Locus 5388

Sequence ID	3R_DroMel_CAF1
Location	14,155,587 – 14,155,680
Length	93
Max. P	0.864013

overview

Window 5

Location	14,155,587 – 14,155,680
Length	93
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	72.78
Mean single sequence MFE	-18.41
Consensus MFE	-5.84
Energy contribution	-6.62
Covariance contribution	0.78
Combinations/Pair	1.33
Mean z-score	-2.35
Structure conservation index	0.32
SVM decision value	0.84
SVM RNA-class probability	0.864013
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14155587 93 + 27905053
CAUAUUUUUGUCUGCGGCAAUGCAGACUAAUGUGAUUCAAUUAAUCUUUUCGCGUUUUUACCUCGAAGAUUCCU-UUUUUAUUUAUA------UUUAUUC
((((((...(((((((....))))))).))))))........(((((((..(.((....)))..)))))))...-............------....... ( -17.80)
>DroSec_CAF1 148447 90 + 1
CAUAUUUUUGUCUGCGGCAAUGCAGACUAAUGUGAUUCAAUUAAUCUUUUCGCGUUUU---CGCGAAGAUUCCG-UUUUCAUUUAUA------UUUAUUC
((((((...(((((((....))))))).))))))............((((((((....---)))))))).....-............------....... ( -24.00)
>DroSim_CAF1 33766 93 + 1
CAUAUUUUUGUCUGCGGCAAUGCAGACUAAUGUGAUUCAAUUAAUCUUUUCGCGUUUUUACCGCGAAGAUUCCG-UUUUCAUUUAUA------UUUAUUC
((((((...(((((((....))))))).))))))............((((((((.......)))))))).....-............------....... ( -23.20)
>DroEre_CAF1 27519 87 + 1
CAUAUUUUUGCAUGUGGCAACGCAGACUAAUGUGGUUCAAUUAAUCUUUUCGCGUUUUUACCUCGAAGAUGCCU-UUUUU------A------UUUACUC
((((((...(..((((....))))..).)))))).................((((((((.....))))))))..-.....------.------....... ( -16.60)
>DroAna_CAF1 25596 88 + 1
CAUAUUUUUGUAUGUGGAAACUCAGACUAAUGUAAUUCAAUUAAUCUUCCAGUGGGUUCUUCUCUUAAAUCCCCCCUUUU------A------UCCCUCC
(((((....)))))((((.....(((.((((........)))).)))))))..(((..............))).......------.------....... (  -8.94)
>DroPer_CAF1 30645 95 + 1
CAUAUUUUUGUGUGUAGAGUCGCCGACUAAUGUAAUUCAAUUAAUCUUCCGGCGUCGG--CGUUGGAG--UCUG-CUCUCUUCUCUCUCCUUCUCUCUUC
(((((....))))).((((..((.(((((((........))))....(((((((....--))))))))--)).)-).))))................... ( -19.90)
>consensus
CAUAUUUUUGUCUGCGGCAACGCAGACUAAUGUGAUUCAAUUAAUCUUUUCGCGUUUUUACCUCGAAGAUUCCG_UUUUCAUUUAUA______UUUAUUC
((((((...((.((((....)))).)).))))))............((((((...........))))))............................... ( -5.84 =  -6.62 +   0.78)

alignment

secondary structure

dotplot

Window 6

Location	14,155,587 – 14,155,680
Length	93
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	72.78
Mean single sequence MFE	-18.14
Consensus MFE	-5.66
Energy contribution	-5.55
Covariance contribution	-0.11
Combinations/Pair	1.27
Mean z-score	-2.11
Structure conservation index	0.31
SVM decision value	0.14
SVM RNA-class probability	0.601876
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14155587 93 - 27905053
GAAUAAA------UAUAAAUAAAAA-AGGAAUCUUCGAGGUAAAAACGCGAAAAGAUUAAUUGAAUCACAUUAGUCUGCAUUGCCGCAGACAAAAAUAUG
.......------...........(-(..((((((((.(.......).)))..)))))..))...........((((((......))))))......... ( -15.20)
>DroSec_CAF1 148447 90 - 1
GAAUAAA------UAUAAAUGAAAA-CGGAAUCUUCGCG---AAAACGCGAAAAGAUUAAUUGAAUCACAUUAGUCUGCAUUGCCGCAGACAAAAAUAUG
.......------....((((....-.......((((((---....))))))..((((.....)))).)))).((((((......))))))......... ( -20.50)
>DroSim_CAF1 33766 93 - 1
GAAUAAA------UAUAAAUGAAAA-CGGAAUCUUCGCGGUAAAAACGCGAAAAGAUUAAUUGAAUCACAUUAGUCUGCAUUGCCGCAGACAAAAAUAUG
.......------....((((....-.......((((((.......))))))..((((.....)))).)))).((((((......))))))......... ( -21.50)
>DroEre_CAF1 27519 87 - 1
GAGUAAA------U------AAAAA-AGGCAUCUUCGAGGUAAAAACGCGAAAAGAUUAAUUGAACCACAUUAGUCUGCGUUGCCACAUGCAAAAAUAUG
.......------.------.....-.((((((.....)))...(((((....((((((((........))))))))))))))))............... ( -14.80)
>DroAna_CAF1 25596 88 - 1
GGAGGGA------U------AAAAGGGGGGAUUUAAGAGAAGAACCCACUGGAAGAUUAAUUGAAUUACAUUAGUCUGAGUUUCCACAUACAAAAAUAUG
(((((..------.------...(((((...(((....)))...))).))...((((((((........))))))))...)))))............... ( -14.50)
>DroPer_CAF1 30645 95 - 1
GAAGAGAGAAGGAGAGAGAAGAGAG-CAGA--CUCCAACG--CCGACGCCGGAAGAUUAAUUGAAUUACAUUAGUCGGCGACUCUACACACAAAAAUAUG
....((((..((((...........-....--))))..((--(((((..(....)..((((........))))))))))).))))............... ( -22.36)
>consensus
GAAUAAA______UAUAAAUAAAAA_CGGAAUCUUCGAGGUAAAAACGCGAAAAGAUUAAUUGAAUCACAUUAGUCUGCAUUGCCACAGACAAAAAUAUG
...........................((....((((.(.......).)))).((((((((........))))))))......))............... ( -5.66 =  -5.55 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:30 2006