AutoCloner

Multiple sequence alignment - TraesCS2D01G287600

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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	TraesCS2D01G287600	chr2D	100.000	4633	0	0	1	4633	367998231	367993599	0.000000e+00	8556.0
1	TraesCS2D01G287600	chr2D	96.699	515	15	2	1	514	443481088	443480575	0.000000e+00	856.0
2	TraesCS2D01G287600	chr2D	96.126	413	14	2	1	413	184111094	184111504	0.000000e+00	673.0
3	TraesCS2D01G287600	chr2D	84.742	426	31	15	1	411	604047016	604046610	3.360000e-106	396.0
4	TraesCS2D01G287600	chr2D	87.538	329	35	4	2249	2576	410406807	410407130	4.380000e-100	375.0
5	TraesCS2D01G287600	chr2D	97.059	102	3	0	316	417	443480672	443480571	6.160000e-39	172.0
6	TraesCS2D01G287600	chr2D	100.000	47	0	0	372	418	602570011	602569965	2.300000e-13	87.9
7	TraesCS2D01G287600	chr2D	83.158	95	11	5	325	417	427515578	427515487	1.070000e-11	82.4
8	TraesCS2D01G287600	chr2D	81.250	96	13	5	325	418	427532543	427532451	6.430000e-09	73.1
9	TraesCS2D01G287600	chr2B	96.184	2463	58	10	2201	4633	436997503	436995047	0.000000e+00	3995.0
10	TraesCS2D01G287600	chr2B	97.365	1670	37	2	536	2204	436999288	436997625	0.000000e+00	2833.0
11	TraesCS2D01G287600	chr2B	85.165	182	27	0	5	186	97971933	97971752	2.200000e-43	187.0
12	TraesCS2D01G287600	chr2A	96.332	1554	25	5	2428	3961	498091656	498090115	0.000000e+00	2525.0
13	TraesCS2D01G287600	chr2A	96.801	1094	26	6	1339	2431	498093022	498091937	0.000000e+00	1818.0
14	TraesCS2D01G287600	chr2A	97.139	699	17	3	3938	4633	498089939	498089241	0.000000e+00	1177.0
15	TraesCS2D01G287600	chr2A	92.565	807	44	7	536	1335	498093865	498093068	0.000000e+00	1144.0
16	TraesCS2D01G287600	chr2A	86.275	102	11	3	980	1078	498093502	498093401	1.760000e-19	108.0
17	TraesCS2D01G287600	chr3D	96.163	417	16	0	1	417	560101492	560101908	0.000000e+00	682.0
18	TraesCS2D01G287600	chr3D	89.796	98	10	0	3767	3864	138076232	138076329	4.870000e-25	126.0
19	TraesCS2D01G287600	chr3D	92.857	56	3	1	372	426	187945	188000	3.840000e-11	80.5
20	TraesCS2D01G287600	chr1D	90.032	311	23	7	2257	2566	236959112	236959415	3.360000e-106	396.0
21	TraesCS2D01G287600	chr1D	93.103	87	6	0	3775	3861	332956432	332956518	1.350000e-25	128.0
22	TraesCS2D01G287600	chr1D	97.917	48	1	0	372	419	401143036	401142989	2.970000e-12	84.2
23	TraesCS2D01G287600	chr1D	83.158	95	11	5	325	417	217007083	217007174	1.070000e-11	82.4
24	TraesCS2D01G287600	chr1D	97.826	46	1	0	372	417	113846549	113846594	3.840000e-11	80.5
25	TraesCS2D01G287600	chr1D	92.727	55	3	1	1018	1072	196551626	196551679	1.380000e-10	78.7
26	TraesCS2D01G287600	chr1D	91.304	46	4	0	372	417	382225695	382225740	3.870000e-06	63.9
27	TraesCS2D01G287600	chr7B	89.423	312	28	3	2257	2567	313152759	313152452	5.620000e-104	388.0
28	TraesCS2D01G287600	chr7B	83.135	421	45	16	5	420	610600750	610600351	1.230000e-95	361.0
