Locus 2887

Sequence ID	3L_DroMel_CAF1
Location	8,254,132 – 8,254,346
Length	214
Max. P	0.995594

overview

Window 0

Location	8,254,132 – 8,254,226
Length	94
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	79.92
Mean single sequence MFE	-9.43
Consensus MFE	-6.50
Energy contribution	-6.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.69
SVM decision value	0.51
SVM RNA-class probability	0.763614
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8254132 94 + 23771897
CACAUUCGU-ACAUCAUCUCGAUAAAA----------ACCAACAAACAACGUACA--AAUCCAUCGAA--UCCGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCA
.......((-((......(((((....----------....((.......))...--.....))))).--...))))...........(((((((.....)).))))). ( -11.19)
>DroGri_CAF1 93492 94 + 1
CACAUUCAAAACUUCAC------AAAA-AAA---AAAAUCAACAACAAAAAAAAA--AUACCAUCGCA--U-CGUAUUAAACUUUUUAGAAUCGGACAAUCCAGGUUCA
.................------....-...---....................(--((((.......--.-.)))))..........(((((((.....)).))))). (  -7.00)
>DroEre_CAF1 81140 93 + 1
CACAUUCGU-ACAUCAUCUCGAUAAAA----------ACCAACAAACAACGUACA--AAUCCAUCGAA--U-CGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCA
.......((-((......(((((....----------....((.......))...--.....))))).--.-.))))...........(((((((.....)).))))). ( -10.79)
>DroWil_CAF1 98271 88 + 1
CACA------AAAAAAUCUC----AAA----------UCAAACAAACAACGUACAAAAAUCCAUCGAAAAU-CGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCA
....------..........----...----------.............((((.....((....))....-.))))...........(((((((.....)).))))). (  -8.20)
>DroYak_CAF1 81475 103 + 1
CACAUUCGU-ACAUCAUCACGAUAAAAAAAAAAACAAAUCAACAAACAACGUACA--AAUCCAUCGAA--U-CGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCA
.....((((-........))))............................((((.--..((....)).--.-.))))...........(((((((.....)).))))). ( -10.70)
>DroAna_CAF1 79527 100 + 1
CUCAUUUCA-ACUUCAUCUCGAUAAAAAACCA---AAACCAACAAACAACGUACA--AAUCCAUCGAA--U-CGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCA
.........-......................---...............((((.--..((....)).--.-.))))...........(((((((.....)).))))). (  -8.70)
>consensus
CACAUUCGU_ACAUCAUCUCGAUAAAA__________ACCAACAAACAACGUACA__AAUCCAUCGAA__U_CGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCA
........................................................................................(((((((.....)).))))). ( -6.50 =  -6.50 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	8,254,158 – 8,254,266
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.28
Mean single sequence MFE	-18.10
Consensus MFE	-15.18
Energy contribution	-15.23
Covariance contribution	0.06
Combinations/Pair	1.06
Mean z-score	-2.44
Structure conservation index	0.84
SVM decision value	1.15
SVM RNA-class probability	0.922239
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8254158 108 + 23771897
--------ACCAACAAACAACGUACA--AAUCCAUCGAA--UCCGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACGCUUCACAUCC
--------.............((...--........(((--((.((..(((.....)))(((((((.....)).))))).)).))))).(((((((((.....))))..))))))).... ( -18.80)
>DroPse_CAF1 77943 108 + 1
-----CAAACCAACAAACAACGUACA--ACUCCAUCGA---U-CGUACUAAACUU-UUAGAAUCGGACAAUCCAGGUUCCACAGAUUCCGAAGUUAGGAAAAUCCUAACGCUUCACAUAC
-----................((((.--..........---.-.))))......(-(..(((((((.....)).(....)...)))))..))((((((.....))))))........... ( -17.52)
>DroGri_CAF1 93514 112 + 1
AA---AAAAUCAACAACAAAAAAAAA--AUACCAUCGCA--U-CGUAUUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACUCUUCACAUAC
..---..((((..............(--((((.......--.-.)))))..........(((((((.....)).)))))....))))..(((((((((.....)))))))..))...... ( -17.60)
>DroWil_CAF1 98288 111 + 1
--------UCAAACAAACAACGUACAAAAAUCCAUCGAAAAU-CGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACACUUCACAUAC
--------.............((...........(((..(((-(((.....))......(((((((.....)).)))))....)))).))).((((((.....)))))).....)).... ( -17.40)
>DroYak_CAF1 81503 115 + 1
AAAAACAAAUCAACAAACAACGUACA--AAUCCAUCGAA--U-CGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACGCUUCACAUCC
.....................((...--........(((--(-(((.....))......(((((((.....)).)))))....))))).(((((((((.....))))..))))))).... ( -19.70)
>DroMoj_CAF1 98322 95 + 1
--------------------AAAAAC--GAAACAUCGCA--U-UGUAUUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACGCUUCACAUAC
--------------------......--........((.--.-............((..(((((((.....)).(......).)))))..))((((((.....))))))))......... ( -17.60)
>consensus
________ACCAACAAACAACGUACA__AAUCCAUCGAA__U_CGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACGCUUCACAUAC
............................................((.............(((((((.....)).)))))..........(((((((((.....))))..))))))).... (-15.18 = -15.23 +   0.06)

