AutoCloner

Multiple sequence alignment - TraesCS6D01G132600

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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	TraesCS6D01G132600	chr6D	100.000	3904	0	0	1	3904	99796554	99792651	0.000000e+00	7210.0
1	TraesCS6D01G132600	chr6D	88.079	1015	62	13	857	1866	100356066	100355106	0.000000e+00	1149.0
2	TraesCS6D01G132600	chr6D	88.776	490	27	7	1863	2326	100352536	100352049	3.380000e-160	575.0
3	TraesCS6D01G132600	chr6D	86.966	468	37	10	2548	2993	100350318	100349853	4.500000e-139	505.0
4	TraesCS6D01G132600	chr6D	88.235	68	4	4	2216	2280	100352107	100352041	1.160000e-10	78.7
5	TraesCS6D01G132600	chr6D	97.222	36	0	1	3190	3224	100873853	100873818	4.210000e-05	60.2
6	TraesCS6D01G132600	chr6B	93.317	1212	51	6	396	1586	184151169	184149967	0.000000e+00	1762.0
7	TraesCS6D01G132600	chr6B	92.818	905	40	6	1652	2531	184149968	184149064	0.000000e+00	1288.0
8	TraesCS6D01G132600	chr6B	96.758	401	12	1	1	401	184151596	184151197	0.000000e+00	667.0
9	TraesCS6D01G132600	chr6B	86.473	621	27	6	2543	3143	184148997	184148414	2.560000e-176	628.0
10	TraesCS6D01G132600	chr6B	92.237	219	16	1	3223	3441	184148416	184148199	3.790000e-80	309.0
11	TraesCS6D01G132600	chr6B	88.258	264	15	2	3642	3904	184148094	184147846	6.340000e-78	302.0
12	TraesCS6D01G132600	chr6B	88.333	60	6	1	2216	2274	184149327	184149268	1.950000e-08	71.3
13	TraesCS6D01G132600	chr6A	92.915	988	55	8	857	1841	119758675	119757700	0.000000e+00	1423.0
14	TraesCS6D01G132600	chr6A	94.484	562	28	2	2582	3140	119754522	119753961	0.000000e+00	863.0
15	TraesCS6D01G132600	chr6A	95.050	404	13	2	3508	3904	119753611	119753208	2.560000e-176	628.0
16	TraesCS6D01G132600	chr6A	93.932	412	22	3	1811	2220	119757507	119757097	1.540000e-173	619.0
17	TraesCS6D01G132600	chr6A	94.953	317	14	2	2216	2531	119754957	119754642	2.710000e-136	496.0
18	TraesCS6D01G132600	chr6A	90.741	324	9	3	3183	3505	119753959	119753656	2.810000e-111	412.0
19	TraesCS6D01G132600	chr6A	77.893	484	72	22	401	856	70226406	70225930	6.430000e-68	268.0
20	TraesCS6D01G132600	chr6A	88.636	88	9	1	3145	3231	66089058	66089145	5.330000e-19	106.0
21	TraesCS6D01G132600	chr6A	98.113	53	1	0	2216	2268	119757079	119757027	4.150000e-15	93.5
22	TraesCS6D01G132600	chr6A	86.585	82	9	2	3145	3224	58312407	58312326	5.370000e-14	89.8
23	TraesCS6D01G132600	chr6A	88.333	60	6	1	2216	2274	119754904	119754845	1.950000e-08	71.3
24	TraesCS6D01G132600	chr6A	100.000	37	0	0	3504	3540	20250109	20250073	7.000000e-08	69.4
25	TraesCS6D01G132600	chr6A	92.857	42	3	0	3504	3545	213755909	213755950	1.170000e-05	62.1
26	TraesCS6D01G132600	chr5B	79.783	460	84	7	401	855	702366353	702366808	3.760000e-85	326.0
27	TraesCS6D01G132600	chr5B	95.238	42	2	0	3504	3545	330755906	330755865	2.520000e-07	67.6
