AutoCloner

Multiple sequence alignment - TraesCS3A01G090200

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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	TraesCS3A01G090200	chr3A	100.000	2600	0	0	1	2600	57429855	57432454	0.000000e+00	4802.0
1	TraesCS3A01G090200	chr3A	96.095	845	31	2	1506	2349	705144882	705144039	0.000000e+00	1376.0
2	TraesCS3A01G090200	chr3A	85.714	1281	134	38	248	1508	657459365	657460616	0.000000e+00	1306.0
3	TraesCS3A01G090200	chr3A	88.968	843	75	9	669	1507	408196106	408195278	0.000000e+00	1026.0
4	TraesCS3A01G090200	chr3A	96.552	261	9	0	2340	2600	657460606	657460866	1.430000e-117	433.0
5	TraesCS3A01G090200	chr3A	89.552	67	7	0	2340	2406	713098779	713098713	4.610000e-13	86.1
6	TraesCS3A01G090200	chr6A	93.213	1444	70	9	67	1508	422165583	422164166	0.000000e+00	2098.0
7	TraesCS3A01G090200	chr6A	92.803	264	16	1	2340	2600	422164176	422163913	1.890000e-101	379.0
8	TraesCS3A01G090200	chr7A	97.158	915	24	2	594	1508	693449774	693450686	0.000000e+00	1544.0
9	TraesCS3A01G090200	chr7A	96.062	838	33	0	1502	2339	149927814	149928651	0.000000e+00	1365.0
10	TraesCS3A01G090200	chr7A	97.318	261	7	0	2340	2600	693450676	693450936	6.600000e-121	444.0
11	TraesCS3A01G090200	chr2A	97.844	835	18	0	1505	2339	777643750	777644584	0.000000e+00	1443.0
12	TraesCS3A01G090200	chr5A	97.010	836	25	0	1505	2340	662511275	662512110	0.000000e+00	1406.0
13	TraesCS3A01G090200	chr5A	95.868	847	34	1	1505	2350	80113228	80114074	0.000000e+00	1369.0
14	TraesCS3A01G090200	chr5A	96.177	837	31	1	1505	2341	684793828	684792993	0.000000e+00	1367.0
15	TraesCS3A01G090200	chr5A	89.136	1077	88	21	436	1508	94737701	94738752	0.000000e+00	1314.0
16	TraesCS3A01G090200	chr5A	96.935	261	8	0	2340	2600	94738742	94739002	3.070000e-119	438.0
17	TraesCS3A01G090200	chr5A	96.226	53	2	0	2354	2406	700794252	700794304	1.280000e-13	87.9
18	TraesCS3A01G090200	chr1A	96.424	839	28	2	1502	2339	412137648	412138485	0.000000e+00	1382.0
19	TraesCS3A01G090200	chr6D	95.417	851	39	0	1495	2345	193075019	193074169	0.000000e+00	1356.0
20	TraesCS3A01G090200	chr6D	89.845	837	69	8	676	1507	4108884	4108059	0.000000e+00	1061.0
21	TraesCS3A01G090200	chr4A	95.813	836	34	1	1505	2339	71161989	71162824	0.000000e+00	1349.0
22	TraesCS3A01G090200	chr2D	90.555	847	63	13	665	1508	27615364	27614532	0.000000e+00	1105.0
23	TraesCS3A01G090200	chr2D	94.253	261	15	0	2340	2600	27614542	27614282	1.450000e-107	399.0
