AutoCloner

Multiple sequence alignment - TraesCS2D01G338400

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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	TraesCS2D01G338400	chr2D	100.000	5062	0	0	1	5062	431927634	431922573	0.000000e+00	9348.0
1	TraesCS2D01G338400	chr2D	93.299	1925	89	21	869	2762	433016370	433018285	0.000000e+00	2804.0
2	TraesCS2D01G338400	chr2D	94.972	1452	61	7	3039	4489	433021246	433022686	0.000000e+00	2266.0
3	TraesCS2D01G338400	chr2D	89.474	627	58	6	1	624	432874396	432875017	0.000000e+00	785.0
4	TraesCS2D01G338400	chr2D	90.875	537	21	8	4543	5060	433023007	433023534	0.000000e+00	695.0
5	TraesCS2D01G338400	chr2D	95.964	223	9	0	2758	2980	433021013	433021235	3.730000e-96	363.0
6	TraesCS2D01G338400	chr2D	94.393	214	12	0	4285	4498	433022687	433022900	3.780000e-86	329.0
7	TraesCS2D01G338400	chr2D	90.179	112	7	3	652	760	433015926	433016036	5.280000e-30	143.0
8	TraesCS2D01G338400	chr2D	86.441	59	6	2	4787	4844	433023343	433023400	4.230000e-06	63.9
9	TraesCS2D01G338400	chr2A	94.077	2735	94	27	1544	4240	554079770	554077066	0.000000e+00	4091.0
10	TraesCS2D01G338400	chr2A	83.938	1351	162	17	2640	3972	554377416	554376103	0.000000e+00	1242.0
11	TraesCS2D01G338400	chr2A	93.740	639	23	6	819	1457	554080671	554080050	0.000000e+00	942.0
12	TraesCS2D01G338400	chr2A	82.730	608	99	6	47	652	66767836	66767233	2.070000e-148	536.0
13	TraesCS2D01G338400	chr2A	95.506	267	7	2	4233	4498	554077102	554076840	6.060000e-114	422.0
14	TraesCS2D01G338400	chr2A	91.667	228	13	3	4507	4731	554076797	554076573	1.370000e-80	311.0
15	TraesCS2D01G338400	chr2A	92.994	157	7	1	4841	4993	554076519	554076363	5.100000e-55	226.0
16	TraesCS2D01G338400	chr2A	89.583	144	10	2	2465	2603	554377647	554377504	1.450000e-40	178.0
17	TraesCS2D01G338400	chr2A	86.420	162	15	2	4020	4174	554138706	554138545	2.420000e-38	171.0
18	TraesCS2D01G338400	chr2A	86.364	154	14	2	4020	4166	554377993	554378146	1.460000e-35	161.0
19	TraesCS2D01G338400	chr2A	93.478	46	2	1	4802	4847	554076474	554076430	3.270000e-07	67.6
20	TraesCS2D01G338400	chr2B	94.957	2102	67	18	888	2957	511161200	511159106	0.000000e+00	3258.0
21	TraesCS2D01G338400	chr2B	95.318	1303	32	9	2940	4240	511158699	511157424	0.000000e+00	2041.0
22	TraesCS2D01G338400	chr2B	84.761	1319	168	19	2674	3973	511038543	511037239	0.000000e+00	1291.0
23	TraesCS2D01G338400	chr2B	91.228	855	43	19	4233	5062	511157459	511156612	0.000000e+00	1134.0
24	TraesCS2D01G338400	chr2B	80.645	1178	157	40	944	2070	511120605	511119448	0.000000e+00	846.0
