AutoCloner

Multiple sequence alignment - TraesCS6D01G011300

Loading Multiple Alignment...

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	TraesCS6D01G011300	chr6D	100.000	4500	0	0	1	4500	4295942	4291443	0.000000e+00	8311
1	TraesCS6D01G011300	chr6D	79.651	344	47	19	2463	2803	109252891	109253214	4.530000e-55	226
2	TraesCS6D01G011300	chr6D	94.074	135	7	1	914	1047	109250047	109250181	2.120000e-48	204
3	TraesCS6D01G011300	chr6D	78.571	322	55	10	1559	1867	109250949	109251269	2.750000e-47	200
4	TraesCS6D01G011300	chr6B	91.185	3460	199	36	1078	4500	8407736	8411126	0.000000e+00	4602
5	TraesCS6D01G011300	chr6B	98.261	230	4	0	685	914	8407016	8407245	1.950000e-108	403
6	TraesCS6D01G011300	chr6B	96.407	167	4	2	1	166	8406854	8407019	1.590000e-69	274
7	TraesCS6D01G011300	chr6B	100.000	129	0	0	914	1042	8407541	8407669	5.820000e-59	239
8	TraesCS6D01G011300	chr6B	79.598	348	51	17	2464	2803	198399875	198400210	9.740000e-57	231
9	TraesCS6D01G011300	chr6B	79.624	319	48	12	1565	1867	198394812	198395129	3.530000e-51	213
10	TraesCS6D01G011300	chr6B	94.074	135	7	1	914	1047	198393925	198394059	2.120000e-48	204
11	TraesCS6D01G011300	chr6B	86.719	128	16	1	2023	2150	198399508	198399634	1.690000e-29	141
12	TraesCS6D01G011300	chr6A	91.338	1166	80	9	3348	4500	2752106	2750949	0.000000e+00	1574
13	TraesCS6D01G011300	chr6A	95.965	917	30	4	1	915	2766603	2765692	0.000000e+00	1482
14	TraesCS6D01G011300	chr6A	95.259	907	40	2	1520	2423	2764887	2763981	0.000000e+00	1434
15	TraesCS6D01G011300	chr6A	90.860	930	64	9	2418	3338	2753074	2752157	0.000000e+00	1227
16	TraesCS6D01G011300	chr6A	91.290	310	14	5	1081	1387	2765184	2764885	1.170000e-110	411
17	TraesCS6D01G011300	chr6A	95.906	171	4	3	914	1081	2765398	2765228	1.590000e-69	274
18	TraesCS6D01G011300	chr6A	80.466	343	49	15	2463	2803	134191718	134192044	3.480000e-61	246
19	TraesCS6D01G011300	chr6A	94.074	135	7	1	914	1047	134188870	134189004	2.120000e-48	204
20	TraesCS6D01G011300	chr6A	78.261	322	56	10	1559	1867	134189774	134190094	1.280000e-45	195
21	TraesCS6D01G011300	chr4D	80.560	643	86	28	1320	1954	493798102	493797491	4.100000e-125	459
22	TraesCS6D01G011300	chr4D	81.076	502	78	10	2342	2839	493796668	493796180	7.060000e-103	385
23	TraesCS6D01G011300	chr4D	83.571	140	17	4	2019	2153	493796906	493796768	4.730000e-25	126
24	TraesCS6D01G011300	chr4D	87.850	107	10	3	976	1081	493798549	493798445	6.110000e-24	122
25	TraesCS6D01G011300	chr4B	79.782	643	93	27	1319	1954	631415888	631415276	2.490000e-117	433
