AutoCloner

Multiple sequence alignment - TraesCS4A01G204700

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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	TraesCS4A01G204700	chr4A	100.000	7912	0	0	1	7912	496996901	497004812	0.000000e+00	14611.0
1	TraesCS4A01G204700	chr4D	96.931	7200	156	37	692	7877	84268946	84276094	0.000000e+00	12011.0
2	TraesCS4A01G204700	chr4D	90.267	637	52	5	2	631	84268290	84268923	0.000000e+00	824.0
3	TraesCS4A01G204700	chr4B	95.584	3329	88	12	918	4214	119259891	119263192	0.000000e+00	5278.0
4	TraesCS4A01G204700	chr4B	93.319	1811	75	16	5887	7681	119270386	119272166	0.000000e+00	2632.0
5	TraesCS4A01G204700	chr4B	96.556	813	20	3	4222	5029	119263232	119264041	0.000000e+00	1339.0
6	TraesCS4A01G204700	chr4B	86.379	903	78	22	1	891	119258945	119259814	0.000000e+00	944.0
7	TraesCS4A01G204700	chr4B	97.490	518	13	0	5294	5811	119264349	119264866	0.000000e+00	885.0
8	TraesCS4A01G204700	chr4B	86.047	215	22	4	1	208	70549281	70549494	2.870000e-54	224.0
9	TraesCS4A01G204700	chr4B	88.439	173	16	4	7706	7876	119272161	119272331	1.040000e-48	206.0
10	TraesCS4A01G204700	chr1D	89.995	2169	189	16	975	3139	54918727	54916583	0.000000e+00	2778.0
11	TraesCS4A01G204700	chr1D	90.715	1594	97	22	4224	5805	54915461	54913907	0.000000e+00	2076.0
12	TraesCS4A01G204700	chr1D	87.652	988	95	20	6076	7050	54913630	54912657	0.000000e+00	1123.0
13	TraesCS4A01G204700	chr1D	85.699	965	64	30	3236	4140	54916585	54915635	0.000000e+00	950.0
14	TraesCS4A01G204700	chr1B	89.886	2185	177	24	975	3144	90418185	90420340	0.000000e+00	2771.0
15	TraesCS4A01G204700	chr1B	91.075	1591	106	20	4224	5803	90421682	90423247	0.000000e+00	2119.0
16	TraesCS4A01G204700	chr1B	86.659	832	82	19	6233	7050	90423886	90424702	0.000000e+00	894.0
17	TraesCS4A01G204700	chr1B	91.320	553	34	5	3592	4141	90420967	90421508	0.000000e+00	743.0
18	TraesCS4A01G204700	chr1B	78.967	794	131	23	3	767	558287997	558288783	7.080000e-140	508.0
19	TraesCS4A01G204700	chr1B	92.857	70	5	0	3137	3206	428722561	428722492	1.400000e-17	102.0
20	TraesCS4A01G204700	chr1A	89.628	2179	189	20	975	3144	53910404	53908254	0.000000e+00	2737.0
21	TraesCS4A01G204700	chr1A	89.718	1595	116	24	4224	5803	53907177	53905616	0.000000e+00	1993.0
22	TraesCS4A01G204700	chr1A	88.838	869	77	10	6138	6992	53905036	53904174	0.000000e+00	1050.0
23	TraesCS4A01G204700	chr1A	91.455	550	33	5	3595	4141	53907887	53907349	0.000000e+00	743.0
24	TraesCS4A01G204700	chr1A	100.000	37	0	0	7876	7912	66446892	66446856	1.420000e-07	69.4
25	TraesCS4A01G204700	chr6D	85.039	508	63	8	1	501	43553865	43554366	9.160000e-139	505.0
26	TraesCS4A01G204700	chr6D	77.250	800	121	30	2	773	419441792	419441026	5.710000e-111	412.0
27	TraesCS4A01G204700	chr6D	90.741	54	5	0	3154	3207	365847308	365847361	1.100000e-08	73.1
28	TraesCS4A01G204700	chr6D	100.000	37	0	0	7876	7912	367386766	367386802	1.420000e-07	69.4
