AutoCloner

Multiple sequence alignment - TraesCS7B01G304700

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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	TraesCS7B01G304700	chr7B	100.000	3842	0	0	1	3842	546010431	546014272	0.000000e+00	7095.0
1	TraesCS7B01G304700	chr7B	94.161	137	7	1	476	611	546010846	546010982	1.400000e-49	207.0
2	TraesCS7B01G304700	chr7B	94.161	137	7	1	416	552	546010906	546011041	1.400000e-49	207.0
3	TraesCS7B01G304700	chr7B	83.243	185	27	3	713	895	123665720	123665902	2.370000e-37	167.0
4	TraesCS7B01G304700	chr7B	96.875	32	0	1	750	781	515283418	515283448	7.000000e-03	52.8
5	TraesCS7B01G304700	chr7D	96.240	2952	81	11	896	3842	515464532	515467458	0.000000e+00	4809.0
6	TraesCS7B01G304700	chr7D	87.017	362	31	5	529	874	603143788	603144149	1.000000e-105	394.0
7	TraesCS7B01G304700	chr7D	85.976	328	33	8	23	338	603143438	603143764	4.750000e-89	339.0
8	TraesCS7B01G304700	chr7D	93.506	77	5	0	469	545	603143788	603143864	8.720000e-22	115.0
9	TraesCS7B01G304700	chr7A	96.041	2955	104	8	895	3842	589121197	589124145	0.000000e+00	4796.0
10	TraesCS7B01G304700	chr7A	85.409	514	49	14	1	489	695852125	695852637	9.520000e-141	510.0
11	TraesCS7B01G304700	chr7A	85.411	377	40	4	533	894	695852561	695852937	1.010000e-100	377.0
12	TraesCS7B01G304700	chr1A	99.441	894	5	0	1	894	114349359	114348466	0.000000e+00	1624.0
13	TraesCS7B01G304700	chr1A	97.826	552	11	1	1	552	562949199	562948649	0.000000e+00	952.0
14	TraesCS7B01G304700	chr1A	98.568	419	6	0	476	894	562948784	562948366	0.000000e+00	741.0
15	TraesCS7B01G304700	chr1A	94.161	137	7	1	416	552	114348884	114348749	1.400000e-49	207.0
16	TraesCS7B01G304700	chr1A	94.161	137	7	1	476	611	114348944	114348808	1.400000e-49	207.0
17	TraesCS7B01G304700	chr6A	79.371	509	64	15	1	485	557419047	557419538	1.720000e-83	320.0
18	TraesCS7B01G304700	chr2A	84.422	199	26	5	699	894	206301696	206301500	1.410000e-44	191.0
19	TraesCS7B01G304700	chr2A	80.315	127	22	3	276	400	35839173	35839048	4.090000e-15	93.5
20	TraesCS7B01G304700	chr3A	84.000	200	26	6	699	894	567989151	567988954	1.820000e-43	187.0
21	TraesCS7B01G304700	chr2D	82.540	126	20	2	278	402	523168221	523168345	4.060000e-20	110.0
22	TraesCS7B01G304700	chr5A	100.000	28	0	0	743	770	461260725	461260698	7.000000e-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	TraesCS7B01G304700	chr7B	546010431	546014272	3841	False	2503.000000	7095	96.107333	1	3842	3	chr7B.!!$F3	3841
