Locus 3575

Sequence ID	3R_DroMel_CAF1
Location	9,672,779 – 9,672,959
Length	180
Max. P	0.981239

overview

Window 9

Location	9,672,779 – 9,672,880
Length	101
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.83
Mean single sequence MFE	-36.72
Consensus MFE	-30.01
Energy contribution	-30.01
Covariance contribution	-0.00
Combinations/Pair	1.15
Mean z-score	-2.27
Structure conservation index	0.82
SVM decision value	1.73
SVM RNA-class probability	0.974201
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9672779 101 - 27905053
GCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGCGCUGCCACAAAGGUGUUGCUCAUGCUCGG----------AUCUGAGUAUCUGGGAAAUGCAAAUCCAGUUAAUCACUGAA
......(((((((((((..((((((.---------.......))))))....(((((.((((((((((.----------...))))))..)))).))))).....))).))))))))... ( -33.70)
>DroSec_CAF1 64465 101 - 1
GCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGCGCUGCCACAAAGGCGUUGCUCAUGCUCGG----------AUCUGAGUGUCUGGGAAAUGCAAAUCCAGUUAAUCACUGAA
......(((((((((((..((((((.---------.......))))))....(((((.((((((((((.----------...))))))..)))).))))).....))).))))))))... ( -35.00)
>DroSim_CAF1 67396 101 - 1
GCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGCGCUGCCACAAAGGCGUUGCUCAUGCUCGG----------AUCUGAGUGUCUGGGAAAUGCAAAUCCAGUUAAUCACUGAA
......(((((((((((..((((((.---------.......))))))....(((((.((((((((((.----------...))))))..)))).))))).....))).))))))))... ( -35.00)
>DroEre_CAF1 65650 118 - 1
GCCAAGAGUGAUUGCCGAGGUGGCAAUGGAGCUGAUUGGAGCUGCCACAAAGGUGUUGCUAAUGCU--GGUAUCUGGGUAUCUGGGUAUCUGGGAAAUGCAAAUCCAGUUGAUCACUGAA
......((((((((((...((((((.....(((......)))))))))...))).((((...(.((--((((((..(....)..)))))).)).)...))))........)))))))... ( -35.90)
>DroYak_CAF1 69484 111 - 1
GCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGAGCUGCCACAAAGGUGUUGCUAAUGCUCGGGUAUCUGGCUAUCCGGGUAUCUGGGAAAUGCAAAUCCAGUUAAUCACUGAA
......(((((((((((..((((((.---------.......))))))...(((.((((.....(((((((((((((....)))))))))))))....)))))))))).))))))))... ( -44.00)
>consensus
GCCAAGAGUGAUUGCUGAGGUGGCAA_________UUGGCGCUGCCACAAAGGUGUUGCUCAUGCUCGG__________AUCUGAGUAUCUGGGAAAUGCAAAUCCAGUUAAUCACUGAA
......(((((((((((..((((((.................))))))....(((((.(((((((((((............))))))))..))).))))).....))).))))))))... (-30.01 = -30.01 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	9,672,819 – 9,672,919
Length	100
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.33
Mean single sequence MFE	-36.46
Consensus MFE	-31.83
Energy contribution	-32.23
Covariance contribution	0.40
Combinations/Pair	1.07
Mean z-score	-1.94
Structure conservation index	0.87
SVM decision value	1.54
SVM RNA-class probability	0.962637
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9672819 100 - 27905053
UAUGUCGUUUGACACAUUUAAUUGG-AGUCAAUUGGCCGGGCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGCGCUGCCACAAAGGUGUUGCUCAUGCUCGG----------A
...((((.(((((.((......)).-.))))).))))(((((...(((..((.(((...((((((.---------.......))))))...)))))..)))..))))).----------. ( -35.60)
>DroSec_CAF1 64505 100 - 1
UAUGUCGUUUGACACAUUUAAUUGG-AGUCAAUUGGCCGGGCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGCGCUGCCACAAAGGCGUUGCUCAUGCUCGG----------A
...((((.(((((.((......)).-.))))).))))(((((...(((..((.(((...((((((.---------.......))))))...)))))..)))..))))).----------. ( -38.20)
>DroSim_CAF1 67436 100 - 1
UAUGUCGUUUGACACAUUUAAUUGG-AGUCAAUUGGCCGGGCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGCGCUGCCACAAAGGCGUUGCUCAUGCUCGG----------A
...((((.(((((.((......)).-.))))).))))(((((...(((..((.(((...((((((.---------.......))))))...)))))..)))..))))).----------. ( -38.20)
>DroEre_CAF1 65690 118 - 1
CAUGUCGUUUGACACAUUUAAUUGGAAGUCAAUUGGCCGGGCCAAGAGUGAUUGCCGAGGUGGCAAUGGAGCUGAUUGGAGCUGCCACAAAGGUGUUGCUAAUGCU--GGUAUCUGGGUA
....(((.(((((.((......))...))))).)))((((((((..((..((.(((...((((((.....(((......)))))))))...)))))..)).....)--)))..))))... ( -32.80)
>DroYak_CAF1 69524 111 - 1
UAUGUCGCUUGACACAUUUAAUUGGAAGUCAAUUGGCCGGGCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGAGCUGCCACAAAGGUGUUGCUAAUGCUCGGGUAUCUGGCUA
..((((....))))............(((((..((.((((((....((..((.(((...((((((.---------.......))))))...)))))..))...)))))).))..))))). ( -37.50)
>consensus
UAUGUCGUUUGACACAUUUAAUUGG_AGUCAAUUGGCCGGGCCAAGAGUGAUUGCUGAGGUGGCAA_________UUGGCGCUGCCACAAAGGUGUUGCUCAUGCUCGG__________A
...((((.(((((.((......))...))))).))))(((((...(((..((.(((...((((((.................))))))...)))))..)))..)))))............ (-31.83 = -32.23 +   0.40)

