AutoCloner

Multiple sequence alignment - TraesCS6D01G400300

Loading Multiple Alignment...

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	TraesCS6D01G400300	chr6D	100.000	4165	0	0	1	4165	470095737	470099901	0.000000e+00	7692.0
1	TraesCS6D01G400300	chr6D	92.165	1889	77	22	229	2115	470298669	470296850	0.000000e+00	2603.0
2	TraesCS6D01G400300	chr6D	93.499	1769	83	6	2427	4165	470296671	470294905	0.000000e+00	2601.0
3	TraesCS6D01G400300	chr6D	93.122	189	4	2	2199	2387	470296850	470296671	6.860000e-68	268.0
4	TraesCS6D01G400300	chr6D	88.750	160	12	1	1	160	470299730	470299577	1.530000e-44	191.0
5	TraesCS6D01G400300	chr6D	83.974	156	11	5	1	156	470302934	470302793	2.020000e-28	137.0
6	TraesCS6D01G400300	chr6A	92.233	1944	92	23	229	2163	614959721	614961614	0.000000e+00	2699.0
7	TraesCS6D01G400300	chr6A	93.563	1709	79	17	2485	4165	614961841	614963546	0.000000e+00	2518.0
8	TraesCS6D01G400300	chr6A	77.404	1040	201	24	3147	4160	27105882	27104851	4.640000e-164	588.0
9	TraesCS6D01G400300	chr6A	77.657	922	192	13	3147	4061	27008061	27007147	2.190000e-152	549.0
10	TraesCS6D01G400300	chr6A	77.210	724	157	8	3150	3869	27061780	27061061	2.320000e-112	416.0
11	TraesCS6D01G400300	chr6A	91.497	294	6	2	2146	2439	614961565	614961839	1.820000e-103	387.0
12	TraesCS6D01G400300	chr6A	92.500	160	12	0	1	160	614977539	614977380	3.240000e-56	230.0
13	TraesCS6D01G400300	chr6A	76.667	330	47	14	3858	4160	27059796	27059470	5.580000e-34	156.0
14	TraesCS6D01G400300	chrUn	79.369	1522	259	31	2570	4051	95818117	95819623	0.000000e+00	1020.0
15	TraesCS6D01G400300	chrUn	78.836	1512	283	26	2575	4061	96126507	96125008	0.000000e+00	985.0
16	TraesCS6D01G400300	chrUn	77.467	1642	307	30	2575	4160	96156377	96154743	0.000000e+00	924.0
17	TraesCS6D01G400300	chrUn	78.307	1512	261	39	2572	4049	95985476	95986954	0.000000e+00	913.0
18	TraesCS6D01G400300	chrUn	77.611	1532	295	34	2554	4049	96230241	96228722	0.000000e+00	885.0
19	TraesCS6D01G400300	chrUn	76.888	1536	307	27	2562	4061	96217867	96216344	0.000000e+00	826.0
20	TraesCS6D01G400300	chrUn	76.928	1530	279	36	2563	4055	95709614	95711106	0.000000e+00	802.0
21	TraesCS6D01G400300	chrUn	75.167	1047	218	29	3147	4160	96297888	96296851	4.910000e-124	455.0
22	TraesCS6D01G400300	chrUn	76.113	741	151	20	3322	4054	96286268	96285546	8.510000e-97	364.0
23	TraesCS6D01G400300	chrUn	79.762	420	77	5	997	1412	50646651	50646236	8.750000e-77	298.0
24	TraesCS6D01G400300	chr6B	76.699	1545	310	29	2554	4061	47092718	47091187	0.000000e+00	813.0
25	TraesCS6D01G400300	chr6B	77.297	1110	200	33	1001	2088	47271373	47270294	1.280000e-169	606.0
26	TraesCS6D01G400300	chr6B	89.703	437	27	8	858	1293	716432632	716432213	3.660000e-150	542.0
27	TraesCS6D01G400300	chr6B	77.083	912	195	14	3150	4054	46925887	46924983	7.980000e-142	514.0
28	TraesCS6D01G400300	chr6B	75.768	912	203	17	3147	4049	46948046	46947144	1.060000e-120	444.0
29	TraesCS6D01G400300	chr6B	74.973	911	208	17	3150	4054	46960924	46960028	6.490000e-108	401.0
