AutoCloner

Multiple sequence alignment - TraesCS2D01G442700

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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	TraesCS2D01G442700	chr2D	100.000	3917	0	0	1	3917	553254573	553250657	0.000000e+00	7234
1	TraesCS2D01G442700	chr2B	94.995	2877	101	23	309	3162	659004511	659001655	0.000000e+00	4475
2	TraesCS2D01G442700	chr2B	94.272	611	25	7	2530	3138	658997077	658996475	0.000000e+00	926
3	TraesCS2D01G442700	chr2B	89.644	309	17	8	1	307	659004865	659004570	2.860000e-101	379
4	TraesCS2D01G442700	chr2A	96.387	2159	58	10	989	3138	693429940	693427793	0.000000e+00	3537
5	TraesCS2D01G442700	chr2A	85.169	445	19	12	502	942	693430413	693430012	2.820000e-111	412
6	TraesCS2D01G442700	chr5B	92.857	770	39	6	3157	3917	208704871	208704109	0.000000e+00	1103
7	TraesCS2D01G442700	chr5B	89.833	777	51	9	3159	3912	474051570	474050799	0.000000e+00	972
8	TraesCS2D01G442700	chr5B	84.874	476	56	12	3158	3623	420574414	420574883	2.130000e-127	466
9	TraesCS2D01G442700	chr5B	84.783	322	32	6	3608	3917	420574945	420575261	1.370000e-79	307
10	TraesCS2D01G442700	chr6A	92.458	769	45	6	3158	3917	576223283	576224047	0.000000e+00	1086
11	TraesCS2D01G442700	chr6A	81.573	1297	202	22	1638	2920	493842838	493844111	0.000000e+00	1037
12	TraesCS2D01G442700	chr6A	92.493	706	40	6	3221	3917	576397482	576398183	0.000000e+00	998
13	TraesCS2D01G442700	chr6A	80.802	1297	212	20	1638	2920	493756655	493757928	0.000000e+00	981
14	TraesCS2D01G442700	chr6A	80.663	1267	210	20	1667	2920	495153701	495152457	0.000000e+00	950
15	TraesCS2D01G442700	chr6A	80.124	1293	224	17	1638	2918	494047348	494048619	0.000000e+00	933
16	TraesCS2D01G442700	chr6A	80.568	916	145	19	1641	2544	494880285	494879391	0.000000e+00	675
17	TraesCS2D01G442700	chr6A	89.732	224	22	1	1230	1453	493842509	493842731	6.410000e-73	285
18	TraesCS2D01G442700	chr6A	89.286	224	23	1	1230	1453	495154059	495153837	2.980000e-71	279
19	TraesCS2D01G442700	chr6A	90.141	213	21	0	1241	1453	493756339	493756551	1.070000e-70	278
20	TraesCS2D01G442700	chr6D	81.596	1266	196	18	1667	2918	350204727	350203485	0.000000e+00	1013
21	TraesCS2D01G442700	chr6D	81.096	1296	210	20	1638	2920	349031771	349033044	0.000000e+00	1003
22	TraesCS2D01G442700	chr6D	80.478	1296	218	22	1638	2920	348861708	348862981	0.000000e+00	959
23	TraesCS2D01G442700	chr6D	88.596	228	25	1	1225	1452	28244891	28244665	3.860000e-70	276
24	TraesCS2D01G442700	chr6D	88.839	224	24	1	1230	1453	350205043	350204821	1.390000e-69	274
25	TraesCS2D01G442700	chr6D	88.789	223	24	1	1230	1452	348861379	348861600	4.990000e-69	272
26	TraesCS2D01G442700	chr6B	80.603	1294	216	21	1638	2918	529890222	529891493	0.000000e+00	966
