AutoCloner

Multiple sequence alignment - TraesCS7D01G462800

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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	TraesCS7D01G462800	chr7D	100.000	3723	0	0	1	3723	578123967	578127689	0.000000e+00	6876.0
1	TraesCS7D01G462800	chr7D	89.310	1188	96	9	1293	2462	578049790	578050964	0.000000e+00	1461.0
2	TraesCS7D01G462800	chr7D	84.615	1339	143	24	1295	2588	578064758	578066078	0.000000e+00	1273.0
3	TraesCS7D01G462800	chr7D	95.312	192	9	0	968	1159	578049522	578049713	4.670000e-79	305.0
4	TraesCS7D01G462800	chr7D	84.356	326	29	9	45	350	578046196	578046519	2.170000e-77	300.0
5	TraesCS7D01G462800	chr7D	75.320	547	91	28	3067	3600	578051606	578052121	4.840000e-54	222.0
6	TraesCS7D01G462800	chr7D	82.684	231	37	2	2594	2824	578071957	578072184	6.300000e-48	202.0
7	TraesCS7D01G462800	chr7D	89.062	64	3	1	644	707	578043420	578043479	3.990000e-10	76.8
8	TraesCS7D01G462800	chr7D	93.478	46	3	0	304	349	578055020	578055065	6.670000e-08	69.4
9	TraesCS7D01G462800	chr7B	83.463	2443	281	61	1309	3702	641755489	641753121	0.000000e+00	2159.0
10	TraesCS7D01G462800	chr7B	86.611	1322	134	17	1170	2466	641783812	641782509	0.000000e+00	1421.0
11	TraesCS7D01G462800	chr7B	86.548	1182	117	12	1298	2451	641807230	641806063	0.000000e+00	1264.0
12	TraesCS7D01G462800	chr7B	84.495	1019	116	21	2696	3702	641782427	641781439	0.000000e+00	968.0
13	TraesCS7D01G462800	chr7B	83.274	837	106	11	1293	2105	641855530	641854704	0.000000e+00	739.0
14	TraesCS7D01G462800	chr7B	89.293	467	27	12	852	1306	641764791	641764336	6.980000e-157	564.0
15	TraesCS7D01G462800	chr7B	87.377	507	43	9	5	491	641768518	641768013	2.510000e-156	562.0
16	TraesCS7D01G462800	chr7B	80.000	470	64	16	3	449	641862062	641861600	1.670000e-83	320.0
17	TraesCS7D01G462800	chr7B	78.654	520	61	25	2	489	641871900	641871399	2.170000e-77	300.0
18	TraesCS7D01G462800	chr7B	92.105	152	9	1	1016	1167	641787928	641787780	1.050000e-50	211.0
19	TraesCS7D01G462800	chr7B	88.321	137	10	6	538	673	641794176	641794045	3.850000e-35	159.0
20	TraesCS7D01G462800	chr7B	89.683	126	7	3	651	775	641765008	641764888	4.980000e-34	156.0
21	TraesCS7D01G462800	chr7B	90.179	112	4	3	665	775	641788876	641788981	5.010000e-29	139.0
22	TraesCS7D01G462800	chr7B	95.181	83	1	3	534	615	641765080	641765000	1.090000e-25	128.0
23	TraesCS7D01G462800	chr7B	88.060	67	6	2	904	970	641866935	641866871	1.110000e-10	78.7
24	TraesCS7D01G462800	chr7B	96.774	31	1	0	304	334	641810463	641810433	7.000000e-03	52.8
25	TraesCS7D01G462800	chr7A	93.960	1192	61	7	2518	3700	670264403	670263214	0.000000e+00	1792.0
26	TraesCS7D01G462800	chr7A	84.507	1775	179	51	1293	3006	670269978	670268239	0.000000e+00	1666.0
27	TraesCS7D01G462800	chr7A	88.775	1069	83	11	1458	2492	670265539	670264474	0.000000e+00	1275.0
