AutoCloner

Multiple sequence alignment - TraesCS1B01G242800

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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	TraesCS1B01G242800	chr1B	100.000	2564	0	0	1	2564	431031995	431034558	0.000000e+00	4735
1	TraesCS1B01G242800	chr1B	85.305	1395	148	33	666	2039	430618410	430617052	0.000000e+00	1387
2	TraesCS1B01G242800	chr1B	87.267	644	79	3	1	642	119275497	119274855	0.000000e+00	732
3	TraesCS1B01G242800	chr1B	87.267	644	77	5	1	642	300959075	300958435	0.000000e+00	730
4	TraesCS1B01G242800	chr1D	93.151	1942	88	24	640	2564	318722080	318723993	0.000000e+00	2808
5	TraesCS1B01G242800	chr1D	85.947	1409	149	30	649	2039	318498440	318497063	0.000000e+00	1459
6	TraesCS1B01G242800	chr1A	93.271	1932	83	16	640	2564	405093023	405091132	0.000000e+00	2804
7	TraesCS1B01G242800	chr1A	86.190	1412	137	37	649	2039	399826696	399825322	0.000000e+00	1474
8	TraesCS1B01G242800	chr7D	88.043	644	71	4	6	643	539759091	539758448	0.000000e+00	758
9	TraesCS1B01G242800	chr7D	86.936	643	80	4	1	640	168429063	168428422	0.000000e+00	719
10	TraesCS1B01G242800	chr3B	86.997	646	79	3	4	644	708602651	708603296	0.000000e+00	723
11	TraesCS1B01G242800	chr3B	86.583	641	85	1	1	640	758765256	758765896	0.000000e+00	706
12	TraesCS1B01G242800	chr4D	85.759	646	88	4	1	643	29640445	29639801	0.000000e+00	680
13	TraesCS1B01G242800	chr6D	85.779	661	70	17	3	644	411224812	411224157	0.000000e+00	678
14	TraesCS1B01G242800	chr5D	84.779	657	79	15	3	644	93059948	93060598	7.740000e-180	640

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	TraesCS1B01G242800	chr1B	431031995	431034558	2563	False	4735	4735	100.000	1	2564	1	chr1B.!!$F1	2563
1	TraesCS1B01G242800	chr1B	430617052	430618410	1358	True	1387	1387	85.305	666	2039	1	chr1B.!!$R3	1373
2	TraesCS1B01G242800	chr1B	119274855	119275497	642	True	732	732	87.267	1	642	1	chr1B.!!$R1	641
3	TraesCS1B01G242800	chr1B	300958435	300959075	640	True	730	730	87.267	1	642	1	chr1B.!!$R2	641
4	TraesCS1B01G242800	chr1D	318722080	318723993	1913	False	2808	2808	93.151	640	2564	1	chr1D.!!$F1	1924
5	TraesCS1B01G242800	chr1D	318497063	318498440	1377	True	1459	1459	85.947	649	2039	1	chr1D.!!$R1	1390
6	TraesCS1B01G242800	chr1A	405091132	405093023	1891	True	2804	2804	93.271	640	2564	1	chr1A.!!$R2	1924
7	TraesCS1B01G242800	chr1A	399825322	399826696	1374	True	1474	1474	86.190	649	2039	1	chr1A.!!$R1	1390