28	TraesCS6D01G132600	chr5B	100.000	34	0	0	3504	3537	602247108	602247141	3.260000e-06	63.9
29	TraesCS6D01G132600	chr7B	84.429	289	36	5	396	679	205632187	205631903	3.840000e-70	276.0
30	TraesCS6D01G132600	chr7B	97.436	39	1	0	3504	3542	126550008	126550046	2.520000e-07	67.6
31	TraesCS6D01G132600	chr4D	81.682	333	42	8	401	719	8829067	8829394	3.870000e-65	259.0
32	TraesCS6D01G132600	chr2D	84.848	264	32	5	423	681	506519415	506519155	3.870000e-65	259.0
33	TraesCS6D01G132600	chr3B	77.381	420	65	19	401	796	527663038	527662625	5.080000e-54	222.0
34	TraesCS6D01G132600	chr3B	95.349	43	2	0	3141	3183	76432157	76432115	7.000000e-08	69.4
35	TraesCS6D01G132600	chr4B	80.769	286	39	10	401	674	16805967	16806248	3.950000e-50	209.0
36	TraesCS6D01G132600	chr1D	78.930	299	44	9	401	683	1815041	1815336	6.660000e-43	185.0
37	TraesCS6D01G132600	chr1D	86.207	87	9	3	596	681	467236783	467236867	1.490000e-14	91.6
38	TraesCS6D01G132600	chr1D	84.091	88	7	5	565	650	204795651	204795569	1.160000e-10	78.7
39	TraesCS6D01G132600	chr1D	93.333	45	3	0	3504	3548	275947656	275947612	2.520000e-07	67.6
40	TraesCS6D01G132600	chr4A	78.603	229	33	7	464	678	741531727	741531953	1.890000e-28	137.0
41	TraesCS6D01G132600	chr5D	83.942	137	18	3	548	681	242616570	242616705	1.140000e-25	128.0
42	TraesCS6D01G132600	chr7D	84.375	128	16	4	548	675	454095052	454094929	5.300000e-24	122.0
43	TraesCS6D01G132600	chr5A	88.506	87	6	3	3141	3224	101414562	101414477	6.900000e-18	102.0
44	TraesCS6D01G132600	chr3D	90.000	80	7	1	3146	3224	383596970	383596891	6.900000e-18	102.0
45	TraesCS6D01G132600	chr3D	88.889	54	4	2	3505	3557	15951524	15951576	9.050000e-07	65.8
46	TraesCS6D01G132600	chr2A	90.000	80	7	1	3146	3224	679913083	679913004	6.900000e-18	102.0
47	TraesCS6D01G132600	chr2B	97.500	40	0	1	3504	3542	790112975	790112936	2.520000e-07	67.6

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	TraesCS6D01G132600	chr6D	99792651	99796554	3903	True	7210.000000	7210	100.000000	1	3904	1	chr6D.!!$R1	3903
1	TraesCS6D01G132600	chr6D	100349853	100356066	6213	True	576.925000	1149	88.014000	857	2993	4	chr6D.!!$R3	2136
2	TraesCS6D01G132600	chr6B	184147846	184151596	3750	True	718.185714	1762	91.170571	1	3904	7	chr6B.!!$R1	3903
3	TraesCS6D01G132600	chr6A	119753208	119758675	5467	True	575.725000	1423	93.565125	857	3904	8	chr6A.!!$R4	3047

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
459	492	0.037303	ACTTGAGCATGGTGTCCCTG	59.963	55.0	0.00	0.00	4.45	F
732	765	0.179062	GACCGCTGGCATGATCTCTT	60.179	55.0	0.00	0.00	2.85	F
984	1036	0.179134	ACATCGCGGCTACTCTGAAC	60.179	55.0	6.13	0.00	3.18	F
1387	1445	0.249573	TCTGTTCGGTGGAAACGGTC	60.250	55.0	0.00	33.05	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1320	1378	0.964358	CGGGAGTTCACCTCGGTAGT	60.964	60.000	0.00	41.46	2.73	R
