Locus 1472

Sequence ID	X_DroMel_CAF1
Location	4,407,979 – 4,408,113
Length	134
Max. P	0.999734

overview

Window 5

Location	4,407,979 – 4,408,074
Length	95
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	78.54
Mean single sequence MFE	-28.77
Consensus MFE	-21.46
Energy contribution	-22.02
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-2.05
Structure conservation index	0.75
SVM decision value	1.46
SVM RNA-class probability	0.956114
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4407979 95 + 22224390
-----------------UAAAGUUUAA--CUGCAUA-ACAAUUGUAUGUGUUGUUUUUUUUGCAGUGUUGGCCCAAAUUGGAGCCAAAGUUGGACGGUUUUUGGGCCAGGCACGA
-----------------.........(--(((((.(-(((((.......)))))).....)))))).((((((((((......(((....)))......))))))))))...... ( -29.70)
>DroSec_CAF1 10485 94 + 1
-----------------UAAUGUUUUAUCCUUGAUA-AGAAUUGUAUGUAUU---UUUUUGGCAGUGCUGGCCCAAAUUGGAGCCAAAGUUGGUCUGUUUUUGGGACAGGCACGA
-----------------.....(((((((...))))-)))............---.........(((((..((((((.((((.(((....)))))))..))))))...))))).. ( -23.80)
>DroSim_CAF1 10578 96 + 1
-----------------UAAUGUUUAAUCCUUGAUA-AGAAUUGUAUGUGUU-UUUUUUUGGCAGUGCUGGCCCAAAUUGGAGCCAAAGUUGGUCUGUUUUUGGGCCAGGCACGA
-----------------...........((..((.(-(((((.......)))-)))))..))..(((((((((((((.((((.(((....)))))))..))))))))).)))).. ( -29.10)
>DroEre_CAF1 11303 109 + 1
GAAGGCAUUUAAUACGGCUAUGUGUUA---UUGAUAAACAAUUGUGUGUGCU---UUUUCCGCAGUGCUGGCCCAAAUUGGAGCCAAAGUUGGACUGUUUUUGGGCAAGGCACGA
((((((((.(((((((....)))))))---.......(((....))))))))---)))......(((((.(((((((..(.(((((....))).)).).)))))))..))))).. ( -32.50)
>consensus
_________________UAAUGUUUAA__CUUGAUA_ACAAUUGUAUGUGUU___UUUUUGGCAGUGCUGGCCCAAAUUGGAGCCAAAGUUGGACUGUUUUUGGGCCAGGCACGA
................................................................(((((((((((((..(.(((((....))).)).).))))))))).)))).. (-21.46 = -22.02 +   0.56)

