Locus 5385

Sequence ID	3L_DroMel_CAF1
Location	14,799,407 – 14,799,635
Length	228
Max. P	0.866993

overview

Window 1

Location	14,799,407 – 14,799,526
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	86.05
Mean single sequence MFE	-19.83
Consensus MFE	-12.64
Energy contribution	-13.64
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.06
Structure conservation index	0.64
SVM decision value	0.06
SVM RNA-class probability	0.562741
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14799407 119 + 23771897
UCAUGUAAAAAAUAAAUUUACAUUUGACCAUAAAAUGAUUUCAAACAGCAUUUAAGGCUGAAUUUACAAUAAUUCCCUUCUGCUAUACGCACUCGAUAAAUGCUUGAUUAAAUCAUGUU
..(((((((.......)))))))...........(((((((.....(((((((((((..(((((......))))))))..(((.....))).....)))))))).....)))))))... ( -20.30)
>DroSec_CAF1 34864 119 + 1
UCACGUAAAAAAUAAAUUUACAUUUGCCCAUAAAAUGAUGUCAAACAGCAUUUAAGGCUGAAUUUACAAUAAUUCCCGUCUGCUAUACGCACUCGAUAAAUGCUAGUUUAAAUCAUGUU
....(((((.......))))).............(((((...((((((((((((((((.(((((......)))))..))))((.....))......)))))))).))))..)))))... ( -22.40)
>DroSim_CAF1 27807 119 + 1
UCACGUAAAAAAUAAAUUUAUAUUUGCCCAUAAAAUGAUUUCAAACAGCAUUUAUGUCUGAAUUUACAAUAAUACCCGUCUGCUAUACGCACUCGAUAAAUGCUAGAUUAAAUCAUGUC
..................................(((((((.....(((((((((((........)).........((..(((.....)))..))))))))))).....)))))))... ( -16.60)
>DroEre_CAF1 34462 117 + 1
UCACGUAAUAAAUAAAUUUUCAUUUACACAUUAUAUGAUUUCAAACAGCAUUUACCGCUGAAUUUACAAUAAUUCCCUUCUGCUAUACGCACUCGGCAAAUGCUUGAUUA--UCAUGUU
....((((...............)))).....(((((((.(((...(((((((.(((..(((((......))))).....(((.....)))..))).))))))))))..)--)))))). ( -20.96)
>DroYak_CAF1 36765 106 + 1
UCACGUAUUAAAUGAGUU-------------UAUAUGAUUUCAAACAGCAUUUAACGUUGAAUUUACAAUAAUUCCCUUCUGCUAUACGCACUCGAUAAAUGCUUGAUUAAAUCAUGUU
..................-------------.(((((((((.....((((((((.((..(((((......))))).....(((.....)))..)).)))))))).....))))))))). ( -18.90)
>consensus
UCACGUAAAAAAUAAAUUUACAUUUGCCCAUAAAAUGAUUUCAAACAGCAUUUAAGGCUGAAUUUACAAUAAUUCCCUUCUGCUAUACGCACUCGAUAAAUGCUUGAUUAAAUCAUGUU
..................................(((((((.....((((((((.....(((((......))))).....(((.....))).....)))))))).....)))))))... (-12.64 = -13.64 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	14,799,407 – 14,799,526
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	86.05
Mean single sequence MFE	-25.50
Consensus MFE	-16.66
Energy contribution	-17.14
Covariance contribution	0.48
Combinations/Pair	1.08
Mean z-score	-1.88
Structure conservation index	0.65
SVM decision value	-0.01
SVM RNA-class probability	0.527517
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14799407 119 - 23771897
AACAUGAUUUAAUCAAGCAUUUAUCGAGUGCGUAUAGCAGAAGGGAAUUAUUGUAAAUUCAGCCUUAAAUGCUGUUUGAAAUCAUUUUAUGGUCAAAUGUAAAUUUAUUUUUUACAUGA
...((((((...((((((((((...))))))..((((((.(((((((((......)))))..))))...))))))))))))))))...........(((((((.......))))))).. ( -25.10)
>DroSec_CAF1 34864 119 - 1
AACAUGAUUUAAACUAGCAUUUAUCGAGUGCGUAUAGCAGACGGGAAUUAUUGUAAAUUCAGCCUUAAAUGCUGUUUGACAUCAUUUUAUGGGCAAAUGUAAAUUUAUUUUUUACGUGA
...(((((((((((.(((((((((((..(((.....)))..)))(((((......))))).....)))))))))))))).)))))...........(((((((.......))))))).. ( -26.90)
>DroSim_CAF1 27807 119 - 1
GACAUGAUUUAAUCUAGCAUUUAUCGAGUGCGUAUAGCAGACGGGUAUUAUUGUAAAUUCAGACAUAAAUGCUGUUUGAAAUCAUUUUAUGGGCAAAUAUAAAUUUAUUUUUUACGUGA
...(((((((....((((((((((((..(((.....)))..))).......(((........))))))))))))....))))))).(((((...(((((......)))))....))))) ( -21.60)
>DroEre_CAF1 34462 117 - 1
AACAUGA--UAAUCAAGCAUUUGCCGAGUGCGUAUAGCAGAAGGGAAUUAUUGUAAAUUCAGCGGUAAAUGCUGUUUGAAAUCAUAUAAUGUGUAAAUGAAAAUUUAUUUAUUACGUGA
.......--...((((((((((((((..(((.....))).....(((((......)))))..)))))))))))...)))..(((..(((((.((((((....)))))).)))))..))) ( -31.70)
>DroYak_CAF1 36765 106 - 1
AACAUGAUUUAAUCAAGCAUUUAUCGAGUGCGUAUAGCAGAAGGGAAUUAUUGUAAAUUCAACGUUAAAUGCUGUUUGAAAUCAUAUA-------------AACUCAUUUAAUACGUGA
...(((((((.....((((((((.((..(((.....))).....(((((......)))))..)).)))))))).....)))))))...-------------.................. ( -22.20)
>consensus
AACAUGAUUUAAUCAAGCAUUUAUCGAGUGCGUAUAGCAGAAGGGAAUUAUUGUAAAUUCAGCCUUAAAUGCUGUUUGAAAUCAUUUUAUGGGCAAAUGUAAAUUUAUUUUUUACGUGA
...(((((((.....((((((((((...(((.....)))...))(((((......))))).....)))))))).....))))))).................................. (-16.66 = -17.14 +   0.48)

