AutoCloner

Multiple sequence alignment - TraesCS4B01G064100

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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	TraesCS4B01G064100	chr4B	100.000	5464	0	0	1	5464	56990265	56984802	0.000000e+00	10091.0
1	TraesCS4B01G064100	chr4B	86.327	373	32	9	117	484	12847956	12848314	6.640000e-104	388.0
2	TraesCS4B01G064100	chr4B	94.595	37	2	0	5070	5106	201526931	201526895	2.130000e-04	58.4
3	TraesCS4B01G064100	chr4A	92.978	2364	116	23	552	2881	562286677	562284330	0.000000e+00	3400.0
4	TraesCS4B01G064100	chr4A	93.487	2088	86	19	3021	5097	562283872	562281824	0.000000e+00	3057.0
5	TraesCS4B01G064100	chr4A	94.465	271	14	1	5195	5464	562281751	562281481	3.040000e-112	416.0
6	TraesCS4B01G064100	chr4A	96.183	131	4	1	2894	3023	562284064	562283934	4.290000e-51	213.0
7	TraesCS4B01G064100	chr4A	87.755	49	5	1	5074	5122	521302928	521302881	7.650000e-04	56.5
8	TraesCS4B01G064100	chr4A	100.000	28	0	0	2883	2910	562284213	562284186	1.000000e-02	52.8
9	TraesCS4B01G064100	chr4D	96.697	1332	40	3	2786	4116	39210914	39209586	0.000000e+00	2213.0
10	TraesCS4B01G064100	chr4D	97.002	934	22	5	1861	2790	39211945	39211014	0.000000e+00	1565.0
11	TraesCS4B01G064100	chr4D	90.538	1152	67	19	542	1676	39213071	39211945	0.000000e+00	1485.0
12	TraesCS4B01G064100	chr4D	92.579	822	33	12	4205	5023	39209346	39208550	0.000000e+00	1155.0
13	TraesCS4B01G064100	chr4D	87.169	491	45	8	1	484	139307998	139307519	4.810000e-150	542.0
14	TraesCS4B01G064100	chr4D	86.151	491	50	8	1	486	470857937	470857460	1.050000e-141	514.0
15	TraesCS4B01G064100	chr4D	93.949	314	11	5	5157	5464	39208321	39208010	8.290000e-128	468.0
16	TraesCS4B01G064100	chr2D	88.211	492	41	7	1	486	640638248	640637768	6.140000e-159	571.0
17	TraesCS4B01G064100	chr2D	85.872	453	38	8	1	439	403192252	403191812	4.990000e-125	459.0
18	TraesCS4B01G064100	chr2D	82.305	486	52	21	1	459	22416468	22415990	1.850000e-104	390.0
19	TraesCS4B01G064100	chr1D	86.939	490	44	13	4	486	5530351	5529875	2.900000e-147	532.0
20	TraesCS4B01G064100	chr5B	85.947	491	40	8	1	487	691261417	691261882	1.060000e-136	497.0
21	TraesCS4B01G064100	chr5B	94.872	39	2	0	5073	5111	534670579	534670541	1.640000e-05	62.1
22	TraesCS4B01G064100	chr5B	92.683	41	2	1	5074	5114	412286384	412286423	2.130000e-04	58.4
23	TraesCS4B01G064100	chr6B	85.540	491	44	15	1	486	24344669	24344201	6.360000e-134	488.0
24	TraesCS4B01G064100	chr6B	85.132	491	46	15	1	486	24261450	24260982	1.380000e-130	477.0
25	TraesCS4B01G064100	chr6A	84.158	505	49	13	1	487	6016967	6016476	1.390000e-125	460.0
26	TraesCS4B01G064100	chr2B	84.254	489	44	14	1	484	49671159	49671619	3.880000e-121	446.0
27	TraesCS4B01G064100	chr2B	83.436	489	48	14	1	484	49701324	49701784	1.820000e-114	424.0
28	TraesCS4B01G064100	chr2B	86.269	335	28	9	160	489	798010773	798010452	1.130000e-91	348.0
29	TraesCS4B01G064100	chr2B	85.484	310	27	9	185	489	797751012	797750716	1.910000e-79	307.0
30	TraesCS4B01G064100	chrUn	83.436	489	48	14	1	484	291354370	291354830	1.820000e-114	424.0
31	TraesCS4B01G064100	chrUn	83.436	489	48	14	1	484	345371752	345372212	1.820000e-114	424.0
32	TraesCS4B01G064100	chr3A	86.761	355	31	7	1	351	728973610	728973952	1.110000e-101	381.0
33	TraesCS4B01G064100	chr6D	91.667	48	4	0	5075	5122	421774295	421774248	3.530000e-07	67.6
34	TraesCS4B01G064100	chr5D	93.023	43	2	1	5070	5112	213216821	213216862	1.640000e-05	62.1
35	TraesCS4B01G064100	chr5D	94.595	37	2	0	5070	5106	28421398	28421434	2.130000e-04	58.4
36	TraesCS4B01G064100	chr3D	94.872	39	2	0	5070	5108	20751861	20751823	1.640000e-05	62.1

