AutoCloner

Multiple sequence alignment - TraesCS6D01G354400

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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	TraesCS6D01G354400	chr6D	100.000	3719	0	0	1	3719	449845556	449841838	0.000000e+00	6868.0
1	TraesCS6D01G354400	chr6D	88.935	2178	195	23	870	3033	449818499	449816354	0.000000e+00	2645.0
2	TraesCS6D01G354400	chr6D	78.333	1080	177	34	1057	2118	452082762	452081722	0.000000e+00	645.0
3	TraesCS6D01G354400	chr6D	75.345	941	169	41	1867	2789	450168337	450167442	9.680000e-106	394.0
4	TraesCS6D01G354400	chr6D	82.479	468	62	14	1655	2118	462409647	462409196	3.480000e-105	392.0
5	TraesCS6D01G354400	chr6D	72.637	1312	283	54	1441	2709	450212096	450210818	7.590000e-97	364.0
6	TraesCS6D01G354400	chr6D	92.308	52	4	0	3029	3080	449815548	449815497	1.430000e-09	75.0
7	TraesCS6D01G354400	chr6D	93.182	44	2	1	1064	1107	380495624	380495666	3.100000e-06	63.9
8	TraesCS6D01G354400	chr6D	93.182	44	2	1	1064	1107	380565618	380565660	3.100000e-06	63.9
9	TraesCS6D01G354400	chr6B	94.504	3639	152	16	111	3719	682417004	682420624	0.000000e+00	5568.0
10	TraesCS6D01G354400	chr6B	89.918	1220	89	22	1863	3080	681929816	681928629	0.000000e+00	1541.0
11	TraesCS6D01G354400	chr6B	92.694	1054	77	0	902	1955	681930869	681929816	0.000000e+00	1520.0
12	TraesCS6D01G354400	chr6B	73.770	1971	395	82	870	2783	682662256	682660351	0.000000e+00	664.0
13	TraesCS6D01G354400	chr6B	87.821	312	13	6	111	416	681931191	681930899	3.560000e-90	342.0
14	TraesCS6D01G354400	chr6B	78.373	541	100	8	2173	2709	682707636	682707109	5.950000e-88	335.0
15	TraesCS6D01G354400	chr6B	93.182	44	2	1	1064	1107	567764986	567765028	3.100000e-06	63.9
16	TraesCS6D01G354400	chr6B	93.182	44	2	1	1064	1107	567844261	567844303	3.100000e-06	63.9
17	TraesCS6D01G354400	chr6A	94.646	1158	60	2	815	1970	595490133	595488976	0.000000e+00	1794.0
18	TraesCS6D01G354400	chr6A	86.704	1617	103	41	2122	3650	595488471	595486879	0.000000e+00	1692.0
19	TraesCS6D01G354400	chr6A	93.459	688	30	6	111	787	595490813	595490130	0.000000e+00	1007.0
20	TraesCS6D01G354400	chr6A	73.806	1779	351	77	1062	2783	595664810	595663090	6.870000e-167	597.0
21	TraesCS6D01G354400	chr6A	77.332	1072	171	31	1071	2127	609163391	609162377	5.390000e-158	568.0
22	TraesCS6D01G354400	chr6A	95.556	135	4	2	2007	2139	595488786	595488652	8.090000e-52	215.0
23	TraesCS6D01G354400	chr6A	93.182	44	2	1	1064	1107	522044537	522044579	3.100000e-06	63.9
24	TraesCS6D01G354400	chr3B	82.326	877	89	38	33	871	653623372	653622524	0.000000e+00	701.0