alignment

secondary structure

dotplot

Window 1

Location	9,672,849 – 9,672,959
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.53
Mean single sequence MFE	-26.60
Consensus MFE	-22.26
Energy contribution	-22.10
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.40
Structure conservation index	0.84
SVM decision value	0.31
SVM RNA-class probability	0.684125
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9672849 110 + 27905053
GCCAA---------UUGCCACCUCAGCAAUCACUCUUGGCCCGGCCAAUUGACU-CCAAUUAAAUGUGUCAAACGACAUAGACCGUUAACACGCCACGUCUGGCAUUGAGACCACUAGCU
((..(---------((((.......)))))..(((...(((.(((.(((((...-.)))))....((((..((((........)))).)))).....))).)))...))).......)). ( -23.60)
>DroSec_CAF1 64535 110 + 1
GCCAA---------UUGCCACCUCAGCAAUCACUCUUGGCCCGGCCAAUUGACU-CCAAUUAAAUGUGUCAAACGACAUAGACCGUUAACACGCCACGUCUGGCAUUGAGACCACUAGCU
((..(---------((((.......)))))..(((...(((.(((.(((((...-.)))))....((((..((((........)))).)))).....))).)))...))).......)). ( -23.60)
>DroSim_CAF1 67466 110 + 1
GCCAA---------UUGCCACCUCAGCAAUCACUCUUGGCCCGGCCAAUUGACU-CCAAUUAAAUGUGUCAAACGACAUAGACCGUUAACACGCCACGUCUGGCAUUGAGACCACUAGCU
((..(---------((((.......)))))..(((...(((.(((.(((((...-.)))))....((((..((((........)))).)))).....))).)))...))).......)). ( -23.60)
>DroEre_CAF1 65728 120 + 1
UCCAAUCAGCUCCAUUGCCACCUCGGCAAUCACUCUUGGCCCGGCCAAUUGACUUCCAAUUAAAUGUGUCAAACGACAUGGACCGUUAACACGCCAAGUCUGGCAUUGAGACCACUAGCU
.......((((..((((((.....))))))...(((..(..((((((((((.....)))))....(((((....))))))).))).......((((....)))).)..))).....)))) ( -30.50)
>DroYak_CAF1 69564 111 + 1
UCCAA---------UUGCCACCUCAGCAAUCACUCUUGGCCCGGCCAAUUGACUUCCAAUUAAAUGUGUCAAGCGACAUAGGCCGUUAACACGCCAAGUCGGGCAUUGAGACCACUAGCU
....(---------((((.......)))))..(((...(((((((.(((((.....)))))...((((((....))))))(((.((....)))))..)))))))...))).......... ( -31.70)
>consensus
GCCAA_________UUGCCACCUCAGCAAUCACUCUUGGCCCGGCCAAUUGACU_CCAAUUAAAUGUGUCAAACGACAUAGACCGUUAACACGCCACGUCUGGCAUUGAGACCACUAGCU
..............((((.......))))...(((...(((.(((.(((((.....)))))....((((..((((........)))).)))).....))).)))...))).......... (-22.26 = -22.10 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	9,672,849 – 9,672,959