8	TraesCS1B01G242800	chr7D	539758448	539759091	643	True	758	758	88.043	6	643	1	chr7D.!!$R2	637
9	TraesCS1B01G242800	chr7D	168428422	168429063	641	True	719	719	86.936	1	640	1	chr7D.!!$R1	639
10	TraesCS1B01G242800	chr3B	708602651	708603296	645	False	723	723	86.997	4	644	1	chr3B.!!$F1	640
11	TraesCS1B01G242800	chr3B	758765256	758765896	640	False	706	706	86.583	1	640	1	chr3B.!!$F2	639
12	TraesCS1B01G242800	chr4D	29639801	29640445	644	True	680	680	85.759	1	643	1	chr4D.!!$R1	642
13	TraesCS1B01G242800	chr6D	411224157	411224812	655	True	678	678	85.779	3	644	1	chr6D.!!$R1	641
14	TraesCS1B01G242800	chr5D	93059948	93060598	650	False	640	640	84.779	3	644	1	chr5D.!!$F1	641

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
554	571	0.035056	AGAAAAGATGGGTCTGGGCG	60.035	55.0	0.0	0.0	34.13	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1898	1952	0.108377	TTCTGTCACGCACACACAGT	60.108	50.0	0.0	0.0	38.94	3.55	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
28	29	4.208686	CGTCTCCCAGTAGCGCCC	62.209	72.222	2.29	0.00	0.00	6.13
35	36	2.417516	CAGTAGCGCCCGCATACT	59.582	61.111	15.50	14.89	44.88	2.12
55	56	1.153745	CAGCGCTGAGGTACTGTCC	60.154	63.158	33.66	0.00	41.55	4.02
197	202	2.594592	GGTCGTGCTTGCCCTTGT	60.595	61.111	0.00	0.00	0.00	3.16
198	203	2.193536	GGTCGTGCTTGCCCTTGTT	61.194	57.895	0.00	0.00	0.00	2.83
313	327	1.229209	AGTGGGGAGTGTGGACGAT	60.229	57.895	0.00	0.00	0.00	3.73
345	359	1.405463	GGCTTCGGCATTTAAGAAGGG	59.595	52.381	6.57	0.00	43.96	3.95
378	393	3.845259	GGGCGGATGACAGGCGTA	61.845	66.667	0.00	0.00	37.61	4.42
413	428	1.459450	GTATTGATGTTGGCGGGTGT	58.541	50.000	0.00	0.00	0.00	4.16
479	496	4.243008	TCCGTTTGCTGTCCGCCA	62.243	61.111	0.00	0.00	38.05	5.69
483	500	2.664851	TTTGCTGTCCGCCACGAG	60.665	61.111	0.00	0.00	38.05	4.18
534	551	1.969589	GTCGGCCCGGACACAAAAT	60.970	57.895	0.73	0.00	36.91	1.82
535	552	0.674269	GTCGGCCCGGACACAAAATA	60.674	55.000	0.73	0.00	36.91	1.40
538	555	1.828979	GGCCCGGACACAAAATAGAA	58.171	50.000	0.73	0.00	0.00	2.10
554	571	0.035056	AGAAAAGATGGGTCTGGGCG	60.035	55.000	0.00	0.00	34.13	6.13
555	572	0.322546	GAAAAGATGGGTCTGGGCGT	60.323	55.000	0.00	0.00	34.13	5.68
557	574	0.112412	AAAGATGGGTCTGGGCGTTT	59.888	50.000	0.00	0.00	34.13	3.60
582	599	0.994995	CTGAGCTGATCGGTTTGTCG	59.005	55.000	2.89	0.00	0.00	4.35
646	663	2.525368	GGTGGAGTTGGCCTAACAAAT	58.475	47.619	16.93	0.00	41.88	2.32
655	672	1.676006	GGCCTAACAAATCCATCACCG	59.324	52.381	0.00	0.00	0.00	4.94
