Locus 1443

Sequence ID	2L_DroMel_CAF1
Location	3,838,278 – 3,838,386
Length	108
Max. P	0.825234

overview

Window 8

Location	3,838,278 – 3,838,386
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.94
Mean single sequence MFE	-37.30
Consensus MFE	-24.94
Energy contribution	-26.17
Covariance contribution	1.22
Combinations/Pair	1.21
Mean z-score	-1.81
Structure conservation index	0.67
SVM decision value	0.70
SVM RNA-class probability	0.825234
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3838278 108 + 22407834
CACCGCC----CUU--------CGUCGCACCACCCACGAGCAGUGAGCUCUACCAGCGAUUGCAGUACCAACAGCUGUUGCAUCAACAUGCGGCAGCCGCCGCUCUGGCGGCUCAUCAAA
.......----...--------.((((((........((((.....)))).....(((((.((.((....)).)).))))).......))))))(((((((.....)))))))....... ( -35.90)
>DroSec_CAF1 27146 108 + 1
CUCCACC----CUU--------UGUUGCACCACCCACGAGCAGUGAACUCUACCAGCGAUUGCAGUACCAACAGCUGUUGCAUCAACAUGCGGCAGCCGCCGCCCUGGCGGCUCAUCAAA
.......----...--------(((((.......(((.....)))..........((....)).....)))))((((((((((....)))))))))).(((((....)))))........ ( -32.40)
>DroEre_CAF1 31737 108 + 1
CGCCGCC----CUU--------CGUUGCACCACCCACGAGCAGUGAGCUCUACCAGCGAUUGCAGUACCAACAGCUGUUGCACCAACAUGCGGCAGCCGCCGCACUGGCGGCUCAUCAAA
.((((((----...--------.((((..........((((.....)))).....(((((.((.((....)).)).)))))..)))).((((((....))))))..))))))........ ( -40.60)
>DroWil_CAF1 51238 120 + 1
CGCCAUCAGUCCAACCUAAUCCCGCCGCCGCCGCCGCAAGCACGGAACUGUAUCAGCGUCUGCAGUAUCAACAGUUGUUGCAUCAACAUGCAGCGGCAGCCGCUUUGGCGGCACAUCAAA
.......................(((((((..((.((......((.((((((........)))))).))....((((((((((....)))))))))).)).))..)))))))........ ( -40.10)
>DroYak_CAF1 28509 108 + 1
CUCCGCC----CUU--------UGUUGCACCGCCCACGAGCAGUGAGCUCUACCAGCGAUUGCAGUACCAACAGCUGUUGCAUCAACAUGCGGCAGCCGCCGCAUUGGCGGCACAUCAAA
..(((((----..(--------((.((((.(((....((((.....)))).....)))...(((((.......))))))))).))).(((((((....))))))).)))))......... ( -37.70)
>DroAna_CAF1 28393 104 + 1
-UCCGCC----CUU--------CGUGACCCCGCCCACGAGC---GAGCUCUACCAGCGCCUGCAGUACCAGCAGCUCCUGCACCAGCACGCGGCCGCCGCGGCUCUGGCGGCCCACCAGC
-......----..(--------((((........)))))((---(.(((....(((...((((.......))))...)))....))).)))((((((((......))))))))....... ( -37.10)
>consensus
CUCCGCC____CUU________CGUUGCACCACCCACGAGCAGUGAGCUCUACCAGCGAUUGCAGUACCAACAGCUGUUGCAUCAACAUGCGGCAGCCGCCGCUCUGGCGGCUCAUCAAA
.......................(((((.........((((.....)))).....(((((.((.((....)).)).)))))........))))).((((((.....))))))........ (-24.94 = -26.17 +   1.22)

alignment

secondary structure

dotplot

Window 9

Location	3,838,278 – 3,838,386
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.94
Mean single sequence MFE	-47.53
Consensus MFE	-33.49
Energy contribution	-34.80
Covariance contribution	1.31
Combinations/Pair	1.24
Mean z-score	-1.55
Structure conservation index	0.70
SVM decision value	0.53
SVM RNA-class probability	0.769575
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3838278 108 - 22407834
UUUGAUGAGCCGCCAGAGCGGCGGCUGCCGCAUGUUGAUGCAACAGCUGUUGGUACUGCAAUCGCUGGUAGAGCUCACUGCUCGUGGGUGGUGCGACG--------AAG----GGCGGUG
........((((((....(((((((((..((((....))))..)))))))))((((..(...(((.(((((......))))).))).)..))))....--------...----)))))). ( -46.10)
>DroSec_CAF1 27146 108 - 1
UUUGAUGAGCCGCCAGGGCGGCGGCUGCCGCAUGUUGAUGCAACAGCUGUUGGUACUGCAAUCGCUGGUAGAGUUCACUGCUCGUGGGUGGUGCAACA--------AAG----GGUGGAG
.........(((((....(((((((((..((((....))))..)))))))))((((..(...(((.(((((......))))).))).)..))))....--------...----))))).. ( -42.50)
>DroEre_CAF1 31737 108 - 1
UUUGAUGAGCCGCCAGUGCGGCGGCUGCCGCAUGUUGGUGCAACAGCUGUUGGUACUGCAAUCGCUGGUAGAGCUCACUGCUCGUGGGUGGUGCAACG--------AAG----GGCGGCG
........(((((((((((((((((((..((((....))))..)))))))).)))))(((.(((((....((((.....))))...))))))))....--------...----)))))). ( -49.20)
>DroWil_CAF1 51238 120 - 1
UUUGAUGUGCCGCCAAAGCGGCUGCCGCUGCAUGUUGAUGCAACAACUGUUGAUACUGCAGACGCUGAUACAGUUCCGUGCUUGCGGCGGCGGCGGCGGGAUUAGGUUGGACUGAUGGCG
........(((.((...((.((((((((((((.......(((..((((((.......((....))....))))))...))).)))))))))))).)).))(((((......)))))))). ( -49.60)
>DroYak_CAF1 28509 108 - 1
UUUGAUGUGCCGCCAAUGCGGCGGCUGCCGCAUGUUGAUGCAACAGCUGUUGGUACUGCAAUCGCUGGUAGAGCUCACUGCUCGUGGGCGGUGCAACA--------AAG----GGCGGAG
.........(((((....(((((((((..((((....))))..)))))))))(((((((...(((.(((((......))))).))).)))))))....--------...----))))).. ( -46.90)
>DroAna_CAF1 28393 104 - 1
GCUGGUGGGCCGCCAGAGCCGCGGCGGCCGCGUGCUGGUGCAGGAGCUGCUGGUACUGCAGGCGCUGGUAGAGCUC---GCUCGUGGGCGGGGUCACG--------AAG----GGCGGA-
((..((((((((((........)))))))((((((..((((....)).))..)))).))...)))..)).((.(((---(((....)))))).)).(.--------...----).....- ( -50.90)
>consensus
UUUGAUGAGCCGCCAGAGCGGCGGCUGCCGCAUGUUGAUGCAACAGCUGUUGGUACUGCAAUCGCUGGUAGAGCUCACUGCUCGUGGGUGGUGCAACG________AAG____GGCGGAG
.........(((((....(((((((((..((((....))))..)))))))))(((((((...(((.(((((......))))).))).)))))))...................))))).. (-33.49 = -34.80 +   1.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:47 2006