AutoCloner

Multiple sequence alignment - TraesCS6B01G042100

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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	TraesCS6B01G042100	chr6B	100.000	3365	0	0	1	3365	25957237	25960601	0.000000e+00	6215.0
1	TraesCS6B01G042100	chr2A	99.131	3337	27	2	31	3365	25040209	25036873	0.000000e+00	6000.0
2	TraesCS6B01G042100	chr2A	81.926	675	122	0	2691	3365	751722128	751722802	3.770000e-159	571.0
3	TraesCS6B01G042100	chr6D	98.923	1672	16	2	1695	3365	5494961	5496631	0.000000e+00	2987.0
4	TraesCS6B01G042100	chr6D	98.240	966	17	0	745	1710	5493964	5494929	0.000000e+00	1690.0
5	TraesCS6B01G042100	chr6D	96.208	712	24	2	33	741	5493205	5493916	0.000000e+00	1162.0
6	TraesCS6B01G042100	chr3B	99.246	663	5	0	745	1407	22075835	22075173	0.000000e+00	1197.0
7	TraesCS6B01G042100	chr3B	95.967	719	20	4	32	741	22076601	22075883	0.000000e+00	1158.0
8	TraesCS6B01G042100	chr3B	99.296	142	1	0	3224	3365	22075175	22075034	1.200000e-64	257.0
9	TraesCS6B01G042100	chr3B	72.494	389	94	11	1305	1688	125866249	125866629	2.740000e-21	113.0
10	TraesCS6B01G042100	chr1B	99.246	663	4	1	745	1407	7414532	7415193	0.000000e+00	1195.0
11	TraesCS6B01G042100	chr1B	96.503	715	21	4	31	741	7413770	7414484	0.000000e+00	1179.0
12	TraesCS6B01G042100	chr1B	99.296	142	1	0	3224	3365	7415191	7415332	1.200000e-64	257.0
13	TraesCS6B01G042100	chr1B	94.872	39	2	0	4	42	434418134	434418096	1.010000e-05	62.1
14	TraesCS6B01G042100	chr4D	98.908	458	5	0	2903	3360	430796499	430796956	0.000000e+00	819.0
15	TraesCS6B01G042100	chr1A	83.099	639	102	6	2691	3326	52566309	52566944	8.100000e-161	577.0
16	TraesCS6B01G042100	chr1A	82.547	636	106	5	2691	3324	52561325	52560693	3.790000e-154	555.0
17	TraesCS6B01G042100	chr1A	92.308	39	3	0	4	42	477033551	477033513	4.690000e-04	56.5
18	TraesCS6B01G042100	chr5A	77.138	1076	139	67	33	1051	546793161	546792136	2.970000e-145	525.0
19	TraesCS6B01G042100	chr5A	72.895	380	90	11	1314	1688	694511823	694511452	5.900000e-23	119.0
20	TraesCS6B01G042100	chr7A	85.904	376	53	0	2949	3324	208088988	208089363	5.230000e-108	401.0
21	TraesCS6B01G042100	chr5B	78.295	258	52	4	2091	2345	70441046	70441302	2.690000e-36	163.0
22	TraesCS6B01G042100	chr5B	94.595	37	2	0	7	43	589996980	589996944	1.300000e-04	58.4
23	TraesCS6B01G042100	chr1D	72.895	380	90	11	1314	1688	172863844	172863473	5.900000e-23	119.0
24	TraesCS6B01G042100	chr2B	72.632	380	91	11	1314	1688	777556645	777556274	2.740000e-21	113.0
25	TraesCS6B01G042100	chr2B	94.737	38	2	0	4	41	528572895	528572932	3.630000e-05	60.2
