AutoCloner

Multiple sequence alignment - TraesCS2B01G598300

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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	TraesCS2B01G598300	chr2B	100.000	4067	0	0	1	4067	781148702	781152768	0.000000e+00	7511.0
1	TraesCS2B01G598300	chr2B	91.308	2508	141	45	1578	4039	781085479	781083003	0.000000e+00	3352.0
2	TraesCS2B01G598300	chr2B	85.818	3180	291	74	394	3466	780875794	780872668	0.000000e+00	3227.0
3	TraesCS2B01G598300	chr2B	85.162	1449	143	41	2047	3466	780829667	780828262	0.000000e+00	1419.0
4	TraesCS2B01G598300	chr2B	83.178	214	17	5	3783	3995	780872351	780872156	1.160000e-40	178.0
5	TraesCS2B01G598300	chr2D	88.826	3007	243	43	1	2942	651430702	651433680	0.000000e+00	3605.0
6	TraesCS2B01G598300	chr2D	87.118	2391	247	31	903	3260	117631153	117633515	0.000000e+00	2652.0
7	TraesCS2B01G598300	chr2D	86.695	1646	160	27	1869	3466	651422738	651421104	0.000000e+00	1772.0
8	TraesCS2B01G598300	chr2D	85.017	1802	181	43	1033	2800	651574821	651576567	0.000000e+00	1749.0
9	TraesCS2B01G598300	chr2D	90.171	234	12	6	3020	3251	651433693	651433917	1.110000e-75	294.0
10	TraesCS2B01G598300	chr2D	81.461	356	54	9	3610	3958	651598008	651598358	8.610000e-72	281.0
11	TraesCS2B01G598300	chr2D	90.148	203	13	6	3270	3466	651490175	651490376	1.450000e-64	257.0
12	TraesCS2B01G598300	chr2D	88.318	214	23	2	3783	3995	651528194	651528406	5.220000e-64	255.0
13	TraesCS2B01G598300	chr2D	88.479	217	17	8	3257	3466	651597410	651597625	5.220000e-64	255.0
14	TraesCS2B01G598300	chr2D	86.341	205	25	3	3580	3781	651527948	651528152	1.900000e-53	220.0
15	TraesCS2B01G598300	chr2D	84.466	206	13	5	3791	3995	651490632	651490819	6.940000e-43	185.0
16	TraesCS2B01G598300	chr2D	90.226	133	12	1	3583	3714	651490452	651490584	5.400000e-39	172.0
17	TraesCS2B01G598300	chr2D	86.441	59	5	3	3580	3636	651597793	651597850	1.220000e-05	62.1
18	TraesCS2B01G598300	chr2A	90.868	2431	188	14	776	3196	776171025	776168619	0.000000e+00	3229.0
19	TraesCS2B01G598300	chr2A	87.026	2320	227	32	900	3197	776212835	776215102	0.000000e+00	2549.0
20	TraesCS2B01G598300	chr2A	81.509	411	23	16	3411	3769	776168479	776168070	5.140000e-74	289.0
21	TraesCS2B01G598300	chr2A	95.833	48	2	0	3783	3830	776168016	776167969	1.210000e-10	78.7
22	TraesCS2B01G598300	chr2A	95.238	42	2	0	833	874	776212789	776212830	2.620000e-07	67.6
23	TraesCS2B01G598300	chr6D	87.568	2389	236	31	906	3260	69108803	69106442	0.000000e+00	2710.0
