AutoCloner

Multiple sequence alignment - TraesCS6D01G364600

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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	TraesCS6D01G364600	chr6D	100.000	6570	0	0	1	6570	454256104	454249535	0.000000e+00	12133.0
1	TraesCS6D01G364600	chr6D	86.255	2561	254	53	3070	5599	454127284	454129777	0.000000e+00	2689.0
2	TraesCS6D01G364600	chr6D	83.910	2368	288	60	3294	5620	454215451	454217766	0.000000e+00	2176.0
3	TraesCS6D01G364600	chr6D	86.150	1704	190	27	3938	5620	454224354	454226032	0.000000e+00	1797.0
4	TraesCS6D01G364600	chr6D	88.558	1241	64	34	1476	2701	454125630	454126807	0.000000e+00	1434.0
5	TraesCS6D01G364600	chr6D	83.483	999	98	37	706	1666	454221444	454222413	0.000000e+00	869.0
6	TraesCS6D01G364600	chr6D	89.455	569	23	13	1997	2563	454222645	454223178	0.000000e+00	684.0
7	TraesCS6D01G364600	chr6D	98.276	348	6	0	2037	2384	454213569	454213916	1.570000e-170	610.0
8	TraesCS6D01G364600	chr6D	81.295	834	83	32	997	1796	454212647	454213441	5.630000e-170	608.0
9	TraesCS6D01G364600	chr6D	86.556	543	39	12	894	1428	454124954	454125470	9.560000e-158	568.0
10	TraesCS6D01G364600	chr6D	82.392	602	64	25	3291	3869	454223528	454224110	2.750000e-133	486.0
11	TraesCS6D01G364600	chr6D	89.591	269	23	5	3277	3544	6097041	6096777	2.940000e-88	337.0
12	TraesCS6D01G364600	chr6D	88.889	216	8	8	2762	2977	454126798	454126997	1.090000e-62	252.0
13	TraesCS6D01G364600	chr6D	80.247	324	26	16	2413	2720	454214921	454215222	6.680000e-50	209.0
14	TraesCS6D01G364600	chr6D	92.308	65	4	1	1871	1935	454213439	454213502	2.520000e-14	91.6
15	TraesCS6D01G364600	chr6D	88.235	68	1	4	1868	1935	454222537	454222597	2.540000e-09	75.0
16	TraesCS6D01G364600	chr6A	96.506	3406	97	14	3171	6568	600459343	600455952	0.000000e+00	5611.0
17	TraesCS6D01G364600	chr6A	86.981	3180	196	111	28	3116	600462525	600459473	0.000000e+00	3378.0
18	TraesCS6D01G364600	chr6A	86.424	2335	235	50	3316	5616	600394106	600396392	0.000000e+00	2481.0
19	TraesCS6D01G364600	chr6A	89.821	1896	110	45	705	2564	600391444	600393292	0.000000e+00	2355.0
20	TraesCS6D01G364600	chr6A	82.172	488	55	22	3010	3486	426299375	426298909	2.220000e-104	390.0
21	TraesCS6D01G364600	chr6A	78.378	222	22	15	444	649	600391215	600391426	3.220000e-23	121.0
22	TraesCS6D01G364600	chr6B	95.426	3345	121	12	3243	6570	690734988	690731659	0.000000e+00	5301.0
23	TraesCS6D01G364600	chr6B	89.780	3229	153	62	28	3155	690738186	690735034	0.000000e+00	3971.0
24	TraesCS6D01G364600	chr6B	83.914	2381	281	71	3291	5620	690449345	690451674	0.000000e+00	2182.0
25	TraesCS6D01G364600	chr6B	85.773	1933	225	41	3712	5618	690441517	690443425	0.000000e+00	2001.0
26	TraesCS6D01G364600	chr6B	86.932	1255	131	19	4362	5608	690330182	690331411	0.000000e+00	1378.0
27	TraesCS6D01G364600	chr6B	87.190	968	73	25	980	1934	690316376	690317305	0.000000e+00	1053.0
28	TraesCS6D01G364600	chr6B	85.356	956	94	25	747	1673	690447254	690448192	0.000000e+00	948.0
