Locus 9723

Sequence ID 3R_DroMel_CAF1
Location 25,729,175 – 25,729,318
Length 143
Max. P 0.588978
window15532 window15533

overview

Window 2

Location 25,729,175 – 25,729,294
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.12
Mean single sequence MFE -38.08
Consensus MFE -23.80
Energy contribution -25.80
Covariance contribution 2.00
Combinations/Pair 1.21
Mean z-score -1.61
Structure conservation index 0.62
SVM decision value 0.04
SVM RNA-class probability 0.554489
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25729175 119 - 27905053
UACCAAAUUCCCC-UUCAAGUCUGCCUCACUUUGGGCAUUGGCUUGACCAGUGGAACCAUCAAUUUGGGGGCCACAAUGGAUGGAAAUUCGGUGGCCGCGCUAUCCAUCAGCACCGCCAA
.(((((.((((..-.((((((((((((......)))))..)))))))(((((((..(((......)))...))))..)))..)))).)).)))(((.(.(((.......))).).))).. ( -40.70)
>DroPse_CAF1 25970 119 - 1
U-UCAAUUGCUCAAUUGCAGUGUGCCUGACAUUCAAGAUUAGCGUACUAAGUGGGUCAGUAGAUGUAGGUGUCACCAUGGAUGGAAAUUCGAUGACAAAGUUCACCAUCAGCACUGCGUC
.-..............(((((((..(((((...((...((((....)))).)).)))))..((((..(((((((...(((((....))))).)))))....))..)))).)))))))... ( -31.10)
>DroSec_CAF1 24497 118 - 1
U-UCAAAUUCCCC-UUCAAGUCUGUCUCACUUUGGGCAUUGGCUUGACCAGUGGAACCAUCAAUUUGGGGGCCACAAUGGAUGGAAAUUCGGUGGCCGCGUUCGCCAUCAGCACCACCAA
.-.....((((..-.((((((((((((......)))))..)))))))(((((((..(((......)))...))))..)))..))))....(((((..((...........)).))))).. ( -37.10)
>DroSim_CAF1 24972 118 - 1
U-UUAAAUUCCCC-UUCAAGUCUGCCUCACUUUGGGCAUUGGCUUGACCAGUGGAACCAUCAAUUUGGGGGCCACAAUGGAUGGAAAUGCGGUGGCCGCGUUCGCCAUCAGCACCACCAA
.-...........-.((((((((((((......)))))..)))))))...((((..(((......)))...))))..(((.(((...(((((((((.......)))))).))))))))). ( -41.30)
>DroEre_CAF1 25647 117 - 1
U-UAAAAUUCCCC-CU-AAGUCUGCGUAUCCUUGGGCCUCGGCUUGACCAGUGGAACCAUCAAUUUAGGGGCCACAAUGGAUGGGAAUUCGGUGGCCGCGUUCUCCAUCAGCACCACCCA
.-...(((((((.-..-..(....)..(((((((((((((((.....)).(((....))).......)))))).))).))))))))))).(((((..((...........)).))))).. ( -36.20)
>DroYak_CAF1 25346 118 - 1
U-UCACAUUCUCC-CUCAAGUGUGCCUCACUUUGGGCAUCGGCUUGACCAGUGGAACCAUCAAUUUGGGGGCCACAAUGGAUGGAAAUGCGGUCGCCGCGUUUGCCAUCAGCACCACCAA
.-...((((....-.((((((((((((......))))))..))))))...((((..(((......)))...))))))))(((((((((((((...)))))))).)))))........... ( -42.10)
>consensus
U_UCAAAUUCCCC_UUCAAGUCUGCCUCACUUUGGGCAUUGGCUUGACCAGUGGAACCAUCAAUUUGGGGGCCACAAUGGAUGGAAAUUCGGUGGCCGCGUUCGCCAUCAGCACCACCAA
...............((((((((((((......)))))..)))))))...((((..(((......))).((((((...((((....)))).))))))................))))... (-23.80 = -25.80 +   2.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 25,729,215 – 25,729,318
Length 103
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 69.49
Mean single sequence MFE -23.85
Consensus MFE -13.50
Energy contribution -15.58
Covariance contribution 2.09
Combinations/Pair 1.11
Mean z-score -1.31
Structure conservation index 0.57
SVM decision value 0.11
SVM RNA-class probability 0.588978
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25729215 103 - 27905053
C-------ACAUUCAUAUAACC-CU----UACCUUA--UACCAAAUUCCCC-UUCAAGUCUGCCUCACUUUGGGCAUUGGCUUGACCAGUGGAACCAUCAAUUUGGGGGCCACAAUGG
.-------..............-..----.......--..(((........-.((((((((((((......)))))..)))))))...((((..(((......)))...))))..))) ( -26.30)
>DroPse_CAF1 26010 112 - 1
CCAAAACA---GUAGUACAGUACGUUCUAUAAUUCC--U-UCAAUUGCUCAAUUGCAGUGUGCCUGACAUUCAAGAUUAGCGUACUAAGUGGGUCAGUAGAUGUAGGUGUCACCAUGG
........---((..(((..(((((.((((....((--(-.(.(((((......)))))(((((((((......).)))).))))...).)))...))))))))).)))..))..... ( -23.00)
>DroSec_CAF1 24537 102 - 1
C-------ACUUUCCUAUAACC-CU----UACCUUA--U-UCAAAUUCCCC-UUCAAGUCUGUCUCACUUUGGGCAUUGGCUUGACCAGUGGAACCAUCAAUUUGGGGGCCACAAUGG
.-------............((-(.----.......--.-.....((((.(-(((((((((((((......)))))..)))))))..)).))))(((......))))))......... ( -22.70)
>DroSim_CAF1 25012 104 - 1
C-------ACUUUCUUAUAACC-CU----UACCUUACCU-UUAAAUUCCCC-UUCAAGUCUGCCUCACUUUGGGCAUUGGCUUGACCAGUGGAACCAUCAAUUUGGGGGCCACAAUGG
.-------............((-(.----..........-.....((((.(-(((((((((((((......)))))..)))))))..)).))))(((......))))))......... ( -25.40)
>DroEre_CAF1 25687 93 - 1
U-------AC-------------UUUCCUUACCUCA--U-UAAAAUUCCCC-CU-AAGUCUGCGUAUCCUUGGGCCUCGGCUUGACCAGUGGAACCAUCAAUUUAGGGGCCACAAUGG
.-------..-------------.............--.-........(((-((-((((.((.((.(((((((((....))....)))).)))))))...)))))))))......... ( -20.80)
>DroYak_CAF1 25386 103 - 1
U-------AU-AACAUAUACCC-CUUCC--CCCUCA--U-UCACAUUCUCC-CUCAAGUGUGCCUCACUUUGGGCAUCGGCUUGACCAGUGGAACCAUCAAUUUGGGGGCCACAAUGG
.-------..-...........-.....--......--.-...((((....-.((((((((((((......))))))..))))))...((((..(((......)))...)))))))). ( -24.90)
>consensus
C_______AC_UUCAUAUAACC_CU____UACCUCA__U_UCAAAUUCCCC_UUCAAGUCUGCCUCACUUUGGGCAUUGGCUUGACCAGUGGAACCAUCAAUUUGGGGGCCACAAUGG
.....................................................((((((((((((......)))))..)))))))...((((..((.........))..))))..... (-13.50 = -15.58 +   2.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:40:42 2006