24	TraesCS2B01G598300	chr6D	81.108	2202	307	62	1035	3210	458990768	458988650	0.000000e+00	1661.0
25	TraesCS2B01G598300	chr6D	80.944	2204	328	49	1035	3210	459064402	459062263	0.000000e+00	1659.0
26	TraesCS2B01G598300	chr6D	88.785	107	12	0	831	937	459064550	459064444	9.170000e-27	132.0
27	TraesCS2B01G598300	chr5B	79.797	2262	368	54	997	3213	703859467	703857250	0.000000e+00	1563.0
28	TraesCS2B01G598300	chr6B	81.192	1393	213	30	1035	2413	698121810	698120453	0.000000e+00	1075.0
29	TraesCS2B01G598300	chr6B	85.714	98	14	0	838	935	698121951	698121854	2.000000e-18	104.0
30	TraesCS2B01G598300	chrUn	86.839	927	112	7	1277	2196	23720256	23719333	0.000000e+00	1027.0
31	TraesCS2B01G598300	chrUn	84.300	1121	99	34	2396	3490	23718990	23717921	0.000000e+00	1024.0
32	TraesCS2B01G598300	chr5D	91.176	442	23	6	906	1347	548473929	548473504	1.630000e-163	586.0
33	TraesCS2B01G598300	chr5D	73.127	1455	315	61	822	2230	552741867	552740443	6.200000e-123	451.0
34	TraesCS2B01G598300	chr3D	91.011	445	24	6	903	1347	68368790	68369218	1.630000e-163	586.0

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	TraesCS2B01G598300	chr2B	781148702	781152768	4066	False	7511.000000	7511	100.000000	1	4067	1	chr2B.!!$F1	4066
1	TraesCS2B01G598300	chr2B	781083003	781085479	2476	True	3352.000000	3352	91.308000	1578	4039	1	chr2B.!!$R2	2461
2	TraesCS2B01G598300	chr2B	780872156	780875794	3638	True	1702.500000	3227	84.498000	394	3995	2	chr2B.!!$R3	3601
3	TraesCS2B01G598300	chr2B	780828262	780829667	1405	True	1419.000000	1419	85.162000	2047	3466	1	chr2B.!!$R1	1419
4	TraesCS2B01G598300	chr2D	117631153	117633515	2362	False	2652.000000	2652	87.118000	903	3260	1	chr2D.!!$F1	2357
5	TraesCS2B01G598300	chr2D	651430702	651433917	3215	False	1949.500000	3605	89.498500	1	3251	2	chr2D.!!$F3	3250
6	TraesCS2B01G598300	chr2D	651421104	651422738	1634	True	1772.000000	1772	86.695000	1869	3466	1	chr2D.!!$R1	1597
7	TraesCS2B01G598300	chr2D	651574821	651576567	1746	False	1749.000000	1749	85.017000	1033	2800	1	chr2D.!!$F2	1767
8	TraesCS2B01G598300	chr2D	651490175	651490819	644	False	204.666667	257	88.280000	3270	3995	3	chr2D.!!$F4	725
9	TraesCS2B01G598300	chr2A	776212789	776215102	2313	False	1308.300000	2549	91.132000	833	3197	2	chr2A.!!$F1	2364
10	TraesCS2B01G598300	chr2A	776167969	776171025	3056	True	1198.900000	3229	89.403333	776	3830	3	chr2A.!!$R1	3054
