Locus 7417

Sequence ID	3L_DroMel_CAF1
Location	19,970,531 – 19,970,662
Length	131
Max. P	0.991045

overview

Window 7

Location	19,970,531 – 19,970,622
Length	91
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.04
Mean single sequence MFE	-30.55
Consensus MFE	-19.88
Energy contribution	-20.35
Covariance contribution	0.47
Combinations/Pair	1.24
Mean z-score	-2.06
Structure conservation index	0.65
SVM decision value	1.92
SVM RNA-class probability	0.982766
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19970531 91 + 23771897
ACGAGU----------------------AUCCGUGCCGACA---UUGCAGCCAAAAUGUUGAACUCACUCCG--AAUGGAGUUUAUCUCCGUAUUUUGAGUGGGUUUU--CCGGCGCGUG
......----------------------...((((((((((---((........))))).((((((((((.(--(((((((.....))))))..)).)))))))))).--.))))))).. ( -34.70)
>DroSec_CAF1 61478 91 + 1
ACGAGU----------------------AUCUGUGCCGACA---UUGCAGCCAAAAUGUUGAACUCACUCCG--AAUGGAGUUUACCUCCGGAUUUUGAGUGGAUUUU--UCGGCGCGUG
......----------------------....(((((((((---((........))))..(((..(((((.(--(((((((.....))))..)))).)))))..))).--)))))))... ( -27.50)
>DroSim_CAF1 20093 91 + 1
ACGAGU----------------------AUCUGUGCCGACG---UUGCAGCCAAAAUGUUGAACUCACUCCG--AAUGGAGUUUAUCUCCGGAUUUUGAGUGGAUUUU--CCGGCGCGUG
......----------------------....((((((..(---((.((((......)))))))((((((.(--(((((((.....))))..)))).)))))).....--.))))))... ( -28.60)
>DroEre_CAF1 12547 90 + 1
ACGAGU----------------------AUUCCUGCCGACA---UUGCAGUCAAAAUGUUGGACUCACUCUG--AAAGGAGUUUAUCUCCAGAUUUUGAGUGAGUUUU--G-GGCGCAUG
....((----------------------...(((.((((((---((........))))))))((((((((.(--((.((((.....))))...))).))))))))...--)-)).))... ( -28.50)
>DroYak_CAF1 12513 91 + 1
ACGAGU----------------------AUCCGUGCCGACA---UUGCAGUCAACAUGUUGAACUCACUCUG--AAUGGAGUUUAUCUCCAGACUUUGAGUGAGUUUU--GUGACGCAUG
......----------------------...(((((.(((.---.....)))..(((...((((((((((.(--..(((((.....)))))..)...)))))))))).--)))..))))) ( -30.80)
>DroAna_CAF1 12201 119 + 1
ACGAGUCACCGAAAAUAUCUCAAGGGAUAUAUGUGCAAUCCUUUUUGGAGCUCCCAACUUUAACUCACUCAGCCGAAGGAGUCUGGCUCCACAA-CUGAGUGACUUUGGCCCAGCGCAUG
.((......))...((((((....))))))((((((..(((.....)))....((((.......((((((((.....((((.....))))....-))))))))..))))....)))))). ( -33.20)
>consensus
ACGAGU______________________AUCCGUGCCGACA___UUGCAGCCAAAAUGUUGAACUCACUCCG__AAUGGAGUUUAUCUCCAGAUUUUGAGUGAGUUUU__CCGGCGCAUG
................................((((((.........((((......))))...((((((......(((((.....)))))......))))))........))))))... (-19.88 = -20.35 +   0.47)

