AutoCloner

Multiple sequence alignment - TraesCS3B01G305000

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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	TraesCS3B01G305000	chr3B	100.000	2480	0	0	1	2480	489700768	489698289	0.000000e+00	4580.0
1	TraesCS3B01G305000	chr7D	90.595	1446	112	14	508	1950	379771364	379772788	0.000000e+00	1895.0
2	TraesCS3B01G305000	chr7D	84.605	1455	195	21	509	1951	491884807	491883370	0.000000e+00	1419.0
3	TraesCS3B01G305000	chr7D	92.717	508	33	4	1	507	605786926	605786422	0.000000e+00	730.0
4	TraesCS3B01G305000	chr1A	89.241	1450	149	5	508	1951	380575647	380577095	0.000000e+00	1807.0
5	TraesCS3B01G305000	chr7B	89.850	1330	118	7	508	1833	241524564	241523248	0.000000e+00	1692.0
6	TraesCS3B01G305000	chr7B	88.502	1409	132	11	529	1919	582657413	582656017	0.000000e+00	1677.0
7	TraesCS3B01G305000	chr7B	84.182	1454	204	24	508	1948	581803869	581805309	0.000000e+00	1387.0
8	TraesCS3B01G305000	chr1B	89.542	1224	122	2	508	1725	410325576	410326799	0.000000e+00	1546.0
9	TraesCS3B01G305000	chr2B	84.844	1445	200	13	514	1950	229793227	229791794	0.000000e+00	1437.0
10	TraesCS3B01G305000	chr2B	84.349	1444	201	19	521	1948	655760743	655759309	0.000000e+00	1391.0
11	TraesCS3B01G305000	chr3A	96.415	530	18	1	1951	2480	498788215	498787687	0.000000e+00	872.0
12	TraesCS3B01G305000	chr5D	94.685	508	23	4	1	507	443607678	443607174	0.000000e+00	785.0
13	TraesCS3B01G305000	chr5D	94.153	496	25	4	13	507	298160903	298161395	0.000000e+00	752.0
14	TraesCS3B01G305000	chr5D	92.745	510	32	5	1	508	349584256	349584762	0.000000e+00	732.0
15	TraesCS3B01G305000	chr1D	93.124	509	31	4	1	507	373968137	373968643	0.000000e+00	743.0
16	TraesCS3B01G305000	chr4D	93.561	497	28	4	12	507	493983377	493982884	0.000000e+00	737.0
17	TraesCS3B01G305000	chr2D	93.561	497	28	4	13	508	329854840	329855333	0.000000e+00	737.0
18	TraesCS3B01G305000	chr2D	92.731	509	33	4	1	508	346650500	346651005	0.000000e+00	732.0
19	TraesCS3B01G305000	chr2D	93.042	503	31	4	6	507	365504478	365504977	0.000000e+00	732.0
20	TraesCS3B01G305000	chr3D	97.778	405	7	2	2076	2480	375699667	375699265	0.000000e+00	697.0
21	TraesCS3B01G305000	chr3D	95.789	95	4	0	1951	2045	375699988	375699894	1.190000e-33	154.0
22	TraesCS3B01G305000	chr3D	95.918	49	2	0	2040	2088	375699724	375699676	2.040000e-11	80.5

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	TraesCS3B01G305000	chr3B	489698289	489700768	2479	True	4580.0	4580	100.000	1	2480	1	chr3B.!!$R1	2479
1	TraesCS3B01G305000	chr7D	379771364	379772788	1424	False	1895.0	1895	90.595	508	1950	1	chr7D.!!$F1	1442
2	TraesCS3B01G305000	chr7D	491883370	491884807	1437	True	1419.0	1419	84.605	509	1951	1	chr7D.!!$R1	1442
