AutoCloner

Multiple sequence alignment - TraesCS4B01G082500

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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	TraesCS4B01G082500	chr4B	100.000	3811	0	0	1	3811	81359174	81362984	0.000000e+00	7038.0
1	TraesCS4B01G082500	chr4B	96.148	649	25	0	3163	3811	604539206	604539854	0.000000e+00	1061.0
2	TraesCS4B01G082500	chr4D	95.880	1966	32	7	913	2830	54810906	54808942	0.000000e+00	3136.0
3	TraesCS4B01G082500	chr4D	92.774	941	49	14	1	932	54811845	54810915	0.000000e+00	1343.0
4	TraesCS4B01G082500	chr4D	91.011	267	15	3	2899	3162	54808943	54808683	6.060000e-93	351.0
5	TraesCS4B01G082500	chr4A	92.129	2198	103	24	1	2157	542260594	542262762	0.000000e+00	3037.0
6	TraesCS4B01G082500	chr4A	97.050	1017	20	3	2156	3162	542262795	542263811	0.000000e+00	1703.0
7	TraesCS4B01G082500	chr4A	96.600	647	21	1	3165	3811	728114294	728114939	0.000000e+00	1072.0
8	TraesCS4B01G082500	chr1B	96.302	649	24	0	3163	3811	72804309	72803661	0.000000e+00	1066.0
9	TraesCS4B01G082500	chr1B	96.012	652	26	0	3160	3811	6250356	6249705	0.000000e+00	1061.0
10	TraesCS4B01G082500	chr3B	96.296	648	23	1	3164	3811	24390151	24390797	0.000000e+00	1062.0
11	TraesCS4B01G082500	chr3B	95.846	650	27	0	3162	3811	621475342	621475991	0.000000e+00	1051.0
12	TraesCS4B01G082500	chr6B	95.994	649	25	1	3163	3811	576208365	576209012	0.000000e+00	1053.0
13	TraesCS4B01G082500	chr6B	95.988	648	26	0	3164	3811	641300853	641301500	0.000000e+00	1053.0
14	TraesCS4B01G082500	chr1D	95.833	648	27	0	3164	3811	486402827	486402180	0.000000e+00	1048.0
15	TraesCS4B01G082500	chr1D	96.296	54	1	1	290	342	48391460	48391407	1.890000e-13	87.9
16	TraesCS4B01G082500	chr6D	96.296	54	1	1	290	342	304099449	304099396	1.890000e-13	87.9
17	TraesCS4B01G082500	chr5D	96.296	54	1	1	290	342	241947603	241947550	1.890000e-13	87.9
18	TraesCS4B01G082500	chr5D	96.296	54	1	1	290	342	294634485	294634432	1.890000e-13	87.9
19	TraesCS4B01G082500	chr5A	96.296	54	1	1	290	342	311937134	311937081	1.890000e-13	87.9
20	TraesCS4B01G082500	chr3D	96.296	54	1	1	290	342	71517681	71517734	1.890000e-13	87.9
21	TraesCS4B01G082500	chr3D	96.296	54	1	1	290	342	426451862	426451915	1.890000e-13	87.9

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	TraesCS4B01G082500	chr4B	81359174	81362984	3810	False	7038	7038	100.000000	1	3811	1	chr4B.!!$F1	3810
1	TraesCS4B01G082500	chr4B	604539206	604539854	648	False	1061	1061	96.148000	3163	3811	1	chr4B.!!$F2	648
2	TraesCS4B01G082500	chr4D	54808683	54811845	3162	True	1610	3136	93.221667	1	3162	3	chr4D.!!$R1	3161
3	TraesCS4B01G082500	chr4A	542260594	542263811	3217	False	2370	3037	94.589500	1	3162	2	chr4A.!!$F2	3161
