AutoCloner

Multiple sequence alignment - TraesCS1A01G031800

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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	TraesCS1A01G031800	chr1A	100.000	6551	0	0	1	6551	14595115	14588565	0.000000e+00	12098.0
1	TraesCS1A01G031800	chr1A	87.240	1152	136	6	1198	2346	14615550	14614407	0.000000e+00	1303.0
2	TraesCS1A01G031800	chr1A	81.460	1014	143	21	3586	4594	14605472	14604499	0.000000e+00	789.0
3	TraesCS1A01G031800	chr1A	81.868	182	31	2	4169	4349	532530722	532530902	1.140000e-32	152.0
4	TraesCS1A01G031800	chr1A	73.864	264	53	11	3185	3441	532629419	532629165	2.520000e-14	91.6
5	TraesCS1A01G031800	chr1A	100.000	28	0	0	5667	5694	16394024	16393997	1.200000e-02	52.8
6	TraesCS1A01G031800	chr1B	93.152	5155	251	42	1069	6188	19038919	19044006	0.000000e+00	7470.0
7	TraesCS1A01G031800	chr1B	89.325	3288	253	51	2485	5715	19048468	19051714	0.000000e+00	4037.0
8	TraesCS1A01G031800	chr1B	85.751	1158	141	17	1218	2366	19232416	19231274	0.000000e+00	1203.0
9	TraesCS1A01G031800	chr1B	91.578	843	58	10	5712	6550	19057678	19058511	0.000000e+00	1151.0
10	TraesCS1A01G031800	chr1B	91.036	714	34	16	249	932	19036576	19037289	0.000000e+00	937.0
11	TraesCS1A01G031800	chr1B	84.894	801	114	6	3780	4578	19219864	19219069	0.000000e+00	802.0
12	TraesCS1A01G031800	chr1B	78.151	833	107	27	251	1031	19308109	19307300	1.660000e-125	460.0
13	TraesCS1A01G031800	chr1B	86.413	184	19	3	1	181	19308289	19308109	5.180000e-46	196.0
14	TraesCS1A01G031800	chr1B	84.058	207	6	6	1	181	19036371	19036576	2.430000e-39	174.0
15	TraesCS1A01G031800	chr1B	80.769	182	33	2	4169	4349	588232236	588232416	2.460000e-29	141.0
16	TraesCS1A01G031800	chr1B	90.588	85	8	0	3630	3714	19219983	19219899	5.370000e-21	113.0
17	TraesCS1A01G031800	chr1B	74.242	264	52	11	3185	3441	588327516	588327262	5.410000e-16	97.1
18	TraesCS1A01G031800	chr1D	94.543	4673	201	22	1070	5715	13325393	13320748	0.000000e+00	7167.0
19	TraesCS1A01G031800	chr1D	92.553	2417	148	16	3320	5715	13313858	13311453	0.000000e+00	3437.0
20	TraesCS1A01G031800	chr1D	90.606	841	66	10	5715	6551	13310890	13310059	0.000000e+00	1103.0
21	TraesCS1A01G031800	chr1D	93.198	691	21	6	406	1071	13327056	13326367	0.000000e+00	992.0
22	TraesCS1A01G031800	chr1D	91.371	591	41	5	5961	6551	13319987	13319407	0.000000e+00	800.0
23	TraesCS1A01G031800	chr1D	79.177	1167	214	22	1197	2352	13371135	13369987	0.000000e+00	782.0
24	TraesCS1A01G031800	chr1D	83.154	837	87	31	2497	3310	13314730	13313925	0.000000e+00	715.0
25	TraesCS1A01G031800	chr1D	78.471	1138	207	26	1229	2352	14259881	14258768	0.000000e+00	710.0
26	TraesCS1A01G031800	chr1D	81.658	796	125	12	3803	4594	13368370	13367592	5.540000e-180	641.0
27	TraesCS1A01G031800	chr1D	80.359	835	118	22	3569	4397	14257490	14256696	5.660000e-165	592.0
28	TraesCS1A01G031800	chr1D	79.521	459	62	11	603	1031	13376141	13375685	1.380000e-76	298.0
29	TraesCS1A01G031800	chr1D	91.960	199	15	1	5715	5912	13320186	13319988	1.800000e-70	278.0
30	TraesCS1A01G031800	chr1D	94.231	156	9	0	253	408	13348695	13348540	8.490000e-59	239.0
