AutoCloner

Multiple sequence alignment - TraesCS3B01G061900

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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	TraesCS3B01G061900	chr3B	100.000	2371	0	0	1	2371	34011476	34013846	0.000000e+00	4379.0
1	TraesCS3B01G061900	chr3B	93.851	1740	82	12	636	2371	34158001	34159719	0.000000e+00	2597.0
2	TraesCS3B01G061900	chr3B	93.793	1740	83	12	636	2371	34213880	34215598	0.000000e+00	2591.0
3	TraesCS3B01G061900	chr3B	93.739	1741	83	13	636	2371	34107158	34108877	0.000000e+00	2588.0
4	TraesCS3B01G061900	chr3B	98.131	642	7	2	1	638	34212140	34212780	0.000000e+00	1114.0
5	TraesCS3B01G061900	chr3B	98.529	612	9	0	27	638	34105446	34106057	0.000000e+00	1081.0
6	TraesCS3B01G061900	chr3B	98.754	562	7	0	77	638	34156363	34156924	0.000000e+00	1000.0
7	TraesCS3B01G061900	chr3B	80.741	540	76	14	1216	1749	34111519	34112036	1.710000e-106	396.0
8	TraesCS3B01G061900	chr3B	80.370	540	78	14	1216	1749	34162215	34162732	3.700000e-103	385.0
9	TraesCS3B01G061900	chr3B	80.000	540	80	14	1216	1749	34218318	34218835	8.000000e-100	374.0
10	TraesCS3B01G061900	chr3B	100.000	32	0	0	52	83	34011558	34011527	2.540000e-05	60.2
11	TraesCS3B01G061900	chr3B	100.000	32	0	0	52	83	34212225	34212194	2.540000e-05	60.2
12	TraesCS3B01G061900	chr3A	90.403	2209	135	34	170	2371	28878374	28880512	0.000000e+00	2833.0
13	TraesCS3B01G061900	chr3A	88.688	442	38	8	1557	1987	28891738	28892178	1.610000e-146	529.0
14	TraesCS3B01G061900	chrUn	93.793	1740	83	12	636	2371	278731583	278729865	0.000000e+00	2591.0

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	TraesCS3B01G061900	chr3B	34011476	34013846	2370	False	4379.000000	4379	100.000000	1	2371	1	chr3B.!!$F1	2370
1	TraesCS3B01G061900	chr3B	34212140	34218835	6695	False	1359.666667	2591	90.641333	1	2371	3	chr3B.!!$F4	2370
2	TraesCS3B01G061900	chr3B	34105446	34112036	6590	False	1355.000000	2588	91.003000	27	2371	3	chr3B.!!$F2	2344
3	TraesCS3B01G061900	chr3B	34156363	34162732	6369	False	1327.333333	2597	90.991667	77	2371	3	chr3B.!!$F3	2294
4	TraesCS3B01G061900	chr3A	28878374	28880512	2138	False	2833.000000	2833	90.403000	170	2371	1	chr3A.!!$F1	2201
5	TraesCS3B01G061900	chrUn	278729865	278731583	1718	True	2591.000000	2591	93.793000	636	2371	1	chrUn.!!$R1	1735

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
955	2064	0.763035	ACCTCCCAGTAAACACGCTT	59.237	50.0	0.0	0.0	0.0	4.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2237	3349	0.108585	AAACCACGACTGCACTGGAT	59.891	50.0	0.0	0.0	0.0	3.41	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
91	95	3.030882	GCCGAGGTCGATTAGCGC	61.031	66.667	0.00	0.00	43.02	5.92
