AutoCloner

Multiple sequence alignment - TraesCS3D01G484800

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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	TraesCS3D01G484800	chr3D	100.000	3248	0	0	1	3248	581824812	581821565	0.000000e+00	5999
1	TraesCS3D01G484800	chr3D	87.500	568	61	5	2681	3248	556639254	556638697	0.000000e+00	647
2	TraesCS3D01G484800	chr3D	81.780	236	36	5	2042	2271	581790756	581790522	1.190000e-44	191
3	TraesCS3D01G484800	chr3A	90.380	2682	164	39	1	2659	716262872	716265482	0.000000e+00	3437
4	TraesCS3D01G484800	chr3A	90.667	75	6	1	2672	2745	170969191	170969265	7.420000e-17	99
5	TraesCS3D01G484800	chr3B	93.740	1262	73	5	1011	2266	776226678	776227939	0.000000e+00	1888
6	TraesCS3D01G484800	chr3B	89.728	808	52	12	1	800	776225683	776226467	0.000000e+00	1003
7	TraesCS3D01G484800	chr3B	92.574	202	15	0	826	1027	776226454	776226655	1.140000e-74	291
8	TraesCS3D01G484800	chr3B	88.517	209	15	5	2338	2546	776227930	776228129	9.000000e-61	244
9	TraesCS3D01G484800	chr5A	82.051	858	89	38	4	813	565598549	565597709	0.000000e+00	671
10	TraesCS3D01G484800	chr1A	81.702	858	91	38	5	813	80807845	80807005	0.000000e+00	654
11	TraesCS3D01G484800	chr7D	88.069	461	33	9	380	822	67550329	67550785	7.980000e-146	527
12	TraesCS3D01G484800	chr7D	90.488	389	36	1	2860	3248	194713808	194714195	2.230000e-141	512
13	TraesCS3D01G484800	chr7D	88.636	308	26	4	1	307	67549991	67550290	1.840000e-97	366
14	TraesCS3D01G484800	chr7D	92.391	184	13	1	2681	2864	194712900	194713082	8.940000e-66	261
15	TraesCS3D01G484800	chr2D	87.852	461	34	9	380	822	54822236	54822692	3.710000e-144	521
16	TraesCS3D01G484800	chr2D	86.947	452	37	11	380	813	442838672	442838225	3.770000e-134	488
17	TraesCS3D01G484800	chr2D	79.514	576	91	20	2681	3248	52624909	52625465	5.080000e-103	385
18	TraesCS3D01G484800	chr2D	87.500	328	32	4	1	327	442839004	442838685	1.420000e-98	370
19	TraesCS3D01G484800	chr2D	78.609	575	97	23	2681	3248	573488491	573487936	1.110000e-94	357
20	TraesCS3D01G484800	chr2D	87.338	308	30	4	1	307	54821898	54822197	8.630000e-91	344
21	TraesCS3D01G484800	chr6B	90.957	376	29	3	439	813	91483255	91482884	4.840000e-138	501
22	TraesCS3D01G484800	chr6B	85.671	328	38	4	1	327	91483654	91483335	1.440000e-88	337
23	TraesCS3D01G484800	chr5D	87.361	451	35	10	380	813	543759304	543758859	6.260000e-137	497
24	TraesCS3D01G484800	chr5D	88.636	308	26	4	1	307	543759642	543759343	1.840000e-97	366
25	TraesCS3D01G484800	chr5D	78.322	572	105	17	2681	3248	398821249	398821805	5.160000e-93	351
26	TraesCS3D01G484800	chr5D	78.087	575	103	20	2681	3248	35118196	35118754	3.100000e-90	342
27	TraesCS3D01G484800	chr1D	87.361	451	35	10	380	813	429377088	429376643	6.260000e-137	497
28	TraesCS3D01G484800	chr1D	78.694	582	97	25	2677	3248	64205369	64205933	2.380000e-96	363
29	TraesCS3D01G484800	chr1D	87.338	308	30	4	1	307	429377426	429377127	8.630000e-91	344
30	TraesCS3D01G484800	chr6D	88.636	308	26	4	1	307	429637678	429637379	1.840000e-97	366
