AutoCloner

Multiple sequence alignment - TraesCS1A01G166400

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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	TraesCS1A01G166400	chr1A	100.000	4651	0	0	1	4651	299102405	299107055	0.000000e+00	8589
1	TraesCS1A01G166400	chr1B	97.073	3826	102	5	833	4651	329941452	329945274	0.000000e+00	6436
2	TraesCS1A01G166400	chr1B	90.831	349	18	2	1	335	329941119	329941467	5.490000e-124	455
3	TraesCS1A01G166400	chr1D	97.184	3658	89	5	1002	4651	248113080	248109429	0.000000e+00	6172
4	TraesCS1A01G166400	chr1D	97.628	2403	55	2	1002	3404	248203493	248201093	0.000000e+00	4120
5	TraesCS1A01G166400	chr1D	97.657	1195	25	1	3457	4651	248201094	248199903	0.000000e+00	2049
6	TraesCS1A01G166400	chr1D	92.105	342	18	2	1	333	248113687	248113346	1.510000e-129	473
7	TraesCS1A01G166400	chr1D	92.105	342	18	2	1	333	248204122	248203781	1.510000e-129	473
8	TraesCS1A01G166400	chr1D	93.750	272	12	4	832	1098	248113351	248113080	2.020000e-108	403
9	TraesCS1A01G166400	chr1D	93.704	270	14	2	832	1098	248203786	248203517	7.250000e-108	401
10	TraesCS1A01G166400	chr1D	82.500	160	17	3	42	191	248113429	248113271	3.780000e-26	130
11	TraesCS1A01G166400	chr1D	82.500	160	17	3	42	191	248203864	248203706	3.780000e-26	130
12	TraesCS1A01G166400	chr2B	82.191	3588	518	62	1085	4603	66751439	66754974	0.000000e+00	2974
13	TraesCS1A01G166400	chr2A	82.938	2110	288	38	1396	3447	43197359	43199454	0.000000e+00	1836
14	TraesCS1A01G166400	chr2A	78.944	1743	291	34	1074	2756	43940625	43938899	0.000000e+00	1116
15	TraesCS1A01G166400	chr2A	84.411	1129	166	6	3480	4603	43199460	43200583	0.000000e+00	1101
16	TraesCS1A01G166400	chr2A	84.018	1120	171	6	3486	4603	43820023	43818910	0.000000e+00	1070
17	TraesCS1A01G166400	chr2A	83.929	1120	171	6	3486	4603	43902287	43901175	0.000000e+00	1062
18	TraesCS1A01G166400	chr2A	83.839	1120	174	5	3486	4603	43844311	43843197	0.000000e+00	1059
19	TraesCS1A01G166400	chr2A	85.281	693	98	3	2755	3445	43928701	43928011	0.000000e+00	712
20	TraesCS1A01G166400	chr2D	83.790	1752	237	29	1737	3454	38370640	38372378	0.000000e+00	1618
21	TraesCS1A01G166400	chr2D	85.515	1077	142	9	2376	3447	38197345	38198412	0.000000e+00	1112
22	TraesCS1A01G166400	chr2D	83.839	1120	162	9	3486	4603	38372383	38373485	0.000000e+00	1048
23	TraesCS1A01G166400	chr2D	89.357	498	38	9	330	826	346401435	346400952	3.080000e-171	612
24	TraesCS1A01G166400	chr2D	79.779	816	111	18	1559	2346	38196420	38197209	1.140000e-150	544
25	TraesCS1A01G166400	chr2D	84.848	165	20	3	3480	3643	38198418	38198578	1.340000e-35	161
