AutoCloner

Multiple sequence alignment - TraesCS5A01G545200

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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	TraesCS5A01G545200	chr5A	100.000	2830	0	0	1	2830	700371322	700374151	0.000000e+00	5227.0
1	TraesCS5A01G545200	chr5A	92.393	2432	130	37	439	2830	699561648	699564064	0.000000e+00	3415.0
2	TraesCS5A01G545200	chr5A	94.940	2174	84	18	671	2830	699708136	699710297	0.000000e+00	3382.0
3	TraesCS5A01G545200	chr5A	94.718	2177	86	21	671	2830	699629488	699631652	0.000000e+00	3356.0
4	TraesCS5A01G545200	chr5A	100.000	33	0	0	345	377	699571904	699571936	8.470000e-06	62.1
5	TraesCS5A01G545200	chr5A	100.000	33	0	0	345	377	699639593	699639625	8.470000e-06	62.1
6	TraesCS5A01G545200	chrUn	92.393	2432	130	37	439	2830	278955344	278952928	0.000000e+00	3415.0
7	TraesCS5A01G545200	chrUn	90.369	2357	169	35	438	2769	110271527	110269204	0.000000e+00	3042.0
8	TraesCS5A01G545200	chrUn	90.119	2358	173	37	438	2769	110209123	110206800	0.000000e+00	3009.0
9	TraesCS5A01G545200	chrUn	90.830	1614	129	11	1157	2757	110306215	110304608	0.000000e+00	2143.0
10	TraesCS5A01G545200	chrUn	90.830	1614	129	11	1157	2757	110320435	110318828	0.000000e+00	2143.0
11	TraesCS5A01G545200	chrUn	90.830	1614	129	11	1157	2757	187710510	187708903	0.000000e+00	2143.0
12	TraesCS5A01G545200	chrUn	92.654	667	35	10	1	661	110328008	110327350	0.000000e+00	948.0
13	TraesCS5A01G545200	chrUn	82.262	389	57	9	831	1209	190755937	190756323	2.720000e-85	326.0
14	TraesCS5A01G545200	chrUn	96.104	77	3	0	2754	2830	110206767	110206691	2.960000e-25	126.0
15	TraesCS5A01G545200	chrUn	93.506	77	5	0	2754	2830	110269171	110269095	6.410000e-22	115.0
16	TraesCS5A01G545200	chrUn	88.462	78	5	2	521	594	184188259	184188336	1.080000e-14	91.6
17	TraesCS5A01G545200	chrUn	88.462	78	5	2	521	594	184215927	184216004	1.080000e-14	91.6
18	TraesCS5A01G545200	chrUn	88.462	78	5	2	521	594	247790167	247790090	1.080000e-14	91.6
19	TraesCS5A01G545200	chrUn	88.462	78	5	2	521	594	263570098	263570021	1.080000e-14	91.6
20	TraesCS5A01G545200	chrUn	88.462	78	5	2	521	594	272712116	272712039	1.080000e-14	91.6
21	TraesCS5A01G545200	chrUn	88.462	78	5	2	521	594	303326100	303326023	1.080000e-14	91.6
22	TraesCS5A01G545200	chrUn	77.372	137	28	2	460	594	156634949	156635084	8.410000e-11	78.7
23	TraesCS5A01G545200	chrUn	100.000	33	0	0	345	377	156740367	156740399	8.470000e-06	62.1
24	TraesCS5A01G545200	chr4B	89.236	2750	206	38	1	2685	660447440	660444716	0.000000e+00	3356.0
25	TraesCS5A01G545200	chr4B	90.896	2076	142	20	1	2044	660418132	660416072	0.000000e+00	2743.0
