AutoCloner

Multiple sequence alignment - TraesCS6A01G033100

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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	TraesCS6A01G033100	chr6A	100.000	3527	0	0	1	3527	16401697	16398171	0.000000e+00	6514
1	TraesCS6A01G033100	chr6A	91.495	2469	186	12	317	2781	16410705	16408257	0.000000e+00	3374
2	TraesCS6A01G033100	chr6A	85.303	1735	243	8	797	2526	15953615	15951888	0.000000e+00	1781
3	TraesCS6A01G033100	chr6A	84.837	1774	251	13	782	2548	16100377	16098615	0.000000e+00	1770
4	TraesCS6A01G033100	chr6D	92.883	2993	194	12	317	3299	15799954	15796971	0.000000e+00	4329
5	TraesCS6A01G033100	chr6D	91.545	2815	182	11	2	2777	15809864	15807067	0.000000e+00	3829
6	TraesCS6A01G033100	chr6D	83.159	2102	288	39	457	2531	15748504	15746442	0.000000e+00	1860
7	TraesCS6A01G033100	chr6D	85.566	1739	239	9	797	2530	15385360	15383629	0.000000e+00	1810
8	TraesCS6A01G033100	chr6D	85.405	1754	242	9	782	2530	15419827	15418083	0.000000e+00	1808
9	TraesCS6A01G033100	chr6D	90.270	740	55	5	318	1055	15784683	15783959	0.000000e+00	952
10	TraesCS6A01G033100	chr6D	90.033	301	19	2	1	301	15800283	15799994	2.570000e-101	379
11	TraesCS6A01G033100	chr6D	81.443	194	24	7	3338	3527	15796853	15796668	7.890000e-32	148
12	TraesCS6A01G033100	chr6D	90.722	97	7	2	188	284	15784783	15784689	1.030000e-25	128
13	TraesCS6A01G033100	chr6B	92.447	2979	208	11	333	3299	27820914	27817941	0.000000e+00	4239
14	TraesCS6A01G033100	chr6B	93.585	2572	153	8	318	2883	27806954	27804389	0.000000e+00	3825
15	TraesCS6A01G033100	chr6B	87.988	333	27	7	1	320	27807385	27807053	7.140000e-102	381
16	TraesCS6A01G033100	chr6B	89.671	213	20	2	2912	3123	27804388	27804177	1.610000e-68	270
17	TraesCS6A01G033100	chr6B	86.207	116	11	4	3187	3299	27804184	27804071	1.720000e-23	121

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	TraesCS6A01G033100	chr6A	16398171	16401697	3526	True	6514.000000	6514	100.000000	1	3527	1	chr6A.!!$R3	3526
1	TraesCS6A01G033100	chr6A	16408257	16410705	2448	True	3374.000000	3374	91.495000	317	2781	1	chr6A.!!$R4	2464
2	TraesCS6A01G033100	chr6A	15951888	15953615	1727	True	1781.000000	1781	85.303000	797	2526	1	chr6A.!!$R1	1729
3	TraesCS6A01G033100	chr6A	16098615	16100377	1762	True	1770.000000	1770	84.837000	782	2548	1	chr6A.!!$R2	1766
4	TraesCS6A01G033100	chr6D	15807067	15809864	2797	True	3829.000000	3829	91.545000	2	2777	1	chr6D.!!$R4	2775
5	TraesCS6A01G033100	chr6D	15746442	15748504	2062	True	1860.000000	1860	83.159000	457	2531	1	chr6D.!!$R3	2074
6	TraesCS6A01G033100	chr6D	15383629	15385360	1731	True	1810.000000	1810	85.566000	797	2530	1	chr6D.!!$R1	1733
7	TraesCS6A01G033100	chr6D	15418083	15419827	1744	True	1808.000000	1808	85.405000	782	2530	1	chr6D.!!$R2	1748
8	TraesCS6A01G033100	chr6D	15796668	15800283	3615	True	1618.666667	4329	88.119667	1	3527	3	chr6D.!!$R6	3526
