AutoCloner

Multiple sequence alignment - TraesCS1B01G199200

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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	TraesCS1B01G199200	chr1B	100.000	5825	0	0	2315	8139	357424001	357418177	0.000000e+00	10757.0
1	TraesCS1B01G199200	chr1B	100.000	2013	0	0	1	2013	357426315	357424303	0.000000e+00	3718.0
2	TraesCS1B01G199200	chr1B	82.528	269	24	9	7887	8134	329909406	329909672	1.780000e-51	215.0
3	TraesCS1B01G199200	chr1B	87.654	162	17	2	7981	8139	575139493	575139654	1.390000e-42	185.0
4	TraesCS1B01G199200	chr1B	88.199	161	9	6	7982	8134	603564443	603564285	5.020000e-42	183.0
5	TraesCS1B01G199200	chr1A	95.256	1834	71	6	5924	7742	327536339	327538171	0.000000e+00	2891.0
6	TraesCS1B01G199200	chr1A	95.430	1466	35	11	4456	5895	327534887	327536346	0.000000e+00	2307.0
7	TraesCS1B01G199200	chr1A	94.422	1004	49	4	2326	3323	327532959	327533961	0.000000e+00	1537.0
8	TraesCS1B01G199200	chr1A	95.851	940	29	5	1078	2013	327531759	327532692	0.000000e+00	1511.0
9	TraesCS1B01G199200	chr1A	92.949	936	53	9	3434	4359	327533957	327534889	0.000000e+00	1351.0
10	TraesCS1B01G199200	chr1A	85.278	1080	61	41	15	1034	327530713	327531754	0.000000e+00	1024.0
11	TraesCS1B01G199200	chr1A	79.639	388	40	18	7781	8139	327538284	327538661	8.160000e-60	243.0
12	TraesCS1B01G199200	chr1A	86.957	161	19	2	7981	8139	520858689	520858849	6.490000e-41	180.0
13	TraesCS1B01G199200	chr1D	92.480	1835	87	23	4456	6255	255498644	255500462	0.000000e+00	2577.0
14	TraesCS1B01G199200	chr1D	95.704	1513	55	6	6256	7765	255500506	255502011	0.000000e+00	2425.0
15	TraesCS1B01G199200	chr1D	93.031	1564	58	25	1	1538	255493237	255494775	0.000000e+00	2237.0
16	TraesCS1B01G199200	chr1D	91.471	938	40	14	3434	4359	255497737	255498646	0.000000e+00	1253.0
17	TraesCS1B01G199200	chr1D	95.223	649	28	2	2535	3180	255496440	255497088	0.000000e+00	1024.0
18	TraesCS1B01G199200	chr1D	93.182	484	12	4	1538	2013	255495676	255496146	0.000000e+00	691.0
19	TraesCS1B01G199200	chr1D	92.072	391	20	6	7756	8139	255502029	255502415	2.580000e-149	540.0
20	TraesCS1B01G199200	chr1D	97.653	213	5	0	2337	2549	255496188	255496400	4.640000e-97	366.0
21	TraesCS1B01G199200	chr1D	93.548	155	7	1	3172	3323	255497587	255497741	2.290000e-55	228.0
22	TraesCS1B01G199200	chr1D	78.415	366	40	21	7807	8139	34949689	34950048	1.390000e-47	202.0
23	TraesCS1B01G199200	chr1D	95.161	124	5	1	3322	3445	28313637	28313515	2.320000e-45	195.0
24	TraesCS1B01G199200	chr1D	92.562	121	7	2	4356	4475	445993578	445993697	1.090000e-38	172.0
25	TraesCS1B01G199200	chr5A	83.065	248	24	11	7906	8139	6481712	6481469	8.280000e-50	209.0
26	TraesCS1B01G199200	chr3D	77.500	400	53	15	7774	8139	30290227	30289831	1.070000e-48	206.0
