AutoCloner

Multiple sequence alignment - TraesCS6D01G086200

Loading Multiple Alignment...

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	TraesCS6D01G086200	chr6D	100.000	2693	0	0	1	2693	51625028	51622336	0.000000e+00	4974
1	TraesCS6D01G086200	chr6D	89.639	2712	256	16	1	2693	53309039	53311744	0.000000e+00	3428
2	TraesCS6D01G086200	chr6D	82.558	86	13	2	1394	1478	52007902	52007986	1.030000e-09	75
3	TraesCS6D01G086200	chr6B	93.046	2344	147	9	1	2331	118823737	118821397	0.000000e+00	3411
4	TraesCS6D01G086200	chr6B	87.490	2382	264	22	1	2360	76599530	76597161	0.000000e+00	2717
5	TraesCS6D01G086200	chr6B	86.747	1411	165	11	966	2360	76733990	76732586	0.000000e+00	1550
6	TraesCS6D01G086200	chr6B	88.248	919	98	9	1	913	76742365	76741451	0.000000e+00	1090
7	TraesCS6D01G086200	chr6B	93.640	283	17	1	2318	2600	118784783	118784502	3.210000e-114	422
8	TraesCS6D01G086200	chr6B	92.308	91	7	0	2603	2693	118672379	118672289	2.180000e-26	130
9	TraesCS6D01G086200	chr6A	88.809	2493	251	18	1	2476	62490084	62487603	0.000000e+00	3033
10	TraesCS6D01G086200	chr6A	86.959	2009	202	28	571	2558	42389528	42387559	0.000000e+00	2204
11	TraesCS6D01G086200	chr6A	86.517	2010	201	31	571	2558	42208617	42206656	0.000000e+00	2146
12	TraesCS6D01G086200	chr6A	88.889	531	53	5	1	528	42209142	42208615	0.000000e+00	649
13	TraesCS6D01G086200	chr6A	88.701	531	54	5	1	528	42390053	42389526	0.000000e+00	643
14	TraesCS6D01G086200	chr6A	86.385	426	53	3	2272	2693	62659930	62659506	6.790000e-126	460
15	TraesCS6D01G086200	chrUn	89.339	1754	166	12	823	2558	105245674	105247424	0.000000e+00	2183
16	TraesCS6D01G086200	chrUn	88.301	624	62	5	1	621	105245058	105245673	0.000000e+00	737
17	TraesCS6D01G086200	chrUn	88.312	385	40	4	1	382	345248662	345248280	8.790000e-125	457

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	TraesCS6D01G086200	chr6D	51622336	51625028	2692	True	4974.0	4974	100.000	1	2693	1	chr6D.!!$R1	2692
1	TraesCS6D01G086200	chr6D	53309039	53311744	2705	False	3428.0	3428	89.639	1	2693	1	chr6D.!!$F2	2692
2	TraesCS6D01G086200	chr6B	118821397	118823737	2340	True	3411.0	3411	93.046	1	2331	1	chr6B.!!$R6	2330
3	TraesCS6D01G086200	chr6B	76597161	76599530	2369	True	2717.0	2717	87.490	1	2360	1	chr6B.!!$R1	2359
4	TraesCS6D01G086200	chr6B	76732586	76733990	1404	True	1550.0	1550	86.747	966	2360	1	chr6B.!!$R2	1394
5	TraesCS6D01G086200	chr6B	76741451	76742365	914	True	1090.0	1090	88.248	1	913	1	chr6B.!!$R3	912
6	TraesCS6D01G086200	chr6A	62487603	62490084	2481	True	3033.0	3033	88.809	1	2476	1	chr6A.!!$R1	2475
7	TraesCS6D01G086200	chr6A	42387559	42390053	2494	True	1423.5	2204	87.830	1	2558	2	chr6A.!!$R4	2557
8	TraesCS6D01G086200	chr6A	42206656	42209142	2486	True	1397.5	2146	87.703	1	2558	2	chr6A.!!$R3	2557
9	TraesCS6D01G086200	chrUn	105245058	105247424	2366	False	1460.0	2183	88.820	1	2558	2	chrUn.!!$F1	2557