31	TraesCS1A01G031800	chr1D	75.780	545	89	33	3183	3714	13368926	13368412	1.100000e-57	235.0
32	TraesCS1A01G031800	chr1D	84.878	205	29	2	4412	4616	14256636	14256434	8.610000e-49	206.0
33	TraesCS1A01G031800	chr1D	95.868	121	4	1	62	181	13348815	13348695	1.860000e-45	195.0
34	TraesCS1A01G031800	chr1D	89.683	126	11	1	1070	1195	13371344	13371221	6.800000e-35	159.0
35	TraesCS1A01G031800	chr1D	86.861	137	18	0	4433	4569	452623314	452623178	3.160000e-33	154.0
36	TraesCS1A01G031800	chr1D	90.698	86	7	1	3630	3714	452624078	452623993	5.370000e-21	113.0
37	TraesCS1A01G031800	chr1D	93.220	59	4	0	4436	4494	433925956	433926014	3.250000e-13	87.9
38	TraesCS1A01G031800	chr1D	100.000	28	0	0	5667	5694	15308380	15308353	1.200000e-02	52.8
39	TraesCS1A01G031800	chr5D	94.828	58	3	0	3351	3408	553344920	553344863	2.520000e-14	91.6
40	TraesCS1A01G031800	chr5B	92.188	64	5	0	3351	3414	697379531	697379468	2.520000e-14	91.6
41	TraesCS1A01G031800	chr5B	100.000	28	0	0	5667	5694	527760410	527760437	1.200000e-02	52.8
42	TraesCS1A01G031800	chr3D	100.000	29	0	0	5667	5695	573685391	573685419	3.000000e-03	54.7
43	TraesCS1A01G031800	chr2B	100.000	28	0	0	5667	5694	680079790	680079817	1.200000e-02	52.8

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	TraesCS1A01G031800	chr1A	14588565	14595115	6550	True	12098.000000	12098	100.000000	1	6551	1	chr1A.!!$R1	6550
1	TraesCS1A01G031800	chr1A	14614407	14615550	1143	True	1303.000000	1303	87.240000	1198	2346	1	chr1A.!!$R3	1148
2	TraesCS1A01G031800	chr1A	14604499	14605472	973	True	789.000000	789	81.460000	3586	4594	1	chr1A.!!$R2	1008
3	TraesCS1A01G031800	chr1B	19048468	19051714	3246	False	4037.000000	4037	89.325000	2485	5715	1	chr1B.!!$F1	3230
4	TraesCS1A01G031800	chr1B	19036371	19044006	7635	False	2860.333333	7470	89.415333	1	6188	3	chr1B.!!$F4	6187
5	TraesCS1A01G031800	chr1B	19231274	19232416	1142	True	1203.000000	1203	85.751000	1218	2366	1	chr1B.!!$R1	1148
6	TraesCS1A01G031800	chr1B	19057678	19058511	833	False	1151.000000	1151	91.578000	5712	6550	1	chr1B.!!$F2	838
7	TraesCS1A01G031800	chr1B	19219069	19219983	914	True	457.500000	802	87.741000	3630	4578	2	chr1B.!!$R3	948
8	TraesCS1A01G031800	chr1B	19307300	19308289	989	True	328.000000	460	82.282000	1	1031	2	chr1B.!!$R4	1030
9	TraesCS1A01G031800	chr1D	13319407	13327056	7649	True	2309.250000	7167	92.768000	406	6551	4	chr1D.!!$R4	6145
10	TraesCS1A01G031800	chr1D	13310059	13314730	4671	True	1751.666667	3437	88.771000	2497	6551	3	chr1D.!!$R3	4054
11	TraesCS1A01G031800	chr1D	14256434	14259881	3447	True	502.666667	710	81.236000	1229	4616	3	chr1D.!!$R7	3387
12	TraesCS1A01G031800	chr1D	13367592	13371344	3752	True	454.250000	782	81.574500	1070	4594	4	chr1D.!!$R6	3524

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
197	225	0.167908	GGTGTGTGTGTGTGTGTGTG	59.832	55.000	0.00	0.00	0.00	3.82	F
199	227	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82	F
1659	3378	0.318360	CGTAGTCTTGCCACACGACA	60.318	55.000	6.93	0.00	35.51	4.35	F
1685	3404	1.453015	GGTGTGCCTGGTGAACACA	60.453	57.895	22.19	13.69	44.77	3.72	F