9	TraesCS6A01G033100	chr6D	15783959	15784783	824	True	540.000000	952	90.496000	188	1055	2	chr6D.!!$R5	867
10	TraesCS6A01G033100	chr6B	27817941	27820914	2973	True	4239.000000	4239	92.447000	333	3299	1	chr6B.!!$R1	2966
11	TraesCS6A01G033100	chr6B	27804071	27807385	3314	True	1149.250000	3825	89.362750	1	3299	4	chr6B.!!$R2	3298

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
961	1110	2.142356	CTCTGAGAGCTCCAAGGAGA	57.858	55.0	19.99	4.01	44.53	3.71	F
2142	2295	0.612732	ACGGTGTCATCCCCTTCGTA	60.613	55.0	0.00	0.00	0.00	3.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2397	2550	1.199615	GTAGGCCCTTGCTCTTCTCT	58.800	55.0	0.0	0.0	37.74	3.10	R
3343	3581	0.105964	TGCTTATATTCGGGCTGCGT	59.894	50.0	0.0	0.0	0.00	5.24	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
404	520	2.223803	ACCTGCAGACTACAGCTAGT	57.776	50.000	17.39	0.00	35.77	2.57
486	604	3.310774	CGGAATATCTCAACCTGCAAGTG	59.689	47.826	0.00	0.00	0.00	3.16
490	608	2.418368	TCTCAACCTGCAAGTGTTGT	57.582	45.000	17.79	0.00	42.19	3.32
740	862	6.397272	TGGAGTGATGGTTTGCATTAATTTC	58.603	36.000	0.00	0.00	0.00	2.17
779	906	7.233553	TGAATGGAATACTGGAACGATCTAGAT	59.766	37.037	12.98	4.47	37.58	1.98
961	1110	2.142356	CTCTGAGAGCTCCAAGGAGA	57.858	55.000	19.99	4.01	44.53	3.71
982	1132	5.700183	AGAAAGGAAGAAGAAGCTTTCCTT	58.300	37.500	19.38	19.38	37.18	3.36
1372	1525	1.067364	CAGCAGTGTTTTGCATGTCCA	59.933	47.619	0.00	0.00	46.47	4.02
1641	1794	2.936498	CGTACCAGGAATGATGTTGGTC	59.064	50.000	0.00	0.00	42.66	4.02
1683	1836	1.750399	CATGGGGCAAGACCTTCCG	60.750	63.158	0.00	0.00	39.10	4.30
2044	2197	1.464734	CTTCTGCCTCTGTCTCGGTA	58.535	55.000	0.00	0.00	0.00	4.02
2085	2238	3.021695	CTCAATCACATGCATGGTCCTT	58.978	45.455	29.41	14.45	0.00	3.36
2142	2295	0.612732	ACGGTGTCATCCCCTTCGTA	60.613	55.000	0.00	0.00	0.00	3.43
2235	2388	1.601166	TCCTCTTCTTCACGTCGTCA	58.399	50.000	0.00	0.00	0.00	4.35
2418	2571	1.488393	GAGAAGAGCAAGGGCCTACAT	59.512	52.381	6.41	0.00	42.56	2.29
2798	2954	3.270027	TGTGGATCCATGTTCATCGTTC	58.730	45.455	19.62	0.27	0.00	3.95
2806	2962	6.480524	TCCATGTTCATCGTTCTTTTGTAG	57.519	37.500	0.00	0.00	0.00	2.74
2817	2973	7.017498	TCGTTCTTTTGTAGTTTTGCACATA	57.983	32.000	0.00	0.00	0.00	2.29
2854	3010	2.635915	AGGTGACAATGGAAACCGACTA	59.364	45.455	0.00	0.00	37.78	2.59
2873	3029	3.899980	ACTACCTTTGGTTAGTCGACCTT	59.100	43.478	13.01	0.00	40.47	3.50
2910	3067	1.072332	TGGTGGCGCTGCTCTTAAA	59.928	52.632	7.64	0.00	0.00	1.52
2914	3071	1.535462	GTGGCGCTGCTCTTAAAGAAA	59.465	47.619	7.64	0.00	0.00	2.52
2963	3120	7.377766	TCTTTTGTAATTCAGCATCTGTACC	57.622	36.000	0.00	0.00	32.61	3.34
3013	3170	1.311859	CAAAGTCTGCTTGCACTCCA	58.688	50.000	0.00	0.00	34.71	3.86
3084	3241	2.449464	CCTCTTGGATGATTGCACCAA	58.551	47.619	5.68	5.68	40.68	3.67
3126	3283	5.582689	AACTCTCAAGTTTCCCACAAAAG	57.417	39.130	0.00	0.00	43.28	2.27
3159	3316	3.945434	GATGATGCCACGCTGCGG	61.945	66.667	26.95	14.65	0.00	5.69
3200	3359	4.611367	ACTAGTGCTCCCTACATTGTAGT	58.389	43.478	19.76	4.96	0.00	2.73
