AutoCloner

Multiple sequence alignment - TraesCS1B01G019500

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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	TraesCS1B01G019500	chr1B	100.000	4511	0	0	1	4511	9160801	9165311	0.000000e+00	8331.0
1	TraesCS1B01G019500	chr1B	93.593	4292	202	19	98	4355	8868103	8863851	0.000000e+00	6335.0
2	TraesCS1B01G019500	chr1B	81.206	2671	404	59	993	3606	10007492	10004863	0.000000e+00	2061.0
3	TraesCS1B01G019500	chr1B	81.287	839	125	17	926	1747	9281198	9282021	0.000000e+00	651.0
4	TraesCS1B01G019500	chr1B	88.732	142	15	1	4357	4497	8862192	8862051	6.000000e-39	172.0
5	TraesCS1B01G019500	chr1B	96.842	95	3	0	1	95	52486629	52486535	4.670000e-35	159.0
6	TraesCS1B01G019500	chr1B	94.681	94	5	0	1	94	52151356	52151263	3.640000e-31	147.0
7	TraesCS1B01G019500	chr1B	92.857	84	6	0	5	88	52148076	52147993	6.130000e-24	122.0
8	TraesCS1B01G019500	chr1D	92.469	4302	230	34	98	4355	6722461	6718210	0.000000e+00	6063.0
9	TraesCS1B01G019500	chr1D	83.390	2655	362	44	938	3552	6898393	6901008	0.000000e+00	2386.0
10	TraesCS1B01G019500	chr1D	82.202	2697	377	52	988	3629	407672556	407669908	0.000000e+00	2226.0
11	TraesCS1B01G019500	chr1D	81.048	2844	445	52	846	3626	6714782	6711970	0.000000e+00	2180.0
12	TraesCS1B01G019500	chr1D	80.905	2739	414	59	952	3629	6913119	6915809	0.000000e+00	2060.0
13	TraesCS1B01G019500	chr1D	88.386	663	38	13	440	1087	6692395	6691757	0.000000e+00	761.0
14	TraesCS1B01G019500	chr1D	96.970	99	3	0	1	99	35925204	35925302	2.790000e-37	167.0
15	TraesCS1B01G019500	chr1D	93.617	47	2	1	491	537	6692435	6692390	8.100000e-08	69.4
16	TraesCS1B01G019500	chr1A	92.924	3929	216	34	443	4355	8160377	8156495	0.000000e+00	5659.0
17	TraesCS1B01G019500	chr1A	82.740	2781	361	49	850	3556	8326967	8329702	0.000000e+00	2366.0
18	TraesCS1B01G019500	chr1A	81.898	2635	422	26	936	3537	8144565	8141953	0.000000e+00	2172.0
19	TraesCS1B01G019500	chr1A	81.983	2642	388	43	938	3529	8331893	8334496	0.000000e+00	2161.0
20	TraesCS1B01G019500	chr1A	88.484	686	58	7	607	1288	8089150	8088482	0.000000e+00	809.0
21	TraesCS1B01G019500	chr1A	87.897	661	76	4	983	1643	8337974	8338630	0.000000e+00	774.0
22	TraesCS1B01G019500	chr1A	82.910	433	42	11	98	518	8089843	8089431	1.190000e-95	361.0
23	TraesCS1B01G019500	chr1A	90.830	229	18	2	98	323	8169922	8169694	2.040000e-78	303.0
24	TraesCS1B01G019500	chr1A	86.473	207	19	6	3528	3729	7831016	7831218	7.600000e-53	219.0
25	TraesCS1B01G019500	chr1A	95.960	99	3	1	1	99	51166229	51166132	4.670000e-35	159.0