26	TraesCS1A01G166400	chr4A	94.280	507	25	3	330	834	498208203	498208707	0.000000e+00	773
27	TraesCS1A01G166400	chr7D	89.683	504	35	7	330	833	548813926	548814412	1.100000e-175	627
28	TraesCS1A01G166400	chr5D	89.484	504	40	7	330	833	401380685	401380195	3.950000e-175	625
29	TraesCS1A01G166400	chr5D	89.307	505	40	7	330	833	417725257	417725748	5.110000e-174	621
30	TraesCS1A01G166400	chr5D	89.044	502	42	6	330	831	502657374	502656886	1.110000e-170	610
31	TraesCS1A01G166400	chrUn	89.216	510	40	8	330	838	43651915	43651420	1.420000e-174	623
32	TraesCS1A01G166400	chrUn	89.157	498	42	5	335	832	27118821	27119306	1.110000e-170	610
33	TraesCS1A01G166400	chr4D	89.066	503	42	6	330	832	445487728	445488217	3.080000e-171	612
34	TraesCS1A01G166400	chr6D	83.898	118	19	0	1804	1921	290247901	290247784	3.800000e-21	113
35	TraesCS1A01G166400	chr6A	84.685	111	17	0	1811	1921	434531649	434531759	1.370000e-20	111

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	TraesCS1A01G166400	chr1A	299102405	299107055	4650	False	8589.000000	8589	100.000000	1	4651	1	chr1A.!!$F1	4650
1	TraesCS1A01G166400	chr1B	329941119	329945274	4155	False	3445.500000	6436	93.952000	1	4651	2	chr1B.!!$F1	4650
2	TraesCS1A01G166400	chr1D	248109429	248113687	4258	True	1794.500000	6172	91.384750	1	4651	4	chr1D.!!$R1	4650
3	TraesCS1A01G166400	chr1D	248199903	248204122	4219	True	1434.600000	4120	92.718800	1	4651	5	chr1D.!!$R2	4650
4	TraesCS1A01G166400	chr2B	66751439	66754974	3535	False	2974.000000	2974	82.191000	1085	4603	1	chr2B.!!$F1	3518
5	TraesCS1A01G166400	chr2A	43197359	43200583	3224	False	1468.500000	1836	83.674500	1396	4603	2	chr2A.!!$F1	3207
6	TraesCS1A01G166400	chr2A	43938899	43940625	1726	True	1116.000000	1116	78.944000	1074	2756	1	chr2A.!!$R5	1682
7	TraesCS1A01G166400	chr2A	43818910	43820023	1113	True	1070.000000	1070	84.018000	3486	4603	1	chr2A.!!$R1	1117
8	TraesCS1A01G166400	chr2A	43901175	43902287	1112	True	1062.000000	1062	83.929000	3486	4603	1	chr2A.!!$R3	1117
9	TraesCS1A01G166400	chr2A	43843197	43844311	1114	True	1059.000000	1059	83.839000	3486	4603	1	chr2A.!!$R2	1117
10	TraesCS1A01G166400	chr2A	43928011	43928701	690	True	712.000000	712	85.281000	2755	3445	1	chr2A.!!$R4	690
11	TraesCS1A01G166400	chr2D	38370640	38373485	2845	False	1333.000000	1618	83.814500	1737	4603	2	chr2D.!!$F2	2866
12	TraesCS1A01G166400	chr2D	38196420	38198578	2158	False	605.666667	1112	83.380667	1559	3643	3	chr2D.!!$F1	2084
13	TraesCS1A01G166400	chr4A	498208203	498208707	504	False	773.000000	773	94.280000	330	834	1	chr4A.!!$F1	504

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
