AutoCloner

Multiple sequence alignment - TraesCS6D01G239500

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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	TraesCS6D01G239500	chr6D	100.000	7479	0	0	394	7872	340437470	340444948	0.000000e+00	13812.0
1	TraesCS6D01G239500	chr6D	92.708	768	43	6	7109	7872	441246426	441247184	0.000000e+00	1096.0
2	TraesCS6D01G239500	chr6D	100.000	261	0	0	1	261	340437077	340437337	4.400000e-132	483.0
3	TraesCS6D01G239500	chr6D	100.000	44	0	0	8056	8099	40425230	40425187	1.870000e-11	82.4
4	TraesCS6D01G239500	chr6D	100.000	44	0	0	8056	8099	302705096	302705139	1.870000e-11	82.4
5	TraesCS6D01G239500	chr6D	100.000	44	0	0	8056	8099	340445132	340445175	1.870000e-11	82.4
6	TraesCS6D01G239500	chr6B	98.087	3555	38	7	824	4376	480388255	480384729	0.000000e+00	6161.0
7	TraesCS6D01G239500	chr6B	98.187	1710	24	2	4377	6079	480384405	480382696	0.000000e+00	2979.0
8	TraesCS6D01G239500	chr6B	92.322	1042	44	15	6098	7108	480382607	480381571	0.000000e+00	1448.0
9	TraesCS6D01G239500	chr6A	94.190	3666	148	30	840	4466	480617116	480620755	0.000000e+00	5529.0
10	TraesCS6D01G239500	chr6A	93.519	2407	102	24	4745	7108	480620773	480623168	0.000000e+00	3531.0
11	TraesCS6D01G239500	chr6A	88.028	284	19	7	575	844	480613547	480613829	1.010000e-83	322.0
12	TraesCS6D01G239500	chr6A	88.593	263	20	4	575	829	480613971	480614231	2.190000e-80	311.0
13	TraesCS6D01G239500	chr6A	85.714	70	5	3	3241	3305	480619450	480619519	1.460000e-07	69.4
14	TraesCS6D01G239500	chr2D	95.065	770	24	5	7108	7872	35460349	35459589	0.000000e+00	1199.0
15	TraesCS6D01G239500	chr2D	93.951	777	34	5	7109	7872	325765454	325766230	0.000000e+00	1162.0
16	TraesCS6D01G239500	chr2D	91.157	769	48	14	7109	7872	129867552	129868305	0.000000e+00	1026.0
17	TraesCS6D01G239500	chr2D	88.687	769	63	14	7108	7870	25428842	25428092	0.000000e+00	917.0
18	TraesCS6D01G239500	chr2D	95.918	49	1	1	4659	4706	17030776	17030824	2.420000e-10	78.7
19	TraesCS6D01G239500	chrUn	92.969	768	41	9	7109	7872	43797215	43796457	0.000000e+00	1107.0
20	TraesCS6D01G239500	chr5D	91.203	773	45	12	7109	7872	438610027	438610785	0.000000e+00	1029.0
21	TraesCS6D01G239500	chr5D	100.000	44	0	0	8056	8099	367735449	367735492	1.870000e-11	82.4
22	TraesCS6D01G239500	chr3D	90.649	770	61	8	7109	7872	608278173	608278937	0.000000e+00	1013.0
23	TraesCS6D01G239500	chr3D	78.873	213	37	5	5050	5258	584118625	584118417	3.940000e-28	137.0
24	TraesCS6D01G239500	chr3D	100.000	44	0	0	8056	8099	3214838	3214795	1.870000e-11	82.4
