AutoCloner

Multiple sequence alignment - TraesCS2A01G397500

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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	TraesCS2A01G397500	chr2A	100.000	2201	0	0	1	2201	651438720	651436520	0.000000e+00	4065
1	TraesCS2A01G397500	chr2A	98.965	1546	16	0	103	1648	726901231	726902776	0.000000e+00	2767
2	TraesCS2A01G397500	chr2A	98.734	553	7	0	1649	2201	651391769	651391217	0.000000e+00	983
3	TraesCS2A01G397500	chr2A	99.107	112	1	0	1	112	651438205	651438094	3.710000e-48	202
4	TraesCS2A01G397500	chr3D	98.771	1546	19	0	103	1648	589258304	589259849	0.000000e+00	2750
5	TraesCS2A01G397500	chr3D	95.118	553	27	0	1649	2201	183570028	183570580	0.000000e+00	872
6	TraesCS2A01G397500	chr3D	95.281	551	25	1	1651	2201	291420810	291420261	0.000000e+00	872
7	TraesCS2A01G397500	chr3D	99.107	112	1	0	1	112	213401528	213401417	3.710000e-48	202
8	TraesCS2A01G397500	chr3D	100.000	109	0	0	1	109	589258717	589258825	3.710000e-48	202
9	TraesCS2A01G397500	chr3B	98.771	1546	19	0	103	1648	201569563	201571108	0.000000e+00	2750
10	TraesCS2A01G397500	chr2D	98.706	1546	19	1	103	1648	591990896	591989352	0.000000e+00	2743
11	TraesCS2A01G397500	chr2D	95.118	553	27	0	1649	2201	370260758	370260206	0.000000e+00	872
12	TraesCS2A01G397500	chr7B	98.642	1546	20	1	103	1648	662732137	662730593	0.000000e+00	2737
13	TraesCS2A01G397500	chr7B	98.512	1546	22	1	103	1648	663094202	663095746	0.000000e+00	2726
14	TraesCS2A01G397500	chr7B	100.000	109	0	0	1	109	622433159	622433267	3.710000e-48	202
15	TraesCS2A01G397500	chr7A	98.383	1546	25	0	103	1648	258305590	258307135	0.000000e+00	2717
16	TraesCS2A01G397500	chr6B	98.383	1546	25	0	103	1648	450085026	450083481	0.000000e+00	2717
17	TraesCS2A01G397500	chr6B	99.107	112	1	0	1	112	450084613	450084502	3.710000e-48	202
18	TraesCS2A01G397500	chr1D	98.383	1546	25	0	103	1648	254530830	254529285	0.000000e+00	2717
19	TraesCS2A01G397500	chr4D	95.298	553	26	0	1649	2201	421777992	421778544	0.000000e+00	878
20	TraesCS2A01G397500	chr4D	95.118	553	27	0	1649	2201	404433324	404433876	0.000000e+00	872
21	TraesCS2A01G397500	chr4D	95.109	552	25	2	1650	2201	103174553	103174004	0.000000e+00	869
22	TraesCS2A01G397500	chr4D	99.107	112	1	0	1	112	338468562	338468451	3.710000e-48	202
23	TraesCS2A01G397500	chr1A	95.118	553	27	0	1649	2201	387204896	387204344	0.000000e+00	872
24	TraesCS2A01G397500	chr6D	94.937	553	28	0	1649	2201	378323215	378322663	0.000000e+00	867
