AutoCloner

Multiple sequence alignment - TraesCS1B01G138100

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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	TraesCS1B01G138100	chr1B	100.000	4326	0	0	1	4326	177839345	177835020	0.000000e+00	7989.0
1	TraesCS1B01G138100	chr1B	88.034	117	9	2	3660	3776	1823677	1823566	2.710000e-27	134.0
2	TraesCS1B01G138100	chr1B	86.325	117	11	3	3660	3776	666933558	666933669	5.870000e-24	122.0
3	TraesCS1B01G138100	chr1B	95.312	64	3	0	4263	4326	177811140	177811077	7.650000e-18	102.0
4	TraesCS1B01G138100	chr1B	83.178	107	16	2	4010	4115	158531307	158531202	3.560000e-16	97.1
5	TraesCS1B01G138100	chr1D	94.293	2243	77	28	56	2277	116006329	116004117	0.000000e+00	3386.0
6	TraesCS1B01G138100	chr1D	96.438	1151	37	4	2309	3456	116004120	116002971	0.000000e+00	1895.0
7	TraesCS1B01G138100	chr1D	94.286	175	7	1	3467	3641	128530466	128530637	9.220000e-67	265.0
8	TraesCS1B01G138100	chr1D	91.489	47	4	0	3843	3889	437855315	437855361	1.000000e-06	65.8
9	TraesCS1B01G138100	chr1A	93.858	2133	76	22	58	2152	127078579	127076464	0.000000e+00	3162.0
10	TraesCS1B01G138100	chr1A	95.311	1301	45	7	2184	3475	127076467	127075174	0.000000e+00	2050.0
11	TraesCS1B01G138100	chr1A	82.108	408	48	14	3942	4326	432625910	432625505	4.170000e-85	326.0
12	TraesCS1B01G138100	chr1A	92.818	181	10	1	3462	3642	90767726	90767549	4.290000e-65	259.0
13	TraesCS1B01G138100	chr1A	88.485	165	19	0	4162	4326	127074594	127074430	2.640000e-47	200.0
14	TraesCS1B01G138100	chr1A	91.892	37	3	0	3787	3823	475311171	475311135	8.000000e-03	52.8
15	TraesCS1B01G138100	chr1A	100.000	28	0	0	3788	3815	564450555	564450582	8.000000e-03	52.8
16	TraesCS1B01G138100	chr5A	84.424	321	19	10	3459	3778	436260748	436260458	1.970000e-73	287.0
17	TraesCS1B01G138100	chr5A	95.322	171	5	1	3474	3644	367790241	367790074	7.130000e-68	268.0
18	TraesCS1B01G138100	chr5A	79.143	350	54	15	3942	4285	146935700	146935364	1.570000e-54	224.0
19	TraesCS1B01G138100	chr5A	92.424	66	5	0	1730	1795	57375666	57375601	1.280000e-15	95.3
20	TraesCS1B01G138100	chr5A	82.292	96	17	0	1694	1789	575658615	575658710	2.770000e-12	84.2
21	TraesCS1B01G138100	chr5A	95.455	44	2	0	3846	3889	549400456	549400499	2.160000e-08	71.3
22	TraesCS1B01G138100	chr7D	85.714	259	31	5	3948	4201	270711981	270711724	7.130000e-68	268.0
23	TraesCS1B01G138100	chr7D	89.109	202	19	2	3455	3656	519969083	519968885	9.290000e-62	248.0
24	TraesCS1B01G138100	chr7D	100.000	45	0	0	3890	3934	141135481	141135525	2.770000e-12	84.2
