AutoCloner

Multiple sequence alignment - TraesCS2A01G541800

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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	TraesCS2A01G541800	chr2A	100.000	2516	0	0	1	2516	752978215	752975700	0.000000e+00	4647.0
1	TraesCS2A01G541800	chr2A	84.472	1288	161	23	824	2098	753004613	753003352	0.000000e+00	1234.0
2	TraesCS2A01G541800	chr2A	91.323	461	21	9	159	619	753043530	753043089	1.650000e-171	612.0
3	TraesCS2A01G541800	chr2A	80.709	508	55	23	306	792	752997211	752996726	3.080000e-94	355.0
4	TraesCS2A01G541800	chr2A	79.702	537	66	22	277	792	753005125	753004611	5.150000e-92	348.0
5	TraesCS2A01G541800	chr2A	95.484	155	5	2	2	154	30697228	30697074	1.930000e-61	246.0
6	TraesCS2A01G541800	chr2A	85.714	91	8	3	2358	2448	752994750	752994665	9.580000e-15	91.6
7	TraesCS2A01G541800	chr2A	85.714	91	8	3	2358	2448	753002886	753002801	9.580000e-15	91.6
8	TraesCS2A01G541800	chr2A	76.608	171	22	9	2203	2359	752994940	752994774	7.460000e-11	78.7
9	TraesCS2A01G541800	chr2A	76.023	171	23	9	2203	2359	753003076	753002910	3.470000e-09	73.1
10	TraesCS2A01G541800	chr2D	93.190	2364	76	20	159	2448	621130383	621128031	0.000000e+00	3395.0
11	TraesCS2A01G541800	chr2D	83.124	1831	215	48	307	2098	621314114	621312339	0.000000e+00	1583.0
12	TraesCS2A01G541800	chr2D	84.790	1545	176	43	572	2100	621265827	621264326	0.000000e+00	1496.0
13	TraesCS2A01G541800	chr2D	84.663	1441	166	31	776	2187	621140962	621139548	0.000000e+00	1386.0
14	TraesCS2A01G541800	chr2D	87.912	91	7	2	2358	2448	621311873	621311787	1.230000e-18	104.0
15	TraesCS2A01G541800	chr2D	94.203	69	0	1	2448	2516	621127999	621127935	4.430000e-18	102.0
16	TraesCS2A01G541800	chr2D	78.363	171	19	12	2203	2359	621312063	621311897	7.410000e-16	95.3
17	TraesCS2A01G541800	chrUn	91.956	2014	93	21	497	2448	314618913	314616907	0.000000e+00	2758.0
18	TraesCS2A01G541800	chrUn	84.244	1409	176	30	802	2181	338975293	338976684	0.000000e+00	1330.0
19	TraesCS2A01G541800	chrUn	87.903	248	23	4	537	778	329049716	329049470	4.100000e-73	285.0
20	TraesCS2A01G541800	chrUn	88.430	242	21	4	537	772	338975052	338975292	4.100000e-73	285.0
21	TraesCS2A01G541800	chrUn	88.430	242	21	4	537	772	342892905	342893145	4.100000e-73	285.0
22	TraesCS2A01G541800	chrUn	88.430	242	21	4	537	772	417387460	417387700	4.100000e-73	285.0
23	TraesCS2A01G541800	chrUn	95.455	154	5	2	2	153	471489003	471488850	6.950000e-61	244.0
24	TraesCS2A01G541800	chrUn	94.631	149	6	2	358	505	314619485	314619338	1.950000e-56	230.0