27	TraesCS2D01G442700	chr6B	80.495	1292	219	19	1641	2920	530851842	530850572	0.000000e+00	959
28	TraesCS2D01G442700	chr6B	84.744	780	87	13	3151	3913	142735767	142736531	0.000000e+00	752
29	TraesCS2D01G442700	chr6B	89.286	224	23	1	1230	1453	529889893	529890115	2.980000e-71	279
30	TraesCS2D01G442700	chrUn	85.863	771	82	12	3164	3913	928652	927888	0.000000e+00	795
31	TraesCS2D01G442700	chrUn	85.714	777	84	12	3158	3913	951049	951819	0.000000e+00	795
32	TraesCS2D01G442700	chr1A	85.863	771	82	12	3164	3913	514591872	514591108	0.000000e+00	795
33	TraesCS2D01G442700	chr1A	85.038	782	83	16	3158	3917	9965007	9965776	0.000000e+00	765
34	TraesCS2D01G442700	chr5D	88.667	450	33	6	3477	3913	294330399	294330843	2.070000e-147	532
35	TraesCS2D01G442700	chr3A	87.640	356	28	8	3576	3917	680763037	680763390	2.190000e-107	399
36	TraesCS2D01G442700	chr7A	91.379	232	17	3	3687	3917	234527842	234528071	8.170000e-82	315
37	TraesCS2D01G442700	chr7D	83.871	124	20	0	3151	3274	27507996	27508119	6.880000e-23	119

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	TraesCS2D01G442700	chr2D	553250657	553254573	3916	True	7234.0	7234	100.0000	1	3917	1	chr2D.!!$R1	3916
1	TraesCS2D01G442700	chr2B	659001655	659004865	3210	True	2427.0	4475	92.3195	1	3162	2	chr2B.!!$R2	3161
2	TraesCS2D01G442700	chr2B	658996475	658997077	602	True	926.0	926	94.2720	2530	3138	1	chr2B.!!$R1	608
3	TraesCS2D01G442700	chr2A	693427793	693430413	2620	True	1974.5	3537	90.7780	502	3138	2	chr2A.!!$R1	2636
4	TraesCS2D01G442700	chr5B	208704109	208704871	762	True	1103.0	1103	92.8570	3157	3917	1	chr5B.!!$R1	760
5	TraesCS2D01G442700	chr5B	474050799	474051570	771	True	972.0	972	89.8330	3159	3912	1	chr5B.!!$R2	753
6	TraesCS2D01G442700	chr5B	420574414	420575261	847	False	386.5	466	84.8285	3158	3917	2	chr5B.!!$F1	759
7	TraesCS2D01G442700	chr6A	576223283	576224047	764	False	1086.0	1086	92.4580	3158	3917	1	chr6A.!!$F2	759
8	TraesCS2D01G442700	chr6A	576397482	576398183	701	False	998.0	998	92.4930	3221	3917	1	chr6A.!!$F3	696
9	TraesCS2D01G442700	chr6A	494047348	494048619	1271	False	933.0	933	80.1240	1638	2918	1	chr6A.!!$F1	1280
10	TraesCS2D01G442700	chr6A	494879391	494880285	894	True	675.0	675	80.5680	1641	2544	1	chr6A.!!$R1	903
11	TraesCS2D01G442700	chr6A	493842509	493844111	1602	False	661.0	1037	85.6525	1230	2920	2	chr6A.!!$F5	1690
12	TraesCS2D01G442700	chr6A	493756339	493757928	1589	False	629.5	981	85.4715	1241	2920	2	chr6A.!!$F4	1679
13	TraesCS2D01G442700	chr6A	495152457	495154059	1602	True	614.5	950	84.9745	1230	2920	2	chr6A.!!$R2	1690
14	TraesCS2D01G442700	chr6D	349031771	349033044	1273	False	1003.0	1003	81.0960	1638	2920	1	chr6D.!!$F1	1282
