AutoCloner

Multiple sequence alignment - TraesCS1D01G204100

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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	TraesCS1D01G204100	chr1D	100.000	2720	0	0	1	2720	288937651	288940370	0.000000e+00	5024.0
1	TraesCS1D01G204100	chr1D	82.759	638	79	17	2009	2636	10376491	10377107	8.570000e-150	540.0
2	TraesCS1D01G204100	chr1D	82.540	126	20	2	1	125	462469688	462469812	2.860000e-20	110.0
3	TraesCS1D01G204100	chr1D	86.207	87	12	0	12	98	208754772	208754858	8.020000e-16	95.3
4	TraesCS1D01G204100	chr1B	92.177	1534	63	20	473	1965	390467112	390468629	0.000000e+00	2115.0
5	TraesCS1D01G204100	chr1B	90.735	993	80	6	1737	2720	390470948	390471937	0.000000e+00	1314.0
6	TraesCS1D01G204100	chr1B	84.066	364	48	6	123	476	390464300	390464663	2.590000e-90	342.0
7	TraesCS1D01G204100	chr1B	94.643	168	9	0	1571	1738	390470738	390470905	7.470000e-66	261.0
8	TraesCS1D01G204100	chr1B	95.968	124	5	0	1	124	390464108	390464231	4.590000e-48	202.0
9	TraesCS1D01G204100	chr1A	89.964	1664	100	27	127	1743	361234600	361236243	0.000000e+00	2085.0
10	TraesCS1D01G204100	chr1A	80.601	732	128	14	1993	2720	540185505	540186226	1.100000e-153	553.0
11	TraesCS1D01G204100	chr1A	91.200	125	11	0	1	125	361234404	361234528	1.300000e-38	171.0
12	TraesCS1D01G204100	chr1A	82.796	93	16	0	12	104	554277052	554276960	1.740000e-12	84.2
13	TraesCS1D01G204100	chr1A	82.292	96	17	0	3	98	554296316	554296411	1.740000e-12	84.2
14	TraesCS1D01G204100	chr3A	84.135	769	107	10	1963	2720	69265079	69264315	0.000000e+00	730.0
15	TraesCS1D01G204100	chr3A	82.921	404	65	4	2319	2720	68271470	68271069	7.160000e-96	361.0
16	TraesCS1D01G204100	chr7D	82.177	735	117	12	1994	2720	607028858	607028130	1.070000e-173	619.0
17	TraesCS1D01G204100	chr7D	86.066	122	16	1	3	124	470276022	470275902	2.200000e-26	130.0
18	TraesCS1D01G204100	chr6D	83.667	649	86	10	1962	2592	267726575	267727221	6.480000e-166	593.0
19	TraesCS1D01G204100	chr6D	81.667	120	22	0	1	120	333367435	333367316	1.720000e-17	100.0
20	TraesCS1D01G204100	chr2A	81.754	707	112	6	2019	2720	179349455	179350149	2.350000e-160	575.0
21	TraesCS1D01G204100	chr2A	79.630	216	31	10	2005	2214	468523252	468523044	2.820000e-30	143.0
22	TraesCS1D01G204100	chr2A	85.366	123	18	0	3	125	475866999	475866877	7.910000e-26	128.0
23	TraesCS1D01G204100	chr2A	78.571	182	32	4	2006	2181	84541661	84541481	2.210000e-21	113.0
