AutoCloner

Multiple sequence alignment - TraesCS6D01G096300

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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	TraesCS6D01G096300	chr6D	100.000	2888	0	0	1	2888	60488980	60486093	0.000000e+00	5334.0
1	TraesCS6D01G096300	chr6D	100.000	282	0	0	3278	3559	60485703	60485422	4.070000e-144	521.0
2	TraesCS6D01G096300	chr6A	94.287	2818	88	30	90	2881	77101021	77098251	0.000000e+00	4244.0
3	TraesCS6D01G096300	chr6A	89.860	286	24	2	3278	3559	77098217	77097933	2.610000e-96	363.0
4	TraesCS6D01G096300	chr6A	90.071	141	12	1	1	139	77101141	77101001	7.850000e-42	182.0
5	TraesCS6D01G096300	chr6A	84.348	115	12	2	1	109	77109618	77109504	1.350000e-19	108.0
6	TraesCS6D01G096300	chr6B	92.255	2350	101	37	579	2888	134665246	134662938	0.000000e+00	3256.0
7	TraesCS6D01G096300	chr6B	88.699	292	17	10	291	578	134665562	134665283	3.400000e-90	342.0
8	TraesCS6D01G096300	chr2A	86.251	2131	127	79	747	2807	175467327	175469361	0.000000e+00	2159.0
9	TraesCS6D01G096300	chr2A	88.462	156	12	4	592	746	175467126	175467276	2.180000e-42	183.0
10	TraesCS6D01G096300	chr2B	86.231	2128	116	70	747	2807	223153836	223155853	0.000000e+00	2143.0
11	TraesCS6D01G096300	chr2B	89.375	160	10	5	588	746	223153632	223153785	1.010000e-45	195.0
12	TraesCS6D01G096300	chr2B	87.755	49	4	2	2764	2810	223155950	223155998	4.960000e-04	56.5
13	TraesCS6D01G096300	chr2D	86.055	2137	117	80	747	2807	175330904	175332935	0.000000e+00	2128.0
14	TraesCS6D01G096300	chr2D	89.809	157	10	4	591	746	175330702	175330853	2.800000e-46	196.0
15	TraesCS6D01G096300	chr4D	98.969	97	1	0	896	992	484166802	484166706	1.310000e-39	174.0
16	TraesCS6D01G096300	chr4D	82.963	135	21	2	1105	1238	304690191	304690324	1.740000e-23	121.0
17	TraesCS6D01G096300	chr3D	87.586	145	18	0	1453	1597	148224359	148224503	6.110000e-38	169.0
18	TraesCS6D01G096300	chr3B	86.577	149	19	1	1450	1597	214284993	214284845	2.840000e-36	163.0
19	TraesCS6D01G096300	chr3A	86.577	149	19	1	1450	1597	165088449	165088301	2.840000e-36	163.0
20	TraesCS6D01G096300	chr1D	83.562	146	16	6	1104	1245	359666065	359665924	2.880000e-26	130.0
21	TraesCS6D01G096300	chr1D	82.474	97	15	1	181	275	345484653	345484749	2.280000e-12	84.2
22	TraesCS6D01G096300	chr5D	76.955	243	36	12	1479	1720	519277448	519277671	1.740000e-23	121.0
23	TraesCS6D01G096300	chr4B	82.963	135	21	2	1105	1238	380653478	380653611	1.740000e-23	121.0
24	TraesCS6D01G096300	chr4A	82.963	135	21	2	1105	1238	174157472	174157339	1.740000e-23	121.0