2029	3751	2.034879	CGCCCGAGCTCAACAATGT	61.035	57.895	15.40	0.00	36.60	2.71	F
2587	4340	1.105167	ATGGGATGGCTTGACATGCG	61.105	55.000	7.19	0.00	39.74	4.73	F
4158	6972	0.179048	TGGCGGCGATGATGATTCTT	60.179	50.000	12.98	0.00	0.00	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1647	3366	0.250081	TGCACTATGTCGTGTGGCAA	60.250	50.000	0.00	37.24	4.52	R
1730	3449	1.204704	TGTGGGTAGAGCGACATCTTG	59.795	52.381	0.00	0.00	3.02	R
2526	4279	1.614317	GGGTCACCCATCCAGTTCTTG	60.614	57.143	8.52	44.65	3.02	R
2577	4330	1.650912	GGCATAGCCGCATGTCAAG	59.349	57.895	0.00	39.62	3.02	R
4008	6820	0.669619	CATTGTTGTGTGCTGGCTCA	59.330	50.000	0.00	0.00	4.26	R
4164	6978	2.167693	TGAACCGGCGATTCTCAACTAT	59.832	45.455	16.09	0.00	2.12	R
5968	9420	0.947244	CAGTCAGTGTGTTCTTGCCC	59.053	55.000	0.00	0.00	5.36	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
49	52	1.915141	AGTTTGGGATGCAGGTCAAG	58.085	50.000	0.00	0.00	0.00	3.02
54	57	2.265367	TGGGATGCAGGTCAAGTCTTA	58.735	47.619	0.00	0.00	0.00	2.10
93	96	6.294361	ACCTTGCAGATAGTACACACAATA	57.706	37.500	0.00	0.00	0.00	1.90
172	200	2.482494	AGATCCTCGGAGTTCCCAAAT	58.518	47.619	4.02	0.00	34.14	2.32
173	201	2.436173	AGATCCTCGGAGTTCCCAAATC	59.564	50.000	4.02	0.00	34.14	2.17
174	202	1.651737	TCCTCGGAGTTCCCAAATCA	58.348	50.000	4.02	0.00	34.14	2.57
175	203	2.196595	TCCTCGGAGTTCCCAAATCAT	58.803	47.619	4.02	0.00	34.14	2.45
178	206	3.129287	CCTCGGAGTTCCCAAATCATTTG	59.871	47.826	2.80	2.80	40.32	2.32
190	218	4.431809	CAAATCATTTGGTGTGTGTGTGT	58.568	39.130	1.73	0.00	37.01	3.72
191	219	3.713858	ATCATTTGGTGTGTGTGTGTG	57.286	42.857	0.00	0.00	0.00	3.82
192	220	2.441410	TCATTTGGTGTGTGTGTGTGT	58.559	42.857	0.00	0.00	0.00	3.72
193	221	2.163211	TCATTTGGTGTGTGTGTGTGTG	59.837	45.455	0.00	0.00	0.00	3.82
194	222	1.610363	TTTGGTGTGTGTGTGTGTGT	58.390	45.000	0.00	0.00	0.00	3.72
195	223	0.877743	TTGGTGTGTGTGTGTGTGTG	59.122	50.000	0.00	0.00	0.00	3.82
196	224	0.250510	TGGTGTGTGTGTGTGTGTGT	60.251	50.000	0.00	0.00	0.00	3.72
197	225	0.167908	GGTGTGTGTGTGTGTGTGTG	59.832	55.000	0.00	0.00	0.00	3.82
198	226	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
199	227	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
200	228	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
201	229	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
202	230	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
203	231	1.136085	GTGTGTGTGTGTGTGTGTGTC	60.136	52.381	0.00	0.00	0.00	3.67
204	232	1.270571	TGTGTGTGTGTGTGTGTGTCT	60.271	47.619	0.00	0.00	0.00	3.41
205	233	2.028930	TGTGTGTGTGTGTGTGTGTCTA	60.029	45.455	0.00	0.00	0.00	2.59
206	234	3.194861	GTGTGTGTGTGTGTGTGTCTAT	58.805	45.455	0.00	0.00	0.00	1.98
207	235	4.142138	TGTGTGTGTGTGTGTGTGTCTATA	60.142	41.667	0.00	0.00	0.00	1.31
208	236	4.988540	GTGTGTGTGTGTGTGTGTCTATAT	59.011	41.667	0.00	0.00	0.00	0.86
209	237	6.153756	GTGTGTGTGTGTGTGTGTCTATATA	58.846	40.000	0.00	0.00	0.00	0.86
210	238	6.811665	GTGTGTGTGTGTGTGTGTCTATATAT	59.188	38.462	0.00	0.00	0.00	0.86
211	239	7.971722	GTGTGTGTGTGTGTGTGTCTATATATA	59.028	37.037	0.00	0.00	0.00	0.86
