Locus 6729

Sequence ID	3R_DroMel_CAF1
Location	17,728,657 – 17,728,778
Length	121
Max. P	0.740211

overview

Window 6

Location	17,728,657 – 17,728,752
Length	95
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	71.01
Mean single sequence MFE	-23.30
Consensus MFE	-7.09
Energy contribution	-8.82
Covariance contribution	1.73
Combinations/Pair	1.32
Mean z-score	-2.13
Structure conservation index	0.30
SVM decision value	0.45
SVM RNA-class probability	0.740211
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17728657 95 + 27905053
UAAAAAAC--UGUCAGGCUGGCAGAGUUCUUU-UGGCCAGGCGAAUUGGAUUUAUU-UAGCCAAUGUUU-UUCCAAUUCAUAUAU----GAAUGUAUUGGCCAA-
.......(--((((.....))))).......(-(((((((..((((((((..((((-.....))))...-.))))))))((((..----..)))).))))))))- ( -25.90)
>DroVir_CAF1 20152 88 + 1
--AAAAACGCUGGCAUACUGACAAAAGGCAGCCCGGCUG------CUGCACAUAUUUUAGCCAAC--UU-UU------AAAAUAUGUUGCCAUUUGUUGGCCAAG
--........((((.....((((((.((((((...))))------))(((((((((((((.....--..-))------)))))))).)))..)))))).)))).. ( -26.10)
>DroSec_CAF1 17771 91 + 1
UAAAAAAC--UGACAGGCUGGUGGAGUUCUUU-UGGCUAGUCGAAUUGGAUUUAUU-UAGCCAAUGUUU-UUCCAAUUUAUAUAU--------GUAUUGGCCAA-
........--.....(((..((((((.....(-(((((((..((((...))))..)-))))))).....-)))))...(((....--------))))..)))..- ( -21.30)
>DroSim_CAF1 18045 91 + 1
UAAAAAAC--UAGCAGGCUGGUGGAGUUCUUU-UGGCCAGUCGAAUUGGAUUUAUU-UAGCCAAUGUUU-UUCCAAUUCAUAUAU--------GUAUUGGCCAA-
........--..((.(((((((.(((....))-).)))))))((((((((..((((-.....))))...-.))))))))......--------......))...- ( -24.80)
>DroEre_CAF1 20188 81 + 1
------------GCAGGCUGGUAGAGUUCUUU-UGGCCAGGCAAAUUGGAUUUAUU-UAGCCCAUGUUU-UGCCAAUUCACAUAU--------GUAUUGGCCAA-
------------...(((..(((.(......(-((((.(((((...(((.......-....))))))))-.)))))........)--------.)))..)))..- ( -22.14)
>DroYak_CAF1 19312 92 + 1
UAAAAAAC--UGGCAGGCUGUUAGAGUUCCUU-UAACCAGGCGAAUUGAAUUUAUU-UAGUCCAUGUUUUUUCCAAUUCAUACAU--------GUACUGGCCAA-
........--((((.(.(((((((((...)))-))).))).)..............-((((.(((((..............))))--------).)))))))).- ( -19.54)
>consensus
UAAAAAAC__UGGCAGGCUGGUAGAGUUCUUU_UGGCCAGGCGAAUUGGAUUUAUU_UAGCCAAUGUUU_UUCCAAUUCAUAUAU________GUAUUGGCCAA_
...............((((((((..(((......))).....((((((((.....................))))))))...............))))))))... ( -7.09 =  -8.82 +   1.73)

