Locus 4923

Sequence ID	3R_DroMel_CAF1
Location	12,914,791 – 12,915,022
Length	231
Max. P	0.684826

overview

Window 8

Location	12,914,791 – 12,914,911
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.67
Mean single sequence MFE	-44.47
Consensus MFE	-30.11
Energy contribution	-30.12
Covariance contribution	0.01
Combinations/Pair	1.46
Mean z-score	-1.89
Structure conservation index	0.68
SVM decision value	0.20
SVM RNA-class probability	0.630625
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12914791 120 - 27905053
UCCCUCUCACGUCGGCGAAGCAACACGGCCUGCAUGUGGUGACGAUGCUCCUGCUCGUCACCAUAGGCGUACUUUGCCCGCAACUCGUCUCGUUUGUGAGAGUGUUUACGGUACAUCUUA
...((((((((..(((((.(....((((..(((.(((((((((((.((....)))))))))))))((((.....)))).)))..)))))))))))))))))).................. ( -45.30)
>DroPse_CAF1 7459 120 - 1
UCCCUCUCACGACGCCGAUGUAGCAAAGCCUGCAUGUGAUGGCGGUGCUCCUGCUCAUCGUCGUAGGCGUACUUGGCACGUAGCUCGUCGCGCUUGCACGAGUGUGUGCGAUACAUUUUG
....((.(((.(((((((((.((((.(((((((........)))).)))..)))))))))..((((((((((..(((.....))).)).))))))))....))))))).))......... ( -41.60)
>DroEre_CAF1 3244 120 - 1
UCCCUCUCACGUCGGCGAAGCAACACCGCCUGCAUGUGGUGACGAUGCUCCUGCUCGUCAUCGUAGGCGUACUUUGCCCGCAGCUCGUCCCGCUUGUGAGAGUGUUUACGGUACAUCUUA
...(((((((((.(((((((......(((((((....((((((((.((....)))))))))))))))))..))))))).))(((.......))).))))))).................. ( -47.30)
>DroYak_CAF1 3274 120 - 1
UCCCUCUCACGUCGACGAAGCAGCACAGCCUGCAUGUGGUGACGAUGCUCCUGCUCGUCACCGUAGGCAUACUUGGCCCGCAACUCGUCCCGUUUGUGAGAGUGUUUACGGUACAUCUUA
...((((((((..(((((.((((......))))....((((((((.((....))))))))))(..(((.......)))..)...))))).....)))))))).................. ( -44.40)
>DroAna_CAF1 3191 120 - 1
UCUUUCUCGCGCCGUCGGUGCAGCAGGGCUUGCAUGUGGUGGCGAUGCUCUUGUUCGUCAUCAUAAGCGUACUUGGCCCUCAGCUCGUCCCGCUUGUGGGAAUGUUUUCUGUACAUCUUU
...((((((((..(.(((..(((((((((((((.(((((((((((.((....))))))))))))).))).....))))))..))).)..)))).)))))))).................. ( -44.10)
>DroPer_CAF1 3141 120 - 1
UCCCUCUCACGACGCCGAUGUAGCAAAGCCUGCAUGUGAUGGCGGUGCUCCUGUUCAUCGUCGUAGGCGUACUUGGCACGCAGCUCGUCGCGCUUGCACGAGUGUGUGCGAUACAUUUUG
.......((.((((((.((((((......))))))...(((((((((........))))))))).))))).).))(((((((.(((((.((....))))))))))))))........... ( -44.10)
>consensus
UCCCUCUCACGUCGCCGAAGCAGCACAGCCUGCAUGUGGUGACGAUGCUCCUGCUCGUCAUCGUAGGCGUACUUGGCCCGCAGCUCGUCCCGCUUGUGAGAGUGUUUACGGUACAUCUUA
...((((((((.((((((.((.((...((((((.(((((((((((.((....))))))))))))).))).....)))..)).)))))..)))..)))))))).................. (-30.11 = -30.12 +   0.01)

alignment

secondary structure

dotplot

Window 9

Location	12,914,911 – 12,915,022
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.59
Mean single sequence MFE	-39.47
Consensus MFE	-23.63
Energy contribution	-24.97
Covariance contribution	1.34
Combinations/Pair	1.25
Mean z-score	-1.76
Structure conservation index	0.60
SVM decision value	0.31
SVM RNA-class probability	0.684826
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12914911 111 + 27905053
GCGCCAGCUUGCAUAUCUGGCGUCUACGCCGAUGCAAUGCGUCUACUC---------CAGCGGCCAUCAUAUGAGACGCAAGAAUCUGCGUAAGCGGCGCAUAAACUCCUGGAUGUUUGA
(((((.((((((.((((.((((....))))))))...(((((((.(..---------...............)))))))).........))))))))))).(((((........))))). ( -39.63)
>DroSec_CAF1 11501 111 + 1
GCGCCAGCUGGCCUACCUGGCGUCGACGCCGAUGCAAUGCGUCUACUC---------CAGCGGCCAUCAUAUGAGACGCAAGAAUCUGCGUAAGCGGCGCAUAAACUCCUGGAUAUUUGA
(((((.(((((((...((((.((.(((((.........))))).)).)---------))).))))..........(((((......))))).)))))))).................... ( -42.40)
>DroSim_CAF1 10214 111 + 1
GCGCCAGCUGGCCUACCUGGCGUCGACGCCGAUGCAAUGCGUCUACUC---------CAGCGGCCAUCAUAUGAGACGCAAGAAUCUGCGUAAGCGGCGCAUAAACUCCUGGAUAUUUGA
(((((.(((((((...((((.((.(((((.........))))).)).)---------))).))))..........(((((......))))).)))))))).................... ( -42.40)
>DroEre_CAF1 3364 111 + 1
GCGCCAACUGGCUUACCUGGCUUCUAGGCCGAUGGAAUGCGUCUACUC---------CAGGGGUCAUUACAUGAGACGCAAAUAUUUGCGUAAGCGGCGCAUAAACUCCUGGAUGUUUGA
(((((....)))...(((((((....)))))..))...)).((.((((---------(((((((.......((..((((((....))))))...))........))))))))).))..)) ( -35.56)
>DroYak_CAF1 3394 111 + 1
GCGCCAAUUGGCCUACCUGGCUUCUACGCCGAUGCAAUGCCUCUACUC---------CAACAGCCAUCAUAUGAGACGCAAGAAUCUGCGUAAGCGGCGCAUAAGCUCCUGCAUGUUUGA
(((((....((((.....))))..(((((.(((....(((.(((.(..---------...............)))).)))...))).)))))...))))).(((((........))))). ( -30.83)
>DroAna_CAF1 3311 120 + 1
GCGCCACCUGGCUUACCUGACAUCCAGUCCACGACACUGCCGCCUCUCAGUCAGUGUCGGUGGGCACCACUCUCGGCGCAAGCAUCUGAGCAAGCGCCGAGCCGACUCUUCGUUAUUCGA
..(((....))).....((((.....(((((((((((((.(........).))))))).))))))......((((((((..((......))..))))))))..........))))..... ( -46.00)
>consensus
GCGCCAGCUGGCCUACCUGGCGUCUACGCCGAUGCAAUGCGUCUACUC_________CAGCGGCCAUCAUAUGAGACGCAAGAAUCUGCGUAAGCGGCGCAUAAACUCCUGGAUAUUUGA
(((((...(((((.....((((....))))(((((...)))))..................))))).........(((((......)))))....))))).................... (-23.63 = -24.97 +   1.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:09 2006