1	TraesCS7B01G304700	chr7D	515464532	515467458	2926	False	4809.000000	4809	96.240000	896	3842	1	chr7D.!!$F1	2946
2	TraesCS7B01G304700	chr7D	603143438	603144149	711	False	282.666667	394	88.833000	23	874	3	chr7D.!!$F2	851
3	TraesCS7B01G304700	chr7A	589121197	589124145	2948	False	4796.000000	4796	96.041000	895	3842	1	chr7A.!!$F1	2947
4	TraesCS7B01G304700	chr7A	695852125	695852937	812	False	443.500000	510	85.410000	1	894	2	chr7A.!!$F2	893
5	TraesCS7B01G304700	chr1A	562948366	562949199	833	True	846.500000	952	98.197000	1	894	2	chr1A.!!$R2	893
6	TraesCS7B01G304700	chr1A	114348466	114349359	893	True	679.333333	1624	95.921000	1	894	3	chr1A.!!$R1	893

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
584	656	0.671781	GGTGGAGCTAGCAGTGTGTG	60.672	60.000	18.83	0.00	0.0	3.82	F
940	1020	1.401905	GCATTCCTCCGCGAGAAAAAT	59.598	47.619	8.23	3.26	0.0	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1755	1837	1.494721	TGCCTCACCCTCTTCAAGTTT	59.505	47.619	0.0	0.0	0.00	2.66	R
2871	2957	0.462047	AATCACGGGACAGAATCGCC	60.462	55.000	0.0	0.0	36.94	5.54	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
388	400	2.335092	TACGCCCTACCTCCTCCTCG	62.335	65.000	0.00	0.00	0.00	4.63
506	578	2.359169	ATCACAGATGGCGGTCGGT	61.359	57.895	0.00	0.00	0.00	4.69
511	583	2.818274	GATGGCGGTCGGTTGGAC	60.818	66.667	0.00	0.00	45.31	4.02
557	629	3.274586	CGGCGGCCATCACAGATG	61.275	66.667	20.71	0.07	0.00	2.90
558	630	2.903855	GGCGGCCATCACAGATGG	60.904	66.667	19.22	19.22	41.99	3.51
563	635	4.131376	CCATCACAGATGGCGGTC	57.869	61.111	12.64	0.00	31.75	4.79
564	636	1.884464	CCATCACAGATGGCGGTCG	60.884	63.158	12.64	0.00	31.75	4.79
565	637	1.884464	CATCACAGATGGCGGTCGG	60.884	63.158	0.00	0.00	0.00	4.79
566	638	3.094062	ATCACAGATGGCGGTCGGG	62.094	63.158	0.00	0.00	0.00	5.14
567	639	4.082523	CACAGATGGCGGTCGGGT	62.083	66.667	0.00	0.00	0.00	5.28
568	640	4.082523	ACAGATGGCGGTCGGGTG	62.083	66.667	0.00	0.00	0.00	4.61
569	641	4.838152	CAGATGGCGGTCGGGTGG	62.838	72.222	0.00	0.00	0.00	4.61
571	643	4.530857	GATGGCGGTCGGGTGGAG	62.531	72.222	0.00	0.00	0.00	3.86
575	647	4.208686	GCGGTCGGGTGGAGCTAG	62.209	72.222	0.00	0.00	41.03	3.42
576	648	4.208686	CGGTCGGGTGGAGCTAGC	62.209	72.222	6.62	6.62	41.03	3.42
577	649	3.075005	GGTCGGGTGGAGCTAGCA	61.075	66.667	18.83	0.00	40.05	3.49
578	650	2.496817	GTCGGGTGGAGCTAGCAG	59.503	66.667	18.83	0.00	0.00	4.24
579	651	2.037367	TCGGGTGGAGCTAGCAGT	59.963	61.111	18.83	0.00	0.00	4.40
