AutoCloner

Multiple sequence alignment - TraesCS2A01G361400

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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	TraesCS2A01G361400	chr2A	100.000	3476	0	0	1	3476	605309934	605313409	0.000000e+00	6420.0
1	TraesCS2A01G361400	chr3D	93.961	1987	96	12	874	2845	597266059	597264082	0.000000e+00	2983.0
2	TraesCS2A01G361400	chr3D	88.558	1512	147	9	988	2488	596993908	596995404	0.000000e+00	1810.0
3	TraesCS2A01G361400	chr3D	95.622	434	19	0	98	531	597266844	597266411	0.000000e+00	697.0
4	TraesCS2A01G361400	chr3D	86.529	631	67	13	2595	3213	596995434	596996058	0.000000e+00	678.0
5	TraesCS2A01G361400	chr3D	93.909	197	12	0	527	723	597266351	597266155	7.290000e-77	298.0
6	TraesCS2A01G361400	chr3B	91.196	1840	114	18	730	2540	804113727	804111907	0.000000e+00	2457.0
7	TraesCS2A01G361400	chr3B	87.269	1516	167	9	984	2488	803513072	803511572	0.000000e+00	1707.0
8	TraesCS2A01G361400	chr3B	88.980	980	87	6	1517	2488	803334588	803333622	0.000000e+00	1192.0
9	TraesCS2A01G361400	chr3B	93.974	780	27	8	2532	3303	804111724	804110957	0.000000e+00	1162.0
10	TraesCS2A01G361400	chr3B	83.905	758	80	25	2580	3312	803540646	803541386	0.000000e+00	686.0
11	TraesCS2A01G361400	chr3B	84.690	516	59	15	2573	3070	803363474	803362961	6.700000e-137	497.0
12	TraesCS2A01G361400	chr3B	84.690	516	59	15	2573	3070	803461213	803460700	6.700000e-137	497.0
13	TraesCS2A01G361400	chr3B	84.283	509	61	14	2579	3070	803511522	803511016	2.430000e-131	479.0
14	TraesCS2A01G361400	chr3B	86.835	357	30	5	2148	2488	803561078	803561433	1.960000e-102	383.0
15	TraesCS2A01G361400	chr3B	93.956	182	6	5	3295	3476	804109939	804109763	1.590000e-68	270.0
16	TraesCS2A01G361400	chr3B	85.593	236	19	8	3069	3300	803324888	803324664	2.090000e-57	233.0
17	TraesCS2A01G361400	chr3B	84.190	253	21	10	298	531	804114118	804113866	9.710000e-56	228.0
18	TraesCS2A01G361400	chr3B	84.746	236	21	8	3069	3300	803496995	803496771	4.520000e-54	222.0
19	TraesCS2A01G361400	chr3B	96.053	76	3	0	530	605	804113801	804113726	1.310000e-24	124.0
20	TraesCS2A01G361400	chr3B	89.899	99	5	3	1	99	675577166	675577259	4.710000e-24	122.0
21	TraesCS2A01G361400	chr3B	88.660	97	6	2	1	97	31849163	31849254	2.840000e-21	113.0
22	TraesCS2A01G361400	chrUn	86.986	1629	156	25	1534	3132	277309201	277307599	0.000000e+00	1783.0
23	TraesCS2A01G361400	chrUn	88.980	980	87	7	1517	2488	303788917	303789883	0.000000e+00	1192.0