27	TraesCS1B01G199200	chr3D	89.032	155	17	0	7985	8139	457907567	457907413	8.340000e-45	193.0
28	TraesCS1B01G199200	chr3D	98.113	106	2	0	4356	4461	529790944	529790839	1.390000e-42	185.0
29	TraesCS1B01G199200	chr4B	97.479	119	3	0	3320	3438	628068095	628067977	3.850000e-48	204.0
30	TraesCS1B01G199200	chr4B	91.200	125	7	4	4356	4479	272861393	272861272	5.050000e-37	167.0
31	TraesCS1B01G199200	chr5B	95.902	122	5	0	3320	3441	403545836	403545715	1.790000e-46	198.0
32	TraesCS1B01G199200	chr5B	95.161	124	6	0	3315	3438	611922696	611922819	6.440000e-46	196.0
33	TraesCS1B01G199200	chr5B	95.161	124	5	1	3320	3443	571209384	571209262	2.320000e-45	195.0
34	TraesCS1B01G199200	chr5B	95.122	123	5	1	3320	3442	451432869	451432990	8.340000e-45	193.0
35	TraesCS1B01G199200	chr5B	94.690	113	4	2	4356	4466	138779427	138779315	3.020000e-39	174.0
36	TraesCS1B01G199200	chr5B	81.043	211	32	7	7905	8108	17569566	17569775	2.350000e-35	161.0
37	TraesCS1B01G199200	chr2D	93.939	132	5	3	3319	3448	158283412	158283282	6.440000e-46	196.0
38	TraesCS1B01G199200	chr4D	93.798	129	6	2	3315	3441	72256255	72256127	8.340000e-45	193.0
39	TraesCS1B01G199200	chr4D	93.913	115	6	1	4356	4469	195030545	195030659	1.090000e-38	172.0
40	TraesCS1B01G199200	chr4D	79.781	183	33	4	7800	7980	55714924	55714744	6.630000e-26	130.0
41	TraesCS1B01G199200	chr4A	91.367	139	9	2	3303	3438	544199299	544199437	3.880000e-43	187.0
42	TraesCS1B01G199200	chr4A	98.077	104	2	0	4356	4459	362098359	362098462	1.800000e-41	182.0
43	TraesCS1B01G199200	chr4A	91.667	132	7	4	4356	4486	596221223	596221351	6.490000e-41	180.0
44	TraesCS1B01G199200	chr7A	77.874	348	43	16	7821	8139	241740867	241741209	1.390000e-42	185.0
45	TraesCS1B01G199200	chr7A	79.085	153	19	10	7830	7980	63441114	63441255	8.700000e-15	93.5
46	TraesCS1B01G199200	chr3B	92.437	119	7	2	4356	4474	809849029	809849145	1.400000e-37	169.0
47	TraesCS1B01G199200	chr3B	91.200	125	8	3	4356	4480	272137348	272137469	5.050000e-37	167.0
48	TraesCS1B01G199200	chr3B	79.524	210	33	9	7774	7980	24357535	24357737	3.060000e-29	141.0
49	TraesCS1B01G199200	chr3B	79.426	209	34	8	7774	7980	24378906	24379107	1.100000e-28	139.0
50	TraesCS1B01G199200	chr5D	79.310	116	15	5	5403	5512	543310973	543310861	1.130000e-08	73.1

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	TraesCS1B01G199200	chr1B	357418177	357426315	8138	True	7237.500000	10757	100.000000	1	8139	2	chr1B.!!$R2	8138
1	TraesCS1B01G199200	chr1A	327530713	327538661	7948	False	1552.000000	2891	91.260714	15	8139	7	chr1A.!!$F2	8124
2	TraesCS1B01G199200	chr1D	255493237	255502415	9178	False	1260.111111	2577	93.818222	1	8139	9	chr1D.!!$F3	8138

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
