Locus 2220

Sequence ID	X_DroMel_CAF1
Location	5,988,915 – 5,989,067
Length	152
Max. P	0.992355

overview

Window 1

Location	5,988,915 – 5,989,027
Length	112
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	87.68
Mean single sequence MFE	-29.08
Consensus MFE	-23.69
Energy contribution	-24.92
Covariance contribution	1.23
Combinations/Pair	1.03
Mean z-score	-2.06
Structure conservation index	0.81
SVM decision value	1.36
SVM RNA-class probability	0.946096
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5988915 112 + 22224390
AAGUUGAACUUAAAUUAGUUUAGCCAAAGCUGUUUGAUUGCUUCUCGUACCGAACUGAAAUGCAACCAGGGCCAAGUUGCACCGCAGCCCAGCCACAAAAUCACUUUGGCUC
....((((((......))))))(((((((...((((.((((...(((........)))...))))....(((...(((((...)))))...))).))))....))))))).. ( -28.60)
>DroSec_CAF1 4033 112 + 1
AAGUUGAACUCAAAUUAGUUUAGCCAAAGCUGUUUGAUUGCUUCUCGUACCGAACUAAAAUGCAACCAGGGCAAAGUUGCACCGCAGCCCAGCCACAAAAUCACUUUGGCUC
....((((((......))))))((((((((((.((((((.....(((...))).....))).))).)))(((...(((((...)))))...))).........))))))).. ( -26.80)
>DroSim_CAF1 5655 112 + 1
AAGUUGAACUUAAAUUAGUUUAGCCAAAGCUGUUUGAUUGCUUCUCGUACCGAACUGAAAUGCAACCAGGGCAAAGUUGCACCGCAGCCCAGCCACAAAAUCACUUUGGCUC
....((((((......))))))(((((((...((((.((((...(((........)))...))))....(((...(((((...)))))...))).))))....))))))).. ( -28.60)
>DroEre_CAF1 3887 90 + 1
AAGUUGCACUUAAAUUAGUUUAGCCAAAGCAGUUUGAUU----------------------GCAACCAGGGCGAAGUUGCACCGCAGCCCAGCCACAAAAUCGCUGCGGCUG
..((((((.(((((((.((((.....))))))))))).)----------------------)))))..(((((....))).)).(((((((((.........)))).))))) ( -30.20)
>DroYak_CAF1 6018 112 + 1
AAGUUGAACUUAAAUUAGUUUAGCCAAAGCAGUUUGAUUGCUUCUCAUACCAAAUUGAAAUGCAACCAGGGCGAAGUUGCACCGCAGCCCAGCCACAAAAUCACUUUGGCUC
....((((((......))))))(((((((...((((.((((...(((........)))...))))....(((...(((((...)))))...))).))))....))))))).. ( -31.20)
>consensus
AAGUUGAACUUAAAUUAGUUUAGCCAAAGCUGUUUGAUUGCUUCUCGUACCGAACUGAAAUGCAACCAGGGCAAAGUUGCACCGCAGCCCAGCCACAAAAUCACUUUGGCUC
....((((((......))))))(((((((...((((.((((...(((........)))...))))....(((...(((((...)))))...))).))))....))))))).. (-23.69 = -24.92 +   1.23)