212	240	8.691797	TGTGTGTGTGTGTGTGTCTATATATAT	58.308	33.333	0.00	0.00	0.00	0.86
368	405	1.072806	AGTGCAATGCAGGTCTCTTCA	59.927	47.619	8.73	0.00	40.08	3.02
383	420	7.066645	CAGGTCTCTTCAATCATAAAATGAGCA	59.933	37.037	0.00	0.00	43.53	4.26
479	517	2.673775	TTTCCCTTGTCCATTGCTCA	57.326	45.000	0.00	0.00	0.00	4.26
557	596	1.197812	ATTTGGCCAATTGGAGAGCC	58.802	50.000	29.02	20.88	45.96	4.70
558	597	0.904394	TTTGGCCAATTGGAGAGCCC	60.904	55.000	29.02	18.67	45.14	5.19
578	618	8.548877	AGAGCCCAAAGTTAAGAATAGTAATCA	58.451	33.333	0.00	0.00	0.00	2.57
793	834	1.000955	CCGGCCTCGAGTAATAAGCAT	59.999	52.381	12.31	0.00	39.00	3.79
794	835	2.061773	CGGCCTCGAGTAATAAGCATG	58.938	52.381	12.31	0.00	39.00	4.06
796	837	3.060602	GGCCTCGAGTAATAAGCATGAC	58.939	50.000	12.31	0.00	0.00	3.06
797	838	3.492656	GGCCTCGAGTAATAAGCATGACA	60.493	47.826	12.31	0.00	0.00	3.58
798	839	4.119862	GCCTCGAGTAATAAGCATGACAA	58.880	43.478	12.31	0.00	0.00	3.18
799	840	4.210120	GCCTCGAGTAATAAGCATGACAAG	59.790	45.833	12.31	0.00	0.00	3.16
806	873	8.700644	CGAGTAATAAGCATGACAAGTATTACC	58.299	37.037	0.00	1.60	0.00	2.85
946	1029	5.388408	AAGACTTTCTAGTACAAGGACCG	57.612	43.478	0.00	0.00	33.84	4.79
975	1059	1.143073	ACCACCCTTTGTCTTGTCCTC	59.857	52.381	0.00	0.00	0.00	3.71
1156	2790	3.497879	GGCAACGTACTCCATGGC	58.502	61.111	6.96	0.00	0.00	4.40
1195	2829	4.067896	GCAGAGGTATCTCTCTCTCTCTG	58.932	52.174	1.34	12.23	46.79	3.35
1249	2967	5.761003	TGCCTCATTTACATTGCATATTCG	58.239	37.500	0.00	0.00	0.00	3.34
1413	3132	3.692406	GGCGGTCCAGGAACGTCT	61.692	66.667	27.76	0.00	44.46	4.18
1471	3190	2.662866	CTACACGTTAGGATCCCTGGA	58.337	52.381	8.55	0.00	34.61	3.86
1499	3218	2.158959	CAAGTACCTCTTCCGCGCG	61.159	63.158	25.67	25.67	33.63	6.86
1535	3254	2.801679	CAACTACGACGGCCTTAACAAA	59.198	45.455	0.00	0.00	0.00	2.83
1610	3329	2.530661	TCGTGGTGGGGGTTGGAT	60.531	61.111	0.00	0.00	0.00	3.41
1611	3330	2.361104	CGTGGTGGGGGTTGGATG	60.361	66.667	0.00	0.00	0.00	3.51
1647	3366	1.043673	GGTGGAGGCCATCGTAGTCT	61.044	60.000	5.01	0.00	35.28	3.24
1659	3378	0.318360	CGTAGTCTTGCCACACGACA	60.318	55.000	6.93	0.00	35.51	4.35
1661	3380	2.414957	CGTAGTCTTGCCACACGACATA	60.415	50.000	6.93	0.00	35.51	2.29
1685	3404	1.453015	GGTGTGCCTGGTGAACACA	60.453	57.895	22.19	13.69	44.77	3.72
1888	3610	4.192000	CACGATGTGGGCAGAGAC	57.808	61.111	0.00	0.00	0.00	3.36
1977	3699	3.874873	CGATCAAGCCGCTGAACA	58.125	55.556	0.00	0.00	0.00	3.18
2029	3751	2.034879	CGCCCGAGCTCAACAATGT	61.035	57.895	15.40	0.00	36.60	2.71
2370	4103	8.859236	AGCACATATTGACATCTAATAAGCAT	57.141	30.769	0.00	0.00	0.00	3.79
2583	4336	4.342427	GCATGGGATGGCTTGACA	57.658	55.556	0.00	0.00	0.00	3.58
2587	4340	1.105167	ATGGGATGGCTTGACATGCG	61.105	55.000	7.19	0.00	39.74	4.73
2636	4408	8.353423	AGGATCACAAGCATGTAAGTTATTTT	57.647	30.769	0.00	0.00	37.82	1.82
2642	4414	9.341899	CACAAGCATGTAAGTTATTTTTACTCC	57.658	33.333	0.00	0.00	37.82	3.85
2746	5301	9.631452	GGGAATTCAAGAAAAGTCAGAAATAAG	57.369	33.333	7.93	0.00	0.00	1.73
2827	5382	5.710099	GGGTTTCCTATCATTGTCTTGTTCA	59.290	40.000	0.00	0.00	0.00	3.18
