AutoCloner

Multiple sequence alignment - TraesCS1B01G060800

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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	TraesCS1B01G060800	chr1B	100.000	3574	0	0	1	3574	44798607	44802180	0.000000e+00	6601.0
1	TraesCS1B01G060800	chr1B	92.258	775	44	12	2648	3415	44601527	44602292	0.000000e+00	1085.0
2	TraesCS1B01G060800	chr1B	92.000	125	7	3	3446	3567	44609293	44609417	4.740000e-39	172.0
3	TraesCS1B01G060800	chr2D	91.599	2202	129	18	343	2507	19554985	19557167	0.000000e+00	2990.0
4	TraesCS1B01G060800	chr2D	85.090	1442	145	37	1080	2471	10220610	10219189	0.000000e+00	1408.0
5	TraesCS1B01G060800	chr2D	93.004	243	14	2	1	240	19554566	19554808	5.680000e-93	351.0
6	TraesCS1B01G060800	chr2D	81.844	347	36	14	2271	2593	19520588	19520931	2.120000e-67	267.0
7	TraesCS1B01G060800	chr2D	95.238	42	2	0	2542	2583	19557263	19557304	2.300000e-07	67.6
8	TraesCS1B01G060800	chr3D	90.437	2196	117	32	346	2507	589673932	589671796	0.000000e+00	2806.0
9	TraesCS1B01G060800	chr3D	91.393	244	17	2	1	240	589674355	589674112	7.400000e-87	331.0
10	TraesCS1B01G060800	chr3D	95.238	42	2	0	2542	2583	589671700	589671659	2.300000e-07	67.6
11	TraesCS1B01G060800	chrUn	93.475	1548	71	13	1724	3243	3510691	3509146	0.000000e+00	2272.0
12	TraesCS1B01G060800	chrUn	91.968	1133	61	11	2139	3243	366506591	366505461	0.000000e+00	1561.0
13	TraesCS1B01G060800	chrUn	96.316	923	28	4	298	1219	3514236	3513319	0.000000e+00	1511.0
14	TraesCS1B01G060800	chrUn	96.208	923	29	4	298	1219	324102936	324102019	0.000000e+00	1506.0
15	TraesCS1B01G060800	chrUn	84.674	1442	154	35	1075	2468	12288510	12287088	0.000000e+00	1376.0
16	TraesCS1B01G060800	chrUn	97.399	692	18	0	2752	3443	400709731	400709040	0.000000e+00	1179.0
17	TraesCS1B01G060800	chrUn	97.888	663	9	3	557	1219	244467129	244466472	0.000000e+00	1142.0
18	TraesCS1B01G060800	chrUn	97.930	483	10	0	1217	1699	3511169	3510687	0.000000e+00	837.0
19	TraesCS1B01G060800	chrUn	100.000	327	0	0	1	327	320429415	320429741	3.950000e-169	604.0
20	TraesCS1B01G060800	chrUn	100.000	327	0	0	1	327	320432771	320433097	3.950000e-169	604.0
21	TraesCS1B01G060800	chrUn	100.000	327	0	0	1	327	351823721	351824047	3.950000e-169	604.0
22	TraesCS1B01G060800	chrUn	100.000	327	0	0	1	327	412405038	412405364	3.950000e-169	604.0
23	TraesCS1B01G060800	chrUn	76.428	963	188	26	1174	2130	359563179	359564108	5.360000e-133	484.0
24	TraesCS1B01G060800	chrUn	92.923	325	18	4	3249	3570	3505658	3505336	5.400000e-128	468.0
25	TraesCS1B01G060800	chrUn	92.923	325	18	4	3249	3570	244455963	244455641	5.400000e-128	468.0
26	TraesCS1B01G060800	chrUn	95.417	240	11	0	1	240	3514592	3514353	2.010000e-102	383.0
