Locus 4883

Sequence ID	dm3.chr2R
Location	16,196,972 – 16,197,077
Length	105
Max. P	0.999866

overview

Window 1

Location	16,196,972 – 16,197,077
Length	105
Sequences	11
Columns	112
Reading direction	forward
Mean pairwise identity	68.91
Shannon entropy	0.67858
G+C content	0.48998
Mean single sequence MFE	-25.03
Consensus MFE	-13.18
Energy contribution	-13.50
Covariance contribution	0.32
Combinations/Pair	1.12
Mean z-score	-1.21
Structure conservation index	0.53
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.82
SVM RNA-class probability	0.969606
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16196972 105 + 21146708
UUCGGAACUCUAAGUUGCAGCUGCGUUGUCAAUGUCUU----UUAUCGCCUGUUCCUCCAUCUUCGUUUCCGUUUC---CGUAGCAGCGACAUCCUUAGGCUCCUUUAACUG
...(((.(.(((((((((.((((((.((..((((....----......................))))..))....---)))))).)))))....))))).)))........ ( -19.27, z-score =  -0.67, R)
>droGri2.scaffold_15245 13672676 105 + 18325388
UUCAAAUGUCUAAGGUGCAGCUGCUUCGUUAGAUUGCU--CCUUGCU-----GUUGUCCUUGUUGGUGGUUGGCGGCGUUGCUGCAGCGGCAUUCUUAGGCUGCUUUAACUG
.......(((((((((((.(((((.((....))..((.--...((((-----((((.((........)).))))))))..)).))))).))).))))))))........... ( -34.60, z-score =  -0.96, R)
>droVir3.scaffold_12875 9543649 88 - 20611582
--UCCUCGUCUAAGUUGCAGCUGUUUCGUCGUUGUGCU--CCUCG-------AUUGCCUUCAUGGACAAC-------------GCAGCGGCAUUCUUAGGCUGCUUUAACUG
--..........((((((((((.....(((((((((.(--((..(-------(......))..)))...)-------------)))))))).......))))))...)))). ( -26.90, z-score =  -2.01, R)
>droWil1.scaffold_181009 1344694 111 + 3585778
UUUGGAACUCUAAGUUGCAGCUGCUUCGUCGAGAUGAUGAUGUUGUUGAUUGUUGGUCAACUGGGAAAUCUCUUCCGU-UUGGGCAGCAACAUUCUUAGGCUCCUUUAACUG
...(((.(.(((((.((((((.((.(((((.....))))).)).)))).((((((.((((.(((((......))))).-)))).))))))))..)))))).)))........ ( -32.90, z-score =  -1.79, R)
>droPer1.super_4 5171729 87 + 7162766
UUUGGAACACUAAGUUGCAGCUGCUGUGUCAGGGUCUU----UC--------------------UCCAUCUCUUCGGGAC-UUGCAGCGACAUCCUUAGGCUCCUUUAACCG
...(((.(.(((((.((..(((((...(((.(((....----..--------------------)))....(....))))-..)))))..))..)))))).)))........ ( -25.70, z-score =  -1.58, R)