29	TraesCS6D01G364600	chr6B	88.817	617	27	18	1997	2607	690448429	690449009	0.000000e+00	719.0
30	TraesCS6D01G364600	chr6B	94.495	436	20	2	1960	2392	690318360	690318794	0.000000e+00	669.0
31	TraesCS6D01G364600	chr6B	81.896	823	77	32	999	1796	690437565	690438340	4.320000e-176	628.0
32	TraesCS6D01G364600	chr6B	89.216	510	24	15	1871	2374	690438338	690438822	5.630000e-170	608.0
33	TraesCS6D01G364600	chr6B	85.337	416	40	9	3960	4373	690327745	690328141	1.710000e-110	411.0
34	TraesCS6D01G364600	chr6B	90.335	269	24	2	3277	3544	636562572	636562839	1.050000e-92	351.0
35	TraesCS6D01G364600	chr6B	84.191	272	21	12	3011	3278	368566057	368565804	1.830000e-60	244.0
36	TraesCS6D01G364600	chr6B	92.208	154	10	2	5468	5620	690452516	690452668	3.990000e-52	217.0
37	TraesCS6D01G364600	chr6B	79.866	298	29	16	2413	2689	690439981	690440268	8.700000e-44	189.0
38	TraesCS6D01G364600	chr6B	86.957	69	2	7	1869	1935	690448318	690448381	3.290000e-08	71.3
39	TraesCS6D01G364600	chr4B	92.877	351	22	3	2631	2980	475719241	475718893	2.110000e-139	507.0
40	TraesCS6D01G364600	chr4B	90.083	121	9	1	3034	3154	475718887	475718770	3.170000e-33	154.0
41	TraesCS6D01G364600	chr7D	84.583	480	40	15	3099	3562	590894609	590895070	4.670000e-121	446.0
42	TraesCS6D01G364600	chr7D	89.591	269	26	2	3277	3544	567630481	567630214	2.270000e-89	340.0
43	TraesCS6D01G364600	chr1B	91.824	318	22	2	2664	2980	46515926	46515612	2.170000e-119	440.0
44	TraesCS6D01G364600	chr1B	90.083	121	9	1	3034	3154	46515606	46515489	3.170000e-33	154.0
45	TraesCS6D01G364600	chr3B	82.365	499	46	18	3010	3485	200105740	200105261	4.770000e-106	396.0
46	TraesCS6D01G364600	chr3B	82.129	498	47	18	3011	3485	200086991	200086513	7.990000e-104	388.0
47	TraesCS6D01G364600	chr3B	88.136	118	9	2	3166	3283	181804740	181804628	1.150000e-27	135.0
48	TraesCS6D01G364600	chr4A	81.557	488	60	21	3010	3486	31215454	31214986	6.220000e-100	375.0
49	TraesCS6D01G364600	chr4A	91.489	47	3	1	2784	2830	718965460	718965505	5.500000e-06	63.9
50	TraesCS6D01G364600	chr7B	89.259	270	25	4	3276	3544	242513482	242513748	1.060000e-87	335.0
51	TraesCS6D01G364600	chr3D	89.219	269	26	3	3277	3544	529249854	529249588	3.800000e-87	333.0
52	TraesCS6D01G364600	chr3D	81.053	95	13	2	2784	2878	139731999	139732088	3.290000e-08	71.3
53	TraesCS6D01G364600	chr5B	90.678	118	6	2	3166	3283	667470306	667470194	1.140000e-32	152.0
54	TraesCS6D01G364600	chr5D	88.983	118	8	2	3166	3283	448114385	448114497	2.470000e-29	141.0
55	TraesCS6D01G364600	chr5D	89.474	114	7	2	3166	3279	445140910	445140802	8.880000e-29	139.0
56	TraesCS6D01G364600	chrUn	91.489	47	3	1	2784	2830	384036762	384036807	5.500000e-06	63.9
57	TraesCS6D01G364600	chr2B	93.182	44	2	1	2787	2830	632572915	632572873	5.500000e-06	63.9

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	TraesCS6D01G364600	chr6D	454249535	454256104	6569	True	12133.000000	12133	100.000000	1	6570	1	chr6D.!!$R2	6569
