Locus 13427

Sequence ID dm3.chrX
Location 6,487,453 – 6,487,586
Length 133
Max. P 0.769869
window18489 window18490 window18491

overview

Window 9

Location 6,487,453 – 6,487,573
Length 120
Sequences 12
Columns 120
Reading direction forward
Mean pairwise identity 74.22
Shannon entropy 0.57383
G+C content 0.56736
Mean single sequence MFE -43.64
Consensus MFE -19.37
Energy contribution -19.12
Covariance contribution -0.25
Combinations/Pair 1.48
Mean z-score -1.49
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.64
SVM RNA-class probability 0.769869
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6487453 120 + 22422827
UUCGCUCGACUCGUUCGCUAUCCAUUUGCUCGCAGUCAAUUGCUGCGCAUAAUGGCCUCACUAAUGGCCAGCCAAAAGAUGCUGGCCAAAAGACUCAGCGAGAACUAUGUGUCGCGCUAU
...((.((((.((((((((..((((((((..(((((.....)))))))).))))).....((..((((((((........))))))))..))....))))).....))).)))).))... ( -44.20, z-score =  -3.43, R)
>droSim1.chrX 5094737 120 + 17042790
UUCUCUCGACUCGUUCGCUUUCCAUUUGCCCGCAGCCAAUUGCUGCGCAUAAUGGCCUCACUAAUGGCCAGCAAUAAGAUGCUGGCCAAAAGACUCAGCGAGAACUAUGUGUCGCGCUAU
......((((.((((((((..((((((((..(((((.....)))))))).))))).....((..(((((((((......)))))))))..))....))))).....))).))))...... ( -42.70, z-score =  -3.41, R)
>droSec1.super_4 5865495 120 - 6179234
UUCUCUCGACUCGUUCGCUAUCCAUUUGCCCGCAGCCAAUUGCUGCGCAUAAUGGCCUCACUAAUGGCCAGCAAUAAGAUGCUGGCCAAAAGACUCAGCGAGAACUAUGUGUCGCGCUAU
......((((.((((((((..((((((((..(((((.....)))))))).))))).....((..(((((((((......)))))))))..))....))))).....))).))))...... ( -43.30, z-score =  -3.60, R)
>droYak2.chrX 2454071 120 + 21770863
UUCGCUCGACUCGUUCGAUACCCAGCUGCUCGCAGCCAGUUGCUGCACAUAAUGGCCUCACUAAUGGCCAGCAAGAAGAUGCUGGCCAAAAGACUCAGCGAGAACUAUGUAUCGCGCUAU
............((.((((((..((...(((((.((((..((.....))...))))....((..(((((((((......)))))))))..)).....)))))..))..)))))).))... ( -41.80, z-score =  -2.29, R)
>droEre2.scaffold_4690 15418775 120 + 18748788
UUCUCUCGACUCGUUCGAUACCCAGCUGCUCGCAGUCAGUUGCUGCGCAUAAUGGCCUCACUAAUGGCCAGCAAGAAGAUGCUGGCCAGGAGACUCAGCGAGAACUAUGUAUCGCGCUAU
............((.((((((..((...(((((.((((..(((...)))...))))(((.....(((((((((......))))))))).))).....)))))..))..)))))).))... ( -43.80, z-score =  -1.86, R)
>droAna3.scaffold_12929 3049083 120 + 3277472
UUCACUCGCCUGGUCCGCUACUCGCCCGCCCGCAGCAAGCUGCUGCGCAUCGUGGCCUCGCUGAUGGCCAGCAAAAAGCCGCUCGCCAGCCGUCUCAGCGGCGCCUACAUCGCCCGCUAC
......((.(((((..((.....(((((..((((((.....))))))...)).)))...((((.....))))........))..))))).))....(((((.((.......))))))).. ( -43.00, z-score =  -0.12, R)
>dp4.chrXL_group1e 5351176 120 + 12523060
UUCGCGCGACUCGUACGCCACUCACCAGCACGCAGCAAACUGCUGGGCAUUCUGGCCGCCCUGAUGGCCAACAAAAAGAUGCUAUCGAGCCGGCUUAGCGAGGCCUAUGUGGGUCGCUAC
