Locus 4577

Sequence ID	3L_DroMel_CAF1
Location	13,122,875 – 13,123,068
Length	193
Max. P	0.999982

overview

Window 5

Location	13,122,875 – 13,122,988
Length	113
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	97.35
Mean single sequence MFE	-30.00
Consensus MFE	-28.60
Energy contribution	-28.23
Covariance contribution	-0.38
Combinations/Pair	1.06
Mean z-score	-2.12
Structure conservation index	0.95
SVM decision value	1.05
SVM RNA-class probability	0.906407
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13122875 113 + 23771897
AUCGAAGCCUUUCAUUCCUCGGCGUGUUCGCAUUUAAAUAAUGGUCCAAGAUUAUCAAUUAAGCCGUUGGCCAAAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAUA
((((((........)))...((((((....((((.....))))((((..(.....).........(((((((((........))))))))).....))))))))))...))). ( -31.00)
>DroSec_CAF1 110770 113 + 1
AUCGAAGCCUUUCAUUCCUCGGCGUGUUCGCAUUUAAAUAAUGGUCAAAGAUUAUCAAUUAAGCCGUUGGCCAAAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAAA
..............(((...(((((((((((..((((.(.((((((...)))))).).)))))).(((((((((........))))))))).....))).))))))...))). ( -29.50)
>DroSim_CAF1 108948 113 + 1
AUCGAAGCCUUUCAUUCCUCGGCGUGUUCGCAUUUAAAUAAUGGUCAAAGAUUAUCAAUUAAGCCGUUGGCCAAAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAAA
..............(((...(((((((((((..((((.(.((((((...)))))).).)))))).(((((((((........))))))))).....))).))))))...))). ( -29.50)
>DroYak_CAF1 110998 113 + 1
AUCGAAGCCUUUCAUUCCUCGGCGUGUUCGCUUUUGAAUAAUGGUCAAAGAUUAUCAAUUAAGCCGUUGGCCAAAUUAAUAGUUGGUCGACUAAAAGGACCACGCCCUCGAAA
..............(((...(((((((((((((((((.((((........))))))))..)))).(((((((((........))))))))).....))).))))))...))). ( -30.00)
>consensus
AUCGAAGCCUUUCAUUCCUCGGCGUGUUCGCAUUUAAAUAAUGGUCAAAGAUUAUCAAUUAAGCCGUUGGCCAAAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAAA
.(((((........)))...(((((((((((..((((.(.((((((...)))))).).)))))).(((((((((........))))))))).....))).))))))...)).. (-28.60 = -28.23 +  -0.38)

