AutoCloner

Multiple sequence alignment - TraesCS2D01G007500

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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	TraesCS2D01G007500	chr2D	100.000	7222	0	0	1	7222	4037112	4044333	0.000000e+00	13337.0
1	TraesCS2D01G007500	chr2D	98.507	5024	65	7	6	5026	3985183	3990199	0.000000e+00	8853.0
2	TraesCS2D01G007500	chr2D	98.423	2156	31	3	5068	7222	3990493	3992646	0.000000e+00	3790.0
3	TraesCS2D01G007500	chr2D	88.836	421	39	6	4598	5011	559830203	559829784	1.800000e-140	510.0
4	TraesCS2D01G007500	chr2D	94.056	286	16	1	6937	7222	59540725	59541009	4.000000e-117	433.0
5	TraesCS2D01G007500	chr2B	93.610	4069	222	26	1	4049	7076325	7072275	0.000000e+00	6039.0
6	TraesCS2D01G007500	chr2B	93.536	4069	226	26	1	4049	7118007	7113956	0.000000e+00	6023.0
7	TraesCS2D01G007500	chr2B	93.512	4069	225	27	1	4049	7150567	7146518	0.000000e+00	6015.0
8	TraesCS2D01G007500	chr2B	93.417	4071	232	27	1	4049	454731331	454735387	0.000000e+00	6000.0
9	TraesCS2D01G007500	chr2B	93.315	4069	240	18	3	4049	6969431	6973489	0.000000e+00	5978.0
10	TraesCS2D01G007500	chr2B	92.873	4069	233	25	3	4049	6889021	6893054	0.000000e+00	5854.0
11	TraesCS2D01G007500	chr2B	93.305	3943	229	26	1	3922	454758021	454761949	0.000000e+00	5786.0
12	TraesCS2D01G007500	chr2B	92.338	4072	252	30	1	4049	454808906	454804872	0.000000e+00	5736.0
13	TraesCS2D01G007500	chr2B	93.627	3813	209	25	257	4049	7037396	7033598	0.000000e+00	5664.0
14	TraesCS2D01G007500	chr2B	92.329	1838	91	17	5070	6893	6974172	6975973	0.000000e+00	2567.0
15	TraesCS2D01G007500	chr2B	94.641	933	37	7	5050	5972	7071639	7070710	0.000000e+00	1434.0
16	TraesCS2D01G007500	chr2B	94.624	930	38	7	5052	5972	7127140	7126214	0.000000e+00	1430.0
17	TraesCS2D01G007500	chr2B	94.421	932	38	6	5052	5972	7113307	7112379	0.000000e+00	1421.0
18	TraesCS2D01G007500	chr2B	94.421	932	38	7	5052	5972	454736044	454736972	0.000000e+00	1421.0
19	TraesCS2D01G007500	chr2B	94.574	645	26	6	5070	5707	6893739	6894381	0.000000e+00	989.0
20	TraesCS2D01G007500	chr2B	96.289	512	18	1	4095	4605	6893198	6893709	0.000000e+00	839.0
21	TraesCS2D01G007500	chr2B	95.703	512	21	1	4095	4605	6973633	6974144	0.000000e+00	822.0
22	TraesCS2D01G007500	chr2B	96.122	490	19	0	4095	4584	7072133	7071644	0.000000e+00	800.0
23	TraesCS2D01G007500	chr2B	96.122	490	19	0	4095	4584	7113813	7113324	0.000000e+00	800.0
24	TraesCS2D01G007500	chr2B	96.122	490	19	0	4095	4584	454735530	454736019	0.000000e+00	800.0