25	TraesCS2D01G338400	chr2B	95.522	201	8	1	2959	3159	787960589	787960788	2.270000e-83	320.0
26	TraesCS2D01G338400	chr2B	95.349	43	2	0	4802	4844	511156788	511156746	9.090000e-08	69.4
27	TraesCS2D01G338400	chr7B	83.908	609	90	8	47	652	748331732	748331129	4.400000e-160	575.0
28	TraesCS2D01G338400	chr7B	82.587	603	101	4	53	652	104298968	104298367	3.470000e-146	529.0
29	TraesCS2D01G338400	chr3D	83.388	608	95	6	48	652	562513974	562514578	4.430000e-155	558.0
30	TraesCS2D01G338400	chr5D	82.753	603	100	4	53	652	76031159	76030558	7.460000e-148	534.0
31	TraesCS2D01G338400	chr7D	82.529	601	102	3	53	651	133886919	133887518	4.490000e-145	525.0
32	TraesCS2D01G338400	chr7D	82.508	606	94	11	54	652	251355465	251354865	5.810000e-144	521.0
33	TraesCS2D01G338400	chr7D	82.314	605	100	6	53	652	136414280	136414882	7.510000e-143	518.0

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	TraesCS2D01G338400	chr2D	431922573	431927634	5061	True	9348.000000	9348	100.000000	1	5062	1	chr2D.!!$R1	5061
1	TraesCS2D01G338400	chr2D	433015926	433023534	7608	False	951.985714	2804	92.303286	652	5060	7	chr2D.!!$F2	4408
2	TraesCS2D01G338400	chr2D	432874396	432875017	621	False	785.000000	785	89.474000	1	624	1	chr2D.!!$F1	623
3	TraesCS2D01G338400	chr2A	554076363	554080671	4308	True	1009.933333	4091	93.577000	819	4993	6	chr2A.!!$R3	4174
4	TraesCS2D01G338400	chr2A	554376103	554377647	1544	True	710.000000	1242	86.760500	2465	3972	2	chr2A.!!$R4	1507
5	TraesCS2D01G338400	chr2A	66767233	66767836	603	True	536.000000	536	82.730000	47	652	1	chr2A.!!$R1	605
6	TraesCS2D01G338400	chr2B	511156612	511161200	4588	True	1625.600000	3258	94.213000	888	5062	4	chr2B.!!$R3	4174
7	TraesCS2D01G338400	chr2B	511037239	511038543	1304	True	1291.000000	1291	84.761000	2674	3973	1	chr2B.!!$R1	1299
8	TraesCS2D01G338400	chr2B	511119448	511120605	1157	True	846.000000	846	80.645000	944	2070	1	chr2B.!!$R2	1126
9	TraesCS2D01G338400	chr7B	748331129	748331732	603	True	575.000000	575	83.908000	47	652	1	chr7B.!!$R2	605
10	TraesCS2D01G338400	chr7B	104298367	104298968	601	True	529.000000	529	82.587000	53	652	1	chr7B.!!$R1	599
11	TraesCS2D01G338400	chr3D	562513974	562514578	604	False	558.000000	558	83.388000	48	652	1	chr3D.!!$F1	604
12	TraesCS2D01G338400	chr5D	76030558	76031159	601	True	534.000000	534	82.753000	53	652	1	chr5D.!!$R1	599
13	TraesCS2D01G338400	chr7D	133886919	133887518	599	False	525.000000	525	82.529000	53	651	1	chr7D.!!$F1	598
