AutoCloner

Multiple sequence alignment - TraesCS4A01G016400

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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	TraesCS4A01G016400	chr4A	100.000	6870	0	0	1	6870	11182282	11189151	0.000000e+00	12687.0
1	TraesCS4A01G016400	chr4D	92.193	2946	142	43	2969	5870	457504132	457501231	0.000000e+00	4085.0
2	TraesCS4A01G016400	chr4D	88.053	3005	198	69	1	2927	457507138	457504217	0.000000e+00	3411.0
3	TraesCS4A01G016400	chr4D	91.954	522	23	6	5922	6434	457501218	457500707	0.000000e+00	713.0
4	TraesCS4A01G016400	chr4D	91.160	362	22	6	6073	6434	457498148	457497797	3.730000e-132	483.0
5	TraesCS4A01G016400	chr4B	89.870	2458	157	39	1	2399	571474787	571472363	0.000000e+00	3075.0
6	TraesCS4A01G016400	chr4B	90.808	2252	98	41	4491	6701	571470360	571468177	0.000000e+00	2911.0
7	TraesCS4A01G016400	chr4B	91.731	1040	49	12	3423	4441	571471386	571470363	0.000000e+00	1410.0
8	TraesCS4A01G016400	chr4B	91.224	433	29	3	2969	3393	571471815	571471384	1.280000e-161	580.0
9	TraesCS4A01G016400	chr4B	94.624	279	9	3	2502	2780	571472254	571471982	1.770000e-115	427.0
10	TraesCS4A01G016400	chr4B	85.350	157	22	1	6702	6857	53190626	53190782	1.980000e-35	161.0
11	TraesCS4A01G016400	chr7A	84.069	408	39	11	2511	2899	170288198	170288598	3.030000e-98	370.0
12	TraesCS4A01G016400	chr7A	87.135	171	17	5	6702	6870	35593699	35593532	9.100000e-44	189.0
13	TraesCS4A01G016400	chr7B	88.235	170	16	4	6702	6870	49608898	49609064	4.200000e-47	200.0
14	TraesCS4A01G016400	chr1D	87.059	170	19	3	6702	6870	64115332	64115165	9.100000e-44	189.0
15	TraesCS4A01G016400	chr1D	85.294	170	23	2	6702	6870	86114839	86114671	2.550000e-39	174.0
16	TraesCS4A01G016400	chr1D	93.478	46	3	0	4444	4489	333492168	333492213	1.240000e-07	69.4
17	TraesCS4A01G016400	chr2B	86.047	172	18	6	6701	6870	45036407	45036240	5.470000e-41	180.0
18	TraesCS4A01G016400	chr3D	87.261	157	18	2	6716	6870	41428750	41428594	1.970000e-40	178.0
19	TraesCS4A01G016400	chr3D	84.211	171	24	3	6702	6870	47601005	47601174	5.510000e-36	163.0
20	TraesCS4A01G016400	chr7D	84.024	169	24	3	6702	6870	440005490	440005325	7.130000e-35	159.0
21	TraesCS4A01G016400	chr1B	84.177	158	11	1	3828	3971	6714117	6713960	2.580000e-29	141.0
22	TraesCS4A01G016400	chr1B	84.177	158	11	1	3828	3971	6718503	6718346	2.580000e-29	141.0
23	TraesCS4A01G016400	chr1B	83.544	158	12	1	3828	3971	6705284	6705127	1.200000e-27	135.0
24	TraesCS4A01G016400	chr1B	82.911	158	13	1	3828	3971	6709701	6709544	5.590000e-26	130.0
25	TraesCS4A01G016400	chr1B	82.278	158	14	1	3828	3971	6701107	6700950	2.600000e-24	124.0
26	TraesCS4A01G016400	chr1B	94.444	72	4	0	3828	3899	6721662	6721591	2.030000e-20	111.0
27	TraesCS4A01G016400	chr1B	94.444	72	4	0	3828	3899	6725258	6725187	2.030000e-20	111.0

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	TraesCS4A01G016400	chr4A	11182282	11189151	6869	False	12687.0	12687	100.0000	1	6870	1	chr4A.!!$F1	6869
1	TraesCS4A01G016400	chr4D	457497797	457507138	9341	True	2173.0	4085	90.8400	1	6434	4	chr4D.!!$R1	6433
2	TraesCS4A01G016400	chr4B	571468177	571474787	6610	True	1680.6	3075	91.6514	1	6701	5	chr4B.!!$R1	6700

