AutoCloner

Multiple sequence alignment - TraesCS2B01G343600

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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	TraesCS2B01G343600	chr2B	100.000	3252	0	0	1	3252	489417782	489421033	0.000000e+00	6006.0
1	TraesCS2B01G343600	chr2B	92.500	80	5	1	3085	3163	614917139	614917218	2.650000e-21	113.0
2	TraesCS2B01G343600	chr2B	89.024	82	8	1	3086	3166	168851945	168852026	2.060000e-17	100.0
3	TraesCS2B01G343600	chr2D	93.514	2467	72	42	670	3087	417543513	417545940	0.000000e+00	3589.0
4	TraesCS2B01G343600	chr2D	79.710	276	41	5	1259	1520	53649287	53649561	5.540000e-43	185.0
5	TraesCS2B01G343600	chr2D	98.795	83	1	0	3170	3252	417545954	417546036	7.270000e-32	148.0
6	TraesCS2B01G343600	chr2A	91.663	2291	80	37	670	2891	572616429	572614181	0.000000e+00	3070.0
7	TraesCS2B01G343600	chr2A	99.560	455	2	0	1	455	742797394	742797848	0.000000e+00	830.0
8	TraesCS2B01G343600	chr2A	95.455	154	7	0	2935	3088	572614184	572614031	2.510000e-61	246.0
9	TraesCS2B01G343600	chr2A	95.745	94	2	2	3159	3252	572614034	572613943	2.020000e-32	150.0
10	TraesCS2B01G343600	chr1B	97.015	670	14	1	1	670	419967104	419967767	0.000000e+00	1122.0
11	TraesCS2B01G343600	chr1B	93.883	703	11	4	1	671	65587451	65586749	0.000000e+00	1031.0
12	TraesCS2B01G343600	chr1B	99.341	455	3	0	1	455	167951380	167950926	0.000000e+00	824.0
13	TraesCS2B01G343600	chr1B	99.341	455	3	0	1	455	303582519	303582065	0.000000e+00	824.0
14	TraesCS2B01G343600	chr1B	96.774	217	7	0	457	673	167950892	167950676	2.380000e-96	363.0
15	TraesCS2B01G343600	chr7B	96.588	674	11	3	1	673	570467995	570467333	0.000000e+00	1107.0
16	TraesCS2B01G343600	chr7B	96.774	217	7	0	457	673	74089239	74089455	2.380000e-96	363.0
17	TraesCS2B01G343600	chr7B	81.057	227	35	7	1280	1499	455272022	455271797	1.200000e-39	174.0
18	TraesCS2B01G343600	chr1A	99.560	455	2	0	1	455	521318381	521318835	0.000000e+00	830.0
19	TraesCS2B01G343600	chr5A	99.341	455	3	0	1	455	400069391	400068937	0.000000e+00	824.0
20	TraesCS2B01G343600	chr5A	99.341	455	3	0	1	455	521677535	521677989	0.000000e+00	824.0
21	TraesCS2B01G343600	chr5A	97.183	213	6	0	457	669	687717056	687716844	8.580000e-96	361.0
22	TraesCS2B01G343600	chr3B	96.833	221	7	0	457	677	798435864	798436084	1.430000e-98	370.0
23	TraesCS2B01G343600	chr3B	89.286	84	7	2	3081	3162	5175445	5175528	1.600000e-18	104.0
24	TraesCS2B01G343600	chr3B	77.397	146	25	5	1035	1176	583392857	583392716	2.690000e-11	80.5