29	TraesCS4A01G204700	chr6D	100.000	37	0	0	7876	7912	435935523	435935487	1.420000e-07	69.4
30	TraesCS4A01G204700	chr2D	76.463	803	151	29	4	773	194048755	194049552	1.240000e-107	401.0
31	TraesCS4A01G204700	chr3B	86.364	374	33	12	6379	6750	7294731	7294374	7.440000e-105	392.0
32	TraesCS4A01G204700	chr3B	82.432	74	13	0	3134	3207	434051744	434051817	1.840000e-06	65.8
33	TraesCS4A01G204700	chr7D	78.221	652	106	19	1	631	83409031	83408395	1.250000e-102	385.0
34	TraesCS4A01G204700	chr5D	75.467	803	139	37	1	757	76212301	76213091	9.830000e-89	339.0
35	TraesCS4A01G204700	chr2A	78.042	378	68	8	1	365	208563793	208563418	2.870000e-54	224.0
36	TraesCS4A01G204700	chr2A	100.000	39	0	0	7874	7912	30698372	30698334	1.100000e-08	73.1
37	TraesCS4A01G204700	chr2A	100.000	39	0	0	7874	7912	499296136	499296174	1.100000e-08	73.1
38	TraesCS4A01G204700	chr2A	97.561	41	0	1	7872	7912	613342803	613342842	1.420000e-07	69.4
39	TraesCS4A01G204700	chr7A	75.714	210	36	12	571	773	662417584	662417383	3.040000e-14	91.6
40	TraesCS4A01G204700	chr7B	93.220	59	4	0	3149	3207	611724061	611724003	3.930000e-13	87.9
41	TraesCS4A01G204700	chr3D	87.324	71	9	0	3137	3207	73896454	73896384	1.830000e-11	82.4
42	TraesCS4A01G204700	chr3D	92.593	54	4	0	3154	3207	604669426	604669479	2.370000e-10	78.7
43	TraesCS4A01G204700	chr6A	92.593	54	4	0	3154	3207	506643253	506643306	2.370000e-10	78.7
44	TraesCS4A01G204700	chr6A	100.000	39	0	0	7874	7912	45023138	45023176	1.100000e-08	73.1
45	TraesCS4A01G204700	chr6B	100.000	38	0	0	7875	7912	692586379	692586342	3.960000e-08	71.3
46	TraesCS4A01G204700	chr5A	93.617	47	2	1	7867	7912	332216893	332216847	1.420000e-07	69.4

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	TraesCS4A01G204700	chr4A	496996901	497004812	7911	False	14611.00	14611	100.00000	1	7912	1	chr4A.!!$F1	7911
1	TraesCS4A01G204700	chr4D	84268290	84276094	7804	False	6417.50	12011	93.59900	2	7877	2	chr4D.!!$F1	7875
2	TraesCS4A01G204700	chr4B	119258945	119264866	5921	False	2111.50	5278	94.00225	1	5811	4	chr4B.!!$F2	5810
3	TraesCS4A01G204700	chr4B	119270386	119272331	1945	False	1419.00	2632	90.87900	5887	7876	2	chr4B.!!$F3	1989
4	TraesCS4A01G204700	chr1D	54912657	54918727	6070	True	1731.75	2778	88.51525	975	7050	4	chr1D.!!$R1	6075
5	TraesCS4A01G204700	chr1B	90418185	90424702	6517	False	1631.75	2771	89.73500	975	7050	4	chr1B.!!$F2	6075
6	TraesCS4A01G204700	chr1B	558287997	558288783	786	False	508.00	508	78.96700	3	767	1	chr1B.!!$F1	764
7	TraesCS4A01G204700	chr1A	53904174	53910404	6230	True	1630.75	2737	89.90975	975	6992	4	chr1A.!!$R2	6017
8	TraesCS4A01G204700	chr6D	43553865	43554366	501	False	505.00	505	85.03900	1	501	1	chr6D.!!$F1	500
9	TraesCS4A01G204700	chr6D	419441026	419441792	766	True	412.00	412	77.25000	2	773	1	chr6D.!!$R1	771
10	TraesCS4A01G204700	chr2D	194048755	194049552	797	False	401.00	401	76.46300	4	773	1	chr2D.!!$F1	769
