AutoCloner

Multiple sequence alignment - TraesCS7B01G390700

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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	TraesCS7B01G390700	chr7B	100.000	2813	0	0	1	2813	657084008	657086820	0.000000e+00	5195.0
1	TraesCS7B01G390700	chr7B	84.029	1509	193	29	634	2114	657663279	657661791	0.000000e+00	1408.0
2	TraesCS7B01G390700	chr7B	80.920	1630	213	53	522	2117	656529695	656528130	0.000000e+00	1197.0
3	TraesCS7B01G390700	chr7B	80.850	1530	233	38	634	2114	657313575	657315093	0.000000e+00	1147.0
4	TraesCS7B01G390700	chr7B	79.913	1613	249	38	634	2190	656928801	656930394	0.000000e+00	1114.0
5	TraesCS7B01G390700	chr7B	78.092	1415	225	40	572	1946	657420492	657421861	0.000000e+00	817.0
6	TraesCS7B01G390700	chr7B	83.890	838	84	29	1810	2611	657077133	657077955	0.000000e+00	752.0
7	TraesCS7B01G390700	chr7B	86.480	429	49	9	2243	2668	656550288	656549866	1.970000e-126	462.0
8	TraesCS7B01G390700	chr7B	80.550	509	86	7	634	1129	657338848	657339356	2.050000e-101	379.0
9	TraesCS7B01G390700	chr7B	85.794	359	45	6	2243	2598	657077963	657078318	2.650000e-100	375.0
10	TraesCS7B01G390700	chr7B	89.474	228	23	1	2251	2478	610766503	610766277	1.280000e-73	287.0
11	TraesCS7B01G390700	chr7D	91.850	2405	138	27	443	2807	586700026	586702412	0.000000e+00	3302.0
12	TraesCS7B01G390700	chr7D	78.629	2101	343	51	634	2668	586508922	586506862	0.000000e+00	1295.0
13	TraesCS7B01G390700	chr7D	88.219	1078	82	20	244	1303	586502261	586501211	0.000000e+00	1245.0
14	TraesCS7B01G390700	chr7D	80.686	1517	229	37	634	2114	586708185	586709673	0.000000e+00	1120.0
15	TraesCS7B01G390700	chr7D	83.951	891	116	17	1467	2343	586501062	586500185	0.000000e+00	828.0
16	TraesCS7B01G390700	chr7D	76.557	1493	256	43	522	1953	586754219	586755678	0.000000e+00	732.0
17	TraesCS7B01G390700	chr7A	88.810	1984	147	36	131	2055	677824803	677826770	0.000000e+00	2364.0
18	TraesCS7B01G390700	chr7A	83.333	1590	225	20	556	2114	678146284	678144704	0.000000e+00	1432.0
19	TraesCS7B01G390700	chr7A	79.971	2057	277	64	634	2598	677821388	677823401	0.000000e+00	1391.0
20	TraesCS7B01G390700	chr7A	80.139	1299	210	30	634	1896	677833050	677834336	0.000000e+00	926.0
21	TraesCS7B01G390700	chr7A	76.194	1487	270	37	634	2068	677839001	677840455	0.000000e+00	708.0
22	TraesCS7B01G390700	chr7A	76.845	1179	197	31	588	1727	677995527	677994386	1.870000e-166	595.0
