AutoCloner

Multiple sequence alignment - TraesCS6D01G014200

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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	TraesCS6D01G014200	chr6D	100.000	4033	0	0	1	4033	5979563	5975531	0.000000e+00	7448
1	TraesCS6D01G014200	chr6D	90.196	102	9	1	992	1093	471075284	471075384	9.100000e-27	132
2	TraesCS6D01G014200	chr6A	89.665	2032	139	41	84	2087	5322520	5320532	0.000000e+00	2523
3	TraesCS6D01G014200	chr6A	92.172	792	51	9	2130	2912	5320304	5319515	0.000000e+00	1109
4	TraesCS6D01G014200	chr6A	88.099	563	37	7	2911	3451	5319422	5318868	3.400000e-180	641
5	TraesCS6D01G014200	chr6A	91.358	324	26	2	2588	2909	5762025	5762348	3.700000e-120	442
6	TraesCS6D01G014200	chr6A	91.049	324	27	2	2588	2909	5663825	5664148	1.720000e-118	436
7	TraesCS6D01G014200	chr6A	86.688	308	32	6	1682	1982	370232962	370233267	2.320000e-87	333
8	TraesCS6D01G014200	chr6B	88.881	1448	99	33	709	2112	11289147	11287718	0.000000e+00	1725
9	TraesCS6D01G014200	chr6B	93.893	786	42	5	2130	2912	11287498	11286716	0.000000e+00	1181
10	TraesCS6D01G014200	chr6B	88.566	551	36	15	2911	3451	11286580	11286047	0.000000e+00	643
11	TraesCS6D01G014200	chr6B	83.587	591	65	11	2344	2909	125020692	125021275	3.570000e-145	525
12	TraesCS6D01G014200	chr6B	82.569	327	23	14	1	301	11289756	11289438	1.440000e-64	257
13	TraesCS6D01G014200	chr6B	82.166	314	36	11	362	672	11289440	11289144	6.690000e-63	252
14	TraesCS6D01G014200	chr6B	85.930	199	20	7	2139	2335	4147934	4148126	5.280000e-49	206
15	TraesCS6D01G014200	chr6B	85.572	201	21	7	2137	2335	159090894	159090700	1.900000e-48	204
16	TraesCS6D01G014200	chr6B	91.176	102	8	1	992	1093	719480381	719480281	1.950000e-28	137
17	TraesCS6D01G014200	chr2A	86.661	1087	100	24	992	2063	137931820	137932876	0.000000e+00	1162
18	TraesCS6D01G014200	chr2A	84.370	595	65	16	2340	2909	137933339	137933930	3.520000e-155	558
19	TraesCS6D01G014200	chr2A	80.193	414	61	11	2911	3309	137934035	137934442	1.420000e-74	291
20	TraesCS6D01G014200	chr2A	83.333	348	25	11	3454	3779	677394471	677394135	1.420000e-74	291
21	TraesCS6D01G014200	chr2A	84.689	209	24	8	2130	2335	137933097	137933300	6.830000e-48	202
22	TraesCS6D01G014200	chr2A	95.238	63	3	0	3971	4033	677394140	677394078	2.560000e-17	100
23	TraesCS6D01G014200	chr2D	86.759	1080	93	32	994	2046	131277189	131278245	0.000000e+00	1157
24	TraesCS6D01G014200	chr2D	82.392	602	71	20	2335	2912	131278698	131279288	3.620000e-135	492
25	TraesCS6D01G014200	chr2D	87.829	304	14	4	3540	3821	533031963	533031661	6.460000e-88	335
26	TraesCS6D01G014200	chr2D	94.419	215	12	0	3819	4033	483761549	483761335	8.350000e-87	331
27	TraesCS6D01G014200	chr2D	80.535	411	57	13	2911	3309	131279350	131279749	1.100000e-75	294
28	TraesCS6D01G014200	chr2D	89.189	185	19	1	3850	4033	533031663	533031479	3.140000e-56	230
29	TraesCS6D01G014200	chr2B	86.461	1071	102	32	992	2046	184772874	184773917	0.000000e+00	1134
30	TraesCS6D01G014200	chr2B	84.653	606	59	15	2335	2909	184774288	184774890	1.260000e-159	573
