AutoCloner

Multiple sequence alignment - TraesCS2D01G266000

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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	TraesCS2D01G266000	chr2D	100.000	8616	0	0	1	8616	324605627	324597012	0.000000e+00	15911.0
1	TraesCS2D01G266000	chr2D	91.379	232	20	0	6401	6632	324598996	324598765	1.400000e-82	318.0
2	TraesCS2D01G266000	chr2D	91.379	232	20	0	6632	6863	324599227	324598996	1.400000e-82	318.0
3	TraesCS2D01G266000	chr2D	95.833	96	4	0	4663	4758	324600869	324600774	1.160000e-33	156.0
4	TraesCS2D01G266000	chr2D	95.833	96	4	0	4759	4854	324600965	324600870	1.160000e-33	156.0
5	TraesCS2D01G266000	chr2D	80.420	143	19	8	335	476	633845908	633845774	5.500000e-17	100.0
6	TraesCS2D01G266000	chr2A	96.560	8633	255	23	10	8616	394010306	394018922	0.000000e+00	14259.0
7	TraesCS2D01G266000	chr2A	91.810	232	19	0	6632	6863	394016712	394016943	3.000000e-84	324.0
8	TraesCS2D01G266000	chr2A	92.140	229	18	0	6401	6629	394016943	394017171	3.000000e-84	324.0
9	TraesCS2D01G266000	chr2A	80.967	331	56	7	5356	5681	724109749	724109421	1.110000e-63	255.0
10	TraesCS2D01G266000	chr2A	94.792	96	5	0	4759	4854	394014975	394015070	5.390000e-32	150.0
11	TraesCS2D01G266000	chr2A	94.792	96	5	0	4663	4758	394015071	394015166	5.390000e-32	150.0
12	TraesCS2D01G266000	chr2A	77.848	158	30	5	117	272	29649922	29649768	9.210000e-15	93.5
13	TraesCS2D01G266000	chr2B	95.941	6874	226	17	117	6968	393475403	393468561	0.000000e+00	11099.0
14	TraesCS2D01G266000	chr2B	97.173	1627	29	8	6991	8616	393468568	393466958	0.000000e+00	2734.0
15	TraesCS2D01G266000	chr2B	92.672	232	17	0	6401	6632	393468897	393468666	1.390000e-87	335.0
16	TraesCS2D01G266000	chr2B	92.672	232	17	0	6632	6863	393469128	393468897	1.390000e-87	335.0
17	TraesCS2D01G266000	chr2B	96.875	96	3	0	4759	4854	393470863	393470768	2.490000e-35	161.0
18	TraesCS2D01G266000	chr2B	93.750	96	6	0	4663	4758	393470767	393470672	2.510000e-30	145.0
19	TraesCS2D01G266000	chr5A	79.726	365	70	4	5356	5719	568571331	568571692	2.390000e-65	261.0
20	TraesCS2D01G266000	chrUn	80.665	331	57	7	5356	5681	69802415	69802087	5.160000e-62	250.0
21	TraesCS2D01G266000	chr4A	80.363	331	58	7	5356	5681	2619845	2620173	2.400000e-60	244.0
22	TraesCS2D01G266000	chr7A	79.697	330	62	5	5356	5681	619254372	619254044	5.200000e-57	233.0
