AutoCloner

Multiple sequence alignment - TraesCS2D01G002500

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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	TraesCS2D01G002500	chr2D	100.000	3434	0	0	1	3434	2013184	2016617	0.000000e+00	6342.0
1	TraesCS2D01G002500	chr2D	87.895	950	88	22	2492	3434	102715218	102716147	0.000000e+00	1092.0
2	TraesCS2D01G002500	chr2D	85.417	288	34	5	1018	1298	2237396	2237682	3.350000e-75	292.0
3	TraesCS2D01G002500	chr2D	84.681	235	19	3	566	800	2165232	2165449	5.770000e-53	219.0
4	TraesCS2D01G002500	chr2D	89.262	149	15	1	30	178	2150237	2150384	5.850000e-43	185.0
5	TraesCS2D01G002500	chr2D	94.828	58	3	0	825	882	4326044	4326101	1.310000e-14	91.6
6	TraesCS2D01G002500	chr2D	94.828	58	3	0	825	882	4351238	4351295	1.310000e-14	91.6
7	TraesCS2D01G002500	chr2D	94.828	58	3	0	825	882	4382762	4382819	1.310000e-14	91.6
8	TraesCS2D01G002500	chr2B	94.671	1201	64	0	1292	2492	477607	478807	0.000000e+00	1864.0
9	TraesCS2D01G002500	chr2B	93.959	1225	50	1	1292	2492	64317	65541	0.000000e+00	1831.0
10	TraesCS2D01G002500	chr2B	92.816	1225	54	5	1292	2492	178574	179788	0.000000e+00	1744.0
11	TraesCS2D01G002500	chr2B	94.212	933	26	13	2495	3425	359504081	359503175	0.000000e+00	1399.0
12	TraesCS2D01G002500	chr2B	95.694	627	23	4	676	1302	63610	64232	0.000000e+00	1005.0
13	TraesCS2D01G002500	chr2B	95.534	627	24	4	676	1302	177867	178489	0.000000e+00	1000.0
14	TraesCS2D01G002500	chr2B	81.029	1186	194	17	1291	2466	9198665	9197501	0.000000e+00	915.0
15	TraesCS2D01G002500	chr2B	96.118	541	18	3	762	1302	476985	477522	0.000000e+00	880.0
16	TraesCS2D01G002500	chr2B	79.647	1189	204	27	1291	2466	30989798	30988635	0.000000e+00	821.0
17	TraesCS2D01G002500	chr2B	79.664	1190	199	35	1291	2466	31048232	31049392	0.000000e+00	817.0
18	TraesCS2D01G002500	chr2B	78.822	1138	204	20	1348	2474	6731900	6730789	0.000000e+00	732.0
19	TraesCS2D01G002500	chr2B	83.737	289	37	8	1018	1298	1329932	1330218	7.310000e-67	265.0
20	TraesCS2D01G002500	chr2B	91.111	180	15	1	1	180	476771	476949	3.420000e-60	243.0
21	TraesCS2D01G002500	chr2B	89.130	184	14	5	1	180	63416	63597	1.240000e-54	224.0
22	TraesCS2D01G002500	chr2B	89.130	184	14	5	1	180	177673	177854	1.240000e-54	224.0
23	TraesCS2D01G002500	chr2B	91.667	60	4	1	824	882	6779690	6779631	7.900000e-12	82.4
24	TraesCS2D01G002500	chr2A	91.590	1201	91	1	1292	2492	1915935	1917125	0.000000e+00	1650.0
25	TraesCS2D01G002500	chr2A	90.411	730	59	6	1708	2434	1884701	1885422	0.000000e+00	950.0
26	TraesCS2D01G002500	chr2A	80.808	1188	192	22	1291	2466	2876592	2877755	0.000000e+00	898.0
27	TraesCS2D01G002500	chr2A	84.493	503	57	3	1292	1794	1884223	1884704	8.620000e-131	477.0
28	TraesCS2D01G002500	chr2A	87.437	398	36	5	897	1294	1883749	1884132	2.430000e-121	446.0
29	TraesCS2D01G002500	chr2A	84.350	377	24	12	209	574	1882340	1882692	1.530000e-88	337.0
30	TraesCS2D01G002500	chr2A	91.429	210	10	1	2	211	1908273	1908474	7.260000e-72	281.0
31	TraesCS2D01G002500	chr2A	84.946	279	34	5	1023	1294	2405968	2406245	3.380000e-70	276.0