14	TraesCS2D01G338400	chr7D	251354865	251355465	600	True	521.000000	521	82.508000	54	652	1	chr7D.!!$R1	598
15	TraesCS2D01G338400	chr7D	136414280	136414882	602	False	518.000000	518	82.314000	53	652	1	chr7D.!!$F2	599

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	End Stability	Orientation
258	261	0.325296	ACGGTGGCTCCCTGAAGATA	60.325	55.000	1.98	F
1028	1267	0.318762	ACCAGAAAGAGAGCGGTGAC	59.681	55.000	3.67	F
1517	1777	0.804989	CCATGCGTTTCACCTTCTCC	59.195	55.000	3.71	F
3123	6855	2.699954	CCAAACTGTGATCGTAGGCTT	58.300	47.619	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1111	1356	0.392706	TCACGCATCGCCTTATCCAT	59.607	50.000	0.00	0.00	3.41	R
2877	6183	1.818674	AGTGGCCGGCAGAAAAATAAG	59.181	47.619	30.85	0.00	1.73	R
3205	6939	5.638596	AAAAAGACCGGTGGAACATAATC	57.361	39.130	14.63	44.52	1.75	R
4499	8445	0.182537	CACAGTCTGGTTGTTGGGGA	59.817	55.000	4.53	0.00	4.81	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
23	24	0.530870	CTAGAAGCCGGGCAGTAAGC	60.531	60.000	23.09	3.33	44.65	3.09
45	46	4.508124	GCATCCAAAGTCATACCTCTTACG	59.492	45.833	0.00	0.00	0.00	3.18
122	124	1.667154	CCAGTCCGCCTCATCTTCGA	61.667	60.000	0.00	0.00	0.00	3.71
153	155	1.227943	CATAGGGGCGTGGTGGATG	60.228	63.158	0.00	0.00	0.00	3.51
166	168	2.124151	GGATGCCGACCATTGCCT	60.124	61.111	0.00	0.00	33.29	4.75
188	191	3.146847	ACGGAGGGCTTTGTTTTTAGAG	58.853	45.455	0.00	0.00	0.00	2.43
189	192	2.095212	CGGAGGGCTTTGTTTTTAGAGC	60.095	50.000	0.00	0.00	0.00	4.09
208	211	8.603242	TTAGAGCTTTCTTCGAGTTTTGTTAT	57.397	30.769	0.00	0.00	0.00	1.89
219	222	5.354513	TCGAGTTTTGTTATGGTTTGTGTCA	59.645	36.000	0.00	0.00	0.00	3.58
243	246	1.302351	AGGAAGACGAGACGACGGT	60.302	57.895	0.00	0.00	37.61	4.83
258	261	0.325296	ACGGTGGCTCCCTGAAGATA	60.325	55.000	0.00	0.00	0.00	1.98
265	268	5.163195	GGTGGCTCCCTGAAGATAGAATAAA	60.163	44.000	0.00	0.00	0.00	1.40
344	348	1.375523	GGTGTGCCTCCGACGAATT	60.376	57.895	0.00	0.00	0.00	2.17
356	360	4.062293	TCCGACGAATTTGTCTTTGATGT	58.938	39.130	20.99	0.00	36.71	3.06
361	365	7.537306	CCGACGAATTTGTCTTTGATGTATTTT	59.463	33.333	20.99	0.00	36.71	1.82
396	400	6.588756	GGTCGTTCTTCATCTATGTTTGTGTA	59.411	38.462	0.00	0.00	0.00	2.90
415	419	5.189180	GTGTATCTTCAGCTTGGATCCTTT	58.811	41.667	14.23	0.00	0.00	3.11
458	462	2.645802	GTGGTGGTTGTTGTTCTGGTA	58.354	47.619	0.00	0.00	0.00	3.25
459	463	3.018149	GTGGTGGTTGTTGTTCTGGTAA	58.982	45.455	0.00	0.00	0.00	2.85
463	467	3.380320	GTGGTTGTTGTTCTGGTAAGCTT	59.620	43.478	3.48	3.48	0.00	3.74
653	658	9.181805	CTAGTGTTTATTGTACTACCATGATCG	57.818	37.037	0.00	0.00	0.00	3.69
