AutoCloner

Multiple sequence alignment - TraesCS5B01G361400

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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	TraesCS5B01G361400	chr5B	100.000	2597	0	0	1	2597	541109000	541111596	0.000000e+00	4796
1	TraesCS5B01G361400	chr5B	90.995	2632	171	23	1	2597	134553016	134550416	0.000000e+00	3487
2	TraesCS5B01G361400	chr5B	89.594	2614	208	27	1	2597	194199775	194197209	0.000000e+00	3262
3	TraesCS5B01G361400	chr5B	88.876	2643	234	32	1	2597	180053208	180055836	0.000000e+00	3197
4	TraesCS5B01G361400	chr5B	84.582	467	60	10	2136	2597	400988026	400987567	1.100000e-123	453
5	TraesCS5B01G361400	chr2B	92.563	2622	162	15	1	2597	675965690	675963077	0.000000e+00	3731
6	TraesCS5B01G361400	chr3B	91.524	2631	167	33	1	2597	543859818	543857210	0.000000e+00	3572
7	TraesCS5B01G361400	chr7B	91.223	2632	185	23	1	2597	16169342	16166722	0.000000e+00	3539
8	TraesCS5B01G361400	chr7B	91.337	2551	180	23	78	2597	655033402	655030862	0.000000e+00	3448
9	TraesCS5B01G361400	chr7B	90.530	2376	201	17	1	2370	330999775	330997418	0.000000e+00	3120
10	TraesCS5B01G361400	chr7B	86.265	415	47	7	2186	2597	330997461	330997054	2.370000e-120	442
11	TraesCS5B01G361400	chr1B	90.684	2630	198	29	1	2595	547568707	547566090	0.000000e+00	3456
12	TraesCS5B01G361400	chr6B	90.674	2627	201	25	1	2597	169048046	169050658	0.000000e+00	3454
13	TraesCS5B01G361400	chr6B	90.498	2610	223	21	1	2597	698944610	698942013	0.000000e+00	3422
14	TraesCS5B01G361400	chr6B	84.222	450	61	9	2151	2596	571749872	571749429	1.850000e-116	429
15	TraesCS5B01G361400	chr4B	85.545	422	51	9	2182	2597	552007280	552007697	1.430000e-117	433

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	TraesCS5B01G361400	chr5B	541109000	541111596	2596	False	4796	4796	100.0000	1	2597	1	chr5B.!!$F2	2596
1	TraesCS5B01G361400	chr5B	134550416	134553016	2600	True	3487	3487	90.9950	1	2597	1	chr5B.!!$R1	2596
2	TraesCS5B01G361400	chr5B	194197209	194199775	2566	True	3262	3262	89.5940	1	2597	1	chr5B.!!$R2	2596
3	TraesCS5B01G361400	chr5B	180053208	180055836	2628	False	3197	3197	88.8760	1	2597	1	chr5B.!!$F1	2596
4	TraesCS5B01G361400	chr2B	675963077	675965690	2613	True	3731	3731	92.5630	1	2597	1	chr2B.!!$R1	2596
5	TraesCS5B01G361400	chr3B	543857210	543859818	2608	True	3572	3572	91.5240	1	2597	1	chr3B.!!$R1	2596
6	TraesCS5B01G361400	chr7B	16166722	16169342	2620	True	3539	3539	91.2230	1	2597	1	chr7B.!!$R1	2596
7	TraesCS5B01G361400	chr7B	655030862	655033402	2540	True	3448	3448	91.3370	78	2597	1	chr7B.!!$R2	2519
8	TraesCS5B01G361400	chr7B	330997054	330999775	2721	True	1781	3120	88.3975	1	2597	2	chr7B.!!$R3	2596
9	TraesCS5B01G361400	chr1B	547566090	547568707	2617	True	3456	3456	90.6840	1	2595	1	chr1B.!!$R1	2594