2949	5514	6.489127	TTACGTTCACCCTTGAATTGTATG	57.511	37.500	0.00	0.00	43.72	2.39
2955	5520	6.449635	TCACCCTTGAATTGTATGTATTGC	57.550	37.500	0.00	0.00	0.00	3.56
3225	5872	8.744652	CCTCCAGTGGTCTAAATAGTGATATAG	58.255	40.741	9.54	0.00	0.00	1.31
3238	5885	9.935241	AAATAGTGATATAGCATCATCTTTCGT	57.065	29.630	0.00	0.00	0.00	3.85
3409	6126	3.359033	TCAATTCCAGATGCCCTTTCAG	58.641	45.455	0.00	0.00	0.00	3.02
3445	6167	3.758554	GACAGTCATGTAAGTTGGGCAAT	59.241	43.478	0.00	0.00	40.68	3.56
3472	6214	5.896073	AGCCCTAACTAATTAGCAGACAT	57.104	39.130	12.54	0.00	37.12	3.06
3506	6250	5.232202	CACACTCGGACACAATATATGACAC	59.768	44.000	0.00	0.00	0.00	3.67
3509	6253	7.145323	CACTCGGACACAATATATGACACATA	58.855	38.462	0.00	0.00	0.00	2.29
3513	6257	7.982354	TCGGACACAATATATGACACATACAAA	59.018	33.333	0.00	0.00	0.00	2.83
3620	6374	6.609237	ACATATATTGTGTGTCTGATGTGC	57.391	37.500	0.00	0.00	37.11	4.57
3757	6511	9.301897	ACTTGATAAATTCCACTAAGCTTCTTT	57.698	29.630	0.00	0.00	0.00	2.52
3854	6654	1.730121	GCACTGACGGCAATTCATGTG	60.730	52.381	0.00	0.00	0.00	3.21
3875	6675	2.643933	GCTTGCTGCTAAAAGGAAGG	57.356	50.000	0.00	0.00	43.62	3.46
4158	6972	0.179048	TGGCGGCGATGATGATTCTT	60.179	50.000	12.98	0.00	0.00	2.52
4164	6978	3.063861	CGGCGATGATGATTCTTTGTGAA	59.936	43.478	0.00	0.00	39.24	3.18
4292	7106	2.027192	GGAAGATGGTACTCAAGTGGCA	60.027	50.000	0.00	0.00	0.00	4.92
4479	7342	6.596888	GGATTCATCACAAGAATCTTGTCTCA	59.403	38.462	24.21	12.48	46.60	3.27
4606	7469	5.530915	GGCTAACAAAAAGGATTTGGCTTTT	59.469	36.000	5.96	0.00	39.02	2.27
4625	7488	7.775093	TGGCTTTTAACTCATATAGTGAATGCT	59.225	33.333	0.00	0.00	38.88	3.79
4636	7499	1.377202	TGAATGCTCAAGTCGCCCC	60.377	57.895	0.00	0.00	0.00	5.80
4784	7664	4.395583	GTGCACGCTCAAGCTGCC	62.396	66.667	17.69	9.67	41.28	4.85
4804	7684	4.072839	GCCCTTCAATAGTTATGGCCTAC	58.927	47.826	3.32	0.00	0.00	3.18
4818	7698	3.692690	TGGCCTACTTTTGTATTCACCC	58.307	45.455	3.32	0.00	33.96	4.61
4832	7712	3.281727	TTCACCCAGAGGCACATTATC	57.718	47.619	0.00	0.00	36.11	1.75
4833	7713	1.490490	TCACCCAGAGGCACATTATCC	59.510	52.381	0.00	0.00	36.11	2.59
5058	7938	1.669760	CACGCTCGCTTTTACCCCA	60.670	57.895	0.00	0.00	0.00	4.96
5061	7941	1.298667	GCTCGCTTTTACCCCAGGA	59.701	57.895	0.00	0.00	0.00	3.86
5094	7974	2.106683	GTACCAGGCCACGATGCAC	61.107	63.158	5.01	0.00	0.00	4.57
5472	8352	2.284798	CTAGTGCGCAGTCCACCGAT	62.285	60.000	23.41	0.00	33.75	4.18
5749	9196	3.793559	AGTGTAGTTTCATCATACCGGC	58.206	45.455	0.00	0.00	0.00	6.13
5772	9219	1.134007	CCATGAGCAGAACCTGGCATA	60.134	52.381	0.00	0.00	31.21	3.14
5774	9221	2.627515	TGAGCAGAACCTGGCATATC	57.372	50.000	0.00	0.00	31.21	1.63
5799	9246	0.884259	CAACAGCCATCACCGTCACA	60.884	55.000	0.00	0.00	0.00	3.58
5877	9325	4.778534	ATGAAGCAGACAAAATCACTGG	57.221	40.909	0.00	0.00	33.00	4.00
5886	9334	7.665559	AGCAGACAAAATCACTGGAATAACTTA	59.334	33.333	0.00	0.00	33.00	2.24
6076	9532	4.517075	TCGCTTGATTTACCATGACACAAA	59.483	37.500	0.00	0.00	0.00	2.83
6097	9555	7.121759	CACAAATCTGGGATAGAACAGTCATTT	59.878	37.037	0.00	0.00	39.30	2.32
