Locus 2169

Sequence ID	X_DroMel_CAF1
Location	5,877,653 – 5,877,783
Length	130
Max. P	0.977643

overview

Window 4

Location	5,877,653 – 5,877,747
Length	94
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	81.18
Mean single sequence MFE	-36.67
Consensus MFE	-24.28
Energy contribution	-24.20
Covariance contribution	-0.08
Combinations/Pair	1.14
Mean z-score	-4.00
Structure conservation index	0.66
SVM decision value	1.67
SVM RNA-class probability	0.970852
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5877653 94 + 22224390
AC------GAGGACUCCGUUUUCGACUUUUU----CGAGAAUUGGGCAUUCCCAGACGACUGACAUUAAU-UAGUUGUCUGGGAAUUGGC-CGCCGGAAUGGGGAA
..------.....((((((((((((.....)----))))))).((.(((((((((((((((((......)-)))))))))))))).)).)-)........)))).. ( -40.70)
>DroSec_CAF1 82391 95 + 1
AC------GAGGACUCCGUUUUCGACUUUUU----CGAGAAUUGGGCAUUCCCAGACGACUGACAUUAAUUUAGUUGUCUGGGAAUUGGC-CGCCGGAAUUGGGAA
.(------((....(((((((((((.....)----))))))..((.(((((((((((((((((.......))))))))))))))).)).)-)..)))).))).... ( -39.00)
>DroSim_CAF1 85113 94 + 1
AC------GAGGACUCCGUUUUCGACUUUUU----CGAGAAUUGGGCAUUCCCAGACGACUGACAUUAAU-UAGUUGUCUGGGAAUUGGC-CGCCGGAAUUGGGAA
.(------((....(((((((((((.....)----))))))..((.(((((((((((((((((......)-)))))))))))))).)).)-)..)))).))).... ( -39.40)
>DroEre_CAF1 80439 88 + 1
AC------GAGGACUCCGC----------UUCGACUGAGAAUUGGGCAUUCCCAGACGACUGACAUUAAU-UAGUUGUCUGGGAAUUGGC-CGCCGGAAUUGGGAA
.(------((((......)----------)))).(..(...((.(((((((((((((((((((......)-)))))))))))))))....-.))).)).)..)... ( -35.60)
>DroYak_CAF1 88699 95 + 1
AC------GAGGACUCCCUUU---ACUUUUUGGACCGAGAAUUGCGCAUUCCCAGACGACUGACAUUAAU-UAGUUGUCUGGGAAUUGGC-CGCCGGAAUUGGGAA
..------......((((...---.((....)).(((.(....((.(((((((((((((((((......)-)))))))))))))).))))-..))))....)))). ( -34.80)
>DroAna_CAF1 87086 84 + 1
ACCGAACAGAGGACUCCAUCU---------------G------AGGCAUUCCCAGACGGUUGACAUUAAU-UAGUUGUCUGGGAAUUGUCUCUCCCAAAAUAGGAG
......((((((...)).)))---------------)------((((((((((((((..((((......)-)))..))))))))).)))))((((.......)))) ( -30.50)
>consensus
AC______GAGGACUCCGUUU___ACUUUUU____CGAGAAUUGGGCAUUCCCAGACGACUGACAUUAAU_UAGUUGUCUGGGAAUUGGC_CGCCGGAAUUGGGAA
..............(((...............................((((((((((((((.........))))))))))))))((((....)))).....))). (-24.28 = -24.20 +  -0.08)