180	181	0.106708	AGCAGCGAAGGTTCTGTTCA	59.893	50.0	0.00	0.00	33.74	3.18	F
996	1025	0.669077	GACGGCCGAGAGACATACAT	59.331	55.0	35.90	3.54	0.00	2.29	F
2038	2219	0.797249	CCAAGTCGTAACCGAGCTCG	60.797	60.0	29.06	29.06	45.26	5.03	F
2702	3005	2.128771	AATGTTGTTCTATGCGCCCT	57.871	45.0	4.18	0.00	0.00	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1825	2006	0.106519	CCAAGGCCTTCCATTCCGAT	60.107	55.0	17.29	0.00	33.74	4.18	R
2702	3005	0.697658	TCTGGTGGATGGCATCAACA	59.302	50.0	30.72	21.94	34.80	3.33	R
3450	3769	0.473886	CCCTCAGTATCCCCCGGAAT	60.474	60.0	0.73	0.00	34.34	3.01	R
4451	4773	0.036952	CCTCACATGTGAAGGTCGCT	60.037	55.0	27.63	0.00	39.39	4.93	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
49	50	1.658686	CGCTTCTCCTACGCAGAGGT	61.659	60.000	1.00	0.00	37.88	3.85
103	104	3.797353	GGCTGGCGGAATCAGGGA	61.797	66.667	0.00	0.00	33.16	4.20
154	155	3.431055	TTGGTGCGCTTCCAAGTG	58.569	55.556	25.31	0.00	39.62	3.16
156	157	0.537143	TTGGTGCGCTTCCAAGTGAT	60.537	50.000	25.31	0.00	39.62	3.06
180	181	0.106708	AGCAGCGAAGGTTCTGTTCA	59.893	50.000	0.00	0.00	33.74	3.18
186	187	4.690748	CAGCGAAGGTTCTGTTCATTCTTA	59.309	41.667	0.00	0.00	33.74	2.10
201	210	7.016760	TGTTCATTCTTATCCCGGGAATATACA	59.983	37.037	30.84	18.40	0.00	2.29
214	223	5.660460	GGGAATATACAAGGCTTGTTTTGG	58.340	41.667	35.13	8.34	42.22	3.28
239	248	3.706373	CGGCTACACCTGGGCAGT	61.706	66.667	0.00	0.00	35.61	4.40
267	282	2.125912	CGCAGAGGCTTACAGCGT	60.126	61.111	13.20	0.00	43.62	5.07
271	286	1.071605	CAGAGGCTTACAGCGTGAAC	58.928	55.000	0.00	0.00	43.62	3.18
290	305	2.358615	ATTGGCTGCTTGCGACGA	60.359	55.556	0.00	0.00	44.05	4.20
312	327	1.887707	CGACTGGCGGAATTAGGGC	60.888	63.158	0.00	0.00	36.03	5.19
416	441	2.746904	CACAACCAAGTTGATGGCGATA	59.253	45.455	14.05	0.00	45.28	2.92
434	459	2.040009	TATGTGAAGGGGCTAGGCGC	62.040	60.000	23.85	23.85	40.84	6.53
476	501	3.779183	AGGTGTTCTCTGGATGATGATGT	59.221	43.478	0.00	0.00	0.00	3.06
500	525	1.134580	TGCTGCTCTGCTCTACATTCC	60.135	52.381	0.00	0.00	0.00	3.01
505	530	0.975556	TCTGCTCTACATTCCGCCCA	60.976	55.000	0.00	0.00	0.00	5.36
523	548	1.212688	CCATGGTTGTGATAGGAGGCA	59.787	52.381	2.57	0.00	0.00	4.75
529	554	2.042686	TGTGATAGGAGGCATTGTGC	57.957	50.000	0.00	0.00	44.08	4.57
574	599	4.084223	CGCGGCTAGAAAACTTTTGAAGTA	60.084	41.667	0.00	0.00	41.91	2.24
606	633	2.249413	ATTGCTCCTCTGGCACCTCG	62.249	60.000	0.00	0.00	39.55	4.63
662	689	3.697619	AGACCCAAACTAAGTAGGTGC	57.302	47.619	0.00	0.00	0.00	5.01
666	693	3.137728	ACCCAAACTAAGTAGGTGCTGTT	59.862	43.478	0.00	0.00	0.00	3.16
675	702	4.699925	AGTAGGTGCTGTTAGGTTTTCA	57.300	40.909	0.00	0.00	0.00	2.69
