AutoCloner

Multiple sequence alignment - TraesCS6D01G285400

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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	TraesCS6D01G285400	chr6D	100.000	6026	0	0	1	6026	393651122	393657147	0.000000e+00	11129.0
1	TraesCS6D01G285400	chr6B	94.716	2971	108	19	1	2946	588831262	588834208	0.000000e+00	4571.0
2	TraesCS6D01G285400	chr6B	95.152	1980	80	10	3450	5423	588834657	588836626	0.000000e+00	3110.0
3	TraesCS6D01G285400	chr6B	92.074	757	36	9	5255	6003	588905962	588906702	0.000000e+00	1044.0
4	TraesCS6D01G285400	chr6B	93.598	328	17	3	3126	3450	588834288	588834614	2.520000e-133	486.0
5	TraesCS6D01G285400	chr6B	98.113	53	1	0	2163	2215	8403634	8403582	6.430000e-15	93.5
6	TraesCS6D01G285400	chr6A	93.384	1965	71	23	3440	5393	540045897	540047813	0.000000e+00	2854.0
7	TraesCS6D01G285400	chr6A	94.258	1428	69	8	745	2167	540042827	540044246	0.000000e+00	2170.0
8	TraesCS6D01G285400	chr6A	92.072	719	29	8	9	713	540042120	540042824	0.000000e+00	987.0
9	TraesCS6D01G285400	chr6A	91.876	677	22	9	5335	6003	540048030	540048681	0.000000e+00	915.0
10	TraesCS6D01G285400	chr6A	93.688	602	34	4	2647	3246	540044705	540045304	0.000000e+00	898.0
11	TraesCS6D01G285400	chr6A	92.043	465	34	3	2227	2690	540044245	540044707	0.000000e+00	651.0
12	TraesCS6D01G285400	chr6A	90.698	215	19	1	3236	3450	540045641	540045854	9.890000e-73	285.0
13	TraesCS6D01G285400	chr6A	90.732	205	15	3	5111	5314	540047841	540048042	2.770000e-68	270.0
14	TraesCS6D01G285400	chr1D	85.782	211	27	2	4972	5179	408251607	408251397	2.830000e-53	220.0
15	TraesCS6D01G285400	chr1D	89.928	139	12	2	5223	5360	408251388	408251251	1.730000e-40	178.0
16	TraesCS6D01G285400	chr1A	84.977	213	29	2	4970	5179	504252651	504252439	4.730000e-51	213.0
17	TraesCS6D01G285400	chr1A	94.828	58	3	0	2158	2215	558377637	558377580	2.310000e-14	91.6
18	TraesCS6D01G285400	chr1A	87.013	77	4	2	2158	2228	66895531	66895607	1.390000e-11	82.4
19	TraesCS6D01G285400	chr2A	89.928	139	12	2	5223	5360	40831948	40832085	1.730000e-40	178.0
20	TraesCS6D01G285400	chr2A	96.552	58	2	0	2158	2215	367831954	367832011	4.970000e-16	97.1
21	TraesCS6D01G285400	chr2A	100.000	52	0	0	2164	2215	478110585	478110534	4.970000e-16	97.1
22	TraesCS6D01G285400	chr5A	86.325	117	15	1	4029	4144	646004266	646004382	6.340000e-25	126.0
23	TraesCS6D01G285400	chr4A	85.246	122	7	5	4028	4138	195968437	195968558	1.370000e-21	115.0
24	TraesCS6D01G285400	chr4B	83.607	122	9	5	4028	4138	364042714	364042835	2.970000e-18	104.0
25	TraesCS6D01G285400	chr7A	96.552	58	2	0	2158	2215	721264939	721264996	4.970000e-16	97.1
26	TraesCS6D01G285400	chr5D	88.000	75	7	2	4034	4106	1328104	1328030	2.990000e-13	87.9
27	TraesCS6D01G285400	chr2B	93.443	61	1	2	2155	2215	716971376	716971433	2.990000e-13	87.9
28	TraesCS6D01G285400	chr2B	87.838	74	7	2	4034	4105	369214137	369214064	1.080000e-12	86.1
29	TraesCS6D01G285400	chr1B	92.063	63	3	2	2154	2215	529474285	529474346	2.990000e-13	87.9
30	TraesCS6D01G285400	chr3B	87.838	74	7	2	4034	4105	638815361	638815434	1.080000e-12	86.1
31	TraesCS6D01G285400	chr3B	84.337	83	11	2	4034	4114	379021718	379021636	5.010000e-11	80.5

