AutoCloner

Multiple sequence alignment - TraesCS7A01G071400

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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	TraesCS7A01G071400	chr7A	100.000	6665	0	0	1	6665	37094440	37087776	0.000000e+00	12309.0
1	TraesCS7A01G071400	chr7A	88.020	409	29	5	5818	6207	85813668	85814075	3.640000e-127	466.0
2	TraesCS7A01G071400	chr7A	96.266	241	5	1	566	802	37088863	37088623	6.270000e-105	392.0
3	TraesCS7A01G071400	chr7A	96.266	241	5	1	5578	5818	37093875	37093639	6.270000e-105	392.0
4	TraesCS7A01G071400	chr7A	92.500	40	3	0	5079	5118	29542552	29542591	2.600000e-04	58.4
5	TraesCS7A01G071400	chr6B	98.992	5060	46	4	505	5561	629119	634176	0.000000e+00	9057.0
6	TraesCS7A01G071400	chr6B	97.010	301	6	2	505	802	634199	634499	2.770000e-138	503.0
7	TraesCS7A01G071400	chr6B	95.016	321	12	2	6345	6665	11703815	11703499	9.980000e-138	501.0
8	TraesCS7A01G071400	chr6B	94.154	325	11	4	6345	6665	707183252	707182932	7.770000e-134	488.0
9	TraesCS7A01G071400	chr6B	97.521	242	3	3	5578	5818	634260	634499	1.730000e-110	411.0
10	TraesCS7A01G071400	chr6B	97.083	240	3	3	5578	5816	629180	629416	1.040000e-107	401.0
11	TraesCS7A01G071400	chr2A	96.372	1075	37	2	4487	5559	335704930	335706004	0.000000e+00	1768.0
12	TraesCS7A01G071400	chr2A	95.630	801	32	3	3697	4497	335696368	335697165	0.000000e+00	1282.0
13	TraesCS7A01G071400	chr2A	97.460	315	8	0	6351	6665	21211396	21211710	7.610000e-149	538.0
14	TraesCS7A01G071400	chr2A	95.950	321	10	1	6345	6665	736458018	736457701	9.910000e-143	518.0
15	TraesCS7A01G071400	chr2A	96.575	292	9	1	6345	6636	744849332	744849042	3.610000e-132	483.0
16	TraesCS7A01G071400	chr2A	90.268	298	25	3	505	800	335706029	335706324	2.920000e-103	387.0
17	TraesCS7A01G071400	chr2A	89.916	238	20	3	5579	5816	335706091	335706324	3.020000e-78	303.0
18	TraesCS7A01G071400	chr2A	80.952	399	31	18	132	507	21210751	21211127	2.370000e-69	274.0
19	TraesCS7A01G071400	chr1B	92.545	550	22	12	5818	6351	32422312	32422858	0.000000e+00	771.0
20	TraesCS7A01G071400	chr1B	96.037	429	13	3	5923	6351	606008234	606007810	0.000000e+00	695.0
21	TraesCS7A01G071400	chr1B	88.281	512	31	11	25	507	32421810	32422321	2.680000e-163	586.0
22	TraesCS7A01G071400	chrUn	92.518	548	24	11	5818	6351	38658306	38658850	0.000000e+00	769.0
23	TraesCS7A01G071400	chrUn	88.258	511	32	10	25	507	38657805	38658315	2.680000e-163	586.0
24	TraesCS7A01G071400	chrUn	98.413	315	5	0	6351	6665	401014339	401014653	7.550000e-154	555.0
25	TraesCS7A01G071400	chrUn	89.695	262	12	9	5818	6066	478574227	478574486	3.000000e-83	320.0
26	TraesCS7A01G071400	chrUn	81.203	399	30	18	132	507	367366796	367366420	5.090000e-71	279.0
27	TraesCS7A01G071400	chr5B	92.058	554	21	12	5818	6351	591688759	591688209	0.000000e+00	758.0
28	TraesCS7A01G071400	chr5B	95.632	435	15	3	5917	6351	19065535	19065965	0.000000e+00	695.0
29	TraesCS7A01G071400	chr5B	87.867	511	32	12	27	507	591689260	591688750	2.080000e-159	573.0
30	TraesCS7A01G071400	chr2B	92.153	548	26	11	5818	6351	576686194	576685650	0.000000e+00	758.0