25	TraesCS1B01G138100	chr7D	96.000	50	1	1	3887	3935	84326818	84326769	3.590000e-11	80.5
26	TraesCS1B01G138100	chr7D	97.368	38	1	0	3852	3889	600490439	600490402	1.000000e-06	65.8
27	TraesCS1B01G138100	chr5D	94.767	172	5	2	3474	3644	445106652	445106484	9.220000e-67	265.0
28	TraesCS1B01G138100	chr5D	88.095	210	18	5	3440	3647	64274867	64275071	4.320000e-60	243.0
29	TraesCS1B01G138100	chr5D	88.182	110	9	1	3682	3787	279302838	279302729	1.260000e-25	128.0
30	TraesCS1B01G138100	chr5D	86.842	114	9	4	3660	3773	241946305	241946412	5.870000e-24	122.0
31	TraesCS1B01G138100	chr5D	78.453	181	34	5	3942	4119	443309853	443310031	3.540000e-21	113.0
32	TraesCS1B01G138100	chr5D	95.238	63	3	0	1727	1789	66756451	66756513	2.750000e-17	100.0
33	TraesCS1B01G138100	chr5D	83.333	96	16	0	1694	1789	457777221	457777316	5.960000e-14	89.8
34	TraesCS1B01G138100	chr5D	95.556	45	2	0	3788	3832	150835347	150835303	6.000000e-09	73.1
35	TraesCS1B01G138100	chr5D	100.000	31	0	0	3271	3301	21021100	21021070	1.680000e-04	58.4
36	TraesCS1B01G138100	chr3B	93.820	178	8	1	3466	3643	499167810	499167636	9.220000e-67	265.0
37	TraesCS1B01G138100	chr3B	86.667	135	18	0	1673	1807	126921207	126921341	2.690000e-32	150.0
38	TraesCS1B01G138100	chr3B	85.124	121	13	3	3656	3776	755450075	755449960	7.600000e-23	119.0
39	TraesCS1B01G138100	chr3B	86.364	88	9	3	4002	4088	415648489	415648404	4.610000e-15	93.5
40	TraesCS1B01G138100	chr3D	87.500	216	22	3	3442	3657	496740156	496739946	1.200000e-60	244.0
41	TraesCS1B01G138100	chr3D	81.553	206	23	8	1094	1287	81206732	81206934	5.790000e-34	156.0
42	TraesCS1B01G138100	chr3D	75.477	367	54	21	1441	1795	81207160	81207502	3.490000e-31	147.0
43	TraesCS1B01G138100	chr3D	87.500	112	9	1	3660	3771	583473251	583473357	1.630000e-24	124.0
44	TraesCS1B01G138100	chr3D	86.325	117	11	2	3660	3776	130497918	130498029	5.870000e-24	122.0
45	TraesCS1B01G138100	chr3D	96.078	51	1	1	3887	3936	545176667	545176717	9.970000e-12	82.4
46	TraesCS1B01G138100	chr2D	79.167	264	50	5	3942	4201	50440580	50440318	1.240000e-40	178.0
47	TraesCS1B01G138100	chr2D	84.733	131	12	2	3660	3787	373883454	373883579	1.630000e-24	124.0
48	TraesCS1B01G138100	chr2D	91.489	47	3	1	3788	3833	616608452	616608406	3.610000e-06	63.9
49	TraesCS1B01G138100	chr2D	100.000	31	0	0	3271	3301	209185675	209185645	1.680000e-04	58.4
50	TraesCS1B01G138100	chr2D	90.476	42	4	0	3789	3830	206242376	206242335	6.040000e-04	56.5
51	TraesCS1B01G138100	chr3A	86.667	135	18	0	1673	1807	95477817	95477951	2.690000e-32	150.0
