Locus 4446

Sequence ID 3L_DroMel_CAF1
Location 12,949,331 – 12,949,636
Length 305
Max. P 0.981561
window6910 window6911 window6912 window6913 window6914

overview

Window 0

Location 12,949,331 – 12,949,438
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.64
Mean single sequence MFE -33.68
Consensus MFE -25.04
Energy contribution -27.04
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.74
SVM decision value 1.19
SVM RNA-class probability 0.928538
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12949331 107 - 23771897
AGUCUGGGCCUGGCCA------------AAAAGCGCAACACGAAAGGCGCUUAAGUGCUGUGGCUUUGGGUUAGGGAUGGGUAAAGAAAACUCAUCAAG-CAUGAAAAUCACGUAAAGAA
..(((...(((((((.------------.((((((((...(....)((((....))))))).))))).)))))))(((((((.......)))))))..(-(.((.....)).))..))). ( -31.70)
>DroSec_CAF1 66527 119 - 1
AGUCUGGGCCUGGCCAAAAAGAGGGCCAAAAAGCGCAACACGAAAGGCGCUUAAGUGCUGUGGCUUUGGGUUAGGGAUGGGUAAAGAAAACUCAUCAAG-CAUGAAAAUCACGUAAAAAU
..(((((.(((((((........))))).((((((((...(....)((((....))))))).))))))).)))))(((((((.......)))))))..(-(.((.....)).))...... ( -34.80)
>DroSim_CAF1 71354 119 - 1
AGUCUGGGCCUGGCCAAAAAGAGGGCCAAAAAGCGCAACACGAAAGGCGCUUAAGUGCUGUGGCUUUGGGUUAGGGAUGGGUAAAGAAAACUCAUCAAG-CAUGAAAAUCACGUAAAAAU
..(((((.(((((((........))))).((((((((...(....)((((....))))))).))))))).)))))(((((((.......)))))))..(-(.((.....)).))...... ( -34.80)
>DroEre_CAF1 72559 119 - 1
AGUCUGGGCCUGGCCAAAAAGAGGGCCAA-AAGCGCAACACGAAAGGCGCUUAAGUGCUGUGGCUUUGGAUUAGGGAUGGGCAAAGAAAACUCAUCAGGCCAUGAAUAUCACGUAAAUAU
......(((((((((........)))).(-(((((((...(....)((((....))))))).)))))........((((((.........)))))))))))................... ( -34.20)
>DroYak_CAF1 70435 114 - 1
AGUCU------GGCCAAAAAGAGGGCCAAAAAGCGCAACACGAAAGGCGCUUAAGUGCUGUGGCUUUGGAUUAGUGAUGGGUAACGAAGACUCAUCAAGCCAUGAAAAUCACGUAAAUAU
....(------((((........)))))..((((((....(....)))))))..(((.(((((((.........((((((((.......))))))))))))))).....)))........ ( -32.90)
>consensus
AGUCUGGGCCUGGCCAAAAAGAGGGCCAAAAAGCGCAACACGAAAGGCGCUUAAGUGCUGUGGCUUUGGGUUAGGGAUGGGUAAAGAAAACUCAUCAAG_CAUGAAAAUCACGUAAAAAU
..(((((.((.(((((.....((.((....((((((....(....)))))))..)).)).)))))..)).)))))(((((((.......)))))))........................ (-25.04 = -27.04 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 12,949,410 – 12,949,516
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.46
Mean single sequence MFE -33.80
Consensus MFE -24.56
Energy contribution -25.32
Covariance contribution 0.76
Combinations/Pair 1.04
Mean z-score -1.96
Structure conservation index 0.73
SVM decision value 0.16
SVM RNA-class probability 0.613366
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12949410 106 - 23771897
AAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGCUC--GCUGCUCUAACCACAGUCUGGGCCUGGCCA------------AAAAGCGCAACA
.(((...((....(((((...)))))....))..)))....((((((((((....))((((((.--...((((..((....))..))))..)))))------------).)))))))).. ( -25.60)
>DroSec_CAF1 66606 120 - 1
AAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGCUGGGGCUGCUCUAACCACAGUCUGGGCCUGGCCAAAAAGAGGGCCAAAAAGCGCAACA
.(((...((....(((((...)))))....))..)))....((((((((..........((((.((((((.........)))))).))))(((((........)))))..)))))))).. ( -38.60)
>DroSim_CAF1 71433 120 - 1
AAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGCUGGGGCUGCUCUAACCACAGUCUGGGCCUGGCCAAAAAGAGGGCCAAAAAGCGCAACA
.(((...((....(((((...)))))....))..)))....((((((((..........((((.((((((.........)))))).))))(((((........)))))..)))))))).. ( -38.60)
>DroEre_CAF1 72639 117 - 1
AAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGAUG--GCUGCUCUAACCGCAGUCUGGGCCUGGCCAAAAAGAGGGCCAA-AAGCGCAACA
.(((...((....(((((...)))))....))..)))....((((((((..........((..(--(((((.......))))))....))(((((........))))).-)))))))).. ( -33.60)
>DroYak_CAF1 70515 112 - 1
AAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGCUG--GCUGCUCUAACCGCAGUCU------GGCCAAAAAGAGGGCCAAAAAGCGCAACA
......((.....(((((((((((.....(..(((....)))..)(((.((....))..)))))--))))))...)))((..(.(------((((........))))).)..)))).... ( -32.60)
>consensus
AAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGCUG__GCUGCUCUAACCACAGUCUGGGCCUGGCCAAAAAGAGGGCCAAAAAGCGCAACA
..(((.((....((((((((((.......(..(((....)))..)(((.((....))..)))....))))))...))))............((((........)))).....)).))).. (-24.56 = -25.32 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 12,949,438 – 12,949,556
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.04
Mean single sequence MFE -26.60
Consensus MFE -23.78
Energy contribution -23.74
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -1.17
Structure conservation index 0.89
SVM decision value 0.08
SVM RNA-class probability 0.573270
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12949438 118 - 23771897
AAAAAAAAAAAGGAAACGAGAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGCUC--GCUGCUCUAACCAC
...........(....)......(((..((..(....)...))..)))....((((((((((.......(..(((....)))..)(((.((....))..)))..--))))))...)))). ( -26.60)
>DroSec_CAF1 66646 116 - 1
AAAA----AAAGGGAACGAGAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGCUGGGGCUGCUCUAACCAC
....----...(....)......(((..((..(....)...))..)))....((((((((((..(....(..(((....)))..)(((.((....))..))).)..))))))...)))). ( -26.40)
>DroSim_CAF1 71473 116 - 1
AAAA----AAAGGGAACGAGAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGCUGGGGCUGCUCUAACCAC
....----...(....)......(((..((..(....)...))..)))....((((((((((..(....(..(((....)))..)(((.((....))..))).)..))))))...)))). ( -26.40)
>DroEre_CAF1 72678 113 - 1
AAA-----AAAGGGAACGAGGGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGAUG--GCUGCUCUAACCGC
...-----...(....)..((..(((..((..(....)...))..)))....(((.((((((((..(((((..........((((....))))..)))))..))--))))))))).)).. ( -26.70)
>DroYak_CAF1 70549 113 - 1
AAA-----AAAGGGAACGAGGGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGCUG--GCUGCUCUAACCGC
...-----...(....)..((..(((..((..(....)...))..)))....(((.((((((((.....(..(((....)))..)(((.((....))..)))))--))))))))).)).. ( -26.90)
>consensus
AAAA____AAAGGGAACGAGAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUUUUUGCGCUUGUAAUAACUUGGCUG__GCUGCUCUAACCAC
...........(....)......(((..((..(....)...))..)))....((((((((((.......(..(((....)))..)(((.((....))..)))....))))))...)))). (-23.78 = -23.74 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,949,476 – 12,949,596
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.43
Mean single sequence MFE -20.92
Consensus MFE -18.36
Energy contribution -18.56
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.88
SVM decision value 1.21
SVM RNA-class probability 0.930739
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12949476 120 - 23771897
ACUGAAAGCCAAACAUUACACGAAAAUUUUGUGUUAAAUUAAAAAAAAAAAGGAAACGAGAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUU
.......((((..((((((((((.....)))))).................(....)......(((..((..(....)...))..)))..)))).))))..................... ( -20.00)
>DroSec_CAF1 66686 116 - 1