31	TraesCS7A01G071400	chr2B	88.063	511	33	10	25	507	576686695	576686185	1.250000e-161	580.0
32	TraesCS7A01G071400	chr2B	96.573	321	8	1	6345	6665	721698462	721698779	4.580000e-146	529.0
33	TraesCS7A01G071400	chr2B	90.385	208	15	2	305	507	109402872	109403079	1.100000e-67	268.0
34	TraesCS7A01G071400	chr3B	96.270	429	12	3	5923	6351	182540516	182540092	0.000000e+00	701.0
35	TraesCS7A01G071400	chr3B	95.632	435	15	3	5917	6351	216365207	216365637	0.000000e+00	695.0
36	TraesCS7A01G071400	chr7B	96.037	429	13	3	5923	6351	337276806	337276382	0.000000e+00	695.0
37	TraesCS7A01G071400	chr7B	99.048	315	3	0	6351	6665	585483687	585483373	3.490000e-157	566.0
38	TraesCS7A01G071400	chr7B	88.020	409	29	5	5818	6207	537736423	537736016	3.640000e-127	466.0
39	TraesCS7A01G071400	chr7B	80.460	522	41	22	25	507	585484455	585483956	6.400000e-90	342.0
40	TraesCS7A01G071400	chr7B	90.385	208	15	4	305	507	686133302	686133509	1.100000e-67	268.0
41	TraesCS7A01G071400	chr7B	94.444	36	2	0	4571	4606	60072798	60072763	1.000000e-03	56.5
42	TraesCS7A01G071400	chr5A	96.037	429	13	3	5923	6351	373558852	373558428	0.000000e+00	695.0
43	TraesCS7A01G071400	chr5A	87.990	408	30	6	5818	6207	395305759	395306165	1.310000e-126	464.0
44	TraesCS7A01G071400	chr5A	87.775	409	30	5	5818	6207	549369009	549368602	1.690000e-125	460.0
45	TraesCS7A01G071400	chr4B	95.402	435	16	3	5917	6351	235043375	235043805	0.000000e+00	689.0
46	TraesCS7A01G071400	chr4B	95.804	429	14	3	5923	6351	281361480	281361056	0.000000e+00	689.0
47	TraesCS7A01G071400	chr1A	95.402	435	16	3	5917	6351	551839157	551839587	0.000000e+00	689.0
48	TraesCS7A01G071400	chr4A	96.262	321	9	1	6345	6665	622187608	622187925	2.130000e-144	523.0
49	TraesCS7A01G071400	chr6D	90.385	208	15	2	305	507	94293433	94293226	1.100000e-67	268.0
50	TraesCS7A01G071400	chr6D	89.904	208	16	2	305	507	34848919	34848712	5.130000e-66	263.0
51	TraesCS7A01G071400	chr6D	73.418	316	78	5	4677	4989	162270691	162271003	5.460000e-21	113.0
52	TraesCS7A01G071400	chr1D	90.385	208	15	2	305	507	87845841	87845634	1.100000e-67	268.0
53	TraesCS7A01G071400	chr4D	94.805	77	4	0	171	247	337055216	337055140	3.260000e-23	121.0
54	TraesCS7A01G071400	chr6A	80.519	154	26	4	4676	4827	503590799	503590950	1.520000e-21	115.0
55	TraesCS7A01G071400	chr5D	79.839	124	21	3	2030	2151	398574771	398574892	3.310000e-13	87.9
56	TraesCS7A01G071400	chr3D	94.444	36	2	0	4571	4606	15038039	15038004	1.000000e-03	56.5

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	TraesCS7A01G071400	chr7A	37087776	37094440	6664	True	12309.000000	12309	100.000000	1	6665	1	chr7A.!!$R1	6664
1	TraesCS7A01G071400	chr6B	629119	634176	5057	False	9057.000000	9057	98.992000	505	5561	1	chr6B.!!$F1	5056
2	TraesCS7A01G071400	chr2A	335696368	335697165	797	False	1282.000000	1282	95.630000	3697	4497	1	chr2A.!!$F1	800
3	TraesCS7A01G071400	chr2A	335704930	335706324	1394	False	819.333333	1768	92.185333	505	5816	3	chr2A.!!$F3	5311
4	TraesCS7A01G071400	chr2A	21210751	21211710	959	False	406.000000	538	89.206000	132	6665	2	chr2A.!!$F2	6533