25	TraesCS2A01G397500	chr7D	99.107	112	1	0	1	112	231537700	231537589	3.710000e-48	202
26	TraesCS2A01G397500	chr5D	100.000	109	0	0	1	109	503259966	503260074	3.710000e-48	202
27	TraesCS2A01G397500	chr3A	100.000	109	0	0	1	109	66000669	66000777	3.710000e-48	202

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	TraesCS2A01G397500	chr2A	651436520	651438720	2200	True	2133.5	4065	99.5535	1	2201	2	chr2A.!!$R2	2200
1	TraesCS2A01G397500	chr2A	726901231	726902776	1545	False	2767.0	2767	98.9650	103	1648	1	chr2A.!!$F1	1545
2	TraesCS2A01G397500	chr2A	651391217	651391769	552	True	983.0	983	98.7340	1649	2201	1	chr2A.!!$R1	552
3	TraesCS2A01G397500	chr3D	589258304	589259849	1545	False	1476.0	2750	99.3855	1	1648	2	chr3D.!!$F2	1647
4	TraesCS2A01G397500	chr3D	183570028	183570580	552	False	872.0	872	95.1180	1649	2201	1	chr3D.!!$F1	552
5	TraesCS2A01G397500	chr3D	291420261	291420810	549	True	872.0	872	95.2810	1651	2201	1	chr3D.!!$R2	550
6	TraesCS2A01G397500	chr3B	201569563	201571108	1545	False	2750.0	2750	98.7710	103	1648	1	chr3B.!!$F1	1545
7	TraesCS2A01G397500	chr2D	591989352	591990896	1544	True	2743.0	2743	98.7060	103	1648	1	chr2D.!!$R2	1545
8	TraesCS2A01G397500	chr2D	370260206	370260758	552	True	872.0	872	95.1180	1649	2201	1	chr2D.!!$R1	552
9	TraesCS2A01G397500	chr7B	662730593	662732137	1544	True	2737.0	2737	98.6420	103	1648	1	chr7B.!!$R1	1545
10	TraesCS2A01G397500	chr7B	663094202	663095746	1544	False	2726.0	2726	98.5120	103	1648	1	chr7B.!!$F2	1545
11	TraesCS2A01G397500	chr7A	258305590	258307135	1545	False	2717.0	2717	98.3830	103	1648	1	chr7A.!!$F1	1545
12	TraesCS2A01G397500	chr6B	450083481	450085026	1545	True	1459.5	2717	98.7450	1	1648	2	chr6B.!!$R1	1647
13	TraesCS2A01G397500	chr1D	254529285	254530830	1545	True	2717.0	2717	98.3830	103	1648	1	chr1D.!!$R1	1545
14	TraesCS2A01G397500	chr4D	421777992	421778544	552	False	878.0	878	95.2980	1649	2201	1	chr4D.!!$F2	552
15	TraesCS2A01G397500	chr4D	404433324	404433876	552	False	872.0	872	95.1180	1649	2201	1	chr4D.!!$F1	552
16	TraesCS2A01G397500	chr4D	103174004	103174553	549	True	869.0	869	95.1090	1650	2201	1	chr4D.!!$R1	551
17	TraesCS2A01G397500	chr1A	387204344	387204896	552	True	872.0	872	95.1180	1649	2201	1	chr1A.!!$R1	552
18	TraesCS2A01G397500	chr6D	378322663	378323215	552	True	867.0	867	94.9370	1649	2201	1	chr6D.!!$R1	552

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
61	62	0.030369	CCCTACAGTATCGTCACCGC	59.97	60.0	0.0	0.0	0.0	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1260	1262	0.249868	CGTGAGCTGGGTTCAGAACA	60.25	55.0	15.36	0.0	43.49	3.18	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
