Locus 3955

Sequence ID	3L_DroMel_CAF1
Location	11,491,739 – 11,492,004
Length	265
Max. P	0.992598

overview

Window 6

Location	11,491,739 – 11,491,856
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.97
Mean single sequence MFE	-43.57
Consensus MFE	-30.92
Energy contribution	-31.07
Covariance contribution	0.14
Combinations/Pair	1.20
Mean z-score	-1.93
Structure conservation index	0.71
SVM decision value	0.27
SVM RNA-class probability	0.661249
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11491739 117 - 23771897
CCCGGUAAUGCCAACGGUUGACUGGCUGCCGCCAGAAAGCUGGGCAACAGCACCUGUCGCUGGUACAAAUCGAUCAGCUGCUUAAACUGCAACAGAUUCAUAUUCAGAGCUGGUCCC---
.(((((..((((..(((((..(((((....)))))..)))))))))((((...)))).)))))........((((((((((.......))....((.......))..))))))))..--- ( -38.30)
>DroPse_CAF1 13066 112 - 1
--------CGGCAUCGGCUGGCUGGCCGCGGCCAGGAAGCUGGGCAGGAGCACCUGCCUCUGGUACAGGUCGAUCAGCUGUUUGAACUGCAGCAGAUUCAGAUUCAGACCCGAUUCCGAU
--------(((.((((((((..(((((...(((((......(((((((....))))))))))))...)))))..)))).((((((((((.(.....).))).))))))).)))).))).. ( -50.60)
>DroSec_CAF1 6806 117 - 1
CCCGGUAAUGCCAACGGUUGACUGGCUGCGGCCAAAAAGCUGGGCAACAGCACCUGUCGCUGGUACAAAUCGAUCAGCUGCUUAAACUGCAACAGAUUCAUAUUCAGAGCUGGUCCC---
.(((((..((((..(((((...((((....))))...)))))))))((((...)))).)))))........((((((((((.......))....((.......))..))))))))..--- ( -35.40)
>DroPer_CAF1 3286 107 - 1
--------CGGCAUCGGCUGGCUGGCCGCGGCCAGGAAGCUGGGCAGGAGCACCUGCCUCUGGUACAGGUCGAUCAGCUGUUUGAACUGCAGCAGAUUCAGAUUCAGACCCGAUC-----
--------(((....(((((..(((((...(((((......(((((((....))))))))))))...)))))..)))))((((((((((.(.....).))).))))))))))...----- ( -46.30)
>DroEre_CAF1 2493 117 - 1
CCCGGUAACGCCAGUGGUUGGCUGGCUGCCGCCAGAAAGCUGGGCAGCAGCACCUGUCGCUGGUACAAAUCGAUCAGCUGCUUAAACUGCAGCAGAUUCAUAUUCAAAGCUGGUCCC---
.(((((...((((((((..((...(((((.(((((....)).))).))))).))..)))))))).......((((.(((((.......))))).))))..........)))))....--- ( -47.20)
>DroYak_CAF1 3165 117 - 1
CCCGGCAACGCCAACGGUUGACUGGCUGCCGCAAGAAAGCUGGGCAGCAGCACCUGCCGCUGGUACAAAUCGAUCAGCUGCUUGAACUGCAGCAGAUUCAUAUUCAACGCUGGUCCC---
.(((((...((((.((((((.(((.(((((((......))..))))))))))...)))).)))).......((((.(((((.......))))).))))..........)))))....--- ( -43.60)
>consensus
CCCGGUAACGCCAACGGUUGACUGGCUGCCGCCAGAAAGCUGGGCAGCAGCACCUGCCGCUGGUACAAAUCGAUCAGCUGCUUAAACUGCAGCAGAUUCAUAUUCAGAGCUGGUCCC___
.........((((.(((((..(((((....)))))..)))))(((((......)))))..)))).......((((.(((((.......))))).((.......))......))))..... (-30.92 = -31.07 +   0.14)

