AutoCloner

Multiple sequence alignment - TraesCS4B01G351700

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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	TraesCS4B01G351700	chr4B	100.000	3883	0	0	1	3883	643664983	643668865	0.000000e+00	7171.0
1	TraesCS4B01G351700	chr4B	90.010	1992	122	35	607	2577	643764542	643766477	0.000000e+00	2505.0
2	TraesCS4B01G351700	chr4B	81.283	561	73	17	2630	3167	643766574	643767125	3.590000e-115	425.0
3	TraesCS4B01G351700	chr4B	88.757	169	11	4	296	459	643764016	643764181	2.370000e-47	200.0
4	TraesCS4B01G351700	chr4B	94.253	87	4	1	528	613	643764176	643764262	8.750000e-27	132.0
5	TraesCS4B01G351700	chr4D	95.452	3408	120	13	200	3591	500392860	500396248	0.000000e+00	5402.0
6	TraesCS4B01G351700	chr4D	78.488	172	23	9	3274	3444	16648160	16648002	2.470000e-17	100.0
7	TraesCS4B01G351700	chr4D	81.111	90	7	4	455	534	98453261	98453172	3.240000e-06	63.9
8	TraesCS4B01G351700	chr5A	94.320	3292	157	13	602	3883	681135191	681138462	0.000000e+00	5016.0
9	TraesCS4B01G351700	chr5A	93.771	3291	156	22	606	3883	681205559	681208813	0.000000e+00	4896.0
10	TraesCS4B01G351700	chr5A	95.147	1669	66	7	1197	2865	681090338	681091991	0.000000e+00	2619.0
11	TraesCS4B01G351700	chr5A	94.967	1669	68	7	1197	2865	681162655	681164307	0.000000e+00	2603.0
12	TraesCS4B01G351700	chr5A	92.968	1479	93	7	2147	3623	681255570	681257039	0.000000e+00	2145.0
13	TraesCS4B01G351700	chr5A	92.170	1341	94	7	2546	3883	681065638	681066970	0.000000e+00	1884.0
14	TraesCS4B01G351700	chr5A	94.188	1170	51	3	2	1162	681084012	681085173	0.000000e+00	1768.0
15	TraesCS4B01G351700	chr5A	94.188	1170	51	3	2	1162	681156331	681157492	0.000000e+00	1768.0
16	TraesCS4B01G351700	chr5A	90.868	1117	77	13	1039	2155	681254301	681255392	0.000000e+00	1474.0
17	TraesCS4B01G351700	chr5A	92.320	612	35	4	3	603	681204844	681205454	0.000000e+00	859.0
18	TraesCS4B01G351700	chr5A	93.231	325	21	1	3	327	681134410	681134733	9.760000e-131	477.0
19	TraesCS4B01G351700	chr5A	91.520	342	29	0	3303	3644	681164304	681164645	4.540000e-129	472.0
20	TraesCS4B01G351700	chr5A	90.351	342	31	1	3303	3644	681091988	681092327	7.650000e-122	448.0
21	TraesCS4B01G351700	chr5A	92.419	277	12	2	607	881	681248250	681248519	1.690000e-103	387.0
22	TraesCS4B01G351700	chr5A	91.039	279	18	2	332	603	681134808	681135086	1.700000e-98	370.0
23	TraesCS4B01G351700	chr5A	89.041	146	9	2	908	1046	681249926	681250071	1.430000e-39	174.0
24	TraesCS4B01G351700	chr5A	93.023	86	6	0	528	613	681247885	681247970	4.070000e-25	126.0
25	TraesCS4B01G351700	chrUn	95.650	1954	62	8	602	2544	321512134	321514075	0.000000e+00	3116.0
