Locus 3183

Sequence ID	2L_DroMel_CAF1
Location	9,106,335 – 9,106,520
Length	185
Max. P	0.943508

overview

Window 3

Location	9,106,335 – 9,106,451
Length	116
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	79.94
Mean single sequence MFE	-26.52
Consensus MFE	-15.20
Energy contribution	-16.07
Covariance contribution	0.87
Combinations/Pair	1.31
Mean z-score	-2.12
Structure conservation index	0.57
SVM decision value	0.58
SVM RNA-class probability	0.787410
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9106335 116 - 22407834
CGCGUUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAUUUUCUCGCGAAUGGAAUU---CAAUGAAAUUUCAAAACUUACCCAUUAUUGAUAAAUAUUUAAUGCGCAUAAUUUA
.(((((((.((((((((((.........)))))))))).))).........(((((....(---((((((..................)))))))....)))))...))))........ ( -26.77)
>DroVir_CAF1 39634 103 - 1
-----UGUUGUUUUUGCUAUUAAUUAAUUUAAAACAUUAGCAUUUGCG--------UU-UGUGUCGGCAAAAAUACGCAAAUUGC--GUGGCUAUUUAAUAUUUUAUGCAUAUAAUUUA
-----(((((((((((((.((((.....)))).(((...((....)).--------..-)))...)))))))))).)))...(((--((((............)))))))......... ( -17.50)
>DroSec_CAF1 8510 116 - 1
CGCGUUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAUUUUCUCGCGAGUGGAAUU---CAAUAAAAUUUCAAAACUUACCCAUUAUUGACAAAUAUUUAAUGCGCAUAAUUUA
.(((((((.((((((((((.........)))))))))).))).((((.(....).)))).(---((((((..................)))))))............))))........ ( -26.97)
>DroSim_CAF1 8593 116 - 1
CGCGUUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAUUUUCUCGCGAGUGGAAUU---CAAUAAAAUUUCAAAACUUACCCAUUAUUGAUAAAUAUUUAAUGCGCAUAAUUUA
.(((((((.((((((((((.........)))))))))).))).((((.(....).)))).(---((((((..................)))))))............))))........ ( -27.07)
>DroEre_CAF1 8685 116 - 1
CGCGUUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAAUUUCUCGCGAGUGGAAUU---CAAUCAAAUUUCAAAACUUGCCCAUGUUUGAUAAAUAUUUAAUGCGCAUAAUUUA
.(((((((.((((((((((.........)))))))))).))).......((((((((((((---......))))))...))))))......................))))........ ( -30.40)
>DroYak_CAF1 13306 116 - 1
CGCGGUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAUUUUCUCGCUAGUAGAAUU---CAAUAAAAUUUGAAAACUGGCCCAUGAUUGAUAAAUAUUUAAUGAGCAUAAUUUA
.(((((((.((((((((((.........)))))))))).))).......((((((....((---(((......))))).)))))))).(.(((((.......))))).)))........ ( -30.40)
>consensus
CGCGUUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAUUUUCUCGCGAGUGGAAUU___CAAUAAAAUUUCAAAACUUACCCAUGAUUGAUAAAUAUUUAAUGCGCAUAAUUUA
.....(((.((((((((((.........)))))))))).))).......(((....((((....((((((..................))))))......))))....)))........ (-15.20 = -16.07 +   0.87)

