AutoCloner

Multiple sequence alignment - TraesCS3D01G000700

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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	TraesCS3D01G000700	chr3D	100.000	2366	0	0	1	2366	480757	478392	0.000000e+00	4370.0
1	TraesCS3D01G000700	chr3D	83.188	345	50	6	3	345	468194508	468194846	2.280000e-80	309.0
2	TraesCS3D01G000700	chr3D	92.683	41	3	0	1793	1833	333394324	333394364	2.540000e-05	60.2
3	TraesCS3D01G000700	chr3A	95.538	874	31	5	241	1109	9072680	9073550	0.000000e+00	1391.0
4	TraesCS3D01G000700	chr3A	94.423	771	26	8	1140	1894	9073550	9074319	0.000000e+00	1170.0
5	TraesCS3D01G000700	chr3A	96.804	219	7	0	1880	2098	9082346	9082564	1.340000e-97	366.0
6	TraesCS3D01G000700	chr3A	97.630	211	5	0	2156	2366	9084418	9084628	1.730000e-96	363.0
7	TraesCS3D01G000700	chr3A	86.854	213	18	1	1	213	9072487	9072689	1.830000e-56	230.0
8	TraesCS3D01G000700	chr3A	73.529	408	74	25	938	1328	9223986	9224376	8.880000e-25	124.0
9	TraesCS3D01G000700	chr3A	100.000	46	0	0	2094	2139	9084380	9084425	4.190000e-13	86.1
10	TraesCS3D01G000700	chr3B	81.709	1170	115	43	768	1902	5817443	5816338	0.000000e+00	883.0
11	TraesCS3D01G000700	chr3B	82.922	931	88	28	795	1695	6085288	6086177	0.000000e+00	773.0
12	TraesCS3D01G000700	chr3B	85.060	502	36	14	765	1255	6104148	6104621	2.130000e-130	475.0
13	TraesCS3D01G000700	chr3B	90.343	321	24	3	1893	2210	5814875	5814559	4.700000e-112	414.0
14	TraesCS3D01G000700	chr3B	88.462	208	24	0	1399	1606	6110054	6110261	3.900000e-63	252.0
15	TraesCS3D01G000700	chr3B	86.364	110	5	5	612	711	6104036	6104145	6.910000e-21	111.0
16	TraesCS3D01G000700	chr3B	79.000	100	14	6	938	1031	6130891	6130989	7.060000e-06	62.1
17	TraesCS3D01G000700	chr3B	91.111	45	3	1	718	762	779581021	779580978	2.540000e-05	60.2
18	TraesCS3D01G000700	chrUn	85.282	496	34	14	771	1255	35553607	35553140	2.130000e-130	475.0
19	TraesCS3D01G000700	chrUn	85.060	502	36	14	765	1255	293672019	293672492	2.130000e-130	475.0
20	TraesCS3D01G000700	chrUn	80.095	633	78	30	1292	1896	34338496	34339108	6.040000e-116	427.0
21	TraesCS3D01G000700	chrUn	86.364	110	5	5	612	711	35553725	35553616	6.910000e-21	111.0
22	TraesCS3D01G000700	chrUn	86.364	110	5	5	612	711	293671907	293672016	6.910000e-21	111.0
23	TraesCS3D01G000700	chr6B	85.263	380	50	5	4	380	469297307	469296931	1.030000e-103	387.0
24	TraesCS3D01G000700	chr6B	100.000	28	0	0	1802	1829	9093206	9093233	4.000000e-03	52.8
25	TraesCS3D01G000700	chr1D	83.641	379	55	7	3	378	425307533	425307159	1.350000e-92	350.0
26	TraesCS3D01G000700	chr1D	81.771	384	57	11	1	380	130305369	130305743	2.280000e-80	309.0