25	TraesCS6D01G239500	chr3D	100.000	44	0	0	8056	8099	497233263	497233306	1.870000e-11	82.4
26	TraesCS6D01G239500	chr1D	90.272	771	56	11	7109	7872	79143734	79144492	0.000000e+00	990.0
27	TraesCS6D01G239500	chr1D	100.000	44	0	0	8056	8099	7456548	7456505	1.870000e-11	82.4
28	TraesCS6D01G239500	chr1D	100.000	44	0	0	8056	8099	28632069	28632112	1.870000e-11	82.4
29	TraesCS6D01G239500	chr3A	90.013	771	56	14	7109	7872	37370778	37371534	0.000000e+00	977.0
30	TraesCS6D01G239500	chr3A	78.333	120	21	4	4597	4711	40822501	40822620	1.130000e-08	73.1
31	TraesCS6D01G239500	chr1B	90.909	264	21	2	1	261	622709837	622709574	1.290000e-92	351.0
32	TraesCS6D01G239500	chr1B	90.968	155	13	1	420	573	622709412	622709258	2.960000e-49	207.0
33	TraesCS6D01G239500	chr3B	90.076	262	25	1	1	261	145683838	145683577	1.010000e-88	339.0
34	TraesCS6D01G239500	chr3B	90.968	155	13	1	420	573	145683417	145683263	2.960000e-49	207.0
35	TraesCS6D01G239500	chr3B	90.728	151	13	1	420	569	145686367	145686517	4.960000e-47	200.0
36	TraesCS6D01G239500	chr3B	89.720	107	8	3	4604	4710	821553646	821553543	5.100000e-27	134.0
37	TraesCS6D01G239500	chr4A	89.516	248	24	1	16	261	464888311	464888064	6.100000e-81	313.0
38	TraesCS6D01G239500	chr5B	87.963	108	10	2	4603	4709	212190196	212190091	3.070000e-24	124.0
39	TraesCS6D01G239500	chr5A	87.963	108	10	2	4603	4709	225789900	225790005	3.070000e-24	124.0
40	TraesCS6D01G239500	chr7D	82.474	97	15	2	586	681	98401833	98401738	5.210000e-12	84.2
41	TraesCS6D01G239500	chr4D	100.000	44	0	0	8056	8099	16511071	16511114	1.870000e-11	82.4
42	TraesCS6D01G239500	chr4D	100.000	44	0	0	8056	8099	19758539	19758582	1.870000e-11	82.4
43	TraesCS6D01G239500	chr2A	78.740	127	15	10	600	720	20878929	20878809	3.130000e-09	75.0
44	TraesCS6D01G239500	chr2A	100.000	28	0	0	34	61	558653712	558653685	1.500000e-02	52.8
45	TraesCS6D01G239500	chr7B	88.136	59	7	0	4604	4662	643459622	643459564	4.060000e-08	71.3
46	TraesCS6D01G239500	chr2B	96.875	32	1	0	4679	4710	38631775	38631744	4.000000e-03	54.7

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	TraesCS6D01G239500	chr6D	340437077	340445175	8098	False	4792.466667	13812	100.000000	1	8099	3	chr6D.!!$F3	8098
1	TraesCS6D01G239500	chr6D	441246426	441247184	758	False	1096.000000	1096	92.708000	7109	7872	1	chr6D.!!$F2	763
2	TraesCS6D01G239500	chr6B	480381571	480388255	6684	True	3529.333333	6161	96.198667	824	7108	3	chr6B.!!$R1	6284
3	TraesCS6D01G239500	chr6A	480613547	480623168	9621	False	1952.480000	5529	90.008800	575	7108	5	chr6A.!!$F1	6533
