Locus 4099

Sequence ID	2R_DroMel_CAF1
Location	13,491,669 – 13,491,831
Length	162
Max. P	0.746617

overview

Window 4

Location	13,491,669 – 13,491,768
Length	99
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	81.43
Mean single sequence MFE	-33.13
Consensus MFE	-22.83
Energy contribution	-22.22
Covariance contribution	-0.61
Combinations/Pair	1.29
Mean z-score	-1.82
Structure conservation index	0.69
SVM decision value	0.46
SVM RNA-class probability	0.746617
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13491669 99 - 20766785
CGGCCGCAAGCAUGUGGAUUAAAAAUGCUCGCGCACGGUGCGCCA----------GAU----CCAGCCAUUUGGCAGGCAAACUGCCAUUAA-AGCCAGGCUAUAAACACGGCG-
..(((((.(((((...........))))).))((..(((..((((----------(((----......))))))).(((.....))).....-.)))..)).........))).- ( -32.90)
>DroPse_CAF1 38068 113 - 1
CGGCCGCAAGCAUGUGGAUUAAAAAUGCCCGCACACGACACGACGACGGCGACGGCAACACAGCGGCCAUUUGGCAGGCAAACUGCCAUUAA-AGCCAGGCCAUAAACAUACCA-
.((((....((.((((.........(((((((...((......))...)))..)))).))))))(((....((((((.....))))))....-.))).))))............- ( -38.80)
>DroSec_CAF1 40244 99 - 1
CGGCCGCAAGCAUGUGGAUUAAAAAUGCCCGCGCACGGUGCGCCA----------GAU----CCAGUCAUUUGGCAGGCAAACUGCCAUUAA-AGCCAGGCCAUAAACACGGCG-
.((((....((...((((((.....((((((....))).)))...----------)))----)))......((((((.....))))))....-.))..))))............- ( -32.40)
>DroYak_CAF1 42197 100 - 1
CGGCCGCAAGCAUGUGGAUUAAAAAUGCCCGCGCACGGUGCUGCA----------GAU----CCAGCCAUUUGGCAGGCAAACUGCCAUUAA-AGCCAGGCCAUAAACACGGCCA
.((((....)....((((((......(((((....))).))....----------)))----))))))...((((((.....))))))....-.....((((........)))). ( -34.60)
>DroAna_CAF1 42053 100 - 1
CGGCCGCAAGCAUGUGGAUUAAAAAUGCCCGCGCACGGUGUACGG----------CAG----CCAACCAUUUGGCAGGCAAACUGCUAUUAAAAGCCAGCUCAUAAACACAGCG-
.........((.((((.........((((((....))).))).((----------(.(----((((....))))).(((.....))).......)))..........)))))).- ( -26.10)
>DroPer_CAF1 46116 113 - 1
CGGCCGCAAGCAUGUGGAUUAAAAAUGCCCGCACACGACACGACGACGACGACGGCAACACAGCGGCCAUUUGGCAGGCAAACUGCCAUUAA-AGCCAGGCCAUAAACAUACCA-
.((((....((.((((.........((((((....((......))....))..)))).))))))(((....((((((.....))))))....-.))).))))............- ( -34.00)
>consensus
CGGCCGCAAGCAUGUGGAUUAAAAAUGCCCGCGCACGGUGCGCCA__________CAU____CCAGCCAUUUGGCAGGCAAACUGCCAUUAA_AGCCAGGCCAUAAACACAGCG_
.((((....((.(((((...........)))))......................................((((((.....))))))......))..))))............. (-22.83 = -22.22 +  -0.61)

