AutoCloner

Multiple sequence alignment - TraesCS7A01G037000

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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	TraesCS7A01G037000	chr7A	100.000	4409	0	0	1	4409	16646243	16641835	0.000000e+00	8142.0
1	TraesCS7A01G037000	chr7D	97.599	3874	73	7	537	4409	17253479	17249625	0.000000e+00	6621.0
2	TraesCS7A01G037000	chr7D	88.485	495	35	6	1	482	17254070	17253585	2.960000e-161	579.0
3	TraesCS7A01G037000	chr7D	87.500	80	10	0	1	80	562385912	562385833	4.700000e-15	93.5
4	TraesCS7A01G037000	chr4A	86.058	2740	302	47	915	3625	717018669	717021357	0.000000e+00	2870.0
5	TraesCS7A01G037000	chr4A	82.619	1772	242	35	974	2733	676537969	676536252	0.000000e+00	1506.0
6	TraesCS7A01G037000	chr4A	82.766	499	58	17	3618	4101	717021375	717021860	1.900000e-113	420.0
7	TraesCS7A01G037000	chr4A	84.069	408	46	8	42	434	538830830	538831233	4.160000e-100	375.0
8	TraesCS7A01G037000	chr4A	75.934	482	57	30	42	466	692631616	692631137	4.500000e-45	193.0
9	TraesCS7A01G037000	chr4A	77.817	284	43	12	1	280	535037760	535037493	1.640000e-34	158.0
10	TraesCS7A01G037000	chr4A	84.746	59	8	1	3519	3576	676535487	676535429	1.710000e-04	58.4
11	TraesCS7A01G037000	chr5D	85.310	1661	208	21	896	2542	344829351	344830989	0.000000e+00	1683.0
12	TraesCS7A01G037000	chr5D	80.550	982	129	36	2538	3497	344831054	344831995	0.000000e+00	699.0
13	TraesCS7A01G037000	chr5D	85.463	454	47	9	42	480	432035423	432034974	5.200000e-124	455.0
14	TraesCS7A01G037000	chr5D	84.728	478	39	18	42	501	514926988	514926527	8.700000e-122	448.0
15	TraesCS7A01G037000	chr5D	84.858	317	29	9	43	343	260097578	260097265	7.170000e-78	302.0
16	TraesCS7A01G037000	chr5B	84.755	1653	214	22	898	2542	406934894	406933272	0.000000e+00	1622.0
17	TraesCS7A01G037000	chr5B	80.258	542	87	11	2972	3497	406931574	406931037	1.490000e-104	390.0
18	TraesCS7A01G037000	chr5B	84.085	377	39	7	2538	2914	406933210	406932855	1.170000e-90	344.0
19	TraesCS7A01G037000	chr6D	83.142	522	58	15	1	506	338516446	338515939	2.420000e-122	449.0
20	TraesCS7A01G037000	chr6D	83.368	487	53	15	1	466	22716400	22716879	4.080000e-115	425.0
21	TraesCS7A01G037000	chr6D	81.153	451	36	18	42	480	94774272	94773859	2.560000e-82	316.0
22	TraesCS7A01G037000	chr6D	78.193	321	45	14	42	340	54790359	54790676	9.740000e-42	182.0
23	TraesCS7A01G037000	chr2D	84.649	456	41	15	45	485	120549148	120549589	1.130000e-115	427.0
24	TraesCS7A01G037000	chr2D	80.988	405	43	12	42	434	651540477	651540859	1.550000e-74	291.0
25	TraesCS7A01G037000	chr2A	81.898	453	44	18	70	490	606810315	606809869	9.080000e-92	348.0