30	TraesCS6D01G400300	chr6B	86.250	160	19	1	1	157	716396571	716396412	1.990000e-38	171.0
31	TraesCS6D01G400300	chr6B	86.047	86	10	1	75	160	716494827	716494744	1.590000e-14	91.6
32	TraesCS6D01G400300	chr3A	75.626	1038	214	25	3147	4154	686910751	686911779	2.910000e-131	479.0
33	TraesCS6D01G400300	chr7A	75.070	1067	242	14	1001	2049	486924271	486925331	3.770000e-130	475.0
34	TraesCS6D01G400300	chr7A	78.423	482	87	13	940	1412	20025340	20025813	8.750000e-77	298.0
35	TraesCS6D01G400300	chr7D	79.303	459	76	15	937	1384	19925149	19925599	1.880000e-78	303.0
36	TraesCS6D01G400300	chr7D	79.286	420	78	6	997	1412	19861988	19862402	6.820000e-73	285.0
37	TraesCS6D01G400300	chr7D	79.587	387	71	5	997	1379	19815812	19816194	1.910000e-68	270.0
38	TraesCS6D01G400300	chr7D	77.951	449	85	10	937	1379	19742779	19743219	6.860000e-68	268.0
39	TraesCS6D01G400300	chr7B	71.548	956	226	36	3228	4165	747525349	747524422	2.520000e-52	217.0

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	TraesCS6D01G400300	chr6D	470095737	470099901	4164	False	7692	7692	100.0000	1	4165	1	chr6D.!!$F1	4164
1	TraesCS6D01G400300	chr6D	470294905	470302934	8029	True	1160	2603	90.3020	1	4165	5	chr6D.!!$R1	4164
2	TraesCS6D01G400300	chr6A	614959721	614963546	3825	False	1868	2699	92.4310	229	4165	3	chr6A.!!$F1	3936
3	TraesCS6D01G400300	chr6A	27104851	27105882	1031	True	588	588	77.4040	3147	4160	1	chr6A.!!$R2	1013
4	TraesCS6D01G400300	chr6A	27007147	27008061	914	True	549	549	77.6570	3147	4061	1	chr6A.!!$R1	914
5	TraesCS6D01G400300	chr6A	27059470	27061780	2310	True	286	416	76.9385	3150	4160	2	chr6A.!!$R4	1010
6	TraesCS6D01G400300	chrUn	95818117	95819623	1506	False	1020	1020	79.3690	2570	4051	1	chrUn.!!$F2	1481
7	TraesCS6D01G400300	chrUn	96125008	96126507	1499	True	985	985	78.8360	2575	4061	1	chrUn.!!$R2	1486
8	TraesCS6D01G400300	chrUn	96154743	96156377	1634	True	924	924	77.4670	2575	4160	1	chrUn.!!$R3	1585
9	TraesCS6D01G400300	chrUn	95985476	95986954	1478	False	913	913	78.3070	2572	4049	1	chrUn.!!$F3	1477
10	TraesCS6D01G400300	chrUn	96228722	96230241	1519	True	885	885	77.6110	2554	4049	1	chrUn.!!$R5	1495
11	TraesCS6D01G400300	chrUn	96216344	96217867	1523	True	826	826	76.8880	2562	4061	1	chrUn.!!$R4	1499
12	TraesCS6D01G400300	chrUn	95709614	95711106	1492	False	802	802	76.9280	2563	4055	1	chrUn.!!$F1	1492
13	TraesCS6D01G400300	chrUn	96296851	96297888	1037	True	455	455	75.1670	3147	4160	1	chrUn.!!$R7	1013
14	TraesCS6D01G400300	chrUn	96285546	96286268	722	True	364	364	76.1130	3322	4054	1	chrUn.!!$R6	732
15	TraesCS6D01G400300	chr6B	47091187	47092718	1531	True	813	813	76.6990	2554	4061	1	chr6B.!!$R4	1507
16	TraesCS6D01G400300	chr6B	47270294	47271373	1079	True	606	606	77.2970	1001	2088	1	chr6B.!!$R5	1087
17	TraesCS6D01G400300	chr6B	46924983	46925887	904	True	514	514	77.0830	3150	4054	1	chr6B.!!$R1	904
18	TraesCS6D01G400300	chr6B	46947144	46948046	902	True	444	444	75.7680	3147	4049	1	chr6B.!!$R2	902
19	TraesCS6D01G400300	chr6B	46960028	46960924	896	True	401	401	74.9730	3150	4054	1	chr6B.!!$R3	904
