AutoCloner

Multiple sequence alignment - TraesCS1A01G270200

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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	TraesCS1A01G270200	chr1A	100.000	4243	0	0	1	4243	464246320	464250562	0.000000e+00	7836
1	TraesCS1A01G270200	chr1B	96.105	2028	61	8	2226	4243	488819072	488821091	0.000000e+00	3291
2	TraesCS1A01G270200	chr1B	93.581	1075	59	7	1159	2227	488817764	488818834	0.000000e+00	1594
3	TraesCS1A01G270200	chr1B	87.333	150	8	5	983	1131	488817302	488817441	1.220000e-35	161
4	TraesCS1A01G270200	chr1D	91.174	2198	100	29	1143	3298	365434016	365436161	0.000000e+00	2898
5	TraesCS1A01G270200	chr1D	94.426	915	40	5	3337	4243	365436158	365437069	0.000000e+00	1397
6	TraesCS1A01G270200	chr1D	92.593	135	9	1	983	1116	365433565	365433699	4.330000e-45	193
7	TraesCS1A01G270200	chr7A	96.213	977	33	3	1	973	4496148	4495172	0.000000e+00	1596
8	TraesCS1A01G270200	chr7A	95.506	979	40	4	1	976	36165315	36164338	0.000000e+00	1561
9	TraesCS1A01G270200	chr3A	95.795	975	39	2	1	973	40346824	40347798	0.000000e+00	1572
10	TraesCS1A01G270200	chr6A	95.436	986	43	2	1	984	122685136	122684151	0.000000e+00	1570
11	TraesCS1A01G270200	chr5A	95.325	984	42	4	1	981	464187783	464188765	0.000000e+00	1559
12	TraesCS1A01G270200	chr4B	95.594	976	35	5	1	973	626419933	626418963	0.000000e+00	1557
13	TraesCS1A01G270200	chrUn	95.492	976	40	4	1	973	309083522	309082548	0.000000e+00	1555
14	TraesCS1A01G270200	chr6B	95.492	976	40	4	1	973	711657824	711658798	0.000000e+00	1555
15	TraesCS1A01G270200	chr3B	95.306	980	43	3	1	979	828517402	828516425	0.000000e+00	1552

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	TraesCS1A01G270200	chr1A	464246320	464250562	4242	False	7836	7836	100.000000	1	4243	1	chr1A.!!$F1	4242
1	TraesCS1A01G270200	chr1B	488817302	488821091	3789	False	1682	3291	92.339667	983	4243	3	chr1B.!!$F1	3260
2	TraesCS1A01G270200	chr1D	365433565	365437069	3504	False	1496	2898	92.731000	983	4243	3	chr1D.!!$F1	3260
3	TraesCS1A01G270200	chr7A	4495172	4496148	976	True	1596	1596	96.213000	1	973	1	chr7A.!!$R1	972
4	TraesCS1A01G270200	chr7A	36164338	36165315	977	True	1561	1561	95.506000	1	976	1	chr7A.!!$R2	975
5	TraesCS1A01G270200	chr3A	40346824	40347798	974	False	1572	1572	95.795000	1	973	1	chr3A.!!$F1	972
6	TraesCS1A01G270200	chr6A	122684151	122685136	985	True	1570	1570	95.436000	1	984	1	chr6A.!!$R1	983
7	TraesCS1A01G270200	chr5A	464187783	464188765	982	False	1559	1559	95.325000	1	981	1	chr5A.!!$F1	980
