AutoCloner

Multiple sequence alignment - TraesCS7B01G091000

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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	TraesCS7B01G091000	chr7B	100.000	2315	0	0	1	2315	105229199	105226885	0.000000e+00	4276
1	TraesCS7B01G091000	chr7B	96.170	1462	49	1	854	2315	663100025	663098571	0.000000e+00	2383
2	TraesCS7B01G091000	chr7B	96.158	859	30	3	1	856	663100918	663100060	0.000000e+00	1400
3	TraesCS7B01G091000	chr6D	96.170	1462	49	1	854	2315	389246422	389244968	0.000000e+00	2383
4	TraesCS7B01G091000	chr6D	96.042	859	31	3	1	856	389247315	389246457	0.000000e+00	1395
5	TraesCS7B01G091000	chr3B	95.964	1462	53	1	854	2315	201538921	201540376	0.000000e+00	2368
6	TraesCS7B01G091000	chr2A	95.964	1462	52	1	854	2315	726907055	726905601	0.000000e+00	2366
7	TraesCS7B01G091000	chr2A	95.398	1456	61	3	860	2315	335846718	335848167	0.000000e+00	2313
8	TraesCS7B01G091000	chr2A	95.809	859	33	3	1	856	726907948	726907090	0.000000e+00	1384
9	TraesCS7B01G091000	chr2B	95.890	1460	53	2	856	2315	474920332	474921784	0.000000e+00	2357
10	TraesCS7B01G091000	chr2B	93.659	410	19	2	855	1264	110643900	110644302	7.070000e-170	606
11	TraesCS7B01G091000	chr4A	94.888	1467	65	2	854	2315	583869513	583868052	0.000000e+00	2285
12	TraesCS7B01G091000	chr5D	93.639	1462	73	7	854	2315	523003807	523002366	0.000000e+00	2167
13	TraesCS7B01G091000	chr5D	96.042	859	31	3	1	856	503243779	503244637	0.000000e+00	1395
14	TraesCS7B01G091000	chr5D	94.394	553	26	1	854	1406	432357067	432356520	0.000000e+00	845
15	TraesCS7B01G091000	chr7D	93.238	1464	92	6	854	2315	88622017	88620559	0.000000e+00	2148
16	TraesCS7B01G091000	chr6B	93.209	1443	91	2	873	2315	678790761	678789326	0.000000e+00	2115
17	TraesCS7B01G091000	chrUn	95.809	859	33	3	1	856	216507611	216506753	0.000000e+00	1384
18	TraesCS7B01G091000	chr3D	95.809	859	32	4	1	856	589265016	589264159	0.000000e+00	1384
19	TraesCS7B01G091000	chr2D	95.809	859	33	3	1	856	272554288	272555146	0.000000e+00	1384
20	TraesCS7B01G091000	chr3A	95.693	859	34	3	1	856	66006625	66005767	0.000000e+00	1378
21	TraesCS7B01G091000	chr1D	95.693	859	34	3	1	856	254383514	254382656	0.000000e+00	1378

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	TraesCS7B01G091000	chr7B	105226885	105229199	2314	True	4276.0	4276	100.0000	1	2315	1	chr7B.!!$R1	2314
1	TraesCS7B01G091000	chr7B	663098571	663100918	2347	True	1891.5	2383	96.1640	1	2315	2	chr7B.!!$R2	2314
2	TraesCS7B01G091000	chr6D	389244968	389247315	2347	True	1889.0	2383	96.1060	1	2315	2	chr6D.!!$R1	2314
