AutoCloner

Multiple sequence alignment - TraesCS2D01G118800

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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	TraesCS2D01G118800	chr2D	100.000	3378	0	0	1	3378	68562685	68559308	0.000000e+00	6239
1	TraesCS2D01G118800	chr2D	95.923	2600	85	9	1	2591	68584838	68582251	0.000000e+00	4194
2	TraesCS2D01G118800	chr2D	95.117	2601	88	11	1	2591	68621990	68619419	0.000000e+00	4063
3	TraesCS2D01G118800	chr2D	97.118	798	18	5	2583	3378	68619401	68618607	0.000000e+00	1341
4	TraesCS2D01G118800	chr2D	96.883	802	20	5	2580	3378	68582236	68581437	0.000000e+00	1338
5	TraesCS2D01G118800	chr2D	86.692	263	30	5	485	746	68618966	68619224	1.530000e-73	287
6	TraesCS2D01G118800	chr2D	85.577	208	24	4	2796	3001	22816940	22817143	2.640000e-51	213
7	TraesCS2D01G118800	chr4A	92.007	1689	99	15	768	2432	629478937	629477261	0.000000e+00	2338
8	TraesCS2D01G118800	chr4A	84.946	279	36	5	490	766	741250619	741250893	9.230000e-71	278
9	TraesCS2D01G118800	chr5D	92.336	1644	90	20	765	2382	539022547	539024180	0.000000e+00	2305
10	TraesCS2D01G118800	chr5D	85.714	273	33	5	497	768	224086460	224086193	1.980000e-72	283
11	TraesCS2D01G118800	chr5B	92.165	1621	96	14	768	2382	680601482	680603077	0.000000e+00	2261
12	TraesCS2D01G118800	chr5B	91.971	274	21	1	3106	3378	626657410	626657137	1.900000e-102	383
13	TraesCS2D01G118800	chr5B	91.971	274	21	1	3106	3378	629728078	629727805	1.900000e-102	383
14	TraesCS2D01G118800	chr5B	89.212	241	26	0	1	241	513650984	513651224	5.480000e-78	302
15	TraesCS2D01G118800	chr5B	85.455	275	32	6	497	768	247230795	247231064	2.570000e-71	279
16	TraesCS2D01G118800	chr7D	92.391	276	19	2	3104	3378	515031074	515031348	3.160000e-105	392
17	TraesCS2D01G118800	chr7A	92.075	265	20	1	3105	3368	8681053	8681317	4.120000e-99	372
18	TraesCS2D01G118800	chr7A	92.045	264	20	1	3105	3367	251143246	251142983	1.480000e-98	370
19	TraesCS2D01G118800	chr7A	90.511	274	25	1	3106	3378	8676482	8676755	8.910000e-96	361
20	TraesCS2D01G118800	chr6D	93.776	241	15	0	1	241	134265950	134265710	2.480000e-96	363
21	TraesCS2D01G118800	chr6D	87.313	268	30	4	497	763	205268379	205268115	1.520000e-78	303
22	TraesCS2D01G118800	chr3B	90.288	278	26	1	3102	3378	704021902	704021625	2.480000e-96	363
23	TraesCS2D01G118800	chr2B	87.417	302	32	4	2702	3001	114040069	114040366	3.230000e-90	342
24	TraesCS2D01G118800	chr2B	85.537	242	31	3	1	240	705713834	705713595	2.010000e-62	250
25	TraesCS2D01G118800	chr2B	81.090	312	50	8	2702	3005	585899410	585899720	1.210000e-59	241
26	TraesCS2D01G118800	chr2B	93.333	75	5	0	1857	1931	400351688	400351614	9.910000e-21	111
27	TraesCS2D01G118800	chr1B	88.750	240	24	3	500	739	616824294	616824530	1.190000e-74	291
