AutoCloner

Multiple sequence alignment - TraesCS3D01G161500

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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	TraesCS3D01G161500	chr3D	100.000	1320	0	0	1218	2537	132275088	132276407	0.000000e+00	2438.0
1	TraesCS3D01G161500	chr3D	100.000	670	0	0	466	1135	132274336	132275005	0.000000e+00	1238.0
2	TraesCS3D01G161500	chr3D	100.000	326	0	0	1	326	132273871	132274196	1.160000e-168	603.0
3	TraesCS3D01G161500	chr3D	100.000	194	0	0	2731	2924	132276601	132276794	2.770000e-95	359.0
4	TraesCS3D01G161500	chr3D	81.063	301	54	3	4	301	572654645	572654945	1.350000e-58	237.0
5	TraesCS3D01G161500	chr3D	82.000	100	10	5	2387	2478	48350467	48350566	8.690000e-11	78.7
6	TraesCS3D01G161500	chr3B	97.149	1333	24	8	1218	2537	188877184	188878515	0.000000e+00	2239.0
7	TraesCS3D01G161500	chr3B	93.884	654	24	9	487	1134	188876567	188877210	0.000000e+00	972.0
8	TraesCS3D01G161500	chr3B	92.239	670	31	10	466	1131	189917780	189917128	0.000000e+00	929.0
9	TraesCS3D01G161500	chr3B	97.977	346	7	0	1218	1563	189921661	189921316	4.170000e-168	601.0
10	TraesCS3D01G161500	chr3B	85.586	333	37	6	1	323	188874038	188874369	3.610000e-89	339.0
11	TraesCS3D01G161500	chr3B	92.784	194	14	0	2731	2924	188878670	188878863	6.170000e-72	281.0
12	TraesCS3D01G161500	chr3B	88.265	196	22	1	128	322	189917994	189917799	1.750000e-57	233.0
13	TraesCS3D01G161500	chr3B	80.189	106	10	7	2384	2478	446747955	446748060	5.230000e-08	69.4
14	TraesCS3D01G161500	chr3A	91.920	1349	53	22	1236	2537	145667222	145668561	0.000000e+00	1836.0
15	TraesCS3D01G161500	chr3A	91.317	357	30	1	486	841	145666003	145666359	1.220000e-133	486.0
16	TraesCS3D01G161500	chr3A	92.727	275	17	3	841	1115	145666524	145666795	7.600000e-106	394.0
17	TraesCS3D01G161500	chr7D	84.875	562	66	12	1251	1807	470837422	470837969	1.530000e-152	549.0
18	TraesCS3D01G161500	chr7B	84.314	561	71	10	1251	1807	494434785	494435332	1.540000e-147	532.0
19	TraesCS3D01G161500	chr7B	100.000	29	0	0	2427	2455	149853809	149853781	1.000000e-03	54.7
20	TraesCS3D01G161500	chr7A	83.957	561	73	10	1251	1807	527995927	527995380	3.340000e-144	521.0
21	TraesCS3D01G161500	chr5B	81.350	311	54	4	4	312	375796035	375796343	1.740000e-62	250.0
22	TraesCS3D01G161500	chr5B	83.168	101	11	3	2384	2482	690707359	690707263	1.440000e-13	87.9
23	TraesCS3D01G161500	chr6D	82.131	291	46	5	27	312	293319494	293319205	8.090000e-61	244.0
24	TraesCS3D01G161500	chr5D	81.029	311	54	5	4	312	324368599	324368906	2.910000e-60	243.0
25	TraesCS3D01G161500	chr5D	81.818	77	10	3	2384	2457	299395846	299395921	8.750000e-06	62.1
26	TraesCS3D01G161500	chr1B	80.745	322	48	12	1482	1796	373628644	373628958	3.770000e-59	239.0