alignment

secondary structure

dotplot

Window 2

Location	5,988,915 – 5,989,027
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	87.68
Mean single sequence MFE	-35.90
Consensus MFE	-29.40
Energy contribution	-29.62
Covariance contribution	0.22
Combinations/Pair	1.13
Mean z-score	-2.56
Structure conservation index	0.82
SVM decision value	2.32
SVM RNA-class probability	0.992355
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5988915 112 - 22224390
GAGCCAAAGUGAUUUUGUGGCUGGGCUGCGGUGCAACUUGGCCCUGGUUGCAUUUCAGUUCGGUACGAGAAGCAAUCAAACAGCUUUGGCUAAACUAAUUUAAGUUCAACUU
.(((((((((..(((((((.((((((((..((((((((.......))))))))..))))))))))))))).(........).))))))))).((((......))))...... ( -39.70)
>DroSec_CAF1 4033 112 - 1
GAGCCAAAGUGAUUUUGUGGCUGGGCUGCGGUGCAACUUUGCCCUGGUUGCAUUUUAGUUCGGUACGAGAAGCAAUCAAACAGCUUUGGCUAAACUAAUUUGAGUUCAACUU
.(((((((((..(((((((.((((((((..((((((((.......))))))))..))))))))))))))).(........).))))))))).((((......))))...... ( -38.10)
>DroSim_CAF1 5655 112 - 1
GAGCCAAAGUGAUUUUGUGGCUGGGCUGCGGUGCAACUUUGCCCUGGUUGCAUUUCAGUUCGGUACGAGAAGCAAUCAAACAGCUUUGGCUAAACUAAUUUAAGUUCAACUU
.(((((((((..(((((((.((((((((..((((((((.......))))))))..))))))))))))))).(........).))))))))).((((......))))...... ( -39.70)
>DroEre_CAF1 3887 90 - 1
CAGCCGCAGCGAUUUUGUGGCUGGGCUGCGGUGCAACUUCGCCCUGGUUGC----------------------AAUCAAACUGCUUUGGCUAAACUAAUUUAAGUGCAACUU
.(((((.((((...(((..((..((..((((.......))))))..))..)----------------------))......)))).)))))..................... ( -27.90)
>DroYak_CAF1 6018 112 - 1
GAGCCAAAGUGAUUUUGUGGCUGGGCUGCGGUGCAACUUCGCCCUGGUUGCAUUUCAAUUUGGUAUGAGAAGCAAUCAAACUGCUUUGGCUAAACUAAUUUAAGUUCAACUU
.(((((((((((...((..((..((..((((.......))))))..))..))..)).....(((.(((.......))).)))))))))))).((((......))))...... ( -34.10)
>consensus
GAGCCAAAGUGAUUUUGUGGCUGGGCUGCGGUGCAACUUCGCCCUGGUUGCAUUUCAGUUCGGUACGAGAAGCAAUCAAACAGCUUUGGCUAAACUAAUUUAAGUUCAACUU
.(((((((((........(((..((.(((...))).))..))).(((((((.((((.((.....)))))).)))))))....)))))))))..................... (-29.40 = -29.62 +   0.22)

alignment

secondary structure

dotplot

Window 3

Location	5,988,947 – 5,989,067
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.89
Mean single sequence MFE	-39.35
Consensus MFE	-35.29
Energy contribution	-35.85
Covariance contribution	0.56
Combinations/Pair	1.13
Mean z-score	-2.05
Structure conservation index	0.90
SVM decision value	1.21
SVM RNA-class probability	0.931605
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5988947 120 - 22224390
AAAGUGUGGUUGAGUCGAGUCGAGUUGAACUGUAAGCUGGGAGCCAAAGUGAUUUUGUGGCUGGGCUGCGGUGCAACUUGGCCCUGGUUGCAUUUCAGUUCGGUACGAGAAGCAAUCAAA
......((((((..(((..((((..((((.(((((.(..((.(((((..((...(((..((...))..)))..))..)))))))..)))))).))))..))))..)))....)))))).. ( -45.20)
>DroSec_CAF1 4065 120 - 1
AAAGUGUGGUUGAGUCGAGUCGAGUUGAACUGUAAGCUGGGAGCCAAAGUGAUUUUGUGGCUGGGCUGCGGUGCAACUUUGCCCUGGUUGCAUUUUAGUUCGGUACGAGAAGCAAUCAAA
......((((((..(((..((((..((((.(((((.(..((.((.(((((....(((..((...))..)))....)))))))))..)))))).))))..))))..)))....)))))).. ( -39.70)
>DroSim_CAF1 5687 120 - 1
AAAGUGUGGUCGAGUCGAGUCGAGUUGAACUGUAAGCUGGGAGCCAAAGUGAUUUUGUGGCUGGGCUGCGGUGCAACUUUGCCCUGGUUGCAUUUCAGUUCGGUACGAGAAGCAAUCAAA
....((..(((((.(((...))).))).))..)).(((((...)).......(((((((.((((((((..((((((((.......))))))))..))))))))))))))))))....... ( -38.50)
>DroYak_CAF1 6050 116 - 1
AAAGUGUGGUUG----GAAUUGAGUGGAAGUGUAAGCUGGGAGCCAAAGUGAUUUUGUGGCUGGGCUGCGGUGCAACUUCGCCCUGGUUGCAUUUCAAUUUGGUAUGAGAAGCAAUCAAA
....(((..((.----(.((..(((.(((((((((.(..((.((..((((....(((..((...))..)))....)))).))))..)))))))))).)))..)).).))..)))...... ( -34.00)
>consensus
AAAGUGUGGUUGAGUCGAGUCGAGUUGAACUGUAAGCUGGGAGCCAAAGUGAUUUUGUGGCUGGGCUGCGGUGCAACUUUGCCCUGGUUGCAUUUCAGUUCGGUACGAGAAGCAAUCAAA
......((((((..(((..((((((((((.(((((.(..((.((.(((((....(((..((...))..)))....)))))))))..)))))).))))))))))..)))....)))))).. (-35.29 = -35.85 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:08 2006