23	TraesCS2D01G266000	chr6D	86.364	220	19	8	336	545	15375828	15375610	6.730000e-56	230.0
24	TraesCS2D01G266000	chr6D	82.803	157	27	0	397	553	372345579	372345735	3.240000e-29	141.0
25	TraesCS2D01G266000	chr6D	74.828	290	70	3	24	312	125977346	125977059	2.520000e-25	128.0
26	TraesCS2D01G266000	chr3A	78.098	347	70	5	5377	5719	31814403	31814747	1.880000e-51	215.0
27	TraesCS2D01G266000	chr1B	83.784	222	26	1	335	546	638956611	638956832	1.470000e-47	202.0
28	TraesCS2D01G266000	chr6A	77.778	306	63	5	29	331	448362594	448362897	5.310000e-42	183.0
29	TraesCS2D01G266000	chr1D	86.709	158	21	0	389	546	379907466	379907309	8.890000e-40	176.0
30	TraesCS2D01G266000	chr4B	75.439	171	41	1	22	192	393456549	393456718	1.990000e-11	82.4
31	TraesCS2D01G266000	chr3B	79.487	117	15	4	335	442	809614175	809614059	3.340000e-09	75.0
32	TraesCS2D01G266000	chr3D	88.889	54	5	1	389	442	602460836	602460784	2.010000e-06	65.8
33	TraesCS2D01G266000	chr3D	87.037	54	6	1	389	442	602379126	602379074	9.340000e-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	TraesCS2D01G266000	chr2D	324597012	324605627	8615	True	15911.0	15911	100.00000	1	8616	1	chr2D.!!$R1	8615
1	TraesCS2D01G266000	chr2D	324598765	324600965	2200	True	237.0	318	93.60600	4663	6863	4	chr2D.!!$R3	2200
2	TraesCS2D01G266000	chr2A	394010306	394018922	8616	False	3041.4	14259	94.01880	10	8616	5	chr2A.!!$F1	8606
3	TraesCS2D01G266000	chr2B	393466958	393475403	8445	True	6916.5	11099	96.55700	117	8616	2	chr2B.!!$R1	8499
4	TraesCS2D01G266000	chr2B	393468666	393470863	2197	True	244.0	335	93.99225	4663	6863	4	chr2B.!!$R2	2200

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
119	120	0.100861	GGACGAACTCGAGGTGGATC	59.899	60.000	20.11	12.12	43.02	3.36	F
120	121	0.248134	GACGAACTCGAGGTGGATCG	60.248	60.000	20.11	19.12	44.07	3.69	F
244	245	0.830648	CCGTAATTCTCCTCCCTGCA	59.169	55.000	0.00	0.00	0.00	4.41	F
283	284	1.847088	GGGCAGAGGGGAGACTAATTT	59.153	52.381	0.00	0.00	0.00	1.82	F
2768	2801	1.203492	GGGTAGGGGAGATGATGGGAT	60.203	57.143	0.00	0.00	0.00	3.85	F
3318	3354	1.148310	CCGTTGCTCTTGTCACGAAT	58.852	50.000	0.00	0.00	0.00	3.34	F
3389	3425	2.415983	TCAGAAGGAGTTGGAAGGGA	57.584	50.000	0.00	0.00	0.00	4.20	F
3957	3993	2.499289	AGTAGAGGATGCAGAACAGGTG	59.501	50.000	0.00	0.00	0.00	4.00	F
4567	4606	0.892755	AGTACCCGAAGTGAATGCGA	59.107	50.000	0.00	0.00	0.00	5.10	F