580	652	2.185350	CGGGTGGAGCTAGCAGTG	59.815	66.667	18.83	0.00	0.00	3.66
581	653	2.650116	CGGGTGGAGCTAGCAGTGT	61.650	63.158	18.83	0.00	0.00	3.55
582	654	1.078848	GGGTGGAGCTAGCAGTGTG	60.079	63.158	18.83	0.00	0.00	3.82
583	655	1.674057	GGTGGAGCTAGCAGTGTGT	59.326	57.895	18.83	0.00	0.00	3.72
584	656	0.671781	GGTGGAGCTAGCAGTGTGTG	60.672	60.000	18.83	0.00	0.00	3.82
585	657	0.671781	GTGGAGCTAGCAGTGTGTGG	60.672	60.000	18.83	0.00	0.00	4.17
586	658	1.743252	GGAGCTAGCAGTGTGTGGC	60.743	63.158	18.83	0.00	0.00	5.01
587	659	1.743252	GAGCTAGCAGTGTGTGGCC	60.743	63.158	18.83	0.00	0.00	5.36
588	660	3.121030	GCTAGCAGTGTGTGGCCG	61.121	66.667	10.63	0.00	0.00	6.13
589	661	2.656646	CTAGCAGTGTGTGGCCGA	59.343	61.111	0.00	0.00	0.00	5.54
590	662	1.446792	CTAGCAGTGTGTGGCCGAG	60.447	63.158	0.00	0.00	0.00	4.63
591	663	2.159819	CTAGCAGTGTGTGGCCGAGT	62.160	60.000	0.00	0.00	0.00	4.18
592	664	2.434658	TAGCAGTGTGTGGCCGAGTG	62.435	60.000	0.00	0.00	0.00	3.51
593	665	2.666190	CAGTGTGTGGCCGAGTGG	60.666	66.667	0.00	0.00	38.77	4.00
605	677	4.819761	GAGTGGCATGAGCGGCGA	62.820	66.667	12.98	0.00	43.41	5.54
825	905	3.663995	TGTCATGAGTGGCAATTTTGG	57.336	42.857	0.00	0.00	36.93	3.28
940	1020	1.401905	GCATTCCTCCGCGAGAAAAAT	59.598	47.619	8.23	3.26	0.00	1.82
1068	1150	2.835431	CTCCTCGACGCCCAGGAT	60.835	66.667	4.40	0.00	38.18	3.24
1626	1708	2.964740	CCTGATGGGATATGCTACACG	58.035	52.381	0.00	0.00	37.23	4.49
1755	1837	1.756538	TCAATGATGACAGCGCTAGGA	59.243	47.619	10.99	0.00	0.00	2.94
2013	2095	2.037772	ACAGATGGATAGGGAATGCGAC	59.962	50.000	0.00	0.00	0.00	5.19
2167	2249	3.834231	AGACCTTTATGCAAAATGTGGCT	59.166	39.130	0.00	0.00	0.00	4.75
2238	2320	5.981315	CACAATTACTTGGAATGCCATGATC	59.019	40.000	12.62	0.00	45.46	2.92
2794	2876	3.951775	TGTCAAATGTTAATGGGGCAC	57.048	42.857	0.00	0.00	0.00	5.01
2814	2896	4.020543	CACCTTCAGAACTAGTAGCCTCT	58.979	47.826	0.00	0.00	0.00	3.69
2831	2913	3.323115	GCCTCTGAGGACATCATCACATA	59.677	47.826	27.53	0.00	37.67	2.29
2869	2955	5.841957	ACATTTTCTGTCTCTGCTTTTGT	57.158	34.783	0.00	0.00	29.94	2.83
2870	2956	6.212888	ACATTTTCTGTCTCTGCTTTTGTT	57.787	33.333	0.00	0.00	29.94	2.83
2871	2957	6.038356	ACATTTTCTGTCTCTGCTTTTGTTG	58.962	36.000	0.00	0.00	29.94	3.33
2872	2958	4.637483	TTTCTGTCTCTGCTTTTGTTGG	57.363	40.909	0.00	0.00	0.00	3.77
2884	2970	1.243902	TTTGTTGGCGATTCTGTCCC	58.756	50.000	0.00	0.00	0.00	4.46
3190	3278	4.884164	AGGCTGTCTATTTATTGGCTTCAC	59.116	41.667	0.00	0.00	0.00	3.18