2537	9085	1.136828	AGCAAGGGTACAAGTCACCA	58.863	50.000	0.00	37.84	4.17	R
2820	9441	0.674895	ATCTGCACGAACAGGAAGCC	60.675	55.000	9.07	38.26	4.35	R
3141	9775	1.222298	ACATTATAGGACGGAGGGGGT	59.778	52.381	0.00	0.00	4.95	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
123	124	5.233083	TGATGCCCATCTAACCATAAGAG	57.767	43.478	9.44	0.00	38.60	2.85
130	131	4.503991	CCATCTAACCATAAGAGCCAGGAC	60.504	50.000	0.00	0.00	0.00	3.85
186	187	1.257750	TGCAGTGTATCAGCCCGACT	61.258	55.000	0.00	0.00	0.00	4.18
201	202	2.555325	CCCGACTAAAAAGGGGTGTTTC	59.445	50.000	0.00	0.00	41.43	2.78
221	222	1.016627	CGATACACCTGGCAACCATG	58.983	55.000	0.00	0.00	30.82	3.66
222	223	1.392589	GATACACCTGGCAACCATGG	58.607	55.000	11.19	11.19	30.82	3.66
229	230	1.039068	CTGGCAACCATGGTGAAACA	58.961	50.000	20.60	14.16	32.30	2.83
239	240	5.436175	ACCATGGTGAAACAATCGATATGA	58.564	37.500	18.99	0.00	39.98	2.15
263	264	2.319410	CTAGAGGGAGGAGGTGGGGG	62.319	70.000	0.00	0.00	0.00	5.40
272	273	1.532238	GAGGTGGGGGTGAATAGGC	59.468	63.158	0.00	0.00	0.00	3.93
314	315	7.431376	GCTCTTTTAATCAAATTACGGTTAGCC	59.569	37.037	0.00	0.00	0.00	3.93
458	491	0.326264	GACTTGAGCATGGTGTCCCT	59.674	55.000	0.00	0.00	0.00	4.20
459	492	0.037303	ACTTGAGCATGGTGTCCCTG	59.963	55.000	0.00	0.00	0.00	4.45
528	561	5.766670	GCTTGGTGATTGATCTATGATGGAA	59.233	40.000	0.00	0.00	0.00	3.53
650	683	2.027073	TGCGTCGGCATGAACTGTC	61.027	57.895	0.00	0.00	46.21	3.51
655	688	2.263077	GTCGGCATGAACTGTCTAGTG	58.737	52.381	0.00	0.00	37.19	2.74
732	765	0.179062	GACCGCTGGCATGATCTCTT	60.179	55.000	0.00	0.00	0.00	2.85
734	767	0.463295	CCGCTGGCATGATCTCTTGT	60.463	55.000	0.00	0.00	0.00	3.16
775	808	7.316544	AGTTCAAATTATTTTCTACGCGGAT	57.683	32.000	12.47	0.00	0.00	4.18
776	809	7.186804	AGTTCAAATTATTTTCTACGCGGATG	58.813	34.615	12.47	0.00	0.00	3.51
800	833	2.561549	TTAGGTCGGCCGGTTAAGCG	62.562	60.000	27.83	19.73	40.50	4.68
804	837	3.505184	CGGCCGGTTAAGCGCATT	61.505	61.111	20.10	3.50	0.00	3.56
818	851	1.290009	GCATTGGTTGGACACAGGC	59.710	57.895	0.00	0.00	0.00	4.85
823	856	0.321210	TGGTTGGACACAGGCGTATG	60.321	55.000	0.00	0.00	0.00	2.39
826	859	0.682292	TTGGACACAGGCGTATGACA	59.318	50.000	0.00	0.00	0.00	3.58
916	965	0.393808	TTTATTCGGCTCACCAGGGC	60.394	55.000	0.00	0.00	34.57	5.19
952	1004	1.484444	AAGAGACCAGTCCACCAGCC	61.484	60.000	0.00	0.00	0.00	4.85
953	1005	2.930562	AGACCAGTCCACCAGCCC	60.931	66.667	0.00	0.00	0.00	5.19
954	1006	3.249189	GACCAGTCCACCAGCCCA	61.249	66.667	0.00	0.00	0.00	5.36
955	1007	3.553095	GACCAGTCCACCAGCCCAC	62.553	68.421	0.00	0.00	0.00	4.61
956	1008	4.351054	CCAGTCCACCAGCCCACC	62.351	72.222	0.00	0.00	0.00	4.61
957	1009	3.569210	CAGTCCACCAGCCCACCA	61.569	66.667	0.00	0.00	0.00	4.17
