AutoCloner

Multiple sequence alignment - TraesCS2D01G425500

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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	TraesCS2D01G425500	chr2D	100.000	4159	0	0	1	4159	537927608	537931766	0.000000e+00	7681.0
1	TraesCS2D01G425500	chr2D	90.323	124	12	0	4036	4159	440325008	440324885	3.330000e-36	163.0
2	TraesCS2D01G425500	chr2D	90.244	123	12	0	4036	4158	592616358	592616236	1.200000e-35	161.0
3	TraesCS2D01G425500	chr2D	74.772	329	70	11	1048	1368	629074190	629074513	7.250000e-28	135.0
4	TraesCS2D01G425500	chr2D	88.710	62	7	0	1632	1693	629074954	629075015	4.460000e-10	76.8
5	TraesCS2D01G425500	chr2A	96.913	2462	62	5	735	3183	680261222	680263682	0.000000e+00	4113.0
6	TraesCS2D01G425500	chr2A	90.043	693	39	8	3360	4046	680264403	680265071	0.000000e+00	870.0
7	TraesCS2D01G425500	chr2A	85.311	531	71	7	212	737	537233564	537234092	3.660000e-150	542.0
8	TraesCS2D01G425500	chr2A	93.636	220	4	3	3164	3373	680263695	680263914	1.870000e-83	320.0
9	TraesCS2D01G425500	chr2A	91.935	124	8	2	4036	4159	583841336	583841215	5.530000e-39	172.0
10	TraesCS2D01G425500	chr2A	74.242	330	70	13	1048	1368	758880901	758881224	1.570000e-24	124.0
11	TraesCS2D01G425500	chr2A	91.935	62	5	0	1632	1693	758881632	758881693	2.060000e-13	87.9
12	TraesCS2D01G425500	chr2B	94.407	2199	103	8	1964	4159	640607191	640609372	0.000000e+00	3362.0
13	TraesCS2D01G425500	chr2B	96.535	1241	42	1	735	1975	640598699	640599938	0.000000e+00	2052.0
14	TraesCS2D01G425500	chr2B	80.967	641	103	14	107	739	758876413	758877042	1.340000e-134	490.0
15	TraesCS2D01G425500	chr2B	86.290	124	17	0	4036	4159	89331073	89330950	7.250000e-28	135.0
16	TraesCS2D01G425500	chr2B	74.030	335	74	11	1048	1374	772121945	772121616	1.570000e-24	124.0
17	TraesCS2D01G425500	chr3D	88.018	676	72	8	69	737	561491717	561491044	0.000000e+00	791.0
18	TraesCS2D01G425500	chr3D	83.877	583	80	10	160	737	24569136	24569709	1.020000e-150	544.0
19	TraesCS2D01G425500	chr6A	73.736	1641	366	48	1513	3107	22547423	22549044	2.150000e-162	582.0
20	TraesCS2D01G425500	chr6A	89.565	115	11	1	4046	4159	2919373	2919259	1.210000e-30	145.0
21	TraesCS2D01G425500	chr6A	89.189	74	4	3	1295	1366	410583755	410583684	5.730000e-14	89.8
22	TraesCS2D01G425500	chr5B	84.563	583	76	10	160	737	710236198	710235625	2.170000e-157	566.0
23	TraesCS2D01G425500	chr7B	84.391	583	77	9	160	737	380072740	380073313	1.010000e-155	560.0
24	TraesCS2D01G425500	chr7B	84.391	583	77	10	160	737	648274080	648273507	1.010000e-155	560.0
25	TraesCS2D01G425500	chr1B	84.220	583	75	10	160	737	192142023	192141453	6.080000e-153	551.0
26	TraesCS2D01G425500	chr6B	73.366	1652	369	55	1505	3107	38926021	38927650	7.860000e-152	547.0