alignment

secondary structure

dotplot

Window 6

Location	13,122,908 – 13,123,028
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.67
Mean single sequence MFE	-34.36
Consensus MFE	-31.24
Energy contribution	-31.64
Covariance contribution	0.40
Combinations/Pair	1.06
Mean z-score	-2.08
Structure conservation index	0.91
SVM decision value	2.90
SVM RNA-class probability	0.997658
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13122908 120 + 23771897
UUAAAUAAUGGUCCAAGAUUAUCAAUUAAGCCGUUGGCCAAAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAUACCAAUGCCUCCUGGACAUGGAGUCCUGCAUGGCUGUGCUA
........((((((..(.....).........(((((((((........))))))))).....)))))).((((..(((.(((.((((....)).))))).)))..)...)))....... ( -34.90)
>DroSec_CAF1 110803 120 + 1
UUAAAUAAUGGUCAAAGAUUAUCAAUUAAGCCGUUGGCCAAAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAAACCAAUGCCUCUAGGACAUGGAGUCCUGCACGGCUGUGCUA
.......((((((...))))))......(((((((((((((........)))))))))....(((((..((.((((((..........))))))...))..)))))....))))...... ( -35.80)
>DroSim_CAF1 108981 120 + 1
UUAAAUAAUGGUCAAAGAUUAUCAAUUAAGCCGUUGGCCAAAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAAACCAAUGCCUCUAGGACAUGGAGUCCUGCACGGCUGUGCUA
.......((((((...))))))......(((((((((((((........)))))))))....(((((..((.((((((..........))))))...))..)))))....))))...... ( -35.80)
>DroEre_CAF1 107513 120 + 1
UUGAAUAAUGGUCAAAGAUUAUCAAUUAAGCCGUUGGCCAAAUUAAUAGUUGGUCGACUAAAAGGGCCACGCCCCAGAAAGCAAUGCCUCUAGGACAUGAAGUCCUGCACGGCUGUGCUA
((((.((((........)))))))).......(((((((((........))))))))).....((((...)))).....((((..(((..((((((.....))))))...)))..)))). ( -34.80)
>DroYak_CAF1 111031 120 + 1
UUGAAUAAUGGUCAAAGAUUAUCAAUUAAGCCGUUGGCCAAAUUAAUAGUUGGUCGACUAAAAGGACCACGCCCUCGAAACCAAUGCCUCUAGGACAUGGAGUCCUGCACGGCUGUGCUA
((((.((((........))))))))...(((((((((((((........)))))))))....(((((..((....))...(((.((((....)).))))).)))))....))))...... ( -30.50)
>consensus
UUAAAUAAUGGUCAAAGAUUAUCAAUUAAGCCGUUGGCCAAAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAAACCAAUGCCUCUAGGACAUGGAGUCCUGCACGGCUGUGCUA
.......((((((...))))))......(((((((((((((........)))))))))....(((((..((.((((((..........))))))...))..)))))....))))...... (-31.24 = -31.64 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	13,122,908 – 13,123,028
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.67
Mean single sequence MFE	-41.92
Consensus MFE	-39.98
Energy contribution	-40.74
Covariance contribution	0.76
Combinations/Pair	1.10
Mean z-score	-3.70
Structure conservation index	0.95
SVM decision value	5.28
SVM RNA-class probability	0.999982
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13122908 120 - 23771897
UAGCACAGCCAUGCAGGACUCCAUGUCCAGGAGGCAUUGGUAUCUAGGGCGUGGUCCUUUUAGUCGGCCAACUAUUAAUUUGGCCAACGGCUUAAUUGAUAAUCUUGGACCAUUAUUUAA
..(((......)))((((..((((((((.(((.((....)).))).)))))))))))).......((((((.((((((((.((((...)))).))))))))...)))).))......... ( -38.10)
>DroSec_CAF1 110803 120 - 1
UAGCACAGCCGUGCAGGACUCCAUGUCCUAGAGGCAUUGGUUUCUAGGGCGUGGUCCUUUUAGUCGGCCAACUAUUAAUUUGGCCAACGGCUUAAUUGAUAAUCUUUGACCAUUAUUUAA
......((((((..((((..(((((((((((((((....))))))))))))))))))).......((((((........)))))).))))))............................ ( -46.00)
>DroSim_CAF1 108981 120 - 1
UAGCACAGCCGUGCAGGACUCCAUGUCCUAGAGGCAUUGGUUUCUAGGGCGUGGUCCUUUUAGUCGGCCAACUAUUAAUUUGGCCAACGGCUUAAUUGAUAAUCUUUGACCAUUAUUUAA
......((((((..((((..(((((((((((((((....))))))))))))))))))).......((((((........)))))).))))))............................ ( -46.00)
>DroEre_CAF1 107513 120 - 1
UAGCACAGCCGUGCAGGACUUCAUGUCCUAGAGGCAUUGCUUUCUGGGGCGUGGCCCUUUUAGUCGACCAACUAUUAAUUUGGCCAACGGCUUAAUUGAUAAUCUUUGACCAUUAUUCAA
..((((....))))(((...(((((((((((((((...)).))))))))))))).)))....(((((.....((((((((.((((...)))).))))))))....))))).......... ( -38.30)
>DroYak_CAF1 111031 120 - 1
UAGCACAGCCGUGCAGGACUCCAUGUCCUAGAGGCAUUGGUUUCGAGGGCGUGGUCCUUUUAGUCGACCAACUAUUAAUUUGGCCAACGGCUUAAUUGAUAAUCUUUGACCAUUAUUCAA
..((((....))))((((..(((((((((.(((((....))))).)))))))))))))....(((((.....((((((((.((((...)))).))))))))....))))).......... ( -41.20)
>consensus
UAGCACAGCCGUGCAGGACUCCAUGUCCUAGAGGCAUUGGUUUCUAGGGCGUGGUCCUUUUAGUCGGCCAACUAUUAAUUUGGCCAACGGCUUAAUUGAUAAUCUUUGACCAUUAUUUAA
..((((....))))((((..(((((((((((((((....)))))))))))))))))))....(((((.....((((((((.((((...)))).))))))))....))))).......... (-39.98 = -40.74 +   0.76)