3204	3363	8.171400	ACTAGTGCTCCCTACATTGTAGTATAT	58.829	37.037	19.76	4.82	0.00	0.86
3239	3398	0.537143	TTGCCCTTGTGCAGTACCAG	60.537	55.000	0.00	0.00	43.21	4.00
3241	3400	2.066340	CCCTTGTGCAGTACCAGGA	58.934	57.895	10.10	0.00	43.30	3.86
3270	3431	0.457853	CGAAGGCGACGGATGAAAGA	60.458	55.000	0.00	0.00	40.82	2.52
3289	3450	9.793252	ATGAAAGAACATGCATACAACTAAATC	57.207	29.630	0.00	0.00	0.00	2.17
3329	3524	9.827411	CTAGCAAAAGTAGCTAAAAACTTTAGG	57.173	33.333	11.72	9.00	43.35	2.69
3330	3525	7.145985	AGCAAAAGTAGCTAAAAACTTTAGGC	58.854	34.615	19.06	19.06	43.35	3.93
3332	3527	8.294577	GCAAAAGTAGCTAAAAACTTTAGGCTA	58.705	33.333	19.24	0.00	43.35	3.93
3335	3530	8.507524	AAGTAGCTAAAAACTTTAGGCTATGG	57.492	34.615	0.00	0.00	34.97	2.74
3336	3531	5.836821	AGCTAAAAACTTTAGGCTATGGC	57.163	39.130	0.00	0.00	37.82	4.40
3343	3581	2.965831	ACTTTAGGCTATGGCTGATCGA	59.034	45.455	0.00	0.00	39.30	3.59
3373	3611	4.443739	CCGAATATAAGCAACCACCCTACA	60.444	45.833	0.00	0.00	0.00	2.74
3381	3619	1.345415	CAACCACCCTACACCGTACTT	59.655	52.381	0.00	0.00	0.00	2.24
3386	3624	3.350833	CACCCTACACCGTACTTACTCT	58.649	50.000	0.00	0.00	0.00	3.24
3390	3628	5.104360	ACCCTACACCGTACTTACTCTATGA	60.104	44.000	0.00	0.00	0.00	2.15
3404	3642	7.923344	ACTTACTCTATGATCTTGCATGTGTAC	59.077	37.037	0.00	0.00	0.00	2.90
3410	3648	2.744318	TTGCATGTGTACGGGCCG	60.744	61.111	27.06	27.06	0.00	6.13
3411	3649	4.769063	TGCATGTGTACGGGCCGG	62.769	66.667	31.78	11.52	0.00	6.13
3416	3654	1.906105	ATGTGTACGGGCCGGAATGT	61.906	55.000	31.78	11.45	0.00	2.71
3417	3655	1.812507	GTGTACGGGCCGGAATGTC	60.813	63.158	31.78	10.59	0.00	3.06
3418	3656	2.284276	TGTACGGGCCGGAATGTCA	61.284	57.895	31.78	13.56	0.00	3.58
3419	3657	1.520787	GTACGGGCCGGAATGTCAG	60.521	63.158	31.78	0.00	0.00	3.51
3423	3661	1.832912	GGGCCGGAATGTCAGAGAT	59.167	57.895	5.05	0.00	0.00	2.75
3426	3664	2.158813	GGGCCGGAATGTCAGAGATTTA	60.159	50.000	5.05	0.00	0.00	1.40
3427	3665	3.134458	GGCCGGAATGTCAGAGATTTAG	58.866	50.000	5.05	0.00	0.00	1.85
3432	3670	6.073548	GCCGGAATGTCAGAGATTTAGTATTG	60.074	42.308	5.05	0.00	0.00	1.90
3435	3673	8.969267	CGGAATGTCAGAGATTTAGTATTGTAC	58.031	37.037	0.00	0.00	0.00	2.90
3492	3730	9.883142	CTATTTTTCTTCTAGATCCTCAGTTGT	57.117	33.333	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	61	8.825667	TCAAACTTAAATTAATTTGGGCAGTC	57.174	30.769	21.19	0.00	33.72	3.51
145	155	6.194235	AGGAGGTTCCACAAAAATGCATATA	58.806	36.000	0.00	0.00	39.61	0.86
404	520	3.087370	TGACTCTAGGTAGCTGCAGAA	57.913	47.619	20.43	0.50	0.00	3.02
486	604	6.338937	AGGGTTTATTCGATCTGACTACAAC	58.661	40.000	0.00	0.00	0.00	3.32
490	608	6.238953	GCTGTAGGGTTTATTCGATCTGACTA	60.239	42.308	0.00	0.00	0.00	2.59
606	727	3.788227	TGTTGAACTTATCAGGGCTGT	57.212	42.857	0.00	0.00	39.77	4.40
740	862	7.648112	CAGTATTCCATTCATTTTGATCTGCTG	59.352	37.037	0.00	0.00	0.00	4.41
779	906	0.601841	GCTCCCGACGTTTCCTTTCA	60.602	55.000	0.00	0.00	0.00	2.69