11	TraesCS4A01G204700	chr7D	83408395	83409031	636	True	385.00	385	78.22100	1	631	1	chr7D.!!$R1	630
12	TraesCS4A01G204700	chr5D	76212301	76213091	790	False	339.00	339	75.46700	1	757	1	chr5D.!!$F1	756

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	Hairpin	End Stability	Orientation
534	605	0.169672	CGAGGACGAGGACGCTTAAA	59.830	55.000	0.00	43.96	1.52	F
689	773	0.461339	TTCGCGCCACCTTAGGAATC	60.461	55.000	4.77	0.00	2.52	F
773	858	0.593008	GCCGACCCAAACGAACAAAC	60.593	55.000	0.00	0.00	2.93	F
2148	2308	1.411977	TCCACCAAAAGTTGCACCATG	59.588	47.619	0.00	0.00	3.66	F
2555	2715	1.691196	CCCTGCTTTGTTCCTTGTCA	58.309	50.000	0.00	0.00	3.58	F
4272	4856	3.105283	ACTTAAGAGACGTTATGCCCCT	58.895	45.455	10.09	0.00	4.79	F
5129	5808	2.232696	TCATGAATTCCAACCGACGAGA	59.767	45.455	2.27	0.00	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1760	1920	0.908198	AGAATCTGGTGCACTCCTCC	59.092	55.000	17.98	0.00	0.00	4.30	R
2255	2415	1.078709	CCACTGTAAGATGCACCGTG	58.921	55.000	0.00	0.00	37.43	4.94	R
3291	3462	6.189859	AGATTGCTCATTTTTCTACCCATGA	58.810	36.000	0.00	0.00	0.00	3.07	R
4454	5041	3.498397	AGTGAGCCATTTTACAGACAACG	59.502	43.478	0.00	0.00	0.00	4.10	R
5129	5808	8.129211	GTGCATGTTTTAGTCTAGTTTTCACTT	58.871	33.333	0.00	0.00	34.06	3.16	R
6603	7793	2.610433	CTGCAGACGAGCTTTATGTCA	58.390	47.619	8.42	1.93	35.09	3.58	R
7624	8844	0.179094	ACTTCACGTGCGAAAGACCA	60.179	50.000	19.05	0.00	0.00	4.02	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
51	53	1.042229	TCCTCCGTGAAAACGAGGAA	58.958	50.000	13.38	2.99	36.91	3.36
89	100	3.217743	GGAGGAGGAGGCGTACCG	61.218	72.222	0.00	0.00	42.76	4.02
294	331	2.435805	GGAGATGTACCTGGAGCAATGA	59.564	50.000	0.00	0.00	0.00	2.57
305	342	4.183686	GCAATGACGGCAGCGCAT	62.184	61.111	11.47	0.00	0.00	4.73
349	395	4.121669	GGCGACTCGAGCAGCTGA	62.122	66.667	25.23	0.00	36.08	4.26
376	446	2.837291	CTGAGGCGGAGGAGGAGG	60.837	72.222	0.00	0.00	0.00	4.30
377	447	3.347590	TGAGGCGGAGGAGGAGGA	61.348	66.667	0.00	0.00	0.00	3.71
378	448	2.520741	GAGGCGGAGGAGGAGGAG	60.521	72.222	0.00	0.00	0.00	3.69
379	449	4.150454	AGGCGGAGGAGGAGGAGG	62.150	72.222	0.00	0.00	0.00	4.30
380	450	4.144727	GGCGGAGGAGGAGGAGGA	62.145	72.222	0.00	0.00	0.00	3.71
381	451	2.042843	GCGGAGGAGGAGGAGGAA	60.043	66.667	0.00	0.00	0.00	3.36
497	568	4.814294	GCGCCAACCCTCGTCGAT	62.814	66.667	0.00	0.00	0.00	3.59
533	604	0.957395	ACGAGGACGAGGACGCTTAA	60.957	55.000	0.00	0.00	43.96	1.85
534	605	0.169672	CGAGGACGAGGACGCTTAAA	59.830	55.000	0.00	0.00	43.96	1.52
558	633	1.597199	GCGCGCCTCCTAATTTTTAGC	60.597	52.381	23.24	0.00	0.00	3.09
606	685	0.802607	GTGGACTCGTGGATTCTCGC	60.803	60.000	0.00	0.00	0.00	5.03
689	773	0.461339	TTCGCGCCACCTTAGGAATC	60.461	55.000	4.77	0.00	0.00	2.52
690	774	1.153449	CGCGCCACCTTAGGAATCA	60.153	57.895	4.77	0.00	0.00	2.57
773	858	0.593008	GCCGACCCAAACGAACAAAC	60.593	55.000	0.00	0.00	0.00	2.93