26	TraesCS1B01G019500	chr4B	85.089	3380	419	43	193	3537	36636640	36633311	0.000000e+00	3371.0
27	TraesCS1B01G019500	chr4B	91.398	93	8	0	98	190	36639246	36639154	1.320000e-25	128.0
28	TraesCS1B01G019500	chr5B	83.521	2749	359	42	850	3552	549547824	549550524	0.000000e+00	2481.0
29	TraesCS1B01G019500	chr2B	81.775	2760	402	53	935	3640	548623925	548626637	0.000000e+00	2217.0
30	TraesCS1B01G019500	chr2A	82.112	2661	386	45	935	3539	611302766	611305392	0.000000e+00	2194.0
31	TraesCS1B01G019500	chr2D	94.737	95	4	1	1	95	514250565	514250472	3.640000e-31	147.0
32	TraesCS1B01G019500	chr2D	94.030	67	3	1	3745	3811	469993474	469993539	2.870000e-17	100.0
33	TraesCS1B01G019500	chr3A	90.625	96	6	3	3	96	163683876	163683782	1.700000e-24	124.0
34	TraesCS1B01G019500	chr6D	90.000	90	7	2	12	100	76626419	76626507	1.030000e-21	115.0
35	TraesCS1B01G019500	chr3B	87.500	96	12	0	1	96	162299352	162299447	1.330000e-20	111.0
36	TraesCS1B01G019500	chr7D	100.000	29	0	0	516	544	634664423	634664395	2.000000e-03	54.7

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	TraesCS1B01G019500	chr1B	9160801	9165311	4510	False	8331.0	8331	100.000000	1	4511	1	chr1B.!!$F1	4510
1	TraesCS1B01G019500	chr1B	8862051	8868103	6052	True	3253.5	6335	91.162500	98	4497	2	chr1B.!!$R3	4399
2	TraesCS1B01G019500	chr1B	10004863	10007492	2629	True	2061.0	2061	81.206000	993	3606	1	chr1B.!!$R1	2613
3	TraesCS1B01G019500	chr1B	9281198	9282021	823	False	651.0	651	81.287000	926	1747	1	chr1B.!!$F2	821
4	TraesCS1B01G019500	chr1D	6711970	6722461	10491	True	4121.5	6063	86.758500	98	4355	2	chr1D.!!$R3	4257
5	TraesCS1B01G019500	chr1D	6898393	6901008	2615	False	2386.0	2386	83.390000	938	3552	1	chr1D.!!$F1	2614
6	TraesCS1B01G019500	chr1D	407669908	407672556	2648	True	2226.0	2226	82.202000	988	3629	1	chr1D.!!$R1	2641
7	TraesCS1B01G019500	chr1D	6913119	6915809	2690	False	2060.0	2060	80.905000	952	3629	1	chr1D.!!$F2	2677
8	TraesCS1B01G019500	chr1D	6691757	6692435	678	True	415.2	761	91.001500	440	1087	2	chr1D.!!$R2	647
9	TraesCS1B01G019500	chr1A	8156495	8160377	3882	True	5659.0	5659	92.924000	443	4355	1	chr1A.!!$R2	3912
10	TraesCS1B01G019500	chr1A	8141953	8144565	2612	True	2172.0	2172	81.898000	936	3537	1	chr1A.!!$R1	2601
11	TraesCS1B01G019500	chr1A	8326967	8338630	11663	False	1767.0	2366	84.206667	850	3556	3	chr1A.!!$F2	2706
12	TraesCS1B01G019500	chr1A	8088482	8089843	1361	True	585.0	809	85.697000	98	1288	2	chr1A.!!$R5	1190
13	TraesCS1B01G019500	chr4B	36633311	36639246	5935	True	1749.5	3371	88.243500	98	3537	2	chr4B.!!$R1	3439