7028	7071	2.563179	TCTGAACAAGAGCAGACCTACC	59.437	50.000	0.00	0.00	36.31	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1755	1788	2.362503	ATCTCACGCAGGTCCCGA	60.363	61.111	0.00	0.00	0.00	5.14	R
2451	2484	1.194781	TTTTCCGCTCCCTCTCTGCT	61.195	55.000	0.00	0.00	0.00	4.24	R
2768	2801	3.445008	ACCAGAGACTTAGCCATGAAGA	58.555	45.455	0.00	0.00	0.00	2.87	R
2864	2897	2.277084	ACACCACTGTCTCGTCAAAAC	58.723	47.619	0.00	0.00	0.00	2.43	R
4140	4176	0.907486	CATCTCCAGGCTCCTCAACA	59.093	55.000	0.00	0.00	0.00	3.33	R
4141	4177	0.908198	ACATCTCCAGGCTCCTCAAC	59.092	55.000	0.00	0.00	0.00	3.18	R
4401	4440	2.857186	TGGTTTCTGCATGCTCTACA	57.143	45.000	20.33	7.69	0.00	2.74	R
6984	7027	6.703607	AGACGCTTCATCATTTTCTATACCAG	59.296	38.462	0.00	0.00	0.00	4.00	R
7153	7196	1.890489	GGTCGGCCAAATTTACTGGTT	59.110	47.619	0.00	0.00	36.24	3.67	R
8466	8511	1.891919	GCAGTCGGCCACTTTGACA	60.892	57.895	2.24	0.00	35.09	3.58	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
47	48	3.203487	ACAAGAAACCCTAACCTCACCAA	59.797	43.478	0.00	0.00	0.00	3.67
61	62	0.405585	CACCAACCCAAGGAGATGGT	59.594	55.000	5.08	5.08	44.95	3.55
71	72	6.584950	ACCCAAGGAGATGGTAGGAATATAT	58.415	40.000	0.00	0.00	38.91	0.86
90	91	2.182030	CCGGAGCTCTGTCGGTTC	59.818	66.667	21.06	0.00	39.04	3.62
95	96	1.587933	GAGCTCTGTCGGTTCCGTCT	61.588	60.000	6.43	1.10	0.00	4.18
113	114	2.082231	TCTAGTTGGACGAACTCGAGG	58.918	52.381	18.41	1.00	41.37	4.63
119	120	0.100861	GGACGAACTCGAGGTGGATC	59.899	60.000	20.11	12.12	43.02	3.36
120	121	0.248134	GACGAACTCGAGGTGGATCG	60.248	60.000	20.11	19.12	44.07	3.69
126	127	2.892640	CGAGGTGGATCGAAGCCA	59.107	61.111	6.30	6.30	45.56	4.75
219	220	2.232941	CCTAAACTGTTAGCCGGAGTCA	59.767	50.000	5.05	0.00	36.19	3.41
228	229	4.003788	CCGGAGTCAAGGCACCGT	62.004	66.667	9.52	0.00	43.22	4.83
241	242	0.831307	GCACCGTAATTCTCCTCCCT	59.169	55.000	0.00	0.00	0.00	4.20
244	245	0.830648	CCGTAATTCTCCTCCCTGCA	59.169	55.000	0.00	0.00	0.00	4.41
283	284	1.847088	GGGCAGAGGGGAGACTAATTT	59.153	52.381	0.00	0.00	0.00	1.82
332	333	3.463585	TGTAACCCTAGCCGCCGG	61.464	66.667	0.00	0.00	0.00	6.13
451	462	7.665559	ACATATAATTCCTATCACGTGCCAAAT	59.334	33.333	11.67	1.19	0.00	2.32
480	495	7.773224	TGGATTGGTAATAAAACGACTCATCAT	59.227	33.333	0.00	0.00	0.00	2.45
515	530	6.916440	TCAATAGAACTCGCTACACTAAACA	58.084	36.000	0.00	0.00	0.00	2.83