.....((((((((((.(((.....((((((..........))))))((.....(((((.(.(((((((............))))))).).)))))..))..))).)))..)))))))... ( -42.90, z-score =  -0.58, R)
>droPer1.super_21 262449 120 + 1645244
UUCGCGCGACUCGUACGGCACUCACCAGCACGCAGCAAACUGCUGGGCAUUCUGGCCGCCCUGAUGGCCAGCAAAAAGAUGCUAUCGAGCCGGCUUAGCGAGGCCUAUGUGGGUCGCUAC
.....((((((((...(((.....((((((..........))))))((((((((((((......)))))))......)))))......)))(((((....)))))....))))))))... ( -47.50, z-score =  -1.08, R)
>droWil1.scaffold_181150 1769472 120 + 4952429
UUCACACGAUUGGUACGCUAUUCGCCGGCACGUAGCCAACUCUUACGCAUAUUGGCUUCCCUAAUGGCCAGCAAGAAAAUGCUGGCGAAUCGCCUGAGCGAGGUCUAUGUCGGUCGCUAU
......((((((..(.(((.(((((((((((((((.......)))))....((((((........))))))........))))))))))((((....)))))))...)..)))))).... ( -38.00, z-score =  -0.80, R)
>droVir3.scaffold_12928 524942 120 + 7717345
UUCCGUCCACUCGUACGCUACACAUCGGCGCGCGGCAAGCUGCUCCGCAUUGUGGCCGCCUUGAUGGCCAGCAACAAGACGCUGCCGCAUCGCCUCAGCGAAGCCUAUGUGGGCCGCUAU
....((((((..(..((((.......))))..)(((..((((....((..((((((.(((.....))).(((........)))))))))..))..))))...)))...))))))...... ( -44.20, z-score =   0.15, R)
>droMoj3.scaffold_6328 1484026 120 + 4453435
UUCCGUCGUCUGGUCCGUUACACAUCGGCCCGCGGCAAGCUGCUGCGCAUUGUGGCAGCUUUGAUGGCCAGCAACAAGGCGCUGCCGCGGCGCCUCAGCGAUGCCUAUGUGGGCCGCUUU
..(((.....)))............((((((((((((.((((..((((...((((((((.......(((........))))))))))).))))..))))..))))...)))))))).... ( -54.21, z-score =  -0.75, R)
>droGri2.scaffold_15203 6944480 120 + 11997470
UUCCAUCGACUCGUACGCUACAUACCGGCACGAAGCAAGCUGCUGCGGAUCGUUGUCGAUUUGAUGACGAAUAACAAGGCGGUAACGCGUCGCCUCAGCGAUGCAUAUGUUGGCCGCAUU
............((..(((((((((((.(.((.(((.....))).))..((((..((.....))..)))).......).)))))..(((((((....)))))))...)).)))).))... ( -38.10, z-score =  -0.08, R)
>consensus
UUCGCUCGACUCGUACGCUACCCACCUGCACGCAGCAAACUGCUGCGCAUAAUGGCCUCACUAAUGGCCAGCAAAAAGAUGCUGGCCAAACGACUCAGCGAGGCCUAUGUGGCGCGCUAU
...........................((..(((((.....)))))((((..(((((........))))).........(((((...........)))))......)))).....))... (-19.37 = -19.12 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,487,493 – 6,487,586
Length 93
Sequences 12
Columns 111
Reading direction forward
Mean pairwise identity 63.43
Shannon entropy 0.78171
G+C content 0.56568
Mean single sequence MFE -36.02
Consensus MFE -12.51
Energy contribution -12.30
Covariance contribution -0.21
Combinations/Pair 1.42
Mean z-score -0.93
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.532797
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6487493 93 + 22422827
UGCUGCGCAUAAUGGCCUCACUAAUGGCCAGCCAAAAGAUGCUGGCCAAAAGACUCAGCGAGAACUAUGUGUCGCGCUAUGAGGUGGUGGCCG------------------
