AutoCloner

Multiple sequence alignment - TraesCS4D01G264700

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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	TraesCS4D01G264700	chr4D	100.000	4995	0	0	1	4995	435066646	435061652	0.000000e+00	9225.0
1	TraesCS4D01G264700	chr4D	89.419	1342	111	21	2703	4031	82293380	82292057	0.000000e+00	1663.0
2	TraesCS4D01G264700	chr4D	87.259	934	75	20	4031	4951	82292025	82291123	0.000000e+00	1026.0
3	TraesCS4D01G264700	chr4D	84.132	939	114	23	1778	2705	82294353	82293439	0.000000e+00	876.0
4	TraesCS4D01G264700	chr4D	87.015	747	73	15	522	1258	82295844	82295112	0.000000e+00	821.0
5	TraesCS4D01G264700	chr4D	88.462	234	21	5	1550	1780	428936388	428936158	1.370000e-70	278.0
6	TraesCS4D01G264700	chr4D	88.034	234	20	7	1550	1778	22018379	22018609	2.290000e-68	270.0
7	TraesCS4D01G264700	chr4D	87.387	222	20	3	1263	1483	82294565	82294351	1.070000e-61	248.0
8	TraesCS4D01G264700	chr4D	94.366	71	3	1	1483	1552	22018347	22018417	1.900000e-19	108.0
9	TraesCS4D01G264700	chr4A	93.360	2771	114	30	1921	4665	36413876	36411150	0.000000e+00	4034.0
10	TraesCS4D01G264700	chr4A	87.242	2281	201	52	1778	4031	492533340	492531123	0.000000e+00	2518.0
11	TraesCS4D01G264700	chr4A	86.510	934	82	21	4031	4951	492531092	492530190	0.000000e+00	987.0
12	TraesCS4D01G264700	chr4A	91.054	626	50	5	199	822	36415597	36414976	0.000000e+00	841.0
13	TraesCS4D01G264700	chr4A	95.409	501	15	6	825	1319	36414940	36414442	0.000000e+00	791.0
14	TraesCS4D01G264700	chr4A	87.891	479	48	6	790	1267	492534760	492534291	5.650000e-154	555.0
15	TraesCS4D01G264700	chr4A	90.909	330	21	4	1550	1879	36414307	36413987	7.680000e-118	435.0
16	TraesCS4D01G264700	chr4A	86.695	233	25	5	1550	1778	579865416	579865186	2.310000e-63	254.0
17	TraesCS4D01G264700	chr4A	86.036	222	23	3	1263	1483	492533552	492533338	1.080000e-56	231.0
18	TraesCS4D01G264700	chr4A	89.119	193	5	6	1363	1553	36414446	36414268	5.030000e-55	226.0
19	TraesCS4D01G264700	chr4A	91.781	73	4	2	1483	1553	37347249	37347321	3.180000e-17	100.0
20	TraesCS4D01G264700	chr4A	89.024	82	7	2	1483	1562	579865448	579865367	3.180000e-17	100.0
21	TraesCS4D01G264700	chr4A	95.652	46	2	0	1874	1919	36413948	36413903	1.930000e-09	75.0
22	TraesCS4D01G264700	chr4A	97.297	37	0	1	4954	4990	13753828	13753793	1.500000e-05	62.1
23	TraesCS4D01G264700	chr4A	100.000	28	0	0	4962	4989	603501924	603501897	9.000000e-03	52.8
24	TraesCS4D01G264700	chr4B	93.186	1849	65	21	1501	3304	535249757	535247925	0.000000e+00	2660.0
25	TraesCS4D01G264700	chr4B	89.129	1481	97	21	6	1446	535252453	535250997	0.000000e+00	1784.0
26	TraesCS4D01G264700	chr4B	89.650	1343	109	19	2704	4031	116214332	116213005	0.000000e+00	1683.0
27	TraesCS4D01G264700	chr4B	92.809	737	40	6	3303	4031	535247770	535247039	0.000000e+00	1055.0
28	TraesCS4D01G264700	chr4B	90.793	706	34	16	4028	4730	535246981	535246304	0.000000e+00	915.0
29	TraesCS4D01G264700	chr4B	87.277	786	82	14	1921	2705	116215169	116214401	0.000000e+00	881.0
