Locus 503

Sequence ID 3L_DroMel_CAF1
Location 1,472,428 – 1,472,588
Length 160
Max. P 0.802706
window753 window754

overview

Window 3

Location 1,472,428 – 1,472,528
Length 100
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 78.35
Mean single sequence MFE -26.62
Consensus MFE -21.09
Energy contribution -20.53
Covariance contribution -0.55
Combinations/Pair 1.25
Mean z-score -1.26
Structure conservation index 0.79
SVM decision value 0.62
SVM RNA-class probability 0.802706
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1472428 100 + 23771897
UGGGGUUGGGGGGGCCUGUGAAAUCAGUUUGUUGCAAUUUGACG-UUACUAGAAUUGUUGCACU-UUCCGCGGGCCCAGAGAGAU---A-CUUCCGG-A-UAAUCAUA
....(((.((.(((((((((.((..(((..((.(((((((....-......))))))).)))))-)).))))))))).(((....---.-))))).)-)-)....... ( -26.50)
>DroPse_CAF1 159573 99 + 1
UGU-------GUGGCCUGUGAAAUUA-UUUGUUACAAUUUGUCGCUCGUUGGAAUUGUUGCACUACUUUGCGGGCCCAGAAAGAACUUAGAUUCCAU-UUUAAUCAUA
(.(-------(.((((((..((....-..(((.(((((((..(....)...))))))).)))....))..)))))))).).........((((....-...))))... ( -21.60)
>DroSim_CAF1 117510 93 + 1
UGG-------GGGGCCUGUGAAAUCAGUUUGUUGCAAUUUGACA-UGACUGGAAUUGCUGCACU-UUUCGCGGGCCCAGAGAGAU---A-CUUCCGG-A-UAAUCAUA
..(-------(((((((((((((..(((..((.(((((((.(..-....).))))))).)))))-)))))))))))).(((....---.-)))))..-.-........ ( -30.70)
>DroYak_CAF1 125554 95 + 1
GGG-------GGGGCCUGUGAAAUCAGUUUGCUGCAAUUUGACG-UGACUGGAAUUGUUGCACU-UUUCGCGGGCCCAGAGAAAU---A-CUUUCGGUGUUAAUCAUA
...-------.((((((((((((..(((..((.(((((((.(..-....).))))))).)))))-)))))))))))).((..(((---(-(.....)))))..))... ( -34.60)
>DroAna_CAF1 127678 93 + 1
UAU-------UUGGCCCGUGACAUUA-UUUGUUACAAUUUGUCG-CCUUUGGAAUUGUUGCACGAGUUCGCGGGCCCAGAAAGAU---A-AUUCCGG-U-UAAUCAUA
...-------..(((((((((.(((.-..(((.(((((((....-......))))))).)))..))))))))))))......(((---(-((....)-)-).)))... ( -24.70)
>DroPer_CAF1 162193 99 + 1
UGU-------GUGGCCUGUGAAAUUA-UUUGUUACAAUUUGUCGCUCGUUGGAAUUGUUGCACUACUUUGCGGGCCCAGAAAGAACUUAGAUUCCAU-UUUAAUCAUA
(.(-------(.((((((..((....-..(((.(((((((..(....)...))))))).)))....))..)))))))).).........((((....-...))))... ( -21.60)
>consensus
UGG_______GGGGCCUGUGAAAUCA_UUUGUUACAAUUUGACG_UCACUGGAAUUGUUGCACU_UUUCGCGGGCCCAGAAAGAU___A_AUUCCGG_U_UAAUCAUA
............((((((((((.......(((.(((((((...........))))))).)))....))))))))))................................ (-21.09 = -20.53 +  -0.55)

alignment

Postscript

secondary structure

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dotplot

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Window 4

Location 1,472,498 – 1,472,588
Length 90
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 74.27
Mean single sequence MFE -20.81
Consensus MFE -12.81
Energy contribution -12.92
Covariance contribution 0.11
Combinations/Pair 1.35
Mean z-score -1.40
Structure conservation index 0.62
SVM decision value 0.41
SVM RNA-class probability 0.726651
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1472498 90 + 23771897
GGCCCAGAGAGAU----A-CUUCCGGA-UAAUCAUAGGCU-----GCUGGUUUUCAAUACCAUAGUCUAUUUCAUGGCCGGCAAACAAAUUUCCUUUUUGC------
((((..(((((((----.-........-..))).((((((-----(.((((.......)))))))))))))))..)))).(((((...........)))))------ ( -21.30)
>DroVir_CAF1 129462 100 + 1
GGGCCAGAGAAAAUAUGAUAUUCCGUU-UAAUCAUAGACUAA--AAUCGGUGCUCAAUACCUUAGCCUAUUUCAUGCCCGGAAUACAUUUUUA-UUUUUGUUUU---
....(((((((((.(((.(((((((..-((...((((.((((--....((((.....)))))))).))))....))..)))))))))).))).-))))))....--- ( -18.80)
>DroPse_CAF1 159637 100 + 1
GGCCCAGAAAGAAC-UUAGAUUCCAUUUUAAUCAUAGGCUAA--AAUUGGUAAUCAAUACCUUAGUCUAUUUCAUGCAUGGAACACAGUUUUCUUUUUUCU-UU---
.....(((((((((-(....((((((.......(((((((((--....((((.....))))))))))))).......))))))...)))..)))))))...-..--- ( -20.24)
>DroEre_CAF1 124776 99 + 1
GGCCCAGAGAGAU----A-CUUCCGGAUUAAUCAUAGGCUAU--AGCUGGUCAUCAAUACCAUAGCUUAUUUCAUGGCCGGCAGACAUAUACCCUUUUUUU-UUGCA
((((..(((((((----.-...........))).(((((((.--...((((.......)))))))))))))))..)))).(((((...............)-)))). ( -19.96)
>DroMoj_CAF1 107582 98 + 1
GGGCCAGAGUAAA--UGAUAUUCCGUU-UAAUCAUAGGCUAA--AUCGGGUACUCAAUACCUUAGCCUAUUUCAUGCCCGGAAUACAGUUUGU-UUUUUGAUUU---
....(((((((((--(..(((((((..-((...((((((((.--...(((((.....)))))))))))))....))..)))))))..))))).-.)))))....--- ( -26.00)
>DroAna_CAF1 127741 96 + 1
GGCCCAGAAAGAU----A-AUUCCGGU-UAAUCAUAGGCUAAAU-CCCGGUAAUCAAUACCUUAGUCUAUUUCAUGCCCGGCAAACAUAUUUCUAUUUUUA-UU---
.....(((((...----.-...((((.-.....(((((((((..-...((((.....))))))))))))).......))))........))))).......-..--- ( -18.58)
>consensus
GGCCCAGAGAGAA____A_AUUCCGGU_UAAUCAUAGGCUAA__AACUGGUAAUCAAUACCUUAGCCUAUUUCAUGCCCGGAAAACAUAUUUC_UUUUUGU_UU___
......................((((.......(((((((((......((((.....))))))))))))).......)))).......................... (-12.81 = -12.92 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:41 2006