AutoCloner

Multiple sequence alignment - TraesCS2A01G392300

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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	TraesCS2A01G392300	chr2A	100.000	6133	0	0	1	6133	642574854	642568722	0.000000e+00	11326.0
1	TraesCS2A01G392300	chr2B	93.906	4283	167	39	1770	6016	584116149	584111925	0.000000e+00	6377.0
2	TraesCS2A01G392300	chr2B	94.383	1086	43	6	1	1070	584117837	584116754	0.000000e+00	1652.0
3	TraesCS2A01G392300	chr2B	89.620	973	83	13	3147	4119	734355396	734356350	0.000000e+00	1221.0
4	TraesCS2A01G392300	chr2B	94.071	506	24	4	1057	1557	584116736	584116232	0.000000e+00	763.0
5	TraesCS2A01G392300	chr2B	84.343	198	18	3	2235	2424	734354923	734355115	1.360000e-41	182.0
6	TraesCS2A01G392300	chr2B	91.597	119	9	1	6016	6133	584111794	584111676	4.920000e-36	163.0
7	TraesCS2A01G392300	chr2B	85.057	87	7	6	1562	1647	411139536	411139455	3.940000e-12	84.2
8	TraesCS2A01G392300	chr2D	94.583	2640	93	15	3408	6016	498028855	498026235	0.000000e+00	4037.0
9	TraesCS2A01G392300	chr2D	91.527	1133	53	16	2211	3324	498029958	498028850	0.000000e+00	1520.0
10	TraesCS2A01G392300	chr2D	89.301	1187	56	30	1	1126	498032645	498031469	0.000000e+00	1423.0
11	TraesCS2A01G392300	chr2D	91.152	486	25	7	1620	2104	498030786	498030318	1.440000e-180	643.0
12	TraesCS2A01G392300	chr2D	92.670	191	8	4	1145	1330	498031232	498031043	2.820000e-68	270.0
13	TraesCS2A01G392300	chr2D	87.200	250	9	5	1318	1562	498031014	498030783	4.710000e-66	263.0
14	TraesCS2A01G392300	chr2D	90.083	121	8	3	6016	6133	498026074	498025955	2.960000e-33	154.0
15	TraesCS2A01G392300	chr2D	82.692	104	17	1	6024	6126	88053646	88053749	2.350000e-14	91.6
16	TraesCS2A01G392300	chr2D	81.915	94	15	2	6040	6132	62035456	62035548	1.830000e-10	78.7
17	TraesCS2A01G392300	chr1B	90.246	1179	93	17	3150	4326	117783295	117782137	0.000000e+00	1520.0
18	TraesCS2A01G392300	chr1B	86.364	198	15	2	2235	2424	117783772	117783579	8.060000e-49	206.0
19	TraesCS2A01G392300	chr3B	90.076	1179	95	17	3150	4326	16704871	16703713	0.000000e+00	1509.0
20	TraesCS2A01G392300	chr3B	84.343	198	19	2	2235	2424	16705348	16705155	3.780000e-42	183.0
21	TraesCS2A01G392300	chr1D	89.487	1189	96	18	3147	4326	18772943	18771775	0.000000e+00	1476.0
22	TraesCS2A01G392300	chr1D	83.505	194	21	6	2235	2424	18773410	18773224	2.940000e-38	171.0
23	TraesCS2A01G392300	chr6B	89.492	1180	99	19	3150	4326	16554896	16553739	0.000000e+00	1469.0
24	TraesCS2A01G392300	chr3A	89.900	1000	83	11	3333	4323	523893841	523894831	0.000000e+00	1271.0
25	TraesCS2A01G392300	chr3D	92.453	53	3	1	5917	5969	143003782	143003731	2.370000e-09	75.0
26	TraesCS2A01G392300	chr5B	97.619	42	1	0	1577	1618	412805699	412805740	8.530000e-09	73.1
27	TraesCS2A01G392300	chr5B	91.667	48	4	0	1571	1618	462751235	462751282	3.970000e-07	67.6
28	TraesCS2A01G392300	chr7B	88.889	54	5	1	1564	1617	686143811	686143759	1.430000e-06	65.8

