Locus 3491

Sequence ID 2R_DroMel_CAF1
Location 11,702,785 – 11,703,001
Length 216
Max. P 0.869221
window5689 window5690 window5691

overview

Window 9

Location 11,702,785 – 11,702,904
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.76
Mean single sequence MFE -28.72
Consensus MFE -23.73
Energy contribution -23.54
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -1.47
Structure conservation index 0.83
SVM decision value 0.03
SVM RNA-class probability 0.549856
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11702785 119 - 20766785
UACAU-UUACAACAAAACAGUAGAAAAACAAACAGAAAGAGAAAAGCGAGCUGAUAAGGCCAAAGGGGCCGGGUUCGUUCGGAGUCCGUACGAACGAACAGUCCACCGAAUAAUCCAAUC
....(-((((.........))))).......................(..(((....((((.....))))..((((((.(((...))).))))))...)))..)................ ( -24.70)
>DroSim_CAF1 998 115 - 1
UACAU-UUACAACAAAACAGCAGAAAAACAAACAGAAAGAGACAAGCGAGCUGAUAAGGCCAAAGGGGCCGGGUUCGUUCGGAGUCCGUACG----AACAGUCCACCGAAUAAUCCAAUC
.....-...........((((............................))))....((((.....))))(((((.((((((.(..(.....----....)..).))))))))))).... ( -23.89)
>DroEre_CAF1 1004 114 - 1
UCGAU-UUACAACAAAACAGCAGAAAAACAAACAGAAGGGGC-AAGCGAGCUGAUAAGGCCAAAGGGGCCGGGUUCGUUCGGAGUCCGUACG----AACAGUCCGCCGAAUAAUCCAAUC
.....-...............................(((..-...((.((.(((..((((.....))))..((((((.(((...))).)))----))).))).)))).....))).... ( -28.70)
>DroYak_CAF1 1005 115 - 1
CUGUUUUUACAACAAAACAGCAGAAAAACAAACAGAAGGAGA-CAGCGGGCUGAUAAGGCCAAAGGGGCCGGGUUCGUUCGGAGUCCGUACG----AACAGUCCGCCGAAUAAUCCAAUC
(((((((......))))))).................(((..-(.(((((((.....((((.....))))..((((((.(((...))).)))----)))))))))).).....))).... ( -37.60)
>consensus
UACAU_UUACAACAAAACAGCAGAAAAACAAACAGAAAGAGA_AAGCGAGCUGAUAAGGCCAAAGGGGCCGGGUUCGUUCGGAGUCCGUACG____AACAGUCCACCGAAUAAUCCAAUC
.................((((............................))))....((((.....))))(((((.((((((.(..(((........)).)..).))))))))))).... (-23.73 = -23.54 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 11,702,865 – 11,702,968
Length 103
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 77.13
Mean single sequence MFE -31.30
Consensus MFE -12.88
Energy contribution -14.88
Covariance contribution 2.00
Combinations/Pair 1.19
Mean z-score -3.11
Structure conservation index 0.41
SVM decision value 0.86
SVM RNA-class probability 0.869221
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11702865 103 + 20766785
UCUUUCUGUUUGUUUUUCUACUGUUUUGUUGUAA-AUGUAUGU----ACAUAUGCCU--------UUAUAUGUAUAUGCAAGCACACAGCUUGCCGGCGAACACAGACAAACUGAG
....((.((((((.......(((((((((((...-....((((----(((((((...--------.)))))))))))((((((.....))))))))))))).)))))))))).)). ( -30.71)
>DroSim_CAF1 1074 107 + 1
UCUUUCUGUUUGUUUUUCUGCUGUUUUGUUGUAA-AUGUAUGUAUUUACAUAUACCU--------UCAUAUGUAUAUGCAAGCACACAGCUUGCCGGCGAACACAGACACACUGAG
