AutoCloner

Multiple sequence alignment - TraesCS7B01G231300

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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	TraesCS7B01G231300	chr7B	100.000	5349	0	0	1	5349	433872824	433867476	0.000000e+00	9878.0
1	TraesCS7B01G231300	chr7B	92.654	5173	216	59	74	5126	434365691	434360563	0.000000e+00	7297.0
2	TraesCS7B01G231300	chr7B	92.491	1638	87	15	820	2434	212775890	212777514	0.000000e+00	2311.0
3	TraesCS7B01G231300	chr7B	82.406	773	103	23	4598	5349	212779783	212780543	1.260000e-180	643.0
4	TraesCS7B01G231300	chr7B	80.339	885	92	35	74	897	434173476	434172613	3.570000e-166	595.0
5	TraesCS7B01G231300	chr7B	82.231	529	53	13	298	789	212775371	212775895	8.290000e-113	418.0
6	TraesCS7B01G231300	chr7B	85.294	340	31	10	2436	2756	212777600	212777939	3.090000e-87	333.0
7	TraesCS7B01G231300	chr7B	89.535	86	4	4	3175	3255	212778020	212778105	2.640000e-18	104.0
8	TraesCS7B01G231300	chr7D	93.122	4987	249	48	430	5349	417931814	417926855	0.000000e+00	7223.0
9	TraesCS7B01G231300	chr7D	95.109	2147	72	19	1024	3147	418057180	418055044	0.000000e+00	3352.0
10	TraesCS7B01G231300	chr7D	94.024	2209	105	10	3137	5331	418054078	418051883	0.000000e+00	3323.0
11	TraesCS7B01G231300	chr7D	89.687	1823	121	33	90	1901	418905126	418903360	0.000000e+00	2263.0
12	TraesCS7B01G231300	chr7D	94.379	1441	70	5	3144	4576	418902210	418900773	0.000000e+00	2202.0
13	TraesCS7B01G231300	chr7D	94.240	1441	71	6	3144	4576	418614368	418612932	0.000000e+00	2191.0
14	TraesCS7B01G231300	chr7D	87.756	1609	133	36	3794	5349	418394481	418392884	0.000000e+00	1821.0
15	TraesCS7B01G231300	chr7D	97.286	958	21	3	949	1901	418616974	418616017	0.000000e+00	1620.0
16	TraesCS7B01G231300	chr7D	90.172	1160	62	17	1946	3060	418903361	418902209	0.000000e+00	1463.0
17	TraesCS7B01G231300	chr7D	89.133	773	60	13	4560	5310	418900758	418899988	0.000000e+00	941.0
18	TraesCS7B01G231300	chr7D	88.745	773	62	14	4560	5310	418612917	418612148	0.000000e+00	922.0
19	TraesCS7B01G231300	chr7D	92.807	570	34	5	3243	3809	418396271	418395706	0.000000e+00	819.0
20	TraesCS7B01G231300	chr7D	89.882	593	37	7	1946	2522	418616018	418615433	0.000000e+00	741.0
21	TraesCS7B01G231300	chr7D	89.428	577	30	15	2513	3060	418614941	418614367	0.000000e+00	699.0
22	TraesCS7B01G231300	chr7D	83.706	626	67	20	430	1033	418069747	418069135	4.680000e-155	558.0
23	TraesCS7B01G231300	chr7D	81.363	499	60	18	430	904	418617473	418616984	5.060000e-100	375.0
24	TraesCS7B01G231300	chr7D	87.931	116	11	2	90	203	418617606	418617492	3.360000e-27	134.0
25	TraesCS7B01G231300	chr7A	93.991	3528	138	28	1745	5230	483946292	483942797	0.000000e+00	5273.0
26	TraesCS7B01G231300	chr7A	94.805	1944	65	8	3423	5349	483488808	483486884	0.000000e+00	2998.0
27	TraesCS7B01G231300	chr7A	97.568	1316	25	6	2118	3427	483494288	483492974	0.000000e+00	2246.0
28	TraesCS7B01G231300	chr7A	94.580	941	37	6	759	1693	483495789	483494857	0.000000e+00	1443.0
