AutoCloner

Multiple sequence alignment - TraesCS7A01G145500

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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	TraesCS7A01G145500	chr7A	100.000	3494	0	0	1	3494	96817047	96813554	0.000000e+00	6453.0
1	TraesCS7A01G145500	chr7A	90.636	2232	139	37	462	2650	97023966	97021762	0.000000e+00	2900.0
2	TraesCS7A01G145500	chr7A	89.685	349	31	4	7	355	96829746	96829403	1.150000e-119	440.0
3	TraesCS7A01G145500	chr7A	89.100	211	16	3	3032	3235	97021202	97020992	4.480000e-64	255.0
4	TraesCS7A01G145500	chr7A	88.068	176	18	2	2712	2885	97021645	97021471	4.570000e-49	206.0
5	TraesCS7A01G145500	chr7A	85.526	152	10	4	3352	3494	97020389	97020241	7.810000e-32	148.0
6	TraesCS7A01G145500	chr7A	75.839	149	24	8	23	170	573855337	573855200	8.100000e-07	65.8
7	TraesCS7A01G145500	chr7D	93.759	3509	159	32	22	3494	93883265	93879781	0.000000e+00	5212.0
8	TraesCS7A01G145500	chr7D	76.510	149	23	8	23	170	506521499	506521362	1.740000e-08	71.3
9	TraesCS7A01G145500	chr7B	91.306	2956	160	50	595	3494	47604970	47602056	0.000000e+00	3945.0
10	TraesCS7A01G145500	chr7B	89.778	1712	103	33	359	2030	47342042	47340363	0.000000e+00	2126.0
11	TraesCS7A01G145500	chr7B	91.866	627	44	6	2031	2650	47340401	47339775	0.000000e+00	869.0
12	TraesCS7A01G145500	chr7B	89.298	299	26	5	13	310	47342451	47342158	1.530000e-98	370.0
13	TraesCS7A01G145500	chr7B	88.028	142	13	4	462	603	47608780	47608643	7.760000e-37	165.0
14	TraesCS7A01G145500	chr7B	91.228	114	10	0	3032	3145	47339215	47339102	4.670000e-34	156.0
15	TraesCS7A01G145500	chr7B	96.610	59	2	0	2890	2948	47339430	47339372	7.980000e-17	99.0

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	TraesCS7A01G145500	chr7A	96813554	96817047	3493	True	6453.00	6453	100.0000	1	3494	1	chr7A.!!$R1	3493
1	TraesCS7A01G145500	chr7A	97020241	97023966	3725	True	877.25	2900	88.3325	462	3494	4	chr7A.!!$R4	3032
2	TraesCS7A01G145500	chr7D	93879781	93883265	3484	True	5212.00	5212	93.7590	22	3494	1	chr7D.!!$R1	3472
3	TraesCS7A01G145500	chr7B	47602056	47608780	6724	True	2055.00	3945	89.6670	462	3494	2	chr7B.!!$R2	3032
4	TraesCS7A01G145500	chr7B	47339102	47342451	3349	True	724.00	2126	91.7560	13	3145	5	chr7B.!!$R1	3132

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
25	26	1.468520	CACATCGCAAAATCGGGAAGT	59.531	47.619	0.00	0.00	30.95	3.01	F
1074	4923	0.449388	GACAGAGGCTTGCCGAATTG	59.551	55.000	5.95	6.17	0.00	2.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2007	5862	0.035630	CCTCAAGCCCCTGTTCTGAG	60.036	60.0	0.0	0.0	0.0	3.35	R
2881	6841	0.954452	CTGGAAACCACTGAACTGGC	59.046	55.0	0.0	0.0	34.2	4.85	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
25	26	1.468520	CACATCGCAAAATCGGGAAGT	59.531	47.619	0.00	0.00	30.95	3.01
