Locus 8439

Sequence ID	X_DroMel_CAF1
Location	20,990,369 – 20,990,559
Length	190
Max. P	0.999725

overview

Window 5

Location	20,990,369 – 20,990,479
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.04
Mean single sequence MFE	-34.08
Consensus MFE	-26.52
Energy contribution	-26.88
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-2.10
Structure conservation index	0.78
SVM decision value	0.97
SVM RNA-class probability	0.891519
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20990369 110 + 22224390
----AGGAUG------AGGAUAGCGAUGAAGACAUAUGCUAAUCUUCAUCGAAGGAAAGCGCCGACAAUGGAUGGUAAUGGCGGAACCCAAAUGGGUGGAAAAUUCCUUUGUCUUUAAUG
----..((((------((((((((((((....))).)))).)))))))))(((((((..((((.((........))...))))..((((....))))......))))))).......... ( -35.70)
>DroSec_CAF1 71889 114 + 1
UUCGUGGAUG------AGGAUAGCGAUGAAGACAUAUGCUAAUCUUCACCGAAGGAGAGCGCCGACAAUGGAUGGUAAUGGCGGGACCCAAAUGGGAGGAAAAUUCCUUUGUCUUUAAUG
.....((.((------((((((((((((....))).)))).)))))))))(((((((..((((.((........))...))))...(((....))).......))))))).......... ( -32.50)
>DroSim_CAF1 82686 114 + 1
UUCGUGGAUG------AGGAUAGCGAUGAAGACAUAUGCUAAUCUUCAUCGAAGGAGAGCGCCGACAAUGGAUGGUAAUGGCGGGACCCAAAUGGGUGGAAAAUUCCUUUGUCUUUAAUG
......((((------((((((((((((....))).)))).)))))))))(((((((..((((.((........))...))))..((((....))))......))))))).......... ( -35.50)
>DroEre_CAF1 14400 114 + 1
CUCGUGGAUG------AGGAUAGCGAUGAAGACAUAUGCUAAUCUUCAUCGAAGGAAAGCGCCGACAAUGGAUGGCAAUGGCAGGACCCAAAUGGGUGGAAAAUUCCUUUGUCUUUAAUG
......((((------((((((((((((....))).)))).)))))))))(((((((...((((.(....).)))).........((((....))))......))))))).......... ( -34.30)
>DroYak_CAF1 16308 120 + 1
UUCGUGGAUGAGAAUGAGGAUAGCGAUGAAGACAUAUGCUAAUCUUCAUCGAUGGAAAGCGCCGACAAUGGAUGGCAAUGGCAGGACCCAAAUGGGUGGAAAAUUCCUUUGUCUUUAAUG
(((((.(((((.....(((.((((((((....))).))))).)))))))).)))))....((((.(....).))))...((((((((((....))))(((....)))))))))....... ( -32.40)
>consensus
UUCGUGGAUG______AGGAUAGCGAUGAAGACAUAUGCUAAUCUUCAUCGAAGGAAAGCGCCGACAAUGGAUGGUAAUGGCGGGACCCAAAUGGGUGGAAAAUUCCUUUGUCUUUAAUG
................((((((.(((((((((..........)))))))))((((((...((((.((.....))....))))...((((....))))......))))))))))))..... (-26.52 = -26.88 +   0.36)

