Locus 4605

Sequence ID 3L_DroMel_CAF1
Location 13,141,848 – 13,142,126
Length 278
Max. P 0.983416
window7220 window7221 window7222 window7223

overview

Window 0

Location 13,141,848 – 13,141,968
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.16
Mean single sequence MFE -25.14
Consensus MFE -21.70
Energy contribution -22.50
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.86
SVM decision value 1.25
SVM RNA-class probability 0.936706
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13141848 120 + 23771897
AGGCACAAAAAGGCAACAAAGGUGCAUAUCUCCUCCUUUCGGACUUUCGGACACAACAAAGCCGGUGUUCUGGCAAAAAGGAAAAUAUGAAUAACCAUUCAAUCAACCAGAAAGAACAAC
..((((.....(....)....))))........(((....)))(((((((..........(((((....))))).............(((((....))))).....)).)))))...... ( -25.10)
>DroSec_CAF1 129521 120 + 1
AGGCACAAAAAGGAAACAACGGUGCAUAUCUCCUCCUUUCGGACUUACGGACACAACAAAGCCGGUGUUCUGGCAAAAAGGGAAAUAUGAAUAACCAUUCAAUCAACCAGAAAGAACAAC
.((........(....)...(((.(((((.((((...((((......)))).........(((((....))))).....)))).)))))....)))..........))............ ( -26.30)
>DroSim_CAF1 129439 120 + 1
AGGCACAAAAAGGCAACAAAGGUGCAUAUCUCCUCCUUUCGGACUUUCGGACACAACAAAGCCGGUGUUCUGGCAAAAAGGGAAAUAUGAAUAACCAUUCAAUCAACCAGAAAGAACAAC
..((((.....(....)....))))........(((....)))(((((............(((((....))))).....((......(((((....))))).....)).)))))...... ( -25.40)
>DroEre_CAF1 126424 119 + 1
AGGCACAAAAAGGCAACAAAGGUGCAUAUCUCCUCCUUUCGGACUUUCGGACACAACAAAGCCGGUGUUGUGGCAAAAAG-AAAAUAUGAAUAACCAUUCAAUCAACCAGAAAGAACAAC
..((((.....(....)....))))..........(((((((.((((..(.(((((((.......))))))).)..))))-......(((((....))))).....)).)))))...... ( -25.80)
>DroYak_CAF1 130884 119 + 1
AGGCACAAAAAGGCAACAAAGGUGCAUAUCUCCUCCUUUCGGACGUUCGGACACAACAAAGCCGGUGUUGUGGCAAAAAG-AAAAUAUGAAUAACCAUUCAAUCAACCAGAAAGAACAAC
..((((.....(....)....))))..........(((((((.........(((((((.......)))))))........-......(((((....))))).....)).)))))...... ( -23.10)
>consensus
AGGCACAAAAAGGCAACAAAGGUGCAUAUCUCCUCCUUUCGGACUUUCGGACACAACAAAGCCGGUGUUCUGGCAAAAAGGAAAAUAUGAAUAACCAUUCAAUCAACCAGAAAGAACAAC
..((((.....(....)....))))........(((....)))(((((((..........(((((....))))).............(((((....))))).....)).)))))...... (-21.70 = -22.50 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 13,141,968 – 13,142,088
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.25
Mean single sequence MFE -27.96
Consensus MFE -25.24
Energy contribution -25.84
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.90
SVM decision value 1.83
SVM RNA-class probability 0.979137
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13141968 120 + 23771897
AAUUUCAACGAGGUGGAGCAAAAAAUAUGGCCAGUCAUUAAUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGAUAUAAA
........((.((.((.(((.......(((....)))((((...(((((.....).((((((((..(((....))).))))))))..))))..))))......))).))))))....... ( -24.40)
>DroSec_CAF1 129641 120 + 1
AAUUUCAACGAGUGGGAGCAAAAAAUAUGGCCAGUCAUUAAUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGAUAUAAA
........((.(.(((.(((.......(((....)))((((...(((((.....).((((((((..(((....))).))))))))..))))..))))......))).))))))....... ( -24.40)
>DroSim_CAF1 129559 120 + 1
AAUUUCAACGAGGGGGAGCAAAAAAUAUGGCCAGUCAUUAAUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGGUAUAAA
...........(((((.(((.......(((....)))((((...(((((.....).((((((((..(((....))).))))))))..))))..))))......))).)))))........ ( -29.90)
>DroEre_CAF1 126543 119 + 1
AAUUUCAACGAGG-GGAGCAAAAAAUAUGUCCAGUCAUUAAUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGAUAUAAA
........((.((-((.(((........(((((.((.........)))))))....((((((((..(((....))).))))))))..................))).))))))....... ( -29.70)
>DroYak_CAF1 131003 120 + 1
AAUUUCAACGAGGGGGAGCAAAAAAUAUGUCCAGUCAUUAAUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGAUAUAAA
...........(((((.(((........(((((.((.........)))))))....((((((((..(((....))).))))))))..................))).)))))........ ( -31.40)
>consensus
AAUUUCAACGAGGGGGAGCAAAAAAUAUGGCCAGUCAUUAAUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGAUAUAAA
...........(((((.(((...............((((......))))((((...((((((((..(((....))).)))))))).)))).............))).)))))........ (-25.24 = -25.84 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 13,142,008 – 13,142,126