26	TraesCS4B01G351700	chrUn	93.231	325	21	1	3	327	321511377	321511700	9.760000e-131	477.0
27	TraesCS4B01G351700	chrUn	92.115	279	15	1	332	603	321511751	321512029	1.690000e-103	387.0
28	TraesCS4B01G351700	chrUn	94.969	159	8	0	3	161	398015164	398015322	2.320000e-62	250.0
29	TraesCS4B01G351700	chr5D	85.000	420	53	9	3466	3881	458530124	458530537	6.000000e-113	418.0
30	TraesCS4B01G351700	chr7D	84.127	441	56	12	3449	3883	156097703	156097271	7.760000e-112	414.0
31	TraesCS4B01G351700	chr1B	83.410	434	61	10	3448	3877	363663239	363663665	3.640000e-105	392.0
32	TraesCS4B01G351700	chr3D	81.735	438	54	12	3449	3883	290817626	290818040	3.710000e-90	342.0
33	TraesCS4B01G351700	chr1D	80.543	442	56	21	3447	3883	43119817	43119401	2.910000e-81	313.0
34	TraesCS4B01G351700	chr1D	92.683	41	2	1	484	524	462461962	462461923	1.510000e-04	58.4
35	TraesCS4B01G351700	chr2B	85.906	298	35	2	2	299	453063603	453063893	1.050000e-80	311.0
36	TraesCS4B01G351700	chr5B	84.083	289	38	8	3596	3883	530255108	530254827	4.940000e-69	272.0
37	TraesCS4B01G351700	chr3B	100.000	46	0	0	257	302	9372415	9372460	6.910000e-13	86.1
38	TraesCS4B01G351700	chr3B	87.671	73	4	5	455	527	440404857	440404790	3.220000e-11	80.5
39	TraesCS4B01G351700	chr2A	91.837	49	3	1	484	532	613878680	613878727	2.500000e-07	67.6

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	TraesCS4B01G351700	chr4B	643664983	643668865	3882	False	7171.000000	7171	100.000000	1	3883	1	chr4B.!!$F1	3882
1	TraesCS4B01G351700	chr4B	643764016	643767125	3109	False	815.500000	2505	88.575750	296	3167	4	chr4B.!!$F2	2871
2	TraesCS4B01G351700	chr4D	500392860	500396248	3388	False	5402.000000	5402	95.452000	200	3591	1	chr4D.!!$F1	3391
3	TraesCS4B01G351700	chr5A	681204844	681208813	3969	False	2877.500000	4896	93.045500	3	3883	2	chr5A.!!$F7	3880
4	TraesCS4B01G351700	chr5A	681134410	681138462	4052	False	1954.333333	5016	92.863333	3	3883	3	chr5A.!!$F5	3880
5	TraesCS4B01G351700	chr5A	681065638	681066970	1332	False	1884.000000	1884	92.170000	2546	3883	1	chr5A.!!$F1	1337
6	TraesCS4B01G351700	chr5A	681254301	681257039	2738	False	1809.500000	2145	91.918000	1039	3623	2	chr5A.!!$F9	2584
7	TraesCS4B01G351700	chr5A	681084012	681085173	1161	False	1768.000000	1768	94.188000	2	1162	1	chr5A.!!$F2	1160
8	TraesCS4B01G351700	chr5A	681156331	681157492	1161	False	1768.000000	1768	94.188000	2	1162	1	chr5A.!!$F3	1160
9	TraesCS4B01G351700	chr5A	681162655	681164645	1990	False	1537.500000	2603	93.243500	1197	3644	2	chr5A.!!$F6	2447
