AutoCloner

Multiple sequence alignment - TraesCS2A01G259500

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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	TraesCS2A01G259500	chr2A	100.000	5178	0	0	1	5178	407743618	407738441	0.000000e+00	9563.0
1	TraesCS2A01G259500	chr2A	85.185	135	20	0	1001	1135	183549660	183549794	6.990000e-29	139.0
2	TraesCS2A01G259500	chr2D	93.021	1834	66	27	1	1811	323073720	323075514	0.000000e+00	2621.0
3	TraesCS2A01G259500	chr2D	96.626	1393	21	6	2971	4345	323076770	323078154	0.000000e+00	2289.0
4	TraesCS2A01G259500	chr2D	91.051	771	24	12	1808	2553	323075594	323076344	0.000000e+00	1000.0
5	TraesCS2A01G259500	chr2D	91.818	440	36	0	4737	5176	323078563	323079002	9.530000e-172	614.0
6	TraesCS2A01G259500	chr2D	92.429	317	11	6	2635	2942	323076385	323076697	1.710000e-119	440.0
7	TraesCS2A01G259500	chr2D	91.765	255	12	2	4489	4742	323078179	323078425	3.840000e-91	346.0
8	TraesCS2A01G259500	chr2D	97.959	98	2	0	4343	4440	22958382	22958479	2.480000e-38	171.0
9	TraesCS2A01G259500	chr2D	83.704	135	22	0	1001	1135	166610516	166610382	1.510000e-25	128.0
10	TraesCS2A01G259500	chr2B	95.665	1384	39	8	2986	4354	390925436	390926813	0.000000e+00	2204.0
11	TraesCS2A01G259500	chr2B	93.219	1106	41	14	853	1951	390923168	390924246	0.000000e+00	1596.0
12	TraesCS2A01G259500	chr2B	83.716	872	52	35	1	855	390920229	390921027	0.000000e+00	741.0
13	TraesCS2A01G259500	chr2B	90.424	543	46	5	4639	5178	390938406	390938945	0.000000e+00	710.0
14	TraesCS2A01G259500	chr2B	91.975	486	16	8	2486	2953	390924811	390925291	0.000000e+00	660.0
15	TraesCS2A01G259500	chr2B	88.298	470	18	12	1993	2448	390924243	390924689	3.550000e-146	529.0
16	TraesCS2A01G259500	chr2B	91.791	134	8	3	4434	4566	390926819	390926950	3.180000e-42	183.0
17	TraesCS2A01G259500	chr2B	96.000	100	2	2	4342	4441	493852646	493852743	1.490000e-35	161.0
18	TraesCS2A01G259500	chr2B	83.333	138	23	0	998	1135	231232744	231232881	1.510000e-25	128.0
19	TraesCS2A01G259500	chr2B	97.619	42	1	0	4558	4599	390929763	390929804	7.190000e-09	73.1
20	TraesCS2A01G259500	chr3B	84.962	1064	157	1	3071	4134	761936950	761938010	0.000000e+00	1075.0
21	TraesCS2A01G259500	chr3B	82.868	1074	175	7	3071	4141	761902288	761903355	0.000000e+00	955.0
22	TraesCS2A01G259500	chr3B	94.393	107	3	3	4350	4454	52905168	52905273	1.490000e-35	161.0
23	TraesCS2A01G259500	chr3B	96.000	100	2	2	4343	4441	512457410	512457508	1.490000e-35	161.0
24	TraesCS2A01G259500	chr3A	84.939	1069	153	6	3071	4134	706922883	706923948	0.000000e+00	1075.0
25	TraesCS2A01G259500	chr3A	82.698	1075	175	9	3071	4141	706851447	706852514	0.000000e+00	944.0
26	TraesCS2A01G259500	chr3A	94.444	36	1	1	2053	2088	46003693	46003727	3.000000e-03	54.7
27	TraesCS2A01G259500	chr3A	100.000	28	0	0	2947	2974	509019727	509019754	9.000000e-03	52.8
28	TraesCS2A01G259500	chr3D	84.398	1064	163	1	3071	4134	572046002	572044942	0.000000e+00	1042.0
29	TraesCS2A01G259500	chr3D	83.054	1074	173	7	3071	4141	572101762	572100695	0.000000e+00	966.0
30	TraesCS2A01G259500	chr3D	82.514	1058	182	1	3071	4128	572085473	572084419	0.000000e+00	926.0
31	TraesCS2A01G259500	chr3D	78.484	488	72	20	4710	5178	185721027	185721500	6.560000e-74	289.0
32	TraesCS2A01G259500	chr3D	74.624	532	103	25	4646	5154	433419064	433418542	6.800000e-49	206.0
33	TraesCS2A01G259500	chr1A	79.903	413	70	9	4746	5148	521947057	521947466	1.820000e-74	291.0
34	TraesCS2A01G259500	chr7B	79.065	449	67	20	4745	5178	278906169	278906605	3.050000e-72	283.0
35	TraesCS2A01G259500	chr7B	88.189	127	12	3	4333	4458	695952570	695952694	1.160000e-31	148.0
36	TraesCS2A01G259500	chr5B	96.117	103	2	2	4343	4444	345770303	345770202	3.210000e-37	167.0
37	TraesCS2A01G259500	chr4A	97.938	97	1	1	4347	4443	650851207	650851302	3.210000e-37	167.0
38	TraesCS2A01G259500	chr4A	97.938	97	1	1	4347	4443	650861410	650861505	3.210000e-37	167.0
39	TraesCS2A01G259500	chr4A	96.000	100	2	2	4343	4441	723335662	723335564	1.490000e-35	161.0

