AutoCloner

Multiple sequence alignment - TraesCS3B01G049400

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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	TraesCS3B01G049400	chr3B	100.000	2699	0	0	1	2699	24932342	24935040	0.000000e+00	4985
1	TraesCS3B01G049400	chr3B	79.448	652	103	14	1013	1657	30363602	30364229	1.480000e-117	433
2	TraesCS3B01G049400	chr3B	79.237	655	99	19	1013	1657	29976626	29977253	3.210000e-114	422
3	TraesCS3B01G049400	chr3B	79.785	465	75	8	1197	1657	29981207	29981656	1.210000e-83	320
4	TraesCS3B01G049400	chr3D	85.994	1785	169	28	282	2015	17361277	17363031	0.000000e+00	1836
5	TraesCS3B01G049400	chr3D	82.875	1092	147	20	670	1743	17533165	17532096	0.000000e+00	944
6	TraesCS3B01G049400	chr3D	90.120	668	55	9	2035	2699	17363551	17364210	0.000000e+00	857
7	TraesCS3B01G049400	chr3D	82.918	562	48	20	2	523	17528336	17527783	1.890000e-126	462
8	TraesCS3B01G049400	chr3D	84.753	446	38	12	100	523	17533849	17533412	1.160000e-113	420
9	TraesCS3B01G049400	chr3D	80.600	433	68	8	967	1392	11335686	11336109	1.210000e-83	320
10	TraesCS3B01G049400	chr3D	82.609	322	35	9	665	985	17527548	17527247	5.730000e-67	265
11	TraesCS3B01G049400	chr3D	88.350	103	12	0	1173	1275	17527244	17527142	1.010000e-24	124
12	TraesCS3B01G049400	chr3A	85.592	1402	129	27	665	2015	19486432	19485053	0.000000e+00	1402
13	TraesCS3B01G049400	chr3A	83.608	1092	139	19	667	1743	19357266	19358332	0.000000e+00	989
14	TraesCS3B01G049400	chr3A	89.767	645	56	7	2035	2675	19484636	19483998	0.000000e+00	817
15	TraesCS3B01G049400	chr3A	82.983	523	49	14	3	490	19487085	19486568	1.150000e-118	436
16	TraesCS3B01G049400	chr3A	77.855	718	119	13	1015	1719	26413685	26414375	2.500000e-110	409
17	TraesCS3B01G049400	chr3A	77.893	579	78	24	1173	1722	19283677	19284234	5.610000e-82	315
18	TraesCS3B01G049400	chr3A	77.799	527	83	14	1238	1752	26449965	26450469	7.310000e-76	294
19	TraesCS3B01G049400	chr3A	74.725	728	139	23	1007	1718	26245526	26246224	1.580000e-72	283
20	TraesCS3B01G049400	chr3A	81.657	338	29	11	212	523	19356365	19356695	1.600000e-62	250
21	TraesCS3B01G049400	chr3A	92.708	96	6	1	114	209	19356031	19356125	1.300000e-28	137
22	TraesCS3B01G049400	chr7B	73.038	497	96	17	1077	1567	64280275	64280739	1.010000e-29	141

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	TraesCS3B01G049400	chr3B	24932342	24935040	2698	False	4985.000000	4985	100.000	1	2699	1	chr3B.!!$F1	2698
1	TraesCS3B01G049400	chr3B	30363602	30364229	627	False	433.000000	433	79.448	1013	1657	1	chr3B.!!$F2	644
2	TraesCS3B01G049400	chr3B	29976626	29981656	5030	False	371.000000	422	79.511	1013	1657	2	chr3B.!!$F3	644
3	TraesCS3B01G049400	chr3D	17361277	17364210	2933	False	1346.500000	1836	88.057	282	2699	2	chr3D.!!$F2	2417
4	TraesCS3B01G049400	chr3D	17527142	17533849	6707	True	443.000000	944	84.301	2	1743	5	chr3D.!!$R1	1741
5	TraesCS3B01G049400	chr3A	19483998	19487085	3087	True	885.000000	1402	86.114	3	2675	3	chr3A.!!$R1	2672
6	TraesCS3B01G049400	chr3A	19356031	19358332	2301	False	458.666667	989	85.991	114	1743	3	chr3A.!!$F5	1629
7	TraesCS3B01G049400	chr3A	26413685	26414375	690	False	409.000000	409	77.855	1015	1719	1	chr3A.!!$F3	704
8	TraesCS3B01G049400	chr3A	19283677	19284234	557	False	315.000000	315	77.893	1173	1722	1	chr3A.!!$F1	549
9	TraesCS3B01G049400	chr3A	26449965	26450469	504	False	294.000000	294	77.799	1238	1752	1	chr3A.!!$F4	514
10	TraesCS3B01G049400	chr3A	26245526	26246224	698	False	283.000000	283	74.725	1007	1718	1	chr3A.!!$F2	711