5	TraesCS7A01G071400	chr1B	32421810	32422858	1048	False	678.500000	771	90.413000	25	6351	2	chr1B.!!$F1	6326
6	TraesCS7A01G071400	chrUn	38657805	38658850	1045	False	677.500000	769	90.388000	25	6351	2	chrUn.!!$F3	6326
7	TraesCS7A01G071400	chr5B	591688209	591689260	1051	True	665.500000	758	89.962500	27	6351	2	chr5B.!!$R1	6324
8	TraesCS7A01G071400	chr2B	576685650	576686695	1045	True	669.000000	758	90.108000	25	6351	2	chr2B.!!$R1	6326
9	TraesCS7A01G071400	chr7B	585483373	585484455	1082	True	454.000000	566	89.754000	25	6665	2	chr7B.!!$R4	6640

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
764	811	0.036294	CCCGTCTTCCCTCTGTTTCC	60.036	60.000	0.00	0.00	0.00	3.13	F
1068	1115	0.169009	GATTCGGCACCAAGCTTGAC	59.831	55.000	28.05	15.66	44.79	3.18	F
1839	1886	0.676466	CCTCCTTGGCACGCATACAA	60.676	55.000	0.00	0.00	0.00	2.41	F
3026	3073	0.875728	TTTTGTGTGGATTACGGGCG	59.124	50.000	0.00	0.00	0.00	6.13	F
3249	3296	1.004918	GACCAACGCACCAGCTACT	60.005	57.895	0.00	0.00	39.10	2.57	F
3621	3668	4.893524	TGGATATCAAAGCCTCTTACTCGA	59.106	41.667	4.83	0.00	0.00	4.04	F
5576	5623	0.100146	GAGGTTCTTCGCCGTCGTAT	59.900	55.000	0.00	0.00	36.96	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2007	2054	1.007387	GAAGCAAAGGCCGTTGGTG	60.007	57.895	31.89	10.52	42.56	4.17	R
3022	3069	0.102300	GTGGCATCATTTAACCGCCC	59.898	55.000	0.00	0.00	42.27	6.13	R
3078	3125	1.089920	CTGCCAATTCGTCCAAGAGG	58.910	55.000	0.00	0.00	0.00	3.69	R
3961	4008	2.361757	CAGTGCCCAATTGTTGTTCAGA	59.638	45.455	4.43	0.00	0.00	3.27	R
4127	4174	3.963129	TGGGTAACATCCAGAATCCAAC	58.037	45.455	0.00	0.00	39.74	3.77	R
5599	5713	0.392193	CTTGATGCGCCTCTGAACCT	60.392	55.000	13.93	0.00	0.00	3.50	R
6534	6670	0.588252	ACGCATCTTATCATTGCCGC	59.412	50.000	0.00	0.00	32.76	6.53	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
18	19	1.784062	CTCGAAGCAAACAGAGGCG	59.216	57.895	0.00	0.00	34.54	5.52
19	20	0.667487	CTCGAAGCAAACAGAGGCGA	60.667	55.000	0.00	0.00	34.54	5.54
20	21	0.667487	TCGAAGCAAACAGAGGCGAG	60.667	55.000	0.00	0.00	34.54	5.03
21	22	1.630244	CGAAGCAAACAGAGGCGAGG	61.630	60.000	0.00	0.00	34.54	4.63
22	23	0.603975	GAAGCAAACAGAGGCGAGGT	60.604	55.000	0.00	0.00	34.54	3.85
23	24	0.685097	AAGCAAACAGAGGCGAGGTA	59.315	50.000	0.00	0.00	34.54	3.08
136	153	1.005394	GACTTGTTCCTTCCGGCGA	60.005	57.895	9.30	0.00	0.00	5.54
179	196	2.186826	GTGTTCCTTGCGGCAGTGT	61.187	57.895	1.67	0.00	0.00	3.55
285	318	1.492176	ACCTAGGCTGCTGCAACATAT	59.508	47.619	17.89	0.00	41.91	1.78
286	319	2.149578	CCTAGGCTGCTGCAACATATC	58.850	52.381	17.89	0.00	41.91	1.63
287	320	2.224475	CCTAGGCTGCTGCAACATATCT	60.224	50.000	17.89	5.77	41.91	1.98
289	322	0.585357	GGCTGCTGCAACATATCTCG	59.415	55.000	17.89	0.00	41.91	4.04
290	323	0.041488	GCTGCTGCAACATATCTCGC	60.041	55.000	11.11	0.00	39.41	5.03
291	324	1.579698	CTGCTGCAACATATCTCGCT	58.420	50.000	3.02	0.00	0.00	4.93
292	325	1.526041	CTGCTGCAACATATCTCGCTC	59.474	52.381	3.02	0.00	0.00	5.03
293	326	1.137675	TGCTGCAACATATCTCGCTCT	59.862	47.619	0.00	0.00	0.00	4.09
294	327	1.791785	GCTGCAACATATCTCGCTCTC	59.208	52.381	0.00	0.00	0.00	3.20
295	328	2.800985	GCTGCAACATATCTCGCTCTCA	60.801	50.000	0.00	0.00	0.00	3.27
