AutoCloner

Multiple sequence alignment - TraesCS4A01G281100

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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	TraesCS4A01G281100	chr4A	100.000	3020	0	0	1	3020	589485132	589488151	0.000000e+00	5578.0
1	TraesCS4A01G281100	chr4A	91.375	800	60	4	1	791	662057859	662057060	0.000000e+00	1086.0
2	TraesCS4A01G281100	chr3A	97.702	1001	23	0	2020	3020	200681495	200680495	0.000000e+00	1722.0
3	TraesCS4A01G281100	chr3A	90.217	1012	76	7	2019	3019	23370293	23371292	0.000000e+00	1299.0
4	TraesCS4A01G281100	chr3A	87.734	587	51	12	2019	2602	556992143	556991575	0.000000e+00	665.0
5	TraesCS4A01G281100	chr3A	71.995	732	175	27	73	789	372173106	372172390	3.970000e-44	189.0
6	TraesCS4A01G281100	chr5D	96.903	1001	31	0	2020	3020	477398486	477397486	0.000000e+00	1677.0
7	TraesCS4A01G281100	chr7D	96.707	1002	32	1	2020	3020	135936320	135937321	0.000000e+00	1666.0
8	TraesCS4A01G281100	chr7D	96.502	972	34	0	2049	3020	4599022	4599993	0.000000e+00	1607.0
9	TraesCS4A01G281100	chr7D	75.332	377	83	8	1135	1506	5187741	5188112	4.000000e-39	172.0
10	TraesCS4A01G281100	chr1D	96.119	1005	38	1	2016	3020	405082682	405081679	0.000000e+00	1639.0
11	TraesCS4A01G281100	chr4D	96.016	1004	37	3	2019	3020	300858937	300859939	0.000000e+00	1629.0
12	TraesCS4A01G281100	chr4D	88.802	893	76	7	1072	1955	12988866	12989743	0.000000e+00	1074.0
13	TraesCS4A01G281100	chr4D	85.285	965	127	6	1000	1958	12138910	12137955	0.000000e+00	981.0
14	TraesCS4A01G281100	chr4D	93.836	292	11	3	789	1073	12973743	12974034	1.660000e-117	433.0
15	TraesCS4A01G281100	chr4D	95.312	64	3	0	1956	2019	12137888	12137825	5.330000e-18	102.0
16	TraesCS4A01G281100	chr4D	89.062	64	7	0	1956	2019	12989815	12989878	2.500000e-11	80.5
17	TraesCS4A01G281100	chr4D	81.373	102	14	5	800	898	12139172	12139073	8.980000e-11	78.7
18	TraesCS4A01G281100	chr5B	92.703	973	45	6	2049	3020	709010829	709009882	0.000000e+00	1380.0
19	TraesCS4A01G281100	chr3B	92.395	789	55	4	1	788	104265955	104266739	0.000000e+00	1120.0
20	TraesCS4A01G281100	chr3B	78.202	367	76	4	1161	1525	147553278	147553642	6.510000e-57	231.0
21	TraesCS4A01G281100	chr2B	92.152	790	60	2	1	790	753067576	753068363	0.000000e+00	1114.0
22	TraesCS4A01G281100	chr2B	91.793	792	64	1	1	792	32146766	32147556	0.000000e+00	1101.0
23	TraesCS4A01G281100	chr7B	91.772	790	64	1	1	790	123741203	123741991	0.000000e+00	1098.0
24	TraesCS4A01G281100	chr7B	91.656	791	65	1	1	791	635904170	635904959	0.000000e+00	1094.0
25	TraesCS4A01G281100	chr1B	91.551	793	66	1	1	793	361010660	361009869	0.000000e+00	1092.0
26	TraesCS4A01G281100	chr5A	91.635	789	59	4	1	789	395283686	395284467	0.000000e+00	1085.0