28	TraesCS7D01G462800	chr7A	81.818	495	64	17	12	491	670267083	670266600	3.490000e-105	392.0
29	TraesCS7D01G462800	chr7A	76.719	640	103	27	3057	3686	670268236	670267633	7.760000e-82	315.0
30	TraesCS7D01G462800	chr7A	88.618	123	14	0	1298	1420	670265661	670265539	2.320000e-32	150.0
31	TraesCS7D01G462800	chr7A	87.838	74	7	2	897	970	670274651	670274580	6.630000e-13	86.1
32	TraesCS7D01G462800	chr7A	86.486	74	9	1	897	970	670275392	670275320	3.080000e-11	80.5
33	TraesCS7D01G462800	chr3D	76.239	787	145	21	1613	2376	512908196	512908963	2.710000e-101	379.0
34	TraesCS7D01G462800	chr3D	78.723	94	13	6	2828	2918	357426453	357426364	5.190000e-04	56.5
35	TraesCS7D01G462800	chr3B	76.299	789	126	29	1613	2376	675559928	675560680	7.600000e-97	364.0
36	TraesCS7D01G462800	chr3B	79.348	92	13	5	2829	2918	459102601	459102514	4.020000e-05	60.2
37	TraesCS7D01G462800	chr6B	90.541	74	6	1	897	970	79948154	79948082	3.060000e-16	97.1
38	TraesCS7D01G462800	chr6B	90.541	74	6	1	897	970	80001645	80001573	3.060000e-16	97.1
39	TraesCS7D01G462800	chrUn	89.855	69	5	2	903	970	27627599	27627532	1.840000e-13	87.9
40	TraesCS7D01G462800	chrUn	87.838	74	6	2	897	970	27528256	27528186	2.380000e-12	84.2
41	TraesCS7D01G462800	chr6A	87.143	70	6	3	903	970	46569656	46569588	3.990000e-10	76.8
42	TraesCS7D01G462800	chr5A	84.706	85	1	4	503	575	680399557	680399641	1.430000e-09	75.0
43	TraesCS7D01G462800	chr4D	97.297	37	1	0	2826	2862	400201945	400201981	3.100000e-06	63.9
44	TraesCS7D01G462800	chr4D	100.000	28	0	0	2827	2854	395958241	395958214	7.000000e-03	52.8
45	TraesCS7D01G462800	chr5D	79.570	93	14	4	2827	2918	58120221	58120133	1.120000e-05	62.1
46	TraesCS7D01G462800	chr6D	94.737	38	2	0	2825	2862	83109193	83109230	4.020000e-05	60.2

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	TraesCS7D01G462800	chr7D	578123967	578127689	3722	False	6876.000000	6876	100.000000	1	3723	1	chr7D.!!$F3	3722
1	TraesCS7D01G462800	chr7D	578064758	578066078	1320	False	1273.000000	1273	84.615000	1295	2588	1	chr7D.!!$F1	1293
2	TraesCS7D01G462800	chr7D	578043420	578055065	11645	False	405.700000	1461	87.806333	45	3600	6	chr7D.!!$F4	3555
3	TraesCS7D01G462800	chr7B	641753121	641755489	2368	True	2159.000000	2159	83.463000	1309	3702	1	chr7B.!!$R1	2393
4	TraesCS7D01G462800	chr7B	641781439	641787928	6489	True	866.666667	1421	87.737000	1016	3702	3	chr7B.!!$R8	2686
5	TraesCS7D01G462800	chr7B	641854704	641855530	826	True	739.000000	739	83.274000	1293	2105	1	chr7B.!!$R3	812
6	TraesCS7D01G462800	chr7B	641806063	641810463	4400	True	658.400000	1264	91.661000	304	2451	2	chr7B.!!$R9	2147
7	TraesCS7D01G462800	chr7B	641764336	641768518	4182	True	352.500000	564	90.383500	5	1306	4	chr7B.!!$R7	1301