25	TraesCS2A01G541800	chrUn	91.875	160	9	4	2	159	118289114	118288957	1.170000e-53	220.0
26	TraesCS2A01G541800	chrUn	92.126	127	6	2	209	333	314619607	314619483	2.570000e-40	176.0
27	TraesCS2A01G541800	chrUn	86.184	152	18	1	307	455	329049877	329049726	7.200000e-36	161.0
28	TraesCS2A01G541800	chrUn	92.537	67	1	1	2450	2516	314616873	314616811	2.660000e-15	93.5
29	TraesCS2A01G541800	chr2B	94.487	1687	58	10	358	2017	762063805	762062127	0.000000e+00	2567.0
30	TraesCS2A01G541800	chr2B	83.667	1647	184	45	572	2177	762072154	762070552	0.000000e+00	1472.0
31	TraesCS2A01G541800	chr2B	92.035	452	6	3	2027	2448	762050037	762049586	2.140000e-170	608.0
32	TraesCS2A01G541800	chr2B	91.477	176	12	2	159	333	762063976	762063803	3.230000e-59	239.0
33	TraesCS2A01G541800	chr5A	96.875	160	3	2	2	159	203869440	203869599	1.480000e-67	267.0
34	TraesCS2A01G541800	chr1A	95.092	163	6	2	2	162	454355356	454355194	3.210000e-64	255.0
35	TraesCS2A01G541800	chr7A	95.031	161	5	2	2	159	602423393	602423553	1.490000e-62	250.0
36	TraesCS2A01G541800	chr4A	96.026	151	4	2	2	150	551327245	551327395	6.950000e-61	244.0
37	TraesCS2A01G541800	chr4D	91.875	160	10	3	2	159	275356771	275356929	1.170000e-53	220.0
38	TraesCS2A01G541800	chr4D	91.875	160	10	3	2	159	348933423	348933265	1.170000e-53	220.0

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	TraesCS2A01G541800	chr2A	752975700	752978215	2515	True	4647.000	4647	100.00000	1	2516	1	chr2A.!!$R2	2515
1	TraesCS2A01G541800	chr2A	753002801	753005125	2324	True	436.675	1234	81.47775	277	2448	4	chr2A.!!$R5	2171
2	TraesCS2A01G541800	chr2D	621127935	621130383	2448	True	1748.500	3395	93.69650	159	2516	2	chr2D.!!$R3	2357
3	TraesCS2A01G541800	chr2D	621264326	621265827	1501	True	1496.000	1496	84.79000	572	2100	1	chr2D.!!$R2	1528
4	TraesCS2A01G541800	chr2D	621139548	621140962	1414	True	1386.000	1386	84.66300	776	2187	1	chr2D.!!$R1	1411
5	TraesCS2A01G541800	chr2D	621311787	621314114	2327	True	594.100	1583	83.13300	307	2448	3	chr2D.!!$R4	2141
6	TraesCS2A01G541800	chrUn	314616811	314619607	2796	True	814.375	2758	92.81250	209	2516	4	chrUn.!!$R3	2307
7	TraesCS2A01G541800	chrUn	338975052	338976684	1632	False	807.500	1330	86.33700	537	2181	2	chrUn.!!$F3	1644
8	TraesCS2A01G541800	chr2B	762070552	762072154	1602	True	1472.000	1472	83.66700	572	2177	1	chr2B.!!$R2	1605
9	TraesCS2A01G541800	chr2B	762062127	762063976	1849	True	1403.000	2567	92.98200	159	2017	2	chr2B.!!$R3	1858

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
157	158	0.249447	CAGGGTGATGAATAGCGCGA	60.249	55.0	12.10	0.0	0.00	5.87	F