27	TraesCS4A01G281100	chr1A	87.975	790	94	1	1	790	556597276	556596488	0.000000e+00	931.0
28	TraesCS4A01G281100	chr4B	84.101	912	132	6	1000	1910	22177105	22178004	0.000000e+00	869.0
29	TraesCS4A01G281100	chr4B	77.670	103	19	3	800	898	22250922	22251024	3.250000e-05	60.2
30	TraesCS4A01G281100	chr6B	92.226	566	38	4	2018	2582	612269057	612268497	0.000000e+00	797.0
31	TraesCS4A01G281100	chr6B	95.153	392	16	3	2629	3020	612220747	612220359	1.540000e-172	616.0
32	TraesCS4A01G281100	chr3D	88.444	450	49	3	2020	2468	30500007	30499560	9.530000e-150	540.0
33	TraesCS4A01G281100	chr7A	76.923	377	77	8	1135	1506	6531894	6532265	3.950000e-49	206.0

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	TraesCS4A01G281100	chr4A	589485132	589488151	3019	False	5578.000000	5578	100.000000	1	3020	1	chr4A.!!$F1	3019
1	TraesCS4A01G281100	chr4A	662057060	662057859	799	True	1086.000000	1086	91.375000	1	791	1	chr4A.!!$R1	790
2	TraesCS4A01G281100	chr3A	200680495	200681495	1000	True	1722.000000	1722	97.702000	2020	3020	1	chr3A.!!$R1	1000
3	TraesCS4A01G281100	chr3A	23370293	23371292	999	False	1299.000000	1299	90.217000	2019	3019	1	chr3A.!!$F1	1000
4	TraesCS4A01G281100	chr3A	556991575	556992143	568	True	665.000000	665	87.734000	2019	2602	1	chr3A.!!$R3	583
5	TraesCS4A01G281100	chr5D	477397486	477398486	1000	True	1677.000000	1677	96.903000	2020	3020	1	chr5D.!!$R1	1000
6	TraesCS4A01G281100	chr7D	135936320	135937321	1001	False	1666.000000	1666	96.707000	2020	3020	1	chr7D.!!$F3	1000
7	TraesCS4A01G281100	chr7D	4599022	4599993	971	False	1607.000000	1607	96.502000	2049	3020	1	chr7D.!!$F1	971
8	TraesCS4A01G281100	chr1D	405081679	405082682	1003	True	1639.000000	1639	96.119000	2016	3020	1	chr1D.!!$R1	1004
9	TraesCS4A01G281100	chr4D	300858937	300859939	1002	False	1629.000000	1629	96.016000	2019	3020	1	chr4D.!!$F2	1001
10	TraesCS4A01G281100	chr4D	12988866	12989878	1012	False	577.250000	1074	88.932000	1072	2019	2	chr4D.!!$F3	947
11	TraesCS4A01G281100	chr4D	12137825	12139172	1347	True	387.233333	981	87.323333	800	2019	3	chr4D.!!$R1	1219
12	TraesCS4A01G281100	chr5B	709009882	709010829	947	True	1380.000000	1380	92.703000	2049	3020	1	chr5B.!!$R1	971
13	TraesCS4A01G281100	chr3B	104265955	104266739	784	False	1120.000000	1120	92.395000	1	788	1	chr3B.!!$F1	787
14	TraesCS4A01G281100	chr2B	753067576	753068363	787	False	1114.000000	1114	92.152000	1	790	1	chr2B.!!$F2	789
15	TraesCS4A01G281100	chr2B	32146766	32147556	790	False	1101.000000	1101	91.793000	1	792	1	chr2B.!!$F1	791
16	TraesCS4A01G281100	chr7B	123741203	123741991	788	False	1098.000000	1098	91.772000	1	790	1	chr7B.!!$F1	789
17	TraesCS4A01G281100	chr7B	635904170	635904959	789	False	1094.000000	1094	91.656000	1	791	1	chr7B.!!$F2	790