298	331	2.481969	GCAACATATCTCGCTCTCACCA	60.482	50.000	0.00	0.00	0.00	4.17
301	334	3.225940	ACATATCTCGCTCTCACCATCA	58.774	45.455	0.00	0.00	0.00	3.07
302	335	3.638627	ACATATCTCGCTCTCACCATCAA	59.361	43.478	0.00	0.00	0.00	2.57
303	336	2.886862	ATCTCGCTCTCACCATCAAG	57.113	50.000	0.00	0.00	0.00	3.02
316	359	2.289945	ACCATCAAGACCAGCTCTGAAC	60.290	50.000	0.00	0.00	0.00	3.18
360	404	2.361757	AGATCTCGCTCTCACCATCAAG	59.638	50.000	0.00	0.00	0.00	3.02
395	439	3.782046	ACAACCCGTAAGAATGATCTCG	58.218	45.455	0.00	0.00	43.02	4.04
423	467	2.371897	CTTGCCCCCTTCCCTGTGTT	62.372	60.000	0.00	0.00	0.00	3.32
432	476	3.500343	CCTTCCCTGTGTTTCTCCATTT	58.500	45.455	0.00	0.00	0.00	2.32
468	512	3.118149	ACTTGATGGCTAGATCATGCACA	60.118	43.478	11.18	7.58	33.03	4.57
572	616	0.249657	GATCCCGTCAGCTGTGATCC	60.250	60.000	14.67	3.67	34.36	3.36
573	617	0.977627	ATCCCGTCAGCTGTGATCCA	60.978	55.000	14.67	0.00	34.36	3.41
693	739	5.427157	TGCCTATAGATAAGGACCAACAACA	59.573	40.000	0.00	0.00	36.08	3.33
707	753	3.058708	CCAACAACATGTACTGTGCAGAG	60.059	47.826	9.74	9.74	38.39	3.35
721	768	4.654915	TGTGCAGAGAGGAAAATGAATGA	58.345	39.130	0.00	0.00	0.00	2.57
738	785	8.475331	AATGAATGAAAACTGAATTCTGCATC	57.525	30.769	11.86	8.44	32.63	3.91
764	811	0.036294	CCCGTCTTCCCTCTGTTTCC	60.036	60.000	0.00	0.00	0.00	3.13
1068	1115	0.169009	GATTCGGCACCAAGCTTGAC	59.831	55.000	28.05	15.66	44.79	3.18
1168	1215	2.961522	TGAAGAAATTCGCCGTCAAC	57.038	45.000	0.00	0.00	0.00	3.18
1732	1779	3.748568	GGATGAATCCTTGAGTAATCGCC	59.251	47.826	1.86	0.00	43.73	5.54
1839	1886	0.676466	CCTCCTTGGCACGCATACAA	60.676	55.000	0.00	0.00	0.00	2.41
1840	1887	1.164411	CTCCTTGGCACGCATACAAA	58.836	50.000	0.00	0.00	0.00	2.83
2007	2054	1.017701	AACTCCGGGATTTTCGTCGC	61.018	55.000	0.00	0.00	0.00	5.19
2094	2141	4.201891	GCACATGTCCTGATGATTGAAGTC	60.202	45.833	0.00	0.00	0.00	3.01
2287	2334	6.588756	GGTGATGTTGTTGTTAGTCGATTCTA	59.411	38.462	0.00	0.00	0.00	2.10
2364	2411	7.151308	CAGTCACCAAGATATCTCCTATCAAC	58.849	42.308	5.51	0.00	39.03	3.18
2436	2483	2.292267	CTACAATGGTGGTCTCATGGC	58.708	52.381	0.00	0.00	0.00	4.40
2810	2857	1.633432	CAAGTCCTTACCACCCCATCA	59.367	52.381	0.00	0.00	0.00	3.07
2863	2910	3.887716	AGATGCAAGGCCAATCAATACTC	59.112	43.478	5.01	0.00	0.00	2.59
3022	3069	2.287069	TGGCGTTTTTGTGTGGATTACG	60.287	45.455	0.00	0.00	0.00	3.18
3026	3073	0.875728	TTTTGTGTGGATTACGGGCG	59.124	50.000	0.00	0.00	0.00	6.13
3150	3197	2.028658	GGCAGGCTATCATCAGATTCGA	60.029	50.000	0.00	0.00	35.67	3.71
3249	3296	1.004918	GACCAACGCACCAGCTACT	60.005	57.895	0.00	0.00	39.10	2.57
3620	3667	5.201713	TGGATATCAAAGCCTCTTACTCG	57.798	43.478	4.83	0.00	0.00	4.18
3621	3668	4.893524	TGGATATCAAAGCCTCTTACTCGA	59.106	41.667	4.83	0.00	0.00	4.04
3961	4008	5.435686	TCACAAGTCCTTATGCACCTTAT	57.564	39.130	0.00	0.00	0.00	1.73
4127	4174	2.223249	CGTTGTCAGTTTGTCAACCTGG	60.223	50.000	9.94	0.00	41.21	4.45
4148	4195	3.308832	GGTTGGATTCTGGATGTTACCCA	60.309	47.826	0.00	0.00	0.00	4.51
4241	4288	2.678336	GTTTTTCTCTGGATAGTGGCCG	59.322	50.000	0.00	0.00	0.00	6.13
5148	5195	0.608035	TGTTTCAGGTGGGCGATTCC	60.608	55.000	0.00	0.00	0.00	3.01
