AutoCloner

Multiple sequence alignment - TraesCS1A01G172500

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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	TraesCS1A01G172500	chr1A	100.000	3761	0	0	1	3761	308350312	308354072	0.000000e+00	6946.0
1	TraesCS1A01G172500	chr1A	94.435	2839	124	19	268	3084	292891705	292888879	0.000000e+00	4337.0
2	TraesCS1A01G172500	chr1A	93.602	422	26	1	3080	3501	292888066	292887646	2.470000e-176	628.0
3	TraesCS1A01G172500	chr1A	96.460	113	2	1	3651	3761	307054741	307054629	6.420000e-43	185.0
4	TraesCS1A01G172500	chr5A	96.364	3658	101	10	1	3647	10039378	10035742	0.000000e+00	5989.0
5	TraesCS1A01G172500	chr4A	96.844	3042	84	2	226	3255	216815639	216818680	0.000000e+00	5075.0
6	TraesCS1A01G172500	chr4A	91.185	363	11	7	3285	3647	216818679	216819020	1.220000e-129	473.0
7	TraesCS1A01G172500	chr4A	95.855	193	8	0	1	193	216811912	216812104	2.820000e-81	313.0
8	TraesCS1A01G172500	chr4A	97.436	39	0	1	181	218	216815610	216815648	8.720000e-07	65.8
9	TraesCS1A01G172500	chr7D	95.192	2475	88	9	1	2471	287706413	287703966	0.000000e+00	3882.0
10	TraesCS1A01G172500	chr7D	92.940	1119	63	5	2542	3647	287703969	287702854	0.000000e+00	1615.0
11	TraesCS1A01G172500	chr2B	94.157	1814	92	5	1378	3177	63518801	63520614	0.000000e+00	2750.0
12	TraesCS1A01G172500	chr3A	87.500	1320	109	26	2346	3643	91452149	91453434	0.000000e+00	1472.0
13	TraesCS1A01G172500	chr3A	86.894	1320	117	22	2346	3643	425588076	425589361	0.000000e+00	1428.0
14	TraesCS1A01G172500	chr6A	87.273	1320	111	22	2346	3643	571276294	571275010	0.000000e+00	1454.0
15	TraesCS1A01G172500	chr6A	90.968	310	25	2	1681	1989	321271220	321270913	7.520000e-112	414.0
16	TraesCS1A01G172500	chr6A	94.828	116	3	2	3644	3756	453122739	453122624	1.070000e-40	178.0
17	TraesCS1A01G172500	chr6B	95.305	852	33	6	731	1575	708049287	708050138	0.000000e+00	1345.0
18	TraesCS1A01G172500	chr6B	90.523	612	57	1	1681	2291	329470978	329470367	0.000000e+00	808.0
19	TraesCS1A01G172500	chr6B	86.451	679	75	9	2346	3010	329470343	329469668	0.000000e+00	728.0
20	TraesCS1A01G172500	chr6B	93.162	117	4	3	3643	3756	247023185	247023300	6.460000e-38	169.0
21	TraesCS1A01G172500	chr1D	95.300	851	34	5	731	1575	420674348	420673498	0.000000e+00	1345.0
22	TraesCS1A01G172500	chr1D	94.249	852	41	7	731	1575	78367242	78368092	0.000000e+00	1295.0
23	TraesCS1A01G172500	chr2D	94.830	851	38	5	731	1575	207541028	207541878	0.000000e+00	1323.0
24	TraesCS1A01G172500	chr2A	85.080	1307	159	17	2346	3635	285231428	285232715	0.000000e+00	1301.0
25	TraesCS1A01G172500	chr2A	91.467	375	31	1	1916	2290	285231030	285231403	7.200000e-142	514.0
26	TraesCS1A01G172500	chr2A	94.690	113	3	2	3647	3756	715995805	715995917	4.990000e-39	172.0
27	TraesCS1A01G172500	chr2A	93.913	115	4	2	3645	3756	260533547	260533661	1.800000e-38	171.0
28	TraesCS1A01G172500	chr7B	93.890	851	45	6	731	1575	164689096	164689945	0.000000e+00	1277.0
