Locus 3576

Sequence ID	3R_DroMel_CAF1
Location	9,673,398 – 9,673,613
Length	215
Max. P	0.986891

overview

Window 3

Location	9,673,398 – 9,673,511
Length	113
Sequences	3
Columns	115
Reading direction	reverse
Mean pairwise identity	95.36
Mean single sequence MFE	-33.00
Consensus MFE	-32.08
Energy contribution	-31.87
Covariance contribution	-0.22
Combinations/Pair	1.07
Mean z-score	-1.45
Structure conservation index	0.97
SVM decision value	0.07
SVM RNA-class probability	0.569806
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9673398 113 - 27905053
AAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUAAAUUUAUCGUAAAUGCCAUCAGCUGCAGUUGAGGCUGAGCUAAGCUCCUCC--GUAUGUUCAUCCCUCCGUCAUU
((((((((((((((((..((((((((....))).((((.........)))))))))...)))))))))..((((.(((((...((......--))..)))))..))))))))))) ( -36.60)
>DroSec_CAF1 65085 115 - 1
AAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUAAAUUUAUCGUAAAUGCCAUCAGCUGUAGUUGAGGCUGAGCUGAGCUCCUCCACGUACGUUCGUCCCUCCGUCAUU
.(..(((((((....)))))))..).....(((..(((((..............(((.(((((....)))))))).((((...)))).......)))))..)))........... ( -33.80)
>DroSim_CAF1 68023 115 - 1
AAUGAUUCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUAAAUUUAUCGUAAAUGCCAUCAGCUACAGUUGAGGCUGAGCUGAGCUCCUCCACGUACGUUCGUCCCUCCGUCAUU
..((((.((((....))))....))))(((((((((((.........)))))..((..((((((.((((....))))))))))))......(((......)))......)))))) ( -28.60)
>consensus
AAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUAAAUUUAUCGUAAAUGCCAUCAGCUGCAGUUGAGGCUGAGCUGAGCUCCUCCACGUACGUUCGUCCCUCCGUCAUU
((((((((((((((((..((((((((....))).((((.........)))))))))...)))))))))..((((.(((((.(.((........)).))))))..))))))))))) (-32.08 = -31.87 +  -0.22)

alignment

secondary structure

dotplot

Window 4

Location	9,673,431 – 9,673,551
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.83
Mean single sequence MFE	-31.10
Consensus MFE	-23.38
Energy contribution	-24.02
Covariance contribution	0.64
Combinations/Pair	1.05
Mean z-score	-2.08
Structure conservation index	0.75
SVM decision value	0.51
SVM RNA-class probability	0.762242
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9673431 120 + 27905053
GCUCAGCCUCAACUGCAGCUGAUGGCAUUUACGAUAAAUUUACGCAAGUCAUUUGACAACGCUGCAACUGCAGCAUCAUUAUGCAGGCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCA
(((((((..(....)..)))))((((((.............((....)).(((((((...(((((....)))))........((((....))))...).)))))))))).)).....)). ( -31.90)
>DroSec_CAF1 65120 120 + 1
GCUCAGCCUCAACUACAGCUGAUGGCAUUUACGAUAAAUUUACGCAAGUCAUUUGACAACGCUGCAACUGCAGCAUCAUUAUGCAGCCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCA
(((((((..........)))))((((((...............(((.(((....)))...(((((....))))).......)))((((........)))).....)))).)).....)). ( -31.10)
>DroSim_CAF1 68058 120 + 1
GCUCAGCCUCAACUGUAGCUGAUGGCAUUUACGAUAAAUUUACGCAAGUCAUUUGACAACGCUGCAACUGCAGAAUCAUUAUGCAGCCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCA
(((((((..(....)..)))))((((((...............(((.(((....)))....((((....))))........)))((((........)))).....)))).)).....)). ( -28.90)
>DroEre_CAF1 66347 106 + 1
--------------GCAGCUGAUGGCACUUACGAUAAAUUUACGCAAGUCAUUUGACAACGCUGCAACUGCAGCAUCAUUAUGCAGCCGACGGCCAGGCUCAAAAAUGCACAAAUAUGCA
--------------(((((((.((((.(....)..........(((.(((....)))...(((((....))))).......))).)))).))))...((........)).......))). ( -29.70)
>DroYak_CAF1 70180 120 + 1
GCUCAGCCUCAACUGCAGCUGAUGGCAUUUACGAUAAAUUUACGCAAGUCAUUUGACAACGCUGCAACUGCAGCAUCAUUAUGCAGCCGACGGCCAGGCUCAAAUAUGCACAAAUAUGCA
(((..(((((..(((((..((((((.......(.(((((..((....)).))))).)...(((((....))))).)))))))))))..)).)))..))).......((((......)))) ( -33.90)
>consensus
GCUCAGCCUCAACUGCAGCUGAUGGCAUUUACGAUAAAUUUACGCAAGUCAUUUGACAACGCUGCAACUGCAGCAUCAUUAUGCAGCCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCA
..............(((.......((((...............(((.(((....)))...(((((....))))).......)))((((........)))).....)))).......))). (-23.38 = -24.02 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	9,673,431 – 9,673,551
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.83
Mean single sequence MFE	-38.94
Consensus MFE	-31.48
Energy contribution	-33.48
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-2.34
Structure conservation index	0.81
SVM decision value	1.91
SVM RNA-class probability	0.982408
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9673431 120 - 27905053
UGCAUAUUUGUGCAUAUUUGAGCCUGGCAGUCGCCUGCAUAAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUAAAUUUAUCGUAAAUGCCAUCAGCUGCAGUUGAGGCUGAGC
(((((....)))))...((.(((((.((((....))))........((((((((((..((((((((....))).((((.........)))))))))...))))))))))..))))).)). ( -40.30)
>DroSec_CAF1 65120 120 - 1
UGCAUAUUUGUGCAUAUUUGAGCCUGGCAGUCGGCUGCAUAAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUAAAUUUAUCGUAAAUGCCAUCAGCUGUAGUUGAGGCUGAGC
(((((....)))))...((.(((((((((((((..((....(..(((((((....)))))))..)))..))))(((((.........))))).)))))(((((....))))))))).)). ( -41.00)
>DroSim_CAF1 68058 120 - 1
UGCAUAUUUGUGCAUAUUUGAGCCUGGCAGUCGGCUGCAUAAUGAUUCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUAAAUUUAUCGUAAAUGCCAUCAGCUACAGUUGAGGCUGAGC
(((((....)))))...((.((((((((((.((((((((.........))))))))).((((.(((....)))..))))..............)))))(((((....))))))))).)). ( -38.40)
>DroEre_CAF1 66347 106 - 1
UGCAUAUUUGUGCAUUUUUGAGCCUGGCCGUCGGCUGCAUAAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUAAAUUUAUCGUAAGUGCCAUCAGCUGC--------------
(((((....)))))...........(((.(..(((..(((.(..(((((((....)))))))..)...)))(((((((.........))))))))))..).)))..-------------- ( -32.50)
>DroYak_CAF1 70180 120 - 1
UGCAUAUUUGUGCAUAUUUGAGCCUGGCCGUCGGCUGCAUAAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUAAAUUUAUCGUAAAUGCCAUCAGCUGCAGUUGAGGCUGAGC
(((((....))))).......((..((((.(((((((((...(((((((((....)))))...(((....)))(((((.........))))).....))))..)))))))))))))..)) ( -42.50)
>consensus
UGCAUAUUUGUGCAUAUUUGAGCCUGGCAGUCGGCUGCAUAAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUAAAUUUAUCGUAAAUGCCAUCAGCUGCAGUUGAGGCUGAGC
(((((....)))))......((((((((.((((..((....(..(((((((....)))))))..)))..))))(((((.........)))))..))))(((((....))))))))).... (-31.48 = -33.48 +   2.00)

