AutoCloner

Multiple sequence alignment - TraesCS2B01G027700

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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	TraesCS2B01G027700	chr2B	100.000	3476	0	0	1	3476	13059779	13056304	0.000000e+00	6420.0
1	TraesCS2B01G027700	chr2B	83.506	1546	213	23	998	2526	138993293	138991773	0.000000e+00	1404.0
2	TraesCS2B01G027700	chr2B	82.714	1533	242	11	998	2517	768807004	768805482	0.000000e+00	1341.0
3	TraesCS2B01G027700	chr2B	82.299	1531	244	16	998	2511	12422311	12423831	0.000000e+00	1301.0
4	TraesCS2B01G027700	chr2B	82.600	1500	230	19	1031	2511	11518287	11516800	0.000000e+00	1295.0
5	TraesCS2B01G027700	chr2B	80.578	1627	263	27	998	2611	13068506	13066920	0.000000e+00	1205.0
6	TraesCS2B01G027700	chr2B	84.918	305	42	2	2217	2517	11225257	11224953	4.360000e-79	305.0
7	TraesCS2B01G027700	chr2B	86.667	90	9	3	2686	2774	13063940	13063853	2.860000e-16	97.1
8	TraesCS2B01G027700	chr2D	98.145	2426	43	2	429	2854	9753776	9751353	0.000000e+00	4229.0
9	TraesCS2B01G027700	chr2D	83.485	1538	209	24	998	2517	85929585	85928075	0.000000e+00	1391.0
10	TraesCS2B01G027700	chr2D	82.959	1514	240	10	998	2502	19587012	19588516	0.000000e+00	1351.0
11	TraesCS2B01G027700	chr2D	82.203	1534	240	19	998	2511	9604745	9606265	0.000000e+00	1290.0
12	TraesCS2B01G027700	chr2D	81.800	1533	251	18	998	2517	9371512	9373029	0.000000e+00	1260.0
13	TraesCS2B01G027700	chr2D	80.050	1604	253	34	1266	2853	9758263	9756711	0.000000e+00	1127.0
14	TraesCS2B01G027700	chr2D	95.067	446	14	2	3	444	9755564	9755123	0.000000e+00	695.0
15	TraesCS2B01G027700	chr2D	75.849	265	37	20	598	845	9792401	9792147	3.670000e-20	110.0
16	TraesCS2B01G027700	chr2A	96.828	1986	46	4	148	2129	9090094	9088122	0.000000e+00	3302.0
17	TraesCS2B01G027700	chr2A	81.860	1527	246	19	998	2505	8707392	8708906	0.000000e+00	1256.0
18	TraesCS2B01G027700	chr2A	80.935	1626	258	25	998	2611	9094485	9092900	0.000000e+00	1238.0
19	TraesCS2B01G027700	chr2A	81.348	1528	245	18	998	2517	9982950	9984445	0.000000e+00	1206.0
20	TraesCS2B01G027700	chr2A	96.199	684	16	2	2127	2804	9066210	9065531	0.000000e+00	1110.0
21	TraesCS2B01G027700	chr5D	95.462	639	20	5	2847	3476	550608242	550608880	0.000000e+00	1011.0
22	TraesCS2B01G027700	chr5D	95.283	636	21	5	2850	3476	542461833	542461198	0.000000e+00	1000.0
23	TraesCS2B01G027700	chr5D	82.558	86	13	2	574	657	404501571	404501486	1.340000e-09	75.0
24	TraesCS2B01G027700	chr6D	95.149	639	22	2	2847	3476	19378735	19379373	0.000000e+00	1000.0
25	TraesCS2B01G027700	chr3D	95.283	636	21	5	2850	3476	430363751	430363116	0.000000e+00	1000.0
26	TraesCS2B01G027700	chrUn	94.969	636	23	2	2850	3476	61940479	61939844	0.000000e+00	989.0
27	TraesCS2B01G027700	chrUn	94.836	639	24	2	2847	3476	391915778	391916416	0.000000e+00	989.0
28	TraesCS2B01G027700	chrUn	94.679	639	25	2	2847	3476	329182541	329183179	0.000000e+00	983.0