26	TraesCS5A01G545200	chr4B	83.690	1214	157	25	799	1993	660248184	660246993	0.000000e+00	1107.0
27	TraesCS5A01G545200	chr4B	82.393	1329	173	36	800	2104	660337354	660336063	0.000000e+00	1101.0
28	TraesCS5A01G545200	chr4B	77.536	138	26	4	460	594	660284868	660284733	8.410000e-11	78.7
29	TraesCS5A01G545200	chr4B	94.737	38	1	1	345	382	660322838	660322802	1.100000e-04	58.4

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	TraesCS5A01G545200	chr5A	700371322	700374151	2829	False	5227.0	5227	100.0000	1	2830	1	chr5A.!!$F6	2829
1	TraesCS5A01G545200	chr5A	699561648	699564064	2416	False	3415.0	3415	92.3930	439	2830	1	chr5A.!!$F1	2391
2	TraesCS5A01G545200	chr5A	699708136	699710297	2161	False	3382.0	3382	94.9400	671	2830	1	chr5A.!!$F5	2159
3	TraesCS5A01G545200	chr5A	699629488	699631652	2164	False	3356.0	3356	94.7180	671	2830	1	chr5A.!!$F3	2159
4	TraesCS5A01G545200	chrUn	278952928	278955344	2416	True	3415.0	3415	92.3930	439	2830	1	chrUn.!!$R8	2391
5	TraesCS5A01G545200	chrUn	110304608	110306215	1607	True	2143.0	2143	90.8300	1157	2757	1	chrUn.!!$R1	1600
6	TraesCS5A01G545200	chrUn	110318828	110320435	1607	True	2143.0	2143	90.8300	1157	2757	1	chrUn.!!$R2	1600
7	TraesCS5A01G545200	chrUn	187708903	187710510	1607	True	2143.0	2143	90.8300	1157	2757	1	chrUn.!!$R4	1600
8	TraesCS5A01G545200	chrUn	110269095	110271527	2432	True	1578.5	3042	91.9375	438	2830	2	chrUn.!!$R11	2392
9	TraesCS5A01G545200	chrUn	110206691	110209123	2432	True	1567.5	3009	93.1115	438	2830	2	chrUn.!!$R10	2392
10	TraesCS5A01G545200	chrUn	110327350	110328008	658	True	948.0	948	92.6540	1	661	1	chrUn.!!$R3	660
11	TraesCS5A01G545200	chr4B	660444716	660447440	2724	True	3356.0	3356	89.2360	1	2685	1	chr4B.!!$R6	2684
12	TraesCS5A01G545200	chr4B	660416072	660418132	2060	True	2743.0	2743	90.8960	1	2044	1	chr4B.!!$R5	2043
13	TraesCS5A01G545200	chr4B	660246993	660248184	1191	True	1107.0	1107	83.6900	799	1993	1	chr4B.!!$R1	1194
14	TraesCS5A01G545200	chr4B	660336063	660337354	1291	True	1101.0	1101	82.3930	800	2104	1	chr4B.!!$R4	1304

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
894	967	0.409092	TCCATTGCCCACAGGTTCAT	59.591	50.0	0.0	0.0	34.57	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2068	2187	3.518992	TCGGAACAAGGGGAAAAGAAT	57.481	42.857	0.0	0.0	0.0	2.4	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
58	59	3.041469	GCTGGGCAGGGAGAAGGAG	62.041	68.421	0.00	0.00	0.00	3.69
61	62	3.803162	GGCAGGGAGAAGGAGGGC	61.803	72.222	0.00	0.00	0.00	5.19
94	95	2.040464	ATCCAGGAGGCGGTGGAT	60.040	61.111	11.23	11.23	46.56	3.41
97	98	2.671070	CAGGAGGCGGTGGATGTT	59.329	61.111	0.00	0.00	0.00	2.71