alignment

secondary structure

dotplot

Window 4

Location	9,106,375 – 9,106,488
Length	113
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	78.95
Mean single sequence MFE	-22.24
Consensus MFE	-12.74
Energy contribution	-13.78
Covariance contribution	1.04
Combinations/Pair	1.17
Mean z-score	-2.50
Structure conservation index	0.57
SVM decision value	1.31
SVM RNA-class probability	0.940649
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9106375 113 + 22407834
UUUGAAAUUUCAUUG---AAUUCCAUUCGCGAGAAAAUGCAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACAACGCGACAAAAC--AAACAAUUAGUCCACGAACUCGAUUAAAUU
.....(((((.((((---(.(((...(((((.....(((((((((((((.....))))))))..)))))......)))))......--.........(....)))).))))).))))) ( -25.30)
>DroVir_CAF1 39672 95 + 1
UGCGUAUUUUUGCCGACACA-AA--------CGCAAAUGCUAAUGUUUUAAAUUAAUUAAUAGCAAAAACAACA------ACAAACGAAAGCAAUUA----ACG----UCAUUUUAGU
.(((......))).(((...-..--------......(((((..(((.......)))...))))).........------.....(....)......----..)----))........ (  -9.50)
>DroSec_CAF1 8550 113 + 1
UUUGAAAUUUUAUUG---AAUUCCACUCGCGAGAAAAUGCAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACAACGCGUCAAAAC--AAACAAUUAGUCCACGAACUCGAUUAAAAU
......(((((((((---(.(((....((((.....(((((((((((((.....))))))))..)))))......)))).......--.........(....)))).)))).)))))) ( -22.60)
>DroSim_CAF1 8633 113 + 1
UUUGAAAUUUUAUUG---AAUUCCACUCGCGAGAAAAUGCAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACAACGCGACAAAAC--AAACAAUUAGUCCACGAACUCGAUUAAAAU
......(((((((((---(.(((...(((((.....(((((((((((((.....))))))))..)))))......)))))......--.........(....)))).)))).)))))) ( -24.40)
>DroEre_CAF1 8725 113 + 1
UUUGAAAUUUGAUUG---AAUUCCACUCGCGAGAAAUUGCAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACAACGCGACAAAAC--AAACAAUUAGUCCACGAACUCAAUUAAAAU
.......((((((((---(.(((...(((((......((((((((((((.....))))))))..)))).......)))))......--.........(....)))).))))))))).. ( -27.72)
>DroYak_CAF1 13346 113 + 1
UUUCAAAUUUUAUUG---AAUUCUACUAGCGAGAAAAUGCAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACACCGCGACAAAAC--AAACAAUUAGUCCACGAACUCGAUUAAAAU
......(((((((((---(.(((.....(((.....(((((((((((((.....))))))))..)))))......)))(((.....--.........)))...))).)))).)))))) ( -23.94)
>consensus
UUUGAAAUUUUAUUG___AAUUCCACUCGCGAGAAAAUGCAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACAACGCGACAAAAC__AAACAAUUAGUCCACGAACUCGAUUAAAAU
..........................(((((.....(((((((((((((.....))))))))..)))))......)))))...................................... (-12.74 = -13.78 +   1.04)

alignment

secondary structure

dotplot

Window 5

Location	9,106,375 – 9,106,488
Length	113
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	78.95
Mean single sequence MFE	-29.40
Consensus MFE	-17.21
Energy contribution	-18.55
Covariance contribution	1.34
Combinations/Pair	1.21
Mean z-score	-2.48
Structure conservation index	0.59
SVM decision value	1.34
SVM RNA-class probability	0.943508
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9106375 113 - 22407834
AAUUUAAUCGAGUUCGUGGACUAAUUGUUU--GUUUUGUCGCGUUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAUUUUCUCGCGAAUGGAAUU---CAAUGAAAUUUCAAA
.........(((((((..(((.....))).--.)....(((((.(((.((((((((((.........)))))))))).)))......)))))...)))))---).............. ( -32.30)
>DroVir_CAF1 39672 95 - 1
ACUAAAAUGA----CGU----UAAUUGCUUUCGUUUGU------UGUUGUUUUUGCUAUUAAUUAAUUUAAAACAUUAGCAUUUGCG--------UU-UGUGUCGGCAAAAAUACGCA
....((((((----.((----.....))..))))))..------(((((((((((((.((((.....)))).(((...((....)).--------..-)))...)))))))))).))) ( -15.50)
>DroSec_CAF1 8550 113 - 1
AUUUUAAUCGAGUUCGUGGACUAAUUGUUU--GUUUUGACGCGUUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAUUUUCUCGCGAGUGGAAUU---CAAUAAAAUUUCAAA
.........(((((((..(((.....))).--.).....((((.(((.((((((((((.........)))))))))).)))......))))....)))))---).............. ( -31.00)
>DroSim_CAF1 8633 113 - 1
AUUUUAAUCGAGUUCGUGGACUAAUUGUUU--GUUUUGUCGCGUUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAUUUUCUCGCGAGUGGAAUU---CAAUAAAAUUUCAAA
.........(((((((..(((.....))).--.)....(((((.(((.((((((((((.........)))))))))).)))......)))))...)))))---).............. ( -32.30)
>DroEre_CAF1 8725 113 - 1
AUUUUAAUUGAGUUCGUGGACUAAUUGUUU--GUUUUGUCGCGUUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAAUUUCUCGCGAGUGGAAUU---CAAUCAAAUUUCAAA
..(((.((((((((((..(((.....))).--.)....(((((((((.((((((((((.........)))))))))).)))).....)))))...)))))---)))).)))....... ( -35.20)
>DroYak_CAF1 13346 113 - 1
AUUUUAAUCGAGUUCGUGGACUAAUUGUUU--GUUUUGUCGCGGUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAUUUUCUCGCUAGUAGAAUU---CAAUAAAAUUUGAAA
.(((((..((((..(((((...(((.....--)))...)))))((((.((((((((((.........)))))))))).))))...))))....)))))((---(((......))))). ( -30.10)
>consensus
AUUUUAAUCGAGUUCGUGGACUAAUUGUUU__GUUUUGUCGCGUUGUUGAUGCAGCAAUACAGCGAUUUGCUGCAUUUGCAUUUUCUCGCGAGUGGAAUU___CAAUAAAAUUUCAAA
..........((((....))))..(((((...(((((((((((.(((.((((((((((.........)))))))))).)))......))))).)))))).....)))))......... (-17.21 = -18.55 +   1.34)

