AutoCloner

Multiple sequence alignment - TraesCS7B01G476200

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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	TraesCS7B01G476200	chr7B	100.000	2583	0	0	1	2583	732423916	732426498	0.000000e+00	4771.0
1	TraesCS7B01G476200	chr7B	95.500	1111	39	8	720	1828	732591900	732590799	0.000000e+00	1764.0
2	TraesCS7B01G476200	chr7B	93.631	785	35	9	1813	2583	732585017	732584234	0.000000e+00	1158.0
3	TraesCS7B01G476200	chr7B	97.143	35	1	0	2306	2340	479644481	479644447	2.780000e-05	60.2
4	TraesCS7B01G476200	chr7D	87.618	1914	157	29	718	2578	629630620	629628734	0.000000e+00	2148.0
5	TraesCS7B01G476200	chr5B	96.245	719	24	3	1	717	15143870	15143153	0.000000e+00	1175.0
6	TraesCS7B01G476200	chr5B	82.143	280	42	6	2306	2583	541095685	541095412	1.550000e-57	233.0
7	TraesCS7B01G476200	chr7A	92.996	257	16	1	718	974	725679063	725678809	8.730000e-100	374.0
8	TraesCS7B01G476200	chr7A	84.680	359	38	4	1788	2129	725652562	725652204	2.460000e-90	342.0
9	TraesCS7B01G476200	chr7A	92.157	102	8	0	1685	1786	725678802	725678701	7.450000e-31	145.0
10	TraesCS7B01G476200	chr7A	97.059	34	1	0	2303	2336	7331872	7331905	9.980000e-05	58.4
11	TraesCS7B01G476200	chrUn	85.714	266	34	4	218	481	89684801	89684538	7.040000e-71	278.0
12	TraesCS7B01G476200	chrUn	84.234	222	29	4	496	715	89684552	89684335	7.240000e-51	211.0
13	TraesCS7B01G476200	chr1A	76.792	293	61	7	2295	2583	299269294	299269583	9.570000e-35	158.0
14	TraesCS7B01G476200	chr2D	76.642	274	40	15	2295	2553	20938806	20939070	2.090000e-26	130.0
15	TraesCS7B01G476200	chr3D	85.556	90	12	1	2296	2384	40498073	40497984	2.740000e-15	93.5
16	TraesCS7B01G476200	chr6B	84.337	83	12	1	2303	2384	9809448	9809530	2.130000e-11	80.5
17	TraesCS7B01G476200	chr3B	91.071	56	4	1	2302	2357	528135311	528135257	9.910000e-10	75.0

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	TraesCS7B01G476200	chr7B	732423916	732426498	2582	False	4771	4771	100.000	1	2583	1	chr7B.!!$F1	2582
1	TraesCS7B01G476200	chr7B	732590799	732591900	1101	True	1764	1764	95.500	720	1828	1	chr7B.!!$R3	1108
2	TraesCS7B01G476200	chr7B	732584234	732585017	783	True	1158	1158	93.631	1813	2583	1	chr7B.!!$R2	770
3	TraesCS7B01G476200	chr7D	629628734	629630620	1886	True	2148	2148	87.618	718	2578	1	chr7D.!!$R1	1860
4	TraesCS7B01G476200	chr5B	15143153	15143870	717	True	1175	1175	96.245	1	717	1	chr5B.!!$R1	716

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
163	164	0.250513	GTGACATCACCCTGTCCCTC	59.749	60.0	0.18	0.0	43.99	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1611	1642	0.969894	AGAGCCGTACATAGCATCCC	59.03	55.0	0.0	0.0	0.0	3.85	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
