Locus 7521

Sequence ID	2L_DroMel_CAF1
Location	20,863,241 – 20,863,340
Length	99
Max. P	0.786089

overview

Window 7

Location	20,863,241 – 20,863,340
Length	99
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	79.54
Mean single sequence MFE	-26.02
Consensus MFE	-16.99
Energy contribution	-17.18
Covariance contribution	0.20
Combinations/Pair	1.10
Mean z-score	-1.70
Structure conservation index	0.65
SVM decision value	0.57
SVM RNA-class probability	0.786089
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20863241 99 + 22407834
UACAAGCUUGACUUUUCAGAUUGUGUAUGGGAUAAACGCCCAUCGCGAUUGCUCUAUGACCGGGCGAUUUUUCACCCUACAGU-UUAUACAUAAUCAUG-----A
...............((((((((((((((((((((.(((.....))).))).)))......(((.((....)).)))......-.))))))))))).))-----) ( -23.90)
>DroVir_CAF1 59864 88 + 1
UACAGACUUGACUUUUCAGAUUGUGUAUGGGAUAGACACCCAUGGCGAUGGCUCUAUGACCGGGCGACUUUUCGCCCUGUAUACA----CA-------------A
.......((((....)))).((((((((((.(((((...((((....)))).)))))..))((((((....))))))...)))))----))-------------) ( -27.00)
>DroPse_CAF1 50823 90 + 1
UACAGACUUGACUUUUCAGAUUGUGUAUGGGAUAGACGCCCAUCGCGAUAGCUCUAUGACCGGGCGACUUUUCGCCCUAUAUA-UGGUAA--------------A
.......((((....))))((((((.(((((.......))))))))))).(((.((((...((((((....))))))..))))-.)))..--------------. ( -25.40)
>DroGri_CAF1 41136 88 + 1
UACAGACUUGACUUUUGAGAUUGUGUAUGGGAUAGACGCCCAUGGCGAUGGCUCUAUGACCGGGCGACUUUUCGCCCUGUUUAGU----GG-------------U
.....(((.(((....((((((((.((((((.......)))))))))))..))).......((((((....)))))).))).)))----..-------------. ( -25.80)
>DroWil_CAF1 64293 103 + 1
CACAAACUUUACUUUUCAGAUUAUGUAUGGGAUAAACGCCCAUGGCAAUGGCUCUAUGACCAGGCGACUUUUCGCCCUAUAU--AUAUAUAUAGUAUUUGGUCAA
.................((((((((((((((.......))))).)).)))).))).(((((((((((....)))))((((((--....))))))....)))))). ( -26.80)
>DroPer_CAF1 53672 90 + 1
UACAGACUUGACUUUUCAGAUUGUGUAUGGGAUAGACGCCCAUCGCGAUAGCUCUAUGACCGGGCGACUUUUCGCCCUACAUA-UGGUAA--------------A
.......((((....))))((((((.(((((.......))))))))))).(((.((((...((((((....))))))..))))-.)))..--------------. ( -27.20)
>consensus
UACAGACUUGACUUUUCAGAUUGUGUAUGGGAUAGACGCCCAUCGCGAUGGCUCUAUGACCGGGCGACUUUUCGCCCUAUAUA_U__UAAA_____________A
.................((((((((((((((.......))))).)).)))).)))......((((((....))))))............................ (-16.99 = -17.18 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	20,863,241 – 20,863,340
Length	99
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	79.54
Mean single sequence MFE	-23.65
Consensus MFE	-18.55
Energy contribution	-18.22
Covariance contribution	-0.33
Combinations/Pair	1.17
Mean z-score	-1.33
Structure conservation index	0.78
SVM decision value	0.50
SVM RNA-class probability	0.760777
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20863241 99 - 22407834
U-----CAUGAUUAUGUAUAA-ACUGUAGGGUGAAAAAUCGCCCGGUCAUAGAGCAAUCGCGAUGGGCGUUUAUCCCAUACACAAUCUGAAAAGUCAAGCUUGUA
(-----((.((((.(((((((-((....((((((....))))))(.((((.((....))...)))).)))))).....)))).))))))).(((.....)))... ( -24.10)
>DroVir_CAF1 59864 88 - 1
U-------------UG----UGUAUACAGGGCGAAAAGUCGCCCGGUCAUAGAGCCAUCGCCAUGGGUGUCUAUCCCAUACACAAUCUGAAAAGUCAAGUCUGUA
(-------------((----(((((...((((((....))))))((..(((((..((((......))))))))).)))))))))).((....))........... ( -26.80)
>DroPse_CAF1 50823 90 - 1
U--------------UUACCA-UAUAUAGGGCGAAAAGUCGCCCGGUCAUAGAGCUAUCGCGAUGGGCGUCUAUCCCAUACACAAUCUGAAAAGUCAAGUCUGUA
.--------------......-......((((((....))))))....(((((((....)).(((((.......)))))....................))))). ( -20.80)
>DroGri_CAF1 41136 88 - 1
A-------------CC----ACUAAACAGGGCGAAAAGUCGCCCGGUCAUAGAGCCAUCGCCAUGGGCGUCUAUCCCAUACACAAUCUCAAAAGUCAAGUCUGUA
.-------------..----(((..((.((((((....))))))((..((((((((.........))).))))).))................))..)))..... ( -22.30)
>DroWil_CAF1 64293 103 - 1
UUGACCAAAUACUAUAUAUAU--AUAUAGGGCGAAAAGUCGCCUGGUCAUAGAGCCAUUGCCAUGGGCGUUUAUCCCAUACAUAAUCUGAAAAGUAAAGUUUGUG
.((((((....((((((....--))))))(((((....)))))))))))((((.....((..(((((.......))))).))...))))................ ( -26.40)
>DroPer_CAF1 53672 90 - 1
U--------------UUACCA-UAUGUAGGGCGAAAAGUCGCCCGGUCAUAGAGCUAUCGCGAUGGGCGUCUAUCCCAUACACAAUCUGAAAAGUCAAGUCUGUA
.--------------......-((((..((((((....))))))...))))..((....)).(((((.......)))))..(((..((((....)).))..))). ( -21.50)
>consensus
U_____________UGUA__A_UAUAUAGGGCGAAAAGUCGCCCGGUCAUAGAGCCAUCGCCAUGGGCGUCUAUCCCAUACACAAUCUGAAAAGUCAAGUCUGUA
............................((((((....))))))....(((((((....)).(((((.......)))))....................))))). (-18.55 = -18.22 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:51 2006