3464	3555	6.283544	TGGCATATGCAAGAATCTCAAAAA	57.716	33.333	28.07	0.00	44.36	1.94
3580	3671	1.471119	TAGTAGTCGGTGCTTCCTGG	58.529	55.000	0.00	0.00	0.00	4.45
3593	3684	4.156739	GTGCTTCCTGGTTATTTCCTCTTG	59.843	45.833	0.00	0.00	0.00	3.02
3655	3746	8.517056	TCGTTGTCACAAGTAGTAATGATTAGA	58.483	33.333	0.00	0.00	0.00	2.10
3756	3849	5.353394	ACCTCAGATTACGCCATTTTAGA	57.647	39.130	0.00	0.00	0.00	2.10
3798	3891	5.658468	TGCATTTTGATGTGTGTTTGAGAA	58.342	33.333	0.00	0.00	0.00	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
388	400	2.383527	CCGTTCGCTTGCCTGAGAC	61.384	63.158	0.00	0.00	0.00	3.36
506	578	2.280797	GCACACTGCTCGGTCCAA	60.281	61.111	0.00	0.00	40.96	3.53
549	621	3.770040	CCCGACCGCCATCTGTGA	61.770	66.667	0.00	0.00	0.00	3.58
550	622	4.082523	ACCCGACCGCCATCTGTG	62.083	66.667	0.00	0.00	0.00	3.66
551	623	4.082523	CACCCGACCGCCATCTGT	62.083	66.667	0.00	0.00	0.00	3.41
552	624	4.838152	CCACCCGACCGCCATCTG	62.838	72.222	0.00	0.00	0.00	2.90
558	630	4.208686	CTAGCTCCACCCGACCGC	62.209	72.222	0.00	0.00	0.00	5.68
559	631	4.208686	GCTAGCTCCACCCGACCG	62.209	72.222	7.70	0.00	0.00	4.79
560	632	3.075005	TGCTAGCTCCACCCGACC	61.075	66.667	17.23	0.00	0.00	4.79
561	633	2.352032	ACTGCTAGCTCCACCCGAC	61.352	63.158	17.23	0.00	0.00	4.79
562	634	2.037367	ACTGCTAGCTCCACCCGA	59.963	61.111	17.23	0.00	0.00	5.14
563	635	2.185350	CACTGCTAGCTCCACCCG	59.815	66.667	17.23	0.00	0.00	5.28
564	636	1.078848	CACACTGCTAGCTCCACCC	60.079	63.158	17.23	0.00	0.00	4.61
565	637	0.671781	CACACACTGCTAGCTCCACC	60.672	60.000	17.23	0.00	0.00	4.61
566	638	0.671781	CCACACACTGCTAGCTCCAC	60.672	60.000	17.23	0.00	0.00	4.02
567	639	1.673477	CCACACACTGCTAGCTCCA	59.327	57.895	17.23	0.00	0.00	3.86
568	640	1.743252	GCCACACACTGCTAGCTCC	60.743	63.158	17.23	0.00	0.00	4.70
569	641	1.743252	GGCCACACACTGCTAGCTC	60.743	63.158	17.23	0.00	0.00	4.09
570	642	2.348998	GGCCACACACTGCTAGCT	59.651	61.111	17.23	0.00	0.00	3.32
571	643	3.121030	CGGCCACACACTGCTAGC	61.121	66.667	8.10	8.10	0.00	3.42
572	644	1.446792	CTCGGCCACACACTGCTAG	60.447	63.158	2.24	0.00	0.00	3.42
573	645	2.207229	ACTCGGCCACACACTGCTA	61.207	57.895	2.24	0.00	0.00	3.49
574	646	3.550431	ACTCGGCCACACACTGCT	61.550	61.111	2.24	0.00	0.00	4.24
575	647	3.349006	CACTCGGCCACACACTGC	61.349	66.667	2.24	0.00	0.00	4.40
576	648	2.666190	CCACTCGGCCACACACTG	60.666	66.667	2.24	0.00	0.00	3.66
588	660	4.819761	TCGCCGCTCATGCCACTC	62.820	66.667	0.00	0.00	35.36	3.51
