AutoCloner

Multiple sequence alignment - TraesCS3D01G434600

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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	TraesCS3D01G434600	chr3D	100.000	2550	0	0	1	2550	547002766	547000217	0.000000e+00	4710.0
1	TraesCS3D01G434600	chr3A	90.352	1420	95	26	27	1431	683549669	683548277	0.000000e+00	1825.0
2	TraesCS3D01G434600	chr3A	88.063	821	70	17	28	830	683683966	683683156	0.000000e+00	948.0
3	TraesCS3D01G434600	chr3A	93.770	610	36	2	834	1442	24199928	24200536	0.000000e+00	915.0
4	TraesCS3D01G434600	chr3A	93.377	604	37	3	830	1431	683681868	683681266	0.000000e+00	891.0
5	TraesCS3D01G434600	chr3A	84.160	827	63	21	1542	2332	683681246	683680452	0.000000e+00	739.0
6	TraesCS3D01G434600	chr3A	88.791	455	36	4	1542	1985	683548257	683547807	6.200000e-151	544.0
7	TraesCS3D01G434600	chr3A	86.720	497	26	11	2055	2542	683547565	683547100	1.350000e-142	516.0
8	TraesCS3D01G434600	chr3A	87.898	314	26	3	1728	2029	24201305	24201618	2.410000e-95	359.0
9	TraesCS3D01G434600	chr3A	93.004	243	13	3	1451	1693	24200515	24200753	4.040000e-93	351.0
10	TraesCS3D01G434600	chr3A	92.653	245	14	3	28	271	24198874	24199115	1.450000e-92	350.0
11	TraesCS3D01G434600	chr3A	89.583	96	5	1	715	810	24199842	24199932	1.600000e-22	117.0
12	TraesCS3D01G434600	chr3A	97.143	35	1	0	1	35	629018096	629018062	2.740000e-05	60.2
13	TraesCS3D01G434600	chr4B	95.315	747	33	2	696	1442	604887924	604888668	0.000000e+00	1184.0
14	TraesCS3D01G434600	chr4B	92.391	276	17	3	28	302	604887663	604887935	8.550000e-105	390.0
15	TraesCS3D01G434600	chr4B	94.545	165	6	2	1522	1684	604888784	604888947	4.210000e-63	252.0
16	TraesCS3D01G434600	chr3B	94.370	746	40	2	696	1440	724187667	724186923	0.000000e+00	1144.0
17	TraesCS3D01G434600	chr3B	89.542	918	54	14	1651	2542	724186679	724185778	0.000000e+00	1125.0
18	TraesCS3D01G434600	chr3B	88.803	259	21	7	31	285	724188025	724187771	6.850000e-81	311.0
19	TraesCS3D01G434600	chr3B	93.500	200	8	4	1454	1652	724186939	724186744	2.480000e-75	292.0
20	TraesCS3D01G434600	chr3B	97.727	44	0	1	1986	2029	805483897	805483939	9.780000e-10	75.0
21	TraesCS3D01G434600	chr2A	92.168	715	28	5	731	1442	5291440	5290751	0.000000e+00	985.0
22	TraesCS3D01G434600	chr2A	90.816	588	37	6	1454	2029	5290770	5290188	0.000000e+00	771.0
23	TraesCS3D01G434600	chr2A	88.945	199	16	3	28	224	5292113	5291919	9.120000e-60	241.0
24	TraesCS3D01G434600	chr2D	88.144	388	32	7	321	697	71203459	71203075	1.390000e-122	449.0
25	TraesCS3D01G434600	chr2D	80.500	400	49	17	314	697	35778517	35778131	1.930000e-71	279.0