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	TraesCS6D01G285400	chr6D	393651122	393657147	6025	False	11129.000000	11129	100.000000	1	6026	1	chr6D.!!$F1	6025
1	TraesCS6D01G285400	chr6B	588831262	588836626	5364	False	2722.333333	4571	94.488667	1	5423	3	chr6B.!!$F2	5422
2	TraesCS6D01G285400	chr6B	588905962	588906702	740	False	1044.000000	1044	92.074000	5255	6003	1	chr6B.!!$F1	748
3	TraesCS6D01G285400	chr6A	540042120	540048681	6561	False	1128.750000	2854	92.343875	9	6003	8	chr6A.!!$F1	5994

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
93	95	0.453793	ATCTTCTCTCCACACTCGCG	59.546	55.000	0.00	0.0	0.00	5.87	F
1209	1242	0.167470	CCAACGATGCAAGCACTCAG	59.833	55.000	0.00	0.0	0.00	3.35	F
1218	1251	1.065564	GCAAGCACTCAGAAGGGAGAT	60.066	52.381	0.00	0.0	38.30	2.75	F
1383	1416	1.145738	ACTGTGCCAGAAAATGAGGGT	59.854	47.619	8.91	0.0	35.18	4.34	F
2726	2807	1.341531	GTGGGGTGTGAGATCCTATCG	59.658	57.143	0.00	0.0	0.00	2.92	F
3465	3950	0.034896	AACTGGTTCTGGCACTACCG	59.965	55.000	8.32	6.3	43.94	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1218	1251	0.610174	GATCAGTGCCACTGGACTCA	59.390	55.000	23.85	5.32	45.94	3.41	R
2894	2976	1.012486	GTCCGGTTTGTGTCTAGGCG	61.012	60.000	0.00	0.00	0.00	5.52	R
3038	3120	2.958355	CCAGGTTGACAAACAGGACATT	59.042	45.455	8.97	0.00	38.10	2.71	R
3365	3795	1.340795	ACCTACCTACACTCCTGGACG	60.341	57.143	0.00	0.00	0.00	4.79	R
3953	4444	0.321298	ACTGAAGCACCGCCGTATTT	60.321	50.000	0.00	0.00	0.00	1.40	R
5349	6125	0.034670	AGAAGCTGGCTCATGGGAAC	60.035	55.000	0.00	0.00	0.00	3.62	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
56	57	1.521010	CGCACTCTCAGCCCTCATG	60.521	63.158	0.00	0.00	0.00	3.07
93	95	0.453793	ATCTTCTCTCCACACTCGCG	59.546	55.000	0.00	0.00	0.00	5.87
94	96	0.605589	TCTTCTCTCCACACTCGCGA	60.606	55.000	9.26	9.26	0.00	5.87
231	233	1.361204	ACTCCCACATCACCACATCA	58.639	50.000	0.00	0.00	0.00	3.07
284	288	9.620660	CCCCATTTATATTAATAAAACGAGCAC	57.379	33.333	0.00	0.00	40.16	4.40
331	335	3.884318	TGGTGTAGTGCTGCCAGA	58.116	55.556	0.00	0.00	0.00	3.86
431	445	1.487231	CGCGAGATAAAATCCGCCG	59.513	57.895	0.00	0.00	42.16	6.46
432	446	1.860078	GCGAGATAAAATCCGCCGG	59.140	57.895	0.00	0.00	40.56	6.13
433	447	0.599204	GCGAGATAAAATCCGCCGGA	60.599	55.000	8.97	8.97	40.56	5.14
435	449	1.509703	GAGATAAAATCCGCCGGACC	58.490	55.000	8.62	0.00	32.98	4.46
454	470	2.513897	CCGCGATTTCCCCCACTC	60.514	66.667	8.23	0.00	0.00	3.51
660	689	6.030228	CCGTTGATAGATTTTTCCAGCTTTC	58.970	40.000	0.00	0.00	0.00	2.62
720	749	7.063898	GGATATTTCTTCTTTTGCTTTCTTGGC	59.936	37.037	0.00	0.00	0.00	4.52
724	753	1.277495	CTTTTGCTTTCTTGGCCGCG	61.277	55.000	0.00	0.00	0.00	6.46
909	939	2.079925	GTTTGGGATGCTCTGTGTCTC	58.920	52.381	0.00	0.00	0.00	3.36
1137	1170	3.167485	TCTGAATTCCTTGCCTGCAATT	58.833	40.909	4.84	0.00	35.20	2.32
1171	1204	1.609061	CGGAGATTGGTGTCTTGCACT	60.609	52.381	0.00	0.00	46.86	4.40
1173	1206	2.498167	GAGATTGGTGTCTTGCACTGT	58.502	47.619	0.00	0.00	46.86	3.55
1209	1242	0.167470	CCAACGATGCAAGCACTCAG	59.833	55.000	0.00	0.00	0.00	3.35
1218	1251	1.065564	GCAAGCACTCAGAAGGGAGAT	60.066	52.381	0.00	0.00	38.30	2.75
1263	1296	1.490574	AGGTCCCGAAGAATGAGGAG	58.509	55.000	0.00	0.00	0.00	3.69
1274	1307	4.500499	AGAATGAGGAGGTTGATGAAGG	57.500	45.455	0.00	0.00	0.00	3.46
1326	1359	2.504367	CACTCGGTTGACCCTTTGAAT	58.496	47.619	0.00	0.00	0.00	2.57
1383	1416	1.145738	ACTGTGCCAGAAAATGAGGGT	59.854	47.619	8.91	0.00	35.18	4.34
1443	1476	4.836125	TCTCAGCATTGTCAAAAAGGAC	57.164	40.909	0.00	0.00	38.29	3.85