52	TraesCS1B01G138100	chr3A	86.747	83	10	1	1441	1522	95477584	95477666	1.660000e-14	91.6
53	TraesCS1B01G138100	chr3A	100.000	45	0	0	3890	3934	647021286	647021330	2.770000e-12	84.2
54	TraesCS1B01G138100	chr4D	86.777	121	11	1	3656	3776	40952276	40952161	3.510000e-26	130.0
55	TraesCS1B01G138100	chr4D	100.000	38	0	0	3852	3889	326379924	326379887	2.160000e-08	71.3
56	TraesCS1B01G138100	chr4D	95.556	45	1	1	3845	3889	427269615	427269658	2.160000e-08	71.3
57	TraesCS1B01G138100	chr6B	86.325	117	12	2	3660	3776	256326159	256326271	1.630000e-24	124.0
58	TraesCS1B01G138100	chr6B	79.348	184	30	8	3942	4119	694447605	694447786	5.870000e-24	122.0
59	TraesCS1B01G138100	chr6B	84.071	113	13	4	3942	4049	310390884	310390996	2.130000e-18	104.0
60	TraesCS1B01G138100	chr6B	97.727	44	1	0	3846	3889	437150784	437150741	4.640000e-10	76.8
61	TraesCS1B01G138100	chr6B	95.349	43	2	0	3788	3830	225541849	225541891	7.760000e-08	69.4
62	TraesCS1B01G138100	chr6B	76.364	110	24	2	3942	4049	632431504	632431613	1.680000e-04	58.4
63	TraesCS1B01G138100	chr6D	79.348	184	30	7	3942	4119	456647892	456648073	5.870000e-24	122.0
64	TraesCS1B01G138100	chr5B	93.939	66	4	0	1730	1795	64265119	64265054	2.750000e-17	100.0
65	TraesCS1B01G138100	chr5B	83.333	96	16	0	1694	1789	559992274	559992369	5.960000e-14	89.8
66	TraesCS1B01G138100	chr5B	97.872	47	1	0	3888	3934	56695161	56695207	9.970000e-12	82.4
67	TraesCS1B01G138100	chr5B	97.368	38	1	0	3852	3889	563123151	563123188	1.000000e-06	65.8
68	TraesCS1B01G138100	chr7B	76.923	182	37	5	3942	4119	411357431	411357611	9.900000e-17	99.0
69	TraesCS1B01G138100	chr7B	82.143	112	17	3	3942	4050	193801060	193800949	4.610000e-15	93.5
70	TraesCS1B01G138100	chr7B	97.778	45	1	0	3890	3934	611239570	611239614	1.290000e-10	78.7
71	TraesCS1B01G138100	chr6A	96.000	50	1	1	3886	3934	64321628	64321677	3.590000e-11	80.5
72	TraesCS1B01G138100	chr2B	94.231	52	3	0	3883	3934	799555105	799555054	3.590000e-11	80.5
73	TraesCS1B01G138100	chr4B	87.302	63	6	1	3889	3951	556997974	556998034	2.160000e-08	71.3
74	TraesCS1B01G138100	chr7A	91.489	47	4	0	3843	3889	24673625	24673671	1.000000e-06	65.8
75	TraesCS1B01G138100	chr2A	93.182	44	3	0	3787	3830	656371991	656372034	1.000000e-06	65.8
76	TraesCS1B01G138100	chr2A	91.489	47	4	0	3843	3889	731536423	731536469	1.000000e-06	65.8

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	TraesCS1B01G138100	chr1B	177835020	177839345	4325	True	7989.0	7989	100.000000	1	4326	1	chr1B.!!$R4	4325
1	TraesCS1B01G138100	chr1D	116002971	116006329	3358	True	2640.5	3386	95.365500	56	3456	2	chr1D.!!$R1	3400