29	TraesCS1A01G172500	chr7B	95.614	114	2	2	3646	3756	644495574	644495461	2.980000e-41	180.0
30	TraesCS1A01G172500	chr1B	87.865	1063	90	12	2382	3426	601126593	601125552	0.000000e+00	1212.0
31	TraesCS1A01G172500	chr1B	93.366	618	33	1	1681	2290	601127441	601126824	0.000000e+00	907.0
32	TraesCS1A01G172500	chr1B	93.220	118	4	3	3642	3756	62025681	62025797	1.800000e-38	171.0
33	TraesCS1A01G172500	chr1B	85.393	89	9	3	3555	3643	601110397	601110313	5.170000e-14	89.8
34	TraesCS1A01G172500	chr7A	85.626	1127	110	20	2535	3643	501097020	501095928	0.000000e+00	1136.0
35	TraesCS1A01G172500	chr7A	93.966	116	4	2	3644	3756	552450753	552450638	4.990000e-39	172.0
36	TraesCS1A01G172500	chr7A	93.966	116	4	2	3644	3756	552451786	552451671	4.990000e-39	172.0
37	TraesCS1A01G172500	chr6D	91.909	309	25	0	1681	1989	232767056	232766748	2.070000e-117	433.0
38	TraesCS1A01G172500	chr6D	86.957	230	28	2	2698	2927	232766774	232766547	1.340000e-64	257.0
39	TraesCS1A01G172500	chr5D	92.035	113	6	3	1574	1683	483521136	483521248	5.030000e-34	156.0
40	TraesCS1A01G172500	chr4B	92.035	113	6	3	1574	1683	525412158	525412046	5.030000e-34	156.0
41	TraesCS1A01G172500	chr4B	91.071	112	7	3	1575	1683	525277690	525277579	8.420000e-32	148.0
42	TraesCS1A01G172500	chr4B	89.381	113	9	3	1574	1683	525295901	525296013	5.070000e-29	139.0

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	TraesCS1A01G172500	chr1A	308350312	308354072	3760	False	6946.0	6946	100.0000	1	3761	1	chr1A.!!$F1	3760
1	TraesCS1A01G172500	chr1A	292887646	292891705	4059	True	2482.5	4337	94.0185	268	3501	2	chr1A.!!$R2	3233
2	TraesCS1A01G172500	chr5A	10035742	10039378	3636	True	5989.0	5989	96.3640	1	3647	1	chr5A.!!$R1	3646
3	TraesCS1A01G172500	chr4A	216811912	216819020	7108	False	1481.7	5075	95.3300	1	3647	4	chr4A.!!$F1	3646
4	TraesCS1A01G172500	chr7D	287702854	287706413	3559	True	2748.5	3882	94.0660	1	3647	2	chr7D.!!$R1	3646
5	TraesCS1A01G172500	chr2B	63518801	63520614	1813	False	2750.0	2750	94.1570	1378	3177	1	chr2B.!!$F1	1799
6	TraesCS1A01G172500	chr3A	91452149	91453434	1285	False	1472.0	1472	87.5000	2346	3643	1	chr3A.!!$F1	1297
7	TraesCS1A01G172500	chr3A	425588076	425589361	1285	False	1428.0	1428	86.8940	2346	3643	1	chr3A.!!$F2	1297
8	TraesCS1A01G172500	chr6A	571275010	571276294	1284	True	1454.0	1454	87.2730	2346	3643	1	chr6A.!!$R3	1297
9	TraesCS1A01G172500	chr6B	708049287	708050138	851	False	1345.0	1345	95.3050	731	1575	1	chr6B.!!$F2	844
10	TraesCS1A01G172500	chr6B	329469668	329470978	1310	True	768.0	808	88.4870	1681	3010	2	chr6B.!!$R1	1329
11	TraesCS1A01G172500	chr1D	420673498	420674348	850	True	1345.0	1345	95.3000	731	1575	1	chr1D.!!$R1	844
12	TraesCS1A01G172500	chr1D	78367242	78368092	850	False	1295.0	1295	94.2490	731	1575	1	chr1D.!!$F1	844
13	TraesCS1A01G172500	chr2D	207541028	207541878	850	False	1323.0	1323	94.8300	731	1575	1	chr2D.!!$F1	844
14	TraesCS1A01G172500	chr2A	285231030	285232715	1685	False	907.5	1301	88.2735	1916	3635	2	chr2A.!!$F3	1719
