AutoCloner

Multiple sequence alignment - TraesCS4D01G250100

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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	TraesCS4D01G250100	chr4D	100.000	5132	0	0	1	5132	419110161	419105030	0.000000e+00	9478.0
1	TraesCS4D01G250100	chr4B	96.321	4566	133	12	204	4760	516863510	516858971	0.000000e+00	7468.0
2	TraesCS4D01G250100	chr4B	96.131	336	13	0	4797	5132	516858976	516858641	2.700000e-152	549.0
3	TraesCS4D01G250100	chr4A	95.678	4327	155	20	53	4365	46045861	46050169	0.000000e+00	6926.0
4	TraesCS4D01G250100	chr4A	88.307	573	51	9	311	876	239788467	239789030	0.000000e+00	673.0
5	TraesCS4D01G250100	chr4A	87.260	573	58	10	311	876	355345080	355344516	1.560000e-179	640.0
6	TraesCS4D01G250100	chr4A	90.099	101	10	0	4598	4698	612564741	612564641	1.160000e-26	132.0
7	TraesCS4D01G250100	chr5B	87.264	2010	157	46	2393	4365	526590675	526588728	0.000000e+00	2202.0
8	TraesCS4D01G250100	chr5B	85.205	757	82	16	911	1645	526592280	526591532	0.000000e+00	750.0
9	TraesCS4D01G250100	chr5B	81.595	652	87	19	1647	2275	526591370	526590729	4.580000e-140	508.0
10	TraesCS4D01G250100	chr5D	88.956	1485	123	21	2897	4365	433023480	433022021	0.000000e+00	1796.0
11	TraesCS4D01G250100	chr5D	83.038	1409	170	39	911	2275	433025467	433024084	0.000000e+00	1214.0
12	TraesCS4D01G250100	chr5D	89.255	577	43	9	311	876	41527380	41526812	0.000000e+00	704.0
13	TraesCS4D01G250100	chr5D	91.365	498	31	7	2393	2888	433024031	433023544	0.000000e+00	671.0
14	TraesCS4D01G250100	chr5A	89.799	1147	70	29	2395	3520	547648652	547647532	0.000000e+00	1426.0
15	TraesCS4D01G250100	chr5A	83.234	1008	122	27	911	1881	547650647	547649650	0.000000e+00	881.0
16	TraesCS4D01G250100	chr5A	85.185	864	86	20	3518	4365	547647470	547646633	0.000000e+00	848.0
17	TraesCS4D01G250100	chr5A	83.461	393	50	9	1816	2196	547649256	547648867	8.180000e-93	351.0
18	TraesCS4D01G250100	chr5A	94.064	219	11	1	4916	5132	613468948	613469166	1.070000e-86	331.0
19	TraesCS4D01G250100	chr5A	77.231	650	86	28	3386	4028	3309376	3308782	1.780000e-84	324.0
20	TraesCS4D01G250100	chr3B	89.672	1036	79	11	773	1792	818294368	818293345	0.000000e+00	1295.0
21	TraesCS4D01G250100	chr3B	87.805	574	52	9	312	876	725604736	725605300	0.000000e+00	656.0
22	TraesCS4D01G250100	chr3B	91.228	171	15	0	821	991	828472074	828472244	3.090000e-57	233.0
23	TraesCS4D01G250100	chr3B	93.000	100	7	0	4597	4696	128063928	128063829	4.140000e-31	147.0