8	TraesCS7D01G462800	chr7B	641871399	641871900	501	True	300.000000	300	78.654000	2	489	1	chr7B.!!$R6	487
9	TraesCS7D01G462800	chr7A	670263214	670269978	6764	True	931.666667	1792	85.732833	12	3700	6	chr7A.!!$R1	3688
10	TraesCS7D01G462800	chr3D	512908196	512908963	767	False	379.000000	379	76.239000	1613	2376	1	chr3D.!!$F1	763
11	TraesCS7D01G462800	chr3B	675559928	675560680	752	False	364.000000	364	76.299000	1613	2376	1	chr3B.!!$F1	763

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	Hairpin	End Stability	Orientation
408	5934	0.173481	CCAGCGTGAACAGCTAGCTA	59.827	55.0	18.86	44.06	3.32	F
495	8046	0.250989	CTCCTCTCTAGGTAGGCCGG	60.251	65.0	0.00	44.09	6.13	F
1666	17418	0.318762	GAACACGAAGGTCAGGAGCT	59.681	55.0	0.00	41.53	4.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1731	17483	1.076705	GGGGCCTCTGTTGAATCCC	60.077	63.158	0.84	34.77	3.85	R
2132	17934	2.037136	GTGCTGCGTGAGGAAGCAT	61.037	57.895	11.42	42.95	3.79	R
3294	19266	0.172803	GACCTAATCACTGGCGACGT	59.827	55.000	0.00	0.00	4.34	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
67	3832	8.695456	AGAAAAAGTTTGGAGTATGTTGAATGT	58.305	29.630	0.00	0.00	0.00	2.71
139	3918	7.621428	AAGAACTTATGACATGATGAGTTGG	57.379	36.000	8.68	0.00	33.55	3.77
140	3919	5.587844	AGAACTTATGACATGATGAGTTGGC	59.412	40.000	8.68	0.00	33.55	4.52
141	3920	5.108187	ACTTATGACATGATGAGTTGGCT	57.892	39.130	0.00	0.00	0.00	4.75
142	3921	6.239217	ACTTATGACATGATGAGTTGGCTA	57.761	37.500	0.00	0.00	0.00	3.93
155	3934	9.056005	TGATGAGTTGGCTATATGATGTTAAAC	57.944	33.333	0.00	0.00	0.00	2.01
253	4033	3.455910	CCATCCCCTTCAGACTTGTGATA	59.544	47.826	0.00	0.00	0.00	2.15
263	4043	8.642432	CCTTCAGACTTGTGATATCCACTTATA	58.358	37.037	0.00	0.00	45.86	0.98
292	4075	1.971167	TGTGATTTCCACCAGCCGC	60.971	57.895	0.00	0.00	45.09	6.53
294	4077	2.435938	GATTTCCACCAGCCGCGA	60.436	61.111	8.23	0.00	0.00	5.87
295	4078	2.436646	ATTTCCACCAGCCGCGAG	60.437	61.111	8.23	0.00	0.00	5.03
343	4464	3.578688	GGTTTGATGAAGTGGCATTCAC	58.421	45.455	12.42	8.69	41.76	3.18
363	5876	7.862512	TTCACATGCATGTATTATGTCTGAA	57.137	32.000	30.92	21.99	39.39	3.02
366	5879	9.558396	TCACATGCATGTATTATGTCTGAAATA	57.442	29.630	30.92	0.00	39.39	1.40
383	5903	4.657039	TGAAATACCCCTGGTGATACTACC	59.343	45.833	0.00	0.00	41.24	3.18
406	5932	1.079819	TCCAGCGTGAACAGCTAGC	60.080	57.895	6.62	6.62	44.06	3.42
407	5933	1.079543	CCAGCGTGAACAGCTAGCT	60.080	57.895	12.68	12.68	44.06	3.32
408	5934	0.173481	CCAGCGTGAACAGCTAGCTA	59.827	55.000	18.86	0.00	44.06	3.32
409	5935	1.554392	CAGCGTGAACAGCTAGCTAG	58.446	55.000	18.86	16.84	44.06	3.42
414	5940	2.414293	CGTGAACAGCTAGCTAGTCGTT	60.414	50.000	18.86	21.99	0.00	3.85
451	5987	6.488006	TCCATTTTTCACTCTCTTTCTTCCTG	59.512	38.462	0.00	0.00	0.00	3.86
495	8046	0.250989	CTCCTCTCTAGGTAGGCCGG	60.251	65.000	0.00	0.00	44.09	6.13