27	TraesCS3D01G000700	chr1D	81.868	364	56	8	22	380	122776976	122776618	4.940000e-77	298.0
28	TraesCS3D01G000700	chr2B	82.447	376	58	8	3	376	448370835	448371204	2.930000e-84	322.0
29	TraesCS3D01G000700	chr7B	83.102	361	49	9	19	375	645254301	645254653	3.790000e-83	318.0
30	TraesCS3D01G000700	chr7B	100.000	29	0	0	718	746	40436072	40436100	1.000000e-03	54.7
31	TraesCS3D01G000700	chr2D	83.193	357	51	8	1	351	118115844	118115491	3.790000e-83	318.0
32	TraesCS3D01G000700	chr6A	79.373	383	67	11	1	379	25014102	25014476	2.330000e-65	259.0
33	TraesCS3D01G000700	chr5B	96.875	32	1	0	1802	1833	579367541	579367510	1.000000e-03	54.7
34	TraesCS3D01G000700	chr1A	96.875	32	1	0	1802	1833	536658424	536658393	1.000000e-03	54.7

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	TraesCS3D01G000700	chr3D	478392	480757	2365	True	4370.000000	4370	100.000000	1	2366	1	chr3D.!!$R1	2365
1	TraesCS3D01G000700	chr3A	9072487	9074319	1832	False	930.333333	1391	92.271667	1	1894	3	chr3A.!!$F2	1893
2	TraesCS3D01G000700	chr3A	9082346	9084628	2282	False	271.700000	366	98.144667	1880	2366	3	chr3A.!!$F3	486
3	TraesCS3D01G000700	chr3B	6085288	6086177	889	False	773.000000	773	82.922000	795	1695	1	chr3B.!!$F1	900
4	TraesCS3D01G000700	chr3B	5814559	5817443	2884	True	648.500000	883	86.026000	768	2210	2	chr3B.!!$R2	1442
5	TraesCS3D01G000700	chr3B	6104036	6104621	585	False	293.000000	475	85.712000	612	1255	2	chr3B.!!$F4	643
6	TraesCS3D01G000700	chrUn	34338496	34339108	612	False	427.000000	427	80.095000	1292	1896	1	chrUn.!!$F1	604
7	TraesCS3D01G000700	chrUn	35553140	35553725	585	True	293.000000	475	85.823000	612	1255	2	chrUn.!!$R1	643
8	TraesCS3D01G000700	chrUn	293671907	293672492	585	False	293.000000	475	85.712000	612	1255	2	chrUn.!!$F2	643

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
542	543	0.952984	GCTCAGCTGGTGAACCACTC	60.953	60.0	15.13	0.0	42.01	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1977	3554	0.804933	GGCCGACGACAACAGGTATC	60.805	60.0	0.0	0.0	0.0	2.24	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
53	54	2.687935	AGGAAGATGTGCACACGTTTTT	59.312	40.909	24.37	8.13	0.00	1.94
57	58	6.205853	AGGAAGATGTGCACACGTTTTTATTA	59.794	34.615	24.37	0.00	0.00	0.98
58	59	6.858993	GGAAGATGTGCACACGTTTTTATTAA	59.141	34.615	24.37	0.00	0.00	1.40
59	60	7.380065	GGAAGATGTGCACACGTTTTTATTAAA	59.620	33.333	24.37	0.00	0.00	1.52
86	87	2.688666	ATGAAGCCCTCGCCTCCA	60.689	61.111	0.00	0.00	34.57	3.86
97	98	3.181450	CCCTCGCCTCCATCTAGAAAAAT	60.181	47.826	0.00	0.00	0.00	1.82
