AutoCloner

Multiple sequence alignment - TraesCS6B01G228000

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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	TraesCS6B01G228000	chr6B	100.000	6077	0	0	1	6077	355874837	355880913	0.000000e+00	11223.0
1	TraesCS6B01G228000	chr6B	96.295	3914	126	11	16	3916	343409201	343405294	0.000000e+00	6407.0
2	TraesCS6B01G228000	chr6B	95.841	3607	129	13	1	3593	356870048	356873647	0.000000e+00	5810.0
3	TraesCS6B01G228000	chr6B	96.381	3067	100	8	15	3074	405326665	405323603	0.000000e+00	5038.0
4	TraesCS6B01G228000	chr6B	95.806	2170	84	6	3912	6077	341735821	341733655	0.000000e+00	3496.0
5	TraesCS6B01G228000	chr6B	97.792	317	6	1	3597	3913	356873733	356874048	4.140000e-151	545.0
6	TraesCS6B01G228000	chr6B	82.891	339	43	10	1644	1970	269686092	269685757	2.140000e-74	291.0
7	TraesCS6B01G228000	chr6B	78.816	321	50	9	562	878	191974629	191974323	3.710000e-47	200.0
8	TraesCS6B01G228000	chr6B	84.564	149	20	3	2143	2289	191963619	191963472	1.770000e-30	145.0
9	TraesCS6B01G228000	chr2B	95.624	2171	82	11	3912	6077	345639091	345636929	0.000000e+00	3470.0
10	TraesCS6B01G228000	chr2B	95.166	2172	95	8	3912	6077	591519654	591521821	0.000000e+00	3421.0
11	TraesCS6B01G228000	chr7B	95.262	2174	91	6	3912	6077	246865931	246863762	0.000000e+00	3434.0
12	TraesCS6B01G228000	chr7B	95.021	2169	97	9	3912	6077	399139071	399141231	0.000000e+00	3397.0
13	TraesCS6B01G228000	chr7B	94.686	2183	103	9	3904	6077	73610836	73613014	0.000000e+00	3376.0
14	TraesCS6B01G228000	chr7B	82.249	169	18	8	3754	3916	22136737	22136575	1.060000e-27	135.0
15	TraesCS6B01G228000	chr3B	95.258	2172	92	8	3912	6077	284028555	284030721	0.000000e+00	3430.0
16	TraesCS6B01G228000	chr3B	95.025	2171	94	11	3912	6077	461837502	461835341	0.000000e+00	3398.0
17	TraesCS6B01G228000	chr5B	95.126	2175	92	7	3912	6077	422904804	422902635	0.000000e+00	3417.0
18	TraesCS6B01G228000	chr5B	82.997	347	46	6	1635	1970	261359354	261359010	9.900000e-78	302.0
19	TraesCS6B01G228000	chr5B	82.421	347	49	6	1635	1970	257827815	257828160	5.960000e-75	292.0
20	TraesCS6B01G228000	chr5B	81.897	348	49	7	1635	1970	258006939	258006594	1.290000e-71	281.0
21	TraesCS6B01G228000	chr5B	82.915	199	28	6	3721	3913	258004024	258003826	2.250000e-39	174.0
22	TraesCS6B01G228000	chr5B	82.090	201	26	8	3720	3913	257835620	257835817	4.870000e-36	163.0