26	TraesCS6D01G011300	chr4B	82.292	384	52	12	2464	2839	631414006	631413631	7.260000e-83	318
27	TraesCS6D01G011300	chr4B	91.716	169	11	2	914	1081	631416426	631416260	9.740000e-57	231
28	TraesCS6D01G011300	chr4B	82.222	180	23	6	1979	2153	631414451	631414276	3.630000e-31	147
29	TraesCS6D01G011300	chr5A	82.283	508	77	12	1456	1961	672573314	672573810	1.160000e-115	427
30	TraesCS6D01G011300	chr5A	81.842	380	56	11	2464	2836	672575071	672575444	1.570000e-79	307
31	TraesCS6D01G011300	chr5A	92.169	166	10	2	914	1078	672572658	672572821	9.740000e-57	231
32	TraesCS6D01G011300	chr5A	81.667	180	24	6	1979	2153	672574626	672574801	1.690000e-29	141
33	TraesCS6D01G011300	chr1B	85.195	385	47	2	3853	4227	683110952	683111336	1.960000e-103	387
34	TraesCS6D01G011300	chr1D	81.395	129	23	1	4078	4206	460602687	460602814	2.210000e-18	104

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	TraesCS6D01G011300	chr6D	4291443	4295942	4499	True	8311.00	8311	100.000000	1	4500	1	chr6D.!!$R1	4499
1	TraesCS6D01G011300	chr6D	109250047	109253214	3167	False	210.00	226	84.098667	914	2803	3	chr6D.!!$F1	1889
2	TraesCS6D01G011300	chr6B	8406854	8411126	4272	False	1379.50	4602	96.463250	1	4500	4	chr6B.!!$F1	4499
3	TraesCS6D01G011300	chr6B	198393925	198395129	1204	False	208.50	213	86.849000	914	1867	2	chr6B.!!$F2	953
4	TraesCS6D01G011300	chr6A	2750949	2753074	2125	True	1400.50	1574	91.099000	2418	4500	2	chr6A.!!$R1	2082
5	TraesCS6D01G011300	chr6A	2763981	2766603	2622	True	900.25	1482	94.605000	1	2423	4	chr6A.!!$R2	2422
6	TraesCS6D01G011300	chr6A	134188870	134192044	3174	False	215.00	246	84.267000	914	2803	3	chr6A.!!$F1	1889
7	TraesCS6D01G011300	chr4D	493796180	493798549	2369	True	273.00	459	83.264250	976	2839	4	chr4D.!!$R1	1863
8	TraesCS6D01G011300	chr4B	631413631	631416426	2795	True	282.25	433	84.003000	914	2839	4	chr4B.!!$R1	1925
9	TraesCS6D01G011300	chr5A	672572658	672575444	2786	False	276.50	427	84.490250	914	2836	4	chr5A.!!$F1	1922

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
168	170	0.833287	TCCACCTTGAGATGCTAGGC	59.167	55.000	0.00	0.00	42.45	3.93	F
265	267	1.339631	CGGAACCCCATAGAAACAGCA	60.340	52.381	0.00	0.00	0.00	4.41	F
1223	1625	0.107993	ACCTGGAGACATCATGCACG	60.108	55.000	0.00	0.00	41.51	5.34	F
1225	1627	1.004595	CTGGAGACATCATGCACGTG	58.995	55.000	12.28	12.28	41.51	4.49	F
2677	4852	0.108186	TCTTCATAGGCCTGCGTGTG	60.108	55.000	17.99	6.55	0.00	3.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1205	1607	0.107993	ACGTGCATGATGTCTCCAGG	60.108	55.000	14.17	0.00	0.00	4.45	R
