AutoCloner

Multiple sequence alignment - TraesCS4A01G168100

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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	TraesCS4A01G168100	chr4A	100.000	3644	0	0	1	3644	418291095	418287452	0.000000e+00	6730.0
1	TraesCS4A01G168100	chr6D	95.047	3654	157	18	1	3644	197263424	197267063	0.000000e+00	5723.0
2	TraesCS4A01G168100	chr6D	93.968	2669	125	13	462	3098	338138091	338135427	0.000000e+00	4004.0
3	TraesCS4A01G168100	chr6D	88.210	1391	132	19	2267	3644	245496821	245498192	0.000000e+00	1631.0
4	TraesCS4A01G168100	chr6D	86.994	1384	153	15	2267	3637	245569550	245570919	0.000000e+00	1533.0
5	TraesCS4A01G168100	chr6D	94.050	437	19	1	3	432	338138526	338138090	0.000000e+00	656.0
6	TraesCS4A01G168100	chr2D	94.776	3656	164	15	1	3644	161651781	161648141	0.000000e+00	5668.0
7	TraesCS4A01G168100	chr2B	93.574	3657	215	17	2	3644	430822838	430819188	0.000000e+00	5433.0
8	TraesCS4A01G168100	chr2B	92.688	930	65	3	2707	3633	669355657	669356586	0.000000e+00	1338.0
9	TraesCS4A01G168100	chr2B	92.332	939	65	3	2707	3644	602888718	602887786	0.000000e+00	1328.0
10	TraesCS4A01G168100	chr3A	92.293	3685	222	20	1	3644	216936512	216940175	0.000000e+00	5175.0
11	TraesCS4A01G168100	chr3A	94.616	2916	138	9	1	2911	217011979	217014880	0.000000e+00	4497.0
12	TraesCS4A01G168100	chr6A	89.647	1787	135	24	430	2199	568172595	568174348	0.000000e+00	2230.0
13	TraesCS4A01G168100	chr3B	94.774	1435	70	5	1365	2797	241261628	241260197	0.000000e+00	2230.0
14	TraesCS4A01G168100	chr4B	94.130	1431	78	6	1365	2791	199721268	199722696	0.000000e+00	2172.0
15	TraesCS4A01G168100	chr4B	91.811	1331	86	15	508	1824	527931247	527929926	0.000000e+00	1832.0
16	TraesCS4A01G168100	chr4B	90.987	1054	77	14	430	1469	631901768	631902817	0.000000e+00	1404.0
17	TraesCS4A01G168100	chr4B	87.437	199	19	6	112	307	195136031	195135836	1.320000e-54	224.0
18	TraesCS4A01G168100	chr7A	92.944	1488	100	5	1822	3305	276742028	276743514	0.000000e+00	2161.0
19	TraesCS4A01G168100	chr1A	89.747	1385	118	16	2267	3636	489151194	489152569	0.000000e+00	1749.0
20	TraesCS4A01G168100	chr5B	94.785	882	41	4	1	879	357076092	357075213	0.000000e+00	1369.0
21	TraesCS4A01G168100	chr5B	86.284	401	36	14	8	401	472026382	472025994	5.630000e-113	418.0
22	TraesCS4A01G168100	chr6B	91.304	69	3	3	4	69	353096111	353096043	1.390000e-14	91.6
23	TraesCS4A01G168100	chr4D	93.333	60	2	2	1	58	37441313	37441372	1.800000e-13	87.9

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	TraesCS4A01G168100	chr4A	418287452	418291095	3643	True	6730	6730	100.000	1	3644	1	chr4A.!!$R1	3643
1	TraesCS4A01G168100	chr6D	197263424	197267063	3639	False	5723	5723	95.047	1	3644	1	chr6D.!!$F1	3643
2	TraesCS4A01G168100	chr6D	338135427	338138526	3099	True	2330	4004	94.009	3	3098	2	chr6D.!!$R1	3095
