AutoCloner

Multiple sequence alignment - TraesCS3B01G196900

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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	TraesCS3B01G196900	chr3B	100.000	3995	0	0	1	3995	223961842	223965836	0.000000e+00	7378.0
1	TraesCS3B01G196900	chr3B	90.576	191	17	1	2877	3067	223658720	223658909	6.630000e-63	252.0
2	TraesCS3B01G196900	chr3D	97.022	3996	73	8	1	3995	152822160	152826110	0.000000e+00	6678.0
3	TraesCS3B01G196900	chr3D	89.231	195	20	1	2873	3067	153078509	153078702	3.990000e-60	243.0
4	TraesCS3B01G196900	chr3A	98.054	2364	35	4	1	2363	177705073	177702720	0.000000e+00	4100.0
5	TraesCS3B01G196900	chr3A	95.737	1642	43	4	2358	3995	177686375	177684757	0.000000e+00	2619.0
6	TraesCS3B01G196900	chr3A	90.816	196	17	1	2873	3067	177111122	177110927	1.100000e-65	261.0
7	TraesCS3B01G196900	chr2A	78.171	1640	280	44	1049	2634	705264682	705266297	0.000000e+00	974.0
8	TraesCS3B01G196900	chr2A	79.771	786	124	15	1882	2633	704754687	704753903	4.540000e-149	538.0
9	TraesCS3B01G196900	chr2A	93.916	263	8	2	102	363	1217920	1217665	1.350000e-104	390.0
10	TraesCS3B01G196900	chr2B	77.339	1646	300	40	1044	2633	675534128	675535756	0.000000e+00	905.0
11	TraesCS3B01G196900	chr2B	79.363	785	129	13	1882	2633	675334071	675333287	4.580000e-144	521.0
12	TraesCS3B01G196900	chr2D	76.886	1644	307	35	1044	2633	564476327	564477951	0.000000e+00	863.0
13	TraesCS3B01G196900	chr2D	76.634	1652	305	56	1022	2634	564418719	564420328	0.000000e+00	837.0
14	TraesCS3B01G196900	chr2D	79.745	785	126	11	1882	2633	564072002	564071218	4.540000e-149	538.0
15	TraesCS3B01G196900	chr6A	91.155	407	23	4	102	502	108078635	108079034	1.260000e-149	540.0
16	TraesCS3B01G196900	chr7D	90.663	407	25	4	102	502	239729549	239729948	2.730000e-146	529.0
17	TraesCS3B01G196900	chr5A	90.663	407	25	4	102	502	565536224	565536623	2.730000e-146	529.0
18	TraesCS3B01G196900	chr4B	79.301	715	115	16	1949	2633	22438650	22437939	1.680000e-128	470.0
19	TraesCS3B01G196900	chr4B	79.048	525	96	11	2117	2628	22488446	22487923	8.220000e-92	348.0
20	TraesCS3B01G196900	chr5D	100.000	29	0	0	3842	3870	550833680	550833652	2.000000e-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	TraesCS3B01G196900	chr3B	223961842	223965836	3994	False	7378	7378	100.000	1	3995	1	chr3B.!!$F2	3994
1	TraesCS3B01G196900	chr3D	152822160	152826110	3950	False	6678	6678	97.022	1	3995	1	chr3D.!!$F1	3994