538	553	3.465588	CCCACTCCCCTTCCCAAATATTA	59.534	47.826	0.00	0.00	0.00	0.98
546	561	4.707934	CCCTTCCCAAATATTACCAAACGT	59.292	41.667	0.00	0.00	0.00	3.99
565	580	7.805542	CCAAACGTGTTGTTAATGTAATCATCA	59.194	33.333	0.00	0.00	40.84	3.07
692	715	5.883661	CATTAGTGCAGGGACAAATAACTG	58.116	41.667	0.00	0.00	0.00	3.16
1755	1788	2.494918	GTGCTCGCGTCCCTGTAT	59.505	61.111	5.77	0.00	0.00	2.29
2451	2484	2.751436	GCAGCCATGGAAGCCGAA	60.751	61.111	18.40	0.00	0.00	4.30
2768	2801	1.203492	GGGTAGGGGAGATGATGGGAT	60.203	57.143	0.00	0.00	0.00	3.85
3058	3091	8.759481	AGAATACAGTGATCTCTTGACTGATA	57.241	34.615	15.01	6.19	39.64	2.15
3109	3142	2.802816	GCTATCACAGTTGATAAGCCCG	59.197	50.000	0.00	0.00	42.93	6.13
3213	3246	2.025898	GAGGCTACAGGTAGACCAGAC	58.974	57.143	8.67	0.00	42.18	3.51
3237	3270	2.375174	AGGCACCATTGTTACTCAGGAA	59.625	45.455	0.00	0.00	0.00	3.36
3272	3305	2.869801	CCAAACTTGCAGTTGACGAGTA	59.130	45.455	8.07	0.00	38.66	2.59
3318	3354	1.148310	CCGTTGCTCTTGTCACGAAT	58.852	50.000	0.00	0.00	0.00	3.34
3348	3384	5.188359	AGAAGAAAAGGGTAATGTAGCGGTA	59.812	40.000	0.00	0.00	0.00	4.02
3389	3425	2.415983	TCAGAAGGAGTTGGAAGGGA	57.584	50.000	0.00	0.00	0.00	4.20
3539	3575	4.524316	ATGATGTTGGTGAATGTGTTGG	57.476	40.909	0.00	0.00	0.00	3.77
3541	3577	4.151121	TGATGTTGGTGAATGTGTTGGAT	58.849	39.130	0.00	0.00	0.00	3.41
3549	3585	4.022068	GGTGAATGTGTTGGATTGTCATGT	60.022	41.667	0.00	0.00	0.00	3.21
3656	3692	6.676189	AGGGAGATTTCCTGTAAAGAAGAGAT	59.324	38.462	1.74	0.00	43.49	2.75
3670	3706	3.843027	AGAAGAGATTGGAGGAGAAAGCA	59.157	43.478	0.00	0.00	0.00	3.91
3757	3793	7.102346	AGAATGTGGAGAAGACATTACTCTTG	58.898	38.462	0.00	0.00	42.74	3.02
3774	3810	6.773976	ACTCTTGTGGAAAAAGACAATGAA	57.226	33.333	0.00	0.00	34.58	2.57
3957	3993	2.499289	AGTAGAGGATGCAGAACAGGTG	59.501	50.000	0.00	0.00	0.00	4.00
4002	4038	3.070115	TGCAAATGAGGGGCACAAT	57.930	47.368	0.00	0.00	31.58	2.71
4139	4175	7.308710	CGGTAAGAGATTAACAGGGAGAGATAC	60.309	44.444	0.00	0.00	0.00	2.24
4140	4176	7.726738	GGTAAGAGATTAACAGGGAGAGATACT	59.273	40.741	0.00	0.00	0.00	2.12
4141	4177	7.595819	AAGAGATTAACAGGGAGAGATACTG	57.404	40.000	0.00	0.00	38.19	2.74
4170	4209	2.943199	GCCTGGAGATGTTCTTGAAGGG	60.943	54.545	0.00	0.00	0.00	3.95
4361	4400	9.710900	AAAAATAAAAGGAACTCATAAGCCAAG	57.289	29.630	0.00	0.00	38.49	3.61
4401	4440	5.833131	TGGTAAGCTTCAGGAAGTTTTTGAT	59.167	36.000	14.80	0.00	41.17	2.57
