Locus 3765

Sequence ID	2L_DroMel_CAF1
Location	10,963,792 – 10,963,971
Length	179
Max. P	0.988543

overview

Window 6

Location	10,963,792 – 10,963,902
Length	110
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	66.91
Mean single sequence MFE	-22.87
Consensus MFE	-13.20
Energy contribution	-13.20
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.21
Structure conservation index	0.58
SVM decision value	2.12
SVM RNA-class probability	0.988543
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10963792 110 + 22407834
UCCCAUGAAUUUAACCAUUUAAACAUCCAA----UGUUAGUUUUUAACAGACAAUUAAUUCAG-GGGACAAUAUCUUUCACUGGCCGCAUAAAGCGGCCUCCAAUUCGAAACUUC
((((.((((((..........(((((...)----)))).((((.....))))....)))))).-))))..............((((((.....))))))................ ( -24.50)
>DroSec_CAF1 46554 97 + 1
UCCCAUAAAUUAAACCAUUUAAACAUCCAA----AGUUAGUUUUUAACAGACAAUUGAUU--------------CUUUCACUGGCCGCUUAAAGCGGCCUCCGAUUCGAAACUUC
.............................(----((((.((((.....))))..((((.(--------------(.......((((((.....))))))...)).))))))))). ( -17.40)
>DroSim_CAF1 53467 97 + 1
UCCCAUAAAUUAAACCAUUUAAACAUCCAA----UGUUAGUUUUUAACAGACAAUUGAUU--------------CUUUCACUGGCCGCUUAAAGCGGCCUCCGAUUCGAAACUUC
...........................(((----((((.((.....)).))).)))).((--------------(..((...((((((.....))))))...))...)))..... ( -17.70)
>DroEre_CAF1 47135 97 + 1
UU-CAUAAACUGAAG-------------AA----UGUCAGUAUUUUGUUGGUGGUUGAUGCAAGGGGACAAUAUCUUUCACUGGCCGCAUAAAGCGGCCUCCAAUUCGAAACUUC
((-(....(((((..-------------..----..))))).....((((((((..((((...(....)..))))..)))).((((((.....))))))..))))..)))..... ( -27.50)
>DroYak_CAF1 48771 110 + 1
UC-CAUAAACGGAAGUAUUCAAGCAUCCAA----UGUUAGUAUUUGGUUGGUUGUUGAUACAGGGGGGCAAUAUCUUUCACUGGCCGCUUAAAGCGGCCUACAAUUCGAAACUUC
..-......((((.((((((((.((.((((----.........)))).)).)))..))))).(..(((.....)))..)...((((((.....)))))).....))))....... ( -29.60)
>DroAna_CAF1 61430 95 + 1
UC-CAUUAAUUUAAUU-UUAAGACUUCCCACUGCAAUAAGUAUUUC-----------UGUCUA-GCGACAAUAU------CUGGCCGCGUAAAGCGGCCACAAUUUGAAAACUGC
..-.............-...((((.....(((......))).....-----------.)))).-....(((...------.(((((((.....)))))))....)))........ ( -20.50)
>consensus
UC_CAUAAAUUAAACCAUUUAAACAUCCAA____UGUUAGUAUUUAACAGACAAUUGAUUCA__GGGACAAUAUCUUUCACUGGCCGCUUAAAGCGGCCUCCAAUUCGAAACUUC
..................................................................................((((((.....))))))................ (-13.20 = -13.20 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	10,963,792 – 10,963,902
Length	110
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	66.91
Mean single sequence MFE	-23.89
Consensus MFE	-13.82
Energy contribution	-13.82
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.19
Structure conservation index	0.58
SVM decision value	0.09
SVM RNA-class probability	0.576724
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10963792 110 - 22407834
GAAGUUUCGAAUUGGAGGCCGCUUUAUGCGGCCAGUGAAAGAUAUUGUCCC-CUGAAUUAAUUGUCUGUUAAAAACUAACA----UUGGAUGUUUAAAUGGUUAAAUUCAUGGGA
................((((((.....))))))..............((((-.(((((((((..(...(((((..(((...----.)))...))))))..))).)))))).)))) ( -27.10)
>DroSec_CAF1 46554 97 - 1
GAAGUUUCGAAUCGGAGGCCGCUUUAAGCGGCCAGUGAAAG--------------AAUCAAUUGUCUGUUAAAAACUAACU----UUGGAUGUUUAAAUGGUUUAAUUUAUGGGA
..(((((..((.((((((((((.....))))))..(((...--------------..)))....))))))..)))))..((----.(((((..............))))).)).. ( -20.54)
>DroSim_CAF1 53467 97 - 1
GAAGUUUCGAAUCGGAGGCCGCUUUAAGCGGCCAGUGAAAG--------------AAUCAAUUGUCUGUUAAAAACUAACA----UUGGAUGUUUAAAUGGUUUAAUUUAUGGGA