15	TraesCS2D01G442700	chr6D	350203485	350205043	1558	True	643.5	1013	85.2175	1230	2918	2	chr6D.!!$R2	1688
16	TraesCS2D01G442700	chr6D	348861379	348862981	1602	False	615.5	959	84.6335	1230	2920	2	chr6D.!!$F2	1690
17	TraesCS2D01G442700	chr6B	530850572	530851842	1270	True	959.0	959	80.4950	1641	2920	1	chr6B.!!$R1	1279
18	TraesCS2D01G442700	chr6B	142735767	142736531	764	False	752.0	752	84.7440	3151	3913	1	chr6B.!!$F1	762
19	TraesCS2D01G442700	chr6B	529889893	529891493	1600	False	622.5	966	84.9445	1230	2918	2	chr6B.!!$F2	1688
20	TraesCS2D01G442700	chrUn	927888	928652	764	True	795.0	795	85.8630	3164	3913	1	chrUn.!!$R1	749
21	TraesCS2D01G442700	chrUn	951049	951819	770	False	795.0	795	85.7140	3158	3913	1	chrUn.!!$F1	755
22	TraesCS2D01G442700	chr1A	514591108	514591872	764	True	795.0	795	85.8630	3164	3913	1	chr1A.!!$R1	749
23	TraesCS2D01G442700	chr1A	9965007	9965776	769	False	765.0	765	85.0380	3158	3917	1	chr1A.!!$F1	759

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	Hairpin	End Stability	Orientation
209	210	0.179032	TTGCTCTTCAGTTTCCCGCA	60.179	50.000	0.00	5.69	F
912	981	0.985490	ATCTCACCCTCCAAGGCTCC	60.985	60.000	32.73	4.70	F
1476	1572	1.066454	GTAAGCACACACCCAAACCAC	59.934	52.381	0.00	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1183	1279	0.755079	TTGCTCTCTATCAGCGGCAT	59.245	50.000	1.45	40.01	4.40	R
2238	2421	1.227380	GATGCTCGTCGCCCAGATT	60.227	57.895	0.00	38.05	2.40	R
2928	3114	0.026803	GTACGCCGACGAGTAACGAT	59.973	55.000	0.00	45.77	3.73	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
28	29	3.786635	CTGATGTAACAGTCAGTAGCCC	58.213	50.000	0.00	37.62	5.19
63	64	1.187087	GGATTCACAGAGACGGTCCT	58.813	55.000	4.14	0.00	3.85
65	66	0.811915	ATTCACAGAGACGGTCCTCG	59.188	55.000	4.14	45.88	4.63
174	175	2.017049	GCATTTCACCTTACCGATGCT	58.983	47.619	0.00	37.49	3.79
176	177	2.851263	TTTCACCTTACCGATGCTGT	57.149	45.000	0.00	0.00	4.40
184	185	2.157834	TACCGATGCTGTTCACGTTT	57.842	45.000	0.00	0.00	3.60
209	210	0.179032	TTGCTCTTCAGTTTCCCGCA	60.179	50.000	0.00	0.00	5.69
224	230	6.097839	AGTTTCCCGCAAGATAAGTATAGTGA	59.902	38.462	0.00	43.02	3.41
225	231	5.707242	TCCCGCAAGATAAGTATAGTGAG	57.293	43.478	0.00	43.02	3.51
234	240	7.847711	AGATAAGTATAGTGAGTTGGAGCAT	57.152	36.000	0.00	0.00	3.79
235	241	8.941995	AGATAAGTATAGTGAGTTGGAGCATA	57.058	34.615	0.00	0.00	3.14
236	242	8.798402	AGATAAGTATAGTGAGTTGGAGCATAC	58.202	37.037	0.00	0.00	2.39
237	243	8.713708	ATAAGTATAGTGAGTTGGAGCATACT	57.286	34.615	0.00	30.95	2.12
238	244	6.642707	AGTATAGTGAGTTGGAGCATACTC	57.357	41.667	0.00	42.66	2.59
239	245	6.369629	AGTATAGTGAGTTGGAGCATACTCT	58.630	40.000	0.00	42.98	3.24
240	246	7.519057	AGTATAGTGAGTTGGAGCATACTCTA	58.481	38.462	0.00	42.98	2.43