209	219	2.123077	CCCGCTCCTCCTCCTCAT	60.123	66.667	0.00	0.00	0.00	2.90
210	220	2.206536	CCCGCTCCTCCTCCTCATC	61.207	68.421	0.00	0.00	0.00	2.92
211	221	2.206536	CCGCTCCTCCTCCTCATCC	61.207	68.421	0.00	0.00	0.00	3.51
212	222	1.152567	CGCTCCTCCTCCTCATCCT	60.153	63.158	0.00	0.00	0.00	3.24
213	223	1.178534	CGCTCCTCCTCCTCATCCTC	61.179	65.000	0.00	0.00	0.00	3.71
273	283	1.030488	CCAGAGAAGGCTGCCATGTG	61.030	60.000	22.65	14.16	34.56	3.21
285	295	3.631144	CTGCCATGTGTGTTGTTGTAAG	58.369	45.455	0.00	0.00	0.00	2.34
387	401	4.157105	TGAACTGGTCATGCATGATGAAAG	59.843	41.667	30.89	24.52	42.96	2.62
462	491	3.429141	ATCGCCGTGTCGTCGTCT	61.429	61.111	0.00	0.00	0.00	4.18
474	503	1.782181	GTCGTCTTCGCTTCTTGCC	59.218	57.895	0.00	0.00	38.78	4.52
480	509	3.254014	TTCGCTTCTTGCCGCAAGC	62.254	57.895	25.53	15.65	40.84	4.01
489	518	2.980233	GCCGCAAGCACTCAACCT	60.980	61.111	0.00	0.00	42.97	3.50
656	689	9.201989	ACAATCCAGACTGTTACTCATATCTAA	57.798	33.333	0.93	0.00	0.00	2.10
661	694	8.519526	CCAGACTGTTACTCATATCTAATCCTC	58.480	40.741	0.93	0.00	0.00	3.71
662	695	9.072375	CAGACTGTTACTCATATCTAATCCTCA	57.928	37.037	0.00	0.00	0.00	3.86
663	696	9.295825	AGACTGTTACTCATATCTAATCCTCAG	57.704	37.037	0.00	0.00	0.00	3.35
664	697	7.891561	ACTGTTACTCATATCTAATCCTCAGC	58.108	38.462	0.00	0.00	0.00	4.26
665	698	7.039363	ACTGTTACTCATATCTAATCCTCAGCC	60.039	40.741	0.00	0.00	0.00	4.85
694	758	5.744171	TCAGATGGAGTAGCTTAATTTGCA	58.256	37.500	0.00	0.00	0.00	4.08
739	803	2.092323	GGAAATGTGTCCCTAAGGCAC	58.908	52.381	0.00	0.00	39.33	5.01
792	862	5.392380	CAAAGATTTGAGTATGGCTGACCAC	60.392	44.000	0.00	0.00	44.39	4.16
810	880	3.059188	ACCACGTCTCAAAAGTTTATGCG	60.059	43.478	0.00	0.00	0.00	4.73
888	959	2.292267	GACTATGTCCATTGCCCACAG	58.708	52.381	0.00	0.00	0.00	3.66
894	967	0.409092	TCCATTGCCCACAGGTTCAT	59.591	50.000	0.00	0.00	34.57	2.57
981	1078	6.887002	ACAGGAAAACAAGAGAAAAGAAGAGT	59.113	34.615	0.00	0.00	0.00	3.24
1130	1230	5.188948	ACATGCATTCACCAGGTACTACTTA	59.811	40.000	0.00	0.00	36.02	2.24
1460	1562	1.587522	ATGCTCCCTTGGGCCAGAAT	61.588	55.000	6.23	0.00	0.00	2.40
2022	2127	8.150296	TGTTTATCACACGGATATGATCTCATT	58.850	33.333	0.00	0.00	38.27	2.57
2378	2500	8.527810	TGGTTCAAACTCTTGTAAGTTCAATTT	58.472	29.630	0.00	0.00	38.52	1.82
2615	2758	9.034800	ACCGCCCAAAAATGAATATTATATGAT	57.965	29.630	0.00	0.00	0.00	2.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
94	95	1.445410	CGGGATCTCGACGCAAACA	60.445	57.895	10.16	0.00	0.00	2.83
208	218	1.957877	GAAGCTACCTACAGCGAGGAT	59.042	52.381	9.09	0.00	46.52	3.24
209	219	1.390565	GAAGCTACCTACAGCGAGGA	58.609	55.000	9.09	0.00	46.52	3.71
