AutoCloner

Multiple sequence alignment - TraesCS5D01G035500

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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	TraesCS5D01G035500	chr5D	100.000	4631	0	0	1	4631	34887299	34891929	0.000000e+00	8552.0
1	TraesCS5D01G035500	chr5D	94.118	2788	144	11	974	3753	34803075	34805850	0.000000e+00	4222.0
2	TraesCS5D01G035500	chr5D	85.542	2483	300	37	974	3438	34797988	34800429	0.000000e+00	2542.0
3	TraesCS5D01G035500	chr5D	84.276	1679	207	32	974	2623	34869649	34871299	0.000000e+00	1585.0
4	TraesCS5D01G035500	chr5D	90.909	198	18	0	3400	3597	34875591	34875788	2.750000e-67	267.0
5	TraesCS5D01G035500	chr5D	94.545	55	2	1	4576	4629	311481668	311481722	2.970000e-12	84.2
6	TraesCS5D01G035500	chr5D	89.062	64	5	2	898	960	34797939	34798001	1.380000e-10	78.7
7	TraesCS5D01G035500	chr5A	97.454	3810	69	16	598	4398	23173498	23177288	0.000000e+00	6473.0
8	TraesCS5D01G035500	chr5A	91.397	3057	221	19	463	3501	23616073	23613041	0.000000e+00	4150.0
9	TraesCS5D01G035500	chr5A	92.165	485	15	7	1	479	23622066	23621599	0.000000e+00	664.0
10	TraesCS5D01G035500	chr5A	86.555	238	26	6	3856	4089	23612843	23612608	1.650000e-64	257.0
11	TraesCS5D01G035500	chr5A	91.724	145	8	3	4477	4618	23177285	23177428	1.020000e-46	198.0
12	TraesCS5D01G035500	chr5A	92.063	63	1	1	3694	3752	23612949	23612887	8.260000e-13	86.1
13	TraesCS5D01G035500	chr5A	94.545	55	2	1	4576	4629	499620129	499620075	2.970000e-12	84.2
14	TraesCS5D01G035500	chr5B	95.759	3230	122	7	1072	4291	26306902	26303678	0.000000e+00	5192.0
15	TraesCS5D01G035500	chr5B	87.515	3356	322	49	433	3752	26005591	26008885	0.000000e+00	3786.0
16	TraesCS5D01G035500	chr5B	85.318	2813	333	48	974	3756	25993206	25995968	0.000000e+00	2833.0
17	TraesCS5D01G035500	chr5B	85.466	2649	320	34	974	3597	26324041	26321433	0.000000e+00	2699.0
18	TraesCS5D01G035500	chr5B	85.459	447	27	18	1	442	26005126	26005539	9.210000e-117	431.0
19	TraesCS5D01G035500	chr5B	96.364	55	1	1	4576	4629	649420036	649419982	6.380000e-14	89.8
20	TraesCS5D01G035500	chr5B	87.500	64	5	3	898	960	26324089	26324028	2.310000e-08	71.3
21	TraesCS5D01G035500	chr5B	90.741	54	1	1	4276	4329	26303628	26303579	8.310000e-08	69.4
22	TraesCS5D01G035500	chr3B	88.146	3020	290	33	677	3663	638313387	638310403	0.000000e+00	3531.0
23	TraesCS5D01G035500	chr3B	82.464	211	28	3	4370	4572	812654228	812654019	4.760000e-40	176.0
24	TraesCS5D01G035500	chr3A	89.177	2624	249	17	1049	3663	621847736	621845139	0.000000e+00	3240.0
25	TraesCS5D01G035500	chr3A	84.936	312	34	8	697	1000	621848569	621848263	2.090000e-78	303.0
26	TraesCS5D01G035500	chr3A	94.545	55	2	1	4576	4629	9379715	9379769	2.970000e-12	84.2