3	TraesCS4A01G168100	chr6D	245496821	245498192	1371	False	1631	1631	88.210	2267	3644	1	chr6D.!!$F2	1377
4	TraesCS4A01G168100	chr6D	245569550	245570919	1369	False	1533	1533	86.994	2267	3637	1	chr6D.!!$F3	1370
5	TraesCS4A01G168100	chr2D	161648141	161651781	3640	True	5668	5668	94.776	1	3644	1	chr2D.!!$R1	3643
6	TraesCS4A01G168100	chr2B	430819188	430822838	3650	True	5433	5433	93.574	2	3644	1	chr2B.!!$R1	3642
7	TraesCS4A01G168100	chr2B	669355657	669356586	929	False	1338	1338	92.688	2707	3633	1	chr2B.!!$F1	926
8	TraesCS4A01G168100	chr2B	602887786	602888718	932	True	1328	1328	92.332	2707	3644	1	chr2B.!!$R2	937
9	TraesCS4A01G168100	chr3A	216936512	216940175	3663	False	5175	5175	92.293	1	3644	1	chr3A.!!$F1	3643
10	TraesCS4A01G168100	chr3A	217011979	217014880	2901	False	4497	4497	94.616	1	2911	1	chr3A.!!$F2	2910
11	TraesCS4A01G168100	chr6A	568172595	568174348	1753	False	2230	2230	89.647	430	2199	1	chr6A.!!$F1	1769
12	TraesCS4A01G168100	chr3B	241260197	241261628	1431	True	2230	2230	94.774	1365	2797	1	chr3B.!!$R1	1432
13	TraesCS4A01G168100	chr4B	199721268	199722696	1428	False	2172	2172	94.130	1365	2791	1	chr4B.!!$F1	1426
14	TraesCS4A01G168100	chr4B	527929926	527931247	1321	True	1832	1832	91.811	508	1824	1	chr4B.!!$R2	1316
15	TraesCS4A01G168100	chr4B	631901768	631902817	1049	False	1404	1404	90.987	430	1469	1	chr4B.!!$F2	1039
16	TraesCS4A01G168100	chr7A	276742028	276743514	1486	False	2161	2161	92.944	1822	3305	1	chr7A.!!$F1	1483
17	TraesCS4A01G168100	chr1A	489151194	489152569	1375	False	1749	1749	89.747	2267	3636	1	chr1A.!!$F1	1369
18	TraesCS4A01G168100	chr5B	357075213	357076092	879	True	1369	1369	94.785	1	879	1	chr5B.!!$R1	878

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
553	563	0.173708	CTCCCAAGTCCACGCTAGTC	59.826	60.000	0.00	0.0	0.00	2.59	F
1799	1880	1.000060	GCTGCTTTGCAATGTCTCCAA	60.000	47.619	13.29	0.0	38.41	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1931	2013	0.393402	TTACCTCGTCGCTAGGCTGA	60.393	55.000	0.0	0.0	37.67	4.26	R
3263	3406	1.193874	GTTTGTACTGAGCGGGTTTCG	59.806	52.381	0.0	0.0	42.76	3.46	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
144	145	7.445096	TGACTTCTTTGCACAAAATCAGATCTA	59.555	33.333	0.00	0.00	0.00	1.98
192	193	2.165641	TCTGTATCGTACTGCACCTTGG	59.834	50.000	0.00	0.00	0.00	3.61
249	250	1.699083	TCTGTGCAATCAGACTTGGGA	59.301	47.619	3.01	0.00	39.20	4.37
336	337	7.602517	ATTGCTAAGTGATAGTCTGAACAAC	57.397	36.000	0.00	0.00	33.87	3.32
337	338	6.346477	TGCTAAGTGATAGTCTGAACAACT	57.654	37.500	0.00	0.00	33.87	3.16
347	348	5.825593	AGTCTGAACAACTGATAAGGGAA	57.174	39.130	0.00	0.00	0.00	3.97
418	428	2.621070	AGTCTAAACCAAGGGAGCTGA	58.379	47.619	0.00	0.00	0.00	4.26
547	557	1.608717	CCTCTCCTCCCAAGTCCACG	61.609	65.000	0.00	0.00	0.00	4.94
