AutoCloner

Multiple sequence alignment - TraesCS7D01G242800

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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	TraesCS7D01G242800	chr7D	100.000	2262	0	0	1	2262	208635176	208637437	0.000	4178.0
1	TraesCS7D01G242800	chr7D	97.219	2265	57	5	2	2262	203499964	203502226	0.000	3829.0
2	TraesCS7D01G242800	chr7D	97.130	2265	59	5	2	2262	381923966	381926228	0.000	3818.0
3	TraesCS7D01G242800	chr7D	97.043	2266	60	5	2	2262	382050043	382052306	0.000	3807.0
4	TraesCS7D01G242800	chr7D	97.042	2265	58	6	2	2262	381973802	381971543	0.000	3803.0
5	TraesCS7D01G242800	chr7D	100.000	29	0	0	2568	2596	208637743	208637771	0.001	54.7
6	TraesCS7D01G242800	chr5A	97.220	2266	56	5	2	2262	19248879	19246616	0.000	3829.0
7	TraesCS7D01G242800	chr7B	97.085	2264	61	4	2	2262	716878815	716876554	0.000	3810.0
8	TraesCS7D01G242800	chr7B	96.952	2264	64	4	2	2262	742989411	742991672	0.000	3794.0
9	TraesCS7D01G242800	chr6D	97.084	2263	60	5	2	2260	124517487	124519747	0.000	3808.0
10	TraesCS7D01G242800	chr1A	96.998	2265	62	5	2	2262	498691262	498689000	0.000	3801.0
11	TraesCS7D01G242800	chr1A	100.000	29	0	0	2568	2596	498688933	498688905	0.001	54.7
12	TraesCS7D01G242800	chr2B	100.000	29	0	0	2568	2596	391163303	391163331	0.001	54.7

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	TraesCS7D01G242800	chr7D	208635176	208637771	2595	False	2116.35	4178	100.000	1	2596	2	chr7D.!!$F4	2595
1	TraesCS7D01G242800	chr7D	203499964	203502226	2262	False	3829.00	3829	97.219	2	2262	1	chr7D.!!$F1	2260
2	TraesCS7D01G242800	chr7D	381923966	381926228	2262	False	3818.00	3818	97.130	2	2262	1	chr7D.!!$F2	2260
3	TraesCS7D01G242800	chr7D	382050043	382052306	2263	False	3807.00	3807	97.043	2	2262	1	chr7D.!!$F3	2260
4	TraesCS7D01G242800	chr7D	381971543	381973802	2259	True	3803.00	3803	97.042	2	2262	1	chr7D.!!$R1	2260
5	TraesCS7D01G242800	chr5A	19246616	19248879	2263	True	3829.00	3829	97.220	2	2262	1	chr5A.!!$R1	2260
6	TraesCS7D01G242800	chr7B	716876554	716878815	2261	True	3810.00	3810	97.085	2	2262	1	chr7B.!!$R1	2260
7	TraesCS7D01G242800	chr7B	742989411	742991672	2261	False	3794.00	3794	96.952	2	2262	1	chr7B.!!$F1	2260
8	TraesCS7D01G242800	chr6D	124517487	124519747	2260	False	3808.00	3808	97.084	2	2260	1	chr6D.!!$F1	2258
9	TraesCS7D01G242800	chr1A	498688905	498691262	2357	True	1927.85	3801	98.499	2	2596	2	chr1A.!!$R1	2594

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
284	285	0.550914	AACACAGGAAAGCACCCTCA	59.449	50.000	0.0	0.0	0.0	3.86	F
659	664	1.282157	GAAAGGGGTCCATGTAGCTGT	59.718	52.381	0.0	0.0	0.0	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1560	1568	1.142262	GGCCACCCAACGACCTATAAT	59.858	52.381	0.0	0.0	0.0	1.28	R
1768	1776	2.302733	GGCCAACTTCCATTCACCAAAT	59.697	45.455	0.0	0.0	0.0	2.32	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
29	30	2.092049	AGAGTTCGTTTTTGGGTTCCCT	60.092	45.455	9.43	0.00	0.00	4.20
163	164	1.988846	CCCCTCCCTCTGTCTTTTTCT	59.011	52.381	0.00	0.00	0.00	2.52
