AutoCloner

Multiple sequence alignment - TraesCS6B01G155500

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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	TraesCS6B01G155500	chr6B	100.000	3566	0	0	1	3566	158165704	158169269	0.000000e+00	6586.0
1	TraesCS6B01G155500	chr6D	92.741	3568	206	20	1	3562	83161768	83165288	0.000000e+00	5105.0
2	TraesCS6B01G155500	chr6D	80.106	754	128	16	2064	2802	20558293	20557547	3.130000e-150	542.0
3	TraesCS6B01G155500	chr6A	93.784	3314	178	11	269	3566	100262447	100265748	0.000000e+00	4953.0
4	TraesCS6B01G155500	chr6A	84.173	278	12	15	15	279	100234204	100234462	1.280000e-59	241.0
5	TraesCS6B01G155500	chr5A	83.052	2130	298	41	787	2874	18762786	18764894	0.000000e+00	1875.0
6	TraesCS6B01G155500	chr5A	81.592	603	95	7	2962	3562	18764898	18765486	5.350000e-133	484.0
7	TraesCS6B01G155500	chr2B	83.898	1683	250	16	1206	2869	754921157	754922837	0.000000e+00	1587.0
8	TraesCS6B01G155500	chr2B	82.947	604	98	4	2962	3564	754922846	754923445	1.130000e-149	540.0
9	TraesCS6B01G155500	chr2B	82.222	90	14	2	987	1075	8636140	8636052	3.820000e-10	76.8
10	TraesCS6B01G155500	chr2B	82.222	90	14	2	987	1075	8666547	8666635	3.820000e-10	76.8
11	TraesCS6B01G155500	chr7B	83.594	1536	242	8	1207	2734	747197088	747198621	0.000000e+00	1432.0
12	TraesCS6B01G155500	chr7B	82.401	608	99	5	2963	3566	747198778	747199381	1.130000e-144	523.0
13	TraesCS6B01G155500	chr7A	82.196	1685	272	20	1207	2868	708362089	708363768	0.000000e+00	1424.0
14	TraesCS6B01G155500	chr7A	82.516	612	99	5	2959	3566	708363775	708364382	6.780000e-147	531.0
15	TraesCS6B01G155500	chr7A	95.000	40	2	0	472	511	708361118	708361157	2.970000e-06	63.9
16	TraesCS6B01G155500	chr3D	82.597	1540	253	12	1207	2735	600154336	600155871	0.000000e+00	1345.0
17	TraesCS6B01G155500	chr3D	81.038	559	85	13	3009	3561	600156100	600156643	3.290000e-115	425.0
18	TraesCS6B01G155500	chr1D	77.076	1409	292	27	1337	2732	79141607	79140217	0.000000e+00	784.0
19	TraesCS6B01G155500	chr1B	75.781	1408	312	26	1337	2732	130023877	130022487	0.000000e+00	684.0

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	TraesCS6B01G155500	chr6B	158165704	158169269	3565	False	6586.000000	6586	100.000000	1	3566	1	chr6B.!!$F1	3565
1	TraesCS6B01G155500	chr6D	83161768	83165288	3520	False	5105.000000	5105	92.741000	1	3562	1	chr6D.!!$F1	3561
2	TraesCS6B01G155500	chr6D	20557547	20558293	746	True	542.000000	542	80.106000	2064	2802	1	chr6D.!!$R1	738