2	TraesCS3B01G196900	chr3A	177702720	177705073	2353	True	4100	4100	98.054	1	2363	1	chr3A.!!$R3	2362
3	TraesCS3B01G196900	chr3A	177684757	177686375	1618	True	2619	2619	95.737	2358	3995	1	chr3A.!!$R2	1637
4	TraesCS3B01G196900	chr2A	705264682	705266297	1615	False	974	974	78.171	1049	2634	1	chr2A.!!$F1	1585
5	TraesCS3B01G196900	chr2A	704753903	704754687	784	True	538	538	79.771	1882	2633	1	chr2A.!!$R2	751
6	TraesCS3B01G196900	chr2B	675534128	675535756	1628	False	905	905	77.339	1044	2633	1	chr2B.!!$F1	1589
7	TraesCS3B01G196900	chr2B	675333287	675334071	784	True	521	521	79.363	1882	2633	1	chr2B.!!$R1	751
8	TraesCS3B01G196900	chr2D	564476327	564477951	1624	False	863	863	76.886	1044	2633	1	chr2D.!!$F2	1589
9	TraesCS3B01G196900	chr2D	564418719	564420328	1609	False	837	837	76.634	1022	2634	1	chr2D.!!$F1	1612
10	TraesCS3B01G196900	chr2D	564071218	564072002	784	True	538	538	79.745	1882	2633	1	chr2D.!!$R1	751
11	TraesCS3B01G196900	chr4B	22437939	22438650	711	True	470	470	79.301	1949	2633	1	chr4B.!!$R1	684
12	TraesCS3B01G196900	chr4B	22487923	22488446	523	True	348	348	79.048	2117	2628	1	chr4B.!!$R2	511

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
514	515	0.834612	ACCACTTTGGACTTCGGTCA	59.165	50.000	0.0	0.0	46.11	4.02	F
1858	1881	2.036217	CTCATTGCCTTGGTTTTGCTCA	59.964	45.455	0.0	0.0	0.00	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2337	2414	1.374631	GTCGAGTGCAGATGCCACA	60.375	57.895	1.72	0.00	41.18	4.17	R
3652	3730	0.454196	AACAAAAGCGCTTTCGTGGT	59.546	45.000	33.69	25.13	38.14	4.16	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
62	63	5.401531	AGCAGATGAACAGCAATGAATTT	57.598	34.783	0.00	0.00	33.37	1.82
63	64	5.168569	AGCAGATGAACAGCAATGAATTTG	58.831	37.500	0.00	0.00	38.43	2.32
90	91	2.409371	CGAAACTCTGTTAACGCCGTTC	60.409	50.000	5.42	0.00	0.00	3.95
131	132	7.711846	ACATTGCTGTTTAACAAAGTCATACA	58.288	30.769	0.00	0.00	28.70	2.29
132	133	8.359642	ACATTGCTGTTTAACAAAGTCATACAT	58.640	29.630	0.00	0.00	28.70	2.29
133	134	8.641155	CATTGCTGTTTAACAAAGTCATACATG	58.359	33.333	0.00	0.00	0.00	3.21
134	135	7.503521	TGCTGTTTAACAAAGTCATACATGA	57.496	32.000	0.00	0.00	0.00	3.07
135	136	8.109705	TGCTGTTTAACAAAGTCATACATGAT	57.890	30.769	0.00	0.00	39.30	2.45
136	137	9.225436	TGCTGTTTAACAAAGTCATACATGATA	57.775	29.630	0.00	0.00	39.30	2.15
137	138	9.490663	GCTGTTTAACAAAGTCATACATGATAC	57.509	33.333	0.00	0.00	39.30	2.24
197	198	3.879892	GCCAGAAGATTAATCCAGTCCAC	59.120	47.826	11.92	0.00	0.00	4.02
225	226	4.260132	GCGATGTTTGACATTTTTGTTGCA	60.260	37.500	0.00	0.00	39.27	4.08
