Locus 4574

Sequence ID	3L_DroMel_CAF1
Location	13,121,531 – 13,121,765
Length	234
Max. P	0.999551

overview

Window 2

Location	13,121,531 – 13,121,651
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.95
Mean single sequence MFE	-28.76
Consensus MFE	-26.20
Energy contribution	-26.24
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.12
Structure conservation index	0.91
SVM decision value	0.04
SVM RNA-class probability	0.554732
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13121531 120 + 23771897
UGCAGGCUAUAUGGUGAAAUAUAAAAACAUUAUUAAUCAAUGUCCAGGAAAACCGGGGCAGGACACAAAAGCUGGAAGUUGGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGACGGGA
..((((..((((((..(..................((((((.(((((.....((......)).(......)))))).))))))((((((....)))))).)..)))))).))))...... ( -26.70)
>DroSec_CAF1 109436 118 + 1
UGCAGGCUAUAUGGCGAAAUAUAAAAACAUUAUUAAUCAAUGUCCAGGAAAAGCGGGGCAGGACACAAAAGCUGGAAGUUGGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGACGG--
..((((..(((((((((..................((((((.(((((.....((...)).(....).....))))).))))))((((((....)))))).))))))))).))))....-- ( -28.50)
>DroSim_CAF1 107604 118 + 1
UGCAGGCUAUAUGGCGAAAUAUAAAAACAUUAUUAAUCAAUGUCCAGGAAAAGCGGGGCAGGACACAAAAGCUGGAAGUUGGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGACGG--
..((((..(((((((((..................((((((.(((((.....((...)).(....).....))))).))))))((((((....)))))).))))))))).))))....-- ( -28.50)
>DroEre_CAF1 106131 118 + 1
UGCAGGCUAUAUGGCCAAAUAUAAAAACAUUAUUAAUCAAUGUCCAGGAAAAGCAGGGCAGGGCACGAAAGCUGGAAGUUGGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGGCGG--
....((((....)))).........(((.......((((((.(((((.....((........)).(....)))))).))))))((((((....)))))))))((((......))))..-- ( -32.60)
>DroYak_CAF1 109655 113 + 1
UGCAGGCUAUAUGGCGAAAUAUAAAAACAUUAUUAAUCAAUGUCCAGGAAAAGCAG-----GGCACAAAAGCUGGAAGUUGGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGACGG--
..((((..(((((((((..................((((((.(((((.........-----..........))))).))))))((((((....)))))).))))))))).))))....-- ( -27.51)
>consensus
UGCAGGCUAUAUGGCGAAAUAUAAAAACAUUAUUAAUCAAUGUCCAGGAAAAGCGGGGCAGGACACAAAAGCUGGAAGUUGGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGACGG__
..((((..(((((((((..................((((((.(((((........................))))).))))))((((((....)))))).))))))))).))))...... (-26.20 = -26.24 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	13,121,571 – 13,121,691
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.25
Mean single sequence MFE	-42.74
Consensus MFE	-36.87
Energy contribution	-36.75
Covariance contribution	-0.12
Combinations/Pair	1.11
Mean z-score	-2.96
Structure conservation index	0.86
SVM decision value	3.71
SVM RNA-class probability	0.999551
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13121571 120 - 23771897
GUCCGGGAAUCCCCCAAGGGGCGCGAAAUUGGGACAGCCGUCCCGUCAAAGACAUGGCAACAGUAAGCUUACUUACUACCAACUUCCAGCUUUUGUGUCCUGCCCCGGUUUUCCUGGACA
(((((((((..((....(((((((((((((((((..(((((...(((...))))))))...((((((....))))))......)))))).))))))))))).....))..))))))))). ( -51.60)
>DroSec_CAF1 109476 117 - 1
GUC-GGGAAUCCCCCAAGGGGUGCGAAAUUGGGACAGCCG--CCGUCAAAGACAUGGCAACAGUAAGCUUACUUACUACCAACUUCCAGCUUUUGUGUCCUGCCCCGCUUUUCCUGGACA
(((-(((((........((((..(((((((((((..((((--..(((...))).))))...((((((....))))))......)))))).)))))..)))).........))))).))). ( -37.23)
>DroSim_CAF1 107644 117 - 1