553	563	0.173708	CTCCCAAGTCCACGCTAGTC	59.826	60.000	0.00	0.00	0.00	2.59
625	635	6.936900	AGTAGGTGTTCTTAGTTCAGTACGTA	59.063	38.462	0.00	0.00	0.00	3.57
675	686	9.191995	CATATAAGATAGTACGATGTTTGTGCA	57.808	33.333	3.75	0.00	0.00	4.57
1072	1123	2.650116	ATGCGCGTCTCCTTCCTGT	61.650	57.895	8.43	0.00	0.00	4.00
1156	1207	2.124736	CAACCCCATGGCGTCGAT	60.125	61.111	6.09	0.00	33.59	3.59
1245	1298	6.929049	CAGTTCACTGTACCTAGAACAATCAA	59.071	38.462	17.89	0.00	42.01	2.57
1303	1356	5.236047	TGTGTTTACTGCAAAAATTGATGCC	59.764	36.000	11.85	0.00	41.87	4.40
1462	1515	7.041721	TCATGTGGTTGTAAGCTCTAACTATG	58.958	38.462	0.00	1.37	0.00	2.23
1577	1636	8.180267	CACACAGGATCTTTATAAGAGCAAAAG	58.820	37.037	6.96	0.00	45.44	2.27
1673	1754	7.332213	TCAATGACAGAAAAACATGAGTTCA	57.668	32.000	0.00	0.00	36.84	3.18
1694	1775	9.710900	AGTTCAAAAAGTTTTTGACTCTTGAAT	57.289	25.926	33.11	19.33	43.98	2.57
1734	1815	7.853377	ACGATATGTGTACTGTTGATAATCG	57.147	36.000	0.00	0.00	0.00	3.34
1799	1880	1.000060	GCTGCTTTGCAATGTCTCCAA	60.000	47.619	13.29	0.00	38.41	3.53
1858	1939	3.414700	CGTGCACGCTCCAACCTC	61.415	66.667	28.16	0.00	0.00	3.85
1865	1946	1.381327	CGCTCCAACCTCTCCCCTA	60.381	63.158	0.00	0.00	0.00	3.53
1951	2033	0.454600	CAGCCTAGCGACGAGGTAAA	59.545	55.000	0.00	0.00	36.37	2.01
1960	2042	3.130516	AGCGACGAGGTAAATCATCTTCA	59.869	43.478	0.00	0.00	0.00	3.02
1962	2044	4.149046	GCGACGAGGTAAATCATCTTCATC	59.851	45.833	0.00	0.00	0.00	2.92
1967	2049	4.769688	AGGTAAATCATCTTCATCGTGCA	58.230	39.130	0.00	0.00	0.00	4.57
2094	2177	5.577945	GTGCATTATGCTTTAAATGTGCAGT	59.422	36.000	18.44	0.00	45.31	4.40
2364	2450	0.981183	TACGGACATCTTGGGCTTGT	59.019	50.000	0.00	0.00	0.00	3.16
2370	2456	1.427368	ACATCTTGGGCTTGTTGGGTA	59.573	47.619	0.00	0.00	0.00	3.69
2543	2633	4.816392	TCACATTCTTGCTGTACACGTAT	58.184	39.130	0.00	0.00	0.00	3.06
2548	2638	7.062956	CACATTCTTGCTGTACACGTATCTTTA	59.937	37.037	0.00	0.00	0.00	1.85
2666	2757	5.999205	ATGGTTGTGGAGCAATTTAATGA	57.001	34.783	0.00	0.00	39.57	2.57
2746	2837	5.250774	AGGTTGTACCATACTGAAATCTGGT	59.749	40.000	0.00	0.00	41.95	4.00
2853	2944	5.447778	AGGGGATGATCATTCATATGTCC	57.552	43.478	16.02	7.67	42.73	4.02
2903	2996	9.673454	AAAAAGTATTTACATCGGTTCAAACTC	57.327	29.630	0.00	0.00	37.28	3.01
2911	3019	3.887621	TCGGTTCAAACTCAGGGATAG	57.112	47.619	0.00	0.00	0.00	2.08
3013	3147	6.952935	TCATTAAAAACAAACACAACGCTT	57.047	29.167	0.00	0.00	0.00	4.68
3072	3207	6.147656	GCTCAAACAAAAATAAACCTCATGGG	59.852	38.462	0.00	0.00	41.89	4.00
3199	3342	8.669946	TCATGCAATTTTAGGTACGATGATAA	57.330	30.769	0.00	0.00	0.00	1.75
3374	3526	6.020971	TCAGTACGAACACACACATAGATT	57.979	37.500	0.00	0.00	0.00	2.40
3379	3531	8.900781	AGTACGAACACACACATAGATTAGTAT	58.099	33.333	0.00	0.00	0.00	2.12
3406	3558	4.381411	ACTCTGTTTTTCCGGAGAGAAAG	58.619	43.478	19.72	9.41	37.09	2.62
