Locus 1461

Sequence ID	2L_DroMel_CAF1
Location	3,870,638 – 3,870,772
Length	134
Max. P	0.663273

overview

Window 9

Location	3,870,638 – 3,870,752
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.93
Mean single sequence MFE	-40.99
Consensus MFE	-27.33
Energy contribution	-27.87
Covariance contribution	0.53
Combinations/Pair	1.25
Mean z-score	-2.29
Structure conservation index	0.67
SVM decision value	0.07
SVM RNA-class probability	0.567890
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3870638 114 + 22407834
UGCUACUUACGAAGGCCCAGCUCGAGAACGAGCGAAAGAUUCAGCAGCUGCAGAUGCAGGCCAUCAAUGCGCUGUGGAAAAAGGUGUCCACCAUGGA---GGUGGAUCCCAAGGGAA---
...............(((.(((((....)))))......(((.(((((.(((((((.....))))..)))))))).)))...((..((((((.....---))))))..))..)))..--- ( -41.80)
>DroVir_CAF1 25091 114 + 1
UGCUGCUGACUAAGGCGCAGCUGCAGAACGAGCGCAAAAUCCAACAGCUUCAGAUGCAGGCCAUCAAUGCGCUGUGGAAAAAGGUGUCUACCAUGCA---AGUAGAUCCCAAGGCUG---
(((.((((.(......))))).))).....(((......((((.((((....((((.....)))).....))))))))....((..(((((......---.)))))..))...))).--- ( -32.80)
>DroPse_CAF1 12723 120 + 1
UGCGGCUGACCAAGGCGCAGCUGGAGAACGAGCGCAAGAUCCAACAGCUGCAAAUGCAGGCCAUCAAUGCGCUGUGGAAGAAGGUGUCCACCAUGCAUGUGGUGGAUCCUAAGGCAGCAG
(((.(((..(((.((((((((((......((.(....).))...)))))))....(((.........)))))).)))....(((.(((((((((....))))))))))))..))).))). ( -49.10)
>DroWil_CAF1 20511 114 + 1
UGCUGCUGACCAAGGCGCAGCUGGAGAACGAACGAAAGAUUCAACAGUUGCAAAUGCAGGCCAUUAAUGCACUGUGGAAGAAGGUUUCCACAAUGGAAAUUGUGGACACAAAAG------
..((.((..((.....(((((((..(((....(....).)))..)))))))....((((((.......)).)))))).)).))((.((((((((....)))))))).)).....------ ( -35.70)
>DroMoj_CAF1 16339 114 + 1
UGAUAAUGACCAAGGUGCAGCUGCAGAACGAGCGCAAGAUACAACAGCUGCAAAUGCAGGCCAUCAAUGCGCUGUGGAAGAAGGUGUCCACCAUGCA---GGUGGACCCGAAGGCUG---
......((....(..((((((((.........(....)......))))))))..).))((((.((......((.....))..((.(((((((.....---))))))))))).)))).--- ( -37.46)
>DroPer_CAF1 13315 120 + 1
UGCGGCUGACCAAGGCGCAGCUGGAGAACGAGCGCAAGAUCCAACAGCUGCAAAUGCAGGCCAUCAAUGCGCUGUGGAAGAAGGUGUCCACCAUGCAUGUGGUGGAUCCUAAGGCAGCAG
(((.(((..(((.((((((((((......((.(....).))...)))))))....(((.........)))))).)))....(((.(((((((((....))))))))))))..))).))). ( -49.10)
>consensus
UGCUGCUGACCAAGGCGCAGCUGGAGAACGAGCGCAAGAUCCAACAGCUGCAAAUGCAGGCCAUCAAUGCGCUGUGGAAGAAGGUGUCCACCAUGCA___GGUGGAUCCCAAGGCAG___
.........(((.((((((((((......((.(....).))...)))))))....(((.........)))))).))).....((.(((((((........)))))))))........... (-27.33 = -27.87 +   0.53)