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	TraesCS6D01G096300	chr6D	60485422	60488980	3558	True	2927.500000	5334	100.0000	1	3559	2	chr6D.!!$R1	3558
1	TraesCS6D01G096300	chr6A	77097933	77101141	3208	True	1596.333333	4244	91.4060	1	3559	3	chr6A.!!$R2	3558
2	TraesCS6D01G096300	chr6B	134662938	134665562	2624	True	1799.000000	3256	90.4770	291	2888	2	chr6B.!!$R1	2597
3	TraesCS6D01G096300	chr2A	175467126	175469361	2235	False	1171.000000	2159	87.3565	592	2807	2	chr2A.!!$F1	2215
4	TraesCS6D01G096300	chr2B	223153632	223155998	2366	False	798.166667	2143	87.7870	588	2810	3	chr2B.!!$F1	2222
5	TraesCS6D01G096300	chr2D	175330702	175332935	2233	False	1162.000000	2128	87.9320	591	2807	2	chr2D.!!$F1	2216

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
843	994	0.047176	TCTCCTCTCCTCTCCTCCCT	59.953	60.0	0.00	0.00	0.0	4.20	F
1279	1476	0.377554	ATCTCGTCGGTCGTGCTTAG	59.622	55.0	0.00	0.00	40.8	2.18	F
1832	2051	0.110599	CGATCGCACGGTCTAGCTAG	60.111	60.0	15.01	15.01	0.0	3.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1699	1914	1.514087	GTCGGTGAGGCGGTATTCA	59.486	57.895	0.00	0.00	2.57	R
2088	2328	2.169978	CCTGATGATGGAGCAGTGAAGA	59.830	50.000	0.00	36.24	2.87	R
3307	3623	1.036707	GAGTAGCTAGACCAGGCCAG	58.963	60.000	5.01	0.00	4.85	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
20	21	1.608590	ACCAATCCAAAAGACTGTGCG	59.391	47.619	0.00	0.00	0.00	5.34
21	22	1.666888	CCAATCCAAAAGACTGTGCGC	60.667	52.381	0.00	0.00	0.00	6.09
28	29	0.957395	AAAGACTGTGCGCCAGATGG	60.957	55.000	26.07	7.00	44.49	3.51
43	44	5.066375	CGCCAGATGGAGAAACATTTATGAA	59.934	40.000	2.18	0.00	37.14	2.57
85	86	2.930950	ACTAGCAGCAGGTTGTTTTCA	58.069	42.857	0.00	0.00	0.00	2.69
159	193	4.822026	TGACTTAGGAACTTTCTAGCAGC	58.178	43.478	0.00	0.00	41.75	5.25
164	198	2.235898	AGGAACTTTCTAGCAGCCAGAG	59.764	50.000	0.00	0.00	27.25	3.35
238	272	1.133792	ACTTGAACTCTGGTGGGTTGG	60.134	52.381	0.00	0.00	0.00	3.77
248	282	0.107165	GGTGGGTTGGAGATACCTGC	60.107	60.000	0.00	0.00	39.86	4.85
249	283	0.618458	GTGGGTTGGAGATACCTGCA	59.382	55.000	0.00	0.00	39.06	4.41
256	290	4.141482	GGTTGGAGATACCTGCATTCCTAA	60.141	45.833	0.00	0.00	40.50	2.69
257	291	4.689612	TGGAGATACCTGCATTCCTAAC	57.310	45.455	0.00	0.00	35.75	2.34
258	292	3.391296	TGGAGATACCTGCATTCCTAACC	59.609	47.826	0.00	0.00	35.75	2.85
269	305	6.000246	TGCATTCCTAACCATCTAATCACA	58.000	37.500	0.00	0.00	0.00	3.58
334	370	2.069273	GTGTCTGAAATGAGGTCACCG	58.931	52.381	0.00	0.00	0.00	4.94
349	385	4.285260	AGGTCACCGTGTTAAAAGAGGTAT	59.715	41.667	0.00	0.00	33.30	2.73
