Locus 4971

Sequence ID	3L_DroMel_CAF1
Location	13,727,369 – 13,727,617
Length	248
Max. P	0.980937

overview

Window 3

Location	13,727,369 – 13,727,476
Length	107
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	94.77
Mean single sequence MFE	-28.26
Consensus MFE	-25.52
Energy contribution	-26.00
Covariance contribution	0.48
Combinations/Pair	1.04
Mean z-score	-1.42
Structure conservation index	0.90
SVM decision value	1.00
SVM RNA-class probability	0.898851
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13727369 107 + 23771897
GCAAUGAUAACCCUGCAAACAUGGCCCUGGCCCAAAACGUUGAAAAUUAAACGCCCGGUAGGGGAGUCUACCAAAAUAUUUAUGGCAGCAGCAAAGGGCAGCUGGCA-----
.....(((..((((((......(((....))).....((((........))))....))))))..)))..............((.((((.((.....)).)))).))----- ( -30.90)
>DroSec_CAF1 134299 107 + 1
GCAAUGAUAACCCAGCAAACAUGGCCCUGGCCCAAAACGUUGAAAAUUAAACGCCCGGUAGGGGAGUCUACCAAAAUAUUUAUGACAGCAGCAAAGGGCAGCUGGCA-----
...........(((((......(((....)))......(((........)))((((((((((....))))))..........((....)).....)))).)))))..----- ( -29.00)
>DroSim_CAF1 145084 107 + 1
GCAAUGAUAACCCAGCAAACAUGGCCCUGGCCCAAAACGUUGAAAAUUAAACGCCCGGUAGGGGAGUCUACCAAAAUAUUUAUGACAGCAGCAAAGGGCAGCUGGCA-----
...........(((((......(((....)))......(((........)))((((((((((....))))))..........((....)).....)))).)))))..----- ( -29.00)
>DroEre_CAF1 140979 107 + 1
GCAAUGAUAACCCAGCAAACAUGGCCCUGGCCCAAAACGUUGAAAAUUAAACGGCCGGUAGGAGAGUCUACCAAAAUAUUUAUGACAGCAGCAAAGGGCAGCUGGCA-----
...........(((((.......(((((((((......(((........)))))))((((((....))))))......................))))).)))))..----- ( -28.70)
>DroYak_CAF1 144790 109 + 1
GCAAUGAUAACCCGGCAAACAUGGCCCUGGCCCAAAACGUUGAAAAUUAAACGCCCGGCAGGAGAGUCUACCAAAAUAUUUAUGACAGCAG---AGGGCAGCUGGCAAACUG
...........(((((......(((....)))......(((........)))((((((.(((....))).))..........((....)).---.)))).)))))....... ( -23.70)
>consensus
GCAAUGAUAACCCAGCAAACAUGGCCCUGGCCCAAAACGUUGAAAAUUAAACGCCCGGUAGGGGAGUCUACCAAAAUAUUUAUGACAGCAGCAAAGGGCAGCUGGCA_____
...........(((((......(((....)))......(((........)))((((((((((....))))))..........((....)).....)))).)))))....... (-25.52 = -26.00 +   0.48)

