Locus 1722

Sequence ID	2R_DroMel_CAF1
Location	6,477,276 – 6,477,441
Length	165
Max. P	0.815367

overview

Window 4

Location	6,477,276 – 6,477,369
Length	93
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	87.03
Mean single sequence MFE	-23.28
Consensus MFE	-16.94
Energy contribution	-16.74
Covariance contribution	-0.20
Combinations/Pair	1.16
Mean z-score	-1.79
Structure conservation index	0.73
SVM decision value	0.27
SVM RNA-class probability	0.660731
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6477276 93 + 20766785
--UCGGGACUUUGGCUAGCUCAUUAAAUUUUCCAUUCCAUUUUUUGAGCUCUGCUUUGGCUGCGUUGUGUGCAACAAAAUGUUGCCA-UCGACCAC
--...((.((..(((.((((((..((((..........))))..))))))..)))..))))(.((((((.(((((.....)))))))-.))))).. ( -25.40)
>DroSec_CAF1 45408 93 + 1
--UCGGGACUUUGGCUAGCUCAUUAAAUUUUCCAUUCCAUUUUUUGAGCUCUGCUUUGGCUGCGUUGUGUGCAACAAAAUGUUGCCA-UCGACCAC
--...((.((..(((.((((((..((((..........))))..))))))..)))..))))(.((((((.(((((.....)))))))-.))))).. ( -25.40)
>DroEre_CAF1 43574 90 + 1
--UCGGGACUUUGGCUAGCUCAUUAAAUUUUCCAUUCCAUUUUUUGAGCUCUGCUUUGACUGCGUUGUGUGCAACAAAAUGUUGCCA-UCGGC---
--.(((......(((.((((((..((((..........))))..))))))..)))....))).((((((.(((((.....)))))))-.))))--- ( -22.30)
>DroYak_CAF1 48101 90 + 1
--UUGGGACUUUGGCUAGCUCAUUAAAUUUUCCAUUCCAUUUUUUGAGCUCUGCUUUGGCUGCGUUGUGUGCAACAAAAUGUUGCCA-UCGGC---
--...((.((..(((.((((((..((((..........))))..))))))..)))..))))..((((((.(((((.....)))))))-.))))--- ( -24.00)
>DroAna_CAF1 45382 86 + 1
CUUUGGGACUCUGGCUAGCUCAUUAAAUUUUCC-----AUUUUUUGUGCGAUGCUUU--CUAUGUUUUGAGCAGCAAAAUGUUGCCCCAUGGC---
((.((((.....(((..((.((..((((.....-----))))..)).))...)))..--...........(((((.....))))))))).)).--- ( -19.30)
>consensus
__UCGGGACUUUGGCUAGCUCAUUAAAUUUUCCAUUCCAUUUUUUGAGCUCUGCUUUGGCUGCGUUGUGUGCAACAAAAUGUUGCCA_UCGGC___
...(((......(((.((((((..((((..........))))..))))))..)))....))).((((...(((((.....)))))....))))... (-16.94 = -16.74 +  -0.20)

alignment

secondary structure

dotplot

Window 5

Location	6,477,338 – 6,477,441
Length	103
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	80.45
Mean single sequence MFE	-28.17
Consensus MFE	-15.69
Energy contribution	-17.92
Covariance contribution	2.22
Combinations/Pair	1.14
Mean z-score	-1.94
Structure conservation index	0.56
SVM decision value	0.11
SVM RNA-class probability	0.586745
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6477338 103 + 20766785
UUGUGUGCAACAAAAUGUUGCCA-UCGACCAC----CAGUGGGAAUCCCCGGAGCCUUUGGCCCCGGCCAA-AAGCAAUCAAAAGUCAAUGGGCAACACUUAAAAUGUC
((((.....))))..(((((((.-..(((...----...((((....))))..((.((((((....)))))-).))........)))....)))))))........... ( -31.50)
>DroSec_CAF1 45470 103 + 1
UUGUGUGCAACAAAAUGUUGCCA-UCGACCAC----CAGUGGGAAUCCCCGGAGCCUUUGGACCCGGCCAA-AAGCAAUCAAAAGUCAAUGGGCAACACUUAAAAUGUC
((((.....))))..(((((((.-..(((...----...((((....))))..((.(((((......))))-).))........)))....)))))))........... ( -26.70)
>DroEre_CAF1 43636 100 + 1
UUGUGUGCAACAAAAUGUUGCCA-UCGGC-------CAGCGGGAAUCCCCGGAGCCUUUGGCCCCGGCCAA-AAGCAAUCAAAAGUCAAUGGGCAACACUUAAAAUGUC
..(((((((((.....)))))..-...((-------(..((((....))))..((.((((((....)))))-).))...............))).)))).......... ( -33.20)
>DroYak_CAF1 48163 100 + 1
UUGUGUGCAACAAAAUGUUGCCA-UCGGC-------CAGCGGGAAUCCCCGGAGCCUUUGGCCCCGGCCAA-AAGCAAUCAAAAGUCAAUGGGCAACACUUAAAAUGUC
..(((((((((.....)))))..-...((-------(..((((....))))..((.((((((....)))))-).))...............))).)))).......... ( -33.20)
>DroMoj_CAF1 38983 90 + 1
------ACAGCAAA---UAGCAA-UUCAGC--UGCGUAUCCGUAUUCCCAGUAG-----AGCCAAAGCCAA-AAGUAAUCAAACGUCAAUGG-GAACACUUAAAAUGUC
------...(((..---((((..-....))--)).......((.((((((...(-----(((....))...-..((......)).))..)))-))).))......))). ( -12.80)
>DroAna_CAF1 45439 101 + 1
UUUUGAGCAGCAAAAUGUUGCCCCAUGGC-------CAUC-GGAAUUCCCGCAGGCUUUGGCCCUGGCCAAAAAGCAAUCAAAAGUCAAUGGGCAACACUUAAAAUGUC
(((((((........((((((((..((((-------...(-((.....)))...((((((((....))))..))))........))))..))))))))))))))).... ( -31.60)
>consensus
UUGUGUGCAACAAAAUGUUGCCA_UCGAC_______CAGCGGGAAUCCCCGGAGCCUUUGGCCCCGGCCAA_AAGCAAUCAAAAGUCAAUGGGCAACACUUAAAAUGUC
...............(((((((....(((..........((((....))))..((..(((((....)))))...))........)))....)))))))........... (-15.69 = -17.92 +   2.22)