11	TraesCS2B01G598300	chr6D	69106442	69108803	2361	True	2710.000000	2710	87.568000	906	3260	1	chr6D.!!$R1	2354
12	TraesCS2B01G598300	chr6D	458988650	458990768	2118	True	1661.000000	1661	81.108000	1035	3210	1	chr6D.!!$R2	2175
13	TraesCS2B01G598300	chr6D	459062263	459064550	2287	True	895.500000	1659	84.864500	831	3210	2	chr6D.!!$R3	2379
14	TraesCS2B01G598300	chr5B	703857250	703859467	2217	True	1563.000000	1563	79.797000	997	3213	1	chr5B.!!$R1	2216
15	TraesCS2B01G598300	chr6B	698120453	698121951	1498	True	589.500000	1075	83.453000	838	2413	2	chr6B.!!$R1	1575
16	TraesCS2B01G598300	chrUn	23717921	23720256	2335	True	1025.500000	1027	85.569500	1277	3490	2	chrUn.!!$R1	2213
17	TraesCS2B01G598300	chr5D	552740443	552741867	1424	True	451.000000	451	73.127000	822	2230	1	chr5D.!!$R2	1408

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	Hairpin	End Stability	Orientation
188	190	0.179073	CCCATCGGCGTTGAGATTCT	60.179	55.000	18.84	0.00	2.40	F
190	192	0.302890	CATCGGCGTTGAGATTCTGC	59.697	55.000	12.41	0.00	4.26	F
619	645	1.071699	TGTACTTTGCACCTCTCCCAC	59.928	52.381	0.00	0.00	4.61	F
1712	1817	0.869454	CGGATTGAGCTCGTCTCTGC	60.869	60.000	9.64	42.38	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1453	1553	0.333993	AAGGCCATGAACTCCTGCAT	59.666	50.000	5.01	0.00	0.00	3.96	R
1712	1817	1.026718	CACTTGCCTAAGCTTCGGGG	61.027	60.000	18.01	12.73	40.80	5.73	R
2445	2742	1.519719	CAGGGCTCTCCTCTTTCCG	59.480	63.158	0.00	0.00	46.12	4.30	R
3466	3881	0.107410	AACAGCACACCTTTGACCGA	60.107	50.000	0.00	0.00	0.00	4.69	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
83	84	1.079336	GGAACCGAGTGGCACTACC	60.079	63.158	22.11	14.54	39.70	3.18
107	108	6.040504	CCATCTATGTAGTACAGGTAAGCACA	59.959	42.308	9.25	0.00	0.00	4.57
124	126	5.783100	AGCACAACAAAAACTCACAAATG	57.217	34.783	0.00	0.00	0.00	2.32
163	165	4.201980	GCGATTATGGTTTTTCTACCCCAC	60.202	45.833	0.00	0.00	37.39	4.61
170	172	0.978907	TTTTCTACCCCACGGACTCC	59.021	55.000	0.00	0.00	0.00	3.85
188	190	0.179073	CCCATCGGCGTTGAGATTCT	60.179	55.000	18.84	0.00	0.00	2.40
190	192	0.302890	CATCGGCGTTGAGATTCTGC	59.697	55.000	12.41	0.00	0.00	4.26
203	205	3.825160	TTCTGCTGTGACCACCGGC	62.825	63.158	0.00	3.47	0.00	6.13
204	206	4.320456	CTGCTGTGACCACCGGCT	62.320	66.667	0.00	0.00	32.83	5.52
231	254	2.337583	GCGCACTCTGACTGAATACAA	58.662	47.619	0.30	0.00	0.00	2.41
254	277	2.882137	TCGGGAATCCAAGTTTTGTGAC	59.118	45.455	0.09	0.00	0.00	3.67