111	112	3.359515	TACCCACCACGCGATTCCG	62.360	63.158	15.93	0.00	39.16	4.30
163	164	0.250513	GTGACATCACCCTGTCCCTC	59.749	60.000	0.18	0.00	43.99	4.30
186	187	1.658686	CCCTCCCAGTTCGAGAGACG	61.659	65.000	0.46	0.00	41.84	4.18
261	262	4.695231	CGCCGTCGTCGTTCACCT	62.695	66.667	0.71	0.00	35.01	4.00
321	322	1.153549	CCCCTTTCTCTCTTCGGCG	60.154	63.158	0.00	0.00	0.00	6.46
323	324	1.079819	CCTTTCTCTCTTCGGCGCA	60.080	57.895	10.83	0.00	0.00	6.09
376	377	2.893398	GCGTAGTGGTAGCTGCCT	59.107	61.111	22.25	5.05	0.00	4.75
411	412	2.113351	GCCCCCTTAATCCTCGCC	59.887	66.667	0.00	0.00	0.00	5.54
549	551	2.040278	ACAGGAGGAGCTGAGGGG	59.960	66.667	0.00	0.00	0.00	4.79
590	592	2.029970	TCAAAGCACAAGACGACGAAAC	59.970	45.455	0.00	0.00	0.00	2.78
598	600	1.957695	GACGACGAAACCCACCACC	60.958	63.158	0.00	0.00	0.00	4.61
621	623	2.446994	TCCCTTGTGTGGTCGGGT	60.447	61.111	0.00	0.00	37.92	5.28
626	628	2.510613	CCTTGTGTGGTCGGGTTTATT	58.489	47.619	0.00	0.00	0.00	1.40
648	650	2.822418	TTACGTGGCGTGATCGTGGG	62.822	60.000	0.00	0.00	41.39	4.61
788	791	4.006989	ACGCAGATTGTATGCCTGTAAAA	58.993	39.130	0.00	0.00	40.67	1.52
852	856	5.663456	TGCAATCTTTCTCATTTATTGGCC	58.337	37.500	0.00	0.00	0.00	5.36
914	920	0.817634	TGGTTGTGGTGTGCTACAGC	60.818	55.000	10.34	10.34	46.05	4.40
926	932	1.762957	TGCTACAGCCAATCCCTCTAC	59.237	52.381	0.00	0.00	41.18	2.59
938	944	0.747255	CCCTCTACACCCATCAGACG	59.253	60.000	0.00	0.00	0.00	4.18
963	969	4.917415	TCGATCATCGTGCATATAGTTGTG	59.083	41.667	7.00	0.00	41.35	3.33
964	970	4.681483	CGATCATCGTGCATATAGTTGTGT	59.319	41.667	0.00	0.00	34.72	3.72
965	971	5.164148	CGATCATCGTGCATATAGTTGTGTC	60.164	44.000	0.00	0.00	34.72	3.67
966	972	5.004922	TCATCGTGCATATAGTTGTGTCA	57.995	39.130	0.00	0.00	0.00	3.58
967	973	5.415221	TCATCGTGCATATAGTTGTGTCAA	58.585	37.500	0.00	0.00	0.00	3.18
968	974	6.048509	TCATCGTGCATATAGTTGTGTCAAT	58.951	36.000	0.00	0.00	0.00	2.57
969	975	5.966636	TCGTGCATATAGTTGTGTCAATC	57.033	39.130	0.00	0.00	0.00	2.67
972	978	5.331830	CGTGCATATAGTTGTGTCAATCGAG	60.332	44.000	0.00	0.00	0.00	4.04
974	980	6.422100	GTGCATATAGTTGTGTCAATCGAGAT	59.578	38.462	0.00	0.00	0.00	2.75
977	983	7.618139	GCATATAGTTGTGTCAATCGAGATTCG	60.618	40.741	0.00	0.00	42.10	3.34
1234	1263	7.335171	AGGTACCTAACAAAATGGAAATCGTAC	59.665	37.037	14.41	0.00	0.00	3.67
1250	1279	9.111702	GGAAATCGTACATAAGTATACTCGAAC	57.888	37.037	13.87	9.53	31.61	3.95
1252	1281	9.875675	AAATCGTACATAAGTATACTCGAACTC	57.124	33.333	13.87	2.04	31.61	3.01
1256	1285	9.955310	CGTACATAAGTATACTCGAACTCATAG	57.045	37.037	5.70	0.00	31.84	2.23
1290	1321	6.192970	ACCGGATCTTATGATTTTCCATCT	57.807	37.500	9.46	0.00	32.19	2.90
1305	1336	7.477144	TTTTCCATCTATATGTGTGCTTACG	57.523	36.000	0.00	0.00	0.00	3.18