2	TraesCS1B01G138100	chr1A	127074430	127078579	4149	True	1804.0	3162	92.551333	58	4326	3	chr1A.!!$R4	4268

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
732	757	0.178992	GGGAATGGGGATTGCGATGA	60.179	55.000	0.00	0.00	0.00	2.92	F
834	859	0.240945	GAATGCAAATATCGGCGGGG	59.759	55.000	7.21	0.00	0.00	5.73	F
858	883	0.909843	GCATCGCGACAAGAAATTGC	59.090	50.000	12.93	11.62	0.00	3.56	F
1507	1554	1.215647	CGACCTCAAGGCTTACGCT	59.784	57.895	0.00	0.00	39.32	5.07	F
2365	2416	1.151668	CAGCTGTTCAGTTTCTCGGG	58.848	55.000	5.25	0.00	0.00	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2297	2348	0.594602	CATCATTCGCCGCCAATCAT	59.405	50.000	0.00	0.00	2.45	R
2299	2350	1.370900	GCATCATTCGCCGCCAATC	60.371	57.895	0.00	0.00	2.67	R
2300	2351	1.789078	GAGCATCATTCGCCGCCAAT	61.789	55.000	0.00	33.17	3.16	R
3316	3376	1.609501	CTCGGGAGAACAGGGACCA	60.610	63.158	0.00	39.18	4.02	R
4022	4136	0.101759	TACGGCTAGCGTTGGATGTC	59.898	55.000	15.48	0.00	3.06	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
23	24	5.855235	GCTTGGTTAGTTTAGTAGAAAGCG	58.145	41.667	0.00	0.00	0.00	4.68
24	25	5.407691	GCTTGGTTAGTTTAGTAGAAAGCGT	59.592	40.000	0.00	0.00	0.00	5.07
25	26	6.073385	GCTTGGTTAGTTTAGTAGAAAGCGTT	60.073	38.462	0.00	0.00	0.00	4.84
26	27	7.519488	GCTTGGTTAGTTTAGTAGAAAGCGTTT	60.519	37.037	0.00	0.00	0.00	3.60
27	28	7.790823	TGGTTAGTTTAGTAGAAAGCGTTTT	57.209	32.000	0.00	0.00	0.00	2.43
28	29	8.212317	TGGTTAGTTTAGTAGAAAGCGTTTTT	57.788	30.769	0.00	0.00	0.00	1.94
29	30	8.124199	TGGTTAGTTTAGTAGAAAGCGTTTTTG	58.876	33.333	0.00	0.00	0.00	2.44
30	31	8.124823	GGTTAGTTTAGTAGAAAGCGTTTTTGT	58.875	33.333	0.00	0.00	0.00	2.83
31	32	9.494479	GTTAGTTTAGTAGAAAGCGTTTTTGTT	57.506	29.630	0.00	0.00	0.00	2.83
33	34	8.975410	AGTTTAGTAGAAAGCGTTTTTGTTTT	57.025	26.923	0.00	0.00	0.00	2.43
34	35	8.856247	AGTTTAGTAGAAAGCGTTTTTGTTTTG	58.144	29.630	0.00	0.00	0.00	2.44
35	36	8.852380	GTTTAGTAGAAAGCGTTTTTGTTTTGA	58.148	29.630	0.00	0.00	0.00	2.69
36	37	6.864560	AGTAGAAAGCGTTTTTGTTTTGAC	57.135	33.333	0.00	0.00	0.00	3.18
37	38	6.383415	AGTAGAAAGCGTTTTTGTTTTGACA	58.617	32.000	0.00	0.00	0.00	3.58
38	39	6.864165	AGTAGAAAGCGTTTTTGTTTTGACAA	59.136	30.769	0.00	0.00	0.00	3.18
39	40	6.532365	AGAAAGCGTTTTTGTTTTGACAAA	57.468	29.167	0.00	0.00	37.77	2.83
40	41	6.949449	AGAAAGCGTTTTTGTTTTGACAAAA	58.051	28.000	9.30	9.30	44.71	2.44
51	52	9.840427	TTTTGTTTTGACAAAAAGAGAGAGTAG	57.160	29.630	14.75	0.00	43.82	2.57
52	53	8.786826	TTGTTTTGACAAAAAGAGAGAGTAGA	57.213	30.769	14.75	0.00	35.96	2.59
