Locus 4248

Sequence ID	3R_DroMel_CAF1
Location	11,385,011 – 11,385,163
Length	152
Max. P	0.990715

overview

Window 4

Location	11,385,011 – 11,385,125
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.91
Mean single sequence MFE	-32.68
Consensus MFE	-31.28
Energy contribution	-31.32
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.71
Structure conservation index	0.96
SVM decision value	2.23
SVM RNA-class probability	0.990715
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11385011 114 + 27905053
------UGCCAAACUUAAUGAAAGGGCCGGCUGAAACGUGUAAAGUGCUUUUGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAA
------...((.((((.......((((((((........))..(((((((.(((.((((......))))))).))))))).........))))))...((((....)))))))).))... ( -31.90)
>DroSec_CAF1 132720 114 + 1
------UGCCAAACUUAAUGAAAGGGCCGGCUGAAACGUGUAAAGUGCUUUUGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAA
------...((.((((.......((((((((........))..(((((((.(((.((((......))))))).))))))).........))))))...((((....)))))))).))... ( -31.90)
>DroSim_CAF1 123842 114 + 1
------UGCCAAACUUAAUGAAAGGGCCGGCUGAAACGUGUAAAGUGCUUUUGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAA
------...((.((((.......((((((((........))..(((((((.(((.((((......))))))).))))))).........))))))...((((....)))))))).))... ( -31.90)
>DroEre_CAF1 120154 114 + 1
------UGCCAAACCUAAUGAAAGGGCCGGCUGAAACGUGUAAAGUGCUUUCGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAA
------.......(((((((...((((((((........))..(((((((..((.((((......))))))..))))))).........))))))..)))))))................ ( -31.10)
>DroYak_CAF1 123436 120 + 1
UGCCUAUGCCAAACUUAAUGAAGGGGCCGGCUGAAACGUGUAAAGUGCUUUUGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAA
....(((((.............(((((((((........))..(((((((.(((.((((......))))))).))))))).........))))))).(((((....))))).)))))... ( -36.60)
>consensus
______UGCCAAACUUAAUGAAAGGGCCGGCUGAAACGUGUAAAGUGCUUUUGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAA
.............(((((((...((((((((........))..(((((((.(((.((((......))))))).))))))).........))))))..)))))))................ (-31.28 = -31.32 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	11,385,011 – 11,385,125
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.91
Mean single sequence MFE	-29.06
Consensus MFE	-28.10
Energy contribution	-27.62
Covariance contribution	-0.48
Combinations/Pair	1.10
Mean z-score	-1.66
Structure conservation index	0.97
SVM decision value	2.18
SVM RNA-class probability	0.989701
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11385011 114 - 27905053
UUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCAAAAGCACUUUACACGUUUCAGCCGGCCCUUUCAUUAAGUUUGGCA------
..(((.((((((((....))))..((((((............(((((.((((((........))).))).)))))........((....)).))))))......)))).)))..------ ( -27.30)
>DroSec_CAF1 132720 114 - 1
UUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCAAAAGCACUUUACACGUUUCAGCCGGCCCUUUCAUUAAGUUUGGCA------
..(((.((((((((....))))..((((((............(((((.((((((........))).))).)))))........((....)).))))))......)))).)))..------ ( -27.30)
>DroSim_CAF1 123842 114 - 1
UUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCAAAAGCACUUUACACGUUUCAGCCGGCCCUUUCAUUAAGUUUGGCA------
..(((.((((((((....))))..((((((............(((((.((((((........))).))).)))))........((....)).))))))......)))).)))..------ ( -27.30)
>DroEre_CAF1 120154 114 - 1
UUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCGAAAGCACUUUACACGUUUCAGCCGGCCCUUUCAUUAGGUUUGGCA------
.........(((((..(((((...((((((............(((((.((((((........))).))).)))))........((....)).))))))....)))))..)))))------ ( -32.90)
>DroYak_CAF1 123436 120 - 1
UUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCAAAAGCACUUUACACGUUUCAGCCGGCCCCUUCAUUAAGUUUGGCAUAGGCA
...((.((((((((....))))..((((((............(((((.((((((........))).))).)))))........((....)).))))))......)))).))((....)). ( -30.50)
>consensus
UUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCAAAAGCACUUUACACGUUUCAGCCGGCCCUUUCAUUAAGUUUGGCA______
..(((.((((((((....))))..((((((............(((((.((((((........))).))).)))))........((....)).))))))......)))).)))........ (-28.10 = -27.62 +  -0.48)