27	TraesCS2D01G425500	chr6B	88.750	80	4	4	1294	1370	472613844	472613767	4.430000e-15	93.5
28	TraesCS2D01G425500	chr6D	73.114	1644	371	55	1513	3107	24022881	24024502	4.760000e-144	521.0
29	TraesCS2D01G425500	chr6D	80.975	636	102	16	109	736	445913562	445912938	1.740000e-133	486.0
30	TraesCS2D01G425500	chr6D	89.916	119	12	0	4036	4154	414461172	414461290	2.000000e-33	154.0
31	TraesCS2D01G425500	chr6D	89.189	74	4	3	1295	1366	304735864	304735935	5.730000e-14	89.8
32	TraesCS2D01G425500	chr5A	74.561	570	128	13	110	673	644871658	644872216	2.500000e-57	233.0
33	TraesCS2D01G425500	chr1D	87.705	122	14	1	4036	4156	268725068	268725189	1.560000e-29	141.0
34	TraesCS2D01G425500	chr7A	84.127	126	18	2	4036	4159	42265576	42265701	2.030000e-23	121.0
35	TraesCS2D01G425500	chr3A	95.455	44	2	0	15	58	470843212	470843255	2.070000e-08	71.3

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	TraesCS2D01G425500	chr2D	537927608	537931766	4158	False	7681.000000	7681	100.000000	1	4159	1	chr2D.!!$F1	4158
1	TraesCS2D01G425500	chr2A	680261222	680265071	3849	False	1767.666667	4113	93.530667	735	4046	3	chr2A.!!$F2	3311
2	TraesCS2D01G425500	chr2A	537233564	537234092	528	False	542.000000	542	85.311000	212	737	1	chr2A.!!$F1	525
3	TraesCS2D01G425500	chr2B	640607191	640609372	2181	False	3362.000000	3362	94.407000	1964	4159	1	chr2B.!!$F2	2195
4	TraesCS2D01G425500	chr2B	640598699	640599938	1239	False	2052.000000	2052	96.535000	735	1975	1	chr2B.!!$F1	1240
5	TraesCS2D01G425500	chr2B	758876413	758877042	629	False	490.000000	490	80.967000	107	739	1	chr2B.!!$F3	632
6	TraesCS2D01G425500	chr3D	561491044	561491717	673	True	791.000000	791	88.018000	69	737	1	chr3D.!!$R1	668
7	TraesCS2D01G425500	chr3D	24569136	24569709	573	False	544.000000	544	83.877000	160	737	1	chr3D.!!$F1	577
8	TraesCS2D01G425500	chr6A	22547423	22549044	1621	False	582.000000	582	73.736000	1513	3107	1	chr6A.!!$F1	1594
9	TraesCS2D01G425500	chr5B	710235625	710236198	573	True	566.000000	566	84.563000	160	737	1	chr5B.!!$R1	577
10	TraesCS2D01G425500	chr7B	380072740	380073313	573	False	560.000000	560	84.391000	160	737	1	chr7B.!!$F1	577
11	TraesCS2D01G425500	chr7B	648273507	648274080	573	True	560.000000	560	84.391000	160	737	1	chr7B.!!$R1	577
12	TraesCS2D01G425500	chr1B	192141453	192142023	570	True	551.000000	551	84.220000	160	737	1	chr1B.!!$R1	577
13	TraesCS2D01G425500	chr6B	38926021	38927650	1629	False	547.000000	547	73.366000	1505	3107	1	chr6B.!!$F1	1602
14	TraesCS2D01G425500	chr6D	24022881	24024502	1621	False	521.000000	521	73.114000	1513	3107	1	chr6D.!!$F1	1594
15	TraesCS2D01G425500	chr6D	445912938	445913562	624	True	486.000000	486	80.975000	109	736	1	chr6D.!!$R1	627
16	TraesCS2D01G425500	chr5A	644871658	644872216	558	False	233.000000	233	74.561000	110	673	1	chr5A.!!$F1	563

