AutoCloner

Multiple sequence alignment - TraesCS4A01G344400

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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	TraesCS4A01G344400	chr4A	100.000	3534	0	0	1	3534	624294216	624290683	0.000000e+00	6527.0
1	TraesCS4A01G344400	chr5A	96.386	3403	91	13	138	3534	638408071	638404695	0.000000e+00	5574.0
2	TraesCS4A01G344400	chr5A	98.305	1711	28	1	1824	3534	631794043	631792334	0.000000e+00	2998.0
3	TraesCS4A01G344400	chr5A	92.097	911	39	14	138	1021	631794977	631794073	0.000000e+00	1253.0
4	TraesCS4A01G344400	chr1B	94.916	3147	137	8	402	3534	506333303	506336440	0.000000e+00	4903.0
5	TraesCS4A01G344400	chr1B	88.129	278	19	4	138	415	506333005	506333268	5.690000e-83	318.0
6	TraesCS4A01G344400	chr1B	91.429	70	6	0	4	73	9168540	9168471	2.900000e-16	97.1
7	TraesCS4A01G344400	chr7A	96.747	2890	75	10	134	3020	659713750	659716623	0.000000e+00	4798.0
8	TraesCS4A01G344400	chr7A	89.579	2495	238	17	1021	3505	2611847	2614329	0.000000e+00	3147.0
9	TraesCS4A01G344400	chr7A	97.500	40	1	0	330	369	659713884	659713923	6.330000e-08	69.4
10	TraesCS4A01G344400	chr5B	97.196	2675	61	4	874	3534	669738618	669741292	0.000000e+00	4512.0
11	TraesCS4A01G344400	chr5B	91.195	1908	153	11	961	2865	537974528	537972633	0.000000e+00	2579.0
12	TraesCS4A01G344400	chr5B	92.780	554	22	5	135	688	669738062	669738597	0.000000e+00	785.0
13	TraesCS4A01G344400	chr5B	83.721	172	24	4	135	305	550147925	550148093	3.650000e-35	159.0
14	TraesCS4A01G344400	chr5B	90.411	73	7	0	1	73	498835193	498835265	2.900000e-16	97.1
15	TraesCS4A01G344400	chr6B	94.281	2588	142	6	947	3532	294340981	294343564	0.000000e+00	3954.0
16	TraesCS4A01G344400	chr6B	86.147	231	26	6	725	951	90312544	90312772	9.800000e-61	244.0
17	TraesCS4A01G344400	chr6B	85.799	169	19	5	135	301	90311924	90312089	1.300000e-39	174.0
18	TraesCS4A01G344400	chr7B	92.674	2307	160	7	1192	3497	712180109	712177811	0.000000e+00	3315.0
19	TraesCS4A01G344400	chr7B	88.060	67	7	1	13	79	723203247	723203182	1.050000e-10	78.7
20	TraesCS4A01G344400	chr7B	88.060	67	7	1	13	79	723389495	723389430	1.050000e-10	78.7
21	TraesCS4A01G344400	chr2B	93.566	1865	117	3	1672	3534	397051322	397053185	0.000000e+00	2776.0
22	TraesCS4A01G344400	chr2B	95.963	867	35	0	2668	3534	122982608	122983474	0.000000e+00	1408.0
23	TraesCS4A01G344400	chr2B	88.483	903	53	18	135	1000	581621490	581622378	0.000000e+00	1044.0
24	TraesCS4A01G344400	chr2B	89.394	132	14	0	3382	3513	800217067	800216936	2.180000e-37	167.0