236	237	7.040823	TGACATTTTTGTTGCACTTTCCTTTTT	60.041	29.630	0.00	0.00	0.00	1.94
514	515	0.834612	ACCACTTTGGACTTCGGTCA	59.165	50.000	0.00	0.00	46.11	4.02
692	694	5.532779	AGACAAATCCAAGGTTTTGACTCTC	59.467	40.000	22.76	13.07	36.14	3.20
914	916	5.597182	TCGATACTGAAAGGCTTAGTGGTAT	59.403	40.000	11.96	11.90	39.30	2.73
984	986	3.438216	TGGTGAGATTGCAGAAATCCA	57.562	42.857	0.00	0.00	45.10	3.41
996	998	3.434299	GCAGAAATCCAAGCACCATTTTG	59.566	43.478	0.00	0.00	0.00	2.44
1461	1478	2.159366	CGACACGAGAAAGAGCTACCAT	60.159	50.000	0.00	0.00	0.00	3.55
1600	1617	6.643388	AGTATCATCTACAACAGCACATCAA	58.357	36.000	0.00	0.00	0.00	2.57
1858	1881	2.036217	CTCATTGCCTTGGTTTTGCTCA	59.964	45.455	0.00	0.00	0.00	4.26
2337	2414	3.006967	GGCGATACAGGATAATCTGTGGT	59.993	47.826	7.65	0.00	46.29	4.16
2661	2738	8.210265	TCCATGCTATATGACACACAAGAAATA	58.790	33.333	0.00	0.00	0.00	1.40
2662	2739	8.285394	CCATGCTATATGACACACAAGAAATAC	58.715	37.037	0.00	0.00	0.00	1.89
2712	2789	0.039618	GCCTGGGGAAAGTCATGGAA	59.960	55.000	0.00	0.00	0.00	3.53
2756	2833	1.202463	AGTGTATGACGAGATGCAGGC	60.202	52.381	0.00	0.00	0.00	4.85
3004	3081	4.838423	TCACAGGAAGGTGAGTATCTCAAA	59.162	41.667	0.88	0.00	42.46	2.69
3131	3208	3.007635	GCAACTCCGCCTAAATGTACTT	58.992	45.455	0.00	0.00	0.00	2.24
3132	3209	3.439129	GCAACTCCGCCTAAATGTACTTT	59.561	43.478	0.00	0.00	0.00	2.66
3133	3210	4.082949	GCAACTCCGCCTAAATGTACTTTT	60.083	41.667	11.09	11.09	0.00	2.27
3134	3211	5.122711	GCAACTCCGCCTAAATGTACTTTTA	59.877	40.000	12.03	12.03	0.00	1.52
3135	3212	6.183360	GCAACTCCGCCTAAATGTACTTTTAT	60.183	38.462	12.77	0.00	0.00	1.40
3136	3213	7.627726	GCAACTCCGCCTAAATGTACTTTTATT	60.628	37.037	12.77	2.61	0.00	1.40
3137	3214	8.885722	CAACTCCGCCTAAATGTACTTTTATTA	58.114	33.333	12.77	0.00	0.00	0.98
3138	3215	9.623000	AACTCCGCCTAAATGTACTTTTATTAT	57.377	29.630	12.77	0.00	0.00	1.28
3266	3343	4.956700	TCTCGACCAAGACTTAGGATCAAT	59.043	41.667	9.74	0.00	0.00	2.57
3312	3389	6.126854	GGTGGTGATCTAAAGTGTTACCCTAT	60.127	42.308	0.00	0.00	0.00	2.57
3342	3419	3.374402	CAGACGGCTCGGACCAGT	61.374	66.667	0.00	0.00	0.00	4.00
3355	3432	4.986783	TCGGACCAGTCATCATAGACTAT	58.013	43.478	0.00	0.00	46.65	2.12
3521	3599	1.409521	CCAGAAACAGACCACCAACCA	60.410	52.381	0.00	0.00	0.00	3.67
3588	3666	2.132762	GTGCACACTGTACACCACTAC	58.867	52.381	13.17	0.00	33.03	2.73
3661	3739	5.338614	CACTAAGGTGTAAACCACGAAAG	57.661	43.478	4.48	0.00	45.52	2.62
3669	3747	1.555477	AAACCACGAAAGCGCTTTTG	58.445	45.000	37.17	37.17	42.48	2.44
