Locus 6493

Sequence ID	3L_DroMel_CAF1
Location	17,258,342 – 17,258,523
Length	181
Max. P	0.976184

overview

Window 4

Location	17,258,342 – 17,258,449
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.37
Mean single sequence MFE	-27.78
Consensus MFE	-21.76
Energy contribution	-21.52
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-2.46
Structure conservation index	0.78
SVM decision value	1.76
SVM RNA-class probability	0.976184
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17258342 107 + 23771897
CAUCCCUUGUGGAAAUUAUUUUAAUUUUUCACGCAACCGAAAAGCGGAAAUUCCAAUUAAAACGCAUCAGCGCAUUGAGAUACUCCGCAUUCGGCAUC------UGCAUCCGC-------
........(((((((..........)))))))(((.(((((..(((((...((((((.....(((....))).)))).))...))))).)))))....------)))......------- ( -26.30)
>DroSec_CAF1 142008 108 + 1
CAUCCCUUGUGGAAAUUAUUUUAAUUUUUCACGCAACCGAAAAGCGGAAAUUCCAAUUAAAACGCAUCAGCGCAUUGAGAUUCUCCGCAUUCGGCAUC------UGCAUCCGC------A
.......(((((((((((...)))))......(((.(((((..((((((((..((((.....(((....))).))))..))).))))).)))))....------))).)))))------) ( -27.30)
>DroSim_CAF1 136864 114 + 1
CAUCCCUUGUGGAAAUUAUUUUAAUUUUUCACGCAACCGAAAAGCGGAAAUUCCAAUUAAAACGCAUCAGCGCAUUGAGAUACUCCGCAUUCGGCAUC------UGCAUCCGCAUACGCA
........(((((((..........)))))))((..(((((..(((((...((((((.....(((....))).)))).))...))))).)))))....------(((....)))...)). ( -28.10)
>DroEre_CAF1 145099 107 + 1
CAUCCCUUGUGGAAAUUAUUUUAAUUUUUCACGCAACCGAAGAGCGGAAAUUCCAAUUAAAACGCAUCAGCGCAUUGAGAUACUCCGC-------------AUCUGCAUCCGCAGCCGCA
........(((((((..........)))))))((.........(((((...((((((.....(((....))).)))).))...)))))-------------..((((....))))..)). ( -25.70)
>DroYak_CAF1 149239 120 + 1
CAUCCCUUGUGGAAAUUAUUUUAAUUUUUCACGCAACCGAAGAGCGGAAAUUCCAAUUAAAACGCAUCAGCGCAUUGAGAUACUCCGCAUUCGGCAUCUGCAUCUGCAUCCGCAUCCGCA
.......((((((...................(((.(((((..(((((...((((((.....(((....))).)))).))...))))).)))))....)))...(((....))))))))) ( -31.50)
>consensus
CAUCCCUUGUGGAAAUUAUUUUAAUUUUUCACGCAACCGAAAAGCGGAAAUUCCAAUUAAAACGCAUCAGCGCAUUGAGAUACUCCGCAUUCGGCAUC______UGCAUCCGCA__CGCA
........(((((............(((((........)))))(((((...((((((.....(((....))).)))).))...)))))....................)))))....... (-21.76 = -21.52 +  -0.24)