1432	2038	2.565841	CCTCTTAAGGCCAGTGCATAC	58.434	52.381	5.01	0.00	40.13	2.39	R
2677	4852	0.179000	AATCACGCTCCATCTCACCC	59.821	55.000	0.00	0.00	0.00	4.61	R
2862	5037	1.956629	ATGGCTACCGACGGGACAAG	61.957	60.000	20.00	10.77	36.97	3.16	R
4287	6541	0.507358	GCGAGAACAACCAGAACGTC	59.493	55.000	0.00	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
124	126	2.157668	GCACCGACCATTCATATTAGCG	59.842	50.000	0.00	0.00	0.00	4.26
164	166	1.949799	AGAGTCCACCTTGAGATGCT	58.050	50.000	0.00	0.00	0.00	3.79
168	170	0.833287	TCCACCTTGAGATGCTAGGC	59.167	55.000	0.00	0.00	42.45	3.93
232	234	6.884280	ATTGAGCTATCTAAATTTTCCGGG	57.116	37.500	0.00	0.00	0.00	5.73
235	237	6.419791	TGAGCTATCTAAATTTTCCGGGAAA	58.580	36.000	18.03	18.03	0.00	3.13
246	248	1.519408	TCCGGGAAAGAAAGAAAGCG	58.481	50.000	0.00	0.00	0.00	4.68
265	267	1.339631	CGGAACCCCATAGAAACAGCA	60.340	52.381	0.00	0.00	0.00	4.41
282	284	3.005554	CAGCATGTCGAAGGTTGAGATT	58.994	45.455	0.00	0.00	0.00	2.40
283	285	3.438087	CAGCATGTCGAAGGTTGAGATTT	59.562	43.478	0.00	0.00	0.00	2.17
399	401	7.484007	GCTGTTCTCATTTCTCAACATACATTG	59.516	37.037	0.00	0.00	0.00	2.82
440	442	9.777297	CCCCACCCATATAATTTTTAATTCAAG	57.223	33.333	0.00	0.00	0.00	3.02
509	511	7.760340	AGTTACACCTCTTGATATTTCGACTTC	59.240	37.037	0.00	0.00	0.00	3.01
557	559	6.777526	TGAGTTTTGTTTCCAACAGTTTTG	57.222	33.333	0.00	0.00	43.27	2.44
649	651	5.961272	CCCAAACTGGCTAAAATTATTCGT	58.039	37.500	0.00	0.00	35.79	3.85
671	673	6.594547	TCGTATCCTCTAATCTGTCTATTCGG	59.405	42.308	0.00	0.00	0.00	4.30
705	707	3.437049	CACTACAGTTCCTAAAAGCCAGC	59.563	47.826	0.00	0.00	0.00	4.85
868	870	9.562408	TTAACAGACAGGTGACAATTGTTATTA	57.438	29.630	13.36	0.00	31.86	0.98
1065	1365	8.562052	GTTATATTGTATACCCGGTTCCTTTTG	58.438	37.037	0.00	0.00	0.00	2.44
1076	1446	4.202111	CCGGTTCCTTTTGTGTTGATTTCT	60.202	41.667	0.00	0.00	0.00	2.52
1088	1458	6.801575	TGTGTTGATTTCTTTTAGTTGGGTC	58.198	36.000	0.00	0.00	0.00	4.46
1205	1607	5.240623	TCAGACATCATGTTTGTGGGTTTAC	59.759	40.000	8.12	0.00	34.49	2.01
1221	1623	3.609853	GTTTACCTGGAGACATCATGCA	58.390	45.455	0.00	0.00	41.51	3.96
1223	1625	0.107993	ACCTGGAGACATCATGCACG	60.108	55.000	0.00	0.00	41.51	5.34
1225	1627	1.004595	CTGGAGACATCATGCACGTG	58.995	55.000	12.28	12.28	41.51	4.49
1297	1813	4.456280	AGTTGAAGATACTCATGCGACA	57.544	40.909	0.00	0.00	0.00	4.35
1432	2038	3.553922	GGATTATCCAGTCTTCCAGCTCG	60.554	52.174	6.34	0.00	36.28	5.03
1723	2530	7.201565	GCTGATAAAGTTGAAGACATGAGGTAC	60.202	40.741	0.00	0.00	0.00	3.34
1837	2659	2.028112	TCAAGCACGGCTTCAACTATCT	60.028	45.455	7.99	0.00	46.77	1.98