25	TraesCS6D01G354400	chr1A	93.277	119	8	0	109	227	583526054	583526172	3.820000e-40	176.0
26	TraesCS6D01G354400	chr1A	82.143	196	28	6	676	868	16760004	16760195	1.070000e-35	161.0
27	TraesCS6D01G354400	chr2B	78.061	196	25	10	676	868	32053338	32053518	1.410000e-19	108.0

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	TraesCS6D01G354400	chr6D	449841838	449845556	3718	True	6868.000000	6868	100.000000	1	3719	1	chr6D.!!$R1	3718
1	TraesCS6D01G354400	chr6D	449815497	449818499	3002	True	1360.000000	2645	90.621500	870	3080	2	chr6D.!!$R6	2210
2	TraesCS6D01G354400	chr6D	452081722	452082762	1040	True	645.000000	645	78.333000	1057	2118	1	chr6D.!!$R4	1061
3	TraesCS6D01G354400	chr6D	450167442	450168337	895	True	394.000000	394	75.345000	1867	2789	1	chr6D.!!$R2	922
4	TraesCS6D01G354400	chr6D	450210818	450212096	1278	True	364.000000	364	72.637000	1441	2709	1	chr6D.!!$R3	1268
5	TraesCS6D01G354400	chr6B	682417004	682420624	3620	False	5568.000000	5568	94.504000	111	3719	1	chr6B.!!$F3	3608
6	TraesCS6D01G354400	chr6B	681928629	681931191	2562	True	1134.333333	1541	90.144333	111	3080	3	chr6B.!!$R3	2969
7	TraesCS6D01G354400	chr6B	682660351	682662256	1905	True	664.000000	664	73.770000	870	2783	1	chr6B.!!$R1	1913
8	TraesCS6D01G354400	chr6B	682707109	682707636	527	True	335.000000	335	78.373000	2173	2709	1	chr6B.!!$R2	536
9	TraesCS6D01G354400	chr6A	595486879	595490813	3934	True	1177.000000	1794	92.591250	111	3650	4	chr6A.!!$R3	3539
10	TraesCS6D01G354400	chr6A	595663090	595664810	1720	True	597.000000	597	73.806000	1062	2783	1	chr6A.!!$R1	1721
11	TraesCS6D01G354400	chr6A	609162377	609163391	1014	True	568.000000	568	77.332000	1071	2127	1	chr6A.!!$R2	1056
12	TraesCS6D01G354400	chr3B	653622524	653623372	848	True	701.000000	701	82.326000	33	871	1	chr3B.!!$R1	838

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
368	416	0.596577	GGGGCACGGTTTTCTTCTTC	59.403	55.0	0.0	0.0	0.0	2.87	F
1529	1714	0.393537	AGCTGCCAGGTGTTAGATGC	60.394	55.0	0.0	0.0	0.0	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1779	1974	2.050144	TCTTCCCTAGTGCATCCATCC	58.950	52.381	0.00	0.00	0.00	3.51	R
3525	5162	0.607620	GGCAAAATACAGGCCTTGCA	59.392	50.000	22.83	3.81	44.72	4.08	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
80	81	3.260100	ACCTCCCTGCCCCTGTTG	61.260	66.667	0.00	0.00	0.00	3.33
305	353	1.006400	CTGAAATTGGGGCCTCTCCTT	59.994	52.381	3.07	0.00	34.39	3.36
368	416	0.596577	GGGGCACGGTTTTCTTCTTC	59.403	55.000	0.00	0.00	0.00	2.87
382	434	7.353497	GTTTTCTTCTTCTACTGCTAAACACC	58.647	38.462	0.00	0.00	0.00	4.16
