Locus 5321

Sequence ID	3L_DroMel_CAF1
Location	14,684,960 – 14,685,176
Length	216
Max. P	0.992584

overview

Window 0

Location	14,684,960 – 14,685,061
Length	101
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	90.44
Mean single sequence MFE	-36.64
Consensus MFE	-31.46
Energy contribution	-32.02
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.89
Structure conservation index	0.86
SVM decision value	1.72
SVM RNA-class probability	0.974092
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14684960 101 - 23771897
GGGGCAAGAAGGAGUAU----GGGGG-CGGAUGACACCCGAAUCGCGGUGGCAUCUCUGGCACAGGAAUUACCAAUUCAAAUGUCAGGCUAUGGCGAAACAUUUCA
...........(((.((----(.(((-.(.....).)))...((((.(((((....((((((...((((.....))))...))))))))))).))))..)))))). ( -30.00)
>DroSec_CAF1 35375 102 - 1
GGGGCAAGGAGGAGUGU----GGCUGUUGGUUGGCACCCGAAUCGCGGUGGCAUCUCUGGCACAGGAAUUACCAAUUCAAAUGUCAGGCUAUGGCGAAACACUUCA
..........(((((((----((.((((....)))).))...((((.(((((....((((((...((((.....))))...))))))))))).)))).))))))). ( -35.20)
>DroSim_CAF1 36506 102 - 1
GGGGCAAGAAGGAGUGU----GGCUGUUGGUUGGCACCCGAAUCGCGGUGGCAUCUCUGGCACAGGAAUUACCAAUUCAAAUGUCAGGCUAUGGCGAAACACUUCA
..........(((((((----((.((((....)))).))...((((.(((((....((((((...((((.....))))...))))))))))).)))).))))))). ( -35.20)
>DroEre_CAF1 35518 99 - 1
GGGGCAU---GGAGUGU----GGGGGGUGGCUGCCACCCGAAACGCGGUGGCAUCUCUGGCACUGGAAUUACCAAUUCAAAUGUCAGGCUAUGGCGAAACACUUCA
......(---(((((((----...((((((...))))))....(((.(((((....((((((...((((.....))))...))))))))))).)))..)))))))) ( -39.90)
>DroYak_CAF1 36260 106 - 1
GGGGCAAGAAGGAGUGUUUUGGGGGGGUGGAUGCCACGCGAGUCGCGGUGGCAUCUCUGGCACAGGAAUUACCAAUUCAAAUGUCAGGCUAUGGCGAAACACUUCA
..........(((((((((((....(((((((((((((((...))).)))))))))((((((...((((.....))))...)))))))))....))))))))))). ( -42.90)
>consensus
GGGGCAAGAAGGAGUGU____GGGGGGUGGAUGCCACCCGAAUCGCGGUGGCAUCUCUGGCACAGGAAUUACCAAUUCAAAUGUCAGGCUAUGGCGAAACACUUCA
..........(((((((....(((.(((....))).)))...((((.(((((....((((((...((((.....))))...))))))))))).)))).))))))). (-31.46 = -32.02 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	14,685,034 – 14,685,138
Length	104
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	79.34
Mean single sequence MFE	-24.84
Consensus MFE	-18.76
Energy contribution	-19.60
Covariance contribution	0.84
Combinations/Pair	1.05
Mean z-score	-2.57
Structure conservation index	0.76
SVM decision value	2.34
SVM RNA-class probability	0.992584
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14685034 104 + 23771897
AUCCG-CCCCCAUACUCCUUC--------UUGCCCCUUUUGGGCAUAUCUACGCACACCACACAACGGAAAUUGCCUUUUUUGCGCGACUUCCGCUUCUGUGCG---AGCCCCCUU
....(-(..............--------.(((((.....)))))......((((((........(((((.(((((......).)))).)))))....))))))---.))...... ( -26.40)
>DroSec_CAF1 35449 105 + 1
AACCAACAGCCACACUCCUCC--------UUGCCCCUUUUGGGCAUAUCUACGCACACCAUACAACGGAAAUUGCCUUUUUUGCGCGACUUCCGCUUCUGUGCG---AGUCCCCUU
.............((((....--------.(((((.....))))).......(((((........(((((.(((((......).)))).)))))....))))))---)))...... ( -26.60)
>DroSim_CAF1 36580 105 + 1
AACCAACAGCCACACUCCUUC--------UUGCCCCUUUUGGGCAUAUCUACGCACACCACACAACGGAAAUUGCCUUUUUUGCGCGACUUCCGCUUCUGUGCG---AGUCCCCUU
.............((((....--------.(((((.....))))).......(((((........(((((.(((((......).)))).)))))....))))))---)))...... ( -26.60)
>DroEre_CAF1 35592 105 + 1
AGCCACCCCCCACACUCC-----------AUGCCCCUUUCGGCCAUUUCUGCGCACACCACACAACGGAAAUUGCCUUUUUUGCGCGACUUCCGCUUCUGUGCGAACGAACCCCUU
..................-----------..(((......)))...(((..((((((........(((((.(((((......).)))).)))))....))))))...)))...... ( -21.60)
>DroAna_CAF1 31721 105 + 1
----UACCGCCACCAUCCUCCCGAAAAACCAGCCAUAUUUGCGC----CUGCUCAUACCGCACAACGGAAAUUGCCUUUUUUGCGCGACUUCCGCUUUUGUGCG---AGUCUCAGU
----...........................((((....)).))----..(((.(.((((((((((((((.(((((......).)))).)))))...)))))))---.)).).))) ( -23.00)
>consensus
AACCAACCGCCACACUCCUCC________UUGCCCCUUUUGGGCAUAUCUACGCACACCACACAACGGAAAUUGCCUUUUUUGCGCGACUUCCGCUUCUGUGCG___AGUCCCCUU
..............................(((((.....)))))......((((((........(((((.(((((......).)))).)))))....))))))............ (-18.76 = -19.60 +   0.84)