26	TraesCS3D01G434600	chr2D	83.537	164	8	6	1848	1992	141501409	141501246	4.430000e-28	135.0
27	TraesCS3D01G434600	chr7D	85.287	401	41	11	314	699	457216115	457215718	5.110000e-107	398.0
28	TraesCS3D01G434600	chr1D	85.250	400	42	9	315	700	459833165	459832769	1.840000e-106	396.0
29	TraesCS3D01G434600	chr1D	92.683	41	1	2	1	41	137225178	137225216	9.850000e-05	58.4
30	TraesCS3D01G434600	chr7B	82.512	406	49	11	314	699	713466620	713467023	1.130000e-88	337.0
31	TraesCS3D01G434600	chr7B	97.143	35	1	0	1	35	417898160	417898194	2.740000e-05	60.2
32	TraesCS3D01G434600	chr6D	82.532	395	55	11	314	697	56208088	56208479	4.070000e-88	335.0
33	TraesCS3D01G434600	chr6D	97.059	34	1	0	1	34	48458106	48458139	9.850000e-05	58.4
34	TraesCS3D01G434600	chr4A	84.302	344	36	11	302	631	689845681	689845342	1.140000e-83	320.0
35	TraesCS3D01G434600	chr2B	81.683	404	47	15	314	697	189614818	189615214	6.850000e-81	311.0
36	TraesCS3D01G434600	chr2B	100.000	42	0	0	1988	2029	681332041	681332000	7.560000e-11	78.7
37	TraesCS3D01G434600	chr1A	80.856	397	59	15	314	697	36604833	36604441	1.920000e-76	296.0
38	TraesCS3D01G434600	chr7A	80.402	398	51	19	322	697	509139359	509138967	6.950000e-71	278.0
39	TraesCS3D01G434600	chr7A	83.796	216	21	4	1786	1992	115587397	115587607	2.590000e-45	193.0
40	TraesCS3D01G434600	chr7A	87.302	63	5	2	1967	2029	454290732	454290791	4.550000e-08	69.4
41	TraesCS3D01G434600	chr7A	95.000	40	1	1	1	39	653383924	653383963	7.620000e-06	62.1
42	TraesCS3D01G434600	chr6A	85.976	164	9	5	1843	1992	156673949	156674112	2.030000e-36	163.0
43	TraesCS3D01G434600	chr6A	84.810	158	11	4	1848	1992	519768333	519768176	2.040000e-31	147.0
44	TraesCS3D01G434600	chrUn	97.727	44	0	1	1986	2029	75923114	75923156	9.780000e-10	75.0
45	TraesCS3D01G434600	chr6B	95.745	47	1	1	1986	2032	9987642	9987597	9.780000e-10	75.0
46	TraesCS3D01G434600	chr6B	90.741	54	2	3	1986	2038	664040591	664040540	4.550000e-08	69.4
47	TraesCS3D01G434600	chr6B	94.595	37	1	1	1	37	51001162	51001197	3.540000e-04	56.5
48	TraesCS3D01G434600	chr1B	97.727	44	0	1	1986	2029	299716739	299716697	9.780000e-10	75.0
49	TraesCS3D01G434600	chr5A	97.222	36	1	0	1	36	299095862	299095827	7.620000e-06	62.1
50	TraesCS3D01G434600	chr5A	90.698	43	2	2	1	42	475324396	475324355	3.540000e-04	56.5
51	TraesCS3D01G434600	chr4D	100.000	33	0	0	1	33	100572245	100572277	7.620000e-06	62.1

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	TraesCS3D01G434600	chr3D	547000217	547002766	2549	True	4710.000000	4710	100.000000	1	2550	1	chr3D.!!$R1	2549
1	TraesCS3D01G434600	chr3A	683547100	683549669	2569	True	961.666667	1825	88.621000	27	2542	3	chr3A.!!$R2	2515