15	TraesCS1A01G172500	chr7B	164689096	164689945	849	False	1277.0	1277	93.8900	731	1575	1	chr7B.!!$F1	844
16	TraesCS1A01G172500	chr1B	601125552	601127441	1889	True	1059.5	1212	90.6155	1681	3426	2	chr1B.!!$R2	1745
17	TraesCS1A01G172500	chr7A	501095928	501097020	1092	True	1136.0	1136	85.6260	2535	3643	1	chr7A.!!$R1	1108
18	TraesCS1A01G172500	chr6D	232766547	232767056	509	True	345.0	433	89.4330	1681	2927	2	chr6D.!!$R1	1246

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
223	3743	0.387202	CGACTGGAGTGGCTATGAGG	59.613	60.0	0.0	0.0	0.0	3.86	F
1387	4920	0.101219	GCCTTTTGATCGACCATGCC	59.899	55.0	0.0	0.0	0.0	4.40	F
1844	5380	0.387239	GCGCACTGAATTGTTGGACC	60.387	55.0	0.3	0.0	0.0	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2173	5719	0.179034	GATTGATCTCAAGGCCGGCT	60.179	55.0	28.56	9.77	39.47	5.52	R
2668	6408	0.037877	AGCTGCTCTGCTGAAACCAT	59.962	50.0	0.00	0.00	42.33	3.55	R
3668	8263	0.179134	GACGGACGCAGAAGCACTAT	60.179	55.0	0.00	0.00	42.27	2.12	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
106	107	2.427245	CCGTCGCAGGGAGAGGATT	61.427	63.158	3.50	0.00	0.00	3.01
220	3740	2.145958	CATCGACTGGAGTGGCTATG	57.854	55.000	0.00	0.00	0.00	2.23
221	3741	1.683385	CATCGACTGGAGTGGCTATGA	59.317	52.381	0.00	0.00	0.00	2.15
222	3742	1.393603	TCGACTGGAGTGGCTATGAG	58.606	55.000	0.00	0.00	0.00	2.90
223	3743	0.387202	CGACTGGAGTGGCTATGAGG	59.613	60.000	0.00	0.00	0.00	3.86
224	3744	1.490574	GACTGGAGTGGCTATGAGGT	58.509	55.000	0.00	0.00	0.00	3.85
225	3745	1.834263	GACTGGAGTGGCTATGAGGTT	59.166	52.381	0.00	0.00	0.00	3.50
226	3746	1.556911	ACTGGAGTGGCTATGAGGTTG	59.443	52.381	0.00	0.00	0.00	3.77
227	3747	0.911769	TGGAGTGGCTATGAGGTTGG	59.088	55.000	0.00	0.00	0.00	3.77
228	3748	1.204146	GGAGTGGCTATGAGGTTGGA	58.796	55.000	0.00	0.00	0.00	3.53
229	3749	1.139853	GGAGTGGCTATGAGGTTGGAG	59.860	57.143	0.00	0.00	0.00	3.86
230	3750	1.834263	GAGTGGCTATGAGGTTGGAGT	59.166	52.381	0.00	0.00	0.00	3.85
231	3751	1.556911	AGTGGCTATGAGGTTGGAGTG	59.443	52.381	0.00	0.00	0.00	3.51
232	3752	0.911769	TGGCTATGAGGTTGGAGTGG	59.088	55.000	0.00	0.00	0.00	4.00
235	3755	1.762957	GCTATGAGGTTGGAGTGGCTA	59.237	52.381	0.00	0.00	0.00	3.93
672	4199	2.231964	TGTCGCGAACAAGGGTAATAGT	59.768	45.455	12.06	0.00	34.03	2.12
733	4260	5.106396	CCATCTCAGCCAACTTAACTTTCAG	60.106	44.000	0.00	0.00	0.00	3.02
742	4269	6.034577	GCCAACTTAACTTTCAGTTTGTTCAC	59.965	38.462	0.00	0.00	39.51	3.18
1387	4920	0.101219	GCCTTTTGATCGACCATGCC	59.899	55.000	0.00	0.00	0.00	4.40
1630	5165	7.887381	TCTATTGAAATCTAGAGGATCGGTTC	58.113	38.462	0.00	0.00	42.67	3.62
1844	5380	0.387239	GCGCACTGAATTGTTGGACC	60.387	55.000	0.30	0.00	0.00	4.46
2173	5719	1.241165	CAGCACTTGCATTGGACAGA	58.759	50.000	3.62	0.00	45.16	3.41
2184	5730	3.706373	GGACAGAGCCGGCCTTGA	61.706	66.667	28.51	0.00	0.00	3.02
2232	5778	2.633967	TCGTACTTGGAGCAAAAGGGTA	59.366	45.455	0.00	0.00	0.00	3.69
