AutoCloner

Multiple sequence alignment - TraesCS1A01G125900

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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	TraesCS1A01G125900	chr1A	100.000	2531	0	0	1	2531	150859632	150862162	0.000000e+00	4674.0
1	TraesCS1A01G125900	chr1D	96.465	792	25	2	771	1560	140056110	140055320	0.000000e+00	1304.0
2	TraesCS1A01G125900	chr1D	88.053	226	13	1	2320	2531	140055219	140054994	3.230000e-64	255.0
3	TraesCS1A01G125900	chr1B	96.091	793	26	4	771	1560	198486112	198486902	0.000000e+00	1288.0
4	TraesCS1A01G125900	chr1B	81.743	241	14	9	2320	2531	198487000	198487239	9.310000e-40	174.0
5	TraesCS1A01G125900	chr3A	95.014	702	18	5	1636	2322	165096325	165095626	0.000000e+00	1086.0
6	TraesCS1A01G125900	chr3A	94.571	700	23	1	1634	2318	724138936	724139635	0.000000e+00	1068.0
7	TraesCS1A01G125900	chr5A	95.122	697	19	1	1637	2318	682896437	682897133	0.000000e+00	1085.0
8	TraesCS1A01G125900	chr5A	84.021	776	97	11	1	774	493407888	493407138	0.000000e+00	721.0
9	TraesCS1A01G125900	chr5A	83.212	274	32	9	1633	1905	607947144	607947404	3.250000e-59	239.0
10	TraesCS1A01G125900	chr5A	79.672	305	33	14	2016	2318	607947464	607947741	2.570000e-45	193.0
11	TraesCS1A01G125900	chr5A	97.872	47	1	0	2017	2063	671555800	671555754	5.800000e-12	82.4
12	TraesCS1A01G125900	chr7A	93.211	707	23	6	1636	2318	8544831	8544126	0.000000e+00	1016.0
13	TraesCS1A01G125900	chr7A	84.154	751	87	16	3	749	117277856	117278578	0.000000e+00	699.0
14	TraesCS1A01G125900	chr7A	83.333	774	96	16	1	771	725558924	725558181	0.000000e+00	684.0
15	TraesCS1A01G125900	chr7A	79.503	322	47	11	1636	1950	78705263	78704954	7.090000e-51	211.0
16	TraesCS1A01G125900	chr7A	84.951	206	28	2	2131	2333	80323588	80323383	3.300000e-49	206.0
17	TraesCS1A01G125900	chr7A	79.062	320	49	11	1636	1948	148408948	148408640	1.190000e-48	204.0
18	TraesCS1A01G125900	chr7A	85.311	177	26	0	2142	2318	254431670	254431846	1.550000e-42	183.0
19	TraesCS1A01G125900	chr7A	90.196	51	5	0	2031	2081	15523435	15523485	1.620000e-07	67.6
20	TraesCS1A01G125900	chr7D	85.530	774	84	12	1	772	112180284	112181031	0.000000e+00	784.0
21	TraesCS1A01G125900	chr7D	85.638	188	27	0	2131	2318	436458414	436458601	5.520000e-47	198.0
22	TraesCS1A01G125900	chr7D	75.168	149	31	6	569	713	572267786	572267932	5.840000e-07	65.8
23	TraesCS1A01G125900	chr6D	83.760	782	86	20	1	774	354537005	354537753	0.000000e+00	702.0
24	TraesCS1A01G125900	chr2D	83.810	735	92	14	1	735	560955488	560956195	0.000000e+00	673.0