.(((((..((((((..((((((.....))))))..((((..--------------.(((...(((..((.....))..)))----...))).))))..)))))))))))...... ( -21.80)
>DroEre_CAF1 47135 97 - 1
GAAGUUUCGAAUUGGAGGCCGCUUUAUGCGGCCAGUGAAAGAUAUUGUCCCCUUGCAUCAACCACCAACAAAAUACUGACA----UU-------------CUUCAGUUUAUG-AA
...........((((.((((((.....)))))).(..(..(((...)))...)..)........))))((....(((((..----..-------------..)))))...))-.. ( -22.00)
>DroYak_CAF1 48771 110 - 1
GAAGUUUCGAAUUGUAGGCCGCUUUAAGCGGCCAGUGAAAGAUAUUGCCCCCCUGUAUCAACAACCAACCAAAUACUAACA----UUGGAUGCUUGAAUACUUCCGUUUAUG-GA
((((((((((.((((.((((((.....)))))).......(((((.........))))).)))).((.((((.........----)))).)).))))).)))))........-.. ( -26.90)
>DroAna_CAF1 61430 95 - 1
GCAGUUUUCAAAUUGUGGCCGCUUUACGCGGCCAG------AUAUUGUCGC-UAGACA-----------GAAAUACUUAUUGCAGUGGGAAGUCUUAA-AAUUAAAUUAAUG-GA
..((.((((..(((((((((((.....))))))..------...(((((..-..))))-----------)...........)))))..)))).))...-.............-.. ( -25.00)
>consensus
GAAGUUUCGAAUUGGAGGCCGCUUUAAGCGGCCAGUGAAAGAUAUUGUCCC__UGAAUCAAUUGUCUGUUAAAAACUAACA____UUGGAUGUUUAAAUGGUUAAAUUUAUG_GA
................((((((.....)))))).................................................................................. (-13.82 = -13.82 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	10,963,828 – 10,963,938
Length	110
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	71.31
Mean single sequence MFE	-24.65
Consensus MFE	-15.09
Energy contribution	-15.37
Covariance contribution	0.28
Combinations/Pair	1.21
Mean z-score	-1.57
Structure conservation index	0.61
SVM decision value	1.04
SVM RNA-class probability	0.904764
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10963828 110 + 22407834
UUUUUAACAGACAAUUAAUUCAG-GGGACAAUAUCUUUCACUGGCCGCAUAAAGCGGCCUCCAAUUCGAAACUUCACUUUUGCCUC----AAGAGCAUUAUACACUGAGCGAAAU
..................(((.(-(((.(((...........((((((.....))))))........((....))....)))))))----....((.(((.....)))))))).. ( -21.00)
>DroSec_CAF1 46590 97 + 1
UUUUUAACAGACAAUUGAUU--------------CUUUCACUGGCCGCUUAAAGCGGCCUCCGAUUCGAAACUUCACUUUUGCUUC----AAGAGCAUUAUACACUGAGCGAAAU
.......(((....((((.(--------------(.......((((((.....))))))...)).))))...........(((((.----..))))).......)))........ ( -20.80)
>DroSim_CAF1 53503 97 + 1
UUUUUAACAGACAAUUGAUU--------------CUUUCACUGGCCGCUUAAAGCGGCCUCCGAUUCGAAACUUCACUUUUGCUCC----AAGAGCAUUAUACACUGAGCGAAAU
.......(((....((((.(--------------(.......((((((.....))))))...)).))))...........(((((.----..))))).......)))........ ( -22.40)
>DroEre_CAF1 47157 111 + 1
UAUUUUGUUGGUGGUUGAUGCAAGGGGACAAUAUCUUUCACUGGCCGCAUAAAGCGGCCUCCAAUUCGAAACUUCACUUUUGCUUC----GCGAAUAUUAUACACUGAGCGAAAU
.((((((((((((.(((..(((((((((..............((((((.....))))))..............)).)))))))...----.)))........)))).)))))))) ( -29.19)
>DroYak_CAF1 48806 111 + 1
UAUUUGGUUGGUUGUUGAUACAGGGGGGCAAUAUCUUUCACUGGCCGCUUAAAGCGGCCUACAAUUCGAAACUUCACUGUAGCUUC----AAGAGCCUUAUACACUGAGCGAAAU
..((..((.((((.((((((((((..((......))..)...((((((.....)))))).................)))))...))----)).))))......))..))...... ( -30.30)
>DroAna_CAF1 61468 97 + 1
UAUUUC-----------UGUCUA-GCGACAAUAU------CUGGCCGCGUAAAGCGGCCACAAUUUGAAAACUGCACUUUUCUUUUUUUUUUUACCACAUUACACUGGGAGAAAG
..((((-----------(.((((-(.(.......------.(((((((.....)))))))......(((((......)))))....................).)))))))))). ( -24.20)
>consensus
UAUUUAACAGACAAUUGAUUCA__GGGACAAUAUCUUUCACUGGCCGCUUAAAGCGGCCUCCAAUUCGAAACUUCACUUUUGCUUC____AAGAGCAUUAUACACUGAGCGAAAU
..........................................((((((.....))))))..................((((((((.....................)))))))). (-15.09 = -15.37 +   0.28)