alignment

secondary structure

dotplot

Window 8

Location	19,970,531 – 19,970,622
Length	91
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.04
Mean single sequence MFE	-27.75
Consensus MFE	-16.66
Energy contribution	-16.57
Covariance contribution	-0.08
Combinations/Pair	1.22
Mean z-score	-2.00
Structure conservation index	0.60
SVM decision value	1.62
SVM RNA-class probability	0.967950
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19970531 91 - 23771897
CACGCGCCGG--AAAACCCACUCAAAAUACGGAGAUAAACUCCAUU--CGGAGUGAGUUCAACAUUUUGGCUGCAA---UGUCGGCACGGAU----------------------ACUCGU
..((.(((((--......((..((((((...(((....(((((...--.)))))...)))...))))))..))...---..))))).))...----------------------...... ( -25.80)
>DroSec_CAF1 61478 91 - 1
CACGCGCCGA--AAAAUCCACUCAAAAUCCGGAGGUAAACUCCAUU--CGGAGUGAGUUCAACAUUUUGGCUGCAA---UGUCGGCACAGAU----------------------ACUCGU
...(((((((--((.....(((((...((((((((......)).))--)))).)))))......))))))).))..---((((......)))----------------------)..... ( -28.10)
>DroSim_CAF1 20093 91 - 1
CACGCGCCGG--AAAAUCCACUCAAAAUCCGGAGAUAAACUCCAUU--CGGAGUGAGUUCAACAUUUUGGCUGCAA---CGUCGGCACAGAU----------------------ACUCGU
...(((((((--((.....(((((...((((((...........))--)))).)))))......))))))).))..---.(((......)))----------------------...... ( -23.70)
>DroEre_CAF1 12547 90 - 1
CAUGCGCC-C--AAAACUCACUCAAAAUCUGGAGAUAAACUCCUUU--CAGAGUGAGUCCAACAUUUUGACUGCAA---UGUCGGCAGGAAU----------------------ACUCGU
.....(((-.--...((((((((..((...((((.....)))).))--..))))))))..........(((.....---.))))))......----------------------...... ( -24.10)
>DroYak_CAF1 12513 91 - 1
CAUGCGUCAC--AAAACUCACUCAAAGUCUGGAGAUAAACUCCAUU--CAGAGUGAGUUCAACAUGUUGACUGCAA---UGUCGGCACGGAU----------------------ACUCGU
.....(((..--..(((((((((...(..(((((.....)))))..--).)))))))))...(.(((((((.....---.))))))).))))----------------------...... ( -28.00)
>DroAna_CAF1 12201 119 - 1
CAUGCGCUGGGCCAAAGUCACUCAG-UUGUGGAGCCAGACUCCUUCGGCUGAGUGAGUUAAAGUUGGGAGCUCCAAAAAGGAUUGCACAUAUAUCCCUUGAGAUAUUUUCGGUGACUCGU
....(((((((...((.((((((((-(((.((((.....))))..))))))))))).))......(((((((((.....)))..)).......))))..........)))))))...... ( -36.81)
>consensus
CACGCGCCGG__AAAACCCACUCAAAAUCCGGAGAUAAACUCCAUU__CGGAGUGAGUUCAACAUUUUGGCUGCAA___UGUCGGCACAGAU______________________ACUCGU
.....(((......(((.(((((.......((((.....)))).......))))).))).........(((.........)))))).................................. (-16.66 = -16.57 +  -0.08)

alignment

secondary structure

dotplot

Window 9

Location	19,970,549 – 19,970,662
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.98
Mean single sequence MFE	-36.82
Consensus MFE	-23.64
Energy contribution	-24.25
Covariance contribution	0.61
Combinations/Pair	1.33
Mean z-score	-2.75
Structure conservation index	0.64
SVM decision value	1.95
SVM RNA-class probability	0.983539
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19970549 113 + 23771897
A---UUGCAGCCAAAAUGUUGAACUCACUCCG--AAUGGAGUUUAUCUCCGUAUUUUGAGUGGGUUUU--CCGGCGCGUGCGCUGGAUUCGACUCCAUUUUUGGGCAAUUGUUUGAAAAU
(---((((..((((((.(((((((((((((.(--(((((((.....))))))..)).))))))))..(--((((((....))))))).))))).....)))))))))))........... ( -41.80)
>DroSec_CAF1 61496 113 + 1
A---UUGCAGCCAAAAUGUUGAACUCACUCCG--AAUGGAGUUUACCUCCGGAUUUUGAGUGGAUUUU--UCGGCGCGUGCGCUGGAUUCGACUCCAUUUUUGAGCAAUUGUUUGAAAAU
.---.............((((((.((((((.(--(((((((.....))))..)))).))))))....(--((((((....)))))))))))))...(((((..(((....)))..))))) ( -32.90)
>DroSim_CAF1 20111 113 + 1
G---UUGCAGCCAAAAUGUUGAACUCACUCCG--AAUGGAGUUUAUCUCCGGAUUUUGAGUGGAUUUU--CCGGCGCGUGCGCUGGAUUCGACUCCAUUUUUGGGCAAUUGUUUGAGAAU
(---((((..((((((.((((((.((((((.(--(((((((.....))))..)))).))))))....(--((((((....))))))))))))).....)))))))))))........... ( -38.70)
>DroEre_CAF1 12565 112 + 1
A---UUGCAGUCAAAAUGUUGGACUCACUCUG--AAAGGAGUUUAUCUCCAGAUUUUGAGUGAGUUUU--G-GGCGCAUGCGCUGGAUUUGACUCCAUUUUUGGGCAGUUGUUUGAGAAU
.---.((.(((((((......(((((((((.(--((.((((.....))))...))).)))))))))((--.-((((....)))).))))))))).))((((..(((....)))..)))). ( -38.10)
>DroYak_CAF1 12531 113 + 1
A---UUGCAGUCAACAUGUUGAACUCACUCUG--AAUGGAGUUUAUCUCCAGACUUUGAGUGAGUUUU--GUGACGCAUGCGCUAGAUUUGACUCCAUUUUUGGGCAAUUGUUUGAAAAU
.---.(((.((((.((....((((((((((.(--..(((((.....)))))..)...)))))))))))--))))))))(((.(((((..((....))..))))))))............. ( -36.30)
>DroAna_CAF1 12241 117 + 1
CUUUUUGGAGCUCCCAACUUUAACUCACUCAGCCGAAGGAGUCUGGCUCCACAA-CUGAGUGACUUUGGCCCAGCGCAUGCGUUUAUUUCGGCUCCAGAUCCGAA--GCCUCACCAGCAU
...(((((((((.((((.......((((((((.....((((.....))))....-))))))))..))))...((((....))))......)))))))))......--((.......)).. ( -33.10)
>consensus
A___UUGCAGCCAAAAUGUUGAACUCACUCCG__AAUGGAGUUUAUCUCCAGAUUUUGAGUGAGUUUU__CCGGCGCAUGCGCUGGAUUCGACUCCAUUUUUGGGCAAUUGUUUGAAAAU
.................((((((.((((((......(((((.....)))))......))))))........(((((....)))))..))))))...(((((..(((....)))..))))) (-23.64 = -24.25 +   0.61)