26	TraesCS7A01G037000	chr2A	82.857	385	50	5	41	412	69297066	69297447	9.140000e-87	331.0
27	TraesCS7A01G037000	chr2A	73.535	529	110	13	1804	2320	750416650	750417160	1.630000e-39	174.0
28	TraesCS7A01G037000	chr1D	72.264	530	113	16	1805	2320	486743517	486743008	2.770000e-27	134.0
29	TraesCS7A01G037000	chr1D	71.456	529	119	16	1805	2320	396188548	396189057	1.300000e-20	111.0
30	TraesCS7A01G037000	chr1A	87.179	78	8	2	1809	1885	584340889	584340813	2.180000e-13	87.9
31	TraesCS7A01G037000	chr4B	87.013	77	7	3	407	480	161877566	161877490	2.830000e-12	84.2

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	TraesCS7A01G037000	chr7A	16641835	16646243	4408	True	8142.000000	8142	100.000000	1	4409	1	chr7A.!!$R1	4408
1	TraesCS7A01G037000	chr7D	17249625	17254070	4445	True	3600.000000	6621	93.042000	1	4409	2	chr7D.!!$R2	4408
2	TraesCS7A01G037000	chr4A	717018669	717021860	3191	False	1645.000000	2870	84.412000	915	4101	2	chr4A.!!$F2	3186
3	TraesCS7A01G037000	chr4A	676535429	676537969	2540	True	782.200000	1506	83.682500	974	3576	2	chr4A.!!$R3	2602
4	TraesCS7A01G037000	chr5D	344829351	344831995	2644	False	1191.000000	1683	82.930000	896	3497	2	chr5D.!!$F1	2601
5	TraesCS7A01G037000	chr5B	406931037	406934894	3857	True	785.333333	1622	83.032667	898	3497	3	chr5B.!!$R1	2599
6	TraesCS7A01G037000	chr6D	338515939	338516446	507	True	449.000000	449	83.142000	1	506	1	chr6D.!!$R2	505

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
106	107	0.322277	GATGATGAGGCGGCCATGAT	60.322	55.000	23.09	13.17	0.00	2.45	F
531	573	0.958876	ATTTTTCGAGACCGTGGGGC	60.959	55.000	0.00	0.00	36.48	5.80	F
896	977	1.136000	CACACACACACACACACACAG	60.136	52.381	0.00	0.00	0.00	3.66	F
1721	1826	1.153086	AGTTGGATCCAGATGGCGC	60.153	57.895	15.53	0.00	34.44	6.53	F
1936	2041	1.475441	GAAGATCCGCAAGCTCGTCG	61.475	60.000	0.00	0.00	0.00	5.12	F
2945	4369	1.818060	CAAATTCAATCGCCAGTGGGA	59.182	47.619	12.15	7.06	37.89	4.37	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1721	1826	0.035056	GACCAGGTGATCCTTGTGGG	60.035	60.000	0.00	0.00	43.07	4.61	R
2433	2550	1.524002	CATCCTCCATGTGAGCGGT	59.476	57.895	5.86	0.00	39.98	5.68	R
2601	2787	0.250295	TGAGGTTTCTTGGCCACTCG	60.250	55.000	3.88	0.00	0.00	4.18	R
2945	4369	0.955919	GAAAGGTAGCTTGCCACGCT	60.956	55.000	8.16	0.04	41.35	5.07	R
3006	4439	1.071605	GGTGATCAGTGTTCTCGCAC	58.928	55.000	0.00	0.00	39.51	5.34	R
4388	5939	0.175760	TAGGTGAGGTTCTGCATCGC	59.824	55.000	0.00	0.00	37.64	4.58	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
