AutoCloner

Multiple sequence alignment - TraesCS3D01G189100

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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	TraesCS3D01G189100	chr3D	100.000	2339	0	0	1	2339	177015445	177013107	0.000000e+00	4320.0
1	TraesCS3D01G189100	chr3D	87.209	86	10	1	1460	1544	418785204	418785119	1.910000e-16	97.1
2	TraesCS3D01G189100	chr6D	95.528	1364	59	2	1	1362	462399749	462398386	0.000000e+00	2180.0
3	TraesCS3D01G189100	chr6D	95.088	1364	62	5	1	1362	452072048	452070688	0.000000e+00	2143.0
4	TraesCS3D01G189100	chr1D	95.165	1365	64	2	1	1363	176360147	176361511	0.000000e+00	2154.0
5	TraesCS3D01G189100	chr1D	94.648	1364	70	3	1	1362	356880593	356881955	0.000000e+00	2111.0
6	TraesCS3D01G189100	chr7D	94.733	1367	68	4	1	1364	219850273	219848908	0.000000e+00	2122.0
7	TraesCS3D01G189100	chr2B	94.277	1363	75	3	1	1362	325636806	325638166	0.000000e+00	2082.0
8	TraesCS3D01G189100	chr5B	94.204	1363	78	1	1	1362	684172822	684174184	0.000000e+00	2078.0
9	TraesCS3D01G189100	chr2A	94.057	1363	79	2	1	1362	382856646	382855285	0.000000e+00	2067.0
10	TraesCS3D01G189100	chr2A	86.792	106	7	6	1567	1669	83008924	83009025	6.830000e-21	111.0
11	TraesCS3D01G189100	chr4B	93.732	1372	77	4	1	1364	364053868	364052498	0.000000e+00	2049.0
12	TraesCS3D01G189100	chr4B	83.333	216	31	3	1450	1664	626017412	626017623	6.600000e-46	195.0
13	TraesCS3D01G189100	chr4B	83.333	186	30	1	1720	1905	489370351	489370167	1.110000e-38	171.0
14	TraesCS3D01G189100	chr4B	97.674	43	1	0	1514	1556	617394236	617394194	8.960000e-10	75.0
15	TraesCS3D01G189100	chr3A	87.821	780	65	12	1361	2135	217352020	217351266	0.000000e+00	887.0
16	TraesCS3D01G189100	chr3A	84.733	131	19	1	1476	1606	649165438	649165567	1.890000e-26	130.0
17	TraesCS3D01G189100	chr3B	92.322	521	28	4	1821	2339	255982638	255982128	0.000000e+00	730.0
18	TraesCS3D01G189100	chr3B	92.657	463	31	3	1359	1819	255983337	255982876	0.000000e+00	664.0
19	TraesCS3D01G189100	chr3B	86.228	167	19	4	1450	1614	676772285	676772449	6.640000e-41	178.0
20	TraesCS3D01G189100	chr3B	87.500	72	9	0	1365	1436	670203943	670203872	1.490000e-12	84.2
21	TraesCS3D01G189100	chr5D	89.610	77	8	0	1359	1435	126260620	126260544	5.320000e-17	99.0
22	TraesCS3D01G189100	chr4A	89.474	76	8	0	1361	1436	679680536	679680611	1.910000e-16	97.1
23	TraesCS3D01G189100	chr4A	93.023	43	3	0	1514	1556	595655223	595655181	1.940000e-06	63.9
24	TraesCS3D01G189100	chr4A	92.105	38	3	0	1800	1837	212296	212333	1.000000e-03	54.7