2	TraesCS3D01G434600	chr3A	683680452	683683966	3514	True	859.333333	948	88.533333	28	2332	3	chr3A.!!$R3	2304
3	TraesCS3D01G434600	chr3A	24198874	24201618	2744	False	418.400000	915	91.381600	28	2029	5	chr3A.!!$F1	2001
4	TraesCS3D01G434600	chr4B	604887663	604888947	1284	False	608.666667	1184	94.083667	28	1684	3	chr4B.!!$F1	1656
5	TraesCS3D01G434600	chr3B	724185778	724188025	2247	True	718.000000	1144	91.553750	31	2542	4	chr3B.!!$R1	2511
6	TraesCS3D01G434600	chr2A	5290188	5292113	1925	True	665.666667	985	90.643000	28	2029	3	chr2A.!!$R1	2001

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
38	40	1.067821	CGGAGGGAGTAGAACTCATGC	59.932	57.143	9.15	2.1	46.79	4.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2030	4512	0.236711	CTAACAGCACAGCACAGCAC	59.763	55.0	0.0	0.0	0.0	4.4	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
24	25	6.607004	AGACATATATTTAGGAACGGAGGG	57.393	41.667	0.00	0.00	0.00	4.30
25	26	6.320518	AGACATATATTTAGGAACGGAGGGA	58.679	40.000	0.00	0.00	0.00	4.20
38	40	1.067821	CGGAGGGAGTAGAACTCATGC	59.932	57.143	9.15	2.10	46.79	4.06
50	52	5.886960	AGAACTCATGCATGACCTTTTAC	57.113	39.130	25.42	11.91	32.50	2.01
63	65	3.623703	ACCTTTTACGTGTTCACCCTTT	58.376	40.909	0.00	0.00	0.00	3.11
271	279	7.393234	CCATTTTGATCTTAAGAACAGGGTGTA	59.607	37.037	14.24	0.00	0.00	2.90
281	627	5.772393	AGAACAGGGTGTACCATCAATAA	57.228	39.130	3.11	0.00	43.89	1.40
289	640	8.677300	CAGGGTGTACCATCAATAAATATATGC	58.323	37.037	3.11	0.00	43.89	3.14
316	667	3.513225	CCATAGCTGGCCAAACGG	58.487	61.111	7.01	0.00	35.23	4.44
350	711	2.565834	AGCCACGATTATTATACGGGCT	59.434	45.455	0.00	0.00	43.20	5.19
511	1012	9.674705	ACATGTTGGGCCATATAGAGATATATA	57.325	33.333	7.26	0.00	0.00	0.86
580	1081	2.439156	CCCTAGCAGCCCAAGCAC	60.439	66.667	0.00	0.00	43.56	4.40
633	1141	4.722700	GTGTCGTGCCTGGCCCAT	62.723	66.667	17.53	0.00	0.00	4.00
687	1195	1.543944	GGTTGGTCCAGCCCATTTGG	61.544	60.000	13.75	0.00	33.60	3.28
752	1260	7.505258	TGAAAGGTTTGGGAGGAAAATTTTAG	58.495	34.615	2.75	0.00	0.00	1.85
954	2751	3.446873	TGGATAAGCGTTGATGCCAAAAT	59.553	39.130	0.00	0.00	33.49	1.82
1270	3069	2.433604	TGCAGAAGAGATGGGATCTGAC	59.566	50.000	5.85	0.00	40.38	3.51
1282	3081	1.079503	GATCTGACGGTTGTGAAGGC	58.920	55.000	0.00	0.00	0.00	4.35
1287	3086	1.586154	GACGGTTGTGAAGGCCATGG	61.586	60.000	7.63	7.63	0.00	3.66
1436	3236	6.313905	CGATCTACCAATTTAGGCATATGTCC	59.686	42.308	3.04	5.90	0.00	4.02
1442	3242	5.215160	CAATTTAGGCATATGTCCTTTCGC	58.785	41.667	19.50	0.00	35.21	4.70
1443	3243	2.148916	TAGGCATATGTCCTTTCGCG	57.851	50.000	19.50	0.00	35.21	5.87
