Locus 1621

Sequence ID	2L_DroMel_CAF1
Location	4,348,951 – 4,349,133
Length	182
Max. P	0.993826

overview

Window 4

Location	4,348,951 – 4,349,053
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.58
Mean single sequence MFE	-40.60
Consensus MFE	-32.20
Energy contribution	-33.82
Covariance contribution	1.62
Combinations/Pair	1.06
Mean z-score	-2.40
Structure conservation index	0.79
SVM decision value	1.80
SVM RNA-class probability	0.977697
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4348951 102 + 22407834
UCUGUUAACUACGCCGCCAUUUGUCUGCAGUUGGUAAGAUGGUAGCUUAGUCACUUGGC------------------AACUGGCAACAACUAACUGUUAACUGGGCCCAGACCUGGGCCA
...((((((......((((..((.(((.(((((.(.....).)))))))).))..))))------------------...((....)).......))))))..((((((....)))))). ( -34.10)
>DroSec_CAF1 17662 112 + 1
UCUGUUAACUUUGCCGCCAUUUGUCUGCAGUUGGUAAGAUGGUAGCUUAGUCACUUGGCAGUGCG---GCAACUGCCAACUGGCAACAACUAACUGUUAACUGGG-----ACCUCGGCCA
............((((((....((..((((((((((((.......))).((((.((((((((...---...)))))))).))))....)))))))))..))..))-----....)))).. ( -37.30)
>DroSim_CAF1 18409 117 + 1
UCUGUUAACUUUGCCGCCAUUUGUCUGCAGUUGGUAAGAUGGUAGCUUAGUCACUUGGCAGUGCG---GCAACUGCCAACUGGCAACAACUAACUGUUAACUGGGCCCAGACCUGGGCCA
...((((((...((..((((((..((......))..))))))..))...((((.((((((((...---...)))))))).))))...........))))))..((((((....)))))). ( -46.80)
>DroEre_CAF1 22916 117 + 1
UCUGUUAACUUUGCCGACAGUUGUCUGCAGUUGGUAAGAUGGUGGCUUAGUCACUUGGCAGCUCG---GCAACUGCCAACUGGCAACAACUAACUGUUAACUGGGCCUAGACCUGGGCCA
...((((((...((.(((....))).))(((((((.....((((((...))))))((((((....---....))))))..((....)))))))))))))))..((((((....)))))). ( -43.00)
>DroYak_CAF1 19164 120 + 1
UCUGUUAACUUUGCCGCCAUUUGUCUGCAGUUGGUAUGAUGGUAGCUUAGUCACUUGGCAGCUCGGCGGCAACUGCCAACUGGCAACAACUAACUGUUAACUGGGCUUAGACCUGGGCCA
...((((((.((((((((..(..(((((.....))).))..).((((..(((....))))))).)))))))).((((....))))..........))))))..((((((....)))))). ( -41.80)
>consensus
UCUGUUAACUUUGCCGCCAUUUGUCUGCAGUUGGUAAGAUGGUAGCUUAGUCACUUGGCAGCGCG___GCAACUGCCAACUGGCAACAACUAACUGUUAACUGGGCCCAGACCUGGGCCA
...((((((...((.((((((...((......))...)))))).))...((((.(((((((...........))))))).))))...........))))))..((((((....)))))). (-32.20 = -33.82 +   1.62)

