Locus 4423

Sequence ID	3L_DroMel_CAF1
Location	12,914,732 – 12,914,904
Length	172
Max. P	0.962542

overview

Window 6

Location	12,914,732 – 12,914,840
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.84
Mean single sequence MFE	-18.71
Consensus MFE	-10.38
Energy contribution	-11.05
Covariance contribution	0.67
Combinations/Pair	1.25
Mean z-score	-1.97
Structure conservation index	0.55
SVM decision value	0.47
SVM RNA-class probability	0.748023
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12914732 108 + 23771897
AUGCGGCCACCA----UUAUAAGCCUUCUUU---UUUUUUUGUGCAU----AACCAUAAACCAGGCUUAUGGGCAAAAAA-AAAAAUCAAACUAAAAUGUAGCCAAACAAUGAAUAAUAU
....(((...((----((..........(((---(((((((((.(((----((((........)).))))).))))))))-))))..........))))..)))................ ( -22.55)
>DroSec_CAF1 35487 110 + 1
AUGCGGCCACCAUUCAUUAUAAGCCUGCUUU------UUUUGUGCAU----AACCAUAAACCAGGCUUAUGGGCAAAAAAAAAAAAUCAAACUAAAAUGUAGCCAAACAAUGAAUAAUAU
...........((((((((((((((((....------.((((((...----...)))))).))))))))).(((...........................)))....)))))))..... ( -20.83)
>DroSim_CAF1 34523 106 + 1
AUGCGGCCACCA----UUAUAAGCCUGCUUU------UUUUGUGCAU----AACCAUAAACCAGGCUUAUGGGCAAAAAAAAAAAAACAAACUAAAAUGUAGCCAAACAAUGAAUAAUAU
....(((.....----(((((((((((....------.((((((...----...)))))).)))))))))))..............(((........))).)))................ ( -19.90)
>DroEre_CAF1 40792 97 + 1
AUGCGGCCACCA----UUAUAAGCCUGAUAUU------UUUUUGAAU----AACCAUAAACCAGGCUUAAGGGUAAAAAGAA---------CUAAAUUGUAGCCAAACAAUGAAUAAUAU
....(((.(((.----...((((((((.....------.........----..........))))))))..))).......(---------(......)).)))................ ( -17.06)
>DroYak_CAF1 38241 109 + 1
AUGCGACCACCA----UUAUAAGCCAGAUUUUUUUUUUUUUUUGAAU----AACCAUAAACCAGGCUUAUGGGCAAAAAAAA---AACUAGCUAAAAUGUAGCCAAACAAUGAAUAAUAU
..........((----((...............(((((((((((...----..((((((.......)))))).)))))))))---))...((((.....)))).....))))........ ( -15.80)
>DroPer_CAF1 39753 102 + 1
AAGCGGCUACCA----UGAAAGGCCUGCUUU------UU--GUCCAGCAGCCACAAUAAACCAGGCUUACUA------AGAAAAAAGUGAACUAAAAAGUAACCAAAUGAUGAAUAAUAU
....((.(((..----.....(((.((((..------..--....)))))))...........((.(((((.------.......))))).)).....))).))................ ( -16.10)
>consensus
AUGCGGCCACCA____UUAUAAGCCUGCUUU______UUUUGUGCAU____AACCAUAAACCAGGCUUAUGGGCAAAAAAAAAAAAACAAACUAAAAUGUAGCCAAACAAUGAAUAAUAU
....(((.........(((((((((((..................................)))))))))))..................((......)).)))................ (-10.38 = -11.05 +   0.67)

