Locus 8050

Sequence ID	3L_DroMel_CAF1
Location	21,223,177 – 21,223,417
Length	240
Max. P	0.848558

overview

Window 5

Location	21,223,177 – 21,223,297
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.83
Mean single sequence MFE	-55.85
Consensus MFE	-51.65
Energy contribution	-51.65
Covariance contribution	-0.00
Combinations/Pair	1.05
Mean z-score	-1.86
Structure conservation index	0.92
SVM decision value	0.78
SVM RNA-class probability	0.848558
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21223177 120 + 23771897
CUCGGCCGGCGAGGAAGUGCAAGUGUCGGAGGCAUCUAGUGGCACGGCAUCCACCACCGUUGUUGCCACGAGCACGGCCAGCAGCACUGGUGGCCCCUCCGGCGGCAGCUUUUUUGCCCU
.......(((((((((((((....((((((((......((((((((((..........)))).))))))......(((((.((....)).))))))))))))).))).)))))))))).. ( -55.90)
>DroSim_CAF1 90218 120 + 1
CUCGGCCGGCGAGGAAGUGCAAGUGUCGGAGGCAUCCAGUGGCACGGCAUCCACCACCGUUGUGGCCACGAGCACGGCCAGCAGCACUGGUGGCCCCUCUGGCGGCAGCUUUUUUGCCCU
.......(((((((((((((....((((((((......((((((((((..........))))).)))))......(((((.((....)).))))))))))))).))).)))))))))).. ( -53.70)
>DroEre_CAF1 42601 120 + 1
CACGGCCGGCGAAGAAGUGCAAGUGUCGGAGGCAUCCAGUGCCACGGCAUCAACGACCGUUGUGGCCACGAGCACGGCCAGCAGCACUGGUGGCCCCUCCGGCGGCAGCUUUUUUGCCCU
.......(((((((((((((....((((((((......(((((..(((..((((....))))..)))..).))))(((((.((....)).))))))))))))).))).)))))))))).. ( -58.00)
>DroYak_CAF1 147756 120 + 1
CACGGCCGGCGAAGAAGUGCAAGUGUCGGAGGCAUCUAGUGCCACGGCAUCCACCACCGUUGUUGCCACGAGCACGGCCAGCAGCACUGGUGGCCCCUCUGGCGGCAGCUUUUUUGCCCU
.......((((((((((((...((((((..(((((...))))).)))))).)))....((((((((((.(((...(((((.((....)).))))).)))))))))))))))))))))).. ( -55.80)
>consensus
CACGGCCGGCGAAGAAGUGCAAGUGUCGGAGGCAUCCAGUGCCACGGCAUCCACCACCGUUGUGGCCACGAGCACGGCCAGCAGCACUGGUGGCCCCUCCGGCGGCAGCUUUUUUGCCCU
.......(((((((((((((....((((((((......((((((((((..........))))).)))))......(((((.((....)).))))))))))))).))).)))))))))).. (-51.65 = -51.65 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	21,223,217 – 21,223,337
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-52.40
Consensus MFE	-47.58
Energy contribution	-48.08
Covariance contribution	0.50
Combinations/Pair	1.03
Mean z-score	-1.62
Structure conservation index	0.91
SVM decision value	0.19
SVM RNA-class probability	0.626756
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21223217 120 + 23771897
GGCACGGCAUCCACCACCGUUGUUGCCACGAGCACGGCCAGCAGCACUGGUGGCCCCUCCGGCGGCAGCUUUUUUGCCCUGGAGGAGUUUACGGAGACAAAGACCGACUAGGAUUGGCCC
.....(((..((((((..(((((((((........)).)))))))..))))))(((((((((.(((((.....)))))))))))).((((..(....)..))))......))....))). ( -48.50)
>DroSim_CAF1 90258 120 + 1
GGCACGGCAUCCACCACCGUUGUGGCCACGAGCACGGCCAGCAGCACUGGUGGCCCCUCUGGCGGCAGCUUUUUUGCCCUGGAGGAGUUUACGGAGACAAAGGCCGACUAGGAUUGGCCC
(((.((..((((((((..(((((((((........))))).))))..))))((((((((..(.(((((.....))))))..)))).......(....)...)))).....))))))))). ( -53.10)
>DroEre_CAF1 42641 120 + 1
GCCACGGCAUCAACGACCGUUGUGGCCACGAGCACGGCCAGCAGCACUGGUGGCCCCUCCGGCGGCAGCUUUUUUGCCCUGGAGGAGUUUUCGGAGACAAAGGCCGACUAGGAUUGGCCU
((((((((..........))))))))..((((.(((((((.((....)).)))))(((((((.(((((.....)))))))))))).)).)))).......(((((((......))))))) ( -56.90)
>DroYak_CAF1 147796 120 + 1
GCCACGGCAUCCACCACCGUUGUUGCCACGAGCACGGCCAGCAGCACUGGUGGCCCCUCUGGCGGCAGCUUUUUUGCCCUGGAGGAGUUUACGGAGACAAAGGCCGACUAGGAUUGGCCU
((((....((((((((..(((((((((........)).)))))))..))))((((((((..(.(((((.....))))))..)))).......(....)...)))).....)))))))).. ( -51.10)
>consensus
GCCACGGCAUCCACCACCGUUGUGGCCACGAGCACGGCCAGCAGCACUGGUGGCCCCUCCGGCGGCAGCUUUUUUGCCCUGGAGGAGUUUACGGAGACAAAGGCCGACUAGGAUUGGCCC
.....(((..........(((((((((........))))).)))).((((((((((((((((.(((((.....)))))))))))).......(....)...)))).))))).....))). (-47.58 = -48.08 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	21,223,257 – 21,223,377
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.83
Mean single sequence MFE	-50.32
Consensus MFE	-47.86
Energy contribution	-47.42
Covariance contribution	-0.44
Combinations/Pair	1.09
Mean z-score	-1.74
Structure conservation index	0.95
SVM decision value	0.70
SVM RNA-class probability	0.827362
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21223257 120 + 23771897
GCAGCACUGGUGGCCCCUCCGGCGGCAGCUUUUUUGCCCUGGAGGAGUUUACGGAGACAAAGACCGACUAGGAUUGGCCCUAGGGGCGUGGUCAUGACCACUAUACCAUACUGGCAUGCG
(((((..(((((((((((((((.(((((.....)))))))))))(.((((..(....)..)))))..(((((......)))))))))(((((....)))))..))))).....)).))). ( -50.40)
>DroSim_CAF1 90298 120 + 1
GCAGCACUGGUGGCCCCUCUGGCGGCAGCUUUUUUGCCCUGGAGGAGUUUACGGAGACAAAGGCCGACUAGGAUUGGCCCUAGGGGCGUGGUCAUGACCACUACACCAUAUUGGCAUGCG
(((((..((((((((((((..(.(((((.....))))))..)).........(....)...((((((......))))))...)))))(((((....)))))..))))).....)).))). ( -51.50)
>DroEre_CAF1 42681 120 + 1
GCAGCACUGGUGGCCCCUCCGGCGGCAGCUUUUUUGCCCUGGAGGAGUUUUCGGAGACAAAGGCCGACUAGGAUUGGCCUUAGGGGCGUGGCCAUGACCAUUAUACCAUACUGGCAUGCG
(((((..(((((((((((((((.(((((.....)))))))))).........(....).((((((((......)))))))).)))))((((......))))..))))).....)).))). ( -49.80)
>DroYak_CAF1 147836 120 + 1
GCAGCACUGGUGGCCCCUCUGGCGGCAGCUUUUUUGCCCUGGAGGAGUUUACGGAGACAAAGGCCGACUAGGAUUGGCCUUAGGGGCGUGGCGAUGACCACUAUACCAUACUGGCAUGCG
(((((..((((((((((((..(.(((((.....))))))..)).........(....).((((((((......)))))))).)))))((((......))))..))))).....)).))). ( -49.60)
>consensus
GCAGCACUGGUGGCCCCUCCGGCGGCAGCUUUUUUGCCCUGGAGGAGUUUACGGAGACAAAGGCCGACUAGGAUUGGCCCUAGGGGCGUGGCCAUGACCACUAUACCAUACUGGCAUGCG
(((((.((((((((((((((((.(((((.....)))))))))))).......(....)...)))).))))).....((((...))))((((......))))............)).))). (-47.86 = -47.42 +  -0.44)