18	TraesCS4A01G281100	chr1B	361009869	361010660	791	True	1092.000000	1092	91.551000	1	793	1	chr1B.!!$R1	792
19	TraesCS4A01G281100	chr5A	395283686	395284467	781	False	1085.000000	1085	91.635000	1	789	1	chr5A.!!$F1	788
20	TraesCS4A01G281100	chr1A	556596488	556597276	788	True	931.000000	931	87.975000	1	790	1	chr1A.!!$R1	789
21	TraesCS4A01G281100	chr4B	22177105	22178004	899	False	869.000000	869	84.101000	1000	1910	1	chr4B.!!$F1	910
22	TraesCS4A01G281100	chr6B	612268497	612269057	560	True	797.000000	797	92.226000	2018	2582	1	chr6B.!!$R2	564

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
722	733	0.036010	CGGGCTGTCTGGTCTCAAAT	60.036	55.0	0.0	0.0	0.00	2.32	F
1497	1579	0.035439	ACCCATTCACCCGTGACATC	60.035	55.0	0.0	0.0	39.66	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1655	1737	0.325296	TTGCGTCTCCAGGGAGGTAT	60.325	55.0	15.08	0.0	42.20	2.73	R
2997	3170	0.121197	TTCCAGTGGAAGGGGAGGAT	59.879	55.0	21.05	0.0	36.71	3.24	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	2.483014	AAATGGTTGATCGTTCGGGA	57.517	45.000	0.00	0.00	0.00	5.14
56	57	1.825474	CTAGAACACATCCTGGTCGGT	59.175	52.381	0.00	0.00	42.12	4.69
140	141	1.262640	GGTACCTGTGGTGGATCCGT	61.263	60.000	7.39	0.00	36.19	4.69
155	156	1.443872	CCGTCGCCAGTACACTCAC	60.444	63.158	0.00	0.00	0.00	3.51
169	170	5.721960	AGTACACTCACAATGGTAATCCTCT	59.278	40.000	0.00	0.00	34.23	3.69
195	196	4.696877	CAGCATTCAAATGGCCTATATCGA	59.303	41.667	3.32	0.00	36.90	3.59
206	207	4.342378	TGGCCTATATCGATCCTTGCTATC	59.658	45.833	0.00	0.00	0.00	2.08
244	245	2.362077	AGGCAAATGCGAAGAAAACTGT	59.638	40.909	0.00	0.00	43.26	3.55
279	280	4.168291	GGGAGAAGCCGGAGCCTG	62.168	72.222	5.05	0.00	41.25	4.85
306	307	8.659925	ATTTGTCAAACTAAATGTTGATGCAA	57.340	26.923	0.00	0.00	39.13	4.08
377	378	0.871722	TGAATGGACCGTTTCTTGCG	59.128	50.000	0.00	0.00	0.00	4.85
389	391	1.846007	TTCTTGCGGCCCAATGTATT	58.154	45.000	0.00	0.00	31.91	1.89
418	420	1.538047	GTGGCATCAAGTGTGGTCAT	58.462	50.000	0.00	0.00	0.00	3.06
621	623	6.670695	AGGTCAAATTTAAGCATTGTCCTT	57.329	33.333	8.73	0.00	38.76	3.36
722	733	0.036010	CGGGCTGTCTGGTCTCAAAT	60.036	55.000	0.00	0.00	0.00	2.32
747	758	5.873179	TGTGGACGATGTAATTCCTTTTC	57.127	39.130	0.00	0.00	0.00	2.29
832	844	1.277326	TGCACGCATCAGATTCGTAC	58.723	50.000	7.82	3.36	34.81	3.67
833	845	1.277326	GCACGCATCAGATTCGTACA	58.723	50.000	7.82	0.00	34.81	2.90
834	846	1.658596	GCACGCATCAGATTCGTACAA	59.341	47.619	7.82	0.00	34.81	2.41
835	847	2.285220	GCACGCATCAGATTCGTACAAT	59.715	45.455	7.82	0.00	34.81	2.71
836	848	3.602491	GCACGCATCAGATTCGTACAATC	60.602	47.826	7.82	8.94	34.81	2.67
837	849	3.060272	CACGCATCAGATTCGTACAATCC	60.060	47.826	7.82	0.77	34.81	3.01
838	850	2.153817	CGCATCAGATTCGTACAATCCG	59.846	50.000	11.86	5.27	0.00	4.18