10	TraesCS4B01G351700	chr5A	681090338	681092327	1989	False	1533.500000	2619	92.749000	1197	3644	2	chr5A.!!$F4	2447
11	TraesCS4B01G351700	chr5A	681247885	681250071	2186	False	229.000000	387	91.494333	528	1046	3	chr5A.!!$F8	518
12	TraesCS4B01G351700	chrUn	321511377	321514075	2698	False	1326.666667	3116	93.665333	3	2544	3	chrUn.!!$F2	2541

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
971	2828	1.137086	TGCTCGAAGGCTATCTCCAAC	59.863	52.381	0.00	0.0	0.00	3.77	F
1713	3584	0.748005	ACTGCAGCAACCGACTGTTT	60.748	50.000	15.27	0.0	37.47	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2223	4287	2.787249	CAGCCGTTTGGATGCTCG	59.213	61.111	0.0	0.0	46.14	5.03	R
3485	5626	0.380378	GACAAACAGCGGACAAAGCA	59.620	50.000	0.0	0.0	37.01	3.91	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
47	48	1.633171	CGCGCCGAAGAAGATCTTG	59.367	57.895	14.00	0.00	36.73	3.02
53	54	3.274288	GCCGAAGAAGATCTTGACCATT	58.726	45.455	14.00	0.00	36.73	3.16
80	81	1.191535	CCCTTCCAGGTCATCGTACA	58.808	55.000	0.00	0.00	31.93	2.90
83	84	1.548719	CTTCCAGGTCATCGTACACCA	59.451	52.381	3.19	0.00	34.80	4.17
126	127	2.159071	AGCATAGCAGCTCTGACTTCAG	60.159	50.000	11.90	0.00	42.18	3.02
156	157	4.142665	CGAAGACCAAGACGAAGATACTCA	60.143	45.833	0.00	0.00	0.00	3.41
162	163	4.156922	CCAAGACGAAGATACTCAGACACT	59.843	45.833	0.00	0.00	0.00	3.55
166	167	2.678836	CGAAGATACTCAGACACTCCGT	59.321	50.000	0.00	0.00	0.00	4.69
193	194	1.545651	GCCCACTAACAAGGTCTTGCT	60.546	52.381	10.31	1.58	44.03	3.91
245	246	2.260869	GCCACACAAGCCGTCACAT	61.261	57.895	0.00	0.00	0.00	3.21
327	328	5.129634	TCACTAGCCTTTCATGACAACAAA	58.870	37.500	0.00	0.00	0.00	2.83
329	330	3.354089	AGCCTTTCATGACAACAAACG	57.646	42.857	0.00	0.00	0.00	3.60
450	533	7.272144	ACAAGGAAATTCCACTAGTATCCTT	57.728	36.000	15.21	12.65	44.41	3.36
479	566	4.974399	ACTCCCTCCGATCCAAATTAATC	58.026	43.478	0.00	0.00	0.00	1.75
528	615	5.424895	TGTCAATTAATTTGGATTGGAGGGG	59.575	40.000	0.00	0.00	35.92	4.79
746	1214	7.545265	CGCCCACCCATATTCAAATATTTATTG	59.455	37.037	0.00	0.00	29.35	1.90
956	2806	1.151668	CCTCCTTGTCACTTTGCTCG	58.848	55.000	0.00	0.00	0.00	5.03
971	2828	1.137086	TGCTCGAAGGCTATCTCCAAC	59.863	52.381	0.00	0.00	0.00	3.77
1007	2875	1.819632	CAGCGACAGTAATGGGGGC	60.820	63.158	0.00	0.00	0.00	5.80
1254	3122	6.385176	TCTCTCCTTCTCATGGTTGTCATATT	59.615	38.462	0.00	0.00	34.12	1.28
1256	3124	8.267620	TCTCCTTCTCATGGTTGTCATATTAT	57.732	34.615	0.00	0.00	34.12	1.28
1515	3383	3.190118	GCTTTCACCTTCCAGATTCACAG	59.810	47.826	0.00	0.00	0.00	3.66
1614	3482	2.892640	CCTTCATCCTCGCGGTCA	59.107	61.111	6.13	0.00	0.00	4.02
1632	3500	5.689819	CGGTCATTTTCAGGTAAACAAGAG	58.310	41.667	0.00	0.00	0.00	2.85