25	TraesCS1A01G125900	chr2D	79.814	322	43	16	1636	1948	492074059	492073751	5.480000e-52	215.0
26	TraesCS1A01G125900	chr4A	81.912	774	112	12	1	772	420544843	420544096	1.650000e-176	628.0
27	TraesCS1A01G125900	chr4A	82.657	715	85	22	1	713	80138088	80137411	4.660000e-167	597.0
28	TraesCS1A01G125900	chr3D	81.596	777	114	16	1	774	602794818	602795568	1.290000e-172	616.0
29	TraesCS1A01G125900	chr3D	84.694	98	15	0	1271	1368	104293043	104292946	5.760000e-17	99.0
30	TraesCS1A01G125900	chr4D	85.204	588	79	6	1	584	481035163	481035746	4.660000e-167	597.0
31	TraesCS1A01G125900	chrUn	91.789	341	13	6	1993	2318	12351958	12352298	6.380000e-126	460.0
32	TraesCS1A01G125900	chrUn	94.500	200	11	0	1636	1835	12351569	12351768	2.450000e-80	309.0
33	TraesCS1A01G125900	chrUn	92.000	100	8	0	1864	1963	12351769	12351868	9.440000e-30	141.0
34	TraesCS1A01G125900	chr2B	82.090	201	29	7	2131	2327	57109225	57109422	5.600000e-37	165.0
35	TraesCS1A01G125900	chr5D	80.597	201	37	2	573	772	116070568	116070767	1.210000e-33	154.0
36	TraesCS1A01G125900	chr2A	87.379	103	12	1	2133	2234	767552314	767552212	1.590000e-22	117.0
37	TraesCS1A01G125900	chr3B	74.793	242	43	15	1271	1500	155418923	155418688	2.680000e-15	93.5

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	TraesCS1A01G125900	chr1A	150859632	150862162	2530	False	4674.000000	4674	100.000	1	2531	1	chr1A.!!$F1	2530
1	TraesCS1A01G125900	chr1D	140054994	140056110	1116	True	779.500000	1304	92.259	771	2531	2	chr1D.!!$R1	1760
2	TraesCS1A01G125900	chr1B	198486112	198487239	1127	False	731.000000	1288	88.917	771	2531	2	chr1B.!!$F1	1760
3	TraesCS1A01G125900	chr3A	165095626	165096325	699	True	1086.000000	1086	95.014	1636	2322	1	chr3A.!!$R1	686
4	TraesCS1A01G125900	chr3A	724138936	724139635	699	False	1068.000000	1068	94.571	1634	2318	1	chr3A.!!$F1	684
5	TraesCS1A01G125900	chr5A	682896437	682897133	696	False	1085.000000	1085	95.122	1637	2318	1	chr5A.!!$F1	681
6	TraesCS1A01G125900	chr5A	493407138	493407888	750	True	721.000000	721	84.021	1	774	1	chr5A.!!$R1	773
7	TraesCS1A01G125900	chr5A	607947144	607947741	597	False	216.000000	239	81.442	1633	2318	2	chr5A.!!$F2	685
8	TraesCS1A01G125900	chr7A	8544126	8544831	705	True	1016.000000	1016	93.211	1636	2318	1	chr7A.!!$R1	682
9	TraesCS1A01G125900	chr7A	117277856	117278578	722	False	699.000000	699	84.154	3	749	1	chr7A.!!$F2	746
10	TraesCS1A01G125900	chr7A	725558181	725558924	743	True	684.000000	684	83.333	1	771	1	chr7A.!!$R5	770
