AutoCloner

Multiple sequence alignment - TraesCS3A01G393600

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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	TraesCS3A01G393600	chr3A	100.000	2796	0	0	775	3570	641557838	641560633	0.000000e+00	5164
1	TraesCS3A01G393600	chr3A	100.000	541	0	0	1	541	641557064	641557604	0.000000e+00	1000
2	TraesCS3A01G393600	chr3D	94.467	2747	103	29	843	3569	502125436	502128153	0.000000e+00	4185
3	TraesCS3A01G393600	chr3D	94.669	544	26	2	1	541	502121874	502122417	0.000000e+00	841
4	TraesCS3A01G393600	chr3D	92.893	197	12	2	3374	3570	7569628	7569822	5.830000e-73	285
5	TraesCS3A01G393600	chr3B	90.645	1550	105	16	2028	3570	663408466	663409982	0.000000e+00	2023
6	TraesCS3A01G393600	chr3B	89.935	1550	116	17	2028	3570	663335446	663336962	0.000000e+00	1962
7	TraesCS3A01G393600	chr3B	88.771	757	53	7	789	1544	663363837	663364562	0.000000e+00	898
8	TraesCS3A01G393600	chr3B	87.450	757	62	10	789	1544	663291015	663291739	0.000000e+00	841
9	TraesCS3A01G393600	chr3B	89.971	339	31	3	1	338	663290399	663290735	5.470000e-118	435
10	TraesCS3A01G393600	chr3B	89.971	339	31	3	1	338	663363221	663363557	5.470000e-118	435
11	TraesCS3A01G393600	chr3B	94.304	158	8	1	384	541	663290744	663290900	1.280000e-59	241
12	TraesCS3A01G393600	chr3B	94.304	158	8	1	384	541	663363566	663363722	1.280000e-59	241
13	TraesCS3A01G393600	chr5B	92.717	508	37	0	1056	1563	448132742	448132235	0.000000e+00	734
14	TraesCS3A01G393600	chr5B	88.555	533	59	2	2057	2588	448131081	448130550	0.000000e+00	645
15	TraesCS3A01G393600	chr5B	84.221	526	69	11	2855	3368	647385266	647384743	1.910000e-137	499
16	TraesCS3A01G393600	chr5B	85.955	356	50	0	1616	1971	448131918	448131563	7.230000e-102	381
17	TraesCS3A01G393600	chr5A	90.450	555	49	3	1021	1574	476669822	476669271	0.000000e+00	728
18	TraesCS3A01G393600	chr5A	88.555	533	59	2	2057	2588	476668257	476667726	0.000000e+00	645
19	TraesCS3A01G393600	chr5A	86.798	356	47	0	1616	1971	476668909	476668554	7.180000e-107	398
20	TraesCS3A01G393600	chr5D	88.067	595	58	10	992	1574	375312378	375311785	0.000000e+00	693
21	TraesCS3A01G393600	chr5D	88.743	533	58	2	2057	2588	375310749	375310218	0.000000e+00	651
22	TraesCS3A01G393600	chr5D	84.473	541	59	19	2849	3368	514919868	514919332	8.840000e-141	510
23	TraesCS3A01G393600	chr5D	87.360	356	45	0	1616	1971	375311410	375311055	3.320000e-110	409
24	TraesCS3A01G393600	chr5D	87.088	364	32	12	2984	3333	124720571	124720209	7.180000e-107	398
25	TraesCS3A01G393600	chr5D	91.509	212	13	5	3360	3570	420452959	420453166	1.620000e-73	287
