Locus 4085

Sequence ID	2L_DroMel_CAF1
Location	11,774,839 – 11,774,986
Length	147
Max. P	0.991675

overview

Window 6

Location	11,774,839 – 11,774,957
Length	118
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.75
Mean single sequence MFE	-32.44
Consensus MFE	-22.26
Energy contribution	-22.85
Covariance contribution	0.59
Combinations/Pair	1.11
Mean z-score	-1.22
Structure conservation index	0.69
SVM decision value	-0.05
SVM RNA-class probability	0.508316
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11774839 118 + 22407834
UGUUGUCCAAUUCAGUAAUCCAAGGCAUCAGGAACAGCCGACCAUUCCUCCAGAGGGCCCUUGGAUGUAACAGCCCUCCUGGAGGAUUCU--CUUUCGUGCGCCCGAUUCAGUUUUCUGU
............(((.((..(...(.(((.((....(((((....(((((((((((((..(((....)))..))))).))))))))....--...))).)).)).))).).)..))))). ( -33.50)
>DroSec_CAF1 32865 118 + 1
UGUUGUCCAAUUCAGUAAUCCAAGGCAUCAGGAACAGCCGACCAUUCCUCCAGUGGGCCCUUGGAUGUAACAGCCCUCCUGGAGGAUUCC--CUUUCGUGCGCCCGAUUCCGUUUUCUGU
............(((........((.(((.((....(((((....((((((((.((((..(((....)))..))))..))))))))....--...))).)).)).))).)).....))). ( -33.82)
>DroSim_CAF1 31966 118 + 1
UGUUGUCCAAUUCAGUAAUCCAAGGCAUCAGGAACAGCCGACCAUUCCUCCAGAGGGCCCUUGGAUGUAACAGCCCUCCUGGAGGAUUCC--CUUUCGUGCGCCCGAUUCCGUUUUCUGU
............(((........((.(((.((....(((((....(((((((((((((..(((....)))..))))).))))))))....--...))).)).)).))).)).....))). ( -36.22)
>DroEre_CAF1 43219 113 + 1
UGUUGUCCAAUUCAGUAAUCCAAGGCAUCAGGAACAGCCGACGAUUCCUCCAGAGGGCCCUUGGAAGUAACAGCCCUCCUGGAGGAUUCC--CUC-----CUCCCGAUUCCGCUUUCUGU
............(((........((.(((.(((..((.....((.(((((((((((((..(((....)))..))))).)))))))).)).--)).-----.))).))).)).....))). ( -33.52)
>DroYak_CAF1 34332 99 + 1
UGUUGUCCAAUUCAGUAAUCCAAGGCAUCAGGAACAGCCGACAAUUCCUCCAGAGGGCCCUUGGAUGUAACAGCCCUCCUGGAGGAU---------------------UCCGUUUUCUGU
((.((((................)))).))...((((..(((...(((((((((((((..(((....)))..))))).)))))))).---------------------...)))..)))) ( -29.99)
>DroAna_CAF1 35147 116 + 1
GGUUGUCCAAUUCACUAAACCAAGGCAUCAAAAUUAGCCUUGAGAACCUCUAGAGUGCCAUCGACCAUAACCAAGCUCCUGCAGGACUCGAGCUUUUGU---UUUGUUUCAGCUUU-UAU
(((((....((((.......((((((..........))))))((.....)).)))).....)))))......(((((...(((((((..........))---)))))...))))).-... ( -27.60)
>consensus
UGUUGUCCAAUUCAGUAAUCCAAGGCAUCAGGAACAGCCGACCAUUCCUCCAGAGGGCCCUUGGAUGUAACAGCCCUCCUGGAGGAUUCC__CUUUCGU_CGCCCGAUUCCGUUUUCUGU
.......................(((..........)))......(((((((((((((..(((....)))..))))).)))))))).................................. (-22.26 = -22.85 +   0.59)