alignment

secondary structure

dotplot

Window 7

Location	12,914,732 – 12,914,840
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.84
Mean single sequence MFE	-26.75
Consensus MFE	-13.70
Energy contribution	-14.59
Covariance contribution	0.89
Combinations/Pair	1.25
Mean z-score	-2.86
Structure conservation index	0.51
SVM decision value	1.54
SVM RNA-class probability	0.962542
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12914732 108 - 23771897
AUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUGAUUUUU-UUUUUUGCCCAUAAGCCUGGUUUAUGGUU----AUGCACAAAAAAA---AAAGAAGGCUUAUAA----UGGUGGCCGCAU
................(((((((((..(((((..(((((-((((((((((((((((...))))))))..----..))).)))))))---)))..)))))...))----).)))))).... ( -30.10)
>DroSec_CAF1 35487 110 - 1
AUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUGAUUUUUUUUUUUUGCCCAUAAGCCUGGUUUAUGGUU----AUGCACAAAA------AAAGCAGGCUUAUAAUGAAUGGUGGCCGCAU
.(((((((((((((..((((.((........))...((((((((.(((((((((((...))))))))..----..))).))))------))))..)))).)))))))))))))....... ( -27.90)
>DroSim_CAF1 34523 106 - 1
AUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUGUUUUUUUUUUUUUGCCCAUAAGCCUGGUUUAUGGUU----AUGCACAAAA------AAAGCAGGCUUAUAA----UGGUGGCCGCAU
................(((((((((..((((((((((((((....(((((((((((...))))))))..----..))).))))------))))))))))...))----).)))))).... ( -31.30)
>DroEre_CAF1 40792 97 - 1
AUAUUAUUCAUUGUUUGGCUACAAUUUAG---------UUCUUUUUACCCUUAAGCCUGGUUUAUGGUU----AUUCAAAAA------AAUAUCAGGCUUAUAA----UGGUGGCCGCAU
................((((((......(---------(.......))...((((((((((...(((..----..)))....------...))))))))))...----..)))))).... ( -21.20)
>DroYak_CAF1 38241 109 - 1
AUAUUAUUCAUUGUUUGGCUACAUUUUAGCUAGUU---UUUUUUUUGCCCAUAAGCCUGGUUUAUGGUU----AUUCAAAAAAAAAAAAAAAUCUGGCUUAUAA----UGGUGGUCGCAU
................(((((((((..((((((((---(((((((((.((((((((...))))))))..----...)))))))))))......))))))...))----).)))))).... ( -27.10)
>DroPer_CAF1 39753 102 - 1
AUAUUAUUCAUCAUUUGGUUACUUUUUAGUUCACUUUUUUCU------UAGUAAGCCUGGUUUAUUGUGGCUGCUGGAC--AA------AAAGCAGGCCUUUCA----UGGUAGCCGCUU
................(((((((....((..(.((((((..(------(((((.(((...........)))))))))..--))------))))..)..))....----.))))))).... ( -22.90)
>consensus
AUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUGAUUUUUUUUUUUUGCCCAUAAGCCUGGUUUAUGGUU____AUGCACAAAA______AAAGCAGGCUUAUAA____UGGUGGCCGCAU
................((((((......((................))..(((((((((.(((..........................))).)))))))))........)))))).... (-13.70 = -14.59 +   0.89)

