AutoCloner

Multiple sequence alignment - TraesCS4D01G265500

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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	TraesCS4D01G265500	chr4D	100.000	3218	0	0	1	3218	435625981	435629198	0.000000e+00	5943.0
1	TraesCS4D01G265500	chr4B	93.802	2033	84	28	607	2621	536894387	536896395	0.000000e+00	3018.0
2	TraesCS4D01G265500	chr4B	91.429	455	27	7	1	449	536893799	536894247	5.900000e-172	614.0
3	TraesCS4D01G265500	chr4A	94.954	1843	59	15	467	2288	37006497	37008326	0.000000e+00	2857.0
4	TraesCS4D01G265500	chr4A	94.901	608	22	4	2613	3218	306966634	306967234	0.000000e+00	942.0
5	TraesCS4D01G265500	chr4A	93.388	605	31	4	2616	3218	528728602	528729199	0.000000e+00	887.0
6	TraesCS4D01G265500	chr4A	93.028	459	20	6	1	447	37005971	37006429	0.000000e+00	660.0
7	TraesCS4D01G265500	chr4A	95.484	155	7	0	2334	2488	37008321	37008475	6.890000e-62	248.0
8	TraesCS4D01G265500	chr5D	96.173	601	15	3	2616	3215	37836824	37837417	0.000000e+00	976.0
9	TraesCS4D01G265500	chr5D	93.750	576	27	2	2645	3218	292992288	292992856	0.000000e+00	856.0
10	TraesCS4D01G265500	chr2D	94.901	608	22	4	2612	3218	432003264	432003863	0.000000e+00	942.0
11	TraesCS4D01G265500	chr2D	93.399	606	30	7	2616	3218	46851848	46851250	0.000000e+00	889.0
12	TraesCS4D01G265500	chr2D	95.616	479	20	1	2741	3218	348597627	348598105	0.000000e+00	767.0
13	TraesCS4D01G265500	chr1A	94.876	605	22	3	2616	3218	513383603	513383006	0.000000e+00	937.0
14	TraesCS4D01G265500	chr7B	92.562	605	31	3	2616	3218	692719420	692720012	0.000000e+00	856.0
15	TraesCS4D01G265500	chr5B	89.951	607	44	9	2607	3204	533413924	533414522	0.000000e+00	767.0
16	TraesCS4D01G265500	chr3D	92.500	120	7	2	2608	2726	613710162	613710044	1.540000e-38	171.0
17	TraesCS4D01G265500	chr2A	91.453	117	10	0	2607	2723	763348453	763348569	9.240000e-36	161.0
18	TraesCS4D01G265500	chr2A	94.118	34	2	0	1048	1081	153456779	153456746	6.000000e-03	52.8

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	TraesCS4D01G265500	chr4D	435625981	435629198	3217	False	5943	5943	100.000000	1	3218	1	chr4D.!!$F1	3217
1	TraesCS4D01G265500	chr4B	536893799	536896395	2596	False	1816	3018	92.615500	1	2621	2	chr4B.!!$F1	2620
2	TraesCS4D01G265500	chr4A	37005971	37008475	2504	False	1255	2857	94.488667	1	2488	3	chr4A.!!$F3	2487
3	TraesCS4D01G265500	chr4A	306966634	306967234	600	False	942	942	94.901000	2613	3218	1	chr4A.!!$F1	605
4	TraesCS4D01G265500	chr4A	528728602	528729199	597	False	887	887	93.388000	2616	3218	1	chr4A.!!$F2	602
5	TraesCS4D01G265500	chr5D	37836824	37837417	593	False	976	976	96.173000	2616	3215	1	chr5D.!!$F1	599
6	TraesCS4D01G265500	chr5D	292992288	292992856	568	False	856	856	93.750000	2645	3218	1	chr5D.!!$F2	573