23	TraesCS6B01G228000	chr5B	82.065	184	26	4	2113	2289	257833995	257834178	3.790000e-32	150.0
24	TraesCS6B01G228000	chr5B	82.386	176	22	7	3745	3914	261346433	261346261	1.770000e-30	145.0
25	TraesCS6B01G228000	chr5B	83.333	150	22	3	2143	2289	258005614	258005465	1.060000e-27	135.0
26	TraesCS6B01G228000	chr4D	92.256	891	56	8	1635	2517	153903166	153902281	0.000000e+00	1251.0
27	TraesCS6B01G228000	chr4D	94.412	340	17	1	1296	1635	153926741	153926404	6.980000e-144	521.0
28	TraesCS6B01G228000	chr4D	94.613	297	15	1	3618	3913	153902006	153901710	5.550000e-125	459.0
29	TraesCS6B01G228000	chr4D	91.197	284	22	2	3374	3657	153902284	153902004	3.440000e-102	383.0
30	TraesCS6B01G228000	chr4D	100.000	29	0	0	2385	2413	478049711	478049739	3.000000e-03	54.7
31	TraesCS6B01G228000	chr6D	89.286	196	18	3	1644	1837	256574421	256574227	6.090000e-60	243.0
32	TraesCS6B01G228000	chr6D	83.333	174	28	1	3742	3914	256574221	256574048	6.300000e-35	159.0
33	TraesCS6B01G228000	chr7D	79.348	184	31	7	3735	3913	553981333	553981152	8.270000e-24	122.0
34	TraesCS6B01G228000	chr3D	94.595	37	0	1	2400	2436	47782006	47782040	8.510000e-04	56.5

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	TraesCS6B01G228000	chr6B	355874837	355880913	6076	False	11223.000000	11223	100.000000	1	6077	1	chr6B.!!$F1	6076
1	TraesCS6B01G228000	chr6B	343405294	343409201	3907	True	6407.000000	6407	96.295000	16	3916	1	chr6B.!!$R5	3900
2	TraesCS6B01G228000	chr6B	405323603	405326665	3062	True	5038.000000	5038	96.381000	15	3074	1	chr6B.!!$R6	3059
3	TraesCS6B01G228000	chr6B	341733655	341735821	2166	True	3496.000000	3496	95.806000	3912	6077	1	chr6B.!!$R4	2165
4	TraesCS6B01G228000	chr6B	356870048	356874048	4000	False	3177.500000	5810	96.816500	1	3913	2	chr6B.!!$F2	3912
5	TraesCS6B01G228000	chr2B	345636929	345639091	2162	True	3470.000000	3470	95.624000	3912	6077	1	chr2B.!!$R1	2165
6	TraesCS6B01G228000	chr2B	591519654	591521821	2167	False	3421.000000	3421	95.166000	3912	6077	1	chr2B.!!$F1	2165
7	TraesCS6B01G228000	chr7B	246863762	246865931	2169	True	3434.000000	3434	95.262000	3912	6077	1	chr7B.!!$R2	2165
8	TraesCS6B01G228000	chr7B	399139071	399141231	2160	False	3397.000000	3397	95.021000	3912	6077	1	chr7B.!!$F2	2165
9	TraesCS6B01G228000	chr7B	73610836	73613014	2178	False	3376.000000	3376	94.686000	3904	6077	1	chr7B.!!$F1	2173
10	TraesCS6B01G228000	chr3B	284028555	284030721	2166	False	3430.000000	3430	95.258000	3912	6077	1	chr3B.!!$F1	2165