30	TraesCS4D01G264700	chr4B	85.065	770	70	25	531	1267	116216857	116216100	0.000000e+00	743.0
31	TraesCS4D01G264700	chr4B	90.873	504	26	11	4456	4951	116212697	116212206	0.000000e+00	658.0
32	TraesCS4D01G264700	chr4B	93.015	272	14	3	4680	4951	535226632	535226366	4.690000e-105	392.0
33	TraesCS4D01G264700	chr4B	86.228	334	23	9	4372	4695	535237222	535236902	1.720000e-89	340.0
34	TraesCS4D01G264700	chr4B	88.696	230	15	6	1255	1483	116215527	116215308	2.290000e-68	270.0
35	TraesCS4D01G264700	chr4B	89.189	74	8	0	1778	1851	116215310	116215237	5.320000e-15	93.5
36	TraesCS4D01G264700	chr4B	88.235	68	7	1	1438	1504	535250164	535250097	4.150000e-11	80.5
37	TraesCS4D01G264700	chr5B	89.333	225	22	2	1555	1777	536311621	536311397	1.060000e-71	281.0
38	TraesCS4D01G264700	chr2A	86.752	234	22	7	1550	1778	637227787	637227558	8.300000e-63	252.0
39	TraesCS4D01G264700	chr2A	74.556	169	36	5	16	183	605032907	605033069	3.230000e-07	67.6
40	TraesCS4D01G264700	chr2A	100.000	28	0	0	4962	4989	499766429	499766402	9.000000e-03	52.8
41	TraesCS4D01G264700	chr6B	86.695	233	20	8	1550	1777	523958175	523958401	1.070000e-61	248.0
42	TraesCS4D01G264700	chrUn	86.087	230	26	5	1555	1781	1482177	1481951	5.000000e-60	243.0
43	TraesCS4D01G264700	chr7A	84.889	225	24	8	1557	1777	513209760	513209978	8.420000e-53	219.0
44	TraesCS4D01G264700	chr7A	97.059	34	1	0	4956	4989	260695	260662	1.940000e-04	58.4
45	TraesCS4D01G264700	chr3B	90.000	80	6	2	1476	1553	601408291	601408212	8.850000e-18	102.0
46	TraesCS4D01G264700	chr3B	86.667	90	9	3	1476	1562	117300599	117300510	4.120000e-16	97.1
47	TraesCS4D01G264700	chr1A	98.246	57	1	0	1497	1553	581437313	581437257	3.180000e-17	100.0
48	TraesCS4D01G264700	chr7B	89.610	77	6	2	1479	1553	497083643	497083719	4.120000e-16	97.1
49	TraesCS4D01G264700	chr2D	95.238	42	2	0	4954	4995	598272421	598272380	3.230000e-07	67.6
50	TraesCS4D01G264700	chr2D	76.852	108	19	6	76	181	3026543	3026646	6.990000e-04	56.5
51	TraesCS4D01G264700	chr3A	74.118	170	30	12	14	181	587584726	587584569	1.940000e-04	58.4
52	TraesCS4D01G264700	chr3A	94.286	35	2	0	4955	4989	33641203	33641169	3.000000e-03	54.7
53	TraesCS4D01G264700	chr3A	94.286	35	2	0	4956	4990	634690127	634690161	3.000000e-03	54.7
54	TraesCS4D01G264700	chr3A	94.286	35	2	0	4956	4990	639422892	639422926	3.000000e-03	54.7
55	TraesCS4D01G264700	chr5D	94.444	36	0	1	2693	2726	318483133	318483168	3.000000e-03	54.7
56	TraesCS4D01G264700	chr1B	100.000	28	0	0	4962	4989	112351171	112351144	9.000000e-03	52.8

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	TraesCS4D01G264700	chr4D	435061652	435066646	4994	True	9225.000000	9225	100.000000	1	4995	1	chr4D.!!$R2	4994
1	TraesCS4D01G264700	chr4D	82291123	82295844	4721	True	926.800000	1663	87.042400	522	4951	5	chr4D.!!$R3	4429
2	TraesCS4D01G264700	chr4A	492530190	492534760	4570	True	1072.750000	2518	86.919750	790	4951	4	chr4A.!!$R4	4161
3	TraesCS4D01G264700	chr4A	36411150	36415597	4447	True	1067.000000	4034	92.583833	199	4665	6	chr4A.!!$R3	4466