alignment

secondary structure

dotplot

Window 8

Location	21,223,297 – 21,223,417
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-30.25
Consensus MFE	-26.88
Energy contribution	-27.12
Covariance contribution	0.25
Combinations/Pair	1.16
Mean z-score	-1.49
Structure conservation index	0.89
SVM decision value	0.21
SVM RNA-class probability	0.636156
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21223297 120 - 23771897
CAGUUCACGCUGGUGAUUCCUUUAACUUACCAGUCCUCUUCGCAUGCCAGUAUGGUAUAGUGGUCAUGACCACGCCCCUAGGGCCAAUCCUAGUCGGUCUUUGUCUCCGUAAACUCCUCC
.((((.((((((((((..........))))))))((.....(((((((.....))))).(((((....)))))))..((((((....))))))..))...........)).))))..... ( -31.60)
>DroSim_CAF1 90338 119 - 1
CAGUUUACGCUGGA-CUUCCUUUAACUUACCAGUCCUCUUCGCAUGCCAAUAUGGUGUAGUGGUCAUGACCACGCCCCUAGGGCCAAUCCUAGUCGGCCUUUGUCUCCGUAAACUCCUCC
.((((((((..(((-(...........................(((((.....))))).(((((....)))))(((.((((((....))))))..)))....)))).))))))))..... ( -33.40)
>DroEre_CAF1 42721 120 - 1
CAGUUCACGCUGGUACUUCCAUUAACUUACCAGUCCUCUUCGCAUGCCAGUAUGGUAUAAUGGUCAUGGCCACGCCCCUAAGGCCAAUCCUAGUCGGCCUUUGUCUCCGAAAACUCCUCC
.((((...(((((((............)))))))....((((((((((.....)))))..((((....)))).))....((((((..........)))))).......)))))))..... ( -27.00)
>DroYak_CAF1 147876 120 - 1
CAGUCCACGCUGGUACUUCCGUUAACUUACCAGUCCUCUUCGCAUGCCAGUAUGGUAUAGUGGUCAUCGCCACGCCCCUAAGGCCAAUCCUAGUCGGCCUUUGUCUCCGUAAACUCCUCC
..(.(((((((((((............))))))).........(((((.....))))).)))).)......(((.....((((((..........))))))......))).......... ( -29.00)
>consensus
CAGUUCACGCUGGUACUUCCUUUAACUUACCAGUCCUCUUCGCAUGCCAGUAUGGUAUAGUGGUCAUGACCACGCCCCUAAGGCCAAUCCUAGUCGGCCUUUGUCUCCGUAAACUCCUCC
.((((.(((((((((............))))))).......(((((((.....))))).(((((....)))))))....((((((..........)))))).......)).))))..... (-26.88 = -27.12 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:57 2006