24	TraesCS3A01G090200	chr1D	89.349	845	74	8	667	1507	62345645	62346477	0.000000e+00	1048.0
25	TraesCS3A01G090200	chr4D	89.461	835	73	7	676	1507	30305718	30304896	0.000000e+00	1040.0
26	TraesCS3A01G090200	chr3D	78.947	1102	183	32	422	1507	134264155	134263087	0.000000e+00	704.0
27	TraesCS3A01G090200	chr3D	96.169	261	10	0	2340	2600	386603609	386603349	6.650000e-116	427.0
28	TraesCS3A01G090200	chr7D	95.019	261	13	0	2340	2600	69496721	69496981	6.700000e-111	411.0

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	TraesCS3A01G090200	chr3A	57429855	57432454	2599	False	4802.0	4802	100.0000	1	2600	1	chr3A.!!$F1	2599
1	TraesCS3A01G090200	chr3A	705144039	705144882	843	True	1376.0	1376	96.0950	1506	2349	1	chr3A.!!$R2	843
2	TraesCS3A01G090200	chr3A	408195278	408196106	828	True	1026.0	1026	88.9680	669	1507	1	chr3A.!!$R1	838
3	TraesCS3A01G090200	chr3A	657459365	657460866	1501	False	869.5	1306	91.1330	248	2600	2	chr3A.!!$F2	2352
4	TraesCS3A01G090200	chr6A	422163913	422165583	1670	True	1238.5	2098	93.0080	67	2600	2	chr6A.!!$R1	2533
5	TraesCS3A01G090200	chr7A	149927814	149928651	837	False	1365.0	1365	96.0620	1502	2339	1	chr7A.!!$F1	837
6	TraesCS3A01G090200	chr7A	693449774	693450936	1162	False	994.0	1544	97.2380	594	2600	2	chr7A.!!$F2	2006
7	TraesCS3A01G090200	chr2A	777643750	777644584	834	False	1443.0	1443	97.8440	1505	2339	1	chr2A.!!$F1	834
8	TraesCS3A01G090200	chr5A	662511275	662512110	835	False	1406.0	1406	97.0100	1505	2340	1	chr5A.!!$F2	835
9	TraesCS3A01G090200	chr5A	80113228	80114074	846	False	1369.0	1369	95.8680	1505	2350	1	chr5A.!!$F1	845
10	TraesCS3A01G090200	chr5A	684792993	684793828	835	True	1367.0	1367	96.1770	1505	2341	1	chr5A.!!$R1	836
11	TraesCS3A01G090200	chr5A	94737701	94739002	1301	False	876.0	1314	93.0355	436	2600	2	chr5A.!!$F4	2164
12	TraesCS3A01G090200	chr1A	412137648	412138485	837	False	1382.0	1382	96.4240	1502	2339	1	chr1A.!!$F1	837
13	TraesCS3A01G090200	chr6D	193074169	193075019	850	True	1356.0	1356	95.4170	1495	2345	1	chr6D.!!$R2	850
14	TraesCS3A01G090200	chr6D	4108059	4108884	825	True	1061.0	1061	89.8450	676	1507	1	chr6D.!!$R1	831
15	TraesCS3A01G090200	chr4A	71161989	71162824	835	False	1349.0	1349	95.8130	1505	2339	1	chr4A.!!$F1	834
16	TraesCS3A01G090200	chr2D	27614282	27615364	1082	True	752.0	1105	92.4040	665	2600	2	chr2D.!!$R1	1935