GUC-GGGAAUCCCCCAAGGGGCGCGAAAUUGGGACACCCG--CCGUCAAAGACAUGGCAACAGUAAGCUUACUUACUACCAACUUCCAGCUUUUGUGUCCUGCCCCGCUUUUCCUGGACA
(((-(((((........(((((((((((((((((.....(--((((.......)))))...((((((....))))))......)))))).))))))))))).........))))).))). ( -39.43)
>DroEre_CAF1 106171 117 - 1
CUC-GGGAAUCCCCCAAGGGGCGCGAAAUUGGGACAGCCG--CCGCCAAAGACAUGGCAACAGUAAGCUUACUUACUACCAACUUCCAGCUUUCGUGCCCUGCCCUGCUUUUCCUGGACA
.((-(((((........(((((((((((((((((......--..((((......))))...((((((....))))))......)))))).))))))))))).........)))))))... ( -43.63)
>DroYak_CAF1 109695 112 - 1
GUC-GGGAAUCCCCCAAGGGGCGCGAAAUUGGGACAGCCG--CCGUCAAAGACAUGGCAACAGUAAGCUUACUUACUACCAACUUCCAGCUUUUGUGCC-----CUGCUUUUCCUGGACA
(((-(((.....)))..(((((((((((((((((..((((--..(((...))).))))...((((((....))))))......)))))).)))))))))-----))..........))). ( -41.80)
>consensus
GUC_GGGAAUCCCCCAAGGGGCGCGAAAUUGGGACAGCCG__CCGUCAAAGACAUGGCAACAGUAAGCUUACUUACUACCAACUUCCAGCUUUUGUGUCCUGCCCCGCUUUUCCUGGACA
(((.(((((........(((((((((((((((((..........((((......))))...((((((....))))))......)))))).))))))))))).........))))).))). (-36.87 = -36.75 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	13,121,611 – 13,121,729
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.66
Mean single sequence MFE	-43.28
Consensus MFE	-28.08
Energy contribution	-29.44
Covariance contribution	1.36
Combinations/Pair	1.16
Mean z-score	-2.17
Structure conservation index	0.65
SVM decision value	0.16
SVM RNA-class probability	0.611177
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13121611 118 + 23771897
GGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGACGGGACGGCUGUCCCAAUUUCGCGCCCCUUGGGGGAUUCCCGGACGAUUGCUAAAGCUGGAAAAAGGG-GAUCCCCC-AAAACAA
(((((((((....))))))...((...(((...)))(((((....)))))......)))))..(((((((((((((........((....))........)))-))))))))-))..... ( -46.79)
>DroSec_CAF1 109516 103 + 1
GGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGACGG--CGGCUGUCCCAAUUUCGCACCCCUUGGGGGAUUCCC-GACGAUUGCUGG------AAAAAGGG-GAUCCCC-------AA
(((((((((....))))))((((((..(((...)))))--))))..............))).....((((((((((-............------.....)))-)))))))-------.. ( -35.83)
>DroSim_CAF1 107684 108 + 1
GGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGACGG--CGGGUGUCCCAAUUUCGCGCCCCUUGGGGGAUUCCC-GACGAUUGCUAAAGCGGCAAAAAGGG-GAUCCCC-------A-
..(((((((....)))))))..(((..(((...)))))--)((((((.........))))))....((((((((((-.....(((((.....)))))...)))-)))))))-------.- ( -43.60)
>DroEre_CAF1 106211 113 + 1
GGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGGCGG--CGGCUGUCCCAAUUUCGCGCCCCUUGGGGGAUUCCC-GAGGAUAGCUAACGCUGGAGGAAGGG-GGUGCCCCAAAAG---
((.((((((....))))))(((((((......))))))--)(((...(((..((((...(((((((((.....)))-))))..(((....))))).))))..)-)).))))).....--- ( -48.50)
>DroYak_CAF1 109730 116 + 1
GGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGACGG--CGGCUGUCCCAAUUUCGCGCCCCUUGGGGGAUUCCC-GACGAUAGCUAAAGCUGGAAAAAGGGGGGUUCCCCCAAAGCA-
((.((((((....))))))((((((..(((...)))))--))))....))........((...(((((((((((((-.....((((....))))......)))))..)))))))).)).- ( -41.70)
>consensus
GGUAGUAAGUAAGCUUACUGUUGCCAUGUCUUUGACGG__CGGCUGUCCCAAUUUCGCGCCCCUUGGGGGAUUCCC_GACGAUUGCUAAAGCUGGAAAAAGGG_GAUCCCCC_AAA__A_
(((((((((....))))))...(((.((((...))))....)))..............)))....(((((((((((......((((....))))......))).))))))))........ (-28.08 = -29.44 +   1.36)