901	990	4.207165	CACAACAGGGGAGGGTAAATATG	58.793	47.826	0.00	0.00	0.00	1.78
902	991	3.204382	ACAACAGGGGAGGGTAAATATGG	59.796	47.826	0.00	0.00	0.00	2.74
903	992	3.448277	ACAGGGGAGGGTAAATATGGA	57.552	47.619	0.00	0.00	0.00	3.41
904	993	3.053826	ACAGGGGAGGGTAAATATGGAC	58.946	50.000	0.00	0.00	0.00	4.02
906	995	3.722101	CAGGGGAGGGTAAATATGGACTT	59.278	47.826	0.00	0.00	0.00	3.01
937	1075	6.938030	AGGTACTAATATGGACTTCTCTCGAG	59.062	42.308	5.93	5.93	36.02	4.04
1415	1572	6.127925	TGCTATTGAAATTTCGATTGTGAGCT	60.128	34.615	26.61	9.50	33.27	4.09
1468	1626	2.225467	GCCCCTTGATGTTCTATCTGC	58.775	52.381	0.00	0.00	0.00	4.26
1537	1695	5.450965	GCCACAAAGCATCATATTTACAGCT	60.451	40.000	0.00	0.00	0.00	4.24
1655	1815	8.549338	AAAACTTTAGCTTACCAGTGTCTATC	57.451	34.615	0.00	0.00	0.00	2.08
1760	1920	7.572523	TGAATTCCCACTTGATAGCTTATTG	57.427	36.000	2.27	0.00	0.00	1.90
1901	2061	9.543783	GTTATCTTTCTTCCCTTCGTGTATAAT	57.456	33.333	0.00	0.00	0.00	1.28
2107	2267	6.041979	AGTTTTTGAGGGTGATAAAATGCAGT	59.958	34.615	0.00	0.00	0.00	4.40
2148	2308	1.411977	TCCACCAAAAGTTGCACCATG	59.588	47.619	0.00	0.00	0.00	3.66
2255	2415	3.893200	TCCATGCAGAAATGAATCCCATC	59.107	43.478	0.00	0.00	33.53	3.51
2555	2715	1.691196	CCCTGCTTTGTTCCTTGTCA	58.309	50.000	0.00	0.00	0.00	3.58
3207	3377	7.278461	ACGTATTTCAGTGCTAGATACATCT	57.722	36.000	0.00	0.00	40.86	2.90
3286	3457	5.888982	TCTTAACATTATCTCCCTCACCC	57.111	43.478	0.00	0.00	0.00	4.61
3287	3458	5.538877	TCTTAACATTATCTCCCTCACCCT	58.461	41.667	0.00	0.00	0.00	4.34
3288	3459	5.366768	TCTTAACATTATCTCCCTCACCCTG	59.633	44.000	0.00	0.00	0.00	4.45
3289	3460	3.136641	ACATTATCTCCCTCACCCTGT	57.863	47.619	0.00	0.00	0.00	4.00
3290	3461	4.280789	ACATTATCTCCCTCACCCTGTA	57.719	45.455	0.00	0.00	0.00	2.74
3291	3462	4.832492	ACATTATCTCCCTCACCCTGTAT	58.168	43.478	0.00	0.00	0.00	2.29
3292	3463	4.841246	ACATTATCTCCCTCACCCTGTATC	59.159	45.833	0.00	0.00	0.00	2.24
3293	3464	4.552883	TTATCTCCCTCACCCTGTATCA	57.447	45.455	0.00	0.00	0.00	2.15
3294	3465	3.645053	ATCTCCCTCACCCTGTATCAT	57.355	47.619	0.00	0.00	0.00	2.45
3384	3558	8.160765	TCTCAAATGTTTATCCCTTAGTGTTCA	58.839	33.333	0.00	0.00	0.00	3.18
4235	4818	7.223387	GGGTGAAATGACAATTATCTTGCATTC	59.777	37.037	0.00	0.00	31.17	2.67
4272	4856	3.105283	ACTTAAGAGACGTTATGCCCCT	58.895	45.455	10.09	0.00	0.00	4.79
4407	4994	7.367285	TGACAAGCCTAATGTTGAAATAACAC	58.633	34.615	0.00	0.00	32.37	3.32
4425	5012	4.015872	ACACGGTTGTCCAGTTGATAAT	57.984	40.909	0.00	0.00	0.00	1.28
4850	5437	6.431234	TGATATCATAGAAAGTAGCGAGCTGA	59.569	38.462	7.99	0.00	0.00	4.26
5129	5808	2.232696	TCATGAATTCCAACCGACGAGA	59.767	45.455	2.27	0.00	0.00	4.04
5157	5837	7.587757	GTGAAAACTAGACTAAAACATGCACAG	59.412	37.037	0.00	0.00	0.00	3.66
5315	6003	7.440255	TGATCTGTAGAACATAGCACAATGATG	59.560	37.037	0.00	0.00	0.00	3.07
5903	6718	7.700322	TGCAAATTAGATTAGATCTGACGTC	57.300	36.000	9.11	9.11	40.51	4.34
6406	7595	4.853468	TCCTTGCTTGGGTTACATATGA	57.147	40.909	10.38	0.00	0.00	2.15