32	TraesCS2D01G002500	chr2A	83.468	248	16	12	676	911	1882749	1882983	1.250000e-49	207.0
33	TraesCS2D01G002500	chr2A	82.110	218	27	8	1	207	1881863	1882079	3.520000e-40	176.0
34	TraesCS2D01G002500	chrUn	95.718	864	29	4	2573	3434	325526514	325527371	0.000000e+00	1384.0
35	TraesCS2D01G002500	chrUn	87.083	929	95	20	2506	3425	201290054	201290966	0.000000e+00	1027.0
36	TraesCS2D01G002500	chrUn	86.972	284	29	5	1018	1294	15864958	15865240	2.570000e-81	313.0
37	TraesCS2D01G002500	chrUn	91.667	60	4	1	824	882	339338959	339338900	7.900000e-12	82.4
38	TraesCS2D01G002500	chr3A	90.612	948	74	12	2495	3434	726399638	726400578	0.000000e+00	1243.0
39	TraesCS2D01G002500	chr4D	90.399	927	80	8	2511	3434	222413715	222414635	0.000000e+00	1210.0
40	TraesCS2D01G002500	chr5D	96.518	718	22	3	2720	3434	2601277	2600560	0.000000e+00	1184.0
41	TraesCS2D01G002500	chr6B	87.432	923	89	22	2513	3425	558817412	558818317	0.000000e+00	1037.0
42	TraesCS2D01G002500	chr5B	87.177	928	97	19	2506	3425	497221339	497222252	0.000000e+00	1035.0
43	TraesCS2D01G002500	chr3D	86.282	277	38	0	1022	1298	1347326	1347050	5.570000e-78	302.0

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	TraesCS2D01G002500	chr2D	2013184	2016617	3433	False	6342.000000	6342	100.000000	1	3434	1	chr2D.!!$F1	3433
1	TraesCS2D01G002500	chr2D	102715218	102716147	929	False	1092.000000	1092	87.895000	2492	3434	1	chr2D.!!$F8	942
2	TraesCS2D01G002500	chr2B	359503175	359504081	906	True	1399.000000	1399	94.212000	2495	3425	1	chr2B.!!$R5	930
3	TraesCS2D01G002500	chr2B	63416	65541	2125	False	1020.000000	1831	92.927667	1	2492	3	chr2B.!!$F3	2491
4	TraesCS2D01G002500	chr2B	476771	478807	2036	False	995.666667	1864	93.966667	1	2492	3	chr2B.!!$F5	2491
5	TraesCS2D01G002500	chr2B	177673	179788	2115	False	989.333333	1744	92.493333	1	2492	3	chr2B.!!$F4	2491
6	TraesCS2D01G002500	chr2B	9197501	9198665	1164	True	915.000000	915	81.029000	1291	2466	1	chr2B.!!$R3	1175
7	TraesCS2D01G002500	chr2B	30988635	30989798	1163	True	821.000000	821	79.647000	1291	2466	1	chr2B.!!$R4	1175
8	TraesCS2D01G002500	chr2B	31048232	31049392	1160	False	817.000000	817	79.664000	1291	2466	1	chr2B.!!$F2	1175
9	TraesCS2D01G002500	chr2B	6730789	6731900	1111	True	732.000000	732	78.822000	1348	2474	1	chr2B.!!$R1	1126
10	TraesCS2D01G002500	chr2A	1915935	1917125	1190	False	1650.000000	1650	91.590000	1292	2492	1	chr2A.!!$F2	1200
11	TraesCS2D01G002500	chr2A	2876592	2877755	1163	False	898.000000	898	80.808000	1291	2466	1	chr2A.!!$F4	1175
12	TraesCS2D01G002500	chr2A	1881863	1885422	3559	False	432.166667	950	85.378167	1	2434	6	chr2A.!!$F5	2433
13	TraesCS2D01G002500	chrUn	325526514	325527371	857	False	1384.000000	1384	95.718000	2573	3434	1	chrUn.!!$F3	861
14	TraesCS2D01G002500	chrUn	201290054	201290966	912	False	1027.000000	1027	87.083000	2506	3425	1	chrUn.!!$F2	919
15	TraesCS2D01G002500	chr3A	726399638	726400578	940	False	1243.000000	1243	90.612000	2495	3434	1	chr3A.!!$F1	939
16	TraesCS2D01G002500	chr4D	222413715	222414635	920	False	1210.000000	1210	90.399000	2511	3434	1	chr4D.!!$F1	923
