Locus 2032

Sequence ID 3R_DroMel_CAF1
Location 5,763,170 – 5,763,328
Length 158
Max. P 0.996798
window3333 window3334

overview

Window 3

Location 5,763,170 – 5,763,267
Length 97
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 68.48
Mean single sequence MFE -26.11
Consensus MFE -7.14
Energy contribution -7.47
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.76
Structure conservation index 0.27
SVM decision value 1.85
SVM RNA-class probability 0.979850
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5763170 97 - 27905053
CCACUGUGUUCG-UGAG-AUCACAGUGGGUAAAUGGCAGCUACAAAUCUGACAUUA-----AAGGAACUUGGCAAUAACAUUUAUAUACAAAAUCUGGCUUUAA
((((((((.((.-...)-).))))))))(((((((...((((....(((.......-----.)))....)))).....)))))))................... ( -26.70)
>DroPse_CAF1 60955 82 - 1
CCAGUGUCGCCUACGGGUGGCACAGUGGCAACAC--------ACACUCACACACAA-----GAGGAAGUGG-CA--------UACAUGGAAGAGAAUAUUUUAG
(((((((((((....)))))))).(((....)))--------.((((..(......-----..)..)))).-..--------....)))............... ( -28.10)
>DroSec_CAF1 55397 97 - 1
CCACUGUCUUCG-UGAG-AGAACAGUGUGUAAAUGGCAGCCACAAAGCUGACAUUA-----AAGGAACUAGGCAAUAAAAUGUAUAUAAAAAAUAUGGCUUUAA
.((((((..((.-...)-)..))))))....((((.((((......)))).)))).-----........((((.(((................))).))))... ( -20.59)
>DroSim_CAF1 55590 97 - 1
CCACUGUCUUCG-UGAG-AGAACAGUGGGUAAAUGGCAGCUACAAAGCUGACAUUA-----AAGGAACUAGGCAAUAAAAUGUAUAUAAAAAAUAUGGCUUUAA
(((((((..((.-...)-)..)))))))...((((.(((((....))))).)))).-----........((((.(((................))).))))... ( -25.69)
>DroEre_CAF1 50591 102 - 1
CCACUGUGUUCA-UGUG-AGAACAGUGGGUAAAUGGCUGAUACAAAUGAGGCAUUAUGGUUAGGAAACUUGGCAAGAACACUUAUAUUAAGUAGCUGGCAUUAA
(((((((.(((.-...)-)).)))))))((....(((((......(((((...((.((.(.((....)).).)).))...)))))......))))).))..... ( -25.80)
>DroYak_CAF1 39289 102 - 1
CCACUGUGUUCA-UGUG-AGAACAGUGGGCAAAUGGCUGCCACAAAUGAGGCAUUAUGGCUAAGAGACUUGGCAAGAACAAUCAUAUAAAGUAUGUGGCAUUAA
(((((((.(((.-...)-)).)))))))((.....))(((((((......((.(((((((((((...))))))..((....)).))))).)).))))))).... ( -29.80)
>consensus
CCACUGUCUUCG_UGAG_AGAACAGUGGGUAAAUGGCAGCUACAAAUCAGACAUUA_____AAGGAACUUGGCAAUAACAUUUAUAUAAAAAAUAUGGCUUUAA
(((((((..............)))))))............................................................................ ( -7.14 =  -7.47 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,763,238 – 5,763,328
Length 90
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 73.11
Mean single sequence MFE -34.04
Consensus MFE -11.15
Energy contribution -11.35
Covariance contribution 0.20
Combinations/Pair 1.29
Mean z-score -3.33
Structure conservation index 0.33
SVM decision value 2.75
SVM RNA-class probability 0.996798
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5763238 90 - 27905053
UCCUGCUGCAACAAUUUAGCGGUACUUGACUGACCAGCCGGCAGCAGACCAUGGGAAUUGCCCACUGUGUUCG-UGAG-AUCACAGUGGGUA
((((((((........))))(((...((.(((.((....))))))).)))..))))..(((((((((((.((.-...)-).))))))))))) ( -39.50)
>DroPse_CAF1 61006 79 - 1
----GCUGCAACGAUUUAGCGGUACUUG------CAACC---GCAAGACCAUGGGAAUUACCCAGUGUCGCCUACGGGUGGCACAGUGGCAA
----((..(...........(((.((((------(....---)))))))).((((.....))))((((((((....)))))))).)..)).. ( -37.80)
>DroSim_CAF1 55658 90 - 1
UGCUGCUGCAACAAUUUAGCGGUACUUGACUGACCAGCCGGCAGCAGACCAUGGGAAUUGCCCACUGUCUUCG-UGAG-AGAACAGUGGGUA
..(((((((..........((((.....))))........)))))))...........((((((((((..((.-...)-)..)))))))))) ( -36.87)
>DroEre_CAF1 50664 87 - 1
---UGCUGCAACAAUUUAGCGGUACUUGACUGGCCGACCAGCAGCAGACCAUGGGAAUUGCCCACUGUGUUCA-UGUG-AGAACAGUGGGUA
---.((((........))))(((..(((.((((....)))))))...)))........((((((((((.(((.-...)-)).)))))))))) ( -31.00)
>DroAna_CAF1 6701 75 - 1
----GCUGC-ACAAUUUAGCGGUACUCGGCUGACCA----------GGCCAUGGGAAAUACCCAUUAUAGCCGCCGGG-AGUACAGUGGUU-
----((((.-((..((..(((((....((((.....----------))))(((((.....)))))....)))))..))-.)).))))....- ( -24.90)
>DroPer_CAF1 60483 79 - 1
----GCUGCAACGAUUUAGCGGUACUUG------CAACC---ACAAGACCAUGGGAAUUACCCAGUGUCGCCUACGGGUGGCACAGUGGCAA
----((..(...........(((.((((------.....---.))))))).((((.....))))((((((((....)))))))).)..)).. ( -34.20)
>consensus
____GCUGCAACAAUUUAGCGGUACUUGACUGACCAACC___AGCAGACCAUGGGAAUUACCCACUGUCGCCG_CGGG_AGCACAGUGGGUA
....(((((.........)))))......................................(((((((.((.........)))))))))... (-11.15 = -11.35 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:46 2006