alignment

secondary structure

dotplot

Window 2

Location	8,254,187 – 8,254,306
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	97.30
Mean single sequence MFE	-24.98
Consensus MFE	-23.03
Energy contribution	-23.08
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-2.01
Structure conservation index	0.92
SVM decision value	2.59
SVM RNA-class probability	0.995594
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8254187 119 + 23771897
-UCCGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACGCUUCACAUCCCAAUUACAGAAUAUGACACACUCGGCUCCGAGUCCGACAA
-......((((.....))))..((((((....((.((((....(....)(((((((((.....))))..)))))..............)))).))......(((....)))))))))... ( -24.30)
>DroVir_CAF1 98577 118 + 1
-U-CGUAUUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACGCUUCACAUACCAAUUACAGAAUAUGACACACUCGGCUCCGAGUCCGACAA
-(-((((((..........(((((((.....)).)))))..........(((((((((.....))))..)))))...............)))))))...(((((....)))))....... ( -26.60)
>DroPse_CAF1 77974 117 + 1
-U-CGUACUAAACUU-UUAGAAUCGGACAAUCCAGGUUCCACAGAUUCCGAAGUUAGGAAAAUCCUAACGCUUCACAUACCAAUUACAGAAUAUGACACACUCGGCUCCGAGUCCGACAA
-(-((((.......(-(..(((((((.....)).(....)...)))))..))((((((.....))))))......................)))))...(((((....)))))....... ( -24.10)
>DroGri_CAF1 93548 118 + 1
-U-CGUAUUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACUCUUCACAUACCAAUUACAGAAUAUGACACACUCGGCUCCGAGUCCGACAA
-(-((((((..........(((((((.....)).)))))..........(((((((((.....)))))))..))...............)))))))...(((((....)))))....... ( -26.30)
>DroWil_CAF1 98320 119 + 1
AU-CGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACACUUCACAUACCAAUUACAGAAUAUGACACACUCGGCUCCGAGUCCGACAA
.(-((((............(((((((.....)).)))))..........(((((((((.....))))..))))).................)))))...(((((....)))))....... ( -24.30)
>DroMoj_CAF1 98339 118 + 1
-U-UGUAUUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACGCUUCACAUACCAAUUACAGAAUAUGACACACUCGGCUCCGAGUCCGACAA
-(-((((............(((((((.....)).)))))..........(((((((((.....))))..)))))..........)))))..........(((((....)))))....... ( -24.30)
>consensus
_U_CGUACUAAACUUUUUAGAAUCGGACAAUCCAGGUUCAACAGAUUCCGAAGUUAGGAAAAUCCUAACGCUUCACAUACCAAUUACAGAAUAUGACACACUCGGCUCCGAGUCCGACAA
......................((((((....((.((((....(....)(((((((((.....))))..)))))..............)))).))......(((....)))))))))... (-23.03 = -23.08 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	8,254,187 – 8,254,306
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	97.30
Mean single sequence MFE	-32.25
Consensus MFE	-30.34
Energy contribution	-30.40
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.25
Structure conservation index	0.94
SVM decision value	1.18
SVM RNA-class probability	0.927366
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8254187 119 - 23771897
UUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGGAUGUGAAGCGUUAGGAUUUUCCUAACUUCGGAAUCUGUUGAACCUGGAUUGUCCGAUUCUAAAAAGUUUAGUACGGA-
..(((((((......(((((.((.(((((((((......))))))))).))((((((.....)))))))))))(((((.........))))))))))))....................- ( -36.00)
>DroVir_CAF1 98577 118 - 1
UUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGUAUGUGAAGCGUUAGGAUUUUCCUAACUUCGGAAUCUGUUGAACCUGGAUUGUCCGAUUCUAAAAAGUUUAAUACG-A-
..(((((((......(((((.((.((((((.((......)).)))))).))((((((.....)))))))))))(((((.........))))))))))))..................-.- ( -32.10)
>DroPse_CAF1 77974 117 - 1
UUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGUAUGUGAAGCGUUAGGAUUUUCCUAACUUCGGAAUCUGUGGAACCUGGAUUGUCCGAUUCUAA-AAGUUUAGUACG-A-
..(((((((......(((((.((.((((((.((......)).)))))).))((((((.....)))))))))))((((((.(....)))))))))))))).....-............-.- ( -33.10)
>DroGri_CAF1 93548 118 - 1
UUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGUAUGUGAAGAGUUAGGAUUUUCCUAACUUCGGAAUCUGUUGAACCUGGAUUGUCCGAUUCUAAAAAGUUUAAUACG-A-
..(((((((......((((.....((((((.((......)).))))))..(((((((.....)))))))))))(((((.........))))))))))))..................-.- ( -30.40)
>DroWil_CAF1 98320 119 - 1
UUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGUAUGUGAAGUGUUAGGAUUUUCCUAACUUCGGAAUCUGUUGAACCUGGAUUGUCCGAUUCUAAAAAGUUUAGUACG-AU
..(((((((......(((((....((((((.((......)).))))))...((((((.....)))))))))))(((((.........))))))))))))..................-.. ( -29.80)
>DroMoj_CAF1 98339 118 - 1
UUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGUAUGUGAAGCGUUAGGAUUUUCCUAACUUCGGAAUCUGUUGAACCUGGAUUGUCCGAUUCUAAAAAGUUUAAUACA-A-
..(((((((......(((((.((.((((((.((......)).)))))).))((((((.....)))))))))))(((((.........))))))))))))..................-.- ( -32.10)
>consensus
UUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGUAUGUGAAGCGUUAGGAUUUUCCUAACUUCGGAAUCUGUUGAACCUGGAUUGUCCGAUUCUAAAAAGUUUAAUACG_A_
..(((((((......(((((.((.((((((.((......)).)))))).))((((((.....)))))))))))(((((.........))))))))))))..................... (-30.34 = -30.40 +   0.06)

