AutoCloner

Multiple sequence alignment - TraesCS7B01G290000

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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	TraesCS7B01G290000	chr7B	100.000	2267	0	0	1	2267	526387115	526384849	0.000000e+00	4187.0
1	TraesCS7B01G290000	chr7B	89.288	1419	78	36	1	1400	526239720	526238357	0.000000e+00	1711.0
2	TraesCS7B01G290000	chr7B	89.225	761	65	10	621	1373	526234782	526234031	0.000000e+00	935.0
3	TraesCS7B01G290000	chr7B	82.058	719	74	27	1462	2140	708672553	708673256	1.520000e-156	562.0
4	TraesCS7B01G290000	chr7B	90.476	252	10	8	373	623	526235697	526235459	1.010000e-83	320.0
5	TraesCS7B01G290000	chr7B	79.302	430	58	19	1462	1878	151654813	151654402	2.870000e-69	272.0
6	TraesCS7B01G290000	chr7B	76.109	293	46	15	1871	2141	551066073	551065783	5.080000e-27	132.0
7	TraesCS7B01G290000	chr7B	90.110	91	8	1	1870	1959	84461027	84460937	1.420000e-22	117.0
8	TraesCS7B01G290000	chr7D	94.130	1448	62	15	1	1436	497901348	497899912	0.000000e+00	2182.0
9	TraesCS7B01G290000	chr7D	92.777	443	25	5	937	1373	497895355	497894914	3.180000e-178	634.0
10	TraesCS7B01G290000	chr7D	91.630	454	19	12	362	814	497899920	497899485	5.350000e-171	610.0
11	TraesCS7B01G290000	chr7A	93.031	1478	75	15	1	1462	563477372	563475907	0.000000e+00	2134.0
12	TraesCS7B01G290000	chr7A	80.556	720	89	29	1462	2141	708467856	708468564	7.230000e-140	507.0
13	TraesCS7B01G290000	chr7A	98.780	82	1	0	2186	2267	563475909	563475828	1.810000e-31	147.0
14	TraesCS7B01G290000	chr1B	80.028	726	99	24	1462	2144	175929672	175928950	1.560000e-136	496.0
15	TraesCS7B01G290000	chr1B	77.298	718	103	33	1462	2132	419391750	419392454	3.560000e-98	368.0
16	TraesCS7B01G290000	chr1B	91.000	100	7	2	1870	1967	484001959	484002058	1.410000e-27	134.0
17	TraesCS7B01G290000	chr3B	79.863	730	93	29	1462	2144	253501185	253500463	3.390000e-133	484.0
18	TraesCS7B01G290000	chr5D	80.220	728	72	42	1460	2141	426153870	426154571	4.380000e-132	481.0
19	TraesCS7B01G290000	chr5D	90.476	63	6	0	992	1054	507375397	507375335	1.440000e-12	84.2
20	TraesCS7B01G290000	chr6B	79.172	725	95	31	1462	2148	680779545	680780251	3.430000e-123	451.0
21	TraesCS7B01G290000	chr6B	89.879	247	25	0	992	1238	116108135	116108381	3.630000e-83	318.0
22	TraesCS7B01G290000	chr6B	77.174	276	47	15	1872	2134	37985992	37986264	1.810000e-31	147.0
23	TraesCS7B01G290000	chr6B	76.812	276	48	15	1872	2134	37988240	37988512	8.440000e-30	141.0
24	TraesCS7B01G290000	chr6B	88.889	99	10	1	1870	1967	70926019	70926117	1.100000e-23	121.0
25	TraesCS7B01G290000	chr1D	79.970	674	73	30	1519	2137	462486673	462486007	7.430000e-120	440.0
26	TraesCS7B01G290000	chr1D	97.849	93	2	0	499	591	399767195	399767103	6.480000e-36	161.0
27	TraesCS7B01G290000	chr6D	81.004	558	54	29	1622	2141	9133351	9132808	1.630000e-106	396.0