25	TraesCS2B01G343600	chr3B	90.909	55	5	0	1038	1092	22505935	22505881	1.250000e-09	75.0
26	TraesCS2B01G343600	chr6B	96.774	217	7	0	457	673	47437441	47437225	2.380000e-96	363.0
27	TraesCS2B01G343600	chr7A	97.183	213	6	0	457	669	708293364	708293152	8.580000e-96	361.0
28	TraesCS2B01G343600	chr7A	95.556	225	8	2	457	681	549396107	549395885	3.080000e-95	359.0
29	TraesCS2B01G343600	chr7A	81.858	226	35	5	1280	1499	489163234	489163459	5.540000e-43	185.0
30	TraesCS2B01G343600	chr5B	97.183	213	6	0	457	669	158896903	158897115	8.580000e-96	361.0
31	TraesCS2B01G343600	chr5B	80.667	150	23	3	1036	1182	461141441	461141295	9.540000e-21	111.0
32	TraesCS2B01G343600	chr5B	89.157	83	7	2	3080	3162	255305556	255305636	5.740000e-18	102.0
33	TraesCS2B01G343600	chr4A	84.677	248	35	2	1268	1512	173630690	173630937	9.010000e-61	244.0
34	TraesCS2B01G343600	chr4A	93.506	77	2	1	3086	3162	90090690	90090617	9.540000e-21	111.0
35	TraesCS2B01G343600	chr4A	89.655	87	5	2	3086	3169	735837496	735837411	1.230000e-19	108.0
36	TraesCS2B01G343600	chr4D	84.274	248	36	2	1268	1512	305141322	305141569	4.190000e-59	239.0
37	TraesCS2B01G343600	chr4D	88.776	98	8	3	3086	3181	43548946	43548850	2.050000e-22	117.0
38	TraesCS2B01G343600	chr4B	84.211	247	36	2	1268	1511	381374103	381374349	1.510000e-58	237.0
39	TraesCS2B01G343600	chr7D	81.223	229	37	5	1277	1499	438368646	438368874	2.580000e-41	180.0
40	TraesCS2B01G343600	chr7D	85.714	70	10	0	1036	1105	215096454	215096385	1.250000e-09	75.0
41	TraesCS2B01G343600	chr5D	81.333	150	22	3	1036	1182	384348078	384347932	2.050000e-22	117.0
42	TraesCS2B01G343600	chr5D	93.590	78	3	1	3087	3162	465200378	465200301	7.370000e-22	115.0
43	TraesCS2B01G343600	chr5D	90.476	63	5	1	1035	1096	519277281	519277343	7.480000e-12	82.4
44	TraesCS2B01G343600	chr6D	87.879	99	7	5	3069	3165	63834825	63834730	9.540000e-21	111.0
45	TraesCS2B01G343600	chr3D	78.082	146	24	5	1035	1176	445038185	445038044	5.780000e-13	86.1

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	TraesCS2B01G343600	chr2B	489417782	489421033	3251	False	6006.000000	6006	100.000000	1	3252	1	chr2B.!!$F2	3251
1	TraesCS2B01G343600	chr2D	417543513	417546036	2523	False	1868.500000	3589	96.154500	670	3252	2	chr2D.!!$F2	2582
2	TraesCS2B01G343600	chr2A	572613943	572616429	2486	True	1155.333333	3070	94.287667	670	3252	3	chr2A.!!$R1	2582
3	TraesCS2B01G343600	chr1B	419967104	419967767	663	False	1122.000000	1122	97.015000	1	670	1	chr1B.!!$F1	669
4	TraesCS2B01G343600	chr1B	65586749	65587451	702	True	1031.000000	1031	93.883000	1	671	1	chr1B.!!$R1	670