17	TraesCS2D01G002500	chr5D	2600560	2601277	717	True	1184.000000	1184	96.518000	2720	3434	1	chr5D.!!$R1	714
18	TraesCS2D01G002500	chr6B	558817412	558818317	905	False	1037.000000	1037	87.432000	2513	3425	1	chr6B.!!$F1	912
19	TraesCS2D01G002500	chr5B	497221339	497222252	913	False	1035.000000	1035	87.177000	2506	3425	1	chr5B.!!$F1	919

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
604	911	0.528924	ATCACACATGCCATGCACAC	59.471	50.0	4.17	43.04	3.82	F
1236	2334	0.389948	GGATGCGGTTCTTCGTCACT	60.390	55.0	0.00	0.00	3.41	F
1607	2892	0.108329	AGGTGGCTAAACATCGGTCG	60.108	55.0	0.00	0.00	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1528	2813	0.257039	AATCCCACCTCCATGACTGC	59.743	55.000	0.00	0.00	4.40	R
2059	3511	1.470805	CGGCATAATATCATCGGCGGA	60.471	52.381	7.21	41.37	5.54	R
2874	4339	3.195610	CCTTCTTATTTTTCCCACTGGGC	59.804	47.826	9.60	43.94	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
54	55	2.258755	CATGCACGTACGAACAGATGA	58.741	47.619	24.41	0.00	0.00	2.92
86	87	1.545582	TGCAATTTACTTCAGCCAGCC	59.454	47.619	0.00	0.00	0.00	4.85
106	107	1.290955	GGCACACAGTACTGCCGTA	59.709	57.895	22.90	0.00	43.56	4.02
107	110	0.736325	GGCACACAGTACTGCCGTAG	60.736	60.000	22.90	14.34	43.56	3.51
108	111	1.352156	GCACACAGTACTGCCGTAGC	61.352	60.000	22.90	18.99	40.48	3.58
158	161	9.508567	GGACAATTGAGAAAATTATAAGTCAGC	57.491	33.333	13.59	0.00	0.00	4.26
167	170	3.507103	TTATAAGTCAGCGCCGTACAA	57.493	42.857	2.29	0.00	0.00	2.41
170	173	0.796312	AAGTCAGCGCCGTACAAATG	59.204	50.000	2.29	0.00	0.00	2.32
176	184	2.095969	CAGCGCCGTACAAATGAGAAAA	60.096	45.455	2.29	0.00	0.00	2.29
191	228	0.592247	GAAAATATGCACGCGGCCAG	60.592	55.000	12.47	0.00	43.89	4.85
193	230	1.714899	AAATATGCACGCGGCCAGAC	61.715	55.000	12.47	0.00	43.89	3.51
207	244	0.953471	CCAGACGGGTCGATTGCAAA	60.953	55.000	1.71	0.00	34.09	3.68
214	510	5.408604	AGACGGGTCGATTGCAAATATATTC	59.591	40.000	1.71	0.00	34.09	1.75
238	537	3.790126	ACCTTTGCCATCCTAAACCATT	58.210	40.909	0.00	0.00	0.00	3.16
260	559	2.292267	CAGTCTTATGGTGGCCACATC	58.708	52.381	35.78	20.74	35.80	3.06
264	563	0.747644	TTATGGTGGCCACATCGCTG	60.748	55.000	35.78	0.00	35.80	5.18
265	564	2.607411	TATGGTGGCCACATCGCTGG	62.607	60.000	35.78	0.00	35.80	4.85
268	567	3.321648	TGGCCACATCGCTGGAGT	61.322	61.111	0.00	0.00	32.30	3.85
287	586	2.293677	AGTGTGTACTTGACCGAGACTG	59.706	50.000	0.00	0.00	31.66	3.51
319	618	1.702299	CTGGCGATCAACGTTCGAC	59.298	57.895	12.06	9.60	44.92	4.20
332	631	1.450905	CGTTCGACGTCAACCTCTTTC	59.549	52.381	17.16	0.00	36.74	2.62
348	647	5.208503	CCTCTTTCTTCTTTTTCTTGACGC	58.791	41.667	0.00	0.00	0.00	5.19
355	654	2.157668	TCTTTTTCTTGACGCGATGAGC	59.842	45.455	15.93	0.00	43.95	4.26
366	665	4.925861	GATGAGCAGCCGGGAGCC	62.926	72.222	2.18	0.00	45.47	4.70
419	718	2.424956	GTGGGCATGGAGAATTCAAGTC	59.575	50.000	8.44	0.00	0.00	3.01
422	721	1.672881	GCATGGAGAATTCAAGTCGGG	59.327	52.381	8.44	0.00	0.00	5.14
431	730	0.601558	TTCAAGTCGGGAAGGAGACG	59.398	55.000	0.00	0.00	41.86	4.18