28	TraesCS7B01G290000	chrUn	76.838	721	111	35	1462	2132	36497731	36498445	2.770000e-94	355.0
29	TraesCS7B01G290000	chr3A	77.661	667	90	32	1454	2075	336891453	336890801	3.580000e-93	351.0
30	TraesCS7B01G290000	chr5A	79.406	539	66	22	1649	2144	241189662	241189126	2.790000e-89	339.0
31	TraesCS7B01G290000	chr5A	79.874	318	39	11	1674	1967	332295853	332295537	2.280000e-50	209.0
32	TraesCS7B01G290000	chr5A	91.209	91	7	1	1870	1959	524193581	524193671	3.060000e-24	122.0
33	TraesCS7B01G290000	chr2D	77.778	504	73	22	1676	2142	76556473	76556974	7.980000e-70	274.0
34	TraesCS7B01G290000	chr3D	81.293	294	36	9	755	1037	603233016	603232731	1.050000e-53	220.0
35	TraesCS7B01G290000	chr3D	90.110	91	8	1	1870	1959	254459896	254459986	1.420000e-22	117.0
36	TraesCS7B01G290000	chr5B	80.224	268	40	9	1454	1717	162818658	162818916	2.970000e-44	189.0
37	TraesCS7B01G290000	chr4B	79.070	301	36	10	1692	1967	648568841	648569139	4.970000e-42	182.0
38	TraesCS7B01G290000	chr4B	90.110	91	8	1	1870	1959	534369716	534369806	1.420000e-22	117.0

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	TraesCS7B01G290000	chr7B	526384849	526387115	2266	True	4187.000000	4187	100.0000	1	2267	1	chr7B.!!$R3	2266
1	TraesCS7B01G290000	chr7B	526234031	526239720	5689	True	988.666667	1711	89.6630	1	1400	3	chr7B.!!$R5	1399
2	TraesCS7B01G290000	chr7B	708672553	708673256	703	False	562.000000	562	82.0580	1462	2140	1	chr7B.!!$F1	678
3	TraesCS7B01G290000	chr7D	497899485	497901348	1863	True	1396.000000	2182	92.8800	1	1436	2	chr7D.!!$R2	1435
4	TraesCS7B01G290000	chr7A	563475828	563477372	1544	True	1140.500000	2134	95.9055	1	2267	2	chr7A.!!$R1	2266
5	TraesCS7B01G290000	chr7A	708467856	708468564	708	False	507.000000	507	80.5560	1462	2141	1	chr7A.!!$F1	679
6	TraesCS7B01G290000	chr1B	175928950	175929672	722	True	496.000000	496	80.0280	1462	2144	1	chr1B.!!$R1	682
7	TraesCS7B01G290000	chr1B	419391750	419392454	704	False	368.000000	368	77.2980	1462	2132	1	chr1B.!!$F1	670
8	TraesCS7B01G290000	chr3B	253500463	253501185	722	True	484.000000	484	79.8630	1462	2144	1	chr3B.!!$R1	682
9	TraesCS7B01G290000	chr5D	426153870	426154571	701	False	481.000000	481	80.2200	1460	2141	1	chr5D.!!$F1	681
10	TraesCS7B01G290000	chr6B	680779545	680780251	706	False	451.000000	451	79.1720	1462	2148	1	chr6B.!!$F3	686
11	TraesCS7B01G290000	chr1D	462486007	462486673	666	True	440.000000	440	79.9700	1519	2137	1	chr1D.!!$R2	618
12	TraesCS7B01G290000	chr6D	9132808	9133351	543	True	396.000000	396	81.0040	1622	2141	1	chr6D.!!$R1	519
13	TraesCS7B01G290000	chrUn	36497731	36498445	714	False	355.000000	355	76.8380	1462	2132	1	chrUn.!!$F1	670
14	TraesCS7B01G290000	chr3A	336890801	336891453	652	True	351.000000	351	77.6610	1454	2075	1	chr3A.!!$R1	621