221	224	0.593128	ACGGCAATCACTGTGCTTTC	59.407	50.0	2.12	0.0	41.88	2.62	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1170	1691	1.078159	TGTGCCTGAGGGGAGTACTTA	59.922	52.381	0.00	0.0	37.23	2.24	R
1529	2052	1.089481	AATACACATGTGCCCGCGAG	61.089	55.000	25.68	0.0	0.00	5.03	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
34	35	7.599630	TTTTTACGGCGAGTACATATTTTCT	57.400	32.000	16.62	0.00	34.56	2.52
35	36	7.599630	TTTTACGGCGAGTACATATTTTCTT	57.400	32.000	16.62	0.00	34.56	2.52
36	37	8.700722	TTTTACGGCGAGTACATATTTTCTTA	57.299	30.769	16.62	0.00	34.56	2.10
37	38	8.876275	TTTACGGCGAGTACATATTTTCTTAT	57.124	30.769	16.62	0.00	34.56	1.73
38	39	6.764877	ACGGCGAGTACATATTTTCTTATG	57.235	37.500	16.62	0.00	35.98	1.90
39	40	6.278363	ACGGCGAGTACATATTTTCTTATGT	58.722	36.000	16.62	2.97	43.45	2.29
40	41	6.759827	ACGGCGAGTACATATTTTCTTATGTT	59.240	34.615	16.62	0.00	41.73	2.71
41	42	7.042925	ACGGCGAGTACATATTTTCTTATGTTC	60.043	37.037	16.62	0.00	41.73	3.18
42	43	7.169308	CGGCGAGTACATATTTTCTTATGTTCT	59.831	37.037	0.00	3.52	41.73	3.01
43	44	8.488764	GGCGAGTACATATTTTCTTATGTTCTC	58.511	37.037	15.53	15.53	44.80	2.87
44	45	9.250624	GCGAGTACATATTTTCTTATGTTCTCT	57.749	33.333	19.72	10.44	45.38	3.10
101	102	5.874831	GTAAAATACGGTGCATTGATGTCA	58.125	37.500	0.00	0.00	0.00	3.58
102	103	5.384063	AAAATACGGTGCATTGATGTCAA	57.616	34.783	0.00	0.00	40.51	3.18
103	104	5.384063	AAATACGGTGCATTGATGTCAAA	57.616	34.783	0.00	0.00	39.55	2.69
104	105	5.384063	AATACGGTGCATTGATGTCAAAA	57.616	34.783	0.00	0.00	39.55	2.44
105	106	3.940209	ACGGTGCATTGATGTCAAAAT	57.060	38.095	0.00	0.00	39.55	1.82
106	107	6.691754	ATACGGTGCATTGATGTCAAAATA	57.308	33.333	0.00	0.00	39.55	1.40
107	108	4.985413	ACGGTGCATTGATGTCAAAATAG	58.015	39.130	0.00	0.00	39.55	1.73
108	109	4.699735	ACGGTGCATTGATGTCAAAATAGA	59.300	37.500	0.00	0.00	39.55	1.98
109	110	5.163723	ACGGTGCATTGATGTCAAAATAGAG	60.164	40.000	0.00	0.00	39.55	2.43
110	111	5.065090	CGGTGCATTGATGTCAAAATAGAGA	59.935	40.000	0.00	0.00	39.55	3.10
111	112	6.493116	GGTGCATTGATGTCAAAATAGAGAG	58.507	40.000	0.00	0.00	39.55	3.20
112	113	6.459298	GGTGCATTGATGTCAAAATAGAGAGG	60.459	42.308	0.00	0.00	39.55	3.69
113	114	5.591472	TGCATTGATGTCAAAATAGAGAGGG	59.409	40.000	0.00	0.00	39.55	4.30
114	115	5.009410	GCATTGATGTCAAAATAGAGAGGGG	59.991	44.000	0.00	0.00	39.55	4.79
115	116	6.359804	CATTGATGTCAAAATAGAGAGGGGA	58.640	40.000	0.00	0.00	39.55	4.81
116	117	6.581388	TTGATGTCAAAATAGAGAGGGGAT	57.419	37.500	0.00	0.00	32.11	3.85
117	118	5.933617	TGATGTCAAAATAGAGAGGGGATG	58.066	41.667	0.00	0.00	0.00	3.51