25	TraesCS4A01G344400	chr2B	95.833	72	3	0	1	72	643299727	643299656	2.230000e-22	117.0
26	TraesCS4A01G344400	chr5D	91.614	1908	145	10	962	2865	441937339	441935443	0.000000e+00	2623.0
27	TraesCS4A01G344400	chr3B	90.680	794	69	4	2742	3534	758628855	758629644	0.000000e+00	1051.0
28	TraesCS4A01G344400	chr3B	75.833	600	82	34	132	716	758627515	758628066	2.720000e-61	246.0
29	TraesCS4A01G344400	chr3B	93.590	78	5	0	1	78	615529748	615529671	2.230000e-22	117.0
30	TraesCS4A01G344400	chr3B	91.667	84	5	2	725	806	758628118	758628201	8.020000e-22	115.0
31	TraesCS4A01G344400	chr3B	89.286	84	6	3	844	925	50989541	50989623	6.240000e-18	102.0
32	TraesCS4A01G344400	chr7D	85.782	211	17	8	726	925	151827016	151826808	9.940000e-51	211.0
33	TraesCS4A01G344400	chr6A	97.222	72	2	0	1	72	613643063	613643134	4.790000e-24	122.0
34	TraesCS4A01G344400	chr3A	87.234	94	12	0	732	825	21334226	21334133	1.340000e-19	108.0
35	TraesCS4A01G344400	chr3D	92.958	71	5	0	3	73	15698793	15698723	1.740000e-18	104.0
36	TraesCS4A01G344400	chr6D	88.406	69	6	2	11	78	144563499	144563566	8.130000e-12	82.4

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	TraesCS4A01G344400	chr4A	624290683	624294216	3533	True	6527.000000	6527	100.0000	1	3534	1	chr4A.!!$R1	3533
1	TraesCS4A01G344400	chr5A	638404695	638408071	3376	True	5574.000000	5574	96.3860	138	3534	1	chr5A.!!$R1	3396
2	TraesCS4A01G344400	chr5A	631792334	631794977	2643	True	2125.500000	2998	95.2010	138	3534	2	chr5A.!!$R2	3396
3	TraesCS4A01G344400	chr1B	506333005	506336440	3435	False	2610.500000	4903	91.5225	138	3534	2	chr1B.!!$F1	3396
4	TraesCS4A01G344400	chr7A	2611847	2614329	2482	False	3147.000000	3147	89.5790	1021	3505	1	chr7A.!!$F1	2484
5	TraesCS4A01G344400	chr7A	659713750	659716623	2873	False	2433.700000	4798	97.1235	134	3020	2	chr7A.!!$F2	2886
6	TraesCS4A01G344400	chr5B	669738062	669741292	3230	False	2648.500000	4512	94.9880	135	3534	2	chr5B.!!$F3	3399
7	TraesCS4A01G344400	chr5B	537972633	537974528	1895	True	2579.000000	2579	91.1950	961	2865	1	chr5B.!!$R1	1904
8	TraesCS4A01G344400	chr6B	294340981	294343564	2583	False	3954.000000	3954	94.2810	947	3532	1	chr6B.!!$F1	2585
9	TraesCS4A01G344400	chr6B	90311924	90312772	848	False	209.000000	244	85.9730	135	951	2	chr6B.!!$F2	816
10	TraesCS4A01G344400	chr7B	712177811	712180109	2298	True	3315.000000	3315	92.6740	1192	3497	1	chr7B.!!$R1	2305