3	TraesCS7B01G091000	chr3B	201538921	201540376	1455	False	2368.0	2368	95.9640	854	2315	1	chr3B.!!$F1	1461
4	TraesCS7B01G091000	chr2A	335846718	335848167	1449	False	2313.0	2313	95.3980	860	2315	1	chr2A.!!$F1	1455
5	TraesCS7B01G091000	chr2A	726905601	726907948	2347	True	1875.0	2366	95.8865	1	2315	2	chr2A.!!$R1	2314
6	TraesCS7B01G091000	chr2B	474920332	474921784	1452	False	2357.0	2357	95.8900	856	2315	1	chr2B.!!$F2	1459
7	TraesCS7B01G091000	chr4A	583868052	583869513	1461	True	2285.0	2285	94.8880	854	2315	1	chr4A.!!$R1	1461
8	TraesCS7B01G091000	chr5D	523002366	523003807	1441	True	2167.0	2167	93.6390	854	2315	1	chr5D.!!$R2	1461
9	TraesCS7B01G091000	chr5D	503243779	503244637	858	False	1395.0	1395	96.0420	1	856	1	chr5D.!!$F1	855
10	TraesCS7B01G091000	chr5D	432356520	432357067	547	True	845.0	845	94.3940	854	1406	1	chr5D.!!$R1	552
11	TraesCS7B01G091000	chr7D	88620559	88622017	1458	True	2148.0	2148	93.2380	854	2315	1	chr7D.!!$R1	1461
12	TraesCS7B01G091000	chr6B	678789326	678790761	1435	True	2115.0	2115	93.2090	873	2315	1	chr6B.!!$R1	1442
13	TraesCS7B01G091000	chrUn	216506753	216507611	858	True	1384.0	1384	95.8090	1	856	1	chrUn.!!$R1	855
14	TraesCS7B01G091000	chr3D	589264159	589265016	857	True	1384.0	1384	95.8090	1	856	1	chr3D.!!$R1	855
15	TraesCS7B01G091000	chr2D	272554288	272555146	858	False	1384.0	1384	95.8090	1	856	1	chr2D.!!$F1	855
16	TraesCS7B01G091000	chr3A	66005767	66006625	858	True	1378.0	1378	95.6930	1	856	1	chr3A.!!$R1	855
17	TraesCS7B01G091000	chr1D	254382656	254383514	858	True	1378.0	1378	95.6930	1	856	1	chr1D.!!$R1	855

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
117	118	0.251253	TGGTGCATGGCTGTCATCAA	60.251	50.0	0.0	0.0	32.92	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1699	1749	0.458025	GACCTCGCCCGTGAAGTAAG	60.458	60.0	0.0	0.0	0.0	2.34	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
96	97	0.321671	CCTCAGGAACGTGGACACAT	59.678	55.000	3.12	0.00	0.00	3.21
113	114	1.075305	ATGTGGTGCATGGCTGTCA	59.925	52.632	0.00	0.00	36.26	3.58
117	118	0.251253	TGGTGCATGGCTGTCATCAA	60.251	50.000	0.00	0.00	32.92	2.57
124	125	0.392706	TGGCTGTCATCAACTCGTGT	59.607	50.000	0.00	0.00	0.00	4.49
176	177	2.356695	GTGCAACCCTCGTGTTTAGTTT	59.643	45.455	0.00	0.00	0.00	2.66
178	179	2.876550	GCAACCCTCGTGTTTAGTTTCT	59.123	45.455	0.00	0.00	0.00	2.52
190	191	9.403110	TCGTGTTTAGTTTCTACTATGAGTTTC	57.597	33.333	0.00	0.00	36.76	2.78
213	214	2.030562	CTGAACAGACCGCCGGTT	59.969	61.111	11.54	0.00	35.25	4.44