958	1010	3.252284	AGTCCACCAGCCCACCAG	61.252	66.667	0.00	0.00	0.00	4.00
984	1036	0.179134	ACATCGCGGCTACTCTGAAC	60.179	55.000	6.13	0.00	0.00	3.18
1134	1187	1.135053	GTCTCCGACTACTTCAAGCCC	60.135	57.143	0.00	0.00	0.00	5.19
1185	1239	0.448593	CTCTCTCCGTTCGTCTGTCC	59.551	60.000	0.00	0.00	0.00	4.02
1333	1391	1.100510	CCGATGACTACCGAGGTGAA	58.899	55.000	4.80	0.00	0.00	3.18
1387	1445	0.249573	TCTGTTCGGTGGAAACGGTC	60.250	55.000	0.00	0.00	33.05	4.79
1410	1468	6.961554	GTCACGATACTTAAATTTGGAAGCTG	59.038	38.462	0.00	0.00	0.00	4.24
1465	1523	3.247006	TCTCTCTGTTGGAATTACGCC	57.753	47.619	0.00	0.00	0.00	5.68
1479	1537	1.870055	TACGCCGTCCTTCTGTCCAC	61.870	60.000	0.00	0.00	0.00	4.02
1491	1549	7.500992	GTCCTTCTGTCCACATATGAGAAATA	58.499	38.462	10.38	0.00	0.00	1.40
1606	1664	9.612066	GTACCAGAGTGTAGTTACTTAGATAGT	57.388	37.037	0.00	0.00	41.04	2.12
1699	1757	2.971330	ACCACAGAAATGGCCATTGAAA	59.029	40.909	31.28	0.00	44.33	2.69
1718	1776	6.951062	TGAAATGTGACATGGTCTTTTACA	57.049	33.333	0.00	0.00	33.15	2.41
1791	1849	5.123979	CCTTACTCCTGGCAGAATGTAAAAC	59.876	44.000	17.94	0.00	39.31	2.43
1823	1881	7.660208	AGGGATACTAGGTTTGCAAATATAACG	59.340	37.037	16.21	5.06	0.00	3.18
1849	2130	7.646548	TGTATATCTGGACTATAGTGATGGC	57.353	40.000	10.90	0.00	0.00	4.40
1856	2137	6.379417	TCTGGACTATAGTGATGGCATGATAG	59.621	42.308	10.90	8.93	32.25	2.08
1866	4720	2.934887	TGGCATGATAGGATGTTGGTG	58.065	47.619	0.00	0.00	0.00	4.17
1890	4744	5.230942	ACACTCTACTCTTCCATGTTTTCG	58.769	41.667	0.00	0.00	0.00	3.46
1894	4748	6.154706	ACTCTACTCTTCCATGTTTTCGGTAT	59.845	38.462	0.00	0.00	0.00	2.73
1936	4792	5.250235	TCTTCCTGTATGTTGATCGAGTC	57.750	43.478	0.00	0.00	0.00	3.36
2213	5071	4.948341	TGAGTTGTTAAGCCTCTGTACA	57.052	40.909	0.00	0.00	0.00	2.90
2287	7289	7.447374	AAATATTTGGTTGATGACTGTCGAA	57.553	32.000	0.00	0.00	0.00	3.71
2511	9059	4.607584	AGCTTCCATCCCCCATATATTTGA	59.392	41.667	0.00	0.00	0.00	2.69
2531	9079	6.709018	TTGATAGACGACTATTGACCATGA	57.291	37.500	8.78	0.00	39.16	3.07
2532	9080	6.073327	TGATAGACGACTATTGACCATGAC	57.927	41.667	8.78	0.00	39.16	3.06
2533	9081	5.828328	TGATAGACGACTATTGACCATGACT	59.172	40.000	8.78	0.00	39.16	3.41
2536	9084	4.220821	AGACGACTATTGACCATGACTGTT	59.779	41.667	0.00	0.00	0.00	3.16
2537	9085	4.894784	ACGACTATTGACCATGACTGTTT	58.105	39.130	0.00	0.00	0.00	2.83
2541	9089	4.761739	ACTATTGACCATGACTGTTTGGTG	59.238	41.667	17.73	8.20	46.14	4.17
2571	9174	3.553508	CCCTTGCTTGGTGAGTTTGATTG	60.554	47.826	0.00	0.00	0.00	2.67
2598	9215	9.739276	TGTTAGTAATTCCACATTCTCTTCATT	57.261	29.630	0.00	0.00	0.00	2.57
2619	9236	2.497138	TCTGTTCAATGGACACTGCTG	58.503	47.619	0.00	0.00	0.00	4.41
2644	9261	7.377397	TGTGCAAACTAAACATTATTGTTCGTC	59.623	33.333	3.60	0.00	45.30	4.20
2687	9304	2.565834	GTTCCTGGACCTACTTGTGCTA	59.434	50.000	0.00	0.00	0.00	3.49