29	TraesCS2B01G027700	chr7D	94.969	636	23	5	2850	3476	64984012	64983377	0.000000e+00	989.0
30	TraesCS2B01G027700	chr7D	94.969	636	23	5	2850	3476	633529062	633528427	0.000000e+00	989.0

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	TraesCS2B01G027700	chr2B	13056304	13059779	3475	True	6420.00	6420	100.000000	1	3476	1	chr2B.!!$R3	3475
1	TraesCS2B01G027700	chr2B	138991773	138993293	1520	True	1404.00	1404	83.506000	998	2526	1	chr2B.!!$R4	1528
2	TraesCS2B01G027700	chr2B	768805482	768807004	1522	True	1341.00	1341	82.714000	998	2517	1	chr2B.!!$R5	1519
3	TraesCS2B01G027700	chr2B	12422311	12423831	1520	False	1301.00	1301	82.299000	998	2511	1	chr2B.!!$F1	1513
4	TraesCS2B01G027700	chr2B	11516800	11518287	1487	True	1295.00	1295	82.600000	1031	2511	1	chr2B.!!$R2	1480
5	TraesCS2B01G027700	chr2B	13063853	13068506	4653	True	651.05	1205	83.622500	998	2774	2	chr2B.!!$R6	1776
6	TraesCS2B01G027700	chr2D	9751353	9758263	6910	True	2017.00	4229	91.087333	3	2854	3	chr2D.!!$R3	2851
7	TraesCS2B01G027700	chr2D	85928075	85929585	1510	True	1391.00	1391	83.485000	998	2517	1	chr2D.!!$R2	1519
8	TraesCS2B01G027700	chr2D	19587012	19588516	1504	False	1351.00	1351	82.959000	998	2502	1	chr2D.!!$F3	1504
9	TraesCS2B01G027700	chr2D	9604745	9606265	1520	False	1290.00	1290	82.203000	998	2511	1	chr2D.!!$F2	1513
10	TraesCS2B01G027700	chr2D	9371512	9373029	1517	False	1260.00	1260	81.800000	998	2517	1	chr2D.!!$F1	1519
11	TraesCS2B01G027700	chr2A	9088122	9094485	6363	True	2270.00	3302	88.881500	148	2611	2	chr2A.!!$R2	2463
12	TraesCS2B01G027700	chr2A	8707392	8708906	1514	False	1256.00	1256	81.860000	998	2505	1	chr2A.!!$F1	1507
13	TraesCS2B01G027700	chr2A	9982950	9984445	1495	False	1206.00	1206	81.348000	998	2517	1	chr2A.!!$F2	1519
14	TraesCS2B01G027700	chr2A	9065531	9066210	679	True	1110.00	1110	96.199000	2127	2804	1	chr2A.!!$R1	677
15	TraesCS2B01G027700	chr5D	550608242	550608880	638	False	1011.00	1011	95.462000	2847	3476	1	chr5D.!!$F1	629
16	TraesCS2B01G027700	chr5D	542461198	542461833	635	True	1000.00	1000	95.283000	2850	3476	1	chr5D.!!$R2	626
17	TraesCS2B01G027700	chr6D	19378735	19379373	638	False	1000.00	1000	95.149000	2847	3476	1	chr6D.!!$F1	629
18	TraesCS2B01G027700	chr3D	430363116	430363751	635	True	1000.00	1000	95.283000	2850	3476	1	chr3D.!!$R1	626
19	TraesCS2B01G027700	chrUn	61939844	61940479	635	True	989.00	989	94.969000	2850	3476	1	chrUn.!!$R1	626
20	TraesCS2B01G027700	chrUn	391915778	391916416	638	False	989.00	989	94.836000	2847	3476	1	chrUn.!!$F2	629
21	TraesCS2B01G027700	chrUn	329182541	329183179	638	False	983.00	983	94.679000	2847	3476	1	chrUn.!!$F1	629
22	TraesCS2B01G027700	chr7D	64983377	64984012	635	True	989.00	989	94.969000	2850	3476	1	chr7D.!!$R1	626
23	TraesCS2B01G027700	chr7D	633528427	633529062	635	True	989.00	989	94.969000	2850	3476	1	chr7D.!!$R2	626

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