25	TraesCS2D01G007500	chr2B	95.714	490	21	0	4095	4584	7033455	7032966	0.000000e+00	789.0
26	TraesCS2D01G007500	chr2B	93.763	497	20	2	4104	4599	454804720	454804234	0.000000e+00	736.0
27	TraesCS2D01G007500	chr2B	95.323	449	21	0	4095	4543	7146375	7145927	0.000000e+00	713.0
28	TraesCS2D01G007500	chr2B	91.358	162	12	2	6778	6937	112833675	112833836	3.390000e-53	220.0
29	TraesCS2D01G007500	chr2B	100.000	46	0	0	4539	4584	7127202	7127157	1.290000e-12	86.1
30	TraesCS2D01G007500	chrUn	94.319	1197	59	7	5070	6258	11585410	11584215	0.000000e+00	1825.0
31	TraesCS2D01G007500	chrUn	94.629	931	37	7	5052	5972	370046861	370045934	0.000000e+00	1430.0
32	TraesCS2D01G007500	chrUn	94.421	932	38	8	5052	5972	357089407	357088479	0.000000e+00	1421.0
33	TraesCS2D01G007500	chrUn	96.122	490	19	0	4095	4584	357089913	357089424	0.000000e+00	800.0
34	TraesCS2D01G007500	chrUn	95.610	205	6	1	5768	5972	421242490	421242289	6.990000e-85	326.0
35	TraesCS2D01G007500	chrUn	93.443	61	3	1	4039	4099	324495686	324495745	9.980000e-14	89.8
36	TraesCS2D01G007500	chrUn	93.443	61	3	1	4039	4099	332390691	332390632	9.980000e-14	89.8
37	TraesCS2D01G007500	chr3B	90.709	409	33	5	4607	5012	42739186	42738780	2.290000e-149	540.0
38	TraesCS2D01G007500	chr3B	89.951	408	36	5	4607	5012	815467254	815466850	8.300000e-144	521.0
39	TraesCS2D01G007500	chr7A	90.441	408	33	6	4607	5011	26466035	26465631	3.840000e-147	532.0
40	TraesCS2D01G007500	chr7D	90.000	410	36	5	4607	5012	538352159	538352567	6.420000e-145	525.0
41	TraesCS2D01G007500	chr5B	89.731	409	37	4	4607	5012	122614474	122614880	1.070000e-142	518.0
42	TraesCS2D01G007500	chr5D	89.461	408	41	2	4607	5012	505367005	505367412	1.390000e-141	514.0
43	TraesCS2D01G007500	chr5D	94.035	285	17	0	6938	7222	312859158	312859442	4.000000e-117	433.0
44	TraesCS2D01G007500	chr5D	88.312	77	6	1	6705	6778	560791654	560791578	9.980000e-14	89.8
45	TraesCS2D01G007500	chr1D	88.862	413	40	5	4606	5016	97311020	97311428	3.010000e-138	503.0
46	TraesCS2D01G007500	chr1D	93.772	289	17	1	6934	7222	399747363	399747650	4.000000e-117	433.0
47	TraesCS2D01G007500	chr3D	94.425	287	16	0	6936	7222	467716010	467715724	6.650000e-120	442.0
48	TraesCS2D01G007500	chr6D	94.386	285	16	0	6938	7222	65031339	65031055	8.600000e-119	438.0
49	TraesCS2D01G007500	chr6D	86.957	161	14	2	6778	6937	283229861	283229707	2.680000e-39	174.0
50	TraesCS2D01G007500	chr4D	94.681	282	14	1	6936	7217	169952653	169952933	3.090000e-118	436.0