2245	5791	5.951747	AGCAAAAGGGTAAATATTCTGCAGA	59.048	36.000	13.74	13.74	0.00	4.26
2425	6165	0.975556	GGGCCCCGTGATTTTGGAAT	60.976	55.000	12.23	0.00	0.00	3.01
2526	6266	5.323371	TCAAGCAAGCACTAACAAACTTT	57.677	34.783	0.00	0.00	0.00	2.66
2597	6337	4.283403	GCTTGCAGCGTTGGCCAA	62.283	61.111	16.05	16.05	41.24	4.52
2604	6344	0.597568	CAGCGTTGGCCAAGAATTCA	59.402	50.000	21.21	0.00	41.24	2.57
2608	6348	2.922335	GCGTTGGCCAAGAATTCAGAAC	60.922	50.000	21.21	2.09	0.00	3.01
2668	6408	4.997395	GCCCGCTTATGATCTCTGAATTTA	59.003	41.667	0.00	0.00	0.00	1.40
2683	6423	5.124457	TCTGAATTTATGGTTTCAGCAGAGC	59.876	40.000	7.60	0.00	45.41	4.09
2732	6475	3.813150	AGGTTGTGCCTCTCCCTC	58.187	61.111	0.00	0.00	46.96	4.30
2763	6506	4.344359	TGGCAATTTCAAGGGGTAAAAC	57.656	40.909	0.00	0.00	0.00	2.43
2770	6514	5.666474	TTTCAAGGGGTAAAACTAAGGGA	57.334	39.130	0.00	0.00	0.00	4.20
3106	7694	2.203056	CAGCGCCCGGATCAATGA	60.203	61.111	0.73	0.00	0.00	2.57
3255	7843	2.096248	CTCCTCTTACTTGAGCGTCCT	58.904	52.381	0.00	0.00	33.02	3.85
3373	7962	2.748647	TCGATGGTCGGAGTCGCA	60.749	61.111	0.00	0.00	40.88	5.10
3587	8182	0.645496	TAGATTGGGGGCTGGTAGGA	59.355	55.000	0.00	0.00	0.00	2.94
3647	8242	6.091123	ACGTTTGCTCTACGACAAAATATC	57.909	37.500	11.65	0.00	41.33	1.63
3648	8243	5.867716	ACGTTTGCTCTACGACAAAATATCT	59.132	36.000	11.65	0.00	41.33	1.98
3649	8244	6.367969	ACGTTTGCTCTACGACAAAATATCTT	59.632	34.615	11.65	0.00	41.33	2.40
3650	8245	7.095355	ACGTTTGCTCTACGACAAAATATCTTT	60.095	33.333	11.65	0.00	41.33	2.52
3651	8246	7.422746	CGTTTGCTCTACGACAAAATATCTTTC	59.577	37.037	0.00	0.00	41.33	2.62
3652	8247	6.903883	TGCTCTACGACAAAATATCTTTCC	57.096	37.500	0.00	0.00	0.00	3.13
3653	8248	5.815740	TGCTCTACGACAAAATATCTTTCCC	59.184	40.000	0.00	0.00	0.00	3.97
3654	8249	6.049790	GCTCTACGACAAAATATCTTTCCCT	58.950	40.000	0.00	0.00	0.00	4.20
3655	8250	7.147794	TGCTCTACGACAAAATATCTTTCCCTA	60.148	37.037	0.00	0.00	0.00	3.53
3656	8251	7.169476	GCTCTACGACAAAATATCTTTCCCTAC	59.831	40.741	0.00	0.00	0.00	3.18
3657	8252	8.302515	TCTACGACAAAATATCTTTCCCTACT	57.697	34.615	0.00	0.00	0.00	2.57
3658	8253	9.412460	TCTACGACAAAATATCTTTCCCTACTA	57.588	33.333	0.00	0.00	0.00	1.82
3681	8276	8.818057	ACTAATAAAGTAAATAGTGCTTCTGCG	58.182	33.333	0.00	0.00	38.29	5.18
3682	8277	7.611213	AATAAAGTAAATAGTGCTTCTGCGT	57.389	32.000	0.00	0.00	43.34	5.24
3683	8278	5.532025	AAAGTAAATAGTGCTTCTGCGTC	57.468	39.130	0.00	0.00	43.34	5.19
3684	8279	3.522553	AGTAAATAGTGCTTCTGCGTCC	58.477	45.455	0.00	0.00	43.34	4.79
3685	8280	1.359848	AAATAGTGCTTCTGCGTCCG	58.640	50.000	0.00	0.00	43.34	4.79
3686	8281	0.246635	AATAGTGCTTCTGCGTCCGT	59.753	50.000	0.00	0.00	43.34	4.69
3687	8282	0.179134	ATAGTGCTTCTGCGTCCGTC	60.179	55.000	0.00	0.00	43.34	4.79
3688	8283	1.520600	TAGTGCTTCTGCGTCCGTCA	61.521	55.000	0.00	0.00	43.34	4.35
3689	8284	1.738099	GTGCTTCTGCGTCCGTCAT	60.738	57.895	0.00	0.00	43.34	3.06
3690	8285	0.457853	GTGCTTCTGCGTCCGTCATA	60.458	55.000	0.00	0.00	43.34	2.15