658	663	8.753175	GTTTATTGTACTACCATGATCGTCTTC	58.247	37.037	0.00	0.00	0.00	2.87
676	681	3.890756	TCTTCACACTTTCACCATTGCAT	59.109	39.130	0.00	0.00	0.00	3.96
677	682	5.048782	GTCTTCACACTTTCACCATTGCATA	60.049	40.000	0.00	0.00	0.00	3.14
684	689	4.391830	ACTTTCACCATTGCATACAGTACG	59.608	41.667	0.00	0.00	0.00	3.67
718	723	9.913310	AAATGAAAAGAAAATGTCCCCTAAAAA	57.087	25.926	0.00	0.00	0.00	1.94
720	725	8.900983	TGAAAAGAAAATGTCCCCTAAAAATG	57.099	30.769	0.00	0.00	0.00	2.32
721	726	8.709308	TGAAAAGAAAATGTCCCCTAAAAATGA	58.291	29.630	0.00	0.00	0.00	2.57
722	727	9.554395	GAAAAGAAAATGTCCCCTAAAAATGAA	57.446	29.630	0.00	0.00	0.00	2.57
727	732	9.378551	GAAAATGTCCCCTAAAAATGAAATACC	57.621	33.333	0.00	0.00	0.00	2.73
760	768	8.729805	AGGCAAATGAAATACTTTTTGTGAAA	57.270	26.923	0.00	0.00	0.00	2.69
762	770	7.587392	GGCAAATGAAATACTTTTTGTGAAAGC	59.413	33.333	0.00	0.00	0.00	3.51
763	771	7.318674	GCAAATGAAATACTTTTTGTGAAAGCG	59.681	33.333	0.00	0.00	0.00	4.68
764	772	7.406799	AATGAAATACTTTTTGTGAAAGCGG	57.593	32.000	0.00	0.00	0.00	5.52
766	774	6.565234	TGAAATACTTTTTGTGAAAGCGGAA	58.435	32.000	0.00	0.00	0.00	4.30
767	775	7.036220	TGAAATACTTTTTGTGAAAGCGGAAA	58.964	30.769	0.00	0.00	0.00	3.13
769	777	6.822073	ATACTTTTTGTGAAAGCGGAAAAC	57.178	33.333	0.00	0.00	0.00	2.43
771	779	2.196295	TTTGTGAAAGCGGAAAACGG	57.804	45.000	0.00	0.00	44.51	4.44
773	781	1.380524	TGTGAAAGCGGAAAACGGAA	58.619	45.000	0.00	0.00	44.51	4.30
774	782	1.743958	TGTGAAAGCGGAAAACGGAAA	59.256	42.857	0.00	0.00	44.51	3.13
775	783	2.114056	GTGAAAGCGGAAAACGGAAAC	58.886	47.619	0.00	0.00	44.51	2.78
776	784	1.065851	TGAAAGCGGAAAACGGAAACC	59.934	47.619	0.00	0.00	44.51	3.27
777	785	0.386476	AAAGCGGAAAACGGAAACCC	59.614	50.000	0.00	0.00	44.51	4.11
779	787	0.466739	AGCGGAAAACGGAAACCCTT	60.467	50.000	0.00	0.00	44.51	3.95
781	789	1.202440	GCGGAAAACGGAAACCCTTTT	60.202	47.619	0.00	0.00	44.51	2.27
782	790	2.739287	GCGGAAAACGGAAACCCTTTTT	60.739	45.455	0.00	0.00	44.51	1.94
807	815	4.734652	TTTTTAGGGCCTGCTCGG	57.265	55.556	18.53	0.00	0.00	4.63
816	824	2.282462	CCTGCTCGGCCTTTGGTT	60.282	61.111	0.00	0.00	0.00	3.67
817	825	2.335712	CCTGCTCGGCCTTTGGTTC	61.336	63.158	0.00	0.00	0.00	3.62
895	1128	0.673644	ATTATAGCGCATGGGCCGAC	60.674	55.000	29.03	4.07	36.38	4.79
964	1203	1.028905	TTTCCAACTTCGCAACCCAG	58.971	50.000	0.00	0.00	0.00	4.45
1027	1266	1.048601	AACCAGAAAGAGAGCGGTGA	58.951	50.000	0.00	0.00	0.00	4.02
1028	1267	0.318762	ACCAGAAAGAGAGCGGTGAC	59.681	55.000	0.00	0.00	0.00	3.67