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.65
Mean single sequence MFE -27.41
Consensus MFE -26.87
Energy contribution -26.71
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.62
Structure conservation index 0.98
SVM decision value 1.94
SVM RNA-class probability 0.983416
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13142008 118 + 23771897
AUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGAUAUAAAGCGGCGAACCAUAUUUUUUGCCAUGC--UUAAGCCGCACA
((((((..((......((((((((..(((....))).))))))))....(((............)))))..))))))...((((((((........))))))..((--....)).))... ( -27.70)
>DroSec_CAF1 129681 120 + 1
AUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGAUAUAAAGCGGCGAACCAUAUUUUUUACCAUGCUCUUAAGCCGCACA
......((((......((((((((..(((....))).)))))))).........(((((((((((((((.............))))...)))))))))))))))(((....)))...... ( -27.52)
>DroSim_CAF1 129599 120 + 1
AUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGGUAUAAAGCGGCGAACCAUAUUUUUUACCAUGCUCUUAAGCCGCACA
......((((......((((((((..(((....))).)))))))).........(((((((((((((((.............))))...)))))))))))))))(((....)))...... ( -27.52)
>DroEre_CAF1 126582 118 + 1
AUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGAUAUAAAGCGGCGAACCAUAUUUUUUACCAUGC--UUAAGCCGCACA
((((((..((......((((((((..(((....))).))))))))....(((............)))))..))))))...(((((....(((..........))).--....)))))... ( -27.40)
>DroYak_CAF1 131043 118 + 1
AUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGAUAUAAAGCGGCGAACCAUAUUUUUUACCAACC--UUAAGCCGCACA
((((((..((......((((((((..(((....))).))))))))....(((............)))))..))))))...(((((.....................--....)))))... ( -26.91)
>consensus
AUAUCGAUGGAUUACAUGCGUUCAGCAUUUUACGAUAUGAGCGCAAAAUCGUUUUAAAAAAUAUGCGCCCCCGAUAUAAAGCGGCGAACCAUAUUUUUUACCAUGC__UUAAGCCGCACA
((((((..((......((((((((..(((....))).))))))))....(((............)))))..))))))...(((((...........................)))))... (-26.87 = -26.71 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,142,008 – 13,142,126
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.65
Mean single sequence MFE -31.21
Consensus MFE -27.46
Energy contribution -27.50
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.36
Structure conservation index 0.88
SVM decision value 0.10
SVM RNA-class probability 0.585637
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13142008 118 - 23771897
UGUGCGGCUUAA--GCAUGGCAAAAAAUAUGGUUCGCCGCUUUAUAUCGGGGGCGCAUAUUUUUUAAAACGAUUUUGCGCUCAUAUCGUAAAAUGCUGAACGCAUGUAAUCCAUCGAUAU
...(((((..((--.((((........)))).)).)))))...((((((((((((((..................)))))))..........((((.....))))........))))))) ( -31.07)
>DroSec_CAF1 129681 120 - 1
UGUGCGGCUUAAGAGCAUGGUAAAAAAUAUGGUUCGCCGCUUUAUAUCGGGGGCGCAUAUUUUUUAAAACGAUUUUGCGCUCAUAUCGUAAAAUGCUGAACGCAUGUAAUCCAUCGAUAU
.((((((((....))).((.(((((((((((((((.(((........))))))).)))))))))))...))....)))))..((((((....((((.....)))).........)))))) ( -30.52)
>DroSim_CAF1 129599 120 - 1
UGUGCGGCUUAAGAGCAUGGUAAAAAAUAUGGUUCGCCGCUUUAUACCGGGGGCGCAUAUUUUUUAAAACGAUUUUGCGCUCAUAUCGUAAAAUGCUGAACGCAUGUAAUCCAUCGAUAU
.((((((((....))).((.(((((((((((((((.(((........))))))).)))))))))))...))....)))))..((((((....((((.....)))).........)))))) ( -30.72)
>DroEre_CAF1 126582 118 - 1
UGUGCGGCUUAA--GCAUGGUAAAAAAUAUGGUUCGCCGCUUUAUAUCGGGGGCGCAUAUUUUUUAAAACGAUUUUGCGCUCAUAUCGUAAAAUGCUGAACGCAUGUAAUCCAUCGAUAU
.(((((.....(--((.((.(((((((((((((((.(((........))))))).)))))))))))...))((((((((.......)))))))))))...)))))............... ( -31.70)
>DroYak_CAF1 131043 118 - 1
UGUGCGGCUUAA--GGUUGGUAAAAAAUAUGGUUCGCCGCUUUAUAUCGGGGGCGCAUAUUUUUUAAAACGAUUUUGCGCUCAUAUCGUAAAAUGCUGAACGCAUGUAAUCCAUCGAUAU
.....(((.(((--(((((.(((((((((((((((.(((........))))))).)))))))))))...)))))))).))).((((((....((((.....)))).........)))))) ( -32.02)
>consensus
UGUGCGGCUUAA__GCAUGGUAAAAAAUAUGGUUCGCCGCUUUAUAUCGGGGGCGCAUAUUUUUUAAAACGAUUUUGCGCUCAUAUCGUAAAAUGCUGAACGCAUGUAAUCCAUCGAUAU
.(((((((......))..(((((((((((((((((.(((........))))))).))))))))))......((((((((.......)))))))))))...)))))............... (-27.46 = -27.50 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:14 2006