Locus 571

Sequence ID	3R_DroMel_CAF1
Location	2,132,685 – 2,132,878
Length	193
Max. P	0.997927

overview

Window 8

Location	2,132,685 – 2,132,801
Length	116
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	82.39
Mean single sequence MFE	-30.50
Consensus MFE	-22.44
Energy contribution	-23.28
Covariance contribution	0.84
Combinations/Pair	1.23
Mean z-score	-2.45
Structure conservation index	0.74
SVM decision value	1.65
SVM RNA-class probability	0.970009
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2132685 116 + 27905053
AAAUCCU-UUUUUUCAGAAAGUGCCGUGAUAGUCUGCAUAUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACUAAAACACUGAUAGUUGGUUCCAGUAACCAAUUAUC
.....((-(((.....)))))(((.(((((.((((((....((((((......))))))..))))))....))))))))...........(((((((((((.....))))))))))) ( -32.90)
>DroSec_CAF1 276041 117 + 1
AAAUCUUAUUUUUUCAGCAAGUGCCGUGGUAGUCUGCCUCUUAGGAAUACAUUUUUCUACGGCGGUCAUCGACCACGCAACAAAACCACUGAUAGUUGGAUCCAGUGACCAAUUAUC
....................((..((((((.(.(((((...((((((......)))))).))))).)....))))))..)).........(((((((((.((....))))))))))) ( -31.00)
>DroSim_CAF1 295476 117 + 1
AAAUCAUAUUUUUUCAGCAAGUGCCGUGGUAGUCUGCCUCUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACAAAACCACUGAUAGUUGGUUCCAGUGACCAAUUAUC
....................((..((((((.(((((((...((((((......)))))).)))))))....))))))..)).........(((((((((((.....))))))))))) ( -34.20)
>DroEre_CAF1 280221 117 + 1
AAAUUCUAUUUGUAUAGCAAGUGCAAUAAUAGUCUGCAUAUUUAAAGUACAUUUUUGUACGGCGGAGACUGAUCACGUAUUAAAGCCACAGAUAGUUGGUGCUAAAAGCCAACUAUC
.....((((((((((.....)))))..)))))..............(((((....)))))((((....)((((.....))))..)))...((((((((((.......)))))))))) ( -27.90)
>DroYak_CAF1 280865 117 + 1
AAAUUCUUUUUGUUUAGCAAGUGCAAUGAUAGUCUUCAUAUUAAGAAUACAUUUUUGUACGGCGGAGGCUGAUCACGUAAUAAAACCACAGAUAGUUGGUGCCAGUAGCCAACUAUC
..........((.(((((..((((((.(((.((.(((.......))).))))).)))))).......))))).))...............((((((((((.......)))))))))) ( -26.50)
>consensus
AAAUCCUAUUUUUUCAGCAAGUGCCGUGAUAGUCUGCAUAUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACAAAACCACUGAUAGUUGGUUCCAGUAACCAAUUAUC
.....................(((.(((((.((((((....((((((......))))))..))))))....))))))))...........((((((((((.......)))))))))) (-22.44 = -23.28 +   0.84)

