AutoCloner

Multiple sequence alignment - TraesCS2B01G310400

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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	TraesCS2B01G310400	chr2B	100.000	3174	0	0	1	3174	443222664	443225837	0.000000e+00	5862.0
1	TraesCS2B01G310400	chr2B	97.674	1978	17	6	410	2371	443148952	443146988	0.000000e+00	3371.0
2	TraesCS2B01G310400	chr2B	96.499	657	22	1	2518	3174	526409930	526409275	0.000000e+00	1085.0
3	TraesCS2B01G310400	chr2B	92.754	69	3	1	2440	2506	443146984	443146916	7.250000e-17	99.0
4	TraesCS2B01G310400	chr2D	94.098	2406	91	18	3	2380	373749606	373751988	0.000000e+00	3609.0
5	TraesCS2B01G310400	chr2D	94.171	1990	78	20	409	2380	373654258	373652289	0.000000e+00	2998.0
6	TraesCS2B01G310400	chr2A	91.481	2019	94	40	411	2380	505080486	505078497	0.000000e+00	2704.0
7	TraesCS2B01G310400	chr2A	90.481	1975	110	34	583	2506	505208566	505210513	0.000000e+00	2534.0
8	TraesCS2B01G310400	chr3B	99.233	652	5	0	2522	3173	542502204	542501553	0.000000e+00	1177.0
9	TraesCS2B01G310400	chr5B	97.409	656	16	1	2519	3174	280466029	280466683	0.000000e+00	1116.0
10	TraesCS2B01G310400	chr5B	96.031	655	25	1	2520	3174	82155635	82154982	0.000000e+00	1064.0
11	TraesCS2B01G310400	chr7B	96.799	656	20	1	2519	3174	504236931	504236277	0.000000e+00	1094.0
12	TraesCS2B01G310400	chr7B	96.478	653	22	1	2522	3174	5497345	5497996	0.000000e+00	1077.0
13	TraesCS2B01G310400	chr4B	96.183	655	24	1	2520	3174	223363865	223363212	0.000000e+00	1070.0
14	TraesCS2B01G310400	chrUn	96.024	654	23	3	2521	3173	315282861	315282210	0.000000e+00	1061.0
15	TraesCS2B01G310400	chrUn	95.719	654	25	3	2521	3173	327315881	327316532	0.000000e+00	1050.0
16	TraesCS2B01G310400	chrUn	89.583	48	4	1	359	406	77472655	77472609	3.420000e-05	60.2
17	TraesCS2B01G310400	chr3D	76.439	556	112	15	1419	1963	566081016	566081563	1.860000e-72	283.0
18	TraesCS2B01G310400	chr1A	75.844	563	118	17	1412	1965	11555200	11555753	1.450000e-68	270.0
19	TraesCS2B01G310400	chr1D	75.401	561	124	12	1412	1965	9745218	9745771	3.140000e-65	259.0
20	TraesCS2B01G310400	chr1B	75.404	557	119	14	1418	1965	14138344	14138891	1.460000e-63	254.0

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	TraesCS2B01G310400	chr2B	443222664	443225837	3173	False	5862	5862	100.000	1	3174	1	chr2B.!!$F1	3173
1	TraesCS2B01G310400	chr2B	443146916	443148952	2036	True	1735	3371	95.214	410	2506	2	chr2B.!!$R2	2096
2	TraesCS2B01G310400	chr2B	526409275	526409930	655	True	1085	1085	96.499	2518	3174	1	chr2B.!!$R1	656
3	TraesCS2B01G310400	chr2D	373749606	373751988	2382	False	3609	3609	94.098	3	2380	1	chr2D.!!$F1	2377
4	TraesCS2B01G310400	chr2D	373652289	373654258	1969	True	2998	2998	94.171	409	2380	1	chr2D.!!$R1	1971
5	TraesCS2B01G310400	chr2A	505078497	505080486	1989	True	2704	2704	91.481	411	2380	1	chr2A.!!$R1	1969
6	TraesCS2B01G310400	chr2A	505208566	505210513	1947	False	2534	2534	90.481	583	2506	1	chr2A.!!$F1	1923