5	TraesCS2B01G343600	chr1B	167950676	167951380	704	True	593.500000	824	98.057500	1	673	2	chr1B.!!$R3	672
6	TraesCS2B01G343600	chr7B	570467333	570467995	662	True	1107.000000	1107	96.588000	1	673	1	chr7B.!!$R2	672

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
463	496	1.079681	CGGGGTTCGACGGATGAAA	60.080	57.895	0.0	0.0	42.43	2.69	F
1757	1824	0.110644	GTCGTCCGCAGCAAAGAAAG	60.111	55.000	0.0	0.0	0.00	2.62	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1906	1973	0.032952	CCGTCGGGTTGAAGAACTGA	59.967	55.0	2.34	0.0	32.15	3.41	R
2868	2969	0.468226	CCTAATACCAAGCTCGCCCA	59.532	55.0	0.00	0.0	0.00	5.36	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
209	210	3.128349	GCGAATATACACCGAACCATGT	58.872	45.455	0.00	0.00	0.00	3.21
461	494	2.361483	TCGGGGTTCGACGGATGA	60.361	61.111	0.00	0.00	43.74	2.92
463	496	1.079681	CGGGGTTCGACGGATGAAA	60.080	57.895	0.00	0.00	42.43	2.69
576	609	2.631428	GTGCTTTTGTGCGCTCGA	59.369	55.556	9.73	0.87	40.01	4.04
703	737	2.752238	CCCTCTCGCGTCCAGACT	60.752	66.667	5.77	0.00	0.00	3.24
810	844	7.711339	CGATTGAGTCCATATCATCATCATCAT	59.289	37.037	0.00	0.00	0.00	2.45
811	845	8.966069	ATTGAGTCCATATCATCATCATCATC	57.034	34.615	0.00	0.00	0.00	2.92
812	846	7.490657	TGAGTCCATATCATCATCATCATCA	57.509	36.000	0.00	0.00	0.00	3.07
817	851	8.041919	GTCCATATCATCATCATCATCAGTTCT	58.958	37.037	0.00	0.00	0.00	3.01
871	913	2.632996	TCGGATCTCTCTCTCTCTCTCC	59.367	54.545	0.00	0.00	0.00	3.71
872	914	2.289694	CGGATCTCTCTCTCTCTCTCCC	60.290	59.091	0.00	0.00	0.00	4.30
873	915	2.982488	GGATCTCTCTCTCTCTCTCCCT	59.018	54.545	0.00	0.00	0.00	4.20
874	916	3.008485	GGATCTCTCTCTCTCTCTCCCTC	59.992	56.522	0.00	0.00	0.00	4.30
875	917	3.421394	TCTCTCTCTCTCTCTCCCTCT	57.579	52.381	0.00	0.00	0.00	3.69
876	918	3.309296	TCTCTCTCTCTCTCTCCCTCTC	58.691	54.545	0.00	0.00	0.00	3.20
884	926	2.368548	TCTCTCTCCCTCTCTCTCATCG	59.631	54.545	0.00	0.00	0.00	3.84
987	1029	4.079253	TGTTTGGTTGATTTCTAGAGGGC	58.921	43.478	0.00	0.00	0.00	5.19
988	1030	3.366052	TTGGTTGATTTCTAGAGGGCC	57.634	47.619	0.00	0.00	0.00	5.80
1204	1246	1.985159	ACCTCTTCATGCACCAACCTA	59.015	47.619	0.00	0.00	0.00	3.08
1248	1290	2.427453	ACGAGCTACCGAATTGATCAGT	59.573	45.455	1.33	0.00	0.00	3.41
1250	1292	3.046390	GAGCTACCGAATTGATCAGTCG	58.954	50.000	18.90	18.90	34.58	4.18
1253	1295	3.733988	GCTACCGAATTGATCAGTCGACA	60.734	47.826	24.55	14.26	36.92	4.35
1566	1628	4.776322	CAGGGCCGCATCGTCCAA	62.776	66.667	0.00	0.00	0.00	3.53
