Locus 552

Sequence ID	3R_DroMel_CAF1
Location	2,052,639 – 2,052,768
Length	129
Max. P	0.767380

overview

Window 9

Location	2,052,639 – 2,052,757
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	70.43
Mean single sequence MFE	-23.46
Consensus MFE	-10.42
Energy contribution	-11.38
Covariance contribution	0.96
Combinations/Pair	1.22
Mean z-score	-1.77
Structure conservation index	0.44
SVM decision value	0.40
SVM RNA-class probability	0.720878
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2052639 118 + 27905053
CUUUUACAUAAGGC--CGAUUGAAAUUGAAAUUUGGUAACCGUAAGAACAGUGACAUGUCAUUGUUCUUGUUGAAUAAUUUUGAUUCCAGCCAGAAAAAGGACUUAAAAGGACUUUAUCU
...........(((--....((.(((..(((((...((((...(((((((((((....)))))))))))))))...)))))..))).)))))(((.((((..((....))..)))).))) ( -31.90)
>DroSec_CAF1 196104 118 + 1
CUUUUACUUAACGC--CCUCUUAAAUUCAAAUUUGGUAACCGUAACAACAAUGAUAUUUCAUUGUUCUGGUUGAAUAAUUUUGAUUCCAACCCAAAAAAGGACUUAAAAGGACUUUAAUU
.......((((.(.--(((.((((.(((...(((((((((((....((((((((....)))))))).)))))).......(((....))).)))))...))).)))).))).).)))).. ( -21.40)
>DroSim_CAF1 201093 118 + 1
CUUUUACAUAACGC--CCUCUUAAAUUCAAAUUUGGUAACCGUAAGAACAAUGAUAUUUCAUUGUUCUGGUUGAAUAAUUUUGAUUCCAACCUAAAAAAGGACUUAAAAGGACUUUAAUU
..............--(((.((((..(((((.(((.(((((...((((((((((....)))))))))))))))..))).)))))......(((.....)))..)))).)))......... ( -25.40)
>DroEre_CAF1 195991 116 + 1
CGUUUGCAUAAGAC--UGACUUAAAUACAGAUUUGUUGG-CGUAAGAACAAUGAUAUACCACUGUGCUGGUCGAAUAGUUUCGAUUUAAGCUUAAAACAGCACCUAAAUGGAUAUGUA-G
....((((((.(.(--((........((((..(..(((.-(....)..)))..).......))))(((.((((((....))))))...)))......)))).((.....)).))))))-. ( -21.50)
>DroYak_CAF1 199435 95 + 1
CUUUUACAUAAGACGUCGAUUUAAAUAUAGAAUUGUUAGCCAUAAGAACAAUGAAAUAUCAUUGUGCUGCUUGCCUAGUUUCGAUAUGAGUCAAA-------------------------
.................((((((.((...(((...((((.((..((.(((((((....))))))).))...)).)))).))).)).))))))...------------------------- ( -17.10)
>consensus
CUUUUACAUAAGGC__CGACUUAAAUUCAAAUUUGGUAACCGUAAGAACAAUGAUAUAUCAUUGUUCUGGUUGAAUAAUUUUGAUUCCAGCCAAAAAAAGGACUUAAAAGGACUUUAA_U
.......................(((..(((((...(((((...((((((((((....)))))))))))))))...)))))..))).................................. (-10.42 = -11.38 +   0.96)