3	TraesCS6B01G155500	chr6A	100262447	100265748	3301	False	4953.000000	4953	93.784000	269	3566	1	chr6A.!!$F2	3297
4	TraesCS6B01G155500	chr5A	18762786	18765486	2700	False	1179.500000	1875	82.322000	787	3562	2	chr5A.!!$F1	2775
5	TraesCS6B01G155500	chr2B	754921157	754923445	2288	False	1063.500000	1587	83.422500	1206	3564	2	chr2B.!!$F2	2358
6	TraesCS6B01G155500	chr7B	747197088	747199381	2293	False	977.500000	1432	82.997500	1207	3566	2	chr7B.!!$F1	2359
7	TraesCS6B01G155500	chr7A	708361118	708364382	3264	False	672.966667	1424	86.570667	472	3566	3	chr7A.!!$F1	3094
8	TraesCS6B01G155500	chr3D	600154336	600156643	2307	False	885.000000	1345	81.817500	1207	3561	2	chr3D.!!$F1	2354
9	TraesCS6B01G155500	chr1D	79140217	79141607	1390	True	784.000000	784	77.076000	1337	2732	1	chr1D.!!$R1	1395
10	TraesCS6B01G155500	chr1B	130022487	130023877	1390	True	684.000000	684	75.781000	1337	2732	1	chr1B.!!$R1	1395

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
616	678	0.252761	TTCCGCATGATCTGAAGCCA	59.747	50.000	0.00	0.0	0.0	4.75	F
1319	1611	2.032620	TGATCTAGAGCTTCGGAACCC	58.967	52.381	9.79	0.0	0.0	4.11	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1482	1786	1.137513	GTGTGAAAGTCGTCTTCCCG	58.862	55.000	0.0	0.0	32.9	5.14	R
2849	3204	1.724654	CGGACAAGAAAATGGCGAACG	60.725	52.381	0.0	0.0	0.0	3.95	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
22	23	4.651585	GCAGATAGCAGAGAGGCG	57.348	61.111	0.00	0.00	44.79	5.52
23	24	1.664333	GCAGATAGCAGAGAGGCGC	60.664	63.158	0.00	0.00	44.79	6.53
44	45	4.674101	CGCGATTTTTCCATGTGGTAATGT	60.674	41.667	0.00	0.00	36.34	2.71
197	198	0.320771	TTTCTCTTGCGCAGGGAGAC	60.321	55.000	30.90	0.00	31.61	3.36
237	238	0.831711	ATTGGTGGCTTGGTGTTCCC	60.832	55.000	0.00	0.00	0.00	3.97
240	241	1.179174	GGTGGCTTGGTGTTCCCTTC	61.179	60.000	0.00	0.00	0.00	3.46
302	304	0.962356	AACTTCGCTCCATTGGCCAG	60.962	55.000	5.11	0.00	0.00	4.85
332	334	1.518572	CCCCTGATTCCGTTCGTCG	60.519	63.158	0.00	0.00	39.52	5.12
337	339	4.430765	ATTCCGTTCGTCGCCGCT	62.431	61.111	0.00	0.00	38.35	5.52
365	368	4.269523	TCCGCTGGTTTGCTGCCT	62.270	61.111	0.00	0.00	0.00	4.75
470	483	5.574970	ATGTATTTCCCTTCCCAGAGATC	57.425	43.478	0.00	0.00	0.00	2.75
604	666	2.516930	CCCGGCATTCTTCCGCAT	60.517	61.111	0.00	0.00	45.19	4.73
616	678	0.252761	TTCCGCATGATCTGAAGCCA	59.747	50.000	0.00	0.00	0.00	4.75
751	813	4.285292	CAAGAACATTCCTATTGATGCGC	58.715	43.478	0.00	0.00	0.00	6.09
801	880	3.005539	AGCGTGAGGATGGCCACT	61.006	61.111	8.16	0.00	36.29	4.00