4	TraesCS4B01G082500	chr4A	728114294	728114939	645	False	1072	1072	96.600000	3165	3811	1	chr4A.!!$F1	646
5	TraesCS4B01G082500	chr1B	72803661	72804309	648	True	1066	1066	96.302000	3163	3811	1	chr1B.!!$R2	648
6	TraesCS4B01G082500	chr1B	6249705	6250356	651	True	1061	1061	96.012000	3160	3811	1	chr1B.!!$R1	651
7	TraesCS4B01G082500	chr3B	24390151	24390797	646	False	1062	1062	96.296000	3164	3811	1	chr3B.!!$F1	647
8	TraesCS4B01G082500	chr3B	621475342	621475991	649	False	1051	1051	95.846000	3162	3811	1	chr3B.!!$F2	649
9	TraesCS4B01G082500	chr6B	576208365	576209012	647	False	1053	1053	95.994000	3163	3811	1	chr6B.!!$F1	648
10	TraesCS4B01G082500	chr6B	641300853	641301500	647	False	1053	1053	95.988000	3164	3811	1	chr6B.!!$F2	647
11	TraesCS4B01G082500	chr1D	486402180	486402827	647	True	1048	1048	95.833000	3164	3811	1	chr1D.!!$R2	647

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
136	142	0.696501	TTTGGTCTAGTTGCTCCCCC	59.303	55.0	0.00	0.0	0.00	5.40	F
1089	1134	0.040058	AGCAGATGCCACATTTCCCA	59.960	50.0	0.14	0.0	43.38	4.37	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1119	1164	1.523758	GTGGTGCAGGTAGAACAAGG	58.476	55.000	0.0	0.0	0.0	3.61	R
3132	3251	3.834231	CCCAATGATGTTCAGGAAAAGGT	59.166	43.478	0.0	0.0	0.0	3.50	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
45	51	2.327592	CGCTTTGCAACAGTCGCA	59.672	55.556	0.00	0.00	37.68	5.10
53	59	1.296392	CAACAGTCGCATCAGGGGA	59.704	57.895	0.00	0.00	35.89	4.81
55	61	1.138859	CAACAGTCGCATCAGGGGATA	59.861	52.381	0.00	0.00	40.92	2.59
80	86	6.600822	AGTTAGATGTGCTGCATTGAGTAATT	59.399	34.615	5.27	0.00	38.06	1.40
93	99	7.033185	GCATTGAGTAATTTGGTCGGTTTATT	58.967	34.615	0.00	0.00	0.00	1.40
94	100	8.185505	GCATTGAGTAATTTGGTCGGTTTATTA	58.814	33.333	0.00	0.00	0.00	0.98
102	108	6.687081	TTTGGTCGGTTTATTATAGGCAAG	57.313	37.500	0.00	0.00	0.00	4.01
136	142	0.696501	TTTGGTCTAGTTGCTCCCCC	59.303	55.000	0.00	0.00	0.00	5.40
140	146	3.083997	CTAGTTGCTCCCCCGGCT	61.084	66.667	0.00	0.00	0.00	5.52
187	193	6.406370	AGAACCGATTCTCACATGTATTTGA	58.594	36.000	0.00	0.00	41.63	2.69
319	325	0.737715	GTGCTAGAAGCTCCCACACG	60.738	60.000	0.00	0.00	42.97	4.49
371	377	5.204409	GCATTGGCAGATGATTAAATCCA	57.796	39.130	11.99	0.00	40.72	3.41
376	382	9.938280	CATTGGCAGATGATTAAATCCAATAAT	57.062	29.630	0.00	0.00	39.86	1.28
467	478	1.347062	TGGAGACATGTGTAGGTGCA	58.653	50.000	1.15	0.00	33.40	4.57
482	493	2.171448	AGGTGCAGTAGCCATAAAGGAG	59.829	50.000	0.00	0.00	41.22	3.69
494	505	2.806945	TAAAGGAGATTGTGGGCCAG	57.193	50.000	6.40	0.00	0.00	4.85
538	550	6.243148	TCCAAGTAACCTTTTTCCTATCACC	58.757	40.000	0.00	0.00	0.00	4.02
539	551	6.045106	TCCAAGTAACCTTTTTCCTATCACCT	59.955	38.462	0.00	0.00	0.00	4.00