11	TraesCS4A01G344400	chr2B	397051322	397053185	1863	False	2776.000000	2776	93.5660	1672	3534	1	chr2B.!!$F2	1862
12	TraesCS4A01G344400	chr2B	122982608	122983474	866	False	1408.000000	1408	95.9630	2668	3534	1	chr2B.!!$F1	866
13	TraesCS4A01G344400	chr2B	581621490	581622378	888	False	1044.000000	1044	88.4830	135	1000	1	chr2B.!!$F3	865
14	TraesCS4A01G344400	chr5D	441935443	441937339	1896	True	2623.000000	2623	91.6140	962	2865	1	chr5D.!!$R1	1903
15	TraesCS4A01G344400	chr3B	758627515	758629644	2129	False	470.666667	1051	86.0600	132	3534	3	chr3B.!!$F2	3402

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	Hairpin	End Stability	Orientation
112	113	0.317160	CGACTCCAACTACAGCCACA	59.683	55.000	0.00	4.17	F
120	121	0.987294	ACTACAGCCACAATCCAGCT	59.013	50.000	37.32	4.24	F
530	680	1.005037	CAAGCGACACCAGGCTACA	60.005	57.895	38.88	2.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1728	1961	0.240945	CACCACGGTCAAAAGCATCC	59.759	55.000	0.00	3.51	R
2244	2487	3.804036	CAACAGAGACAACCACCAACTA	58.196	45.455	0.00	2.24	R
2733	2985	5.308825	CCAACCACTCTCTCTTAATGTTGT	58.691	41.667	32.16	3.32	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
27	28	9.772973	ATTTCAACAACAGTCTACATAGTTACA	57.227	29.630	0.00	0.00	0.00	2.41
28	29	9.602568	TTTCAACAACAGTCTACATAGTTACAA	57.397	29.630	0.00	0.00	0.00	2.41
29	30	9.772973	TTCAACAACAGTCTACATAGTTACAAT	57.227	29.630	0.00	0.00	0.00	2.71
30	31	9.772973	TCAACAACAGTCTACATAGTTACAATT	57.227	29.630	0.00	0.00	0.00	2.32
35	36	8.922058	ACAGTCTACATAGTTACAATTTACCG	57.078	34.615	0.00	0.00	0.00	4.02
36	37	8.742777	ACAGTCTACATAGTTACAATTTACCGA	58.257	33.333	0.00	0.00	0.00	4.69
37	38	9.017669	CAGTCTACATAGTTACAATTTACCGAC	57.982	37.037	0.00	0.00	0.00	4.79
38	39	8.742777	AGTCTACATAGTTACAATTTACCGACA	58.257	33.333	0.00	0.00	0.00	4.35
39	40	9.017669	GTCTACATAGTTACAATTTACCGACAG	57.982	37.037	0.00	0.00	0.00	3.51
40	41	8.192774	TCTACATAGTTACAATTTACCGACAGG	58.807	37.037	0.00	0.00	45.13	4.00
41	42	5.583457	ACATAGTTACAATTTACCGACAGGC	59.417	40.000	0.00	0.00	42.76	4.85
42	43	2.997986	AGTTACAATTTACCGACAGGCG	59.002	45.455	0.00	0.00	42.76	5.52
43	44	1.361793	TACAATTTACCGACAGGCGC	58.638	50.000	0.00	0.00	42.76	6.53
44	45	1.060308	CAATTTACCGACAGGCGCG	59.940	57.895	0.00	0.00	42.76	6.86
71	72	4.570663	CGCGCGGGCTAAGCTAGT	62.571	66.667	24.84	0.00	36.88	2.57
72	73	2.202892	GCGCGGGCTAAGCTAGTT	60.203	61.111	18.33	0.00	35.83	2.24
73	74	1.814169	GCGCGGGCTAAGCTAGTTT	60.814	57.895	18.33	0.00	35.83	2.66
74	75	2.006772	CGCGGGCTAAGCTAGTTTG	58.993	57.895	0.00	0.00	0.00	2.93