284	285	0.550914	AACACAGGAAAGCACCCTCA	59.449	50.000	0.00	0.00	0.00	3.86
294	295	6.152661	CAGGAAAGCACCCTCATTTTGTAATA	59.847	38.462	0.00	0.00	0.00	0.98
422	425	2.480555	GAATGCCTGCCGACGTTG	59.519	61.111	0.00	0.00	0.00	4.10
461	464	4.508584	CCCTTACCACTAAAGGAAAGGCTT	60.509	45.833	3.44	0.00	45.41	4.35
473	476	1.423794	AAAGGCTTGACGAAGGGGGA	61.424	55.000	0.00	0.00	0.00	4.81
481	485	4.642429	CTTGACGAAGGGGGAATATTAGG	58.358	47.826	0.00	0.00	0.00	2.69
484	488	2.105993	ACGAAGGGGGAATATTAGGTGC	59.894	50.000	0.00	0.00	0.00	5.01
496	500	6.316890	GGAATATTAGGTGCGTAAGGAAAACA	59.683	38.462	0.00	0.00	41.83	2.83
520	524	3.906014	TCGGAGATTGAGATGTCGATC	57.094	47.619	11.40	11.40	42.22	3.69
623	628	4.065281	CTCGGACCGGGAAAGCGT	62.065	66.667	8.50	0.00	0.00	5.07
659	664	1.282157	GAAAGGGGTCCATGTAGCTGT	59.718	52.381	0.00	0.00	0.00	4.40
728	733	5.485353	AGAGAATCCACTTCAGATAACCACA	59.515	40.000	0.00	0.00	36.24	4.17
811	816	3.549423	CGAGAGTGGAGTTACGTGAACAA	60.549	47.826	0.00	0.00	40.86	2.83
936	944	1.742308	TGTGGGGCCCTATCTATTCC	58.258	55.000	25.93	1.56	0.00	3.01
939	947	3.181389	TGTGGGGCCCTATCTATTCCATA	60.181	47.826	25.93	2.65	0.00	2.74
1061	1069	5.586243	CGGTGACATCATTCCTTTCTATTGT	59.414	40.000	0.00	0.00	0.00	2.71
1254	1262	6.985117	TGGACATGTAGGTTATATTCGTACC	58.015	40.000	0.00	0.00	0.00	3.34
1386	1394	4.595762	ACCCGTGTCAAATATATAGCGT	57.404	40.909	0.00	0.00	0.00	5.07
1454	1462	8.497745	ACCTTCTCCATTACAATGTTCTCATAT	58.502	33.333	0.00	0.00	34.60	1.78
1462	1470	5.824904	ACAATGTTCTCATATGCAGGAAC	57.175	39.130	19.53	19.53	38.64	3.62
1560	1568	2.447443	CAGTGGGAGTAGTGACTAGCA	58.553	52.381	0.00	0.00	35.45	3.49
1576	1584	3.965347	ACTAGCATTATAGGTCGTTGGGT	59.035	43.478	0.00	0.00	0.00	4.51
1649	1657	0.895100	ACCGGACACGTAGCTTACCA	60.895	55.000	9.46	0.00	38.78	3.25
1683	1691	3.154710	CACAGATGGGAATGCATGCTAT	58.845	45.455	20.33	7.43	0.00	2.97
1692	1700	4.098349	GGGAATGCATGCTATGAAAGACAA	59.902	41.667	20.33	0.00	0.00	3.18
1699	1707	4.265904	TGCTATGAAAGACAAGGTCGAA	57.734	40.909	0.00	0.00	37.67	3.71
1768	1776	2.492088	CACTACACGAGATGAACCTGGA	59.508	50.000	0.00	0.00	0.00	3.86
1827	1835	2.158330	CAGTTACTGCGCGCGATCA	61.158	57.895	37.18	22.16	0.00	2.92
1834	1842	1.467342	ACTGCGCGCGATCATATACTA	59.533	47.619	37.18	2.45	0.00	1.82
1870	1878	2.733593	GTTGGAACGACGCGAGCT	60.734	61.111	15.93	0.00	0.00	4.09
1894	1902	1.202580	CCGAGCCTCGATTCCTTTCAT	60.203	52.381	17.19	0.00	43.74	2.57
1998	2007	5.799827	TTCCATTTTCGTTGGGAAAGAAT	57.200	34.783	0.00	0.00	44.95	2.40
2014	2023	1.153168	AATGGCGAAGTCCATCCGG	60.153	57.895	0.00	0.00	41.99	5.14
2084	2093	2.677524	GCATGCAGAAGGGGCACA	60.678	61.111	14.21	0.00	45.23	4.57
2171	2180	1.070601	GTGCTTTGTTTCCTGGCCAAT	59.929	47.619	7.01	0.00	0.00	3.16
2208	2217	6.406177	GGGCTGATTGCAAAAGATATCTGAAA	60.406	38.462	5.86	0.00	45.15	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.114767	ACCCAAAAACGAACTCTGTTTACTA	58.885	36.000	0.00	0.00	38.52	1.82