27	TraesCS5D01G035500	chr3D	90.020	1493	121	15	2174	3663	478560080	478558613	0.000000e+00	1906.0
28	TraesCS5D01G035500	chr3D	89.840	374	33	3	1807	2178	478632474	478632104	4.190000e-130	475.0
29	TraesCS5D01G035500	chr3D	85.942	377	42	10	879	1251	478639003	478638634	4.340000e-105	392.0
30	TraesCS5D01G035500	chr3D	95.918	49	1	1	4576	4623	450885689	450885641	1.380000e-10	78.7
31	TraesCS5D01G035500	chr2A	85.222	203	22	6	4373	4572	555335296	555335099	7.860000e-48	202.0
32	TraesCS5D01G035500	chr4A	96.364	55	1	1	4576	4629	220023131	220023185	6.380000e-14	89.8
33	TraesCS5D01G035500	chr2D	87.013	77	10	0	3782	3858	114223078	114223002	2.300000e-13	87.9
34	TraesCS5D01G035500	chr7D	92.982	57	3	1	4576	4631	514994309	514994365	1.070000e-11	82.4
35	TraesCS5D01G035500	chr1D	92.727	55	2	2	4576	4629	437843855	437843802	1.380000e-10	78.7
36	TraesCS5D01G035500	chr7B	86.364	66	8	1	3794	3858	21656101	21656036	2.310000e-08	71.3
37	TraesCS5D01G035500	chr7B	86.154	65	9	0	3794	3858	539786277	539786213	2.310000e-08	71.3
38	TraesCS5D01G035500	chr7A	84.615	65	10	0	3794	3858	581848383	581848319	1.080000e-06	65.8

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	TraesCS5D01G035500	chr5D	34887299	34891929	4630	False	8552.00	8552	100.0000	1	4631	1	chr5D.!!$F3	4630
1	TraesCS5D01G035500	chr5D	34797939	34805850	7911	False	2280.90	4222	89.5740	898	3753	3	chr5D.!!$F5	2855
2	TraesCS5D01G035500	chr5D	34869649	34871299	1650	False	1585.00	1585	84.2760	974	2623	1	chr5D.!!$F1	1649
3	TraesCS5D01G035500	chr5A	23173498	23177428	3930	False	3335.50	6473	94.5890	598	4618	2	chr5A.!!$F1	4020
4	TraesCS5D01G035500	chr5A	23612608	23616073	3465	True	1497.70	4150	90.0050	463	4089	3	chr5A.!!$R3	3626
5	TraesCS5D01G035500	chr5B	25993206	25995968	2762	False	2833.00	2833	85.3180	974	3756	1	chr5B.!!$F1	2782
6	TraesCS5D01G035500	chr5B	26303579	26306902	3323	True	2630.70	5192	93.2500	1072	4329	2	chr5B.!!$R2	3257
7	TraesCS5D01G035500	chr5B	26005126	26008885	3759	False	2108.50	3786	86.4870	1	3752	2	chr5B.!!$F2	3751
8	TraesCS5D01G035500	chr5B	26321433	26324089	2656	True	1385.15	2699	86.4830	898	3597	2	chr5B.!!$R3	2699
9	TraesCS5D01G035500	chr3B	638310403	638313387	2984	True	3531.00	3531	88.1460	677	3663	1	chr3B.!!$R1	2986
10	TraesCS5D01G035500	chr3A	621845139	621848569	3430	True	1771.50	3240	87.0565	697	3663	2	chr3A.!!$R1	2966
11	TraesCS5D01G035500	chr3D	478558613	478560080	1467	True	1906.00	1906	90.0200	2174	3663	1	chr3D.!!$R2	1489

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	Hairpin	End Stability	Orientation
847	928	0.250727	TGCAGCAGTAGTTTCACCCC	60.251	55.000	0.00	4.95	F