29	TraesCS7B01G231300	chr7A	94.737	912	33	8	788	1693	483947192	483946290	0.000000e+00	1404.0
30	TraesCS7B01G231300	chr7A	91.757	643	46	4	3169	3809	483746833	483746196	0.000000e+00	887.0
31	TraesCS7B01G231300	chr7A	92.487	599	33	5	3797	4389	483744965	483744373	0.000000e+00	846.0
32	TraesCS7B01G231300	chr7A	97.113	381	10	1	1745	2125	483494859	483494480	4.520000e-180	641.0
33	TraesCS7B01G231300	chr7A	81.352	488	50	16	321	771	499341310	499341793	5.090000e-95	359.0
34	TraesCS7B01G231300	chr5B	91.562	320	21	4	1247	1560	101893620	101893939	2.290000e-118	436.0
35	TraesCS7B01G231300	chr5B	93.583	187	11	1	1576	1761	290922982	290922796	1.470000e-70	278.0
36	TraesCS7B01G231300	chr4A	90.698	258	18	1	1009	1266	375969013	375968762	6.640000e-89	339.0
37	TraesCS7B01G231300	chr3D	92.308	39	3	0	1910	1948	75637699	75637737	7.480000e-04	56.5
38	TraesCS7B01G231300	chr3D	92.308	39	3	0	1910	1948	75664236	75664274	7.480000e-04	56.5
39	TraesCS7B01G231300	chr3A	92.308	39	3	0	1910	1948	90078127	90078165	7.480000e-04	56.5

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	TraesCS7B01G231300	chr7B	433867476	433872824	5348	True	9878.000000	9878	100.000000	1	5349	1	chr7B.!!$R1	5348
1	TraesCS7B01G231300	chr7B	434360563	434365691	5128	True	7297.000000	7297	92.654000	74	5126	1	chr7B.!!$R3	5052
2	TraesCS7B01G231300	chr7B	212775371	212780543	5172	False	761.800000	2311	86.391400	298	5349	5	chr7B.!!$F1	5051
3	TraesCS7B01G231300	chr7B	434172613	434173476	863	True	595.000000	595	80.339000	74	897	1	chr7B.!!$R2	823
4	TraesCS7B01G231300	chr7D	417926855	417931814	4959	True	7223.000000	7223	93.122000	430	5349	1	chr7D.!!$R1	4919
5	TraesCS7B01G231300	chr7D	418051883	418057180	5297	True	3337.500000	3352	94.566500	1024	5331	2	chr7D.!!$R3	4307
6	TraesCS7B01G231300	chr7D	418899988	418905126	5138	True	1717.250000	2263	90.842750	90	5310	4	chr7D.!!$R6	5220
7	TraesCS7B01G231300	chr7D	418392884	418396271	3387	True	1320.000000	1821	90.281500	3243	5349	2	chr7D.!!$R4	2106
8	TraesCS7B01G231300	chr7D	418612148	418617606	5458	True	954.571429	2191	89.839286	90	5310	7	chr7D.!!$R5	5220
9	TraesCS7B01G231300	chr7D	418069135	418069747	612	True	558.000000	558	83.706000	430	1033	1	chr7D.!!$R2	603
10	TraesCS7B01G231300	chr7A	483942797	483947192	4395	True	3338.500000	5273	94.364000	788	5230	2	chr7A.!!$R4	4442
11	TraesCS7B01G231300	chr7A	483486884	483488808	1924	True	2998.000000	2998	94.805000	3423	5349	1	chr7A.!!$R1	1926
12	TraesCS7B01G231300	chr7A	483492974	483495789	2815	True	1443.333333	2246	96.420333	759	3427	3	chr7A.!!$R2	2668
13	TraesCS7B01G231300	chr7A	483744373	483746833	2460	True	866.500000	887	92.122000	3169	4389	2	chr7A.!!$R3	1220

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
83	84	0.038892	GTTTACCAGCGTGACGGAGA	60.039	55.000	7.25	0.00	0.00	3.71	F
153	155	0.106318	GATGCCAGGCCAGAATCCTT	60.106	55.000	9.64	0.00	0.00	3.36	F