alignment

secondary structure

dotplot

Window 0

Location	19,970,549 – 19,970,662
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.98
Mean single sequence MFE	-33.58
Consensus MFE	-21.61
Energy contribution	-21.81
Covariance contribution	0.20
Combinations/Pair	1.22
Mean z-score	-3.39
Structure conservation index	0.64
SVM decision value	2.25
SVM RNA-class probability	0.991045
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19970549 113 - 23771897
AUUUUCAAACAAUUGCCCAAAAAUGGAGUCGAAUCCAGCGCACGCGCCGG--AAAACCCACUCAAAAUACGGAGAUAAACUCCAUU--CGGAGUGAGUUCAACAUUUUGGCUGCAA---U
...........((((((((....)))((((((((((.(((....))).))--).(((.(((((..(((..((((.....)))))))--..))))).)))......)))))))))))---) ( -32.40)
>DroSec_CAF1 61496 113 - 1
AUUUUCAAACAAUUGCUCAAAAAUGGAGUCGAAUCCAGCGCACGCGCCGA--AAAAUCCACUCAAAAUCCGGAGGUAAACUCCAUU--CGGAGUGAGUUCAACAUUUUGGCUGCAA---U
...........(((((.......((((......))))((....))(((((--((.....(((((...((((((((......)).))--)))).)))))......))))))).))))---) ( -33.00)
>DroSim_CAF1 20111 113 - 1
AUUCUCAAACAAUUGCCCAAAAAUGGAGUCGAAUCCAGCGCACGCGCCGG--AAAAUCCACUCAAAAUCCGGAGAUAAACUCCAUU--CGGAGUGAGUUCAACAUUUUGGCUGCAA---C
............((((((((((..(((......(((.(((....))).))--)...)))(((((...((((((...........))--)))).)))))......))))))..))))---. ( -31.30)
>DroEre_CAF1 12565 112 - 1
AUUCUCAAACAACUGCCCAAAAAUGGAGUCAAAUCCAGCGCAUGCGCC-C--AAAACUCACUCAAAAUCUGGAGAUAAACUCCUUU--CAGAGUGAGUCCAACAUUUUGACUGCAA---U
.............((((((....)))(((((((....(((....))).-.--...((((((((..((...((((.....)))).))--..)))))))).......)))))))))).---. ( -30.10)
>DroYak_CAF1 12531 113 - 1
AUUUUCAAACAAUUGCCCAAAAAUGGAGUCAAAUCUAGCGCAUGCGUCAC--AAAACUCACUCAAAGUCUGGAGAUAAACUCCAUU--CAGAGUGAGUUCAACAUGUUGACUGCAA---U
...........((((((((....)))((((((.....(((....)))...--..(((((((((...(..(((((.....)))))..--).))))))))).......))))))))))---) ( -31.00)
>DroAna_CAF1 12241 117 - 1
AUGCUGGUGAGGC--UUCGGAUCUGGAGCCGAAAUAAACGCAUGCGCUGGGCCAAAGUCACUCAG-UUGUGGAGCCAGACUCCUUCGGCUGAGUGAGUUAAAGUUGGGAGCUCCAAAAAG
((((..((..(((--((((....)))))))...))....))))((.((.(((..((.((((((((-(((.((((.....))))..))))))))))).))...))).)).))......... ( -43.70)
>consensus
AUUCUCAAACAAUUGCCCAAAAAUGGAGUCGAAUCCAGCGCACGCGCCGG__AAAACCCACUCAAAAUCCGGAGAUAAACUCCAUU__CGGAGUGAGUUCAACAUUUUGGCUGCAA___U
.......................((.((((((.....(((....))).......(((.(((((.......((((.....)))).......))))).))).......)))))).))..... (-21.61 = -21.81 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:30 2006