AutoCloner

Multiple sequence alignment - TraesCS1A01G419200

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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	TraesCS1A01G419200	chr1A	100.000	2369	0	0	1	2369	576140161	576137793	0.000000e+00	4375.0
1	TraesCS1A01G419200	chr1A	88.797	1696	92	37	5	1669	576204519	576202891	0.000000e+00	1989.0
2	TraesCS1A01G419200	chr1A	90.085	706	53	9	1668	2357	576202854	576202150	0.000000e+00	900.0
3	TraesCS1A01G419200	chr1A	84.900	351	44	5	1027	1369	576078222	576077873	1.740000e-91	346.0
4	TraesCS1A01G419200	chr1A	83.594	128	12	7	1549	1672	576077757	576077635	6.920000e-21	111.0
5	TraesCS1A01G419200	chr1D	88.790	1686	120	20	5	1669	479760369	479758732	0.000000e+00	2002.0
6	TraesCS1A01G419200	chr1D	86.209	1675	148	41	7	1669	479751775	479750172	0.000000e+00	1736.0
7	TraesCS1A01G419200	chr1D	91.011	712	42	9	1668	2357	479750136	479749425	0.000000e+00	941.0
8	TraesCS1A01G419200	chr1D	90.476	651	53	7	1714	2357	479758615	479757967	0.000000e+00	850.0
9	TraesCS1A01G419200	chr1D	89.604	404	21	7	1983	2365	479722164	479721761	5.880000e-136	494.0
10	TraesCS1A01G419200	chr1D	88.800	250	25	1	1028	1277	479737842	479737596	1.060000e-78	303.0
11	TraesCS1A01G419200	chr1D	85.124	121	9	7	1549	1665	479737354	479737239	5.350000e-22	115.0
12	TraesCS1A01G419200	chr1B	89.043	1150	77	21	543	1669	667930469	667931592	0.000000e+00	1380.0
13	TraesCS1A01G419200	chr1B	92.157	714	41	6	966	1669	667975792	667975084	0.000000e+00	994.0
14	TraesCS1A01G419200	chr1B	91.489	705	36	12	984	1669	667997262	667996563	0.000000e+00	948.0
15	TraesCS1A01G419200	chr1B	90.442	701	50	13	1668	2357	667975048	667974354	0.000000e+00	907.0
16	TraesCS1A01G419200	chr1B	90.435	690	33	16	995	1669	668031084	668030413	0.000000e+00	878.0
17	TraesCS1A01G419200	chr1B	83.404	940	81	33	5	930	668031975	668031097	0.000000e+00	802.0
18	TraesCS1A01G419200	chr1B	91.297	563	43	4	1789	2345	668029994	668029432	0.000000e+00	763.0
19	TraesCS1A01G419200	chr1B	90.182	550	36	10	1786	2320	667932023	667932569	0.000000e+00	701.0
20	TraesCS1A01G419200	chr1B	91.475	434	29	4	1778	2207	667996255	667995826	7.290000e-165	590.0
21	TraesCS1A01G419200	chr1B	88.889	477	41	3	5	481	667930000	667930464	5.680000e-161	577.0
22	TraesCS1A01G419200	chr1B	83.090	686	65	15	5	678	667976825	667976179	5.680000e-161	577.0
23	TraesCS1A01G419200	chr1B	84.715	615	51	14	329	930	667997846	667997262	2.040000e-160	575.0
24	TraesCS1A01G419200	chr1B	79.641	334	33	14	5	338	667998666	667998368	8.580000e-50	207.0