1065	5779	0.923729	AGAGCAGGAGGAGGAGGAGA	60.924	60.000	0.00	3.71	F
2294	7045	1.067060	CACGGAGACACACTCAACTCA	59.933	52.381	46.54	3.41	F
2624	7382	1.407258	CCTCCAAGAAGCTCCTAGTCG	59.593	57.143	0.00	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2093	6841	0.242017	ACGCAAATCTCTTGCCAAGC	59.758	50.000	0.00	0.00	42.10	4.01	R
2444	7202	2.224018	TGCTTGCAGACAAATTTGGACC	60.224	45.455	21.74	10.54	34.74	4.46	R
3341	8099	1.003580	TGTTGAGCAGGATCTTCCCAC	59.996	52.381	0.00	0.00	37.19	4.61	R
4453	9322	0.030603	GGGAGGGAGGAAGAGGTGAT	60.031	60.000	0.00	0.00	0.00	3.06	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
34	35	6.999456	CGAAGCAACCTTTAACAATTTGTTT	58.001	32.000	19.15	5.05	41.45	2.83
374	376	9.995957	GAAGAAGAATTAACTAATCAGAAAGCC	57.004	33.333	0.00	0.00	0.00	4.35
375	377	9.746457	AAGAAGAATTAACTAATCAGAAAGCCT	57.254	29.630	0.00	0.00	0.00	4.58
389	391	9.520515	AATCAGAAAGCCTTAAGAAATACAGAA	57.479	29.630	3.36	0.00	0.00	3.02
434	439	1.276705	TGCCGGTAGCTTGACACATAA	59.723	47.619	1.90	0.00	44.23	1.90
435	440	1.664151	GCCGGTAGCTTGACACATAAC	59.336	52.381	1.90	0.00	38.99	1.89
436	441	2.677037	GCCGGTAGCTTGACACATAACT	60.677	50.000	1.90	0.00	38.99	2.24
555	626	4.641645	CACAACAGGCCTGGGCGA	62.642	66.667	35.42	0.00	43.06	5.54
588	661	1.087501	GGGAACACAATTCGGAGAGC	58.912	55.000	0.00	0.00	38.43	4.09
847	928	0.250727	TGCAGCAGTAGTTTCACCCC	60.251	55.000	0.00	0.00	0.00	4.95
851	932	2.026822	CAGCAGTAGTTTCACCCCAGAT	60.027	50.000	0.00	0.00	0.00	2.90
896	977	9.993454	TTCCATCAGTTGAATGAGATAGATAAG	57.007	33.333	0.00	0.00	31.44	1.73
929	5122	5.581874	CAGTGGTTTTCTTGCTGTGATTTTT	59.418	36.000	0.00	0.00	0.00	1.94
930	5123	5.581874	AGTGGTTTTCTTGCTGTGATTTTTG	59.418	36.000	0.00	0.00	0.00	2.44
1033	5263	1.604378	GGGGAGGATATCATGCCGG	59.396	63.158	19.84	0.00	39.11	6.13
1050	5758	2.363172	GGGGGAGGTCAGTGAGAGC	61.363	68.421	0.00	0.00	45.07	4.09
1065	5779	0.923729	AGAGCAGGAGGAGGAGGAGA	60.924	60.000	0.00	0.00	0.00	3.71
1973	6712	4.070716	GAGCAACTATTGGAGATGGATGG	58.929	47.826	0.00	0.00	0.00	3.51
2093	6841	2.343101	TCGAATTAGTTTGTCAGGGCG	58.657	47.619	0.00	0.00	0.00	6.13
2294	7045	1.067060	CACGGAGACACACTCAACTCA	59.933	52.381	0.00	0.00	46.54	3.41
2624	7382	1.407258	CCTCCAAGAAGCTCCTAGTCG	59.593	57.143	0.00	0.00	0.00	4.18
3012	7770	3.414486	GCCACCGGCCTATGTTAAT	57.586	52.632	0.00	0.00	44.06	1.40
3021	7779	3.569701	CGGCCTATGTTAATGGAATGCTT	59.430	43.478	0.00	0.00	0.00	3.91
3341	8099	2.509052	TTAGCTGTTGATCCCGATCG	57.491	50.000	8.51	8.51	40.63	3.69
3771	8569	4.574674	TTATTGACTGCCTGATGTTCCT	57.425	40.909	0.00	0.00	0.00	3.36
4161	8963	7.613801	TGACAGCATACAAATTACCCATAGTTT	59.386	33.333	0.00	0.00	0.00	2.66