5378	5425	2.262915	GTCTCTGCCACCTCCACG	59.737	66.667	0.00	0.00	0.00	4.94
5388	5435	0.880278	CACCTCCACGTGTGTTCCAG	60.880	60.000	15.65	0.00	0.00	3.86
5561	5608	0.831307	GCTCCTATTTGGGACGAGGT	59.169	55.000	0.00	0.00	36.20	3.85
5564	5611	2.766828	CTCCTATTTGGGACGAGGTTCT	59.233	50.000	0.00	0.00	36.20	3.01
5566	5613	3.197116	TCCTATTTGGGACGAGGTTCTTC	59.803	47.826	0.00	0.00	36.20	2.87
5567	5614	2.094762	ATTTGGGACGAGGTTCTTCG	57.905	50.000	2.97	2.97	45.70	3.79
5568	5615	0.601841	TTTGGGACGAGGTTCTTCGC	60.602	55.000	4.36	0.00	44.15	4.70
5569	5616	2.125633	GGGACGAGGTTCTTCGCC	60.126	66.667	4.36	6.72	44.15	5.54
5570	5617	2.506438	GGACGAGGTTCTTCGCCG	60.506	66.667	4.36	0.00	44.15	6.46
5571	5618	2.257676	GACGAGGTTCTTCGCCGT	59.742	61.111	4.36	0.00	44.15	5.68
5572	5619	1.800713	GACGAGGTTCTTCGCCGTC	60.801	63.158	4.36	0.00	44.15	4.79
5574	5621	2.257676	GAGGTTCTTCGCCGTCGT	59.742	61.111	0.00	0.00	36.96	4.34
5575	5622	1.503542	GAGGTTCTTCGCCGTCGTA	59.496	57.895	0.00	0.00	36.96	3.43
5576	5623	0.100146	GAGGTTCTTCGCCGTCGTAT	59.900	55.000	0.00	0.00	36.96	3.06
5577	5624	0.529378	AGGTTCTTCGCCGTCGTATT	59.471	50.000	0.00	0.00	36.96	1.89
5585	5699	1.537289	CGCCGTCGTATTGTGATCCG	61.537	60.000	0.00	0.00	0.00	4.18
5599	5713	4.443621	TGTGATCCGTTTGACAACTAACA	58.556	39.130	0.00	0.00	32.90	2.41
5610	5724	3.067833	GACAACTAACAGGTTCAGAGGC	58.932	50.000	0.00	0.00	0.00	4.70
5614	5728	0.613260	TAACAGGTTCAGAGGCGCAT	59.387	50.000	10.83	0.00	0.00	4.73
5626	5740	3.818787	GCGCATCAAGGCAGGGTG	61.819	66.667	0.30	0.00	0.00	4.61
5627	5741	2.360350	CGCATCAAGGCAGGGTGT	60.360	61.111	0.00	0.00	0.00	4.16
5628	5742	2.693762	CGCATCAAGGCAGGGTGTG	61.694	63.158	0.00	0.00	0.00	3.82
5648	5762	3.415983	TGTGTGTGTGTGGGGCCT	61.416	61.111	0.84	0.00	0.00	5.19
5681	5795	2.216750	TAAGGCGAGTGCGTGTACCC	62.217	60.000	0.00	0.00	44.10	3.69
5705	5819	6.331061	CGTATGCCTATAGATAAGGACCAAC	58.669	44.000	0.00	0.00	36.08	3.77
5714	5828	5.161943	AGATAAGGACCAACAACCTGTAC	57.838	43.478	0.00	0.00	36.56	2.90
5717	5831	2.124411	AGGACCAACAACCTGTACTGT	58.876	47.619	0.00	0.00	34.99	3.55
5721	5835	1.603802	CCAACAACCTGTACTGTGCAG	59.396	52.381	17.58	17.58	0.00	4.41
5723	5837	2.533266	ACAACCTGTACTGTGCAGAG	57.467	50.000	24.66	17.03	36.12	3.35
5725	5839	2.036475	ACAACCTGTACTGTGCAGAGAG	59.964	50.000	24.66	15.72	36.12	3.20
5743	5857	6.618811	CAGAGAGGAAAATGAATGGAAACTG	58.381	40.000	0.00	0.00	0.00	3.16
5766	5880	1.070445	CTGCATCTCATCCCCCGTC	59.930	63.158	0.00	0.00	0.00	4.79
5775	5889	1.383248	ATCCCCCGTCTTCCCTCTG	60.383	63.158	0.00	0.00	0.00	3.35
5789	5903	1.918957	CCCTCTGTTTCTCATCCCCTT	59.081	52.381	0.00	0.00	0.00	3.95
5791	5905	2.843113	CCTCTGTTTCTCATCCCCTTCT	59.157	50.000	0.00	0.00	0.00	2.85
5792	5906	3.265479	CCTCTGTTTCTCATCCCCTTCTT	59.735	47.826	0.00	0.00	0.00	2.52
5793	5907	4.260170	CTCTGTTTCTCATCCCCTTCTTG	58.740	47.826	0.00	0.00	0.00	3.02
5800	5914	3.118629	TCTCATCCCCTTCTTGTGATTCG	60.119	47.826	0.00	0.00	0.00	3.34
5802	5916	0.391130	TCCCCTTCTTGTGATTCGCG	60.391	55.000	0.00	0.00	0.00	5.87
5841	5955	1.271379	ACATGCAGCATTTGGTCTGTG	59.729	47.619	4.69	0.00	33.09	3.66