23	TraesCS7B01G390700	chr4B	89.474	228	23	1	2251	2478	366572868	366572642	1.280000e-73	287.0
24	TraesCS7B01G390700	chr1B	89.474	228	23	1	2251	2478	447990103	447990329	1.280000e-73	287.0
25	TraesCS7B01G390700	chr5B	89.035	228	24	1	2251	2478	638209991	638209765	5.930000e-72	281.0
26	TraesCS7B01G390700	chr5B	91.379	58	5	0	2133	2190	638210179	638210122	2.320000e-11	80.5
27	TraesCS7B01G390700	chr3B	85.926	135	14	3	2	133	723523934	723523802	3.780000e-29	139.0
28	TraesCS7B01G390700	chr3B	84.426	122	11	5	1	117	781627293	781627411	2.290000e-21	113.0
29	TraesCS7B01G390700	chr1D	87.603	121	11	2	2	118	484472263	484472383	1.360000e-28	137.0
30	TraesCS7B01G390700	chr3D	83.448	145	10	11	1	140	49476188	49476053	3.810000e-24	122.0
31	TraesCS7B01G390700	chr2D	88.660	97	8	1	2	95	422093734	422093638	6.370000e-22	115.0
32	TraesCS7B01G390700	chr2B	83.333	132	14	5	2	128	621780530	621780402	6.370000e-22	115.0
33	TraesCS7B01G390700	chr2B	81.395	129	19	3	2	127	775436802	775436928	1.780000e-17	100.0
34	TraesCS7B01G390700	chr4D	82.443	131	19	2	2	129	111131785	111131656	8.240000e-21	111.0
35	TraesCS7B01G390700	chr2A	83.740	123	11	6	3	118	599448460	599448340	1.070000e-19	108.0

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	TraesCS7B01G390700	chr7B	657084008	657086820	2812	False	5195.0	5195	100.0000	1	2813	1	chr7B.!!$F2	2812
1	TraesCS7B01G390700	chr7B	657661791	657663279	1488	True	1408.0	1408	84.0290	634	2114	1	chr7B.!!$R4	1480
2	TraesCS7B01G390700	chr7B	656528130	656529695	1565	True	1197.0	1197	80.9200	522	2117	1	chr7B.!!$R2	1595
3	TraesCS7B01G390700	chr7B	657313575	657315093	1518	False	1147.0	1147	80.8500	634	2114	1	chr7B.!!$F3	1480
4	TraesCS7B01G390700	chr7B	656928801	656930394	1593	False	1114.0	1114	79.9130	634	2190	1	chr7B.!!$F1	1556
5	TraesCS7B01G390700	chr7B	657420492	657421861	1369	False	817.0	817	78.0920	572	1946	1	chr7B.!!$F5	1374
6	TraesCS7B01G390700	chr7B	657077133	657078318	1185	False	563.5	752	84.8420	1810	2611	2	chr7B.!!$F6	801
7	TraesCS7B01G390700	chr7B	657338848	657339356	508	False	379.0	379	80.5500	634	1129	1	chr7B.!!$F4	495
8	TraesCS7B01G390700	chr7D	586700026	586702412	2386	False	3302.0	3302	91.8500	443	2807	1	chr7D.!!$F1	2364
9	TraesCS7B01G390700	chr7D	586506862	586508922	2060	True	1295.0	1295	78.6290	634	2668	1	chr7D.!!$R1	2034
10	TraesCS7B01G390700	chr7D	586708185	586709673	1488	False	1120.0	1120	80.6860	634	2114	1	chr7D.!!$F2	1480