4	TraesCS6D01G239500	chr2D	35459589	35460349	760	True	1199.000000	1199	95.065000	7108	7872	1	chr2D.!!$R2	764
5	TraesCS6D01G239500	chr2D	325765454	325766230	776	False	1162.000000	1162	93.951000	7109	7872	1	chr2D.!!$F3	763
6	TraesCS6D01G239500	chr2D	129867552	129868305	753	False	1026.000000	1026	91.157000	7109	7872	1	chr2D.!!$F2	763
7	TraesCS6D01G239500	chr2D	25428092	25428842	750	True	917.000000	917	88.687000	7108	7870	1	chr2D.!!$R1	762
8	TraesCS6D01G239500	chrUn	43796457	43797215	758	True	1107.000000	1107	92.969000	7109	7872	1	chrUn.!!$R1	763
9	TraesCS6D01G239500	chr5D	438610027	438610785	758	False	1029.000000	1029	91.203000	7109	7872	1	chr5D.!!$F2	763
10	TraesCS6D01G239500	chr3D	608278173	608278937	764	False	1013.000000	1013	90.649000	7109	7872	1	chr3D.!!$F2	763
11	TraesCS6D01G239500	chr1D	79143734	79144492	758	False	990.000000	990	90.272000	7109	7872	1	chr1D.!!$F2	763
12	TraesCS6D01G239500	chr3A	37370778	37371534	756	False	977.000000	977	90.013000	7109	7872	1	chr3A.!!$F1	763
13	TraesCS6D01G239500	chr1B	622709258	622709837	579	True	279.000000	351	90.938500	1	573	2	chr1B.!!$R1	572
14	TraesCS6D01G239500	chr3B	145683263	145683838	575	True	273.000000	339	90.522000	1	573	2	chr3B.!!$R2	572

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
569	639	0.720590	GCGCCGGTTACAAACGATTA	59.279	50.000	1.90	0.00	0.00	1.75	F
1080	4462	0.323629	TTCCCACTGTTCCATCGTCC	59.676	55.000	0.00	0.00	0.00	4.79	F
2588	5984	7.065563	GCTTGATTATATGCTAGCTATTGCAGT	59.934	37.037	17.23	7.17	42.74	4.40	F
2835	6234	9.132521	CCATTTCAACATTTTCACTAGATGTTC	57.867	33.333	0.00	0.00	40.84	3.18	F
4643	8381	3.740141	GCTCGATAGTTCATTTTCCCGGA	60.740	47.826	0.73	0.00	37.40	5.14	F
4694	8432	1.676635	GTGGGCTTAAACGGGACCC	60.677	63.158	0.00	0.00	41.24	4.46	F
6083	9836	2.628657	CCGCCCTAGCAGTAGTATCTTT	59.371	50.000	0.00	0.00	39.83	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2142	5529	6.269315	TCACGTACAAAATTGAAATTGCTGT	58.731	32.000	0.00	8.17	32.90	4.40	R
2848	6247	8.900983	ACAAAACAAATGCACCTTATGTTATT	57.099	26.923	0.00	0.00	33.39	1.40	R
3481	6882	2.642311	TCAGAATAGAGGGTGGCACAAA	59.358	45.455	20.82	0.00	44.16	2.83	R
4677	8415	2.758434	GGGTCCCGTTTAAGCCCA	59.242	61.111	0.00	0.00	39.13	5.36	R
6361	10186	0.822164	GCAAAAGCATCAGCCTGGAT	59.178	50.000	0.00	0.00	43.56	3.41	R
6688	10527	2.950309	CTCCGCACCACTATACTACAGT	59.050	50.000	0.00	0.00	0.00	3.55	R