22	23	4.818534	TTTTATCATTCTGGCATCGAGC	57.181	40.909	0.00	0.00	44.65	5.03
23	24	3.758755	TTATCATTCTGGCATCGAGCT	57.241	42.857	6.78	0.00	44.79	4.09
24	25	4.871933	TTATCATTCTGGCATCGAGCTA	57.128	40.909	6.78	0.79	44.79	3.32
25	26	3.977134	ATCATTCTGGCATCGAGCTAT	57.023	42.857	6.78	0.00	44.79	2.97
26	27	3.758755	TCATTCTGGCATCGAGCTATT	57.241	42.857	6.78	0.00	44.79	1.73
27	28	4.077300	TCATTCTGGCATCGAGCTATTT	57.923	40.909	6.78	0.00	44.79	1.40
28	29	4.454678	TCATTCTGGCATCGAGCTATTTT	58.545	39.130	6.78	0.00	44.79	1.82
29	30	4.274214	TCATTCTGGCATCGAGCTATTTTG	59.726	41.667	6.78	0.00	44.79	2.44
30	31	1.942657	TCTGGCATCGAGCTATTTTGC	59.057	47.619	6.78	2.04	44.79	3.68
31	32	3.853623	GGCATCGAGCTATTTTGCC	57.146	52.632	8.10	8.10	45.31	4.52
32	33	0.040958	GGCATCGAGCTATTTTGCCG	60.041	55.000	8.10	0.00	42.97	5.69
33	34	0.658536	GCATCGAGCTATTTTGCCGC	60.659	55.000	0.00	0.00	41.15	6.53
34	35	0.657312	CATCGAGCTATTTTGCCGCA	59.343	50.000	0.00	0.00	0.00	5.69
35	36	0.940126	ATCGAGCTATTTTGCCGCAG	59.060	50.000	0.00	0.00	0.00	5.18
48	49	2.363795	CGCAGGACCTCCCCTACA	60.364	66.667	0.00	0.00	34.07	2.74
49	50	2.427245	CGCAGGACCTCCCCTACAG	61.427	68.421	0.00	0.00	34.07	2.74
50	51	1.306226	GCAGGACCTCCCCTACAGT	60.306	63.158	0.00	0.00	34.07	3.55
51	52	0.032416	GCAGGACCTCCCCTACAGTA	60.032	60.000	0.00	0.00	34.07	2.74
52	53	1.413227	GCAGGACCTCCCCTACAGTAT	60.413	57.143	0.00	0.00	34.07	2.12
53	54	2.599677	CAGGACCTCCCCTACAGTATC	58.400	57.143	0.00	0.00	34.07	2.24
54	55	1.145325	AGGACCTCCCCTACAGTATCG	59.855	57.143	0.00	0.00	34.07	2.92
55	56	1.133544	GGACCTCCCCTACAGTATCGT	60.134	57.143	0.00	0.00	0.00	3.73
56	57	2.228925	GACCTCCCCTACAGTATCGTC	58.771	57.143	0.00	0.00	0.00	4.20
57	58	1.567649	ACCTCCCCTACAGTATCGTCA	59.432	52.381	0.00	0.00	0.00	4.35
58	59	1.955080	CCTCCCCTACAGTATCGTCAC	59.045	57.143	0.00	0.00	0.00	3.67
59	60	1.955080	CTCCCCTACAGTATCGTCACC	59.045	57.143	0.00	0.00	0.00	4.02
60	61	0.666913	CCCCTACAGTATCGTCACCG	59.333	60.000	0.00	0.00	0.00	4.94
61	62	0.030369	CCCTACAGTATCGTCACCGC	59.970	60.000	0.00	0.00	0.00	5.68
62	63	0.736636	CCTACAGTATCGTCACCGCA	59.263	55.000	0.00	0.00	0.00	5.69
63	64	1.268589	CCTACAGTATCGTCACCGCAG	60.269	57.143	0.00	0.00	0.00	5.18
64	65	1.400846	CTACAGTATCGTCACCGCAGT	59.599	52.381	0.00	0.00	0.00	4.40
65	66	1.456296	ACAGTATCGTCACCGCAGTA	58.544	50.000	0.00	0.00	0.00	2.74
66	67	1.400846	ACAGTATCGTCACCGCAGTAG	59.599	52.381	0.00	0.00	0.00	2.57