5888	6002	5.220228	CGATGTAGAGTTCGGTTTTGTGATC	60.220	44.000	0.00	0.00	0.00	2.92
6197	6325	3.343941	AGCTGCGGGTTTAGTTTGATA	57.656	42.857	0.00	0.00	0.00	2.15
6254	6388	7.065803	GCAATGTGACACATATATATGGGGTAC	59.934	40.741	25.27	21.86	41.37	3.34
6264	6398	9.213777	ACATATATATGGGGTACTGTAGGATTG	57.786	37.037	23.44	0.00	38.00	2.67
6534	6670	7.697352	TTGATTTTGCTTGTCAACATAACAG	57.303	32.000	0.00	0.00	33.73	3.16
6567	6703	0.749649	ATGCGTTGCCCTTGTGAAAA	59.250	45.000	0.00	0.00	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	0.667487	CTCGCCTCTGTTTGCTTCGA	60.667	55.000	0.00	0.00	0.00	3.71
2	3	1.630244	CCTCGCCTCTGTTTGCTTCG	61.630	60.000	0.00	0.00	0.00	3.79
3	4	0.603975	ACCTCGCCTCTGTTTGCTTC	60.604	55.000	0.00	0.00	0.00	3.86
5	6	0.247736	CTACCTCGCCTCTGTTTGCT	59.752	55.000	0.00	0.00	0.00	3.91
6	7	1.362406	GCTACCTCGCCTCTGTTTGC	61.362	60.000	0.00	0.00	0.00	3.68
7	8	1.078759	CGCTACCTCGCCTCTGTTTG	61.079	60.000	0.00	0.00	0.00	2.93
8	9	1.215647	CGCTACCTCGCCTCTGTTT	59.784	57.895	0.00	0.00	0.00	2.83
9	10	2.711922	CCGCTACCTCGCCTCTGTT	61.712	63.158	0.00	0.00	0.00	3.16
10	11	3.141488	CCGCTACCTCGCCTCTGT	61.141	66.667	0.00	0.00	0.00	3.41
11	12	4.577246	GCCGCTACCTCGCCTCTG	62.577	72.222	0.00	0.00	0.00	3.35
285	318	1.474478	GTCTTGATGGTGAGAGCGAGA	59.526	52.381	0.00	0.00	0.00	4.04
286	319	1.470632	GGTCTTGATGGTGAGAGCGAG	60.471	57.143	0.00	0.00	31.66	5.03
287	320	0.532573	GGTCTTGATGGTGAGAGCGA	59.467	55.000	0.00	0.00	31.66	4.93
289	322	2.011046	GCTGGTCTTGATGGTGAGAGC	61.011	57.143	0.00	0.00	40.02	4.09
290	323	1.554160	AGCTGGTCTTGATGGTGAGAG	59.446	52.381	0.00	0.00	0.00	3.20
291	324	1.552337	GAGCTGGTCTTGATGGTGAGA	59.448	52.381	0.00	0.00	0.00	3.27
292	325	1.554160	AGAGCTGGTCTTGATGGTGAG	59.446	52.381	3.02	0.00	27.07	3.51
293	326	1.277273	CAGAGCTGGTCTTGATGGTGA	59.723	52.381	6.64	0.00	30.64	4.02
294	327	1.277273	TCAGAGCTGGTCTTGATGGTG	59.723	52.381	6.64	0.00	30.64	4.17
295	328	1.649321	TCAGAGCTGGTCTTGATGGT	58.351	50.000	6.64	0.00	30.64	3.55
298	331	1.980765	TGGTTCAGAGCTGGTCTTGAT	59.019	47.619	6.64	0.00	30.64	2.57
301	334	1.202818	GGTTGGTTCAGAGCTGGTCTT	60.203	52.381	6.64	0.00	30.64	3.01
302	335	0.398318	GGTTGGTTCAGAGCTGGTCT	59.602	55.000	3.02	3.02	35.00	3.85
303	336	0.951040	CGGTTGGTTCAGAGCTGGTC	60.951	60.000	0.00	0.00	0.00	4.02
316	359	3.423154	GCTTGGAGCGTCGGTTGG	61.423	66.667	0.00	0.00	0.00	3.77
374	418	3.782046	CGAGATCATTCTTACGGGTTGT	58.218	45.455	0.00	0.00	30.30	3.32
395	439	4.432741	GGGGGCAAGGACAGAGGC	62.433	72.222	0.00	0.00	0.00	4.70
432	476	4.640201	GCCATCAAGTACTCCAAGCAAATA	59.360	41.667	0.00	0.00	0.00	1.40
468	512	4.648762	TCCACATTTCCACAAACACTTGAT	59.351	37.500	0.00	0.00	36.33	2.57
572	616	6.293626	CCTCTGAACCTGTTAGTTGTCAAATG	60.294	42.308	0.00	0.00	0.00	2.32
573	617	5.765182	CCTCTGAACCTGTTAGTTGTCAAAT	59.235	40.000	0.00	0.00	0.00	2.32
693	739	4.623932	TTTTCCTCTCTGCACAGTACAT	57.376	40.909	0.00	0.00	0.00	2.29
707	753	9.702494	AGAATTCAGTTTTCATTCATTTTCCTC	57.298	29.630	8.44	0.00	30.51	3.71
721	768	5.126707	GGGATGAGATGCAGAATTCAGTTTT	59.873	40.000	8.44	0.00	0.00	2.43