4459	4498	2.185004	TAAGGGAGTTGCAGACAAGC	57.815	50.000	0.00	0.00	36.16	4.01
4472	4511	4.040376	GCAGACAAGCAGTTTGAAGAAAG	58.960	43.478	3.67	0.00	39.21	2.62
4567	4606	0.892755	AGTACCCGAAGTGAATGCGA	59.107	50.000	0.00	0.00	0.00	5.10
6990	7033	3.963428	GACAGAGTTGTCCACTGGTAT	57.037	47.619	0.00	0.00	46.47	2.73
6994	7037	5.084519	ACAGAGTTGTCCACTGGTATAGAA	58.915	41.667	0.00	0.00	35.01	2.10
7028	7071	2.563179	TCTGAACAAGAGCAGACCTACC	59.437	50.000	0.00	0.00	36.31	3.18
7068	7111	3.041211	CTCCTTCAGGTATGGATCACCA	58.959	50.000	3.73	0.00	42.66	4.17
7153	7196	2.028130	CCAGTAAACACAGGTTGCCAA	58.972	47.619	0.00	0.00	37.30	4.52
7491	7534	1.135489	AGATGTGCAAAATGCTCGCAG	60.135	47.619	3.78	0.00	45.31	5.18
7635	7678	7.416664	GCATTGACCTTTTAATTAGCTCCATGA	60.417	37.037	0.00	0.00	0.00	3.07
7774	7817	5.593095	ACCTTTTCTCTTGGGTGAAGTTTAC	59.407	40.000	0.00	0.00	32.90	2.01
7941	7984	9.691362	TGCAAAGTTAGTTTCTCATAAAATTCC	57.309	29.630	0.00	0.00	0.00	3.01
7952	7995	5.644636	TCTCATAAAATTCCGGGTGTGTAAC	59.355	40.000	0.00	0.00	37.35	2.50
8191	8236	2.353803	GGCTCGTCAACCACTTGTATCT	60.354	50.000	0.00	0.00	0.00	1.98
8485	8530	1.598130	GTCAAAGTGGCCGACTGCT	60.598	57.895	8.37	0.00	40.92	4.24
8488	8533	3.553095	AAAGTGGCCGACTGCTCCC	62.553	63.158	8.37	0.00	40.92	4.30

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.741401	TGAGCGTCGGCAGGATTTG	60.741	57.895	0.00	0.00	43.41	2.32
2	3	2.125512	GTGAGCGTCGGCAGGATT	60.126	61.111	0.00	0.00	43.41	3.01
3	4	4.498520	CGTGAGCGTCGGCAGGAT	62.499	66.667	0.00	0.00	43.41	3.24
27	28	3.436035	GGTTGGTGAGGTTAGGGTTTCTT	60.436	47.826	0.00	0.00	0.00	2.52
47	48	2.661176	TTCCTACCATCTCCTTGGGT	57.339	50.000	0.00	0.00	41.35	4.51
61	62	3.701542	CAGAGCTCCGGCATATATTCCTA	59.298	47.826	10.93	0.00	41.70	2.94
95	96	1.538512	CACCTCGAGTTCGTCCAACTA	59.461	52.381	12.31	0.00	46.10	2.24
113	114	0.537188	TCTTCCTGGCTTCGATCCAC	59.463	55.000	3.08	0.00	0.00	4.02
119	120	0.035458	AGTTGGTCTTCCTGGCTTCG	59.965	55.000	0.00	0.00	34.23	3.79
120	121	1.814793	GAGTTGGTCTTCCTGGCTTC	58.185	55.000	0.00	0.00	34.23	3.86
126	127	3.231818	TCTTCTTCGAGTTGGTCTTCCT	58.768	45.455	0.00	0.00	34.23	3.36
219	220	1.209747	GGAGGAGAATTACGGTGCCTT	59.790	52.381	0.00	0.00	0.00	4.35
228	229	0.839946	GGCTGCAGGGAGGAGAATTA	59.160	55.000	17.12	0.00	38.04	1.40
263	264	1.512735	AATTAGTCTCCCCTCTGCCC	58.487	55.000	0.00	0.00	0.00	5.36