39	40	2.289694	CGGGAAGTTCATCACCAACTCT	60.290	50.000	5.01	0.00	32.71	3.24
43	44	5.513267	GGGAAGTTCATCACCAACTCTAAGT	60.513	44.000	5.01	0.00	32.71	2.24
77	78	5.945191	TGATCACTTGTGGCAAATTCATAGA	59.055	36.000	0.00	0.00	0.00	1.98
138	139	9.860898	GATTATTAATTCATTTGGACCCTATGC	57.139	33.333	0.00	0.00	0.00	3.14
139	140	6.670695	ATTAATTCATTTGGACCCTATGCC	57.329	37.500	0.00	0.00	0.00	4.40
155	156	4.621034	CCTATGCCGTGTTTGATTTTGAAC	59.379	41.667	0.00	0.00	0.00	3.18
163	164	7.372135	GCCGTGTTTGATTTTGAACATTTAAAC	59.628	33.333	0.00	0.00	37.98	2.01
197	198	5.748152	ACGAACTTGAAATGTTGGTGAAATG	59.252	36.000	0.00	0.00	40.41	2.32
303	308	6.831976	AGAGAGGAAGAAGTAGCAAAGAAAA	58.168	36.000	0.00	0.00	0.00	2.29
318	324	7.890515	AGCAAAGAAAAGAAAATAGAGGGAAG	58.109	34.615	0.00	0.00	0.00	3.46
338	344	4.797800	AGTAAGTTTTAGACGAGGGTCC	57.202	45.455	0.00	0.00	44.54	4.46
340	346	3.679824	AAGTTTTAGACGAGGGTCCAG	57.320	47.619	0.00	0.00	44.54	3.86
341	347	1.900486	AGTTTTAGACGAGGGTCCAGG	59.100	52.381	0.00	0.00	44.54	4.45
355	361	6.183360	CGAGGGTCCAGGTGAAAATAATTTAC	60.183	42.308	0.00	0.00	0.00	2.01
362	467	9.226606	TCCAGGTGAAAATAATTTACACTACAG	57.773	33.333	0.00	0.00	32.22	2.74
573	696	2.582978	CTGCTGCTGCTGCTCCTA	59.417	61.111	27.67	10.41	40.48	2.94
605	4409	1.496429	CATACCCCAGCCAATCTCCTT	59.504	52.381	0.00	0.00	0.00	3.36
667	4479	3.211963	CCATTGCCGGGCTAGCAC	61.212	66.667	21.46	13.06	40.69	4.40
668	4480	2.438254	CATTGCCGGGCTAGCACA	60.438	61.111	18.96	6.33	40.69	4.57
669	4481	2.124570	ATTGCCGGGCTAGCACAG	60.125	61.111	18.96	6.85	40.69	3.66
807	4622	2.178912	TCAAATTCCGGCGATATCCC	57.821	50.000	9.30	0.00	0.00	3.85
982	4806	4.757692	AGGGAAATTGGGGAAACATACAA	58.242	39.130	0.00	0.00	0.00	2.41
1004	4853	3.935315	CAGAGCTCTGTTTCTTCATGGA	58.065	45.455	31.71	0.00	39.09	3.41
1074	4923	0.449388	GACAGAGGCTTGCCGAATTG	59.551	55.000	5.95	6.17	0.00	2.32
1079	4928	2.690778	GGCTTGCCGAATTGCTCGT	61.691	57.895	0.00	0.00	46.65	4.18
1101	4950	1.549170	GTCCATCGTCTGTTACCCAGT	59.451	52.381	0.00	0.00	42.19	4.00
1181	5030	2.564771	CATATTCGCCAGCCTTGAGAA	58.435	47.619	0.00	0.00	0.00	2.87
1224	5073	2.879070	CGTCTGCTCATCATGGCGC	61.879	63.158	0.00	0.00	0.00	6.53
1273	5122	0.673022	GCTCTTCAGGCAGACACAGG	60.673	60.000	0.00	0.00	0.00	4.00
1308	5157	1.817099	CACCTCTGAATCTGCCGGC	60.817	63.158	22.73	22.73	0.00	6.13
1444	5293	1.890979	GCCGACGATAGGTCCGAGA	60.891	63.158	0.00	0.00	42.99	4.04
1660	5515	1.340114	ACCTCTTCGGGAAGGCATTTC	60.340	52.381	8.46	0.00	38.88	2.17
1680	5535	2.702478	TCTGTCATCTGATCCATCCACC	59.298	50.000	0.00	0.00	0.00	4.61
1797	5652	8.804743	CATGTTGATTATGCAGATTGTTTCTTC	58.195	33.333	0.00	0.00	29.93	2.87
2007	5862	1.141858	GGTTGGGAGGATGAGGATGTC	59.858	57.143	0.00	0.00	0.00	3.06
2097	5952	2.528127	TCGGGGCTGGAACCTGAA	60.528	61.111	2.01	0.00	40.34	3.02