970	1052	3.081133	CGCACGACAGGGAAATCG	58.919	61.111	0.00	0.00	43.97	3.34
1261	1553	2.840038	AGGATGGCAGACATTGTACAGA	59.160	45.455	0.00	0.00	40.72	3.41
1319	1611	2.032620	TGATCTAGAGCTTCGGAACCC	58.967	52.381	9.79	0.00	0.00	4.11
1482	1786	1.869824	TTGTTGGCCCAGGGGGTATC	61.870	60.000	7.91	0.00	46.51	2.24
1503	1807	2.135933	GGGAAGACGACTTTCACACAG	58.864	52.381	8.19	0.00	36.39	3.66
1783	2090	6.157994	AGAGGCAAGAGGTAACATGGTTATTA	59.842	38.462	0.00	0.00	41.41	0.98
2096	2403	5.453762	CCAGTGACTATGACATTATGCCAGA	60.454	44.000	0.00	0.00	0.00	3.86
2463	2778	7.095899	CCATCTGTACGTCATTTGTCTATCATG	60.096	40.741	0.00	0.00	0.00	3.07
2465	2780	6.972901	TCTGTACGTCATTTGTCTATCATGAC	59.027	38.462	0.00	0.00	38.49	3.06
2669	2985	8.547967	TTCTTTTATCCGGAGCATATTATGAC	57.452	34.615	11.34	1.12	0.00	3.06
2787	3115	6.401394	TCAAGATTGTATCACCTGAGAGTTG	58.599	40.000	0.00	0.00	0.00	3.16
2823	3151	2.815158	ACAGTGTCCACCTTGGTTTTT	58.185	42.857	0.00	0.00	39.03	1.94
2833	3188	5.768164	TCCACCTTGGTTTTTCAAGAGATAC	59.232	40.000	6.21	0.00	44.98	2.24
2849	3204	7.705325	TCAAGAGATACGAGCAACCTTATAAAC	59.295	37.037	0.00	0.00	0.00	2.01
2877	3232	3.557054	CCATTTTCTTGTCCGAGACAGGA	60.557	47.826	12.57	12.57	44.68	3.86
2886	3241	0.390472	CCGAGACAGGAACCTTCAGC	60.390	60.000	0.00	0.00	0.00	4.26
2924	3285	6.991938	TGTGGGAAAACTGGAATTATTTCAG	58.008	36.000	11.43	11.43	34.31	3.02
2984	3345	6.003326	AGGTTTTGAATTTAGGCAAATTGGG	58.997	36.000	10.82	0.00	42.97	4.12
2993	3354	2.028733	GCAAATTGGGCAGTTGGCG	61.029	57.895	0.00	0.00	46.16	5.69
3088	3449	4.083324	ACTGATGCACAAAATCCACTTACG	60.083	41.667	0.00	0.00	0.00	3.18
3313	3683	2.291605	GCAATTTTCCACCTCTAGGGGT	60.292	50.000	9.09	9.09	36.70	4.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	4.562394	CACATTACCACATGGAAAAATCGC	59.438	41.667	4.53	0.00	38.94	4.58
23	24	5.948588	TCACATTACCACATGGAAAAATCG	58.051	37.500	4.53	0.91	38.94	3.34
133	134	1.302033	GTGTGCAGGTCACCAGAGG	60.302	63.158	0.00	0.00	45.03	3.69
197	198	3.889815	TGAGTGGAGGCTGAATTATTGG	58.110	45.455	0.00	0.00	0.00	3.16
302	304	4.486503	CAGGGGAGCTGAGCAGGC	62.487	72.222	7.39	0.00	0.00	4.85
390	393	1.468054	GCACAAAGATGATTGGCGTCC	60.468	52.381	0.00	0.00	34.56	4.79
470	483	4.211374	GCAACCAAGTTCAGTACACTACAG	59.789	45.833	0.00	0.00	0.00	2.74
540	571	2.158696	AGGATGGAATACTGGCTTCAGC	60.159	50.000	0.00	0.00	34.91	4.26
541	572	3.390639	AGAGGATGGAATACTGGCTTCAG	59.609	47.826	0.00	0.00	37.92	3.02
542	573	3.387962	AGAGGATGGAATACTGGCTTCA	58.612	45.455	0.00	0.00	37.92	3.02
