Locus 5028

Sequence ID dm3.chr2R
Location 17,211,690 – 17,211,799
Length 109
Max. P 0.972967
window6904 window6905

overview

Window 4

Location 17,211,690 – 17,211,799
Length 109
Sequences 12
Columns 110
Reading direction forward
Mean pairwise identity 87.63
Shannon entropy 0.28886
G+C content 0.53326
Mean single sequence MFE -37.70
Consensus MFE -30.47
Energy contribution -30.86
Covariance contribution 0.38
Combinations/Pair 1.21
Mean z-score -1.70
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.06
SVM RNA-class probability 0.883213
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17211690 109 + 21146708
CAGAUGUCUCAAACAUGAAUGAAGGUAAUUCAGCAGGAGGGGGGCAUGAAGGGCUCAGCCCGG-CCCCUCCUGCUGUGCCAGACCGCGUAACUCCACAUUCAACGGAAAU
...............((((((..((((...(((((((((((((((.(((.....))))))...-)))))))))))))))).(....).........))))))........ ( -39.50, z-score =  -1.63, R)
>droSim1.chr2R 15863899 109 + 19596830
CAGAUGUCUCAAACAUGAAUGAAGGUAAUUCAGCAGGAGGGGGGCAUGAAGGGCUCAGCCCGG-CCCCUCCUGCUGUGCCAGACCGCGUAACUCCACAUUCAACGGAAAU
...............((((((..((((...(((((((((((((((.(((.....))))))...-)))))))))))))))).(....).........))))))........ ( -39.50, z-score =  -1.63, R)
>droSec1.super_9 543050 109 + 3197100
CAGAUGUCUCAAACAUGAAUGAAGGUAAUUCAGCAGGAGGGGGGCAUGAAGGGCUCAGCCCGG-CCCCUCCUGCUGUGCCAGACCGCGUAACUCCACAUUCAACGGAAAU
...............((((((..((((...(((((((((((((((.(((.....))))))...-)))))))))))))))).(....).........))))))........ ( -39.50, z-score =  -1.63, R)
>droYak2.chr2R 9162584 109 - 21139217
UAGAUGUCUCAAACAUGAAUGAAGGUAAUUCAGCAGGAGGGGGGCAUGAAGGGCUCAGCCCGG-CCCCUCCUGCUGUGCCAGACCGCGUAACUCCACAUUCAACGGAAAC
...............((((((..((((...(((((((((((((((.(((.....))))))...-)))))))))))))))).(....).........))))))..(....) ( -39.60, z-score =  -1.87, R)
>droEre2.scaffold_4845 11355475 109 + 22589142
CAGAUGUCUCAAACAUGAAUGAAGGUAAUUCAGCAGGAGGGGGGCAUGAAGGGCUCAGCCCGG-CCCCUCCUGCUGUGCCAGACCGCGUAACUCCACAUUUAACGGAAAC
..(..((((((....))).....((((...(((((((((((((((.(((.....))))))...-)))))))))))))))).)))..).....(((.........)))... ( -38.80, z-score =  -1.67, R)
>droAna3.scaffold_13266 5013863 109 + 19884421
CAGAUGUCUCAAACAUGAAUGAAGGUAAUUCAGCAGGAGGGGGGCAUGAAGGGCUCAGCCCGG-CCCCUCCUGCUGUGCCAGACCGCGUAACUUCAUACUCAACGGAAAA
...............(((((((((......(((((((((((((((.(((.....))))))...-)))))))))))).((......))....))))))..)))........ ( -39.10, z-score =  -1.66, R)
>dp4.chr3 9976957 109 - 19779522
CAGAUGUCUCAAACAUGAAUGAAGGUAAUUCAGCAGGAGGGGGGCAUGAAGGGCUAAGCCCGG-CCCCUCCUGCUGUGUCAGACCGCGUAACUUUACACUCUACGGAAAA
...((((.(((....))).....(((....((((((((..(((((.....((((...)))).)-))))))))))))......)))))))..........((....))... ( -37.30, z-score =  -1.53, R)
>droPer1.super_4 2044218 109 - 7162766
CAGAUGUCUCAAACAUGAAUGAAGGUAAUUCAGCAGGAGGGGGGCAUGAAGGGCUAAGCCCGG-CCCCUCCUGCUGUGUCAGACCGCGUAACUUUACACUCUACGGAAAA
...((((.(((....))).....(((....((((((((..(((((.....((((...)))).)-))))))))))))......)))))))..........((....))... ( -37.30, z-score =  -1.53, R)
