AutoCloner

Multiple sequence alignment - TraesCS6A01G395100

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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	TraesCS6A01G395100	chr6A	100.000	3426	0	0	1	3426	608121376	608117951	0.000000e+00	6327
1	TraesCS6A01G395100	chr6D	93.213	3477	124	50	1	3426	461457747	461454332	0.000000e+00	5011
2	TraesCS6A01G395100	chr6D	82.869	251	36	7	458	705	137799495	137799249	5.760000e-53	219
3	TraesCS6A01G395100	chr6B	94.251	1548	46	18	1892	3426	703289728	703288211	0.000000e+00	2326
4	TraesCS6A01G395100	chr6B	87.195	492	37	17	983	1469	703290764	703290294	1.400000e-148	536
5	TraesCS6A01G395100	chr6B	76.261	337	62	14	18	343	7819545	7819874	2.740000e-36	163
6	TraesCS6A01G395100	chr6B	80.597	201	24	12	117	312	577167675	577167485	1.280000e-29	141
7	TraesCS6A01G395100	chr6B	77.778	243	32	15	81	321	614302254	614302032	2.770000e-26	130
8	TraesCS6A01G395100	chr4D	72.973	925	172	53	18	902	224473290	224472404	5.680000e-63	252
9	TraesCS6A01G395100	chr3D	84.959	246	29	6	458	698	393649534	393649292	3.420000e-60	243
10	TraesCS6A01G395100	chr7D	76.681	476	74	27	235	699	553460870	553460421	2.660000e-56	230
11	TraesCS6A01G395100	chr7D	75.745	235	44	11	119	346	53923294	53923522	4.680000e-19	106
12	TraesCS6A01G395100	chr7A	84.783	230	26	8	673	895	584112613	584112386	4.450000e-54	222
13	TraesCS6A01G395100	chr7A	77.591	357	54	20	235	576	276923555	276923900	3.490000e-45	193
14	TraesCS6A01G395100	chr3B	83.607	244	27	9	458	698	513551000	513550767	2.070000e-52	217
15	TraesCS6A01G395100	chr5D	83.051	236	26	10	673	897	544289710	544289942	5.800000e-48	202
16	TraesCS6A01G395100	chr5D	80.916	262	28	20	653	901	548794420	548794168	1.620000e-43	187
17	TraesCS6A01G395100	chr5D	80.612	196	21	14	235	423	480909627	480909812	5.960000e-28	135
18	TraesCS6A01G395100	chr5A	83.710	221	27	8	472	687	597312230	597312014	2.090000e-47	200
19	TraesCS6A01G395100	chr5A	81.532	222	27	9	678	895	574861665	574861876	1.630000e-38	171
20	TraesCS6A01G395100	chr5A	75.862	319	53	20	103	411	680204582	680204886	1.280000e-29	141
21	TraesCS6A01G395100	chr4B	80.952	252	39	8	458	705	47644389	47644635	1.250000e-44	191
22	TraesCS6A01G395100	chr4B	79.457	258	44	8	457	711	122276283	122276032	1.260000e-39	174
23	TraesCS6A01G395100	chr4B	80.252	238	35	9	666	894	524656495	524656261	5.880000e-38	169
24	TraesCS6A01G395100	chr4B	76.737	331	47	20	10	321	377998282	377998601	1.270000e-34	158
25	TraesCS6A01G395100	chr4A	82.949	217	22	12	687	895	569852728	569852519	7.550000e-42	182
26	TraesCS6A01G395100	chr3A	77.439	328	52	17	117	433	16684376	16684060	3.510000e-40	176
27	TraesCS6A01G395100	chr3A	79.915	234	32	13	671	893	464482849	464482620	1.270000e-34	158