20	TraesCS6D01G400300	chr3A	686910751	686911779	1028	False	479	479	75.6260	3147	4154	1	chr3A.!!$F1	1007
21	TraesCS6D01G400300	chr7A	486924271	486925331	1060	False	475	475	75.0700	1001	2049	1	chr7A.!!$F2	1048
22	TraesCS6D01G400300	chr7B	747524422	747525349	927	True	217	217	71.5480	3228	4165	1	chr7B.!!$R1	937

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
529	4595	0.099968	TTCTTCTACCGCATCCGTCG	59.900	55.0	0.00	0.00	0.00	5.12	F
987	5060	0.767375	AGCCTGAGCCTGAGAACAAA	59.233	50.0	0.00	0.00	41.25	2.83	F
1884	5969	1.317431	TGTGGAGCCATGAAGCATGC	61.317	55.0	10.51	10.51	40.20	4.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2333	6421	0.687354	TGGGAGAGAAGCTGTTCACC	59.313	55.000	5.86	5.86	34.82	4.02	R
2387	6475	1.926511	GCAAGTGGGGATTCGCTGTG	61.927	60.000	0.40	0.00	0.00	3.66	R
3568	7682	1.267806	CACCAAACACCATCTGTCTGC	59.732	52.381	0.00	0.00	30.29	4.26	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
20	21	2.589014	GCAGTGCATGAGCTACAAAAC	58.411	47.619	11.09	0.00	42.74	2.43
36	37	9.162764	AGCTACAAAACATATACGATGAAACTT	57.837	29.630	0.00	0.00	0.00	2.66
58	59	6.719370	ACTTTCCAAAAGCATATCACAGGTAA	59.281	34.615	0.00	0.00	0.00	2.85
99	3298	9.836864	TTACTAGGTTACGATAACTCTGACATA	57.163	33.333	0.00	0.00	0.00	2.29
100	3299	8.743085	ACTAGGTTACGATAACTCTGACATAA	57.257	34.615	0.00	0.00	0.00	1.90
138	3337	7.145985	TCGTTTTGGAGATCATAGCTACATAC	58.854	38.462	0.00	0.00	0.00	2.39
141	3340	4.918588	TGGAGATCATAGCTACATACGGA	58.081	43.478	0.00	0.00	0.00	4.69
142	3341	5.321927	TGGAGATCATAGCTACATACGGAA	58.678	41.667	0.00	0.00	0.00	4.30
143	3342	5.773176	TGGAGATCATAGCTACATACGGAAA	59.227	40.000	0.00	0.00	0.00	3.13
144	3343	6.266786	TGGAGATCATAGCTACATACGGAAAA	59.733	38.462	0.00	0.00	0.00	2.29
145	3344	6.809196	GGAGATCATAGCTACATACGGAAAAG	59.191	42.308	0.00	0.00	0.00	2.27
146	3345	7.291411	AGATCATAGCTACATACGGAAAAGT	57.709	36.000	0.00	0.00	0.00	2.66
147	3346	8.405418	AGATCATAGCTACATACGGAAAAGTA	57.595	34.615	0.00	0.00	0.00	2.24
148	3347	9.026121	AGATCATAGCTACATACGGAAAAGTAT	57.974	33.333	0.00	0.00	37.78	2.12
151	3350	9.293404	TCATAGCTACATACGGAAAAGTATACT	57.707	33.333	0.00	0.00	35.72	2.12
152	3351	9.343103	CATAGCTACATACGGAAAAGTATACTG	57.657	37.037	6.06	0.00	35.72	2.74
153	3352	7.344095	AGCTACATACGGAAAAGTATACTGT	57.656	36.000	6.06	0.00	35.72	3.55
154	3353	7.779073	AGCTACATACGGAAAAGTATACTGTT	58.221	34.615	8.09	8.09	35.72	3.16
155	3354	8.255905	AGCTACATACGGAAAAGTATACTGTTT	58.744	33.333	9.71	10.34	35.72	2.83
156	3355	8.876790	GCTACATACGGAAAAGTATACTGTTTT	58.123	33.333	9.71	6.05	35.72	2.43
158	3357	8.836268	ACATACGGAAAAGTATACTGTTTTCA	57.164	30.769	22.58	9.97	42.17	2.69
159	3358	8.715088	ACATACGGAAAAGTATACTGTTTTCAC	58.285	33.333	22.58	14.78	42.17	3.18
160	3359	6.549912	ACGGAAAAGTATACTGTTTTCACC	57.450	37.500	22.58	13.60	42.17	4.02
161	3360	5.178067	ACGGAAAAGTATACTGTTTTCACCG	59.822	40.000	22.77	22.77	42.17	4.94
162	3361	5.388111	GGAAAAGTATACTGTTTTCACCGC	58.612	41.667	22.58	9.02	42.17	5.68