24	TraesCS1D01G204100	chr7B	81.085	719	115	15	2008	2720	692622424	692623127	3.060000e-154	555.0
25	TraesCS1D01G204100	chr7B	95.074	203	10	0	1422	1624	481813695	481813897	1.220000e-83	320.0
26	TraesCS1D01G204100	chr6B	80.913	723	117	16	2015	2720	71303245	71303963	3.960000e-153	551.0
27	TraesCS1D01G204100	chr3D	90.400	125	12	0	1	125	348920158	348920034	6.030000e-37	165.0
28	TraesCS1D01G204100	chr6A	86.325	117	10	5	241	351	594822345	594822229	3.680000e-24	122.0
29	TraesCS1D01G204100	chr6A	79.775	89	14	3	7	93	530501747	530501833	8.130000e-06	62.1

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	TraesCS1D01G204100	chr1D	288937651	288940370	2719	False	5024.0	5024	100.0000	1	2720	1	chr1D.!!$F3	2719
1	TraesCS1D01G204100	chr1D	10376491	10377107	616	False	540.0	540	82.7590	2009	2636	1	chr1D.!!$F1	627
2	TraesCS1D01G204100	chr1B	390464108	390471937	7829	False	846.8	2115	91.5178	1	2720	5	chr1B.!!$F1	2719
3	TraesCS1D01G204100	chr1A	361234404	361236243	1839	False	1128.0	2085	90.5820	1	1743	2	chr1A.!!$F3	1742
4	TraesCS1D01G204100	chr1A	540185505	540186226	721	False	553.0	553	80.6010	1993	2720	1	chr1A.!!$F1	727
5	TraesCS1D01G204100	chr3A	69264315	69265079	764	True	730.0	730	84.1350	1963	2720	1	chr3A.!!$R2	757
6	TraesCS1D01G204100	chr7D	607028130	607028858	728	True	619.0	619	82.1770	1994	2720	1	chr7D.!!$R2	726
7	TraesCS1D01G204100	chr6D	267726575	267727221	646	False	593.0	593	83.6670	1962	2592	1	chr6D.!!$F1	630
8	TraesCS1D01G204100	chr2A	179349455	179350149	694	False	575.0	575	81.7540	2019	2720	1	chr2A.!!$F1	701
9	TraesCS1D01G204100	chr7B	692622424	692623127	703	False	555.0	555	81.0850	2008	2720	1	chr7B.!!$F2	712
10	TraesCS1D01G204100	chr6B	71303245	71303963	718	False	551.0	551	80.9130	2015	2720	1	chr6B.!!$F1	705

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
992	3560	0.248296	GATCTCTCACGAGTCACGCC	60.248	60.0	0.0	0.0	46.94	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2614	7813	0.536006	GTGGAGCACTGAGTTGCCTT	60.536	55.0	3.93	0.0	44.14	4.35	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
84	85	1.387539	GAAGAGAAGAAGGCCATGGC	58.612	55.000	29.47	29.47	41.06	4.40
104	105	1.384525	CGAGGAGAGGAAGACGATGT	58.615	55.000	0.00	0.00	0.00	3.06
125	126	4.644685	TGTTGGAAGAAAAGAAGGTGAAGG	59.355	41.667	0.00	0.00	0.00	3.46
183	254	1.821061	CGGAGAAGGAGGCCGCATAT	61.821	60.000	9.31	0.00	38.46	1.78
186	257	1.227943	GAAGGAGGCCGCATATGCA	60.228	57.895	26.52	0.00	42.21	3.96