17	TraesCS3A01G090200	chr1D	62345645	62346477	832	False	1048.0	1048	89.3490	667	1507	1	chr1D.!!$F1	840
18	TraesCS3A01G090200	chr4D	30304896	30305718	822	True	1040.0	1040	89.4610	676	1507	1	chr4D.!!$R1	831
19	TraesCS3A01G090200	chr3D	134263087	134264155	1068	True	704.0	704	78.9470	422	1507	1	chr3D.!!$R1	1085

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
33	34	0.033699	GGAAGAATGGGAAGCTGGCT	60.034	55.0	0.0	0.0	0.0	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1881	1924	2.346766	ATGACAGCCACACAACTTGA	57.653	45.0	0.0	0.0	0.0	3.02	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
19	20	4.373116	GCTGGTCGTGGCGGAAGA	62.373	66.667	0.00	0.00	0.00	2.87
20	21	2.342279	CTGGTCGTGGCGGAAGAA	59.658	61.111	0.00	0.00	0.00	2.52
21	22	1.079127	CTGGTCGTGGCGGAAGAAT	60.079	57.895	0.00	0.00	0.00	2.40
22	23	1.361668	CTGGTCGTGGCGGAAGAATG	61.362	60.000	0.00	0.00	0.00	2.67
23	24	2.106683	GGTCGTGGCGGAAGAATGG	61.107	63.158	0.00	0.00	0.00	3.16
24	25	2.106683	GTCGTGGCGGAAGAATGGG	61.107	63.158	0.00	0.00	0.00	4.00
25	26	2.267642	CGTGGCGGAAGAATGGGA	59.732	61.111	0.00	0.00	0.00	4.37
26	27	1.376683	CGTGGCGGAAGAATGGGAA	60.377	57.895	0.00	0.00	0.00	3.97
27	28	1.369091	CGTGGCGGAAGAATGGGAAG	61.369	60.000	0.00	0.00	0.00	3.46
28	29	1.378514	TGGCGGAAGAATGGGAAGC	60.379	57.895	0.00	0.00	0.00	3.86
29	30	1.077429	GGCGGAAGAATGGGAAGCT	60.077	57.895	0.00	0.00	0.00	3.74
30	31	1.379642	GGCGGAAGAATGGGAAGCTG	61.380	60.000	0.00	0.00	0.00	4.24
31	32	1.379642	GCGGAAGAATGGGAAGCTGG	61.380	60.000	0.00	0.00	0.00	4.85
32	33	1.379642	CGGAAGAATGGGAAGCTGGC	61.380	60.000	0.00	0.00	0.00	4.85
33	34	0.033699	GGAAGAATGGGAAGCTGGCT	60.034	55.000	0.00	0.00	0.00	4.75
34	35	1.387539	GAAGAATGGGAAGCTGGCTC	58.612	55.000	0.00	0.00	0.00	4.70
35	36	0.393537	AAGAATGGGAAGCTGGCTCG	60.394	55.000	0.00	0.00	0.00	5.03
36	37	1.078143	GAATGGGAAGCTGGCTCGT	60.078	57.895	0.00	0.00	0.00	4.18
37	38	0.678048	GAATGGGAAGCTGGCTCGTT	60.678	55.000	0.00	0.00	0.00	3.85
38	39	0.251341	AATGGGAAGCTGGCTCGTTT	60.251	50.000	0.00	0.00	0.00	3.60
39	40	0.251341	ATGGGAAGCTGGCTCGTTTT	60.251	50.000	0.00	0.00	0.00	2.43
40	41	0.889186	TGGGAAGCTGGCTCGTTTTC	60.889	55.000	0.00	0.00	0.00	2.29
41	42	1.497722	GGAAGCTGGCTCGTTTTCG	59.502	57.895	0.00	0.00	45.64	3.46
42	43	1.154395	GAAGCTGGCTCGTTTTCGC	60.154	57.895	0.00	0.00	43.73	4.70
43	44	1.569479	GAAGCTGGCTCGTTTTCGCT	61.569	55.000	0.00	0.00	43.73	4.93
44	45	1.569479	AAGCTGGCTCGTTTTCGCTC	61.569	55.000	0.00	0.00	43.73	5.03