75	76	0.739813	CGCGGGCTAAGCTAGTTTGT	60.740	55.000	0.00	0.00	0.00	2.83
76	77	1.470285	CGCGGGCTAAGCTAGTTTGTA	60.470	52.381	0.00	0.00	0.00	2.41
77	78	1.931841	GCGGGCTAAGCTAGTTTGTAC	59.068	52.381	1.54	0.00	0.00	2.90
78	79	2.675889	GCGGGCTAAGCTAGTTTGTACA	60.676	50.000	1.54	0.00	0.00	2.90
79	80	3.592059	CGGGCTAAGCTAGTTTGTACAA	58.408	45.455	3.59	3.59	0.00	2.41
80	81	3.370061	CGGGCTAAGCTAGTTTGTACAAC	59.630	47.826	8.07	4.01	0.00	3.32
81	82	3.688185	GGGCTAAGCTAGTTTGTACAACC	59.312	47.826	8.07	0.30	0.00	3.77
82	83	4.320870	GGCTAAGCTAGTTTGTACAACCA	58.679	43.478	8.07	0.00	0.00	3.67
83	84	4.758165	GGCTAAGCTAGTTTGTACAACCAA	59.242	41.667	8.07	0.00	0.00	3.67
84	85	5.334646	GGCTAAGCTAGTTTGTACAACCAAC	60.335	44.000	8.07	4.21	0.00	3.77
85	86	5.334646	GCTAAGCTAGTTTGTACAACCAACC	60.335	44.000	8.07	0.00	0.00	3.77
86	87	4.159244	AGCTAGTTTGTACAACCAACCA	57.841	40.909	8.07	0.00	0.00	3.67
87	88	4.528920	AGCTAGTTTGTACAACCAACCAA	58.471	39.130	8.07	0.00	0.00	3.67
88	89	4.337274	AGCTAGTTTGTACAACCAACCAAC	59.663	41.667	8.07	1.87	0.00	3.77
89	90	4.337274	GCTAGTTTGTACAACCAACCAACT	59.663	41.667	8.07	9.71	36.89	3.16
90	91	5.528320	GCTAGTTTGTACAACCAACCAACTA	59.472	40.000	8.07	10.33	35.28	2.24
91	92	6.206048	GCTAGTTTGTACAACCAACCAACTAT	59.794	38.462	8.07	0.00	35.65	2.12
92	93	7.255346	GCTAGTTTGTACAACCAACCAACTATT	60.255	37.037	8.07	0.00	35.65	1.73
93	94	7.034685	AGTTTGTACAACCAACCAACTATTC	57.965	36.000	8.07	0.00	32.72	1.75
94	95	5.676532	TTGTACAACCAACCAACTATTCG	57.323	39.130	3.59	0.00	0.00	3.34
95	96	4.958509	TGTACAACCAACCAACTATTCGA	58.041	39.130	0.00	0.00	0.00	3.71
96	97	4.751098	TGTACAACCAACCAACTATTCGAC	59.249	41.667	0.00	0.00	0.00	4.20
97	98	4.081322	ACAACCAACCAACTATTCGACT	57.919	40.909	0.00	0.00	0.00	4.18
98	99	4.062991	ACAACCAACCAACTATTCGACTC	58.937	43.478	0.00	0.00	0.00	3.36
99	100	3.329929	ACCAACCAACTATTCGACTCC	57.670	47.619	0.00	0.00	0.00	3.85
100	101	2.635915	ACCAACCAACTATTCGACTCCA	59.364	45.455	0.00	0.00	0.00	3.86
101	102	3.071892	ACCAACCAACTATTCGACTCCAA	59.928	43.478	0.00	0.00	0.00	3.53
102	103	3.435671	CCAACCAACTATTCGACTCCAAC	59.564	47.826	0.00	0.00	0.00	3.77
103	104	4.315803	CAACCAACTATTCGACTCCAACT	58.684	43.478	0.00	0.00	0.00	3.16
104	105	5.475719	CAACCAACTATTCGACTCCAACTA	58.524	41.667	0.00	0.00	0.00	2.24
105	106	5.069501	ACCAACTATTCGACTCCAACTAC	57.930	43.478	0.00	0.00	0.00	2.73
106	107	4.525487	ACCAACTATTCGACTCCAACTACA	59.475	41.667	0.00	0.00	0.00	2.74
