AutoCloner

Multiple sequence alignment - TraesCS4D01G313500

Loading Multiple Alignment...

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	TraesCS4D01G313500	chr4D	100.000	2282	0	0	1	2282	479532635	479530354	0.000000e+00	4215
1	TraesCS4D01G313500	chr5D	95.753	1342	29	6	131	1445	3887239	3885899	0.000000e+00	2137
2	TraesCS4D01G313500	chr5D	93.333	120	4	2	56	171	3887349	3887230	8.380000e-40	174
3	TraesCS4D01G313500	chr5D	98.413	63	1	0	1	63	3885837	3885899	6.660000e-21	111
4	TraesCS4D01G313500	chr4B	91.573	1068	73	6	394	1445	38752369	38753435	0.000000e+00	1458
5	TraesCS4D01G313500	chr4B	91.487	1069	72	8	394	1445	63041856	63040790	0.000000e+00	1452
6	TraesCS4D01G313500	chr4B	91.992	487	32	5	1800	2282	606760914	606760431	0.000000e+00	676
7	TraesCS4D01G313500	chr4B	93.995	383	19	1	1	379	38752005	38752387	5.470000e-161	577
8	TraesCS4D01G313500	chr4B	93.995	383	19	1	1	379	63042220	63041838	5.470000e-161	577
9	TraesCS4D01G313500	chr4B	93.296	358	17	3	1444	1801	606763015	606762665	2.600000e-144	521
10	TraesCS4D01G313500	chr5A	91.199	1068	77	6	394	1445	60332146	60331080	0.000000e+00	1435
11	TraesCS4D01G313500	chr5A	93.473	383	21	1	1	379	60332510	60332128	1.180000e-157	566
12	TraesCS4D01G313500	chr4A	85.246	854	88	24	1441	2282	685834234	685833407	0.000000e+00	845
13	TraesCS4D01G313500	chr4A	83.465	508	58	15	392	884	738859969	738859473	1.240000e-122	449
14	TraesCS4D01G313500	chr4A	86.590	261	23	5	1193	1446	738859242	738858987	6.210000e-71	278
15	TraesCS4D01G313500	chr2B	82.060	903	100	31	32	919	378536985	378537840	0.000000e+00	713
16	TraesCS4D01G313500	chr7B	81.899	790	90	25	71	847	605317446	605316697	3.220000e-173	617
17	TraesCS4D01G313500	chr7B	85.769	260	26	3	1193	1445	605315065	605314810	4.830000e-67	265
18	TraesCS4D01G313500	chr7B	85.769	260	26	3	1193	1445	605316287	605316032	4.830000e-67	265
19	TraesCS4D01G313500	chr1D	86.972	545	52	8	914	1445	55034867	55034329	1.510000e-166	595
20	TraesCS4D01G313500	chr1D	86.667	540	56	8	914	1444	69585653	69585121	3.270000e-163	584
21	TraesCS4D01G313500	chr3A	86.740	543	54	10	910	1443	521359080	521359613	2.530000e-164	588
22	TraesCS4D01G313500	chr7D	86.614	508	53	7	918	1416	24043956	24043455	4.290000e-152	547
23	TraesCS4D01G313500	chr5B	85.421	535	56	18	919	1449	533109400	533109916	9.280000e-149	536
24	TraesCS4D01G313500	chr5B	82.834	367	44	11	32	379	533108476	533108842	6.120000e-81	311
25	TraesCS4D01G313500	chrUn	93.675	332	20	1	394	724	479777238	479776907	1.570000e-136	496