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
950	962	0.104409	AAAGGAGTGAGGTGAGGGGT	60.104	55.0	0.0	0.0	0.0	4.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1811	1839	1.040646	TGGTTGTCTCAACGAGCTCT	58.959	50.0	12.85	0.0	38.01	4.09	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
93	95	2.779742	CTTTGGGTGGCGATTGGGGA	62.780	60.000	0.00	0.00	0.00	4.81
113	115	9.928618	TTGGGGAAATACATTGAATATAACTCA	57.071	29.630	0.00	0.00	0.00	3.41
248	255	8.779303	ACTTTGAATGTGTTATCATACGTTTCA	58.221	29.630	0.00	0.00	0.00	2.69
263	271	2.643551	GTTTCATCGGGATGGTGTGAT	58.356	47.619	8.68	0.00	39.24	3.06
278	286	5.857822	GGTGTGATGTAGACCAACTAAAC	57.142	43.478	0.00	0.00	42.21	2.01
280	289	4.387862	GTGTGATGTAGACCAACTAAACGG	59.612	45.833	0.00	0.00	32.49	4.44
327	336	5.925397	TGTTAGTGGCAATGCACAATAAAAG	59.075	36.000	7.79	0.00	30.31	2.27
416	426	6.560253	AACTCTATTCAACCAACATCACAC	57.440	37.500	0.00	0.00	0.00	3.82
457	467	8.400947	ACAATTCTTTGATGTAGTATGCATGAC	58.599	33.333	10.16	5.38	43.13	3.06
471	482	5.910637	ATGCATGACACAAATTTTCACAC	57.089	34.783	0.00	0.00	0.00	3.82
519	531	2.418368	TGCCCATTACATCCACAGTC	57.582	50.000	0.00	0.00	0.00	3.51
702	714	3.255149	ACTTTGAGAAGAAGCAGCAATGG	59.745	43.478	0.00	0.00	36.69	3.16
729	741	2.238521	GCCATGTCCTTTGGAAGTTCA	58.761	47.619	5.01	0.00	36.26	3.18
733	745	5.009631	CCATGTCCTTTGGAAGTTCACATA	58.990	41.667	5.01	0.00	36.26	2.29
740	752	8.360390	GTCCTTTGGAAGTTCACATATCTTTTT	58.640	33.333	5.01	0.00	31.38	1.94
780	792	1.606668	TGACCATCCGTTCTTGCAAAC	59.393	47.619	0.00	0.00	0.00	2.93
950	962	0.104409	AAAGGAGTGAGGTGAGGGGT	60.104	55.000	0.00	0.00	0.00	4.95
1063	1076	3.171388	ACAGATCCGATGGCCCCC	61.171	66.667	0.00	0.00	0.00	5.40
1114	1127	1.086067	CAAGCGACCATGACGAGCAT	61.086	55.000	14.41	0.00	37.85	3.79
1311	1330	1.003118	CAACCTTCTTCATGTCGGGGA	59.997	52.381	0.00	0.00	0.00	4.81
1384	1403	2.477694	CGTGAACAAGAAGCAAGCACAA	60.478	45.455	0.00	0.00	0.00	3.33
1421	1440	2.281002	TTGCAGAGCAGCGCTTGA	60.281	55.556	7.50	0.00	39.88	3.02
1492	1511	2.482664	GCTGGAGAATGAGAAGATGCGA	60.483	50.000	0.00	0.00	0.00	5.10
1545	1564	1.347817	CGCAAGGAGTTCGAGCTCAC	61.348	60.000	27.43	17.66	37.24	3.51
1558	1577	2.195567	GCTCACTGTTGCCAAGCCA	61.196	57.895	0.00	0.00	0.00	4.75
1587	1606	0.394216	TAGGGTGTGTGCATGCATCC	60.394	55.000	25.64	21.41	36.17	3.51
1604	1623	3.150767	CATCCGGGTTGTTTTCCAGTAA	58.849	45.455	0.00	0.00	0.00	2.24
1811	1839	1.968493	AGAGAACCTCCGTACTTTGCA	59.032	47.619	0.00	0.00	0.00	4.08
1852	1880	3.066208	AGGAGGAGGCTTTCATGGATA	57.934	47.619	0.00	0.00	0.00	2.59
1875	1912	4.699257	AGAATCATCTCACTCTTGCCAAAC	59.301	41.667	0.00	0.00	0.00	2.93
1901	1938	2.913617	CCTTCACCCCCTTCTTTCTACT	59.086	50.000	0.00	0.00	0.00	2.57
1932	1969	6.767902	TCATTGCTTAATACCTCTCCACATTC	59.232	38.462	0.00	0.00	0.00	2.67
2064	2107	3.117398	AGCTCCTTTATCCATGGCATCAA	60.117	43.478	6.96	0.00	0.00	2.57
