Locus 3346

Sequence ID	3R_DroMel_CAF1
Location	9,012,004 – 9,012,164
Length	160
Max. P	0.989760

overview

Window 7

Location	9,012,004 – 9,012,124
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.67
Mean single sequence MFE	-32.87
Consensus MFE	-22.50
Energy contribution	-24.50
Covariance contribution	2.00
Combinations/Pair	1.11
Mean z-score	-3.55
Structure conservation index	0.68
SVM decision value	1.42
SVM RNA-class probability	0.951872
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9012004 120 + 27905053
CUGGACAAAAGCCUCUGGCUUACCAGCCUCCACAUAAACUUGCACUUUAUCCAGUGCAUUGGCUAUGAAAUCAUCGUUUGAUAGCUCAUUCCGCUCCUGCUGGCUUUCGUCCUCUAUUUC
..((((.((((((...((((....))))............((((((......))))))..((((((.((((....)))).))))))......((....)).)))))).))))........ ( -35.00)
>DroSec_CAF1 125979 120 + 1
CUGGACAAAAGCGUCUGGCUUACCAGCCUGCACAUAAACUUGCACUUUAUCCAGUGCAUUGGCUAUGAAAUCAUCAUUUGAUAGCUCCUUCCGCUCCUGCUGGCUUUCGUCCUUUAUUUC
..((((..((((.....)))).(((((..((.........((((((......))))))..((((((.((((....)))).))))))......))....))))).....))))........ ( -34.20)
>DroSim_CAF1 129219 120 + 1
CUGGACAAAAGCCUCUGGCUUACCAGCCUGCACAUAAACUUGCACUUUAUCCAGUGCAUUGGCUAUGAAAUCAUCAUUUGAUAGCUCCUUCCGCUCCUGCUGGCUUUCGUCCUUUAUUUC
..((((.((((((...((((....)))).(((........((((((......))))))..((((((.((((....)))).))))))...........))).)))))).))))........ ( -36.40)
>DroEre_CAF1 132018 120 + 1
CUGGACAAAAGCCUCCGUCUUACCAGCCUCCACAUAGACUUGCACAUUAUCCAGAGCCUUGGCUAUGCCCCUUUCCUUCGAUGGCUCCUUCUGAUCCUGCUGGCUUUCGUCCUUUAUUUC
..((((.((((((...((((...............))))..(((.((((....(((((..(((...)))....((....)).)))))....))))..))).)))))).))))........ ( -27.96)
>DroYak_CAF1 137310 120 + 1
CUGGACAAAAGCCUCUGGCUUACCAGCCUCGACAUAGACUUGCACAUUAUCCAGGGCCUUGGCUAUGUUCCUUUCUUUCGAUAGAUCCCUCUGAUCCUGUUGGCUUUCGUCCUUUAUUUC
..((((.((((((...((((....))))..(((((((.((.((.(........).))...)))))))))..........((((((((.....))).))))))))))).))))........ ( -30.80)
>consensus
CUGGACAAAAGCCUCUGGCUUACCAGCCUCCACAUAAACUUGCACUUUAUCCAGUGCAUUGGCUAUGAAAUCAUCAUUUGAUAGCUCCUUCCGCUCCUGCUGGCUUUCGUCCUUUAUUUC
..((((..((((.....)))).(((((..............((((........))))...((((((.((((....)))).))))))............))))).....))))........ (-22.50 = -24.50 +   2.00)