502	8053	0.745468	CTAGGTAGGCCGGTTGAGAC	59.255	60.000	1.90	0.00	40.50	3.36
615	11346	1.377333	CCCTTTGGCGTCCTCTTCC	60.377	63.158	0.00	0.00	0.00	3.46
622	11353	2.394563	GCGTCCTCTTCCTGCAAGC	61.395	63.158	0.00	0.00	31.26	4.01
625	11373	2.217038	TCCTCTTCCTGCAAGCGGT	61.217	57.895	0.00	0.00	38.09	5.68
669	11460	0.655733	CGTCCTTTCACGCTGTGTTT	59.344	50.000	8.22	0.00	34.79	2.83
768	11584	5.759506	TTTTGCGTGAGGATTTAACAAGA	57.240	34.783	0.00	0.00	0.00	3.02
769	11585	5.356882	TTTGCGTGAGGATTTAACAAGAG	57.643	39.130	0.00	0.00	0.00	2.85
771	11587	3.007506	TGCGTGAGGATTTAACAAGAGGA	59.992	43.478	0.00	0.00	0.00	3.71
779	11646	6.026186	AGGATTTAACAAGAGGAAGAGAGGA	58.974	40.000	0.00	0.00	0.00	3.71
786	11653	4.594920	ACAAGAGGAAGAGAGGAATCACAA	59.405	41.667	0.00	0.00	0.00	3.33
790	11657	3.913163	AGGAAGAGAGGAATCACAACCTT	59.087	43.478	0.00	0.00	36.57	3.50
861	11728	2.691409	TTTTCGGGGCTAGAGACATG	57.309	50.000	0.00	0.00	0.00	3.21
862	11729	1.568504	TTTCGGGGCTAGAGACATGT	58.431	50.000	0.00	0.00	0.00	3.21
879	11746	8.170730	AGAGACATGTATATATAGTGGTCACCA	58.829	37.037	0.00	0.00	0.00	4.17
1147	12925	4.020617	CTCCTTCTGGTGGCGCCA	62.021	66.667	29.03	29.03	46.95	5.69
1187	16930	1.434696	CGGCATCCCATTCACAAGC	59.565	57.895	0.00	0.00	0.00	4.01
1282	17034	3.389002	TCCTCGTCATTGATGATCACCAT	59.611	43.478	8.97	0.00	39.30	3.55
1530	17282	1.216064	TTGGCCAGATCCACTATGCT	58.784	50.000	5.11	0.00	35.50	3.79
1666	17418	0.318762	GAACACGAAGGTCAGGAGCT	59.681	55.000	0.00	0.00	41.53	4.09
1695	17447	1.526686	CTGCAGCCACAAGGTCACA	60.527	57.895	0.00	0.00	37.19	3.58
1705	17457	2.439960	AAGGTCACAGTGCCGGACA	61.440	57.895	5.05	0.00	33.26	4.02
1739	17491	1.376683	CCGGCTTCGTGGGATTCAA	60.377	57.895	0.00	0.00	0.00	2.69
1743	17495	1.610624	GGCTTCGTGGGATTCAACAGA	60.611	52.381	0.00	0.00	0.00	3.41
1750	17503	1.452108	GGATTCAACAGAGGCCCCG	60.452	63.158	0.00	0.00	0.00	5.73
1752	17505	1.002134	ATTCAACAGAGGCCCCGTG	60.002	57.895	0.00	0.00	0.00	4.94
1779	17532	2.440247	TCGCAGCTCCGGATCTCA	60.440	61.111	3.57	0.00	0.00	3.27
1973	17759	2.433318	GCAGCTCCTCACCGACAC	60.433	66.667	0.00	0.00	0.00	3.67
2112	17914	4.021925	GCCTGGCTCCGGTGAACT	62.022	66.667	12.43	0.00	0.00	3.01
2246	18049	2.613223	GCAGAACTACTTCTTCGCCCTT	60.613	50.000	0.00	0.00	34.20	3.95
2463	18276	1.069823	AGTTCCAGCTAGATCATGCGG	59.930	52.381	0.00	5.21	0.00	5.69
2464	18277	0.394192	TTCCAGCTAGATCATGCGGG	59.606	55.000	18.06	18.06	44.00	6.13
2465	18278	0.760567	TCCAGCTAGATCATGCGGGT	60.761	55.000	21.31	0.77	43.31	5.28
2476	18290	1.841277	TCATGCGGGTGGGTAATAACT	59.159	47.619	0.00	0.00	0.00	2.24
2503	18383	1.000506	TCAGGTTGCTCGGACAAGTAC	59.999	52.381	0.00	0.00	0.00	2.73
2504	18384	1.000955	CAGGTTGCTCGGACAAGTACT	59.999	52.381	0.00	0.00	0.00	2.73