283	284	2.678934	AACTCCAGCGAGCCCGTA	60.679	61.111	0.00	0.00	40.03	4.02
451	462	7.613585	TGAGTCGTTTTATTACCAATCCACTA	58.386	34.615	0.00	0.00	0.00	2.74
480	495	8.397575	AGCGAGTTCTATTGAGATTAGACATA	57.602	34.615	0.00	0.00	0.00	2.29
503	518	2.614734	GGGAGTGGGTGTTTAGTGTAGC	60.615	54.545	0.00	0.00	0.00	3.58
515	530	0.780090	ATTTGGGAAGGGGAGTGGGT	60.780	55.000	0.00	0.00	0.00	4.51
538	553	7.028926	TGATTACATTAACAACACGTTTGGT	57.971	32.000	12.79	9.72	39.14	3.67
546	561	6.726379	TCCCCTGATGATTACATTAACAACA	58.274	36.000	0.00	0.00	36.82	3.33
1755	1788	2.362503	ATCTCACGCAGGTCCCGA	60.363	61.111	0.00	0.00	0.00	5.14
2451	2484	1.194781	TTTTCCGCTCCCTCTCTGCT	61.195	55.000	0.00	0.00	0.00	4.24
2768	2801	3.445008	ACCAGAGACTTAGCCATGAAGA	58.555	45.455	0.00	0.00	0.00	2.87
2864	2897	2.277084	ACACCACTGTCTCGTCAAAAC	58.723	47.619	0.00	0.00	0.00	2.43
2983	3016	3.181390	ACCTCCTCAGGCATATTAGGGAT	60.181	47.826	0.00	0.00	45.05	3.85
3018	3051	7.500892	TCACTGTATTCTTCTCTCTCCATAGAC	59.499	40.741	0.00	0.00	0.00	2.59
3058	3091	7.799081	TCTATGACATCCTCACTGAAATCAAT	58.201	34.615	0.00	0.00	0.00	2.57
3109	3142	1.615392	AGGTGCACTGGAGAAATTTGC	59.385	47.619	17.98	0.00	0.00	3.68
3183	3216	1.354040	CTGTAGCCTCAAGACGCTTG	58.646	55.000	11.78	11.78	36.53	4.01
3195	3228	0.739561	CGTCTGGTCTACCTGTAGCC	59.260	60.000	0.02	5.41	36.48	3.93
3213	3246	2.416547	CTGAGTAACAATGGTGCCTTCG	59.583	50.000	0.00	0.00	0.00	3.79
3237	3270	4.502087	GCAAGTTTGGCTTTCTTCTCCAAT	60.502	41.667	0.00	0.00	39.36	3.16
3299	3335	1.136252	CATTCGTGACAAGAGCAACGG	60.136	52.381	0.00	0.00	0.00	4.44
3318	3354	7.769044	GCTACATTACCCTTTTCTTCTATGTCA	59.231	37.037	0.00	0.00	0.00	3.58
3348	3384	1.831736	ACTACGGCACCTTCAATAGCT	59.168	47.619	0.00	0.00	0.00	3.32
3361	3397	2.737252	CAACTCCTTCTGAAACTACGGC	59.263	50.000	0.00	0.00	0.00	5.68
3389	3425	1.686236	ATGACTTGTTCCCTCCCCAT	58.314	50.000	0.00	0.00	0.00	4.00
3539	3575	9.950496	AAGTATCCTCCATTATACATGACAATC	57.050	33.333	0.00	0.00	32.14	2.67
3541	3577	8.713971	ACAAGTATCCTCCATTATACATGACAA	58.286	33.333	0.00	0.00	33.60	3.18
3549	3585	5.307976	AGCAGCACAAGTATCCTCCATTATA	59.692	40.000	0.00	0.00	0.00	0.98
3601	3637	1.535088	GCGACAAAATCTAAAGCGGC	58.465	50.000	0.00	0.00	0.00	6.53
3656	3692	4.267536	CATCTGATTGCTTTCTCCTCCAA	58.732	43.478	0.00	0.00	0.00	3.53
3670	3706	5.873712	CGCTATCTTTCATAGCCATCTGATT	59.126	40.000	7.81	0.00	42.89	2.57