2711	9328	5.804639	AGCTTACAGTTGACCAACATGATA	58.195	37.500	14.42	0.07	43.47	2.15
2759	9376	3.754323	TCATTTTGTTAGCCGGTTAGGTG	59.246	43.478	1.90	0.00	43.70	4.00
2820	9441	8.438676	AATTTTATCAGATTGTCCTAACTCGG	57.561	34.615	0.00	0.00	0.00	4.63
3075	9706	1.765904	TCAGTCTGTGTTGCCAACCTA	59.234	47.619	4.90	0.00	0.00	3.08
3140	9774	5.821470	CAGTTCATTTGTCAGCCTATCAGAT	59.179	40.000	0.00	0.00	0.00	2.90
3141	9775	6.988580	CAGTTCATTTGTCAGCCTATCAGATA	59.011	38.462	0.00	0.00	0.00	1.98
3142	9776	6.989169	AGTTCATTTGTCAGCCTATCAGATAC	59.011	38.462	0.00	0.00	0.00	2.24
3143	9777	5.858381	TCATTTGTCAGCCTATCAGATACC	58.142	41.667	0.00	0.00	0.00	2.73
3144	9778	4.689612	TTTGTCAGCCTATCAGATACCC	57.310	45.455	0.00	0.00	0.00	3.69
3145	9779	2.609747	TGTCAGCCTATCAGATACCCC	58.390	52.381	0.00	0.00	0.00	4.95
3146	9780	1.903183	GTCAGCCTATCAGATACCCCC	59.097	57.143	0.00	0.00	0.00	5.40
3147	9781	1.795786	TCAGCCTATCAGATACCCCCT	59.204	52.381	0.00	0.00	0.00	4.79
3148	9782	2.183679	CAGCCTATCAGATACCCCCTC	58.816	57.143	0.00	0.00	0.00	4.30
3149	9783	1.079658	AGCCTATCAGATACCCCCTCC	59.920	57.143	0.00	0.00	0.00	4.30
3150	9784	1.853963	CCTATCAGATACCCCCTCCG	58.146	60.000	0.00	0.00	0.00	4.63
3151	9785	1.077334	CCTATCAGATACCCCCTCCGT	59.923	57.143	0.00	0.00	0.00	4.69
3152	9786	2.448453	CTATCAGATACCCCCTCCGTC	58.552	57.143	0.00	0.00	0.00	4.79
3153	9787	0.178929	ATCAGATACCCCCTCCGTCC	60.179	60.000	0.00	0.00	0.00	4.79
3154	9788	1.233369	CAGATACCCCCTCCGTCCT	59.767	63.158	0.00	0.00	0.00	3.85
3155	9789	0.481567	CAGATACCCCCTCCGTCCTA	59.518	60.000	0.00	0.00	0.00	2.94
3156	9790	1.077334	CAGATACCCCCTCCGTCCTAT	59.923	57.143	0.00	0.00	0.00	2.57
3157	9791	2.310945	CAGATACCCCCTCCGTCCTATA	59.689	54.545	0.00	0.00	0.00	1.31
3158	9792	2.998910	AGATACCCCCTCCGTCCTATAA	59.001	50.000	0.00	0.00	0.00	0.98
3159	9793	3.601537	AGATACCCCCTCCGTCCTATAAT	59.398	47.826	0.00	0.00	0.00	1.28
3160	9794	2.025636	ACCCCCTCCGTCCTATAATG	57.974	55.000	0.00	0.00	0.00	1.90
3161	9795	1.222298	ACCCCCTCCGTCCTATAATGT	59.778	52.381	0.00	0.00	0.00	2.71
3162	9796	2.452047	ACCCCCTCCGTCCTATAATGTA	59.548	50.000	0.00	0.00	0.00	2.29
3163	9797	3.116629	ACCCCCTCCGTCCTATAATGTAA	60.117	47.826	0.00	0.00	0.00	2.41
3164	9798	3.514309	CCCCCTCCGTCCTATAATGTAAG	59.486	52.174	0.00	0.00	0.00	2.34
3165	9799	4.413760	CCCCTCCGTCCTATAATGTAAGA	58.586	47.826	0.00	0.00	0.00	2.10
3166	9800	5.024118	CCCCTCCGTCCTATAATGTAAGAT	58.976	45.833	0.00	0.00	0.00	2.40
3167	9801	5.127356	CCCCTCCGTCCTATAATGTAAGATC	59.873	48.000	0.00	0.00	0.00	2.75
3168	9802	5.952947	CCCTCCGTCCTATAATGTAAGATCT	59.047	44.000	0.00	0.00	0.00	2.75
3169	9803	6.437793	CCCTCCGTCCTATAATGTAAGATCTT	59.562	42.308	13.56	13.56	0.00	2.40
3170	9804	7.038941	CCCTCCGTCCTATAATGTAAGATCTTT	60.039	40.741	14.36	0.00	0.00	2.52