24	TraesCS4D01G250100	chr3B	97.297	37	0	1	230	265	818294973	818294937	1.540000e-05	62.1
25	TraesCS4D01G250100	chr3D	86.104	1101	94	31	253	1311	608387907	608388990	0.000000e+00	1131.0
26	TraesCS4D01G250100	chr3D	92.617	149	8	1	1374	1519	608388991	608389139	1.450000e-50	211.0
27	TraesCS4D01G250100	chr2D	90.029	692	56	7	311	997	566786818	566786135	0.000000e+00	883.0
28	TraesCS4D01G250100	chr3A	90.986	588	48	5	1209	1792	740914034	740913448	0.000000e+00	787.0
29	TraesCS4D01G250100	chr3A	89.428	577	49	6	605	1171	740914616	740914042	0.000000e+00	717.0
30	TraesCS4D01G250100	chr3A	93.925	214	11	1	4921	5132	57723184	57722971	6.410000e-84	322.0
31	TraesCS4D01G250100	chr1A	87.108	574	57	9	311	876	19277986	19277422	7.250000e-178	634.0
32	TraesCS4D01G250100	chr1A	87.108	574	57	7	311	876	19392134	19391570	7.250000e-178	634.0
33	TraesCS4D01G250100	chr2B	94.828	174	9	0	821	994	775266600	775266773	6.550000e-69	272.0
34	TraesCS4D01G250100	chr2B	92.473	186	12	2	4916	5099	798843549	798843364	1.100000e-66	265.0
35	TraesCS4D01G250100	chr2B	92.529	174	13	0	821	994	753389823	753389996	3.070000e-62	250.0
36	TraesCS4D01G250100	chr7B	94.565	92	5	0	4605	4696	609750510	609750601	5.360000e-30	143.0
37	TraesCS4D01G250100	chrUn	92.708	96	7	0	4601	4696	178186372	178186277	6.930000e-29	139.0
38	TraesCS4D01G250100	chr6B	92.708	96	7	0	4601	4696	604111056	604110961	6.930000e-29	139.0

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	TraesCS4D01G250100	chr4D	419105030	419110161	5131	True	9478.000000	9478	100.000000	1	5132	1	chr4D.!!$R1	5131
1	TraesCS4D01G250100	chr4B	516858641	516863510	4869	True	4008.500000	7468	96.226000	204	5132	2	chr4B.!!$R1	4928
2	TraesCS4D01G250100	chr4A	46045861	46050169	4308	False	6926.000000	6926	95.678000	53	4365	1	chr4A.!!$F1	4312
3	TraesCS4D01G250100	chr4A	239788467	239789030	563	False	673.000000	673	88.307000	311	876	1	chr4A.!!$F2	565
4	TraesCS4D01G250100	chr4A	355344516	355345080	564	True	640.000000	640	87.260000	311	876	1	chr4A.!!$R1	565
5	TraesCS4D01G250100	chr5B	526588728	526592280	3552	True	1153.333333	2202	84.688000	911	4365	3	chr5B.!!$R1	3454
6	TraesCS4D01G250100	chr5D	433022021	433025467	3446	True	1227.000000	1796	87.786333	911	4365	3	chr5D.!!$R2	3454
7	TraesCS4D01G250100	chr5D	41526812	41527380	568	True	704.000000	704	89.255000	311	876	1	chr5D.!!$R1	565
8	TraesCS4D01G250100	chr5A	547646633	547650647	4014	True	876.500000	1426	85.419750	911	4365	4	chr5A.!!$R2	3454
