Locus 4573

Sequence ID	X_DroMel_CAF1
Location	11,999,145 – 11,999,398
Length	253
Max. P	0.909466

overview

Window 8

Location	11,999,145 – 11,999,249
Length	104
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	78.67
Mean single sequence MFE	-20.82
Consensus MFE	-17.01
Energy contribution	-16.45
Covariance contribution	-0.56
Combinations/Pair	1.14
Mean z-score	-1.79
Structure conservation index	0.82
SVM decision value	1.07
SVM RNA-class probability	0.909466
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11999145 104 + 22224390
CUUCUACGCAUAUAAAUUUGUAUGCGUUGCACUGAAAUUUGCAACAGUUACAAUUACAACGAUAAAAGCCGGUGGCAGCAACAGCAAA---CAUGCAACCAUGCCCA
.......(((((((....)))))))((((((........))))))..............((........))(.((((......(((..---..))).....))))). ( -21.90)
>DroSec_CAF1 38125 87 + 1
---GUACGCAUAUAAAUUUGUAUGUGUGGCACUGAAAAUUGCAACAGUUACAAUUACAACGAUAAAAGCCGG-GGC------AGCAAC---CAUGCAA-------CA
---.((((((((((....))))))))))(((.((....((((....(((........))).......((...-.))------.)))).---)))))..-------.. ( -17.80)
>DroEre_CAF1 36864 83 + 1
-----ACGCAUAUAAAUUUGUAUGCGUAGCAGUCGAAUUUGCAACAGUUACAAUUACAACGAUAAAGGCCG--GGC------GGCAAC---CAUGCCAC--------
-----(((((((((....))))))))).((((......))))........................(((..--((.------.....)---)..)))..-------- ( -19.80)
>DroYak_CAF1 37596 90 + 1
-----GCGCAUAUAAAAUUGUAUGCGUCGCAGUGAAAUUUGCAACAGUUACAAUUACAACGAUAAAAGCUGG-GGC------AGCAACACACAUGCCACCA-----A
-----(((((((((....))))))))).((((((....((((..(((((...(((.....)))...))))).-.))------)).....))).))).....-----. ( -23.80)
>consensus
_____ACGCAUAUAAAUUUGUAUGCGUAGCACUGAAAUUUGCAACAGUUACAAUUACAACGAUAAAAGCCGG_GGC______AGCAAC___CAUGCAAC_______A
.....(((((((((....))))))))).(((.......((((....(((........))).......(((...))).......))))......)))........... (-17.01 = -16.45 +  -0.56)

alignment

secondary structure

dotplot

Window 9

Location	11,999,249 – 11,999,365
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	78.74
Mean single sequence MFE	-30.58
Consensus MFE	-17.61
Energy contribution	-18.11
Covariance contribution	0.50
Combinations/Pair	1.23
Mean z-score	-2.10
Structure conservation index	0.58
SVM decision value	0.58
SVM RNA-class probability	0.787499
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11999249 116 - 22224390
CUUUUUUUUGGGCCAUGUCGUGUGUUCAUUUGUCUGUGUGCUCGUUUCAUCGUUUGGCUUUUGCCAUUUGACUGAGCGCAUAAU----AAAAAUUGGCACAUAUUUUUGGUUUCAGUGUG
.......((((((((....((((((..((((...((((((((((.....(((..((((....))))..))).))))))))))..----..))))..)))))).....))).))))).... ( -35.40)
>DroSec_CAF1 38212 114 - 1
CUCUU-UUUGGGCCACGUCGUGUGUUCAUUUGUCUGUGUGCA-GCGGCAUCGUUUGGCUUUUGCCAUUUGACUGAGCGCACAAU----AAAAAUUGGCACAUAUUUUUGGUUUCAGUGUG
.....-.((((((((....((((((..((((...(((((((.-.(((..(((..((((....))))..)))))).)))))))..----..))))..)))))).....))).))))).... ( -34.20)
>DroEre_CAF1 36947 87 - 1
-------------------------UCAUUUGCCUG--UGCA-GCGGCAUCGUUCGGCUUUUGCCGUUUGACUGAGCGCAUAAU----AAAAAUUGGCACAUAUUUUUGGUUUCAGUGU-
-------------------------.((((.(((((--(((.-(((.(((((..((((....))))..))).))..))).((((----....))))))))).......)))...)))).- ( -23.11)
>DroYak_CAF1 37686 116 - 1
CUUU--UUUGGGCCAUGUCGUAUGUUCAUUUGUGUGAAUGCA-GCGACAUCGUUUGGCUUUUGCCGUUUGACUGAGCGUAUAAUAUGUAAAAAUUGGCACAUAUUUUUGGUUU-GGUGUG
....--...((((.(((((((..((((((....))))))...-))))))).))))(((....))).....((..(((....(((((((..........)))))))....))).-.))... ( -29.60)
>consensus
CUUU__UUUGGGCCAUGUCGUGUGUUCAUUUGUCUGUGUGCA_GCGGCAUCGUUUGGCUUUUGCCAUUUGACUGAGCGCAUAAU____AAAAAUUGGCACAUAUUUUUGGUUUCAGUGUG
...................(((((((((...((......))........(((..((((....))))..))).)))))))))...............((((...............)))). (-17.61 = -18.11 +   0.50)

alignment

secondary structure

dotplot

Window 0

Location	11,999,285 – 11,999,398
Length	113
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	83.19
Mean single sequence MFE	-34.17
Consensus MFE	-27.40
Energy contribution	-26.63
Covariance contribution	-0.77
Combinations/Pair	1.13
Mean z-score	-1.52
Structure conservation index	0.80
SVM decision value	0.06
SVM RNA-class probability	0.562007
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11999285 113 - 22224390
-------CAUUUUAACCGCGACUGUCCAAACGGUUAGCCACUUUUUUUUGGGCCAUGUCGUGUGUUCAUUUGUCUGUGUGCUCGUUUCAUCGUUUGGCUUUUGCCAUUUGACUGAGCGCA
-------((..(.(((((((((.(((((((.(((.....)))....)))))))...)))))).))).)..))....((((((((.....(((..((((....))))..))).)))))))) ( -35.20)
>DroSec_CAF1 38248 111 - 1
-------CAUUUUAACCGCGGCUGUCUAAACGGUUAGCCACUCUU-UUUGGGCCACGUCGUGUGUUCAUUUGUCUGUGUGCA-GCGGCAUCGUUUGGCUUUUGCCAUUUGACUGAGCGCA
-------..........(((((.(((((((.((.........)).-)))))))...)))))(((((((...(((.(((.(((-(.(((........))).)))))))..)))))))))). ( -31.90)
>DroYak_CAF1 37725 117 - 1
ACCUGUGCGUUUAAACCGCCGCUGUCCAAAGGGUUAGCUACUUU--UUUGGGCCAUGUCGUAUGUUCAUUUGUGUGAAUGCA-GCGACAUCGUUUGGCUUUUGCCGUUUGACUGAGCGUA
.....((((((((....(((((((.((....)).))))..(...--...))))..((((((..((((((....))))))...-))))))(((..((((....))))..))).)))))))) ( -35.40)
>consensus
_______CAUUUUAACCGCGGCUGUCCAAACGGUUAGCCACUUUU_UUUGGGCCAUGUCGUGUGUUCAUUUGUCUGUGUGCA_GCGACAUCGUUUGGCUUUUGCCAUUUGACUGAGCGCA
.................(((((.(((((((.(((.....)))....)))))))...)))))(((((((...((......))........(((..((((....))))..))).))))))). (-27.40 = -26.63 +  -0.77)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:29 2006