6431	7620	8.986477	AAATGCTTTCTGTATTATGTTGGTTC	57.014	30.769	0.00	0.00	30.81	3.62
6603	7793	1.913762	AGAAGGCTACACCGGTGCT	60.914	57.895	34.26	22.43	46.52	4.40
6720	7913	6.974932	TTTTCACTAGAAGCTTGCTGATAG	57.025	37.500	2.10	10.79	34.71	2.08
6992	8193	4.457603	CCTCATCTTCTCCATACTACCTCG	59.542	50.000	0.00	0.00	0.00	4.63
7106	8314	3.187942	AGTGCCAGCTATGATATGGGAT	58.812	45.455	0.00	0.00	36.77	3.85
7225	8440	1.672881	GCTCCGAAGAATCCATGTTGG	59.327	52.381	0.00	0.00	39.43	3.77
7367	8584	6.570957	GCATGTCATGAGTTTCATCCTTTTCA	60.571	38.462	17.24	0.00	34.28	2.69
7373	8590	6.764308	TGAGTTTCATCCTTTTCATGGATC	57.236	37.500	0.00	0.00	41.94	3.36
7570	8787	7.596248	CACATTTAGACCTGTTCCAAATGAAAG	59.404	37.037	11.67	0.67	38.34	2.62
7606	8826	4.478203	TGTTCCAAATGAAACTGATCCCA	58.522	39.130	0.00	0.00	33.94	4.37
7620	8840	2.244510	TGATCCCACCAGTAATGGCATT	59.755	45.455	18.01	18.01	35.74	3.56
7624	8844	2.621407	CCCACCAGTAATGGCATTGAGT	60.621	50.000	22.57	10.99	35.74	3.41
7631	8851	4.460382	CAGTAATGGCATTGAGTGGTCTTT	59.540	41.667	22.57	0.00	0.00	2.52
7683	8904	2.648613	ATCCCTGCTCGAGATCCCGT	62.649	60.000	18.75	0.00	0.00	5.28
7702	8931	0.539518	TGATCGCGGGATGAAAAGGA	59.460	50.000	20.80	0.00	31.51	3.36
7796	9031	8.441312	TCTATTTTAAAGGACAAGAAACACGT	57.559	30.769	0.00	0.00	0.00	4.49
7837	9072	6.569179	TGCACCTCCTTTTCAAATTACTAC	57.431	37.500	0.00	0.00	0.00	2.73
7842	9077	6.433093	ACCTCCTTTTCAAATTACTACGCATT	59.567	34.615	0.00	0.00	0.00	3.56
7843	9078	7.039993	ACCTCCTTTTCAAATTACTACGCATTT	60.040	33.333	0.00	0.00	0.00	2.32
7877	9112	5.524511	TTTACGCATCACACATGAACTAC	57.475	39.130	0.00	0.00	38.69	2.73
7878	9113	3.319137	ACGCATCACACATGAACTACT	57.681	42.857	0.00	0.00	38.69	2.57
7879	9114	3.254060	ACGCATCACACATGAACTACTC	58.746	45.455	0.00	0.00	38.69	2.59
7880	9115	2.604914	CGCATCACACATGAACTACTCC	59.395	50.000	0.00	0.00	38.69	3.85
7881	9116	2.939103	GCATCACACATGAACTACTCCC	59.061	50.000	0.00	0.00	38.69	4.30
7882	9117	3.369892	GCATCACACATGAACTACTCCCT	60.370	47.826	0.00	0.00	38.69	4.20
7883	9118	4.437239	CATCACACATGAACTACTCCCTC	58.563	47.826	0.00	0.00	38.69	4.30
7884	9119	2.832129	TCACACATGAACTACTCCCTCC	59.168	50.000	0.00	0.00	0.00	4.30
7885	9120	2.567169	CACACATGAACTACTCCCTCCA	59.433	50.000	0.00	0.00	0.00	3.86
7886	9121	3.198635	CACACATGAACTACTCCCTCCAT	59.801	47.826	0.00	0.00	0.00	3.41
7887	9122	3.846588	ACACATGAACTACTCCCTCCATT	59.153	43.478	0.00	0.00	0.00	3.16
7888	9123	4.289672	ACACATGAACTACTCCCTCCATTT	59.710	41.667	0.00	0.00	0.00	2.32
7889	9124	4.878397	CACATGAACTACTCCCTCCATTTC	59.122	45.833	0.00	0.00	0.00	2.17
7890	9125	4.536090	ACATGAACTACTCCCTCCATTTCA	59.464	41.667	0.00	0.00	0.00	2.69
7891	9126	4.553330	TGAACTACTCCCTCCATTTCAC	57.447	45.455	0.00	0.00	0.00	3.18
7892	9127	3.907474	TGAACTACTCCCTCCATTTCACA	59.093	43.478	0.00	0.00	0.00	3.58
7893	9128	4.349636	TGAACTACTCCCTCCATTTCACAA	59.650	41.667	0.00	0.00	0.00	3.33
