Locus 5386

Sequence ID	2L_DroMel_CAF1
Location	15,364,805 – 15,364,938
Length	133
Max. P	0.973969

overview

Window 5

Location	15,364,805 – 15,364,898
Length	93
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	77.67
Mean single sequence MFE	-31.35
Consensus MFE	-21.32
Energy contribution	-21.18
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-1.11
Structure conservation index	0.68
SVM decision value	0.05
SVM RNA-class probability	0.558623
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15364805 93 + 22407834
-----------------CUCGAGACUUGAGAGGUAGGUUCACCUGUUUAUGCCAGAUUACUGGCAUGCGAUUAAAAUCACCUGCGCAAGCUUUUGCGCCCACGCAGUCGA----
-----------------.....((((((..(((((((....)))...((((((((....))))))))...........))))((((((....))))))...)).))))..---- ( -28.70)
>DroEre_CAF1 117062 100 + 1
-----CUGGA-----GACUUGAGACUUGAGAGGUAGGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCAUCUGCGCAAGCUUUUGCGCCCACGCAGUGGA----
-----..(..-----..).(((...((((..(.((((....))))..((((((((....)))))))))..))))..)))...((((((....))))))((((...)))).---- ( -28.20)
>DroWil_CAF1 184646 84 + 1
------------------------------GGCGAGGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCACCUGCGCAAGCUUUUGCGCCCACGCAGUUGGCCAU
------------------------------(((.(((....)))...((((((((....))))))))..........((.(((((...((....)).....))))).))))).. ( -28.60)
>DroYak_CAF1 116796 105 + 1
-----UCGGAUUCGGAGCUUGAGACUUGAGAGGUAGGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCACCUGCGCAAGCUUUUGCGCCCACGCAGUAGA----
-----........((.((..(((.((((....((((((.........((((((((....)))))))).(((....))))))))).)))))))..))..))..........---- ( -31.50)
>DroAna_CAF1 118685 95 + 1
--------GAGUCG---GUGGAGUCUUCGGU----GGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCACCUGCGCAAGCUUUUGCGCCCACGCAGUCGC----
--------((.(.(---((((.......(((----((((.....(((((((((((....)))))))).)))...))))))).((((((....)))))))))).)).))..---- ( -33.20)
>DroPer_CAF1 113495 106 + 1
CGCAGUCGCAGUCGGAGUCGGAGUCUUCGGA----GGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCACCUGCGCAGGCUUUUGCGCCCACGCAGCCGA----
...((((((((((((((((((..((....))----((....))........)).)))))).))).)))))))........(((((..(((......)))..)))))....---- ( -37.90)
>consensus
________GA_______CUGGAGACUUGAGAGGUAGGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCACCUGCGCAAGCUUUUGCGCCCACGCAGUCGA____
..........................................((((.((((((((....))))))))...............((((((....))))))....))))........ (-21.32 = -21.18 +  -0.14)