alignment

secondary structure

dotplot

Window 6

Location	20,990,369 – 20,990,479
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.04
Mean single sequence MFE	-27.25
Consensus MFE	-24.82
Energy contribution	-24.86
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-2.45
Structure conservation index	0.91
SVM decision value	3.95
SVM RNA-class probability	0.999725
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20990369 110 - 22224390
CAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUUCCGCCAUUACCAUCCAUUGUCGGCGCUUUCCUUCGAUGAAGAUUAGCAUAUGUCUUCAUCGCUAUCCU------CAUCCU----
...........((((((......((((....))))..((((................))))..))))))((((((((((........)))))))))).......------......---- ( -27.29)
>DroSec_CAF1 71889 114 - 1
CAUUAAAGACAAAGGAAUUUUCCUCCCAUUUGGGUCCCGCCAUUACCAUCCAUUGUCGGCGCUCUCCUUCGGUGAAGAUUAGCAUAUGUCUUCAUCGCUAUCCU------CAUCCACGAA
.......(((((((((....))))(((....)))..................)))))((..........((((((((((........)))))))))).......------...))..... ( -25.25)
>DroSim_CAF1 82686 114 - 1
CAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCCGCCAUUACCAUCCAUUGUCGGCGCUCUCCUUCGAUGAAGAUUAGCAUAUGUCUUCAUCGCUAUCCU------CAUCCACGAA
.......(((((.(((....)))((((....)))).................)))))((..........((((((((((........)))))))))).......------...))..... ( -27.15)
>DroEre_CAF1 14400 114 - 1
CAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCUGCCAUUGCCAUCCAUUGUCGGCGCUUUCCUUCGAUGAAGAUUAGCAUAUGUCUUCAUCGCUAUCCU------CAUCCACGAG
.......(((((.(((.......((((....))))...((....))..))).)))))((..........((((((((((........)))))))))).......------...))..... ( -28.85)
>DroYak_CAF1 16308 120 - 1
CAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCUGCCAUUGCCAUCCAUUGUCGGCGCUUUCCAUCGAUGAAGAUUAGCAUAUGUCUUCAUCGCUAUCCUCAUUCUCAUCCACGAA
.......(((((.(((.......((((....))))...((....))..))).)))))((......))..((((((((((........))))))))))....................... ( -27.70)
>consensus
CAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCCGCCAUUACCAUCCAUUGUCGGCGCUUUCCUUCGAUGAAGAUUAGCAUAUGUCUUCAUCGCUAUCCU______CAUCCACGAA
.......(((((.(((....)))((((....)))).................)))))............((((((((((........))))))))))....................... (-24.82 = -24.86 +   0.04)

