AutoCloner

Multiple sequence alignment - TraesCS1D01G076700

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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	TraesCS1D01G076700	chr1D	100.000	3103	0	0	1	3103	58764124	58761022	0.000000e+00	5731
1	TraesCS1D01G076700	chr1D	89.902	2347	218	13	1	2340	58628614	58626280	0.000000e+00	3003
2	TraesCS1D01G076700	chr1D	84.043	1479	225	11	802	2275	36623655	36622183	0.000000e+00	1413
3	TraesCS1D01G076700	chr1D	83.704	1485	222	19	801	2275	38367077	38365603	0.000000e+00	1384
4	TraesCS1D01G076700	chr1D	83.604	1476	240	2	801	2275	38559351	38557877	0.000000e+00	1384
5	TraesCS1D01G076700	chr1D	82.307	1543	259	14	801	2336	50023566	50025101	0.000000e+00	1325
6	TraesCS1D01G076700	chr1D	81.505	784	137	7	26	803	49956361	49957142	3.370000e-179	638
7	TraesCS1D01G076700	chr1B	94.378	2437	134	3	1	2435	94233214	94230779	0.000000e+00	3738
8	TraesCS1D01G076700	chr1B	82.254	2316	358	35	32	2336	94327166	94324893	0.000000e+00	1951
9	TraesCS1D01G076700	chr1B	96.918	584	12	1	2471	3048	94230785	94230202	0.000000e+00	974
10	TraesCS1D01G076700	chr1B	96.667	60	2	0	3044	3103	94230167	94230108	1.970000e-17	100
11	TraesCS1D01G076700	chr1A	89.705	2341	222	13	7	2340	57405787	57403459	0.000000e+00	2970
12	TraesCS1D01G076700	chr1A	92.712	1523	104	5	1	1517	57640145	57638624	0.000000e+00	2191
13	TraesCS1D01G076700	chr1A	81.899	2254	390	17	33	2275	37512149	37509903	0.000000e+00	1886
14	TraesCS1D01G076700	chr1A	84.003	1469	231	4	801	2267	37504384	37502918	0.000000e+00	1408
15	TraesCS1D01G076700	chr1A	96.205	448	17	0	2554	3001	57638625	57638178	0.000000e+00	734
16	TraesCS1D01G076700	chr1A	82.487	788	130	8	24	807	49346853	49347636	0.000000e+00	684
17	TraesCS1D01G076700	chr1A	80.892	785	140	9	26	803	49293482	49294263	7.360000e-171	610

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	TraesCS1D01G076700	chr1D	58761022	58764124	3102	True	5731.0	5731	100.000000	1	3103	1	chr1D.!!$R5	3102
1	TraesCS1D01G076700	chr1D	58626280	58628614	2334	True	3003.0	3003	89.902000	1	2340	1	chr1D.!!$R4	2339
2	TraesCS1D01G076700	chr1D	36622183	36623655	1472	True	1413.0	1413	84.043000	802	2275	1	chr1D.!!$R1	1473
3	TraesCS1D01G076700	chr1D	38365603	38367077	1474	True	1384.0	1384	83.704000	801	2275	1	chr1D.!!$R2	1474
4	TraesCS1D01G076700	chr1D	38557877	38559351	1474	True	1384.0	1384	83.604000	801	2275	1	chr1D.!!$R3	1474
5	TraesCS1D01G076700	chr1D	50023566	50025101	1535	False	1325.0	1325	82.307000	801	2336	1	chr1D.!!$F2	1535
6	TraesCS1D01G076700	chr1D	49956361	49957142	781	False	638.0	638	81.505000	26	803	1	chr1D.!!$F1	777
7	TraesCS1D01G076700	chr1B	94324893	94327166	2273	True	1951.0	1951	82.254000	32	2336	1	chr1B.!!$R1	2304