11	TraesCS1A01G125900	chr7D	112180284	112181031	747	False	784.000000	784	85.530	1	772	1	chr7D.!!$F1	771
12	TraesCS1A01G125900	chr6D	354537005	354537753	748	False	702.000000	702	83.760	1	774	1	chr6D.!!$F1	773
13	TraesCS1A01G125900	chr2D	560955488	560956195	707	False	673.000000	673	83.810	1	735	1	chr2D.!!$F1	734
14	TraesCS1A01G125900	chr4A	420544096	420544843	747	True	628.000000	628	81.912	1	772	1	chr4A.!!$R2	771
15	TraesCS1A01G125900	chr4A	80137411	80138088	677	True	597.000000	597	82.657	1	713	1	chr4A.!!$R1	712
16	TraesCS1A01G125900	chr3D	602794818	602795568	750	False	616.000000	616	81.596	1	774	1	chr3D.!!$F1	773
17	TraesCS1A01G125900	chr4D	481035163	481035746	583	False	597.000000	597	85.204	1	584	1	chr4D.!!$F1	583
18	TraesCS1A01G125900	chrUn	12351569	12352298	729	False	303.333333	460	92.763	1636	2318	3	chrUn.!!$F1	682

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
550	560	0.32121	TTTCGGGCATGTGTGATCGT	60.321	50.0	0.0	0.0	0.0	3.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2465	2644	0.443869	GTACTTGCCGTCGTCGAGTA	59.556	55.0	2.98	0.0	39.71	2.59	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
74	75	3.423154	GCCGACGCCAAGAACAGG	61.423	66.667	0.00	0.00	0.00	4.00
100	101	3.274288	CAAAGAGGAAGGAGAAATCCGG	58.726	50.000	0.00	0.00	40.78	5.14
105	106	3.310860	AAGGAGAAATCCGGCGCGT	62.311	57.895	8.43	0.00	34.28	6.01
107	108	2.508439	GAGAAATCCGGCGCGTGA	60.508	61.111	8.43	0.00	0.00	4.35
159	160	0.980423	GCTTGACCTTCTCAGGACCT	59.020	55.000	0.00	0.00	44.19	3.85
189	190	1.000607	CGAAGAAGAGGAACACCGACA	60.001	52.381	0.00	0.00	0.00	4.35
252	253	1.669440	GTCAAGGCGTGGTACCTGA	59.331	57.895	14.36	4.20	37.67	3.86
255	256	1.904865	AAGGCGTGGTACCTGACGA	60.905	57.895	24.49	0.00	37.67	4.20
275	276	2.182842	GCGCGGCCTCATCTTGAAT	61.183	57.895	8.83	0.00	0.00	2.57
365	375	2.434185	GATGAAGCGGTGCCGACA	60.434	61.111	15.45	10.78	42.83	4.35
376	386	4.612412	GCCGACACCGACCACCAA	62.612	66.667	0.00	0.00	38.22	3.67
397	407	2.666190	GAGCACAGAAGCCACGCA	60.666	61.111	0.00	0.00	34.23	5.24
400	410	2.037136	GCACAGAAGCCACGCAGAT	61.037	57.895	0.00	0.00	0.00	2.90
451	461	2.672996	CAGTCCCACGCCAAAGGG	60.673	66.667	0.00	0.00	46.90	3.95
471	481	1.579084	GCCCGCCGTTTGATGTGTTA	61.579	55.000	0.00	0.00	0.00	2.41
481	491	6.256975	GCCGTTTGATGTGTTACATGTCTATA	59.743	38.462	0.00	0.00	39.27	1.31
492	502	7.707035	GTGTTACATGTCTATACTTCCTTCCTG	59.293	40.741	0.00	0.00	0.00	3.86
514	524	1.153353	GATCGTTGAACTTTCGGGCA	58.847	50.000	0.00	0.00	0.00	5.36
515	525	1.737793	GATCGTTGAACTTTCGGGCAT	59.262	47.619	0.00	0.00	0.00	4.40
