AutoCloner

Multiple sequence alignment - TraesCS7D01G379700

Loading Multiple Alignment...

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	TraesCS7D01G379700	chr7D	100.000	3238	0	0	1	3238	491874971	491871734	0.000000e+00	5980.0
1	TraesCS7D01G379700	chr7D	91.649	1401	85	24	1599	2976	493203681	493205072	0.000000e+00	1910.0
2	TraesCS7D01G379700	chr7D	89.021	1430	109	32	1595	3001	493560538	493561942	0.000000e+00	1727.0
3	TraesCS7D01G379700	chr7D	97.780	946	18	2	1	945	426446484	426447427	0.000000e+00	1628.0
4	TraesCS7D01G379700	chr7D	85.630	508	43	12	970	1450	493203148	493203652	1.270000e-139	507.0
5	TraesCS7D01G379700	chr7D	100.000	268	0	0	3689	3956	491871283	491871016	2.750000e-136	496.0
6	TraesCS7D01G379700	chr7D	88.850	287	26	4	1127	1409	493559960	493560244	8.140000e-92	348.0
7	TraesCS7D01G379700	chr7D	91.473	129	9	1	164	290	532013943	532014071	4.060000e-40	176.0
8	TraesCS7D01G379700	chr7D	96.154	52	2	0	894	945	619199705	619199756	7.040000e-13	86.1
9	TraesCS7D01G379700	chr7D	82.474	97	10	5	3072	3166	575899037	575899128	1.180000e-10	78.7
10	TraesCS7D01G379700	chr7D	80.412	97	14	5	3072	3166	488555282	488555375	7.090000e-08	69.4
11	TraesCS7D01G379700	chr7D	95.122	41	0	2	3038	3078	2087301	2087263	3.300000e-06	63.9
12	TraesCS7D01G379700	chr7D	92.857	42	1	2	3038	3078	117242278	117242318	4.270000e-05	60.2
13	TraesCS7D01G379700	chr7B	93.026	2151	83	25	945	3056	521197891	521195769	0.000000e+00	3079.0
14	TraesCS7D01G379700	chr7B	94.574	1548	55	7	1552	3076	521150665	521149124	0.000000e+00	2366.0
15	TraesCS7D01G379700	chr7B	89.979	1427	79	28	1603	3001	522142075	522143465	0.000000e+00	1784.0
16	TraesCS7D01G379700	chr7B	91.700	494	27	6	976	1455	522141555	522142048	0.000000e+00	673.0
17	TraesCS7D01G379700	chr7B	93.862	391	19	3	945	1331	521151246	521150857	5.700000e-163	584.0
18	TraesCS7D01G379700	chr7B	86.667	240	32	0	3717	3956	521148868	521148629	2.340000e-67	267.0
19	TraesCS7D01G379700	chr7B	92.063	63	5	0	3162	3224	521149029	521148967	5.440000e-14	89.8
20	TraesCS7D01G379700	chr7A	94.901	1510	49	7	1552	3039	558109982	558108479	0.000000e+00	2337.0
21	TraesCS7D01G379700	chr7A	91.422	1399	86	25	1601	2976	559361783	559363170	0.000000e+00	1888.0
22	TraesCS7D01G379700	chr7A	92.265	905	56	5	1552	2448	559386812	559387710	0.000000e+00	1271.0
23	TraesCS7D01G379700	chr7A	91.837	392	23	5	945	1331	558110564	558110177	4.500000e-149	538.0
24	TraesCS7D01G379700	chr7A	88.339	283	29	4	2490	2770	559388039	559388319	1.760000e-88	337.0
25	TraesCS7D01G379700	chr7A	82.997	347	32	17	991	1331	559361345	559361670	5.000000e-74	289.0