26	TraesCS4D01G313500	chrUn	96.203	79	3	0	301	379	479777298	479777220	1.840000e-26	130
27	TraesCS4D01G313500	chr2A	83.708	534	62	8	916	1445	61484792	61485304	4.410000e-132	481
28	TraesCS4D01G313500	chr2A	84.279	458	57	8	998	1445	702409800	702410252	1.250000e-117	433
29	TraesCS4D01G313500	chr3B	83.514	461	57	10	396	848	738720995	738721444	1.630000e-111	412
30	TraesCS4D01G313500	chr3B	85.227	352	46	5	32	379	738720661	738721010	7.750000e-95	357
31	TraesCS4D01G313500	chr1A	82.071	396	53	6	1	379	561062923	561063317	2.830000e-84	322
32	TraesCS4D01G313500	chr6B	84.962	266	29	3	1187	1445	679742835	679743096	2.250000e-65	259

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	TraesCS4D01G313500	chr4D	479530354	479532635	2281	True	4215.000000	4215	100.0000	1	2282	1	chr4D.!!$R1	2281
1	TraesCS4D01G313500	chr5D	3885899	3887349	1450	True	1155.500000	2137	94.5430	56	1445	2	chr5D.!!$R1	1389
2	TraesCS4D01G313500	chr4B	38752005	38753435	1430	False	1017.500000	1458	92.7840	1	1445	2	chr4B.!!$F1	1444
3	TraesCS4D01G313500	chr4B	63040790	63042220	1430	True	1014.500000	1452	92.7410	1	1445	2	chr4B.!!$R1	1444
4	TraesCS4D01G313500	chr4B	606760431	606763015	2584	True	598.500000	676	92.6440	1444	2282	2	chr4B.!!$R2	838
5	TraesCS4D01G313500	chr5A	60331080	60332510	1430	True	1000.500000	1435	92.3360	1	1445	2	chr5A.!!$R1	1444
6	TraesCS4D01G313500	chr4A	685833407	685834234	827	True	845.000000	845	85.2460	1441	2282	1	chr4A.!!$R1	841
7	TraesCS4D01G313500	chr4A	738858987	738859969	982	True	363.500000	449	85.0275	392	1446	2	chr4A.!!$R2	1054
8	TraesCS4D01G313500	chr2B	378536985	378537840	855	False	713.000000	713	82.0600	32	919	1	chr2B.!!$F1	887
9	TraesCS4D01G313500	chr7B	605314810	605317446	2636	True	382.333333	617	84.4790	71	1445	3	chr7B.!!$R1	1374
10	TraesCS4D01G313500	chr1D	55034329	55034867	538	True	595.000000	595	86.9720	914	1445	1	chr1D.!!$R1	531
11	TraesCS4D01G313500	chr1D	69585121	69585653	532	True	584.000000	584	86.6670	914	1444	1	chr1D.!!$R2	530
12	TraesCS4D01G313500	chr3A	521359080	521359613	533	False	588.000000	588	86.7400	910	1443	1	chr3A.!!$F1	533
13	TraesCS4D01G313500	chr7D	24043455	24043956	501	True	547.000000	547	86.6140	918	1416	1	chr7D.!!$R1	498
14	TraesCS4D01G313500	chr5B	533108476	533109916	1440	False	423.500000	536	84.1275	32	1449	2	chr5B.!!$F1	1417
15	TraesCS4D01G313500	chr2A	61484792	61485304	512	False	481.000000	481	83.7080	916	1445	1	chr2A.!!$F1	529