266	267	0.901580	CATCATGCCCCTTATGCCCC	60.902	60.000	0.00	0.00	0.00	5.80
290	292	0.394938	ACACACGTGCTACAATGGGA	59.605	50.000	17.22	0.00	0.00	4.37
326	329	1.736586	CTCGCGAGGGTGAGCTAAT	59.263	57.895	28.40	0.00	43.25	1.73
361	364	0.901827	TCAGTTCGGATTGCAGGCTA	59.098	50.000	0.00	0.00	0.00	3.93
432	435	1.153784	GCGGTGAATACGTTCCCGA	60.154	57.895	16.45	0.00	44.20	5.14
443	446	0.320073	CGTTCCCGAGCCTTGTACAA	60.320	55.000	8.28	8.28	35.63	2.41
450	453	0.887387	GAGCCTTGTACAAACCGCCA	60.887	55.000	10.03	0.00	0.00	5.69
451	454	0.466555	AGCCTTGTACAAACCGCCAA	60.467	50.000	10.03	0.00	0.00	4.52
468	471	3.658709	GCCAATCACACTATAGGAGCTC	58.341	50.000	4.71	4.71	0.00	4.09
474	477	2.820197	CACACTATAGGAGCTCGCCATA	59.180	50.000	7.83	4.21	0.00	2.74
572	576	2.967397	CCGTACTGGAAGGTGCGA	59.033	61.111	6.67	0.00	45.39	5.10
699	703	8.712228	AAACTTGGATATGGAAGTCTTCTTTT	57.288	30.769	12.31	1.00	33.64	2.27
718	722	8.810990	TTCTTTTGTTTAGGGTGAAGTAAGAA	57.189	30.769	0.00	0.00	0.00	2.52
832	836	1.113788	CGGCATGGGGATGTCAAAAT	58.886	50.000	0.00	0.00	0.00	1.82
843	847	4.467438	GGGATGTCAAAATGAAAGGGATGT	59.533	41.667	0.00	0.00	0.00	3.06
894	935	3.916544	TAGAGCGCGCCCCTGATG	61.917	66.667	30.33	0.00	0.00	3.07
959	1000	5.499313	TGGATAGTTCAATGTGCTCATCAA	58.501	37.500	1.01	0.00	32.56	2.57
980	1021	1.983224	CCTGACCCGAAGATGTGGT	59.017	57.895	0.00	0.00	34.33	4.16
1025	1066	3.616560	GCGTACTCCTCCTGTTTGAATCA	60.617	47.826	0.00	0.00	0.00	2.57
1096	1137	4.560739	TCAGGTGAGATCCCATGTAGATT	58.439	43.478	0.00	0.00	0.00	2.40
1127	1168	2.933287	ACTTGTGGGATCCGGGCA	60.933	61.111	5.45	1.36	0.00	5.36
1234	1282	3.074412	CAAGCATAGGTTGAGGTTCGTT	58.926	45.455	3.01	0.00	42.72	3.85
1263	1311	3.769300	GGGAAAATGGAGCACCTAACAAT	59.231	43.478	0.71	0.00	37.04	2.71
1281	1329	3.890756	ACAATGCATCTTCACAGACCAAA	59.109	39.130	0.00	0.00	0.00	3.28
1316	1364	1.075374	CCCTTTCATTCTGGGGTGACA	59.925	52.381	0.00	0.00	37.37	3.58
1331	1379	1.822990	GTGACAGAGGGATCGTACCAA	59.177	52.381	0.00	0.00	0.00	3.67
1530	1578	1.625315	GCCTTCCTTTTTCTGCCCATT	59.375	47.619	0.00	0.00	0.00	3.16
1553	1601	4.352595	TGGAGTTATTTCCCAAGGACTTGA	59.647	41.667	13.35	0.00	40.31	3.02
1597	1647	1.202580	AGAAGCACACTTGAAGAGCGT	60.203	47.619	0.00	0.00	35.82	5.07
1607	1657	3.251729	ACTTGAAGAGCGTAGTACAACGA	59.748	43.478	0.00	0.00	45.68	3.85
1623	1673	0.608130	ACGAGGAGTTGTATGCTGCA	59.392	50.000	4.13	4.13	0.00	4.41
1784	1834	7.491682	AGAATAGAAGAAGCATCTGACTCTTC	58.508	38.462	10.87	10.87	35.59	2.87
1865	1921	3.428725	GCAATTGGGTCATTGCGATTACA	60.429	43.478	7.72	0.00	42.78	2.41