558	570	3.311596	ACCTGTAAAACTGAAGCGTGAAC	59.688	43.478	0.00	0.00	0.00	3.18
583	595	5.553123	ACCACATACCTGTTTTAATCGACA	58.447	37.500	0.00	0.00	31.62	4.35
593	605	4.451096	TGTTTTAATCGACAGGTCTGCTTC	59.549	41.667	0.00	0.00	0.00	3.86
720	734	4.627611	CATGGTTTGCTTAGATGGTCAG	57.372	45.455	0.00	0.00	0.00	3.51
873	890	6.671190	TGATTCAGCATCTTTGTGTTAGTTG	58.329	36.000	0.00	0.00	32.34	3.16
874	891	6.486320	TGATTCAGCATCTTTGTGTTAGTTGA	59.514	34.615	0.00	0.00	32.34	3.18
876	893	6.882610	TCAGCATCTTTGTGTTAGTTGAAT	57.117	33.333	0.00	0.00	0.00	2.57
954	999	3.565902	GTGCTCTGTTTTCAGTTTAGCCT	59.434	43.478	0.00	0.00	46.98	4.58
960	1005	4.274147	TGTTTTCAGTTTAGCCTGGTTGA	58.726	39.130	0.00	0.00	33.14	3.18
973	1018	2.069273	CTGGTTGATCCTCGACAACAC	58.931	52.381	15.80	7.98	45.27	3.32
1009	1054	2.029739	TCAGTTCATGCAATGCAACCTG	60.030	45.455	13.45	14.94	46.21	4.00
1086	1131	2.097142	GTCAGAGCAGATGCCACATTTC	59.903	50.000	0.14	0.00	43.38	2.17
1089	1134	0.040058	AGCAGATGCCACATTTCCCA	59.960	50.000	0.14	0.00	43.38	4.37
1220	1265	9.807386	GTTTTATACTGTATGTGTTTCACTGTC	57.193	33.333	10.51	0.00	35.11	3.51
1431	1477	2.564062	ACCTTGGGTTCATTTGCATCAG	59.436	45.455	0.00	0.00	27.29	2.90
1483	1530	4.255833	TGTTTGCCACTTCATTCCATTC	57.744	40.909	0.00	0.00	0.00	2.67
1958	2029	6.874664	TGTGATATTGCTACTTTCGGTTTACA	59.125	34.615	0.00	0.00	0.00	2.41
1990	2061	5.437060	AGGAACTTCAGAACTTTGCTTGTA	58.563	37.500	0.00	0.00	27.25	2.41
2894	3003	2.037772	GGTCAGTCATCTGTGGTCTGTT	59.962	50.000	0.00	0.00	41.91	3.16
3131	3250	1.073548	GCGAGTGGGGGTGGTTTTA	59.926	57.895	0.00	0.00	0.00	1.52
3132	3251	0.537828	GCGAGTGGGGGTGGTTTTAA	60.538	55.000	0.00	0.00	0.00	1.52
3231	3350	4.924305	AGTACAAGTCACGTAAAGACCA	57.076	40.909	0.00	0.00	36.68	4.02
3257	3376	7.715657	ACATGACAAAACTGAAAAGATAGCAA	58.284	30.769	0.00	0.00	0.00	3.91
3263	3382	9.382275	ACAAAACTGAAAAGATAGCAAAACATT	57.618	25.926	0.00	0.00	0.00	2.71
3500	3619	1.144057	CTAGCATCCCACCACGACC	59.856	63.158	0.00	0.00	0.00	4.79
3689	3808	1.300697	GACACAGGTCCACCACGAC	60.301	63.158	0.00	0.00	38.12	4.34
3696	3815	3.307108	TCCACCACGACGATGCCA	61.307	61.111	0.00	0.00	0.00	4.92
3762	3881	0.906775	TCCCCAACAATAGGACCGAC	59.093	55.000	0.00	0.00	0.00	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	46	2.891580	TCTAACTATCCCCTGATGCGAC	59.108	50.000	0.00	0.00	32.18	5.19
45	51	4.285517	CAGCACATCTAACTATCCCCTGAT	59.714	45.833	0.00	0.00	34.87	2.90
53	59	5.678583	ACTCAATGCAGCACATCTAACTAT	58.321	37.500	0.00	0.00	38.34	2.12
55	61	3.947868	ACTCAATGCAGCACATCTAACT	58.052	40.909	0.00	0.00	38.34	2.24
80	86	5.991861	TCTTGCCTATAATAAACCGACCAA	58.008	37.500	0.00	0.00	0.00	3.67