alignment

secondary structure

dotplot

Window 6

Location	9,106,411 – 9,106,520
Length	109
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	82.05
Mean single sequence MFE	-17.11
Consensus MFE	-10.50
Energy contribution	-11.83
Covariance contribution	1.34
Combinations/Pair	1.20
Mean z-score	-2.21
Structure conservation index	0.61
SVM decision value	0.32
SVM RNA-class probability	0.687000
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9106411 109 + 22407834
CAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACAACGCGACAAAAC--AAACAAUUAGUCCACGAACUCGAUUAAAUUUAAUUUAUAAUCAGUUUGAUGAAUAAA--AAAAU
....((((((((.........))))))))(((.....(.(((.....--.........)))).((((((.(((((...........))))))))))).))).....--..... ( -19.44)
>DroVir_CAF1 39702 99 + 1
CUAAUGUUUUAAAUUAAUUAAUAGCAAAAACAACA------ACAAACGAAAGCAAUUA----ACG----UCAUUUUAGUCUAUUGACUAUCAGCUCAAAUAAUACAACAAAGG
......................(((..........------.....(....)......----...----......(((((....)))))...))).................. (  -7.80)
>DroSec_CAF1 8586 109 + 1
CAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACAACGCGUCAAAAC--AAACAAUUAGUCCACGAACUCGAUUAAAAUUAAUUUAUAAUCAGUUUGAUGAAUAAA--AAAAU
...(((((((((.........))))))))).................--............((((((((.(((((.((.....)).))))))))))).))......--..... ( -19.50)
>DroSim_CAF1 8669 109 + 1
CAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACAACGCGACAAAAC--AAACAAUUAGUCCACGAACUCGAUUAAAAUUAAUUUAUAAUCAGUUUGAUGAAUAAA--AAAAU
....((((((((.........))))))))(((.....(.(((.....--.........)))).((((((.(((((.((.....)).))))))))))).))).....--..... ( -20.44)
>DroEre_CAF1 8761 110 + 1
CAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACAACGCGACAAAAC--AAACAAUUAGUCCACGAACUCAAUUAAAAUUAAUUUAUAAUCAGUUUGAUGAAUAAAA-AAAAU
....((((((((.........))))))))(((.....(.(((.....--.........)))).((((((..((((.((.....)).)))).)))))).)))......-..... ( -16.04)
>DroYak_CAF1 13382 111 + 1
CAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACACCGCGACAAAAC--AAACAAUUAGUCCACGAACUCGAUUAAAAUUAAUAUAUAAUCAGUUUGAUGAAUAAAAAAAAAU
....((((((((.........))))))))(((.....(.(((.....--.........)))).((((((.(((((...........))))))))))).)))............ ( -19.44)
>consensus
CAAAUGCAGCAAAUCGCUGUAUUGCUGCAUCAACAACGCGACAAAAC__AAACAAUUAGUCCACGAACUCGAUUAAAAUUAAUUUAUAAUCAGUUUGAUGAAUAAA__AAAAU
...(((((((((.........))))))))).................................((((((.(((((...........)))))))))))................ (-10.50 = -11.83 +   1.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:19 2006