Locus 1581

Sequence ID	2R_DroMel_CAF1
Location	5,941,912 – 5,942,147
Length	235
Max. P	0.974568

overview

Window 8

Location	5,941,912 – 5,942,032
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.69
Mean single sequence MFE	-31.53
Consensus MFE	-28.61
Energy contribution	-28.98
Covariance contribution	0.37
Combinations/Pair	1.06
Mean z-score	-2.77
Structure conservation index	0.91
SVM decision value	1.73
SVM RNA-class probability	0.974568
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5941912 120 + 20766785
UGUAGAAUAAUCAAAACUGACUUGCUAGCAAUGUUAAAAAGUGCAGAAAGCAUUGGCUAAUAUCGUUUGGCUAUUGAUUUUUUGCAUUUUCGUGCAUGCAAUUUUGUAGCUGUAGUUGUU
..............(((((....(((((((.(((...(((((((((((((((.(((((((......))))))).)).)))))))))))))...)))))).......))))..)))))... ( -32.71)
>DroSec_CAF1 83994 120 + 1
UGUAGAAUAAUCAAAGUUGACUUGCUAGGAAUGUUAAUAAGUGCAGAAAGCAUUGGCUAAUUUCGUUUGGCUAUUGAUUUUUUGCAUUUUCGUGCAUGCAAUUUUGUAGCUGUAGUUGUU
.....((((((...(((((..((((.....((((....((((((((((((((.(((((((......))))))).)).))))))))))))....)))))))).....)))))...)))))) ( -31.30)
>DroSim_CAF1 81841 120 + 1
UGUAGAAUUAUCAAAAUUGACUUGCUAGCAAUGUUAAAAAGUGCAGAAAGCAUUGGCUAAUUUCGUUUGGCUAUUGAUUUUUUGCAUUUUCGUGCAUGCAAUUUUGUAGCUGUAGUUGUU
.....((((((((((((((...(((((((...)))).(((((((((((((((.(((((((......))))))).)).)))))))))))))...)))..)))))))).....))))))... ( -32.00)
>DroYak_CAF1 86747 120 + 1
UGUAGAAUAAUCAAAACUAACUUGCUAGCAAUAUUUAAAAGUGCAAAAAGCAUUGGCUAAUUUCGUUUGGCUAUUGAUUUUUUGCAUUUUCGUGCAUGCAAUUUUGUAGCUGUAGUUGUU
.................(((((.((.(((........(((((((((((((((.(((((((......))))))).)).)))))))))))))..((((........)))))))))))))).. ( -30.10)
>consensus
UGUAGAAUAAUCAAAACUGACUUGCUAGCAAUGUUAAAAAGUGCAGAAAGCAUUGGCUAAUUUCGUUUGGCUAUUGAUUUUUUGCAUUUUCGUGCAUGCAAUUUUGUAGCUGUAGUUGUU
..................((((.(((((((.(((...(((((((((((((((.(((((((......))))))).)).)))))))))))))...)))))).......))))...))))... (-28.61 = -28.98 +   0.37)

alignment

secondary structure

dotplot

Window 9

Location	5,941,952 – 5,942,072
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	98.75
Mean single sequence MFE	-40.62
Consensus MFE	-40.66
Energy contribution	-40.48
Covariance contribution	-0.19
Combinations/Pair	1.02
Mean z-score	-4.51
Structure conservation index	1.00
SVM decision value	1.03
SVM RNA-class probability	0.904051
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5941952 120 + 20766785
GUGCAGAAAGCAUUGGCUAAUAUCGUUUGGCUAUUGAUUUUUUGCAUUUUCGUGCAUGCAAUUUUGUAGCUGUAGUUGUUGCUGUUGUAUUUUUUUGUGCUGCAGCUGCGCGUCGCAACU
((((((((((((.(((((((......))))))).)).))))))))))....(((.((((......(((((((((((...(((....))).........)))))))))))))))))).... ( -40.50)
>DroSec_CAF1 84034 120 + 1
GUGCAGAAAGCAUUGGCUAAUUUCGUUUGGCUAUUGAUUUUUUGCAUUUUCGUGCAUGCAAUUUUGUAGCUGUAGUUGUUGCUGUUGUAUUUUUUUGUGCUGCAGCUGCGCGUCGCAACU
((((((((((((.(((((((......))))))).)).))))))))))....(((.((((......(((((((((((...(((....))).........)))))))))))))))))).... ( -40.50)
>DroSim_CAF1 81881 120 + 1
GUGCAGAAAGCAUUGGCUAAUUUCGUUUGGCUAUUGAUUUUUUGCAUUUUCGUGCAUGCAAUUUUGUAGCUGUAGUUGUUGCUGUUGUAUUUUUUUGUGCUGCAGCUGCGCGUCGCAACU
((((((((((((.(((((((......))))))).)).))))))))))....(((.((((......(((((((((((...(((....))).........)))))))))))))))))).... ( -40.50)
>DroYak_CAF1 86787 119 + 1
GUGCAAAAAGCAUUGGCUAAUUUCGUUUGGCUAUUGAUUUUUUGCAUUUUCGUGCAUGCAAUUUUGUAGCUGUAGUUGUUGCUGUUGUAUUU-UUUGUGCUGCAGCUGCGCGUCGCAACU
((((((((((((.(((((((......))))))).)).))))))))))....(((.((((......(((((((((((...(((....)))...-.....)))))))))))))))))).... ( -41.00)
>consensus
GUGCAGAAAGCAUUGGCUAAUUUCGUUUGGCUAUUGAUUUUUUGCAUUUUCGUGCAUGCAAUUUUGUAGCUGUAGUUGUUGCUGUUGUAUUUUUUUGUGCUGCAGCUGCGCGUCGCAACU
((((((((((((.(((((((......))))))).)).))))))))))....(((.((((......(((((((((((...(((....))).........)))))))))))))))))).... (-40.66 = -40.48 +  -0.19)