26	TraesCS7D01G379700	chr7A	86.166	253	29	4	1127	1377	559385994	559386242	6.520000e-68	268.0
27	TraesCS7D01G379700	chr7A	90.667	75	3	2	1459	1529	558110054	558109980	3.250000e-16	97.1
28	TraesCS7D01G379700	chr4D	98.312	948	14	2	1	946	25399972	25400919	0.000000e+00	1661.0
29	TraesCS7D01G379700	chr4D	82.353	136	22	2	1184	1318	455693547	455693681	2.500000e-22	117.0
30	TraesCS7D01G379700	chr1D	97.725	967	18	4	1	964	474450453	474449488	0.000000e+00	1661.0
31	TraesCS7D01G379700	chr1D	91.473	129	9	1	164	290	99653122	99652994	4.060000e-40	176.0
32	TraesCS7D01G379700	chr1D	96.078	51	2	0	897	947	454522194	454522244	2.530000e-12	84.2
33	TraesCS7D01G379700	chr6D	95.238	672	17	5	290	946	429397018	429396347	0.000000e+00	1050.0
34	TraesCS7D01G379700	chr6D	90.909	44	0	2	3038	3078	389647674	389647716	5.520000e-04	56.5
35	TraesCS7D01G379700	chr6A	82.725	822	133	7	1624	2442	564975151	564975966	0.000000e+00	723.0
36	TraesCS7D01G379700	chr1B	85.320	688	58	19	290	940	526210892	526210211	0.000000e+00	671.0
37	TraesCS7D01G379700	chr1B	85.029	688	60	19	290	940	526226505	526225824	0.000000e+00	660.0
38	TraesCS7D01G379700	chr3A	95.862	290	12	0	1	290	743489215	743488926	1.660000e-128	470.0
39	TraesCS7D01G379700	chr3A	95.833	168	7	0	1	168	436464172	436464339	5.040000e-69	272.0
40	TraesCS7D01G379700	chr5D	96.786	280	9	0	1	280	385111580	385111301	5.990000e-128	468.0
41	TraesCS7D01G379700	chr5D	90.698	129	10	1	164	290	34067992	34067864	1.890000e-38	171.0
42	TraesCS7D01G379700	chr5D	83.529	85	8	5	3082	3166	384139375	384139453	1.520000e-09	75.0
43	TraesCS7D01G379700	chr5D	81.690	71	8	4	3096	3166	326204859	326204924	2.000000e-03	54.7
44	TraesCS7D01G379700	chr4B	95.172	290	14	0	1	290	80005493	80005782	3.600000e-125	459.0
45	TraesCS7D01G379700	chr4B	85.714	77	9	2	872	946	81324636	81324712	3.280000e-11	80.5
46	TraesCS7D01G379700	chr3B	97.024	168	5	0	1	168	425389465	425389298	2.330000e-72	283.0
47	TraesCS7D01G379700	chr3B	89.655	58	4	2	290	347	40198567	40198622	5.480000e-09	73.1
48	TraesCS7D01G379700	chr3B	92.857	42	2	1	3038	3078	673096120	673096161	4.270000e-05	60.2
49	TraesCS7D01G379700	chr3D	94.578	166	9	0	1	166	299600457	299600292	1.410000e-64	257.0
50	TraesCS7D01G379700	chr3D	88.028	142	10	3	290	425	22935563	22935703	1.140000e-35	161.0
51	TraesCS7D01G379700	chr5B	86.316	95	8	3	3072	3166	446356988	446357077	9.050000e-17	99.0
52	TraesCS7D01G379700	chr2B	82.292	96	13	3	3073	3166	122648820	122648913	3.280000e-11	80.5
53	TraesCS7D01G379700	chr2B	94.872	39	0	2	3038	3076	760152398	760152434	4.270000e-05	60.2