28	TraesCS2D01G118800	chr1B	86.508	252	33	1	2751	3001	616824546	616824295	3.320000e-70	276
29	TraesCS2D01G118800	chr3D	87.500	248	25	5	500	746	53620261	53620503	7.140000e-72	281
30	TraesCS2D01G118800	chr3D	85.356	239	30	5	2760	2994	54001784	54002021	3.370000e-60	243
31	TraesCS2D01G118800	chr6B	83.828	303	40	5	2702	3001	633680716	633681012	2.570000e-71	279
32	TraesCS2D01G118800	chr1A	83.402	241	13	1	1	241	588135255	588135042	7.390000e-47	198
33	TraesCS2D01G118800	chr2A	87.586	145	11	4	356	493	66376166	66376310	9.700000e-36	161
34	TraesCS2D01G118800	chr2A	88.430	121	10	2	356	472	66481964	66482084	3.510000e-30	143
35	TraesCS2D01G118800	chr2A	94.667	75	4	0	1857	1931	440069814	440069740	2.130000e-22	117

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	TraesCS2D01G118800	chr2D	68559308	68562685	3377	True	6239	6239	100.0000	1	3378	1	chr2D.!!$R1	3377
1	TraesCS2D01G118800	chr2D	68581437	68584838	3401	True	2766	4194	96.4030	1	3378	2	chr2D.!!$R2	3377
2	TraesCS2D01G118800	chr2D	68618607	68621990	3383	True	2702	4063	96.1175	1	3378	2	chr2D.!!$R3	3377
3	TraesCS2D01G118800	chr4A	629477261	629478937	1676	True	2338	2338	92.0070	768	2432	1	chr4A.!!$R1	1664
4	TraesCS2D01G118800	chr5D	539022547	539024180	1633	False	2305	2305	92.3360	765	2382	1	chr5D.!!$F1	1617
5	TraesCS2D01G118800	chr5B	680601482	680603077	1595	False	2261	2261	92.1650	768	2382	1	chr5B.!!$F3	1614

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
231	233	0.528017	GCCAGCCCAAAAGTAAGAGC	59.472	55.0	0.0	0.00	0.00	4.09	F
378	380	0.881118	GGTTCACACCACATTCGCAT	59.119	50.0	0.0	0.00	43.61	4.73	F
1456	1471	0.461870	GATGTACGCCATGCTGGACA	60.462	55.0	6.4	3.28	40.96	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1290	1302	1.026182	GGCTGACGATCATGTTGGCA	61.026	55.000	0.00	0.00	0.00	4.92	R
1655	1676	1.587054	CCGAGGAACTTGACGAGCT	59.413	57.895	0.00	0.00	44.22	4.09	R
2780	2873	0.378257	GAATACACATGCACGCAGGG	59.622	55.000	8.69	0.41	31.33	4.45	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
144	145	1.066071	GGTTCTTCACACCTAGGCCTC	60.066	57.143	9.68	0.00	0.00	4.70
225	227	1.043022	CTCTTTGCCAGCCCAAAAGT	58.957	50.000	0.00	0.00	34.59	2.66
227	229	2.627699	CTCTTTGCCAGCCCAAAAGTAA	59.372	45.455	0.00	0.00	34.59	2.24
228	230	2.627699	TCTTTGCCAGCCCAAAAGTAAG	59.372	45.455	0.00	0.00	34.59	2.34
229	231	2.373335	TTGCCAGCCCAAAAGTAAGA	57.627	45.000	0.00	0.00	0.00	2.10
230	232	1.909700	TGCCAGCCCAAAAGTAAGAG	58.090	50.000	0.00	0.00	0.00	2.85
231	233	0.528017	GCCAGCCCAAAAGTAAGAGC	59.472	55.000	0.00	0.00	0.00	4.09
232	234	1.909700	CCAGCCCAAAAGTAAGAGCA	58.090	50.000	0.00	0.00	0.00	4.26
240	242	4.074970	CCAAAAGTAAGAGCACATCCACT	58.925	43.478	0.00	0.00	0.00	4.00
310	312	6.545666	TGTGCAGAGTTTGGAGAAAAGAAATA	59.454	34.615	0.00	0.00	0.00	1.40