516	526	0.871722	TCGTTGAACTTTCGGGCATG	59.128	50.000	0.00	0.00	0.00	4.06
517	527	0.591170	CGTTGAACTTTCGGGCATGT	59.409	50.000	0.00	0.00	0.00	3.21
518	528	1.001815	CGTTGAACTTTCGGGCATGTT	60.002	47.619	0.00	0.00	0.00	2.71
519	529	2.542824	CGTTGAACTTTCGGGCATGTTT	60.543	45.455	0.00	0.00	0.00	2.83
520	530	2.791383	TGAACTTTCGGGCATGTTTG	57.209	45.000	0.00	0.00	0.00	2.93
521	531	2.302260	TGAACTTTCGGGCATGTTTGA	58.698	42.857	0.00	0.00	0.00	2.69
522	532	2.890311	TGAACTTTCGGGCATGTTTGAT	59.110	40.909	0.00	0.00	0.00	2.57
523	533	3.057596	TGAACTTTCGGGCATGTTTGATC	60.058	43.478	0.00	0.00	0.00	2.92
524	534	2.513753	ACTTTCGGGCATGTTTGATCA	58.486	42.857	0.00	0.00	0.00	2.92
525	535	2.228822	ACTTTCGGGCATGTTTGATCAC	59.771	45.455	0.00	0.00	0.00	3.06
526	536	1.173043	TTCGGGCATGTTTGATCACC	58.827	50.000	0.00	0.00	0.00	4.02
527	537	1.024046	TCGGGCATGTTTGATCACCG	61.024	55.000	11.34	11.34	41.06	4.94
528	538	1.024046	CGGGCATGTTTGATCACCGA	61.024	55.000	12.01	0.00	42.19	4.69
529	539	1.173043	GGGCATGTTTGATCACCGAA	58.827	50.000	0.00	0.00	0.00	4.30
530	540	1.135402	GGGCATGTTTGATCACCGAAC	60.135	52.381	0.00	0.00	39.19	3.95
531	541	1.812571	GGCATGTTTGATCACCGAACT	59.187	47.619	9.54	0.00	39.42	3.01
532	542	2.228822	GGCATGTTTGATCACCGAACTT	59.771	45.455	9.54	1.90	39.42	2.66
533	543	3.305335	GGCATGTTTGATCACCGAACTTT	60.305	43.478	9.54	0.00	39.42	2.66
534	544	3.914364	GCATGTTTGATCACCGAACTTTC	59.086	43.478	9.54	0.00	39.42	2.62
550	560	0.321210	TTTCGGGCATGTGTGATCGT	60.321	50.000	0.00	0.00	0.00	3.73
567	577	1.474879	TCGTCGAACTGTGGCATGATA	59.525	47.619	0.00	0.00	0.00	2.15
663	677	2.156051	GACGTCTGGGAGCCGAAACT	62.156	60.000	8.70	0.00	0.00	2.66
680	694	0.473886	ACTTGAGGGTGTGGCTAGGT	60.474	55.000	0.00	0.00	0.00	3.08
697	712	1.826921	GTACTCGATCGCCCCAGGA	60.827	63.158	11.09	0.00	0.00	3.86
779	796	5.092105	CGAGTGAAGATGCTCTAATATCCG	58.908	45.833	0.00	0.00	0.00	4.18
784	801	2.899900	AGATGCTCTAATATCCGCACCA	59.100	45.455	0.00	0.00	34.93	4.17
796	813	2.260154	CGCACCATGTGACAAGCCA	61.260	57.895	0.00	0.00	35.23	4.75
806	823	3.561143	TGTGACAAGCCAAATTGGTACT	58.439	40.909	14.17	0.00	40.46	2.73
809	826	4.517453	GTGACAAGCCAAATTGGTACTACA	59.483	41.667	14.17	6.57	40.46	2.74
825	842	5.815740	GGTACTACATCATCGAAAACCATGT	59.184	40.000	0.00	0.00	0.00	3.21
842	859	0.660488	TGTGCACGTGTGACATTTCC	59.340	50.000	18.38	0.00	0.00	3.13
852	869	4.326826	GTGTGACATTTCCATCTCTTCCA	58.673	43.478	0.00	0.00	0.00	3.53
1010	1032	3.054361	AGCCGATAACAAATGGAGAAGGT	60.054	43.478	0.00	0.00	0.00	3.50
