Locus 4458

Sequence ID dm3.chr2R
Location 13,164,076 – 13,164,180
Length 104
Max. P 0.999287
window6106 window6107

overview

Window 6

Location 13,164,076 – 13,164,180
Length 104
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 60.98
Shannon entropy 0.75251
G+C content 0.28342
Mean single sequence MFE -22.53
Consensus MFE -7.60
Energy contribution -10.16
Covariance contribution 2.56
Combinations/Pair 1.35
Mean z-score -3.05
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.76
SVM RNA-class probability 0.999287
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13164076 104 + 21146708
ACCUUAAAAAAAAAUAAACAUAGAGAAAA--------UCGGUUAUUAAUUGAGCGUUAAUUUGUUCA----AAAAUAUGAACAACAAAUUUGGGAUUUUCUCUGUGUAAACUGUAA
.................((((((((((((--------(((.(((.....))).)......(((((((----......))))))).........))))))))))))))......... ( -26.00, z-score =  -4.68, R)
>droEre2.scaffold_4845 9897807 115 - 22589142
ACCCUGAAGAACAA-AAACAUAGAGAAAACCGGAAAAUCGGUUACUAAUUGAGUAGUAUGUCUUUCAUUCAAAAAUUUGAACACCAAGUCUGUGAUUUUCUCUGUGUGAACUGUAG
..........(((.-..(((((((((((((((((.....((((((((......))))).........(((((....))))).)))...)))).).))))))))))))....))).. ( -25.30, z-score =  -1.68, R)
>droYak2.chr2R 2829833 113 - 21139217
ACCCCAAAAAAAAAGAAACAUAGAGAAAAACGGAGAAUCGGUGACUAAUUGAGUAGUAAUUCAUUCA---AAAAAUUUAAACACCAAAUCUGGGAUUUUCUCUGUGUAAACUAAAA
.................((((((((((((.((((.....((((..(((((((((........)))))---).....)))..))))...))))...))))))))))))......... ( -24.50, z-score =  -3.02, R)
>droSec1.super_1 10665831 101 + 14215200
-ACUAAAAAAAAAAAAAAAACAGAGAAAAUCGGAAAAUCGGUGAUUAUUU----------UUGUUCA----AAAAUAUGAACACCAAAUUUGGGAUUUUCUCUGUGUAAACUGUAA
-..................((((((((((((..(((...((((.((((.(----------((.....----.))).)))).))))...)))..))))))))))))........... ( -24.20, z-score =  -4.26, R)
>droSim1.chr2R 11892489 98 + 19596830
--ACUUAAAAAAAA--AACAUAGAGAAAAUCGGAAAAUCGGUGAUUAUUU----------UUGUUCA----AAAAUGUGAACACCAAAUUUGUGAUUUUCUCUGUGUAAACUGUAA
--............--.(((((((((((((((.(((...((((.((((.(----------((.....----.))).)))).))))...))).)))))))))))))))......... ( -29.60, z-score =  -6.03, R)
>droVir3.scaffold_12875 7859069 86 + 20611582
---AGAUCAAAUAUGAAAAAAAGAAUGUAACAAAAGCUUAAGAAUUGAACGGCAUAAAUCGUGUUUA----GAAUCAUAAUUAUCGAAUCCAG-----------------------
---.((((((((((((......(.......)....(((............))).....)))))))).----).))).................----------------------- (  -5.60, z-score =   1.39, R)
>consensus
_CCCUAAAAAAAAA_AAACAUAGAGAAAAACGGAAAAUCGGUGAUUAAUUGAG___UA__UUGUUCA____AAAAUAUGAACACCAAAUCUGGGAUUUUCUCUGUGUAAACUGUAA
.................((((((((((((..........((((.((((............................)))).))))..........))))))))))))......... ( -7.60 = -10.16 +   2.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 13,164,076 – 13,164,180
Length 104
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 60.98
Shannon entropy 0.75251
G+C content 0.28342
Mean single sequence MFE -20.75
Consensus MFE -5.09
Energy contribution -7.01
Covariance contribution 1.92
Combinations/Pair 1.35
Mean z-score -2.52
Structure conservation index 0.25
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.84
SVM RNA-class probability 0.970691
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13164076 104 - 21146708
UUACAGUUUACACAGAGAAAAUCCCAAAUUUGUUGUUCAUAUUUU----UGAACAAAUUAACGCUCAAUUAAUAACCGA--------UUUUCUCUAUGUUUAUUUUUUUUUAAGGU
....(((..(((.((((((((((.........(((((((......----)))))))(((((.......)))))....))--------)))))))).)))..)))............ ( -20.80, z-score =  -3.56, R)
>droEre2.scaffold_4845 9897807 115 + 22589142
CUACAGUUCACACAGAGAAAAUCACAGACUUGGUGUUCAAAUUUUUGAAUGAAAGACAUACUACUCAAUUAGUAACCGAUUUUCCGGUUUUCUCUAUGUUU-UUGUUCUUCAGGGU
..((((...(((.((((((((((..(((.(((((((((((....))))))........(((((......)))))))))).)))..)))))))))).)))..-)))).......... ( -25.90, z-score =  -1.40, R)
>droYak2.chr2R 2829833 113 + 21139217
UUUUAGUUUACACAGAGAAAAUCCCAGAUUUGGUGUUUAAAUUUUU---UGAAUGAAUUACUACUCAAUUAGUCACCGAUUCUCCGUUUUUCUCUAUGUUUCUUUUUUUUUGGGGU
....((...(((.((((((((....(((.((((((.((((.....(---(((.((......)).)))))))).)))))).)))....)))))))).)))..))............. ( -21.70, z-score =  -1.18, R)
>droSec1.super_1 10665831 101 - 14215200
UUACAGUUUACACAGAGAAAAUCCCAAAUUUGGUGUUCAUAUUUU----UGAACAA----------AAAUAAUCACCGAUUUUCCGAUUUUCUCUGUUUUUUUUUUUUUUUUAGU-
...........((((((((((((..(((.((((((....((((((----(....))----------)))))..)))))).)))..))))))))))))..................- ( -26.70, z-score =  -5.90, R)
>droSim1.chr2R 11892489 98 - 19596830
UUACAGUUUACACAGAGAAAAUCACAAAUUUGGUGUUCACAUUUU----UGAACAA----------AAAUAAUCACCGAUUUUCCGAUUUUCUCUAUGUU--UUUUUUUUAAGU--
.........(((.((((((((((..(((.((((((.....(((((----(....))----------))))...)))))).)))..)))))))))).))).--............-- ( -23.10, z-score =  -4.27, R)
>droVir3.scaffold_12875 7859069 86 - 20611582
-----------------------CUGGAUUCGAUAAUUAUGAUUC----UAAACACGAUUUAUGCCGUUCAAUUCUUAAGCUUUUGUUACAUUCUUUUUUUCAUAUUUGAUCU---
-----------------------..((((.(((....(((((...----.....(((........)))..........(((....)))............))))).)))))))--- (  -6.30, z-score =   1.21, R)
>consensus
UUACAGUUUACACAGAGAAAAUCCCAAAUUUGGUGUUCAUAUUUU____UGAACAA__UA___CUCAAUUAAUCACCGAUUUUCCGAUUUUCUCUAUGUUU_UUUUUUUUUAGGG_
.............((((((((....(((.((((((......................................)))))).)))....))))))))..................... ( -5.09 =  -7.01 +   1.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:29:32 2011