Locus 3791

Sequence ID	3L_DroMel_CAF1
Location	10,948,589 – 10,948,726
Length	137
Max. P	0.956687

overview

Window 9

Location	10,948,589 – 10,948,696
Length	107
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	82.90
Mean single sequence MFE	-35.41
Consensus MFE	-22.52
Energy contribution	-23.22
Covariance contribution	0.70
Combinations/Pair	1.19
Mean z-score	-2.16
Structure conservation index	0.64
SVM decision value	0.15
SVM RNA-class probability	0.607032
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10948589 107 + 23771897
GAACGAGGAGAUCGGAGCUACUUAACUGGCUAUGAGGAAAUUAGCCUCGUAGCCAGG-----AGCUCAGCUUUUCUGGCCUUUUGC-CCCUUUGCCACAAACUAAGCCCAUCC
....((((((....(((((......((((((((((((.......)))))))))))).-----)))))..))))))((((.......-......))))................ ( -37.62)
>DroSec_CAF1 80934 106 + 1
GAACGAGGAGAUCGGAGCUACUUAACUGGCUAUGAGGAAAUUAGCCUCGUAGCCAGG-----AGCUGAACUUUUCUGGCCUU-UUC-CCCUUUGCAACAAACUAAGCCCAUCC
....((((((.((..((((......((((((((((((.......)))))))))))).-----)))))).))))))(((.(((-...-................))).)))... ( -32.91)
>DroSim_CAF1 77458 107 + 1
GAACGAGUAGAUCGGAGCUACUUAACUGGCUAUGAGGAAAUUAGCCUCGUAGCCAGG-----AGCUGAGCUUUUCUGGCCUUUUUC-CCCUUUGCAACAAUCUAAGCCCAUCC
(((.(((((((..((((((......((((((((((((.......)))))))))))).-----.....))))))))))..))).)))-.......................... ( -32.70)
>DroEre_CAF1 81154 106 + 1
GAACGAGGAGAUCGGAGGUACUUAACUGGCUAUGAGGAAAUUAGCCUCGUAGCCAGG-----AGCUACGCUUUUCUGGCCUU-UCC-CCCUUUGCACCAAGCGAAGUCCAUCC
....(..(((..(((((........((((((((((((.......))))))))))))(-----(((...)))))))))..)))-..)-..((((((.....))))))....... ( -38.60)
>DroYak_CAF1 82756 107 + 1
GAACGAGGAGAUCGCUGGUACUUAACUGGCUAUGAGGAAAUUAGCCUCGUGGCCAGG-----AGCUAAGCUUUUCUGGCCUU-UUCCCCUUUUGCACCCAGCUAAGACCAUCC
......(((((..((..(.......((((((((((((.......))))))))))))(-----(((...))))..)..))..)-)))).(((..((.....)).)))....... ( -35.80)
>DroAna_CAF1 75667 102 + 1
GGAGGAGG----CGGAGAUAGAU-GCUGGCCAUGAGGAAAUUAGCCUCUUAGCCAAGAACAGAGCUUGGCUUUUCUGGCCUGUUAC-CGCUUC-----AUACUGAGCUAAUCC
....((((----(((.(((((..-((..(....((((.......))))..(((((((.......)))))))...)..))))))).)-))))))-----............... ( -34.80)
>consensus
GAACGAGGAGAUCGGAGCUACUUAACUGGCUAUGAGGAAAUUAGCCUCGUAGCCAGG_____AGCUAAGCUUUUCUGGCCUU_UUC_CCCUUUGCAACAAACUAAGCCCAUCC
...(((((.................((((((((((((.......)))))))))))).......((((........))))..........)))))................... (-22.52 = -23.22 +   0.70)