1302	1324	1.069427	GCTGCTCGAGCTGGATGAT	59.931	57.895	35.63	0.00	45.21	2.45
1492	1514	1.241990	CCTCGAGACCACCGTCAAGA	61.242	60.000	15.71	0.00	41.87	3.02
1560	1582	4.827087	GCTGGCTCGCTGCTGCTA	62.827	66.667	14.03	1.49	42.39	3.49
1566	1620	2.884146	CTCGCTGCTGCTAGCTAAG	58.116	57.895	17.23	11.43	42.97	2.18
1609	1664	9.851686	ACAAGATAGAAATGGATGTATTTGCTA	57.148	29.630	0.00	0.00	30.78	3.49
1671	1726	5.395768	GGTGCATCATACTACCTCTGAAAGT	60.396	44.000	0.00	0.00	33.76	2.66
1674	1729	6.070824	TGCATCATACTACCTCTGAAAGTGAA	60.071	38.462	0.00	0.00	33.76	3.18
1675	1730	6.256757	GCATCATACTACCTCTGAAAGTGAAC	59.743	42.308	0.00	0.00	33.76	3.18
1712	1776	2.981997	CCGTTGATTAGCGGGGTAC	58.018	57.895	4.76	0.00	45.65	3.34
1813	1877	0.750546	ATGATCAACAGCGCATGCCT	60.751	50.000	13.15	7.52	44.31	4.75
1850	1915	2.591072	CCTGACTGCCTGAGTGCCT	61.591	63.158	0.00	0.00	33.83	4.75
1956	2021	3.406361	CGTCGTCGCTGCAGCTTT	61.406	61.111	34.22	0.00	39.32	3.51
1969	2072	1.407989	GCAGCTTTCTATGAGGCCACT	60.408	52.381	5.01	0.00	0.00	4.00
2027	2152	9.758651	CATGTATCCACAAATGATCAATCAATT	57.241	29.630	0.00	0.00	38.10	2.32
2209	2359	9.601810	ATTTTCTAAGTCTTCCAATTTTACCCT	57.398	29.630	0.00	0.00	0.00	4.34
2318	2468	1.659098	GATGCACCGTAAAAGGTCTCG	59.341	52.381	0.00	0.00	43.89	4.04
2320	2470	1.202557	TGCACCGTAAAAGGTCTCGTT	60.203	47.619	0.00	0.00	43.89	3.85
2321	2471	1.193874	GCACCGTAAAAGGTCTCGTTG	59.806	52.381	0.00	0.00	43.89	4.10
2322	2472	2.476821	CACCGTAAAAGGTCTCGTTGT	58.523	47.619	0.00	0.00	43.89	3.32
2323	2473	2.867975	CACCGTAAAAGGTCTCGTTGTT	59.132	45.455	0.00	0.00	43.89	2.83
2324	2474	3.310501	CACCGTAAAAGGTCTCGTTGTTT	59.689	43.478	0.00	0.00	43.89	2.83
2325	2475	3.940852	ACCGTAAAAGGTCTCGTTGTTTT	59.059	39.130	0.00	0.00	41.46	2.43
2326	2476	4.034394	ACCGTAAAAGGTCTCGTTGTTTTC	59.966	41.667	0.00	0.00	41.46	2.29
2351	2501	8.363390	TCTCTATTATGATTAGTGCCAAGAGTG	58.637	37.037	0.00	0.00	0.00	3.51
2382	2533	4.567959	GCTTCCCATGTGCAATGAATAAAC	59.432	41.667	9.56	0.00	0.00	2.01
2389	2540	7.378461	CCCATGTGCAATGAATAAACGTATTAC	59.622	37.037	9.56	0.00	29.69	1.89
2422	2573	9.539194	TGATGTCTATACATGTCTATCCATCTT	57.461	33.333	19.69	1.36	46.49	2.40
2430	2581	7.383102	ACATGTCTATCCATCTTTGTGTTTC	57.617	36.000	0.00	0.00	0.00	2.78
2465	2644	1.048601	ATTCCGAGTGTGGAGTGTGT	58.951	50.000	0.00	0.00	39.72	3.72

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	1.400242	CGATGCACTGCTCGATCGATA	60.400	52.381	19.78	10.03	40.06	2.92
74	75	1.746991	CTCCTTCCTCTTTGCGGCC	60.747	63.158	0.00	0.00	0.00	6.13