31	TraesCS6D01G014200	chr2B	90.390	333	25	6	3707	4033	632567985	632567654	8.010000e-117	431
32	TraesCS6D01G014200	chr2B	90.226	266	16	4	3454	3709	246373210	246373475	4.990000e-89	339
33	TraesCS6D01G014200	chr2B	92.116	241	18	1	3762	4001	246373635	246373875	4.990000e-89	339
34	TraesCS6D01G014200	chr2B	81.955	399	50	14	2925	3309	184774969	184775359	6.500000e-83	318
35	TraesCS6D01G014200	chr3B	90.017	601	32	11	3454	4033	733551339	733551932	0.000000e+00	752
36	TraesCS6D01G014200	chr1B	87.500	616	39	13	3454	4033	562510828	562511441	0.000000e+00	676
37	TraesCS6D01G014200	chr7D	88.690	504	30	6	3556	4033	184582208	184581706	1.250000e-164	590
38	TraesCS6D01G014200	chr7D	86.070	201	20	7	2137	2335	636156814	636156620	4.080000e-50	209
39	TraesCS6D01G014200	chr7D	85.572	201	21	8	2137	2335	64418813	64418619	1.900000e-48	204
40	TraesCS6D01G014200	chr1D	83.139	599	71	13	2335	2909	360102712	360103304	1.660000e-143	520
41	TraesCS6D01G014200	chr1D	85.572	201	21	7	2137	2335	360102484	360102678	1.900000e-48	204
42	TraesCS6D01G014200	chr5B	82.125	593	76	12	2344	2912	206760151	206759565	7.840000e-132	481
43	TraesCS6D01G014200	chr5B	86.070	201	20	8	2137	2335	206760388	206760194	4.080000e-50	209
44	TraesCS6D01G014200	chrUn	88.319	351	36	3	2344	2689	317269849	317269499	2.240000e-112	416
45	TraesCS6D01G014200	chr7B	89.552	335	21	7	3707	4033	154178310	154177982	2.900000e-111	412
46	TraesCS6D01G014200	chr7B	87.013	308	31	7	1682	1982	701399776	701400081	4.990000e-89	339
47	TraesCS6D01G014200	chr7B	86.688	308	32	7	1682	1982	645437115	645436810	2.320000e-87	333
48	TraesCS6D01G014200	chr1A	83.617	470	30	17	3454	3876	570247307	570246838	8.120000e-107	398
49	TraesCS6D01G014200	chr3A	86.688	308	32	6	1682	1982	667843705	667844010	2.320000e-87	333

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	TraesCS6D01G014200	chr6D	5975531	5979563	4032	True	7448.000000	7448	100.000000	1	4033	1	chr6D.!!$R1	4032
1	TraesCS6D01G014200	chr6A	5318868	5322520	3652	True	1424.333333	2523	89.978667	84	3451	3	chr6A.!!$R1	3367
2	TraesCS6D01G014200	chr6B	11286047	11289756	3709	True	811.600000	1725	87.215000	1	3451	5	chr6B.!!$R3	3450
3	TraesCS6D01G014200	chr6B	125020692	125021275	583	False	525.000000	525	83.587000	2344	2909	1	chr6B.!!$F2	565
4	TraesCS6D01G014200	chr2A	137931820	137934442	2622	False	553.250000	1162	83.978250	992	3309	4	chr2A.!!$F1	2317
5	TraesCS6D01G014200	chr2D	131277189	131279749	2560	False	647.666667	1157	83.228667	994	3309	3	chr2D.!!$F1	2315
6	TraesCS6D01G014200	chr2B	184772874	184775359	2485	False	675.000000	1134	84.356333	992	3309	3	chr2B.!!$F1	2317
7	TraesCS6D01G014200	chr2B	246373210	246373875	665	False	339.000000	339	91.171000	3454	4001	2	chr2B.!!$F2	547
8	TraesCS6D01G014200	chr3B	733551339	733551932	593	False	752.000000	752	90.017000	3454	4033	1	chr3B.!!$F1	579
9	TraesCS6D01G014200	chr1B	562510828	562511441	613	False	676.000000	676	87.500000	3454	4033	1	chr1B.!!$F1	579