27	TraesCS3D01G161500	chr1B	79.381	291	51	7	4	291	329761921	329762205	2.300000e-46	196.0
28	TraesCS3D01G161500	chr1B	77.469	324	62	9	4	319	565917582	565917902	1.790000e-42	183.0
29	TraesCS3D01G161500	chr1B	77.419	279	55	8	1393	1667	529998501	529998227	3.020000e-35	159.0
30	TraesCS3D01G161500	chr6B	78.979	333	55	9	2	323	487122729	487122401	2.280000e-51	213.0
31	TraesCS3D01G161500	chr6B	84.466	103	8	5	2384	2478	716341287	716341389	8.630000e-16	95.3
32	TraesCS3D01G161500	chr1D	77.656	273	53	8	1393	1661	392697091	392697359	3.020000e-35	159.0
33	TraesCS3D01G161500	chr1D	81.373	102	10	8	2384	2478	379782826	379782925	1.120000e-09	75.0
34	TraesCS3D01G161500	chr1A	76.703	279	57	8	1393	1667	492652702	492652428	6.530000e-32	148.0
35	TraesCS3D01G161500	chr2D	78.155	206	43	2	2	206	615577843	615577639	2.360000e-26	130.0
36	TraesCS3D01G161500	chr2D	90.385	52	2	3	2384	2432	485466140	485466191	6.760000e-07	65.8
37	TraesCS3D01G161500	chr5A	97.561	41	1	0	2384	2424	488022089	488022129	1.450000e-08	71.3

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	TraesCS3D01G161500	chr3D	132273871	132276794	2923	False	1159.500000	2438	100.00000	1	2924	4	chr3D.!!$F3	2923
1	TraesCS3D01G161500	chr3B	188874038	188878863	4825	False	957.750000	2239	92.35075	1	2924	4	chr3B.!!$F2	2923
2	TraesCS3D01G161500	chr3B	189917128	189921661	4533	True	587.666667	929	92.82700	128	1563	3	chr3B.!!$R1	1435
3	TraesCS3D01G161500	chr3A	145666003	145668561	2558	False	905.333333	1836	91.98800	486	2537	3	chr3A.!!$F1	2051
4	TraesCS3D01G161500	chr7D	470837422	470837969	547	False	549.000000	549	84.87500	1251	1807	1	chr7D.!!$F1	556
5	TraesCS3D01G161500	chr7B	494434785	494435332	547	False	532.000000	532	84.31400	1251	1807	1	chr7B.!!$F1	556
6	TraesCS3D01G161500	chr7A	527995380	527995927	547	True	521.000000	521	83.95700	1251	1807	1	chr7A.!!$R1	556

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	Hairpin	End Stability	Orientation
135	136	0.032952	CGAAGAACAGACCCACCGAA	59.967	55.0	0.00	4.30	F
148	158	0.179100	CACCGAAGACCAGCATCGAT	60.179	55.0	39.91	3.59	F
549	2724	0.922626	GGAGGAGGGGAAAGCTTGAT	59.077	55.0	0.00	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1114	3453	0.105709	CCCCTCTCTCTCTTCCTCCC	60.106	65.000	4.30	R
1116	3455	3.531821	CCCCCTCTCTCTCTTCCTC	57.468	63.158	3.71	R
2341	8639	3.002348	CACCCGAAAACAGTCTTGACTTC	59.998	47.826	3.01	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	0.535335	GTCGTCATGCTAAGACCCCA	59.465	55.000	0.00	0.00	32.41	4.96
27	28	2.628178	TCGTCATGCTAAGACCCCATAG	59.372	50.000	0.00	0.00	32.41	2.23
28	29	2.289072	CGTCATGCTAAGACCCCATAGG	60.289	54.545	0.00	0.00	43.78	2.57
33	34	2.124411	GCTAAGACCCCATAGGACCAA	58.876	52.381	0.00	0.00	39.89	3.67