31	TraesCS3D01G484800	chr6D	85.057	348	48	4	2903	3248	464504323	464503978	5.160000e-93	351
32	TraesCS3D01G484800	chr4A	86.462	325	35	4	4	327	619883298	619882982	6.670000e-92	348
33	TraesCS3D01G484800	chr4D	84.241	349	50	5	2903	3248	480130266	480129920	5.190000e-88	335
34	TraesCS3D01G484800	chr7A	77.969	581	95	25	2680	3246	24756912	24757473	1.870000e-87	333
35	TraesCS3D01G484800	chr2B	96.078	102	4	0	1049	1150	789982245	789982346	2.000000e-37	167
36	TraesCS3D01G484800	chr2B	88.372	86	9	1	2681	2765	282965905	282965820	5.730000e-18	102
37	TraesCS3D01G484800	chr2B	88.095	84	9	1	2683	2765	453066114	453066197	7.420000e-17	99
38	TraesCS3D01G484800	chrUn	87.778	90	9	2	2671	2758	65778999	65778910	1.590000e-18	104
39	TraesCS3D01G484800	chr4B	88.506	87	9	1	2680	2765	575817215	575817129	1.590000e-18	104
40	TraesCS3D01G484800	chr4B	87.356	87	10	1	2680	2765	575842506	575842420	7.420000e-17	99

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	TraesCS3D01G484800	chr3D	581821565	581824812	3247	True	5999.0	5999	100.00000	1	3248	1	chr3D.!!$R3	3247
1	TraesCS3D01G484800	chr3D	556638697	556639254	557	True	647.0	647	87.50000	2681	3248	1	chr3D.!!$R1	567
2	TraesCS3D01G484800	chr3A	716262872	716265482	2610	False	3437.0	3437	90.38000	1	2659	1	chr3A.!!$F2	2658
3	TraesCS3D01G484800	chr3B	776225683	776228129	2446	False	856.5	1888	91.13975	1	2546	4	chr3B.!!$F1	2545
4	TraesCS3D01G484800	chr5A	565597709	565598549	840	True	671.0	671	82.05100	4	813	1	chr5A.!!$R1	809
5	TraesCS3D01G484800	chr1A	80807005	80807845	840	True	654.0	654	81.70200	5	813	1	chr1A.!!$R1	808
6	TraesCS3D01G484800	chr7D	67549991	67550785	794	False	446.5	527	88.35250	1	822	2	chr7D.!!$F1	821
7	TraesCS3D01G484800	chr7D	194712900	194714195	1295	False	386.5	512	91.43950	2681	3248	2	chr7D.!!$F2	567
8	TraesCS3D01G484800	chr2D	54821898	54822692	794	False	432.5	521	87.59500	1	822	2	chr2D.!!$F2	821
9	TraesCS3D01G484800	chr2D	442838225	442839004	779	True	429.0	488	87.22350	1	813	2	chr2D.!!$R2	812
10	TraesCS3D01G484800	chr2D	52624909	52625465	556	False	385.0	385	79.51400	2681	3248	1	chr2D.!!$F1	567
11	TraesCS3D01G484800	chr2D	573487936	573488491	555	True	357.0	357	78.60900	2681	3248	1	chr2D.!!$R1	567
12	TraesCS3D01G484800	chr6B	91482884	91483654	770	True	419.0	501	88.31400	1	813	2	chr6B.!!$R1	812
13	TraesCS3D01G484800	chr5D	543758859	543759642	783	True	431.5	497	87.99850	1	813	2	chr5D.!!$R1	812
14	TraesCS3D01G484800	chr5D	398821249	398821805	556	False	351.0	351	78.32200	2681	3248	1	chr5D.!!$F2	567
15	TraesCS3D01G484800	chr5D	35118196	35118754	558	False	342.0	342	78.08700	2681	3248	1	chr5D.!!$F1	567
16	TraesCS3D01G484800	chr1D	429376643	429377426	783	True	420.5	497	87.34950	1	813	2	chr1D.!!$R1	812
17	TraesCS3D01G484800	chr1D	64205369	64205933	564	False	363.0	363	78.69400	2677	3248	1	chr1D.!!$F1	571
18	TraesCS3D01G484800	chr7A	24756912	24757473	561	False	333.0	333	77.96900	2680	3246	1	chr7A.!!$F1	566