alignment

secondary structure

dotplot

Window 9

Location	2,132,723 – 2,132,841
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	83.64
Mean single sequence MFE	-32.76
Consensus MFE	-21.73
Energy contribution	-21.77
Covariance contribution	0.04
Combinations/Pair	1.25
Mean z-score	-3.36
Structure conservation index	0.66
SVM decision value	2.26
SVM RNA-class probability	0.991260
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2132723 118 + 27905053
AUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACUAAAACACUGAUAGUUGGUUCCAGUAACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUC
....((((((..(((((((...(((((......)).)))..........(((((((((((((.....))))))))))))))))))))..))))))....(((((.....))))).... ( -36.40)
>DroSec_CAF1 276080 109 + 1
CUUAGGAAUACAUUUUUCUACGGCGGUCAUCGACCACGCAACAAAACCACUGAUAGUUGGAUCCAGUGACCAAUUAUCAAAGAAAGAA---------UCGGAAUUGCCCAUUCCCAUC
....(((((...(((((((.((..((((...)))).))............((((((((((.((....)))))))))))).))))))).---------..((......))))))).... ( -27.20)
>DroSim_CAF1 295515 118 + 1
CUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACAAAACCACUGAUAGUUGGUUCCAGUGACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUC
....((((((..(((((((...(((((......)).)))..........(((((((((((((.....))))))))))))))))))))..))))))....(((((.....))))).... ( -36.80)
>DroEre_CAF1 280260 118 + 1
AUUUAAAGUACAUUUUUGUACGGCGGAGACUGAUCACGUAUUAAAGCCACAGAUAGUUGGUGCUAAAAGCCAACUAUCAGAGAAUGAAAUAUUCCGGUCGGAAUUGCCCAUUCCCAUC
.......(((((....)))))((((....)((((.....))))..)))...((((((((((.......)))))))))).(.(((((....(((((....)))))....))))).)... ( -35.30)
>DroYak_CAF1 280904 118 + 1
AUUAAGAAUACAUUUUUGUACGGCGGAGGCUGAUCACGUAAUAAAACCACAGAUAGUUGGUGCCAGUAGCCAACUAUCAGAGAAAGAAAUAUUCCGUUCAGAAUUGCCUAUUCCCAUU
.....(((((((.(((((...(((((((.((..((..((......))....((((((((((.......)))))))))).))...)).....)))))))))))).))..)))))..... ( -28.10)
>consensus
AUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACAAAACCACUGAUAGUUGGUUCCAGUAACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUC
..((((((......)))))).(((((...((((..............(.((((((((((((.......)))))))))))).)...............))))..))))).......... (-21.73 = -21.77 +   0.04)

