AutoCloner

Multiple sequence alignment - TraesCS3D01G232300

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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	TraesCS3D01G232300	chr3D	100.000	3323	0	0	1	3323	319516723	319520045	0.000000e+00	6137.0
1	TraesCS3D01G232300	chr3B	96.352	2440	54	11	754	3174	400652851	400650428	0.000000e+00	3980.0
2	TraesCS3D01G232300	chr3B	98.592	71	1	0	3253	3323	400650422	400650352	3.480000e-25	126.0
3	TraesCS3D01G232300	chr3A	94.617	2601	83	19	754	3323	406300548	406297974	0.000000e+00	3975.0
4	TraesCS3D01G232300	chr3A	95.441	680	29	2	1	679	605018860	605018182	0.000000e+00	1083.0
5	TraesCS3D01G232300	chr5D	97.920	673	12	2	1	671	373939050	373938378	0.000000e+00	1164.0
6	TraesCS3D01G232300	chr7D	97.177	673	15	3	1	670	271296310	271296981	0.000000e+00	1134.0
7	TraesCS3D01G232300	chr7D	86.111	72	8	2	1292	1362	134178487	134178417	3.550000e-10	76.8
8	TraesCS3D01G232300	chr6A	96.736	674	18	3	1	671	593810531	593809859	0.000000e+00	1120.0
9	TraesCS3D01G232300	chr7B	96.307	677	20	4	1	673	675587411	675586736	0.000000e+00	1107.0
10	TraesCS3D01G232300	chr4A	96.137	673	22	3	1	669	4254641	4253969	0.000000e+00	1096.0
11	TraesCS3D01G232300	chr2B	96.000	675	23	3	1	671	5762057	5762731	0.000000e+00	1094.0
12	TraesCS3D01G232300	chr6B	95.846	674	25	3	1	671	234236873	234237546	0.000000e+00	1086.0
13	TraesCS3D01G232300	chr1A	95.710	676	24	4	1	671	453791742	453792417	0.000000e+00	1083.0
14	TraesCS3D01G232300	chr7A	86.111	72	8	2	1292	1362	133058771	133058701	3.550000e-10	76.8

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	TraesCS3D01G232300	chr3D	319516723	319520045	3322	False	6137	6137	100.000	1	3323	1	chr3D.!!$F1	3322
1	TraesCS3D01G232300	chr3B	400650352	400652851	2499	True	2053	3980	97.472	754	3323	2	chr3B.!!$R1	2569
2	TraesCS3D01G232300	chr3A	406297974	406300548	2574	True	3975	3975	94.617	754	3323	1	chr3A.!!$R1	2569
3	TraesCS3D01G232300	chr3A	605018182	605018860	678	True	1083	1083	95.441	1	679	1	chr3A.!!$R2	678
4	TraesCS3D01G232300	chr5D	373938378	373939050	672	True	1164	1164	97.920	1	671	1	chr5D.!!$R1	670
5	TraesCS3D01G232300	chr7D	271296310	271296981	671	False	1134	1134	97.177	1	670	1	chr7D.!!$F1	669
6	TraesCS3D01G232300	chr6A	593809859	593810531	672	True	1120	1120	96.736	1	671	1	chr6A.!!$R1	670
7	TraesCS3D01G232300	chr7B	675586736	675587411	675	True	1107	1107	96.307	1	673	1	chr7B.!!$R1	672
8	TraesCS3D01G232300	chr4A	4253969	4254641	672	True	1096	1096	96.137	1	669	1	chr4A.!!$R1	668
9	TraesCS3D01G232300	chr2B	5762057	5762731	674	False	1094	1094	96.000	1	671	1	chr2B.!!$F1	670
10	TraesCS3D01G232300	chr6B	234236873	234237546	673	False	1086	1086	95.846	1	671	1	chr6B.!!$F1	670
