Locus 1884

Sequence ID	2L_DroMel_CAF1
Location	5,181,171 – 5,181,306
Length	135
Max. P	0.994340

overview

Window 7

Location	5,181,171 – 5,181,266
Length	95
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	67.54
Mean single sequence MFE	-23.15
Consensus MFE	-13.07
Energy contribution	-13.32
Covariance contribution	0.25
Combinations/Pair	1.07
Mean z-score	-2.47
Structure conservation index	0.56
SVM decision value	2.47
SVM RNA-class probability	0.994340
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5181171 95 + 22407834
-------------AACCGUCUCCACCACCAGCUCCUUCUCCUAAUACCUCAGGUAUGUCAUGGGCUGCUAUAGCCGCCCAUAAUGUGCCAGAACCAGUUCAACAUAUU
-------------......................................(((((((.((((((.((....)).)))))).))))))).(((....)))........ ( -22.90)
>DroGri_CAF1 90150 98 + 1
----ACAAUAGCCAAACUA------UUUCCGCUCCAAUUCCAUCUACCUCUGGCAUGUCAUGGGCGGCAAUCGCUGCACACAAUGUUCCUGAACCUGCUCAACAAAUA
----..(((((.....)))------)).......................(((((..(((.(((((((....)))))((.....)).)))))...))).))....... ( -14.80)
>DroSec_CAF1 59009 95 + 1
-------------AACCGUCUCCACCACCAGCUCCUUCUCCUUAUACCUCUGGUAUGUCAUGGGCUGCUAUAGCCGCCCACAAUGUGCCAGAACCAGUUCAACAUAUU
-------------...................................((((((((((..(((((.((....)).)))))..))))))))))................ ( -25.40)
>DroMoj_CAF1 118641 98 + 1
----ACAAUAGCCAAUCGA------CUCCAGCACCCAUUCCGAUUACAUCAGGUAUGUCAUGGGCGGCAAUCGCUGCUCAUAAUGUUCCAGAGCCUCCACAACAAAUC
----......((((((((.------...............)))))......((.((((.(((((((((....))))))))).)))).)).).)).............. ( -20.89)
>DroAna_CAF1 62508 105 + 1
CAAGAAGUUAAGGAA---UCUUCAGCUCCUGUACCGUCUCCGGUCACAUCUGGGAUGUCUUGGGCAGCGAUAGCUGCGCACAAUGUACCAGAACCUGCUCAACAAAUA
...((((........---.))))(((...(((((((....)))).)))(((((.((((..((.(((((....))))).))..)))).)))))....)))......... ( -31.00)
>DroPer_CAF1 71911 86 + 1
-------------AA---------ACACCCGCUCCUUCUCCCUACACUUCUGGUAUGUCGUGGGCAGCCAUAGCCGCCCACAAUGUUCCAGAACCUGCACAACAAAUA
-------------..---------.......................((((((.((((.((((((.((....)).)))))).)))).))))))............... ( -23.90)
>consensus
_____________AA_CGU______CACCAGCUCCUUCUCCGUAUACCUCUGGUAUGUCAUGGGCAGCAAUAGCCGCCCACAAUGUUCCAGAACCUGCUCAACAAAUA
................................................((.((.((((..(((((.((....)).)))))..)))).)).))................ (-13.07 = -13.32 +   0.25)

alignment

secondary structure

dotplot

Window 8

Location	5,181,186 – 5,181,306
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	73.17
Mean single sequence MFE	-29.84
Consensus MFE	-14.27
Energy contribution	-14.68
Covariance contribution	0.42
Combinations/Pair	1.12
Mean z-score	-1.69
Structure conservation index	0.48
SVM decision value	0.10
SVM RNA-class probability	0.582383
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5181186 120 + 22407834
CAGCUCCUUCUCCUAAUACCUCAGGUAUGUCAUGGGCUGCUAUAGCCGCCCAUAAUGUGCCAGAACCAGUUCAACAUAUUCGACCCCUCCAAGCUGAGGCCAAACCAACUGUCGUUGAAG
((((..(...........((((((((((((.((((((.((....)).)))))).))))))).(((....)))......................)))))...........)..))))... ( -32.05)
>DroGri_CAF1 90168 120 + 1
CCGCUCCAAUUCCAUCUACCUCUGGCAUGUCAUGGGCGGCAAUCGCUGCACACAAUGUUCCUGAACCUGCUCAACAAAUACGACCUCUUCAAAUUGAAACUAAGGAAAUUACUUUAGAAA
......(((((...........(((((..(((.(((((((....)))))((.....)).)))))...))).))........((.....)).)))))...((((((......))))))... ( -19.00)
>DroYak_CAF1 60662 120 + 1
CAGCUCCUUCUCCUUAUACCUCUGGUAUGUCAUGGGCUGCAAUUGCCGCCCAUAAUGUGCCAGAACCUGUUCAACAAAUUCGACCCCUUCCAGUUGAGGCCAAGCCAACUAUCGUUGAAG
....................((((((((((.((((((.((....)).)))))).)))))))))).....((((((....(((((........)))))(((...))).......)))))). ( -39.50)
>DroMoj_CAF1 118659 120 + 1
CAGCACCCAUUCCGAUUACAUCAGGUAUGUCAUGGGCGGCAAUCGCUGCUCAUAAUGUUCCAGAGCCUCCACAACAAAUCAGACUUAUUCAAAUUGAAUCAAAACCAUCAACAUUUGACA
..((.........(((...))).((.((((.(((((((((....))))))))).)))).))...))......................(((((((((..........)))..)))))).. ( -21.00)
>DroAna_CAF1 62533 120 + 1
CUGUACCGUCUCCGGUCACAUCUGGGAUGUCUUGGGCAGCGAUAGCUGCGCACAAUGUACCAGAACCUGCUCAACAAAUAAGACCCCUUUUGGUAGAAACGAAAUCGGUUGUGGUUGAAG
.(((((((....)))).)))(((((.((((..((.(((((....))))).))..)))).)))))......(((((......((((..(((((.......)))))..))))...))))).. ( -38.10)
>DroPer_CAF1 71917 120 + 1
CCGCUCCUUCUCCCUACACUUCUGGUAUGUCGUGGGCAGCCAUAGCCGCCCACAAUGUUCCAGAACCUGCACAACAAAUACGUCCGCUUCAAAUUGAAACCAAGUCCAUAAUUGUUGAAG
...................((((((.((((.((((((.((....)).)))))).)))).))))))......((((((.((.(..(..(((.....))).....)..).)).))))))... ( -29.40)
>consensus
CAGCUCCUUCUCCGUAUACCUCUGGUAUGUCAUGGGCAGCAAUAGCCGCCCACAAUGUUCCAGAACCUGCUCAACAAAUACGACCCCUUCAAAUUGAAACCAAACCAACUAUCGUUGAAG
....................((.((.((((.((((((.((....)).)))))).)))).)).))........................................................ (-14.27 = -14.68 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:43 2006