alignment

secondary structure

dotplot

Window 5

Location	5,877,653 – 5,877,747
Length	94
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	81.18
Mean single sequence MFE	-29.69
Consensus MFE	-20.42
Energy contribution	-20.78
Covariance contribution	0.36
Combinations/Pair	1.05
Mean z-score	-3.18
Structure conservation index	0.69
SVM decision value	1.37
SVM RNA-class probability	0.947126
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5877653 94 - 22224390
UUCCCCAUUCCGGCG-GCCAAUUCCCAGACAACUA-AUUAAUGUCAGUCGUCUGGGAAUGCCCAAUUCUCG----AAAAAGUCGAAAACGGAGUCCUC------GU
......(((((((.(-((..((((((((((.(((.-((....)).))).)))))))))))))).....(((----(.....))))...))))))....------.. ( -32.00)
>DroSec_CAF1 82391 95 - 1
UUCCCAAUUCCGGCG-GCCAAUUCCCAGACAACUAAAUUAAUGUCAGUCGUCUGGGAAUGCCCAAUUCUCG----AAAAAGUCGAAAACGGAGUCCUC------GU
......(((((((.(-((..((((((((((.(((...........))).)))))))))))))).....(((----(.....))))...))))))....------.. ( -30.80)
>DroSim_CAF1 85113 94 - 1
UUCCCAAUUCCGGCG-GCCAAUUCCCAGACAACUA-AUUAAUGUCAGUCGUCUGGGAAUGCCCAAUUCUCG----AAAAAGUCGAAAACGGAGUCCUC------GU
......(((((((.(-((..((((((((((.(((.-((....)).))).)))))))))))))).....(((----(.....))))...))))))....------.. ( -32.00)
>DroEre_CAF1 80439 88 - 1
UUCCCAAUUCCGGCG-GCCAAUUCCCAGACAACUA-AUUAAUGUCAGUCGUCUGGGAAUGCCCAAUUCUCAGUCGAA----------GCGGAGUCCUC------GU
......(((((((.(-((..((((((((((.(((.-((....)).))).))))))))))))))..(((......)))----------.))))))....------.. ( -29.30)
>DroYak_CAF1 88699 95 - 1
UUCCCAAUUCCGGCG-GCCAAUUCCCAGACAACUA-AUUAAUGUCAGUCGUCUGGGAAUGCGCAAUUCUCGGUCCAAAAAGU---AAAGGGAGUCCUC------GU
(((((....((((..-((((.(((((((((.(((.-((....)).))).))))))))))).)).....))))..(.....).---...))))).....------.. ( -27.50)
>DroAna_CAF1 87086 84 - 1
CUCCUAUUUUGGGAGAGACAAUUCCCAGACAACUA-AUUAAUGUCAACCGUCUGGGAAUGCCU------C---------------AGAUGGAGUCCUCUGUUCGGU
(((((.....))))).....((((((((((.....-.............))))))))))(((.------(---------------(((.((...))))))...))) ( -26.57)
>consensus
UUCCCAAUUCCGGCG_GCCAAUUCCCAGACAACUA_AUUAAUGUCAGUCGUCUGGGAAUGCCCAAUUCUCG____AAAAAGU___AAACGGAGUCCUC______GU
((((.......((....)).((((((((((.(((...........))).))))))))))..............................))))............. (-20.42 = -20.78 +   0.36)

alignment

secondary structure

dotplot

Window 6

Location	5,877,673 – 5,877,783
Length	110
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	80.39
Mean single sequence MFE	-42.47
Consensus MFE	-28.39
Energy contribution	-30.98
Covariance contribution	2.60
Combinations/Pair	1.06
Mean z-score	-3.95
Structure conservation index	0.67
SVM decision value	1.80
SVM RNA-class probability	0.977643
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5877673 110 + 22224390
UUUUU----CGAGAAUUGGGCAUUCCCAGACGACUGACAUUAAU-UAGUUGUCUGGGAAUUGGCCGCCGGAAUGGGGAAUU-UUCCUGUUUUUGGGAAGAGGAUGCAUCC---AAUGCG
(((((----(.......((.(((((((((((((((((......)-)))))))))))))).)).)).((((((..((((...-.))))..))))))))))))...((((..---.)))). ( -43.90)
>DroSec_CAF1 82411 111 + 1
UUUUU----CGAGAAUUGGGCAUUCCCAGACGACUGACAUUAAUUUAGUUGUCUGGGAAUUGGCCGCCGGAAUUGGGAAUU-UUCCUGUUUUUGGGGAGAGGCUGCAUCC---AAUGCG
.....----((...(((((((((((((((((((((((.......)))))))))))))))).((((.((((((..((((...-.))))..)))))).....))))))..))---))).)) ( -44.00)
>DroSim_CAF1 85133 110 + 1
UUUUU----CGAGAAUUGGGCAUUCCCAGACGACUGACAUUAAU-UAGUUGUCUGGGAAUUGGCCGCCGGAAUUGGGAAUU-UUCCUGCUUUUGGGGAGAGGCUGCAUCC---AAUGCG
.....----((...(((((((((((((((((((((((......)-))))))))))))))).((((.((((((..((((...-.))))..)))))).....))))))..))---))).)) ( -44.40)
>DroEre_CAF1 80452 110 + 1
---UUCGACUGAGAAUUGGGCAUUCCCAGACGACUGACAUUAAU-UAGUUGUCUGGGAAUUGGCCGCCGGAAUUGGGAAUU-UUCCUG-UUUUGCCUAGAGGCUGCAUCC---AAUGCA
---(((......)))..((.(((((((((((((((((......)-)))))))))))))).)).))((.(((...((((...-.))))(-(...(((....))).)).)))---...)). ( -41.70)
>DroYak_CAF1 88716 114 + 1
UUUUUGGACCGAGAAUUGCGCAUUCCCAGACGACUGACAUUAAU-UAGUUGUCUGGGAAUUGGCCGCCGGAAUUGGGAAUUUUUCCUG-UUUUGACUAGUGGCUGCAUCC---AAUGCA
...(((((........(((..((((((((((((((((......)-))))))))))))))).((((((((((((.((((....)))).)-)))))....))))))))))))---)).... ( -44.30)
>DroPer_CAF1 105659 93 + 1
UCCGU----C-----UCCCGGCUCCCCAGGCGAUUGACAUUAAU-UAGUUGUCUGGGAAUUUGCCUCCCCAGUUGGU-------------AUUGGGAAGAGGC---AUUCGAUAAUGCU
.....----.-----....(((..(((((((((((((......)-))))))))))))....((((((((((((....-------------))))))..)))))---).........))) ( -36.50)
>consensus
UUUUU____CGAGAAUUGGGCAUUCCCAGACGACUGACAUUAAU_UAGUUGUCUGGGAAUUGGCCGCCGGAAUUGGGAAUU_UUCCUG_UUUUGGGAAGAGGCUGCAUCC___AAUGCG
.....................(((((((((((((((.........))))))))))))))).((((.((((((.(((((.....))))).)))))).....))))((((......)))). (-28.39 = -30.98 +   2.60)