1913	1969	7.121759	GGCGGTAATGATAGTATCTTGTACCTA	59.878	40.741	21.99	4.32	0.00	3.08
1948	2004	7.122799	GCTCACTTTTTCTAAGTAATGGGGAAT	59.877	37.037	0.00	0.00	0.00	3.01
1965	2021	2.614057	GGAATAGGACTGAAACATGCCG	59.386	50.000	0.00	0.00	0.00	5.69
2007	2063	8.039603	AGACAAAAAGATGGGTTTTCAAAAAC	57.960	30.769	9.37	9.37	45.70	2.43
2014	2070	5.826208	AGATGGGTTTTCAAAAACGTAGAGT	59.174	36.000	11.15	0.00	47.00	3.24
2195	2251	4.159120	GAGCGAAATGTAGCAAAAGGAAC	58.841	43.478	0.00	0.00	35.48	3.62
2212	2268	1.400494	GAACGAAAATCCATGGACCGG	59.600	52.381	18.99	0.00	0.00	5.28
2254	2310	2.040178	GGAACTACGAGATCACCCCAT	58.960	52.381	0.00	0.00	0.00	4.00
2266	2322	3.727258	CCCCATGGACGCCCTCAA	61.727	66.667	15.22	0.00	0.00	3.02
2268	2324	2.350895	CCATGGACGCCCTCAACA	59.649	61.111	5.56	0.00	0.00	3.33
2297	2353	1.000521	ACGGACCGACCATAGACCA	60.001	57.895	23.38	0.00	38.90	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	1.896220	AGGTTCTTCGCTTTGCATCA	58.104	45.000	0.00	0.00	0.00	3.07
81	82	0.250295	CCACATGTGTCCACGTTCCT	60.250	55.000	23.79	0.00	0.00	3.36
96	97	0.961857	GATGACAGCCATGCACCACA	60.962	55.000	0.00	0.00	35.17	4.17
113	114	2.295349	ACACCTTACGACACGAGTTGAT	59.705	45.455	7.27	0.00	33.15	2.57
117	118	1.269413	CCAACACCTTACGACACGAGT	60.269	52.381	0.00	0.00	0.00	4.18
124	125	3.642848	AGACTTAACCCAACACCTTACGA	59.357	43.478	0.00	0.00	0.00	3.43
156	157	2.335316	AACTAAACACGAGGGTTGCA	57.665	45.000	0.00	0.00	0.00	4.08
176	177	5.258841	TCAGGGTTCGAAACTCATAGTAGA	58.741	41.667	13.88	0.00	33.06	2.59
178	179	5.244402	TGTTCAGGGTTCGAAACTCATAGTA	59.756	40.000	13.88	0.00	33.06	1.82
190	191	2.027625	GCGGTCTGTTCAGGGTTCG	61.028	63.158	0.00	1.64	0.00	3.95
213	214	1.831736	CTCTCCTTCCTCCGGCTTAAA	59.168	52.381	0.00	0.00	0.00	1.52
266	267	2.431942	GTAGCACGTGTGTCCCCG	60.432	66.667	18.38	0.00	0.00	5.73
290	292	1.218316	GATCGCGACCTTTGTCCCT	59.782	57.895	12.93	0.00	38.32	4.20
326	329	1.213430	ACTGAGGACGGGTTTTTGGAA	59.787	47.619	0.00	0.00	0.00	3.53
361	364	1.580845	GCTTCATGCAGGCGAGTTGT	61.581	55.000	0.00	0.00	42.31	3.32
432	435	0.466555	TTGGCGGTTTGTACAAGGCT	60.467	50.000	20.49	0.00	32.75	4.58
443	446	2.769663	TCCTATAGTGTGATTGGCGGTT	59.230	45.455	0.00	0.00	0.00	4.44
450	453	2.297597	GGCGAGCTCCTATAGTGTGATT	59.702	50.000	8.47	0.00	0.00	2.57
451	454	1.889829	GGCGAGCTCCTATAGTGTGAT	59.110	52.381	8.47	0.00	0.00	3.06
468	471	4.821805	AGGGTAATGACTTCAAATATGGCG	59.178	41.667	0.00	0.00	0.00	5.69
474	477	6.243148	ACGGTTAAGGGTAATGACTTCAAAT	58.757	36.000	0.00	0.00	0.00	2.32
699	703	5.529800	GCTTGTTCTTACTTCACCCTAAACA	59.470	40.000	0.00	0.00	0.00	2.83