357	359	3.081804	TCGACTGATAGCTGAAGTGACA	58.918	45.455	0.00	0.00	0.00	3.58
378	380	0.881118	GGTTCACACCACATTCGCAT	59.119	50.000	0.00	0.00	43.61	4.73
428	430	3.326747	GTCACAACTATCGTCTTTGCCT	58.673	45.455	0.00	0.00	0.00	4.75
469	471	3.055719	CATCACACACCCCGCACC	61.056	66.667	0.00	0.00	0.00	5.01
550	552	3.241530	TGGCGCCCACTTCAGTCT	61.242	61.111	26.77	0.00	0.00	3.24
552	554	2.343758	GCGCCCACTTCAGTCTCA	59.656	61.111	0.00	0.00	0.00	3.27
866	872	2.535317	AGGGAACATGGGGTGGCT	60.535	61.111	0.00	0.00	0.00	4.75
981	987	3.257375	AGGTGTTCAAGACATACGTGCTA	59.743	43.478	0.00	0.00	41.10	3.49
1004	1010	2.341257	GCAGACGACAGTGTTCATGAT	58.659	47.619	0.00	0.00	0.00	2.45
1122	1128	2.047274	CTCACCACCAACGGCGAT	60.047	61.111	16.62	0.00	0.00	4.58
1260	1272	4.538283	CGCGTGCTCGTCCTCGAT	62.538	66.667	10.18	0.00	45.21	3.59
1300	1312	2.821378	CTCAAGGTCATTGCCAACATGA	59.179	45.455	0.00	0.00	38.89	3.07
1423	1438	4.161295	CCTTCCATCGCGGCCTCA	62.161	66.667	6.13	0.00	33.14	3.86
1456	1471	0.461870	GATGTACGCCATGCTGGACA	60.462	55.000	6.40	3.28	40.96	4.02
1622	1643	0.614979	ATCCTGACGCTACTGGTGGT	60.615	55.000	0.00	0.00	0.00	4.16
1640	1661	4.697756	CGGCCACGACACCACCAT	62.698	66.667	2.24	0.00	44.60	3.55
2220	2244	4.988716	TGAGTCGCTGTCCCCCGT	62.989	66.667	0.00	0.00	0.00	5.28
2346	2394	0.102844	GTGCGCATGCCCAATAACAT	59.897	50.000	15.91	0.00	41.78	2.71
2451	2513	6.438259	TGTGTAGTTACTCTACTGATGCTC	57.562	41.667	0.00	0.00	46.50	4.26
2500	2562	7.041780	AGCGATATTTTCAGGCTATTTGTACTG	60.042	37.037	0.00	0.00	31.03	2.74
2747	2840	4.715130	TCCGACCAGGTGGGAGGG	62.715	72.222	19.24	1.84	35.59	4.30
2770	2863	9.095700	AGGGTCTTTTAATAACTGGCAATTTTA	57.904	29.630	0.00	0.00	0.00	1.52
2908	3002	2.040178	GGACCGTAGATGACCCTCAAT	58.960	52.381	0.00	0.00	0.00	2.57
2947	3041	5.071370	TGTATTTCGGGTGTTTGTAACCAT	58.929	37.500	0.00	0.00	39.65	3.55
3001	3095	5.712152	AGGCCTTGTAGTGAATTTTTCTG	57.288	39.130	0.00	0.00	0.00	3.02
3056	3150	1.195674	GCACTTCGGCTCTGACTTTTC	59.804	52.381	0.00	0.00	0.00	2.29
3079	3173	3.643763	ACAACTGAAGTCGTCATCAGAC	58.356	45.455	19.11	0.00	44.64	3.51
3140	3234	1.269883	ACGGTCACTGTAATTGCGTCA	60.270	47.619	0.00	0.00	0.00	4.35
3258	3352	1.578583	GTACACGCAGTTTGACCACT	58.421	50.000	0.00	0.00	41.61	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
109	110	0.951040	GAACCTAGCACTGCAAGCGT	60.951	55.000	3.30	0.00	37.60	5.07
144	145	4.082787	AGTTTGCAAACCTACATCATTCGG	60.083	41.667	33.09	0.00	39.71	4.30
225	227	2.159043	GCAGCTAGTGGATGTGCTCTTA	60.159	50.000	0.00	0.00	33.03	2.10
227	229	0.177604	GCAGCTAGTGGATGTGCTCT	59.822	55.000	0.00	0.00	33.03	4.09
228	230	0.107993	TGCAGCTAGTGGATGTGCTC	60.108	55.000	0.00	0.00	35.11	4.26
229	231	0.325933	TTGCAGCTAGTGGATGTGCT	59.674	50.000	0.00	0.00	35.11	4.40
230	232	0.731417	CTTGCAGCTAGTGGATGTGC	59.269	55.000	0.00	0.00	33.29	4.57