3691	8286	0.245266	TGCTTCTGCGTCCGTCATAA	59.755	50.000	0.00	0.00	43.34	1.90
3692	8287	1.337354	TGCTTCTGCGTCCGTCATAAA	60.337	47.619	0.00	0.00	43.34	1.40
3693	8288	1.730064	GCTTCTGCGTCCGTCATAAAA	59.270	47.619	0.00	0.00	0.00	1.52
3694	8289	2.158841	GCTTCTGCGTCCGTCATAAAAA	59.841	45.455	0.00	0.00	0.00	1.94
3712	8307	2.871096	AAATACCCTCGAAGTTGGCA	57.129	45.000	0.00	0.00	0.00	4.92
3713	8308	2.871096	AATACCCTCGAAGTTGGCAA	57.129	45.000	0.00	0.00	0.00	4.52
3714	8309	2.871096	ATACCCTCGAAGTTGGCAAA	57.129	45.000	0.00	0.00	0.00	3.68
3715	8310	2.642154	TACCCTCGAAGTTGGCAAAA	57.358	45.000	0.00	0.00	0.00	2.44
3716	8311	1.995376	ACCCTCGAAGTTGGCAAAAT	58.005	45.000	0.00	0.00	0.00	1.82
3717	8312	2.316108	ACCCTCGAAGTTGGCAAAATT	58.684	42.857	0.00	0.00	0.00	1.82
3718	8313	2.698274	ACCCTCGAAGTTGGCAAAATTT	59.302	40.909	0.00	0.00	0.00	1.82
3719	8314	3.892588	ACCCTCGAAGTTGGCAAAATTTA	59.107	39.130	0.00	0.00	0.00	1.40
3720	8315	4.234574	CCCTCGAAGTTGGCAAAATTTAC	58.765	43.478	0.00	0.00	0.00	2.01
3721	8316	4.234574	CCTCGAAGTTGGCAAAATTTACC	58.765	43.478	0.00	3.69	0.00	2.85
3722	8317	4.234574	CTCGAAGTTGGCAAAATTTACCC	58.765	43.478	0.00	4.36	0.00	3.69
3723	8318	3.637229	TCGAAGTTGGCAAAATTTACCCA	59.363	39.130	0.00	6.66	0.00	4.51
3724	8319	3.738791	CGAAGTTGGCAAAATTTACCCAC	59.261	43.478	0.00	7.49	0.00	4.61
3725	8320	3.762407	AGTTGGCAAAATTTACCCACC	57.238	42.857	0.00	3.57	0.00	4.61
3726	8321	3.041946	AGTTGGCAAAATTTACCCACCA	58.958	40.909	0.00	2.34	0.00	4.17
3727	8322	3.456277	AGTTGGCAAAATTTACCCACCAA	59.544	39.130	0.00	7.44	33.50	3.67
3728	8323	4.103943	AGTTGGCAAAATTTACCCACCAAT	59.896	37.500	0.00	0.00	37.95	3.16
3729	8324	4.013267	TGGCAAAATTTACCCACCAATG	57.987	40.909	7.51	0.00	0.00	2.82
3730	8325	2.746904	GGCAAAATTTACCCACCAATGC	59.253	45.455	0.00	0.00	0.00	3.56
3731	8326	2.746904	GCAAAATTTACCCACCAATGCC	59.253	45.455	0.00	0.00	0.00	4.40
3732	8327	3.808618	GCAAAATTTACCCACCAATGCCA	60.809	43.478	0.00	0.00	0.00	4.92
3733	8328	4.587891	CAAAATTTACCCACCAATGCCAT	58.412	39.130	0.00	0.00	0.00	4.40
3734	8329	4.486125	AAATTTACCCACCAATGCCATC	57.514	40.909	0.00	0.00	0.00	3.51
3735	8330	1.859302	TTTACCCACCAATGCCATCC	58.141	50.000	0.00	0.00	0.00	3.51
3736	8331	0.395036	TTACCCACCAATGCCATCCG	60.395	55.000	0.00	0.00	0.00	4.18
3737	8332	1.567208	TACCCACCAATGCCATCCGT	61.567	55.000	0.00	0.00	0.00	4.69
3738	8333	1.225983	CCCACCAATGCCATCCGTA	59.774	57.895	0.00	0.00	0.00	4.02
3739	8334	0.395036	CCCACCAATGCCATCCGTAA	60.395	55.000	0.00	0.00	0.00	3.18
3740	8335	1.024271	CCACCAATGCCATCCGTAAG	58.976	55.000	0.00	0.00	0.00	2.34
3741	8336	1.681780	CCACCAATGCCATCCGTAAGT	60.682	52.381	0.00	0.00	0.00	2.24
3742	8337	1.401552	CACCAATGCCATCCGTAAGTG	59.598	52.381	0.00	0.00	0.00	3.16
3743	8338	1.024271	CCAATGCCATCCGTAAGTGG	58.976	55.000	0.00	0.00	38.55	4.00
3750	8345	2.941428	CCATCCGTAAGTGGCAAAAAC	58.059	47.619	0.00	0.00	0.00	2.43
3751	8346	2.580589	CATCCGTAAGTGGCAAAAACG	58.419	47.619	9.11	9.11	0.00	3.60