1867	2689	7.907214	AAGATTTATTGTACTCAGGTGTGTC	57.093	36.000	0.00	0.00	0.00	3.67
1875	2697	6.754702	TGTACTCAGGTGTGTCTCTTATAC	57.245	41.667	0.00	0.00	0.00	1.47
1883	2705	4.863131	GGTGTGTCTCTTATACCAAGTTCG	59.137	45.833	0.00	0.00	0.00	3.95
1942	2766	6.861572	TGTGTCGACTAGATTTAACTGAACTG	59.138	38.462	17.92	0.00	0.00	3.16
1944	2768	5.805994	GTCGACTAGATTTAACTGAACTGGG	59.194	44.000	8.70	0.00	0.00	4.45
1977	4084	8.176365	GATAGTTGATCATGCAGAATTGCTATC	58.824	37.037	0.00	1.28	41.54	2.08
2120	4229	2.568956	AGAAGCTGAAGCACATGGTAGA	59.431	45.455	4.90	0.00	45.16	2.59
2208	4326	1.140312	GATCTATTCCCCAGGGTGCA	58.860	55.000	4.22	0.00	36.47	4.57
2238	4356	9.819267	AGTGCCTTAGTTTCATAGTTTATAGTC	57.181	33.333	0.00	0.00	0.00	2.59
2259	4378	7.594351	AGTCTAGATCATAACAGCATTCTGA	57.406	36.000	0.00	0.00	42.95	3.27
2430	4595	7.605691	AGGAGATCTCATTTGTAACTTCTTGTG	59.394	37.037	23.85	0.00	0.00	3.33
2458	4626	6.237942	GCTCTGTAAATAGCCGCATGTATATG	60.238	42.308	0.00	0.00	33.64	1.78
2459	4627	6.930731	TCTGTAAATAGCCGCATGTATATGA	58.069	36.000	3.28	0.00	36.36	2.15
2460	4628	7.382898	TCTGTAAATAGCCGCATGTATATGAA	58.617	34.615	3.28	0.00	36.36	2.57
2461	4629	7.875554	TCTGTAAATAGCCGCATGTATATGAAA	59.124	33.333	3.28	0.00	36.36	2.69
2468	4636	7.312657	AGCCGCATGTATATGAAATTATGAG	57.687	36.000	3.28	0.00	36.36	2.90
2616	4787	9.595823	GGTTTAATGAGTATGAAGCTTACAGTA	57.404	33.333	0.00	0.00	0.00	2.74
2653	4825	9.927668	AATGTTGTTCCTTGTCTTAAAATATGG	57.072	29.630	0.00	0.00	0.00	2.74
2677	4852	0.108186	TCTTCATAGGCCTGCGTGTG	60.108	55.000	17.99	6.55	0.00	3.82
2862	5037	4.835199	ACGCATACTATTGTTGTCGTTC	57.165	40.909	0.00	0.00	0.00	3.95
3011	5192	0.238817	GCGGAACATGCGGTTTGTTA	59.761	50.000	0.00	0.00	40.63	2.41
3153	5334	3.502211	GGAAGCGAGAATGGTTCTTTTCA	59.498	43.478	5.77	0.00	43.89	2.69
3203	5384	7.273712	GGATTTTACTTACCCTCTCCTAGTTG	58.726	42.308	0.00	0.00	0.00	3.16
3244	5431	4.505922	CGTTTGCCTAATTTTTGTTGCTCA	59.494	37.500	0.00	0.00	0.00	4.26
3257	5444	8.806429	TTTTTGTTGCTCAGATAATCCTCATA	57.194	30.769	0.00	0.00	0.00	2.15
3273	5460	6.560003	TCCTCATATCCTTTCAAGTTGCTA	57.440	37.500	0.00	0.00	0.00	3.49
3298	5485	7.624549	AGTGCATCTCTGAGAAACCTTATTTA	58.375	34.615	12.00	0.00	0.00	1.40
3378	5607	6.818644	TGAAACATTATCTCTAGAACCAGTGC	59.181	38.462	0.00	0.00	0.00	4.40
3380	5609	5.911752	ACATTATCTCTAGAACCAGTGCTG	58.088	41.667	0.00	0.00	0.00	4.41
3408	5637	5.276461	TGCTTGAATCCTGTCGTATATGT	57.724	39.130	0.00	0.00	0.00	2.29
3416	5645	4.028131	TCCTGTCGTATATGTTGAACCCT	58.972	43.478	0.00	0.00	0.00	4.34
3417	5646	4.119862	CCTGTCGTATATGTTGAACCCTG	58.880	47.826	0.00	0.00	0.00	4.45