67	68	1.669265	CAGTATCGTCACCGCAGTAGA	59.331	52.381	0.00	0.00	0.00	2.59
68	69	1.941294	AGTATCGTCACCGCAGTAGAG	59.059	52.381	0.00	0.00	0.00	2.43
69	70	1.669779	GTATCGTCACCGCAGTAGAGT	59.330	52.381	0.00	0.00	0.00	3.24
70	71	1.174783	ATCGTCACCGCAGTAGAGTT	58.825	50.000	0.00	0.00	0.00	3.01
71	72	0.956633	TCGTCACCGCAGTAGAGTTT	59.043	50.000	0.00	0.00	0.00	2.66
72	73	2.153645	TCGTCACCGCAGTAGAGTTTA	58.846	47.619	0.00	0.00	0.00	2.01
73	74	2.553602	TCGTCACCGCAGTAGAGTTTAA	59.446	45.455	0.00	0.00	0.00	1.52
74	75	2.660236	CGTCACCGCAGTAGAGTTTAAC	59.340	50.000	0.00	0.00	0.00	2.01
75	76	2.991866	GTCACCGCAGTAGAGTTTAACC	59.008	50.000	0.00	0.00	0.00	2.85
76	77	2.629137	TCACCGCAGTAGAGTTTAACCA	59.371	45.455	0.00	0.00	0.00	3.67
77	78	2.735134	CACCGCAGTAGAGTTTAACCAC	59.265	50.000	0.00	0.00	0.00	4.16
78	79	2.289257	ACCGCAGTAGAGTTTAACCACC	60.289	50.000	0.00	0.00	0.00	4.61
79	80	2.289195	CCGCAGTAGAGTTTAACCACCA	60.289	50.000	0.00	0.00	0.00	4.17
80	81	3.395639	CGCAGTAGAGTTTAACCACCAA	58.604	45.455	0.00	0.00	0.00	3.67
81	82	3.810941	CGCAGTAGAGTTTAACCACCAAA	59.189	43.478	0.00	0.00	0.00	3.28
82	83	4.454504	CGCAGTAGAGTTTAACCACCAAAT	59.545	41.667	0.00	0.00	0.00	2.32
83	84	5.048991	CGCAGTAGAGTTTAACCACCAAATT	60.049	40.000	0.00	0.00	0.00	1.82
84	85	6.379386	GCAGTAGAGTTTAACCACCAAATTC	58.621	40.000	0.00	0.00	0.00	2.17
85	86	6.599437	CAGTAGAGTTTAACCACCAAATTCG	58.401	40.000	0.00	0.00	29.71	3.34
86	87	5.704053	AGTAGAGTTTAACCACCAAATTCGG	59.296	40.000	0.00	0.00	29.71	4.30
87	88	3.824443	AGAGTTTAACCACCAAATTCGGG	59.176	43.478	0.00	0.00	29.71	5.14
88	89	3.822167	GAGTTTAACCACCAAATTCGGGA	59.178	43.478	3.29	0.00	0.00	5.14
89	90	4.412843	AGTTTAACCACCAAATTCGGGAT	58.587	39.130	3.29	0.00	0.00	3.85
90	91	4.219725	AGTTTAACCACCAAATTCGGGATG	59.780	41.667	3.29	0.00	0.00	3.51
91	92	1.555967	AACCACCAAATTCGGGATGG	58.444	50.000	3.29	8.81	40.16	3.51
92	93	0.701731	ACCACCAAATTCGGGATGGA	59.298	50.000	17.07	0.00	37.66	3.41
93	94	1.287739	ACCACCAAATTCGGGATGGAT	59.712	47.619	17.07	6.18	37.66	3.41
94	95	2.292192	ACCACCAAATTCGGGATGGATT	60.292	45.455	17.07	2.47	37.66	3.01
95	96	2.101249	CCACCAAATTCGGGATGGATTG	59.899	50.000	0.04	0.00	37.66	2.67
96	97	2.101249	CACCAAATTCGGGATGGATTGG	59.899	50.000	0.04	0.00	42.29	3.16
97	98	2.292192	ACCAAATTCGGGATGGATTGGT	60.292	45.455	2.31	2.31	44.13	3.67
98	99	2.101249	CCAAATTCGGGATGGATTGGTG	59.899	50.000	0.00	0.00	36.27	4.17
99	100	2.760092	CAAATTCGGGATGGATTGGTGT	59.240	45.455	0.00	0.00	0.00	4.16