859	4923	0.395862	TTTGGTTTGGGCCGTTCAGA	60.396	50.000	0.0	0.0	0.00	3.27	F
1548	5622	2.223340	ACACGCTGAGAAGCAAAAACTG	60.223	45.455	0.0	0.0	34.41	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1726	5802	1.679032	GGTCCTGCCATGGTCAAGTAC	60.679	57.143	14.67	6.05	37.17	2.73	R
3340	12949	0.660488	TAATATGTTGCGGCCTTGCG	59.340	50.000	0.00	0.00	37.81	4.85	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
23	2721	1.444895	GCACCTTCATGCAAAGCGG	60.445	57.895	0.00	0.00	45.39	5.52
133	2831	9.857656	ATCAATGGACAAGTTACATATCTTCAT	57.142	29.630	0.00	0.00	0.00	2.57
153	2851	8.705594	TCTTCATAAAGATTACTCAAGTAGGGG	58.294	37.037	0.00	0.00	36.59	4.79
154	2852	6.827727	TCATAAAGATTACTCAAGTAGGGGC	58.172	40.000	0.00	0.00	0.00	5.80
352	3054	4.465886	TCGGTGAGGAAAATGGAAAAAGA	58.534	39.130	0.00	0.00	0.00	2.52
367	3069	5.868801	TGGAAAAAGAAAAGAACAGCAACAG	59.131	36.000	0.00	0.00	0.00	3.16
386	3088	4.781934	ACAGCGGGCTAGAAATTTAGAAT	58.218	39.130	0.00	0.00	0.00	2.40
449	4513	5.768164	GGAAACTCAACTTCCTTTATGGTGA	59.232	40.000	0.00	0.00	39.49	4.02
568	4632	4.145052	CAAAGGTAGAAAGGGGGCATATC	58.855	47.826	0.00	0.00	0.00	1.63
659	4723	4.304110	CACGGTCAAACTTTGCTAGAGTA	58.696	43.478	0.00	0.00	0.00	2.59
697	4761	5.470777	TCCTCGTGTGTAAAATGTAAAAGGG	59.529	40.000	0.00	0.00	0.00	3.95
859	4923	0.395862	TTTGGTTTGGGCCGTTCAGA	60.396	50.000	0.00	0.00	0.00	3.27
897	4961	3.139077	CAACCCACTACTCCAGTCAAAC	58.861	50.000	0.00	0.00	34.26	2.93
971	5035	5.326069	ACTTGGAAGAGAGCAGTCTAGTTA	58.674	41.667	0.00	0.00	30.97	2.24
995	5059	2.857483	TCTCCAGAGAGATCGACCATC	58.143	52.381	0.00	0.00	44.42	3.51
1548	5622	2.223340	ACACGCTGAGAAGCAAAAACTG	60.223	45.455	0.00	0.00	34.41	3.16
1726	5802	2.276732	TGGAGACAGCCTTTTGAAGG	57.723	50.000	2.33	2.33	43.96	3.46
1923	5999	8.388853	GTGAAACCGATTTTCCTAAGTATTCTC	58.611	37.037	6.92	0.00	42.80	2.87
2085	6161	3.895232	AAGGTCGCAGATGTATTGAGT	57.105	42.857	0.00	0.00	40.67	3.41
2252	6331	3.881688	GCTTCACATCCACTTAGCATGAT	59.118	43.478	0.00	0.00	0.00	2.45
2415	6497	2.154198	TCATTTCGTTACAAGTCGTGCG	59.846	45.455	0.00	0.00	0.00	5.34
2669	9633	8.695456	GGTACATTTTATCAATCCAACAATCCT	58.305	33.333	0.00	0.00	0.00	3.24
2968	12332	7.496346	TTACTCAGGACATTCCTCAAGTTAT	57.504	36.000	10.59	0.00	45.66	1.89
3063	12672	4.699522	ACAAGGCTTCGGGTCCGC	62.700	66.667	4.27	0.00	39.59	5.54
3066	12675	2.363975	AAGGCTTCGGGTCCGCATA	61.364	57.895	4.27	0.00	39.59	3.14
3247	12856	2.234300	TATCGTCCGATTTGCCTTCC	57.766	50.000	7.57	0.00	36.17	3.46
3340	12949	4.584327	AACCCACTCAAACAGCATTTAC	57.416	40.909	0.00	0.00	0.00	2.01
3368	12977	3.815401	GCCGCAACATATTAGATGGAGTT	59.185	43.478	0.00	0.00	0.00	3.01
3467	13766	7.402862	ACAAAGCCTATGATAAGGTTAAGTGT	58.597	34.615	0.00	0.00	39.02	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	0.877071	CTTTGCATGAAGGTGCTCGT	59.123	50.000	0.00	0.00	45.27	4.18
3	4	0.455633	CGCTTTGCATGAAGGTGCTC	60.456	55.000	0.00	0.00	45.27	4.26