3	TraesCS3B01G305000	chr7D	605786422	605786926	504	True	730.0	730	92.717	1	507	1	chr7D.!!$R2	506
4	TraesCS3B01G305000	chr1A	380575647	380577095	1448	False	1807.0	1807	89.241	508	1951	1	chr1A.!!$F1	1443
5	TraesCS3B01G305000	chr7B	241523248	241524564	1316	True	1692.0	1692	89.850	508	1833	1	chr7B.!!$R1	1325
6	TraesCS3B01G305000	chr7B	582656017	582657413	1396	True	1677.0	1677	88.502	529	1919	1	chr7B.!!$R2	1390
7	TraesCS3B01G305000	chr7B	581803869	581805309	1440	False	1387.0	1387	84.182	508	1948	1	chr7B.!!$F1	1440
8	TraesCS3B01G305000	chr1B	410325576	410326799	1223	False	1546.0	1546	89.542	508	1725	1	chr1B.!!$F1	1217
9	TraesCS3B01G305000	chr2B	229791794	229793227	1433	True	1437.0	1437	84.844	514	1950	1	chr2B.!!$R1	1436
10	TraesCS3B01G305000	chr2B	655759309	655760743	1434	True	1391.0	1391	84.349	521	1948	1	chr2B.!!$R2	1427
11	TraesCS3B01G305000	chr3A	498787687	498788215	528	True	872.0	872	96.415	1951	2480	1	chr3A.!!$R1	529
12	TraesCS3B01G305000	chr5D	443607174	443607678	504	True	785.0	785	94.685	1	507	1	chr5D.!!$R1	506
13	TraesCS3B01G305000	chr5D	349584256	349584762	506	False	732.0	732	92.745	1	508	1	chr5D.!!$F2	507
14	TraesCS3B01G305000	chr1D	373968137	373968643	506	False	743.0	743	93.124	1	507	1	chr1D.!!$F1	506
15	TraesCS3B01G305000	chr2D	346650500	346651005	505	False	732.0	732	92.731	1	508	1	chr2D.!!$F2	507
16	TraesCS3B01G305000	chr3D	375699265	375699988	723	True	310.5	697	96.495	1951	2480	3	chr3D.!!$R1	529

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
883	889	0.179026	AGCTGCAGCATACAGATGGG	60.179	55.0	38.24	0.0	45.16	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2088	2353	0.901827	TAGAAGAATGTCGCAGGGCA	59.098	50.0	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
23	24	3.852578	ACCACATAGGGGAACTCTCAATT	59.147	43.478	0.00	0.00	43.89	2.32
123	124	1.207791	GGAGACTGGGGACATGATGT	58.792	55.000	0.00	0.00	41.51	3.06
151	152	2.043349	TTCGGGCCCTCTCGATGA	60.043	61.111	22.43	4.41	35.25	2.92
190	191	5.123936	TCCTGCTTGATTGATCTTGATGAG	58.876	41.667	0.00	0.00	0.00	2.90
252	253	4.944177	TGGCTAAACCCTAGAAGTCTAGT	58.056	43.478	13.10	0.00	43.34	2.57
280	282	5.745312	TGATTATGATTGCCTCTACGGAT	57.255	39.130	0.00	0.00	33.16	4.18
301	303	8.716779	ACGGATTAAACCCTCCAGTTTATATAA	58.283	33.333	0.00	0.00	40.80	0.98
326	329	0.401541	GGAGGGGCCTAGGGTTGTAT	60.402	60.000	11.72	0.00	0.00	2.29
341	344	3.998341	GGTTGTATAGAGTCGGTTTGCAA	59.002	43.478	0.00	0.00	0.00	4.08
633	637	5.124617	TCAAGCAAGTGTTGTATGTTGTTGA	59.875	36.000	0.00	0.00	0.00	3.18
701	705	1.293924	CAAGATTCGCACTAGCCCAG	58.706	55.000	0.00	0.00	37.52	4.45
883	889	0.179026	AGCTGCAGCATACAGATGGG	60.179	55.000	38.24	0.00	45.16	4.00