28	TraesCS6A01G395100	chr2D	80.000	250	38	11	469	709	606038762	606039008	1.260000e-39	174
29	TraesCS6A01G395100	chr2D	80.000	195	26	13	120	306	601507824	601508013	7.710000e-27	132
30	TraesCS6A01G395100	chr2D	88.710	62	5	2	362	422	6180649	6180589	1.320000e-09	75
31	TraesCS6A01G395100	chr1A	75.749	334	56	22	103	423	103690387	103690708	9.910000e-31	145
32	TraesCS6A01G395100	chr2B	78.302	212	33	10	117	321	33514547	33514342	1.290000e-24	124

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	TraesCS6A01G395100	chr6A	608117951	608121376	3425	True	6327	6327	100.000	1	3426	1	chr6A.!!$R1	3425
1	TraesCS6A01G395100	chr6D	461454332	461457747	3415	True	5011	5011	93.213	1	3426	1	chr6D.!!$R2	3425
2	TraesCS6A01G395100	chr6B	703288211	703290764	2553	True	1431	2326	90.723	983	3426	2	chr6B.!!$R3	2443
3	TraesCS6A01G395100	chr4D	224472404	224473290	886	True	252	252	72.973	18	902	1	chr4D.!!$R1	884

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
941	1262	1.078356	TCCTGTCGAGAGTCTCCGG	60.078	63.158	14.61	9.76	0.00	5.14	F
1818	2480	0.183492	AGTTCCTGCAAAGACTGGCA	59.817	50.000	2.47	2.47	38.52	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1978	2640	0.179137	TGCTCGCTTCGATGATCGTT	60.179	50.0	15.06	0.0	41.35	3.85	R
3295	3973	0.179004	ACCAAACACCCGATTGCTCA	60.179	50.0	0.00	0.0	0.00	4.26	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
78	79	9.801873	CTCTTTCTTTTGGTTTTCATTCTACAA	57.198	29.630	0.00	0.00	0.00	2.41
542	728	7.127686	CACACTGAAAAATTTCCAAATGCTTC	58.872	34.615	3.60	0.00	36.36	3.86
630	921	9.740239	ATATGATCAACTTTTCACACATATTGC	57.260	29.630	0.00	0.00	0.00	3.56
633	924	7.542824	TGATCAACTTTTCACACATATTGCATG	59.457	33.333	0.00	0.00	0.00	4.06
705	1010	9.947669	TTTTTCAATGCTTGATTAACCATTTTG	57.052	25.926	0.41	0.00	39.84	2.44
741	1046	8.445275	TCAACTTTTCACACACATTGTATAGT	57.555	30.769	0.00	0.00	35.67	2.12
754	1059	7.603404	ACACATTGTATAGTTTTTGCATGCATT	59.397	29.630	23.37	7.73	0.00	3.56
760	1065	8.023706	TGTATAGTTTTTGCATGCATTTTCGTA	58.976	29.630	23.37	9.68	0.00	3.43
817	1122	9.985730	AACATTTTTCAGATGCTTGATTAAGAA	57.014	25.926	0.58	0.00	35.92	2.52
937	1258	4.505918	CCATATAGGTCCTGTCGAGAGTCT	60.506	50.000	8.95	5.81	0.00	3.24
941	1262	1.078356	TCCTGTCGAGAGTCTCCGG	60.078	63.158	14.61	9.76	0.00	5.14
1056	1377	2.449312	AGGCTGCCTCCTCTGTCT	59.551	61.111	17.22	0.00	0.00	3.41
1057	1378	1.988956	AGGCTGCCTCCTCTGTCTG	60.989	63.158	17.22	0.00	0.00	3.51
1064	1388	1.181786	CCTCCTCTGTCTGTCTGTCC	58.818	60.000	0.00	0.00	0.00	4.02
1286	1611	1.597027	CCCGCCGCTTAAATCCGAT	60.597	57.895	0.00	0.00	0.00	4.18
1324	1649	4.175337	GGCCAGGATACCGCAGCA	62.175	66.667	0.00	0.00	34.11	4.41
1375	1708	5.302568	AGGTGTTTTTCTGATTTGATGCTGA	59.697	36.000	0.00	0.00	0.00	4.26
1397	1730	3.439540	CCCCGCCGTGAATGGTTG	61.440	66.667	0.00	0.00	0.00	3.77