1111	1356	3.838271	GTGGCGAGATGGAGGCGA	61.838	66.667	0.00	0.00	35.52	5.54
1116	1361	1.970639	CGAGATGGAGGCGATGGAT	59.029	57.895	0.00	0.00	0.00	3.41
1195	1443	1.379642	GCGGATGGCAAAGAAGGAGG	61.380	60.000	0.00	0.00	42.87	4.30
1282	1542	2.029623	CGACGGGGAGGAAGATCTTAA	58.970	52.381	8.25	0.00	0.00	1.85
1489	1749	3.875134	TGACATGTCATTGATGCAGCTAG	59.125	43.478	24.56	0.00	34.14	3.42
1497	1757	1.352083	TGATGCAGCTAGTATCCCCC	58.648	55.000	2.53	0.00	38.44	5.40
1517	1777	0.804989	CCATGCGTTTCACCTTCTCC	59.195	55.000	0.00	0.00	0.00	3.71
1584	2037	3.817647	AGTTGCAGAAATTGACCAGAGTC	59.182	43.478	0.00	0.00	43.83	3.36
1863	2341	5.843673	TCAATGTGAAGGCTTTGTTGTTA	57.156	34.783	0.00	0.00	0.00	2.41
1898	2397	9.816354	ATAAATATGCAAGTTTGGTGGTAATTC	57.184	29.630	9.25	0.00	0.00	2.17
1950	2456	7.649533	ATGTTTATGGCATCTCTTCATGAAA	57.350	32.000	9.88	0.00	0.00	2.69
2420	2929	5.430417	TGTGATGGGAATTAGGCCTAAACTA	59.570	40.000	28.50	18.86	0.00	2.24
2603	3118	7.715249	GCATGTTTCCAGGTATATAGAAGTCAA	59.285	37.037	0.00	0.00	0.00	3.18
2605	3120	9.838339	ATGTTTCCAGGTATATAGAAGTCAAAG	57.162	33.333	0.00	0.00	0.00	2.77
2607	3122	9.886132	GTTTCCAGGTATATAGAAGTCAAAGAA	57.114	33.333	0.00	0.00	0.00	2.52
2702	3268	3.321111	ACGTAGTCCATTGTCTGTCTGTT	59.679	43.478	0.00	0.00	29.74	3.16
2877	6183	6.165659	ACGTGCAACTGAACAAATATACTC	57.834	37.500	0.00	0.00	31.75	2.59
2893	6200	6.803154	ATATACTCTTATTTTTCTGCCGGC	57.197	37.500	22.73	22.73	0.00	6.13
3123	6855	2.699954	CCAAACTGTGATCGTAGGCTT	58.300	47.619	0.00	0.00	0.00	4.35
3205	6939	4.508461	AACACATGTCATTGTCACCATG	57.492	40.909	0.00	0.00	40.34	3.66
3219	6953	3.312421	GTCACCATGATTATGTTCCACCG	59.688	47.826	0.00	0.00	32.21	4.94
3785	7524	3.431486	GGATCAGGTTGTGGAGAGTCATC	60.431	52.174	0.00	0.00	0.00	2.92
3994	7733	4.034510	AGCTGTCGCATTTTAAGTGCTATC	59.965	41.667	10.51	2.19	40.37	2.08
4066	7805	8.044309	TGGATAAAGTTAGATTTTCATCGGTGA	58.956	33.333	0.00	0.00	34.17	4.02
4086	7825	6.183360	CGGTGATGTGTTGGCTTAATTCTAAT	60.183	38.462	0.00	0.00	0.00	1.73
4087	7826	7.011950	CGGTGATGTGTTGGCTTAATTCTAATA	59.988	37.037	0.00	0.00	0.00	0.98
4088	7827	8.682710	GGTGATGTGTTGGCTTAATTCTAATAA	58.317	33.333	0.00	0.00	0.00	1.40
4155	7894	2.420022	CCTGCCACATTTACTGCTACAC	59.580	50.000	0.00	0.00	0.00	2.90
4181	7920	8.419076	TCGTAACATCGGCGTATATACTATTA	57.581	34.615	6.85	0.00	0.00	0.98
4470	8416	4.610333	TGGGAGCTTAGACAATCTACAGA	58.390	43.478	0.00	0.00	0.00	3.41
4498	8444	3.205282	CCCCATATCCTCCCCAAATATCC	59.795	52.174	0.00	0.00	0.00	2.59
4499	8445	4.122211	CCCATATCCTCCCCAAATATCCT	58.878	47.826	0.00	0.00	0.00	3.24
