AutoCloner

Multiple sequence alignment - TraesCS1A01G145200

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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	TraesCS1A01G145200	chr1A	100.000	4709	0	0	1	4709	251376090	251371382	0.000000e+00	8696.0
1	TraesCS1A01G145200	chr1A	97.935	3825	72	4	889	4709	540641929	540638108	0.000000e+00	6619.0
2	TraesCS1A01G145200	chr1A	96.124	258	8	2	3865	4120	204828795	204829052	2.030000e-113	420.0
3	TraesCS1A01G145200	chr1A	95.385	260	9	3	3864	4120	367443136	367442877	1.220000e-110	411.0
4	TraesCS1A01G145200	chr1A	93.213	221	10	3	118	333	540643285	540643065	2.110000e-83	320.0
5	TraesCS1A01G145200	chr1A	100.000	102	0	0	335	436	251375655	251375554	6.220000e-44	189.0
6	TraesCS1A01G145200	chr1A	100.000	102	0	0	436	537	251375756	251375655	6.220000e-44	189.0
7	TraesCS1A01G145200	chr6B	98.521	4597	53	4	120	4709	22940689	22936101	0.000000e+00	8098.0
8	TraesCS1A01G145200	chr6B	100.000	102	0	0	436	537	22940474	22940373	6.220000e-44	189.0
9	TraesCS1A01G145200	chr7A	98.422	3295	45	3	335	3626	1867891	1871181	0.000000e+00	5790.0
10	TraesCS1A01G145200	chr7A	98.165	1090	19	1	3621	4709	1875503	1876592	0.000000e+00	1901.0
11	TraesCS1A01G145200	chr7A	91.169	419	10	3	120	537	1867398	1867790	1.150000e-150	544.0
12	TraesCS1A01G145200	chr7A	95.437	263	8	3	3862	4120	586627785	586627523	2.620000e-112	416.0
13	TraesCS1A01G145200	chr7A	99.015	203	2	0	335	537	1867790	1867992	9.630000e-97	364.0
14	TraesCS1A01G145200	chr7A	98.522	203	3	0	335	537	1867689	1867891	4.480000e-95	359.0
15	TraesCS1A01G145200	chr7A	100.000	102	0	0	335	436	1867992	1868093	6.220000e-44	189.0
16	TraesCS1A01G145200	chr6D	96.548	3447	91	7	430	3872	79952331	79948909	0.000000e+00	5681.0
17	TraesCS1A01G145200	chr6D	86.834	319	22	8	120	436	79952533	79952233	5.840000e-89	339.0
18	TraesCS1A01G145200	chr2D	96.172	3474	95	11	430	3872	623393288	623396754	0.000000e+00	5644.0
19	TraesCS1A01G145200	chr2D	91.723	447	35	1	4117	4563	623396755	623397199	1.860000e-173	619.0
20	TraesCS1A01G145200	chr2D	86.025	322	24	12	117	434	623393090	623393394	4.540000e-85	326.0
21	TraesCS1A01G145200	chr1B	95.013	3369	141	8	508	3872	20778141	20781486	0.000000e+00	5265.0
22	TraesCS1A01G145200	chr1B	89.865	592	51	6	4117	4704	20781487	20782073	0.000000e+00	752.0
23	TraesCS1A01G145200	chr1B	88.802	509	52	4	4199	4707	20782386	20782889	1.860000e-173	619.0
24	TraesCS1A01G145200	chr1B	93.275	342	23	0	508	849	20754803	20755144	5.440000e-139	505.0
25	TraesCS1A01G145200	chr1B	86.392	316	35	6	120	434	20777833	20778141	5.840000e-89	339.0
26	TraesCS1A01G145200	chr1B	84.232	241	30	7	120	353	20754529	20754768	1.320000e-55	228.0
27	TraesCS1A01G145200	chr1B	94.915	118	6	0	1	118	280181675	280181558	8.050000e-43	185.0