848	863	5.766702	TTCGTACAATCCGACAACATAAC	57.233	39.130	0.00	0.00	33.41	1.89
854	869	7.042321	CGTACAATCCGACAACATAACCATTAT	60.042	37.037	0.00	0.00	0.00	1.28
856	871	8.740123	ACAATCCGACAACATAACCATTATTA	57.260	30.769	0.00	0.00	0.00	0.98
857	872	8.836413	ACAATCCGACAACATAACCATTATTAG	58.164	33.333	0.00	0.00	0.00	1.73
861	876	8.885722	TCCGACAACATAACCATTATTAGTTTC	58.114	33.333	0.00	0.00	0.00	2.78
865	880	8.889717	ACAACATAACCATTATTAGTTTCCTCG	58.110	33.333	0.00	0.00	0.00	4.63
867	882	8.433421	ACATAACCATTATTAGTTTCCTCGTG	57.567	34.615	0.00	0.00	0.00	4.35
892	907	3.937079	ACAAGGCAGCGGTAATTAAGTAC	59.063	43.478	4.49	4.49	0.00	2.73
898	913	4.743644	GCAGCGGTAATTAAGTACTCGATT	59.256	41.667	20.40	2.44	0.00	3.34
900	915	5.975344	CAGCGGTAATTAAGTACTCGATTCA	59.025	40.000	20.40	0.00	0.00	2.57
901	916	6.641314	CAGCGGTAATTAAGTACTCGATTCAT	59.359	38.462	20.40	5.10	0.00	2.57
903	918	8.355169	AGCGGTAATTAAGTACTCGATTCATTA	58.645	33.333	20.40	0.00	0.00	1.90
904	919	9.136952	GCGGTAATTAAGTACTCGATTCATTAT	57.863	33.333	20.40	0.00	0.00	1.28
913	962	8.162878	AGTACTCGATTCATTATACTCCGAAA	57.837	34.615	0.00	0.00	0.00	3.46
948	1012	0.039437	TCGCCTCTCAAACTCACGAC	60.039	55.000	0.00	0.00	0.00	4.34
974	1038	2.536761	TCGTTTCCGAAACCACATCT	57.463	45.000	16.61	0.00	40.86	2.90
975	1039	2.409975	TCGTTTCCGAAACCACATCTC	58.590	47.619	16.61	0.00	40.86	2.75
979	1043	1.449601	CCGAAACCACATCTCCCGG	60.450	63.158	0.00	0.00	0.00	5.73
981	1045	2.046314	AAACCACATCTCCCGGCG	60.046	61.111	0.00	0.00	0.00	6.46
982	1046	2.515996	GAAACCACATCTCCCGGCGA	62.516	60.000	9.30	0.00	0.00	5.54
984	1048	3.770040	CCACATCTCCCGGCGACA	61.770	66.667	9.30	0.00	0.00	4.35
985	1049	2.202797	CACATCTCCCGGCGACAG	60.203	66.667	9.30	3.16	0.00	3.51
989	1053	1.982395	ATCTCCCGGCGACAGTCAA	60.982	57.895	9.30	0.00	0.00	3.18
990	1054	2.227089	ATCTCCCGGCGACAGTCAAC	62.227	60.000	9.30	0.00	0.00	3.18
994	1070	1.594293	CCGGCGACAGTCAACAACT	60.594	57.895	9.30	0.00	39.44	3.16
997	1073	0.782384	GGCGACAGTCAACAACTACG	59.218	55.000	0.41	0.00	36.07	3.51
998	1074	1.484356	GCGACAGTCAACAACTACGT	58.516	50.000	0.41	0.00	38.41	3.57
1006	1082	3.433274	AGTCAACAACTACGTGATGCATG	59.567	43.478	2.46	0.00	36.07	4.06
1007	1083	2.741517	TCAACAACTACGTGATGCATGG	59.258	45.455	2.46	0.00	0.00	3.66
1020	1096	2.440147	CATGGCACCACCTTCCCA	59.560	61.111	0.00	0.00	40.22	4.37
1023	1099	3.971702	GGCACCACCTTCCCAGCT	61.972	66.667	0.00	0.00	34.51	4.24
1025	1101	3.160585	CACCACCTTCCCAGCTGA	58.839	61.111	17.39	0.00	0.00	4.26
1026	1102	1.002868	CACCACCTTCCCAGCTGAG	60.003	63.158	17.39	0.39	0.00	3.35
1039	1115	1.060266	CAGCTGAGAAACGAAGATGCG	59.940	52.381	8.42	0.00	37.29	4.73
1052	1131	1.343069	AGATGCGTATCTCCTTCCCC	58.657	55.000	10.51	0.00	39.46	4.81