771	1880	8.815565	ATGTTTTGGGTGTATATCAACATACA	57.184	30.769	0.00	0.00	38.71	2.29
955	2064	0.763035	ACCTCCCAGTAAACACGCTT	59.237	50.000	0.00	0.00	0.00	4.68
960	2069	2.103432	TCCCAGTAAACACGCTTTCTCA	59.897	45.455	0.00	0.00	0.00	3.27
961	2070	2.875933	CCCAGTAAACACGCTTTCTCAA	59.124	45.455	0.00	0.00	0.00	3.02
966	2075	5.177511	CAGTAAACACGCTTTCTCAATCTCA	59.822	40.000	0.00	0.00	0.00	3.27
967	2076	5.758296	AGTAAACACGCTTTCTCAATCTCAA	59.242	36.000	0.00	0.00	0.00	3.02
971	2080	4.629200	ACACGCTTTCTCAATCTCAATCTC	59.371	41.667	0.00	0.00	0.00	2.75
976	2085	6.576185	GCTTTCTCAATCTCAATCTCTCTCT	58.424	40.000	0.00	0.00	0.00	3.10
977	2086	6.698766	GCTTTCTCAATCTCAATCTCTCTCTC	59.301	42.308	0.00	0.00	0.00	3.20
978	2087	7.631161	GCTTTCTCAATCTCAATCTCTCTCTCA	60.631	40.741	0.00	0.00	0.00	3.27
979	2088	6.947644	TCTCAATCTCAATCTCTCTCTCAG	57.052	41.667	0.00	0.00	0.00	3.35
980	2089	5.829391	TCTCAATCTCAATCTCTCTCTCAGG	59.171	44.000	0.00	0.00	0.00	3.86
1068	2177	3.445450	CGCTGCTATCCTCAGGTATGTAT	59.555	47.826	0.00	0.00	32.41	2.29
1100	2209	8.075593	AGCATGTTTTGTGATCAATTTTGTAC	57.924	30.769	0.00	0.00	33.32	2.90
1364	2473	2.130272	ACTGTACTCCATCTCAGCGA	57.870	50.000	0.00	0.00	0.00	4.93
1397	2506	7.383300	GCAGTGATTGTTGCTTAATTTTTCTCT	59.617	33.333	0.00	0.00	37.35	3.10
1403	2512	8.419076	TTGTTGCTTAATTTTTCTCTGTTTCC	57.581	30.769	0.00	0.00	0.00	3.13
1472	2581	6.310711	GTCAAATACTCCTACTTGGAAACTCG	59.689	42.308	0.00	0.00	45.63	4.18
1632	2743	7.922382	AGTCTCCTTGATTTATCTTCCTTTGA	58.078	34.615	0.00	0.00	0.00	2.69
1633	2744	7.826744	AGTCTCCTTGATTTATCTTCCTTTGAC	59.173	37.037	0.00	0.00	0.00	3.18
1664	2775	5.649782	AAATTGATGGAGCTCGTGAAATT	57.350	34.783	7.83	8.66	0.00	1.82
1670	2781	3.411446	TGGAGCTCGTGAAATTGTGAAT	58.589	40.909	7.83	0.00	0.00	2.57
1708	2819	8.912787	ATAACGCACATATATAGCTAGTGTTC	57.087	34.615	10.66	2.75	32.99	3.18
1717	2828	2.349297	AGCTAGTGTTCGTCCTTTCG	57.651	50.000	0.00	0.00	0.00	3.46
1729	2840	2.480419	CGTCCTTTCGAGCTGACAATTT	59.520	45.455	0.00	0.00	0.00	1.82
1738	2849	7.485418	TTCGAGCTGACAATTTGTTTAGTAA	57.515	32.000	3.08	0.00	0.00	2.24
1740	2851	8.094798	TCGAGCTGACAATTTGTTTAGTAATT	57.905	30.769	3.08	0.00	0.00	1.40
1741	2852	8.227791	TCGAGCTGACAATTTGTTTAGTAATTC	58.772	33.333	3.08	3.41	0.00	2.17
1742	2853	7.214449	CGAGCTGACAATTTGTTTAGTAATTCG	59.786	37.037	3.08	9.62	0.00	3.34
1743	2854	7.871853	AGCTGACAATTTGTTTAGTAATTCGT	58.128	30.769	3.08	0.00	0.00	3.85
1819	2930	3.181538	GCGTCGTCATTGATCAAACGTAA	60.182	43.478	24.45	10.09	36.55	3.18
1855	2967	3.001330	GTCCTTCGGCTACAATGAATTCG	59.999	47.826	0.04	0.00	0.00	3.34
1943	3055	2.166254	CACATGCACTATCCCAAAACCC	59.834	50.000	0.00	0.00	0.00	4.11