11	TraesCS3D01G232300	chr1A	453791742	453792417	675	False	1083	1083	95.710	1	671	1	chr1A.!!$F1	670

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
916	938	0.178813	AACCCTTCCTACCCACCCAT	60.179	55.0	0.00	0.0	0.00	4.00	F
1972	1994	1.667236	GAACATGCCATCGTCCATGA	58.333	50.0	7.53	0.0	40.92	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2105	2127	0.478507	ATAAGGCCCCATACCAGCAC	59.521	55.000	0.0	0.0	0.0	4.40	R
3174	3214	2.813754	TGAGGAAGAAACTGAATTGGCG	59.186	45.455	0.0	0.0	0.0	5.69	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	1.668151	GTTTCTTCGCCTGGCTCGT	60.668	57.895	17.92	0.00	0.00	4.18
304	305	1.153107	CATCAGCAGCATCGGGGAA	60.153	57.895	0.00	0.00	0.00	3.97
358	359	1.070289	GTTTCGAAGTCCACCACCTCT	59.930	52.381	0.00	0.00	0.00	3.69
710	719	9.520515	AATCTTTACAACCTGTTTACATCATCT	57.479	29.630	0.00	0.00	0.00	2.90
711	720	8.918202	TCTTTACAACCTGTTTACATCATCTT	57.082	30.769	0.00	0.00	0.00	2.40
732	741	9.750125	CATCTTATTATTTGTTTTAAGGAGCCC	57.250	33.333	0.00	0.00	0.00	5.19
733	742	7.992008	TCTTATTATTTGTTTTAAGGAGCCCG	58.008	34.615	0.00	0.00	0.00	6.13
734	743	7.612633	TCTTATTATTTGTTTTAAGGAGCCCGT	59.387	33.333	0.00	0.00	0.00	5.28
735	744	6.599356	ATTATTTGTTTTAAGGAGCCCGTT	57.401	33.333	0.00	0.00	0.00	4.44
736	745	3.719173	TTTGTTTTAAGGAGCCCGTTG	57.281	42.857	0.00	0.00	0.00	4.10
737	746	0.955905	TGTTTTAAGGAGCCCGTTGC	59.044	50.000	0.00	0.00	41.71	4.17
738	747	0.955905	GTTTTAAGGAGCCCGTTGCA	59.044	50.000	0.00	0.00	44.83	4.08
739	748	1.338655	GTTTTAAGGAGCCCGTTGCAA	59.661	47.619	0.00	0.00	44.83	4.08
740	749	0.955905	TTTAAGGAGCCCGTTGCAAC	59.044	50.000	19.89	19.89	44.83	4.17
782	791	1.556564	AGACAACTCGTGAACGTGTG	58.443	50.000	10.87	8.12	43.95	3.82
784	793	1.275657	CAACTCGTGAACGTGTGCC	59.724	57.895	10.87	0.00	43.95	5.01
886	908	1.540363	CCCGATTGATCCTACCCAACG	60.540	57.143	0.00	0.00	0.00	4.10
916	938	0.178813	AACCCTTCCTACCCACCCAT	60.179	55.000	0.00	0.00	0.00	4.00
977	999	4.442454	CCCTTTTCCTCCCCCGCC	62.442	72.222	0.00	0.00	0.00	6.13
978	1000	4.796495	CCTTTTCCTCCCCCGCCG	62.796	72.222	0.00	0.00	0.00	6.46
1873	1895	2.592308	GGCTTGGGCTAGGTGGAG	59.408	66.667	0.00	0.00	38.73	3.86
1972	1994	1.667236	GAACATGCCATCGTCCATGA	58.333	50.000	7.53	0.00	40.92	3.07
2105	2127	1.457346	GGCTCATCTCAGTTTGGTGG	58.543	55.000	0.00	0.00	0.00	4.61
2366	2388	5.469084	GCTGGTGTTACTTGCTTTTACTAGT	59.531	40.000	0.00	0.00	0.00	2.57
2394	2416	4.142071	TGTGCTTGTTTTGAAGTGGCATAA	60.142	37.500	0.00	0.00	0.00	1.90
2528	2558	2.101082	TGTTGCATTGTTGTCATGCTGT	59.899	40.909	6.46	0.00	41.52	4.40
2609	2641	6.521162	TGAACTAGCAATCTGTAAGTTGACA	58.479	36.000	0.00	0.00	30.83	3.58
2611	2643	7.331934	TGAACTAGCAATCTGTAAGTTGACATC	59.668	37.037	0.00	0.00	30.83	3.06
2658	2690	0.763035	GGTCGGTATGGGGTTGCTAT	59.237	55.000	0.00	0.00	0.00	2.97
