AutoCloner

Multiple sequence alignment - TraesCS3D01G203200

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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	TraesCS3D01G203200	chr3D	100.000	2459	0	0	1	2459	252333502	252331044	0.000000e+00	4542
1	TraesCS3D01G203200	chr3D	97.683	259	6	0	1	259	579163782	579164040	1.730000e-121	446
2	TraesCS3D01G203200	chr1D	95.840	2404	87	4	1	2401	447755856	447753463	0.000000e+00	3873
3	TraesCS3D01G203200	chr5D	96.345	2189	75	3	217	2401	530733965	530736152	0.000000e+00	3594
4	TraesCS3D01G203200	chr5D	96.468	2180	68	3	217	2395	320661370	320663541	0.000000e+00	3591
5	TraesCS3D01G203200	chr5D	96.113	2187	74	4	217	2402	363006232	363008408	0.000000e+00	3557
6	TraesCS3D01G203200	chr5D	95.757	2192	89	2	217	2404	134488989	134486798	0.000000e+00	3530
7	TraesCS3D01G203200	chr5D	95.751	2189	81	6	217	2401	350368764	350366584	0.000000e+00	3517
8	TraesCS3D01G203200	chr5D	98.456	259	4	0	1	259	363005954	363006212	8.010000e-125	457
9	TraesCS3D01G203200	chr2D	95.930	2187	75	4	217	2401	114667580	114665406	0.000000e+00	3533
10	TraesCS3D01G203200	chr2D	97.692	260	5	1	1	259	82210809	82210550	1.730000e-121	446
11	TraesCS3D01G203200	chr2D	97.683	259	6	0	1	259	114667858	114667600	1.730000e-121	446
12	TraesCS3D01G203200	chr7D	95.753	2190	83	6	217	2401	550636653	550638837	0.000000e+00	3520
13	TraesCS3D01G203200	chr7D	97.683	259	6	0	1	259	604446938	604447196	1.730000e-121	446
14	TraesCS3D01G203200	chr4A	95.492	2196	89	5	217	2407	574553949	574551759	0.000000e+00	3498
15	TraesCS3D01G203200	chr4B	97.297	259	7	0	1	259	525306362	525306620	8.070000e-120	440
16	TraesCS3D01G203200	chr1A	96.911	259	8	0	1	259	50970775	50970517	3.760000e-118	435
17	TraesCS3D01G203200	chr1A	96.911	259	8	0	1	259	104231958	104231700	3.760000e-118	435
18	TraesCS3D01G203200	chr3A	100.000	59	0	0	2401	2459	332227622	332227680	2.590000e-20	110

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	TraesCS3D01G203200	chr3D	252331044	252333502	2458	True	4542.0	4542	100.0000	1	2459	1	chr3D.!!$R1	2458
1	TraesCS3D01G203200	chr1D	447753463	447755856	2393	True	3873.0	3873	95.8400	1	2401	1	chr1D.!!$R1	2400
2	TraesCS3D01G203200	chr5D	530733965	530736152	2187	False	3594.0	3594	96.3450	217	2401	1	chr5D.!!$F2	2184
3	TraesCS3D01G203200	chr5D	320661370	320663541	2171	False	3591.0	3591	96.4680	217	2395	1	chr5D.!!$F1	2178
4	TraesCS3D01G203200	chr5D	134486798	134488989	2191	True	3530.0	3530	95.7570	217	2404	1	chr5D.!!$R1	2187
5	TraesCS3D01G203200	chr5D	350366584	350368764	2180	True	3517.0	3517	95.7510	217	2401	1	chr5D.!!$R2	2184
6	TraesCS3D01G203200	chr5D	363005954	363008408	2454	False	2007.0	3557	97.2845	1	2402	2	chr5D.!!$F3	2401
7	TraesCS3D01G203200	chr2D	114665406	114667858	2452	True	1989.5	3533	96.8065	1	2401	2	chr2D.!!$R2	2400
