AutoCloner

Multiple sequence alignment - TraesCS3D01G458700

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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	TraesCS3D01G458700	chr3D	100.000	2723	0	0	1	2723	564053328	564056050	0.000000e+00	5029.0
1	TraesCS3D01G458700	chr3D	91.905	210	16	1	2451	2659	15362086	15362295	2.650000e-75	292.0
2	TraesCS3D01G458700	chr3D	87.500	72	7	2	2444	2513	17157723	17157652	6.250000e-12	82.4
3	TraesCS3D01G458700	chr3D	88.136	59	6	1	2412	2469	194687275	194687217	4.870000e-08	69.4
4	TraesCS3D01G458700	chr2D	97.258	1532	41	1	301	1831	9008784	9010315	0.000000e+00	2595.0
5	TraesCS3D01G458700	chr2D	83.232	1473	227	12	303	1764	8670729	8672192	0.000000e+00	1334.0
6	TraesCS3D01G458700	chr2D	82.237	1475	210	33	309	1750	9753161	9751706	0.000000e+00	1225.0
7	TraesCS3D01G458700	chr2D	80.080	1506	248	29	302	1766	9643014	9644508	0.000000e+00	1072.0
8	TraesCS3D01G458700	chr2D	95.618	502	11	3	2227	2723	9010616	9011111	0.000000e+00	795.0
9	TraesCS3D01G458700	chr2D	89.316	234	18	2	22	255	9008270	9008496	1.230000e-73	287.0
10	TraesCS3D01G458700	chr2D	95.588	68	3	0	1871	1938	9010548	9010615	2.870000e-20	110.0
11	TraesCS3D01G458700	chr2B	96.608	1533	51	1	301	1832	11907069	11905537	0.000000e+00	2542.0
12	TraesCS3D01G458700	chr2B	81.370	1358	222	13	381	1725	11389681	11391020	0.000000e+00	1077.0
13	TraesCS3D01G458700	chr2B	79.827	1507	250	30	302	1766	11454188	11452694	0.000000e+00	1050.0
14	TraesCS3D01G458700	chr2B	91.304	575	42	5	1899	2472	11905186	11904619	0.000000e+00	778.0
15	TraesCS3D01G458700	chr2B	95.941	271	9	2	2455	2723	9706495	9706765	3.220000e-119	438.0
16	TraesCS3D01G458700	chr2B	89.051	274	14	5	1	258	11913273	11913000	2.610000e-85	326.0
17	TraesCS3D01G458700	chr2A	94.522	1570	70	10	301	1854	8413148	8414717	0.000000e+00	2409.0
18	TraesCS3D01G458700	chr2A	96.543	1128	35	4	721	1845	8034405	8033279	0.000000e+00	1864.0
19	TraesCS3D01G458700	chr2A	95.524	782	26	7	1945	2723	8033099	8032324	0.000000e+00	1242.0
20	TraesCS3D01G458700	chr2A	81.283	1325	220	10	411	1725	7741769	7743075	0.000000e+00	1048.0
21	TraesCS3D01G458700	chr2A	95.364	604	22	4	1863	2465	8027330	8026732	0.000000e+00	955.0
22	TraesCS3D01G458700	chr2A	95.785	261	10	1	2464	2723	8023945	8023685	1.170000e-113	420.0
23	TraesCS3D01G458700	chr2A	87.324	213	25	2	1931	2143	8414872	8415082	2.710000e-60	243.0
