Locus 3926

Sequence ID 2L_DroMel_CAF1
Location 11,464,258 – 11,464,446
Length 188
Max. P 0.863204
window6189 window6190 window6191

overview

Window 9

Location 11,464,258 – 11,464,356
Length 98
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 94.57
Mean single sequence MFE -23.08
Consensus MFE -21.90
Energy contribution -21.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.25
Structure conservation index 0.95
SVM decision value 0.84
SVM RNA-class probability 0.863204
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11464258 98 + 22407834
-AAAAGGAAAAUAAAAUCUGCACCAGUUCGGGGGAAUCCCCUCCA-----CAACCACGUGCUGGCAUUGCGCGACACAAA---AGGCGAGCAACAAA-AAAUCGCUCU
-..................((........(((((.....))))).-----......(((((.......))))).......---..))((((......-.....)))). ( -22.00)
>DroSec_CAF1 27816 101 + 1
-AAAAGGAAAAUAAAAUCUGCACCAGUUCGGGGGAAUCCCCUCCA-----CAACCACGUGCUGGCAUUGCGCGACACAAACACAGGCGAGCAACAAA-AAAUCGCUCU
-...............((((.........(((((.....))))).-----......(((((.......))))).........)))).((((......-.....)))). ( -22.10)
>DroSim_CAF1 30128 102 + 1
-AAAAGGAAAAUAAAAUCUGCACCAGUUCGGGGGAAUCCCCUCCA-----CAACCACGUGCUGGCAUUGCGCGACACAAACACAGGCGAGCAACAAAAAAAUCGCUCU
-...............((((.........(((((.....))))).-----......(((((.......))))).........)))).((((............)))). ( -22.00)
>DroEre_CAF1 28146 99 + 1
GAAAAGGGAAAUAAAAUCUGCACCGGUUCGGGGGAAUCCCCUCCA-----CAACCACGUGCUGGCAUUGCGCGACACAAA---AGGCGAGCAACAAA-AAAUCGCUCU
...................((...((((.(((((.....))))).-----.)))).(((((.......))))).......---..))((((......-.....)))). ( -25.40)
>DroYak_CAF1 28658 104 + 1
GAAAAGGAAAAUAAAAUCUGCACCAGUUCGGGGGAAUCCCCUCCAACAACCAACCACGUGCUGGCAUUGCGCGACACAAA---AGGCGAGCAACAAA-AAAUCGCUCU
...................((....(((.(((((....))))).))).........(((((.......))))).......---..))((((......-.....)))). ( -23.90)
>consensus
_AAAAGGAAAAUAAAAUCUGCACCAGUUCGGGGGAAUCCCCUCCA_____CAACCACGUGCUGGCAUUGCGCGACACAAA___AGGCGAGCAACAAA_AAAUCGCUCU
...................((........(((((.....)))))............(((((.......)))))............))((((............)))). (-21.90 = -21.90 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 11,464,258 – 11,464,356
Length 98
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 94.57
Mean single sequence MFE -31.26
Consensus MFE -25.90
Energy contribution -25.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.35
Structure conservation index 0.83
SVM decision value 0.01
SVM RNA-class probability 0.538675
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11464258 98 - 22407834
AGAGCGAUUU-UUUGUUGCUCGCCU---UUUGUGUCGCGCAAUGCCAGCACGUGGUUG-----UGGAGGGGAUUCCCCCGAACUGGUGCAGAUUUUAUUUUCCUUUU-
.(((((((..-...)))))))....---((((..((.((((..((((.....))))))-----))..((((....)))).....))..))))...............- ( -29.40)
>DroSec_CAF1 27816 101 - 1
AGAGCGAUUU-UUUGUUGCUCGCCUGUGUUUGUGUCGCGCAAUGCCAGCACGUGGUUG-----UGGAGGGGAUUCCCCCGAACUGGUGCAGAUUUUAUUUUCCUUUU-
.(((((((..-...)))))))..((((..(((((...))))).(((((((((....))-----))..((((....))))...)))))))))................- ( -31.60)
>DroSim_CAF1 30128 102 - 1