11	TraesCS6B01G228000	chr3B	461835341	461837502	2161	True	3398.000000	3398	95.025000	3912	6077	1	chr3B.!!$R1	2165
12	TraesCS6B01G228000	chr5B	422902635	422904804	2169	True	3417.000000	3417	95.126000	3912	6077	1	chr5B.!!$R3	2165
13	TraesCS6B01G228000	chr4D	153901710	153903166	1456	True	697.666667	1251	92.688667	1635	3913	3	chr4D.!!$R2	2278

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
756	762	0.033699	GGGTCTGGTCTAGGTACCGT	60.034	60.0	6.18	0.00	42.91	4.83	F
1210	1216	0.107654	AATGAAGCGGTACCAGCTCC	60.108	55.0	24.77	16.83	45.31	4.70	F
1933	1942	0.391130	TCCGCGGTCCATCTCTTTTG	60.391	55.0	27.15	0.00	0.00	2.44	F
3679	3823	0.109226	CACGGGAGAGGACGACTTTC	60.109	60.0	0.00	0.00	0.00	2.62	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2692	2710	1.296392	CATGACCAGAACCGCTCCA	59.704	57.895	0.00	0.0	0.00	3.86	R
3180	3199	0.844661	ATATGGGCGCCCCTTGGATA	60.845	55.000	41.75	30.4	45.70	2.59	R
3739	3883	0.456221	ATGCCACCGAAGAGACTACG	59.544	55.000	0.00	0.0	0.00	3.51	R
5561	5721	1.546029	ACTCTGAATGCAGTGCTACGA	59.454	47.619	17.60	5.0	42.84	3.43	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
76	79	2.451490	TCAGTTGTTTTGTGGCCAAGA	58.549	42.857	7.24	0.00	0.00	3.02
180	186	7.201609	GGTCTCATATTAAATGTCGCTCAAACA	60.202	37.037	0.00	0.00	0.00	2.83
191	197	5.961272	TGTCGCTCAAACAGATGTATCTTA	58.039	37.500	0.00	0.00	34.22	2.10
215	221	9.826574	TTACACTTTGATACGGCTAGATATTTT	57.173	29.630	0.00	0.00	0.00	1.82
441	447	6.037172	TCTGCGGTTTCTATATCTTTTTGCTC	59.963	38.462	0.00	0.00	0.00	4.26
442	448	5.645929	TGCGGTTTCTATATCTTTTTGCTCA	59.354	36.000	0.00	0.00	0.00	4.26
602	608	2.232941	TGTTGTCTACCGATGAACTCCC	59.767	50.000	0.00	0.00	0.00	4.30
606	612	4.543689	TGTCTACCGATGAACTCCCTTAT	58.456	43.478	0.00	0.00	0.00	1.73
628	634	0.526954	CCGCTAGTAATCGGCGTTGT	60.527	55.000	6.85	0.00	46.23	3.32
652	658	1.151810	TCACTCCCAAGCTCCCCTT	60.152	57.895	0.00	0.00	0.00	3.95
653	659	0.118346	TCACTCCCAAGCTCCCCTTA	59.882	55.000	0.00	0.00	31.00	2.69
675	681	4.916041	ATTTCCTCTGTTGGTCTCATGA	57.084	40.909	0.00	0.00	0.00	3.07
756	762	0.033699	GGGTCTGGTCTAGGTACCGT	60.034	60.000	6.18	0.00	42.91	4.83
943	949	1.202976	AGCAGCATGGAGTTTGAGGTT	60.203	47.619	0.00	0.00	35.86	3.50
1025	1031	1.065998	GGTTTGTATCCACACCGGCTA	60.066	52.381	0.00	0.00	32.06	3.93
1035	1041	3.157680	ACCGGCTAGTTGCAAGGT	58.842	55.556	0.00	9.43	45.03	3.50
1143	1149	0.475044	TAACAGGCGGAGTTTTGGGT	59.525	50.000	0.00	0.00	0.00	4.51