alignment

secondary structure

dotplot

Window 4

Location	8,254,226 – 8,254,346
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.00
Mean single sequence MFE	-39.25
Consensus MFE	-35.84
Energy contribution	-35.62
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.56
Structure conservation index	0.91
SVM decision value	1.44
SVM RNA-class probability	0.953730
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8254226 120 - 23771897
UCGAUACUUGGCCGAGUUUAGAGCUCGCGCAGACACAUCAUUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGGAUGUGAAGCGUUAGGAUUUUCCUAACUUCGGAAUCUGU
((((.((((((((((((((...((....)).((((......)))))))))))..)))))))((.(((((((((......))))))))).))((((((.....)))))).))))....... ( -43.00)
>DroVir_CAF1 98615 120 - 1
GCGAUAUUUGGCCGAGUUAAGAGCGCGCGCGGACACAUCAUUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGUAUGUGAAGCGUUAGGAUUUUCCUAACUUCGGAAUCUGU
((.(((((((((((((((....((....)).((((......)))).))))))..))))))))).((((((.((......)).)))))).))((((((.....))))))............ ( -37.90)
>DroGri_CAF1 93586 120 - 1
GCGAUAUUUGGCCGAGUUAAGAGCGCGUGCAGACACAUCGUUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGUAUGUGAAGAGUUAGGAUUUUCCUAACUUCGGAAUCUGU
.(((((((((((((((((.(.((((.(((....)))..)))).)..))))))..))))))))).((((((.((......)).)))))).((((((((.....))))))))))........ ( -36.90)
>DroWil_CAF1 98359 120 - 1
GCGAUAUUUGGCCGAGUUAAGAGCGCGUGCAGACACAUCAUUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGUAUGUGAAGUGUUAGGAUUUUCCUAACUUCGGAAUCUGU
.(((((((((((((((((....((....)).((((......)))).))))))..))))))))).((((((.((......)).))))))...((((((.....))))))..))........ ( -34.60)
>DroMoj_CAF1 98377 120 - 1
GCGAUAUUUGGCCGAGUUAAGAGCGCGGGCGGACACAUCAUUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGUAUGUGAAGCGUUAGGAUUUUCCUAACUUCGGAAUCUGU
((.(((((((((((((((....((....)).((((......)))).))))))..))))))))).((((((.((......)).)))))).))((((((.....))))))............ ( -37.50)
>DroAna_CAF1 79627 120 - 1
GCGAUACUUGGCCGAGUUUAGCGCGCGUGCAGACACAUCAUUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGGAUGUGAAGCGUUAGGAUUUUCCUAACUUCGGAAUCUGU
((.((((((((((((((((.(((....))).((((......)))))))))))..))))))))).(((((((((......))))))))).))((((((.....))))))............ ( -45.60)
>consensus
GCGAUAUUUGGCCGAGUUAAGAGCGCGUGCAGACACAUCAUUGUCGGACUCGGAGCCGAGUGUGUCAUAUUCUGUAAUUGGUAUGUGAAGCGUUAGGAUUUUCCUAACUUCGGAAUCUGU
.(((((((((((((((((....((....)).((((......)))).))))))..))))))))).((((((.((......)).))))))...((((((.....))))))..))........ (-35.84 = -35.62 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:17 2006