24	TraesCS2A01G361400	chrUn	88.980	980	87	7	1517	2488	308985222	308986188	0.000000e+00	1192.0
25	TraesCS2A01G361400	chrUn	85.169	236	20	10	3069	3300	292088138	292087914	9.710000e-56	228.0
26	TraesCS2A01G361400	chrUn	85.169	236	20	10	3069	3300	312304713	312304489	9.710000e-56	228.0
27	TraesCS2A01G361400	chrUn	88.660	97	6	2	1	97	354813562	354813653	2.840000e-21	113.0
28	TraesCS2A01G361400	chrUn	88.660	97	6	2	1	97	401389727	401389636	2.840000e-21	113.0
29	TraesCS2A01G361400	chrUn	90.588	85	3	2	13	97	343006312	343006391	1.320000e-19	108.0
30	TraesCS2A01G361400	chrUn	100.000	43	0	0	55	97	314951300	314951258	2.880000e-11	80.5
31	TraesCS2A01G361400	chr3A	86.986	1629	156	25	1534	3132	727185498	727187100	0.000000e+00	1783.0
32	TraesCS2A01G361400	chr3A	87.648	1522	159	11	1015	2512	727180666	727182182	0.000000e+00	1742.0
33	TraesCS2A01G361400	chr3A	90.365	903	64	10	960	1862	727365357	727366236	0.000000e+00	1164.0
34	TraesCS2A01G361400	chr3A	90.092	434	37	1	98	531	727364164	727364591	3.030000e-155	558.0
35	TraesCS2A01G361400	chr3A	95.184	353	15	2	2806	3157	727371945	727372296	1.090000e-154	556.0
36	TraesCS2A01G361400	chr3A	88.110	328	22	8	527	841	727364651	727364974	1.180000e-99	374.0
37	TraesCS2A01G361400	chr3A	92.821	195	7	2	3156	3350	727372511	727372698	3.420000e-70	276.0
38	TraesCS2A01G361400	chr3A	93.233	133	9	0	3344	3476	727372940	727373072	2.740000e-46	196.0
39	TraesCS2A01G361400	chr3A	88.462	78	9	0	874	951	727364970	727365047	1.030000e-15	95.3
40	TraesCS2A01G361400	chr4B	83.041	1598	214	27	997	2552	86359292	86360874	0.000000e+00	1397.0
41	TraesCS2A01G361400	chr4A	82.737	1593	212	30	1015	2553	538906749	538905166	0.000000e+00	1360.0
42	TraesCS2A01G361400	chr7B	91.667	84	7	0	527	610	496667075	496666992	2.190000e-22	117.0
43	TraesCS2A01G361400	chr7A	88.660	97	7	1	1	97	610647027	610647119	7.880000e-22	115.0
44	TraesCS2A01G361400	chr5A	88.660	97	6	1	1	97	671268469	671268560	2.840000e-21	113.0
45	TraesCS2A01G361400	chr5A	84.000	100	11	2	1	99	401752077	401752172	1.330000e-14	91.6
46	TraesCS2A01G361400	chr6B	93.750	64	4	0	527	590	715585999	715586062	2.860000e-16	97.1
47	TraesCS2A01G361400	chr6D	90.909	44	4	0	468	511	472450425	472450382	3.750000e-05	60.2
48	TraesCS2A01G361400	chr7D	96.875	32	0	1	399	429	471241309	471241278	6.000000e-03	52.8

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	TraesCS2A01G361400	chr2A	605309934	605313409	3475	False	6420.000000	6420	100.000000	1	3476	1	chr2A.!!$F1	3475