1113	1192	3.357079	GGCGCATATTCCAGGCCG	61.357	66.667	10.83	0.00	33.58	6.13
1114	1193	2.280797	GCGCATATTCCAGGCCGA	60.281	61.111	0.30	0.00	0.00	5.54
1143	1222	1.209261	TCGCTGCATGGAGATTTGGTA	59.791	47.619	19.59	0.00	0.00	3.25
1149	1228	2.213499	CATGGAGATTTGGTACGCCTC	58.787	52.381	0.00	0.00	35.27	4.70
1180	1262	1.169577	CGTGCTAGCCGGAGATCTAT	58.830	55.000	13.29	0.00	0.00	1.98
1323	1405	3.468140	GGCCTCTACCCCGGACAC	61.468	72.222	0.73	0.00	0.00	3.67
1353	1435	1.291132	GTGGCTACATCCGCTTCTTC	58.709	55.000	0.00	0.00	33.93	2.87
1442	1524	2.367377	CCATGGCCTCCTCCTCCA	60.367	66.667	3.32	0.00	0.00	3.86
1443	1525	2.450320	CCATGGCCTCCTCCTCCAG	61.450	68.421	3.32	0.00	32.78	3.86
1497	1579	0.035439	ACCCATTCACCCGTGACATC	60.035	55.000	0.00	0.00	39.66	3.06
1500	1582	0.999406	CATTCACCCGTGACATCGTC	59.001	55.000	0.00	0.00	39.66	4.20
1503	1585	1.800315	CACCCGTGACATCGTCGAC	60.800	63.158	5.18	5.18	34.95	4.20
1511	1593	0.458025	GACATCGTCGACCTTCCACC	60.458	60.000	10.58	0.00	0.00	4.61
1528	1610	2.487428	CTCTCACCACTCTCGCCG	59.513	66.667	0.00	0.00	0.00	6.46
1596	1678	0.608640	TCTCCACTTCGGCTTCCTTC	59.391	55.000	0.00	0.00	33.14	3.46
1665	1747	2.808206	GGCCGTGGATACCTCCCTG	61.808	68.421	0.00	0.00	41.29	4.45
1668	1750	1.115930	CCGTGGATACCTCCCTGGAG	61.116	65.000	6.20	6.20	41.29	3.86
1670	1752	1.415200	GTGGATACCTCCCTGGAGAC	58.585	60.000	14.86	0.00	44.53	3.36
1691	1773	2.017049	GCAATGGACGATGCTAGGTTT	58.983	47.619	0.00	0.00	39.46	3.27
1719	1801	1.755783	AGGGTGGTCGTATCCGGTC	60.756	63.158	0.00	0.00	33.95	4.79
1742	1824	1.563111	TTACACGGCAAGCTATACGC	58.437	50.000	4.08	0.00	39.57	4.42
1743	1825	0.456628	TACACGGCAAGCTATACGCA	59.543	50.000	4.08	0.00	42.61	5.24
1752	1834	4.092091	GGCAAGCTATACGCAGTTGATATC	59.908	45.833	0.00	0.00	37.78	1.63
1816	1904	2.815211	CGGCACACCACCATCGAG	60.815	66.667	0.00	0.00	34.57	4.04
1817	1905	3.127533	GGCACACCACCATCGAGC	61.128	66.667	0.00	0.00	35.26	5.03
1876	1964	1.338973	ACAAACAACGCCTCTACTCGA	59.661	47.619	0.00	0.00	0.00	4.04
1879	1967	1.583967	CAACGCCTCTACTCGAGCG	60.584	63.158	13.61	12.81	41.66	5.03
1919	2007	2.864343	CGGAAATCTTAGTGGTTAGCCG	59.136	50.000	0.00	0.00	37.67	5.52
1999	2158	1.379527	CAAGGCATTTCCTACCGTCC	58.620	55.000	0.00	0.00	46.94	4.79
2250	2412	3.876341	AGTTTGACCGTTAAGTTGACCA	58.124	40.909	0.00	0.00	0.00	4.02
2263	2425	4.908601	AGTTGACCATTATGACAGGTGA	57.091	40.909	0.00	0.00	35.36	4.02
2314	2477	6.151648	TCTCTGTATCTTCCTTTGGCATTTTG	59.848	38.462	0.00	0.00	0.00	2.44
2357	2520	1.386533	CTATGCTGCTTTCAGTGGGG	58.613	55.000	0.00	0.00	42.29	4.96
2558	2721	1.376424	GCAAGGAGCAGTAGCAGCA	60.376	57.895	0.00	0.00	45.49	4.41
2616	2782	4.749310	CGCAAGCCGAGCTCCTGT	62.749	66.667	8.47	0.00	38.25	4.00