14	TraesCS1B01G019500	chr5B	549547824	549550524	2700	False	2481.0	2481	83.521000	850	3552	1	chr5B.!!$F1	2702
15	TraesCS1B01G019500	chr2B	548623925	548626637	2712	False	2217.0	2217	81.775000	935	3640	1	chr2B.!!$F1	2705
16	TraesCS1B01G019500	chr2A	611302766	611305392	2626	False	2194.0	2194	82.112000	935	3539	1	chr2A.!!$F1	2604

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
481	3012	0.178953	ATTGTCTTGTTGGCTGGCCT	60.179	50.0	13.05	36.94	5.19	F
1787	4687	0.032117	ATGGATCCACGGACCAGAGA	60.032	55.0	18.99	37.12	3.10	F
2088	4988	0.179108	GGGAGTTTGAGGATCGGACG	60.179	60.0	0.00	38.61	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
2066	4966	1.278127	TCCGATCCTCAAACTCCCAAC	59.722	52.381	3.77	R
3051	5985	3.580895	GGCTAAAATCCCTTCCCACAAAA	59.419	43.478	2.44	R
3918	7446	1.707989	TGGTTCTGGGAGGCAATGTTA	59.292	47.619	2.41	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
74	75	6.849085	TTTTTCTCATTAGCCCATAAAGCA	57.151	33.333	0.00	0.00	0.00	3.91
75	76	5.835113	TTTCTCATTAGCCCATAAAGCAC	57.165	39.130	0.00	0.00	0.00	4.40
76	77	4.778213	TCTCATTAGCCCATAAAGCACT	57.222	40.909	0.00	0.00	0.00	4.40
77	78	5.116084	TCTCATTAGCCCATAAAGCACTT	57.884	39.130	0.00	0.00	0.00	3.16
78	79	5.509498	TCTCATTAGCCCATAAAGCACTTT	58.491	37.500	0.70	0.70	36.63	2.66
79	80	5.951747	TCTCATTAGCCCATAAAGCACTTTT	59.048	36.000	0.20	0.00	34.23	2.27
80	81	6.437162	TCTCATTAGCCCATAAAGCACTTTTT	59.563	34.615	0.20	0.00	34.23	1.94
81	82	7.613801	TCTCATTAGCCCATAAAGCACTTTTTA	59.386	33.333	0.20	0.00	34.23	1.52
82	83	8.305046	TCATTAGCCCATAAAGCACTTTTTAT	57.695	30.769	0.20	0.00	34.43	1.40
83	84	9.415008	TCATTAGCCCATAAAGCACTTTTTATA	57.585	29.630	0.20	0.00	32.84	0.98
132	133	1.635817	ATGGTCCCATAGCACGCCTT	61.636	55.000	0.00	0.00	38.70	4.35
173	174	4.357918	ACATGTGAGTCTAATATGGGCC	57.642	45.455	0.00	0.00	0.00	5.80
179	182	4.021016	GTGAGTCTAATATGGGCCCTAGTG	60.021	50.000	25.70	8.50	0.00	2.74
236	2750	8.803235	TCTAGCTCACTCTTATGTGTTTTAAGA	58.197	33.333	0.00	0.00	38.90	2.10
327	2851	6.366061	GGTCTTAGGTGTTGATTTTGCATTTC	59.634	38.462	0.00	0.00	0.00	2.17
342	2866	6.603237	TTGCATTTCTAGTATTCGACCATG	57.397	37.500	0.00	0.00	0.00	3.66
380	2904	9.589461	TTCTGGGTTGGTTAGTAAAATGATTAA	57.411	29.630	0.00	0.00	0.00	1.40
478	3009	2.624838	AGTTCATTGTCTTGTTGGCTGG	59.375	45.455	0.00	0.00	0.00	4.85
481	3012	0.178953	ATTGTCTTGTTGGCTGGCCT	60.179	50.000	13.05	0.00	36.94	5.19
583	3114	3.066203	CAGCTTTCGTGGTAAGTTTGGTT	59.934	43.478	0.00	0.00	0.00	3.67
590	3121	2.691011	GTGGTAAGTTTGGTTGAAGCCA	59.309	45.455	0.00	0.00	36.62	4.75
643	3396	4.342772	CTTTTGTGGAAAACTCACGACTG	58.657	43.478	0.00	0.00	37.91	3.51