286	309	1.209504	CTTCTTTGATGGGCTCCGGTA	59.790	52.381	0.00	0.00	0.00	4.02
313	336	1.250840	GGGCAGTGCGAAGGGAAAAT	61.251	55.000	9.45	0.00	0.00	1.82
374	397	3.366374	GCTTAAACATGTGGAGCTTGACC	60.366	47.826	16.69	0.00	0.00	4.02
403	426	3.138283	TCATTGGTGAGGAGGTGTTCTTT	59.862	43.478	0.00	0.00	0.00	2.52
583	607	2.754002	AGTTTCACTAGAGCGTAGGGAC	59.246	50.000	0.00	0.00	0.00	4.46
614	638	2.902705	TTCGTGTACTTTGCACCTCT	57.097	45.000	0.00	0.00	33.61	3.69
619	645	1.071699	TGTACTTTGCACCTCTCCCAC	59.928	52.381	0.00	0.00	0.00	4.61
624	650	3.181434	ACTTTGCACCTCTCCCACAATAA	60.181	43.478	0.00	0.00	0.00	1.40
628	654	3.274288	GCACCTCTCCCACAATAAGAAG	58.726	50.000	0.00	0.00	0.00	2.85
700	741	2.764128	TCTCCCCGTCCATCCAGC	60.764	66.667	0.00	0.00	0.00	4.85
701	742	3.866582	CTCCCCGTCCATCCAGCC	61.867	72.222	0.00	0.00	0.00	4.85
730	772	3.402681	CCCCGGCCACACTCATCT	61.403	66.667	2.24	0.00	0.00	2.90
1179	1261	2.356313	CTCTCGCGTGTGCACCTT	60.356	61.111	15.69	0.00	42.97	3.50
1406	1497	2.154462	CACCGAATGCCTTGAGTTCTT	58.846	47.619	0.00	0.00	0.00	2.52
1453	1553	3.491619	GCTGGACAGCGAGATTGAGAATA	60.492	47.826	8.72	0.00	45.29	1.75
1712	1817	0.869454	CGGATTGAGCTCGTCTCTGC	60.869	60.000	9.64	0.00	42.38	4.26
1815	1920	5.038033	CGAGGTGTAATGCTCTCTTCTAAC	58.962	45.833	0.00	0.00	0.00	2.34
1822	1927	1.618837	TGCTCTCTTCTAACGCCAAGT	59.381	47.619	0.00	0.00	0.00	3.16
2059	2195	1.137872	CCGAAGCAGCTCACTCCTATT	59.862	52.381	0.00	0.00	0.00	1.73
2068	2204	5.182001	GCAGCTCACTCCTATTTTCAGAAAA	59.818	40.000	10.80	10.80	34.41	2.29
2334	2510	9.849607	CATATCACAAATACTAAAAGTAGTGCG	57.150	33.333	0.00	0.00	40.89	5.34
2771	3144	1.067582	GTATCAAGACGCCCGAGGG	59.932	63.158	3.22	3.22	38.57	4.30
2870	3243	0.179000	GGGTGCGAGGATGAAGACAT	59.821	55.000	0.00	0.00	39.67	3.06
3079	3452	4.963318	ATCTGTTGACGGATATGGTCAT	57.037	40.909	3.67	0.00	43.37	3.06
3082	3455	2.158827	TGTTGACGGATATGGTCATGGG	60.159	50.000	6.95	0.00	43.37	4.00
3136	3509	0.170561	GCAGCTTGAGCAATGACTGG	59.829	55.000	5.70	0.00	45.16	4.00
3139	3512	0.610232	GCTTGAGCAATGACTGGGGT	60.610	55.000	0.00	0.00	41.59	4.95
3188	3570	7.893124	TCTAGTTATCGGTAACCTGAGAATT	57.107	36.000	14.91	0.00	40.88	2.17
3198	3580	1.012841	CCTGAGAATTCTTGCTCGGC	58.987	55.000	9.87	0.00	36.44	5.54
3252	3634	3.391296	GGTAGCCTGGGAATAGTTGATCA	59.609	47.826	0.00	0.00	0.00	2.92
3283	3681	5.817296	GTGTACTTGAATCTGGATGCATGTA	59.183	40.000	2.46	11.12	36.48	2.29
3323	3721	2.351726	GAGTAATTGCGCACCTACCTTG	59.648	50.000	11.12	0.00	0.00	3.61
