AutoCloner

Multiple sequence alignment - TraesCS7B01G176000

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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	TraesCS7B01G176000	chr7B	100.000	2732	0	0	1	2732	247460923	247463654	0.000000e+00	5046
1	TraesCS7B01G176000	chr7B	96.246	2744	91	3	1	2732	743005939	743008682	0.000000e+00	4486
2	TraesCS7B01G176000	chrUn	96.392	2744	87	4	1	2732	186191539	186188796	0.000000e+00	4508
3	TraesCS7B01G176000	chr7A	96.060	2741	98	3	1	2732	120880326	120883065	0.000000e+00	4455
4	TraesCS7B01G176000	chr7D	95.993	2745	90	8	1	2732	579029615	579032352	0.000000e+00	4442
5	TraesCS7B01G176000	chr4B	95.792	2733	101	5	12	2732	209271422	209268692	0.000000e+00	4397
6	TraesCS7B01G176000	chr1D	95.441	2742	97	11	1	2732	212467973	212465250	0.000000e+00	4346
7	TraesCS7B01G176000	chr1D	95.368	1986	79	4	756	2732	269438072	269436091	0.000000e+00	3145
8	TraesCS7B01G176000	chr1D	93.304	224	7	1	2517	2732	275769283	275769506	9.440000e-85	324
9	TraesCS7B01G176000	chr6D	95.295	2742	118	4	1	2732	369918130	369915390	0.000000e+00	4338
10	TraesCS7B01G176000	chr6D	95.432	2671	109	5	73	2732	283154172	283151504	0.000000e+00	4244
11	TraesCS7B01G176000	chr6A	94.825	2744	126	7	1	2732	79143554	79146293	0.000000e+00	4266
12	TraesCS7B01G176000	chr6A	94.412	680	30	1	2061	2732	375819080	375818401	0.000000e+00	1038
13	TraesCS7B01G176000	chr2B	92.566	2744	186	7	1	2732	343522134	343524871	0.000000e+00	3921
14	TraesCS7B01G176000	chr5D	93.963	1524	82	3	1217	2732	79789550	79788029	0.000000e+00	2296
15	TraesCS7B01G176000	chr4D	95.019	803	32	1	1938	2732	123554355	123555157	0.000000e+00	1254
16	TraesCS7B01G176000	chr4D	94.645	803	35	1	1938	2732	123339904	123340706	0.000000e+00	1238

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	TraesCS7B01G176000	chr7B	247460923	247463654	2731	False	5046	5046	100.000	1	2732	1	chr7B.!!$F1	2731
1	TraesCS7B01G176000	chr7B	743005939	743008682	2743	False	4486	4486	96.246	1	2732	1	chr7B.!!$F2	2731
2	TraesCS7B01G176000	chrUn	186188796	186191539	2743	True	4508	4508	96.392	1	2732	1	chrUn.!!$R1	2731
3	TraesCS7B01G176000	chr7A	120880326	120883065	2739	False	4455	4455	96.060	1	2732	1	chr7A.!!$F1	2731
4	TraesCS7B01G176000	chr7D	579029615	579032352	2737	False	4442	4442	95.993	1	2732	1	chr7D.!!$F1	2731
5	TraesCS7B01G176000	chr4B	209268692	209271422	2730	True	4397	4397	95.792	12	2732	1	chr4B.!!$R1	2720
6	TraesCS7B01G176000	chr1D	212465250	212467973	2723	True	4346	4346	95.441	1	2732	1	chr1D.!!$R1	2731
7	TraesCS7B01G176000	chr1D	269436091	269438072	1981	True	3145	3145	95.368	756	2732	1	chr1D.!!$R2	1976