AGAGCGAUUUUUUUGUUGCUCGCCUGUGUUUGUGUCGCGCAAUGCCAGCACGUGGUUG-----UGGAGGGGAUUCCCCCGAACUGGUGCAGAUUUUAUUUUCCUUUU-
.(((((((......)))))))..((((..(((((...))))).(((((((((....))-----))..((((....))))...)))))))))................- ( -31.80)
>DroEre_CAF1 28146 99 - 1
AGAGCGAUUU-UUUGUUGCUCGCCU---UUUGUGUCGCGCAAUGCCAGCACGUGGUUG-----UGGAGGGGAUUCCCCCGAACCGGUGCAGAUUUUAUUUCCCUUUUC
.(((((((..-...)))))))((..---.(((((...))))).))..((((.(((((.-----(((.(((....)))))))))))))))................... ( -31.70)
>DroYak_CAF1 28658 104 - 1
AGAGCGAUUU-UUUGUUGCUCGCCU---UUUGUGUCGCGCAAUGCCAGCACGUGGUUGGUUGUUGGAGGGGAUUCCCCCGAACUGGUGCAGAUUUUAUUUUCCUUUUC
.(((((((..-...)))))))....---((((..((...((((((((((.....))))).)))))..((((....)))).....))..))))................ ( -31.80)
>consensus
AGAGCGAUUU_UUUGUUGCUCGCCU___UUUGUGUCGCGCAAUGCCAGCACGUGGUUG_____UGGAGGGGAUUCCCCCGAACUGGUGCAGAUUUUAUUUUCCUUUU_
.(((((((......)))))))............(((((((...((((.....))))...........((((....))))......)))).)))............... (-25.90 = -25.90 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 11,464,356 – 11,464,446
Length 90
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 80.56
Mean single sequence MFE -34.77
Consensus MFE -19.38
Energy contribution -20.44
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -1.89
Structure conservation index 0.56
SVM decision value 0.01
SVM RNA-class probability 0.540887
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11464356 90 - 22407834
U--CUCCCAAGGAUAUGCCCUUACAGGAGGCUGG-------CGGGGGUAACGGCGGGGAAAGUGUCCUGGCAGCCGCUUUUGGGGCCUGUCAUUGUCCC
.--....(((.((((.(((((...(((.(((((.-------(((((...((..........)).))))).))))).)))..))))).)))).))).... ( -34.60)
>DroPse_CAF1 28638 77 - 1
UCUCUCCCAAGGAUAUGCCGUUACGG-CAGCAGC-------A--------------AGAGCGUGUCCUGGCAGCCGCUCUUGGGGCCUGUCAUUGUCCC
..........((((((((((...)))-))((..(-------(--------------(((((((((....)))..))))))))..)).......))))). ( -28.10)
>DroSec_CAF1 27917 76 - 1
U--CUCCCAAGGAUAUGCCCUUACAGGCGGCUGG-------CG------------GGGAAAG--UCCUGGCAGCCGCUUUUGGGGCCUGUCAUUGUCCC
.--....(((.((((.(((((...(((((((((.-------((------------(((....--))))).)))))))))..))))).)))).))).... ( -40.10)
>DroSim_CAF1 30230 78 - 1
U--CUCCCAAGGAUAUGCCCUUACAGGCGGCUGG-------CG------------GGGAAAGUGUCCUGGCAGCCGCUUUUGGGGCCUGUCAUUGUCCC
.--....(((.((((.(((((...(((((((((.-------((------------(((......))))).)))))))))..))))).)))).))).... ( -40.30)
>DroEre_CAF1 28245 75 - 1
---CUCCCAAGGAUAUGCCCUUACAGGCGGGCAG---------------------GGGAAAGUGUCCUGGCAGCCGCUUUUGGGGCCUGUCAUUGUCCC
---....(((.((((.(((((...((((((((..---------------------((((.....)))).))..))))))..))))).)))).))).... ( -28.90)
>DroYak_CAF1 28762 97 - 1
U--CUCCCAAGGAUAUGCCCUUACAGGCGGGAAGAGGGGAGAGGGGGUAACGGCGGGGAAAGUGUCCUGGCAGCCGCUUUUGGGGCCUGUCAUUGUCCC
(--(((((.......((((......)))).......)))))).(((..((.((((((((.....))).....(((.(....).)))))))).))..))) ( -36.64)
>consensus
U__CUCCCAAGGAUAUGCCCUUACAGGCGGCUGG_______CG____________GGGAAAGUGUCCUGGCAGCCGCUUUUGGGGCCUGUCAUUGUCCC
.......(((.((((.(((((...(((((((........................((((.....))))....)))))))..))))).)))).))).... (-19.38 = -20.44 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:57 2006