163	3362	5.049267	GGAAAAGTATACTGTTTTCACCGCA	60.049	40.000	22.58	0.00	42.17	5.69
164	3363	6.380095	AAAAGTATACTGTTTTCACCGCAA	57.620	33.333	6.06	0.00	0.00	4.85
165	3364	6.380095	AAAGTATACTGTTTTCACCGCAAA	57.620	33.333	6.06	0.00	0.00	3.68
166	3365	6.380095	AAGTATACTGTTTTCACCGCAAAA	57.620	33.333	6.06	0.00	0.00	2.44
220	3419	7.986085	AATAGTTGTTACACATCAGCTTTCT	57.014	32.000	0.00	0.00	0.00	2.52
222	3421	6.064846	AGTTGTTACACATCAGCTTTCTTG	57.935	37.500	0.00	0.00	0.00	3.02
223	3422	5.009010	AGTTGTTACACATCAGCTTTCTTGG	59.991	40.000	0.00	0.00	0.00	3.61
224	3423	4.460263	TGTTACACATCAGCTTTCTTGGT	58.540	39.130	0.00	0.00	0.00	3.67
226	3425	3.213206	ACACATCAGCTTTCTTGGTCA	57.787	42.857	0.00	0.00	0.00	4.02
245	4309	3.020984	TCAATTTCGAGGTATTTGGGCC	58.979	45.455	0.00	0.00	0.00	5.80
284	4348	4.683832	CCTAATGTGTCTACAGTGCCTAC	58.316	47.826	0.00	0.00	40.79	3.18
319	4384	2.363975	GCCGTGGTATCAGGGGTGA	61.364	63.158	16.27	0.00	46.08	4.02
325	4390	1.614241	GGTATCAGGGGTGACGTGCT	61.614	60.000	0.00	0.00	35.01	4.40
326	4391	1.108776	GTATCAGGGGTGACGTGCTA	58.891	55.000	0.00	0.00	35.01	3.49
331	4397	2.056223	GGGGTGACGTGCTAGGCTA	61.056	63.158	0.00	0.00	0.00	3.93
397	4463	1.607178	CCATCTGGCCAGGTTTGCA	60.607	57.895	32.23	12.73	0.00	4.08
399	4465	0.899720	CATCTGGCCAGGTTTGCATT	59.100	50.000	32.23	4.90	0.00	3.56
411	4477	2.017049	GTTTGCATTAGATCCGCCTGT	58.983	47.619	0.00	0.00	0.00	4.00
512	4578	3.491652	GAAGCTGACGCGGCCTTC	61.492	66.667	10.82	12.82	42.32	3.46
513	4579	3.941657	GAAGCTGACGCGGCCTTCT	62.942	63.158	19.87	7.68	42.32	2.85
514	4580	3.537206	AAGCTGACGCGGCCTTCTT	62.537	57.895	10.82	7.11	42.32	2.52
515	4581	3.491652	GCTGACGCGGCCTTCTTC	61.492	66.667	10.82	0.00	0.00	2.87
516	4582	2.262915	CTGACGCGGCCTTCTTCT	59.737	61.111	10.82	0.00	0.00	2.85
517	4583	1.511305	CTGACGCGGCCTTCTTCTA	59.489	57.895	10.82	0.00	0.00	2.10
518	4584	0.802607	CTGACGCGGCCTTCTTCTAC	60.803	60.000	10.82	0.00	0.00	2.59
519	4585	1.518792	GACGCGGCCTTCTTCTACC	60.519	63.158	12.47	0.00	0.00	3.18
522	4588	2.577059	CGGCCTTCTTCTACCGCA	59.423	61.111	0.00	0.00	39.08	5.69
523	4589	1.144057	CGGCCTTCTTCTACCGCAT	59.856	57.895	0.00	0.00	39.08	4.73
524	4590	0.876342	CGGCCTTCTTCTACCGCATC	60.876	60.000	0.00	0.00	39.08	3.91
525	4591	0.533085	GGCCTTCTTCTACCGCATCC	60.533	60.000	0.00	0.00	0.00	3.51
526	4592	0.876342	GCCTTCTTCTACCGCATCCG	60.876	60.000	0.00	0.00	0.00	4.18
527	4593	0.460311	CCTTCTTCTACCGCATCCGT	59.540	55.000	0.00	0.00	0.00	4.69
528	4594	1.536284	CCTTCTTCTACCGCATCCGTC	60.536	57.143	0.00	0.00	0.00	4.79
529	4595	0.099968	TTCTTCTACCGCATCCGTCG	59.900	55.000	0.00	0.00	0.00	5.12
530	4596	1.944676	CTTCTACCGCATCCGTCGC	60.945	63.158	0.00	0.00	0.00	5.19
531	4597	3.420214	TTCTACCGCATCCGTCGCC	62.420	63.158	0.00	0.00	0.00	5.54
629	4695	0.846693	CGGAGATGGAGGGGGAAAAT	59.153	55.000	0.00	0.00	0.00	1.82
900	4973	1.226542	GCCCAAGCTAAGTACCCCC	59.773	63.158	0.00	0.00	35.50	5.40
901	4974	1.279749	GCCCAAGCTAAGTACCCCCT	61.280	60.000	0.00	0.00	35.50	4.79
902	4975	1.973201	GCCCAAGCTAAGTACCCCCTA	60.973	57.143	0.00	0.00	35.50	3.53