26	TraesCS3A01G393600	chr5D	92.893	197	12	2	3374	3570	420457906	420458100	5.830000e-73	285
27	TraesCS3A01G393600	chr5D	92.929	198	11	3	3374	3570	496923824	496923629	5.830000e-73	285
28	TraesCS3A01G393600	chr6B	85.714	399	39	12	2952	3333	10229500	10229897	4.290000e-109	405
29	TraesCS3A01G393600	chr1A	85.279	394	42	13	2952	3333	518475894	518476283	3.340000e-105	392
30	TraesCS3A01G393600	chr1D	84.352	409	44	13	2937	3329	442456380	442455976	2.010000e-102	383
31	TraesCS3A01G393600	chr2B	85.893	319	25	12	2952	3252	526461484	526461800	4.450000e-84	322
32	TraesCS3A01G393600	chr4A	92.893	197	13	1	3374	3570	740983029	740982834	5.830000e-73	285
33	TraesCS3A01G393600	chr4A	92.105	76	6	0	2606	2681	556604743	556604668	1.360000e-19	108
34	TraesCS3A01G393600	chrUn	92.462	199	13	2	3372	3570	74787154	74786958	2.100000e-72	283
35	TraesCS3A01G393600	chr7D	92.893	197	11	3	3374	3570	528576666	528576859	2.100000e-72	283
36	TraesCS3A01G393600	chr4D	90.541	74	7	0	2608	2681	55489307	55489234	8.160000e-17	99

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	TraesCS3A01G393600	chr3A	641557064	641560633	3569	False	3082.000000	5164	100.000000	1	3570	2	chr3A.!!$F1	3569
1	TraesCS3A01G393600	chr3D	502121874	502128153	6279	False	2513.000000	4185	94.568000	1	3569	2	chr3D.!!$F2	3568
2	TraesCS3A01G393600	chr3B	663408466	663409982	1516	False	2023.000000	2023	90.645000	2028	3570	1	chr3B.!!$F2	1542
3	TraesCS3A01G393600	chr3B	663335446	663336962	1516	False	1962.000000	1962	89.935000	2028	3570	1	chr3B.!!$F1	1542
4	TraesCS3A01G393600	chr3B	663363221	663364562	1341	False	524.666667	898	91.015333	1	1544	3	chr3B.!!$F4	1543
5	TraesCS3A01G393600	chr3B	663290399	663291739	1340	False	505.666667	841	90.575000	1	1544	3	chr3B.!!$F3	1543
6	TraesCS3A01G393600	chr5B	448130550	448132742	2192	True	586.666667	734	89.075667	1056	2588	3	chr5B.!!$R2	1532
7	TraesCS3A01G393600	chr5B	647384743	647385266	523	True	499.000000	499	84.221000	2855	3368	1	chr5B.!!$R1	513
8	TraesCS3A01G393600	chr5A	476667726	476669822	2096	True	590.333333	728	88.601000	1021	2588	3	chr5A.!!$R1	1567
9	TraesCS3A01G393600	chr5D	375310218	375312378	2160	True	584.333333	693	88.056667	992	2588	3	chr5D.!!$R4	1596
10	TraesCS3A01G393600	chr5D	514919332	514919868	536	True	510.000000	510	84.473000	2849	3368	1	chr5D.!!$R3	519

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
990	3861	0.038159	AGAGGAAAGAGTCAACGCCG	60.038	55.0	0.00	0.0	0.0	6.46	F
1563	4450	0.036858	GGTGAGCGCTTCTTCTTCCT	60.037	55.0	13.26	0.0	0.0	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2474	6188	0.329596	ACATCCCACCCTTTGAGCTC	59.670	55.0	6.82	6.82	0.0	4.09	R
