Locus 5932

Sequence ID	3L_DroMel_CAF1
Location	15,913,568 – 15,913,871
Length	303
Max. P	0.988452

overview

Window 3

Location	15,913,568 – 15,913,684
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.39
Mean single sequence MFE	-31.72
Consensus MFE	-17.70
Energy contribution	-17.54
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.72
Structure conservation index	0.56
SVM decision value	0.02
SVM RNA-class probability	0.543848
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15913568 116 + 23771897
GGCCCGGUCCAAUCAUUGUAGUGUUCGUAAAUUGAAAGUGAAAUGGAAUGGCCGUCGGUCAGAUGUGUGUGUGGUACUAUAUGUUCAUACAUGU----GUACUACUAUGCUUCGAGCAAC
((((...((((.(((((.((((........))))..)))))..))))..))))...(.((.((.(((((.(((((((.((((((....))))))----)))))))))))).)))).)... ( -36.30)
>DroSec_CAF1 15314 98 + 1
GGCCCGGUCCACUCAUUGUAGUGUUCGUAAAUUGAAAGUGAAAUGGAAUGGCCGCCGGUCAGAU------------------GUUCAUACAUAU----GUACUACUAUGCAUCGAGCAAC
((((...((((.(((((.((((........))))..)))))..))))..))))((((((((...------------------((...(((....----)))..))..)).)))).))... ( -24.50)
>DroSim_CAF1 15515 102 + 1
GGCCCGGUCCACUCAUCGUAGUGUUCGUAAAUUGAAAGUGAAAUGGAAUGGCCGCCGGUCAGAU------------------GUUCAUACAUAUGUAUGUACUACUAUGCAUCGAGCAAC
((((...((((.((((..((((........))))...))))..))))..))))((((((((...------------------((.(((((....))))).)).....)).)))).))... ( -28.60)
>DroEre_CAF1 12982 110 + 1
GGCCCGGUCUAGUCAUUGUAGUGCUCGUAAAUUGAAAGUGAAAUGGAAUGGCCGCUGGUACUACAAGUA--UACAAGU----AUAUGUACAUAU----GUACUGCUGUGCAGCCAGCAAC
((((...((((.(((((.((((........))))..)))))..))))..))))((((((..((((.(((--(....))----)).))))....(----((((....)))))))))))... ( -33.30)
>DroYak_CAF1 13145 107 + 1
GGCCCGGUCCACUCAUUGUAGUGUUCGUAAAUUGAAAGUGAAAUGGAAUGGCCGCUGGUACUACACUCG--UAGGUAC----AUAUAUACAUAU----GUAC---AGUGCAUCCAGCAAC
((((...((((.(((((.((((........))))..)))))..))))..))))(((((..((((....)--)))((((----((((....))))----))))---.......)))))... ( -35.90)
>consensus
GGCCCGGUCCACUCAUUGUAGUGUUCGUAAAUUGAAAGUGAAAUGGAAUGGCCGCCGGUCAGAU_______U__________GUUCAUACAUAU____GUACUACUAUGCAUCGAGCAAC
((((...((((.((((..((((........))))...))))..))))..))))......................................................(((.....))).. (-17.70 = -17.54 +  -0.16)