2997	3170	2.031012	CAGAGCTCCGCAACACCA	59.969	61.111	10.93	0.00	0.00	4.17
3010	3183	0.477597	AACACCATCCTCCCCTTCCA	60.478	55.000	0.00	0.00	0.00	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	7.071698	ACCAGGATGTGTTCTAGTATGATTGAT	59.928	37.037	0.00	0.00	0.00	2.57
56	57	1.150536	GGGCACTTGTCTTGGTGGA	59.849	57.895	0.00	0.00	34.41	4.02
140	141	1.337728	CCATTGTGAGTGTACTGGCGA	60.338	52.381	0.00	0.00	0.00	5.54
169	170	2.530460	AGGCCATTTGAATGCTGGTA	57.470	45.000	5.01	0.00	35.08	3.25
195	196	9.646427	GTCGAAATTATTAGAGATAGCAAGGAT	57.354	33.333	0.00	0.00	0.00	3.24
206	207	6.677781	TTTGCCTGGTCGAAATTATTAGAG	57.322	37.500	0.00	0.00	0.00	2.43
244	245	2.106338	TCCCATCTGTCTTGCACTGAAA	59.894	45.455	0.00	0.00	36.61	2.69
279	280	7.384660	TGCATCAACATTTAGTTTGACAAATCC	59.615	33.333	3.49	0.00	38.74	3.01
306	307	3.000727	CTCCTTCTTCGGCATAAAACGT	58.999	45.455	0.00	0.00	0.00	3.99
316	317	1.219393	GCTCCCACTCCTTCTTCGG	59.781	63.158	0.00	0.00	0.00	4.30
347	348	3.198635	ACGGTCCATTCACATCTCTGATT	59.801	43.478	0.00	0.00	0.00	2.57
377	378	3.951680	CGGGGATATAAATACATTGGGCC	59.048	47.826	0.00	0.00	0.00	5.80
389	391	2.708861	ACTTGATGCCACGGGGATATAA	59.291	45.455	8.67	0.00	32.75	0.98
418	420	1.073025	ATTGCCAGTGCTTCCGTCA	59.927	52.632	0.00	0.00	38.71	4.35
533	535	1.141657	GCAGCTTCATCCCACCATCTA	59.858	52.381	0.00	0.00	0.00	1.98
621	623	2.791567	CGCCGCTTTATTTGCATTACA	58.208	42.857	0.00	0.00	0.00	2.41
722	733	4.819105	AGGAATTACATCGTCCACAAGA	57.181	40.909	0.00	0.00	33.57	3.02
747	758	6.436261	CATCATGGCTAGCTTTATTGACTTG	58.564	40.000	15.72	4.03	0.00	3.16
793	805	3.491267	GCAAGATAAGGATTCGAACCGAG	59.509	47.826	0.00	0.00	37.14	4.63
794	806	3.118920	TGCAAGATAAGGATTCGAACCGA	60.119	43.478	0.00	0.00	0.00	4.69
795	807	3.001330	GTGCAAGATAAGGATTCGAACCG	59.999	47.826	0.00	0.00	0.00	4.44
796	808	3.001330	CGTGCAAGATAAGGATTCGAACC	59.999	47.826	0.00	4.22	0.00	3.62
797	809	3.544244	GCGTGCAAGATAAGGATTCGAAC	60.544	47.826	2.99	0.00	0.00	3.95
798	810	2.607635	GCGTGCAAGATAAGGATTCGAA	59.392	45.455	2.99	0.00	0.00	3.71
803	815	3.136763	CTGATGCGTGCAAGATAAGGAT	58.863	45.455	2.99	0.00	0.00	3.24
832	844	8.836413	ACTAATAATGGTTATGTTGTCGGATTG	58.164	33.333	0.00	0.00	0.00	2.67
833	845	8.974060	ACTAATAATGGTTATGTTGTCGGATT	57.026	30.769	0.00	0.00	0.00	3.01
834	846	8.974060	AACTAATAATGGTTATGTTGTCGGAT	57.026	30.769	0.00	0.00	0.00	4.18
835	847	8.795842	AAACTAATAATGGTTATGTTGTCGGA	57.204	30.769	0.00	0.00	29.08	4.55
836	848	8.126700	GGAAACTAATAATGGTTATGTTGTCGG	58.873	37.037	0.00	0.00	29.08	4.79
837	849	8.889717	AGGAAACTAATAATGGTTATGTTGTCG	58.110	33.333	0.00	0.00	40.61	4.35
848	863	4.035208	GTGCCACGAGGAAACTAATAATGG	59.965	45.833	1.86	0.00	44.43	3.16
854	869	2.489971	CTTGTGCCACGAGGAAACTAA	58.510	47.619	1.86	0.00	44.43	2.24
