AutoCloner

Multiple sequence alignment - TraesCS6B01G350000

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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	TraesCS6B01G350000	chr6B	100.000	2567	0	0	1	2567	615166075	615168641	0.000000e+00	4741
1	TraesCS6B01G350000	chr6B	93.445	1968	72	19	635	2567	615229964	615231909	0.000000e+00	2867
2	TraesCS6B01G350000	chr6B	87.916	1291	94	32	639	1891	615275109	615276375	0.000000e+00	1463
3	TraesCS6B01G350000	chr6B	81.849	584	77	15	997	1561	615605438	615606011	5.000000e-127	464
4	TraesCS6B01G350000	chr6B	79.866	596	71	29	11	563	615273866	615274455	8.610000e-105	390
5	TraesCS6B01G350000	chr6B	78.894	597	77	29	11	564	615228719	615229309	2.430000e-95	359
6	TraesCS6B01G350000	chr6B	84.878	205	23	7	1897	2096	615276683	615276884	1.560000e-47	200
7	TraesCS6B01G350000	chr6D	88.596	1631	110	34	11	1589	409515304	409516910	0.000000e+00	1912
8	TraesCS6B01G350000	chr6D	92.525	1097	49	16	638	1716	409583814	409584895	0.000000e+00	1541
9	TraesCS6B01G350000	chr6D	88.228	790	60	9	1684	2443	409516947	409517733	0.000000e+00	913
10	TraesCS6B01G350000	chr6D	82.109	531	63	24	997	1502	409655215	409655738	2.360000e-115	425
11	TraesCS6B01G350000	chr6D	83.491	424	55	9	11	422	409582571	409582991	5.180000e-102	381
12	TraesCS6B01G350000	chr6A	89.167	1117	65	25	684	1772	554855272	554856360	0.000000e+00	1341
13	TraesCS6B01G350000	chr6A	92.893	605	34	6	86	688	554854634	554855231	0.000000e+00	870
14	TraesCS6B01G350000	chr6A	80.579	587	88	16	997	1561	555088983	555089565	1.820000e-116	429
15	TraesCS6B01G350000	chr1B	83.142	261	34	6	2283	2540	45351568	45351315	1.990000e-56	230
16	TraesCS6B01G350000	chr4D	81.661	289	39	9	2269	2552	449043292	449043013	7.150000e-56	228
17	TraesCS6B01G350000	chr5A	82.511	223	33	5	2257	2475	595543352	595543132	9.370000e-45	191
18	TraesCS6B01G350000	chr4A	82.870	216	33	3	2260	2472	45331411	45331197	9.370000e-45	191
19	TraesCS6B01G350000	chr5D	79.167	288	47	6	2257	2539	476159694	476159415	1.210000e-43	187
20	TraesCS6B01G350000	chr3A	81.696	224	37	4	2257	2477	11572974	11572752	1.570000e-42	183
21	TraesCS6B01G350000	chr5B	81.982	222	33	6	2258	2474	491441396	491441177	5.640000e-42	182
22	TraesCS6B01G350000	chr1D	84.146	164	26	0	1334	1497	366475659	366475496	2.640000e-35	159

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	TraesCS6B01G350000	chr6B	615166075	615168641	2566	False	4741.000000	4741	100.0000	1	2567	1	chr6B.!!$F1	2566
1	TraesCS6B01G350000	chr6B	615228719	615231909	3190	False	1613.000000	2867	86.1695	11	2567	2	chr6B.!!$F3	2556
2	TraesCS6B01G350000	chr6B	615273866	615276884	3018	False	684.333333	1463	84.2200	11	2096	3	chr6B.!!$F4	2085
3	TraesCS6B01G350000	chr6B	615605438	615606011	573	False	464.000000	464	81.8490	997	1561	1	chr6B.!!$F2	564