10	TraesCS6D01G014200	chr7D	184581706	184582208	502	True	590.000000	590	88.690000	3556	4033	1	chr7D.!!$R2	477
11	TraesCS6D01G014200	chr1D	360102484	360103304	820	False	362.000000	520	84.355500	2137	2909	2	chr1D.!!$F1	772
12	TraesCS6D01G014200	chr5B	206759565	206760388	823	True	345.000000	481	84.097500	2137	2912	2	chr5B.!!$R1	775

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
19	20	0.323629	TGGGCCGAGAAGAACGAAAT	59.676	50.0	0.00	0.00	2.17	F
50	51	0.392998	AGCCGTCAGCCCATTAGTTG	60.393	55.0	0.00	45.47	3.16	F
131	136	0.536460	CCTCCCTCTACTCCTCGCTC	60.536	65.0	0.00	0.00	5.03	F
1338	1420	0.322636	TCTGTCTGTCTCCCTCGGTC	60.323	60.0	0.00	0.00	4.79	F
2753	3167	0.249868	TTGTGGTGTTCGAGAGCCAG	60.250	55.0	4.49	0.00	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1107	1169	0.035598	TTCGATTCGGTTCAAGGGCA	59.964	50.000	6.18	0.00	5.36	R
1338	1420	1.276415	GCTGCACTTCTCTAAGCTCG	58.724	55.000	0.00	36.05	5.03	R
1644	1740	3.904136	AGCAGACAACAAACATACAGC	57.096	42.857	0.00	0.00	4.40	R
2941	3507	0.250945	TAGCAACCGGGCAAATGTCA	60.251	50.000	6.32	35.83	3.58	R
3875	4637	1.078709	CGACTGTGGCGATGTTTGAT	58.921	50.000	0.00	0.00	2.57	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
19	20	0.323629	TGGGCCGAGAAGAACGAAAT	59.676	50.000	0.00	0.00	0.00	2.17
46	47	0.978667	TGGTAGCCGTCAGCCCATTA	60.979	55.000	0.00	0.00	45.47	1.90
50	51	0.392998	AGCCGTCAGCCCATTAGTTG	60.393	55.000	0.00	0.00	45.47	3.16
131	136	0.536460	CCTCCCTCTACTCCTCGCTC	60.536	65.000	0.00	0.00	0.00	5.03
159	164	1.043673	GCTCCGCCTCCTTTCCTCTA	61.044	60.000	0.00	0.00	0.00	2.43
228	259	3.148279	CCGTAAGCTCCCTCCGCT	61.148	66.667	0.00	0.00	39.94	5.52
243	274	4.475135	GCTCCTCCTTCCCCGTGC	62.475	72.222	0.00	0.00	0.00	5.34
259	290	1.202222	CGTGCCTTCTTCATTGATGCC	60.202	52.381	0.00	0.00	0.00	4.40
279	310	1.002544	CACCCAGAGAACAGTCTTCCC	59.997	57.143	0.00	0.00	32.80	3.97
280	311	0.615850	CCCAGAGAACAGTCTTCCCC	59.384	60.000	0.00	0.00	32.80	4.81
338	373	0.678950	CCTAGCTAGCTCTCCTTGGC	59.321	60.000	23.26	0.00	0.00	4.52
355	390	2.329267	TGGCACTCGAGGATGGAATAT	58.671	47.619	18.41	0.00	0.00	1.28
372	407	9.423061	GATGGAATATATTGCCAAATGTTTACC	57.577	33.333	13.70	0.23	34.95	2.85
373	408	7.429633	TGGAATATATTGCCAAATGTTTACCG	58.570	34.615	13.70	0.00	0.00	4.02
374	409	7.285629	TGGAATATATTGCCAAATGTTTACCGA	59.714	33.333	13.70	0.00	0.00	4.69
382	417	5.531659	TGCCAAATGTTTACCGAAGAAAGTA	59.468	36.000	0.00	0.00	0.00	2.24
385	420	7.095102	GCCAAATGTTTACCGAAGAAAGTAGTA	60.095	37.037	0.00	0.00	0.00	1.82
403	438	7.086685	AGTAGTATTCTTTTTCCTGTTCCCA	57.913	36.000	0.00	0.00	0.00	4.37
427	462	2.736978	CTCGATAAGCATGCTCTCGTT	58.263	47.619	33.50	19.17	34.71	3.85
439	474	5.220739	GCATGCTCTCGTTTCTATTGATTGT	60.221	40.000	11.37	0.00	0.00	2.71
444	479	6.738649	GCTCTCGTTTCTATTGATTGTTTGAC	59.261	38.462	0.00	0.00	0.00	3.18
480	515	4.628333	CCTTTCTTTTGATTCTACGCGGTA	59.372	41.667	12.47	0.00	0.00	4.02
484	519	4.624024	TCTTTTGATTCTACGCGGTACTTG	59.376	41.667	12.47	0.00	0.00	3.16
486	521	4.700268	TTGATTCTACGCGGTACTTGTA	57.300	40.909	12.47	0.00	0.00	2.41