4	TraesCS4D01G264700	chr4B	535246304	535252453	6149	True	1298.900000	2660	90.830400	6	4730	5	chr4B.!!$R4	4724
5	TraesCS4D01G264700	chr4B	116212206	116216857	4651	True	721.416667	1683	88.458333	531	4951	6	chr4B.!!$R3	4420

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
74	75	0.259356	TGTCAACCGGTTTCCCCTTT	59.741	50.0	19.55	0.00	3.11	F
1492	3264	0.105039	CATCTTCACTACCCCCTCGC	59.895	60.0	0.00	0.00	5.03	F
2561	4771	0.593518	TGGTGCGTGATTTTGCGTTG	60.594	50.0	0.00	0.00	4.10	F
3506	5965	2.215942	ACCAGTTTGGGTATTCAGGC	57.784	50.0	0.00	43.37	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1997	4194	0.949105	CTCCAACCGAAGAACACCCG	60.949	60.000	0.00	0.00	5.28	R
2667	4877	1.609072	GGACCAGGCTTTGTTTGACTC	59.391	52.381	0.00	0.00	3.36	R
3611	6084	0.247460	CCACAGAGTCTTGATCGCCA	59.753	55.000	0.00	0.00	5.69	R
4737	7313	0.033920	GTCTGCTTTTGGCCTTTGGG	59.966	55.000	3.32	40.92	4.12	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
45	46	5.758784	AGTAGTGTTTCTTTTACTGACAGGC	59.241	40.000	7.51	0.00	0.00	4.85
67	68	3.086282	AGAACTGTTTGTCAACCGGTTT	58.914	40.909	19.55	0.00	31.89	3.27
69	70	1.746787	ACTGTTTGTCAACCGGTTTCC	59.253	47.619	19.55	11.66	31.02	3.13
74	75	0.259356	TGTCAACCGGTTTCCCCTTT	59.741	50.000	19.55	0.00	0.00	3.11
80	81	1.151908	CGGTTTCCCCTTTCCACCA	59.848	57.895	0.00	0.00	0.00	4.17
91	92	2.718609	CCTTTCCACCATATCCCTCCAT	59.281	50.000	0.00	0.00	0.00	3.41
94	95	3.073411	TCCACCATATCCCTCCATTGA	57.927	47.619	0.00	0.00	0.00	2.57
96	97	3.989558	TCCACCATATCCCTCCATTGATT	59.010	43.478	0.00	0.00	0.00	2.57
97	98	4.043310	TCCACCATATCCCTCCATTGATTC	59.957	45.833	0.00	0.00	0.00	2.52
129	130	2.649531	TCTGAATTTTCCCACCACGT	57.350	45.000	0.00	0.00	0.00	4.49
131	132	2.158740	TCTGAATTTTCCCACCACGTCA	60.159	45.455	0.00	0.00	0.00	4.35
142	143	3.071023	CCCACCACGTCAGATATAACCAT	59.929	47.826	0.00	0.00	0.00	3.55
151	152	6.322969	ACGTCAGATATAACCATACCTCACAA	59.677	38.462	0.00	0.00	0.00	3.33
154	155	8.150945	GTCAGATATAACCATACCTCACAACAT	58.849	37.037	0.00	0.00	0.00	2.71
155	156	8.150296	TCAGATATAACCATACCTCACAACATG	58.850	37.037	0.00	0.00	0.00	3.21
174	175	4.098349	ACATGCCGCTCAATCACATTAATT	59.902	37.500	0.00	0.00	0.00	1.40
305	306	1.366319	AGACACAAAGGGGCAGATCT	58.634	50.000	0.00	0.00	0.00	2.75
341	342	5.395435	CCCATCAAACCATGTCAATGCAATA	60.395	40.000	0.00	0.00	31.93	1.90
344	345	6.094193	TCAAACCATGTCAATGCAATAACA	57.906	33.333	0.00	0.00	31.93	2.41
345	346	6.519382	TCAAACCATGTCAATGCAATAACAA	58.481	32.000	0.00	0.00	31.93	2.83
348	349	7.599630	AACCATGTCAATGCAATAACAAATC	57.400	32.000	0.00	0.00	31.93	2.17
350	351	7.037438	ACCATGTCAATGCAATAACAAATCTC	58.963	34.615	0.00	0.00	31.93	2.75
353	354	5.094812	GTCAATGCAATAACAAATCTCGCA	58.905	37.500	0.00	0.00	0.00	5.10
366	367	5.356190	ACAAATCTCGCATCAATGATGAACT	59.644	36.000	25.77	3.33	42.09	3.01
658	666	6.869388	AGGAGACTTTTCGACTCAAAAGATAC	59.131	38.462	12.96	3.78	43.41	2.24
771	795	2.605837	TCAGCACCGCCGAATTTATA	57.394	45.000	0.00	0.00	0.00	0.98