.............((((((((...((((((((........)))))))).....(((((((.((.(.....))).)))..)))))))).)))).------------------ ( -36.10, z-score =  -2.30, R)
>droSim1.chrX 5094777 97 + 17042790
UGCUGCGCAUAAUGGCCUCACUAAUGGCCAGCAAUAAGAUGCUGGCCAAAAGACUCAGCGAGAACUAUGUGUCGCGCUAUGAGGUGGUGACCCGUCA--------------
....(((....((.((((((((..(((((((((......)))))))))..))....((((.((.(.....))).)))).)))))).))....)))..-------------- ( -36.00, z-score =  -2.20, R)
>droSec1.super_4 5865535 97 - 6179234
UGCUGCGCAUAAUGGCCUCACUAAUGGCCAGCAAUAAGAUGCUGGCCAAAAGACUCAGCGAGAACUAUGUGUCGCGCUAUGAGGUGGGGACCGGUCA--------------
............(((((((((...(((((((((......))))))))).....(((((((.((.(.....))).)))..)))))))))).)))....-------------- ( -38.20, z-score =  -2.43, R)
>droYak2.chrX 2454111 90 + 21770863
UGCUGCACAUAAUGGCCUCACUAAUGGCCAGCAAGAAGAUGCUGGCCAAAAGACUCAGCGAGAACUAUGUAUCGCGCUAUGAGGUUGCCG---------------------
.............(((((((((..(((((((((......)))))))))..))....((((.((........)).)))).)))))))....--------------------- ( -32.20, z-score =  -2.58, R)
>droEre2.scaffold_4690 15418815 90 + 18748788
UGCUGCGCAUAAUGGCCUCACUAAUGGCCAGCAAGAAGAUGCUGGCCAGGAGACUCAGCGAGAACUAUGUAUCGCGCUAUGAGGUUGCCG---------------------
....(.(((.....((((((((..(((((((((......)))))))))..))....((((.((........)).)))).)))))))))).--------------------- ( -35.30, z-score =  -2.38, R)
>droAna3.scaffold_12929 3049123 98 + 3277472
UGCUGCGCAUCGUGGCCUCGCUGAUGGCCAGCAAAAAGCCGCUCGCCAGCCGUCUCAGCGGCGCCUACAUCGCCCGCUACGGCCAGGACUGGGAGCUG-------------
((((((.(((((((....))).))))).))))).......((((.(((((((((..(((((.((.......)))))))..)))..)).))))))))..------------- ( -40.30, z-score =   0.19, R)
>dp4.chrXL_group1e 5351216 111 + 12523060
UGCUGGGCAUUCUGGCCGCCCUGAUGGCCAACAAAAAGAUGCUAUCGAGCCGGCUUAGCGAGGCCUAUGUGGGUCGCUACAAUACAAAACAGACGCAAGAUGGGGAUGAUG
.(((((((....((((((......))))))..........(((....)))..)))))))....(((((.((.(((................))).))..)))))....... ( -31.49, z-score =   0.65, R)
>droPer1.super_21 262489 111 + 1645244
UGCUGGGCAUUCUGGCCGCCCUGAUGGCCAGCAAAAAGAUGCUAUCGAGCCGGCUUAGCGAGGCCUAUGUGGGUCGCUACAAUACAAAACAGACGCAAGAUGGGGAUGAUG
((((((.((((..((....)).)))).))))))......(.(((((..((.(((((....)))))..(((((....))))).............))..))))).)...... ( -33.70, z-score =   0.50, R)
>droWil1.scaffold_181150 1769512 97 + 4952429
UCUUACGCAUAUUGGCUUCCCUAAUGGCCAGCAAGAAAAUGCUGGCGAAUCGCCUGAGCGAGGUCUAUGUCGGUCGCUAUGGAGUCGCGUCUGGCCA--------------
.............((((((.......(((((((......))))))).....((....))))))))...(((((.(((.........))).)))))..-------------- ( -30.40, z-score =   0.22, R)
>droVir3.scaffold_12928 524982 103 + 7717345
UGCUCCGCAUUGUGGCCGCCUUGAUGGCCAGCAACAAGACGCUGCCGCAUCGCCUCAGCGAAGCCUAUGUGGGCCGCUAUGCUGUGUCCC---AGACAGAGGCACA-----
