Locus 7302

Sequence ID	3R_DroMel_CAF1
Location	19,279,267 – 19,279,388
Length	121
Max. P	0.991357

overview

Window 5

Location	19,279,267 – 19,279,371
Length	104
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	76.02
Mean single sequence MFE	-37.30
Consensus MFE	-16.38
Energy contribution	-21.62
Covariance contribution	5.24
Combinations/Pair	1.17
Mean z-score	-2.99
Structure conservation index	0.44
SVM decision value	2.26
SVM RNA-class probability	0.991357
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19279267 104 + 27905053
AUAAGCAAUAGGCCAGGCUAGCUGAAUG--------------AAUGGUUGGAGGAUGGCGGCUGGAUGGAUGGCC-AAAAGAAGCUGGCCAGUGCGUGAGCAGGCCCAAAGCAUGGGCG
..........((((((.((((((.....--------------...))))))....((((.(((....)).).)))-).......))))))..(((....))).(((((.....))))). ( -38.10)
>DroGri_CAF1 88558 85 + 1
AUAAGUUGCA----AGCUGAGAAGAA-------------------GGCUGCAGC--GAAGACUGGA--GUUGGCCUGAAACUGGCAGCCCAGUGCGUGAGAAG-UUAAAAGCA------
....((((((----.(((........-------------------)))))))))--....(((((.--((((.((.......))))))))))).(....)...-.........------ ( -26.50)
>DroSec_CAF1 74755 104 + 1
AUAAGCAAUAGACCAGGCUAGCUGAAUG--------------AAUGGAUGGAGGAUGGCGGCUGGAUGGAUGGCC-AAAAGAAGCUGGCCAGUGCGUGAGCAGGCCCAAAGCAUGGGCG
............(((..(((((((....--------------..(......)......))))))).))).(((((-(........)))))).(((....))).(((((.....))))). ( -35.80)
>DroSim_CAF1 77015 104 + 1
AUAAGCAAUAGGCCAGGCUAGCUGAAUG--------------AGUGGAUGGAGGAUGGCGGCUGGAUGGAUGGCC-AAAAGAAGCUGGCCAGUGCGUGAGCAGGCCCAAAGCAUGGGCG
..........((((((((((.((..((.--------------.....))...)).))))(((((......)))))-........))))))..(((....))).(((((.....))))). ( -37.20)
>DroEre_CAF1 76427 104 + 1
AUAAGCCAUAGGCUUGGCUAGCUGAAUG--------------GGUGGAUGGCGGAUGGCGGCUGGAUGGAUGGCC-AAAAGAAGCUGGCCACUGCGUGAGCAGGUCCGAAGCAGGGGCG
....(((((..(((...(((.((....)--------------).)))..)))..))))).(((...(((((((((-(........))))).((((....))))))))).)))....... ( -43.10)
>DroYak_CAF1 79483 118 + 1
AUAAGCAAUAGGCCAGGCGUGCUGAAUGCAUGCUUGGAGGAUGGGGGAUGUAGGAUGGCGGCUAGAUGGAUGGCC-AAAAGAAGCUGGCCAGUGCGUGAGCUGGCCCAAAGCAGGGGCU
............((((((((((.....))))))))))...................((((((((......)))))-.......((((((((((......)))))))...)))....))) ( -43.10)
>consensus
AUAAGCAAUAGGCCAGGCUAGCUGAAUG______________AGUGGAUGGAGGAUGGCGGCUGGAUGGAUGGCC_AAAAGAAGCUGGCCAGUGCGUGAGCAGGCCCAAAGCAUGGGCG
....((....((((.((((((((.............................(.....)(((((......))))).......))))))))..(((....)))))))....))....... (-16.38 = -21.62 +   5.24)