8	TraesCS1D01G076700	chr1B	94230108	94233214	3106	True	1604.0	3738	95.987667	1	3103	3	chr1B.!!$R2	3102
9	TraesCS1D01G076700	chr1A	57403459	57405787	2328	True	2970.0	2970	89.705000	7	2340	1	chr1A.!!$R3	2333
10	TraesCS1D01G076700	chr1A	37509903	37512149	2246	True	1886.0	1886	81.899000	33	2275	1	chr1A.!!$R2	2242
11	TraesCS1D01G076700	chr1A	57638178	57640145	1967	True	1462.5	2191	94.458500	1	3001	2	chr1A.!!$R4	3000
12	TraesCS1D01G076700	chr1A	37502918	37504384	1466	True	1408.0	1408	84.003000	801	2267	1	chr1A.!!$R1	1466
13	TraesCS1D01G076700	chr1A	49346853	49347636	783	False	684.0	684	82.487000	24	807	1	chr1A.!!$F2	783
14	TraesCS1D01G076700	chr1A	49293482	49294263	781	False	610.0	610	80.892000	26	803	1	chr1A.!!$F1	777

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
441	442	0.24746	CAAGACGGACAGATGAGGCA	59.753	55.000	0.0	0.0	0.00	4.75	F
456	457	1.15415	GGCAATCAACGTGCTGCTC	60.154	57.895	0.0	0.0	41.88	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1364	1376	1.566231	ACCCTTCCTTCCTTGCATAGG	59.434	52.381	8.22	8.22	46.27	2.57	R
2324	2343	2.367567	TCTCGGCTGAAACTGTACCTTT	59.632	45.455	0.00	0.00	0.00	3.11	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
233	234	1.893919	GCTCTCGGCCTCTTCAACCT	61.894	60.000	0.00	0.00	34.27	3.50
260	261	3.612247	GAGAAGAAGCAGGGCCGCA	62.612	63.158	19.61	0.00	0.00	5.69
294	295	3.407698	CACAACCTGCACCTACAACATA	58.592	45.455	0.00	0.00	0.00	2.29
363	364	3.302347	CTTCGGCCGCTTCCTGAGT	62.302	63.158	23.51	0.00	0.00	3.41
395	396	1.787847	CAAACCAGATCGTCGCCAC	59.212	57.895	0.00	0.00	0.00	5.01
441	442	0.247460	CAAGACGGACAGATGAGGCA	59.753	55.000	0.00	0.00	0.00	4.75
456	457	1.154150	GGCAATCAACGTGCTGCTC	60.154	57.895	0.00	0.00	41.88	4.26
471	472	2.103771	GCTGCTCCATAGGATGTCTGAA	59.896	50.000	0.00	0.00	0.00	3.02
837	849	5.249393	ACTTGGAACTCATTCATGTACTCCT	59.751	40.000	0.00	0.00	36.46	3.69
1112	1124	3.004734	CCGAAATGCAGGAACAAAGAGTT	59.995	43.478	0.00	0.00	44.93	3.01
1117	1129	4.689612	TGCAGGAACAAAGAGTTAGTCT	57.310	40.909	0.00	0.00	41.51	3.24
1269	1281	7.398829	TCTAATTCAGGGCTTTTGTACACATA	58.601	34.615	0.00	0.00	0.00	2.29
1364	1376	6.147821	TGTTCTTCAGCTCAGTAATAAACAGC	59.852	38.462	0.00	0.00	0.00	4.40
2198	2214	4.453819	GCTTCAACTACTTCACTGATGCTT	59.546	41.667	0.00	0.00	36.53	3.91
2324	2343	6.544928	TTGTATATGAGCAGAACTCCTCAA	57.455	37.500	0.00	0.00	45.61	3.02
2342	2361	2.875933	TCAAAAGGTACAGTTTCAGCCG	59.124	45.455	0.00	0.00	0.00	5.52
2357	2376	4.409342	CCGAGAAGGCAGATGACG	57.591	61.111	0.00	0.00	0.00	4.35
2358	2377	1.513158	CCGAGAAGGCAGATGACGT	59.487	57.895	0.00	0.00	0.00	4.34