alignment

secondary structure

dotplot

Window 7

Location	11,491,776 – 11,491,896
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.17
Mean single sequence MFE	-46.06
Consensus MFE	-38.78
Energy contribution	-40.18
Covariance contribution	1.40
Combinations/Pair	1.08
Mean z-score	-1.26
Structure conservation index	0.84
SVM decision value	-0.02
SVM RNA-class probability	0.525656
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11491776 120 - 23771897
GUCCAGAAGAGGCCCUGAAACUCCAGGACCUGCUGCUGAACCCGGUAAUGCCAACGGUUGACUGGCUGCCGCCAGAAAGCUGGGCAACAGCACCUGUCGCUGGUACAAAUCGAUCAGCUG
.......(((((.((((......)))).))).))(((((...((((..((((..(((((..(((((....)))))..)))))(((.((((...)))).)))))))...)))).))))).. ( -42.80)
>DroSec_CAF1 6843 120 - 1
GUCCAGAAGGGAUCCUGAAGCUCCAGGACCUGCUGCUGAACCCGGUAAUGCCAACGGUUGACUGGCUGCGGCCAAAAAGCUGGGCAACAGCACCUGUCGCUGGUACAAAUCGAUCAGCUG
((((((..(((.(((((......))))))))(((((.....(((((...(((...)))..)))))..))))).......)))))).((((...)))).((((((........)))))).. ( -43.10)
>DroSim_CAF1 740 120 - 1
GUCCAGAAGGGAUCCUGAAGCUCCAGGACCUGCUGCUGAGCCCGGUAAUGCCAACGGUUGACUGGCUGCCGCCAGGAAGCUGGGCAACAGCACCUGUCGCUGGUACAAAUCGAUCAGCUG
...(((..(((.(((((......))))))))..(((((.((((((.....))...((((..(((((....)))))..))))))))..))))).)))..((((((........)))))).. ( -48.80)
>DroEre_CAF1 2530 120 - 1
GUCCAGCAGGGGUCCUGAAACUGCGGGACCUGCUCCUGAUCCCGGUAACGCCAGUGGUUGGCUGGCUGCCGCCAGAAAGCUGGGCAGCAGCACCUGUCGCUGGUACAAAUCGAUCAGCUG
.....((((((((((((......)))))))((((.(((....(((((..((((((.....)))))))))))((((....)))).))).))))))))).((((((........)))))).. ( -52.80)
>DroYak_CAF1 3202 120 - 1
GUCCAGAAGUGGUCCCGACACUGCAGGACCUGCUCCUGAACCCGGCAACGCCAACGGUUGACUGGCUGCCGCAAGAAAGCUGGGCAGCAGCACCUGCCGCUGGUACAAAUCGAUCAGCUG
((.(((.((((((((.(......).))))).))).))).))..((((..((...(((....)))((((((((......))..)))))).))...))))((((((........)))))).. ( -42.80)
>consensus
GUCCAGAAGGGGUCCUGAAACUCCAGGACCUGCUGCUGAACCCGGUAAUGCCAACGGUUGACUGGCUGCCGCCAGAAAGCUGGGCAACAGCACCUGUCGCUGGUACAAAUCGAUCAGCUG
...(((...((((((((......))))))))((((.((..((((((...)))...((((..(((((....)))))..))))))))).))))..)))..((((((........)))))).. (-38.78 = -40.18 +   1.40)