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
528	541	0.623723	ATGCGTTTGTCCTATGGGGT	59.376	50.0	0.00	0.00	36.25	4.95	F
1410	1433	0.374758	CATGTACATGCGCACTGGTC	59.625	55.0	22.27	10.24	31.39	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2390	2443	0.800683	TCGCGATGTTCATGTCCGTC	60.801	55.0	3.71	0.0	0.0	4.79	R
3311	3411	0.742281	CAGGAAGGTGACATGGCGAG	60.742	60.0	0.00	0.0	0.0	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
23	24	4.801330	AACCTATGATCGTTCACTCACA	57.199	40.909	0.00	0.00	33.85	3.58
24	25	4.801330	ACCTATGATCGTTCACTCACAA	57.199	40.909	0.00	0.00	33.85	3.33
25	26	5.147330	ACCTATGATCGTTCACTCACAAA	57.853	39.130	0.00	0.00	33.85	2.83
26	27	5.734720	ACCTATGATCGTTCACTCACAAAT	58.265	37.500	0.00	0.00	33.85	2.32
27	28	6.173339	ACCTATGATCGTTCACTCACAAATT	58.827	36.000	0.00	0.00	33.85	1.82
28	29	6.313905	ACCTATGATCGTTCACTCACAAATTC	59.686	38.462	0.00	0.00	33.85	2.17
29	30	6.536582	CCTATGATCGTTCACTCACAAATTCT	59.463	38.462	0.00	0.00	33.85	2.40
30	31	6.808008	ATGATCGTTCACTCACAAATTCTT	57.192	33.333	0.00	0.00	33.85	2.52
31	32	7.905604	ATGATCGTTCACTCACAAATTCTTA	57.094	32.000	0.00	0.00	33.85	2.10
32	33	7.722795	TGATCGTTCACTCACAAATTCTTAA	57.277	32.000	0.00	0.00	0.00	1.85
33	34	8.148807	TGATCGTTCACTCACAAATTCTTAAA	57.851	30.769	0.00	0.00	0.00	1.52
34	35	8.616942	TGATCGTTCACTCACAAATTCTTAAAA	58.383	29.630	0.00	0.00	0.00	1.52
35	36	9.445786	GATCGTTCACTCACAAATTCTTAAAAA	57.554	29.630	0.00	0.00	0.00	1.94
36	37	9.965824	ATCGTTCACTCACAAATTCTTAAAAAT	57.034	25.926	0.00	0.00	0.00	1.82
37	38	9.445786	TCGTTCACTCACAAATTCTTAAAAATC	57.554	29.630	0.00	0.00	0.00	2.17
38	39	9.232082	CGTTCACTCACAAATTCTTAAAAATCA	57.768	29.630	0.00	0.00	0.00	2.57
40	41	8.801715	TCACTCACAAATTCTTAAAAATCAGC	57.198	30.769	0.00	0.00	0.00	4.26
41	42	8.632679	TCACTCACAAATTCTTAAAAATCAGCT	58.367	29.630	0.00	0.00	0.00	4.24
42	43	8.909671	CACTCACAAATTCTTAAAAATCAGCTC	58.090	33.333	0.00	0.00	0.00	4.09
43	44	7.805071	ACTCACAAATTCTTAAAAATCAGCTCG	59.195	33.333	0.00	0.00	0.00	5.03
44	45	6.582295	TCACAAATTCTTAAAAATCAGCTCGC	59.418	34.615	0.00	0.00	0.00	5.03
45	46	6.363088	CACAAATTCTTAAAAATCAGCTCGCA	59.637	34.615	0.00	0.00	0.00	5.10
46	47	6.922957	ACAAATTCTTAAAAATCAGCTCGCAA	59.077	30.769	0.00	0.00	0.00	4.85
47	48	6.934561	AATTCTTAAAAATCAGCTCGCAAC	57.065	33.333	0.00	0.00	0.00	4.17
48	49	5.431420	TTCTTAAAAATCAGCTCGCAACA	57.569	34.783	0.00	0.00	0.00	3.33
49	50	4.783242	TCTTAAAAATCAGCTCGCAACAC	58.217	39.130	0.00	0.00	0.00	3.32
50	51	4.274705	TCTTAAAAATCAGCTCGCAACACA	59.725	37.500	0.00	0.00	0.00	3.72
51	52	3.648339	AAAAATCAGCTCGCAACACAT	57.352	38.095	0.00	0.00	0.00	3.21
52	53	4.764679	AAAAATCAGCTCGCAACACATA	57.235	36.364	0.00	0.00	0.00	2.29