593	665	4.819761	TGAGGTCGCCGCTCATGC	62.820	66.667	0.00	0.00	0.00	4.06
594	666	2.584418	CTGAGGTCGCCGCTCATG	60.584	66.667	0.00	0.00	0.00	3.07
595	667	4.521062	GCTGAGGTCGCCGCTCAT	62.521	66.667	0.00	0.00	0.00	2.90
765	845	2.646798	TGCCATTTGCCCCCTTTTATTT	59.353	40.909	0.00	0.00	40.16	1.40
825	905	3.582714	CCACTTTCAAGATTGGCTTCC	57.417	47.619	0.00	0.00	33.60	3.46
940	1020	0.945265	CCCGGCGTCGTGTTCTTTTA	60.945	55.000	9.28	0.00	33.95	1.52
1152	1234	2.035312	AGGCAGTACCCGAGACGT	59.965	61.111	0.00	0.00	40.58	4.34
1194	1276	1.310933	GGTAGCGGTCGTTGAGGAGA	61.311	60.000	0.00	0.00	0.00	3.71
1755	1837	1.494721	TGCCTCACCCTCTTCAAGTTT	59.505	47.619	0.00	0.00	0.00	2.66
1781	1863	4.827087	CCTGAGCATGCGCCTCGT	62.827	66.667	19.19	0.00	39.83	4.18
1965	2047	2.989840	CAGCACAAGAACCTTCTCGTAG	59.010	50.000	0.00	0.00	36.28	3.51
2013	2095	2.894126	AGTCCCCAAGCTATATGAGTCG	59.106	50.000	0.00	0.00	0.00	4.18
2151	2233	5.123820	GTCTACAGAGCCACATTTTGCATAA	59.876	40.000	0.00	0.00	0.00	1.90
2794	2876	4.274147	TCAGAGGCTACTAGTTCTGAAGG	58.726	47.826	18.44	0.00	42.08	3.46
2814	2896	5.874897	TGTCATATGTGATGATGTCCTCA	57.125	39.130	1.90	0.00	36.60	3.86
2831	2913	7.285401	ACAGAAAATGTTAAGGTCAGTTGTCAT	59.715	33.333	0.00	0.00	39.96	3.06
2869	2955	1.375396	CACGGGACAGAATCGCCAA	60.375	57.895	0.00	0.00	36.94	4.52
2870	2956	1.613317	ATCACGGGACAGAATCGCCA	61.613	55.000	0.00	0.00	36.94	5.69
2871	2957	0.462047	AATCACGGGACAGAATCGCC	60.462	55.000	0.00	0.00	36.94	5.54
2872	2958	0.652592	CAATCACGGGACAGAATCGC	59.347	55.000	0.00	0.00	36.92	4.58
2884	2970	4.318333	CGAATGACTCATAAGCCAATCACG	60.318	45.833	0.00	0.00	0.00	4.35
3177	3265	7.517614	TGTGATTACAAGTGAAGCCAATAAA	57.482	32.000	0.00	0.00	32.88	1.40
3264	3352	8.356533	CATTATTAATGGAAGCGAGCATTTTT	57.643	30.769	8.30	0.00	35.23	1.94
3265	3353	7.935338	CATTATTAATGGAAGCGAGCATTTT	57.065	32.000	8.30	0.00	35.23	1.82
3435	3526	8.672823	TGAGATTCTTGCATATGCCATATATC	57.327	34.615	24.54	18.26	41.18	1.63
3503	3594	9.128107	CGAAAACTATTTACATGCATCAAACTT	57.872	29.630	0.00	0.00	0.00	2.66
3580	3671	8.394121	GTCTCATGAATGTCAAGAGGAAATAAC	58.606	37.037	9.81	0.00	41.19	1.89
3593	3684	6.592994	TCTGTGATTTCAGTCTCATGAATGTC	59.407	38.462	0.00	0.00	38.90	3.06
3804	3900	3.053917	TCATTGTCTAAGGCTTAACCCCC	60.054	47.826	8.54	0.00	40.58	5.40
3805	3901	4.230745	TCATTGTCTAAGGCTTAACCCC	57.769	45.455	8.54	0.00	40.58	4.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.