alignment

secondary structure

dotplot

Window 8

Location	11,491,816 – 11,491,936
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.50
Mean single sequence MFE	-48.68
Consensus MFE	-41.04
Energy contribution	-41.08
Covariance contribution	0.04
Combinations/Pair	1.19
Mean z-score	-2.30
Structure conservation index	0.84
SVM decision value	2.33
SVM RNA-class probability	0.992535
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11491816 120 + 23771897
GCUUUCUGGCGGCAGCCAGUCAACCGUUGGCAUUACCGGGUUCAGCAGCAGGUCCUGGAGUUUCAGGGCCUCUUCUGGACAUGCGCAUUUUGCUUGAGAAUGCCGCUCAACAGAAGCUAA
((((((((((....)))))......((((((........((((((.((.(((((((((....))))))))))).))))))..(.(((((((.....)))))))))).)))).)))))... ( -49.20)
>DroSec_CAF1 6883 120 + 1
GCUUUUUGGCCGCAGCCAGUCAACCGUUGGCAUUACCGGGUUCAGCAGCAGGUCCUGGAGCUUCAGGAUCCCUUCUGGACAUGCGCAUUUUGCUGGAGAAUGCCGCUCAACAGAAGCUAA
((((((((((....)))).......((((((........((((((.((..((((((((....)))))))).)).))))))..(.(((((((.....)))))))))).))))))))))... ( -41.40)
>DroSim_CAF1 780 120 + 1
GCUUCCUGGCGGCAGCCAGUCAACCGUUGGCAUUACCGGGCUCAGCAGCAGGUCCUGGAGCUUCAGGAUCCCUUCUGGACAUGCGCAUUUUGCUGGAGAAUGCCGCUCAACAGAAGCUAA
(((((.((((((((.((((.(((....((((((..(((((((....))).((((((((....))))))))....))))..)))).))..)))))))....)))))).))...)))))... ( -48.20)
>DroEre_CAF1 2570 120 + 1
GCUUUCUGGCGGCAGCCAGCCAACCACUGGCGUUACCGGGAUCAGGAGCAGGUCCCGCAGUUUCAGGACCCCUGCUGGACAUGCGACUCUUGCUGGAGAAUGCCGCUCAACAAAAGCUAA
(((((.(((((((((((((.......)))))....((((.(..((..(((.((((.((((...........)))).)))).)))..))..).))))....)))))).))...)))))... ( -50.00)
>DroYak_CAF1 3242 120 + 1
GCUUUCUUGCGGCAGCCAGUCAACCGUUGGCGUUGCCGGGUUCAGGAGCAGGUCCUGCAGUGUCGGGACCACUUCUGGACAUGCGACUCCUGCUGGAGAAUGCCGCUCAACAGAAGCUAA
(((((...((((((.(((((........((.(((((...(((((((((..(((((((......))))))).)))))))))..))))).)).)))))....))))))......)))))... ( -54.60)
>consensus
GCUUUCUGGCGGCAGCCAGUCAACCGUUGGCAUUACCGGGUUCAGCAGCAGGUCCUGGAGUUUCAGGACCCCUUCUGGACAUGCGCAUUUUGCUGGAGAAUGCCGCUCAACAGAAGCUAA
(((((..(((((((.(((((......((((.....))))((((((.((..(((((((......))))))).)).))))))...........)))))....))))))).....)))))... (-41.04 = -41.08 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	11,491,856 – 11,491,973
Length	117
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	90.85
Mean single sequence MFE	-44.66
Consensus MFE	-37.10
Energy contribution	-38.18
Covariance contribution	1.08
Combinations/Pair	1.14
Mean z-score	-2.34
Structure conservation index	0.83
SVM decision value	2.34
SVM RNA-class probability	0.992598
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11491856 117 + 23771897
UUCAGCAGCAGGUCCUGGAGUUUCAGGGCCUCUUCUGGACAUGCGCAUUUUGCUUGAGAAUGCCGCUCAACAGAAGCUAAUGCUGCUCAAUGCAGCCGCAAGUGCAACGGCAAGUGC
...(((((((((((((((....)))))))).((((((.....(((((((((.....)))))).)))....))))))....)))))))..........(((..(((....)))..))) ( -45.80)
>DroSec_CAF1 6923 117 + 1
UUCAGCAGCAGGUCCUGGAGCUUCAGGAUCCCUUCUGGACAUGCGCAUUUUGCUGGAGAAUGCCGCUCAACAGAAGCUAAUGCUGCUCAAUGCAGCUGCAAGUGCAACGGCAAGUGC
...(((((((((((((((....)))))))).((((((.....(((((((((.....)))))).)))....))))))....)))))))..........(((..(((....)))..))) ( -43.30)
>DroSim_CAF1 820 117 + 1
CUCAGCAGCAGGUCCUGGAGCUUCAGGAUCCCUUCUGGACAUGCGCAUUUUGCUGGAGAAUGCCGCUCAACAGAAGCUAAUGCUGCUGAAUGCAGCUGCAAGUGCAACGGCAAGUGC
.(((((((((((((((((....)))))))).((((((.....(((((((((.....)))))).)))....))))))....)))))))))........(((..(((....)))..))) ( -48.30)
>DroEre_CAF1 2610 117 + 1
AUCAGGAGCAGGUCCCGCAGUUUCAGGACCCCUGCUGGACAUGCGACUCUUGCUGGAGAAUGCCGCUCAACAAAAGCUAAUGCUCCUCAAUGCAGCGGCAAGUGCAACGGCAAGUGC
...((..(((.((((.((((...........)))).)))).)))..))(((((((..(..(((((((((.....(((....)))......)).)))))))....)..)))))))... ( -42.80)
>DroYak_CAF1 3282 117 + 1
UUCAGGAGCAGGUCCUGCAGUGUCGGGACCACUUCUGGACAUGCGACUCCUGCUGGAGAAUGCCGCUCAACAGAAGCUAAUGCUGCUCAAUGCAGCUGCAAGUGCAACAGCAAGUGC
......(((.(((((((......)))))))..(((((.....(((.((((....)))).....)))....))))))))...(((((.....))))).(((..(((....)))..))) ( -43.10)
>consensus
UUCAGCAGCAGGUCCUGGAGUUUCAGGACCCCUUCUGGACAUGCGCAUUUUGCUGGAGAAUGCCGCUCAACAGAAGCUAAUGCUGCUCAAUGCAGCUGCAAGUGCAACGGCAAGUGC
...((((((((((((((......))))))).((((((.....(((((((((.....)))))).)))....))))))....)))))))..........(((..(((....)))..))) (-37.10 = -38.18 +   1.08)