25	TraesCS1A01G419200	chr1B	92.174	115	5	2	798	909	667975901	667975788	2.440000e-35	159.0
26	TraesCS1A01G419200	chr1B	87.500	128	4	5	1668	1783	668030376	668030249	1.140000e-28	137.0
27	TraesCS1A01G419200	chr1B	87.179	117	3	7	1668	1772	667931630	667931746	3.200000e-24	122.0
28	TraesCS1A01G419200	chr1B	98.438	64	1	0	1714	1777	667996445	667996382	1.920000e-21	113.0
29	TraesCS1A01G419200	chr1B	94.737	57	2	1	1610	1666	667966261	667966316	1.170000e-13	87.9

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	TraesCS1A01G419200	chr1A	576137793	576140161	2368	True	4375.00	4375	100.00000	1	2369	1	chr1A.!!$R1	2368
1	TraesCS1A01G419200	chr1A	576202150	576204519	2369	True	1444.50	1989	89.44100	5	2357	2	chr1A.!!$R3	2352
2	TraesCS1A01G419200	chr1A	576077635	576078222	587	True	228.50	346	84.24700	1027	1672	2	chr1A.!!$R2	645
3	TraesCS1A01G419200	chr1D	479757967	479760369	2402	True	1426.00	2002	89.63300	5	2357	2	chr1D.!!$R4	2352
4	TraesCS1A01G419200	chr1D	479749425	479751775	2350	True	1338.50	1736	88.61000	7	2357	2	chr1D.!!$R3	2350
5	TraesCS1A01G419200	chr1D	479737239	479737842	603	True	209.00	303	86.96200	1028	1665	2	chr1D.!!$R2	637
6	TraesCS1A01G419200	chr1B	667930000	667932569	2569	False	695.00	1380	88.82325	5	2320	4	chr1B.!!$F2	2315
7	TraesCS1A01G419200	chr1B	667974354	667976825	2471	True	659.25	994	89.46575	5	2357	4	chr1B.!!$R1	2352
8	TraesCS1A01G419200	chr1B	668029432	668031975	2543	True	645.00	878	88.15900	5	2345	4	chr1B.!!$R3	2340
9	TraesCS1A01G419200	chr1B	667995826	667998666	2840	True	486.60	948	89.15160	5	2207	5	chr1B.!!$R2	2202

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
918	1717	0.395311	CCATCTCACCAGCAGCCAAT	60.395	55.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1874	3200	0.038892	TGCGTGTTCTCCGTCCTTAC	60.039	55.0	0.0	0.0	0.0	2.34	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
40	41	3.589988	TCTCTCATCCGAAAAGCAAGAC	58.410	45.455	0.00	0.00	0.00	3.01
50	51	3.313526	CGAAAAGCAAGACATATCCTGGG	59.686	47.826	0.00	0.00	0.00	4.45
71	72	4.054825	CATGGCCAACACGCACCC	62.055	66.667	10.96	0.00	0.00	4.61
72	73	4.594854	ATGGCCAACACGCACCCA	62.595	61.111	10.96	0.00	0.00	4.51
78	79	1.358759	CAACACGCACCCACTTTCC	59.641	57.895	0.00	0.00	0.00	3.13
147	148	7.794349	GCGACATGATGCTCTTAAAATAACTAC	59.206	37.037	0.00	0.00	0.00	2.73
148	149	9.035607	CGACATGATGCTCTTAAAATAACTACT	57.964	33.333	0.00	0.00	0.00	2.57
286	297	4.518970	AGTAACAACCCAACATTACTGCAG	59.481	41.667	13.48	13.48	36.69	4.41
323	871	3.548745	AGAATCAAGATCATCACGCCA	57.451	42.857	0.00	0.00	0.00	5.69
325	873	2.251409	ATCAAGATCATCACGCCAGG	57.749	50.000	0.00	0.00	0.00	4.45