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
612	624	0.037697	TACTACACAAGTGCGCCAGG	60.038	55.0	4.18	0.00	39.39	4.45	F
647	665	0.384309	GTGATGGATAGCACGGACGA	59.616	55.0	0.00	0.00	33.04	4.20	F
1823	1895	0.246635	TTCTCGTGTCAAGGCTAGCC	59.753	55.0	27.19	27.19	0.00	3.93	F
2633	2756	0.178981	ATGGGTAGGTGGATGCATGC	60.179	55.0	11.82	11.82	0.00	4.06	F
2707	2830	0.106569	TTGCCTGGCCATATGGAGTG	60.107	55.0	26.47	12.81	37.39	3.51	F
4453	4661	0.033306	ACTACTCCTTCCCTCCGTCC	60.033	60.0	0.00	0.00	0.00	4.79	F
4454	4662	0.033405	CTACTCCTTCCCTCCGTCCA	60.033	60.0	0.00	0.00	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1776	1848	0.243907	GAGAAGCTGCACGTCCTACA	59.756	55.0	1.02	0.00	0.00	2.74	R
2482	2605	0.454285	GTGTGTGTGTGTGTGTGTGC	60.454	55.0	0.00	0.00	0.00	4.57	R
2670	2793	0.106519	AAGTCCACTTGCCAAGCTGT	60.107	50.0	3.88	0.00	34.38	4.40	R
3491	3678	0.250513	GTCTGCGTCTTCCCCATCTT	59.749	55.0	0.00	0.00	0.00	2.40	R
4643	4862	0.173481	TCTCCTTGGCGAAGATCACG	59.827	55.0	10.40	7.74	0.00	4.35	R
5393	5637	0.035056	ATCAAGTGGCGGAAGGGAAG	60.035	55.0	0.00	0.00	0.00	3.46	R
6268	6560	0.110238	CATCCAAAACAGTGCGTCGG	60.110	55.0	0.00	0.00	0.00	4.79	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
22	23	1.152881	AGGAATCGCCAATGGGAGC	60.153	57.895	0.00	0.00	40.02	4.70
28	29	2.274104	GCCAATGGGAGCGGGTTA	59.726	61.111	0.00	0.00	35.59	2.85
58	61	3.069016	TGTTACCTGCAGAGACGAAGAAA	59.931	43.478	17.39	0.00	0.00	2.52
59	62	2.910688	ACCTGCAGAGACGAAGAAAA	57.089	45.000	17.39	0.00	0.00	2.29
66	69	3.804873	GCAGAGACGAAGAAAAGAACTGT	59.195	43.478	0.00	0.00	0.00	3.55
91	94	0.179062	CTTCTGCTCTCCGGAATGGG	60.179	60.000	5.23	0.00	38.14	4.00
110	113	1.115326	GGGGATAGGTTGGGCAATGC	61.115	60.000	0.00	0.00	0.00	3.56
122	125	1.810853	GCAATGCGATTGGCCAACC	60.811	57.895	23.27	11.09	42.61	3.77
140	143	1.445410	CGAGGCGACCGATTGTTCA	60.445	57.895	0.00	0.00	0.00	3.18
155	158	2.929641	TGTTCAGATGAGGCAACAACA	58.070	42.857	0.00	0.00	41.41	3.33
157	160	1.511850	TCAGATGAGGCAACAACACG	58.488	50.000	0.00	0.00	41.41	4.49
190	193	0.323360	CATCCACGGGAAACATGGGT	60.323	55.000	0.00	0.00	38.38	4.51
222	225	3.189287	GCAGAGTTCAAATGACGATGGTT	59.811	43.478	0.00	0.00	0.00	3.67
244	247	0.163788	CACATTTGTCTCGTGCGGAC	59.836	55.000	0.00	0.00	0.00	4.79
280	283	1.041447	ACGGATCGGGGAATTCGAGT	61.041	55.000	5.18	0.00	40.09	4.18
403	412	3.103742	TCAAATAGATGCCCCAAAACCC	58.896	45.455	0.00	0.00	0.00	4.11
470	479	7.119262	GTGCACTACAATAGATAAACCAAGTGT	59.881	37.037	10.32	0.00	35.43	3.55
554	563	8.517878	CAGGATATGGCCTCATTAAAAACATAG	58.482	37.037	3.32	0.00	35.66	2.23
555	564	7.177392	AGGATATGGCCTCATTAAAAACATAGC	59.823	37.037	3.32	0.00	30.76	2.97
556	565	7.039784	GGATATGGCCTCATTAAAAACATAGCA	60.040	37.037	3.32	0.00	34.96	3.49
607	619	4.106029	AGTACCATACTACACAAGTGCG	57.894	45.455	0.00	0.00	39.39	5.34
612	624	0.037697	TACTACACAAGTGCGCCAGG	60.038	55.000	4.18	0.00	39.39	4.45
613	625	2.031919	TACACAAGTGCGCCAGGG	59.968	61.111	4.18	0.00	0.00	4.45
647	665	0.384309	GTGATGGATAGCACGGACGA	59.616	55.000	0.00	0.00	33.04	4.20
648	666	0.384309	TGATGGATAGCACGGACGAC	59.616	55.000	0.00	0.00	0.00	4.34

