Locus 2635

Sequence ID	X_DroMel_CAF1
Location	7,037,428 – 7,037,549
Length	121
Max. P	0.736483

overview

Window 9

Location	7,037,428 – 7,037,520
Length	92
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	66.71
Mean single sequence MFE	-19.55
Consensus MFE	-5.78
Energy contribution	-6.28
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.30
SVM decision value	0.44
SVM RNA-class probability	0.736483
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7037428 92 + 22224390
CCGUUGGCCAA--AACAAUUUAUGGCCAU------CAAACGAUCGCUGGAUGCACUGGAAA-AA---CUCAA-GAGCUGCACAAACUACCAACUAUCAAUCAUGC
..(.((((((.--.........)))))).------)....(((.(.(((.((((((.((..-..---.))..-.)).)))).......))).).)))........ ( -14.80)
>DroSec_CAF1 28914 84 + 1
CCGUUGGCCAA--AACAAUUUAUGGCCAU------CAAACGAUGGCU-AAUGCACUGAGAA-AA---CUCAG-GAGCUGCACAAGCC-------ACCAAUCAUAC
..(.((((((.--.........)))))).------)....(.(((((-..(((((((((..-..---)))))-....))))..))))-------).)........ ( -26.00)
>DroSim_CAF1 28997 92 + 1
CCGUUGGCCAA--AACAAUUUAUGGCCAU------CAAACGAUGGAU-GAUGCACUGAGAA-AAAAACUGUU-UGUUUGUACAAACAAACAA--ACCAAUCAUAC
((((((((((.--.........)))))).------......))))((-(((......((..-.....))(((-(((((((....))))))))--))..))))).. ( -20.81)
>DroEre_CAF1 28615 81 + 1
CCGUUGGCCAA--AACAAUUUGUGGCCAU------CAAACGAUCGCU-GAUGCACUGAGAAAAA---CGCAA-CAGUUGCACAAACUAA-------CCAU----U
.(((((((((.--.........)))))).------...)))...(((-(.(((...........---.))).-))))............-------....----. ( -15.20)
>DroYak_CAF1 27330 84 + 1
CCGUUGGCCAAAAAACAAUUUAUGGCCAU-----ACAAACGAUCGCU-GAUGCACUGAGAGAAA---UUCAA-GCGGUGCAUAAACUAA-------CUAU----U
..((((((((.(((....))).)))))).-----))...........-.((((((((.((....---))...-.)))))))).......-------....----. ( -21.20)
>DroAna_CAF1 72872 89 + 1
CCGUUGGCCAA--AACGAUUUAAAGCAAGAGGCUAAGAGCUGUCUUA-GAUGCACUUGGAGAAA-AGGGGUUAACGAUUCAGA------------AAAAUCCUAU
.((((((((..--...........(((.....((((((....)))))-).))).(((......)-)).)))))))).......------------.......... ( -19.30)
>consensus
CCGUUGGCCAA__AACAAUUUAUGGCCAU______CAAACGAUCGCU_GAUGCACUGAGAA_AA___CUCAA_GAGCUGCACAAACUAA_______CAAUCAUAC
....((((((............))))))............................................................................. ( -5.78 =  -6.28 +   0.50)