7	TraesCS4D01G265500	chr2D	432003264	432003863	599	False	942	942	94.901000	2612	3218	1	chr2D.!!$F2	606
8	TraesCS4D01G265500	chr2D	46851250	46851848	598	True	889	889	93.399000	2616	3218	1	chr2D.!!$R1	602
9	TraesCS4D01G265500	chr1A	513383006	513383603	597	True	937	937	94.876000	2616	3218	1	chr1A.!!$R1	602
10	TraesCS4D01G265500	chr7B	692719420	692720012	592	False	856	856	92.562000	2616	3218	1	chr7B.!!$F1	602
11	TraesCS4D01G265500	chr5B	533413924	533414522	598	False	767	767	89.951000	2607	3204	1	chr5B.!!$F1	597

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
355	370	0.107508	CATCAATCAGTCCGCCCACT	60.108	55.0	0.0	0.0	0.0	4.00	F
1037	1150	0.248866	CTCGTTGGTTTGTTGGTGGC	60.249	55.0	0.0	0.0	0.0	5.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2148	2264	0.108424	GCATGAGCTTCTCCTCGTGT	60.108	55.0	11.64	0.0	46.0	4.49	R
2724	2853	0.597568	CTTTGCCCTTTGCGTCATCA	59.402	50.0	0.00	0.0	45.6	3.07	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
109	113	1.262417	CTCCGATCATGCATCCGTTTG	59.738	52.381	0.00	0.00	0.00	2.93
233	240	1.004927	CATAACCGCTAAAGCTCACGC	60.005	52.381	0.00	0.00	39.32	5.34
274	286	4.893036	CGAATCCATCGTATCACATCAC	57.107	45.455	0.00	0.00	46.52	3.06
275	287	4.298332	CGAATCCATCGTATCACATCACA	58.702	43.478	0.00	0.00	46.52	3.58
276	288	4.925646	CGAATCCATCGTATCACATCACAT	59.074	41.667	0.00	0.00	46.52	3.21
355	370	0.107508	CATCAATCAGTCCGCCCACT	60.108	55.000	0.00	0.00	0.00	4.00
358	373	2.596851	AATCAGTCCGCCCACTGCT	61.597	57.895	5.03	0.00	43.18	4.24
360	375	4.320456	CAGTCCGCCCACTGCTGT	62.320	66.667	0.00	0.00	37.58	4.40
447	465	7.520451	ACTCCAGTGGTAAAAGGTATTTTTC	57.480	36.000	9.54	0.00	39.61	2.29
450	468	9.292195	CTCCAGTGGTAAAAGGTATTTTTCTTA	57.708	33.333	9.54	0.00	39.61	2.10
451	469	9.070179	TCCAGTGGTAAAAGGTATTTTTCTTAC	57.930	33.333	9.54	0.00	39.61	2.34
452	470	8.852135	CCAGTGGTAAAAGGTATTTTTCTTACA	58.148	33.333	0.00	0.00	39.61	2.41
502	582	2.957402	AGTTGGTCAGCTTTGATCCA	57.043	45.000	0.00	0.00	0.00	3.41
503	583	3.446442	AGTTGGTCAGCTTTGATCCAT	57.554	42.857	0.00	0.00	0.00	3.41
504	584	3.087031	AGTTGGTCAGCTTTGATCCATG	58.913	45.455	0.00	0.00	0.00	3.66
505	585	2.821969	GTTGGTCAGCTTTGATCCATGT	59.178	45.455	0.00	0.00	0.00	3.21
506	586	2.439409	TGGTCAGCTTTGATCCATGTG	58.561	47.619	0.00	0.00	0.00	3.21
507	587	1.133790	GGTCAGCTTTGATCCATGTGC	59.866	52.381	0.00	0.00	0.00	4.57
508	588	2.089980	GTCAGCTTTGATCCATGTGCT	58.910	47.619	0.00	0.00	0.00	4.40
509	589	2.097142	GTCAGCTTTGATCCATGTGCTC	59.903	50.000	0.00	0.00	0.00	4.26
510	590	1.404391	CAGCTTTGATCCATGTGCTCC	59.596	52.381	0.00	0.00	0.00	4.70
521	601	2.686915	CCATGTGCTCCTTTCAGATTCC	59.313	50.000	0.00	0.00	0.00	3.01
528	608	4.042062	TGCTCCTTTCAGATTCCTCTTCAA	59.958	41.667	0.00	0.00	0.00	2.69