903	4976	2.047830	CCCAAGCTAAGTACCCCCTAG	58.952	57.143	0.00	0.00	0.00	3.02
904	4977	2.359994	CCCAAGCTAAGTACCCCCTAGA	60.360	54.545	0.00	0.00	0.00	2.43
905	4978	2.699321	CCAAGCTAAGTACCCCCTAGAC	59.301	54.545	0.00	0.00	0.00	2.59
921	4994	4.224370	CCCTAGACTACTAACCAAGGCAAA	59.776	45.833	0.00	0.00	0.00	3.68
936	5009	1.336332	GGCAAAACACACACACACACA	60.336	47.619	0.00	0.00	0.00	3.72
937	5010	2.398498	GCAAAACACACACACACACAA	58.602	42.857	0.00	0.00	0.00	3.33
938	5011	2.154772	GCAAAACACACACACACACAAC	59.845	45.455	0.00	0.00	0.00	3.32
939	5012	3.375642	CAAAACACACACACACACAACA	58.624	40.909	0.00	0.00	0.00	3.33
940	5013	2.697431	AACACACACACACACAACAC	57.303	45.000	0.00	0.00	0.00	3.32
941	5014	1.598882	ACACACACACACACAACACA	58.401	45.000	0.00	0.00	0.00	3.72
942	5015	1.265635	ACACACACACACACAACACAC	59.734	47.619	0.00	0.00	0.00	3.82
943	5016	1.265365	CACACACACACACAACACACA	59.735	47.619	0.00	0.00	0.00	3.72
944	5017	1.265635	ACACACACACACAACACACAC	59.734	47.619	0.00	0.00	0.00	3.82
945	5018	1.265365	CACACACACACAACACACACA	59.735	47.619	0.00	0.00	0.00	3.72
946	5019	1.265635	ACACACACACAACACACACAC	59.734	47.619	0.00	0.00	0.00	3.82
987	5060	0.767375	AGCCTGAGCCTGAGAACAAA	59.233	50.000	0.00	0.00	41.25	2.83
1221	5294	2.202878	AAGCGCGCCATGTACGAT	60.203	55.556	30.33	1.73	0.00	3.73
1435	5514	1.531423	TGCTTCGTACGAGGACTCTT	58.469	50.000	29.03	0.00	0.00	2.85
1478	5560	1.337071	CTTATCTACCAGCCGCGAGAA	59.663	52.381	8.23	0.00	0.00	2.87
1518	5600	1.460689	AGGTGTGGTCGGGGAGAAA	60.461	57.895	0.00	0.00	0.00	2.52
1571	5653	2.027745	TCATGGTGAGAAGAACTGAGGC	60.028	50.000	0.00	0.00	0.00	4.70
1584	5666	1.856265	CTGAGGCGGAAACCAGCAAC	61.856	60.000	0.00	0.00	34.54	4.17
1644	5726	1.773856	TTGGTGGGATCGGCAAGACA	61.774	55.000	0.00	0.00	0.00	3.41
1884	5969	1.317431	TGTGGAGCCATGAAGCATGC	61.317	55.000	10.51	10.51	40.20	4.06
1913	6001	2.298729	TGCTTGAAACACCCCTTAATGC	59.701	45.455	0.00	0.00	0.00	3.56
2263	6351	3.694734	GCATACAACATATGCACACCAC	58.305	45.455	12.82	0.00	46.89	4.16
2264	6352	3.128415	GCATACAACATATGCACACCACA	59.872	43.478	12.82	0.00	46.89	4.17
2265	6353	4.661125	CATACAACATATGCACACCACAC	58.339	43.478	1.58	0.00	0.00	3.82
2266	6354	2.580962	ACAACATATGCACACCACACA	58.419	42.857	1.58	0.00	0.00	3.72
2267	6355	2.293122	ACAACATATGCACACCACACAC	59.707	45.455	1.58	0.00	0.00	3.82
2268	6356	2.268762	ACATATGCACACCACACACA	57.731	45.000	1.58	0.00	0.00	3.72
2269	6357	1.879380	ACATATGCACACCACACACAC	59.121	47.619	1.58	0.00	0.00	3.82
2270	6358	1.878734	CATATGCACACCACACACACA	59.121	47.619	0.00	0.00	0.00	3.72
2333	6421	9.727627	GTTTTAATCAAATCTAGCTTGATGAGG	57.272	33.333	11.51	4.81	41.56	3.86
2387	6475	7.330946	GGCAATTTAATTTCAGTACCTTGGTTC	59.669	37.037	0.00	0.00	0.00	3.62
2881	6970	0.517316	CCTAAAAGTGCTGCGTGGTC	59.483	55.000	0.00	0.00	0.00	4.02
2893	6982	1.539388	TGCGTGGTCTAAAAATGGCAG	59.461	47.619	0.00	0.00	0.00	4.85
3010	7099	6.387220	AGGAACCTTATAGAGCCAGTTACAAT	59.613	38.462	0.00	0.00	0.00	2.71
3187	7301	3.005554	CTGGAGTTCCTTACATGCACAG	58.994	50.000	0.00	0.00	36.82	3.66
