AutoCloner

Multiple sequence alignment - TraesCS3B01G363600

Loading Multiple Alignment...

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	TraesCS3B01G363600	chr3B	100.000	2405	0	0	1	2405	575448925	575446521	0.000000e+00	4442.0
1	TraesCS3B01G363600	chr5B	93.939	1254	59	8	1168	2405	16283939	16285191	0.000000e+00	1879.0
2	TraesCS3B01G363600	chr1B	93.871	930	48	5	1483	2405	286759173	286760100	0.000000e+00	1393.0
3	TraesCS3B01G363600	chr1B	90.549	984	76	8	859	1830	38110864	38111842	0.000000e+00	1286.0
4	TraesCS3B01G363600	chr1B	92.061	781	48	6	681	1451	286758402	286759178	0.000000e+00	1086.0
5	TraesCS3B01G363600	chr1B	95.331	514	22	2	1894	2405	38111954	38112467	0.000000e+00	815.0
6	TraesCS3B01G363600	chr1B	95.122	123	6	0	680	802	38110732	38110854	6.780000e-46	195.0
7	TraesCS3B01G363600	chr1B	85.256	156	19	3	1958	2111	661148030	661148183	8.900000e-35	158.0
8	TraesCS3B01G363600	chr1B	85.714	91	13	0	1264	1354	661137071	661137161	1.970000e-16	97.1
9	TraesCS3B01G363600	chr1D	95.876	679	27	1	3	681	409609827	409609150	0.000000e+00	1098.0
10	TraesCS3B01G363600	chr1D	95.294	680	28	2	3	681	96986993	96986317	0.000000e+00	1075.0
11	TraesCS3B01G363600	chr1D	82.390	318	39	5	2010	2325	475249464	475249766	6.590000e-66	261.0
12	TraesCS3B01G363600	chr1D	89.116	147	11	4	2168	2309	318391136	318391282	6.830000e-41	178.0
13	TraesCS3B01G363600	chr1D	85.714	91	13	0	1264	1354	475239258	475239348	1.970000e-16	97.1
14	TraesCS3B01G363600	chr7D	95.723	678	27	2	3	678	310912338	310913015	0.000000e+00	1090.0
15	TraesCS3B01G363600	chr7D	95.322	684	27	3	3	681	134279777	134279094	0.000000e+00	1081.0
16	TraesCS3B01G363600	chr7D	76.471	187	41	3	679	865	159085470	159085287	5.470000e-17	99.0
17	TraesCS3B01G363600	chr7D	88.000	75	9	0	681	755	159083369	159083295	3.290000e-14	89.8
18	TraesCS3B01G363600	chr7D	93.478	46	3	0	688	733	582058459	582058504	4.290000e-08	69.4
19	TraesCS3B01G363600	chr3D	95.441	680	27	2	3	681	178476468	178475792	0.000000e+00	1081.0
20	TraesCS3B01G363600	chr3D	95.294	680	28	2	3	681	518395818	518395142	0.000000e+00	1075.0
21	TraesCS3B01G363600	chrUn	95.315	683	26	3	1	681	20068932	20068254	0.000000e+00	1079.0
22	TraesCS3B01G363600	chr5D	95.441	680	26	2	3	681	505291259	505290584	0.000000e+00	1079.0
23	TraesCS3B01G363600	chr6D	95.294	680	28	3	3	681	369888439	369887763	0.000000e+00	1075.0
24	TraesCS3B01G363600	chr4B	89.853	749	69	4	1663	2405	120577255	120578002	0.000000e+00	955.0
25	TraesCS3B01G363600	chr4B	85.524	677	71	14	680	1349	120511566	120512222	0.000000e+00	682.0
26	TraesCS3B01G363600	chr4B	86.232	138	11	1	1504	1641	120577144	120577273	2.490000e-30	143.0
27	TraesCS3B01G363600	chr6A	85.589	569	74	7	1782	2345	147978714	147978149	7.410000e-165	590.0
28	TraesCS3B01G363600	chr7B	81.270	630	75	24	1721	2342	611603965	611604559	1.010000e-128	470.0
29	TraesCS3B01G363600	chr4A	89.385	179	18	1	2168	2345	607632595	607632417	8.650000e-55	224.0
30	TraesCS3B01G363600	chr7A	88.742	151	11	5	2165	2309	46133235	46133385	1.900000e-41	180.0