9	TraesCS4D01G250100	chr5A	3308782	3309376	594	True	324.000000	324	77.231000	3386	4028	1	chr5A.!!$R1	642
10	TraesCS4D01G250100	chr3B	818293345	818294973	1628	True	678.550000	1295	93.484500	230	1792	2	chr3B.!!$R2	1562
11	TraesCS4D01G250100	chr3B	725604736	725605300	564	False	656.000000	656	87.805000	312	876	1	chr3B.!!$F1	564
12	TraesCS4D01G250100	chr3D	608387907	608389139	1232	False	671.000000	1131	89.360500	253	1519	2	chr3D.!!$F1	1266
13	TraesCS4D01G250100	chr2D	566786135	566786818	683	True	883.000000	883	90.029000	311	997	1	chr2D.!!$R1	686
14	TraesCS4D01G250100	chr3A	740913448	740914616	1168	True	752.000000	787	90.207000	605	1792	2	chr3A.!!$R2	1187
15	TraesCS4D01G250100	chr1A	19277422	19277986	564	True	634.000000	634	87.108000	311	876	1	chr1A.!!$R1	565
16	TraesCS4D01G250100	chr1A	19391570	19392134	564	True	634.000000	634	87.108000	311	876	1	chr1A.!!$R2	565

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
143	144	0.179073	TTTCTAGCGATCTGGCTGGC	60.179	55.000	5.46	0.00	44.50	4.85	F
1008	1284	1.523711	CGTAGGTGCCATGGCGATT	60.524	57.895	30.87	20.09	45.51	3.34	F
1215	1504	2.486203	TGTCACCGTTACAAATGATGGC	59.514	45.455	0.00	0.00	0.00	4.40	F
2290	3345	3.608316	TGTTTGCATTAATCCTTGGGC	57.392	42.857	0.00	0.00	0.00	5.36	F
3456	4585	2.602878	CAAGCATGCACAATTGTCCTC	58.397	47.619	21.98	1.65	0.00	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1846	2811	2.292569	CACAGAAGTGCACTGCTTTCAT	59.707	45.455	25.62	8.18	39.21	2.57	R
2351	3406	0.179045	AATCAGCGATACCAGGTGCC	60.179	55.000	0.76	0.00	37.07	5.01	R
2771	3839	1.408340	CCAATGAACAAGTGTGGTGCA	59.592	47.619	0.00	0.00	0.00	4.57	R
3891	5090	1.689233	TCCATGAGCTTACCCCGCT	60.689	57.895	0.00	0.00	41.15	5.52	R
4749	5979	0.108615	GTCACTGCCGTGCATAGACT	60.109	55.000	2.98	0.00	40.99	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
61	62	6.330004	TGAGCAATTTTGAGACATAGCAAA	57.670	33.333	0.00	0.00	32.63	3.68
74	75	5.245301	AGACATAGCAAACCCGCATATAGTA	59.755	40.000	0.00	0.00	0.00	1.82
75	76	5.479306	ACATAGCAAACCCGCATATAGTAG	58.521	41.667	0.00	0.00	0.00	2.57
76	77	5.011738	ACATAGCAAACCCGCATATAGTAGT	59.988	40.000	0.00	0.00	0.00	2.73
77	78	6.209986	ACATAGCAAACCCGCATATAGTAGTA	59.790	38.462	0.00	0.00	0.00	1.82
93	94	1.132500	AGTATTGGTCTAGGCAGCCC	58.868	55.000	8.22	0.00	0.00	5.19
114	115	1.090052	GCAGGCCGAAACTAGCGATT	61.090	55.000	0.00	0.00	0.00	3.34
116	117	0.535335	AGGCCGAAACTAGCGATTGA	59.465	50.000	0.00	0.00	0.00	2.57