847	946	0.112606	TTGTAAATGGGCCGGACCAA	59.887	50.000	38.01	16.06	45.13	3.67	F
1320	1438	1.333636	CCTCCTCGGACAGCTGGATT	61.334	60.000	19.93	0.00	33.16	3.01	F
1923	2120	4.043435	ACTCCCTAGCTTGGAAAACAATCT	59.957	41.667	16.43	0.00	38.88	2.40	F
3014	4069	4.286032	TCTGCACCCCTGTATATTCCATAC	59.714	45.833	0.00	0.00	0.00	2.39	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1923	2120	0.768622	CCCTCCGCCCCACAATATAA	59.231	55.000	0.00	0.00	0.98	R
1935	2145	1.896465	AGCAAGATATACTCCCTCCGC	59.104	52.381	0.00	0.00	5.54	R
2371	2791	3.441500	TCTCAGCTAGACCTTCACAGA	57.558	47.619	0.00	0.00	3.41	R
3155	5188	2.668632	CGGCCTTGGCTGTAGGAA	59.331	61.111	12.07	34.56	3.36	R
3336	5782	1.956297	CCTCGTACTCGTCTCTCCAT	58.044	55.000	0.00	38.33	3.41	R
4858	8687	0.178068	TTAGGCTCCTCAATCGGTGC	59.822	55.000	0.00	41.56	5.01	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
24	25	3.212538	CGAGAAATAGTCGCCGCG	58.787	61.111	6.39	6.39	0.00	6.46
25	26	2.917656	CGAGAAATAGTCGCCGCGC	61.918	63.158	8.21	0.00	0.00	6.86
26	27	1.589196	GAGAAATAGTCGCCGCGCT	60.589	57.895	8.21	11.17	0.00	5.92
27	28	1.541439	GAGAAATAGTCGCCGCGCTC	61.541	60.000	8.21	3.19	0.00	5.03
28	29	2.585247	AAATAGTCGCCGCGCTCC	60.585	61.111	8.21	0.00	0.00	4.70
29	30	4.587189	AATAGTCGCCGCGCTCCC	62.587	66.667	8.21	0.00	0.00	4.30
37	38	3.431725	CCGCGCTCCCCTTTTCAC	61.432	66.667	5.56	0.00	0.00	3.18
38	39	2.358737	CGCGCTCCCCTTTTCACT	60.359	61.111	5.56	0.00	0.00	3.41
39	40	2.391389	CGCGCTCCCCTTTTCACTC	61.391	63.158	5.56	0.00	0.00	3.51
40	41	1.003233	GCGCTCCCCTTTTCACTCT	60.003	57.895	0.00	0.00	0.00	3.24
41	42	1.021920	GCGCTCCCCTTTTCACTCTC	61.022	60.000	0.00	0.00	0.00	3.20
42	43	0.321671	CGCTCCCCTTTTCACTCTCA	59.678	55.000	0.00	0.00	0.00	3.27
43	44	1.814793	GCTCCCCTTTTCACTCTCAC	58.185	55.000	0.00	0.00	0.00	3.51
44	45	1.072331	GCTCCCCTTTTCACTCTCACA	59.928	52.381	0.00	0.00	0.00	3.58
45	46	2.487265	GCTCCCCTTTTCACTCTCACAA	60.487	50.000	0.00	0.00	0.00	3.33
46	47	3.820557	CTCCCCTTTTCACTCTCACAAA	58.179	45.455	0.00	0.00	0.00	2.83
47	48	4.207165	CTCCCCTTTTCACTCTCACAAAA	58.793	43.478	0.00	0.00	0.00	2.44
48	49	4.803452	TCCCCTTTTCACTCTCACAAAAT	58.197	39.130	0.00	0.00	0.00	1.82
49	50	4.827284	TCCCCTTTTCACTCTCACAAAATC	59.173	41.667	0.00	0.00	0.00	2.17
50	51	4.829492	CCCCTTTTCACTCTCACAAAATCT	59.171	41.667	0.00	0.00	0.00	2.40
51	52	6.003950	CCCCTTTTCACTCTCACAAAATCTA	58.996	40.000	0.00	0.00	0.00	1.98
52	53	6.490040	CCCCTTTTCACTCTCACAAAATCTAA	59.510	38.462	0.00	0.00	0.00	2.10
53	54	7.014230	CCCCTTTTCACTCTCACAAAATCTAAA	59.986	37.037	0.00	0.00	0.00	1.85
54	55	8.579863	CCCTTTTCACTCTCACAAAATCTAAAT	58.420	33.333	0.00	0.00	0.00	1.40
55	56	9.971922	CCTTTTCACTCTCACAAAATCTAAATT	57.028	29.630	0.00	0.00	0.00	1.82
64	65	9.109393	TCTCACAAAATCTAAATTATCTTCCCG	57.891	33.333	0.00	0.00	0.00	5.14
65	66	8.801882	TCACAAAATCTAAATTATCTTCCCGT	57.198	30.769	0.00	0.00	0.00	5.28
66	67	9.238368	TCACAAAATCTAAATTATCTTCCCGTT	57.762	29.630	0.00	0.00	0.00	4.44