500	536	6.334989	CGGTACTTGTATGTTGTCCAGATTA	58.665	40.000	0.00	0.00	0.00	1.75
503	539	8.472413	GGTACTTGTATGTTGTCCAGATTAGTA	58.528	37.037	0.00	0.00	0.00	1.82
555	591	6.386654	GGTGTAAATTTGTCTGGTTGGTATG	58.613	40.000	0.00	0.00	0.00	2.39
556	592	6.015772	GGTGTAAATTTGTCTGGTTGGTATGT	60.016	38.462	0.00	0.00	0.00	2.29
557	593	7.430441	GTGTAAATTTGTCTGGTTGGTATGTT	58.570	34.615	0.00	0.00	0.00	2.71
558	594	7.593644	GTGTAAATTTGTCTGGTTGGTATGTTC	59.406	37.037	0.00	0.00	0.00	3.18
559	595	5.722021	AATTTGTCTGGTTGGTATGTTCC	57.278	39.130	0.00	0.00	0.00	3.62
595	631	2.293122	TGCTCCGGAAGAATTTTGTGTG	59.707	45.455	5.23	0.00	0.00	3.82
600	636	4.274950	TCCGGAAGAATTTTGTGTGAGAAC	59.725	41.667	0.00	0.00	0.00	3.01
614	650	2.224314	GTGAGAACAGTGCAGCTAAACC	59.776	50.000	0.00	0.00	0.00	3.27
617	653	3.555966	AGAACAGTGCAGCTAAACCTTT	58.444	40.909	0.00	0.00	0.00	3.11
633	669	7.494298	GCTAAACCTTTGAGTTGGAAATCAAAA	59.506	33.333	14.01	1.55	42.96	2.44
680	717	3.576078	CCCAGCTGTATGAATGGGTTA	57.424	47.619	13.81	0.00	46.19	2.85
697	734	5.565509	TGGGTTAACAGCAATGATTGACTA	58.434	37.500	9.76	0.00	0.00	2.59
699	736	6.318648	TGGGTTAACAGCAATGATTGACTATC	59.681	38.462	9.76	0.00	0.00	2.08
701	738	6.422223	GTTAACAGCAATGATTGACTATCGG	58.578	40.000	9.76	0.00	35.94	4.18
712	749	6.216569	TGATTGACTATCGGAGTTTCTATGC	58.783	40.000	0.00	0.00	39.06	3.14
722	759	4.376146	GGAGTTTCTATGCTGTCCAGATC	58.624	47.826	0.00	0.00	0.00	2.75
797	838	2.082231	CCGTAGTTGTCTCTCCGAGAA	58.918	52.381	0.00	0.00	40.59	2.87
815	856	8.615878	TCCGAGAAGAATTTTTGTCAGAATAA	57.384	30.769	6.67	0.00	0.00	1.40
832	873	9.512435	GTCAGAATAATAGTGTAGCTAAACGAA	57.488	33.333	8.44	1.72	32.72	3.85
835	876	7.646922	AGAATAATAGTGTAGCTAAACGAACGG	59.353	37.037	8.44	0.00	32.72	4.44
836	877	4.970662	ATAGTGTAGCTAAACGAACGGA	57.029	40.909	8.44	0.00	32.72	4.69
870	915	5.709164	ACAGTAATGGTTACTCTGTACTCGT	59.291	40.000	0.00	0.00	44.32	4.18
909	954	5.339008	TGCTGTAGGAATGTCGTCTTATT	57.661	39.130	0.00	0.00	0.00	1.40
935	984	6.149129	TCATACTCACCTACAGCTGTTATG	57.851	41.667	27.06	22.34	0.00	1.90
957	1006	1.680735	TGCACATTTGACAACCTGACC	59.319	47.619	4.38	0.00	0.00	4.02
959	1008	2.362077	GCACATTTGACAACCTGACCTT	59.638	45.455	4.38	0.00	0.00	3.50
961	1010	4.362279	CACATTTGACAACCTGACCTTTG	58.638	43.478	4.38	0.00	0.00	2.77
964	1013	2.136298	TGACAACCTGACCTTTGCAA	57.864	45.000	0.00	0.00	0.00	4.08
1099	1152	3.667429	GATTTCCTGGTGCGTGCGC	62.667	63.158	9.85	9.85	42.35	6.09
1134	1196	2.081462	GAACCGAATCGAACCCAACAT	58.919	47.619	3.36	0.00	0.00	2.71
1157	1223	0.596082	GGAAAACACCCACACATCCG	59.404	55.000	0.00	0.00	0.00	4.18
1192	1261	3.311106	CCTGATGTTGTGTTGTGATTGC	58.689	45.455	0.00	0.00	0.00	3.56
1193	1262	2.975193	CTGATGTTGTGTTGTGATTGCG	59.025	45.455	0.00	0.00	0.00	4.85
1338	1420	0.322636	TCTGTCTGTCTCCCTCGGTC	60.323	60.000	0.00	0.00	0.00	4.79
1387	1470	3.049344	GGAGGGGTCTGGTCTTGATATT	58.951	50.000	0.00	0.00	0.00	1.28
1389	1472	3.970640	GAGGGGTCTGGTCTTGATATTCT	59.029	47.826	0.00	0.00	0.00	2.40