644	3397	2.971660	TGTGGAAAACTCACGACTGA	57.028	45.000	0.00	0.00	37.91	3.41
687	3440	3.526534	CACTTAGTGGAAGCCTCTTAGC	58.473	50.000	4.14	0.00	38.92	3.09
688	3441	2.502130	ACTTAGTGGAAGCCTCTTAGCC	59.498	50.000	0.00	0.00	38.92	3.93
689	3442	2.552093	TAGTGGAAGCCTCTTAGCCT	57.448	50.000	0.00	0.00	0.00	4.58
690	3443	1.199615	AGTGGAAGCCTCTTAGCCTC	58.800	55.000	0.00	0.00	0.00	4.70
709	3462	3.511540	CCTCATGACTGACTTGGACACTA	59.488	47.826	0.00	0.00	0.00	2.74
776	3529	1.344763	GTAATCCCTGCCGACTAGCAT	59.655	52.381	0.00	0.00	43.09	3.79
812	3572	6.094881	TGAAAATAGTGCCAGCCTTGTATTAC	59.905	38.462	0.00	0.00	0.00	1.89
1311	4208	6.488006	ACATTAACTCAACACAGCTCAAGATT	59.512	34.615	0.00	0.00	0.00	2.40
1325	4222	3.329386	TCAAGATTTCAAGAGACGGCAG	58.671	45.455	0.00	0.00	0.00	4.85
1444	4344	0.037697	CACCACTAGTGCTGCCGTTA	60.038	55.000	17.86	0.00	40.28	3.18
1474	4374	3.096092	ACTGGAAACCTTGCTGTGAAAA	58.904	40.909	0.00	0.00	32.34	2.29
1787	4687	0.032117	ATGGATCCACGGACCAGAGA	60.032	55.000	18.99	0.00	37.12	3.10
1803	4703	5.892348	ACCAGAGACTTGATTAACCCAATT	58.108	37.500	0.00	0.00	0.00	2.32
2088	4988	0.179108	GGGAGTTTGAGGATCGGACG	60.179	60.000	0.00	0.00	38.61	4.79
2160	5069	3.692101	TCACAAGTTCAACGGACATGTTT	59.308	39.130	0.00	0.00	27.54	2.83
2179	5088	4.405358	TGTTTCAGCCCATTTCTCAAGTTT	59.595	37.500	0.00	0.00	0.00	2.66
2187	5096	3.004734	CCATTTCTCAAGTTTCGTTGCCT	59.995	43.478	0.00	0.00	0.00	4.75
2189	5098	3.691049	TTCTCAAGTTTCGTTGCCTTG	57.309	42.857	0.00	0.00	37.51	3.61
2283	5198	6.448006	CACTGCTTATTCCTATAACGCTAGT	58.552	40.000	0.00	0.00	0.00	2.57
2293	5208	6.944096	TCCTATAACGCTAGTAGATGCTCTA	58.056	40.000	0.00	0.00	0.00	2.43
2700	5625	4.938226	ACTATAGCAGTGAAAAGGCTTGAC	59.062	41.667	0.00	0.00	39.01	3.18
2797	5722	4.339872	AAATTGATTGGTTTCTGCTGCA	57.660	36.364	0.88	0.88	0.00	4.41
2808	5733	2.502142	TCTGCTGCAAAGGTGATCAT	57.498	45.000	3.02	0.00	0.00	2.45
2859	5784	6.821616	AATAGGTCTCTTGATGGTCATCTT	57.178	37.500	11.62	0.00	38.60	2.40
3051	5985	2.597510	GACTTTGGGTTGGCGGCT	60.598	61.111	11.43	0.00	0.00	5.52
3178	6112	2.745281	GTTTACAGCTTCGGCATGGTAA	59.255	45.455	0.00	0.00	44.74	2.85
3206	6140	4.226168	GGAAATCATATCGGGAAGGAGGAT	59.774	45.833	0.00	0.00	0.00	3.24
3207	6141	5.423886	GAAATCATATCGGGAAGGAGGATC	58.576	45.833	0.00	0.00	0.00	3.36
3245	6179	6.041409	ACATCATACTACACTAGAAGCAGCAT	59.959	38.462	0.00	0.00	0.00	3.79
3246	6180	6.078202	TCATACTACACTAGAAGCAGCATC	57.922	41.667	0.00	0.00	0.00	3.91
3247	6181	5.594317	TCATACTACACTAGAAGCAGCATCA	59.406	40.000	0.00	0.00	0.00	3.07