121	122	3.546218	GCCGAAACTAGCGATTGATTTCC	60.546	47.826	0.00	0.00	0.00	3.13
125	126	6.314784	CGAAACTAGCGATTGATTTCCTTTT	58.685	36.000	0.00	0.00	0.00	2.27
132	133	4.730521	GCGATTGATTTCCTTTTTCTAGCG	59.269	41.667	0.00	0.00	0.00	4.26
140	141	2.501723	TCCTTTTTCTAGCGATCTGGCT	59.498	45.455	0.65	0.65	46.88	4.75
141	142	2.611292	CCTTTTTCTAGCGATCTGGCTG	59.389	50.000	5.46	0.00	44.50	4.85
142	143	2.315925	TTTTCTAGCGATCTGGCTGG	57.684	50.000	5.46	2.88	44.50	4.85
143	144	0.179073	TTTCTAGCGATCTGGCTGGC	60.179	55.000	5.46	0.00	44.50	4.85
144	145	2.030262	CTAGCGATCTGGCTGGCC	59.970	66.667	4.43	4.43	44.50	5.36
145	146	2.763710	TAGCGATCTGGCTGGCCA	60.764	61.111	13.96	13.96	44.50	5.36
146	147	2.985512	CTAGCGATCTGGCTGGCCAC	62.986	65.000	10.55	0.00	44.50	5.01
192	193	4.082523	ATACGCGGGCTGCTGTGT	62.083	61.111	17.54	11.27	43.27	3.72
198	199	4.996434	GGGCTGCTGTGTGACGCT	62.996	66.667	0.00	0.00	0.00	5.07
199	200	3.720193	GGCTGCTGTGTGACGCTG	61.720	66.667	0.00	0.00	0.00	5.18
200	201	4.380628	GCTGCTGTGTGACGCTGC	62.381	66.667	19.10	19.10	42.32	5.25
201	202	2.664185	CTGCTGTGTGACGCTGCT	60.664	61.111	24.49	0.00	39.07	4.24
331	332	2.764128	GAGATCCACCCGCCCTCA	60.764	66.667	0.00	0.00	0.00	3.86
341	342	2.685380	CGCCCTCAACCTCTCCCT	60.685	66.667	0.00	0.00	0.00	4.20
373	378	4.764771	CCGTCCCCGAGGTACCCA	62.765	72.222	8.74	0.00	35.63	4.51
374	379	3.455469	CGTCCCCGAGGTACCCAC	61.455	72.222	8.74	2.17	35.63	4.61
375	380	3.079478	GTCCCCGAGGTACCCACC	61.079	72.222	8.74	0.00	46.19	4.61
679	927	9.669353	CAGACTGCAAAATCCATATATTGTTAC	57.331	33.333	0.00	0.00	0.00	2.50
932	1206	5.931532	ACTTTGTAGAATCATTGTTCAGCG	58.068	37.500	0.00	0.00	0.00	5.18
1008	1284	1.523711	CGTAGGTGCCATGGCGATT	60.524	57.895	30.87	20.09	45.51	3.34
1185	1470	2.743718	CTTCAGTCCACTGGCCGT	59.256	61.111	6.87	0.00	43.91	5.68
1215	1504	2.486203	TGTCACCGTTACAAATGATGGC	59.514	45.455	0.00	0.00	0.00	4.40
1371	1665	4.265856	TCTTATAGCTTCTCCTGACCCA	57.734	45.455	0.00	0.00	0.00	4.51
1561	1865	8.127150	ACATGAAGATTCATCCGATGACTATA	57.873	34.615	10.73	0.00	45.62	1.31
1575	1879	7.039011	TCCGATGACTATAATTGCAGGTAATCT	60.039	37.037	0.00	0.00	0.00	2.40
1707	2185	6.128090	ACAATAACAACATCTGCAGATCAGTG	60.128	38.462	26.44	23.24	43.32	3.66
2290	3345	3.608316	TGTTTGCATTAATCCTTGGGC	57.392	42.857	0.00	0.00	0.00	5.36
2350	3405	4.174704	TCACTTCCGGGAATACTAGCTA	57.825	45.455	10.44	0.00	0.00	3.32
2351	3406	4.142790	TCACTTCCGGGAATACTAGCTAG	58.857	47.826	19.44	19.44	0.00	3.42