29	TraesCS2D01G287600	chr7B	85.185	243	18	10	193	418	293117196	293116955	2.790000e-57	233.0
30	TraesCS2D01G287600	chr7B	88.333	120	14	0	7	126	293117313	293117194	1.340000e-30	145.0
31	TraesCS2D01G287600	chr7B	92.222	90	7	0	3775	3864	34327076	34326987	1.350000e-25	128.0
32	TraesCS2D01G287600	chr7A	89.389	311	30	3	2258	2566	219650153	219649844	5.620000e-104	388.0
33	TraesCS2D01G287600	chr6D	89.137	313	28	3	2256	2566	445740073	445740381	7.270000e-103	385.0
34	TraesCS2D01G287600	chr6D	97.826	46	1	0	372	417	393646628	393646583	3.840000e-11	80.5
35	TraesCS2D01G287600	chr6D	97.778	45	1	0	373	417	393646791	393646747	1.380000e-10	78.7
36	TraesCS2D01G287600	chr6D	95.556	45	2	0	374	418	36129231	36129275	6.430000e-09	73.1
37	TraesCS2D01G287600	chr6D	93.182	44	3	0	375	418	176820249	176820206	1.080000e-06	65.8
38	TraesCS2D01G287600	chr4B	89.355	310	27	4	2258	2566	588920436	588920132	7.270000e-103	385.0
39	TraesCS2D01G287600	chr4B	89.137	313	26	6	2257	2566	484781736	484782043	2.620000e-102	383.0
40	TraesCS2D01G287600	chr1B	83.894	416	45	13	7	417	528481954	528482352	1.220000e-100	377.0
41	TraesCS2D01G287600	chr1B	96.078	51	1	1	372	421	119175614	119175664	1.070000e-11	82.4
42	TraesCS2D01G287600	chr3B	83.095	420	46	12	5	418	21926155	21925755	4.410000e-95	359.0
43	TraesCS2D01G287600	chr5B	85.279	197	26	3	5	200	536466089	536466283	2.830000e-47	200.0
44	TraesCS2D01G287600	chr5B	92.222	90	7	0	3775	3864	222371367	222371278	1.350000e-25	128.0
45	TraesCS2D01G287600	chr5D	93.333	90	6	0	3775	3864	65990587	65990498	2.910000e-27	134.0
46	TraesCS2D01G287600	chr5D	97.917	48	1	0	372	419	443810081	443810128	2.970000e-12	84.2
47	TraesCS2D01G287600	chr5D	97.917	48	1	0	372	419	475866376	475866423	2.970000e-12	84.2
48	TraesCS2D01G287600	chr5D	97.917	48	1	0	372	419	475867178	475867225	2.970000e-12	84.2
49	TraesCS2D01G287600	chr5D	97.917	48	1	0	372	419	475867979	475868026	2.970000e-12	84.2
50	TraesCS2D01G287600	chr5D	97.917	48	1	0	372	419	475868778	475868825	2.970000e-12	84.2
51	TraesCS2D01G287600	chr5D	88.235	68	6	2	372	437	294562774	294562707	3.840000e-11	80.5
52	TraesCS2D01G287600	chr5A	91.000	100	8	1	3765	3864	239529946	239529848	2.910000e-27	134.0
53	TraesCS2D01G287600	chr4D	91.489	94	8	0	3771	3864	289339911	289339818	3.760000e-26	130.0
54	TraesCS2D01G287600	chr7D	100.000	46	0	0	372	417	213056698	213056743	8.260000e-13	86.1
55	TraesCS2D01G287600	chr1A	97.826	46	1	0	372	417	360985504	360985459	3.840000e-11	80.5
56	TraesCS2D01G287600	chrUn	95.556	45	2	0	374	418	479100332	479100376	6.430000e-09	73.1

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	TraesCS2D01G287600	chr2D	367993599	367998231	4632	True	8556.0	8556	100.0000	1	4633	1	chr2D.!!$R1	4632
1	TraesCS2D01G287600	chr2D	443480571	443481088	517	True	514.0	856	96.8790	1	514	2	chr2D.!!$R6	513