54	TraesCS7D01G379700	chr2B	92.683	41	2	1	3039	3078	4502756	4502796	1.540000e-04	58.4
55	TraesCS7D01G379700	chr2A	91.228	57	3	2	892	946	398350354	398350410	4.240000e-10	76.8
56	TraesCS7D01G379700	chr2A	91.228	57	3	2	892	946	398969247	398969191	4.240000e-10	76.8
57	TraesCS7D01G379700	chr2A	82.278	79	11	3	3080	3157	649483410	649483334	9.180000e-07	65.8
58	TraesCS7D01G379700	chr2D	81.818	88	13	3	3080	3166	600327274	600327359	1.970000e-08	71.3
59	TraesCS7D01G379700	chrUn	81.053	95	9	8	3072	3166	88060654	88060739	2.550000e-07	67.6
60	TraesCS7D01G379700	chrUn	94.872	39	1	1	3037	3075	65665403	65665440	4.270000e-05	60.2
61	TraesCS7D01G379700	chr4A	95.000	40	0	2	3038	3077	743388083	743388046	1.190000e-05	62.1

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	TraesCS7D01G379700	chr7D	491871016	491874971	3955	True	3238.000000	5980	100.000000	1	3956	2	chr7D.!!$R2	3955
1	TraesCS7D01G379700	chr7D	426446484	426447427	943	False	1628.000000	1628	97.780000	1	945	1	chr7D.!!$F2	944
2	TraesCS7D01G379700	chr7D	493203148	493205072	1924	False	1208.500000	1910	88.639500	970	2976	2	chr7D.!!$F7	2006
3	TraesCS7D01G379700	chr7D	493559960	493561942	1982	False	1037.500000	1727	88.935500	1127	3001	2	chr7D.!!$F8	1874
4	TraesCS7D01G379700	chr7B	521195769	521197891	2122	True	3079.000000	3079	93.026000	945	3056	1	chr7B.!!$R1	2111
5	TraesCS7D01G379700	chr7B	522141555	522143465	1910	False	1228.500000	1784	90.839500	976	3001	2	chr7B.!!$F1	2025
6	TraesCS7D01G379700	chr7B	521148629	521151246	2617	True	826.700000	2366	91.791500	945	3956	4	chr7B.!!$R2	3011
7	TraesCS7D01G379700	chr7A	559361345	559363170	1825	False	1088.500000	1888	87.209500	991	2976	2	chr7A.!!$F1	1985
8	TraesCS7D01G379700	chr7A	558108479	558110564	2085	True	990.700000	2337	92.468333	945	3039	3	chr7A.!!$R1	2094
9	TraesCS7D01G379700	chr7A	559385994	559388319	2325	False	625.333333	1271	88.923333	1127	2770	3	chr7A.!!$F2	1643
10	TraesCS7D01G379700	chr4D	25399972	25400919	947	False	1661.000000	1661	98.312000	1	946	1	chr4D.!!$F1	945
11	TraesCS7D01G379700	chr1D	474449488	474450453	965	True	1661.000000	1661	97.725000	1	964	1	chr1D.!!$R2	963
12	TraesCS7D01G379700	chr6D	429396347	429397018	671	True	1050.000000	1050	95.238000	290	946	1	chr6D.!!$R1	656
13	TraesCS7D01G379700	chr6A	564975151	564975966	815	False	723.000000	723	82.725000	1624	2442	1	chr6A.!!$F1	818
14	TraesCS7D01G379700	chr1B	526210211	526210892	681	True	671.000000	671	85.320000	290	940	1	chr1B.!!$R1	650
15	TraesCS7D01G379700	chr1B	526225824	526226505	681	True	660.000000	660	85.029000	290	940	1	chr1B.!!$R2	650

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