693	720	1.152830	ACCCCATGGTGCTCGTTTT	59.847	52.632	11.73	0.00	45.58	2.43
701	728	1.154225	GTGCTCGTTTTGATGGCGG	60.154	57.895	0.00	0.00	0.00	6.13
707	734	3.439540	TTTTGATGGCGGGCGAGC	61.440	61.111	0.00	0.00	0.00	5.03
719	746	2.193536	GGCGAGCACAGTGGGTTTT	61.194	57.895	1.84	0.00	0.00	2.43
720	747	1.282875	GCGAGCACAGTGGGTTTTC	59.717	57.895	1.84	0.00	0.00	2.29
764	791	3.604582	CTTCTCTTTCCTTGCTACCTGG	58.395	50.000	0.00	0.00	0.00	4.45
775	802	2.239400	TGCTACCTGGATGTATCGGAG	58.761	52.381	0.00	0.00	0.00	4.63
789	816	5.657474	TGTATCGGAGACTGTTGTATTTCC	58.343	41.667	4.23	0.00	42.51	3.13
811	838	5.889289	TCCGTTTATCTTAAATGGAAAGGGG	59.111	40.000	15.32	0.00	41.08	4.79
814	841	6.183360	CGTTTATCTTAAATGGAAAGGGGCAT	60.183	38.462	0.00	0.00	0.00	4.40
897	924	5.335191	CCTCACTGCAAACAATAAGGTTCTC	60.335	44.000	0.00	0.00	0.00	2.87
996	1025	0.669077	GACGGCCGAGAGACATACAT	59.331	55.000	35.90	3.54	0.00	2.29
1020	1050	4.406456	AGATGAACTCAGTGACAGAGAGT	58.594	43.478	12.13	5.82	43.98	3.24
1044	1146	5.540337	TGGATTGAACTCAGTTACAGAGAGT	59.460	40.000	11.67	5.65	43.98	3.24
1046	1148	5.854010	TTGAACTCAGTTACAGAGAGTGT	57.146	39.130	11.67	0.93	41.45	3.55
1068	1218	3.812156	TTGAACTCGGTGACAGAAAGA	57.188	42.857	0.00	0.00	0.00	2.52
1179	1329	3.442273	TCAACTTCACCACCAAACTGAAC	59.558	43.478	0.00	0.00	0.00	3.18
1292	1442	1.852309	TCCATGTGCCCTATTGTGGAT	59.148	47.619	0.00	0.00	31.24	3.41
1441	1591	2.432628	CGTGGTGCGACCTTCTCC	60.433	66.667	6.83	0.00	44.77	3.71
1638	1798	4.931661	AAAGGACATGGATGAATCATGC	57.068	40.909	7.84	7.84	44.09	4.06
1653	1813	9.502145	GATGAATCATGCGAAAAACTAATACAA	57.498	29.630	0.00	0.00	0.00	2.41
1688	1869	5.797934	CCAAAATACAACAAACGCGTGATAT	59.202	36.000	14.98	1.88	0.00	1.63
1745	1926	1.235724	GAGGAGAAAACCCACAACCG	58.764	55.000	0.00	0.00	0.00	4.44
1796	1977	4.515361	CTTCTCATGCATCTGACTTCCTT	58.485	43.478	0.00	0.00	0.00	3.36
1825	2006	1.270839	GGCTAAAGCTGGTGTCTGTCA	60.271	52.381	1.39	0.00	41.70	3.58
1950	2131	4.915158	GTATCTAACGGCCACTCTAGTT	57.085	45.455	2.24	0.00	0.00	2.24
1990	2171	2.846950	AGCCACAGGGTACTATTCCTT	58.153	47.619	0.00	0.00	36.17	3.36
2038	2219	0.797249	CCAAGTCGTAACCGAGCTCG	60.797	60.000	29.06	29.06	45.26	5.03
2155	2337	5.939764	AGAGCATCACCAAATGTAGACTA	57.060	39.130	0.00	0.00	37.82	2.59
2549	2849	7.266922	TGATAACGCTAACTTTGTTCCTTTT	57.733	32.000	0.00	0.00	0.00	2.27
2702	3005	2.128771	AATGTTGTTCTATGCGCCCT	57.871	45.000	4.18	0.00	0.00	5.19
2802	3105	4.208460	CAGCTGCAAATGAGTTGTTGAAAG	59.792	41.667	0.00	0.00	39.63	2.62
2906	3209	5.465051	CGATGTATCCTTTCGACATCAGAT	58.535	41.667	13.07	1.33	46.43	2.90