200	271	1.587547	TATGCAGCAACGACAACACA	58.412	45.000	0.00	0.00	0.00	3.72
206	277	0.383949	GCAACGACAACACATTGGGT	59.616	50.000	0.00	0.00	40.42	4.51
238	310	7.603784	GGTTCAGAATTATTTTTGCATGGACTT	59.396	33.333	0.00	0.00	0.00	3.01
252	324	4.708177	CATGGACTTCCGGACTGATATTT	58.292	43.478	1.83	0.00	39.43	1.40
319	393	3.316308	GGTTGTGATAAGGCATGTGATCC	59.684	47.826	0.00	0.00	0.00	3.36
336	410	1.299850	CCGACGCGCTATGGATCAA	60.300	57.895	5.73	0.00	0.00	2.57
398	478	7.394016	ACATAATATCATTGAATGACCGCCTA	58.606	34.615	10.45	0.00	43.01	3.93
427	513	1.752833	GGACTGGTCCCTTGTTCGT	59.247	57.895	8.48	0.00	43.94	3.85
439	525	3.369471	CCCTTGTTCGTGGATAGACACAT	60.369	47.826	0.00	0.00	41.38	3.21
445	531	5.163550	TGTTCGTGGATAGACACATAAGGAG	60.164	44.000	0.00	0.00	41.38	3.69
522	3065	7.229306	TCCTTCGTCGGTAAGTATATGTATGTT	59.771	37.037	0.00	0.00	0.00	2.71
526	3069	9.236691	TCGTCGGTAAGTATATGTATGTTTTTC	57.763	33.333	0.00	0.00	0.00	2.29
608	3163	7.663493	ACATAGTCTTTCTGAAGAGAAAAAGGG	59.337	37.037	0.00	0.00	45.57	3.95
909	3477	2.436469	CCAGTGCCACGCATAGCA	60.436	61.111	0.00	0.00	41.91	3.49
979	3547	5.435291	GTTGATCACTTGGATTGGATCTCT	58.565	41.667	0.00	0.00	37.60	3.10
985	3553	3.131933	ACTTGGATTGGATCTCTCACGAG	59.868	47.826	0.00	0.00	38.67	4.18
986	3554	2.739943	TGGATTGGATCTCTCACGAGT	58.260	47.619	0.00	0.00	38.45	4.18
992	3560	0.248296	GATCTCTCACGAGTCACGCC	60.248	60.000	0.00	0.00	46.94	5.68
998	3566	3.911698	ACGAGTCACGCCTGCACA	61.912	61.111	0.00	0.00	46.94	4.57
1180	3748	4.021925	GCAGACCGGCCCTGTCTT	62.022	66.667	17.69	3.73	41.02	3.01
1235	3811	3.575965	ACCCATTCGTTTCTTTGCATC	57.424	42.857	0.00	0.00	0.00	3.91
1306	3882	0.854062	CGGCACAAAACTTGCATGTG	59.146	50.000	12.08	12.08	45.54	3.21
1398	3979	1.304547	CCTCCGAGGAGTGGACAGT	60.305	63.158	17.04	0.00	37.67	3.55
1619	4206	3.695022	GACGCGGCTACGGTGATGT	62.695	63.158	12.47	0.00	41.36	3.06
1731	4318	0.666274	TCATGTGACGGCTTGACGAC	60.666	55.000	1.78	0.00	37.61	4.34
1759	6916	9.784531	ATATTCGTGGAACTATCATGAATCTTT	57.215	29.630	12.85	0.00	43.39	2.52
1794	6951	7.344093	TGAGATTGTAGTGAATCTGATCTCCTT	59.656	37.037	0.00	0.00	41.78	3.36
1799	6956	1.139654	TGAATCTGATCTCCTTGCCGG	59.860	52.381	0.00	0.00	0.00	6.13
1821	6978	5.625150	GGATGCAAATGTATTACTCCCTCT	58.375	41.667	0.00	0.00	0.00	3.69
1822	6979	5.471456	GGATGCAAATGTATTACTCCCTCTG	59.529	44.000	0.00	0.00	0.00	3.35
1852	7010	8.141909	TGTACTAAGCAGCTACAAGTAATATGG	58.858	37.037	11.79	0.00	0.00	2.74
1855	7013	8.432805	ACTAAGCAGCTACAAGTAATATGGATT	58.567	33.333	0.00	0.00	0.00	3.01