8	TraesCS7B01G176000	chr6D	369915390	369918130	2740	True	4338	4338	95.295	1	2732	1	chr6D.!!$R2	2731
9	TraesCS7B01G176000	chr6D	283151504	283154172	2668	True	4244	4244	95.432	73	2732	1	chr6D.!!$R1	2659
10	TraesCS7B01G176000	chr6A	79143554	79146293	2739	False	4266	4266	94.825	1	2732	1	chr6A.!!$F1	2731
11	TraesCS7B01G176000	chr6A	375818401	375819080	679	True	1038	1038	94.412	2061	2732	1	chr6A.!!$R1	671
12	TraesCS7B01G176000	chr2B	343522134	343524871	2737	False	3921	3921	92.566	1	2732	1	chr2B.!!$F1	2731
13	TraesCS7B01G176000	chr5D	79788029	79789550	1521	True	2296	2296	93.963	1217	2732	1	chr5D.!!$R1	1515
14	TraesCS7B01G176000	chr4D	123554355	123555157	802	False	1254	1254	95.019	1938	2732	1	chr4D.!!$F2	794
15	TraesCS7B01G176000	chr4D	123339904	123340706	802	False	1238	1238	94.645	1938	2732	1	chr4D.!!$F1	794

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
303	304	0.528017	TCGAAAGAGCTGAGCACGAT	59.472	50.0	7.39	0.0	34.84	3.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2253	2278	1.007038	CGAACGAAGGACCCGTCAA	60.007	57.895	0.0	0.0	39.57	3.18	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
101	102	1.670811	GGACCATATTCACGCAACTGG	59.329	52.381	0.00	0.00	0.00	4.00
110	111	2.571212	TCACGCAACTGGTTCTTTCAT	58.429	42.857	0.00	0.00	0.00	2.57
136	137	5.344743	TCTCCAAGCGTCTTATCAAGATT	57.655	39.130	0.00	0.00	40.18	2.40
139	140	5.245531	TCCAAGCGTCTTATCAAGATTTGT	58.754	37.500	0.00	0.00	40.18	2.83
178	179	8.083828	AGGATCTGTTTTCTTTAGAGATGCTA	57.916	34.615	0.00	0.00	39.30	3.49
249	250	3.812167	GCTTGGAAGTGGAACAGAGGATT	60.812	47.826	0.00	0.00	41.80	3.01
278	279	1.995542	AGAAATCCCCAAGAGCAAGGA	59.004	47.619	0.00	0.00	0.00	3.36
303	304	0.528017	TCGAAAGAGCTGAGCACGAT	59.472	50.000	7.39	0.00	34.84	3.73
316	317	0.654683	GCACGATCATGCTCTTGACC	59.345	55.000	6.50	0.00	42.62	4.02
326	327	5.376625	TCATGCTCTTGACCTGTTTAAGTT	58.623	37.500	0.00	0.00	0.00	2.66
520	540	2.753452	TGGCTCTTCTCTACTAACCACG	59.247	50.000	0.00	0.00	0.00	4.94
550	570	6.874278	TTGGGACTCTCTATTTCATCTTCA	57.126	37.500	0.00	0.00	0.00	3.02
596	616	3.195610	ACATGCTTCTCCGTACTGATTCA	59.804	43.478	0.00	0.00	0.00	2.57
618	638	2.738938	GGAATTAGCCCGACCCGGT	61.739	63.158	0.00	0.00	46.80	5.28
844	864	6.071051	GCTCCTATTAAGCTCAGCCTTAGTAT	60.071	42.308	0.00	0.00	36.80	2.12
1098	1118	1.855295	TATCACTTCCGGTACTGGCA	58.145	50.000	16.58	4.05	0.00	4.92
1122	1142	7.632680	GCAGGGGCAATTACAATGTTATTAACT	60.633	37.037	7.99	0.00	40.72	2.24
1213	1234	2.178912	TTGGTTCTTCGGTCATCCAC	57.821	50.000	0.00	0.00	0.00	4.02
1215	1236	1.628340	TGGTTCTTCGGTCATCCACAT	59.372	47.619	0.00	0.00	0.00	3.21