4500	8446	4.166919	CCCATATCCTCCCCAAATATCCTC	59.833	50.000	0.00	0.00	0.00	3.71
4501	8447	4.166919	CCATATCCTCCCCAAATATCCTCC	59.833	50.000	0.00	0.00	0.00	4.30
4505	8485	2.143602	CTCCCCAAATATCCTCCCCAA	58.856	52.381	0.00	0.00	0.00	4.12
4931	8995	1.298859	ACGGCCGAGCTGTCAAATTC	61.299	55.000	35.90	0.00	45.94	2.17
5000	9064	7.092716	TCCAAATCGACTTAAACAGTAGTACC	58.907	38.462	0.00	0.00	35.01	3.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	2.436417	TGACTTTGGATGCTTACTGCC	58.564	47.619	0.00	0.00	42.00	4.85
23	24	5.661458	ACGTAAGAGGTATGACTTTGGATG	58.339	41.667	0.00	0.00	43.62	3.51
34	35	3.220940	GAGGTGGCTACGTAAGAGGTAT	58.779	50.000	0.00	0.00	43.62	2.73
45	46	3.418684	TTTTTGAGAGGAGGTGGCTAC	57.581	47.619	0.00	0.00	0.00	3.58
153	155	2.895372	CCGTAGGCAATGGTCGGC	60.895	66.667	0.00	0.00	46.14	5.54
166	168	4.320870	CTCTAAAAACAAAGCCCTCCGTA	58.679	43.478	0.00	0.00	0.00	4.02
188	191	5.758924	ACCATAACAAAACTCGAAGAAAGC	58.241	37.500	0.00	0.00	34.09	3.51
189	192	7.700656	ACAAACCATAACAAAACTCGAAGAAAG	59.299	33.333	0.00	0.00	34.09	2.62
208	211	1.142667	TCCTGAGCATGACACAAACCA	59.857	47.619	0.00	0.00	0.00	3.67
219	222	0.453793	CGTCTCGTCTTCCTGAGCAT	59.546	55.000	0.00	0.00	32.20	3.79
243	246	5.667626	ACTTTATTCTATCTTCAGGGAGCCA	59.332	40.000	0.00	0.00	0.00	4.75
258	261	3.451402	AGGCGGGGAAAACTTTATTCT	57.549	42.857	0.00	0.00	0.00	2.40
265	268	2.675371	GGCTAGGCGGGGAAAACT	59.325	61.111	0.00	0.00	0.00	2.66
289	293	4.228567	TGCTCGACGCACCACCAA	62.229	61.111	5.59	0.00	45.47	3.67
344	348	9.730705	AGATCTGAGAAAATACATCAAAGACAA	57.269	29.630	0.00	0.00	0.00	3.18
356	360	6.531503	AGAACGACCAGATCTGAGAAAATA	57.468	37.500	24.62	0.00	30.25	1.40
361	365	3.421844	TGAAGAACGACCAGATCTGAGA	58.578	45.455	24.62	0.00	31.94	3.27
396	400	3.198635	TCGAAAGGATCCAAGCTGAAGAT	59.801	43.478	15.82	0.00	0.00	2.40
415	419	4.919168	CCGATTAAAAGTGGCGTATATCGA	59.081	41.667	0.00	0.00	42.86	3.59
553	557	1.974236	ACTGAAGCTAGTGAAGGTGCT	59.026	47.619	0.00	0.00	35.65	4.40
629	634	7.553334	ACGATCATGGTAGTACAATAAACACT	58.447	34.615	2.06	0.00	0.00	3.55
636	641	6.127451	TGTGAAGACGATCATGGTAGTACAAT	60.127	38.462	2.06	0.00	0.00	2.71
644	649	3.685139	AAGTGTGAAGACGATCATGGT	57.315	42.857	0.00	0.00	0.00	3.55
653	658	3.066621	TGCAATGGTGAAAGTGTGAAGAC	59.933	43.478	0.00	0.00	0.00	3.01
658	663	4.022935	ACTGTATGCAATGGTGAAAGTGTG	60.023	41.667	0.00	0.00	0.00	3.82
734	742	9.823647	TTTCACAAAAAGTATTTCATTTGCCTA	57.176	25.926	0.00	0.00	37.28	3.93