6102	9560	9.607333	ATCTGGGATAGAACAGTCATTTATCTA	57.393	33.333	0.00	0.00	39.30	1.98
6130	9588	1.210478	ACCAGTTGCGGCATAGAGATT	59.790	47.619	2.28	0.00	0.00	2.40
6133	9591	2.938451	CAGTTGCGGCATAGAGATTGAA	59.062	45.455	2.28	0.00	0.00	2.69
6137	9595	4.335400	TGCGGCATAGAGATTGAATACA	57.665	40.909	0.00	0.00	0.00	2.29
6267	9725	7.540299	ACTACTGCAGAGAGTAAATTGAGTAC	58.460	38.462	23.35	0.00	0.00	2.73
6324	9783	9.521841	TTATGGTCTTATGGATCTAGTGTCTAG	57.478	37.037	0.00	0.00	0.00	2.43
6333	9792	6.377080	TGGATCTAGTGTCTAGTCCATCATT	58.623	40.000	16.36	0.00	31.24	2.57
6401	9860	2.060284	CCAACAATGGTGCATTTCACG	58.940	47.619	0.00	0.00	46.56	4.35
6417	9876	1.135199	TCACGAGCTGATTACCGTTCC	60.135	52.381	0.00	0.00	32.50	3.62
6426	9885	0.544697	ATTACCGTTCCGCATTCCCT	59.455	50.000	0.00	0.00	0.00	4.20
6533	9993	0.731417	GAGCTCATTTGCTGTGCGAT	59.269	50.000	9.40	0.00	46.51	4.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
77	80	7.735326	ACCCTTCTTATTGTGTGTACTATCT	57.265	36.000	0.00	0.00	0.00	1.98
93	96	2.308866	CCCTTCACCACATACCCTTCTT	59.691	50.000	0.00	0.00	0.00	2.52
172	200	2.163211	CACACACACACACACCAAATGA	59.837	45.455	0.00	0.00	0.00	2.57
173	201	2.094803	ACACACACACACACACCAAATG	60.095	45.455	0.00	0.00	0.00	2.32
174	202	2.094803	CACACACACACACACACCAAAT	60.095	45.455	0.00	0.00	0.00	2.32
175	203	1.268079	CACACACACACACACACCAAA	59.732	47.619	0.00	0.00	0.00	3.28
178	206	0.167908	CACACACACACACACACACC	59.832	55.000	0.00	0.00	0.00	4.16
180	208	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
181	209	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
182	210	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
183	211	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
184	212	1.152510	GACACACACACACACACACA	58.847	50.000	0.00	0.00	0.00	3.72
185	213	1.438651	AGACACACACACACACACAC	58.561	50.000	0.00	0.00	0.00	3.82
186	214	3.535280	ATAGACACACACACACACACA	57.465	42.857	0.00	0.00	0.00	3.72
263	294	9.927668	CAGAAACTGTTGTCCCAAAATATTTAT	57.072	29.630	0.01	0.00	0.00	1.40
278	309	9.643693	AAAAATATCATTAGGCAGAAACTGTTG	57.356	29.630	0.00	0.00	33.43	3.33
383	420	0.685097	ACCGGTCAACTGCACTGTAT	59.315	50.000	0.00	0.00	0.00	2.29
479	517	4.832266	TGGTTAAAGAGTTGAATGTGGCAT	59.168	37.500	0.00	0.00	0.00	4.40
578	618	2.419574	GGTCGTGGTGCATTAGGTATGT	60.420	50.000	0.00	0.00	36.57	2.29
731	772	9.929180	ACTCGCATATGTTATACATGTAAATCT	57.071	29.630	10.14	0.00	39.53	2.40
741	782	7.178712	AGCTTCAAACTCGCATATGTTATAC	57.821	36.000	4.29	0.00	0.00	1.47
793	834	4.689071	CGTGCATAGGGTAATACTTGTCA	58.311	43.478	0.00	0.00	0.00	3.58
794	835	3.493503	GCGTGCATAGGGTAATACTTGTC	59.506	47.826	0.00	0.00	0.00	3.18
796	837	3.728845	AGCGTGCATAGGGTAATACTTG	58.271	45.455	0.00	0.00	0.00	3.16
797	838	4.831155	TCTAGCGTGCATAGGGTAATACTT	59.169	41.667	0.00	0.00	0.00	2.24
798	839	4.404640	TCTAGCGTGCATAGGGTAATACT	58.595	43.478	0.00	0.00	0.00	2.12
799	840	4.778534	TCTAGCGTGCATAGGGTAATAC	57.221	45.455	0.00	0.00	0.00	1.89
806	873	5.355630	ACATCTACTATCTAGCGTGCATAGG	59.644	44.000	0.00	0.00	0.00	2.57
1014	1100	7.330262	CCTTGCCAGTATTTTCACCAAATAAT	58.670	34.615	0.00	0.00	38.77	1.28