53	54	1.437573	CGCTATGAAGACGGAGCCA	59.562	57.895	0.00	0.00	0.00	4.75
74	75	2.125552	CTCGCCGCCATGAAGACA	60.126	61.111	0.00	0.00	0.00	3.41
106	107	0.322277	GATGATGAGGCGGCCATGAT	60.322	55.000	23.09	13.17	0.00	2.45
117	118	4.854924	CCATGATGTGGGCGCGGA	62.855	66.667	8.83	0.00	44.79	5.54
135	136	2.731691	GAAAGACTGGGCGTGGCTGA	62.732	60.000	0.00	0.00	0.00	4.26
206	217	1.969589	GGGGCCGTCATCGTGTTTT	60.970	57.895	0.00	0.00	35.01	2.43
211	222	2.481185	GGCCGTCATCGTGTTTTAAGAA	59.519	45.455	0.00	0.00	35.01	2.52
276	291	4.278513	CCACGGGCAGGGGTTCAA	62.279	66.667	0.00	0.00	39.08	2.69
280	295	2.991540	GGGCAGGGGTTCAACAGC	60.992	66.667	0.00	0.00	0.00	4.40
281	296	3.365265	GGCAGGGGTTCAACAGCG	61.365	66.667	0.00	0.00	0.00	5.18
282	297	2.594592	GCAGGGGTTCAACAGCGT	60.595	61.111	0.00	0.00	0.00	5.07
403	431	5.873164	AGAACACCGTAATTTATGTCCTGTC	59.127	40.000	0.00	0.00	0.00	3.51
438	466	5.164954	TGTAATGTTTGCCGAATTTTAGCC	58.835	37.500	0.00	0.00	0.00	3.93
491	533	4.760047	GAGGCGGCGGCTGAGAAA	62.760	66.667	40.95	0.00	38.98	2.52
506	548	1.374252	GAAACCGCTCGCCTTCAGA	60.374	57.895	0.00	0.00	0.00	3.27
508	550	1.021390	AAACCGCTCGCCTTCAGATG	61.021	55.000	0.00	0.00	0.00	2.90
509	551	2.587194	CCGCTCGCCTTCAGATGG	60.587	66.667	0.00	0.00	0.00	3.51
511	553	2.169789	CGCTCGCCTTCAGATGGTG	61.170	63.158	9.25	9.25	36.49	4.17
512	554	1.219124	GCTCGCCTTCAGATGGTGA	59.781	57.895	15.92	15.92	41.23	4.02
515	557	2.636830	CTCGCCTTCAGATGGTGATTT	58.363	47.619	16.87	0.00	42.36	2.17
516	558	3.012518	CTCGCCTTCAGATGGTGATTTT	58.987	45.455	16.87	0.00	42.36	1.82
517	559	3.420893	TCGCCTTCAGATGGTGATTTTT	58.579	40.909	13.42	0.00	38.95	1.94
518	560	3.440173	TCGCCTTCAGATGGTGATTTTTC	59.560	43.478	13.42	0.00	38.95	2.29
519	561	3.728864	CGCCTTCAGATGGTGATTTTTCG	60.729	47.826	9.87	0.00	37.26	3.46
520	562	3.440173	GCCTTCAGATGGTGATTTTTCGA	59.560	43.478	4.31	0.00	34.17	3.71
522	564	4.937620	CCTTCAGATGGTGATTTTTCGAGA	59.062	41.667	0.00	0.00	34.17	4.04
523	565	5.163814	CCTTCAGATGGTGATTTTTCGAGAC	60.164	44.000	0.00	0.00	34.17	3.36
524	566	4.253685	TCAGATGGTGATTTTTCGAGACC	58.746	43.478	0.00	0.00	0.00	3.85
525	567	3.062639	CAGATGGTGATTTTTCGAGACCG	59.937	47.826	0.00	0.00	37.07	4.79
526	568	2.536761	TGGTGATTTTTCGAGACCGT	57.463	45.000	0.00	0.00	37.05	4.83
527	569	2.139917	TGGTGATTTTTCGAGACCGTG	58.860	47.619	0.00	0.00	37.05	4.94
528	570	1.463444	GGTGATTTTTCGAGACCGTGG	59.537	52.381	0.00	0.00	37.05	4.94
529	571	1.463444	GTGATTTTTCGAGACCGTGGG	59.537	52.381	0.00	0.00	37.05	4.61
531	573	0.958876	ATTTTTCGAGACCGTGGGGC	60.959	55.000	0.00	0.00	36.48	5.80
532	574	3.540367	TTTTCGAGACCGTGGGGCC	62.540	63.158	0.00	0.00	36.48	5.80