4261	9064	7.621832	TTTAATGTCGAAAAATGCAGACAAG	57.378	32.000	8.11	0.00	45.17	3.16
4373	9242	3.374402	CTCCTCGCTCACCACGGT	61.374	66.667	0.00	0.00	0.00	4.83
4374	9243	3.633094	CTCCTCGCTCACCACGGTG	62.633	68.421	10.09	10.09	46.64	4.94
4399	9268	3.702048	CGGGACCCGTCACCACAT	61.702	66.667	25.54	0.00	42.73	3.21
4400	9269	2.267961	GGGACCCGTCACCACATC	59.732	66.667	0.00	0.00	0.00	3.06
4401	9270	2.589157	GGGACCCGTCACCACATCA	61.589	63.158	0.00	0.00	0.00	3.07
4402	9271	1.602237	GGACCCGTCACCACATCAT	59.398	57.895	0.00	0.00	0.00	2.45
4403	9272	0.462047	GGACCCGTCACCACATCATC	60.462	60.000	0.00	0.00	0.00	2.92
4404	9273	0.537188	GACCCGTCACCACATCATCT	59.463	55.000	0.00	0.00	0.00	2.90
4405	9274	0.537188	ACCCGTCACCACATCATCTC	59.463	55.000	0.00	0.00	0.00	2.75
4406	9275	0.179073	CCCGTCACCACATCATCTCC	60.179	60.000	0.00	0.00	0.00	3.71
4407	9276	0.826715	CCGTCACCACATCATCTCCT	59.173	55.000	0.00	0.00	0.00	3.69
4408	9277	1.208052	CCGTCACCACATCATCTCCTT	59.792	52.381	0.00	0.00	0.00	3.36
4409	9278	2.544685	CGTCACCACATCATCTCCTTC	58.455	52.381	0.00	0.00	0.00	3.46
4410	9279	2.544685	GTCACCACATCATCTCCTTCG	58.455	52.381	0.00	0.00	0.00	3.79
4411	9280	1.134699	TCACCACATCATCTCCTTCGC	60.135	52.381	0.00	0.00	0.00	4.70
4412	9281	0.904649	ACCACATCATCTCCTTCGCA	59.095	50.000	0.00	0.00	0.00	5.10
4413	9282	1.134580	ACCACATCATCTCCTTCGCAG	60.135	52.381	0.00	0.00	0.00	5.18
4414	9283	0.935898	CACATCATCTCCTTCGCAGC	59.064	55.000	0.00	0.00	0.00	5.25
4415	9284	0.829333	ACATCATCTCCTTCGCAGCT	59.171	50.000	0.00	0.00	0.00	4.24
4416	9285	1.202510	ACATCATCTCCTTCGCAGCTC	60.203	52.381	0.00	0.00	0.00	4.09
4417	9286	1.068895	CATCATCTCCTTCGCAGCTCT	59.931	52.381	0.00	0.00	0.00	4.09
4418	9287	0.743688	TCATCTCCTTCGCAGCTCTC	59.256	55.000	0.00	0.00	0.00	3.20
4419	9288	0.459078	CATCTCCTTCGCAGCTCTCA	59.541	55.000	0.00	0.00	0.00	3.27
4420	9289	0.746063	ATCTCCTTCGCAGCTCTCAG	59.254	55.000	0.00	0.00	0.00	3.35
4421	9290	1.519013	CTCCTTCGCAGCTCTCAGC	60.519	63.158	0.00	0.00	42.84	4.26
4430	9299	4.434685	GCTCTCAGCTCCCGAATG	57.565	61.111	0.00	0.00	38.45	2.67
4431	9300	1.819229	GCTCTCAGCTCCCGAATGA	59.181	57.895	0.00	0.00	38.45	2.57
4432	9301	0.529555	GCTCTCAGCTCCCGAATGAC	60.530	60.000	0.00	0.00	38.45	3.06
4433	9302	0.103937	CTCTCAGCTCCCGAATGACC	59.896	60.000	0.00	0.00	0.00	4.02
4434	9303	0.614697	TCTCAGCTCCCGAATGACCA	60.615	55.000	0.00	0.00	0.00	4.02
4435	9304	0.460987	CTCAGCTCCCGAATGACCAC	60.461	60.000	0.00	0.00	0.00	4.16
4436	9305	0.904865	TCAGCTCCCGAATGACCACT	60.905	55.000	0.00	0.00	0.00	4.00
4437	9306	0.460987	CAGCTCCCGAATGACCACTC	60.461	60.000	0.00	0.00	0.00	3.51