210	220	0.386113	GGAAGCTACCTACAGCGAGG	59.614	60.000	0.00	1.23	46.52	4.63
211	221	0.029567	CGGAAGCTACCTACAGCGAG	59.970	60.000	0.00	0.00	46.52	5.03
212	222	1.381928	CCGGAAGCTACCTACAGCGA	61.382	60.000	0.00	0.00	46.52	4.93
213	223	1.065928	CCGGAAGCTACCTACAGCG	59.934	63.158	0.00	0.00	46.52	5.18
273	283	4.475944	GTCCATGCATCTTACAACAACAC	58.524	43.478	0.00	0.00	0.00	3.32
285	295	2.224695	TGGATGATCAGGTCCATGCATC	60.225	50.000	13.08	0.00	39.51	3.91
387	401	3.735746	GTGGTTAACATCTTGCAAAGTGC	59.264	43.478	8.10	0.00	46.34	4.40
403	423	8.134202	TCATCTGATCTTAACAAGAGTGGTTA	57.866	34.615	0.00	0.00	41.61	2.85
462	491	2.945984	CTTGCGGCAAGAAGCGAA	59.054	55.556	33.39	1.46	43.42	4.70
474	503	0.236711	CAAGAGGTTGAGTGCTTGCG	59.763	55.000	0.00	0.00	35.46	4.85
480	509	4.342862	TTTCTCTCCAAGAGGTTGAGTG	57.657	45.455	4.24	0.00	42.54	3.51
489	518	4.655963	CCTGGTCAAATTTCTCTCCAAGA	58.344	43.478	0.00	0.00	0.00	3.02
594	627	4.644234	TGGTCAAATATGAAATCGTGGCAT	59.356	37.500	0.00	0.00	37.30	4.40
656	689	2.073252	TCTGATGTACGGCTGAGGAT	57.927	50.000	0.00	0.00	0.00	3.24
661	694	1.410517	ACTCCATCTGATGTACGGCTG	59.589	52.381	15.95	0.00	0.00	4.85
662	695	1.781786	ACTCCATCTGATGTACGGCT	58.218	50.000	15.95	0.00	0.00	5.52
663	696	2.608261	GCTACTCCATCTGATGTACGGC	60.608	54.545	15.95	9.64	0.00	5.68
664	697	2.887783	AGCTACTCCATCTGATGTACGG	59.112	50.000	15.95	1.39	0.00	4.02
665	698	4.576216	AAGCTACTCCATCTGATGTACG	57.424	45.455	15.95	6.69	0.00	3.67
733	797	3.595190	AGTTCCCTTTTAGTGTGCCTT	57.405	42.857	0.00	0.00	0.00	4.35
739	803	7.703058	ATTACCATCAAGTTCCCTTTTAGTG	57.297	36.000	0.00	0.00	0.00	2.74
792	862	7.007099	GGTTATTTCGCATAAACTTTTGAGACG	59.993	37.037	0.00	0.00	0.00	4.18
810	880	5.105064	TGGCTGGTGACTACTAGGTTATTTC	60.105	44.000	0.00	0.00	36.06	2.17
823	893	0.546267	ATGGTCTCTGGCTGGTGACT	60.546	55.000	14.10	0.00	0.00	3.41
824	894	0.326264	AATGGTCTCTGGCTGGTGAC	59.674	55.000	8.88	8.88	0.00	3.67
888	959	1.729149	GCGCAACAAGCAGTATGAACC	60.729	52.381	0.30	0.00	46.13	3.62
894	967	2.971660	TATAGGCGCAACAAGCAGTA	57.028	45.000	10.83	0.00	46.13	2.74
981	1078	5.221481	TGCCATTTGATTTGAGCTTCTTTCA	60.221	36.000	0.00	0.00	0.00	2.69
1130	1230	1.694696	AGGACGAGAAAGCAGGAAGTT	59.305	47.619	0.00	0.00	0.00	2.66
1460	1562	2.666207	GGGTGCGTATGTGGTGGA	59.334	61.111	0.00	0.00	0.00	4.02
1556	1658	5.983720	CACCTTCGAGAAGAACTTGTTTCTA	59.016	40.000	13.90	0.00	44.41	2.10
2031	2141	6.103997	TGAGAAATACGACACATTAGAACCC	58.896	40.000	0.00	0.00	0.00	4.11
2068	2187	3.518992	TCGGAACAAGGGGAAAAGAAT	57.481	42.857	0.00	0.00	0.00	2.40
2615	2758	6.031751	ACAGGCTTGTTACAAAGAAACAAA	57.968	33.333	0.00	0.00	43.98	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.