737	745	7.318674	CGCTTTCACAAAAAGTATTTCATTTGC	59.681	33.333	0.00	0.00	37.28	3.68
755	763	2.114056	GTTTCCGTTTTCCGCTTTCAC	58.886	47.619	0.00	0.00	34.38	3.18
760	768	0.466739	AAGGGTTTCCGTTTTCCGCT	60.467	50.000	0.00	0.00	38.33	5.52
762	770	2.875087	AAAAGGGTTTCCGTTTTCCG	57.125	45.000	11.69	0.00	44.79	4.30
790	798	4.734652	CCGAGCAGGCCCTAAAAA	57.265	55.556	0.00	0.00	0.00	1.94
799	807	2.282462	AACCAAAGGCCGAGCAGG	60.282	61.111	0.00	0.00	44.97	4.85
800	808	1.301677	GAGAACCAAAGGCCGAGCAG	61.302	60.000	0.00	0.00	0.00	4.24
801	809	1.302511	GAGAACCAAAGGCCGAGCA	60.303	57.895	0.00	0.00	0.00	4.26
802	810	1.003233	AGAGAACCAAAGGCCGAGC	60.003	57.895	0.00	0.00	0.00	5.03
803	811	0.610687	AGAGAGAACCAAAGGCCGAG	59.389	55.000	0.00	0.00	0.00	4.63
804	812	1.002087	GAAGAGAGAACCAAAGGCCGA	59.998	52.381	0.00	0.00	0.00	5.54
805	813	1.270839	TGAAGAGAGAACCAAAGGCCG	60.271	52.381	0.00	0.00	0.00	6.13
806	814	2.155279	GTGAAGAGAGAACCAAAGGCC	58.845	52.381	0.00	0.00	0.00	5.19
807	815	2.810852	CTGTGAAGAGAGAACCAAAGGC	59.189	50.000	0.00	0.00	0.00	4.35
808	816	4.314121	CTCTGTGAAGAGAGAACCAAAGG	58.686	47.826	0.00	0.00	41.95	3.11
809	817	4.039730	TCCTCTGTGAAGAGAGAACCAAAG	59.960	45.833	6.07	0.00	41.95	2.77
810	818	3.967326	TCCTCTGTGAAGAGAGAACCAAA	59.033	43.478	6.07	0.00	41.95	3.28
811	819	3.576861	TCCTCTGTGAAGAGAGAACCAA	58.423	45.455	6.07	0.00	41.95	3.67
812	820	3.244887	TCCTCTGTGAAGAGAGAACCA	57.755	47.619	6.07	0.00	41.95	3.67
813	821	4.608948	TTTCCTCTGTGAAGAGAGAACC	57.391	45.455	6.07	0.00	41.95	3.62
895	1128	2.607771	CGGATGTGTTGGGCTTCTTTTG	60.608	50.000	0.00	0.00	0.00	2.44
964	1203	2.202703	CGACGATCGGGTTGGGTC	60.203	66.667	20.98	4.79	36.00	4.46
989	1228	0.038892	TTGGTGTACGCGAGAAGGAC	60.039	55.000	15.93	0.90	0.00	3.85
1111	1356	0.392706	TCACGCATCGCCTTATCCAT	59.607	50.000	0.00	0.00	0.00	3.41
1116	1361	1.358725	GCTTGTCACGCATCGCCTTA	61.359	55.000	0.00	0.00	0.00	2.69
1195	1443	2.520741	CTCCGCCTCCTCCTCCTC	60.521	72.222	0.00	0.00	0.00	3.71
1463	1723	4.598062	CTGCATCAATGACATGTCACATC	58.402	43.478	30.09	15.74	43.11	3.06
1464	1724	3.181490	GCTGCATCAATGACATGTCACAT	60.181	43.478	30.09	19.06	43.11	3.21
1497	1757	0.804989	GAGAAGGTGAAACGCATGGG	59.195	55.000	8.44	8.44	38.12	4.00
1584	2037	1.522355	CATCCAGCGGCCACTGTAG	60.522	63.158	19.22	5.41	35.83	2.74
1898	2397	5.433855	CATTGAAATTTCGCACAAACAAGG	58.566	37.500	13.34	0.00	0.00	3.61
2177	2685	4.722526	ACCATTACATAAGGGCAGCATA	57.277	40.909	2.27	0.00	40.59	3.14
2294	2802	2.777094	TGAGATTGTCCGTTGCATTCA	58.223	42.857	0.00	0.00	0.00	2.57