>dp4.chr3 9854268 87 + 19779522
UUUGGAACUCUAAGUUGCAGCUGCUGUGUCAGGGUCUU----UC--------------------CCCAUCUCUUCGGGAC-UUGCAGCGACAUCCUUAGGCUCCUUUAACCG
...(((.(.(((((.((..(((((...(((.(((....----..--------------------)))....(....))))-..)))))..))..)))))).)))........ ( -28.20, z-score =  -2.24, R)
>droAna3.scaffold_13266 16798407 108 - 19884421
UUCGGAACUCUAAGUUGCAGCUGCAUUGUCAGUGUCUU----UUAACUCCCGCUUAGUGAUCGUCUCGUCCCCUCCGGACGUUGCAGCGACAUCCUUAGGCUCCUUUAACUG
...(((.(.(((((.((..((((((..((((.((....----............)).)))).....(((((.....))))).))))))..))..)))))).)))........ ( -28.29, z-score =  -1.69, R)
>droEre2.scaffold_4845 10348185 105 + 22589142
UUCGGAACUCUAAGUUGCAGCUGCGUUGUCAGUGUCUU----UUAUCGCCUGUUUCUCCAUCUUCGUUUCCGUUUC---CGUAGCAGCGACAUCCUUAGGCUCCUUUAACUG
...(((.(.(((((((((.((((((....(((.((...----.....)))))............((....))....---)))))).)))))....))))).)))........ ( -20.60, z-score =  -0.80, R)
>droYak2.chr2R 8133221 105 - 21139217
UUCGGAACUCUAAGUUGCAGCUGCGUUGUCACUGUCUU----UUAUCGCCUGUUUCUCCAUCUUCGUUUCCGUUUC---CGUAGCAGCGACAUCCUUAGGCUCCUUUAACUG
...(((.(.(((((.((..((((((..(..((.((...----.....))..))..)..)...........((....---))..)))))..))..)))))).)))........ ( -17.70, z-score =   0.04, R)
>droSec1.super_1 13762826 105 + 14215200
UUCGGAACUCUAAGUUGCAGCUGCGUUGUCAGUGUCUU----UUAUCGCCUGUUCCUCCAUCUUCGUUUCCGUUUC---CGUAGCAGCGACAUCCUUAGGCUCCUUUAACUG
...(((.(.(((((((((.((((((....(((.((...----.....)))))............((....))....---)))))).)))))....))))).)))........ ( -20.60, z-score =  -0.81, R)
>droSim1.chr2R 14855807 105 + 19596830
UUCGGAACUCUAAGUUGCAGCUGCGUUGUCAGUGUCUU----UUAUCGCCUGUUCCUCCAUCUUCGUUUCCGUUUC---CGUAGCAGCGACAUCCUUAGGCUCCUUUAACUG
...(((.(.(((((((((.((((((....(((.((...----.....)))))............((....))....---)))))).)))))....))))).)))........ ( -20.60, z-score =  -0.81, R)
>consensus
UUCGGAACUCUAAGUUGCAGCUGCGUUGUCAGUGUCUU____UUAUCGCCUGUUUCUCCAUCUUCGUUUCCGUUUC___CGUAGCAGCGACAUCCUUAGGCUCCUUUAACUG
...(((.(.(((((.((..(((((...........................................................)))))..))..)))))).)))........ (-13.18 = -13.50 +   0.32)