11	TraesCS7B01G390700	chr7D	586500185	586502261	2076	True	1036.5	1245	86.0850	244	2343	2	chr7D.!!$R2	2099
12	TraesCS7B01G390700	chr7D	586754219	586755678	1459	False	732.0	732	76.5570	522	1953	1	chr7D.!!$F3	1431
13	TraesCS7B01G390700	chr7A	677821388	677826770	5382	False	1877.5	2364	84.3905	131	2598	2	chr7A.!!$F3	2467
14	TraesCS7B01G390700	chr7A	678144704	678146284	1580	True	1432.0	1432	83.3330	556	2114	1	chr7A.!!$R2	1558
15	TraesCS7B01G390700	chr7A	677833050	677834336	1286	False	926.0	926	80.1390	634	1896	1	chr7A.!!$F1	1262
16	TraesCS7B01G390700	chr7A	677839001	677840455	1454	False	708.0	708	76.1940	634	2068	1	chr7A.!!$F2	1434
17	TraesCS7B01G390700	chr7A	677994386	677995527	1141	True	595.0	595	76.8450	588	1727	1	chr7A.!!$R1	1139

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
486	3798	0.462759	GTGGGCCTTCTCCTCAATCG	60.463	60.000	4.53	0.0	0.00	3.34	F
1164	4594	1.078848	CCAGAACTGGGGCTCGAAG	60.079	63.158	12.54	0.0	46.81	3.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1756	5272	1.674057	GTAGGCAGGACAGCAGTGT	59.326	57.895	0.0	0.0	40.71	3.55	R
2076	5634	2.095919	GCTTAGCCAAAACAGGTACACG	60.096	50.000	0.0	0.0	0.00	4.49	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	3.951332	TTTCGGCTCGCTTCAGTG	58.049	55.556	0.00	0.00	0.00	3.66
18	19	1.069090	TTTCGGCTCGCTTCAGTGT	59.931	52.632	0.00	0.00	0.00	3.55
19	20	0.531974	TTTCGGCTCGCTTCAGTGTT	60.532	50.000	0.00	0.00	0.00	3.32
20	21	0.531974	TTCGGCTCGCTTCAGTGTTT	60.532	50.000	0.00	0.00	0.00	2.83
21	22	1.205064	CGGCTCGCTTCAGTGTTTG	59.795	57.895	0.00	0.00	0.00	2.93
22	23	1.498865	CGGCTCGCTTCAGTGTTTGT	61.499	55.000	0.00	0.00	0.00	2.83
24	25	1.871039	GGCTCGCTTCAGTGTTTGTAA	59.129	47.619	0.00	0.00	0.00	2.41
25	26	2.484264	GGCTCGCTTCAGTGTTTGTAAT	59.516	45.455	0.00	0.00	0.00	1.89
27	28	3.722082	GCTCGCTTCAGTGTTTGTAATCG	60.722	47.826	0.00	0.00	0.00	3.34
29	30	2.724839	CGCTTCAGTGTTTGTAATCGCC	60.725	50.000	0.00	0.00	0.00	5.54
30	31	2.724839	GCTTCAGTGTTTGTAATCGCCG	60.725	50.000	0.00	0.00	0.00	6.46
32	33	0.796312	CAGTGTTTGTAATCGCCGCT	59.204	50.000	0.00	0.00	0.00	5.52
33	34	1.996898	CAGTGTTTGTAATCGCCGCTA	59.003	47.619	0.00	0.00	0.00	4.26
34	35	2.029244	CAGTGTTTGTAATCGCCGCTAG	59.971	50.000	0.00	0.00	0.00	3.42
35	36	1.326548	GTGTTTGTAATCGCCGCTAGG	59.673	52.381	0.00	0.00	41.62	3.02
43	44	3.849951	CGCCGCTAGGTGGTCCAT	61.850	66.667	0.00	0.00	44.11	3.41
