AutoCloner

Multiple sequence alignment - TraesCS1A01G346900

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	TraesCS1A01G346900	chr1A	100.000	1675	0	0	950	2624	533162329	533164003	0.000000e+00	3094.0
1	TraesCS1A01G346900	chr1A	100.000	648	0	0	1	648	533161380	533162027	0.000000e+00	1197.0
2	TraesCS1A01G346900	chr1A	89.026	729	74	4	1750	2472	533209109	533209837	0.000000e+00	898.0
3	TraesCS1A01G346900	chr1B	96.673	1653	37	9	975	2624	589488290	589489927	0.000000e+00	2732.0
4	TraesCS1A01G346900	chr1B	84.013	638	29	33	10	588	589487428	589488051	1.780000e-151	545.0
5	TraesCS1A01G346900	chr1B	86.609	463	50	7	2141	2600	589491243	589491696	3.900000e-138	501.0
6	TraesCS1A01G346900	chr1B	89.164	323	30	2	2193	2513	589756428	589756747	5.260000e-107	398.0
7	TraesCS1A01G346900	chr1B	85.263	95	5	6	2432	2521	589756421	589756511	3.600000e-14	89.8
8	TraesCS1A01G346900	chr1D	96.570	1487	29	11	1144	2624	435932755	435934225	0.000000e+00	2444.0
9	TraesCS1A01G346900	chr1D	89.431	738	75	2	1738	2472	435951497	435952234	0.000000e+00	928.0
10	TraesCS1A01G346900	chr1D	89.362	423	13	16	208	603	435931769	435932186	1.080000e-138	503.0
11	TraesCS1A01G346900	chr1D	83.388	307	44	4	1976	2280	435952260	435952561	7.150000e-71	278.0
12	TraesCS1A01G346900	chr1D	89.767	215	12	5	10	224	435931548	435931752	1.550000e-67	267.0
13	TraesCS1A01G346900	chr1D	94.845	97	3	1	2	96	415286866	415286962	1.630000e-32	150.0
14	TraesCS1A01G346900	chr1D	94.845	97	3	1	2	96	415287513	415287609	1.630000e-32	150.0
15	TraesCS1A01G346900	chr7A	98.889	90	1	0	4	93	78420161	78420250	7.520000e-36	161.0
16	TraesCS1A01G346900	chr4A	100.000	86	0	0	11	96	717815888	717815803	2.700000e-35	159.0
17	TraesCS1A01G346900	chr4A	97.802	91	2	0	6	96	717265720	717265810	9.720000e-35	158.0
18	TraesCS1A01G346900	chr4A	97.802	91	2	0	6	96	717798550	717798460	9.720000e-35	158.0
19	TraesCS1A01G346900	chr2B	93.137	102	3	3	11	112	180419772	180419869	2.100000e-31	147.0

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	TraesCS1A01G346900	chr1A	533161380	533164003	2623	False	2145.500000	3094	100.000000	1	2624	2	chr1A.!!$F2	2623
1	TraesCS1A01G346900	chr1A	533209109	533209837	728	False	898.000000	898	89.026000	1750	2472	1	chr1A.!!$F1	722
2	TraesCS1A01G346900	chr1B	589487428	589491696	4268	False	1259.333333	2732	89.098333	10	2624	3	chr1B.!!$F1	2614
3	TraesCS1A01G346900	chr1D	435931548	435934225	2677	False	1071.333333	2444	91.899667	10	2624	3	chr1D.!!$F2	2614
4	TraesCS1A01G346900	chr1D	435951497	435952561	1064	False	603.000000	928	86.409500	1738	2472	2	chr1D.!!$F3	734

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
243	279	0.108329	CACTGTCCCCACCATCGTAC	60.108	60.0	0.0	0.0	0.0	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1680	1808	2.678336	GTCGAATCCCATTCCTGACAAC	59.322	50.0	0.0	0.0	35.89	3.32	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
