Locus 8765

Sequence ID	3R_DroMel_CAF1
Location	23,399,869 – 23,400,002
Length	133
Max. P	0.974457

overview

Window 9

Location	23,399,869 – 23,399,970
Length	101
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	88.04
Mean single sequence MFE	-33.78
Consensus MFE	-27.46
Energy contribution	-28.50
Covariance contribution	1.04
Combinations/Pair	1.08
Mean z-score	-2.24
Structure conservation index	0.81
SVM decision value	1.73
SVM RNA-class probability	0.974457
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23399869 101 + 27905053
--------GGAGGAGUUG-----CUUCUUC-GCCAGAAGACAAAGUUGGCAACUCGAUUGAAAAAGUUGCUGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCG
--------....((((((-----(((((((-....))))).......))))))))(((.(......(((((.((((.......)))).)))))....(((....)))..).))). ( -31.01)
>DroSec_CAF1 14417 103 + 1
--------GAAGGAGUAGUUCUUCUUCUUG-GCCAGAAGACAAAGUUGGCAACUCGAUGGCA---GUUGCUGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCG
--------(((((((.....)))))))(((-(((((....((..(((((((((((....).)---)))))).((((.......)))).....)))..)).))))))))....... ( -35.70)
>DroSim_CAF1 14413 106 + 1
--------GAAGGAGUAGUUCUUCUUCUUG-GCCAGAAGACAAAGUUGGCAACUCGAUGGCAAAAGUUGCUGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCG
--------(((((((.....)))))))(((-(((((....((...(((.((......)).)))...(((((.((((.......)))).)))))....)).))))))))....... ( -35.70)
>DroEre_CAF1 17516 105 + 1
-------AGUAGGAGAA--UCUUGCGCUUG-GCCAGAAGACAAAGUUGGCAACUCGAUUGAAAAAGUUGCUGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCG
-------.(((((....--.)))))(((((-(((((...........(....).(((((.....)))))))))))))))....((((.(((........))).))))........ ( -34.10)
>DroYak_CAF1 15371 113 + 1
AGCGGAAAGUAGGAGCA--UCUUGCGCUUGGGCCAGAAGACAAAGUUGGCAACUCGAUUGAAAAAGUUGCUGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCG
...((..(((....((.--....))(((...((((...(((...((..((((((..........))))))..))...)))...)))).)))........)))..))......... ( -32.40)
>consensus
________GAAGGAGUAG_UCUUCUUCUUG_GCCAGAAGACAAAGUUGGCAACUCGAUUGAAAAAGUUGCUGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCG
........(((((((.....)))))))....((((...(((...((..((((((..........))))))..))...)))...)))).(((...(....)...)))......... (-27.46 = -28.50 +   1.04)

alignment

secondary structure

dotplot

Window 0

Location	23,399,869 – 23,399,970
Length	101
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	88.04
Mean single sequence MFE	-31.14
Consensus MFE	-21.64
Energy contribution	-22.24
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.80
Structure conservation index	0.69
SVM decision value	1.04
SVM RNA-class probability	0.905552
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23399869 101 - 27905053
CGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCAGCAACUUUUUCAAUCGAGUUGCCAACUUUGUCUUCUGGC-GAAGAAG-----CAACUCCUCC--------
.((.(((((((((((...(((..((.....))..))).)))))))..))))...))....(((((((...(((((((....)))-))))..)-----))))))....-------- ( -32.00)
>DroSec_CAF1 14417 103 - 1
CGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCAGCAAC---UGCCAUCGAGUUGCCAACUUUGUCUUCUGGC-CAAGAAGAAGAACUACUCCUUC--------
.(((((((((((.((.((.....)).))))).(((..(((((((((((((---(.......))))))((....)).....))))-))))..))))))))).))....-------- ( -31.10)
>DroSim_CAF1 14413 106 - 1
CGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCAGCAACUUUUGCCAUCGAGUUGCCAACUUUGUCUUCUGGC-CAAGAAGAAGAACUACUCCUUC--------
.(((((((((((.((.((.....)).))))).(((..(((((((((((((((........)))))))((....)).....))))-))))..))))))))).))....-------- ( -32.10)
>DroEre_CAF1 17516 105 - 1
CGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCAGCAACUUUUUCAAUCGAGUUGCCAACUUUGUCUUCUGGC-CAAGCGCAAGA--UUCUCCUACU-------
.....((((((((((.((..(((.....((((.......))))..(((((((........))))))).)))..))....)))))-)))))......--..........------- ( -31.60)
>DroYak_CAF1 15371 113 - 1
CGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCAGCAACUUUUUCAAUCGAGUUGCCAACUUUGUCUUCUGGCCCAAGCGCAAGA--UGCUCCUACUUUCCGCU
.....((((((((((.((..(((.....((((.......))))..(((((((........))))))).)))..))....)))).))))))((....--.)).............. ( -28.90)
>consensus
CGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCAGCAACUUUUUCAAUCGAGUUGCCAACUUUGUCUUCUGGC_CAAGAAGAAGA_CUACUCCUAC________
.....(..((((.((.((.....)).))))))..)..(((((((((((((((........)))))))((....)).....)))).)))).......................... (-21.64 = -22.24 +   0.60)