8	TraesCS1A01G270200	chr4B	626418963	626419933	970	True	1557	1557	95.594000	1	973	1	chr4B.!!$R1	972
9	TraesCS1A01G270200	chrUn	309082548	309083522	974	True	1555	1555	95.492000	1	973	1	chrUn.!!$R1	972
10	TraesCS1A01G270200	chr6B	711657824	711658798	974	False	1555	1555	95.492000	1	973	1	chr6B.!!$F1	972
11	TraesCS1A01G270200	chr3B	828516425	828517402	977	True	1552	1552	95.306000	1	979	1	chr3B.!!$R1	978

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
872	874	0.523966	AAGTGAGAGAGGCGACGAAG	59.476	55.0	0.00	0.00	0.0	3.79	F
1252	1558	0.460987	CAGTCTCCGGTCATTGAGCC	60.461	60.0	10.11	3.23	0.0	4.70	F
1299	1607	1.092348	GTGATTAGTCAAACCCCGCC	58.908	55.0	0.00	0.00	35.8	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1909	2235	4.188937	ACCAGAATGCCAATGGATATGT	57.811	40.909	2.05	0.00	37.54	2.29	R
2879	3447	3.933332	GACGCCTAATCTAGTTTGCAACT	59.067	43.478	0.00	2.51	45.40	3.16	R
3243	3826	4.005650	CTGATACAATTGACCACTGCAGT	58.994	43.478	15.25	15.25	0.00	4.40	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	2.596851	GGAGGTGAGGCAGCAAGGA	61.597	63.158	0.00	0.00	33.95	3.36
195	196	2.100631	CGGCGCTTGATTCGTTCCT	61.101	57.895	7.64	0.00	0.00	3.36
423	425	5.306678	AGGGGAATTGCTTGTGAAAATAACA	59.693	36.000	0.00	0.00	0.00	2.41
497	499	6.374613	CAGATTCCCTTAAAACTGGTAGGAAC	59.625	42.308	0.00	0.00	34.91	3.62
504	506	4.895668	AAAACTGGTAGGAACGGATACA	57.104	40.909	0.00	0.00	0.00	2.29
583	585	7.115236	TGCATGAAAACGAATCATCAAGAAAAG	59.885	33.333	0.00	0.00	35.38	2.27
656	658	2.733956	ACAGTTTCTGCCCAAACAAGA	58.266	42.857	9.57	0.00	38.53	3.02
807	809	6.884295	TCAGTATGGAAAATTCTGATCCGTTT	59.116	34.615	0.00	0.00	35.96	3.60
814	816	8.079809	TGGAAAATTCTGATCCGTTTAGTTTTC	58.920	33.333	0.00	0.00	35.96	2.29
858	860	7.227711	TGAAGTGAAAATAAACCGATGAAGTGA	59.772	33.333	0.00	0.00	0.00	3.41
860	862	6.934645	AGTGAAAATAAACCGATGAAGTGAGA	59.065	34.615	0.00	0.00	0.00	3.27
872	874	0.523966	AAGTGAGAGAGGCGACGAAG	59.476	55.000	0.00	0.00	0.00	3.79
958	965	0.528470	GCGAGACTACCAACTGCTCT	59.472	55.000	0.00	0.00	0.00	4.09
1086	1094	3.866582	ATCGCCTGCCCTACAGCC	61.867	66.667	0.00	0.00	45.78	4.85
1131	1139	4.084888	CCGGCCGACGCTTTCAAC	62.085	66.667	30.73	0.00	42.52	3.18
1132	1140	4.084888	CGGCCGACGCTTTCAACC	62.085	66.667	24.07	0.00	34.82	3.77
1133	1141	3.733960	GGCCGACGCTTTCAACCC	61.734	66.667	0.00	0.00	34.44	4.11
1134	1142	3.733960	GCCGACGCTTTCAACCCC	61.734	66.667	0.00	0.00	0.00	4.95
1135	1143	3.053896	CCGACGCTTTCAACCCCC	61.054	66.667	0.00	0.00	0.00	5.40
1249	1555	1.215382	CGCAGTCTCCGGTCATTGA	59.785	57.895	0.00	0.00	0.00	2.57