1390	1473	3.970640	AGGGGTCTGGTCTTGATATTCTC	59.029	47.826	0.00	0.00	0.00	2.87
1391	1474	3.711704	GGGGTCTGGTCTTGATATTCTCA	59.288	47.826	0.00	0.00	0.00	3.27
1491	1578	3.248602	CGCAAGGTATCCTTTACTGCATC	59.751	47.826	9.73	0.00	41.69	3.91
1502	1589	5.880332	TCCTTTACTGCATCACAAGGTATTC	59.120	40.000	11.74	0.00	36.23	1.75
1675	1771	5.843673	TTGTTGTCTGCTTACAAATTCCA	57.156	34.783	6.09	0.00	40.85	3.53
1904	2002	7.538575	ACACATCAATTACCAGTAAATGAAGC	58.461	34.615	11.28	0.00	38.15	3.86
2113	2268	1.282157	AGGGTAATTCAGAGTGGTGCC	59.718	52.381	0.00	0.00	0.00	5.01
2132	2289	9.672673	GTGGTGCCTGTTAGAAATATATATGAT	57.327	33.333	0.00	0.00	0.00	2.45
2150	2483	4.689612	TGATAGCTTGGTGGTAATCTCC	57.310	45.455	0.00	0.00	31.94	3.71
2258	2602	4.877378	ACACGGAGGTTGTAGTAATTCA	57.123	40.909	0.00	0.00	0.00	2.57
2277	2623	9.490663	GTAATTCATACATCACTACAGTTTTGC	57.509	33.333	0.00	0.00	34.46	3.68
2390	2772	3.181458	TGCGGAAGGGATTTATACCAGTC	60.181	47.826	0.00	0.00	31.13	3.51
2396	2778	2.363359	GGGATTTATACCAGTCGACCGT	59.637	50.000	13.01	11.49	0.00	4.83
2454	2837	3.395639	TGTTGCTAACTACAACCGGAAG	58.604	45.455	9.46	1.51	45.42	3.46
2489	2878	5.006746	ACGCTGTAGATTAATAAGCTGTTGC	59.993	40.000	0.45	1.89	40.05	4.17
2629	3019	5.356882	TTGTAAGTAACACTTGATGCTGC	57.643	39.130	1.84	0.00	39.11	5.25
2638	3028	3.377485	ACACTTGATGCTGCTCATTGATC	59.623	43.478	0.00	0.00	35.05	2.92
2703	3112	2.252976	TTGCCTGCAAATTTCAACCC	57.747	45.000	1.31	0.00	32.44	4.11
2745	3157	2.875933	AGGTACACAATTGTGGTGTTCG	59.124	45.455	35.20	14.56	46.75	3.95
2753	3167	0.249868	TTGTGGTGTTCGAGAGCCAG	60.250	55.000	4.49	0.00	0.00	4.85
2872	3296	0.401738	CACCAGTGTTCATCCCAGGT	59.598	55.000	0.00	0.00	0.00	4.00
2879	3303	1.962807	TGTTCATCCCAGGTTTTGCTG	59.037	47.619	0.00	0.00	0.00	4.41
2909	3333	2.780065	TGTGCTGTGCTTCAATTGTC	57.220	45.000	5.13	0.00	0.00	3.18
2928	3494	4.256110	TGTCTTCTGATTGTATGCTGTGG	58.744	43.478	0.00	0.00	0.00	4.17
2938	3504	0.839277	TATGCTGTGGGAGGTGATGG	59.161	55.000	0.00	0.00	0.00	3.51
2941	3507	1.611419	CTGTGGGAGGTGATGGCAT	59.389	57.895	0.00	0.00	0.00	4.40
2944	3510	0.749454	GTGGGAGGTGATGGCATGAC	60.749	60.000	3.81	6.63	0.00	3.06
2967	3533	0.600557	TGCCCGGTTGCTAATGTTTG	59.399	50.000	0.00	0.00	0.00	2.93
3061	3628	5.845614	AGAGAAGGCAGATGGATCTTTATCT	59.154	40.000	0.00	0.00	34.22	1.98
3083	3650	2.750637	GGAGCGACGGGACTCTGA	60.751	66.667	0.00	0.00	33.29	3.27
3125	3695	5.911178	TCTATTTTAGTGGGGATGAGATGGT	59.089	40.000	0.00	0.00	0.00	3.55
3235	3808	5.863935	GCTGTGGTGGAAAATTAATGAACTC	59.136	40.000	0.00	0.00	0.00	3.01
3314	3917	8.639428	CCATATAATTAGTGTTGATTCGTCTCG	58.361	37.037	0.00	0.00	0.00	4.04
3361	3969	4.526970	GGACCTTGAATGCCATCTTAAGA	58.473	43.478	7.82	7.82	0.00	2.10
3451	4059	9.490663	CGACCATTTCTTAGATTAATTTGTGTC	57.509	33.333	0.00	0.00	0.00	3.67
3491	4099	7.441017	TGACTGAAAATAAAATTTGGGTCAGG	58.559	34.615	15.95	5.11	32.12	3.86
3634	4260	2.019337	CATGCAGCTGCGCTTATCA	58.981	52.632	32.11	14.60	45.83	2.15
3726	4371	3.246619	CCTTAGACTTTCTCACGCTGAC	58.753	50.000	0.00	0.00	0.00	3.51