alignment

secondary structure

dotplot

Window 5

Location	13,491,704 – 13,491,808
Length	104
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	77.82
Mean single sequence MFE	-25.90
Consensus MFE	-16.76
Energy contribution	-15.93
Covariance contribution	-0.83
Combinations/Pair	1.33
Mean z-score	-1.30
Structure conservation index	0.65
SVM decision value	0.14
SVM RNA-class probability	0.601900
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13491704 104 + 20766785
CCUGCCAAAUGGCUGG----AUC----------UGGCGCACCGUGCGCGAGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCCCUCUUAG
((.(((....))).))----...----------.(((((.....))((((((((...........)))))))).)))..(((((((....)))))))..................... ( -28.00)
>DroPse_CAF1 38103 118 + 1
CCUGCCAAAUGGCCGCUGUGUUGCCGUCGCCGUCGUCGUGUCGUGUGCGGGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCUCUGUUUU
........((((((((.......(((.(((((.(.....).)).))))))((((...........))))..))))))))(((((((....)))))))..................... ( -29.50)
>DroWil_CAF1 454 92 + 1
CAUGCCCUGUGUUUGU----AUA----------UGU----GUGUGUGUGGGUAUUUUUAAUCCACAUGCUUGCGGCUGUGUCAUUUUCAUAAAUUACUUUUAUUGUUUUU--------
((((((..((((....----)))----------)((----(.((((((((((.......)))))))))).)))))).)))..............................-------- ( -17.90)
>DroYak_CAF1 42233 104 + 1
CCUGCCAAAUGGCUGG----AUC----------UGCAGCACCGUGCGCGGGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCCCUCUUAG
...(((....))).((----(..----------.((((...((..(((((((((...........)))))))))..)).(((((((....))))))).....))))..)))....... ( -25.60)
>DroAna_CAF1 42089 104 + 1
CCUGCCAAAUGGUUGG----CUG----------CCGUACACCGUGCGCGGGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCUCUCUUAG
...(((((....))))----).(----------((((((...))))((((((((...........)))))))))))...(((((((....)))))))..................... ( -25.70)
>DroPer_CAF1 46151 118 + 1
CCUGCCAAAUGGCCGCUGUGUUGCCGUCGUCGUCGUCGUGUCGUGUGCGGGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCUCUGUUUU
........((((((((......((((.((....)).)).)).(((((.(((.........))).)))))..))))))))(((((((....)))))))..................... ( -28.70)
>consensus
CCUGCCAAAUGGCUGG____AUG__________CGUCGCACCGUGCGCGGGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCUCUCUUAG
...(((....)))............................((..(((((((((...........)))))))))..)).(((((((....)))))))..................... (-16.76 = -15.93 +  -0.83)

alignment

secondary structure

dotplot

Window 6

Location	13,491,730 – 13,491,831
Length	101
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	80.04
Mean single sequence MFE	-19.17
Consensus MFE	-16.39
Energy contribution	-16.03
Covariance contribution	-0.36
Combinations/Pair	1.11
Mean z-score	-1.16
Structure conservation index	0.86
SVM decision value	0.19
SVM RNA-class probability	0.626251
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13491730 101 + 20766785
CCGUGCGCGAGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCCCUCUUAGCCAAC---------AGAACCA----ACCACACGCCG---
.((((.((((((((...........))))))))(((...(((((((....))))))).......(........)...)))...---------.......----....))))...--- ( -19.90)
>DroPse_CAF1 38143 84 + 1
UCGUGUGCGGGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCUCUGUUUUCA------------------------------GUCG---
.((..(((((((((...........)))))))))..)).(((((((....)))))))..............(((....))------------------------------)...--- ( -15.70)
>DroEre_CAF1 40669 101 + 1
CCGUGCGCGGGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCCCUCUUAGCCAAC---------AGAGCCA----ACCACGCGCCG---
..((((((((((((...........))))))))(((...(((((((....))))))).....(((((.............)))---------)).))).----.....))))..--- ( -23.82)
>DroYak_CAF1 42259 105 + 1
CCGUGCGCGGGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCCCUCUUAGCCAAC---------AGAACCAACCAACCACACGCCG---
.((((.((((((((...........))))))))(((...(((((((....))))))).......(........)...)))...---------...............))))...--- ( -19.10)
>DroAna_CAF1 42115 113 + 1
CCGUGCGCGGGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCUCUCUUAGCAAACGCAUAUAGCAUAACCA----CACUCACUCCACAC
..((((((((((((...........)))))))).((.(((((((((....))))))).....(((((.........))))))))).....)))).....----.............. ( -20.80)
>DroPer_CAF1 46191 84 + 1
UCGUGUGCGGGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCUCUGUUUUCA------------------------------GUCG---
.((..(((((((((...........)))))))))..)).(((((((....)))))))..............(((....))------------------------------)...--- ( -15.70)
>consensus
CCGUGCGCGGGCAUUUUUAAUCCACAUGCUUGCGGCCGUGUAAUUUUCAUAAAUUACUUUUAUUGUUUUCCCUCUUAGCAAAC_________AGAACCA____ACCACACGCCG___
.((..(((((((((...........)))))))))..)).(((((((....)))))))............................................................ (-16.39 = -16.03 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:49 2006