2368	2387	3.006323	AGGCAGATGACGTAATGAGGATC	59.994	47.826	0.00	0.00	0.00	3.36
2435	2454	0.909133	GGATGGTTTGGGGCCACAAT	60.909	55.000	23.96	6.18	39.03	2.71
2436	2455	0.249955	GATGGTTTGGGGCCACAATG	59.750	55.000	23.96	0.00	39.03	2.82
2437	2456	0.178909	ATGGTTTGGGGCCACAATGA	60.179	50.000	23.96	4.14	39.03	2.57
2438	2457	0.178909	TGGTTTGGGGCCACAATGAT	60.179	50.000	23.96	0.00	0.00	2.45
2439	2458	0.536724	GGTTTGGGGCCACAATGATC	59.463	55.000	23.96	3.55	0.00	2.92
2440	2459	1.560505	GTTTGGGGCCACAATGATCT	58.439	50.000	23.96	0.00	0.00	2.75
2441	2460	1.205417	GTTTGGGGCCACAATGATCTG	59.795	52.381	23.96	0.00	0.00	2.90
2442	2461	0.971959	TTGGGGCCACAATGATCTGC	60.972	55.000	18.93	0.00	0.00	4.26
2443	2462	1.076485	GGGGCCACAATGATCTGCT	60.076	57.895	4.39	0.00	0.00	4.24
2444	2463	1.389609	GGGGCCACAATGATCTGCTG	61.390	60.000	4.39	0.00	0.00	4.41
2445	2464	0.682209	GGGCCACAATGATCTGCTGT	60.682	55.000	4.39	0.00	0.00	4.40
2446	2465	1.408683	GGGCCACAATGATCTGCTGTA	60.409	52.381	4.39	0.00	0.00	2.74
2447	2466	2.368439	GGCCACAATGATCTGCTGTAA	58.632	47.619	0.00	0.00	0.00	2.41
2448	2467	2.954318	GGCCACAATGATCTGCTGTAAT	59.046	45.455	0.00	0.00	0.00	1.89
2449	2468	4.136796	GGCCACAATGATCTGCTGTAATA	58.863	43.478	0.00	0.00	0.00	0.98
2450	2469	4.763793	GGCCACAATGATCTGCTGTAATAT	59.236	41.667	0.00	0.00	0.00	1.28
2451	2470	5.242393	GGCCACAATGATCTGCTGTAATATT	59.758	40.000	0.00	0.00	0.00	1.28
2452	2471	6.147581	GCCACAATGATCTGCTGTAATATTG	58.852	40.000	0.00	0.00	0.00	1.90
2453	2472	6.016860	GCCACAATGATCTGCTGTAATATTGA	60.017	38.462	0.00	0.00	0.00	2.57
2454	2473	7.309012	GCCACAATGATCTGCTGTAATATTGAT	60.309	37.037	0.00	0.00	0.00	2.57
2455	2474	9.223099	CCACAATGATCTGCTGTAATATTGATA	57.777	33.333	0.00	0.00	0.00	2.15
2460	2479	8.822652	TGATCTGCTGTAATATTGATACTGTG	57.177	34.615	0.00	0.00	0.00	3.66
2461	2480	8.641541	TGATCTGCTGTAATATTGATACTGTGA	58.358	33.333	0.00	0.00	0.00	3.58
2462	2481	9.650539	GATCTGCTGTAATATTGATACTGTGAT	57.349	33.333	0.00	2.37	0.00	3.06
2463	2482	9.650539	ATCTGCTGTAATATTGATACTGTGATC	57.349	33.333	0.00	0.00	0.00	2.92
2464	2483	8.641541	TCTGCTGTAATATTGATACTGTGATCA	58.358	33.333	0.00	0.00	33.96	2.92
2465	2484	9.264719	CTGCTGTAATATTGATACTGTGATCAA	57.735	33.333	0.00	12.03	46.93	2.57
2473	2492	6.484364	TTGATACTGTGATCAATAGAGCCA	57.516	37.500	13.53	6.31	40.18	4.75
2474	2493	5.847304	TGATACTGTGATCAATAGAGCCAC	58.153	41.667	13.53	0.00	32.84	5.01
2475	2494	5.363580	TGATACTGTGATCAATAGAGCCACA	59.636	40.000	13.53	0.00	38.27	4.17
2476	2495	4.558226	ACTGTGATCAATAGAGCCACAA	57.442	40.909	13.53	0.00	39.29	3.33
2733	2758	5.106555	GCTTTTGTGATCAGCTTAGCACTAA	60.107	40.000	16.54	12.55	36.72	2.24
2820	2845	6.018016	CGAAAAATGTCAAGGCCAAAAGAAAT	60.018	34.615	5.01	0.00	0.00	2.17