568	649	2.548057	CTCTAACAGCGGTGCAAAAGAA	59.452	45.455	15.82	0.00	0.00	2.52
679	760	1.946081	TCAGAATGCGCACTTTTGACA	59.054	42.857	14.90	0.00	34.76	3.58
692	773	1.764571	TTTGACAGGACCCCACCTCG	61.765	60.000	0.00	0.00	38.32	4.63
751	832	1.663161	GGAGTAAAGCAAAGCACGCAC	60.663	52.381	0.00	0.00	0.00	5.34
766	847	1.875963	GCACCACGGGATCAAACAG	59.124	57.895	0.00	0.00	0.00	3.16
792	873	2.045926	GCGTTGAGTGAGGGCCAT	60.046	61.111	6.18	0.00	0.00	4.40
896	977	1.136000	CACACACACACACACACACAG	60.136	52.381	0.00	0.00	0.00	3.66
898	979	1.394572	CACACACACACACACACAGAG	59.605	52.381	0.00	0.00	0.00	3.35
900	981	1.929169	CACACACACACACACAGAGAG	59.071	52.381	0.00	0.00	0.00	3.20
902	983	2.159184	ACACACACACACACAGAGAGAG	60.159	50.000	0.00	0.00	0.00	3.20
904	985	2.360483	ACACACACACACAGAGAGAGAG	59.640	50.000	0.00	0.00	0.00	3.20
906	987	2.884012	ACACACACACAGAGAGAGAGAG	59.116	50.000	0.00	0.00	0.00	3.20
908	989	3.189080	CACACACACAGAGAGAGAGAGAG	59.811	52.174	0.00	0.00	0.00	3.20
909	990	3.072330	ACACACACAGAGAGAGAGAGAGA	59.928	47.826	0.00	0.00	0.00	3.10
910	991	3.686241	CACACACAGAGAGAGAGAGAGAG	59.314	52.174	0.00	0.00	0.00	3.20
911	992	3.582647	ACACACAGAGAGAGAGAGAGAGA	59.417	47.826	0.00	0.00	0.00	3.10
912	993	4.186926	CACACAGAGAGAGAGAGAGAGAG	58.813	52.174	0.00	0.00	0.00	3.20
913	994	4.081476	CACACAGAGAGAGAGAGAGAGAGA	60.081	50.000	0.00	0.00	0.00	3.10
914	995	4.161189	ACACAGAGAGAGAGAGAGAGAGAG	59.839	50.000	0.00	0.00	0.00	3.20
915	996	4.403752	CACAGAGAGAGAGAGAGAGAGAGA	59.596	50.000	0.00	0.00	0.00	3.10
916	997	4.648762	ACAGAGAGAGAGAGAGAGAGAGAG	59.351	50.000	0.00	0.00	0.00	3.20
922	1003	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
972	1077	1.676967	GGCTAAGGCTGCTGCAACT	60.677	57.895	17.89	1.93	41.91	3.16
976	1081	2.910199	CTAAGGCTGCTGCAACTATCA	58.090	47.619	17.89	0.00	41.91	2.15
1721	1826	1.153086	AGTTGGATCCAGATGGCGC	60.153	57.895	15.53	0.00	34.44	6.53
1936	2041	1.475441	GAAGATCCGCAAGCTCGTCG	61.475	60.000	0.00	0.00	0.00	5.12
2601	2787	4.836825	TCAGATCAAATGAGAAGGTGGTC	58.163	43.478	0.00	0.00	0.00	4.02
2700	2892	2.992124	TCTTCAACACGGTCAAGGAA	57.008	45.000	0.00	0.00	0.00	3.36
2917	4341	3.201353	TCCAAGAAATTGACCACGTCA	57.799	42.857	0.00	0.00	41.09	4.35
2945	4369	1.818060	CAAATTCAATCGCCAGTGGGA	59.182	47.619	12.15	7.06	37.89	4.37
3006	4439	1.374758	GGAGACAGTCCACAAGCCG	60.375	63.158	0.00	0.00	46.10	5.52
3276	4721	2.270205	CACGGGAGGCATCTTGCT	59.730	61.111	0.00	0.00	44.28	3.91
3699	5239	9.337987	TCCTCGATGGTACTAGTGGATATCCAA	62.338	44.444	26.14	10.93	41.73	3.53