ACUGAAAGCCAAACAUUACACGAAAAUUGUGUGUUAAAUUAAAA----AAAGGGAACGAGAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUU
.(((...((((.....(((((((...)))))))...........----...............(((..((..(....)...))..)))....))))..)))................... ( -19.30)
>DroSim_CAF1 71513 116 - 1
ACUGAAAGCCAAACAUUACACGAAAAUUGUGUGUUAAAUUAAAA----AAAGGGAACGAGAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUU
.(((...((((.....(((((((...)))))))...........----...............(((..((..(....)...))..)))....))))..)))................... ( -19.30)
>DroEre_CAF1 72716 115 - 1
GCUGAAAGCCAAACAUUACACGAAAAUUGUGUGUUAAAUUAAA-----AAAGGGAACGAGGGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUU
((((...((((.....(((((((...)))))))..........-----...............(((..((..(....)...))..)))....))))..)))).................. ( -23.00)
>DroYak_CAF1 70587 115 - 1
GCUGAAAGCCAAACAUUACACGAAAAUUGUGUGUUAAAUUAAA-----AAAGGGAACGAGGGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUU
((((...((((.....(((((((...)))))))..........-----...............(((..((..(....)...))..)))....))))..)))).................. ( -23.00)
>consensus
ACUGAAAGCCAAACAUUACACGAAAAUUGUGUGUUAAAUUAAAA____AAAGGGAACGAGAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGCAGCUACUUAAGUGAAAAUAUU
.(((...((((.....(((((((...)))))))..................(....)......(((..((..(....)...))..)))....))))..)))................... (-18.36 = -18.56 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,949,516 – 12,949,636
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.96
Mean single sequence MFE -23.52
Consensus MFE -21.38
Energy contribution -21.22
Covariance contribution -0.16
Combinations/Pair 1.11
Mean z-score -1.66
Structure conservation index 0.91
SVM decision value 1.89
SVM RNA-class probability 0.981561
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12949516 120 - 23771897
CCCGAAGAUUGUAAAAUGUUCUUGCUCAAAAGAGCAGCGAACUGAAAGCCAAACAUUACACGAAAAUUUUGUGUUAAAUUAAAAAAAAAAAGGAAACGAGAGAGCUUGAUGUUGGAAAUA
.((((..(((.......((((((((((....)))))).))))...(((((.......((((((.....)))))).................(....)....).))))))).))))..... ( -23.90)
>DroSec_CAF1 66726 116 - 1
UCCGAAGAUUGUAAAAUGUUCUUGCUCAAAAGAGCAGCGAACUGAAAGCCAAACAUUACACGAAAAUUGUGUGUUAAAUUAAAA----AAAGGGAACGAGAGAGCUUGAUGUUGGAAAUA
(((((..(((.......((((((((((....)))))).))))...(((((......(((((((...)))))))...........----...(....)....).))))))).))))).... ( -24.30)
>DroSim_CAF1 71553 116 - 1
UCCGAAGAUUGUAAAAUGUUCUUGUUCAAAAGAGCAGCGAACUGAAAGCCAAACAUUACACGAAAAUUGUGUGUUAAAUUAAAA----AAAGGGAACGAGAGAGCUUGAUGUUGGAAAUA
(((((..(((.......((((((((((....)))))).))))...(((((......(((((((...)))))))...........----...(....)....).))))))).))))).... ( -21.90)
>DroEre_CAF1 72756 115 - 1
UACGAAGAUUGUGAAAUGUUCUUGCUCAAAAGGGCAGCGAGCUGAAAGCCAAACAUUACACGAAAAUUGUGUGUUAAAUUAAA-----AAAGGGAACGAGGGAGCUUGAUGUUGGAAAUA
.................((((((((((....)))))).))))......((((.((((((((((...)))))))..........-----........((((....)))))))))))..... ( -23.20)
>DroYak_CAF1 70627 115 - 1
UUCGAAGAUUGUGAAAUGUUCUCGCUCAAAAGAGCAGCGAGCUGAAAGCCAAACAUUACACGAAAAUUGUGUGUUAAAUUAAA-----AAAGGGAACGAGGGAGCUUGAUGUUGGAAAUA
(((.((.(((.......((((((((((....))))((((.((.....))).......((((((...)))))))))........-----...))))))(((....)))))).)).)))... ( -24.30)
>consensus
UCCGAAGAUUGUAAAAUGUUCUUGCUCAAAAGAGCAGCGAACUGAAAGCCAAACAUUACACGAAAAUUGUGUGUUAAAUUAAAA____AAAGGGAACGAGAGAGCUUGAUGUUGGAAAUA
.................((((((((((....)))))).))))......((((.((((((((((...))))))).......................((((....)))))))))))..... (-21.38 = -21.22 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:10 2006