1	TraesCS2A01G361400	chr3D	597264082	597266844	2762	True	1326.000000	2983	94.497333	98	2845	3	chr3D.!!$R1	2747
2	TraesCS2A01G361400	chr3D	596993908	596996058	2150	False	1244.000000	1810	87.543500	988	3213	2	chr3D.!!$F1	2225
3	TraesCS2A01G361400	chr3B	803333622	803334588	966	True	1192.000000	1192	88.980000	1517	2488	1	chr3B.!!$R2	971
4	TraesCS2A01G361400	chr3B	803511016	803513072	2056	True	1093.000000	1707	85.776000	984	3070	2	chr3B.!!$R6	2086
5	TraesCS2A01G361400	chr3B	804109763	804114118	4355	True	848.200000	2457	91.873800	298	3476	5	chr3B.!!$R7	3178
6	TraesCS2A01G361400	chr3B	803540646	803541386	740	False	686.000000	686	83.905000	2580	3312	1	chr3B.!!$F3	732
7	TraesCS2A01G361400	chr3B	803362961	803363474	513	True	497.000000	497	84.690000	2573	3070	1	chr3B.!!$R3	497
8	TraesCS2A01G361400	chr3B	803460700	803461213	513	True	497.000000	497	84.690000	2573	3070	1	chr3B.!!$R4	497
9	TraesCS2A01G361400	chrUn	277307599	277309201	1602	True	1783.000000	1783	86.986000	1534	3132	1	chrUn.!!$R1	1598
10	TraesCS2A01G361400	chrUn	303788917	303789883	966	False	1192.000000	1192	88.980000	1517	2488	1	chrUn.!!$F1	971
11	TraesCS2A01G361400	chrUn	308985222	308986188	966	False	1192.000000	1192	88.980000	1517	2488	1	chrUn.!!$F2	971
12	TraesCS2A01G361400	chr3A	727180666	727187100	6434	False	1762.500000	1783	87.317000	1015	3132	2	chr3A.!!$F1	2117
13	TraesCS2A01G361400	chr3A	727364164	727366236	2072	False	547.825000	1164	89.257250	98	1862	4	chr3A.!!$F2	1764
14	TraesCS2A01G361400	chr3A	727371945	727373072	1127	False	342.666667	556	93.746000	2806	3476	3	chr3A.!!$F3	670
15	TraesCS2A01G361400	chr4B	86359292	86360874	1582	False	1397.000000	1397	83.041000	997	2552	1	chr4B.!!$F1	1555
16	TraesCS2A01G361400	chr4A	538905166	538906749	1583	True	1360.000000	1360	82.737000	1015	2553	1	chr4A.!!$R1	1538

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	Hairpin	End Stability	Orientation
21	22	0.322366	GCTTTTCTCAGGCTCAGGCT	60.322	55.0	0.00	39.66	4.58	F
443	463	0.675083	TGTTTCTACGGCTTCGACCA	59.325	50.0	0.00	37.63	4.02	F
565	651	0.728542	CAGCATTGCAGCATCACGTA	59.271	50.0	11.91	36.85	3.57	F
869	974	0.733150	GTGGGCTCCTAATGCGAAAC	59.267	55.0	0.00	0.00	2.78	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1065	1474	0.036388	CCACCACATTGTACTCCGCT	60.036	55.000	0.00	0.00	5.52	R
1378	1790	1.937924	GCCCAATACTCCTGCCCCTT	61.938	60.000	0.00	0.00	3.95	R
1398	1810	2.353406	GCAATTGCTGACCTTCTTGCAT	60.353	45.455	23.21	38.96	3.96	R