45	46	1.367840	GCCGCTAGGTGGTCCATAG	59.632	63.158	0.00	0.00	40.50	2.23
46	47	1.113517	GCCGCTAGGTGGTCCATAGA	61.114	60.000	0.00	0.00	40.50	1.98
47	48	1.633774	CCGCTAGGTGGTCCATAGAT	58.366	55.000	0.00	0.00	35.89	1.98
48	49	1.546476	CCGCTAGGTGGTCCATAGATC	59.454	57.143	0.00	0.00	35.89	2.75
49	50	2.520069	CGCTAGGTGGTCCATAGATCT	58.480	52.381	0.00	0.00	35.89	2.75
50	51	3.561528	CCGCTAGGTGGTCCATAGATCTA	60.562	52.174	4.57	4.57	35.89	1.98
51	52	3.692101	CGCTAGGTGGTCCATAGATCTAG	59.308	52.174	8.70	3.77	35.89	2.43
52	53	4.565861	CGCTAGGTGGTCCATAGATCTAGA	60.566	50.000	8.70	0.00	35.89	2.43
55	56	3.138653	AGGTGGTCCATAGATCTAGACGT	59.861	47.826	8.70	0.00	35.89	4.34
56	57	4.350225	AGGTGGTCCATAGATCTAGACGTA	59.650	45.833	8.70	2.03	35.89	3.57
57	58	5.068636	GGTGGTCCATAGATCTAGACGTAA	58.931	45.833	8.70	0.00	0.00	3.18
59	60	6.208994	GGTGGTCCATAGATCTAGACGTAATT	59.791	42.308	8.70	0.00	0.00	1.40
60	61	7.255871	GGTGGTCCATAGATCTAGACGTAATTT	60.256	40.741	8.70	0.00	0.00	1.82
61	62	8.142551	GTGGTCCATAGATCTAGACGTAATTTT	58.857	37.037	8.70	0.00	0.00	1.82
90	91	6.516739	TTTCTTGTGTTTGTTGTACCATGA	57.483	33.333	0.00	0.00	0.00	3.07
91	92	6.707440	TTCTTGTGTTTGTTGTACCATGAT	57.293	33.333	0.00	0.00	0.00	2.45
94	95	6.319911	TCTTGTGTTTGTTGTACCATGATTGA	59.680	34.615	0.00	0.00	0.00	2.57
95	96	6.456795	TGTGTTTGTTGTACCATGATTGAA	57.543	33.333	0.00	0.00	0.00	2.69
96	97	6.502652	TGTGTTTGTTGTACCATGATTGAAG	58.497	36.000	0.00	0.00	0.00	3.02
97	98	6.319911	TGTGTTTGTTGTACCATGATTGAAGA	59.680	34.615	0.00	0.00	0.00	2.87
98	99	6.636850	GTGTTTGTTGTACCATGATTGAAGAC	59.363	38.462	0.00	0.00	0.00	3.01
99	100	5.605564	TTGTTGTACCATGATTGAAGACG	57.394	39.130	0.00	0.00	0.00	4.18
100	101	4.888917	TGTTGTACCATGATTGAAGACGA	58.111	39.130	0.00	0.00	0.00	4.20
101	102	5.301555	TGTTGTACCATGATTGAAGACGAA	58.698	37.500	0.00	0.00	0.00	3.85
102	103	5.937540	TGTTGTACCATGATTGAAGACGAAT	59.062	36.000	0.00	0.00	0.00	3.34
103	104	7.100409	TGTTGTACCATGATTGAAGACGAATA	58.900	34.615	0.00	0.00	0.00	1.75
104	105	7.277760	TGTTGTACCATGATTGAAGACGAATAG	59.722	37.037	0.00	0.00	0.00	1.73
105	106	7.107639	TGTACCATGATTGAAGACGAATAGA	57.892	36.000	0.00	0.00	0.00	1.98
106	107	7.726216	TGTACCATGATTGAAGACGAATAGAT	58.274	34.615	0.00	0.00	0.00	1.98
124	125	8.943909	GAATAGATCGAAAGTTTTCCTAGGAA	57.056	34.615	20.72	20.72	33.68	3.36
125	126	9.379791	GAATAGATCGAAAGTTTTCCTAGGAAA	57.620	33.333	29.41	29.41	41.69	3.13
