Locus 8477

Sequence ID X_DroMel_CAF1
Location 21,043,147 – 21,043,458
Length 311
Max. P 0.999970
window13929 window13930 window13931 window13932 window13933 window13934 window13935 window13936 window13937

overview

Window 9

Location 21,043,147 – 21,043,267
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.42
Mean single sequence MFE -30.38
Consensus MFE -26.74
Energy contribution -26.74
Covariance contribution 0.00
Combinations/Pair 1.11
Mean z-score -1.72
Structure conservation index 0.88
SVM decision value 1.61
SVM RNA-class probability 0.967618
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21043147 120 + 22224390
GUAUCAACAAUACCACCGCUGUUGCUGCAGCACCACCAACUGAAAGCACUGAAAUCCACUACAAUGGAGGCAUUUAAUAGCAGCCCGAUGCACUUUCAUUGGAGUUUCCACUCCGAGGGC
.................(((((....)))))....((...((((((...((...((((......))))..)).......(((......))).))))))(((((((....))))))))).. ( -29.50)
>DroSec_CAF1 13576 120 + 1
GUAUCACCAAUACCACCCCAGCUGGUGCAGCACCACCAACUAAAAGCACUGGAAUCCACUACAAUGGCGGCAUUUAAUAGCAGCCCGGUGCACUUUUAUUGGAGUUUCCACUCCAAGUGC
....(((((.............)))))..((((............(((((((...(((......)))..((........))...))))))).......(((((((....))))))))))) ( -31.12)
>DroSim_CAF1 14094 120 + 1
GUAUCACCAAUACCACCCCAGCUGGUGCAGCACCACCAACUAAAAGCACUGGAAUCCACUACAAUGGCGGCAUUUAAUAGCAGCCCGGUGCACUUUCAUUGGAGUUUCCACUCCAAGUGC
....(((((.............)))))..((((............(((((((...(((......)))..((........))...))))))).......(((((((....))))))))))) ( -31.12)
>DroEre_CAF1 14328 120 + 1
GUAUCACCAAUACCCGUCCAGCUCCGGCAGCACAACCAACUAAAAGCACUGAAAUCCACUACAAUGGCGGCAUUCAAUAGCAGCCCGGUGCAUUUUCAUUGGAGUUUCCACUCCAAGUGC
.............(((........)))..((((............((((((..............(((.((........)).))))))))).......(((((((....))))))))))) ( -28.53)
>DroYak_CAF1 15536 120 + 1
GUAUCACCAAUACCAGCUCAGUUGCUGCAGCACAACCAACUAAAAGCACUGAAAUCCACUACAAUGGCGGCAUUCACUAGCAGCCCGGUGCAUUUUUAUUGGAGUUUCCACUCCAAGUGC
.............((((......))))..((((............((((((..............(((.((........)).))))))))).......(((((((....))))))))))) ( -31.63)
>consensus
GUAUCACCAAUACCACCCCAGCUGCUGCAGCACCACCAACUAAAAGCACUGAAAUCCACUACAAUGGCGGCAUUUAAUAGCAGCCCGGUGCACUUUCAUUGGAGUUUCCACUCCAAGUGC
.............((((......))))..((((............((((((....(((......))).(((...........))))))))).......(((((((....))))))))))) (-26.74 = -26.74 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 21,043,147 – 21,043,267
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.42
Mean single sequence MFE -43.84
Consensus MFE -32.98
Energy contribution -34.14
Covariance contribution 1.16
Combinations/Pair 1.14
Mean z-score -2.46
Structure conservation index 0.75
SVM decision value 1.15
SVM RNA-class probability 0.923024
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21043147 120 - 22224390