1	TraesCS6D01G364600	chr6D	454124954	454129777	4823	False	1235.750000	2689	87.564500	894	5599	4	chr6D.!!$F1	4705
2	TraesCS6D01G364600	chr6D	454212647	454226032	13385	False	760.560000	2176	86.575100	706	5620	10	chr6D.!!$F2	4914
3	TraesCS6D01G364600	chr6A	600455952	600462525	6573	True	4494.500000	5611	91.743500	28	6568	2	chr6A.!!$R2	6540
4	TraesCS6D01G364600	chr6A	600391215	600396392	5177	False	1652.333333	2481	84.874333	444	5616	3	chr6A.!!$F1	5172
5	TraesCS6D01G364600	chr6B	690731659	690738186	6527	True	4636.000000	5301	92.603000	28	6570	2	chr6B.!!$R2	6542
6	TraesCS6D01G364600	chr6B	690327745	690331411	3666	False	894.500000	1378	86.134500	3960	5608	2	chr6B.!!$F3	1648
7	TraesCS6D01G364600	chr6B	690316376	690318794	2418	False	861.000000	1053	90.842500	980	2392	2	chr6B.!!$F2	1412
8	TraesCS6D01G364600	chr6B	690437565	690452668	15103	False	840.366667	2182	86.000333	747	5620	9	chr6B.!!$F4	4873

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
351	371	0.109597	CTAAAGCAGGCAAGGCAACG	60.110	55.000	0.00	0.0	46.39	4.10	F
356	376	0.672401	GCAGGCAAGGCAACGTAGTA	60.672	55.000	0.00	0.0	45.00	1.82	F
1461	11709	0.249447	TGCGGCTGATTATCCGTCTG	60.249	55.000	0.00	0.0	46.79	3.51	F
2405	13847	0.451783	CGCCATGGCCAACTAGTTTC	59.548	55.000	30.79	0.6	37.98	2.78	F
3179	15682	1.001764	CAGAAGTGGATGGGCAGCA	60.002	57.895	0.00	0.0	0.00	4.41	F
3447	15960	1.324383	TCAGACCTACAAGACACGCA	58.676	50.000	0.00	0.0	0.00	5.24	F
3704	16229	1.734465	CAGAATTCCAACTCTGCGGTC	59.266	52.381	0.65	0.0	33.17	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1390	11631	0.460109	CATGCTTGTCCGTGGATCGA	60.460	55.000	0.00	42.86	3.59	R
1898	12275	0.852777	CACGCGTAAAGGATGATCGG	59.147	55.000	13.44	0.00	4.18	R
3157	15660	0.112995	TGCCCATCCACTTCTGCTTT	59.887	50.000	0.00	0.00	3.51	R
3964	16690	0.752743	TGCTGCACAAGAGCAAAGGT	60.753	50.000	0.00	43.47	3.50	R
4502	19293	0.465097	CCTGGATCGCAAGGCAAGAT	60.465	55.000	0.00	38.47	2.40	R
4503	19294	1.078214	CCTGGATCGCAAGGCAAGA	60.078	57.895	0.00	38.47	3.02	R
5586	21402	2.616510	GGGAGCATGCTGTTACACTCTT	60.617	50.000	28.27	0.00	2.85	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
60	63	4.508128	ACGGCCATAGCGACACGG	62.508	66.667	2.24	0.00	41.24	4.94
78	85	4.175337	CACGGGGTGCGGATCCAT	62.175	66.667	9.05	0.00	0.00	3.41
79	86	3.861797	ACGGGGTGCGGATCCATC	61.862	66.667	9.05	3.12	0.00	3.51
81	88	2.839098	GGGGTGCGGATCCATCAT	59.161	61.111	9.05	0.00	0.00	2.45
106	113	9.836864	ATATACATACCGTATGGATCTACGTAA	57.163	33.333	17.99	1.74	38.98	3.18
108	115	9.836864	ATACATACCGTATGGATCTACGTAATA	57.163	33.333	20.23	2.53	42.21	0.98
181	201	1.593787	CGGATGAGTGGCAGAGTGT	59.406	57.895	0.00	0.00	0.00	3.55
285	305	2.359975	ACCGCACCAAGCTTAGCC	60.360	61.111	0.00	0.00	42.61	3.93
287	307	2.401766	CCGCACCAAGCTTAGCCAG	61.402	63.158	0.00	0.00	42.61	4.85
296	316	3.077617	GCTTAGCCAGCTCCAGAAG	57.922	57.895	0.00	0.00	46.27	2.85
313	333	7.482654	TCCAGAAGCAAAATTATATGAGACG	57.517	36.000	0.00	0.00	0.00	4.18
315	335	7.439356	TCCAGAAGCAAAATTATATGAGACGAG	59.561	37.037	0.00	0.00	0.00	4.18