1444	3244	0.464036	AGGCATATGTCCTTTCGCGA	59.536	50.000	3.71	3.71	0.00	5.87
1445	3245	1.134521	AGGCATATGTCCTTTCGCGAA	60.135	47.619	19.38	19.38	0.00	4.70
1446	3246	1.668751	GGCATATGTCCTTTCGCGAAA	59.331	47.619	30.47	30.47	0.00	3.46
1447	3247	2.096819	GGCATATGTCCTTTCGCGAAAA	59.903	45.455	31.68	19.38	0.00	2.29
1448	3248	3.426963	GGCATATGTCCTTTCGCGAAAAA	60.427	43.478	31.68	21.10	0.00	1.94
1842	4299	1.697432	TCCGTTGGTCTCTTGGACATT	59.303	47.619	0.00	0.00	46.16	2.71
1843	4300	2.076863	CCGTTGGTCTCTTGGACATTC	58.923	52.381	0.00	0.00	46.16	2.67
1891	4348	3.930229	CAGATCGTCCATTTTGTTACGGA	59.070	43.478	0.00	0.00	36.08	4.69
2030	4512	9.988815	AGTGCTCAGTTATAATGTATCTAAAGG	57.011	33.333	0.00	0.00	0.00	3.11
2031	4513	9.765795	GTGCTCAGTTATAATGTATCTAAAGGT	57.234	33.333	0.00	0.00	0.00	3.50
2032	4514	9.764363	TGCTCAGTTATAATGTATCTAAAGGTG	57.236	33.333	0.00	0.00	0.00	4.00
2033	4515	8.713271	GCTCAGTTATAATGTATCTAAAGGTGC	58.287	37.037	0.00	0.00	0.00	5.01
2080	4763	2.252747	CTGTGTTGTGCTGTGTTGTTG	58.747	47.619	0.00	0.00	0.00	3.33
2134	4823	2.081462	CGTTTTACACATCCAGGACCC	58.919	52.381	0.00	0.00	0.00	4.46
2135	4824	2.290071	CGTTTTACACATCCAGGACCCT	60.290	50.000	0.00	0.00	0.00	4.34
2136	4825	3.055675	CGTTTTACACATCCAGGACCCTA	60.056	47.826	0.00	0.00	0.00	3.53
2137	4826	4.259356	GTTTTACACATCCAGGACCCTAC	58.741	47.826	0.00	0.00	0.00	3.18
2140	4829	2.562296	ACACATCCAGGACCCTACATT	58.438	47.619	0.00	0.00	0.00	2.71
2144	4833	4.881850	CACATCCAGGACCCTACATTTTAC	59.118	45.833	0.00	0.00	0.00	2.01
2145	4834	4.788617	ACATCCAGGACCCTACATTTTACT	59.211	41.667	0.00	0.00	0.00	2.24
2156	4845	7.913789	ACCCTACATTTTACTCACTGAACATA	58.086	34.615	0.00	0.00	0.00	2.29
2169	4858	8.314751	ACTCACTGAACATAGCTACATTTTACT	58.685	33.333	0.00	0.00	0.00	2.24
2170	4859	8.703604	TCACTGAACATAGCTACATTTTACTC	57.296	34.615	0.00	0.00	0.00	2.59
2171	4860	8.531982	TCACTGAACATAGCTACATTTTACTCT	58.468	33.333	0.00	0.00	0.00	3.24
2172	4861	8.812329	CACTGAACATAGCTACATTTTACTCTC	58.188	37.037	0.00	0.00	0.00	3.20
2173	4862	8.754080	ACTGAACATAGCTACATTTTACTCTCT	58.246	33.333	0.00	0.00	0.00	3.10
2174	4863	9.243637	CTGAACATAGCTACATTTTACTCTCTC	57.756	37.037	0.00	0.00	0.00	3.20
2175	4864	8.972127	TGAACATAGCTACATTTTACTCTCTCT	58.028	33.333	0.00	0.00	0.00	3.10
2176	4865	9.458374	GAACATAGCTACATTTTACTCTCTCTC	57.542	37.037	0.00	0.00	0.00	3.20
2177	4866	8.760980	ACATAGCTACATTTTACTCTCTCTCT	57.239	34.615	0.00	0.00	0.00	3.10
2178	4867	8.846211	ACATAGCTACATTTTACTCTCTCTCTC	58.154	37.037	0.00	0.00	0.00	3.20
2179	4868	9.066892	CATAGCTACATTTTACTCTCTCTCTCT	57.933	37.037	0.00	0.00	0.00	3.10