2592	7632	2.028420	TCCTCCAAGCAATGATCACG	57.972	50.000	0.00	0.00	4.35	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
18	19	2.865492	GGGCTTTTCTCAGGCTCAG	58.135	57.895	0.00	0.00	39.35	3.35
19	20	0.679321	GGGCTTTTCTCAGGCTCAGG	60.679	60.000	0.00	0.00	39.35	3.86
20	21	1.311651	GGCTTTTCTCAGGCTCAGGC	61.312	60.000	0.00	0.00	36.41	4.85
21	22	0.322366	GCTTTTCTCAGGCTCAGGCT	60.322	55.000	0.00	0.00	39.66	4.58
22	23	1.885790	GCTTTTCTCAGGCTCAGGCTT	60.886	52.381	0.00	0.00	35.88	4.35
23	24	2.512705	CTTTTCTCAGGCTCAGGCTTT	58.487	47.619	0.00	0.00	35.88	3.51
24	25	3.679389	CTTTTCTCAGGCTCAGGCTTTA	58.321	45.455	0.00	0.00	35.88	1.85
25	26	2.770164	TTCTCAGGCTCAGGCTTTAC	57.230	50.000	0.00	0.00	35.88	2.01
26	27	1.644509	TCTCAGGCTCAGGCTTTACA	58.355	50.000	0.00	0.00	35.88	2.41
27	28	2.191400	TCTCAGGCTCAGGCTTTACAT	58.809	47.619	0.00	0.00	35.88	2.29
28	29	2.573462	TCTCAGGCTCAGGCTTTACATT	59.427	45.455	0.00	0.00	35.88	2.71
29	30	3.009473	TCTCAGGCTCAGGCTTTACATTT	59.991	43.478	0.00	0.00	35.88	2.32
30	31	3.760684	CTCAGGCTCAGGCTTTACATTTT	59.239	43.478	0.00	0.00	35.88	1.82
31	32	4.917385	TCAGGCTCAGGCTTTACATTTTA	58.083	39.130	0.00	0.00	35.88	1.52
32	33	4.943705	TCAGGCTCAGGCTTTACATTTTAG	59.056	41.667	0.00	0.00	35.88	1.85
33	34	3.696548	AGGCTCAGGCTTTACATTTTAGC	59.303	43.478	0.00	0.00	33.67	3.09
34	35	3.443681	GGCTCAGGCTTTACATTTTAGCA	59.556	43.478	0.00	0.00	36.64	3.49
35	36	4.415735	GCTCAGGCTTTACATTTTAGCAC	58.584	43.478	0.00	0.00	36.64	4.40
36	37	4.675408	GCTCAGGCTTTACATTTTAGCACC	60.675	45.833	0.00	0.00	36.64	5.01
37	38	3.438781	TCAGGCTTTACATTTTAGCACCG	59.561	43.478	0.00	0.00	36.64	4.94
38	39	2.752903	AGGCTTTACATTTTAGCACCGG	59.247	45.455	0.00	0.00	36.64	5.28
39	40	2.159296	GGCTTTACATTTTAGCACCGGG	60.159	50.000	6.32	0.00	36.64	5.73
40	41	2.734175	GCTTTACATTTTAGCACCGGGC	60.734	50.000	6.32	6.61	45.30	6.13
49	50	4.522971	GCACCGGGCTTTCTAGAG	57.477	61.111	6.32	0.00	40.25	2.43
50	51	1.815840	GCACCGGGCTTTCTAGAGC	60.816	63.158	6.32	0.00	41.96	4.09
56	57	2.203084	GCTTTCTAGAGCCCGGCC	60.203	66.667	5.55	0.00	36.66	6.13
57	58	2.506472	CTTTCTAGAGCCCGGCCC	59.494	66.667	5.55	0.00	0.00	5.80
58	59	3.447025	CTTTCTAGAGCCCGGCCCG	62.447	68.421	5.55	0.00	0.00	6.13
94	95	3.470888	CCGAGAGATGCCCGGGTT	61.471	66.667	24.63	10.53	39.59	4.11
95	96	2.584608	CGAGAGATGCCCGGGTTT	59.415	61.111	24.63	10.09	0.00	3.27
96	97	1.682451	CCGAGAGATGCCCGGGTTTA	61.682	60.000	24.63	9.73	39.59	2.01
316	317	1.811266	GTCACGGTGATGCTGCGAT	60.811	57.895	14.78	0.00	0.00	4.58