24	TraesCS3D01G458700	chr2A	87.204	211	7	3	48	258	8412539	8412729	3.530000e-54	222.0
25	TraesCS3D01G458700	chr2A	91.429	70	4	2	2457	2525	179425768	179425836	8.030000e-16	95.3
26	TraesCS3D01G458700	chrUn	97.467	1145	27	2	721	1863	335085453	335086597	0.000000e+00	1953.0
27	TraesCS3D01G458700	chrUn	97.387	1148	28	2	721	1866	416897230	416896083	0.000000e+00	1953.0
28	TraesCS3D01G458700	chrUn	88.136	59	6	1	2412	2469	62694537	62694595	4.870000e-08	69.4
29	TraesCS3D01G458700	chr6B	86.905	84	7	4	2455	2536	2841879	2841798	1.040000e-14	91.6
30	TraesCS3D01G458700	chr7A	85.393	89	8	5	2458	2543	68552503	68552589	1.340000e-13	87.9
31	TraesCS3D01G458700	chr6A	88.136	59	6	1	2412	2469	457604314	457604372	4.870000e-08	69.4
32	TraesCS3D01G458700	chr5D	88.136	59	6	1	2412	2469	46341086	46341144	4.870000e-08	69.4

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	TraesCS3D01G458700	chr3D	564053328	564056050	2722	False	5029.00	5029	100.000000	1	2723	1	chr3D.!!$F2	2722
1	TraesCS3D01G458700	chr2D	8670729	8672192	1463	False	1334.00	1334	83.232000	303	1764	1	chr2D.!!$F1	1461
2	TraesCS3D01G458700	chr2D	9751706	9753161	1455	True	1225.00	1225	82.237000	309	1750	1	chr2D.!!$R1	1441
3	TraesCS3D01G458700	chr2D	9643014	9644508	1494	False	1072.00	1072	80.080000	302	1766	1	chr2D.!!$F2	1464
4	TraesCS3D01G458700	chr2D	9008270	9011111	2841	False	946.75	2595	94.445000	22	2723	4	chr2D.!!$F3	2701
5	TraesCS3D01G458700	chr2B	11904619	11907069	2450	True	1660.00	2542	93.956000	301	2472	2	chr2B.!!$R3	2171
6	TraesCS3D01G458700	chr2B	11389681	11391020	1339	False	1077.00	1077	81.370000	381	1725	1	chr2B.!!$F2	1344
7	TraesCS3D01G458700	chr2B	11452694	11454188	1494	True	1050.00	1050	79.827000	302	1766	1	chr2B.!!$R1	1464
8	TraesCS3D01G458700	chr2A	8032324	8034405	2081	True	1553.00	1864	96.033500	721	2723	2	chr2A.!!$R2	2002
9	TraesCS3D01G458700	chr2A	7741769	7743075	1306	False	1048.00	1048	81.283000	411	1725	1	chr2A.!!$F1	1314
10	TraesCS3D01G458700	chr2A	8412539	8415082	2543	False	958.00	2409	89.683333	48	2143	3	chr2A.!!$F3	2095
11	TraesCS3D01G458700	chr2A	8023685	8027330	3645	True	687.50	955	95.574500	1863	2723	2	chr2A.!!$R1	860
12	TraesCS3D01G458700	chrUn	335085453	335086597	1144	False	1953.00	1953	97.467000	721	1863	1	chrUn.!!$F2	1142
13	TraesCS3D01G458700	chrUn	416896083	416897230	1147	True	1953.00	1953	97.387000	721	1866	1	chrUn.!!$R1	1145

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