27	TraesCS1B01G060800	chrUn	95.000	240	12	0	1	240	324103292	324103053	9.370000e-101	377.0
28	TraesCS1B01G060800	chrUn	87.500	144	15	2	3430	3570	400709026	400708883	2.860000e-36	163.0
29	TraesCS1B01G060800	chr2A	80.995	1547	223	38	934	2438	10486962	10485445	0.000000e+00	1162.0
30	TraesCS1B01G060800	chr2B	81.487	1372	203	33	1096	2437	4493310	4494660	0.000000e+00	1079.0
31	TraesCS1B01G060800	chr2B	76.428	963	188	26	1174	2130	3839218	3840147	5.360000e-133	484.0
32	TraesCS1B01G060800	chr2B	87.817	197	18	5	1971	2164	38731794	38731601	3.590000e-55	226.0
33	TraesCS1B01G060800	chr1A	88.739	222	25	0	3222	3443	29106655	29106876	4.550000e-69	272.0

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	TraesCS1B01G060800	chr1B	44798607	44802180	3573	False	6601.0	6601	100.000000	1	3574	1	chr1B.!!$F3	3573
1	TraesCS1B01G060800	chr1B	44601527	44602292	765	False	1085.0	1085	92.258000	2648	3415	1	chr1B.!!$F1	767
2	TraesCS1B01G060800	chr2D	10219189	10220610	1421	True	1408.0	1408	85.090000	1080	2471	1	chr2D.!!$R1	1391
3	TraesCS1B01G060800	chr2D	19554566	19557304	2738	False	1136.2	2990	93.280333	1	2583	3	chr2D.!!$F2	2582
4	TraesCS1B01G060800	chr3D	589671659	589674355	2696	True	1068.2	2806	92.356000	1	2583	3	chr3D.!!$R1	2582
5	TraesCS1B01G060800	chrUn	366505461	366506591	1130	True	1561.0	1561	91.968000	2139	3243	1	chrUn.!!$R4	1104
6	TraesCS1B01G060800	chrUn	12287088	12288510	1422	True	1376.0	1376	84.674000	1075	2468	1	chrUn.!!$R1	1393
7	TraesCS1B01G060800	chrUn	244466472	244467129	657	True	1142.0	1142	97.888000	557	1219	1	chrUn.!!$R3	662
8	TraesCS1B01G060800	chrUn	3505336	3514592	9256	True	1094.2	2272	95.212200	1	3570	5	chrUn.!!$R5	3569
9	TraesCS1B01G060800	chrUn	324102019	324103292	1273	True	941.5	1506	95.604000	1	1219	2	chrUn.!!$R6	1218
10	TraesCS1B01G060800	chrUn	400708883	400709731	848	True	671.0	1179	92.449500	2752	3570	2	chrUn.!!$R7	818
11	TraesCS1B01G060800	chrUn	320429415	320433097	3682	False	604.0	604	100.000000	1	327	2	chrUn.!!$F4	326
12	TraesCS1B01G060800	chrUn	359563179	359564108	929	False	484.0	484	76.428000	1174	2130	1	chrUn.!!$F2	956
13	TraesCS1B01G060800	chr2A	10485445	10486962	1517	True	1162.0	1162	80.995000	934	2438	1	chr2A.!!$R1	1504
14	TraesCS1B01G060800	chr2B	4493310	4494660	1350	False	1079.0	1079	81.487000	1096	2437	1	chr2B.!!$F2	1341
15	TraesCS1B01G060800	chr2B	3839218	3840147	929	False	484.0	484	76.428000	1174	2130	1	chr2B.!!$F1	956

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
327	424	1.135402	CGTGGAGCAGGTTTTAATGCC	60.135	52.381	0.00	0.0	43.6	4.40	F