alignment

secondary structure

dotplot

Window 6

Location	19,279,267 – 19,279,371
Length	104
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	76.02
Mean single sequence MFE	-25.61
Consensus MFE	-11.73
Energy contribution	-13.25
Covariance contribution	1.52
Combinations/Pair	1.13
Mean z-score	-2.05
Structure conservation index	0.46
SVM decision value	0.45
SVM RNA-class probability	0.741420
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19279267 104 - 27905053
CGCCCAUGCUUUGGGCCUGCUCACGCACUGGCCAGCUUCUUUU-GGCCAUCCAUCCAGCCGCCAUCCUCCAACCAUU--------------CAUUCAGCUAGCCUGGCCUAUUGCUUAU
.......((..((((((.(((.......(((((((......))-))))).......(((..................--------------......))))))..))))))..)).... ( -26.36)
>DroGri_CAF1 88558 85 - 1
------UGCUUUUAA-CUUCUCACGCACUGGGCUGCCAGUUUCAGGCCAAC--UCCAGUCUUC--GCUGCAGCC-------------------UUCUUCUCAGCU----UGCAACUUAU
------.........-........((((((((((((.(((...((((....--....))))..--)))))))))-------------------.......)))..----)))....... ( -18.81)
>DroSec_CAF1 74755 104 - 1
CGCCCAUGCUUUGGGCCUGCUCACGCACUGGCCAGCUUCUUUU-GGCCAUCCAUCCAGCCGCCAUCCUCCAUCCAUU--------------CAUUCAGCUAGCCUGGUCUAUUGCUUAU
.......((..((((((.(((.......(((((((......))-))))).......(((..................--------------......))))))..))))))..)).... ( -23.66)
>DroSim_CAF1 77015 104 - 1
CGCCCAUGCUUUGGGCCUGCUCACGCACUGGCCAGCUUCUUUU-GGCCAUCCAUCCAGCCGCCAUCCUCCAUCCACU--------------CAUUCAGCUAGCCUGGCCUAUUGCUUAU
.......((..((((((.(((.......(((((((......))-))))).......(((..................--------------......))))))..))))))..)).... ( -26.36)
>DroEre_CAF1 76427 104 - 1
CGCCCCUGCUUCGGACCUGCUCACGCAGUGGCCAGCUUCUUUU-GGCCAUCCAUCCAGCCGCCAUCCGCCAUCCACC--------------CAUUCAGCUAGCCAAGCCUAUGGCUUAU
.((..(((..(.(((.((((....))))(((((((......))-)))))))))..)))..))...............--------------.........(((((......)))))... ( -26.10)
>DroYak_CAF1 79483 118 - 1
AGCCCCUGCUUUGGGCCAGCUCACGCACUGGCCAGCUUCUUUU-GGCCAUCCAUCUAGCCGCCAUCCUACAUCCCCCAUCCUCCAAGCAUGCAUUCAGCACGCCUGGCCUAUUGCUUAU
.......((..((((((((.........(((((((......))-))))).....................................((.(((.....))).))))))))))..)).... ( -32.40)
>consensus
CGCCCAUGCUUUGGGCCUGCUCACGCACUGGCCAGCUUCUUUU_GGCCAUCCAUCCAGCCGCCAUCCUCCAUCCACU______________CAUUCAGCUAGCCUGGCCUAUUGCUUAU
.......((..((((((.((....))..(((((...........)))))........................................................))))))..)).... (-11.73 = -13.25 +   1.52)

alignment

secondary structure

dotplot

Window 7

Location	19,279,295 – 19,279,388
Length	93
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	70.13
Mean single sequence MFE	-31.92
Consensus MFE	-9.15
Energy contribution	-11.27
Covariance contribution	2.11
Combinations/Pair	1.12
Mean z-score	-2.02
Structure conservation index	0.29
SVM decision value	0.09
SVM RNA-class probability	0.579793
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19279295 93 + 27905053
---AAUGGUUGGAGGAUGGCGGCUGGAUGGAUGGCC-AAAAGAAGCUGGCCAGUGCGUGAGCAGGCCCAAAGCAUGGGCGUGCCGAAGAGG-GGUAUC
---..((((..(........(((((......)))))-........)..)))).(((....))).(((((.....)))))(((((.......-))))). ( -31.99)
>DroVir_CAF1 94518 80 + 1
------GGCUGCAGC--UUAGACUGGG--GUUGGCCCGAAACUGGCAGGCGAGUGCGUGAGAAG-UUAAAAGCC-------GACACAGAGGUGGCGGC
------.(((((.((--((...(((..--((((((....((((..((.((....)).))...))-))....)))-------))).))))))).))))) ( -29.50)
>DroGri_CAF1 88580 80 + 1
------GGCUGCAGC--GAAGACUGGA--GUUGGCCUGAAACUGGCAGCCCAGUGCGUGAGAAG-UUAAAAGCA-------GCCGCAGAGGUGGCGCU
------((((...((--(...(((((.--((((.((.......))))))))))).)))....))-))...(((.-------(((((....)))))))) ( -29.70)
>DroSim_CAF1 77043 94 + 1
---AGUGGAUGGAGGAUGGCGGCUGGAUGGAUGGCC-AAAAGAAGCUGGCCAGUGCGUGAGCAGGCCCAAAGCAUGGGCGUGCCGUAGAGGGGGUAUC
---....((((.......(((((........(((((-(........)))))).(((....))).(((((.....)))))..)))))........)))) ( -32.36)
>DroEre_CAF1 76455 91 + 1
---GGUGGAUGGCGGAUGGCGGCUGGAUGGAUGGCC-AAAAGAAGCUGGCCACUGCGUGAGCAGGUCCGAAGCAGGGGCGUGCCGCAGAGGGGG-A--
---........(((((((.(.(((...(((((((((-(........))))).((((....))))))))).)))...).))).))))........-.-- ( -37.40)
>DroYak_CAF1 79522 94 + 1
GAUGGGGGAUGUAGGAUGGCGGCUAGAUGGAUGGCC-AAAAGAAGCUGGCCAGUGCGUGAGCUGGCCCAAAGCAGGGGCUUGCCGUAGAGGGGG-A--
...............((((((((((......)))))-.....((((((((((((......))))))).........))))))))))........-.-- ( -30.60)
>consensus
____GUGGAUGGAGGAUGGCGGCUGGAUGGAUGGCC_AAAAGAAGCUGGCCAGUGCGUGAGCAGGCCCAAAGCA_GGGCGUGCCGCAGAGGGGG_A_C
.................(((.(((.(.....(((((...........))))).....).)))..((((.......))))..))).............. ( -9.15 = -11.27 +   2.11)