1251	1557	1.086634	GCAGTCTCCGGTCATTGAGC	61.087	60.000	0.00	5.77	0.00	4.26
1252	1558	0.460987	CAGTCTCCGGTCATTGAGCC	60.461	60.000	10.11	3.23	0.00	4.70
1289	1595	5.163713	GCTTGGTTTCATCCAGTGATTAGTC	60.164	44.000	0.00	0.00	38.80	2.59
1299	1607	1.092348	GTGATTAGTCAAACCCCGCC	58.908	55.000	0.00	0.00	35.80	6.13
1370	1678	2.420022	CTGCTCTTACGATTGGTTTGGG	59.580	50.000	0.00	0.00	0.00	4.12
1390	1698	1.277557	GAGACCTGTCCATGTCTTGCT	59.722	52.381	6.67	0.00	41.74	3.91
1434	1744	6.157471	GGAAAGGGGTCCTGTTTAGACTAATA	59.843	42.308	0.00	0.00	32.13	0.98
1489	1799	9.746711	GCTATATAATTGAAGCAAATGAGTACG	57.253	33.333	0.00	0.00	35.05	3.67
1492	1802	4.685169	ATTGAAGCAAATGAGTACGGTG	57.315	40.909	0.00	0.00	0.00	4.94
1525	1835	9.811995	GTTTCTTTAGGTTGTGGATTACTTTTT	57.188	29.630	0.00	0.00	0.00	1.94
1546	1856	2.235891	GATTTGGACCTTTGGTTCCGT	58.764	47.619	0.00	0.00	35.25	4.69
1572	1882	2.004583	TCCTCGTATCCGTGCAAAAG	57.995	50.000	0.00	0.00	35.01	2.27
1602	1912	5.287274	CACTTCATAGTGTTCGTAGCTTCAG	59.713	44.000	0.00	0.00	45.46	3.02
1747	2060	3.640967	TGTTTATGTTTCAAAGCCTGCCT	59.359	39.130	0.00	0.00	0.00	4.75
1909	2235	4.278170	GTCCTGATTGTTTGTGTTCATGGA	59.722	41.667	0.00	0.00	0.00	3.41
2004	2330	9.527157	AACATATCTAGATGATAGTACTGCAGT	57.473	33.333	25.12	25.12	40.58	4.40
2143	2471	4.083565	GGTTTTCTGTTATGGGCCAACTA	58.916	43.478	11.89	0.00	0.00	2.24
2145	2473	5.163550	GGTTTTCTGTTATGGGCCAACTATC	60.164	44.000	11.89	0.00	0.00	2.08
2229	2796	6.646653	AGCATGATACCTGTTATGTGATAACG	59.353	38.462	0.00	0.00	46.22	3.18
2252	2819	7.633621	ACGTGTTAGCCTTTTTCTTTTAGTAC	58.366	34.615	0.00	0.00	0.00	2.73
2253	2820	7.280652	ACGTGTTAGCCTTTTTCTTTTAGTACA	59.719	33.333	0.00	0.00	0.00	2.90
2254	2821	7.797123	CGTGTTAGCCTTTTTCTTTTAGTACAG	59.203	37.037	0.00	0.00	0.00	2.74
2255	2822	8.618677	GTGTTAGCCTTTTTCTTTTAGTACAGT	58.381	33.333	0.00	0.00	0.00	3.55
2256	2823	9.835389	TGTTAGCCTTTTTCTTTTAGTACAGTA	57.165	29.630	0.00	0.00	0.00	2.74
2467	3035	6.263168	ACTTTCTAATGAAACTCTGGGTGTTG	59.737	38.462	0.00	0.00	37.27	3.33
2493	3061	3.895656	TGTAGCACTAGTCACTCAAGGTT	59.104	43.478	0.00	0.00	0.00	3.50
2507	3075	5.473162	CACTCAAGGTTTTGACCATGATGTA	59.527	40.000	4.23	0.00	38.37	2.29
2879	3447	3.244422	ACTGGAACTTTGATGAAGCCGTA	60.244	43.478	0.00	0.00	39.04	4.02
2922	3490	1.177401	GCTGTTCCCAGTTGGATTCC	58.823	55.000	0.00	0.00	44.66	3.01
3243	3826	5.170021	GCATTTCTTTGCCACATGATAACA	58.830	37.500	0.00	0.00	36.60	2.41
3304	3887	6.569693	GCACAAAACTTGCGTAAAAATTCATC	59.430	34.615	0.00	0.00	0.00	2.92
3526	4110	2.630137	GCAAATCGCTCGCAAGTTC	58.370	52.632	0.00	0.00	37.77	3.01