235	3531	7.362574	GCACTTTACCAATGGCTAGTTATTCAA	60.363	37.037	0.00	0.00	0.00	2.69
241	3537	8.766994	ACCAATGGCTAGTTATTCAATTATGT	57.233	30.769	0.00	0.00	0.00	2.29
277	3573	9.816787	ACCCAGACCACTAATTAATAAAAAGAA	57.183	29.630	0.00	0.00	0.00	2.52
292	3598	7.951530	ATAAAAAGAAAAACTGGTGCATGAG	57.048	32.000	0.00	0.00	0.00	2.90
311	3617	3.010420	GAGCCACTCTAAAATCCACACC	58.990	50.000	0.00	0.00	0.00	4.16
312	3618	2.375174	AGCCACTCTAAAATCCACACCA	59.625	45.455	0.00	0.00	0.00	4.17
313	3619	3.153919	GCCACTCTAAAATCCACACCAA	58.846	45.455	0.00	0.00	0.00	3.67
476	3788	3.119096	GCTTCGTCGTGGGCCTTC	61.119	66.667	4.53	0.00	0.00	3.46
480	3792	3.382832	CGTCGTGGGCCTTCTCCT	61.383	66.667	4.53	0.00	0.00	3.69
486	3798	0.462759	GTGGGCCTTCTCCTCAATCG	60.463	60.000	4.53	0.00	0.00	3.34
487	3799	1.524849	GGGCCTTCTCCTCAATCGC	60.525	63.158	0.84	0.00	0.00	4.58
497	3809	1.137675	TCCTCAATCGCAGACCATCAG	59.862	52.381	0.00	0.00	42.51	2.90
507	3819	1.517832	GACCATCAGTCAGTCCCCG	59.482	63.158	0.00	0.00	45.55	5.73
749	4121	4.147449	CCTGGCGCGACCTCATCA	62.147	66.667	10.82	0.00	40.22	3.07
766	4138	2.115910	ACCGACCCCGTGTACAGA	59.884	61.111	0.00	0.00	0.00	3.41
1164	4594	1.078848	CCAGAACTGGGGCTCGAAG	60.079	63.158	12.54	0.00	46.81	3.79
1181	4611	3.515502	TCGAAGAAATCCCTGTCTGTGAT	59.484	43.478	0.00	0.00	0.00	3.06
1223	4653	1.985159	AGAAACTGGTGCATGGGTAGA	59.015	47.619	0.00	0.00	0.00	2.59
1319	4775	3.102972	ACCTGCTCACATATCAGTCTGT	58.897	45.455	0.00	0.00	0.00	3.41
1336	4792	2.036604	TCTGTGTTGGCGATAGTTGACA	59.963	45.455	0.00	0.00	39.35	3.58
1338	4794	1.463444	GTGTTGGCGATAGTTGACACC	59.537	52.381	0.00	0.00	37.74	4.16
1374	4837	1.442526	GAACCATCCTGCTGCCGATG	61.443	60.000	15.95	15.95	36.45	3.84
1408	4877	2.084546	GTTTCTCAGGTTTCATCGGGG	58.915	52.381	0.00	0.00	0.00	5.73
1756	5272	9.327628	CATTTATGCAATTTTTCCCATATGTGA	57.672	29.630	1.24	0.00	0.00	3.58
1879	5412	3.963665	TCCGTTGCATTTTCAAGTGAAG	58.036	40.909	0.00	0.00	35.21	3.02
2016	5569	2.604914	CTCATGGATGTGTTAGTGCGAC	59.395	50.000	0.00	0.00	0.00	5.19
2068	5626	5.050490	GCAACAAGTACGGATGTATGAGAT	58.950	41.667	3.04	0.00	32.11	2.75
2076	5634	4.495422	ACGGATGTATGAGATATTTCCGC	58.505	43.478	8.25	0.00	41.71	5.54
2177	5735	2.361757	TGTTCTGTGCCTTTTGATGTGG	59.638	45.455	0.00	0.00	0.00	4.17
2205	5785	2.462456	TGAGGCAGTGTGTTCTGATC	57.538	50.000	0.00	0.00	37.61	2.92
2211	5794	3.755378	GGCAGTGTGTTCTGATCTGAATT	59.245	43.478	16.85	0.86	37.61	2.17