316	336	7.068341	CAGAAGCAAAATTATATGAGACGAGC	58.932	38.462	0.00	0.00	0.00	5.03
317	337	5.582439	AGCAAAATTATATGAGACGAGCG	57.418	39.130	0.00	0.00	0.00	5.03
318	338	5.289595	AGCAAAATTATATGAGACGAGCGA	58.710	37.500	0.00	0.00	0.00	4.93
319	339	5.403766	AGCAAAATTATATGAGACGAGCGAG	59.596	40.000	0.00	0.00	0.00	5.03
345	365	2.411547	CGAACGAACTAAAGCAGGCAAG	60.412	50.000	0.00	0.00	0.00	4.01
349	369	1.613437	GAACTAAAGCAGGCAAGGCAA	59.387	47.619	0.00	0.00	0.00	4.52
350	370	0.961753	ACTAAAGCAGGCAAGGCAAC	59.038	50.000	0.00	0.00	0.00	4.17
351	371	0.109597	CTAAAGCAGGCAAGGCAACG	60.110	55.000	0.00	0.00	46.39	4.10
353	373	0.821711	AAAGCAGGCAAGGCAACGTA	60.822	50.000	0.00	0.00	46.39	3.57
356	376	0.672401	GCAGGCAAGGCAACGTAGTA	60.672	55.000	0.00	0.00	45.00	1.82
420	443	1.531365	CCACCCTTTCCTTGCTGCA	60.531	57.895	0.00	0.00	0.00	4.41
429	452	1.171308	TCCTTGCTGCATCTGCTTTC	58.829	50.000	1.84	0.00	42.66	2.62
434	457	1.015868	GCTGCATCTGCTTTCTCTCC	58.984	55.000	3.53	0.00	42.66	3.71
520	562	2.083774	CCGCATTGTGTCCACTACAAT	58.916	47.619	0.00	0.00	46.54	2.71
708	765	3.180189	GCACACACACATTCATTTGTTCG	59.820	43.478	0.00	0.00	0.00	3.95
746	803	3.843619	AGAGGGAAAAAGAGAGAAGGGAG	59.156	47.826	0.00	0.00	0.00	4.30
747	804	2.916269	AGGGAAAAAGAGAGAAGGGAGG	59.084	50.000	0.00	0.00	0.00	4.30
756	813	2.499693	GAGAGAAGGGAGGGAAAGAGTG	59.500	54.545	0.00	0.00	0.00	3.51
1390	11631	2.901042	GATTCGGGGGAGCTCGTT	59.099	61.111	7.83	0.00	0.00	3.85
1461	11709	0.249447	TGCGGCTGATTATCCGTCTG	60.249	55.000	0.00	0.00	46.79	3.51
1639	11990	2.508891	CGACGTCAAGCGCATCCTC	61.509	63.158	17.16	0.00	46.11	3.71
1801	12152	2.358267	GTCAGGTAGGTGTCCATACTCG	59.642	54.545	0.00	0.00	0.00	4.18
1883	12260	0.603707	CACGTCCCAGCACATGAACT	60.604	55.000	0.00	0.00	0.00	3.01
1898	12275	1.957765	GAACTCCACTACCGGCCTCC	61.958	65.000	0.00	0.00	0.00	4.30
1958	13386	1.300233	GCACCATCTCGACCGATCC	60.300	63.158	0.00	0.00	0.00	3.36
2402	13844	2.272146	CCGCCATGGCCAACTAGT	59.728	61.111	30.79	0.00	37.98	2.57
2403	13845	1.378514	CCGCCATGGCCAACTAGTT	60.379	57.895	30.79	1.12	37.98	2.24
2405	13847	0.451783	CGCCATGGCCAACTAGTTTC	59.548	55.000	30.79	0.60	37.98	2.78
2408	13874	2.562738	GCCATGGCCAACTAGTTTCTTT	59.437	45.455	27.24	0.00	34.56	2.52
2411	13877	2.500229	TGGCCAACTAGTTTCTTTCCG	58.500	47.619	0.61	0.00	0.00	4.30
2442	13908	3.755378	GCCATGAGAACTGTGACATCTTT	59.245	43.478	0.00	0.00	0.00	2.52
2443	13909	4.379186	GCCATGAGAACTGTGACATCTTTG	60.379	45.833	0.00	0.00	0.00	2.77
2444	13910	4.155462	CCATGAGAACTGTGACATCTTTGG	59.845	45.833	0.00	5.36	0.00	3.28
2445	13911	3.743521	TGAGAACTGTGACATCTTTGGG	58.256	45.455	0.00	0.00	0.00	4.12
2446	13912	3.077359	GAGAACTGTGACATCTTTGGGG	58.923	50.000	0.00	0.00	0.00	4.96
2447	13913	2.443255	AGAACTGTGACATCTTTGGGGT	59.557	45.455	0.00	0.00	0.00	4.95
2448	13914	2.276732	ACTGTGACATCTTTGGGGTG	57.723	50.000	0.00	0.00	0.00	4.61
2449	13915	1.202927	ACTGTGACATCTTTGGGGTGG	60.203	52.381	0.00	0.00	0.00	4.61