4438	9307	1.519455	GCTCCCGAATGACCACTCG	60.519	63.158	0.00	0.00	34.83	4.18
4439	9308	1.890894	CTCCCGAATGACCACTCGT	59.109	57.895	0.34	0.00	33.17	4.18
4440	9309	0.179134	CTCCCGAATGACCACTCGTC	60.179	60.000	0.34	0.00	42.33	4.20
4441	9310	1.153628	CCCGAATGACCACTCGTCC	60.154	63.158	0.34	0.00	41.18	4.79
4442	9311	1.589630	CCGAATGACCACTCGTCCA	59.410	57.895	0.34	0.00	41.18	4.02
4443	9312	0.736325	CCGAATGACCACTCGTCCAC	60.736	60.000	0.34	0.00	41.18	4.02
4444	9313	0.736325	CGAATGACCACTCGTCCACC	60.736	60.000	0.00	0.00	41.18	4.61
4445	9314	0.608640	GAATGACCACTCGTCCACCT	59.391	55.000	0.00	0.00	41.18	4.00
4446	9315	0.608640	AATGACCACTCGTCCACCTC	59.391	55.000	0.00	0.00	41.18	3.85
4447	9316	0.541998	ATGACCACTCGTCCACCTCA	60.542	55.000	0.00	0.00	41.18	3.86
4448	9317	0.541998	TGACCACTCGTCCACCTCAT	60.542	55.000	0.00	0.00	41.18	2.90
4449	9318	0.173708	GACCACTCGTCCACCTCATC	59.826	60.000	0.00	0.00	35.23	2.92
4450	9319	1.258445	ACCACTCGTCCACCTCATCC	61.258	60.000	0.00	0.00	0.00	3.51
4451	9320	0.972983	CCACTCGTCCACCTCATCCT	60.973	60.000	0.00	0.00	0.00	3.24
4452	9321	0.174389	CACTCGTCCACCTCATCCTG	59.826	60.000	0.00	0.00	0.00	3.86
4453	9322	0.039764	ACTCGTCCACCTCATCCTGA	59.960	55.000	0.00	0.00	0.00	3.86
4454	9323	1.342474	ACTCGTCCACCTCATCCTGAT	60.342	52.381	0.00	0.00	0.00	2.90
4455	9324	1.339610	CTCGTCCACCTCATCCTGATC	59.660	57.143	0.00	0.00	0.00	2.92
4456	9325	1.114627	CGTCCACCTCATCCTGATCA	58.885	55.000	0.00	0.00	0.00	2.92
4457	9326	1.202463	CGTCCACCTCATCCTGATCAC	60.202	57.143	0.00	0.00	0.00	3.06
4458	9327	1.139853	GTCCACCTCATCCTGATCACC	59.860	57.143	0.00	0.00	0.00	4.02
4459	9328	1.008815	TCCACCTCATCCTGATCACCT	59.991	52.381	0.00	0.00	0.00	4.00
4460	9329	1.415659	CCACCTCATCCTGATCACCTC	59.584	57.143	0.00	0.00	0.00	3.85
4461	9330	2.396608	CACCTCATCCTGATCACCTCT	58.603	52.381	0.00	0.00	0.00	3.69
4462	9331	2.770802	CACCTCATCCTGATCACCTCTT	59.229	50.000	0.00	0.00	0.00	2.85
4463	9332	3.037549	ACCTCATCCTGATCACCTCTTC	58.962	50.000	0.00	0.00	0.00	2.87
4464	9333	2.368221	CCTCATCCTGATCACCTCTTCC	59.632	54.545	0.00	0.00	0.00	3.46
4465	9334	3.307506	CTCATCCTGATCACCTCTTCCT	58.692	50.000	0.00	0.00	0.00	3.36
4466	9335	3.303938	TCATCCTGATCACCTCTTCCTC	58.696	50.000	0.00	0.00	0.00	3.71
4467	9336	2.166907	TCCTGATCACCTCTTCCTCC	57.833	55.000	0.00	0.00	0.00	4.30
4468	9337	1.127343	CCTGATCACCTCTTCCTCCC	58.873	60.000	0.00	0.00	0.00	4.30
4469	9338	1.343884	CCTGATCACCTCTTCCTCCCT	60.344	57.143	0.00	0.00	0.00	4.20
4470	9339	2.038659	CTGATCACCTCTTCCTCCCTC	58.961	57.143	0.00	0.00	0.00	4.30
4471	9340	1.343478	TGATCACCTCTTCCTCCCTCC	60.343	57.143	0.00	0.00	0.00	4.30
4472	9341	0.030603	ATCACCTCTTCCTCCCTCCC	60.031	60.000	0.00	0.00	0.00	4.30