25	TraesCS3D01G189100	chr2D	85.714	91	13	0	1815	1905	348178580	348178670	1.910000e-16	97.1
26	TraesCS3D01G189100	chr4D	93.023	43	3	0	1514	1556	472429926	472429968	1.940000e-06	63.9

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	TraesCS3D01G189100	chr3D	177013107	177015445	2338	True	4320	4320	100.0000	1	2339	1	chr3D.!!$R1	2338
1	TraesCS3D01G189100	chr6D	462398386	462399749	1363	True	2180	2180	95.5280	1	1362	1	chr6D.!!$R2	1361
2	TraesCS3D01G189100	chr6D	452070688	452072048	1360	True	2143	2143	95.0880	1	1362	1	chr6D.!!$R1	1361
3	TraesCS3D01G189100	chr1D	176360147	176361511	1364	False	2154	2154	95.1650	1	1363	1	chr1D.!!$F1	1362
4	TraesCS3D01G189100	chr1D	356880593	356881955	1362	False	2111	2111	94.6480	1	1362	1	chr1D.!!$F2	1361
5	TraesCS3D01G189100	chr7D	219848908	219850273	1365	True	2122	2122	94.7330	1	1364	1	chr7D.!!$R1	1363
6	TraesCS3D01G189100	chr2B	325636806	325638166	1360	False	2082	2082	94.2770	1	1362	1	chr2B.!!$F1	1361
7	TraesCS3D01G189100	chr5B	684172822	684174184	1362	False	2078	2078	94.2040	1	1362	1	chr5B.!!$F1	1361
8	TraesCS3D01G189100	chr2A	382855285	382856646	1361	True	2067	2067	94.0570	1	1362	1	chr2A.!!$R1	1361
9	TraesCS3D01G189100	chr4B	364052498	364053868	1370	True	2049	2049	93.7320	1	1364	1	chr4B.!!$R1	1363
10	TraesCS3D01G189100	chr3A	217351266	217352020	754	True	887	887	87.8210	1361	2135	1	chr3A.!!$R1	774
11	TraesCS3D01G189100	chr3B	255982128	255983337	1209	True	697	730	92.4895	1359	2339	2	chr3B.!!$R2	980

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
481	483	0.179004	TGAAGGTCACGCCCATTTGT	60.179	50.0	0.0	0.0	38.26	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2097	2348	1.68766	TGCATGCACAAGTTTGACCAT	59.312	42.857	18.46	0.0	0.0	3.55	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
61	62	4.137543	GGATCCCAAATTGTGCTACTAGG	58.862	47.826	0.00	0.00	0.00	3.02
110	111	5.161943	ACTGTTAACTAAGGTGGGTGATC	57.838	43.478	7.22	0.00	0.00	2.92
112	113	6.021030	ACTGTTAACTAAGGTGGGTGATCTA	58.979	40.000	7.22	0.00	0.00	1.98
139	140	2.771943	TCCTGCTTCGAATACTTGGGAT	59.228	45.455	0.00	0.00	0.00	3.85
145	146	4.271291	GCTTCGAATACTTGGGATGAAGAC	59.729	45.833	0.00	0.00	34.71	3.01
193	194	3.511699	TGATGTTCAACGGATTCTCTCG	58.488	45.455	0.00	0.00	0.00	4.04
276	277	1.795286	GTTCTCAGTTCGGTCTGCTTG	59.205	52.381	3.54	0.00	35.63	4.01
322	323	7.858382	CAGTATGGAAGTAGACTAAGACATTCG	59.142	40.741	0.00	0.00	0.00	3.34
339	341	2.186826	CGAATGGGATGGGGCGAAC	61.187	63.158	0.00	0.00	0.00	3.95
386	388	6.918067	AGATATGGAAGTTATCATGTCCGA	57.082	37.500	9.99	0.00	33.74	4.55
