Locus 5470

Sequence ID	2R_DroMel_CAF1
Location	17,608,662 – 17,608,853
Length	191
Max. P	0.991237

overview

Window 7

Location	17,608,662 – 17,608,758
Length	96
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	78.23
Mean single sequence MFE	-28.18
Consensus MFE	-15.19
Energy contribution	-15.07
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-2.06
Structure conservation index	0.54
SVM decision value	0.17
SVM RNA-class probability	0.614836
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17608662 96 - 20766785
CACCACUGCCCCCCA--------UCAACUGGGCAAUCACUGACAUCGCAG---------UGGCAUGGUUU-UCGGGGCUAUUCCAAAUAGAUAUCAUUCAAAGAUAUA------UUUCUC
.......(((((...--------..((((..((...(((((......)))---------))))..)))).-..)))))............(((((.......))))).------...... ( -21.10)
>DroSec_CAF1 23335 99 - 1
CACCACUGCCCCCCA--------UCAACUGGGCAAUCACUGACAUCGCAG---------AGGCAUGGUUU-UGGGGGCUAUUCCAAAUAGAUAUCAUUGAGAGAUAUA---AUAAUUAUC
.((((.((((.((((--------.....))))......(((......)))---------.))))))))((-(((((....)))))))...(((((.......))))).---......... ( -22.70)
>DroSim_CAF1 24110 99 - 1
CACCACUGCCCCCCA--------UCAACUGGGCAAUCACUGACAUCGCAG---------AGGCAUGGUUU-UGGGGGCUAUUCCAAAUAGAUAUCAUUGAGAGAUAUA---AUAAUUCUC
.((((.((((.((((--------.....))))......(((......)))---------.))))))))((-(((((....)))))))...(((((.......))))).---......... ( -22.70)
>DroYak_CAF1 25062 120 - 1
CACCACUGCCCCCCACCAACCGACCAACUGGGCAAUCACUGACAUCGCAGUGAUUGCAGGGGCAUGGAUUUUUGGGGUAAUCCCAGAAAGAUAUUCGUGGAAGAAAUUAUCAAAAAUAUU
..(((.((((((.......(((......)))((((((((((......)))))))))).))))))))).((((((((.....))))))))((((((..(((((....)).)))..)))))) ( -46.20)
>consensus
CACCACUGCCCCCCA________UCAACUGGGCAAUCACUGACAUCGCAG_________AGGCAUGGUUU_UGGGGGCUAUUCCAAAUAGAUAUCAUUGAAAGAUAUA___AUAAUUAUC
..(((.((((.((((.............))))......(((......)))..........))))))).......(((....)))......(((((.......)))))............. (-15.19 = -15.07 +  -0.12)

alignment

secondary structure

dotplot

Window 8

Location	17,608,696 – 17,608,787
Length	91
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	79.14
Mean single sequence MFE	-30.51
Consensus MFE	-15.91
Energy contribution	-15.95
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.98
Structure conservation index	0.52
SVM decision value	0.34
SVM RNA-class probability	0.694375
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17608696 91 - 20766785
GUUACAAUAAUAACAGCCGUGAUUCCCGACACCACUGCCCCCCA--------UCAACUGGGCAAUCACUGACAUCGCAG---------UGGCAUGGUUU-UCGGGGCUA
((((......))))((((.(((...(((...(((((((..((((--------.....))))((.....)).....))))---------)))..)))...-))).)))). ( -28.70)
>DroSec_CAF1 23372 91 - 1
GUUACAAUAAUAACAGCCGUGAUUCCCGACACCACUGCCCCCCA--------UCAACUGGGCAAUCACUGACAUCGCAG---------AGGCAUGGUUU-UGGGGGCUA
((((......))))((((......(((((.((((.((((.((((--------.....))))......(((......)))---------.)))))))).)-)))))))). ( -29.20)
>DroSim_CAF1 24147 91 - 1
GUUACAAUAAUAACAGCCGUGAUUCCCGACACCACUGCCCCCCA--------UCAACUGGGCAAUCACUGACAUCGCAG---------AGGCAUGGUUU-UGGGGGCUA
((((......))))((((......(((((.((((.((((.((((--------.....))))......(((......)))---------.)))))))).)-)))))))). ( -29.20)
>DroEre_CAF1 25121 94 - 1
GUUACACUAAUAACAGCCGUGAUUCCCGACACCA--------------CCAACCCACUGGGCAAUCACCGACUUCGCAGUGGCGGCAGGGGCAUGAACC-UGGGGGCAU
((((......)))).(((((((((((((......--------------.........)))).)))))).....((((....))))((((........))-))..))).. ( -25.16)
>DroYak_CAF1 25102 109 - 1
GUUACACUAAUAACAGCCGUGAUUCCCGACACCACUGCCCCCCACCAACCGACCAACUGGGCAAUCACUGACAUCGCAGUGAUUGCAGGGGCAUGGAUUUUUGGGGUAA
((((......)))).........((((((..(((.((((((.......(((......)))((((((((((......)))))))))).)))))))))....))))))... ( -40.30)
>consensus
GUUACAAUAAUAACAGCCGUGAUUCCCGACACCACUGCCCCCCA________UCAACUGGGCAAUCACUGACAUCGCAG_________AGGCAUGGUUU_UGGGGGCUA
((((......)))).(((((((((((((.............................)))).))))))...(((.((.............))))).........))).. (-15.91 = -15.95 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	17,608,726 – 17,608,827
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.46
Mean single sequence MFE	-29.26
Consensus MFE	-18.67
Energy contribution	-19.70
Covariance contribution	1.03
Combinations/Pair	1.18
Mean z-score	-2.53
Structure conservation index	0.64
SVM decision value	2.26
SVM RNA-class probability	0.991237
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17608726 101 - 20766785
CCGGGAUCGCGGUCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACAAUAAUAAC-----------AGCCGUGAUUCCCGACACCACUGCCCCCCA--------UCAACUGGGCAAUCACU
.((((((((((((......(((....)))((((((((.....))))))))....-----------.))))))).))))).......(((((....--------......)))))...... ( -32.70)
>DroVir_CAF1 32366 95 - 1
GCGCCG----UGUCCAUUUGGUAAUAUCUUUGCCGUAAUUGUAACAGUAAUGAUAAUGCCCAGCUAGCCGUGAUGCCUAAUGCCCAUGCUCAUUA--------UUAG-------------
(.((.(----((..((((.((((.((((.((((.((.......)).)))).))))..((.......)).....)))).))))..))))).)....--------....------------- ( -16.40)
>DroSec_CAF1 23402 101 - 1
CCGGGAUCGCGGCCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACAAUAAUAAC-----------AGCCGUGAUUCCCGACACCACUGCCCCCCA--------UCAACUGGGCAAUCACU
.((((((((((((......(((....)))((((((((.....))))))))....-----------.))))))).))))).......(((((....--------......)))))...... ( -34.70)
>DroSim_CAF1 24177 101 - 1
CCGGGAUCGCGGCCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACAAUAAUAAC-----------AGCCGUGAUUCCCGACACCACUGCCCCCCA--------UCAACUGGGCAAUCACU
.((((((((((((......(((....)))((((((((.....))))))))....-----------.))))))).))))).......(((((....--------......)))))...... ( -34.70)
>DroEre_CAF1 25160 95 - 1
CCGGGAUCGCGGUCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACACUAAUAAC-----------AGCCGUGAUUCCCGACACCA--------------CCAACCCACUGGGCAAUCACC
.((((((((((((.......((((((....))))))...(((((......))))-----------)))))))).)))))......--------------(((......)))......... ( -26.60)
>DroYak_CAF1 25142 109 - 1
CCGGGAUCGCGGUCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACACUAAUAAC-----------AGCCGUGAUUCCCGACACCACUGCCCCCCACCAACCGACCAACUGGGCAAUCACU
.((((((((((((.......((((((....))))))...(((((......))))-----------)))))))).))))).......(((((..................)))))...... ( -30.47)
>consensus
CCGGGAUCGCGGUCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACAAUAAUAAC___________AGCCGUGAUUCCCGACACCACUGCCCCCCA________UCAACUGGGCAAUCACU
..(((((((((((......(((....)))((((((((.....))))))))................)))))))))))........................................... (-18.67 = -19.70 +   1.03)