2197	6052	6.033831	CGTATTTAAAGTGGATTTTGCTGCAG	59.966	38.462	10.11	10.11	32.01	4.41
2248	6103	3.214328	GACAGTGTGATGTTTCTTGGGT	58.786	45.455	0.00	0.00	32.25	4.51
2300	6155	7.042456	CGATGAATATCCACAGTTAAAGTCCAG	60.042	40.741	0.00	0.00	0.00	3.86
2350	6211	6.161381	GGCTATTATCATTTTGGAAGCATGG	58.839	40.000	0.00	0.00	0.00	3.66
2408	6269	5.662211	AATTGCACTGTTGAAAGAATTGC	57.338	34.783	0.00	0.00	0.00	3.56
2652	6517	0.107459	TATGTGGTGCGCTAATGGCA	60.107	50.000	9.73	0.00	41.91	4.92
3161	7243	0.475906	GATGACAGGGATGGAAGGGG	59.524	60.000	0.00	0.00	0.00	4.79
3383	7987	6.491403	ACTTTTTCAGATTGCTCACTGGTATT	59.509	34.615	0.00	0.00	35.20	1.89
3450	8060	7.612677	ACGAGTTCCATCTTAGAATTTACACT	58.387	34.615	0.00	0.00	0.00	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	0.170116	TTCCCGATTTTGCGATGTGC	59.830	50.000	0.00	0.00	46.70	4.57
5	6	1.468520	ACTTCCCGATTTTGCGATGTG	59.531	47.619	0.00	0.00	0.00	3.21
6	7	1.821216	ACTTCCCGATTTTGCGATGT	58.179	45.000	0.00	0.00	0.00	3.06
7	8	2.161410	TGAACTTCCCGATTTTGCGATG	59.839	45.455	0.00	0.00	0.00	3.84
8	9	2.432444	TGAACTTCCCGATTTTGCGAT	58.568	42.857	0.00	0.00	0.00	4.58
9	10	1.885560	TGAACTTCCCGATTTTGCGA	58.114	45.000	0.00	0.00	0.00	5.10
10	11	2.161410	TGATGAACTTCCCGATTTTGCG	59.839	45.455	0.00	0.00	0.00	4.85
11	12	3.501950	GTGATGAACTTCCCGATTTTGC	58.498	45.455	0.00	0.00	0.00	3.68
12	13	3.505680	TGGTGATGAACTTCCCGATTTTG	59.494	43.478	0.00	0.00	0.00	2.44
13	14	3.761897	TGGTGATGAACTTCCCGATTTT	58.238	40.909	0.00	0.00	0.00	1.82
14	15	3.433306	TGGTGATGAACTTCCCGATTT	57.567	42.857	0.00	0.00	0.00	2.17
15	16	3.081804	GTTGGTGATGAACTTCCCGATT	58.918	45.455	0.00	0.00	0.00	3.34
16	17	2.305927	AGTTGGTGATGAACTTCCCGAT	59.694	45.455	0.00	0.00	28.94	4.18
19	20	3.425162	AGAGTTGGTGATGAACTTCCC	57.575	47.619	0.00	0.00	33.71	3.97
49	50	6.623486	TGAATTTGCCACAAGTGATCAATAG	58.377	36.000	0.00	0.00	0.00	1.73
51	52	5.471556	TGAATTTGCCACAAGTGATCAAT	57.528	34.783	0.00	0.00	0.00	2.57
138	139	8.599774	AGTTTAAATGTTCAAAATCAAACACGG	58.400	29.630	0.00	0.00	38.14	4.94
139	140	9.965748	AAGTTTAAATGTTCAAAATCAAACACG	57.034	25.926	0.00	0.00	38.14	4.49
155	156	9.459276	CAAGTTCGTTGTTTTCAAGTTTAAATG	57.541	29.630	0.00	0.00	40.74	2.32
163	164	7.276953	ACATTTCAAGTTCGTTGTTTTCAAG	57.723	32.000	0.00	0.00	40.74	3.02
170	171	4.156922	TCACCAACATTTCAAGTTCGTTGT	59.843	37.500	0.00	0.00	37.43	3.32
197	198	7.307493	TGACATGAGTATTTCTAATGCACAC	57.693	36.000	0.00	0.00	38.32	3.82
318	324	4.492611	CTGGACCCTCGTCTAAAACTTAC	58.507	47.826	0.00	0.00	39.15	2.34
338	344	8.730680	AGCTGTAGTGTAAATTATTTTCACCTG	58.269	33.333	19.00	12.02	0.00	4.00
340	346	8.512138	ACAGCTGTAGTGTAAATTATTTTCACC	58.488	33.333	20.16	9.20	0.00	4.02
362	467	3.935828	CCTCCTTCTAAACTTGCTACAGC	59.064	47.826	0.00	0.00	42.50	4.40
438	556	0.332632	TGGAAGGCCAGCTTAAGCAT	59.667	50.000	28.39	11.48	45.16	3.79