3278	7392	2.223829	CCCTGCCTACGAACTCTACATG	60.224	54.545	0.00	0.00	0.00	3.21
3491	7605	4.944317	GGCAGCTGAGGTATCTTAACTTTT	59.056	41.667	20.43	0.00	0.00	2.27
3550	7664	9.793259	TTCTGTGTTCTAACAAATCTAAGGAAT	57.207	29.630	0.00	0.00	41.21	3.01
3568	7682	3.726517	CTGCGTGGGTTTCCAGCG	61.727	66.667	0.00	0.00	45.05	5.18
3696	7810	2.298163	CAAAGGCAAAGCTTGGTGAGAT	59.702	45.455	0.00	0.00	0.00	2.75
3891	9288	1.077429	GGCTCCCAAGGTGGATGAC	60.077	63.158	0.00	0.00	40.96	3.06
4000	9400	0.112995	AGCTCCCATGTTTGCAGGAA	59.887	50.000	0.00	0.00	0.00	3.36
4004	9404	3.592059	CTCCCATGTTTGCAGGAAATTG	58.408	45.455	0.00	0.00	0.00	2.32
4008	9408	3.742369	CCATGTTTGCAGGAAATTGACAC	59.258	43.478	0.00	0.00	0.00	3.67
4055	9455	3.010420	GTTGGACCTGAATTCCTACAGC	58.990	50.000	2.27	0.00	38.37	4.40
4058	9458	0.919710	ACCTGAATTCCTACAGCCCC	59.080	55.000	2.27	0.00	33.40	5.80
4061	9461	1.561542	CTGAATTCCTACAGCCCCACT	59.438	52.381	2.27	0.00	0.00	4.00
4062	9462	1.992557	TGAATTCCTACAGCCCCACTT	59.007	47.619	2.27	0.00	0.00	3.16
4063	9463	3.186283	TGAATTCCTACAGCCCCACTTA	58.814	45.455	2.27	0.00	0.00	2.24
4064	9464	3.199946	TGAATTCCTACAGCCCCACTTAG	59.800	47.826	2.27	0.00	0.00	2.18
4067	9467	1.327690	CCTACAGCCCCACTTAGCGA	61.328	60.000	0.00	0.00	0.00	4.93
4098	9522	5.004821	CGTTTCCGAGATTACAGAAGATGTG	59.995	44.000	0.00	0.00	38.50	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	6.019075	TCGTATATGTTTTGTAGCTCATGCAC	60.019	38.462	0.00	0.00	42.74	4.57
20	21	7.967854	TGCTTTTGGAAAGTTTCATCGTATATG	59.032	33.333	17.16	0.27	0.00	1.78
36	37	6.491745	TGTTTACCTGTGATATGCTTTTGGAA	59.508	34.615	0.00	0.00	0.00	3.53
100	3299	7.148355	TCTCCAAAACGAGTAACAACTTTTT	57.852	32.000	0.00	0.00	0.00	1.94
114	3313	6.088217	CGTATGTAGCTATGATCTCCAAAACG	59.912	42.308	0.00	0.15	0.00	3.60
120	3319	5.899120	TTCCGTATGTAGCTATGATCTCC	57.101	43.478	0.00	0.00	0.00	3.71
138	3337	5.614760	CGGTGAAAACAGTATACTTTTCCG	58.385	41.667	20.05	16.38	36.10	4.30
141	3340	6.380095	TTGCGGTGAAAACAGTATACTTTT	57.620	33.333	1.56	2.29	0.00	2.27
142	3341	6.380095	TTTGCGGTGAAAACAGTATACTTT	57.620	33.333	1.56	0.00	0.00	2.66
143	3342	6.380095	TTTTGCGGTGAAAACAGTATACTT	57.620	33.333	1.56	0.00	0.00	2.24
144	3343	6.380095	TTTTTGCGGTGAAAACAGTATACT	57.620	33.333	0.00	0.00	0.00	2.12
203	3402	4.515191	TGACCAAGAAAGCTGATGTGTAAC	59.485	41.667	0.00	0.00	37.35	2.50
204	3403	4.713553	TGACCAAGAAAGCTGATGTGTAA	58.286	39.130	0.00	0.00	0.00	2.41
206	3405	3.213206	TGACCAAGAAAGCTGATGTGT	57.787	42.857	0.00	0.00	0.00	3.72
207	3406	4.778534	ATTGACCAAGAAAGCTGATGTG	57.221	40.909	0.00	0.00	0.00	3.21
208	3407	5.563475	CGAAATTGACCAAGAAAGCTGATGT	60.563	40.000	0.00	0.00	0.00	3.06
210	3409	4.761739	TCGAAATTGACCAAGAAAGCTGAT	59.238	37.500	0.00	0.00	0.00	2.90
211	3410	4.133820	TCGAAATTGACCAAGAAAGCTGA	58.866	39.130	0.00	0.00	0.00	4.26
212	3411	4.470462	CTCGAAATTGACCAAGAAAGCTG	58.530	43.478	0.00	0.00	0.00	4.24
214	3413	3.253432	ACCTCGAAATTGACCAAGAAAGC	59.747	43.478	0.00	0.00	0.00	3.51
215	3414	6.743575	ATACCTCGAAATTGACCAAGAAAG	57.256	37.500	0.00	0.00	0.00	2.62
