Locus 7110

Sequence ID	X_DroMel_CAF1
Location	17,855,267 – 17,855,447
Length	180
Max. P	0.989887

overview

Window 7

Location	17,855,267 – 17,855,382
Length	115
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	86.26
Mean single sequence MFE	-34.44
Consensus MFE	-26.85
Energy contribution	-27.73
Covariance contribution	0.88
Combinations/Pair	1.15
Mean z-score	-2.43
Structure conservation index	0.78
SVM decision value	1.65
SVM RNA-class probability	0.969953
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17855267 115 - 22224390
CAAAUUAAAUGACACGAACUGUCGGCUCAAAAUGCCGACAUUUAGUUAGGCCCCAGCUUAGCACACACGCCCACUGGUUGGGUUUCAAAUUUUGUGGUGUAGCUAAGAAUAUUGA
..............(((..(((((((.......)))))))((((((((.(((.((((...))......(((((.....))))).........)).))).))))))))....))). ( -31.30)
>DroSec_CAF1 112844 115 - 1
CAAAUCAAAUGACAAGAACUGUCGGCUCAAAAUGCCGACAUUUAGUUAGGCCCCAGCUUAGCACACACCCGCACUGCUUGGGUCUCAAAUUUUGGGGUGUAGCUGAGAAUAUUGA
....((((...........(((((((.......)))))))((((((((.((((((((...))....(((((.......))))).........)))))).))))))))....)))) ( -38.10)
>DroSim_CAF1 89958 115 - 1
CAAAUUAAAUGACAAGAACUGUCGGCUCAAAAUGCCGACAUUUAGUUAGGCCCCAGCUUAGCACACACCCGCACUGCUUGGGCCUCAAAUUUUGGGGUGUAGCUGAGAAUAUUGA
............(((....(((((((.......)))))))((((((((.((((((((((((((...........))).))))).........)))))).))))))))....))). ( -36.70)
>DroEre_CAF1 116564 104 - 1
CAAAUUAAAUGACAAGAACUGUCGGCUCAAACUGACGACAUUUAGUUAGGCCCCAGCUUAACACAUACCCC-----------CCACCGAUUUUGGGGUGUAGCUAAGCAUAUGGG
..........((((.....))))((((..((((((......)))))).))))((((((((.....(((.((-----------(((.......))))).)))..)))))...))). ( -28.20)
>DroYak_CAF1 114800 115 - 1
CAAAUUAAAUGACAAGAACUGUCGGCUCAAAAUGCCGACAUUUAGUUAGGCCCCAGCCUAACACACACCUCCGCCGCUUGGGCCACUGAAUUUGGGGUGGAGCUAAGCAUAUUGA
............(((....(((((((.......)))))))....(((((((....))))))).............((((((.(((((........)))))..))))))...))). ( -37.90)
>consensus
CAAAUUAAAUGACAAGAACUGUCGGCUCAAAAUGCCGACAUUUAGUUAGGCCCCAGCUUAGCACACACCCCCACUGCUUGGGCCUCAAAUUUUGGGGUGUAGCUAAGAAUAUUGA
...................(((((((.......)))))))((((((((.((((((((((((................)))))).........)))))).))))))))........ (-26.85 = -27.73 +   0.88)