2505	18385	2.230508	CAGGTTGCTCGGACAAGTACTA	59.769	50.000	0.00	0.00	0.00	1.82
2506	18386	2.230750	AGGTTGCTCGGACAAGTACTAC	59.769	50.000	0.00	0.00	0.00	2.73
2507	18387	2.230750	GGTTGCTCGGACAAGTACTACT	59.769	50.000	0.00	0.00	0.00	2.57
2508	18388	3.441572	GGTTGCTCGGACAAGTACTACTA	59.558	47.826	0.00	0.00	0.00	1.82
2533	18413	7.661040	AGTTGGATTGTATTTTGAGTTTCCAG	58.339	34.615	0.00	0.00	33.83	3.86
2616	18500	9.241317	CATTAGAATTTGAGGTTATGTGCATTC	57.759	33.333	0.00	0.00	0.00	2.67
2770	18664	5.105917	TGTTGTTGTTTGTTCTCCCTCTTTC	60.106	40.000	0.00	0.00	0.00	2.62
2817	18711	4.906437	GCTTTTGTTCACTTCGATCTGTTC	59.094	41.667	0.00	0.00	0.00	3.18
2864	18817	6.814644	TGTTCACCCATTTTAGTCTGTATACG	59.185	38.462	0.00	0.00	0.00	3.06
2918	18880	0.170561	CGTGTGAACGGAGGGAGTAG	59.829	60.000	0.00	0.00	0.00	2.57
2962	18924	9.125026	GCTCTTCCTTCATATCCAATTTCTTTA	57.875	33.333	0.00	0.00	0.00	1.85
3010	18972	8.576442	ACAGAAAAGGTTAATCAATGTTTCGAT	58.424	29.630	0.00	0.00	0.00	3.59
3043	19005	0.394080	GCTTCATCAGCTCTTGCCCT	60.394	55.000	0.00	0.00	46.27	5.19
3268	19240	6.378280	AGTTCAACAGAAATGAAGGAGTTTGT	59.622	34.615	0.00	0.00	37.46	2.83
3287	19259	7.840489	AGTTTGTAAATCGCAAATGTTTTGAG	58.160	30.769	4.24	1.13	38.00	3.02
3294	19266	1.662876	GCAAATGTTTTGAGCGCTCGA	60.663	47.619	30.75	27.40	0.00	4.04
3425	19397	1.089920	ACATGTGGAGAATCAAGCGC	58.910	50.000	0.00	0.00	36.25	5.92
3466	19447	2.726821	CATGCCAAGATACACCTGGTT	58.273	47.619	0.00	0.00	0.00	3.67
3521	19503	1.328279	TCGTCAGAAACTGCCTCAGA	58.672	50.000	0.29	0.00	35.18	3.27
3536	19518	1.262950	CTCAGATCTCGGACTAGCACG	59.737	57.143	0.00	0.59	0.00	5.34
3544	19526	1.338973	TCGGACTAGCACGAAACACTT	59.661	47.619	6.87	0.00	36.01	3.16
3565	19547	2.202756	GTTCCGGAGCTAGTGCCG	60.203	66.667	11.59	15.67	46.80	5.69
3570	19552	4.577246	GGAGCTAGTGCCGGAGCG	62.577	72.222	5.05	0.00	43.72	5.03
3587	19579	3.400590	GGCACCGTCGTCGTTGTC	61.401	66.667	1.45	0.00	32.23	3.18
3588	19580	3.749373	GCACCGTCGTCGTTGTCG	61.749	66.667	1.45	0.00	32.23	4.35
3589	19581	2.352686	CACCGTCGTCGTTGTCGT	60.353	61.111	0.71	0.00	38.33	4.34
3590	19582	2.051882	ACCGTCGTCGTTGTCGTC	60.052	61.111	0.71	0.00	38.33	4.20
3591	19583	2.798262	CCGTCGTCGTTGTCGTCC	60.798	66.667	0.71	0.00	38.33	4.79
3594	19586	1.594269	CGTCGTCGTTGTCGTCCAAG	61.594	60.000	0.00	0.00	38.33	3.61
3634	19627	1.481772	CAACCCAATGGCCGAATCAAT	59.518	47.619	0.00	0.00	33.59	2.57
3702	19698	3.928727	TCGTTTATAGCGGTATCCCTG	57.071	47.619	10.99	0.76	0.00	4.45
3703	19699	2.029649	TCGTTTATAGCGGTATCCCTGC	60.030	50.000	10.99	0.00	0.00	4.85
3704	19700	2.288579	CGTTTATAGCGGTATCCCTGCA	60.289	50.000	10.99	0.00	34.17	4.41
3705	19701	3.616560	CGTTTATAGCGGTATCCCTGCAT	60.617	47.826	10.99	0.00	34.17	3.96
3706	19702	3.610040	TTATAGCGGTATCCCTGCATG	57.390	47.619	10.99	0.00	34.17	4.06