107	108	5.103000	CCAACTATTCGACTCCAACTACAG	58.897	45.833	0.00	0.00	0.00	2.74
108	109	4.373348	ACTATTCGACTCCAACTACAGC	57.627	45.455	0.00	0.00	0.00	4.40
109	110	2.674796	ATTCGACTCCAACTACAGCC	57.325	50.000	0.00	0.00	0.00	4.85
110	111	1.334160	TTCGACTCCAACTACAGCCA	58.666	50.000	0.00	0.00	0.00	4.75
111	112	0.601558	TCGACTCCAACTACAGCCAC	59.398	55.000	0.00	0.00	0.00	5.01
112	113	0.317160	CGACTCCAACTACAGCCACA	59.683	55.000	0.00	0.00	0.00	4.17
113	114	1.270094	CGACTCCAACTACAGCCACAA	60.270	52.381	0.00	0.00	0.00	3.33
114	115	2.612972	CGACTCCAACTACAGCCACAAT	60.613	50.000	0.00	0.00	0.00	2.71
115	116	3.003480	GACTCCAACTACAGCCACAATC	58.997	50.000	0.00	0.00	0.00	2.67
116	117	2.290323	ACTCCAACTACAGCCACAATCC	60.290	50.000	0.00	0.00	0.00	3.01
117	118	1.702401	TCCAACTACAGCCACAATCCA	59.298	47.619	0.00	0.00	0.00	3.41
118	119	2.086869	CCAACTACAGCCACAATCCAG	58.913	52.381	0.00	0.00	0.00	3.86
119	120	1.470098	CAACTACAGCCACAATCCAGC	59.530	52.381	0.00	0.00	0.00	4.85
120	121	0.987294	ACTACAGCCACAATCCAGCT	59.013	50.000	0.00	0.00	37.32	4.24
121	122	2.187958	ACTACAGCCACAATCCAGCTA	58.812	47.619	0.00	0.00	34.38	3.32
122	123	2.774234	ACTACAGCCACAATCCAGCTAT	59.226	45.455	0.00	0.00	34.38	2.97
123	124	2.338577	ACAGCCACAATCCAGCTATC	57.661	50.000	0.00	0.00	34.38	2.08
124	125	1.842562	ACAGCCACAATCCAGCTATCT	59.157	47.619	0.00	0.00	34.38	1.98
125	126	3.041211	ACAGCCACAATCCAGCTATCTA	58.959	45.455	0.00	0.00	34.38	1.98
126	127	3.070734	ACAGCCACAATCCAGCTATCTAG	59.929	47.826	0.00	0.00	34.38	2.43
127	128	3.070734	CAGCCACAATCCAGCTATCTAGT	59.929	47.826	0.00	0.00	34.38	2.57
128	129	4.281941	CAGCCACAATCCAGCTATCTAGTA	59.718	45.833	0.00	0.00	34.38	1.82
129	130	4.526262	AGCCACAATCCAGCTATCTAGTAG	59.474	45.833	0.00	0.00	34.38	2.57
530	680	1.005037	CAAGCGACACCAGGCTACA	60.005	57.895	0.00	0.00	38.88	2.74
567	719	1.889829	CAGTCGTTCCTCAACCTCTCT	59.110	52.381	0.00	0.00	0.00	3.10
594	746	4.760047	TCTGGCTTCGGCTTCGGC	62.760	66.667	0.00	0.00	41.44	5.54
595	747	4.767255	CTGGCTTCGGCTTCGGCT	62.767	66.667	0.00	0.00	41.44	5.52
596	748	4.329545	TGGCTTCGGCTTCGGCTT	62.330	61.111	0.00	0.00	41.44	4.35
882	1088	1.136336	GTAAGAAGACGGCAACTTGCG	60.136	52.381	7.67	5.96	46.21	4.85
1098	1326	2.094675	CCACCTCCTAACATTGCCAAG	58.905	52.381	0.00	0.00	0.00	3.61
1184	1412	8.424918	TCCTCCTAATATTCAAGATCAAGTGAC	58.575	37.037	0.00	0.00	0.00	3.67
1311	1539	6.322201	GGTACAAAACTCATCCATGGATTGAT	59.678	38.462	25.20	12.28	31.62	2.57
1670	1900	5.441500	TGACGAATCCTCTACTTCTCTGAT	58.558	41.667	0.00	0.00	0.00	2.90