alignment

secondary structure

dotplot

Window 7

Location	17,728,686 – 17,728,778
Length	92
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	84.56
Mean single sequence MFE	-23.23
Consensus MFE	-15.31
Energy contribution	-17.71
Covariance contribution	2.40
Combinations/Pair	1.15
Mean z-score	-1.93
Structure conservation index	0.66
SVM decision value	0.23
SVM RNA-class probability	0.646250
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17728686 92 + 27905053
UUGGCCAGGCGAAUUGGAUUUAUUUAGCCAAUGUUU-UUCCAAUUCAUAUAUGAAUGUAUUGGCCAACGGGCCACAGCUGCUGUUGCACUUGC
.(((((.(((((((((((..((((.....))))...-.))))))))(((((....)))))..)))....)))))(((.(((....))).))). ( -26.70)
>DroSec_CAF1 17800 88 + 1
UUGGCUAGUCGAAUUGGAUUUAUUUAGCCAAUGUUU-UUCCAAUUUAUAUAU----GUAUUGGCCAACGGGCAACAGCUGCUGCUGCACUUGC
((((((((((((((((((..((((.....))))...-.))))))))......----).)))))))))...((((((((....))))...)))) ( -21.70)
>DroSim_CAF1 18074 88 + 1
UUGGCCAGUCGAAUUGGAUUUAUUUAGCCAAUGUUU-UUCCAAUUCAUAUAU----GUAUUGGCCAACGGGCAACAGCUGCUGUUGCACUUGC
((((((((((((((((((..((((.....))))...-.))))))))......----).)))))))))...(((((((...)))))))...... ( -27.70)
>DroEre_CAF1 20207 74 + 1
UUGGCCAGGCAAAUUGGAUUUAUUUAGCCCAUGUUU-UGCCAAUUCACAUAU----GUAUUGGCCAACGGGCAACAGCU--------------
(((((((((((((.(((...........)))...))-)))).....((....----))..)))))))..(((....)))-------------- ( -21.30)
>DroYak_CAF1 19341 89 + 1
UUAACCAGGCGAAUUGAAUUUAUUUAGUCCAUGUUUUUUCCAAUUCAUACAU----GUACUGGCCAACGGGCAACAGCUGCUGUUGCACUUGC
....((.(((((((...))))...((((.(((((..............))))----).)))))))...))(((((((...)))))))...... ( -18.74)
>consensus
UUGGCCAGGCGAAUUGGAUUUAUUUAGCCAAUGUUU_UUCCAAUUCAUAUAU____GUAUUGGCCAACGGGCAACAGCUGCUGUUGCACUUGC
((((((((..((((((((....................)))))))).(((......)))))))))))...(((((((...)))))))...... (-15.31 = -17.71 +   2.40)

alignment

secondary structure

dotplot

Window 8

Location	17,728,686 – 17,728,778
Length	92
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	84.56
Mean single sequence MFE	-21.64
Consensus MFE	-14.85
Energy contribution	-16.01
Covariance contribution	1.16
Combinations/Pair	1.28
Mean z-score	-1.97
Structure conservation index	0.69
SVM decision value	0.42
SVM RNA-class probability	0.728088
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17728686 92 - 27905053
GCAAGUGCAACAGCAGCUGUGGCCCGUUGGCCAAUACAUUCAUAUAUGAAUUGGAA-AAACAUUGGCUAAAUAAAUCCAAUUCGCCUGGCCAA
(((..(((....)))..)))((((.(((..(((((.(((......))).)))))..-.)))...(((................))).)))).. ( -23.69)
>DroSec_CAF1 17800 88 - 1
GCAAGUGCAGCAGCAGCUGUUGCCCGUUGGCCAAUAC----AUAUAUAAAUUGGAA-AAACAUUGGCUAAAUAAAUCCAAUUCGACUAGCCAA
....(.(((((((...))))))).)(((..(((((..----........)))))..-.))).(((((((.................))))))) ( -20.53)
>DroSim_CAF1 18074 88 - 1
GCAAGUGCAACAGCAGCUGUUGCCCGUUGGCCAAUAC----AUAUAUGAAUUGGAA-AAACAUUGGCUAAAUAAAUCCAAUUCGACUGGCCAA
....(.(((((((...))))))).).((((((((((.----...)))((((((((.-..................))))))))...))))))) ( -24.41)
>DroEre_CAF1 20207 74 - 1
--------------AGCUGUUGCCCGUUGGCCAAUAC----AUAUGUGAAUUGGCA-AAACAUGGGCUAAAUAAAUCCAAUUUGCCUGGCCAA
--------------.((....))...(((((((.(((----....)))....((((-((...(((..(.....)..))).))))))))))))) ( -20.20)
>DroYak_CAF1 19341 89 - 1
GCAAGUGCAACAGCAGCUGUUGCCCGUUGGCCAGUAC----AUGUAUGAAUUGGAAAAAACAUGGACUAAAUAAAUUCAAUUCGCCUGGUUAA
....(.(((((((...))))))).).((((((((((.----...)).((((((((....................))))))))..)))))))) ( -19.35)
>consensus
GCAAGUGCAACAGCAGCUGUUGCCCGUUGGCCAAUAC____AUAUAUGAAUUGGAA_AAACAUUGGCUAAAUAAAUCCAAUUCGCCUGGCCAA
......(((((((...)))))))...((((((((((........)))((((((((....................))))))))...))))))) (-14.85 = -16.01 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:29 2006