alignment

secondary structure

dotplot

Window 4

Location	15,913,608 – 15,913,724
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.13
Mean single sequence MFE	-30.92
Consensus MFE	-14.68
Energy contribution	-14.68
Covariance contribution	-0.00
Combinations/Pair	1.11
Mean z-score	-2.11
Structure conservation index	0.47
SVM decision value	0.90
SVM RNA-class probability	0.877854
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15913608 116 + 23771897
AAAUGGAAUGGCCGUCGGUCAGAUGUGUGUGUGGUACUAUAUGUUCAUACAUGU----GUACUACUAUGCUUCGAGCAACAAGUGUUUUAUCAACAGAGCGACAGGCGUCCGAACAAAAG
...((((...(((((((.((.((.(((((.(((((((.((((((....))))))----)))))))))))).))(((((.....)))))........)).)))).))).))))........ ( -37.90)
>DroSec_CAF1 15354 98 + 1
AAAUGGAAUGGCCGCCGGUCAGAU------------------GUUCAUACAUAU----GUACUACUAUGCAUCGAGCAACAAGUGUUUUAUCAACUGAGCGACAGGCGUCCGGACAAAAG
...((((...(((..((.((((.(------------------(.....((((.(----((.......(((.....)))))).)))).....)).)))).))...))).))))........ ( -24.21)
>DroSim_CAF1 15555 102 + 1
AAAUGGAAUGGCCGCCGGUCAGAU------------------GUUCAUACAUAUGUAUGUACUACUAUGCAUCGAGCAACAAGUGUUUUAUCAACUGAGCGACAGGCGUCCGGACAAAAG
...((...(((.((((.(((.(((------------------((.(((((....))))).........)))))..((....(((.........)))..))))).)))).)))..)).... ( -27.00)
>DroEre_CAF1 13022 110 + 1
AAAUGGAAUGGCCGCUGGUACUACAAGUA--UACAAGU----AUAUGUACAUAU----GUACUGCUGUGCAGCCAGCAACAAGUGUUUUAUCAACACAGAGACAGGCGUCCGGACAAAAG
...((((...(((((((((..((((.(((--(....))----)).))))....(----((((....))))))))))).....(((((.....))))).......))).))))........ ( -32.30)
>DroYak_CAF1 13185 107 + 1
AAAUGGAAUGGCCGCUGGUACUACACUCG--UAGGUAC----AUAUAUACAUAU----GUAC---AGUGCAUCCAGCAACAAGUGUUUUAUCAACACAGAGACAGGCGUCCGGACAAAAG
...((((...((((((((..((((....)--)))((((----((((....))))----))))---.......))))).....(((((.....))))).......))).))))........ ( -33.20)
>consensus
AAAUGGAAUGGCCGCCGGUCAGAU_______U__________GUUCAUACAUAU____GUACUACUAUGCAUCGAGCAACAAGUGUUUUAUCAACAGAGCGACAGGCGUCCGGACAAAAG
...((...(((.((((.(((...........................(((........)))......(((.....)))......................))).)))).)))..)).... (-14.68 = -14.68 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	15,913,608 – 15,913,724
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.13
Mean single sequence MFE	-28.72
Consensus MFE	-14.74
Energy contribution	-15.10
Covariance contribution	0.36
Combinations/Pair	1.10
Mean z-score	-1.87
Structure conservation index	0.51
SVM decision value	0.29
SVM RNA-class probability	0.670323
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15913608 116 - 23771897
CUUUUGUUCGGACGCCUGUCGCUCUGUUGAUAAAACACUUGUUGCUCGAAGCAUAGUAGUAC----ACAUGUAUGAACAUAUAGUACCACACACACAUCUGACCGACGGCCAUUCCAUUU
.........(((.(((.((((.((...((.............(((.....)))..((.((((----..((((....))))...)))).)).....))...)).)))))))...))).... ( -23.60)
>DroSec_CAF1 15354 98 - 1
CUUUUGUCCGGACGCCUGUCGCUCAGUUGAUAAAACACUUGUUGCUCGAUGCAUAGUAGUAC----AUAUGUAUGAAC------------------AUCUGACCGGCGGCCAUUCCAUUU
.........(((.(((.((((.((((.((.......(((...(((.....))).))).((((----....))))...)------------------).)))).)))))))...))).... ( -25.20)
>DroSim_CAF1 15555 102 - 1
CUUUUGUCCGGACGCCUGUCGCUCAGUUGAUAAAACACUUGUUGCUCGAUGCAUAGUAGUACAUACAUAUGUAUGAAC------------------AUCUGACCGGCGGCCAUUCCAUUU
.........(((.(((.((((.((((.((.....(((((...(((.....))).))).)).(((((....)))))..)------------------).)))).)))))))...))).... ( -28.60)
>DroEre_CAF1 13022 110 - 1
CUUUUGUCCGGACGCCUGUCUCUGUGUUGAUAAAACACUUGUUGCUGGCUGCACAGCAGUAC----AUAUGUACAUAU----ACUUGUA--UACUUGUAGUACCAGCGGCCAUUCCAUUU
.........(((.(((.......(((((.....))))).....(((((((((...))))(((----(..((((((...----...))))--))..))))...))))))))...))).... ( -32.30)
>DroYak_CAF1 13185 107 - 1
CUUUUGUCCGGACGCCUGUCUCUGUGUUGAUAAAACACUUGUUGCUGGAUGCACU---GUAC----AUAUGUAUAUAU----GUACCUA--CGAGUGUAGUACCAGCGGCCAUUCCAUUU
.........(((.(((.......(((((.....))))).....(((((.((((((---((((----((((....))))----))))...--..))))))...))))))))...))).... ( -33.90)
>consensus
CUUUUGUCCGGACGCCUGUCGCUCUGUUGAUAAAACACUUGUUGCUCGAUGCAUAGUAGUAC____AUAUGUAUGAAC__________A_______AUCUGACCGGCGGCCAUUCCAUUU
.........(((.(((.((((.((.(((.....)))(((...(((.....)))....)))........................................)).)))))))...))).... (-14.74 = -15.10 +   0.36)

