Locus 5455

Sequence ID dm3.chr2R
Location 20,413,577 – 20,413,683
Length 106
Max. P 0.998699
window7487 window7488

overview

Window 7

Location 20,413,577 – 20,413,683
Length 106
Sequences 7
Columns 118
Reading direction forward
Mean pairwise identity 63.32
Shannon entropy 0.71329
G+C content 0.40883
Mean single sequence MFE -25.01
Consensus MFE -9.15
Energy contribution -10.45
Covariance contribution 1.30
Combinations/Pair 1.42
Mean z-score -1.06
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.564255
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 20413577 106 + 21146708
AUUAGUGAUGUUAAAAAACAUCG-----AUGCAUCUGCCAUCGAU---ACGUGAGGCCUUCAUGUU--CUUGGCCAUA--CCAUCGAUGACUUUCUCGCUCCCGAUUGCUUAGCAAGU
.....(((((((....)))))))-----.(((......(((((((---..(((.((((........--...)))).))--).)))))))........((........))...)))... ( -27.60, z-score =  -1.72, R)
>droAna3.scaffold_13266 15961342 82 + 19884421
---------------------------GUUUUUGAUGAAAAGUAAUCGGCAUAGUUUCCCAACACU--GCCUGCCAUU-UUCCUCAGU--AUUUUUCAACACCAAUUCUAUAGU----
---------------------------.....((.(((((((((...((((((((........)))--)..))))...-........)--)))))))).)).............---- ( -11.04, z-score =  -1.00, R)
>droEre2.scaffold_4845 21782592 106 + 22589142
AUUAGUGAUGUUAAAAAACAUCG-----AUGCAUCUGCCAUCGAU---ACGUGGGGCCGUGAUGUU--CUGGGCCGUA--CUAUCGAUGACUUCCUCGGUAGCGAUUGCUUAGCAAGU
....((((((((....)))))).-----..(((..((((((((((---(.(((.((((..(.....--)..)))).))--)))))))))(((.....))).)))..)))...)).... ( -33.40, z-score =  -1.58, R)
>droYak2.chr2R 20382094 106 + 21139217
AUUAGUGAUGUUAAAAAACAUCG-----AUGCAUCUGCCAUCGAU---ACGUGGGGCCUUGAUGUU--CUGGACCGUA--CUAUCGAUAACUUCCUCGGUAGCGAUUGCUUAGCAAGU
....((((((((....)))))).-----..(((.(((((((((((---(.(((.((((........--..)).)).))--)))))))).........)))))....)))...)).... ( -27.50, z-score =  -0.73, R)
>droSec1.super_23 287813 106 + 989336
AUUAGUGAUGUUAAAAAACAUCG-----AUGCAUCUGCCAUCGAU---AUGUGGGGCCUUCAUGUU--CUUGGCCAUA--CCAUCGAUGACUUUCUCGCUGUCGAUUGCUUAGCAAUU
.....(((((((....)))))))-----.(((....((.((((((---(.((((((...((((...--..(((.....--)))...))))...))))))))))))).))...)))... ( -29.00, z-score =  -1.64, R)
>droSim1.chr2R 18874051 106 + 19596830
AUUAGUGAUGUUAAAAAACAUCG-----AUGCAUCUGCCAUCGAU---AUGUGGGGCCUUCAUGUU--CUUGGCCGUA--CCAUCGAUGACUUUCUCGCUGUCGAUUGCUUAGCAAGU
.....(((((((....)))))))-----.(((......(((((((---..(((.((((........--...)))).))--).)))))))........((........))...)))... ( -29.70, z-score =  -1.44, R)
>droWil1.scaffold_180699 2032133 115 + 2593675
AUUAAUUUUAUGUAAACAUGUAGUAAACGUGUAGAUAAAAACGAUUAAACGUGUAGAUACAAAAUUUACUUCGCCGCAAUUUAUCGAUUGGGUUUUUCUU--CGAUUA-UUAGUAAUU
(((((((((((.(..((((((.....))))))).)))))).(((..(((...((((((.....))))))...(((.(((((....)))))))).)))..)--))....-))))).... ( -16.80, z-score =   0.69, R)
>consensus
AUUAGUGAUGUUAAAAAACAUCG_____AUGCAUCUGCCAUCGAU___ACGUGGGGCCUUCAUGUU__CUUGGCCGUA__CCAUCGAUGACUUUCUCGCUACCGAUUGCUUAGCAAGU
......((((((....))))))................(((((((......((.((((.............)))).))....)))))))............................. ( -9.15 = -10.45 +   1.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 20,413,577 – 20,413,683
