Locus 2021

Sequence ID	3R_DroMel_CAF1
Location	5,736,082 – 5,736,215
Length	133
Max. P	0.990386

overview

Window 3

Location	5,736,082 – 5,736,176
Length	94
Sequences	3
Columns	94
Reading direction	forward
Mean pairwise identity	95.04
Mean single sequence MFE	-35.43
Consensus MFE	-34.76
Energy contribution	-34.10
Covariance contribution	-0.66
Combinations/Pair	1.10
Mean z-score	-2.85
Structure conservation index	0.98
SVM decision value	2.21
SVM RNA-class probability	0.990386
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5736082 94 + 27905053
UGGCUGGCUCAUUGGCUUCAGUAUUGGGCCAAUGAUUGGCUAACCGAGCCCUGCAUGUCACUUGAUCGAUGGUUACAAAGCCAUAAGCCAUCAU
((((((((((((((((((.......))))))))))..((((.....))))......))).........((((((....)))))).))))).... ( -31.10)
>DroSec_CAF1 27653 94 + 1
UGGCUGGCUCAUUGGCUCCAUUAUUGGGCCAAUGAUUGGCUAACCGAGCCCUGCAUGGCACUUGAUCGAUGGCUGCACGGCCAUAAGCCAUCAU
((((..(.((((((((.(((....))))))))))))..)))).....(((......)))........(((((((...........))))))).. ( -38.80)
>DroSim_CAF1 28289 94 + 1
UGGCUGGCUCAUUGGCUCCAUUAUUGGGCCAAUGAUUGGCUAACCGAGCCCUGCAUGGCACUUGAUCGAUGGUUGCACGGCCAUAAGCCAUCAU
((((..(.((((((((.(((....))))))))))))..)))).....(((......)))........(((((((...........))))))).. ( -36.40)
>consensus
UGGCUGGCUCAUUGGCUCCAUUAUUGGGCCAAUGAUUGGCUAACCGAGCCCUGCAUGGCACUUGAUCGAUGGUUGCACGGCCAUAAGCCAUCAU
((((((((((((((((.(((....)))))))))))((((....)))))))..................((((((....)))))).))))).... (-34.76 = -34.10 +  -0.66)