1187	1193	0.960364	GCTTGGAATTGCCGAGGACA	60.960	55.000	0.00	0.00	46.81	4.02
1188	1194	1.755179	CTTGGAATTGCCGAGGACAT	58.245	50.000	0.00	0.00	43.53	3.06
1191	1197	1.557371	TGGAATTGCCGAGGACATACA	59.443	47.619	0.00	0.00	40.66	2.29
1210	1216	0.107654	AATGAAGCGGTACCAGCTCC	60.108	55.000	24.77	16.83	45.31	4.70
1211	1217	0.978146	ATGAAGCGGTACCAGCTCCT	60.978	55.000	24.77	14.47	45.31	3.69
1242	1250	7.489113	CCTTTAGTTTAATTTTGCGATGCAGAT	59.511	33.333	0.00	0.00	40.61	2.90
1250	1258	3.457610	TTGCGATGCAGATCATACAGA	57.542	42.857	0.00	0.00	40.61	3.41
1283	1291	2.684881	CCTGAGGACATTGGTTATGCAC	59.315	50.000	0.00	0.00	37.81	4.57
1612	1620	5.184287	TGATGAGTGGACGTTGTCACTATAA	59.816	40.000	16.36	8.78	33.68	0.98
1614	1622	4.763279	TGAGTGGACGTTGTCACTATAAGA	59.237	41.667	16.36	1.74	33.68	2.10
1787	1796	7.715249	TGCAGGAAACTAATTATCCATGTACTC	59.285	37.037	6.41	0.00	40.21	2.59
1933	1942	0.391130	TCCGCGGTCCATCTCTTTTG	60.391	55.000	27.15	0.00	0.00	2.44
1953	1962	7.442364	TCTTTTGGTGACTCTTGAGAATGTTAG	59.558	37.037	4.49	0.00	0.00	2.34
1972	1981	9.920946	AATGTTAGGTATAGATGTCCATGTTTT	57.079	29.630	0.00	0.00	0.00	2.43
2094	2108	3.964688	TGAGTGGTTCTCTCAGTTGGTAA	59.035	43.478	0.00	0.00	43.13	2.85
2095	2109	4.407621	TGAGTGGTTCTCTCAGTTGGTAAA	59.592	41.667	0.00	0.00	43.13	2.01
2096	2110	5.104693	TGAGTGGTTCTCTCAGTTGGTAAAA	60.105	40.000	0.00	0.00	43.13	1.52
2137	2151	3.999663	GCTTCTAGCTATACCTGCCAATG	59.000	47.826	0.00	0.00	38.45	2.82
2309	2324	3.816994	ACCCTATACTTTTTCGGATGGC	58.183	45.455	0.00	0.00	0.00	4.40
2331	2346	5.397559	GGCTGGGGTACAACTTACATATCTT	60.398	44.000	0.00	0.00	0.00	2.40
2523	2540	3.118038	GGTTGCCATCCCTCTATTGTACA	60.118	47.826	0.00	0.00	0.00	2.90
2692	2710	8.116026	ACTTGAGGGAAATGTAAGTATGGAAAT	58.884	33.333	0.00	0.00	30.45	2.17
2909	2928	2.887360	CGCTGGAAGGGGCAAATG	59.113	61.111	0.00	0.00	44.19	2.32
2962	2981	4.627035	AGAGCAAACTTTGAACACAAAAGC	59.373	37.500	5.65	0.00	33.92	3.51
3141	3160	1.147600	GGTGTCGTTGGGTGGAGTT	59.852	57.895	0.00	0.00	0.00	3.01
3180	3199	2.787473	TCCAACAGAGATTTGGCGAT	57.213	45.000	0.00	0.00	42.96	4.58
3211	3230	1.670811	CGCCCATATGAAGGTGAACAC	59.329	52.381	3.65	0.00	35.58	3.32
3246	3265	2.310233	GCGCTTGCAAGTCTGACGA	61.310	57.895	26.55	0.00	38.92	4.20
3248	3267	0.111089	CGCTTGCAAGTCTGACGAAC	60.111	55.000	26.55	6.59	0.00	3.95
3286	3305	0.320683	TTCAGGTGTGCGTGATGGAG	60.321	55.000	0.00	0.00	38.98	3.86
