AutoCloner

Multiple sequence alignment - TraesCS5D01G119800

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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	TraesCS5D01G119800	chr5D	100.000	3620	0	0	1	3620	167036231	167039850	0.000000	6685.0
1	TraesCS5D01G119800	chr5D	98.276	696	11	1	2926	3620	167047194	167047889	0.000000	1218.0
2	TraesCS5D01G119800	chr5D	94.978	697	32	3	2926	3620	341322034	341322729	0.000000	1090.0
3	TraesCS5D01G119800	chr5D	96.970	33	0	1	477	508	402742626	402742658	0.002000	54.7
4	TraesCS5D01G119800	chr5D	96.970	33	0	1	477	508	402745787	402745819	0.002000	54.7
5	TraesCS5D01G119800	chr5A	98.735	2371	28	2	556	2926	218604473	218602105	0.000000	4211.0
6	TraesCS5D01G119800	chr5A	97.248	545	9	2	1	544	218604995	218604456	0.000000	918.0
7	TraesCS5D01G119800	chr3D	95.409	697	30	2	2926	3620	442345602	442344906	0.000000	1109.0
8	TraesCS5D01G119800	chr3D	94.684	696	34	3	2926	3620	362692758	362692065	0.000000	1077.0
9	TraesCS5D01G119800	chr2D	95.122	697	31	3	2926	3620	84157798	84158493	0.000000	1096.0
10	TraesCS5D01G119800	chr2D	94.835	697	32	4	2926	3620	72084440	72083746	0.000000	1085.0
11	TraesCS5D01G119800	chr4D	94.692	697	34	3	2926	3620	348028291	348027596	0.000000	1079.0
12	TraesCS5D01G119800	chr1D	94.556	698	35	3	2926	3620	246490791	246490094	0.000000	1075.0
13	TraesCS5D01G119800	chr1D	94.564	699	33	5	2926	3620	246501796	246501099	0.000000	1075.0
14	TraesCS5D01G119800	chr7D	94.444	36	2	0	477	512	332491734	332491699	0.000505	56.5
15	TraesCS5D01G119800	chr7D	94.444	36	2	0	477	512	638202608	638202573	0.000505	56.5
16	TraesCS5D01G119800	chr4A	100.000	30	0	0	477	506	282173817	282173846	0.000505	56.5
17	TraesCS5D01G119800	chr4A	100.000	30	0	0	477	506	334112645	334112674	0.000505	56.5
18	TraesCS5D01G119800	chr4A	81.818	66	10	2	440	504	318656866	318656930	0.002000	54.7
19	TraesCS5D01G119800	chr2A	94.444	36	2	0	477	512	298238752	298238717	0.000505	56.5

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	TraesCS5D01G119800	chr5D	167036231	167039850	3619	False	6685.0	6685	100.0000	1	3620	1	chr5D.!!$F1	3619
1	TraesCS5D01G119800	chr5D	167047194	167047889	695	False	1218.0	1218	98.2760	2926	3620	1	chr5D.!!$F2	694
2	TraesCS5D01G119800	chr5D	341322034	341322729	695	False	1090.0	1090	94.9780	2926	3620	1	chr5D.!!$F3	694
3	TraesCS5D01G119800	chr5A	218602105	218604995	2890	True	2564.5	4211	97.9915	1	2926	2	chr5A.!!$R1	2925
4	TraesCS5D01G119800	chr3D	442344906	442345602	696	True	1109.0	1109	95.4090	2926	3620	1	chr3D.!!$R2	694
5	TraesCS5D01G119800	chr3D	362692065	362692758	693	True	1077.0	1077	94.6840	2926	3620	1	chr3D.!!$R1	694
6	TraesCS5D01G119800	chr2D	84157798	84158493	695	False	1096.0	1096	95.1220	2926	3620	1	chr2D.!!$F1	694
7	TraesCS5D01G119800	chr2D	72083746	72084440	694	True	1085.0	1085	94.8350	2926	3620	1	chr2D.!!$R1	694