2771	3839	9.855021	GTTAGTAAAATGTTGATTTGGTATGCT	57.145	29.630	0.00	0.00	31.83	3.79
2772	3840	9.853555	TTAGTAAAATGTTGATTTGGTATGCTG	57.146	29.630	0.00	0.00	31.83	4.41
2896	4025	4.021456	GGGTATGTTCTTTCAAACCCTTGG	60.021	45.833	1.03	0.00	42.74	3.61
3169	4298	8.835439	AGAAACAGAAAATGAGAGAGAAAGTTC	58.165	33.333	0.00	0.00	0.00	3.01
3396	4525	6.014755	AGCTCATCGAAGAGATTATGATTGGA	60.015	38.462	21.19	0.00	43.63	3.53
3456	4585	2.602878	CAAGCATGCACAATTGTCCTC	58.397	47.619	21.98	1.65	0.00	3.71
3891	5090	2.686405	GCTGGAATTGATGTCATCAGCA	59.314	45.455	14.98	2.78	43.66	4.41
4582	5812	9.486497	TCTTTATATCTTTGTCAGATGAGCATC	57.514	33.333	2.27	2.27	42.76	3.91
4743	5973	4.897140	ACCCAACATGAATGGATTTGTTG	58.103	39.130	19.54	7.48	45.29	3.33
4757	5987	7.792374	TGGATTTGTTGATTCTAGTCTATGC	57.208	36.000	0.00	0.00	0.00	3.14
4758	5988	7.337938	TGGATTTGTTGATTCTAGTCTATGCA	58.662	34.615	0.00	0.00	0.00	3.96
4759	5989	7.280876	TGGATTTGTTGATTCTAGTCTATGCAC	59.719	37.037	0.00	0.00	0.00	4.57
4760	5990	6.647212	TTTGTTGATTCTAGTCTATGCACG	57.353	37.500	0.00	0.00	0.00	5.34
4761	5991	4.682787	TGTTGATTCTAGTCTATGCACGG	58.317	43.478	0.00	0.00	0.00	4.94
4762	5992	3.371102	TGATTCTAGTCTATGCACGGC	57.629	47.619	0.00	0.00	0.00	5.68
4763	5993	2.693074	TGATTCTAGTCTATGCACGGCA	59.307	45.455	0.00	1.01	44.86	5.69
4764	5994	2.871182	TTCTAGTCTATGCACGGCAG	57.129	50.000	0.00	0.00	43.65	4.85
4765	5995	1.763968	TCTAGTCTATGCACGGCAGT	58.236	50.000	0.00	0.00	43.65	4.40
4775	6005	2.029666	ACGGCAGTGACTGTGCTC	59.970	61.111	14.82	0.00	40.97	4.26
4776	6006	2.740055	CGGCAGTGACTGTGCTCC	60.740	66.667	14.82	5.70	40.97	4.70
4777	6007	2.746359	GGCAGTGACTGTGCTCCT	59.254	61.111	14.82	0.00	40.97	3.69
4778	6008	1.375268	GGCAGTGACTGTGCTCCTC	60.375	63.158	14.82	0.00	40.97	3.71
4779	6009	1.735920	GCAGTGACTGTGCTCCTCG	60.736	63.158	14.82	0.00	37.96	4.63
4780	6010	1.080230	CAGTGACTGTGCTCCTCGG	60.080	63.158	4.01	0.00	0.00	4.63
4781	6011	2.262915	GTGACTGTGCTCCTCGGG	59.737	66.667	0.00	0.00	0.00	5.14
4782	6012	3.695606	TGACTGTGCTCCTCGGGC	61.696	66.667	0.00	0.00	0.00	6.13
4783	6013	4.803426	GACTGTGCTCCTCGGGCG	62.803	72.222	0.00	0.00	0.00	6.13
4785	6015	4.803426	CTGTGCTCCTCGGGCGTC	62.803	72.222	0.00	0.00	0.00	5.19
4823	6053	0.173255	CGGGTGGATGTTTGCAATCC	59.827	55.000	10.15	10.15	35.12	3.01
4840	6070	1.003355	CCTGTGGAATCGGTGTGCT	60.003	57.895	0.00	0.00	0.00	4.40
4856	6086	5.222631	GGTGTGCTAACTGAAATTTTCCTG	58.777	41.667	6.68	2.83	0.00	3.86
4928	6158	0.304705	CCATATGCTGCGTTCGGTTC	59.695	55.000	0.00	0.00	0.00	3.62