3468	3621	5.705441	TGAATGGTTGCGAAGTAGAGAAAAT	59.295	36.000	0.00	0.00	0.00	1.82
3475	3628	6.801539	TGCGAAGTAGAGAAAATGTTCAAT	57.198	33.333	0.00	0.00	36.09	2.57
3477	3630	7.963981	TGCGAAGTAGAGAAAATGTTCAATAG	58.036	34.615	0.00	0.00	36.09	1.73
3497	3650	9.567776	TCAATAGGACTAAGTTTCACATTTTCA	57.432	29.630	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
192	193	1.355718	TGGATGGGATGAAGGGAGCC	61.356	60.000	0.00	0.00	0.00	4.70
263	264	7.121759	CCAACAATTCAGAACTAAGATCACCAT	59.878	37.037	0.00	0.00	0.00	3.55
307	308	8.604890	GTTCAGACTATCACTTAGCAATTAACC	58.395	37.037	0.00	0.00	0.00	2.85
336	337	3.355378	TGCACAATGGTTCCCTTATCAG	58.645	45.455	0.00	0.00	0.00	2.90
337	338	3.448093	TGCACAATGGTTCCCTTATCA	57.552	42.857	0.00	0.00	0.00	2.15
347	348	7.090173	GTGTTTCAATAGTAATGCACAATGGT	58.910	34.615	0.00	0.00	0.00	3.55
350	351	7.814107	CCTTGTGTTTCAATAGTAATGCACAAT	59.186	33.333	9.11	0.00	42.25	2.71
351	352	7.144661	CCTTGTGTTTCAATAGTAATGCACAA	58.855	34.615	0.00	0.00	41.38	3.33
397	398	3.786553	TCAGCTCCCTTGGTTTAGACTA	58.213	45.455	0.00	0.00	0.00	2.59
418	428	1.307647	GGGGAGGATTGGTGCACAT	59.692	57.895	20.43	3.94	0.00	3.21
547	557	6.183360	CCTCTGCTTTTTGTGATAAGACTAGC	60.183	42.308	0.00	0.00	0.00	3.42
553	563	6.373774	AGACATCCTCTGCTTTTTGTGATAAG	59.626	38.462	0.00	0.00	0.00	1.73
612	622	7.498239	ACATGAGATAGCTTACGTACTGAACTA	59.502	37.037	0.00	0.00	0.00	2.24
625	635	6.716628	TGTTTTCCAAGAACATGAGATAGCTT	59.283	34.615	0.00	0.00	32.44	3.74
973	1016	3.003173	CGGGGCCTTCCTCAGTCA	61.003	66.667	0.84	0.00	35.33	3.41
1031	1082	1.138859	GAACAAAGGGTGGCTGCTTTT	59.861	47.619	0.00	0.00	0.00	2.27
1042	1093	2.504681	GCGCATGCGAACAAAGGG	60.505	61.111	41.98	11.73	42.83	3.95
1072	1123	0.973496	TGGCGCATACCTAGGTGACA	60.973	55.000	25.33	13.21	32.55	3.58
1106	1157	3.070159	GGCTATGTGAGTAGGAAGCATCA	59.930	47.826	0.00	0.00	0.00	3.07
1156	1207	1.596260	CTCGCGACTAACTCGACCATA	59.404	52.381	3.71	0.00	46.14	2.74
1245	1298	4.837298	TCAGAATCAGGAGATGGATCGAAT	59.163	41.667	0.00	0.00	33.90	3.34
1462	1515	5.351458	ACTCATTTTTCTCTTTGTTGCCAC	58.649	37.500	0.00	0.00	0.00	5.01
1549	1608	7.418337	TGCTCTTATAAAGATCCTGTGTGTA	57.582	36.000	0.00	0.00	36.82	2.90
1577	1636	8.296713	TGAACTTACAGATTTCCATTTTGTAGC	58.703	33.333	0.00	0.00	0.00	3.58
1640	1699	6.974048	TGTTTTTCTGTCATTGAACTGATGTG	59.026	34.615	0.00	0.00	0.00	3.21
1701	1782	9.083080	CAACAGTACACATATCGTATCTTTCAA	57.917	33.333	0.00	0.00	0.00	2.69
1734	1815	7.414436	TCTAAAGTTGAGTAACACATGTTTGC	58.586	34.615	1.98	0.00	39.30	3.68
1799	1880	2.755655	CGTCATGGAGAAGTAGGACTGT	59.244	50.000	0.00	0.00	0.00	3.55
1858	1939	3.631046	GGGGCTGCGATAGGGGAG	61.631	72.222	0.00	0.00	0.00	4.30
1865	1946	4.101448	GAGTGGTGGGGCTGCGAT	62.101	66.667	0.00	0.00	0.00	4.58
1931	2013	0.393402	TTACCTCGTCGCTAGGCTGA	60.393	55.000	0.00	0.00	37.67	4.26