8	TraesCS5D01G119800	chr4D	348027596	348028291	695	True	1079.0	1079	94.6920	2926	3620	1	chr4D.!!$R1	694
9	TraesCS5D01G119800	chr1D	246490094	246490791	697	True	1075.0	1075	94.5560	2926	3620	1	chr1D.!!$R1	694
10	TraesCS5D01G119800	chr1D	246501099	246501796	697	True	1075.0	1075	94.5640	2926	3620	1	chr1D.!!$R2	694

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
793	795	0.032615	AAACCTGGGTTGAAGTGCCA	60.033	50.0	5.73	0.0	38.47	4.92	F
1718	1720	0.034670	ACTGAAGAGGAGGCCATTGC	60.035	55.0	5.01	0.0	0.00	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1747	1749	0.395586	TTGCTGGTTGTTCTGCCACT	60.396	50.0	0.00	0.0	0.0	4.00	R
2950	2953	1.124780	TTTGGACCAACACTCCGAGA	58.875	50.0	6.36	0.0	0.0	4.04	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
181	182	2.578021	ACCCTATGCTGGACATGAAGTT	59.422	45.455	0.00	0.00	40.06	2.66
182	183	2.947652	CCCTATGCTGGACATGAAGTTG	59.052	50.000	0.00	0.00	40.06	3.16
355	357	8.668510	TGCTTGAATCCTTCATATCTAAGAAC	57.331	34.615	0.00	0.00	39.84	3.01
384	386	3.965347	TGTTCCCTAATGAGGTAGTAGCC	59.035	47.826	0.00	0.00	41.95	3.93
480	482	1.468520	GTTGATGATGGGTTCGTGGTG	59.531	52.381	0.00	0.00	0.00	4.17
494	496	3.839778	TCGTGGTGATGTCCATAGGATA	58.160	45.455	0.00	0.00	39.81	2.59
495	497	3.572682	TCGTGGTGATGTCCATAGGATAC	59.427	47.826	0.00	0.00	39.81	2.24
496	498	3.574396	CGTGGTGATGTCCATAGGATACT	59.426	47.826	0.00	0.00	41.08	2.12
497	499	4.321304	CGTGGTGATGTCCATAGGATACTC	60.321	50.000	0.00	0.00	41.12	2.59
498	500	4.021016	GTGGTGATGTCCATAGGATACTCC	60.021	50.000	0.00	0.00	41.12	3.85
536	538	3.153919	GGTTTATGGTTGAGGTTGCAGA	58.846	45.455	0.00	0.00	0.00	4.26
537	539	3.572255	GGTTTATGGTTGAGGTTGCAGAA	59.428	43.478	0.00	0.00	0.00	3.02
538	540	4.038642	GGTTTATGGTTGAGGTTGCAGAAA	59.961	41.667	0.00	0.00	0.00	2.52
539	541	5.222631	GTTTATGGTTGAGGTTGCAGAAAG	58.777	41.667	0.00	0.00	0.00	2.62
540	542	1.032014	TGGTTGAGGTTGCAGAAAGC	58.968	50.000	0.00	0.00	45.96	3.51
541	543	0.315251	GGTTGAGGTTGCAGAAAGCC	59.685	55.000	0.00	0.00	44.83	4.35
542	544	0.315251	GTTGAGGTTGCAGAAAGCCC	59.685	55.000	0.00	0.00	44.83	5.19
543	545	0.827507	TTGAGGTTGCAGAAAGCCCC	60.828	55.000	0.00	0.00	44.83	5.80
544	546	2.282462	AGGTTGCAGAAAGCCCCG	60.282	61.111	0.00	0.00	44.83	5.73
545	547	4.056125	GGTTGCAGAAAGCCCCGC	62.056	66.667	0.00	0.00	44.83	6.13
546	548	3.294493	GTTGCAGAAAGCCCCGCA	61.294	61.111	0.00	0.00	44.83	5.69
547	549	2.520500	TTGCAGAAAGCCCCGCAA	60.521	55.556	0.00	0.00	44.83	4.85
548	550	2.130426	TTGCAGAAAGCCCCGCAAA	61.130	52.632	0.00	0.00	44.83	3.68
549	551	1.680522	TTGCAGAAAGCCCCGCAAAA	61.681	50.000	0.00	0.00	44.83	2.44
550	552	1.068921	GCAGAAAGCCCCGCAAAAA	59.931	52.632	0.00	0.00	37.23	1.94
793	795	0.032615	AAACCTGGGTTGAAGTGCCA	60.033	50.000	5.73	0.00	38.47	4.92
807	809	4.040461	TGAAGTGCCACTAGCTAAGAAACT	59.960	41.667	0.00	0.00	44.23	2.66