674	692	1.271707	CGTTGTACATCCCAAACCCCT	60.272	52.381	0.00	0.00	0.00	4.79
698	717	2.708325	GAGCCAATGTTATCTCCCCTCT	59.292	50.000	0.00	0.00	0.00	3.69
712	731	9.962835	TTATCTCCCCTCTACCTTCTTATAAAA	57.037	33.333	0.00	0.00	0.00	1.52
726	746	5.050685	TCTTATAAAACCCCCATTCCCTCT	58.949	41.667	0.00	0.00	0.00	3.69
788	808	8.421784	TCTTCTCAACTCATACAGTTTAGTTGT	58.578	33.333	16.16	0.00	43.38	3.32
838	864	0.172352	GTCTCTGGTGCTCCTCTTCG	59.828	60.000	6.34	0.00	34.23	3.79
1003	1042	4.260355	CATCAAGCGCCGCCATGG	62.260	66.667	7.63	7.63	42.50	3.66
1097	1136	2.596631	GCATGGCCCGATGCTGAT	60.597	61.111	18.43	0.00	44.57	2.90
1120	1159	0.390866	CTGCCTCGTCAGCATCAACT	60.391	55.000	0.00	0.00	40.04	3.16
1219	1258	1.006805	GATGAGGAGGCGTCATCGG	60.007	63.158	15.38	0.00	42.83	4.18
1532	1571	1.888018	CCGAGCCCAAGAACGACTA	59.112	57.895	0.00	0.00	0.00	2.59
1605	1646	3.195698	GCGCCGAGCTACCAAAGG	61.196	66.667	0.00	0.00	44.04	3.11
1663	1706	0.179084	CATATCCCGGCGTCTGTGTT	60.179	55.000	6.01	0.00	0.00	3.32
1681	1724	0.324943	TTGCTGTCCCTTAGCTGACC	59.675	55.000	0.00	0.00	41.66	4.02
1793	1839	6.227522	TCAGTTTTTCTGATCGGTGTGATAA	58.772	36.000	0.42	0.00	46.77	1.75
1812	1858	5.357878	TGATAAACATTTGGATCAGTGGCTC	59.642	40.000	0.00	0.00	0.00	4.70
1892	1946	9.904732	AGGGGTATATCATATAGACTTGCATAT	57.095	33.333	0.00	0.00	0.00	1.78
1893	1947	9.935241	GGGGTATATCATATAGACTTGCATATG	57.065	37.037	0.00	0.00	36.75	1.78
1954	2013	8.187354	AGATCGTAGTATCGTACATATGTGAG	57.813	38.462	18.81	11.71	0.00	3.51
1970	2030	9.277783	ACATATGTGAGTTATAATGGAAAGCTC	57.722	33.333	7.78	0.00	0.00	4.09
2076	2137	2.224209	GGGACGGTACCTCATTACATGG	60.224	54.545	10.90	0.00	0.00	3.66
2133	2194	4.624604	GCCGGGAAAGTAGAAGTCCAATTA	60.625	45.833	2.18	0.00	32.70	1.40
2137	2198	6.653740	CGGGAAAGTAGAAGTCCAATTAAACT	59.346	38.462	0.00	0.00	32.70	2.66
2138	2199	7.174426	CGGGAAAGTAGAAGTCCAATTAAACTT	59.826	37.037	4.72	4.72	38.40	2.66
2196	2258	7.484140	AGTATCGTATGCATGATAGTGTATGG	58.516	38.462	10.16	0.00	35.74	2.74
2214	2276	9.755122	AGTGTATGGTATCTCTATAGTGCATAA	57.245	33.333	0.00	0.00	0.00	1.90
2234	2296	8.865978	TGCATAATATCAACGACCGTATTTATC	58.134	33.333	0.00	0.00	0.00	1.75
2427	2498	2.810274	CACACCATTCTGTGAGGTCTTG	59.190	50.000	0.00	0.00	43.77	3.02
2513	2584	7.118200	CTCACCGGAGTAGTAGGAAACTTCC	62.118	52.000	9.46	0.00	40.78	3.46
2530	2601	3.880490	ACTTCCTTCGTTTACAACATGCA	59.120	39.130	0.00	0.00	0.00	3.96