26	TraesCS6B01G042100	chrUn	81.651	109	16	4	1311	1417	74787545	74787651	1.660000e-13	87.9
27	TraesCS6B01G042100	chrUn	94.737	38	2	0	5	42	24697969	24697932	3.630000e-05	60.2
28	TraesCS6B01G042100	chr7D	90.698	43	4	0	1	43	439239035	439239077	1.300000e-04	58.4
29	TraesCS6B01G042100	chr7D	92.308	39	3	0	4	42	49828864	49828826	4.690000e-04	56.5
30	TraesCS6B01G042100	chr3D	92.308	39	3	0	4	42	20348849	20348811	4.690000e-04	56.5
31	TraesCS6B01G042100	chr2D	90.909	44	1	3	1	42	87247304	87247262	4.690000e-04	56.5

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	TraesCS6B01G042100	chr6B	25957237	25960601	3364	False	6215.000000	6215	100.000000	1	3365	1	chr6B.!!$F1	3364
1	TraesCS6B01G042100	chr2A	25036873	25040209	3336	True	6000.000000	6000	99.131000	31	3365	1	chr2A.!!$R1	3334
2	TraesCS6B01G042100	chr2A	751722128	751722802	674	False	571.000000	571	81.926000	2691	3365	1	chr2A.!!$F1	674
3	TraesCS6B01G042100	chr6D	5493205	5496631	3426	False	1946.333333	2987	97.790333	33	3365	3	chr6D.!!$F1	3332
4	TraesCS6B01G042100	chr3B	22075034	22076601	1567	True	870.666667	1197	98.169667	32	3365	3	chr3B.!!$R1	3333
5	TraesCS6B01G042100	chr1B	7413770	7415332	1562	False	877.000000	1195	98.348333	31	3365	3	chr1B.!!$F1	3334
6	TraesCS6B01G042100	chr1A	52566309	52566944	635	False	577.000000	577	83.099000	2691	3326	1	chr1A.!!$F1	635
7	TraesCS6B01G042100	chr1A	52560693	52561325	632	True	555.000000	555	82.547000	2691	3324	1	chr1A.!!$R1	633
8	TraesCS6B01G042100	chr5A	546792136	546793161	1025	True	525.000000	525	77.138000	33	1051	1	chr5A.!!$R1	1018

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
661	702	0.539986	GTTGATGGTAGGGGCGAAGA	59.460	55.0	0.0	0.0	0.0	2.87	F
918	1026	5.016173	AGTGCTGTATTTTTATGCCTTGGA	58.984	37.5	0.0	0.0	0.0	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1778	1887	0.745468	AGATCTTCCTTCGGCGTACC	59.255	55.0	6.85	0.0	0.0	3.34	R
2894	3003	0.951558	ATCCGTGGCTTGTTGTGTTC	59.048	50.0	0.00	0.0	0.0	3.18	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
20	21	2.955342	AGATAGTACTCCCTCCGTCC	57.045	55.000	0.00	0.00	0.00	4.79
21	22	1.424684	AGATAGTACTCCCTCCGTCCC	59.575	57.143	0.00	0.00	0.00	4.46
22	23	1.144503	GATAGTACTCCCTCCGTCCCA	59.855	57.143	0.00	0.00	0.00	4.37
23	24	1.229131	TAGTACTCCCTCCGTCCCAT	58.771	55.000	0.00	0.00	0.00	4.00
24	25	1.229131	AGTACTCCCTCCGTCCCATA	58.771	55.000	0.00	0.00	0.00	2.74
25	26	1.572415	AGTACTCCCTCCGTCCCATAA	59.428	52.381	0.00	0.00	0.00	1.90