4473	9342	2.060980	CACCTCTTCCTCCCTCCCG	61.061	68.421	0.00	0.00	0.00	5.14
4474	9343	2.246874	ACCTCTTCCTCCCTCCCGA	61.247	63.158	0.00	0.00	0.00	5.14
4475	9344	1.234529	CCTCTTCCTCCCTCCCGAT	59.765	63.158	0.00	0.00	0.00	4.18
4476	9345	0.830023	CCTCTTCCTCCCTCCCGATC	60.830	65.000	0.00	0.00	0.00	3.69
4477	9346	0.830023	CTCTTCCTCCCTCCCGATCC	60.830	65.000	0.00	0.00	0.00	3.36
4478	9347	1.075226	CTTCCTCCCTCCCGATCCA	60.075	63.158	0.00	0.00	0.00	3.41
4497	9366	2.439156	GGAGGGGCAGATGTGTGC	60.439	66.667	0.00	0.00	43.19	4.57
4573	9442	0.387878	CTCTCCTGTGACACGACAGC	60.388	60.000	0.22	0.00	41.85	4.40
4604	9473	2.520500	TGCACCCGCATTTGTGGT	60.521	55.556	9.19	0.00	45.36	4.16
4605	9474	2.049248	GCACCCGCATTTGTGGTG	60.049	61.111	9.19	11.78	43.97	4.17
4606	9475	2.049248	CACCCGCATTTGTGGTGC	60.049	61.111	9.19	0.00	43.97	5.01
4607	9476	2.203480	ACCCGCATTTGTGGTGCT	60.203	55.556	9.19	0.00	43.97	4.40
4608	9477	1.074072	ACCCGCATTTGTGGTGCTA	59.926	52.632	9.19	0.00	43.97	3.49
4609	9478	1.241315	ACCCGCATTTGTGGTGCTAC	61.241	55.000	9.19	0.00	43.97	3.58
4610	9479	1.506262	CCGCATTTGTGGTGCTACC	59.494	57.895	1.88	0.00	40.69	3.18
4611	9480	1.134487	CGCATTTGTGGTGCTACCG	59.866	57.895	0.00	0.00	42.58	4.02
4613	9482	1.241315	GCATTTGTGGTGCTACCGGT	61.241	55.000	13.98	13.98	42.58	5.28
4614	9483	0.521291	CATTTGTGGTGCTACCGGTG	59.479	55.000	19.93	8.61	42.58	4.94
4615	9484	1.241315	ATTTGTGGTGCTACCGGTGC	61.241	55.000	19.93	19.04	42.58	5.01
4616	9485	2.610532	TTTGTGGTGCTACCGGTGCA	62.611	55.000	19.93	21.51	42.58	4.57
4621	9490	2.920384	TGCTACCGGTGCACTGGA	60.920	61.111	44.14	27.99	45.36	3.86
4622	9491	2.290287	TGCTACCGGTGCACTGGAT	61.290	57.895	44.14	30.66	45.36	3.41
4623	9492	1.815421	GCTACCGGTGCACTGGATG	60.815	63.158	44.14	33.87	45.36	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
408	413	2.289756	TGTCAAGCTACCGGCATAAACA	60.290	45.455	0.00	0.00	44.79	2.83
538	609	3.925630	ATCGCCCAGGCCTGTTGTG	62.926	63.158	30.63	25.32	37.98	3.33
539	610	2.713531	AAATCGCCCAGGCCTGTTGT	62.714	55.000	30.63	9.57	37.98	3.32
550	621	0.850856	CTTACGCTACGAAATCGCCC	59.149	55.000	2.15	0.00	44.43	6.13
555	626	3.256558	GTGTTCCCTTACGCTACGAAAT	58.743	45.455	0.00	0.00	0.00	2.17
588	661	7.318909	GCGAGTGTGAATATTTATTTGTCGATG	59.681	37.037	9.75	0.00	0.00	3.84
814	889	1.153005	CTGCAGAAGGGGATCTGGC	60.153	63.158	8.42	0.46	45.60	4.85
847	928	4.686972	TCAAACAGCTCGGATCTAATCTG	58.313	43.478	0.00	0.00	36.99	2.90
851	932	4.081142	TGGAATCAAACAGCTCGGATCTAA	60.081	41.667	0.00	0.00	0.00	2.10
929	5122	2.658373	GATGCAATCAACACATGGCA	57.342	45.000	0.00	0.00	44.70	4.92
1033	5263	1.610673	TGCTCTCACTGACCTCCCC	60.611	63.158	0.00	0.00	0.00	4.81