1595	1657	4.182693	ACATCTTTTCACCATGCATGTG	57.817	40.909	24.58	20.71	0.00	3.21
1596	1658	3.575256	ACATCTTTTCACCATGCATGTGT	59.425	39.130	24.58	18.38	0.00	3.72
1597	1659	3.646611	TCTTTTCACCATGCATGTGTG	57.353	42.857	28.34	28.34	33.28	3.82
1598	1660	2.957680	TCTTTTCACCATGCATGTGTGT	59.042	40.909	30.53	19.44	33.55	3.72
1599	1661	4.140536	TCTTTTCACCATGCATGTGTGTA	58.859	39.130	30.53	24.32	33.55	2.90
1600	1662	4.766373	TCTTTTCACCATGCATGTGTGTAT	59.234	37.500	30.53	10.16	33.55	2.29
1601	1663	4.700268	TTTCACCATGCATGTGTGTATC	57.300	40.909	30.53	0.00	33.55	2.24
1633	1700	8.971073	TGTGATCGATCATATATACTTGGTCAT	58.029	33.333	29.53	0.00	39.30	3.06
1645	1712	4.877378	ACTTGGTCATTCGTAGTAACCA	57.123	40.909	0.00	0.00	38.20	3.67
1757	1824	0.110644	GTCGTCCGCAGCAAAGAAAG	60.111	55.000	0.00	0.00	0.00	2.62
2217	2287	1.807142	CTCTTCTTCCTTCGGCCAAAC	59.193	52.381	2.24	0.00	0.00	2.93
2298	2368	0.461870	TTCGTGGCGAAGGATGGATG	60.462	55.000	0.00	0.00	41.05	3.51
2308	2378	5.491982	GCGAAGGATGGATGGATTATTAGT	58.508	41.667	0.00	0.00	0.00	2.24
2363	2433	0.878086	GCGAGGGATCAAGCTAGCAC	60.878	60.000	18.83	2.59	0.00	4.40
2364	2434	0.249657	CGAGGGATCAAGCTAGCACC	60.250	60.000	18.83	11.31	0.00	5.01
2365	2435	0.249657	GAGGGATCAAGCTAGCACCG	60.250	60.000	18.83	4.51	0.00	4.94
2366	2436	1.227674	GGGATCAAGCTAGCACCGG	60.228	63.158	18.83	0.00	0.00	5.28
2451	2522	6.322712	TGATTTGGGGGTGTAATTAGCATTAC	59.677	38.462	1.00	1.00	43.67	1.89
2502	2577	9.918630	AGTATATTTCATTATCATTTTGCCAGC	57.081	29.630	0.00	0.00	0.00	4.85
2507	2582	9.841295	ATTTCATTATCATTTTGCCAGCTTAAT	57.159	25.926	0.00	0.00	0.00	1.40
2508	2583	9.669887	TTTCATTATCATTTTGCCAGCTTAATT	57.330	25.926	0.00	0.00	0.00	1.40
2558	2635	0.451135	GCAGCTGCGTTCGTTAAGTG	60.451	55.000	25.23	0.00	0.00	3.16
2560	2637	1.525197	CAGCTGCGTTCGTTAAGTGAA	59.475	47.619	0.00	0.00	0.00	3.18
2561	2638	1.792949	AGCTGCGTTCGTTAAGTGAAG	59.207	47.619	0.00	0.00	0.00	3.02
2563	2640	2.412089	GCTGCGTTCGTTAAGTGAAGAT	59.588	45.455	0.00	0.00	0.00	2.40
2652	2753	4.124970	GACGGAAACCTAACAGTTTGACT	58.875	43.478	0.00	0.00	40.01	3.41
2671	2772	9.257651	GTTTGACTTGTTGTGATAGTAGTTAGT	57.742	33.333	0.00	0.00	0.00	2.24
2878	2979	0.745845	GACATGATGTGGGCGAGCTT	60.746	55.000	1.23	0.00	0.00	3.74
2879	2980	1.028330	ACATGATGTGGGCGAGCTTG	61.028	55.000	0.00	0.00	0.00	4.01
2917	3018	2.423892	ACCGCAACAACACATAACAACA	59.576	40.909	0.00	0.00	0.00	3.33
2927	3028	3.554324	ACACATAACAACACTCGTGTCAC	59.446	43.478	2.81	0.00	44.13	3.67
2932	3033	2.639065	ACAACACTCGTGTCACCAATT	58.361	42.857	2.81	0.00	44.13	2.32