241	247	6.892658	ATAGTGAGTTGGAGCATACTCTAG	57.107	41.667	0.00	42.98	2.43
242	248	4.861196	AGTGAGTTGGAGCATACTCTAGA	58.139	43.478	0.00	42.98	2.43
243	249	5.454062	AGTGAGTTGGAGCATACTCTAGAT	58.546	41.667	0.00	42.98	1.98
244	250	6.606069	AGTGAGTTGGAGCATACTCTAGATA	58.394	40.000	0.00	42.98	1.98
245	251	7.063593	AGTGAGTTGGAGCATACTCTAGATAA	58.936	38.462	0.00	42.98	1.75
256	262	9.113838	AGCATACTCTAGATAAATTTGTGGTTG	57.886	33.333	0.00	0.00	3.77
259	265	7.383102	ACTCTAGATAAATTTGTGGTTGCAG	57.617	36.000	0.00	0.00	4.41
286	292	6.270927	TGGTTAGGATTATGCTCTCTGCTAAT	59.729	38.462	0.00	43.37	1.73
287	293	6.816140	GGTTAGGATTATGCTCTCTGCTAATC	59.184	42.308	0.00	43.37	1.75

Showing 1 to 25 of 76 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
125	126	5.403466	GCAAATTAAGTTCAGGCTTTCAGTG	59.597	40.000	0.00	0.00	3.66
128	129	5.528043	TGCAAATTAAGTTCAGGCTTTCA	57.472	34.783	0.00	0.00	2.69
174	175	3.625764	AGAGCAAGCTTAAAACGTGAACA	59.374	39.130	0.00	0.00	3.18
176	177	4.334203	TGAAGAGCAAGCTTAAAACGTGAA	59.666	37.500	0.00	0.00	3.18
184	185	3.821033	GGGAAACTGAAGAGCAAGCTTAA	59.179	43.478	0.00	0.00	1.85
209	210	7.661536	TGCTCCAACTCACTATACTTATCTT	57.338	36.000	0.00	0.00	2.40
224	230	9.553064	CAAATTTATCTAGAGTATGCTCCAACT	57.447	33.333	7.25	42.59	3.16
225	231	9.331282	ACAAATTTATCTAGAGTATGCTCCAAC	57.669	33.333	7.25	42.59	3.77
234	240	7.065803	GCTGCAACCACAAATTTATCTAGAGTA	59.934	37.037	0.00	0.00	2.59
235	241	6.127897	GCTGCAACCACAAATTTATCTAGAGT	60.128	38.462	0.00	0.00	3.24
236	242	6.094603	AGCTGCAACCACAAATTTATCTAGAG	59.905	38.462	1.02	0.00	2.43
237	243	5.945784	AGCTGCAACCACAAATTTATCTAGA	59.054	36.000	1.02	0.00	2.43
238	244	6.032094	CAGCTGCAACCACAAATTTATCTAG	58.968	40.000	0.00	0.00	2.43
239	245	5.105797	CCAGCTGCAACCACAAATTTATCTA	60.106	40.000	8.66	0.00	1.98
240	246	4.322198	CCAGCTGCAACCACAAATTTATCT	60.322	41.667	8.66	0.00	1.98
241	247	3.928375	CCAGCTGCAACCACAAATTTATC	59.072	43.478	8.66	0.00	1.75
242	248	3.324556	ACCAGCTGCAACCACAAATTTAT	59.675	39.130	8.66	0.00	1.40
243	249	2.697751	ACCAGCTGCAACCACAAATTTA	59.302	40.909	8.66	0.00	1.40
244	250	1.485895	ACCAGCTGCAACCACAAATTT	59.514	42.857	8.66	0.00	1.82
245	251	1.122227	ACCAGCTGCAACCACAAATT	58.878	45.000	8.66	0.00	1.82
256	262	2.810852	GAGCATAATCCTAACCAGCTGC	59.189	50.000	8.66	0.00	5.25
259	265	4.314121	CAGAGAGCATAATCCTAACCAGC	58.686	47.826	0.00	0.00	4.85
289	295	5.520022	AAAACGTATATGAAACGCTTCGT	57.480	34.783	0.00	44.04	3.85
290	296	7.355354	GCAATAAAACGTATATGAAACGCTTCG	60.355	37.037	0.00	44.04	3.79
307	313	1.732405	GCCAGCTCACCGCAATAAAAC	60.732	52.381	0.00	42.61	2.43

Showing 1 to 25 of 68 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.