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	TraesCS2A01G259500	chr2A	407738441	407743618	5177	True	9563.000000	9563	100.000000	1	5178	1	chr2A.!!$R1	5177
1	TraesCS2A01G259500	chr2D	323073720	323079002	5282	False	1218.333333	2621	92.785000	1	5176	6	chr2D.!!$F2	5175
2	TraesCS2A01G259500	chr2B	390920229	390929804	9575	False	855.157143	2204	91.754714	1	4599	7	chr2B.!!$F4	4598
3	TraesCS2A01G259500	chr2B	390938406	390938945	539	False	710.000000	710	90.424000	4639	5178	1	chr2B.!!$F2	539
4	TraesCS2A01G259500	chr3B	761936950	761938010	1060	False	1075.000000	1075	84.962000	3071	4134	1	chr3B.!!$F4	1063
5	TraesCS2A01G259500	chr3B	761902288	761903355	1067	False	955.000000	955	82.868000	3071	4141	1	chr3B.!!$F3	1070
6	TraesCS2A01G259500	chr3A	706922883	706923948	1065	False	1075.000000	1075	84.939000	3071	4134	1	chr3A.!!$F4	1063
7	TraesCS2A01G259500	chr3A	706851447	706852514	1067	False	944.000000	944	82.698000	3071	4141	1	chr3A.!!$F3	1070
8	TraesCS2A01G259500	chr3D	572044942	572046002	1060	True	1042.000000	1042	84.398000	3071	4134	1	chr3D.!!$R2	1063
9	TraesCS2A01G259500	chr3D	572100695	572101762	1067	True	966.000000	966	83.054000	3071	4141	1	chr3D.!!$R4	1070
10	TraesCS2A01G259500	chr3D	572084419	572085473	1054	True	926.000000	926	82.514000	3071	4128	1	chr3D.!!$R3	1057
11	TraesCS2A01G259500	chr3D	433418542	433419064	522	True	206.000000	206	74.624000	4646	5154	1	chr3D.!!$R1	508

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
633	654	1.067821	TGAATTTGAACCAACGGTGCC	59.932	47.619	0.00	0.00	35.34	5.01	F
1926	4201	0.107268	TCCATCCATGTCGAGCCATG	59.893	55.000	8.64	8.64	41.52	3.66	F
2204	4479	1.146774	TGATGCTCCCCAAAGTCCAAA	59.853	47.619	0.00	0.00	0.00	3.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
2419	4709	0.106708	TCAACAGCCCATCCTATCGC	59.893	55.000	4.58	R
3790	6323	0.035630	GGCAGATGAAGAGCACCACT	60.036	55.000	4.00	R
4180	6713	1.366435	AGCTAGGGAAGGAAGGAAGGA	59.634	52.381	3.36	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	Self end TH	Hairpin	End Stability
28	29	5.685841	TCAACATCGAAAAAGATCCGAAAC	58.314	37.500	0.00	0.00	35.87	2.78
29	30	5.237561	TCAACATCGAAAAAGATCCGAAACA	59.762	36.000	0.00	0.00	35.87	2.83
104	105	5.126396	AGAAACAGCATGATCGATCGATA	57.874	39.130	29.45	17.81	39.69	2.92
105	106	4.920340	AGAAACAGCATGATCGATCGATAC	59.080	41.667	29.45	21.57	39.69	2.24
197	212	2.186826	GGTCCGAATTCATGGCCGG	61.187	63.158	6.22	0.00	43.02	6.13
227	242	5.050159	GCAGTAAAGCACCCAAAAAGATTTG	60.050	40.000	0.00	0.00	44.50	2.32
298	313	3.153919	TCCCACGAAAATAAAGCTGCTT	58.846	40.909	9.53	9.53	0.00	3.91
505	520	5.705441	AGACGATTCTTTGGACTTGCATTAA	59.295	36.000	0.00	0.00	0.00	1.40
506	521	5.699839	ACGATTCTTTGGACTTGCATTAAC	58.300	37.500	0.00	0.00	0.00	2.01
508	523	6.653320	ACGATTCTTTGGACTTGCATTAACTA	59.347	34.615	0.00	0.00	0.00	2.24
509	524	7.148407	ACGATTCTTTGGACTTGCATTAACTAG	60.148	37.037	0.00	0.00	0.00	2.57
510	525	7.064609	CGATTCTTTGGACTTGCATTAACTAGA	59.935	37.037	0.00	0.00	0.00	2.43
511	526	8.814038	ATTCTTTGGACTTGCATTAACTAGAT	57.186	30.769	0.00	0.00	0.00	1.98
513	528	9.733556	TTCTTTGGACTTGCATTAACTAGATTA	57.266	29.630	0.00	0.00	0.00	1.75
514	529	9.383519	TCTTTGGACTTGCATTAACTAGATTAG	57.616	33.333	0.00	0.00	0.00	1.73
560	579	3.003113	AACTCGCGCACTACTCCCC	62.003	63.158	8.75	0.00	0.00	4.81
561	580	4.208686	CTCGCGCACTACTCCCCC	62.209	72.222	8.75	0.00	0.00	5.40
562	581	4.753662	TCGCGCACTACTCCCCCT	62.754	66.667	8.75	0.00	0.00	4.79
563	582	3.771160	CGCGCACTACTCCCCCTT	61.771	66.667	8.75	0.00	0.00	3.95
597	618	1.532437	ACGAATGAGTGTGTGTGCATG	59.468	47.619	0.00	0.00	0.00	4.06
633	654	1.067821	TGAATTTGAACCAACGGTGCC	59.932	47.619	0.00	0.00	35.34	5.01
731	752	5.817816	AGTTTAAGATAATGCCTCCAACTCG	59.182	40.000	0.00	0.00	0.00	4.18
756	777	3.870538	TCATATTTGCAGCCATCTCCT	57.129	42.857	0.00	0.00	0.00	3.69
758	779	4.645535	TCATATTTGCAGCCATCTCCTAC	58.354	43.478	0.00	0.00	0.00	3.18
770	795	4.263994	GCCATCTCCTACCTATCTAGTCCA	60.264	50.000	0.00	0.00	0.00	4.02