3016	3041	7.012421	TCTGAAAGGTTTAAAGCTTCTCAAGAC	59.988	37.037	27.71	15.27	45.17	3.01
3017	3042	6.039382	TGAAAGGTTTAAAGCTTCTCAAGACC	59.961	38.462	27.71	12.84	45.17	3.85
3020	3045	2.094762	TAAAGCTTCTCAAGACCGGC	57.905	50.000	0.00	0.00	0.00	6.13
3048	3073	1.676014	GGACGGTTGGAGATGGACAAG	60.676	57.143	0.00	0.00	0.00	3.16
3049	3074	1.275291	GACGGTTGGAGATGGACAAGA	59.725	52.381	0.00	0.00	0.00	3.02
3092	3156	4.126208	TCGAATTTTGCATGCATTGGAT	57.874	36.364	23.37	10.23	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
78	79	2.280797	TGGTGTGCGTCTTCAGGC	60.281	61.111	0.00	0.00	0.00	4.85
294	295	1.376942	GCAGCAGCTGTCCATGAGT	60.377	57.895	23.60	0.00	37.91	3.41
395	396	2.190488	GAGGCACTTGAGGAGGGTGG	62.190	65.000	0.00	0.00	41.55	4.61
441	442	2.283298	CTATGGAGCAGCACGTTGATT	58.717	47.619	0.00	0.00	0.00	2.57
456	457	4.607293	TCCGAATTCAGACATCCTATGG	57.393	45.455	6.22	0.00	33.60	2.74
471	472	3.206150	GACATTAGGCACACATCCGAAT	58.794	45.455	0.00	0.00	30.57	3.34
807	815	6.970484	ACATGAATGAGTTCCAAGTAACAAC	58.030	36.000	0.00	0.00	33.26	3.32
837	849	3.276857	TGCTTTTTCCATGCTTGCAAAA	58.723	36.364	0.00	0.00	0.00	2.44
891	903	1.153756	CAGGTTTGAGGCCCTTGGT	59.846	57.895	0.00	0.00	0.00	3.67
987	999	6.095440	GCTACAATACCATTGTCTTCCATTGT	59.905	38.462	7.76	0.00	38.36	2.71
1112	1124	1.644509	AGGTGCACACATCCAGACTA	58.355	50.000	20.43	0.00	0.00	2.59
1181	1193	7.434307	GCAATCATCTCATTTAGTTTGTCCATG	59.566	37.037	0.00	0.00	0.00	3.66
1269	1281	3.493176	GCCTTTGCTTTCACCAAATCACT	60.493	43.478	0.00	0.00	32.34	3.41
1364	1376	1.566231	ACCCTTCCTTCCTTGCATAGG	59.434	52.381	8.22	8.22	46.27	2.57
1890	1902	3.256631	TCTCTTCCCTTAACCGTGTACAC	59.743	47.826	16.32	16.32	0.00	2.90
2324	2343	2.367567	TCTCGGCTGAAACTGTACCTTT	59.632	45.455	0.00	0.00	0.00	3.11
2342	2361	4.046938	TCATTACGTCATCTGCCTTCTC	57.953	45.455	0.00	0.00	0.00	2.87
2351	2370	6.763610	AGAAAAAGGATCCTCATTACGTCATC	59.236	38.462	16.52	6.94	0.00	2.92
2357	2376	8.964476	TCATACAGAAAAAGGATCCTCATTAC	57.036	34.615	16.52	6.29	0.00	1.89
2358	2377	9.618890	CTTCATACAGAAAAAGGATCCTCATTA	57.381	33.333	16.52	0.42	35.40	1.90
2368	2387	8.572855	AAGAGGAATCTTCATACAGAAAAAGG	57.427	34.615	0.00	0.00	35.40	3.11
2398	2417	4.406972	CCATCCTCATACAGTCCTCTCAAA	59.593	45.833	0.00	0.00	0.00	2.69
2435	2454	8.641541	TCACAGTATCAATATTACAGCAGATCA	58.358	33.333	0.00	0.00	0.00	2.92
2436	2455	9.650539	ATCACAGTATCAATATTACAGCAGATC	57.349	33.333	0.00	0.00	0.00	2.75
2437	2456	9.650539	GATCACAGTATCAATATTACAGCAGAT	57.349	33.333	0.00	0.00	0.00	2.90
2438	2457	8.641541	TGATCACAGTATCAATATTACAGCAGA	58.358	33.333	0.00	0.00	32.97	4.26
2439	2458	8.822652	TGATCACAGTATCAATATTACAGCAG	57.177	34.615	0.00	0.00	32.97	4.24