alignment

secondary structure

dotplot

Window 0

Location	2,132,763 – 2,132,878
Length	115
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	82.75
Mean single sequence MFE	-26.16
Consensus MFE	-17.46
Energy contribution	-18.46
Covariance contribution	1.00
Combinations/Pair	1.15
Mean z-score	-3.91
Structure conservation index	0.67
SVM decision value	2.96
SVM RNA-class probability	0.997927
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2132763 115 + 27905053
ACUAAAACACUGAUAGUUGGUUCCAGUAACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUCAAACUAAACUAUGGGAAUCAACAAAUUUA---UAAAAAUG
.........(((((((((((((.....)))))))))))))...........((((....))))(((...((((((((...........))))))))...))).....---........ ( -28.30)
>DroSec_CAF1 276120 109 + 1
ACAAAACCACUGAUAGUUGGAUCCAGUGACCAAUUAUCAAAGAAAGAA---------UCGGAAUUGCCCAUUCCCAUCAAACUAAACUAUGGGAAUCAACAAUUUCCUAUUAAAAAUG
..........((((((((((.((....)))))))))))).........---------..(((((((...((((((((...........))))))))...)))))))............ ( -25.40)
>DroSim_CAF1 295555 118 + 1
ACAAAACCACUGAUAGUUGGUUCCAGUGACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUCAAACUAAACUAUAGGAAUCAACAAUUUCCUAUUAAAAAUG
.........(((((((((((((.....))))))))))))).(((.(....(((((....)))))....).)))...............(((((((........)))))))........ ( -28.20)
>DroEre_CAF1 280300 115 + 1
UUAAAGCCACAGAUAGUUGGUGCUAAAAGCCAACUAUCAGAGAAUGAAAUAUUCCGGUCGGAAUUGCCCAUUCCCAUCAAACUAAACUAUGGUAAUCAGCCAAUUUA---UAAUAAUA
.....((((..((((((((((.......)))))))))).(.(((((....(((((....)))))....))))).)..............))))..............---........ ( -28.70)
>DroYak_CAF1 280944 115 + 1
AUAAAACCACAGAUAGUUGGUGCCAGUAGCCAACUAUCAGAGAAAGAAAUAUUCCGUUCAGAAUUGCCUAUUCCCAUUAAACUGAACUAUGACAAUCAACAAAUUUA---UAAUAAUA
(((((......((((((((((.......)))))))))).................((((((...((........)).....))))))................))))---)....... ( -20.20)
>consensus
ACAAAACCACUGAUAGUUGGUUCCAGUAACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUCAAACUAAACUAUGGGAAUCAACAAAUUUA___UAAAAAUG
.........((((((((((((.......))))))))))))...................(((.(((...((((((((...........))))))))...))).)))............ (-17.46 = -18.46 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	2,132,763 – 2,132,878
Length	115
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	82.75
Mean single sequence MFE	-29.24
Consensus MFE	-19.36
Energy contribution	-20.40
Covariance contribution	1.04
Combinations/Pair	1.18
Mean z-score	-2.36
Structure conservation index	0.66
SVM decision value	1.10
SVM RNA-class probability	0.915900
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2132763 115 - 27905053
CAUUUUUA---UAAAUUUGUUGAUUCCCAUAGUUUAGUUUGAUGGGAAUGGGCAAUUCCGAACGGAAUAUUUCUUUCUCUGAUAAUUGGUUACUGGAACCAACUAUCAGUGUUUUAGU
........---......((((.((((((((...........)))))))).))))(((((....)))))........(.((((((.((((((.....)))))).)))))).)....... ( -31.50)
>DroSec_CAF1 276120 109 - 1
CAUUUUUAAUAGGAAAUUGUUGAUUCCCAUAGUUUAGUUUGAUGGGAAUGGGCAAUUCCGA---------UUCUUUCUUUGAUAAUUGGUCACUGGAUCCAACUAUCAGUGGUUUUGU
...........((((.(((((.((((((((...........)))))))).)))))))))..---------.....((.((((((.((((((....)).)))).)))))).))...... ( -29.80)
>DroSim_CAF1 295555 118 - 1
CAUUUUUAAUAGGAAAUUGUUGAUUCCUAUAGUUUAGUUUGAUGGGAAUGGGCAAUUCCGAACGGAAUAUUUCUUUCUCUGAUAAUUGGUCACUGGAACCAACUAUCAGUGGUUUUGU
..........(((((((((((.((((((((...........)))))))).))))(((((....))))))))))))((.((((((.((((((....).))))).)))))).))...... ( -31.80)
>DroEre_CAF1 280300 115 - 1
UAUUAUUA---UAAAUUGGCUGAUUACCAUAGUUUAGUUUGAUGGGAAUGGGCAAUUCCGACCGGAAUAUUUCAUUCUCUGAUAGUUGGCUUUUAGCACCAACUAUCUGUGGCUUUAA
........---...............(((((............(((((((((..(((((....)))))..))))))))).(((((((((.........))))))))))))))...... ( -30.10)
>DroYak_CAF1 280944 115 - 1
UAUUAUUA---UAAAUUUGUUGAUUGUCAUAGUUCAGUUUAAUGGGAAUAGGCAAUUCUGAACGGAAUAUUUCUUUCUCUGAUAGUUGGCUACUGGCACCAACUAUCUGUGGUUUUAU
((..((((---((..(((((((((((((....((((......))))....)))))))...))))))..............(((((((((.........)))))))))))))))..)). ( -23.00)
>consensus
CAUUUUUA___UAAAUUUGUUGAUUCCCAUAGUUUAGUUUGAUGGGAAUGGGCAAUUCCGAACGGAAUAUUUCUUUCUCUGAUAAUUGGUUACUGGAACCAACUAUCAGUGGUUUUGU
................(((((.((((((((...........)))))))).)))))((((....)))).........(.((((((.((((.........)))).)))))).)....... (-19.36 = -20.40 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:24 2006