3250	6184	3.692257	ACACTAGAAGCAGCATCAGTT	57.308	42.857	0.00	0.00	0.00	3.16
3253	6187	3.868077	CACTAGAAGCAGCATCAGTTACC	59.132	47.826	0.00	0.00	0.00	2.85
3357	6297	5.598005	ACATGGTGACTTCAATTTGGAAGAA	59.402	36.000	11.40	0.00	45.66	2.52
3514	6464	2.675348	GCTCTAACAGAACACTGATGCC	59.325	50.000	0.00	0.00	35.80	4.40
3606	6577	7.118723	TGTAATGTGGAGCAGAAGGAATAAAT	58.881	34.615	0.00	0.00	0.00	1.40
3615	6586	7.213178	AGCAGAAGGAATAAATAAAGGAGGA	57.787	36.000	0.00	0.00	0.00	3.71
3629	6600	0.961753	GGAGGAAACCTTGCAGTTGG	59.038	55.000	0.00	0.00	31.76	3.77
3702	6912	7.624360	AATATGGTCGTGCTAGAAATTTTCA	57.376	32.000	11.53	0.00	0.00	2.69
3918	7446	3.689347	TGTTACTGCTGCCATTCATCTT	58.311	40.909	0.00	0.00	0.00	2.40
3944	7472	2.747855	CTCCCAGAACCAAGCCGC	60.748	66.667	0.00	0.00	0.00	6.53
4039	7640	3.056322	GGATCTTGCTCCATTTGTTGCTT	60.056	43.478	0.00	0.00	35.24	3.91
4141	8207	0.647925	GTTTCGCCAGCTTCGAGATC	59.352	55.000	7.73	0.00	37.26	2.75
4142	8208	0.532573	TTTCGCCAGCTTCGAGATCT	59.467	50.000	0.00	0.00	37.26	2.75
4165	8231	0.806868	CCATGACTGCTTGCGACATT	59.193	50.000	0.00	0.00	0.00	2.71
4183	8249	1.865865	TTCCAGCAACAGTTCTCGAC	58.134	50.000	0.00	0.00	0.00	4.20
4265	8331	4.340666	TGCCAGAATGCTCAAACTTAAACA	59.659	37.500	0.00	0.00	31.97	2.83
4289	8355	4.378356	CGCTTGAAGCTGTGCAAAAGTATA	60.378	41.667	15.92	0.00	39.60	1.47
4313	8379	4.081862	TCTGCCTAGTTGCAACTATAACGT	60.082	41.667	33.45	14.13	41.51	3.99
4351	8417	2.887152	GACTGTGGCTGAAGTGGAAAAT	59.113	45.455	0.00	0.00	0.00	1.82
4355	8421	5.539955	ACTGTGGCTGAAGTGGAAAATAATT	59.460	36.000	0.00	0.00	0.00	1.40
4356	8422	6.719370	ACTGTGGCTGAAGTGGAAAATAATTA	59.281	34.615	0.00	0.00	0.00	1.40
4357	8423	7.397192	ACTGTGGCTGAAGTGGAAAATAATTAT	59.603	33.333	0.00	0.00	0.00	1.28
4358	8424	7.771183	TGTGGCTGAAGTGGAAAATAATTATC	58.229	34.615	0.00	0.00	0.00	1.75
4359	8425	7.615365	TGTGGCTGAAGTGGAAAATAATTATCT	59.385	33.333	0.00	0.00	0.00	1.98
4360	8426	7.917505	GTGGCTGAAGTGGAAAATAATTATCTG	59.082	37.037	0.00	0.00	0.00	2.90
4374	14393	8.437360	AATAATTATCTGCAACGATGAGTGAA	57.563	30.769	0.00	0.00	0.00	3.18
4381	14400	2.096218	GCAACGATGAGTGAAGTGGTTC	60.096	50.000	0.00	0.00	0.00	3.62
4399	14418	4.590222	TGGTTCGGGTTCTCTAAGTAAAGT	59.410	41.667	0.00	0.00	0.00	2.66
4401	14420	5.279156	GGTTCGGGTTCTCTAAGTAAAGTGA	60.279	44.000	0.00	0.00	0.00	3.41
4404	15164	6.819284	TCGGGTTCTCTAAGTAAAGTGAAAA	58.181	36.000	0.00	0.00	32.49	2.29
4406	15166	7.440255	TCGGGTTCTCTAAGTAAAGTGAAAAAG	59.560	37.037	0.00	0.00	32.49	2.27
4442	15202	1.336887	CCGACGATGAGTGAAGTGGTT	60.337	52.381	0.00	0.00	0.00	3.67