28	29	0.102481	AACAGTCGAACGACAGTGCT	59.898	50.0	25.13	9.88	46.76	4.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1875	2526	1.050988	ATCTAGACAGTGCCCCGCAT	61.051	55.0	0.0	0.0	41.91	4.73	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
24	25	1.847818	TGGAAACAGTCGAACGACAG	58.152	50.000	25.13	20.45	46.76	3.51
25	26	1.135527	TGGAAACAGTCGAACGACAGT	59.864	47.619	25.13	21.03	46.76	3.55
26	27	1.521423	GGAAACAGTCGAACGACAGTG	59.479	52.381	25.13	18.51	46.76	3.66
27	28	0.928229	AAACAGTCGAACGACAGTGC	59.072	50.000	25.13	2.40	46.76	4.40
28	29	0.102481	AACAGTCGAACGACAGTGCT	59.898	50.000	25.13	9.88	46.76	4.40
29	30	0.102481	ACAGTCGAACGACAGTGCTT	59.898	50.000	25.13	4.70	46.76	3.91
30	31	0.778815	CAGTCGAACGACAGTGCTTC	59.221	55.000	25.13	0.40	46.76	3.86
31	32	0.318784	AGTCGAACGACAGTGCTTCC	60.319	55.000	25.13	0.00	46.76	3.46
32	33	0.596600	GTCGAACGACAGTGCTTCCA	60.597	55.000	20.00	0.00	44.02	3.53
33	34	0.317160	TCGAACGACAGTGCTTCCAT	59.683	50.000	0.00	0.00	0.00	3.41
39	40	5.533482	GAACGACAGTGCTTCCATATATCT	58.467	41.667	0.00	0.00	0.00	1.98
87	88	1.064803	CATCTCGTCTCGTCTCCCTTG	59.935	57.143	0.00	0.00	0.00	3.61
113	114	2.125912	GTGCCGATCGCTGTCACT	60.126	61.111	10.32	0.00	38.78	3.41
204	205	6.364568	TGCAGTGGCTGTCATTATCTATAT	57.635	37.500	0.00	0.00	41.91	0.86
205	206	6.772605	TGCAGTGGCTGTCATTATCTATATT	58.227	36.000	0.00	0.00	41.91	1.28
226	227	3.300388	TCTAGAGCTGGATCGATTTGGT	58.700	45.455	0.00	0.00	0.00	3.67
229	230	1.091771	AGCTGGATCGATTTGGTGCG	61.092	55.000	0.00	0.00	0.00	5.34
240	241	4.094294	TCGATTTGGTGCGGAAAATAGAAG	59.906	41.667	0.00	0.00	28.51	2.85
268	600	6.414694	TCTGGTACGTAGCGTAAATTATTTCG	59.585	38.462	19.02	0.00	43.95	3.46
306	689	3.016736	GCAGCTTTACCTAATCAAGCCA	58.983	45.455	0.00	0.00	43.40	4.75
342	725	1.939838	GCTGAACAAGTACCACCCGAG	60.940	57.143	0.00	0.00	0.00	4.63
580	963	6.609212	AGGTTAGCATCAAAGACTCATCTAGA	59.391	38.462	0.00	0.00	33.57	2.43
780	1166	4.733887	CGACATCTATCTTTACACCGACAC	59.266	45.833	0.00	0.00	0.00	3.67
870	1266	1.272037	TGATGCACCAGCCATTCTTCA	60.272	47.619	0.00	0.00	41.13	3.02
926	1322	1.454572	GGTTGCTCATGTGTGTGGCA	61.455	55.000	0.00	0.00	35.04	4.92
946	1342	4.667420	GAAAGGGTTCGCTCGTGA	57.333	55.556	0.00	0.00	0.00	4.35
1306	1718	2.166829	TGCACACACAAGGTTCACTTT	58.833	42.857	0.00	0.00	37.29	2.66
2003	2771	4.065088	CTCCGAAACTTCTGAACATTCCA	58.935	43.478	0.00	0.00	0.00	3.53