16	TraesCS4D01G313500	chr3B	738720661	738721444	783	False	384.500000	412	84.3705	32	848	2	chr3B.!!$F1	816

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
425	509	1.153107	CCTTGATGCATCTGCCGGA	60.153	57.895	26.32	3.04	41.18	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2170	5499	0.461339	GGCCATAGCGTCGAGGAAAA	60.461	55.0	9.75	0.0	41.24	2.29	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	1.526917	CCCACCCAGCGATGGATTC	60.527	63.158	24.05	0.00	38.34	2.52
111	114	2.056223	GGCAATCAGGCAGGCACAT	61.056	57.895	0.00	0.00	43.51	3.21
118	121	3.423539	TCAGGCAGGCACATATATTCC	57.576	47.619	0.00	0.00	0.00	3.01
150	153	1.298863	CGACGCCCGATGTTCGTAT	60.299	57.895	0.00	0.00	41.76	3.06
362	414	2.050144	ACCCAATCGCTCATCAGGTAT	58.950	47.619	0.00	0.00	0.00	2.73
363	415	2.037772	ACCCAATCGCTCATCAGGTATC	59.962	50.000	0.00	0.00	0.00	2.24
369	421	6.036844	CCAATCGCTCATCAGGTATCATATTG	59.963	42.308	0.00	0.00	0.00	1.90
370	422	5.728637	TCGCTCATCAGGTATCATATTGT	57.271	39.130	0.00	0.00	0.00	2.71
371	423	5.714047	TCGCTCATCAGGTATCATATTGTC	58.286	41.667	0.00	0.00	0.00	3.18
372	424	4.560427	CGCTCATCAGGTATCATATTGTCG	59.440	45.833	0.00	0.00	0.00	4.35
373	425	5.473931	GCTCATCAGGTATCATATTGTCGT	58.526	41.667	0.00	0.00	0.00	4.34
374	426	5.928839	GCTCATCAGGTATCATATTGTCGTT	59.071	40.000	0.00	0.00	0.00	3.85
375	427	6.090088	GCTCATCAGGTATCATATTGTCGTTC	59.910	42.308	0.00	0.00	0.00	3.95
376	428	6.455647	TCATCAGGTATCATATTGTCGTTCC	58.544	40.000	0.00	0.00	0.00	3.62
377	429	6.267699	TCATCAGGTATCATATTGTCGTTCCT	59.732	38.462	0.00	0.00	0.00	3.36
378	430	6.479972	TCAGGTATCATATTGTCGTTCCTT	57.520	37.500	0.00	0.00	0.00	3.36
379	431	6.884832	TCAGGTATCATATTGTCGTTCCTTT	58.115	36.000	0.00	0.00	0.00	3.11
380	432	6.984474	TCAGGTATCATATTGTCGTTCCTTTC	59.016	38.462	0.00	0.00	0.00	2.62
381	433	6.202954	CAGGTATCATATTGTCGTTCCTTTCC	59.797	42.308	0.00	0.00	0.00	3.13
382	434	6.099845	AGGTATCATATTGTCGTTCCTTTCCT	59.900	38.462	0.00	0.00	0.00	3.36
383	435	6.202954	GGTATCATATTGTCGTTCCTTTCCTG	59.797	42.308	0.00	0.00	0.00	3.86
384	436	3.938963	TCATATTGTCGTTCCTTTCCTGC	59.061	43.478	0.00	0.00	0.00	4.85
385	437	2.270352	ATTGTCGTTCCTTTCCTGCA	57.730	45.000	0.00	0.00	0.00	4.41
386	438	2.045561	TTGTCGTTCCTTTCCTGCAA	57.954	45.000	0.00	0.00	0.00	4.08
387	439	2.045561	TGTCGTTCCTTTCCTGCAAA	57.954	45.000	0.00	0.00	0.00	3.68
388	440	2.370349	TGTCGTTCCTTTCCTGCAAAA	58.630	42.857	0.00	0.00	0.00	2.44