216	3415	7.367285	CAAATACCTCGAAATTGACCAAGAAA	58.633	34.615	0.00	0.00	0.00	2.52
217	3416	6.072175	CCAAATACCTCGAAATTGACCAAGAA	60.072	38.462	0.00	0.00	0.00	2.52
220	3419	4.461081	CCCAAATACCTCGAAATTGACCAA	59.539	41.667	0.00	0.00	0.00	3.67
222	3421	3.181490	GCCCAAATACCTCGAAATTGACC	60.181	47.826	0.00	0.00	0.00	4.02
223	3422	3.181490	GGCCCAAATACCTCGAAATTGAC	60.181	47.826	0.00	0.00	0.00	3.18
224	3423	3.020984	GGCCCAAATACCTCGAAATTGA	58.979	45.455	0.00	0.00	0.00	2.57
226	3425	3.023832	CAGGCCCAAATACCTCGAAATT	58.976	45.455	0.00	0.00	32.56	1.82
267	4331	0.885879	CGGTAGGCACTGTAGACACA	59.114	55.000	0.00	0.00	41.52	3.72
268	4332	0.886563	ACGGTAGGCACTGTAGACAC	59.113	55.000	0.56	0.00	42.67	3.67
301	4366	2.189521	CACCCCTGATACCACGGC	59.810	66.667	0.00	0.00	0.00	5.68
307	4372	1.067212	CTAGCACGTCACCCCTGATAC	59.933	57.143	0.00	0.00	0.00	2.24
319	4384	2.042843	AGCCCTAGCCTAGCACGT	60.043	61.111	0.00	0.00	41.25	4.49
395	4461	0.394565	AGGACAGGCGGATCTAATGC	59.605	55.000	0.00	0.00	0.00	3.56
397	4463	0.394565	GCAGGACAGGCGGATCTAAT	59.605	55.000	0.00	0.00	0.00	1.73
399	4465	2.134287	GGCAGGACAGGCGGATCTA	61.134	63.158	0.00	0.00	0.00	1.98
411	4477	3.075005	GTAGAGTGGCCGGCAGGA	61.075	66.667	30.85	8.59	41.02	3.86
502	4568	2.577593	GGTAGAAGAAGGCCGCGT	59.422	61.111	4.92	0.00	0.00	6.01
506	4572	0.533085	GGATGCGGTAGAAGAAGGCC	60.533	60.000	0.00	0.00	0.00	5.19
507	4573	0.876342	CGGATGCGGTAGAAGAAGGC	60.876	60.000	0.00	0.00	0.00	4.35
508	4574	0.460311	ACGGATGCGGTAGAAGAAGG	59.540	55.000	12.44	0.00	0.00	3.46
509	4575	1.841450	GACGGATGCGGTAGAAGAAG	58.159	55.000	12.44	0.00	0.00	2.85
510	4576	0.099968	CGACGGATGCGGTAGAAGAA	59.900	55.000	12.44	0.00	0.00	2.52
511	4577	1.725665	CGACGGATGCGGTAGAAGA	59.274	57.895	12.44	0.00	0.00	2.87
512	4578	1.944676	GCGACGGATGCGGTAGAAG	60.945	63.158	12.44	0.00	0.00	2.85
513	4579	2.103538	GCGACGGATGCGGTAGAA	59.896	61.111	12.44	0.00	0.00	2.10
514	4580	3.896133	GGCGACGGATGCGGTAGA	61.896	66.667	12.44	0.00	0.00	2.59
613	4679	0.846693	CCGATTTTCCCCCTCCATCT	59.153	55.000	0.00	0.00	0.00	2.90
655	4721	2.626780	CCAGAGTCACCAGCGTCGA	61.627	63.158	0.00	0.00	0.00	4.20
662	4728	3.680786	CGGTCGCCAGAGTCACCA	61.681	66.667	0.00	0.00	0.00	4.17
900	4973	6.147328	GTGTTTTGCCTTGGTTAGTAGTCTAG	59.853	42.308	0.00	0.00	0.00	2.43
901	4974	5.993441	GTGTTTTGCCTTGGTTAGTAGTCTA	59.007	40.000	0.00	0.00	0.00	2.59
902	4975	4.820173	GTGTTTTGCCTTGGTTAGTAGTCT	59.180	41.667	0.00	0.00	0.00	3.24
903	4976	4.577283	TGTGTTTTGCCTTGGTTAGTAGTC	59.423	41.667	0.00	0.00	0.00	2.59
904	4977	4.337274	GTGTGTTTTGCCTTGGTTAGTAGT	59.663	41.667	0.00	0.00	0.00	2.73
905	4978	4.336993	TGTGTGTTTTGCCTTGGTTAGTAG	59.663	41.667	0.00	0.00	0.00	2.57
921	4994	1.950216	TGTGTTGTGTGTGTGTGTGTT	59.050	42.857	0.00	0.00	0.00	3.32
936	5009	5.392595	GGTTAATCAACAGTGTGTGTGTGTT	60.393	40.000	0.00	0.00	40.26	3.32
937	5010	4.095782	GGTTAATCAACAGTGTGTGTGTGT	59.904	41.667	0.00	0.00	40.26	3.72
938	5011	4.095632	TGGTTAATCAACAGTGTGTGTGTG	59.904	41.667	0.00	0.00	40.26	3.82
939	5012	4.265893	TGGTTAATCAACAGTGTGTGTGT	58.734	39.130	0.00	0.00	40.26	3.72