45	46	2.317609	GCTGGCTCGTTTTCGCTCA	61.318	57.895	0.00	0.00	43.73	4.26
46	47	1.493311	CTGGCTCGTTTTCGCTCAC	59.507	57.895	0.00	0.00	43.73	3.51
47	48	2.215478	CTGGCTCGTTTTCGCTCACG	62.215	60.000	0.00	0.00	43.73	4.35
48	49	2.308039	GGCTCGTTTTCGCTCACGT	61.308	57.895	0.00	0.00	43.73	4.49
49	50	1.563173	GCTCGTTTTCGCTCACGTT	59.437	52.632	0.00	0.00	43.73	3.99
50	51	0.718220	GCTCGTTTTCGCTCACGTTG	60.718	55.000	0.00	0.00	43.73	4.10
51	52	0.575390	CTCGTTTTCGCTCACGTTGT	59.425	50.000	0.00	0.00	43.73	3.32
52	53	1.782569	CTCGTTTTCGCTCACGTTGTA	59.217	47.619	0.00	0.00	43.73	2.41
53	54	2.396601	TCGTTTTCGCTCACGTTGTAT	58.603	42.857	0.00	0.00	43.73	2.29
54	55	2.796031	TCGTTTTCGCTCACGTTGTATT	59.204	40.909	0.00	0.00	43.73	1.89
55	56	3.980134	TCGTTTTCGCTCACGTTGTATTA	59.020	39.130	0.00	0.00	43.73	0.98
56	57	4.088923	TCGTTTTCGCTCACGTTGTATTAG	59.911	41.667	0.00	0.00	43.73	1.73
57	58	4.088923	CGTTTTCGCTCACGTTGTATTAGA	59.911	41.667	0.00	0.00	41.18	2.10
58	59	5.387649	CGTTTTCGCTCACGTTGTATTAGAA	60.388	40.000	0.00	0.00	41.18	2.10
59	60	5.756950	TTTCGCTCACGTTGTATTAGAAG	57.243	39.130	0.00	0.00	41.18	2.85
60	61	3.766151	TCGCTCACGTTGTATTAGAAGG	58.234	45.455	0.00	0.00	41.18	3.46
61	62	3.441222	TCGCTCACGTTGTATTAGAAGGA	59.559	43.478	0.85	0.00	41.18	3.36
62	63	4.097437	TCGCTCACGTTGTATTAGAAGGAT	59.903	41.667	0.85	0.00	41.18	3.24
63	64	4.207224	CGCTCACGTTGTATTAGAAGGATG	59.793	45.833	0.85	0.00	33.53	3.51
64	65	5.348986	GCTCACGTTGTATTAGAAGGATGA	58.651	41.667	0.85	1.35	0.00	2.92
65	66	5.232414	GCTCACGTTGTATTAGAAGGATGAC	59.768	44.000	0.85	0.00	0.00	3.06
69	70	6.418226	CACGTTGTATTAGAAGGATGACTAGC	59.582	42.308	0.85	0.00	0.00	3.42
91	92	2.629050	ATTAGCGCTCGGATGCACGT	62.629	55.000	16.34	0.00	34.94	4.49
107	108	2.167900	GCACGTTGGTTACTCCCTCTAT	59.832	50.000	0.00	0.00	34.77	1.98
110	111	5.346522	CACGTTGGTTACTCCCTCTATAAC	58.653	45.833	0.00	0.00	34.77	1.89
118	119	0.825010	TCCCTCTATAACCGGGCGTC	60.825	60.000	6.32	0.00	37.89	5.19
123	124	1.611977	TCTATAACCGGGCGTCAGATG	59.388	52.381	6.32	0.00	0.00	2.90
134	135	1.575244	CGTCAGATGGGCTGTGTATG	58.425	55.000	0.00	0.00	45.14	2.39
162	163	5.578776	TCAGTATGTAGTACACGCATGAAG	58.421	41.667	4.80	0.00	37.40	3.02
166	167	4.245845	TGTAGTACACGCATGAAGTTGA	57.754	40.909	0.00	0.00	0.00	3.18
169	170	3.925379	AGTACACGCATGAAGTTGATGA	58.075	40.909	6.49	0.00	0.00	2.92
172	173	2.481568	ACACGCATGAAGTTGATGACTG	59.518	45.455	6.49	2.78	39.00	3.51