alignment

secondary structure

dotplot

Window 5

Location	4,348,951 – 4,349,053
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.58
Mean single sequence MFE	-36.14
Consensus MFE	-26.68
Energy contribution	-28.11
Covariance contribution	1.43
Combinations/Pair	1.06
Mean z-score	-1.55
Structure conservation index	0.74
SVM decision value	-0.05
SVM RNA-class probability	0.510307
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4348951 102 - 22407834
UGGCCCAGGUCUGGGCCCAGUUAACAGUUAGUUGUUGCCAGUU------------------GCCAAGUGACUAAGCUACCAUCUUACCAACUGCAGACAAAUGGCGGCGUAGUUAACAGA
.((((((....))))))..((((((.......((((((((.((------------------((..(((...((((.......))))...))))))).....))))))))..))))))... ( -31.40)
>DroSec_CAF1 17662 112 - 1
UGGCCGAGGU-----CCCAGUUAACAGUUAGUUGUUGCCAGUUGGCAGUUGC---CGCACUGCCAAGUGACUAAGCUACCAUCUUACCAACUGCAGACAAAUGGCGGCAAAGUUAACAGA
.(((....))-----)...((((((......((((((((((((.(((((((.---..((((....))))..((((.......)))).))))))).)))...))))))))).))))))... ( -33.50)
>DroSim_CAF1 18409 117 - 1
UGGCCCAGGUCUGGGCCCAGUUAACAGUUAGUUGUUGCCAGUUGGCAGUUGC---CGCACUGCCAAGUGACUAAGCUACCAUCUUACCAACUGCAGACAAAUGGCGGCAAAGUUAACAGA
.((((((....))))))..((((((......((((((((((((.(((((((.---..((((....))))..((((.......)))).))))))).)))...))))))))).))))))... ( -43.20)
>DroEre_CAF1 22916 117 - 1
UGGCCCAGGUCUAGGCCCAGUUAACAGUUAGUUGUUGCCAGUUGGCAGUUGC---CGAGCUGCCAAGUGACUAAGCCACCAUCUUACCAACUGCAGACAACUGUCGGCAAAGUUAACAGA
.((((........))))..((((((....(((((....((.(((((((((..---..))))))))).))..((((.......)))).)))))((.(((....))).))...))))))... ( -37.40)
>DroYak_CAF1 19164 120 - 1
UGGCCCAGGUCUAAGCCCAGUUAACAGUUAGUUGUUGCCAGUUGGCAGUUGCCGCCGAGCUGCCAAGUGACUAAGCUACCAUCAUACCAACUGCAGACAAAUGGCGGCAAAGUUAACAGA
.(((....)))........((((((.........(((((....)))))(((((((((..((((..(((.....................))))))).....))))))))).))))))... ( -35.20)
>consensus
UGGCCCAGGUCUAGGCCCAGUUAACAGUUAGUUGUUGCCAGUUGGCAGUUGC___CGAACUGCCAAGUGACUAAGCUACCAUCUUACCAACUGCAGACAAAUGGCGGCAAAGUUAACAGA
.((((........))))..((((((..(((((......((.((((((((.........)))))))).)))))))(((.((((..................)))).)))...))))))... (-26.68 = -28.11 +   1.43)