3425	3840	4.082463	GGAACAGAGGTTGACTGTAGAGAG	60.082	50.000	0.00	0.00	46.01	3.20
3466	3881	6.899393	TTTGCTATGTGTTGAGAAATTCCT	57.101	33.333	0.00	0.00	0.00	3.36
3467	3882	6.500684	TTGCTATGTGTTGAGAAATTCCTC	57.499	37.500	0.00	0.00	0.00	3.71
3468	3883	4.631377	TGCTATGTGTTGAGAAATTCCTCG	59.369	41.667	0.00	0.00	35.99	4.63
3469	3884	4.034510	GCTATGTGTTGAGAAATTCCTCGG	59.965	45.833	0.00	0.00	35.99	4.63
3473	3888	3.813166	GTGTTGAGAAATTCCTCGGTCAA	59.187	43.478	0.00	0.00	35.99	3.18
3478	3909	3.412386	AGAAATTCCTCGGTCAAAGGTG	58.588	45.455	0.00	0.00	35.29	4.00
3656	4122	7.594714	ACATAGTCTACCAATGTCGATGATAC	58.405	38.462	0.00	0.00	0.00	2.24
3714	4181	8.999431	CAGAGGTACTTTAGTCTTTTGCATTAA	58.001	33.333	0.00	0.00	41.55	1.40
3715	4182	9.569122	AGAGGTACTTTAGTCTTTTGCATTAAA	57.431	29.630	0.00	0.00	41.55	1.52
3717	4184	9.127277	AGGTACTTTAGTCTTTTGCATTAAACA	57.873	29.630	0.00	0.00	27.25	2.83
3739	4206	2.294512	CCCTCAGAAAGTGTTCAAAGGC	59.705	50.000	0.00	0.00	36.82	4.35
3766	4233	4.787135	TCCACATATATTTCAGCACCCA	57.213	40.909	0.00	0.00	0.00	4.51
3769	4236	5.073554	TCCACATATATTTCAGCACCCAGAT	59.926	40.000	0.00	0.00	0.00	2.90
3770	4237	5.413833	CCACATATATTTCAGCACCCAGATC	59.586	44.000	0.00	0.00	0.00	2.75
3771	4238	5.121298	CACATATATTTCAGCACCCAGATCG	59.879	44.000	0.00	0.00	0.00	3.69
3785	4252	2.871099	ATCGGCCGATCGATCTCG	59.129	61.111	34.60	20.69	45.43	4.04
3835	4342	0.314935	AACAATGCCAAGTTCCGCAG	59.685	50.000	1.06	0.00	38.64	5.18
3849	4356	1.745890	CGCAGGAATCGGTATCCCA	59.254	57.895	0.00	0.00	37.71	4.37
3857	4364	0.180406	ATCGGTATCCCACACAAGGC	59.820	55.000	0.00	0.00	0.00	4.35
3913	4420	3.199508	AGATGTGAATGTCTCCTTCAGGG	59.800	47.826	0.00	0.00	33.49	4.45
3916	4423	0.915364	GAATGTCTCCTTCAGGGGCT	59.085	55.000	0.00	0.00	35.00	5.19
3960	4467	4.582701	TCAAAGAATTCAAACATGGCGT	57.417	36.364	8.44	0.00	0.00	5.68
3961	4468	4.297510	TCAAAGAATTCAAACATGGCGTG	58.702	39.130	8.44	4.87	0.00	5.34
3983	4490	3.181487	GGCTGCACACGGATTCAAAATAT	60.181	43.478	0.50	0.00	0.00	1.28
4002	4509	2.561478	TCCTGCCTGGTTTGAACTAC	57.439	50.000	0.00	0.00	37.07	2.73
4006	4513	3.214328	CTGCCTGGTTTGAACTACAAGT	58.786	45.455	0.00	0.00	39.77	3.16
4018	4525	3.784701	ACTACAAGTATCACGCTCCAG	57.215	47.619	0.00	0.00	0.00	3.86
4039	4546	7.441836	TCCAGTTACGCATCATTCTACATATT	58.558	34.615	0.00	0.00	0.00	1.28
4040	4547	8.581578	TCCAGTTACGCATCATTCTACATATTA	58.418	33.333	0.00	0.00	0.00	0.98