28	TraesCS1A01G145200	chr2A	97.777	3014	55	5	730	3740	765414896	765411892	0.000000e+00	5184.0
29	TraesCS1A01G145200	chr2A	94.818	3030	119	10	871	3869	43903285	43906307	0.000000e+00	4691.0
30	TraesCS1A01G145200	chr2A	94.705	3022	122	11	882	3872	43821069	43824083	0.000000e+00	4660.0
31	TraesCS1A01G145200	chr2A	94.178	1838	76	4	2065	3872	43911760	43913596	0.000000e+00	2772.0
32	TraesCS1A01G145200	chr2A	95.097	1183	55	2	3527	4709	765411901	765410722	0.000000e+00	1860.0
33	TraesCS1A01G145200	chr2A	93.701	635	18	6	120	753	765415452	765414839	0.000000e+00	931.0
34	TraesCS1A01G145200	chr2A	91.312	587	46	3	4117	4703	43824084	43824665	0.000000e+00	797.0
35	TraesCS1A01G145200	chr2A	90.227	573	51	4	4117	4687	43848340	43848909	0.000000e+00	743.0
36	TraesCS1A01G145200	chr2A	90.769	455	39	2	4117	4571	43906311	43906762	5.210000e-169	604.0
37	TraesCS1A01G145200	chr2A	95.000	260	12	1	3862	4120	160813242	160812983	1.580000e-109	407.0
38	TraesCS1A01G145200	chr2A	90.000	190	15	3	4520	4709	43913680	43913865	4.710000e-60	243.0
39	TraesCS1A01G145200	chr2A	99.020	102	1	0	335	436	765415156	765415055	2.890000e-42	183.0
40	TraesCS1A01G145200	chr2A	97.248	109	2	1	430	537	765415264	765415156	2.890000e-42	183.0
41	TraesCS1A01G145200	chr5D	97.411	2781	68	2	1095	3872	488176510	488179289	0.000000e+00	4734.0
42	TraesCS1A01G145200	chr3A	96.032	252	8	2	3871	4120	22933661	22933410	4.390000e-110	409.0
43	TraesCS1A01G145200	chr1D	97.458	118	3	0	1	118	199623661	199623544	7.990000e-48	202.0
44	TraesCS1A01G145200	chr5A	84.416	77	8	4	118	192	553530391	553530317	6.540000e-09	73.1
45	TraesCS1A01G145200	chr7D	83.562	73	10	2	117	188	42920698	42920769	3.040000e-07	67.6

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	TraesCS1A01G145200	chr1A	251371382	251376090	4708	True	3024.666667	8696	100.000000	1	4709	3	chr1A.!!$R2	4708
1	TraesCS1A01G145200	chr1A	540638108	540643285	5177	True	3469.500000	6619	95.574000	118	4709	2	chr1A.!!$R3	4591
2	TraesCS1A01G145200	chr6B	22936101	22940689	4588	True	4143.500000	8098	99.260500	120	4709	2	chr6B.!!$R1	4589
3	TraesCS1A01G145200	chr7A	1875503	1876592	1089	False	1901.000000	1901	98.165000	3621	4709	1	chr7A.!!$F1	1088
4	TraesCS1A01G145200	chr7A	1867398	1871181	3783	False	1449.200000	5790	97.425600	120	3626	5	chr7A.!!$F2	3506
5	TraesCS1A01G145200	chr6D	79948909	79952533	3624	True	3010.000000	5681	91.691000	120	3872	2	chr6D.!!$R1	3752
6	TraesCS1A01G145200	chr2D	623393090	623397199	4109	False	2196.333333	5644	91.306667	117	4563	3	chr2D.!!$F1	4446
7	TraesCS1A01G145200	chr1B	20777833	20782889	5056	False	1743.750000	5265	90.018000	120	4707	4	chr1B.!!$F2	4587
8	TraesCS1A01G145200	chr1B	20754529	20755144	615	False	366.500000	505	88.753500	120	849	2	chr1B.!!$F1	729