alignment

secondary structure

dotplot

Window 6

Location	11,385,045 – 11,385,163
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.31
Mean single sequence MFE	-35.12
Consensus MFE	-32.34
Energy contribution	-33.14
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.13
Structure conservation index	0.92
SVM decision value	0.01
SVM RNA-class probability	0.537047
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11385045 118 + 27905053
UAAAGUGCUUUUGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAAUGGGCGGCAUUUGCCGGCUAGUCCAUCGUGAUGUAAUG--
...(((((((.(((.((((......))))))).)))))))...((((..(((((((......)))...............(((.((((....)))).)))).))))))).........-- ( -34.70)
>DroSec_CAF1 132754 120 + 1
UAAAGUGCUUUUGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAAUGGGCGGCAUUUGCUGGCUAGUCCAGCGUGAUGUAAUAGC
...(((((((.(((.((((......))))))).)))))))......(((((.((((((((((....))))).........)))).).)))))(((((.....)))))............. ( -35.80)
>DroSim_CAF1 123876 120 + 1
UAAAGUGCUUUUGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAAUGGGCGGCAUUUGCUGGCUAGUCCAGCGUGAUGUAAUAGC
...(((((((.(((.((((......))))))).)))))))......(((((.((((((((((....))))).........)))).).)))))(((((.....)))))............. ( -35.80)
>DroEre_CAF1 120188 118 + 1
UAAAGUGCUUUCGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAAUGGGCGGCAUUUGCUGGCUAGUACAGCGUGAUGUGAUG--
....(((((.(((((....))))).))...)))..(((((((....(((((.((((((((((....))))).........)))).).)))))((((.......)))))))))))....-- ( -32.80)
>DroYak_CAF1 123476 118 + 1
UAAAGUGCUUUUGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAAUGGGCGGCAUUUGCUGGCUAGCCCAGCGUGAUGUGAUG--
...(((((((.(((.((((......))))))).)))))))........((.((..((((((.(((....((....))...(((.((((....)))).))).)))))))))..)).)).-- ( -36.50)
>consensus
UAAAGUGCUUUUGGUGUCUGCCGAUGGACCCACAAGCAUUAUAAUGAAAUGGCCCCAUGUUAGGGAUAACAAGUAUGAAAUGGGCGGCAUUUGCUGGCUAGUCCAGCGUGAUGUAAUG__
...(((((((.(((.((((......))))))).)))))))......(((((.((((((((((....))))).........)))).).)))))(((((.....)))))............. (-32.34 = -33.14 +   0.80)

alignment

secondary structure

dotplot

Window 7

Location	11,385,045 – 11,385,163
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.31
Mean single sequence MFE	-29.42
Consensus MFE	-26.94
Energy contribution	-27.02
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.65
Structure conservation index	0.92
SVM decision value	1.72
SVM RNA-class probability	0.974078
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11385045 118 - 27905053
--CAUUACAUCACGAUGGACUAGCCGGCAAAUGCCGCCCAUUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCAAAAGCACUUUA
--..........((((((((((((.(((....)))((((..........(((((....)))))..))))..............)))....)))))))))..................... ( -29.50)
>DroSec_CAF1 132754 120 - 1
GCUAUUACAUCACGCUGGACUAGCCAGCAAAUGCCGCCCAUUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCAAAAGCACUUUA
(((..........(((((.....)))))...(((((.............(((((....)))))((((.((((..(((....)))...)))).)))).))))).........)))...... ( -31.60)
>DroSim_CAF1 123876 120 - 1
GCUAUUACAUCACGCUGGACUAGCCAGCAAAUGCCGCCCAUUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCAAAAGCACUUUA
(((..........(((((.....)))))...(((((.............(((((....)))))((((.((((..(((....)))...)))).)))).))))).........)))...... ( -31.60)
>DroEre_CAF1 120188 118 - 1
--CAUCACAUCACGCUGUACUAGCCAGCAAAUGCCGCCCAUUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCGAAAGCACUUUA
--.......((..((((.......))))...(((((.............(((((....)))))((((.((((..(((....)))...)))).)))).)))))......)).......... ( -25.00)
>DroYak_CAF1 123476 118 - 1
--CAUCACAUCACGCUGGGCUAGCCAGCAAAUGCCGCCCAUUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCAAAAGCACUUUA
--...........(((((.....)))))(((((..((((..........(((((....)))))..)))))))))........(((((.((((((........))).))).)))))..... ( -29.40)
>consensus
__CAUUACAUCACGCUGGACUAGCCAGCAAAUGCCGCCCAUUUCAUACUUGUUAUCCCUAACAUGGGGCCAUUUCAUUAUAAUGCUUGUGGGUCCAUCGGCAGACACCAAAAGCACUUUA
.............(((((.....)))))(((((..((((..........(((((....)))))..)))))))))........(((((.((((((........))).))).)))))..... (-26.94 = -27.02 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:29 2006