GCCCUCGGAGUGGAAACUCCAAUGAAAGUGCAUCGGGCUGCUAUUAAAUGCCUCCAUUGUAGUGGAUUUCAGUGCUUUCAGUUGGUGGUGCUGCAGCAACAGCGGUGGUAUUGUUGAUAC
......(((((....)))))..((((((..(....(((...........)))(((((....))))).....)..))))))((..(..((((..(.((....)).)..))))..)..)).. ( -43.70)
>DroSec_CAF1 13576 120 - 1
GCACUUGGAGUGGAAACUCCAAUAAAAGUGCACCGGGCUGCUAUUAAAUGCCGCCAUUGUAGUGGAUUCCAGUGCUUUUAGUUGGUGGUGCUGCACCAGCUGGGGUGGUAUUGGUGAUAC
(((((((((((....)))))).....)))))(((((....))....(((((((((...(((.(((...))).)))..((((((((((......))))))))))))))))))))))..... ( -48.70)
>DroSim_CAF1 14094 120 - 1
GCACUUGGAGUGGAAACUCCAAUGAAAGUGCACCGGGCUGCUAUUAAAUGCCGCCAUUGUAGUGGAUUCCAGUGCUUUUAGUUGGUGGUGCUGCACCAGCUGGGGUGGUAUUGGUGAUAC
(((((((((((....)))))).....)))))(((((....))....(((((((((...(((.(((...))).)))..((((((((((......))))))))))))))))))))))..... ( -48.70)
>DroEre_CAF1 14328 120 - 1
GCACUUGGAGUGGAAACUCCAAUGAAAAUGCACCGGGCUGCUAUUGAAUGCCGCCAUUGUAGUGGAUUUCAGUGCUUUUAGUUGGUUGUGCUGCCGGAGCUGGACGGGUAUUGGUGAUAC
.((((((((((....)))))).....(((((.(((....((.((((((..((((.......))))..)))))))).((((((((((......))))..)))))))))))))))))).... ( -38.70)
>DroYak_CAF1 15536 120 - 1
GCACUUGGAGUGGAAACUCCAAUAAAAAUGCACCGGGCUGCUAGUGAAUGCCGCCAUUGUAGUGGAUUUCAGUGCUUUUAGUUGGUUGUGCUGCAGCAACUGAGCUGGUAUUGGUGAUAC
.((((((((((....)))))))......((((...(((.((........)).)))..)))))))....((((((((((((((((.(((.....)))))))))))..))))))))...... ( -39.40)
>consensus
GCACUUGGAGUGGAAACUCCAAUGAAAGUGCACCGGGCUGCUAUUAAAUGCCGCCAUUGUAGUGGAUUUCAGUGCUUUUAGUUGGUGGUGCUGCAGCAGCUGGGGUGGUAUUGGUGAUAC
.((((((((((....)))))))......((((...(((.((........)).)))..)))))))....((((((((((((((((.((......)).))))))))..))))))))...... (-32.98 = -34.14 +   1.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 21,043,187 – 21,043,307
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.33
Mean single sequence MFE -40.10
Consensus MFE -39.14
Energy contribution -38.98
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -1.90
Structure conservation index 0.98
SVM decision value 3.30
SVM RNA-class probability 0.998954
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21043187 120 + 22224390
UGAAAGCACUGAAAUCCACUACAAUGGAGGCAUUUAAUAGCAGCCCGAUGCACUUUCAUUGGAGUUUCCACUCCGAGGGCCGGCGAUCCGAUCGGAUCGGGCAUCAAUUUCGUGCUGUGC
....(((((.((((((((......)))).((........)).(((((((.(.......(((((((....))))))).(..(((....)))..)).))))))).....))))))))).... ( -40.50)
>DroSec_CAF1 13616 120 + 1
UAAAAGCACUGGAAUCCACUACAAUGGCGGCAUUUAAUAGCAGCCCGGUGCACUUUUAUUGGAGUUUCCACUCCAAGUGCCGGCGAUCCGAUCGGAUCGGGCAUCAAUUUCGUGCUGUGC
.....((((...........((...(((.((........)).)))..))((((.....(((((((....)))))))(((((..((((((....))))))))))).......)))).)))) ( -40.70)
>DroSim_CAF1 14134 120 + 1
