AutoCloner

Multiple sequence alignment - TraesCS5B01G173000

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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	TraesCS5B01G173000	chr5B	100.000	4579	0	0	1	4579	317889437	317884859	0.000000e+00	8456.0
1	TraesCS5B01G173000	chr5B	97.010	301	9	0	4278	4578	324614480	324614780	1.470000e-139	507.0
2	TraesCS5B01G173000	chr5B	95.341	279	11	1	3997	4273	324597373	324597651	4.200000e-120	442.0
3	TraesCS5B01G173000	chr5B	83.178	107	12	5	4169	4272	614834803	614834906	4.880000e-15	93.5
4	TraesCS5B01G173000	chr5A	95.306	3451	86	20	731	4144	372931278	372934689	0.000000e+00	5406.0
5	TraesCS5B01G173000	chr5D	96.339	2595	53	16	1448	4007	280307428	280304841	0.000000e+00	4228.0
6	TraesCS5B01G173000	chr5D	97.339	451	8	2	1012	1459	280309743	280309294	0.000000e+00	763.0
7	TraesCS5B01G173000	chr5D	94.865	370	14	5	3915	4281	280304846	280304479	1.430000e-159	573.0
8	TraesCS5B01G173000	chr5D	94.702	302	7	2	4278	4579	280304312	280304020	1.160000e-125	460.0
9	TraesCS5B01G173000	chr3D	90.723	733	63	3	1	728	5057560	5058292	0.000000e+00	972.0
10	TraesCS5B01G173000	chr3D	80.544	735	134	7	1	728	468968117	468968849	1.440000e-154	556.0
11	TraesCS5B01G173000	chr3D	84.112	107	12	3	4173	4279	342717356	342717255	1.050000e-16	99.0
12	TraesCS5B01G173000	chr4A	89.139	755	75	5	1	748	86461166	86460412	0.000000e+00	933.0
13	TraesCS5B01G173000	chr4A	88.904	730	75	4	1	728	13290341	13291066	0.000000e+00	894.0
14	TraesCS5B01G173000	chr1A	88.798	732	78	3	1	730	489153669	489152940	0.000000e+00	894.0
15	TraesCS5B01G173000	chr1A	77.205	737	149	17	3	727	171042316	171043045	3.300000e-111	412.0
16	TraesCS5B01G173000	chr4B	82.466	730	118	7	8	730	72165306	72164580	8.360000e-177	630.0
17	TraesCS5B01G173000	chr4B	89.908	109	8	2	4172	4279	439317133	439317239	2.220000e-28	137.0
18	TraesCS5B01G173000	chr7A	80.628	733	133	7	1	727	513369259	513368530	4.000000e-155	558.0
19	TraesCS5B01G173000	chr7A	88.660	97	10	1	4178	4273	571312104	571312200	2.890000e-22	117.0
20	TraesCS5B01G173000	chr7B	76.461	599	123	14	139	726	248504990	248504399	4.450000e-80	309.0
21	TraesCS5B01G173000	chr2D	79.639	388	73	5	3193	3577	349732377	349731993	1.620000e-69	274.0
22	TraesCS5B01G173000	chr2D	85.714	119	12	5	4156	4273	370824167	370824281	2.240000e-23	121.0
23	TraesCS5B01G173000	chr2A	78.182	385	84	0	3193	3577	465554689	465554305	3.540000e-61	246.0
24	TraesCS5B01G173000	chr3B	83.200	125	17	2	4155	4279	776098313	776098433	1.350000e-20	111.0
25	TraesCS5B01G173000	chr3B	74.654	217	41	13	107	316	729592194	729591985	2.940000e-12	84.2