2	TraesCS2D01G287600	chr2B	436995047	436999288	4241	True	3414.0	3995	96.7745	536	4633	2	chr2B.!!$R2	4097
3	TraesCS2D01G287600	chr2A	498089241	498093865	4624	True	1354.4	2525	93.8224	536	4633	5	chr2A.!!$R1	4097

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
456	457	0.108963	CGATCGAGTAGGAGGAGGGT	59.891	60.000	10.26	0.0	0.00	4.34	F
1231	1234	0.036388	CGCTTGCCCCTTCTACAAGA	60.036	55.000	6.18	0.0	42.71	3.02	F
2226	2402	1.065926	TCCTAATGCTGTGCTGTCTGG	60.066	52.381	0.00	0.0	0.00	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2226	2402	1.098050	AAAGACGCTCATGGCCATTC	58.902	50.000	17.92	11.15	37.74	2.67	R
3219	3680	2.596904	TATACGGTTCAGCTTCTGGC	57.403	50.000	0.00	0.00	42.19	4.85	R
4114	4802	1.372683	CTCAGGGGTGTCAGGTGTG	59.627	63.158	0.00	0.00	0.00	3.82	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
27	28	3.634072	CGTGCCGATAGCTGCTGC	61.634	66.667	13.43	7.62	44.23	5.25
42	43	2.043551	TGCTGGTGGTGTTTGGCA	60.044	55.556	0.00	0.00	0.00	4.92
359	360	2.041819	GTGGGAGGAGGGGTCGAT	60.042	66.667	0.00	0.00	0.00	3.59
370	371	0.179092	GGGGTCGATGAAAGGTACGG	60.179	60.000	0.00	0.00	0.00	4.02
446	447	0.745486	TGGGAAGACGCGATCGAGTA	60.745	55.000	24.49	5.09	39.41	2.59
456	457	0.108963	CGATCGAGTAGGAGGAGGGT	59.891	60.000	10.26	0.00	0.00	4.34
461	462	1.477195	CGAGTAGGAGGAGGGTTCGAT	60.477	57.143	0.00	0.00	0.00	3.59
482	483	3.411446	TGAAAGGTACGACGTAAGAGGA	58.589	45.455	9.72	0.00	43.62	3.71
485	486	2.903798	AGGTACGACGTAAGAGGAGAG	58.096	52.381	9.72	0.00	43.62	3.20
643	645	1.003928	ACACCCTATTCGTTTCCCACC	59.996	52.381	0.00	0.00	0.00	4.61
647	649	1.408266	CCTATTCGTTTCCCACCCCAG	60.408	57.143	0.00	0.00	0.00	4.45
763	765	2.808321	GACGCCGAAACCGACCTC	60.808	66.667	0.00	0.00	0.00	3.85
936	939	2.926200	CGCTGGAACAATAGAGACAGTG	59.074	50.000	0.00	0.00	38.70	3.66
1060	1063	3.323758	TTCCAGGCGTGGGGAATCG	62.324	63.158	24.54	0.00	45.11	3.34
1123	1126	4.150454	CTCGGGCCTCCTCCTCCT	62.150	72.222	0.84	0.00	0.00	3.69
1124	1127	4.144727	TCGGGCCTCCTCCTCCTC	62.145	72.222	0.84	0.00	0.00	3.71
1125	1128	4.150454	CGGGCCTCCTCCTCCTCT	62.150	72.222	0.84	0.00	0.00	3.69
1126	1129	2.123033	GGGCCTCCTCCTCCTCTC	60.123	72.222	0.84	0.00	0.00	3.20
1231	1234	0.036388	CGCTTGCCCCTTCTACAAGA	60.036	55.000	6.18	0.00	42.71	3.02
1485	1536	6.257193	GCTTATTTTCTCAGCCATTTCCATTG	59.743	38.462	0.00	0.00	0.00	2.82
1642	1693	4.479056	TGACCTCTCCTATTCTCTACCACT	59.521	45.833	0.00	0.00	0.00	4.00
2155	2206	7.625185	GCAATTTCTCAAGCTTTAGAGGTACTG	60.625	40.741	10.14	6.67	41.55	2.74
2170	2221	5.905913	AGAGGTACTGTATAGCTGGGATTTT	59.094	40.000	0.00	0.00	41.55	1.82
2226	2402	1.065926	TCCTAATGCTGTGCTGTCTGG	60.066	52.381	0.00	0.00	0.00	3.86
2426	2887	1.620819	GACACTCAGCTCTTCCTCCAA	59.379	52.381	0.00	0.00	0.00	3.53
3196	3657	7.350110	CATGGATTATGTGTTTTGTTGAACC	57.650	36.000	0.00	0.00	31.92	3.62