alignment

secondary structure

dotplot

Window 0

Location	5,941,952 – 5,942,072
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	98.75
Mean single sequence MFE	-20.59
Consensus MFE	-20.56
Energy contribution	-20.37
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-1.73
Structure conservation index	1.00
SVM decision value	0.20
SVM RNA-class probability	0.631220
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5941952 120 - 20766785
AGUUGCGACGCGCAGCUGCAGCACAAAAAAAUACAACAGCAACAACUACAGCUACAAAAUUGCAUGCACGAAAAUGCAAAAAAUCAAUAGCCAAACGAUAUUAGCCAAUGCUUUCUGCAC
(((((((...)))))))((((.............................((((.....((((((........))))))........))))...........(((....)))..)))).. ( -20.82)
>DroSec_CAF1 84034 120 - 1
AGUUGCGACGCGCAGCUGCAGCACAAAAAAAUACAACAGCAACAACUACAGCUACAAAAUUGCAUGCACGAAAAUGCAAAAAAUCAAUAGCCAAACGAAAUUAGCCAAUGCUUUCUGCAC
(((((((...)))))))((((.............................((((.....((((((........))))))........))))...........(((....)))..)))).. ( -20.82)
>DroSim_CAF1 81881 120 - 1
AGUUGCGACGCGCAGCUGCAGCACAAAAAAAUACAACAGCAACAACUACAGCUACAAAAUUGCAUGCACGAAAAUGCAAAAAAUCAAUAGCCAAACGAAAUUAGCCAAUGCUUUCUGCAC
(((((((...)))))))((((.............................((((.....((((((........))))))........))))...........(((....)))..)))).. ( -20.82)
>DroYak_CAF1 86787 119 - 1
AGUUGCGACGCGCAGCUGCAGCACAAA-AAAUACAACAGCAACAACUACAGCUACAAAAUUGCAUGCACGAAAAUGCAAAAAAUCAAUAGCCAAACGAAAUUAGCCAAUGCUUUUUGCAC
(((((((...)))))))(((((.....-.........(((..........)))......((((((........))))))..........))...........(((....)))...))).. ( -19.90)
>consensus
AGUUGCGACGCGCAGCUGCAGCACAAAAAAAUACAACAGCAACAACUACAGCUACAAAAUUGCAUGCACGAAAAUGCAAAAAAUCAAUAGCCAAACGAAAUUAGCCAAUGCUUUCUGCAC
(((((((...)))))))((((.............................((((.....((((((........))))))........))))...........(((....)))..)))).. (-20.56 = -20.37 +  -0.19)

alignment

secondary structure

dotplot

Window 1

Location	5,942,032 – 5,942,147
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.58
Mean single sequence MFE	-19.24
Consensus MFE	-18.60
Energy contribution	-18.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.97
SVM decision value	0.94
SVM RNA-class probability	0.886014
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5942032 115 - 20766785
ACUCUCUCAAUCACUCGUGCACUCU-CUUUCGUUAACUGACCCAAAAUACAA----ACAACAACAGCAACAGCAGUUUACAGUUGCGACGCGCAGCUGCAGCACAAAAAAAUACAACAGC
................((((.....-..........................----.........((....))......((((((((...))))))))..))))................ ( -18.60)
>DroSec_CAF1 84114 119 - 1
ACGCUCUCACUCACUCGUGCACUCU-CUUUCGUUAACUGACCCAAAAUACAAAACAACAACAACAGCAACAGCAGUUUACAGUUGCGACGCGCAGCUGCAGCACAAAAAAAUACAACAGC
................((((.....-.......................................((....))......((((((((...))))))))..))))................ ( -18.60)
>DroSim_CAF1 81961 120 - 1
ACUCUCUCACUCACUCGUGCACUCUUCUUUCGUUAACUGACCCAAAAUACAAAACAACAACAACAGCAACAGCAGUUUACAGUUGCGACGCGCAGCUGCAGCACAAAAAAAUACAACAGC
................((((.............................................((....))......((((((((...))))))))..))))................ ( -18.60)
>DroYak_CAF1 86867 114 - 1
ACUCUCUCACUCACUCGUGCACUCU-CUUUUGUUAACUGACCCCAAAUAUAA-ACAA---CAACAGCAACAGCAGAUUACAGUUGCGACGCGCAGCUGCAGCACAAA-AAAUACAACAGC
................((((....(-((.(((((..(((.............-....---...))).))))).)))...((((((((...))))))))..))))...-............ ( -21.15)
>consensus
ACUCUCUCACUCACUCGUGCACUCU_CUUUCGUUAACUGACCCAAAAUACAA_ACAACAACAACAGCAACAGCAGUUUACAGUUGCGACGCGCAGCUGCAGCACAAAAAAAUACAACAGC
................((((.............................................((....))......((((((((...))))))))..))))................ (-18.60 = -18.60 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:03 2006