51	TraesCS2D01G007500	chr4A	94.386	285	14	1	6938	7222	166240902	166240620	3.090000e-118	436.0
52	TraesCS2D01G007500	chr4A	95.294	85	4	0	6853	6937	697510549	697510633	1.260000e-27	135.0
53	TraesCS2D01G007500	chr7B	93.448	290	17	2	6933	7222	153475569	153475282	5.180000e-116	429.0

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	TraesCS2D01G007500	chr2D	4037112	4044333	7221	False	13337.000000	13337	100.000000	1	7222	1	chr2D.!!$F1	7221
1	TraesCS2D01G007500	chr2D	3985183	3992646	7463	False	6321.500000	8853	98.465000	6	7222	2	chr2D.!!$F3	7216
2	TraesCS2D01G007500	chr2B	454758021	454761949	3928	False	5786.000000	5786	93.305000	1	3922	1	chr2B.!!$F2	3921
3	TraesCS2D01G007500	chr2B	7145927	7150567	4640	True	3364.000000	6015	94.417500	1	4543	2	chr2B.!!$R5	4542
4	TraesCS2D01G007500	chr2B	454804234	454808906	4672	True	3236.000000	5736	93.050500	1	4599	2	chr2B.!!$R6	4598
5	TraesCS2D01G007500	chr2B	7032966	7037396	4430	True	3226.500000	5664	94.670500	257	4584	2	chr2B.!!$R1	4327
6	TraesCS2D01G007500	chr2B	6969431	6975973	6542	False	3122.333333	5978	93.782333	3	6893	3	chr2B.!!$F4	6890
7	TraesCS2D01G007500	chr2B	7070710	7076325	5615	True	2757.666667	6039	94.791000	1	5972	3	chr2B.!!$R2	5971
8	TraesCS2D01G007500	chr2B	7112379	7118007	5628	True	2748.000000	6023	94.693000	1	5972	3	chr2B.!!$R3	5971
9	TraesCS2D01G007500	chr2B	454731331	454736972	5641	False	2740.333333	6000	94.653333	1	5972	3	chr2B.!!$F5	5971
10	TraesCS2D01G007500	chr2B	6889021	6894381	5360	False	2560.666667	5854	94.578667	3	5707	3	chr2B.!!$F3	5704
11	TraesCS2D01G007500	chr2B	7126214	7127202	988	True	758.050000	1430	97.312000	4539	5972	2	chr2B.!!$R4	1433
12	TraesCS2D01G007500	chrUn	11584215	11585410	1195	True	1825.000000	1825	94.319000	5070	6258	1	chrUn.!!$R1	1188
13	TraesCS2D01G007500	chrUn	370045934	370046861	927	True	1430.000000	1430	94.629000	5052	5972	1	chrUn.!!$R3	920
14	TraesCS2D01G007500	chrUn	357088479	357089913	1434	True	1110.500000	1421	95.271500	4095	5972	2	chrUn.!!$R5	1877

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
411	414	0.324943	ATTCGCCCGGCTGCTAATAT	59.675	50.000	8.05	0.00	0.00	1.28	F
507	518	1.968704	AGAGACCTGCATGCATGATG	58.031	50.000	30.64	19.58	34.84	3.07	F
1420	1440	1.407618	GGTTAATTTCCATGGCGTCCC	59.592	52.381	6.96	0.00	0.00	4.46	F
2230	2264	1.401905	GGATGACGCTTAGGGCAAAAG	59.598	52.381	0.00	0.00	41.91	2.27	F