26	TraesCS5B01G173000	chr6B	82.540	126	11	5	4155	4279	73356028	73356143	2.910000e-17	100.0
27	TraesCS5B01G173000	chr6B	79.545	88	18	0	105	192	712655903	712655816	3.820000e-06	63.9
28	TraesCS5B01G173000	chr4D	73.311	296	67	11	12	300	180671273	180671563	1.050000e-16	99.0

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	TraesCS5B01G173000	chr5B	317884859	317889437	4578	True	8456	8456	100.00000	1	4579	1	chr5B.!!$R1	4578
1	TraesCS5B01G173000	chr5A	372931278	372934689	3411	False	5406	5406	95.30600	731	4144	1	chr5A.!!$F1	3413
2	TraesCS5B01G173000	chr5D	280304020	280309743	5723	True	1506	4228	95.81125	1012	4579	4	chr5D.!!$R1	3567
3	TraesCS5B01G173000	chr3D	5057560	5058292	732	False	972	972	90.72300	1	728	1	chr3D.!!$F1	727
4	TraesCS5B01G173000	chr3D	468968117	468968849	732	False	556	556	80.54400	1	728	1	chr3D.!!$F2	727
5	TraesCS5B01G173000	chr4A	86460412	86461166	754	True	933	933	89.13900	1	748	1	chr4A.!!$R1	747
6	TraesCS5B01G173000	chr4A	13290341	13291066	725	False	894	894	88.90400	1	728	1	chr4A.!!$F1	727
7	TraesCS5B01G173000	chr1A	489152940	489153669	729	True	894	894	88.79800	1	730	1	chr1A.!!$R1	729
8	TraesCS5B01G173000	chr1A	171042316	171043045	729	False	412	412	77.20500	3	727	1	chr1A.!!$F1	724
9	TraesCS5B01G173000	chr4B	72164580	72165306	726	True	630	630	82.46600	8	730	1	chr4B.!!$R1	722
10	TraesCS5B01G173000	chr7A	513368530	513369259	729	True	558	558	80.62800	1	727	1	chr7A.!!$R1	726
11	TraesCS5B01G173000	chr7B	248504399	248504990	591	True	309	309	76.46100	139	726	1	chr7B.!!$R1	587

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
860	870	0.033504	TCACTCACGCCCAAGAAGTC	59.966	55.000	0.0	0.0	0.00	3.01	F
864	874	0.033504	TCACGCCCAAGAAGTCACTC	59.966	55.000	0.0	0.0	0.00	3.51	F
867	877	0.034059	CGCCCAAGAAGTCACTCACT	59.966	55.000	0.0	0.0	36.64	3.41	F
894	904	0.454196	AAGACAAAACCACGGCACAC	59.546	50.000	0.0	0.0	0.00	3.82	F
922	932	0.936600	TCGTGAGTTGTACGTGTCGA	59.063	50.000	0.0	0.0	41.91	4.20	F
1496	3392	1.830477	GTGGCTCTGTTCCTCTCTCAT	59.170	52.381	0.0	0.0	0.00	2.90	F
3380	5312	1.604308	CATCCTTGCTGTGGTGGCA	60.604	57.895	0.0	0.0	37.97	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2150	4081	1.488705	TTGGCTCTCGGGGTCACATT	61.489	55.000	0.00	0.0	0.00	2.71	R
2568	4500	3.338249	CGGCTTGAGAAAGGAAGATGAA	58.662	45.455	0.00	0.0	0.00	2.57	R
2825	4757	5.509498	AGCCCATTAAAAGCACTTCTATCA	58.491	37.500	0.00	0.0	0.00	2.15	R
2996	4928	1.909700	ATCCGCACACTCCAAAACAT	58.090	45.000	0.00	0.0	0.00	2.71	R
3380	5312	0.726827	CAAATGCAGGCACGTACGAT	59.273	50.000	24.41	3.1	0.00	3.73	R
3461	5393	1.005097	ACAATGCTGAGATGGAAGGCA	59.995	47.619	0.00	0.0	37.32	4.75	R