alignment

secondary structure

dotplot

Window 6

Location	6,477,338 – 6,477,441
Length	103
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	80.45
Mean single sequence MFE	-35.53
Consensus MFE	-17.04
Energy contribution	-19.85
Covariance contribution	2.81
Combinations/Pair	1.08
Mean z-score	-2.75
Structure conservation index	0.48
SVM decision value	0.66
SVM RNA-class probability	0.815367
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6477338 103 - 20766785
GACAUUUUAAGUGUUGCCCAUUGACUUUUGAUUGCUU-UUGGCCGGGGCCAAAGGCUCCGGGGAUUCCCACUG----GUGGUCGA-UGGCAACAUUUUGUUGCACACAA
((((....((((((((((.(((((((.......((((-(((((....))))))))).((((((....)).)))----).))))))-)))))))))))))))........ ( -43.50)
>DroSec_CAF1 45470 103 - 1
GACAUUUUAAGUGUUGCCCAUUGACUUUUGAUUGCUU-UUGGCCGGGUCCAAAGGCUCCGGGGAUUCCCACUG----GUGGUCGA-UGGCAACAUUUUGUUGCACACAA
((((....((((((((((.(((((((.......((((-((((......)))))))).((((((....)).)))----).))))))-)))))))))))))))........ ( -37.90)
>DroEre_CAF1 43636 100 - 1
GACAUUUUAAGUGUUGCCCAUUGACUUUUGAUUGCUU-UUGGCCGGGGCCAAAGGCUCCGGGGAUUCCCGCUG-------GCCGA-UGGCAACAUUUUGUUGCACACAA
..........((((.((.....(((...((.(((((.-((((((((((((...))))))(((....)))...)-------)))))-.)))))))....))))))))).. ( -38.30)
>DroYak_CAF1 48163 100 - 1
GACAUUUUAAGUGUUGCCCAUUGACUUUUGAUUGCUU-UUGGCCGGGGCCAAAGGCUCCGGGGAUUCCCGCUG-------GCCGA-UGGCAACAUUUUGUUGCACACAA
..........((((.((.....(((...((.(((((.-((((((((((((...))))))(((....)))...)-------)))))-.)))))))....))))))))).. ( -38.30)
>DroMoj_CAF1 38983 90 - 1
GACAUUUUAAGUGUUC-CCAUUGACGUUUGAUUACUU-UUGGCUUUGGCU-----CUACUGGGAAUACGGAUACGCA--GCUGAA-UUGCUA---UUUGCUGU------
..........((((((-(((.....((......))..-..(((....)))-----....)))))))))......(((--((.(((-(....)---))))))))------ ( -20.70)
>DroAna_CAF1 45439 101 - 1
GACAUUUUAAGUGUUGCCCAUUGACUUUUGAUUGCUUUUUGGCCAGGGCCAAAGCCUGCGGGAAUUCC-GAUG-------GCCAUGGGGCAACAUUUUGCUGCUCAAAA
((((....(((((((((((..((..............((((((....))))))(((..(((.....))-)..)-------))))..)))))))))))...)).)).... ( -34.50)
>consensus
GACAUUUUAAGUGUUGCCCAUUGACUUUUGAUUGCUU_UUGGCCGGGGCCAAAGGCUCCGGGGAUUCCCGCUG_______GCCGA_UGGCAACAUUUUGUUGCACACAA
..((....((((((((((...............((((.(((((....)))))))))..((((....)))).................))))))))))...))....... (-17.04 = -19.85 +   2.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:39 2006