137	138	8.210946	TCACCTTCATCTAGAAAAAGAAGTGAA	58.789	33.333	17.52	11.31	35.40	3.18
138	139	8.840321	CACCTTCATCTAGAAAAAGAAGTGAAA	58.160	33.333	15.53	0.00	35.40	2.69
139	140	9.408648	ACCTTCATCTAGAAAAAGAAGTGAAAA	57.591	29.630	15.53	0.00	35.40	2.29
175	176	1.382522	ATCAATGCAACCTACCAGCG	58.617	50.000	0.00	0.00	0.00	5.18
179	180	3.188786	GCAACCTACCAGCGAGCG	61.189	66.667	0.00	0.00	0.00	5.03
184	185	2.701780	CCTACCAGCGAGCGTCACT	61.702	63.158	0.00	0.00	0.00	3.41
240	241	7.687941	GGTTCATCACCTTCATCTAAAAAGA	57.312	36.000	0.00	0.00	43.29	2.52
241	242	8.110860	GGTTCATCACCTTCATCTAAAAAGAA	57.889	34.615	0.00	0.00	43.29	2.52
242	243	8.576442	GGTTCATCACCTTCATCTAAAAAGAAA	58.424	33.333	0.00	0.00	43.29	2.52
243	244	9.965824	GTTCATCACCTTCATCTAAAAAGAAAA	57.034	29.630	0.00	0.00	0.00	2.29
313	314	1.980036	AGCTTTTTCACCATGGCCAAT	59.020	42.857	10.96	0.00	0.00	3.16
355	356	2.133742	CTGGTTGGCTGCCTTTCACG	62.134	60.000	21.03	0.24	0.00	4.35
356	357	2.193536	GGTTGGCTGCCTTTCACGT	61.194	57.895	21.03	0.00	0.00	4.49
392	393	8.047310	TGGGTTTAATAGTCTCTTCATCTTTCC	58.953	37.037	0.00	0.00	0.00	3.13
405	406	4.214310	TCATCTTTCCTGGCTGTTTTCAA	58.786	39.130	0.00	0.00	0.00	2.69
431	432	1.538849	GCAAGCTTGGGGTGTTCAAAG	60.539	52.381	27.10	0.00	0.00	2.77
542	543	0.952984	GCTCAGCTGGTGAACCACTC	60.953	60.000	15.13	0.00	42.01	3.51
553	554	3.128349	GTGAACCACTCGCTCTTTGTTA	58.872	45.455	0.00	0.00	0.00	2.41
558	559	1.136336	CACTCGCTCTTTGTTAACGGC	60.136	52.381	0.26	0.00	0.00	5.68
711	722	3.085208	GCTATGCTGCAGCTGGTAA	57.915	52.632	36.61	18.93	42.66	2.85
729	743	4.713321	TGGTAACATGTACCTACTTCCTCC	59.287	45.833	18.99	0.73	46.17	4.30
793	808	1.463444	GCTGTCACGCGGTTTCTTAAT	59.537	47.619	12.47	0.00	0.00	1.40
794	809	2.669434	GCTGTCACGCGGTTTCTTAATA	59.331	45.455	12.47	0.00	0.00	0.98
1290	1361	2.280797	GACTGCAGCGACAACCCA	60.281	61.111	15.27	0.00	0.00	4.51
1330	1404	2.759973	CTACTCCTCCGGCAGCCA	60.760	66.667	13.30	0.00	0.00	4.75
1352	1426	2.184579	GGACGTACCTCCTGCTGC	59.815	66.667	3.83	0.00	35.41	5.25
1370	1444	4.012374	GCTGCCAGCCATATGTAATGTAT	58.988	43.478	5.06	0.00	34.48	2.29
1376	1450	5.396484	CAGCCATATGTAATGTATGCTTGC	58.604	41.667	1.24	0.00	0.00	4.01
1379	1453	4.455533	CCATATGTAATGTATGCTTGCCGT	59.544	41.667	1.24	0.00	0.00	5.68
1571	1655	9.838339	ATTCTATTGAGTGTAAATTAGTCCAGG	57.162	33.333	0.00	0.00	0.00	4.45
1812	1917	0.376852	ATGAACACACGCACACACAC	59.623	50.000	0.00	0.00	0.00	3.82
1896	2001	9.408648	TCCTCCTTCCATTAAATTGTCTTTATC	57.591	33.333	0.00	0.00	0.00	1.75
1898	2003	9.109393	CTCCTTCCATTAAATTGTCTTTATCGA	57.891	33.333	0.00	0.00	0.00	3.59