538	618	6.070021	TCAGATTCCTCTTCAATTAAGCTGGA	60.070	38.462	0.00	0.00	36.45	3.86
561	641	3.691118	CCATACAGTATGCAAGCTTGTGT	59.309	43.478	26.55	22.67	42.53	3.72
562	642	4.437794	CCATACAGTATGCAAGCTTGTGTG	60.438	45.833	26.55	17.84	42.53	3.82
566	646	3.070018	AGTATGCAAGCTTGTGTGTCTC	58.930	45.455	26.55	9.43	0.00	3.36
585	665	2.812591	CTCAAATTCTCAGTGTGCAGCT	59.187	45.455	0.00	0.00	0.00	4.24
596	676	2.431782	AGTGTGCAGCTCAAATTTTGGT	59.568	40.909	9.18	0.00	0.00	3.67
599	679	4.808364	GTGTGCAGCTCAAATTTTGGTTAA	59.192	37.500	9.18	0.00	0.00	2.01
608	688	7.599998	AGCTCAAATTTTGGTTAACTATTGCAG	59.400	33.333	9.18	2.94	0.00	4.41
629	715	0.320771	CACTGCCTCACACCTACCAC	60.321	60.000	0.00	0.00	0.00	4.16
630	716	0.762842	ACTGCCTCACACCTACCACA	60.763	55.000	0.00	0.00	0.00	4.17
631	717	0.320771	CTGCCTCACACCTACCACAC	60.321	60.000	0.00	0.00	0.00	3.82
649	735	3.614176	CACACACACACTGATCTAATCCG	59.386	47.826	0.00	0.00	0.00	4.18
674	762	1.304713	AAGTGCAAGATGGGGCCAG	60.305	57.895	4.39	0.00	0.00	4.85
761	849	1.685148	GAAGCCAAGACCCCATCATC	58.315	55.000	0.00	0.00	0.00	2.92
762	850	1.213926	GAAGCCAAGACCCCATCATCT	59.786	52.381	0.00	0.00	0.00	2.90
763	851	1.302907	AGCCAAGACCCCATCATCTT	58.697	50.000	0.00	0.00	35.51	2.40
764	852	1.213926	AGCCAAGACCCCATCATCTTC	59.786	52.381	0.00	0.00	32.77	2.87
843	935	5.622687	GCCATCATCACATTTCACAATCACA	60.623	40.000	0.00	0.00	0.00	3.58
849	941	3.569277	CACATTTCACAATCACACCTCCA	59.431	43.478	0.00	0.00	0.00	3.86
938	1030	3.337889	CACTGACACACGCCACCG	61.338	66.667	0.00	0.00	41.14	4.94
1037	1150	0.248866	CTCGTTGGTTTGTTGGTGGC	60.249	55.000	0.00	0.00	0.00	5.01
1938	2054	3.952628	CTTCCGGCCCAAGACGACC	62.953	68.421	0.00	0.00	0.00	4.79
2016	2132	2.356673	GTCGGGGTGGTGAACGTC	60.357	66.667	0.00	0.00	0.00	4.34
2028	2144	0.472471	TGAACGTCTTCCAGGGCTTT	59.528	50.000	0.00	0.00	0.00	3.51
2233	2357	3.716539	TAGCTAGCGCGCCTTGGTG	62.717	63.158	30.33	12.57	42.32	4.17
2289	2413	3.998672	GGGAGACACGGCCACGAA	61.999	66.667	2.24	0.00	44.60	3.85
2290	2414	2.737376	GGAGACACGGCCACGAAC	60.737	66.667	2.24	0.00	44.60	3.95
2291	2415	3.103911	GAGACACGGCCACGAACG	61.104	66.667	2.24	0.00	44.60	3.95
2292	2416	3.547249	GAGACACGGCCACGAACGA	62.547	63.158	2.24	0.00	44.60	3.85
2537	2666	9.062674	GTTTCACTTTTTCAGTTTCTCAGTAAC	57.937	33.333	0.00	0.00	30.92	2.50
2568	2697	3.797256	CGACTAGCCGATTCTTGGTAAAG	59.203	47.826	0.00	0.00	34.45	1.85
2584	2713	3.689649	GGTAAAGAAGCCACGTCATGAAT	59.310	43.478	0.00	0.00	0.00	2.57
2594	2723	4.605968	CCACGTCATGAATTGTGAACAAA	58.394	39.130	19.91	0.00	39.55	2.83
2599	2728	5.222631	GTCATGAATTGTGAACAAAGGTCC	58.777	41.667	0.00	0.00	39.55	4.46
2600	2729	4.280677	TCATGAATTGTGAACAAAGGTCCC	59.719	41.667	0.00	0.00	39.55	4.46
2724	2853	6.494893	TTGAAATAATGAGTACTTTGCGCT	57.505	33.333	9.73	0.00	0.00	5.92