Showing 1 to 25 of 155 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	3.425162	AGCTTCCTTGTTTCGGATCTT	57.575	42.857	0.00	0.00	0.00	2.40
18	19	3.339141	GAAGCTTCCTTGTTTCGGATCT	58.661	45.455	15.97	0.00	0.00	2.75
78	79	5.122239	TCGATCGATCATGCTGTTTCTTTTT	59.878	36.000	24.40	0.00	0.00	1.94
79	80	4.631377	TCGATCGATCATGCTGTTTCTTTT	59.369	37.500	24.40	0.00	0.00	2.27
84	85	4.445718	GTGTATCGATCGATCATGCTGTTT	59.554	41.667	32.50	9.73	36.17	2.83
104	105	0.253347	ATCCCTGGGATGGTCAGTGT	60.253	55.000	27.29	0.01	41.43	3.55
105	106	1.806496	TATCCCTGGGATGGTCAGTG	58.194	55.000	33.71	0.00	43.06	3.66
227	242	1.134995	TCGTGATGGTGAGTCATGAGC	60.135	52.381	0.00	0.00	36.86	4.26
328	343	4.216472	ACCAGCGAGAAGATTTCCTTTTTC	59.784	41.667	0.00	0.00	34.68	2.29
334	349	5.048991	TGTTTTAACCAGCGAGAAGATTTCC	60.049	40.000	0.00	0.00	0.00	3.13
335	350	5.997385	TGTTTTAACCAGCGAGAAGATTTC	58.003	37.500	0.00	0.00	0.00	2.17
336	351	5.531287	ACTGTTTTAACCAGCGAGAAGATTT	59.469	36.000	0.00	0.00	0.00	2.17
337	352	5.063880	ACTGTTTTAACCAGCGAGAAGATT	58.936	37.500	0.00	0.00	0.00	2.40
338	353	4.642429	ACTGTTTTAACCAGCGAGAAGAT	58.358	39.130	0.00	0.00	0.00	2.40
339	354	4.067972	ACTGTTTTAACCAGCGAGAAGA	57.932	40.909	0.00	0.00	0.00	2.87
340	355	4.813296	AACTGTTTTAACCAGCGAGAAG	57.187	40.909	0.00	0.00	0.00	2.85
505	520	8.651589	TGGATGGTCGAATAATCTAATCTAGT	57.348	34.615	0.00	0.00	0.00	2.57
506	521	9.743057	GATGGATGGTCGAATAATCTAATCTAG	57.257	37.037	0.00	0.00	0.00	2.43
508	523	7.122799	TCGATGGATGGTCGAATAATCTAATCT	59.877	37.037	0.00	0.00	44.25	2.40
509	524	7.258441	TCGATGGATGGTCGAATAATCTAATC	58.742	38.462	0.00	0.00	44.25	1.75
510	525	7.170393	TCGATGGATGGTCGAATAATCTAAT	57.830	36.000	0.00	0.00	44.25	1.73
511	526	6.584185	TCGATGGATGGTCGAATAATCTAA	57.416	37.500	0.00	0.00	44.25	2.10
526	545	3.190079	CGAGTTGTGTTGATCGATGGAT	58.810	45.455	0.54	0.00	37.35	3.41
561	580	4.452733	GTCTCCCGTCCGGCCAAG	62.453	72.222	2.24	0.00	0.00	3.61
597	618	8.537223	GTTCAAATTCAATCACATGCATACATC	58.463	33.333	0.00	0.00	32.87	3.06

Showing 1 to 25 of 166 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.