AutoCloner

Multiple sequence alignment - TraesCS6D01G325200

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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	TraesCS6D01G325200	chr6D	100.000	4069	0	0	1	4069	431316861	431320929	0.000000e+00	7515.0
1	TraesCS6D01G325200	chr6D	88.462	52	4	2	3260	3310	20494320	20494370	1.220000e-05	62.1
2	TraesCS6D01G325200	chr6A	95.681	3056	87	13	224	3267	578072946	578075968	0.000000e+00	4870.0
3	TraesCS6D01G325200	chr6A	97.414	232	5	1	1	232	578072650	578072880	1.060000e-105	394.0
4	TraesCS6D01G325200	chr6B	95.775	1562	64	1	778	2337	651018832	651020393	0.000000e+00	2518.0
5	TraesCS6D01G325200	chr6B	92.445	953	44	9	2323	3267	651020411	651021343	0.000000e+00	1336.0
6	TraesCS6D01G325200	chr6B	94.684	790	30	5	1	782	651013108	651013893	0.000000e+00	1216.0
7	TraesCS6D01G325200	chr5A	94.010	768	31	9	3308	4069	7815957	7815199	0.000000e+00	1149.0
8	TraesCS6D01G325200	chr5A	93.478	46	3	0	3268	3313	7816044	7815999	7.300000e-08	69.4
9	TraesCS6D01G325200	chr2B	81.420	662	85	21	3387	4022	539367116	539367765	1.310000e-139	507.0
10	TraesCS6D01G325200	chr3B	81.402	371	46	11	3674	4022	521686661	521686292	8.610000e-72	281.0
11	TraesCS6D01G325200	chr4D	93.478	46	3	0	3268	3313	234724547	234724502	7.300000e-08	69.4
12	TraesCS6D01G325200	chr4A	93.478	46	3	0	3268	3313	368295829	368295784	7.300000e-08	69.4
13	TraesCS6D01G325200	chr3D	90.385	52	4	1	3263	3313	190250476	190250425	2.620000e-07	67.6
14	TraesCS6D01G325200	chr4B	100.000	34	0	0	3268	3301	429024972	429025005	3.400000e-06	63.9
15	TraesCS6D01G325200	chr7A	91.304	46	2	1	3258	3301	323483726	323483771	1.220000e-05	62.1
16	TraesCS6D01G325200	chr7D	88.235	51	4	1	3262	3310	285420056	285420106	4.390000e-05	60.2
17	TraesCS6D01G325200	chr5B	88.235	51	4	2	3267	3316	337980952	337980903	4.390000e-05	60.2

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	TraesCS6D01G325200	chr6D	431316861	431320929	4068	False	7515.0	7515	100.0000	1	4069	1	chr6D.!!$F2	4068
1	TraesCS6D01G325200	chr6A	578072650	578075968	3318	False	2632.0	4870	96.5475	1	3267	2	chr6A.!!$F1	3266
2	TraesCS6D01G325200	chr6B	651018832	651021343	2511	False	1927.0	2518	94.1100	778	3267	2	chr6B.!!$F2	2489
3	TraesCS6D01G325200	chr6B	651013108	651013893	785	False	1216.0	1216	94.6840	1	782	1	chr6B.!!$F1	781
4	TraesCS6D01G325200	chr5A	7815199	7816044	845	True	609.2	1149	93.7440	3268	4069	2	chr5A.!!$R1	801
5	TraesCS6D01G325200	chr2B	539367116	539367765	649	False	507.0	507	81.4200	3387	4022	1	chr2B.!!$F1	635

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	Hairpin	End Stability	Orientation
469	548	0.033601	TTAATTGCATCCCCACCGCT	60.034	50.000	0.00	0.00	5.52	F
511	590	1.070445	CGCTCATCAGATCCACCCC	59.930	63.158	0.00	0.00	4.95	F
1568	1652	0.178990	ACCTGCTTTTCCGAAGCCTT	60.179	50.000	8.15	42.36	4.35	F
1753	1837	2.498441	TCATTACCTATGGGGCCTTGT	58.502	47.619	0.84	39.10	3.16	F