882	884	9.593565	AGGGAGATTAAAGAGAAATCTGTTTTT	57.406	29.630	10.35	0.69	42.38	1.94
1058	1060	1.936547	CTCGCCCTCATCAAAAGCTAC	59.063	52.381	0.00	0.00	0.00	3.58
1718	1720	0.034670	ACTGAAGAGGAGGCCATTGC	60.035	55.000	5.01	0.00	0.00	3.56
1801	1803	4.081642	GCTATAACTCTTCACAGGTCACCA	60.082	45.833	0.00	0.00	0.00	4.17
1803	1805	1.051812	ACTCTTCACAGGTCACCAGG	58.948	55.000	0.00	0.00	0.00	4.45
1824	1826	2.928116	GGAATCATGCAAAGCTTTCTGC	59.072	45.455	14.88	14.88	43.29	4.26
1880	1882	4.920340	GTCATCGAGGTCACATCATGTATC	59.080	45.833	0.00	0.00	0.00	2.24
2198	2200	7.795047	TCTGCTGATAGGAACATGAAGAAATA	58.205	34.615	0.00	0.00	0.00	1.40
2322	2324	5.360714	AGATCTCTCAGAGGATGAACAGAAC	59.639	44.000	0.57	0.00	37.52	3.01
2442	2444	5.513788	CCCTCTTCCACTCTCTCATTTTGAA	60.514	44.000	0.00	0.00	0.00	2.69
2622	2624	4.463891	AGTCCCTCAAAGCCATGTTAAATG	59.536	41.667	0.00	0.00	0.00	2.32
2632	2634	3.258123	GCCATGTTAAATGGTGGTTGTCT	59.742	43.478	3.05	0.00	41.17	3.41
2740	2742	2.103153	ATCATGTCGGTGGGATAGGT	57.897	50.000	0.00	0.00	0.00	3.08
2805	2807	9.684448	TCTTGTTCTGCTAATCTAATCGAATAG	57.316	33.333	0.76	0.76	0.00	1.73
2806	2808	9.684448	CTTGTTCTGCTAATCTAATCGAATAGA	57.316	33.333	12.47	12.47	36.41	1.98
2921	2923	1.592064	TTGTCGCACTGCTGAATTCA	58.408	45.000	8.12	8.12	0.00	2.57
2996	2999	2.510012	CTTGCAGCGCCATCTCGA	60.510	61.111	2.29	0.00	0.00	4.04
2997	3000	2.047370	TTGCAGCGCCATCTCGAA	60.047	55.556	2.29	0.00	0.00	3.71
3002	3005	1.293924	CAGCGCCATCTCGAAGAAAT	58.706	50.000	2.29	0.00	34.09	2.17
3005	3008	3.309682	CAGCGCCATCTCGAAGAAATTTA	59.690	43.478	2.29	0.00	34.09	1.40
3078	3081	0.179076	TACGTGCGACTCCTATCGGA	60.179	55.000	0.00	0.00	42.49	4.55
3142	3148	3.979948	TGTCGAAATGTCTTGTAACCGA	58.020	40.909	0.00	0.00	0.00	4.69
3278	3286	1.739929	CGCGGTTGTGTGGCAGATA	60.740	57.895	0.00	0.00	0.00	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	83	3.192844	GGAACATCCGACAAGTCAGACTA	59.807	47.826	2.64	0.00	0.00	2.59
181	182	5.497464	TGTCCAACAAGTCAGATATTCCA	57.503	39.130	0.00	0.00	0.00	3.53
182	183	6.115446	TGATGTCCAACAAGTCAGATATTCC	58.885	40.000	0.00	0.00	0.00	3.01
355	357	2.355756	CCTCATTAGGGAACATTGTGCG	59.644	50.000	0.00	0.00	39.48	5.34
384	386	6.803154	TCCTATACACTCATATGAGACGTG	57.197	41.667	34.16	25.19	44.74	4.49
494	496	2.289882	CCATGGTGATATGATGCGGAGT	60.290	50.000	2.57	0.00	0.00	3.85
495	497	2.353323	CCATGGTGATATGATGCGGAG	58.647	52.381	2.57	0.00	0.00	4.63
496	498	1.003464	CCCATGGTGATATGATGCGGA	59.997	52.381	11.73	0.00	0.00	5.54
497	499	1.271543	ACCCATGGTGATATGATGCGG	60.272	52.381	11.73	0.00	32.98	5.69
498	500	2.189594	ACCCATGGTGATATGATGCG	57.810	50.000	11.73	0.00	32.98	4.73
525	527	1.228552	GGGGCTTTCTGCAACCTCA	60.229	57.895	0.00	0.00	45.15	3.86
528	530	4.056125	GCGGGGCTTTCTGCAACC	62.056	66.667	0.00	0.00	45.15	3.77
547	549	4.112634	GCTTTCCGCAACTTCTTCTTTTT	58.887	39.130	0.00	0.00	38.92	1.94