2128	2899	5.237127	GCATGATTCCACTCGTCATTTATCA	59.763	40.000	0.00	0.00	30.57	2.15
2410	3188	5.478233	TCAATAAATTGATGTTCGACCGG	57.522	39.130	0.00	0.00	41.51	5.28
2681	6248	0.107831	CCGAGACACCCTTCCAACAA	59.892	55.000	0.00	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.726017	TGTCGTTCGACTGTTTCCAGAAAC	61.726	45.833	22.49	14.88	41.50	2.78
1	2	2.861935	GTCGTTCGACTGTTTCCAGAAA	59.138	45.455	16.50	0.00	41.50	2.52
2	3	2.159212	TGTCGTTCGACTGTTTCCAGAA	60.159	45.455	22.49	0.00	41.50	3.02
3	4	1.406180	TGTCGTTCGACTGTTTCCAGA	59.594	47.619	22.49	0.48	41.50	3.86
5	6	1.135527	ACTGTCGTTCGACTGTTTCCA	59.864	47.619	24.22	5.87	42.02	3.53
6	7	1.521423	CACTGTCGTTCGACTGTTTCC	59.479	52.381	26.22	3.24	42.53	3.13
7	8	1.071436	GCACTGTCGTTCGACTGTTTC	60.071	52.381	26.22	19.35	42.53	2.78
8	9	0.928229	GCACTGTCGTTCGACTGTTT	59.072	50.000	26.22	10.80	42.53	2.83
9	10	0.102481	AGCACTGTCGTTCGACTGTT	59.898	50.000	26.22	15.56	42.53	3.16
10	11	0.102481	AAGCACTGTCGTTCGACTGT	59.898	50.000	24.22	24.22	44.27	3.55
11	12	0.778815	GAAGCACTGTCGTTCGACTG	59.221	55.000	23.19	23.19	39.12	3.51
12	13	0.318784	GGAAGCACTGTCGTTCGACT	60.319	55.000	22.49	4.84	36.23	4.18
13	14	0.596600	TGGAAGCACTGTCGTTCGAC	60.597	55.000	16.85	16.85	35.84	4.20
14	15	0.317160	ATGGAAGCACTGTCGTTCGA	59.683	50.000	0.00	0.00	0.00	3.71
15	16	1.990799	TATGGAAGCACTGTCGTTCG	58.009	50.000	0.00	0.00	0.00	3.95
16	17	5.533482	AGATATATGGAAGCACTGTCGTTC	58.467	41.667	0.00	0.00	0.00	3.95
17	18	5.537300	AGATATATGGAAGCACTGTCGTT	57.463	39.130	0.00	0.00	0.00	3.85
18	19	5.537300	AAGATATATGGAAGCACTGTCGT	57.463	39.130	0.00	0.00	0.00	4.34
19	20	6.914259	TCTAAGATATATGGAAGCACTGTCG	58.086	40.000	0.00	0.00	0.00	4.35
20	21	8.983724	GTTTCTAAGATATATGGAAGCACTGTC	58.016	37.037	0.00	0.00	0.00	3.51
21	22	8.486210	TGTTTCTAAGATATATGGAAGCACTGT	58.514	33.333	0.00	0.00	0.00	3.55
22	23	8.893219	TGTTTCTAAGATATATGGAAGCACTG	57.107	34.615	0.00	0.00	0.00	3.66
23	24	8.709308	ACTGTTTCTAAGATATATGGAAGCACT	58.291	33.333	0.00	0.00	0.00	4.40
24	25	8.894768	ACTGTTTCTAAGATATATGGAAGCAC	57.105	34.615	0.00	0.00	0.00	4.40
25	26	7.867909	CGACTGTTTCTAAGATATATGGAAGCA	59.132	37.037	0.00	4.48	0.00	3.91
26	27	8.082852	TCGACTGTTTCTAAGATATATGGAAGC	58.917	37.037	0.00	0.00	0.00	3.86
27	28	9.967346	TTCGACTGTTTCTAAGATATATGGAAG	57.033	33.333	0.00	0.00	0.00	3.46
28	29	9.745880	GTTCGACTGTTTCTAAGATATATGGAA	57.254	33.333	0.00	0.00	0.00	3.53