3085	3186	6.152661	TGGTGGATCCAGTTCATGAAAATTAC	59.847	38.462	16.81	0.00	41.93	1.89
3088	3189	8.398665	GTGGATCCAGTTCATGAAAATTACTAC	58.601	37.037	16.81	5.34	0.00	2.73
3089	3190	8.328758	TGGATCCAGTTCATGAAAATTACTACT	58.671	33.333	11.44	0.00	0.00	2.57
3090	3191	8.831550	GGATCCAGTTCATGAAAATTACTACTC	58.168	37.037	10.35	1.55	0.00	2.59
3091	3192	8.738645	ATCCAGTTCATGAAAATTACTACTCC	57.261	34.615	10.35	0.00	0.00	3.85
3092	3193	7.110155	TCCAGTTCATGAAAATTACTACTCCC	58.890	38.462	10.35	0.00	0.00	4.30
3093	3194	7.037586	TCCAGTTCATGAAAATTACTACTCCCT	60.038	37.037	10.35	0.00	0.00	4.20
3094	3195	7.281100	CCAGTTCATGAAAATTACTACTCCCTC	59.719	40.741	10.35	0.00	0.00	4.30
3095	3196	7.281100	CAGTTCATGAAAATTACTACTCCCTCC	59.719	40.741	10.35	0.00	0.00	4.30
3096	3197	5.914033	TCATGAAAATTACTACTCCCTCCG	58.086	41.667	0.00	0.00	0.00	4.63
3097	3198	5.424252	TCATGAAAATTACTACTCCCTCCGT	59.576	40.000	0.00	0.00	0.00	4.69
3098	3199	5.334724	TGAAAATTACTACTCCCTCCGTC	57.665	43.478	0.00	0.00	0.00	4.79
3099	3200	4.161001	TGAAAATTACTACTCCCTCCGTCC	59.839	45.833	0.00	0.00	0.00	4.79
3100	3201	2.378378	ATTACTACTCCCTCCGTCCC	57.622	55.000	0.00	0.00	0.00	4.46
3101	3202	1.002069	TTACTACTCCCTCCGTCCCA	58.998	55.000	0.00	0.00	0.00	4.37
3102	3203	1.229131	TACTACTCCCTCCGTCCCAT	58.771	55.000	0.00	0.00	0.00	4.00
3103	3204	1.229131	ACTACTCCCTCCGTCCCATA	58.771	55.000	0.00	0.00	0.00	2.74
3104	3205	1.572415	ACTACTCCCTCCGTCCCATAA	59.428	52.381	0.00	0.00	0.00	1.90
3105	3206	2.179424	ACTACTCCCTCCGTCCCATAAT	59.821	50.000	0.00	0.00	0.00	1.28
3106	3207	1.424638	ACTCCCTCCGTCCCATAATG	58.575	55.000	0.00	0.00	0.00	1.90
3107	3208	1.344087	ACTCCCTCCGTCCCATAATGT	60.344	52.381	0.00	0.00	0.00	2.71
3108	3209	2.090943	ACTCCCTCCGTCCCATAATGTA	60.091	50.000	0.00	0.00	0.00	2.29
3109	3210	2.969950	CTCCCTCCGTCCCATAATGTAA	59.030	50.000	0.00	0.00	0.00	2.41
3110	3211	2.969950	TCCCTCCGTCCCATAATGTAAG	59.030	50.000	0.00	0.00	0.00	2.34
3111	3212	2.969950	CCCTCCGTCCCATAATGTAAGA	59.030	50.000	0.00	0.00	0.00	2.10
3112	3213	3.244112	CCCTCCGTCCCATAATGTAAGAC	60.244	52.174	0.00	0.00	0.00	3.01
3113	3214	3.386726	CCTCCGTCCCATAATGTAAGACA	59.613	47.826	0.00	0.00	0.00	3.41
3114	3215	4.040461	CCTCCGTCCCATAATGTAAGACAT	59.960	45.833	0.00	0.00	41.31	3.06
3116	3217	5.996644	TCCGTCCCATAATGTAAGACATTT	58.003	37.500	9.92	0.00	45.80	2.32
3117	3218	6.419791	TCCGTCCCATAATGTAAGACATTTT	58.580	36.000	9.92	0.33	45.80	1.82
3118	3219	6.887545	TCCGTCCCATAATGTAAGACATTTTT	59.112	34.615	9.92	0.00	45.80	1.94