362	363	0.955919	CTCCAACGAAGGCCCAACTC	60.956	60.000	0.00	0.00	0.00	3.01
443	463	0.675083	TGTTTCTACGGCTTCGACCA	59.325	50.000	0.00	0.00	37.63	4.02
565	651	0.728542	CAGCATTGCAGCATCACGTA	59.271	50.000	11.91	0.00	36.85	3.57
770	858	5.929992	ACTTCATCCGACTGTTTTTAATCGA	59.070	36.000	0.00	0.00	36.70	3.59
816	915	6.586868	AGTACGTGAAGTAGTCTCGATTAG	57.413	41.667	0.00	0.00	44.19	1.73
843	942	4.949856	GTGGGATGTGACTTGTATTCCAAT	59.050	41.667	0.00	0.00	31.44	3.16
854	953	6.522054	ACTTGTATTCCAATCGTATAGTGGG	58.478	40.000	0.00	0.00	43.78	4.61
866	971	1.717032	ATAGTGGGCTCCTAATGCGA	58.283	50.000	0.00	0.00	0.00	5.10
869	974	0.733150	GTGGGCTCCTAATGCGAAAC	59.267	55.000	0.00	0.00	0.00	2.78
897	1002	2.681778	CCCTGAGACGAGCTGGGT	60.682	66.667	0.00	0.00	39.08	4.51
900	1005	1.214062	CTGAGACGAGCTGGGTCAC	59.786	63.158	14.91	10.11	36.87	3.67
1013	1422	2.131183	GCGGAAGATGAGCAGTCATAC	58.869	52.381	0.00	0.00	43.92	2.39
1033	1442	3.292500	CTCTCGCTGCTGCTGGTGA	62.293	63.158	14.03	8.58	36.97	4.02
1089	1501	3.132289	CGGAGTACAATGTGGTGGACTAT	59.868	47.826	0.00	0.00	43.04	2.12
1398	1810	2.689691	GGGGCAGGAGTATTGGGCA	61.690	63.158	0.00	0.00	0.00	5.36
1411	1823	0.178967	TTGGGCATGCAAGAAGGTCA	60.179	50.000	21.36	1.43	0.00	4.02
1467	1910	6.638468	GTGATGACATGAACTTCTTGGTTTTC	59.362	38.462	0.00	0.00	0.00	2.29
1515	1958	2.590575	CTTGTGACGGGCGTTGGT	60.591	61.111	0.00	0.00	0.00	3.67
1627	2074	1.522355	ATGGCCATCTTCGACTGCG	60.522	57.895	14.09	0.00	39.35	5.18
1631	2078	3.918220	CATCTTCGACTGCGCCGC	61.918	66.667	4.18	0.00	37.46	6.53
1762	2209	1.080093	GGCGACGATTGTGTCTCCA	60.080	57.895	0.00	0.00	42.14	3.86
1940	2402	2.419198	GATCGCAGCATCGGGAGT	59.581	61.111	0.00	0.00	0.00	3.85
1943	2405	0.823769	ATCGCAGCATCGGGAGTCTA	60.824	55.000	0.00	0.00	0.00	2.59
1946	2408	2.045280	CAGCATCGGGAGTCTAGGG	58.955	63.158	0.00	0.00	0.00	3.53
1990	2452	0.898789	AGGAACGTGACGGTGGAGAT	60.899	55.000	10.66	0.00	0.00	2.75
2132	2594	1.805345	CTCGTCGACCAGAACTACTGT	59.195	52.381	10.58	0.00	44.40	3.55
2370	7189	1.748122	CTGCAGCGGGATCAAGCTT	60.748	57.895	10.89	0.00	42.52	3.74
2575	7615	5.747565	CACAGTTGCGTAAGATCAAAAAGA	58.252	37.500	0.00	0.00	43.02	2.52
2576	7616	6.198687	CACAGTTGCGTAAGATCAAAAAGAA	58.801	36.000	0.00	0.00	43.02	2.52
2608	7649	2.689553	TAGCGTGATCATTGCTTGGA	57.310	45.000	24.69	9.45	40.06	3.53
2890	7944	5.336744	CGGAAAGCGGCTTGATAAATTTTA	58.663	37.500	17.16	0.00	0.00	1.52
2891	7945	5.455525	CGGAAAGCGGCTTGATAAATTTTAG	59.544	40.000	17.16	0.00	0.00	1.85
