Locus 5980

Sequence ID	2L_DroMel_CAF1
Location	16,865,409 – 16,865,637
Length	228
Max. P	0.998995

overview

Window 8

Location	16,865,409 – 16,865,510
Length	101
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	84.98
Mean single sequence MFE	-52.05
Consensus MFE	-34.09
Energy contribution	-34.12
Covariance contribution	0.03
Combinations/Pair	1.14
Mean z-score	-3.72
Structure conservation index	0.65
SVM decision value	0.62
SVM RNA-class probability	0.801950
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16865409 101 + 22407834
GGCCAACAAACUGGUAGCGUCUGGUGUGGCGAGCCAACAAAAGGCUGGCAGAGCGGCCAACACCGGACCCGGCCCGAAACUGAAUCCGGGUC------CGGGUCUGG
((((..((.((..(......)..)).))((.((((.......)))).)).....))))....((((((((((((((..........)))).)------))))))))) ( -52.10)
>DroPse_CAF1 27359 98 + 1
GGCCAAGAAACUGGUAGCGUCUGGUGUUGCGAGCCAACAAAAGGCUGGCA-----GCCAACACCGGACCGGACC-GGGGCUACA--CGGCCCCGGGACCGGGAC-GG
.((((......))))...((.((((..(((.((((.......)))).)))-----)))))).(((..((((.((-((((((...--.))))))))..))))..)-)) ( -52.50)
>DroSim_CAF1 7394 101 + 1
GGCCAACAAACUGGUAGCGUCUGGUGUGGCGAGCCAACAAAAGGCUGGCAGGGCGGCCAACACCGGACCCGGCCAGAAACUGAAUCCGGGUC------CGGGUCUGG
((((..((.((..(......)..)).))((.((((.......)))).)).....))))....((((((((((.(((...)))...)))))))------)))...... ( -47.80)
>DroEre_CAF1 37224 107 + 1
GGCCAACAAACUGGUAGCGUCUGGUGUGGCGAGCCAACAAAAGGCUGGCAGGGCGGCCAACACCGGACCCGGCCCGAAUCUGAAUCCGGGUCCGGGUCCGGGUCUGG
((((..((.((..(......)..)).))((.((((.......)))).)).....))))....((((((((((((((.(((((....))))).)))).)))))))))) ( -58.30)
>DroYak_CAF1 141 101 + 1
GGCCAACAAACUGGUAGCGUCUGGUGUGGCGAGCCAACAAAAGGCUGGCAGGGCGGCCAACACCGGACCCGGCCCGAAUCUGAAUCCGGGUC------CGGGCCUGG
.((((......))))...(((((((((.((.((((.......)))).)).((....)).)))))))))((((((((.(((((....))))).------)))))).)) ( -49.10)
>DroPer_CAF1 29542 98 + 1
GGCCAAGAAACUGGUAGCGUCUGGUGUUGCGAGCCAACAAAAGGCUGGCA-----GCCAACACCGGACCGGACC-GGGGCUACA--CGGCCCCGGGACCGGGAC-GG
.((((......))))...((.((((..(((.((((.......)))).)))-----)))))).(((..((((.((-((((((...--.))))))))..))))..)-)) ( -52.50)
>consensus
GGCCAACAAACUGGUAGCGUCUGGUGUGGCGAGCCAACAAAAGGCUGGCAGGGCGGCCAACACCGGACCCGGCCCGAAACUGAAUCCGGGUC______CGGGUCUGG
((((......(.(((...(((((((((....((((.......))))(((......))).)))))))))...))).).(((((....))))).........))))... (-34.09 = -34.12 +   0.03)

