Locus 6311

Sequence ID	X_DroMel_CAF1
Location	15,973,907 – 15,974,187
Length	280
Max. P	0.998038

overview

Window 8

Location	15,973,907 – 15,974,027
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.09
Mean single sequence MFE	-22.63
Consensus MFE	-17.49
Energy contribution	-18.80
Covariance contribution	1.31
Combinations/Pair	1.14
Mean z-score	-1.46
Structure conservation index	0.77
SVM decision value	-0.02
SVM RNA-class probability	0.525912
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15973907 120 + 22224390
AAAUACAUAUAUUUUCUACAUUUCGGAAAUGCCUGAAAAGGUGAAUAUAGCUAUGUAUAUUUCACAUAAUAAUAUCAGGGCCAACAAUGUUAUUAGUGUGUGAAAAUAAAAGCUUAGUUU
..(((((((.((((((........))))))((((....)))).........))))))).(((((((((.(((((.((..(....)..)).))))).)))))))))............... ( -26.00)
>DroSec_CAF1 41797 112 + 1
A----UAUAUAUUUUCUACAUUUCGGAAACGCCUGAAAAGGUGACUAUACCU----AUAAUUCACAUAAUAAUAUCAGGGCCAACAAUGUUAUUAGUGUGUGAAAAUAAAAGCUUGGUUU
.----.......(((((.......)))))(((((....)))))((((.....----....((((((((.(((((.((..(....)..)).))))).))))))))..........)))).. ( -21.81)
>DroSim_CAF1 32964 112 + 1
A----UAUAUAUUUUCUACAUUUCGGAAACGCCUGAAAGGGUGACUAUACCU----AUAAUUCACAUAAUAAUAUCAGGGCCAACAAUGUUAUUAGUGUGUGAAAAUAAAAGCUUGGUUU
.----.......(((((.......)))))(((((....)))))((((.....----....((((((((.(((((.((..(....)..)).))))).))))))))..........)))).. ( -21.71)
>DroEre_CAF1 40631 112 + 1
A----AAUGUAUUUUGUAUAUUUCGGAAACGCCUGAAAAGGUGACUAUACUU----AUAAUUCAUUUAAUAAUAUCAGGGCCAACAAUGUUAUUAGUGUGUGAAAAUAAAAGCAUAGUUU
(----(((((((...)))))))).(....)((((....))))((((((.(((----.((.(((((((((((((((...(.....).))))))))))...)))))..)).))).)))))). ( -21.00)
>consensus
A____UAUAUAUUUUCUACAUUUCGGAAACGCCUGAAAAGGUGACUAUACCU____AUAAUUCACAUAAUAAUAUCAGGGCCAACAAUGUUAUUAGUGUGUGAAAAUAAAAGCUUAGUUU
.............................(((((....))))).................((((((((.(((((.((..(....)..)).))))).))))))))................ (-17.49 = -18.80 +   1.31)