alignment

secondary structure

dotplot

Window 6

Location	4,348,991 – 4,349,093
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.91
Mean single sequence MFE	-36.94
Consensus MFE	-29.04
Energy contribution	-30.26
Covariance contribution	1.22
Combinations/Pair	1.06
Mean z-score	-1.48
Structure conservation index	0.79
SVM decision value	0.09
SVM RNA-class probability	0.580958
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4348991 102 + 22407834
GGUAGCUUAGUCACUUGGC------------------AACUGGCAACAACUAACUGUUAACUGGGCCCAGACCUGGGCCAGGUACGCCCCCAACAUGCAUUCCAACAUGCCAUGCGAAAG
((..(((((((...(((.(------------------....).)))..)))))......(((.((((((....)))))).)))..))..))..(((((((......))).))))...... ( -27.90)
>DroSec_CAF1 17702 112 + 1
GGUAGCUUAGUCACUUGGCAGUGCG---GCAACUGCCAACUGGCAACAACUAACUGUUAACUGGG-----ACCUCGGCCAGGUACGCCCCCAACAUGCAUUCCGACAUGCCAUGCGAAAG
((..((...((((.((((((((...---...)))))))).))))...........((...((((.-----.......))))..))))..))..(((((((......))).))))...... ( -33.40)
>DroSim_CAF1 18449 117 + 1
GGUAGCUUAGUCACUUGGCAGUGCG---GCAACUGCCAACUGGCAACAACUAACUGUUAACUGGGCCCAGACCUGGGCCAGGUACGCCCCCAACAUGCAUUCCAACAUGCCAUGCGAAAG
((..((...((((.((((((((...---...)))))))).))))((((......)))).(((.((((((....)))))).)))..))..))..(((((((......))).))))...... ( -42.50)
>DroEre_CAF1 22956 116 + 1
GGUGGCUUAGUCACUUGGCAGCUCG---GCAACUGCCAACUGGCAACAACUAACUGUUAACUGGGCCUAGACCUGGGCCAGGC-CGCCCCCAACAUGCAUUCCAACAUGCCAUGCGAAAG
((((((((.((((.(((((((....---....))))))).))))((((......)))).....((((((....))))))))))-)))).....(((((((......))).))))...... ( -43.50)
>DroYak_CAF1 19204 119 + 1
GGUAGCUUAGUCACUUGGCAGCUCGGCGGCAACUGCCAACUGGCAACAACUAACUGUUAACUGGGCUUAGACCUGGGCCAGGC-CGCCCCCAACAUGCAUUCCAACAUGCCAUGCGAAAG
((..((...(((....))).....((((((....)))..(((((((((......))))..(..((......))..))))))))-)))..))..(((((((......))).))))...... ( -37.40)
>consensus
GGUAGCUUAGUCACUUGGCAGCGCG___GCAACUGCCAACUGGCAACAACUAACUGUUAACUGGGCCCAGACCUGGGCCAGGUACGCCCCCAACAUGCAUUCCAACAUGCCAUGCGAAAG
((..((...((((.(((((((...........))))))).))))((((......))))..((((.((((....))))))))....))..))..(((((((......))).))))...... (-29.04 = -30.26 +   1.22)