alignment

secondary structure

dotplot

Window 9

Location	16,865,449 – 16,865,547
Length	98
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	93.43
Mean single sequence MFE	-48.74
Consensus MFE	-36.02
Energy contribution	-36.50
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-2.15
Structure conservation index	0.74
SVM decision value	0.27
SVM RNA-class probability	0.663822
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16865449 98 + 22407834
AAGGCUGGCAGAGCGGCCAACACCGGACCCGGCCCGAAACUGAAUCCGGGUC------CGGGUCUGGGUCCGUGUCCGUGUCCGGGUUGGUUUCGCAGCAUCUA
...((((...(((..((((((.((((((((((((((..........)))).)------)))))))))........(((....)))))))))))).))))..... ( -46.60)
>DroSec_CAF1 4985 98 + 1
AAGGCUGGCAGGGCGGCCAACACCGGACCCGGCCAGAAACUGAAUCCGGGUC------CGGGUCUGGGUCCGUGUCCGUGUCCGGGUUGGAUCCGCAGCAUCUA
...((((...(((...(((((.((((((((((.(((...)))...)))))))------)))..(((((..((....))..)))))))))).))).))))..... ( -47.30)
>DroSim_CAF1 7434 98 + 1
AAGGCUGGCAGGGCGGCCAACACCGGACCCGGCCAGAAACUGAAUCCGGGUC------CGGGUCUGGGUCCGUGUCCGUGUCCGGGUUGGAUCCGCAGCAUCUA
...((((...(((...(((((.((((((((((.(((...)))...)))))))------)))..(((((..((....))..)))))))))).))).))))..... ( -47.30)
>DroEre_CAF1 37264 104 + 1
AAGGCUGGCAGGGCGGCCAACACCGGACCCGGCCCGAAUCUGAAUCCGGGUCCGGGUCCGGGUCUGGGUCCGUGUCCGUGUCCGCGUUGGAUCCGCAACAUCUA
...((.(((((((((.(..((.((((((((((((((.(((((....))))).)))).))))))))))))..)))))).)))).))((((......))))..... ( -53.10)
>DroYak_CAF1 181 98 + 1
AAGGCUGGCAGGGCGGCCAACACCGGACCCGGCCCGAAUCUGAAUCCGGGUC------CGGGCCUGGGACCGUGUCCGUGUCCGGGUUGGAUCCGCAACAUCUA
.(((.((.....(((((((((.((((((.(((((((.(((((....))))).------))))))..((((...))))).)))))))))))..))))..))))). ( -49.40)
>consensus
AAGGCUGGCAGGGCGGCCAACACCGGACCCGGCCCGAAACUGAAUCCGGGUC______CGGGUCUGGGUCCGUGUCCGUGUCCGGGUUGGAUCCGCAGCAUCUA
............((((((((((((((((((((((((...(((....))).........)))))).))))))).))(((....))))))))..))))........ (-36.02 = -36.50 +   0.48)