alignment

secondary structure

dotplot

Window 9

Location	15,974,027 – 15,974,147
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.50
Mean single sequence MFE	-28.46
Consensus MFE	-27.06
Energy contribution	-27.46
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.84
Structure conservation index	0.95
SVM decision value	2.08
SVM RNA-class probability	0.987558
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15974027 120 + 22224390
UACGGCAUUUGCGUUCAUGGAAACUGUUUGGCAUGCGUGUUAAUUUGAAUAUAAAAGCAUAUUAAAAACGCGCCGCAACGCUCUUAAUUUCUCAAGCCACCAAAUGCAUGAUUAAUUCAU
....(((((((.((....(....).....(((..(((((((......(((((......)))))...))))))).((...))..............))))))))))))((((.....)))) ( -24.70)
>DroSec_CAF1 41909 120 + 1
UACGGCAUUUGCGUUCAUGGAAACUGUUUGGCAUGCGUGUUAAUUUGAAUAUAAAAGCAUAUUAAAAACGCGCUGCAACGCGCUUAAUUUCUCAAGCCAUCAAAUGCAUGAUUAAUUCAU
....(((((((((((...(....)......(((.(((((((......(((((......)))))...)))))))))))))))((((........))))....))))))((((.....)))) ( -29.40)
>DroSim_CAF1 33076 120 + 1
UACGGCAUUUGCGUUCAUGGAAACUGUUUGGCAUGCGUGUUAAUUUGAAUAUAAAAGCAUAUUAAAAACGCGCUGCAACGCGCUUAAUUUCUCAAGCCAUCAAAUGCAUGAUUAAUUCAU
....(((((((((((...(....)......(((.(((((((......(((((......)))))...)))))))))))))))((((........))))....))))))((((.....)))) ( -29.40)
>DroEre_CAF1 40743 120 + 1
UACGGCAUUUGCGUUCAUGGAAACUGUUUGGCAUGCGUGUUAAUUUGAAUAUAAAAGCAUAUUAAAAACGCGCUGCAACGCGCUUAAUUUCUCAAGCCACCAAAUGCAUGAUUAAUUCAU
....(((((((((((...(....)......(((.(((((((......(((((......)))))...)))))))))))))))((((........))))....))))))((((.....)))) ( -29.40)
>DroYak_CAF1 24520 120 + 1
UACGGCAUUUGCGUUCAUGGAAACUGUUUGGCAUGCGUGUUAAUUUGAAUAUAAAAGCAUAUUAAAAACGCGCUGCAACGCGCUUAAUUUCUCAAGCCACAAAAUGCAUGAUUAAUUCAU
....(((((((((((...(....)......(((.(((((((......(((((......)))))...)))))))))))))))((((........))))....))))))((((.....)))) ( -29.40)
>consensus
UACGGCAUUUGCGUUCAUGGAAACUGUUUGGCAUGCGUGUUAAUUUGAAUAUAAAAGCAUAUUAAAAACGCGCUGCAACGCGCUUAAUUUCUCAAGCCACCAAAUGCAUGAUUAAUUCAU
....(((((((((((...(....)......(((.(((((((......(((((......)))))...)))))))))))))))((((........))))....))))))((((.....)))) (-27.06 = -27.46 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	15,974,027 – 15,974,147
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.50
Mean single sequence MFE	-27.99
Consensus MFE	-27.26
Energy contribution	-27.30
Covariance contribution	0.04
Combinations/Pair	1.02
Mean z-score	-1.49
Structure conservation index	0.97
SVM decision value	1.19
SVM RNA-class probability	0.927863
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15974027 120 - 22224390
AUGAAUUAAUCAUGCAUUUGGUGGCUUGAGAAAUUAAGAGCGUUGCGGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUAACACGCAUGCCAAACAGUUUCCAUGAACGCAAAUGCCGUA
((((.....))))(((((((.((((.......(((((((((((......)))))))))))((((....................))))))))....((((....)))).))))))).... ( -25.75)
>DroSec_CAF1 41909 120 - 1
AUGAAUUAAUCAUGCAUUUGAUGGCUUGAGAAAUUAAGCGCGUUGCAGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUAACACGCAUGCCAAACAGUUUCCAUGAACGCAAAUGCCGUA
((((.....))))((((((....((((((....))))))(((((((((((.((((((((((((....)))))).)))..))).))).)))....((.......))))))))))))).... ( -28.70)
>DroSim_CAF1 33076 120 - 1
AUGAAUUAAUCAUGCAUUUGAUGGCUUGAGAAAUUAAGCGCGUUGCAGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUAACACGCAUGCCAAACAGUUUCCAUGAACGCAAAUGCCGUA