alignment

secondary structure

dotplot

Window 6

Location	4,407,979 – 4,408,074
Length	95
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	78.54
Mean single sequence MFE	-22.67
Consensus MFE	-18.52
Energy contribution	-19.52
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-3.24
Structure conservation index	0.82
SVM decision value	3.97
SVM RNA-class probability	0.999734
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4407979 95 - 22224390
UCGUGCCUGGCCCAAAAACCGUCCAACUUUGGCUCCAAUUUGGGCCAACACUGCAAAAAAAACAACACAUACAAUUGU-UAUGCAG--UUAAACUUUA-----------------
.......(((((((((......(((....)))......)))))))))..((((((.....(((((.........))))-).)))))--).........----------------- ( -22.60)
>DroSec_CAF1 10485 94 - 1
UCGUGCCUGUCCCAAAAACAGACCAACUUUGGCUCCAAUUUGGGCCAGCACUGCCAAAAA---AAUACAUACAAUUCU-UAUCAAGGAUAAAACAUUA-----------------
..((((.((.((((((...((.(((....)))))....)))))).)))))).........---..........(((((-.....))))).........----------------- ( -18.60)
>DroSim_CAF1 10578 96 - 1
UCGUGCCUGGCCCAAAAACAGACCAACUUUGGCUCCAAUUUGGGCCAGCACUGCCAAAAAAA-AACACAUACAAUUCU-UAUCAAGGAUUAAACAUUA-----------------
..((((.(((((((((...((.(((....)))))....)))))))))))))...........-.........((((((-.....))))))........----------------- ( -26.60)
>DroEre_CAF1 11303 109 - 1
UCGUGCCUUGCCCAAAAACAGUCCAACUUUGGCUCCAAUUUGGGCCAGCACUGCGGAAAA---AGCACACACAAUUGUUUAUCAA---UAACACAUAGCCGUAUUAAAUGCCUUC
..((((...(((((((...((.(((....)))))....)))))))..))))(((((...(---((((........))))).....---..........)))))............ ( -22.87)
>consensus
UCGUGCCUGGCCCAAAAACAGACCAACUUUGGCUCCAAUUUGGGCCAGCACUGCCAAAAA___AACACAUACAAUUCU_UAUCAAG__UAAAACAUUA_________________
..((((.(((((((((...((.(((....)))))....)))))))))))))................................................................ (-18.52 = -19.52 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	4,407,996 – 4,408,113
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.73
Mean single sequence MFE	-38.28
Consensus MFE	-26.46
Energy contribution	-26.54
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-3.05
Structure conservation index	0.69
SVM decision value	1.68
SVM RNA-class probability	0.971726
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4407996 117 + 22224390
-ACAAUUGUAUGUGUUGUUUUUUUUGCAGUGUUGGCCCAAAUUGGAGCCAAAGUUGGACGGUUUUUGGGCC-AGGCACGAGCCAAGAAACCGCAGAAAUGCAGCUUGCACUAAGAAA-AC
-.....((((...(((((..(((((((.((..(((((((((......(((....)))......))))))))-)(((....))).....)).))))))).))))).))))........-.. ( -38.50)
>DroSec_CAF1 10504 114 + 1
-AGAAUUGUAUGUAUU---UUUUUGGCAGUGCUGGCCCAAAUUGGAGCCAAAGUUGGUCUGUUUUUGGGAC-AGGCACGAGCCAAGAAACCGCAGAAAUGCAGCUUGCACUAAGAAA-AC
-.....((((.((..(---((((((((.(((((..((((((.((((.(((....)))))))..))))))..-.)))))..)))))))))..(((....))).)).))))........-.. ( -40.20)
>DroSim_CAF1 10597 116 + 1
-AGAAUUGUAUGUGUU-UUUUUUUGGCAGUGCUGGCCCAAAUUGGAGCCAAAGUUGGUCUGUUUUUGGGCC-AGGCACGAGCCAAGAAACCGCAGAAAUGCAGCUUGCACUAAGAAA-AC
-..........((((.-.(((((((((.(((((((((((((.((((.(((....)))))))..))))))))-).))))..)))))))))..(((....))).....)))).......-.. ( -46.10)
>DroEre_CAF1 11336 115 + 1
AACAAUUGUGUGUGCU---UUUUCCGCAGUGCUGGCCCAAAUUGGAGCCAAAGUUGGACUGUUUUUGGGCA-AGGCACGAGCCAAGAAACCGCAGAAAUGCAGCUUGCACUAAGAAA-AA
.......(((((.(((---.((((.((.(((((.(((((((..(.(((((....))).)).).))))))).-.)))))..))...))))..(((....)))))).))))).......-.. ( -37.20)
>DroYak_CAF1 10726 102 + 1
---------------U---UUUCCCCCAGUGCUGGCCCAAUUUGGAGUCAAAGUAGGACGGUUUUUGGACAAAGGCACGAGCCAAGAAACCGCAGAAAUGCAGCUUGCACUAAGAAAAAA
---------------(---((((....(((((((((((.....)).))))((((.....(((((((.......(((....))).)))))))(((....))).)))))))))..))))).. ( -29.40)
>consensus
_ACAAUUGUAUGUGUU___UUUUUCGCAGUGCUGGCCCAAAUUGGAGCCAAAGUUGGACUGUUUUUGGGCC_AGGCACGAGCCAAGAAACCGCAGAAAUGCAGCUUGCACUAAGAAA_AC
...........................(((((((((((.....)).))))((((((....(((((((((....(((....)))......)).))))))).)))))))))))......... (-26.46 = -26.54 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	4,407,996 – 4,408,113
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.73
Mean single sequence MFE	-35.93
Consensus MFE	-27.92
Energy contribution	-28.56
Covariance contribution	0.64
Combinations/Pair	1.10
Mean z-score	-3.50
Structure conservation index	0.78
SVM decision value	2.99
SVM RNA-class probability	0.998027
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4407996 117 - 22224390
GU-UUUCUUAGUGCAAGCUGCAUUUCUGCGGUUUCUUGGCUCGUGCCU-GGCCCAAAAACCGUCCAACUUUGGCUCCAAUUUGGGCCAACACUGCAAAAAAAACAACACAUACAAUUGU-
((-(((.....(((((((((((....))))))))...(((....)))(-((((((((......(((....)))......))))))))).....)))...)))))...............- ( -33.50)
>DroSec_CAF1 10504 114 - 1
GU-UUUCUUAGUGCAAGCUGCAUUUCUGCGGUUUCUUGGCUCGUGCCU-GUCCCAAAAACAGACCAACUUUGGCUCCAAUUUGGGCCAGCACUGCCAAAAA---AAUACAUACAAUUCU-
..-.......(((.((((((((....)))))))).(((((..((((.(-(.((((((...((.(((....)))))....)))))).)))))).)))))...---..)))..........- ( -32.70)
>DroSim_CAF1 10597 116 - 1
GU-UUUCUUAGUGCAAGCUGCAUUUCUGCGGUUUCUUGGCUCGUGCCU-GGCCCAAAAACAGACCAACUUUGGCUCCAAUUUGGGCCAGCACUGCCAAAAAAA-AACACAUACAAUUCU-
..-.......(((.((((((((....)))))))).(((((..((((.(-((((((((...((.(((....)))))....))))))))))))).))))).....-..)))..........- ( -41.50)
>DroEre_CAF1 11336 115 - 1
UU-UUUCUUAGUGCAAGCUGCAUUUCUGCGGUUUCUUGGCUCGUGCCU-UGCCCAAAAACAGUCCAACUUUGGCUCCAAUUUGGGCCAGCACUGCGGAAAA---AGCACACACAAUUGUU
((-(((((((((((((((((((....))))))))...(((....))).-.(((((((...((.(((....)))))....)))))))..)))))).))))))---)............... ( -37.10)
>DroYak_CAF1 10726 102 - 1
UUUUUUCUUAGUGCAAGCUGCAUUUCUGCGGUUUCUUGGCUCGUGCCUUUGUCCAAAAACCGUCCUACUUUGACUCCAAAUUGGGCCAGCACUGGGGGAAA---A---------------
.(((..((((((((((((((((....))))))))..(((((((.......(((.(((...........)))))).......)))))))))))))))..)))---.--------------- ( -34.84)
>consensus
GU_UUUCUUAGUGCAAGCUGCAUUUCUGCGGUUUCUUGGCUCGUGCCU_GGCCCAAAAACAGUCCAACUUUGGCUCCAAUUUGGGCCAGCACUGCCAAAAA___AACACAUACAAUUCU_
...(((..((((((((((((((....))))))))...(((....)))..((((((((......((......))......)))))))).))))))..)))..................... (-27.92 = -28.56 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:14 2006