2125	2168	4.021016	AGTGTGGACTAGTCAAAGATCACC	60.021	45.833	23.91	13.82	0.00	4.02
2150	2193	5.308237	AGGAAGACAGAGTAAGATGTTGGTT	59.692	40.000	0.00	0.00	0.00	3.67
2159	2202	8.607459	CAGAGTAAGATGTTGGTTTATGTCATC	58.393	37.037	0.00	0.00	36.25	2.92
2211	2254	6.602179	CACACACGTCAAATTTGAGACATAT	58.398	36.000	21.05	3.86	37.98	1.78
2253	2297	9.434559	GTCTTTTGTGTTCACTATGTAGAAAAC	57.565	33.333	4.59	0.00	33.54	2.43
2269	2313	8.738199	TGTAGAAAACGTCTTTGACTAGTATG	57.262	34.615	0.00	0.00	37.84	2.39
2382	2432	7.851228	TCTTCACTACTTTGATACATCATGGT	58.149	34.615	0.00	0.00	36.56	3.55
2389	2439	4.904253	TTGATACATCATGGTACGTCGA	57.096	40.909	0.00	0.00	36.56	4.20
2418	2468	3.965347	TCTTGTACCTATTAGCCCCTCAC	59.035	47.826	0.00	0.00	0.00	3.51
2419	2469	2.313317	TGTACCTATTAGCCCCTCACG	58.687	52.381	0.00	0.00	0.00	4.35
2445	2495	1.689984	TGCACATGTGAGGCTTGAAA	58.310	45.000	29.80	0.00	0.00	2.69
2586	2640	0.322906	GGCAAGGAGCTAGTTGGCTT	60.323	55.000	20.84	0.00	43.87	4.35
2597	2652	2.191128	AGTTGGCTTCCATGTGAGTC	57.809	50.000	0.00	0.00	31.53	3.36
2600	2655	1.059098	TGGCTTCCATGTGAGTCACT	58.941	50.000	23.29	7.08	35.11	3.41
2603	2658	2.355513	GGCTTCCATGTGAGTCACTGAT	60.356	50.000	23.29	7.51	35.11	2.90
2605	2660	3.868077	GCTTCCATGTGAGTCACTGATAC	59.132	47.826	23.29	9.09	35.11	2.24
2611	2666	5.702670	CCATGTGAGTCACTGATACAAACTT	59.297	40.000	23.29	0.00	35.11	2.66
2617	2672	9.813080	GTGAGTCACTGATACAAACTTTTATTC	57.187	33.333	16.26	0.00	0.00	1.75
2631	2686	9.530129	CAAACTTTTATTCGTACTTCATCTGTC	57.470	33.333	0.00	0.00	0.00	3.51
2636	2691	3.850122	TCGTACTTCATCTGTCACCAG	57.150	47.619	0.00	0.00	40.25	4.00
2655	2710	8.017946	GTCACCAGAAGACAATAAATGTTTCTC	58.982	37.037	0.00	0.00	44.12	2.87
2663	2718	9.442047	AAGACAATAAATGTTTCTCTAGACAGG	57.558	33.333	0.00	0.00	44.12	4.00
2674	2729	5.745312	TCTCTAGACAGGAAAATGCAAGA	57.255	39.130	0.00	0.00	0.00	3.02
2677	2732	3.863142	AGACAGGAAAATGCAAGATGC	57.137	42.857	0.00	0.00	45.29	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	5.594317	ACACTTTCTAACACCAGCAGAAAAT	59.406	36.000	0.00	0.00	37.72	1.82
10	11	4.900635	AAACACTTTCTAACACCAGCAG	57.099	40.909	0.00	0.00	0.00	4.24
154	159	4.586841	TCAACCGGATTGGAACTTGATTTT	59.413	37.500	9.46	0.00	42.00	1.82
160	167	6.887545	TGTAATAATCAACCGGATTGGAACTT	59.112	34.615	9.46	4.99	45.70	2.66
248	255	2.365617	GTCTACATCACACCATCCCGAT	59.634	50.000	0.00	0.00	0.00	4.18
263	271	2.607499	TCCCCGTTTAGTTGGTCTACA	58.393	47.619	0.00	0.00	0.00	2.74
278	286	6.490721	ACTGATATCTTACTCTAACTTCCCCG	59.509	42.308	3.98	0.00	0.00	5.73
280	289	8.240267	ACACTGATATCTTACTCTAACTTCCC	57.760	38.462	3.98	0.00	0.00	3.97
371	381	6.883217	AGTTTCTACATCATGAGCACAAGAAT	59.117	34.615	0.09	0.00	0.00	2.40
457	467	6.250089	GCAAAAAGGAGTGTGAAAATTTGTG	58.750	36.000	0.00	0.00	0.00	3.33
471	482	1.681264	ACTCAAACCGGCAAAAAGGAG	59.319	47.619	0.00	1.64	0.00	3.69