867	882	1.595093	AATTACCGCTGCCTTGTGCC	61.595	55.000	0.00	0.00	40.16	5.01
878	893	7.404139	AATGAATCGAGTACTTAATTACCGC	57.596	36.000	0.00	0.00	0.00	5.68
892	907	7.694388	TTGTTTCGGAGTATAATGAATCGAG	57.306	36.000	0.00	0.00	0.00	4.04
898	913	8.786826	ACTTGATTTGTTTCGGAGTATAATGA	57.213	30.769	0.00	0.00	0.00	2.57
900	915	9.840427	CAAACTTGATTTGTTTCGGAGTATAAT	57.160	29.630	0.00	0.00	42.46	1.28
930	994	1.009389	GGTCGTGAGTTTGAGAGGCG	61.009	60.000	0.00	0.00	0.00	5.52
964	1028	2.046314	CGCCGGGAGATGTGGTTT	60.046	61.111	2.18	0.00	0.00	3.27
965	1029	3.000819	TCGCCGGGAGATGTGGTT	61.001	61.111	2.18	0.00	0.00	3.67
966	1030	3.771160	GTCGCCGGGAGATGTGGT	61.771	66.667	2.18	0.00	0.00	4.16
967	1031	3.723235	CTGTCGCCGGGAGATGTGG	62.723	68.421	2.18	0.00	0.00	4.17
969	1033	2.680352	ACTGTCGCCGGGAGATGT	60.680	61.111	2.18	3.78	0.00	3.06
970	1034	2.105128	GACTGTCGCCGGGAGATG	59.895	66.667	2.18	3.14	0.00	2.90
971	1035	1.982395	TTGACTGTCGCCGGGAGAT	60.982	57.895	2.18	0.00	0.00	2.75
973	1037	2.432628	GTTGACTGTCGCCGGGAG	60.433	66.667	2.18	0.00	0.00	4.30
974	1038	2.798364	TTGTTGACTGTCGCCGGGA	61.798	57.895	2.18	0.00	0.00	5.14
975	1039	2.280524	TTGTTGACTGTCGCCGGG	60.281	61.111	2.18	0.00	0.00	5.73
979	1043	1.189446	CACGTAGTTGTTGACTGTCGC	59.811	52.381	2.98	0.00	41.61	5.19
981	1045	3.120991	GCATCACGTAGTTGTTGACTGTC	60.121	47.826	0.00	0.00	41.61	3.51
982	1046	2.800544	GCATCACGTAGTTGTTGACTGT	59.199	45.455	0.00	0.00	41.61	3.55
984	1048	3.106242	TGCATCACGTAGTTGTTGACT	57.894	42.857	0.00	0.00	41.61	3.41
985	1049	3.424829	CCATGCATCACGTAGTTGTTGAC	60.425	47.826	0.00	0.00	41.61	3.18
989	1053	1.086696	GCCATGCATCACGTAGTTGT	58.913	50.000	0.00	0.00	41.61	3.32
990	1054	1.085893	TGCCATGCATCACGTAGTTG	58.914	50.000	0.00	0.00	32.17	3.16
994	1070	1.298014	TGGTGCCATGCATCACGTA	59.702	52.632	11.23	2.39	45.28	3.57
1006	1082	3.971702	AGCTGGGAAGGTGGTGCC	61.972	66.667	0.00	0.00	37.58	5.01
1007	1083	2.674380	CAGCTGGGAAGGTGGTGC	60.674	66.667	5.57	0.00	34.04	5.01
1020	1096	1.337260	ACGCATCTTCGTTTCTCAGCT	60.337	47.619	0.00	0.00	40.07	4.24
1023	1099	4.371855	AGATACGCATCTTCGTTTCTCA	57.628	40.909	0.00	0.00	43.61	3.27
1026	1102	3.707793	AGGAGATACGCATCTTCGTTTC	58.292	45.455	0.00	0.00	41.21	2.78
1039	1115	1.473497	GGAGGCGGGGAAGGAGATAC	61.473	65.000	0.00	0.00	0.00	2.24
1113	1192	3.023949	ATGCAGCGAGTCCCAGGTC	62.024	63.158	0.00	0.00	0.00	3.85
1114	1193	3.005539	ATGCAGCGAGTCCCAGGT	61.006	61.111	0.00	0.00	0.00	4.00
1122	1201	0.661552	CCAAATCTCCATGCAGCGAG	59.338	55.000	6.50	6.50	0.00	5.03
1162	1241	2.353208	CCAATAGATCTCCGGCTAGCAC	60.353	54.545	18.24	5.06	0.00	4.40
1167	1246	2.390225	AGTCCAATAGATCTCCGGCT	57.610	50.000	0.00	0.00	0.00	5.52
1257	1339	4.547367	GGGTGGAAGCGGGGATCG	62.547	72.222	0.00	0.00	42.76	3.69