9	TraesCS1A01G145200	chr2A	43821069	43824665	3596	False	2728.500000	4660	93.008500	882	4703	2	chr2A.!!$F2	3821
10	TraesCS1A01G145200	chr2A	43903285	43906762	3477	False	2647.500000	4691	92.793500	871	4571	2	chr2A.!!$F3	3700
11	TraesCS1A01G145200	chr2A	765410722	765415452	4730	True	1668.200000	5184	96.568600	120	4709	5	chr2A.!!$R2	4589
12	TraesCS1A01G145200	chr2A	43911760	43913865	2105	False	1507.500000	2772	92.089000	2065	4709	2	chr2A.!!$F4	2644
13	TraesCS1A01G145200	chr2A	43848340	43848909	569	False	743.000000	743	90.227000	4117	4687	1	chr2A.!!$F1	570
14	TraesCS1A01G145200	chr5D	488176510	488179289	2779	False	4734.000000	4734	97.411000	1095	3872	1	chr5D.!!$F1	2777

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
116	117	0.106769	TGCTGCAAAAGTCTCCACCA	60.107	50.000	0.00	0.00	0.00	4.17	F
1626	2248	1.067425	TGATGTGCAAAAGGCTGATGC	60.067	47.619	15.63	15.63	45.15	3.91	F
1809	2431	0.321653	CTCCGTTATATGGCAGCCCC	60.322	60.000	9.64	0.00	0.00	5.80	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1809	2431	1.462616	TTCGCCATCCATGTCCTTTG	58.537	50.000	0.00	0.0	0.00	2.77	R
3171	3798	3.973973	TGGATTCCGGACATTTCCTAGAT	59.026	43.478	1.83	0.0	40.23	1.98	R
3742	4601	0.732571	CACGGGTTCGAATCCCATTG	59.267	55.000	21.74	17.2	44.81	2.82	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
17	18	2.598394	GCTGCCACTTTCTGCCCA	60.598	61.111	0.00	0.00	0.00	5.36
18	19	1.980772	GCTGCCACTTTCTGCCCAT	60.981	57.895	0.00	0.00	0.00	4.00
19	20	0.680921	GCTGCCACTTTCTGCCCATA	60.681	55.000	0.00	0.00	0.00	2.74
20	21	2.025863	GCTGCCACTTTCTGCCCATAT	61.026	52.381	0.00	0.00	0.00	1.78
21	22	2.381911	CTGCCACTTTCTGCCCATATT	58.618	47.619	0.00	0.00	0.00	1.28
22	23	2.762327	CTGCCACTTTCTGCCCATATTT	59.238	45.455	0.00	0.00	0.00	1.40
23	24	2.760092	TGCCACTTTCTGCCCATATTTC	59.240	45.455	0.00	0.00	0.00	2.17
24	25	2.760092	GCCACTTTCTGCCCATATTTCA	59.240	45.455	0.00	0.00	0.00	2.69
25	26	3.429410	GCCACTTTCTGCCCATATTTCAC	60.429	47.826	0.00	0.00	0.00	3.18
26	27	4.019174	CCACTTTCTGCCCATATTTCACT	58.981	43.478	0.00	0.00	0.00	3.41
27	28	4.142315	CCACTTTCTGCCCATATTTCACTG	60.142	45.833	0.00	0.00	0.00	3.66
28	29	4.460382	CACTTTCTGCCCATATTTCACTGT	59.540	41.667	0.00	0.00	0.00	3.55
29	30	4.702131	ACTTTCTGCCCATATTTCACTGTC	59.298	41.667	0.00	0.00	0.00	3.51
30	31	3.998913	TCTGCCCATATTTCACTGTCA	57.001	42.857	0.00	0.00	0.00	3.58
31	32	3.609853	TCTGCCCATATTTCACTGTCAC	58.390	45.455	0.00	0.00	0.00	3.67
32	33	3.264193	TCTGCCCATATTTCACTGTCACT	59.736	43.478	0.00	0.00	0.00	3.41
33	34	3.609853	TGCCCATATTTCACTGTCACTC	58.390	45.455	0.00	0.00	0.00	3.51
34	35	3.264193	TGCCCATATTTCACTGTCACTCT	59.736	43.478	0.00	0.00	0.00	3.24
35	36	4.469586	TGCCCATATTTCACTGTCACTCTA	59.530	41.667	0.00	0.00	0.00	2.43
36	37	5.130975	TGCCCATATTTCACTGTCACTCTAT	59.869	40.000	0.00	0.00	0.00	1.98
37	38	5.698545	GCCCATATTTCACTGTCACTCTATC	59.301	44.000	0.00	0.00	0.00	2.08