2083	2326	5.728637	TCTGAGTCACTAAAGAATGCTCA	57.271	39.130	0.00	0.00	32.14	4.26
2244	2487	3.940852	TCATTGCTATGCTCATCGTTTGT	59.059	39.130	3.00	0.00	0.00	2.83
2733	2985	0.321346	TGATGTCAAAGCTCGGCTGA	59.679	50.000	0.00	0.00	39.62	4.26
2950	3818	0.036388	GAGATGGACCACCGCTTCAA	60.036	55.000	0.00	0.00	39.42	2.69
3173	4041	5.479724	TGATGATGTTCAAAGTTTGGCCATA	59.520	36.000	6.09	0.00	0.00	2.74
3364	4232	4.937201	TGATGATATGTTACACCGAGCT	57.063	40.909	0.00	0.00	0.00	4.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	9.772973	ATTGTAACTATGTAGACTGTTGTTGAA	57.227	29.630	0.00	0.00	0.00	2.69
9	10	9.362539	CGGTAAATTGTAACTATGTAGACTGTT	57.637	33.333	0.00	0.00	0.00	3.16
10	11	8.742777	TCGGTAAATTGTAACTATGTAGACTGT	58.257	33.333	0.00	0.00	0.00	3.55
11	12	9.017669	GTCGGTAAATTGTAACTATGTAGACTG	57.982	37.037	0.00	0.00	0.00	3.51
12	13	8.742777	TGTCGGTAAATTGTAACTATGTAGACT	58.257	33.333	0.00	0.00	0.00	3.24
13	14	8.915871	TGTCGGTAAATTGTAACTATGTAGAC	57.084	34.615	0.00	0.00	0.00	2.59
14	15	8.192774	CCTGTCGGTAAATTGTAACTATGTAGA	58.807	37.037	0.00	0.00	0.00	2.59
15	16	7.042925	GCCTGTCGGTAAATTGTAACTATGTAG	60.043	40.741	0.00	0.00	0.00	2.74
16	17	6.757947	GCCTGTCGGTAAATTGTAACTATGTA	59.242	38.462	0.00	0.00	0.00	2.29
17	18	5.583457	GCCTGTCGGTAAATTGTAACTATGT	59.417	40.000	0.00	0.00	0.00	2.29
18	19	5.276678	CGCCTGTCGGTAAATTGTAACTATG	60.277	44.000	0.00	0.00	33.78	2.23
19	20	4.807304	CGCCTGTCGGTAAATTGTAACTAT	59.193	41.667	0.00	0.00	33.78	2.12
20	21	4.175516	CGCCTGTCGGTAAATTGTAACTA	58.824	43.478	0.00	0.00	33.78	2.24
21	22	2.997986	CGCCTGTCGGTAAATTGTAACT	59.002	45.455	0.00	0.00	33.78	2.24
22	23	2.475022	GCGCCTGTCGGTAAATTGTAAC	60.475	50.000	0.00	0.00	38.94	2.50
23	24	1.733360	GCGCCTGTCGGTAAATTGTAA	59.267	47.619	0.00	0.00	38.94	2.41
24	25	1.361793	GCGCCTGTCGGTAAATTGTA	58.638	50.000	0.00	0.00	38.94	2.41
25	26	1.632046	CGCGCCTGTCGGTAAATTGT	61.632	55.000	0.00	0.00	38.94	2.71
26	27	1.060308	CGCGCCTGTCGGTAAATTG	59.940	57.895	0.00	0.00	38.94	2.32
27	28	2.104253	CCGCGCCTGTCGGTAAATT	61.104	57.895	0.00	0.00	41.85	1.82
28	29	2.510691	CCGCGCCTGTCGGTAAAT	60.511	61.111	0.00	0.00	41.85	1.40
54	55	4.570663	ACTAGCTTAGCCCGCGCG	62.571	66.667	25.67	25.67	41.18	6.86
55	56	1.814169	AAACTAGCTTAGCCCGCGC	60.814	57.895	0.00	0.00	0.00	6.86
56	57	0.739813	ACAAACTAGCTTAGCCCGCG	60.740	55.000	0.00	0.00	0.00	6.46
57	58	1.931841	GTACAAACTAGCTTAGCCCGC	59.068	52.381	0.00	0.00	0.00	6.13
58	59	3.241067	TGTACAAACTAGCTTAGCCCG	57.759	47.619	0.00	0.00	0.00	6.13