221	222	6.040391	TGGTATTTCTTTTTCTCACCACTTGG	59.960	38.462	0.00	0.00	42.17	3.61
235	236	0.740737	ACTTGGCCGCTAAATCATGC	59.259	50.000	0.00	0.00	0.00	4.06
237	238	0.455410	TTGGCCGCTAAATCATGCAC	59.545	50.000	0.00	0.00	0.00	4.57
240	241	1.534595	GGCCGCTAAATCATGCACTTG	60.535	52.381	0.00	0.00	0.00	3.16
244	245	3.367292	CCGCTAAATCATGCACTTGGTTT	60.367	43.478	4.11	4.11	34.43	3.27
304	306	4.218417	ACACATGGATTAGTTCTGTTTGCC	59.782	41.667	0.00	0.00	0.00	4.52
307	309	1.132453	GGATTAGTTCTGTTTGCCGCC	59.868	52.381	0.00	0.00	0.00	6.13
331	333	3.106242	TCATCAGTTAACTGCACGTGT	57.894	42.857	27.49	8.66	43.46	4.49
338	340	5.005971	TCAGTTAACTGCACGTGTTTTAGTC	59.994	40.000	27.49	8.94	43.46	2.59
340	342	3.668596	AACTGCACGTGTTTTAGTCAC	57.331	42.857	18.38	0.00	0.00	3.67
341	343	2.623535	ACTGCACGTGTTTTAGTCACA	58.376	42.857	18.38	1.92	35.79	3.58
344	346	2.939756	TGCACGTGTTTTAGTCACACAT	59.060	40.909	18.38	0.00	44.14	3.21
346	348	3.001838	GCACGTGTTTTAGTCACACATCA	59.998	43.478	18.38	0.00	44.14	3.07
375	397	1.538047	TCTTTTGGGCTGCATGAGTC	58.462	50.000	0.50	0.00	0.00	3.36
410	432	5.391950	GCACGTCCATATAATTAGGCAATGG	60.392	44.000	10.51	10.51	38.76	3.16
433	457	5.345702	GTTGTTCCCCGCTTATTTAATTCC	58.654	41.667	0.00	0.00	0.00	3.01
434	458	4.601084	TGTTCCCCGCTTATTTAATTCCA	58.399	39.130	0.00	0.00	0.00	3.53
536	563	2.543031	GGAACCAACGAGAAGTTTTGGC	60.543	50.000	4.29	0.00	43.18	4.52
551	578	7.447238	AGAAGTTTTGGCTTAACACTGCTATAA	59.553	33.333	0.89	0.00	0.00	0.98
603	630	7.980099	AGTTTAGTACTGCATGGTTACATACTC	59.020	37.037	5.39	0.00	35.19	2.59
610	637	4.261801	GCATGGTTACATACTCACCAACT	58.738	43.478	0.00	0.00	43.85	3.16
644	671	5.475719	TCGTGAATTCGTGATTATATCCCC	58.524	41.667	0.04	0.00	0.00	4.81
858	891	5.948758	TGCCATGTTATTAATCAGACCAACA	59.051	36.000	0.00	0.00	0.00	3.33
994	1035	3.615155	GGCTCCTAAACTCAATTGAGCT	58.385	45.455	30.95	19.44	45.79	4.09
1097	1138	1.352687	GAGAAGGCTCCAGTTCCCTTT	59.647	52.381	0.00	0.00	38.99	3.11
1344	1385	6.433716	TGATCATGAAAATGCTCACCACTAAA	59.566	34.615	0.00	0.00	0.00	1.85
1522	1563	3.753294	ATCACTGTTCAAGAACTCGGT	57.247	42.857	13.49	7.47	41.67	4.69
1817	1860	4.930963	TGCTATTTGTGTTGAACCTTGTG	58.069	39.130	0.00	0.00	0.00	3.33
1881	1924	4.015764	TGTTATGTGTGGCTGCATATTGT	58.984	39.130	0.50	0.00	0.00	2.71
2125	2168	2.493414	ATAGGCCTACGAGCTACGAT	57.507	50.000	16.61	0.00	45.77	3.73