1947	3059	3.309296	TGCACTATCCCAAAACCCAAAA	58.691	40.909	0.00	0.00	0.00	2.44
1948	3060	3.711704	TGCACTATCCCAAAACCCAAAAA	59.288	39.130	0.00	0.00	0.00	1.94
1955	3067	6.694445	ATCCCAAAACCCAAAAATCATACA	57.306	33.333	0.00	0.00	0.00	2.29
2022	3134	2.365941	TGGTAGTCAATGTCGTCCACAA	59.634	45.455	0.00	0.00	38.97	3.33
2103	3215	3.713003	TCAAGAAGGCTAGACAGGATGA	58.287	45.455	0.00	0.00	39.69	2.92
2129	3241	2.674852	CGGATATGCGATCCCAATGAAG	59.325	50.000	11.65	0.00	34.76	3.02
2158	3270	5.239525	GTGTTTCTCATCTAGTTTTGCCACT	59.760	40.000	0.00	0.00	0.00	4.00
2213	3325	4.021925	ACCAGCCCAGCCGTTCTC	62.022	66.667	0.00	0.00	0.00	2.87
2237	3349	2.378038	GAATCATTGGGGCTTGCTACA	58.622	47.619	0.00	0.00	0.00	2.74
2251	3363	0.108615	GCTACATCCAGTGCAGTCGT	60.109	55.000	0.00	0.00	0.00	4.34
2278	3392	1.308069	GCACGGGACACATTGCTGAT	61.308	55.000	0.00	0.00	32.00	2.90
2307	3421	2.417516	CGCAATCGACCCGGATCT	59.582	61.111	0.73	0.00	38.10	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
91	95	4.467198	ACTAAATGACCACGGAGTTAGG	57.533	45.455	0.00	0.00	41.61	2.69
638	643	6.830912	ACAGCTCATCTACTAATGGCATTAA	58.169	36.000	19.68	6.60	0.00	1.40
648	1755	6.156256	ACCCAAAACATACAGCTCATCTACTA	59.844	38.462	0.00	0.00	0.00	1.82
734	1843	5.357878	ACACCCAAAACATACAGCTCATATG	59.642	40.000	11.43	11.43	36.32	1.78
771	1880	7.776618	TCATCGGTCTGTATCCTATAAATGT	57.223	36.000	0.00	0.00	0.00	2.71
955	2064	6.321945	CCTGAGAGAGAGATTGAGATTGAGAA	59.678	42.308	0.00	0.00	0.00	2.87
960	2069	5.395546	GCAACCTGAGAGAGAGATTGAGATT	60.396	44.000	0.00	0.00	0.00	2.40
961	2070	4.099881	GCAACCTGAGAGAGAGATTGAGAT	59.900	45.833	0.00	0.00	0.00	2.75
966	2075	2.235898	GTGGCAACCTGAGAGAGAGATT	59.764	50.000	0.00	0.00	0.00	2.40
967	2076	1.830477	GTGGCAACCTGAGAGAGAGAT	59.170	52.381	0.00	0.00	0.00	2.75
980	2089	0.883833	CCTGTCTTGATGGTGGCAAC	59.116	55.000	0.00	0.00	0.00	4.17
995	2104	2.803956	TGTAGAACGACCTCATCCTGT	58.196	47.619	0.00	0.00	0.00	4.00
1068	2177	4.099113	TGATCACAAAACATGCTCCAAACA	59.901	37.500	0.00	0.00	0.00	2.83
1100	2209	0.870307	CGATAGTGGAAAGGTCGCCG	60.870	60.000	0.00	0.00	0.00	6.46
1134	2243	6.594744	TCCAGCATATAAAGATTGCAGAGAA	58.405	36.000	0.00	0.00	38.84	2.87
1187	2296	2.437716	CCGCCACCATTAGCCGTT	60.438	61.111	0.00	0.00	0.00	4.44
1307	2416	1.647545	CGGCATCACAATCGCCAACT	61.648	55.000	0.00	0.00	46.60	3.16
1439	2548	5.026790	AGTAGGAGTATTTGACAGGAAGCT	58.973	41.667	0.00	0.00	0.00	3.74
1443	2552	5.338632	TCCAAGTAGGAGTATTTGACAGGA	58.661	41.667	0.00	0.00	43.07	3.86
1472	2581	6.630443	CGATGAAATTTCTGACATTCCGATTC	59.370	38.462	18.64	0.00	0.00	2.52
1632	2743	3.871594	GCTCCATCAATTTACTACGCTGT	59.128	43.478	0.00	0.00	0.00	4.40