2180	4869	7.568199	AGCTACATTTTACTCTCTCTCTCTC	57.432	40.000	0.00	0.00	0.00	3.20
2181	4870	7.346471	AGCTACATTTTACTCTCTCTCTCTCT	58.654	38.462	0.00	0.00	0.00	3.10
2182	4871	7.499232	AGCTACATTTTACTCTCTCTCTCTCTC	59.501	40.741	0.00	0.00	0.00	3.20
2183	4872	7.499232	GCTACATTTTACTCTCTCTCTCTCTCT	59.501	40.741	0.00	0.00	0.00	3.10
2184	4873	7.865706	ACATTTTACTCTCTCTCTCTCTCTC	57.134	40.000	0.00	0.00	0.00	3.20
2185	4874	7.402054	ACATTTTACTCTCTCTCTCTCTCTCA	58.598	38.462	0.00	0.00	0.00	3.27
2186	4875	7.336931	ACATTTTACTCTCTCTCTCTCTCTCAC	59.663	40.741	0.00	0.00	0.00	3.51
2187	4876	6.367374	TTTACTCTCTCTCTCTCTCTCACA	57.633	41.667	0.00	0.00	0.00	3.58
2188	4877	4.207891	ACTCTCTCTCTCTCTCTCACAC	57.792	50.000	0.00	0.00	0.00	3.82
2189	4878	3.582647	ACTCTCTCTCTCTCTCTCACACA	59.417	47.826	0.00	0.00	0.00	3.72
2190	4879	3.935203	CTCTCTCTCTCTCTCTCACACAC	59.065	52.174	0.00	0.00	0.00	3.82
2204	4913	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2294	5003	2.460669	AGAGAAATGATGCCCAAACCC	58.539	47.619	0.00	0.00	0.00	4.11
2389	5098	0.697658	TGATGGGTCAATGCACAGGA	59.302	50.000	0.00	0.00	0.00	3.86
2430	5139	1.425066	ACAGCAAAGGGAGATCCAACA	59.575	47.619	0.47	0.00	38.24	3.33
2431	5140	2.158475	ACAGCAAAGGGAGATCCAACAA	60.158	45.455	0.47	0.00	38.24	2.83
2432	5141	2.490903	CAGCAAAGGGAGATCCAACAAG	59.509	50.000	0.47	0.00	38.24	3.16
2500	5218	0.038166	TTGTTGTCCCCAGGCTCATC	59.962	55.000	0.00	0.00	0.00	2.92
2537	5255	7.444487	ACATCACCATCATCATCTTACATGAAG	59.556	37.037	0.00	0.00	32.76	3.02
2542	5260	6.655425	CCATCATCATCTTACATGAAGCTCAT	59.345	38.462	0.00	0.00	37.65	2.90
2543	5261	7.175119	CCATCATCATCTTACATGAAGCTCATT	59.825	37.037	0.00	0.00	34.28	2.57
2544	5262	7.725818	TCATCATCTTACATGAAGCTCATTC	57.274	36.000	0.00	0.00	34.28	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.785963	TCCCTCCGTTCCTAAATATATGTCTT	59.214	38.462	0.00	0.00	0.00	3.01
1	2	6.320518	TCCCTCCGTTCCTAAATATATGTCT	58.679	40.000	0.00	0.00	0.00	3.41
2	3	6.210984	ACTCCCTCCGTTCCTAAATATATGTC	59.789	42.308	0.00	0.00	0.00	3.06
3	4	6.082707	ACTCCCTCCGTTCCTAAATATATGT	58.917	40.000	0.00	0.00	0.00	2.29
4	5	6.607004	ACTCCCTCCGTTCCTAAATATATG	57.393	41.667	0.00	0.00	0.00	1.78
5	6	7.706674	TCTACTCCCTCCGTTCCTAAATATAT	58.293	38.462	0.00	0.00	0.00	0.86
6	7	7.095183	TCTACTCCCTCCGTTCCTAAATATA	57.905	40.000	0.00	0.00	0.00	0.86
7	8	5.961897	TCTACTCCCTCCGTTCCTAAATAT	58.038	41.667	0.00	0.00	0.00	1.28
8	9	5.393068	TCTACTCCCTCCGTTCCTAAATA	57.607	43.478	0.00	0.00	0.00	1.40
9	10	4.261411	TCTACTCCCTCCGTTCCTAAAT	57.739	45.455	0.00	0.00	0.00	1.40
10	11	3.744940	TCTACTCCCTCCGTTCCTAAA	57.255	47.619	0.00	0.00	0.00	1.85