4	TraesCS6B01G350000	chr6D	409515304	409517733	2429	False	1412.500000	1912	88.4120	11	2443	2	chr6D.!!$F2	2432
5	TraesCS6B01G350000	chr6D	409582571	409584895	2324	False	961.000000	1541	88.0080	11	1716	2	chr6D.!!$F3	1705
6	TraesCS6B01G350000	chr6D	409655215	409655738	523	False	425.000000	425	82.1090	997	1502	1	chr6D.!!$F1	505
7	TraesCS6B01G350000	chr6A	554854634	554856360	1726	False	1105.500000	1341	91.0300	86	1772	2	chr6A.!!$F2	1686
8	TraesCS6B01G350000	chr6A	555088983	555089565	582	False	429.000000	429	80.5790	997	1561	1	chr6A.!!$F1	564

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
248	272	0.046397	AGGAGGGGAGGGTAAAGCAT	59.954	55.0	0.0	0.0	0.0	3.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1822	3070	0.251634	CTGAAGAAGAGGGAGTGGCC	59.748	60.0	0.0	0.0	0.0	5.36	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
56	72	8.477419	TTTTGATTTTCCATAAGAACCTGTCT	57.523	30.769	0.00	0.00	38.69	3.41
63	79	5.419542	TCCATAAGAACCTGTCTGAAATCG	58.580	41.667	0.00	0.00	36.40	3.34
65	81	5.063944	CCATAAGAACCTGTCTGAAATCGTG	59.936	44.000	0.00	0.00	36.40	4.35
76	92	4.386049	GTCTGAAATCGTGGTTGTCTGTAG	59.614	45.833	0.00	0.00	0.00	2.74
79	95	2.656560	ATCGTGGTTGTCTGTAGAGC	57.343	50.000	0.00	0.00	0.00	4.09
87	103	3.552273	GGTTGTCTGTAGAGCGACTTGAA	60.552	47.826	0.00	0.00	0.00	2.69
104	120	6.368791	CGACTTGAAAGTGAAGATACCATCAA	59.631	38.462	0.00	0.00	39.88	2.57
149	169	5.692204	ACATGACAAAGAGTAAGAGACGTTG	59.308	40.000	0.00	0.00	0.00	4.10
160	180	7.980099	AGAGTAAGAGACGTTGAAGAAAGAAAA	59.020	33.333	0.00	0.00	0.00	2.29
168	188	6.263344	ACGTTGAAGAAAGAAAACTTAAGGC	58.737	36.000	7.53	0.00	0.00	4.35
169	189	6.127842	ACGTTGAAGAAAGAAAACTTAAGGCA	60.128	34.615	7.53	0.00	0.00	4.75
170	190	6.196538	CGTTGAAGAAAGAAAACTTAAGGCAC	59.803	38.462	7.53	0.00	0.00	5.01
171	191	6.767524	TGAAGAAAGAAAACTTAAGGCACA	57.232	33.333	7.53	0.00	0.00	4.57
192	216	6.424207	GCACATTTTTATTAACCGGACCAAAA	59.576	34.615	9.46	4.89	0.00	2.44
248	272	0.046397	AGGAGGGGAGGGTAAAGCAT	59.954	55.000	0.00	0.00	0.00	3.79
257	281	1.288932	AGGGTAAAGCATGGAGGCAAT	59.711	47.619	0.00	0.00	35.83	3.56
272	296	3.036091	AGGCAATTTGGAGCATTAGCAT	58.964	40.909	0.00	0.00	45.49	3.79
278	302	3.632643	TTGGAGCATTAGCATCAGACA	57.367	42.857	0.00	0.00	45.49	3.41
383	408	3.445805	ACAAATCCACCAACAAAACGACT	59.554	39.130	0.00	0.00	0.00	4.18
395	420	1.415374	AAACGACTGACAACGATCGG	58.585	50.000	20.98	4.82	38.88	4.18
419	444	5.508994	GCATTGTTTAAGGGCACACTAGTTT	60.509	40.000	0.00	0.00	0.00	2.66
608	922	7.284034	AGCAGTATACAATTGGATTTCAGAAGG	59.716	37.037	8.85	0.00	0.00	3.46
674	1653	8.494016	GCTTTAGAAGATTAGCCAAAAGTCTA	57.506	34.615	0.00	0.00	0.00	2.59
689	1710	6.594159	CCAAAAGTCTAATGGTACCAGTAGTG	59.406	42.308	35.92	28.25	42.87	2.74