Showing 1 to 25 of 378 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	3.621268	CAGGTAACACATGTCATAACCCG	59.379	47.826	0.00	0.00	41.41	5.28
28	29	3.261643	TCTCTGCAGGTAACACATGTCAT	59.738	43.478	15.13	0.00	41.41	3.06
58	61	6.120507	AGAGCAGAAGGAATTACAGTTCTT	57.879	37.500	0.00	0.00	0.00	2.52
59	62	5.337975	GGAGAGCAGAAGGAATTACAGTTCT	60.338	44.000	0.00	0.00	0.00	3.01
66	69	2.747177	TCCGGAGAGCAGAAGGAATTA	58.253	47.619	0.00	0.00	0.00	1.40
91	94	1.115326	GCATTGCCCAACCTATCCCC	61.115	60.000	0.00	0.00	0.00	4.81
103	106	1.810853	GTTGGCCAATCGCATTGCC	60.811	57.895	23.66	0.66	40.31	4.52
106	109	1.656818	CTCGGTTGGCCAATCGCATT	61.657	55.000	39.99	0.00	44.00	3.56
110	113	3.508840	GCCTCGGTTGGCCAATCG	61.509	66.667	39.37	39.37	46.82	3.34
117	120	3.659089	AATCGGTCGCCTCGGTTGG	62.659	63.158	0.00	0.00	29.09	3.77
122	125	1.413767	CTGAACAATCGGTCGCCTCG	61.414	60.000	0.00	0.00	0.00	4.63
127	130	2.196749	CCTCATCTGAACAATCGGTCG	58.803	52.381	0.00	0.00	33.40	4.79
140	143	1.512926	GTCGTGTTGTTGCCTCATCT	58.487	50.000	0.00	0.00	0.00	2.90
155	158	0.944311	GATGAACACTGCCACGTCGT	60.944	55.000	0.00	0.00	0.00	4.34
157	160	0.602638	TGGATGAACACTGCCACGTC	60.603	55.000	0.00	0.00	0.00	4.34
190	193	3.500448	TTGAACTCTGCCCATTACACA	57.500	42.857	0.00	0.00	0.00	3.72
222	225	1.418373	CGCACGAGACAAATGTGAGA	58.582	50.000	0.00	0.00	35.77	3.27
261	264	1.041447	ACTCGAATTCCCCGATCCGT	61.041	55.000	0.00	0.00	35.35	4.69
280	283	1.699730	TCTCGGTTTGTGTCTCTCCA	58.300	50.000	0.00	0.00	0.00	3.86
304	312	5.048991	CCAACGGTAAAGTGCTTAAGTCATT	60.049	40.000	4.02	0.00	0.00	2.57
305	313	4.454504	CCAACGGTAAAGTGCTTAAGTCAT	59.545	41.667	4.02	0.00	0.00	3.06
306	314	3.810941	CCAACGGTAAAGTGCTTAAGTCA	59.189	43.478	4.02	0.00	0.00	3.41
307	315	4.060205	TCCAACGGTAAAGTGCTTAAGTC	58.940	43.478	4.02	0.00	0.00	3.01
308	316	4.075963	TCCAACGGTAAAGTGCTTAAGT	57.924	40.909	4.02	0.00	0.00	2.24
309	317	4.693566	TGATCCAACGGTAAAGTGCTTAAG	59.306	41.667	0.00	0.00	0.00	1.85

Showing 1 to 25 of 380 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.