118	119	5.667172	TGATGTCAAAATAGAGAGGGGATGA	59.333	40.000	0.00	0.00	0.00	2.92
119	120	6.331042	TGATGTCAAAATAGAGAGGGGATGAT	59.669	38.462	0.00	0.00	0.00	2.45
120	121	5.933617	TGTCAAAATAGAGAGGGGATGATG	58.066	41.667	0.00	0.00	0.00	3.07
121	122	5.667172	TGTCAAAATAGAGAGGGGATGATGA	59.333	40.000	0.00	0.00	0.00	2.92
122	123	6.158520	TGTCAAAATAGAGAGGGGATGATGAA	59.841	38.462	0.00	0.00	0.00	2.57
123	124	7.147248	TGTCAAAATAGAGAGGGGATGATGAAT	60.147	37.037	0.00	0.00	0.00	2.57
124	125	8.378565	GTCAAAATAGAGAGGGGATGATGAATA	58.621	37.037	0.00	0.00	0.00	1.75
125	126	8.948362	TCAAAATAGAGAGGGGATGATGAATAA	58.052	33.333	0.00	0.00	0.00	1.40
126	127	9.007901	CAAAATAGAGAGGGGATGATGAATAAC	57.992	37.037	0.00	0.00	0.00	1.89
127	128	8.517323	AAATAGAGAGGGGATGATGAATAACT	57.483	34.615	0.00	0.00	0.00	2.24
128	129	9.621239	AAATAGAGAGGGGATGATGAATAACTA	57.379	33.333	0.00	0.00	0.00	2.24
129	130	9.796242	AATAGAGAGGGGATGATGAATAACTAT	57.204	33.333	0.00	0.00	0.00	2.12
130	131	9.796242	ATAGAGAGGGGATGATGAATAACTATT	57.204	33.333	0.00	0.00	0.00	1.73
131	132	8.144862	AGAGAGGGGATGATGAATAACTATTC	57.855	38.462	2.99	2.99	41.81	1.75
142	143	5.940617	TGAATAACTATTCATCACCCAGGG	58.059	41.667	2.85	2.85	45.03	4.45
143	144	5.431731	TGAATAACTATTCATCACCCAGGGT	59.568	40.000	4.76	4.76	45.03	4.34
144	145	5.765182	GAATAACTATTCATCACCCAGGGTG	59.235	44.000	31.06	31.06	45.61	4.61
154	155	0.469917	ACCCAGGGTGATGAATAGCG	59.530	55.000	11.70	0.00	32.98	4.26
155	156	0.886490	CCCAGGGTGATGAATAGCGC	60.886	60.000	0.00	0.00	0.00	5.92
156	157	1.224069	CCAGGGTGATGAATAGCGCG	61.224	60.000	0.00	0.00	0.00	6.86
157	158	0.249447	CAGGGTGATGAATAGCGCGA	60.249	55.000	12.10	0.00	0.00	5.87
175	176	1.726791	CGACAAGCACGAGCAACTATT	59.273	47.619	7.77	0.00	45.49	1.73
180	181	4.094887	ACAAGCACGAGCAACTATTATTGG	59.905	41.667	7.77	0.00	45.49	3.16
221	224	0.593128	ACGGCAATCACTGTGCTTTC	59.407	50.000	2.12	0.00	41.88	2.62
502	963	6.715344	TTTCGCAGGTGTACTTGTAATTAG	57.285	37.500	0.00	0.00	0.00	1.73
597	1059	6.795144	ATAATGCTTTGGACAATTGGATCA	57.205	33.333	10.83	2.08	0.00	2.92
661	1151	0.654683	GTAGACCGCGTCGATACTGT	59.345	55.000	4.92	0.00	37.67	3.55
694	1185	1.852067	AACGCGTGAAATGGTCAGCC	61.852	55.000	14.98	0.00	36.74	4.85
727	1218	1.141881	CCCGGTCTTCACATCCTCG	59.858	63.158	0.00	0.00	0.00	4.63
785	1292	4.131649	TCCCACCTACACACAATATTCG	57.868	45.455	0.00	0.00	0.00	3.34
822	1332	5.924254	CAGGTACACAAACTTCATTCTACGA	59.076	40.000	0.00	0.00	0.00	3.43
1282	1803	1.340017	CCGGGAATGATGTTGTCACCT	60.340	52.381	0.00	0.00	40.28	4.00
1382	1903	0.030705	ATGCCAGGCTCCTCCTCTAA	60.031	55.000	14.15	0.00	45.52	2.10