961	1110	4.830046	GGAAGGAAAGCTTCTTCTTCCTTT	59.170	41.667	29.07	16.76	39.30	3.11
1372	1525	0.761187	CCACCAGGACCATCGATGAT	59.239	55.000	26.86	10.22	36.89	2.45
1641	1794	2.047274	ACGAGCAACCCCATCACG	60.047	61.111	0.00	0.00	0.00	4.35
1683	1836	1.034292	GGCTCCTCAAGTTGCCATCC	61.034	60.000	0.00	0.00	44.34	3.51
2044	2197	2.221299	TGGGAAGGGTAGTTGCGCT	61.221	57.895	9.73	0.00	0.00	5.92
2085	2238	1.476891	GCCTCGACACAGATGGAGTAA	59.523	52.381	0.00	0.00	0.00	2.24
2235	2388	2.904434	CCCTTTACCTGTGGAGTACTGT	59.096	50.000	0.00	0.00	0.00	3.55
2361	2514	1.747898	GCAGCGTAGTACTCCTCCTCT	60.748	57.143	0.00	0.00	0.00	3.69
2397	2550	1.199615	GTAGGCCCTTGCTCTTCTCT	58.800	55.000	0.00	0.00	37.74	3.10
2418	2571	1.355796	CGAACTTGATGCCCGCGTTA	61.356	55.000	4.92	0.00	0.00	3.18
2473	2626	2.043248	AGGTACGGCGAGGATGGT	60.043	61.111	16.62	0.00	0.00	3.55
2590	2743	5.456621	ACCCTAGAGGAACGTACACGTATG	61.457	50.000	7.97	0.00	45.99	2.39
2591	2744	3.370953	ACCCTAGAGGAACGTACACGTAT	60.371	47.826	7.97	0.00	45.99	3.06
2788	2944	6.470877	TGCAAAACTACAAAAGAACGATGAAC	59.529	34.615	0.00	0.00	0.00	3.18
2806	2962	6.709145	TGAAGCATCAAATATGTGCAAAAC	57.291	33.333	0.00	0.00	36.59	2.43
2854	3010	3.135167	TCAAAGGTCGACTAACCAAAGGT	59.865	43.478	16.46	0.00	42.12	3.50
2910	3067	8.910351	AAACTGACAAGCTAACTCTTATTTCT	57.090	30.769	0.00	0.00	0.00	2.52
2957	3114	1.520787	GGTTGGCCGATCGGTACAG	60.521	63.158	33.33	9.96	37.65	2.74
2963	3120	1.376683	TTGGAAGGTTGGCCGATCG	60.377	57.895	8.51	8.51	40.50	3.69
3012	3169	1.193874	GCCAGTTCTCCGTAAAACGTG	59.806	52.381	0.00	0.00	40.58	4.49
3013	3170	1.069668	AGCCAGTTCTCCGTAAAACGT	59.930	47.619	0.00	0.00	40.58	3.99
3022	3179	1.107114	TCTCATCGAGCCAGTTCTCC	58.893	55.000	0.00	0.00	0.00	3.71
3126	3283	5.352293	GGCATCATCTTCCATTTGTTTTTCC	59.648	40.000	0.00	0.00	0.00	3.13
3239	3398	2.815647	CCTTCGACGCCAGCTTCC	60.816	66.667	0.00	0.00	0.00	3.46
3325	3520	1.269723	CGTCGATCAGCCATAGCCTAA	59.730	52.381	0.00	0.00	41.25	2.69
3326	3521	0.881796	CGTCGATCAGCCATAGCCTA	59.118	55.000	0.00	0.00	41.25	3.93
3328	3523	2.024319	GCGTCGATCAGCCATAGCC	61.024	63.158	0.00	0.00	41.25	3.93
3329	3524	1.280886	CTGCGTCGATCAGCCATAGC	61.281	60.000	0.00	0.00	40.32	2.97
3330	3525	2.806577	CTGCGTCGATCAGCCATAG	58.193	57.895	0.00	0.00	0.00	2.23
3336	3531	2.960957	ATTCGGGCTGCGTCGATCAG	62.961	60.000	15.23	11.80	35.25	2.90
3343	3581	0.105964	TGCTTATATTCGGGCTGCGT	59.894	50.000	0.00	0.00	0.00	5.24
3373	3611	5.593095	TGCAAGATCATAGAGTAAGTACGGT	59.407	40.000	0.00	0.00	0.00	4.83
3381	3619	6.438763	CGTACACATGCAAGATCATAGAGTA	58.561	40.000	0.00	0.00	0.00	2.59
3386	3624	3.727726	CCCGTACACATGCAAGATCATA	58.272	45.455	0.00	0.00	0.00	2.15
3390	3628	0.748005	GGCCCGTACACATGCAAGAT	60.748	55.000	0.00	0.00	0.00	2.40
3404	3642	2.032860	ATCTCTGACATTCCGGCCCG	62.033	60.000	0.00	0.00	0.00	6.13
3466	3704	9.883142	ACAACTGAGGATCTAGAAGAAAAATAG	57.117	33.333	0.00	0.00	34.92	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.