365	401	4.103311	AGAGGTATCCCTTGATTAGTTGCC	59.897	45.833	0.00	0.00	42.86	4.52
366	402	3.138468	AGGTATCCCTTGATTAGTTGCCC	59.862	47.826	0.00	0.00	38.13	5.36
368	404	0.254747	TCCCTTGATTAGTTGCCCCG	59.745	55.000	0.00	0.00	0.00	5.73
369	405	0.254747	CCCTTGATTAGTTGCCCCGA	59.745	55.000	0.00	0.00	0.00	5.14
371	407	1.668419	CTTGATTAGTTGCCCCGAGG	58.332	55.000	0.00	0.00	0.00	4.63
372	408	1.209504	CTTGATTAGTTGCCCCGAGGA	59.790	52.381	0.00	0.00	33.47	3.71
373	409	1.507140	TGATTAGTTGCCCCGAGGAT	58.493	50.000	0.00	0.00	33.47	3.24
375	411	2.367567	TGATTAGTTGCCCCGAGGATAC	59.632	50.000	0.00	0.00	33.47	2.24
772	903	1.004918	CTCTCCTCGCCACGGTTTT	60.005	57.895	0.00	0.00	0.00	2.43
789	927	3.561120	TTCACAGCCGCCCCGAAAT	62.561	57.895	0.00	0.00	0.00	2.17
819	957	2.182791	CACCGCAGATCACTCGCT	59.817	61.111	0.00	0.00	0.00	4.93
841	992	0.478507	CCTCTCCTCTCCTCTCCTCC	59.521	65.000	0.00	0.00	0.00	4.30
842	993	0.478507	CTCTCCTCTCCTCTCCTCCC	59.521	65.000	0.00	0.00	0.00	4.30
843	994	0.047176	TCTCCTCTCCTCTCCTCCCT	59.953	60.000	0.00	0.00	0.00	4.20
844	995	0.478507	CTCCTCTCCTCTCCTCCCTC	59.521	65.000	0.00	0.00	0.00	4.30
993	1176	3.934457	GCTAGCTAGCTAAGGGAAGAG	57.066	52.381	33.71	13.39	45.62	2.85
1270	1463	5.180868	GGTATGTTATGTCTATCTCGTCGGT	59.819	44.000	0.00	0.00	0.00	4.69
1279	1476	0.377554	ATCTCGTCGGTCGTGCTTAG	59.622	55.000	0.00	0.00	40.80	2.18
1298	1495	1.268352	AGTTTATCAAGCGCCGCAAAA	59.732	42.857	13.36	0.55	0.00	2.44
1699	1914	3.833650	TCAAAACCAACTGGATCATGCAT	59.166	39.130	1.86	0.00	38.94	3.96
1702	1917	3.090210	ACCAACTGGATCATGCATGAA	57.910	42.857	31.79	15.77	38.35	2.57
1830	2049	1.818363	TCGATCGCACGGTCTAGCT	60.818	57.895	11.09	0.00	0.00	3.32
1831	2050	0.531311	TCGATCGCACGGTCTAGCTA	60.531	55.000	11.09	0.00	0.00	3.32
1832	2051	0.110599	CGATCGCACGGTCTAGCTAG	60.111	60.000	15.01	15.01	0.00	3.42
1833	2052	0.386226	GATCGCACGGTCTAGCTAGC	60.386	60.000	16.35	6.62	0.00	3.42
2088	2328	0.321564	TGGCAGCAACTACGCTTCAT	60.322	50.000	0.00	0.00	41.38	2.57
2267	2516	1.738099	CCCGTTCAACTGGCTCGAG	60.738	63.158	8.45	8.45	0.00	4.04
2274	2523	3.288308	AACTGGCTCGAGGCGTCAG	62.288	63.158	30.84	24.74	44.42	3.51
2763	3060	5.565045	GCGAACTTGCTAGCCATATAGTAGT	60.565	44.000	13.29	0.20	0.00	2.73
3307	3623	6.238648	ACAATCCCCAGTCGGATATAATTTC	58.761	40.000	0.00	0.00	42.05	2.17
3313	3629	4.263068	CCAGTCGGATATAATTTCTGGCCT	60.263	45.833	3.32	0.00	35.37	5.19
3325	3641	0.631753	TCTGGCCTGGTCTAGCTACT	59.368	55.000	10.07	0.00	0.00	2.57
3343	3659	9.743057	CTAGCTACTCATCATGTATAAATAGGC	57.257	37.037	0.00	0.00	0.00	3.93