3707	19703	0.036010	ATAGCGGTATCCCTGCATGC	60.036	55.000	11.82	11.82	34.17	4.06
3708	19704	1.406860	TAGCGGTATCCCTGCATGCA	61.407	55.000	21.29	21.29	34.17	3.96
3709	19705	1.601759	GCGGTATCCCTGCATGCAT	60.602	57.895	22.97	9.00	32.67	3.96
3711	19707	1.293963	CGGTATCCCTGCATGCATCG	61.294	60.000	22.97	14.18	0.00	3.84
3713	19709	1.302752	TATCCCTGCATGCATCGCC	60.303	57.895	22.97	0.00	0.00	5.54
3717	19713	2.712944	CCTGCATGCATCGCCCAAA	61.713	57.895	22.97	0.00	0.00	3.28
3718	19714	1.440060	CTGCATGCATCGCCCAAAT	59.560	52.632	22.97	0.00	0.00	2.32
3719	19715	0.874175	CTGCATGCATCGCCCAAATG	60.874	55.000	22.97	0.79	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
120	3899	8.880750	CATATAGCCAACTCATCATGTCATAAG	58.119	37.037	0.00	0.00	0.00	1.73
253	4033	6.882140	TCACACGGTTCAAAATATAAGTGGAT	59.118	34.615	0.00	0.00	33.18	3.41
263	4043	4.616953	GTGGAAATCACACGGTTCAAAAT	58.383	39.130	0.00	0.00	45.39	1.82
292	4075	5.812127	TGTCCAAAACTGATATGATCACTCG	59.188	40.000	0.00	0.00	35.06	4.18
294	4077	7.613022	ACATTGTCCAAAACTGATATGATCACT	59.387	33.333	0.00	0.00	35.06	3.41
295	4078	7.699391	CACATTGTCCAAAACTGATATGATCAC	59.301	37.037	0.00	0.00	35.06	3.06
343	4464	8.239314	GGGTATTTCAGACATAATACATGCATG	58.761	37.037	25.09	25.09	38.42	4.06
344	4465	7.394359	GGGGTATTTCAGACATAATACATGCAT	59.606	37.037	0.00	0.00	38.42	3.96
345	4466	6.714810	GGGGTATTTCAGACATAATACATGCA	59.285	38.462	0.00	0.00	38.42	3.96
346	4467	6.942576	AGGGGTATTTCAGACATAATACATGC	59.057	38.462	0.00	0.00	38.42	4.06
351	4476	6.617784	TCACCAGGGGTATTTCAGACATAATA	59.382	38.462	0.00	0.00	32.11	0.98
363	5876	4.289837	TGGTAGTATCACCAGGGGTATT	57.710	45.455	0.00	0.00	43.76	1.89
383	5903	0.445436	GCTGTTCACGCTGGAGATTG	59.555	55.000	0.00	0.00	0.00	2.67
406	5932	4.142160	TGGAATCAGACATGGAACGACTAG	60.142	45.833	0.00	0.00	0.00	2.57
407	5933	3.767131	TGGAATCAGACATGGAACGACTA	59.233	43.478	0.00	0.00	0.00	2.59
408	5934	2.567169	TGGAATCAGACATGGAACGACT	59.433	45.455	0.00	0.00	0.00	4.18
409	5935	2.972625	TGGAATCAGACATGGAACGAC	58.027	47.619	0.00	0.00	0.00	4.34
414	5940	6.012113	AGTGAAAAATGGAATCAGACATGGA	58.988	36.000	0.00	0.00	0.00	3.41
451	5987	4.038282	TCAAATCATATCACTGCCAATGCC	59.962	41.667	0.00	0.00	36.33	4.40
495	8046	3.506844	ACGGGTCTCTCTAAAGTCTCAAC	59.493	47.826	0.00	0.00	0.00	3.18
502	8053	1.404315	GCACCACGGGTCTCTCTAAAG	60.404	57.143	0.00	0.00	31.02	1.85
637	11385	4.864334	GGACGGAGGCCATGGCTG	62.864	72.222	34.70	23.30	38.98	4.85
648	11396	1.300620	CACAGCGTGAAAGGACGGA	60.301	57.895	3.04	0.00	39.81	4.69
650	11398	0.655733	AAACACAGCGTGAAAGGACG	59.344	50.000	14.18	0.00	42.42	4.79
655	11403	1.542030	ACCAACAAACACAGCGTGAAA	59.458	42.857	14.18	0.00	36.96	2.69
669	11460	4.142271	ACGAAATTTCTGCTTGAACCAACA	60.142	37.500	15.92	0.00	33.88	3.33
753	11547	6.070538	CCTCTCTTCCTCTTGTTAAATCCTCA	60.071	42.308	0.00	0.00	0.00	3.86