alignment

secondary structure

dotplot

Window 4

Location	5,736,082 – 5,736,176
Length	94
Sequences	3
Columns	94
Reading direction	reverse
Mean pairwise identity	95.04
Mean single sequence MFE	-34.90
Consensus MFE	-32.47
Energy contribution	-32.37
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-2.87
Structure conservation index	0.93
SVM decision value	1.72
SVM RNA-class probability	0.973807
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5736082 94 - 27905053
AUGAUGGCUUAUGGCUUUGUAACCAUCGAUCAAGUGACAUGCAGGGCUCGGUUAGCCAAUCAUUGGCCCAAUACUGAAGCCAAUGAGCCAGCCA
....(((((((((((((((((............((.....)).(((((.((((....))))...)))))..))).)))))).)))))))).... ( -29.90)
>DroSec_CAF1 27653 94 - 1
AUGAUGGCUUAUGGCCGUGCAGCCAUCGAUCAAGUGCCAUGCAGGGCUCGGUUAGCCAAUCAUUGGCCCAAUAAUGGAGCCAAUGAGCCAGCCA
.(((((((((((....))).)))))))).....(.(((......))).)((((.((...(((((((((((....))).)))))))))).)))). ( -38.70)
>DroSim_CAF1 28289 94 - 1
AUGAUGGCUUAUGGCCGUGCAACCAUCGAUCAAGUGCCAUGCAGGGCUCGGUUAGCCAAUCAUUGGCCCAAUAAUGGAGCCAAUGAGCCAGCCA
....(((((..(((((.((((..(((.......)))...)))).))).))...))))).(((((((((((....))).))))))))........ ( -36.10)
>consensus
AUGAUGGCUUAUGGCCGUGCAACCAUCGAUCAAGUGCCAUGCAGGGCUCGGUUAGCCAAUCAUUGGCCCAAUAAUGGAGCCAAUGAGCCAGCCA
....(((((..(((((.((((..(((.......)))...)))).))).))...))))).(((((((((((....))).))))))))........ (-32.47 = -32.37 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	5,736,098 – 5,736,215
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.78
Mean single sequence MFE	-33.08
Consensus MFE	-19.67
Energy contribution	-21.12
Covariance contribution	1.45
Combinations/Pair	1.15
Mean z-score	-2.09
Structure conservation index	0.59
SVM decision value	0.92
SVM RNA-class probability	0.882112
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5736098 117 + 27905053
UUCAGUAUUGGGCCAAUGAUUGGCUAACCGAGCCC--UGCAUGUCACUUGAUCGAUGGUUACAAAGCCAUAAGCCAUCAUUAGCCAUGUGGCAAUUUAU-AUGCUGGCUUCACUUCGAUC
......(((((((((.....)))))....(((((.--.((((((....((((.(((((((...........)))))))))))(((....))).....))-)))).))))).....)))). ( -32.40)
>DroSec_CAF1 27669 117 + 1
UCCAUUAUUGGGCCAAUGAUUGGCUAACCGAGCCC--UGCAUGGCACUUGAUCGAUGGCUGCACGGCCAUAAGCCAUCAUUAGCCAUGUGGCAAUUUAU-AUGCUGGCUUCACUUCGAUC
.(((....)))((((.((...((((.....)))).--..))))))....(((((((((((....))))).((((((.(((..(((....))).......-))).))))))....)))))) ( -40.10)
>DroSim_CAF1 28305 117 + 1
UCCAUUAUUGGGCCAAUGAUUGGCUAACCGAGCCC--UGCAUGGCACUUGAUCGAUGGUUGCACGGCCAUAAGCCAUCAUUAGCCAUGUGGCAAUUUAU-AUGCUGGCUUCACUUCGAUC
.(((....)))((((.((...((((.....)))).--..))))))....(((((((((((....))))).((((((.(((..(((....))).......-))).))))))....)))))) ( -37.60)
>DroEre_CAF1 23357 109 + 1
UUCAUUAUUGG-CCAA-------ACAACCGAGCCC--UGCAUGGCACUUGAUCGAUGGUUCCACAGCCAUAAGCCAUCAUUAGCCAUGUGGCAAUUUAU-AUGCUGGCUUUACUCCGAUC
.((......((-....-------....))(((((.--.(((((((...((((..(((((......))))).....))))...)))))))((((......-.)))))))))......)).. ( -27.90)
>DroYak_CAF1 11118 109 + 1
UUCAGUAUUGG-CCAA-------CCAACCGAGCCC--UGCAUGGCACUUGAUCGAUGGCUCCAAAGCCAUAAGCCAUCAUUAGCCAUGUGGCAAUUUAU-AUGCUGGCUUUACUUCGAUC
.((((((((((-....-------))))....(((.--.(((((((...((((..((((((....)))))).....))))...)))))))))).......-.))))))............. ( -33.30)
>DroPer_CAF1 33328 101 + 1
-UCAUUAGCAGG-----------------AGGCCCUGUGCAU-ACAUUUGAUAGAUGGAUGCCGAGCACUAAGUCAUCAUUAGCUCGAUACCCAUUUAUCAUGAUCAACGGACUCUGAUU
-......(((((-----------------....)))))....-.....((((((((((.((.(((((...............))))).)).)))))))))).(((((........))))) ( -27.16)
>consensus
UUCAUUAUUGGGCCAA_______CUAACCGAGCCC__UGCAUGGCACUUGAUCGAUGGUUGCACAGCCAUAAGCCAUCAUUAGCCAUGUGGCAAUUUAU_AUGCUGGCUUCACUUCGAUC
.............................(((((....(((((((...((((.(((((((...........))))))))))))))))))((((........))))))))).......... (-19.67 = -21.12 +   1.45)