968	1009	1.898472	TCCAGAGAAGAAGAGTGCAGG	59.102	52.381	0.00	0.0	0.0	4.85	F
2058	2647	0.687920	TGGCCAAGGTGTACATCGAA	59.312	50.000	0.61	0.0	0.0	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2464	3053	0.262580	CATGAATCATGGGGTGGGGT	59.737	55.0	15.09	0.0	38.11	4.95	R
3218	4209	0.532573	ACATGGCGACGAGACTGAAT	59.467	50.0	0.00	0.0	0.00	2.57	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
119	120	3.325753	GCTGGCCCTGAGGACTGT	61.326	66.667	0.00	0.00	44.45	3.55
641	645	4.380444	GCCCATCATTTTCACACGTAATGT	60.380	41.667	7.63	0.00	44.81	2.71
968	1009	1.898472	TCCAGAGAAGAAGAGTGCAGG	59.102	52.381	0.00	0.00	0.00	4.85
989	1035	1.989165	GAACAGTGTGAGATCGACAGC	59.011	52.381	0.00	0.00	0.00	4.40
1016	1062	1.815421	CGATGGGGAAGAACGGCAG	60.815	63.158	0.00	0.00	0.00	4.85
1107	1159	1.884075	TACGCACGCTCATGGTTCCT	61.884	55.000	0.00	0.00	0.00	3.36
1161	1232	2.038426	CCGTGGGAGCATAATGGATGTA	59.962	50.000	0.00	0.00	37.90	2.29
1445	1566	4.754618	TGACAACATGCTAAGTTCGATTGT	59.245	37.500	0.00	0.00	0.00	2.71
1544	2120	1.164411	TGAAATTGTACCAGCTGCGG	58.836	50.000	8.66	0.00	0.00	5.69
1545	2121	1.165270	GAAATTGTACCAGCTGCGGT	58.835	50.000	8.66	17.55	43.46	5.68
1576	2152	5.990745	AAAAATGTGCAAATACGATCACG	57.009	34.783	0.00	0.00	45.75	4.35
1577	2153	4.937696	AAATGTGCAAATACGATCACGA	57.062	36.364	0.00	0.00	42.66	4.35
1578	2154	4.937696	AATGTGCAAATACGATCACGAA	57.062	36.364	0.00	0.00	42.66	3.85
1879	2468	3.066190	CCTACTCCGACGGCACCA	61.066	66.667	9.66	0.00	0.00	4.17
2058	2647	0.687920	TGGCCAAGGTGTACATCGAA	59.312	50.000	0.61	0.00	0.00	3.71
2581	3493	3.830994	GATGAGATCGCGGCGCTGA	62.831	63.158	30.54	26.62	0.00	4.26
2815	3738	0.615331	GAAGCCTCCACTGATCCACA	59.385	55.000	0.00	0.00	0.00	4.17
2822	3745	2.932614	CTCCACTGATCCACAATTCGAC	59.067	50.000	0.00	0.00	0.00	4.20
2826	3749	1.927174	CTGATCCACAATTCGACCGAC	59.073	52.381	0.00	0.00	0.00	4.79
3062	4011	5.409520	GTCAAGTGACATAACATGCAAGAGA	59.590	40.000	6.57	0.00	44.18	3.10
3069	4018	6.936335	TGACATAACATGCAAGAGAGAAGAAA	59.064	34.615	0.00	0.00	0.00	2.52
3071	4020	7.588512	ACATAACATGCAAGAGAGAAGAAAAC	58.411	34.615	0.00	0.00	0.00	2.43
3074	4023	5.825507	ACATGCAAGAGAGAAGAAAACAAC	58.174	37.500	0.00	0.00	0.00	3.32
3075	4024	5.591877	ACATGCAAGAGAGAAGAAAACAACT	59.408	36.000	0.00	0.00	0.00	3.16
3076	4025	5.490139	TGCAAGAGAGAAGAAAACAACTG	57.510	39.130	0.00	0.00	0.00	3.16
3078	4027	5.065218	TGCAAGAGAGAAGAAAACAACTGAC	59.935	40.000	0.00	0.00	0.00	3.51
3082	4031	8.830580	CAAGAGAGAAGAAAACAACTGACATAA	58.169	33.333	0.00	0.00	0.00	1.90
3083	4032	8.371770	AGAGAGAAGAAAACAACTGACATAAC	57.628	34.615	0.00	0.00	0.00	1.89