3757	4419	1.076350	ACTCTACACTGTCCTGCTCCT	59.924	52.381	0.00	0.00	0.00	3.69
3758	4420	1.476085	CTCTACACTGTCCTGCTCCTG	59.524	57.143	0.00	0.00	0.00	3.86
3806	4564	0.036010	AGCTAGCTTCGCATGTTGGT	60.036	50.000	12.68	0.00	0.00	3.67
3875	4637	4.124238	CTCCTGTCTCGTTGGTTAAAACA	58.876	43.478	0.00	0.00	0.00	2.83
3885	4648	5.910166	TCGTTGGTTAAAACATCAAACATCG	59.090	36.000	0.00	0.00	36.41	3.84
3906	4669	0.888619	CACAGTCGGGAGTGCTTCTA	59.111	55.000	3.47	0.00	35.19	2.10
3916	4679	4.261197	CGGGAGTGCTTCTATAAAAATGCC	60.261	45.833	0.00	0.00	0.00	4.40
3965	4731	7.750458	CGATCATATTTACATCCGAAAAATGGG	59.250	37.037	0.00	0.00	0.00	4.00
4020	4786	5.225642	TGCACACAATTCGCATGAAAATTA	58.774	33.333	0.00	0.00	37.71	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	2.203877	ACGGCTACCAAGGGTCCA	60.204	61.111	0.00	0.00	37.09	4.02
46	47	2.231721	GGCTCGACTTAGGTCTTCAACT	59.768	50.000	3.27	0.00	40.10	3.16
50	51	0.525882	GCGGCTCGACTTAGGTCTTC	60.526	60.000	3.27	0.00	40.10	2.87
228	259	3.864983	AAGGCACGGGGAAGGAGGA	62.865	63.158	0.00	0.00	0.00	3.71
241	272	1.820519	GTGGCATCAATGAAGAAGGCA	59.179	47.619	0.00	0.00	39.07	4.75
243	274	1.753073	GGGTGGCATCAATGAAGAAGG	59.247	52.381	0.00	0.00	0.00	3.46
259	290	1.002544	GGGAAGACTGTTCTCTGGGTG	59.997	57.143	0.00	0.00	0.00	4.61
279	310	3.355626	TGCATCGAGAAGAAGATACGG	57.644	47.619	0.00	0.00	0.00	4.02
280	311	3.487574	GGTTGCATCGAGAAGAAGATACG	59.512	47.826	0.00	0.00	0.00	3.06
325	360	0.323451	TCGAGTGCCAAGGAGAGCTA	60.323	55.000	0.00	0.00	0.00	3.32
326	361	1.603236	CTCGAGTGCCAAGGAGAGCT	61.603	60.000	3.62	0.00	0.00	4.09
327	362	1.153667	CTCGAGTGCCAAGGAGAGC	60.154	63.158	3.62	0.00	0.00	4.09
328	363	0.967887	TCCTCGAGTGCCAAGGAGAG	60.968	60.000	12.31	0.00	34.26	3.20
338	373	4.872691	GGCAATATATTCCATCCTCGAGTG	59.127	45.833	12.31	3.72	0.00	3.51
355	390	6.576662	TTCTTCGGTAAACATTTGGCAATA	57.423	33.333	0.00	0.00	0.00	1.90
372	407	8.989980	ACAGGAAAAAGAATACTACTTTCTTCG	58.010	33.333	0.00	0.00	41.38	3.79
423	458	7.962964	AGAGTCAAACAATCAATAGAAACGA	57.037	32.000	0.00	0.00	0.00	3.85
439	474	5.601313	AGAAAGGCCGGTATATAGAGTCAAA	59.399	40.000	1.90	0.00	0.00	2.69
444	479	6.522054	TCAAAAGAAAGGCCGGTATATAGAG	58.478	40.000	1.90	0.00	0.00	2.43
480	515	9.959721	AAATACTAATCTGGACAACATACAAGT	57.040	29.630	0.00	0.00	0.00	3.16
528	564	4.283212	CCAACCAGACAAATTTACACCCAT	59.717	41.667	0.00	0.00	0.00	4.00
532	568	6.977213	ACATACCAACCAGACAAATTTACAC	58.023	36.000	0.00	0.00	0.00	2.90
555	591	2.358247	ACGACCATGGCACGGAAC	60.358	61.111	27.25	0.00	0.00	3.62
556	592	2.047655	GACGACCATGGCACGGAA	60.048	61.111	27.25	0.00	0.00	4.30
557	593	2.994995	AGACGACCATGGCACGGA	60.995	61.111	27.25	0.00	0.00	4.69
558	594	2.815211	CAGACGACCATGGCACGG	60.815	66.667	27.25	0.00	0.00	4.94
559	595	3.490759	GCAGACGACCATGGCACG	61.491	66.667	23.94	23.94	0.00	5.34
595	631	2.772287	AGGTTTAGCTGCACTGTTCTC	58.228	47.619	1.02	0.00	0.00	2.87
600	636	2.880890	ACTCAAAGGTTTAGCTGCACTG	59.119	45.455	1.02	0.00	0.00	3.66
617	653	9.270640	CAACCATTAATTTTGATTTCCAACTCA	57.729	29.630	1.67	0.00	33.85	3.41