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	TraesCS4B01G064100	chr4B	56984802	56990265	5463	True	10091.00	10091	100.0000	1	5464	1	chr4B.!!$R1	5463
1	TraesCS4B01G064100	chr4A	562281481	562286677	5196	True	1427.76	3400	95.4226	552	5464	5	chr4A.!!$R2	4912
2	TraesCS4B01G064100	chr4D	39208010	39213071	5061	True	1377.20	2213	94.1530	542	5464	5	chr4D.!!$R3	4922

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	Hairpin	End Stability	Orientation
30	31	0.035056	GCAACCTGGACTGCATACCT	60.035	55.000	16.91	38.48	3.08	F
97	98	0.035630	AGCAGAATCTGGTGGAGCAC	60.036	55.000	14.70	40.87	4.40	F
421	422	0.036294	GCCCCAGAGCCGATTATACC	60.036	60.000	0.00	0.00	2.73	F
469	470	0.106868	TGCCTCCTGAGATGCCAATG	60.107	55.000	0.00	33.08	2.82	F
531	532	0.249911	GGCTGGAAGACACGTCTTGT	60.250	55.000	16.84	46.27	3.16	F
990	1013	0.253327	CTAGAAGCTTCCACCCACCC	59.747	60.000	22.81	0.00	4.61	F
1517	1552	0.905357	AGAACCGTGATAGCCAGCTT	59.095	50.000	0.00	0.00	3.74	F
1529	1564	1.280133	AGCCAGCTTGACATGCTAGAA	59.720	47.619	14.86	38.92	2.10	F
2619	2668	1.618837	GCTAGAAGGATATGGGACGCA	59.381	52.381	0.00	0.00	5.24	F
3693	4166	0.035458	AGCAGGCAGAGTACAACACC	59.965	55.000	0.00	0.00	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1503	1538	1.596260	CATGTCAAGCTGGCTATCACG	59.404	52.381	0.00	0.00	0.00	4.35	R
1577	1612	1.668047	GCAGAGCGCAAAAATCAGCTT	60.668	47.619	11.47	0.00	40.39	3.74	R
1590	1625	2.029244	CCGTTACACAAATAGCAGAGCG	59.971	50.000	0.00	0.00	0.00	5.03	R
1720	1759	3.310774	CCACATCAAGCCTAATCAAGACG	59.689	47.826	0.00	0.00	0.00	4.18	R
1774	1813	3.347077	AAGGTCTGATCCTTGAGCTTG	57.653	47.619	17.87	0.00	45.50	4.01	R
2773	2823	2.149973	AAGGGAAGGATCATGCAACC	57.850	50.000	0.00	0.00	0.00	3.77	R
3015	3423	3.974871	TTCGTACTATCATGTAGCGCA	57.025	42.857	11.47	0.00	0.00	6.09	R
3287	3760	4.164796	ACAGATATTGAGGAGTGCAATCCA	59.835	41.667	32.85	14.86	42.26	3.41	R
3911	4384	0.250124	TGCAGTGGGTACGGTTTCAG	60.250	55.000	0.00	0.00	0.00	3.02	R
5222	5977	0.539051	CTCGGCCTCTTCCTGACAAT	59.461	55.000	0.00	0.00	0.00	2.71	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
28	29	2.482326	GGCAACCTGGACTGCATAC	58.518	57.895	21.20	6.31	40.46	2.39
29	30	1.032114	GGCAACCTGGACTGCATACC	61.032	60.000	21.20	0.00	40.46	2.73
30	31	0.035056	GCAACCTGGACTGCATACCT	60.035	55.000	16.91	0.00	38.48	3.08
31	32	2.014068	GCAACCTGGACTGCATACCTC	61.014	57.143	16.91	0.00	38.48	3.85
32	33	1.278985	CAACCTGGACTGCATACCTCA	59.721	52.381	0.00	0.00	0.00	3.86
33	34	1.198713	ACCTGGACTGCATACCTCAG	58.801	55.000	0.00	4.01	37.56	3.35
34	35	1.198713	CCTGGACTGCATACCTCAGT	58.801	55.000	10.02	0.00	46.46	3.41
35	36	2.292257	ACCTGGACTGCATACCTCAGTA	60.292	50.000	0.00	0.00	44.09	2.74
36	37	2.968574	CCTGGACTGCATACCTCAGTAT	59.031	50.000	10.02	0.00	44.09	2.12
44	45	3.990318	CATACCTCAGTATGCGTCAGA	57.010	47.619	0.61	0.00	46.95	3.27
45	46	4.307443	CATACCTCAGTATGCGTCAGAA	57.693	45.455	0.61	0.00	46.95	3.02
46	47	2.949451	ACCTCAGTATGCGTCAGAAG	57.051	50.000	0.00	0.00	34.76	2.85
47	48	2.447443	ACCTCAGTATGCGTCAGAAGA	58.553	47.619	0.00	0.00	34.76	2.87
48	49	3.027412	ACCTCAGTATGCGTCAGAAGAT	58.973	45.455	0.00	0.00	34.76	2.40
49	50	3.067461	ACCTCAGTATGCGTCAGAAGATC	59.933	47.826	0.00	0.00	34.76	2.75
50	51	3.551863	CCTCAGTATGCGTCAGAAGATCC	60.552	52.174	0.00	0.00	34.76	3.36
51	52	2.033424	TCAGTATGCGTCAGAAGATCCG	59.967	50.000	0.00	0.00	34.76	4.18
52	53	2.033424	CAGTATGCGTCAGAAGATCCGA	59.967	50.000	0.00	0.00	0.00	4.55
53	54	2.292016	AGTATGCGTCAGAAGATCCGAG	59.708	50.000	0.00	0.00	0.00	4.63
54	55	1.393603	ATGCGTCAGAAGATCCGAGA	58.606	50.000	0.00	0.00	0.00	4.04
55	56	0.452184	TGCGTCAGAAGATCCGAGAC	59.548	55.000	0.00	0.00	0.00	3.36
56	57	0.248702	GCGTCAGAAGATCCGAGACC	60.249	60.000	0.00	0.00	0.00	3.85
57	58	0.382515	CGTCAGAAGATCCGAGACCC	59.617	60.000	0.00	0.00	0.00	4.46
58	59	1.475403	GTCAGAAGATCCGAGACCCA	58.525	55.000	0.00	0.00	0.00	4.51
59	60	1.135333	GTCAGAAGATCCGAGACCCAC	59.865	57.143	0.00	0.00	0.00	4.61