7	TraesCS2B01G310400	chr3B	542501553	542502204	651	True	1177	1177	99.233	2522	3173	1	chr3B.!!$R1	651
8	TraesCS2B01G310400	chr5B	280466029	280466683	654	False	1116	1116	97.409	2519	3174	1	chr5B.!!$F1	655
9	TraesCS2B01G310400	chr5B	82154982	82155635	653	True	1064	1064	96.031	2520	3174	1	chr5B.!!$R1	654
10	TraesCS2B01G310400	chr7B	504236277	504236931	654	True	1094	1094	96.799	2519	3174	1	chr7B.!!$R1	655
11	TraesCS2B01G310400	chr7B	5497345	5497996	651	False	1077	1077	96.478	2522	3174	1	chr7B.!!$F1	652
12	TraesCS2B01G310400	chr4B	223363212	223363865	653	True	1070	1070	96.183	2520	3174	1	chr4B.!!$R1	654
13	TraesCS2B01G310400	chrUn	315282210	315282861	651	True	1061	1061	96.024	2521	3173	1	chrUn.!!$R2	652
14	TraesCS2B01G310400	chrUn	327315881	327316532	651	False	1050	1050	95.719	2521	3173	1	chrUn.!!$F1	652
15	TraesCS2B01G310400	chr3D	566081016	566081563	547	False	283	283	76.439	1419	1963	1	chr3D.!!$F1	544
16	TraesCS2B01G310400	chr1A	11555200	11555753	553	False	270	270	75.844	1412	1965	1	chr1A.!!$F1	553
17	TraesCS2B01G310400	chr1D	9745218	9745771	553	False	259	259	75.401	1412	1965	1	chr1D.!!$F1	553
18	TraesCS2B01G310400	chr1B	14138344	14138891	547	False	254	254	75.404	1418	1965	1	chr1B.!!$F1	547

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
94	95	0.034089	GGCTGCAGTTTAGGACCCAT	60.034	55.0	16.64	0.0	0.0	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2198	2277	3.1877	GCACACTTACGAGGGTAATGAG	58.812	50.0	0.0	0.0	37.45	2.9	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
19	20	1.854227	GGCAGCGTGGTAGAGATAAC	58.146	55.000	0.00	0.00	0.00	1.89
94	95	0.034089	GGCTGCAGTTTAGGACCCAT	60.034	55.000	16.64	0.00	0.00	4.00
96	97	1.340017	GCTGCAGTTTAGGACCCATGA	60.340	52.381	16.64	0.00	0.00	3.07
107	108	2.240162	GACCCATGACGTCCCACTCC	62.240	65.000	14.12	0.00	0.00	3.85
109	110	0.686441	CCCATGACGTCCCACTCCTA	60.686	60.000	14.12	0.00	0.00	2.94
124	125	4.773149	CCACTCCTACTTAGAGAAAGGTGT	59.227	45.833	0.00	0.00	39.73	4.16
136	137	4.838986	AGAGAAAGGTGTACCAGAAGCTTA	59.161	41.667	0.00	0.00	38.89	3.09
201	202	2.222013	GGAACAACGGGGGAGGAGT	61.222	63.158	0.00	0.00	0.00	3.85
227	228	1.685820	GGACCCTTCCCTTCCACAG	59.314	63.158	0.00	0.00	35.57	3.66
251	252	2.228822	ACATTGATCCGAAAAGCCACAC	59.771	45.455	0.00	0.00	0.00	3.82
258	259	1.879380	CCGAAAAGCCACACATTCAGA	59.121	47.619	0.00	0.00	0.00	3.27
260	261	2.549754	CGAAAAGCCACACATTCAGAGT	59.450	45.455	0.00	0.00	0.00	3.24
261	262	3.607775	CGAAAAGCCACACATTCAGAGTG	60.608	47.826	0.00	0.00	42.56	3.51
290	291	3.229156	AACCCGCGAACACGATCCA	62.229	57.895	8.23	0.00	34.06	3.41
302	303	1.446792	CGATCCAGCGCAGAACACT	60.447	57.895	11.47	0.00	0.00	3.55
343	344	3.931130	CGTGTGCCGCGTTGTTCA	61.931	61.111	4.92	0.00	32.40	3.18
350	351	1.841663	GCCGCGTTGTTCACAGTCAT	61.842	55.000	4.92	0.00	0.00	3.06
351	352	0.110688	CCGCGTTGTTCACAGTCATG	60.111	55.000	4.92	0.00	0.00	3.07
367	368	2.032894	GTCATGGCGGATTTCGTGTATG	60.033	50.000	0.00	0.00	41.72	2.39