4991	6221	1.332997	GAAAGATTCCCTGATGCAGCG	59.667	52.381	0.00	0.00	0.00	5.18
4994	6224	1.098050	GATTCCCTGATGCAGCGTTT	58.902	50.000	0.00	0.00	0.00	3.60
4995	6225	0.813184	ATTCCCTGATGCAGCGTTTG	59.187	50.000	0.00	0.00	0.00	2.93
5017	6247	3.068873	GGTCTGCAGGGATGAAGTACTAG	59.931	52.174	15.13	0.00	0.00	2.57
5028	6258	8.235230	AGGGATGAAGTACTAGAATTCCATAGA	58.765	37.037	0.65	0.00	0.00	1.98
5045	6275	6.407202	TCCATAGAAAAGTTTCTGTAGCCTC	58.593	40.000	15.09	0.00	46.34	4.70
5053	6283	2.737252	GTTTCTGTAGCCTCCAGTTTCG	59.263	50.000	0.00	0.00	0.00	3.46
5072	6302	1.202177	CGCGGGAAATCAAACATCCAG	60.202	52.381	0.00	0.00	34.82	3.86
5089	6319	0.179230	CAGCGAGCTCTTTTTCTGCG	60.179	55.000	12.85	0.00	0.00	5.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	7.208777	TGCTATGTCTCAAAATTGCTCAAAAA	58.791	30.769	0.00	0.00	0.00	1.94
35	36	6.747125	TGCTATGTCTCAAAATTGCTCAAAA	58.253	32.000	0.00	0.00	0.00	2.44
36	37	6.330004	TGCTATGTCTCAAAATTGCTCAAA	57.670	33.333	0.00	0.00	0.00	2.69
37	38	5.963176	TGCTATGTCTCAAAATTGCTCAA	57.037	34.783	0.00	0.00	0.00	3.02
38	39	5.963176	TTGCTATGTCTCAAAATTGCTCA	57.037	34.783	0.00	0.00	0.00	4.26
39	40	5.574443	GGTTTGCTATGTCTCAAAATTGCTC	59.426	40.000	0.00	0.00	34.44	4.26
40	41	5.473039	GGTTTGCTATGTCTCAAAATTGCT	58.527	37.500	0.00	0.00	34.44	3.91
41	42	4.627035	GGGTTTGCTATGTCTCAAAATTGC	59.373	41.667	0.00	0.00	34.44	3.56
42	43	4.858692	CGGGTTTGCTATGTCTCAAAATTG	59.141	41.667	0.00	0.00	34.44	2.32
43	44	4.618227	GCGGGTTTGCTATGTCTCAAAATT	60.618	41.667	0.00	0.00	34.44	1.82
44	45	3.119495	GCGGGTTTGCTATGTCTCAAAAT	60.119	43.478	0.00	0.00	34.44	1.82
45	46	2.227865	GCGGGTTTGCTATGTCTCAAAA	59.772	45.455	0.00	0.00	34.44	2.44
46	47	1.810151	GCGGGTTTGCTATGTCTCAAA	59.190	47.619	0.00	0.00	0.00	2.69
47	48	1.271108	TGCGGGTTTGCTATGTCTCAA	60.271	47.619	0.00	0.00	35.36	3.02
48	49	0.323302	TGCGGGTTTGCTATGTCTCA	59.677	50.000	0.00	0.00	35.36	3.27
49	50	1.668419	ATGCGGGTTTGCTATGTCTC	58.332	50.000	0.00	0.00	35.36	3.36
50	51	3.492102	ATATGCGGGTTTGCTATGTCT	57.508	42.857	0.00	0.00	35.36	3.41
51	52	4.315803	ACTATATGCGGGTTTGCTATGTC	58.684	43.478	0.00	0.00	35.36	3.06
55	56	6.845758	ATACTACTATATGCGGGTTTGCTA	57.154	37.500	0.00	0.00	35.36	3.49
61	62	5.331069	AGACCAATACTACTATATGCGGGT	58.669	41.667	0.00	0.00	0.00	5.28
97	98	0.535335	TCAATCGCTAGTTTCGGCCT	59.465	50.000	0.00	0.00	0.00	5.19
114	115	5.586243	CCAGATCGCTAGAAAAAGGAAATCA	59.414	40.000	0.00	0.00	0.00	2.57