2906	2942	1.086696	CCAACGTGCCCTTCACATAG	58.913	55.000	0.00	0.00	45.92	2.23	F
3521	3562	0.611714	ATCGTGTGGTGGAGGGTTAC	59.388	55.000	0.00	0.00	0.00	2.50	F
4992	5157	1.378250	GCAGGTGCAGATGAGCCTT	60.378	57.895	2.28	0.00	41.59	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1268	1288	3.076621	TCCATGCATATTTCTCATCGCC	58.923	45.455	0.00	0.00	0.00	5.54	R
2136	2169	3.134262	GGGACAAGGGTTAGCTAGGTAAG	59.866	52.174	14.53	5.61	0.00	2.34	R
2630	2665	2.821378	CCACATTGTCAATGGAGCTTCA	59.179	45.455	25.59	0.00	43.21	3.02	R
3521	3562	2.034066	AACACGGAGGCCCATGTG	59.966	61.111	15.17	15.17	38.28	3.21	R
4343	4508	6.202937	TCTTTGTTTGCATGTTAACCTAACG	58.797	36.000	2.48	0.00	41.50	3.18	R
5040	5205	0.908198	AGAGAGAGATGCACAACCCC	59.092	55.000	0.00	0.00	0.00	4.95	R
6934	7401	2.209838	ATGTTGGAGACGTATCAGCG	57.790	50.000	12.92	0.00	37.94	5.18	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
36	37	7.761249	GGTAATGAATGCATGCCCTAATTTATC	59.239	37.037	16.68	3.35	34.26	1.75
40	41	7.003482	TGAATGCATGCCCTAATTTATCAGTA	58.997	34.615	16.68	0.00	0.00	2.74
118	119	6.266330	CACATGTGACTATCTATCCTTCCTCA	59.734	42.308	21.64	0.00	0.00	3.86
411	414	0.324943	ATTCGCCCGGCTGCTAATAT	59.675	50.000	8.05	0.00	0.00	1.28
440	443	6.762661	TCATGCATTCATCTTAAACTCGATGA	59.237	34.615	0.00	1.97	42.96	2.92
507	518	1.968704	AGAGACCTGCATGCATGATG	58.031	50.000	30.64	19.58	34.84	3.07
645	656	3.588511	TTGGGGCTGCCATGGTCA	61.589	61.111	22.05	10.98	0.00	4.02
734	746	6.923508	AGTAACTTTGATTTAACTTTGGCAGC	59.076	34.615	0.00	0.00	0.00	5.25
934	951	4.502962	CTGGAGTTTTCTGATCTGAGGTC	58.497	47.826	2.33	0.00	0.00	3.85
1420	1440	1.407618	GGTTAATTTCCATGGCGTCCC	59.592	52.381	6.96	0.00	0.00	4.46
1669	1694	2.436646	CCACTACTTGCAGGCCCG	60.437	66.667	0.00	0.00	0.00	6.13
1692	1717	7.438459	CCCGAGTAGGAACACATTTCTAATTAG	59.562	40.741	6.11	6.11	45.00	1.73
2136	2169	2.517650	TGGTTTTGGCGACATTTTCC	57.482	45.000	0.00	0.00	42.32	3.13
2230	2264	1.401905	GGATGACGCTTAGGGCAAAAG	59.598	52.381	0.00	0.00	41.91	2.27
2776	2812	8.029522	AGGACACTATTATGTCTATACAATGCG	58.970	37.037	5.92	0.00	46.85	4.73
2906	2942	1.086696	CCAACGTGCCCTTCACATAG	58.913	55.000	0.00	0.00	45.92	2.23
2992	3028	3.469008	CATAACCCGATGCTACTGGAA	57.531	47.619	0.00	0.00	0.00	3.53
3521	3562	0.611714	ATCGTGTGGTGGAGGGTTAC	59.388	55.000	0.00	0.00	0.00	2.50
4088	4229	7.602517	AGTCTTAACACAATAGCACTCATTC	57.397	36.000	0.00	0.00	0.00	2.67
4649	4814	2.036571	CATCTGCACCTGCGCTCAA	61.037	57.895	9.73	0.00	45.83	3.02