1381	1402	4.634012	ATGTTTACTGTGGGCTTAGACA	57.366	40.909	0.00	0.00	0.00	3.41
1388	1409	5.636903	ACTGTGGGCTTAGACATTGATAT	57.363	39.130	0.00	0.00	0.00	1.63
1424	1445	2.232208	CCGCAGCTACCATGATCATAGA	59.768	50.000	8.15	0.00	0.00	1.98
1591	1612	3.070159	TGGGCTAGACATTGCTCTACATC	59.930	47.826	0.00	0.00	0.00	3.06
1730	1751	8.432805	TGAAACTTTAGGCCAAATCCATTTTTA	58.567	29.630	5.01	0.00	0.00	1.52
1798	1820	1.377987	GGCTTTCGGGTATGCCACA	60.378	57.895	1.04	0.00	44.34	4.17
1809	1831	4.412075	TGCCACATCGCATTCCAA	57.588	50.000	0.00	0.00	32.62	3.53
1944	1966	5.759763	GGAAAGAACCAAAAATGTGCAGAAT	59.240	36.000	0.00	0.00	0.00	2.40
1953	1975	2.592102	ATGTGCAGAATGTCCTTGGT	57.408	45.000	0.00	0.00	39.31	3.67
1979	2001	6.068010	TGTTGAACAGAATCCAACCATACTT	58.932	36.000	0.00	0.00	39.36	2.24
2020	2042	1.816224	TCCGGCCTTTCATACTTTTGC	59.184	47.619	0.00	0.00	0.00	3.68
2172	2197	5.893824	CCCACAGATTAGGAAGGCTTTTATT	59.106	40.000	0.00	0.00	0.00	1.40
2222	2247	4.620086	TCCTTCTTGGTGGAGATAGGTA	57.380	45.455	0.00	0.00	37.07	3.08
2253	2278	3.640029	TCCAACCTAAGTCAGTTCGAACT	59.360	43.478	24.93	24.93	40.60	3.01
2263	2288	0.033090	AGTTCGAACTTGACGGGTCC	59.967	55.000	24.93	0.00	35.21	4.46
2349	2376	3.973973	TCATATGTCGAAGAAGGGGGAAT	59.026	43.478	1.90	0.00	39.69	3.01
2413	2441	4.263771	ACCGTCATTTAAGGACCAAGGATT	60.264	41.667	8.64	0.00	31.55	3.01
2428	2456	0.579156	GGATTCGATGTGAGAAGCGC	59.421	55.000	0.00	0.00	35.11	5.92
2434	2462	0.390340	GATGTGAGAAGCGCAGGTCA	60.390	55.000	11.47	5.75	40.93	4.02
2445	2473	1.519719	GCAGGTCAGAGTAGCAGGG	59.480	63.158	0.00	0.00	0.00	4.45
2507	2535	7.870954	TGTAACGAGATGAATTAGAACACTTGT	59.129	33.333	0.00	0.00	0.00	3.16
2639	2667	2.576191	AGTTAGCCAAGTTATCCTGCCA	59.424	45.455	0.00	0.00	0.00	4.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
101	102	4.222114	CGCTTGGAGAACAATGAAAGAAC	58.778	43.478	0.00	0.00	38.65	3.01
110	111	4.265904	TGATAAGACGCTTGGAGAACAA	57.734	40.909	2.86	0.00	37.55	2.83
136	137	1.203428	TCCTCCCTCATTCTCCCACAA	60.203	52.381	0.00	0.00	0.00	3.33
139	140	1.582624	AGATCCTCCCTCATTCTCCCA	59.417	52.381	0.00	0.00	0.00	4.37
229	230	3.557054	CGAATCCTCTGTTCCACTTCCAA	60.557	47.826	0.00	0.00	0.00	3.53
278	279	2.036475	TGCTCAGCTCTTTCGAGACTTT	59.964	45.455	0.00	0.00	39.74	2.66
303	304	4.973168	ACTTAAACAGGTCAAGAGCATGA	58.027	39.130	0.00	0.00	0.00	3.07
316	317	9.810545	CCTTCTAAGATCCTCTAACTTAAACAG	57.189	37.037	0.00	0.00	0.00	3.16
326	327	9.953429	TTTCTAATTCCCTTCTAAGATCCTCTA	57.047	33.333	0.00	0.00	0.00	2.43
359	379	3.719871	TCAGAATTACAGAGCTACCCCA	58.280	45.455	0.00	0.00	0.00	4.96
370	390	9.224267	CTGGAAGAGAAAAGAATCAGAATTACA	57.776	33.333	0.00	0.00	34.07	2.41