3154	3255	8.786826	AAAAACGTCTTACATTATGAGATGGA	57.213	30.769	0.00	0.00	34.85	3.41
3155	3256	8.425577	AAAACGTCTTACATTATGAGATGGAG	57.574	34.615	0.00	0.00	34.85	3.86
3156	3257	6.090483	ACGTCTTACATTATGAGATGGAGG	57.910	41.667	0.00	0.00	34.85	4.30
3157	3258	5.011125	ACGTCTTACATTATGAGATGGAGGG	59.989	44.000	0.00	0.00	34.85	4.30
3158	3259	5.243954	CGTCTTACATTATGAGATGGAGGGA	59.756	44.000	0.00	0.00	0.00	4.20
3159	3260	6.571344	CGTCTTACATTATGAGATGGAGGGAG	60.571	46.154	0.00	0.00	0.00	4.30
3160	3261	6.268847	GTCTTACATTATGAGATGGAGGGAGT	59.731	42.308	0.00	0.00	0.00	3.85
3161	3262	7.451877	GTCTTACATTATGAGATGGAGGGAGTA	59.548	40.741	0.00	0.00	0.00	2.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
209	210	7.465116	GTCCATACTATAGGGGTAGAACACTA	58.535	42.308	4.43	0.00	0.00	2.74
275	276	2.421751	TTCTCGATCTCGTCCTTCCT	57.578	50.000	0.00	0.00	40.80	3.36
598	631	3.120979	CTCGTGCGGCATAGACGGA	62.121	63.158	5.72	0.00	32.98	4.69
628	661	0.172803	GTGTGGCGTCGATAGGAACT	59.827	55.000	0.00	0.00	46.37	3.01
703	737	4.420168	GCGCTTAAATACTGGAATTTGCA	58.580	39.130	0.00	0.00	31.63	4.08
843	885	3.202151	AGAGAGAGAGATCCGAAGAAGGT	59.798	47.826	0.00	0.00	0.00	3.50
871	913	2.030007	GGATTGAGCGATGAGAGAGAGG	60.030	54.545	0.00	0.00	0.00	3.69
872	914	2.622470	TGGATTGAGCGATGAGAGAGAG	59.378	50.000	0.00	0.00	0.00	3.20
873	915	2.622470	CTGGATTGAGCGATGAGAGAGA	59.378	50.000	0.00	0.00	0.00	3.10
874	916	2.863312	GCTGGATTGAGCGATGAGAGAG	60.863	54.545	0.00	0.00	0.00	3.20
875	917	1.068281	GCTGGATTGAGCGATGAGAGA	59.932	52.381	0.00	0.00	0.00	3.10
876	918	1.500108	GCTGGATTGAGCGATGAGAG	58.500	55.000	0.00	0.00	0.00	3.20
924	966	2.542020	TGGATGAAACAGAAGCACGA	57.458	45.000	0.00	0.00	0.00	4.35
925	967	2.743664	TCATGGATGAAACAGAAGCACG	59.256	45.455	0.00	0.00	33.08	5.34
926	968	4.978083	ATCATGGATGAAACAGAAGCAC	57.022	40.909	0.00	0.00	40.69	4.40
987	1029	2.229784	GTGCTCCATCACTTCCTTTTGG	59.770	50.000	0.00	0.00	36.07	3.28
988	1030	2.095567	CGTGCTCCATCACTTCCTTTTG	60.096	50.000	0.00	0.00	34.92	2.44
1204	1246	4.838423	TGGGTTCTATCGTATGGATCACAT	59.162	41.667	0.00	0.00	43.68	3.21
1248	1290	3.868123	GCGCTGCATGCATGTCGA	61.868	61.111	28.99	15.21	43.06	4.20
1250	1292	2.277949	CAGCGCTGCATGCATGTC	60.278	61.111	26.68	18.98	43.06	3.06
1360	1422	2.267961	CCGGTGGCCTTCCAGTAC	59.732	66.667	3.32	0.00	44.48	2.73
1465	1527	1.904771	CATGACCCAGCCGGACTTA	59.095	57.895	5.05	0.00	34.64	2.24
1566	1628	4.098914	TGGTGAAAAGATGTTGCTACCT	57.901	40.909	0.00	0.00	0.00	3.08
1595	1657	4.805719	TGATCGATCACAAGCAAGATACAC	59.194	41.667	23.99	0.00	0.00	2.90