3740	5280	0.035534	AATGCATGGTACTGTGCGGA	60.036	50.000	0.00	3.18	41.94	5.54
3804	5344	6.339587	TGTGAACTTTTCTCCAACAGTTTT	57.660	33.333	0.00	0.00	29.43	2.43
3805	5345	7.455641	TGTGAACTTTTCTCCAACAGTTTTA	57.544	32.000	0.00	0.00	29.43	1.52
3901	5442	2.356135	CACGGCACCTGCTAGTAAAAT	58.644	47.619	0.00	0.00	41.70	1.82
3973	5517	7.104290	GTCCAGGAACAACTAGCTTAAGTTAT	58.896	38.462	4.02	0.00	37.61	1.89
3993	5537	1.122019	AGCCATACGGAGGGGATGAC	61.122	60.000	0.00	0.00	0.00	3.06
4005	5549	5.454755	CGGAGGGGATGACTAACACAATTAT	60.455	44.000	0.00	0.00	0.00	1.28
4140	5691	4.696479	AGATACAAGGTGCCAAGGATAG	57.304	45.455	0.00	0.00	0.00	2.08
4145	5696	2.493547	GGTGCCAAGGATAGCAACC	58.506	57.895	0.00	0.00	40.94	3.77
4206	5757	0.035630	GAGCACTGCATGGAGTCCTT	60.036	55.000	17.98	5.70	0.00	3.36
4212	5763	1.483827	CTGCATGGAGTCCTTAGAGCA	59.516	52.381	11.33	11.67	0.00	4.26
4220	5771	3.553922	GGAGTCCTTAGAGCAATCATCGG	60.554	52.174	0.41	0.00	0.00	4.18
4221	5772	3.034635	AGTCCTTAGAGCAATCATCGGT	58.965	45.455	0.00	0.00	0.00	4.69
4250	5801	0.244178	AACGGAGAGAAGAACGGAGC	59.756	55.000	0.00	0.00	0.00	4.70
4285	5836	4.473559	AGAGACTAGTAGACAGAGGAAGCT	59.526	45.833	3.59	0.00	0.00	3.74
4372	5923	1.153568	CCTCGCGCTGGATCAAAGA	60.154	57.895	5.56	0.00	0.00	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	1.112113	GACCTGGCTCCGTCTTCATA	58.888	55.000	0.00	0.00	0.00	2.15
39	40	0.616111	AGACCTGGCTCCGTCTTCAT	60.616	55.000	0.00	0.00	35.84	2.57
53	54	3.376935	CTTCATGGCGGCGAGACCT	62.377	63.158	12.98	0.00	35.61	3.85
66	67	1.519719	GCTCCGGCTCTGTCTTCAT	59.480	57.895	0.00	0.00	35.22	2.57
92	93	2.124612	CACATCATGGCCGCCTCA	60.125	61.111	11.61	0.00	0.00	3.86
106	107	3.936203	AGTCTTTCCGCGCCCACA	61.936	61.111	0.00	0.00	0.00	4.17
117	118	2.281761	CAGCCACGCCCAGTCTTT	60.282	61.111	0.00	0.00	0.00	2.52
182	193	2.998949	GATGACGGCCCCTTCCTT	59.001	61.111	0.00	0.00	0.00	3.36
192	203	4.148891	GCTTTCTTAAAACACGATGACGG	58.851	43.478	0.00	0.00	44.46	4.79
206	217	2.991728	CGTCGTCGTCGCTTTCTTA	58.008	52.632	0.00	0.00	36.96	2.10
261	272	3.491598	CTGTTGAACCCCTGCCCGT	62.492	63.158	0.00	0.00	0.00	5.28
276	291	0.039074	CTCCTTCTTCACGACGCTGT	60.039	55.000	0.00	0.00	0.00	4.40
280	295	1.540267	TCCTTCTCCTTCTTCACGACG	59.460	52.381	0.00	0.00	0.00	5.12
281	296	2.668834	CGTCCTTCTCCTTCTTCACGAC	60.669	54.545	0.00	0.00	0.00	4.34
282	297	1.540267	CGTCCTTCTCCTTCTTCACGA	59.460	52.381	0.00	0.00	0.00	4.35
377	404	6.815142	ACAGGACATAAATTACGGTGTTCTAC	59.185	38.462	0.00	0.00	29.52	2.59
378	405	6.938507	ACAGGACATAAATTACGGTGTTCTA	58.061	36.000	0.00	0.00	29.52	2.10