414	434	3.435275	GGGGCTGGAAGAGAAAAGAAAT	58.565	45.455	0.00	0.00	34.07	2.17
520	540	7.546250	TGAAATAGAGAGTCCCAATATCCTC	57.454	40.000	0.00	0.00	0.00	3.71
596	616	1.278127	CGGGTCGGGCTAATTCCATAT	59.722	52.381	0.00	0.00	0.00	1.78
618	638	5.331906	TGATTCCCACCAAGAATTTGATCA	58.668	37.500	0.00	0.00	36.36	2.92
703	723	3.494924	CCAAATCCACCTATCATCGCTGA	60.495	47.826	0.00	0.00	35.41	4.26
811	831	4.100189	TGAGCTTAATAGGAGCAAGAGACC	59.900	45.833	0.00	0.00	42.56	3.85
844	864	1.752198	AAGTGTCGCTGCCCACTTA	59.248	52.632	23.06	0.00	46.97	2.24
1098	1118	7.617723	TCAGTTAATAACATTGTAATTGCCCCT	59.382	33.333	5.89	0.00	0.00	4.79
1166	1187	7.017551	AGAGATGCTGGTATAATATTGGGTCAA	59.982	37.037	0.00	0.00	0.00	3.18
1167	1188	6.501805	AGAGATGCTGGTATAATATTGGGTCA	59.498	38.462	0.00	0.00	0.00	4.02
1213	1234	6.148976	CCAGGCAGAATGAGAATATACACATG	59.851	42.308	0.00	0.00	39.69	3.21
1215	1236	5.366477	TCCAGGCAGAATGAGAATATACACA	59.634	40.000	0.00	0.00	39.69	3.72
1265	1286	5.432885	GACCGATTTTCTTGAAAAGGTCA	57.567	39.130	25.67	5.21	46.79	4.02
1282	1303	1.816961	GCCTAGATACCCGAAGACCGA	60.817	57.143	0.00	0.00	41.76	4.69
1381	1402	3.809832	GTGAAGTAGGCACGCATATCAAT	59.190	43.478	0.00	0.00	0.00	2.57
1388	1409	2.048597	CGGTGAAGTAGGCACGCA	60.049	61.111	0.00	0.00	37.13	5.24
1424	1445	2.307496	TTTGATTCCTGTGGGCACAT	57.693	45.000	0.00	0.00	41.01	3.21
1730	1751	5.648092	CAGATTAACCCCGAAAAAGTGATCT	59.352	40.000	0.00	0.00	0.00	2.75
1798	1820	5.336213	GCATCTGGATAATTTGGAATGCGAT	60.336	40.000	0.00	0.00	0.00	4.58
1975	1997	4.521256	GGCTTTGTACCAACCATTCAAGTA	59.479	41.667	0.00	0.00	0.00	2.24
1979	2001	2.158385	AGGGCTTTGTACCAACCATTCA	60.158	45.455	0.00	0.00	0.00	2.57
2020	2042	5.178438	GTCTCTTTTACAGCAGGAAGTTCTG	59.822	44.000	2.25	0.76	37.79	3.02
2172	2197	2.102757	TGGTTACGTAGTTCAGTTGGCA	59.897	45.455	0.00	0.00	37.78	4.92
2222	2247	1.132495	ACTTAGGTTGGACCAGGACCT	60.132	52.381	19.62	19.62	45.38	3.85
2253	2278	1.007038	CGAACGAAGGACCCGTCAA	60.007	57.895	0.00	0.00	39.57	3.18
2263	2288	2.917971	GAGATTCTCCACACGAACGAAG	59.082	50.000	1.97	0.00	0.00	3.79
2316	2343	6.939622	TCTTCGACATATGAATATGCCTCAT	58.060	36.000	10.38	0.00	42.98	2.90
2396	2424	5.590259	CACATCGAATCCTTGGTCCTTAAAT	59.410	40.000	0.00	0.00	0.00	1.40
2413	2441	1.153765	CCTGCGCTTCTCACATCGA	60.154	57.895	9.73	0.00	0.00	3.59
2428	2456	0.616111	ACCCCTGCTACTCTGACCTG	60.616	60.000	0.00	0.00	0.00	4.00
2434	2462	0.106167	TCGCATACCCCTGCTACTCT	60.106	55.000	0.00	0.00	40.06	3.24
2639	2667	4.563140	TCGGGGTGCTTTATCTAAACTT	57.437	40.909	0.00	0.00	0.00	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.