10	TraesCS5B01G361400	chr6B	169048046	169050658	2612	False	3454	3454	90.6740	1	2597	1	chr6B.!!$F1	2596
11	TraesCS5B01G361400	chr6B	698942013	698944610	2597	True	3422	3422	90.4980	1	2597	1	chr6B.!!$R2	2596

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
495	504	0.599204	GAGTTCGTGAGGCCAAACGA	60.599	55.0	24.13	24.13	46.33	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2019	2090	0.320334	TGCATCGACCGCAGAAAAGA	60.32	50.0	7.24	0.0	33.55	2.52	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
97	98	2.263895	TACCATTAGGAGTGCCACCT	57.736	50.000	0.00	0.00	41.05	4.00
156	157	2.882876	GCGGAAGACTACGAGCCA	59.117	61.111	3.89	0.00	0.00	4.75
162	163	1.133407	GAAGACTACGAGCCAGAGGTG	59.867	57.143	0.00	0.00	0.00	4.00
189	190	1.133668	ACAAAGGAGCAGAACCAGCTT	60.134	47.619	0.00	0.00	43.58	3.74
201	202	4.024048	CAGAACCAGCTTTACGACATTGTT	60.024	41.667	0.00	0.00	0.00	2.83
203	204	5.408604	AGAACCAGCTTTACGACATTGTTAG	59.591	40.000	0.00	0.00	0.00	2.34
293	295	7.177216	ACCACATAATCTCTCATTTTGCTTTGA	59.823	33.333	0.00	0.00	0.00	2.69
466	475	3.044059	GACGTACGTCGACCTGGGG	62.044	68.421	30.48	0.00	42.86	4.96
480	489	1.915078	CTGGGGGATCTTGCCGAGTT	61.915	60.000	0.00	0.00	0.00	3.01
495	504	0.599204	GAGTTCGTGAGGCCAAACGA	60.599	55.000	24.13	24.13	46.33	3.85
560	569	7.722728	ACATCAACAAGCATATGGATATGTCTT	59.277	33.333	4.56	8.63	41.63	3.01
631	640	3.253432	GTGACTTCCACCACAAAATCCTC	59.747	47.826	0.00	0.00	39.86	3.71
667	676	2.948979	TCAACACGGTGAATTCAAGCTT	59.051	40.909	16.29	0.00	0.00	3.74
673	682	4.024048	CACGGTGAATTCAAGCTTACACTT	60.024	41.667	10.35	0.00	0.00	3.16
699	708	7.496346	AGAAATATGTGAGTACTCCTTCCAA	57.504	36.000	20.11	0.00	0.00	3.53
707	716	3.744660	AGTACTCCTTCCAAGTTTGCAG	58.255	45.455	0.00	0.00	0.00	4.41
736	749	2.825532	ACATGGTATGGTTTTCTGCCAC	59.174	45.455	0.00	0.00	39.03	5.01
814	830	9.255304	GTAAACTAACTTTTTGATTTGCATCCA	57.745	29.630	0.00	0.00	0.00	3.41
852	868	6.038382	TGGCAACTTCAAAGTAAAATACACGA	59.962	34.615	0.00	0.00	38.57	4.35
863	879	8.609478	AAGTAAAATACACGACAACTTTTGTG	57.391	30.769	0.00	0.00	45.52	3.33
1113	1134	4.563061	GCTTTGAGGTGCTTGATTCAATT	58.437	39.130	0.00	0.00	30.45	2.32
1121	1142	2.811431	TGCTTGATTCAATTCGTTCGGT	59.189	40.909	0.00	0.00	0.00	4.69
1146	1167	2.194271	GATGCAGACCTTACTACGCAC	58.806	52.381	0.00	0.00	31.22	5.34
1245	1266	1.138047	CGATTGAGTACGTGGCGACC	61.138	60.000	0.00	0.00	0.00	4.79
1377	1403	1.001378	CCTTTTTGCGAGTTCACCTGG	60.001	52.381	0.00	0.00	0.00	4.45
1386	1413	3.792124	GCGAGTTCACCTGGTTCTTTTTG	60.792	47.826	0.00	0.00	0.00	2.44
1391	1418	5.712917	AGTTCACCTGGTTCTTTTTGTTGTA	59.287	36.000	0.00	0.00	0.00	2.41
1414	1441	0.249911	GACGGACTGTGGCTTTCACT	60.250	55.000	0.00	0.00	46.20	3.41
1425	1452	5.263599	TGTGGCTTTCACTCATTGGAATAT	58.736	37.500	0.00	0.00	46.20	1.28