1633	2744	4.122776	AGCTCCATCAATTTACTACGCTG	58.877	43.478	0.00	0.00	0.00	5.18
1664	2775	5.334491	CGTTATAACTTGCACACCATTCACA	60.334	40.000	13.56	0.00	0.00	3.58
1670	2781	2.495084	TGCGTTATAACTTGCACACCA	58.505	42.857	13.56	0.00	31.31	4.17
1704	2815	0.671796	TCAGCTCGAAAGGACGAACA	59.328	50.000	0.00	0.00	41.67	3.18
1708	2819	1.714794	ATTGTCAGCTCGAAAGGACG	58.285	50.000	5.79	0.00	33.04	4.79
1717	2828	8.015658	ACGAATTACTAAACAAATTGTCAGCTC	58.984	33.333	0.00	0.00	0.00	4.09
1740	2851	9.084164	GCTTCTATTTCTTCATTACTAACACGA	57.916	33.333	0.00	0.00	0.00	4.35
1741	2852	8.328864	GGCTTCTATTTCTTCATTACTAACACG	58.671	37.037	0.00	0.00	0.00	4.49
1742	2853	9.162764	TGGCTTCTATTTCTTCATTACTAACAC	57.837	33.333	0.00	0.00	0.00	3.32
1743	2854	9.905713	ATGGCTTCTATTTCTTCATTACTAACA	57.094	29.630	0.00	0.00	0.00	2.41
1761	2872	1.203052	CCGTGCATGAAAATGGCTTCT	59.797	47.619	7.72	0.00	0.00	2.85
1819	2930	2.031870	GAAGGACAAAACCCACTTGCT	58.968	47.619	0.00	0.00	0.00	3.91
1855	2967	9.448294	GATGATCTTTAAAGATTGAAGATGTGC	57.552	33.333	27.24	13.52	45.39	4.57
1943	3055	4.665212	ACTGCATCGCTGTATGATTTTTG	58.335	39.130	0.00	0.00	38.85	2.44
1947	3059	3.183793	TGACTGCATCGCTGTATGATT	57.816	42.857	0.00	0.00	40.59	2.57
1948	3060	2.896745	TGACTGCATCGCTGTATGAT	57.103	45.000	0.00	0.00	40.59	2.45
1955	3067	5.007430	CAGATAAAGATTTGACTGCATCGCT	59.993	40.000	0.00	0.00	0.00	4.93
2000	3112	2.565391	TGTGGACGACATTGACTACCAT	59.435	45.455	0.00	0.00	0.00	3.55
2022	3134	1.217183	TCCCTCCTACTCCTATTGCGT	59.783	52.381	0.00	0.00	0.00	5.24
2103	3215	1.628340	TGGGATCGCATATCCGGAAAT	59.372	47.619	9.01	0.00	39.07	2.17
2129	3241	6.088616	GCAAAACTAGATGAGAAACACAATGC	59.911	38.462	0.00	0.00	0.00	3.56
2158	3270	1.597854	CAAGAACTGGCGTGGCTCA	60.598	57.895	0.00	0.00	0.00	4.26
2200	3312	4.785453	CCTGGAGAACGGCTGGGC	62.785	72.222	0.00	0.00	0.00	5.36
2213	3325	1.117150	CAAGCCCCAATGATTCCTGG	58.883	55.000	0.00	0.00	0.00	4.45
2237	3349	0.108585	AAACCACGACTGCACTGGAT	59.891	50.000	0.00	0.00	0.00	3.41
2251	3363	4.858680	TGTCCCGTGCGCAAACCA	62.859	61.111	14.00	1.48	0.00	3.67
2278	3392	1.077787	GATTGCGGTCCCCATCACA	60.078	57.895	0.00	0.00	0.00	3.58
2291	3405	0.663568	CGTAGATCCGGGTCGATTGC	60.664	60.000	9.59	0.00	0.00	3.56
2292	3406	0.666913	ACGTAGATCCGGGTCGATTG	59.333	55.000	9.59	3.76	0.00	2.67
2293	3407	1.066605	CAACGTAGATCCGGGTCGATT	59.933	52.381	9.59	0.00	0.00	3.34
2294	3408	0.666913	CAACGTAGATCCGGGTCGAT	59.333	55.000	9.59	0.00	0.00	3.59
2295	3409	0.392863	TCAACGTAGATCCGGGTCGA	60.393	55.000	9.59	0.00	0.00	4.20
2307	3421	1.368641	GATGCACAGCCATCAACGTA	58.631	50.000	0.00	0.00	40.96	3.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.