67	68	9.855021	CACAAAATCTAAATTATCTTCCCGTTT	57.145	29.630	0.00	0.00	0.00	3.60
71	72	9.689501	AAATCTAAATTATCTTCCCGTTTACCA	57.310	29.630	0.00	0.00	0.00	3.25
72	73	8.904099	ATCTAAATTATCTTCCCGTTTACCAG	57.096	34.615	0.00	0.00	0.00	4.00
83	84	0.038892	GTTTACCAGCGTGACGGAGA	60.039	55.000	7.25	0.00	0.00	3.71
84	85	0.242825	TTTACCAGCGTGACGGAGAG	59.757	55.000	7.25	0.00	0.00	3.20
86	87	2.759641	TACCAGCGTGACGGAGAGGT	62.760	60.000	7.25	0.00	0.00	3.85
87	88	2.651361	CAGCGTGACGGAGAGGTT	59.349	61.111	7.25	0.00	0.00	3.50
152	154	1.284111	TGATGCCAGGCCAGAATCCT	61.284	55.000	9.64	0.00	0.00	3.24
153	155	0.106318	GATGCCAGGCCAGAATCCTT	60.106	55.000	9.64	0.00	0.00	3.36
205	209	0.730834	CGTGACAGAGCAAGTCGAGG	60.731	60.000	0.00	0.00	38.83	4.63
209	213	1.079543	CAGAGCAAGTCGAGGTGGG	60.080	63.158	0.00	0.00	0.00	4.61
261	265	3.047280	TGGTGCGGTCGATGTTGC	61.047	61.111	0.00	0.00	0.00	4.17
287	291	0.523546	CAAGTGATAGCGCGACGACT	60.524	55.000	12.10	0.00	0.00	4.18
288	292	0.170561	AAGTGATAGCGCGACGACTT	59.829	50.000	12.10	6.96	0.00	3.01
294	298	1.721664	TAGCGCGACGACTTAGGCAT	61.722	55.000	12.10	0.00	0.00	4.40
296	300	0.663568	GCGCGACGACTTAGGCATAT	60.664	55.000	12.10	0.00	0.00	1.78
299	303	2.470821	GCGACGACTTAGGCATATGTT	58.529	47.619	4.29	0.00	0.00	2.71
317	321	1.062587	GTTGAAATCCATGAGGCGACG	59.937	52.381	0.00	0.00	33.74	5.12
318	322	0.461870	TGAAATCCATGAGGCGACGG	60.462	55.000	0.00	0.00	33.74	4.79
319	323	1.153168	AAATCCATGAGGCGACGGG	60.153	57.895	0.00	0.00	33.74	5.28
320	324	3.757248	AATCCATGAGGCGACGGGC	62.757	63.158	0.00	0.00	42.51	6.13
322	326	4.552365	CCATGAGGCGACGGGCAT	62.552	66.667	0.00	0.00	46.16	4.40
323	327	3.274586	CATGAGGCGACGGGCATG	61.275	66.667	7.28	7.28	46.16	4.06
324	328	4.552365	ATGAGGCGACGGGCATGG	62.552	66.667	0.00	0.00	46.16	3.66
350	368	1.678970	GAATTCCAAGCCGGCCAGT	60.679	57.895	26.15	5.80	33.14	4.00
383	401	1.424403	CGACGTGGTTGACATTAGCA	58.576	50.000	0.00	0.00	0.00	3.49
408	426	0.671781	AAGTGACCGTGCAGAGATGC	60.672	55.000	0.00	0.00	0.00	3.91
409	427	2.125952	TGACCGTGCAGAGATGCG	60.126	61.111	0.00	0.00	37.69	4.73
410	428	2.125912	GACCGTGCAGAGATGCGT	60.126	61.111	0.00	0.00	37.69	5.24
416	445	1.678360	GTGCAGAGATGCGTTTGTTG	58.322	50.000	0.00	0.00	37.69	3.33
419	448	1.135859	GCAGAGATGCGTTTGTTGAGG	60.136	52.381	0.00	0.00	0.00	3.86
489	521	8.687824	ATATGTTCATGTTTCCGAAAAATGTC	57.312	30.769	19.29	14.90	0.00	3.06
496	548	3.624326	TTCCGAAAAATGTCTGTGCTG	57.376	42.857	0.00	0.00	0.00	4.41
661	734	5.463061	AGTTGGCATTTTCAAAATGTTCTCG	59.537	36.000	21.35	0.00	0.00	4.04
740	816	5.006844	TGTTGCTTCAAGAAAACGAACGATA	59.993	36.000	0.14	0.00	0.00	2.92
741	817	5.856126	TGCTTCAAGAAAACGAACGATAT	57.144	34.783	0.14	0.00	0.00	1.63
843	942	0.699399	TCCTTTGTAAATGGGCCGGA	59.301	50.000	5.05	0.00	41.22	5.14
847	946	0.112606	TTGTAAATGGGCCGGACCAA	59.887	50.000	38.01	16.06	45.13	3.67
1273	1376	2.282958	TCTTGGGACCGTCGAGCT	60.283	61.111	0.00	0.00	0.00	4.09
1320	1438	1.333636	CCTCCTCGGACAGCTGGATT	61.334	60.000	19.93	0.00	33.16	3.01
