Locus 1876

Sequence ID dm3.chr2L
Location 14,518,087 – 14,518,159
Length 72
Max. P 0.901079
window2585 window2586

overview

Window 5

Location 14,518,087 – 14,518,159
Length 72
Sequences 13
Columns 78
Reading direction forward
Mean pairwise identity 84.19
Shannon entropy 0.34414
G+C content 0.63926
Mean single sequence MFE -29.85
Consensus MFE -26.18
Energy contribution -24.26
Covariance contribution -1.92
Combinations/Pair 1.67
Mean z-score -1.22
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.99
SVM RNA-class probability 0.868769
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14518087 72 + 23011544
GAAGCAUCGG-----UGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUG
....((((((-----..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))) ( -30.80, z-score =  -0.82, R)
>droAna3.scaffold_12913 128343 72 - 441482
AGAGCAUCGG-----UGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUG
....((((((-----..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))) ( -30.80, z-score =  -0.73, R)
>droEre2.scaffold_4929 6275463 72 + 26641161
GAAGCAUCGG-----UGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUG
....((((((-----..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))) ( -30.80, z-score =  -0.82, R)
>droYak2.chr2L 14627550 72 + 22324452
GAAGCAUCGG-----UGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUG
....((((((-----..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))) ( -30.80, z-score =  -0.82, R)
>droSec1.super_3 781237 72 + 7220098
AAAGCAUCGG-----UGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUG
....((((((-----..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))) ( -30.80, z-score =  -0.94, R)
>droPer1.super_5 6189145 71 - 6813705
-AAGCAUCGG-----UGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUG
-...((((((-----..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))) ( -30.80, z-score =  -0.94, R)
>dp4.chr4_group4 1436228 71 + 6586962
-AAGCAUCGG-----UGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUG
-...((((((-----..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))) ( -30.80, z-score =  -0.94, R)
>droWil1.scaffold_180701 2121832 76 - 3904529
AAAGCAUCUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUG--
...((((((.((((........))))...)))).(((((.......)))))..))(((((.......)))))....-- ( -21.50, z-score =  -0.44, R)
>droGri2.scaffold_15252 11469071 69 + 17193109
---GCAUCGG-----UGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUG
---.((((((-----..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))) ( -30.80, z-score =  -0.99, R)
>droMoj3.scaffold_6500 23189631 69 + 32352404
---GCAUCGG-----UGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUG
---.((((((-----..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))) ( -30.80, z-score =  -0.99, R)
>droVir3.scaffold_12963 203613 69 - 20206255
---GCAUCGG-----UGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUG
---.((((((-----..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))) ( -30.80, z-score =  -0.99, R)
>apiMel3.Group14 2180898 72 + 8318479
GUAGCACUGC-----UGGUGUAGUGGU-AUCAUGCAAGAUUCCCAUUCUUGCGACCCGGGUUCGAUUCCCGGGCAGUG
(((.((((((-----....)))))).)-))...((((((.......))))))(.((((((.......))))))).... ( -30.20, z-score =  -3.23, R)
>triCas2.ChLG8 12282827 72 + 15773733
ACAGCACUGC-----UAGUGUAGUGGU-AUCAUGCAAGAUUCCCAUUCUUGCGACCCGGGUUCGAUUCCCGGGCAGUG
....((((((-----....))))))..-.....((((((.......))))))(.((((((.......))))))).... ( -28.40, z-score =  -3.19, R)
>consensus
_AAGCAUCGG_____UGGUUCAGUGGU_AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUG
....((((((.......((((........))))((((((.......))))))...(((((.......))))))))))) (-26.18 = -24.26 +  -1.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 14,518,087 – 14,518,159
Length 72
Sequences 13
Columns 78
Reading direction reverse
Mean pairwise identity 84.19
Shannon entropy 0.34414
G+C content 0.63926
Mean single sequence MFE -27.18
Consensus MFE -22.39
Energy contribution -21.22
Covariance contribution -1.17
Combinations/Pair 1.50
Mean z-score -1.51
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.15
SVM RNA-class probability 0.901079
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14518087 72 - 23011544
CAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCA-----CCGAUGCUUC
(((((((((((.......)))))((((((.((...)).)))).)).....-............-----)))))).... ( -28.00, z-score =  -1.31, R)
>droAna3.scaffold_12913 128343 72 + 441482
CAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCA-----CCGAUGCUCU
(((((((((((.......)))))((((((.((...)).)))).)).....-............-----)))))).... ( -28.00, z-score =  -1.21, R)
>droEre2.scaffold_4929 6275463 72 - 26641161
CAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCA-----CCGAUGCUUC
(((((((((((.......)))))((((((.((...)).)))).)).....-............-----)))))).... ( -28.00, z-score =  -1.31, R)
>droYak2.chr2L 14627550 72 - 22324452
CAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCA-----CCGAUGCUUC
(((((((((((.......)))))((((((.((...)).)))).)).....-............-----)))))).... ( -28.00, z-score =  -1.31, R)
>droSec1.super_3 781237 72 - 7220098
CAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCA-----CCGAUGCUUU
(((((((((((.......)))))((((((.((...)).)))).)).....-............-----)))))).... ( -28.00, z-score =  -1.33, R)
>droPer1.super_5 6189145 71 + 6813705
CAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCA-----CCGAUGCUU-
(((((((((((.......)))))((((((.((...)).)))).)).....-............-----))))))...- ( -28.00, z-score =  -1.36, R)
>dp4.chr4_group4 1436228 71 - 6586962
CAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCA-----CCGAUGCUU-
(((((((((((.......)))))((((((.((...)).)))).)).....-............-----))))))...- ( -28.00, z-score =  -1.36, R)
>droWil1.scaffold_180701 2121832 76 + 3904529
--CAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAGAUGCUUU
--....(((((.......)))))(((((((((((....)))((....))................))))))..))... ( -23.20, z-score =  -0.99, R)
>droGri2.scaffold_15252 11469071 69 - 17193109
CAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCA-----CCGAUGC---
(((((((((((.......)))))((((((.((...)).)))).)).....-............-----)))))).--- ( -28.00, z-score =  -1.47, R)
>droMoj3.scaffold_6500 23189631 69 - 32352404
CAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCA-----CCGAUGC---
(((((((((((.......)))))((((((.((...)).)))).)).....-............-----)))))).--- ( -28.00, z-score =  -1.47, R)
>droVir3.scaffold_12963 203613 69 + 20206255
CAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCA-----CCGAUGC---
(((((((((((.......)))))((((((.((...)).)))).)).....-............-----)))))).--- ( -28.00, z-score =  -1.47, R)
>apiMel3.Group14 2180898 72 - 8318479
CACUGCCCGGGAAUCGAACCCGGGUCGCAAGAAUGGGAAUCUUGCAUGAU-ACCACUACACCA-----GCAGUGCUAC
(((((((((((.......)))))...((((((.......)))))).....-............-----)))))).... ( -25.10, z-score =  -2.70, R)
>triCas2.ChLG8 12282827 72 - 15773733
CACUGCCCGGGAAUCGAACCCGGGUCGCAAGAAUGGGAAUCUUGCAUGAU-ACCACUACACUA-----GCAGUGCUGU
(((((((((((.......)))))...((((((.......)))))).....-............-----)))))).... ( -25.10, z-score =  -2.32, R)
>consensus
CAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU_ACCACUGAACCA_____CCGAUGCUU_
(((((((((((.......)))))...((.(((.......))).)).......................)))))).... (-22.39 = -21.22 +  -1.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:40:34 2011