7290	11163	0.409092	TGCCATCAACCAGGACCAAT	59.591	50.000	0.00	0.00	0.00	3.16	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
83	85	3.709633	TCACCATCGGCAGCTGCT	61.710	61.111	35.82	16.13	41.70	4.24
104	106	2.465813	AGCTTCTAGCATCTGGTCACT	58.534	47.619	1.09	0.00	45.56	3.41
147	149	0.745486	CGGTTGCAGCATCTGGATGA	60.745	55.000	13.96	0.00	41.20	2.92
172	176	4.877251	GTGGGTTGTACAAAGTGACTGTAA	59.123	41.667	10.51	0.00	31.27	2.41
176	180	5.449304	GTTGTACAAAGTGACTGTAATGGC	58.551	41.667	10.51	0.00	31.27	4.40
204	208	1.883084	CGCCTCCATGTAACTCCGC	60.883	63.158	0.00	0.00	0.00	5.54
212	216	1.134401	CATGTAACTCCGCCCATCACT	60.134	52.381	0.00	0.00	0.00	3.41
229	233	2.040145	TCACTGGTTTCAGCATCCATGA	59.960	45.455	0.00	0.00	44.59	3.07
422	426	4.415332	GCCGGCGTCGACAGAGAA	62.415	66.667	12.58	0.00	39.00	2.87
503	573	4.746309	TGCATGGGGCCACTGCTC	62.746	66.667	23.98	5.74	43.89	4.26
511	581	2.743928	GCCACTGCTCCCTTCGTG	60.744	66.667	0.00	0.00	33.53	4.35
512	582	2.743928	CCACTGCTCCCTTCGTGC	60.744	66.667	0.00	0.00	0.00	5.34
569	639	0.720590	GCGCCGGTTACAAACGATTA	59.279	50.000	1.90	0.00	0.00	1.75
573	643	3.520569	GCCGGTTACAAACGATTACCTA	58.479	45.455	1.90	0.00	0.00	3.08
574	644	3.932089	GCCGGTTACAAACGATTACCTAA	59.068	43.478	1.90	0.00	0.00	2.69
575	645	4.201714	GCCGGTTACAAACGATTACCTAAC	60.202	45.833	1.90	0.00	0.00	2.34
576	646	5.170748	CCGGTTACAAACGATTACCTAACT	58.829	41.667	0.00	0.00	0.00	2.24
577	647	5.639082	CCGGTTACAAACGATTACCTAACTT	59.361	40.000	0.00	0.00	0.00	2.66
578	648	6.147656	CCGGTTACAAACGATTACCTAACTTT	59.852	38.462	0.00	0.00	0.00	2.66
615	685	8.672823	TCGTGAGCTAAGAATACTCTTACATA	57.327	34.615	0.00	0.00	42.17	2.29
616	686	8.557864	TCGTGAGCTAAGAATACTCTTACATAC	58.442	37.037	0.00	0.00	42.17	2.39
669	746	8.470040	AGCACTTATTGATGCATTTGTTTTAG	57.530	30.769	0.00	0.00	44.59	1.85
731	808	6.548441	TTACTAGTTCAAATGTCCAAACGG	57.452	37.500	0.00	0.00	0.00	4.44
739	816	4.395854	TCAAATGTCCAAACGGATGAGATG	59.604	41.667	0.00	0.00	34.24	2.90
751	828	1.948721	ATGAGATGTGAGCGGCGACA	61.949	55.000	12.98	6.74	0.00	4.35
1019	4394	1.526225	GAGCAAAGTATCCGCCCCC	60.526	63.158	0.00	0.00	0.00	5.40
1020	4395	1.984288	GAGCAAAGTATCCGCCCCCT	61.984	60.000	0.00	0.00	0.00	4.79
1021	4396	1.076995	GCAAAGTATCCGCCCCCTT	60.077	57.895	0.00	0.00	0.00	3.95
1080	4462	0.323629	TTCCCACTGTTCCATCGTCC	59.676	55.000	0.00	0.00	0.00	4.79
2142	5529	7.636579	TGTACTGACAGGTATACTTCCTCTTA	58.363	38.462	7.51	0.00	32.37	2.10
2588	5984	7.065563	GCTTGATTATATGCTAGCTATTGCAGT	59.934	37.037	17.23	7.17	42.74	4.40
2835	6234	9.132521	CCATTTCAACATTTTCACTAGATGTTC	57.867	33.333	0.00	0.00	40.84	3.18