26	27	2.179424	AGTACTCCCTCCGTCCCATAAT	59.821	50.000	0.00	0.00	0.00	1.28
27	28	1.424638	ACTCCCTCCGTCCCATAATG	58.575	55.000	0.00	0.00	0.00	1.90
28	29	1.344087	ACTCCCTCCGTCCCATAATGT	60.344	52.381	0.00	0.00	0.00	2.71
29	30	2.090943	ACTCCCTCCGTCCCATAATGTA	60.091	50.000	0.00	0.00	0.00	2.29
58	59	7.093322	CTTCTTTGGATCGAAGGATTTTCAT	57.907	36.000	3.16	0.00	34.45	2.57
63	64	6.247229	TGGATCGAAGGATTTTCATAGGAA	57.753	37.500	0.00	0.00	31.51	3.36
64	65	6.055588	TGGATCGAAGGATTTTCATAGGAAC	58.944	40.000	0.00	0.00	31.51	3.62
221	228	1.661112	GGAAAGATTCCTGACGCGAAG	59.339	52.381	15.93	10.12	46.57	3.79
661	702	0.539986	GTTGATGGTAGGGGCGAAGA	59.460	55.000	0.00	0.00	0.00	2.87
918	1026	5.016173	AGTGCTGTATTTTTATGCCTTGGA	58.984	37.500	0.00	0.00	0.00	3.53
1779	1888	2.945447	TTGTTGGACGTATAGGTCGG	57.055	50.000	17.01	0.00	37.82	4.79
2091	2200	4.013050	AGAAGCAAAATCCTACAAGCTCC	58.987	43.478	0.00	0.00	0.00	4.70
2177	2286	4.810191	TTGAGGAGAAGAAACTAGAGGC	57.190	45.455	0.00	0.00	0.00	4.70
2819	2928	3.930229	CCATTTGGCACATCAACAATCTG	59.070	43.478	0.00	0.00	39.30	2.90
2894	3003	3.373748	TGTAGGCGTATGAAATTGTGCAG	59.626	43.478	0.00	0.00	0.00	4.41
3033	3142	2.844946	TGAGCATGACGAAGGTTGAAA	58.155	42.857	0.00	0.00	0.00	2.69
3263	5238	7.075121	TGTACATGCACAAATTTTAAGTCGAG	58.925	34.615	0.00	0.00	0.00	4.04

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.641815	GGGACGGAGGGAGTACTATCTA	59.358	54.545	0.00	0.00	0.00	1.98
1	2	1.424684	GGGACGGAGGGAGTACTATCT	59.575	57.143	0.00	0.00	0.00	1.98
2	3	1.144503	TGGGACGGAGGGAGTACTATC	59.855	57.143	0.00	0.00	0.00	2.08
3	4	1.229131	TGGGACGGAGGGAGTACTAT	58.771	55.000	0.00	0.00	0.00	2.12
4	5	1.229131	ATGGGACGGAGGGAGTACTA	58.771	55.000	0.00	0.00	0.00	1.82
5	6	1.229131	TATGGGACGGAGGGAGTACT	58.771	55.000	0.00	0.00	0.00	2.73
6	7	2.077687	TTATGGGACGGAGGGAGTAC	57.922	55.000	0.00	0.00	0.00	2.73
7	8	2.090943	ACATTATGGGACGGAGGGAGTA	60.091	50.000	0.00	0.00	0.00	2.59
8	9	1.344087	ACATTATGGGACGGAGGGAGT	60.344	52.381	0.00	0.00	0.00	3.85
9	10	1.424638	ACATTATGGGACGGAGGGAG	58.575	55.000	0.00	0.00	0.00	4.30
10	11	2.779429	TACATTATGGGACGGAGGGA	57.221	50.000	0.00	0.00	0.00	4.20
11	12	2.038557	CCTTACATTATGGGACGGAGGG	59.961	54.545	0.00	0.00	0.00	4.30
12	13	2.550208	GCCTTACATTATGGGACGGAGG	60.550	54.545	0.00	0.00	0.00	4.30
13	14	2.550208	GGCCTTACATTATGGGACGGAG	60.550	54.545	0.00	0.00	0.00	4.63
14	15	1.418637	GGCCTTACATTATGGGACGGA	59.581	52.381	0.00	0.00	0.00	4.69
15	16	1.420138	AGGCCTTACATTATGGGACGG	59.580	52.381	0.00	0.00	30.99	4.79
16	17	2.930826	AGGCCTTACATTATGGGACG	57.069	50.000	0.00	0.00	30.99	4.79