1002	2540	0.107459	GGAGCAGCTTAAGTCCCAGG	60.107	60.000	4.02	0.0	0.0	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2146	6726	1.274770	CATGCATGCAGCTCGTACG	59.725	57.895	26.69	9.53	45.94	3.67	R
2700	7414	2.180946	ATGTGTGGATGCTCCTAGGA	57.819	50.000	11.98	11.98	37.46	2.94	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
327	424	1.135402	CGTGGAGCAGGTTTTAATGCC	60.135	52.381	0.00	0.00	43.60	4.40
912	2446	8.283291	ACTTGAGTTTATTCAAATTCAGTCGTC	58.717	33.333	0.00	0.00	40.27	4.20
913	2447	6.817396	TGAGTTTATTCAAATTCAGTCGTCG	58.183	36.000	0.00	0.00	35.98	5.12
914	2448	6.422701	TGAGTTTATTCAAATTCAGTCGTCGT	59.577	34.615	0.00	0.00	35.98	4.34
1002	2540	0.107459	GGAGCAGCTTAAGTCCCAGG	60.107	60.000	4.02	0.00	0.00	4.45
2004	6584	2.380084	TGATGAGAAGGCGGTAACAC	57.620	50.000	0.00	0.00	0.00	3.32
2345	6991	3.287222	GTTATCTTTGGGCCATGCTGTA	58.713	45.455	7.26	0.00	0.00	2.74
2346	6992	2.062971	ATCTTTGGGCCATGCTGTAG	57.937	50.000	7.26	0.00	0.00	2.74
2365	7014	3.237268	AGGGCATAACAAGACCAACAA	57.763	42.857	0.00	0.00	36.27	2.83
2583	7295	7.412891	GCTTTGGGTCAAATAAATGTATGTTGC	60.413	37.037	0.00	0.00	32.70	4.17
2584	7296	5.971763	TGGGTCAAATAAATGTATGTTGCC	58.028	37.500	0.00	0.00	0.00	4.52
2638	7352	5.121380	AGCATGGGATGTATGTTCTTCTT	57.879	39.130	0.00	0.00	0.00	2.52
2700	7414	3.983044	AGATGGTAGCGGAAAAAGAGT	57.017	42.857	0.00	0.00	0.00	3.24
2707	7421	2.537143	AGCGGAAAAAGAGTCCTAGGA	58.463	47.619	7.62	7.62	32.53	2.94
3213	7950	2.202932	CTGGCTCCATCGAACCGG	60.203	66.667	0.00	0.00	0.00	5.28
3216	7953	4.814294	GCTCCATCGAACCGGCGT	62.814	66.667	6.01	0.00	0.00	5.68
3301	11521	0.179089	CGATCTCTTCACCAGCCTGG	60.179	60.000	9.83	9.83	45.02	4.45
3389	11609	2.324860	GTTTGGCTCCATTTAACGTGC	58.675	47.619	0.00	0.00	0.00	5.34
3396	11616	2.679837	CTCCATTTAACGTGCTCAGCAT	59.320	45.455	0.54	0.00	41.91	3.79
3406	11626	0.608130	TGCTCAGCATCGTACAACCT	59.392	50.000	0.00	0.00	31.71	3.50
3408	11628	2.159240	TGCTCAGCATCGTACAACCTAG	60.159	50.000	0.00	0.00	31.71	3.02
3409	11629	2.799917	GCTCAGCATCGTACAACCTAGG	60.800	54.545	7.41	7.41	0.00	3.02
3416	11638	4.463186	GCATCGTACAACCTAGGGAGATAT	59.537	45.833	14.81	0.00	0.00	1.63
3525	11774	6.289834	CAGCTAGAACTGATTCATGGATCTT	58.710	40.000	15.17	1.90	40.25	2.40
3526	11775	6.424509	CAGCTAGAACTGATTCATGGATCTTC	59.575	42.308	15.17	10.96	40.25	2.87
3567	11819	6.853720	TGAATCTGACAGTTAGTGTACTAGC	58.146	40.000	1.59	0.00	40.56	3.42
3570	11822	7.795482	ATCTGACAGTTAGTGTACTAGCTAG	57.205	40.000	19.44	19.44	40.56	3.42
3571	11823	6.709281	TCTGACAGTTAGTGTACTAGCTAGT	58.291	40.000	28.50	28.50	40.56	2.57
3572	11824	7.166851	TCTGACAGTTAGTGTACTAGCTAGTT	58.833	38.462	30.40	15.59	40.56	2.24