389	441	2.755655	TGTCGTTCCTTTCCTGCAAAAA	59.244	40.909	0.00	0.00	0.00	1.94
425	509	1.153107	CCTTGATGCATCTGCCGGA	60.153	57.895	26.32	3.04	41.18	5.14
735	2030	2.289569	ACACCAAAATCGGCCGTAAGTA	60.290	45.455	27.15	5.24	0.00	2.24
784	2084	4.093998	CACATGCACAATCTCCTAGTGTTC	59.906	45.833	0.00	0.00	33.16	3.18
824	2124	6.761242	CACACTCCTGATATTTACGATCCAAA	59.239	38.462	0.00	0.00	0.00	3.28
893	2193	4.675063	AAGGGCCTATGAAAGAGGAAAA	57.325	40.909	6.41	0.00	35.99	2.29
964	2481	7.900352	GCTAGTTTATTCAAAAGATGTCGACAG	59.100	37.037	24.41	9.12	0.00	3.51
1413	2978	2.152016	GCCCTGAGTTTTAGTTTCGCT	58.848	47.619	0.00	0.00	0.00	4.93
1438	3003	0.704076	CCCCCAAAATCTCAGGACCA	59.296	55.000	0.00	0.00	0.00	4.02
1460	3025	0.109342	CCTGGTGATGGAGGGCATAC	59.891	60.000	0.00	0.00	0.00	2.39
1700	3270	2.604046	AGATGCCCATTCTACGACAC	57.396	50.000	0.00	0.00	0.00	3.67
1844	5167	1.017387	GCCACCGCCAGAATTTCTAG	58.983	55.000	0.00	0.00	0.00	2.43
1849	5172	2.028385	ACCGCCAGAATTTCTAGTCGTT	60.028	45.455	0.00	0.00	0.00	3.85
1956	5281	8.572855	AGAAGATTTTTCTGGTCCTAAATGAG	57.427	34.615	0.00	0.00	0.00	2.90
1959	5284	8.572855	AGATTTTTCTGGTCCTAAATGAGAAG	57.427	34.615	0.00	0.00	0.00	2.85
1971	5296	5.189934	CCTAAATGAGAAGGTACTGAGGGTT	59.810	44.000	0.00	0.00	40.86	4.11
1974	5299	3.791320	TGAGAAGGTACTGAGGGTTGAT	58.209	45.455	0.00	0.00	40.86	2.57
1982	5307	0.606401	CTGAGGGTTGATGCGGTGTT	60.606	55.000	0.00	0.00	0.00	3.32
2145	5472	3.088532	AGTGTCTTGGTGCTTTTGTTGA	58.911	40.909	0.00	0.00	0.00	3.18
2150	5477	5.108517	GTCTTGGTGCTTTTGTTGATTTGA	58.891	37.500	0.00	0.00	0.00	2.69
2151	5478	5.005682	GTCTTGGTGCTTTTGTTGATTTGAC	59.994	40.000	0.00	0.00	0.00	3.18
2170	5499	2.952310	GACTTTTTGTGGAGCTGGAGTT	59.048	45.455	0.00	0.00	0.00	3.01
2220	5549	2.548067	CGGTCCATAGGGTGATGCTAAC	60.548	54.545	0.00	0.00	34.93	2.34
2249	5578	3.853355	AGCCAATAGGGAGACATCAAG	57.147	47.619	0.00	0.00	40.01	3.02
2250	5579	3.387962	AGCCAATAGGGAGACATCAAGA	58.612	45.455	0.00	0.00	40.01	3.02
2261	5591	7.018150	AGGGAGACATCAAGATTGATCTCTAT	58.982	38.462	18.64	9.90	45.62	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	1.727880	TCGCTCCCGAAATAACAAACG	59.272	47.619	0.00	0.00	41.17	3.60
30	31	2.035155	TGAAGGACTCGCTCCCGA	59.965	61.111	0.00	0.00	40.53	5.14
150	153	4.728102	CGTCGGCGGCAGTACCAA	62.728	66.667	13.62	0.00	39.03	3.67
362	414	3.938963	GCAGGAAAGGAACGACAATATGA	59.061	43.478	0.00	0.00	0.00	2.15
363	415	3.689161	TGCAGGAAAGGAACGACAATATG	59.311	43.478	0.00	0.00	0.00	1.78
369	421	3.430333	TTTTTGCAGGAAAGGAACGAC	57.570	42.857	0.00	0.00	0.00	4.34