583	625	0.107606	CCGAGACCGAGAGAGAAGGA	60.108	60.000	0.00	38.22	3.36	F
586	628	1.404035	GAGACCGAGAGAGAAGGAAGC	59.596	57.143	0.00	0.00	3.86	F
1488	1566	2.490903	GCCCATGCCATCTATGTGAATC	59.509	50.000	0.00	0.00	2.52	F
2725	3766	0.036294	GAAGCTACCCGACTTTGCCT	60.036	55.000	0.00	0.00	4.75	F
3338	4892	0.032813	AATACTCCCTCCGTCCGGAA	60.033	55.000	5.23	44.66	4.30	F
3341	4895	0.032813	ACTCCCTCCGTCCGGAAATA	60.033	55.000	5.23	44.66	1.40	F
3343	4897	0.032813	TCCCTCCGTCCGGAAATACT	60.033	55.000	5.23	44.66	2.12	F
4373	5945	0.330604	AATGTGCCAGAGCCATGAGT	59.669	50.000	0.00	38.69	3.41	F
5047	6645	0.109827	CGGCACACATTTTGATGCGA	60.110	50.000	0.00	39.02	5.10	F
6348	8009	0.390492	AACTGCTTTTGCCAAGCTCC	59.610	50.000	16.39	46.87	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1488	1566	1.225475	GCAACGACTCGAATGCACG	60.225	57.895	21.07	0.00	40.55	5.34	R
1513	1591	1.896220	TTTCAGCAGCTAACCACCAG	58.104	50.000	0.00	0.00	0.00	4.00	R
3321	4875	0.032813	ATTTCCGGACGGAGGGAGTA	60.033	55.000	13.64	0.00	46.06	2.59	R
4356	5928	0.607217	CAACTCATGGCTCTGGCACA	60.607	55.000	0.00	0.00	41.84	4.57	R
4395	5967	0.714180	TGGGGTAGGCTAGAGGTGAA	59.286	55.000	0.00	0.00	0.00	3.18	R
4396	5968	0.714180	TTGGGGTAGGCTAGAGGTGA	59.286	55.000	0.00	0.00	0.00	4.02	R
4398	5970	0.717196	AGTTGGGGTAGGCTAGAGGT	59.283	55.000	0.00	0.00	0.00	3.85	R
5990	7600	1.971357	CATTAGGGGATACGTCTGGCT	59.029	52.381	0.00	0.00	37.60	4.75	R
6784	8453	0.106819	GATTGTGATGGAGGCTGGCT	60.107	55.000	2.24	2.24	0.00	4.75	R
7787	9560	0.469331	ACCGTTCCCTCTGTCTCACA	60.469	55.000	0.00	0.00	0.00	3.58	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
31	32	2.842496	AGCTGAACAGATCTGATTGGGA	59.158	45.455	29.27	5.72	0.00	4.37
66	67	3.681897	AGCAAGCTCAACAAGAATACTCG	59.318	43.478	0.00	0.00	0.00	4.18
127	136	6.039941	TGAAGAAGCCTAGCATCTAGAAGTAC	59.960	42.308	0.00	0.00	35.50	2.73
137	146	7.921786	AGCATCTAGAAGTACTATCTAGCTG	57.078	40.000	23.85	23.85	43.92	4.24
139	148	7.606456	AGCATCTAGAAGTACTATCTAGCTGAC	59.394	40.741	27.72	22.41	42.26	3.51
140	149	7.606456	GCATCTAGAAGTACTATCTAGCTGACT	59.394	40.741	27.72	14.56	42.26	3.41
169	185	1.452145	GGCTGTGCCGGAACAAGAAA	61.452	55.000	18.16	0.00	39.62	2.52
233	259	2.125512	CGAAGGAGTGGGGAAGCG	60.126	66.667	0.00	0.00	0.00	4.68
234	260	2.436824	GAAGGAGTGGGGAAGCGC	60.437	66.667	0.00	0.00	0.00	5.92
307	333	0.528684	CTCCTCGAAGCCGAACATCC	60.529	60.000	0.00	0.00	45.04	3.51
506	544	4.270153	TCACCTGGGGCTGGGAGT	62.270	66.667	0.00	0.00	0.00	3.85
576	618	3.432588	ACGCACCGAGACCGAGAG	61.433	66.667	0.00	0.00	38.22	3.20
577	619	3.125573	CGCACCGAGACCGAGAGA	61.126	66.667	0.00	0.00	38.22	3.10
582	624	0.393267	ACCGAGACCGAGAGAGAAGG	60.393	60.000	0.00	0.00	38.22	3.46
583	625	0.107606	CCGAGACCGAGAGAGAAGGA	60.108	60.000	0.00	0.00	38.22	3.36