UAAAAGCACUGGAAUCCACUACAAUGGCGGCAUUUAAUAGCAGCCCGGUGCACUUUCAUUGGAGUUUCCACUCCAAGUGCCGGCGAUCCGAUCGGAUCGGGCAUCAAUUUCGUGCUGUGC
.....((((...........((...(((.((........)).)))..))((((.....(((((((....)))))))(((((..((((((....))))))))))).......)))).)))) ( -40.70)
>DroEre_CAF1 14368 120 + 1
UAAAAGCACUGAAAUCCACUACAAUGGCGGCAUUCAAUAGCAGCCCGGUGCAUUUUCAUUGGAGUUUCCACUCCAAGUGCCGGCGAUCCGAUCAGAUCGGGCAUCAAUUUCGUGCUGUGC
....((((((((((..((((.....(((.((........)).))).))))...)))))(((((((....)))))))(((((..(((((......)))))))))).......))))).... ( -37.60)
>DroYak_CAF1 15576 120 + 1
UAAAAGCACUGAAAUCCACUACAAUGGCGGCAUUCACUAGCAGCCCGGUGCAUUUUUAUUGGAGUUUCCACUCCAAGUGCCGGCGAUCCGAUCGGAUCGGGCAUCAAUUUCGUGCUGUCC
....(((((.(((((..........(((.((........)).))).(((((.......(((((((....))))))).......((((((....)))))).))))).)))))))))).... ( -41.00)
>consensus
UAAAAGCACUGAAAUCCACUACAAUGGCGGCAUUUAAUAGCAGCCCGGUGCACUUUCAUUGGAGUUUCCACUCCAAGUGCCGGCGAUCCGAUCGGAUCGGGCAUCAAUUUCGUGCUGUGC
....(((((.(((((..........(((.((........)).))).(((((.......(((((((....))))))).......((((((....)))))).))))).)))))))))).... (-39.14 = -38.98 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 21,043,187 – 21,043,307
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.33
Mean single sequence MFE -45.36
Consensus MFE -42.82
Energy contribution -43.46
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -3.00
Structure conservation index 0.94
SVM decision value 5.04
SVM RNA-class probability 0.999970
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21043187 120 - 22224390
GCACAGCACGAAAUUGAUGCCCGAUCCGAUCGGAUCGCCGGCCCUCGGAGUGGAAACUCCAAUGAAAGUGCAUCGGGCUGCUAUUAAAUGCCUCCAUUGUAGUGGAUUUCAGUGCUUUCA
((((.((((......((.(((((((((....))))))..)))..))(((((....))))).......))))....(((...........)))(((((....))))).....))))..... ( -42.70)
>DroSec_CAF1 13616 120 - 1
GCACAGCACGAAAUUGAUGCCCGAUCCGAUCGGAUCGCCGGCACUUGGAGUGGAAACUCCAAUAAAAGUGCACCGGGCUGCUAUUAAAUGCCGCCAUUGUAGUGGAUUCCAGUGCUUUUA
((((.((((........((((((((((....))))))..)))).(((((((....))))))).....))))...((.(..((((..((((....))))))))..)...)).))))..... ( -46.20)
>DroSim_CAF1 14134 120 - 1
GCACAGCACGAAAUUGAUGCCCGAUCCGAUCGGAUCGCCGGCACUUGGAGUGGAAACUCCAAUGAAAGUGCACCGGGCUGCUAUUAAAUGCCGCCAUUGUAGUGGAUUCCAGUGCUUUUA
((((.((((........((((((((((....))))))..)))).(((((((....))))))).....))))...((.(..((((..((((....))))))))..)...)).))))..... ( -46.20)
>DroEre_CAF1 14368 120 - 1
GCACAGCACGAAAUUGAUGCCCGAUCUGAUCGGAUCGCCGGCACUUGGAGUGGAAACUCCAAUGAAAAUGCACCGGGCUGCUAUUGAAUGCCGCCAUUGUAGUGGAUUUCAGUGCUUUUA
....(((((((((((.(((((((((((....))))))..)))..(((((((....)))))))......((((...(((.((........)).)))..)))))).)))))).))))).... ( -44.70)
>DroYak_CAF1 15576 120 - 1
GGACAGCACGAAAUUGAUGCCCGAUCCGAUCGGAUCGCCGGCACUUGGAGUGGAAACUCCAAUAAAAAUGCACCGGGCUGCUAGUGAAUGCCGCCAUUGUAGUGGAUUUCAGUGCUUUUA