3527	4111	0.110238	GCAAATCGCTCGCAAGTTCA	60.110	50.000	0.00	0.00	37.77	3.18
3535	4119	1.597937	GCTCGCAAGTTCACAACCAAG	60.598	52.381	0.00	0.00	39.48	3.61
3615	4199	5.349543	GGCATGCTTTTAATATAATGCTGGC	59.650	40.000	18.92	0.00	40.15	4.85
3619	4203	6.437928	TGCTTTTAATATAATGCTGGCGAAG	58.562	36.000	0.00	0.00	0.00	3.79
3641	4225	2.636768	GCCTTCAGCACGCTATTTTT	57.363	45.000	0.00	0.00	42.97	1.94
3755	4339	2.325583	TACGAATGCCCTTGTCATCC	57.674	50.000	0.00	0.00	0.00	3.51
3770	4354	1.570024	TCATCCCCAAATGCATCTCCA	59.430	47.619	0.00	0.00	0.00	3.86
4085	4676	9.110502	CTTACCTGAGGTTCTGATATTTTTACC	57.889	37.037	10.53	0.00	37.09	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
94	95	0.676151	CTTCCTTGCTGCCTCACCTC	60.676	60.000	0.00	0.00	0.00	3.85
111	112	2.551459	GACAGCTTCAATGTGCAGTCTT	59.449	45.455	14.56	0.00	40.78	3.01
195	196	4.641645	CCAAGCTCCACGCCACCA	62.642	66.667	0.00	0.00	40.39	4.17
423	425	1.582937	CGCTAAGTCGTCGTCGCAT	60.583	57.895	0.00	0.00	36.96	4.73
497	499	5.657470	ATCAACGTCATCAATTGTATCCG	57.343	39.130	5.13	7.01	0.00	4.18
504	506	8.397906	CACCACTATTTATCAACGTCATCAATT	58.602	33.333	0.00	0.00	0.00	2.32
604	606	6.989169	GCAGAGATTAGAAAGCTTCCTATGAA	59.011	38.462	0.00	0.00	0.00	2.57
618	620	6.360370	AACTGTTTGGTAGCAGAGATTAGA	57.640	37.500	0.00	0.00	36.62	2.10
656	658	6.348213	CCGAATCACGTCCATAACTTTTCTTT	60.348	38.462	0.00	0.00	40.78	2.52
781	783	6.595682	ACGGATCAGAATTTTCCATACTGAT	58.404	36.000	0.00	0.00	46.42	2.90
794	796	6.649557	ACGAAGAAAACTAAACGGATCAGAAT	59.350	34.615	0.00	0.00	0.00	2.40
807	809	5.047847	CCTCTCACACAACGAAGAAAACTA	58.952	41.667	0.00	0.00	0.00	2.24
814	816	1.068588	TCACCCTCTCACACAACGAAG	59.931	52.381	0.00	0.00	0.00	3.79
858	860	2.494073	AGATTTTCTTCGTCGCCTCTCT	59.506	45.455	0.00	0.00	0.00	3.10
860	862	3.731264	CGTAGATTTTCTTCGTCGCCTCT	60.731	47.826	0.00	0.00	33.49	3.69
872	874	6.092748	TGTAGGTTAACCGTCGTAGATTTTC	58.907	40.000	18.91	0.00	40.67	2.29
902	907	2.424302	CCACCACTTTCGTCCGGT	59.576	61.111	0.00	0.00	0.00	5.28
979	986	3.263425	ACGGGCAAAAGGAGATAAGAAGA	59.737	43.478	0.00	0.00	0.00	2.87
996	1003	0.733150	GATGCAAGAAAGGTACGGGC	59.267	55.000	0.00	0.00	0.00	6.13
1098	1106	3.537874	GGGACGGTAGGCTGCGAT	61.538	66.667	0.00	0.00	0.00	4.58
1116	1124	3.733960	GGGTTGAAAGCGTCGGCC	61.734	66.667	0.00	0.00	41.24	6.13
1141	1149	3.732849	GAGAGGCCTTGGGGTGGG	61.733	72.222	6.77	0.00	34.45	4.61
1172	1475	1.455773	AGATCGGGAGCGGTGATGA	60.456	57.895	0.00	0.00	0.00	2.92
1181	1487	2.256764	CGATGCGGAGATCGGGAG	59.743	66.667	0.00	0.00	41.29	4.30
1249	1555	2.356535	CCAAGCTCATACCTCAAAGGCT	60.357	50.000	0.00	0.00	39.63	4.58
