Locus 2022

Sequence ID	2L_DroMel_CAF1
Location	5,478,715 – 5,478,898
Length	183
Max. P	0.835717

overview

Window 4

Location	5,478,715 – 5,478,827
Length	112
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	79.77
Mean single sequence MFE	-36.88
Consensus MFE	-22.95
Energy contribution	-23.48
Covariance contribution	0.53
Combinations/Pair	1.04
Mean z-score	-1.87
Structure conservation index	0.62
SVM decision value	0.58
SVM RNA-class probability	0.789406
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5478715 112 + 22407834
UCGGUGGCGGU---GGUAUCUGAAA--UAUACGAG-AGUCCCCGGUUGGCAGUUACCGGUUACCGGUUGUGGGUCCAAGGCAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAA
((((.(((..(---.((((......--.)))).).-.))).))))((((((((((((((...))))).((((((.........))))))(((((....))))).....))))))))). ( -36.70)
>DroPse_CAF1 116694 98 + 1
------------------CAUGGUAUG-GUCCGUUUGGUCCCCGGUCGCCAGUUACCGGUUACCGGG-GUCGGUCCCAGGUAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAA
------------------..(((((.(-(.(((......(((((((.(((.......))).))))))-).))).))..((.....))(((((((....)))))))......))))).. ( -37.00)
>DroEre_CAF1 99081 108 + 1
UCGGUGG------CGGUGUCUGAAA--UAUACGAG-AGUCCCCGGUUGGCAGUUACCGGUUACCGGUUGUGGGUCCA-GGCAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAA
....(((------(((((((((...--..(((((.-.((..(((((........)))))..))...)))))....))-)))......(((((((....)))))))....))))))).. ( -35.70)
>DroYak_CAF1 106506 115 + 1
UCGGUGGCGGUGGCGGUGUGUGAAA--UAUACGAG-AGUCCCCGGUUGGCAGUUACCGGUUACCGGUUGUGGGUCCAAGGCAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAA
.(((((((((.(((..((((((...--))))))..-.)))))((((........)))))))))))(((((((((.........))))(((((((....))))))).)))))....... ( -37.80)
>DroAna_CAF1 105884 115 + 1
UCGGUGGCACU---GUAUUCCGGAAUAUAUACGAGAAGUCCCCGGUUGGCAGUUACCGGUUGCCGGUUGUGGGUCCGAGGCAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAA
((((.((.(((---....((((.........)).)))))))))))(((((((((...((.((((((........))..))))...))(((((((....)))))))...))))))))). ( -37.10)
>DroPer_CAF1 117406 98 + 1
------------------CAUGGUAUG-GUCCGUUUGGUCCCCGGUCGCCAGUUACCGGUUACCGGG-GUCGGUCCCAGGUAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAA
------------------..(((((.(-(.(((......(((((((.(((.......))).))))))-).))).))..((.....))(((((((....)))))))......))))).. ( -37.00)
>consensus
UCGGUGG_______GGU_UCUGAAA__UAUACGAG_AGUCCCCGGUUGGCAGUUACCGGUUACCGGUUGUGGGUCCAAGGCAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAA
.....................................((..(((((........)))))..))(((((((........((.....))(((((((....))))))).)))))))..... (-22.95 = -23.48 +   0.53)