alignment

secondary structure

dotplot

Window 6

Location	9,673,471 – 9,673,591
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-33.28
Consensus MFE	-29.06
Energy contribution	-29.66
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.19
Structure conservation index	0.87
SVM decision value	2.06
SVM RNA-class probability	0.986891
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9673471 120 + 27905053
UACGCAAGUCAUUUGACAACGCUGCAACUGCAGCAUCAUUAUGCAGGCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCAAAGCAGCUACUGAUUAUUGUCGAAAGUUGUUAGCAGAAGA
..(((..(((....)))...(((((....)))))............))).((((............((((......)))).(((((((..((((....))))..))))))).)))).... ( -33.60)
>DroSec_CAF1 65160 120 + 1
UACGCAAGUCAUUUGACAACGCUGCAACUGCAGCAUCAUUAUGCAGCCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCAAAGCAGCUACUGAUUAUUGUCGAAAGUUGUUAGCAGAAGA
...(((.(((....)))...(((((....))))).......((.((((........))))))....))).......(((..(((((((..((((....))))..))))))).)))..... ( -32.80)
>DroSim_CAF1 68098 120 + 1
UACGCAAGUCAUUUGACAACGCUGCAACUGCAGAAUCAUUAUGCAGCCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCAAAGCAGCUACUGAUUAUUGUCGAAAGUUGUUAGCAGAAGA
.((....))...(((((((((((((...((((.........))))(((........))).......((((......))))..)))))...((((....))))...))))))))....... ( -29.90)
>DroEre_CAF1 66373 120 + 1
UACGCAAGUCAUUUGACAACGCUGCAACUGCAGCAUCAUUAUGCAGCCGACGGCCAGGCUCAAAAAUGCACAAAUAUGCAAAGCAGCUACUGAUGAUUGUCGAAUGUUGUUAGCAGAAGA
...((....((((((((((.(((((....))))).((((((.((((((........))))......((((......)))).....))...))))))))))))))))......))...... ( -36.40)
>DroYak_CAF1 70220 120 + 1
UACGCAAGUCAUUUGACAACGCUGCAACUGCAGCAUCAUUAUGCAGCCGACGGCCAGGCUCAAAUAUGCACAAAUAUGCAAAGCAGCUACUGAUGAUUGUCGAAAGUUGUUAGCAGAAGA
.((....))...(((((((((((((....)))))(((((((.((((((........))))......((((......)))).....))...)))))))........))))))))....... ( -33.70)
>consensus
UACGCAAGUCAUUUGACAACGCUGCAACUGCAGCAUCAUUAUGCAGCCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCAAAGCAGCUACUGAUUAUUGUCGAAAGUUGUUAGCAGAAGA
...(((.(((....)))...(((((....))))).......((.((((........))))))....))).......(((..(((((((..((((....))))..))))))).)))..... (-29.06 = -29.66 +   0.60)