alignment

secondary structure

dotplot

Window 4

Location	13,727,403 – 13,727,512
Length	109
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	94.14
Mean single sequence MFE	-31.14
Consensus MFE	-25.22
Energy contribution	-25.26
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.23
Structure conservation index	0.81
SVM decision value	1.64
SVM RNA-class probability	0.969400
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13727403 109 + 23771897
AAACGUUGAAAAUUAAACGCCCGGUAGGGGAGUCUACCAAAAUAUUUAUGGCAGCAGCAAAGGGCAGCUGGCA---------ACGGAGACAACGUUGCGUAUGCGUCAUAUUAAUGGA
...((((((.........((((((((((....))))))............((....))...)))).((..(((---------(((.......))))))....))......)))))).. ( -31.70)
>DroSec_CAF1 134333 109 + 1
AAACGUUGAAAAUUAAACGCCCGGUAGGGGAGUCUACCAAAAUAUUUAUGACAGCAGCAAAGGGCAGCUGGCA---------ACGGAGACAACGUUGCGUAUGCGUCAUAUUAAUGGA
...((((........)))).((((((((....))))))........((((((..((((........))))(((---------(((.......))))))......)))))).....)). ( -32.10)
>DroSim_CAF1 145118 109 + 1
AAACGUUGAAAAUUAAACGCCCGGUAGGGGAGUCUACCAAAAUAUUUAUGACAGCAGCAAAGGGCAGCUGGCA---------ACGGAGACAACGUUGCGUAUGCGUCAUAUUAAUGGA
...((((........)))).((((((((....))))))........((((((..((((........))))(((---------(((.......))))))......)))))).....)). ( -32.10)
>DroEre_CAF1 141013 109 + 1
AAACGUUGAAAAUUAAACGGCCGGUAGGAGAGUCUACCAAAAUAUUUAUGACAGCAGCAAAGGGCAGCUGGCA---------ACGGAGACAACGUUGCGUAUGCGUCAUAUUAAUGGA
...((((........)))).((((((((....))))))........((((((..((((........))))(((---------(((.......))))))......)))))).....)). ( -32.90)
>DroYak_CAF1 144824 115 + 1
AAACGUUGAAAAUUAAACGCCCGGCAGGAGAGUCUACCAAAAUAUUUAUGACAGCAG---AGGGCAGCUGGCAAACUGGCAAACGGAGACAACGUUGCGUAUGCGUCAUAUUAAUGGA
...((((........)))).((((.(((....))).))........((((((.(((.---.(.(((((..((......))....(....)...))))).).))))))))).....)). ( -26.90)
>consensus
AAACGUUGAAAAUUAAACGCCCGGUAGGGGAGUCUACCAAAAUAUUUAUGACAGCAGCAAAGGGCAGCUGGCA_________ACGGAGACAACGUUGCGUAUGCGUCAUAUUAAUGGA
...((((........)))).((((((((....))))))........((((((.(((.....(.(((((.(.............)(....)...))))).).))))))))).....)). (-25.22 = -25.26 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	13,727,403 – 13,727,512
Length	109
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	94.14
Mean single sequence MFE	-28.34
Consensus MFE	-23.06
Energy contribution	-23.10
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.33
Structure conservation index	0.81
SVM decision value	1.87
SVM RNA-class probability	0.980937
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13727403 109 - 23771897
UCCAUUAAUAUGACGCAUACGCAACGUUGUCUCCGU---------UGCCAGCUGCCCUUUGCUGCUGCCAUAAAUAUUUUGGUAGACUCCCCUACCGGGCGUUUAAUUUUCAACGUUU
...........(((((....((((((.......)))---------)))((((.((.....)).))))...........(((((((......))))))))))))............... ( -26.90)
>DroSec_CAF1 134333 109 - 1
UCCAUUAAUAUGACGCAUACGCAACGUUGUCUCCGU---------UGCCAGCUGCCCUUUGCUGCUGUCAUAAAUAUUUUGGUAGACUCCCCUACCGGGCGUUUAAUUUUCAACGUUU
.((.....((((((......((((((.......)))---------)))((((........))))..))))))........(((((......)))))))(((((........))))).. ( -30.00)
>DroSim_CAF1 145118 109 - 1
UCCAUUAAUAUGACGCAUACGCAACGUUGUCUCCGU---------UGCCAGCUGCCCUUUGCUGCUGUCAUAAAUAUUUUGGUAGACUCCCCUACCGGGCGUUUAAUUUUCAACGUUU
.((.....((((((......((((((.......)))---------)))((((........))))..))))))........(((((......)))))))(((((........))))).. ( -30.00)