11	12	3.011032	AGTTCTACTCCCTCCGTTCCTAA	59.989	47.826	0.00	0.00	0.00	2.69
12	13	2.579860	AGTTCTACTCCCTCCGTTCCTA	59.420	50.000	0.00	0.00	0.00	2.94
13	14	1.358445	AGTTCTACTCCCTCCGTTCCT	59.642	52.381	0.00	0.00	0.00	3.36
14	15	1.750206	GAGTTCTACTCCCTCCGTTCC	59.250	57.143	0.00	0.00	39.28	3.62
15	16	2.444421	TGAGTTCTACTCCCTCCGTTC	58.556	52.381	4.52	0.00	44.44	3.95
16	17	2.599408	TGAGTTCTACTCCCTCCGTT	57.401	50.000	4.52	0.00	44.44	4.44
17	18	2.379972	CATGAGTTCTACTCCCTCCGT	58.620	52.381	4.52	0.00	44.44	4.69
18	19	1.067821	GCATGAGTTCTACTCCCTCCG	59.932	57.143	0.00	0.00	44.44	4.63
19	20	2.111384	TGCATGAGTTCTACTCCCTCC	58.889	52.381	0.00	0.00	44.44	4.30
20	21	3.386078	TCATGCATGAGTTCTACTCCCTC	59.614	47.826	25.42	0.00	44.44	4.30
21	22	3.133721	GTCATGCATGAGTTCTACTCCCT	59.866	47.826	29.38	0.00	44.44	4.20
22	23	3.462021	GTCATGCATGAGTTCTACTCCC	58.538	50.000	29.38	10.03	44.44	4.30
23	24	3.133721	AGGTCATGCATGAGTTCTACTCC	59.866	47.826	29.38	22.19	44.44	3.85
24	25	4.399004	AGGTCATGCATGAGTTCTACTC	57.601	45.455	29.38	14.55	45.26	2.59
25	26	4.833478	AAGGTCATGCATGAGTTCTACT	57.167	40.909	29.38	16.53	37.51	2.57
38	40	3.058501	GGGTGAACACGTAAAAGGTCATG	60.059	47.826	0.00	0.00	0.00	3.07
50	52	4.513692	TCAACAATCTAAAGGGTGAACACG	59.486	41.667	0.00	0.00	0.00	4.49
63	65	5.585820	ATGCATGCATGTTCAACAATCTA	57.414	34.783	31.74	0.00	35.03	1.98
281	627	9.618890	CAGCTATGGTACCAATTAGCATATATT	57.381	33.333	33.70	18.65	45.72	1.28
331	692	3.678072	CACAGCCCGTATAATAATCGTGG	59.322	47.826	0.00	0.00	0.00	4.94
470	889	6.533723	GCCCAACATGTAAAAATAGGCTAAAC	59.466	38.462	0.00	0.00	35.00	2.01
551	1052	2.052690	GCTAGGGTGAGCACTCGGA	61.053	63.158	0.16	0.00	42.36	4.55
563	1064	2.439156	GTGCTTGGGCTGCTAGGG	60.439	66.667	0.00	0.00	39.59	3.53
603	1111	3.122971	GACACGGGCTAAACGGGC	61.123	66.667	0.00	0.00	38.56	6.13
1081	2879	1.997606	GTCCTTTACCCATGTTCGTCG	59.002	52.381	0.00	0.00	0.00	5.12
1232	3031	5.001237	TCTGCATCCATTAGCAAACAATG	57.999	39.130	0.00	0.00	40.73	2.82
1270	3069	0.322098	TACCATGGCCTTCACAACCG	60.322	55.000	13.04	0.00	0.00	4.44
1282	3081	0.684153	CCCAGGTTTGGCTACCATGG	60.684	60.000	11.19	11.19	43.58	3.66
1287	3086	3.191182	CCATCCCAGGTTTGGCTAC	57.809	57.895	0.00	0.00	43.58	3.58
1411	3210	6.313905	GGACATATGCCTAAATTGGTAGATCG	59.686	42.308	1.58	0.00	0.00	3.69
1448	3248	7.642669	CACGAGATGACATATGCCTAATTTTT	58.357	34.615	1.58	0.00	0.00	1.94
1449	3249	6.293626	GCACGAGATGACATATGCCTAATTTT	60.294	38.462	1.58	0.00	0.00	1.82
1450	3250	5.180117	GCACGAGATGACATATGCCTAATTT	59.820	40.000	1.58	0.00	0.00	1.82
1451	3251	4.692625	GCACGAGATGACATATGCCTAATT	59.307	41.667	1.58	0.00	0.00	1.40
