Locus 518

Sequence ID	2L_DroMel_CAF1
Location	1,583,414 – 1,583,537
Length	123
Max. P	0.999957

overview

Window 1

Location	1,583,414 – 1,583,518
Length	104
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	73.02
Mean single sequence MFE	-29.82
Consensus MFE	-16.79
Energy contribution	-20.96
Covariance contribution	4.17
Combinations/Pair	1.11
Mean z-score	-2.65
Structure conservation index	0.56
SVM decision value	3.18
SVM RNA-class probability	0.998678
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1583414 104 + 22407834
UGACGUUUUUGGCACUCUGCUUAAAACUCGCUUUAGAAGC--------ACAGAGUGACCAUGCACCGCAACGGCAUUUCCGUCACUGUGCAAGGUAACACUGUCUUC-ACAAA
.((.(((((.(((.....))).)))))))......((((.--------((((.((.(((.(((((.(..((((.....))))..).))))).))).)).))))))))-..... ( -34.90)
>DroSec_CAF1 61912 104 + 1
UGACGUUUUCGGCACUCUGCUUAAAACUUGCCUUAGAAGC--------ACAGAGUGACCAUGCACCGGAACGGUAUUUCCGUCACUGUGCAAGGUCAUACUGUAUUC-ACAAU
....(((((.(((.....))).)))))........(((..--------((((.((((((.(((((.(..((((.....))))..).))))).)))))).)))).)))-..... ( -38.60)
>DroSim_CAF1 64204 104 + 1
UGACGUUUUUGGAACUCUGCUUAAAACUUGGCUUAGAAGC--------ACAGAGUGAGCAUGCACCGCAACGGAAUUUCCGUCACUGUGCAAGGUCAUACUGUUUUC-ACAAU
........(((.......(((........)))...((((.--------((((.((((.(.(((((.(..((((.....))))..).))))).).)))).))))))))-.))). ( -29.20)
>DroEre_CAF1 63082 101 + 1
UCACGUUUUUGGCACUUUGCCUAAAACUUGCUUCUAAAGCACGAGGGCACAGAGUGACCAUGC-----------AAUUCCGCCACUGUGCAAGGUCACACUAUCUUGCAUAA-
....((...(((((((((((((....(.((((.....)))).).)))))..))))).))).))-----------...........((((((((((......)))))))))).- ( -29.70)
>DroYak_CAF1 62046 85 + 1
-------------GCUCUGCCUAA-AUUUGCUUUCAAAGC--------ACAGAGUUACCAUGCUUCCCUACGGUAUUUCAGCCACUGUGCAAGGUCACACUGUCUUG------
-------------.....((((..-.((((....))))((--------(((((((......))).......(((......))).)))))).))))............------ ( -16.70)
>consensus
UGACGUUUUUGGCACUCUGCUUAAAACUUGCUUUAGAAGC________ACAGAGUGACCAUGCACCGCAACGGUAUUUCCGUCACUGUGCAAGGUCACACUGUCUUC_ACAA_
....(((((.(((.....))).))))).....................((((.((((((.(((((.(..((((.....))))..).))))).)))))).)))).......... (-16.79 = -20.96 +   4.17)

alignment

secondary structure

dotplot

Window 2

Location	1,583,414 – 1,583,518
Length	104
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	73.02
Mean single sequence MFE	-31.93
Consensus MFE	-20.68
Energy contribution	-24.24
Covariance contribution	3.56
Combinations/Pair	1.14
Mean z-score	-2.31
Structure conservation index	0.65
SVM decision value	2.61
SVM RNA-class probability	0.995781
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1583414 104 - 22407834
UUUGU-GAAGACAGUGUUACCUUGCACAGUGACGGAAAUGCCGUUGCGGUGCAUGGUCACUCUGU--------GCUUCUAAAGCGAGUUUUAAGCAGAGUGCCAAAAACGUCA
((((.-((((((((.((.(((.(((((.(..((((.....))))..).))))).))).)).))))--------.))))))))..(((((((..((.....))..))))).)). ( -39.20)
>DroSec_CAF1 61912 104 - 1
AUUGU-GAAUACAGUAUGACCUUGCACAGUGACGGAAAUACCGUUCCGGUGCAUGGUCACUCUGU--------GCUUCUAAGGCAAGUUUUAAGCAGAGUGCCGAAAACGUCA
.....-((((((((..(((((.(((((.(..((((.....))))..).))))).)))))..))))--------).)))...(((..(((((..((.....))..)))))))). ( -37.90)
>DroSim_CAF1 64204 104 - 1
AUUGU-GAAAACAGUAUGACCUUGCACAGUGACGGAAAUUCCGUUGCGGUGCAUGCUCACUCUGU--------GCUUCUAAGCCAAGUUUUAAGCAGAGUUCCAAAAACGUCA
(((((-....))))).((((..(((((.(..((((.....))))..).))))).....(((((((--------(((....)))..........))))))).........)))) ( -32.90)
>DroEre_CAF1 63082 101 - 1
-UUAUGCAAGAUAGUGUGACCUUGCACAGUGGCGGAAUU-----------GCAUGGUCACUCUGUGCCCUCGUGCUUUAGAAGCAAGUUUUAGGCAAAGUGCCAAAAACGUGA
-...(((...((((.((((((.((((..((......)))-----------))).)))))).))))((......)).......))).(((((.(((.....))).))))).... ( -29.70)
>DroYak_CAF1 62046 85 - 1
------CAAGACAGUGUGACCUUGCACAGUGGCUGAAAUACCGUAGGGAAGCAUGGUAACUCUGU--------GCUUUGAAAGCAAAU-UUAGGCAGAGC-------------
------....((((.((.(((.(((.(((...))).....((....))..))).))).)).))))--------((((((.........-.....))))))------------- ( -19.94)
>consensus
_UUGU_GAAGACAGUGUGACCUUGCACAGUGACGGAAAUACCGUUGCGGUGCAUGGUCACUCUGU________GCUUCUAAAGCAAGUUUUAAGCAGAGUGCCAAAAACGUCA
..........((((.((((((.(((((.(((((((.....))))))).))))).)))))).))))........((((..((......))..)))).................. (-20.68 = -24.24 +   3.56)