1857	7015	6.000219	AGCAGCTACAAGTAATATGGATTGG	59.000	40.000	0.00	0.00	0.00	3.16
1865	7023	7.006509	ACAAGTAATATGGATTGGAGGGATTG	58.993	38.462	0.00	0.00	0.00	2.67
1869	7027	3.763557	ATGGATTGGAGGGATTGTGTT	57.236	42.857	0.00	0.00	0.00	3.32
1870	7028	4.879295	ATGGATTGGAGGGATTGTGTTA	57.121	40.909	0.00	0.00	0.00	2.41
1945	7103	3.712091	AGTATAGTACAGTTGCTCCGC	57.288	47.619	0.00	0.00	0.00	5.54
1958	7116	4.973055	TCCGCGGGTGTTGGAACG	62.973	66.667	27.83	0.00	0.00	3.95
2151	7318	2.345244	CTGCTTCTGACGCCCTGT	59.655	61.111	3.54	0.00	0.00	4.00
2371	7565	4.805768	CGCCCCATTAACCCCGCA	62.806	66.667	0.00	0.00	0.00	5.69
2378	7574	1.684869	CCATTAACCCCGCATGGAAGT	60.685	52.381	0.00	0.00	40.10	3.01
2411	7607	2.586635	TGCCACACGTCCGTTCAC	60.587	61.111	0.00	0.00	0.00	3.18
2461	7658	1.755008	GAGCTCCTACTGTCCGCCT	60.755	63.158	0.87	0.00	0.00	5.52
2548	7745	0.325933	CCACCACTCTTCTGATGGCA	59.674	55.000	0.00	0.00	36.96	4.92
2577	7774	1.405526	GCAGTTCTCCGGCATACAAGA	60.406	52.381	0.00	0.00	0.00	3.02
2650	7849	3.636231	CCTTCCGTGCCTCACCCA	61.636	66.667	0.00	0.00	0.00	4.51
2664	7863	0.738389	CACCCAACGAAGCAAGTTGT	59.262	50.000	14.70	0.00	45.31	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
84	85	0.665835	CATCGTCTTCCTCTCCTCGG	59.334	60.000	0.00	0.00	0.00	4.63
104	105	4.644685	CACCTTCACCTTCTTTTCTTCCAA	59.355	41.667	0.00	0.00	0.00	3.53
125	126	3.423154	CCGCCGCCTTCAACTCAC	61.423	66.667	0.00	0.00	0.00	3.51
177	248	0.096802	TTGTCGTTGCTGCATATGCG	59.903	50.000	22.21	17.15	45.83	4.73
183	254	0.737804	AATGTGTTGTCGTTGCTGCA	59.262	45.000	0.00	0.00	0.00	4.41
186	257	0.667993	CCCAATGTGTTGTCGTTGCT	59.332	50.000	0.00	0.00	34.23	3.91
200	271	1.444933	TCTGAACCTCCACACCCAAT	58.555	50.000	0.00	0.00	0.00	3.16
206	277	6.041409	TGCAAAAATAATTCTGAACCTCCACA	59.959	34.615	0.00	0.00	0.00	4.17
256	328	9.539825	TGTTTAAGTTTTTACATGCATGTTCAT	57.460	25.926	35.45	14.88	41.97	2.57
292	365	5.069648	TCACATGCCTTATCACAACCAAAAA	59.930	36.000	0.00	0.00	0.00	1.94
298	372	3.002656	CGGATCACATGCCTTATCACAAC	59.997	47.826	0.00	0.00	0.00	3.32
306	380	1.815421	GCGTCGGATCACATGCCTT	60.815	57.895	0.00	0.00	0.00	4.35
319	393	1.139989	ATTTGATCCATAGCGCGTCG	58.860	50.000	8.43	0.00	0.00	5.12
376	456	6.170506	GGTAGGCGGTCATTCAATGATATTA	58.829	40.000	2.67	0.00	42.04	0.98
427	513	7.255836	CCGTAAATCTCCTTATGTGTCTATCCA	60.256	40.741	0.00	0.00	0.00	3.41
439	525	1.766496	CCCTGCCCGTAAATCTCCTTA	59.234	52.381	0.00	0.00	0.00	2.69