3355	3816	7.095102	GCATTTCCAAACTTGCATACATTTTCT	60.095	33.333	0.00	0.00	35.22	2.52
3469	3930	4.403734	TGAAGGTAAATCCCCAAACTGTC	58.596	43.478	0.00	0.00	36.75	3.51
3624	4085	0.695924	TTTCCGGGAATGGCTCAAGA	59.304	50.000	10.86	0.00	0.00	3.02
3730	4191	6.035758	CGCCTTCCTACATTTAACAGTCTAAC	59.964	42.308	0.00	0.00	0.00	2.34
3735	4196	8.786826	TCCTACATTTAACAGTCTAACAATGG	57.213	34.615	0.00	0.00	0.00	3.16
3746	4207	8.099364	ACAGTCTAACAATGGTTTGTATCTTG	57.901	34.615	0.00	0.00	45.30	3.02
3781	4242	7.708051	TCTGTGGAGAATATTTTCTACTCTCG	58.292	38.462	19.00	8.64	42.50	4.04
3802	4263	3.306166	CGCCGTCCTAAAATAAGTGTCTG	59.694	47.826	0.00	0.00	0.00	3.51
3858	4319	6.805713	ACAAAGTTGAGACACTTATTTTGGG	58.194	36.000	0.00	0.00	35.87	4.12
4034	4717	2.543777	TGCGAGGAAACACTAAAGCT	57.456	45.000	0.00	0.00	0.00	3.74
4035	4718	2.846193	TGCGAGGAAACACTAAAGCTT	58.154	42.857	0.00	0.00	0.00	3.74
4188	4876	1.064314	TGTACTGGCCCACAAACTGTT	60.064	47.619	0.00	0.00	0.00	3.16
4261	4949	0.039256	TGAAGATGGCAGCGTTTTGC	60.039	50.000	0.00	0.88	46.98	3.68
4462	5153	7.933577	TCAGTCAAATACATGTTCTTCACTCTT	59.066	33.333	2.30	0.00	0.00	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	2.202395	CCCTGCCAAACACCACCAG	61.202	63.158	0.00	0.00	0.00	4.00
89	90	0.105349	CCGGGTAGGGTTCCCATCTA	60.105	60.000	10.73	0.00	44.81	1.98
259	260	1.190643	CCTCTTTCTCCCTCTCGCTT	58.809	55.000	0.00	0.00	0.00	4.68
359	360	1.203052	CCTCTTACGCCGTACCTTTCA	59.797	52.381	0.00	0.00	0.00	2.69
370	371	1.318158	TTCCGTCTCCCCTCTTACGC	61.318	60.000	0.00	0.00	34.13	4.42
425	426	2.180769	CGATCGCGTCTTCCCACA	59.819	61.111	5.77	0.00	0.00	4.17
446	447	1.834263	CTTTCATCGAACCCTCCTCCT	59.166	52.381	0.00	0.00	0.00	3.69
456	457	2.995466	ACGTCGTACCTTTCATCGAA	57.005	45.000	0.00	0.00	34.23	3.71
461	462	3.411446	TCCTCTTACGTCGTACCTTTCA	58.589	45.455	4.17	0.00	0.00	2.69
516	518	9.555411	TGTGGTATCTCTATCTCTATCTCTACT	57.445	37.037	0.00	0.00	0.00	2.57
517	519	9.817809	CTGTGGTATCTCTATCTCTATCTCTAC	57.182	40.741	0.00	0.00	0.00	2.59
518	520	9.777008	TCTGTGGTATCTCTATCTCTATCTCTA	57.223	37.037	0.00	0.00	0.00	2.43
519	521	8.540388	GTCTGTGGTATCTCTATCTCTATCTCT	58.460	40.741	0.00	0.00	0.00	3.10
520	522	7.769044	GGTCTGTGGTATCTCTATCTCTATCTC	59.231	44.444	0.00	0.00	0.00	2.75
521	523	7.580688	CGGTCTGTGGTATCTCTATCTCTATCT	60.581	44.444	0.00	0.00	0.00	1.98
522	524	6.537301	CGGTCTGTGGTATCTCTATCTCTATC	59.463	46.154	0.00	0.00	0.00	2.08
523	525	6.213802	TCGGTCTGTGGTATCTCTATCTCTAT	59.786	42.308	0.00	0.00	0.00	1.98
524	526	5.543020	TCGGTCTGTGGTATCTCTATCTCTA	59.457	44.000	0.00	0.00	0.00	2.43
525	527	4.348461	TCGGTCTGTGGTATCTCTATCTCT	59.652	45.833	0.00	0.00	0.00	3.10
526	528	4.643463	TCGGTCTGTGGTATCTCTATCTC	58.357	47.826	0.00	0.00	0.00	2.75
527	529	4.708576	TCGGTCTGTGGTATCTCTATCT	57.291	45.455	0.00	0.00	0.00	1.98