53	54	4.970662	AAAATCAGCTCGCAACACATAT	57.029	36.364	0.00	0.00	0.00	1.78
54	55	6.435430	AAAAATCAGCTCGCAACACATATA	57.565	33.333	0.00	0.00	0.00	0.86
55	56	6.435430	AAAATCAGCTCGCAACACATATAA	57.565	33.333	0.00	0.00	0.00	0.98
56	57	6.435430	AAATCAGCTCGCAACACATATAAA	57.565	33.333	0.00	0.00	0.00	1.40
57	58	6.624352	AATCAGCTCGCAACACATATAAAT	57.376	33.333	0.00	0.00	0.00	1.40
58	59	5.408204	TCAGCTCGCAACACATATAAATG	57.592	39.130	0.00	0.00	39.17	2.32
59	60	5.115480	TCAGCTCGCAACACATATAAATGA	58.885	37.500	0.00	0.00	36.54	2.57
60	61	5.234972	TCAGCTCGCAACACATATAAATGAG	59.765	40.000	0.00	0.00	36.54	2.90
61	62	5.234972	CAGCTCGCAACACATATAAATGAGA	59.765	40.000	0.00	0.00	36.54	3.27
62	63	5.235186	AGCTCGCAACACATATAAATGAGAC	59.765	40.000	0.00	0.00	36.54	3.36
63	64	5.006649	GCTCGCAACACATATAAATGAGACA	59.993	40.000	0.00	0.00	36.54	3.41
64	65	6.344572	TCGCAACACATATAAATGAGACAC	57.655	37.500	0.00	0.00	36.54	3.67
65	66	5.005299	TCGCAACACATATAAATGAGACACG	59.995	40.000	0.00	0.00	36.54	4.49
66	67	4.963953	GCAACACATATAAATGAGACACGC	59.036	41.667	0.00	0.00	36.54	5.34
67	68	5.447144	GCAACACATATAAATGAGACACGCA	60.447	40.000	0.00	0.00	36.54	5.24
210	213	1.115930	GCGGGAGGGCTTCAGATCTA	61.116	60.000	0.00	0.00	0.00	1.98
221	230	8.147244	AGGGCTTCAGATCTAGTTTTTAGTTA	57.853	34.615	0.00	0.00	0.00	2.24
305	317	6.973642	TCTGAAAATGGAATAATGTCCTCCT	58.026	36.000	0.00	0.00	38.62	3.69
333	346	1.287815	CTCGTTCCGGCTGTGTGTA	59.712	57.895	0.00	0.00	0.00	2.90
464	477	3.079578	CTGTGTGTCTGCAGGATGAATT	58.920	45.455	15.13	0.00	39.69	2.17
484	497	2.749776	TCTTTCGATCAACGCTTCACA	58.250	42.857	0.00	0.00	42.26	3.58
509	522	1.022451	GGCGGCGGTTGTTATTCTGA	61.022	55.000	9.78	0.00	0.00	3.27
516	529	3.669557	GCGGTTGTTATTCTGATGCGTTT	60.670	43.478	0.00	0.00	0.00	3.60
528	541	0.623723	ATGCGTTTGTCCTATGGGGT	59.376	50.000	0.00	0.00	36.25	4.95
601	616	0.692419	ATGAGGAAGGGGCGATGAGT	60.692	55.000	0.00	0.00	0.00	3.41
624	639	2.281484	GCCTTCGGCTCACACCAA	60.281	61.111	0.00	0.00	46.69	3.67
729	745	7.776933	TGATGAATAGATCGGAAGTTTTCTG	57.223	36.000	0.00	0.00	37.39	3.02
774	793	3.988517	GTGAGTGCGGATATTAAGCTACC	59.011	47.826	0.00	0.00	0.00	3.18
1059	1078	2.801631	GGGGATGGAGGACGAGCAG	61.802	68.421	0.00	0.00	0.00	4.24
1125	1144	3.248171	GAGACGATCACGGTGCGC	61.248	66.667	0.00	0.00	44.46	6.09
1410	1433	0.374758	CATGTACATGCGCACTGGTC	59.625	55.000	22.27	10.24	31.39	4.02
1465	1488	1.467342	GTTTGGGACGTACATTCTGGC	59.533	52.381	0.00	0.00	0.00	4.85
1580	1603	2.821366	AGCTTCGCCGGCATCTTG	60.821	61.111	28.98	9.94	0.00	3.02
1843	1866	3.119708	GCTTTTCGACGAGGGTTCTACTA	60.120	47.826	0.00	0.00	0.00	1.82
1911	1934	2.314246	AGATCACCATCTCGATGCTCA	58.686	47.619	0.00	0.00	33.71	4.26
2753	2809	1.438651	TCGCCATGACCGAGAAAAAG	58.561	50.000	0.00	0.00	0.00	2.27