2925	3228	9.886132	CATCAGATCAATATTCCACATCAGATA	57.114	33.333	0.00	0.00	0.00	1.98
3094	3397	5.136105	AGGAAGATGTGAAGAAAGCTTGTT	58.864	37.500	0.00	0.00	33.61	2.83
3100	3403	4.269183	TGTGAAGAAAGCTTGTTGAGGAA	58.731	39.130	0.00	0.00	33.61	3.36
3450	3769	5.968167	TCTAAGGTTATGAAAGGGAAGGCTA	59.032	40.000	0.00	0.00	0.00	3.93
3560	3879	1.479323	CACCATCTGAAAGGCATTGGG	59.521	52.381	0.00	0.00	35.21	4.12
3648	3967	0.475906	AGGAAAGCTGGAGCACTTGT	59.524	50.000	0.65	0.00	45.16	3.16
3905	4224	2.363680	CGGACTAAGCACATCTCTGGAT	59.636	50.000	0.00	0.00	0.00	3.41
3957	4276	2.876550	GCGGTTGGACAGTCTAAACTTT	59.123	45.455	12.47	0.00	31.71	2.66
4097	4419	9.502091	GTATTTATTATTCCCTGCTGTATCACA	57.498	33.333	0.00	0.00	0.00	3.58
4148	4470	4.080638	GGAGAGGAAGGTCTCATTGTCATT	60.081	45.833	3.44	0.00	44.29	2.57
4207	4529	4.341783	AGGACCTGCTGCTGCCAC	62.342	66.667	13.47	1.98	38.71	5.01
4217	4539	2.358615	GCTGCCACGATGGACACA	60.359	61.111	8.04	0.00	40.96	3.72
4257	4579	5.906113	ACAGAGAAGAAGAGCGAGAATTA	57.094	39.130	0.00	0.00	0.00	1.40
4272	4594	3.974642	GAGAATTAGGAGGGGAGCCTTTA	59.025	47.826	0.00	0.00	36.96	1.85
4451	4773	6.249192	TCTCTCTAGTCTCAACAGAATCCAA	58.751	40.000	0.00	0.00	0.00	3.53
4539	4861	3.894427	GCAAGTATCTCAGATCTCCTCCA	59.106	47.826	0.00	0.00	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	4.261888	CGCTGTAAACCTCTGCGT	57.738	55.556	8.52	0.00	44.06	5.24
49	50	1.202132	GCCAATGATTCGCGCTGTAAA	60.202	47.619	5.56	0.00	0.00	2.01
154	155	1.589716	AACCTTCGCTGCTTGCCATC	61.590	55.000	0.00	0.00	38.78	3.51
156	157	2.203337	AACCTTCGCTGCTTGCCA	60.203	55.556	0.00	0.00	38.78	4.92
180	181	6.578439	GCCTTGTATATTCCCGGGATAAGAAT	60.578	42.308	27.48	17.25	34.68	2.40
186	187	2.632537	AGCCTTGTATATTCCCGGGAT	58.367	47.619	27.48	16.98	0.00	3.85
201	210	0.958822	CGCCTACCAAAACAAGCCTT	59.041	50.000	0.00	0.00	0.00	4.35
214	223	4.886121	GGTGTAGCCGCCGCCTAC	62.886	72.222	0.00	0.00	34.57	3.18
267	282	1.667151	GCAAGCAGCCAATGGTTCA	59.333	52.632	0.00	0.00	46.55	3.18
271	286	2.180017	GTCGCAAGCAGCCAATGG	59.820	61.111	0.00	0.00	41.38	3.16
290	305	0.103208	CTAATTCCGCCAGTCGCTCT	59.897	55.000	0.00	0.00	36.73	4.09
307	322	4.499116	GCTCCTCCCTGGGCCCTA	62.499	72.222	25.70	8.68	36.20	3.53
416	441	2.911143	CGCCTAGCCCCTTCACAT	59.089	61.111	0.00	0.00	0.00	3.21
434	459	4.760047	CCCTTGTCTCCCGTGGCG	62.760	72.222	0.00	0.00	0.00	5.69
476	501	0.390866	GTAGAGCAGAGCAGCAGCAA	60.391	55.000	3.17	0.00	45.49	3.91
500	525	0.180171	TCCTATCACAACCATGGGCG	59.820	55.000	18.09	9.01	0.00	6.13
505	530	3.053395	ACAATGCCTCCTATCACAACCAT	60.053	43.478	0.00	0.00	0.00	3.55