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	TraesCS2A01G392300	chr2A	642568722	642574854	6132	True	11326.000000	11326	100.000000	1	6133	1	chr2A.!!$R1	6132
1	TraesCS2A01G392300	chr2B	584111676	584117837	6161	True	2238.750000	6377	93.489250	1	6133	4	chr2B.!!$R2	6132
2	TraesCS2A01G392300	chr2B	734354923	734356350	1427	False	701.500000	1221	86.981500	2235	4119	2	chr2B.!!$F1	1884
3	TraesCS2A01G392300	chr2D	498025955	498032645	6690	True	1187.142857	4037	90.930857	1	6133	7	chr2D.!!$R1	6132
4	TraesCS2A01G392300	chr1B	117782137	117783772	1635	True	863.000000	1520	88.305000	2235	4326	2	chr1B.!!$R1	2091
5	TraesCS2A01G392300	chr3B	16703713	16705348	1635	True	846.000000	1509	87.209500	2235	4326	2	chr3B.!!$R1	2091
6	TraesCS2A01G392300	chr1D	18771775	18773410	1635	True	823.500000	1476	86.496000	2235	4326	2	chr1D.!!$R1	2091
7	TraesCS2A01G392300	chr6B	16553739	16554896	1157	True	1469.000000	1469	89.492000	3150	4326	1	chr6B.!!$R1	1176
8	TraesCS2A01G392300	chr3A	523893841	523894831	990	False	1271.000000	1271	89.900000	3333	4323	1	chr3A.!!$F1	990

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
617	637	1.945819	GCAGGCTTCGGTTTCATCAGA	60.946	52.381	0.00	0.0	0.0	3.27	F
1885	2259	0.033366	GGGCATGTGGGTTGTTTGTC	59.967	55.000	0.00	0.0	0.0	3.18	F
2555	3219	0.108992	TTACAGCGGATGTCGTGTCC	60.109	55.000	0.45	0.0	42.7	4.02	F
2831	3530	0.617935	TCTCCGGAATTGGCATGTCA	59.382	50.000	5.23	0.0	0.0	3.58	F
3018	3720	1.500474	ATGATCCGTGGATGGTGTCT	58.500	50.000	6.03	0.0	34.6	3.41	F
4313	5026	2.292267	ACTGTGAGACTGGTTTTGCTG	58.708	47.619	0.00	0.0	0.0	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2101	2476	0.099968	TCTTATCTCCCGTCGCGTTG	59.900	55.000	5.77	0.00	0.00	4.10	R
2816	3515	1.473677	ACATGTGACATGCCAATTCCG	59.526	47.619	24.32	0.00	0.00	4.30	R
3366	4070	2.117156	GGTGCGCTGCAGGATCATT	61.117	57.895	17.12	0.00	40.08	2.57	R
4758	5474	1.202604	CCGCCCGTAATAAGATGGTGT	60.203	52.381	0.00	0.00	0.00	4.16	R
4978	5698	2.448453	AGAAGGGACTCTGTACGAAGG	58.552	52.381	0.00	0.00	38.49	3.46	R
5950	6701	0.521242	CGCACGTGCATAAAGGCTTC	60.521	55.000	37.03	6.34	42.21	3.86	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
31	32	3.469008	TTCTCTCAAAGAAAGCGGACA	57.531	42.857	0.00	0.00	41.10	4.02
94	95	2.540931	CAGTGCAACACCAATTTTCAGC	59.459	45.455	0.00	0.00	41.43	4.26
343	344	6.213195	GGATTAATCTGGTGATGGAGAGAGAT	59.787	42.308	14.95	0.00	32.44	2.75
352	353	5.512232	GGTGATGGAGAGAGATTATGGAACC	60.512	48.000	0.00	0.00	0.00	3.62
355	356	4.483950	TGGAGAGAGATTATGGAACCGAT	58.516	43.478	0.00	0.00	0.00	4.18
379	380	2.283529	GCTCAGGGAGGTTCGGACA	61.284	63.158	0.00	0.00	0.00	4.02
617	637	1.945819	GCAGGCTTCGGTTTCATCAGA	60.946	52.381	0.00	0.00	0.00	3.27
619	639	2.417933	CAGGCTTCGGTTTCATCAGAAG	59.582	50.000	0.00	0.21	40.62	2.85
621	641	2.615493	GGCTTCGGTTTCATCAGAAGGA	60.615	50.000	6.25	0.00	39.04	3.36
636	656	4.281688	TCAGAAGGAAAAATGGGCTGAAAG	59.718	41.667	0.00	0.00	0.00	2.62
651	671	4.899048	CTGAAAGAGAGCCCAGGAAGGC	62.899	59.091	0.00	0.00	46.57	4.35
701	721	7.093245	TGCATGGCCATATTTTATGCATAGAAT	60.093	33.333	20.30	21.99	46.31	2.40
704	724	9.705103	ATGGCCATATTTTATGCATAGAATAGT	57.295	29.630	25.30	15.48	0.00	2.12
872	893	9.868389	GTATAACCGTATACAAAAATGTTAGCC	57.132	33.333	3.32	0.00	41.21	3.93
974	1032	2.900122	TGTTTGCTTAGCTTGATCGC	57.100	45.000	5.60	0.00	0.00	4.58
1012	1072	1.407851	CCTGGACCATGGTCATGACTG	60.408	57.143	38.83	25.72	46.20	3.51
1030	1090	1.411977	CTGGTGGAGCAGATGTAGGAG	59.588	57.143	0.00	0.00	0.00	3.69
1032	1092	0.105778	GTGGAGCAGATGTAGGAGGC	59.894	60.000	0.00	0.00	0.00	4.70
1157	1466	9.060347	TGATAAAGAAGAGATGCATATGGTTTC	57.940	33.333	0.00	0.24	0.00	2.78
1224	1538	6.265577	AGTACCATTCGCATTGCTTTATTTC	58.734	36.000	7.12	0.00	0.00	2.17
1235	1549	5.743026	TTGCTTTATTTCGCCGAATATCA	57.257	34.783	0.00	0.00	0.00	2.15
1236	1550	5.090652	TGCTTTATTTCGCCGAATATCAC	57.909	39.130	0.00	0.00	0.00	3.06
1360	1721	7.506114	AGATGTTCAAAGTTTACACAGTAGGA	58.494	34.615	5.53	0.00	0.00	2.94
1383	1744	3.546020	GGGAATTATCGTGTTGATGTGCG	60.546	47.826	0.00	0.00	37.99	5.34
1384	1745	2.737467	ATTATCGTGTTGATGTGCGC	57.263	45.000	0.00	0.00	37.99	6.09