alignment

secondary structure

dotplot

Window 0

Location	11,491,856 – 11,491,973
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	90.85
Mean single sequence MFE	-43.62
Consensus MFE	-35.52
Energy contribution	-36.36
Covariance contribution	0.84
Combinations/Pair	1.15
Mean z-score	-1.92
Structure conservation index	0.81
SVM decision value	1.28
SVM RNA-class probability	0.939967
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11491856 117 - 23771897
GCACUUGCCGUUGCACUUGCGGCUGCAUUGAGCAGCAUUAGCUUCUGUUGAGCGGCAUUCUCAAGCAAAAUGCGCAUGUCCAGAAGAGGCCCUGAAACUCCAGGACCUGCUGCUGAA
(((...(((((.......)))))))).((.((((((.....((((((....(((.((((.........))))))).....))))))(((.((((......)))).))))))))).)) ( -41.80)
>DroSec_CAF1 6923 117 - 1
GCACUUGCCGUUGCACUUGCAGCUGCAUUGAGCAGCAUUAGCUUCUGUUGAGCGGCAUUCUCCAGCAAAAUGCGCAUGUCCAGAAGGGAUCCUGAAGCUCCAGGACCUGCUGCUGAA
.....(((.(((((....))))).)))((.(((((((....((((((....(((.((((.........))))))).....))))))((.(((((......)))))))))))))).)) ( -42.50)
>DroSim_CAF1 820 117 - 1
GCACUUGCCGUUGCACUUGCAGCUGCAUUCAGCAGCAUUAGCUUCUGUUGAGCGGCAUUCUCCAGCAAAAUGCGCAUGUCCAGAAGGGAUCCUGAAGCUCCAGGACCUGCUGCUGAG
.....(((.(((((....))))).))).(((((((((....((((((....(((.((((.........))))))).....))))))((.(((((......)))))))))))))))). ( -46.40)
>DroEre_CAF1 2610 117 - 1
GCACUUGCCGUUGCACUUGCCGCUGCAUUGAGGAGCAUUAGCUUUUGUUGAGCGGCAUUCUCCAGCAAGAGUCGCAUGUCCAGCAGGGGUCCUGAAACUGCGGGACCUGCUCCUGAU
((((((...((((....(((((((.((...((((((....))))))..))))))))).....))))..)))).)).....(((.((((((((((......)))))))).)).))).. ( -44.60)
>DroYak_CAF1 3282 117 - 1
GCACUUGCUGUUGCACUUGCAGCUGCAUUGAGCAGCAUUAGCUUCUGUUGAGCGGCAUUCUCCAGCAGGAGUCGCAUGUCCAGAAGUGGUCCCGACACUGCAGGACCUGCUCCUGAA
(((..(((....)))..))).(((((.....)))))....((((((((((((.......)).)))))))))).(((.((((...((((.......))))...)))).)))....... ( -42.80)
>consensus
GCACUUGCCGUUGCACUUGCAGCUGCAUUGAGCAGCAUUAGCUUCUGUUGAGCGGCAUUCUCCAGCAAAAUGCGCAUGUCCAGAAGGGGUCCUGAAACUCCAGGACCUGCUGCUGAA
.....(((.(((((....))))).)))...((((((.....((((((....(((((........))......))).....))))))((((((((......))))))))))))))... (-35.52 = -36.36 +   0.84)

