AutoCloner

Multiple sequence alignment - TraesCS7A01G288100

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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	TraesCS7A01G288100	chr7A	100.000	2330	0	0	1	2330	346769590	346767261	0.000000e+00	4303.0
1	TraesCS7A01G288100	chr4A	94.178	2336	123	9	1	2330	622161371	622163699	0.000000e+00	3548.0
2	TraesCS7A01G288100	chr4A	86.068	323	38	4	1979	2296	716535122	716534802	7.970000e-90	340.0
3	TraesCS7A01G288100	chr2B	94.158	2328	129	7	1	2326	631840	634162	0.000000e+00	3539.0
4	TraesCS7A01G288100	chr2B	93.145	2334	135	11	1	2330	488701816	488704128	0.000000e+00	3400.0
5	TraesCS7A01G288100	chr1A	94.042	2333	131	8	1	2330	143378962	143376635	0.000000e+00	3531.0
6	TraesCS7A01G288100	chr1A	93.675	1834	109	7	1	1831	480976001	480974172	0.000000e+00	2737.0
7	TraesCS7A01G288100	chr3D	95.630	1602	68	2	730	2330	124495014	124493414	0.000000e+00	2569.0
8	TraesCS7A01G288100	chr3D	95.225	733	33	2	1	731	124495794	124495062	0.000000e+00	1158.0
9	TraesCS7A01G288100	chr7B	94.359	585	32	1	1	585	511463900	511463317	0.000000e+00	896.0
10	TraesCS7A01G288100	chr1B	89.544	373	36	3	44	416	200035723	200035354	9.750000e-129	470.0
11	TraesCS7A01G288100	chr6A	85.809	451	51	8	44	493	239316430	239316868	1.260000e-127	466.0
12	TraesCS7A01G288100	chr5A	87.761	335	30	5	1836	2164	219128348	219128677	4.700000e-102	381.0
13	TraesCS7A01G288100	chr5A	86.527	334	34	4	1836	2164	208947309	208947636	7.920000e-95	357.0
14	TraesCS7A01G288100	chr3B	86.986	292	25	3	1858	2136	462621384	462621093	1.340000e-82	316.0
15	TraesCS7A01G288100	chrUn	87.402	254	26	3	1911	2158	402215522	402215775	1.050000e-73	287.0
16	TraesCS7A01G288100	chrUn	89.189	74	4	1	1836	1909	388630247	388630316	3.190000e-14	89.8

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	TraesCS7A01G288100	chr7A	346767261	346769590	2329	True	4303.0	4303	100.0000	1	2330	1	chr7A.!!$R1	2329
1	TraesCS7A01G288100	chr4A	622161371	622163699	2328	False	3548.0	3548	94.1780	1	2330	1	chr4A.!!$F1	2329
2	TraesCS7A01G288100	chr2B	631840	634162	2322	False	3539.0	3539	94.1580	1	2326	1	chr2B.!!$F1	2325
3	TraesCS7A01G288100	chr2B	488701816	488704128	2312	False	3400.0	3400	93.1450	1	2330	1	chr2B.!!$F2	2329
4	TraesCS7A01G288100	chr1A	143376635	143378962	2327	True	3531.0	3531	94.0420	1	2330	1	chr1A.!!$R1	2329
5	TraesCS7A01G288100	chr1A	480974172	480976001	1829	True	2737.0	2737	93.6750	1	1831	1	chr1A.!!$R2	1830
6	TraesCS7A01G288100	chr3D	124493414	124495794	2380	True	1863.5	2569	95.4275	1	2330	2	chr3D.!!$R1	2329
7	TraesCS7A01G288100	chr7B	511463317	511463900	583	True	896.0	896	94.3590	1	585	1	chr7B.!!$R1	584

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
640	652	0.909623	CTTAGTGGTTCCGGGGTCAT	59.09	55.0	0.0	0.0	0.0	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2208	2288	0.597568	CCAAAACAGCGCTTGGATCA	59.402	50.0	19.1	0.0	44.16	2.92	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
43	46	1.065854	AGCATCAACTCCTTCCTTCCG	60.066	52.381	0.00	0.00	0.00	4.30
167	173	6.982141	CGCAAGTAAATACTACTGGGATTACA	59.018	38.462	4.26	0.00	34.99	2.41