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
186	223	0.550432	TATTGGTGCCCATGCTAGCA	59.450	50.0	21.85	21.85	38.71	3.49	F
348	423	0.761323	TGGGGTGGACTCTGAACGAA	60.761	55.0	0.00	0.00	0.00	3.85	F
1849	1987	0.322456	TGCGCCAAATTAGGACTGCT	60.322	50.0	4.18	0.00	0.00	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1829	1967	0.099436	GCAGTCCTAATTTGGCGCAG	59.901	55.0	10.83	0.00	0.00	5.18	R
1903	2041	0.392461	GCCCATAGACAAGGCACGAA	60.392	55.0	0.00	0.00	46.34	3.85	R
2852	3028	0.593128	CTAGCAGCGCTGGTTTGTTT	59.407	50.0	42.66	11.91	40.10	2.83	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
75	83	1.160137	CCTGTTCCTCTTTCCTTGCG	58.840	55.000	0.00	0.00	0.00	4.85
105	113	1.172180	TTTGCAAGTCCAAGCTCGGG	61.172	55.000	0.00	0.00	0.00	5.14
169	206	5.431765	ACTAGCAAAGCTGTAACTGCATAT	58.568	37.500	1.04	0.00	40.10	1.78
186	223	0.550432	TATTGGTGCCCATGCTAGCA	59.450	50.000	21.85	21.85	38.71	3.49
260	297	7.432350	AATTCAGTCTAAAACAGAGAAGCAG	57.568	36.000	0.00	0.00	32.51	4.24
277	314	2.327081	CAGAATCACTGCTGTTGTGC	57.673	50.000	0.00	0.00	39.86	4.57
307	344	3.418684	AGTACCAGCTGAATTTCGGTT	57.581	42.857	17.39	0.00	0.00	4.44
332	407	1.672356	CTTTGTCTGACGCCCTGGG	60.672	63.158	8.86	8.86	0.00	4.45
344	419	1.538876	CCCTGGGGTGGACTCTGAA	60.539	63.158	4.27	0.00	0.00	3.02
346	421	1.293498	CTGGGGTGGACTCTGAACG	59.707	63.158	0.00	0.00	0.00	3.95
347	422	1.152419	TGGGGTGGACTCTGAACGA	60.152	57.895	0.00	0.00	0.00	3.85
348	423	0.761323	TGGGGTGGACTCTGAACGAA	60.761	55.000	0.00	0.00	0.00	3.85
361	436	5.465724	ACTCTGAACGAATCCTGTAAACAAC	59.534	40.000	0.00	0.00	0.00	3.32
370	445	1.605232	CCTGTAAACAACGACCCCAAC	59.395	52.381	0.00	0.00	0.00	3.77
394	469	4.505922	CACGAGCCTCATTTCTTCAGATAC	59.494	45.833	0.00	0.00	0.00	2.24
501	592	6.952358	ACATCTTAAAGTGTAGGTCTCCTGTA	59.048	38.462	0.00	0.00	34.61	2.74
502	593	7.453752	ACATCTTAAAGTGTAGGTCTCCTGTAA	59.546	37.037	0.00	0.00	34.61	2.41
503	594	7.224522	TCTTAAAGTGTAGGTCTCCTGTAAC	57.775	40.000	0.00	0.00	34.61	2.50
504	595	6.779049	TCTTAAAGTGTAGGTCTCCTGTAACA	59.221	38.462	0.00	0.00	34.61	2.41
632	724	4.456911	TGTTTTGGATGCTCTCTCATTCAC	59.543	41.667	0.00	0.00	31.99	3.18
687	780	4.571176	ACAGTTGAGAAGAAAAACTCGGTC	59.429	41.667	0.00	0.00	36.11	4.79
746	839	4.407365	CAAAACCCTCCAACAACTATCCT	58.593	43.478	0.00	0.00	0.00	3.24
747	840	3.721087	AACCCTCCAACAACTATCCTG	57.279	47.619	0.00	0.00	0.00	3.86
831	924	7.012138	CAGCTGCAGTTTGTTCTATCTGATTAT	59.988	37.037	16.64	0.00	0.00	1.28
890	983	7.854422	TGTTCTATGAATATCGTACAGTCGAAC	59.146	37.037	0.00	0.00	42.99	3.95
912	1005	7.094549	CGAACCAGTGGTGATATTTTCCTTTTA	60.095	37.037	17.56	0.00	35.34	1.52
974	1067	1.420138	TGAAGGAACAAGGGAGTGTCC	59.580	52.381	0.00	0.00	35.23	4.02
976	1069	1.059913	AGGAACAAGGGAGTGTCCTG	58.940	55.000	0.00	0.00	37.20	3.86
1086	1220	4.709886	TCTGAACCTGAATACGATCTTCCA	59.290	41.667	0.00	0.00	0.00	3.53
1128	1262	6.852420	TTTACTACTCCTGCACAGAGTATT	57.148	37.500	17.90	15.52	31.93	1.89
1227	1361	7.243604	TGGCCTGAATGAACTATTTGAATTT	57.756	32.000	3.32	0.00	0.00	1.82