alignment

secondary structure

dotplot

Window 0

Location	16,865,449 – 16,865,547
Length	98
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	93.43
Mean single sequence MFE	-46.52
Consensus MFE	-37.02
Energy contribution	-37.58
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.17
Structure conservation index	0.80
SVM decision value	1.35
SVM RNA-class probability	0.944980
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16865449 98 - 22407834
UAGAUGCUGCGAAACCAACCCGGACACGGACACGGACCCAGACCCG------GACCCGGAUUCAGUUUCGGGCCGGGUCCGGUGUUGGCCGCUCUGCCAGCCUU
.....((.(((...(((((((((((..((........))....(((------(.((((((......)))))))))))))))).))))).)))...))....... ( -43.60)
>DroSec_CAF1 4985 98 - 1
UAGAUGCUGCGGAUCCAACCCGGACACGGACACGGACCCAGACCCG------GACCCGGAUUCAGUUUCUGGCCGGGUCCGGUGUUGGCCGCCCUGCCAGCCUU
.....(((((((.......(((....)))...(((.((..((((((------(((((((...(((...))).)))))))))).))))))))..))).))))... ( -44.20)
>DroSim_CAF1 7434 98 - 1
UAGAUGCUGCGGAUCCAACCCGGACACGGACACGGACCCAGACCCG------GACCCGGAUUCAGUUUCUGGCCGGGUCCGGUGUUGGCCGCCCUGCCAGCCUU
.....(((((((.......(((....)))...(((.((..((((((------(((((((...(((...))).)))))))))).))))))))..))).))))... ( -44.20)
>DroEre_CAF1 37264 104 - 1
UAGAUGUUGCGGAUCCAACGCGGACACGGACACGGACCCAGACCCGGACCCGGACCCGGAUUCAGAUUCGGGCCGGGUCCGGUGUUGGCCGCCCUGCCAGCCUU
....(((((((.......))).)))).((.((.((..((((..((((((((((.(((((((....)))))))))))))))))..))))...)).))))...... ( -52.40)
>DroYak_CAF1 181 98 - 1
UAGAUGUUGCGGAUCCAACCCGGACACGGACACGGUCCCAGGCCCG------GACCCGGAUUCAGAUUCGGGCCGGGUCCGGUGUUGGCCGCCCUGCCAGCCUU
........((((..(((((((((((.((....))))))..((((((------(.(((((((....)))))))))))))).)).)))))))))............ ( -48.20)
>consensus
UAGAUGCUGCGGAUCCAACCCGGACACGGACACGGACCCAGACCCG______GACCCGGAUUCAGUUUCGGGCCGGGUCCGGUGUUGGCCGCCCUGCCAGCCUU
.....((.((((..(((((((((((.(((...(((........)))........((((((......))))))))).)))))).)))))))))...))....... (-37.02 = -37.58 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	16,865,547 – 16,865,637
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	99.11
Mean single sequence MFE	-32.84
Consensus MFE	-32.22
Energy contribution	-32.42
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.37
Structure conservation index	0.98
SVM decision value	3.32
SVM RNA-class probability	0.998995
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16865547 90 - 22407834
CCUGUUUUUGUUGUUGGCCGGCCACUCUUCUUGGCUGGCUACGCGUCAAAUUGAGACCCAAACUCCGCUCAAUUGGCAGCCGUGAUGCCG
........((.(((((((((((((.......)))))))))).))).))(((((((............)))))))((((.......)))). ( -28.90)
>DroSec_CAF1 5083 90 - 1
CCUGUUUUUGUUGUUGGCCGGCCACUCUUCUUGGCUGGCUACGCGUCAAAUUGAGACCCAAACUCCGCUCAAUUGGCAGCCGUGCUGCCG
........((.(((((((((((((.......)))))))))).))).))(((((((............)))))))((((((...)))))). ( -33.50)
>DroSim_CAF1 7532 90 - 1
CCUGUUUUUGUUGUUGGCCGGCCAAUCUUCUUGGCUGGCUACGCGUCAAAUUGAGACCCAAACUCCGCUCAAUUGGCAGCCGUGCUGCCG
........((.((((((((((((((.....))))))))))).))).))(((((((............)))))))((((((...)))))). ( -34.80)
>DroEre_CAF1 37368 90 - 1
CCUGUUUUUGUUGUUGGCCGGCCACUCUUCUUGGCUGGCUACGCGUCAAAUUGAGACCCAAACUCCGCUCAAUUGGCAGCCGUGCUGCCG
........((.(((((((((((((.......)))))))))).))).))(((((((............)))))))((((((...)))))). ( -33.50)
>DroYak_CAF1 279 90 - 1
CCUGUUUUUGUUGUUGGCCGGCCACUCUUCUUGGCUGGCUACGCGUCAAAUUGAGACCCAAACUCCGCUCAAUUGGCAGCCGUGCUGCCG
........((.(((((((((((((.......)))))))))).))).))(((((((............)))))))((((((...)))))). ( -33.50)
>consensus
CCUGUUUUUGUUGUUGGCCGGCCACUCUUCUUGGCUGGCUACGCGUCAAAUUGAGACCCAAACUCCGCUCAAUUGGCAGCCGUGCUGCCG
........((.(((((((((((((.......)))))))))).))).))(((((((............)))))))((((((...)))))). (-32.22 = -32.42 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:04 2006