alignment

secondary structure

dotplot

Window 6

Location	15,913,724 – 15,913,839
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.04
Mean single sequence MFE	-31.52
Consensus MFE	-28.70
Energy contribution	-29.10
Covariance contribution	0.40
Combinations/Pair	1.06
Mean z-score	-1.39
Structure conservation index	0.91
SVM decision value	0.97
SVM RNA-class probability	0.892926
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15913724 115 - 23771897
UUGUUAUUAAUAAUAUUAGUA-----UGUGAUAUUAACGGGACUGCAGCCUCCAUUGUGCCGGCGGUGGAAACCCUUUGGCACGCGAACUCAAUUUUCCUAGGCUGACAGUUUAUAAUUC
..........((((((((...-----..))))))))...((((((((((((.....(((((((.((.(....))).)))))))..(((.......)))..)))))).))))))....... ( -34.60)
>DroSec_CAF1 15452 115 - 1
UUGUUAUUAAUAAUAUUAGUA-----UGUGAUAUUAACGGGACUGCAGCCUCCAUUGUGUCGGCGGUGGAAACCCUUUGGCACGCGAACUCAAUUUUCCUAGGCUGACAGUUUAGAAUGC
..........((((((((...-----..)))))))).(..(((((((((((.....(((((((.((.(....))).)))))))..(((.......)))..)))))).)))))..)..... ( -32.40)
>DroSim_CAF1 15657 115 - 1
UUGUUAUUAAUAAUAUUAGUA-----UGUGAUAUUAACGGGACUGCAGCCUCCAUUGUGCCGGCGGUGGAAACCCUUUGGCACGCGAACUCAAUUUUCCUAGGCUGACAGUUUAUAAUGC
....(((((.((((((((...-----..))))))))...((((((((((((.....(((((((.((.(....))).)))))))..(((.......)))..)))))).)))))).))))). ( -35.10)
>DroEre_CAF1 13132 115 - 1
UUGUUAUUAAUAAUAUUAGUA-----UGUGAUAUUAACUGGACUGCAGCCUCCUUUGUGGCGGCGGUGGAAACCCUUUGGCAUGCGAACUCAAUUUUCCUAGGCUGACAGUUUAUAAUGC
....(((((.((((((((...-----..))))))))..(((((((((((((.....(((.(((.((.(....))).))).)))..(((.......)))..)))))).)))))))))))). ( -29.00)
>DroYak_CAF1 13292 120 - 1
UUGUUAUUAAUAAUAUUAGUACGAGAUGUGAUAUUAACUGGACUGCAGCCUCCUUUCUGGCGGCGGUGGAAACCCUUUGGCAUGCGAACUCAAUUUUCCUAGGCUGACAGUUUAUAAUGC
....(((((.((((((((..........))))))))..(((((((((((((......((.(((.((.(....))).))).))...(((.......)))..)))))).)))))))))))). ( -26.50)
>consensus
UUGUUAUUAAUAAUAUUAGUA_____UGUGAUAUUAACGGGACUGCAGCCUCCAUUGUGCCGGCGGUGGAAACCCUUUGGCACGCGAACUCAAUUUUCCUAGGCUGACAGUUUAUAAUGC
..........((((((((..........))))))))...((((((((((((.....(((((((.((.(....))).)))))))..(((.......)))..)))))).))))))....... (-28.70 = -29.10 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	15,913,764 – 15,913,871