3326	3345	1.003108	TACATTACATGTGTGCGCCG	58.997	50.000	9.11	0.00	44.60	6.46
3349	3368	4.242336	TCCAGTCTCTGATCTAGCTTGA	57.758	45.455	0.00	0.00	32.44	3.02
3427	3450	1.783284	GGGCAAGTGCTAACAAAAGC	58.217	50.000	2.85	0.00	43.08	3.51
3460	3484	2.288666	GTTAGCTTGATCAATCCGGCA	58.711	47.619	16.86	3.76	0.00	5.69
3474	3498	2.267351	CGGCATCCACAACTTGGCA	61.267	57.895	0.00	0.00	46.47	4.92
3595	3701	4.973168	AGCAATCAACCTCTTGTACTTCA	58.027	39.130	0.00	0.00	0.00	3.02
3599	3705	4.395959	TCAACCTCTTGTACTTCACGTT	57.604	40.909	0.00	0.00	0.00	3.99
3632	3775	3.673594	GCTTCGTAGAGTTTGAGCTAGCA	60.674	47.826	18.83	0.00	38.43	3.49
3679	3823	0.109226	CACGGGAGAGGACGACTTTC	60.109	60.000	0.00	0.00	0.00	2.62
3739	3883	5.359009	GTGGGTTTTTCTAGGGTATAAAGGC	59.641	44.000	0.00	0.00	0.00	4.35
3946	4091	1.153842	GGGTTTGGCATACGCAAGC	60.154	57.895	17.74	5.06	45.62	4.01
4002	4147	1.140052	TCAAGAGAAGGGACGCACAAA	59.860	47.619	0.00	0.00	0.00	2.83
4062	4207	3.834489	TCAAAAAGGATTGGCTGCAAA	57.166	38.095	0.50	0.00	0.00	3.68
4078	4223	4.645956	CTGCAAAGCAAAGATTAGAGTCG	58.354	43.478	0.00	0.00	38.41	4.18
4261	4406	3.181468	ACATGCTCAGATGATGTCGATGT	60.181	43.478	0.00	0.00	0.00	3.06
4315	4460	0.750546	ACATACTAGCCGCGACTGGA	60.751	55.000	13.58	0.00	0.00	3.86
4326	4472	3.255725	CCGCGACTGGATAACAAGTAAA	58.744	45.455	8.23	0.00	0.00	2.01
4427	4573	7.068103	TCTGAAAATGCAGGAAACAGAAGTTTA	59.932	33.333	9.70	0.00	39.98	2.01
4557	4703	5.771165	ACCGTGTAAGAAACATATTTTGGGT	59.229	36.000	0.00	0.00	41.10	4.51
4643	4789	9.284594	CGTATAAAACTAACAAATTCCACATGG	57.715	33.333	0.00	0.00	0.00	3.66
4686	4832	4.507710	GTGAACCATCATCTACAGAGCAA	58.492	43.478	0.00	0.00	38.01	3.91
4855	5010	7.716799	TTGGTGCACTTATATTTCTTCCATT	57.283	32.000	17.98	0.00	0.00	3.16
4971	5128	3.263170	TCCCACAAACTCTGCATAAGCTA	59.737	43.478	0.00	0.00	42.74	3.32
5005	5162	7.340699	GCATATCATGAAGAAGTACAAAGACG	58.659	38.462	0.00	0.00	0.00	4.18
5019	5176	1.248785	AAGACGACCTCGCCTTGCTA	61.249	55.000	0.00	0.00	40.42	3.49
5142	5300	2.553086	ACAACTTGTAAGGCGACGAAA	58.447	42.857	0.00	0.00	0.00	3.46
5192	5350	3.907894	GAGTGGATCTCGGCTTACTAG	57.092	52.381	0.00	0.00	33.25	2.57
5204	5362	7.166167	TCTCGGCTTACTAGAAGGAAATTTTT	58.834	34.615	0.00	0.00	0.00	1.94
5561	5721	7.750229	TGCAGATTTCAAAGAAACACTCTAT	57.250	32.000	0.00	0.00	32.46	1.98
5581	5741	1.546029	TCGTAGCACTGCATTCAGAGT	59.454	47.619	3.30	0.00	42.95	3.24
5621	5781	3.507233	ACCCGACAAAGTATCTCGTACAA	59.493	43.478	0.00	0.00	35.67	2.41