alignment

secondary structure

dotplot

Window 3

Location	14,799,526 – 14,799,635
Length	109
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.66
Mean single sequence MFE	-25.21
Consensus MFE	-16.14
Energy contribution	-17.58
Covariance contribution	1.45
Combinations/Pair	1.13
Mean z-score	-2.63
Structure conservation index	0.64
SVM decision value	0.85
SVM RNA-class probability	0.866993
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14799526 109 + 23771897
U--AUAUCA---------CUCGACGAAAAAAUAAUCGACGACUUAAAAUCCUCGAAUGGAUUACAGUGUUGAACAUUGUAAUCCUUAAAGAAGAUUUUGAUGCGCAUUACAGCAAGCCAC
.--......---------.(((.(((........))).))).((((((((.((....(((((((((((.....))))))))))).....)).))))))))(((........)))...... ( -28.90)
>DroSec_CAF1 34983 109 + 1
C--AUAUGA---------CUCGACGAAAAAAUAAUCGACGAUUUAAAAUCCUCGAAUGGAUUACAGUGUUGAACAUUGUAAUCCUUAAAGAAGAUUUUGAUGCGCAUUACAGCAAGCCAC
.--......---------.(((.(((........))).))).((((((((.((....(((((((((((.....))))))))))).....)).))))))))(((........)))...... ( -29.10)
>DroSim_CAF1 27926 109 + 1
U--AUAUCA---------CUCGACGAAAAAAUAAUCGACGAUUUAAAAUCCUCGAAUGGAUUACAGUGUUGAACAUUGUAAUCCUUAAAGAAGAUUUUGAUGCGCAUUACAGCAAGCCAC
.--......---------.(((.(((........))).))).((((((((.((....(((((((((((.....))))))))))).....)).))))))))(((........)))...... ( -29.10)
>DroEre_CAF1 34579 120 + 1
UUUUUAUCAUAGACCAAAAAAAACACAAAAAAAAUCGACGAUUUAAAAUCCUCGAAUGGAUUACAGUGUUGAACAAAGUAAUCCUUAAAGAAGAUUUUGAUGCGCAUUACAGCAAGCCAC
..........................................((((((((.((....(((((((..((.....))..))))))).....)).))))))))(((........)))...... ( -20.50)
>DroYak_CAF1 36871 109 + 1
U--AUAUCA---------AUCGACAGAGAAAAAAACGACGAUUUAAAGUCCUCGAAUGGAUUACAGUGUUGAACAAAGUAAUCCUUAAAGAAGAUUUUGAUGCGCAUUACAGCAAGCCAC
.--......---------........................((((((((.((....(((((((..((.....))..))))))).....)).))))))))(((........)))...... ( -20.50)
>DroAna_CAF1 33257 106 + 1
U--CCAUCA---------GUCAGCAUAUAAAC--UGGCAGCUUUAA-CCGGAACAUUGGCUUAUAGGUUUUUACAAUGUAAUCCUUAAAGAAGAUUUUGAUGCGCAUUAUAGCGGACCAC
.--.(((((---------(((((........)--))))..((((((-..(((((((((...............))))))..))))))))).......)))))(((......)))...... ( -23.16)
>consensus
U__AUAUCA_________CUCGACAAAAAAAUAAUCGACGAUUUAAAAUCCUCGAAUGGAUUACAGUGUUGAACAAUGUAAUCCUUAAAGAAGAUUUUGAUGCGCAUUACAGCAAGCCAC
..........................................((((((((.((....((((((((.((.....)).)))))))).....)).))))))))(((........)))...... (-16.14 = -17.58 +   1.45)