382	383	4.819630	TCGTGTATGTTCTTTTCTGCCTTT	59.180	37.500	0.00	0.00	0.00	3.11
385	386	7.174253	TCGTGTATGTTCTTTTCTGCCTTTTAT	59.826	33.333	0.00	0.00	0.00	1.40
400	401	9.930158	TCTGCCTTTTATAAAAATATGGTACCT	57.070	29.630	14.36	1.08	0.00	3.08
2198	2277	1.366111	TACCGCGAGCTGATTTTGCC	61.366	55.000	8.23	0.00	0.00	4.52
2289	2383	5.637006	TTGGTTTCAGAATAAATCACCGG	57.363	39.130	0.00	0.00	29.35	5.28
2290	2384	4.013728	TGGTTTCAGAATAAATCACCGGG	58.986	43.478	6.32	0.00	0.00	5.73
2306	2403	1.671742	GGGTGGTGATGTCGTGTCT	59.328	57.895	0.00	0.00	0.00	3.41
2330	2427	4.552355	TGTGTGTTAGTCAATCGATCGTT	58.448	39.130	15.94	3.47	0.00	3.85
2371	2474	4.235762	AGGCGTTGCTCGGTGTGT	62.236	61.111	4.36	0.00	40.26	3.72
2372	2475	4.012895	GGCGTTGCTCGGTGTGTG	62.013	66.667	4.36	0.00	40.26	3.82
2398	2501	1.915769	GGATAGGATCGGCAGGGCT	60.916	63.158	0.00	0.00	0.00	5.19
2401	2504	1.772819	ATAGGATCGGCAGGGCTTGG	61.773	60.000	0.00	0.00	0.00	3.61
2410	2513	1.376037	CAGGGCTTGGTCCGAAGAC	60.376	63.158	5.53	2.69	42.73	3.01
2421	2524	2.076863	GTCCGAAGACCAAACCAGATG	58.923	52.381	0.00	0.00	37.00	2.90
2422	2525	0.804989	CCGAAGACCAAACCAGATGC	59.195	55.000	0.00	0.00	0.00	3.91
2423	2526	1.522668	CGAAGACCAAACCAGATGCA	58.477	50.000	0.00	0.00	0.00	3.96
2424	2527	2.086869	CGAAGACCAAACCAGATGCAT	58.913	47.619	0.00	0.00	0.00	3.96
2433	2543	1.153309	CCAGATGCATGTCGAGCCA	60.153	57.895	2.46	0.00	0.00	4.75
2439	2549	1.089112	TGCATGTCGAGCCAATCTTG	58.911	50.000	0.00	0.00	0.00	3.02
2506	2621	9.824534	GAACAATCAAGTTTGTTTTTCATGTTT	57.175	25.926	9.77	0.00	46.84	2.83
2507	2622	9.824534	AACAATCAAGTTTGTTTTTCATGTTTC	57.175	25.926	3.98	0.00	45.14	2.78
2508	2623	9.218440	ACAATCAAGTTTGTTTTTCATGTTTCT	57.782	25.926	0.00	0.00	36.43	2.52
2512	2627	9.567848	TCAAGTTTGTTTTTCATGTTTCTAGAC	57.432	29.630	0.00	0.00	0.00	2.59
2513	2628	8.523464	CAAGTTTGTTTTTCATGTTTCTAGACG	58.477	33.333	0.00	0.00	0.00	4.18
2514	2629	7.193595	AGTTTGTTTTTCATGTTTCTAGACGG	58.806	34.615	0.00	0.00	0.00	4.79
2515	2630	6.687081	TTGTTTTTCATGTTTCTAGACGGT	57.313	33.333	0.00	0.00	0.00	4.83
2516	2631	6.055231	TGTTTTTCATGTTTCTAGACGGTG	57.945	37.500	0.00	0.00	0.00	4.94
2828	2944	1.153168	CCATGGCCTTCCGATTCGT	60.153	57.895	3.32	0.00	34.14	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.538419	GGTTATCTCTACCACGCTGCC	60.538	57.143	0.00	0.00	35.67	4.85
1	2	1.136305	TGGTTATCTCTACCACGCTGC	59.864	52.381	0.00	0.00	40.65	5.25
9	10	7.870445	GGATTCTGTTGATCTGGTTATCTCTAC	59.130	40.741	0.00	0.00	0.00	2.59
15	16	6.995091	GCTAAGGATTCTGTTGATCTGGTTAT	59.005	38.462	0.00	0.00	0.00	1.89
16	17	6.349300	GCTAAGGATTCTGTTGATCTGGTTA	58.651	40.000	0.00	0.00	0.00	2.85
19	20	4.133078	GGCTAAGGATTCTGTTGATCTGG	58.867	47.826	0.00	0.00	0.00	3.86
59	60	1.065854	CAGCCTCTCTACCCAAACAGG	60.066	57.143	0.00	0.00	37.03	4.00
94	95	2.306805	TCTAAGTAGGAGTGGGACGTCA	59.693	50.000	18.91	0.00	0.00	4.35
96	97	2.575279	TCTCTAAGTAGGAGTGGGACGT	59.425	50.000	0.00	0.00	33.06	4.34