>droWil1.scaffold_180697 1465779 109 + 4168966
CAGAUGUCUCAAACAUGAAUGAAGGUAAUUCAGCAGGAGGGGGGCACGAAGGGCUAAGCCCGG-CCCCUCCUGCUGUGCAAGACCGCGUUACGUUACAAACUACGGAAAA
..(((((.(((....))).....(((....((((((((..(((((.....((((...)))).)-))))))))))))......)))))))).(((........)))..... ( -38.60, z-score =  -2.06, R)
>droVir3.scaffold_12875 2542493 107 - 20611582
CAGAUGUCUCAA-CAUGAAUGAACGUAUUCAGCCAGGAGGGGGGCAUGAAGG-CUAAGCCCGGGCCCCUCCUGCUGUGUCAGACCGUGUAACGUUACA-UCAACGGUAAA
..(((((..(.(-((((..(((.......((((.(((((((((((.......-....)))....))))))))))))..)))...)))))...)..)))-))......... ( -35.10, z-score =  -0.91, R)
>droGri2.scaffold_15245 14127781 109 - 18325388
CAGAUGUCUCAAACAUGAAUGAAGGUAAUUCAGCAGGAGGGGGGCAUGAAGGGCUAAGCCCGG-CCCCUCCUGCUGUGUCAGACCGUGUAACGUUACUAUCAACGGAAAA
............(((((..(((........((((((((..(((((.....((((...)))).)-))))))))))))..)))...)))))..((((......))))..... ( -38.00, z-score =  -1.91, R)
>anoGam1.chr2L 26876184 106 + 48795086
CAGAUGUAUAAAAAAUGAAUGAAGGCGAUACGGCGGGAGGGCAACGUG---GUCGAAACCAGG-CCCUUCCUGCUGGAAUUGAUCGAAACACAUCAACUGCAACUAACAC
..(((((..................((((.((((((((((((....((---((....)))).)-))).))))))))......))))....)))))............... ( -30.15, z-score =  -2.40, R)
>consensus
CAGAUGUCUCAAACAUGAAUGAAGGUAAUUCAGCAGGAGGGGGGCAUGAAGGGCUAAGCCCGG_CCCCUCCUGCUGUGCCAGACCGCGUAACUUCACAUUCAACGGAAAA
.......................(((....((((((((((((........((((...))))...))))))))))))......)))......................... (-30.47 = -30.86 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 17,211,690 – 17,211,799
Length 109
Sequences 12
Columns 110
Reading direction reverse
Mean pairwise identity 87.63
Shannon entropy 0.28886
G+C content 0.53326
Mean single sequence MFE -39.11
Consensus MFE -29.38
Energy contribution -29.29
Covariance contribution -0.09
Combinations/Pair 1.43
Mean z-score -2.41
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.88
SVM RNA-class probability 0.972967
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17211690 109 - 21146708
AUUUCCGUUGAAUGUGGAGUUACGCGGUCUGGCACAGCAGGAGGGG-CCGGGCUGAGCCCUUCAUGCCCCCCUCCUGCUGAAUUACCUUCAUUCAUGUUUGAGACAUCUG
.((((...((((((.((((((..((......)).((((((((((((-...(((((((...)))).))))))))))))))))))).))..)))))).....))))...... ( -42.90, z-score =  -2.57, R)
>droSim1.chr2R 15863899 109 - 19596830
AUUUCCGUUGAAUGUGGAGUUACGCGGUCUGGCACAGCAGGAGGGG-CCGGGCUGAGCCCUUCAUGCCCCCCUCCUGCUGAAUUACCUUCAUUCAUGUUUGAGACAUCUG
.((((...((((((.((((((..((......)).((((((((((((-...(((((((...)))).))))))))))))))))))).))..)))))).....))))...... ( -42.90, z-score =  -2.57, R)
>droSec1.super_9 543050 109 - 3197100
AUUUCCGUUGAAUGUGGAGUUACGCGGUCUGGCACAGCAGGAGGGG-CCGGGCUGAGCCCUUCAUGCCCCCCUCCUGCUGAAUUACCUUCAUUCAUGUUUGAGACAUCUG
.((((...((((((.((((((..((......)).((((((((((((-...(((((((...)))).))))))))))))))))))).))..)))))).....))))...... ( -42.90, z-score =  -2.57, R)
>droYak2.chr2R 9162584 109 + 21139217