2960	3016	0.686441	CCGTGATCTACCTGTGGGGA	60.686	60.000	0.00	0.00	38.76	4.81
3341	3441	1.064825	ACCTTCCTGGAACCGTTCAT	58.935	50.000	13.23	0.00	39.71	2.57
3389	3991	1.302671	TTTAACCCAACGCCCCTCG	60.303	57.895	0.00	0.00	45.38	4.63
3544	4150	3.063997	CACACCTCGCATTCAAGAATACC	59.936	47.826	0.00	0.00	0.00	2.73
3545	4151	2.614057	CACCTCGCATTCAAGAATACCC	59.386	50.000	0.00	0.00	0.00	3.69
3546	4152	2.222027	CCTCGCATTCAAGAATACCCC	58.778	52.381	0.00	0.00	0.00	4.95
3547	4153	1.867233	CTCGCATTCAAGAATACCCCG	59.133	52.381	0.00	0.00	0.00	5.73
3548	4154	0.307760	CGCATTCAAGAATACCCCGC	59.692	55.000	0.00	0.00	0.00	6.13
3549	4155	0.668535	GCATTCAAGAATACCCCGCC	59.331	55.000	0.00	0.00	0.00	6.13
3550	4156	1.318576	CATTCAAGAATACCCCGCCC	58.681	55.000	0.00	0.00	0.00	6.13
3551	4157	1.133792	CATTCAAGAATACCCCGCCCT	60.134	52.381	0.00	0.00	0.00	5.19
3552	4158	0.544697	TTCAAGAATACCCCGCCCTC	59.455	55.000	0.00	0.00	0.00	4.30
3553	4159	1.148498	CAAGAATACCCCGCCCTCC	59.852	63.158	0.00	0.00	0.00	4.30
3554	4160	2.440817	AAGAATACCCCGCCCTCCG	61.441	63.158	0.00	0.00	0.00	4.63
3555	4161	4.620937	GAATACCCCGCCCTCCGC	62.621	72.222	0.00	0.00	35.03	5.54
3610	4233	2.047274	CCCGATCTGCAACGGTGT	60.047	61.111	19.87	0.00	46.53	4.16
3664	4287	1.178534	CCCTCCATGTGGTTTTGCGT	61.179	55.000	0.00	0.00	36.34	5.24
3790	4413	2.171003	CCACCCCAAAGTCAAATCTCC	58.829	52.381	0.00	0.00	0.00	3.71
3794	4417	4.082026	CACCCCAAAGTCAAATCTCCAATC	60.082	45.833	0.00	0.00	0.00	2.67
3810	4433	1.952296	CAATCTCCAGGGCTAATGTGC	59.048	52.381	0.00	0.00	0.00	4.57
3830	4453	2.615869	CTTGCTCCTGCTCTAGTTGTC	58.384	52.381	0.00	0.00	40.48	3.18
3832	4455	0.528470	GCTCCTGCTCTAGTTGTCGT	59.472	55.000	0.00	0.00	36.03	4.34
3834	4457	2.359531	GCTCCTGCTCTAGTTGTCGTAT	59.640	50.000	0.00	0.00	36.03	3.06
3876	4499	1.097547	CCTAGCCTTCAATGCCACGG	61.098	60.000	0.00	0.00	0.00	4.94
3920	4543	4.129737	CCCGTCTCGCCACATCGT	62.130	66.667	0.00	0.00	0.00	3.73
3994	4617	2.968206	GACCGACCTTGCTACCGT	59.032	61.111	0.00	0.00	0.00	4.83
4043	4666	8.924511	TCCCTTAGGATTTCATGAATGATAAC	57.075	34.615	9.40	0.00	37.19	1.89
4049	4672	6.040166	AGGATTTCATGAATGATAACTGCCAC	59.960	38.462	9.40	0.00	36.56	5.01
4052	4675	3.622612	TCATGAATGATAACTGCCACACG	59.377	43.478	0.00	0.00	0.00	4.49
4056	4679	2.078849	TGATAACTGCCACACGTCAG	57.921	50.000	0.74	0.74	36.45	3.51
4072	4695	3.314331	AGGTGTGTGGCTCTCCGG	61.314	66.667	0.00	0.00	34.14	5.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.275494	TGTGAGTGAACGATCATAGGTTTA	57.725	37.500	0.00	0.00	38.01	2.01
1	2	5.147330	TGTGAGTGAACGATCATAGGTTT	57.853	39.130	0.00	0.00	38.01	3.27
2	3	4.801330	TGTGAGTGAACGATCATAGGTT	57.199	40.909	0.00	0.00	38.01	3.50
5	6	7.531280	AGAATTTGTGAGTGAACGATCATAG	57.469	36.000	0.00	0.00	38.01	2.23
6	7	7.905604	AAGAATTTGTGAGTGAACGATCATA	57.094	32.000	0.00	0.00	38.01	2.15