651	688	6.545666	CCATTCATACAGCTGGGTGTTTAATA	59.454	38.462	19.93	0.00	31.46	0.98
680	717	4.769688	TCCGATAGTCAATCATTGCTGTT	58.230	39.130	0.00	0.00	33.87	3.16
697	734	2.766263	TGGACAGCATAGAAACTCCGAT	59.234	45.455	0.00	0.00	0.00	4.18
699	736	2.166459	TCTGGACAGCATAGAAACTCCG	59.834	50.000	0.00	0.00	0.00	4.63
701	738	4.141846	TGGATCTGGACAGCATAGAAACTC	60.142	45.833	0.00	0.00	0.00	3.01
712	749	6.531923	AGTAAATGATGATGGATCTGGACAG	58.468	40.000	0.00	0.00	31.55	3.51
744	781	6.220930	GGACTAATTTACAGCGGTATCATCA	58.779	40.000	0.00	0.00	0.00	3.07
753	790	5.061808	GCATATACCGGACTAATTTACAGCG	59.938	44.000	9.46	0.00	0.00	5.18
815	856	4.970662	TCCGTTCGTTTAGCTACACTAT	57.029	40.909	8.34	0.00	0.00	2.12
822	863	4.319984	GGTTTTTCATCCGTTCGTTTAGCT	60.320	41.667	0.00	0.00	0.00	3.32
832	873	4.217550	CCATTACTGTGGTTTTTCATCCGT	59.782	41.667	0.00	0.00	34.46	4.69
870	915	3.327757	ACAGCAGGGTGTTCAATCTAGAA	59.672	43.478	0.00	0.00	0.00	2.10
901	946	9.613957	CTGTAGGTGAGTATGAATAATAAGACG	57.386	37.037	0.00	0.00	0.00	4.18
902	947	9.413048	GCTGTAGGTGAGTATGAATAATAAGAC	57.587	37.037	0.00	0.00	0.00	3.01
909	954	6.791867	AACAGCTGTAGGTGAGTATGAATA	57.208	37.500	22.01	0.00	45.66	1.75
935	984	3.115554	GTCAGGTTGTCAAATGTGCAAC	58.884	45.455	12.23	12.23	39.24	4.17
957	1006	4.009675	TGTAGCTCCCTGTAATTGCAAAG	58.990	43.478	1.71	0.00	0.00	2.77
959	1008	3.712016	TGTAGCTCCCTGTAATTGCAA	57.288	42.857	0.00	0.00	0.00	4.08
961	1010	5.215252	TCTATGTAGCTCCCTGTAATTGC	57.785	43.478	0.00	0.00	0.00	3.56
964	1013	5.081315	ACCTCTATGTAGCTCCCTGTAAT	57.919	43.478	0.00	0.00	0.00	1.89
1099	1152	1.372128	GTTCAAGGGCAAGCAAGCG	60.372	57.895	0.00	0.00	34.64	4.68
1107	1169	0.035598	TTCGATTCGGTTCAAGGGCA	59.964	50.000	6.18	0.00	0.00	5.36
1111	1173	1.803334	TGGGTTCGATTCGGTTCAAG	58.197	50.000	6.18	0.00	0.00	3.02
1134	1196	3.892588	GGATGTGTGGGTGTTTTCCTTTA	59.107	43.478	0.00	0.00	0.00	1.85
1157	1223	4.918810	ACATCAGGGACAAGAACAAAAC	57.081	40.909	0.00	0.00	0.00	2.43
1193	1262	2.595009	CTTTCCCCTCCAGCGGCTAC	62.595	65.000	0.26	0.00	0.00	3.58
1338	1420	1.276415	GCTGCACTTCTCTAAGCTCG	58.724	55.000	0.00	0.00	36.05	5.03
1387	1470	4.709397	ACAACCAAACCAACAAAGATGAGA	59.291	37.500	0.00	0.00	0.00	3.27
1389	1472	5.413309	AACAACCAAACCAACAAAGATGA	57.587	34.783	0.00	0.00	0.00	2.92
1390	1473	6.493449	AAAACAACCAAACCAACAAAGATG	57.507	33.333	0.00	0.00	0.00	2.90
1391	1474	6.569418	GCAAAAACAACCAAACCAACAAAGAT	60.569	34.615	0.00	0.00	0.00	2.40
1482	1569	5.079689	TCGAATACCTTGTGATGCAGTAA	57.920	39.130	0.00	0.00	0.00	2.24
1491	1578	6.960992	CACACACAAATATCGAATACCTTGTG	59.039	38.462	19.21	19.21	42.20	3.33
1502	1589	5.115472	GCAGAAAACACACACACAAATATCG	59.885	40.000	0.00	0.00	0.00	2.92
1644	1740	3.904136	AGCAGACAACAAACATACAGC	57.096	42.857	0.00	0.00	0.00	4.40
1675	1771	4.413520	ACCTGATATACCAAGAACATGCCT	59.586	41.667	0.00	0.00	0.00	4.75
2132	2289	3.450904	ACAGGAGATTACCACCAAGCTA	58.549	45.455	0.00	0.00	0.00	3.32
2235	2572	6.343716	TGAATTACTACAACCTCCGTGTTA	57.656	37.500	0.00	0.00	0.00	2.41
2258	2602	6.942576	AGGAAAGCAAAACTGTAGTGATGTAT	59.057	34.615	0.00	0.00	0.00	2.29
