Locus 2937

Sequence ID	2L_DroMel_CAF1
Location	8,432,251 – 8,432,450
Length	199
Max. P	0.696694

overview

Window 9

Location	8,432,251 – 8,432,351
Length	100
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	75.02
Mean single sequence MFE	-38.18
Consensus MFE	-19.09
Energy contribution	-19.17
Covariance contribution	0.07
Combinations/Pair	1.29
Mean z-score	-1.81
Structure conservation index	0.50
SVM decision value	0.34
SVM RNA-class probability	0.696694
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8432251 100 - 22407834
CUGCAGCGCAAGCAACUGGAGGCCUCGGCCCAGGAGGAGGC----------AGACCAG--CUGCAUCCCGAUACGGAUCCCA-----AUCCGGACUCGGGCGGCCAACUGCCAAACG
.((((((....))..((((..(((((..(....)..)))))----------...))))--.)))).(((((..(((((....-----)))))...))))).(((.....)))..... ( -42.10)
>DroSec_CAF1 5333 100 - 1
CUGCAGCGCAAGCAACUGGAGGCUUCGGCCCAGGAGGAGGC----------AGAUCAA--CUGCAUCCCGAUACGGAUCCCA-----AUCCGGACUCCGGCGACCAACUGCCAAACG
.....((....))..((((..((....))))))..((((((----------((.....--)))).........(((((....-----)))))..))))((((......))))..... ( -36.50)
>DroSim_CAF1 5315 100 - 1
CUGCAGCGCAAGAAACUGGAGGCUUCGGCCCAGGAGGAGGC----------AGACCAA--CUGCAUCCCGAUACGGAUCCCA-----AUCCGGACUCGGGCGACCAACUGCCAAACG
..(((((....)...((((..((....))))))..((..((----------((.....--))))..(((((..(((((....-----)))))...)))))...))..))))...... ( -35.10)
>DroEre_CAF1 5321 100 - 1
CUGCAGCGCAAGCAACUGGAGGCUUCCGCUCAGGAGGAGGC----------AGACCAG--CUGCAACCUGAUACGGAUACCA-----GUCCAGACGCUGGCAGCCAACUACCAAACG
(((((((((..(((.((((..((((((........))))))----------...))))--.)))..........((((....-----)))).).)))).)))).............. ( -36.10)
>DroYak_CAF1 5454 100 - 1
CUGCAGCGUAAGCAACUGGAGGCUUCCGCUCAGGAGGAGGC----------AGACCAG--CUGCAUCCCGAUACGGAUCCCA-----AUCCAGACACUGGCGACCAACUGCCAAGCA
..((.((....))..(((((((..((((.((.(((....((----------((.....--)))).))).))..))))..)).-----.)))))....(((((......))))).)). ( -36.30)
>DroAna_CAF1 5856 110 - 1
CAACAG------CUGCUGGAGGCAGCAGCCCAGGAGGCUGCGUUAGAAGCCAACCCAGAUCUGGAGCUAGGCAUAGAACCCAUCAGUGCCCAGUCGGUGG-AGACGUCCACCGAAUC
...(((------...((((.(((.((((((.....)))))).......)))...))))..)))...((.(((((.((.....)).))))).))(((((((-(....))))))))... ( -43.00)
>consensus
CUGCAGCGCAAGCAACUGGAGGCUUCGGCCCAGGAGGAGGC__________AGACCAG__CUGCAUCCCGAUACGGAUCCCA_____AUCCAGACUCUGGCGACCAACUGCCAAACG
.....((....))..(((((.(((((..(....)..))))).......................((((......))))..........))))).....((((......))))..... (-19.09 = -19.17 +   0.07)