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	TraesCS3B01G363600	chr3B	575446521	575448925	2404	True	4442.000000	4442	100.000000	1	2405	1	chr3B.!!$R1	2404
1	TraesCS3B01G363600	chr5B	16283939	16285191	1252	False	1879.000000	1879	93.939000	1168	2405	1	chr5B.!!$F1	1237
2	TraesCS3B01G363600	chr1B	286758402	286760100	1698	False	1239.500000	1393	92.966000	681	2405	2	chr1B.!!$F4	1724
3	TraesCS3B01G363600	chr1B	38110732	38112467	1735	False	765.333333	1286	93.667333	680	2405	3	chr1B.!!$F3	1725
4	TraesCS3B01G363600	chr1D	409609150	409609827	677	True	1098.000000	1098	95.876000	3	681	1	chr1D.!!$R2	678
5	TraesCS3B01G363600	chr1D	96986317	96986993	676	True	1075.000000	1075	95.294000	3	681	1	chr1D.!!$R1	678
6	TraesCS3B01G363600	chr7D	310912338	310913015	677	False	1090.000000	1090	95.723000	3	678	1	chr7D.!!$F1	675
7	TraesCS3B01G363600	chr7D	134279094	134279777	683	True	1081.000000	1081	95.322000	3	681	1	chr7D.!!$R1	678
8	TraesCS3B01G363600	chr3D	178475792	178476468	676	True	1081.000000	1081	95.441000	3	681	1	chr3D.!!$R1	678
9	TraesCS3B01G363600	chr3D	518395142	518395818	676	True	1075.000000	1075	95.294000	3	681	1	chr3D.!!$R2	678
10	TraesCS3B01G363600	chrUn	20068254	20068932	678	True	1079.000000	1079	95.315000	1	681	1	chrUn.!!$R1	680
11	TraesCS3B01G363600	chr5D	505290584	505291259	675	True	1079.000000	1079	95.441000	3	681	1	chr5D.!!$R1	678
12	TraesCS3B01G363600	chr6D	369887763	369888439	676	True	1075.000000	1075	95.294000	3	681	1	chr6D.!!$R1	678
13	TraesCS3B01G363600	chr4B	120511566	120512222	656	False	682.000000	682	85.524000	680	1349	1	chr4B.!!$F1	669
14	TraesCS3B01G363600	chr4B	120577144	120578002	858	False	549.000000	955	88.042500	1504	2405	2	chr4B.!!$F2	901
15	TraesCS3B01G363600	chr6A	147978149	147978714	565	True	590.000000	590	85.589000	1782	2345	1	chr6A.!!$R1	563
16	TraesCS3B01G363600	chr7B	611603965	611604559	594	False	470.000000	470	81.270000	1721	2342	1	chr7B.!!$F1	621

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
748	760	0.396811	GCCTCGGCTACCCATAACAT	59.603	55.0	0.0	0.0	38.26	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1771	1805	1.311859	CAAGTGAGCAGCCAGTTCAA	58.688	50.0	0.0	0.0	39.28	2.69	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
94	96	7.606839	AGTTAGAGCTAGTTTGGGTTGAAATAC	59.393	37.037	0.00	0.00	0.00	1.89
199	202	8.050930	GGTTCTAATTGGGTTAGTTATCCTTGA	58.949	37.037	0.00	0.00	40.58	3.02
416	428	2.028876	CACCGGTTGTTTTTCTCCCTT	58.971	47.619	2.97	0.00	0.00	3.95
430	442	3.276091	CCTTTGTCGTGCGTGGCA	61.276	61.111	0.00	0.00	35.60	4.92
432	444	2.202946	TTTGTCGTGCGTGGCAGA	60.203	55.556	0.00	0.00	40.08	4.26
495	507	1.887198	GTTCCTTCTCTGTCTCACGGA	59.113	52.381	0.00	0.00	31.67	4.69
514	526	3.496130	CGGACATATCATTGGTCTTGCTC	59.504	47.826	0.00	0.00	0.00	4.26
540	552	6.128688	GCTCTAGCGCTAATTCTAATTTGGAG	60.129	42.308	19.37	16.24	0.00	3.86
645	657	5.441718	TTCTAGATGCCCAAAGATTCAGT	57.558	39.130	0.00	0.00	0.00	3.41
673	685	6.055588	CCTTTCTAGGTGTTTCAGTTTCAGA	58.944	40.000	0.00	0.00	36.74	3.27