46	47	2.281070	ACCAACGCACCAGAGCAG	60.281	61.111	0.00	0.00	0.00	4.24
57	58	1.744368	CAGAGCAGCAACCATCGCT	60.744	57.895	0.00	0.00	41.47	4.93
70	71	5.563842	CAACCATCGCTGATAAAGAAAGTC	58.436	41.667	0.00	0.00	0.00	3.01
101	102	6.538742	TCGGAAGGATCAAATCTGTAAACATC	59.461	38.462	0.00	0.00	0.00	3.06
102	103	6.540189	CGGAAGGATCAAATCTGTAAACATCT	59.460	38.462	0.00	0.00	0.00	2.90
127	128	5.659048	ATGAAGACAAACGAAGAACAGAC	57.341	39.130	0.00	0.00	0.00	3.51
131	132	2.285977	ACAAACGAAGAACAGACCCAC	58.714	47.619	0.00	0.00	0.00	4.61
132	133	1.602377	CAAACGAAGAACAGACCCACC	59.398	52.381	0.00	0.00	0.00	4.61
133	134	0.249741	AACGAAGAACAGACCCACCG	60.250	55.000	0.00	0.00	0.00	4.94
135	136	0.032952	CGAAGAACAGACCCACCGAA	59.967	55.000	0.00	0.00	0.00	4.30
136	137	1.797025	GAAGAACAGACCCACCGAAG	58.203	55.000	0.00	0.00	0.00	3.79
137	138	1.343465	GAAGAACAGACCCACCGAAGA	59.657	52.381	0.00	0.00	0.00	2.87
142	143	2.047179	GACCCACCGAAGACCAGC	60.047	66.667	0.00	0.00	0.00	4.85
148	158	0.179100	CACCGAAGACCAGCATCGAT	60.179	55.000	0.00	0.00	39.91	3.59
155	165	3.548745	AGACCAGCATCGATTGAATCA	57.451	42.857	5.95	0.00	0.00	2.57
156	166	4.082665	AGACCAGCATCGATTGAATCAT	57.917	40.909	5.95	0.00	0.00	2.45
160	170	1.534163	AGCATCGATTGAATCATGCGG	59.466	47.619	23.60	4.52	42.84	5.69
166	176	2.507484	GATTGAATCATGCGGGATCCA	58.493	47.619	15.23	0.00	0.00	3.41
177	187	1.522569	GGGATCCAAGGGAGACACG	59.477	63.158	15.23	0.00	34.05	4.49
187	197	2.430921	GAGACACGCCTCCACACG	60.431	66.667	0.00	0.00	0.00	4.49
218	228	3.686622	GCTAGATGCACCATCGGAA	57.313	52.632	0.00	0.00	44.67	4.30
247	257	9.547753	GGAATAGTACATGTGAGACATTATTGT	57.452	33.333	9.11	0.00	36.53	2.71
256	266	6.406370	TGTGAGACATTATTGTTACTGAGGG	58.594	40.000	0.00	0.00	35.79	4.30
265	275	4.345859	TTGTTACTGAGGGACATCGTTT	57.654	40.909	0.00	0.00	0.00	3.60
290	300	3.049674	ACAGCGCCAACCATGACG	61.050	61.111	2.29	0.00	35.33	4.35
293	303	2.126888	GCGCCAACCATGACGTTG	60.127	61.111	0.00	7.61	42.31	4.10
549	2724	0.922626	GGAGGAGGGGAAAGCTTGAT	59.077	55.000	0.00	0.00	0.00	2.57
664	2839	2.438868	TCACGGCGATGATATTGAGG	57.561	50.000	16.62	0.00	0.00	3.86
1045	3384	6.095300	CCAATCTGCAAATACTACATCAACCA	59.905	38.462	0.00	0.00	0.00	3.67
1112	3451	4.444022	CCAGAGAAGAGAGAGAGAGAGAGG	60.444	54.167	0.00	0.00	0.00	3.69
1113	3452	4.163078	CAGAGAAGAGAGAGAGAGAGAGGT	59.837	50.000	0.00	0.00	0.00	3.85
1114	3453	4.163078	AGAGAAGAGAGAGAGAGAGAGGTG	59.837	50.000	0.00	0.00	0.00	4.00
1115	3454	3.200825	AGAAGAGAGAGAGAGAGAGGTGG	59.799	52.174	0.00	0.00	0.00	4.61
1116	3455	1.846439	AGAGAGAGAGAGAGAGGTGGG	59.154	57.143	0.00	0.00	0.00	4.61
1117	3456	1.843851	GAGAGAGAGAGAGAGGTGGGA	59.156	57.143	0.00	0.00	0.00	4.37