100	101	2.057137	ATTCGGGATGGATTGGTGTG	57.943	50.000	0.00	0.00	0.00	3.82
101	102	0.034574	TTCGGGATGGATTGGTGTGG	60.035	55.000	0.00	0.00	0.00	4.17
106	107	1.005924	GGATGGATTGGTGTGGTTCCT	59.994	52.381	0.00	0.00	0.00	3.36
372	373	1.082690	GGAAAGCGCCTTTCTCTCTG	58.917	55.000	22.65	0.00	46.20	3.35
987	989	8.651389	CCTTATCCTATTTCCATACTTCTGTCA	58.349	37.037	0.00	0.00	0.00	3.58
1260	1262	0.526662	GGACCGAACTGTCTCACGAT	59.473	55.000	0.00	0.00	35.54	3.73
1454	1456	3.636231	CCCTTCCACTCGGCACCA	61.636	66.667	0.00	0.00	0.00	4.17
1554	1556	2.350895	CCAATGTCCGTCTGGCCA	59.649	61.111	4.71	4.71	34.14	5.36
1571	1573	1.691196	CCAGAGGAAACCTTTGCACA	58.309	50.000	0.00	0.00	34.82	4.57
1666	1668	7.201644	GGGTCTGAGTAATGACAACATACATTG	60.202	40.741	0.00	0.00	37.32	2.82
1710	1712	1.001706	CTTGCCCGAGATTCGATCGTA	60.002	52.381	15.94	5.83	43.74	3.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	4.077300	AGCTCGATGCCAGAATGATAAA	57.923	40.909	3.66	0.00	44.23	1.40
3	4	3.758755	AGCTCGATGCCAGAATGATAA	57.241	42.857	3.66	0.00	44.23	1.75
4	5	5.411831	AATAGCTCGATGCCAGAATGATA	57.588	39.130	0.00	0.00	44.23	2.15
5	6	3.977134	ATAGCTCGATGCCAGAATGAT	57.023	42.857	0.00	0.00	44.23	2.45
6	7	3.758755	AATAGCTCGATGCCAGAATGA	57.241	42.857	0.00	0.00	44.23	2.57
7	8	4.534168	CAAAATAGCTCGATGCCAGAATG	58.466	43.478	0.00	0.00	44.23	2.67
8	9	3.004106	GCAAAATAGCTCGATGCCAGAAT	59.996	43.478	0.00	0.00	44.23	2.40
9	10	2.355756	GCAAAATAGCTCGATGCCAGAA	59.644	45.455	0.00	0.00	44.23	3.02
10	11	1.942657	GCAAAATAGCTCGATGCCAGA	59.057	47.619	0.00	0.00	44.23	3.86
11	12	2.396160	GCAAAATAGCTCGATGCCAG	57.604	50.000	0.00	0.00	44.23	4.85
14	15	0.658536	GCGGCAAAATAGCTCGATGC	60.659	55.000	0.00	0.00	43.29	3.91
15	16	0.657312	TGCGGCAAAATAGCTCGATG	59.343	50.000	0.00	0.00	32.44	3.84
16	17	0.940126	CTGCGGCAAAATAGCTCGAT	59.060	50.000	3.44	0.00	32.44	3.59
17	18	1.089481	CCTGCGGCAAAATAGCTCGA	61.089	55.000	3.44	0.00	32.44	4.04
18	19	1.089481	TCCTGCGGCAAAATAGCTCG	61.089	55.000	3.44	0.00	34.17	5.03
19	20	0.378610	GTCCTGCGGCAAAATAGCTC	59.621	55.000	3.44	0.00	34.17	4.09
20	21	1.032114	GGTCCTGCGGCAAAATAGCT	61.032	55.000	3.44	0.00	34.17	3.32
21	22	1.032114	AGGTCCTGCGGCAAAATAGC	61.032	55.000	3.44	0.00	0.00	2.97
22	23	1.017387	GAGGTCCTGCGGCAAAATAG	58.983	55.000	3.44	0.00	0.00	1.73
23	24	0.393808	GGAGGTCCTGCGGCAAAATA	60.394	55.000	3.44	0.00	0.00	1.40
24	25	1.678970	GGAGGTCCTGCGGCAAAAT	60.679	57.895	3.44	0.00	0.00	1.82
25	26	2.282180	GGAGGTCCTGCGGCAAAA	60.282	61.111	3.44	0.00	0.00	2.44
