Locus 1861

Sequence ID 2R_DroMel_CAF1
Location 6,994,089 – 6,994,216
Length 127
Max. P 0.986337
window3089 window3090

overview

Window 9

Location 6,994,089 – 6,994,186
Length 97
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 76.41
Mean single sequence MFE -22.65
Consensus MFE -15.18
Energy contribution -16.02
Covariance contribution 0.84
Combinations/Pair 1.22
Mean z-score -2.44
Structure conservation index 0.67
SVM decision value 2.04
SVM RNA-class probability 0.986337
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6994089 97 - 20766785
CCUUAAC--------CAAAUGACUGCC---AUCAAGUGGCUUAAAUCACUCUCCA--UUCGCCACUUGAACCACAUGAUCCAUGGACUUACCCGAGAUUCCAGGGGAUUA--------
.......--------............---.(((((((((...............--...)))))))))......((((((.(((((((....)))..))))..))))))-------- ( -23.67)
>DroPse_CAF1 24213 109 - 1
UCUUAGCUUGACUCGAAAAU-----CC---UUGUAAUAG-CAAAAUCACUUUCUAAUUUUCCCACCCGAACCGCAGGACCCAUAGAACCCACAGGGAUUCCAGGGGAUUACAGAUUGC
.....(((..((..(.....-----.)---..))...))-).......(..(((....(((((..((........)).......((((((...))).)))..)))))....)))..). ( -17.20)
>DroSec_CAF1 22648 97 - 1
CCUUAAC--------CAAUUAACUCCC---AUCAAGUGGCCUAAAUCACUCUCUA--UUCGCCACUUGAACCACAUGAUCCAUGGACUUACCCGAGAUUCCAGGGGAUUA--------
.......--------............---.(((((((((...............--...)))))))))......((((((.(((((((....)))..))))..))))))-------- ( -23.17)
>DroSim_CAF1 20909 97 - 1
CCUCAAC--------CAAAUAACUGCC---AUCAAGUGGCCUAAAUCACUCUCCA--UUCGCCACUUGAACCACAUGAUCCAUGGACUUACCCGAGAUUCCAGGGGAUUA--------
.......--------............---.(((((((((...............--...)))))))))......((((((.(((((((....)))..))))..))))))-------- ( -23.17)
>DroEre_CAF1 25331 99 - 1
GCUUAAC--------AA-AUAGCUGCUUAGCUCAAGUGGCUUAAAUCACACUCCA--CUCGCCGCUGGAACCACAUGAUCCAUGGACUCACCCGAGAUUCCAGGGGUUUA--------
.......--------..-..(((..(((.....)))..)))..............--...(((.((((((...((((...))))..(((....))).)))))).)))...-------- ( -24.70)
>DroYak_CAF1 23196 97 - 1
CCUUAAC--------AAAAUAACUGCC---AUCAAGUGGCUUAAAUCACUCUCCA--UUCGCCACUUGAACCACAUGAUCCAUGGAUUCACUCGAGAUUCCAGGACAUUA--------
.......--------............---.(((((((((...............--...))))))))).....(((.(((.((((.((......)).))))))))))..-------- ( -23.97)
>consensus
CCUUAAC________AAAAUAACUGCC___AUCAAGUGGCCUAAAUCACUCUCCA__UUCGCCACUUGAACCACAUGAUCCAUGGACUCACCCGAGAUUCCAGGGGAUUA________
...............................(((((((((....................))))))))).........(((.((((.((......)).)))))))............. (-15.18 = -16.02 +   0.84)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,994,119 – 6,994,216
Length 97
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 76.70
Mean single sequence MFE -17.86
Consensus MFE -8.84
Energy contribution -10.23
Covariance contribution 1.39
Combinations/Pair 1.15
Mean z-score -2.52
Structure conservation index 0.50
SVM decision value 1.57
SVM RNA-class probability 0.964840
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6994119 97 - 20766785
ACUAGCUGAGCAAGCUAAUAAAGGUAAACACCUUAAC--------CAAAUGACUGCC---AUCAAGUGGCUUAAAUCACUCUCCA--UUCGCCACUUGAACCACAUGAUC
..(((((.....)))))...(((((....)))))...--------............---.(((((((((...............--...)))))))))........... ( -22.17)
>DroSec_CAF1 22678 97 - 1
ACUAGCAGAGCAAGCUAAUAAAGGUAAACACCUUAAC--------CAAUUAACUCCC---AUCAAGUGGCCUAAAUCACUCUCUA--UUCGCCACUUGAACCACAUGAUC
..((((.......))))...(((((....)))))...--------............---.(((((((((...............--...)))))))))........... ( -19.37)
>DroSim_CAF1 20939 97 - 1
ACUAGCUGAGCAAGCUAAUAAAGGUAAACACCUCAAC--------CAAAUAACUGCC---AUCAAGUGGCCUAAAUCACUCUCCA--UUCGCCACUUGAACCACAUGAUC
..(((((.....)))))....((((....))))....--------............---.(((((((((...............--...)))))))))........... ( -20.17)
>DroEre_CAF1 25361 98 - 1
ACUAGC-UAACAAGCUAAUAAAAGUAAACAGCUUAAC--------AA-AUAGCUGCUUAGCUCAAGUGGCUUAAAUCACACUCCA--CUCGCCGCUGGAACCACAUGAUC
....((-(((..(((((....((((.....))))...--------..-.)))))..)))))((.((((((...............--...)))))).))........... ( -19.77)
>DroYak_CAF1 23226 97 - 1
ACUAGCACAGCAAGCUAAUAAAGCUAAACACCUUAAC--------AAAAUAACUGCC---AUCAAGUGGCUUAAAUCACUCUCCA--UUCGCCACUUGAACCACAUGAUC
............((((.....))))............--------............---.(((((((((...............--...)))))))))........... ( -16.37)
>DroPer_CAF1 24243 97 - 1
ACCUUU-CAAGGAGCUAAUCAA---AAACGUCUUUGCUUGACUCGAAAAU-----CC---UUGUAAUAG-CAAAAUCACUUUCUAAUUUUCCCACCCGAACCGCAGGAUC
.(((..-..)))..........---....(..((((((..((..(.....-----.)---..))...))-))))..)..................((........))... (  -9.30)
>consensus
ACUAGC_GAGCAAGCUAAUAAAGGUAAACACCUUAAC________AAAAUAACUGCC___AUCAAGUGGCCUAAAUCACUCUCCA__UUCGCCACUUGAACCACAUGAUC
..((((.......))))............................................(((((((((....................)))))))))........... ( -8.84 = -10.23 +   1.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:01 2006