1634	3502	5.768164	GGTCATTTTCAGGTAAACAAGAGGA	59.232	40.000	0.00	0.00	0.00	3.71
1635	3503	6.072452	GGTCATTTTCAGGTAAACAAGAGGAG	60.072	42.308	0.00	0.00	0.00	3.69
1636	3504	5.473504	TCATTTTCAGGTAAACAAGAGGAGC	59.526	40.000	0.00	0.00	0.00	4.70
1637	3505	3.418684	TTCAGGTAAACAAGAGGAGCC	57.581	47.619	0.00	0.00	0.00	4.70
1638	3506	2.621070	TCAGGTAAACAAGAGGAGCCT	58.379	47.619	0.00	0.00	0.00	4.58
1639	3507	2.303022	TCAGGTAAACAAGAGGAGCCTG	59.697	50.000	0.00	0.00	42.26	4.85
1640	3508	1.630878	AGGTAAACAAGAGGAGCCTGG	59.369	52.381	0.00	0.00	0.00	4.45
1641	3509	1.351350	GGTAAACAAGAGGAGCCTGGT	59.649	52.381	0.00	0.00	0.00	4.00
1642	3510	2.570302	GGTAAACAAGAGGAGCCTGGTA	59.430	50.000	0.00	0.00	0.00	3.25
1643	3511	3.369576	GGTAAACAAGAGGAGCCTGGTAG	60.370	52.174	0.00	0.00	0.00	3.18
1644	3512	1.280457	AACAAGAGGAGCCTGGTAGG	58.720	55.000	0.00	0.00	38.80	3.18
1648	3516	1.799933	AGAGGAGCCTGGTAGGAATG	58.200	55.000	0.00	0.00	37.67	2.67
1653	3521	4.047883	AGGAGCCTGGTAGGAATGTAATT	58.952	43.478	0.00	0.00	37.67	1.40
1700	3570	2.744494	GCCATAGAGGAAGGAACTGCAG	60.744	54.545	13.48	13.48	41.22	4.41
1713	3584	0.748005	ACTGCAGCAACCGACTGTTT	60.748	50.000	15.27	0.00	37.47	2.83
2098	3973	4.587584	CTCCGAGGGAGTATTACCTTTC	57.412	50.000	3.45	0.00	44.25	2.62
2223	4287	1.809619	TCGCTACATGCTTCGTGGC	60.810	57.895	0.00	0.00	40.11	5.01
2373	4437	2.708216	TCAGTTCACTTTGTGGCTCA	57.292	45.000	0.00	0.00	33.87	4.26
2602	4692	7.217200	TCCATCCTATGTTAATAAGTGCAGAC	58.783	38.462	0.00	0.00	0.00	3.51
2774	4891	5.700402	TTCTAGCTGGGCTCTATCTTTTT	57.300	39.130	0.00	0.00	40.44	1.94
2805	4922	5.938710	GGAAAGAGAAAAGAATCGGTACCTT	59.061	40.000	10.90	0.00	0.00	3.50
3004	5137	6.460537	CCATTCATCCAATTTGATCATCACGT	60.461	38.462	0.00	0.00	0.00	4.49
3005	5138	7.255208	CCATTCATCCAATTTGATCATCACGTA	60.255	37.037	0.00	0.00	0.00	3.57
3006	5139	6.603237	TCATCCAATTTGATCATCACGTAC	57.397	37.500	0.00	0.00	0.00	3.67
3007	5140	5.234116	TCATCCAATTTGATCATCACGTACG	59.766	40.000	15.01	15.01	0.00	3.67
3042	5177	9.211410	TCAATATCCCAAAATGTTGATTATGGT	57.789	29.630	0.00	0.00	36.83	3.55
3043	5178	9.835389	CAATATCCCAAAATGTTGATTATGGTT	57.165	29.630	0.00	0.00	36.83	3.67
3102	5238	8.370182	ACCAGAAAGTGAAAATAGCAAAATGAT	58.630	29.630	0.00	0.00	0.00	2.45
3200	5336	2.124403	CTCCACTGCCTCATGCCC	60.124	66.667	0.00	0.00	40.16	5.36
3227	5363	2.755655	TCCTGTCTGAAAGGATCGAGAC	59.244	50.000	12.71	0.00	38.96	3.36
3326	5463	3.021269	ACACAAATGAACGAGCTACGA	57.979	42.857	11.64	0.00	45.77	3.43
3366	5503	4.729746	GCACGGGGAAACGAAGATTTATTC	60.730	45.833	0.00	0.00	37.61	1.75