4443	15203	2.404215	CGACGATGAGTGAAGTGGTTT	58.596	47.619	0.00	0.00	0.00	3.27
4453	15213	0.591659	GAAGTGGTTTGGGTTCTCGC	59.408	55.000	0.00	0.00	0.00	5.03
4498	15276	3.230976	TCGCAGCCCTAAGAGAATCATA	58.769	45.455	0.00	0.00	37.82	2.15
4499	15277	3.641436	TCGCAGCCCTAAGAGAATCATAA	59.359	43.478	0.00	0.00	37.82	1.90
4500	15278	3.743396	CGCAGCCCTAAGAGAATCATAAC	59.257	47.826	0.00	0.00	37.82	1.89
4501	15279	4.502259	CGCAGCCCTAAGAGAATCATAACT	60.502	45.833	0.00	0.00	37.82	2.24
4502	15280	4.994217	GCAGCCCTAAGAGAATCATAACTC	59.006	45.833	0.00	0.00	37.82	3.01
4503	15281	5.453903	GCAGCCCTAAGAGAATCATAACTCA	60.454	44.000	0.00	0.00	37.82	3.41
4506	15284	8.370940	CAGCCCTAAGAGAATCATAACTCATTA	58.629	37.037	0.00	0.00	37.82	1.90
4508	15286	9.160496	GCCCTAAGAGAATCATAACTCATTATG	57.840	37.037	0.00	1.37	46.29	1.90
4509	15287	9.160496	CCCTAAGAGAATCATAACTCATTATGC	57.840	37.037	0.00	0.00	45.07	3.14
4510	15288	9.716531	CCTAAGAGAATCATAACTCATTATGCA	57.283	33.333	0.00	0.00	45.07	3.96

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	52	6.437162	AGTGCTTTATGGGCTAATGAGAAAAA	59.563	34.615	0.00	0.00	0.00	1.94
52	53	5.951747	AGTGCTTTATGGGCTAATGAGAAAA	59.048	36.000	0.00	0.00	0.00	2.29
53	54	5.509498	AGTGCTTTATGGGCTAATGAGAAA	58.491	37.500	0.00	0.00	0.00	2.52
54	55	5.116084	AGTGCTTTATGGGCTAATGAGAA	57.884	39.130	0.00	0.00	0.00	2.87
55	56	4.778213	AGTGCTTTATGGGCTAATGAGA	57.222	40.909	0.00	0.00	0.00	3.27
56	57	5.841957	AAAGTGCTTTATGGGCTAATGAG	57.158	39.130	0.00	0.00	0.00	2.90
57	58	6.603940	AAAAAGTGCTTTATGGGCTAATGA	57.396	33.333	0.00	0.00	31.63	2.57
127	128	6.097356	TCAGTACTGTAATTCAACTAAGGCG	58.903	40.000	21.99	0.00	0.00	5.52
132	133	9.203421	CACATGTTCAGTACTGTAATTCAACTA	57.797	33.333	21.99	9.26	0.00	2.24
173	174	0.611896	CCAAAAGGGGTGGCACTAGG	60.612	60.000	18.45	5.48	0.00	3.02
179	182	3.181449	ACAAAATAACCAAAAGGGGTGGC	60.181	43.478	0.00	0.00	41.32	5.01
262	2776	5.681105	CGACCACAAACAGAAATACAACAAG	59.319	40.000	0.00	0.00	0.00	3.16
327	2851	6.662414	TTTGCTTTCATGGTCGAATACTAG	57.338	37.500	0.00	0.00	0.00	2.57
342	2866	5.793817	ACCAACCCAGAAATATTTGCTTTC	58.206	37.500	5.17	0.00	33.69	2.62
416	2942	0.550914	AGACCAGAAAAGGCACCACA	59.449	50.000	0.00	0.00	0.00	4.17
460	2991	0.961019	GCCAGCCAACAAGACAATGA	59.039	50.000	0.00	0.00	0.00	2.57
478	3009	3.371898	GGCATGCTAATTGTCAAAAAGGC	59.628	43.478	18.92	0.00	0.00	4.35
481	3012	3.986572	CACGGCATGCTAATTGTCAAAAA	59.013	39.130	18.92	0.00	0.00	1.94
583	3114	3.753815	TCAAGTCAATCATGTGGCTTCA	58.246	40.909	0.45	0.00	41.48	3.02
590	3121	2.426024	GCCATGCTCAAGTCAATCATGT	59.574	45.455	0.00	0.00	34.36	3.21