7	8	6.808008	AAGAATTTGTGAGTGAACGATCAT	57.192	33.333	0.00	0.00	38.01	2.45
8	9	7.722795	TTAAGAATTTGTGAGTGAACGATCA	57.277	32.000	0.00	0.00	0.00	2.92
9	10	9.445786	TTTTTAAGAATTTGTGAGTGAACGATC	57.554	29.630	0.00	0.00	0.00	3.69
10	11	9.965824	ATTTTTAAGAATTTGTGAGTGAACGAT	57.034	25.926	0.00	0.00	0.00	3.73
11	12	9.445786	GATTTTTAAGAATTTGTGAGTGAACGA	57.554	29.630	0.00	0.00	0.00	3.85
12	13	9.232082	TGATTTTTAAGAATTTGTGAGTGAACG	57.768	29.630	0.00	0.00	0.00	3.95
14	15	9.248291	GCTGATTTTTAAGAATTTGTGAGTGAA	57.752	29.630	0.00	0.00	0.00	3.18
15	16	8.632679	AGCTGATTTTTAAGAATTTGTGAGTGA	58.367	29.630	0.00	0.00	0.00	3.41
16	17	8.807667	AGCTGATTTTTAAGAATTTGTGAGTG	57.192	30.769	0.00	0.00	0.00	3.51
17	18	7.805071	CGAGCTGATTTTTAAGAATTTGTGAGT	59.195	33.333	0.00	0.00	0.00	3.41
18	19	7.201299	GCGAGCTGATTTTTAAGAATTTGTGAG	60.201	37.037	0.00	0.00	0.00	3.51
19	20	6.582295	GCGAGCTGATTTTTAAGAATTTGTGA	59.418	34.615	0.00	0.00	0.00	3.58
20	21	6.363088	TGCGAGCTGATTTTTAAGAATTTGTG	59.637	34.615	0.00	0.00	0.00	3.33
21	22	6.446318	TGCGAGCTGATTTTTAAGAATTTGT	58.554	32.000	0.00	0.00	0.00	2.83
22	23	6.932901	TGCGAGCTGATTTTTAAGAATTTG	57.067	33.333	0.00	0.00	0.00	2.32
23	24	6.922957	TGTTGCGAGCTGATTTTTAAGAATTT	59.077	30.769	0.00	0.00	0.00	1.82
24	25	6.363357	GTGTTGCGAGCTGATTTTTAAGAATT	59.637	34.615	0.00	0.00	0.00	2.17
25	26	5.858581	GTGTTGCGAGCTGATTTTTAAGAAT	59.141	36.000	0.00	0.00	0.00	2.40
26	27	5.212194	GTGTTGCGAGCTGATTTTTAAGAA	58.788	37.500	0.00	0.00	0.00	2.52
27	28	4.274705	TGTGTTGCGAGCTGATTTTTAAGA	59.725	37.500	0.00	0.00	0.00	2.10
28	29	4.536065	TGTGTTGCGAGCTGATTTTTAAG	58.464	39.130	0.00	0.00	0.00	1.85
29	30	4.560136	TGTGTTGCGAGCTGATTTTTAA	57.440	36.364	0.00	0.00	0.00	1.52
30	31	4.764679	ATGTGTTGCGAGCTGATTTTTA	57.235	36.364	0.00	0.00	0.00	1.52
31	32	3.648339	ATGTGTTGCGAGCTGATTTTT	57.352	38.095	0.00	0.00	0.00	1.94
32	33	4.970662	ATATGTGTTGCGAGCTGATTTT	57.029	36.364	0.00	0.00	0.00	1.82
33	34	6.435430	TTTATATGTGTTGCGAGCTGATTT	57.565	33.333	0.00	0.00	0.00	2.17
34	35	6.260714	TCATTTATATGTGTTGCGAGCTGATT	59.739	34.615	0.00	0.00	33.34	2.57
35	36	5.759763	TCATTTATATGTGTTGCGAGCTGAT	59.240	36.000	0.00	0.00	33.34	2.90
36	37	5.115480	TCATTTATATGTGTTGCGAGCTGA	58.885	37.500	0.00	0.00	33.34	4.26
37	38	5.234972	TCTCATTTATATGTGTTGCGAGCTG	59.765	40.000	0.00	0.00	33.34	4.24
38	39	5.235186	GTCTCATTTATATGTGTTGCGAGCT	59.765	40.000	0.00	0.00	33.34	4.09
39	40	5.006649	TGTCTCATTTATATGTGTTGCGAGC	59.993	40.000	0.00	0.00	33.34	5.03
40	41	6.414079	GTGTCTCATTTATATGTGTTGCGAG	58.586	40.000	0.00	0.00	33.34	5.03
41	42	5.005299	CGTGTCTCATTTATATGTGTTGCGA	59.995	40.000	0.00	0.00	33.34	5.10
42	43	5.190342	CGTGTCTCATTTATATGTGTTGCG	58.810	41.667	0.00	0.00	33.34	4.85