1447	1780	2.291209	TCTAGGTCGTGTGGGTTGTA	57.709	50.000	0.00	0.00	0.00	2.41
1453	1786	2.032071	GTGTGGGTTGTAGGCGCT	59.968	61.111	7.64	0.00	0.00	5.92
1470	1803	1.611673	CGCTGGTGGGAGTTGAAATCT	60.612	52.381	0.00	0.00	0.00	2.40
1527	1860	3.492102	TCTAATTAGGACAGGCCATGC	57.508	47.619	12.54	0.00	40.02	4.06
1545	1878	5.619086	GCCATGCTTTCTTTTCTTTACGCTA	60.619	40.000	0.00	0.00	0.00	4.26
1551	1884	8.726988	TGCTTTCTTTTCTTTACGCTATGTTAT	58.273	29.630	0.00	0.00	0.00	1.89
1733	2395	1.135746	GCATCTCAGCTGTTTGCACTC	60.136	52.381	23.65	3.79	45.94	3.51
1734	2396	1.467734	CATCTCAGCTGTTTGCACTCC	59.532	52.381	14.67	0.00	45.94	3.85
1752	2414	1.233285	CCTGCAACACCACTGAGCTC	61.233	60.000	6.82	6.82	0.00	4.09
1818	2480	0.183492	AGTTCCTGCAAAGACTGGCA	59.817	50.000	2.47	2.47	38.52	4.92
1819	2481	1.032014	GTTCCTGCAAAGACTGGCAA	58.968	50.000	3.92	0.00	39.93	4.52
1830	2492	5.531634	CAAAGACTGGCAAATAAGCTGAAA	58.468	37.500	0.00	0.00	34.17	2.69
1869	2531	8.975410	ATTTCATTTTATCATGTGTGTGTCAG	57.025	30.769	0.00	0.00	0.00	3.51
1921	2583	3.875865	GGCCAACCGGATACTCTTT	57.124	52.632	9.46	0.00	0.00	2.52
1978	2640	1.151810	AGGCTTGAGGTCCCTCCAA	60.152	57.895	10.77	4.84	42.09	3.53
2028	2690	2.244117	AATGAGCGTCGCCATGACCT	62.244	55.000	14.86	0.00	45.23	3.85
2046	2708	0.176680	CTGGAGGATCACAAGACCGG	59.823	60.000	0.00	0.00	36.25	5.28
2378	3046	1.920835	AGCTTCACCCTGGAGGACC	60.921	63.158	0.00	0.00	39.89	4.46
2497	3168	2.036733	CTGTCACCTCCTTACCGAAACA	59.963	50.000	0.00	0.00	0.00	2.83
2534	3205	4.070716	CTCAGTTTCATGGCTTCTCAAGT	58.929	43.478	0.00	0.00	0.00	3.16
2548	3219	2.072298	CTCAAGTGGAGTACAAGCTGC	58.928	52.381	0.00	0.00	38.90	5.25
2615	3286	4.662966	TGGACTACCCACACTCTAGTAA	57.337	45.455	0.00	0.00	40.82	2.24
2650	3321	4.405358	TCCTTTCTTGTCCAAGCATGTTTT	59.595	37.500	2.09	0.00	38.28	2.43
2651	3322	5.104982	TCCTTTCTTGTCCAAGCATGTTTTT	60.105	36.000	2.09	0.00	38.28	1.94
2652	3323	5.234972	CCTTTCTTGTCCAAGCATGTTTTTC	59.765	40.000	2.09	0.00	38.28	2.29
2653	3324	4.320608	TCTTGTCCAAGCATGTTTTTCC	57.679	40.909	2.09	0.00	38.28	3.13
2654	3325	2.791383	TGTCCAAGCATGTTTTTCCG	57.209	45.000	0.00	0.00	0.00	4.30
2655	3326	2.302260	TGTCCAAGCATGTTTTTCCGA	58.698	42.857	0.00	0.00	0.00	4.55
2657	3328	2.552315	GTCCAAGCATGTTTTTCCGAGA	59.448	45.455	0.00	0.00	0.00	4.04
2658	3329	2.813754	TCCAAGCATGTTTTTCCGAGAG	59.186	45.455	0.00	0.00	0.00	3.20
2659	3330	2.813754	CCAAGCATGTTTTTCCGAGAGA	59.186	45.455	0.00	0.00	0.00	3.10
2717	3388	8.507524	AACCTCTAGTTTAACTGGAATATTGC	57.492	34.615	12.04	0.00	35.25	3.56
2814	3485	6.062095	AGTACAGTACAGCCAGAAACAATTT	58.938	36.000	13.37	0.00	0.00	1.82
2840	3511	4.846779	TTTGCACCTCAAATGTTACTCC	57.153	40.909	0.00	0.00	39.58	3.85
2979	3654	5.809001	TCAACATCCTGCTCTTTACATCTT	58.191	37.500	0.00	0.00	0.00	2.40