450	749	1.525995	CCACCACGCTTTCACCACT	60.526	57.895	0.00	0.00	0.00	4.00
471	770	3.566130	GCTATGAGCCCATCCATCC	57.434	57.895	0.00	0.00	34.48	3.51
473	772	1.074405	GCTATGAGCCCATCCATCCAA	59.926	52.381	0.00	0.00	34.48	3.53
491	790	3.118482	TCCAAAAGTTTGAGCCAATGCAA	60.118	39.130	5.34	0.00	40.55	4.08
501	800	4.449131	TGAGCCAATGCAAAACAAAATCA	58.551	34.783	0.00	0.00	41.13	2.57
576	883	6.358178	TCGATAGATGTCACTCTCCTTAGTT	58.642	40.000	0.00	0.00	42.67	2.24
577	884	6.261158	TCGATAGATGTCACTCTCCTTAGTTG	59.739	42.308	0.00	0.00	42.67	3.16
578	885	6.514212	CGATAGATGTCACTCTCCTTAGTTGG	60.514	46.154	0.00	0.00	39.76	3.77
579	886	4.678256	AGATGTCACTCTCCTTAGTTGGA	58.322	43.478	0.00	0.00	34.52	3.53
590	897	6.531503	CTCCTTAGTTGGAGTAGAATCACA	57.468	41.667	2.62	0.00	46.33	3.58
591	898	6.282199	TCCTTAGTTGGAGTAGAATCACAC	57.718	41.667	0.00	0.00	0.00	3.82
592	899	5.778241	TCCTTAGTTGGAGTAGAATCACACA	59.222	40.000	0.00	0.00	0.00	3.72
593	900	6.440647	TCCTTAGTTGGAGTAGAATCACACAT	59.559	38.462	0.00	0.00	0.00	3.21
594	901	6.536582	CCTTAGTTGGAGTAGAATCACACATG	59.463	42.308	0.00	0.00	0.00	3.21
595	902	4.256920	AGTTGGAGTAGAATCACACATGC	58.743	43.478	0.00	0.00	0.00	4.06
596	903	3.266510	TGGAGTAGAATCACACATGCC	57.733	47.619	0.00	0.00	0.00	4.40
597	904	2.571202	TGGAGTAGAATCACACATGCCA	59.429	45.455	0.00	0.00	0.00	4.92
598	905	3.200605	TGGAGTAGAATCACACATGCCAT	59.799	43.478	0.00	0.00	0.00	4.40
599	906	3.562973	GGAGTAGAATCACACATGCCATG	59.437	47.826	2.40	2.40	0.00	3.66
600	907	2.947652	AGTAGAATCACACATGCCATGC	59.052	45.455	4.17	0.00	0.00	4.06
601	908	1.842052	AGAATCACACATGCCATGCA	58.158	45.000	4.17	0.00	44.86	3.96
602	909	1.475280	AGAATCACACATGCCATGCAC	59.525	47.619	4.17	0.00	43.04	4.57
603	910	1.202817	GAATCACACATGCCATGCACA	59.797	47.619	4.17	0.00	43.04	4.57
604	911	0.528924	ATCACACATGCCATGCACAC	59.471	50.000	4.17	0.00	43.04	3.82
614	921	1.332997	GCCATGCACACTTCTAGCATC	59.667	52.381	0.00	0.00	46.39	3.91
620	927	3.769300	TGCACACTTCTAGCATCTTCCTA	59.231	43.478	0.00	0.00	32.55	2.94
630	937	8.948631	TTCTAGCATCTTCCTAATTACAAGTG	57.051	34.615	0.00	0.00	0.00	3.16
632	939	8.198109	TCTAGCATCTTCCTAATTACAAGTGTC	58.802	37.037	0.00	0.00	0.00	3.67
633	940	6.951971	AGCATCTTCCTAATTACAAGTGTCT	58.048	36.000	0.00	0.00	0.00	3.41
634	941	7.044798	AGCATCTTCCTAATTACAAGTGTCTC	58.955	38.462	0.00	0.00	0.00	3.36
635	942	7.044798	GCATCTTCCTAATTACAAGTGTCTCT	58.955	38.462	0.00	0.00	0.00	3.10
636	943	7.010923	GCATCTTCCTAATTACAAGTGTCTCTG	59.989	40.741	0.00	0.00	0.00	3.35
637	944	6.398918	TCTTCCTAATTACAAGTGTCTCTGC	58.601	40.000	0.00	0.00	0.00	4.26
638	945	6.211584	TCTTCCTAATTACAAGTGTCTCTGCT	59.788	38.462	0.00	0.00	0.00	4.24
639	946	5.724328	TCCTAATTACAAGTGTCTCTGCTG	58.276	41.667	0.00	0.00	0.00	4.41
640	947	5.480422	TCCTAATTACAAGTGTCTCTGCTGA	59.520	40.000	0.00	0.00	0.00	4.26
642	949	6.312426	CCTAATTACAAGTGTCTCTGCTGAAG	59.688	42.308	0.00	0.00	0.00	3.02
643	950	4.937201	TTACAAGTGTCTCTGCTGAAGA	57.063	40.909	0.00	0.00	0.00	2.87
646	953	3.873952	ACAAGTGTCTCTGCTGAAGAAAC	59.126	43.478	0.00	0.84	33.37	2.78