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
856	1592	0.112412	AGCGGTGGTTGAGGGAATTT	59.888	50.0	0.0	0.0	0.0	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2563	8633	0.976641	TCGAGCACATCTCCTGGTTT	59.023	50.0	0.0	0.0	38.62	3.27	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	5.458779	AGCGACACTTTGCTTTTATTGTTTC	59.541	36.000	0.00	0.00	39.78	2.78
36	37	5.523552	ACACTTTGCTTTTATTGTTTCCTGC	59.476	36.000	0.00	0.00	0.00	4.85
43	44	6.159293	GCTTTTATTGTTTCCTGCTTAAGCT	58.841	36.000	26.90	7.12	42.66	3.74
51	52	4.634012	TTCCTGCTTAAGCTACCAAGAA	57.366	40.909	26.90	16.43	42.66	2.52
62	63	5.695851	AGCTACCAAGAACTGAAAACATG	57.304	39.130	0.00	0.00	0.00	3.21
76	77	1.341080	AACATGCCTTGAAACTGGGG	58.659	50.000	0.00	0.00	0.00	4.96
77	78	0.188342	ACATGCCTTGAAACTGGGGT	59.812	50.000	0.00	0.00	0.00	4.95
102	115	1.133325	TGGCCCTTAGTTTTTCAGCCA	60.133	47.619	0.00	0.00	46.16	4.75
155	168	1.298014	GCCACTGTCTCCCCTTCTG	59.702	63.158	0.00	0.00	0.00	3.02
194	207	3.648982	CGTGCTCGTTGGCAAGCA	61.649	61.111	8.22	8.22	45.83	3.91
201	214	2.192861	CGTTGGCAAGCAACCTCCA	61.193	57.895	0.00	0.00	0.00	3.86
240	490	2.286872	GTCAGGCACCATTGATCTCTG	58.713	52.381	0.00	0.00	0.00	3.35
279	529	2.220479	GAGGTTACTCGCCGCTAATT	57.780	50.000	0.00	0.00	33.35	1.40
328	598	0.673644	TAACTCTGGAAAGGCTGCGC	60.674	55.000	0.00	0.00	0.00	6.09
404	674	7.203255	AGAATCGTTTTTCTTTTCCCTGTAG	57.797	36.000	0.00	0.00	31.94	2.74
600	1305	6.701841	TCTTTTTCATCGGATACTGACATAGC	59.298	38.462	0.00	0.00	0.00	2.97
625	1330	4.422073	ACCTGTCAAGTCTGAATGTTGA	57.578	40.909	0.00	0.00	31.88	3.18
662	1377	4.929808	TCTGGCATCTAAAACTTTCTCGAC	59.070	41.667	0.00	0.00	0.00	4.20
677	1408	4.352600	TCTCGACGAAGGAATCTTGTAC	57.647	45.455	0.00	0.00	32.52	2.90
712	1445	2.311124	AAGCATGAAGTAGCCGGTAC	57.689	50.000	1.90	4.64	0.00	3.34
765	1499	1.147153	TCACATCACGGGCACACAA	59.853	52.632	0.00	0.00	0.00	3.33
774	1508	0.888736	CGGGCACACAAAGGTCATGA	60.889	55.000	0.00	0.00	0.00	3.07
806	1542	2.682856	CCCGTCAATGGTGTTAGGATTG	59.317	50.000	0.00	0.00	0.00	2.67
827	1563	1.672881	GAGATTCAGAAACCATGGCCG	59.327	52.381	13.04	0.00	0.00	6.13
856	1592	0.112412	AGCGGTGGTTGAGGGAATTT	59.888	50.000	0.00	0.00	0.00	1.82