7894	9129	5.014123	TGAACTACTCCCTCCATTTCACAAT	59.986	40.000	0.00	0.00	0.00	2.71
7895	9130	4.848357	ACTACTCCCTCCATTTCACAATG	58.152	43.478	0.00	0.00	39.79	2.82
7896	9131	3.814504	ACTCCCTCCATTTCACAATGT	57.185	42.857	0.00	0.00	38.58	2.71
7897	9132	4.927267	ACTCCCTCCATTTCACAATGTA	57.073	40.909	0.00	0.00	38.58	2.29
7898	9133	4.848357	ACTCCCTCCATTTCACAATGTAG	58.152	43.478	0.00	0.00	38.58	2.74
7899	9134	4.289672	ACTCCCTCCATTTCACAATGTAGT	59.710	41.667	0.00	0.00	38.58	2.73
7900	9135	4.588899	TCCCTCCATTTCACAATGTAGTG	58.411	43.478	0.00	0.00	38.58	2.74
7901	9136	3.129287	CCCTCCATTTCACAATGTAGTGC	59.871	47.826	0.00	0.00	38.58	4.40
7902	9137	4.012374	CCTCCATTTCACAATGTAGTGCT	58.988	43.478	0.00	0.00	38.58	4.40
7903	9138	4.460382	CCTCCATTTCACAATGTAGTGCTT	59.540	41.667	0.00	0.00	38.58	3.91
7904	9139	5.392380	CCTCCATTTCACAATGTAGTGCTTC	60.392	44.000	0.00	0.00	38.58	3.86
7905	9140	4.458989	TCCATTTCACAATGTAGTGCTTCC	59.541	41.667	0.00	0.00	38.58	3.46
7906	9141	4.460382	CCATTTCACAATGTAGTGCTTCCT	59.540	41.667	0.00	0.00	38.58	3.36
7907	9142	5.392380	CCATTTCACAATGTAGTGCTTCCTC	60.392	44.000	0.00	0.00	38.58	3.71
7908	9143	4.623932	TTCACAATGTAGTGCTTCCTCT	57.376	40.909	0.00	0.00	39.35	3.69
7909	9144	5.738619	TTCACAATGTAGTGCTTCCTCTA	57.261	39.130	0.00	0.00	39.35	2.43
7910	9145	5.939764	TCACAATGTAGTGCTTCCTCTAT	57.060	39.130	0.00	0.00	39.35	1.98
7911	9146	5.907207	TCACAATGTAGTGCTTCCTCTATC	58.093	41.667	0.00	0.00	39.35	2.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
97	108	4.776322	CGCCATGGCCTCCGACAA	62.776	66.667	30.79	0.00	37.98	3.18
270	307	0.671251	GCTCCAGGTACATCTCCTCG	59.329	60.000	0.00	0.00	32.37	4.63
332	378	3.633094	TTCAGCTGCTCGAGTCGCC	62.633	63.158	15.13	1.67	0.00	5.54
357	403	4.382541	TCCTCCTCCGCCTCAGCA	62.383	66.667	0.00	0.00	39.83	4.41
360	430	3.347590	TCCTCCTCCTCCGCCTCA	61.348	66.667	0.00	0.00	0.00	3.86
376	446	2.280592	ACGGGCACAACGTTCCTC	60.281	61.111	0.00	0.00	42.70	3.71
377	447	2.590575	CACGGGCACAACGTTCCT	60.591	61.111	0.00	0.00	43.58	3.36
378	448	3.656045	CCACGGGCACAACGTTCC	61.656	66.667	0.00	0.00	43.58	3.62
379	449	2.898343	ACCACGGGCACAACGTTC	60.898	61.111	0.00	0.00	43.58	3.95
380	450	3.206246	CACCACGGGCACAACGTT	61.206	61.111	0.00	0.00	43.58	3.99
485	556	1.654954	CGGTGAGATCGACGAGGGTT	61.655	60.000	3.01	0.00	0.00	4.11
488	559	2.716244	CCGGTGAGATCGACGAGG	59.284	66.667	3.01	0.00	0.00	4.63
533	604	0.676782	AATTAGGAGGCGCGCTGTTT	60.677	50.000	32.29	16.68	0.00	2.83
534	605	0.676782	AAATTAGGAGGCGCGCTGTT	60.677	50.000	32.29	17.07	0.00	3.16
606	685	1.254284	TTAATGCCGGCCACAAAGGG	61.254	55.000	26.77	0.00	38.09	3.95
689	773	2.738521	CCAACGCTGACCCGACTG	60.739	66.667	0.00	0.00	0.00	3.51
690	774	2.915659	TCCAACGCTGACCCGACT	60.916	61.111	0.00	0.00	0.00	4.18
901	990	6.553852	TCCATATTAGTACCTCCTTCAAGTCC	59.446	42.308	0.00	0.00	0.00	3.85
902	991	7.288158	AGTCCATATTAGTACCTCCTTCAAGTC	59.712	40.741	0.00	0.00	0.00	3.01