2467	13947	1.749258	GTGGGGGCTGACGGATTTC	60.749	63.158	0.00	0.00	0.00	2.17
2468	13948	2.124278	GGGGGCTGACGGATTTCC	60.124	66.667	0.00	0.00	0.00	3.13
2582	14068	7.919313	AGGTACGTACGTCATAATTAACATG	57.081	36.000	26.53	0.00	0.00	3.21
2583	14069	7.483307	AGGTACGTACGTCATAATTAACATGT	58.517	34.615	26.53	0.00	0.00	3.21
2734	14905	6.782000	ACTCCTCATCAGCTATAATCAAGACT	59.218	38.462	0.00	0.00	0.00	3.24
2755	14926	3.044235	TGGCTAGTGAGTGACATGTTG	57.956	47.619	0.00	0.00	0.00	3.33
3135	15638	8.486210	TCAACTAGGATTATCAAATAGCACAGT	58.514	33.333	0.00	0.00	0.00	3.55
3155	15658	5.163301	ACAGTTAGTGATCTGTGTGGTTCTT	60.163	40.000	0.00	0.00	42.30	2.52
3156	15659	6.041637	ACAGTTAGTGATCTGTGTGGTTCTTA	59.958	38.462	0.00	0.00	42.30	2.10
3157	15660	6.929049	CAGTTAGTGATCTGTGTGGTTCTTAA	59.071	38.462	0.00	0.00	0.00	1.85
3158	15661	7.441157	CAGTTAGTGATCTGTGTGGTTCTTAAA	59.559	37.037	0.00	0.00	0.00	1.52
3159	15662	7.990886	AGTTAGTGATCTGTGTGGTTCTTAAAA	59.009	33.333	0.00	0.00	0.00	1.52
3160	15663	6.867662	AGTGATCTGTGTGGTTCTTAAAAG	57.132	37.500	0.00	0.00	0.00	2.27
3161	15664	5.239525	AGTGATCTGTGTGGTTCTTAAAAGC	59.760	40.000	0.00	0.00	0.00	3.51
3162	15665	5.008613	GTGATCTGTGTGGTTCTTAAAAGCA	59.991	40.000	0.00	0.00	0.00	3.91
3163	15666	5.239306	TGATCTGTGTGGTTCTTAAAAGCAG	59.761	40.000	0.00	0.00	0.00	4.24
3164	15667	4.776349	TCTGTGTGGTTCTTAAAAGCAGA	58.224	39.130	0.00	0.00	0.00	4.26
3169	15672	4.338118	TGTGGTTCTTAAAAGCAGAAGTGG	59.662	41.667	0.00	0.00	30.72	4.00
3179	15682	1.001764	CAGAAGTGGATGGGCAGCA	60.002	57.895	0.00	0.00	0.00	4.41
3252	15755	1.827969	GAGACTAGCCCAGCTCTGAAA	59.172	52.381	0.00	0.00	40.44	2.69
3446	15959	2.433868	TTCAGACCTACAAGACACGC	57.566	50.000	0.00	0.00	0.00	5.34
3447	15960	1.324383	TCAGACCTACAAGACACGCA	58.676	50.000	0.00	0.00	0.00	5.24
3448	15961	1.893137	TCAGACCTACAAGACACGCAT	59.107	47.619	0.00	0.00	0.00	4.73
3461	15974	6.072508	ACAAGACACGCATACAGAATGAATTT	60.073	34.615	0.00	0.00	39.69	1.82
3644	16167	2.634815	AGGCAGGCACATAGATTCAG	57.365	50.000	0.00	0.00	0.00	3.02
3646	16169	2.709934	AGGCAGGCACATAGATTCAGAT	59.290	45.455	0.00	0.00	0.00	2.90
3670	16195	3.096852	TCACAGTCCTACCATGTACCTG	58.903	50.000	0.00	0.00	0.00	4.00
3692	16217	6.331369	TGTGGTGAAGAAATTCAGAATTCC	57.669	37.500	8.90	5.61	0.00	3.01
3704	16229	1.734465	CAGAATTCCAACTCTGCGGTC	59.266	52.381	0.65	0.00	33.17	4.79
3899	16602	4.730657	CTCTGTTCTTGGCATGATTTCAC	58.269	43.478	3.72	0.44	0.00	3.18
3909	16612	5.964758	TGGCATGATTTCACTTTATTCCAC	58.035	37.500	0.00	0.00	0.00	4.02
3964	16690	3.197766	CCTTGGCCTGACAGTAGATTGTA	59.802	47.826	3.32	0.00	0.00	2.41
4015	16741	2.033757	AGCCTGCACTGCTTCCTG	59.966	61.111	1.98	0.00	34.87	3.86
4233	16959	2.104963	GGGGGCTCATAGTGGTAAGAAG	59.895	54.545	0.00	0.00	0.00	2.85
4270	16997	4.141505	TGTGGAACCAGAAGATGACTTTCA	60.142	41.667	0.00	0.00	33.84	2.69
4271	16998	5.006386	GTGGAACCAGAAGATGACTTTCAT	58.994	41.667	0.00	0.00	40.34	2.57
4277	17004	5.645497	ACCAGAAGATGACTTTCATACTTGC	59.355	40.000	0.00	0.00	37.20	4.01