alignment

secondary structure

dotplot

Window 2

Location	16,196,972 – 16,197,077
Length	105
Sequences	11
Columns	112
Reading direction	reverse
Mean pairwise identity	68.91
Shannon entropy	0.67858
G+C content	0.48998
Mean single sequence MFE	-30.18
Consensus MFE	-18.90
Energy contribution	-19.25
Covariance contribution	0.36
Combinations/Pair	1.17
Mean z-score	-2.81
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	4.63
SVM RNA-class probability	0.999866
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16196972 105 - 21146708
CAGUUAAAGGAGCCUAAGGAUGUCGCUGCUACG---GAAACGGAAACGAAGAUGGAGGAACAGGCGAUAA----AAGACAUUGACAACGCAGCUGCAACUUAGAGUUCCGAA
........((((((((((..(((.(((((..((---....))....((....((......))..))....----..............))))).))).))))).)))))... ( -31.80, z-score =  -3.63, R)
>droGri2.scaffold_15245 13672676 105 - 18325388
CAGUUAAAGCAGCCUAAGAAUGCCGCUGCAGCAACGCCGCCAACCACCAACAAGGACAAC-----AGCAAGG--AGCAAUCUAACGAAGCAGCUGCACCUUAGACAUUUGAA
...(((((...(.(((((..(((.(((((.((..(...((......((.....)).....-----.))..).--.))..((....)).))))).))).))))).).))))). ( -23.70, z-score =  -0.72, R)
>droVir3.scaffold_12875 9543649 88 + 20611582
CAGUUAAAGCAGCCUAAGAAUGCCGCUGC-------------GUUGUCCAUGAAGGCAAU-------CGAGG--AGCACAACGACGAAACAGCUGCAACUUAGACGAGGA--
...........(.(((((..(((.((((.-------------.(((((..((...((...-------.....--.)).))..)))))..)))).))).))))).).....-- ( -20.30, z-score =   0.22, R)
>droWil1.scaffold_181009 1344694 111 - 3585778
CAGUUAAAGGAGCCUAAGAAUGUUGCUGCCCAA-ACGGAAGAGAUUUCCCAGUUGACCAACAAUCAACAACAUCAUCAUCUCGACGAAGCAGCUGCAACUUAGAGUUCCAAA
........((((((((((..(((.(((((((..-..))..(((((......(((((.......))))).........)))))......))))).))).))))).)))))... ( -31.46, z-score =  -3.79, R)
>droPer1.super_4 5171729 87 - 7162766
CGGUUAAAGGAGCCUAAGGAUGUCGCUGCAA-GUCCCGAAGAGAUGGA--------------------GA----AAGACCCUGACACAGCAGCUGCAACUUAGUGUUCCAAA
........((((((((((..(((.(((((..-((((((......)))(--------------------(.----......)))))...))))).))).))))).)))))... ( -26.60, z-score =  -1.91, R)
>dp4.chr3 9854268 87 - 19779522
CGGUUAAAGGAGCCUAAGGAUGUCGCUGCAA-GUCCCGAAGAGAUGGG--------------------GA----AAGACCCUGACACAGCAGCUGCAACUUAGAGUUCCAAA
........((((((((((..(((.(((((..-(((.......)))(((--------------------..----....))).......))))).))).))))).)))))... ( -30.80, z-score =  -2.74, R)
>droAna3.scaffold_13266 16798407 108 + 19884421
CAGUUAAAGGAGCCUAAGGAUGUCGCUGCAACGUCCGGAGGGGACGAGACGAUCACUAAGCGGGAGUUAA----AAGACACUGACAAUGCAGCUGCAACUUAGAGUUCCGAA
........((((((((((..(((.((((((.(((((.....))))).............((((..(((..----..))).))).)..)))))).))).))))).)))))... ( -37.90, z-score =  -3.32, R)
>droEre2.scaffold_4845 10348185 105 - 22589142
CAGUUAAAGGAGCCUAAGGAUGUCGCUGCUACG---GAAACGGAAACGAAGAUGGAGAAACAGGCGAUAA----AAGACACUGACAACGCAGCUGCAACUUAGAGUUCCGAA
........((((((((((..(((.(((((..((---....))....((....((......))..))....----..............))))).))).))))).)))))... ( -31.80, z-score =  -3.71, R)
>droYak2.chr2R 8133221 105 + 21139217
CAGUUAAAGGAGCCUAAGGAUGUCGCUGCUACG---GAAACGGAAACGAAGAUGGAGAAACAGGCGAUAA----AAGACAGUGACAACGCAGCUGCAACUUAGAGUUCCGAA
........((((((((((..((((((((((.((---....))....((....((......))..))....----.)).))))))))..((....))..))))).)))))... ( -34.00, z-score =  -4.34, R)
>droSec1.super_1 13762826 105 - 14215200
CAGUUAAAGGAGCCUAAGGAUGUCGCUGCUACG---GAAACGGAAACGAAGAUGGAGGAACAGGCGAUAA----AAGACACUGACAACGCAGCUGCAACUUAGAGUUCCGAA
........((((((((((..(((.(((((..((---....))....((....((......))..))....----..............))))).))).))))).)))))... ( -31.80, z-score =  -3.47, R)
>droSim1.chr2R 14855807 105 - 19596830
CAGUUAAAGGAGCCUAAGGAUGUCGCUGCUACG---GAAACGGAAACGAAGAUGGAGGAACAGGCGAUAA----AAGACACUGACAACGCAGCUGCAACUUAGAGUUCCGAA
........((((((((((..(((.(((((..((---....))....((....((......))..))....----..............))))).))).))))).)))))... ( -31.80, z-score =  -3.47, R)
>consensus
CAGUUAAAGGAGCCUAAGGAUGUCGCUGCUACG___GAAACGGAAACGAAGAUGGAGAAACAGGCGAUAA____AAGACACUGACAAAGCAGCUGCAACUUAGAGUUCCGAA
........((((((((((..(((.(((((...........................................................))))).))).))))).)))))... (-18.90 = -19.25 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:37:58 2011