1596	1658	5.009854	TGATCGATCACAAGCAAGATACA	57.990	39.130	23.99	0.00	0.00	2.29
1597	1659	7.824704	ATATGATCGATCACAAGCAAGATAC	57.175	36.000	29.49	0.00	40.03	2.24
1599	1661	9.526713	GTATATATGATCGATCACAAGCAAGAT	57.473	33.333	29.49	13.25	40.03	2.40
1600	1662	8.743714	AGTATATATGATCGATCACAAGCAAGA	58.256	33.333	29.49	10.03	40.03	3.02
1601	1663	8.923609	AGTATATATGATCGATCACAAGCAAG	57.076	34.615	29.49	0.00	40.03	4.01
1633	1700	1.591183	GGCCGGTGGTTACTACGAA	59.409	57.895	1.90	0.00	0.00	3.85
1744	1811	2.126734	CCGCCTTTCTTTGCTGCG	60.127	61.111	0.00	0.00	44.47	5.18
1800	1867	3.083997	GAGGGAGCGGGGTGACAT	61.084	66.667	0.00	0.00	0.00	3.06
1906	1973	0.032952	CCGTCGGGTTGAAGAACTGA	59.967	55.000	2.34	0.00	32.15	3.41
1963	2030	0.599060	GGGAGTATGACGAGGCTAGC	59.401	60.000	6.04	6.04	0.00	3.42
2298	2368	5.562113	GCACCGGTAAATGCACTAATAATCC	60.562	44.000	6.87	0.00	41.65	3.01
2308	2378	3.275617	AATCTAGCACCGGTAAATGCA	57.724	42.857	6.87	0.00	44.59	3.96
2354	2424	2.175035	TTAACGGCCGGTGCTAGCTT	62.175	55.000	29.82	12.62	37.74	3.74
2363	2433	1.658994	TGAAGCTAATTAACGGCCGG	58.341	50.000	31.76	10.83	0.00	6.13
2364	2434	3.064820	ACAATGAAGCTAATTAACGGCCG	59.935	43.478	26.86	26.86	0.00	6.13
2365	2435	4.351192	CACAATGAAGCTAATTAACGGCC	58.649	43.478	0.00	0.00	0.00	6.13
2366	2436	4.142469	ACCACAATGAAGCTAATTAACGGC	60.142	41.667	0.00	0.00	0.00	5.68
2451	2522	3.751479	TGTCGATGGATCCCAATACAG	57.249	47.619	9.90	0.00	36.95	2.74
2524	2599	3.549625	GCAGCTGCCAACTTGCTAATATC	60.550	47.826	28.76	0.00	35.05	1.63
2525	2600	2.360165	GCAGCTGCCAACTTGCTAATAT	59.640	45.455	28.76	0.00	35.05	1.28
2526	2601	1.745087	GCAGCTGCCAACTTGCTAATA	59.255	47.619	28.76	0.00	35.05	0.98
2527	2602	0.529378	GCAGCTGCCAACTTGCTAAT	59.471	50.000	28.76	0.00	35.05	1.73
2528	2603	1.855213	CGCAGCTGCCAACTTGCTAA	61.855	55.000	32.07	0.00	37.91	3.09
2530	2605	3.667282	CGCAGCTGCCAACTTGCT	61.667	61.111	32.07	0.00	37.91	3.91
2532	2607	1.370900	GAACGCAGCTGCCAACTTG	60.371	57.895	32.07	19.26	37.91	3.16
2533	2608	2.896801	CGAACGCAGCTGCCAACTT	61.897	57.895	32.07	17.78	37.91	2.66
2584	2684	9.130312	GCTAGCTACTCACAACATACAATATAC	57.870	37.037	7.70	0.00	0.00	1.47
2587	2687	7.348080	AGCTAGCTACTCACAACATACAATA	57.652	36.000	17.69	0.00	0.00	1.90
2588	2688	6.227298	AGCTAGCTACTCACAACATACAAT	57.773	37.500	17.69	0.00	0.00	2.71
2590	2690	5.886474	ACTAGCTAGCTACTCACAACATACA	59.114	40.000	20.67	0.00	0.00	2.29
2591	2691	6.183360	ACACTAGCTAGCTACTCACAACATAC	60.183	42.308	20.67	0.00	0.00	2.39