1571	1707	9.640963	ATTACTATAAGGTATTCACGATTGCTC	57.359	33.333	0.00	0.00	0.00	4.26
1573	1709	7.148641	ACTATAAGGTATTCACGATTGCTCTG	58.851	38.462	0.00	0.00	0.00	3.35
1582	1718	9.341899	GTATTCACGATTGCTCTGTTAAATTTT	57.658	29.630	0.00	0.00	0.00	1.82
1584	1720	9.906660	ATTCACGATTGCTCTGTTAAATTTTTA	57.093	25.926	0.00	0.00	0.00	1.52
1609	1745	2.871022	TGTTGTGCCAAACATGCAATTC	59.129	40.909	0.00	0.00	41.06	2.17
1625	1761	4.951715	TGCAATTCCAAGTATCATGCTCTT	59.048	37.500	0.00	0.00	33.66	2.85
1654	1790	1.291877	ATGTTTCTGACGACGCAGGC	61.292	55.000	15.85	9.42	36.55	4.85
1679	1815	2.222819	GCTTCAGTTAACGGATCAAGCG	60.223	50.000	9.31	0.00	0.00	4.68
1680	1816	2.004583	TCAGTTAACGGATCAAGCGG	57.995	50.000	4.18	0.00	0.00	5.52
1696	1832	2.229792	AGCGGCTGAAGAAAATGACAA	58.770	42.857	0.00	0.00	0.00	3.18
1700	1836	4.358851	CGGCTGAAGAAAATGACAAAACA	58.641	39.130	0.00	0.00	0.00	2.83
1775	1913	9.833182	GCTGAAAAGGTTTGTATTTTTCAAAAA	57.167	25.926	11.34	0.00	45.07	1.94
1783	1921	7.430793	GGTTTGTATTTTTCAAAAACCATGCAC	59.569	33.333	10.03	0.00	45.87	4.57
1797	1935	8.761575	AAAACCATGCACAGAAAGTTATATTG	57.238	30.769	0.00	0.00	0.00	1.90
1849	1987	0.322456	TGCGCCAAATTAGGACTGCT	60.322	50.000	4.18	0.00	0.00	4.24
1967	2105	4.889409	TGAAGAAGTTGATTGGTGAAAGCT	59.111	37.500	0.00	0.00	33.76	3.74
1988	2126	1.609208	TGCCAAGGTTTCTCTTCTGC	58.391	50.000	0.00	0.00	0.00	4.26
1990	2128	1.819305	GCCAAGGTTTCTCTTCTGCCA	60.819	52.381	0.00	0.00	0.00	4.92
1992	2130	2.294512	CCAAGGTTTCTCTTCTGCCAAC	59.705	50.000	0.00	0.00	0.00	3.77
2042	2188	9.630098	AATTCATGTTATTTGCAGAGTTACTTG	57.370	29.630	0.00	0.00	0.00	3.16
2178	2324	8.598041	ACAGTAAACAAGAAGAGGAGTATGATT	58.402	33.333	0.00	0.00	0.00	2.57
2265	2411	7.669427	CAGAATGAGATCTTTAGCTGTAGGAT	58.331	38.462	0.00	0.00	39.69	3.24
2270	2416	4.898265	AGATCTTTAGCTGTAGGATCTGCA	59.102	41.667	18.38	0.00	40.73	4.41
2303	2449	1.545841	GGGTTTTCCTGAATTCGCCT	58.454	50.000	0.04	0.00	40.46	5.52
2305	2451	2.352715	GGGTTTTCCTGAATTCGCCTTG	60.353	50.000	0.04	0.00	40.46	3.61
2306	2452	2.352715	GGTTTTCCTGAATTCGCCTTGG	60.353	50.000	0.04	0.00	36.94	3.61
2307	2453	1.544724	TTTCCTGAATTCGCCTTGGG	58.455	50.000	0.04	0.00	0.00	4.12
2308	2454	0.695924	TTCCTGAATTCGCCTTGGGA	59.304	50.000	0.04	0.00	0.00	4.37
2309	2455	0.918983	TCCTGAATTCGCCTTGGGAT	59.081	50.000	0.04	0.00	0.00	3.85
2310	2456	1.027357	CCTGAATTCGCCTTGGGATG	58.973	55.000	0.04	0.00	0.00	3.51
2311	2457	0.383231	CTGAATTCGCCTTGGGATGC	59.617	55.000	0.04	0.00	0.00	3.91
2312	2458	0.034186	TGAATTCGCCTTGGGATGCT	60.034	50.000	0.04	0.00	0.00	3.79
2313	2459	1.211703	TGAATTCGCCTTGGGATGCTA	59.788	47.619	0.04	0.00	0.00	3.49
2314	2460	1.604278	GAATTCGCCTTGGGATGCTAC	59.396	52.381	0.00	0.00	0.00	3.58
2315	2461	0.179018	ATTCGCCTTGGGATGCTACC	60.179	55.000	0.00	0.00	0.00	3.18
2316	2462	1.558167	TTCGCCTTGGGATGCTACCA	61.558	55.000	2.59	0.00	35.88	3.25
2327	2473	4.166725	TGGGATGCTACCAGAGAATTCATT	59.833	41.667	8.44	0.00	33.23	2.57