alignment

secondary structure

dotplot

Window 1

Location	11,491,896 – 11,492,004
Length	108
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	87.10
Mean single sequence MFE	-37.06
Consensus MFE	-30.20
Energy contribution	-31.12
Covariance contribution	0.92
Combinations/Pair	1.07
Mean z-score	-2.01
Structure conservation index	0.81
SVM decision value	1.22
SVM RNA-class probability	0.931733
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11491896 108 + 23771897
AUGCGCAUUUUGCUUGAGAAUGCCGCUCAACAGAAGCUAAUGCUGCUCAAUGCAGCCGCAAGUGCAACGGCAAGUGCAGUGGCAGC---------CACAACAAUCAACUCCGGUCAA
.(((((.(((((.(((((.......))))))))))(((...(((((.....))))).((....))...)))..)))))((((...)---------)))................... ( -31.00)
>DroSec_CAF1 6963 108 + 1
AUGCGCAUUUUGCUGGAGAAUGCCGCUCAACAGAAGCUAAUGCUGCUCAAUGCAGCUGCAAGUGCAACGGCAAGUGCAGUGGCAGC---------CACAACAAUGGACUCCGGUCAA
...........(((((((..((((((...............(((((.....)))))((((..(((....)))..)))))))))).(---------((......))).)))))))... ( -39.70)
>DroSim_CAF1 860 108 + 1
AUGCGCAUUUUGCUGGAGAAUGCCGCUCAACAGAAGCUAAUGCUGCUGAAUGCAGCUGCAAGUGCAACGGCAAGUGCAGUGGCAGC---------CACAACAAUGGACUAAGGUCAA
.....(((((((.(((....((((((....(((.(((....))).)))...)).((((((..(((....)))..)))))))))).)---------))))).))))(((....))).. ( -38.20)
>DroEre_CAF1 2650 117 + 1
AUGCGACUCUUGCUGGAGAAUGCCGCUCAACAAAAGCUAAUGCUCCUCAAUGCAGCGGCAAGUGCAACGGCAAGUGCGGUGGCAAGUGCGGCAACCACAACGAUGAAUUCCGGCCAG
...((.(.(((((((..(..(((((((((.....(((....)))......)).)))))))....)..))))))).))).((((..(((.(....))))..((........)))))). ( -39.80)
>DroYak_CAF1 3322 108 + 1
AUGCGACUCCUGCUGGAGAAUGCCGCUCAACAGAAGCUAAUGCUGCUCAAUGCAGCUGCAAGUGCAACAGCAAGUGCCGUGGCAAG---------CACAACCAUGGACUCCGGGCAA
.(((..((((....))))..((((((...............(((((.....))))).(((..(((....)))..))).)))))).)---------))...((.(((...)))))... ( -36.60)
>consensus
AUGCGCAUUUUGCUGGAGAAUGCCGCUCAACAGAAGCUAAUGCUGCUCAAUGCAGCUGCAAGUGCAACGGCAAGUGCAGUGGCAGC_________CACAACAAUGGACUCCGGUCAA
..........((((((((..(((((((..............(((((.....))))).(((..(((....)))..)))))))))).............((....))..)))))).)). (-30.20 = -31.12 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:56 2006