115	119	1.284715	CGTCGTGGTGTGCTAGACA	59.715	57.895	0.00	0.00	32.57	3.41
167	171	0.164002	GTTCCGCTGCTTCGAAGAAC	59.836	55.000	28.95	17.82	45.90	3.01
171	175	0.436531	CGCTGCTTCGAAGAACAGAC	59.563	55.000	28.95	18.61	45.90	3.51
177	181	3.064820	TGCTTCGAAGAACAGACCAAAAC	59.935	43.478	28.95	6.50	45.90	2.43
179	183	2.567985	TCGAAGAACAGACCAAAACCC	58.432	47.619	0.00	0.00	0.00	4.11
205	209	0.976641	TGGTCAACTCCTCGAATGCT	59.023	50.000	0.00	0.00	0.00	3.79
215	251	2.014093	CTCGAATGCTCCAACGCGAC	62.014	60.000	15.93	0.00	0.00	5.19
235	271	2.431942	CGTACGCACTGTCCCCAC	60.432	66.667	0.52	0.00	0.00	4.61
237	273	2.524640	TACGCACTGTCCCCACCA	60.525	61.111	0.00	0.00	0.00	4.17
238	274	1.916273	TACGCACTGTCCCCACCAT	60.916	57.895	0.00	0.00	0.00	3.55
241	277	3.068881	CACTGTCCCCACCATCGT	58.931	61.111	0.00	0.00	0.00	3.73
242	278	1.895020	GCACTGTCCCCACCATCGTA	61.895	60.000	0.00	0.00	0.00	3.43
243	279	0.108329	CACTGTCCCCACCATCGTAC	60.108	60.000	0.00	0.00	0.00	3.67
279	330	0.250038	CTGCACACCAGCTACTGTGT	60.250	55.000	19.19	14.67	40.05	3.72
319	371	4.514577	CGTCTAGCCCACCAGCCG	62.515	72.222	0.00	0.00	0.00	5.52
448	516	4.798344	CTGGGCAGGCAGAGCAGG	62.798	72.222	0.00	0.00	0.00	4.85
451	519	4.792804	GGCAGGCAGAGCAGGGTC	62.793	72.222	0.00	0.00	0.00	4.46
555	644	0.324275	ATTAATGCCGCCAACCACCT	60.324	50.000	0.00	0.00	0.00	4.00
579	668	0.406361	ATCCACCCCGCAAAACCTAA	59.594	50.000	0.00	0.00	0.00	2.69
603	692	1.684391	GCACAAATACCCCCACCCC	60.684	63.158	0.00	0.00	0.00	4.95
604	693	1.379309	CACAAATACCCCCACCCCG	60.379	63.158	0.00	0.00	0.00	5.73
605	694	2.441348	CAAATACCCCCACCCCGC	60.441	66.667	0.00	0.00	0.00	6.13
606	695	3.746436	AAATACCCCCACCCCGCC	61.746	66.667	0.00	0.00	0.00	6.13
1144	1267	4.596585	CCCACCACCACCACCACC	62.597	72.222	0.00	0.00	0.00	4.61
1145	1268	3.814906	CCACCACCACCACCACCA	61.815	66.667	0.00	0.00	0.00	4.17
1147	1270	3.816090	ACCACCACCACCACCACC	61.816	66.667	0.00	0.00	0.00	4.61
1148	1271	3.814906	CCACCACCACCACCACCA	61.815	66.667	0.00	0.00	0.00	4.17
1149	1272	2.203337	CACCACCACCACCACCAG	60.203	66.667	0.00	0.00	0.00	4.00
1150	1273	3.498071	ACCACCACCACCACCAGG	61.498	66.667	0.00	0.00	42.21	4.45
1151	1274	4.284550	CCACCACCACCACCAGGG	62.285	72.222	0.00	0.00	44.81	4.45
1152	1275	4.974721	CACCACCACCACCAGGGC	62.975	72.222	0.00	0.00	42.05	5.19
1709	1837	6.000219	CAGGAATGGGATTCGACTTGATTAT	59.000	40.000	0.00	0.00	40.17	1.28
2033	2164	6.802608	TCGTTATTCGAGGTATGATTCTGTT	58.197	36.000	0.00	0.00	44.01	3.16
2236	2368	8.882415	ACGTTACTTCTATATATGTTGGTTGG	57.118	34.615	0.00	0.00	0.00	3.77
2360	2496	2.006888	ACGAATCAATGTTACTGCCGG	58.993	47.619	0.00	0.00	0.00	6.13
2421	2835	1.684450	TGTCGTCTACTTTGAGCCACA	59.316	47.619	0.00	0.00	0.00	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.830755	ACTACAACGACTTGGATGTACCT	59.169	43.478	0.00	0.00	39.86	3.08