2677	2709	9.438291	GTTGCTATGTTAATGATGTATTGTGTC	57.562	33.333	0.00	0.00	0.00	3.67
2689	2721	5.878332	TGTATTGTGTCACATGTTCCATC	57.122	39.130	6.48	0.00	0.00	3.51
2690	2722	5.559770	TGTATTGTGTCACATGTTCCATCT	58.440	37.500	6.48	0.00	0.00	2.90
2813	2845	2.224137	TGATGCATCCCTCGCTCTAAAG	60.224	50.000	23.67	0.00	0.00	1.85
2835	2867	3.181480	GGGTATTGTGTTTGTGTGTTGCT	60.181	43.478	0.00	0.00	0.00	3.91
2923	2955	2.948979	AGCTGTTGTTTTTGGACGATCA	59.051	40.909	0.00	0.00	0.00	2.92
2939	2971	3.563808	ACGATCAAGCTTTGCTGTTGTTA	59.436	39.130	0.00	0.00	39.62	2.41
3051	3090	4.744939	TGACAGCAGTTGGCAAACAATCA	61.745	43.478	6.76	0.00	43.52	2.57
3130	3170	7.039434	TGGCCATTTAGATGTTTGTTAATGTCA	60.039	33.333	0.00	0.00	0.00	3.58
3174	3214	8.009974	GTGATGAGGTTTTACATATATTGCGTC	58.990	37.037	0.00	0.00	0.00	5.19
3177	3217	4.212636	AGGTTTTACATATATTGCGTCGCC	59.787	41.667	15.88	0.00	0.00	5.54
3198	3238	4.083057	GCCAATTCAGTTTCTTCCTCAGAC	60.083	45.833	0.00	0.00	0.00	3.51
3203	3243	2.234908	CAGTTTCTTCCTCAGACCCGAT	59.765	50.000	0.00	0.00	0.00	4.18
3216	3256	3.991972	CCCGATACCCTTGGGTTTT	57.008	52.632	17.30	5.20	43.16	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
111	112	1.626321	TCCATAAGCGGTTCTGGACAA	59.374	47.619	25.33	8.58	34.74	3.18
304	305	5.733253	AGTCCACGACTTTAGGCCTACCT	62.733	52.174	13.46	0.00	44.69	3.08
358	359	4.655921	CGCAAGCCTATTGGGGAA	57.344	55.556	0.00	0.00	35.12	3.97
684	693	9.520515	AGATGATGTAAACAGGTTGTAAAGATT	57.479	29.630	0.00	0.00	0.00	2.40
685	694	9.520515	AAGATGATGTAAACAGGTTGTAAAGAT	57.479	29.630	0.00	0.00	0.00	2.40
686	695	8.918202	AAGATGATGTAAACAGGTTGTAAAGA	57.082	30.769	0.00	0.00	0.00	2.52
706	715	9.750125	GGGCTCCTTAAAACAAATAATAAGATG	57.250	33.333	0.00	0.00	0.00	2.90
707	716	8.630037	CGGGCTCCTTAAAACAAATAATAAGAT	58.370	33.333	0.00	0.00	0.00	2.40
708	717	7.612633	ACGGGCTCCTTAAAACAAATAATAAGA	59.387	33.333	0.00	0.00	0.00	2.10
709	718	7.768240	ACGGGCTCCTTAAAACAAATAATAAG	58.232	34.615	0.00	0.00	0.00	1.73
710	719	7.706100	ACGGGCTCCTTAAAACAAATAATAA	57.294	32.000	0.00	0.00	0.00	1.40
711	720	7.540299	CAACGGGCTCCTTAAAACAAATAATA	58.460	34.615	0.00	0.00	0.00	0.98
712	721	6.394809	CAACGGGCTCCTTAAAACAAATAAT	58.605	36.000	0.00	0.00	0.00	1.28
713	722	5.774630	CAACGGGCTCCTTAAAACAAATAA	58.225	37.500	0.00	0.00	0.00	1.40
714	723	4.321378	GCAACGGGCTCCTTAAAACAAATA	60.321	41.667	0.00	0.00	40.25	1.40
715	724	3.554129	GCAACGGGCTCCTTAAAACAAAT	60.554	43.478	0.00	0.00	40.25	2.32
716	725	2.223852	GCAACGGGCTCCTTAAAACAAA	60.224	45.455	0.00	0.00	40.25	2.83
717	726	1.338655	GCAACGGGCTCCTTAAAACAA	59.661	47.619	0.00	0.00	40.25	2.83
718	727	0.955905	GCAACGGGCTCCTTAAAACA	59.044	50.000	0.00	0.00	40.25	2.83