116	117	4.336713	GCCAGATCGCTAGAAAAAGGAAAT	59.663	41.667	0.00	0.00	0.00	2.17
121	122	2.611292	CCAGCCAGATCGCTAGAAAAAG	59.389	50.000	0.00	0.00	36.82	2.27
125	126	1.443407	GCCAGCCAGATCGCTAGAA	59.557	57.895	0.00	0.00	36.82	2.10
132	133	2.487532	GCATGTGGCCAGCCAGATC	61.488	63.158	17.76	9.71	45.49	2.75
140	141	3.445888	CAAGTGTGCATGTGGCCA	58.554	55.556	0.00	0.00	43.89	5.36
189	190	4.017877	GGCACAGCAGCGTCACAC	62.018	66.667	0.00	0.00	34.64	3.82
224	225	3.493440	CTTAAACGGGGCGCGTCC	61.493	66.667	29.70	24.67	0.00	4.79
331	332	2.364448	GGAGGCGAGGGAGAGGTT	60.364	66.667	0.00	0.00	0.00	3.50
541	777	3.760684	GGAAAACAAGCAGATCAGATGGT	59.239	43.478	0.00	0.00	0.00	3.55
635	881	6.035866	GCAGTCTGAATGAGATCAGTAAACTG	59.964	42.308	9.58	15.04	44.50	3.16
679	927	2.084610	TGATCTGGCACTTGTCGAAG	57.915	50.000	0.00	0.00	35.07	3.79
899	1173	6.061022	TGATTCTACAAAGTATTGCCTCCA	57.939	37.500	0.00	0.00	40.34	3.86
932	1206	5.784578	AAGAACCCCACATAAACAAAGAC	57.215	39.130	0.00	0.00	0.00	3.01
1008	1284	2.698274	TGTGGTCTTGACTAAGTCTGCA	59.302	45.455	0.61	0.00	35.38	4.41
1072	1356	2.529780	TCTTTTGCCCAAACTGCATG	57.470	45.000	0.00	0.00	38.76	4.06
1215	1504	4.213270	TGAAGTGACTTCAAAATGGTAGCG	59.787	41.667	24.40	0.00	45.84	4.26
1561	1865	8.184192	CGTCTAAAATGAAGATTACCTGCAATT	58.816	33.333	0.00	0.00	33.18	2.32
1575	1879	8.346300	TGTTGAATAAACTGCGTCTAAAATGAA	58.654	29.630	0.00	0.00	39.70	2.57
1707	2185	6.638468	GTCATTTTCCAAACTTCACATGTCTC	59.362	38.462	0.00	0.00	0.00	3.36
1770	2249	8.082672	AGGGAGCTGCTTTTAATCATTTAAAT	57.917	30.769	2.53	0.00	37.20	1.40
1846	2811	2.292569	CACAGAAGTGCACTGCTTTCAT	59.707	45.455	25.62	8.18	39.21	2.57
2290	3345	6.724893	AAAATGGGGAAAATAAGTATCCGG	57.275	37.500	0.00	0.00	33.90	5.14
2319	3374	2.103094	TCCCGGAAGTGATGCTCATTAG	59.897	50.000	0.73	0.00	0.00	1.73
2337	3392	2.300437	CAGGTGCCTAGCTAGTATTCCC	59.700	54.545	19.31	11.07	32.36	3.97
2350	3405	1.050988	ATCAGCGATACCAGGTGCCT	61.051	55.000	0.76	0.00	37.07	4.75
2351	3406	0.179045	AATCAGCGATACCAGGTGCC	60.179	55.000	0.76	0.00	37.07	5.01
2771	3839	1.408340	CCAATGAACAAGTGTGGTGCA	59.592	47.619	0.00	0.00	0.00	4.57
2772	3840	1.408702	ACCAATGAACAAGTGTGGTGC	59.591	47.619	0.00	0.00	41.05	5.01
3169	4298	2.767394	TCCCATGGCCAATGATTTTCTG	59.233	45.455	10.96	0.00	38.72	3.02
3396	4525	3.522750	AGAAATGAATCAGCCTGTCCTCT	59.477	43.478	0.00	0.00	0.00	3.69
3447	4576	2.026449	CCTTGCTCCTCTGAGGACAATT	60.026	50.000	26.93	0.00	40.06	2.32
3480	4609	5.449177	GCATGATAAGGAGCTACACCAAAAC	60.449	44.000	0.00	0.00	0.00	2.43