903	992	7.133483	AGTCCATATTAGTACCTCCTTCAAGT	58.867	38.462	0.00	0.00	0.00	3.16
904	993	7.604657	AGTCCATATTAGTACCTCCTTCAAG	57.395	40.000	0.00	0.00	0.00	3.02
906	995	7.363031	AGAAGTCCATATTAGTACCTCCTTCA	58.637	38.462	0.00	0.00	0.00	3.02
1415	1572	4.955811	ACATCTACACAGTCAAAGGTCA	57.044	40.909	0.00	0.00	0.00	4.02
1468	1626	7.808381	GGATCAATCAGCACATATTCAATTGAG	59.192	37.037	8.41	0.00	35.74	3.02
1537	1695	7.093354	TGTGTTAATCTTGTTTTCAGCAACAA	58.907	30.769	0.78	0.78	43.00	2.83
1655	1815	4.560035	CAGCTGACTTGAACAAAACAACAG	59.440	41.667	8.42	0.00	0.00	3.16
1760	1920	0.908198	AGAATCTGGTGCACTCCTCC	59.092	55.000	17.98	0.00	0.00	4.30
1901	2061	6.867799	TTTATAGTTTCGTATTCGCGACAA	57.132	33.333	9.15	0.00	40.85	3.18
2107	2267	7.055378	GTGGAACTAGACTAAGGTAGAGATCA	58.945	42.308	0.00	0.00	0.00	2.92
2148	2308	4.749099	CAGACTCTGACTTATTATGGCTGC	59.251	45.833	0.00	0.00	32.44	5.25
2255	2415	1.078709	CCACTGTAAGATGCACCGTG	58.921	55.000	0.00	0.00	37.43	4.94
3286	3457	6.543465	TGCTCATTTTTCTACCCATGATACAG	59.457	38.462	0.00	0.00	0.00	2.74
3287	3458	6.422333	TGCTCATTTTTCTACCCATGATACA	58.578	36.000	0.00	0.00	0.00	2.29
3288	3459	6.942532	TGCTCATTTTTCTACCCATGATAC	57.057	37.500	0.00	0.00	0.00	2.24
3289	3460	8.000709	AGATTGCTCATTTTTCTACCCATGATA	58.999	33.333	0.00	0.00	0.00	2.15
3290	3461	6.837568	AGATTGCTCATTTTTCTACCCATGAT	59.162	34.615	0.00	0.00	0.00	2.45
3291	3462	6.189859	AGATTGCTCATTTTTCTACCCATGA	58.810	36.000	0.00	0.00	0.00	3.07
3292	3463	6.461110	AGATTGCTCATTTTTCTACCCATG	57.539	37.500	0.00	0.00	0.00	3.66
3293	3464	7.486407	AAAGATTGCTCATTTTTCTACCCAT	57.514	32.000	0.00	0.00	0.00	4.00
3294	3465	6.916360	AAAGATTGCTCATTTTTCTACCCA	57.084	33.333	0.00	0.00	0.00	4.51
3363	3537	9.927668	CATTTTGAACACTAAGGGATAAACATT	57.072	29.630	0.00	0.00	0.00	2.71
4235	4818	9.344309	GTCTCTTAAGTAGCACAAAGTACTTAG	57.656	37.037	8.92	3.51	40.88	2.18
4272	4856	9.850628	GAAGTGACACAAGTAACAGTATATACA	57.149	33.333	15.18	0.00	30.87	2.29
4407	4994	5.371115	ACAAATTATCAACTGGACAACCG	57.629	39.130	0.00	0.00	39.42	4.44
4437	5024	8.873830	ACAGACAACGAATTAATCAACTATGAG	58.126	33.333	0.00	0.00	39.39	2.90
4454	5041	3.498397	AGTGAGCCATTTTACAGACAACG	59.502	43.478	0.00	0.00	0.00	4.10
5129	5808	8.129211	GTGCATGTTTTAGTCTAGTTTTCACTT	58.871	33.333	0.00	0.00	34.06	3.16
5157	5837	7.856145	AACAGAACTTCATATCATCCTGAAC	57.144	36.000	0.00	0.00	0.00	3.18
5315	6003	4.713792	ACAGGAAATGATGGGAGGTATC	57.286	45.455	0.00	0.00	0.00	2.24
5397	6087	6.095440	GGATGGCTTCAATTAACTGCTTCTTA	59.905	38.462	2.60	0.00	0.00	2.10
5903	6718	7.646130	CCAGTAGAAGCTAAAGAAATCGTAGAG	59.354	40.741	0.00	0.00	43.63	2.43
5920	6735	4.641396	TGTGTGGAATCAACCAGTAGAAG	58.359	43.478	0.00	0.00	40.85	2.85
6406	7595	8.584157	TGAACCAACATAATACAGAAAGCATTT	58.416	29.630	0.00	0.00	43.98	2.32
6431	7620	9.874215	CTAGTGCATACATCATTCATTTAGTTG	57.126	33.333	0.00	0.00	0.00	3.16
6603	7793	2.610433	CTGCAGACGAGCTTTATGTCA	58.390	47.619	8.42	1.93	35.09	3.58