4342	6552	2.362077	ACTGCATTTGTTCTGTTGGGAC	59.638	45.455	0.00	0.0	0.00	4.46	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
26	27	1.302832	CTGTTTCTCTTGGCCGGCT	60.303	57.895	28.56	0.00	0.00	5.52
192	193	1.935327	CTGGACTTCGGACCGGAGAC	61.935	65.000	29.25	22.02	38.18	3.36
199	200	2.838693	GGACCGGAGACCTAGGCC	60.839	72.222	9.46	0.00	0.00	5.19
242	243	4.337836	TCAAACTGCTTCACATGCTTACAA	59.662	37.500	0.00	0.00	0.00	2.41
301	304	1.374947	GCTAGGGAAGTGTGGCACA	59.625	57.895	17.96	17.96	36.74	4.57
334	337	1.280998	AGCTTAACTTGGCCGTGGTAT	59.719	47.619	0.00	0.00	0.00	2.73
397	400	2.152016	CAAGGAGAGGGTTTCGGAAAC	58.848	52.381	22.26	22.26	40.65	2.78
421	424	2.484651	CTCAAGAGAGGTTTCGACTCGA	59.515	50.000	0.00	0.00	39.90	4.04
501	504	3.732849	GCCCAACAGCTAGCCCCT	61.733	66.667	12.13	0.00	0.00	4.79
543	546	6.204882	TGATCTTAAGAGATATTCGCGAGTGA	59.795	38.462	15.03	0.00	42.66	3.41
596	600	2.515854	ACGCTTTGTGAGAGAGTAGGA	58.484	47.619	0.00	0.00	0.00	2.94
615	621	2.094234	GGATTGTAATGGTGTTGGGTGC	60.094	50.000	0.00	0.00	0.00	5.01
680	689	5.703876	CCTCTCTTGTAAATTTGTTGCTCC	58.296	41.667	0.00	0.00	0.00	4.70
787	797	4.479619	GACAGAAAATCATGTGTGCTTCC	58.520	43.478	0.00	0.00	0.00	3.46
836	846	1.666553	TGCGCTTTACACGTCCCAG	60.667	57.895	9.73	0.00	0.00	4.45
849	859	0.039074	GTCCCAGTCACTCACTCACG	60.039	60.000	0.00	0.00	30.26	4.35
851	861	1.373497	CCAGTCACTCACTCACGCC	60.373	63.158	0.00	0.00	30.26	5.68
853	863	1.832608	AGTCACTCACTCACGCCCA	60.833	57.895	0.00	0.00	0.00	5.36
854	864	1.069090	GTCACTCACTCACGCCCAA	59.931	57.895	0.00	0.00	0.00	4.12
855	865	0.946221	GTCACTCACTCACGCCCAAG	60.946	60.000	0.00	0.00	0.00	3.61
856	866	1.112916	TCACTCACTCACGCCCAAGA	61.113	55.000	0.00	0.00	0.00	3.02
857	867	0.249868	CACTCACTCACGCCCAAGAA	60.250	55.000	0.00	0.00	0.00	2.52
858	868	0.034059	ACTCACTCACGCCCAAGAAG	59.966	55.000	0.00	0.00	0.00	2.85
859	869	0.034059	CTCACTCACGCCCAAGAAGT	59.966	55.000	0.00	0.00	0.00	3.01
860	870	0.033504	TCACTCACGCCCAAGAAGTC	59.966	55.000	0.00	0.00	0.00	3.01
861	871	0.249868	CACTCACGCCCAAGAAGTCA	60.250	55.000	0.00	0.00	0.00	3.41
862	872	0.249911	ACTCACGCCCAAGAAGTCAC	60.250	55.000	0.00	0.00	0.00	3.67
863	873	0.034059	CTCACGCCCAAGAAGTCACT	59.966	55.000	0.00	0.00	0.00	3.41
864	874	0.033504	TCACGCCCAAGAAGTCACTC	59.966	55.000	0.00	0.00	0.00	3.51
865	875	0.249868	CACGCCCAAGAAGTCACTCA	60.250	55.000	0.00	0.00	0.00	3.41
866	876	0.249911	ACGCCCAAGAAGTCACTCAC	60.250	55.000	0.00	0.00	0.00	3.51
867	877	0.034059	CGCCCAAGAAGTCACTCACT	59.966	55.000	0.00	0.00	36.64	3.41
868	878	1.802069	GCCCAAGAAGTCACTCACTC	58.198	55.000	0.00	0.00	32.30	3.51