1977	3554	4.533919	ACTGTCTTTCCTCATGTCTCAG	57.466	45.455	0.00	0.00	0.00	3.35
1994	3571	1.471287	TCAGATACCTGTTGTCGTCGG	59.529	52.381	0.00	0.00	41.16	4.79
1995	3572	0.172803	AGATACCTGTTGTCGTCGGC	59.827	55.000	0.00	0.00	0.00	5.54
2156	5555	8.039603	TGCCACTAATTTACATGACTACTTTG	57.960	34.615	0.00	0.00	0.00	2.77
2263	5663	7.646548	ACTAGAGAATACTTGCATCTACACA	57.353	36.000	0.00	0.00	0.00	3.72
2314	5714	1.201424	AACAACCCTCGGGATAGTCC	58.799	55.000	9.43	0.00	38.96	3.85
2325	5725	5.480642	TCGGGATAGTCCAGTACTACTAG	57.519	47.826	10.50	0.00	43.47	2.57
2362	5762	7.652300	ACCATATAACAATGCATGTACGTAG	57.348	36.000	0.00	0.00	42.99	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	3.257561	CGGCGCCAGAAGATGACG	61.258	66.667	28.98	3.82	37.90	4.35
59	60	3.879892	GCGAGGGCTTCATCTATCTTTTT	59.120	43.478	0.00	0.00	35.83	1.94
64	65	0.972883	AGGCGAGGGCTTCATCTATC	59.027	55.000	0.00	0.00	39.81	2.08
71	72	1.115930	TAGATGGAGGCGAGGGCTTC	61.116	60.000	0.00	0.00	43.99	3.86
78	79	9.621629	TTTTAATATTTTTCTAGATGGAGGCGA	57.378	29.630	0.00	0.00	0.00	5.54
175	176	1.416434	GCTACGCAAAGTGACGCTC	59.584	57.895	0.00	0.00	0.00	5.03
179	180	0.796927	GAAGGGCTACGCAAAGTGAC	59.203	55.000	0.00	0.00	0.00	3.67
184	185	2.772077	TACATGAAGGGCTACGCAAA	57.228	45.000	0.00	0.00	0.00	3.68
217	218	9.965824	TTTTCTTTTTAGATGAAGGTGATGAAC	57.034	29.630	0.00	0.00	0.00	3.18
270	271	9.987272	AGCTTTTGGGATATTATTTTTAGATGC	57.013	29.630	0.00	0.00	0.00	3.91
287	288	3.140623	CCATGGTGAAAAAGCTTTTGGG	58.859	45.455	24.50	13.12	0.00	4.12
303	304	1.434696	GCGAACTGATTGGCCATGG	59.565	57.895	6.09	7.63	33.70	3.66
313	314	2.741985	CCATGTGGCGCGAACTGA	60.742	61.111	12.10	0.00	0.00	3.41
392	393	1.606224	GCCACCATTGAAAACAGCCAG	60.606	52.381	0.00	0.00	0.00	4.85
405	406	2.284112	CCCCAAGCTTGCCACCAT	60.284	61.111	21.43	0.00	0.00	3.55
473	474	3.135994	TCTCCTACCAACGAAAACAAGC	58.864	45.455	0.00	0.00	0.00	4.01
542	543	0.452784	GCTGCCGTTAACAAAGAGCG	60.453	55.000	6.39	0.00	0.00	5.03
553	554	0.534873	AAAAACAACAGGCTGCCGTT	59.465	45.000	15.89	18.57	0.00	4.44
574	575	1.164411	TGTATCACCGCTGGCTTTTG	58.836	50.000	0.00	0.00	0.00	2.44
575	576	1.539827	GTTGTATCACCGCTGGCTTTT	59.460	47.619	0.00	0.00	0.00	2.27
576	577	1.165270	GTTGTATCACCGCTGGCTTT	58.835	50.000	0.00	0.00	0.00	3.51
711	722	3.022406	GACGGAGGAAGTAGGTACATGT	58.978	50.000	2.69	2.69	0.00	3.21
713	724	3.053842	TGAGACGGAGGAAGTAGGTACAT	60.054	47.826	0.00	0.00	0.00	2.29
714	725	2.306805	TGAGACGGAGGAAGTAGGTACA	59.693	50.000	0.00	0.00	0.00	2.90
758	772	6.143278	CGCGTGACAGCTAACACATAATATAA	59.857	38.462	18.13	0.00	36.91	0.98