GUUUCCGUUGAAUGUGGAGUUACGCGGUCUGGCACAGCAGGAGGGG-CCGGGCUGAGCCCUUCAUGCCCCCCUCCUGCUGAAUUACCUUCAUUCAUGUUUGAGACAUCUA
(((((...((((((.((((((..((......)).((((((((((((-...(((((((...)))).))))))))))))))))))).))..)))))).....)))))..... ( -46.50, z-score =  -3.44, R)
>droEre2.scaffold_4845 11355475 109 - 22589142
GUUUCCGUUAAAUGUGGAGUUACGCGGUCUGGCACAGCAGGAGGGG-CCGGGCUGAGCCCUUCAUGCCCCCCUCCUGCUGAAUUACCUUCAUUCAUGUUUGAGACAUCUG
(((((........((((((....((......)).((((((((((((-...(((((((...)))).)))))))))))))))......))))))........)))))..... ( -43.29, z-score =  -2.82, R)
>droAna3.scaffold_13266 5013863 109 - 19884421
UUUUCCGUUGAGUAUGAAGUUACGCGGUCUGGCACAGCAGGAGGGG-CCGGGCUGAGCCCUUCAUGCCCCCCUCCUGCUGAAUUACCUUCAUUCAUGUUUGAGACAUCUG
.((((...(((..((((((....((......)).((((((((((((-...(((((((...)))).)))))))))))))))......))))))))).....))))...... ( -40.20, z-score =  -2.25, R)
>dp4.chr3 9976957 109 + 19779522
UUUUCCGUAGAGUGUAAAGUUACGCGGUCUGACACAGCAGGAGGGG-CCGGGCUUAGCCCUUCAUGCCCCCCUCCUGCUGAAUUACCUUCAUUCAUGUUUGAGACAUCUG
.......(((((((((....))))).((((.(.(((((((((((((-..((((...))))........))))))))))(((((.......)))))))).).)))).)))) ( -39.00, z-score =  -2.73, R)
>droPer1.super_4 2044218 109 + 7162766
UUUUCCGUAGAGUGUAAAGUUACGCGGUCUGACACAGCAGGAGGGG-CCGGGCUUAGCCCUUCAUGCCCCCCUCCUGCUGAAUUACCUUCAUUCAUGUUUGAGACAUCUG
.......(((((((((....))))).((((.(.(((((((((((((-..((((...))))........))))))))))(((((.......)))))))).).)))).)))) ( -39.00, z-score =  -2.73, R)
>droWil1.scaffold_180697 1465779 109 - 4168966
UUUUCCGUAGUUUGUAACGUAACGCGGUCUUGCACAGCAGGAGGGG-CCGGGCUUAGCCCUUCGUGCCCCCCUCCUGCUGAAUUACCUUCAUUCAUGUUUGAGACAUCUG
.....(((.(((........))))))((((((.(((((((((((((-..((((...))))........))))))))))(((((.......)))))))).))))))..... ( -36.80, z-score =  -2.22, R)
>droVir3.scaffold_12875 2542493 107 + 20611582
UUUACCGUUGA-UGUAACGUUACACGGUCUGACACAGCAGGAGGGGCCCGGGCUUAG-CCUUCAUGCCCCCCUCCUGGCUGAAUACGUUCAUUCAUG-UUGAGACAUCUG
((((.(((.((-((.(((((.....(......).((((((((((((....(((....-.......))))))))))).))))...))))))))).)))-.))))....... ( -34.00, z-score =  -1.21, R)
>droGri2.scaffold_15245 14127781 109 + 18325388
UUUUCCGUUGAUAGUAACGUUACACGGUCUGACACAGCAGGAGGGG-CCGGGCUUAGCCCUUCAUGCCCCCCUCCUGCUGAAUUACCUUCAUUCAUGUUUGAGACAUCUG
........(((..((((.((((.......)))).((((((((((((-..((((...))))........))))))))))))..))))..)))((((....))))....... ( -36.00, z-score =  -2.55, R)
>anoGam1.chr2L 26876184 106 - 48795086
GUGUUAGUUGCAGUUGAUGUGUUUCGAUCAAUUCCAGCAGGAAGGG-CCUGGUUUCGAC---CACGUUGCCCUCCCGCCGUAUCGCCUUCAUUCAUUUUUUAUACAUCUG
((((..((((.(((((((........))))))).)))).((.((((-(.((((....))---))....))))).)).........................))))..... ( -25.80, z-score =  -1.25, R)
>consensus
UUUUCCGUUGAAUGUGAAGUUACGCGGUCUGGCACAGCAGGAGGGG_CCGGGCUGAGCCCUUCAUGCCCCCCUCCUGCUGAAUUACCUUCAUUCAUGUUUGAGACAUCUG
.........(((.((((.((((.......)))).(((((((((((....((((............)))))))))))))))..)))).))).((((....))))....... (-29.38 = -29.29 +  -0.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:40:31 2011