2729	2858	2.741759	TGAGTACTTTGCGCTGATGA	57.258	45.000	9.73	0.00	0.00	2.92
2731	2860	1.321743	GAGTACTTTGCGCTGATGACG	59.678	52.381	9.73	0.00	0.00	4.35
2996	3127	4.397103	AGAATCATCGTTGCATGTGTCATT	59.603	37.500	0.00	0.00	0.00	2.57
3037	3168	7.926674	TCATTGTCTAAGCAAATCTTCATGA	57.073	32.000	0.00	0.00	36.25	3.07
3171	3310	2.223900	TGAGGAGCTCTGCAACATATCG	60.224	50.000	14.64	0.00	0.00	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
233	240	1.064060	GATCGGCTGGGAAATGTTTCG	59.936	52.381	0.00	0.00	38.06	3.46
502	582	3.522750	AGAGGAATCTGAAAGGAGCACAT	59.477	43.478	0.00	0.00	0.00	3.21
503	583	2.909006	AGAGGAATCTGAAAGGAGCACA	59.091	45.455	0.00	0.00	0.00	4.57
504	584	3.625649	AGAGGAATCTGAAAGGAGCAC	57.374	47.619	0.00	0.00	0.00	4.40
505	585	3.584406	TGAAGAGGAATCTGAAAGGAGCA	59.416	43.478	0.00	0.00	0.00	4.26
506	586	4.213564	TGAAGAGGAATCTGAAAGGAGC	57.786	45.455	0.00	0.00	0.00	4.70
507	587	8.798859	TTAATTGAAGAGGAATCTGAAAGGAG	57.201	34.615	0.00	0.00	0.00	3.69
508	588	7.337942	GCTTAATTGAAGAGGAATCTGAAAGGA	59.662	37.037	0.00	0.00	37.33	3.36
509	589	7.338957	AGCTTAATTGAAGAGGAATCTGAAAGG	59.661	37.037	0.00	0.00	37.33	3.11
510	590	8.182881	CAGCTTAATTGAAGAGGAATCTGAAAG	58.817	37.037	0.00	0.00	37.33	2.62
521	601	6.115446	TGTATGGTCCAGCTTAATTGAAGAG	58.885	40.000	0.00	0.00	37.33	2.85
528	608	5.163205	TGCATACTGTATGGTCCAGCTTAAT	60.163	40.000	24.75	0.00	36.68	1.40
538	618	3.691118	CACAAGCTTGCATACTGTATGGT	59.309	43.478	26.27	12.19	36.68	3.55
561	641	3.807553	TGCACACTGAGAATTTGAGACA	58.192	40.909	0.00	0.00	0.00	3.41
562	642	3.364764	GCTGCACACTGAGAATTTGAGAC	60.365	47.826	0.00	0.00	0.00	3.36
566	646	2.551032	TGAGCTGCACACTGAGAATTTG	59.449	45.455	1.02	0.00	0.00	2.32
585	665	8.417106	TGACTGCAATAGTTAACCAAAATTTGA	58.583	29.630	7.37	0.00	40.53	2.69
608	688	0.037232	GGTAGGTGTGAGGCAGTGAC	60.037	60.000	0.00	0.00	0.00	3.67
618	698	1.134521	AGTGTGTGTGTGGTAGGTGTG	60.135	52.381	0.00	0.00	0.00	3.82
629	715	3.190079	CCGGATTAGATCAGTGTGTGTG	58.810	50.000	0.00	0.00	0.00	3.82
630	716	2.168521	CCCGGATTAGATCAGTGTGTGT	59.831	50.000	0.73	0.00	0.00	3.72
631	717	2.430694	TCCCGGATTAGATCAGTGTGTG	59.569	50.000	0.73	0.00	0.00	3.82
649	735	1.318158	CCATCTTGCACTTGCCTCCC	61.318	60.000	0.00	0.00	41.18	4.30
674	762	0.250901	ATCTGTGTGGTGCCCAACTC	60.251	55.000	0.00	0.00	34.18	3.01
761	849	4.837050	GTGTATTTCGTTTCGTTTCGGAAG	59.163	41.667	0.00	0.00	0.00	3.46
762	850	4.269603	TGTGTATTTCGTTTCGTTTCGGAA	59.730	37.500	0.00	0.00	0.00	4.30
763	851	3.801050	TGTGTATTTCGTTTCGTTTCGGA	59.199	39.130	0.00	0.00	0.00	4.55
764	852	4.118023	TGTGTATTTCGTTTCGTTTCGG	57.882	40.909	0.00	0.00	0.00	4.30
843	935	1.420532	TAGTGGGGCGTTTTGGAGGT	61.421	55.000	0.00	0.00	0.00	3.85
849	941	1.042229	GGGTTTTAGTGGGGCGTTTT	58.958	50.000	0.00	0.00	0.00	2.43