Showing 1 to 25 of 339 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.928396	AGGTTGCCCGTAGCTGGT	60.928	61.111	0.00	0.00	44.23	4.00
1	2	2.436646	CAGGTTGCCCGTAGCTGG	60.437	66.667	0.00	0.00	44.23	4.85
2	3	2.436646	CCAGGTTGCCCGTAGCTG	60.437	66.667	0.00	0.00	44.23	4.24
3	4	2.606519	TCCAGGTTGCCCGTAGCT	60.607	61.111	0.00	0.00	44.23	3.32
4	5	2.436115	GTCCAGGTTGCCCGTAGC	60.436	66.667	0.00	0.00	44.14	3.58
5	6	1.079127	CAGTCCAGGTTGCCCGTAG	60.079	63.158	0.00	0.00	35.12	3.51
6	7	3.065306	CAGTCCAGGTTGCCCGTA	58.935	61.111	0.00	0.00	35.12	4.02
7	8	4.643387	GCAGTCCAGGTTGCCCGT	62.643	66.667	7.29	0.00	34.28	5.28
8	9	2.535485	TATGCAGTCCAGGTTGCCCG	62.535	60.000	13.83	0.00	39.54	6.13
9	10	1.032114	GTATGCAGTCCAGGTTGCCC	61.032	60.000	13.83	2.01	39.54	5.36
10	11	1.032114	GGTATGCAGTCCAGGTTGCC	61.032	60.000	13.83	2.09	39.54	4.52
11	12	0.035056	AGGTATGCAGTCCAGGTTGC	60.035	55.000	11.65	10.65	40.67	4.17
12	13	1.278985	TGAGGTATGCAGTCCAGGTTG	59.721	52.381	11.65	0.00	0.00	3.77
13	14	1.556911	CTGAGGTATGCAGTCCAGGTT	59.443	52.381	11.65	0.00	0.00	3.50
14	15	1.198713	CTGAGGTATGCAGTCCAGGT	58.801	55.000	11.65	0.00	0.00	4.00
15	16	1.198713	ACTGAGGTATGCAGTCCAGG	58.801	55.000	11.65	4.69	42.62	4.45
16	17	3.987547	CATACTGAGGTATGCAGTCCAG	58.012	50.000	11.65	7.52	45.56	3.86
25	26	4.207955	TCTTCTGACGCATACTGAGGTAT	58.792	43.478	0.00	0.00	39.02	2.73
26	27	3.617284	TCTTCTGACGCATACTGAGGTA	58.383	45.455	0.00	0.00	0.00	3.08
27	28	2.447443	TCTTCTGACGCATACTGAGGT	58.553	47.619	0.00	0.00	0.00	3.85
28	29	3.551863	GGATCTTCTGACGCATACTGAGG	60.552	52.174	0.00	0.00	0.00	3.86
29	30	3.637432	GGATCTTCTGACGCATACTGAG	58.363	50.000	0.00	0.00	0.00	3.35
30	31	2.033424	CGGATCTTCTGACGCATACTGA	59.967	50.000	0.00	0.00	0.00	3.41
31	32	2.033424	TCGGATCTTCTGACGCATACTG	59.967	50.000	0.00	0.00	0.00	2.74
32	33	2.292016	CTCGGATCTTCTGACGCATACT	59.708	50.000	0.00	0.00	0.00	2.12

Showing 1 to 25 of 374 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.