53	54	8.964476	TGTTTTGACAAAAAGAGAGAGTAGAT	57.036	30.769	14.75	0.00	35.96	1.98
54	55	8.830580	TGTTTTGACAAAAAGAGAGAGTAGATG	58.169	33.333	14.75	0.00	35.96	2.90
55	56	7.969536	TTTGACAAAAAGAGAGAGTAGATGG	57.030	36.000	0.00	0.00	0.00	3.51
56	57	6.672266	TGACAAAAAGAGAGAGTAGATGGT	57.328	37.500	0.00	0.00	0.00	3.55
57	58	7.067496	TGACAAAAAGAGAGAGTAGATGGTT	57.933	36.000	0.00	0.00	0.00	3.67
58	59	6.931281	TGACAAAAAGAGAGAGTAGATGGTTG	59.069	38.462	0.00	0.00	0.00	3.77

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
1	2	7.417496	AACGCTTTCTACTAAACTAACCAAG	57.583	36.000	0.00	0.00	0.00	3.61
8	9	8.856247	CAAAACAAAAACGCTTTCTACTAAACT	58.144	29.630	0.00	0.00	0.00	2.66
9	10	8.852380	TCAAAACAAAAACGCTTTCTACTAAAC	58.148	29.630	0.00	0.00	0.00	2.01
13	14	6.383415	TGTCAAAACAAAAACGCTTTCTACT	58.617	32.000	0.00	0.00	30.70	2.57
14	15	6.620253	TGTCAAAACAAAAACGCTTTCTAC	57.380	33.333	0.00	0.00	30.70	2.59
27	28	8.786826	TCTACTCTCTCTTTTTGTCAAAACAA	57.213	30.769	10.29	1.44	43.58	2.83
28	29	8.830580	CATCTACTCTCTCTTTTTGTCAAAACA	58.169	33.333	10.29	0.11	0.00	2.83
29	30	8.286097	CCATCTACTCTCTCTTTTTGTCAAAAC	58.714	37.037	10.29	0.00	0.00	2.43
30	31	7.993183	ACCATCTACTCTCTCTTTTTGTCAAAA	59.007	33.333	6.65	6.65	0.00	2.44
31	32	7.509546	ACCATCTACTCTCTCTTTTTGTCAAA	58.490	34.615	0.00	0.00	0.00	2.69
32	33	7.067496	ACCATCTACTCTCTCTTTTTGTCAA	57.933	36.000	0.00	0.00	0.00	3.18
33	34	6.672266	ACCATCTACTCTCTCTTTTTGTCA	57.328	37.500	0.00	0.00	0.00	3.58
34	35	6.370166	CCAACCATCTACTCTCTCTTTTTGTC	59.630	42.308	0.00	0.00	0.00	3.18
35	36	6.183361	ACCAACCATCTACTCTCTCTTTTTGT	60.183	38.462	0.00	0.00	0.00	2.83
36	37	6.148480	CACCAACCATCTACTCTCTCTTTTTG	59.852	42.308	0.00	0.00	0.00	2.44
37	38	6.183361	ACACCAACCATCTACTCTCTCTTTTT	60.183	38.462	0.00	0.00	0.00	1.94
38	39	5.308237	ACACCAACCATCTACTCTCTCTTTT	59.692	40.000	0.00	0.00	0.00	2.27
39	40	4.841246	ACACCAACCATCTACTCTCTCTTT	59.159	41.667	0.00	0.00	0.00	2.52
40	41	4.421131	ACACCAACCATCTACTCTCTCTT	58.579	43.478	0.00	0.00	0.00	2.85
41	42	4.054359	ACACCAACCATCTACTCTCTCT	57.946	45.455	0.00	0.00	0.00	3.10
42	43	4.951094	ACTACACCAACCATCTACTCTCTC	59.049	45.833	0.00	0.00	0.00	3.20
43	44	4.936802	ACTACACCAACCATCTACTCTCT	58.063	43.478	0.00	0.00	0.00	3.10
44	45	6.963083	ATACTACACCAACCATCTACTCTC	57.037	41.667	0.00	0.00	0.00	3.20
45	46	7.735326	AAATACTACACCAACCATCTACTCT	57.265	36.000	0.00	0.00	0.00	3.24
46	47	8.788325	AAAAATACTACACCAACCATCTACTC	57.212	34.615	0.00	0.00	0.00	2.59

Showing 1 to 25 of 377 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.