523	548	5.105146	CCTGAGACTTAGACCTTAGCACAAT	60.105	44.000	0.00	0.00	0.00	2.71
529	554	3.634910	GGAGCCTGAGACTTAGACCTTAG	59.365	52.174	0.00	0.00	0.00	2.18
574	599	6.433404	CCAGAGGAGCAATATTTAGCATGAAT	59.567	38.462	0.00	0.00	0.00	2.57
591	618	1.821061	AACACGAGGTGCCAGAGGAG	61.821	60.000	0.00	0.00	36.98	3.69
606	633	1.068588	GGGGAGAAAAGGCACAAACAC	59.931	52.381	0.00	0.00	0.00	3.32
662	689	2.825532	CCATGGGGTGAAAACCTAACAG	59.174	50.000	2.85	0.00	0.00	3.16
701	728	2.130073	GAAAACCCACTGTGCTCGCC	62.130	60.000	1.29	0.00	0.00	5.54
707	734	0.670162	CTGCCAGAAAACCCACTGTG	59.330	55.000	0.00	0.00	32.93	3.66
719	746	0.880278	GAGTTCAACGCACTGCCAGA	60.880	55.000	0.00	0.00	0.00	3.86
720	747	1.571460	GAGTTCAACGCACTGCCAG	59.429	57.895	0.00	0.00	0.00	4.85
764	791	6.421202	GGAAATACAACAGTCTCCGATACATC	59.579	42.308	0.00	0.00	0.00	3.06
789	816	5.126384	TGCCCCTTTCCATTTAAGATAAACG	59.874	40.000	0.00	0.00	0.00	3.60
838	865	3.730761	CAAGCCGTCACTGCTGCC	61.731	66.667	0.00	0.00	39.48	4.85
839	866	0.740868	TATCAAGCCGTCACTGCTGC	60.741	55.000	0.00	0.00	39.48	5.25
840	867	1.945387	ATATCAAGCCGTCACTGCTG	58.055	50.000	0.00	0.00	39.48	4.41
841	868	2.283298	CAATATCAAGCCGTCACTGCT	58.717	47.619	0.00	0.00	41.89	4.24
842	869	1.331756	CCAATATCAAGCCGTCACTGC	59.668	52.381	0.00	0.00	0.00	4.40
843	870	2.352651	CACCAATATCAAGCCGTCACTG	59.647	50.000	0.00	0.00	0.00	3.66
844	871	2.632377	CACCAATATCAAGCCGTCACT	58.368	47.619	0.00	0.00	0.00	3.41
845	872	1.064060	GCACCAATATCAAGCCGTCAC	59.936	52.381	0.00	0.00	0.00	3.67
846	873	1.378531	GCACCAATATCAAGCCGTCA	58.621	50.000	0.00	0.00	0.00	4.35
847	874	0.304705	CGCACCAATATCAAGCCGTC	59.695	55.000	0.00	0.00	0.00	4.79
897	924	4.737855	TGATTAGGGGAGAAGAACGAAG	57.262	45.455	0.00	0.00	0.00	3.79
996	1025	6.007076	ACTCTCTGTCACTGAGTTCATCTTA	58.993	40.000	11.17	0.00	37.76	2.10
1020	1050	5.540337	ACTCTCTGTAACTGAGTTCAATCCA	59.460	40.000	0.00	0.00	37.76	3.41
1044	1146	4.594123	TTCTGTCACCGAGTTCAATACA	57.406	40.909	0.00	0.00	0.00	2.29
1046	1148	5.227908	GTCTTTCTGTCACCGAGTTCAATA	58.772	41.667	0.00	0.00	0.00	1.90
1056	1158	4.058817	AGTTCAATCGTCTTTCTGTCACC	58.941	43.478	0.00	0.00	0.00	4.02
1068	1218	5.941058	TCTCTCTCTTACTGAGTTCAATCGT	59.059	40.000	0.00	0.00	43.13	3.73
1179	1329	1.234821	TTACTTTGGCACGCCTCTTG	58.765	50.000	9.92	0.00	36.94	3.02
1292	1442	5.600226	AGACCAGATCTCTAGCAAACTGCA	61.600	45.833	0.00	0.00	38.65	4.41
1441	1591	2.422479	TGAACTGATCTTCGGTAGGACG	59.578	50.000	0.00	0.00	34.28	4.79
1638	1798	7.955864	GCCTTGTACTCTTGTATTAGTTTTTCG	59.044	37.037	0.00	0.00	0.00	3.46
1653	1813	5.381757	TGTTGTATTTTGGCCTTGTACTCT	58.618	37.500	3.32	0.00	0.00	3.24