alignment

secondary structure

dotplot

Window 0

Location	17,608,758 – 17,608,853
Length	95
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	83.93
Mean single sequence MFE	-31.08
Consensus MFE	-21.16
Energy contribution	-23.55
Covariance contribution	2.39
Combinations/Pair	1.10
Mean z-score	-2.23
Structure conservation index	0.68
SVM decision value	0.09
SVM RNA-class probability	0.579684
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17608758 95 - 20766785
--------------CCAACAGCGCUACCGUUGGCCAUUUGCCGGGAUCGCGGUCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACAAUAAUAACAGCCGUGAUUCCCGA
--------------....(((((....))))).........((((((((((((......(((....)))((((((((.....)))))))).....))))))).))))). ( -30.40)
>DroSec_CAF1 23434 95 - 1
--------------CCACCAGCGCUACCGUUGGCCAUUUGCCGGGAUCGCGGCCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACAAUAAUAACAGCCGUGAUUCCCGA
--------------...((((((....))))))........((((((((((((......(((....)))((((((((.....)))))))).....))))))).))))). ( -34.80)
>DroSim_CAF1 24209 95 - 1
--------------CCGCCAGCGCUACCGUUGGCCAUUUGCCGGGAUCGCGGCCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACAAUAAUAACAGCCGUGAUUCCCGA
--------------..(((((((....))))))).......((((((((((((......(((....)))((((((((.....)))))))).....))))))).))))). ( -38.40)
>DroEre_CAF1 25186 104 - 1
UCC-----ACGACUCCAACAGCGCUACCGUUGGCCAUUUGCCGGGAUCGCGGUCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACACUAAUAACAGCCGUGAUUCCCGA
...-----..........(((((....))))).........((((((((((((.......((((((....))))))...(((((......)))))))))))).))))). ( -28.80)
>DroYak_CAF1 25182 109 - 1
UCAACCACUCCACUCCACCGGCGCUACCGUUGGCCAUUUGCCGGGAUCGCGGUCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACACUAAUAACAGCCGUGAUUCCCGA
.................((((((....))))))........((((((((((((.......((((((....))))))...(((((......)))))))))))).))))). ( -30.40)
>DroAna_CAF1 23864 82 - 1
--------------C--CGAGAGCUACCGUUGGCCAUUUGGCGGGAUCGC---CCAUUUGGCAAUGCCUUUGUUGUAAUUGUAACAAUAAUAGCAGAAGGG--------
--------------.--.........((....((((..(((((....)).---)))..))))..(((..(((((((.......)))))))..)))...)).-------- ( -23.70)
>consensus
______________CCACCAGCGCUACCGUUGGCCAUUUGCCGGGAUCGCGGUCCAUUUGGCAAUAGCUUUGUUGUAAUUGUUACAAUAAUAACAGCCGUGAUUCCCGA
.................((((((....))))))........((((((((((((......(((....))).((((((.((((...)))).))))))))))))).))))). (-21.16 = -23.55 +   2.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:42 2006