2819	2937	1.606668	ACCAAACAATGTACACTGCCG	59.393	47.619	3.81	0.00	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1515	1599	1.463553	AAGTCCAAAAGCCCTTGCCG	61.464	55.000	0.00	38.69	5.69	R
2393	2509	4.092968	GGTACGAACTGATTAAGCAACTGG	59.907	45.833	0.00	0.00	4.00	R
2806	2924	1.086696	GTCATGCGGCAGTGTACATT	58.913	50.000	9.25	0.00	2.71	R
3025	3151	3.817084	CACTTCTCCAGCAACATCTGAAA	59.183	43.478	0.00	36.19	2.69	R
3724	3905	6.147328	ACATTTCAGTTTAAACGTCCTAGCTC	59.853	38.462	12.54	0.00	4.09	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
130	131	4.816385	CCAATAGAATCGTTGTGCCATACT	59.184	41.667	1.98	0.00	0.00	2.12
204	205	3.652869	ACACTTCCTCTTCCTTGGAATCA	59.347	43.478	2.24	0.00	40.98	2.57
318	393	2.637872	AGGATGACTCGGGTTTCTTGAA	59.362	45.455	0.00	0.00	0.00	2.69
469	548	0.033601	TTAATTGCATCCCCACCGCT	60.034	50.000	0.00	0.00	0.00	5.52
500	579	1.290203	TCGATTTTGAGCCGCTCATC	58.710	50.000	23.48	16.55	40.39	2.92
511	590	1.070445	CGCTCATCAGATCCACCCC	59.930	63.158	0.00	0.00	0.00	4.95
512	591	1.453669	GCTCATCAGATCCACCCCC	59.546	63.158	0.00	0.00	0.00	5.40
675	754	9.598517	CCTAAAGAGTATACTACTAGGTATCCG	57.401	40.741	18.27	2.11	39.59	4.18
755	834	5.068636	CAGCTAGGACATTTATTCCAGCAT	58.931	41.667	12.35	0.00	38.62	3.79
976	1057	2.158081	ACCCCAGATCTCTAATCCTCCC	60.158	54.545	0.00	0.00	0.00	4.30
1515	1599	2.095161	CGTACCGATCAATAGAGGGAGC	60.095	54.545	0.00	0.00	0.00	4.70
1568	1652	0.178990	ACCTGCTTTTCCGAAGCCTT	60.179	50.000	8.15	0.00	42.36	4.35
1752	1836	3.562176	GGATCATTACCTATGGGGCCTTG	60.562	52.174	0.84	0.00	39.10	3.61
1753	1837	2.498441	TCATTACCTATGGGGCCTTGT	58.502	47.619	0.84	0.00	39.10	3.16
2208	2292	2.639347	ATGATGTGATCATCGGCCCTTA	59.361	45.455	0.00	0.00	46.62	2.69
2349	2465	7.907389	TCTCTAAAGATAGTGGTGACATGTTT	58.093	34.615	0.00	0.00	46.14	2.83
2393	2509	4.337555	AGAGCAAAAGATACCATCATGTGC	59.662	41.667	0.00	0.00	33.93	4.57
2411	2527	3.253188	TGTGCCAGTTGCTTAATCAGTTC	59.747	43.478	0.00	0.00	42.00	3.01
2436	2552	7.934665	TCGTACCAAACTACATTATGCCATATT	59.065	33.333	0.00	0.00	0.00	1.28
2675	2792	4.155462	ACAGCATACTTCTTGTTGATGCAG	59.845	41.667	7.79	2.44	40.98	4.41
2701	2818	9.810545	GCAGGCAATTGGTTTTATTAACTTATA	57.189	29.630	7.72	0.00	0.00	0.98
2749	2867	5.895636	TGCAGAAGAAGAAAAAGACAACA	57.104	34.783	0.00	0.00	0.00	3.33
2819	2937	1.606668	ACCAAACAATGTACACTGCCG	59.393	47.619	3.81	0.00	0.00	5.69
2850	2968	3.936372	TGAGTAACGAGCAGCTAGTTT	57.064	42.857	23.88	9.05	32.15	2.66
3074	3200	2.158957	TCGGGACCATGCTTAGATTCAC	60.159	50.000	0.00	0.00	0.00	3.18
3128	3254	5.634118	TGCCCCCTTCAAATAAGATCTATG	58.366	41.667	0.00	0.00	0.00	2.23
3129	3255	4.460731	GCCCCCTTCAAATAAGATCTATGC	59.539	45.833	0.00	0.00	0.00	3.14
3130	3256	5.012893	CCCCCTTCAAATAAGATCTATGCC	58.987	45.833	0.00	0.00	0.00	4.40
3131	3257	5.458069	CCCCCTTCAAATAAGATCTATGCCA	60.458	44.000	0.00	0.00	0.00	4.92