1	2	4.184079	ACTACAACGACTTGGATGTACC	57.816	45.455	0.00	0.00	39.54	3.34
2	3	7.642978	CACTATACTACAACGACTTGGATGTAC	59.357	40.741	0.00	0.00	0.00	2.90
3	4	7.201758	CCACTATACTACAACGACTTGGATGTA	60.202	40.741	0.00	0.00	0.00	2.29
4	5	6.405508	CCACTATACTACAACGACTTGGATGT	60.406	42.308	0.00	0.00	0.00	3.06
5	6	5.977725	CCACTATACTACAACGACTTGGATG	59.022	44.000	0.00	0.00	0.00	3.51
6	7	5.655532	ACCACTATACTACAACGACTTGGAT	59.344	40.000	0.00	0.00	0.00	3.41
7	8	5.012239	ACCACTATACTACAACGACTTGGA	58.988	41.667	0.00	0.00	0.00	3.53
8	9	5.320549	ACCACTATACTACAACGACTTGG	57.679	43.478	0.00	0.00	0.00	3.61
97	101	0.729478	CTGTCTAGCACACCACGACG	60.729	60.000	0.00	0.00	0.00	5.12
115	119	2.224523	AGCTCTCGATAGCAGAGTAGCT	60.225	50.000	22.93	14.37	45.30	3.32
167	171	1.340889	CATGGTGTGGGTTTTGGTCTG	59.659	52.381	0.00	0.00	0.00	3.51
179	183	1.813513	GAGGAGTTGACCATGGTGTG	58.186	55.000	25.52	0.00	0.00	3.82
205	209	4.054825	GTACGGGGTCGCGTTGGA	62.055	66.667	17.44	0.00	40.63	3.53
215	251	4.446413	GGGACAGTGCGTACGGGG	62.446	72.222	18.39	0.36	0.00	5.73
235	271	1.658673	GAGCCGGGTAGTACGATGG	59.341	63.158	5.91	0.00	0.00	3.51
237	273	0.106708	TACGAGCCGGGTAGTACGAT	59.893	55.000	20.76	7.45	0.00	3.73
238	274	0.530650	CTACGAGCCGGGTAGTACGA	60.531	60.000	20.76	5.20	34.13	3.43
241	277	1.526917	GCCTACGAGCCGGGTAGTA	60.527	63.158	22.68	22.68	36.48	1.82
242	278	2.832201	GCCTACGAGCCGGGTAGT	60.832	66.667	22.89	22.89	36.48	2.73
243	279	3.603671	GGCCTACGAGCCGGGTAG	61.604	72.222	5.91	9.79	44.57	3.18
279	330	2.429250	TCCTGTTCTTGTTGACTGACGA	59.571	45.455	0.00	0.00	0.00	4.20
326	378	3.351416	GGCGGTGTGAAACGGGAC	61.351	66.667	0.00	0.00	42.39	4.46
439	507	4.154347	CCCTCGACCCTGCTCTGC	62.154	72.222	0.00	0.00	0.00	4.26
440	508	3.465403	CCCCTCGACCCTGCTCTG	61.465	72.222	0.00	0.00	0.00	3.35
442	510	3.151022	CTCCCCTCGACCCTGCTC	61.151	72.222	0.00	0.00	0.00	4.26
555	644	2.398840	TTTTGCGGGGTGGATGTCGA	62.399	55.000	0.00	0.00	0.00	4.20
579	668	2.046285	GGGGTATTTGTGCGCTGCT	61.046	57.895	9.73	0.00	0.00	4.24
1024	1113	3.224324	GTAGCCGAGGCCGATGGA	61.224	66.667	10.95	0.00	43.17	3.41
1025	1114	4.647615	CGTAGCCGAGGCCGATGG	62.648	72.222	10.95	1.04	43.17	3.51
1680	1808	2.678336	GTCGAATCCCATTCCTGACAAC	59.322	50.000	0.00	0.00	35.89	3.32
1709	1837	4.080243	ACCTCTCCTGACGATCTCTCTAAA	60.080	45.833	0.00	0.00	0.00	1.85
1790	1918	4.631377	TCCATCGATCTACTGCAAAACTTG	59.369	41.667	0.00	0.00	0.00	3.16
2235	2367	5.233263	CGACAAGAAGAGCTCTATTTAAGCC	59.767	44.000	18.59	2.04	40.75	4.35
2236	2368	5.808030	ACGACAAGAAGAGCTCTATTTAAGC	59.192	40.000	18.59	3.59	40.14	3.09
2337	2473	3.483574	CGGCAGTAACATTGATTCGTGAC	60.484	47.826	0.00	0.00	0.00	3.67
2360	2496	5.858381	TGTTATCCACTTGATCTAGGATGC	58.142	41.667	9.03	7.18	40.86	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.