alignment

secondary structure

dotplot

Window 4

Location	14,799,526 – 14,799,635
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.66
Mean single sequence MFE	-25.99
Consensus MFE	-16.09
Energy contribution	-17.48
Covariance contribution	1.39
Combinations/Pair	1.20
Mean z-score	-1.83
Structure conservation index	0.62
SVM decision value	0.12
SVM RNA-class probability	0.595382
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14799526 109 - 23771897
GUGGCUUGCUGUAAUGCGCAUCAAAAUCUUCUUUAAGGAUUACAAUGUUCAACACUGUAAUCCAUUCGAGGAUUUUAAGUCGUCGAUUAUUUUUUCGUCGAG---------UGAUAU--A
...((..((......))))((((((((((((.....((((((((.((.....)).))))))))....))))))))).(.(((.(((........))).))).---------))))..--. ( -29.00)
>DroSec_CAF1 34983 109 - 1
GUGGCUUGCUGUAAUGCGCAUCAAAAUCUUCUUUAAGGAUUACAAUGUUCAACACUGUAAUCCAUUCGAGGAUUUUAAAUCGUCGAUUAUUUUUUCGUCGAG---------UCAUAU--G
(((((..((......)).....(((((((((.....((((((((.((.....)).))))))))....)))))))))...(((.(((........))).))))---------))))..--. ( -31.10)
>DroSim_CAF1 27926 109 - 1
GUGGCUUGCUGUAAUGCGCAUCAAAAUCUUCUUUAAGGAUUACAAUGUUCAACACUGUAAUCCAUUCGAGGAUUUUAAAUCGUCGAUUAUUUUUUCGUCGAG---------UGAUAU--A
...((..((......))))((((((((((((.....((((((((.((.....)).))))))))....)))))))))...(((.(((........))).))).---------.)))..--. ( -28.70)
>DroEre_CAF1 34579 120 - 1
GUGGCUUGCUGUAAUGCGCAUCAAAAUCUUCUUUAAGGAUUACUUUGUUCAACACUGUAAUCCAUUCGAGGAUUUUAAAUCGUCGAUUUUUUUUGUGUUUUUUUUGGUCUAUGAUAAAAA
..((((.........(((((..((((((........(((((((..((.....))..)))))))....((.(((.....))).))))))))...))))).......))))........... ( -26.09)
>DroYak_CAF1 36871 109 - 1
GUGGCUUGCUGUAAUGCGCAUCAAAAUCUUCUUUAAGGAUUACUUUGUUCAACACUGUAAUCCAUUCGAGGACUUUAAAUCGUCGUUUUUUUCUCUGUCGAU---------UGAUAU--A
...((..((......))))((((((.(((((.....(((((((..((.....))..)))))))....))))).))).(((((.((..........)).))))---------))))..--. ( -20.50)
>DroAna_CAF1 33257 106 - 1
GUGGUCCGCUAUAAUGCGCAUCAAAAUCUUCUUUAAGGAUUACAUUGUAAAAACCUAUAAGCCAAUGUUCCGG-UUAAAGCUGCCA--GUUUAUAUGCUGAC---------UGAUGG--A
.((((.(((......))).)))).......(((((.(((..((((((...............)))))))))..-.)))))((..((--(((........)))---------))..))--. ( -20.56)
>consensus
GUGGCUUGCUGUAAUGCGCAUCAAAAUCUUCUUUAAGGAUUACAAUGUUCAACACUGUAAUCCAUUCGAGGAUUUUAAAUCGUCGAUUAUUUUUUCGUCGAG_________UGAUAU__A
..(((.(((......)))....(((((((((.....((((((((.((.....)).))))))))....)))))))))....................)))..................... (-16.09 = -17.48 +   1.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:03 2006