3085	4034	8.682936	AGAGAAGAAAACAACTGACATAACAT	57.317	30.769	0.00	0.00	0.00	2.71
3086	4035	8.562892	AGAGAAGAAAACAACTGACATAACATG	58.437	33.333	0.00	0.00	0.00	3.21
3087	4036	7.141363	AGAAGAAAACAACTGACATAACATGC	58.859	34.615	0.00	0.00	0.00	4.06
3088	4037	6.389830	AGAAAACAACTGACATAACATGCA	57.610	33.333	0.00	0.00	0.00	3.96
3089	4038	6.804677	AGAAAACAACTGACATAACATGCAA	58.195	32.000	0.00	0.00	0.00	4.08
3090	4039	6.919662	AGAAAACAACTGACATAACATGCAAG	59.080	34.615	0.00	0.00	0.00	4.01
3091	4040	6.389830	AAACAACTGACATAACATGCAAGA	57.610	33.333	0.00	0.00	0.00	3.02
3092	4041	5.618056	ACAACTGACATAACATGCAAGAG	57.382	39.130	0.00	0.00	0.00	2.85
3093	4042	5.308014	ACAACTGACATAACATGCAAGAGA	58.692	37.500	0.00	0.00	0.00	3.10
3094	4043	5.410746	ACAACTGACATAACATGCAAGAGAG	59.589	40.000	0.00	0.00	0.00	3.20
3095	4044	5.411831	ACTGACATAACATGCAAGAGAGA	57.588	39.130	0.00	0.00	0.00	3.10
3096	4045	5.798132	ACTGACATAACATGCAAGAGAGAA	58.202	37.500	0.00	0.00	0.00	2.87
3097	4046	5.873712	ACTGACATAACATGCAAGAGAGAAG	59.126	40.000	0.00	0.00	0.00	2.85
3098	4047	6.041423	TGACATAACATGCAAGAGAGAAGA	57.959	37.500	0.00	0.00	0.00	2.87
3099	4048	6.466812	TGACATAACATGCAAGAGAGAAGAA	58.533	36.000	0.00	0.00	0.00	2.52
3100	4049	6.936335	TGACATAACATGCAAGAGAGAAGAAA	59.064	34.615	0.00	0.00	0.00	2.52
3101	4050	7.445096	TGACATAACATGCAAGAGAGAAGAAAA	59.555	33.333	0.00	0.00	0.00	2.29
3102	4051	7.588512	ACATAACATGCAAGAGAGAAGAAAAC	58.411	34.615	0.00	0.00	0.00	2.43
3103	4052	7.229306	ACATAACATGCAAGAGAGAAGAAAACA	59.771	33.333	0.00	0.00	0.00	2.83
3104	4053	6.455360	AACATGCAAGAGAGAAGAAAACAA	57.545	33.333	0.00	0.00	0.00	2.83
3105	4054	6.645790	ACATGCAAGAGAGAAGAAAACAAT	57.354	33.333	0.00	0.00	0.00	2.71
3106	4055	7.047460	ACATGCAAGAGAGAAGAAAACAATT	57.953	32.000	0.00	0.00	0.00	2.32
3107	4056	6.921857	ACATGCAAGAGAGAAGAAAACAATTG	59.078	34.615	3.24	3.24	0.00	2.32
3108	4057	6.698008	TGCAAGAGAGAAGAAAACAATTGA	57.302	33.333	13.59	0.00	0.00	2.57
3109	4058	7.099266	TGCAAGAGAGAAGAAAACAATTGAA	57.901	32.000	13.59	0.00	0.00	2.69
3110	4059	7.546358	TGCAAGAGAGAAGAAAACAATTGAAA	58.454	30.769	13.59	0.00	0.00	2.69
3111	4060	7.703621	TGCAAGAGAGAAGAAAACAATTGAAAG	59.296	33.333	13.59	0.00	0.00	2.62
3112	4061	7.168804	GCAAGAGAGAAGAAAACAATTGAAAGG	59.831	37.037	13.59	0.00	0.00	3.11
3113	4062	8.408601	CAAGAGAGAAGAAAACAATTGAAAGGA	58.591	33.333	13.59	0.00	0.00	3.36
3114	4063	8.525290	AGAGAGAAGAAAACAATTGAAAGGAA	57.475	30.769	13.59	0.00	0.00	3.36
3115	4064	8.971073	AGAGAGAAGAAAACAATTGAAAGGAAA	58.029	29.630	13.59	0.00	0.00	3.13
3116	4065	9.586435	GAGAGAAGAAAACAATTGAAAGGAAAA	57.414	29.630	13.59	0.00	0.00	2.29