445	531	1.807226	GCAACCCTGCCCGTAAATC	59.193	57.895	0.00	0.00	43.26	2.17
522	3065	5.642063	ACTCGAGATTAGCCGAAATTGAAAA	59.358	36.000	21.68	0.00	34.17	2.29
526	3069	6.771188	ATAACTCGAGATTAGCCGAAATTG	57.229	37.500	21.68	0.00	34.17	2.32
909	3477	1.874872	GATCGACCGAGTAGCTAGCTT	59.125	52.381	24.88	5.38	0.00	3.74
923	3491	1.719600	ACAAGCTCTTGCAGATCGAC	58.280	50.000	9.36	0.00	44.03	4.20
979	3547	3.601685	TGCAGGCGTGACTCGTGA	61.602	61.111	11.29	0.00	42.13	4.35
985	3553	2.557805	CATGTGTGCAGGCGTGAC	59.442	61.111	11.29	6.34	0.00	3.67
986	3554	2.669229	CCATGTGTGCAGGCGTGA	60.669	61.111	11.29	0.00	0.00	4.35
992	3560	3.434319	GGTCCGCCATGTGTGCAG	61.434	66.667	0.00	0.00	34.09	4.41
998	3566	2.607750	AGACCAGGTCCGCCATGT	60.608	61.111	16.72	0.00	37.19	3.21
1109	3677	4.796231	GGTGACGATGCGCGGAGT	62.796	66.667	8.83	0.00	46.49	3.85
1180	3748	3.552384	ACGCGGGTGAACCTGGAA	61.552	61.111	12.47	0.00	42.72	3.53
1277	3853	1.677052	GTTTTGTGCCGGTCAGGTAAA	59.323	47.619	1.90	1.66	43.70	2.01
1278	3854	1.134037	AGTTTTGTGCCGGTCAGGTAA	60.134	47.619	1.90	0.00	43.70	2.85
1306	3882	2.433318	GAGCTCCACCGTCTGCAC	60.433	66.667	0.87	0.00	0.00	4.57
1425	4006	2.677524	TACCCCGTCACCCTCACG	60.678	66.667	0.00	0.00	36.99	4.35
1619	4206	2.047655	GGCCGTGACGATCACCAA	60.048	61.111	6.54	0.00	44.20	3.67
1731	4318	7.757173	AGATTCATGATAGTTCCACGAATATCG	59.243	37.037	0.00	0.00	46.93	2.92
1759	6916	8.251026	AGATTCACTACAATCTCATCGTACAAA	58.749	33.333	0.00	0.00	38.53	2.83
1799	6956	6.291377	TCAGAGGGAGTAATACATTTGCATC	58.709	40.000	0.00	0.00	0.00	3.91
1821	6978	6.464222	ACTTGTAGCTGCTTAGTACAAATCA	58.536	36.000	7.79	0.00	36.48	2.57
1822	6979	6.969828	ACTTGTAGCTGCTTAGTACAAATC	57.030	37.500	7.79	0.00	36.48	2.17
1945	7103	1.503818	CCTTCACGTTCCAACACCCG	61.504	60.000	0.00	0.00	0.00	5.28
1958	7116	1.614413	CCGCCTAGAGATACCCTTCAC	59.386	57.143	0.00	0.00	0.00	3.18
2151	7318	1.432023	GGAGGGGTTCTTTGGTGGGA	61.432	60.000	0.00	0.00	0.00	4.37
2371	7565	3.447944	GGAGTAGGTTTCTCGACTTCCAT	59.552	47.826	0.00	0.00	33.26	3.41
2378	7574	1.183549	GGCAGGAGTAGGTTTCTCGA	58.816	55.000	0.00	0.00	33.26	4.04
2411	7607	1.812093	TTTAATGTCGGCCCGCTCG	60.812	57.895	0.00	0.00	0.00	5.03
2461	7658	4.866486	GCGTCTTCCCTCGTTTAAATAGAA	59.134	41.667	0.00	0.00	0.00	2.10
2614	7813	0.536006	GTGGAGCACTGAGTTGCCTT	60.536	55.000	3.93	0.00	44.14	4.35
2650	7849	1.647084	GGCGACAACTTGCTTCGTT	59.353	52.632	4.33	0.00	35.17	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.