8	TraesCS3D01G203200	chr7D	550636653	550638837	2184	False	3520.0	3520	95.7530	217	2401	1	chr7D.!!$F1	2184
9	TraesCS3D01G203200	chr4A	574551759	574553949	2190	True	3498.0	3498	95.4920	217	2407	1	chr4A.!!$R1	2190

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
909	979	1.556911	CTGTCCACCATTGCCTACTCT	59.443	52.381	0.0	0.0	0.0	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2416	2497	0.03716	GGGTGTTTGGGTGTCGGTAT	59.963	55.0	0.0	0.0	0.0	2.73	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
46	47	6.872628	TTGATCTAGATGCATGGTTGATTC	57.127	37.500	10.74	0.00	0.00	2.52
57	58	3.417069	TGGTTGATTCGTGGTCTGATT	57.583	42.857	0.00	0.00	0.00	2.57
249	250	7.910584	TGCTATGATAGTGATGAACCATGTAT	58.089	34.615	0.92	0.00	0.00	2.29
260	323	6.813152	TGATGAACCATGTATATGTATGCTCG	59.187	38.462	0.00	0.00	32.21	5.03
357	421	2.478709	CGCAGACGCAAGATCTTAGTCT	60.479	50.000	27.00	27.00	38.99	3.24
470	534	3.634448	CGAGTCTGATTCCCTCTATGTGT	59.366	47.826	0.00	0.00	0.00	3.72
616	686	2.287644	CGTGCTGAACAAGATGTGTGAA	59.712	45.455	0.00	0.00	40.60	3.18
747	817	3.322828	GTGTACAACCACCTGAGGAAGTA	59.677	47.826	4.99	0.00	0.00	2.24
759	829	5.104444	ACCTGAGGAAGTAGAGAAGTCGATA	60.104	44.000	4.99	0.00	0.00	2.92
795	865	1.658686	CTGAGAGACCTTAGCGGCGT	61.659	60.000	9.37	0.00	35.61	5.68
820	890	1.699083	TGGGATGAGAACACTTGCTCA	59.301	47.619	0.00	0.00	44.43	4.26
909	979	1.556911	CTGTCCACCATTGCCTACTCT	59.443	52.381	0.00	0.00	0.00	3.24
984	1054	2.174639	TGAGTTCCTCAACACACCCATT	59.825	45.455	0.00	0.00	37.57	3.16
1097	1167	1.229658	CTGACTTCCCTGGGACCCT	60.230	63.158	16.85	0.00	0.00	4.34
1173	1248	2.682563	GCCATTTGACCCCGTTGATAGA	60.683	50.000	0.00	0.00	0.00	1.98
1219	1294	3.070878	GGAGGAGGAGATCAATGTCTTCC	59.929	52.174	9.51	9.51	43.81	3.46
1226	1301	1.063174	GATCAATGTCTTCCGCAGCAC	59.937	52.381	0.00	0.00	0.00	4.40
1291	1366	2.044650	CCCTCGACGTCCACCCTA	60.045	66.667	10.58	0.00	0.00	3.53
1417	1492	1.977009	ATGGTCGACGCTCACAGGA	60.977	57.895	9.92	0.00	0.00	3.86
1420	1495	1.506718	GTCGACGCTCACAGGATGA	59.493	57.895	0.00	0.00	39.69	2.92
1489	1564	1.759293	CTGTGAGCGTGCATGATCCG	61.759	60.000	20.81	5.47	0.00	4.18
1839	1919	1.285280	TGCTAGGGCAAGTGGTATGT	58.715	50.000	0.00	0.00	46.36	2.29
1901	1981	1.985473	AGAAGCCAATGCACAAGTGA	58.015	45.000	4.04	0.00	41.13	3.41
1917	1997	5.291858	CACAAGTGACATCGTATAGCAACAT	59.708	40.000	0.00	0.00	0.00	2.71
2167	2247	3.710165	GGTAAGCTCACCAACTAGGGTAT	59.290	47.826	0.00	0.00	43.89	2.73
2204	2285	3.468770	TGTACACGTATGCAACCAAACT	58.531	40.909	0.00	0.00	0.00	2.66
2404	2485	1.066752	GAACCAAACACGCCCCAAC	59.933	57.895	0.00	0.00	0.00	3.77
2407	2488	2.727544	CAAACACGCCCCAACTGG	59.272	61.111	0.00	0.00	0.00	4.00
2408	2489	1.826054	CAAACACGCCCCAACTGGA	60.826	57.895	0.00	0.00	37.39	3.86