548	550	3.490933	GGCTTTCCGCAACTTCTTCTTTT	60.491	43.478	0.00	0.00	41.67	2.27
549	551	2.034685	GGCTTTCCGCAACTTCTTCTTT	59.965	45.455	0.00	0.00	41.67	2.52
550	552	1.609072	GGCTTTCCGCAACTTCTTCTT	59.391	47.619	0.00	0.00	41.67	2.52
551	553	1.239347	GGCTTTCCGCAACTTCTTCT	58.761	50.000	0.00	0.00	41.67	2.85
552	554	0.241213	GGGCTTTCCGCAACTTCTTC	59.759	55.000	0.00	0.00	41.67	2.87
553	555	1.179174	GGGGCTTTCCGCAACTTCTT	61.179	55.000	0.00	0.00	44.12	2.52
554	556	1.603739	GGGGCTTTCCGCAACTTCT	60.604	57.895	0.00	0.00	44.12	2.85
555	557	2.962569	GGGGCTTTCCGCAACTTC	59.037	61.111	0.00	0.00	44.12	3.01
561	563	0.954452	CAAGATATGGGGCTTTCCGC	59.046	55.000	0.00	0.00	44.87	5.54
562	564	1.609208	CCAAGATATGGGGCTTTCCG	58.391	55.000	0.00	0.00	46.27	4.30
765	767	5.773176	ACTTCAACCCAGGTTTTATGGTAAG	59.227	40.000	0.00	0.00	36.00	2.34
793	795	2.913617	AGCCCCAAGTTTCTTAGCTAGT	59.086	45.455	0.00	0.00	0.00	2.57
807	809	5.376756	ACCGTAGATAAATAAAGCCCCAA	57.623	39.130	0.00	0.00	0.00	4.12
1058	1060	4.216472	TCCGAAGATCTGATTCTGATACCG	59.784	45.833	0.00	9.27	0.00	4.02
1747	1749	0.395586	TTGCTGGTTGTTCTGCCACT	60.396	50.000	0.00	0.00	0.00	4.00
1801	1803	3.194968	CAGAAAGCTTTGCATGATTCCCT	59.805	43.478	18.30	0.00	0.00	4.20
1803	1805	2.928116	GCAGAAAGCTTTGCATGATTCC	59.072	45.455	18.30	0.00	40.02	3.01
1824	1826	2.513204	CTGCCATCCGCCAGAGTG	60.513	66.667	0.00	0.00	36.24	3.51
1880	1882	2.558359	GGGACTTCATTCAAACCACCTG	59.442	50.000	0.00	0.00	0.00	4.00
1950	1952	2.099141	TCAAGCCTTGAAGATCACCG	57.901	50.000	4.27	0.00	36.59	4.94
2177	2179	9.565090	TTGGATATTTCTTCATGTTCCTATCAG	57.435	33.333	0.00	0.00	0.00	2.90
2198	2200	6.357579	TCAAAATTATTGGTGTGCTTGGAT	57.642	33.333	0.00	0.00	0.00	3.41
2322	2324	4.621991	CTCCATCTACGTCAGGGTTAATG	58.378	47.826	0.00	0.00	0.00	1.90
2442	2444	1.204146	ACCGTTGCTCATACAGGGAT	58.796	50.000	0.00	0.00	0.00	3.85
2551	2553	5.708697	TGAACTTCATGTTGCTGATCTCATT	59.291	36.000	0.00	0.00	39.30	2.57
2665	2667	2.485814	GCTCAGCGAGGAAACAAAATCT	59.514	45.455	7.50	0.00	0.00	2.40
2850	2852	2.512692	ATCCAAGCATACAAGTGGCA	57.487	45.000	0.00	0.00	0.00	4.92
2921	2923	3.436035	GGCCCGGGGAGTAAAATAATTCT	60.436	47.826	25.28	0.00	0.00	2.40
2950	2953	1.124780	TTTGGACCAACACTCCGAGA	58.875	50.000	6.36	0.00	0.00	4.04
2991	2994	4.261801	CCAGCCCTTAAATTTCTTCGAGA	58.738	43.478	0.00	0.00	0.00	4.04
2996	2999	7.612065	ACTAAAACCAGCCCTTAAATTTCTT	57.388	32.000	0.00	0.00	0.00	2.52
2997	3000	7.070696	ACAACTAAAACCAGCCCTTAAATTTCT	59.929	33.333	0.00	0.00	0.00	2.52
3002	3005	5.239087	CGTACAACTAAAACCAGCCCTTAAA	59.761	40.000	0.00	0.00	0.00	1.52
3005	3008	3.143728	CGTACAACTAAAACCAGCCCTT	58.856	45.455	0.00	0.00	0.00	3.95
3193	3199	6.493802	ACTTATCCCATTATAAGCTCTCACGA	59.506	38.462	0.00	0.00	41.29	4.35
3278	3286	4.830600	ACAACCGGACATTAACAAATTCCT	59.169	37.500	9.46	0.00	0.00	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.