2319	6274	5.678107	GCATTGCTAAGATTTTCTGGGTCTG	60.678	44.000	0.16	0.00	0.00	3.51
2361	6317	9.166173	TGATGTTATATTCACAGAAGTTTCCAG	57.834	33.333	0.00	0.00	0.00	3.86
2372	6328	5.702670	ACAGAAGTTTCCAGATGTGTACATG	59.297	40.000	0.00	0.00	36.57	3.21
2532	6491	9.262358	GATTATCTAGTTTAATTTCTGGCGTCT	57.738	33.333	0.00	0.00	0.00	4.18
2560	6519	1.593196	ACAGTGTTGGTGAACCATCG	58.407	50.000	2.34	0.00	46.97	3.84
2569	6529	5.533154	TGTTGGTGAACCATCGATTTAACTT	59.467	36.000	2.34	0.00	46.97	2.66
2580	6540	6.381801	CATCGATTTAACTTTGTTCCAGCTT	58.618	36.000	0.00	0.00	0.00	3.74
2598	6558	6.664816	TCCAGCTTCAACAATTTAGGATGAAT	59.335	34.615	0.00	0.00	30.39	2.57
2616	6576	9.343994	AGGATGAATGTATTATCCCTTGTCTAT	57.656	33.333	0.00	0.00	41.00	1.98
2725	6685	2.509569	TGTCACGCAATGGTTAATGGT	58.490	42.857	0.00	0.00	0.00	3.55
2807	6767	4.560128	CCGTATGAATGGGTATGAGACAG	58.440	47.826	0.00	0.00	0.00	3.51
2808	6768	4.280929	CCGTATGAATGGGTATGAGACAGA	59.719	45.833	0.00	0.00	0.00	3.41
2809	6769	5.221441	CCGTATGAATGGGTATGAGACAGAA	60.221	44.000	0.00	0.00	0.00	3.02
2810	6770	6.459066	CGTATGAATGGGTATGAGACAGAAT	58.541	40.000	0.00	0.00	0.00	2.40
2811	6771	6.931281	CGTATGAATGGGTATGAGACAGAATT	59.069	38.462	0.00	0.00	0.00	2.17
2812	6772	8.088365	CGTATGAATGGGTATGAGACAGAATTA	58.912	37.037	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	1.205064	CAAACACTGAAGCGAGCCG	59.795	57.895	0.00	0.00	0.00	5.52
6	7	3.722082	GCGATTACAAACACTGAAGCGAG	60.722	47.826	0.00	0.00	0.00	5.03
7	8	2.156891	GCGATTACAAACACTGAAGCGA	59.843	45.455	0.00	0.00	0.00	4.93
9	10	2.724839	CGGCGATTACAAACACTGAAGC	60.725	50.000	0.00	0.00	0.00	3.86
10	11	2.724839	GCGGCGATTACAAACACTGAAG	60.725	50.000	12.98	0.00	0.00	3.02
11	12	1.195900	GCGGCGATTACAAACACTGAA	59.804	47.619	12.98	0.00	0.00	3.02
13	14	0.796312	AGCGGCGATTACAAACACTG	59.204	50.000	12.98	0.00	0.00	3.66
14	15	2.268298	CTAGCGGCGATTACAAACACT	58.732	47.619	12.98	0.00	0.00	3.55
15	16	1.326548	CCTAGCGGCGATTACAAACAC	59.673	52.381	12.98	0.00	0.00	3.32
16	17	1.066716	ACCTAGCGGCGATTACAAACA	60.067	47.619	12.98	0.00	0.00	2.83
17	18	1.326548	CACCTAGCGGCGATTACAAAC	59.673	52.381	12.98	0.00	0.00	2.93
18	19	1.647346	CACCTAGCGGCGATTACAAA	58.353	50.000	12.98	0.00	0.00	2.83
19	20	0.179094	CCACCTAGCGGCGATTACAA	60.179	55.000	12.98	0.00	0.00	2.41
20	21	1.324740	ACCACCTAGCGGCGATTACA	61.325	55.000	12.98	0.00	0.00	2.41
21	22	0.596859	GACCACCTAGCGGCGATTAC	60.597	60.000	12.98	0.00	0.00	1.89