2409	2490	1.152830	AAACACGCCCCAACTGGAT	59.847	52.632	0.00	0.00	37.39	3.41
2410	2491	1.178534	AAACACGCCCCAACTGGATG	61.179	55.000	0.00	0.00	37.39	3.51
2411	2492	2.751436	CACGCCCCAACTGGATGG	60.751	66.667	0.00	0.00	40.35	3.51
2412	2493	3.256960	ACGCCCCAACTGGATGGT	61.257	61.111	0.00	0.00	38.91	3.55
2413	2494	2.751436	CGCCCCAACTGGATGGTG	60.751	66.667	0.00	0.00	38.91	4.17
2414	2495	2.440599	GCCCCAACTGGATGGTGT	59.559	61.111	0.00	0.00	38.91	4.16
2415	2496	1.678970	GCCCCAACTGGATGGTGTC	60.679	63.158	0.00	0.00	38.91	3.67
2416	2497	1.767036	CCCCAACTGGATGGTGTCA	59.233	57.895	0.00	0.00	38.91	3.58
2417	2498	0.332632	CCCCAACTGGATGGTGTCAT	59.667	55.000	0.00	0.00	38.91	3.06
2418	2499	1.563879	CCCCAACTGGATGGTGTCATA	59.436	52.381	0.00	0.00	38.91	2.15
2419	2500	2.643551	CCCAACTGGATGGTGTCATAC	58.356	52.381	0.00	0.00	38.91	2.39
2420	2501	2.643551	CCAACTGGATGGTGTCATACC	58.356	52.381	0.00	0.00	43.53	2.73
2421	2502	3.000067	CCAACTGGATGGTGTCATACCG	61.000	54.545	0.00	0.00	45.18	4.02
2422	2503	5.251847	CCAACTGGATGGTGTCATACCGA	62.252	52.174	0.00	0.00	45.18	4.69
2432	2513	2.172851	GTCATACCGACACCCAAACA	57.827	50.000	0.00	0.00	44.69	2.83
2433	2514	1.802365	GTCATACCGACACCCAAACAC	59.198	52.381	0.00	0.00	44.69	3.32
2434	2515	1.161843	CATACCGACACCCAAACACC	58.838	55.000	0.00	0.00	0.00	4.16
2435	2516	0.037160	ATACCGACACCCAAACACCC	59.963	55.000	0.00	0.00	0.00	4.61
2436	2517	1.343431	TACCGACACCCAAACACCCA	61.343	55.000	0.00	0.00	0.00	4.51
2437	2518	1.896660	CCGACACCCAAACACCCAG	60.897	63.158	0.00	0.00	0.00	4.45
2438	2519	1.147376	CGACACCCAAACACCCAGA	59.853	57.895	0.00	0.00	0.00	3.86
2439	2520	1.164041	CGACACCCAAACACCCAGAC	61.164	60.000	0.00	0.00	0.00	3.51
2440	2521	1.153046	ACACCCAAACACCCAGACG	60.153	57.895	0.00	0.00	0.00	4.18
2441	2522	1.896660	CACCCAAACACCCAGACGG	60.897	63.158	0.00	0.00	37.81	4.79
2454	2535	3.311110	GACGGGCCTGTCTGGTCA	61.311	66.667	33.52	0.00	43.75	4.02
2455	2536	3.302347	GACGGGCCTGTCTGGTCAG	62.302	68.421	33.52	0.70	43.75	3.51
2456	2537	3.314331	CGGGCCTGTCTGGTCAGT	61.314	66.667	2.29	0.00	43.75	3.41
2457	2538	2.348998	GGGCCTGTCTGGTCAGTG	59.651	66.667	0.84	0.00	43.75	3.66
2458	2539	2.520536	GGGCCTGTCTGGTCAGTGT	61.521	63.158	0.84	0.00	43.75	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	1.462283	CAGCTCACAAATCAGACCACG	59.538	52.381	0.00	0.00	0.00	4.94
57	58	3.719268	ACCAACCATATCAGCTCACAA	57.281	42.857	0.00	0.00	0.00	3.33
249	250	3.809279	CCATGAAAGCACGAGCATACATA	59.191	43.478	7.77	0.00	45.49	2.29
260	323	1.133025	CCGGACAATCCATGAAAGCAC	59.867	52.381	0.00	0.00	35.91	4.40
302	366	1.006832	AATCGTAGCACGCATTGACC	58.993	50.000	4.15	0.00	42.21	4.02
357	421	4.308458	CGGACACGACAAGGGCCA	62.308	66.667	6.18	0.00	44.60	5.36
493	557	0.811219	CGGCAGCAGCAGCAGTATTA	60.811	55.000	12.41	0.00	45.49	0.98