3502	5731	6.808704	GCCTGAAATTAACCAAAGAATGACTC	59.191	38.462	0.00	0.00	0.00	3.36
3545	5775	1.938585	TCTCGAAGGGTGATTGGAGT	58.061	50.000	0.00	0.00	36.66	3.85
3548	5778	2.496070	CTCGAAGGGTGATTGGAGTGTA	59.504	50.000	0.00	0.00	32.26	2.90
3566	5796	1.952102	TATGAGGTGAACCGGTCCGC	61.952	60.000	8.04	7.70	42.08	5.54
3624	5854	2.555199	ACACGATAGCTCTTGGCATTC	58.445	47.619	0.00	0.00	44.79	2.67
3667	5898	4.566004	TGCGAAATTAGTTCTGTAGCTGT	58.434	39.130	0.00	0.00	33.70	4.40
3681	5912	7.410120	TCTGTAGCTGTCTTGATATGAAGAA	57.590	36.000	6.17	0.00	33.73	2.52
3844	6094	6.697455	ACGTATGCCGAATAGAGCAATATATG	59.303	38.462	0.00	0.00	43.36	1.78
3987	6241	0.669619	TGAACTCGTCGTTGCAGGTA	59.330	50.000	0.00	0.00	35.56	3.08
3990	6244	0.319297	ACTCGTCGTTGCAGGTAACC	60.319	55.000	0.00	0.00	37.17	2.85
4022	6276	0.802607	GTGGCGGTCATCTTCGTCTC	60.803	60.000	0.00	0.00	31.68	3.36
4026	6280	1.511305	GGTCATCTTCGTCTCGGCA	59.489	57.895	0.00	0.00	0.00	5.69
4031	6285	2.685387	ATCTTCGTCTCGGCATCGGC	62.685	60.000	0.00	0.00	40.13	5.54
4061	6315	4.284860	CTCGATGGCGGCGATGGA	62.285	66.667	12.98	5.85	37.13	3.41
4139	6393	0.249322	CACCTTGTCGACCTCGTTGT	60.249	55.000	14.12	0.00	40.80	3.32
4150	6404	1.674057	CTCGTTGTCTCCTTGCCCT	59.326	57.895	0.00	0.00	0.00	5.19
4164	6418	4.809496	CCCTGGAGCGCTGCCATT	62.809	66.667	26.87	0.00	34.33	3.16
4179	6433	1.528824	CATTCCGGAGTCCATGCCT	59.471	57.895	10.49	0.00	0.00	4.75
4308	6562	0.878523	CGTTCTGGTTGTTCTCGCCA	60.879	55.000	0.00	0.00	0.00	5.69
4386	6640	3.771160	GTGGAGGACATCGCCGGT	61.771	66.667	1.90	0.00	38.24	5.28
4389	6643	2.511600	GAGGACATCGCCGGTTGG	60.512	66.667	1.90	0.00	38.77	3.77
4406	6660	1.925972	GGGGCAGAAGGAAGAGGGT	60.926	63.158	0.00	0.00	0.00	4.34
4410	6664	0.687354	GCAGAAGGAAGAGGGTGACA	59.313	55.000	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
232	234	2.030185	GGGGTTCCGCTTTCTTTCTTTC	60.030	50.000	0.00	0.00	0.00	2.62
235	237	0.476771	TGGGGTTCCGCTTTCTTTCT	59.523	50.000	7.39	0.00	35.24	2.52
246	248	2.507407	TGCTGTTTCTATGGGGTTCC	57.493	50.000	0.00	0.00	0.00	3.62
399	401	3.433740	GGGTGGGGATGAGATACAGAAAC	60.434	52.174	0.00	0.00	0.00	2.78
440	442	4.839121	TGACAGTCCATATACAACCCAAC	58.161	43.478	0.00	0.00	0.00	3.77
503	505	7.143514	ACTTAAACTACCTAGTCAGAAGTCG	57.856	40.000	0.00	0.00	34.99	4.18
584	586	4.276678	ACCAGATCATCCATTACAAATGCG	59.723	41.667	0.00	0.00	0.00	4.73
667	669	8.836268	AACTGTAGTGAAAAATGTATACCGAA	57.164	30.769	0.00	0.00	0.00	4.30
669	671	7.548075	AGGAACTGTAGTGAAAAATGTATACCG	59.452	37.037	0.00	0.00	37.18	4.02