3752	8347	1.950828	TCCGTAAGTGGCAAAAACGA	58.049	45.000	15.63	2.88	35.66	3.85
3753	8348	2.496111	TCCGTAAGTGGCAAAAACGAT	58.504	42.857	15.63	0.00	35.66	3.73
3754	8349	2.879646	TCCGTAAGTGGCAAAAACGATT	59.120	40.909	15.63	0.00	35.66	3.34
3755	8350	3.058777	TCCGTAAGTGGCAAAAACGATTC	60.059	43.478	15.63	0.00	35.66	2.52
3756	8351	2.900046	CGTAAGTGGCAAAAACGATTCG	59.100	45.455	4.14	4.14	35.66	3.34
3757	8352	3.605231	CGTAAGTGGCAAAAACGATTCGT	60.605	43.478	5.75	5.75	43.97	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
52	53	1.186200	CTCTCCCCGTCAACATCTCA	58.814	55.000	0.00	0.00	0.00	3.27
95	96	2.370445	CCCGCACAATCCTCTCCCT	61.370	63.158	0.00	0.00	0.00	4.20
216	3736	3.643320	TCATAGCCACTCCAACCTCATAG	59.357	47.826	0.00	0.00	0.00	2.23
217	3737	3.643320	CTCATAGCCACTCCAACCTCATA	59.357	47.826	0.00	0.00	0.00	2.15
218	3738	2.437281	CTCATAGCCACTCCAACCTCAT	59.563	50.000	0.00	0.00	0.00	2.90
219	3739	1.833630	CTCATAGCCACTCCAACCTCA	59.166	52.381	0.00	0.00	0.00	3.86
220	3740	1.139853	CCTCATAGCCACTCCAACCTC	59.860	57.143	0.00	0.00	0.00	3.85
221	3741	1.207791	CCTCATAGCCACTCCAACCT	58.792	55.000	0.00	0.00	0.00	3.50
222	3742	0.181350	CCCTCATAGCCACTCCAACC	59.819	60.000	0.00	0.00	0.00	3.77
223	3743	0.181350	CCCCTCATAGCCACTCCAAC	59.819	60.000	0.00	0.00	0.00	3.77
224	3744	0.988145	CCCCCTCATAGCCACTCCAA	60.988	60.000	0.00	0.00	0.00	3.53
225	3745	1.384502	CCCCCTCATAGCCACTCCA	60.385	63.158	0.00	0.00	0.00	3.86
226	3746	1.074471	TCCCCCTCATAGCCACTCC	60.074	63.158	0.00	0.00	0.00	3.85
227	3747	0.105453	TCTCCCCCTCATAGCCACTC	60.105	60.000	0.00	0.00	0.00	3.51
228	3748	0.105246	CTCTCCCCCTCATAGCCACT	60.105	60.000	0.00	0.00	0.00	4.00
229	3749	0.105453	TCTCTCCCCCTCATAGCCAC	60.105	60.000	0.00	0.00	0.00	5.01
230	3750	0.189574	CTCTCTCCCCCTCATAGCCA	59.810	60.000	0.00	0.00	0.00	4.75
231	3751	0.189822	ACTCTCTCCCCCTCATAGCC	59.810	60.000	0.00	0.00	0.00	3.93
232	3752	1.133325	TCACTCTCTCCCCCTCATAGC	60.133	57.143	0.00	0.00	0.00	2.97
235	3755	1.217689	CTCTCACTCTCTCCCCCTCAT	59.782	57.143	0.00	0.00	0.00	2.90
326	3846	2.519063	CACCCACACAGCCTTGCA	60.519	61.111	0.00	0.00	0.00	4.08
351	3872	4.395959	ACAAGAGTGGAACAACGAACTA	57.604	40.909	0.00	0.00	44.16	2.24
672	4199	2.031870	CAGTCTGATGGATCGTGGGTA	58.968	52.381	0.00	0.00	0.00	3.69
1387	4920	6.211515	ACTGCACTAAAGAGCTTTTTGAATG	58.788	36.000	12.27	8.45	34.23	2.67
1630	5165	7.979444	TCTTCTAGTACCTCAACAAAAATGG	57.021	36.000	0.00	0.00	0.00	3.16
1857	5393	5.467735	TCCGATGCTTGACAGATGAATTATG	59.532	40.000	0.00	0.00	0.00	1.90
2173	5719	0.179034	GATTGATCTCAAGGCCGGCT	60.179	55.000	28.56	9.77	39.47	5.52
2184	5730	8.897752	GGCTACAGAATTTAGTTTGATTGATCT	58.102	33.333	0.00	0.00	0.00	2.75
2232	5778	2.545526	CGACGGCATCTGCAGAATATTT	59.454	45.455	22.50	5.30	44.36	1.40
2262	5808	1.767759	ATAACAACATGCCCTCTGCC	58.232	50.000	0.00	0.00	40.16	4.85
2526	6266	5.001874	ACGCTACTGATACTATGATCCGAA	58.998	41.667	0.00	0.00	0.00	4.30
2597	6337	3.262915	CCTCTCCTGGTGTTCTGAATTCT	59.737	47.826	7.05	0.00	0.00	2.40