3117	4066	9.942850	AGAGAAGAAAACAATTGAAAGGAAAAA	57.057	25.926	13.59	0.00	0.00	1.94
3166	4115	3.146847	TCACGGATATAGCATCGACTGT	58.853	45.455	0.00	0.00	0.00	3.55
3168	4117	2.254459	CGGATATAGCATCGACTGTGC	58.746	52.381	1.15	1.15	42.81	4.57
3211	4202	7.017055	GCTCATGCATAAATTTGTTTTGGAAC	58.983	34.615	0.00	0.00	39.41	3.62
3229	4220	4.039245	TGGAACAAGAAGATTCAGTCTCGT	59.961	41.667	0.00	0.00	31.98	4.18
3230	4221	4.623595	GGAACAAGAAGATTCAGTCTCGTC	59.376	45.833	0.00	0.00	35.67	4.20
3231	4222	3.827625	ACAAGAAGATTCAGTCTCGTCG	58.172	45.455	0.00	0.00	35.67	5.12
3232	4223	2.553079	AGAAGATTCAGTCTCGTCGC	57.447	50.000	0.00	0.00	35.67	5.19
3233	4224	1.133407	AGAAGATTCAGTCTCGTCGCC	59.867	52.381	0.00	0.00	35.67	5.54
3235	4226	1.107114	AGATTCAGTCTCGTCGCCAT	58.893	50.000	0.00	0.00	28.45	4.40
3236	4227	1.202348	AGATTCAGTCTCGTCGCCATG	60.202	52.381	0.00	0.00	28.45	3.66
3237	4228	0.532573	ATTCAGTCTCGTCGCCATGT	59.467	50.000	0.00	0.00	0.00	3.21
3780	4771	3.262936	CGTGGAAGGCATCGCAAA	58.737	55.556	0.00	0.00	0.00	3.68
3784	4775	0.035534	TGGAAGGCATCGCAAAGCTA	60.036	50.000	0.00	0.00	0.00	3.32
3811	4802	2.898840	CATGGTGGCAGCGGCTAG	60.899	66.667	12.58	0.00	40.87	3.42
3812	4803	4.181010	ATGGTGGCAGCGGCTAGG	62.181	66.667	12.58	0.00	40.87	3.02
3822	4813	4.609018	CGGCTAGGGATGGGCACG	62.609	72.222	0.00	0.00	0.00	5.34
3836	4827	2.782222	GCACGACCCGGATCTAGCA	61.782	63.158	0.73	0.00	0.00	3.49
3867	4858	4.265056	GGGTGGCGTGAGTGGGTT	62.265	66.667	0.00	0.00	0.00	4.11
3871	4862	2.668550	GGCGTGAGTGGGTTGGTC	60.669	66.667	0.00	0.00	0.00	4.02
3879	4870	2.197324	TGGGTTGGTCTTGGTGGC	59.803	61.111	0.00	0.00	0.00	5.01
3884	4875	1.827789	TTGGTCTTGGTGGCTGTGC	60.828	57.895	0.00	0.00	0.00	4.57
3889	4880	0.764890	TCTTGGTGGCTGTGCTACTT	59.235	50.000	6.06	0.00	39.93	2.24
3899	4890	2.034066	TGCTACTTGGGCAGCACC	59.966	61.111	0.00	0.00	42.68	5.01
3908	4899	1.271127	TGGGCAGCACCATACTAGCA	61.271	55.000	0.00	0.00	42.05	3.49
3910	4901	1.162800	GGCAGCACCATACTAGCAGC	61.163	60.000	0.00	0.00	39.64	5.25
3911	4902	1.162800	GCAGCACCATACTAGCAGCC	61.163	60.000	0.00	0.00	35.14	4.85
3912	4903	0.178767	CAGCACCATACTAGCAGCCA	59.821	55.000	0.00	0.00	0.00	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
119	120	2.991190	CCAGAAGCGCGTAACTTTTCTA	59.009	45.455	8.43	0.00	0.00	2.10
968	1009	2.600731	CTGTCGATCTCACACTGTTCC	58.399	52.381	0.00	0.00	0.00	3.62
1016	1062	2.282040	AGAAGCAGCACAGGTGGC	60.282	61.111	1.10	0.00	0.00	5.01
1161	1232	5.105269	TGCAACAAGATTATGGCATGAACAT	60.105	36.000	10.98	2.43	0.00	2.71
1303	1380	0.991920	GACCTTGGGTGGAGATGGAA	59.008	55.000	0.00	0.00	35.25	3.53