2956	8019	9.171877	CCAAGAGCAGAAATATTTAACTCTCTT	57.828	33.333	19.54	19.08	38.47	2.85
3035	8100	7.223971	TGCTATCTATGTCAAACAACCGTTATC	59.776	37.037	0.00	0.00	33.99	1.75
3120	8190	4.334443	CGGCGAAATAAGAGTTCACATTG	58.666	43.478	0.00	0.00	0.00	2.82
3253	8541	9.165035	CAGGGTATTTTCAAAACCGTAGTAATA	57.835	33.333	0.00	0.00	33.89	0.98
3254	8542	9.387257	AGGGTATTTTCAAAACCGTAGTAATAG	57.613	33.333	0.00	0.00	33.89	1.73
3255	8543	9.166173	GGGTATTTTCAAAACCGTAGTAATAGT	57.834	33.333	0.00	0.00	33.89	2.12
3352	9916	9.424319	TCTGTGAAAACTAGTATGCTTTAGAAG	57.576	33.333	0.00	0.00	0.00	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.679321	CCTGAGCCTGAGAAAAGCCC	60.679	60.000	0.00	0.00	0.00	5.19
1	2	1.311651	GCCTGAGCCTGAGAAAAGCC	61.312	60.000	0.00	0.00	0.00	4.35
2	3	0.322366	AGCCTGAGCCTGAGAAAAGC	60.322	55.000	0.00	0.00	41.25	3.51
3	4	2.197283	AAGCCTGAGCCTGAGAAAAG	57.803	50.000	0.00	0.00	41.25	2.27
4	5	2.664402	AAAGCCTGAGCCTGAGAAAA	57.336	45.000	0.00	0.00	41.25	2.29
5	6	2.371841	TGTAAAGCCTGAGCCTGAGAAA	59.628	45.455	0.00	0.00	41.25	2.52
6	7	1.977854	TGTAAAGCCTGAGCCTGAGAA	59.022	47.619	0.00	0.00	41.25	2.87
7	8	1.644509	TGTAAAGCCTGAGCCTGAGA	58.355	50.000	0.00	0.00	41.25	3.27
8	9	2.706339	ATGTAAAGCCTGAGCCTGAG	57.294	50.000	0.00	0.00	41.25	3.35
9	10	3.439857	AAATGTAAAGCCTGAGCCTGA	57.560	42.857	0.00	0.00	41.25	3.86
10	11	4.439289	GCTAAAATGTAAAGCCTGAGCCTG	60.439	45.833	0.00	0.00	41.25	4.85
11	12	3.696548	GCTAAAATGTAAAGCCTGAGCCT	59.303	43.478	0.00	0.00	41.25	4.58
12	13	3.443681	TGCTAAAATGTAAAGCCTGAGCC	59.556	43.478	0.00	0.00	41.25	4.70
13	14	4.415735	GTGCTAAAATGTAAAGCCTGAGC	58.584	43.478	0.00	0.00	35.33	4.26
14	15	4.437390	CGGTGCTAAAATGTAAAGCCTGAG	60.437	45.833	0.00	0.00	35.33	3.35
15	16	3.438781	CGGTGCTAAAATGTAAAGCCTGA	59.561	43.478	0.00	0.00	35.33	3.86
16	17	3.427503	CCGGTGCTAAAATGTAAAGCCTG	60.428	47.826	0.00	0.00	35.33	4.85
17	18	2.752903	CCGGTGCTAAAATGTAAAGCCT	59.247	45.455	0.00	0.00	35.33	4.58
18	19	2.159296	CCCGGTGCTAAAATGTAAAGCC	60.159	50.000	0.00	0.00	35.33	4.35
19	20	2.734175	GCCCGGTGCTAAAATGTAAAGC	60.734	50.000	0.00	0.00	36.87	3.51
20	21	3.145212	GCCCGGTGCTAAAATGTAAAG	57.855	47.619	0.00	0.00	36.87	1.85
32	33	1.815840	GCTCTAGAAAGCCCGGTGC	60.816	63.158	0.00	3.33	36.22	5.01
33	34	4.522971	GCTCTAGAAAGCCCGGTG	57.477	61.111	0.00	0.00	36.22	4.94
39	40	2.203084	GGCCGGGCTCTAGAAAGC	60.203	66.667	22.87	0.00	41.73	3.51
40	41	2.506472	GGGCCGGGCTCTAGAAAG	59.494	66.667	28.80	0.00	0.00	2.62