394	396	6.072673	GGAAGTTATCATGTCCGACAAAAGTT	60.073	38.462	5.07	7.08	0.00	2.66
457	459	0.935196	GGGTTACGCTCGCAAATAGG	59.065	55.000	0.00	0.00	0.00	2.57
481	483	0.179004	TGAAGGTCACGCCCATTTGT	60.179	50.000	0.00	0.00	38.26	2.83
593	595	6.965500	GGATGATATCATTGATAAAGCTTGCG	59.035	38.462	19.11	0.00	36.57	4.85
620	622	3.241530	TTGCTGGAGAGGCGGTGT	61.242	61.111	0.00	0.00	0.00	4.16
652	654	2.972713	ACTACTTCTGCCAGACCAAGAA	59.027	45.455	0.00	0.00	0.00	2.52
699	701	4.754618	TGTGCGTGAAATGATTACTGTCTT	59.245	37.500	0.00	0.00	0.00	3.01
754	756	2.092968	AGTGCACAAGGAGACAACTCAA	60.093	45.455	21.04	0.00	44.22	3.02
1078	1087	9.350357	GATGTAATCGCCTTATTATTAACTCGA	57.650	33.333	0.00	0.00	31.13	4.04
1107	1116	5.457197	CCTGGAGGTGATTGATACCATGAAT	60.457	44.000	0.00	0.00	40.74	2.57
1230	1239	7.992033	AGAGAAGCAAATAAAGTAGCTCATGAT	59.008	33.333	0.00	0.00	36.07	2.45
1472	1484	7.662669	ACGAGTAGGCCTTAAAAGTTTGAAATA	59.337	33.333	12.58	0.00	0.00	1.40
1506	1519	7.122948	TGGGTCTTAAATGTGTGTAAGTTGTTT	59.877	33.333	0.00	0.00	0.00	2.83
1538	1551	7.013942	GGGTCCTAAAAGTATTTCAAGTGTGTT	59.986	37.037	0.00	0.00	37.28	3.32
1554	1567	9.280174	TCAAGTGTGTTAAATAGGTCCTAAAAG	57.720	33.333	1.78	0.00	0.00	2.27
1563	1576	2.893424	AGGTCCTAAAAGTCACGGGTA	58.107	47.619	0.00	0.00	0.00	3.69
1582	1595	9.932207	CACGGGTAAAAATACATATATAGGACA	57.068	33.333	0.54	0.00	0.00	4.02
1628	1641	3.305720	AGGACCTACTTGACACACTTGA	58.694	45.455	0.00	0.00	0.00	3.02
1630	1643	4.058817	GGACCTACTTGACACACTTGAAG	58.941	47.826	0.00	0.00	0.00	3.02
1633	1646	6.420913	ACCTACTTGACACACTTGAAGTAT	57.579	37.500	0.00	0.00	32.04	2.12
1638	1651	9.438291	CTACTTGACACACTTGAAGTATTTTTG	57.562	33.333	0.00	0.00	32.04	2.44
1665	1679	8.803235	GGACCTCCAATGTATTTTACTCTTTTT	58.197	33.333	0.00	0.00	35.64	1.94
1674	1688	8.891671	TGTATTTTACTCTTTTTAGACGGTGT	57.108	30.769	0.00	0.00	0.00	4.16
1684	1698	6.987992	TCTTTTTAGACGGTGTGTGTTTCTAT	59.012	34.615	0.00	0.00	0.00	1.98
1716	1730	4.351407	TCCAGTTAAGGTTGGTCATGGTTA	59.649	41.667	0.00	0.00	35.89	2.85
1733	1747	9.900710	GTCATGGTTAGAGTAACATAGATAGTG	57.099	37.037	0.00	0.00	40.39	2.74
1734	1748	8.577296	TCATGGTTAGAGTAACATAGATAGTGC	58.423	37.037	0.00	0.00	40.39	4.40
1752	1766	0.748450	GCCATGCATGCCACATAAGT	59.252	50.000	21.69	0.00	0.00	2.24
1852	2102	6.757897	TTTTCCAATGCGAAATGACTCTAT	57.242	33.333	0.00	0.00	32.00	1.98
1908	2158	4.349930	ACCTATGACACAACCCACTACTTT	59.650	41.667	0.00	0.00	0.00	2.66
1947	2197	8.880750	GCCTAACTAAGTTTAACTAGACAATGG	58.119	37.037	0.00	0.00	0.00	3.16