43	44	4.963953	GCGTGTCTCATTTATATGTGTTGC	59.036	41.667	0.00	0.00	33.34	4.17
44	45	5.959527	GTGCGTGTCTCATTTATATGTGTTG	59.040	40.000	0.00	0.00	33.34	3.33
45	46	5.220397	CGTGCGTGTCTCATTTATATGTGTT	60.220	40.000	0.00	0.00	33.34	3.32
46	47	4.267690	CGTGCGTGTCTCATTTATATGTGT	59.732	41.667	0.00	0.00	33.34	3.72
47	48	4.751172	CGTGCGTGTCTCATTTATATGTG	58.249	43.478	0.00	0.00	33.34	3.21
48	49	3.245284	GCGTGCGTGTCTCATTTATATGT	59.755	43.478	0.00	0.00	33.34	2.29
49	50	3.362986	GGCGTGCGTGTCTCATTTATATG	60.363	47.826	0.00	0.00	0.00	1.78
50	51	2.800544	GGCGTGCGTGTCTCATTTATAT	59.199	45.455	0.00	0.00	0.00	0.86
51	52	2.159156	AGGCGTGCGTGTCTCATTTATA	60.159	45.455	0.00	0.00	0.00	0.98
52	53	1.006832	GGCGTGCGTGTCTCATTTAT	58.993	50.000	0.00	0.00	0.00	1.40
53	54	0.037697	AGGCGTGCGTGTCTCATTTA	60.038	50.000	0.00	0.00	0.00	1.40
54	55	1.291877	GAGGCGTGCGTGTCTCATTT	61.292	55.000	4.88	0.00	0.00	2.32
55	56	1.738099	GAGGCGTGCGTGTCTCATT	60.738	57.895	4.88	0.00	0.00	2.57
56	57	2.125912	GAGGCGTGCGTGTCTCAT	60.126	61.111	4.88	0.00	0.00	2.90
57	58	2.931068	ATGAGGCGTGCGTGTCTCA	61.931	57.895	13.75	13.75	40.04	3.27
58	59	2.125912	ATGAGGCGTGCGTGTCTC	60.126	61.111	2.87	2.87	0.00	3.36
59	60	2.433145	CATGAGGCGTGCGTGTCT	60.433	61.111	0.00	0.00	0.00	3.41
60	61	4.152625	GCATGAGGCGTGCGTGTC	62.153	66.667	0.00	0.00	36.64	3.67
84	85	3.070302	ACAGCCTAATTGCCTAGCTAGTC	59.930	47.826	19.31	7.49	0.00	2.59
305	317	3.145551	GGAACGAGGGCTAGGCGA	61.146	66.667	10.58	0.00	0.00	5.54
326	339	3.883489	CCTCCGATGAGACTATACACACA	59.117	47.826	0.00	0.00	41.42	3.72
333	346	0.178987	ACGCCCTCCGATGAGACTAT	60.179	55.000	0.00	0.00	41.42	2.12
484	497	2.581208	TAACAACCGCCGCCGATGAT	62.581	55.000	0.00	0.00	36.29	2.45
509	522	0.623723	ACCCCATAGGACAAACGCAT	59.376	50.000	0.00	0.00	39.89	4.73
516	529	2.116238	GTGCTAAGACCCCATAGGACA	58.884	52.381	0.00	0.00	39.45	4.02
528	541	0.524862	GGGAAGTCGTCGTGCTAAGA	59.475	55.000	0.00	0.00	0.00	2.10
588	601	4.473520	CGCCACTCATCGCCCCTT	62.474	66.667	0.00	0.00	0.00	3.95
618	633	3.250744	CGACGACTACAATCATTGGTGT	58.749	45.455	1.58	0.00	34.12	4.16
624	639	2.950309	ACCTAGCGACGACTACAATCAT	59.050	45.455	0.00	0.00	0.00	2.45
739	758	1.129998	GCACTCACACTTGCATAGCTG	59.870	52.381	0.00	0.00	38.68	4.24
799	818	1.264288	GTGATGCTAAACATAGCCGCC	59.736	52.381	5.47	0.00	42.17	6.13
895	914	2.041153	CAACTCTTGGGTTGGTGGC	58.959	57.895	5.52	0.00	41.78	5.01
1236	1255	2.176273	CAGGCGCGGGATGAAGAAG	61.176	63.158	8.83	0.00	0.00	2.85
1243	1262	4.552365	CATCCACAGGCGCGGGAT	62.552	66.667	8.83	8.26	42.04	3.85
1425	1448	1.097232	CCACCTGCACATACACATGG	58.903	55.000	0.00	0.00	36.39	3.66
1465	1488	2.806856	GCCGAGTGCTTGCTCATCG	61.807	63.158	7.37	7.37	35.33	3.84
1781	1804	4.284550	GCCTGGAAGCCACACCCA	62.285	66.667	0.00	0.00	0.00	4.51