38	39	6.686378	GCCCATATTTCACTGTCACTCTATCA	60.686	42.308	0.00	0.00	0.00	2.15
39	40	6.927936	CCCATATTTCACTGTCACTCTATCAG	59.072	42.308	0.00	0.00	35.60	2.90
40	41	6.423302	CCATATTTCACTGTCACTCTATCAGC	59.577	42.308	0.00	0.00	33.12	4.26
41	42	3.494045	TTCACTGTCACTCTATCAGCG	57.506	47.619	0.00	0.00	33.12	5.18
42	43	2.437413	TCACTGTCACTCTATCAGCGT	58.563	47.619	0.00	0.00	33.12	5.07
43	44	2.420372	TCACTGTCACTCTATCAGCGTC	59.580	50.000	0.00	0.00	33.12	5.19
44	45	1.746220	ACTGTCACTCTATCAGCGTCC	59.254	52.381	0.00	0.00	33.12	4.79
45	46	1.745653	CTGTCACTCTATCAGCGTCCA	59.254	52.381	0.00	0.00	0.00	4.02
46	47	2.164422	CTGTCACTCTATCAGCGTCCAA	59.836	50.000	0.00	0.00	0.00	3.53
47	48	2.164422	TGTCACTCTATCAGCGTCCAAG	59.836	50.000	0.00	0.00	0.00	3.61
48	49	1.135139	TCACTCTATCAGCGTCCAAGC	59.865	52.381	0.00	0.00	37.41	4.01
58	59	2.873133	GCGTCCAAGCTACTGTATCT	57.127	50.000	0.00	0.00	0.00	1.98
59	60	2.733517	GCGTCCAAGCTACTGTATCTC	58.266	52.381	0.00	0.00	0.00	2.75
60	61	2.855187	GCGTCCAAGCTACTGTATCTCG	60.855	54.545	0.00	0.00	0.00	4.04
61	62	2.287069	CGTCCAAGCTACTGTATCTCGG	60.287	54.545	0.00	0.00	0.00	4.63
62	63	2.950309	GTCCAAGCTACTGTATCTCGGA	59.050	50.000	0.00	0.00	0.00	4.55
63	64	3.380637	GTCCAAGCTACTGTATCTCGGAA	59.619	47.826	0.19	0.00	0.00	4.30
64	65	4.038162	GTCCAAGCTACTGTATCTCGGAAT	59.962	45.833	0.19	0.00	0.00	3.01
65	66	4.649674	TCCAAGCTACTGTATCTCGGAATT	59.350	41.667	0.00	0.00	0.00	2.17
66	67	5.128827	TCCAAGCTACTGTATCTCGGAATTT	59.871	40.000	0.00	0.00	0.00	1.82
67	68	5.235186	CCAAGCTACTGTATCTCGGAATTTG	59.765	44.000	0.00	0.00	0.00	2.32
68	69	4.950050	AGCTACTGTATCTCGGAATTTGG	58.050	43.478	0.00	0.00	0.00	3.28
69	70	4.058817	GCTACTGTATCTCGGAATTTGGG	58.941	47.826	0.00	0.00	0.00	4.12
70	71	4.443034	GCTACTGTATCTCGGAATTTGGGT	60.443	45.833	0.00	0.00	0.00	4.51
71	72	3.873910	ACTGTATCTCGGAATTTGGGTG	58.126	45.455	0.00	0.00	0.00	4.61
72	73	2.614057	CTGTATCTCGGAATTTGGGTGC	59.386	50.000	0.00	0.00	0.00	5.01
73	74	2.238646	TGTATCTCGGAATTTGGGTGCT	59.761	45.455	0.00	0.00	0.00	4.40
74	75	2.044123	ATCTCGGAATTTGGGTGCTC	57.956	50.000	0.00	0.00	0.00	4.26
75	76	0.391130	TCTCGGAATTTGGGTGCTCG	60.391	55.000	0.00	0.00	0.00	5.03
76	77	1.982073	CTCGGAATTTGGGTGCTCGC	61.982	60.000	0.00	0.00	0.00	5.03
77	78	2.331893	CGGAATTTGGGTGCTCGCA	61.332	57.895	0.87	0.87	34.75	5.10
78	79	1.212751	GGAATTTGGGTGCTCGCAC	59.787	57.895	13.37	13.37	45.49	5.34
90	91	0.853419	GCTCGCACGTTATTAGAGCC	59.147	55.000	13.28	1.20	46.00	4.70
91	92	1.801395	GCTCGCACGTTATTAGAGCCA	60.801	52.381	13.28	0.00	46.00	4.75
92	93	2.743938	CTCGCACGTTATTAGAGCCAT	58.256	47.619	0.00	0.00	0.00	4.40
93	94	3.855895	GCTCGCACGTTATTAGAGCCATA	60.856	47.826	13.28	0.00	46.00	2.74
94	95	3.897325	TCGCACGTTATTAGAGCCATAG	58.103	45.455	0.00	0.00	0.00	2.23