6	7	1.444895	GCCGCTTTGCATGAAGGTG	60.445	57.895	0.00	0.00	0.00	4.00
23	2721	4.521062	ACTGATCTCGCCGGCTGC	62.521	66.667	26.68	9.33	0.00	5.25
78	2776	0.250640	CTCCTGTTGGTTCTGCAGCT	60.251	55.000	9.47	0.00	34.23	4.24
131	2829	6.831976	AGCCCCTACTTGAGTAATCTTTATG	58.168	40.000	0.00	0.00	0.00	1.90
133	2831	6.672657	AGAAGCCCCTACTTGAGTAATCTTTA	59.327	38.462	0.00	0.00	0.00	1.85
191	2893	9.590451	CATTTCCTTGATTTTACACAGCATAAT	57.410	29.630	0.00	0.00	0.00	1.28
192	2894	8.584157	ACATTTCCTTGATTTTACACAGCATAA	58.416	29.630	0.00	0.00	0.00	1.90
227	2929	8.859090	TGATGTACATTTCCTTGATTTTTGACT	58.141	29.630	10.30	0.00	0.00	3.41
260	2962	5.360999	AGCATTGTGTACTGCTATACTCTCA	59.639	40.000	5.59	0.00	46.49	3.27
327	3029	3.502123	TTCCATTTTCCTCACCGAAGT	57.498	42.857	0.00	0.00	0.00	3.01
352	3054	0.385390	CCCGCTGTTGCTGTTCTTTT	59.615	50.000	0.00	0.00	36.97	2.27
367	3069	7.674471	ATTCTATTCTAAATTTCTAGCCCGC	57.326	36.000	0.00	0.00	0.00	6.13
449	4513	1.271597	GGGGTGTCTCTGTTCATGCTT	60.272	52.381	0.00	0.00	0.00	3.91
568	4632	1.157870	AACTCGTTGGCAAGGACACG	61.158	55.000	17.89	10.29	0.00	4.49
659	4723	2.634940	CACGAGGAATATCATCCACCCT	59.365	50.000	0.00	0.00	42.27	4.34
697	4761	2.353109	GCATTTGTCTTTCTTGGGGCTC	60.353	50.000	0.00	0.00	0.00	4.70
751	4815	9.123902	CTCACAATAGGTCCAAATTAATCATGA	57.876	33.333	0.00	0.00	0.00	3.07
761	4825	9.575868	TGTTTTTATACTCACAATAGGTCCAAA	57.424	29.630	0.00	0.00	0.00	3.28
859	4923	4.142038	GGGTTGGTGACACTGATACTTTT	58.858	43.478	5.39	0.00	42.67	2.27
897	4961	5.130145	AGAAGTCTCCAGGGATGACTAAATG	59.870	44.000	15.87	0.00	39.78	2.32
995	5059	1.619654	TTTGACAACCTCCATGGCTG	58.380	50.000	6.96	2.46	40.22	4.85
1255	5325	1.270839	ACTGTCTTGGATGGTTCGGTG	60.271	52.381	0.00	0.00	0.00	4.94
1548	5622	1.763634	GCTGCAACAAGAAGCTCAAC	58.236	50.000	0.00	0.00	46.23	3.18
1726	5802	1.679032	GGTCCTGCCATGGTCAAGTAC	60.679	57.143	14.67	6.05	37.17	2.73
2085	6161	2.145397	ACTGAGCATCGAGGTTCCTA	57.855	50.000	11.42	0.00	38.61	2.94
2415	6497	3.806521	CACTAGCTTCATGTGTATCCTGC	59.193	47.826	0.00	0.00	0.00	4.85
2669	9633	5.981088	TTTGTACGTTATCTACAGGTGGA	57.019	39.130	0.00	0.00	0.00	4.02
2890	10584	3.181476	TGAAGGTCCAAAAAGCTCTTTGC	60.181	43.478	7.01	0.00	43.29	3.68
2951	10786	4.336713	GCTTCCATAACTTGAGGAATGTCC	59.663	45.833	0.00	0.00	40.39	4.02
2968	12332	3.866883	GGAATTCATTTTCCGCTTCCA	57.133	42.857	7.93	0.00	36.12	3.53
3054	12663	1.143183	GAAAGCTATGCGGACCCGA	59.857	57.895	13.24	0.00	42.83	5.14
3063	12672	1.936547	GAACTCTGCGGGAAAGCTATG	59.063	52.381	0.00	0.00	38.13	2.23
3066	12675	1.267121	TAGAACTCTGCGGGAAAGCT	58.733	50.000	0.00	0.00	38.13	3.74
3340	12949	0.660488	TAATATGTTGCGGCCTTGCG	59.340	50.000	0.00	0.00	37.81	4.85
3443	13211	7.012421	GGACACTTAACCTTATCATAGGCTTTG	59.988	40.741	0.00	0.00	38.99	2.77
3452	13751	6.697641	AGAAAGGGACACTTAACCTTATCA	57.302	37.500	0.00	0.00	43.49	2.15

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.