3573	11825	8.316946	TCTGACAGTTAGTGTACTAGCTAGTTA	58.683	37.037	30.40	17.47	40.56	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
344	457	1.866925	GCCGCAGTAACCACAAGAC	59.133	57.895	0.00	0.00	0.00	3.01
470	583	2.631012	ATTTGGGAGATGAGGCGGCC	62.631	60.000	12.11	12.11	0.00	6.13
472	585	2.638480	TTATTTGGGAGATGAGGCGG	57.362	50.000	0.00	0.00	0.00	6.13
633	1481	3.801594	GCCACACCCATTAAAAATATGCG	59.198	43.478	0.00	0.00	0.00	4.73
642	1490	6.508030	TTGAGATATAGCCACACCCATTAA	57.492	37.500	0.00	0.00	0.00	1.40
721	1579	8.440833	ACGAAGATCCGTGTAGAAAAATAAAAG	58.559	33.333	0.00	0.00	41.70	2.27
912	2446	5.466819	TGTATGAACAACTACTCAGGAACG	58.533	41.667	0.00	0.00	30.91	3.95
913	2447	8.033038	TGTATGTATGAACAACTACTCAGGAAC	58.967	37.037	0.00	0.00	39.58	3.62
914	2448	8.129496	TGTATGTATGAACAACTACTCAGGAA	57.871	34.615	0.00	0.00	39.58	3.36
1002	2540	1.128692	GTATTCTCTGCGTTGTGGTGC	59.871	52.381	0.00	0.00	0.00	5.01
2004	6584	3.775654	GCCCTCCGACTCCACCAG	61.776	72.222	0.00	0.00	0.00	4.00
2146	6726	1.274770	CATGCATGCAGCTCGTACG	59.725	57.895	26.69	9.53	45.94	3.67
2345	6991	2.969821	TGTTGGTCTTGTTATGCCCT	57.030	45.000	0.00	0.00	0.00	5.19
2346	6992	3.153919	TCTTGTTGGTCTTGTTATGCCC	58.846	45.455	0.00	0.00	0.00	5.36
2365	7014	8.891985	TGTAGCTGATAATATGGAGAATCTCT	57.108	34.615	10.38	0.00	33.73	3.10
2442	7091	4.758688	TGCATGTAGAGTTGTAGACCATG	58.241	43.478	0.00	0.00	31.39	3.66
2609	7321	4.858850	ACATACATCCCATGCTCAAAAGA	58.141	39.130	0.00	0.00	0.00	2.52
2610	7322	5.359009	AGAACATACATCCCATGCTCAAAAG	59.641	40.000	0.00	0.00	0.00	2.27
2638	7352	7.051696	AGGGAGGGAAATGGTTTTATAAGAA	57.948	36.000	0.00	0.00	0.00	2.52
2700	7414	2.180946	ATGTGTGGATGCTCCTAGGA	57.819	50.000	11.98	11.98	37.46	2.94
2707	7421	6.334989	CACATAAAATGAATGTGTGGATGCT	58.665	36.000	7.81	0.00	45.91	3.79
3213	7950	2.886124	GCTAAGGGACGAGCACGC	60.886	66.667	2.62	0.00	43.96	5.34
3216	7953	0.612174	AGTGAGCTAAGGGACGAGCA	60.612	55.000	0.00	0.00	43.15	4.26
3301	11521	3.065371	CCCTTGCCACGATTAGATTGAAC	59.935	47.826	0.00	0.00	0.00	3.18
3303	11523	2.421388	CCCCTTGCCACGATTAGATTGA	60.421	50.000	0.00	0.00	0.00	2.57
3389	11609	2.223829	CCCTAGGTTGTACGATGCTGAG	60.224	54.545	8.29	0.00	0.00	3.35
3396	11616	5.698104	TCAATATCTCCCTAGGTTGTACGA	58.302	41.667	8.29	0.00	0.00	3.43
3406	11626	9.672673	CTTTCAGTTTTTCTCAATATCTCCCTA	57.327	33.333	0.00	0.00	0.00	3.53
3408	11628	7.254137	GCTTTCAGTTTTTCTCAATATCTCCC	58.746	38.462	0.00	0.00	0.00	4.30
3409	11629	6.963805	CGCTTTCAGTTTTTCTCAATATCTCC	59.036	38.462	0.00	0.00	0.00	3.71
3416	11638	2.425312	TGCCGCTTTCAGTTTTTCTCAA	59.575	40.909	0.00	0.00	0.00	3.02
3533	11785	1.059913	GTCAGATTCATCCCCCGGAT	58.940	55.000	0.73	0.00	44.21	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.