.((.(((((((((((.(((((((((((....))))))..)))..(((((((....)))))))......((((...(((.((........)).)))..)))))).)))))).))))).)). ( -47.00)
>consensus
GCACAGCACGAAAUUGAUGCCCGAUCCGAUCGGAUCGCCGGCACUUGGAGUGGAAACUCCAAUGAAAGUGCACCGGGCUGCUAUUAAAUGCCGCCAUUGUAGUGGAUUUCAGUGCUUUUA
....(((((((((((.(((((((((((....))))))..)))..(((((((....)))))))......((((...(((.((........)).)))..)))))).)))))).))))).... (-42.82 = -43.46 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 21,043,227 – 21,043,347
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.00
Mean single sequence MFE -42.09
Consensus MFE -39.92
Energy contribution -39.80
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.91
Structure conservation index 0.95
SVM decision value 2.92
SVM RNA-class probability 0.997734
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21043227 120 + 22224390
CAGCCCGAUGCACUUUCAUUGGAGUUUCCACUCCGAGGGCCGGCGAUCCGAUCGGAUCGGGCAUCAAUUUCGUGCUGUGCCUGACAGCGGCUGUCGCUUAUAAAUUGCAGAUUCCACAAA
(((((.(((((.......(((((((....))))))).......((((((....)))))).)))))........(((((.....))))))))))..((.........))............ ( -41.00)
>DroSec_CAF1 13656 120 + 1
CAGCCCGGUGCACUUUUAUUGGAGUUUCCACUCCAAGUGCCGGCGAUCCGAUCGGAUCGGGCAUCAAUUUCGUGCUGUGCCUGACAGCGGCUGUCGCUUAUAAAUUGCAGAUUCCACAAA
..((((((..(.......(((((((....))))))))..))...(((((....))))))))).........(((((((.....)))))((..(((((.........)).))).))))... ( -40.81)
>DroSim_CAF1 14174 120 + 1
CAGCCCGGUGCACUUUCAUUGGAGUUUCCACUCCAAGUGCCGGCGAUCCGAUCGGAUCGGGCAUCAAUUUCGUGCUGUGCCUGACAGCGGCUGUCGCUUAUAAAUUGCAGAUUCCACAAA
..((((((..(.......(((((((....))))))))..))...(((((....))))))))).........(((((((.....)))))((..(((((.........)).))).))))... ( -40.81)
>DroEre_CAF1 14408 120 + 1
CAGCCCGGUGCAUUUUCAUUGGAGUUUCCACUCCAAGUGCCGGCGAUCCGAUCAGAUCGGGCAUCAAUUUCGUGCUGUGCCUGACAGCGGCUGUCGCUUAUAAAUUGCAGAGCCCACAAA
..((((((..(.......(((((((....))))))))..))...((((......)))))))).........(((((((.....)))))((((.(.((.........))).)))).))... ( -39.71)
>DroYak_CAF1 15616 120 + 1
CAGCCCGGUGCAUUUUUAUUGGAGUUUCCACUCCAAGUGCCGGCGAUCCGAUCGGAUCGGGCAUCAAUUUCGUGCUGUCCCUGACAGCGGCUGUCGCUUAUAAAUUGCAGUGCCCACAAA
..(((.((..(.......(((((((....))))))))..)))))(((((....)))))((((((((((((...((((((...))))))(((....)))...))))))..))))))..... ( -48.11)
>consensus
CAGCCCGGUGCACUUUCAUUGGAGUUUCCACUCCAAGUGCCGGCGAUCCGAUCGGAUCGGGCAUCAAUUUCGUGCUGUGCCUGACAGCGGCUGUCGCUUAUAAAUUGCAGAUUCCACAAA
(((((.(((((.......(((((((....))))))).......((((((....)))))).)))))........(((((.....))))))))))..((.........))............ (-39.92 = -39.80 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 21,043,227 – 21,043,347
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.00
Mean single sequence MFE -44.10
Consensus MFE -40.96
Energy contribution -41.20
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -2.18
