Locus 2997

Sequence ID	3R_DroMel_CAF1
Location	8,029,535 – 8,029,633
Length	98
Max. P	0.947848

overview

Window 2

Location	8,029,535 – 8,029,633
Length	98
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	79.80
Mean single sequence MFE	-19.38
Consensus MFE	-11.89
Energy contribution	-13.00
Covariance contribution	1.11
Combinations/Pair	1.04
Mean z-score	-2.19
Structure conservation index	0.61
SVM decision value	0.90
SVM RNA-class probability	0.878105
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8029535 98 + 27905053
-GGGG----UGGUGAAGGAA--GGAAAGAAAACUAAAUGCACAUUUAACAAUAAAUGAGCAACGUUUUUCGGAAAUUAACUUUCAACAACAUGUGUUGAAAUGCA
-....----...((((((..--.....(((((.....(((.((((((....)))))).)))....))))).........)))))).((((....))))....... ( -15.59)
>DroVir_CAF1 214292 103 + 1
-AGAAAGAAAGGAAAAUGGCAGCAAAAGAAAACCAAAUGCGCAUUUAGCAG-AAAUGAGCUGCGUUUUCCGAAAAUUAACUUUCAACAACAUGUGUUGAAAUGCA
-.........((((((((.((((....(.....)...(((.......))).-......))))))))))))..........((((((((.....)))))))).... ( -24.20)
>DroYak_CAF1 100219 99 + 1
AGGGA----UGGCAAACAGA--CGAAAGAAAACUAAAUGCACAUUUAACAAUAAAUGAGCAACGUUUUUCGGAAAUUAACUUUCAACAACAUGUGUUGAAAUGCA
.....----..(((......--(((((((........(((.((((((....)))))).)))...))))))).........((((((((.....))))))))))). ( -20.60)
>DroMoj_CAF1 165195 103 + 1
-AGGGAACAAGGAAAAUGGCAGCAAAAGAAAUCCAAAUGCGCACUUAGCAG-AAAUGAGCUGCGUUUUCAGAAAAUUAACUUUCAACAACAUGUGUUGAAAUGCA
-.(....)...(((((((.((((....(.....)...(((.......))).-......)))))))))))...........((((((((.....)))))))).... ( -20.90)
>DroAna_CAF1 104001 92 + 1
-A---------AUGAAAAUA--GCAAAGAAAACUAAAUGCGCAUUUAACAAUAAAUGAGAAACGUU-UUCGGAAAUUAACUUUCAACAACAUGUGUUGAAACGCA
-.---------.........--((...((((((......(.((((((....)))))).)....)))-)))..........((((((((.....)))))))).)). ( -16.90)
>DroPer_CAF1 112338 93 + 1
-A-------GUGCGAA-GGA--GAAAAGAAAACUAAAUGCACAUUUAACAAUAAAUGAGCAACGUUUUU-GGAAAUUAACUUUCAACAACAUGUGUUGAAAUGCA
-.-------.((((..-...--.....((((((....(((.((((((....)))))).)))..))))))-..........((((((((.....)))))))))))) ( -18.10)
>consensus
_AGG_____AGGAAAAUGGA__CAAAAGAAAACUAAAUGCACAUUUAACAAUAAAUGAGCAACGUUUUUCGGAAAUUAACUUUCAACAACAUGUGUUGAAAUGCA
...........................((((((....(((.((((((....)))))).)))..))))))...........((((((((.....)))))))).... (-11.89 = -13.00 +   1.11)

alignment

secondary structure

dotplot

Window 3

Location	8,029,535 – 8,029,633
Length	98
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	79.80
Mean single sequence MFE	-20.53
Consensus MFE	-12.24
Energy contribution	-13.38
Covariance contribution	1.14
Combinations/Pair	1.08
Mean z-score	-2.72
Structure conservation index	0.60
SVM decision value	1.38
SVM RNA-class probability	0.947848
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8029535 98 - 27905053
UGCAUUUCAACACAUGUUGUUGAAAGUUAAUUUCCGAAAAACGUUGCUCAUUUAUUGUUAAAUGUGCAUUUAGUUUUCUUUCC--UUCCUUCACCA----CCCC-
....((((((((.....))))))))..........(((((....(((.((((((....)))))).))).....))))).....--...........----....- ( -18.40)
>DroVir_CAF1 214292 103 - 1
UGCAUUUCAACACAUGUUGUUGAAAGUUAAUUUUCGGAAAACGCAGCUCAUUU-CUGCUAAAUGCGCAUUUGGUUUUCUUUUGCUGCCAUUUUCCUUUCUUUCU-
....((((((((.....))))))))..........((((((.(((((......-..(((((((....)))))))........)))))..)))))).........- ( -26.39)
>DroYak_CAF1 100219 99 - 1
UGCAUUUCAACACAUGUUGUUGAAAGUUAAUUUCCGAAAAACGUUGCUCAUUUAUUGUUAAAUGUGCAUUUAGUUUUCUUUCG--UCUGUUUGCCA----UCCCU
.(((((((((((.....)))))))).........((((((((..(((.((((((....)))))).)))....)))...)))))--......)))..----..... ( -20.80)
>DroMoj_CAF1 165195 103 - 1
UGCAUUUCAACACAUGUUGUUGAAAGUUAAUUUUCUGAAAACGCAGCUCAUUU-CUGCUAAGUGCGCAUUUGGAUUUCUUUUGCUGCCAUUUUCCUUGUUCCCU-
.(((((((((((.....))))))))...........(((((.(((((......-...((((((....)))))).........)))))..)))))..))).....- ( -20.97)
>DroAna_CAF1 104001 92 - 1
UGCGUUUCAACACAUGUUGUUGAAAGUUAAUUUCCGAA-AACGUUUCUCAUUUAUUGUUAAAUGCGCAUUUAGUUUUCUUUGC--UAUUUUCAU---------U-
.(((((((((((.....))))))))..........(((-(((....(.((((((....)))))).)......))))))..)))--.........---------.- ( -16.50)
>DroPer_CAF1 112338 93 - 1
UGCAUUUCAACACAUGUUGUUGAAAGUUAAUUUCC-AAAAACGUUGCUCAUUUAUUGUUAAAUGUGCAUUUAGUUUUCUUUUC--UCC-UUCGCAC-------U-
(((.((((((((.....))))))))..........-.(((((..(((.((((((....)))))).)))....)))))......--...-...))).-------.- ( -20.10)
>consensus
UGCAUUUCAACACAUGUUGUUGAAAGUUAAUUUCCGAAAAACGUUGCUCAUUUAUUGUUAAAUGCGCAUUUAGUUUUCUUUUC__UCCAUUCACCA_____CCU_
.((.((((((((.....))))))))))........(((((....(((.((((((....)))))).))).....)))))........................... (-12.24 = -13.38 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:45 2006