738	785	1.383248	AGGGAAGACGGGGGATGAG	60.383	63.158	0.00	0.00	0.00	2.90
764	811	2.292267	CGAATCACAAGAAGGGGATGG	58.708	52.381	0.00	0.00	0.00	3.51
800	847	2.037772	ACCAAGCTCTGAGTACCAACTG	59.962	50.000	6.53	0.00	35.56	3.16
1415	1462	1.811965	CCAAATCGATCCACAACAGCA	59.188	47.619	0.00	0.00	0.00	4.41
1727	1774	1.994507	CTGAGAGACGAACCGGCGAT	61.995	60.000	9.30	0.00	41.28	4.58
1732	1779	2.052157	GACAAACTGAGAGACGAACCG	58.948	52.381	0.00	0.00	0.00	4.44
1839	1886	1.375326	GTGTTCCGCCTCCTCCTTT	59.625	57.895	0.00	0.00	0.00	3.11
1840	1887	2.593956	GGTGTTCCGCCTCCTCCTT	61.594	63.158	0.00	0.00	0.00	3.36
2007	2054	1.007387	GAAGCAAAGGCCGTTGGTG	60.007	57.895	31.89	10.52	42.56	4.17
2094	2141	1.202770	AGAACTTCACCAAACTCCCCG	60.203	52.381	0.00	0.00	0.00	5.73
2364	2411	1.586154	GACCATTGGCCACCTTGACG	61.586	60.000	3.88	0.00	0.00	4.35
2810	2857	3.322828	GGTAATTGCATGATCCAAGGCAT	59.677	43.478	0.00	0.00	35.98	4.40
3022	3069	0.102300	GTGGCATCATTTAACCGCCC	59.898	55.000	0.00	0.00	42.27	6.13
3026	3073	4.396790	TCTTTACCGTGGCATCATTTAACC	59.603	41.667	0.00	0.00	0.00	2.85
3078	3125	1.089920	CTGCCAATTCGTCCAAGAGG	58.910	55.000	0.00	0.00	0.00	3.69
3150	3197	2.359900	GGTTCATCTTCCTCACGCATT	58.640	47.619	0.00	0.00	0.00	3.56
3249	3296	3.509184	TGGAATTCATCACGCATTGGAAA	59.491	39.130	7.93	0.00	0.00	3.13
3482	3529	6.748333	TTGCAGAAGTTTTCTCAGGATATG	57.252	37.500	0.00	0.00	38.11	1.78
3484	3531	5.649395	CCATTGCAGAAGTTTTCTCAGGATA	59.351	40.000	0.00	0.00	38.11	2.59
3620	3667	5.007332	TGAAAACCTTTCTTCGTAAGCAGTC	59.993	40.000	1.22	0.00	37.18	3.51
3621	3668	4.879545	TGAAAACCTTTCTTCGTAAGCAGT	59.120	37.500	1.22	0.00	37.18	4.40
3961	4008	2.361757	CAGTGCCCAATTGTTGTTCAGA	59.638	45.455	4.43	0.00	0.00	3.27
4127	4174	3.963129	TGGGTAACATCCAGAATCCAAC	58.037	45.455	0.00	0.00	39.74	3.77
4148	4195	7.195646	CGCAACAACATCCAATTCATAAGTAT	58.804	34.615	0.00	0.00	0.00	2.12
5378	5425	2.030805	GCTGAACAATCCTGGAACACAC	60.031	50.000	0.00	0.00	0.00	3.82
5388	5435	0.674895	ACGGCTGAGCTGAACAATCC	60.675	55.000	21.86	0.00	38.46	3.01
5561	5608	1.068402	TCACAATACGACGGCGAAGAA	60.068	47.619	22.49	0.00	41.64	2.52
5564	5611	1.552226	GATCACAATACGACGGCGAA	58.448	50.000	22.49	0.00	41.64	4.70
5566	5613	1.537289	CGGATCACAATACGACGGCG	61.537	60.000	10.39	10.39	42.13	6.46
5567	5614	0.526954	ACGGATCACAATACGACGGC	60.527	55.000	0.00	0.00	42.13	5.68
5568	5615	1.917273	AACGGATCACAATACGACGG	58.083	50.000	0.00	0.00	42.13	4.79
5569	5616	2.918600	TCAAACGGATCACAATACGACG	59.081	45.455	0.00	0.00	42.13	5.12
5570	5617	3.676172	TGTCAAACGGATCACAATACGAC	59.324	43.478	0.00	0.00	42.13	4.34
5571	5618	3.915536	TGTCAAACGGATCACAATACGA	58.084	40.909	0.00	0.00	42.13	3.43
5572	5619	4.151689	AGTTGTCAAACGGATCACAATACG	59.848	41.667	0.00	0.00	45.21	3.06
5574	5621	6.706716	TGTTAGTTGTCAAACGGATCACAATA	59.293	34.615	0.00	0.00	41.45	1.90
5575	5622	5.529430	TGTTAGTTGTCAAACGGATCACAAT	59.471	36.000	0.00	0.00	41.45	2.71
5576	5623	4.876679	TGTTAGTTGTCAAACGGATCACAA	59.123	37.500	0.00	0.00	41.45	3.33
5577	5624	4.443621	TGTTAGTTGTCAAACGGATCACA	58.556	39.130	0.00	0.00	41.45	3.58
5585	5699	5.007724	CCTCTGAACCTGTTAGTTGTCAAAC	59.992	44.000	0.00	0.00	36.47	2.93