683	3436	3.055819	GTCCAAGTCAGTCATGAGGCTAA	60.056	47.826	0.00	0.00	35.66	3.09
684	3437	2.497675	GTCCAAGTCAGTCATGAGGCTA	59.502	50.000	0.00	0.00	35.66	3.93
685	3438	1.277557	GTCCAAGTCAGTCATGAGGCT	59.722	52.381	0.00	0.00	35.66	4.58
686	3439	1.002430	TGTCCAAGTCAGTCATGAGGC	59.998	52.381	0.00	0.00	35.66	4.70
687	3440	2.301296	AGTGTCCAAGTCAGTCATGAGG	59.699	50.000	0.00	0.00	35.66	3.86
688	3441	3.674528	AGTGTCCAAGTCAGTCATGAG	57.325	47.619	0.00	0.00	35.66	2.90
689	3442	3.511540	CCTAGTGTCCAAGTCAGTCATGA	59.488	47.826	0.00	0.00	0.00	3.07
690	3443	3.259374	ACCTAGTGTCCAAGTCAGTCATG	59.741	47.826	0.00	0.00	0.00	3.07
709	3462	4.154942	ACTTTCAATGATGCTTTCCACCT	58.845	39.130	0.00	0.00	0.00	4.00
776	3529	7.517614	TGGCACTATTTTCATGAAAACTACA	57.482	32.000	30.64	20.82	42.32	2.74
812	3572	0.103208	GGTGCCACTATCTCTCCGTG	59.897	60.000	0.00	0.00	0.00	4.94
1444	4344	3.319122	GCAAGGTTTCCAGTGTTCAAGAT	59.681	43.478	0.00	0.00	0.00	2.40
1474	4374	3.713248	TCAGACAATGGGCTATCTGTGAT	59.287	43.478	4.06	0.00	39.68	3.06
1787	4687	8.865090	TGTCAACATAAATTGGGTTAATCAAGT	58.135	29.630	0.00	0.00	0.00	3.16
1803	4703	5.875224	TCCTCTTGGTCATTGTCAACATAA	58.125	37.500	0.00	0.00	34.23	1.90
1875	4775	9.868160	TTTATCAGACCAGAGATATCTAGTGAA	57.132	33.333	4.89	0.00	0.00	3.18
2066	4966	1.278127	TCCGATCCTCAAACTCCCAAC	59.722	52.381	0.00	0.00	0.00	3.77
2088	4988	3.817647	GTGTATTTCTGATGCATCCTCCC	59.182	47.826	23.67	6.11	0.00	4.30
2160	5069	2.813754	CGAAACTTGAGAAATGGGCTGA	59.186	45.455	0.00	0.00	0.00	4.26
2187	5096	2.315176	ACTATGCTTTGTGGGTTGCAA	58.685	42.857	0.00	0.00	38.96	4.08
2189	5098	2.676076	CAACTATGCTTTGTGGGTTGC	58.324	47.619	0.00	0.00	0.00	4.17
2293	5208	3.979501	AAGCAAGTCCCCATTCCATAT	57.020	42.857	0.00	0.00	0.00	1.78
2454	5370	5.772393	TGAACATGAGTAACCCAATACCT	57.228	39.130	0.00	0.00	0.00	3.08
2770	5695	7.598493	GCAGCAGAAACCAATCAATTTTACTAA	59.402	33.333	0.00	0.00	0.00	2.24
2797	5722	6.779860	ACACAAGTAACCTATGATCACCTTT	58.220	36.000	0.00	0.00	0.00	3.11
2859	5784	5.477984	AGCAGTGGCATCATTTCTCTTAAAA	59.522	36.000	0.00	0.00	44.61	1.52
2944	5878	5.706833	TGCATTTGTGACAACTCTGATGTAT	59.293	36.000	0.00	0.00	0.00	2.29
3051	5985	3.580895	GGCTAAAATCCCTTCCCACAAAA	59.419	43.478	0.00	0.00	0.00	2.44
3178	6112	5.072741	CCTTCCCGATATGATTTCCAACAT	58.927	41.667	0.00	0.00	0.00	2.71
3206	6140	6.611613	AGTATGATGTTTCAAGTGAGGAGA	57.388	37.500	0.00	0.00	34.96	3.71
3207	6141	7.276658	GTGTAGTATGATGTTTCAAGTGAGGAG	59.723	40.741	0.00	0.00	34.96	3.69
3245	6179	7.065324	GGAAATATTCGACATTGTGGTAACTGA	59.935	37.037	0.00	0.00	37.61	3.41