647	954	4.125703	CAAGTGTCTCTGCTGAAGAAACT	58.874	43.478	8.88	8.88	33.37	2.66
648	955	5.163405	ACAAGTGTCTCTGCTGAAGAAACTA	60.163	40.000	12.77	0.00	33.37	2.24
649	956	4.877282	AGTGTCTCTGCTGAAGAAACTAC	58.123	43.478	11.51	0.00	33.37	2.73
651	958	4.920927	GTGTCTCTGCTGAAGAAACTACTC	59.079	45.833	0.00	0.00	33.37	2.59
652	959	4.021894	TGTCTCTGCTGAAGAAACTACTCC	60.022	45.833	0.00	0.00	33.37	3.85
653	960	4.021894	GTCTCTGCTGAAGAAACTACTCCA	60.022	45.833	0.00	0.00	33.37	3.86
654	961	4.588951	TCTCTGCTGAAGAAACTACTCCAA	59.411	41.667	0.00	0.00	33.37	3.53
655	962	4.632153	TCTGCTGAAGAAACTACTCCAAC	58.368	43.478	0.00	0.00	29.54	3.77
656	963	4.345257	TCTGCTGAAGAAACTACTCCAACT	59.655	41.667	0.00	0.00	29.54	3.16
658	965	5.539048	TGCTGAAGAAACTACTCCAACTAC	58.461	41.667	0.00	0.00	0.00	2.73
659	966	5.304614	TGCTGAAGAAACTACTCCAACTACT	59.695	40.000	0.00	0.00	0.00	2.57
660	967	5.635700	GCTGAAGAAACTACTCCAACTACTG	59.364	44.000	0.00	0.00	0.00	2.74
717	1024	1.734117	GCACATGGCTTGCGAAACC	60.734	57.895	0.00	0.00	40.25	3.27
723	1030	1.610363	TGGCTTGCGAAACCATGTAA	58.390	45.000	0.00	0.00	0.00	2.41
736	1043	4.789012	ACCATGTAAGCAAAAGATGTGG	57.211	40.909	0.00	0.00	0.00	4.17
782	1089	6.385467	ACTGAAGAGCTAGGTTAGGATTGATT	59.615	38.462	0.00	0.00	0.00	2.57
968	2066	4.407945	AGCCACGTCCATTATAAAGGTAGT	59.592	41.667	6.63	5.56	0.00	2.73
998	2096	3.315191	ACACTACTGCCAACAATGTCAAC	59.685	43.478	0.00	0.00	0.00	3.18
1042	2140	4.098155	TGTGCTACTTGTTCCCCTATACA	58.902	43.478	0.00	0.00	0.00	2.29
1173	2271	1.949847	ATCTCACCTTGGTCCTCGCG	61.950	60.000	0.00	0.00	0.00	5.87
1236	2334	0.389948	GGATGCGGTTCTTCGTCACT	60.390	55.000	0.00	0.00	0.00	3.41
1356	2640	2.124109	TGCCGCAACAAGGTGGAA	60.124	55.556	0.00	0.00	41.00	3.53
1444	2729	5.547465	TGATGTCGAGGTTTATGTTTGACT	58.453	37.500	0.00	0.00	0.00	3.41
1528	2813	1.571460	GCTGTGGTTGCTCTGAACG	59.429	57.895	0.00	0.00	0.00	3.95
1607	2892	0.108329	AGGTGGCTAAACATCGGTCG	60.108	55.000	0.00	0.00	0.00	4.79
1774	3220	4.710375	TGTCTTCCTACCCAGACTATGTTC	59.290	45.833	1.31	0.00	40.24	3.18
1816	3262	4.418392	CAAGAACATTGGCTACATGCTTC	58.582	43.478	0.00	0.00	42.39	3.86
1876	3328	0.320073	TTACAACCTCGCCCAGAACG	60.320	55.000	0.00	0.00	0.00	3.95
2035	3487	2.173519	CTCTTAGGTTGTACCCACCGA	58.826	52.381	5.83	0.00	39.75	4.69
2172	3624	2.100197	TGGGGTAATGACTGTCTCGAG	58.900	52.381	5.93	5.93	0.00	4.04
2195	3647	1.972588	AACCCAGATAGGTGGCTCTT	58.027	50.000	0.00	0.00	40.05	2.85
2252	3704	3.131046	CACAAGTTCTTGGCCTTCAACTT	59.869	43.478	16.35	16.35	39.20	2.66
2443	3898	8.200792	AGAAGCGAGAGATGTAACATTAGATTT	58.799	33.333	0.00	0.00	0.00	2.17
2521	3980	3.761752	AGAGGAAAAACGAGAGAGAGAGG	59.238	47.826	0.00	0.00	0.00	3.69
2522	3981	2.829120	AGGAAAAACGAGAGAGAGAGGG	59.171	50.000	0.00	0.00	0.00	4.30
2525	3984	3.945981	AAAACGAGAGAGAGAGGGAAC	57.054	47.619	0.00	0.00	0.00	3.62
2570	4029	7.989741	GTCTTCTCATTGATTGAAGATTAGGGA	59.010	37.037	16.79	0.00	44.98	4.20
2653	4114	7.492669	CCGACATAGCAGGGATTAACATATTAG	59.507	40.741	0.00	0.00	0.00	1.73
2717	4178	3.441572	GCTTGTCCTTGTGAGTATGCATT	59.558	43.478	3.54	0.00	0.00	3.56