1051	1137	5.814764	TGCAAAGTACGTTTGGAAACTTA	57.185	34.783	15.16	0.00	42.93	2.24
1156	2790	4.081030	CTGTCAAGCTGTGCGCGG	62.081	66.667	8.83	0.38	45.59	6.46
1195	2829	4.135747	AGAGAGAGAAGCCAATAACAGC	57.864	45.455	0.00	0.00	0.00	4.40
1249	2967	3.435105	TGTTGATGAAACCTGCACAAC	57.565	42.857	0.00	0.00	38.06	3.32
1343	3062	2.719354	GTGCCGGTGTTGGTGAAC	59.281	61.111	1.90	0.00	0.00	3.18
1350	3069	2.667199	GTAAGGCGTGCCGGTGTT	60.667	61.111	1.90	0.00	41.95	3.32
1413	3132	2.260869	GGAAACTTCGCAGGCTGCA	61.261	57.895	35.94	21.62	45.36	4.41
1471	3190	0.971447	GAGGTACTTGAGGCCCGACT	60.971	60.000	0.00	0.00	41.55	4.18
1499	3218	3.546670	CGTAGTTGCCATAGAGAAACGTC	59.453	47.826	0.00	0.00	0.00	4.34
1610	3329	2.741092	GTCGCCCTGTTGTCCTCA	59.259	61.111	0.00	0.00	0.00	3.86
1611	3330	2.432628	CGTCGCCCTGTTGTCCTC	60.433	66.667	0.00	0.00	0.00	3.71
1647	3366	0.250081	TGCACTATGTCGTGTGGCAA	60.250	50.000	0.00	0.00	37.24	4.52
1730	3449	1.204704	TGTGGGTAGAGCGACATCTTG	59.795	52.381	0.00	0.00	0.00	3.02
1888	3610	3.862402	CCCTCTCGGTCGTCGTCG	61.862	72.222	0.00	0.00	40.32	5.12
2129	3857	3.646715	CCCGGGACCCAGCTTTCA	61.647	66.667	18.48	0.00	0.00	2.69
2494	4247	3.741860	GGCCTTGATCGCCATGAG	58.258	61.111	5.33	0.00	46.27	2.90
2526	4279	1.614317	GGGTCACCCATCCAGTTCTTG	60.614	57.143	8.52	0.00	44.65	3.02
2577	4330	1.650912	GGCATAGCCGCATGTCAAG	59.349	57.895	0.00	0.00	39.62	3.02
2929	5494	6.677781	ATACATACAATTCAAGGGTGAACG	57.322	37.500	0.00	0.00	46.40	3.95
2949	5514	6.956299	AAGCTTCAAATGTGAATGCAATAC	57.044	33.333	17.11	0.00	42.85	1.89
3225	5872	4.801147	TTAGATGCACGAAAGATGATGC	57.199	40.909	0.00	0.00	38.59	3.91
3238	5885	3.939740	ATTGGAGAGCCTTTAGATGCA	57.060	42.857	0.00	0.00	34.31	3.96
3387	6104	3.958798	CTGAAAGGGCATCTGGAATTGAT	59.041	43.478	0.00	0.00	0.00	2.57
3409	6126	5.877012	ACATGACTGTCAATGATGGTAACTC	59.123	40.000	15.31	0.00	37.61	3.01
3445	6167	8.930527	TGTCTGCTAATTAGTTAGGGCTAATTA	58.069	33.333	13.91	13.98	44.89	1.40
3472	6214	3.991773	GTGTCCGAGTGTGTAAATAAGCA	59.008	43.478	0.00	0.00	0.00	3.91
3605	6359	2.158769	AGGAAAGCACATCAGACACACA	60.159	45.455	0.00	0.00	0.00	3.72
3614	6368	6.112058	ACAAATCTCTAGAGGAAAGCACATC	58.888	40.000	19.67	0.00	0.00	3.06
3617	6371	5.580297	CAGACAAATCTCTAGAGGAAAGCAC	59.420	44.000	19.67	6.71	30.42	4.40
3620	6374	5.115480	GCCAGACAAATCTCTAGAGGAAAG	58.885	45.833	19.67	10.14	30.42	2.62
3768	6522	9.590451	CAAGTTAATTAATGAAGTCCATGCAAT	57.410	29.630	0.31	0.00	35.24	3.56
3771	6525	7.547227	ACCAAGTTAATTAATGAAGTCCATGC	58.453	34.615	0.31	0.00	35.24	4.06
3772	6526	8.190784	GGACCAAGTTAATTAATGAAGTCCATG	58.809	37.037	22.60	6.72	39.83	3.66
3773	6527	8.116026	AGGACCAAGTTAATTAATGAAGTCCAT	58.884	33.333	25.92	16.23	41.98	3.41
3774	6528	7.466804	AGGACCAAGTTAATTAATGAAGTCCA	58.533	34.615	25.92	0.00	41.98	4.02
3932	6738	3.100671	AGAACAAGACTAGTAGGGCCAG	58.899	50.000	6.18	0.00	0.00	4.85
4008	6820	0.669619	CATTGTTGTGTGCTGGCTCA	59.330	50.000	0.00	0.00	0.00	4.26
4158	6972	3.616821	CGGCGATTCTCAACTATTCACAA	59.383	43.478	0.00	0.00	0.00	3.33
4164	6978	2.167693	TGAACCGGCGATTCTCAACTAT	59.832	45.455	16.09	0.00	0.00	2.12