alignment

secondary structure

dotplot

Window 5

Location	17,258,342 – 17,258,449
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.37
Mean single sequence MFE	-33.12
Consensus MFE	-26.60
Energy contribution	-27.80
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.80
SVM decision value	0.66
SVM RNA-class probability	0.815326
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17258342 107 - 23771897
-------GCGGAUGCA------GAUGCCGAAUGCGGAGUAUCUCAAUGCGCUGAUGCGUUUUAAUUGGAAUUUCCGCUUUUCGGUUGCGUGAAAAAUUAAAAUAAUUUCCACAAGGGAUG
-------....(((((------...((((((.((((((.((..((((((((....))))....))))..))))))))..)))))))))))................((((....)))).. ( -32.50)
>DroSec_CAF1 142008 108 - 1
U------GCGGAUGCA------GAUGCCGAAUGCGGAGAAUCUCAAUGCGCUGAUGCGUUUUAAUUGGAAUUUCCGCUUUUCGGUUGCGUGAAAAAUUAAAAUAAUUUCCACAAGGGAUG
.------....(((((------...((((((.(((((((.((.((((((((....))))....)))))).)))))))..)))))))))))................((((....)))).. ( -34.30)
>DroSim_CAF1 136864 114 - 1
UGCGUAUGCGGAUGCA------GAUGCCGAAUGCGGAGUAUCUCAAUGCGCUGAUGCGUUUUAAUUGGAAUUUCCGCUUUUCGGUUGCGUGAAAAAUUAAAAUAAUUUCCACAAGGGAUG
.((((((((....)))------...((((((.((((((.((..((((((((....))))....))))..))))))))..)))))))))))................((((....)))).. ( -33.70)
>DroEre_CAF1 145099 107 - 1
UGCGGCUGCGGAUGCAGAU-------------GCGGAGUAUCUCAAUGCGCUGAUGCGUUUUAAUUGGAAUUUCCGCUCUUCGGUUGCGUGAAAAAUUAAAAUAAUUUCCACAAGGGAUG
.(((((((.(((.......-------------((((((.((..((((((((....))))....))))..))))))))))).)))))))..................((((....)))).. ( -29.61)
>DroYak_CAF1 149239 120 - 1
UGCGGAUGCGGAUGCAGAUGCAGAUGCCGAAUGCGGAGUAUCUCAAUGCGCUGAUGCGUUUUAAUUGGAAUUUCCGCUCUUCGGUUGCGUGAAAAAUUAAAAUAAUUUCCACAAGGGAUG
((.((((((....))).(((((...((((((.((((((.((..((((((((....))))....))))..))))))))..))))))))))).................))).))....... ( -35.50)
>consensus
UGCG__UGCGGAUGCA______GAUGCCGAAUGCGGAGUAUCUCAAUGCGCUGAUGCGUUUUAAUUGGAAUUUCCGCUUUUCGGUUGCGUGAAAAAUUAAAAUAAUUUCCACAAGGGAUG
...........(((((.........((((((.((((((.((..((((((((....))))....))))..))))))))..)))))))))))................((((....)))).. (-26.60 = -27.80 +   1.20)

alignment

secondary structure

dotplot

Window 6

Location	17,258,382 – 17,258,483
Length	101
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.02
Mean single sequence MFE	-26.15
Consensus MFE	-20.35
Energy contribution	-20.35
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.37
Structure conservation index	0.78
SVM decision value	-0.05
SVM RNA-class probability	0.509852
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17258382 101 + 23771897
AAAGCGGAAAUUCCAAUUAAAACGCAUCAGCGCAUUGAGAUACUCCGCAUUCGGCAUC------UGCAUCCGC------------AUAC-GCAUCCGCAUUUCGUAUCCGAAUCCGAAAG
...(((((...((((((.....(((....))).)))).))...))))).(((((....------(((....((------------....-))....))).((((....)))).))))).. ( -23.30)
>DroSec_CAF1 142048 107 + 1
AAAGCGGAAAUUCCAAUUAAAACGCAUCAGCGCAUUGAGAUUCUCCGCAUUCGGCAUC------UGCAUCCGC------AUCCGCAUAC-GCAUCCGCAUUUCGUAUCCGAAUCCGAAAG
...((((((((..((((.....(((....))).))))..))).))))).(((((....------(((....))------)..((.((((-(.(........)))))).))...))))).. ( -25.50)
>DroSim_CAF1 136904 113 + 1
AAAGCGGAAAUUCCAAUUAAAACGCAUCAGCGCAUUGAGAUACUCCGCAUUCGGCAUC------UGCAUCCGCAUACGCAUCCGCAUAU-GCAUCCGCAUUUCGUAUCCAAAUCCGAAAG
...(((((...((((((.....(((....))).)))).))...))))).(((((.((.------((.....(((((.((....)).)))-))....((.....))...)).))))))).. ( -26.50)
>DroYak_CAF1 149279 120 + 1
AGAGCGGAAAUUCCAAUUAAAACGCAUCAGCGCAUUGAGAUACUCCGCAUUCGGCAUCUGCAUCUGCAUCCGCAUCCGCAUCCGCAUAUGGCAUCCGCAUAUCGCAUCCGAAUCCGAAAG
...(((((...((((((.....(((....))).)))).))...))))).(((((..(((((...(((....)))...)))...(((((((.......))))).))....))..))))).. ( -29.30)
>consensus
AAAGCGGAAAUUCCAAUUAAAACGCAUCAGCGCAUUGAGAUACUCCGCAUUCGGCAUC______UGCAUCCGC______AUCCGCAUAC_GCAUCCGCAUUUCGUAUCCGAAUCCGAAAG
...(((((...((((((.....(((....))).)))).))...))))).(((((...........((....)).................((....))...............))))).. (-20.35 = -20.35 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	17,258,382 – 17,258,483
Length	101
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.02
Mean single sequence MFE	-38.53
Consensus MFE	-29.49
Energy contribution	-29.55
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-2.21
Structure conservation index	0.77
SVM decision value	1.01
SVM RNA-class probability	0.899461
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17258382 101 - 23771897
CUUUCGGAUUCGGAUACGAAAUGCGGAUGC-GUAU------------GCGGAUGCA------GAUGCCGAAUGCGGAGUAUCUCAAUGCGCUGAUGCGUUUUAAUUGGAAUUUCCGCUUU
..(((((.((((....)))).((((..(((-....------------)))..))))------....))))).((((((.((..((((((((....))))....))))..))))))))... ( -33.80)
>DroSec_CAF1 142048 107 - 1
CUUUCGGAUUCGGAUACGAAAUGCGGAUGC-GUAUGCGGAU------GCGGAUGCA------GAUGCCGAAUGCGGAGAAUCUCAAUGCGCUGAUGCGUUUUAAUUGGAAUUUCCGCUUU
..(((((.((((....)))).((((..(((-((......))------)))..))))------....))))).(((((((.((.((((((((....))))....)))))).)))))))... ( -38.10)
>DroSim_CAF1 136904 113 - 1
CUUUCGGAUUUGGAUACGAAAUGCGGAUGC-AUAUGCGGAUGCGUAUGCGGAUGCA------GAUGCCGAAUGCGGAGUAUCUCAAUGCGCUGAUGCGUUUUAAUUGGAAUUUCCGCUUU
..(((((.((((....)))).((((..(((-((((((....)))))))))..))))------....))))).((((((.((..((((((((....))))....))))..))))))))... ( -42.40)
>DroYak_CAF1 149279 120 - 1
CUUUCGGAUUCGGAUGCGAUAUGCGGAUGCCAUAUGCGGAUGCGGAUGCGGAUGCAGAUGCAGAUGCCGAAUGCGGAGUAUCUCAAUGCGCUGAUGCGUUUUAAUUGGAAUUUCCGCUCU
.......((((((.((((...((((..(((.((.(((....))).)))))..))))..))))....))))))((((((.((..((((((((....))))....))))..))))))))... ( -39.80)
>consensus
CUUUCGGAUUCGGAUACGAAAUGCGGAUGC_AUAUGCGGAU______GCGGAUGCA______GAUGCCGAAUGCGGAGUAUCUCAAUGCGCUGAUGCGUUUUAAUUGGAAUUUCCGCUUU
..(((((.((((....)))).((((..(((.................)))..))))..........))))).((((((.((..((((((((....))))....))))..))))))))... (-29.49 = -29.55 +   0.06)