2978	4446	7.998964	ACCTTTGAAGAAGGAGAAAACTCATTA	59.001	33.333	11.52	0.00	39.81	1.90
3029	4497	9.752961	GCTTTGTATACTTTCCTTTAAAAACCA	57.247	29.630	4.17	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	49	0.992072	CAAGGCACGTACGTCATCTG	59.008	55.000	19.94	8.27	0.00	2.90
54	55	0.948678	AAATTGCAAGGCACGTACGT	59.051	45.000	16.72	16.72	38.71	3.57
158	161	4.670621	GCATATTTTCTCATTTGTACGGCG	59.329	41.667	4.80	4.80	0.00	6.46
167	170	2.541588	GCCGCGTGCATATTTTCTCATT	60.542	45.455	13.61	0.00	40.77	2.57
170	173	0.317020	GGCCGCGTGCATATTTTCTC	60.317	55.000	18.87	0.00	43.89	2.87
176	184	2.588877	GTCTGGCCGCGTGCATAT	60.589	61.111	18.87	0.00	43.89	1.78
191	228	5.408604	AGAATATATTTGCAATCGACCCGTC	59.591	40.000	0.00	0.00	0.00	4.79
193	230	5.862924	AGAATATATTTGCAATCGACCCG	57.137	39.130	0.00	0.00	0.00	5.28
214	510	4.340617	TGGTTTAGGATGGCAAAGGTTAG	58.659	43.478	0.00	0.00	0.00	2.34
222	518	2.101783	CTGCAATGGTTTAGGATGGCA	58.898	47.619	0.00	0.00	0.00	4.92
238	537	0.322456	GTGGCCACCATAAGACTGCA	60.322	55.000	26.31	0.00	35.28	4.41
251	550	3.321648	ACTCCAGCGATGTGGCCA	61.322	61.111	0.00	0.00	37.53	5.36
252	551	2.821366	CACTCCAGCGATGTGGCC	60.821	66.667	0.00	0.00	37.53	5.36
253	552	2.046892	ACACTCCAGCGATGTGGC	60.047	61.111	0.00	0.00	37.53	5.01
260	559	1.419374	GTCAAGTACACACTCCAGCG	58.581	55.000	0.00	0.00	32.29	5.18
264	563	1.884579	TCTCGGTCAAGTACACACTCC	59.115	52.381	0.00	0.00	32.29	3.85
265	564	2.553172	AGTCTCGGTCAAGTACACACTC	59.447	50.000	0.00	0.00	32.29	3.51
268	567	2.034179	CACAGTCTCGGTCAAGTACACA	59.966	50.000	0.00	0.00	0.00	3.72
287	586	3.297620	CCAGCCAAGCCACACCAC	61.298	66.667	0.00	0.00	0.00	4.16
319	618	6.364945	AGAAAAAGAAGAAAGAGGTTGACG	57.635	37.500	0.00	0.00	0.00	4.35
320	619	7.698550	GTCAAGAAAAAGAAGAAAGAGGTTGAC	59.301	37.037	0.00	0.00	34.12	3.18
323	622	6.678164	GCGTCAAGAAAAAGAAGAAAGAGGTT	60.678	38.462	0.00	0.00	0.00	3.50
332	631	4.389645	CTCATCGCGTCAAGAAAAAGAAG	58.610	43.478	5.77	0.00	0.00	2.85
370	669	4.899239	CTGAGCCCCGACGATGCC	62.899	72.222	0.00	0.00	0.00	4.40
371	670	3.838271	TCTGAGCCCCGACGATGC	61.838	66.667	0.00	0.00	0.00	3.91
372	671	2.105128	GTCTGAGCCCCGACGATG	59.895	66.667	0.00	0.00	0.00	3.84
419	718	4.452733	GGTGGCGTCTCCTTCCCG	62.453	72.222	0.00	0.00	35.26	5.14
422	721	2.432628	CGTGGTGGCGTCTCCTTC	60.433	66.667	9.85	2.13	35.26	3.46
431	730	2.904866	TGGTGAAAGCGTGGTGGC	60.905	61.111	0.00	0.00	36.92	5.01
469	768	2.433604	TGCATTGGCTCAAACTTTTGGA	59.566	40.909	1.94	0.00	41.91	3.53
471	770	4.879104	TTTGCATTGGCTCAAACTTTTG	57.121	36.364	0.00	0.00	41.91	2.44
473	772	4.260170	TGTTTTGCATTGGCTCAAACTTT	58.740	34.783	8.81	0.00	41.04	2.66
574	881	3.375299	GGCATGTGTGATTCTACTCCAAC	59.625	47.826	0.00	0.00	0.00	3.77
576	883	2.571202	TGGCATGTGTGATTCTACTCCA	59.429	45.455	0.00	0.00	0.00	3.86
577	884	3.266510	TGGCATGTGTGATTCTACTCC	57.733	47.619	0.00	0.00	0.00	3.85
578	885	3.003068	GCATGGCATGTGTGATTCTACTC	59.997	47.826	26.94	3.45	0.00	2.59
579	886	2.947652	GCATGGCATGTGTGATTCTACT	59.052	45.455	26.94	0.00	0.00	2.57
580	887	2.684374	TGCATGGCATGTGTGATTCTAC	59.316	45.455	26.94	8.20	31.71	2.59