((((.....))))((((((....((((((....))))))(((((((((((.((((((((((((....)))))).)))..))).))).)))....((.......))))))))))))).... ( -28.70)
>DroEre_CAF1 40743 120 - 1
AUGAAUUAAUCAUGCAUUUGGUGGCUUGAGAAAUUAAGCGCGUUGCAGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUAACACGCAUGCCAAACAGUUUCCAUGAACGCAAAUGCCGUA
((((.....))))((((((....((((((....))))))(((((((((((.((((((((((((....)))))).)))..))).))).)))....((.......))))))))))))).... ( -28.70)
>DroYak_CAF1 24520 120 - 1
AUGAAUUAAUCAUGCAUUUUGUGGCUUGAGAAAUUAAGCGCGUUGCAGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUAACACGCAUGCCAAACAGUUUCCAUGAACGCAAAUGCCGUA
((((.....))))((((((....((((((....))))))(((((((((((.((((((((((((....)))))).)))..))).))).)))....((.......))))))))))))).... ( -28.10)
>consensus
AUGAAUUAAUCAUGCAUUUGGUGGCUUGAGAAAUUAAGCGCGUUGCAGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUAACACGCAUGCCAAACAGUUUCCAUGAACGCAAAUGCCGUA
((((.....))))((((((....((((((....))))))(((((((((((.((((((((((((....)))))).)))..))).))).)))....((.......))))))))))))).... (-27.26 = -27.30 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	15,974,067 – 15,974,187
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.00
Mean single sequence MFE	-34.07
Consensus MFE	-31.56
Energy contribution	-31.44
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-2.13
Structure conservation index	0.93
SVM decision value	2.99
SVM RNA-class probability	0.998038
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15974067 120 - 22224390
ACCGGUUGACAAUUCUCUGGGAAAAUCUGGCUGCCGCGCAAUGAAUUAAUCAUGCAUUUGGUGGCUUGAGAAAUUAAGAGCGUUGCGGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUA
....((((.((((.((((.......((.(((..(((.(((.(((.....))))))...)))..))).)).......)))).))))))))((((.......))))................ ( -30.64)
>DroSec_CAF1 41949 120 - 1
ACCGGUUGACAAUUCUCUGGGAAAAUCUGGCUGCCGCGCAAUGAAUUAAUCAUGCAUUUGAUGGCUUGAGAAAUUAAGCGCGUUGCAGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUA
.((((..((....)).))))(((......(((((.((((.........((((......)))).((((((....)))))))))).)))))((((.......)))).......)))...... ( -35.00)
>DroSim_CAF1 33116 120 - 1
ACCGGUUGACAAUUCUCUGGGAAAAUCUGGCUGCCGCGCAAUGAAUUAAUCAUGCAUUUGAUGGCUUGAGAAAUUAAGCGCGUUGCAGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUA
.((((..((....)).))))(((......(((((.((((.........((((......)))).((((((....)))))))))).)))))((((.......)))).......)))...... ( -35.00)
>DroEre_CAF1 40783 120 - 1
CCCGGUUGACAAUUGUCUGGGAAAAUCUGGCUGCCGCGCAAUGAAUUAAUCAUGCAUUUGGUGGCUUGAGAAAUUAAGCGCGUUGCAGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUA
((((...(((....)))))))........(((((.((((.........((((......)))).((((((....)))))))))).)))))((((.......))))................ ( -35.20)
>DroYak_CAF1 24560 120 - 1
CCCGGUUGACAAUUCUCUGGGAAAAACUGGCUGUCGCGCAAUGAAUUAAUCAUGCAUUUUGUGGCUUGAGAAAUUAAGCGCGUUGCAGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUA
(((((..((....)).)))))((((((..(((((.((((.((((.....))))..........((((((....)))))))))).)))))..))))))....................... ( -34.50)
>consensus
ACCGGUUGACAAUUCUCUGGGAAAAUCUGGCUGCCGCGCAAUGAAUUAAUCAUGCAUUUGGUGGCUUGAGAAAUUAAGCGCGUUGCAGCGCGUUUUUAAUAUGCUUUUAUAUUCAAAUUA
.((((...........))))(((......(((((.((((.((((.....))))..........((((((....)))))))))).)))))((((.......)))).......)))...... (-31.56 = -31.44 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:21 2006