4041	4548	9.371136	CCAGTTACGCATCATTCTACATATTAT	57.629	33.333	0.00	0.00	0.00	1.28
4046	4553	8.694975	ACGCATCATTCTACATATTATGACTC	57.305	34.615	10.62	0.00	30.51	3.36
4047	4554	8.306761	ACGCATCATTCTACATATTATGACTCA	58.693	33.333	10.62	0.00	30.51	3.41
4048	4555	9.143631	CGCATCATTCTACATATTATGACTCAA	57.856	33.333	10.62	0.00	30.51	3.02
4055	4562	9.868160	TTCTACATATTATGACTCAAGAGAGGA	57.132	33.333	10.62	0.00	46.44	3.71
4056	4563	9.290988	TCTACATATTATGACTCAAGAGAGGAC	57.709	37.037	10.62	0.00	46.44	3.85
4057	4564	7.296628	ACATATTATGACTCAAGAGAGGACC	57.703	40.000	10.62	0.00	46.44	4.46
4058	4565	6.841229	ACATATTATGACTCAAGAGAGGACCA	59.159	38.462	10.62	0.00	46.44	4.02
4059	4566	7.512058	ACATATTATGACTCAAGAGAGGACCAT	59.488	37.037	10.62	1.38	46.44	3.55
4060	4567	5.860941	TTATGACTCAAGAGAGGACCATC	57.139	43.478	3.73	0.00	46.44	3.51
4061	4568	2.461695	TGACTCAAGAGAGGACCATCC	58.538	52.381	3.73	0.00	46.44	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
65	66	1.079336	GGTAGTGCCACTCGGTTCC	60.079	63.158	0.00	0.00	37.17	3.62
66	67	1.669440	TGGTAGTGCCACTCGGTTC	59.331	57.895	0.00	0.00	43.61	3.62
67	68	3.879844	TGGTAGTGCCACTCGGTT	58.120	55.556	0.00	0.00	43.61	4.44
83	84	7.039313	TGTGCTTACCTGTACTACATAGATG	57.961	40.000	0.00	0.00	0.00	2.90
91	92	6.824704	AGTTTTTGTTGTGCTTACCTGTACTA	59.175	34.615	0.00	0.00	0.00	1.82
124	126	2.668550	GCCTGGGGTGTCGTTCAC	60.669	66.667	0.00	5.28	45.47	3.18
132	134	0.106719	AACCATAATCGCCTGGGGTG	60.107	55.000	10.81	1.53	36.82	4.61
133	135	0.629058	AAACCATAATCGCCTGGGGT	59.371	50.000	10.81	0.00	36.82	4.95
163	165	4.143333	AACGCCGATGGGAGTCCG	62.143	66.667	3.15	0.00	46.50	4.79
170	172	0.933097	CAGAATCTCAACGCCGATGG	59.067	55.000	0.00	0.00	0.00	3.51
188	190	2.920384	TAGCCGGTGGTCACAGCA	60.920	61.111	1.90	0.00	45.16	4.41
190	192	2.227089	GAGGTAGCCGGTGGTCACAG	62.227	65.000	1.90	0.00	0.00	3.66
203	205	2.103143	CAGAGTGCGCGGAGGTAG	59.897	66.667	8.83	0.00	0.00	3.18
204	206	2.360726	TCAGAGTGCGCGGAGGTA	60.361	61.111	8.83	0.00	0.00	3.08
231	254	4.022329	GTCACAAAACTTGGATTCCCGATT	60.022	41.667	0.00	0.00	34.29	3.34
254	277	4.157289	CCATCAAAGAAGAAGACACCATGG	59.843	45.833	11.19	11.19	0.00	3.66
299	322	1.668751	TCGCATATTTTCCCTTCGCAC	59.331	47.619	0.00	0.00	0.00	5.34
301	324	2.350772	CCATCGCATATTTTCCCTTCGC	60.351	50.000	0.00	0.00	0.00	4.70
303	326	5.712152	AATCCATCGCATATTTTCCCTTC	57.288	39.130	0.00	0.00	0.00	3.46
313	336	1.142667	TGCCTCCAAATCCATCGCATA	59.857	47.619	0.00	0.00	0.00	3.14