3171	9805	8.368668	CCTCCGTCCTATAATGTAAGATCTTTT	58.631	37.037	14.36	4.67	0.00	2.27
3172	9806	9.765795	CTCCGTCCTATAATGTAAGATCTTTTT	57.234	33.333	14.36	8.07	0.00	1.94
3351	9986	7.650890	TCATAATTATAAGTGCCAATGTGCTG	58.349	34.615	0.00	0.00	0.00	4.41
3372	10007	0.036388	CGCTGCTCCCAACCTAAGAA	60.036	55.000	0.00	0.00	0.00	2.52
3446	10081	9.911788	ATCATTTCTAACACCAAGATAGATTGT	57.088	29.630	0.00	0.00	32.45	2.71
3487	10122	6.255453	TGCAAGACTTAAACATGACTTTTTGC	59.745	34.615	0.00	4.22	37.23	3.68
3505	10140	6.732896	TTTTGCCATTTTTCCAAGGTACTA	57.267	33.333	0.00	0.00	38.49	1.82
3506	10141	6.732896	TTTGCCATTTTTCCAAGGTACTAA	57.267	33.333	0.00	0.00	38.49	2.24
3510	10187	5.158494	CCATTTTTCCAAGGTACTAAACGC	58.842	41.667	0.00	0.00	38.49	4.84
3604	10291	1.083489	GCACAAGCGTGGTAGCATAA	58.917	50.000	4.26	0.00	43.81	1.90
3616	10303	6.625362	CGTGGTAGCATAATACATGAGAGAT	58.375	40.000	0.00	0.00	0.00	2.75
3628	10315	3.843027	ACATGAGAGATGTCCTGGAAACT	59.157	43.478	0.00	0.00	0.00	2.66
3787	10475	5.793817	TCTTCCAGAACTCGATGAAAATCA	58.206	37.500	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
123	124	1.084370	GCACATACGAGTGTCCTGGC	61.084	60.000	0.00	0.00	41.52	4.85
130	131	4.152223	TGAGAATTGTTGCACATACGAGTG	59.848	41.667	0.00	0.00	42.37	3.51
186	187	4.761227	GTGTATCGGAAACACCCCTTTTTA	59.239	41.667	4.99	0.00	41.10	1.52
201	202	0.107214	ATGGTTGCCAGGTGTATCGG	60.107	55.000	0.00	0.00	36.75	4.18
229	230	6.379703	CCTCCCTCTAGTCAATCATATCGATT	59.620	42.308	1.71	0.00	45.60	3.34
239	240	2.359781	CCACCTCCTCCCTCTAGTCAAT	60.360	54.545	0.00	0.00	0.00	2.57
263	264	7.428472	GCTAAAAATTCGTAGTTGCCTATTCAC	59.572	37.037	0.00	0.00	0.00	3.18
306	307	3.112580	CAACTTGTTTTGTGGCTAACCG	58.887	45.455	0.00	0.00	39.70	4.44
314	315	7.023575	GGCATATCTAGACAACTTGTTTTGTG	58.976	38.462	0.00	0.00	39.88	3.33
458	491	0.034896	GAACCAAGGCCTCTTCGTCA	59.965	55.000	5.23	0.00	0.00	4.35
459	492	1.014564	CGAACCAAGGCCTCTTCGTC	61.015	60.000	22.90	11.04	32.65	4.20
544	577	0.106769	TTGTGGTCATGCCGGCATAT	60.107	50.000	39.94	20.26	41.21	1.78
679	712	1.429148	GAGTTTATGCTGGCGACGGG	61.429	60.000	0.00	0.00	37.13	5.28
681	714	0.647410	CAGAGTTTATGCTGGCGACG	59.353	55.000	0.00	0.00	0.00	5.12
701	734	1.750399	AGCGGTCATTGCCATCACC	60.750	57.895	0.00	0.00	0.00	4.02
703	736	1.750018	CCAGCGGTCATTGCCATCA	60.750	57.895	0.00	0.00	0.00	3.07
732	765	4.411256	ACTTAGAAAAAGGTCCGTGACA	57.589	40.909	6.41	0.00	33.68	3.58
734	767	5.026038	TGAACTTAGAAAAAGGTCCGTGA	57.974	39.130	0.63	0.00	33.14	4.35
771	804	1.605712	GGCCGACCTAATTCTCATCCG	60.606	57.143	0.00	0.00	0.00	4.18
775	808	0.974010	ACCGGCCGACCTAATTCTCA	60.974	55.000	30.73	0.00	0.00	3.27
776	809	0.177373	AACCGGCCGACCTAATTCTC	59.823	55.000	30.73	0.00	0.00	2.87
800	833	1.290009	GCCTGTGTCCAACCAATGC	59.710	57.895	0.00	0.00	0.00	3.56