3404	7150	0.749049	GCTTCAAATGGCCATCTCCC	59.251	55.0	21.08	1.94	0.0	4.30	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
146	149	1.067974	CTACTTGACACGTCACCACCA	59.932	52.381	0.00	0.00	39.66	4.17
187	190	1.255667	GCCACCAGTAAGTCTCCCGA	61.256	60.000	0.00	0.00	0.00	5.14
275	278	1.621814	CGACAAGTGGGACCTCCTTTA	59.378	52.381	0.00	0.00	36.20	1.85
475	479	3.876914	TCAGCAGTTAGTTTTGGTGTCAG	59.123	43.478	3.96	0.00	41.99	3.51
819	823	2.688507	ACAGTTGTGGTGATGATCGAC	58.311	47.619	0.00	0.00	0.00	4.20
988	3859	0.793250	GCAGAGGAAAGAGTCAACGC	59.207	55.000	0.00	0.00	0.00	4.84
990	3861	0.038159	AGAGGAAAGAGTCAACGCCG	60.038	55.000	0.00	0.00	0.00	6.46
994	3866	2.171489	GAAAGAGTCAACGCCGCACC	62.171	60.000	0.00	0.00	0.00	5.01
1495	4382	3.796443	TCGGCTTCGTCGACTCCG	61.796	66.667	21.72	21.72	33.73	4.63
1563	4450	0.036858	GGTGAGCGCTTCTTCTTCCT	60.037	55.000	13.26	0.00	0.00	3.36
1570	4457	0.176910	GCTTCTTCTTCCTCCCCTCG	59.823	60.000	0.00	0.00	0.00	4.63
1600	4702	2.508663	GGCCGTTACCGAGACAGC	60.509	66.667	0.00	0.00	35.63	4.40
1732	5034	1.179814	ACGGGATCGACATAGAGGGC	61.180	60.000	0.00	0.00	40.11	5.19
1755	5057	1.438651	AACAACACGATCATCACCGG	58.561	50.000	0.00	0.00	0.00	5.28
1825	5127	1.680338	GCCCTGTTCACAACTTGACT	58.320	50.000	0.00	0.00	32.26	3.41
1849	5151	4.778143	AACTGCCGGATCCGCACC	62.778	66.667	29.12	18.15	38.24	5.01
1879	5181	3.853671	GTGCTATCAAATTTGGAAGTGCG	59.146	43.478	17.90	2.16	0.00	5.34
1884	5186	2.226437	TCAAATTTGGAAGTGCGAGCTC	59.774	45.455	17.90	2.73	0.00	4.09
1894	5196	0.793250	GTGCGAGCTCCTTCAACTTC	59.207	55.000	8.47	0.00	0.00	3.01
1984	5350	3.469739	TGGAGGTAACGACTTTGTTTCC	58.530	45.455	0.00	0.00	46.39	3.13
1996	5362	4.273318	ACTTTGTTTCCTCTTCTTGCAGT	58.727	39.130	0.00	0.00	0.00	4.40
1997	5497	4.096984	ACTTTGTTTCCTCTTCTTGCAGTG	59.903	41.667	0.00	0.00	0.00	3.66
2000	5500	1.888215	TTCCTCTTCTTGCAGTGCTG	58.112	50.000	17.60	9.42	0.00	4.41
2053	5634	8.158169	TCAGCTATTTGCATTAAGGAATACTG	57.842	34.615	0.00	0.00	45.94	2.74
2055	5769	7.013655	CAGCTATTTGCATTAAGGAATACTGGT	59.986	37.037	0.00	0.00	45.94	4.00
2125	5839	2.402305	TCAAACATCAAAATGCGCACC	58.598	42.857	14.90	0.00	36.26	5.01
2272	5986	2.766313	GAAAATGGTGTTTTCCTGGCC	58.234	47.619	0.00	0.00	33.54	5.36
2474	6188	1.885887	GGATGAGATGGTCGAGAGGAG	59.114	57.143	0.00	0.00	0.00	3.69
2475	6189	2.488167	GGATGAGATGGTCGAGAGGAGA	60.488	54.545	0.00	0.00	0.00	3.71
2476	6190	2.340210	TGAGATGGTCGAGAGGAGAG	57.660	55.000	0.00	0.00	0.00	3.20
2595	6309	5.833667	AGACCACCTGAATCTCAATCGTATA	59.166	40.000	0.00	0.00	0.00	1.47
2815	6533	1.268625	GTCCTTTGGCCGAAACGAAAT	59.731	47.619	6.92	0.00	0.00	2.17