15	TraesCS7B01G290000	chr5A	241189126	241189662	536	True	339.000000	339	79.4060	1649	2144	1	chr5A.!!$R1	495
16	TraesCS7B01G290000	chr2D	76556473	76556974	501	False	274.000000	274	77.7780	1676	2142	1	chr2D.!!$F1	466

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
112	115	0.815734	CGACCAGGTGGATACGACTT	59.184	55.0	0.0	0.0	42.51	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1792	5875	1.278985	ACCAGTGGCGATCTGAATTGA	59.721	47.619	9.78	0.0	35.2	2.57	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
92	93	1.270147	ACAAGTTAGAGACACACCGGC	60.270	52.381	0.00	0.00	0.00	6.13
112	115	0.815734	CGACCAGGTGGATACGACTT	59.184	55.000	0.00	0.00	42.51	3.01
113	116	1.203994	CGACCAGGTGGATACGACTTT	59.796	52.381	0.00	0.00	42.51	2.66
114	117	2.618053	GACCAGGTGGATACGACTTTG	58.382	52.381	0.00	0.00	42.51	2.77
115	118	1.975680	ACCAGGTGGATACGACTTTGT	59.024	47.619	2.10	0.00	42.51	2.83
218	221	1.509644	CGCAGCTGAACCACACACAT	61.510	55.000	20.43	0.00	0.00	3.21
623	633	3.651562	CGAAATTCTCGCGGTTGTAAT	57.348	42.857	6.13	0.00	41.49	1.89
740	753	3.479269	CGCTTCCACGACGCTTCC	61.479	66.667	0.00	0.00	34.06	3.46
835	855	1.146485	TTTCCGACGGTCAAAGCCA	59.854	52.632	14.79	0.00	0.00	4.75
880	900	2.158127	TCCCTATATAACAAGCCCGGGA	60.158	50.000	29.31	0.71	37.14	5.14
939	973	1.977188	CTCGCACATAGACGACACAA	58.023	50.000	0.00	0.00	34.08	3.33
986	1028	2.403252	ATTTACCTGCTTCCCAGTCG	57.597	50.000	0.00	0.00	40.06	4.18
1178	1220	1.745320	GATGCTATCCGGACGGTGGT	61.745	60.000	6.12	0.00	36.47	4.16
1333	1375	2.365617	GAGGAGGCGTAGGATGATTCAA	59.634	50.000	0.00	0.00	0.00	2.69
1431	1474	6.256539	AGTGTGTATATCTGTCTGATTTTGCG	59.743	38.462	0.00	0.00	36.65	4.85
1434	1477	6.700081	GTGTATATCTGTCTGATTTTGCGGTA	59.300	38.462	0.00	0.00	36.65	4.02
1483	1542	0.032952	AGCAAAAGAGTCCGTGCGTA	59.967	50.000	5.04	0.00	41.90	4.42
1485	1544	1.779569	CAAAAGAGTCCGTGCGTAGT	58.220	50.000	0.00	0.00	0.00	2.73
1507	1783	9.099454	GTAGTAATGGGAGAGAAAATAACACAG	57.901	37.037	0.00	0.00	0.00	3.66
1508	1784	7.690256	AGTAATGGGAGAGAAAATAACACAGT	58.310	34.615	0.00	0.00	0.00	3.55
1509	1785	8.164070	AGTAATGGGAGAGAAAATAACACAGTT	58.836	33.333	0.00	0.00	0.00	3.16
1511	1787	7.839680	ATGGGAGAGAAAATAACACAGTTTT	57.160	32.000	0.00	0.00	0.00	2.43
1512	1788	7.272037	TGGGAGAGAAAATAACACAGTTTTC	57.728	36.000	3.15	3.15	42.03	2.29
1534	1811	6.757897	TCAACCCAATAATCATGACTCAAC	57.242	37.500	0.00	0.00	0.00	3.18
1558	3533	4.412528	ACCCTAATAGGTCCATGTCCTTTC	59.587	45.833	11.14	0.00	33.81	2.62
1589	3564	3.243468	TGACATCACATTTGTGTTGCTGG	60.243	43.478	17.46	4.12	45.03	4.85
1664	3678	3.058115	CGTCTCTCTCGCTCTCTCA	57.942	57.895	0.00	0.00	0.00	3.27
1736	3772	2.034558	CCGTTTTTCAGAGGTGTGCATT	59.965	45.455	0.00	0.00	0.00	3.56
1975	6092	7.672983	AAGATATGTATAATTTGTCTGCGGG	57.327	36.000	0.00	0.00	0.00	6.13