869	879	1.070758	GCCCAAGAAGTCACTCACTCA	59.929	52.381	0.00	0.00	32.30	3.41
876	886	1.069090	GTCACTCACTCACGCCCAA	59.931	57.895	0.00	0.00	0.00	4.12
894	904	0.454196	AAGACAAAACCACGGCACAC	59.546	50.000	0.00	0.00	0.00	3.82
898	908	2.025155	ACAAAACCACGGCACACATAA	58.975	42.857	0.00	0.00	0.00	1.90
899	909	2.625790	ACAAAACCACGGCACACATAAT	59.374	40.909	0.00	0.00	0.00	1.28
911	921	4.181578	GCACACATAATACCTCGTGAGTT	58.818	43.478	0.00	0.00	33.56	3.01
922	932	0.936600	TCGTGAGTTGTACGTGTCGA	59.063	50.000	0.00	0.00	41.91	4.20
997	1007	2.158330	CGTACGCGATTGCTGCTGA	61.158	57.895	15.93	0.00	41.33	4.26
1261	1274	6.555315	GTCAGTATCTACCCAAATTTGCTTG	58.445	40.000	12.92	5.93	0.00	4.01
1269	1282	3.582208	ACCCAAATTTGCTTGGCATCTTA	59.418	39.130	12.92	0.00	43.97	2.10
1333	1352	3.293337	AGAATATTGGAGCTGCAATGCA	58.707	40.909	35.42	21.71	36.92	3.96
1496	3392	1.830477	GTGGCTCTGTTCCTCTCTCAT	59.170	52.381	0.00	0.00	0.00	2.90
1500	3396	3.197549	GGCTCTGTTCCTCTCTCATCTTT	59.802	47.826	0.00	0.00	0.00	2.52
1889	3814	8.675705	TCGCATGATCTCTTTATTCCAAAATA	57.324	30.769	0.00	0.00	0.00	1.40
1952	3878	9.783256	AGTCATGTAACAAGTTTTTGTAAAGAC	57.217	29.630	0.00	0.00	46.54	3.01
2240	4172	6.426937	TGTGTATTCTACTTTTCCTGTTGCTC	59.573	38.462	0.00	0.00	0.00	4.26
2329	4261	8.766994	ATAATTGGCACTACTTTTATGGTGAT	57.233	30.769	0.00	0.00	33.10	3.06
2825	4757	2.094545	GCTTTTCGACCATCCATTTGCT	60.095	45.455	0.00	0.00	0.00	3.91
2996	4928	7.856145	TGTATGTATCATGTTTGTGTATGCA	57.144	32.000	0.00	0.00	0.00	3.96
3380	5312	1.604308	CATCCTTGCTGTGGTGGCA	60.604	57.895	0.00	0.00	37.97	4.92
3461	5393	1.738099	CGCTTTCGTGCTGCCTACT	60.738	57.895	0.00	0.00	0.00	2.57
3578	5510	3.239449	TGGAACCTTCACTGCTCTCTAA	58.761	45.455	0.00	0.00	0.00	2.10
3640	5572	0.602905	GGTGTGTACAGGTCAGGTGC	60.603	60.000	0.00	0.00	0.00	5.01
3662	5594	7.548780	GGTGCAATTATAAACCACATGACAAAT	59.451	33.333	0.00	0.00	32.69	2.32
3664	5596	9.149225	TGCAATTATAAACCACATGACAAATTC	57.851	29.630	0.00	0.00	0.00	2.17
3707	5639	8.814038	AGCAATAGAAAAGAAACACCATCTAT	57.186	30.769	0.00	0.00	32.90	1.98
3729	5661	9.467258	TCTATAAGAAGACGACGAAAAGAAAAA	57.533	29.630	0.00	0.00	0.00	1.94
3794	5726	0.820871	CTCGAAGGAAGCCTAGCTGT	59.179	55.000	0.00	0.00	39.62	4.40
3877	5809	2.548067	GGTAGCGCATGGTAGCTTATGT	60.548	50.000	11.47	0.00	44.15	2.29
4016	6036	5.594926	TCGTATAAAAACGAGGAAGGATCC	58.405	41.667	2.48	2.48	46.29	3.36
4024	6044	3.426917	GGAAGGATCCTTGGGGCA	58.573	61.111	31.79	0.00	42.93	5.36
4025	6045	1.933629	GGAAGGATCCTTGGGGCAT	59.066	57.895	31.79	5.52	42.93	4.40
4026	6046	0.262876	GGAAGGATCCTTGGGGCATT	59.737	55.000	31.79	4.65	42.93	3.56
4027	6047	1.697284	GAAGGATCCTTGGGGCATTC	58.303	55.000	31.79	10.89	36.26	2.67