22	23	1.737816	GACCACCTAGCGGCGATTA	59.262	57.895	12.98	0.50	0.00	1.75
24	25	3.537874	GGACCACCTAGCGGCGAT	61.538	66.667	12.98	7.15	0.00	4.58
25	26	2.914756	TATGGACCACCTAGCGGCGA	62.915	60.000	12.98	0.00	37.04	5.54
27	28	1.113517	TCTATGGACCACCTAGCGGC	61.114	60.000	0.00	0.00	37.04	6.53
29	30	2.520069	AGATCTATGGACCACCTAGCG	58.480	52.381	0.00	0.00	37.04	4.26
30	31	4.703093	GTCTAGATCTATGGACCACCTAGC	59.297	50.000	2.11	0.00	37.04	3.42
32	33	4.350225	ACGTCTAGATCTATGGACCACCTA	59.650	45.833	13.67	0.00	37.04	3.08
33	34	3.138653	ACGTCTAGATCTATGGACCACCT	59.861	47.826	13.67	0.00	37.04	4.00
34	35	3.488363	ACGTCTAGATCTATGGACCACC	58.512	50.000	13.67	0.00	0.00	4.61
35	36	6.821031	ATTACGTCTAGATCTATGGACCAC	57.179	41.667	13.67	0.00	0.00	4.16
82	83	7.061210	CGATCTATTCGTCTTCAATCATGGTAC	59.939	40.741	0.00	0.00	43.01	3.34
83	84	7.084486	CGATCTATTCGTCTTCAATCATGGTA	58.916	38.462	0.00	0.00	43.01	3.25
85	86	6.386897	CGATCTATTCGTCTTCAATCATGG	57.613	41.667	0.00	0.00	43.01	3.66
99	100	8.943909	TTCCTAGGAAAACTTTCGATCTATTC	57.056	34.615	22.27	0.00	38.06	1.75
100	101	9.734984	TTTTCCTAGGAAAACTTTCGATCTATT	57.265	29.630	35.59	0.00	45.59	1.73
130	131	9.958180	TTTAGATCTGGAAACATATTTGAGTCA	57.042	29.630	5.18	0.00	41.51	3.41
132	133	9.965902	ACTTTAGATCTGGAAACATATTTGAGT	57.034	29.630	5.18	0.00	41.51	3.41
193	3480	8.697292	TGGTAAAGTGCTTGGTTTATTTTTACT	58.303	29.630	0.00	0.00	32.94	2.24
201	3488	4.262249	GCCATTGGTAAAGTGCTTGGTTTA	60.262	41.667	4.26	0.00	0.00	2.01
216	3505	8.766994	ACATAATTGAATAACTAGCCATTGGT	57.233	30.769	4.26	0.00	0.00	3.67
275	3571	1.340889	TGGCTCATGCACCAGTTTTTC	59.659	47.619	2.65	0.00	41.91	2.29
277	3573	0.675633	GTGGCTCATGCACCAGTTTT	59.324	50.000	6.76	0.00	41.91	2.43
279	3575	0.607489	GAGTGGCTCATGCACCAGTT	60.607	55.000	13.51	3.84	39.76	3.16
286	3592	3.065925	GTGGATTTTAGAGTGGCTCATGC	59.934	47.826	0.00	0.00	38.76	4.06
289	3595	3.559171	GGTGTGGATTTTAGAGTGGCTCA	60.559	47.826	0.00	0.00	32.06	4.26
292	3598	2.790433	TGGTGTGGATTTTAGAGTGGC	58.210	47.619	0.00	0.00	0.00	5.01
330	3639	7.760131	TTCAAAGTTGAGCTGAAAAATTGAG	57.240	32.000	0.00	0.00	38.61	3.02
335	3644	9.218440	AGAAAATTTCAAAGTTGAGCTGAAAAA	57.782	25.926	8.55	0.00	41.14	1.94
464	3776	1.827399	TTGAGGAGAAGGCCCACGAC	61.827	60.000	0.00	0.00	0.00	4.34
476	3788	1.137675	TGATGGTCTGCGATTGAGGAG	59.862	52.381	0.00	0.00	0.00	3.69
480	3792	1.550072	TGACTGATGGTCTGCGATTGA	59.450	47.619	0.00	0.00	44.74	2.57