5676	5836	4.046286	AGGCATAATTTCCAAGTGGTCA	57.954	40.909	0.00	0.00	36.34	4.02
5677	5837	3.763897	AGGCATAATTTCCAAGTGGTCAC	59.236	43.478	0.00	0.00	36.34	3.67
5721	5881	3.990092	ACGAATGTGAGTGCAAACTCTA	58.010	40.909	7.35	0.00	37.62	2.43
5726	5886	4.400529	TGTGAGTGCAAACTCTAGACAA	57.599	40.909	7.35	0.00	37.62	3.18
5813	5977	9.841295	ACTTACTGAACTTTAAAAGTCCACATA	57.159	29.630	0.00	0.00	41.91	2.29
5966	6138	4.615912	GCTCTTTTGCGTCCATGTGTTATT	60.616	41.667	0.00	0.00	0.00	1.40
6059	6231	6.976349	GCAAGATCAGATGCAATGTTTGATAA	59.024	34.615	11.79	0.00	42.12	1.75
6063	6235	8.195436	AGATCAGATGCAATGTTTGATAAAAGG	58.805	33.333	0.00	0.00	0.00	3.11

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
180	186	6.924060	GCCGTATCAAAGTGTAAGATACATCT	59.076	38.462	11.08	0.00	42.52	2.90
191	197	8.732746	AAAAATATCTAGCCGTATCAAAGTGT	57.267	30.769	0.00	0.00	0.00	3.55
215	221	8.998377	CGTCCCATATTAATGTTGATCACATAA	58.002	33.333	0.00	0.00	46.23	1.90
441	447	3.642705	GCTAAAGCCCAACTCAGTTTTG	58.357	45.455	0.00	0.00	34.31	2.44
525	531	1.196012	GGGATCGGAACTTCTGGAGT	58.804	55.000	0.00	0.00	41.47	3.85
628	634	1.107114	GAGCTTGGGAGTGAGATCGA	58.893	55.000	0.00	0.00	0.00	3.59
652	658	6.173339	GTCATGAGACCAACAGAGGAAATTA	58.827	40.000	0.00	0.00	38.89	1.40
653	659	5.006386	GTCATGAGACCAACAGAGGAAATT	58.994	41.667	0.00	0.00	38.89	1.82
675	681	1.679032	GGAAGATAAGCAAGGTGGCGT	60.679	52.381	0.00	0.00	39.27	5.68
711	717	0.814010	GCACCAACGACCTGAACTGT	60.814	55.000	0.00	0.00	0.00	3.55
904	910	0.895530	TTCACTCGCTTACCTCCCAG	59.104	55.000	0.00	0.00	0.00	4.45
905	911	0.895530	CTTCACTCGCTTACCTCCCA	59.104	55.000	0.00	0.00	0.00	4.37
906	912	0.460459	GCTTCACTCGCTTACCTCCC	60.460	60.000	0.00	0.00	0.00	4.30
972	978	0.319405	GGCTGAAAAGTGCCTTGCAT	59.681	50.000	0.00	0.00	45.26	3.96
1025	1031	0.685097	TCCTTAGCGACCTTGCAACT	59.315	50.000	0.00	0.00	37.31	3.16
1035	1041	2.037251	GGCTTATCCACATCCTTAGCGA	59.963	50.000	0.00	0.00	34.01	4.93
1140	1146	1.548719	GGCACAAACCCAAATCTACCC	59.451	52.381	0.00	0.00	0.00	3.69
1143	1149	4.650972	ACTAGGCACAAACCCAAATCTA	57.349	40.909	0.00	0.00	0.00	1.98
1187	1193	2.170607	AGCTGGTACCGCTTCATTGTAT	59.829	45.455	20.83	1.74	32.98	2.29
1188	1194	1.553248	AGCTGGTACCGCTTCATTGTA	59.447	47.619	20.83	0.00	32.98	2.41
1191	1197	0.107654	GGAGCTGGTACCGCTTCATT	60.108	55.000	25.16	9.16	37.96	2.57
1210	1216	8.029642	TCGCAAAATTAAACTAAAGGAGAGAG	57.970	34.615	0.00	0.00	0.00	3.20