alignment

secondary structure

dotplot

Window 0

Location	10,948,589 – 10,948,696
Length	107
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	82.90
Mean single sequence MFE	-34.95
Consensus MFE	-22.85
Energy contribution	-23.75
Covariance contribution	0.89
Combinations/Pair	1.27
Mean z-score	-1.71
Structure conservation index	0.65
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10948589 107 - 23771897
GGAUGGGCUUAGUUUGUGGCAAAGGG-GCAAAAGGCCAGAAAAGCUGAGCU-----CCUGGCUACGAGGCUAAUUUCCUCAUAGCCAGUUAAGUAGCUCCGAUCUCCUCGUUC
(((.(((((((((((.((((......-.......))))...))))))))))-----)(((((((.((((.......)))).))))))).........)))............. ( -38.22)
>DroSec_CAF1 80934 106 - 1
GGAUGGGCUUAGUUUGUUGCAAAGGG-GAA-AAGGCCAGAAAAGUUCAGCU-----CCUGGCUACGAGGCUAAUUUCCUCAUAGCCAGUUAAGUAGCUCCGAUCUCCUCGUUC
((((((((((..(((.((....)).)-)).-.))))).....((.((((((-----((((((((.((((.......)))).)))))))....).))))..)).))...))))) ( -28.90)
>DroSim_CAF1 77458 107 - 1
GGAUGGGCUUAGAUUGUUGCAAAGGG-GAAAAAGGCCAGAAAAGCUCAGCU-----CCUGGCUACGAGGCUAAUUUCCUCAUAGCCAGUUAAGUAGCUCCGAUCUACUCGUUC
(((((((..(((((((..((..((((-(.....(((.......)))...))-----)))(((((.((((.......)))).))))).........))..)))))))))))))) ( -36.40)
>DroEre_CAF1 81154 106 - 1
GGAUGGACUUCGCUUGGUGCAAAGGG-GGA-AAGGCCAGAAAAGCGUAGCU-----CCUGGCUACGAGGCUAAUUUCCUCAUAGCCAGUUAAGUACCUCCGAUCUCCUCGUUC
.((.(((..(((...(((((...(((-((.-.(.((.......)).)..))-----)))(((((.((((.......)))).)))))......)))))..)))..))))).... ( -37.60)
>DroYak_CAF1 82756 107 - 1
GGAUGGUCUUAGCUGGGUGCAAAAGGGGAA-AAGGCCAGAAAAGCUUAGCU-----CCUGGCCACGAGGCUAAUUUCCUCAUAGCCAGUUAAGUACCAGCGAUCUCCUCGUUC
...(((((((((((((.((...........-..((((((...(((...)))-----.))))))..((((.......)))).)).))))))))).))))((((.....)))).. ( -38.20)
>DroAna_CAF1 75667 102 - 1
GGAUUAGCUCAGUAU-----GAAGCG-GUAACAGGCCAGAAAAGCCAAGCUCUGUUCUUGGCUAAGAGGCUAAUUUCCUCAUGGCCAGC-AUCUAUCUCCG----CCUCCUCC
(((...((..((...-----((.(((-....).(((((....(((((((.......)))))))..((((.......)))).))))).))-.))...))..)----).)))... ( -30.40)
>consensus
GGAUGGGCUUAGUUUGUUGCAAAGGG_GAA_AAGGCCAGAAAAGCUCAGCU_____CCUGGCUACGAGGCUAAUUUCCUCAUAGCCAGUUAAGUAGCUCCGAUCUCCUCGUUC
(((((((........(((((.............(((.......)))...........(((((((.((((.......)))).)))))))....))))).........))))))) (-22.85 = -23.75 +   0.89)

alignment

secondary structure

dotplot

Window 1

Location	10,948,629 – 10,948,726
Length	97
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	78.89
Mean single sequence MFE	-27.69
Consensus MFE	-19.46
Energy contribution	-20.27
Covariance contribution	0.81
Combinations/Pair	1.14
Mean z-score	-2.30
Structure conservation index	0.70
SVM decision value	1.47
SVM RNA-class probability	0.956687
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10948629 97 + 23771897
UUAGCCUCGUAGCCAGG-----AGCUCAGCUUUUCUGGCCUUUUGC-CCCUUUGCCACAAACUAAGCCCAUCCUUAGAUGGGAAAACC---AACACAGAGAGCUAU
.(((((((((.((.(((-----.((...(((.....))).....))-.)))..)).))........((((((....))))))......---......))).)))). ( -27.40)
>DroSec_CAF1 80974 96 + 1
UUAGCCUCGUAGCCAGG-----AGCUGAACUUUUCUGGCCUU-UUC-CCCUUUGCAACAAACUAAGCCCAUCCUUAGAUGGGAAAACC---AACACAGAGAGCUAU
.(((((((...((((((-----((.......)))))))).((-(((-((.((((...))))(((((......)))))..)))))))..---......))).)))). ( -27.60)
>DroSim_CAF1 77498 97 + 1
UUAGCCUCGUAGCCAGG-----AGCUGAGCUUUUCUGGCCUUUUUC-CCCUUUGCAACAAUCUAAGCCCAUCCUUAGAUGGGAAAACC---AACACAGAGAGCUAU
.(((((((...((((((-----(((...))))..)))))..(((((-((..........(((((((......))))))))))))))..---......))).)))). ( -29.80)
>DroEre_CAF1 81194 96 + 1
UUAGCCUCGUAGCCAGG-----AGCUACGCUUUUCUGGCCUU-UCC-CCCUUUGCACCAAGCGAAGUCCAUCCUUAGAUGGUAAAACC---CACACAGAGAGUUAA
.(((((((...((((((-----(((...))))..)))))...-...-..((((((.....)))))).(((((....))))).......---......))).)))). ( -26.40)
>DroYak_CAF1 82796 97 + 1
UUAGCCUCGUGGCCAGG-----AGCUAAGCUUUUCUGGCCUU-UUCCCCUUUUGCACCCAGCUAAGACCAUCCUUAGAUGGUUUGCCC---GACACAGAGAGUUAA
.(((((((..(((((((-----(((...))))..))))))..-..........(((.(((.(((((......))))).)))..)))..---......))).)))). ( -29.50)
>DroAna_CAF1 75702 96 + 1
UUAGCCUCUUAGCCAAGAACAGAGCUUGGCUUUUCUGGCCUGUUAC-CGCUUC-----AUACUGAGCUAAUCCUUGGAUGGGCUUCCUCAAAACACUGCGAG----
...(((....(((((((.......))))))).....))).......-(((...-----....((((..(..((......))..)..)))).......)))..---- ( -25.44)
>consensus
UUAGCCUCGUAGCCAGG_____AGCUAAGCUUUUCUGGCCUU_UUC_CCCUUUGCAACAAACUAAGCCCAUCCUUAGAUGGGAAAACC___AACACAGAGAGCUAU
.(((((((...((((((.....(((...)))..))))))...........................((((((....))))))...............))).)))). (-19.46 = -20.27 +   0.81)