alignment

secondary structure

dotplot

Window 0

Location	2,052,639 – 2,052,757
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	70.43
Mean single sequence MFE	-23.84
Consensus MFE	-7.88
Energy contribution	-8.40
Covariance contribution	0.52
Combinations/Pair	1.20
Mean z-score	-1.86
Structure conservation index	0.33
SVM decision value	0.52
SVM RNA-class probability	0.767380
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2052639 118 - 27905053
AGAUAAAGUCCUUUUAAGUCCUUUUUCUGGCUGGAAUCAAAAUUAUUCAACAAGAACAAUGACAUGUCACUGUUCUUACGGUUACCAAAUUUCAAUUUCAAUCG--GCCUUAUGUAAAAG
(((.((((..((....))..)))).)))((((((.................(((((((.(((....))).)))))))..((...))...............)))--)))........... ( -23.20)
>DroSec_CAF1 196104 118 - 1
AAUUAAAGUCCUUUUAAGUCCUUUUUUGGGUUGGAAUCAAAAUUAUUCAACCAGAACAAUGAAAUAUCAUUGUUGUUACGGUUACCAAAUUUGAAUUUAAGAGG--GCGUUAAGUAAAAG
..((((.((((((((((((.(...(((((((((((..........)))))))..((((((((....))))))))...........))))...).))))))))))--)).))))....... ( -31.30)
>DroSim_CAF1 201093 118 - 1
AAUUAAAGUCCUUUUAAGUCCUUUUUUAGGUUGGAAUCAAAAUUAUUCAACCAGAACAAUGAAAUAUCAUUGUUCUUACGGUUACCAAAUUUGAAUUUAAGAGG--GCGUUAUGUAAAAG
.......((((((((((((.(.......(((((((..........)))))))((((((((((....))))))))))................).))))))))))--))............ ( -31.60)
>DroEre_CAF1 195991 116 - 1
C-UACAUAUCCAUUUAGGUGCUGUUUUAAGCUUAAAUCGAAACUAUUCGACCAGCACAGUGGUAUAUCAUUGUUCUUACG-CCAACAAAUCUGUAUUUAAGUCA--GUCUUAUGCAAACG
.-........(((....((((((.((((....))))(((((....))))).)))))).)))(((((..((((..((((..-...(((....)))...)))).))--))..)))))..... ( -19.20)
>DroYak_CAF1 199435 95 - 1
-------------------------UUUGACUCAUAUCGAAACUAGGCAAGCAGCACAAUGAUAUUUCAUUGUUCUUAUGGCUAACAAUUCUAUAUUUAAAUCGACGUCUUAUGUAAAAG
-------------------------...(((((((((.(((..(((.((...((.(((((((....))))))).))..)).)))....))).)))).......)).)))........... ( -13.91)
>consensus
A_UUAAAGUCCUUUUAAGUCCUUUUUUAGGCUGGAAUCAAAAUUAUUCAACCAGAACAAUGAAAUAUCAUUGUUCUUACGGUUACCAAAUUUGAAUUUAAGUCG__GCCUUAUGUAAAAG
....................................................((((((((((....))))))))))............................................ ( -7.88 =  -8.40 +   0.52)

alignment

secondary structure

dotplot

Window 1

Location	2,052,677 – 2,052,768
Length	91
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	67.62
Mean single sequence MFE	-20.62
Consensus MFE	-10.88
Energy contribution	-11.62
Covariance contribution	0.75
Combinations/Pair	1.25
Mean z-score	-1.60
Structure conservation index	0.53
SVM decision value	0.49
SVM RNA-class probability	0.755013
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2052677 91 + 27905053
CGUAAGAACAGUGACAUGUCAUUGUUCUUGUUGAAUAAUUUUGAUUCCAGCCAGAAAAAGGACUUAAAAGGACUUUAUCUUACGCGAUAAC-----------------------
..((((((((((((....))))))))))))...................((.(((.((((..((....))..)))).)))...))......----------------------- ( -22.30)
>DroSec_CAF1 196142 114 + 1
CGUAACAACAAUGAUAUUUCAUUGUUCUGGUUGAAUAAUUUUGAUUCCAACCCAAAAAAGGACUUAAAAGGACUUUAAUUUACGCGAUAACAACUUUUUGGACAGUGCUUAAAC
.((((.((((((((....))))))))..((((((((.......))).)))))....((((..((....))..))))...))))(((....(((....))).....)))...... ( -19.60)
>DroSim_CAF1 201131 114 + 1
CGUAAGAACAAUGAUAUUUCAUUGUUCUGGUUGAAUAAUUUUGAUUCCAACCUAAAAAAGGACUUAAAAGGACUUUAAUUUACGCGAUAACAACUUUUUGGACAGUGCCUAAAC
....((((((((((....))))))))))((((((((.......))).)))))....((((..((....))..))))..((((.(((....(((....))).....))).)))). ( -24.30)
>DroEre_CAF1 196028 82 + 1
CGUAAGAACAAUGAUAUACCACUGUGCUGGUCGAAUAGUUUCGAUUUAAGCUUAAAACAGCACCUAAAUGGAUAUGUA-G-AAU------------------------------
.............((((((((..((((((((((((....))))))(((....)))..)))))).....))).))))).-.-...------------------------------ ( -16.30)
>consensus
CGUAAGAACAAUGAUAUUUCAUUGUUCUGGUUGAAUAAUUUUGAUUCCAACCUAAAAAAGGACUUAAAAGGACUUUAAUUUACGCGAUAAC_______________________
....((((((((((....))))))))))((((((((.......)))).)))).....((((.((.....)).))))...................................... (-10.88 = -11.62 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:54 2006