3757	3793	5.514274	TCACCTTCATTGTCTTTTTCCAC	57.486	39.130	0.00	0.00	0.00	4.02
3957	3993	7.599998	CCTCCATTTGCCATAGTATTAATTTGC	59.400	37.037	0.00	0.00	0.00	3.68
4002	4038	4.284490	ACATCCTCTACTTCAGCAACTTCA	59.716	41.667	0.00	0.00	0.00	3.02
4106	4142	4.928601	TGTTAATCTCTTACCGTCATCCG	58.071	43.478	0.00	0.00	0.00	4.18
4139	4175	1.134461	CATCTCCAGGCTCCTCAACAG	60.134	57.143	0.00	0.00	0.00	3.16
4140	4176	0.907486	CATCTCCAGGCTCCTCAACA	59.093	55.000	0.00	0.00	0.00	3.33
4141	4177	0.908198	ACATCTCCAGGCTCCTCAAC	59.092	55.000	0.00	0.00	0.00	3.18
4170	4209	1.865788	TTTCCGCTTCTGCATGTGCC	61.866	55.000	2.07	0.00	41.18	5.01
4341	4380	4.089361	CCCTTGGCTTATGAGTTCCTTTT	58.911	43.478	0.00	0.00	0.00	2.27
4361	4400	4.262678	GCTTACCATCAGTATCTTCCTCCC	60.263	50.000	0.00	0.00	0.00	4.30
4401	4440	2.857186	TGGTTTCTGCATGCTCTACA	57.143	45.000	20.33	7.69	0.00	2.74
4459	4498	8.400947	TCTCAATTCAGAACTTTCTTCAAACTG	58.599	33.333	0.00	0.00	34.74	3.16
4472	4511	9.050601	CAATCCCTATACTTCTCAATTCAGAAC	57.949	37.037	0.00	0.00	0.00	3.01
4567	4606	3.826729	GTCCCATTGGCTTGTTCTACTTT	59.173	43.478	0.00	0.00	0.00	2.66
6984	7027	6.703607	AGACGCTTCATCATTTTCTATACCAG	59.296	38.462	0.00	0.00	0.00	4.00
6990	7033	5.931724	TGTTCAGACGCTTCATCATTTTCTA	59.068	36.000	0.00	0.00	0.00	2.10
6994	7037	4.756642	TCTTGTTCAGACGCTTCATCATTT	59.243	37.500	0.00	0.00	0.00	2.32
7028	7071	2.419324	GAGCAATTGAAGCACTCTCTGG	59.581	50.000	10.34	0.00	0.00	3.86
7068	7111	5.766590	CCCCTTTGTTATTATTCTCACCCT	58.233	41.667	0.00	0.00	0.00	4.34
7153	7196	1.890489	GGTCGGCCAAATTTACTGGTT	59.110	47.619	0.00	0.00	36.24	3.67
7188	7231	5.461032	ACTGCTACTATGTATTCTCCTGC	57.539	43.478	0.00	0.00	0.00	4.85
7491	7534	4.081420	TCTCCATCCTAGTTTTCTCAGCAC	60.081	45.833	0.00	0.00	0.00	4.40
7694	7737	1.535462	ACAAACTAGCGTGCATTGGTC	59.465	47.619	0.00	0.00	0.00	4.02
7774	7817	9.480053	TTCATTCAGGAAAGCAAAGAATTTAAG	57.520	29.630	0.00	0.00	35.03	1.85
7829	7872	3.904339	ACTACACATGAACTTCTGGAGGT	59.096	43.478	0.00	0.00	0.00	3.85
7962	8005	9.021807	ACAGAGCTACAAGTTACTTATAAGTCA	57.978	33.333	21.25	8.43	40.37	3.41
7963	8006	9.857957	AACAGAGCTACAAGTTACTTATAAGTC	57.142	33.333	21.25	8.65	40.37	3.01
8191	8236	8.697507	TGAGCAATGAACTCTGTATCTCTATA	57.302	34.615	0.00	0.00	35.12	1.31
8466	8511	1.891919	GCAGTCGGCCACTTTGACA	60.892	57.895	2.24	0.00	35.09	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.