alignment

secondary structure

dotplot

Window 8

Location	9,012,004 – 9,012,124
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.67
Mean single sequence MFE	-45.34
Consensus MFE	-31.04
Energy contribution	-34.32
Covariance contribution	3.28
Combinations/Pair	1.09
Mean z-score	-5.25
Structure conservation index	0.68
SVM decision value	2.07
SVM RNA-class probability	0.987265
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9012004 120 - 27905053
GAAAUAGAGGACGAAAGCCAGCAGGAGCGGAAUGAGCUAUCAAACGAUGAUUUCAUAGCCAAUGCACUGGAUAAAGUGCAAGUUUAUGUGGAGGCUGGUAAGCCAGAGGCUUUUGUCCAG
........(((((((((((.(((.((((((.(((((.((((....))))..)))))..))..((((((......)))))).)))).)))...((((....))))...))))))))))).. ( -46.30)
>DroSec_CAF1 125979 120 - 1
GAAAUAAAGGACGAAAGCCAGCAGGAGCGGAAGGAGCUAUCAAAUGAUGAUUUCAUAGCCAAUGCACUGGAUAAAGUGCAAGUUUAUGUGCAGGCUGGUAAGCCAGACGCUUUUGUCCAG
........((((((((((..(((.((((((..((((.((((....)))).))))....))..((((((......)))))).))))...))).((((....))))....)))))))))).. ( -43.20)
>DroSim_CAF1 129219 120 - 1
GAAAUAAAGGACGAAAGCCAGCAGGAGCGGAAGGAGCUAUCAAAUGAUGAUUUCAUAGCCAAUGCACUGGAUAAAGUGCAAGUUUAUGUGCAGGCUGGUAAGCCAGAGGCUUUUGUCCAG
........(((((((((((.(((.((((((..((((.((((....)))).))))....))..((((((......)))))).))))...))).((((....))))...))))))))))).. ( -47.30)
>DroEre_CAF1 132018 120 - 1
GAAAUAAAGGACGAAAGCCAGCAGGAUCAGAAGGAGCCAUCGAAGGAAAGGGGCAUAGCCAAGGCUCUGGAUAAUGUGCAAGUCUAUGUGGAGGCUGGUAAGACGGAGGCUUUUGUCCAG
........(((((((((((.(((..(((....((((((.((....))....(((...)))..)))))).)))..)))((.(((((......))))).))........))))))))))).. ( -46.70)
>DroYak_CAF1 137310 120 - 1
GAAAUAAAGGACGAAAGCCAACAGGAUCAGAGGGAUCUAUCGAAAGAAAGGAACAUAGCCAAGGCCCUGGAUAAUGUGCAAGUCUAUGUCGAGGCUGGUAAGCCAGAGGCUUUUGUCCAG
........(((((((((((.(((..(((..((((.(((.((....))..((.......)).))))))).)))..)))...............((((....))))...))))))))))).. ( -43.20)
>consensus
GAAAUAAAGGACGAAAGCCAGCAGGAGCGGAAGGAGCUAUCAAAUGAUGAUUUCAUAGCCAAUGCACUGGAUAAAGUGCAAGUUUAUGUGGAGGCUGGUAAGCCAGAGGCUUUUGUCCAG
........(((((((((((.(((.((((....((((.((((....)))).)))).........(((((......)))))..)))).)))...((((....))))...))))))))))).. (-31.04 = -34.32 +   3.28)

alignment

secondary structure

dotplot

Window 9

Location	9,012,044 – 9,012,164
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.00
Mean single sequence MFE	-31.12
Consensus MFE	-26.23
Energy contribution	-28.23
Covariance contribution	2.00
Combinations/Pair	1.09
Mean z-score	-3.13
Structure conservation index	0.84
SVM decision value	2.18
SVM RNA-class probability	0.989760
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9012044 120 + 27905053
UGCACUUUAUCCAGUGCAUUGGCUAUGAAAUCAUCGUUUGAUAGCUCAUUCCGCUCCUGCUGGCUUUCGUCCUCUAUUUCCUGUGCCAGCAACUGCUGAAGCUUGAUCAUUUGCUCCUUG
((((((......))))))..((((((.((((....)))).))))))..(((.((...(((((((....................)))))))...)).)))((..........))...... ( -30.95)
>DroSec_CAF1 126019 120 + 1
UGCACUUUAUCCAGUGCAUUGGCUAUGAAAUCAUCAUUUGAUAGCUCCUUCCGCUCCUGCUGGCUUUCGUCCUUUAUUUCCUCUGCCAGCAACUGCUGAAGCUUGAUAAUUUGCUCCUUA
.(((..(((((.((......((((((.((((....)))).)))))).((((.((...(((((((....................)))))))...)).)))))).)))))..)))...... ( -34.05)
>DroSim_CAF1 129259 120 + 1
UGCACUUUAUCCAGUGCAUUGGCUAUGAAAUCAUCAUUUGAUAGCUCCUUCCGCUCCUGCUGGCUUUCGUCCUUUAUUUCCUCUGCCAGCAACUGCUGAAGCUUGAUAAUUUGCUCCUUA
.(((..(((((.((......((((((.((((....)))).)))))).((((.((...(((((((....................)))))))...)).)))))).)))))..)))...... ( -34.05)
>DroEre_CAF1 132058 120 + 1
UGCACAUUAUCCAGAGCCUUGGCUAUGCCCCUUUCCUUCGAUGGCUCCUUCUGAUCCUGCUGGCUUUCGUCCUUUAUUUCCUCUGCCAGUAACUGCUGAAGCUUUAGCAUCUGCUCCUUA
.............((((....((((.(((....((....)).)))..((((.(....(((((((....................)))))))....).))))...))))....)))).... ( -25.45)
>consensus
UGCACUUUAUCCAGUGCAUUGGCUAUGAAAUCAUCAUUUGAUAGCUCCUUCCGCUCCUGCUGGCUUUCGUCCUUUAUUUCCUCUGCCAGCAACUGCUGAAGCUUGAUAAUUUGCUCCUUA
.(((..(((((.((......((((((.((((....)))).)))))).((((.((...(((((((....................)))))))...)).)))))).)))))..)))...... (-26.23 = -28.23 +   2.00)