3516	6917	8.538701	CCCTCTATTCTGAACTATCATGCTAAT	58.461	37.037	0.00	0.00	34.37	1.73
3814	7215	4.993905	TCGTGTGAGAATGGTATGTAGTG	58.006	43.478	0.00	0.00	0.00	2.74
4029	7430	7.286775	TGTTAATTGCTCTACCTTTGGAGTTTT	59.713	33.333	0.00	0.00	32.67	2.43
4030	7431	6.731292	AATTGCTCTACCTTTGGAGTTTTT	57.269	33.333	0.00	0.00	32.67	1.94
4593	8331	5.367060	GGGATAGATGTGGATAGGATTACCC	59.633	48.000	0.00	0.00	36.73	3.69
4643	8381	3.740141	GCTCGATAGTTCATTTTCCCGGA	60.740	47.826	0.73	0.00	37.40	5.14
4694	8432	1.676635	GTGGGCTTAAACGGGACCC	60.677	63.158	0.00	0.00	41.24	4.46
4713	8451	3.267551	ACCCGGTTTACATCCCTAAACAT	59.732	43.478	0.00	0.00	38.05	2.71
4926	8668	4.798882	AGACACCAAAATTTACAGACCCA	58.201	39.130	0.00	0.00	0.00	4.51
5732	9480	4.813027	ACTGATGGAATTTGTGCAATGAC	58.187	39.130	0.00	0.00	0.00	3.06
6083	9836	2.628657	CCGCCCTAGCAGTAGTATCTTT	59.371	50.000	0.00	0.00	39.83	2.52
6085	9838	4.443034	CCGCCCTAGCAGTAGTATCTTTTT	60.443	45.833	0.00	0.00	39.83	1.94
6127	9950	4.433022	CGAACGTCAGCTGTTTACATCTTC	60.433	45.833	14.67	5.13	0.00	2.87
6292	10115	6.585322	GCATTTGAATTTCAGGTTCTCTCTTG	59.415	38.462	0.00	0.00	0.00	3.02
6453	10278	5.245301	ACAGGTAACCATTTAAAGGCCTTTC	59.755	40.000	33.64	15.73	33.19	2.62
6590	10423	6.017400	TCTCTCAAAATTCAATGCTGGTTC	57.983	37.500	0.00	0.00	0.00	3.62
6646	10479	5.351465	TGCTTTATTCTCTTACGCCTCTTTG	59.649	40.000	0.00	0.00	0.00	2.77
6721	10564	3.071479	TGGTGCGGAGATTTGAGTTAAC	58.929	45.455	0.00	0.00	0.00	2.01
6729	10572	6.402226	GCGGAGATTTGAGTTAACTAACTTGG	60.402	42.308	8.42	2.32	45.84	3.61
6732	10575	8.933807	GGAGATTTGAGTTAACTAACTTGGTAC	58.066	37.037	8.42	0.00	45.84	3.34
6733	10576	8.530269	AGATTTGAGTTAACTAACTTGGTACG	57.470	34.615	8.42	0.00	45.84	3.67
6851	10694	2.235898	GTCTGCTCTTGAAGACCTGGAT	59.764	50.000	0.00	0.00	41.91	3.41
6863	10706	5.190528	TGAAGACCTGGATAGCAAGAAAGAT	59.809	40.000	0.00	0.00	0.00	2.40
6963	10833	6.680197	AGGGATTTATATGCATACAGGGATCT	59.320	38.462	8.99	0.16	0.00	2.75
7032	10902	7.036220	CGATTGACTTACTGTCTTATTGACCT	58.964	38.462	0.00	0.00	45.54	3.85
7060	10930	2.958355	ACACAGGATTGTTGGTCCTTTG	59.042	45.455	6.74	6.74	43.52	2.77
7132	11002	7.166167	TCACTAGTAGAAAAAGGGCCTTTTAG	58.834	38.462	37.12	30.38	41.98	1.85
7148	11018	0.841594	TTAGCCCGGTTGGTAAGGGT	60.842	55.000	0.00	0.00	46.69	4.34
7154	11024	2.040145	CCCGGTTGGTAAGGGTCTTTTA	59.960	50.000	0.00	0.00	40.27	1.52
7304	11184	0.623723	GGCCTATTGGTCCTGGTTGA	59.376	55.000	0.00	0.00	35.27	3.18
7331	11211	1.205460	AACCGGGACCAGTAGGCATT	61.205	55.000	6.32	0.00	39.06	3.56