1211	1217	7.972832	TCGCAAAATTAAACTAAAGGAGAGA	57.027	32.000	0.00	0.00	0.00	3.10
1242	1250	2.965831	GGCAGGACACCTATCTGTATGA	59.034	50.000	0.00	0.00	29.64	2.15
1283	1291	5.008019	AGCAGCAAACATACGGAATAATCTG	59.992	40.000	0.00	0.00	37.98	2.90
1341	1349	5.201713	TGATAGCGAGTGAATAAAGAGGG	57.798	43.478	0.00	0.00	0.00	4.30
1402	1410	3.711190	GTGGATGGGGCCTCAATAAATTT	59.289	43.478	10.86	0.00	0.00	1.82
1787	1796	2.477863	GCCAGCCTTTTACATAAGCACG	60.478	50.000	0.00	0.00	0.00	5.34
1933	1942	5.153950	ACCTAACATTCTCAAGAGTCACC	57.846	43.478	0.00	0.00	0.00	4.02
1953	1962	8.603242	ACGATAAAAACATGGACATCTATACC	57.397	34.615	0.00	0.00	0.00	2.73
2029	2042	3.181454	TGGAAAGACAACAGAAGAGGTCC	60.181	47.826	0.00	0.00	0.00	4.46
2094	2108	7.446625	AGAAGCATGACTATTTCAGACTGTTTT	59.553	33.333	1.59	0.00	37.77	2.43
2095	2109	6.939163	AGAAGCATGACTATTTCAGACTGTTT	59.061	34.615	1.59	0.00	37.77	2.83
2096	2110	6.471146	AGAAGCATGACTATTTCAGACTGTT	58.529	36.000	1.59	0.00	37.77	3.16
2137	2151	4.851558	GTGGTGCAATTTTCTCGTATGAAC	59.148	41.667	0.00	0.00	0.00	3.18
2309	2324	6.538742	CACAAGATATGTAAGTTGTACCCCAG	59.461	42.308	0.00	0.00	41.46	4.45
2331	2346	5.034852	TGAGGACAGAGAAAAACATCACA	57.965	39.130	0.00	0.00	0.00	3.58
2635	2652	7.659390	ACTTTTGTGTTCAGGTTTTGATTGAAA	59.341	29.630	0.00	0.00	35.27	2.69
2692	2710	1.296392	CATGACCAGAACCGCTCCA	59.704	57.895	0.00	0.00	0.00	3.86
2759	2777	7.361889	GATCAACTATGCTTGATCGATGATT	57.638	36.000	0.54	0.00	44.05	2.57
2889	2908	2.142292	ATTTGCCCCTTCCAGCGACT	62.142	55.000	0.00	0.00	0.00	4.18
2905	2924	4.017222	TGGATCTCCAAGATTGTCCCATTT	60.017	41.667	0.00	0.00	44.35	2.32
2962	2981	2.089980	CAGAACTGATTCCTTGCCCTG	58.910	52.381	0.00	0.00	35.18	4.45
3141	3160	8.058235	TGTTGGATATCCTCAATTGTCCAATTA	58.942	33.333	21.87	14.56	40.30	1.40
3180	3199	0.844661	ATATGGGCGCCCCTTGGATA	60.845	55.000	41.75	30.40	45.70	2.59
3211	3230	1.660333	GCGCTTCCAAGTTTCACTTCG	60.660	52.381	0.00	0.00	36.03	3.79
3246	3265	7.123355	TGAAACCAATCTGAATTTCCAAGTT	57.877	32.000	0.00	0.00	31.39	2.66
3248	3267	6.161381	CCTGAAACCAATCTGAATTTCCAAG	58.839	40.000	0.00	0.00	31.39	3.61
3326	3345	4.826733	TCAAGCTAGATCAGAGACTGGATC	59.173	45.833	0.00	5.84	31.51	3.36
3349	3368	7.972277	AGAATACGAATACTCACGTACAAACAT	59.028	33.333	0.00	0.00	45.25	2.71
3427	3450	9.859427	TTGATCAAGCTAACCTATTCAATTTTG	57.141	29.630	3.38	0.00	0.00	2.44
3474	3498	0.819582	CATCTGGCCGGAAAGCAATT	59.180	50.000	20.61	0.00	0.00	2.32