393	445	9.725019	AGATGCATCAAGGAACGAAAATATATA	57.275	29.630	27.81	0.00	0.00	0.86
394	446	8.509690	CAGATGCATCAAGGAACGAAAATATAT	58.490	33.333	27.81	0.00	0.00	0.86
395	447	7.520453	GCAGATGCATCAAGGAACGAAAATATA	60.520	37.037	27.81	0.00	41.59	0.86
425	509	1.068281	TGCATCAATTGTTGCACGGTT	59.932	42.857	30.93	0.00	43.41	4.44
459	550	9.877178	TGATTTTACCAATTTAAAACACACTGT	57.123	25.926	0.00	0.00	34.53	3.55
735	2030	4.649674	TGAATTACCTACATTCTCGGAGCT	59.350	41.667	0.00	0.00	32.63	4.09
1062	2608	6.202954	GCACAGTAAATAAGATGCGATAAGGT	59.797	38.462	0.00	0.00	0.00	3.50
1309	2860	5.008019	AGCACTTAAATGAATCAGTATGCGG	59.992	40.000	0.00	0.00	34.76	5.69
1413	2978	2.944390	AGATTTTGGGGGCCCGGA	60.944	61.111	17.79	4.08	39.42	5.14
1438	3003	2.693864	CCCTCCATCACCAGGGCT	60.694	66.667	0.00	0.00	43.29	5.19
1460	3025	6.489127	TGTTTCCACACATAACGAATTAGG	57.511	37.500	0.00	0.00	0.00	2.69
1700	3270	4.389077	AGCTGGAAGTTCTAACGAATTTCG	59.611	41.667	16.84	16.84	43.10	3.46
1808	5131	1.968493	TGGCGGTTGTCTTCTACTCTT	59.032	47.619	0.00	0.00	0.00	2.85
1825	5148	1.017387	CTAGAAATTCTGGCGGTGGC	58.983	55.000	5.64	0.00	38.90	5.01
1844	5167	2.476519	CGCTAGAAGTGAGGAGAACGAC	60.477	54.545	0.00	0.00	0.00	4.34
1849	5172	1.004394	TGACCGCTAGAAGTGAGGAGA	59.996	52.381	0.00	0.00	0.00	3.71
1897	5220	5.993106	TTGAAACACATGTATGAACGTCA	57.007	34.783	0.00	0.00	0.00	4.35
1900	5224	7.738345	TGAGTATTGAAACACATGTATGAACG	58.262	34.615	0.00	0.00	0.00	3.95
1942	5267	5.422331	TCAGTACCTTCTCATTTAGGACCAG	59.578	44.000	0.00	0.00	35.45	4.00
1956	5281	2.633488	GCATCAACCCTCAGTACCTTC	58.367	52.381	0.00	0.00	0.00	3.46
1959	5284	0.462047	CCGCATCAACCCTCAGTACC	60.462	60.000	0.00	0.00	0.00	3.34
1971	5296	1.383523	TGTTCAACAACACCGCATCA	58.616	45.000	0.00	0.00	37.61	3.07
1974	5299	4.202060	ACATTTATGTTCAACAACACCGCA	60.202	37.500	0.00	0.00	45.47	5.69
1982	5307	8.806429	ATACCAGATGACATTTATGTTCAACA	57.194	30.769	0.00	0.00	41.95	3.33
2065	5390	5.106197	TGCGACGACATAAACCTTAACTCTA	60.106	40.000	0.00	0.00	0.00	2.43
2145	5472	3.960102	TCCAGCTCCACAAAAAGTCAAAT	59.040	39.130	0.00	0.00	0.00	2.32
2150	5477	2.736670	ACTCCAGCTCCACAAAAAGT	57.263	45.000	0.00	0.00	0.00	2.66
2151	5478	4.391405	AAAACTCCAGCTCCACAAAAAG	57.609	40.909	0.00	0.00	0.00	2.27
2170	5499	0.461339	GGCCATAGCGTCGAGGAAAA	60.461	55.000	9.75	0.00	41.24	2.29
2250	5579	9.254133	CGTCTGTGACATAAAATAGAGATCAAT	57.746	33.333	0.00	0.00	32.09	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.