692	1713	7.401955	AAGTCTAATGGTACCAGTAGTGTAC	57.598	40.000	35.92	29.01	42.87	2.90
694	1715	6.602406	AGTCTAATGGTACCAGTAGTGTACAG	59.398	42.308	35.92	20.34	42.87	2.74
695	1716	6.376581	GTCTAATGGTACCAGTAGTGTACAGT	59.623	42.308	35.92	8.55	42.87	3.55
696	1717	6.950041	TCTAATGGTACCAGTAGTGTACAGTT	59.050	38.462	35.92	18.21	42.87	3.16
697	1718	6.429521	AATGGTACCAGTAGTGTACAGTTT	57.570	37.500	21.41	1.58	40.24	2.66
698	1719	5.204409	TGGTACCAGTAGTGTACAGTTTG	57.796	43.478	11.60	8.04	40.24	2.93
699	1720	4.894705	TGGTACCAGTAGTGTACAGTTTGA	59.105	41.667	11.60	0.00	40.24	2.69
701	1722	6.720748	TGGTACCAGTAGTGTACAGTTTGATA	59.279	38.462	11.60	0.00	40.24	2.15
702	1723	7.031975	GGTACCAGTAGTGTACAGTTTGATAC	58.968	42.308	8.85	9.21	40.24	2.24
703	1724	6.912951	ACCAGTAGTGTACAGTTTGATACT	57.087	37.500	8.85	2.85	37.68	2.12
704	1725	8.950210	GTACCAGTAGTGTACAGTTTGATACTA	58.050	37.037	8.85	0.00	38.71	1.82
705	1726	7.824672	ACCAGTAGTGTACAGTTTGATACTAC	58.175	38.462	8.85	8.05	40.25	2.73
826	1853	2.693069	CATTTTCTCACTCACTCGCCT	58.307	47.619	0.00	0.00	0.00	5.52
843	1870	2.706890	GCCTGTTCCCACGATAAGAAA	58.293	47.619	0.00	0.00	0.00	2.52
982	2054	1.338107	TCTCCGAGGAGAGCAAAACA	58.662	50.000	17.24	0.00	45.26	2.83
1415	2544	2.662596	CAAGTGGCTCGGCACCTA	59.337	61.111	18.42	0.00	0.00	3.08
1523	2664	2.868331	CGCATCGTCGTCGTCGTT	60.868	61.111	11.41	0.87	38.33	3.85
1822	3070	0.830648	TTTGCCTATCTCCCCGTGAG	59.169	55.000	0.00	0.00	42.90	3.51
1894	3446	7.624360	TTGCGACAATTTTCCTCAGTATAAT	57.376	32.000	0.00	0.00	0.00	1.28
1923	3475	0.713883	CGGACTCGTTTGGTCATTCG	59.286	55.000	0.00	0.00	35.61	3.34
1939	3494	5.460419	GGTCATTCGACAAGTCAGATGATAC	59.540	44.000	14.52	9.69	44.54	2.24
2010	3565	0.684535	TGGCATCTCTCGTTCCAACA	59.315	50.000	0.00	0.00	0.00	3.33
2031	3586	2.665185	AGACACGGCTGCGAAACC	60.665	61.111	0.00	0.00	0.00	3.27
2060	3615	1.476085	CACAGGCAAACCACAACTCAA	59.524	47.619	0.00	0.00	39.06	3.02
2071	3626	1.608590	CACAACTCAAAGCGGTTGGAT	59.391	47.619	4.61	0.00	44.71	3.41
2072	3627	2.811431	CACAACTCAAAGCGGTTGGATA	59.189	45.455	4.61	0.00	44.71	2.59
2368	3925	3.003897	TGATTTTTGTGCCTACAACCGAC	59.996	43.478	0.00	0.00	45.91	4.79
2424	3981	1.654602	GTAAGAGCCGAGCGAGAAAAC	59.345	52.381	0.00	0.00	0.00	2.43
2544	4102	0.895100	GGCAATTGAGTGGCCAGACA	60.895	55.000	5.11	6.70	46.92	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
56	72	4.556233	CTCTACAGACAACCACGATTTCA	58.444	43.478	0.00	0.00	0.00	2.69
63	79	1.269998	AGTCGCTCTACAGACAACCAC	59.730	52.381	0.00	0.00	39.67	4.16
65	81	2.030185	TCAAGTCGCTCTACAGACAACC	60.030	50.000	0.00	0.00	39.67	3.77
76	92	4.327627	GGTATCTTCACTTTCAAGTCGCTC	59.672	45.833	0.00	0.00	37.08	5.03
79	95	5.869344	TGATGGTATCTTCACTTTCAAGTCG	59.131	40.000	0.00	0.00	37.08	4.18
87	103	7.231317	ACAAATGTGTTGATGGTATCTTCACTT	59.769	33.333	13.34	8.00	32.58	3.16