528	530	4.023021	GGTTCGGTCTGTGGTATCTCTATC	60.023	50.000	0.00	0.00	0.00	2.08
529	531	3.890147	GGTTCGGTCTGTGGTATCTCTAT	59.110	47.826	0.00	0.00	0.00	1.98
530	532	3.285484	GGTTCGGTCTGTGGTATCTCTA	58.715	50.000	0.00	0.00	0.00	2.43
531	533	2.100989	GGTTCGGTCTGTGGTATCTCT	58.899	52.381	0.00	0.00	0.00	3.10
532	534	1.822990	TGGTTCGGTCTGTGGTATCTC	59.177	52.381	0.00	0.00	0.00	2.75
533	535	1.933021	TGGTTCGGTCTGTGGTATCT	58.067	50.000	0.00	0.00	0.00	1.98
534	536	2.618053	CTTGGTTCGGTCTGTGGTATC	58.382	52.381	0.00	0.00	0.00	2.24
647	649	4.097361	GAACGGGGAGGAGTGGCC	62.097	72.222	0.00	0.00	0.00	5.36
926	929	2.646175	GGGCCGCACACTGTCTCTA	61.646	63.158	0.00	0.00	0.00	2.43
1123	1126	3.565449	CCAGAAGGAGAAGGAGAAGGAGA	60.565	52.174	0.00	0.00	36.89	3.71
1124	1127	2.765699	CCAGAAGGAGAAGGAGAAGGAG	59.234	54.545	0.00	0.00	36.89	3.69
1125	1128	2.112691	ACCAGAAGGAGAAGGAGAAGGA	59.887	50.000	0.00	0.00	38.69	3.36
1126	1129	2.235898	CACCAGAAGGAGAAGGAGAAGG	59.764	54.545	0.00	0.00	38.69	3.46
1231	1234	2.241176	TGCAGGAATTACCGGGAATCTT	59.759	45.455	13.67	0.00	44.74	2.40
1485	1536	3.624410	GGTTAACCCACCGTAATGATCAC	59.376	47.826	14.16	0.00	0.00	3.06
1521	1572	5.069251	AGTGCAGTACAATAGATAGGACCAC	59.931	44.000	0.00	0.00	0.00	4.16
1642	1693	2.094182	GGTACTACTGCTGCTGCTGTTA	60.094	50.000	27.87	15.52	46.76	2.41
2170	2221	7.609918	TGGCAAGAAAGACAGCAATAAATAGTA	59.390	33.333	0.00	0.00	0.00	1.82
2226	2402	1.098050	AAAGACGCTCATGGCCATTC	58.902	50.000	17.92	11.15	37.74	2.67
2365	2541	6.520272	TGCATGCAAGTTTTAAACAGGTTAT	58.480	32.000	20.30	0.00	0.00	1.89
2426	2887	4.242475	CACATGCATGCAAGAAAACTGAT	58.758	39.130	28.20	3.45	0.00	2.90
3219	3680	2.596904	TATACGGTTCAGCTTCTGGC	57.403	50.000	0.00	0.00	42.19	4.85
3355	3816	3.806949	AACAGAACTCATAAAGGGGCA	57.193	42.857	0.00	0.00	0.00	5.36
3469	3930	4.846137	GCAGCAAAGACTAACAATGTAACG	59.154	41.667	0.00	0.00	0.00	3.18
3624	4085	1.524002	CCTCCATCCATCACGTGCT	59.476	57.895	11.67	0.00	0.00	4.40
3730	4191	8.606040	AAAATTCACCAAGATACAAACCATTG	57.394	30.769	0.00	0.00	42.46	2.82
3735	4196	8.755018	CACAGAAAAATTCACCAAGATACAAAC	58.245	33.333	0.00	0.00	0.00	2.93
3746	4207	9.710900	AAAATATTCTCCACAGAAAAATTCACC	57.289	29.630	0.00	0.00	42.14	4.02
3779	4240	3.194116	AGACACTTATTTTAGGACGGCGA	59.806	43.478	16.62	0.00	0.00	5.54
3781	4242	4.501071	TCAGACACTTATTTTAGGACGGC	58.499	43.478	0.00	0.00	0.00	5.68
3858	4319	5.376625	TGGGACATAAATAAGGCATCTGTC	58.623	41.667	0.00	0.00	0.00	3.51
4018	4701	6.378710	AGACAAAAGCTTTAGTGTTTCCTC	57.621	37.500	13.10	2.25	0.00	3.71
4114	4802	1.372683	CTCAGGGGTGTCAGGTGTG	59.627	63.158	0.00	0.00	0.00	3.82
4188	4876	1.939381	GCGACACAATACAGGCAGACA	60.939	52.381	0.00	0.00	0.00	3.41
4261	4949	1.875576	GCATACTGGATCCGGAAGCAG	60.876	57.143	27.90	10.29	0.00	4.24
4455	5146	4.019411	TGTGGATGCTGGAATAAAGAGTGA	60.019	41.667	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.