1951	2033	3.766068	AGGATGCACGATGAAGATGAT	57.234	42.857	0.00	0.00	0.00	2.45
1960	2042	2.203070	GGGCGAAGGATGCACGAT	60.203	61.111	7.84	0.00	0.00	3.73
1962	2044	3.499737	GTGGGCGAAGGATGCACG	61.500	66.667	0.00	0.00	39.07	5.34
1967	2049	2.579201	CGACAGTGGGCGAAGGAT	59.421	61.111	1.91	0.00	0.00	3.24
2052	2135	2.854185	GCACTGAAAAGAACACACAAGC	59.146	45.455	0.00	0.00	0.00	4.01
2094	2177	4.299586	TGTATCATTTTGCCTCAGGACA	57.700	40.909	0.00	0.00	0.00	4.02
2208	2292	6.264744	GTGAAATGTGATTCAGGATCCATGAT	59.735	38.462	15.82	3.89	39.84	2.45
2209	2293	5.591472	GTGAAATGTGATTCAGGATCCATGA	59.409	40.000	15.82	11.85	39.84	3.07
2301	2387	5.669477	ACACTGCACAAAAATATGGTGTTT	58.331	33.333	0.00	0.00	33.71	2.83
2364	2450	3.561313	GGGCTTCTTGATTCTGTACCCAA	60.561	47.826	0.00	0.00	34.82	4.12
2370	2456	4.038271	TGATTGGGCTTCTTGATTCTGT	57.962	40.909	0.00	0.00	0.00	3.41
2543	2633	5.939764	ATGGTGCATCTACAGACTAAAGA	57.060	39.130	0.00	0.00	0.00	2.52
2548	2638	4.655649	TCCATTATGGTGCATCTACAGACT	59.344	41.667	11.39	0.00	39.03	3.24
2611	2702	2.531522	AAAACCTGCCAAAGATGCAC	57.468	45.000	0.00	0.00	34.46	4.57
2666	2757	9.140286	CAATGTATACTTTAGTACATAGCGCAT	57.860	33.333	11.47	0.00	39.83	4.73
2746	2837	7.737972	TGTAAATACTTTTTGCTAGACTGCA	57.262	32.000	0.00	0.00	41.65	4.41
2893	2986	3.010420	GTGCTATCCCTGAGTTTGAACC	58.990	50.000	0.00	0.00	0.00	3.62
2903	2996	3.005554	CTGTGAACTTGTGCTATCCCTG	58.994	50.000	0.00	0.00	0.00	4.45
2911	3019	5.405269	ACTTTTGTTTTCTGTGAACTTGTGC	59.595	36.000	0.00	0.00	0.00	4.57
3072	3207	8.690840	CGACTTGAACTTTTACCATTTGAATTC	58.309	33.333	0.00	0.00	0.00	2.17
3182	3324	9.454585	CAATCTACGTTATCATCGTACCTAAAA	57.545	33.333	0.00	0.00	41.72	1.52
3199	3342	7.876068	TCCTCATAACTTTTCAACAATCTACGT	59.124	33.333	0.00	0.00	0.00	3.57
3263	3406	1.193874	GTTTGTACTGAGCGGGTTTCG	59.806	52.381	0.00	0.00	42.76	3.46
3305	3455	4.997395	TGAATTCTTCTGAAAACGGAGGAG	59.003	41.667	7.05	0.00	35.63	3.69
3374	3526	6.660521	TCCGGAAAAACAGAGTACTCATACTA	59.339	38.462	24.44	0.00	41.98	1.82
3379	3531	3.893200	TCTCCGGAAAAACAGAGTACTCA	59.107	43.478	24.44	0.00	0.00	3.41
3406	3558	4.632153	ACGGTAAGATCCATTGTGCTATC	58.368	43.478	0.00	0.00	0.00	2.08
3440	3593	3.994392	TCTACTTCGCAACCATTCAAGAC	59.006	43.478	0.00	0.00	0.00	3.01
3445	3598	5.607119	TTTTCTCTACTTCGCAACCATTC	57.393	39.130	0.00	0.00	0.00	2.67
3468	3621	8.918202	AATGTGAAACTTAGTCCTATTGAACA	57.082	30.769	0.00	0.00	38.04	3.18
3477	3630	8.515414	AGCTATTGAAAATGTGAAACTTAGTCC	58.485	33.333	0.00	0.00	38.04	3.85
3507	3660	4.232188	TGGGGCAAACAATATACCGTTA	57.768	40.909	0.00	0.00	0.00	3.18
3519	3672	2.131972	GTTTGTCGAAATGGGGCAAAC	58.868	47.619	6.29	6.29	40.96	2.93
3552	3705	5.118357	CGGTCAAATTTGATTTTGAATGCGA	59.882	36.000	23.05	0.00	44.71	5.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.