26	27	4.344865	GGGAGGTCCTGCGGCAAA	62.345	66.667	3.44	0.00	35.95	3.68
30	31	3.155167	GTAGGGGAGGTCCTGCGG	61.155	72.222	4.05	0.00	37.75	5.69
31	32	2.363795	TGTAGGGGAGGTCCTGCG	60.364	66.667	4.05	0.00	41.57	5.18
32	33	0.032416	TACTGTAGGGGAGGTCCTGC	60.032	60.000	0.73	0.73	39.54	4.85
33	34	2.599677	GATACTGTAGGGGAGGTCCTG	58.400	57.143	0.00	0.00	37.75	3.86
34	35	1.145325	CGATACTGTAGGGGAGGTCCT	59.855	57.143	0.00	0.00	40.79	3.85
35	36	1.133544	ACGATACTGTAGGGGAGGTCC	60.134	57.143	0.00	0.00	0.00	4.46
36	37	2.228925	GACGATACTGTAGGGGAGGTC	58.771	57.143	0.00	0.00	0.00	3.85
37	38	1.567649	TGACGATACTGTAGGGGAGGT	59.432	52.381	0.00	0.00	0.00	3.85
38	39	1.955080	GTGACGATACTGTAGGGGAGG	59.045	57.143	0.00	0.00	0.00	4.30
39	40	1.955080	GGTGACGATACTGTAGGGGAG	59.045	57.143	0.00	0.00	0.00	4.30
40	41	2.062971	GGTGACGATACTGTAGGGGA	57.937	55.000	0.00	0.00	0.00	4.81
54	55	2.991866	GGTTAAACTCTACTGCGGTGAC	59.008	50.000	8.92	0.00	0.00	3.67
55	56	2.629137	TGGTTAAACTCTACTGCGGTGA	59.371	45.455	8.92	3.03	0.00	4.02
56	57	2.735134	GTGGTTAAACTCTACTGCGGTG	59.265	50.000	8.92	0.00	0.00	4.94
57	58	2.289257	GGTGGTTAAACTCTACTGCGGT	60.289	50.000	2.42	2.42	0.00	5.68
58	59	2.289195	TGGTGGTTAAACTCTACTGCGG	60.289	50.000	0.00	0.00	0.00	5.69
59	60	3.034721	TGGTGGTTAAACTCTACTGCG	57.965	47.619	0.00	0.00	0.00	5.18
60	61	5.959618	ATTTGGTGGTTAAACTCTACTGC	57.040	39.130	0.00	0.00	0.00	4.40
61	62	6.348213	CCGAATTTGGTGGTTAAACTCTACTG	60.348	42.308	3.21	0.00	0.00	2.74
62	63	5.704053	CCGAATTTGGTGGTTAAACTCTACT	59.296	40.000	3.21	0.00	0.00	2.57
63	64	5.106436	CCCGAATTTGGTGGTTAAACTCTAC	60.106	44.000	10.97	0.00	0.00	2.59
64	65	5.005094	CCCGAATTTGGTGGTTAAACTCTA	58.995	41.667	10.97	0.00	0.00	2.43
65	66	3.824443	CCCGAATTTGGTGGTTAAACTCT	59.176	43.478	10.97	0.00	0.00	3.24
66	67	3.822167	TCCCGAATTTGGTGGTTAAACTC	59.178	43.478	10.97	0.00	0.00	3.01
67	68	3.834938	TCCCGAATTTGGTGGTTAAACT	58.165	40.909	10.97	0.00	0.00	2.66
68	69	4.490743	CATCCCGAATTTGGTGGTTAAAC	58.509	43.478	10.97	0.00	0.00	2.01
69	70	3.511934	CCATCCCGAATTTGGTGGTTAAA	59.488	43.478	10.97	0.00	0.00	1.52
70	71	3.093057	CCATCCCGAATTTGGTGGTTAA	58.907	45.455	10.97	0.00	0.00	2.01
71	72	2.309162	TCCATCCCGAATTTGGTGGTTA	59.691	45.455	17.18	1.37	0.00	2.85
72	73	1.076350	TCCATCCCGAATTTGGTGGTT	59.924	47.619	17.18	0.00	0.00	3.67
73	74	0.701731	TCCATCCCGAATTTGGTGGT	59.298	50.000	17.18	1.66	0.00	4.16
74	75	2.071778	ATCCATCCCGAATTTGGTGG	57.928	50.000	13.21	13.21	0.00	4.61
75	76	2.101249	CCAATCCATCCCGAATTTGGTG	59.899	50.000	10.97	3.36	31.19	4.17