1251	1557	3.356529	ACCAAGCTCATACCTCAAAGG	57.643	47.619	0.00	0.00	42.49	3.11
1252	1558	4.761739	TGAAACCAAGCTCATACCTCAAAG	59.238	41.667	0.00	0.00	0.00	2.77
1390	1698	1.344438	CCTACGGGCAGAATCATAGCA	59.656	52.381	0.00	0.00	0.00	3.49
1410	1718	5.494390	TTAGTCTAAACAGGACCCCTTTC	57.506	43.478	0.00	0.00	34.56	2.62
1489	1799	4.665833	ACCTAAAGAAACAAAAGGCACC	57.334	40.909	0.00	0.00	0.00	5.01
1492	1802	4.808895	CCACAACCTAAAGAAACAAAAGGC	59.191	41.667	0.00	0.00	0.00	4.35
1525	1835	2.235016	CGGAACCAAAGGTCCAAATCA	58.765	47.619	0.00	0.00	33.12	2.57
1602	1912	6.538263	ACCATCTCCCTAATTCTCATTAAGC	58.462	40.000	0.00	0.00	0.00	3.09
1747	2060	6.347969	CGATTTCTTCATTCTTTGAGCAGACA	60.348	38.462	0.00	0.00	35.27	3.41
1909	2235	4.188937	ACCAGAATGCCAATGGATATGT	57.811	40.909	2.05	0.00	37.54	2.29
1980	2306	8.620416	GGACTGCAGTACTATCATCTAGATATG	58.380	40.741	22.46	0.00	38.50	1.78
2089	2415	4.277672	CCATGTTCAGGGCTCATATTTCTG	59.722	45.833	0.00	0.00	0.00	3.02
2143	2471	6.549242	TGCATCTAATCATTCATGGGAAGAT	58.451	36.000	0.00	0.00	36.25	2.40
2145	2473	6.040054	TGTTGCATCTAATCATTCATGGGAAG	59.960	38.462	0.00	0.00	36.25	3.46
2229	2796	8.618677	ACTGTACTAAAAGAAAAAGGCTAACAC	58.381	33.333	0.00	0.00	0.00	3.32
2256	2823	9.379791	ACAGCGTTAGTTAGAAGCTTAATTTAT	57.620	29.630	0.00	0.00	35.82	1.40
2269	2836	7.277981	AGGAATCAAACATACAGCGTTAGTTAG	59.722	37.037	0.00	0.00	0.00	2.34
2275	2842	4.323417	TGAGGAATCAAACATACAGCGTT	58.677	39.130	0.00	0.00	0.00	4.84
2337	2904	4.288670	TCTCGCTACATAGAAAAGGACG	57.711	45.455	0.00	0.00	0.00	4.79
2493	3061	7.284261	TCTGTTTCAACTTACATCATGGTCAAA	59.716	33.333	0.00	0.00	0.00	2.69
2879	3447	3.933332	GACGCCTAATCTAGTTTGCAACT	59.067	43.478	0.00	2.51	45.40	3.16
2922	3490	4.098044	TCCTCCTGAATAAGTAAGAGTGCG	59.902	45.833	0.00	0.00	0.00	5.34
3243	3826	4.005650	CTGATACAATTGACCACTGCAGT	58.994	43.478	15.25	15.25	0.00	4.40
3341	3924	9.667107	TTTATGGAGAAGTACTTAACATCCTTG	57.333	33.333	20.61	0.00	31.87	3.61
3380	3964	4.177537	TCACTGATTTGGGTGGAAAAGA	57.822	40.909	0.00	0.00	34.57	2.52
3535	4119	8.094798	TGTACAACAGATAGTTCACCATTTTC	57.905	34.615	0.00	0.00	38.74	2.29
3641	4225	1.747367	CCCTGCCGCGGTTCAATAA	60.747	57.895	28.70	2.98	0.00	1.40
3742	4326	0.413037	ATTTGGGGATGACAAGGGCA	59.587	50.000	0.00	0.00	0.00	5.36
3743	4327	0.826062	CATTTGGGGATGACAAGGGC	59.174	55.000	0.00	0.00	0.00	5.19
3755	4339	0.259647	TCCCTGGAGATGCATTTGGG	59.740	55.000	0.00	8.69	34.76	4.12
3770	4354	4.379243	CAGGTCGCGCTTGTCCCT	62.379	66.667	5.56	0.00	0.00	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.