327	875	1.137675	TCAAGATCATCACGCCAGGAG	59.862	52.381	0.00	0.00	0.00	3.69
432	982	5.707298	ACATGCACACTTCAAAGCTAATAGT	59.293	36.000	0.00	0.00	0.00	2.12
463	1013	7.850492	GCTTAATTTGGTGTAACAAAAAGCTTG	59.150	33.333	17.92	0.00	44.18	4.01
532	1084	4.248859	CCTCTTTCGGTATCTGCATATGG	58.751	47.826	4.56	0.00	0.00	2.74
567	1122	6.868864	TGTCTCAACTTTAAGTATGAGAGCAC	59.131	38.462	25.32	19.21	40.03	4.40
657	1230	2.279517	GATGCCGAGGCGATTCGT	60.280	61.111	9.78	0.00	45.51	3.85
669	1242	0.511221	CGATTCGTGACGCAAAAGGT	59.489	50.000	0.00	0.00	0.00	3.50
832	1567	1.795768	TTATCATCCATCTTCGCCGC	58.204	50.000	0.00	0.00	0.00	6.53
875	1610	4.347292	TCCTCCTCGAGTGCTATAAGTAGA	59.653	45.833	12.31	0.00	0.00	2.59
894	1629	2.635427	AGAACCTCTTCTCACACCTTCC	59.365	50.000	0.00	0.00	30.11	3.46
918	1717	0.395311	CCATCTCACCAGCAGCCAAT	60.395	55.000	0.00	0.00	0.00	3.16
988	1787	1.000060	TCGTTCGAGGAACCAATCGTT	60.000	47.619	3.15	0.00	39.14	3.85
992	1791	1.067142	TCGAGGAACCAATCGTTGAGG	60.067	52.381	0.00	0.00	39.86	3.86
1023	1822	0.674581	CTTCCCTGTCAATGAGCGCA	60.675	55.000	11.47	0.00	0.00	6.09
1077	1876	3.726517	GCGTTGGCAGTGCACGAT	61.727	61.111	26.57	0.00	39.62	3.73
1230	2029	3.007323	GCCTACCGTCCCCCTTGT	61.007	66.667	0.00	0.00	0.00	3.16
1233	2032	1.305887	CTACCGTCCCCCTTGTCCT	60.306	63.158	0.00	0.00	0.00	3.85
1374	2209	4.541705	AGCACTTGAAGATCTAGCTAGGA	58.458	43.478	20.58	8.01	0.00	2.94
1527	2370	5.977725	GTCAATGTATACATGCACGACTAGT	59.022	40.000	18.94	0.00	36.56	2.57
1575	2429	6.330278	GCAGATGCATGCATGTTCATAATAT	58.670	36.000	36.73	10.02	45.77	1.28
1581	2444	8.393671	TGCATGCATGTTCATAATATTAGTGA	57.606	30.769	26.79	3.11	0.00	3.41
1722	2674	5.114785	TGCCAAATATGTTACACACACAC	57.885	39.130	0.00	0.00	38.61	3.82
1837	3162	3.483954	CCACAATAGAGGCAGTGGG	57.516	57.895	0.00	0.00	45.96	4.61
1949	3276	6.935741	ACAAATCACACTACTACAAAGCAA	57.064	33.333	0.00	0.00	0.00	3.91
2272	3621	2.347490	CTGAGTCCCACCCGGTTG	59.653	66.667	0.00	0.00	0.00	3.77
2294	3643	3.947910	ATGTGGCAAAATGGTCAAGAG	57.052	42.857	0.00	0.00	0.00	2.85
2295	3644	2.942804	TGTGGCAAAATGGTCAAGAGA	58.057	42.857	0.00	0.00	0.00	3.10
2299	3648	5.163322	TGTGGCAAAATGGTCAAGAGAAAAT	60.163	36.000	0.00	0.00	0.00	1.82
2336	3686	1.632589	AAACAAGCCCTTCATGGTCC	58.367	50.000	0.00	0.00	0.00	4.46
2359	3709	7.744276	GTCCACAAGTCAACAAAATTCAAAAAC	59.256	33.333	0.00	0.00	0.00	2.43
2360	3710	7.442364	TCCACAAGTCAACAAAATTCAAAAACA	59.558	29.630	0.00	0.00	0.00	2.83
2361	3711	8.235905	CCACAAGTCAACAAAATTCAAAAACAT	58.764	29.630	0.00	0.00	0.00	2.71
2362	3712	9.053135	CACAAGTCAACAAAATTCAAAAACATG	57.947	29.630	0.00	0.00	0.00	3.21