alignment

secondary structure

dotplot

Window 2

Location	14,685,034 – 14,685,138
Length	104
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	79.34
Mean single sequence MFE	-32.89
Consensus MFE	-22.36
Energy contribution	-23.20
Covariance contribution	0.84
Combinations/Pair	1.05
Mean z-score	-1.86
Structure conservation index	0.68
SVM decision value	0.76
SVM RNA-class probability	0.843951
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14685034 104 - 23771897
AAGGGGGCU---CGCACAGAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUGUGGUGUGCGUAGAUAUGCCCAAAAGGGGCAA--------GAAGGAGUAUGGGGG-CGGAU
......(((---(.((((..(((((((((.((.(......))).))))))))).))))..((((.......(((((.....))))).--------......))))..)))-).... ( -34.14)
>DroSec_CAF1 35449 105 - 1
AAGGGGACU---CGCACAGAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUAUGGUGUGCGUAGAUAUGCCCAAAAGGGGCAA--------GGAGGAGUGUGGCUGUUGGUU
....(.(((---((((((..(((((((((.((.(......))).)))))))))......))))).......(((((.....))))).--------....)))).)........... ( -32.50)
>DroSim_CAF1 36580 105 - 1
AAGGGGACU---CGCACAGAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUGUGGUGUGCGUAGAUAUGCCCAAAAGGGGCAA--------GAAGGAGUGUGGCUGUUGGUU
....(.(((---((((((..(((((((((.((.(......))).)))))))))......))))).......(((((.....))))).--------....)))).)........... ( -32.50)
>DroEre_CAF1 35592 105 - 1
AAGGGGUUCGUUCGCACAGAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUGUGGUGUGCGCAGAAAUGGCCGAAAGGGGCAU-----------GGAGUGUGGGGGGUGGCU
....(((((.(((((((...(((((((((.((.(......))).))))))))).......((((.((....)).((....)).))))-----------...))))))).))..))) ( -33.10)
>DroAna_CAF1 31721 105 - 1
ACUGAGACU---CGCACAAAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUGCGGUAUGAGCAG----GCGCAAAUAUGGCUGGUUUUUCGGGAGGAUGGUGGCGGUA----
.(((..((.---((((((...((((((((.((.(......))).)))))))))))))))).....)))----.......(((.((((.(..(((....))).).)))).)))---- ( -32.20)
>consensus
AAGGGGACU___CGCACAGAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUGUGGUGUGCGUAGAUAUGCCCAAAAGGGGCAA________GAAGGAGUGUGGCGGUUGGUU
............((((((...((((((((.((.(......))).)))))))))))))).............(((((.....))))).............................. (-22.36 = -23.20 +   0.84)