alignment

secondary structure

dotplot

Window 7

Location	5,877,673 – 5,877,783
Length	110
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	80.39
Mean single sequence MFE	-31.21
Consensus MFE	-19.60
Energy contribution	-20.70
Covariance contribution	1.10
Combinations/Pair	1.08
Mean z-score	-2.82
Structure conservation index	0.63
SVM decision value	1.34
SVM RNA-class probability	0.944351
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5877673 110 - 22224390
CGCAUU---GGAUGCAUCCUCUUCCCAAAAACAGGAA-AAUUCCCCAUUCCGGCGGCCAAUUCCCAGACAACUA-AUUAAUGUCAGUCGUCUGGGAAUGCCCAAUUCUCG----AAAAA
.((...---(((((.......((((........))))-.......)))))..))(((..((((((((((.(((.-((....)).))).))))))))))))).........----..... ( -31.04)
>DroSec_CAF1 82411 111 - 1
CGCAUU---GGAUGCAGCCUCUCCCCAAAAACAGGAA-AAUUCCCAAUUCCGGCGGCCAAUUCCCAGACAACUAAAUUAAUGUCAGUCGUCUGGGAAUGCCCAAUUCUCG----AAAAA
.(.(((---((..((.(((..(((.........))).-.....((......)).)))..((((((((((.(((...........))).))))))))))))))))).)...----..... ( -28.10)
>DroSim_CAF1 85133 110 - 1
CGCAUU---GGAUGCAGCCUCUCCCCAAAAGCAGGAA-AAUUCCCAAUUCCGGCGGCCAAUUCCCAGACAACUA-AUUAAUGUCAGUCGUCUGGGAAUGCCCAAUUCUCG----AAAAA
.((((.---..))))...............((.((((-.........)))).))(((..((((((((((.(((.-((....)).))).))))))))))))).........----..... ( -30.20)
>DroEre_CAF1 80452 110 - 1
UGCAUU---GGAUGCAGCCUCUAGGCAAAA-CAGGAA-AAUUCCCAAUUCCGGCGGCCAAUUCCCAGACAACUA-AUUAAUGUCAGUCGUCUGGGAAUGCCCAAUUCUCAGUCGAA---
.(((((---((.(((.(((....)))....-..((((-.........)))).))).))))(((((((((.(((.-((....)).))).))))))))))))................--- ( -33.90)
>DroYak_CAF1 88716 114 - 1
UGCAUU---GGAUGCAGCCACUAGUCAAAA-CAGGAAAAAUUCCCAAUUCCGGCGGCCAAUUCCCAGACAACUA-AUUAAUGUCAGUCGUCUGGGAAUGCGCAAUUCUCGGUCCAAAAA
....((---((((...(((....((....)-).((((..........))))))).((((.(((((((((.(((.-((....)).))).))))))))))).))........))))))... ( -34.50)
>DroPer_CAF1 105659 93 - 1
AGCAUUAUCGAAU---GCCUCUUCCCAAU-------------ACCAACUGGGGAGGCAAAUUCCCAGACAACUA-AUUAAUGUCAAUCGCCUGGGGAGCCGGGA-----G----ACGGA
............(---(((((..((((..-------------......)))))))))).....((.((((....-.....))))..((.(((((....))))).-----)----).)). ( -29.50)
>consensus
CGCAUU___GGAUGCAGCCUCUACCCAAAA_CAGGAA_AAUUCCCAAUUCCGGCGGCCAAUUCCCAGACAACUA_AUUAAUGUCAGUCGUCUGGGAAUGCCCAAUUCUCG____AAAAA
.(((((....))))).(((.((...........(((.....))).......)).)))..((((((((((.(((...........))).))))))))))..................... (-19.60 = -20.70 +   1.10)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:48 2006