149	169	8.648557	AAATGTGCCTTAAGTTTTCTTTCTTC	57.351	30.769	0.97	0.00	40.91	2.87
160	180	7.177041	TCCGGTTAATAAAAATGTGCCTTAAGT	59.823	33.333	0.00	0.00	0.00	2.24
168	188	7.095565	GGTTTTGGTCCGGTTAATAAAAATGTG	60.096	37.037	0.00	0.00	0.00	3.21
169	189	6.930164	GGTTTTGGTCCGGTTAATAAAAATGT	59.070	34.615	0.00	0.00	0.00	2.71
170	190	6.369340	GGGTTTTGGTCCGGTTAATAAAAATG	59.631	38.462	0.00	0.00	0.00	2.32
171	191	6.042897	TGGGTTTTGGTCCGGTTAATAAAAAT	59.957	34.615	0.00	0.00	0.00	1.82
192	216	7.339466	GTGGATGATGTATTTTCTTTAGTGGGT	59.661	37.037	0.00	0.00	0.00	4.51
248	272	1.941377	AATGCTCCAAATTGCCTCCA	58.059	45.000	0.00	0.00	0.00	3.86
257	281	3.954200	TGTCTGATGCTAATGCTCCAAA	58.046	40.909	0.00	0.00	40.48	3.28
272	296	0.543277	GGCACCTCCATCATGTCTGA	59.457	55.000	0.00	0.00	35.41	3.27
345	369	6.701400	GTGGATTTGTAGCACTTTTTCATTGT	59.299	34.615	0.00	0.00	0.00	2.71
395	420	3.506067	ACTAGTGTGCCCTTAAACAATGC	59.494	43.478	0.00	0.00	0.00	3.56
419	444	0.703488	TGGGTGAGAATGCAATGGGA	59.297	50.000	0.00	0.00	0.00	4.37
566	622	9.015367	TGTATACTGCTATTTTACCAGCAAAAA	57.985	29.630	4.17	0.00	46.55	1.94
567	623	8.568676	TGTATACTGCTATTTTACCAGCAAAA	57.431	30.769	4.17	0.00	46.55	2.44
662	1641	4.042934	ACTGGTACCATTAGACTTTTGGCT	59.957	41.667	16.75	0.00	42.92	4.75
674	1653	6.042322	TCAAACTGTACACTACTGGTACCATT	59.958	38.462	16.75	13.04	40.24	3.16
677	1656	5.458041	TCAAACTGTACACTACTGGTACC	57.542	43.478	4.43	4.43	40.24	3.34
701	1722	8.894768	AGATAGATTTTACCTACGTACGTAGT	57.105	34.615	38.99	30.99	44.71	2.73
811	1838	0.598562	GAACAGGCGAGTGAGTGAGA	59.401	55.000	0.00	0.00	0.00	3.27
826	1853	4.610605	TCACTTTCTTATCGTGGGAACA	57.389	40.909	0.00	0.00	38.70	3.18
843	1870	2.102438	CATGTCCACGCGCATCACT	61.102	57.895	5.73	0.00	0.00	3.41
1509	2641	2.467946	AAGCCAACGACGACGACGAT	62.468	55.000	25.15	11.68	42.66	3.73
1523	2664	4.978099	AGAAGAATCAGAAACAGAAGCCA	58.022	39.130	0.00	0.00	0.00	4.75
1562	2703	1.003839	CTGCCCGGCAAGTTCTACA	60.004	57.895	14.45	0.00	38.41	2.74
1822	3070	0.251634	CTGAAGAAGAGGGAGTGGCC	59.748	60.000	0.00	0.00	0.00	5.36
1894	3446	4.521639	ACCAAACGAGTCCGCTCATATATA	59.478	41.667	0.00	0.00	41.71	0.86
1923	3475	4.113354	GTTCCGGTATCATCTGACTTGTC	58.887	47.826	0.00	0.00	0.00	3.18
1939	3494	2.705730	TGTGTATCACCAATGTTCCGG	58.294	47.619	0.00	0.00	32.73	5.14
2010	3565	0.602638	TTTCGCAGCCGTGTCTGAAT	60.603	50.000	1.43	0.00	36.19	2.57
2031	3586	1.600413	GGTTTGCCTGTGCTTCGAAAG	60.600	52.381	0.00	0.00	38.71	2.62
2060	3615	8.962679	TGAAAATAAATAGTTATCCAACCGCTT	58.037	29.630	0.00	0.00	35.05	4.68
2424	3981	4.151689	TGACTTTTCATCTAAAACTCGCGG	59.848	41.667	6.13	0.00	33.49	6.46
2544	4102	1.852067	GCACGCACCCGTCAATTCTT	61.852	55.000	0.00	0.00	46.39	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.