4734	4899	9.552114	GTAGATAATTTATTGCATGATGTCTGC	57.448	33.333	0.00	0.00	40.10	4.26
4742	4907	3.093814	TGCATGATGTCTGCTCCAAATT	58.906	40.909	0.00	0.00	40.34	1.82
4992	5157	1.378250	GCAGGTGCAGATGAGCCTT	60.378	57.895	2.28	0.00	41.59	4.35
5028	5193	8.830915	TGGATATTCCCATATAACTCTCTCTC	57.169	38.462	0.00	0.00	35.03	3.20
5030	5195	9.487442	GGATATTCCCATATAACTCTCTCTCTT	57.513	37.037	0.00	0.00	0.00	2.85
5040	5205	4.052159	ACTCTCTCTCTTTGTGTGTGTG	57.948	45.455	0.00	0.00	0.00	3.82
5041	5206	3.181471	ACTCTCTCTCTTTGTGTGTGTGG	60.181	47.826	0.00	0.00	0.00	4.17
5132	5568	2.137523	GTTTGCATGCAGGTCCAAAAG	58.862	47.619	21.50	0.00	0.00	2.27
5422	5871	4.635765	TGCATACATGTTACTTGCTCCTTC	59.364	41.667	2.30	0.00	34.47	3.46
6422	6882	6.544928	TCTGATAGTCCAACAAGAGCAATA	57.455	37.500	0.00	0.00	0.00	1.90
6691	7156	1.810151	TGCCAAGACAATCTTTACGGC	59.190	47.619	10.13	10.13	41.08	5.68
6934	7401	1.967319	TTTCCCGCATCTCCAATAGC	58.033	50.000	0.00	0.00	0.00	2.97
6952	7419	0.457853	GCGCTGATACGTCTCCAACA	60.458	55.000	0.00	0.00	34.88	3.33
7066	7533	4.831710	ACTAACCTATTAACCTAGAGCCCG	59.168	45.833	0.00	0.00	0.00	6.13
7112	7579	6.388259	TTGTTTTTGAGTTTCGCAGAAAAG	57.612	33.333	5.51	0.00	45.90	2.27
7168	7635	2.552315	TCGCAGTGATTTTTCTTGGACC	59.448	45.455	0.00	0.00	0.00	4.46
7205	7672	3.498774	ACTTGGAGTGCAAGTCAGAAT	57.501	42.857	22.87	0.69	38.37	2.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
118	119	4.648626	TTGCTGCCGCTTCCTGCT	62.649	61.111	0.70	0.00	40.11	4.24
146	147	6.320418	TGCTATTCTACTCCGTGATTGAACTA	59.680	38.462	0.00	0.00	0.00	2.24
507	518	1.669779	GTTGTGATCTCTCAGGCATGC	59.330	52.381	9.90	9.90	30.18	4.06
508	519	2.981898	TGTTGTGATCTCTCAGGCATG	58.018	47.619	0.00	0.00	30.18	4.06
509	520	3.708403	TTGTTGTGATCTCTCAGGCAT	57.292	42.857	0.00	0.00	30.18	4.40
510	521	3.708403	ATTGTTGTGATCTCTCAGGCA	57.292	42.857	0.00	0.00	30.18	4.75
511	522	3.128242	CCAATTGTTGTGATCTCTCAGGC	59.872	47.826	4.43	0.00	30.18	4.85
512	523	3.128242	GCCAATTGTTGTGATCTCTCAGG	59.872	47.826	4.43	0.00	30.18	3.86
513	524	3.754850	TGCCAATTGTTGTGATCTCTCAG	59.245	43.478	4.43	0.00	30.18	3.35
514	525	3.753815	TGCCAATTGTTGTGATCTCTCA	58.246	40.909	4.43	0.00	0.00	3.27
1018	1037	8.946085	TGTTCAGAATTTACATCCACATACTTC	58.054	33.333	0.00	0.00	0.00	3.01
1268	1288	3.076621	TCCATGCATATTTCTCATCGCC	58.923	45.455	0.00	0.00	0.00	5.54
1269	1289	3.120060	GGTCCATGCATATTTCTCATCGC	60.120	47.826	0.00	0.00	0.00	4.58
1669	1694	8.718102	TGCTAATTAGAAATGTGTTCCTACTC	57.282	34.615	16.85	0.00	0.00	2.59