alignment

secondary structure

dotplot

Window 8

Location	17,258,422 – 17,258,523
Length	101
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.43
Mean single sequence MFE	-35.46
Consensus MFE	-23.42
Energy contribution	-23.98
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.50
Structure conservation index	0.66
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17258422 101 - 23771897
UUUGGAUUCGGAUCCUGACUCUGAUUCUGAUUCUGUUUCUCUUUCGGAUUCGGAUACGAAAUGCGGAUGC-GUAU------------GCGGAUGCA------GAUGCCGAAUGCGGAGUA
((((.((((((...(((..((((..(((((.((((.........)))).)))))......(((((....)-))))------------.))))..))------)...)))))).))))... ( -30.80)
>DroSec_CAF1 142088 107 - 1
UUUGGAUUCGUAUCCUGACUCUGAUUCUGAUUCUGUUUCUCUUUCGGAUUCGGAUACGAAAUGCGGAUGC-GUAUGCGGAU------GCGGAUGCA------GAUGCCGAAUGCGGAGAA
((((.((((((((((....(((((.(((((.............))))).)))))......(((((....)-))))..))))------)))))).))------))..(((....))).... ( -34.52)
>DroSim_CAF1 136944 113 - 1
UUUGGAUUCGGAUCCUGACUCUGAUUCUGAUUCUGUUUCUCUUUCGGAUUUGGAUACGAAAUGCGGAUGC-AUAUGCGGAUGCGUAUGCGGAUGCA------GAUGCCGAAUGCGGAGUA
((((.(((((((((.....((..(.(((((.............))))).)..)).......((((..(((-((((((....)))))))))..))))------))).)))))).))))... ( -38.82)
>DroYak_CAF1 149319 114 - 1
UUUGGAUUCGGAUCCUGACUCUGAUUC------UGUUUCUCUUUCGGAUUCGGAUGCGAUAUGCGGAUGCCAUAUGCGGAUGCGGAUGCGGAUGCAGAUGCAGAUGCCGAAUGCGGAGUA
((((.((((((...(((..((((..((------(((.(((..((((.((..((((.((.....)).)).))..)).))))...))).)))))..))))..)))...)))))).))))... ( -37.70)
>consensus
UUUGGAUUCGGAUCCUGACUCUGAUUCUGAUUCUGUUUCUCUUUCGGAUUCGGAUACGAAAUGCGGAUGC_AUAUGCGGAU______GCGGAUGCA______GAUGCCGAAUGCGGAGUA
((((.(((((((((((((.(((((....((.......))....))))).))))........((((..(((.................)))..))))......))).)))))).))))... (-23.42 = -23.98 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:08 2006