107	108	7.463961	TTCTGGTACACCTTTCTCTAAGTAG	57.536	40.000	0.00	0.00	36.82	2.57
109	110	5.279556	GCTTCTGGTACACCTTTCTCTAAGT	60.280	44.000	0.00	0.00	36.82	2.24
124	125	2.895404	ACTGACGGTTAAGCTTCTGGTA	59.105	45.455	17.93	0.00	0.00	3.25
201	202	1.383525	GGGAAGGGTCCGGTCCATA	60.384	63.158	19.75	0.00	46.04	2.74
227	228	2.491693	TGGCTTTTCGGATCAATGTTCC	59.508	45.455	0.29	0.29	0.00	3.62
251	252	1.931841	CATCGAGGTGCACTCTGAATG	59.068	52.381	17.98	12.65	44.33	2.67
258	259	1.296715	GGGTTCATCGAGGTGCACT	59.703	57.895	17.98	2.27	0.00	4.40
260	261	2.264480	CGGGTTCATCGAGGTGCA	59.736	61.111	0.00	0.00	0.00	4.57
261	262	3.195698	GCGGGTTCATCGAGGTGC	61.196	66.667	0.00	0.00	0.00	5.01
290	291	2.350522	CAGGATTTAGTGTTCTGCGCT	58.649	47.619	9.73	0.00	41.45	5.92
302	303	2.823959	ACCCGTCTGTACCAGGATTTA	58.176	47.619	0.00	0.00	31.51	1.40
335	336	0.110688	CGCCATGACTGTGAACAACG	60.111	55.000	0.00	0.00	0.00	4.10
343	344	0.036388	ACGAAATCCGCCATGACTGT	60.036	50.000	0.00	0.00	43.32	3.55
350	351	2.004017	GAACATACACGAAATCCGCCA	58.996	47.619	0.00	0.00	43.32	5.69
351	352	2.277084	AGAACATACACGAAATCCGCC	58.723	47.619	0.00	0.00	43.32	6.13
385	386	9.747898	AGTTGTCAATGAGGTACCATATTTTTA	57.252	29.630	15.94	0.03	0.00	1.52
391	392	6.183360	GCTCTAGTTGTCAATGAGGTACCATA	60.183	42.308	15.94	2.17	0.00	2.74
396	397	3.762288	ACGCTCTAGTTGTCAATGAGGTA	59.238	43.478	12.14	0.00	0.00	3.08
399	400	3.794028	GCTACGCTCTAGTTGTCAATGAG	59.206	47.826	8.11	8.11	0.00	2.90
400	401	3.444034	AGCTACGCTCTAGTTGTCAATGA	59.556	43.478	0.00	0.00	30.62	2.57
406	407	2.164624	CTCCAAGCTACGCTCTAGTTGT	59.835	50.000	0.00	0.00	38.25	3.32
2198	2277	3.187700	GCACACTTACGAGGGTAATGAG	58.812	50.000	0.00	0.00	37.45	2.90
2264	2357	6.751888	CCGGTGATTTATTCTGAAACCAAATC	59.248	38.462	18.69	18.69	36.56	2.17
2289	2383	1.531149	CAAAGACACGACATCACCACC	59.469	52.381	0.00	0.00	0.00	4.61
2290	2384	2.032894	CACAAAGACACGACATCACCAC	60.033	50.000	0.00	0.00	0.00	4.16
2306	2403	4.986034	ACGATCGATTGACTAACACACAAA	59.014	37.500	24.34	0.00	0.00	2.83
2330	2427	0.180642	TTCCAACGTTGCCCTACACA	59.819	50.000	22.93	0.00	0.00	3.72
2371	2474	1.550327	CGATCCTATCCTAGCCTGCA	58.450	55.000	0.00	0.00	0.00	4.41
2372	2475	0.820871	CCGATCCTATCCTAGCCTGC	59.179	60.000	0.00	0.00	0.00	4.85
2401	2504	2.076863	CATCTGGTTTGGTCTTCGGAC	58.923	52.381	0.00	0.00	43.76	4.79
2410	2513	1.399440	CTCGACATGCATCTGGTTTGG	59.601	52.381	0.00	0.00	0.00	3.28
2412	2515	1.089920	GCTCGACATGCATCTGGTTT	58.910	50.000	0.00	0.00	0.00	3.27
2415	2518	0.745486	TTGGCTCGACATGCATCTGG	60.745	55.000	0.00	0.00	0.00	3.86
2416	2519	1.263484	GATTGGCTCGACATGCATCTG	59.737	52.381	0.00	0.00	0.00	2.90
2417	2520	1.140452	AGATTGGCTCGACATGCATCT	59.860	47.619	0.00	0.00	0.00	2.90
2418	2521	1.590932	AGATTGGCTCGACATGCATC	58.409	50.000	0.00	0.00	0.00	3.91
2421	2524	0.379669	CCAAGATTGGCTCGACATGC	59.620	55.000	0.00	0.00	42.21	4.06
2828	2944	3.322211	ACATGTCGAAACCCAATACGA	57.678	42.857	0.00	0.00	0.00	3.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.