(((..(((((.((((((........(((.(((........))))))((.((((....)))).)).......)))))).))))..((((..---.)))))..)))..----- ( -39.00, z-score =  -0.18, R)
>droMoj3.scaffold_6328 1484066 101 + 4453435
UGCUGCGCAUUGUGGCAGCUUUGAUGGCCAGCAACAAGGCGCUGCCGCGGCGCCUCAGCGAUGCCUAUGUGGGCCGCUUUGCGCUGCCC---GAGAUUGGAACA-------
.((.(((((..(((((.((......(((..((....((((((((...))))))))..))...)))...))..)))))..))))).))((---(....)))....------- ( -42.80, z-score =   0.32, R)
>droGri2.scaffold_15203 6944520 106 + 11997470
UGCUGCGGAUCGUUGUCGAUUUGAUGACGAAUAACAAGGCGGUAACGCGUCGCCUCAGCGAUGCAUAUGUUGGCCGCAUUGCCCAGCCCUCAGAGAUCGAAGCACA-----
.((((.((.((((..((.....))..))))....(((.(((((((((((((((....)))))))....))).))))).)))))))))...................----- ( -36.80, z-score =  -1.01, R)
>consensus
UGCUGCGCAUAAUGGCCUCACUAAUGGCCAGCAAAAAGAUGCUGGCCAAACGACUCAGCGAGGCCUAUGUGGCGCGCUAUGAGGUGGCCCC_GAGCA______________
......((....(((((........))))).........(((((...........)))))...............)).................................. (-12.51 = -12.30 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,487,493 – 6,487,586
Length 93
Sequences 12
Columns 111
Reading direction reverse
Mean pairwise identity 63.43
Shannon entropy 0.78171
G+C content 0.56568
Mean single sequence MFE -36.06
Consensus MFE -12.05
Energy contribution -11.98
Covariance contribution -0.07
Combinations/Pair 1.47
Mean z-score -1.23
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.46
SVM RNA-class probability 0.704313
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6487493 93 - 22422827
------------------CGGCCACCACCUCAUAGCGCGACACAUAGUUCUCGCUGAGUCUUUUGGCCAGCAUCUUUUGGCUGGCCAUUAGUGAGGCCAUUAUGCGCAGCA
------------------.((......)).....(((((...(((((((((((((((......((((((((........)))))))))))))))))..))))))))).)). ( -34.10, z-score =  -2.24, R)
>droSim1.chrX 5094777 97 - 17042790
--------------UGACGGGUCACCACCUCAUAGCGCGACACAUAGUUCUCGCUGAGUCUUUUGGCCAGCAUCUUAUUGCUGGCCAUUAGUGAGGCCAUUAUGCGCAGCA
--------------(((.((.......)))))..(((((...(((((((((((((((......(((((((((......))))))))))))))))))..))))))))).)). ( -38.30, z-score =  -3.30, R)
>droSec1.super_4 5865535 97 + 6179234
--------------UGACCGGUCCCCACCUCAUAGCGCGACACAUAGUUCUCGCUGAGUCUUUUGGCCAGCAUCUUAUUGCUGGCCAUUAGUGAGGCCAUUAUGCGCAGCA
--------------.....(((....))).....(((((...(((((((((((((((......(((((((((......))))))))))))))))))..))))))))).)). ( -37.10, z-score =  -3.27, R)
>droYak2.chrX 2454111 90 - 21770863
---------------------CGGCAACCUCAUAGCGCGAUACAUAGUUCUCGCUGAGUCUUUUGGCCAGCAUCUUCUUGCUGGCCAUUAGUGAGGCCAUUAUGUGCAGCA
---------------------.(....)........((..(((((((((((((((((......(((((((((......))))))))))))))))))..))))))))..)). ( -37.30, z-score =  -3.71, R)
>droEre2.scaffold_4690 15418815 90 - 18748788