Length 106
Sequences 7
Columns 118
Reading direction reverse
Mean pairwise identity 63.32
Shannon entropy 0.71329
G+C content 0.40883
Mean single sequence MFE -27.30
Consensus MFE -12.31
Energy contribution -14.08
Covariance contribution 1.77
Combinations/Pair 1.44
Mean z-score -2.36
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.45
SVM RNA-class probability 0.998699
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 20413577 106 - 21146708
ACUUGCUAAGCAAUCGGGAGCGAGAAAGUCAUCGAUGG--UAUGGCCAAG--AACAUGAAGGCCUCACGU---AUCGAUGGCAGAUGCAU-----CGAUGUUUUUUAACAUCACUAAU
.........(((.(((....)))....(((((((((((--(..((((...--........))))..)).)---)))))))))...)))..-----.((((((....))))))...... ( -34.60, z-score =  -3.12, R)
>droAna3.scaffold_13266 15961342 82 - 19884421
----ACUAUAGAAUUGGUGUUGAAAAAU--ACUGAGGAA-AAUGGCAGGC--AGUGUUGGGAAACUAUGCCGAUUACUUUUCAUCAAAAAC---------------------------
----......((.(..(((((....)))--))..)((((-(.(((..(((--(....(((....)))))))..))).))))).))......--------------------------- ( -19.80, z-score =  -2.60, R)
>droEre2.scaffold_4845 21782592 106 - 22589142
ACUUGCUAAGCAAUCGCUACCGAGGAAGUCAUCGAUAG--UACGGCCCAG--AACAUCACGGCCCCACGU---AUCGAUGGCAGAUGCAU-----CGAUGUUUUUUAACAUCACUAAU
.((((...(((....)))..))))...(((((((((((--(..((((..(--.....)..))))..)).)---)))))))))........-----.((((((....))))))...... ( -32.30, z-score =  -3.21, R)
>droYak2.chr2R 20382094 106 - 21139217
ACUUGCUAAGCAAUCGCUACCGAGGAAGUUAUCGAUAG--UACGGUCCAG--AACAUCAAGGCCCCACGU---AUCGAUGGCAGAUGCAU-----CGAUGUUUUUUAACAUCACUAAU
.((((...(((....)))..))))...(((((((((((--(..((((..(--.....)..))))..)).)---)))))))))........-----.((((((....))))))...... ( -28.40, z-score =  -2.17, R)
>droSec1.super_23 287813 106 - 989336
AAUUGCUAAGCAAUCGACAGCGAGAAAGUCAUCGAUGG--UAUGGCCAAG--AACAUGAAGGCCCCACAU---AUCGAUGGCAGAUGCAU-----CGAUGUUUUUUAACAUCACUAAU
.........(((.(((....)))....(((((((((((--(..((((...--........))))..)).)---)))))))))...)))..-----.((((((....))))))...... ( -32.10, z-score =  -3.16, R)
>droSim1.chr2R 18874051 106 - 19596830
ACUUGCUAAGCAAUCGACAGCGAGAAAGUCAUCGAUGG--UACGGCCAAG--AACAUGAAGGCCCCACAU---AUCGAUGGCAGAUGCAU-----CGAUGUUUUUUAACAUCACUAAU
.((((((...(....)..))))))...(((((((((((--(..((((...--........))))..)).)---)))))))))........-----.((((((....))))))...... ( -33.40, z-score =  -3.64, R)
>droWil1.scaffold_180699 2032133 115 - 2593675
AAUUACUAA-UAAUCG--AAGAAAAACCCAAUCGAUAAAUUGCGGCGAAGUAAAUUUUGUAUCUACACGUUUAAUCGUUUUUAUCUACACGUUUACUACAUGUUUACAUAAAAUUAAU
.........-......--........((((((......)))).))....((((((..((((..((.((((.((............)).)))).)).)))).))))))........... ( -10.50, z-score =   1.40, R)
>consensus
ACUUGCUAAGCAAUCGAUAGCGAGAAAGUCAUCGAUGG__UACGGCCAAG__AACAUGAAGGCCCCACGU___AUCGAUGGCAGAUGCAU_____CGAUGUUUUUUAACAUCACUAAU
.........(((.(((....)))....(((((((((.......((((.............)))).........)))))))))...)))........((((((....))))))...... (-12.31 = -14.08 +   1.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:48:42 2011