3132	3258	6.251471	CCCCTTCAAATAAGATCTATGCCAT	58.749	40.000	0.00	0.00	0.00	4.40
3133	3259	6.376581	CCCCTTCAAATAAGATCTATGCCATC	59.623	42.308	0.00	0.00	0.00	3.51
3134	3260	7.173722	CCCTTCAAATAAGATCTATGCCATCT	58.826	38.462	0.00	0.00	31.51	2.90
3135	3261	8.324306	CCCTTCAAATAAGATCTATGCCATCTA	58.676	37.037	0.00	0.00	29.97	1.98
3136	3262	9.902684	CCTTCAAATAAGATCTATGCCATCTAT	57.097	33.333	0.00	0.00	29.97	1.98
3257	3383	3.844577	ATTGTTCAAGTCAGAGCATGC	57.155	42.857	10.51	10.51	0.00	4.06
3303	3429	3.366396	TCAGACTACTGATCCCTTGGTC	58.634	50.000	0.00	0.00	46.55	4.02
3349	3523	6.779860	TGTTAGGAGCTGAGTTATTTCCTTT	58.220	36.000	0.00	0.00	39.02	3.11
3385	3559	8.797438	TGCTTCTAGTAATGACTATCACCTATG	58.203	37.037	0.00	0.00	37.53	2.23
3397	3571	1.381872	ACCTATGCTCCCGCTGACT	60.382	57.895	0.00	0.00	36.97	3.41
3414	3588	4.505039	GCTGACTTCTCCACCCTTTCTTAA	60.505	45.833	0.00	0.00	0.00	1.85
3451	3625	7.617041	AGTAACTAACTGCATCCAGAAATTC	57.383	36.000	0.00	0.00	41.77	2.17
3455	3629	2.795329	ACTGCATCCAGAAATTCCGTT	58.205	42.857	0.00	0.00	41.77	4.44
3457	3631	3.689649	ACTGCATCCAGAAATTCCGTTAC	59.310	43.478	0.00	0.00	41.77	2.50
3548	3724	3.713858	TTTGCTTCCAACACACAGATG	57.286	42.857	0.00	0.00	0.00	2.90
3560	3738	9.513906	TCCAACACACAGATGAAGAAATTATTA	57.486	29.630	0.00	0.00	0.00	0.98
3616	3795	7.148606	ACGCAATAATGACATGGAAAAATTGTG	60.149	33.333	17.18	17.18	38.74	3.33
3884	4084	6.345920	AGTGTCTAACTGAAACTTTGTTCG	57.654	37.500	0.00	0.00	40.19	3.95
3905	4105	5.348986	TCGACTGTGTAGGAAGCATAAATC	58.651	41.667	0.00	0.00	0.00	2.17
4059	4261	7.432059	TGAAATGTCTTTACAATGTTGCATGA	58.568	30.769	0.00	0.00	39.58	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	54	3.490348	AGTTATGGCTTATGGTCCATGC	58.510	45.455	15.10	10.00	42.62	4.06
130	131	7.791029	ACATCATCACCTACATAATACACACA	58.209	34.615	0.00	0.00	0.00	3.72
469	548	3.210227	TCAAAATCGAACAAGACTGGCA	58.790	40.909	0.00	0.00	0.00	4.92
474	553	2.839474	CGGCTCAAAATCGAACAAGAC	58.161	47.619	0.00	0.00	0.00	3.01
500	579	0.464452	GTAGTTCGGGGGTGGATCTG	59.536	60.000	0.00	0.00	0.00	2.90
511	590	6.624352	ATCCAATCATTTGATGTAGTTCGG	57.376	37.500	0.00	0.00	34.60	4.30
512	591	7.747799	GCATATCCAATCATTTGATGTAGTTCG	59.252	37.037	0.00	0.00	34.60	3.95
612	691	1.604604	CTTGGTTCTTTCCCTCGCAA	58.395	50.000	0.00	0.00	0.00	4.85
675	754	9.555727	TTGTATTCTAGATTACCCTGTTAATGC	57.444	33.333	17.86	0.00	0.00	3.56
876	955	7.076842	AGCGCTTTGTGCATATATTTATAGG	57.923	36.000	2.64	0.00	42.00	2.57
914	995	0.841961	TCTGCCTCCAATGGATCAGG	59.158	55.000	22.69	14.35	34.89	3.86
976	1057	4.478206	TCAAGGTCTGGAGCTTATCAAG	57.522	45.455	13.54	3.38	46.20	3.02
1515	1599	1.463553	AAGTCCAAAAGCCCTTGCCG	61.464	55.000	0.00	0.00	38.69	5.69
1568	1652	5.642063	GTGTTCGAACCTTCCTGATATTCAA	59.358	40.000	24.78	0.00	0.00	2.69
1617	1701	7.753580	CAGAAACATTTTAATCGAGGGGTTAAC	59.246	37.037	0.00	0.00	0.00	2.01
1752	1836	7.498239	GGTTAATCTCACCAGGGATTTTAGTAC	59.502	40.741	0.00	0.00	34.52	2.73