822	852	6.352137	GGAAACAATGGAATCCAAGCCTAAAT	60.352	38.462	5.89	0.00	36.95	1.40
837	901	3.057734	CCTAAATCCGCGTATCCTCAAC	58.942	50.000	4.92	0.00	0.00	3.18
841	905	2.459060	TCCGCGTATCCTCAACAAAA	57.541	45.000	4.92	0.00	0.00	2.44
917	983	5.188434	CCGGTATATATCACCCGAACTCTA	58.812	45.833	16.01	0.00	43.01	2.43
923	989	1.735386	TCACCCGAACTCTAGACTCG	58.265	55.000	11.07	11.07	0.00	4.18
940	1006	1.204941	CTCGAGAACCCAACCCACTAG	59.795	57.143	6.58	0.00	0.00	2.57
1297	2209	4.351127	TGTACCTTTTCCTCCTCTACTCC	58.649	47.826	0.00	0.00	0.00	3.85
1303	2221	2.830651	TCCTCCTCTACTCCACCTTC	57.169	55.000	0.00	0.00	0.00	3.46
1491	3263	0.753262	CCATCTTCACTACCCCCTCG	59.247	60.000	0.00	0.00	0.00	4.63
1492	3264	0.105039	CATCTTCACTACCCCCTCGC	59.895	60.000	0.00	0.00	0.00	5.03
1494	3266	0.683504	TCTTCACTACCCCCTCGCTC	60.684	60.000	0.00	0.00	0.00	5.03
1495	3267	1.677637	CTTCACTACCCCCTCGCTCC	61.678	65.000	0.00	0.00	0.00	4.70
1496	3268	2.042843	CACTACCCCCTCGCTCCT	60.043	66.667	0.00	0.00	0.00	3.69
1570	3686	5.523369	CCAAATCTGGTCAAAGTCAAACTC	58.477	41.667	0.00	0.00	38.00	3.01
1593	3709	9.097257	ACTCAACAAAGTTTGACCAAATTTATG	57.903	29.630	22.23	7.20	31.37	1.90
1594	3710	9.097257	CTCAACAAAGTTTGACCAAATTTATGT	57.903	29.630	22.23	7.66	31.37	2.29
1595	3711	9.442047	TCAACAAAGTTTGACCAAATTTATGTT	57.558	25.926	22.23	15.92	35.08	2.71
1665	3781	9.507280	AAAGTTAATTTCGTGATGCATCTAATG	57.493	29.630	26.32	13.26	0.00	1.90
1972	4169	4.395854	TGATTGCTAACTGTATGTTGCTGG	59.604	41.667	0.00	0.00	39.55	4.85
1978	4175	6.030228	GCTAACTGTATGTTGCTGGAAAATC	58.970	40.000	0.00	0.00	39.55	2.17
2000	4197	1.221840	CTGATGTTCAGGTCCCGGG	59.778	63.158	16.85	16.85	40.71	5.73
2372	4578	3.609373	ACGTCGATGTAACCGTATGTTTG	59.391	43.478	8.94	0.00	38.42	2.93
2495	4705	2.786777	ACGCGGGTTAGGAAGAATTTT	58.213	42.857	12.47	0.00	0.00	1.82
2539	4749	6.916440	TGCGTTTCAGTTAGTATCTCTGTTA	58.084	36.000	0.00	0.00	0.00	2.41
2561	4771	0.593518	TGGTGCGTGATTTTGCGTTG	60.594	50.000	0.00	0.00	0.00	4.10
2667	4877	7.793948	ATATAAAGGGGGTAGCTGTAAGTAG	57.206	40.000	0.00	0.00	35.30	2.57
2886	5174	6.127366	TGGCCATAAAGAAGGATTGTGATTTC	60.127	38.462	0.00	0.00	0.00	2.17
2981	5269	3.605634	TGGTTGGAGAATATGTTGACGG	58.394	45.455	0.00	0.00	0.00	4.79
2996	5284	2.742774	TGACGGCTATGATGTCATTCG	58.257	47.619	0.19	6.26	37.69	3.34
3119	5413	6.668541	TTTGATTGCTCTTATGTGACTAGC	57.331	37.500	0.00	0.00	0.00	3.42
3269	5563	2.697761	GGCTGGAGCATGTGCAGTG	61.698	63.158	7.83	0.00	46.21	3.66
3299	5593	4.568760	GTGCTTCTATTGCTACTTCTGTCC	59.431	45.833	0.00	0.00	0.00	4.02
3347	5806	9.138596	AGTAAATATGTAAAGAGAGGAGAGTCC	57.861	37.037	0.00	0.00	36.58	3.85
3464	5923	6.017400	ACATCAACATCTTGCCTTTACTTG	57.983	37.500	0.00	0.00	0.00	3.16
3478	5937	6.045955	GCCTTTACTTGAGAGAATAGTGGAG	58.954	44.000	0.00	0.00	0.00	3.86
3506	5965	2.215942	ACCAGTTTGGGTATTCAGGC	57.784	50.000	0.00	0.00	43.37	4.85
3575	6048	6.785191	TCAGATAATTTCTTTCGTTCCATGC	58.215	36.000	0.00	0.00	29.93	4.06
3581	6054	2.351455	TCTTTCGTTCCATGCGCAATA	58.649	42.857	17.11	0.00	0.00	1.90