4028	6048	1.216427	GAAGGATCCTTGGGGCATTCT	59.784	52.381	31.79	2.94	36.26	2.40
4029	6049	0.849417	AGGATCCTTGGGGCATTCTC	59.151	55.000	9.02	0.00	0.00	2.87
4030	6050	0.178978	GGATCCTTGGGGCATTCTCC	60.179	60.000	3.84	0.00	0.00	3.71
4031	6051	0.178978	GATCCTTGGGGCATTCTCCC	60.179	60.000	0.00	0.00	45.80	4.30
4105	6143	1.089920	GTGGCTGCATAGGTGTTCTG	58.910	55.000	0.50	0.00	0.00	3.02
4273	6313	2.224549	CGTGAAGTCCGTGCCAAATTTA	59.775	45.455	0.00	0.00	0.00	1.40
4340	6550	1.012486	CGGAAGAAAACCGTCTCCCG	61.012	60.000	0.00	0.00	44.57	5.14
4341	6551	0.319405	GGAAGAAAACCGTCTCCCGA	59.681	55.000	0.00	0.00	39.56	5.14
4342	6552	1.672145	GGAAGAAAACCGTCTCCCGAG	60.672	57.143	0.00	0.00	39.56	4.63
4343	6553	1.000618	GAAGAAAACCGTCTCCCGAGT	59.999	52.381	0.00	0.00	39.56	4.18
4344	6554	0.602060	AGAAAACCGTCTCCCGAGTC	59.398	55.000	0.00	0.00	39.56	3.36
4345	6555	0.389556	GAAAACCGTCTCCCGAGTCC	60.390	60.000	0.00	0.00	39.56	3.85
4346	6556	1.824224	AAAACCGTCTCCCGAGTCCC	61.824	60.000	0.00	0.00	39.56	4.46
4357	6567	1.476110	CCCGAGTCCCAACAGAACAAA	60.476	52.381	0.00	0.00	0.00	2.83
4459	6669	5.278315	GCGAACTTTGGGATTCAAGTAAGTT	60.278	40.000	0.00	0.00	36.93	2.66
4460	6670	6.072893	GCGAACTTTGGGATTCAAGTAAGTTA	60.073	38.462	0.00	0.00	35.36	2.24
4537	6747	5.904362	AGAGTTTGTTCACTTCTTTGCTT	57.096	34.783	0.00	0.00	0.00	3.91
4541	6751	8.470002	AGAGTTTGTTCACTTCTTTGCTTAAAT	58.530	29.630	0.00	0.00	0.00	1.40
4546	6756	9.730420	TTGTTCACTTCTTTGCTTAAATAACTC	57.270	29.630	0.00	0.00	0.00	3.01
4556	6766	8.862325	TTTGCTTAAATAACTCCATCTTCTCA	57.138	30.769	0.00	0.00	0.00	3.27
4557	6767	8.862325	TTGCTTAAATAACTCCATCTTCTCAA	57.138	30.769	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	4.244066	AGTACGTCGATCTCGCAGTATAT	58.756	43.478	0.00	0.00	39.60	0.86
192	193	3.711059	CTTGCAGCCCAGGCCTAGG	62.711	68.421	13.73	13.73	43.17	3.02
242	243	1.202371	TGTTCAGCGTTGTCTTCGTCT	60.202	47.619	0.00	0.00	0.00	4.18
301	304	5.587844	CCAAGTTAAGCTCATGTAAGCATCT	59.412	40.000	8.91	0.00	45.00	2.90
309	312	1.271379	ACGGCCAAGTTAAGCTCATGT	60.271	47.619	2.24	0.00	0.00	3.21
334	337	0.331616	TCATCCTCTCTGGTCGGTCA	59.668	55.000	0.00	0.00	37.07	4.02
397	400	4.420168	GAGTCGAAACCTCTCTTGAGATG	58.580	47.826	0.41	1.40	42.73	2.90
421	424	3.640407	AGCCACCGCTGTCACCAT	61.640	61.111	0.00	0.00	46.19	3.55
471	474	3.255642	GCTGTTGGGCTGTTCTATTGAAA	59.744	43.478	0.00	0.00	33.52	2.69
501	504	1.919240	TCACTTCCACTAGCTCCGAA	58.081	50.000	0.00	0.00	0.00	4.30
543	546	0.695803	CCCCTAGACCTGCATCCCTT	60.696	60.000	0.00	0.00	0.00	3.95
596	600	1.543802	CGCACCCAACACCATTACAAT	59.456	47.619	0.00	0.00	0.00	2.71