399	491	8.947115	GCTAAACACCTGTCTGTCTATTTAATT	58.053	33.333	0.00	0.00	0.00	1.40
425	517	5.551760	ATGGCGAAATTAGAACTTGTCTG	57.448	39.130	0.00	0.00	37.12	3.51
426	518	3.188460	TGGCGAAATTAGAACTTGTCTGC	59.812	43.478	0.00	0.00	37.12	4.26
429	521	4.083271	GCGAAATTAGAACTTGTCTGCCTT	60.083	41.667	0.00	0.00	37.12	4.35
430	522	5.562890	GCGAAATTAGAACTTGTCTGCCTTT	60.563	40.000	0.00	0.00	37.12	3.11
484	621	3.549471	CGTGTCTGTCTATTCAGATGTGC	59.451	47.826	0.00	0.00	44.59	4.57
492	631	5.530543	TGTCTATTCAGATGTGCACAAAACA	59.469	36.000	25.72	11.65	32.09	2.83
501	640	3.175152	TGTGCACAAAACAAAGTTAGCG	58.825	40.909	19.28	0.00	0.00	4.26
507	646	4.028830	CACAAAACAAAGTTAGCGTGAACG	60.029	41.667	0.00	0.00	43.27	3.95
614	761	9.368674	CAATTTTCCATCTACATTTGCAATGTA	57.631	29.630	15.98	15.98	33.76	2.29
615	762	9.941325	AATTTTCCATCTACATTTGCAATGTAA	57.059	25.926	16.95	11.34	34.50	2.41
616	763	8.984891	TTTTCCATCTACATTTGCAATGTAAG	57.015	30.769	16.95	12.87	34.50	2.34
617	764	7.936496	TTCCATCTACATTTGCAATGTAAGA	57.064	32.000	16.95	15.85	34.50	2.10
618	765	7.936496	TCCATCTACATTTGCAATGTAAGAA	57.064	32.000	16.95	9.83	34.50	2.52
619	766	8.523915	TCCATCTACATTTGCAATGTAAGAAT	57.476	30.769	16.95	11.03	34.50	2.40
620	767	8.407832	TCCATCTACATTTGCAATGTAAGAATG	58.592	33.333	16.95	17.46	34.50	2.67
621	768	8.192774	CCATCTACATTTGCAATGTAAGAATGT	58.807	33.333	13.50	13.50	41.97	2.71
659	813	9.922305	GAATTTGTTACAGTGAGCATTATCTAC	57.078	33.333	0.00	0.00	0.00	2.59
868	1029	7.581213	TTGAATACACTGTGTTCAATTCCTT	57.419	32.000	23.05	0.93	44.36	3.36
910	1071	2.483876	GGGATGTGGTGATACGTGATG	58.516	52.381	0.00	0.00	0.00	3.07
1021	1182	0.962356	GGTCAGCACAAGGTCCATGG	60.962	60.000	4.97	4.97	0.00	3.66
1132	1293	1.913262	TCCTTCTTGCTCTCCCGCA	60.913	57.895	0.00	0.00	38.31	5.69
1268	1450	3.681835	GCGTCTCCGTGACCCAGT	61.682	66.667	1.10	0.00	42.49	4.00
1529	1714	0.393537	AGCTGCCAGGTGTTAGATGC	60.394	55.000	0.00	0.00	0.00	3.91
1779	1974	5.463286	TGTTTTGCTTTGCTATCATGTGAG	58.537	37.500	0.00	0.00	0.00	3.51
1907	2213	3.689161	TGATTCCTATTGCCGTTTGTCAG	59.311	43.478	0.00	0.00	0.00	3.51
2206	2917	7.060600	TCAAAGCATGTACTTTTGTATCTCG	57.939	36.000	0.00	0.00	37.78	4.04
2240	2951	8.258007	TCATGTACTTATGAAGGTAGTTCTTGG	58.742	37.037	0.00	0.00	34.32	3.61
2505	3221	1.073763	AGTTGCCATGTACCTTCTGCA	59.926	47.619	0.00	0.00	0.00	4.41
2631	3347	9.334947	CTCAAGATAGTCAAAATCATATGTGGT	57.665	33.333	1.90	0.00	0.00	4.16
2678	3394	2.028112	ACCGTGCTTTGAAGATGCTCTA	60.028	45.455	0.00	0.00	0.00	2.43