3725	6198	1.142262	AGTAGTTGGTTCCGCAAAGGT	59.858	47.619	0.00	0.00	41.99	3.50
3785	6258	8.694581	TTGCAGATGTCCAATTTGATGATATA	57.305	30.769	0.00	0.00	0.00	0.86
3822	6295	5.466728	TGTAACATCTGTTGCTCTTCTTGAC	59.533	40.000	11.53	0.00	40.55	3.18
4350	6904	3.544684	TGCTAATAGTGGAATGCTGGTG	58.455	45.455	0.00	0.00	0.00	4.17
4366	6920	3.427233	GCTGGTGTGATTTGCTGATCTTC	60.427	47.826	0.00	0.00	0.00	2.87
4367	6921	3.084039	TGGTGTGATTTGCTGATCTTCC	58.916	45.455	0.00	0.00	0.00	3.46
4370	6924	4.005650	GTGTGATTTGCTGATCTTCCTGA	58.994	43.478	0.00	0.00	0.00	3.86
4450	7015	5.123344	ACAAGTGTAACAAACTTCTGTCCAC	59.877	40.000	0.00	0.00	41.43	4.02
4493	7058	1.608055	CATGCTGTGGTGACCTCAAA	58.392	50.000	7.85	0.00	0.00	2.69
4534	7099	2.509964	CAGGGGCAGTTCCTTACCTTAT	59.490	50.000	0.00	0.00	31.06	1.73
4536	7101	4.165372	CAGGGGCAGTTCCTTACCTTATTA	59.835	45.833	0.00	0.00	31.06	0.98
4537	7102	4.412528	AGGGGCAGTTCCTTACCTTATTAG	59.587	45.833	0.00	0.00	34.39	1.73
4540	7105	4.165565	GGCAGTTCCTTACCTTATTAGGGT	59.834	45.833	2.26	2.74	46.58	4.34
4542	7107	6.126681	GGCAGTTCCTTACCTTATTAGGGTTA	60.127	42.308	2.45	0.00	46.58	2.85
4543	7108	7.421030	GGCAGTTCCTTACCTTATTAGGGTTAT	60.421	40.741	2.45	0.00	46.58	1.89
4582	7148	1.224069	CGACCAGTGTGCAAGGACAG	61.224	60.000	0.00	0.00	0.00	3.51
4606	7176	4.583871	AGGTCCAGAAATTAGAACTGCAG	58.416	43.478	13.48	13.48	0.00	4.41
4708	7284	0.676151	CAGAGAAGCTGCCCCAGTTC	60.676	60.000	0.00	0.00	37.90	3.01
4732	7308	1.093159	CTGCATGTCTCTTTGCTCCC	58.907	55.000	0.00	0.00	39.60	4.30
4733	7309	0.322816	TGCATGTCTCTTTGCTCCCC	60.323	55.000	0.00	0.00	39.60	4.81
4734	7310	0.322816	GCATGTCTCTTTGCTCCCCA	60.323	55.000	0.00	0.00	35.95	4.96
4735	7311	1.887956	GCATGTCTCTTTGCTCCCCAA	60.888	52.381	0.00	0.00	35.95	4.12
4736	7312	1.815003	CATGTCTCTTTGCTCCCCAAC	59.185	52.381	0.00	0.00	31.97	3.77
4737	7313	0.110486	TGTCTCTTTGCTCCCCAACC	59.890	55.000	0.00	0.00	31.97	3.77
4753	7329	0.985490	AACCCCAAAGGCCAAAAGCA	60.985	50.000	5.01	0.00	46.50	3.91
4766	7342	4.501400	GGCCAAAAGCAGACAGTAACAATT	60.501	41.667	0.00	0.00	46.50	2.32
4865	7442	2.936498	GGTATCAACGAGGTGACAATGG	59.064	50.000	0.00	0.00	0.00	3.16
4933	7512	8.863049	CAAAGTATTACCATTCAAGAACAATGC	58.137	33.333	0.00	0.00	30.94	3.56
4960	7540	3.790223	TGGAAACATTGGGGCTGC	58.210	55.556	0.00	0.00	33.40	5.25
4961	7541	1.152376	TGGAAACATTGGGGCTGCA	60.152	52.632	0.50	0.00	33.40	4.41
4962	7542	0.544833	TGGAAACATTGGGGCTGCAT	60.545	50.000	0.50	0.00	33.40	3.96
4963	7543	0.108041	GGAAACATTGGGGCTGCATG	60.108	55.000	0.50	0.00	0.00	4.06
4964	7544	0.741927	GAAACATTGGGGCTGCATGC	60.742	55.000	11.82	11.82	41.94	4.06
4965	7545	1.481901	AAACATTGGGGCTGCATGCA	61.482	50.000	21.29	21.29	45.15	3.96
4966	7546	1.268992	AACATTGGGGCTGCATGCAT	61.269	50.000	22.97	0.35	45.15	3.96
4967	7547	1.069090	CATTGGGGCTGCATGCATC	59.931	57.895	22.97	17.75	45.15	3.91
4968	7548	1.075525	ATTGGGGCTGCATGCATCT	60.076	52.632	22.97	0.00	45.15	2.90
4969	7549	0.689745	ATTGGGGCTGCATGCATCTT	60.690	50.000	22.97	0.00	45.15	2.40