2042	6169	6.918569	CGATTCGACTGACTTAAATATGGACT	59.081	38.462	0.00	0.00	0.00	3.85
2156	6291	3.354089	AAAAATGCGACAGACAACCAG	57.646	42.857	0.00	0.00	0.00	4.00
2157	6292	2.254546	AAATGCGACAGACAACCAGA	57.745	45.000	0.00	0.00	0.00	3.86
2158	6293	2.254546	AATGCGACAGACAACCAGAA	57.745	45.000	0.00	0.00	0.00	3.02
2159	6294	1.800805	ATGCGACAGACAACCAGAAG	58.199	50.000	0.00	0.00	0.00	2.85
2160	6295	0.880278	TGCGACAGACAACCAGAAGC	60.880	55.000	0.00	0.00	0.00	3.86
2161	6296	0.880278	GCGACAGACAACCAGAAGCA	60.880	55.000	0.00	0.00	0.00	3.91
2162	6297	0.861837	CGACAGACAACCAGAAGCAC	59.138	55.000	0.00	0.00	0.00	4.40
2163	6298	1.230324	GACAGACAACCAGAAGCACC	58.770	55.000	0.00	0.00	0.00	5.01
2164	6299	0.179018	ACAGACAACCAGAAGCACCC	60.179	55.000	0.00	0.00	0.00	4.61
2165	6300	0.890996	CAGACAACCAGAAGCACCCC	60.891	60.000	0.00	0.00	0.00	4.95
2166	6301	1.966451	GACAACCAGAAGCACCCCG	60.966	63.158	0.00	0.00	0.00	5.73
2167	6302	2.113139	CAACCAGAAGCACCCCGT	59.887	61.111	0.00	0.00	0.00	5.28
2168	6303	2.113139	AACCAGAAGCACCCCGTG	59.887	61.111	0.00	0.00	36.51	4.94
2182	6317	4.647611	CACCCCGTGCATTATTATTAGGA	58.352	43.478	0.00	0.00	0.00	2.94
2183	6318	5.067273	CACCCCGTGCATTATTATTAGGAA	58.933	41.667	0.00	0.00	0.00	3.36
2184	6319	5.533154	CACCCCGTGCATTATTATTAGGAAA	59.467	40.000	0.00	0.00	0.00	3.13
2229	6364	7.074502	CACTTTCTTTGAGTCAGCAAGTTATC	58.925	38.462	4.82	0.00	0.00	1.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
92	93	1.035932	AGTCGTATCCACCTGGTCGG	61.036	60.000	0.00	2.45	39.35	4.79
112	115	0.592637	CTGCTTGACATTCCGCACAA	59.407	50.000	0.00	0.00	0.00	3.33
113	116	0.250252	TCTGCTTGACATTCCGCACA	60.250	50.000	0.00	0.00	0.00	4.57
114	117	0.874390	TTCTGCTTGACATTCCGCAC	59.126	50.000	0.00	0.00	0.00	5.34
115	118	1.739466	GATTCTGCTTGACATTCCGCA	59.261	47.619	0.00	0.00	0.00	5.69
378	382	0.885879	ACAGATGCGGACAGTTCGTA	59.114	50.000	2.44	0.00	0.00	3.43
444	448	0.249398	AGAAATTACGTGCCTCGGCT	59.751	50.000	9.65	0.00	44.69	5.52
623	633	2.747446	GCTTGGAATTCTAGCGTGGAAA	59.253	45.455	14.37	0.00	34.84	3.13
777	797	2.631580	GGAAAATCGGCACCGGCAA	61.632	57.895	9.58	0.00	43.71	4.52
835	855	1.918957	AGGTTGATGGGCTAGCTCTTT	59.081	47.619	17.26	2.87	0.00	2.52
880	900	0.598562	TGTTTGCCGTTGTGTTGTGT	59.401	45.000	0.00	0.00	0.00	3.72
956	997	5.758784	GGAAGCAGGTAAATAAGAATACGCT	59.241	40.000	0.00	0.00	0.00	5.07
967	1009	1.906574	TCGACTGGGAAGCAGGTAAAT	59.093	47.619	0.00	0.00	0.00	1.40
986	1028	2.096657	GCCGCCATTCTTTCTCTCTTTC	59.903	50.000	0.00	0.00	0.00	2.62
1045	1087	2.906897	AAACAGGCACGCCACCAG	60.907	61.111	11.35	0.00	38.92	4.00
1333	1375	9.136323	AGAACTAAAGAAACAATCATGAAACCT	57.864	29.630	0.00	0.00	0.00	3.50
1377	1419	3.684788	TGGTACTTACTCCGTTACTCGTC	59.315	47.826	0.00	0.00	37.94	4.20
1417	1460	4.685169	ATTGTACCGCAAAATCAGACAG	57.315	40.909	0.00	0.00	40.91	3.51