---------------------CGGCAACCUCAUAGCGCGAUACAUAGUUCUCGCUGAGUCUCCUGGCCAGCAUCUUCUUGCUGGCCAUUAGUGAGGCCAUUAUGCGCAGCA
---------------------.(....)......(((((...(((((((((((((((......(((((((((......))))))))))))))))))..))))))))).)). ( -36.00, z-score =  -2.87, R)
>droAna3.scaffold_12929 3049123 98 - 3277472
-------------CAGCUCCCAGUCCUGGCCGUAGCGGGCGAUGUAGGCGCCGCUGAGACGGCUGGCGAGCGGCUUUUUGCUGGCCAUCAGCGAGGCCACGAUGCGCAGCA
-------------..(((....(((.(((((......((((.......))))(((((...(((..(((((......)))))..))).)))))..))))).)))....))). ( -45.20, z-score =  -0.14, R)
>dp4.chrXL_group1e 5351216 111 - 12523060
CAUCAUCCCCAUCUUGCGUCUGUUUUGUAUUGUAGCGACCCACAUAGGCCUCGCUAAGCCGGCUCGAUAGCAUCUUUUUGUUGGCCAUCAGGGCGGCCAGAAUGCCCAGCA
...............(((((((..........((((((.((.....))..)))))).((((.(..(((.((..(.....)...)).)))..).))))))).))))...... ( -29.10, z-score =   0.69, R)
>droPer1.super_21 262489 111 - 1645244
CAUCAUCCCCAUCUUGCGUCUGUUUUGUAUUGUAGCGACCCACAUAGGCCUCGCUAAGCCGGCUCGAUAGCAUCUUUUUGCUGGCCAUCAGGGCGGCCAGAAUGCCCAGCA
...............(((((((..........((((((.((.....))..)))))).((((.(..(((((((......))))....)))..).))))))).))))...... ( -29.60, z-score =   0.86, R)
>droWil1.scaffold_181150 1769512 97 - 4952429
--------------UGGCCAGACGCGACUCCAUAGCGACCGACAUAGACCUCGCUCAGGCGAUUCGCCAGCAUUUUCUUGCUGGCCAUUAGGGAAGCCAAUAUGCGUAAGA
--------------((((....(((.........))).((......((..((((....)))).))(((((((......))))))).....))...))))............ ( -29.30, z-score =  -0.82, R)
>droVir3.scaffold_12928 524982 103 - 7717345
-----UGUGCCUCUGUCU---GGGACACAGCAUAGCGGCCCACAUAGGCUUCGCUGAGGCGAUGCGGCAGCGUCUUGUUGCUGGCCAUCAAGGCGGCCACAAUGCGGAGCA
-----((.(((.((((((---(.....))).)))).))).)).....(((((((((.(((....(((((((.....)))))))(((.....))).))).))..))))))). ( -43.80, z-score =  -0.48, R)
>droMoj3.scaffold_6328 1484066 101 - 4453435
-------UGUUCCAAUCUC---GGGCAGCGCAAAGCGGCCCACAUAGGCAUCGCUGAGGCGCCGCGGCAGCGCCUUGUUGCUGGCCAUCAAAGCUGCCACAAUGCGCAGCA
-------....((......---))((.(((((..(((((((.....(((...)))..)).)))))(((((((((........))).......))))))....))))).)). ( -40.61, z-score =   0.33, R)
>droGri2.scaffold_15203 6944520 106 - 11997470
-----UGUGCUUCGAUCUCUGAGGGCUGGGCAAUGCGGCCAACAUAUGCAUCGCUGAGGCGACGCGUUACCGCCUUGUUAUUCGUCAUCAAAUCGACAACGAUCCGCAGCA
-----..((((.(((((....(((((.((..((((((((........)).((((....)))))))))).))))))).......(((........)))...))).)).)))) ( -32.30, z-score =   0.20, R)
>consensus
______________UGCUC_GAGGCCACCUCAUAGCGCCCCACAUAGGCCUCGCUGAGUCGUCUCGCCAGCAUCUUUUUGCUGGCCAUCAGUGAGGCCAUUAUGCGCAGCA
................................(((((..((.....))...)))))............((((......))))((((........))))............. (-12.05 = -11.98 +  -0.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:21:12 2011