2363	3713	7.750014	ACAAGTCAACAAAATTCAAAAACATGC	59.250	29.630	0.00	0.00	0.00	4.06
2364	3714	6.784176	AGTCAACAAAATTCAAAAACATGCC	58.216	32.000	0.00	0.00	0.00	4.40
2365	3715	6.373774	AGTCAACAAAATTCAAAAACATGCCA	59.626	30.769	0.00	0.00	0.00	4.92
2366	3716	7.067251	AGTCAACAAAATTCAAAAACATGCCAT	59.933	29.630	0.00	0.00	0.00	4.40
2367	3717	7.701501	GTCAACAAAATTCAAAAACATGCCATT	59.298	29.630	0.00	0.00	0.00	3.16
2368	3718	7.914346	TCAACAAAATTCAAAAACATGCCATTC	59.086	29.630	0.00	0.00	0.00	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	9.996554	TGCTTTTCGGATGAGAGAATAATATTA	57.003	29.630	0.00	0.00	0.00	0.98
11	12	8.908786	TGCTTTTCGGATGAGAGAATAATATT	57.091	30.769	0.00	0.00	0.00	1.28
29	30	4.273318	ACCCAGGATATGTCTTGCTTTTC	58.727	43.478	0.00	0.00	30.57	2.29
40	41	0.957395	GCCATGCGACCCAGGATATG	60.957	60.000	0.00	0.00	0.00	1.78
50	51	4.759096	GCGTGTTGGCCATGCGAC	62.759	66.667	22.58	12.44	45.57	5.19
71	72	0.734889	GATGCCATCACCGGAAAGTG	59.265	55.000	9.46	0.00	39.20	3.16
72	73	0.394352	GGATGCCATCACCGGAAAGT	60.394	55.000	9.46	0.00	0.00	2.66
78	79	0.179009	AGATTGGGATGCCATCACCG	60.179	55.000	6.84	0.00	0.00	4.94
113	114	4.996344	AGAGCATCATGTCGCTATCTATG	58.004	43.478	10.86	0.00	38.99	2.23
114	115	5.657826	AAGAGCATCATGTCGCTATCTAT	57.342	39.130	10.86	0.00	38.99	1.98
150	151	8.476657	TGTGAAGTAGCTAGCTATATACGTAG	57.523	38.462	26.59	0.00	0.00	3.51
151	152	8.880750	CATGTGAAGTAGCTAGCTATATACGTA	58.119	37.037	26.59	11.73	0.00	3.57
152	153	7.390996	ACATGTGAAGTAGCTAGCTATATACGT	59.609	37.037	26.59	19.44	0.00	3.57
153	154	7.753659	ACATGTGAAGTAGCTAGCTATATACG	58.246	38.462	26.59	13.02	0.00	3.06
233	244	8.335532	TGAGTGTACCTTAAAAATCTCCAATG	57.664	34.615	0.00	0.00	0.00	2.82
286	297	6.449635	TGATTCTACCACCAACATATTTGC	57.550	37.500	0.00	0.00	0.00	3.68
323	871	2.658807	GGTTCAACCAACTTCCTCCT	57.341	50.000	0.01	0.00	38.42	3.69
379	929	6.811665	TCGATGTTGACTCTTATTTACACCAG	59.188	38.462	0.00	0.00	0.00	4.00
432	982	9.871238	TTTTTGTTACACCAAATTAAGCAAGTA	57.129	25.926	0.00	0.00	34.50	2.24
463	1013	9.574516	AAAATATAGTCCATGGTTAGTGAATCC	57.425	33.333	12.58	0.00	0.00	3.01
556	1108	5.928264	TGCATATACATGTGTGCTCTCATAC	59.072	40.000	23.85	0.88	38.37	2.39
558	1110	4.964593	TGCATATACATGTGTGCTCTCAT	58.035	39.130	23.85	6.51	38.37	2.90
559	1111	4.405116	TGCATATACATGTGTGCTCTCA	57.595	40.909	23.85	9.12	38.37	3.27
560	1112	5.278964	CATGCATATACATGTGTGCTCTC	57.721	43.478	23.85	5.31	42.05	3.20
603	1164	7.689299	TCTCCCTCTCAAAGATTGAAACAATA	58.311	34.615	0.00	0.00	39.58	1.90
607	1168	5.414144	CCTTCTCCCTCTCAAAGATTGAAAC	59.586	44.000	0.00	0.00	39.58	2.78