1447	1573	4.467082	AGGTATTGCAAGAAATCCAATGCA	59.533	37.500	4.94	0.00	46.21	3.96
1473	1599	6.225318	TCTTGATTTGGGAATTTGCAAGAAG	58.775	36.000	0.00	0.00	33.88	2.85
1917	2114	7.849322	AAAATTTACTCCCTAGCTTGGAAAA	57.151	32.000	16.43	9.49	0.00	2.29
1918	2115	6.835819	AATTTACTCCCTAGCTTGGAAAAC	57.164	37.500	16.43	0.00	0.00	2.43
1919	2116	4.986054	TTACTCCCTAGCTTGGAAAACA	57.014	40.909	16.43	0.00	0.00	2.83
1921	2118	4.388577	ACTCCCTAGCTTGGAAAACAAT	57.611	40.909	16.43	0.00	38.65	2.71
1922	2119	4.336280	ACTCCCTAGCTTGGAAAACAATC	58.664	43.478	16.43	0.00	38.65	2.67
1923	2120	4.043435	ACTCCCTAGCTTGGAAAACAATCT	59.957	41.667	16.43	0.00	38.88	2.40
1935	2145	7.416964	TGGAAAACAATCTTATATTGTGGGG	57.583	36.000	4.27	0.00	40.94	4.96
2060	2271	8.474025	AGTTGTGTTATCCATGAAAAGTTTTGA	58.526	29.630	5.36	0.00	0.00	2.69
2371	2791	4.389374	CGGCCCTATGAAAATGTCTGTAT	58.611	43.478	0.00	0.00	0.00	2.29
2592	3630	8.058667	TGTTTACAATCGACTCTTAGGTATCA	57.941	34.615	0.00	0.00	0.00	2.15
2630	3670	8.237811	TGTTATCAGATGCTACTCTACAATGA	57.762	34.615	0.00	0.00	0.00	2.57
2887	3940	7.439157	TTCTTCATTTACATGACCAGTCTTG	57.561	36.000	0.00	11.05	39.28	3.02
3014	4069	4.286032	TCTGCACCCCTGTATATTCCATAC	59.714	45.833	0.00	0.00	0.00	2.39
3155	5188	6.921307	CGCTTTTCTTATAAAAGTGTTGGGTT	59.079	34.615	13.11	0.00	40.76	4.11
3336	5782	0.035725	CTGATGCTGTGAGGGCTTCA	60.036	55.000	0.00	0.00	40.07	3.02
3446	5926	4.608948	AACCTCTCTGTACCTTCAGTTG	57.391	45.455	0.00	0.00	36.85	3.16
3480	5960	1.200716	AGACATCACAAAATGGCTGCG	59.799	47.619	0.00	0.00	43.54	5.18
3944	7713	4.116238	GTCTATAGGAGCAGCTTGTGAAC	58.884	47.826	0.00	0.00	0.00	3.18
4498	8283	4.026356	AGAGAACTTGGTCAAGGAATGG	57.974	45.455	14.29	0.00	42.53	3.16
4650	8475	2.432146	TGGAACTGCATAGTAGGAGCTG	59.568	50.000	0.00	0.00	35.69	4.24
4696	8521	6.956299	CAGCAACTGGAATTTTATGGAAAG	57.044	37.500	0.00	0.00	0.00	2.62
4777	8606	2.058675	CGGAAGGTTCTCCCAGTGT	58.941	57.895	0.00	0.00	34.66	3.55
4779	8608	1.067071	CGGAAGGTTCTCCCAGTGTAC	60.067	57.143	0.00	0.00	34.66	2.90
4781	8610	2.028020	GGAAGGTTCTCCCAGTGTACAG	60.028	54.545	0.00	0.00	34.66	2.74
4791	8620	2.433604	CCCAGTGTACAGAGATGCAGAT	59.566	50.000	0.00	0.00	0.00	2.90
4816	8645	0.659957	GAATCTCATTGCGCTCACCC	59.340	55.000	9.73	0.00	0.00	4.61
4849	8678	0.788391	GCCACTCCGAGTTGTTAACG	59.212	55.000	0.00	0.00	36.23	3.18
4909	8738	3.081710	TCTACGAGTCACCAGATTCCA	57.918	47.619	0.00	0.00	0.00	3.53
5025	8854	1.134995	CATGTCGCAGGAGAGTTGCTA	60.135	52.381	0.00	0.00	39.38	3.49
5172	9032	6.039829	CCTCTTTCCTGTATTTTGGCTATTCC	59.960	42.308	0.00	0.00	0.00	3.01
5190	9050	9.438228	GGCTATTCCCTAAAAATATCACTAGAC	57.562	37.037	0.00	0.00	0.00	2.59
5285	9149	2.035961	TGTGCTAGTCAACTCTGGACAC	59.964	50.000	6.41	0.00	37.74	3.67
5326	9190	5.576774	GGTTGTTTGAGCCAATTATGTTAGC	59.423	40.000	0.00	0.00	0.00	3.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	2.917656	GCGCGGCGACTATTTCTCG	61.918	63.158	28.54	1.54	0.00	4.04
