Locus 673

Sequence ID	3L_DroMel_CAF1
Location	1,996,826 – 1,996,973
Length	147
Max. P	0.745335

overview

Window 6

Location	1,996,826 – 1,996,936
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	84.20
Mean single sequence MFE	-31.24
Consensus MFE	-17.84
Energy contribution	-19.44
Covariance contribution	1.60
Combinations/Pair	1.27
Mean z-score	-2.46
Structure conservation index	0.57
SVM decision value	0.39
SVM RNA-class probability	0.715778
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1996826 110 - 23771897
UCAAUCAUGAAAUUGACAUUCACCAGACCGAAUUCGAGCUCUGAAAAAUGUGGAUUUUGGCCAGGAGGUGAAGAAGCACUGGCCACUUGGCCAACAGAUUUACUCUUGAG
..((((..((((((.(((((...(((((((....)).).))))...))))).))))))(((((((.(((.(........).))).)))))))....)))).......... ( -32.10)
>DroSec_CAF1 47689 107 - 1
UCAAUCAAGAUAUUGAUAUUCAGCAGGCCGAAUUUGAGCUCUGAAAAAUGUCGGUUUUGGCCAGGAGGUGA---AGCACUGGCCACUUGGCCAAAAGAUUUACUCUUGAG
....((((((..((((((((...(((((((....)).)).)))...))))))))(((((((((((.(((.(---.....).))).))))))))))).......)))))). ( -37.10)
>DroSim_CAF1 62520 107 - 1
UCAAUCAAGAAAUUGAUAUUCAGCAGGCCUAAUUCGAGGUCUGAAAAAUGUGGGUUUUGGCCAGGAGGUGA---AGCACUGUCCACUUGGCCAACAGAUUUACUCUUGAG
....((((((((((.(((((...(((((((......)))))))...))))).))))(((((((((.((...---........)).))))))))).........)))))). ( -36.80)
>DroEre_CAF1 53678 107 - 1
UCAAUCAAGAAAUUGAUAUUCAGCAGGCAGAAUUUGAGCUUUGAAAAAUACGAAAAUUGGACAGAAAAUUA---AAUACUGGCCACUUGGCCAACACAUUUACUUUCGAG
...(((((....))))).(((((..(((.........)))))))).....((((((((........)))).---.....(((((....)))))...........)))).. ( -19.00)
>DroYak_CAF1 48800 107 - 1
UCAAUCAAGAAAUUUAUAUUCAGCAGGCAGAAUUUGGGCUUUGAAAAACAUGUGUUUUGGCCAGGAGACGA---AACACUGGCCUCUUGGCUAACACAUUUACUCUUGAG
....((((((........(((((.((.(........).)))))))....((((((..((((((((((.((.---.....))..))))))))))))))))....)))))). ( -31.20)
>consensus
UCAAUCAAGAAAUUGAUAUUCAGCAGGCCGAAUUUGAGCUCUGAAAAAUGUGGGUUUUGGCCAGGAGGUGA___AGCACUGGCCACUUGGCCAACAGAUUUACUCUUGAG
....((((((((((.(((((...((((.(........).))))...))))).))))(((((((((.(((.(........).))).))))))))).........)))))). (-17.84 = -19.44 +   1.60)