1452	3252	4.248859	GCACGAGATGACATATGCCTAAT	58.751	43.478	1.58	0.00	0.00	1.73
1453	3253	3.069443	TGCACGAGATGACATATGCCTAA	59.931	43.478	1.58	0.00	32.02	2.69
1454	3254	2.627699	TGCACGAGATGACATATGCCTA	59.372	45.455	1.58	0.00	32.02	3.93
1455	3255	1.413812	TGCACGAGATGACATATGCCT	59.586	47.619	1.58	0.00	32.02	4.75
1456	3256	1.869774	TGCACGAGATGACATATGCC	58.130	50.000	1.58	0.00	32.02	4.40
1457	3257	2.412455	GCATGCACGAGATGACATATGC	60.412	50.000	14.21	2.27	0.00	3.14
1458	3258	3.064931	AGCATGCACGAGATGACATATG	58.935	45.455	21.98	0.00	0.00	1.78
1459	3259	3.324117	GAGCATGCACGAGATGACATAT	58.676	45.455	21.98	0.00	0.00	1.78
1460	3260	2.747436	GAGCATGCACGAGATGACATA	58.253	47.619	21.98	0.00	0.00	2.29
1461	3261	1.579698	GAGCATGCACGAGATGACAT	58.420	50.000	21.98	0.00	0.00	3.06
1462	3262	0.803380	CGAGCATGCACGAGATGACA	60.803	55.000	30.03	0.00	32.00	3.58
1463	3263	0.526310	TCGAGCATGCACGAGATGAC	60.526	55.000	31.78	6.08	34.45	3.06
1464	3264	0.386838	ATCGAGCATGCACGAGATGA	59.613	50.000	36.10	19.57	41.66	2.92
1465	3265	0.782981	GATCGAGCATGCACGAGATG	59.217	55.000	36.10	12.50	41.66	2.90
1466	3266	0.662672	CGATCGAGCATGCACGAGAT	60.663	55.000	36.10	25.19	41.66	2.75
1467	3267	1.298638	CGATCGAGCATGCACGAGA	60.299	57.895	36.10	20.89	41.66	4.04
1468	3268	2.298629	CCGATCGAGCATGCACGAG	61.299	63.158	36.10	26.13	41.66	4.18
1469	3269	2.278792	CCGATCGAGCATGCACGA	60.279	61.111	35.77	35.77	42.44	4.35
1470	3270	2.583319	ACCGATCGAGCATGCACG	60.583	61.111	28.37	28.37	0.00	5.34
1471	3271	3.009140	CACCGATCGAGCATGCAC	58.991	61.111	21.98	13.43	0.00	4.57
1597	3468	1.252175	TAATCAAGCAAAAGCGGGCA	58.748	45.000	0.00	0.00	0.00	5.36
1792	4247	3.648982	CAGTGTTCGCAGCCGCAA	61.649	61.111	0.00	0.00	38.40	4.85
1938	4404	4.350368	AAGAATTTTTGGCCGTTGGATT	57.650	36.364	0.00	0.00	0.00	3.01
2029	4511	1.165907	TAACAGCACAGCACAGCACC	61.166	55.000	0.00	0.00	0.00	5.01
2030	4512	0.236711	CTAACAGCACAGCACAGCAC	59.763	55.000	0.00	0.00	0.00	4.40
2031	4513	1.509644	GCTAACAGCACAGCACAGCA	61.510	55.000	0.00	0.00	41.89	4.41
2032	4514	1.208614	GCTAACAGCACAGCACAGC	59.791	57.895	0.00	0.00	41.89	4.40
2033	4515	0.604780	AGGCTAACAGCACAGCACAG	60.605	55.000	0.00	0.00	44.75	3.66
2080	4763	1.574702	GGTGTGCGAAGTAACAGGCC	61.575	60.000	0.00	0.00	0.00	5.19
2134	4823	8.709386	AGCTATGTTCAGTGAGTAAAATGTAG	57.291	34.615	0.00	0.00	0.00	2.74
2135	4824	9.582431	GTAGCTATGTTCAGTGAGTAAAATGTA	57.418	33.333	0.00	0.00	0.00	2.29
2136	4825	8.094548	TGTAGCTATGTTCAGTGAGTAAAATGT	58.905	33.333	0.00	0.00	0.00	2.71
2137	4826	8.479313	TGTAGCTATGTTCAGTGAGTAAAATG	57.521	34.615	0.00	0.00	0.00	2.32
2140	4829	9.502091	AAAATGTAGCTATGTTCAGTGAGTAAA	57.498	29.630	0.00	0.00	0.00	2.01