2136	2169	3.134262	GGGACAAGGGTTAGCTAGGTAAG	59.866	52.174	14.53	5.61	0.00	2.34
2230	2264	8.607459	CAACATACATATGTCTTCCTTCAGTTC	58.393	37.037	12.68	0.00	45.55	3.01
2630	2665	2.821378	CCACATTGTCAATGGAGCTTCA	59.179	45.455	25.59	0.00	43.21	3.02
2700	2736	6.661304	AGCTTCCATCTTCACTTTTGAATT	57.339	33.333	0.00	0.00	41.05	2.17
2776	2812	6.202570	GCTCACCATGAATTAGAAGATGAGAC	59.797	42.308	0.00	0.00	34.32	3.36
2827	2863	3.559069	TGATTCAAGATGATGCCTTCCC	58.441	45.455	0.00	0.00	0.00	3.97
2829	2865	5.769484	ACATGATTCAAGATGATGCCTTC	57.231	39.130	0.00	0.00	0.00	3.46
2906	2942	4.427312	CTCTTATTTGTCCTTGGCATTGC	58.573	43.478	0.00	0.00	0.00	3.56
2992	3028	4.102996	AGGTTGAAATCCAATTTGGCAAGT	59.897	37.500	10.76	0.00	37.47	3.16
3521	3562	2.034066	AACACGGAGGCCCATGTG	59.966	61.111	15.17	15.17	38.28	3.21
4088	4229	6.905076	GCAATTGTAACCAGATTGTATGTACG	59.095	38.462	7.40	0.00	34.19	3.67
4343	4508	6.202937	TCTTTGTTTGCATGTTAACCTAACG	58.797	36.000	2.48	0.00	41.50	3.18
4742	4907	7.148188	GCTACTCAGATGTCCAAATGATTTCAA	60.148	37.037	0.00	0.00	0.00	2.69
4992	5157	3.462954	TGGGAATATCCAATTCTGAGCCA	59.537	43.478	0.00	0.00	38.64	4.75
5026	5191	1.405105	CAACCCCACACACACAAAGAG	59.595	52.381	0.00	0.00	0.00	2.85
5028	5193	1.135141	CACAACCCCACACACACAAAG	60.135	52.381	0.00	0.00	0.00	2.77
5030	5195	1.599606	GCACAACCCCACACACACAA	61.600	55.000	0.00	0.00	0.00	3.33
5040	5205	0.908198	AGAGAGAGATGCACAACCCC	59.092	55.000	0.00	0.00	0.00	4.95
5041	5206	1.830477	AGAGAGAGAGATGCACAACCC	59.170	52.381	0.00	0.00	0.00	4.11
5132	5568	1.145803	GCAGGTAACCAGTCACGTTC	58.854	55.000	0.00	0.00	37.17	3.95
5395	5835	6.153340	AGGAGCAAGTAACATGTATGCAATTT	59.847	34.615	20.77	6.75	39.42	1.82
5396	5836	5.653769	AGGAGCAAGTAACATGTATGCAATT	59.346	36.000	20.77	7.02	39.42	2.32
5422	5871	4.067896	ACTTGAGCTTCTTACATGTGTGG	58.932	43.478	9.11	0.00	0.00	4.17
6291	6751	8.757982	AAAGTATGAACAAGCTTATCCATGAT	57.242	30.769	0.00	0.00	0.00	2.45
6542	7007	2.295253	GCTGCTAGCTTTTCTACGGA	57.705	50.000	17.23	0.00	38.45	4.69
6904	7371	3.753272	AGATGCGGGAAAAATATCCATCG	59.247	43.478	0.00	0.00	41.55	3.84
6934	7401	2.209838	ATGTTGGAGACGTATCAGCG	57.790	50.000	12.92	0.00	37.94	5.18
7104	7571	3.504520	TCCGTTTGGTATTCCTTTTCTGC	59.495	43.478	0.00	0.00	36.30	4.26
7112	7579	2.773993	TGGACTCCGTTTGGTATTCC	57.226	50.000	0.00	0.00	36.30	3.01
7168	7635	1.638529	AGTCTCCTGGGTGTCTTCTG	58.361	55.000	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.