alignment

secondary structure

dotplot

Window 7

Location	11,774,839 – 11,774,957
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.75
Mean single sequence MFE	-38.33
Consensus MFE	-26.88
Energy contribution	-27.80
Covariance contribution	0.92
Combinations/Pair	1.14
Mean z-score	-1.77
Structure conservation index	0.70
SVM decision value	0.60
SVM RNA-class probability	0.794499
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11774839 118 - 22407834
ACAGAAAACUGAAUCGGGCGCACGAAAG--AGAAUCCUCCAGGAGGGCUGUUACAUCCAAGGGCCCUCUGGAGGAAUGGUCGGCUGUUCCUGAUGCCUUGGAUUACUGAAUUGGACAACA
.(((.((.(..(((((((.((((....)--.((.((((((((.((((((.((......)).))))))))))))))....))...))).))))))...)..).)).)))............ ( -41.70)
>DroSec_CAF1 32865 118 - 1
ACAGAAAACGGAAUCGGGCGCACGAAAG--GGAAUCCUCCAGGAGGGCUGUUACAUCCAAGGGCCCACUGGAGGAAUGGUCGGCUGUUCCUGAUGCCUUGGAUUACUGAAUUGGACAACA
........(((((((((((((((....)--((((((((((((..(((((.((......)).))))).))))))))..((....)).)))))).)))))..)))).)))............ ( -41.10)
>DroSim_CAF1 31966 118 - 1
ACAGAAAACGGAAUCGGGCGCACGAAAG--GGAAUCCUCCAGGAGGGCUGUUACAUCCAAGGGCCCUCUGGAGGAAUGGUCGGCUGUUCCUGAUGCCUUGGAUUACUGAAUUGGACAACA
........(((((((((((((((....)--((((((((((((.((((((.((......)).))))))))))))))..((....)).)))))).)))))..)))).)))............ ( -42.60)
>DroEre_CAF1 43219 113 - 1
ACAGAAAGCGGAAUCGGGAG-----GAG--GGAAUCCUCCAGGAGGGCUGUUACUUCCAAGGGCCCUCUGGAGGAAUCGUCGGCUGUUCCUGAUGCCUUGGAUUACUGAAUUGGACAACA
.(((.((..((.((((((((-----.((--.((.((((((((.((((((.((......)).)))))))))))))).)).....)).)))))))).)).....)).)))............ ( -43.70)
>DroYak_CAF1 34332 99 - 1
ACAGAAAACGGA---------------------AUCCUCCAGGAGGGCUGUUACAUCCAAGGGCCCUCUGGAGGAAUUGUCGGCUGUUCCUGAUGCCUUGGAUUACUGAAUUGGACAACA
............---------------------.((((((((.((((((.((......)).)))))))))))))).((((((((..........)))(..(....)..)....))))).. ( -35.40)
>DroAna_CAF1 35147 116 - 1
AUA-AAAGCUGAAACAAA---ACAAAAGCUCGAGUCCUGCAGGAGCUUGGUUAUGGUCGAUGGCACUCUAGAGGUUCUCAAGGCUAAUUUUGAUGCCUUGGUUUAGUGAAUUGGACAACC
...-..........((.(---((..((((((..(.....)..)))))).))).))(((.(...((((...(((((..((((((....)))))).))))).....))))...).))).... ( -25.50)
>consensus
ACAGAAAACGGAAUCGGGCG_ACGAAAG__GGAAUCCUCCAGGAGGGCUGUUACAUCCAAGGGCCCUCUGGAGGAAUGGUCGGCUGUUCCUGAUGCCUUGGAUUACUGAAUUGGACAACA
.(((..............................((((((((.((((((.((......)).))))))))))))))......(((..........)))........)))............ (-26.88 = -27.80 +   0.92)

alignment

secondary structure

dotplot

Window 8

Location	11,774,879 – 11,774,986
Length	107
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	73.54
Mean single sequence MFE	-30.48
Consensus MFE	-18.94
Energy contribution	-19.30
Covariance contribution	0.36
Combinations/Pair	1.24
Mean z-score	-1.49
Structure conservation index	0.62
SVM decision value	0.20
SVM RNA-class probability	0.629049
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11774879 107 + 22407834
ACCAUUCCUCCAGAGGGCCCUUGGAUGUAACAGCCCUCCUGGAGGAUUCU--CUUUCGUGCGCCCGAUUCAGUUUUCUGUCUGCCAGGGGCGAGA-UCCCAUUCCUUUCU
.....(((((((((((((..(((....)))..))))).))))))))....--...((...(((((....(((........)))....))))).))-.............. ( -36.10)
>DroSec_CAF1 32905 107 + 1
ACCAUUCCUCCAGUGGGCCCUUGGAUGUAACAGCCCUCCUGGAGGAUUCC--CUUUCGUGCGCCCGAUUCCGUUUUCUGUCUGCCAGUGGCGAGA-UCCCAUUCCUUUCU
.....((((((((.((((..(((....)))..))))..))))))))....--.............(((..((((..(((.....))).))))..)-))............ ( -29.90)
>DroSim_CAF1 32006 107 + 1
ACCAUUCCUCCAGAGGGCCCUUGGAUGUAACAGCCCUCCUGGAGGAUUCC--CUUUCGUGCGCCCGAUUCCGUUUUCUGUCUGCCAGUGGCGAGU-UCCCAUUCCUUUCU
.....(((((((((((((..(((....)))..))))).))))))))....--........((((((....))....(((.....))).))))...-.............. ( -29.80)
>DroEre_CAF1 43259 101 + 1
ACGAUUCCUCCAGAGGGCCCUUGGAAGUAACAGCCCUCCUGGAGGAUUCC--CUC-----CUCCCGAUUCCGCUUUCUGUCUGCCAG-GACGAGGUU-CCCAUUCCUGCU
..((.(((((((((((((..(((....)))..))))).)))))))).))(--(((-----.(((.......((.....))......)-)).))))..-............ ( -33.92)
>DroAna_CAF1 35187 98 + 1
UGAGAACCUCUAGAGUGCCAUCGACCAUAACCAAGCUCCUGCAGGACUCGAGCUUUUGU---UUUGUUUCAGCUUU-UAUCCUCCAGCCGGAGGA-UACCCCU-------
(((((.......((((.((...(........)..((....)).))))))((((....))---))..))))).....-((((((((....))))))-)).....------- ( -22.70)
>consensus
ACCAUUCCUCCAGAGGGCCCUUGGAUGUAACAGCCCUCCUGGAGGAUUCC__CUUUCGUGCGCCCGAUUCCGUUUUCUGUCUGCCAGUGGCGAGA_UCCCAUUCCUUUCU
.....(((((((((((((..(((....)))..))))).)))))))).................................(((((.....)).)))............... (-18.94 = -19.30 +   0.36)