4279	17006	4.872691	AGAAGATGACTTTCATACTTGCGG	59.127	41.667	0.00	0.00	37.20	5.69
5353	20173	0.677731	TGCTGGATTTCTCCCTTGCG	60.678	55.000	0.00	0.00	41.29	4.85
5438	20258	6.146837	CAGCTAGAATCAATATCTCCGGTTTG	59.853	42.308	0.00	0.00	0.00	2.93
5460	20280	4.396790	TGATGTTTTGGTTATAACTCGGGC	59.603	41.667	15.05	4.75	0.00	6.13
5585	21401	6.511416	ACGGATTGATGATAAGACAAGAGAG	58.489	40.000	0.00	0.00	0.00	3.20
5586	21402	6.322456	ACGGATTGATGATAAGACAAGAGAGA	59.678	38.462	0.00	0.00	0.00	3.10
5612	21428	2.368548	TGTAACAGCATGCTCCCGATAT	59.631	45.455	19.68	1.52	42.53	1.63
6473	22299	5.394224	GGTTATCGAAGAGTGATGGAAGTGA	60.394	44.000	0.00	0.00	43.63	3.41
6554	22380	0.391263	GAACTCGTGATTTCGGCCCT	60.391	55.000	0.00	0.00	0.00	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	9.831737	GCATCGCAATGATATATTAAGTTTTCT	57.168	29.630	0.00	0.00	34.83	2.52
15	16	9.611284	TGCATCGCAATGATATATTAAGTTTTC	57.389	29.630	0.00	0.00	34.76	2.29
16	17	9.398170	GTGCATCGCAATGATATATTAAGTTTT	57.602	29.630	0.00	0.00	41.47	2.43
17	18	8.567104	TGTGCATCGCAATGATATATTAAGTTT	58.433	29.630	0.00	0.00	41.47	2.66
18	19	8.017373	GTGTGCATCGCAATGATATATTAAGTT	58.983	33.333	0.00	0.00	41.47	2.66
19	20	7.521529	GTGTGCATCGCAATGATATATTAAGT	58.478	34.615	0.00	0.00	41.47	2.24
20	21	6.679919	CGTGTGCATCGCAATGATATATTAAG	59.320	38.462	0.00	0.00	41.47	1.85
21	22	6.402011	CCGTGTGCATCGCAATGATATATTAA	60.402	38.462	8.40	0.00	41.47	1.40
22	23	5.063312	CCGTGTGCATCGCAATGATATATTA	59.937	40.000	8.40	0.00	41.47	0.98
24	25	3.371898	CCGTGTGCATCGCAATGATATAT	59.628	43.478	8.40	0.00	41.47	0.86
78	85	8.374327	CGTAGATCCATACGGTATGTATATGA	57.626	38.462	22.78	14.42	41.93	2.15
106	113	4.574892	TGGACACATCACACGTTGATTAT	58.425	39.130	9.56	1.44	42.87	1.28
108	115	2.807967	CTGGACACATCACACGTTGATT	59.192	45.455	9.56	0.00	42.87	2.57
122	138	1.802960	CAACTGATCACAGCTGGACAC	59.197	52.381	19.93	10.52	46.95	3.67
288	308	7.439356	TCGTCTCATATAATTTTGCTTCTGGAG	59.561	37.037	0.00	0.00	0.00	3.86
290	310	7.482654	TCGTCTCATATAATTTTGCTTCTGG	57.517	36.000	0.00	0.00	0.00	3.86
292	312	6.074088	CGCTCGTCTCATATAATTTTGCTTCT	60.074	38.462	0.00	0.00	0.00	2.85
293	313	6.067669	CGCTCGTCTCATATAATTTTGCTTC	58.932	40.000	0.00	0.00	0.00	3.86
294	314	5.753438	TCGCTCGTCTCATATAATTTTGCTT	59.247	36.000	0.00	0.00	0.00	3.91
296	316	5.576337	TCGCTCGTCTCATATAATTTTGC	57.424	39.130	0.00	0.00	0.00	3.68
297	317	5.603452	GCTCGCTCGTCTCATATAATTTTG	58.397	41.667	0.00	0.00	0.00	2.44
306	326	1.226435	GTTCGCTCGCTCGTCTCAT	60.226	57.895	0.00	0.00	0.00	2.90
307	327	2.176055	GTTCGCTCGCTCGTCTCA	59.824	61.111	0.00	0.00	0.00	3.27
308	328	2.829577	TTCGTTCGCTCGCTCGTCTC	62.830	60.000	6.05	0.00	0.00	3.36
311	331	2.799916	GTTCGTTCGCTCGCTCGT	60.800	61.111	6.05	0.00	0.00	4.18
313	333	2.078914	TTCGTTCGTTCGCTCGCTC	61.079	57.895	0.00	0.00	0.00	5.03
315	335	1.061799	TAGTTCGTTCGTTCGCTCGC	61.062	55.000	0.00	0.00	0.00	5.03
316	336	1.321016	TTAGTTCGTTCGTTCGCTCG	58.679	50.000	0.00	0.00	0.00	5.03