764	11580	4.815533	TGTGATTCCTCTCTTCCTCTTG	57.184	45.455	0.00	0.00	0.00	3.02
765	11581	4.019771	GGTTGTGATTCCTCTCTTCCTCTT	60.020	45.833	0.00	0.00	0.00	2.85
768	11584	3.525862	AGGTTGTGATTCCTCTCTTCCT	58.474	45.455	0.00	0.00	0.00	3.36
769	11585	3.990959	AGGTTGTGATTCCTCTCTTCC	57.009	47.619	0.00	0.00	0.00	3.46
771	11587	6.441088	AGTTAAGGTTGTGATTCCTCTCTT	57.559	37.500	0.00	0.00	33.09	2.85
841	11708	2.304761	ACATGTCTCTAGCCCCGAAAAA	59.695	45.455	0.00	0.00	0.00	1.94
842	11709	1.906574	ACATGTCTCTAGCCCCGAAAA	59.093	47.619	0.00	0.00	0.00	2.29
843	11710	1.568504	ACATGTCTCTAGCCCCGAAA	58.431	50.000	0.00	0.00	0.00	3.46
844	11711	2.447408	TACATGTCTCTAGCCCCGAA	57.553	50.000	0.00	0.00	0.00	4.30
846	11713	6.999272	ACTATATATACATGTCTCTAGCCCCG	59.001	42.308	0.00	0.00	0.00	5.73
847	11714	7.231722	CCACTATATATACATGTCTCTAGCCCC	59.768	44.444	0.00	0.00	0.00	5.80
849	11716	8.754991	ACCACTATATATACATGTCTCTAGCC	57.245	38.462	0.00	0.00	0.00	3.93
850	11717	9.397280	TGACCACTATATATACATGTCTCTAGC	57.603	37.037	0.00	0.00	0.00	3.42
852	11719	9.682465	GGTGACCACTATATATACATGTCTCTA	57.318	37.037	0.00	0.00	0.00	2.43
853	11720	8.170730	TGGTGACCACTATATATACATGTCTCT	58.829	37.037	0.00	0.00	0.00	3.10
854	11721	8.349568	TGGTGACCACTATATATACATGTCTC	57.650	38.462	0.00	7.63	0.00	3.36
879	11746	1.282157	GATCAACAGGCCCTGGTAAGT	59.718	52.381	16.70	0.00	35.51	2.24
882	11749	1.004277	GTTGATCAACAGGCCCTGGTA	59.996	52.381	29.43	0.00	40.84	3.25
916	11850	5.412904	CACAAAATAGACCTCCCAAGTCTTC	59.587	44.000	0.00	0.00	41.87	2.87
964	11901	1.009829	AATTTCCATGCGCTCTCGAC	58.990	50.000	9.73	0.00	38.10	4.20
995	12764	6.547880	CCTAGTGACCCCTATATATGCAGTAG	59.452	46.154	0.00	0.00	0.00	2.57
1260	17012	2.765699	TGGTGATCATCAATGACGAGGA	59.234	45.455	6.09	0.00	40.03	3.71
1311	17063	2.509336	CGAAGATGAAGGCGCCGT	60.509	61.111	23.20	20.21	0.00	5.68
1423	17175	3.365265	CAAGAAGGTGGGCGTGGC	61.365	66.667	0.00	0.00	0.00	5.01
1424	17176	3.365265	GCAAGAAGGTGGGCGTGG	61.365	66.667	0.00	0.00	0.00	4.94
1425	17177	3.365265	GGCAAGAAGGTGGGCGTG	61.365	66.667	0.00	0.00	0.00	5.34
1438	17190	4.966787	GCCGAAGTGGTGGGGCAA	62.967	66.667	0.00	0.00	44.91	4.52
1530	17282	4.980805	GCGTGGCAAGTCCGGTCA	62.981	66.667	0.00	0.00	37.80	4.02
1573	17325	2.012902	ATGTGCTCTACGTACCGGCC	62.013	60.000	0.00	0.00	0.00	6.13
1666	17418	3.286751	GCTGCAGCCGAACACCAA	61.287	61.111	28.76	0.00	34.31	3.67
1731	17483	1.076705	GGGGCCTCTGTTGAATCCC	60.077	63.158	0.84	0.00	34.77	3.85
1750	17503	2.179517	CTGCGAGACGAGGGACAC	59.820	66.667	0.00	0.00	0.00	3.67
1752	17505	3.404141	GAGCTGCGAGACGAGGGAC	62.404	68.421	0.00	0.00	0.00	4.46
1779	17532	3.368531	GCGTGATGAAGTAGGAGAACCTT	60.369	47.826	0.00	0.00	45.36	3.50
2132	17934	2.037136	GTGCTGCGTGAGGAAGCAT	61.037	57.895	11.42	0.00	42.95	3.79