2604	6344	1.280421	GCAATCCTCTCCTGGTGTTCT	59.720	52.381	0.00	0.00	0.00	3.01
2608	6348	1.153289	CCGCAATCCTCTCCTGGTG	60.153	63.158	0.00	0.00	0.00	4.17
2668	6408	0.037877	AGCTGCTCTGCTGAAACCAT	59.962	50.000	0.00	0.00	42.33	3.55
2683	6423	8.539770	TTTTGAGATTCAGAGTAGTAAAGCTG	57.460	34.615	0.00	0.00	0.00	4.24
2732	6475	5.224888	CCTTGAAATTGCCATGATTATCCG	58.775	41.667	0.00	0.00	0.00	4.18
2763	6506	3.577415	CCCTACCGGTAATTCTCCCTTAG	59.423	52.174	16.65	0.31	0.00	2.18
2770	6514	4.675038	CTCTATCCCCTACCGGTAATTCT	58.325	47.826	16.65	2.41	0.00	2.40
3255	7843	1.338973	GGACGATAGGTACATGGCGAA	59.661	52.381	10.11	0.00	43.77	4.70
3264	7852	1.202903	GCTGGAGGAGGACGATAGGTA	60.203	57.143	0.00	0.00	43.77	3.08
3421	8010	4.416601	CCCGGTCTCCCCTCCCTT	62.417	72.222	0.00	0.00	0.00	3.95
3563	8158	2.498441	ACCAGCCCCCAATCTATAACA	58.502	47.619	0.00	0.00	0.00	2.41
3565	8160	3.116120	TCCTACCAGCCCCCAATCTATAA	60.116	47.826	0.00	0.00	0.00	0.98
3566	8161	2.457126	TCCTACCAGCCCCCAATCTATA	59.543	50.000	0.00	0.00	0.00	1.31
3567	8162	1.225694	TCCTACCAGCCCCCAATCTAT	59.774	52.381	0.00	0.00	0.00	1.98
3655	8250	8.818057	CGCAGAAGCACTATTTACTTTATTAGT	58.182	33.333	0.00	0.00	42.27	2.24
3656	8251	8.818057	ACGCAGAAGCACTATTTACTTTATTAG	58.182	33.333	0.00	0.00	42.27	1.73
3657	8252	8.712285	ACGCAGAAGCACTATTTACTTTATTA	57.288	30.769	0.00	0.00	42.27	0.98
3658	8253	7.201617	GGACGCAGAAGCACTATTTACTTTATT	60.202	37.037	0.00	0.00	42.27	1.40
3659	8254	6.258068	GGACGCAGAAGCACTATTTACTTTAT	59.742	38.462	0.00	0.00	42.27	1.40
3660	8255	5.579511	GGACGCAGAAGCACTATTTACTTTA	59.420	40.000	0.00	0.00	42.27	1.85
3661	8256	4.392138	GGACGCAGAAGCACTATTTACTTT	59.608	41.667	0.00	0.00	42.27	2.66
3662	8257	3.933332	GGACGCAGAAGCACTATTTACTT	59.067	43.478	0.00	0.00	42.27	2.24
3663	8258	3.522553	GGACGCAGAAGCACTATTTACT	58.477	45.455	0.00	0.00	42.27	2.24
3664	8259	2.281762	CGGACGCAGAAGCACTATTTAC	59.718	50.000	0.00	0.00	42.27	2.01
3665	8260	2.094390	ACGGACGCAGAAGCACTATTTA	60.094	45.455	0.00	0.00	42.27	1.40
3666	8261	1.337823	ACGGACGCAGAAGCACTATTT	60.338	47.619	0.00	0.00	42.27	1.40
3667	8262	0.246635	ACGGACGCAGAAGCACTATT	59.753	50.000	0.00	0.00	42.27	1.73
3668	8263	0.179134	GACGGACGCAGAAGCACTAT	60.179	55.000	0.00	0.00	42.27	2.12
3669	8264	1.211969	GACGGACGCAGAAGCACTA	59.788	57.895	0.00	0.00	42.27	2.74
3670	8265	2.049063	GACGGACGCAGAAGCACT	60.049	61.111	0.00	0.00	42.27	4.40
3671	8266	0.457853	TATGACGGACGCAGAAGCAC	60.458	55.000	0.00	0.00	42.27	4.40
3672	8267	0.245266	TTATGACGGACGCAGAAGCA	59.755	50.000	0.00	0.00	42.27	3.91
3673	8268	1.355971	TTTATGACGGACGCAGAAGC	58.644	50.000	0.00	0.00	37.42	3.86
3691	8286	3.492337	TGCCAACTTCGAGGGTATTTTT	58.508	40.909	0.00	0.00	0.00	1.94
3692	8287	3.149005	TGCCAACTTCGAGGGTATTTT	57.851	42.857	0.00	0.00	0.00	1.82
3693	8288	2.871096	TGCCAACTTCGAGGGTATTT	57.129	45.000	0.00	0.00	0.00	1.40
3694	8289	2.871096	TTGCCAACTTCGAGGGTATT	57.129	45.000	0.00	0.00	0.00	1.89