1118	3457	1.846439	AGAGAGAGAGAGAGGTGGGAG	59.154	57.143	0.00	0.00	0.00	4.30
1119	3458	0.926293	AGAGAGAGAGAGGTGGGAGG	59.074	60.000	0.00	0.00	0.00	4.30
1120	3459	0.923358	GAGAGAGAGAGGTGGGAGGA	59.077	60.000	0.00	0.00	0.00	3.71
1121	3460	1.286553	GAGAGAGAGAGGTGGGAGGAA	59.713	57.143	0.00	0.00	0.00	3.36
1122	3461	1.287739	AGAGAGAGAGGTGGGAGGAAG	59.712	57.143	0.00	0.00	0.00	3.46
1123	3462	1.286553	GAGAGAGAGGTGGGAGGAAGA	59.713	57.143	0.00	0.00	0.00	2.87
1124	3463	1.287739	AGAGAGAGGTGGGAGGAAGAG	59.712	57.143	0.00	0.00	0.00	2.85
1125	3464	1.286553	GAGAGAGGTGGGAGGAAGAGA	59.713	57.143	0.00	0.00	0.00	3.10
1126	3465	1.287739	AGAGAGGTGGGAGGAAGAGAG	59.712	57.143	0.00	0.00	0.00	3.20
1127	3466	1.286553	GAGAGGTGGGAGGAAGAGAGA	59.713	57.143	0.00	0.00	0.00	3.10
1128	3467	1.287739	AGAGGTGGGAGGAAGAGAGAG	59.712	57.143	0.00	0.00	0.00	3.20
1129	3468	1.286553	GAGGTGGGAGGAAGAGAGAGA	59.713	57.143	0.00	0.00	0.00	3.10
1130	3469	1.287739	AGGTGGGAGGAAGAGAGAGAG	59.712	57.143	0.00	0.00	0.00	3.20
1131	3470	1.687996	GGTGGGAGGAAGAGAGAGAGG	60.688	61.905	0.00	0.00	0.00	3.69
1132	3471	0.633921	TGGGAGGAAGAGAGAGAGGG	59.366	60.000	0.00	0.00	0.00	4.30
1133	3472	0.105709	GGGAGGAAGAGAGAGAGGGG	60.106	65.000	0.00	0.00	0.00	4.79
1134	3473	0.105709	GGAGGAAGAGAGAGAGGGGG	60.106	65.000	0.00	0.00	0.00	5.40
1664	4569	2.178521	CCTCCGTCACCGAGTTCG	59.821	66.667	0.00	0.00	35.63	3.95
2310	8608	8.443937	GTTCAACATGAGAGTTTTACTGGATAC	58.556	37.037	0.00	0.00	0.00	2.24
2341	8639	9.778993	CACATGTATTCTCTTTATCAAAACAGG	57.221	33.333	0.00	0.00	0.00	4.00
2484	8798	9.104965	GAATATAGTATCGACTGAGATGTAGCT	57.895	37.037	0.00	0.00	36.28	3.32
2756	9070	2.459934	GCCAAACTTAGTGCACACAAC	58.540	47.619	21.04	0.00	0.00	3.32
2785	9099	2.024655	ACACCCTACGGTCTGATCCTTA	60.025	50.000	0.00	0.00	42.04	2.69
2820	9134	0.526211	GCCGACCCAATCAAAGGTTC	59.474	55.000	0.00	0.00	36.17	3.62
2854	9168	4.406001	CTGCCAATCAGAATCATCATCG	57.594	45.455	0.00	0.00	45.72	3.84
2857	9171	2.486982	CCAATCAGAATCATCATCGCCC	59.513	50.000	0.00	0.00	0.00	6.13
2869	9183	3.210012	ATCGCCCACAAACTGCCCT	62.210	57.895	0.00	0.00	0.00	5.19
2872	9186	2.521465	CCCACAAACTGCCCTGCA	60.521	61.111	0.00	0.00	36.92	4.41
2879	9193	4.626081	ACTGCCCTGCACACGTCC	62.626	66.667	0.00	0.00	33.79	4.79
2885	9199	2.281070	CTGCACACGTCCTGCCTT	60.281	61.111	11.34	0.00	33.36	4.35
2887	9201	1.447317	CTGCACACGTCCTGCCTTTT	61.447	55.000	11.34	0.00	33.36	2.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	2.972713	TCCTATGGGGTCTTAGCATGAC	59.027	50.000	0.00	0.00	36.25	3.06
19	20	1.921346	TGCGTTGGTCCTATGGGGT	60.921	57.895	0.00	0.00	36.25	4.95
24	25	0.537188	CTCTGGTGCGTTGGTCCTAT	59.463	55.000	0.00	0.00	0.00	2.57
27	28	3.050275	GCTCTGGTGCGTTGGTCC	61.050	66.667	0.00	0.00	0.00	4.46