1477	1504	1.887242	GTCACAGCTGCAACGGTCA	60.887	57.895	15.27	0.00	0.00	4.02
1534	1561	6.618287	TGACGAATGAAGATTTCAACAAGT	57.382	33.333	0.00	0.00	43.95	3.16
1563	1590	2.490217	CGCGAGTTCGTGGAGGAT	59.510	61.111	0.00	0.00	45.14	3.24
1670	1706	6.947376	ATGTAAGGTACTACCCTTGTTCTT	57.053	37.500	1.19	0.00	44.57	2.52
1714	1753	0.322098	TGTTATGACTGCAACCCCGG	60.322	55.000	0.00	0.00	0.00	5.73
1792	1848	4.647424	TTGTGTGGATGTGAACCTTTTC	57.353	40.909	0.00	0.00	0.00	2.29
1878	1935	1.001378	GGTTGCTGCTTCGAATGTGTT	60.001	47.619	0.00	0.00	0.00	3.32
2018	2089	7.149973	TGGTAGTTTTGATCATATAGCCGTAC	58.850	38.462	0.00	0.00	0.00	3.67
2019	2090	7.014905	TGGTAGTTTTGATCATATAGCCGTACT	59.985	37.037	0.00	0.00	0.00	2.73
2047	2120	1.640428	CGGTCGATGCACATTACACT	58.360	50.000	0.00	0.00	0.00	3.55
2138	2212	6.863275	TCATGGAAATATACGCGATGTAGAT	58.137	36.000	15.93	0.00	36.56	1.98
2176	2251	4.905429	TGGCATTTCTCAGTACAGCTAAA	58.095	39.130	0.00	0.00	0.00	1.85
2177	2252	4.695455	TGGCATTTCTCAGTACAGCTAAAC	59.305	41.667	0.00	0.00	0.00	2.01
2178	2253	4.695455	GGCATTTCTCAGTACAGCTAAACA	59.305	41.667	0.00	0.00	0.00	2.83
2179	2254	5.390991	GGCATTTCTCAGTACAGCTAAACAC	60.391	44.000	0.00	0.00	0.00	3.32
2180	2255	5.179368	GCATTTCTCAGTACAGCTAAACACA	59.821	40.000	0.00	0.00	0.00	3.72
2181	2256	6.293407	GCATTTCTCAGTACAGCTAAACACAA	60.293	38.462	0.00	0.00	0.00	3.33
2184	2259	5.666462	TCTCAGTACAGCTAAACACAACAA	58.334	37.500	0.00	0.00	0.00	2.83
2216	2291	2.408050	AGAACACGACAGATTCAGCAC	58.592	47.619	0.00	0.00	0.00	4.40
2260	2335	2.089980	ACTTGACATGGCAGATTGAGC	58.910	47.619	0.00	0.00	0.00	4.26
2293	2391	4.993028	TGGCAGACCCAATATATTTACCC	58.007	43.478	0.00	0.00	41.82	3.69
2387	2691	6.247229	ACATGGTAACTGCAGTTATCCATA	57.753	37.500	38.61	27.79	42.93	2.74
2502	2811	1.003355	AAGGACCATGTCACAGCGG	60.003	57.895	0.00	0.00	33.68	5.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
156	157	0.111253	CCTTTGTGGCCTTCACCTCT	59.889	55.000	3.32	0.00	45.48	3.69
162	163	0.250901	TCTGCTCCTTTGTGGCCTTC	60.251	55.000	3.32	0.00	35.26	3.46
189	190	4.319622	CCAAAACGCCTAACAATGTCGTAA	60.320	41.667	0.00	0.00	32.71	3.18
201	202	1.466950	CTCGCATTTCCAAAACGCCTA	59.533	47.619	0.00	0.00	0.00	3.93
203	204	0.732538	CCTCGCATTTCCAAAACGCC	60.733	55.000	0.00	0.00	0.00	5.68
230	231	1.072806	TCAGCTCCTTCATGTGCTTGT	59.927	47.619	0.00	0.00	33.03	3.16
402	411	5.675684	TCTGTCCAAACATGAGCTGTATA	57.324	39.130	0.00	0.00	36.98	1.47
466	475	0.108804	TCACGAACTCGGCAAGATCC	60.109	55.000	3.88	0.00	44.95	3.36
495	504	6.091577	TGCAACTACATTCGTCGACATTTTAT	59.908	34.615	17.16	0.00	0.00	1.40
560	569	4.517952	AATGCATGATTGTTTTGTCGGA	57.482	36.364	0.00	0.00	0.00	4.55
631	640	3.976942	CGTGTTGAGCAAAATTCTTCCTG	59.023	43.478	0.00	0.00	0.00	3.86
673	682	8.603898	TGGAAGGAGTACTCACATATTTCTTA	57.396	34.615	23.91	8.28	0.00	2.10