5599	5713	0.392193	CTTGATGCGCCTCTGAACCT	60.392	55.000	13.93	0.00	0.00	3.50
5610	5724	2.360350	ACACCCTGCCTTGATGCG	60.360	61.111	0.00	0.00	0.00	4.73
5614	5728	1.152984	CACACACACCCTGCCTTGA	60.153	57.895	0.00	0.00	0.00	3.02
5626	5740	1.653094	CCCCACACACACACACACAC	61.653	60.000	0.00	0.00	0.00	3.82
5627	5741	1.377856	CCCCACACACACACACACA	60.378	57.895	0.00	0.00	0.00	3.72
5628	5742	2.770589	GCCCCACACACACACACAC	61.771	63.158	0.00	0.00	0.00	3.82
5648	5762	3.041351	CTTACACGCTGGCACGCA	61.041	61.111	8.93	0.00	36.19	5.24
5681	5795	6.071560	TGTTGGTCCTTATCTATAGGCATACG	60.072	42.308	0.00	0.00	32.59	3.06
5705	5819	2.611473	CCTCTCTGCACAGTACAGGTTG	60.611	54.545	0.65	0.00	35.78	3.77
5714	5828	4.142447	CCATTCATTTTCCTCTCTGCACAG	60.142	45.833	0.00	0.00	0.00	3.66
5717	5831	4.305539	TCCATTCATTTTCCTCTCTGCA	57.694	40.909	0.00	0.00	0.00	4.41
5721	5835	6.824305	TCAGTTTCCATTCATTTTCCTCTC	57.176	37.500	0.00	0.00	0.00	3.20
5723	5837	8.309656	AGAATTCAGTTTCCATTCATTTTCCTC	58.690	33.333	8.44	0.00	30.51	3.71
5725	5839	7.148523	GCAGAATTCAGTTTCCATTCATTTTCC	60.149	37.037	8.44	0.00	30.51	3.13
5743	5857	2.512705	GGGGGATGAGATGCAGAATTC	58.487	52.381	0.00	0.00	0.00	2.17
5766	5880	2.092699	GGGGATGAGAAACAGAGGGAAG	60.093	54.545	0.00	0.00	0.00	3.46
5775	5889	4.021102	TCACAAGAAGGGGATGAGAAAC	57.979	45.455	0.00	0.00	0.00	2.78
5789	5903	1.403647	CCCACTACGCGAATCACAAGA	60.404	52.381	15.93	0.00	0.00	3.02
5791	5905	0.604073	TCCCACTACGCGAATCACAA	59.396	50.000	15.93	0.00	0.00	3.33
5792	5906	0.821517	ATCCCACTACGCGAATCACA	59.178	50.000	15.93	0.00	0.00	3.58
5793	5907	2.034305	AGTATCCCACTACGCGAATCAC	59.966	50.000	15.93	0.00	34.98	3.06
5816	5930	5.009310	ACAGACCAAATGCTGCATGTATATG	59.991	40.000	17.00	11.82	35.57	1.78
5817	5931	5.009310	CACAGACCAAATGCTGCATGTATAT	59.991	40.000	17.00	1.08	35.57	0.86
5818	5932	4.336153	CACAGACCAAATGCTGCATGTATA	59.664	41.667	17.00	0.00	35.57	1.47
5819	5933	3.129813	CACAGACCAAATGCTGCATGTAT	59.870	43.478	17.00	4.38	35.57	2.29
5820	5934	2.488937	CACAGACCAAATGCTGCATGTA	59.511	45.455	17.00	0.00	35.57	2.29
5821	5935	1.271379	CACAGACCAAATGCTGCATGT	59.729	47.619	17.00	7.88	35.57	3.21
5822	5936	1.542472	TCACAGACCAAATGCTGCATG	59.458	47.619	17.00	6.05	35.57	4.06
5826	5940	4.508461	TCAAATCACAGACCAAATGCTG	57.492	40.909	0.00	0.00	38.10	4.41
5925	6039	7.450074	ACAAGTCCTGATGTTGTAAGTATCAA	58.550	34.615	0.00	0.00	32.63	2.57
5928	6042	8.135382	ACTACAAGTCCTGATGTTGTAAGTAT	57.865	34.615	0.00	0.00	36.48	2.12
5978	6105	8.083828	AGTCATCATAGAACTGTACATCCTTT	57.916	34.615	0.00	0.00	0.00	3.11
6020	6147	9.507329	AACATTATACAAAGACAGTCTTCACAT	57.493	29.630	16.44	11.33	35.27	3.21
6158	6286	7.169645	CCGCAGCTTGCATATGTAATTATTTTT	59.830	33.333	6.70	0.00	45.36	1.94
6228	6356	5.945784	ACCCCATATATATGTGTCACATTGC	59.054	40.000	23.05	0.00	39.88	3.56
6239	6367	9.213777	ACAATCCTACAGTACCCCATATATATG	57.786	37.037	14.78	14.78	0.00	1.78
6534	6670	0.588252	ACGCATCTTATCATTGCCGC	59.412	50.000	0.00	0.00	32.76	6.53
6567	6703	9.486497	CACTCTGCTGACTTATATTCATACAAT	57.514	33.333	0.00	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.