alignment

secondary structure

dotplot

Window 0

Location	9,012,044 – 9,012,164
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.00
Mean single sequence MFE	-35.44
Consensus MFE	-24.45
Energy contribution	-25.88
Covariance contribution	1.44
Combinations/Pair	1.07
Mean z-score	-3.12
Structure conservation index	0.69
SVM decision value	0.59
SVM RNA-class probability	0.791967
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9012044 120 - 27905053
CAAGGAGCAAAUGAUCAAGCUUCAGCAGUUGCUGGCACAGGAAAUAGAGGACGAAAGCCAGCAGGAGCGGAAUGAGCUAUCAAACGAUGAUUUCAUAGCCAAUGCACUGGAUAAAGUGCA
...(((((..........))))).((..((((((((....................))))))))..))((.(((((.((((....))))..)))))..))..((((((......)))))) ( -33.95)
>DroSec_CAF1 126019 120 - 1
UAAGGAGCAAAUUAUCAAGCUUCAGCAGUUGCUGGCAGAGGAAAUAAAGGACGAAAGCCAGCAGGAGCGGAAGGAGCUAUCAAAUGAUGAUUUCAUAGCCAAUGCACUGGAUAAAGUGCA
...((...(((((((((((((((.((..((((((((....................))))))))..))....))))))......))))))))).....))..((((((......)))))) ( -36.95)
>DroSim_CAF1 129259 120 - 1
UAAGGAGCAAAUUAUCAAGCUUCAGCAGUUGCUGGCAGAGGAAAUAAAGGACGAAAGCCAGCAGGAGCGGAAGGAGCUAUCAAAUGAUGAUUUCAUAGCCAAUGCACUGGAUAAAGUGCA
...((...(((((((((((((((.((..((((((((....................))))))))..))....))))))......))))))))).....))..((((((......)))))) ( -36.95)
>DroEre_CAF1 132058 120 - 1
UAAGGAGCAGAUGCUAAAGCUUCAGCAGUUACUGGCAGAGGAAAUAAAGGACGAAAGCCAGCAGGAUCAGAAGGAGCCAUCGAAGGAAAGGGGCAUAGCCAAGGCUCUGGAUAAUGUGCA
......(((.(((((....((((.((........)).)))).......((.(....))))))...(((....((((((.((....))....(((...)))..)))))).))).)).))). ( -33.90)
>consensus
UAAGGAGCAAAUGAUCAAGCUUCAGCAGUUGCUGGCAGAGGAAAUAAAGGACGAAAGCCAGCAGGAGCGGAAGGAGCUAUCAAAUGAUGAUUUCAUAGCCAAUGCACUGGAUAAAGUGCA
...((........((((((((((.((..((((((((....................))))))))..))....)))))).((....)))))).......))...(((((......))))). (-24.45 = -25.88 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:56 2006