Locus 5018

Sequence ID 3R_DroMel_CAF1
Location 13,233,085 – 13,233,175
Length 90
Max. P 0.996067
window8202 window8203

overview

Window 2

Location 13,233,085 – 13,233,175
Length 90
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 71.27
Mean single sequence MFE -23.38
Consensus MFE -9.68
Energy contribution -9.68
Covariance contribution -0.00
Combinations/Pair 1.27
Mean z-score -2.48
Structure conservation index 0.41
SVM decision value 2.65
SVM RNA-class probability 0.996067
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13233085 90 + 27905053
CUUAU-GACGUUAGUUUACUUACCGAAUUGACGUAGGUCGCAGAAUAAAAUA-----------UGGUUUG------------------GCAUAUGUGUGUUUCUACUAUGAAAUUAUUGU
.....-.((((((((((.......)))))))))).........(((((..((-----------((((..(------------------((((....)))))...))))))...))))).. ( -15.90)
>DroSec_CAF1 261781 119 + 1
GUUAU-GACGUUAAUUUACUUAUCAAAUUGACGUCUUUCACUGAAUAAAAUAAAGCCAAAACAUAUUUUAUUCAGUGAAAGACGUCAAUUUGAUGUGUGUCUCUACCAUGAAAUUAUUGU
.((((-(..((.....(((.((((((((((((((((((((((((((((((((...........)))))))))))))))))))))))))))))))).))).....)))))))......... ( -48.40)
>DroSim_CAF1 247265 90 + 1
GUUAU-GACGUUAAUUUACUUACCAAAUUGACGUCUUUCACUGAAUAAAAUA-----------UGUUUUG------------------GCUUAUGUGUGUCUCUACCAUGAAAUUAUUUU
.....-(((((((((((.......))))))))))).......((((((..((-----------((....(------------------((........))).....))))...)))))). ( -14.90)
>DroEre_CAF1 251455 89 + 1
-UUAUAGGCGUUAGUUUGUUAACCGAAAUGACGCCUUUCGCUGUACAAAAUA-----------UGUUUUG-------------------CGUAUUUGUGGCUCUACACUGUAAUUAAUGU
-....((((((((.((((.....)))).)))))))).......(((((((((-----------((.....-------------------)))))))(((......)))))))........ ( -21.30)
>DroYak_CAF1 262298 90 + 1
GUUAU-GACGUUAAUUUACUAACUGAAUUGACGCCUUUCGCAGAAUAAAAUA-----------UGUUUUG------------------GGGUAUUUGUGGCUCUACACUGAAAUGAAUGU
((((.-.(((((((((((.....))))))))))....((.(((((((.....-----------)))))))------------------.))...)..))))................... ( -16.40)
>consensus
GUUAU_GACGUUAAUUUACUUACCGAAUUGACGUCUUUCGCUGAAUAAAAUA___________UGUUUUG__________________GCGUAUGUGUGUCUCUACAAUGAAAUUAUUGU
......(((((((((((.......)))))))))))..................................................................................... ( -9.68 =  -9.68 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,233,085 – 13,233,175
Length 90
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 71.27
Mean single sequence MFE -18.86
Consensus MFE -3.36
Energy contribution -3.56
Covariance contribution 0.20
Combinations/Pair 1.22
Mean z-score -2.30
Structure conservation index 0.18
SVM decision value 1.76
SVM RNA-class probability 0.976020
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13233085 90 - 27905053
ACAAUAAUUUCAUAGUAGAAACACACAUAUGC------------------CAAACCA-----------UAUUUUAUUCUGCGACCUACGUCAAUUCGGUAAGUAAACUAACGUC-AUAAG
..............((((((......(((((.------------------.....))-----------)))....))))))(((...((......))((.((....)).)))))-..... ( -10.80)
>DroSec_CAF1 261781 119 - 1
ACAAUAAUUUCAUGGUAGAGACACACAUCAAAUUGACGUCUUUCACUGAAUAAAAUAUGUUUUGGCUUUAUUUUAUUCAGUGAAAGACGUCAAUUUGAUAAGUAAAUUAACGUC-AUAAC
...................(((....(((((((((((((((((((((((((((((((.((....))..)))))))))))))))))))))))))))))))..((......)))))-..... ( -47.80)
>DroSim_CAF1 247265 90 - 1
AAAAUAAUUUCAUGGUAGAGACACACAUAAGC------------------CAAAACA-----------UAUUUUAUUCAGUGAAAGACGUCAAUUUGGUAAGUAAAUUAACGUC-AUAAC
.......(((((((((..(........)..))------------------)((((..-----------..)))).....))))))(((((.((((((.....)))))).)))))-..... ( -12.10)
>DroEre_CAF1 251455 89 - 1
ACAUUAAUUACAGUGUAGAGCCACAAAUACG-------------------CAAAACA-----------UAUUUUGUACAGCGAAAGGCGUCAUUUCGGUUAACAAACUAACGCCUAUAA-
............(((......))).....((-------------------(...(((-----------.....)))...)))..((((((......((((....)))).))))))....- ( -14.20)
>DroYak_CAF1 262298 90 - 1
ACAUUCAUUUCAGUGUAGAGCCACAAAUACCC------------------CAAAACA-----------UAUUUUAUUCUGCGAAAGGCGUCAAUUCAGUUAGUAAAUUAACGUC-AUAAC
.............(((((((....(((((...------------------.......-----------)))))..)))))))...(((((.((((.........)))).)))))-..... (  -9.40)
>consensus
ACAAUAAUUUCAUGGUAGAGACACACAUAAGC__________________CAAAACA___________UAUUUUAUUCAGCGAAAGACGUCAAUUCGGUAAGUAAAUUAACGUC_AUAAC
.....................................................................................(((((.((((.........)))).)))))...... ( -3.36 =  -3.56 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:25 2006