3088	3766	5.907197	TGTTACGCAGAGAAAGAAAGAAG	57.093	39.130	0.00	0.00	0.00	2.85
3097	3775	4.693095	AGAGAAAGAAAGAAGCGATGAACC	59.307	41.667	0.00	0.00	0.00	3.62
3099	3777	2.743636	AGAAAGAAGCGATGAACCGA	57.256	45.000	0.00	0.00	0.00	4.69
3100	3778	3.252974	AGAAAGAAGCGATGAACCGAT	57.747	42.857	0.00	0.00	0.00	4.18
3101	3779	3.190874	AGAAAGAAGCGATGAACCGATC	58.809	45.455	0.00	0.00	0.00	3.69
3102	3780	2.672961	AAGAAGCGATGAACCGATCA	57.327	45.000	0.00	0.00	43.67	2.92
3103	3781	2.215907	AGAAGCGATGAACCGATCAG	57.784	50.000	0.00	0.00	42.53	2.90
3104	3782	0.579156	GAAGCGATGAACCGATCAGC	59.421	55.000	0.00	0.00	42.53	4.26
3105	3783	0.176680	AAGCGATGAACCGATCAGCT	59.823	50.000	5.19	3.01	42.36	4.24
3106	3784	0.529337	AGCGATGAACCGATCAGCTG	60.529	55.000	7.63	7.63	42.36	4.24
3107	3785	0.807667	GCGATGAACCGATCAGCTGT	60.808	55.000	14.67	0.42	42.36	4.40
3295	3973	1.156736	GTGTAGCTGCAACCACGAAT	58.843	50.000	5.91	0.00	0.00	3.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	8.669946	AAAACCAAAAGAAAGAGACAAAAACA	57.330	26.923	0.00	0.00	0.00	2.83
50	51	9.452065	GTAGAATGAAAACCAAAAGAAAGAGAC	57.548	33.333	0.00	0.00	0.00	3.36
704	1009	8.246871	TGTGTGAAAAGTTGATCATGTAAAACA	58.753	29.630	0.00	0.00	0.00	2.83
705	1010	8.531530	GTGTGTGAAAAGTTGATCATGTAAAAC	58.468	33.333	0.00	0.00	0.00	2.43
741	1046	7.824704	ATGTATACGAAAATGCATGCAAAAA	57.175	28.000	26.68	0.00	31.89	1.94
782	1087	8.301730	AGCATCTGAAAAATGTTAAATGTGTG	57.698	30.769	0.00	0.00	0.00	3.82
941	1262	2.461945	GGCCTAACGAAGCCGAAGC	61.462	63.158	0.00	0.00	39.87	3.86
955	1276	0.911525	CCGGATCTCCATATGGGCCT	60.912	60.000	21.78	6.26	36.21	5.19
1054	1375	1.590610	GAGCAGAGCGGACAGACAGA	61.591	60.000	0.00	0.00	0.00	3.41
1055	1376	1.153862	GAGCAGAGCGGACAGACAG	60.154	63.158	0.00	0.00	0.00	3.51
1056	1377	2.640302	GGAGCAGAGCGGACAGACA	61.640	63.158	0.00	0.00	0.00	3.41
1057	1378	2.183046	GGAGCAGAGCGGACAGAC	59.817	66.667	0.00	0.00	0.00	3.51
1286	1611	1.101635	ATCGATCCGAGGACAAGCGA	61.102	55.000	0.00	2.60	39.91	4.93
1335	1660	0.844661	ACCTACAATCCCAGCCACCA	60.845	55.000	0.00	0.00	0.00	4.17
1397	1730	0.026285	CGAATCAAATCCCGCGACAC	59.974	55.000	8.23	0.00	0.00	3.67
1447	1780	4.335647	CAACTCCCACCAGCGCCT	62.336	66.667	2.29	0.00	0.00	5.52
1453	1786	3.636300	CACAAAGATTTCAACTCCCACCA	59.364	43.478	0.00	0.00	0.00	4.17
1470	1803	4.216042	CACAGTGCTGGAATCATACACAAA	59.784	41.667	4.11	0.00	34.32	2.83
1551	1884	7.288389	AGCATCCTAAGCCATCAAATCATTTTA	59.712	33.333	0.00	0.00	0.00	1.52
1556	1889	3.887110	CAGCATCCTAAGCCATCAAATCA	59.113	43.478	0.00	0.00	0.00	2.57
1557	1890	3.887716	ACAGCATCCTAAGCCATCAAATC	59.112	43.478	0.00	0.00	0.00	2.17
1558	1891	3.907221	ACAGCATCCTAAGCCATCAAAT	58.093	40.909	0.00	0.00	0.00	2.32
1559	1892	3.370840	ACAGCATCCTAAGCCATCAAA	57.629	42.857	0.00	0.00	0.00	2.69