2535	2606	5.009110	TCCTTCGTTTACAACATGCATGAAA	59.991	36.000	32.75	18.86	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	0.243907	GACAGTACCTCAGCGCTGAA	59.756	55.000	37.16	22.73	39.39	3.02
190	195	1.583495	GGAACTACGGCAACAAGGGC	61.583	60.000	0.00	0.00	0.00	5.19
197	202	1.295423	GGCTCTGGAACTACGGCAA	59.705	57.895	0.00	0.00	0.00	4.52
198	203	2.656069	GGGCTCTGGAACTACGGCA	61.656	63.158	0.00	0.00	0.00	5.69
239	244	1.192146	ACCCTAGCCTCGAACTTGCA	61.192	55.000	0.00	0.00	0.00	4.08
242	247	1.003233	CCAAACCCTAGCCTCGAACTT	59.997	52.381	0.00	0.00	0.00	2.66
331	345	0.455815	CACGGCCCTTCTTAAATGCC	59.544	55.000	0.00	0.00	38.74	4.40
345	359	2.359975	CCAGGGAAAGGTCACGGC	60.360	66.667	0.00	0.00	29.76	5.68
388	403	0.446222	GCCAACATCAATACGCACGT	59.554	50.000	0.00	0.00	0.00	4.49
395	410	1.003696	TCACACCCGCCAACATCAATA	59.996	47.619	0.00	0.00	0.00	1.90
413	428	4.715130	AGGCGGCCACCTACCTCA	62.715	66.667	23.09	0.00	38.67	3.86
457	473	4.072088	GACAGCAAACGGACGCGG	62.072	66.667	12.47	0.00	0.00	6.46
479	496	2.280592	GTGTCGGGTTTGGCTCGT	60.281	61.111	0.00	0.00	42.76	4.18
483	500	0.387565	AAACATGTGTCGGGTTTGGC	59.612	50.000	0.00	0.00	33.78	4.52
493	510	0.660488	TTTCGAGCGCAAACATGTGT	59.340	45.000	11.47	0.00	0.00	3.72
534	551	1.209504	CGCCCAGACCCATCTTTTCTA	59.790	52.381	0.00	0.00	30.42	2.10
535	552	0.035056	CGCCCAGACCCATCTTTTCT	60.035	55.000	0.00	0.00	30.42	2.52
538	555	0.112412	AAACGCCCAGACCCATCTTT	59.888	50.000	0.00	0.00	30.42	2.52
554	571	2.893114	GATCAGCTCAGCGCGCAAAC	62.893	60.000	35.10	19.19	45.59	2.93
555	572	2.743538	ATCAGCTCAGCGCGCAAA	60.744	55.556	35.10	19.60	45.59	3.68
582	599	1.268625	CCGTCTGTTTGGGGTAAAAGC	59.731	52.381	0.00	0.00	0.00	3.51
605	622	3.014085	GCGACCCCATCCTGTTCGA	62.014	63.158	0.00	0.00	0.00	3.71
646	663	1.208535	GGGATGTACAACGGTGATGGA	59.791	52.381	7.88	0.00	0.00	3.41
655	672	2.167662	CAGGGGTTTGGGATGTACAAC	58.832	52.381	0.00	0.00	0.00	3.32
674	692	2.439507	GGGGAGATAACATTGGCTCTCA	59.560	50.000	11.86	0.00	36.65	3.27
698	717	6.355005	GGGAATGGGGGTTTTATAAGAAGGTA	60.355	42.308	0.00	0.00	0.00	3.08
712	731	2.206223	GAAAGTAGAGGGAATGGGGGT	58.794	52.381	0.00	0.00	0.00	4.95
726	746	3.233507	ACGAAGGTAGTGTGGGAAAGTA	58.766	45.455	0.00	0.00	0.00	2.24
788	808	3.259064	CGCGAAGAACAGGGAAAGATAA	58.741	45.455	0.00	0.00	0.00	1.75
838	864	1.473278	AGTTCGTCGTTCAGATCTCCC	59.527	52.381	0.00	0.00	0.00	4.30
954	992	0.034896	TTTGGACGAGAGGAACAGCC	59.965	55.000	0.00	0.00	0.00	4.85