Showing 1 to 25 of 98 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	2.064581	GGATGTACGGTGGGGAGCT	61.065	63.158	0.00	0.00	0.00	4.09
93	95	2.096417	CGTGGACGGAGAAAAATGTGTC	60.096	50.000	0.00	0.00	35.37	3.67
94	96	1.871039	CGTGGACGGAGAAAAATGTGT	59.129	47.619	0.00	0.00	35.37	3.72
154	156	4.106925	GGAGGAGCCTGGCAGTGG	62.107	72.222	22.65	0.28	0.00	4.00
155	157	3.324930	TGGAGGAGCCTGGCAGTG	61.325	66.667	22.65	6.19	37.63	3.66
156	158	3.007920	CTGGAGGAGCCTGGCAGT	61.008	66.667	22.65	4.07	37.63	4.40
157	159	4.486503	GCTGGAGGAGCCTGGCAG	62.487	72.222	22.65	7.75	42.54	4.85
231	233	3.266772	TGCTGGTGATAGAAAATGGAGGT	59.733	43.478	0.00	0.00	0.00	3.85
316	320	0.875059	GGTTTCTGGCAGCACTACAC	59.125	55.000	10.34	0.00	0.00	2.90
331	335	1.302511	CTACCACCTGCAGCGGTTT	60.303	57.895	25.67	9.35	34.29	3.27
349	353	6.442112	GGATATTTGCTGGATCTTTTACTGC	58.558	40.000	0.00	0.00	0.00	4.40
350	354	6.483307	TCGGATATTTGCTGGATCTTTTACTG	59.517	38.462	0.00	0.00	0.00	2.74
431	445	4.870012	GGGAAATCGCGGGGGTCC	62.870	72.222	6.13	8.38	0.00	4.46
432	446	4.870012	GGGGAAATCGCGGGGGTC	62.870	72.222	6.13	0.00	0.00	4.46
454	470	2.875485	TCGAGAGAGGAAACGCGG	59.125	61.111	12.47	0.00	34.84	6.46
1110	1143	4.736759	GCAGGCAAGGAATTCAGATTGATG	60.737	45.833	16.86	14.71	0.00	3.07
1171	1204	2.052779	CCTCTGACTCCACTGCACA	58.947	57.895	0.00	0.00	0.00	4.57
1173	1206	2.587247	GGCCTCTGACTCCACTGCA	61.587	63.158	0.00	0.00	0.00	4.41
1209	1242	1.484240	CCACTGGACTCATCTCCCTTC	59.516	57.143	0.00	0.00	0.00	3.46
1218	1251	0.610174	GATCAGTGCCACTGGACTCA	59.390	55.000	23.85	5.32	45.94	3.41
1263	1296	3.503748	CCTGAACTTCACCTTCATCAACC	59.496	47.826	0.00	0.00	0.00	3.77
1274	1307	0.819259	TGCACAGGCCTGAACTTCAC	60.819	55.000	39.19	18.24	40.13	3.18
1326	1359	2.499205	CCGGCATGGTTCTCGCTA	59.501	61.111	0.00	0.00	0.00	4.26
1383	1416	2.245438	TATCGCCACCATCCGCACAA	62.245	55.000	0.00	0.00	0.00	3.33
1443	1476	5.641209	AGAATCAACAATTTCCTCAGACTCG	59.359	40.000	0.00	0.00	0.00	4.18

Showing 1 to 25 of 88 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.