1353	1435	3.723554	GACGCCTGAGTCTAGGTTG	57.276	57.895	9.48	6.17	40.11	3.77
1442	1524	2.948720	GCGTCCTTGTCCCTCTGCT	61.949	63.158	0.00	0.00	0.00	4.24
1443	1525	2.435059	GCGTCCTTGTCCCTCTGC	60.435	66.667	0.00	0.00	0.00	4.26
1473	1555	2.272146	CGGGTGAATGGGTGGAGG	59.728	66.667	0.00	0.00	0.00	4.30
1497	1579	1.241990	TGAGAGGTGGAAGGTCGACG	61.242	60.000	9.92	0.00	0.00	5.12
1500	1582	1.185618	TGGTGAGAGGTGGAAGGTCG	61.186	60.000	0.00	0.00	0.00	4.79
1503	1585	0.610687	GAGTGGTGAGAGGTGGAAGG	59.389	60.000	0.00	0.00	0.00	3.46
1511	1593	2.487428	CGGCGAGAGTGGTGAGAG	59.513	66.667	0.00	0.00	0.00	3.20
1528	1610	3.451894	CCCCTCGGGCATTTGTGC	61.452	66.667	0.00	0.00	35.35	4.57
1581	1663	1.374758	AGCGAAGGAAGCCGAAGTG	60.375	57.895	0.00	0.00	34.64	3.16
1655	1737	0.325296	TTGCGTCTCCAGGGAGGTAT	60.325	55.000	15.08	0.00	42.20	2.73
1665	1747	1.766143	GCATCGTCCATTGCGTCTCC	61.766	60.000	0.00	0.00	0.00	3.71
1668	1750	0.855349	CTAGCATCGTCCATTGCGTC	59.145	55.000	0.00	0.00	43.61	5.19
1670	1752	0.530650	ACCTAGCATCGTCCATTGCG	60.531	55.000	0.00	0.00	43.61	4.85
1691	1773	2.863484	ACCACCCTGGGCATTCCA	60.863	61.111	14.08	0.00	43.37	3.53
1719	1801	3.425525	CGTATAGCTTGCCGTGTAATGAG	59.574	47.826	0.00	0.00	0.00	2.90
1742	1824	1.866601	TGATTGCCGCGATATCAACTG	59.133	47.619	8.23	0.00	0.00	3.16
1743	1825	2.238942	TGATTGCCGCGATATCAACT	57.761	45.000	8.23	0.00	0.00	3.16
1752	1834	2.202171	GTCACGTTGATTGCCGCG	60.202	61.111	0.00	0.00	0.00	6.46
1764	1846	2.668212	ATTGGTGCACCGGTCACG	60.668	61.111	30.07	8.27	39.43	4.35
1813	1901	3.573772	TTGGTGTGGCTCGAGCTCG	62.574	63.158	34.46	30.03	41.70	5.03
1814	1902	0.884704	TTTTGGTGTGGCTCGAGCTC	60.885	55.000	34.46	26.39	41.70	4.09
1815	1903	1.148273	TTTTGGTGTGGCTCGAGCT	59.852	52.632	34.46	0.00	41.70	4.09
1816	1904	1.166531	AGTTTTGGTGTGGCTCGAGC	61.167	55.000	29.38	29.38	41.14	5.03
1817	1905	0.588252	CAGTTTTGGTGTGGCTCGAG	59.412	55.000	8.45	8.45	0.00	4.04
1876	1964	0.678395	CCATGCTCTACCAGATCGCT	59.322	55.000	0.00	0.00	0.00	4.93
1902	1990	3.675228	CGTCACGGCTAACCACTAAGATT	60.675	47.826	0.00	0.00	34.57	2.40
1919	2007	2.100252	TGGGATAGGAAATCGTCGTCAC	59.900	50.000	0.00	0.00	0.00	3.67
1999	2158	6.412362	ACTCTAGACAATAGTATTGGCCTG	57.588	41.667	22.67	16.08	0.00	4.85
2250	2412	1.212935	GTGGGCCTCACCTGTCATAAT	59.787	52.381	4.53	0.00	40.39	1.28
2603	2769	1.519719	GATGAACAGGAGCTCGGCT	59.480	57.895	7.83	0.00	43.88	5.52
2616	2782	4.794648	CGGCGGCAAGGGGATGAA	62.795	66.667	10.53	0.00	0.00	2.57
2782	2955	1.979693	GGACACCTCGACCTCTGCT	60.980	63.158	0.00	0.00	0.00	4.24
2785	2958	2.361357	CCGGACACCTCGACCTCT	60.361	66.667	0.00	0.00	0.00	3.69
2997	3170	0.121197	TTCCAGTGGAAGGGGAGGAT	59.879	55.000	21.05	0.00	36.71	3.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.