alignment

secondary structure

dotplot

Window 6

Location	15,364,805 – 15,364,898
Length	93
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	77.67
Mean single sequence MFE	-37.11
Consensus MFE	-33.67
Energy contribution	-34.03
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-3.12
Structure conservation index	0.91
SVM decision value	1.72
SVM RNA-class probability	0.973969
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15364805 93 - 22407834
----UCGACUGCGUGGGCGCAAAAGCUUGCGCAGGUGAUUUUAAUCGCAUGCCAGUAAUCUGGCAUAAACAGGUGAACCUACCUCUCAAGUCUCGAG-----------------
----(((((((((..(((......)))..)))))(((((....)))))(((((((....)))))))....(((....)))............)))).----------------- ( -38.20)
>DroEre_CAF1 117062 100 - 1
----UCCACUGCGUGGGCGCAAAAGCUUGCGCAGAUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACCUACCUCUCAAGUCUCAAGUC-----UCCAG-----
----....(((((..(((......)))..)))))..(((((.......(((((((....)))))))....(((....))).......))))).......-----.....----- ( -33.50)
>DroWil_CAF1 184646 84 - 1
AUGGCCAACUGCGUGGGCGCAAAAGCUUGCGCAGGUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACCUCGCC------------------------------
..(((...(((((..(((......)))..)))))(((((....)))))(((((((....)))))))....(((....))).)))------------------------------ ( -37.50)
>DroYak_CAF1 116796 105 - 1
----UCUACUGCGUGGGCGCAAAAGCUUGCGCAGGUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACCUACCUCUCAAGUCUCAAGCUCCGAAUCCGA-----
----....(((((..(((......)))..)))))(((((....)))))(((((((....)))))))....(((....))).............................----- ( -35.70)
>DroAna_CAF1 118685 95 - 1
----GCGACUGCGUGGGCGCAAAAGCUUGCGCAGGUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACC----ACCGAAGACUCCAC---CGACUC--------
----....(((((..(((......)))..)))))(((((....)))))(((((((....))))))).....((((....----...........)))---).....-------- ( -36.06)
>DroPer_CAF1 113495 106 - 1
----UCGGCUGCGUGGGCGCAAAAGCCUGCGCAGGUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACC----UCCGAAGACUCCGACUCCGACUGCGACUGCG
----(((.(((((..(((......)))..))))).)))......(((((((((((....)))))))....(((....))----).....................))))..... ( -41.70)
>consensus
____UCGACUGCGUGGGCGCAAAAGCUUGCGCAGGUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACCUACCUCUCAAGUCUCAAG_______UC________
........(((((..(((......)))..)))))(((((....)))))(((((((....)))))))....(((....))).................................. (-33.67 = -34.03 +   0.36)