76	77	2.292192	ACCAATCCATCCCGAATTTGGT	60.292	45.455	10.97	0.00	41.38	3.67
77	78	2.101249	CACCAATCCATCCCGAATTTGG	59.899	50.000	4.52	4.52	39.55	3.28
78	79	2.760092	ACACCAATCCATCCCGAATTTG	59.240	45.455	0.00	0.00	0.00	2.32
79	80	2.760092	CACACCAATCCATCCCGAATTT	59.240	45.455	0.00	0.00	0.00	1.82
80	81	2.378038	CACACCAATCCATCCCGAATT	58.622	47.619	0.00	0.00	0.00	2.17
81	82	1.410083	CCACACCAATCCATCCCGAAT	60.410	52.381	0.00	0.00	0.00	3.34
82	83	0.034574	CCACACCAATCCATCCCGAA	60.035	55.000	0.00	0.00	0.00	4.30
83	84	1.204786	ACCACACCAATCCATCCCGA	61.205	55.000	0.00	0.00	0.00	5.14
84	85	0.323360	AACCACACCAATCCATCCCG	60.323	55.000	0.00	0.00	0.00	5.14
85	86	1.474330	GAACCACACCAATCCATCCC	58.526	55.000	0.00	0.00	0.00	3.85
86	87	1.005924	AGGAACCACACCAATCCATCC	59.994	52.381	0.00	0.00	34.30	3.51
87	88	2.025887	AGAGGAACCACACCAATCCATC	60.026	50.000	0.00	0.00	34.30	3.51
88	89	1.995542	AGAGGAACCACACCAATCCAT	59.004	47.619	0.00	0.00	34.30	3.41
89	90	1.444933	AGAGGAACCACACCAATCCA	58.555	50.000	0.00	0.00	34.30	3.41
90	91	2.437413	GAAGAGGAACCACACCAATCC	58.563	52.381	0.00	0.00	0.00	3.01
91	92	2.076863	CGAAGAGGAACCACACCAATC	58.923	52.381	0.00	0.00	0.00	2.67
92	93	1.697432	TCGAAGAGGAACCACACCAAT	59.303	47.619	0.00	0.00	0.00	3.16
93	94	1.124780	TCGAAGAGGAACCACACCAA	58.875	50.000	0.00	0.00	0.00	3.67
94	95	0.391597	GTCGAAGAGGAACCACACCA	59.608	55.000	0.00	0.00	36.95	4.17
95	96	0.391597	TGTCGAAGAGGAACCACACC	59.608	55.000	0.00	0.00	36.95	4.16
96	97	2.234300	TTGTCGAAGAGGAACCACAC	57.766	50.000	0.00	0.00	36.95	3.82
97	98	2.992124	TTTGTCGAAGAGGAACCACA	57.008	45.000	0.00	0.00	36.95	4.17
98	99	2.548480	CCTTTTGTCGAAGAGGAACCAC	59.452	50.000	0.00	0.00	36.95	4.16
99	100	2.436542	TCCTTTTGTCGAAGAGGAACCA	59.563	45.455	5.22	0.00	36.95	3.67
100	101	3.121738	TCCTTTTGTCGAAGAGGAACC	57.878	47.619	5.22	0.00	36.95	3.62
101	102	4.814771	TCTTTCCTTTTGTCGAAGAGGAAC	59.185	41.667	15.53	0.00	45.31	3.62
106	107	3.804036	TGCTCTTTCCTTTTGTCGAAGA	58.196	40.909	0.00	0.00	0.00	2.87
1260	1262	0.249868	CGTGAGCTGGGTTCAGAACA	60.250	55.000	15.36	0.00	43.49	3.18
1454	1456	3.127099	TCGGCCTTAGTGATCCGAT	57.873	52.632	0.00	0.00	44.99	4.18
1554	1556	1.215423	AGGTGTGCAAAGGTTTCCTCT	59.785	47.619	0.00	0.00	30.89	3.69
1571	1573	1.350019	CTCCCAAAAGGTAACGGAGGT	59.650	52.381	0.00	0.00	46.39	3.85
1666	1668	6.761714	AGTAACATATCGATGACAAAGGGAAC	59.238	38.462	8.54	0.00	36.48	3.62
2066	2068	4.039245	TCCGTTAGCTTAGCATAATGAGCT	59.961	41.667	7.07	2.10	46.40	4.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.