2419	2565	3.857052	TCCTAGCGACAATCATTTTCGT	58.143	40.909	7.72	0.00	35.17	3.85
2423	2569	2.159627	AGCGACAATCATTTTCGTGACC	59.840	45.455	7.72	0.00	35.17	4.02
2451	2598	6.707440	TGCTTCTCAGGTTTCATTTTAACA	57.293	33.333	0.00	0.00	0.00	2.41
2521	2669	5.738619	TCTGAATGGTCTGTGTAGCTTAA	57.261	39.130	0.00	0.00	0.00	1.85
2522	2670	6.109156	TCTGAATGGTCTGTGTAGCTTAAA	57.891	37.500	0.00	0.00	0.00	1.52
2561	2710	6.653526	TTGGATTGGGTGCAATATCAATAG	57.346	37.500	0.00	0.00	32.79	1.73
2569	2718	8.902540	TGGGTGCAATATCAATAGTAACTTAG	57.097	34.615	0.00	0.00	0.00	2.18
2605	2754	2.281539	TCCGTCACCTAGTTGTGAGA	57.718	50.000	2.43	0.00	45.40	3.27
2614	2763	7.152645	GTCACCTAGTTGTGAGAAAATACAGA	58.847	38.462	2.43	0.00	45.40	3.41
2616	2765	7.819415	TCACCTAGTTGTGAGAAAATACAGATG	59.181	37.037	0.00	0.00	40.22	2.90
2627	2776	6.426587	AGAAAATACAGATGCAACATAGGGT	58.573	36.000	0.00	0.00	0.00	4.34
2648	2797	3.750373	AAACCAGCAGCCGTCGTGT	62.750	57.895	0.00	0.00	0.00	4.49
2650	2799	2.167398	AACCAGCAGCCGTCGTGTAT	62.167	55.000	0.00	0.00	0.00	2.29
2653	2802	1.635844	CAGCAGCCGTCGTGTATAAA	58.364	50.000	0.00	0.00	0.00	1.40
2659	2808	1.999048	CCGTCGTGTATAAACAGGCA	58.001	50.000	0.00	0.00	40.51	4.75
2660	2809	2.339418	CCGTCGTGTATAAACAGGCAA	58.661	47.619	0.00	0.00	40.51	4.52
2661	2810	2.737783	CCGTCGTGTATAAACAGGCAAA	59.262	45.455	0.00	0.00	40.51	3.68
2662	2811	3.181524	CCGTCGTGTATAAACAGGCAAAG	60.182	47.826	0.00	0.00	40.51	2.77
2663	2812	3.676172	CGTCGTGTATAAACAGGCAAAGA	59.324	43.478	0.00	0.00	40.51	2.52
2664	2813	4.328983	CGTCGTGTATAAACAGGCAAAGAT	59.671	41.667	0.00	0.00	40.51	2.40
2665	2814	5.560148	GTCGTGTATAAACAGGCAAAGATG	58.440	41.667	0.00	0.00	40.51	2.90
2666	2815	5.350365	GTCGTGTATAAACAGGCAAAGATGA	59.650	40.000	0.00	0.00	40.51	2.92
2667	2816	5.935206	TCGTGTATAAACAGGCAAAGATGAA	59.065	36.000	0.00	0.00	40.51	2.57
2668	2817	6.597672	TCGTGTATAAACAGGCAAAGATGAAT	59.402	34.615	0.00	0.00	40.51	2.57
2669	2818	7.766738	TCGTGTATAAACAGGCAAAGATGAATA	59.233	33.333	0.00	0.00	40.51	1.75
2670	2819	8.394877	CGTGTATAAACAGGCAAAGATGAATAA	58.605	33.333	0.00	0.00	35.91	1.40
2678	2827	9.590451	AACAGGCAAAGATGAATAATTTACATG	57.410	29.630	0.00	0.00	0.00	3.21
2679	2828	8.970020	ACAGGCAAAGATGAATAATTTACATGA	58.030	29.630	0.00	0.00	0.00	3.07
2761	2913	7.254084	GCATCAAGGTCAAAAAGTTACAAACTG	60.254	37.037	0.00	0.00	41.91	3.16
2802	2964	0.317160	CAGTTCCACACGACCAGCTA	59.683	55.000	0.00	0.00	0.00	3.32
2852	3028	7.416213	GCAGGCACAAATATTACATCCAAACTA	60.416	37.037	0.00	0.00	0.00	2.24
2856	3761	9.632807	GCACAAATATTACATCCAAACTAAACA	57.367	29.630	0.00	0.00	0.00	2.83
2892	3797	5.599999	AGTCCTAGCCAACAGTACATAAG	57.400	43.478	0.00	0.00	0.00	1.73
2893	3798	5.024118	AGTCCTAGCCAACAGTACATAAGT	58.976	41.667	0.00	0.00	0.00	2.24
2948	3854	0.183492	TCTTGTCTTGCCACAGCCTT	59.817	50.000	0.00	0.00	38.69	4.35
3008	3914	0.391661	GCATCGCACTCCTTCTCCAA	60.392	55.000	0.00	0.00	0.00	3.53
3055	3962	5.925506	ATGGCATTTGAAGATCACATCAA	57.074	34.783	0.00	0.00	32.98	2.57