2915	3658	1.901159	CATTTCAATCCCTGGCACCAA	59.099	47.619	0.00	0.00	0.00	3.67
2919	3662	1.707989	TCAATCCCTGGCACCAAGTAA	59.292	47.619	0.00	0.00	0.00	2.24
3027	3770	1.404748	GTAGGAAGACTCGTGTAGGGC	59.595	57.143	0.00	0.00	0.00	5.19
3067	4620	3.056891	CGTAATGTGATTGGGGCAGTTTT	60.057	43.478	0.00	0.00	0.00	2.43
3107	4690	1.468520	CCGCCACCTGTCAATTAACAG	59.531	52.381	1.29	1.29	45.10	3.16
3141	4724	5.576384	TGTGTTCAGTTTCATGTCAAAAAGC	59.424	36.000	0.00	0.00	0.00	3.51
3147	4730	7.771183	TCAGTTTCATGTCAAAAAGCTACTTT	58.229	30.769	0.00	0.00	34.94	2.66
3225	4825	4.934797	TCCAATTGAATCTCCTCCTGTT	57.065	40.909	7.12	0.00	0.00	3.16
3233	4833	1.776662	TCTCCTCCTGTTGTATCCCG	58.223	55.000	0.00	0.00	0.00	5.14
3321	4931	3.194968	GTGGAGGCTTACTTACAGCTGTA	59.805	47.826	22.67	22.67	37.43	2.74
3342	4962	6.000219	TGTACTGGTCTACTTTCTCTACGTT	59.000	40.000	0.00	0.00	0.00	3.99
3351	4971	2.838386	TTCTCTACGTTCCCGAATCG	57.162	50.000	0.00	0.00	37.88	3.34
3381	5001	1.407258	GTTGCTGTGTTTTGCCTACCA	59.593	47.619	0.00	0.00	0.00	3.25
3421	5058	8.692710	TCCTATATTTGTATGACAGAACTCGTT	58.307	33.333	0.00	0.00	0.00	3.85
3468	5105	1.153568	GCAGCTGGAGCATGTCGTA	60.154	57.895	17.12	0.00	45.16	3.43
3480	5117	2.672874	GCATGTCGTAGCAGTTTCATCA	59.327	45.455	0.00	0.00	0.00	3.07
3486	5123	6.163476	TGTCGTAGCAGTTTCATCATAGTTT	58.837	36.000	0.00	0.00	0.00	2.66
3525	5162	2.173996	TCGTTTCCTGAACTTTCCCCTT	59.826	45.455	0.00	0.00	36.06	3.95
3586	5223	0.466739	TCCAGGATCGCGCTAGGTTA	60.467	55.000	5.56	0.00	0.00	2.85
3591	5228	2.628657	AGGATCGCGCTAGGTTATTTCT	59.371	45.455	5.56	0.00	0.00	2.52
3636	5273	5.163248	TGTGTCTCCTGTTACCAGAAAATCA	60.163	40.000	0.00	0.00	41.50	2.57
3714	5351	6.699204	ACTCGATCTGTTACTATGCTGATTTG	59.301	38.462	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	4.826274	TCGTCTCCTGGATCTGATTTTT	57.174	40.909	0.00	0.00	0.00	1.94
29	30	4.508662	GTTCGTCTCCTGGATCTGATTTT	58.491	43.478	0.00	0.00	0.00	1.82
30	31	3.118592	GGTTCGTCTCCTGGATCTGATTT	60.119	47.826	0.00	0.00	0.00	2.17
31	32	2.432510	GGTTCGTCTCCTGGATCTGATT	59.567	50.000	0.00	0.00	0.00	2.57
65	66	2.034687	CACAACAGGGGCAGGGAG	59.965	66.667	0.00	0.00	0.00	4.30
104	105	2.969238	CACATCCGATCGCCTGGC	60.969	66.667	10.32	9.11	0.00	4.85
278	326	1.546029	GGCCCCAATTTCAGAAGTGAC	59.454	52.381	0.00	0.00	32.82	3.67
368	416	4.021894	AGACAGACAGGTGTTTAGCAGTAG	60.022	45.833	0.00	0.00	0.00	2.57
399	491	8.826710	CAGACAAGTTCTAATTTCGCCATTATA	58.173	33.333	0.00	0.00	31.12	0.98
402	494	5.619981	GCAGACAAGTTCTAATTTCGCCATT	60.620	40.000	0.00	0.00	31.12	3.16
407	499	5.613358	AAGGCAGACAAGTTCTAATTTCG	57.387	39.130	0.00	0.00	31.12	3.46