alignment

secondary structure

dotplot

Window 7

Location	15,364,822 – 15,364,938
Length	116
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	83.25
Mean single sequence MFE	-37.05
Consensus MFE	-24.75
Energy contribution	-24.53
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.98
Structure conservation index	0.67
SVM decision value	0.08
SVM RNA-class probability	0.574898
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15364822 116 + 22407834
AGGUUCACCUGUUUAUGCCAGAUUACUGGCAUGCGAUUAAAAUCACCUGCGCAAGCUUUUGCGCCCACGCAGUCGAAGUCUUGGAGUCGCAACUCCAAAAGUCGCAGCUUCGGGUU
......(((((...(((((((....)))))))((((((....((..(((((...((....)).....)))))..))....(((((((....))))))).)))))).....))))). ( -40.90)
>DroPse_CAF1 113569 97 + 1
-GGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCACCUGCGCAGGCUUUUGCGCCCACGCAGC------C--GCAGCCUCAGCCUC----------GCUUCGGGUU
-.....(((((...(((((((....)))))))((((..........(((((..(((......)))..))))).------.--((.......)).))----------))..))))). ( -32.90)
>DroSec_CAF1 110819 116 + 1
AGGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCACCUGCGCAAGCUUUUGCGCCCACACAGUCGAAGUCUUGGAGUCGCAACUCCAAAAGUCGCAGCUUCGGGUU
......(((((...(((((((....)))))))((((((..........((((((....))))))................(((((((....))))))).)))))).....))))). ( -38.40)
>DroEre_CAF1 117086 116 + 1
AGGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCAUCUGCGCAAGCUUUUGCGCCCACGCAGUGGAAGUCUUGGAGUCGCAACUCCAAAAGUCGCAGCUUCGGGUU
......(((((...(((((((....)))))))((((((....(((.(((((...((....)).....)))))))).....(((((((....))))))).)))))).....))))). ( -41.40)
>DroAna_CAF1 118705 98 + 1
-GGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCACCUGCGCAAGCUUUUGCGCCCACGCAGUCGCAGUCC-----------------AAGUCGCAGCUUCGGGUU
-.....(((((...(((((((....)))))))((((((..........((....))..(((((....))))).........-----------------.)))))).....))))). ( -31.70)
>DroPer_CAF1 113526 103 + 1
-GGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCACCUGCGCAGGCUUUUGCGCCCACGCAGCCGAAGCC--GCAGCCGCAGCCUC----------GCUUCGGGUU
-.....(((((...(((((((....)))))))((((..........((((((.((((((.((((....)).)).))))))--...).)))))..))----------))..))))). ( -37.00)
>consensus
_GGUUCACCUGUUUAUGCCAGAUUCCUGGCAUGCGAUUAAAAUCACCUGCGCAAGCUUUUGCGCCCACGCAGUCGAAGUCU_GGAGUCGCAACUCC__AAGUCGCAGCUUCGGGUU
......(((((...(((((((....)))))))(((((....)))....((((((....))))))..........................................))..))))). (-24.75 = -24.53 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	15,364,822 – 15,364,938
Length	116
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	83.25
Mean single sequence MFE	-45.67
Consensus MFE	-33.78
Energy contribution	-33.58
Covariance contribution	-0.19
Combinations/Pair	1.08
Mean z-score	-3.83
Structure conservation index	0.74
SVM decision value	1.33
SVM RNA-class probability	0.942599
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15364822 116 - 22407834
AACCCGAAGCUGCGACUUUUGGAGUUGCGACUCCAAGACUUCGACUGCGUGGGCGCAAAAGCUUGCGCAGGUGAUUUUAAUCGCAUGCCAGUAAUCUGGCAUAAACAGGUGAACCU
....(((((.......(((((((((....)))))))))))))).(((((..(((......)))..)))))(((((....)))))(((((((....)))))))....(((....))) ( -49.21)
>DroPse_CAF1 113569 97 - 1
AACCCGAAGC----------GAGGCUGAGGCUGC--G------GCUGCGUGGGCGCAAAAGCCUGCGCAGGUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACC-
.(((.(..((----------(((((....))).(--(------.(((((..(((......)))..))))).)).......))))(((((((....)))))))...).))).....- ( -42.70)
>DroSec_CAF1 110819 116 - 1
AACCCGAAGCUGCGACUUUUGGAGUUGCGACUCCAAGACUUCGACUGUGUGGGCGCAAAAGCUUGCGCAGGUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACCU
....(((((.......(((((((((....)))))))))))))).(((((..(((......)))..)))))(((((....)))))(((((((....)))))))....(((....))) ( -47.01)
>DroEre_CAF1 117086 116 - 1
AACCCGAAGCUGCGACUUUUGGAGUUGCGACUCCAAGACUUCCACUGCGUGGGCGCAAAAGCUUGCGCAGAUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACCU
...........((((.(((((((((....)))))))))....(((((((..(((......)))..))))).)).......))))(((((((....)))))))....(((....))) ( -46.80)
>DroAna_CAF1 118705 98 - 1
AACCCGAAGCUGCGACUU-----------------GGACUGCGACUGCGUGGGCGCAAAAGCUUGCGCAGGUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACC-
.(((.(.....((((.((-----------------(((...((.(((((..(((......)))..))))).))..)))))))))(((((((....)))))))...).))).....- ( -38.30)
>DroPer_CAF1 113526 103 - 1
AACCCGAAGC----------GAGGCUGCGGCUGC--GGCUUCGGCUGCGUGGGCGCAAAAGCCUGCGCAGGUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACC-
.(((.(...(----------((((((((....))--))))))).(((((..(((......)))..)))))(((((....)))))(((((((....)))))))...).))).....- ( -50.00)
>consensus
AACCCGAAGCUGCGACUU__GGAGUUGCGACUCC_AGACUUCGACUGCGUGGGCGCAAAAGCUUGCGCAGGUGAUUUUAAUCGCAUGCCAGGAAUCUGGCAUAAACAGGUGAACC_
.(((.(......................................(((((..(((......)))..)))))(((((....)))))(((((((....)))))))...).)))...... (-33.78 = -33.58 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:50 2006