2826	6544	3.413558	CGAAACGAAATCGGAAATCACC	58.586	45.455	7.81	0.00	44.95	4.02
3109	6842	7.801716	ATTTTTACATATGACGCACCTATGT	57.198	32.000	10.38	12.66	41.05	2.29
3333	7079	9.235537	TCGTGAATTTGTTATTATCATGCATTG	57.764	29.630	0.00	0.00	0.00	2.82
3370	7116	4.033932	CGCGTATTTCAGAAATGGTCATCA	59.966	41.667	17.38	0.00	32.38	3.07
3404	7150	1.073763	TCCTTCTCATGTGGGTTGTGG	59.926	52.381	0.00	0.00	0.00	4.17
3518	7274	0.909610	ACGTGAGTGGATGGGGATGT	60.910	55.000	0.00	0.00	46.97	3.06
3552	7308	3.982241	GCAGCCACCACCAAGTGC	61.982	66.667	0.00	0.00	36.38	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
92	93	0.676782	TCGTCGGTGCTCAGATCAGA	60.677	55.000	0.00	0.00	0.00	3.27
146	149	1.314730	ACGGCGAGAAATTGTTTGGT	58.685	45.000	16.62	0.00	0.00	3.67
187	190	3.226777	AGATAGAAGGACATAGCAGCGT	58.773	45.455	0.00	0.00	0.00	5.07
375	379	2.741486	AAATGTACAGGCACGCCCGT	62.741	55.000	3.95	2.87	39.21	5.28
382	386	6.656632	TTGAACCATTAAAATGTACAGGCA	57.343	33.333	0.33	0.00	34.60	4.75
449	453	3.316308	CACCAAAACTAACTGCTGAAGCT	59.684	43.478	3.61	0.00	42.66	3.74
491	495	5.514059	AATTTTTCAAATTGCACGGATCG	57.486	34.783	0.00	0.00	0.00	3.69
777	781	9.945904	ACTGTTGTTAGGGTTTTATTTCAAAAA	57.054	25.926	0.00	0.00	0.00	1.94
778	782	9.945904	AACTGTTGTTAGGGTTTTATTTCAAAA	57.054	25.926	0.00	0.00	34.15	2.44
779	783	9.372369	CAACTGTTGTTAGGGTTTTATTTCAAA	57.628	29.630	12.30	0.00	34.60	2.69
780	784	8.532819	ACAACTGTTGTTAGGGTTTTATTTCAA	58.467	29.630	19.85	0.00	42.22	2.69
781	785	7.976734	CACAACTGTTGTTAGGGTTTTATTTCA	59.023	33.333	22.66	0.00	43.23	2.69
782	786	7.436970	CCACAACTGTTGTTAGGGTTTTATTTC	59.563	37.037	22.66	0.00	43.23	2.17
783	787	7.093245	ACCACAACTGTTGTTAGGGTTTTATTT	60.093	33.333	25.07	7.14	43.23	1.40
784	788	6.381707	ACCACAACTGTTGTTAGGGTTTTATT	59.618	34.615	25.07	7.68	43.23	1.40
785	789	5.894964	ACCACAACTGTTGTTAGGGTTTTAT	59.105	36.000	25.07	8.22	43.23	1.40
786	790	5.125739	CACCACAACTGTTGTTAGGGTTTTA	59.874	40.000	23.73	0.00	43.23	1.52
787	791	4.081917	CACCACAACTGTTGTTAGGGTTTT	60.082	41.667	23.73	7.81	43.23	2.43
819	823	2.035832	GGTCCTCAAACCACACATTTGG	59.964	50.000	0.00	0.00	43.04	3.28
859	3729	6.176975	AGATGCATCGTCGATTAAACAAAA	57.823	33.333	20.67	0.00	0.00	2.44
892	3762	6.650427	TCGGTGAGCATGTAATAAGTCTAT	57.350	37.500	0.00	0.00	0.00	1.98
897	3768	5.462398	GGTAGTTCGGTGAGCATGTAATAAG	59.538	44.000	0.00	0.00	0.00	1.73
906	3777	0.601558	GAGTGGTAGTTCGGTGAGCA	59.398	55.000	0.00	0.00	0.00	4.26
907	3778	0.108756	GGAGTGGTAGTTCGGTGAGC	60.109	60.000	0.00	0.00	0.00	4.26
940	3811	3.251245	CGGAGAGTGGTACTATAGCTGTG	59.749	52.174	0.00	0.00	0.00	3.66
994	3866	3.142162	TGATGCTGCCATTGCGGG	61.142	61.111	0.00	0.00	44.47	6.13