1053	1353	3.726291	AATCAACACAAAAGGAACCGG	57.274	42.857	0.00	0.00	0.00	5.28
1065	1365	7.039313	AGACCCAACTAAAAGAAATCAACAC	57.961	36.000	0.00	0.00	0.00	3.32
1076	1446	7.123547	ACATGAACAGAAAAGACCCAACTAAAA	59.876	33.333	0.00	0.00	0.00	1.52
1173	1575	6.702723	CACAAACATGATGTCTGAATTGGTTT	59.297	34.615	5.81	0.00	0.00	3.27
1176	1578	5.165676	CCACAAACATGATGTCTGAATTGG	58.834	41.667	5.81	0.00	0.00	3.16
1205	1607	0.107993	ACGTGCATGATGTCTCCAGG	60.108	55.000	14.17	0.00	0.00	4.45
1221	1623	6.044512	GTTTTGTATCAGAAGACAACACGT	57.955	37.500	1.56	0.00	36.39	4.49
1223	1625	6.127403	GTCGTTTTGTATCAGAAGACAACAC	58.873	40.000	7.39	7.39	36.39	3.32
1225	1627	6.281848	TGTCGTTTTGTATCAGAAGACAAC	57.718	37.500	1.56	0.00	36.39	3.32
1297	1813	6.380079	AATAACTCCACAAGTCAAGATCCT	57.620	37.500	0.00	0.00	37.17	3.24
1432	2038	2.565841	CCTCTTAAGGCCAGTGCATAC	58.434	52.381	5.01	0.00	40.13	2.39
1723	2530	3.383620	TGGCAACCAAAACAATGCTAG	57.616	42.857	0.00	0.00	38.79	3.42
1837	2659	8.792633	CACCTGAGTACAATAAATCTTTTCCAA	58.207	33.333	0.00	0.00	0.00	3.53
1867	2689	6.830114	GTTCATCCGAACTTGGTATAAGAG	57.170	41.667	0.00	0.00	46.72	2.85
2120	4229	6.937436	AGAACGGAACAAAGAAAAGTATGT	57.063	33.333	0.00	0.00	0.00	2.29
2208	4326	5.228945	ACTATGAAACTAAGGCACTGTGT	57.771	39.130	9.86	0.00	40.86	3.72
2258	4377	4.607955	CAATGTTCTGACCATGATGCATC	58.392	43.478	20.14	20.14	0.00	3.91
2259	4378	3.181479	GCAATGTTCTGACCATGATGCAT	60.181	43.478	0.00	0.00	30.19	3.96
2430	4595	3.093717	TGCGGCTATTTACAGAGCTAC	57.906	47.619	0.00	0.00	38.79	3.58
2458	4626	6.749923	AGAACCTGCAGAACTCATAATTTC	57.250	37.500	17.39	2.05	0.00	2.17
2459	4627	6.716628	TCAAGAACCTGCAGAACTCATAATTT	59.283	34.615	17.39	0.00	0.00	1.82
2460	4628	6.240894	TCAAGAACCTGCAGAACTCATAATT	58.759	36.000	17.39	0.00	0.00	1.40
2461	4629	5.809001	TCAAGAACCTGCAGAACTCATAAT	58.191	37.500	17.39	0.00	0.00	1.28
2468	4636	5.448360	GCATCTTATCAAGAACCTGCAGAAC	60.448	44.000	17.39	5.96	39.59	3.01
2616	4787	4.990526	AGGAACAACATTCTCAACAGGAT	58.009	39.130	0.00	0.00	0.00	3.24
2653	4825	2.488153	ACGCAGGCCTATGAAGAAAAAC	59.512	45.455	3.98	0.00	0.00	2.43
2677	4852	0.179000	AATCACGCTCCATCTCACCC	59.821	55.000	0.00	0.00	0.00	4.61
2836	5011	5.514204	ACGACAACAATAGTATGCGTACTTC	59.486	40.000	23.14	11.84	41.35	3.01
2862	5037	1.956629	ATGGCTACCGACGGGACAAG	61.957	60.000	20.00	10.77	36.97	3.16
3011	5192	6.212791	TCTTGAGTTTATGGTTGTAGTAGCCT	59.787	38.462	0.00	0.00	0.00	4.58
3153	5334	9.889128	CCCAAGAAAACAATTAATAATGGTCAT	57.111	29.630	0.00	0.00	0.00	3.06
3244	5431	9.790344	CAACTTGAAAGGATATGAGGATTATCT	57.210	33.333	0.00	0.00	0.00	1.98