alignment

secondary structure

dotplot

Window 6

Location	5,736,098 – 5,736,215
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.78
Mean single sequence MFE	-34.85
Consensus MFE	-18.04
Energy contribution	-19.16
Covariance contribution	1.12
Combinations/Pair	1.19
Mean z-score	-1.90
Structure conservation index	0.52
SVM decision value	0.06
SVM RNA-class probability	0.565515
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5736098 117 - 27905053
GAUCGAAGUGAAGCCAGCAU-AUAAAUUGCCACAUGGCUAAUGAUGGCUUAUGGCUUUGUAACCAUCGAUCAAGUGACAUGCA--GGGCUCGGUUAGCCAAUCAUUGGCCCAAUACUGAA
......((((......(((.-......))).....((((((((((((((..((((((((((..(((.......)))...))))--)))).))...)))).))))))))))...))))... ( -34.80)
>DroSec_CAF1 27669 117 - 1
GAUCGAAGUGAAGCCAGCAU-AUAAAUUGCCACAUGGCUAAUGAUGGCUUAUGGCCGUGCAGCCAUCGAUCAAGUGCCAUGCA--GGGCUCGGUUAGCCAAUCAUUGGCCCAAUAAUGGA
.............((((((.-......))).....((((((((((((((..(((((.((((..(((.......)))...))))--.))).))...)))).))))))))))......))). ( -39.90)
>DroSim_CAF1 28305 117 - 1
GAUCGAAGUGAAGCCAGCAU-AUAAAUUGCCACAUGGCUAAUGAUGGCUUAUGGCCGUGCAACCAUCGAUCAAGUGCCAUGCA--GGGCUCGGUUAGCCAAUCAUUGGCCCAAUAAUGGA
.............((((((.-......))).....((((((((((((((..(((((.((((..(((.......)))...))))--.))).))...)))).))))))))))......))). ( -38.80)
>DroEre_CAF1 23357 109 - 1
GAUCGGAGUAAAGCCAGCAU-AUAAAUUGCCACAUGGCUAAUGAUGGCUUAUGGCUGUGGAACCAUCGAUCAAGUGCCAUGCA--GGGCUCGGUUGU-------UUGG-CCAAUAAUGAA
(((((.(((.((((((.(((-.......(((....)))..))).))))))...)))(((....))))))))..(.(((.....--.))).)((((..-------..))-))......... ( -29.80)
>DroYak_CAF1 11118 109 - 1
GAUCGAAGUAAAGCCAGCAU-AUAAAUUGCCACAUGGCUAAUGAUGGCUUAUGGCUUUGGAGCCAUCGAUCAAGUGCCAUGCA--GGGCUCGGUUGG-------UUGG-CCAAUACUGAA
......((((..((((((..-.......(((.((((((...((((.(...((((((....))))))).))))...))))))..--.))).......)-------))))-)...))))... ( -37.69)
>DroPer_CAF1 33328 101 - 1
AAUCAGAGUCCGUUGAUCAUGAUAAAUGGGUAUCGAGCUAAUGAUGACUUAGUGCUCGGCAUCCAUCUAUCAAAUGU-AUGCACAGGGCCU-----------------CCUGCUAAUGA-
...(((.((((..((..(((((((.((((((..(((((...(((....)))..)))))..)))))).)))))..)).-...))..))))..-----------------.))).......- ( -28.10)
>consensus
GAUCGAAGUGAAGCCAGCAU_AUAAAUUGCCACAUGGCUAAUGAUGGCUUAUGGCUGUGCAACCAUCGAUCAAGUGCCAUGCA__GGGCUCGGUUAG_______UUGGCCCAAUAAUGAA
((((((....((((((.(((........(((....)))..))).)))))).(((........)))))))))..............(((((................)))))......... (-18.04 = -19.16 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:29 2006