105	106	0.739462	GTCATCAACGCCGACCATCA	60.739	55.000	0.00	0.00	0.00	3.07
107	108	1.809619	CGTCATCAACGCCGACCAT	60.810	57.895	0.00	0.00	45.76	3.55
131	132	1.689273	AGAAGGTCAAGCTTCACGTCT	59.311	47.619	20.50	0.00	32.44	4.18
143	144	1.075050	ACGTAGGTCCTGAGAAGGTCA	59.925	52.381	0.00	0.00	0.00	4.02
189	190	2.114670	CCGCCATCAAGAACGCCAT	61.115	57.895	0.00	0.00	0.00	4.40
255	256	2.803155	TTCAAGATGAGGCCGCGCTT	62.803	55.000	5.56	8.30	0.00	4.68
275	276	3.785859	GCTGGCCCGGACATCTGA	61.786	66.667	0.73	0.00	0.00	3.27
321	325	4.364409	GGGCGTCGACGTTGTTGC	62.364	66.667	35.48	19.51	42.22	4.17
365	375	3.622826	CTCGGGTTGGTGGTCGGT	61.623	66.667	0.00	0.00	0.00	4.69
376	386	3.241530	TGGCTTCTGTGCTCGGGT	61.242	61.111	0.00	0.00	0.00	5.28
451	461	4.114997	CACATCAAACGGCGGGCC	62.115	66.667	13.24	0.00	0.00	5.80
471	481	6.440647	TCAACAGGAAGGAAGTATAGACATGT	59.559	38.462	0.00	0.00	0.00	3.21
481	491	3.071023	TCAACGATCAACAGGAAGGAAGT	59.929	43.478	0.00	0.00	0.00	3.01
492	502	2.664698	GCCCGAAAGTTCAACGATCAAC	60.665	50.000	0.00	0.00	0.00	3.18
514	524	4.404507	CGAAAGTTCGGTGATCAAACAT	57.595	40.909	10.56	0.00	46.30	2.71
515	525	3.870723	CGAAAGTTCGGTGATCAAACA	57.129	42.857	10.56	0.00	46.30	2.83
527	537	1.234821	TCACACATGCCCGAAAGTTC	58.765	50.000	0.00	0.00	0.00	3.01
528	538	1.812571	GATCACACATGCCCGAAAGTT	59.187	47.619	0.00	0.00	0.00	2.66
529	539	1.453155	GATCACACATGCCCGAAAGT	58.547	50.000	0.00	0.00	0.00	2.66
530	540	0.374758	CGATCACACATGCCCGAAAG	59.625	55.000	0.00	0.00	0.00	2.62
531	541	0.321210	ACGATCACACATGCCCGAAA	60.321	50.000	0.00	0.00	0.00	3.46
532	542	0.739462	GACGATCACACATGCCCGAA	60.739	55.000	0.00	0.00	0.00	4.30
533	543	1.153647	GACGATCACACATGCCCGA	60.154	57.895	0.00	0.00	0.00	5.14
534	544	2.516589	CGACGATCACACATGCCCG	61.517	63.158	0.00	0.00	0.00	6.13
535	545	0.739462	TTCGACGATCACACATGCCC	60.739	55.000	0.00	0.00	0.00	5.36
536	546	0.370273	GTTCGACGATCACACATGCC	59.630	55.000	0.00	0.00	0.00	4.40
537	547	1.059692	CAGTTCGACGATCACACATGC	59.940	52.381	8.53	0.00	0.00	4.06
538	548	2.091122	CACAGTTCGACGATCACACATG	59.909	50.000	8.53	0.00	0.00	3.21
543	553	0.666274	TGCCACAGTTCGACGATCAC	60.666	55.000	8.53	0.22	0.00	3.06
550	560	3.065233	GCAATTATCATGCCACAGTTCGA	59.935	43.478	0.00	0.00	37.85	3.71
654	668	0.535102	CACACCCTCAAGTTTCGGCT	60.535	55.000	0.00	0.00	0.00	5.52
663	677	1.203262	AGTACCTAGCCACACCCTCAA	60.203	52.381	0.00	0.00	0.00	3.02
680	694	1.826921	GTCCTGGGGCGATCGAGTA	60.827	63.158	21.57	0.20	0.00	2.59