alignment

secondary structure

dotplot

Window 7

Location	1,996,863 – 1,996,973
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	85.39
Mean single sequence MFE	-26.68
Consensus MFE	-19.29
Energy contribution	-20.57
Covariance contribution	1.28
Combinations/Pair	1.14
Mean z-score	-1.91
Structure conservation index	0.72
SVM decision value	0.46
SVM RNA-class probability	0.745335
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1996863 110 + 23771897
CUUCACCUCCUGGCCAAAAUCCACAUUUUUCAGAGCUCGAAUUCGGUCUGGUGAAUGUCAAUUUCAUGAUUGAAUGUGACACAUUCUUUAUGGGCCGGGAAUAUUAUAGA
.......((((((((.((((..((((((.(((((.(.((....)))))))).))))))..))))(((((..(((((.....))))).))))))))))))).......... ( -35.70)
>DroSec_CAF1 47725 108 + 1
--UCACCUCCUGGCCAAAACCGACAUUUUUCAGAGCUCAAAUUCGGCCUGCUGAAUAUCAAUAUCUUGAUUGAAUGUGGCACAUUCUUUAUGGGCCGGGACUAUUAUAGA
--.....((((((((....((.((((((.(((((......((((((....)))))).......)).)))..))))))))..(((.....))))))))))).......... ( -30.32)
>DroSim_CAF1 62556 108 + 1
--UCACCUCCUGGCCAAAACCCACAUUUUUCAGACCUCGAAUUAGGCCUGCUGAAUAUCAAUUUCUUGAUUGAAUGUGGCACAUUCUUUAUGGGCCGGGAAUAUUAUAGA
--.....((((((((.....((((((..(((((.(((......)))....)))))..((((((....))))))))))))..(((.....))))))))))).......... ( -32.90)
>DroEre_CAF1 53714 108 + 1
--UAAUUUUCUGUCCAAUUUUCGUAUUUUUCAAAGCUCAAAUUCUGCCUGCUGAAUAUCAAUUUCUUGAUUGAAUGUGGUACAUUCUUUAUGGGCCUGUAAUAUUGUAGA
--.........(((((......((((((..((..((.........)).))..)))))).............(((((.....)))))....)))))............... ( -13.00)
>DroYak_CAF1 48836 108 + 1
--UCGUCUCCUGGCCAAAACACAUGUUUUUCAAAGCCCAAAUUCUGCCUGCUGAAUAUAAAUUUCUUGAUUGAAUGUGGCACAUUCUUUAUGGGCCUGGAAUAUUGUAAA
--.....(((.(((((((((....))))).....(((((.((((........))))......(((......))))).)))............)))).))).......... ( -21.50)
>consensus
__UCACCUCCUGGCCAAAACCCACAUUUUUCAGAGCUCAAAUUCGGCCUGCUGAAUAUCAAUUUCUUGAUUGAAUGUGGCACAUUCUUUAUGGGCCGGGAAUAUUAUAGA
.......((((((((......(((((((.((((.......((((((....)))))).........))))..)))))))...(((.....))))))))))).......... (-19.29 = -20.57 +   1.28)

alignment

secondary structure

dotplot

Window 8

Location	1,996,863 – 1,996,973
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	85.39
Mean single sequence MFE	-26.54
Consensus MFE	-18.56
Energy contribution	-19.48
Covariance contribution	0.92
Combinations/Pair	1.24
Mean z-score	-1.73
Structure conservation index	0.70
SVM decision value	0.11
SVM RNA-class probability	0.589017
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1996863 110 - 23771897
UCUAUAAUAUUCCCGGCCCAUAAAGAAUGUGUCACAUUCAAUCAUGAAAUUGACAUUCACCAGACCGAAUUCGAGCUCUGAAAAAUGUGGAUUUUGGCCAGGAGGUGAAG
.........((((.((((......(((((.....)))))......((((((.(((((...(((((((....)).).))))...))))).)))))))))).))))...... ( -30.70)
>DroSec_CAF1 47725 108 - 1
UCUAUAAUAGUCCCGGCCCAUAAAGAAUGUGCCACAUUCAAUCAAGAUAUUGAUAUUCAGCAGGCCGAAUUUGAGCUCUGAAAAAUGUCGGUUUUGGCCAGGAGGUGA--
..........(((.((((......(((((.....)))))......((.(((((((((...(((((((....)).)).)))...))))))))).)))))).))).....-- ( -28.20)
>DroSim_CAF1 62556 108 - 1
UCUAUAAUAUUCCCGGCCCAUAAAGAAUGUGCCACAUUCAAUCAAGAAAUUGAUAUUCAGCAGGCCUAAUUCGAGGUCUGAAAAAUGUGGGUUUUGGCCAGGAGGUGA--
.........((((.((((((((.....))))(((((((..(((((....)))))......(((((((......)))))))...))))))).....)))).))))....-- ( -35.70)
>DroEre_CAF1 53714 108 - 1
UCUACAAUAUUACAGGCCCAUAAAGAAUGUACCACAUUCAAUCAAGAAAUUGAUAUUCAGCAGGCAGAAUUUGAGCUUUGAAAAAUACGAAAAUUGGACAGAAAAUUA--
(((............(((......(((((.....))))).(((((....)))))........)))....((..(..((((.......))))..)..)).)))......-- ( -16.60)
>DroYak_CAF1 48836 108 - 1
UUUACAAUAUUCCAGGCCCAUAAAGAAUGUGCCACAUUCAAUCAAGAAAUUUAUAUUCAGCAGGCAGAAUUUGGGCUUUGAAAAACAUGUGUUUUGGCCAGGAGACGA--
.........((((.((((((((..(((((.....)))))................(((((.((.(........).))))))).....))))....)))).))))....-- ( -21.50)
>consensus
UCUAUAAUAUUCCCGGCCCAUAAAGAAUGUGCCACAUUCAAUCAAGAAAUUGAUAUUCAGCAGGCCGAAUUUGAGCUCUGAAAAAUGUGGGUUUUGGCCAGGAGGUGA__
.........((((.((((......(((((.....)))))......((((((.(((((...((((.(........).))))...))))).)))))))))).))))...... (-18.56 = -19.48 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:11 2006