1316	1347	4.308265	TGTGTGCTTACGTGCAACTAATA	58.692	39.130	1.68	0.00	45.12	0.98
1611	1642	0.947244	GTGGAAATAGCGGCATGAGG	59.053	55.000	1.45	0.00	0.00	3.86
1624	1655	2.616510	GGCATGAGGGGATGCTATGTAC	60.617	54.545	0.00	0.00	46.74	2.90
1802	1833	0.841961	TACCTCTACCGAGCTAGGCA	59.158	55.000	13.48	0.00	35.90	4.75
1803	1834	0.186386	ACCTCTACCGAGCTAGGCAT	59.814	55.000	13.48	0.00	35.90	4.40
1823	1854	6.596888	AGGCATGATATGAATAAGGATTGTCG	59.403	38.462	0.00	0.00	0.00	4.35
1836	1867	6.978674	AAGGATTGTCGTTCTATCTCCATA	57.021	37.500	0.00	0.00	0.00	2.74
1879	1910	5.827797	ACCACACATTCAAGTTTGTATGTCT	59.172	36.000	12.36	1.62	44.07	3.41
1998	2029	7.310634	TCAAATCTAATTAGGGGAGCTAGGTA	58.689	38.462	12.54	0.00	0.00	3.08
2045	2085	3.515602	AGAGTGGAGCCAGTCATTTTT	57.484	42.857	22.63	2.78	45.95	1.94
2114	2167	0.250513	GTCATTCTGCCCCGTTCTCT	59.749	55.000	0.00	0.00	0.00	3.10
2120	2173	1.757118	TCTGCCCCGTTCTCTAATCTG	59.243	52.381	0.00	0.00	0.00	2.90
2209	2263	9.152595	GCCTATATATTAACTCTTGTTAGTGCC	57.847	37.037	0.00	0.00	39.49	5.01
2252	2306	8.750416	CGAGATCACTACTAAATCAATTCACAG	58.250	37.037	0.00	0.00	0.00	3.66
2347	2415	5.047377	GCATCAAGAGGATACAAACCCAAAA	60.047	40.000	0.00	0.00	41.41	2.44
2365	2433	3.537206	AAGCACACACTCGGCCTCC	62.537	63.158	0.00	0.00	0.00	4.30
2380	2448	2.290323	GGCCTCCGCATAATTAGGATGT	60.290	50.000	0.32	0.00	36.38	3.06
2500	2572	1.927895	AAGCGATCTGATCCACGTTC	58.072	50.000	11.84	0.00	0.00	3.95
2526	2598	6.926272	GGCAAACTACAACAAAAACCATATCA	59.074	34.615	0.00	0.00	0.00	2.15
2552	2624	3.726557	AACCATCTGATGACACCACAT	57.273	42.857	18.92	0.00	0.00	3.21
2579	2651	3.945285	GAGGAGGTTTCTCAACAACAACA	59.055	43.478	0.00	0.00	41.69	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	1.270571	TGCGTGCAAATCACTCACCTA	60.271	47.619	0.00	0.00	43.46	3.08
119	120	2.041265	GGAGGAAGGGAGAGGGCA	59.959	66.667	0.00	0.00	0.00	5.36
121	122	0.399233	AATCGGAGGAAGGGAGAGGG	60.399	60.000	0.00	0.00	0.00	4.30
186	187	6.146601	AGACCGTAGCCTAGTCTATTTTTC	57.853	41.667	0.00	0.00	39.06	2.29
321	322	3.554692	CGACCAAGCGGATCGTGC	61.555	66.667	0.55	0.55	35.59	5.34
583	585	1.302271	GAGGGTGGTGGGTTTCGTC	60.302	63.158	0.00	0.00	0.00	4.20
590	592	2.689034	GGGAGAGAGGGTGGTGGG	60.689	72.222	0.00	0.00	0.00	4.61
598	600	0.610687	GACCACACAAGGGAGAGAGG	59.389	60.000	0.00	0.00	0.00	3.69
621	623	4.434461	CGATCACGCCACGTAACAAATAAA	60.434	41.667	0.00	0.00	38.32	1.40
626	628	0.318869	ACGATCACGCCACGTAACAA	60.319	50.000	0.00	0.00	43.96	2.83
710	713	7.995488	GGTGAATATATATTCTCCCTCCCAATG	59.005	40.741	30.08	0.00	44.54	2.82
819	823	6.679327	TGAGAAAGATTGCATGATCAGAAG	57.321	37.500	0.09	0.00	0.00	2.85
882	888	1.881324	CACAACCATCACTGCATCACA	59.119	47.619	0.00	0.00	0.00	3.58