Structure conservation index 0.93
SVM decision value 3.39
SVM RNA-class probability 0.999132
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21043227 120 - 22224390
UUUGUGGAAUCUGCAAUUUAUAAGCGACAGCCGCUGUCAGGCACAGCACGAAAUUGAUGCCCGAUCCGAUCGGAUCGCCGGCCCUCGGAGUGGAAACUCCAAUGAAAGUGCAUCGGGCUG
.(((..(...)..)))...........((((((((....)))...((((......((.(((((((((....))))))..)))..))(((((....))))).......))))....))))) ( -42.40)
>DroSec_CAF1 13656 120 - 1
UUUGUGGAAUCUGCAAUUUAUAAGCGACAGCCGCUGUCAGGCACAGCACGAAAUUGAUGCCCGAUCCGAUCGGAUCGCCGGCACUUGGAGUGGAAACUCCAAUAAAAGUGCACCGGGCUG
.(((..(...)..)))...........((((((((....)))...((((........((((((((((....))))))..)))).(((((((....))))))).....))))....))))) ( -44.90)
>DroSim_CAF1 14174 120 - 1
UUUGUGGAAUCUGCAAUUUAUAAGCGACAGCCGCUGUCAGGCACAGCACGAAAUUGAUGCCCGAUCCGAUCGGAUCGCCGGCACUUGGAGUGGAAACUCCAAUGAAAGUGCACCGGGCUG
.(((..(...)..)))...........((((((((....)))...((((........((((((((((....))))))..)))).(((((((....))))))).....))))....))))) ( -44.90)
>DroEre_CAF1 14408 120 - 1
UUUGUGGGCUCUGCAAUUUAUAAGCGACAGCCGCUGUCAGGCACAGCACGAAAUUGAUGCCCGAUCUGAUCGGAUCGCCGGCACUUGGAGUGGAAACUCCAAUGAAAAUGCACCGGGCUG
(((((.((((.(((.........)))..))))(((((.....))))))))))......(((((((((....)))))((...((.(((((((....))))))))).....))...)))).. ( -42.10)
>DroYak_CAF1 15616 120 - 1
UUUGUGGGCACUGCAAUUUAUAAGCGACAGCCGCUGUCAGGGACAGCACGAAAUUGAUGCCCGAUCCGAUCGGAUCGCCGGCACUUGGAGUGGAAACUCCAAUAAAAAUGCACCGGGCUG
.....(((((...((((((....((....)).((((((...))))))...)))))).)))))(((((....)))))(((.(((.(((((((....)))))))......)))....))).. ( -46.20)
>consensus
UUUGUGGAAUCUGCAAUUUAUAAGCGACAGCCGCUGUCAGGCACAGCACGAAAUUGAUGCCCGAUCCGAUCGGAUCGCCGGCACUUGGAGUGGAAACUCCAAUGAAAGUGCACCGGGCUG
.(((..(...)..)))...........((((((((((.....))))).((.......((((((((((....))))))..)))).(((((((....)))))))...........))))))) (-40.96 = -41.20 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 21,043,307 – 21,043,418
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.59
Mean single sequence MFE -37.21
Consensus MFE -29.07
Energy contribution -29.87
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.31
Structure conservation index 0.78
SVM decision value 1.38
SVM RNA-class probability 0.947953
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21043307 111 + 22224390
CUGACAGCGGCUGUCGCUUAUAAAUUGCAGAUUCCACAAAAACAGCAAGAACAACAAGGAC--CAUGCGC-------CAUGGCCACUGUGGCAACAACGGCGACAAGCGCCCUGACAUUU
....(((.((((((((((........(((...(((......................))).--..)))((-------(((((...)))))))......)))))))...))))))...... ( -31.25)
>DroSec_CAF1 13736 118 + 1
CUGACAGCGGCUGUCGCUUAUAAAUUGCAGAUUCCACAAAAACAGCAAGAACAACAAGGGC--CAUGGGCCAUGGGCCAUGGCCACUGUGGCAACAACGGCGACAAGCGCCCUGACAUUU