alignment

secondary structure

dotplot

Window 0

Location	3,870,678 – 3,870,772
Length	94
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	77.16
Mean single sequence MFE	-31.28
Consensus MFE	-19.86
Energy contribution	-20.67
Covariance contribution	0.81
Combinations/Pair	1.14
Mean z-score	-1.39
Structure conservation index	0.63
SVM decision value	0.27
SVM RNA-class probability	0.663273
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3870678 94 + 22407834
UCAGCAGCUGCAGAUGCAGGCCAUCAAUGCGCUGUGGAAAAAGGUGUCCACCAUGGA---GGUGGAUCCCAAGGGAA---UACCUGCUGCUGCGGAACAG
.(((((((.((((.((((.........))))))))......(((((((((((.....---))))))(((....))).---))))))))))))........ ( -37.70)
>DroGri_CAF1 14348 88 + 1
UCAACAGCUGCAGAUGCAGGCCAUCAAUGCGCUGUGGAAAAAGGUGUCCACCAUGCA---GGUCGAACCCAAAGCUG---AACAG----GCUGAGAAC--
....(((((.(((.((..((((.....((((..(((((........)))))..))))---)))).....))...)))---....)----)))).....-- ( -23.50)
>DroYak_CAF1 2306 94 + 1
UCAGCAGCUGCAGAUGCAGGCCAUCAAUGCGCUGUGGAAAAAGGUGUCCACCAUGGA---GGUUGAUCCCAAGGGAA---UACCAGCUACUGGGGAACAG
((.(((((.(((((((.....))))..)))))))).)).....((.(((.((((((.---(((...(((....))).---.)))..))).)))))))).. ( -28.60)
>DroMoj_CAF1 16379 85 + 1
ACAACAGCUGCAAAUGCAGGCCAUCAAUGCGCUGUGGAAGAAGGUGUCCACCAUGCA---GGUGGACCCGAAGGCUG------------GCGGCGAGCAC
......(((((....((.((((.((......((.....))..((.(((((((.....---))))))))))).)))).------------)).)).))).. ( -32.00)
>DroAna_CAF1 17177 94 + 1
CCAGCAACUGCAGAUGCAGGCCAUCAAUGCGCUGUGGAAAAAGGUGUCCACCAUGCA---AGUGGACCCCAAAGGCG---UGCCUCCAGCCGUGGACCAG
.((((..((((....))))((.......))))))(((.....((.((((((......---.)))))).))...(((.---........))).....))). ( -30.80)
>DroPer_CAF1 13355 100 + 1
CCAACAGCUGCAAAUGCAGGCCAUCAAUGCGCUGUGGAAGAAGGUGUCCACCAUGCAUGUGGUGGAUCCUAAGGCAGCAGGACAAGUCGCCGCAGUUUCG
.....((((((......((((((((((((((..(((((........)))))..))))).))))))..)))..(((.((.......)).)))))))))... ( -35.10)
>consensus
UCAACAGCUGCAGAUGCAGGCCAUCAAUGCGCUGUGGAAAAAGGUGUCCACCAUGCA___GGUGGAUCCCAAGGCAG___UACCAGC_GCCGGGGAACAG
...(((((.(((((((.....))))..)))))))).......((.(((((((........))))))).)).............................. (-19.86 = -20.67 +   0.81)

alignment

secondary structure

dotplot

Window 1

Location	3,870,678 – 3,870,772
Length	94
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	77.16
Mean single sequence MFE	-31.64
Consensus MFE	-18.67
Energy contribution	-18.83
Covariance contribution	0.17
Combinations/Pair	1.14
Mean z-score	-1.48
Structure conservation index	0.59
SVM decision value	0.08
SVM RNA-class probability	0.574579
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3870678 94 - 22407834
CUGUUCCGCAGCAGCAGGUA---UUCCCUUGGGAUCCACC---UCCAUGGUGGACACCUUUUUCCACAGCGCAUUGAUGGCCUGCAUCUGCAGCUGCUGA
........(((((((((((.---.(((....)))((((((---.....)))))).))))...........(((..((((.....))))))).))))))). ( -36.10)
>DroGri_CAF1 14348 88 - 1
--GUUCUCAGC----CUGUU---CAGCUUUGGGUUCGACC---UGCAUGGUGGACACCUUUUUCCACAGCGCAUUGAUGGCCUGCAUCUGCAGCUGUUGA
--.......((----((((.---.......((((((.(((---.....))).)).))))......)))).)).(..(((((.(((....))))))))..) ( -25.94)
>DroYak_CAF1 2306 94 - 1
CUGUUCCCCAGUAGCUGGUA---UUCCCUUGGGAUCAACC---UCCAUGGUGGACACCUUUUUCCACAGCGCAUUGAUGGCCUGCAUCUGCAGCUGCUGA
........(((((((((((.---.(((....)))...)))---......(((((........)))))...(((..((((.....))))))))))))))). ( -30.80)
>DroMoj_CAF1 16379 85 - 1
GUGCUCGCCGC------------CAGCCUUCGGGUCCACC---UGCAUGGUGGACACCUUCUUCCACAGCGCAUUGAUGGCCUGCAUUUGCAGCUGUUGU
(((((.((...------------..))....(((((((((---.....))))))).)).........)))))...((((((.(((....))))))))).. ( -30.80)
>DroAna_CAF1 17177 94 - 1
CUGGUCCACGGCUGGAGGCA---CGCCUUUGGGGUCCACU---UGCAUGGUGGACACCUUUUUCCACAGCGCAUUGAUGGCCUGCAUCUGCAGUUGCUGG
.(((.....(((..((((..---..))))..).(((((((---.....))))))).)).....)))((((((.......))((((....))))..)))). ( -34.20)
>DroPer_CAF1 13355 100 - 1
CGAAACUGCGGCGACUUGUCCUGCUGCCUUAGGAUCCACCACAUGCAUGGUGGACACCUUCUUCCACAGCGCAUUGAUGGCCUGCAUUUGCAGCUGUUGG
.(((...((((((........))))))....((.(((((((......)))))))..)))))..((((((((((..((((.....))))))).)))).))) ( -32.00)
>consensus
CUGUUCCCCGGC_GCAGGUA___CUCCCUUGGGAUCCACC___UGCAUGGUGGACACCUUUUUCCACAGCGCAUUGAUGGCCUGCAUCUGCAGCUGCUGA
..............................((..((((((........))))))..))......(((((((((..((((.....))))))).)))).)). (-18.67 = -18.83 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:17 2006