363	386	1.142667	TGAACACATGGTCAAGCTCCA	59.857	47.619	0.00	0.00	39.09	3.86
374	397	2.751259	CCTCCTCACCAATGAACACATG	59.249	50.000	0.00	0.00	33.30	3.21
403	426	2.224113	ACTTGTTCCTTTCGACGGCTTA	60.224	45.455	0.00	0.00	0.00	3.09
583	607	4.237349	AGTACACGAAAATGCCTTTTGG	57.763	40.909	4.31	6.09	44.18	3.28
614	638	7.745717	TCTTCTCTTTTCTTCTTATTGTGGGA	58.254	34.615	0.00	0.00	0.00	4.37
619	645	9.824534	GCTTCTTCTTCTCTTTTCTTCTTATTG	57.175	33.333	0.00	0.00	0.00	1.90
624	650	7.772757	TCTTTGCTTCTTCTTCTCTTTTCTTCT	59.227	33.333	0.00	0.00	0.00	2.85
628	654	6.142139	GCTCTTTGCTTCTTCTTCTCTTTTC	58.858	40.000	0.00	0.00	38.95	2.29
714	756	0.469917	ATTAGATGAGTGTGGCCGGG	59.530	55.000	2.18	0.00	0.00	5.73
730	772	3.380004	GCATTGGATTCGGTGGTTGATTA	59.620	43.478	0.00	0.00	0.00	1.75
1170	1252	2.964925	GCGACGTCAAGGTGCACA	60.965	61.111	20.43	0.00	0.00	4.57
1179	1261	2.254350	CCGAAGTGAGCGACGTCA	59.746	61.111	17.16	0.00	32.98	4.35
1406	1497	2.447572	TGGGCAGCGGGGATATGA	60.448	61.111	0.00	0.00	0.00	2.15
1436	1536	4.056740	CTGCATATTCTCAATCTCGCTGT	58.943	43.478	0.00	0.00	0.00	4.40
1453	1553	0.333993	AAGGCCATGAACTCCTGCAT	59.666	50.000	5.01	0.00	0.00	3.96
1517	1617	3.565482	TCCAAAAGCATGATATTCGAGCC	59.435	43.478	0.00	0.00	0.00	4.70
1712	1817	1.026718	CACTTGCCTAAGCTTCGGGG	61.027	60.000	18.01	12.73	40.80	5.73
2068	2204	3.738281	CGAGAAGAAACACAGTGGTCAGT	60.738	47.826	5.31	0.00	0.00	3.41
2334	2510	4.666402	GCAAAATTACAATGCGGCTTGAAC	60.666	41.667	15.68	0.00	0.00	3.18
2445	2742	1.519719	CAGGGCTCTCCTCTTTCCG	59.480	63.158	0.00	0.00	46.12	4.30
2450	2749	3.693572	AGGCCAGGGCTCTCCTCT	61.694	66.667	10.54	0.00	46.12	3.69
2771	3144	1.301716	TTGGTCTTCTCGGCACTGC	60.302	57.895	0.00	0.00	0.00	4.40
2870	3243	7.885922	TGATAAGCCTTATAAAGTTTGTCACCA	59.114	33.333	6.16	0.00	0.00	4.17
3079	3452	0.324368	ACGAGACCACTAGCATCCCA	60.324	55.000	0.00	0.00	0.00	4.37
3082	3455	3.053455	GCATTACGAGACCACTAGCATC	58.947	50.000	0.00	0.00	0.00	3.91
3139	3512	1.917782	GAATTACAACTGGCGGCGCA	61.918	55.000	34.36	18.35	0.00	6.09
3173	3555	3.600388	AGCAAGAATTCTCAGGTTACCG	58.400	45.455	8.78	0.00	0.00	4.02
3188	3570	4.373116	GGTCCACGCCGAGCAAGA	62.373	66.667	0.00	0.00	0.00	3.02
3198	3580	2.004583	TTAGAATTGCGAGGTCCACG	57.995	50.000	4.11	4.11	0.00	4.94
3283	3681	9.503399	AATTACTCGGTAAACTGAAAGAGAAAT	57.497	29.630	1.45	0.00	30.41	2.17
3466	3881	0.107410	AACAGCACACCTTTGACCGA	60.107	50.000	0.00	0.00	0.00	4.69
3467	3882	0.738389	AAACAGCACACCTTTGACCG	59.262	50.000	0.00	0.00	0.00	4.79
