Locus 1155

Sequence ID	2R_DroMel_CAF1
Location	4,607,152 – 4,607,352
Length	200
Max. P	0.965637

overview

Window 7

Location	4,607,152 – 4,607,251
Length	99
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	81.73
Mean single sequence MFE	-21.85
Consensus MFE	-15.26
Energy contribution	-16.78
Covariance contribution	1.53
Combinations/Pair	1.05
Mean z-score	-2.27
Structure conservation index	0.70
SVM decision value	0.76
SVM RNA-class probability	0.842611
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4607152 99 - 20766785
AAUCUUGCAACAUUGAGUUCUGCAAACAAGCCAGUAGAACUCGAUUUGCAGUUAUAAUCGCUGCACUCACCGGUCGCCUAUCAUAUCU---AUAAUACUUAC
......((.((((((((((((((..........)))))))))))).((((((.......)))))).......)).))...........---........... ( -23.30)
>DroSec_CAF1 7427 99 - 1
AAUCUUGCAACAUUGAGUUCUGCAAACAAGCCAGUAGAACUCGAUUCGCAGUUAUAUUCGCUGCAUUCACGGGUCGCCUACAUUAUUU---AUAAUACUCAC
......((.((((((((((((((..........))))))))))))..(((((.......)))))........)).))...........---........... ( -23.00)
>DroSim_CAF1 7830 99 - 1
AAUCUUGCAACAUUGAGUUCUGCAAACAAGCCAGUAGAACUCGAUUCGCAGUUAUAUUCGCUGCAUUCACGGGUCGCCUACCAUAUCU---AUAAUACUCAC
......((.((((((((((((((..........))))))))))))..(((((.......)))))........)).))...........---........... ( -23.00)
>DroEre_CAF1 7191 99 - 1
AAUCUCGCAACAUUGAGUUCUGCAAACAAGCCAGUAGAACUCGAUUCACAGUUAUAUUCGCUGCAUUCACCGGUCGCCUAUCAUAUCU---GAAUUACUUAC
...........((((((((((((..........))))))))))))...(((.(((((..((.((........)).))..)).))).))---).......... ( -19.30)
>DroYak_CAF1 7571 99 - 1
AAUCUUGCAACAUUGAGUUCUGCAAACAAGCCUAUAGAACUCGAUUCGCAGUUAUAUUCGCUGCAUUUGCUAACUGCCUAACAUAUCU---CAAUUACUUAC
......((((.((((((((((((......))....))))))))))..(((((.......)))))..))))..................---........... ( -20.70)
>DroAna_CAF1 6465 102 - 1
GAUUUUGCAACAUUGAGUUCUGCAAAAAAGCUGGACAUACUAUAAUUGCAGUUAUAUUGGCUGCAAUUAUCAGAACUUUAGGAACUUUGAGAUAAUACUUAC
..............(((((((((......))........((((((((((((((.....)))))))))))).)).......)))))))((((......)))). ( -21.80)
>consensus
AAUCUUGCAACAUUGAGUUCUGCAAACAAGCCAGUAGAACUCGAUUCGCAGUUAUAUUCGCUGCAUUCACCGGUCGCCUACCAUAUCU___AUAAUACUUAC
......((...((((((((((((..........))))))))))))..(((((.......)))))...........))......................... (-15.26 = -16.78 +   1.53)