1050	5758	1.232792	CCCTCTCCTCCTCCTCCTG	59.767	68.421	0.00	0.00	0.00	3.86
1051	5759	2.018086	CCCCTCTCCTCCTCCTCCT	61.018	68.421	0.00	0.00	0.00	3.69
1052	5760	1.595058	TTCCCCTCTCCTCCTCCTCC	61.595	65.000	0.00	0.00	0.00	4.30
1065	5779	2.162906	AGTGGCCATGTGTTCCCCT	61.163	57.895	9.72	0.00	0.00	4.79
1590	6319	4.567537	CCATTGATCAACCTCACCACCTTA	60.568	45.833	11.07	0.00	0.00	2.69
2093	6841	0.242017	ACGCAAATCTCTTGCCAAGC	59.758	50.000	0.00	0.00	42.10	4.01
2444	7202	2.224018	TGCTTGCAGACAAATTTGGACC	60.224	45.455	21.74	10.54	34.74	4.46
2624	7382	5.106157	ACCTTTGTATCAAGCAATGTACTGC	60.106	40.000	0.00	0.00	42.97	4.40
3012	7770	5.508567	TCATTCATCCAGTAAAGCATTCCA	58.491	37.500	0.00	0.00	0.00	3.53
3021	7779	5.255397	ACCTTGGTTCATTCATCCAGTAA	57.745	39.130	0.00	0.00	32.63	2.24
3341	8099	1.003580	TGTTGAGCAGGATCTTCCCAC	59.996	52.381	0.00	0.00	37.19	4.61
3771	8569	6.055588	CAGAGGGAGTTCTTCACAGTAAAAA	58.944	40.000	0.00	0.00	0.00	1.94
3987	8788	2.032799	ACACGGCAAACAACATACACAG	59.967	45.455	0.00	0.00	0.00	3.66
4167	8969	4.210331	GGGCACTCTGGTGATTTATCATT	58.790	43.478	0.00	0.00	45.61	2.57
4293	9161	8.650143	AGTGTCTTCACCCATTGTATTTATTT	57.350	30.769	0.00	0.00	44.83	1.40
4294	9162	9.747898	TTAGTGTCTTCACCCATTGTATTTATT	57.252	29.630	0.00	0.00	44.83	1.40
4295	9163	9.747898	TTTAGTGTCTTCACCCATTGTATTTAT	57.252	29.630	0.00	0.00	44.83	1.40
4296	9164	9.747898	ATTTAGTGTCTTCACCCATTGTATTTA	57.252	29.630	0.00	0.00	44.83	1.40
4333	9201	1.209504	TCCGCTGGTTGAAGGGAATAG	59.790	52.381	0.00	0.00	32.03	1.73
4334	9202	1.281419	TCCGCTGGTTGAAGGGAATA	58.719	50.000	0.00	0.00	32.03	1.75
4404	9273	2.575993	GCTGAGAGCTGCGAAGGA	59.424	61.111	0.00	0.00	38.45	3.36
4413	9282	0.529555	GTCATTCGGGAGCTGAGAGC	60.530	60.000	0.00	0.00	42.84	4.09
4414	9283	0.103937	GGTCATTCGGGAGCTGAGAG	59.896	60.000	0.00	0.00	32.68	3.20
4415	9284	0.614697	TGGTCATTCGGGAGCTGAGA	60.615	55.000	0.00	0.00	36.30	3.27
4416	9285	0.460987	GTGGTCATTCGGGAGCTGAG	60.461	60.000	0.00	0.00	36.30	3.35
4417	9286	0.904865	AGTGGTCATTCGGGAGCTGA	60.905	55.000	0.00	0.00	36.30	4.26
4418	9287	0.460987	GAGTGGTCATTCGGGAGCTG	60.461	60.000	0.00	0.00	36.30	4.24
4419	9288	1.901085	GAGTGGTCATTCGGGAGCT	59.099	57.895	0.00	0.00	36.30	4.09
4420	9289	1.519455	CGAGTGGTCATTCGGGAGC	60.519	63.158	7.79	0.00	36.98	4.70
4421	9290	0.179134	GACGAGTGGTCATTCGGGAG	60.179	60.000	17.54	0.00	45.36	4.30
4422	9291	1.888018	GACGAGTGGTCATTCGGGA	59.112	57.895	17.54	0.00	45.36	5.14
4423	9292	4.496670	GACGAGTGGTCATTCGGG	57.503	61.111	17.54	0.00	45.36	5.14
4430	9299	0.173708	GATGAGGTGGACGAGTGGTC	59.826	60.000	0.00	0.00	45.31	4.02
4431	9300	1.258445	GGATGAGGTGGACGAGTGGT	61.258	60.000	0.00	0.00	0.00	4.16