719	728	0.955905	TGCAACGGGCTCCTTAAAAC	59.044	50.000	3.00	0.00	45.15	2.43
720	729	1.338655	GTTGCAACGGGCTCCTTAAAA	59.661	47.619	14.90	0.00	45.15	1.52
721	730	0.955905	GTTGCAACGGGCTCCTTAAA	59.044	50.000	14.90	0.00	45.15	1.52
722	731	2.636299	GTTGCAACGGGCTCCTTAA	58.364	52.632	14.90	0.00	45.15	1.85
723	732	4.390048	GTTGCAACGGGCTCCTTA	57.610	55.556	14.90	0.00	45.15	2.69
730	739	7.877950	ACATATTTATGTGCGTTGCAACGGG	62.878	44.000	42.59	23.73	45.04	5.28
731	740	4.963320	ACATATTTATGTGCGTTGCAACGG	60.963	41.667	42.59	28.44	45.04	4.44
732	741	4.094911	ACATATTTATGTGCGTTGCAACG	58.905	39.130	40.07	40.07	44.66	4.10
733	742	5.092105	TGACATATTTATGTGCGTTGCAAC	58.908	37.500	19.89	19.89	46.20	4.17
734	743	5.302357	TGACATATTTATGTGCGTTGCAA	57.698	34.783	7.91	0.00	46.20	4.08
735	744	4.954092	TGACATATTTATGTGCGTTGCA	57.046	36.364	7.91	0.00	46.20	4.08
736	745	6.810888	AATTGACATATTTATGTGCGTTGC	57.189	33.333	7.91	0.00	46.20	4.17
748	757	9.825972	CACGAGTTGTCTAAAAATTGACATATT	57.174	29.630	0.00	0.00	41.93	1.28
749	758	9.214957	TCACGAGTTGTCTAAAAATTGACATAT	57.785	29.630	0.00	0.00	41.93	1.78
750	759	8.596271	TCACGAGTTGTCTAAAAATTGACATA	57.404	30.769	0.00	0.00	41.93	2.29
751	760	7.490962	TCACGAGTTGTCTAAAAATTGACAT	57.509	32.000	0.00	0.00	41.93	3.06
752	761	6.912203	TCACGAGTTGTCTAAAAATTGACA	57.088	33.333	0.00	0.00	40.86	3.58
886	908	1.800713	GAAGGGTTCGACGCGACTC	60.801	63.158	15.93	0.00	34.89	3.36
2105	2127	0.478507	ATAAGGCCCCATACCAGCAC	59.521	55.000	0.00	0.00	0.00	4.40
2292	2314	1.555967	GTGGCACATTGGGGTACATT	58.444	50.000	13.86	0.00	44.52	2.71
2366	2388	4.484236	CACTTCAAAACAAGCACACTCAA	58.516	39.130	0.00	0.00	0.00	3.02
2394	2416	5.558844	CGATGCACGACATATTTTGCTACAT	60.559	40.000	0.00	0.00	45.77	2.29
2528	2558	7.363431	TCACATATTCACATAAAACGCAAACA	58.637	30.769	0.00	0.00	0.00	2.83
2658	2690	8.334263	ACATGTGACACAATACATCATTAACA	57.666	30.769	13.23	0.00	35.46	2.41
2689	2721	5.741388	ATAGCACGCTAATCAGGAAAAAG	57.259	39.130	2.32	0.00	31.73	2.27
2690	2722	6.321717	CAAATAGCACGCTAATCAGGAAAAA	58.678	36.000	2.32	0.00	31.73	1.94
2813	2845	3.120041	GCAACACACAAACACAATACCC	58.880	45.455	0.00	0.00	0.00	3.69
2923	2955	5.879777	ACCAAAATTAACAACAGCAAAGCTT	59.120	32.000	0.00	0.00	36.40	3.74
3106	3145	8.243426	TCTGACATTAACAAACATCTAAATGGC	58.757	33.333	0.00	0.00	37.19	4.40
3130	3170	8.847196	CCTCATCACATCAATCAACATATTTCT	58.153	33.333	0.00	0.00	0.00	2.52
3174	3214	2.813754	TGAGGAAGAAACTGAATTGGCG	59.186	45.455	0.00	0.00	0.00	5.69
3177	3217	4.457257	GGGTCTGAGGAAGAAACTGAATTG	59.543	45.833	0.00	0.00	36.40	2.32
3216	3256	8.518430	TGCTCTGGCATTATGAAGTAAATAAA	57.482	30.769	0.00	0.00	44.28	1.40
3239	3279	5.286082	CAGGTTTTACGAAATGTGCTAATGC	59.714	40.000	0.00	0.00	40.20	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.