3273	5460	5.690464	ATAAGGTTTCTCAGAGATGCACT	57.310	39.130	0.00	0.00	0.00	4.40
3298	5485	8.281212	ACGAAAATTTCTGCAGGTAGATTTAT	57.719	30.769	15.13	6.63	0.00	1.40
3364	5593	2.007360	CAGCAGCACTGGTTCTAGAG	57.993	55.000	0.00	0.00	43.19	2.43
3380	5609	0.815734	ACAGGATTCAAGCATGCAGC	59.184	50.000	21.98	0.69	46.19	5.25
3386	5615	5.276461	ACATATACGACAGGATTCAAGCA	57.724	39.130	0.00	0.00	0.00	3.91
3408	5637	3.476552	GACACAATGAGACAGGGTTCAA	58.523	45.455	0.00	0.00	0.00	2.69
3416	5645	1.605457	GCCAGACGACACAATGAGACA	60.605	52.381	0.00	0.00	0.00	3.41
3417	5646	1.071605	GCCAGACGACACAATGAGAC	58.928	55.000	0.00	0.00	0.00	3.36
3502	5731	0.711670	CGGTCCACAATCGTGTTACG	59.288	55.000	0.00	0.00	41.93	3.18
3545	5775	0.899720	GGACCGGTTCACCTCATACA	59.100	55.000	9.42	0.00	0.00	2.29
3548	5778	2.978824	CGGACCGGTTCACCTCAT	59.021	61.111	14.76	0.00	0.00	2.90
3566	5796	2.723322	TCAGCCTTCAGGAATCATGG	57.277	50.000	0.00	0.00	37.39	3.66
3606	5836	3.550437	AAGAATGCCAAGAGCTATCGT	57.450	42.857	0.00	0.00	44.23	3.73
3610	5840	4.144297	ACAACAAAGAATGCCAAGAGCTA	58.856	39.130	0.00	0.00	44.23	3.32
3709	5940	3.117794	TGTTACAGTCGTGGAAACGAAG	58.882	45.455	2.07	1.93	44.12	3.79
3820	6070	7.098503	CATATATTGCTCTATTCGGCATACG	57.901	40.000	0.00	0.00	46.11	3.06
3844	6094	8.997323	AGATTATATTGAGCAAATGTCACTAGC	58.003	33.333	0.00	0.00	0.00	3.42
4022	6276	4.944372	GGAGGTACGCCGATGCCG	62.944	72.222	0.00	0.00	39.41	5.69
4031	6285	1.525535	ATCGAGGACGGGAGGTACG	60.526	63.158	0.00	0.00	40.21	3.67
4098	6352	2.747460	TGCCTCAACGCCTGCATC	60.747	61.111	0.00	0.00	0.00	3.91
4164	6418	3.785859	GCAGGCATGGACTCCGGA	61.786	66.667	2.93	2.93	0.00	5.14
4287	6541	0.507358	GCGAGAACAACCAGAACGTC	59.493	55.000	0.00	0.00	0.00	4.34
4293	6547	0.798776	GATGTGGCGAGAACAACCAG	59.201	55.000	0.00	0.00	33.12	4.00
4308	6562	1.326213	CCGAGACCTGCCAGAGATGT	61.326	60.000	0.00	0.00	0.00	3.06
4344	6598	0.987294	CCATCATCCGGCTCCCTTAT	59.013	55.000	0.00	0.00	0.00	1.73
4366	6620	3.458163	GGCGATGTCCTCCACCGA	61.458	66.667	0.00	0.00	0.00	4.69
4386	6640	1.500783	CCCTCTTCCTTCTGCCCCAA	61.501	60.000	0.00	0.00	0.00	4.12
4389	6643	1.201429	TCACCCTCTTCCTTCTGCCC	61.201	60.000	0.00	0.00	0.00	5.36
4395	6649	1.132689	ACCTCTGTCACCCTCTTCCTT	60.133	52.381	0.00	0.00	0.00	3.36
4397	6651	0.610687	CACCTCTGTCACCCTCTTCC	59.389	60.000	0.00	0.00	0.00	3.46
4406	6660	1.429299	TCTTCCTCCTCACCTCTGTCA	59.571	52.381	0.00	0.00	0.00	3.58
4410	6664	2.938428	ACATCTTCCTCCTCACCTCT	57.062	50.000	0.00	0.00	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.