4292	7106	2.417719	GAATGAGACCGCAACTTCACT	58.582	47.619	0.00	0.00	0.00	3.41
4479	7342	4.336433	CGATCCTTGCAGTAACCAATCATT	59.664	41.667	0.00	0.00	0.00	2.57
4569	7432	8.724229	CCTTTTTGTTAGCCGTAGTTAGTATTT	58.276	33.333	0.00	0.00	0.00	1.40
4606	7469	7.862873	CGACTTGAGCATTCACTATATGAGTTA	59.137	37.037	0.00	0.00	38.99	2.24
4625	7488	2.391724	GAACCACTGGGGCGACTTGA	62.392	60.000	0.00	0.00	42.05	3.02
4636	7499	1.971357	AGTACCTCAGGTGAACCACTG	59.029	52.381	6.61	0.00	36.19	3.66
4784	7664	7.339466	ACAAAAGTAGGCCATAACTATTGAAGG	59.661	37.037	5.01	0.00	0.00	3.46
4804	7684	3.191371	GTGCCTCTGGGTGAATACAAAAG	59.809	47.826	0.00	0.00	34.45	2.27
4833	7713	2.696707	AGTCAAATGCATGCCCAATAGG	59.303	45.455	16.68	0.00	39.47	2.57
4980	7860	1.603456	TCGTCAAGCCAAAATCAGCA	58.397	45.000	0.00	0.00	0.00	4.41
5058	7938	2.068834	ACTCCGGATCAACGTATCCT	57.931	50.000	3.57	0.00	42.91	3.24
5061	7941	2.621998	CTGGTACTCCGGATCAACGTAT	59.378	50.000	3.57	0.00	42.46	3.06
5094	7974	2.027625	GTCGCTCTTGGTCGTTGGG	61.028	63.158	0.00	0.00	0.00	4.12
5709	8589	3.634448	CACTCCTCTCCATCGAGTTGTAT	59.366	47.826	0.00	0.00	34.65	2.29
5713	9156	2.223803	ACACTCCTCTCCATCGAGTT	57.776	50.000	0.00	0.00	34.65	3.01
5749	9196	1.745141	GCCAGGTTCTGCTCATGGTAG	60.745	57.143	0.00	0.00	33.42	3.18
5786	9233	1.066929	TGTGAGATGTGACGGTGATGG	60.067	52.381	0.00	0.00	0.00	3.51
5799	9246	1.649664	GAAGCTGCATCGTGTGAGAT	58.350	50.000	1.02	0.00	0.00	2.75
5843	9291	4.848299	GTCTGCTTCATTTGCTTTCTAACG	59.152	41.667	0.00	0.00	0.00	3.18
5968	9420	0.947244	CAGTCAGTGTGTTCTTGCCC	59.053	55.000	0.00	0.00	0.00	5.36
6076	9532	8.503428	AGATAAATGACTGTTCTATCCCAGAT	57.497	34.615	0.00	0.00	31.77	2.90
6097	9555	4.242475	CGCAACTGGTGTCTGTTTAGATA	58.758	43.478	0.00	0.00	34.94	1.98
6102	9560	1.724582	GCCGCAACTGGTGTCTGTTT	61.725	55.000	0.00	0.00	33.65	2.83
6130	9588	5.570205	TTTGGTTGGGTAGTCTGTATTCA	57.430	39.130	0.00	0.00	0.00	2.57
6133	9591	6.630203	TGTATTTGGTTGGGTAGTCTGTAT	57.370	37.500	0.00	0.00	0.00	2.29
6137	9595	5.497474	GTCATGTATTTGGTTGGGTAGTCT	58.503	41.667	0.00	0.00	0.00	3.24
6193	9651	5.642063	CGCTTGTCTGGTTTCCTTCTTTATA	59.358	40.000	0.00	0.00	0.00	0.98
6194	9652	4.455877	CGCTTGTCTGGTTTCCTTCTTTAT	59.544	41.667	0.00	0.00	0.00	1.40
6195	9653	3.813166	CGCTTGTCTGGTTTCCTTCTTTA	59.187	43.478	0.00	0.00	0.00	1.85
6196	9654	2.618709	CGCTTGTCTGGTTTCCTTCTTT	59.381	45.455	0.00	0.00	0.00	2.52
6197	9655	2.222027	CGCTTGTCTGGTTTCCTTCTT	58.778	47.619	0.00	0.00	0.00	2.52
6198	9656	1.884235	CGCTTGTCTGGTTTCCTTCT	58.116	50.000	0.00	0.00	0.00	2.85
6237	9695	9.772973	TCAATTTACTCTCTGCAGTAGTTTTAA	57.227	29.630	23.16	16.73	30.40	1.52
6246	9704	5.112686	GGGTACTCAATTTACTCTCTGCAG	58.887	45.833	7.63	7.63	0.00	4.41
6324	9783	9.131791	AGGGTTATTAACATGTTAATGATGGAC	57.868	33.333	37.17	27.80	43.36	4.02
6390	9849	2.907910	AATCAGCTCGTGAAATGCAC	57.092	45.000	0.00	0.00	44.21	4.57
6426	9885	1.407258	CCCAAGTGGAAAGTCGCAAAA	59.593	47.619	0.00	0.00	37.39	2.44
6533	9993	3.197614	CGGCTAGGAGACGCTTGA	58.802	61.111	0.00	0.00	41.27	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.