204	211	1.372582	TGACATGCGAGCAATTCTCC	58.627	50.000	0.57	0.00	38.62	3.71
253	264	4.697352	CAGGAGCTAAACTGTTGTGCTATT	59.303	41.667	16.71	8.39	33.83	1.73
271	282	7.065803	TGTGCTATTTTCAGAATTGGTACTAGC	59.934	37.037	0.00	0.00	0.00	3.42
392	403	7.399245	AACTTGTTGGTTCAGTTTAAAGCTA	57.601	32.000	0.00	0.00	0.00	3.32
418	429	4.484872	GGCTTGCGGTAGGGGGAC	62.485	72.222	0.00	0.00	0.00	4.46
472	484	2.735151	TGTGAGTATGATCGGGACTGT	58.265	47.619	0.00	0.00	0.00	3.55
504	516	7.230510	TCTGAAAGTATGTTAGCCAATGTTTGT	59.769	33.333	0.00	0.00	33.76	2.83
562	574	4.013728	GTGCCATGGTAAGTTTGGATGTA	58.986	43.478	14.67	0.00	31.94	2.29
623	635	3.420893	TGCTACAACAATAGCTTGCCTT	58.579	40.909	0.00	0.00	46.54	4.35
632	644	2.781681	TAGCTTGCCTTAGTGGTTCC	57.218	50.000	0.00	0.00	38.35	3.62
640	652	0.909623	CTTAGTGGTTCCGGGGTCAT	59.090	55.000	0.00	0.00	0.00	3.06
901	977	6.149142	CCATTTTGGTGGAATGTAAACATTGG	59.851	38.462	12.85	1.57	42.02	3.16
936	1012	6.151144	AGTTTGATATTTTTCTAGGCGCAAGT	59.849	34.615	10.83	0.00	41.68	3.16
937	1013	6.509418	TTGATATTTTTCTAGGCGCAAGTT	57.491	33.333	10.83	0.00	41.68	2.66
955	1031	3.718723	AGTTATCAGGCTCTTCCAGTCT	58.281	45.455	0.00	0.00	37.68	3.24
982	1058	2.671070	CAGGCCCGAGTCACCATT	59.329	61.111	0.00	0.00	0.00	3.16
998	1074	3.317149	CACCATTATCCTGATGTTGCCAG	59.683	47.826	0.00	0.00	0.00	4.85
1188	1264	5.106277	GCGAGGCTACTTAAAAACAATCCTT	60.106	40.000	0.00	0.00	0.00	3.36
1194	1270	6.861572	GCTACTTAAAAACAATCCTTGGTGAC	59.138	38.462	0.00	0.00	34.12	3.67
1292	1368	4.223320	TGTGGCGAATTCTTGAAGAAAC	57.777	40.909	12.10	8.31	37.82	2.78
1371	1447	9.077674	GTTCTATAGTATACCAAAGATCATGCG	57.922	37.037	0.00	0.00	0.00	4.73
1437	1513	8.736244	TGGCACTAAACATCTTAAGGATAAAAC	58.264	33.333	1.85	0.00	32.64	2.43
1460	1536	4.397417	CAGAAGCAATCTTTAGGAACTGGG	59.603	45.833	0.00	0.00	35.80	4.45
1466	1542	5.192927	CAATCTTTAGGAACTGGGCATGTA	58.807	41.667	0.00	0.00	41.52	2.29
1486	1563	5.216622	TGTATGCTCTATAGAACCCCTGTT	58.783	41.667	3.57	0.00	37.42	3.16
1680	1758	1.221635	CCTGGATCCCACACCCATTA	58.778	55.000	9.90	0.00	0.00	1.90
1688	1766	2.705658	TCCCACACCCATTATAGCTCAG	59.294	50.000	0.00	0.00	0.00	3.35
1698	1776	1.032794	TATAGCTCAGTCCACGCTGG	58.967	55.000	0.00	0.00	39.43	4.85
2049	2127	9.772973	ATCACAATGCAAATATTCATGCTTAAT	57.227	25.926	12.20	0.00	42.97	1.40
2086	2164	2.574006	TTCTGGCAGCAGTGAATCTT	57.426	45.000	10.34	0.00	0.00	2.40
2111	2189	0.179018	AGTTCTGTGTGGCCTTGGAC	60.179	55.000	3.32	0.00	0.00	4.02
2112	2190	1.227823	TTCTGTGTGGCCTTGGACG	60.228	57.895	3.32	0.00	0.00	4.79
2122	2200	1.373570	GCCTTGGACGAATCCTGAAG	58.626	55.000	0.00	0.00	46.43	3.02
2126	2204	3.557054	CCTTGGACGAATCCTGAAGTGAA	60.557	47.826	0.00	0.00	46.43	3.18
2203	2283	6.563381	GCTTTTGCTGAGATGAATTGTTTGTG	60.563	38.462	0.00	0.00	43.35	3.33
2208	2288	5.278169	GCTGAGATGAATTGTTTGTGTCACT	60.278	40.000	4.27	0.00	0.00	3.41
2219	2299	0.950555	TGTGTCACTGATCCAAGCGC	60.951	55.000	0.00	0.00	0.00	5.92
2228	2308	0.598065	GATCCAAGCGCTGTTTTGGT	59.402	50.000	22.01	11.79	43.43	3.67
2287	2367	7.041712	GGTCTCTGCTTAATTGTCTTATAAGCC	60.042	40.741	7.67	0.00	46.88	4.35
2296	2376	4.665833	TGTCTTATAAGCCGTAGTGCAT	57.334	40.909	7.67	0.00	0.00	3.96