2372	2880	3.936661	GCGTTCGATAAAGCCCTAAAAG	58.063	45.455	0.00	0.00	34.45	2.27
2420	2929	5.175859	CACAAAGTGACGTAATATGACCCT	58.824	41.667	0.00	0.00	35.23	4.34
2542	3052	5.647658	TGCACGGAATCATACTCAAATTCTT	59.352	36.000	0.00	0.00	31.53	2.52
2608	3123	9.974980	GGAATAATCAAGAGTTGGTTAACAAAA	57.025	29.630	8.10	0.00	39.48	2.44
2609	3124	8.293867	CGGAATAATCAAGAGTTGGTTAACAAA	58.706	33.333	8.10	0.00	39.48	2.83
2610	3125	7.446013	ACGGAATAATCAAGAGTTGGTTAACAA	59.554	33.333	8.10	0.00	39.48	2.83
2611	3126	6.938030	ACGGAATAATCAAGAGTTGGTTAACA	59.062	34.615	8.10	0.00	39.48	2.41
2702	3268	2.408565	AGTCCCAAACAGAACTGAGGA	58.591	47.619	8.87	6.27	0.00	3.71
2828	6133	5.222079	TCCACACTAAGCATGTCTTGTTA	57.778	39.130	11.24	0.00	36.25	2.41
2877	6183	1.818674	AGTGGCCGGCAGAAAAATAAG	59.181	47.619	30.85	0.00	0.00	1.73
3123	6855	8.843262	CAATGATCAGAATATGTAAGAGGCAAA	58.157	33.333	0.09	0.00	0.00	3.68
3205	6939	5.638596	AAAAAGACCGGTGGAACATAATC	57.361	39.130	14.63	0.00	44.52	1.75
3785	7524	4.738124	TGACTCTTAACATCTTCTCTGCG	58.262	43.478	0.00	0.00	0.00	5.18
4027	7766	3.947834	ACTTTATCCATACAGGCAGCAAC	59.052	43.478	0.00	0.00	37.29	4.17
4066	7805	9.243105	ACTGTTATTAGAATTAAGCCAACACAT	57.757	29.630	0.00	0.00	0.00	3.21
4086	7825	8.863872	TCTGCTAGCATACATAGATACTGTTA	57.136	34.615	19.72	0.00	0.00	2.41
4087	7826	7.450014	ACTCTGCTAGCATACATAGATACTGTT	59.550	37.037	19.72	0.00	0.00	3.16
4088	7827	6.945435	ACTCTGCTAGCATACATAGATACTGT	59.055	38.462	19.72	2.32	0.00	3.55
4155	7894	5.213913	AGTATATACGCCGATGTTACGAG	57.786	43.478	7.23	0.00	35.09	4.18
4470	8416	1.536662	GGAGGATATGGGGCTCCGT	60.537	63.158	1.07	1.07	36.62	4.69
4498	8444	0.474184	ACAGTCTGGTTGTTGGGGAG	59.526	55.000	4.53	0.00	0.00	4.30
4499	8445	0.182537	CACAGTCTGGTTGTTGGGGA	59.817	55.000	4.53	0.00	0.00	4.81
4500	8446	1.455383	GCACAGTCTGGTTGTTGGGG	61.455	60.000	4.53	0.00	0.00	4.96
4501	8447	0.751277	TGCACAGTCTGGTTGTTGGG	60.751	55.000	4.53	0.00	0.00	4.12
4505	8485	1.349026	AGCTATGCACAGTCTGGTTGT	59.651	47.619	4.53	0.00	0.00	3.32
4693	8717	7.984422	TTCTGTCTACATCATCATGTGTTTT	57.016	32.000	0.00	0.00	43.54	2.43
4753	8812	8.101510	CGTATTCAGACTTGTTTTGTTTGTTTG	58.898	33.333	0.00	0.00	0.00	2.93
4759	8818	6.920569	ACTCGTATTCAGACTTGTTTTGTT	57.079	33.333	0.00	0.00	0.00	2.83
4761	8820	6.943981	TGAACTCGTATTCAGACTTGTTTTG	58.056	36.000	0.81	0.00	33.62	2.44
4931	8995	4.154195	GCCACATGTAAGTGTGTTTAGGAG	59.846	45.833	0.00	0.00	46.21	3.69
4966	9030	3.154827	AGTCGATTTGGATTTGGTGGT	57.845	42.857	0.00	0.00	0.00	4.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.