680	689	6.925165	TCGCGTACCTTAATTTTATAGAAGGG	59.075	38.462	5.77	0.00	42.39	3.95
765	775	4.217118	AGGAAGCACACATGATTTTCTGTC	59.783	41.667	0.00	0.00	33.63	3.51
836	846	0.946221	CTTGGGCGTGAGTGAGTGAC	60.946	60.000	0.00	0.00	0.00	3.67
849	859	1.070758	TGAGTGAGTGACTTCTTGGGC	59.929	52.381	0.00	0.00	33.83	5.36
851	861	2.398498	CGTGAGTGAGTGACTTCTTGG	58.602	52.381	0.00	0.00	33.83	3.61
853	863	1.269831	GGCGTGAGTGAGTGACTTCTT	60.270	52.381	0.00	0.00	33.83	2.52
854	864	0.315568	GGCGTGAGTGAGTGACTTCT	59.684	55.000	0.00	0.00	33.83	2.85
855	865	0.667792	GGGCGTGAGTGAGTGACTTC	60.668	60.000	0.00	0.00	33.83	3.01
856	866	1.367840	GGGCGTGAGTGAGTGACTT	59.632	57.895	0.00	0.00	33.83	3.01
857	867	1.399744	TTGGGCGTGAGTGAGTGACT	61.400	55.000	0.00	0.00	37.76	3.41
858	868	0.946221	CTTGGGCGTGAGTGAGTGAC	60.946	60.000	0.00	0.00	0.00	3.67
859	869	1.112916	TCTTGGGCGTGAGTGAGTGA	61.113	55.000	0.00	0.00	0.00	3.41
860	870	0.946221	GTCTTGGGCGTGAGTGAGTG	60.946	60.000	0.00	0.00	0.00	3.51
861	871	1.367840	GTCTTGGGCGTGAGTGAGT	59.632	57.895	0.00	0.00	0.00	3.41
862	872	0.249868	TTGTCTTGGGCGTGAGTGAG	60.250	55.000	0.00	0.00	0.00	3.51
863	873	0.179234	TTTGTCTTGGGCGTGAGTGA	59.821	50.000	0.00	0.00	0.00	3.41
864	874	1.021202	TTTTGTCTTGGGCGTGAGTG	58.979	50.000	0.00	0.00	0.00	3.51
865	875	1.021968	GTTTTGTCTTGGGCGTGAGT	58.978	50.000	0.00	0.00	0.00	3.41
866	876	0.310854	GGTTTTGTCTTGGGCGTGAG	59.689	55.000	0.00	0.00	0.00	3.51
867	877	0.394488	TGGTTTTGTCTTGGGCGTGA	60.394	50.000	0.00	0.00	0.00	4.35
868	878	0.248866	GTGGTTTTGTCTTGGGCGTG	60.249	55.000	0.00	0.00	0.00	5.34
869	879	1.720694	CGTGGTTTTGTCTTGGGCGT	61.721	55.000	0.00	0.00	0.00	5.68
876	886	0.678366	TGTGTGCCGTGGTTTTGTCT	60.678	50.000	0.00	0.00	0.00	3.41
894	904	5.454554	CACGTACAACTCACGAGGTATTATG	59.545	44.000	1.43	0.00	41.91	1.90
898	908	2.816087	ACACGTACAACTCACGAGGTAT	59.184	45.455	1.43	0.00	41.91	2.73
899	909	2.221169	ACACGTACAACTCACGAGGTA	58.779	47.619	1.43	0.00	41.91	3.08
911	921	3.271014	GAGGCCTCGACACGTACA	58.729	61.111	19.06	0.00	0.00	2.90
997	1007	2.273449	CTTTGCCTCCGCCATCCT	59.727	61.111	0.00	0.00	0.00	3.24
1217	1230	1.118838	GAGGAGGAGCATGCAGTAGT	58.881	55.000	21.98	0.00	0.00	2.73
1261	1274	6.128145	GGAGAGAAACAAAAGAGTAAGATGCC	60.128	42.308	0.00	0.00	0.00	4.40
1269	1282	2.104963	AGCGGGAGAGAAACAAAAGAGT	59.895	45.455	0.00	0.00	0.00	3.24
1333	1352	6.043590	TCACCCAATCTGCATATAGACAGAAT	59.956	38.462	10.56	1.60	45.49	2.40
1562	3467	3.930229	CCACCGATTTCATAACGAGACAA	59.070	43.478	0.00	0.00	0.00	3.18
1622	3529	6.463995	AATAGCGCAATCCTTAAAATCCAA	57.536	33.333	11.47	0.00	0.00	3.53
1952	3878	4.752661	TCTTAAACCCGGTTTGAATTCG	57.247	40.909	23.45	5.76	36.37	3.34