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.00
Mean single sequence MFE	-28.47
Consensus MFE	-25.83
Energy contribution	-26.19
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.81
Structure conservation index	0.91
SVM decision value	2.12
SVM RNA-class probability	0.988452
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15913764 107 + 23771897
CCAAAGGGUUUCCACCGCCGGCACAAUGGAGGCUGCAGUCCCGUUAAUAUCACA-----UACUAAUAUUAUUAAUAACAAUGGCUGCAGUCUUGAUUCAAUUUGAUGGCUG--------C
......(((....)))((((.((.(((.((((((((((((..(((((((.....-----.........)))))))......)))))))))))).))).....)).))))..--------. ( -28.64)
>DroSec_CAF1 15492 107 + 1
CCAAAGGGUUUCCACCGCCGACACAAUGGAGGCUGCAGUCCCGUUAAUAUCACA-----UACUAAUAUUAUUAAUAACAAUGGCUGCAGUCUUGAUUCAAUUUGAUGGCUG--------C
......(((....)))((((.((.(((.((((((((((((..(((((((.....-----.........)))))))......)))))))))))).))).....)).))))..--------. ( -28.64)
>DroSim_CAF1 15697 107 + 1
CCAAAGGGUUUCCACCGCCGGCACAAUGGAGGCUGCAGUCCCGUUAAUAUCACA-----UACUAAUAUUAUUAAUAACAAUGGCUGCAGUCUUGAUUCAAUUUGAUGGCUG--------C
......(((....)))((((.((.(((.((((((((((((..(((((((.....-----.........)))))))......)))))))))))).))).....)).))))..--------. ( -28.64)
>DroEre_CAF1 13172 103 + 1
CCAAAGGGUUUCCACCGCCGCCACAAAGGAGGCUGCAGUCCAGUUAAUAUCACA-----UACUAAUAUUAUUAAUAACAAUGACUGCAGUCUUGAUUCAAUUUGAUGG------------
.((((..(..((.....((........))(((((((((((..(((((((.....-----.........)))))))......))))))))))).))..)..))))....------------ ( -23.94)
>DroYak_CAF1 13332 120 + 1
CCAAAGGGUUUCCACCGCCGCCAGAAAGGAGGCUGCAGUCCAGUUAAUAUCACAUCUCGUACUAAUAUUAUUAAUAACAAUGACUGCAGUCUUGAUUCAAUUUGAUGGCUACCCGGUUGC
.(((.((((..(((.((......(((..((((((((((((..(((((((...................)))))))......))))))))))))..)))....)).)))..))))..))). ( -32.51)
>consensus
CCAAAGGGUUUCCACCGCCGCCACAAUGGAGGCUGCAGUCCCGUUAAUAUCACA_____UACUAAUAUUAUUAAUAACAAUGGCUGCAGUCUUGAUUCAAUUUGAUGGCUG________C
......(((....)))((((.((.(((.((((((((((((..(((((((...................)))))))......)))))))))))).))).....)).))))........... (-25.83 = -26.19 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:29 2006