3378	3694	1.589320	GCAACGCATGGTAATTGCATG	59.411	47.619	3.06	0.00	45.38	4.06
3383	3699	1.202203	CATGGTAATTGCATGCACGC	58.798	50.000	22.58	10.48	0.00	5.34
3392	3708	0.027848	TGCATGCACGCGTATGATTG	59.972	50.000	22.77	12.78	37.41	2.67
3405	3721	4.324669	GCGTATGATTGATCTACATGGACG	59.675	45.833	0.00	13.06	32.67	4.79
3406	3722	4.324669	CGTATGATTGATCTACATGGACGC	59.675	45.833	0.00	0.00	0.00	5.19
3419	3735	3.308595	ACATGGACGCACATTGTATAACG	59.691	43.478	0.00	0.00	0.00	3.18
3481	3801	9.747898	ATTGGAGTGGTTTAGTTATTATGTGAA	57.252	29.630	0.00	0.00	0.00	3.18
3508	3828	4.522789	CCCTTATGCGCCAACCTTTTATAT	59.477	41.667	4.18	0.00	0.00	0.86
3553	3873	8.375465	GCTAAATATGCTTGAAAATTGTGTGTC	58.625	33.333	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	0.955428	GTTTCTCCATCTGGCGCACA	60.955	55.000	10.83	3.75	34.44	4.57
20	21	6.455360	TTCATAAATGTTTCTCCATCTGGC	57.545	37.500	0.00	0.00	34.44	4.85
21	22	9.525409	GAATTTCATAAATGTTTCTCCATCTGG	57.475	33.333	0.00	0.00	0.00	3.86
43	44	2.218603	AGCCAACACGAAGAACGAATT	58.781	42.857	0.00	0.00	45.77	2.17
96	97	0.108329	GCGGGAACAACTAGCTGCTA	60.108	55.000	9.34	9.34	0.00	3.49
142	176	3.441101	TCTGGCTGCTAGAAAGTTCCTA	58.559	45.455	13.65	0.00	0.00	2.94
143	177	2.235898	CTCTGGCTGCTAGAAAGTTCCT	59.764	50.000	16.64	0.00	0.00	3.36
159	193	7.718314	TGGATTATCATGATTCTGTTTCTCTGG	59.282	37.037	14.65	0.00	0.00	3.86
216	250	1.807814	ACCCACCAGAGTTCAAGTCT	58.192	50.000	0.00	0.00	0.00	3.24
217	251	2.222027	CAACCCACCAGAGTTCAAGTC	58.778	52.381	0.00	0.00	0.00	3.01
230	264	0.618458	TGCAGGTATCTCCAACCCAC	59.382	55.000	0.00	0.00	37.77	4.61
238	272	4.689612	TGGTTAGGAATGCAGGTATCTC	57.310	45.455	0.00	0.00	0.00	2.75
248	282	6.595682	ACCTGTGATTAGATGGTTAGGAATG	58.404	40.000	0.00	0.00	0.00	2.67
249	283	6.831664	ACCTGTGATTAGATGGTTAGGAAT	57.168	37.500	0.00	0.00	0.00	3.01
349	385	0.254747	CGGGGCAACTAATCAAGGGA	59.745	55.000	0.00	0.00	0.00	4.20
365	401	2.434336	TGACCATTTCAGTATCCTCGGG	59.566	50.000	0.00	0.00	0.00	5.14
366	402	3.458189	GTGACCATTTCAGTATCCTCGG	58.542	50.000	0.00	0.00	33.71	4.63
368	404	2.866762	GCGTGACCATTTCAGTATCCTC	59.133	50.000	0.00	0.00	33.71	3.71
369	405	2.501723	AGCGTGACCATTTCAGTATCCT	59.498	45.455	0.00	0.00	33.71	3.24
371	407	3.262420	ACAGCGTGACCATTTCAGTATC	58.738	45.455	0.00	0.00	33.71	2.24
372	408	3.334583	ACAGCGTGACCATTTCAGTAT	57.665	42.857	0.00	0.00	33.71	2.12
373	409	2.831685	ACAGCGTGACCATTTCAGTA	57.168	45.000	0.00	0.00	33.71	2.74
375	411	4.481930	TTTAACAGCGTGACCATTTCAG	57.518	40.909	0.00	0.00	33.71	3.02
376	412	4.902443	TTTTAACAGCGTGACCATTTCA	57.098	36.364	0.00	0.00	0.00	2.69