alignment

secondary structure

dotplot

Window 9

Location	11,774,879 – 11,774,986
Length	107
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	73.54
Mean single sequence MFE	-37.26
Consensus MFE	-21.46
Energy contribution	-22.26
Covariance contribution	0.80
Combinations/Pair	1.20
Mean z-score	-2.30
Structure conservation index	0.58
SVM decision value	2.28
SVM RNA-class probability	0.991675
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11774879 107 - 22407834
AGAAAGGAAUGGGA-UCUCGCCCCUGGCAGACAGAAAACUGAAUCGGGCGCACGAAAG--AGAAUCCUCCAGGAGGGCUGUUACAUCCAAGGGCCCUCUGGAGGAAUGGU
..............-((((((((....(((........)))....)))))..(....)--))).((((((((.((((((.((......)).))))))))))))))..... ( -40.40)
>DroSec_CAF1 32905 107 - 1
AGAAAGGAAUGGGA-UCUCGCCACUGGCAGACAGAAAACGGAAUCGGGCGCACGAAAG--GGAAUCCUCCAGGAGGGCUGUUACAUCCAAGGGCCCACUGGAGGAAUGGU
..............-(((((((.(((.....)))....((....))))))..(....)--))).((((((((..(((((.((......)).))))).))))))))..... ( -36.80)
>DroSim_CAF1 32006 107 - 1
AGAAAGGAAUGGGA-ACUCGCCACUGGCAGACAGAAAACGGAAUCGGGCGCACGAAAG--GGAAUCCUCCAGGAGGGCUGUUACAUCCAAGGGCCCUCUGGAGGAAUGGU
..............-...((((.(((.....)))....((....))))))..(....)--....((((((((.((((((.((......)).))))))))))))))..... ( -37.80)
>DroEre_CAF1 43259 101 - 1
AGCAGGAAUGGG-AACCUCGUC-CUGGCAGACAGAAAGCGGAAUCGGGAG-----GAG--GGAAUCCUCCAGGAGGGCUGUUACUUCCAAGGGCCCUCUGGAGGAAUCGU
............-..((((.((-((((....(.......)...)))))).-----)))--)((.((((((((.((((((.((......)).)))))))))))))).)).. ( -43.70)
>DroAna_CAF1 35187 98 - 1
-------AGGGGUA-UCCUCCGGCUGGAGGAUA-AAAGCUGAAACAAA---ACAAAAGCUCGAGUCCUGCAGGAGCUUGGUUAUGGUCGAUGGCACUCUAGAGGUUCUCA
-------.((((..-.((((...(((.(((((.-..((((........---.....))))...))))).)))(((....(((((.....))))).)))..)))).)))). ( -27.62)
>consensus
AGAAAGGAAUGGGA_UCUCGCCACUGGCAGACAGAAAACGGAAUCGGGCGCACGAAAG__GGAAUCCUCCAGGAGGGCUGUUACAUCCAAGGGCCCUCUGGAGGAAUGGU
................((.((.....))))..................................((((((((.((((((.((......)).))))))))))))))..... (-21.46 = -22.26 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:59 2006