alignment

secondary structure

dotplot

Window 9

Location	10,963,828 – 10,963,938
Length	110
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	71.31
Mean single sequence MFE	-26.25
Consensus MFE	-19.41
Energy contribution	-19.88
Covariance contribution	0.48
Combinations/Pair	1.22
Mean z-score	-1.39
Structure conservation index	0.74
SVM decision value	1.54
SVM RNA-class probability	0.962751
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10963828 110 - 22407834
AUUUCGCUCAGUGUAUAAUGCUCUU----GAGGCAAAAGUGAAGUUUCGAAUUGGAGGCCGCUUUAUGCGGCCAGUGAAAGAUAUUGUCCC-CUGAAUUAAUUGUCUGUUAAAAA
.......((((.(.((((((.((((----(((((.........)))))........((((((.....)))))).....)))))))))).).-)))).(((((.....)))))... ( -26.90)
>DroSec_CAF1 46590 97 - 1
AUUUCGCUCAGUGUAUAAUGCUCUU----GAAGCAAAAGUGAAGUUUCGAAUCGGAGGCCGCUUUAAGCGGCCAGUGAAAG--------------AAUCAAUUGUCUGUUAAAAA
.(((((((...............((----(((((.........)))))))......((((((.....))))))))))))).--------------.................... ( -24.50)
>DroSim_CAF1 53503 97 - 1
AUUUCGCUCAGUGUAUAAUGCUCUU----GGAGCAAAAGUGAAGUUUCGAAUCGGAGGCCGCUUUAAGCGGCCAGUGAAAG--------------AAUCAAUUGUCUGUUAAAAA
.(((((((..........(((((..----.))))).....................((((((.....))))))))))))).--------------.................... ( -24.80)
>DroEre_CAF1 47157 111 - 1
AUUUCGCUCAGUGUAUAAUAUUCGC----GAAGCAAAAGUGAAGUUUCGAAUUGGAGGCCGCUUUAUGCGGCCAGUGAAAGAUAUUGUCCCCUUGCAUCAACCACCAACAAAAUA
.....((..((.(.(((((((((((----(((((.........)))))........((((((.....)))))).))))...))))))).).)).))................... ( -27.20)
>DroYak_CAF1 48806 111 - 1
AUUUCGCUCAGUGUAUAAGGCUCUU----GAAGCUACAGUGAAGUUUCGAAUUGUAGGCCGCUUUAAGCGGCCAGUGAAAGAUAUUGCCCCCCUGUAUCAACAACCAACCAAAUA
.(((((((...........((..((----((((((.......))))))))...)).((((((.....)))))))))))))(((((.........)))))................ ( -29.00)
>DroAna_CAF1 61468 97 - 1
CUUUCUCCCAGUGUAAUGUGGUAAAAAAAAAAAGAAAAGUGCAGUUUUCAAAUUGUGGCCGCUUUACGCGGCCAG------AUAUUGUCGC-UAGACA-----------GAAAUA
.(((((..(((((((((((..............(((((......)))))......(((((((.....))))))).------)))))).)))-).)..)-----------)))).. ( -25.10)
>consensus
AUUUCGCUCAGUGUAUAAUGCUCUU____GAAGCAAAAGUGAAGUUUCGAAUUGGAGGCCGCUUUAAGCGGCCAGUGAAAGAUAUUGUCCC__UGAAUCAAUUGUCUGUUAAAAA
.(((((((.....................(((((.........)))))........((((((.....)))))))))))))................................... (-19.41 = -19.88 +   0.48)