486	3798	0.107945	GGGACTGACTGATGGTCTGC	60.108	60.000	0.00	0.00	44.37	4.26
487	3799	0.539051	GGGGACTGACTGATGGTCTG	59.461	60.000	0.00	0.00	44.74	3.51
749	4121	1.114722	TTTCTGTACACGGGGTCGGT	61.115	55.000	0.00	0.00	41.39	4.69
766	4138	3.515602	AGGGACTGCACAATCTTCTTT	57.484	42.857	0.00	0.00	37.18	2.52
1104	4531	1.067846	TCGAACACATGGAACTCTCGG	60.068	52.381	0.00	0.00	0.00	4.63
1161	4591	4.813697	GCTATCACAGACAGGGATTTCTTC	59.186	45.833	0.00	0.00	36.88	2.87
1164	4594	4.125703	CTGCTATCACAGACAGGGATTTC	58.874	47.826	0.00	0.00	36.88	2.17
1260	4690	2.452600	AAACTCCAGGCTGACCAAAA	57.547	45.000	17.94	0.00	39.06	2.44
1297	4727	3.517100	ACAGACTGATATGTGAGCAGGTT	59.483	43.478	10.08	0.00	46.38	3.50
1319	4775	1.803334	GGTGTCAACTATCGCCAACA	58.197	50.000	0.00	0.00	34.73	3.33
1338	4794	3.014623	GGTTCTCCATTTTACCCCTTCG	58.985	50.000	0.00	0.00	0.00	3.79
1374	4837	1.732809	GAGAAACCCTTAGCAGCGAAC	59.267	52.381	0.00	0.00	0.00	3.95
1431	4900	1.947456	TGACTATCACGGGAGTCGATG	59.053	52.381	0.00	0.00	44.22	3.84
1756	5272	1.674057	GTAGGCAGGACAGCAGTGT	59.326	57.895	0.00	0.00	40.71	3.55
1879	5412	5.765182	TCTCCCTTTGAATCTTTGTGAAGAC	59.235	40.000	0.00	0.00	44.27	3.01
1941	5482	6.647334	TGAAAACCAATGCAGATCAAACTA	57.353	33.333	0.00	0.00	0.00	2.24
2068	5626	2.747396	AACAGGTACACGCGGAAATA	57.253	45.000	12.47	0.00	0.00	1.40
2076	5634	2.095919	GCTTAGCCAAAACAGGTACACG	60.096	50.000	0.00	0.00	0.00	4.49
2177	5735	3.403038	ACACACTGCCTCATACTTGTTC	58.597	45.455	0.00	0.00	0.00	3.18
2319	6274	4.574599	ACATCAAACCAGAAAGAACAGC	57.425	40.909	0.00	0.00	0.00	4.40
2358	6314	6.371271	TCACATTACAACATGTACACATCTGG	59.629	38.462	0.00	0.00	35.51	3.86
2361	6317	7.973601	TGATCACATTACAACATGTACACATC	58.026	34.615	0.00	0.00	35.51	3.06
2372	6328	5.525012	TGAGCTAGCATGATCACATTACAAC	59.475	40.000	18.83	0.00	34.15	3.32
2532	6491	3.814625	TCACCAACACTGTTGAAGCATA	58.185	40.909	21.38	0.62	0.00	3.14
2560	6519	6.978080	TGTTGAAGCTGGAACAAAGTTAAATC	59.022	34.615	8.07	0.00	38.70	2.17
2569	6529	5.596361	TCCTAAATTGTTGAAGCTGGAACAA	59.404	36.000	20.17	20.17	44.07	2.83
2610	6570	8.896320	TGTTGACAAGTAAAAAGCTATAGACA	57.104	30.769	3.21	0.00	0.00	3.41
2616	6576	7.214381	TCTAGCTGTTGACAAGTAAAAAGCTA	58.786	34.615	17.42	17.42	40.14	3.32
2711	6671	4.244862	CCAGAACAACCATTAACCATTGC	58.755	43.478	0.00	0.00	0.00	3.56
2725	6685	5.376625	ACAAATCTGACTTAGCCAGAACAA	58.623	37.500	1.77	0.00	43.07	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.