678	690	4.589908	AGGTGTTTCAGTTTCAGACTTGT	58.410	39.130	0.00	0.00	36.10	3.16
748	760	0.396811	GCCTCGGCTACCCATAACAT	59.603	55.000	0.00	0.00	38.26	2.71
762	774	9.667107	CTACCCATAACATCACGGATTAATAAT	57.333	33.333	0.00	0.00	0.00	1.28
774	786	6.590292	CACGGATTAATAATAGCCTCACGATT	59.410	38.462	0.00	0.00	0.00	3.34
822	834	8.695456	ACCATTAAAATTATGCTAACCCTCAAG	58.305	33.333	0.00	0.00	0.00	3.02
830	842	2.373836	TGCTAACCCTCAAGCCAAACTA	59.626	45.455	0.00	0.00	37.97	2.24
832	844	3.809324	GCTAACCCTCAAGCCAAACTACA	60.809	47.826	0.00	0.00	32.40	2.74
865	877	2.092882	CGGGCGGACGAAAACTCTC	61.093	63.158	0.00	0.00	35.47	3.20
1044	1066	1.830145	CTTCCAATCCGTCCCCGAT	59.170	57.895	0.00	0.00	35.63	4.18
1063	1085	1.410004	TATCGGCGAGGAGATTGGTT	58.590	50.000	17.22	0.00	0.00	3.67
1142	1164	3.447742	CATCAAGTCGAATGACCGATCA	58.552	45.455	4.44	0.00	46.74	2.92
1172	1194	4.031129	CTGGACTGCAGCCTGGCT	62.031	66.667	17.22	17.22	40.77	4.75
1239	1261	2.202703	GCACGCGGTTACGAGGAT	60.203	61.111	12.47	0.00	44.51	3.24
1319	1343	3.918253	ATGCCGCCGTTGTGGTCAT	62.918	57.895	0.00	0.00	44.42	3.06
1379	1403	2.235016	CGCACCGTGACGTCAAACT	61.235	57.895	21.95	1.70	0.00	2.66
1385	1409	0.852777	CGTGACGTCAAACTGGACAG	59.147	55.000	21.95	0.00	37.66	3.51
1386	1410	0.582005	GTGACGTCAAACTGGACAGC	59.418	55.000	21.95	0.00	37.66	4.40
1455	1482	4.524328	CAGCTCAGTAAAATTTTGGGTCCT	59.476	41.667	13.76	0.71	0.00	3.85
1491	1518	4.278513	CCCGGGGTTTGTGGAGCA	62.279	66.667	14.71	0.00	0.00	4.26
1510	1537	1.067582	CCGGCGTGGTCCTAGATTC	59.932	63.158	6.01	0.00	0.00	2.52
1536	1563	1.130777	TCATGGGATTGGATCGAGCA	58.869	50.000	1.84	0.00	0.00	4.26
1550	1577	1.151777	CGAGCAACCACACGAGTTGT	61.152	55.000	5.62	0.00	45.14	3.32
1603	1630	1.133025	GTGGAATCCAATCACCGCAAG	59.867	52.381	2.31	0.00	34.18	4.01
1667	1694	8.541234	AGAAAGGTAATCTCTTTCCTTAATCGT	58.459	33.333	11.48	0.00	46.65	3.73
1700	1727	0.034670	ATCCACTCCTTCCTTGCTGC	60.035	55.000	0.00	0.00	0.00	5.25
1709	1736	2.092753	CCTTCCTTGCTGCTGAATCCTA	60.093	50.000	0.00	0.00	0.00	2.94
1727	1754	2.092753	CCTACATGTTGTGCTGATCCCT	60.093	50.000	2.30	0.00	0.00	4.20
1729	1756	2.880443	ACATGTTGTGCTGATCCCTTT	58.120	42.857	0.00	0.00	0.00	3.11
1786	1822	0.535780	CCTGTTGAACTGGCTGCTCA	60.536	55.000	8.33	0.00	30.42	4.26
1804	1840	1.150827	CACTTGTTGCTCGATGCTGA	58.849	50.000	8.07	0.00	43.37	4.26
1805	1841	1.532437	CACTTGTTGCTCGATGCTGAA	59.468	47.619	8.07	0.00	43.37	3.02
1867	1984	8.770828	GCTTTGAGTTTCTGTATAGTGTTGTTA	58.229	33.333	0.00	0.00	0.00	2.41
1873	1990	7.172703	AGTTTCTGTATAGTGTTGTTACTTGCC	59.827	37.037	0.00	0.00	32.19	4.52
1911	2028	1.194772	GCTGTTGTTCACGCTAGGAAC	59.805	52.381	4.04	4.04	43.78	3.62
1946	2063	6.021672	ACATGGGATATAGCATCTCTGAGAA	58.978	40.000	12.00	0.00	0.00	2.87
1954	2071	3.027412	AGCATCTCTGAGAACGTACCAT	58.973	45.455	12.00	0.00	0.00	3.55
2256	2385	4.785346	AATGATAGGTCTCCAGCATGTT	57.215	40.909	0.00	0.00	0.00	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
94	96	6.124088	CCTCTTGTTTCGATAATTTGAGGG	57.876	41.667	10.90	0.00	36.03	4.30