alignment

secondary structure

dotplot

Window 0

Location	10,963,867 – 10,963,971
Length	104
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	77.50
Mean single sequence MFE	-30.07
Consensus MFE	-17.73
Energy contribution	-18.40
Covariance contribution	0.67
Combinations/Pair	1.36
Mean z-score	-1.76
Structure conservation index	0.59
SVM decision value	0.59
SVM RNA-class probability	0.793397
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10963867 104 + 22407834
CUGGCCGCAUAAAGCGGCCUCCAAUUCGAAACUUCACUUUUGCCUC----AAGAGCAUUAUACACUGAGCGAAAUCGAAGCCGAACGAUCUUAGUGUCG-------UCUCGCGCA
..((((((.....)))))).....(((((........((((((.((----(..............))))))))))))))((((((((((......))))-------).))).)). ( -29.94)
>DroSec_CAF1 46616 104 + 1
CUGGCCGCUUAAAGCGGCCUCCGAUUCGAAACUUCACUUUUGCUUC----AAGAGCAUUAUACACUGAGCGAAAUCGAAACCGAACGAUGUUAGUAUCG-------UCUCGCGCA
..((((((.....))))))..(((((((............(((((.----..)))))............)).)))))....(((((((((....)))))-------).))).... ( -29.15)
>DroSim_CAF1 53529 104 + 1
CUGGCCGCUUAAAGCGGCCUCCGAUUCGAAACUUCACUUUUGCUCC----AAGAGCAUUAUACACUGAGCGAAAUCGAAGCCGAACGAUGUUAGUAUCG-------UCUCGCGCA
..((((((.....))))))..(((((((............(((((.----..)))))............)).)))))..(((((((((((....)))))-------).))).)). ( -34.85)
>DroEre_CAF1 47197 102 + 1
CUGGCCGCAUAAAGCGGCCUCCAAUUCGAAACUUCACUUUUGCUUC----GCGAAUAUUAUACACUGAGCGAAAUUGCAGCCGAUCGAUCUUAGUGUCG-------UC--ACGCA
..((((((.....))))))......((((..((.((.((((((((.----(.(.........).).)))))))).)).))....)))).....((((..-------..--)))). ( -25.90)
>DroYak_CAF1 48846 102 + 1
CUGGCCGCUUAAAGCGGCCUACAAUUCGAAACUUCACUGUAGCUUC----AAGAGCCUUAUACACUGAGCGAAAUCGAAGUCGAUCGACCUUAGUGCCG-------UC--GCGCA
..((((((.....)))))).....(((((..(((((.((((((((.----..))))....)))).)))).)...)))))(((....)))....((((..-------..--)))). ( -29.10)
>DroAna_CAF1 61490 112 + 1
CUGGCCGCGUAAAGCGGCCACAAUUUGAAAACUGCACUUUUCUUUUUUUUUUUACCACAUUACACUGGGAGAAAGGGAGACCGGU---UCCUUGCUUCUUCGUCAGUGUUAAGCA
.(((((((.....)))))))......(((((......)))))...................((((((((((((((((((.....)---)))))..))))))..))))))...... ( -31.50)
>consensus
CUGGCCGCUUAAAGCGGCCUCCAAUUCGAAACUUCACUUUUGCUUC____AAGAGCAUUAUACACUGAGCGAAAUCGAAGCCGAACGAUCUUAGUGUCG_______UCUCGCGCA
..((((((.....))))))......(((...((((..((((((((.....................))))))))..)))).))).........((((.............)))). (-17.73 = -18.40 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:32 2006