95	96	3.317149	TCGCACGTTATTAGAGCCATAGT	59.683	43.478	0.00	0.00	0.00	2.12
96	97	3.425525	CGCACGTTATTAGAGCCATAGTG	59.574	47.826	0.00	0.00	0.00	2.74
97	98	4.369182	GCACGTTATTAGAGCCATAGTGT	58.631	43.478	0.00	0.00	0.00	3.55
98	99	4.209288	GCACGTTATTAGAGCCATAGTGTG	59.791	45.833	0.00	0.00	0.00	3.82
99	100	4.209288	CACGTTATTAGAGCCATAGTGTGC	59.791	45.833	0.00	0.00	0.00	4.57
100	101	4.099573	ACGTTATTAGAGCCATAGTGTGCT	59.900	41.667	0.00	0.00	41.42	4.40
101	102	4.445718	CGTTATTAGAGCCATAGTGTGCTG	59.554	45.833	0.00	0.00	38.11	4.41
102	103	2.315925	TTAGAGCCATAGTGTGCTGC	57.684	50.000	0.00	0.00	38.11	5.25
103	104	1.194218	TAGAGCCATAGTGTGCTGCA	58.806	50.000	0.00	0.00	38.11	4.41
104	105	0.325933	AGAGCCATAGTGTGCTGCAA	59.674	50.000	2.77	0.00	38.11	4.08
105	106	1.167851	GAGCCATAGTGTGCTGCAAA	58.832	50.000	2.77	0.00	38.11	3.68
106	107	1.541147	GAGCCATAGTGTGCTGCAAAA	59.459	47.619	2.77	0.00	38.11	2.44
107	108	1.542915	AGCCATAGTGTGCTGCAAAAG	59.457	47.619	2.77	0.00	36.23	2.27
108	109	1.270550	GCCATAGTGTGCTGCAAAAGT	59.729	47.619	2.77	1.25	0.00	2.66
109	110	2.669391	GCCATAGTGTGCTGCAAAAGTC	60.669	50.000	2.77	0.00	0.00	3.01
110	111	2.816087	CCATAGTGTGCTGCAAAAGTCT	59.184	45.455	2.77	0.00	0.00	3.24
111	112	3.120060	CCATAGTGTGCTGCAAAAGTCTC	60.120	47.826	2.77	0.00	0.00	3.36
112	113	1.312815	AGTGTGCTGCAAAAGTCTCC	58.687	50.000	2.77	0.00	0.00	3.71
113	114	1.024271	GTGTGCTGCAAAAGTCTCCA	58.976	50.000	2.77	0.00	0.00	3.86
114	115	1.024271	TGTGCTGCAAAAGTCTCCAC	58.976	50.000	2.77	0.00	0.00	4.02
115	116	0.312102	GTGCTGCAAAAGTCTCCACC	59.688	55.000	2.77	0.00	0.00	4.61
116	117	0.106769	TGCTGCAAAAGTCTCCACCA	60.107	50.000	0.00	0.00	0.00	4.17
203	205	8.336235	ACCATTGAATTCTTGAAGGTAGGATAA	58.664	33.333	7.05	0.00	0.00	1.75
469	927	3.077556	TCGCCTCCTTCTCCCTGC	61.078	66.667	0.00	0.00	0.00	4.85
946	1567	2.264109	ACTGCTGTCTATGAACGTCG	57.736	50.000	0.00	0.00	0.00	5.12
976	1597	3.745799	TGGCTCAGTTTCGGACAATAAA	58.254	40.909	0.00	0.00	0.00	1.40
1626	2248	1.067425	TGATGTGCAAAAGGCTGATGC	60.067	47.619	15.63	15.63	45.15	3.91
1809	2431	0.321653	CTCCGTTATATGGCAGCCCC	60.322	60.000	9.64	0.00	0.00	5.80
1830	2452	3.213506	CAAAGGACATGGATGGCGAATA	58.786	45.455	0.00	0.00	36.40	1.75
2262	2886	8.498358	GCTCAAGGATTTTAGGAAATTTGTTTG	58.502	33.333	0.00	0.00	35.65	2.93
2852	3479	0.729140	CCCGTGCGCTCACATTTTTC	60.729	55.000	9.73	0.00	43.28	2.29
3171	3798	0.991146	TCAGGGTCAAGCCAAGCATA	59.009	50.000	0.44	0.00	39.65	3.14
3663	4521	3.084786	ACACTGAAAAGGAGGCAATAGC	58.915	45.455	0.00	0.00	41.10	2.97
3775	4634	0.108138	CCCGTGACCTTGAGGACATC	60.108	60.000	3.59	0.00	41.49	3.06
4376	6063	1.683943	CCTCCACGCATGATTTGGAT	58.316	50.000	9.97	0.00	38.75	3.41
4425	6112	0.956902	ATGTCCGGGCGGTGTTTTAC	60.957	55.000	0.00	0.00	36.47	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	4.019174	AGTGAAATATGGGCAGAAAGTGG	58.981	43.478	0.00	0.00	0.00	4.00