28	29	2.280797	TGCTCTGGTGCGTTGGTC	60.281	61.111	0.00	0.00	35.36	4.02
33	34	2.974698	GTTGCTGCTCTGGTGCGT	60.975	61.111	0.00	0.00	35.36	5.24
46	47	4.142600	ACTTTCTTTATCAGCGATGGTTGC	60.143	41.667	0.00	0.00	0.00	4.17
57	58	6.688637	TCCGATCTACGACTTTCTTTATCA	57.311	37.500	0.00	0.00	45.77	2.15
61	62	4.461781	TCCTTCCGATCTACGACTTTCTTT	59.538	41.667	0.00	0.00	45.77	2.52
70	71	4.920340	CAGATTTGATCCTTCCGATCTACG	59.080	45.833	1.77	0.00	46.65	3.51
101	102	7.794349	GTCTGTTCTTCGTTTGTCTTCATTTAG	59.206	37.037	0.00	0.00	0.00	1.85
102	103	7.254658	GGTCTGTTCTTCGTTTGTCTTCATTTA	60.255	37.037	0.00	0.00	0.00	1.40
127	128	1.450312	GATGCTGGTCTTCGGTGGG	60.450	63.158	0.00	0.00	0.00	4.61
131	132	0.933097	CAATCGATGCTGGTCTTCGG	59.067	55.000	0.00	0.00	41.16	4.30
132	133	1.926561	TCAATCGATGCTGGTCTTCG	58.073	50.000	0.00	0.00	41.88	3.79
133	134	3.873361	TGATTCAATCGATGCTGGTCTTC	59.127	43.478	0.00	0.00	0.00	2.87
135	136	3.548745	TGATTCAATCGATGCTGGTCT	57.451	42.857	0.00	0.00	0.00	3.85
136	137	3.608707	GCATGATTCAATCGATGCTGGTC	60.609	47.826	19.45	0.00	39.02	4.02
137	138	2.292569	GCATGATTCAATCGATGCTGGT	59.707	45.455	19.45	0.00	39.02	4.00
142	143	2.145536	TCCCGCATGATTCAATCGATG	58.854	47.619	0.00	0.00	0.00	3.84
148	158	2.300433	CTTGGATCCCGCATGATTCAA	58.700	47.619	9.90	6.14	37.80	2.69
155	165	1.384502	TCTCCCTTGGATCCCGCAT	60.385	57.895	9.90	0.00	0.00	4.73
156	166	2.040442	TCTCCCTTGGATCCCGCA	59.960	61.111	9.90	0.00	0.00	5.69
160	170	1.153349	GCGTGTCTCCCTTGGATCC	60.153	63.158	4.20	4.20	0.00	3.36
186	196	3.544167	CTAGCATCGTCGGAGGGCG	62.544	68.421	0.00	0.00	33.15	6.13
187	197	1.528292	ATCTAGCATCGTCGGAGGGC	61.528	60.000	0.00	0.00	0.00	5.19
217	227	4.464951	TGTCTCACATGTACTATTCCCGTT	59.535	41.667	0.00	0.00	0.00	4.44
218	228	4.021229	TGTCTCACATGTACTATTCCCGT	58.979	43.478	0.00	0.00	0.00	5.28
228	238	9.586435	CTCAGTAACAATAATGTCTCACATGTA	57.414	33.333	0.00	0.00	37.97	2.29
230	240	7.011763	CCCTCAGTAACAATAATGTCTCACATG	59.988	40.741	0.00	0.00	37.97	3.21
231	241	7.050377	CCCTCAGTAACAATAATGTCTCACAT	58.950	38.462	0.00	0.00	41.31	3.21
234	244	6.212589	TGTCCCTCAGTAACAATAATGTCTCA	59.787	38.462	0.00	0.00	39.40	3.27
247	257	3.604875	GGAAACGATGTCCCTCAGTAA	57.395	47.619	0.00	0.00	0.00	2.24
524	2699	1.692749	TTTCCCCTCCTCCCATCGG	60.693	63.158	0.00	0.00	0.00	4.18
525	2700	1.832912	CTTTCCCCTCCTCCCATCG	59.167	63.158	0.00	0.00	0.00	3.84
526	2701	0.990818	AGCTTTCCCCTCCTCCCATC	60.991	60.000	0.00	0.00	0.00	3.51
528	2703	1.151587	AAGCTTTCCCCTCCTCCCA	60.152	57.895	0.00	0.00	0.00	4.37
529	2704	1.208165	TCAAGCTTTCCCCTCCTCCC	61.208	60.000	0.00	0.00	0.00	4.30
533	2708	4.445557	AAGATATCAAGCTTTCCCCTCC	57.554	45.455	5.32	0.00	0.00	4.30