231	233	2.105006	ACTTGCAGCTAGTGGATGTG	57.895	50.000	8.86	0.00	34.13	3.21
232	234	2.867109	AACTTGCAGCTAGTGGATGT	57.133	45.000	10.46	0.00	36.57	3.06
240	242	1.731709	CACGCATGTAACTTGCAGCTA	59.268	47.619	7.79	0.00	40.14	3.32
310	312	7.721399	ACTCACAAAATGAAATAAGGTCAGTCT	59.279	33.333	0.00	0.00	36.69	3.24
333	335	3.375610	TCACTTCAGCTATCAGTCGACTC	59.624	47.826	16.96	3.84	0.00	3.36
357	359	0.881118	GCGAATGTGGTGTGAACCAT	59.119	50.000	0.11	0.00	42.41	3.55
382	384	0.181587	TCGTGGTTGGTGTGATTGGT	59.818	50.000	0.00	0.00	0.00	3.67
494	496	7.122799	GGCCCTATAGTGAATTTTTCTCTTTGT	59.877	37.037	0.00	0.00	35.37	2.83
550	552	4.554960	TCGGGTATTTGTAACCACATGA	57.445	40.909	0.00	0.00	38.87	3.07
552	554	6.885376	TGTATTTCGGGTATTTGTAACCACAT	59.115	34.615	0.00	0.00	38.87	3.21
753	756	1.074471	GGCAGTGGGGGAGGAGATA	60.074	63.158	0.00	0.00	0.00	1.98
849	855	2.535317	AGCCACCCCATGTTCCCT	60.535	61.111	0.00	0.00	0.00	4.20
866	872	1.906105	GAAGGTATCGCCCACCACCA	61.906	60.000	3.27	0.00	38.62	4.17
923	929	1.419143	CTCTCGCGCAAGAAGCTTG	59.581	57.895	2.10	2.91	42.61	4.01
924	930	1.739562	CCTCTCGCGCAAGAAGCTT	60.740	57.895	8.75	0.00	42.61	3.74
981	987	1.367840	GAACACTGTCGTCTGCCCT	59.632	57.895	0.00	0.00	0.00	5.19
986	992	2.354103	CCCATCATGAACACTGTCGTCT	60.354	50.000	0.00	0.00	0.00	4.18
1260	1272	1.078918	CATGAACTGCGAGGCCTCA	60.079	57.895	31.67	13.79	0.00	3.86
1290	1302	1.026182	GGCTGACGATCATGTTGGCA	61.026	55.000	0.00	0.00	0.00	4.92
1346	1358	3.054361	GGAGGAGATGGCCTTGAAGTTTA	60.054	47.826	3.32	0.00	38.73	2.01
1428	1443	2.491152	GCGTACATCCGGTTCCGA	59.509	61.111	13.08	0.00	0.00	4.55
1655	1676	1.587054	CCGAGGAACTTGACGAGCT	59.413	57.895	0.00	0.00	44.22	4.09
2346	2394	2.039787	TGGCGAGGATGGGGTACA	59.960	61.111	0.00	0.00	0.00	2.90
2471	2533	4.623932	ATAGCCTGAAAATATCGCTCCA	57.376	40.909	0.00	0.00	0.00	3.86
2546	2613	1.686355	TCTTGCCCGTTTGACATTGT	58.314	45.000	0.00	0.00	0.00	2.71
2559	2626	1.960689	TGCCAAGTAAAGGTTCTTGCC	59.039	47.619	0.00	0.00	39.47	4.52
2780	2873	0.378257	GAATACACATGCACGCAGGG	59.622	55.000	8.69	0.41	31.33	4.45
2908	3002	5.587289	GAAATACAGTCACCAAACTTGCAA	58.413	37.500	0.00	0.00	0.00	4.08
2947	3041	1.282382	GGTGCCCACTTTAGTCCCTA	58.718	55.000	0.00	0.00	0.00	3.53
3001	3095	6.738200	CACGTGTGACATATCATTTGAGAAAC	59.262	38.462	7.58	0.00	37.14	2.78
3056	3150	4.854291	GTCTGATGACGACTTCAGTTGTAG	59.146	45.833	22.90	5.34	42.42	2.74
3097	3191	9.550406	CCGTGGGTGTATTTATCTCTTTTATTA	57.450	33.333	0.00	0.00	0.00	0.98
3140	3234	2.365582	GGGTGACCGTATCATGCTTTT	58.634	47.619	0.00	0.00	43.64	2.27
3258	3352	1.890041	CCCAACGAGCGGTCAACAA	60.890	57.895	15.89	0.00	0.00	2.83
3300	3394	1.904287	TTGCTTATTTCCACAGCCGT	58.096	45.000	0.00	0.00	32.11	5.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.