3378	5515	6.594159	ACGAAGATTTATTCCGATGTTCACTT	59.406	34.615	0.00	0.00	0.00	3.16
3385	5522	1.697432	TCCGATGTTCACTTCCTTGGT	59.303	47.619	0.00	0.00	0.00	3.67
3485	5626	2.740826	CGACCCAAATGGACGCGT	60.741	61.111	13.85	13.85	44.79	6.01
3498	5639	4.724697	CGCGTGCTTTGTCCGCTG	62.725	66.667	0.00	0.00	44.92	5.18
3512	5653	0.958091	CCGCTGTTTGTCCATTTGGA	59.042	50.000	0.00	0.00	43.08	3.53
3591	5732	1.001020	TGCGGCCCATTTCATGTCT	60.001	52.632	0.00	0.00	0.00	3.41
3661	5803	1.176527	CCATCGGCCAAAGTTCATGT	58.823	50.000	2.24	0.00	0.00	3.21
3664	5806	1.686355	TCGGCCAAAGTTCATGTTGT	58.314	45.000	2.24	0.00	0.00	3.32
3675	5817	1.138036	CATGTTGTCGCCATGCCAG	59.862	57.895	0.00	0.00	33.90	4.85
3696	5838	1.473258	GGCCAACATACAATGCCAGA	58.527	50.000	0.00	0.00	41.76	3.86
3701	5843	3.346315	CAACATACAATGCCAGACTCCA	58.654	45.455	0.00	0.00	0.00	3.86
3721	5863	2.959507	AAAAAGCCACCACACAGTTC	57.040	45.000	0.00	0.00	0.00	3.01
3722	5864	2.143876	AAAAGCCACCACACAGTTCT	57.856	45.000	0.00	0.00	0.00	3.01
3723	5865	1.392589	AAAGCCACCACACAGTTCTG	58.607	50.000	0.00	0.00	0.00	3.02
3724	5866	0.255890	AAGCCACCACACAGTTCTGT	59.744	50.000	0.00	0.00	0.00	3.41
3773	5917	0.539051	CCAACACACAAAAAGGGGCA	59.461	50.000	0.00	0.00	0.00	5.36
3780	5924	2.368548	ACACAAAAAGGGGCAGGAATTC	59.631	45.455	0.00	0.00	0.00	2.17
3781	5925	1.977854	ACAAAAAGGGGCAGGAATTCC	59.022	47.619	17.31	17.31	0.00	3.01
3788	5932	1.303317	GGCAGGAATTCCACCACGT	60.303	57.895	26.22	1.19	38.89	4.49
3795	5939	1.927174	GAATTCCACCACGTCATCTCG	59.073	52.381	0.00	0.00	0.00	4.04
3805	5949	2.362503	TCATCTCGGCCGTGGTCT	60.363	61.111	27.15	8.49	0.00	3.85
3850	5994	1.026718	AAAAAGGATGGCGCTCTCCG	61.027	55.000	18.73	0.00	36.62	4.63
3869	6013	2.120232	CGCCATAGATCACTCGTTGTC	58.880	52.381	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	3.282374	AAGGGGCGGTCCAATGGTC	62.282	63.158	0.00	0.00	37.22	4.02
80	81	2.373169	TGAGCCTCTTCATTTGAGTGGT	59.627	45.455	0.00	0.00	0.00	4.16
83	84	5.508657	GCTTTTTGAGCCTCTTCATTTGAGT	60.509	40.000	0.00	0.00	46.01	3.41
118	119	3.123804	GTCTTCGCTTGTTCTGAAGTCA	58.876	45.455	0.00	0.00	39.97	3.41
126	127	1.192534	CGTCTTGGTCTTCGCTTGTTC	59.807	52.381	0.00	0.00	0.00	3.18
156	157	1.592223	GCTTGGCTACGGAGTGTCT	59.408	57.895	0.00	0.00	45.73	3.41
162	163	0.905809	TTAGTGGGCTTGGCTACGGA	60.906	55.000	5.18	0.00	0.00	4.69
166	167	1.004277	CCTTGTTAGTGGGCTTGGCTA	59.996	52.381	0.00	0.00	0.00	3.93
193	194	0.970427	TGAGCGATGGTCTGGTAGCA	60.970	55.000	0.00	0.00	40.55	3.49
245	246	2.710902	CGGCGATGTGAGAGGTCCA	61.711	63.158	0.00	0.00	0.00	4.02
450	533	1.143277	GGATCGGAGGGAGTAGTCTGA	59.857	57.143	0.00	0.00	32.61	3.27