7799	11706	4.077300	TCCTCTTGAATTGCTCGCATAT	57.923	40.909	0.00	0.00	0.00	1.78
8081	11988	8.900511	ATAAATGAAACTCGACACAAATGATG	57.099	30.769	0.00	0.00	0.00	3.07
8082	11989	4.747540	TGAAACTCGACACAAATGATGG	57.252	40.909	0.00	0.00	0.00	3.51
8083	11990	4.133820	TGAAACTCGACACAAATGATGGT	58.866	39.130	0.00	0.00	0.00	3.55
8084	11991	5.301555	TGAAACTCGACACAAATGATGGTA	58.698	37.500	0.00	0.00	0.00	3.25
8085	11992	5.760743	TGAAACTCGACACAAATGATGGTAA	59.239	36.000	0.00	0.00	0.00	2.85
8086	11993	6.429692	TGAAACTCGACACAAATGATGGTAAT	59.570	34.615	0.00	0.00	0.00	1.89
8087	11994	7.604545	TGAAACTCGACACAAATGATGGTAATA	59.395	33.333	0.00	0.00	0.00	0.98
8088	11995	7.915293	AACTCGACACAAATGATGGTAATAA	57.085	32.000	0.00	0.00	0.00	1.40
8089	11996	7.915293	ACTCGACACAAATGATGGTAATAAA	57.085	32.000	0.00	0.00	0.00	1.40
8090	11997	8.330466	ACTCGACACAAATGATGGTAATAAAA	57.670	30.769	0.00	0.00	0.00	1.52
8091	11998	8.956426	ACTCGACACAAATGATGGTAATAAAAT	58.044	29.630	0.00	0.00	0.00	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
83	85	3.382865	CAGTGACCAGATGCTAGAAGCTA	59.617	47.826	0.00	0.00	42.97	3.32
90	92	1.644509	ACCACAGTGACCAGATGCTA	58.355	50.000	0.62	0.00	0.00	3.49
147	149	3.882888	CAGTCACTTTGTACAACCCACAT	59.117	43.478	8.07	0.00	0.00	3.21
204	208	1.747355	GATGCTGAAACCAGTGATGGG	59.253	52.381	0.00	0.00	34.23	4.00
212	216	2.874014	TGTTCATGGATGCTGAAACCA	58.126	42.857	0.00	0.00	34.59	3.67
229	233	4.086706	ACCTCAAAATCCGAGAGTTGTT	57.913	40.909	0.00	0.00	31.84	2.83
393	397	1.887707	CGCCGGCTCAGGAAATACC	60.888	63.158	26.68	0.00	39.35	2.73
394	398	1.152383	GACGCCGGCTCAGGAAATAC	61.152	60.000	26.68	0.00	0.00	1.89
415	419	3.305744	GCTCGTTCTCCTTTCTTCTCTGT	60.306	47.826	0.00	0.00	0.00	3.41
419	423	1.067495	CCGCTCGTTCTCCTTTCTTCT	60.067	52.381	0.00	0.00	0.00	2.85
421	425	0.680061	ACCGCTCGTTCTCCTTTCTT	59.320	50.000	0.00	0.00	0.00	2.52
422	426	0.680061	AACCGCTCGTTCTCCTTTCT	59.320	50.000	0.00	0.00	0.00	2.52
459	529	3.318557	CACTCCCGTACCTTATCTTCTCC	59.681	52.174	0.00	0.00	0.00	3.71
683	760	2.370824	GATGATGCTTCACGCGCTGG	62.371	60.000	5.73	0.00	43.27	4.85
710	787	4.710324	TCCGTTTGGACATTTGAACTAGT	58.290	39.130	0.00	0.00	40.17	2.57
731	808	1.066422	TCGCCGCTCACATCTCATC	59.934	57.895	0.00	0.00	0.00	2.92
739	816	2.016704	CCGATATGTCGCCGCTCAC	61.017	63.158	6.31	0.00	46.32	3.51
751	828	1.638529	CTCCCCAGCTTCTCCGATAT	58.361	55.000	0.00	0.00	0.00	1.63
765	842	1.054231	CTATAAACCGTCCCCTCCCC	58.946	60.000	0.00	0.00	0.00	4.81