>DroEre_CAF1 141013 109 - 1
UCCAUUAAUAUGACGCAUACGCAACGUUGUCUCCGU---------UGCCAGCUGCCCUUUGCUGCUGUCAUAAAUAUUUUGGUAGACUCUCCUACCGGCCGUUUAAUUUUCAACGUUU
.((.....((((((......((((((.......)))---------)))((((........))))..))))))........(((((......))))))).((((........))))... ( -27.50)
>DroYak_CAF1 144824 115 - 1
UCCAUUAAUAUGACGCAUACGCAACGUUGUCUCCGUUUGCCAGUUUGCCAGCUGCCCU---CUGCUGUCAUAAAUAUUUUGGUAGACUCUCCUGCCGGGCGUUUAAUUUUCAACGUUU
.((.....(((((((((.((((((((.......)).))))..)).))).(((......---..)))))))))........(((((......)))))))(((((........))))).. ( -27.30)
>consensus
UCCAUUAAUAUGACGCAUACGCAACGUUGUCUCCGU_________UGCCAGCUGCCCUUUGCUGCUGUCAUAAAUAUUUUGGUAGACUCCCCUACCGGGCGUUUAAUUUUCAACGUUU
..............((....))(((((((................((.((((.((.....)).)))).))(((((...(((((((......)))))))..))))).....))))))). (-23.06 = -23.10 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	13,727,512 – 13,727,617
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.71
Mean single sequence MFE	-37.53
Consensus MFE	-26.71
Energy contribution	-26.72
Covariance contribution	0.00
Combinations/Pair	1.13
Mean z-score	-2.95
Structure conservation index	0.71
SVM decision value	1.17
SVM RNA-class probability	0.925749
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13727512 105 + 23771897
CAAGGCUCGG------CCGGUGGAAAUUUUUUGGAAAGCCAAUUUGCGUAUGGUUUUCAAUUAAAAUGUCACAUGAGCUGUAAAACAGUUUGAUGAGCCUG---------UCUCUUCCGU
..(((((((.------...((((..(((((...((((((((.........))))))))....))))).))))..((((((.....))))))..))))))).---------.......... ( -29.60)
>DroPse_CAF1 127527 117 + 1
CAAGGCUCGGGCUCGGGCUGUGGACAUUUUUUGGAAAGCCAAUUUGCGUAUGGUUUUCAAUUAAAAUGUCACAUGAGCUGUAAAACAGUUUGAUGAGCCUGUCGUCCAGGGCCAGG---U
...(((((((((.(((((((((((((((((...((((((((.........))))))))....)))))))).)))((((((.....))))))....))))))..)))).)))))...---. ( -48.90)
>DroEre_CAF1 141122 105 + 1
CAAGGCUCGG------CCGGUGGAAAUUUUUUGGAAAGCCAAUUUGCGUAUGGUUUUCAAUUAAAAUGUCACAUGAGCUGUAAAACAGUUUGAUGAGCCUG---------UCCCCUUCGU
..(((((((.------...((((..(((((...((((((((.........))))))))....))))).))))..((((((.....))))))..))))))).---------.......... ( -29.60)
>DroYak_CAF1 144939 105 + 1
CAAGGCUCGG------GCGGUGGAAAUUUUUUGGAAAGCCAAUUUGCGUAUGGUUUUCAAUUAAAAUGUCACAUGAGCUGUAAAACAGUUUGAUGAGCCUG---------UCUCUUCCGU
..(((((((.------...((((..(((((...((((((((.........))))))))....))))).))))..((((((.....))))))..))))))).---------.......... ( -29.60)
>DroAna_CAF1 195338 111 + 1
CGUGGCUUGG------CCACAGGAUGUUUUUUGGAAAGCCAAUUUGAGUAUGGUUUUCAAUUAAAACGUCACUCGAGCUGUAAAACAGGUUGACGUGGCUACAUUCGAGGUCCAUU---U
.(((((...)------)))).(((((((((...((((((((.........))))))))....)))))(((((((((.(((.....))).)))).)))))..........))))...---. ( -38.60)
>DroPer_CAF1 128909 117 + 1
CAAGGCUCGGGCUCGGGCUGUGGACAUUUUUUGGAAAGCCAAUUUGCGUAUGGUUUUCAAUUAAAAUGUCACAUGAGCUGUAAAACAGUUUGAUGAGCCUGUCGUCCAGGGCCAGG---U
...(((((((((.(((((((((((((((((...((((((((.........))))))))....)))))))).)))((((((.....))))))....))))))..)))).)))))...---. ( -48.90)
>consensus
CAAGGCUCGG______CCGGUGGAAAUUUUUUGGAAAGCCAAUUUGCGUAUGGUUUUCAAUUAAAAUGUCACAUGAGCUGUAAAACAGUUUGAUGAGCCUG_________UCCAUU___U
..(((((((..........(((((.(((((...((((((((.........))))))))....))))).)).)))((((((.....))))))..))))))).................... (-26.71 = -26.72 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:15 2006