1307	1384	0.419459	AGGAGACCTTGGGTGGAGAT	59.581	55.000	0.00	0.00	35.25	2.75
1445	1566	9.853555	ACGAAATAATTAATGAGTTTGCAATCA	57.146	25.926	10.05	7.68	0.00	2.57
1530	2106	3.196039	TCTTTATACCGCAGCTGGTACAA	59.804	43.478	17.12	2.61	46.80	2.41
1573	2149	7.182089	TGTATACTGTATACTTCGTGTTCGTG	58.818	38.462	28.56	0.00	41.21	4.35
1574	2150	7.307493	TGTATACTGTATACTTCGTGTTCGT	57.693	36.000	28.56	0.00	41.21	3.85
1575	2151	8.518660	GTTTGTATACTGTATACTTCGTGTTCG	58.481	37.037	28.56	0.00	41.21	3.95
1576	2152	9.565213	AGTTTGTATACTGTATACTTCGTGTTC	57.435	33.333	28.56	15.17	41.21	3.18
1879	2468	4.309950	GCCGGTGTCGAGGTTGGT	62.310	66.667	1.90	0.00	39.00	3.67
2082	2671	2.847234	TTGTCCCACACCTCGGCT	60.847	61.111	0.00	0.00	0.00	5.52
2462	3051	1.076044	GAATCATGGGGTGGGGTGG	60.076	63.158	0.00	0.00	0.00	4.61
2464	3053	0.262580	CATGAATCATGGGGTGGGGT	59.737	55.000	15.09	0.00	38.11	4.95
2465	3054	0.557238	TCATGAATCATGGGGTGGGG	59.443	55.000	21.58	0.00	41.66	4.96
2581	3493	2.590007	GCGCTTCCTGATCGCCAT	60.590	61.111	0.00	0.00	42.71	4.40
2726	3638	2.968156	CCGACGTTGCGAACCCAA	60.968	61.111	0.00	0.00	0.00	4.12
2815	3738	4.700213	AGAAAATTCATGGTCGGTCGAATT	59.300	37.500	0.00	0.00	39.20	2.17
2822	3745	3.191162	TGCTTCAGAAAATTCATGGTCGG	59.809	43.478	0.00	0.00	0.00	4.79
2826	3749	7.843490	ATCATTTGCTTCAGAAAATTCATGG	57.157	32.000	0.00	0.00	31.03	3.66
3056	4005	6.668541	TGTCAGTTGTTTTCTTCTCTCTTG	57.331	37.500	0.00	0.00	0.00	3.02
3062	4011	7.141363	GCATGTTATGTCAGTTGTTTTCTTCT	58.859	34.615	0.00	0.00	0.00	2.85
3069	4018	5.764686	TCTCTTGCATGTTATGTCAGTTGTT	59.235	36.000	0.00	0.00	0.00	2.83
3071	4020	5.640783	TCTCTCTTGCATGTTATGTCAGTTG	59.359	40.000	0.00	0.00	0.00	3.16
3074	4023	6.104665	TCTTCTCTCTTGCATGTTATGTCAG	58.895	40.000	0.00	0.00	0.00	3.51
3075	4024	6.041423	TCTTCTCTCTTGCATGTTATGTCA	57.959	37.500	0.00	0.00	0.00	3.58
3076	4025	6.974932	TTCTTCTCTCTTGCATGTTATGTC	57.025	37.500	0.00	0.00	0.00	3.06
3078	4027	7.587629	TGTTTTCTTCTCTCTTGCATGTTATG	58.412	34.615	0.00	0.00	0.00	1.90
3082	4031	6.645790	ATTGTTTTCTTCTCTCTTGCATGT	57.354	33.333	0.00	0.00	0.00	3.21
3083	4032	7.143340	TCAATTGTTTTCTTCTCTCTTGCATG	58.857	34.615	5.13	0.00	0.00	4.06
3085	4034	6.698008	TCAATTGTTTTCTTCTCTCTTGCA	57.302	33.333	5.13	0.00	0.00	4.08
3086	4035	7.168804	CCTTTCAATTGTTTTCTTCTCTCTTGC	59.831	37.037	5.13	0.00	0.00	4.01
3087	4036	8.408601	TCCTTTCAATTGTTTTCTTCTCTCTTG	58.591	33.333	5.13	0.00	0.00	3.02
3088	4037	8.525290	TCCTTTCAATTGTTTTCTTCTCTCTT	57.475	30.769	5.13	0.00	0.00	2.85
3089	4038	8.525290	TTCCTTTCAATTGTTTTCTTCTCTCT	57.475	30.769	5.13	0.00	0.00	3.10
3090	4039	9.586435	TTTTCCTTTCAATTGTTTTCTTCTCTC	57.414	29.630	5.13	0.00	0.00	3.20