439	557	1.767036	TGGAAGGCCAGCTTAAGCA	59.233	52.632	28.39	2.11	45.16	3.91
519	640	3.125573	GGGGAAGAGTTTCGCGGC	61.126	66.667	6.13	0.00	44.68	6.53
573	696	0.563672	GGGGTATGGAGAGGAGGAGT	59.436	60.000	0.00	0.00	0.00	3.85
698	4513	2.839474	GAACGAGCTTCCACAAATTCG	58.161	47.619	0.00	0.00	32.91	3.34
854	4670	9.218440	GATACTCCTACTTATAGAACGCTAACT	57.782	37.037	0.00	0.00	0.00	2.24
858	4674	9.165035	GTATGATACTCCTACTTATAGAACGCT	57.835	37.037	0.00	0.00	0.00	5.07
885	4702	2.530151	AGAGGGCAGGCAGGTGAA	60.530	61.111	0.00	0.00	0.00	3.18
886	4703	3.324930	CAGAGGGCAGGCAGGTGA	61.325	66.667	0.00	0.00	0.00	4.02
887	4704	3.618780	GACAGAGGGCAGGCAGGTG	62.619	68.421	0.00	0.00	0.00	4.00
1004	4853	0.837272	ACACCGGGTTATGCTGCTAT	59.163	50.000	6.32	0.00	0.00	2.97
1074	4923	1.583967	CAGACGATGGACGACGAGC	60.584	63.158	0.00	0.00	45.77	5.03
1079	4928	0.813184	GGGTAACAGACGATGGACGA	59.187	55.000	0.00	0.00	41.61	4.20
1235	5084	0.323178	CCCAAGATTGCAGAGCCTGT	60.323	55.000	4.45	0.00	33.43	4.00
1273	5122	0.529992	GTGTATAGGAGGCACGGTGC	60.530	60.000	24.43	24.43	44.08	5.01
1308	5157	1.739562	GAGGCCTGCAACACTCTCG	60.740	63.158	12.00	0.00	0.00	4.04
1444	5293	1.217057	ATGGGGTTGAGGAGGTGCAT	61.217	55.000	0.00	0.00	0.00	3.96
1578	5427	3.530365	GTCGTAGTCGGCTAAGAGC	57.470	57.895	13.08	5.10	41.46	4.09
1586	5435	0.654683	CGTAGGGAAGTCGTAGTCGG	59.345	60.000	0.00	0.00	37.69	4.79
1660	5515	2.547430	CGGTGGATGGATCAGATGACAG	60.547	54.545	0.00	0.00	0.00	3.51
1680	5535	6.366332	GCTTGAGTACCACATAATAATCTCCG	59.634	42.308	0.00	0.00	0.00	4.63
1797	5652	1.674962	GCAAAGAGCAGGCTATCCTTG	59.325	52.381	0.00	6.07	41.93	3.61
1845	5700	3.869623	AGGCGCACTGAGATCAAAT	57.130	47.368	10.83	0.00	0.00	2.32
2007	5862	0.035630	CCTCAAGCCCCTGTTCTGAG	60.036	60.000	0.00	0.00	0.00	3.35
2097	5952	3.534357	ACATCGTCATCCTCCCTATCT	57.466	47.619	0.00	0.00	0.00	1.98
2197	6052	7.065085	TGAGCTAGTAATGTCTTCAAGATTTGC	59.935	37.037	0.00	0.00	0.00	3.68
2202	6057	7.038048	CACATGAGCTAGTAATGTCTTCAAGA	58.962	38.462	0.00	0.00	32.27	3.02
2248	6103	8.243426	GGCACTCAAACAAAGTGATTGATTATA	58.757	33.333	7.42	0.00	45.64	0.98
2350	6211	3.067461	ACTCCAATATCACGCTCACTCTC	59.933	47.826	0.00	0.00	0.00	3.20
2408	6269	1.271543	TGGACCAAAGCTGAGGTGATG	60.272	52.381	14.55	0.00	38.50	3.07
2652	6517	8.683615	CCTATATGCAATGTAAATGATGATGCT	58.316	33.333	0.00	0.00	33.66	3.79
2881	6841	0.954452	CTGGAAACCACTGAACTGGC	59.046	55.000	0.00	0.00	34.20	4.85
3028	7061	5.007039	TCTCGCTGATTTCAAGTGCAATATC	59.993	40.000	0.00	0.00	0.00	1.63
3161	7243	4.338379	AAACTCAGTGAAGTACCTCCAC	57.662	45.455	0.00	0.00	0.00	4.02
3339	7943	8.691661	AAAAAGTACAGGTACATGATGAGTTT	57.308	30.769	15.54	10.76	38.48	2.66
3383	7987	4.912586	TGCTAGGTTTACAATGCCAACTA	58.087	39.130	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.