3086	3995	5.220873	GGTTAGGGAATTTCTTCTCAATCGC	60.221	44.000	0.00	0.00	34.00	4.58
3109	4018	5.516339	GCAATTTTATTCCATGTCGTCCAAG	59.484	40.000	0.00	0.00	0.00	3.61
3123	4032	0.482446	TCCAAGGAGCCCACAACAAT	59.518	50.000	0.00	0.00	0.00	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
88	96	2.032528	CCCGAGCTTGGACTTGCA	59.967	61.111	22.68	0.00	0.00	4.08
89	97	2.347490	TCCCGAGCTTGGACTTGC	59.653	61.111	22.68	0.00	0.00	4.01
260	297	1.605710	ACAGCACAACAGCAGTGATTC	59.394	47.619	0.00	0.00	39.30	2.52
277	314	1.586564	GCTGGTACTAGCGCGACAG	60.587	63.158	15.94	8.26	33.46	3.51
307	344	1.540363	GGCGTCAGACAAAGACCAAGA	60.540	52.381	0.41	0.00	32.41	3.02
336	411	5.227908	TGTTTACAGGATTCGTTCAGAGTC	58.772	41.667	0.00	0.00	35.15	3.36
337	412	5.209818	TGTTTACAGGATTCGTTCAGAGT	57.790	39.130	0.00	0.00	0.00	3.24
338	413	5.388475	CGTTGTTTACAGGATTCGTTCAGAG	60.388	44.000	0.00	0.00	0.00	3.35
339	414	4.446385	CGTTGTTTACAGGATTCGTTCAGA	59.554	41.667	0.00	0.00	0.00	3.27
340	415	4.446385	TCGTTGTTTACAGGATTCGTTCAG	59.554	41.667	0.00	0.00	0.00	3.02
341	416	4.209703	GTCGTTGTTTACAGGATTCGTTCA	59.790	41.667	0.00	0.00	0.00	3.18
344	419	3.062042	GGTCGTTGTTTACAGGATTCGT	58.938	45.455	0.00	0.00	0.00	3.85
346	421	2.745821	GGGGTCGTTGTTTACAGGATTC	59.254	50.000	0.00	0.00	0.00	2.52
347	422	2.106857	TGGGGTCGTTGTTTACAGGATT	59.893	45.455	0.00	0.00	0.00	3.01
348	423	1.700739	TGGGGTCGTTGTTTACAGGAT	59.299	47.619	0.00	0.00	0.00	3.24
370	445	2.005451	CTGAAGAAATGAGGCTCGTGG	58.995	52.381	10.56	0.00	0.00	4.94
394	469	7.865706	AGGCCTTAAGTAGTCAACAATTATG	57.134	36.000	0.00	0.00	0.00	1.90
466	557	7.928706	CCTACACTTTAAGATGTTCTAGATGGG	59.071	40.741	0.00	0.00	0.00	4.00
501	592	0.534877	TGGCGTCAGCTGACATTGTT	60.535	50.000	38.31	0.00	44.99	2.83
502	593	0.952497	CTGGCGTCAGCTGACATTGT	60.952	55.000	38.31	0.00	44.99	2.71
503	594	0.952497	ACTGGCGTCAGCTGACATTG	60.952	55.000	38.31	27.50	44.99	2.82
504	595	0.671781	GACTGGCGTCAGCTGACATT	60.672	55.000	38.31	21.19	44.99	2.71
530	621	7.064371	CAGGACAAAGTCATCTTCTGTAATGAG	59.936	40.741	0.00	0.00	32.76	2.90
547	639	2.227388	GGAAGCATGACACAGGACAAAG	59.773	50.000	0.00	0.00	0.00	2.77
632	724	2.190578	GTCTGATCTTGGGGGCGG	59.809	66.667	0.00	0.00	0.00	6.13
687	780	3.118592	GGACTTGGAGATGAAGTACCTGG	60.119	52.174	0.00	0.00	33.71	4.45
746	839	7.050377	CCTATCTTTCAGTTCATAGCCTTTCA	58.950	38.462	0.00	0.00	0.00	2.69
747	840	7.051000	ACCTATCTTTCAGTTCATAGCCTTTC	58.949	38.462	0.00	0.00	0.00	2.62
890	983	9.942850	ATTTTAAAAGGAAAATATCACCACTGG	57.057	29.630	6.79	0.00	37.27	4.00
960	1053	1.059913	CTCCAGGACACTCCCTTGTT	58.940	55.000	0.00	0.00	37.19	2.83
974	1067	7.587037	TGCCTTGATAAATAAAATCCTCCAG	57.413	36.000	0.00	0.00	0.00	3.86
985	1078	9.585369	TTTGTGGATCATATGCCTTGATAAATA	57.415	29.630	0.00	0.00	34.03	1.40
993	1086	3.907221	AGCTTTGTGGATCATATGCCTT	58.093	40.909	0.00	0.00	0.00	4.35
1047	1181	3.482156	TCAGAGAAAGCAGCAAAGTCT	57.518	42.857	0.00	0.00	0.00	3.24
1110	1244	4.283467	ACAACAATACTCTGTGCAGGAGTA	59.717	41.667	23.23	23.23	46.13	2.59