832	836	4.454504	GCGAGAAAAACTACATCCCTTTCA	59.545	41.667	0.00	0.00	0.00	2.69
894	935	1.154413	CAGGCACAACGACGCAATC	60.154	57.895	0.00	0.00	0.00	2.67
925	966	2.840038	TGAACTATCCATGTGGCTGAGT	59.160	45.455	0.00	0.00	34.44	3.41
959	1000	2.283529	ACATCTTCGGGTCAGGCGT	61.284	57.895	0.00	0.00	0.00	5.68
980	1021	3.084536	TGCTAATGTGCCTTGGATGAA	57.915	42.857	0.00	0.00	0.00	2.57
1096	1137	7.610305	GGATCCCACAAGTGAATAGAAAGTTAA	59.390	37.037	0.00	0.00	0.00	2.01
1151	1199	1.446966	GAGAAGAGAGGTGCCGTGC	60.447	63.158	0.00	0.00	0.00	5.34
1214	1262	3.008049	AGAACGAACCTCAACCTATGCTT	59.992	43.478	0.00	0.00	0.00	3.91
1234	1282	3.091545	GTGCTCCATTTTCCCATTGAGA	58.908	45.455	0.00	0.00	0.00	3.27
1263	1311	3.953612	AGTTTTTGGTCTGTGAAGATGCA	59.046	39.130	0.00	0.00	0.00	3.96
1281	1329	3.581332	TGAAAGGGGTGATCTCGTAGTTT	59.419	43.478	0.00	0.00	0.00	2.66
1316	1364	2.231529	CTCGATTGGTACGATCCCTCT	58.768	52.381	0.00	0.00	39.02	3.69
1355	1403	4.388499	TTTCTCCAGACCGCCGGC	62.388	66.667	19.07	19.07	0.00	6.13
1530	1578	4.352595	TCAAGTCCTTGGGAAATAACTCCA	59.647	41.667	7.16	0.00	40.78	3.86
1553	1601	2.482494	CCCTTCTCCCTCTTACCATGT	58.518	52.381	0.00	0.00	0.00	3.21
1607	1657	2.283298	CGAATGCAGCATACAACTCCT	58.717	47.619	8.75	0.00	0.00	3.69
1623	1673	1.417890	AGCGATTCATCCTTCCCGAAT	59.582	47.619	0.00	0.00	32.15	3.34
1690	1740	1.403647	CCGTGAAGTAAGTCATCGCCA	60.404	52.381	0.00	0.00	0.00	5.69
1699	1749	0.458025	GACCTCGCCCGTGAAGTAAG	60.458	60.000	0.00	0.00	0.00	2.34
1784	1834	1.027357	GCCAAGTGGAGTATGCATGG	58.973	55.000	10.16	0.45	39.99	3.66
1865	1921	4.141390	CCTGGACAATTAGATAGCCAACCT	60.141	45.833	0.00	0.00	0.00	3.50
1913	1969	1.407618	GAAAAAGTGAGCCACCGGTTT	59.592	47.619	2.97	0.00	34.49	3.27
1948	2004	0.613260	AGCGGCATGTTTCAGTCCTA	59.387	50.000	1.45	0.00	0.00	2.94
1965	2021	4.775058	TGTCTCAGTAGAGTCTTTCAGC	57.225	45.455	0.00	0.00	42.66	4.26
2007	2063	2.161030	GCCCATCCTACCTACTCTACG	58.839	57.143	0.00	0.00	0.00	3.51
2014	2070	1.274184	ACCAACTGCCCATCCTACCTA	60.274	52.381	0.00	0.00	0.00	3.08
2109	2165	2.619074	CCAACTTGATCCTCTTCCCCAC	60.619	54.545	0.00	0.00	0.00	4.61
2195	2251	1.724582	GGCCGGTCCATGGATTTTCG	61.725	60.000	19.62	18.06	34.01	3.46
2212	2268	2.043953	GGGTGGAGACAATGGGGC	60.044	66.667	0.00	0.00	46.06	5.80
2254	2310	2.184020	CTGGATGTTGAGGGCGTCCA	62.184	60.000	9.71	6.16	46.38	4.02
2266	2322	2.121832	TCCGTGACCCCTGGATGT	59.878	61.111	0.00	0.00	0.00	3.06
2268	2324	2.687566	GGTCCGTGACCCCTGGAT	60.688	66.667	10.92	0.00	46.19	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.