2277	2623	9.601217	AGCTATATGTTACAAACTACAGGAAAG	57.399	33.333	0.00	0.00	0.00	2.62
2287	2633	8.142994	ACTATGCACAGCTATATGTTACAAAC	57.857	34.615	0.00	0.00	0.00	2.93
2390	2772	1.201769	CGTTCAATTGCTACACGGTCG	60.202	52.381	0.00	0.00	0.00	4.79
2396	2778	1.463056	CGCTTCCGTTCAATTGCTACA	59.537	47.619	0.00	0.00	0.00	2.74
2489	2878	4.571919	TCCACTGTTTTATCCTGGTAACG	58.428	43.478	0.00	0.00	42.51	3.18
2602	2991	3.746940	TCAAGTGTTACTTACAAGGGCC	58.253	45.455	0.00	0.00	36.03	5.80
2703	3112	6.993079	ACCTTTTGCTCCAGGTAAATAAAAG	58.007	36.000	0.00	0.00	41.97	2.27
2727	3139	4.055360	CTCTCGAACACCACAATTGTGTA	58.945	43.478	31.20	10.94	45.78	2.90
2745	3157	1.068055	CACATGGCAAAACTGGCTCTC	60.068	52.381	0.00	0.00	35.21	3.20
2753	3167	5.689961	CCTACAAAGTAACACATGGCAAAAC	59.310	40.000	0.00	0.00	0.00	2.43
2872	3296	6.930164	ACAGCACAAAATATGATTCAGCAAAA	59.070	30.769	0.00	0.00	0.00	2.44
2879	3303	6.094719	TGAAGCACAGCACAAAATATGATTC	58.905	36.000	0.00	0.00	34.06	2.52
2909	3333	3.875727	CTCCCACAGCATACAATCAGAAG	59.124	47.826	0.00	0.00	0.00	2.85
2928	3494	2.062971	AATGTCATGCCATCACCTCC	57.937	50.000	0.00	0.00	0.00	4.30
2938	3504	0.737019	CAACCGGGCAAATGTCATGC	60.737	55.000	6.32	0.00	43.08	4.06
2941	3507	0.250945	TAGCAACCGGGCAAATGTCA	60.251	50.000	6.32	0.00	35.83	3.58
2944	3510	1.204467	ACATTAGCAACCGGGCAAATG	59.796	47.619	6.32	10.66	35.83	2.32
2967	3533	4.745620	GCTTCCGATCTGTATAACCAAGAC	59.254	45.833	0.00	0.00	0.00	3.01
3125	3695	6.095160	ACATACAAAACCAAAGTACGAAACCA	59.905	34.615	0.00	0.00	0.00	3.67
3235	3808	0.322008	AGGGAGCAGGAAAGAAAGCG	60.322	55.000	0.00	0.00	0.00	4.68
3338	3946	2.149973	AAGATGGCATTCAAGGTCCC	57.850	50.000	0.00	0.00	0.00	4.46
3340	3948	6.515272	TTTCTTAAGATGGCATTCAAGGTC	57.485	37.500	5.89	0.00	0.00	3.85
3421	4029	6.867662	ATTAATCTAAGAAATGGTCGCTGG	57.132	37.500	0.00	0.00	0.00	4.85
3428	4036	9.294030	GCTGACACAAATTAATCTAAGAAATGG	57.706	33.333	0.00	0.00	0.00	3.16
3451	4059	0.603569	AGTCAACTGACCGGTAGCTG	59.396	55.000	7.34	7.57	45.85	4.24
3452	4060	0.603569	CAGTCAACTGACCGGTAGCT	59.396	55.000	7.34	0.00	46.59	3.32
3627	4253	1.849219	CTTGCTCTCGACGTGATAAGC	59.151	52.381	0.00	4.40	36.38	3.09
3634	4260	1.772182	CTTTCACTTGCTCTCGACGT	58.228	50.000	0.00	0.00	0.00	4.34
3726	4371	6.207025	AGGACAGTGTAGAGTACTTGTGTTAG	59.793	42.308	0.00	0.00	31.01	2.34
3757	4419	8.195436	GTGTATATGTGCTTCTAGGAACTTACA	58.805	37.037	0.00	0.00	41.75	2.41
3758	4420	8.195436	TGTGTATATGTGCTTCTAGGAACTTAC	58.805	37.037	0.00	0.00	41.75	2.34
3806	4564	1.826487	TGGTCGCATAGCTAGCCGA	60.826	57.895	12.13	10.51	0.00	5.54
3875	4637	1.078709	CGACTGTGGCGATGTTTGAT	58.921	50.000	0.00	0.00	0.00	2.57
3885	4648	3.537206	AAGCACTCCCGACTGTGGC	62.537	63.158	0.00	0.00	34.99	5.01
3906	4669	5.263599	TCTCTGTGGATGTGGCATTTTTAT	58.736	37.500	0.00	0.00	0.00	1.40
3916	4679	2.469274	ACAAGCTCTCTGTGGATGTG	57.531	50.000	0.00	0.00	0.00	3.21
3965	4731	9.687717	CTGTCATTGTTTGTTTTATGTGTTTTC	57.312	29.630	0.00	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.