3759	3837	5.567138	AATTACTAGCAAACATGCCTGAC	57.433	39.130	0.00	0.00	34.90	3.51
3788	3866	1.451387	CATCACACGGCCCTAACCC	60.451	63.158	0.00	0.00	0.00	4.11
3835	3913	0.532196	GCCGTTTATCCTCCTTCCCG	60.532	60.000	0.00	0.00	0.00	5.14
3841	3919	2.563039	TATCCTCCTTCCCGTCCTTT	57.437	50.000	0.00	0.00	0.00	3.11
3968	4050	6.740002	CACGATATGAAGAAGTTGAAAAGCTG	59.260	38.462	0.00	0.00	0.00	4.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	63	3.128349	GTTAACAGAGTTTCGGAGCACA	58.872	45.455	0.00	0.00	0.00	4.57
63	64	2.155155	CGTTAACAGAGTTTCGGAGCAC	59.845	50.000	6.39	0.00	0.00	4.40
90	91	4.398358	AGCAATGTCCAGAAACAGATCATG	59.602	41.667	0.00	0.00	31.50	3.07
131	132	7.069085	CCTCAAATTTTGACCAGGATGTATCAT	59.931	37.037	7.74	0.00	35.46	2.45
132	133	6.377996	CCTCAAATTTTGACCAGGATGTATCA	59.622	38.462	7.74	0.00	35.46	2.15
133	134	6.378280	ACCTCAAATTTTGACCAGGATGTATC	59.622	38.462	17.97	0.00	35.46	2.24
134	135	6.256053	ACCTCAAATTTTGACCAGGATGTAT	58.744	36.000	17.97	0.00	35.46	2.29
135	136	5.640147	ACCTCAAATTTTGACCAGGATGTA	58.360	37.500	17.97	0.00	35.46	2.29
136	137	4.482990	ACCTCAAATTTTGACCAGGATGT	58.517	39.130	17.97	3.04	35.46	3.06
137	138	6.588719	TTACCTCAAATTTTGACCAGGATG	57.411	37.500	17.97	4.72	35.46	3.51
197	198	0.452618	AATGTCAAACATCGCGTGCG	60.453	50.000	5.77	8.14	37.97	5.34
225	226	7.231519	CCCTGTCTATTTGAGAAAAAGGAAAGT	59.768	37.037	0.00	0.00	35.13	2.66
236	237	4.338795	AGAGGTCCCTGTCTATTTGAGA	57.661	45.455	0.00	0.00	0.00	3.27
474	475	8.199449	AGTGGTATTTGATCAAATAAAGCATGG	58.801	33.333	32.42	0.00	42.75	3.66
914	916	9.342308	GTTCATATCCTCCACATATTTCAAGAA	57.658	33.333	0.00	0.00	0.00	2.52
984	986	1.002315	GTCATGGCCAAAATGGTGCTT	59.998	47.619	10.96	0.00	40.46	3.91
1421	1438	4.117685	GTCGAATTCCACGGCTACTATTT	58.882	43.478	0.00	0.00	32.48	1.40
1461	1478	3.289062	TTGCCGTCGAGGTCGTCA	61.289	61.111	4.18	0.00	43.70	4.35
1600	1617	8.292444	TGGCTTACAGATAATACAAAAGCATT	57.708	30.769	6.50	0.00	39.60	3.56
1858	1881	7.202016	ACACAAGAAACGATGAACATGTAAT	57.798	32.000	0.00	0.00	0.00	1.89
2337	2414	1.374631	GTCGAGTGCAGATGCCACA	60.375	57.895	1.72	0.00	41.18	4.17
2514	2591	3.326578	ATGTAGCCCCGTGTGCCA	61.327	61.111	0.00	0.00	0.00	4.92
2661	2738	2.517959	CAGACCCAATCCACAATGTGT	58.482	47.619	12.79	0.00	0.00	3.72
2662	2739	1.820519	CCAGACCCAATCCACAATGTG	59.179	52.381	6.37	6.37	0.00	3.21
2722	2799	2.167398	TACACTCCTCCAAGCACCGC	62.167	60.000	0.00	0.00	0.00	5.68