1483	1542	7.690256	ACTGTGTTATTTTCTCTCCCATTACT	58.310	34.615	0.00	0.00	0.00	2.24
1485	1544	8.934023	AAACTGTGTTATTTTCTCTCCCATTA	57.066	30.769	0.00	0.00	0.00	1.90
1508	1784	7.773489	TGAGTCATGATTATTGGGTTGAAAA	57.227	32.000	0.00	0.00	0.00	2.29
1509	1785	7.232330	TGTTGAGTCATGATTATTGGGTTGAAA	59.768	33.333	0.00	0.00	0.00	2.69
1511	1787	6.150976	GTGTTGAGTCATGATTATTGGGTTGA	59.849	38.462	0.00	0.00	0.00	3.18
1512	1788	6.324819	GTGTTGAGTCATGATTATTGGGTTG	58.675	40.000	0.00	0.00	0.00	3.77
1534	1811	3.318313	AGGACATGGACCTATTAGGGTG	58.682	50.000	14.26	9.22	40.58	4.61
1589	3564	2.202810	GAGCACTGAGGCTACCGC	60.203	66.667	0.00	0.00	45.99	5.68
1736	3772	3.331150	AGAAAACATCGATAACCACGCA	58.669	40.909	0.00	0.00	0.00	5.24
1792	5875	1.278985	ACCAGTGGCGATCTGAATTGA	59.721	47.619	9.78	0.00	35.20	2.57
1975	6092	5.411669	ACCTCTCACATTTCGGTTAATCAAC	59.588	40.000	0.00	0.00	0.00	3.18
2144	6279	1.230324	GGTGCTTCTGGTTGTCTGTC	58.770	55.000	0.00	0.00	0.00	3.51
2145	6280	0.179018	GGGTGCTTCTGGTTGTCTGT	60.179	55.000	0.00	0.00	0.00	3.41
2146	6281	0.890996	GGGGTGCTTCTGGTTGTCTG	60.891	60.000	0.00	0.00	0.00	3.51
2147	6282	1.456287	GGGGTGCTTCTGGTTGTCT	59.544	57.895	0.00	0.00	0.00	3.41
2148	6283	1.966451	CGGGGTGCTTCTGGTTGTC	60.966	63.158	0.00	0.00	0.00	3.18
2149	6284	2.113139	CGGGGTGCTTCTGGTTGT	59.887	61.111	0.00	0.00	0.00	3.32
2150	6285	2.113139	ACGGGGTGCTTCTGGTTG	59.887	61.111	0.00	0.00	0.00	3.77
2151	6286	2.113139	CACGGGGTGCTTCTGGTT	59.887	61.111	0.00	0.00	0.00	3.67
2160	6295	4.647611	TCCTAATAATAATGCACGGGGTG	58.352	43.478	0.00	0.00	36.51	4.61
2161	6296	4.986054	TCCTAATAATAATGCACGGGGT	57.014	40.909	0.00	0.00	0.00	4.95
2162	6297	6.488683	TCTTTTCCTAATAATAATGCACGGGG	59.511	38.462	0.00	0.00	0.00	5.73
2163	6298	7.504924	TCTTTTCCTAATAATAATGCACGGG	57.495	36.000	0.00	0.00	0.00	5.28
2164	6299	8.567948	ACATCTTTTCCTAATAATAATGCACGG	58.432	33.333	0.00	0.00	0.00	4.94
2176	6311	9.213777	TCCATGTCTAGTACATCTTTTCCTAAT	57.786	33.333	0.00	0.00	46.15	1.73
2177	6312	8.603898	TCCATGTCTAGTACATCTTTTCCTAA	57.396	34.615	0.00	0.00	46.15	2.69
2178	6313	8.475639	GTTCCATGTCTAGTACATCTTTTCCTA	58.524	37.037	0.00	0.00	46.15	2.94
2179	6314	7.038302	TGTTCCATGTCTAGTACATCTTTTCCT	60.038	37.037	0.00	0.00	46.15	3.36
2180	6315	7.064728	GTGTTCCATGTCTAGTACATCTTTTCC	59.935	40.741	0.00	0.00	46.15	3.13
2181	6316	7.819900	AGTGTTCCATGTCTAGTACATCTTTTC	59.180	37.037	0.00	0.00	46.15	2.29
2182	6317	7.680730	AGTGTTCCATGTCTAGTACATCTTTT	58.319	34.615	0.00	0.00	46.15	2.27
2183	6318	7.246171	AGTGTTCCATGTCTAGTACATCTTT	57.754	36.000	0.00	0.00	46.15	2.52
2184	6319	6.859112	AGTGTTCCATGTCTAGTACATCTT	57.141	37.500	0.00	0.00	46.15	2.40
2229	6364	7.636150	AGGAACAAGGATAAGTTTCATCATG	57.364	36.000	0.00	0.00	0.00	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.