494	558	2.110967	CGGCAGCAGCAGCAGTATT	61.111	57.895	12.41	0.00	45.49	1.89
495	559	2.513204	CGGCAGCAGCAGCAGTAT	60.513	61.111	12.41	0.00	45.49	2.12
616	686	5.192923	AGTCCTAACTCCACTAGAGATGAGT	59.807	44.000	0.00	0.00	46.50	3.41
747	817	5.197451	ACACTTGGATCTATCGACTTCTCT	58.803	41.667	0.00	0.00	0.00	3.10
759	829	1.980765	TCAGCTTGGACACTTGGATCT	59.019	47.619	0.00	0.00	0.00	2.75
820	890	2.093235	GTGCTCTGCCTCCAGAACTATT	60.093	50.000	0.00	0.00	46.84	1.73
909	979	6.183360	ACACAAGTGTTGTTAGTTGCGATTAA	60.183	34.615	0.00	0.00	43.23	1.40
984	1054	3.866066	GCTGCATCTGGTTGTAGTTCTGA	60.866	47.826	0.00	0.00	32.56	3.27
1097	1167	1.405463	CATCAAGGATCTCGACGTCCA	59.595	52.381	10.58	0.00	36.96	4.02
1173	1248	1.080329	AGGCCTCCTCTCTTCCTCTTT	59.920	52.381	0.00	0.00	0.00	2.52
1226	1301	2.125912	CCTTCACCGCCTCAGTCG	60.126	66.667	0.00	0.00	0.00	4.18
1291	1366	0.253044	ATGACAGCGCCATACAGGTT	59.747	50.000	2.29	0.00	40.61	3.50
1380	1455	2.122167	GGCAACGAACCCAACACCA	61.122	57.895	0.00	0.00	0.00	4.17
1520	1595	1.733360	TGTACGTCGTCATCGTCATCA	59.267	47.619	0.00	0.00	41.72	3.07
1839	1919	2.489971	GAACCTCACCAATGAACACGA	58.510	47.619	0.00	0.00	33.30	4.35
1901	1981	8.793592	TCTATAGTTGATGTTGCTATACGATGT	58.206	33.333	0.00	0.00	0.00	3.06
1917	1997	7.147880	GCTTAGTCTTGAACCCTCTATAGTTGA	60.148	40.741	0.00	0.00	0.00	3.18
2167	2247	4.687018	CGTGTACATGTTGTGCTTACCTTA	59.313	41.667	2.30	0.00	33.97	2.69
2204	2285	0.319986	TAGCGGCACATGAACACGAA	60.320	50.000	0.00	0.00	0.00	3.85
2259	2340	5.726793	CCCTAGTCCCTGCATTAGGTAATAT	59.273	44.000	0.00	0.00	45.80	1.28
2414	2495	1.270947	GGTGTTTGGGTGTCGGTATGA	60.271	52.381	0.00	0.00	0.00	2.15
2415	2496	1.161843	GGTGTTTGGGTGTCGGTATG	58.838	55.000	0.00	0.00	0.00	2.39
2416	2497	0.037160	GGGTGTTTGGGTGTCGGTAT	59.963	55.000	0.00	0.00	0.00	2.73
2417	2498	1.343431	TGGGTGTTTGGGTGTCGGTA	61.343	55.000	0.00	0.00	0.00	4.02
2418	2499	2.193786	GGGTGTTTGGGTGTCGGT	59.806	61.111	0.00	0.00	0.00	4.69
2419	2500	1.896660	CTGGGTGTTTGGGTGTCGG	60.897	63.158	0.00	0.00	0.00	4.79
2420	2501	1.147376	TCTGGGTGTTTGGGTGTCG	59.853	57.895	0.00	0.00	0.00	4.35
2421	2502	1.164041	CGTCTGGGTGTTTGGGTGTC	61.164	60.000	0.00	0.00	0.00	3.67
2422	2503	1.153046	CGTCTGGGTGTTTGGGTGT	60.153	57.895	0.00	0.00	0.00	4.16
2423	2504	1.896660	CCGTCTGGGTGTTTGGGTG	60.897	63.158	0.00	0.00	0.00	4.61
2424	2505	2.513895	CCGTCTGGGTGTTTGGGT	59.486	61.111	0.00	0.00	0.00	4.51
2437	2518	3.302347	CTGACCAGACAGGCCCGTC	62.302	68.421	11.43	11.43	43.14	4.79
2438	2519	3.314331	CTGACCAGACAGGCCCGT	61.314	66.667	0.00	0.00	43.14	5.28
2439	2520	3.314331	ACTGACCAGACAGGCCCG	61.314	66.667	0.00	0.00	43.14	6.13
2440	2521	2.348998	CACTGACCAGACAGGCCC	59.651	66.667	0.00	0.00	43.14	5.80
2441	2522	3.151906	ACACTGACCAGACAGGCC	58.848	61.111	3.76	0.00	43.14	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.