alignment

secondary structure

dotplot

Window 8

Location	19,279,295 – 19,279,388
Length	93
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	70.13
Mean single sequence MFE	-24.65
Consensus MFE	-7.77
Energy contribution	-8.16
Covariance contribution	0.39
Combinations/Pair	1.10
Mean z-score	-2.40
Structure conservation index	0.32
SVM decision value	1.36
SVM RNA-class probability	0.946614
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19279295 93 - 27905053
GAUACC-CCUCUUCGGCACGCCCAUGCUUUGGGCCUGCUCACGCACUGGCCAGCUUCUUUU-GGCCAUCCAUCCAGCCGCCAUCCUCCAACCAUU---
......-.......(((..(((((.....)))))..(((.......(((((((......))-))))).......))).)))..............--- ( -26.44)
>DroVir_CAF1 94518 80 - 1
GCCGCCACCUCUGUGUC-------GGCUUUUAA-CUUCUCACGCACUCGCCUGCCAGUUUCGGGCCAAC--CCCAGUCUAA--GCUGCAGCC------
((((.(((....))).)-------)))......-........((....))((((.(((((.((((....--....))))))--)))))))..------ ( -21.20)
>DroGri_CAF1 88580 80 - 1
AGCGCCACCUCUGCGGC-------UGCUUUUAA-CUUCUCACGCACUGGGCUGCCAGUUUCAGGCCAAC--UCCAGUCUUC--GCUGCAGCC------
((((((........)))-------.))).....-..............((((((.(((...((((....--....))))..--)))))))))------ ( -21.30)
>DroSim_CAF1 77043 94 - 1
GAUACCCCCUCUACGGCACGCCCAUGCUUUGGGCCUGCUCACGCACUGGCCAGCUUCUUUU-GGCCAUCCAUCCAGCCGCCAUCCUCCAUCCACU---
.............((((..(((((.....))))).(((....))).(((((((......))-)))))........))))................--- ( -26.80)
>DroEre_CAF1 76455 91 - 1
--U-CCCCCUCUGCGGCACGCCCCUGCUUCGGACCUGCUCACGCAGUGGCCAGCUUCUUUU-GGCCAUCCAUCCAGCCGCCAUCCGCCAUCCACC---
--.-........(((((..((....))...(((.((((....))))(((((((......))-)))))))).....)))))...............--- ( -28.30)
>DroYak_CAF1 79522 94 - 1
--U-CCCCCUCUACGGCAAGCCCCUGCUUUGGGCCAGCUCACGCACUGGCCAGCUUCUUUU-GGCCAUCCAUCUAGCCGCCAUCCUACAUCCCCCAUC
--.-..........(((..((((.......))))..(((.......(((((((......))-))))).......))).)))................. ( -23.84)
>consensus
G_U_CCCCCUCUGCGGCACGCCC_UGCUUUGGACCUGCUCACGCACUGGCCAGCUUCUUUU_GGCCAUCCAUCCAGCCGCCAUCCUCCAUCCAC____
..............(((........((...............))..(((((...........)))))........))).................... ( -7.77 =  -8.16 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:30 2006