alignment

secondary structure

dotplot

Window 5

Location	13,121,651 – 13,121,765
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.17
Mean single sequence MFE	-45.60
Consensus MFE	-32.64
Energy contribution	-34.16
Covariance contribution	1.52
Combinations/Pair	1.14
Mean z-score	-3.04
Structure conservation index	0.72
SVM decision value	2.66
SVM RNA-class probability	0.996175
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13121651 114 + 23771897
CGGCUGUCCCAAUUUCGCGCCCCUUGGGGGAUUCCCGGACGAUUGCUAAAGCUGGAAAAAGGG-GAUCCCCC-AAAACAAAAAAAAAAAAUGGGGAUGCUG---AGCCACCAGCCGGC-A
((((((.......(((((((((((((((((((((((........((....))........)))-))))))))-))................)))).))).)---))....))))))..-. ( -46.28)
>DroSec_CAF1 109554 101 + 1
CGGCUGUCCCAAUUUCGCACCCCUUGGGGGAUUCCC-GACGAUUGCUGG------AAAAAGGG-GAUCCCC-------AACAAAAAAAAAUGGGGAUGCUG---AGCCACCAGCCGGC-A
((((((.......((((((((((...((((((((((-............------.....)))-)))))))-------.............)))).))).)---))....))))))..-. ( -38.92)
>DroSim_CAF1 107722 102 + 1
CGGGUGUCCCAAUUUCGCGCCCCUUGGGGGAUUCCC-GACGAUUGCUAAAGCGGCAAAAAGGG-GAUCCCC-------A-----AAAAAAUGGGGAUGCUG---AGCCACCAGCCGGC-A
.(((...)))......(((((((((.((((((((((-.....(((((.....)))))...)))-)))))))-------.-----....)).)))).)))..---.(((.......)))-. ( -41.80)
>DroEre_CAF1 106249 107 + 1
CGGCUGUCCCAAUUUCGCGCCCCUUGGGGGAUUCCC-GAGGAUAGCUAACGCUGGAGGAAGGG-GGUGCCCCAAAAG---------GAAUUGGGGAUGCUGUUG-GCCACCAGCCGGC-A
((((((..(((((...(((((((((((((.((((((-.....((((....))))......)))-))).))))))...---------.....)))).))).))))-)....))))))..-. ( -51.40)
>DroYak_CAF1 109768 114 + 1
CGGCUGUCCCAAUUUCGCGCCCCUUGGGGGAUUCCC-GACGAUAGCUAAAGCUGGAAAAAGGGGGGUUCCCCCAAAGCA-----AAAAAUUGGGGAUGCUGCUGGGCCACCAGCCGGCGA
..(((((((((((((...((...(((((((((((((-.....((((....))))......)))))..)))))))).)).-----..))))))))).....(((((....))))))))).. ( -49.60)
>consensus
CGGCUGUCCCAAUUUCGCGCCCCUUGGGGGAUUCCC_GACGAUUGCUAAAGCUGGAAAAAGGG_GAUCCCCC_AAA__A_____AAAAAAUGGGGAUGCUG___AGCCACCAGCCGGC_A
((((((..........(((((((..(((((((((((......((((....))))......))).))))))))...................)))).)))...........)))))).... (-32.64 = -34.16 +   1.52)

alignment

secondary structure

dotplot

Window 6

Location	13,121,651 – 13,121,765
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.17
Mean single sequence MFE	-41.29
Consensus MFE	-27.08
Energy contribution	-27.52
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.78
Structure conservation index	0.66
SVM decision value	0.28
SVM RNA-class probability	0.666009
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13121651 114 - 23771897
U-GCCGGCUGGUGGCU---CAGCAUCCCCAUUUUUUUUUUUUGUUUU-GGGGGAUC-CCCUUUUUCCAGCUUUAGCAAUCGUCCGGGAAUCCCCCAAGGGGCGCGAAAUUGGGACAGCCG
.-..((((((....((---((((..((((................((-(((((((.-(((........((....))........))).))))))))))))).)).....)))).)))))) ( -40.58)
>DroSec_CAF1 109554 101 - 1
U-GCCGGCUGGUGGCU---CAGCAUCCCCAUUUUUUUUUGUU-------GGGGAUC-CCCUUUUU------CCAGCAAUCGUC-GGGAAUCCCCCAAGGGGUGCGAAAUUGGGACAGCCG
.-..((((((....((---(((((((((.........(((((-------((..(..-.....)..------))))))).....-(((.....)))..))))))).....)))).)))))) ( -40.10)
>DroSim_CAF1 107722 102 - 1
U-GCCGGCUGGUGGCU---CAGCAUCCCCAUUUUUU-----U-------GGGGAUC-CCCUUUUUGCCGCUUUAGCAAUCGUC-GGGAAUCCCCCAAGGGGCGCGAAAUUGGGACACCCG
.-.......((((.((---(((.(((((((......-----)-------))))))(-(((((.((((.......)))).....-(((.....))))))))).......))))).)))).. ( -36.10)
>DroEre_CAF1 106249 107 - 1
U-GCCGGCUGGUGGC-CAACAGCAUCCCCAAUUC---------CUUUUGGGGCACC-CCCUUCCUCCAGCGUUAGCUAUCCUC-GGGAAUCCCCCAAGGGGCGCGAAAUUGGGACAGCCG
.-..((((((...((-.....))...((((((((---------(((((((((....-(((.......(((....)))......-)))....)))))))))).....))))))).)))))) ( -41.62)
>DroYak_CAF1 109768 114 - 1
UCGCCGGCUGGUGGCCCAGCAGCAUCCCCAAUUUUU-----UGCUUUGGGGGAACCCCCCUUUUUCCAGCUUUAGCUAUCGUC-GGGAAUCCCCCAAGGGGCGCGAAAUUGGGACAGCCG
....((((((((.((...)).))...(((((((((.-----((((((((((((..(((.........(((....)))......-)))..))))))))..)))).))))))))).)))))) ( -48.06)
>consensus
U_GCCGGCUGGUGGCU___CAGCAUCCCCAUUUUUU_____U__UUU_GGGGGAUC_CCCUUUUUCCAGCUUUAGCAAUCGUC_GGGAAUCCCCCAAGGGGCGCGAAAUUGGGACAGCCG
....((((((...((......)).((((.(((((...............(((.....)))..............((..((......))..((((...)))).))))))).)))))))))) (-27.08 = -27.52 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:07 2006