164	167	8.342270	ACTAACCCAATTAGAACCTCTCTACTA	58.658	37.037	0.81	0.00	42.75	1.82
168	171	6.954352	AACTAACCCAATTAGAACCTCTCT	57.046	37.500	0.81	0.00	42.75	3.10
400	412	3.129813	ACGACAAAGGGAGAAAAACAACC	59.870	43.478	0.00	0.00	0.00	3.77
416	428	2.661537	CTCTGCCACGCACGACAA	60.662	61.111	0.00	0.00	33.79	3.18
430	442	2.136878	CCCTGGTAGATGCGCCTCT	61.137	63.158	19.26	19.26	0.00	3.69
432	444	2.041922	TCCCTGGTAGATGCGCCT	60.042	61.111	4.18	0.00	0.00	5.52
495	507	2.874701	GCGAGCAAGACCAATGATATGT	59.125	45.455	0.00	0.00	0.00	2.29
540	552	6.410540	ACCAAGTTTGATCAGGATCTACTTC	58.589	40.000	18.68	5.28	39.25	3.01
630	642	2.158475	AGGTGAACTGAATCTTTGGGCA	60.158	45.455	0.00	0.00	0.00	5.36
660	672	7.954788	AGAGATACAAGTCTGAAACTGAAAC	57.045	36.000	0.00	0.00	38.58	2.78
701	713	6.316140	GGTGCACTTAGTGATGAATATGTTCA	59.684	38.462	17.40	7.39	40.07	3.18
748	760	5.242171	TCGTGAGGCTATTATTAATCCGTGA	59.758	40.000	0.00	0.00	0.00	4.35
762	774	3.527507	AGGATCCTAATCGTGAGGCTA	57.472	47.619	14.27	0.00	33.73	3.93
830	842	3.584834	GCCCGTCAAAATTGCTAAATGT	58.415	40.909	0.00	0.00	0.00	2.71
832	844	2.416701	CCGCCCGTCAAAATTGCTAAAT	60.417	45.455	0.00	0.00	0.00	1.40
865	877	2.037772	GTGGGATATGCACTACTCTGGG	59.962	54.545	0.00	0.00	0.00	4.45
876	888	4.927782	TGCGGGCGTGGGATATGC	62.928	66.667	0.00	0.00	40.71	3.14
1044	1066	1.068588	CAACCAATCTCCTCGCCGATA	59.931	52.381	0.00	0.00	0.00	2.92
1119	1141	1.548719	TCGGTCATTCGACTTGATGGT	59.451	47.619	0.93	0.00	42.21	3.55
1207	1229	1.598130	GTGCACCTGGAAGACGCTT	60.598	57.895	5.22	0.00	34.07	4.68
1239	1261	1.746239	CATGTGCGTCCATGCCTCA	60.746	57.895	3.97	0.00	36.15	3.86
1379	1403	4.056125	CGAGGAGCACGCTGTCCA	62.056	66.667	0.00	0.00	35.02	4.02
1386	1410	3.456431	CTAGGCGTCGAGGAGCACG	62.456	68.421	9.75	0.00	39.09	5.34
1427	1451	2.200373	AATTTTACTGAGCTGGGCGT	57.800	45.000	0.00	0.00	0.00	5.68
1481	1508	4.555709	ACGCCGGTGCTCCACAAA	62.556	61.111	16.69	0.00	35.86	2.83
1510	1537	3.004002	CGATCCAATCCCATGACATGTTG	59.996	47.826	14.26	11.46	0.00	3.33
1536	1563	0.868602	CGTCGACAACTCGTGTGGTT	60.869	55.000	17.16	0.00	41.96	3.67
1700	1727	4.256110	TCAGCACAACATGTAGGATTCAG	58.744	43.478	0.00	0.00	0.00	3.02
1709	1736	2.559668	CAAAGGGATCAGCACAACATGT	59.440	45.455	0.00	0.00	0.00	3.21
1727	1754	3.215568	CAGCGCCCACCACACAAA	61.216	61.111	2.29	0.00	0.00	2.83
1771	1805	1.311859	CAAGTGAGCAGCCAGTTCAA	58.688	50.000	0.00	0.00	39.28	2.69
1805	1841	2.596631	CACCAAGCCAGCACAGCT	60.597	61.111	0.00	0.00	44.19	4.24
1839	1956	7.282224	ACAACACTATACAGAAACTCAAAGCAA	59.718	33.333	0.00	0.00	0.00	3.91
1911	2028	5.877012	GCTATATCCCATGTTGGTATGTCAG	59.123	44.000	0.00	0.00	35.17	3.51
1946	2063	6.105397	TCTTTTCAAGTCCTTATGGTACGT	57.895	37.500	0.00	0.00	34.23	3.57
1954	2071	4.042809	TCCATGGCTCTTTTCAAGTCCTTA	59.957	41.667	6.96	0.00	0.00	2.69
2245	2374	2.089980	CTCCTTTCCAACATGCTGGAG	58.910	52.381	17.04	7.56	46.20	3.86
2256	2385	5.779241	ATTCAACTCCATACTCCTTTCCA	57.221	39.130	0.00	0.00	0.00	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.