alignment

secondary structure

dotplot

Window 7

Location	4,349,013 – 4,349,133
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.32
Mean single sequence MFE	-31.80
Consensus MFE	-27.96
Energy contribution	-28.16
Covariance contribution	0.20
Combinations/Pair	1.13
Mean z-score	-2.08
Structure conservation index	0.88
SVM decision value	2.43
SVM RNA-class probability	0.993826
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4349013 120 + 22407834
UGGCAACAACUAACUGUUAACUGGGCCCAGACCUGGGCCAGGUACGCCCCCAACAUGCAUUCCAACAUGCCAUGCGAAAGGCAAAUCUAACUGCAUGUUGCAUGCCACUCCAAGACAAAA
(((((..............(((.((((((....)))))).))).......(((((((((........((((........))))........)))))))))..)))))............. ( -38.59)
>DroSec_CAF1 17739 115 + 1
UGGCAACAACUAACUGUUAACUGGG-----ACCUCGGCCAGGUACGCCCCCAACAUGCAUUCCGACAUGCCAUGCGAAAGUCAAACCUAACUGCAUGUUGCAUGCCACUCCAAGACAAAA
(((((..........((...((((.-----.......))))..)).....(((((((((........((....((....))))........)))))))))..)))))............. ( -25.29)
>DroSim_CAF1 18486 120 + 1
UGGCAACAACUAACUGUUAACUGGGCCCAGACCUGGGCCAGGUACGCCCCCAACAUGCAUUCCAACAUGCCAUGCGAAAGUCAAAUCUAACUGCAUGUUGCAUGCCACUGCAAGACAAAA
.(((((((......)))).(((.((((((....)))))).)))..))).......((((......(((((((((((..((......))...))))))..)))))....))))........ ( -34.90)
>DroEre_CAF1 22993 118 + 1
UGGCAACAACUAACUGUUAACUGGGCCUAGACCUGGGCCAGGC-CGCCCCCAACAUGCAUUCCAACAUGCCAUGCGAAAGUCAAAUCUAACUGCAUGUUGCAUGCCACUCCAAGACAA-A
.(((((((......))))..((((.((((....))))))))))-)((...(((((((((........((....((....))))........)))))))))...)).............-. ( -31.39)
>DroYak_CAF1 19244 107 + 1
UGGCAACAACUAACUGUUAACUGGGCUUAGACCUGGGCCAGGC-CGCCCCCAACAUGCAUUCCAACAUGCCAUGCGAAAGUCGAAUCUAACUGCAUGUUGCAUGCCGC------------
.(((((((......))))..((((.((.......)).))))))-)...........((((..((((((((...((....))...........)))))))).))))...------------ ( -28.84)
>consensus
UGGCAACAACUAACUGUUAACUGGGCCCAGACCUGGGCCAGGUACGCCCCCAACAUGCAUUCCAACAUGCCAUGCGAAAGUCAAAUCUAACUGCAUGUUGCAUGCCACUCCAAGACAAAA
.(((((((......))))..((((.((((....))))))))....)))........((((..((((((((..(((....).)).........)))))))).))))............... (-27.96 = -28.16 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	4,349,013 – 4,349,133
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.32
Mean single sequence MFE	-39.66
Consensus MFE	-33.82
Energy contribution	-33.98
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-1.28
Structure conservation index	0.85
SVM decision value	0.05
SVM RNA-class probability	0.559232
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4349013 120 - 22407834
UUUUGUCUUGGAGUGGCAUGCAACAUGCAGUUAGAUUUGCCUUUCGCAUGGCAUGUUGGAAUGCAUGUUGGGGGCGUACCUGGCCCAGGUCUGGGCCCAGUUAACAGUUAGUUGUUGCCA
.............(((((.(((((..((.(((((....(((((..(((((.(((......))))))))..)))))....((((((((....)))).))))))))).))..)))))))))) ( -44.10)
>DroSec_CAF1 17739 115 - 1
UUUUGUCUUGGAGUGGCAUGCAACAUGCAGUUAGGUUUGACUUUCGCAUGGCAUGUCGGAAUGCAUGUUGGGGGCGUACCUGGCCGAGGU-----CCCAGUUAACAGUUAGUUGUUGCCA
.............(((((.(((((..((.(((((.(..((((((.((..(((((((......))))))).(((.....))).)).)))))-----)..).))))).))..)))))))))) ( -34.20)
>DroSim_CAF1 18486 120 - 1
UUUUGUCUUGCAGUGGCAUGCAACAUGCAGUUAGAUUUGACUUUCGCAUGGCAUGUUGGAAUGCAUGUUGGGGGCGUACCUGGCCCAGGUCUGGGCCCAGUUAACAGUUAGUUGUUGCCA
.....(((.(((...((((.((((((((.....((........)).....))))))))..)))).))).)))(((....((((((((....)))).))))..(((((....)))))))). ( -41.10)
>DroEre_CAF1 22993 118 - 1
U-UUGUCUUGGAGUGGCAUGCAACAUGCAGUUAGAUUUGACUUUCGCAUGGCAUGUUGGAAUGCAUGUUGGGGGCG-GCCUGGCCCAGGUCUAGGCCCAGUUAACAGUUAGUUGUUGCCA
.-....((..(....((((.((((((((.....((........)).....))))))))..))))...)..))((((-(((((((....).))))))).....(((((....)))))))). ( -41.40)
>DroYak_CAF1 19244 107 - 1
------------GCGGCAUGCAACAUGCAGUUAGAUUCGACUUUCGCAUGGCAUGUUGGAAUGCAUGUUGGGGGCG-GCCUGGCCCAGGUCUAAGCCCAGUUAACAGUUAGUUGUUGCCA
------------..((((.(((((((((((((......))))...)))).((((......)))).(((((.(((((-(((((...))))))...))))...)))))....))))))))). ( -37.50)
>consensus
UUUUGUCUUGGAGUGGCAUGCAACAUGCAGUUAGAUUUGACUUUCGCAUGGCAUGUUGGAAUGCAUGUUGGGGGCGUACCUGGCCCAGGUCUAGGCCCAGUUAACAGUUAGUUGUUGCCA
..............((((.(((((((((.(..((......))..))))).((((......)))).(((((.((((..(((((...)))))....))))...)))))....))))))))). (-33.82 = -33.98 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:58 2006