545	576	2.971330	CAGAGAGGATGGAATACTGGCT	59.029	50.000	0.00	0.00	37.92	4.75
549	580	6.041865	CACAGAATCAGAGAGGATGGAATACT	59.958	42.308	0.00	0.00	43.38	2.12
604	666	1.421268	AGGTGTTGTGGCTTCAGATCA	59.579	47.619	0.00	0.00	0.00	2.92
616	678	3.692593	GGTTCACTTACACAAGGTGTTGT	59.307	43.478	7.37	4.92	45.08	3.32
801	880	1.448365	CACTGCCGCACTGATAGCA	60.448	57.895	0.00	0.00	0.00	3.49
934	1013	1.700955	GCGTTGTAGAGGATCCCCTA	58.299	55.000	8.55	2.78	44.53	3.53
970	1052	2.674380	CTGGAGTGCAGGGTTGGC	60.674	66.667	3.23	0.00	0.00	4.52
1261	1553	5.046014	CCTTAGCACATATAGGATCCAGCTT	60.046	44.000	15.82	0.00	32.70	3.74
1482	1786	1.137513	GTGTGAAAGTCGTCTTCCCG	58.862	55.000	0.00	0.00	32.90	5.14
1503	1807	5.346281	GCTATTCACCTCTTGATATACGTGC	59.654	44.000	0.00	0.00	32.84	5.34
1783	2090	2.169352	CCTCTGGGATTCGAGTTGTGAT	59.831	50.000	0.00	0.00	33.58	3.06
2020	2327	3.256631	ACTCTTGTCCAATTGTCCAATGC	59.743	43.478	4.43	0.00	0.00	3.56
2368	2683	6.007033	CTCTGATGAGGAGACCATCACTGG	62.007	54.167	0.00	0.00	43.67	4.00
2375	2690	2.042297	AGACACTCTGATGAGGAGACCA	59.958	50.000	0.00	0.00	44.29	4.02
2463	2778	3.182967	GTTGACATCTCCGTCATCTGTC	58.817	50.000	0.00	0.00	45.03	3.51
2465	2780	3.236632	TGTTGACATCTCCGTCATCTG	57.763	47.619	0.00	0.00	45.03	2.90
2525	2840	6.042552	TCCAGCTTTCAATTTTTCACCCAATA	59.957	34.615	0.00	0.00	0.00	1.90
2669	2985	6.429692	TGTGTAAAACATCCTCCACAACATAG	59.570	38.462	0.00	0.00	32.36	2.23
2753	3081	6.238320	GGTGATACAATCTTGAGATGTTGCTC	60.238	42.308	0.00	0.00	34.49	4.26
2787	3115	6.183360	TGGACACTGTTTTTGTCAACATCTAC	60.183	38.462	4.96	0.00	44.47	2.59
2823	3151	5.854010	ATAAGGTTGCTCGTATCTCTTGA	57.146	39.130	0.00	0.00	0.00	3.02
2833	3188	3.779992	GCGAACGTTTATAAGGTTGCTCG	60.780	47.826	0.46	0.00	39.36	5.03
2849	3204	1.724654	CGGACAAGAAAATGGCGAACG	60.725	52.381	0.00	0.00	0.00	3.95
2877	3232	5.489792	TCAGAAGTTCTATGCTGAAGGTT	57.510	39.130	4.74	0.00	34.71	3.50
2886	3241	6.656693	AGTTTTCCCACATCAGAAGTTCTATG	59.343	38.462	4.74	11.72	0.00	2.23
2984	3345	2.193536	ACCAAAGTCCGCCAACTGC	61.194	57.895	0.00	0.00	0.00	4.40
2993	3354	2.365617	TCTCAGTGAGTCACCAAAGTCC	59.634	50.000	19.71	0.00	34.49	3.85
3088	3449	4.793201	ACCCCATTCTAACATTAGCTTCC	58.207	43.478	0.00	0.00	0.00	3.46
3276	3646	5.927281	AAATTGCTCCAAGCTACATCAAT	57.073	34.783	0.11	0.00	42.97	2.57
3313	3683	6.266558	ACCAAGCTCATTAACAAACCATAACA	59.733	34.615	0.00	0.00	0.00	2.41
3317	3687	4.832266	TCACCAAGCTCATTAACAAACCAT	59.168	37.500	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.