2756	2833	3.499737	GCCGCACCACAGAATCCG	61.500	66.667	0.00	0.00	0.00	4.18
2996	3073	1.630369	AGTGCACCAGCCTTTGAGATA	59.370	47.619	14.63	0.00	41.13	1.98
3004	3081	1.073199	GGTACAAGTGCACCAGCCT	59.927	57.895	14.63	0.00	41.13	4.58
3081	3158	1.690985	CCCAGAAGACCCCCTCTCC	60.691	68.421	0.00	0.00	0.00	3.71
3137	3214	9.486497	CTGTATAAACTAGCATGAATCTGACAT	57.514	33.333	0.00	0.00	0.00	3.06
3138	3215	7.928167	CCTGTATAAACTAGCATGAATCTGACA	59.072	37.037	0.00	0.00	0.00	3.58
3312	3389	1.215382	CGTCTGCGATGAGGTTCCA	59.785	57.895	0.00	0.00	41.33	3.53
3342	3419	6.112734	ACAACGCCAAAATAGTCTATGATGA	58.887	36.000	0.00	0.00	0.00	2.92
3355	3432	4.068599	TCATATGACAGACAACGCCAAAA	58.931	39.130	0.00	0.00	0.00	2.44
3466	3544	4.828925	GAGGCCAGTCTCAGCGCC	62.829	72.222	5.01	0.00	41.96	6.53
3467	3545	4.074526	TGAGGCCAGTCTCAGCGC	62.075	66.667	5.01	0.00	38.70	5.92
3468	3546	2.125753	GTGAGGCCAGTCTCAGCG	60.126	66.667	5.01	0.00	43.54	5.18
3470	3548	1.979155	TCGGTGAGGCCAGTCTCAG	60.979	63.158	5.01	0.00	43.54	3.35
3471	3549	2.117423	TCGGTGAGGCCAGTCTCA	59.883	61.111	5.01	0.00	41.03	3.27
3472	3550	1.939769	GAGTCGGTGAGGCCAGTCTC	61.940	65.000	5.01	0.00	36.97	3.36
3473	3551	1.979693	GAGTCGGTGAGGCCAGTCT	60.980	63.158	5.01	0.00	36.97	3.24
3474	3552	2.276116	TGAGTCGGTGAGGCCAGTC	61.276	63.158	5.01	0.00	36.97	3.51
3475	3553	2.203640	TGAGTCGGTGAGGCCAGT	60.204	61.111	5.01	0.00	36.97	4.00
3476	3554	2.219325	GAGTGAGTCGGTGAGGCCAG	62.219	65.000	5.01	0.00	36.97	4.85
3477	3555	2.203640	AGTGAGTCGGTGAGGCCA	60.204	61.111	5.01	0.00	36.97	5.36
3478	3556	1.536943	AAGAGTGAGTCGGTGAGGCC	61.537	60.000	0.00	0.00	0.00	5.19
3479	3557	1.174783	TAAGAGTGAGTCGGTGAGGC	58.825	55.000	0.00	0.00	0.00	4.70
3480	3558	2.480416	GCATAAGAGTGAGTCGGTGAGG	60.480	54.545	0.00	0.00	0.00	3.86
3588	3666	4.436998	GGACGACGACCTGGCCAG	62.437	72.222	26.87	26.87	0.00	4.85
3652	3730	0.454196	AACAAAAGCGCTTTCGTGGT	59.546	45.000	33.69	25.13	38.14	4.16
3661	3739	1.196200	TGCGAAAAGAACAAAAGCGC	58.804	45.000	0.00	0.00	42.87	5.92
3669	3747	6.147038	TCACTTTTGTTTTGCGAAAAGAAC	57.853	33.333	0.00	0.00	40.25	3.01
3705	3783	7.280205	GTGTACCAAGAAAAAGAAGAGAAGACA	59.720	37.037	0.00	0.00	0.00	3.41
3759	3837	2.719046	GCCGTGTGATGTTTTCTTTTCG	59.281	45.455	0.00	0.00	0.00	3.46
3788	3866	2.166254	GGTGGGTTGGTCATGCTTATTG	59.834	50.000	0.00	0.00	0.00	1.90
3835	3913	1.298339	GCGCACACACACAAAGGAC	60.298	57.895	0.30	0.00	0.00	3.85
3968	4050	8.770438	TGCCTCATTATTTATTTGTTTTCACC	57.230	30.769	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.