((....(((((((..(((.((((.(..(((((..-.(((.(((((.(((((((....--------..))))))).))))).))).)))))..).))))))).)))))))....)). ( -30.00)
>DroEre_CAF1 1079 107 + 1
CCCUUCUGUUUGUUUUUCUGCUGUUUUGUUGUAA-AUCGAUGU----AUAUAGGCAUACACACAUGCAUAAGUACAUGC----UGUGUGCUUGCCGGCGGACACAGACACACUGAG
......(((((((...((((((.....((((...-..))))..----.....((((..((((((.((((......))))----))))))..)))))))))).)))))))....... ( -34.60)
>DroYak_CAF1 1080 108 + 1
UCCUUCUGUUUGUUUUUCUGCUGUUUUGUUGUAAAAACAGUGU----ACAUAGGCAUACACACAAACAUAUGUACAUGC----UGUGUGCUUGCCGGCGAGCACAUCCACACUGAG
......((((((((.....((((((((......))))))))..----.....((((..((((((..(((......))).----))))))..))))))))))))............. ( -29.90)
>consensus
UCCUUCUGUUUGUUUUUCUGCUGUUUUGUUGUAA_AUCUAUGU____ACAUAGGCAU________UCAUAUGUACAUGC____ACACAGCUUGCCGGCGAACACAGACACACUGAG
......(((((((..(((.((((..............((((((....))))))........................((((((.....))))))))))))).)))))))....... (-12.88 = -14.88 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 11,702,904 – 11,703,001
Length 97
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 76.83
Mean single sequence MFE -29.98
Consensus MFE -11.27
Energy contribution -15.15
Covariance contribution 3.88
Combinations/Pair 1.11
Mean z-score -2.85
Structure conservation index 0.38
SVM decision value -0.02
SVM RNA-class probability 0.522768
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11702904 97 - 20766785
UUACAUAACAAUACUGUCCGCACACUUUUGUCGCUCAGUUUGUCUGUGUUCGCCGGCAAGCUGUGUGCUUGCAUAUACAUAUAA--------AGGCAUAUGU----ACA
.((((((((((.((((..((.(((....)))))..))))))))........(((.((((((.....)))))).(((....))).--------.))).)))))----).. ( -26.40)
>DroSim_CAF1 1113 101 - 1
UUACAUAAUAAUACUGUUCGCAUACUUUCGCCGCUCAGUGUGUCUGUGUUCGCCGGCAAGCUGUGUGCUUGCAUAUACAUAUGA--------AGGUAUAUGUAAAUACA
..(((((...((((((..(((........).))..))))))...)))))......((((((.....))))))...((((((((.--------...))))))))...... ( -26.00)
>DroEre_CAF1 1118 101 - 1
UUACAUAACAAUACUGUUCGCAUACUUUCGCCUCUCAGUGUGUCUGUGUCCGCCGGCAAGCACACA----GCAUGUACUUAUGCAUGUGUGUAUGCCUAUAU----ACA
..(((((...((((((...((........))....))))))...))))).....((((.(((((((----(((((....))))).))))))).)))).....----... ( -33.50)
>DroYak_CAF1 1120 101 - 1
UUACAUAACAAUACUGUUCGCAUACGUUCGCCGCUCAGUGUGGAUGUGCUCGCCGGCAAGCACACA----GCAUGUACAUAUGUUUGUGUGUAUGCCUAUGU----ACA
.((((((...........((..((((((((((.....).)))))))))..))..((((.(((((((----(((((....)))).)))))))).)))))))))----).. ( -34.00)
>consensus
UUACAUAACAAUACUGUUCGCAUACUUUCGCCGCUCAGUGUGUCUGUGUUCGCCGGCAAGCACACA____GCAUAUACAUAUGA________AGGCAUAUGU____ACA
..(((((...((((((...((........))....))))))...)))))......((((((.....))))))....((((((((..........))))))))....... (-11.27 = -15.15 +   3.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:50 2006