657	1230	1.332375	CTTTTCGGACCTTTTGCGTCA	59.668	47.619	0.00	0.00	40.56	4.35
669	1242	7.052142	GGATCTACCTTTCTATCTTTTCGGA	57.948	40.000	0.00	0.00	35.41	4.55
694	1267	1.227249	TTTTGTCCCCTGGAAGTGGA	58.773	50.000	0.00	0.00	31.38	4.02
751	1325	2.435586	CAGGCCAGCACGAGAAGG	60.436	66.667	5.01	0.00	0.00	3.46
753	1327	3.630013	AGCAGGCCAGCACGAGAA	61.630	61.111	23.38	0.00	36.85	2.87
875	1610	2.635427	GAGGAAGGTGTGAGAAGAGGTT	59.365	50.000	0.00	0.00	0.00	3.50
894	1629	1.810794	GCTGCTGGTGAGATGGATGAG	60.811	57.143	0.00	0.00	0.00	2.90
918	1717	3.093814	TGACCTGAACTACGCTTGGATA	58.906	45.455	0.00	0.00	0.00	2.59
988	1787	1.064463	GGAAGCCATTGATGTCCCTCA	60.064	52.381	0.00	0.00	0.00	3.86
992	1791	1.341383	ACAGGGAAGCCATTGATGTCC	60.341	52.381	0.00	0.00	0.00	4.02
1023	1822	1.068083	CTGCATCGGCGTCCATACT	59.932	57.895	6.85	0.00	45.35	2.12
1145	1944	2.026301	GCTCGTAGTAGCGCCTGG	59.974	66.667	2.29	0.00	31.76	4.45
1277	2076	5.339008	ACTATAAGAAACACAGCGATGGA	57.661	39.130	5.32	0.00	0.00	3.41
1374	2209	1.513858	TGCCCATTACCCGATTACCT	58.486	50.000	0.00	0.00	0.00	3.08
1458	2294	6.074994	GCACACGCTTATGAGTATTACTGTAC	60.075	42.308	0.00	0.00	34.30	2.90
1459	2295	5.975344	GCACACGCTTATGAGTATTACTGTA	59.025	40.000	0.00	0.00	34.30	2.74
1460	2296	4.804139	GCACACGCTTATGAGTATTACTGT	59.196	41.667	0.00	0.00	34.30	3.55
1461	2297	4.803613	TGCACACGCTTATGAGTATTACTG	59.196	41.667	0.00	0.00	39.64	2.74
1462	2298	5.006153	TGCACACGCTTATGAGTATTACT	57.994	39.130	0.00	0.00	39.64	2.24
1527	2370	2.282180	GGCCGACTTTTCTGCCCA	60.282	61.111	0.00	0.00	44.40	5.36
1581	2444	8.871862	GTCGATCTCACGTACATACTTATAGAT	58.128	37.037	0.00	0.00	34.70	1.98
1784	2998	1.208293	GCTAAGCTGTAAGTGCTCCCT	59.792	52.381	0.00	0.00	40.22	4.20
1792	3117	4.424626	TCAACGAGATGCTAAGCTGTAAG	58.575	43.478	0.00	0.00	0.00	2.34
1863	3189	6.630444	TCTCCGTCCTTACTCACATAATAC	57.370	41.667	0.00	0.00	0.00	1.89
1874	3200	0.038892	TGCGTGTTCTCCGTCCTTAC	60.039	55.000	0.00	0.00	0.00	2.34
1875	3201	0.038892	GTGCGTGTTCTCCGTCCTTA	60.039	55.000	0.00	0.00	0.00	2.69
1949	3276	2.713167	AGCAACCCTAGCATGATATGGT	59.287	45.455	11.66	11.66	44.27	3.55
2110	3447	3.245730	ACCATCATCAAAGGGGATGTTGT	60.246	43.478	11.23	2.95	44.00	3.32
2258	3607	0.838987	ACATACAACCGGGTGGGACT	60.839	55.000	26.30	4.74	40.75	3.85
2272	3621	4.458989	TCTCTTGACCATTTTGCCACATAC	59.541	41.667	0.00	0.00	0.00	2.39
2299	3648	8.447053	GGCTTGTTTTTGAATTTTGTTGACTTA	58.553	29.630	0.00	0.00	0.00	2.24
2336	3686	9.053135	CATGTTTTTGAATTTTGTTGACTTGTG	57.947	29.630	0.00	0.00	0.00	3.33

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.