17	18	4.439253	AGAAGGCCTTACATTATGGGAC	57.561	45.455	20.54	0.55	0.00	4.46
18	19	5.200483	CAAAGAAGGCCTTACATTATGGGA	58.800	41.667	20.54	0.00	34.00	4.37
19	20	4.342092	CCAAAGAAGGCCTTACATTATGGG	59.658	45.833	20.54	11.93	34.00	4.00
20	21	5.200483	TCCAAAGAAGGCCTTACATTATGG	58.800	41.667	20.54	19.45	34.00	2.74
21	22	6.293626	CGATCCAAAGAAGGCCTTACATTATG	60.294	42.308	20.54	11.54	34.00	1.90
22	23	5.765182	CGATCCAAAGAAGGCCTTACATTAT	59.235	40.000	20.54	8.18	34.00	1.28
23	24	5.104693	TCGATCCAAAGAAGGCCTTACATTA	60.105	40.000	20.54	3.00	34.00	1.90
24	25	3.947834	CGATCCAAAGAAGGCCTTACATT	59.052	43.478	20.54	11.12	34.00	2.71
25	26	3.199946	TCGATCCAAAGAAGGCCTTACAT	59.800	43.478	20.54	4.55	34.00	2.29
26	27	2.569853	TCGATCCAAAGAAGGCCTTACA	59.430	45.455	20.54	0.00	34.00	2.41
27	28	3.261981	TCGATCCAAAGAAGGCCTTAC	57.738	47.619	20.54	12.29	34.00	2.34
28	29	3.873910	CTTCGATCCAAAGAAGGCCTTA	58.126	45.455	20.54	0.89	39.94	2.69
29	30	2.716217	CTTCGATCCAAAGAAGGCCTT	58.284	47.619	20.65	20.65	39.94	4.35
58	59	5.475564	GGTTTACAATCCAGCAAAGTTCCTA	59.524	40.000	0.00	0.00	0.00	2.94
63	64	4.469657	TGAGGTTTACAATCCAGCAAAGT	58.530	39.130	0.00	0.00	0.00	2.66
64	65	4.082571	CCTGAGGTTTACAATCCAGCAAAG	60.083	45.833	0.00	0.00	0.00	2.77
159	160	0.693049	AATTCCTCTGGGTTCAGCGT	59.307	50.000	0.00	0.00	40.69	5.07
214	221	0.110147	CGAACACTCTCTCTTCGCGT	60.110	55.000	5.77	0.00	31.26	6.01
221	228	0.944311	TTTGGCGCGAACACTCTCTC	60.944	55.000	12.10	0.00	0.00	3.20
374	413	2.190578	CGGGGGATCTGACCTTGC	59.809	66.667	0.00	0.00	0.00	4.01
498	539	1.190643	TGGACGGACTATGTGATGCA	58.809	50.000	0.00	0.00	0.00	3.96
661	702	4.148825	GGACGCCAGCGACATCCT	62.149	66.667	20.32	0.00	42.83	3.24
918	1026	4.186926	CAAGCATGTATGAGCAGTACACT	58.813	43.478	0.00	0.00	35.11	3.55
1778	1887	0.745468	AGATCTTCCTTCGGCGTACC	59.255	55.000	6.85	0.00	0.00	3.34
1779	1888	1.597445	CGAGATCTTCCTTCGGCGTAC	60.597	57.143	6.85	0.00	0.00	3.67
2091	2200	3.208594	TCTTTCATGGAATCCATCTGCG	58.791	45.455	12.63	1.12	43.15	5.18
2177	2286	4.082625	TGCACTTGTGAATGCTAAATGGAG	60.083	41.667	4.79	0.00	42.55	3.86
2484	2593	7.676947	ACAGAGGTCTAGTAAACAAAAGCATA	58.323	34.615	0.00	0.00	0.00	3.14
2819	2928	1.668419	CATGGAGATTGACCCGAACC	58.332	55.000	0.00	0.00	0.00	3.62
2894	3003	0.951558	ATCCGTGGCTTGTTGTGTTC	59.048	50.000	0.00	0.00	0.00	3.18
3033	3142	6.186420	AGGCCACAAAATTACAAGGAATTT	57.814	33.333	5.01	0.00	40.03	1.82
3263	5238	1.317613	TGTCATGGTTGCTTGTGACC	58.682	50.000	0.00	0.00	40.07	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.