1391	1912	0.702902	TCCTCCTCTAAGTCACCCGT	59.297	55.000	0.00	0.00	0.00	5.28
1527	2050	0.035725	TGGCTTGAGTGCATCTCTGG	60.036	55.000	14.60	9.63	43.13	3.86
1529	2052	1.367659	GCTTGAGTGCATCTCTGGAC	58.632	55.000	14.60	0.00	43.51	4.02
1534	2057	1.875813	GTGCATCTCTGGACTCGCG	60.876	63.158	0.00	0.00	40.31	5.87
2017	2557	2.284112	GGGAGTGGGTGACGGGTA	60.284	66.667	0.00	0.00	0.00	3.69
2037	2594	5.063880	GGTACTGCCCTATTATGTTCTTGG	58.936	45.833	0.00	0.00	0.00	3.61
2100	2675	2.765969	CCCAGTCCAGGCACCATT	59.234	61.111	0.00	0.00	0.00	3.16
2225	3026	8.737168	TGGTAGGAAATGATAGATTTCAAGTG	57.263	34.615	8.88	0.00	39.18	3.16
2488	3389	0.834612	AAGTTGTGACGGGGAGTTCA	59.165	50.000	0.00	0.00	0.00	3.18
2489	3390	1.056660	AGTTGTGACGGGGAGTTCAT	58.943	50.000	0.00	0.00	0.00	2.57
2490	3391	2.253610	AGTTGTGACGGGGAGTTCATA	58.746	47.619	0.00	0.00	0.00	2.15
2491	3392	2.838202	AGTTGTGACGGGGAGTTCATAT	59.162	45.455	0.00	0.00	0.00	1.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	9.316730	AGAAAATATGTACTCGCCGTAAAAATA	57.683	29.630	0.00	0.00	0.00	1.40
9	10	8.205131	AGAAAATATGTACTCGCCGTAAAAAT	57.795	30.769	0.00	0.00	0.00	1.82
10	11	7.599630	AGAAAATATGTACTCGCCGTAAAAA	57.400	32.000	0.00	0.00	0.00	1.94
11	12	7.599630	AAGAAAATATGTACTCGCCGTAAAA	57.400	32.000	0.00	0.00	0.00	1.52
12	13	8.757789	CATAAGAAAATATGTACTCGCCGTAAA	58.242	33.333	0.00	0.00	0.00	2.01
13	14	7.922278	ACATAAGAAAATATGTACTCGCCGTAA	59.078	33.333	0.00	0.00	43.04	3.18
14	15	7.428020	ACATAAGAAAATATGTACTCGCCGTA	58.572	34.615	0.00	0.00	43.04	4.02
15	16	6.278363	ACATAAGAAAATATGTACTCGCCGT	58.722	36.000	0.00	0.00	43.04	5.68
16	17	6.764877	ACATAAGAAAATATGTACTCGCCG	57.235	37.500	0.00	0.00	43.04	6.46
17	18	8.366671	AGAACATAAGAAAATATGTACTCGCC	57.633	34.615	0.79	0.00	43.83	5.54
18	19	9.250624	AGAGAACATAAGAAAATATGTACTCGC	57.749	33.333	0.79	0.00	43.83	5.03
77	78	8.303104	TTTGACATCAATGCACCGTATTTTACG	61.303	37.037	0.00	0.22	42.48	3.18
78	79	5.874831	TGACATCAATGCACCGTATTTTAC	58.125	37.500	0.00	0.00	0.00	2.01
79	80	6.502136	TTGACATCAATGCACCGTATTTTA	57.498	33.333	0.00	0.00	0.00	1.52
80	81	5.384063	TTGACATCAATGCACCGTATTTT	57.616	34.783	0.00	0.00	0.00	1.82
81	82	5.384063	TTTGACATCAATGCACCGTATTT	57.616	34.783	0.00	0.00	35.55	1.40
82	83	5.384063	TTTTGACATCAATGCACCGTATT	57.616	34.783	0.00	0.00	35.55	1.89
83	84	5.581126	ATTTTGACATCAATGCACCGTAT	57.419	34.783	0.00	0.00	35.55	3.06
84	85	5.877564	TCTATTTTGACATCAATGCACCGTA	59.122	36.000	0.00	0.00	35.55	4.02
85	86	3.940209	ATTTTGACATCAATGCACCGT	57.060	38.095	0.00	0.00	35.55	4.83