8	9	1.541439	GAGCGCGGCGACTATTTCTC	61.541	60.000	28.54	16.61	0.00	2.87
9	10	1.589196	GAGCGCGGCGACTATTTCT	60.589	57.895	28.54	11.56	0.00	2.52
10	11	2.586773	GGAGCGCGGCGACTATTTC	61.587	63.158	28.54	11.94	0.00	2.17
11	12	2.585247	GGAGCGCGGCGACTATTT	60.585	61.111	28.54	3.04	0.00	1.40
12	13	4.587189	GGGAGCGCGGCGACTATT	62.587	66.667	28.54	4.98	0.00	1.73
20	21	3.431725	GTGAAAAGGGGAGCGCGG	61.432	66.667	8.83	0.00	0.00	6.46
21	22	2.358737	AGTGAAAAGGGGAGCGCG	60.359	61.111	0.00	0.00	0.00	6.86
22	23	1.003233	AGAGTGAAAAGGGGAGCGC	60.003	57.895	0.00	0.00	0.00	5.92
23	24	0.321671	TGAGAGTGAAAAGGGGAGCG	59.678	55.000	0.00	0.00	0.00	5.03
24	25	1.072331	TGTGAGAGTGAAAAGGGGAGC	59.928	52.381	0.00	0.00	0.00	4.70
25	26	3.492102	TTGTGAGAGTGAAAAGGGGAG	57.508	47.619	0.00	0.00	0.00	4.30
26	27	3.943671	TTTGTGAGAGTGAAAAGGGGA	57.056	42.857	0.00	0.00	0.00	4.81
27	28	4.829492	AGATTTTGTGAGAGTGAAAAGGGG	59.171	41.667	0.00	0.00	0.00	4.79
28	29	7.510549	TTAGATTTTGTGAGAGTGAAAAGGG	57.489	36.000	0.00	0.00	0.00	3.95
29	30	9.971922	AATTTAGATTTTGTGAGAGTGAAAAGG	57.028	29.630	0.00	0.00	0.00	3.11
38	39	9.109393	CGGGAAGATAATTTAGATTTTGTGAGA	57.891	33.333	0.00	0.00	0.00	3.27
39	40	8.893727	ACGGGAAGATAATTTAGATTTTGTGAG	58.106	33.333	0.00	0.00	0.00	3.51
40	41	8.801882	ACGGGAAGATAATTTAGATTTTGTGA	57.198	30.769	0.00	0.00	0.00	3.58
41	42	9.855021	AAACGGGAAGATAATTTAGATTTTGTG	57.145	29.630	0.00	0.00	0.00	3.33
45	46	9.689501	TGGTAAACGGGAAGATAATTTAGATTT	57.310	29.630	0.00	0.00	0.00	2.17
46	47	9.338622	CTGGTAAACGGGAAGATAATTTAGATT	57.661	33.333	0.00	0.00	0.00	2.40
47	48	7.444487	GCTGGTAAACGGGAAGATAATTTAGAT	59.556	37.037	0.00	0.00	0.00	1.98
48	49	6.764560	GCTGGTAAACGGGAAGATAATTTAGA	59.235	38.462	0.00	0.00	0.00	2.10
49	50	6.292703	CGCTGGTAAACGGGAAGATAATTTAG	60.293	42.308	0.00	0.00	0.00	1.85
50	51	5.524646	CGCTGGTAAACGGGAAGATAATTTA	59.475	40.000	0.00	0.00	0.00	1.40
51	52	4.334481	CGCTGGTAAACGGGAAGATAATTT	59.666	41.667	0.00	0.00	0.00	1.82
52	53	3.875134	CGCTGGTAAACGGGAAGATAATT	59.125	43.478	0.00	0.00	0.00	1.40
53	54	3.118519	ACGCTGGTAAACGGGAAGATAAT	60.119	43.478	0.00	0.00	0.00	1.28
54	55	2.234414	ACGCTGGTAAACGGGAAGATAA	59.766	45.455	0.00	0.00	0.00	1.75
55	56	1.826720	ACGCTGGTAAACGGGAAGATA	59.173	47.619	0.00	0.00	0.00	1.98
56	57	0.611714	ACGCTGGTAAACGGGAAGAT	59.388	50.000	0.00	0.00	0.00	2.40
57	58	0.320073	CACGCTGGTAAACGGGAAGA	60.320	55.000	0.00	0.00	33.57	2.87
58	59	0.320073	TCACGCTGGTAAACGGGAAG	60.320	55.000	0.00	0.00	39.08	3.46
59	60	0.600782	GTCACGCTGGTAAACGGGAA	60.601	55.000	0.00	0.00	44.44	3.97
60	61	1.005867	GTCACGCTGGTAAACGGGA	60.006	57.895	0.00	0.00	39.88	5.14
61	62	2.377310	CGTCACGCTGGTAAACGGG	61.377	63.158	0.00	0.00	33.38	5.28
62	63	2.377310	CCGTCACGCTGGTAAACGG	61.377	63.158	0.00	0.00	43.65	4.44
63	64	1.342082	CTCCGTCACGCTGGTAAACG	61.342	60.000	0.00	0.00	35.47	3.60
64	65	0.038892	TCTCCGTCACGCTGGTAAAC	60.039	55.000	0.00	0.00	0.00	2.01
65	66	0.242825	CTCTCCGTCACGCTGGTAAA	59.757	55.000	0.00	0.00	0.00	2.01