380	407	5.873164	AGACAGGACATAAATTACGGTGTTC	59.127	40.000	0.00	0.00	0.00	3.18
381	408	5.642063	CAGACAGGACATAAATTACGGTGTT	59.358	40.000	0.00	0.00	0.00	3.32
384	411	4.189231	GCAGACAGGACATAAATTACGGT	58.811	43.478	0.00	0.00	0.00	4.83
385	412	3.560068	GGCAGACAGGACATAAATTACGG	59.440	47.826	0.00	0.00	0.00	4.02
387	414	4.439057	TCGGCAGACAGGACATAAATTAC	58.561	43.478	0.00	0.00	0.00	1.89
388	415	4.746535	TCGGCAGACAGGACATAAATTA	57.253	40.909	0.00	0.00	0.00	1.40
403	431	4.324402	GCAAACATTACAAAGATTCGGCAG	59.676	41.667	0.00	0.00	0.00	4.85
491	533	2.185350	CATCTGAAGGCGAGCGGT	59.815	61.111	0.00	0.00	0.00	5.68
506	548	2.742053	CACGGTCTCGAAAAATCACCAT	59.258	45.455	0.00	0.00	40.11	3.55
508	550	1.463444	CCACGGTCTCGAAAAATCACC	59.537	52.381	0.00	0.00	40.11	4.02
509	551	1.463444	CCCACGGTCTCGAAAAATCAC	59.537	52.381	0.00	0.00	40.11	3.06
511	553	1.084289	CCCCACGGTCTCGAAAAATC	58.916	55.000	0.00	0.00	40.11	2.17
512	554	0.958876	GCCCCACGGTCTCGAAAAAT	60.959	55.000	0.00	0.00	40.11	1.82
515	557	4.011517	GGCCCCACGGTCTCGAAA	62.012	66.667	0.00	0.00	40.11	3.46
531	573	3.280920	GAGCATCTCTAGCCGTTGG	57.719	57.895	0.00	0.00	0.00	3.77
568	649	0.107654	GGTCGCTGGCTATGAACCTT	60.108	55.000	0.00	0.00	0.00	3.50
692	773	1.569479	GACTGTCAAACGGAGCCTGC	61.569	60.000	2.24	0.00	0.00	4.85
698	779	1.070134	CTCCCTTGACTGTCAAACGGA	59.930	52.381	25.65	25.65	35.73	4.69
751	832	2.226330	TGTTTCTGTTTGATCCCGTGG	58.774	47.619	0.00	0.00	0.00	4.94
758	839	6.072508	ACTCAACGCATATGTTTCTGTTTGAT	60.073	34.615	4.29	0.00	0.00	2.57
766	847	3.063997	CCCTCACTCAACGCATATGTTTC	59.936	47.826	4.29	0.00	0.00	2.78
792	873	2.493035	TCTGATGAAGCGCTCAAACAA	58.507	42.857	12.06	0.00	37.67	2.83
896	977	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
898	979	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
900	981	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
902	983	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
904	985	4.280677	CCTCTCTCTCTCTCTCTCTCTCTC	59.719	54.167	0.00	0.00	0.00	3.20
906	987	4.219115	TCCTCTCTCTCTCTCTCTCTCTC	58.781	52.174	0.00	0.00	0.00	3.20
908	989	3.323403	CCTCCTCTCTCTCTCTCTCTCTC	59.677	56.522	0.00	0.00	0.00	3.20
909	990	3.312890	CCTCCTCTCTCTCTCTCTCTCT	58.687	54.545	0.00	0.00	0.00	3.10
910	991	2.370189	CCCTCCTCTCTCTCTCTCTCTC	59.630	59.091	0.00	0.00	0.00	3.20
911	992	2.412591	CCCTCCTCTCTCTCTCTCTCT	58.587	57.143	0.00	0.00	0.00	3.10
912	993	1.421646	CCCCTCCTCTCTCTCTCTCTC	59.578	61.905	0.00	0.00	0.00	3.20
913	994	1.522900	CCCCTCCTCTCTCTCTCTCT	58.477	60.000	0.00	0.00	0.00	3.10
914	995	0.478507	CCCCCTCCTCTCTCTCTCTC	59.521	65.000	0.00	0.00	0.00	3.20