4970	7550	0.905809	TTGGGGCTGCATGCATCTTT	60.906	50.000	22.97	0.00	45.15	2.52
4971	7551	1.324740	TGGGGCTGCATGCATCTTTC	61.325	55.000	22.97	10.97	45.15	2.62
4972	7552	1.041447	GGGGCTGCATGCATCTTTCT	61.041	55.000	22.97	0.00	45.15	2.52
4973	7553	0.102481	GGGCTGCATGCATCTTTCTG	59.898	55.000	22.97	8.76	45.15	3.02
4974	7554	1.100510	GGCTGCATGCATCTTTCTGA	58.899	50.000	22.97	0.00	45.15	3.27
4975	7555	1.681793	GGCTGCATGCATCTTTCTGAT	59.318	47.619	22.97	0.00	45.15	2.90
4984	7564	1.948145	CATCTTTCTGATGCAGAGGCC	59.052	52.381	0.00	0.00	44.96	5.19
4985	7565	0.107993	TCTTTCTGATGCAGAGGCCG	60.108	55.000	0.00	0.00	41.75	6.13
4986	7566	0.107993	CTTTCTGATGCAGAGGCCGA	60.108	55.000	0.00	0.00	41.75	5.54
4987	7567	0.107993	TTTCTGATGCAGAGGCCGAG	60.108	55.000	0.00	0.00	41.75	4.63
4988	7568	1.964608	TTCTGATGCAGAGGCCGAGG	61.965	60.000	0.00	0.00	41.75	4.63
4989	7569	3.457625	CTGATGCAGAGGCCGAGGG	62.458	68.421	0.00	0.00	40.13	4.30
4990	7570	3.474570	GATGCAGAGGCCGAGGGT	61.475	66.667	0.00	0.00	40.13	4.34
4991	7571	2.041922	ATGCAGAGGCCGAGGGTA	60.042	61.111	0.00	0.00	40.13	3.69
4992	7572	1.686325	GATGCAGAGGCCGAGGGTAA	61.686	60.000	0.00	0.00	40.13	2.85
4993	7573	1.056700	ATGCAGAGGCCGAGGGTAAT	61.057	55.000	0.00	0.00	40.13	1.89
4994	7574	1.069935	GCAGAGGCCGAGGGTAATC	59.930	63.158	0.00	0.00	0.00	1.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	2.292267	CAAACAGTTCTGCCTGTCAGT	58.708	47.619	0.00	0.00	44.74	3.41
41	42	2.223572	GGTTGACAAACAGTTCTGCCTG	60.224	50.000	0.00	0.74	38.10	4.85
45	46	2.014128	ACCGGTTGACAAACAGTTCTG	58.986	47.619	0.00	0.00	38.10	3.02
52	53	3.951115	GGGAAACCGGTTGACAAAC	57.049	52.632	23.08	7.56	43.64	2.93
67	68	1.012049	AGGGATATGGTGGAAAGGGGA	59.988	52.381	0.00	0.00	0.00	4.81
69	70	1.425448	GGAGGGATATGGTGGAAAGGG	59.575	57.143	0.00	0.00	0.00	3.95
74	75	3.073411	TCAATGGAGGGATATGGTGGA	57.927	47.619	0.00	0.00	0.00	4.02
129	130	7.669089	TGTTGTGAGGTATGGTTATATCTGA	57.331	36.000	0.00	0.00	30.33	3.27
131	132	6.936900	GCATGTTGTGAGGTATGGTTATATCT	59.063	38.462	0.00	0.00	32.88	1.98
142	143	0.391130	GAGCGGCATGTTGTGAGGTA	60.391	55.000	1.45	0.00	0.00	3.08
151	152	1.466856	AATGTGATTGAGCGGCATGT	58.533	45.000	1.45	0.00	0.00	3.21
154	155	4.717233	AAATTAATGTGATTGAGCGGCA	57.283	36.364	1.45	0.00	0.00	5.69
155	156	5.821204	AGTAAATTAATGTGATTGAGCGGC	58.179	37.500	0.00	0.00	0.00	6.53
187	188	8.579850	AATCTTGCCTGTATTAACTTGATTCA	57.420	30.769	0.00	0.00	0.00	2.57
305	306	3.442273	GGTTTGATGGGCGAGATTTGTTA	59.558	43.478	0.00	0.00	0.00	2.41
341	342	5.823209	TCATCATTGATGCGAGATTTGTT	57.177	34.783	19.74	0.00	39.63	2.83
344	345	5.821470	AGAGTTCATCATTGATGCGAGATTT	59.179	36.000	19.74	3.37	39.63	2.17
345	346	5.366460	AGAGTTCATCATTGATGCGAGATT	58.634	37.500	19.74	4.82	39.63	2.40
348	349	5.333187	GCTAAGAGTTCATCATTGATGCGAG	60.333	44.000	19.74	10.50	39.63	5.03
350	351	4.271776	TGCTAAGAGTTCATCATTGATGCG	59.728	41.667	19.74	0.08	39.63	4.73
353	354	7.876936	AACATGCTAAGAGTTCATCATTGAT	57.123	32.000	0.00	0.00	0.00	2.57