1128	1262	7.877612	ACATATCATGACACTTACAAGACAACA	59.122	33.333	0.00	0.00	0.00	3.33
1159	1293	8.621532	AAGCACAGTAATTAAGTCTTGAATGA	57.378	30.769	0.00	0.00	0.00	2.57
1212	1346	6.493115	TCCCTGCAAGAAATTCAAATAGTTCA	59.507	34.615	0.00	0.00	34.07	3.18
1227	1361	0.620556	GGATTGAGGTCCCTGCAAGA	59.379	55.000	0.00	0.00	34.07	3.02
1259	1393	5.551233	TCTTTGTAATCCCTGTCTTCAGTG	58.449	41.667	0.00	0.00	39.82	3.66
1354	1488	6.487299	AGAAGAAGACTGGGGTAATACATC	57.513	41.667	0.00	0.00	0.00	3.06
1571	1707	8.660373	TGGCACAACAGTTTAAAAATTTAACAG	58.340	29.630	5.38	0.57	30.82	3.16
1609	1745	6.917533	AGAAAACAAAGAGCATGATACTTGG	58.082	36.000	0.00	0.00	0.00	3.61
1625	1761	5.501736	CGTCGTCAGAAACATGAGAAAACAA	60.502	40.000	0.00	0.00	0.00	2.83
1654	1790	3.334691	TGATCCGTTAACTGAAGCCAAG	58.665	45.455	3.71	0.00	0.00	3.61
1679	1815	6.660887	TTTGTTTTGTCATTTTCTTCAGCC	57.339	33.333	0.00	0.00	0.00	4.85
1680	1816	7.742151	ACTTTTGTTTTGTCATTTTCTTCAGC	58.258	30.769	0.00	0.00	0.00	4.26
1700	1836	5.501897	CGCTTCTCTGTTACGAACAACTTTT	60.502	40.000	0.00	0.00	41.61	2.27
1775	1913	7.886629	ATCAATATAACTTTCTGTGCATGGT	57.113	32.000	0.00	0.00	0.00	3.55
1813	1951	2.936498	GCGCAGGTAACAGTGTAATGAT	59.064	45.455	0.30	0.00	35.77	2.45
1829	1967	0.099436	GCAGTCCTAATTTGGCGCAG	59.901	55.000	10.83	0.00	0.00	5.18
1902	2040	1.656652	CCCATAGACAAGGCACGAAG	58.343	55.000	0.00	0.00	0.00	3.79
1903	2041	0.392461	GCCCATAGACAAGGCACGAA	60.392	55.000	0.00	0.00	46.34	3.85
1967	2105	3.347216	GCAGAAGAGAAACCTTGGCATA	58.653	45.455	0.00	0.00	0.00	3.14
1988	2126	8.181573	GGTGTGTGTAAATATAGTGAATGTTGG	58.818	37.037	0.00	0.00	0.00	3.77
1990	2128	7.885922	TGGGTGTGTGTAAATATAGTGAATGTT	59.114	33.333	0.00	0.00	0.00	2.71
1992	2130	7.857734	TGGGTGTGTGTAAATATAGTGAATG	57.142	36.000	0.00	0.00	0.00	2.67
2042	2188	6.532657	CACCAAATCCTGAATATCAAAGCAAC	59.467	38.462	0.00	0.00	0.00	4.17
2151	2297	7.963532	TCATACTCCTCTTCTTGTTTACTGTT	58.036	34.615	0.00	0.00	0.00	3.16
2178	2324	3.873910	CCTAGCTTCGAAAGATTTCCCA	58.126	45.455	0.00	0.00	41.60	4.37
2243	2389	7.669427	CAGATCCTACAGCTAAAGATCTCATT	58.331	38.462	12.38	0.00	41.26	2.57
2303	2449	3.523157	TGAATTCTCTGGTAGCATCCCAA	59.477	43.478	7.05	0.00	0.00	4.12
2305	2451	3.845781	TGAATTCTCTGGTAGCATCCC	57.154	47.619	7.05	0.00	0.00	3.85
2306	2452	4.518211	CCAATGAATTCTCTGGTAGCATCC	59.482	45.833	14.80	0.00	0.00	3.51
2307	2453	5.008415	CACCAATGAATTCTCTGGTAGCATC	59.992	44.000	23.41	0.00	40.23	3.91
2308	2454	4.885907	CACCAATGAATTCTCTGGTAGCAT	59.114	41.667	23.41	6.29	40.23	3.79
2309	2455	4.264253	CACCAATGAATTCTCTGGTAGCA	58.736	43.478	23.41	0.00	40.23	3.49
2310	2456	3.629398	CCACCAATGAATTCTCTGGTAGC	59.371	47.826	23.41	0.00	40.23	3.58
2311	2457	4.637534	CACCACCAATGAATTCTCTGGTAG	59.362	45.833	23.41	20.19	40.23	3.18
2312	2458	4.288366	TCACCACCAATGAATTCTCTGGTA	59.712	41.667	23.41	11.45	40.23	3.25
2313	2459	3.074390	TCACCACCAATGAATTCTCTGGT	59.926	43.478	20.18	20.18	43.01	4.00
2314	2460	3.689347	TCACCACCAATGAATTCTCTGG	58.311	45.455	19.16	19.16	34.95	3.86