alignment

secondary structure

dotplot

Window 1

Location	23,399,894 – 23,400,002
Length	108
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	80.34
Mean single sequence MFE	-33.02
Consensus MFE	-19.43
Energy contribution	-21.42
Covariance contribution	1.99
Combinations/Pair	1.04
Mean z-score	-3.40
Structure conservation index	0.59
SVM decision value	1.69
SVM RNA-class probability	0.972192
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23399894 108 + 27905053
ACAAAGUUGGCAACUCGAUUGAAAAAGUUGC---UGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCGAUUGAUGUUUGUCGAGUUGGCAAUAAAAA---GAG
.....((((.(((((((((.((.....((((---(.((((.......)))).))))).((((.(.(((.....))).).))))...)).))))))))).)))).....---... ( -33.70)
>DroSec_CAF1 14447 105 + 1
ACAAAGUUGGCAACUCGAUGGCA---GUUGC---UGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCGAUUGAUGUUUGUCGAGUUGGCAAUAAAAA---GAA
.....((((.((((((((..(((---.((((---(.((((.......)))).))))).((((.(.(((.....))).).)))).)).)..)))))))).)))).....---... ( -36.10)
>DroSim_CAF1 14443 108 + 1
ACAAAGUUGGCAACUCGAUGGCAAAAGUUGC---UGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCGAUUGAUGUUUGUCGAGUUGGCAAUAAAAA---AAA
.....((((.((((((((((((...((((((---(.((((.......)))).)))).......))).)))((((.(((....)))))))))))))))).)))).....---... ( -36.41)
>DroEre_CAF1 17545 111 + 1
ACAAAGUUGGCAACUCGAUUGAAAAAGUUGC---UGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCGAUUGAUGUUUGUCGAGUUUGCAAUAAAAACCAGAA
.((((.((((((((((((((((.....((((---(.((((.......)))).)))))....(((....))).....)))))))).).))))))).))))............... ( -32.80)
>DroYak_CAF1 15408 102 + 1
ACAAAGUUGGCAACUCGAUUGAAAAAGUUGC---UGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCGAUUGAUGUUUGUCGAGUUAGC---------UAGCA
.....((((((((((((((.((.....((((---(.((((.......)))).))))).((((.(.(((.....))).).))))...)).)))))))).))---------)))). ( -34.40)
>DroPer_CAF1 15927 90 + 1
AAAAAGUUGGCAGCUCGUUGGAAAUUGUUGAAGUUUUCACAGUUAAAUGGCA--------------GGCCAAACUAUCGAUUGGUGUCC-------UGCCAAUCCAAG---AAA
......((((.((((.((.(((((((.....)))))))))))))...(((((--------------((....((((.....))))..))-------)))))..)))).---... ( -24.70)
>consensus
ACAAAGUUGGCAACUCGAUGGAAAAAGUUGC___UGGCCAAGUUGAAUGGCAGGCAAACAAUGGCUGGCCAAACUAUCGAUUGAUGUUUGUCGAGUUGGCAAUAAAAA___GAA
.....((((.(((((((((.....................((((...((((.(((........))).))))))))(((....)))....))))))))).))))........... (-19.43 = -21.42 +   1.99)

alignment

secondary structure

dotplot

Window 2

Location	23,399,894 – 23,400,002
Length	108
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	80.34
Mean single sequence MFE	-26.54
Consensus MFE	-15.27
Energy contribution	-16.33
Covariance contribution	1.06
Combinations/Pair	1.15
Mean z-score	-2.78
Structure conservation index	0.58
SVM decision value	1.20
SVM RNA-class probability	0.930254
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23399894 108 - 27905053
CUC---UUUUUAUUGCCAACUCGACAAACAUCAAUCGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCA---GCAACUUUUUCAAUCGAGUUGCCAACUUUGU
...---......(((.((((((((((((((((....))).)))))............((((..((((.......))))..---)))).........)))))))).)))...... ( -28.10)
>DroSec_CAF1 14447 105 - 1
UUC---UUUUUAUUGCCAACUCGACAAACAUCAAUCGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCA---GCAAC---UGCCAUCGAGUUGCCAACUUUGU
...---......(((.((((((((((((((((....))).)))))(.(((.......((((..((((.......))))..---)))))---)).).)))))))).)))...... ( -28.31)
>DroSim_CAF1 14443 108 - 1
UUU---UUUUUAUUGCCAACUCGACAAACAUCAAUCGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCA---GCAACUUUUGCCAUCGAGUUGCCAACUUUGU
...---......(((.((((((((((((((((....))).)))))....((.(..(((.((..((((.......))))..---)))))..).))..)))))))).)))...... ( -29.50)
>DroEre_CAF1 17545 111 - 1
UUCUGGUUUUUAUUGCAAACUCGACAAACAUCAAUCGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCA---GCAACUUUUUCAAUCGAGUUGCCAACUUUGU
..............((((.(((((((((((((....))).)))))............((((..((((.......))))..---)))).........)))))))))......... ( -25.60)
>DroYak_CAF1 15408 102 - 1
UGCUA---------GCUAACUCGACAAACAUCAAUCGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCA---GCAACUUUUUCAAUCGAGUUGCCAACUUUGU
.....---------((.(((((((((((((((....))).)))))............((((..((((.......))))..---)))).........)))))))))......... ( -25.80)
>DroPer_CAF1 15927 90 - 1
UUU---CUUGGAUUGGCA-------GGACACCAAUCGAUAGUUUGGCC--------------UGCCAUUUAACUGUGAAAACUUCAACAAUUUCCAACGAGCUGCCAACUUUUU
.((---((((((.(((((-------((...((((.(....).))))))--------------))))).......((....))..........))))).)))............. ( -21.90)
>consensus
UUC___UUUUUAUUGCCAACUCGACAAACAUCAAUCGAUAGUUUGGCCAGCCAUUGUUUGCCUGCCAUUCAACUUGGCCA___GCAACUUUUUCAAUCGAGUUGCCAACUUUGU
............(((.((((((((................(..((((..((........))..))))..)......((.....))...........)))))))).)))...... (-15.27 = -16.33 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:16 2006