AutoCloner

Multiple sequence alignment - TraesCS6D01G223500

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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	TraesCS6D01G223500	chr6D	100.000	3994	0	0	1	3994	315626708	315622715	0.000000e+00	7376
1	TraesCS6D01G223500	chr6D	94.895	901	34	3	3105	3994	464213697	464214596	0.000000e+00	1399
2	TraesCS6D01G223500	chr6D	92.786	901	27	3	3104	3994	379092415	379093287	0.000000e+00	1269
3	TraesCS6D01G223500	chr6D	97.159	176	3	2	2528	2703	392897145	392896972	3.020000e-76	296
4	TraesCS6D01G223500	chr6A	96.392	2550	46	11	1	2536	452777670	452775153	0.000000e+00	4157
5	TraesCS6D01G223500	chr6A	95.620	411	9	2	2696	3105	452775156	452774754	0.000000e+00	651
6	TraesCS6D01G223500	chr6B	95.531	2573	61	17	1	2536	511566506	511569061	0.000000e+00	4065
7	TraesCS6D01G223500	chr6B	96.594	411	13	1	2696	3105	511569058	511569468	0.000000e+00	680
8	TraesCS6D01G223500	chr3D	95.560	901	29	2	3104	3994	214959732	214958833	0.000000e+00	1432
9	TraesCS6D01G223500	chr7D	95.551	899	29	2	3106	3994	114468339	114467442	0.000000e+00	1428
10	TraesCS6D01G223500	chr7D	95.117	901	31	3	3104	3994	151541137	151540240	0.000000e+00	1408
11	TraesCS6D01G223500	chr7D	97.674	172	4	0	2531	2702	45837346	45837517	3.020000e-76	296
12	TraesCS6D01G223500	chr3A	95.238	903	30	4	3104	3994	660860781	660861682	0.000000e+00	1417
13	TraesCS6D01G223500	chr2D	95.333	900	28	10	3106	3994	70391946	70391050	0.000000e+00	1417
14	TraesCS6D01G223500	chr2D	94.889	900	34	3	3106	3994	101660883	101659985	0.000000e+00	1397
15	TraesCS6D01G223500	chr2D	94.772	899	35	3	3106	3994	161898505	161897609	0.000000e+00	1389
16	TraesCS6D01G223500	chr2D	95.130	883	32	2	3123	3994	484919097	484919979	0.000000e+00	1382
17	TraesCS6D01G223500	chr2D	94.333	900	34	11	3106	3994	623950340	623949447	0.000000e+00	1363
18	TraesCS6D01G223500	chr5D	94.615	910	35	5	3096	3994	422449114	422448208	0.000000e+00	1397
19	TraesCS6D01G223500	chr5D	93.333	900	27	4	3105	3994	404193743	404194619	0.000000e+00	1299
20	TraesCS6D01G223500	chr5D	93.264	193	8	4	2527	2718	245718446	245718258	3.040000e-71	279
21	TraesCS6D01G223500	chr1D	94.673	901	38	1	3104	3994	84728838	84729738	0.000000e+00	1389
22	TraesCS6D01G223500	chr1D	97.000	400	11	1	3595	3994	464937376	464937774	0.000000e+00	671
23	TraesCS6D01G223500	chr1D	97.688	173	4	0	2532	2704	423269504	423269676	8.390000e-77	298
24	TraesCS6D01G223500	chr1D	97.126	174	4	1	2526	2699	238940208	238940380	3.900000e-75	292
25	TraesCS6D01G223500	chr1D	96.067	178	7	0	2529	2706	345368849	345368672	1.400000e-74	291
26	TraesCS6D01G223500	chr1A	93.021	874	40	8	3106	3959	579858169	579859041	0.000000e+00	1256
27	TraesCS6D01G223500	chr4B	96.154	182	6	1	2519	2700	113961102	113961282	3.020000e-76	296
28	TraesCS6D01G223500	chr4B	93.717	191	10	2	2514	2703	592024214	592024403	6.530000e-73	285
29	TraesCS6D01G223500	chr5A	98.214	168	2	1	2532	2699	362179015	362179181	3.900000e-75	292