59	60	3.688185	GGTTGTACAAACTAGCTTAGCCC	59.312	47.826	16.56	2.23	0.00	5.19
60	61	4.320870	TGGTTGTACAAACTAGCTTAGCC	58.679	43.478	23.51	10.75	31.35	3.93
61	62	5.334646	GGTTGGTTGTACAAACTAGCTTAGC	60.335	44.000	23.90	7.23	35.22	3.09
62	63	5.761234	TGGTTGGTTGTACAAACTAGCTTAG	59.239	40.000	28.51	0.00	38.82	2.18
63	64	5.682659	TGGTTGGTTGTACAAACTAGCTTA	58.317	37.500	28.51	13.67	38.82	3.09
64	65	4.528920	TGGTTGGTTGTACAAACTAGCTT	58.471	39.130	28.51	0.00	38.82	3.74
65	66	4.159244	TGGTTGGTTGTACAAACTAGCT	57.841	40.909	28.51	0.00	38.82	3.32
66	67	4.337274	AGTTGGTTGGTTGTACAAACTAGC	59.663	41.667	24.25	24.25	37.86	3.42
67	68	7.739498	ATAGTTGGTTGGTTGTACAAACTAG	57.261	36.000	23.51	0.00	42.35	2.57
68	69	7.041916	CGAATAGTTGGTTGGTTGTACAAACTA	60.042	37.037	23.51	17.93	42.92	2.24
69	70	6.238538	CGAATAGTTGGTTGGTTGTACAAACT	60.239	38.462	23.51	16.48	41.46	2.66
70	71	5.910723	CGAATAGTTGGTTGGTTGTACAAAC	59.089	40.000	16.98	16.98	38.52	2.93
71	72	5.821470	TCGAATAGTTGGTTGGTTGTACAAA	59.179	36.000	10.51	0.00	31.17	2.83
72	73	5.236911	GTCGAATAGTTGGTTGGTTGTACAA	59.763	40.000	3.59	3.59	0.00	2.41
73	74	4.751098	GTCGAATAGTTGGTTGGTTGTACA	59.249	41.667	0.00	0.00	0.00	2.90
74	75	4.992951	AGTCGAATAGTTGGTTGGTTGTAC	59.007	41.667	0.00	0.00	0.00	2.90
75	76	5.217978	AGTCGAATAGTTGGTTGGTTGTA	57.782	39.130	0.00	0.00	0.00	2.41
76	77	4.062991	GAGTCGAATAGTTGGTTGGTTGT	58.937	43.478	0.00	0.00	0.00	3.32
77	78	3.435671	GGAGTCGAATAGTTGGTTGGTTG	59.564	47.826	0.00	0.00	0.00	3.77
78	79	3.071892	TGGAGTCGAATAGTTGGTTGGTT	59.928	43.478	0.00	0.00	0.00	3.67
79	80	2.635915	TGGAGTCGAATAGTTGGTTGGT	59.364	45.455	0.00	0.00	0.00	3.67
80	81	3.328382	TGGAGTCGAATAGTTGGTTGG	57.672	47.619	0.00	0.00	0.00	3.77
81	82	4.315803	AGTTGGAGTCGAATAGTTGGTTG	58.684	43.478	0.00	0.00	0.00	3.77
82	83	4.618920	AGTTGGAGTCGAATAGTTGGTT	57.381	40.909	0.00	0.00	0.00	3.67
83	84	4.525487	TGTAGTTGGAGTCGAATAGTTGGT	59.475	41.667	0.00	0.00	0.00	3.67
84	85	5.068234	TGTAGTTGGAGTCGAATAGTTGG	57.932	43.478	0.00	0.00	0.00	3.77
85	86	4.563184	GCTGTAGTTGGAGTCGAATAGTTG	59.437	45.833	0.00	0.00	0.00	3.16
86	87	4.381718	GGCTGTAGTTGGAGTCGAATAGTT	60.382	45.833	0.00	0.00	0.00	2.24
87	88	3.130693	GGCTGTAGTTGGAGTCGAATAGT	59.869	47.826	0.00	0.00	0.00	2.12
88	89	3.130516	TGGCTGTAGTTGGAGTCGAATAG	59.869	47.826	0.00	0.00	0.00	1.73
89	90	3.093814	TGGCTGTAGTTGGAGTCGAATA	58.906	45.455	0.00	0.00	0.00	1.75
90	91	1.899814	TGGCTGTAGTTGGAGTCGAAT	59.100	47.619	0.00	0.00	0.00	3.34