....(((.((((((((((......((((................)))).....(((..(((--(((((.(....).))))))))..)))(....)...)))))))...))))))...... ( -42.19)
>DroSim_CAF1 14254 118 + 1
CUGACAGCGGCUGUCGCUUAUAAAUUGCAGAUUCCACAAAAACAGCAAGAACAACAAGGGC--CAUGGGCCAUGGGCCAUUGCCACUGUGGCAACAACGGCGACAAGCGCCCUGACAUUU
....(((.((((((((((......((((................)))).........((.(--((((...))))).)).(((((.....)))))....)))))))...))))))...... ( -35.69)
>DroEre_CAF1 14488 118 + 1
CUGACAGCGGCUGUCGCUUAUAAAUUGCAGAGCCCACAAAAACAGCAAGAACAACAAGGGC--CAUGGGCCAUGGGCCAUGGCCACUAUGGCAACAACGGCGACAAGCGCCCUGACAUUU
....(((.((((((((((......((((...((...........))........(((((((--(((((.(....).)))))))).)).))))))....)))))))...))))))...... ( -41.80)
>DroYak_CAF1 15696 120 + 1
CUGACAGCGGCUGUCGCUUAUAAAUUGCAGUGCCCACAAAAACAGCAAAAACAGCAAGAACAACAAGGGCCAUGGGCCAUGGCCACUAUGGCAACAACGGCGACAAGCGCCCUGACAUUU
....(((.((((((((((......(((...((((..........((.......))..........(((((((((...))))))).))..)))).))).)))))))...))))))...... ( -35.10)
>consensus
CUGACAGCGGCUGUCGCUUAUAAAUUGCAGAUUCCACAAAAACAGCAAGAACAACAAGGGC__CAUGGGCCAUGGGCCAUGGCCACUGUGGCAACAACGGCGACAAGCGCCCUGACAUUU
....(((.((((((((((......((((................))))...............(((((.(....).)))))(((.....)))......)))))))...))))))...... (-29.07 = -29.87 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 21,043,307 – 21,043,418
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.59
Mean single sequence MFE -41.16
Consensus MFE -32.44
Energy contribution -32.80
Covariance contribution 0.36
Combinations/Pair 1.08
Mean z-score -1.54
Structure conservation index 0.79
SVM decision value 0.18
SVM RNA-class probability 0.620249
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21043307 111 - 22224390
AAAUGUCAGGGCGCUUGUCGCCGUUGUUGCCACAGUGGCCAUG-------GCGCAUG--GUCCUUGUUGUUCUUGCUGUUUUUGUGGAAUCUGCAAUUUAUAAGCGACAGCCGCUGUCAG
...((.((((((.(.((.((((((.((..(....)..)).)))-------))))).)--((((((((.....((((.((((.....))))..))))...))))).))).))).))).)). ( -35.90)
>DroSec_CAF1 13736 118 - 1
AAAUGUCAGGGCGCUUGUCGCCGUUGUUGCCACAGUGGCCAUGGCCCAUGGCCCAUG--GCCCUUGUUGUUCUUGCUGUUUUUGUGGAAUCUGCAAUUUAUAAGCGACAGCCGCUGUCAG
...((.(((.(.(((.(((((.((....((.((((.((((((((((...)).)))))--))).)))).))....))(((..(((..(...)..)))...))).))))))))).))).)). ( -44.30)
>DroSim_CAF1 14254 118 - 1
AAAUGUCAGGGCGCUUGUCGCCGUUGUUGCCACAGUGGCAAUGGCCCAUGGCCCAUG--GCCCUUGUUGUUCUUGCUGUUUUUGUGGAAUCUGCAAUUUAUAAGCGACAGCCGCUGUCAG
...((.(((.(.(((.(((((.(((((..((((((..((((..((.((.((((...)--)))..))..))..))))..)...))))).....)))))......))))))))).))).)). ( -40.80)
>DroEre_CAF1 14488 118 - 1
AAAUGUCAGGGCGCUUGUCGCCGUUGUUGCCAUAGUGGCCAUGGCCCAUGGCCCAUG--GCCCUUGUUGUUCUUGCUGUUUUUGUGGGCUCUGCAAUUUAUAAGCGACAGCCGCUGUCAG
...((.(((((((.....))))((((((((....(.((((((((((...)).)))))--))))((((.(..((..(.......)..))..).)))).......))))))))..))).)). ( -44.30)