749	766	0.737715	GCATCTTCACTCGTTCGGCT	60.738	55.000	0.00	0.00	0.00	5.52
779	796	0.388659	TTTGGCTTGTCACATGGTGC	59.611	50.000	0.00	0.00	32.98	5.01
784	801	4.151883	AGTACCAATTTGGCTTGTCACAT	58.848	39.130	15.49	0.00	42.67	3.21
796	813	7.392113	TGGTTTTCGATGATGTAGTACCAATTT	59.608	33.333	0.00	0.00	30.76	1.82
806	823	4.006319	TGCACATGGTTTTCGATGATGTA	58.994	39.130	0.00	0.00	38.95	2.29
809	826	2.159531	CGTGCACATGGTTTTCGATGAT	60.160	45.455	18.64	0.00	38.95	2.45
825	842	1.535028	GATGGAAATGTCACACGTGCA	59.465	47.619	17.22	6.09	0.00	4.57
930	948	0.874175	CGTTTGACTCGCAGTGGTGA	60.874	55.000	0.00	0.00	0.00	4.02
1010	1032	0.964700	CTGCTCAGACTCCTGTGTCA	59.035	55.000	2.61	0.00	41.16	3.58
1560	1582	7.492524	TGTTTCATCTCATCGATTACTTAGCT	58.507	34.615	0.00	0.00	0.00	3.32
1562	1584	9.521503	TCTTGTTTCATCTCATCGATTACTTAG	57.478	33.333	0.00	0.00	0.00	2.18
1566	1620	9.684448	TCTATCTTGTTTCATCTCATCGATTAC	57.316	33.333	0.00	0.00	0.00	1.89
1590	1645	9.499479	CAGACTATAGCAAATACATCCATTTCT	57.501	33.333	0.00	0.00	0.00	2.52
1609	1664	3.074412	CAAACGGGAAGCAACAGACTAT	58.926	45.455	0.00	0.00	0.00	2.12
1671	1726	5.819379	GGCTGAGATGATTCAATACTGTTCA	59.181	40.000	0.00	0.00	0.00	3.18
1674	1729	4.141846	ACGGCTGAGATGATTCAATACTGT	60.142	41.667	0.00	0.00	0.00	3.55
1675	1730	4.375272	ACGGCTGAGATGATTCAATACTG	58.625	43.478	0.00	0.00	0.00	2.74
1813	1877	5.355630	GTCAGGCTAGCTCTGATCGATATTA	59.644	44.000	27.68	9.15	42.36	0.98
1850	1915	1.819305	GCTTGGAGCTCCCACTTGAAA	60.819	52.381	29.95	14.23	46.62	2.69
1920	1985	1.136774	CCGCGACTGATCAAGACGA	59.863	57.895	8.23	0.00	45.25	4.20
2027	2152	5.820423	CCGAGGAAATCACCATGTACAATAA	59.180	40.000	0.00	0.00	0.00	1.40
2318	2468	9.937175	GGCACTAATCATAATAGAGAAAACAAC	57.063	33.333	0.00	0.00	0.00	3.32
2320	2470	9.679661	TTGGCACTAATCATAATAGAGAAAACA	57.320	29.630	0.00	0.00	0.00	2.83
2323	2473	9.770097	CTCTTGGCACTAATCATAATAGAGAAA	57.230	33.333	0.00	0.00	0.00	2.52
2324	2474	8.928448	ACTCTTGGCACTAATCATAATAGAGAA	58.072	33.333	10.43	0.00	32.06	2.87
2325	2475	8.363390	CACTCTTGGCACTAATCATAATAGAGA	58.637	37.037	10.43	0.00	32.06	3.10
2326	2476	7.601886	CCACTCTTGGCACTAATCATAATAGAG	59.398	40.741	0.00	0.00	35.56	2.43
2351	2501	2.825836	CATGGGAAGCGAGCCACC	60.826	66.667	0.00	0.00	0.00	4.61
2389	2540	7.428282	AGACATGTATAGACATCAGACGTAG	57.572	40.000	0.00	0.00	44.82	3.51
2430	2581	5.176223	ACTCGGAATTGTAGTTTTGTACACG	59.824	40.000	0.00	0.00	32.53	4.49
2465	2644	0.443869	GTACTTGCCGTCGTCGAGTA	59.556	55.000	2.98	0.00	39.71	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.