66	67	1.592400	CCTCTCCGTCACGCTGGTAA	61.592	60.000	0.00	0.00	0.00	2.85
67	68	2.044555	CCTCTCCGTCACGCTGGTA	61.045	63.158	0.00	0.00	0.00	3.25
68	69	3.374402	CCTCTCCGTCACGCTGGT	61.374	66.667	0.00	0.00	0.00	4.00
69	70	2.820767	GAACCTCTCCGTCACGCTGG	62.821	65.000	0.00	0.00	0.00	4.85
70	71	1.444553	GAACCTCTCCGTCACGCTG	60.445	63.158	0.00	0.00	0.00	5.18
71	72	2.963371	GAACCTCTCCGTCACGCT	59.037	61.111	0.00	0.00	0.00	5.07
72	73	2.504244	CGAACCTCTCCGTCACGC	60.504	66.667	0.00	0.00	0.00	5.34
226	230	0.729116	CACATCATCACCTTGTCGGC	59.271	55.000	0.00	0.00	35.61	5.54
261	265	1.061131	CGCGCTATCACTTGTTTGGAG	59.939	52.381	5.56	0.00	0.00	3.86
287	291	6.491062	CCTCATGGATTTCAACATATGCCTAA	59.509	38.462	1.58	0.00	34.57	2.69
288	292	6.005823	CCTCATGGATTTCAACATATGCCTA	58.994	40.000	1.58	0.00	34.57	3.93
294	298	3.876914	GTCGCCTCATGGATTTCAACATA	59.123	43.478	0.00	0.00	34.57	2.29
296	300	2.083774	GTCGCCTCATGGATTTCAACA	58.916	47.619	0.00	0.00	34.57	3.33
299	303	0.461870	CCGTCGCCTCATGGATTTCA	60.462	55.000	0.00	0.00	34.57	2.69
317	321	1.334869	GAATTCGACATCACCATGCCC	59.665	52.381	0.00	0.00	32.57	5.36
318	322	1.334869	GGAATTCGACATCACCATGCC	59.665	52.381	0.00	0.00	32.57	4.40
319	323	2.016318	TGGAATTCGACATCACCATGC	58.984	47.619	0.00	0.00	32.57	4.06
320	324	3.488047	GCTTGGAATTCGACATCACCATG	60.488	47.826	0.00	0.00	35.92	3.66
321	325	2.684881	GCTTGGAATTCGACATCACCAT	59.315	45.455	0.00	0.00	0.00	3.55
322	326	2.083774	GCTTGGAATTCGACATCACCA	58.916	47.619	0.00	0.00	0.00	4.17
323	327	1.401905	GGCTTGGAATTCGACATCACC	59.598	52.381	0.00	0.00	0.00	4.02
324	328	1.062587	CGGCTTGGAATTCGACATCAC	59.937	52.381	0.00	0.00	0.00	3.06
325	329	1.368641	CGGCTTGGAATTCGACATCA	58.631	50.000	0.00	0.00	0.00	3.07
350	368	1.064134	CGTCGCATCATCACCTCGA	59.936	57.895	0.00	0.00	0.00	4.04
383	401	0.667487	CTGCACGGTCACTTCGTCAT	60.667	55.000	0.00	0.00	38.94	3.06
489	521	5.809562	TCCAAACAATGTTTTAACAGCACAG	59.190	36.000	8.85	0.00	43.04	3.66
720	796	7.548673	AAAATATCGTTCGTTTTCTTGAAGC	57.451	32.000	0.00	0.00	0.00	3.86
1273	1376	4.408821	GGACGCTCCCATGGTGCA	62.409	66.667	21.71	2.10	41.64	4.57
1320	1438	4.710695	CACGTACGGTCGCTGCCA	62.711	66.667	21.06	0.00	0.00	4.92
1410	1528	7.879677	TCTTGCAATACCTGATTATACATCCAG	59.120	37.037	0.00	0.00	0.00	3.86
1447	1573	6.771573	TCTTGCAAATTCCCAAATCAAGAAT	58.228	32.000	0.00	0.00	33.62	2.40
1473	1599	3.114065	CCAAATCGAGAACGTACTAGGC	58.886	50.000	0.00	0.00	40.69	3.93
1908	2105	7.492344	CCCACAATATAAGATTGTTTTCCAAGC	59.508	37.037	0.00	0.00	39.94	4.01
1909	2106	7.981225	CCCCACAATATAAGATTGTTTTCCAAG	59.019	37.037	0.00	0.00	39.94	3.61
1911	2108	6.127196	GCCCCACAATATAAGATTGTTTTCCA	60.127	38.462	0.00	0.00	39.94	3.53
1912	2109	6.280643	GCCCCACAATATAAGATTGTTTTCC	58.719	40.000	0.00	0.00	39.94	3.13
1913	2110	5.977129	CGCCCCACAATATAAGATTGTTTTC	59.023	40.000	0.00	0.00	39.94	2.29
1917	2114	3.137544	TCCGCCCCACAATATAAGATTGT	59.862	43.478	0.00	0.00	42.38	2.71