730	742	1.206610	ACAGAGTGCAGATAGTGGCAG	59.793	52.381	0.00	0.00	41.35	4.85
736	749	4.272018	GCCACATAAACAGAGTGCAGATAG	59.728	45.833	0.00	0.00	32.09	2.08
814	830	2.586425	AGTTGCCACATAGTTTGCACT	58.414	42.857	0.00	0.00	36.99	4.40
852	868	5.472148	CATCCATGTATGCACAAAAGTTGT	58.528	37.500	0.00	0.00	46.75	3.32
863	879	3.806625	AAAGTTGCCATCCATGTATGC	57.193	42.857	0.00	0.00	0.00	3.14
1113	1134	1.542472	TCTGCATCAACTACCGAACGA	59.458	47.619	0.00	0.00	0.00	3.85
1121	1142	4.439700	GCGTAGTAAGGTCTGCATCAACTA	60.440	45.833	0.00	0.00	0.00	2.24
1245	1266	1.508632	ACGTGTTCCCTTGATTCGTG	58.491	50.000	0.00	0.00	0.00	4.35
1377	1403	4.333372	TCCGTCCTGTACAACAAAAAGAAC	59.667	41.667	0.00	0.00	0.00	3.01
1386	1413	1.604693	CCACAGTCCGTCCTGTACAAC	60.605	57.143	0.00	0.00	43.70	3.32
1391	1418	1.696097	AAAGCCACAGTCCGTCCTGT	61.696	55.000	0.00	0.00	46.40	4.00
1414	1441	6.013898	TCCCACTTTGCAAAATATTCCAATGA	60.014	34.615	13.84	0.00	0.00	2.57
1425	1452	3.634910	GTCTACCTTCCCACTTTGCAAAA	59.365	43.478	13.84	0.00	0.00	2.44
1477	1504	4.764823	TGTGTAAATTTTCCGGAGCTCAAT	59.235	37.500	17.19	3.06	0.00	2.57
1563	1590	4.707105	TCTTGATGACTTTCTTGACAGCA	58.293	39.130	0.00	0.00	0.00	4.41
1670	1706	3.496884	GCACACGGACATAGTTTTTGAGA	59.503	43.478	0.00	0.00	0.00	3.27
1714	1753	2.040178	ACCACTGCATACTAGGCTACC	58.960	52.381	0.00	0.00	0.00	3.18
1792	1848	1.400846	ACGTATCTACTGTCACGCCTG	59.599	52.381	0.00	0.00	37.92	4.85
1833	1890	2.030363	TGGTGCAAACGATGAAACCATC	60.030	45.455	13.00	0.00	40.44	3.51
2009	2080	2.481449	CCGCAGAAAAGAGTACGGCTAT	60.481	50.000	0.00	0.00	33.46	2.97
2018	2089	0.371645	GCATCGACCGCAGAAAAGAG	59.628	55.000	3.85	0.00	0.00	2.85
2019	2090	0.320334	TGCATCGACCGCAGAAAAGA	60.320	50.000	7.24	0.00	33.55	2.52
2145	2219	7.761409	TGTACTGAGAAATGCCATGTTATTTC	58.239	34.615	17.57	17.57	41.38	2.17
2162	2237	5.984233	TTGTTGTGTTTAGCTGTACTGAG	57.016	39.130	3.61	0.00	0.00	3.35
2176	2251	7.540745	GTGTTCTTTGTACTGAATTTGTTGTGT	59.459	33.333	0.00	0.00	0.00	3.72
2177	2252	7.253288	CGTGTTCTTTGTACTGAATTTGTTGTG	60.253	37.037	0.00	0.00	0.00	3.33
2178	2253	6.745450	CGTGTTCTTTGTACTGAATTTGTTGT	59.255	34.615	0.00	0.00	0.00	3.32
2179	2254	6.964370	TCGTGTTCTTTGTACTGAATTTGTTG	59.036	34.615	0.00	0.00	0.00	3.33
2180	2255	6.964934	GTCGTGTTCTTTGTACTGAATTTGTT	59.035	34.615	0.00	0.00	0.00	2.83
2181	2256	6.092944	TGTCGTGTTCTTTGTACTGAATTTGT	59.907	34.615	0.00	0.00	0.00	2.83
2184	2259	6.046593	TCTGTCGTGTTCTTTGTACTGAATT	58.953	36.000	0.00	0.00	0.00	2.17
2260	2335	5.850557	TTGGGTCTGCCATGTTAATTATG	57.149	39.130	0.00	0.00	36.17	1.90
2387	2691	9.793259	TCAGAAGTAGAAGGAAAAATACATTGT	57.207	29.630	0.00	0.00	0.00	2.71
2502	2811	2.929398	CAATCCGTAAGCAAAATTGGGC	59.071	45.455	0.00	0.00	0.00	5.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.