86	87	5.065090	TCTCTATTTTGACATCAATGCACCG	59.935	40.000	0.00	0.00	35.55	4.94
87	88	6.441093	TCTCTATTTTGACATCAATGCACC	57.559	37.500	0.00	0.00	35.55	5.01
88	89	6.459298	CCCTCTCTATTTTGACATCAATGCAC	60.459	42.308	0.00	0.00	35.55	4.57
89	90	5.591472	CCCTCTCTATTTTGACATCAATGCA	59.409	40.000	0.00	0.00	35.55	3.96
90	91	5.009410	CCCCTCTCTATTTTGACATCAATGC	59.991	44.000	0.00	0.00	35.55	3.56
91	92	6.359804	TCCCCTCTCTATTTTGACATCAATG	58.640	40.000	0.00	0.00	35.55	2.82
92	93	6.581388	TCCCCTCTCTATTTTGACATCAAT	57.419	37.500	0.00	0.00	35.55	2.57
93	94	6.158520	TCATCCCCTCTCTATTTTGACATCAA	59.841	38.462	0.00	0.00	0.00	2.57
94	95	5.667172	TCATCCCCTCTCTATTTTGACATCA	59.333	40.000	0.00	0.00	0.00	3.07
95	96	6.179906	TCATCCCCTCTCTATTTTGACATC	57.820	41.667	0.00	0.00	0.00	3.06
96	97	6.331042	TCATCATCCCCTCTCTATTTTGACAT	59.669	38.462	0.00	0.00	0.00	3.06
97	98	5.667172	TCATCATCCCCTCTCTATTTTGACA	59.333	40.000	0.00	0.00	0.00	3.58
98	99	6.179906	TCATCATCCCCTCTCTATTTTGAC	57.820	41.667	0.00	0.00	0.00	3.18
99	100	6.829985	TTCATCATCCCCTCTCTATTTTGA	57.170	37.500	0.00	0.00	0.00	2.69
100	101	9.007901	GTTATTCATCATCCCCTCTCTATTTTG	57.992	37.037	0.00	0.00	0.00	2.44
101	102	8.953665	AGTTATTCATCATCCCCTCTCTATTTT	58.046	33.333	0.00	0.00	0.00	1.82
102	103	8.517323	AGTTATTCATCATCCCCTCTCTATTT	57.483	34.615	0.00	0.00	0.00	1.40
103	104	9.796242	ATAGTTATTCATCATCCCCTCTCTATT	57.204	33.333	0.00	0.00	0.00	1.73
104	105	9.796242	AATAGTTATTCATCATCCCCTCTCTAT	57.204	33.333	0.00	0.00	0.00	1.98
105	106	9.261035	GAATAGTTATTCATCATCCCCTCTCTA	57.739	37.037	6.94	0.00	41.25	2.43
106	107	7.736691	TGAATAGTTATTCATCATCCCCTCTCT	59.263	37.037	9.84	0.00	45.03	3.10
107	108	7.911651	TGAATAGTTATTCATCATCCCCTCTC	58.088	38.462	9.84	0.00	45.03	3.20
108	109	7.878621	TGAATAGTTATTCATCATCCCCTCT	57.121	36.000	9.84	0.00	45.03	3.69
119	120	5.431731	ACCCTGGGTGATGAATAGTTATTCA	59.568	40.000	19.82	14.89	44.20	2.57
120	121	5.941788	ACCCTGGGTGATGAATAGTTATTC	58.058	41.667	19.82	5.18	37.59	1.75
121	122	5.994416	ACCCTGGGTGATGAATAGTTATT	57.006	39.130	19.82	0.00	32.98	1.40
135	136	0.469917	CGCTATTCATCACCCTGGGT	59.530	55.000	14.05	14.05	35.62	4.51
136	137	0.886490	GCGCTATTCATCACCCTGGG	60.886	60.000	12.28	12.28	0.00	4.45
137	138	1.224069	CGCGCTATTCATCACCCTGG	61.224	60.000	5.56	0.00	0.00	4.45
138	139	0.249447	TCGCGCTATTCATCACCCTG	60.249	55.000	5.56	0.00	0.00	4.45
139	140	0.249489	GTCGCGCTATTCATCACCCT	60.249	55.000	5.56	0.00	0.00	4.34
140	141	0.529773	TGTCGCGCTATTCATCACCC	60.530	55.000	5.56	0.00	0.00	4.61
141	142	1.258982	CTTGTCGCGCTATTCATCACC	59.741	52.381	5.56	0.00	0.00	4.02