2293	18099	2.760385	GGCTGCCTAGGACGGACT	60.760	66.667	14.75	0.00	0.00	3.85
2463	18276	2.421073	GACGCCAAAGTTATTACCCACC	59.579	50.000	0.00	0.00	0.00	4.61
2464	18277	3.075884	TGACGCCAAAGTTATTACCCAC	58.924	45.455	0.00	0.00	0.00	4.61
2465	18278	3.340034	CTGACGCCAAAGTTATTACCCA	58.660	45.455	0.00	0.00	0.00	4.51
2476	18290	2.250939	CGAGCAACCTGACGCCAAA	61.251	57.895	0.00	0.00	0.00	3.28
2505	18385	8.793592	GGAAACTCAAAATACAATCCAACTAGT	58.206	33.333	0.00	0.00	0.00	2.57
2506	18386	8.792633	TGGAAACTCAAAATACAATCCAACTAG	58.207	33.333	0.00	0.00	33.06	2.57
2507	18387	8.698973	TGGAAACTCAAAATACAATCCAACTA	57.301	30.769	0.00	0.00	33.06	2.24
2508	18388	7.287696	ACTGGAAACTCAAAATACAATCCAACT	59.712	33.333	0.00	0.00	35.46	3.16
2523	18403	3.138283	AGGGTGATTGAACTGGAAACTCA	59.862	43.478	0.00	0.00	0.00	3.41
2533	18413	1.740025	GTAGCAGCAGGGTGATTGAAC	59.260	52.381	2.13	0.00	0.00	3.18
2616	18500	3.928727	TTTCTTGGAGAGCAATTGCAG	57.071	42.857	30.89	18.36	45.16	4.41
2676	18560	7.643764	CAGGTGCATATAACCTTTAAATCAACG	59.356	37.037	6.55	0.00	46.14	4.10
2731	18620	3.857157	ACAACAAAGGGAAGAGCTACA	57.143	42.857	0.00	0.00	0.00	2.74
2770	18664	5.476091	ACTCAGAGTACAAAGAAAGGGAG	57.524	43.478	0.00	0.00	0.00	4.30
2817	18711	7.810766	ACAAACACACTAAAACACATTTCAG	57.189	32.000	0.00	0.00	32.27	3.02
2907	18860	6.598850	GTCTACCTTATAATCTACTCCCTCCG	59.401	46.154	0.00	0.00	0.00	4.63
2918	18880	8.425703	AGGAAGAGCAAAGTCTACCTTATAATC	58.574	37.037	0.00	0.00	31.48	1.75
2962	18924	3.305398	TGAAACACTTGCACCGTTTTT	57.695	38.095	8.30	4.49	33.18	1.94
3001	18963	2.006888	CGCAGGTACCAATCGAAACAT	58.993	47.619	15.94	0.00	0.00	2.71
3010	18972	0.323302	TGAAGCATCGCAGGTACCAA	59.677	50.000	15.94	0.00	0.00	3.67
3043	19005	5.300286	GGTATCCGCTTACTCCACTTTACTA	59.700	44.000	0.00	0.00	0.00	1.82
3268	19240	6.620621	GAGCGCTCAAAACATTTGCGATTTA	61.621	40.000	31.91	0.00	45.52	1.40
3294	19266	0.172803	GACCTAATCACTGGCGACGT	59.827	55.000	0.00	0.00	0.00	4.34
3466	19447	5.996513	AGACCACATTTGCAATGCATAAAAA	59.003	32.000	9.39	0.00	38.76	1.94
3521	19503	1.816835	TGTTTCGTGCTAGTCCGAGAT	59.183	47.619	6.11	0.00	34.16	2.75
3536	19518	2.031944	GCTCCGGAACTTGAAGTGTTTC	60.032	50.000	5.23	0.00	0.00	2.78
3544	19526	0.246635	GCACTAGCTCCGGAACTTGA	59.753	55.000	20.81	0.37	37.91	3.02
3573	19565	2.051882	GACGACAACGACGACGGT	60.052	61.111	12.58	0.95	44.46	4.83
3582	19574	2.671963	GGCCCCTTGGACGACAAC	60.672	66.667	0.00	0.00	34.76	3.32
3583	19575	3.961414	GGGCCCCTTGGACGACAA	61.961	66.667	12.23	0.00	42.67	3.18
3585	19577	4.410400	CTGGGCCCCTTGGACGAC	62.410	72.222	22.27	0.00	42.67	4.34
3702	19698	2.241880	GCATTTGGGCGATGCATGC	61.242	57.895	11.82	11.82	46.96	4.06
3703	19699	4.021650	GCATTTGGGCGATGCATG	57.978	55.556	2.46	0.00	46.96	4.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.