alignment

secondary structure

dotplot

Window 8

Location	13,122,948 – 13,123,068
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.83
Mean single sequence MFE	-27.99
Consensus MFE	-23.68
Energy contribution	-23.44
Covariance contribution	-0.24
Combinations/Pair	1.14
Mean z-score	-1.53
Structure conservation index	0.85
SVM decision value	0.67
SVM RNA-class probability	0.817457
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13122948 120 + 23771897
AAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAUACCAAUGCCUCCUGGACAUGGAGUCCUGCAUGGCUGUGCUAUCAUUAUUGUCCUCAUUAUGGCAUUAAAAUUAUUUAAUUA
(((((((((((.((((......(((((.........((((.((..(((....((((.....)))).....)))..)).))))......))))).....)))).....))))).)))))). ( -26.46)
>DroSec_CAF1 110843 120 + 1
AAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAAACCAAUGCCUCUAGGACAUGGAGUCCUGCACGGCUGUGCUAUCAUUAUUGUCCUCAUUAUGACAUUAAAAUUAUUUAAUUA
((((((((((((((((......(((((..((.((((((..........))))))...))..)))))...)))))).))))...(((.((((........)))).)))......)))))). ( -28.80)
>DroSim_CAF1 109021 120 + 1
AAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAAACCAAUGCCUCUAGGACAUGGAGUCCUGCACGGCUGUGCUAUCAUUAUUGUCCUCAUUAUGGCAUUAAAAUUAUUUAAUUA
((((((((((((((((......(((((..((.((((((..........))))))...))..)))))...)))))(((((((.((..........)).)))))))...))))).)))))). ( -28.60)
>DroEre_CAF1 107553 120 + 1
AAUUAAUAGUUGGUCGACUAAAAGGGCCACGCCCCAGAAAGCAAUGCCUCUAGGACAUGAAGUCCUGCACGGCUGUGCUAUCAUUACUGUUCUCAUUAUAGCAUUAAAAUUAUUUAAUUA
(((((((((((....)))))...((((...))))..((.((((..(((..((((((.....))))))...)))..)))).)).(((.((((........)))).)))......)))))). ( -28.30)
>DroYak_CAF1 111071 120 + 1
AAUUAAUAGUUGGUCGACUAAAAGGACCACGCCCUCGAAACCAAUGCCUCUAGGACAUGGAGUCCUGCACGGCUGUGCUAUCAUUAUUGUCCUCAUCAUGGCAUUAAAAUUAUUUAAUUA
(((((((((((((((.........))))..............((((((...((((((.........((((....)))).........))))))......))))))..))))).)))))). ( -27.77)
>consensus
AAUUAAUAGUUGGCCGACUAAAAGGACCACGCCCUAGAAACCAAUGCCUCUAGGACAUGGAGUCCUGCACGGCUGUGCUAUCAUUAUUGUCCUCAUUAUGGCAUUAAAAUUAUUUAAUUA
((((((((((((((((......(((((..((.((((((..........))))))...))..)))))...)))))).))))...(((.((((........)))).)))......)))))). (-23.68 = -23.44 +  -0.24)

alignment

secondary structure

dotplot

Window 9

Location	13,122,948 – 13,123,068
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.83
Mean single sequence MFE	-34.96
Consensus MFE	-31.38
Energy contribution	-32.38
Covariance contribution	1.00
Combinations/Pair	1.09
Mean z-score	-2.59
Structure conservation index	0.90
SVM decision value	3.86
SVM RNA-class probability	0.999664
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13122948 120 - 23771897
UAAUUAAAUAAUUUUAAUGCCAUAAUGAGGACAAUAAUGAUAGCACAGCCAUGCAGGACUCCAUGUCCAGGAGGCAUUGGUAUCUAGGGCGUGGUCCUUUUAGUCGGCCAACUAUUAAUU
..((((((....))))))(((((...((((((..........(((......))).......(((((((.(((.((....)).))).)))))))))))))...)).)))............ ( -29.90)
>DroSec_CAF1 110843 120 - 1
UAAUUAAAUAAUUUUAAUGUCAUAAUGAGGACAAUAAUGAUAGCACAGCCGUGCAGGACUCCAUGUCCUAGAGGCAUUGGUUUCUAGGGCGUGGUCCUUUUAGUCGGCCAACUAUUAAUU
.............(((.((((........)))).)))((((((....((((.((((((..(((((((((((((((....)))))))))))))))))))....))))))...))))))... ( -40.50)
>DroSim_CAF1 109021 120 - 1
UAAUUAAAUAAUUUUAAUGCCAUAAUGAGGACAAUAAUGAUAGCACAGCCGUGCAGGACUCCAUGUCCUAGAGGCAUUGGUUUCUAGGGCGUGGUCCUUUUAGUCGGCCAACUAUUAAUU
..((((((....))))))(((((...((((((..........((((....)))).......((((((((((((((....))))))))))))))))))))...)).)))............ ( -40.60)
>DroEre_CAF1 107553 120 - 1
UAAUUAAAUAAUUUUAAUGCUAUAAUGAGAACAGUAAUGAUAGCACAGCCGUGCAGGACUUCAUGUCCUAGAGGCAUUGCUUUCUGGGGCGUGGCCCUUUUAGUCGACCAACUAUUAAUU
..((((((....))))))((((.....((((.(((((((...((((....))))(((((.....))))).....)))))))))))(((((...)))))..))))................ ( -30.60)
>DroYak_CAF1 111071 120 - 1
UAAUUAAAUAAUUUUAAUGCCAUGAUGAGGACAAUAAUGAUAGCACAGCCGUGCAGGACUCCAUGUCCUAGAGGCAUUGGUUUCGAGGGCGUGGUCCUUUUAGUCGACCAACUAUUAAUU
..((((((....))))))....((((((((((..........((((....)))).......((((((((.(((((....))))).))))))))))))))...)))).............. ( -33.20)
>consensus
UAAUUAAAUAAUUUUAAUGCCAUAAUGAGGACAAUAAUGAUAGCACAGCCGUGCAGGACUCCAUGUCCUAGAGGCAUUGGUUUCUAGGGCGUGGUCCUUUUAGUCGGCCAACUAUUAAUU
..((((((....))))))...........(((..........((((....))))((((..(((((((((((((((....)))))))))))))))))))....)))............... (-31.38 = -32.38 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:20 2006