alignment

secondary structure

dotplot

Window 8

Location	4,607,179 – 4,607,288
Length	109
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	79.58
Mean single sequence MFE	-31.41
Consensus MFE	-19.48
Energy contribution	-18.96
Covariance contribution	-0.52
Combinations/Pair	1.38
Mean z-score	-2.01
Structure conservation index	0.62
SVM decision value	0.78
SVM RNA-class probability	0.848611
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4607179 109 + 20766785
CG------GUGAGUGCAGCGAUUAUAACUGCAAAUCGAGUUCUACUGGCUUGUUUGCAGAACUCAAUGUUGCAAGAUUAAUUUGUGAUGCGCAGGGAAAU-GCACUUCACCGAUUG
((------((((((((((((((((((((((((((.((((((.....)))))))))))))(((.....)))...........))))))).))).......)-)))).)))))).... ( -37.01)
>DroSim_CAF1 7857 109 + 1
CC------GUGAAUGCAGCGAAUAUAACUGCGAAUCGAGUUCUACUGGCUUGUUUGCAGAACUCAAUGUUGCAAGAUUAAUUUGUGAUGCGCAAGGAAAU-GCACUUCACCGAUUG
..------.....(((((((.......(((((((.((((((.....))))))))))))).......)))))))....(((((.((((.(.(((......)-)).).)))).))))) ( -30.24)
>DroEre_CAF1 7218 109 + 1
CG------GUGAAUGCAGCGAAUAUAACUGUGAAUCGAGUUCUACUGGCUUGUUUGCAGAACUCAAUGUUGCGAGAUUAAUUUGUGAUUCGCAGGGAAAU-GCACUUCACCGAUUG
((------(((((((((..........((((((((((((((((....((......)))))))))......(((((.....)))))))))))))).....)-))).))))))).... ( -37.76)
>DroYak_CAF1 7598 109 + 1
UA------GCAAAUGCAGCGAAUAUAACUGCGAAUCGAGUUCUAUAGGCUUGUUUGCAGAACUCAAUGUUGCAAGAUUAAUUUGUGAUGCGCAGGGAAAU-GCACUUCACCGAUUG
..------.....(((((((.......(((((((.((((((.....))))))))))))).......)))))))....(((((.((((.(.(((......)-)).).)))).))))) ( -31.24)
>DroAna_CAF1 6495 107 + 1
UG------AUAAUUGCAGCCAAUAUAACUGCAAUUAUAGUAUGUCCAGCUUUUUUGCAGAACUCAAUGUUGCAAAAUCAAGUUGUGGC-CGCAAGGA-AU-CUGCUGUACCAGCUG
..------((((((((((.........))))))))))........(((((.....(((((.......((..(((.......)))..))-(....)..-.)-))))......))))) ( -29.00)
>DroPer_CAF1 7072 114 + 1
UGUUUUUGAAGAUUGCAUCGAAUAUAACUGCAAAUUG-GUUCAUUAAACUUGUUUGCGGAACUCAAUGUUGCAAGAUUAAGUUGUG-UGUGCAGGAAAAUCGUACUAGUCGGAUUG
.((...(((...((((((...((((((((((((((.(-(((.....)))).))))))(.(((.....))).).......)))))))-))))))).....))).))........... ( -23.20)
>consensus
CG______GUGAAUGCAGCGAAUAUAACUGCAAAUCGAGUUCUACUGGCUUGUUUGCAGAACUCAAUGUUGCAAGAUUAAUUUGUGAUGCGCAGGGAAAU_GCACUUCACCGAUUG
.............(((((((.......(((((((.((((((.....))))))))))))).......)))))))........((((.....))))...................... (-19.48 = -18.96 +  -0.52)

alignment

secondary structure

dotplot

Window 9

Location	4,607,179 – 4,607,288
Length	109
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	79.58
Mean single sequence MFE	-30.34
Consensus MFE	-13.90
Energy contribution	-17.52
Covariance contribution	3.61
Combinations/Pair	1.12
Mean z-score	-3.34
Structure conservation index	0.46
SVM decision value	1.58
SVM RNA-class probability	0.965637
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4607179 109 - 20766785
CAAUCGGUGAAGUGC-AUUUCCCUGCGCAUCACAAAUUAAUCUUGCAACAUUGAGUUCUGCAAACAAGCCAGUAGAACUCGAUUUGCAGUUAUAAUCGCUGCACUCAC------CG
....((((((.((((-(.......(((........((((...((((((.((((((((((((..........))))))))))))))))))...))))))))))))))))------)) ( -36.61)
>DroSim_CAF1 7857 109 - 1
CAAUCGGUGAAGUGC-AUUUCCUUGCGCAUCACAAAUUAAUCUUGCAACAUUGAGUUCUGCAAACAAGCCAGUAGAACUCGAUUCGCAGUUAUAUUCGCUGCAUUCAC------GG
....((((((.((((-(......))))).))))................((((((((((((..........))))))))))))..(((((.......))))).....)------). ( -33.60)
>DroEre_CAF1 7218 109 - 1
CAAUCGGUGAAGUGC-AUUUCCCUGCGAAUCACAAAUUAAUCUCGCAACAUUGAGUUCUGCAAACAAGCCAGUAGAACUCGAUUCACAGUUAUAUUCGCUGCAUUCAC------CG
....(((((((.(((-(......(((((..............)))))..((((((((((((..........))))))))))))................)))))))))------)) ( -32.54)
>DroYak_CAF1 7598 109 - 1
CAAUCGGUGAAGUGC-AUUUCCCUGCGCAUCACAAAUUAAUCUUGCAACAUUGAGUUCUGCAAACAAGCCUAUAGAACUCGAUUCGCAGUUAUAUUCGCUGCAUUUGC------UA
.(((..((((.((((-(......))))).))))..)))......((((.((((((((((((......))....))))))))))..(((((.......)))))..))))------.. ( -32.50)
>DroAna_CAF1 6495 107 - 1
CAGCUGGUACAGCAG-AU-UCCUUGCG-GCCACAACUUGAUUUUGCAACAUUGAGUUCUGCAAAAAAGCUGGACAUACUAUAAUUGCAGUUAUAUUGGCUGCAAUUAU------CA
((((((((...((((-..-...)))).-))).........(((((((((.....))..))))))).)))))........((((((((((((.....))))))))))))------.. ( -32.10)
>DroPer_CAF1 7072 114 - 1
CAAUCCGACUAGUACGAUUUUCCUGCACA-CACAACUUAAUCUUGCAACAUUGAGUUCCGCAAACAAGUUUAAUGAAC-CAAUUUGCAGUUAUAUUCGAUGCAAUCUUCAAAAACA
...........((((((..(..(((((..-...((((((((........))))))))..........((((...))))-.....)))))..)...))).))).............. ( -14.70)
>consensus
CAAUCGGUGAAGUGC_AUUUCCCUGCGCAUCACAAAUUAAUCUUGCAACAUUGAGUUCUGCAAACAAGCCAGUAGAACUCGAUUCGCAGUUAUAUUCGCUGCAUUCAC______CA
......((((.((((.........)))).))))................((((((((((((..........))))))))))))..(((((.......))))).............. (-13.90 = -17.52 +   3.61)