29	30	0.395586	CCAATCCATTCGGGGCTTCA	60.396	55.000	0.00	0.00	37.22	3.02
163	164	2.578021	AGAGGGGAAGATTAGCAAAGCA	59.422	45.455	0.00	0.00	0.00	3.91
284	285	4.402474	GGGAAGCTGCAGGTATTACAAAAT	59.598	41.667	20.51	0.00	0.00	1.82
294	295	2.600729	CCTCTGGGAAGCTGCAGGT	61.601	63.158	13.85	13.85	33.58	4.00
335	338	3.603671	GGGGTCCTAGCTACGCCG	61.604	72.222	11.99	0.00	39.75	6.46
461	464	3.389983	CACCTAATATTCCCCCTTCGTCA	59.610	47.826	0.00	0.00	0.00	4.35
473	476	6.882678	AGTGTTTTCCTTACGCACCTAATATT	59.117	34.615	0.00	0.00	0.00	1.28
481	485	3.285745	CGAAAGTGTTTTCCTTACGCAC	58.714	45.455	0.00	0.00	39.63	5.34
484	488	4.053295	TCTCCGAAAGTGTTTTCCTTACG	58.947	43.478	0.00	0.00	39.63	3.18
496	500	3.444034	TCGACATCTCAATCTCCGAAAGT	59.556	43.478	0.00	0.00	0.00	2.66
520	524	6.638468	CCTTCTTCCTTTTCGATGAAAAACAG	59.362	38.462	6.23	3.40	40.34	3.16
611	616	4.572571	TGCCAACGCTTTCCCGGT	62.573	61.111	0.00	0.00	35.36	5.28
623	628	4.202305	CCCCTTTCTTTATGTTGTTGCCAA	60.202	41.667	0.00	0.00	0.00	4.52
681	686	5.717119	TCTTTTGTAGTAGATGTCGAACCC	58.283	41.667	0.00	0.00	0.00	4.11
743	748	1.296392	CTCTCGGCCATTCCACACA	59.704	57.895	2.24	0.00	34.01	3.72
811	816	3.208747	AGTTGTTTTCCATCAGACGGT	57.791	42.857	0.00	0.00	0.00	4.83
936	944	3.475566	TTTCTTGGGGCTCGAGATATG	57.524	47.619	18.75	0.38	35.89	1.78
939	947	1.340114	GGTTTTCTTGGGGCTCGAGAT	60.340	52.381	18.75	0.00	35.89	2.75
1045	1053	8.593945	ATTTTAGGCACAATAGAAAGGAATGA	57.406	30.769	0.00	0.00	0.00	2.57
1254	1262	1.890876	TGGTTCCACATGAGAAACCG	58.109	50.000	6.79	0.00	29.44	4.44
1422	1430	7.200434	ACATTGTAATGGAGAAGGTCATAGT	57.800	36.000	9.22	0.00	40.70	2.12
1454	1462	2.119484	CTAACGGGGGTGTTCCTGCA	62.119	60.000	0.00	0.00	36.66	4.41
1483	1491	6.688813	GGCGAAGAACAAATAGAATTTGCTAG	59.311	38.462	11.32	0.00	32.93	3.42
1560	1568	1.142262	GGCCACCCAACGACCTATAAT	59.858	52.381	0.00	0.00	0.00	1.28
1649	1657	3.006110	CCCATCTGTGTTGCAACTGATTT	59.994	43.478	28.61	9.70	36.82	2.17
1683	1691	4.600692	TCAGATTCGACCTTGTCTTTCA	57.399	40.909	0.00	0.00	0.00	2.69
1692	1700	4.499865	CGGTTGATGTATCAGATTCGACCT	60.500	45.833	14.48	0.00	39.53	3.85
1699	1707	3.632604	AGTCGACGGTTGATGTATCAGAT	59.367	43.478	10.46	0.00	38.19	2.90
1768	1776	2.302733	GGCCAACTTCCATTCACCAAAT	59.697	45.455	0.00	0.00	0.00	2.32
1827	1835	3.163467	GACGGGGAGCACCTTAGTATAT	58.837	50.000	0.00	0.00	40.03	0.86
1877	1885	5.359194	TCTTTATGAAAGGAATCGAGGCT	57.641	39.130	0.00	0.00	39.01	4.58
1894	1902	4.223032	GTCACCTCTGTCCCTTCATCTTTA	59.777	45.833	0.00	0.00	0.00	1.85
1998	2007	2.682136	TCCGGATGGACTTCGCCA	60.682	61.111	0.00	0.00	40.17	5.69
2014	2023	5.825151	CCTCTTATTTCTTCATTGGAGGGTC	59.175	44.000	0.00	0.00	36.44	4.46
2062	2071	2.345760	CCCCTTCTGCATGCGCTTT	61.346	57.895	14.09	0.00	39.64	3.51
2073	2082	4.289672	TCTTTATTTCTCTGTGCCCCTTCT	59.710	41.667	0.00	0.00	0.00	2.85
2084	2093	4.601857	TCCCCCACACTTCTTTATTTCTCT	59.398	41.667	0.00	0.00	0.00	3.10
2171	2180	2.833338	CAATCAGCCCCAAATCCTTGAA	59.167	45.455	0.00	0.00	34.14	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.