1987	3913	6.932400	TCACAATGTGAAAACGGTATTCTAGT	59.068	34.615	14.37	0.00	39.78	2.57
2136	4064	4.862574	GGGTCACATTCCGCTTTAAAAATC	59.137	41.667	0.00	0.00	0.00	2.17
2137	4065	4.322424	GGGGTCACATTCCGCTTTAAAAAT	60.322	41.667	0.00	0.00	35.46	1.82
2143	4074	1.674322	CGGGGTCACATTCCGCTTT	60.674	57.895	0.00	0.00	37.25	3.51
2150	4081	1.488705	TTGGCTCTCGGGGTCACATT	61.489	55.000	0.00	0.00	0.00	2.71
2198	4130	8.966868	AGAATACACATGTTTAACCATTTAGGG	58.033	33.333	0.00	0.00	43.89	3.53
2335	4267	5.878332	AAGATTCGTCATAATGCACACAA	57.122	34.783	0.00	0.00	0.00	3.33
2568	4500	3.338249	CGGCTTGAGAAAGGAAGATGAA	58.662	45.455	0.00	0.00	0.00	2.57
2825	4757	5.509498	AGCCCATTAAAAGCACTTCTATCA	58.491	37.500	0.00	0.00	0.00	2.15
2996	4928	1.909700	ATCCGCACACTCCAAAACAT	58.090	45.000	0.00	0.00	0.00	2.71
3380	5312	0.726827	CAAATGCAGGCACGTACGAT	59.273	50.000	24.41	3.10	0.00	3.73
3461	5393	1.005097	ACAATGCTGAGATGGAAGGCA	59.995	47.619	0.00	0.00	37.32	4.75
3662	5594	5.247862	TGCTTTCTCTCATGTGCATTAGAA	58.752	37.500	0.00	0.00	0.00	2.10
3664	5596	5.556355	TTGCTTTCTCTCATGTGCATTAG	57.444	39.130	0.00	0.00	0.00	1.73
3794	5726	7.202011	GGGATTCTAGTAGATCTTTGTGCCTTA	60.202	40.741	0.00	0.00	0.00	2.69
3877	5809	4.637534	CACCCTACTGCTTAGTACTCGTAA	59.362	45.833	0.00	0.00	0.00	3.18
4030	6050	6.439058	TCCTCATTTTAACTAAACATTGGGGG	59.561	38.462	0.00	0.00	0.00	5.40
4031	6051	7.475137	TCCTCATTTTAACTAAACATTGGGG	57.525	36.000	0.00	0.00	0.00	4.96
4032	6052	8.531146	ACATCCTCATTTTAACTAAACATTGGG	58.469	33.333	0.00	0.00	0.00	4.12
4037	6075	7.721842	TCACCACATCCTCATTTTAACTAAACA	59.278	33.333	0.00	0.00	0.00	2.83
4105	6143	4.273318	AGCTATCATGTTGGTCCCTTTTC	58.727	43.478	0.00	0.00	0.00	2.29
4167	6206	2.901192	TGAATTTACTGTCCACCTCGGA	59.099	45.455	0.00	0.00	43.61	4.55
4273	6313	5.652324	AGACCCTTATACGGATATTCCACT	58.348	41.667	0.00	0.00	35.91	4.00
4340	6550	2.622942	TGCATTTGTTCTGTTGGGACTC	59.377	45.455	0.00	0.00	0.00	3.36
4341	6551	2.624838	CTGCATTTGTTCTGTTGGGACT	59.375	45.455	0.00	0.00	0.00	3.85
4342	6552	2.362077	ACTGCATTTGTTCTGTTGGGAC	59.638	45.455	0.00	0.00	0.00	4.46
4343	6553	2.665165	ACTGCATTTGTTCTGTTGGGA	58.335	42.857	0.00	0.00	0.00	4.37
4344	6554	3.317711	TGTACTGCATTTGTTCTGTTGGG	59.682	43.478	0.00	0.00	0.00	4.12
4345	6555	4.566545	TGTACTGCATTTGTTCTGTTGG	57.433	40.909	0.00	0.00	0.00	3.77
4346	6556	8.746922	AAATATGTACTGCATTTGTTCTGTTG	57.253	30.769	0.00	0.00	38.94	3.33
4357	6567	6.989169	GGTTCTCTCTGAAATATGTACTGCAT	59.011	38.462	0.00	0.00	37.73	3.96
4485	6695	4.973663	GGTACACATCAAAACTTCCGTTTG	59.026	41.667	0.00	0.00	42.28	2.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.