Locus 8733

Sequence ID	3L_DroMel_CAF1
Location	22,781,532 – 22,781,661
Length	129
Max. P	0.975952

overview

Window 1

Location	22,781,532 – 22,781,622
Length	90
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	82.46
Mean single sequence MFE	-29.10
Consensus MFE	-24.02
Energy contribution	-24.18
Covariance contribution	0.16
Combinations/Pair	1.17
Mean z-score	-2.33
Structure conservation index	0.83
SVM decision value	1.76
SVM RNA-class probability	0.975952
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22781532 90 + 23771897
GGUGGCCAUCAGCUGCA---------AAAA-AUCAUUUCAC-A----CUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCA
((((((..((.......---------....-.........(-(----.(((((.....))))).)).(((((((...)))))))))..)))((....))..))). ( -31.10)
>DroSec_CAF1 44215 91 + 1
GGUGGCCAUCAGCUGCA---------AAAAUAUAAUCUCAU-A----CUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCA
((((((..((.......---------...........(((.-.----.(((((.....))))).)))(((((((...)))))))))..)))((....))..))). ( -30.60)
>DroSim_CAF1 46308 91 + 1
GGUGGCCAUCAGCUGCA---------AAAAAAAAAUCUCAU-A----CUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCA
((((((..((.......---------...........(((.-.----.(((((.....))))).)))(((((((...)))))))))..)))((....))..))). ( -30.60)
>DroEre_CAF1 43449 92 + 1
UUCACACAUUAGUUAAA---------AAAAAAGUCUUUCAC-A---CCUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCA
.................---------......(.(((((..-.---..(((((.....)))))....(((((((...)))))))))))).).(((......))). ( -25.90)
>DroYak_CAF1 46725 104 + 1
-UGGCAAACCAGCUAAACUACAAUAUAAAAAAAUCUUUUAAGACUGACUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCA
-.(((...........................................(((((.....)))))((..(((((((...)))))))..))))).(((......))). ( -27.30)
>consensus
GGUGGCCAUCAGCUGCA_________AAAAAAAAAUUUCAC_A____CUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCA
.(((((.....)))))...................((((.........(((((.....)))))....(((((((...)))))))))))....(((......))). (-24.02 = -24.18 +   0.16)