896	902	1.281867	CAGATGGGGGAAGCACTACAA	59.718	52.381	0.00	0.00	0.00	2.41
953	959	4.020307	TCTGAAGTTCACATATGTGCTGGA	60.020	41.667	27.71	16.08	45.25	3.86
1072	1080	0.251634	TGTTGGCTATGCATGTCGGA	59.748	50.000	10.16	0.00	0.00	4.55
1153	1164	4.105057	GGAACTATCCTAGGACTCCTCAGA	59.895	50.000	15.42	0.00	42.93	3.27
1213	1224	0.252696	TGAGAGGGCCTTTGGAGCTA	60.253	55.000	7.89	0.00	0.00	3.32
1222	1233	2.352960	GCCTTTGGAGCTATGAAGAACG	59.647	50.000	0.00	0.00	0.00	3.95
1236	1247	6.555463	ATGAAGAACGGGTTTAAGATCCTA	57.445	37.500	0.00	0.00	0.00	2.94
1251	1262	6.512514	AAGATCCTAGATCAGAAGCCATTT	57.487	37.500	7.30	0.00	0.00	2.32
1255	1266	4.718774	TCCTAGATCAGAAGCCATTTCACT	59.281	41.667	0.00	0.00	38.31	3.41
1330	1343	2.204463	TCCTGCAATGGGGAGTTGATA	58.796	47.619	0.00	0.00	32.10	2.15
1331	1344	2.092429	TCCTGCAATGGGGAGTTGATAC	60.092	50.000	0.00	0.00	32.10	2.24
1369	1382	3.703556	GGAAGATGTGACTCCAGATGAGA	59.296	47.826	0.00	0.00	44.42	3.27
1406	1419	2.022129	GTGTGGAGGCGTTCGACAG	61.022	63.158	0.00	0.00	43.89	3.51
1443	1456	0.779997	AAAGGTTGGAGTGGGCTCAT	59.220	50.000	0.00	0.00	43.37	2.90
1452	1465	1.547372	GAGTGGGCTCATGCAATGTTT	59.453	47.619	0.00	0.00	46.80	2.83
1671	1716	8.766151	GTCATTTGCTAGTAGCTAGAATAAACC	58.234	37.037	22.34	3.22	42.97	3.27
1771	1823	2.235016	TCTTTAGCCGTTTGCAACCAT	58.765	42.857	0.00	0.00	44.83	3.55
1778	1830	1.664588	CCGTTTGCAACCATACAACGG	60.665	52.381	18.89	18.89	35.64	4.44
1805	1857	3.443054	TGTTTAACAATAGCGACGCAC	57.557	42.857	23.70	8.39	0.00	5.34
1834	1902	1.063806	CAGCGTGCTGACTAGTTGTC	58.936	55.000	16.69	0.00	46.30	3.18
1841	1909	1.133407	GCTGACTAGTTGTCTCCCTCG	59.867	57.143	0.00	0.00	45.54	4.63
1881	1950	2.799978	GGCAACCAAACTACATGCAAAC	59.200	45.455	0.00	0.00	38.73	2.93
1886	1955	5.528043	ACCAAACTACATGCAAACATTGA	57.472	34.783	0.00	0.00	32.87	2.57
1898	1967	5.609423	TGCAAACATTGATTTTTAGCCTGT	58.391	33.333	0.00	0.00	0.00	4.00
1904	1973	9.777297	AAACATTGATTTTTAGCCTGTATTTGT	57.223	25.926	0.00	0.00	0.00	2.83
2038	2107	2.278330	GGAACCGGACGTACCCAGT	61.278	63.158	9.46	0.00	34.64	4.00
2051	2295	6.350445	GGACGTACCCAGTCTACAATTTCTTA	60.350	42.308	0.00	0.00	38.58	2.10
2088	2353	1.215647	CCGAGGACACGCTAGCTTT	59.784	57.895	13.93	0.00	0.00	3.51
2151	2416	9.825109	CCTTTACAAATTTTAAAGAAAGGGTCA	57.175	29.630	21.62	0.00	38.36	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	6.038714	GCTTTAATTGAGAGTTCCCCTATGTG	59.961	42.308	0.00	0.00	0.00	3.21
118	119	2.553466	CCCGAACCTGGGTAAAACATCA	60.553	50.000	0.00	0.00	44.76	3.07
151	152	4.632292	AGCAGGAAGTAGGGTATTACCTT	58.368	43.478	12.54	7.74	42.09	3.50
252	253	7.315890	CGTAGAGGCAATCATAATCATACAGA	58.684	38.462	0.00	0.00	0.00	3.41
280	282	9.465199	GGTGTTTATATAAACTGGAGGGTTTAA	57.535	33.333	29.38	10.03	44.36	1.52