3468	3883	2.094234	ACAAAACAGCACACCTTTGACC	60.094	45.455	0.73	0.00	33.84	4.02
3469	3884	3.230743	ACAAAACAGCACACCTTTGAC	57.769	42.857	0.73	0.00	33.84	3.18
3473	3888	2.564947	TCCAAACAAAACAGCACACCTT	59.435	40.909	0.00	0.00	0.00	3.50
3478	3909	5.108517	TCAAGAATCCAAACAAAACAGCAC	58.891	37.500	0.00	0.00	0.00	4.40
3551	3998	3.947834	CTGGTGACCAAAGTGAAAAGAGT	59.052	43.478	5.53	0.00	30.80	3.24
3635	4101	6.656632	ATGTATCATCGACATTGGTAGACT	57.343	37.500	0.00	0.00	33.70	3.24
3656	4122	4.133078	GAGCTGGGTTATCCTCTGAAATG	58.867	47.826	0.00	0.00	36.20	2.32
3715	4182	3.644966	TTGAACACTTTCTGAGGGTGT	57.355	42.857	10.46	10.46	42.62	4.16
3717	4184	3.555966	CCTTTGAACACTTTCTGAGGGT	58.444	45.455	0.00	0.00	46.44	4.34
3739	4206	6.147581	GTGCTGAAATATATGTGGAATGCTG	58.852	40.000	0.00	0.00	0.00	4.41
3769	4236	2.280592	TCGAGATCGATCGGCCGA	60.281	61.111	33.12	33.12	44.22	5.54
3781	4248	3.760035	GGCGTTGGCTCCTCGAGA	61.760	66.667	15.71	0.00	39.81	4.04
3849	4356	0.536006	GAGCAAGTCCAGCCTTGTGT	60.536	55.000	0.00	0.00	43.03	3.72
3857	4364	5.363101	TGCAAATCTATAGAGCAAGTCCAG	58.637	41.667	11.58	0.00	31.42	3.86
3867	4374	7.553760	TCTGCTGAAACATTGCAAATCTATAGA	59.446	33.333	1.71	4.57	36.22	1.98
3913	4420	3.157087	TGGAAGAAGATTGAAACCAGCC	58.843	45.455	0.00	0.00	0.00	4.85
3916	4423	7.790027	TGAAAAATGGAAGAAGATTGAAACCA	58.210	30.769	0.00	0.00	0.00	3.67
3960	4467	0.821301	TTTGAATCCGTGTGCAGCCA	60.821	50.000	0.00	0.00	0.00	4.75
3961	4468	0.313672	TTTTGAATCCGTGTGCAGCC	59.686	50.000	0.00	0.00	0.00	4.85
3983	4490	1.771854	TGTAGTTCAAACCAGGCAGGA	59.228	47.619	1.67	0.00	41.22	3.86
4002	4509	2.852413	CGTAACTGGAGCGTGATACTTG	59.148	50.000	0.00	0.00	0.00	3.16
4006	4513	0.812549	TGCGTAACTGGAGCGTGATA	59.187	50.000	0.00	0.00	0.00	2.15
4039	4546	4.078922	AGGATGGTCCTCTCTTGAGTCATA	60.079	45.833	0.00	0.00	45.66	2.15
4040	4547	3.037549	GGATGGTCCTCTCTTGAGTCAT	58.962	50.000	0.00	0.00	38.61	3.06
4041	4548	2.043664	AGGATGGTCCTCTCTTGAGTCA	59.956	50.000	0.00	0.00	45.66	3.41
4042	4549	2.430332	CAGGATGGTCCTCTCTTGAGTC	59.570	54.545	0.00	0.00	45.66	3.36
4043	4550	2.043664	TCAGGATGGTCCTCTCTTGAGT	59.956	50.000	0.00	0.00	45.66	3.41
4044	4551	2.744760	TCAGGATGGTCCTCTCTTGAG	58.255	52.381	0.00	0.00	45.66	3.02
4045	4552	2.928036	TCAGGATGGTCCTCTCTTGA	57.072	50.000	0.00	3.67	45.66	3.02
4046	4553	3.540314	CTTCAGGATGGTCCTCTCTTG	57.460	52.381	0.00	0.00	45.66	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.