Locus 6670

Sequence ID	2L_DroMel_CAF1
Location	18,710,140 – 18,710,295
Length	155
Max. P	0.998690

overview

Window 5

Location	18,710,140 – 18,710,236
Length	96
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	75.68
Mean single sequence MFE	-24.48
Consensus MFE	-13.73
Energy contribution	-13.72
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.94
Structure conservation index	0.56
SVM decision value	3.05
SVM RNA-class probability	0.998251
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18710140 96 + 22407834
UAAAAAUAAA-------AUAUUAGCCCAGAUUAAAAAAGAAAAA-----------------UAAAUCUUAAAGAUUUGAAUAGCUCAGAUCACAACCAGACUGGUUGGGUUCAAGGCUAG
..........-------....(((((..((......((((....-----------------....))))...(((((((.....))))))).(((((.....)))))...))..))))). ( -20.90)
>DroSec_CAF1 3084 113 + 1
UAAAAAUAAA-------AUAUUGGGCCUGAUUAAAAAACAAUAUGCAAUUCAAUCCUUUGGCAAAGUUUAAAGAUUUGAAUAGCUCAGAUCACAACCAGACUGGUUGGGUUCCAGGCUAA
..........-------......((((((...............((.((((((..((((((......))))))..)))))).))...((((.(((((.....))))))))).)))))).. ( -29.10)
>DroSim_CAF1 2962 113 + 1
UAAAAAAAAA-------AUUUUGCACCUGAUUAAAAAACAAUAUGCCAUUCAAUCCUUUGGCAAAGUUUAAAAAUUUGAAUAGCUCAGAUCACAACCAGACUGGUUGGGUUCCAGGCUAA
........((-------(((((((....((((...................)))).....)))))))))...........(((((..((...(((((.....)))))...))..))))). ( -21.51)
>DroYak_CAF1 2895 120 + 1
AAAUAAUAAAACAAGAAAUUUUGUGCCAGAUUAAAAUGGAAUAGGCAUAGCAAUCCUUCGACCAAAUUUAAAGAUUUAAAUAGCUAAGAUCGCAACCAGACCGGUUGCGUUCCAGGCUAA
..............(((((((((((((................))))))).)))..))).....................(((((..((.(((((((.....))))))).))..))))). ( -26.39)
>consensus
UAAAAAUAAA_______AUAUUGGGCCAGAUUAAAAAACAAUAUGCAAUUCAAUCCUUUGGCAAAGUUUAAAGAUUUGAAUAGCUCAGAUCACAACCAGACUGGUUGGGUUCCAGGCUAA
................................................................................(((((..((...(((((.....)))))...))..))))). (-13.73 = -13.72 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	18,710,140 – 18,710,236
Length	96
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	75.68
Mean single sequence MFE	-24.25
Consensus MFE	-12.43
Energy contribution	-12.67
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.06
Structure conservation index	0.51
SVM decision value	0.24
SVM RNA-class probability	0.650022
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18710140 96 - 22407834
CUAGCCUUGAACCCAACCAGUCUGGUUGUGAUCUGAGCUAUUCAAAUCUUUAAGAUUUA-----------------UUUUUCUUUUUUAAUCUGGGCUAAUAU-------UUUAUUUUUA
.((((((.((...(((((.....))))).(((.((((...)))).)))...((((....-----------------....))))......)).))))))....-------.......... ( -17.70)
>DroSec_CAF1 3084 113 - 1
UUAGCCUGGAACCCAACCAGUCUGGUUGUGAUCUGAGCUAUUCAAAUCUUUAAACUUUGCCAAAGGAUUGAAUUGCAUAUUGUUUUUUAAUCAGGCCCAAUAU-------UUUAUUUUUA
.((((..(((.(.(((((.....))))).).)))..))))..................(((....(((((((..((.....))..))))))).))).......-------.......... ( -25.10)
>DroSim_CAF1 2962 113 - 1
UUAGCCUGGAACCCAACCAGUCUGGUUGUGAUCUGAGCUAUUCAAAUUUUUAAACUUUGCCAAAGGAUUGAAUGGCAUAUUGUUUUUUAAUCAGGUGCAAAAU-------UUUUUUUUUA
.((((..(((.(.(((((.....))))).).)))..))))...............((((((....(((((((..((.....))..)))))))..).)))))..-------.......... ( -26.30)
>DroYak_CAF1 2895 120 - 1
UUAGCCUGGAACGCAACCGGUCUGGUUGCGAUCUUAGCUAUUUAAAUCUUUAAAUUUGGUCGAAGGAUUGCUAUGCCUAUUCCAUUUUAAUCUGGCACAAAAUUUCUUGUUUUAUUAUUU
.((((..(((.(((((((.....))))))).)))..))))..((((.(...((((((.((.(..((((((..(((.......)))..))))))..))).))))))...).))))...... ( -27.90)
>consensus
UUAGCCUGGAACCCAACCAGUCUGGUUGUGAUCUGAGCUAUUCAAAUCUUUAAACUUUGCCAAAGGAUUGAAUUGCAUAUUCUUUUUUAAUCAGGCCCAAAAU_______UUUAUUUUUA
.((((..(((.(.(((((.....))))).).)))..))))................................................................................ (-12.43 = -12.67 +   0.25)