914	920	2.105477	CTGATGGGTGTAGAGGGATTGG	59.895	54.545	0.00	0.00	0.00	3.16
926	932	0.249073	GATCGACCGTCTGATGGGTG	60.249	60.000	19.60	11.33	36.46	4.61
938	944	4.098055	ACTATATGCACGATGATCGACC	57.902	45.455	22.88	11.70	43.74	4.79
969	975	4.023622	TGGCTTCTATCTTCTCGAATCTCG	60.024	45.833	0.00	0.00	42.10	4.04
972	978	5.837437	TCTTGGCTTCTATCTTCTCGAATC	58.163	41.667	0.00	0.00	0.00	2.52
974	980	5.860941	ATCTTGGCTTCTATCTTCTCGAA	57.139	39.130	0.00	0.00	0.00	3.71
985	991	7.609097	TCTGTCTCATATTATCTTGGCTTCT	57.391	36.000	0.00	0.00	0.00	2.85
1250	1279	2.420022	CCGGTTTTGGCAGTTCTATGAG	59.580	50.000	0.00	0.00	0.00	2.90
1252	1281	2.432444	TCCGGTTTTGGCAGTTCTATG	58.568	47.619	0.00	0.00	0.00	2.23
1256	1285	1.534729	AGATCCGGTTTTGGCAGTTC	58.465	50.000	0.00	0.00	0.00	3.01
1290	1321	4.500127	AGTTGCACGTAAGCACACATATA	58.500	39.130	0.00	0.00	45.61	0.86
1300	1331	6.462073	AGTTGTGTATTAGTTGCACGTAAG	57.538	37.500	0.00	0.00	43.23	2.34
1305	1336	7.060633	GCAATTGTAGTTGTGTATTAGTTGCAC	59.939	37.037	7.40	0.00	40.95	4.57
1316	1347	7.039784	ACCTATTTCATGCAATTGTAGTTGTGT	60.040	33.333	7.40	0.00	0.00	3.72
1611	1642	0.969894	AGAGCCGTACATAGCATCCC	59.030	55.000	0.00	0.00	0.00	3.85
1836	1867	8.482943	TGTGTGGTTACTAATCTTGCATAGTAT	58.517	33.333	5.90	0.00	35.25	2.12
1843	1874	6.494893	TGAATGTGTGGTTACTAATCTTGC	57.505	37.500	0.00	0.00	0.00	4.01
1851	1882	7.284489	ACATACAAACTTGAATGTGTGGTTACT	59.716	33.333	7.41	0.00	41.32	2.24
1998	2029	6.072838	CGGCAATGAAGCTATAACAGAATCAT	60.073	38.462	0.00	0.00	34.41	2.45
2209	2263	4.041740	TCTCGGTATGAAATCGAACTGG	57.958	45.455	0.00	0.00	32.35	4.00
2290	2344	7.776969	TGAGCTAATAAATTCTCCATTTGAGCT	59.223	33.333	10.53	10.53	43.04	4.09
2291	2345	7.934457	TGAGCTAATAAATTCTCCATTTGAGC	58.066	34.615	0.00	0.00	41.18	4.26
2296	2350	9.425248	TCCATTTGAGCTAATAAATTCTCCATT	57.575	29.630	0.00	0.00	0.00	3.16
2297	2351	9.075678	CTCCATTTGAGCTAATAAATTCTCCAT	57.924	33.333	0.00	0.00	33.47	3.41
2347	2415	2.031163	GAGGCCGAGTGTGTGCTT	59.969	61.111	0.00	0.00	0.00	3.91
2365	2433	7.477144	TGACTTTGTACATCCTAATTATGCG	57.523	36.000	0.00	0.00	0.00	4.73
2380	2448	4.097135	CCATGTGTTGGTGTTGACTTTGTA	59.903	41.667	0.00	0.00	40.99	2.41
2416	2484	8.462589	TCATATGATTTTGCTATTTGTGGCTA	57.537	30.769	0.00	0.00	0.00	3.93
2418	2486	7.380602	GTCTCATATGATTTTGCTATTTGTGGC	59.619	37.037	5.72	0.00	0.00	5.01
2489	2561	0.250124	AGTTTGCCGAACGTGGATCA	60.250	50.000	0.00	0.00	43.20	2.92
2500	2572	3.512680	TGGTTTTTGTTGTAGTTTGCCG	58.487	40.909	0.00	0.00	0.00	5.69
2526	2598	2.816087	GTGTCATCAGATGGTTTGTGCT	59.184	45.455	10.67	0.00	0.00	4.40
2552	2624	3.493334	TGTTGAGAAACCTCCTCGTCTA	58.507	45.455	0.00	0.00	33.51	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.