alignment

secondary structure

dotplot

Window 8

Location	12,914,765 – 12,914,873
Length	108
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	86.54
Mean single sequence MFE	-20.17
Consensus MFE	-15.63
Energy contribution	-16.32
Covariance contribution	0.70
Combinations/Pair	1.05
Mean z-score	-2.06
Structure conservation index	0.77
SVM decision value	-0.00
SVM RNA-class probability	0.532774
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12914765 108 - 23771897
UCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUGAUUUUU-UUUUUUGCCCAUAAGCCUGGUUUAUGGUUAUGCACA
.......(((((((...((((((((..(((..............))).)))))))).....)))))))....-.....(((((((((((...))))))))....))).. ( -23.24)
>DroSec_CAF1 35521 109 - 1
UCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUGAUUUUUUUUUUUUGCCCAUAAGCCUGGUUUAUGGUUAUGCACA
.......(((((((...((((((((..(((..............))).)))))))).....)))))))..........(((((((((((...))))))))....))).. ( -23.24)
>DroSim_CAF1 34553 109 - 1
UCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUGUUUUUUUUUUUUUGCCCAUAAGCCUGGUUUAUGGUUAUGCACA
........(((((....((((((((..(((..............))).)))))))).)))))................(((((((((((...))))))))....))).. ( -21.24)
>DroEre_CAF1 40822 100 - 1
UCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAAUUUAG---------UUCUUUUUACCCUUAAGCCUGGUUUAUGGUUAUUCAAA
................(((((((((..(((..............))).))))))))).....---------...............((((........))))....... ( -16.74)
>DroYak_CAF1 38277 106 - 1
UCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAUUUUAGCUAGUU---UUUUUUUUGCCCAUAAGCCUGGUUUAUGGUUAUUCAAA
..(((..((((((....((((((((..(((..............))).)))))))).)))))).))).---..........((((((((...))))))))......... ( -24.44)
>DroAna_CAF1 61288 96 - 1
UUACUUUGUUAAAUCCUUGUGGCCAUUGAAUAAAAAUUAUUUAUAGUUUGGUUACACUUUA-----------UUUUUUCGUCCAUAAGCCUCUUUUAUUGUGUUGA--A
.................((((((((.((((((.....)))))).....)))))))).....-----------....((((..(((((..........))))).)))--) ( -12.10)
>consensus
UCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUG_U___UUUUUUUUGCCCAUAAGCCUGGUUUAUGGUUAUGCACA
.................((((((((..(((..............))).)))))))).........................((((((((...))))))))......... (-15.63 = -16.32 +   0.70)

alignment

secondary structure

dotplot

Window 9

Location	12,914,801 – 12,914,904
Length	103
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	86.86
Mean single sequence MFE	-16.40
Consensus MFE	-13.50
Energy contribution	-14.06
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-2.07
Structure conservation index	0.82
SVM decision value	0.44
SVM RNA-class probability	0.738689
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12914801 103 - 23771897
UUAUAACUUUAAUACUUUUGUAUCUUUGCAAUCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUGAUUUUU-
.................(((((....))))).......(((((((...((((((((..(((..............))).)))))))).....)))))))....- ( -17.34)
>DroSec_CAF1 35557 104 - 1
UUAUAACUUUAAUACUUUUGUAUCUUUGCAAUCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUGAUUUUUU
.................(((((....))))).......(((((((...((((((((..(((..............))).)))))))).....)))))))..... ( -17.34)
>DroSim_CAF1 34589 104 - 1
UUAUAACUUUAAUACUUUUGUAUCUUUGCAAUCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUGUUUUUUU
.......(((((((...(((((....)))))......)))))))....((((((((..(((..............))).))))))))................. ( -16.64)
>DroEre_CAF1 40858 95 - 1
UUAUAGUUUUAAUACUUUUGUAUCUUUGCAAUCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAAUUUAG---------UU
.......(((((((...(((((....)))))......)))))))...(((((((((..(((..............))).))))))))).....---------.. ( -17.54)
>DroYak_CAF1 38313 101 - 1
UUAUAAUUUUAAUACUUUUGUAGCUUUGCAAUCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAUUUUAGCUAGUU---UU
.................(((((....)))))..(((..((((((....((((((((..(((..............))).)))))))).)))))).))).---.. ( -18.44)
>DroAna_CAF1 61322 92 - 1
UAAUCAUUUAAAUACC-UUGCAUUUUAGCCAUUACUUUGUUAAAUCCUUGUGGCCAUUGAAUAAAAAUUAUUUAUAGUUUGGUUACACUUUA-----------U
................-......((((((.........))))))....((((((((.((((((.....)))))).....)))))))).....-----------. ( -11.10)
>consensus
UUAUAACUUUAAUACUUUUGUAUCUUUGCAAUCACUUUGUUAAAUCCUUGUGGCCAUUGCAUAAAUAUUAUUCAUUGUUUGGCUACAUUUUAGUUUG_U___UU
.......(((((((...(((((....)))))......)))))))....((((((((..(((..............))).))))))))................. (-13.50 = -14.06 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:17 2006