2233	2276	5.379187	TGCCAATATATTCTCATGTGCAGT	58.621	37.500	0.00	0.00	0.00	4.40
2279	2322	4.590918	TCAGTTAAATGGCCGATTAACCA	58.409	39.130	26.97	17.48	40.98	3.67
2342	2385	3.055675	ACCGAGTTCCCGAACAATGATTA	60.056	43.478	10.07	0.00	43.47	1.75
2428	2471	3.692593	GCGGCTTAAGGTTGAAAGGATAA	59.307	43.478	4.29	0.00	0.00	1.75
2562	2608	2.173669	CACCAAGGCCATCGCTACG	61.174	63.158	5.01	0.00	34.44	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	1.079127	ATTCTTCCGCCACGACCAG	60.079	57.895	0.00	0.00	0.00	4.00
5	6	2.106683	CCATTCTTCCGCCACGACC	61.107	63.158	0.00	0.00	0.00	4.79
6	7	2.106683	CCCATTCTTCCGCCACGAC	61.107	63.158	0.00	0.00	0.00	4.34
8	9	1.369091	CTTCCCATTCTTCCGCCACG	61.369	60.000	0.00	0.00	0.00	4.94
9	10	1.657751	GCTTCCCATTCTTCCGCCAC	61.658	60.000	0.00	0.00	0.00	5.01
12	13	1.379642	CCAGCTTCCCATTCTTCCGC	61.380	60.000	0.00	0.00	0.00	5.54
13	14	1.379642	GCCAGCTTCCCATTCTTCCG	61.380	60.000	0.00	0.00	0.00	4.30
14	15	0.033699	AGCCAGCTTCCCATTCTTCC	60.034	55.000	0.00	0.00	0.00	3.46
15	16	1.387539	GAGCCAGCTTCCCATTCTTC	58.612	55.000	0.00	0.00	0.00	2.87
16	17	0.393537	CGAGCCAGCTTCCCATTCTT	60.394	55.000	0.00	0.00	0.00	2.52
17	18	1.222936	CGAGCCAGCTTCCCATTCT	59.777	57.895	0.00	0.00	0.00	2.40
18	19	0.678048	AACGAGCCAGCTTCCCATTC	60.678	55.000	0.00	0.00	0.00	2.67
19	20	0.251341	AAACGAGCCAGCTTCCCATT	60.251	50.000	0.00	0.00	0.00	3.16
20	21	0.251341	AAAACGAGCCAGCTTCCCAT	60.251	50.000	0.00	0.00	0.00	4.00
21	22	0.889186	GAAAACGAGCCAGCTTCCCA	60.889	55.000	0.00	0.00	0.00	4.37
22	23	1.876664	GAAAACGAGCCAGCTTCCC	59.123	57.895	0.00	0.00	0.00	3.97
23	24	1.497722	CGAAAACGAGCCAGCTTCC	59.502	57.895	0.00	0.00	0.00	3.46
24	25	1.154395	GCGAAAACGAGCCAGCTTC	60.154	57.895	0.00	0.00	0.00	3.86
25	26	1.569479	GAGCGAAAACGAGCCAGCTT	61.569	55.000	0.00	0.00	34.85	3.74
26	27	2.029844	GAGCGAAAACGAGCCAGCT	61.030	57.895	0.00	0.00	37.69	4.24
27	28	2.317609	TGAGCGAAAACGAGCCAGC	61.318	57.895	0.00	0.00	0.00	4.85
28	29	1.493311	GTGAGCGAAAACGAGCCAG	59.507	57.895	0.00	0.00	0.00	4.85
29	30	2.307309	CGTGAGCGAAAACGAGCCA	61.307	57.895	0.00	0.00	42.32	4.75
30	31	1.828331	AACGTGAGCGAAAACGAGCC	61.828	55.000	10.52	0.00	42.32	4.70
31	32	0.718220	CAACGTGAGCGAAAACGAGC	60.718	55.000	10.52	0.00	42.32	5.03
32	33	0.575390	ACAACGTGAGCGAAAACGAG	59.425	50.000	10.52	5.81	42.32	4.18
33	34	1.837648	TACAACGTGAGCGAAAACGA	58.162	45.000	10.52	0.00	42.32	3.85
34	35	2.848562	ATACAACGTGAGCGAAAACG	57.151	45.000	0.00	3.14	45.15	3.60