1113	3997	3.993376	GATGGCCGCCGTGTCGTAA	62.993	63.158	9.46	0.00	0.00	3.18
1397	4284	3.254024	TTCTTCTGGTCGCTGGGCC	62.254	63.158	0.00	0.00	0.00	5.80
1600	4702	9.858217	ATGCAAGCATATGAGAGACTCATCTCG	62.858	44.444	15.95	8.43	46.83	4.04
1726	5028	0.468226	TCGTGTTGTTTGAGCCCTCT	59.532	50.000	0.00	0.00	0.00	3.69
1732	5034	3.423515	CGGTGATGATCGTGTTGTTTGAG	60.424	47.826	0.00	0.00	0.00	3.02
1755	5057	2.176273	CCGGTGTCTATGCTGCAGC	61.176	63.158	31.89	31.89	42.50	5.25
1825	5127	0.605319	GGATCCGGCAGTTTGTCACA	60.605	55.000	0.00	0.00	0.00	3.58
1849	5151	9.512435	CTTCCAAATTTGATAGCACTAGATTTG	57.488	33.333	19.86	9.53	34.49	2.32
1879	5181	2.416701	CCTCTCGAAGTTGAAGGAGCTC	60.417	54.545	4.71	4.71	0.00	4.09
1884	5186	1.719600	CAGCCTCTCGAAGTTGAAGG	58.280	55.000	0.00	0.00	0.00	3.46
1984	5350	2.740981	CCTAACAGCACTGCAAGAAGAG	59.259	50.000	3.30	0.00	37.43	2.85
1985	5351	2.104792	ACCTAACAGCACTGCAAGAAGA	59.895	45.455	3.30	0.00	37.43	2.87
1986	5352	2.225019	CACCTAACAGCACTGCAAGAAG	59.775	50.000	3.30	0.00	37.43	2.85
1996	5362	3.931907	ATAAGATGCCACCTAACAGCA	57.068	42.857	0.00	0.00	41.50	4.41
1997	5497	4.199310	TGAATAAGATGCCACCTAACAGC	58.801	43.478	0.00	0.00	0.00	4.40
2000	5500	5.437060	TCCTTGAATAAGATGCCACCTAAC	58.563	41.667	0.00	0.00	35.92	2.34
2046	5627	6.017109	ACGCATATCCAAATCAACCAGTATTC	60.017	38.462	0.00	0.00	0.00	1.75
2053	5634	7.516627	GCAAAATTACGCATATCCAAATCAACC	60.517	37.037	0.00	0.00	0.00	3.77
2055	5769	7.038048	TGCAAAATTACGCATATCCAAATCAA	58.962	30.769	0.00	0.00	31.95	2.57
2125	5839	4.342862	CCATGAAGGATGGTAGTACCTG	57.657	50.000	20.07	7.34	46.20	4.00
2474	6188	0.329596	ACATCCCACCCTTTGAGCTC	59.670	55.000	6.82	6.82	0.00	4.09
2475	6189	0.779997	AACATCCCACCCTTTGAGCT	59.220	50.000	0.00	0.00	0.00	4.09
2476	6190	2.507407	TAACATCCCACCCTTTGAGC	57.493	50.000	0.00	0.00	0.00	4.26
2815	6533	7.131907	TCAGGAATATTTAGGTGATTTCCGA	57.868	36.000	0.00	0.00	38.10	4.55
2889	6607	3.374042	TTCCCTTCATTATTTCGCCCA	57.626	42.857	0.00	0.00	0.00	5.36
2929	6654	5.588648	GGTCATGGTTTCGAATCCATTTCTA	59.411	40.000	29.81	16.97	41.79	2.10
3254	6999	9.837525	TGAAACATTTTCCAAAAACATTTTGAG	57.162	25.926	15.20	7.21	0.00	3.02
3259	7004	7.095017	ACACGTGAAACATTTTCCAAAAACATT	60.095	29.630	25.01	0.00	35.74	2.71
3333	7079	4.623122	AATACGCGTTGTCAATTTTTGC	57.377	36.364	20.78	0.00	0.00	3.68
3370	7116	6.102321	ACATGAGAAGGATATCCCAACAAGAT	59.898	38.462	18.56	0.00	37.41	2.40
3404	7150	0.749049	GCTTCAAATGGCCATCTCCC	59.251	55.000	21.08	1.94	0.00	4.30
3518	7274	2.883888	GCTGCTGGATGGAGGGTAAAAA	60.884	50.000	0.00	0.00	34.46	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.