1753	1837	7.404980	AGGTTAATCTCACCAGGGATTTTAGTA	59.595	37.037	0.00	0.00	36.67	1.82
2149	2233	8.137437	TCAATTTTGCCTTCTTTTCAAGAGTAG	58.863	33.333	0.00	0.00	39.03	2.57
2167	2251	9.874205	ACATCATAGGGTAAAACATCAATTTTG	57.126	29.630	0.00	0.00	33.80	2.44
2349	2465	6.513884	GCTCTTTTGACACATGAACAAGATCA	60.514	38.462	0.00	0.00	0.00	2.92
2393	2509	4.092968	GGTACGAACTGATTAAGCAACTGG	59.907	45.833	0.00	0.00	0.00	4.00
2411	2527	7.667043	ATATGGCATAATGTAGTTTGGTACG	57.333	36.000	11.86	0.00	0.00	3.67
2480	2597	5.463061	CCAACTTGAGCATGTTTTACCAAAG	59.537	40.000	0.00	0.00	0.00	2.77
2675	2792	8.716646	ATAAGTTAATAAAACCAATTGCCTGC	57.283	30.769	0.00	0.00	0.00	4.85
2716	2833	3.387374	TCTTCTTCTGCAAAAATTGGGCA	59.613	39.130	0.00	0.00	35.96	5.36
2717	2834	3.993920	TCTTCTTCTGCAAAAATTGGGC	58.006	40.909	0.00	0.00	0.00	5.36
2749	2867	4.381292	GCTTGCAGCATATCCAACTTCTTT	60.381	41.667	0.00	0.00	41.89	2.52
2806	2924	1.086696	GTCATGCGGCAGTGTACATT	58.913	50.000	9.25	0.00	0.00	2.71
2819	2937	5.461526	TGCTCGTTACTCATATAGTCATGC	58.538	41.667	0.00	0.00	39.80	4.06
2946	3072	5.653769	CCATTTCATGTTACCTTCATCCTGT	59.346	40.000	0.00	0.00	0.00	4.00
3023	3149	4.889409	ACTTCTCCAGCAACATCTGAAAAA	59.111	37.500	0.00	0.00	36.19	1.94
3024	3150	4.276678	CACTTCTCCAGCAACATCTGAAAA	59.723	41.667	0.00	0.00	36.19	2.29
3025	3151	3.817084	CACTTCTCCAGCAACATCTGAAA	59.183	43.478	0.00	0.00	36.19	2.69
3074	3200	6.018425	GCCATATATATGTCAAGCCTTGATCG	60.018	42.308	19.11	2.69	42.47	3.69
3104	3230	4.821532	AGATCTTATTTGAAGGGGGCAT	57.178	40.909	0.00	0.00	0.00	4.40
3105	3231	5.634118	CATAGATCTTATTTGAAGGGGGCA	58.366	41.667	0.00	0.00	0.00	5.36
3109	3235	7.173722	AGATGGCATAGATCTTATTTGAAGGG	58.826	38.462	0.00	0.00	0.00	3.95
3128	3254	8.019669	GTGTGATAATTTGATGACATAGATGGC	58.980	37.037	0.00	0.00	35.98	4.40
3129	3255	9.059260	TGTGTGATAATTTGATGACATAGATGG	57.941	33.333	0.00	0.00	0.00	3.51
3131	3257	9.842775	ACTGTGTGATAATTTGATGACATAGAT	57.157	29.630	10.16	0.00	35.26	1.98
3257	3383	4.315803	CCTAGCGGTTCCCTAACATAATG	58.684	47.826	0.00	0.00	37.34	1.90
3301	3427	7.181125	ACAATTATACTCCTATCAGATGGGGAC	59.819	40.741	12.74	0.00	0.00	4.46
3303	3429	7.502060	ACAATTATACTCCTATCAGATGGGG	57.498	40.000	12.74	6.39	0.00	4.96
3397	3571	7.695055	TCATGTAATTAAGAAAGGGTGGAGAA	58.305	34.615	0.00	0.00	0.00	2.87
3440	3614	6.708285	ACAACTAGTAACGGAATTTCTGGAT	58.292	36.000	9.94	1.34	0.00	3.41
3451	3625	5.467735	AGCTTACCAAAACAACTAGTAACGG	59.532	40.000	0.00	0.00	0.00	4.44
3455	3629	6.584488	TCACAGCTTACCAAAACAACTAGTA	58.416	36.000	0.00	0.00	0.00	1.82
3457	3631	6.560253	ATCACAGCTTACCAAAACAACTAG	57.440	37.500	0.00	0.00	0.00	2.57
3503	3679	4.750098	CCGTAGTTAGTGGGAAGCATTATG	59.250	45.833	0.00	0.00	0.00	1.90
3724	3905	6.147328	ACATTTCAGTTTAAACGTCCTAGCTC	59.853	38.462	12.54	0.00	0.00	4.09
3884	4084	7.617041	AAAGATTTATGCTTCCTACACAGTC	57.383	36.000	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.