alignment

secondary structure

dotplot

Window 0

Location	7,037,453 – 7,037,549
Length	96
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	70.89
Mean single sequence MFE	-18.78
Consensus MFE	-2.89
Energy contribution	-2.89
Covariance contribution	-0.00
Combinations/Pair	1.17
Mean z-score	-1.66
Structure conservation index	0.15
SVM decision value	0.11
SVM RNA-class probability	0.586165
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7037453 96 + 22224390
AU-CAAACGAUCGCUGGAUGCACUGGAAA-AA---CUCAAGAGCUGCACAAACUACCAACUAUCAAUCAUGCAUAUUAU-CCAUGAA--CUUAAGUAGUUUGGU
((-(((((..(((.(((((((.((.((..-..---.)).)).))((((.....................))))....))-))))))(--(....)).))))))) ( -14.40)
>DroSec_CAF1 28939 88 + 1
AU-CAAACGAUGGCU-AAUGCACUGAGAA-AA---CUCAGGAGCUGCACAAGCC-------ACCAAUCAUACAUAUUAU-CCAUGAU--CUUAAGUAGUUUGGU
((-((((((.(((((-..(((((((((..-..---)))))....))))..))))-------).).....(((.((..((-(...)))--..)).)))))))))) ( -23.50)
>DroSim_CAF1 29022 97 + 1
AU-CAAACGAUGGAU-GAUGCACUGAGAA-AAAAACUGUUUGUUUGUACAAACAAACAA--ACCAAUCAUACAUAUUAU-CCAUGACUACUUAAGUAGUUUGG-
..-......((((((-((((...(((...-.......((((((((((....))))))))--))...)))....))))))-))))((((((....))))))...- ( -24.32)
>DroEre_CAF1 28640 85 + 1
AU-CAAACGAUCGCU-GAUGCACUGAGAAAAA---CGCAACAGUUGCACAAACUAA-------CCAU----UAGAUUGC-CCAUGAA--UUUUAGUAGUUAGGU
..-.....(...(((-(.(((...........---.))).))))..).....((((-------(.((----((((.(..-......)--.)))))).))))).. ( -13.00)
>DroYak_CAF1 27357 87 + 1
AUACAAACGAUCGCU-GAUGCACUGAGAGAAA---UUCAAGCGGUGCAUAAACUAA-------CUAU----UAUAUUGGCCAAUGUA--UUCAAGUAGUUUGUU
..((((((.......-.((((((((.((....---))....))))))))......(-------((..----((((((....))))))--....))).)))))). ( -18.70)
>consensus
AU_CAAACGAUCGCU_GAUGCACUGAGAA_AA___CUCAAGAGCUGCACAAACUAA_____A_CAAUCAU_CAUAUUAU_CCAUGAA__CUUAAGUAGUUUGGU
...(((((..........((((......................)))).......................(((........)))............))))).. ( -2.89 =  -2.89 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	7,037,453 – 7,037,549
Length	96
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	70.89
Mean single sequence MFE	-21.37
Consensus MFE	-2.32
Energy contribution	-2.40
Covariance contribution	0.08
Combinations/Pair	1.22
Mean z-score	-1.66
Structure conservation index	0.11
SVM decision value	0.16
SVM RNA-class probability	0.613527
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7037453 96 - 22224390
ACCAAACUACUUAAG--UUCAUGG-AUAAUAUGCAUGAUUGAUAGUUGGUAGUUUGUGCAGCUCUUGAG---UU-UUUCCAGUGCAUCCAGCGAUCGUUUG-AU
..(((((........--.(((((.-((...)).)))))..(((.(((((.....((..(((((....))---))-......)..)).))))).))))))))-.. ( -20.50)
>DroSec_CAF1 28939 88 - 1
ACCAAACUACUUAAG--AUCAUGG-AUAAUAUGUAUGAUUGGU-------GGCUUGUGCAGCUCCUGAG---UU-UUCUCAGUGCAUU-AGCCAUCGUUUG-AU
..(((((.......(--((((((.-((...)).)))))))(((-------((((.(((((....(((((---..-..)))))))))).-))))))))))))-.. ( -32.50)
>DroSim_CAF1 29022 97 - 1
-CCAAACUACUUAAGUAGUCAUGG-AUAAUAUGUAUGAUUGGU--UUGUUUGUUUGUACAAACAAACAGUUUUU-UUCUCAGUGCAUC-AUCCAUCGUUUG-AU
-.((((((((....)))...((((-((...(((((((((((.(--((((((((....))))))))))))))...-......)))))).-)))))).)))))-.. ( -23.70)
>DroEre_CAF1 28640 85 - 1
ACCUAACUACUAAAA--UUCAUGG-GCAAUCUA----AUGG-------UUAGUUUGUGCAACUGUUGCG---UUUUUCUCAGUGCAUC-AGCGAUCGUUUG-AU
.((((..........--....)))-)..(((.(----((((-------((.(((.(((((.(((.....---.......)))))))).-)))))))))).)-)) ( -16.24)
>DroYak_CAF1 27357 87 - 1
AACAAACUACUUGAA--UACAUUGGCCAAUAUA----AUAG-------UUAGUUUAUGCACCGCUUGAA---UUUCUCUCAGUGCAUC-AGCGAUCGUUUGUAU
.((((((........--.....((((.......----...)-------)))(((.((((((....(((.---......))))))))).-)))....)))))).. ( -13.90)
>consensus
ACCAAACUACUUAAG__UUCAUGG_AUAAUAUG_AUGAUUG_U_____UUAGUUUGUGCAACUCUUGAG___UU_UUCUCAGUGCAUC_AGCGAUCGUUUG_AU
..(((((............................................((....))........................((.....))....)))))... ( -2.32 =  -2.40 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:47 2006