3695	8290	2.871096	TTTGCCAACTTCGAGGGTAT	57.129	45.000	0.00	0.00	0.00	2.73
3696	8291	2.642154	TTTTGCCAACTTCGAGGGTA	57.358	45.000	0.00	0.00	0.00	3.69
3697	8292	1.995376	ATTTTGCCAACTTCGAGGGT	58.005	45.000	0.00	0.00	0.00	4.34
3698	8293	3.385193	AAATTTTGCCAACTTCGAGGG	57.615	42.857	0.00	0.00	0.00	4.30
3699	8294	4.234574	GGTAAATTTTGCCAACTTCGAGG	58.765	43.478	10.96	0.00	35.27	4.63
3700	8295	4.234574	GGGTAAATTTTGCCAACTTCGAG	58.765	43.478	16.68	0.00	37.12	4.04
3701	8296	3.637229	TGGGTAAATTTTGCCAACTTCGA	59.363	39.130	16.68	0.00	37.12	3.71
3702	8297	3.738791	GTGGGTAAATTTTGCCAACTTCG	59.261	43.478	16.68	0.00	36.52	3.79
3703	8298	4.062293	GGTGGGTAAATTTTGCCAACTTC	58.938	43.478	19.44	4.56	39.15	3.01
3704	8299	3.456277	TGGTGGGTAAATTTTGCCAACTT	59.544	39.130	19.44	0.00	39.15	2.66
3705	8300	3.041946	TGGTGGGTAAATTTTGCCAACT	58.958	40.909	19.44	0.00	39.15	3.16
3706	8301	3.477210	TGGTGGGTAAATTTTGCCAAC	57.523	42.857	16.68	15.21	38.51	3.77
3707	8302	4.392940	CATTGGTGGGTAAATTTTGCCAA	58.607	39.130	16.68	3.99	37.12	4.52
3708	8303	3.808618	GCATTGGTGGGTAAATTTTGCCA	60.809	43.478	16.68	2.30	37.12	4.92
3709	8304	2.746904	GCATTGGTGGGTAAATTTTGCC	59.253	45.455	7.66	7.66	34.30	4.52
3710	8305	2.746904	GGCATTGGTGGGTAAATTTTGC	59.253	45.455	0.00	0.00	0.00	3.68
3711	8306	4.013267	TGGCATTGGTGGGTAAATTTTG	57.987	40.909	0.00	0.00	0.00	2.44
3712	8307	4.324176	GGATGGCATTGGTGGGTAAATTTT	60.324	41.667	0.00	0.00	0.00	1.82
3713	8308	3.199727	GGATGGCATTGGTGGGTAAATTT	59.800	43.478	0.00	0.00	0.00	1.82
3714	8309	2.771372	GGATGGCATTGGTGGGTAAATT	59.229	45.455	0.00	0.00	0.00	1.82
3715	8310	2.397597	GGATGGCATTGGTGGGTAAAT	58.602	47.619	0.00	0.00	0.00	1.40
3716	8311	1.859302	GGATGGCATTGGTGGGTAAA	58.141	50.000	0.00	0.00	0.00	2.01
3717	8312	0.395036	CGGATGGCATTGGTGGGTAA	60.395	55.000	0.00	0.00	0.00	2.85
3718	8313	1.225983	CGGATGGCATTGGTGGGTA	59.774	57.895	0.00	0.00	0.00	3.69
3719	8314	1.567208	TACGGATGGCATTGGTGGGT	61.567	55.000	0.00	0.00	0.00	4.51
3720	8315	0.395036	TTACGGATGGCATTGGTGGG	60.395	55.000	0.00	0.00	0.00	4.61
3721	8316	1.024271	CTTACGGATGGCATTGGTGG	58.976	55.000	0.00	0.00	0.00	4.61
3722	8317	1.401552	CACTTACGGATGGCATTGGTG	59.598	52.381	0.00	1.75	0.00	4.17
3723	8318	1.681780	CCACTTACGGATGGCATTGGT	60.682	52.381	0.00	5.51	0.00	3.67
3724	8319	1.024271	CCACTTACGGATGGCATTGG	58.976	55.000	0.00	0.00	0.00	3.16
3730	8325	2.667171	CGTTTTTGCCACTTACGGATGG	60.667	50.000	0.00	0.00	39.16	3.51
3731	8326	2.224549	TCGTTTTTGCCACTTACGGATG	59.775	45.455	0.00	0.00	33.37	3.51
3732	8327	2.496111	TCGTTTTTGCCACTTACGGAT	58.504	42.857	0.00	0.00	33.37	4.18
3733	8328	1.950828	TCGTTTTTGCCACTTACGGA	58.049	45.000	0.00	0.00	33.37	4.69
3734	8329	2.981400	ATCGTTTTTGCCACTTACGG	57.019	45.000	0.00	0.00	33.37	4.02
3735	8330	2.900046	CGAATCGTTTTTGCCACTTACG	59.100	45.455	0.00	0.00	0.00	3.18
3736	8331	3.880610	ACGAATCGTTTTTGCCACTTAC	58.119	40.909	0.96	0.00	36.35	2.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.