3246	6180	7.186804	GGAAATATTCGACATTGTGGTAACTG	58.813	38.462	0.00	0.00	37.61	3.16
3247	6181	6.317893	GGGAAATATTCGACATTGTGGTAACT	59.682	38.462	0.00	0.00	37.61	2.24
3250	6184	5.820423	CAGGGAAATATTCGACATTGTGGTA	59.180	40.000	0.00	0.00	0.00	3.25
3253	6187	5.572211	CACAGGGAAATATTCGACATTGTG	58.428	41.667	0.00	0.00	0.00	3.33
3357	6297	4.427312	CAACTTTGCAAACTCTTTCAGCT	58.573	39.130	8.05	0.00	0.00	4.24
3606	6577	3.876309	ACTGCAAGGTTTCCTCCTTTA	57.124	42.857	0.00	0.00	44.36	1.85
3615	6586	4.590222	AGATGATTTCCAACTGCAAGGTTT	59.410	37.500	0.00	0.00	39.30	3.27
3702	6912	4.512944	CAGCTTACAAGTGACACATCAACT	59.487	41.667	8.59	0.00	36.31	3.16
3918	7446	1.707989	TGGTTCTGGGAGGCAATGTTA	59.292	47.619	0.00	0.00	0.00	2.41
3944	7472	1.856539	ATGGACTGCAGGTTCAGGGG	61.857	60.000	19.93	0.00	36.79	4.79
4141	8207	1.642037	CGCAAGCAGTCATGGTGGAG	61.642	60.000	0.00	0.00	37.19	3.86
4142	8208	1.672030	CGCAAGCAGTCATGGTGGA	60.672	57.895	0.00	0.00	37.19	4.02
4165	8231	1.040646	AGTCGAGAACTGTTGCTGGA	58.959	50.000	0.00	0.00	36.65	3.86
4183	8249	1.679139	TCCCTGCAACAAACAGACAG	58.321	50.000	0.00	0.00	37.32	3.51
4289	8355	5.050490	CGTTATAGTTGCAACTAGGCAGAT	58.950	41.667	35.23	24.39	45.88	2.90
4313	8379	4.696877	CACAGTCCATGCTATCACAGAAAA	59.303	41.667	0.00	0.00	0.00	2.29
4351	8417	7.010460	CACTTCACTCATCGTTGCAGATAATTA	59.990	37.037	0.00	0.00	0.00	1.40
4355	8421	4.176271	CACTTCACTCATCGTTGCAGATA	58.824	43.478	0.00	0.00	0.00	1.98
4356	8422	2.998670	CACTTCACTCATCGTTGCAGAT	59.001	45.455	0.00	0.00	0.00	2.90
4357	8423	2.407090	CACTTCACTCATCGTTGCAGA	58.593	47.619	0.00	0.00	0.00	4.26
4358	8424	1.462283	CCACTTCACTCATCGTTGCAG	59.538	52.381	0.00	0.00	0.00	4.41
4359	8425	1.202639	ACCACTTCACTCATCGTTGCA	60.203	47.619	0.00	0.00	0.00	4.08
4360	8426	1.512926	ACCACTTCACTCATCGTTGC	58.487	50.000	0.00	0.00	0.00	4.17
4374	14393	2.606378	ACTTAGAGAACCCGAACCACT	58.394	47.619	0.00	0.00	0.00	4.00
4381	14400	7.440255	TCTTTTTCACTTTACTTAGAGAACCCG	59.560	37.037	0.00	0.00	0.00	5.28
4399	14418	6.449698	GGCAGATCAAACTCATTCTTTTTCA	58.550	36.000	0.00	0.00	0.00	2.69
4401	14420	5.241506	TCGGCAGATCAAACTCATTCTTTTT	59.758	36.000	0.00	0.00	0.00	1.94
4404	15164	3.686726	GTCGGCAGATCAAACTCATTCTT	59.313	43.478	0.00	0.00	0.00	2.52
4406	15166	2.029728	CGTCGGCAGATCAAACTCATTC	59.970	50.000	0.00	0.00	0.00	2.67
4442	15202	0.034896	GAGAACCAGCGAGAACCCAA	59.965	55.000	0.00	0.00	0.00	4.12
4443	15203	0.832135	AGAGAACCAGCGAGAACCCA	60.832	55.000	0.00	0.00	0.00	4.51
4453	15213	2.027377	AGTCTTGGCATCAGAGAACCAG	60.027	50.000	0.00	0.00	32.79	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.