940	5013	4.891627	TGGTTAATCAACAGTGTGTGTG	57.108	40.909	0.00	0.00	40.26	3.82
941	5014	5.827797	AGATTGGTTAATCAACAGTGTGTGT	59.172	36.000	2.56	0.00	44.14	3.72
942	5015	6.317789	AGATTGGTTAATCAACAGTGTGTG	57.682	37.500	2.56	0.00	44.14	3.82
943	5016	6.959639	AAGATTGGTTAATCAACAGTGTGT	57.040	33.333	2.56	0.00	44.14	3.72
944	5017	7.538678	GCTAAAGATTGGTTAATCAACAGTGTG	59.461	37.037	2.56	0.00	44.14	3.82
945	5018	7.309194	GGCTAAAGATTGGTTAATCAACAGTGT	60.309	37.037	2.56	0.00	44.14	3.55
946	5019	7.029563	GGCTAAAGATTGGTTAATCAACAGTG	58.970	38.462	2.56	0.00	44.14	3.66
987	5060	2.380064	TGGCCATGGTTTCTGTTTCT	57.620	45.000	14.67	0.00	0.00	2.52
1435	5514	1.630369	AGAGGAATGTACCTTGCTGCA	59.370	47.619	9.54	0.00	40.73	4.41
1478	5560	2.893398	GGTCGAGCTCCCACGATT	59.107	61.111	8.47	0.00	40.50	3.34
1518	5600	2.224523	TGCCCTTGTGTCTTCTTCGATT	60.225	45.455	0.00	0.00	0.00	3.34
1571	5653	2.250939	TCTGCGTTGCTGGTTTCCG	61.251	57.895	0.00	0.00	0.00	4.30
1584	5666	1.570813	TGACTCTGTTGTTGTCTGCG	58.429	50.000	0.00	0.00	0.00	5.18
1884	5969	1.334960	GGTGTTTCAAGCACATCACCG	60.335	52.381	6.71	0.00	38.51	4.94
1913	6001	4.162690	GGCTACCTCGGGCCACAG	62.163	72.222	4.39	0.00	46.84	3.66
1947	6035	2.166664	ACGGGCAACTCTTGTATCTCTC	59.833	50.000	0.00	0.00	0.00	3.20
2097	6185	3.845781	TCTCATGTCCAAATAGGGAGC	57.154	47.619	0.00	0.00	37.71	4.70
2263	6351	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2264	6352	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
2265	6353	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2266	6354	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
2267	6355	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2268	6356	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
2269	6357	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2270	6358	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
2333	6421	0.687354	TGGGAGAGAAGCTGTTCACC	59.313	55.000	5.86	5.86	34.82	4.02
2387	6475	1.926511	GCAAGTGGGGATTCGCTGTG	61.927	60.000	0.40	0.00	0.00	3.66
2881	6970	7.068103	TCCACATACCAATACTGCCATTTTTAG	59.932	37.037	0.00	0.00	0.00	1.85
2893	6982	5.408604	CCTTCGCTAATCCACATACCAATAC	59.591	44.000	0.00	0.00	0.00	1.89
3187	7301	8.247562	ACTAATATCAGTGTTCTCAGTGTCTTC	58.752	37.037	3.53	0.00	43.31	2.87
3278	7392	8.441608	CAATACAGCAACATCTATAGATTCTGC	58.558	37.037	25.43	25.43	38.70	4.26
3550	7664	2.281484	GCTGGAAACCCACGCAGA	60.281	61.111	0.00	0.00	32.09	4.26
3568	7682	1.267806	CACCAAACACCATCTGTCTGC	59.732	52.381	0.00	0.00	30.29	4.26
3696	7810	4.974645	AACAAGTGGGTCAGATGAACTA	57.025	40.909	0.00	0.00	31.02	2.24
3891	9288	1.416813	GACCGCTGCTGATCTTGACG	61.417	60.000	0.00	0.00	0.00	4.35
4000	9400	3.419759	GCGCGTCGGGTGTCAATT	61.420	61.111	8.43	0.00	0.00	2.32
4055	9455	3.771160	AGCCGTCGCTAAGTGGGG	61.771	66.667	0.00	0.00	46.08	4.96
4058	9458	3.545481	CGCAGCCGTCGCTAAGTG	61.545	66.667	0.00	0.00	46.25	3.16
4098	9522	6.126409	TCCCATTCCACCATATCAACTAAAC	58.874	40.000	0.00	0.00	0.00	2.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.