93	99	4.037684	GCTACCGAAACTCTCTTGCCTATA	59.962	45.833	0.00	0.00	0.00	1.31
94	100	3.181474	GCTACCGAAACTCTCTTGCCTAT	60.181	47.826	0.00	0.00	0.00	2.57
95	101	2.165845	GCTACCGAAACTCTCTTGCCTA	59.834	50.000	0.00	0.00	0.00	3.93
96	102	1.066787	GCTACCGAAACTCTCTTGCCT	60.067	52.381	0.00	0.00	0.00	4.75
102	108	2.994578	GACCAAAGCTACCGAAACTCTC	59.005	50.000	0.00	0.00	0.00	3.20
140	146	1.754745	GCAGATAGATTGGCGGGGA	59.245	57.895	0.00	0.00	0.00	4.81
144	150	0.394192	TCCTGGCAGATAGATTGGCG	59.606	55.000	17.94	0.00	43.41	5.69
206	212	6.930731	TGCCGTGCTATCATAATTACTCATA	58.069	36.000	0.00	0.00	0.00	2.15
226	232	6.425114	AGCATTAGTAATGATTAGTCTTGCCG	59.575	38.462	24.11	0.00	41.46	5.69
319	325	2.763902	CTTCCCCAACCCCACCTC	59.236	66.667	0.00	0.00	0.00	3.85
467	478	4.141390	CCCACAATCTCCTTTATGGCTACT	60.141	45.833	0.00	0.00	35.26	2.57
482	493	2.450476	AGAAATCACTGGCCCACAATC	58.550	47.619	0.00	0.00	0.00	2.67
494	505	3.748568	GGAGACACTCACCAAGAAATCAC	59.251	47.826	0.00	0.00	31.08	3.06
538	550	4.530094	TGTTCACGCTTCAGTTTTACAG	57.470	40.909	0.00	0.00	0.00	2.74
539	551	4.437659	GGTTGTTCACGCTTCAGTTTTACA	60.438	41.667	0.00	0.00	0.00	2.41
558	570	6.072948	TGTCGATTAAAACAGGTATGTGGTTG	60.073	38.462	0.00	0.00	40.39	3.77
593	605	9.276590	TCTATCACCAAAATATCTATGTTGCAG	57.723	33.333	0.00	0.00	31.07	4.41
741	755	0.524816	GCAGAACGATGCATTGCCAG	60.525	55.000	14.18	4.64	45.77	4.85
848	865	7.175467	TCAACTAACACAAAGATGCTGAATCAT	59.825	33.333	0.00	0.00	37.81	2.45
954	999	1.414550	TGTGTTGTCGAGGATCAACCA	59.585	47.619	12.47	8.26	41.92	3.67
960	1005	2.628178	TGAAGAGTGTGTTGTCGAGGAT	59.372	45.455	0.00	0.00	0.00	3.24
1119	1164	1.523758	GTGGTGCAGGTAGAACAAGG	58.476	55.000	0.00	0.00	0.00	3.61
1220	1265	7.063898	CCTTCCATATGCATACATCGAAGTAAG	59.936	40.741	20.94	1.52	37.74	2.34
1462	1508	3.896888	AGAATGGAATGAAGTGGCAAACA	59.103	39.130	0.00	0.00	0.00	2.83
1643	1690	2.684881	CTGCCATACATCACAAGGGAAC	59.315	50.000	0.00	0.00	0.00	3.62
3131	3250	4.284234	CCCAATGATGTTCAGGAAAAGGTT	59.716	41.667	0.00	0.00	0.00	3.50
3132	3251	3.834231	CCCAATGATGTTCAGGAAAAGGT	59.166	43.478	0.00	0.00	0.00	3.50
3231	3350	7.715657	TGCTATCTTTTCAGTTTTGTCATGTT	58.284	30.769	0.00	0.00	0.00	2.71
3257	3376	3.953612	TGGTGTCAAGCTCAGAAATGTTT	59.046	39.130	0.00	0.00	0.00	2.83
3263	3382	1.581934	CGTTGGTGTCAAGCTCAGAA	58.418	50.000	0.00	0.00	32.92	3.02
3417	3536	1.202675	TCGTTCAACGGTAAGGGCTTT	60.203	47.619	10.69	0.00	42.81	3.51
3500	3619	0.948678	TTTCCTCCTTCGGCGTTTTG	59.051	50.000	6.85	0.00	0.00	2.44
3639	3758	3.578272	TTGCGACGGCGTTTGCTT	61.578	55.556	29.28	2.47	44.10	3.91
3762	3881	0.464452	ATCCTTTCCTAACGAGGCCG	59.536	55.000	0.00	0.00	43.40	6.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.