35	36	5.505165	TCTAATACAACGTGAGCGAAAAC	57.495	39.130	0.00	0.00	42.00	2.43
36	37	5.119588	CCTTCTAATACAACGTGAGCGAAAA	59.880	40.000	0.00	0.00	42.00	2.29
37	38	4.624024	CCTTCTAATACAACGTGAGCGAAA	59.376	41.667	0.00	0.00	42.00	3.46
38	39	4.082625	TCCTTCTAATACAACGTGAGCGAA	60.083	41.667	0.00	0.00	42.00	4.70
39	40	3.441222	TCCTTCTAATACAACGTGAGCGA	59.559	43.478	0.00	0.00	42.00	4.93
40	41	3.766151	TCCTTCTAATACAACGTGAGCG	58.234	45.455	0.00	0.00	44.93	5.03
41	42	5.232414	GTCATCCTTCTAATACAACGTGAGC	59.768	44.000	0.00	0.00	0.00	4.26
42	43	6.565234	AGTCATCCTTCTAATACAACGTGAG	58.435	40.000	0.00	0.00	0.00	3.51
43	44	6.525578	AGTCATCCTTCTAATACAACGTGA	57.474	37.500	0.00	0.00	0.00	4.35
44	45	6.418226	GCTAGTCATCCTTCTAATACAACGTG	59.582	42.308	0.00	0.00	0.00	4.49
45	46	6.321690	AGCTAGTCATCCTTCTAATACAACGT	59.678	38.462	0.00	0.00	0.00	3.99
46	47	6.740110	AGCTAGTCATCCTTCTAATACAACG	58.260	40.000	0.00	0.00	0.00	4.10
47	48	7.717568	TGAGCTAGTCATCCTTCTAATACAAC	58.282	38.462	0.00	0.00	0.00	3.32
48	49	7.898014	TGAGCTAGTCATCCTTCTAATACAA	57.102	36.000	0.00	0.00	0.00	2.41
49	50	8.484214	AATGAGCTAGTCATCCTTCTAATACA	57.516	34.615	7.86	0.00	45.89	2.29
51	52	8.744652	GCTAATGAGCTAGTCATCCTTCTAATA	58.255	37.037	0.00	0.00	45.89	0.98
52	53	7.576666	CGCTAATGAGCTAGTCATCCTTCTAAT	60.577	40.741	0.00	0.00	45.89	1.73
53	54	6.294231	CGCTAATGAGCTAGTCATCCTTCTAA	60.294	42.308	0.00	0.00	45.89	2.10
54	55	5.182190	CGCTAATGAGCTAGTCATCCTTCTA	59.818	44.000	0.00	0.00	45.89	2.10
55	56	4.022416	CGCTAATGAGCTAGTCATCCTTCT	60.022	45.833	0.00	0.00	45.89	2.85
56	57	4.233789	CGCTAATGAGCTAGTCATCCTTC	58.766	47.826	0.00	0.68	45.89	3.46
57	58	3.553922	GCGCTAATGAGCTAGTCATCCTT	60.554	47.826	0.00	0.11	45.89	3.36
58	59	2.029470	GCGCTAATGAGCTAGTCATCCT	60.029	50.000	0.00	0.00	45.89	3.24
59	60	2.029470	AGCGCTAATGAGCTAGTCATCC	60.029	50.000	8.99	1.84	45.89	3.51
60	61	3.296322	AGCGCTAATGAGCTAGTCATC	57.704	47.619	8.99	0.00	45.89	2.92
69	70	0.598419	TGCATCCGAGCGCTAATGAG	60.598	55.000	23.62	11.43	37.31	2.90
91	92	3.962718	CCGGTTATAGAGGGAGTAACCAA	59.037	47.826	12.42	0.00	44.79	3.67
107	108	2.727392	CCCATCTGACGCCCGGTTA	61.727	63.158	0.00	0.00	0.00	2.85
123	124	6.055588	ACATACTGAATAACATACACAGCCC	58.944	40.000	0.00	0.00	32.67	5.19
134	135	7.646526	TCATGCGTGTACTACATACTGAATAAC	59.353	37.037	5.68	0.00	34.56	1.89
169	170	9.541143	CTGGGTCAAACAAATAATTTAAACAGT	57.459	29.630	0.00	0.00	0.00	3.55