alignment

secondary structure

dotplot

Window 2

Location	10,948,629 – 10,948,726
Length	97
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	78.89
Mean single sequence MFE	-30.35
Consensus MFE	-19.64
Energy contribution	-19.75
Covariance contribution	0.11
Combinations/Pair	1.25
Mean z-score	-1.57
Structure conservation index	0.65
SVM decision value	0.46
SVM RNA-class probability	0.744721
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10948629 97 - 23771897
AUAGCUCUCUGUGUU---GGUUUUCCCAUCUAAGGAUGGGCUUAGUUUGUGGCAAAGGG-GCAAAAGGCCAGAAAAGCUGAGCU-----CCUGGCUACGAGGCUAA
.((((.(((......---......((((((....))))))........(((((..((((-((....(((.......)))..)))-----))).)))))))))))). ( -35.50)
>DroSec_CAF1 80974 96 - 1
AUAGCUCUCUGUGUU---GGUUUUCCCAUCUAAGGAUGGGCUUAGUUUGUUGCAAAGGG-GAA-AAGGCCAGAAAAGUUCAGCU-----CCUGGCUACGAGGCUAA
.((((.(((......---..(((((((..(((((......)))))((((...)))).))-)))-))((((((...((.....))-----.))))))..))))))). ( -28.20)
>DroSim_CAF1 77498 97 - 1
AUAGCUCUCUGUGUU---GGUUUUCCCAUCUAAGGAUGGGCUUAGAUUGUUGCAAAGGG-GAAAAAGGCCAGAAAAGCUCAGCU-----CCUGGCUACGAGGCUAA
.((((.(((......---..((((((((((((((......)))))))..........))-))))).((((((...(((...)))-----.))))))..))))))). ( -30.90)
>DroEre_CAF1 81194 96 - 1
UUAACUCUCUGUGUG---GGUUUUACCAUCUAAGGAUGGACUUCGCUUGGUGCAAAGGG-GGA-AAGGCCAGAAAAGCGUAGCU-----CCUGGCUACGAGGCUAA
....((((((.(((.---.......(((((....)))))(((......)))))).))))-)).-..((((.......((((((.-----....)))))).)))).. ( -29.30)
>DroYak_CAF1 82796 97 - 1
UUAACUCUCUGUGUC---GGGCAAACCAUCUAAGGAUGGUCUUAGCUGGGUGCAAAAGGGGAA-AAGGCCAGAAAAGCUUAGCU-----CCUGGCCACGAGGCUAA
....((((.((..((---.(((((((((((....)))))).)).))).))..))..))))...-..((((((...(((...)))-----.)))))).......... ( -33.40)
>DroAna_CAF1 75702 96 - 1
----CUCGCAGUGUUUUGAGGAAGCCCAUCCAAGGAUUAGCUCAGUAU-----GAAGCG-GUAACAGGCCAGAAAAGCCAAGCUCUGUUCUUGGCUAAGAGGCUAA
----.((((..(((.(((((.((..((......)).))..))))).))-----)..)))-).....((((.....(((((((.......)))))))....)))).. ( -24.80)
>consensus
AUAGCUCUCUGUGUU___GGUUUUCCCAUCUAAGGAUGGGCUUAGUUUGUUGCAAAGGG_GAA_AAGGCCAGAAAAGCUCAGCU_____CCUGGCUACGAGGCUAA
....((((((.(((..........((((((....))))))...........))).)))........((((((...(((...)))......))))))..)))..... (-19.64 = -19.75 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:45 2006