Showing 1 to 25 of 73 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	6.292328	GCAGGAAACAATAAAAGCAAAGTGTC	60.292	38.462	0.00	0.00	0.00	3.67
12	13	5.523552	GCAGGAAACAATAAAAGCAAAGTGT	59.476	36.000	0.00	0.00	0.00	3.55
15	16	6.849588	AAGCAGGAAACAATAAAAGCAAAG	57.150	33.333	0.00	0.00	0.00	2.77
32	33	3.686726	CAGTTCTTGGTAGCTTAAGCAGG	59.313	47.826	28.39	9.10	45.16	4.85
36	37	7.259290	TGTTTTCAGTTCTTGGTAGCTTAAG	57.741	36.000	0.00	0.00	0.00	1.85
43	44	4.469657	AGGCATGTTTTCAGTTCTTGGTA	58.530	39.130	0.00	0.00	0.00	3.25
51	52	4.441913	CCAGTTTCAAGGCATGTTTTCAGT	60.442	41.667	0.00	0.00	0.00	3.41
82	83	1.133325	TGGCTGAAAAACTAAGGGCCA	60.133	47.619	6.18	0.00	44.55	5.36
118	131	1.460504	CATGTTGCATCTCAGCCACT	58.539	50.000	0.00	0.00	31.94	4.00
119	132	0.179145	GCATGTTGCATCTCAGCCAC	60.179	55.000	0.00	0.00	44.26	5.01
155	168	4.491602	CGAGAACAAAACGAGATGAGATGC	60.492	45.833	0.00	0.00	0.00	3.91
201	214	5.468540	TGACAGAAACACTACAGTATGCT	57.531	39.130	0.00	0.00	42.53	3.79
240	490	1.302832	CTGGAGTTGGGTGGAGCAC	60.303	63.158	0.00	0.00	0.00	4.40
328	598	1.539065	CCTGTTATGTGCTAGGAGCGG	60.539	57.143	0.00	0.00	46.26	5.52
339	609	0.685097	ACGGAGTGCACCTGTTATGT	59.315	50.000	14.63	0.00	42.51	2.29
404	674	7.439655	GGATAGGTTTGTACAGAGATCACATTC	59.560	40.741	0.00	0.00	0.00	2.67
471	743	7.372396	CGTCGACCAAAAATACATATTAAGCAC	59.628	37.037	10.58	0.00	0.00	4.40
472	744	7.278203	TCGTCGACCAAAAATACATATTAAGCA	59.722	33.333	10.58	0.00	0.00	3.91
473	745	7.623770	TCGTCGACCAAAAATACATATTAAGC	58.376	34.615	10.58	0.00	0.00	3.09
505	780	5.123979	GCAAATTTTAGTCCAGACGGAGATT	59.876	40.000	0.00	0.00	43.99	2.40
506	781	4.636206	GCAAATTTTAGTCCAGACGGAGAT	59.364	41.667	0.00	0.00	43.99	2.75
507	782	4.000988	GCAAATTTTAGTCCAGACGGAGA	58.999	43.478	0.00	0.00	43.99	3.71
508	783	3.751175	TGCAAATTTTAGTCCAGACGGAG	59.249	43.478	0.00	0.00	43.99	4.63
509	784	3.500680	GTGCAAATTTTAGTCCAGACGGA	59.499	43.478	0.00	0.00	39.79	4.69
600	1305	6.427853	TCAACATTCAGACTTGACAGGTAATG	59.572	38.462	9.11	9.11	31.71	1.90

Showing 1 to 25 of 93 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.