804	837	0.321210	CATACGCCTGTGTCCAACCA	60.321	55.000	0.00	0.00	0.00	3.67
818	851	2.173669	CCTGGGCGCTTGTCATACG	61.174	63.158	7.64	0.00	0.00	3.06
831	864	0.107848	ATCCGTTTAAGTCGCCTGGG	60.108	55.000	0.00	0.00	0.00	4.45
832	865	2.589798	TATCCGTTTAAGTCGCCTGG	57.410	50.000	0.00	0.00	0.00	4.45
841	874	4.281182	TGCAAGCCCTTTTTATCCGTTTAA	59.719	37.500	0.00	0.00	0.00	1.52
886	931	0.539669	CCGAATAAAGATGGGCCCCC	60.540	60.000	22.27	11.72	0.00	5.40
1185	1239	3.065371	GTCAACCAAACAGACAGAAGGTG	59.935	47.826	0.00	0.00	32.68	4.00
1320	1378	0.964358	CGGGAGTTCACCTCGGTAGT	60.964	60.000	0.00	0.00	41.46	2.73
1333	1391	1.758514	ACCATCAGATCGCGGGAGT	60.759	57.895	6.13	0.00	0.00	3.85
1387	1445	6.742718	CACAGCTTCCAAATTTAAGTATCGTG	59.257	38.462	0.00	0.00	0.00	4.35
1410	1468	3.245990	GCAGTTTTTCAAATCTGTGCCAC	59.754	43.478	10.60	0.00	37.79	5.01
1465	1523	3.381590	TCTCATATGTGGACAGAAGGACG	59.618	47.826	1.90	0.00	0.00	4.79
1479	1537	4.564372	AGTAGCGCGCATATTTCTCATATG	59.436	41.667	35.10	0.00	35.63	1.78
1582	1640	7.495279	CGACTATCTAAGTAACTACACTCTGGT	59.505	40.741	0.00	0.00	39.07	4.00
1606	1664	6.370442	CACTACCCTGTTGAAATGAATTACGA	59.630	38.462	0.00	0.00	0.00	3.43
1737	1795	1.339610	TCTTTGTTTCCATGCCGGTTG	59.660	47.619	1.90	0.75	35.57	3.77
1742	1800	6.501781	CATCTAAGATCTTTGTTTCCATGCC	58.498	40.000	14.36	0.00	0.00	4.40
1756	1814	5.146010	CCAGGAGTAAGGCATCTAAGATC	57.854	47.826	0.00	0.00	0.00	2.75
1791	1849	4.649674	TGCAAACCTAGTATCCCTAGACAG	59.350	45.833	0.00	0.00	45.21	3.51
1823	1881	8.356657	GCCATCACTATAGTCCAGATATACATC	58.643	40.741	1.26	0.00	0.00	3.06
1849	2130	4.774124	AGTGTCACCAACATCCTATCATG	58.226	43.478	0.00	0.00	40.80	3.07
1856	2137	3.511934	AGAGTAGAGTGTCACCAACATCC	59.488	47.826	0.00	0.00	40.80	3.51
1866	4720	5.346281	CGAAAACATGGAAGAGTAGAGTGTC	59.654	44.000	0.00	0.00	0.00	3.67
1890	4744	3.877508	GGTGCCAAACTCAGACATATACC	59.122	47.826	0.00	0.00	0.00	2.73
1894	4748	3.264193	AGATGGTGCCAAACTCAGACATA	59.736	43.478	0.00	0.00	0.00	2.29
1936	4792	3.181454	ACAGGTAAGTTTCAGACCACCAG	60.181	47.826	0.00	0.00	36.68	4.00
2213	5071	4.134563	GGTCAACAGTCATGTACCAAACT	58.865	43.478	0.00	0.00	39.29	2.66
2287	7289	6.869206	ATGTACCTTACCTGACTAACATGT	57.131	37.500	0.00	0.00	0.00	3.21
2327	7330	9.547279	TCTATGGGAATAGCTCATATTGACTTA	57.453	33.333	0.00	0.00	39.19	2.24
2446	7449	4.396166	ACAGCTCGTCATCTTAAAAATGGG	59.604	41.667	0.00	0.00	0.00	4.00
2455	7458	3.533606	AGCATAACAGCTCGTCATCTT	57.466	42.857	0.00	0.00	42.18	2.40
2458	7461	3.193263	CAGAAGCATAACAGCTCGTCAT	58.807	45.455	0.00	0.00	45.89	3.06
2459	7462	2.029020	ACAGAAGCATAACAGCTCGTCA	60.029	45.455	0.00	0.00	45.89	4.35
2511	9059	5.594725	ACAGTCATGGTCAATAGTCGTCTAT	59.405	40.000	0.00	0.00	38.38	1.98
2531	9079	2.508300	AGGGTACAAGTCACCAAACAGT	59.492	45.455	0.00	0.00	37.84	3.55