alignment

secondary structure

dotplot

Window 3

Location	14,685,061 – 14,685,176
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.28
Mean single sequence MFE	-37.27
Consensus MFE	-24.34
Energy contribution	-25.01
Covariance contribution	0.67
Combinations/Pair	1.19
Mean z-score	-2.18
Structure conservation index	0.65
SVM decision value	0.40
SVM RNA-class probability	0.722372
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14685061 115 - 23771897
GUCUCGCCAAAUGCUGGGUGGGAAAAAAGCGCGAAA--CGAAGGGGGCU---CGCACAGAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUGUGGUGUGCGUAGAUAUGCCCAAAA
.(((((((........))))))).............--(....)((((.---((((((..(((((((((.((.(......))).)))))))))......)))))).......)))).... ( -37.20)
>DroSec_CAF1 35477 117 - 1
GUAUCGCCGAAUGCUGGGUGGGAAAAAAGCGUGAGGGGAGAAGGGGACU---CGCACAGAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUAUGGUGUGCGUAGAUAUGCCCAAAA
...((.((..(((((............)))))..)).))...(((.(((---((((((..(((((((((.((.(......))).)))))))))......)))))).))...).))).... ( -37.10)
>DroSim_CAF1 36608 117 - 1
GUAUCGCCGAAUGCUGGGUGGGAAAAAAGCGUGAGGGGAGAAGGGGACU---CGCACAGAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUGUGGUGUGCGUAGAUAUGCCCAAAA
...((.((..(((((............)))))..)).))...(((.(((---((((((..(((((((((.((.(......))).)))))))))......)))))).))...).))).... ( -37.10)
>DroEre_CAF1 35617 113 - 1
GUAUCGCCGAAUGCUGGGCGGGAAAAAAGCGGA-------AAGGGGUUCGUUCGCACAGAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUGUGGUGUGCGCAGAAAUGGCCGAAA
...((((((....(((.(((.(.....((((((-------......))))))((((((...((((((((.((.(......))).)))))))))))))).).))).)))...))).))).. ( -36.40)
>DroYak_CAF1 36366 108 - 1
GUAUCGCCGAAUGCUGGGCGGGAAAAAAGCGGG-------AAGGCGGCUG-----GCGGAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUGUGGUGUGCGCAGAUAUGGCCGAAA
...((((((.((.(((.(((.(..(..((((((-------((.((((((.-----((....))...))))))((.......))..))))))))...)..).))).))))).))).))).. ( -40.50)
>DroAna_CAF1 31753 107 - 1
GUAUCGCU---CGCUGGGCGGGAAAAUUUCGAGCGG---GACUGAGACU---CGCACAAAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUGCGGUAUGAGCAG----GCGCAAAU
...(((((---.....)))))...........(((.---..(((..((.---((((((...((((((((.((.(......))).)))))))))))))))).....)))----.))).... ( -35.30)
>consensus
GUAUCGCCGAAUGCUGGGCGGGAAAAAAGCGGGAGG___GAAGGGGACU___CGCACAGAAGCGGAAGUCGCGCAAAAAAGGCAAUUUCCGUUGUGUGGUGUGCGCAGAUAUGCCCAAAA
...(((((........))))).....................(((.......((((((..(((((((((.((.(......))).)))))))))......))))))........))).... (-24.34 = -25.01 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:16 2006