41	42	3.467226	CGGGCCGGGCTCTAGAAA	61.467	66.667	28.80	0.00	0.00	2.52
77	78	1.682451	TAAACCCGGGCATCTCTCGG	61.682	60.000	24.08	0.00	43.05	4.63
78	79	0.529992	GTAAACCCGGGCATCTCTCG	60.530	60.000	24.08	0.00	0.00	4.04
79	80	0.831307	AGTAAACCCGGGCATCTCTC	59.169	55.000	24.08	4.87	0.00	3.20
80	81	1.286248	AAGTAAACCCGGGCATCTCT	58.714	50.000	24.08	10.29	0.00	3.10
81	82	2.124277	AAAGTAAACCCGGGCATCTC	57.876	50.000	24.08	7.85	0.00	2.75
82	83	3.349927	GTTAAAGTAAACCCGGGCATCT	58.650	45.455	24.08	11.48	0.00	2.90
83	84	2.096335	CGTTAAAGTAAACCCGGGCATC	59.904	50.000	24.08	9.05	0.00	3.91
84	85	2.086094	CGTTAAAGTAAACCCGGGCAT	58.914	47.619	24.08	12.83	0.00	4.40
85	86	1.521580	CGTTAAAGTAAACCCGGGCA	58.478	50.000	24.08	2.33	0.00	5.36
86	87	0.168788	GCGTTAAAGTAAACCCGGGC	59.831	55.000	24.08	3.45	0.00	6.13
87	88	0.804364	GGCGTTAAAGTAAACCCGGG	59.196	55.000	22.25	22.25	0.00	5.73
88	89	0.804364	GGGCGTTAAAGTAAACCCGG	59.196	55.000	0.00	0.00	29.66	5.73
89	90	0.443478	CGGGCGTTAAAGTAAACCCG	59.557	55.000	12.69	12.69	46.61	5.28
90	91	1.197492	CACGGGCGTTAAAGTAAACCC	59.803	52.381	0.00	0.00	34.51	4.11
91	92	1.197492	CCACGGGCGTTAAAGTAAACC	59.803	52.381	0.00	0.00	0.00	3.27
92	93	1.872952	ACCACGGGCGTTAAAGTAAAC	59.127	47.619	0.00	0.00	0.00	2.01
93	94	2.252976	ACCACGGGCGTTAAAGTAAA	57.747	45.000	0.00	0.00	0.00	2.01
94	95	3.260740	CATACCACGGGCGTTAAAGTAA	58.739	45.455	0.00	0.00	0.00	2.24
95	96	2.891112	CATACCACGGGCGTTAAAGTA	58.109	47.619	0.00	0.00	0.00	2.24
96	97	1.729284	CATACCACGGGCGTTAAAGT	58.271	50.000	0.00	0.00	0.00	2.66
194	195	1.803922	CGTTGCCGTCGTAGCATCA	60.804	57.895	0.00	0.00	40.59	3.07
212	213	2.420022	ACAACATCATCAAAGTAGCGGC	59.580	45.455	0.00	0.00	0.00	6.53
256	257	1.723003	GCGGTTCGTCGTAACATCTTT	59.277	47.619	8.93	0.00	0.00	2.52
286	287	1.332375	CACCGTGACCGTTTGAAACAT	59.668	47.619	8.93	0.00	0.00	2.71
316	317	2.282407	CGTGATCATCCAAGCACATCA	58.718	47.619	0.00	0.00	0.00	3.07
362	363	1.202065	CCGTCGCAACATCATTGAAGG	60.202	52.381	0.00	0.00	0.00	3.46
367	368	1.573829	AACGCCGTCGCAACATCATT	61.574	50.000	0.00	0.00	39.84	2.57
451	471	1.576920	CTCTATCATCGCCGTCGCT	59.423	57.895	0.00	0.00	35.26	4.93
464	484	1.418334	AGCATCCTTGACGCCTCTAT	58.582	50.000	0.00	0.00	0.00	1.98
465	485	1.681793	GTAGCATCCTTGACGCCTCTA	59.318	52.381	0.00	0.00	0.00	2.43
512	532	2.639839	ACACAAGCTTATGGAGTCCTGT	59.360	45.455	9.97	1.12	0.00	4.00
565	651	3.675228	GCTTAGCACGTACCTACACATGT	60.675	47.826	0.00	0.00	0.00	3.21