4432	9301	0.972983	AGGATGAGGTGGACGAGTGG	60.973	60.000	0.00	0.00	0.00	4.00
4433	9302	0.174389	CAGGATGAGGTGGACGAGTG	59.826	60.000	0.00	0.00	39.69	3.51
4434	9303	0.039764	TCAGGATGAGGTGGACGAGT	59.960	55.000	0.00	0.00	42.56	4.18
4435	9304	2.887790	TCAGGATGAGGTGGACGAG	58.112	57.895	0.00	0.00	42.56	4.18
4446	9315	2.368221	GGAGGAAGAGGTGATCAGGATG	59.632	54.545	0.00	0.00	37.54	3.51
4447	9316	2.688477	GGAGGAAGAGGTGATCAGGAT	58.312	52.381	0.00	0.00	0.00	3.24
4448	9317	1.343478	GGGAGGAAGAGGTGATCAGGA	60.343	57.143	0.00	0.00	0.00	3.86
4449	9318	1.127343	GGGAGGAAGAGGTGATCAGG	58.873	60.000	0.00	0.00	0.00	3.86
4450	9319	2.038659	GAGGGAGGAAGAGGTGATCAG	58.961	57.143	0.00	0.00	0.00	2.90
4451	9320	1.343478	GGAGGGAGGAAGAGGTGATCA	60.343	57.143	0.00	0.00	0.00	2.92
4452	9321	1.419381	GGAGGGAGGAAGAGGTGATC	58.581	60.000	0.00	0.00	0.00	2.92
4453	9322	0.030603	GGGAGGGAGGAAGAGGTGAT	60.031	60.000	0.00	0.00	0.00	3.06
4454	9323	1.392534	GGGAGGGAGGAAGAGGTGA	59.607	63.158	0.00	0.00	0.00	4.02
4455	9324	2.060980	CGGGAGGGAGGAAGAGGTG	61.061	68.421	0.00	0.00	0.00	4.00
4456	9325	1.595058	ATCGGGAGGGAGGAAGAGGT	61.595	60.000	0.00	0.00	0.00	3.85
4457	9326	0.830023	GATCGGGAGGGAGGAAGAGG	60.830	65.000	0.00	0.00	0.00	3.69
4458	9327	0.830023	GGATCGGGAGGGAGGAAGAG	60.830	65.000	0.00	0.00	0.00	2.85
4459	9328	1.233369	GGATCGGGAGGGAGGAAGA	59.767	63.158	0.00	0.00	0.00	2.87
4460	9329	1.075226	TGGATCGGGAGGGAGGAAG	60.075	63.158	0.00	0.00	0.00	3.46
4461	9330	1.075226	CTGGATCGGGAGGGAGGAA	60.075	63.158	0.00	0.00	0.00	3.36
4462	9331	2.609339	CTGGATCGGGAGGGAGGA	59.391	66.667	0.00	0.00	0.00	3.71
4463	9332	2.525381	CCTGGATCGGGAGGGAGG	60.525	72.222	0.00	0.00	29.82	4.30
4472	9341	3.554342	CTGCCCCTCCCTGGATCG	61.554	72.222	0.00	0.00	38.35	3.69
4473	9342	1.463018	ATCTGCCCCTCCCTGGATC	60.463	63.158	0.00	0.00	38.35	3.36
4474	9343	1.773391	CATCTGCCCCTCCCTGGAT	60.773	63.158	0.00	0.00	38.35	3.41
4475	9344	2.367377	CATCTGCCCCTCCCTGGA	60.367	66.667	0.00	0.00	38.35	3.86
4476	9345	2.693864	ACATCTGCCCCTCCCTGG	60.694	66.667	0.00	0.00	0.00	4.45
4477	9346	2.304056	ACACATCTGCCCCTCCCTG	61.304	63.158	0.00	0.00	0.00	4.45
4478	9347	2.125912	ACACATCTGCCCCTCCCT	59.874	61.111	0.00	0.00	0.00	4.20
4573	9442	1.299541	GGTGCACCGATACATTCCTG	58.700	55.000	22.49	0.00	0.00	3.86
4597	9466	1.894756	GCACCGGTAGCACCACAAA	60.895	57.895	19.85	0.00	38.47	2.83
4604	9473	2.290287	ATCCAGTGCACCGGTAGCA	61.290	57.895	22.47	22.47	40.19	3.49
4605	9474	1.815421	CATCCAGTGCACCGGTAGC	60.815	63.158	18.59	14.59	0.00	3.58
4606	9475	4.521075	CATCCAGTGCACCGGTAG	57.479	61.111	18.59	8.81	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.