1120	1159	1.410517	GACGAGGAGGATCATGAGCAA	59.589	52.381	13.85	0.00	36.25	3.91
1532	1571	4.675029	CCGGGCCGTCGTCTTTGT	62.675	66.667	26.32	0.00	0.00	2.83
1605	1646	2.507110	TACGTGCTCCTCTGGCTTGC	62.507	60.000	0.00	0.00	0.00	4.01
1649	1690	4.988598	AGCAACACAGACGCCGGG	62.989	66.667	2.18	0.00	0.00	5.73
1663	1706	1.553690	GGGTCAGCTAAGGGACAGCA	61.554	60.000	4.51	0.00	41.66	4.41
1681	1724	2.856039	TACCTCTCCGACCTGCAGGG	62.856	65.000	35.42	19.18	40.27	4.45
1694	1737	2.439883	GGAGCCGACCGTACCTCT	60.440	66.667	0.00	0.00	0.00	3.69
1717	1760	1.400494	ACACAACAAAACAGGAGACGC	59.600	47.619	0.00	0.00	0.00	5.19
1777	1823	5.353956	CCAAATGTTTATCACACCGATCAGA	59.646	40.000	0.00	0.00	38.61	3.27
1788	1834	5.263599	AGCCACTGATCCAAATGTTTATCA	58.736	37.500	0.00	0.00	0.00	2.15
1793	1839	2.450476	GGAGCCACTGATCCAAATGTT	58.550	47.619	0.00	0.00	46.65	2.71
1812	1858	3.670523	CGCACACATCGTCATATAGAAGG	59.329	47.826	0.00	0.00	0.00	3.46
1892	1946	1.003108	CACGCACACACAGTAACACA	58.997	50.000	0.00	0.00	0.00	3.72
1893	1947	1.005347	GTCACGCACACACAGTAACAC	60.005	52.381	0.00	0.00	0.00	3.32
1894	1948	1.282817	GTCACGCACACACAGTAACA	58.717	50.000	0.00	0.00	0.00	2.41
1895	1949	1.257936	CTGTCACGCACACACAGTAAC	59.742	52.381	0.00	0.00	34.08	2.50
1896	1950	1.135333	TCTGTCACGCACACACAGTAA	59.865	47.619	0.00	0.00	38.94	2.24
1897	1951	0.741915	TCTGTCACGCACACACAGTA	59.258	50.000	0.00	0.00	38.94	2.74
1898	1952	0.108377	TTCTGTCACGCACACACAGT	60.108	50.000	0.00	0.00	38.94	3.55
1899	1953	1.220529	ATTCTGTCACGCACACACAG	58.779	50.000	0.00	0.00	39.18	3.66
1954	2013	6.701841	TGTCGATCAGAGCTTTCCATTATAAC	59.298	38.462	0.00	0.00	0.00	1.89
1970	2030	3.441163	CATGCCCAAAAATGTCGATCAG	58.559	45.455	0.00	0.00	0.00	2.90
2076	2137	7.208225	AGCATTTTTCTCCTTCTTGTAGAAC	57.792	36.000	0.00	0.00	29.89	3.01
2133	2194	9.435570	TCCTAACTAGCCTAATCTCATAAGTTT	57.564	33.333	0.00	0.00	0.00	2.66
2177	2239	8.690884	AGAGATACCATACACTATCATGCATAC	58.309	37.037	0.00	0.00	0.00	2.39
2234	2296	6.583050	GGCACTACTATGAGCTATAGAAAACG	59.417	42.308	3.21	0.00	41.10	3.60
2415	2486	1.613925	TCGTTCCTCAAGACCTCACAG	59.386	52.381	0.00	0.00	0.00	3.66
2427	2498	4.326548	GTGTGTTTAGTATGCTCGTTCCTC	59.673	45.833	0.00	0.00	0.00	3.71
2530	2601	7.032580	CGAAGTCACTGAAGTAGATCTTTCAT	58.967	38.462	9.71	0.00	36.40	2.57
2535	2606	3.129638	GCCGAAGTCACTGAAGTAGATCT	59.870	47.826	0.00	0.00	0.00	2.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.