2326	2406	0.332972	GAAATCCCACCCTCCTTGCT	59.667	55.000	0.00	0.00	0.00	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	46	9.601217	AGTAATGTAAATACAGATGGTTGAGAC	57.399	33.333	0.00	0.00	39.92	3.36
182	189	2.353889	GAGAATTGCTCGCATGTCATGT	59.646	45.455	14.26	0.00	33.17	3.21
253	264	9.733556	TTATCTTTGCTAGTACCAATTCTGAAA	57.266	29.630	0.00	0.00	0.00	2.69
271	282	9.499585	CAGAATGTGCAGTTTAGATTATCTTTG	57.500	33.333	0.00	0.00	0.00	2.77
316	327	1.831736	GAAGACTGATTTCCCGAGGGA	59.168	52.381	6.80	6.80	43.52	4.20
356	367	7.592938	TGAACCAACAAGTTATCATGTCATTC	58.407	34.615	0.00	0.00	0.00	2.67
392	403	1.048724	TACCGCAAGCCTCTGCCTAT	61.049	55.000	0.00	0.00	39.26	2.57
418	429	3.181477	TGGTTTTCAACTGGCAGTGATTG	60.181	43.478	22.83	16.02	0.00	2.67
472	484	5.767665	TGGCTAACATACTTTCAGAAAAGCA	59.232	36.000	13.12	1.03	44.82	3.91
530	542	5.570320	ACTTACCATGGCACTACATCTTTT	58.430	37.500	13.04	0.00	0.00	2.27
548	560	6.554334	TTGCAACTCTACATCCAAACTTAC	57.446	37.500	0.00	0.00	0.00	2.34
562	574	5.291971	CAAAGCAGGTTAAATTGCAACTCT	58.708	37.500	0.00	0.00	42.67	3.24
623	635	0.252330	TCATGACCCCGGAACCACTA	60.252	55.000	0.73	0.00	0.00	2.74
632	644	2.288666	CCATGTAAGTTCATGACCCCG	58.711	52.381	13.58	0.00	45.41	5.73
640	652	2.040278	AGAGCAAGCCCATGTAAGTTCA	59.960	45.455	0.00	0.00	0.00	3.18
837	899	9.586435	AACAGAAATTTAGTATAATTGCAAGGC	57.414	29.630	4.94	0.00	0.00	4.35
875	937	6.432403	ATGTTTACATTCCACCAAAATGGT	57.568	33.333	0.00	0.00	42.35	3.55
936	1012	4.219115	CCTAGACTGGAAGAGCCTGATAA	58.781	47.826	0.00	0.00	38.83	1.75
937	1013	3.437198	CCCTAGACTGGAAGAGCCTGATA	60.437	52.174	0.00	0.00	38.83	2.15
1049	1125	1.523758	GGCAACAACACACTCCCTAG	58.476	55.000	0.00	0.00	0.00	3.02
1057	1133	2.115911	GGTGGACGGCAACAACACA	61.116	57.895	0.00	0.00	36.26	3.72
1188	1264	5.863965	TGACAAAGAACATATCAGTCACCA	58.136	37.500	0.00	0.00	34.09	4.17
1194	1270	7.982224	ACATGACATGACAAAGAACATATCAG	58.018	34.615	22.19	0.00	34.28	2.90
1371	1447	9.979270	CATATCTGTTCTGTGACATAAAGAAAC	57.021	33.333	0.00	0.00	32.03	2.78
1437	1513	4.397417	CCCAGTTCCTAAAGATTGCTTCTG	59.603	45.833	0.00	0.00	33.93	3.02
1460	1536	9.580694	AACAGGGGTTCTATAGAGCATACATGC	62.581	44.444	17.19	6.06	43.24	4.06
1486	1563	9.391006	GGTTACAGACAAAATCATGGTATAAGA	57.609	33.333	0.00	0.00	0.00	2.10
1680	1758	0.684479	TCCAGCGTGGACTGAGCTAT	60.684	55.000	3.02	0.00	42.67	2.97
1688	1766	3.044305	GCACACTCCAGCGTGGAC	61.044	66.667	3.02	0.00	42.67	4.02
1698	1776	4.871993	CAATAACTGGAGATGCACACTC	57.128	45.455	12.56	12.56	0.00	3.51
2086	2164	1.148273	GCCACACAGAACTGTCCCA	59.852	57.895	4.38	0.00	42.83	4.37
2111	2189	3.338249	ACACCATTCACTTCAGGATTCG	58.662	45.455	0.00	0.00	0.00	3.34
2112	2190	6.825721	AGATAACACCATTCACTTCAGGATTC	59.174	38.462	0.00	0.00	0.00	2.52
2122	2200	2.722094	TGGGCAGATAACACCATTCAC	58.278	47.619	0.00	0.00	0.00	3.18
2126	2204	3.461085	AGAGAATGGGCAGATAACACCAT	59.539	43.478	0.00	0.00	45.18	3.55
2203	2283	0.671781	ACAGCGCTTGGATCAGTGAC	60.672	55.000	7.50	0.00	0.00	3.67
2208	2288	0.597568	CCAAAACAGCGCTTGGATCA	59.402	50.000	19.10	0.00	44.16	2.92
2287	2367	2.164422	TCCAGAACTCAGATGCACTACG	59.836	50.000	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.