3595	3701	1.429463	GAAGCTGATCGGACAAACGT	58.571	50.000	5.48	0.00	34.94	3.99
3599	3705	2.089201	TCTACGAAGCTGATCGGACAA	58.911	47.619	12.18	0.00	46.82	3.18
3679	3823	5.801947	CCCATGCGTTCATAAGAAAAGAAAG	59.198	40.000	0.00	0.00	35.08	2.62
3739	3883	0.456221	ATGCCACCGAAGAGACTACG	59.544	55.000	0.00	0.00	0.00	3.51
3946	4091	0.457851	TTTGTCCTGTGTTTTGCCCG	59.542	50.000	0.00	0.00	0.00	6.13
4002	4147	4.380973	CGGTGATAATCTGACACAGTCTGT	60.381	45.833	0.00	0.00	36.42	3.41
4261	4406	1.009903	CCACCGAACATACGCGACAA	61.010	55.000	15.93	0.00	0.00	3.18
4274	4419	0.246360	CATGTACTGCAGACCACCGA	59.754	55.000	23.35	0.82	0.00	4.69
4315	4460	6.702723	TGCTCTGTTACGTGTTTACTTGTTAT	59.297	34.615	0.00	0.00	0.00	1.89
4427	4573	4.671831	TCATCTTCAGACTCTTCTCTGGT	58.328	43.478	0.00	0.00	38.62	4.00
4576	4722	6.510799	CGCAGTCTCCAAAATCTTCATATGAC	60.511	42.308	4.48	0.00	0.00	3.06
4643	4789	2.328099	CCACAAAGACTCCCAGCGC	61.328	63.158	0.00	0.00	0.00	5.92
4686	4832	4.740268	CATGAGTGCAACAGCAAATATGT	58.260	39.130	0.00	0.00	41.43	2.29
4706	4852	5.125356	TGATGGTATTGTTTCATCTCGCAT	58.875	37.500	0.00	0.00	38.38	4.73
4971	5128	3.071457	TCTTCATGATATGCCACCGACAT	59.929	43.478	0.00	0.00	0.00	3.06
5005	5162	3.851098	CCTTATATAGCAAGGCGAGGTC	58.149	50.000	3.59	0.00	36.41	3.85
5019	5176	3.181479	TGAGTTTCTCGTGCGCCTTATAT	60.181	43.478	4.18	0.00	32.35	0.86
5130	5288	4.026062	CGAATTCATCATTTCGTCGCCTTA	60.026	41.667	6.22	0.00	39.77	2.69
5142	5300	2.715749	TCCCACAGCGAATTCATCAT	57.284	45.000	6.22	0.00	0.00	2.45
5204	5362	3.532896	GGAAGTCATCCGAGCACAA	57.467	52.632	0.00	0.00	38.79	3.33
5440	5600	5.162794	GCATGATCACAAATGCACTGTTAA	58.837	37.500	12.97	0.00	46.75	2.01
5561	5721	1.546029	ACTCTGAATGCAGTGCTACGA	59.454	47.619	17.60	5.00	42.84	3.43
5621	5781	2.233676	TGCATCCGATCTGTTGTAGTGT	59.766	45.455	0.00	0.00	0.00	3.55
5676	5836	2.296471	ACACCTTTCTCTTCATCGACGT	59.704	45.455	0.00	0.00	0.00	4.34
5677	5837	2.917971	GACACCTTTCTCTTCATCGACG	59.082	50.000	0.00	0.00	0.00	5.12
5721	5881	2.103263	GGAGTCTCACCTGTGTTTGTCT	59.897	50.000	1.47	0.00	0.00	3.41
5726	5886	1.896465	GCTAGGAGTCTCACCTGTGTT	59.104	52.381	1.47	0.00	38.31	3.32
5753	5916	9.578439	CGTGCATGATTATCAGAATCTAGAATA	57.422	33.333	0.00	0.00	0.00	1.75
5770	5934	2.105006	AGTGAGCTTTCGTGCATGAT	57.895	45.000	9.96	0.00	34.99	2.45
5813	5977	8.420222	TCATTTGGTTTTGTGAATTACTCATGT	58.580	29.630	0.00	0.00	36.14	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.