5	6	4.460382	ACAGTGAAATATGGGCAGAAAGTG	59.540	41.667	0.00	0.00	0.00	3.16
6	7	4.666512	ACAGTGAAATATGGGCAGAAAGT	58.333	39.130	0.00	0.00	0.00	2.66
7	8	4.701651	TGACAGTGAAATATGGGCAGAAAG	59.298	41.667	0.00	0.00	0.00	2.62
8	9	4.458989	GTGACAGTGAAATATGGGCAGAAA	59.541	41.667	0.00	0.00	0.00	2.52
9	10	4.009675	GTGACAGTGAAATATGGGCAGAA	58.990	43.478	0.00	0.00	0.00	3.02
10	11	3.264193	AGTGACAGTGAAATATGGGCAGA	59.736	43.478	0.00	0.00	0.00	4.26
11	12	3.614092	AGTGACAGTGAAATATGGGCAG	58.386	45.455	0.00	0.00	0.00	4.85
12	13	3.264193	AGAGTGACAGTGAAATATGGGCA	59.736	43.478	0.00	0.00	0.00	5.36
13	14	3.878778	AGAGTGACAGTGAAATATGGGC	58.121	45.455	0.00	0.00	0.00	5.36
14	15	6.820335	TGATAGAGTGACAGTGAAATATGGG	58.180	40.000	0.00	0.00	0.00	4.00
15	16	6.423302	GCTGATAGAGTGACAGTGAAATATGG	59.577	42.308	0.00	0.00	34.60	2.74
16	17	6.143598	CGCTGATAGAGTGACAGTGAAATATG	59.856	42.308	0.00	0.00	42.41	1.78
17	18	6.183360	ACGCTGATAGAGTGACAGTGAAATAT	60.183	38.462	12.64	0.00	42.41	1.28
18	19	5.125578	ACGCTGATAGAGTGACAGTGAAATA	59.874	40.000	12.64	0.00	42.41	1.40
19	20	4.081972	ACGCTGATAGAGTGACAGTGAAAT	60.082	41.667	12.64	0.00	42.41	2.17
20	21	3.255888	ACGCTGATAGAGTGACAGTGAAA	59.744	43.478	12.64	0.00	42.41	2.69
21	22	2.820197	ACGCTGATAGAGTGACAGTGAA	59.180	45.455	12.64	0.00	42.41	3.18
22	23	2.420372	GACGCTGATAGAGTGACAGTGA	59.580	50.000	12.64	0.00	42.41	3.41
23	24	2.478709	GGACGCTGATAGAGTGACAGTG	60.479	54.545	0.00	0.00	44.40	3.66
24	25	1.746220	GGACGCTGATAGAGTGACAGT	59.254	52.381	0.00	0.00	35.96	3.55
25	26	1.745653	TGGACGCTGATAGAGTGACAG	59.254	52.381	0.00	0.00	35.96	3.51
26	27	1.834188	TGGACGCTGATAGAGTGACA	58.166	50.000	0.00	0.00	35.96	3.58
27	28	2.803451	CTTGGACGCTGATAGAGTGAC	58.197	52.381	0.00	0.00	35.96	3.67
28	29	1.135139	GCTTGGACGCTGATAGAGTGA	59.865	52.381	0.00	0.00	35.96	3.41
29	30	1.135915	AGCTTGGACGCTGATAGAGTG	59.864	52.381	0.00	0.00	39.16	3.51
30	31	1.479709	AGCTTGGACGCTGATAGAGT	58.520	50.000	0.00	0.00	39.16	3.24
31	32	2.621055	AGTAGCTTGGACGCTGATAGAG	59.379	50.000	0.00	0.00	41.12	2.43
32	33	2.359214	CAGTAGCTTGGACGCTGATAGA	59.641	50.000	0.00	0.00	41.12	1.98
33	34	2.099921	ACAGTAGCTTGGACGCTGATAG	59.900	50.000	0.00	0.00	41.12	2.08
34	35	2.100197	ACAGTAGCTTGGACGCTGATA	58.900	47.619	0.00	0.00	41.12	2.15
35	36	0.898320	ACAGTAGCTTGGACGCTGAT	59.102	50.000	0.00	0.00	41.12	2.90
36	37	1.541379	TACAGTAGCTTGGACGCTGA	58.459	50.000	0.00	0.00	41.12	4.26
37	38	2.099921	AGATACAGTAGCTTGGACGCTG	59.900	50.000	0.00	0.00	41.12	5.18
38	39	2.359531	GAGATACAGTAGCTTGGACGCT	59.640	50.000	0.00	0.00	43.83	5.07
39	40	2.733517	GAGATACAGTAGCTTGGACGC	58.266	52.381	0.00	0.00	0.00	5.19
40	41	2.287069	CCGAGATACAGTAGCTTGGACG	60.287	54.545	23.40	11.16	46.50	4.79