1688	1869	2.238646	CAAATGGGGGCTGTACTGAGTA	59.761	50.000	3.61	0.00	0.00	2.59
1745	1926	1.538047	TGGTCCTTTGAGAGCAATGC	58.462	50.000	0.00	0.00	41.08	3.56
1796	1977	2.436646	GCTTTAGCCTCGCCTGCA	60.437	61.111	0.00	0.00	34.31	4.41
1825	2006	0.106519	CCAAGGCCTTCCATTCCGAT	60.107	55.000	17.29	0.00	33.74	4.18
1948	2129	9.109393	TGGCTTTACTTGATGAAGTATATCAAC	57.891	33.333	5.57	0.00	42.92	3.18
1950	2131	8.264347	TGTGGCTTTACTTGATGAAGTATATCA	58.736	33.333	5.57	1.36	42.92	2.15
2038	2219	4.884164	CCTCTTTGTGATGAGGTATTTCCC	59.116	45.833	0.00	0.00	43.49	3.97
2144	2326	6.115448	AGTCAACAGCCTTAGTCTACATTT	57.885	37.500	0.00	0.00	0.00	2.32
2155	2337	6.299805	TGAATACATCTAGTCAACAGCCTT	57.700	37.500	0.00	0.00	0.00	4.35
2702	3005	0.697658	TCTGGTGGATGGCATCAACA	59.302	50.000	30.72	21.94	34.80	3.33
2780	3083	4.142093	ACTTTCAACAACTCATTTGCAGCT	60.142	37.500	0.00	0.00	39.01	4.24
2802	3105	2.911509	TGGCATGCCACCACACAC	60.912	61.111	35.59	6.59	41.89	3.82
2906	3209	8.439964	TCATCCTATCTGATGTGGAATATTGA	57.560	34.615	14.95	11.94	42.24	2.57
2925	3228	7.309255	GCTCATTTGCAATATCATTCTCATCCT	60.309	37.037	0.00	0.00	0.00	3.24
3094	3397	6.126863	TGAAATAGCTTTCTCCTTTCCTCA	57.873	37.500	0.00	0.00	41.18	3.86
3100	3403	4.393371	GCTCGTTGAAATAGCTTTCTCCTT	59.607	41.667	0.00	0.00	41.18	3.36
3450	3769	0.473886	CCCTCAGTATCCCCCGGAAT	60.474	60.000	0.73	0.00	34.34	3.01
3527	3846	4.410099	TCAGATGGTGGCTTCTCAAATTT	58.590	39.130	0.00	0.00	0.00	1.82
3564	3883	1.065636	GTACCTTAGCAGAACCACCCC	60.066	57.143	0.00	0.00	0.00	4.95
3565	3884	1.065636	GGTACCTTAGCAGAACCACCC	60.066	57.143	4.06	0.00	0.00	4.61
3566	3885	1.907255	AGGTACCTTAGCAGAACCACC	59.093	52.381	9.21	0.00	31.36	4.61
3567	3886	2.354805	CCAGGTACCTTAGCAGAACCAC	60.355	54.545	13.15	0.00	31.36	4.16
3648	3967	1.676529	GTGCCTGACATCTAGCGTCTA	59.323	52.381	11.84	0.00	34.37	2.59
3894	4213	2.103373	ACGTGCACTATCCAGAGATGT	58.897	47.619	16.19	0.00	33.67	3.06
3957	4276	2.435805	GACAATGCAGAGATAGGGACCA	59.564	50.000	0.00	0.00	0.00	4.02
4097	4419	5.316167	TGAGCCACTTCAATATTCAAGTGT	58.684	37.500	24.90	11.97	45.49	3.55
4207	4529	1.205655	AGGATGTGTCTGTGTCCATCG	59.794	52.381	0.00	0.00	35.62	3.84
4217	4539	5.010719	TCTCTGTTTTCGTAAGGATGTGTCT	59.989	40.000	0.00	0.00	38.47	3.41
4257	4579	1.216990	CACATAAAGGCTCCCCTCCT	58.783	55.000	0.00	0.00	41.90	3.69
4272	4594	4.706842	ACCAGAACACCTTAAGACACAT	57.293	40.909	3.36	0.00	0.00	3.21
4451	4773	0.036952	CCTCACATGTGAAGGTCGCT	60.037	55.000	27.63	0.00	39.39	4.93
4539	4861	4.164843	ACTCTATTGTTGGTGTGTTGGT	57.835	40.909	0.00	0.00	0.00	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.