479	566	8.425491	CACAACTTTAGTACTAAATCTGTGTCG	58.575	37.037	32.69	21.88	39.51	4.35
528	615	6.406692	TGAGCTAAACCTCTATCATGTACC	57.593	41.667	0.00	0.00	33.02	3.34
795	1265	6.258947	GCAAGATGTCTACACCCTCTAATTTC	59.741	42.308	0.00	0.00	0.00	2.17
956	2806	3.034635	TGGAGAGTTGGAGATAGCCTTC	58.965	50.000	0.00	0.00	0.00	3.46
971	2828	1.239296	TGGACGTACGTGGTGGAGAG	61.239	60.000	28.16	0.00	0.00	3.20
1007	2875	0.039798	TTCCTTCACGTTCGTCGAGG	60.040	55.000	13.72	13.72	42.86	4.63
1107	2975	1.966451	GGTCCAAGCAAGTGACCCG	60.966	63.158	0.00	0.00	42.21	5.28
1233	3101	8.097038	GCTATAATATGACAACCATGAGAAGGA	58.903	37.037	0.00	0.00	36.71	3.36
1234	3102	7.063898	CGCTATAATATGACAACCATGAGAAGG	59.936	40.741	0.00	0.00	36.71	3.46
1254	3122	6.935741	ATTACTTGCCAAATGTTCGCTATA	57.064	33.333	0.00	0.00	0.00	1.31
1256	3124	5.637006	AATTACTTGCCAAATGTTCGCTA	57.363	34.783	0.00	0.00	0.00	4.26
1361	3229	2.079925	GCCTTCAGTGTAAGCTCCTTG	58.920	52.381	0.00	0.00	0.00	3.61
1515	3383	2.109425	ATGTAGGCGAAACCAGGAAC	57.891	50.000	0.00	0.00	43.14	3.62
1614	3482	4.767409	GGCTCCTCTTGTTTACCTGAAAAT	59.233	41.667	0.00	0.00	0.00	1.82
1632	3500	4.439253	AATTACATTCCTACCAGGCTCC	57.561	45.455	0.00	0.00	34.61	4.70
1634	3502	5.968676	TGTAATTACATTCCTACCAGGCT	57.031	39.130	14.35	0.00	34.61	4.58
1635	3503	6.457799	CGTTTGTAATTACATTCCTACCAGGC	60.458	42.308	18.69	0.00	35.89	4.85
1636	3504	6.457799	GCGTTTGTAATTACATTCCTACCAGG	60.458	42.308	18.69	3.92	35.89	4.45
1637	3505	6.457799	GGCGTTTGTAATTACATTCCTACCAG	60.458	42.308	18.69	5.21	35.89	4.00
1638	3506	5.354792	GGCGTTTGTAATTACATTCCTACCA	59.645	40.000	18.69	0.00	35.89	3.25
1639	3507	5.587443	AGGCGTTTGTAATTACATTCCTACC	59.413	40.000	18.69	14.55	35.89	3.18
1640	3508	6.673154	AGGCGTTTGTAATTACATTCCTAC	57.327	37.500	18.69	10.81	35.89	3.18
1641	3509	7.558604	AGTAGGCGTTTGTAATTACATTCCTA	58.441	34.615	18.69	19.66	35.89	2.94
1642	3510	6.412214	AGTAGGCGTTTGTAATTACATTCCT	58.588	36.000	18.69	20.48	35.89	3.36
1643	3511	6.673154	AGTAGGCGTTTGTAATTACATTCC	57.327	37.500	18.69	15.58	35.89	3.01
1644	3512	7.707893	TCCTAGTAGGCGTTTGTAATTACATTC	59.292	37.037	18.69	13.12	33.76	2.67
1648	3516	9.702494	ATATTCCTAGTAGGCGTTTGTAATTAC	57.298	33.333	11.75	8.75	34.61	1.89
1653	3521	6.463331	CCCAATATTCCTAGTAGGCGTTTGTA	60.463	42.308	11.75	0.00	34.61	2.41
2043	3917	7.812191	TGAATTTTGCATGAAATACCTGTACAC	59.188	33.333	0.00	0.00	0.00	2.90
2098	3973	8.968242	GGTCACACTTTGCTTAAGAATTAAAAG	58.032	33.333	6.67	9.42	40.54	2.27
2223	4287	2.787249	CAGCCGTTTGGATGCTCG	59.213	61.111	0.00	0.00	46.14	5.03
2373	4437	5.304686	TGTAAATGAGGACCTTCAACTGT	57.695	39.130	0.00	0.00	0.00	3.55