alignment

secondary structure

dotplot

Window 8

Location	17,855,307 – 17,855,422
Length	115
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	91.39
Mean single sequence MFE	-29.40
Consensus MFE	-25.28
Energy contribution	-25.48
Covariance contribution	0.20
Combinations/Pair	1.15
Mean z-score	-2.04
Structure conservation index	0.86
SVM decision value	2.19
SVM RNA-class probability	0.989887
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17855307 115 - 22224390
GCUUAAUUUCGAACAAGCCGUGAAUCUUCCCGGCAAAUGACAAAUUAAAUGACACGAACUGUCGGCUCAAAAUGCCGACAUUUAGUUAGGCCCCAGCUUAGCACACACGCCCACU
((.....((((.....((((.((....)).)))).(((.....)))........)))).(((((((.......)))))))....(((((((....)))))))......))..... ( -29.40)
>DroSec_CAF1 112884 115 - 1
GCUUAAUUUCGAACAAGCCGUGAAUCUUGCCGGCAAAUGACAAAUCAAAUGACAAGAACUGUCGGCUCAAAAUGCCGACAUUUAGUUAGGCCCCAGCUUAGCACACACCCGCACU
((((..........)))).(((..(((((....((..(((....)))..)).)))))..(((((((.......)))))))....(((((((....))))))).)))......... ( -28.00)
>DroSim_CAF1 89998 115 - 1
GCUUAAUUUCGAACAAGCCGUGAAUCUUGCCGGCAAAUGACAAAUUAAAUGACAAGAACUGUCGGCUCAAAAUGCCGACAUUUAGUUAGGCCCCAGCUUAGCACACACCCGCACU
((((..........)))).(((..(((((.((...(((.....)))...)).)))))..(((((((.......)))))))....(((((((....))))))).)))......... ( -28.40)
>DroEre_CAF1 116597 111 - 1
GCUUAAUUUCGAACGAGCCGUGGAUCUGCCCGGCAAAUGACAAAUUAAAUGACAAGAACUGUCGGCUCAAACUGACGACAUUUAGUUAGGCCCCAGCUUAACACAUACCCC----
..(((((((.......((((.((.....)))))).......)))))))(((........((((((......)))))).......(((((((....))))))).))).....---- ( -24.54)
>DroYak_CAF1 114840 115 - 1
GCUUAAUUUCGAACGAGUCGUGGAUCUCCACGGCAAAUGACAAAUUAAAUGACAAGAACUGUCGGCUCAAAAUGCCGACAUUUAGUUAGGCCCCAGCCUAACACACACCUCCGCC
(((((((((.......(((((((....))))))).......)))))))...........(((((((.......)))))))....(((((((....)))))))..........)). ( -36.64)
>consensus
GCUUAAUUUCGAACAAGCCGUGAAUCUUCCCGGCAAAUGACAAAUUAAAUGACAAGAACUGUCGGCUCAAAAUGCCGACAUUUAGUUAGGCCCCAGCUUAGCACACACCCCCACU
..(((((((.......((((.((....)).)))).......)))))))...........(((((((.......)))))))....(((((((....)))))))............. (-25.28 = -25.48 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	17,855,347 – 17,855,447
Length	100
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	77.08
Mean single sequence MFE	-29.00
Consensus MFE	-20.37
Energy contribution	-22.09
Covariance contribution	1.72
Combinations/Pair	1.12
Mean z-score	-1.21
Structure conservation index	0.70
SVM decision value	0.43
SVM RNA-class probability	0.734587
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17855347 100 + 22224390
GCAUUUUGAGCCGACAGUUCGUGUCAUUUAAUUUGUCAUUUGCCGGGAAGAUUCACGGCUUGUUCGAAAUUAAGCGACGUCUGUUGGCCGCUGUC-GUU--------------GC
(((...(((((((((((....((((.((((((((...((..((((.((....)).))))..))...)))))))).)))).)))))))).....))-).)--------------)) ( -29.60)
>DroPse_CAF1 128134 84 + 1
GU---------------UUCUUGUCAUUUAAUUUGUCAUUUGCCAUGGGG--CCAGAGCUGGGGCCAAAUUAAGCGAUGUCUAAUGGCUCUUUUCCUGU--------------GG
..---------------....((.((.......)).))....((((((((--..((((((.((((.............))))...))))))..))))))--------------)) ( -20.72)
>DroSec_CAF1 112924 100 + 1
GCAUUUUGAGCCGACAGUUCUUGUCAUUUGAUUUGUCAUUUGCCGGCAAGAUUCACGGCUUGUUCGAAAUUAAGCGACGUCUGUUGGCCGCUGUC-UGU--------------GC
((((..((.((((((((....((((.((((((((...((..((((..........))))..))...)))))))).)))).)))))))))).....-.))--------------)) ( -30.30)
>DroSim_CAF1 90038 100 + 1
GCAUUUUGAGCCGACAGUUCUUGUCAUUUAAUUUGUCAUUUGCCGGCAAGAUUCACGGCUUGUUCGAAAUUAAGCGACGUCUGUUGGCCGCUGUC-UGU--------------GC
((((..((.((((((((....((((.((((((((...((..((((..........))))..))...)))))))).)))).)))))))))).....-.))--------------)) ( -30.20)
>DroEre_CAF1 116633 93 + 1
UCAGUUUGAGCCGACAGUUCUUGUCAUUUAAUUUGUCAUUUGCCGGGCAGAUCCACGGCUCGUUCGAAAUUAAGCGACGUCUGUUGGCCGU----------------------GC
...((.((.((((((((....((((.((((((((.......((((((.....)).)))).......)))))))).)))).)))))))))).----------------------)) ( -30.54)
>DroYak_CAF1 114880 114 + 1
GCAUUUUGAGCCGACAGUUCUUGUCAUUUAAUUUGUCAUUUGCCGUGGAGAUCCACGACUCGUUCGAAAUUAAGCGACGUCUGUUGGCCGCUGUC-UGUGUGUCUGUGUAUCGUC
((((...((((((((((....((((.((((((((.......(.(((((....))))).).......)))))))).)))).))))))))(((....-.)))..)).))))...... ( -32.64)
>consensus
GCAUUUUGAGCCGACAGUUCUUGUCAUUUAAUUUGUCAUUUGCCGGGAAGAUCCACGGCUUGUUCGAAAUUAAGCGACGUCUGUUGGCCGCUGUC_UGU______________GC
.........((((((((....((((.((((((((.......((((.((....)).)))).......)))))))).)))).))))))))........................... (-20.37 = -22.09 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:21 2006