alignment

secondary structure

dotplot

Window 2

Location	22,781,553 – 22,781,661
Length	108
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	80.81
Mean single sequence MFE	-36.92
Consensus MFE	-30.47
Energy contribution	-30.47
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.51
Structure conservation index	0.83
SVM decision value	1.38
SVM RNA-class probability	0.948142
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22781553 108 + 23771897
-AUCAUUUCAC-A-----CUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAGUUGAAAUAUAUGUG-UAUAAACUA
-...((((((.-(-----((.((((((((((...((..(((((((...)))))))..)).)))).....(((.....)))....))))))))))))))).......-......... ( -35.60)
>DroVir_CAF1 57461 113 + 1
UAAGAGU--GA-AGAUCACUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAUGGUUAGUUUAGGCGGCAAAAAUGC
.......--..-...(((.(((((.....))))).)))(((((((...)))))))....((((..((..((((((((((.......)))..)))))))..))..))))........ ( -40.10)
>DroGri_CAF1 61672 113 + 1
-AAGAUUUCAA-AGAUC-UUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAUGGUUGAUUUUGCUCAUCGGAAACC
-..(((....(-(((((-..(((((((((((...((..(((((((...)))))))..)).)))).....(((.....)))....))))))).....))))))....)))(....). ( -37.10)
>DroSim_CAF1 46330 108 + 1
-AAAAUCUCAU-A-----CUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAGAUGUGAGGUUGACG-UGUAAACUA
-..((((((((-(-----.((((((((((((...((..(((((((...)))))))..)).)))).....(((.....)))....)))))))).)))))))))....-......... ( -42.30)
>DroEre_CAF1 43471 109 + 1
-AGUCUUUCAC-A---C-CUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAUGUACAAUUCAGUCG-UGUAAACUA
-........((-(---(-..(((((((((((...((..(((((((...)))))))..)).)))).....(((.....)))....))))))).(.((......))))-)))...... ( -32.50)
>DroYak_CAF1 46755 113 + 1
-AAUCUUUUAAGACUGA-CUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAUGCACAAUUUUUUCG-UGUAAACUA
-................-..(((((((((((...((..(((((((...)))))))..)).)))).....(((.....)))....)))))))(((((.........)-))))..... ( -33.90)
>consensus
_AAGAUUUCAA_A___C_CUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAUGUAUAAUUUAGGCG_UGUAAACUA
....................(((((((((((...((..(((((((...)))))))..)).)))).....(((.....)))....)))))))......................... (-30.47 = -30.47 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	22,781,553 – 22,781,661
Length	108
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	80.81
Mean single sequence MFE	-36.84
Consensus MFE	-30.93
Energy contribution	-30.93
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.15
Structure conservation index	0.84
SVM decision value	1.19
SVM RNA-class probability	0.928175
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22781553 108 - 23771897
UAGUUUAUA-CACAUAUAUUUCAACUCCCAUAUUGUCUAGUGGUUAGGAUACCCGGCUCUCACCCGGGAGGCCCGGGUUCAAUUCCCGGUAUGGGAAG-----U-GUGAAAUGAU-
.........-......(((((((((((((((((((......((....((.(((((((((((....)))))..))))))))....))))))))))).))-----)-.)))))))..- ( -37.00)
>DroVir_CAF1 57461 113 - 1
GCAUUUUUGCCGCCUAAACUAACCAUCCCAUAUUGUCUAGUGGUUAGGAUACCCGGCUCUCACCCGGGAGGCCCGGGUUCAAUUCCCGGUAUGGGAAGUGAUCU-UC--ACUCUUA
(((....))).((((...((((((((.............))))))))....(((((.......)))))))))(((((.......)))))..(((((.(((....-.)--))))))) ( -38.62)
>DroGri_CAF1 61672 113 - 1
GGUUUCCGAUGAGCAAAAUCAACCAUCCCAUAUUGUCUAGUGGUUAGGAUACCCGGCUCUCACCCGGGAGGCCCGGGUUCAAUUCCCGGUAUGGGAAA-GAUCU-UUGAAAUCUU-
((((((.(((.......))).....((((((((((......((....((.(((((((((((....)))))..))))))))....))))))))))))..-.....-..))))))..- ( -36.50)
>DroSim_CAF1 46330 108 - 1
UAGUUUACA-CGUCAACCUCACAUCUCCCAUAUUGUCUAGUGGUUAGGAUACCCGGCUCUCACCCGGGAGGCCCGGGUUCAAUUCCCGGUAUGGGAAG-----U-AUGAGAUUUU-
.........-.......((((.(..((((((((((......((....((.(((((((((((....)))))..))))))))....))))))))))))..-----)-.)))).....- ( -36.50)
>DroEre_CAF1 43471 109 - 1
UAGUUUACA-CGACUGAAUUGUACAUCCCAUAUUGUCUAGUGGUUAGGAUACCCGGCUCUCACCCGGGAGGCCCGGGUUCAAUUCCCGGUAUGGGAAG-G---U-GUGAAAGACU-
...((((((-(.((......)).(.((((((((((......((....((.(((((((((((....)))))..))))))))....)))))))))))).)-)---)-))))).....- ( -37.80)
>DroYak_CAF1 46755 113 - 1
UAGUUUACA-CGAAAAAAUUGUGCAUCCCAUAUUGUCUAGUGGUUAGGAUACCCGGCUCUCACCCGGGAGGCCCGGGUUCAAUUCCCGGUAUGGGAAG-UCAGUCUUAAAAGAUU-
.......((-(((.....)))))..((((((((((......((....((.(((((((((((....)))))..))))))))....))))))))))))..-..(((((....)))))- ( -34.60)
>consensus
UAGUUUACA_CGACAAAAUUAAACAUCCCAUAUUGUCUAGUGGUUAGGAUACCCGGCUCUCACCCGGGAGGCCCGGGUUCAAUUCCCGGUAUGGGAAG_G___U_UUGAAAUAUU_
.........................((((((((((......((....((.(((((((((((....)))))..))))))))....)))))))))))).................... (-30.93 = -30.93 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:23:21 2006