alignment

secondary structure

dotplot

Window 0

Location	8,432,311 – 8,432,419
Length	108
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	86.36
Mean single sequence MFE	-40.20
Consensus MFE	-31.15
Energy contribution	-32.54
Covariance contribution	1.39
Combinations/Pair	1.13
Mean z-score	-1.96
Structure conservation index	0.77
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8432311 108 + 22407834
CCUCCUCCUGGGCCGAGGCCUCCAGUUGCUUGCGCUGCAGCUCCAGGCGAUUGAGCAACUCAACCGCGGUCUCCUGGAUCUGCUGCUGCAGCUCGUGCGCAUGCUCGU
.......((((((....))..))))..((.(((((.(((((((((((.(((((.............))))).))))))...))))).)).((....))))).)).... ( -40.12)
>DroSec_CAF1 5393 108 + 1
CCUCCUCCUGGGCCGAAGCCUCCAGUUGCUUGCGCUGCAGCUCCAGGCGAUUGAGCAACUCAACCGCAGUCUCCUGGAUCUGCUGCUGCAGCUCGUGCGCAUGCUCAU
........(((((....((..(.((((((....((.((((.((((((.(((((.............))))).)))))).)))).)).)))))).).))....))))). ( -41.02)
>DroSim_CAF1 5375 108 + 1
CCUCCUCCUGGGCCGAAGCCUCCAGUUUCUUGCGCUGCAGCUCCAGGCGAUUGAGCAACUCAACCGCAGUCUCCUGGAUCUGCUGCUGCAGCUCGUGCGCAUGCUCAU
........(((((.(((((.....))))).(((((.(((((((((((.(((((.............))))).))))))...))))).)).((....))))).))))). ( -40.22)
>DroEre_CAF1 5381 108 + 1
CCUCCUCCUGAGCGGAAGCCUCCAGUUGCUUGCGCUGCAGCUCCAGGCGAUUGAGCAACUCAACCGCAGUCUCCUGGAUCUGCUGCUGCAGCUCGUGCGCAUGCUCGU
.........(((((...((..(.((((((....((.((((.((((((.(((((.............))))).)))))).)))).)).)))))).).))...))))).. ( -43.42)
>DroWil_CAF1 6375 102 + 1
CUUCCU---GGAGUUGUUCGUCGA---GCUUUUGCUGCAACUCCAUUUGAUUGACCAACUGGACCACAUGCUCCUCGAUCUGCUGUUGCAAUUGAUGGGCGUGCUCAU
..((((---((((((((......(---((....)))))))))))).(((......)))..)))...(((((((.(((((.(((....)))))))).)))))))..... ( -33.00)
>DroYak_CAF1 5514 108 + 1
CCUCCUCCUGAGCGGAAGCCUCCAGUUGCUUACGCUGCAGCUCCAGGCGAUUGAGCAACUCAACCGCAGUCUCCUGGAUCUGCUGCUGCAGCUCGUGCGCAUGCUCGU
.........(((((...((..(.((((((....((.((((.((((((.(((((.............))))).)))))).)))).)).)))))).).))...))))).. ( -43.42)
>consensus
CCUCCUCCUGGGCCGAAGCCUCCAGUUGCUUGCGCUGCAGCUCCAGGCGAUUGAGCAACUCAACCGCAGUCUCCUGGAUCUGCUGCUGCAGCUCGUGCGCAUGCUCAU
.........((((....((..(.((((((....((.((((.((((((.(((((.............))))).)))))).)))).)).)))))).).))....)))).. (-31.15 = -32.54 +   1.39)

alignment

secondary structure

dotplot

Window 1

Location	8,432,351 – 8,432,450
Length	99
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	81.92
Mean single sequence MFE	-39.04
Consensus MFE	-17.72
Energy contribution	-17.61
Covariance contribution	-0.11
Combinations/Pair	1.13
Mean z-score	-3.03
Structure conservation index	0.45
SVM decision value	0.26
SVM RNA-class probability	0.657724
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8432351 99 + 22407834
CUCCAGGCGAUUGAGCAACUCAACCGCGGUCUCCUGGAUCUGCUGCUGCAGCUCGUGCGCAUGCUCGUGCAUGUGGCU---------GUGCUGAUGCUGCACAAUUUU
.((((((.(((((.............))))).))))))..(((.((..((((.((.((((((((....)))))).)))---------).))))..)).)))....... ( -37.02)
>DroPse_CAF1 5617 108 + 1
UUCCAUCUGGUUGACCAGCUGGACCACAUGCUCCUCGAUCUGCUGCUGCAGCUCGUGAGCAUGCUCGUGCAUAUGGUUGUGAAAAUUGUGCUGAUGCUGCACAAUUUU
.((((.((((....)))).)))).((((.((((..(((.((((....)))).))).))))((((....)))).....))))((((((((((.......)))))))))) ( -44.30)
>DroSec_CAF1 5433 99 + 1
CUCCAGGCGAUUGAGCAACUCAACCGCAGUCUCCUGGAUCUGCUGCUGCAGCUCGUGCGCAUGCUCAUGCAUGUGACU---------GUGCUGAUGCUGCACAAUUUU
.((((((.(((((.............))))).))))))..(((.((..((((.((..(((((((....)))))))..)---------).))))..)).)))....... ( -38.52)
>DroSim_CAF1 5415 99 + 1
CUCCAGGCGAUUGAGCAACUCAACCGCAGUCUCCUGGAUCUGCUGCUGCAGCUCGUGCGCAUGCUCAUGCAUGUGGCU---------GUGCUGAUGCUGCACAAUUUU
.((((((.(((((.............))))).)))))).....((.(((((((((.(((((.((.(((....))))))---------))))))).))))))))..... ( -38.02)
>DroWil_CAF1 6409 108 + 1
CUCCAUUUGAUUGACCAACUGGACCACAUGCUCCUCGAUCUGCUGUUGCAAUUGAUGGGCGUGCUCAUGCAGAUGAUUGUGAAAAUUAUGCUGAUGCUGCACAAUUUU
.((((.(((......))).))))......((((.(((((.(((....)))))))).))))((((.(((.(((((((((.....)))))).))))))..))))...... ( -32.10)
>DroPer_CAF1 5590 108 + 1
UUCCAUCUGGUUGACCAGCUGGACCACAUGCUCCUCGAUCUGCUGCUGCAGCUCGUGAGCAUGCUCGUGCAUAUGGUUGUGAAAAUUGUGCUGAUGCUGCACAAUUUU
.((((.((((....)))).)))).((((.((((..(((.((((....)))).))).))))((((....)))).....))))((((((((((.......)))))))))) ( -44.30)
>consensus
CUCCAGGCGAUUGACCAACUCAACCACAGGCUCCUCGAUCUGCUGCUGCAGCUCGUGCGCAUGCUCAUGCAUAUGGCU_________GUGCUGAUGCUGCACAAUUUU
........(((((.......................((.((((....)))).))....(((.(((((.((((...............))))))).))))).))))).. (-17.72 = -17.61 +  -0.11)