586	628	1.404035	GAGACCGAGAGAGAAGGAAGC	59.596	57.143	0.00	0.00	0.00	3.86
619	661	3.726517	CACGCGCTTTGGACAGGG	61.727	66.667	5.73	0.00	0.00	4.45
740	782	2.749839	CCAAATTGCCCCTCGCGA	60.750	61.111	9.26	9.26	42.08	5.87
1006	1073	2.615227	ATCGGTTCCTGCCATGGAGC	62.615	60.000	18.40	2.26	37.43	4.70
1086	1153	3.706373	CCGGTGGAGGTGGAGGTG	61.706	72.222	0.00	0.00	0.00	4.00
1087	1154	3.706373	CGGTGGAGGTGGAGGTGG	61.706	72.222	0.00	0.00	0.00	4.61
1088	1155	4.035102	GGTGGAGGTGGAGGTGGC	62.035	72.222	0.00	0.00	0.00	5.01
1488	1566	2.490903	GCCCATGCCATCTATGTGAATC	59.509	50.000	0.00	0.00	0.00	2.52
1513	1591	3.218398	CATTCGAGTCGTTGCTTTGTTC	58.782	45.455	13.12	0.00	0.00	3.18
1581	2560	7.063544	GCTATTCTAGTGTCATTTCGTGTTTCT	59.936	37.037	0.00	0.00	0.00	2.52

Showing 1 to 25 of 241 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	2.381725	TCAGATCTGTTCAGCTGCTG	57.618	50.000	23.31	23.31	0.00	4.41
31	32	3.080319	GAGCTTGCTCAAGTCAATTCCT	58.920	45.455	16.71	0.00	40.45	3.36
66	67	1.372087	CTGCTGGGCTCGTGGAATTC	61.372	60.000	0.00	0.00	0.00	2.17
137	146	1.719600	CACAGCCTGTTGAGCTAGTC	58.280	55.000	0.00	0.00	38.95	2.59
139	148	1.023513	GGCACAGCCTGTTGAGCTAG	61.024	60.000	0.00	0.00	46.69	3.42
140	149	1.003355	GGCACAGCCTGTTGAGCTA	60.003	57.895	0.00	0.00	46.69	3.32
151	167	0.383949	TTTTCTTGTTCCGGCACAGC	59.616	50.000	7.09	0.00	0.00	4.40
169	185	0.679505	TGCGAGTTCTGTGGCTAGTT	59.320	50.000	0.00	0.00	0.00	2.24
307	333	2.587194	CATGGCCGGCGAGAAGAG	60.587	66.667	22.54	1.52	0.00	2.85
351	377	3.984186	CTTGGCCTCTCCCCTCGGA	62.984	68.421	3.32	0.00	36.45	4.55
353	379	1.341156	ATTCTTGGCCTCTCCCCTCG	61.341	60.000	3.32	0.00	0.00	4.63
520	558	4.760047	CCCCTCACCGGCGACTTG	62.760	72.222	9.30	2.14	0.00	3.16
576	618	1.187087	TTCCTCCTCGCTTCCTTCTC	58.813	55.000	0.00	0.00	0.00	2.87
577	619	1.645710	TTTCCTCCTCGCTTCCTTCT	58.354	50.000	0.00	0.00	0.00	2.85
582	624	2.158900	TGATCCATTTCCTCCTCGCTTC	60.159	50.000	0.00	0.00	0.00	3.86
583	625	1.839994	TGATCCATTTCCTCCTCGCTT	59.160	47.619	0.00	0.00	0.00	4.68
586	628	1.858091	CGTGATCCATTTCCTCCTCG	58.142	55.000	0.00	0.00	0.00	4.63
787	829	2.046217	GGCCGAGGGTTGAAGTCC	60.046	66.667	0.00	0.00	0.00	3.85
788	830	2.046217	GGGCCGAGGGTTGAAGTC	60.046	66.667	0.00	0.00	0.00	3.01
870	928	2.203567	TGGGCAAACGGAAAGGGG	60.204	61.111	0.00	0.00	0.00	4.79
1069	1136	3.706373	CACCTCCACCTCCACCGG	61.706	72.222	0.00	0.00	0.00	5.28
1078	1145	4.394712	CTCCACCGCCACCTCCAC	62.395	72.222	0.00	0.00	0.00	4.02
1081	1148	4.083862	GTCCTCCACCGCCACCTC	62.084	72.222	0.00	0.00	0.00	3.85
1084	1151	4.436998	CTCGTCCTCCACCGCCAC	62.437	72.222	0.00	0.00	0.00	5.01
1143	1210	0.679321	CCTTTGCCTCCTCCTGCTTC	60.679	60.000	0.00	0.00	0.00	3.86

Showing 1 to 25 of 256 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.