142	143	1.332377	GCTTGTCGCGCTATTCATCAC	60.332	52.381	5.56	0.00	0.00	3.06
143	144	0.930310	GCTTGTCGCGCTATTCATCA	59.070	50.000	5.56	0.00	0.00	3.07
144	145	0.930310	TGCTTGTCGCGCTATTCATC	59.070	50.000	5.56	0.00	43.27	2.92
145	146	0.652592	GTGCTTGTCGCGCTATTCAT	59.347	50.000	5.56	0.00	45.56	2.57
146	147	1.682867	CGTGCTTGTCGCGCTATTCA	61.683	55.000	5.56	0.00	46.82	2.57
147	148	1.013323	CGTGCTTGTCGCGCTATTC	60.013	57.895	5.56	0.00	46.82	1.75
148	149	3.081133	CGTGCTTGTCGCGCTATT	58.919	55.556	5.56	0.00	46.82	1.73
154	155	1.282248	TAGTTGCTCGTGCTTGTCGC	61.282	55.000	11.19	0.00	40.48	5.19
155	156	1.350193	ATAGTTGCTCGTGCTTGTCG	58.650	50.000	11.19	0.00	40.48	4.35
156	157	5.258622	CAATAATAGTTGCTCGTGCTTGTC	58.741	41.667	11.19	0.00	40.48	3.18
157	158	4.094887	CCAATAATAGTTGCTCGTGCTTGT	59.905	41.667	11.19	0.00	40.48	3.16
180	181	8.979574	GCCGTCAACTATAATAATATCTATGGC	58.020	37.037	0.00	0.00	0.00	4.40
207	208	2.309613	TGCAAGGAAAGCACAGTGATT	58.690	42.857	4.15	0.00	37.02	2.57
237	240	7.608308	AGTGTAGAATCTTGATTTTCTCAGC	57.392	36.000	0.00	0.00	34.68	4.26
238	241	9.868277	ACTAGTGTAGAATCTTGATTTTCTCAG	57.132	33.333	0.00	0.00	34.68	3.35
482	509	6.040247	TGATCTAATTACAAGTACACCTGCG	58.960	40.000	0.00	0.00	0.00	5.18
502	963	8.720562	CCCTAAAATTTTGTTGTTGGAATGATC	58.279	33.333	13.76	0.00	0.00	2.92
566	1028	7.894376	ATTGTCCAAAGCATTATTTTGACAG	57.106	32.000	6.31	0.00	42.38	3.51
597	1059	3.735208	CGATCCACATAGCTTCTGACGTT	60.735	47.826	0.00	0.00	0.00	3.99
661	1151	4.121317	TCACGCGTTCTTTCCTTTTTCTA	58.879	39.130	10.22	0.00	0.00	2.10
727	1218	7.037438	TGGTACGTACTTGATCAAAATAGACC	58.963	38.462	24.07	12.47	0.00	3.85
785	1292	4.394729	TGTGTACCTGGATTTTGGACTTC	58.605	43.478	0.00	0.00	0.00	3.01
822	1332	1.678635	CATGTGCGGTTGGTGGGAT	60.679	57.895	0.00	0.00	0.00	3.85
884	1403	2.526873	AGGCAGTGTCGGGTCCTT	60.527	61.111	0.00	0.00	0.00	3.36
1170	1691	1.078159	TGTGCCTGAGGGGAGTACTTA	59.922	52.381	0.00	0.00	37.23	2.24
1527	2050	2.829043	TACACATGTGCCCGCGAGTC	62.829	60.000	25.68	0.00	0.00	3.36
1529	2052	1.089481	AATACACATGTGCCCGCGAG	61.089	55.000	25.68	0.00	0.00	5.03
1534	2057	9.840427	GAATATACATAAAATACACATGTGCCC	57.160	33.333	25.68	0.00	34.78	5.36
1938	2470	2.951642	ACACCAGAAACAGGAACATGTG	59.048	45.455	0.00	0.00	32.52	3.21
2017	2557	3.117512	CCCCAAGAACATAATAGGGCAGT	60.118	47.826	0.00	0.00	34.93	4.40
2037	2594	1.722034	TAGTGATCATCCTCCAGCCC	58.278	55.000	0.00	0.00	0.00	5.19
2100	2675	8.511321	CAGCTGGTATTTTTACATTACTGAACA	58.489	33.333	5.57	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.