1843	1866	2.289444	ACGTTGGTCATGGAGAAATCGT	60.289	45.455	0.00	0.00	0.00	3.73
1911	1934	1.305046	ACGAGACCAAGGATCCCGT	60.305	57.895	8.55	6.11	0.00	5.28
2100	2123	0.958382	TGCGGGTTCTTGTACATGGC	60.958	55.000	8.74	4.81	0.00	4.40
2390	2443	0.800683	TCGCGATGTTCATGTCCGTC	60.801	55.000	3.71	0.00	0.00	4.79
2429	2482	3.181471	CCCACGAGCTGAAGATGAGTATT	60.181	47.826	0.00	0.00	0.00	1.89
2834	2890	3.716006	CGCCACCTCTTGTGCGTG	61.716	66.667	0.00	0.00	44.01	5.34
2888	2944	2.032681	GGCACGAAGAAGGCCACT	59.967	61.111	5.01	0.00	46.92	4.00
3162	3218	4.789075	ACGCACGTCGAATCCCCG	62.789	66.667	13.06	0.00	41.67	5.73
3311	3411	0.742281	CAGGAAGGTGACATGGCGAG	60.742	60.000	0.00	0.00	0.00	5.03
3341	3441	2.185867	GGCTGTTCGCATCGGGTA	59.814	61.111	0.00	0.00	41.67	3.69
3492	4098	2.613506	GGAACTTCGCCCAACACCG	61.614	63.158	0.00	0.00	0.00	4.94
3525	4131	2.421529	GGGGTATTCTTGAATGCGAGGT	60.422	50.000	6.15	0.00	0.00	3.85
3553	4159	4.504916	CAGAGCGTGGAGGAGGCG	62.505	72.222	0.00	0.00	40.57	5.52
3554	4160	3.363844	GACAGAGCGTGGAGGAGGC	62.364	68.421	0.00	0.00	35.57	4.70
3555	4161	2.888863	GACAGAGCGTGGAGGAGG	59.111	66.667	0.00	0.00	0.00	4.30
3556	4162	1.987704	CTCGACAGAGCGTGGAGGAG	61.988	65.000	0.00	0.00	44.39	3.69
3557	4163	2.033602	TCGACAGAGCGTGGAGGA	59.966	61.111	0.00	0.00	0.00	3.71
3558	4164	2.487428	CTCGACAGAGCGTGGAGG	59.513	66.667	0.00	0.00	44.39	4.30
3559	4165	2.487428	CCTCGACAGAGCGTGGAG	59.513	66.667	0.00	0.00	46.85	3.86
3560	4166	3.062466	CCCTCGACAGAGCGTGGA	61.062	66.667	0.00	0.00	45.07	4.02
3569	4191	3.083349	CATGCCTCCCCCTCGACA	61.083	66.667	0.00	0.00	0.00	4.35
3577	4199	2.440980	GGAAGCACCATGCCTCCC	60.441	66.667	7.14	0.00	45.87	4.30
3759	4382	0.780637	TTGGGGTGGGATTAGCAACA	59.219	50.000	0.00	0.00	0.00	3.33
3790	4413	1.952296	GCACATTAGCCCTGGAGATTG	59.048	52.381	0.00	0.00	0.00	2.67
3794	4417	1.386533	CAAGCACATTAGCCCTGGAG	58.613	55.000	0.00	0.00	34.23	3.86
3810	4433	2.615869	GACAACTAGAGCAGGAGCAAG	58.384	52.381	0.00	0.00	45.49	4.01
3830	4453	1.136363	CGCAACAACACCTCACATACG	60.136	52.381	0.00	0.00	0.00	3.06
3832	4455	1.518325	CCGCAACAACACCTCACATA	58.482	50.000	0.00	0.00	0.00	2.29
3834	4457	2.477176	GCCGCAACAACACCTCACA	61.477	57.895	0.00	0.00	0.00	3.58
3876	4499	2.437895	GCCTAACCTCCGCCCAAC	60.438	66.667	0.00	0.00	0.00	3.77
3928	4551	0.392998	GGCTCAATGTCACCCACGAT	60.393	55.000	0.00	0.00	0.00	3.73
3994	4617	0.320374	CAGCTCGTGGTTCCTTGGTA	59.680	55.000	0.00	0.00	0.00	3.25
4034	4657	3.000041	TGACGTGTGGCAGTTATCATTC	59.000	45.455	0.00	0.00	0.00	2.67
4052	4675	1.004440	GGAGAGCCACACACCTGAC	60.004	63.158	0.00	0.00	0.00	3.51
4072	4695	0.168128	CCATCGAAAAACGTCAGGGC	59.832	55.000	0.00	0.00	43.13	5.19
4105	4728	2.167075	CACTGGAATTTGCCATCCTTCC	59.833	50.000	0.00	0.00	37.30	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.