581	888	2.684374	GTGCATGGCATGTGTGATTCTA	59.316	45.455	26.94	2.22	41.91	2.10
582	889	1.475280	GTGCATGGCATGTGTGATTCT	59.525	47.619	26.94	0.00	41.91	2.40
583	890	1.202817	TGTGCATGGCATGTGTGATTC	59.797	47.619	26.94	10.28	41.91	2.52
584	891	1.067425	GTGTGCATGGCATGTGTGATT	60.067	47.619	26.94	0.00	41.91	2.57
585	892	0.528924	GTGTGCATGGCATGTGTGAT	59.471	50.000	26.94	0.00	41.91	3.06
586	893	0.537828	AGTGTGCATGGCATGTGTGA	60.538	50.000	26.94	7.79	41.91	3.58
587	894	0.315886	AAGTGTGCATGGCATGTGTG	59.684	50.000	26.94	5.35	41.91	3.82
588	895	0.599558	GAAGTGTGCATGGCATGTGT	59.400	50.000	26.94	7.70	41.91	3.72
589	896	0.885879	AGAAGTGTGCATGGCATGTG	59.114	50.000	26.94	6.53	41.91	3.21
590	897	2.362736	CTAGAAGTGTGCATGGCATGT	58.637	47.619	26.94	7.53	41.91	3.21
591	898	1.065102	GCTAGAAGTGTGCATGGCATG	59.935	52.381	22.99	22.99	41.91	4.06
592	899	1.340308	TGCTAGAAGTGTGCATGGCAT	60.340	47.619	0.00	0.00	41.91	4.40
593	900	0.036590	TGCTAGAAGTGTGCATGGCA	59.963	50.000	0.00	0.00	35.60	4.92
594	901	1.332997	GATGCTAGAAGTGTGCATGGC	59.667	52.381	4.36	0.00	45.90	4.40
595	902	2.915349	AGATGCTAGAAGTGTGCATGG	58.085	47.619	4.36	0.00	45.90	3.66
596	903	3.311871	GGAAGATGCTAGAAGTGTGCATG	59.688	47.826	4.36	0.00	45.90	4.06
598	905	2.568956	AGGAAGATGCTAGAAGTGTGCA	59.431	45.455	0.00	0.00	41.13	4.57
599	906	3.258971	AGGAAGATGCTAGAAGTGTGC	57.741	47.619	0.00	0.00	0.00	4.57
600	907	7.981789	TGTAATTAGGAAGATGCTAGAAGTGTG	59.018	37.037	0.00	0.00	0.00	3.82
601	908	8.079211	TGTAATTAGGAAGATGCTAGAAGTGT	57.921	34.615	0.00	0.00	0.00	3.55
602	909	8.948631	TTGTAATTAGGAAGATGCTAGAAGTG	57.051	34.615	0.00	0.00	0.00	3.16
603	910	8.763601	ACTTGTAATTAGGAAGATGCTAGAAGT	58.236	33.333	10.01	0.00	0.00	3.01
604	911	9.039870	CACTTGTAATTAGGAAGATGCTAGAAG	57.960	37.037	10.01	0.00	0.00	2.85
614	921	6.312426	CAGCAGAGACACTTGTAATTAGGAAG	59.688	42.308	3.57	3.57	0.00	3.46
620	927	5.858381	TCTTCAGCAGAGACACTTGTAATT	58.142	37.500	0.00	0.00	0.00	1.40
630	937	4.021894	TGGAGTAGTTTCTTCAGCAGAGAC	60.022	45.833	0.00	0.00	36.96	3.36
632	939	4.527509	TGGAGTAGTTTCTTCAGCAGAG	57.472	45.455	0.00	0.00	31.12	3.35
633	940	4.345257	AGTTGGAGTAGTTTCTTCAGCAGA	59.655	41.667	0.00	0.00	28.54	4.26
634	941	4.636249	AGTTGGAGTAGTTTCTTCAGCAG	58.364	43.478	0.00	0.00	28.54	4.24
635	942	4.689612	AGTTGGAGTAGTTTCTTCAGCA	57.310	40.909	0.00	0.00	28.54	4.41
636	943	5.635700	CAGTAGTTGGAGTAGTTTCTTCAGC	59.364	44.000	0.00	0.00	0.00	4.26
652	959	6.028368	CACAGTCGTAATACTCCAGTAGTTG	58.972	44.000	0.00	0.00	39.80	3.16
653	960	5.392811	GCACAGTCGTAATACTCCAGTAGTT	60.393	44.000	0.00	0.00	39.80	2.24
654	961	4.096081	GCACAGTCGTAATACTCCAGTAGT	59.904	45.833	0.00	0.00	42.62	2.73
655	962	4.095932	TGCACAGTCGTAATACTCCAGTAG	59.904	45.833	0.00	0.00	33.52	2.57
656	963	4.011698	TGCACAGTCGTAATACTCCAGTA	58.988	43.478	0.00	0.00	34.67	2.74
658	965	3.179830	GTGCACAGTCGTAATACTCCAG	58.820	50.000	13.17	0.00	0.00	3.86
659	966	2.094390	GGTGCACAGTCGTAATACTCCA	60.094	50.000	20.43	0.00	0.00	3.86
660	967	2.094390	TGGTGCACAGTCGTAATACTCC	60.094	50.000	20.43	0.00	0.00	3.85