alignment

secondary structure

dotplot

Window 7

Location	20,990,399 – 20,990,519
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.00
Mean single sequence MFE	-29.04
Consensus MFE	-22.36
Energy contribution	-22.60
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.87
Structure conservation index	0.77
SVM decision value	0.35
SVM RNA-class probability	0.702328
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20990399 120 - 22224390
UCACCCCUCAAUUCACAUUAGUUGAUGGAAAAUGCUCAUGCAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUUCCGCCAUUACCAUCCAUUGUCGGCGCUUUCCUUCGAUGAAGAUU
....................(((((.(((((((((....)))))...(((((.(((....)))((((....)))).................)))))......)))).)))))....... ( -25.50)
>DroSec_CAF1 71923 120 - 1
UCGCCCCUCCAUUCACAUUAGUUGAUGGAAAAUGCUCAUGCAUUAAAGACAAAGGAAUUUUCCUCCCAUUUGGGUCCCGCCAUUACCAUCCAUUGUCGGCGCUCUCCUUCGGUGAAGAUU
.((((..((((((.((....)).)))))).(((((....)))))...(((((((((....))))(((....)))..................))))))))).(((((....).).))).. ( -30.50)
>DroSim_CAF1 82720 120 - 1
UCACCCCUCCAUUCACAUUAGUUGAUGGAAAAUGCUCAUGCAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCCGCCAUUACCAUCCAUUGUCGGCGCUCUCCUUCGAUGAAGAUU
.....((((((((.((....)).)))))).(((((....)))))...(((((.(((....)))((((....)))).................))))))).......((((...))))... ( -25.70)
>DroEre_CAF1 14434 120 - 1
UCACCCUUCCUUCCACAUUAGUUGAUGGAAAACGCUCAUGCAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCUGCCAUUGCCAUCCAUUGUCGGCGCUUUCCUUCGAUGAAGAUU
.........((((.......(((((.(((((.((((...........(((((.(((.......((((....))))...((....))..))).))))))))).))))).)))))))))... ( -28.41)
>DroYak_CAF1 16348 120 - 1
UCAGUCUUCCUUCCACAUUAGUUGAUGGAAAAUGCUCAUGCAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCUGCCAUUGCCAUCCAUUGUCGGCGCUUUCCAUCGAUGAAGAUU
..(((((((...........(((((((((((((((....)))))...(((((.(((.......((((....))))...((....))..))).)))))......))))))))))))))))) ( -35.10)
>consensus
UCACCCCUCCAUUCACAUUAGUUGAUGGAAAAUGCUCAUGCAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCCGCCAUUACCAUCCAUUGUCGGCGCUUUCCUUCGAUGAAGAUU
....................(((((.(((.(((((....)))))...(((((.(((....)))((((....)))).................))))).......))).)))))....... (-22.36 = -22.60 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	20,990,439 – 20,990,559
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.20
Mean single sequence MFE	-23.38
Consensus MFE	-20.58
Energy contribution	-21.34
Covariance contribution	0.76
Combinations/Pair	1.03
Mean z-score	-1.26
Structure conservation index	0.88
SVM decision value	0.22
SVM RNA-class probability	0.641733
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20990439 120 - 22224390
GUAACAAUAUUUAAAUGACUAAGCUUUUUUUUUUUAAAUGUCACCCCUCAAUUCACAUUAGUUGAUGGAAAAUGCUCAUGCAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUUCCGC
......................((..............((((..((.((((((......)))))).))..(((((....)))))...))))..(((.......((((....))))))))) ( -22.11)
>DroSec_CAF1 71963 117 - 1
GUAGCAAUAUUUAAAUGACUAAGCUUUU---UUCAAGAUGUCGCCCCUCCAUUCACAUUAGUUGAUGGAAAAUGCUCAUGCAUUAAAGACAAAGGAAUUUUCCUCCCAUUUGGGUCCCGC
...((...(((((((((...........---.......((((.....((((((.((....)).)))))).(((((....)))))...)))).((((....))))..)))))))))...)) ( -24.50)
>DroSim_CAF1 82760 117 - 1
GUAGCAAUAUUUAAAUGACUAAGCUUUU---UUCAAGAUGUCACCCCUCCAUUCACAUUAGUUGAUGGAAAAUGCUCAUGCAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCCGC
...((...(((((((((...........---.......((((.....((((((.((....)).)))))).(((((....)))))...))))..(((....)))...)))))))))...)) ( -24.40)
>DroEre_CAF1 14474 117 - 1
GUAGCCAUAUUUAAAUGACUAAGCAUUU---UUUAAAAUGUCACCCUUCCUUCCACAUUAGUUGAUGGAAAACGCUCAUGCAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCUGC
.(((.(((......))).))).(((...---.......((((....((((.((.((....)).)).))))...((....))......))))..(((....)))((((....))))..))) ( -21.60)
>DroYak_CAF1 16388 117 - 1
AUAGCCAUAUUUAAAUGACUAAGCAUAU---UUUAAAAUGUCAGUCUUCCUUCCACAUUAGUUGAUGGAAAAUGCUCAUGCAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCUGC
.(((.(((......))).))).(((...---............(((((..(((((((.....)).)))))(((((....))))).)))))...(((....)))((((....))))..))) ( -24.30)
>consensus
GUAGCAAUAUUUAAAUGACUAAGCUUUU___UUUAAAAUGUCACCCCUCCAUUCACAUUAGUUGAUGGAAAAUGCUCAUGCAUUAAAGACAAAGGAAUUUUCCACCCAUUUGGGUCCCGC
...((...(((((((((.....................((((.....((((((.((....)).)))))).(((((....)))))...))))..(((....)))...)))))))))...)) (-20.58 = -21.34 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:05 2006