91	92	1.000506	GTGGCTGTAGTTGGAGTCGAA	59.999	52.381	0.00	0.00	0.00	3.71
92	93	0.601558	GTGGCTGTAGTTGGAGTCGA	59.398	55.000	0.00	0.00	0.00	4.20
93	94	0.317160	TGTGGCTGTAGTTGGAGTCG	59.683	55.000	0.00	0.00	0.00	4.18
94	95	2.543777	TTGTGGCTGTAGTTGGAGTC	57.456	50.000	0.00	0.00	0.00	3.36
95	96	2.290323	GGATTGTGGCTGTAGTTGGAGT	60.290	50.000	0.00	0.00	0.00	3.85
96	97	2.290260	TGGATTGTGGCTGTAGTTGGAG	60.290	50.000	0.00	0.00	0.00	3.86
97	98	1.702401	TGGATTGTGGCTGTAGTTGGA	59.298	47.619	0.00	0.00	0.00	3.53
98	99	2.086869	CTGGATTGTGGCTGTAGTTGG	58.913	52.381	0.00	0.00	0.00	3.77
99	100	1.470098	GCTGGATTGTGGCTGTAGTTG	59.530	52.381	0.00	0.00	0.00	3.16
100	101	1.352352	AGCTGGATTGTGGCTGTAGTT	59.648	47.619	0.00	0.00	34.82	2.24
101	102	0.987294	AGCTGGATTGTGGCTGTAGT	59.013	50.000	0.00	0.00	34.82	2.73
102	103	2.988010	TAGCTGGATTGTGGCTGTAG	57.012	50.000	0.00	0.00	37.50	2.74
103	104	3.041211	AGATAGCTGGATTGTGGCTGTA	58.959	45.455	0.00	0.00	37.50	2.74
104	105	1.842562	AGATAGCTGGATTGTGGCTGT	59.157	47.619	0.00	0.00	37.50	4.40
105	106	2.634815	AGATAGCTGGATTGTGGCTG	57.365	50.000	0.00	0.00	37.50	4.85
106	107	3.312890	ACTAGATAGCTGGATTGTGGCT	58.687	45.455	0.00	0.00	39.74	4.75
107	108	3.760580	ACTAGATAGCTGGATTGTGGC	57.239	47.619	0.00	0.00	0.00	5.01
183	184	2.635229	ATCGCTGCTGCTAGGAACCG	62.635	60.000	14.03	0.00	36.97	4.44
266	268	0.319555	CGTGAGAGAAACGAAGGCCA	60.320	55.000	5.01	0.00	43.68	5.36
530	680	1.544691	ACTGGACGAATAGACTGCGTT	59.455	47.619	0.00	0.00	38.51	4.84
567	719	1.208052	CCGAAGCCAGATGAGAGGAAA	59.792	52.381	0.00	0.00	0.00	3.13
934	1142	6.752351	CGAGCTACAACAAGTTCATAGTACAT	59.248	38.462	0.00	0.00	0.00	2.29
1098	1326	9.132521	CGCTCAATATCATTTGGATTAAATTCC	57.867	33.333	0.00	0.00	36.87	3.01
1184	1412	5.278169	GCACCCTTCAATACATATGCTCTTG	60.278	44.000	1.58	4.56	0.00	3.02
1311	1539	2.703536	TGCCTTCTTCCACTCACTGTAA	59.296	45.455	0.00	0.00	0.00	2.41
1728	1961	0.240945	CACCACGGTCAAAAGCATCC	59.759	55.000	0.00	0.00	0.00	3.51
2244	2487	3.804036	CAACAGAGACAACCACCAACTA	58.196	45.455	0.00	0.00	0.00	2.24
2733	2985	5.308825	CCAACCACTCTCTCTTAATGTTGT	58.691	41.667	0.00	0.00	32.16	3.32
2950	3818	2.240667	AGCACACCATTAGCTCCTTCAT	59.759	45.455	0.00	0.00	32.05	2.57
3173	4041	6.773976	TGTTTCTCAGTTTCAACCATCTTT	57.226	33.333	0.00	0.00	0.00	2.52
3364	4232	6.768483	TCATCAACTGACTTGAATAACTCCA	58.232	36.000	0.00	0.00	42.37	3.86
3452	4320	2.736144	TACCGACAGTGCACTAAAGG	57.264	50.000	21.20	22.83	0.00	3.11

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.