41	42	2.950309	TCCGAGATACAGTAGCTTGGAC	59.050	50.000	25.54	1.98	46.91	4.02
43	44	4.592485	ATTCCGAGATACAGTAGCTTGG	57.408	45.455	22.19	22.19	45.23	3.61
44	45	5.235186	CCAAATTCCGAGATACAGTAGCTTG	59.765	44.000	6.14	6.14	0.00	4.01
45	46	5.360591	CCAAATTCCGAGATACAGTAGCTT	58.639	41.667	0.00	0.00	0.00	3.74
46	47	4.202264	CCCAAATTCCGAGATACAGTAGCT	60.202	45.833	0.00	0.00	0.00	3.32
47	48	4.058817	CCCAAATTCCGAGATACAGTAGC	58.941	47.826	0.00	0.00	0.00	3.58
48	49	5.050490	CACCCAAATTCCGAGATACAGTAG	58.950	45.833	0.00	0.00	0.00	2.57
49	50	4.682320	GCACCCAAATTCCGAGATACAGTA	60.682	45.833	0.00	0.00	0.00	2.74
50	51	3.873910	CACCCAAATTCCGAGATACAGT	58.126	45.455	0.00	0.00	0.00	3.55
51	52	2.614057	GCACCCAAATTCCGAGATACAG	59.386	50.000	0.00	0.00	0.00	2.74
52	53	2.238646	AGCACCCAAATTCCGAGATACA	59.761	45.455	0.00	0.00	0.00	2.29
53	54	2.872858	GAGCACCCAAATTCCGAGATAC	59.127	50.000	0.00	0.00	0.00	2.24
54	55	2.483013	CGAGCACCCAAATTCCGAGATA	60.483	50.000	0.00	0.00	0.00	1.98
55	56	1.743772	CGAGCACCCAAATTCCGAGAT	60.744	52.381	0.00	0.00	0.00	2.75
56	57	0.391130	CGAGCACCCAAATTCCGAGA	60.391	55.000	0.00	0.00	0.00	4.04
57	58	1.982073	GCGAGCACCCAAATTCCGAG	61.982	60.000	0.00	0.00	0.00	4.63
58	59	2.038269	GCGAGCACCCAAATTCCGA	61.038	57.895	0.00	0.00	0.00	4.55
59	60	2.331893	TGCGAGCACCCAAATTCCG	61.332	57.895	0.00	0.00	0.00	4.30
60	61	1.212751	GTGCGAGCACCCAAATTCC	59.787	57.895	16.66	0.00	40.79	3.01
61	62	1.154225	CGTGCGAGCACCCAAATTC	60.154	57.895	20.79	0.00	43.49	2.17
62	63	1.452145	AACGTGCGAGCACCCAAATT	61.452	50.000	20.79	6.57	43.49	1.82
63	64	0.604243	TAACGTGCGAGCACCCAAAT	60.604	50.000	20.79	6.82	43.49	2.32
64	65	0.604243	ATAACGTGCGAGCACCCAAA	60.604	50.000	20.79	6.21	43.49	3.28
65	66	0.604243	AATAACGTGCGAGCACCCAA	60.604	50.000	20.79	7.86	43.49	4.12
66	67	0.246910	TAATAACGTGCGAGCACCCA	59.753	50.000	20.79	7.87	43.49	4.51
67	68	0.928229	CTAATAACGTGCGAGCACCC	59.072	55.000	20.79	0.00	43.49	4.61
68	69	1.852895	CTCTAATAACGTGCGAGCACC	59.147	52.381	20.79	5.31	43.49	5.01
69	70	1.255600	GCTCTAATAACGTGCGAGCAC	59.744	52.381	17.42	17.42	44.74	4.40
70	71	1.556564	GCTCTAATAACGTGCGAGCA	58.443	50.000	15.40	0.00	44.74	4.26
71	72	0.853419	GGCTCTAATAACGTGCGAGC	59.147	55.000	13.18	13.18	44.67	5.03
72	73	2.203800	TGGCTCTAATAACGTGCGAG	57.796	50.000	0.00	0.00	0.00	5.03
73	74	2.882927	ATGGCTCTAATAACGTGCGA	57.117	45.000	0.00	0.00	0.00	5.10
74	75	3.425525	CACTATGGCTCTAATAACGTGCG	59.574	47.826	0.00	0.00	0.00	5.34
75	76	4.209288	CACACTATGGCTCTAATAACGTGC	59.791	45.833	0.00	0.00	0.00	5.34
76	77	4.209288	GCACACTATGGCTCTAATAACGTG	59.791	45.833	0.00	0.00	0.00	4.49
77	78	4.099573	AGCACACTATGGCTCTAATAACGT	59.900	41.667	0.00	0.00	34.76	3.99
78	79	4.445718	CAGCACACTATGGCTCTAATAACG	59.554	45.833	0.00	0.00	38.56	3.18
79	80	4.212214	GCAGCACACTATGGCTCTAATAAC	59.788	45.833	0.00	0.00	38.56	1.89