2450	2469	6.127083	TGTGGCTCTATTGATCACAGTATCAA	60.127	38.462	0.00	2.07	46.81	2.57
2451	2470	5.363580	TGTGGCTCTATTGATCACAGTATCA	59.636	40.000	0.00	0.00	34.10	2.15
2452	2471	5.847304	TGTGGCTCTATTGATCACAGTATC	58.153	41.667	0.00	0.00	34.10	2.24
2453	2472	5.876651	TGTGGCTCTATTGATCACAGTAT	57.123	39.130	0.00	0.00	34.10	2.12
2454	2473	5.046663	TGTTGTGGCTCTATTGATCACAGTA	60.047	40.000	0.00	0.00	37.47	2.74
2455	2474	4.256920	GTTGTGGCTCTATTGATCACAGT	58.743	43.478	0.00	0.00	37.47	3.55
2456	2475	4.256110	TGTTGTGGCTCTATTGATCACAG	58.744	43.478	0.00	0.00	37.47	3.66
2457	2476	4.020307	TCTGTTGTGGCTCTATTGATCACA	60.020	41.667	0.00	8.54	35.80	3.58
2458	2477	4.507710	TCTGTTGTGGCTCTATTGATCAC	58.492	43.478	0.00	4.65	0.00	3.06
2459	2478	4.467438	TCTCTGTTGTGGCTCTATTGATCA	59.533	41.667	0.00	0.00	0.00	2.92
2460	2479	5.016051	TCTCTGTTGTGGCTCTATTGATC	57.984	43.478	0.00	0.00	0.00	2.92
2461	2480	5.181748	GTTCTCTGTTGTGGCTCTATTGAT	58.818	41.667	0.00	0.00	0.00	2.57
2462	2481	4.563580	GGTTCTCTGTTGTGGCTCTATTGA	60.564	45.833	0.00	0.00	0.00	2.57
2463	2482	3.686726	GGTTCTCTGTTGTGGCTCTATTG	59.313	47.826	0.00	0.00	0.00	1.90
2464	2483	3.584848	AGGTTCTCTGTTGTGGCTCTATT	59.415	43.478	0.00	0.00	0.00	1.73
2465	2484	3.177228	AGGTTCTCTGTTGTGGCTCTAT	58.823	45.455	0.00	0.00	0.00	1.98
2466	2485	2.609747	AGGTTCTCTGTTGTGGCTCTA	58.390	47.619	0.00	0.00	0.00	2.43
2467	2486	1.428869	AGGTTCTCTGTTGTGGCTCT	58.571	50.000	0.00	0.00	0.00	4.09
2468	2487	2.354203	CCTAGGTTCTCTGTTGTGGCTC	60.354	54.545	0.00	0.00	0.00	4.70
2469	2488	1.625818	CCTAGGTTCTCTGTTGTGGCT	59.374	52.381	0.00	0.00	0.00	4.75
2470	2489	1.623811	TCCTAGGTTCTCTGTTGTGGC	59.376	52.381	9.08	0.00	0.00	5.01
2471	2490	4.559862	ATTCCTAGGTTCTCTGTTGTGG	57.440	45.455	9.08	0.00	0.00	4.17
2472	2491	4.697352	CCAATTCCTAGGTTCTCTGTTGTG	59.303	45.833	9.08	0.00	0.00	3.33
2473	2492	4.351111	ACCAATTCCTAGGTTCTCTGTTGT	59.649	41.667	9.08	0.00	33.39	3.32
2474	2493	4.911390	ACCAATTCCTAGGTTCTCTGTTG	58.089	43.478	9.08	4.93	33.39	3.33
2475	2494	6.697641	TTACCAATTCCTAGGTTCTCTGTT	57.302	37.500	9.08	0.00	39.31	3.16
2476	2495	6.500751	TCTTTACCAATTCCTAGGTTCTCTGT	59.499	38.462	9.08	3.51	39.31	3.41
2733	2758	2.764572	CACCCCCAGTACGTTTCTATCT	59.235	50.000	0.00	0.00	0.00	1.98
2820	2845	0.112995	ACAGAAGCCAAGGCATCCAA	59.887	50.000	14.40	0.00	44.88	3.53
2951	2976	3.573110	ACGACATATACCCTAGGTTGAGC	59.427	47.826	8.29	0.00	37.09	4.26
3016	3041	0.675522	AACCGTCCAACTAATGCCGG	60.676	55.000	0.00	0.00	43.61	6.13
3017	3042	0.446222	CAACCGTCCAACTAATGCCG	59.554	55.000	0.00	0.00	0.00	5.69
3020	3045	3.328382	TCTCCAACCGTCCAACTAATG	57.672	47.619	0.00	0.00	0.00	1.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.