661	968	2.921754	GTGGTGCACAGTCGTAATACTC	59.078	50.000	20.43	0.00	34.08	2.59
662	969	2.297880	TGTGGTGCACAGTCGTAATACT	59.702	45.455	20.43	0.00	39.62	2.12
663	970	2.679450	TGTGGTGCACAGTCGTAATAC	58.321	47.619	20.43	3.73	39.62	1.89
665	972	3.999821	TGTGGTGCACAGTCGTAAT	57.000	47.368	20.43	0.00	39.62	1.89
674	981	3.369546	AGTTAGCAAAATGTGGTGCAC	57.630	42.857	8.80	8.80	43.42	4.57
717	1024	5.375417	TGTCCACATCTTTTGCTTACATG	57.625	39.130	0.00	0.00	0.00	3.21
723	1030	2.957402	TCCTGTCCACATCTTTTGCT	57.043	45.000	0.00	0.00	0.00	3.91
736	1043	3.753797	GTCCTTTCCTTGTCATTCCTGTC	59.246	47.826	0.00	0.00	0.00	3.51
968	2066	5.669164	TGTTGGCAGTAGTGTGTGATATA	57.331	39.130	0.00	0.00	0.00	0.86
998	2096	7.191551	CACAAGTAGCATGGAAATGAACATAG	58.808	38.462	0.00	0.00	0.00	2.23
1042	2140	5.389520	TCTACTGCTAGCCTTGAGATACAT	58.610	41.667	13.29	0.00	0.00	2.29
1173	2271	2.369394	CTGAAGTTGTGGCCTAATCCC	58.631	52.381	3.32	0.00	0.00	3.85
1236	2334	0.392461	GGACATTAGCAGGGTCGCAA	60.392	55.000	0.00	0.00	32.39	4.85
1356	2640	3.359950	GAGCAATGGGAGAAGGATGTTT	58.640	45.455	0.00	0.00	0.00	2.83
1444	2729	4.777896	ACCAAAGAGAGACATAGTAGCCAA	59.222	41.667	0.00	0.00	0.00	4.52
1528	2813	0.257039	AATCCCACCTCCATGACTGC	59.743	55.000	0.00	0.00	0.00	4.40
1607	2892	0.588252	TGTGCAGAGCTTTCTTTCGC	59.412	50.000	0.00	0.00	0.00	4.70
1774	3220	2.205074	GGCATAGGACAAGTCATCGTG	58.795	52.381	2.29	0.00	0.00	4.35
1816	3262	0.604578	CCAATTGTGTCCCTTGCAGG	59.395	55.000	4.43	0.00	34.30	4.85
1876	3328	3.609373	CGGATGATTGACACAATGTTTGC	59.391	43.478	1.64	0.00	0.00	3.68
2035	3487	1.069090	TCTTGCGCTCGAAAGGTGT	59.931	52.632	9.73	0.00	31.74	4.16
2059	3511	1.470805	CGGCATAATATCATCGGCGGA	60.471	52.381	7.21	0.00	41.37	5.54
2101	3553	5.723887	AGAGAGAAATAAGGATGGTGTCACT	59.276	40.000	2.35	0.00	0.00	3.41
2172	3624	4.161102	AGAGCCACCTATCTGGGTTATAC	58.839	47.826	0.00	0.00	42.29	1.47
2195	3647	4.043310	ACCTCAGATTGTTTCCATCTTCCA	59.957	41.667	0.00	0.00	0.00	3.53
2252	3704	1.701024	AGGCATATCCTTGGGCCCA	60.701	57.895	24.45	24.45	44.75	5.36
2443	3898	7.795431	CGTAAGTACGTTTACATAAGACCAA	57.205	36.000	10.02	0.00	44.13	3.67
2492	3947	6.264744	TCTCTCTCGTTTTTCCTCTTTACAGA	59.735	38.462	0.00	0.00	0.00	3.41
2493	3948	6.448006	TCTCTCTCGTTTTTCCTCTTTACAG	58.552	40.000	0.00	0.00	0.00	2.74
2521	3980	4.616181	ATTCATTCCAATCGTTCGTTCC	57.384	40.909	0.00	0.00	0.00	3.62
2522	3981	6.255887	AGACTATTCATTCCAATCGTTCGTTC	59.744	38.462	0.00	0.00	0.00	3.95
2525	3984	6.477033	AGAAGACTATTCATTCCAATCGTTCG	59.523	38.462	0.00	0.00	0.00	3.95
2570	4029	9.484806	AACCGCCTTTGTACTAGGTATATATAT	57.515	33.333	13.79	0.00	35.13	0.86
2751	4212	8.803397	ATGAAGATGATGAACATTCTCAAAGA	57.197	30.769	0.00	0.00	39.56	2.52
2874	4339	3.195610	CCTTCTTATTTTTCCCACTGGGC	59.804	47.826	9.60	0.00	43.94	5.36
2892	4359	4.836125	TGTTGCATCAGTTTTCTCCTTC	57.164	40.909	0.00	0.00	0.00	3.46
3054	4522	9.639601	GGCAATATCTTTTTAAGGTTATATGCC	57.360	33.333	0.00	0.00	0.00	4.40
3092	4560	9.396022	AGTTTTCTCTCAAAGTTTCTCATAACA	57.604	29.630	0.00	0.00	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.