2532	9080	3.208747	AGGGTACAAGTCACCAAACAG	57.791	47.619	0.00	0.00	37.84	3.16
2533	9081	3.283751	CAAGGGTACAAGTCACCAAACA	58.716	45.455	0.00	0.00	37.84	2.83
2536	9084	1.493022	AGCAAGGGTACAAGTCACCAA	59.507	47.619	0.00	0.00	37.84	3.67
2537	9085	1.136828	AGCAAGGGTACAAGTCACCA	58.863	50.000	0.00	0.00	37.84	4.17
2540	9088	1.493022	ACCAAGCAAGGGTACAAGTCA	59.507	47.619	0.00	0.00	36.72	3.41
2541	9089	1.880027	CACCAAGCAAGGGTACAAGTC	59.120	52.381	0.00	0.00	36.72	3.01
2571	9174	8.547967	TGAAGAGAATGTGGAATTACTAACAC	57.452	34.615	0.00	0.00	0.00	3.32
2598	9215	2.880268	CAGCAGTGTCCATTGAACAGAA	59.120	45.455	0.00	0.00	0.00	3.02
2599	9216	2.158769	ACAGCAGTGTCCATTGAACAGA	60.159	45.455	0.00	0.00	26.76	3.41
2644	9261	6.791887	ACAACACACTACAGAATCAATCAG	57.208	37.500	0.00	0.00	0.00	2.90
2687	9304	4.460263	TCATGTTGGTCAACTGTAAGCTT	58.540	39.130	13.96	3.48	41.67	3.74
2711	9328	6.653989	AGGAATATCGACCAAACAAAGAGAT	58.346	36.000	0.00	0.00	0.00	2.75
2759	9376	6.216801	TCAGTAGATACCACATGTTACCAC	57.783	41.667	0.00	0.00	0.00	4.16
2820	9441	0.674895	ATCTGCACGAACAGGAAGCC	60.675	55.000	9.07	0.00	38.26	4.35
3140	9774	2.452047	ACATTATAGGACGGAGGGGGTA	59.548	50.000	0.00	0.00	0.00	3.69
3141	9775	1.222298	ACATTATAGGACGGAGGGGGT	59.778	52.381	0.00	0.00	0.00	4.95
3142	9776	2.025636	ACATTATAGGACGGAGGGGG	57.974	55.000	0.00	0.00	0.00	5.40
3143	9777	4.413760	TCTTACATTATAGGACGGAGGGG	58.586	47.826	0.00	0.00	0.00	4.79
3144	9778	5.952947	AGATCTTACATTATAGGACGGAGGG	59.047	44.000	0.00	0.00	0.00	4.30
3145	9779	7.469537	AAGATCTTACATTATAGGACGGAGG	57.530	40.000	6.06	0.00	0.00	4.30
3146	9780	9.765795	AAAAAGATCTTACATTATAGGACGGAG	57.234	33.333	8.75	0.00	0.00	4.63
3198	9832	6.071984	ACTCCCTCGTCTCATAATGTAAGAT	58.928	40.000	0.00	0.00	0.00	2.40
3211	9845	2.509166	TCACATGTACTCCCTCGTCT	57.491	50.000	0.00	0.00	0.00	4.18
3351	9986	3.622060	TTAGGTTGGGAGCAGCGGC	62.622	63.158	0.00	0.00	41.61	6.53
3487	10122	5.048294	AGCGTTTAGTACCTTGGAAAAATGG	60.048	40.000	0.00	0.00	0.00	3.16
3506	10141	9.490379	CCCTCTGTAAATAAATATAAGAGCGTT	57.510	33.333	0.00	0.00	0.00	4.84
3528	10205	7.558604	AGTACGATCATATCTACTACTCCCTC	58.441	42.308	0.00	0.00	0.00	4.30
3574	10261	3.517602	CACGCTTGTGCTACCTAATACA	58.482	45.455	0.00	0.00	36.68	2.29
3604	10291	5.664908	AGTTTCCAGGACATCTCTCATGTAT	59.335	40.000	0.00	0.00	31.52	2.29
3616	10303	7.831691	TCATTTTTGAATAGTTTCCAGGACA	57.168	32.000	0.00	0.00	0.00	4.02
3677	10364	6.017440	TGTTTCAAGAAATAACCGGTTCTGAG	60.017	38.462	26.16	11.29	34.33	3.35
3787	10475	5.829391	ACGGTTTAGTGGTTTGTTATCCTTT	59.171	36.000	0.00	0.00	0.00	3.11
3860	10548	7.658261	TGTACTACATATTGAGCTGTACCATC	58.342	38.462	0.00	0.00	0.00	3.51
3861	10549	7.597288	TGTACTACATATTGAGCTGTACCAT	57.403	36.000	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.