1950	2201	7.017319	ACTAAGTTTAACTAGACAATGGCCT	57.983	36.000	3.32	0.00	0.00	5.19
2009	2260	7.614192	AGACCAACAAACTAAGGAGAAAAGAAA	59.386	33.333	0.00	0.00	0.00	2.52
2050	2301	4.822026	AGAAAACGGTAGAAGATGGACTG	58.178	43.478	0.00	0.00	0.00	3.51
2083	2334	3.899052	TTATGGAACCACCTTACCTCG	57.101	47.619	0.00	0.00	39.86	4.63
2097	2348	5.104374	CCTTACCTCGTACGCTCAATTTTA	58.896	41.667	11.24	0.00	0.00	1.52
2100	2351	3.869246	ACCTCGTACGCTCAATTTTATGG	59.131	43.478	11.24	0.95	0.00	2.74
2102	2353	4.025979	CCTCGTACGCTCAATTTTATGGTC	60.026	45.833	11.24	0.00	0.00	4.02
2106	2357	5.506832	CGTACGCTCAATTTTATGGTCAAAC	59.493	40.000	0.52	0.00	0.00	2.93
2114	2365	7.215789	TCAATTTTATGGTCAAACTTGTGCAT	58.784	30.769	0.00	0.00	32.73	3.96
2209	2460	6.096987	TGCAACCTAATCCACTAACACAAAAA	59.903	34.615	0.00	0.00	0.00	1.94
2269	2520	5.057149	CCGAGGAGAAAGAGAAAGAAAACA	58.943	41.667	0.00	0.00	0.00	2.83
2322	2573	7.720957	AGATATTACTGCCATACAAATTGCTCA	59.279	33.333	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	4.217510	TCCAGGCATCTTCCCAAATATTG	58.782	43.478	0.00	0.00	0.00	1.90
61	62	3.146847	CCCCTTAGGTGTCACAACTTTC	58.853	50.000	0.00	0.00	31.86	2.62
110	111	7.307632	CCAAGTATTCGAAGCAGGATCAATTAG	60.308	40.741	3.35	0.00	0.00	1.73
112	113	5.297776	CCAAGTATTCGAAGCAGGATCAATT	59.702	40.000	3.35	0.00	0.00	2.32
131	132	4.536090	TGTAATCAGGTCTTCATCCCAAGT	59.464	41.667	0.00	0.00	0.00	3.16
139	140	6.545666	ACATTGTTTGTGTAATCAGGTCTTCA	59.454	34.615	0.00	0.00	37.11	3.02
193	194	4.825546	ATCATGTTGCGAGATTGGAATC	57.174	40.909	0.00	0.00	35.64	2.52
262	263	2.097466	CACAAAACAAGCAGACCGAACT	59.903	45.455	0.00	0.00	0.00	3.01
276	277	1.886542	GATGGTCCCACTCCACAAAAC	59.113	52.381	0.00	0.00	37.81	2.43
322	323	1.828224	GGTTCGCCCCATCCCATTC	60.828	63.158	0.00	0.00	0.00	2.67
436	438	0.806884	TATTTGCGAGCGTAACCCGG	60.807	55.000	0.00	0.00	36.94	5.73
457	459	0.463654	TGGGCGTGACCTTCATATGC	60.464	55.000	0.00	0.00	39.10	3.14
481	483	2.180276	GAACCCTCAGAGCAAGTAGGA	58.820	52.381	0.00	0.00	0.00	2.94
620	622	4.021916	GGCAGAAGTAGTAGGTACTCCAA	58.978	47.826	0.00	0.00	41.50	3.53
652	654	5.387113	TGTGCTAACCCATTATCCTCAAT	57.613	39.130	0.00	0.00	0.00	2.57
692	694	5.841237	ACCATAGATACCATGCTAAGACAGT	59.159	40.000	0.00	0.00	0.00	3.55
699	701	4.140575	TCCCACCATAGATACCATGCTA	57.859	45.455	0.00	0.00	0.00	3.49
754	756	5.484715	CCCATTGAAATCTGAAGTGCATTT	58.515	37.500	0.00	0.00	0.00	2.32
1107	1116	2.693762	CGCCGACTGTCCTCCGTTA	61.694	63.158	1.55	0.00	0.00	3.18
1136	1145	3.634568	AACAATCGTCGAAAATTGCCA	57.365	38.095	16.80	0.00	36.54	4.92