2315	2461	3.693085	CCTCACCACCAATGAATTCTCTG	59.307	47.826	7.05	3.88	0.00	3.35
2316	2462	3.588842	TCCTCACCACCAATGAATTCTCT	59.411	43.478	7.05	0.00	0.00	3.10
2327	2473	0.921166	ATCATGCATCCTCACCACCA	59.079	50.000	0.00	0.00	0.00	4.17
2413	2559	2.158813	AGAAGCAAGAGGGTCACGAAAA	60.159	45.455	0.00	0.00	0.00	2.29
2415	2561	1.000955	GAGAAGCAAGAGGGTCACGAA	59.999	52.381	0.00	0.00	0.00	3.85
2419	2565	0.979665	CCTGAGAAGCAAGAGGGTCA	59.020	55.000	0.00	0.00	0.00	4.02
2423	2569	3.131709	TGAAACCTGAGAAGCAAGAGG	57.868	47.619	0.00	0.00	0.00	3.69
2522	2670	8.655901	ACCCAATCCAATATTACACAAGTTTTT	58.344	29.630	0.00	0.00	0.00	1.94
2528	2676	5.019470	TGCACCCAATCCAATATTACACAA	58.981	37.500	0.00	0.00	0.00	3.33
2540	2689	7.448469	AGTTACTATTGATATTGCACCCAATCC	59.552	37.037	0.00	0.00	41.68	3.01
2578	2727	9.392259	CTCACAACTAGGTGACGGATATATATA	57.608	37.037	16.48	0.00	42.56	0.86
2579	2728	8.107729	TCTCACAACTAGGTGACGGATATATAT	58.892	37.037	16.48	0.00	42.56	0.86
2580	2729	7.455891	TCTCACAACTAGGTGACGGATATATA	58.544	38.462	16.48	0.00	42.56	0.86
2586	2735	2.281539	TCTCACAACTAGGTGACGGA	57.718	50.000	16.48	8.00	42.56	4.69
2587	2736	3.380479	TTTCTCACAACTAGGTGACGG	57.620	47.619	16.48	3.59	42.56	4.79
2588	2737	5.924254	TGTATTTTCTCACAACTAGGTGACG	59.076	40.000	16.48	5.14	42.56	4.35
2593	2742	6.595326	TGCATCTGTATTTTCTCACAACTAGG	59.405	38.462	0.00	0.00	0.00	3.02
2597	2746	6.437928	TGTTGCATCTGTATTTTCTCACAAC	58.562	36.000	0.00	0.00	35.45	3.32
2605	2754	7.573710	TCTACCCTATGTTGCATCTGTATTTT	58.426	34.615	0.00	0.00	0.00	1.82
2614	2763	4.526970	CTGGTTTCTACCCTATGTTGCAT	58.473	43.478	0.00	0.00	44.35	3.96
2616	2765	2.683362	GCTGGTTTCTACCCTATGTTGC	59.317	50.000	0.00	0.00	44.35	4.17
2627	2776	1.080093	CGACGGCTGCTGGTTTCTA	60.080	57.895	13.87	0.00	0.00	2.10
2653	2802	8.970020	TCATGTAAATTATTCATCTTTGCCTGT	58.030	29.630	0.00	0.00	0.00	4.00
2743	2892	7.044052	GCTCATGTCAGTTTGTAACTTTTTGAC	60.044	37.037	0.00	0.00	40.46	3.18
2761	2913	4.093408	TGCTGTTATCTTTTCGCTCATGTC	59.907	41.667	0.00	0.00	0.00	3.06
2802	2964	3.964031	TGCAGAACCTTTATTTTGGTGGT	59.036	39.130	0.00	0.00	36.57	4.16
2852	3028	0.593128	CTAGCAGCGCTGGTTTGTTT	59.407	50.000	42.66	11.91	40.10	2.83
2892	3797	6.258068	GGTGATGCTTGTGGAGTATTAAGTAC	59.742	42.308	0.00	0.00	30.14	2.73
2893	3798	6.346096	GGTGATGCTTGTGGAGTATTAAGTA	58.654	40.000	0.00	0.00	30.14	2.24
2907	3813	3.197790	CCGCTCGGGTGATGCTTG	61.198	66.667	0.00	0.00	0.00	4.01
2948	3854	1.139816	GACGCGCATCAAGACGATCA	61.140	55.000	5.73	0.00	29.21	2.92
2996	3902	0.680061	GACACCGTTGGAGAAGGAGT	59.320	55.000	0.00	0.00	0.00	3.85
3008	3914	0.746063	TTTACAGACGTGGACACCGT	59.254	50.000	0.00	0.00	42.06	4.83
3055	3962	4.586306	AGAAATTCCCTAACCATTCCGT	57.414	40.909	0.00	0.00	0.00	4.69
3086	3995	6.035843	CCTTGGACGACATGGAATAAAATTG	58.964	40.000	0.00	0.00	44.96	2.32
3109	4018	2.649129	GGGCATTGTTGTGGGCTCC	61.649	63.158	0.00	0.00	0.00	4.70
3161	4070	3.640967	CACCATCCTCAAAACCCTGAAAA	59.359	43.478	0.00	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.