3891	5090	1.689233	TCCATGAGCTTACCCCGCT	60.689	57.895	0.00	0.00	41.15	5.52
4156	5379	4.127171	ACTCGGCAAACCATCATACATAC	58.873	43.478	0.00	0.00	34.57	2.39
4422	5651	2.092968	ACCGATTCTGCCATACATGTGT	60.093	45.455	9.11	0.00	0.00	3.72
4582	5812	2.569059	CCTGAATGTGGTCCAGCATAG	58.431	52.381	0.00	0.00	0.00	2.23
4663	5893	3.118542	CAAAGTTTTGCAGCTGTCTTCC	58.881	45.455	16.64	0.00	0.00	3.46
4743	5973	3.243569	ACTGCCGTGCATAGACTAGAATC	60.244	47.826	0.00	0.00	38.13	2.52
4749	5979	0.108615	GTCACTGCCGTGCATAGACT	60.109	55.000	2.98	0.00	40.99	3.24
4757	5987	2.280389	AGCACAGTCACTGCCGTG	60.280	61.111	4.13	1.20	42.59	4.94
4758	5988	2.029666	GAGCACAGTCACTGCCGT	59.970	61.111	4.13	0.00	35.01	5.68
4759	5989	2.740055	GGAGCACAGTCACTGCCG	60.740	66.667	4.13	0.00	35.01	5.69
4760	5990	1.375268	GAGGAGCACAGTCACTGCC	60.375	63.158	4.13	0.00	35.01	4.85
4761	5991	1.735920	CGAGGAGCACAGTCACTGC	60.736	63.158	4.13	0.00	34.37	4.40
4762	5992	1.080230	CCGAGGAGCACAGTCACTG	60.080	63.158	2.22	2.22	37.52	3.66
4763	5993	2.279069	CCCGAGGAGCACAGTCACT	61.279	63.158	0.00	0.00	0.00	3.41
4764	5994	2.262915	CCCGAGGAGCACAGTCAC	59.737	66.667	0.00	0.00	0.00	3.67
4765	5995	3.695606	GCCCGAGGAGCACAGTCA	61.696	66.667	0.00	0.00	0.00	3.41
4766	5996	4.803426	CGCCCGAGGAGCACAGTC	62.803	72.222	0.00	0.00	0.00	3.51
4768	5998	4.803426	GACGCCCGAGGAGCACAG	62.803	72.222	0.00	0.00	0.00	3.66
4792	6022	2.668144	TCCACCCGGAGTTCATTTTT	57.332	45.000	0.73	0.00	35.91	1.94
4823	6053	1.732259	GTTAGCACACCGATTCCACAG	59.268	52.381	0.00	0.00	0.00	3.66
4840	6070	8.792633	CAGTATTCCACAGGAAAATTTCAGTTA	58.207	33.333	8.09	0.00	45.41	2.24
4856	6086	4.265073	AGGAAGCATGAACAGTATTCCAC	58.735	43.478	0.00	0.00	38.92	4.02
4928	6158	4.781934	ACTTTTCCTCCATAAATCCTCCG	58.218	43.478	0.00	0.00	0.00	4.63
4991	6221	1.815003	CTTCATCCCTGCAGACCAAAC	59.185	52.381	17.39	0.00	0.00	2.93
4994	6224	1.555075	GTACTTCATCCCTGCAGACCA	59.445	52.381	17.39	0.00	0.00	4.02
4995	6225	1.834263	AGTACTTCATCCCTGCAGACC	59.166	52.381	17.39	0.00	0.00	3.85
5017	6247	8.184848	GGCTACAGAAACTTTTCTATGGAATTC	58.815	37.037	3.91	0.00	45.23	2.17
5028	6258	4.439253	ACTGGAGGCTACAGAAACTTTT	57.561	40.909	32.96	5.79	39.24	2.27
5045	6275	0.878416	TTGATTTCCCGCGAAACTGG	59.122	50.000	8.23	0.00	40.74	4.00
5053	6283	1.469767	GCTGGATGTTTGATTTCCCGC	60.470	52.381	0.00	0.00	33.55	6.13
5072	6302	1.510833	GCGCAGAAAAAGAGCTCGC	60.511	57.895	8.37	0.94	0.00	5.03

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.