702	714	2.078392	CCAAAGGACATGGCAAATTGC	58.922	47.619	9.87	9.87	44.08	3.56
733	745	8.596293	TGGAGGATTCAAAGCAATTAAAAAGAT	58.404	29.630	0.00	0.00	0.00	2.40
740	752	5.360714	GGTCATGGAGGATTCAAAGCAATTA	59.639	40.000	0.00	0.00	0.00	1.40
780	792	4.373156	TTTCCCTTCTCCTTCTCTTTGG	57.627	45.455	0.00	0.00	0.00	3.28
950	962	4.414182	CAGTTAAATAGATGGGGGTGGGTA	59.586	45.833	0.00	0.00	0.00	3.69
1000	1013	2.603075	TTGAGGTTGCAAGGGCTAAT	57.397	45.000	0.00	0.00	41.91	1.73
1073	1086	2.001361	GCAGAGCGCTTGATGCCAAT	62.001	55.000	24.47	0.00	38.78	3.16
1114	1127	1.591703	CTTGCACCAGACGCTAGGA	59.408	57.895	0.00	0.00	0.00	2.94
1290	1309	0.804989	CCCGACATGAAGAAGGTTGC	59.195	55.000	0.00	0.00	0.00	4.17
1384	1403	3.396685	AGCTCCAGTATCTTGTCCTCT	57.603	47.619	0.00	0.00	0.00	3.69
1421	1440	1.531602	GCTCCTTTGTGGCCCAGTT	60.532	57.895	0.00	0.00	35.26	3.16
1492	1511	0.904865	TGAGCCGGATGTTCTCCAGT	60.905	55.000	5.05	0.00	45.24	4.00
1545	1564	1.138661	TCCTTTTTGGCTTGGCAACAG	59.861	47.619	9.13	8.33	41.97	3.16
1558	1577	3.181434	TGCACACACCCTAGATCCTTTTT	60.181	43.478	0.00	0.00	0.00	1.94
1587	1606	2.031157	CAGCTTACTGGAAAACAACCCG	60.031	50.000	0.00	0.00	40.48	5.28
1604	1623	1.211456	CTCCCCTCTGATTTCCAGCT	58.789	55.000	0.00	0.00	42.62	4.24
1617	1636	3.245407	CCTCCTTTTGTTTCATCTCCCCT	60.245	47.826	0.00	0.00	0.00	4.79
1811	1839	1.040646	TGGTTGTCTCAACGAGCTCT	58.959	50.000	12.85	0.00	38.01	4.09
1852	1880	4.564782	TTGGCAAGAGTGAGATGATTCT	57.435	40.909	0.00	0.00	33.88	2.40
1875	1912	1.076727	GAAGGGGGTGAAGGTTGGG	59.923	63.158	0.00	0.00	0.00	4.12
1901	1938	6.238953	GGAGAGGTATTAAGCAATGACTACGA	60.239	42.308	0.00	0.00	0.00	3.43
1932	1969	4.101585	TGCCTCATCTTAGTATGGTCAAGG	59.898	45.833	0.00	0.00	0.00	3.61
2064	2107	2.229792	ACATGACACATTCAACGCCTT	58.770	42.857	0.00	0.00	37.92	4.35
2125	2168	5.174395	CCAACATCTTACTCTGTCTTCCTG	58.826	45.833	0.00	0.00	0.00	3.86
2150	2193	4.934602	TGCATCACGACAAAGATGACATAA	59.065	37.500	6.60	0.00	43.28	1.90
2159	2202	2.226200	TGGATTGTGCATCACGACAAAG	59.774	45.455	0.00	0.00	37.14	2.77
2211	2254	6.641723	CACAAAAGACAAATATGATGCACACA	59.358	34.615	0.00	0.00	0.00	3.72
2361	2411	6.978659	ACGTACCATGATGTATCAAAGTAGTG	59.021	38.462	0.00	3.21	40.69	2.74
2382	2432	5.957798	AGGTACAAGAATGAAATCGACGTA	58.042	37.500	0.00	0.00	0.00	3.57
2389	2439	7.004691	GGGGCTAATAGGTACAAGAATGAAAT	58.995	38.462	0.00	0.00	0.00	2.17
2445	2495	6.551227	GGGGTTCTTTCTTATTGCATAGGAAT	59.449	38.462	0.00	0.00	31.98	3.01
2586	2640	5.012046	AGTTTGTATCAGTGACTCACATGGA	59.988	40.000	11.80	6.35	36.74	3.41
2605	2660	9.530129	GACAGATGAAGTACGAATAAAAGTTTG	57.470	33.333	0.00	0.00	0.00	2.93
2611	2666	6.693466	TGGTGACAGATGAAGTACGAATAAA	58.307	36.000	0.00	0.00	35.01	1.40
2631	2686	8.103948	AGAGAAACATTTATTGTCTTCTGGTG	57.896	34.615	8.32	0.00	37.68	4.17
2655	2710	4.918037	GCATCTTGCATTTTCCTGTCTAG	58.082	43.478	0.00	0.00	44.26	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.