2592	2692	5.886474	ACACTAGCTAGCTACTCACAACATA	59.114	40.000	20.67	0.00	0.00	2.29
2593	2693	4.707448	ACACTAGCTAGCTACTCACAACAT	59.293	41.667	20.67	0.00	0.00	2.71
2597	2697	3.440522	CACACACTAGCTAGCTACTCACA	59.559	47.826	20.67	1.02	0.00	3.58
2598	2698	3.690139	TCACACACTAGCTAGCTACTCAC	59.310	47.826	20.67	0.00	0.00	3.51
2599	2699	3.951663	TCACACACTAGCTAGCTACTCA	58.048	45.455	20.67	2.24	0.00	3.41
2600	2700	4.576873	TCATCACACACTAGCTAGCTACTC	59.423	45.833	20.67	0.00	0.00	2.59
2652	2753	6.151648	AGCGGTACTAACTACTATCACAACAA	59.848	38.462	0.00	0.00	0.00	2.83
2868	2969	0.468226	CCTAATACCAAGCTCGCCCA	59.532	55.000	0.00	0.00	0.00	5.36
2878	2979	2.810164	GGTTTGCCAACCCTAATACCA	58.190	47.619	8.54	0.00	46.38	3.25
3085	3186	2.376695	TTATGGGACGGAGGGAGTAG	57.623	55.000	0.00	0.00	0.00	2.57
3088	3189	1.424638	ACATTATGGGACGGAGGGAG	58.575	55.000	0.00	0.00	0.00	4.30
3089	3190	2.779429	TACATTATGGGACGGAGGGA	57.221	50.000	0.00	0.00	0.00	4.20
3090	3191	2.969950	TCTTACATTATGGGACGGAGGG	59.030	50.000	0.00	0.00	0.00	4.30
3091	3192	3.386726	TGTCTTACATTATGGGACGGAGG	59.613	47.826	0.00	0.00	0.00	4.30
3092	3193	4.665833	TGTCTTACATTATGGGACGGAG	57.334	45.455	0.00	0.00	0.00	4.63
3093	3194	5.623956	AATGTCTTACATTATGGGACGGA	57.376	39.130	3.51	0.00	46.11	4.69
3129	3230	8.786826	TCCATCTCATAATGTAAGACGTTTTT	57.213	30.769	0.00	0.00	0.00	1.94
3130	3231	7.495934	CCTCCATCTCATAATGTAAGACGTTTT	59.504	37.037	0.00	0.00	0.00	2.43
3131	3232	6.986817	CCTCCATCTCATAATGTAAGACGTTT	59.013	38.462	0.00	0.00	0.00	3.60
3132	3233	6.463049	CCCTCCATCTCATAATGTAAGACGTT	60.463	42.308	0.00	0.00	0.00	3.99
3133	3234	5.011125	CCCTCCATCTCATAATGTAAGACGT	59.989	44.000	0.00	0.00	0.00	4.34
3134	3235	5.243954	TCCCTCCATCTCATAATGTAAGACG	59.756	44.000	0.00	0.00	0.00	4.18
3135	3236	6.268847	ACTCCCTCCATCTCATAATGTAAGAC	59.731	42.308	0.00	0.00	0.00	3.01
3136	3237	6.385443	ACTCCCTCCATCTCATAATGTAAGA	58.615	40.000	0.00	0.00	0.00	2.10
3137	3238	6.678568	ACTCCCTCCATCTCATAATGTAAG	57.321	41.667	0.00	0.00	0.00	2.34
3138	3239	8.742125	AATACTCCCTCCATCTCATAATGTAA	57.258	34.615	0.00	0.00	0.00	2.41
3140	3241	8.923838	ATAATACTCCCTCCATCTCATAATGT	57.076	34.615	0.00	0.00	0.00	2.71
3145	3246	9.653516	CACTATATAATACTCCCTCCATCTCAT	57.346	37.037	0.00	0.00	0.00	2.90
3146	3247	8.624670	ACACTATATAATACTCCCTCCATCTCA	58.375	37.037	0.00	0.00	0.00	3.27
3153	3254	9.804758	GCAACATACACTATATAATACTCCCTC	57.195	37.037	0.00	0.00	0.00	4.30
3154	3255	9.321532	TGCAACATACACTATATAATACTCCCT	57.678	33.333	0.00	0.00	0.00	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.