534	2709	6.125719	AGAAAAGATATCAAGCTTTCCCCTC	58.874	40.000	5.32	0.00	40.36	4.30
535	2710	6.084749	AGAAAAGATATCAAGCTTTCCCCT	57.915	37.500	5.32	0.00	40.36	4.79
536	2711	6.153510	ACAAGAAAAGATATCAAGCTTTCCCC	59.846	38.462	5.32	0.00	40.36	4.81
537	2712	7.163001	ACAAGAAAAGATATCAAGCTTTCCC	57.837	36.000	5.32	0.00	40.36	3.97
664	2839	3.866910	ACGCAATCAATCCAATCAAATGC	59.133	39.130	0.00	0.00	0.00	3.56
870	3209	3.773119	AGCTACCCTATTCCTTTCGTCAA	59.227	43.478	0.00	0.00	0.00	3.18
1045	3384	2.335933	AGGCCTACTTGTGTACCTTGT	58.664	47.619	1.29	0.00	0.00	3.16
1112	3451	1.687996	CCCTCTCTCTCTTCCTCCCAC	60.688	61.905	0.00	0.00	0.00	4.61
1113	3452	0.633921	CCCTCTCTCTCTTCCTCCCA	59.366	60.000	0.00	0.00	0.00	4.37
1114	3453	0.105709	CCCCTCTCTCTCTTCCTCCC	60.106	65.000	0.00	0.00	0.00	4.30
1115	3454	0.105709	CCCCCTCTCTCTCTTCCTCC	60.106	65.000	0.00	0.00	0.00	4.30
1116	3455	3.531821	CCCCCTCTCTCTCTTCCTC	57.468	63.158	0.00	0.00	0.00	3.71
1217	3556	5.136068	TCTCTCTCTCTCTCTCTCTCTCT	57.864	47.826	0.00	0.00	0.00	3.10
1218	3557	5.221422	CCTTCTCTCTCTCTCTCTCTCTCTC	60.221	52.000	0.00	0.00	0.00	3.20
1219	3558	4.653341	CCTTCTCTCTCTCTCTCTCTCTCT	59.347	50.000	0.00	0.00	0.00	3.10
1220	3559	4.202305	CCCTTCTCTCTCTCTCTCTCTCTC	60.202	54.167	0.00	0.00	0.00	3.20
1221	3560	3.713764	CCCTTCTCTCTCTCTCTCTCTCT	59.286	52.174	0.00	0.00	0.00	3.10
1988	8193	8.637281	AAACTAAAACGGAAAATAACACCAAG	57.363	30.769	0.00	0.00	0.00	3.61
2339	8637	3.467803	CCGAAAACAGTCTTGACTTCCT	58.532	45.455	0.00	0.00	0.00	3.36
2341	8639	3.002348	CACCCGAAAACAGTCTTGACTTC	59.998	47.826	0.00	0.00	0.00	3.01
2425	8732	5.895636	ACATCAAGATCCGTGCAAAAATA	57.104	34.783	0.00	0.00	0.00	1.40
2427	8734	5.471797	TCTTACATCAAGATCCGTGCAAAAA	59.528	36.000	0.00	0.00	38.39	1.94
2457	8771	8.884726	GCTACATCTCAGTCGATACTATATTCA	58.115	37.037	0.00	0.00	33.48	2.57
2736	9050	2.159310	TGTTGTGTGCACTAAGTTTGGC	60.159	45.455	19.41	1.66	0.00	4.52
2804	9118	4.766891	TGAATCTGAACCTTTGATTGGGTC	59.233	41.667	0.00	0.00	41.47	4.46
2820	9134	5.319140	TGATTGGCAGAACATTGAATCTG	57.681	39.130	15.32	15.32	44.66	2.90
2846	9160	1.452110	CAGTTTGTGGGCGATGATGA	58.548	50.000	0.00	0.00	0.00	2.92
2854	9168	3.994853	GCAGGGCAGTTTGTGGGC	61.995	66.667	0.00	0.00	0.00	5.36
2857	9171	1.066257	GTGTGCAGGGCAGTTTGTG	59.934	57.895	0.00	0.00	40.08	3.33
2869	9183	1.444119	GAAAAGGCAGGACGTGTGCA	61.444	55.000	18.54	0.00	43.12	4.57
2872	9186	0.468226	TCAGAAAAGGCAGGACGTGT	59.532	50.000	0.00	0.00	0.00	4.49
2879	9193	3.252974	ACGGACTATCAGAAAAGGCAG	57.747	47.619	0.00	0.00	0.00	4.85
2885	9199	2.098607	CGTGGCTACGGACTATCAGAAA	59.901	50.000	15.64	0.00	46.23	2.52
2887	9201	1.306148	CGTGGCTACGGACTATCAGA	58.694	55.000	15.64	0.00	46.23	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.