450	542	4.945246	AGACAGACACGTGTTCAAACTAT	58.055	39.130	24.26	3.39	0.00	2.12
484	621	4.028830	CGTTCACGCTAACTTTGTTTTGTG	60.029	41.667	0.00	0.00	0.00	3.33
501	640	4.992381	AAATAGACAGACAAGCGTTCAC	57.008	40.909	0.00	0.00	0.00	3.18
530	669	6.364165	CGACTACAAACGAGTCCTAATTTCAA	59.636	38.462	0.00	0.00	40.25	2.69
540	679	5.213913	TCATAGTCGACTACAAACGAGTC	57.786	43.478	26.87	0.00	41.39	3.36
583	722	9.770097	TGCAAATGTAGATGGAAAATTGTAAAA	57.230	25.926	0.00	0.00	0.00	1.52
626	773	8.351495	TGCTCACTGTAACAAATTCAAAATTC	57.649	30.769	0.00	0.00	0.00	2.17
910	1071	4.819088	GGAATAGGCAGAGAAACCAAGATC	59.181	45.833	0.00	0.00	0.00	2.75
1021	1182	2.288395	TGTTTCCCTCGTTACGAAGACC	60.288	50.000	9.23	3.27	34.74	3.85
1217	1390	2.167693	ACGAACTTGTTGGAGTCAGTCA	59.832	45.455	2.69	0.00	0.00	3.41
1268	1450	2.772287	TGTCACATACGTTCAATGGCA	58.228	42.857	0.00	0.00	0.00	4.92
1529	1714	7.918033	AGATGTTACAATCTGTCATCTCTAACG	59.082	37.037	5.57	0.00	37.36	3.18
1779	1974	2.050144	TCTTCCCTAGTGCATCCATCC	58.950	52.381	0.00	0.00	0.00	3.51
2140	2623	8.251383	ACCAGATACCGATATTTATATCCCAG	57.749	38.462	4.58	0.00	36.62	4.45
2240	2951	7.712797	TGAAGAGGGTTAAACAAGAAACAATC	58.287	34.615	0.00	0.00	0.00	2.67
2631	3347	3.555966	TCTAGCATCGTCCTTCATCAGA	58.444	45.455	0.00	0.00	0.00	3.27
3027	3770	2.826428	ACGATGATGAAATGGACGGAG	58.174	47.619	0.00	0.00	0.00	4.63
3067	4620	3.614150	CGGCTTTGACTAGCAACTCACTA	60.614	47.826	0.00	0.00	43.02	2.74
3107	4690	5.956642	TGAAACTGAACACAAGGTTTAACC	58.043	37.500	5.91	5.91	40.63	2.85
3209	4809	4.164221	GGGATACAACAGGAGGAGATTCAA	59.836	45.833	0.00	0.00	39.74	2.69
3225	4825	2.026729	TGGAAGAAATGCACGGGATACA	60.027	45.455	0.00	0.00	39.74	2.29
3233	4833	4.730657	CTGAGAACATGGAAGAAATGCAC	58.269	43.478	0.00	0.00	29.34	4.57
3321	4931	4.458642	GGAACGTAGAGAAAGTAGACCAGT	59.541	45.833	0.00	0.00	0.00	4.00
3342	4962	1.138859	ACTTCATGATGCGATTCGGGA	59.861	47.619	8.34	0.00	0.00	5.14
3351	4971	3.293311	AACACAGCAACTTCATGATGC	57.707	42.857	11.10	11.10	40.28	3.91
3404	5024	6.982141	AGTTTACAAACGAGTTCTGTCATACA	59.018	34.615	0.00	0.00	43.51	2.29
3421	5058	5.063204	AGCAAGACATACAGCAGTTTACAA	58.937	37.500	0.00	0.00	0.00	2.41
3468	5105	5.972107	AGCAAAACTATGATGAAACTGCT	57.028	34.783	0.00	0.00	32.97	4.24
3480	5117	8.015658	CGAGCAAAACTAAACTAGCAAAACTAT	58.984	33.333	0.00	0.00	0.00	2.12
3486	5123	5.744666	AACGAGCAAAACTAAACTAGCAA	57.255	34.783	0.00	0.00	0.00	3.91
3525	5162	0.607620	GGCAAAATACAGGCCTTGCA	59.392	50.000	22.83	3.81	44.72	4.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.