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.53
Mean single sequence MFE	-39.34
Consensus MFE	-33.18
Energy contribution	-33.46
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-2.01
Structure conservation index	0.84
SVM decision value	1.88
SVM RNA-class probability	0.981239
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9672849 110 - 27905053
AGCUAGUGGUCUCAAUGCCAGACGUGGCGUGUUAACGGUCUAUGUCGUUUGACACAUUUAAUUGG-AGUCAAUUGGCCGGGCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGC
.(((..((((((....((((((((((((((....)))..)))))))..(((((.((......)).-.))))).)))).))))))..)))(((((((.....)))))---------))... ( -38.10)
>DroSec_CAF1 64535 110 - 1
AGCUAGUGGUCUCAAUGCCAGACGUGGCGUGUUAACGGUCUAUGUCGUUUGACACAUUUAAUUGG-AGUCAAUUGGCCGGGCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGC
.(((..((((((....((((((((((((((....)))..)))))))..(((((.((......)).-.))))).)))).))))))..)))(((((((.....)))))---------))... ( -38.10)
>DroSim_CAF1 67466 110 - 1
AGCUAGUGGUCUCAAUGCCAGACGUGGCGUGUUAACGGUCUAUGUCGUUUGACACAUUUAAUUGG-AGUCAAUUGGCCGGGCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGC
.(((..((((((....((((((((((((((....)))..)))))))..(((((.((......)).-.))))).)))).))))))..)))(((((((.....)))))---------))... ( -38.10)
>DroEre_CAF1 65728 120 - 1
AGCUAGUGGUCUCAAUGCCAGACUUGGCGUGUUAACGGUCCAUGUCGUUUGACACAUUUAAUUGGAAGUCAAUUGGCCGGGCCAAGAGUGAUUGCCGAGGUGGCAAUGGAGCUGAUUGGA
..((((((((..((.(((((..((((((((((((((((......))).)))))))...........(((((.(((((...)))))...))))))))))).))))).))..))).))))). ( -45.70)
>DroYak_CAF1 69564 111 - 1
AGCUAGUGGUCUCAAUGCCCGACUUGGCGUGUUAACGGCCUAUGUCGCUUGACACAUUUAAUUGGAAGUCAAUUGGCCGGGCCAAGAGUGAUUGCUGAGGUGGCAA---------UUGGA
.(((..(((((...(((((......))))).....(((((..((((....)))).....(((((.....)))))))))))))))..)))(((((((.....)))))---------))... ( -36.70)
>consensus
AGCUAGUGGUCUCAAUGCCAGACGUGGCGUGUUAACGGUCUAUGUCGUUUGACACAUUUAAUUGG_AGUCAAUUGGCCGGGCCAAGAGUGAUUGCUGAGGUGGCAA_________UUGGC
.(((..((((((....((((((((((((((....)))..)))))))..(((((.((......))...))))).)))).))))))..)))..(((((.....))))).............. (-33.18 = -33.46 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:43 2006