80	81	4.141733	TGCAGCACACTATGGCTCTAATAA	60.142	41.667	0.00	0.00	38.56	1.40
81	82	3.387699	TGCAGCACACTATGGCTCTAATA	59.612	43.478	0.00	0.00	38.56	0.98
82	83	2.171237	TGCAGCACACTATGGCTCTAAT	59.829	45.455	0.00	0.00	38.56	1.73
83	84	1.554617	TGCAGCACACTATGGCTCTAA	59.445	47.619	0.00	0.00	38.56	2.10
84	85	1.194218	TGCAGCACACTATGGCTCTA	58.806	50.000	0.00	0.00	38.56	2.43
85	86	0.325933	TTGCAGCACACTATGGCTCT	59.674	50.000	0.00	0.00	38.56	4.09
86	87	1.167851	TTTGCAGCACACTATGGCTC	58.832	50.000	0.00	0.00	38.56	4.70
87	88	1.542915	CTTTTGCAGCACACTATGGCT	59.457	47.619	0.00	0.00	42.06	4.75
88	89	1.270550	ACTTTTGCAGCACACTATGGC	59.729	47.619	0.00	0.00	0.00	4.40
89	90	2.816087	AGACTTTTGCAGCACACTATGG	59.184	45.455	0.00	0.00	0.00	2.74
90	91	3.120060	GGAGACTTTTGCAGCACACTATG	60.120	47.826	0.00	0.00	0.00	2.23
91	92	3.077359	GGAGACTTTTGCAGCACACTAT	58.923	45.455	0.00	0.00	0.00	2.12
92	93	2.158827	TGGAGACTTTTGCAGCACACTA	60.159	45.455	0.00	0.00	0.00	2.74
93	94	1.312815	GGAGACTTTTGCAGCACACT	58.687	50.000	0.00	0.00	0.00	3.55
94	95	1.024271	TGGAGACTTTTGCAGCACAC	58.976	50.000	0.00	0.00	0.00	3.82
95	96	1.024271	GTGGAGACTTTTGCAGCACA	58.976	50.000	0.00	0.00	0.00	4.57
96	97	0.312102	GGTGGAGACTTTTGCAGCAC	59.688	55.000	0.00	0.00	36.96	4.40
97	98	0.106769	TGGTGGAGACTTTTGCAGCA	60.107	50.000	0.00	0.00	43.16	4.41
98	99	0.595095	CTGGTGGAGACTTTTGCAGC	59.405	55.000	0.00	0.00	37.41	5.25
99	100	1.242076	CCTGGTGGAGACTTTTGCAG	58.758	55.000	0.00	0.00	34.57	4.41
100	101	0.178992	CCCTGGTGGAGACTTTTGCA	60.179	55.000	0.00	0.00	35.39	4.08
101	102	0.110486	TCCCTGGTGGAGACTTTTGC	59.890	55.000	0.00	0.00	38.61	3.68
203	205	4.764679	TGTCGCACTTAATTTTGATGCT	57.235	36.364	0.00	0.00	34.06	3.79
539	1098	2.155194	CGGAAGCAGCTTCGTCGAG	61.155	63.158	25.64	12.36	40.99	4.04
946	1567	3.426695	CCGAAACTGAGCCATGATGTTTC	60.427	47.826	0.00	6.60	41.46	2.78
1809	2431	1.462616	TTCGCCATCCATGTCCTTTG	58.537	50.000	0.00	0.00	0.00	2.77
2262	2886	2.101415	TCATCGACATCCCAGATGTGAC	59.899	50.000	14.62	1.26	41.63	3.67
2852	3479	6.884836	ACTAAGCCAAGGTATTTTAGAACAGG	59.115	38.462	0.00	0.00	0.00	4.00
3171	3798	3.973973	TGGATTCCGGACATTTCCTAGAT	59.026	43.478	1.83	0.00	40.23	1.98
3574	4432	4.677779	GCCAACTTTTCAGCTCAAGAACAA	60.678	41.667	4.22	0.00	0.00	2.83
3663	4521	8.519492	ACGGTAATTCATTTTGTGATTTTCAG	57.481	30.769	0.00	0.00	36.54	3.02
3742	4601	0.732571	CACGGGTTCGAATCCCATTG	59.267	55.000	21.74	17.20	44.81	2.82
3775	4634	6.485313	TGTTCATTTGGTTAGGTTGTCTAGTG	59.515	38.462	0.00	0.00	0.00	2.74
4007	4876	9.739276	ACCTGACTAATTGACATGAGAAAATAA	57.261	29.630	0.00	0.00	0.00	1.40
4124	4993	9.878599	CAAAATAATTTGCGACCCTAGTTATAG	57.121	33.333	0.00	0.00	39.50	1.31
4376	6063	0.653636	GCGTTCAGTGTCCGTTTTCA	59.346	50.000	6.18	0.00	0.00	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.