Locus 4371

Sequence ID	X_DroMel_CAF1
Location	11,491,876 – 11,492,009
Length	133
Max. P	0.982981

overview

Window 8

Location	11,491,876 – 11,491,969
Length	93
Sequences	3
Columns	97
Reading direction	forward
Mean pairwise identity	75.00
Mean single sequence MFE	-22.47
Consensus MFE	-13.75
Energy contribution	-13.87
Covariance contribution	0.12
Combinations/Pair	1.13
Mean z-score	-1.62
Structure conservation index	0.61
SVM decision value	0.37
SVM RNA-class probability	0.707295
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11491876 93 + 22224390
AUCUGCCACGAUUUGG---CCAACUGGGCUAAGAAGCGAUUCUCAUCUCUCUCACUUUAAAUCCUUUAAAAAGGAUUGA-GUUCAGCCAGCUGAAUU
.........((((..(---(...(((((((..((((.(((....))).)).))......(((((((....))))))).)-))))))...))..)))) ( -22.20)
>DroSec_CAF1 26492 90 + 1
AUCUGCCAGGAUUUGG---CCAACUGGGCUAAGAAGCGAUUCUCCACUCACUCACUUUAAAUCCUU---AAAGGAUUGA-GUUCAGCCAGCUGAAUU
........(((.((((---((.....))))))(((....))))))(((((.((.((((((....))---)))))).)))-))((((....))))... ( -24.20)
>DroAna_CAF1 35391 82 + 1
--UUGUCAGGAUUUUGCUGCAAACUGGGCUAAGAUGCGAUUG----------GACUUAAUGUCCUU---UAAGGAUCGAGGUUCAGCCAACUGUAUU
--(((.(((.......)))))).(((((((..(((.(....(----------(((.....))))..---...).)))..)))))))........... ( -21.00)
>consensus
AUCUGCCAGGAUUUGG___CCAACUGGGCUAAGAAGCGAUUCUC__CUC_CUCACUUUAAAUCCUU___AAAGGAUUGA_GUUCAGCCAGCUGAAUU
.....((((...((((...))))))))((......))......................(((((((....)))))))...((((((....)))))). (-13.75 = -13.87 +   0.12)

alignment

secondary structure

dotplot

Window 9

Location	11,491,876 – 11,491,969
Length	93
Sequences	3
Columns	97
Reading direction	reverse
Mean pairwise identity	75.00
Mean single sequence MFE	-24.37
Consensus MFE	-15.02
Energy contribution	-15.47
Covariance contribution	0.45
Combinations/Pair	1.08
Mean z-score	-2.15
Structure conservation index	0.62
SVM decision value	1.93
SVM RNA-class probability	0.982981
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11491876 93 - 22224390
AAUUCAGCUGGCUGAAC-UCAAUCCUUUUUAAAGGAUUUAAAGUGAGAGAGAUGAGAAUCGCUUCUUAGCCCAGUUGG---CCAAAUCGUGGCAGAU
....(((((((((((..-..(((((((....)))))))..((((((............)))))).)))).)))))))(---(((.....)))).... ( -28.00)
>DroSec_CAF1 26492 90 - 1
AAUUCAGCUGGCUGAAC-UCAAUCCUUU---AAGGAUUUAAAGUGAGUGAGUGGAGAAUCGCUUCUUAGCCCAGUUGG---CCAAAUCCUGGCAGAU
....(((((((((((((-(((.((((((---((....)))))).)).)))))((((.....)))))))).)))))))(---(((.....)))).... ( -30.90)
>DroAna_CAF1 35391 82 - 1
AAUACAGUUGGCUGAACCUCGAUCCUUA---AAGGACAUUAAGUC----------CAAUCGCAUCUUAGCCCAGUUUGCAGCAAAAUCCUGACAA--
.........((((((....((((.....---..((((.....)))----------).))))....))))))(((..(........)..)))....-- ( -14.20)
>consensus
AAUUCAGCUGGCUGAAC_UCAAUCCUUU___AAGGAUUUAAAGUGAG_GAG__GAGAAUCGCUUCUUAGCCCAGUUGG___CCAAAUCCUGGCAGAU
......(((((((((.....(((((((....)))))))....((((............))))...))))))...((((...)))).....))).... (-15.02 = -15.47 +   0.45)

alignment

secondary structure

dotplot

Window 0

Location	11,491,909 – 11,492,009
Length	100
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	68.55
Mean single sequence MFE	-25.79
Consensus MFE	-15.32
Energy contribution	-15.24
Covariance contribution	-0.08
Combinations/Pair	1.24
Mean z-score	-1.47
Structure conservation index	0.59
SVM decision value	0.39
SVM RNA-class probability	0.716676
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11491909 100 + 22224390
---------------CGAUUC---UCAUCUCUCUCACUUUAAAUCCUUUAAAAAGGAUUGA--GUUCAGCCAGCUGAAUUGGGGCUAAGGCCUUGCCACGAUUCGCUGCACAUGCUAAAA
---------------.((..(---(((...............((((((....)))))))))--).))(((((((.((((((.(((.........))).)))))))))).....))).... ( -24.36)
>DroPse_CAF1 38618 112 + 1
AUGUUUCUGUUGCCUCUCUCUCCCCCCCUUCUCUCUCUUUAAAUCCUU---UAAGGAUUGAGAGCUCAUUCAGCUGGAUUGGGGCUAAGGCCUUGCCACGUUUCGUUGCACAC-----AG
......((((.((((......((((.((.((((..(((((((.....)---))))))..))))(((.....))).))...))))...))))..(((.(((...))).))).))-----)) ( -28.20)
>DroSec_CAF1 26525 97 + 1
---------------CGAUUC---UCCACUCACUCACUUUAAAUCCUU---AAAGGAUUGA--GUUCAGCCAGCUGAAUUGGGGCUAAGGCCUCGCCACGUUUCGCUGCACAUGCUAAAA
---------------......---...(((((.((.((((((....))---)))))).)))--))..(((((((.((((((((((....))))))....)))).)))).....))).... ( -25.30)
>DroAna_CAF1 35425 79 + 1
---------------CGAUUG-------------GACUUAAUGUCCUU---UAAGGAUCGAG-GUUCAGCCAACUGUAUUGGGGCUAAGGCCUUGCCACAAUUCGUUGCAC---------
---------------....((-------------(((((...((((..---...))))..))-)))))((.(((...((((.(((.........))).))))..)))))..--------- ( -21.30)
>DroPer_CAF1 40812 109 + 1
AUGUUUCUGUUGCCUCUCUUC---CCCCCUCUCGCUCUUUAAAUCCUU---UAAGGAUUGAGAGCUCAUUCAGCUGGAUUGGGGCUAAGGCCUUGCCACGUUUCGUUGCACAC-----AG
......((((.((((.....(---(((......((((((..(((((..---...)))))))))))..((((....)))).))))...))))..(((.(((...))).))).))-----)) ( -29.80)
>consensus
_______________CGAUUC___CCCCCUCUCUCACUUUAAAUCCUU___UAAGGAUUGAG_GUUCAGCCAGCUGAAUUGGGGCUAAGGCCUUGCCACGUUUCGUUGCACAC_____AA
.........................................(((((((....)))))))...........((((.((((((((((....)))...))).)))).))))............ (-15.32 = -15.24 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:20 2006