alignment

secondary structure

dotplot

Window 7

Location	9,673,471 – 9,673,591
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.67
Mean single sequence MFE	-33.41
Consensus MFE	-31.17
Energy contribution	-31.57
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.93
SVM decision value	1.02
SVM RNA-class probability	0.901808
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9673471 120 - 27905053
UCUUCUGCUAACAACUUUCGACAAUAAUCAGUAGCUGCUUUGCAUAUUUGUGCAUAUUUGAGCCUGGCAGUCGCCUGCAUAAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUA
..............................((((((((...((((..(((((((...........(((....))))))))))..)))).)))))))).((((.(((....)))..)))). ( -33.70)
>DroSec_CAF1 65160 120 - 1
UCUUCUGCUAACAACUUUCGACAAUAAUCAGUAGCUGCUUUGCAUAUUUGUGCAUAUUUGAGCCUGGCAGUCGGCUGCAUAAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUA
..............................((((((((...((((..(((((((.......(((........))))))))))..)))).)))))))).((((.(((....)))..)))). ( -34.01)
>DroSim_CAF1 68098 120 - 1
UCUUCUGCUAACAACUUUCGACAAUAAUCAGUAGCUGCUUUGCAUAUUUGUGCAUAUUUGAGCCUGGCAGUCGGCUGCAUAAUGAUUCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUA
..............................((((((((..(((((....)))))((((((((((........)))).)).)))).....)))))))).((((.(((....)))..)))). ( -29.60)
>DroEre_CAF1 66373 120 - 1
UCUUCUGCUAACAACAUUCGACAAUCAUCAGUAGCUGCUUUGCAUAUUUGUGCAUUUUUGAGCCUGGCCGUCGGCUGCAUAAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUA
......((......((((.((((((.....((((((((...((((..(((((((.......(((........))))))))))..)))).))))))))...)))))).))))....))... ( -35.71)
>DroYak_CAF1 70220 120 - 1
UCUUCUGCUAACAACUUUCGACAAUCAUCAGUAGCUGCUUUGCAUAUUUGUGCAUAUUUGAGCCUGGCCGUCGGCUGCAUAAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUA
..............................((((((((...((((..(((((((.......(((........))))))))))..)))).)))))))).((((.(((....)))..)))). ( -34.01)
>consensus
UCUUCUGCUAACAACUUUCGACAAUAAUCAGUAGCUGCUUUGCAUAUUUGUGCAUAUUUGAGCCUGGCAGUCGGCUGCAUAAUGAUGCUGCAGUUGCAGCGUUGUCAAAUGACUUGCGUA
..............................((((((((...((((..(((((((.......(((........))))))))))..)))).)))))))).((((.(((....)))..)))). (-31.17 = -31.57 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	9,673,511 – 9,673,613
Length	102
Sequences	3
Columns	102
Reading direction	forward
Mean pairwise identity	97.39
Mean single sequence MFE	-26.07
Consensus MFE	-24.12
Energy contribution	-23.90
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-2.44
Structure conservation index	0.93
SVM decision value	1.11
SVM RNA-class probability	0.916574
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9673511 102 + 27905053
AUGCAGGCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCAAAGCAGCUACUGAUUAUUGUCGAAAGUUGUUAGCAGAAGAGCAAAAGCAACAGUAAGAGCAA
..((((....))))...((((.....((((......)))).(((((((..((((....))))..))))))).((......))..............)))).. ( -26.20)
>DroSec_CAF1 65200 102 + 1
AUGCAGCCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCAAAGCAGCUACUGAUUAUUGUCGAAAGUUGUUAGCAGAAGAGCAAAUGCAACAGCAACAGCAA
.(((.(((..((((............((((......)))).(((((((..((((....))))..))))))).))))..).))...(((....)))...))). ( -26.00)
>DroSim_CAF1 68138 102 + 1
AUGCAGCCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCAAAGCAGCUACUGAUUAUUGUCGAAAGUUGUUAGCAGAAGAGCAAAUGCAACAGCAACAGCAA
.(((.(((..((((............((((......)))).(((((((..((((....))))..))))))).))))..).))...(((....)))...))). ( -26.00)
>consensus
AUGCAGCCGACUGCCAGGCUCAAAUAUGCACAAAUAUGCAAAGCAGCUACUGAUUAUUGUCGAAAGUUGUUAGCAGAAGAGCAAAUGCAACAGCAACAGCAA
..((((....))))...((((.....((((......)))).(((((((..((((....))))..))))))).......))))..........((....)).. (-24.12 = -23.90 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:49 2006