317	337	2.470300	GCTTTAGTTCGTTCGTTCGCTC	60.470	50.000	0.00	0.00	0.00	5.03
318	338	1.454653	GCTTTAGTTCGTTCGTTCGCT	59.545	47.619	0.00	0.00	0.00	4.93
319	339	1.190763	TGCTTTAGTTCGTTCGTTCGC	59.809	47.619	0.00	0.00	0.00	4.70
351	371	5.173664	AGAATTAAAGGTGGCACGTACTAC	58.826	41.667	13.85	0.00	0.00	2.73
353	373	4.020485	AGAGAATTAAAGGTGGCACGTACT	60.020	41.667	13.85	6.67	0.00	2.73
356	376	3.244422	TGAGAGAATTAAAGGTGGCACGT	60.244	43.478	12.17	9.66	0.00	4.49
420	443	3.113191	TCAGGAGGAGAGAAAGCAGAT	57.887	47.619	0.00	0.00	0.00	2.90
434	457	0.671472	TTGCATGCGTCACTCAGGAG	60.671	55.000	14.09	0.00	0.00	3.69
697	754	3.001838	CCACTCACGAACGAACAAATGAA	59.998	43.478	0.14	0.00	0.00	2.57
698	755	2.542178	CCACTCACGAACGAACAAATGA	59.458	45.455	0.14	0.00	0.00	2.57
703	760	0.460722	TTCCCACTCACGAACGAACA	59.539	50.000	0.14	0.00	0.00	3.18
708	765	1.067495	CCTCTCTTCCCACTCACGAAC	60.067	57.143	0.00	0.00	0.00	3.95
746	803	0.322546	AACGATGGGCACTCTTTCCC	60.323	55.000	0.00	0.00	42.93	3.97
747	804	1.087501	GAACGATGGGCACTCTTTCC	58.912	55.000	0.00	0.00	0.00	3.13
756	813	1.152383	GGAAGCTACGAACGATGGGC	61.152	60.000	0.14	0.18	0.00	5.36
1134	11319	3.752167	TCCGGAGAGGAGTCCCCC	61.752	72.222	5.25	4.13	45.98	5.40
1390	11631	0.460109	CATGCTTGTCCGTGGATCGA	60.460	55.000	0.00	0.00	42.86	3.59
1461	11709	5.343249	ACACTTCAGTTTCTTGCACAATTC	58.657	37.500	0.00	0.00	0.00	2.17
1898	12275	0.852777	CACGCGTAAAGGATGATCGG	59.147	55.000	13.44	0.00	0.00	4.18
1958	13386	1.943340	TGTCAGAGACTCCGATCGATG	59.057	52.381	18.66	11.13	33.15	3.84
2397	13839	4.025145	CGAAAGCAACGGAAAGAAACTAGT	60.025	41.667	0.00	0.00	0.00	2.57
2398	13840	4.455124	CGAAAGCAACGGAAAGAAACTAG	58.545	43.478	0.00	0.00	0.00	2.57
2399	13841	4.461992	CGAAAGCAACGGAAAGAAACTA	57.538	40.909	0.00	0.00	0.00	2.24
2400	13842	3.334272	CGAAAGCAACGGAAAGAAACT	57.666	42.857	0.00	0.00	0.00	2.66
2448	13914	3.282374	AAATCCGTCAGCCCCCACC	62.282	63.158	0.00	0.00	0.00	4.61
2449	13915	1.749258	GAAATCCGTCAGCCCCCAC	60.749	63.158	0.00	0.00	0.00	4.61
2467	13947	2.582728	TGCAACAGAAAAAGCACAGG	57.417	45.000	0.00	0.00	31.05	4.00
2468	13948	2.798283	CCATGCAACAGAAAAAGCACAG	59.202	45.455	0.00	0.00	40.14	3.66
2582	14068	3.192844	TGTTGCTAGCTAGTGGACAGTAC	59.807	47.826	21.62	7.97	0.00	2.73
2583	14069	3.427573	TGTTGCTAGCTAGTGGACAGTA	58.572	45.455	21.62	2.31	0.00	2.74
2713	14397	6.147492	GCCAAGTCTTGATTATAGCTGATGAG	59.853	42.308	14.42	0.00	0.00	2.90
2734	14905	3.181455	ACAACATGTCACTCACTAGCCAA	60.181	43.478	0.00	0.00	0.00	4.52
2755	14926	3.450096	AGGACGACCCTAAAAGATACCAC	59.550	47.826	0.00	0.00	45.48	4.16
2906	15078	3.513515	TGGCCATCCATTTTCCAAAGTAC	59.486	43.478	0.00	0.00	37.47	2.73
2993	15169	6.764308	TTTTTCTGGATAAAGAGCTGATGG	57.236	37.500	0.00	0.00	0.00	3.51
3116	15534	8.662781	TCACTAACTGTGCTATTTGATAATCC	57.337	34.615	0.00	0.00	45.81	3.01
3135	15638	7.041372	GCTTTTAAGAACCACACAGATCACTAA	60.041	37.037	0.00	0.00	0.00	2.24
3155	15658	2.224992	TGCCCATCCACTTCTGCTTTTA	60.225	45.455	0.00	0.00	0.00	1.52
3156	15659	1.260544	GCCCATCCACTTCTGCTTTT	58.739	50.000	0.00	0.00	0.00	2.27