793	808	7.159372	GGACTTTTCCACATCTGTAAGACTTA	58.841	38.462	0.00	0.00	44.30	2.24
794	809	5.998363	GGACTTTTCCACATCTGTAAGACTT	59.002	40.000	0.00	0.00	44.30	3.01
842	859	3.197790	CATGGAGCTCGCCAACGG	61.198	66.667	7.83	0.00	42.16	4.44
1119	1176	6.953520	TGGAGATCATCTGGTGGTTAATTTTT	59.046	34.615	0.00	0.00	0.00	1.94
1120	1177	6.493166	TGGAGATCATCTGGTGGTTAATTTT	58.507	36.000	0.00	0.00	0.00	1.82
1121	1178	6.078456	TGGAGATCATCTGGTGGTTAATTT	57.922	37.500	0.00	0.00	0.00	1.82
1122	1179	5.715439	TGGAGATCATCTGGTGGTTAATT	57.285	39.130	0.00	0.00	0.00	1.40
1123	1180	5.919348	ATGGAGATCATCTGGTGGTTAAT	57.081	39.130	0.00	0.00	0.00	1.40
1124	1181	6.789457	AGATATGGAGATCATCTGGTGGTTAA	59.211	38.462	0.00	0.00	37.30	2.01
1125	1182	6.326161	AGATATGGAGATCATCTGGTGGTTA	58.674	40.000	0.00	0.00	37.30	2.85
1126	1183	5.161135	AGATATGGAGATCATCTGGTGGTT	58.839	41.667	0.00	0.00	37.30	3.67
1127	1184	4.761086	AGATATGGAGATCATCTGGTGGT	58.239	43.478	0.00	0.00	37.30	4.16
1128	1185	5.247792	TGAAGATATGGAGATCATCTGGTGG	59.752	44.000	0.00	0.00	37.30	4.61
1129	1186	6.014413	AGTGAAGATATGGAGATCATCTGGTG	60.014	42.308	0.00	0.00	37.30	4.17
1130	1187	6.014413	CAGTGAAGATATGGAGATCATCTGGT	60.014	42.308	0.00	0.00	37.30	4.00
1131	1188	6.210984	TCAGTGAAGATATGGAGATCATCTGG	59.789	42.308	0.00	0.00	37.30	3.86
1132	1189	7.229581	TCAGTGAAGATATGGAGATCATCTG	57.770	40.000	0.00	0.00	37.30	2.90
1330	1404	2.035312	AGGAGGTACGTCCGCTGT	59.965	61.111	24.89	8.39	42.05	4.40
1335	1409	2.184579	GCAGCAGGAGGTACGTCC	59.815	66.667	24.14	24.14	36.79	4.79
1352	1426	5.620654	GCAAGCATACATTACATATGGCTGG	60.621	44.000	7.80	2.27	31.75	4.85
1567	1651	4.755123	ACGACTAATTTGTGTTCTTCCTGG	59.245	41.667	0.00	0.00	0.00	4.45
1571	1655	5.401674	AGACGACGACTAATTTGTGTTCTTC	59.598	40.000	0.00	0.00	0.00	2.87
1774	1859	9.998106	GTGTTCATATATGTATGACCCTTACTT	57.002	33.333	11.34	0.00	44.77	2.24
1775	1860	9.154632	TGTGTTCATATATGTATGACCCTTACT	57.845	33.333	11.34	0.00	44.77	2.24
1896	2001	4.748892	TCCATTACTCAGAAAGAAGCTCG	58.251	43.478	0.00	0.00	0.00	5.03
1898	2003	4.512484	GCTCCATTACTCAGAAAGAAGCT	58.488	43.478	0.00	0.00	0.00	3.74
1971	3548	3.728268	CGACGACAACAGGTATCTGAGAC	60.728	52.174	10.76	1.59	43.49	3.36
1977	3554	0.804933	GGCCGACGACAACAGGTATC	60.805	60.000	0.00	0.00	0.00	2.24
1994	3571	1.680249	GGTTCTTCCTCAGTCCATGGC	60.680	57.143	6.96	2.00	0.00	4.40
1995	3572	1.065126	GGGTTCTTCCTCAGTCCATGG	60.065	57.143	4.97	4.97	36.25	3.66
2263	5663	3.181440	TGCTGGTCTTGGAGACTTTGATT	60.181	43.478	7.90	0.00	44.46	2.57
2325	5725	7.690952	TTGTTATATGGTTTGGGAACAGTAC	57.309	36.000	0.00	0.00	44.54	2.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.