1689	2023	9.868277	TGCATACATACATATGATGAAACGATA	57.132	29.630	10.38	0.00	34.94	2.92
1733	2395	1.228063	AGCTCAGTGGTGTTGCAGG	60.228	57.895	0.00	0.00	0.00	4.85
1734	2396	0.533531	TGAGCTCAGTGGTGTTGCAG	60.534	55.000	13.74	0.00	0.00	4.41
1743	2405	2.093816	TCAGTTGGCTATGAGCTCAGTG	60.094	50.000	22.96	17.15	41.99	3.66
1752	2414	2.097142	GCTTCAGCTTCAGTTGGCTATG	59.903	50.000	0.00	0.00	37.00	2.23
1869	2531	3.153735	GCGTCGCAGAAGTAAAAACATC	58.846	45.455	13.44	0.00	39.69	3.06
1921	2583	4.021192	GGGAAGAAAATTCCTGCAATGACA	60.021	41.667	6.60	0.00	38.61	3.58
1978	2640	0.179137	TGCTCGCTTCGATGATCGTT	60.179	50.000	15.06	0.00	41.35	3.85
2002	2664	1.565156	GGCGACGCTCATTTGACACA	61.565	55.000	20.77	0.00	0.00	3.72
2004	2666	0.673333	ATGGCGACGCTCATTTGACA	60.673	50.000	20.77	6.70	0.00	3.58
2008	2670	1.369091	GGTCATGGCGACGCTCATTT	61.369	55.000	20.77	0.00	46.42	2.32
2010	2672	2.202932	GGTCATGGCGACGCTCAT	60.203	61.111	20.77	17.55	46.42	2.90
2028	2690	1.899437	GCCGGTCTTGTGATCCTCCA	61.899	60.000	1.90	0.00	0.00	3.86
2058	2723	4.785453	CAGGGACCGAAGCTGGCC	62.785	72.222	0.00	0.00	0.00	5.36
2077	2745	4.443266	AAGCTCGACTCCGCTGCC	62.443	66.667	0.00	0.00	36.45	4.85
2236	2904	3.831637	AGGTTGTTGCAGCCCCCA	61.832	61.111	0.00	0.00	35.27	4.96
2320	2988	2.525629	TTCACGTCCTGCCCCTGA	60.526	61.111	0.00	0.00	0.00	3.86
2378	3046	3.775654	GACCTGAGACCCGGCCAG	61.776	72.222	2.24	0.00	0.00	4.85
2471	3142	3.896888	TCGGTAAGGAGGTGACAGTTTTA	59.103	43.478	0.00	0.00	0.00	1.52
2472	3143	2.701951	TCGGTAAGGAGGTGACAGTTTT	59.298	45.455	0.00	0.00	0.00	2.43
2473	3144	2.322658	TCGGTAAGGAGGTGACAGTTT	58.677	47.619	0.00	0.00	0.00	2.66
2534	3205	3.578716	AGAACTTAGCAGCTTGTACTCCA	59.421	43.478	0.00	0.00	0.00	3.86
2615	3286	6.267471	TGGACAAGAAAGGATAAAGCACAAAT	59.733	34.615	0.00	0.00	0.00	2.32
2650	3321	5.730296	ATCTTTGTTCTCTTCTCTCGGAA	57.270	39.130	0.00	0.00	0.00	4.30
2651	3322	7.122799	TCAATATCTTTGTTCTCTTCTCTCGGA	59.877	37.037	0.00	0.00	0.00	4.55
2652	3323	7.261325	TCAATATCTTTGTTCTCTTCTCTCGG	58.739	38.462	0.00	0.00	0.00	4.63
2653	3324	8.187480	TCTCAATATCTTTGTTCTCTTCTCTCG	58.813	37.037	0.00	0.00	0.00	4.04
2681	3352	7.235812	AGTTAAACTAGAGGTTCAGAAGGTCAT	59.764	37.037	0.00	0.00	37.12	3.06
2728	3399	8.354426	CCATTCATCATCATACTTGCACATAAA	58.646	33.333	0.00	0.00	0.00	1.40
2838	3509	0.468226	ACTTGTTGCCTTCAGTCGGA	59.532	50.000	0.00	0.00	0.00	4.55
2840	3511	1.581934	TCACTTGTTGCCTTCAGTCG	58.418	50.000	0.00	0.00	0.00	4.18
2979	3654	7.607250	ACAGATTTACCTTTTTGTTGTTGTGA	58.393	30.769	0.00	0.00	0.00	3.58
3011	3689	1.399440	CACAGCATGCATGAGGTGTAC	59.601	52.381	30.64	10.38	43.83	2.90
3088	3766	0.807667	ACAGCTGATCGGTTCATCGC	60.808	55.000	23.35	0.00	32.72	4.58
3295	3973	0.179004	ACCAAACACCCGATTGCTCA	60.179	50.000	0.00	0.00	0.00	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.