2144	4833	8.709386	AGTAAAATGTAGCTATGTTCAGTGAG	57.291	34.615	0.00	0.00	0.00	3.51
2145	4834	8.531982	AGAGTAAAATGTAGCTATGTTCAGTGA	58.468	33.333	0.00	0.00	0.00	3.41
2156	4845	7.346471	AGAGAGAGAGAGAGTAAAATGTAGCT	58.654	38.462	0.00	0.00	0.00	3.32
2169	4858	3.326297	TGTGTGTGAGAGAGAGAGAGAGA	59.674	47.826	0.00	0.00	0.00	3.10
2170	4859	3.436704	GTGTGTGTGAGAGAGAGAGAGAG	59.563	52.174	0.00	0.00	0.00	3.20
2171	4860	3.181450	TGTGTGTGTGAGAGAGAGAGAGA	60.181	47.826	0.00	0.00	0.00	3.10
2172	4861	3.058293	GTGTGTGTGTGAGAGAGAGAGAG	60.058	52.174	0.00	0.00	0.00	3.20
2173	4862	2.881513	GTGTGTGTGTGAGAGAGAGAGA	59.118	50.000	0.00	0.00	0.00	3.10
2174	4863	2.620585	TGTGTGTGTGTGAGAGAGAGAG	59.379	50.000	0.00	0.00	0.00	3.20
2175	4864	2.359214	GTGTGTGTGTGTGAGAGAGAGA	59.641	50.000	0.00	0.00	0.00	3.10
2176	4865	2.099756	TGTGTGTGTGTGTGAGAGAGAG	59.900	50.000	0.00	0.00	0.00	3.20
2177	4866	2.099405	TGTGTGTGTGTGTGAGAGAGA	58.901	47.619	0.00	0.00	0.00	3.10
2178	4867	2.196749	GTGTGTGTGTGTGTGAGAGAG	58.803	52.381	0.00	0.00	0.00	3.20
2179	4868	1.548269	TGTGTGTGTGTGTGTGAGAGA	59.452	47.619	0.00	0.00	0.00	3.10
2180	4869	1.660607	GTGTGTGTGTGTGTGTGAGAG	59.339	52.381	0.00	0.00	0.00	3.20
2181	4870	1.001406	TGTGTGTGTGTGTGTGTGAGA	59.999	47.619	0.00	0.00	0.00	3.27
2182	4871	1.128507	GTGTGTGTGTGTGTGTGTGAG	59.871	52.381	0.00	0.00	0.00	3.51
2183	4872	1.152510	GTGTGTGTGTGTGTGTGTGA	58.847	50.000	0.00	0.00	0.00	3.58
2184	4873	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2185	4874	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
2186	4875	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2187	4876	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
2188	4877	1.155889	AGTGTGTGTGTGTGTGTGTG	58.844	50.000	0.00	0.00	0.00	3.82
2189	4878	1.535028	CAAGTGTGTGTGTGTGTGTGT	59.465	47.619	0.00	0.00	0.00	3.72
2190	4879	1.803555	TCAAGTGTGTGTGTGTGTGTG	59.196	47.619	0.00	0.00	0.00	3.82
2244	4953	1.235281	TGTCTCACCACTCCGACTCG	61.235	60.000	0.00	0.00	0.00	4.18
2309	5018	4.117372	GTCCGTTCGACAAGCGCG	62.117	66.667	0.00	0.00	41.54	6.86
2310	5019	4.117372	CGTCCGTTCGACAAGCGC	62.117	66.667	0.00	0.00	42.07	5.92
2389	5098	0.114364	GGGGGAGGGTGATGTTTTGT	59.886	55.000	0.00	0.00	0.00	2.83
2430	5139	7.129457	TCTGTAGAATGGTGCATATCTTCTT	57.871	36.000	8.45	0.00	0.00	2.52
2431	5140	6.737720	TCTGTAGAATGGTGCATATCTTCT	57.262	37.500	0.00	0.00	0.00	2.85
2432	5141	6.763135	TGTTCTGTAGAATGGTGCATATCTTC	59.237	38.462	0.00	0.00	36.33	2.87
2500	5218	0.323633	TGGTGATGTTCTGGCCATGG	60.324	55.000	5.51	7.63	0.00	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.