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	TraesCS6D01G223500	chr6D	315622715	315626708	3993	True	7376.0	7376	100.0000	1	3994	1	chr6D.!!$R1	3993
1	TraesCS6D01G223500	chr6D	464213697	464214596	899	False	1399.0	1399	94.8950	3105	3994	1	chr6D.!!$F2	889
2	TraesCS6D01G223500	chr6D	379092415	379093287	872	False	1269.0	1269	92.7860	3104	3994	1	chr6D.!!$F1	890
3	TraesCS6D01G223500	chr6A	452774754	452777670	2916	True	2404.0	4157	96.0060	1	3105	2	chr6A.!!$R1	3104
4	TraesCS6D01G223500	chr6B	511566506	511569468	2962	False	2372.5	4065	96.0625	1	3105	2	chr6B.!!$F1	3104
5	TraesCS6D01G223500	chr3D	214958833	214959732	899	True	1432.0	1432	95.5600	3104	3994	1	chr3D.!!$R1	890
6	TraesCS6D01G223500	chr7D	114467442	114468339	897	True	1428.0	1428	95.5510	3106	3994	1	chr7D.!!$R1	888
7	TraesCS6D01G223500	chr7D	151540240	151541137	897	True	1408.0	1408	95.1170	3104	3994	1	chr7D.!!$R2	890
8	TraesCS6D01G223500	chr3A	660860781	660861682	901	False	1417.0	1417	95.2380	3104	3994	1	chr3A.!!$F1	890
9	TraesCS6D01G223500	chr2D	70391050	70391946	896	True	1417.0	1417	95.3330	3106	3994	1	chr2D.!!$R1	888
10	TraesCS6D01G223500	chr2D	101659985	101660883	898	True	1397.0	1397	94.8890	3106	3994	1	chr2D.!!$R2	888
11	TraesCS6D01G223500	chr2D	161897609	161898505	896	True	1389.0	1389	94.7720	3106	3994	1	chr2D.!!$R3	888
12	TraesCS6D01G223500	chr2D	484919097	484919979	882	False	1382.0	1382	95.1300	3123	3994	1	chr2D.!!$F1	871
13	TraesCS6D01G223500	chr2D	623949447	623950340	893	True	1363.0	1363	94.3330	3106	3994	1	chr2D.!!$R4	888
14	TraesCS6D01G223500	chr5D	422448208	422449114	906	True	1397.0	1397	94.6150	3096	3994	1	chr5D.!!$R2	898
15	TraesCS6D01G223500	chr5D	404193743	404194619	876	False	1299.0	1299	93.3330	3105	3994	1	chr5D.!!$F1	889
16	TraesCS6D01G223500	chr1D	84728838	84729738	900	False	1389.0	1389	94.6730	3104	3994	1	chr1D.!!$F1	890
17	TraesCS6D01G223500	chr1A	579858169	579859041	872	False	1256.0	1256	93.0210	3106	3959	1	chr1A.!!$F1	853

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
721	724	2.591133	CCCAAAATAAACCGAACTGCG	58.409	47.619	0.0	0.0	40.47	5.18	F
2436	2481	0.179181	CGGCTGATGTCACAACATGC	60.179	55.000	0.0	0.0	46.20	4.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2578	2623	2.742348	ACATCCGTATGTGGTAGTCCA	58.258	47.619	0.0	0.0	44.79	4.02	R
3415	3466	1.153353	CGACATGGCAACCGTAGTTT	58.847	50.000	0.0	0.0	32.45	2.66	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
262	265	7.044181	TGAAAAGTTCCATTTTTATGCACACA	58.956	30.769	0.00	0.00	32.62	3.72
413	416	9.400638	GATTGTCCGAGAGTTCTTAATATACAG	57.599	37.037	0.00	0.00	0.00	2.74
518	521	2.740981	GTGCATCAGAGAGACCTTGTTG	59.259	50.000	0.00	0.00	0.00	3.33
585	588	9.241919	TGCACATGAAGATATTCCTTTTCTAAA	57.758	29.630	0.00	0.00	0.00	1.85
718	721	4.650131	TGAAACCCCAAAATAAACCGAACT	59.350	37.500	0.00	0.00	0.00	3.01
721	724	2.591133	CCCAAAATAAACCGAACTGCG	58.409	47.619	0.00	0.00	40.47	5.18
1095	1102	1.743252	GGAGCCACAGGAAGCTTCG	60.743	63.158	19.91	9.89	40.11	3.79
1128	1135	1.000486	TCCTCCCCTCGACCTTCTG	60.000	63.158	0.00	0.00	0.00	3.02
1414	1421	1.883544	CTCCAGATGCTGCTGCTCG	60.884	63.158	17.00	8.01	40.48	5.03
1443	1450	7.708752	CACTTGGTCTCTGAACTAATCTTATCC	59.291	40.741	0.00	0.00	0.00	2.59
1547	1554	1.664659	CATCCAGAAGCTTCTTCGCTG	59.335	52.381	26.44	16.13	40.79	5.18
1692	1699	5.415701	AGATTATGCACTTTCGGAATTGTGT	59.584	36.000	18.74	8.45	33.44	3.72
1961	1968	6.841119	TGTACTTGTATGTGTCATGATTTGC	58.159	36.000	0.00	0.00	0.00	3.68
1962	1969	5.963176	ACTTGTATGTGTCATGATTTGCA	57.037	34.783	0.00	0.00	0.00	4.08
1963	1970	5.702865	ACTTGTATGTGTCATGATTTGCAC	58.297	37.500	0.00	2.73	34.76	4.57
2063	2070	7.221828	TGATTCTACACGATCATTTCTTTCG	57.778	36.000	0.00	0.00	38.76	3.46
2158	2165	6.442112	TCACACGATTGTCAATTTGCATTTA	58.558	32.000	0.00	0.00	31.66	1.40
2375	2420	8.475639	AGGTACTATGTCGTTGAATTATGTTCT	58.524	33.333	0.00	0.00	36.02	3.01
2376	2421	8.540492	GGTACTATGTCGTTGAATTATGTTCTG	58.460	37.037	0.00	0.00	0.00	3.02
2377	2422	9.084164	GTACTATGTCGTTGAATTATGTTCTGT	57.916	33.333	0.00	0.00	0.00	3.41
2378	2423	8.547967	ACTATGTCGTTGAATTATGTTCTGTT	57.452	30.769	0.00	0.00	0.00	3.16
2379	2424	8.999431	ACTATGTCGTTGAATTATGTTCTGTTT	58.001	29.630	0.00	0.00	0.00	2.83
2380	2425	9.478019	CTATGTCGTTGAATTATGTTCTGTTTC	57.522	33.333	0.00	0.00	0.00	2.78
2389	2434	9.904198	TGAATTATGTTCTGTTTCTGGATGATA	57.096	29.630	0.00	0.00	0.00	2.15
2436	2481	0.179181	CGGCTGATGTCACAACATGC	60.179	55.000	0.00	0.00	46.20	4.06