1021	4396	1.284408	GCGGCGTGATGTGGAAAAA	59.716	52.632	9.37	0.00	0.00	1.94
1080	4462	4.821589	GAGGGGGTCGAGCGCAAG	62.822	72.222	29.24	2.24	43.44	4.01
2142	5529	6.269315	TCACGTACAAAATTGAAATTGCTGT	58.731	32.000	0.00	8.17	32.90	4.40
2842	6241	9.640952	ACAAATGCACCTTATGTTATTATAGGT	57.359	29.630	0.00	0.00	0.00	3.08
2847	6246	9.988815	ACAAAACAAATGCACCTTATGTTATTA	57.011	25.926	0.00	0.00	33.39	0.98
2848	6247	8.900983	ACAAAACAAATGCACCTTATGTTATT	57.099	26.923	0.00	0.00	33.39	1.40
3481	6882	2.642311	TCAGAATAGAGGGTGGCACAAA	59.358	45.455	20.82	0.00	44.16	2.83
3516	6917	5.373222	AGGCACGGTTAATAAAGATGCATA	58.627	37.500	0.00	0.00	33.24	3.14
4593	8331	6.363357	GCTAAAGCTAACCAAACACAATTCTG	59.637	38.462	0.00	0.00	38.21	3.02
4659	8397	5.254115	AGCCCACTTATGGTCTAAAAGTTC	58.746	41.667	0.00	0.00	45.66	3.01
4660	8398	5.256806	AGCCCACTTATGGTCTAAAAGTT	57.743	39.130	0.00	0.00	45.66	2.66
4677	8415	2.758434	GGGTCCCGTTTAAGCCCA	59.242	61.111	0.00	0.00	39.13	5.36
4694	8432	6.693315	AATCATGTTTAGGGATGTAAACCG	57.307	37.500	0.00	0.00	40.69	4.44
4713	8451	5.032170	TCATATCCTATGCCCAGCTAATCA	58.968	41.667	0.00	0.00	0.00	2.57
4926	8668	1.489481	TCTCATCAGGTCGGCATTCT	58.511	50.000	0.00	0.00	0.00	2.40
5641	9387	6.676237	TGCATGCTTAAAATCGAGTTCATA	57.324	33.333	20.33	0.00	0.00	2.15
5647	9393	3.489738	CCCCTTGCATGCTTAAAATCGAG	60.490	47.826	20.33	3.01	0.00	4.04
5732	9480	5.512788	GGACACAAACTGATTTTATGATGCG	59.487	40.000	0.00	0.00	0.00	4.73
6083	9836	7.323416	CGTTCGATCTCAATTTCATTTCACAAA	59.677	33.333	0.00	0.00	0.00	2.83
6085	9838	6.073276	ACGTTCGATCTCAATTTCATTTCACA	60.073	34.615	0.00	0.00	0.00	3.58
6292	10115	6.797033	CACAACGGAAAACTTGAGATGAATAC	59.203	38.462	0.00	0.00	0.00	1.89
6361	10186	0.822164	GCAAAAGCATCAGCCTGGAT	59.178	50.000	0.00	0.00	43.56	3.41
6565	10394	6.022163	ACCAGCATTGAATTTTGAGAGAAG	57.978	37.500	0.00	0.00	0.00	2.85
6590	10423	6.622549	ACAAGAGGATGTTAGTAGTTTCTCG	58.377	40.000	0.00	0.00	0.00	4.04
6684	10523	5.009310	TCCGCACCACTATACTACAGTAATG	59.991	44.000	0.00	0.00	33.76	1.90
6685	10524	5.135383	TCCGCACCACTATACTACAGTAAT	58.865	41.667	0.00	0.00	33.76	1.89
6686	10525	4.525996	TCCGCACCACTATACTACAGTAA	58.474	43.478	0.00	0.00	33.76	2.24
6687	10526	4.132336	CTCCGCACCACTATACTACAGTA	58.868	47.826	0.00	0.00	34.67	2.74
6688	10527	2.950309	CTCCGCACCACTATACTACAGT	59.050	50.000	0.00	0.00	0.00	3.55
6689	10528	3.211865	TCTCCGCACCACTATACTACAG	58.788	50.000	0.00	0.00	0.00	2.74
6700	10543	3.071479	GTTAACTCAAATCTCCGCACCA	58.929	45.455	0.00	0.00	0.00	4.17