alignment

secondary structure

dotplot

Window 5

Location	5,478,715 – 5,478,827
Length	112
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	79.77
Mean single sequence MFE	-32.41
Consensus MFE	-24.17
Energy contribution	-24.45
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-1.58
Structure conservation index	0.75
SVM decision value	0.70
SVM RNA-class probability	0.826067
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5478715 112 - 22407834
UUUAGCAGUUGUUAUGAGUGUUAACACUCAUGGAUAUGCCUUGGACCCACAACCGGUAACCGGUAACUGCCAACCGGGGACU-CUCGUAUA--UUUCAGAUACC---ACCGCCACCGA
....((((((.(((((((((....)))))))))..................(((((...)))))))))))....(((((...-...((((.--......)))).---....)).))). ( -31.00)
>DroPse_CAF1 116694 98 - 1
UUUAGCAGUUGUUAUGAGUGUUAACACUCAUGGAUAUACCUGGGACCGAC-CCCGGUAACCGGUAACUGGCGACCGGGGACCAAACGGAC-CAUACCAUG------------------
.....(((.(((((((((((....))))))).))))...)))((.(((.(-((((((..((((...))))..)))))))......))).)-)........------------------ ( -35.50)
>DroEre_CAF1 99081 108 - 1
UUUAGCAGUUGUUAUGAGUGUUAACACUCAUGGAUAUGCC-UGGACCCACAACCGGUAACCGGUAACUGCCAACCGGGGACU-CUCGUAUA--UUUCAGACACCG------CCACCGA
....(((....(((((((((....)))))))))...)))(-((((.........(((..(((((........)))))..)))-........--.)))))......------....... ( -29.57)
>DroYak_CAF1 106506 115 - 1
UUUAGCAGUUGUUAUGAGUGUUAACACUCAUGGAUAUGCCUUGGACCCACAACCGGUAACCGGUAACUGCCAACCGGGGACU-CUCGUAUA--UUUCACACACCGCCACCGCCACCGA
....((.(((((((((((((....))))))))(((((((...((........))(((..(((((........)))))..)))-...)))))--))..))).)).))............ ( -29.20)
>DroAna_CAF1 105884 115 - 1
UUUAGCAGUUGUUAUGAGUGUUAACACUCAUGGAUAUGCCUCGGACCCACAACCGGCAACCGGUAACUGCCAACCGGGGACUUCUCGUAUAUAUUCCGGAAUAC---AGUGCCACCGA
....(((....(((((((((....)))))))))...))).((((.......(((((...))))).((((....((((((((.....)).....))))))....)---)))....)))) ( -33.70)
>DroPer_CAF1 117406 98 - 1
UUUAGCAGUUGUUAUGAGUGUUAACACUCAUGGAUAUACCUGGGACCGAC-CCCGGUAACCGGUAACUGGCGACCGGGGACCAAACGGAC-CAUACCAUG------------------
.....(((.(((((((((((....))))))).))))...)))((.(((.(-((((((..((((...))))..)))))))......))).)-)........------------------ ( -35.50)
>consensus
UUUAGCAGUUGUUAUGAGUGUUAACACUCAUGGAUAUGCCUUGGACCCACAACCGGUAACCGGUAACUGCCAACCGGGGACU_CUCGUAUA__UUCCAGA_ACC_______CCACCGA
....(((....(((((((((....)))))))))...)))...((........))(((..(((((........)))))..))).................................... (-24.17 = -24.45 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	5,478,787 – 5,478,898
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	85.94
Mean single sequence MFE	-26.98
Consensus MFE	-23.18
Energy contribution	-23.35
Covariance contribution	0.17
Combinations/Pair	1.13
Mean z-score	-1.97
Structure conservation index	0.86
SVM decision value	0.73
SVM RNA-class probability	0.835717
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5478787 111 + 22407834
GGCAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAAGCCCAUUUUCGCAUGUUGGCAGCUUAUAAAAGUGCAGCACUCGGCCGCAUGGCCAUAUACC---------ACAUAUAUAG
((.((((....(((((((..((((........(((((((.((........))...)))))))........)))).)))))))((((....)))))))).))---------.......... ( -31.39)
>DroPse_CAF1 116752 100 + 1
GGUAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAAGCCCAUUUUCGCAUGUUGGCAGCUUAUAAAACUGCAGCACUCGGCCAUAGAGCCAUA--------------------UAG
((.....))..(((((((...........(((((((.((((....)))).))).))))((((.........)))))))))))(((......)))...--------------------... ( -25.30)
>DroEre_CAF1 99149 109 + 1
GGCAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAAGCCCAUUUUCGCAUGUUGGCAGCUUAUAAAAGUGCAGCGCUCGGCGGUAUGGCCAUAUACC---------ACA--UACAG
((((((((..((((((((..((((........(((((((.((........))...)))))))........)))).))))))))..))))).))).......---------...--..... ( -30.49)
>DroWil_CAF1 144432 100 + 1
GGUAUAUCCAUGAGUGUUAACAUUCAUAACAACUGCUAAAGCCCAUUUUCGCAUGUUGGCAGCUUAUAAAAAUGCAGCACUCGACCAUAGCACCAUA--------------------UAG
(((.(((...((((((((..((((........(((((((.((........))...)))))))........)))).))))))))...)))..)))...--------------------... ( -22.69)
>DroAna_CAF1 105959 120 + 1
GGCAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAAGCCCAUUUUCGCAUGUUGGCAGCUUAUAAAAAUGCAGCACUCGGCCGUGGAGCCAUACAUCCCAUUAGCAACAUAUAUAG
.........(((((((....)))))))......((((((.((........))((((((((.((..........))..(((......)))..)))).))))....)))))).......... ( -26.70)
>DroPer_CAF1 117464 100 + 1
GGUAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAAGCCCAUUUUCGCAUGUUGGCAGCUUAUAAAACUGCAGCACUCGGCCAUAGAGCCAUA--------------------UAG
((.....))..(((((((...........(((((((.((((....)))).))).))))((((.........)))))))))))(((......)))...--------------------... ( -25.30)
>consensus
GGCAUAUCCAUGAGUGUUAACACUCAUAACAACUGCUAAAGCCCAUUUUCGCAUGUUGGCAGCUUAUAAAAAUGCAGCACUCGGCCAUAGAGCCAUA____________________UAG
.((((....(((((((....))))))).....(((((((.((........))...))))))).........)))).......(((......))).......................... (-23.18 = -23.35 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:22 2006