532	570	1.139498	TCACCTTGCCCCATCCTTCA	61.139	55.000	0.00	0.00	0.00	3.02
772	903	3.969250	GATTTCGGGGCGGCTGTGA	62.969	63.158	9.56	1.18	0.00	3.58
789	927	2.879233	GCGGTGGGAGTTCTGGTGA	61.879	63.158	0.00	0.00	0.00	4.02
819	957	1.529796	GAGAGGAGAGGAGAGGCGA	59.470	63.158	0.00	0.00	0.00	5.54
841	992	2.162338	TTACAGCGACGGTTGGGAGG	62.162	60.000	0.00	0.00	0.00	4.30
842	993	1.012486	GTTACAGCGACGGTTGGGAG	61.012	60.000	0.00	0.00	0.00	4.30
843	994	1.005867	GTTACAGCGACGGTTGGGA	60.006	57.895	0.00	0.00	0.00	4.37
844	995	0.881159	TTGTTACAGCGACGGTTGGG	60.881	55.000	0.00	0.00	0.00	4.12
938	1095	0.037882	CGGATGATCCCACCAGATCG	60.038	60.000	5.78	0.00	44.74	3.69
939	1096	0.322975	CCGGATGATCCCACCAGATC	59.677	60.000	5.78	0.00	42.57	2.75
940	1097	0.400525	ACCGGATGATCCCACCAGAT	60.401	55.000	9.46	0.00	31.13	2.90
993	1176	0.322975	CCATGGACCTCATCGGATCC	59.677	60.000	5.56	0.00	32.92	3.36
1279	1476	1.692296	TTTTGCGGCGCTTGATAAAC	58.308	45.000	33.26	0.26	0.00	2.01
1298	1495	4.214545	TCGATTATTTAATTGCGCCGGAAT	59.785	37.500	5.05	0.00	0.00	3.01
1699	1914	1.514087	GTCGGTGAGGCGGTATTCA	59.486	57.895	0.00	0.00	0.00	2.57
1830	2049	5.760253	GCTGGAGAGCAATTAAATACTGCTA	59.240	40.000	0.00	0.00	46.19	3.49
1832	2051	4.853268	GCTGGAGAGCAATTAAATACTGC	58.147	43.478	0.00	0.00	45.46	4.40
2088	2328	2.169978	CCTGATGATGGAGCAGTGAAGA	59.830	50.000	0.00	0.00	36.24	2.87
2521	2782	3.322514	CCGGATATTTGGACGGCAT	57.677	52.632	0.00	0.00	39.85	4.40
2522	2783	4.868026	CCGGATATTTGGACGGCA	57.132	55.556	0.00	0.00	39.85	5.69
2763	3060	8.461249	ACTTCGAAAATACTCCTAGCTATGTA	57.539	34.615	0.00	0.00	0.00	2.29
3296	3612	5.248380	AGACCAGGCCAGAAATTATATCC	57.752	43.478	5.01	0.00	0.00	2.59
3307	3623	1.036707	GAGTAGCTAGACCAGGCCAG	58.963	60.000	5.01	0.00	0.00	4.85
3313	3629	8.706322	TTTATACATGATGAGTAGCTAGACCA	57.294	34.615	0.00	0.00	0.00	4.02
3325	3641	8.311109	ACATACACGCCTATTTATACATGATGA	58.689	33.333	0.00	0.00	0.00	2.92
3343	3659	4.888106	TGCGTTGCTTATTTACATACACG	58.112	39.130	0.00	0.00	0.00	4.49
3378	3694	3.049912	TGTAGATCAATCATACGCGTGC	58.950	45.455	24.59	0.00	0.00	5.34
3383	3699	4.324669	GCGTCCATGTAGATCAATCATACG	59.675	45.833	0.00	5.79	31.23	3.06
3392	3708	3.198068	ACAATGTGCGTCCATGTAGATC	58.802	45.455	0.00	0.00	0.00	2.75
3439	3755	8.548877	ACCACTCCAATATACTAGTTCACAAAT	58.451	33.333	0.00	0.00	0.00	2.32
3455	3771	9.747898	TTCACATAATAACTAAACCACTCCAAT	57.252	29.630	0.00	0.00	0.00	3.16
3459	3775	8.129211	GCCATTCACATAATAACTAAACCACTC	58.871	37.037	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.