172	173	8.769891	CCACTGGGTCAAACAAATAATTTAAAC	58.230	33.333	0.00	0.00	0.00	2.01
221	222	1.534595	CCAAGTGCATGATTTAGCGGC	60.535	52.381	0.00	0.00	0.00	6.53
240	241	1.993369	GCTCACGCTATGGCCAAACC	61.993	60.000	10.96	0.00	39.84	3.27
244	245	1.326951	TAGTGCTCACGCTATGGCCA	61.327	55.000	8.56	8.56	37.86	5.36
304	306	1.860950	CAGTTAACTGATGATCGGGCG	59.139	52.381	28.17	0.00	46.59	6.13
307	309	2.282555	CGTGCAGTTAACTGATGATCGG	59.717	50.000	34.43	14.13	46.59	4.18
341	343	5.221244	GCCCAAAAGAAAACTACACTGATGT	60.221	40.000	0.00	0.00	43.30	3.06
344	346	4.338118	CAGCCCAAAAGAAAACTACACTGA	59.662	41.667	0.00	0.00	0.00	3.41
346	348	3.068165	GCAGCCCAAAAGAAAACTACACT	59.932	43.478	0.00	0.00	0.00	3.55
350	352	3.894427	TCATGCAGCCCAAAAGAAAACTA	59.106	39.130	0.00	0.00	0.00	2.24
353	355	2.699846	ACTCATGCAGCCCAAAAGAAAA	59.300	40.909	0.00	0.00	0.00	2.29
360	382	1.246056	GCTTGACTCATGCAGCCCAA	61.246	55.000	11.16	0.00	35.13	4.12
391	413	7.232534	GGAACAACCATTGCCTAATTATATGGA	59.767	37.037	16.62	0.00	38.39	3.41
410	432	5.105675	TGGAATTAAATAAGCGGGGAACAAC	60.106	40.000	0.00	0.00	0.00	3.32
478	505	7.934457	ACACTTAATGCTCATAAATGACCATC	58.066	34.615	2.11	0.00	33.26	3.51
536	563	8.492673	TCCTGACAATTTATAGCAGTGTTAAG	57.507	34.615	0.00	0.00	0.00	1.85
603	630	4.450757	TCACGATCACATACAAAGTTGGTG	59.549	41.667	0.00	0.00	0.00	4.17
610	637	5.635700	TCACGAATTCACGATCACATACAAA	59.364	36.000	6.22	0.00	37.03	2.83
644	671	4.323553	AGTAGCCGCTTAGATAAAGGTG	57.676	45.455	0.00	0.00	35.58	4.00
942	983	1.879380	TGACGGGTTCAAAGCTGAATG	59.121	47.619	7.71	0.00	43.39	2.67
994	1035	4.175962	AGGAAAGTTAGTCCCATTGAGGA	58.824	43.478	0.00	0.00	41.22	3.71
1097	1138	3.444029	TCATCATCAGAGGACAAGGACA	58.556	45.455	0.00	0.00	28.01	4.02
1344	1385	4.776349	TCACGCCACTTTTACCATCATAT	58.224	39.130	0.00	0.00	0.00	1.78
1522	1563	4.590918	TGGGCATTTAAATGGTAACTCGA	58.409	39.130	25.61	2.22	36.90	4.04
1881	1924	2.346766	ATGACAGCCACACAACTTGA	57.653	45.000	0.00	0.00	0.00	3.02
2154	2197	6.827251	CCACATAATCCAATGCTCATAGCTAT	59.173	38.462	0.00	0.00	42.97	2.97
2279	2322	6.862090	GGTCGACTACTGATTAGCGATTAATT	59.138	38.462	16.46	0.00	38.08	1.40
2342	2385	6.325286	GGTCCACTTCTCCTTCTGAGTATTAT	59.675	42.308	0.00	0.00	42.12	1.28
2391	2434	1.070758	AGCCGCTCTTCTTCTTGAACA	59.929	47.619	0.00	0.00	0.00	3.18
2562	2608	1.763545	CACTTAGGACCCTTAGGCTCC	59.236	57.143	4.44	4.44	36.11	4.70

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.