816	915	0.034896	ACAAGTCACATCCCACGTCC	59.965	55.000	0.00	0.00	0.00	4.79
843	942	2.561419	GCATTAGGAGCCCACTATACGA	59.439	50.000	0.00	0.00	0.00	3.43
854	953	0.461339	TCCCGTTTCGCATTAGGAGC	60.461	55.000	0.00	0.00	0.00	4.70
897	1002	3.703286	ATATTGATCCGAACGACGTGA	57.297	42.857	0.00	0.00	40.78	4.35
900	1005	4.443063	TGCTTTATATTGATCCGAACGACG	59.557	41.667	0.00	0.00	42.18	5.12
986	1395	0.528466	GCTCATCTTCCGCACGATCA	60.528	55.000	0.00	0.00	0.00	2.92
1033	1442	1.968017	CCAGCAGTGCCATCAACGT	60.968	57.895	12.58	0.00	0.00	3.99
1065	1474	0.036388	CCACCACATTGTACTCCGCT	60.036	55.000	0.00	0.00	0.00	5.52
1378	1790	1.937924	GCCCAATACTCCTGCCCCTT	61.938	60.000	0.00	0.00	0.00	3.95
1398	1810	2.353406	GCAATTGCTGACCTTCTTGCAT	60.353	45.455	23.21	0.00	38.96	3.96
1762	2209	2.774351	GGAGGTGCCAGGCCCTAT	60.774	66.667	18.73	1.60	36.34	2.57
1940	2402	2.363795	CCGTCCTGCCACCCTAGA	60.364	66.667	0.00	0.00	0.00	2.43
1943	2405	4.954118	TCACCGTCCTGCCACCCT	62.954	66.667	0.00	0.00	0.00	4.34
1946	2408	3.302347	CTCCTCACCGTCCTGCCAC	62.302	68.421	0.00	0.00	0.00	5.01
2132	2594	3.691342	CAGTCGACCTTGCGGGGA	61.691	66.667	13.01	0.00	40.03	4.81
2317	7136	3.360249	GCAGTTGAACTTCACTGCAAT	57.640	42.857	25.54	0.31	43.89	3.56
2370	7189	4.018490	TGTACGTCAGCCTAATGTTCCTA	58.982	43.478	0.00	0.00	0.00	2.94
2518	7345	9.396022	AGTATTTACAGAAACCATCGAATCAAT	57.604	29.630	0.00	0.00	0.00	2.57
2592	7632	2.028420	TCCTCCAAGCAATGATCACG	57.972	50.000	0.00	0.00	0.00	4.35
2608	7649	2.998493	AGGGTCGCTTTGAGATCCT	58.002	52.632	0.00	0.00	43.99	3.24
2944	8001	5.167303	AGCTCGGGAAAAGAGAGTTAAAT	57.833	39.130	0.00	0.00	37.93	1.40
2956	8019	0.898320	CCTCTCTCAAGCTCGGGAAA	59.102	55.000	0.00	0.00	0.00	3.13
3035	8100	8.327941	ACACATATGCATGTTATAGGCTAAAG	57.672	34.615	10.16	0.00	42.98	1.85
3176	8464	2.802667	CTCGCTCGGGTTGCATTCG	61.803	63.158	0.00	0.00	0.00	3.34
3256	8544	9.031537	CCCAAACTAACCCTAATGTTTTAGATT	57.968	33.333	0.00	0.00	37.59	2.40
3257	8545	8.174757	ACCCAAACTAACCCTAATGTTTTAGAT	58.825	33.333	0.00	0.00	37.59	1.98
3258	8546	7.449086	CACCCAAACTAACCCTAATGTTTTAGA	59.551	37.037	0.00	0.00	37.59	2.10
3320	9634	6.870965	AGCATACTAGTTTTCACAGACTGAAG	59.129	38.462	10.08	1.24	40.12	3.02
3358	9922	8.881262	TCTTTTAGACCAATCTTAGAAAGAGGT	58.119	33.333	1.42	1.42	41.61	3.85
3359	9923	9.898152	ATCTTTTAGACCAATCTTAGAAAGAGG	57.102	33.333	0.00	0.00	41.61	3.69
3375	9939	7.283127	TCACTTGCCATTATCCATCTTTTAGAC	59.717	37.037	0.00	0.00	0.00	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.