Showing 1 to 25 of 179 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	2.887152	GCCTGTCAGTTCTGATGGTTTT	59.113	45.455	18.33	0.00	0.00	2.43
94	95	6.091441	CACCCTCTATTTCTTTCACTTTCTCG	59.909	42.308	0.00	0.00	0.00	4.04
343	344	1.843851	AGCTTCCCATCGGTTCCATAA	59.156	47.619	0.00	0.00	0.00	1.90
352	353	1.445095	CTCCCTGAGCTTCCCATCG	59.555	63.158	0.00	0.00	0.00	3.84
355	356	1.151810	AACCTCCCTGAGCTTCCCA	60.152	57.895	0.00	0.00	0.00	4.37
379	380	3.181476	ACCTGCGCTTGATTTCAGTTTTT	60.181	39.130	9.73	0.00	0.00	1.94
413	414	5.945784	TGATTTCTTTGAACTATGGTGGGAG	59.054	40.000	0.00	0.00	0.00	4.30
617	637	4.482990	TCTCTTTCAGCCCATTTTTCCTT	58.517	39.130	0.00	0.00	0.00	3.36
619	639	3.367806	GCTCTCTTTCAGCCCATTTTTCC	60.368	47.826	0.00	0.00	0.00	3.13
621	641	3.949842	GCTCTCTTTCAGCCCATTTTT	57.050	42.857	0.00	0.00	0.00	1.94
651	671	0.099436	GCAAGCAAATGCCTAGGTCG	59.901	55.000	11.31	0.00	43.38	4.79
802	822	9.595823	GTAGTTCAGGCTATTTTATACTCACAA	57.404	33.333	0.00	0.00	0.00	3.33
880	901	2.290705	GGGTTACCTTGCACATGGTAGT	60.291	50.000	13.31	0.00	40.67	2.73
882	905	1.004979	GGGGTTACCTTGCACATGGTA	59.995	52.381	10.49	10.49	39.30	3.25
884	907	2.578683	GGGGTTACCTTGCACATGG	58.421	57.895	0.00	1.22	36.80	3.66
943	978	7.413475	AGCTAAGCAAACATTATATCGACAG	57.587	36.000	0.00	0.00	0.00	3.51
946	981	8.607441	ATCAAGCTAAGCAAACATTATATCGA	57.393	30.769	0.00	0.00	0.00	3.59
974	1032	1.679898	GTCCACCCCTGTTCTCCAG	59.320	63.158	0.00	0.00	41.15	3.86
1012	1072	0.755686	CCTCCTACATCTGCTCCACC	59.244	60.000	0.00	0.00	0.00	4.61
1030	1090	1.953231	GCATCTTCCAAAGCTGGGCC	61.953	60.000	0.00	0.00	43.71	5.80
1032	1092	1.067354	GTTGCATCTTCCAAAGCTGGG	60.067	52.381	0.00	0.00	43.71	4.45
1074	1165	5.105752	AGTAGCAATGTTCTTCATCGTCTC	58.894	41.667	0.00	0.00	35.48	3.36
1157	1466	8.066595	CCTTTCTAGCATCAATCTTTAATCACG	58.933	37.037	0.00	0.00	0.00	4.35
1224	1538	2.028476	TCCCCATTAGTGATATTCGGCG	60.028	50.000	0.00	0.00	0.00	6.46
1235	1549	4.687219	GCAAGCACTAGATTCCCCATTAGT	60.687	45.833	0.00	0.00	0.00	2.24

Showing 1 to 25 of 154 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.