.69
7735	10667	1.156736	GTGCCACACCACTGACATAC	58.843	55.000	0.00	0.00	33.02	2.39
7810	10742	0.459585	GAGGCGAAATGTAGCACCGA	60.460	55.000	0.00	0.00	34.54	4.69
7834	10810	4.550362	GCGTTATAAACAAATTCGTTCGCA	59.450	37.500	7.24	0.00	38.85	5.10
7884	10860	1.065053	TGTATGTCCACCCCCAATTCG	60.065	52.381	0.00	0.00	0.00	3.34
7887	10863	3.260888	TCCACCCCCAATTCGCCA	61.261	61.111	0.00	0.00	0.00	5.69
7937	10913	8.516694	ATTCTCCAGAAGATGCATGTTTTGCC	62.517	42.308	18.52	3.66	43.22	4.52
7966	10942	4.703897	CATACCCGAATCTAGCTTTGGAA	58.296	43.478	13.34	2.84	32.12	3.53
7967	10943	3.713826	ACCCGAATCTAGCTTTGGAAA	57.286	42.857	13.34	0.00	32.12	3.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
101	103	0.667993	ACAACCATGTTCTTGTGGCG	59.332	50.000	0.00	0.00	39.13	5.69
123	125	8.428063	TGTCCACAAAAGATACCAAATCATTTT	58.572	29.630	0.00	0.00	0.00	1.82
124	126	7.961351	TGTCCACAAAAGATACCAAATCATTT	58.039	30.769	0.00	0.00	0.00	2.32
130	134	7.122055	GGTGATATGTCCACAAAAGATACCAAA	59.878	37.037	0.00	0.00	36.31	3.28
162	166	3.686726	GGTAGTTTCTGCTCAAGTCCATG	59.313	47.826	0.00	0.00	0.00	3.66
163	167	3.617531	CGGTAGTTTCTGCTCAAGTCCAT	60.618	47.826	0.00	0.00	0.00	3.41
209	213	0.250513	AGTCTGTCCATTCGCTTCCC	59.749	55.000	0.00	0.00	0.00	3.97
229	233	1.609072	GAAGACTTGAACTTGGGTGGC	59.391	52.381	0.00	0.00	0.00	5.01
509	521	2.747467	GCCATGACCAGTGCTATGACAT	60.747	50.000	0.00	0.00	0.00	3.06
708	803	0.240145	TAGTGACGCGTGGAACTCAG	59.760	55.000	20.70	0.00	31.75	3.35
839	934	7.309012	GCACTACATCAGCATGGAATCAAATAT	60.309	37.037	0.00	0.00	36.16	1.28
983	1078	4.746729	TGGCATTGTATTTGTGAGCATTC	58.253	39.130	0.00	0.00	0.00	2.67
1083	1178	0.537143	TTTCTGGCGTTGATGGTGCT	60.537	50.000	0.00	0.00	0.00	4.40
1716	3424	3.623703	TGACCATGATTGTATGCAGCTT	58.376	40.909	0.00	0.00	0.00	3.74
2240	3952	3.856638	GCTCCGATATCTTGACTGAGCAG	60.857	52.174	0.34	0.00	42.41	4.24
2278	3990	0.597637	CCATGATAGTCGCGGTGGTC	60.598	60.000	6.13	0.56	0.00	4.02
2322	4034	5.195940	TCTCTCCAATTGCCTCTTTTATGG	58.804	41.667	0.00	0.00	0.00	2.74
2960	4991	6.654161	AGAGGATATTAATGACTGCAGCAATC	59.346	38.462	15.27	11.37	0.00	2.67
3047	5078	6.359804	TGCAGATAAAAATATCAGCTGGAGT	58.640	36.000	15.13	3.08	39.01	3.85
3094	5168	2.184322	GTCTGAAGATCCGGCGCA	59.816	61.111	10.83	0.00	0.00	6.09
4072	6930	7.656137	TGGACGGATATATTAAAACAGAGCTTC	59.344	37.037	0.00	0.00	0.00	3.86
4143	7001	6.538945	TTCCTGAAACAATTTAATAGGGGC	57.461	37.500	0.00	0.00	0.00	5.80
4246	7104	2.174360	TGCTCTGTCTCACTATGCACT	58.826	47.619	0.00	0.00	0.00	4.40
4808	7668	5.381174	ACAATGCGATTATGGATTCCATG	57.619	39.130	25.47	11.60	44.84	3.66
6397	9319	3.526534	GTTGTAGCCTCTGATGTCCTTC	58.473	50.000	0.00	0.00	0.00	3.46
6634	9556	3.341823	CACAGCTATCCTCTGCTTTTGT	58.658	45.455	0.00	0.00	37.44	2.83
7053	9984	6.952773	ACTTATTCAGTAGGCACAAAAACA	57.047	33.333	0.00	0.00	31.97	2.83
7192	10124	0.882927	TTACAGTGTTCCGCTGGTGC	60.883	55.000	0.00	0.00	45.11	5.01
7526	10458	8.010105	TGGCTATGGATTATAGGTTTGGATTTT	58.990	33.333	0.00	0.00	39.36	1.82
7591	10523	7.034685	TGCATAATGTGGATGAGAAATCTTG	57.965	36.000	0.00	0.00	0.00	3.02
7602	10534	7.746243	AGACTAGGATATGCATAATGTGGAT	57.254	36.000	11.13	0.00	42.10	3.41
7648	10580	8.912988	CAATTATGGACAATAATAACCCACTGT	58.087	33.333	0.00	0.00	40.00	3.55
7735	10667	7.498239	CCATATATCCTTGGATTGTATCTGCTG	59.502	40.741	7.52	0.00	34.81	4.41
7770	10702	3.704566	TCGCCTGTAAACTGGACTCATAT	59.295	43.478	9.96	0.00	37.15	1.78
7810	10742	4.784550	GCGAACGAATTTGTTTATAACGCT	59.215	37.500	23.81	0.00	37.21	5.07
7864	10840	1.065053	CGAATTGGGGGTGGACATACA	60.065	52.381	0.00	0.00	0.00	2.29
7884	10860	0.822121	AGGACAGGGTTTTCGTTGGC	60.822	55.000	0.00	0.00	0.00	4.52
7887	10863	0.179001	CCCAGGACAGGGTTTTCGTT	60.179	55.000	0.00	0.00	44.24	3.85
7937	10913	4.516698	AGCTAGATTCGGGTATGCAAATTG	59.483	41.667	0.00	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.