alignment

secondary structure

dotplot

Window 2

Location	8,432,351 – 8,432,450
Length	99
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	81.92
Mean single sequence MFE	-38.10
Consensus MFE	-16.71
Energy contribution	-15.22
Covariance contribution	-1.50
Combinations/Pair	1.39
Mean z-score	-3.12
Structure conservation index	0.44
SVM decision value	0.26
SVM RNA-class probability	0.655787
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8432351 99 - 22407834
AAAAUUGUGCAGCAUCAGCAC---------AGCCACAUGCACGAGCAUGCGCACGAGCUGCAGCAGCAGAUCCAGGAGACCGCGGUUGAGUUGCUCAAUCGCCUGGAG
....((((((.((....))..---------.....(((((....))))).)))))).((((....)))).((((((....)(((((((((...)))))))))))))). ( -36.60)
>DroPse_CAF1 5617 108 - 1
AAAAUUGUGCAGCAUCAGCACAAUUUUCACAACCAUAUGCACGAGCAUGCUCACGAGCUGCAGCAGCAGAUCGAGGAGCAUGUGGUCCAGCUGGUCAACCAGAUGGAA
((((((((((.......)))))))))).....((((((((..(((....))).(((.((((....)))).)))....))))))))((((.((((....)))).)))). ( -45.60)
>DroSec_CAF1 5433 99 - 1
AAAAUUGUGCAGCAUCAGCAC---------AGUCACAUGCAUGAGCAUGCGCACGAGCUGCAGCAGCAGAUCCAGGAGACUGCGGUUGAGUUGCUCAAUCGCCUGGAG
....((((((.((....))..---------.....(((((....))))).)))))).((((....)))).(((((....))(((((((((...)))))))))..))). ( -37.00)
>DroSim_CAF1 5415 99 - 1
AAAAUUGUGCAGCAUCAGCAC---------AGCCACAUGCAUGAGCAUGCGCACGAGCUGCAGCAGCAGAUCCAGGAGACUGCGGUUGAGUUGCUCAAUCGCCUGGAG
....((((((.((....))..---------.....(((((....))))).)))))).((((....)))).(((((....))(((((((((...)))))))))..))). ( -37.00)
>DroWil_CAF1 6409 108 - 1
AAAAUUGUGCAGCAUCAGCAUAAUUUUCACAAUCAUCUGCAUGAGCACGCCCAUCAAUUGCAACAGCAGAUCGAGGAGCAUGUGGUCCAGUUGGUCAAUCAAAUGGAG
((((((((((.......))))))))))((((......(((....))).((((.((..((((....))))...)))).)).)))).((((.((((....)))).)))). ( -26.80)
>DroPer_CAF1 5590 108 - 1
AAAAUUGUGCAGCAUCAGCACAAUUUUCACAACCAUAUGCACGAGCAUGCUCACGAGCUGCAGCAGCAGAUCGAGGAGCAUGUGGUCCAGCUGGUCAACCAGAUGGAA
((((((((((.......)))))))))).....((((((((..(((....))).(((.((((....)))).)))....))))))))((((.((((....)))).)))). ( -45.60)
>consensus
AAAAUUGUGCAGCAUCAGCAC_________AACCACAUGCACGAGCAUGCGCACGAGCUGCAGCAGCAGAUCCAGGAGAAUGCGGUCCAGUUGCUCAAUCACAUGGAG
......((((.......))))...........((((((((....))))).((((..((((((....(........)....))))))...).))).........))).. (-16.71 = -15.22 +  -1.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:59 2006