915	996	0.047176	TCCCCCTCCTCTCTCTCTCT	59.953	60.000	0.00	0.00	0.00	3.10
916	997	0.478507	CTCCCCCTCCTCTCTCTCTC	59.521	65.000	0.00	0.00	0.00	3.20
922	1003	1.376249	ATCCTCCTCCCCCTCCTCTC	61.376	65.000	0.00	0.00	0.00	3.20
972	1077	3.432749	GCTTCTCCAAGGTGAGCATGATA	60.433	47.826	0.00	0.00	32.22	2.15
976	1081	0.990374	AGCTTCTCCAAGGTGAGCAT	59.010	50.000	11.46	0.00	38.97	3.79
1423	1528	3.519913	GTCTCCCCTTTACTTGAGGTGAT	59.480	47.826	0.00	0.00	32.15	3.06
1529	1634	3.047115	ACCTCCTGCTCATCATCAGAAT	58.953	45.455	0.00	0.00	32.26	2.40
1721	1826	0.035056	GACCAGGTGATCCTTGTGGG	60.035	60.000	0.00	0.00	43.07	4.61
2433	2550	1.524002	CATCCTCCATGTGAGCGGT	59.476	57.895	5.86	0.00	39.98	5.68
2601	2787	0.250295	TGAGGTTTCTTGGCCACTCG	60.250	55.000	3.88	0.00	0.00	4.18
2761	2953	5.476945	ACCACACAGATTCATAGTTTTTCCC	59.523	40.000	0.00	0.00	0.00	3.97
2917	4341	5.360714	ACTGGCGATTGAATTTGGATGTAAT	59.639	36.000	0.00	0.00	0.00	1.89
2945	4369	0.955919	GAAAGGTAGCTTGCCACGCT	60.956	55.000	8.16	0.04	41.35	5.07
3006	4439	1.071605	GGTGATCAGTGTTCTCGCAC	58.928	55.000	0.00	0.00	39.51	5.34
3168	4613	3.121030	CCTTCTGCGTGGCCTTCG	61.121	66.667	3.32	10.54	0.00	3.79
3276	4721	1.216444	GATGAGCTCACTGTCGCCA	59.784	57.895	20.97	0.00	0.00	5.69
3702	5242	9.093970	CATGCATTGTCATTTGACTCATTAATT	57.906	29.630	11.67	0.00	44.99	1.40
3703	5243	7.709182	CCATGCATTGTCATTTGACTCATTAAT	59.291	33.333	11.67	0.80	44.99	1.40
3704	5244	7.036829	CCATGCATTGTCATTTGACTCATTAA	58.963	34.615	11.67	0.00	44.99	1.40
3705	5245	6.153170	ACCATGCATTGTCATTTGACTCATTA	59.847	34.615	11.67	0.00	44.99	1.90
3740	5280	8.491958	AGGTCCCACGAGACTAAATATATTTTT	58.508	33.333	15.64	4.12	36.95	1.94
3956	5500	7.866393	CGTATGGCTATAACTTAAGCTAGTTGT	59.134	37.037	11.42	7.79	38.72	3.32
3973	5517	0.485543	TCATCCCCTCCGTATGGCTA	59.514	55.000	0.00	0.00	34.14	3.93
4005	5549	6.947464	AGACGGGAAGATCTTTAAATCAAGA	58.053	36.000	9.87	0.00	37.20	3.02
4140	5691	0.318699	GTTTTCTCGGGCTTGGTTGC	60.319	55.000	0.00	0.00	0.00	4.17
4145	5696	2.731217	CTTGTTGTTTTCTCGGGCTTG	58.269	47.619	0.00	0.00	0.00	4.01
4220	5771	5.721232	TCTTCTCTCCGTTTTCCTAATCAC	58.279	41.667	0.00	0.00	0.00	3.06
4221	5772	5.995565	TCTTCTCTCCGTTTTCCTAATCA	57.004	39.130	0.00	0.00	0.00	2.57
4250	5801	6.315393	GTCTACTAGTCTCTCTCTCAAGTTGG	59.685	46.154	0.00	0.00	0.00	3.77
4285	5836	2.093235	TCCATGTGTTGGCGATGACATA	60.093	45.455	2.89	0.00	46.01	2.29
4388	5939	0.175760	TAGGTGAGGTTCTGCATCGC	59.824	55.000	0.00	0.00	37.64	4.58
4389	5940	2.215907	CTAGGTGAGGTTCTGCATCG	57.784	55.000	0.00	0.00	0.00	3.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.