>DroYak_CAF1 15696 120 - 1
AAAUGUCAGGGCGCUUGUCGCCGUUGUUGCCAUAGUGGCCAUGGCCCAUGGCCCUUGUUGUUCUUGCUGUUUUUGCUGUUUUUGUGGGCACUGCAAUUUAUAAGCGACAGCCGCUGUCAG
...((.(((.(.(((.(((((....(((((...((((.((((((((...))))............((.......)).......)))).)))))))))......))))))))).))).)). ( -40.50)
>consensus
AAAUGUCAGGGCGCUUGUCGCCGUUGUUGCCACAGUGGCCAUGGCCCAUGGCCCAUG__GCCCUUGUUGUUCUUGCUGUUUUUGUGGAAUCUGCAAUUUAUAAGCGACAGCCGCUGUCAG
...((.(((.(.(((.(((((.((....((.((((.((((((((.(....).)))))..))).)))).))....))(((..(((..(...)..)))...))).))))))))).))).)). (-32.44 = -32.80 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 21,043,347 – 21,043,458
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.60
Mean single sequence MFE -35.36
Consensus MFE -27.68
Energy contribution -29.12
Covariance contribution 1.44
Combinations/Pair 1.03
Mean z-score -1.54
Structure conservation index 0.78
SVM decision value 0.03
SVM RNA-class probability 0.547195
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21043347 111 + 22224390
AACAGCAAGAACAACAAGGAC--CAUGCGC-------CAUGGCCACUGUGGCAACAACGGCGACAAGCGCCCUGACAUUUAACAUCCGGUUGAAAUUGUUCAACGCAUUUCCGGUGCUCU
........((((((....(((--(....((-------(((((...)))))))......((((.....))))................))))....))))))...((((.....))))... ( -28.50)
>DroSec_CAF1 13776 118 + 1
AACAGCAAGAACAACAAGGGC--CAUGGGCCAUGGGCCAUGGCCACUGUGGCAACAACGGCGACAAGCGCCCUGACAUUUAACAUCCGGUUGAAAUUGUUCAACGCAUUUCCGGUGCUCU
........((((((((..(((--(((((.(....).))))))))..))((....))..((((.....))))......((((((.....)))))).))))))...((((.....))))... ( -39.50)
>DroSim_CAF1 14294 118 + 1
AACAGCAAGAACAACAAGGGC--CAUGGGCCAUGGGCCAUUGCCACUGUGGCAACAACGGCGACAAGCGCCCUGACAUUUAACAUCCGGUUGAAAUUGUUCAACGCAUUUCCCGUGCUCU
........((((((..(((((--(.((((((...)))).(((((....((....))..))))))).).)))))....((((((.....)))))).))))))...((((.....))))... ( -36.50)
>DroEre_CAF1 14528 118 + 1
AACAGCAAGAACAACAAGGGC--CAUGGGCCAUGGGCCAUGGCCACUAUGGCAACAACGGCGACAAGCGCCCUGACAUUUAACAUCCGGUUGAAAUUGUUCAACGCAUUUCCGGUGCUCU
........((((((..(((((--(((((.(....).)))))))).)).((....))..((((.....))))......((((((.....)))))).))))))...((((.....))))... ( -39.40)
>DroYak_CAF1 15736 120 + 1
AACAGCAAAAACAGCAAGAACAACAAGGGCCAUGGGCCAUGGCCACUAUGGCAACAACGGCGACAAGCGCCCUGACAUUUAACAUCCGGUUGAAAUUGUUCAACGCAUUUCCGGUGCUCU
....((.......))..((((((..(((((.....(((((((...))))))).......((.....)))))))....((((((.....)))))).))))))...((((.....))))... ( -32.90)
>consensus
AACAGCAAGAACAACAAGGGC__CAUGGGCCAUGGGCCAUGGCCACUGUGGCAACAACGGCGACAAGCGCCCUGACAUUUAACAUCCGGUUGAAAUUGUUCAACGCAUUUCCGGUGCUCU
........((((((..(((((..(((((.(....).)))))(((....((....))..))).......)))))....((((((.....)))))).))))))...((((.....))))... (-27.68 = -29.12 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:07 2006