1918	2115	3.750371	TCCGCCCCACAATATAAGATTG	58.250	45.455	0.00	0.00	35.29	2.67
1919	2116	3.244911	CCTCCGCCCCACAATATAAGATT	60.245	47.826	0.00	0.00	0.00	2.40
1921	2118	1.697432	CCTCCGCCCCACAATATAAGA	59.303	52.381	0.00	0.00	0.00	2.10
1922	2119	1.271379	CCCTCCGCCCCACAATATAAG	60.271	57.143	0.00	0.00	0.00	1.73
1923	2120	0.768622	CCCTCCGCCCCACAATATAA	59.231	55.000	0.00	0.00	0.00	0.98
1935	2145	1.896465	AGCAAGATATACTCCCTCCGC	59.104	52.381	0.00	0.00	0.00	5.54
2000	2211	5.266733	AGCACGCAAATTTCAATATGGAT	57.733	34.783	0.00	0.00	0.00	3.41
2371	2791	3.441500	TCTCAGCTAGACCTTCACAGA	57.558	47.619	0.00	0.00	0.00	3.41
2494	3012	9.429359	TGGGCAACAAATGTAATATTTAACAAG	57.571	29.630	0.00	0.00	39.74	3.16
2630	3670	5.278315	GGGTTCACGAAGAAAGTAAGCAAAT	60.278	40.000	0.00	0.00	38.13	2.32
2887	3940	5.410924	ACAAGCCTTGAAGTTGAAGAAAAC	58.589	37.500	12.25	0.00	0.00	2.43
3014	4069	6.021390	CGACGATAGAAGTACACACATTTCAG	60.021	42.308	0.00	0.00	41.38	3.02
3155	5188	2.668632	CGGCCTTGGCTGTAGGAA	59.331	61.111	12.07	0.00	34.56	3.36
3336	5782	1.956297	CCTCGTACTCGTCTCTCCAT	58.044	55.000	0.00	0.00	38.33	3.41
3411	5891	6.468543	ACAGAGAGGTTAAGAAAGGAATGTC	58.531	40.000	0.00	0.00	0.00	3.06
3446	5926	4.455533	TGTGATGTCTGCAAAACCATAGAC	59.544	41.667	0.00	0.00	39.88	2.59
3730	6237	3.534554	TCTGCAGAATCGCACACAATAT	58.465	40.909	15.67	0.00	36.86	1.28
3944	7713	2.513753	AGCTCCTCCTCATGAGATACG	58.486	52.381	24.62	7.33	44.42	3.06
4009	7778	1.999648	TGAACCAGGCAAATGAAGCT	58.000	45.000	0.00	0.00	0.00	3.74
4498	8283	0.886490	CTCACCCCTATTGCATCGGC	60.886	60.000	0.00	0.00	41.68	5.54
4650	8475	9.884465	GCTGGTACAAGTATTATGATGAAATTC	57.116	33.333	0.00	0.00	38.70	2.17
4692	8517	7.161773	TGAGGATTTCACATCATTTCCTTTC	57.838	36.000	0.00	0.00	33.83	2.62
4758	8587	1.296715	CACTGGGAGAACCTTCCGG	59.703	63.158	0.00	0.00	41.25	5.14
4759	8588	1.067071	GTACACTGGGAGAACCTTCCG	60.067	57.143	0.00	0.00	41.11	4.30
4760	8589	1.975680	TGTACACTGGGAGAACCTTCC	59.024	52.381	0.00	0.00	41.11	3.46
4777	8606	5.665916	TTCACTTGATCTGCATCTCTGTA	57.334	39.130	0.00	0.00	0.00	2.74
4779	8608	5.361427	AGATTCACTTGATCTGCATCTCTG	58.639	41.667	0.00	0.00	0.00	3.35
4781	8610	5.358090	TGAGATTCACTTGATCTGCATCTC	58.642	41.667	12.92	12.92	35.52	2.75
4791	8620	2.674852	GAGCGCAATGAGATTCACTTGA	59.325	45.455	11.47	0.00	0.00	3.02
4816	8645	0.615331	AGTGGCACCTGTAGGACATG	59.385	55.000	15.27	0.00	38.94	3.21
4849	8678	0.584396	TCAATCGGTGCAACGTCAAC	59.416	50.000	25.58	0.00	38.12	3.18
4858	8687	0.178068	TTAGGCTCCTCAATCGGTGC	59.822	55.000	0.00	0.00	41.56	5.01
4909	8738	1.700955	AGTGTCACAGTAGGAACCGT	58.299	50.000	5.62	0.00	0.00	4.83
5094	8929	7.448469	CACCCCACATATATAAGGAAGGAAAAG	59.552	40.741	4.58	0.00	0.00	2.27
5190	9050	4.706476	TGGCATTTTGGAAAGAGGTCATAG	59.294	41.667	0.00	0.00	0.00	2.23
5301	9165	5.543507	AACATAATTGGCTCAAACAACCA	57.456	34.783	0.00	0.00	0.00	3.67
5326	9190	4.301072	TTGGTTTCCTACAAGGATCAGG	57.699	45.455	0.00	0.00	45.34	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.