alignment

secondary structure

dotplot

Window 3

Location	1,583,447 – 1,583,537
Length	90
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	71.01
Mean single sequence MFE	-27.61
Consensus MFE	-22.21
Energy contribution	-23.90
Covariance contribution	1.69
Combinations/Pair	1.12
Mean z-score	-2.71
Structure conservation index	0.80
SVM decision value	4.46
SVM RNA-class probability	0.999903
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1583447 90 + 22407834
UAGAAGCACAGAGUGACCAUGCACCGCAACGGCAUUUCCGUCACUGUGCAAGGUAACACUGUCUUCACAAAUAA-CUCG-------------------AUUUUUCACUUU
..((((.((((.((.(((.(((((.(..((((.....))))..).))))).))).)).))))))))........-....-------------------............ ( -27.60)
>DroSec_CAF1 61945 110 + 1
UAGAAGCACAGAGUGACCAUGCACCGGAACGGUAUUUCCGUCACUGUGCAAGGUCAUACUGUAUUCACAAUCAAAAUCGAUGUCGCGUGCUUAUAAGUAUUUUUCACUAU
..(((((((((.((((((.(((((.(..((((.....))))..).))))).)))))).)))).......(((......)))...))(((((....)))))..)))..... ( -35.10)
>DroSim_CAF1 64237 110 + 1
UAGAAGCACAGAGUGAGCAUGCACCGCAACGGAAUUUCCGUCACUGUGCAAGGUCAUACUGUUUUCACAAUCAAAAUCGAUGUCGCUUGCUUAUAAGUAUUUUUCAAAAU
..((((.((((.((((.(.(((((.(..((((.....))))..).))))).).)))).))))))))............((....(((((....))))).....))..... ( -28.60)
>DroYak_CAF1 62065 90 + 1
UCAAAGCACAGAGUUACCAUGCUUCCCUACGGUAUUUCAGCCACUGUGCAAGGUCACACUGUCUUG-------------------AAUGCUU-CAAGUAUUUGUAAAGUU
...(((.((((.((.(((.(((........(((......))).....))).))).)).)))))))(-------------------(((((..-...))))))........ ( -19.12)
>consensus
UAGAAGCACAGAGUGACCAUGCACCGCAACGGUAUUUCCGUCACUGUGCAAGGUCACACUGUCUUCACAAUCAA_AUCG______C_UGCUU_UAAGUAUUUUUCAAUAU
..((((.((((.((((((.(((((.(..((((.....))))..).))))).)))))).))))))))............................................ (-22.21 = -23.90 +   1.69)

alignment

secondary structure

dotplot

Window 4

Location	1,583,447 – 1,583,537
Length	90
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	71.01
Mean single sequence MFE	-31.15
Consensus MFE	-23.41
Energy contribution	-26.73
Covariance contribution	3.31
Combinations/Pair	1.04
Mean z-score	-2.89
Structure conservation index	0.75
SVM decision value	4.87
SVM RNA-class probability	0.999957
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1583447 90 - 22407834
AAAGUGAAAAAU-------------------CGAG-UUAUUUGUGAAGACAGUGUUACCUUGCACAGUGACGGAAAUGCCGUUGCGGUGCAUGGUCACUCUGUGCUUCUA
............-------------------....-........((((((((.((.(((.(((((.(..((((.....))))..).))))).))).)).)))).)))).. ( -33.70)
>DroSec_CAF1 61945 110 - 1
AUAGUGAAAAAUACUUAUAAGCACGCGACAUCGAUUUUGAUUGUGAAUACAGUAUGACCUUGCACAGUGACGGAAAUACCGUUCCGGUGCAUGGUCACUCUGUGCUUCUA
..................((((.(((((((.......)).)))))...((((..(((((.(((((.(..((((.....))))..).))))).)))))..))))))))... ( -35.70)
>DroSim_CAF1 64237 110 - 1
AUUUUGAAAAAUACUUAUAAGCAAGCGACAUCGAUUUUGAUUGUGAAAACAGUAUGACCUUGCACAGUGACGGAAAUUCCGUUGCGGUGCAUGCUCACUCUGUGCUUCUA
...................((.((((..((.((((....))))))...((((..(((.(.(((((.(..((((.....))))..).))))).).)))..)))))))))). ( -31.50)
>DroYak_CAF1 62065 90 - 1
AACUUUACAAAUACUUG-AAGCAUU-------------------CAAGACAGUGUGACCUUGCACAGUGGCUGAAAUACCGUAGGGAAGCAUGGUAACUCUGUGCUUUGA
..((((((.....((((-(.....)-------------------)))).((.((((......)))).))...........))))))((((((((.....))))))))... ( -23.70)
>consensus
AAAGUGAAAAAUACUUA_AAGCA_G______CGAU_UUGAUUGUGAAGACAGUAUGACCUUGCACAGUGACGGAAAUACCGUUGCGGUGCAUGGUCACUCUGUGCUUCUA
............................................((((((((.((((((.(((((.(((((((.....))))))).))))).)))))).)))).)))).. (-23.41 = -26.73 +   3.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:04 2006