301	303	2.687566	CTAGGCCCCTCCGGTGTT	60.688	66.667	0.00	0.00	40.77	3.32
326	329	3.070446	TCCTTCTTTGCAAACCGACTCTA	59.930	43.478	8.05	0.00	0.00	2.43
407	411	5.346270	ACAAGATAAGAAGACTTCCTCCCT	58.654	41.667	11.67	2.30	37.53	4.20
512	516	1.367346	TGGAGGAACATGGCCACTTA	58.633	50.000	8.16	0.00	0.00	2.24
633	637	1.852309	TCATCTCTCCTCTGAGCTCCT	59.148	52.381	12.15	0.00	38.58	3.69
701	705	5.071788	TCACCTTGAAGTATGGATACCATCC	59.928	44.000	6.55	0.00	40.74	3.51
811	816	3.589951	ACCATCTATTGCTCCAATGCT	57.410	42.857	0.94	0.00	35.54	3.79
883	889	1.541588	CTGGCTTTTGTAGTGCTTCCC	59.458	52.381	0.00	0.00	0.00	3.97
896	902	2.089980	CAGCTAGCACATTCTGGCTTT	58.910	47.619	18.83	0.00	46.70	3.51
1072	1080	2.241176	TGAAGGGTGGAAGAACACTTGT	59.759	45.455	0.00	0.00	43.87	3.16
1153	1164	5.059833	GGAGTGTCTGAGATTGAACAGTTT	58.940	41.667	0.00	0.00	35.84	2.66
1213	1224	5.437191	AGGATCTTAAACCCGTTCTTCAT	57.563	39.130	0.00	0.00	0.00	2.57
1222	1233	6.227522	GCTTCTGATCTAGGATCTTAAACCC	58.772	44.000	8.66	0.00	0.00	4.11
1236	1247	4.840716	AGAGTGAAATGGCTTCTGATCT	57.159	40.909	0.00	0.00	34.86	2.75
1251	1262	2.544844	CCTGGGTAGGGTAAGAGTGA	57.455	55.000	0.00	0.00	40.63	3.41
1330	1343	2.035626	CTCCCCCGGCACAAATGT	59.964	61.111	0.00	0.00	0.00	2.71
1331	1344	2.755469	CCTCCCCCGGCACAAATG	60.755	66.667	0.00	0.00	0.00	2.32
1369	1382	0.395686	CCATGGTCGGAGCTGATCAT	59.604	55.000	2.57	0.00	40.30	2.45
1406	1419	0.039256	TTTGTTGCTCCATGCTTCGC	60.039	50.000	0.00	0.00	43.37	4.70
1443	1456	5.069318	TGACCTCTGTTATCAAACATTGCA	58.931	37.500	0.00	0.00	44.43	4.08
1452	1465	4.416516	TCCTTGTCTGACCTCTGTTATCA	58.583	43.478	5.17	0.00	0.00	2.15
1521	1544	1.188219	TGCTGCTTCCTCTTCCTCGT	61.188	55.000	0.00	0.00	0.00	4.18
1834	1902	1.743252	GGCTTTCTGCACGAGGGAG	60.743	63.158	0.00	0.00	45.15	4.30
1841	1909	1.133790	CCTGCATTAGGCTTTCTGCAC	59.866	52.381	12.47	0.00	45.15	4.57
1881	1950	8.034215	TGGACAAATACAGGCTAAAAATCAATG	58.966	33.333	0.00	0.00	0.00	2.82
1886	1955	6.268847	TGGTTGGACAAATACAGGCTAAAAAT	59.731	34.615	0.00	0.00	0.00	1.82
1898	1967	3.139397	AGTTGGGTCTGGTTGGACAAATA	59.861	43.478	0.00	0.00	37.91	1.40
1904	1973	1.217916	TTCAGTTGGGTCTGGTTGGA	58.782	50.000	0.00	0.00	36.25	3.53
2029	2098	6.860080	TCTAAGAAATTGTAGACTGGGTACG	58.140	40.000	0.00	0.00	0.00	3.67
2051	2295	5.762218	CCTCGGATCTATCATTTGCTTTTCT	59.238	40.000	0.00	0.00	0.00	2.52
2088	2353	0.901827	TAGAAGAATGTCGCAGGGCA	59.098	50.000	0.00	0.00	0.00	5.36
2138	2403	6.684613	GCTGTATATCGGTGACCCTTTCTTTA	60.685	42.308	0.00	0.00	0.00	1.85
2151	2416	4.859304	TGTATTTCGGCTGTATATCGGT	57.141	40.909	0.00	0.00	0.00	4.69
2207	2472	6.549736	ACTTGTAAAAATCTAGCCTGTTGGTT	59.450	34.615	0.00	0.00	35.27	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.