29	30	8.074370	CGTTCGACTGTTTCTAAGATATATGGA	58.926	37.037	0.00	0.00	0.00	3.41
30	31	8.074370	TCGTTCGACTGTTTCTAAGATATATGG	58.926	37.037	0.00	0.00	0.00	2.74
31	32	8.893884	GTCGTTCGACTGTTTCTAAGATATATG	58.106	37.037	16.50	0.00	32.82	1.78
32	33	8.618677	TGTCGTTCGACTGTTTCTAAGATATAT	58.381	33.333	22.49	0.00	36.23	0.86
33	34	7.907045	GTGTCGTTCGACTGTTTCTAAGATATA	59.093	37.037	22.49	0.00	36.23	0.86
39	40	4.031418	TGTGTCGTTCGACTGTTTCTAA	57.969	40.909	22.49	1.12	36.23	2.10
68	69	1.384525	CAAGGGAGACGAGACGAGAT	58.615	55.000	0.00	0.00	0.00	2.75
69	70	0.677098	CCAAGGGAGACGAGACGAGA	60.677	60.000	0.00	0.00	0.00	4.04
70	71	0.961358	ACCAAGGGAGACGAGACGAG	60.961	60.000	0.00	0.00	0.00	4.18
71	72	0.538977	AACCAAGGGAGACGAGACGA	60.539	55.000	0.00	0.00	0.00	4.20
72	73	1.132643	CTAACCAAGGGAGACGAGACG	59.867	57.143	0.00	0.00	0.00	4.18
87	88	1.883084	CGATCGGCACCAGCTAACC	60.883	63.158	7.38	0.00	41.70	2.85
128	129	4.369182	CAACCACTAATCCACTATCGTCC	58.631	47.826	0.00	0.00	0.00	4.79
204	205	3.706594	ACCAAATCGATCCAGCTCTAGAA	59.293	43.478	0.00	0.00	0.00	2.10
205	206	3.068732	CACCAAATCGATCCAGCTCTAGA	59.931	47.826	0.00	0.00	0.00	2.43
226	227	3.009723	CCAGAAGCTTCTATTTTCCGCA	58.990	45.455	28.02	0.00	35.34	5.69
229	230	5.176592	ACGTACCAGAAGCTTCTATTTTCC	58.823	41.667	28.02	12.92	35.34	3.13
240	241	2.549633	TTACGCTACGTACCAGAAGC	57.450	50.000	0.00	0.00	42.13	3.86
306	689	4.263639	TGTTCAGCAGGAAGGAGATGAAAT	60.264	41.667	0.00	0.00	35.82	2.17
342	725	2.781595	TTCTTCCGAGCGTGAAGGCC	62.782	60.000	15.77	0.00	39.72	5.19
500	883	0.249868	CTCAAGGTGTCCAAGACGCA	60.250	55.000	10.19	0.00	43.87	5.24
529	912	1.123861	AGCCTGCACTGTCTTGGAGA	61.124	55.000	0.00	0.00	37.11	3.71
580	963	5.452356	GGGAATTGCTAAATACATGCTGCTT	60.452	40.000	0.00	0.00	0.00	3.91
780	1166	0.738389	ATGCCGGCCGAACATAAAAG	59.262	50.000	30.73	7.40	0.00	2.27
946	1342	5.591877	ACTCAAGTGCAAAACAGAAGAGAAT	59.408	36.000	0.00	0.00	0.00	2.40
1168	1574	6.861572	CACTCGTCATAAGACAGAACACTAAA	59.138	38.462	0.00	0.00	45.23	1.85
1875	2526	1.050988	ATCTAGACAGTGCCCCGCAT	61.051	55.000	0.00	0.00	41.91	4.73
2103	2874	2.996249	ATGACGAGTGGAATCATGCT	57.004	45.000	0.00	0.00	31.84	3.79
2227	2999	3.127721	GCCCTGTCACTTAAGATTTGAGC	59.872	47.826	10.09	0.00	0.00	4.26
2410	3188	6.094186	AGGAACACAAGAAGAAAGACACTTTC	59.906	38.462	14.05	14.05	0.00	2.62
2681	6248	0.984230	ATGTTCAGATCACGTGGGGT	59.016	50.000	17.00	1.87	0.00	4.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.