2602	4692	5.278964	GGTCTTAAGAACGTTAGCCAAAG	57.721	43.478	6.78	1.56	0.00	2.77
2635	4746	2.894763	TTGGCAATGCATATCTTGGC	57.105	45.000	15.29	15.29	45.30	4.52
2774	4891	5.473504	CGATTCTTTTCTCTTTCCCCAAAGA	59.526	40.000	0.00	0.00	44.87	2.52
2805	4922	4.968259	TCCTTTGGATTTTCTTCACTCGA	58.032	39.130	0.00	0.00	0.00	4.04
2954	5072	6.513806	TGAGGACATCACAAACAATATTGG	57.486	37.500	19.37	4.67	34.56	3.16
3004	5137	8.632906	TTTTGGGATATTGACCTTTTTACGTA	57.367	30.769	0.00	0.00	0.00	3.57
3005	5138	7.527568	TTTTGGGATATTGACCTTTTTACGT	57.472	32.000	0.00	0.00	0.00	3.57
3006	5139	8.032451	ACATTTTGGGATATTGACCTTTTTACG	58.968	33.333	0.00	0.00	0.00	3.18
3007	5140	9.719355	AACATTTTGGGATATTGACCTTTTTAC	57.281	29.630	0.00	0.00	0.00	2.01
3140	5276	8.790718	GGTCAATGCTTGATGACTTCATATAAT	58.209	33.333	5.95	0.00	44.20	1.28
3153	5289	1.927487	TTGCAGGGTCAATGCTTGAT	58.073	45.000	0.00	0.00	44.17	2.57
3172	5308	5.150715	TGAGGCAGTGGAGAGATACAATAT	58.849	41.667	0.00	0.00	0.00	1.28
3200	5336	4.512484	GATCCTTTCAGACAGGAGGAAAG	58.488	47.826	11.12	0.00	43.96	2.62
3301	5438	5.783654	CGTAGCTCGTTCATTTGTGTTTTAG	59.216	40.000	0.00	0.00	34.52	1.85
3326	5463	2.741878	CGTGCCTTCGATTGTCCCTAAT	60.742	50.000	0.00	0.00	0.00	1.73
3366	5503	1.806542	CACCAAGGAAGTGAACATCGG	59.193	52.381	0.00	0.00	37.42	4.18
3378	5515	1.688311	CGACTATCTCCCCACCAAGGA	60.688	57.143	0.00	0.00	41.22	3.36
3385	5522	0.467474	ACGATGCGACTATCTCCCCA	60.467	55.000	0.00	0.00	0.00	4.96
3485	5626	0.380378	GACAAACAGCGGACAAAGCA	59.620	50.000	0.00	0.00	37.01	3.91
3591	5732	5.341617	CGGGCCTTTTAAAATTTATGCGTA	58.658	37.500	0.84	0.00	0.00	4.42
3623	5765	1.731433	GCATGGCCGCTGACATGATT	61.731	55.000	26.33	0.00	45.55	2.57
3654	5796	0.456653	GGCATGGCGACAACATGAAC	60.457	55.000	2.41	0.00	46.60	3.18
3675	5817	1.226945	GGCATTGTATGTTGGCCGC	60.227	57.895	0.00	0.00	34.56	6.53
3681	5823	3.719268	TGGAGTCTGGCATTGTATGTT	57.281	42.857	0.00	0.00	0.00	2.71
3682	5824	3.719268	TTGGAGTCTGGCATTGTATGT	57.281	42.857	0.00	0.00	0.00	2.29
3707	5849	0.381801	CAACAGAACTGTGTGGTGGC	59.618	55.000	8.25	0.00	44.13	5.01
3757	5901	0.032615	TCCTGCCCCTTTTTGTGTGT	60.033	50.000	0.00	0.00	0.00	3.72
3773	5917	1.909302	AGATGACGTGGTGGAATTCCT	59.091	47.619	24.73	3.55	36.82	3.36
3780	5924	2.509336	GCCGAGATGACGTGGTGG	60.509	66.667	0.00	0.00	0.00	4.61
3781	5925	2.509336	GGCCGAGATGACGTGGTG	60.509	66.667	0.00	0.00	0.00	4.17
3788	5932	1.982395	AAGACCACGGCCGAGATGA	60.982	57.895	35.90	0.00	0.00	2.92
3850	5994	2.120232	CGACAACGAGTGATCTATGGC	58.880	52.381	0.00	0.00	42.66	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.