366	367	2.694213	TGCACGCTAAACATGCTAAGA	58.306	42.857	0.00	0.00	38.60	2.10
436	438	6.126623	TGGTATTAGGCAGGATAACAATCACA	60.127	38.462	0.00	0.00	0.00	3.58
702	710	8.706492	TGAATCATTATTTGTGATTTTGGAGC	57.294	30.769	3.22	0.00	44.10	4.70
732	746	7.439356	GTGCTGAAAAGTGCTGTGATATCTATA	59.561	37.037	3.98	0.00	0.00	1.31
739	761	1.610522	GGTGCTGAAAAGTGCTGTGAT	59.389	47.619	0.00	0.00	0.00	3.06
740	762	1.024271	GGTGCTGAAAAGTGCTGTGA	58.976	50.000	0.00	0.00	0.00	3.58
741	763	0.317269	CGGTGCTGAAAAGTGCTGTG	60.317	55.000	0.00	0.00	0.00	3.66
771	795	5.237236	TCTTTTCCACCGGTTAAGAGATT	57.763	39.130	2.97	0.00	0.00	2.40
822	852	2.028839	TCTTTTGTTGAGGATACGCGGA	60.029	45.455	12.47	0.00	46.39	5.54
917	983	0.471211	TGGGTTGGGTTCTCGAGTCT	60.471	55.000	13.13	0.00	0.00	3.24
923	989	1.278413	GTCCTAGTGGGTTGGGTTCTC	59.722	57.143	0.00	0.00	36.25	2.87
940	1006	4.500826	GGGAGGAGGGGGAGGTCC	62.501	77.778	0.00	0.00	0.00	4.46
1297	2209	2.032549	CAGAACGTGCAAGAAGAAGGTG	60.033	50.000	6.65	0.00	0.00	4.00
1371	2289	3.488553	GGGAGGAAGTTGTTTGTGTTTCG	60.489	47.826	0.00	0.00	0.00	3.46
1453	3225	5.664908	AGATGGTGACCTCAAAGATACTCAT	59.335	40.000	2.11	0.00	0.00	2.90
1553	3669	4.963276	TGTTGAGTTTGACTTTGACCAG	57.037	40.909	0.00	0.00	0.00	4.00
1568	3684	9.097257	ACATAAATTTGGTCAAACTTTGTTGAG	57.903	29.630	0.00	0.00	38.17	3.02
1714	3833	8.195617	TGGTCAAAGTCAAATTTTGAAATGTC	57.804	30.769	13.21	9.87	43.76	3.06
1972	4169	5.123027	GGACCTGAACATCAGTGAGATTTTC	59.877	44.000	0.00	0.00	42.80	2.29
1978	4175	1.404717	CGGGACCTGAACATCAGTGAG	60.405	57.143	0.00	0.00	42.80	3.51
1997	4194	0.949105	CTCCAACCGAAGAACACCCG	60.949	60.000	0.00	0.00	0.00	5.28
2000	4197	1.566018	CGCCTCCAACCGAAGAACAC	61.566	60.000	0.00	0.00	0.00	3.32
2194	4400	3.686726	AGAAGATTGGACACTGCGAATTC	59.313	43.478	0.00	0.00	0.00	2.17
2245	4451	1.402456	CGAAGTGTTGGAGTAGGACCG	60.402	57.143	0.00	0.00	0.00	4.79
2495	4705	6.615088	ACGCAGATTCGTAAAGTAGAACTTA	58.385	36.000	0.00	0.00	41.36	2.24
2539	4749	1.742831	ACGCAAAATCACGCACCATAT	59.257	42.857	0.00	0.00	0.00	1.78
2667	4877	1.609072	GGACCAGGCTTTGTTTGACTC	59.391	52.381	0.00	0.00	0.00	3.36
2886	5174	3.378339	GTTACCGGATGTGTAATCCTCG	58.622	50.000	9.46	0.00	36.07	4.63
2996	5284	2.736144	TGATGGGTAACAGACGTCAC	57.264	50.000	19.50	6.78	39.74	3.67
3090	5384	6.583806	GTCACATAAGAGCAATCAAAAGGTTG	59.416	38.462	0.00	0.00	35.95	3.77
3138	5432	4.177026	CACTCCTAAACTGATCTTGGTCG	58.823	47.826	0.00	0.00	0.00	4.79
3269	5563	5.908341	AGTAGCAATAGAAGCACTTACTCC	58.092	41.667	0.00	0.00	0.00	3.85
3299	5593	6.106877	CTGAAAGTACCAACGGATGTATTG	57.893	41.667	0.00	0.00	0.00	1.90
3347	5806	5.597813	AAGATGAGCAGTTTGTTTACTCG	57.402	39.130	0.00	0.00	0.00	4.18
3464	5923	6.704050	GGTATCTTTTGCTCCACTATTCTCTC	59.296	42.308	0.00	0.00	0.00	3.20
3478	5937	5.914898	ATACCCAAACTGGTATCTTTTGC	57.085	39.130	0.00	0.00	46.37	3.68
3506	5965	7.148523	GGGAGTACGAAAAGGTAAGTTAACATG	60.149	40.741	8.61	0.00	0.00	3.21
3611	6084	0.247460	CCACAGAGTCTTGATCGCCA	59.753	55.000	0.00	0.00	0.00	5.69