3091	4040	9.942850	TTTTTCCTTTCAATTGTTTTCTTCTCT	57.057	25.926	5.13	0.00	0.00	3.10
3137	4086	6.768381	TCGATGCTATATCCGTGAGATCTTAT	59.232	38.462	0.00	0.00	36.33	1.73
3166	4115	2.420547	GCATCCAACAGATACCTCAGCA	60.421	50.000	0.00	0.00	32.37	4.41
3168	4117	3.133542	TGAGCATCCAACAGATACCTCAG	59.866	47.826	0.00	0.00	37.49	3.35
3169	4118	3.106827	TGAGCATCCAACAGATACCTCA	58.893	45.455	0.00	0.00	38.88	3.86
3170	4119	3.827008	TGAGCATCCAACAGATACCTC	57.173	47.619	0.00	0.00	35.00	3.85
3171	4120	3.746751	GCATGAGCATCCAACAGATACCT	60.747	47.826	0.00	0.00	41.58	3.08
3172	4121	2.551459	GCATGAGCATCCAACAGATACC	59.449	50.000	0.00	0.00	41.58	2.73
3211	4202	2.596419	GCGACGAGACTGAATCTTCTTG	59.404	50.000	0.00	0.05	38.00	3.02
3218	4209	0.532573	ACATGGCGACGAGACTGAAT	59.467	50.000	0.00	0.00	0.00	2.57
3220	4211	3.681473	ACATGGCGACGAGACTGA	58.319	55.556	0.00	0.00	0.00	3.41
3711	4702	4.465512	CTGCCATCGCACCGTTGC	62.466	66.667	0.00	0.00	46.21	4.17
3712	4703	3.803082	CCTGCCATCGCACCGTTG	61.803	66.667	0.00	0.00	41.12	4.10
3756	4747	4.738998	TGCCTTCCACGCCCATGG	62.739	66.667	4.14	4.14	41.57	3.66
3758	4749	2.124151	GATGCCTTCCACGCCCAT	60.124	61.111	0.00	0.00	0.00	4.00
3771	4762	2.601741	GCAAGATCTAGCTTTGCGATGC	60.602	50.000	4.42	3.60	0.00	3.91
3777	4768	2.621998	CCATGGGCAAGATCTAGCTTTG	59.378	50.000	2.85	0.00	0.00	2.77
3779	4770	1.849039	ACCATGGGCAAGATCTAGCTT	59.151	47.619	18.09	0.00	0.00	3.74
3780	4771	1.142465	CACCATGGGCAAGATCTAGCT	59.858	52.381	18.09	0.00	0.00	3.32
3807	4798	2.109181	GTCGTGCCCATCCCTAGC	59.891	66.667	0.00	0.00	0.00	3.42
3822	4813	0.605589	CCAGATGCTAGATCCGGGTC	59.394	60.000	6.61	6.61	0.00	4.46
3850	4841	4.265056	AACCCACTCACGCCACCC	62.265	66.667	0.00	0.00	0.00	4.61
3860	4851	1.536676	CCACCAAGACCAACCCACT	59.463	57.895	0.00	0.00	0.00	4.00
3866	4857	1.827789	GCACAGCCACCAAGACCAA	60.828	57.895	0.00	0.00	0.00	3.67
3867	4858	1.414866	TAGCACAGCCACCAAGACCA	61.415	55.000	0.00	0.00	0.00	4.02
3871	4862	0.877071	CAAGTAGCACAGCCACCAAG	59.123	55.000	0.00	0.00	0.00	3.61
3884	4875	1.210478	AGTATGGTGCTGCCCAAGTAG	59.790	52.381	12.73	0.00	38.20	2.57
3889	4880	1.271127	TGCTAGTATGGTGCTGCCCA	61.271	55.000	11.41	11.41	39.27	5.36
3899	4890	2.763933	CATCCACTGGCTGCTAGTATG	58.236	52.381	18.52	15.07	0.00	2.39
3908	4899	3.640407	ACACCGCATCCACTGGCT	61.640	61.111	0.00	0.00	0.00	4.75
3910	4901	2.747460	CCACACCGCATCCACTGG	60.747	66.667	0.00	0.00	0.00	4.00
3911	4902	3.434319	GCCACACCGCATCCACTG	61.434	66.667	0.00	0.00	0.00	3.66
3912	4903	3.640407	AGCCACACCGCATCCACT	61.640	61.111	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.