3157	15660	0.112995	TGCCCATCCACTTCTGCTTT	59.887	50.000	0.00	0.00	0.00	3.51
3158	15661	0.323178	CTGCCCATCCACTTCTGCTT	60.323	55.000	0.00	0.00	0.00	3.91
3159	15662	1.302285	CTGCCCATCCACTTCTGCT	59.698	57.895	0.00	0.00	0.00	4.24
3160	15663	2.413142	GCTGCCCATCCACTTCTGC	61.413	63.158	0.00	0.00	0.00	4.26
3161	15664	1.001764	TGCTGCCCATCCACTTCTG	60.002	57.895	0.00	0.00	0.00	3.02
3162	15665	1.302285	CTGCTGCCCATCCACTTCT	59.698	57.895	0.00	0.00	0.00	2.85
3163	15666	2.413142	GCTGCTGCCCATCCACTTC	61.413	63.158	3.85	0.00	0.00	3.01
3164	15667	2.362120	GCTGCTGCCCATCCACTT	60.362	61.111	3.85	0.00	0.00	3.16
3169	15672	2.235650	TCTATATCTGCTGCTGCCCATC	59.764	50.000	13.47	0.00	38.71	3.51
3179	15682	6.294453	GCACATCACTGTAGTCTATATCTGCT	60.294	42.308	0.00	0.00	33.14	4.24
3206	15709	3.813724	TGCTACTACTGCAGTACTATCGG	59.186	47.826	22.67	13.93	38.80	4.18
3260	15763	9.769093	AAACTATACATCGATTTTGTTACAAGC	57.231	29.630	0.00	0.00	0.00	4.01
3461	15974	7.487509	CGAAATTTCATGGCATGTAAACACATA	59.512	33.333	25.62	1.45	0.00	2.29
3644	16167	6.267928	AGGTACATGGTAGGACTGTGAATATC	59.732	42.308	0.00	0.00	0.00	1.63
3646	16169	5.362717	CAGGTACATGGTAGGACTGTGAATA	59.637	44.000	0.00	0.00	0.00	1.75
3670	16195	6.331369	TGGAATTCTGAATTTCTTCACCAC	57.669	37.500	19.39	4.16	36.46	4.16
3692	16217	6.205784	TGAAAATTTAAAGACCGCAGAGTTG	58.794	36.000	0.00	0.00	0.00	3.16
3704	16229	6.200097	CCGTGAACAACCCTGAAAATTTAAAG	59.800	38.462	0.00	0.00	0.00	1.85
3899	16602	8.834465	CCTAACAATCTGAGATGTGGAATAAAG	58.166	37.037	0.00	0.00	0.00	1.85
3909	16612	4.711399	TGCATCCCTAACAATCTGAGATG	58.289	43.478	0.00	0.00	34.23	2.90
3964	16690	0.752743	TGCTGCACAAGAGCAAAGGT	60.753	50.000	0.00	0.00	43.47	3.50
4015	16741	1.803334	TGAACAGGTTGCATCCGTAC	58.197	50.000	8.17	2.99	0.00	3.67
4233	16959	4.457603	TGGTTCCACATATGTAGTTTGTGC	59.542	41.667	8.32	0.00	39.48	4.57
4277	17004	2.805671	TGACTTCAGTTGCAACATACCG	59.194	45.455	30.11	16.24	0.00	4.02
4279	17006	6.672147	AGAATTGACTTCAGTTGCAACATAC	58.328	36.000	30.11	15.07	36.24	2.39
4502	19293	0.465097	CCTGGATCGCAAGGCAAGAT	60.465	55.000	0.00	0.00	38.47	2.40
4503	19294	1.078214	CCTGGATCGCAAGGCAAGA	60.078	57.895	0.00	0.00	38.47	3.02
5353	20173	2.621998	TCGTCGGATTATCTCCAAGGAC	59.378	50.000	0.00	0.00	45.24	3.85
5431	20251	6.683715	AGTTATAACCAAAACATCAAACCGG	58.316	36.000	12.05	0.00	0.00	5.28
5438	20258	4.396790	TGCCCGAGTTATAACCAAAACATC	59.603	41.667	12.05	0.85	0.00	3.06
5460	20280	3.317149	CCTGCAATCCAGTCAACCATATG	59.683	47.826	0.00	0.00	40.06	1.78
5585	21401	2.675348	GGAGCATGCTGTTACACTCTTC	59.325	50.000	28.27	5.72	0.00	2.87
5586	21402	2.616510	GGGAGCATGCTGTTACACTCTT	60.617	50.000	28.27	0.00	0.00	2.85
5612	21428	5.843019	ACTCTGAACCTAAATTCCCTTGA	57.157	39.130	0.00	0.00	0.00	3.02
6455	22281	2.266554	GCTCACTTCCATCACTCTTCG	58.733	52.381	0.00	0.00	0.00	3.79
6473	22299	3.950397	TGAATTACCGGAGTTCAATGCT	58.050	40.909	9.46	0.00	0.00	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.