alignment

secondary structure

dotplot

Window 0

Location	4,607,251 – 4,607,352
Length	101
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	83.25
Mean single sequence MFE	-27.48
Consensus MFE	-19.51
Energy contribution	-19.68
Covariance contribution	0.17
Combinations/Pair	1.22
Mean z-score	-2.83
Structure conservation index	0.71
SVM decision value	0.73
SVM RNA-class probability	0.834847
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4607251 101 + 20766785
AAUUUGUGAUGCGCAGGGAAAU-GCACUUCACCGAUUGCAAUUCAAAUUGCAGUCACGUGGUCGAGAUUCCAUUGCAGUCUCAACAAA---UUAA-AAAUUAAAAA
(((((((((.((((((((((..-.(...((((.(((((((((....)))))))))..))))..)...)))).)))).)).)).)))))---))..-.......... ( -27.80)
>DroSec_CAF1 7526 101 + 1
AAUUUGUGAUGCGCAAGGAAAU-GCACUUCACCGAUUGCAACUCAAAUUGCAGUCACGUGGUCAAGAAUCCAUUGCAGUCUCAACAAA---UUAA-CAAUUAAAAA
(((((((((.(((((((((...-.....((((.((((((((......))))))))..)))).......))).)))).)).)).)))))---))..-.......... ( -25.86)
>DroSim_CAF1 7929 101 + 1
AAUUUGUGAUGCGCAAGGAAAU-GCACUUCACCGAUUGCAACUCAAAUUGCAGUCACGUGGUCGAGAAUCCAUUGCAGUCUCAACAAA---UUAA-CAAUUAAAAA
(((((((((.(((((((((...-.....((((.((((((((......))))))))..)))).......))).)))).)).)).)))))---))..-.......... ( -25.86)
>DroEre_CAF1 7290 102 + 1
AAUUUGUGAUUCGCAGGGAAAU-GCACUUCACCGAUUGCACUUCAAAUUGCAGUCACGUGGUUGAGAAUCCAUUGCAAUCUCAACAAA---UUAUCCAAAUUAAUG
((((((.(((.(((.(((((..-....))).))(((((((........)))))))..)))(((((((...........)))))))...---..))))))))).... ( -26.20)
>DroYak_CAF1 7670 101 + 1
AAUUUGUGAUGCGCAGGGAAAU-GCACUUCACCGAUUGCAACUGAAGUUGCAGUCACGUGGUCGAGAAUCCAUUGCAGUCUCAACAAA---UUAA-CAACUUAAUA
(((((((((.(((((((((...-.....((((.(((((((((....)))))))))..)))).......))).)))).)).)).)))))---))..-.......... ( -29.16)
>DroPer_CAF1 7149 103 + 1
AAGUUGUG-UGUGCAGGAAAAUCGUACUAGUCGGAUUGCAAUGCAUUUUGCAGUCACGUGGUCUAGAACGCUCUGCUGCUUAAACAGCCCCUUUG-CCAUUAGAA-
..(((((.-...((((.(....(((.((((.((((((((((......)))))))).))....)))).)))...).))))....))))).......-.........- ( -30.00)
>consensus
AAUUUGUGAUGCGCAGGGAAAU_GCACUUCACCGAUUGCAACUCAAAUUGCAGUCACGUGGUCGAGAAUCCAUUGCAGUCUCAACAAA___UUAA_CAAUUAAAAA
..(((((((.(((((((((......(((.....((((((((......))))))))....)))......))).)))).)).)).))))).................. (-19.51 = -19.68 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:51 2006