alignment

secondary structure

dotplot

Window 7

Location	18,710,196 – 18,710,295
Length	99
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.23
Mean single sequence MFE	-27.16
Consensus MFE	-14.90
Energy contribution	-14.94
Covariance contribution	0.04
Combinations/Pair	1.06
Mean z-score	-2.79
Structure conservation index	0.55
SVM decision value	3.19
SVM RNA-class probability	0.998690
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18710196 99 + 22407834
UAGCUCAGAUCACAACCAGACUGGUUGGGUUCAAGGCUAGAUCUAUGUAU------GUAAAA---------------UUCGUCGUAGAAUCAAUGUAUAAUUCAUACAGAGAAGAGAAUG
(((((..((((.(((((.....)))))))))...)))))..((((((.((------(.....---------------..))))))))).((..(((((.....)))))..))........ ( -23.70)
>DroSec_CAF1 3157 99 + 1
UAGCUCAGAUCACAACCAGACUGGUUGGGUUCCAGGCUAAAUAUAUGUAU------GUCAAA---------------AUCUUCGUAAAAUCGAUGUAUAAUACAUACAAAAUACAGAAUG
(((((..((...(((((.....)))))...))..)))))......(((((------((....---------------....(((......)))........)))))))............ ( -22.69)
>DroSim_CAF1 3035 99 + 1
UAGCUCAGAUCACAACCAGACUGGUUGGGUUCCAGGCUAAAUCGAUGUAU------GUCAAA---------------UUCUUCGUAGAAUCGAUGUAUAAUACAUACAAAAUACAGAAUG
(((((..((...(((((.....)))))...))..)))))......(((((------((....---------------....(((......)))........)))))))............ ( -22.69)
>DroEre_CAF1 2983 120 + 1
UAGCUCAGAUCGCAACCAGACUGGUUGCGUUCCAAGCUAAAUCGUUGUAUGUAUAUGUAUAAUACAUGUAUGAAAGGUUCUUCGUAAAAUCUAUGUAUAAUACAUACAUAAUACCGGAUG
(((((..((.(((((((.....))))))).))..)))))..(((...((((((..(((((.(((((((((((((......)))))).....))))))).)))))))))))....)))... ( -37.30)
>DroYak_CAF1 2975 107 + 1
UAGCUAAGAUCGCAACCAGACCGGUUGCGUUCCAGGCUAAAUCUUUCUAU------GUAAAAUAAAUGUAAGUA-------UAGUAUAACCUAUGUAUAGUACCUACAUCCUGUAGGAUG
(((((..((.(((((((.....))))))).))..)))))...........------...........(((.(((-------(.(((((.....))))).)))).)))((((....)))). ( -29.40)
>consensus
UAGCUCAGAUCACAACCAGACUGGUUGGGUUCCAGGCUAAAUCUAUGUAU______GUAAAA_______________UUCUUCGUAAAAUCGAUGUAUAAUACAUACAAAAUACAGAAUG
(((((..((...(((((.....)))))...))..)))))......................................................(((((.....)))))............ (-14.90 = -14.94 +   0.04)

alignment

secondary structure

dotplot

Window 8

Location	18,710,196 – 18,710,295
Length	99
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.23
Mean single sequence MFE	-26.21
Consensus MFE	-13.10
Energy contribution	-13.50
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.57
Structure conservation index	0.50
SVM decision value	2.58
SVM RNA-class probability	0.995462
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18710196 99 - 22407834
CAUUCUCUUCUCUGUAUGAAUUAUACAUUGAUUCUACGACGAA---------------UUUUAC------AUACAUAGAUCUAGCCUUGAACCCAACCAGUCUGGUUGUGAUCUGAGCUA
........(((.((((((...........(((((......)))---------------))...)------))))).)))..((((...((.(.(((((.....))))).).))...)))) ( -18.34)
>DroSec_CAF1 3157 99 - 1
CAUUCUGUAUUUUGUAUGUAUUAUACAUCGAUUUUACGAAGAU---------------UUUGAC------AUACAUAUAUUUAGCCUGGAACCCAACCAGUCUGGUUGUGAUCUGAGCUA
......((((..(((((((........(((......)))....---------------....))------))))).)))).((((..(((.(.(((((.....))))).).)))..)))) ( -22.79)
>DroSim_CAF1 3035 99 - 1
CAUUCUGUAUUUUGUAUGUAUUAUACAUCGAUUCUACGAAGAA---------------UUUGAC------AUACAUCGAUUUAGCCUGGAACCCAACCAGUCUGGUUGUGAUCUGAGCUA
............(((((((...((.(.(((......))).).)---------------)...))------)))))......((((..(((.(.(((((.....))))).).)))..)))) ( -22.80)
>DroEre_CAF1 2983 120 - 1
CAUCCGGUAUUAUGUAUGUAUUAUACAUAGAUUUUACGAAGAACCUUUCAUACAUGUAUUAUACAUAUACAUACAACGAUUUAGCUUGGAACGCAACCAGUCUGGUUGCGAUCUGAGCUA
.(((..((((..(((((((((.((((((.(......)((((....))))....)))))).))))))))).))))...))).(((((..((.(((((((.....))))))).))..))))) ( -38.50)
>DroYak_CAF1 2975 107 - 1
CAUCCUACAGGAUGUAGGUACUAUACAUAGGUUAUACUA-------UACUUACAUUUAUUUUAC------AUAGAAAGAUUUAGCCUGGAACGCAACCGGUCUGGUUGCGAUCUUAGCUA
.........(((((((((((.......(((......)))-------))))))))))).......------...........((((..(((.(((((((.....))))))).)))..)))) ( -28.61)
>consensus
CAUUCUGUAUUAUGUAUGUAUUAUACAUAGAUUCUACGAAGAA_______________UUUUAC______AUACAUAGAUUUAGCCUGGAACCCAACCAGUCUGGUUGUGAUCUGAGCUA
............((((((...))))))......................................................((((..(((.(.(((((.....))))).).)))..)))) (-13.10 = -13.50 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:55 2006