6721	10564	5.412526	TTTTCAAGCACGTACCAAGTTAG	57.587	39.130	0.00	0.00	0.00	2.34
6729	10572	5.103290	TCCTGAAATTTTCAAGCACGTAC	57.897	39.130	12.62	0.00	39.58	3.67
6732	10575	4.858935	TCTTCCTGAAATTTTCAAGCACG	58.141	39.130	12.62	1.59	39.58	5.34
6733	10576	6.076981	TCTCTTCCTGAAATTTTCAAGCAC	57.923	37.500	12.62	0.00	39.58	4.40
6851	10694	8.319057	TCTCCCATTAGTTATCTTTCTTGCTA	57.681	34.615	0.00	0.00	0.00	3.49
6863	10706	9.607333	AAGTATGAGATCATCTCCCATTAGTTA	57.393	33.333	12.37	0.00	42.73	2.24
6918	10761	4.747108	CCCTACTACATTGAGATTGAAGCG	59.253	45.833	0.00	0.00	0.00	4.68
6963	10833	3.120321	AGAGGTGCACGTTTTCATACA	57.880	42.857	14.12	0.00	0.00	2.29
7032	10902	6.385759	AGGACCAACAATCCTGTGTGTATATA	59.614	38.462	0.00	0.00	45.29	0.86
7060	10930	7.695618	GCTGATCAACTTCTATTTGTCAATGTC	59.304	37.037	0.00	0.00	0.00	3.06
7132	11002	2.045634	GACCCTTACCAACCGGGC	60.046	66.667	6.32	0.00	41.86	6.13
7148	11018	5.456548	GGTTCAAAAACCGGGATAAAAGA	57.543	39.130	6.32	0.00	45.33	2.52
7286	11159	2.301346	CATCAACCAGGACCAATAGGC	58.699	52.381	0.00	0.00	39.06	3.93
7290	11163	0.409092	TGCCATCAACCAGGACCAAT	59.591	50.000	0.00	0.00	0.00	3.16
7304	11184	4.360405	GGTCCCGGTTGGTGCCAT	62.360	66.667	0.00	0.00	34.77	4.40
7323	11203	1.999051	CTGACGCGTGAATGCCTAC	59.001	57.895	20.70	0.00	0.00	3.18
7331	11211	1.291184	CCTGAAATGCTGACGCGTGA	61.291	55.000	20.70	7.67	39.65	4.35
7432	11324	9.606631	AGGACACTTTTCTCTATTAATTAGCTG	57.393	33.333	0.00	0.00	0.00	4.24
7449	11341	5.715070	CACGAAGATAAGAGAGGACACTTT	58.285	41.667	0.00	0.00	0.00	2.66
7799	11706	4.343526	GGATGAACTCCTAGCAGAAGATCA	59.656	45.833	0.00	0.00	41.29	2.92
8055	11962	9.345517	CATCATTTGTGTCGAGTTTCATTTATT	57.654	29.630	0.00	0.00	0.00	1.40
8056	11963	7.970061	CCATCATTTGTGTCGAGTTTCATTTAT	59.030	33.333	0.00	0.00	0.00	1.40
8057	11964	7.040755	ACCATCATTTGTGTCGAGTTTCATTTA	60.041	33.333	0.00	0.00	0.00	1.40
8058	11965	6.151691	CCATCATTTGTGTCGAGTTTCATTT	58.848	36.000	0.00	0.00	0.00	2.32
8059	11966	5.241506	ACCATCATTTGTGTCGAGTTTCATT	59.758	36.000	0.00	0.00	0.00	2.57
8060	11967	4.761739	ACCATCATTTGTGTCGAGTTTCAT	59.238	37.500	0.00	0.00	0.00	2.57
8061	11968	4.133820	ACCATCATTTGTGTCGAGTTTCA	58.866	39.130	0.00	0.00	0.00	2.69
8062	11969	4.749245	ACCATCATTTGTGTCGAGTTTC	57.251	40.909	0.00	0.00	0.00	2.78
8063	11970	6.817765	ATTACCATCATTTGTGTCGAGTTT	57.182	33.333	0.00	0.00	0.00	2.66
8064	11971	7.915293	TTATTACCATCATTTGTGTCGAGTT	57.085	32.000	0.00	0.00	0.00	3.01
8065	11972	7.915293	TTTATTACCATCATTTGTGTCGAGT	57.085	32.000	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.