3725	6198	8.577296	GTGTTCATAGCATAGAAGTATACCTGA	58.423	37.037	0.00	0.00	0.00	3.86
3822	6295	1.251251	CCAGCCTCCAACCTTGAAAG	58.749	55.000	0.00	0.00	0.00	2.62
3848	6321	4.585955	AGGTGAGCATATTACCGTACTG	57.414	45.455	0.00	0.00	39.46	2.74
4337	6891	2.927871	GCAAATCACACCAGCATTCCAC	60.928	50.000	0.00	0.00	0.00	4.02
4350	6904	5.633830	TTTCAGGAAGATCAGCAAATCAC	57.366	39.130	0.00	0.00	0.00	3.06
4430	6988	3.001939	CCGTGGACAGAAGTTTGTTACAC	59.998	47.826	0.00	11.95	36.62	2.90
4487	7052	1.376609	GGCACTGCCGGTATTTGAGG	61.377	60.000	3.73	0.00	39.62	3.86
4582	7148	5.003804	TGCAGTTCTAATTTCTGGACCTTC	58.996	41.667	0.00	0.00	0.00	3.46
4595	7162	8.792830	ATATTTTACTCTTGCTGCAGTTCTAA	57.207	30.769	16.64	5.24	0.00	2.10
4638	7208	6.403866	TGCAATGTATTCTTTGTGTCCTTT	57.596	33.333	0.00	0.00	33.21	3.11
4716	7292	1.815003	GTTGGGGAGCAAAGAGACATG	59.185	52.381	0.00	0.00	0.00	3.21
4732	7308	0.108396	CTTTTGGCCTTTGGGGTTGG	59.892	55.000	3.32	0.00	37.43	3.77
4733	7309	0.534877	GCTTTTGGCCTTTGGGGTTG	60.535	55.000	3.32	0.00	37.43	3.77
4734	7310	0.985490	TGCTTTTGGCCTTTGGGGTT	60.985	50.000	3.32	0.00	40.92	4.11
4735	7311	1.383803	TGCTTTTGGCCTTTGGGGT	60.384	52.632	3.32	0.00	40.92	4.95
4736	7312	1.120795	TCTGCTTTTGGCCTTTGGGG	61.121	55.000	3.32	0.00	40.92	4.96
4737	7313	0.033920	GTCTGCTTTTGGCCTTTGGG	59.966	55.000	3.32	0.00	40.92	4.12
4809	7385	4.299586	TCATGACAGCAATTTGGGACTA	57.700	40.909	0.00	0.00	0.00	2.59
4865	7442	2.235016	TGTAAATGGTGCCAAGGTGAC	58.765	47.619	0.00	0.00	0.00	3.67
4933	7512	4.160252	CCCCAATGTTTCCATCCAAGTTAG	59.840	45.833	0.00	0.00	0.00	2.34
4951	7531	0.905809	AAAGATGCATGCAGCCCCAA	60.906	50.000	30.96	2.80	44.83	4.12
4952	7532	1.305465	AAAGATGCATGCAGCCCCA	60.305	52.632	30.96	3.64	44.83	4.96
4953	7533	1.041447	AGAAAGATGCATGCAGCCCC	61.041	55.000	30.96	19.78	44.83	5.80
4954	7534	0.102481	CAGAAAGATGCATGCAGCCC	59.898	55.000	30.96	20.12	44.83	5.19
4955	7535	1.100510	TCAGAAAGATGCATGCAGCC	58.899	50.000	30.96	21.44	44.83	4.85
4956	7536	2.732366	CATCAGAAAGATGCATGCAGC	58.268	47.619	27.98	27.98	46.90	5.25
4965	7545	1.474677	CGGCCTCTGCATCAGAAAGAT	60.475	52.381	0.00	0.00	40.18	2.40
4966	7546	0.107993	CGGCCTCTGCATCAGAAAGA	60.108	55.000	0.00	0.00	40.18	2.52
4967	7547	0.107993	TCGGCCTCTGCATCAGAAAG	60.108	55.000	0.00	0.00	40.18	2.62
4968	7548	0.107993	CTCGGCCTCTGCATCAGAAA	60.108	55.000	0.00	0.00	40.18	2.52
4969	7549	1.519246	CTCGGCCTCTGCATCAGAA	59.481	57.895	0.00	0.00	40.18	3.02
4970	7550	2.429767	CCTCGGCCTCTGCATCAGA	61.430	63.158	0.00	0.00	38.25	3.27
4971	7551	2.108566	CCTCGGCCTCTGCATCAG	59.891	66.667	0.00	0.00	40.13	2.90
4972	7552	2.871795	TACCCTCGGCCTCTGCATCA	62.872	60.000	0.00	0.00	40.13	3.07
4973	7553	1.686325	TTACCCTCGGCCTCTGCATC	61.686	60.000	0.00	0.00	40.13	3.91
4974	7554	1.056700	ATTACCCTCGGCCTCTGCAT	61.057	55.000	0.00	0.00	40.13	3.96
4975	7555	1.686325	GATTACCCTCGGCCTCTGCA	61.686	60.000	0.00	0.00	40.13	4.41
4976	7556	1.069935	GATTACCCTCGGCCTCTGC	59.930	63.158	0.00	0.00	0.00	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.