994	1107	2.456119	CGCCACTCCTCATTGTCGC	61.456	63.158	0.00	0.00	0.00	5.19
1080	1196	3.097728	GTCGACGTCGTGCACCTG	61.098	66.667	34.40	7.16	40.80	4.00
1278	1394	4.207281	TCGGAGAAGGCGGCGATG	62.207	66.667	12.98	0.00	0.00	3.84
1524	1640	1.141234	GGAGTAGCCCTGCACGTAC	59.859	63.158	0.00	0.00	0.00	3.67
1746	1862	3.307906	TGCCCGTAGAACCACGCT	61.308	61.111	0.00	0.00	40.59	5.07
1938	2054	2.448477	GTACTTGCGGTACCGGTTG	58.552	57.895	33.98	8.35	43.53	3.77
2016	2132	0.401738	TGACCTCAAAGCCCTGGAAG	59.598	55.000	0.00	0.00	0.00	3.46
2028	2144	3.083349	CCGAGCCCCATGACCTCA	61.083	66.667	0.00	0.00	0.00	3.86
2148	2264	0.108424	GCATGAGCTTCTCCTCGTGT	60.108	55.000	11.64	0.00	46.00	4.49
2211	2327	0.598680	CAAGGCGCGCTAGCTAGAAT	60.599	55.000	32.29	1.15	42.32	2.40
2288	2412	3.119990	CGCACCCATTCAATTACTTCGTT	60.120	43.478	0.00	0.00	0.00	3.85
2289	2413	2.418628	CGCACCCATTCAATTACTTCGT	59.581	45.455	0.00	0.00	0.00	3.85
2290	2414	2.223249	CCGCACCCATTCAATTACTTCG	60.223	50.000	0.00	0.00	0.00	3.79
2291	2415	2.752903	ACCGCACCCATTCAATTACTTC	59.247	45.455	0.00	0.00	0.00	3.01
2292	2416	2.752903	GACCGCACCCATTCAATTACTT	59.247	45.455	0.00	0.00	0.00	2.24
2410	2534	4.373527	ACAAATAGTACAACGAGCACACA	58.626	39.130	0.00	0.00	0.00	3.72
2547	2676	5.007385	TCTTTACCAAGAATCGGCTAGTC	57.993	43.478	0.00	0.00	35.99	2.59
2568	2697	2.483877	TCACAATTCATGACGTGGCTTC	59.516	45.455	15.49	0.00	0.00	3.86
2571	2700	2.031245	TGTTCACAATTCATGACGTGGC	60.031	45.455	15.49	10.95	0.00	5.01
2599	2728	6.708054	GTCATCTAGTCATATGAACCAAAGGG	59.292	42.308	7.07	0.00	34.06	3.95
2600	2729	6.708054	GGTCATCTAGTCATATGAACCAAAGG	59.292	42.308	7.07	0.00	34.39	3.11
2610	2739	3.305403	CGCAACGGGTCATCTAGTCATAT	60.305	47.826	0.00	0.00	0.00	1.78
2643	2772	4.065281	GGCTTGCTGCTGGCCTTG	62.065	66.667	22.23	0.00	42.31	3.61
2724	2853	0.597568	CTTTGCCCTTTGCGTCATCA	59.402	50.000	0.00	0.00	45.60	3.07
2729	2858	3.615709	GCCCTTTGCCCTTTGCGT	61.616	61.111	0.00	0.00	45.60	5.24
2731	2860	3.286915	CTCGCCCTTTGCCCTTTGC	62.287	63.158	0.00	0.00	41.77	3.68
2732	2861	1.589716	CTCTCGCCCTTTGCCCTTTG	61.590	60.000	0.00	0.00	36.24	2.77
2733	2862	1.303643	CTCTCGCCCTTTGCCCTTT	60.304	57.895	0.00	0.00	36.24	3.11
2734	2863	2.352805	CTCTCGCCCTTTGCCCTT	59.647	61.111	0.00	0.00	36.24	3.95
2735	2864	4.416738	GCTCTCGCCCTTTGCCCT	62.417	66.667	0.00	0.00	36.24	5.19
2736	2865	4.722700	TGCTCTCGCCCTTTGCCC	62.723	66.667	0.00	0.00	36.24	5.36
2737	2866	2.672996	TTGCTCTCGCCCTTTGCC	60.673	61.111	0.00	0.00	36.24	4.52
2906	3036	8.343028	AGATGACCAGACCTATCTATATGATGT	58.657	37.037	0.00	0.00	36.65	3.06
2996	3127	6.878923	AGACAATGAAGTCATTTTCGATACCA	59.121	34.615	12.29	0.00	43.85	3.25
3037	3168	2.434331	CCCACCGAACACACCCAT	59.566	61.111	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.