6720	7913	4.016444	TCCTGGTGGAAATGCAAATAGTC	58.984	43.478	0.00	0.00	39.87	2.59
6992	8193	6.888430	ACAACACGTTAGAATTCAATGACTC	58.112	36.000	8.44	0.00	0.00	3.36
7106	8314	1.745115	CGCCCATTTCTCTTGCCGA	60.745	57.895	0.00	0.00	0.00	5.54
7173	8386	5.014858	AGAATCATTGTGAACATCAGGCTT	58.985	37.500	0.00	0.00	0.00	4.35
7225	8440	3.676291	TTTCCTATTGTTTGGCAAGGC	57.324	42.857	0.00	0.00	40.86	4.35
7239	8454	4.949856	GTCAGCATGGATTCCTTTTTCCTA	59.050	41.667	3.95	0.00	36.16	2.94
7312	8529	5.842907	AGCTTTCACCAGAACCAAAAATAC	58.157	37.500	0.00	0.00	32.39	1.89
7373	8590	7.701539	ATTAGTACTGCTAGATCAGATGGAG	57.298	40.000	5.39	0.00	37.51	3.86
7388	8605	8.251721	AGAGCTACCACTACAAAATTAGTACTG	58.748	37.037	5.39	0.00	30.76	2.74
7459	8676	1.351012	CACGGGTACTCGACTAGCG	59.649	63.158	24.57	0.00	42.69	4.26
7602	8822	1.638070	TCAATGCCATTACTGGTGGGA	59.362	47.619	0.55	0.00	45.10	4.37
7606	8826	2.041620	ACCACTCAATGCCATTACTGGT	59.958	45.455	0.55	6.91	45.10	4.00
7620	8840	0.874175	CACGTGCGAAAGACCACTCA	60.874	55.000	0.82	0.00	0.00	3.41
7624	8844	0.179094	ACTTCACGTGCGAAAGACCA	60.179	50.000	19.05	0.00	0.00	4.02
7631	8851	1.353804	GCCAAAACTTCACGTGCGA	59.646	52.632	11.67	0.50	0.00	5.10
7683	8904	0.539518	TCCTTTTCATCCCGCGATCA	59.460	50.000	8.23	0.00	0.00	2.92
7702	8931	6.189859	TGAACCAAAATGCAGAGGATTCTAT	58.810	36.000	0.00	0.00	30.73	1.98
7785	9020	8.802856	TGAATTGTAAAATTCACGTGTTTCTTG	58.197	29.630	15.76	0.00	42.39	3.02
7796	9031	6.815089	AGGTGCAAGTGAATTGTAAAATTCA	58.185	32.000	15.76	15.76	44.32	2.57
7814	9049	5.180492	CGTAGTAATTTGAAAAGGAGGTGCA	59.820	40.000	0.00	0.00	0.00	4.57
7837	9072	7.123190	TGCGTAAATCAATAACTCTAAATGCG	58.877	34.615	0.00	0.00	0.00	4.73
7842	9077	8.600625	GTGTGATGCGTAAATCAATAACTCTAA	58.399	33.333	0.12	0.00	38.28	2.10
7843	9078	7.762159	TGTGTGATGCGTAAATCAATAACTCTA	59.238	33.333	0.12	0.00	38.28	2.43
7877	9112	4.637534	CACTACATTGTGAAATGGAGGGAG	59.362	45.833	13.76	2.00	45.41	4.30
7878	9113	4.588899	CACTACATTGTGAAATGGAGGGA	58.411	43.478	13.76	0.00	45.41	4.20
7879	9114	3.129287	GCACTACATTGTGAAATGGAGGG	59.871	47.826	13.76	11.18	45.36	4.30
7880	9115	4.012374	AGCACTACATTGTGAAATGGAGG	58.988	43.478	13.76	5.57	43.78	4.30
7881	9116	5.392380	GGAAGCACTACATTGTGAAATGGAG	60.392	44.000	8.77	8.77	44.77	3.86
7882	9117	4.458989	GGAAGCACTACATTGTGAAATGGA	59.541	41.667	0.00	0.00	40.12	3.41
7883	9118	4.460382	AGGAAGCACTACATTGTGAAATGG	59.540	41.667	0.00	0.00	40.12	3.16
7884	9119	5.413833	AGAGGAAGCACTACATTGTGAAATG	59.586	40.000	0.00	0.00	40.12	2.32
7885	9120	5.564550	AGAGGAAGCACTACATTGTGAAAT	58.435	37.500	0.00	0.00	40.12	2.17
7886	9121	4.973168	AGAGGAAGCACTACATTGTGAAA	58.027	39.130	0.00	0.00	40.12	2.69
7887	9122	4.623932	AGAGGAAGCACTACATTGTGAA	57.376	40.909	0.00	0.00	40.12	3.18
7888	9123	5.907207	GATAGAGGAAGCACTACATTGTGA	58.093	41.667	0.00	0.00	40.12	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.