Showing 1 to 25 of 103 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
316	319	9.399403	GCTTAAAAACACTTAAAGATCCAAGAG	57.601	33.333	6.38	2.05	0.00	2.85
413	416	0.814010	ATGTTATCAAGACGCCGGCC	60.814	55.000	23.46	7.92	0.00	6.13
518	521	3.118592	ACCAAGAGGAAGCATACAGCTAC	60.119	47.826	0.00	0.00	46.53	3.58
718	721	1.002403	TCCCTCCCTATCAACCGCA	59.998	57.895	0.00	0.00	0.00	5.69
721	724	0.267960	TCCCTCCCTCCCTATCAACC	59.732	60.000	0.00	0.00	0.00	3.77
1095	1102	2.250741	GAGGAGGAGGAAGCAGCACC	62.251	65.000	0.00	0.00	0.00	5.01
1128	1135	0.455815	CTACGAAATTTGGGGGCTGC	59.544	55.000	5.14	0.00	0.00	5.25
1414	1421	2.246719	AGTTCAGAGACCAAGTGTGC	57.753	50.000	0.00	0.00	0.00	4.57
1692	1699	8.686334	ACTTTCTCAAGTTTTTGCTCATCTTTA	58.314	29.630	0.00	0.00	40.66	1.85
1961	1968	9.904647	GCAAATACAAATGCATTTACATAAGTG	57.095	29.630	23.69	15.73	42.12	3.16
1962	1969	9.650539	TGCAAATACAAATGCATTTACATAAGT	57.349	25.926	23.69	17.67	46.87	2.24
2063	2070	3.261137	ACCCAGTTCTTGTAACCTCTAGC	59.739	47.826	0.00	0.00	0.00	3.42
2436	2481	5.010012	GGAGGCAAAGTTATGTTATCCATGG	59.990	44.000	4.97	4.97	34.86	3.66
2536	2581	5.758784	GTCAAATATTTAGGAACGGAGGGAG	59.241	44.000	0.00	0.00	0.00	4.30
2537	2582	5.427481	AGTCAAATATTTAGGAACGGAGGGA	59.573	40.000	0.00	0.00	0.00	4.20
2538	2583	5.681639	AGTCAAATATTTAGGAACGGAGGG	58.318	41.667	0.00	0.00	0.00	4.30
2539	2584	7.625828	AAAGTCAAATATTTAGGAACGGAGG	57.374	36.000	0.00	0.00	0.00	4.30
2556	2601	9.965824	GTCCATTTGAAATCTCTAAAAAGTCAA	57.034	29.630	0.00	0.00	0.00	3.18
2557	2602	9.354673	AGTCCATTTGAAATCTCTAAAAAGTCA	57.645	29.630	0.00	0.00	0.00	3.41
2561	2606	9.581289	TGGTAGTCCATTTGAAATCTCTAAAAA	57.419	29.630	0.00	0.00	39.03	1.94
2562	2607	9.010029	GTGGTAGTCCATTTGAAATCTCTAAAA	57.990	33.333	0.00	0.00	46.20	1.52
2563	2608	8.160765	TGTGGTAGTCCATTTGAAATCTCTAAA	58.839	33.333	0.00	0.00	46.20	1.85
2564	2609	7.685481	TGTGGTAGTCCATTTGAAATCTCTAA	58.315	34.615	0.00	0.00	46.20	2.10
2565	2610	7.252612	TGTGGTAGTCCATTTGAAATCTCTA	57.747	36.000	0.00	0.00	46.20	2.43
2566	2611	6.126863	TGTGGTAGTCCATTTGAAATCTCT	57.873	37.500	0.00	0.00	46.20	3.10

Showing 1 to 25 of 102 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.