1301	1310	7.876068	AGATAAAAAGTACATCGTTTGTGAGGA	59.124	33.333	0.00	0.00	39.48	3.71
1447	1459	5.934935	TTCAAACTTTTAAGGCCTACTCG	57.065	39.130	5.16	0.00	0.00	4.18
1472	1484	3.813166	CACATTTAAGACCCACGTGAACT	59.187	43.478	19.30	10.08	0.00	3.01
1506	1519	5.046448	TGAAATACTTTTAGGACCCGCAGTA	60.046	40.000	0.00	0.00	0.00	2.74
1509	1522	4.289238	TGAAATACTTTTAGGACCCGCA	57.711	40.909	0.00	0.00	0.00	5.69
1538	1551	5.484998	ACCCGTGACTTTTAGGACCTATTTA	59.515	40.000	0.94	0.00	0.00	1.40
1563	1576	8.946085	CACCGCATGTCCTATATATGTATTTTT	58.054	33.333	0.00	0.00	0.00	1.94
1582	1595	2.552315	AGTTTGAAATCGTTCACCGCAT	59.448	40.909	0.00	0.00	43.52	4.73
1638	1651	6.002653	AGAGTAAAATACATTGGAGGTCCC	57.997	41.667	0.00	0.00	34.29	4.46
1665	1679	4.763279	TGAGATAGAAACACACACCGTCTA	59.237	41.667	0.00	0.00	0.00	2.59
1674	1688	4.089361	TGGAGAGCTGAGATAGAAACACA	58.911	43.478	0.00	0.00	0.00	3.72
1684	1698	3.176924	ACCTTAACTGGAGAGCTGAGA	57.823	47.619	0.00	0.00	0.00	3.27
1716	1730	5.305386	TGCATGGCACTATCTATGTTACTCT	59.695	40.000	0.00	0.00	31.71	3.24
1734	1748	4.652421	TTTACTTATGTGGCATGCATGG	57.348	40.909	27.34	10.90	0.00	3.66
1762	1776	8.268850	TCTTCTCTTTAATTACTTGCCACATC	57.731	34.615	0.00	0.00	0.00	3.06
1812	1826	9.669353	CATTGGAAAATGCTATGTGATAGTAAC	57.331	33.333	0.00	0.00	35.29	2.50
1908	2158	3.170991	AGTTAGGCTAGTCACAGTGGA	57.829	47.619	0.00	0.00	0.00	4.02
2035	2286	3.550437	ACATGCAGTCCATCTTCTACC	57.450	47.619	0.00	0.00	29.71	3.18
2050	2301	7.014230	AGGTGGTTCCATAATTACATTACATGC	59.986	37.037	0.00	0.00	39.02	4.06
2063	2314	3.175594	ACGAGGTAAGGTGGTTCCATAA	58.824	45.455	0.00	0.00	39.02	1.90
2083	2334	6.608610	AGTTTGACCATAAAATTGAGCGTAC	58.391	36.000	0.00	0.00	0.00	3.67
2097	2348	1.687660	TGCATGCACAAGTTTGACCAT	59.312	42.857	18.46	0.00	0.00	3.55
2100	2351	3.015934	TCATGCATGCACAAGTTTGAC	57.984	42.857	25.37	0.00	0.00	3.18
2102	2353	3.845178	AGATCATGCATGCACAAGTTTG	58.155	40.909	25.37	16.46	0.00	2.93
2106	2357	7.423199	ACTAATTAAGATCATGCATGCACAAG	58.577	34.615	25.37	16.12	0.00	3.16
2150	2401	4.084287	ACACTGGGATGAACGAAGTACTA	58.916	43.478	0.00	0.00	45.00	1.82
2228	2479	9.937876	TCTCCTCGGATTCCTGTATATATTTAT	57.062	33.333	0.30	0.00	0.00	1.40
2238	2489	2.763448	CTCTTTCTCCTCGGATTCCTGT	59.237	50.000	0.30	0.00	0.00	4.00
2248	2499	7.321745	TGTTGTTTTCTTTCTCTTTCTCCTC	57.678	36.000	0.00	0.00	0.00	3.71
2301	2552	5.887598	AGATGAGCAATTTGTATGGCAGTAA	59.112	36.000	0.00	0.00	32.73	2.24
2315	2566	3.726557	TTCAAGGTGGAGATGAGCAAT	57.273	42.857	0.00	0.00	0.00	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.