Locus 1287

Sequence ID	2L_DroMel_CAF1
Location	3,416,076 – 3,416,326
Length	250
Max. P	0.785758

overview

Window 6

Location	3,416,076 – 3,416,166
Length	90
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.64
Mean single sequence MFE	-27.44
Consensus MFE	-14.71
Energy contribution	-13.74
Covariance contribution	-0.96
Combinations/Pair	1.44
Mean z-score	-2.03
Structure conservation index	0.54
SVM decision value	0.26
SVM RNA-class probability	0.657801
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3416076 90 + 22407834
CAUA---------UCUCUGGU----CUUCAGCGGCUUUAU----------GUCUAUU--UUUGUAACAUUAUUUUCGAGACGAGCCUCGUUUAAGUGAU--GUUGGGU---CACUGGAGA
....---------((((..((----..((...(((.....----------)))....--....(((((((((((.((((......))))...)))))))--)))))).---.))..)))) ( -25.90)
>DroSec_CAF1 5034 88 + 1
CAUA---------UCUCUGGU----CUUCAGGGGCUUUAU----------GCCUAUU--UUUGUAACAUUAUUUUCGAGACGAGCCUCGUUUAAGUGAU--GUUGGGU---CACUGGA--
....---------..((..((----..((..((((.....----------))))...--....(((((((((((.((((......))))...)))))))--)))))).---.))..))-- ( -25.10)
>DroAna_CAF1 7496 103 + 1
CAAAGUGGCAGGGCCUCUGGUCCGUCUUGUAGACUUUUAU----------GUUUAUUUCUUUGUGGCAUUAUUUUCGAGAUGAGCCUGGU-UAAGUGGU--GUUGGCU---CAUACGAA-
....((.((((((((...))))).....((((((......----------)))))).....))).))......((((..(((((((....-........--...))))---))).))))- ( -27.76)
>DroSim_CAF1 5252 93 + 1
CAUA---------UCUCUGGU----CUUCAGGGGCUUUAU----------GCCUAUU--UUUGUAACAUUAUUUUCGAGACGAGCCUCGUUUAAGUGAU--GUUGGGUCGUCACUGGAGA
....---------.......(----((((((((((.....----------))))...--..(.(((((((((((.((((......))))...)))))))--)))).)......))))))) ( -28.40)
>DroEre_CAF1 5192 89 + 1
CAUA---------UCUCUGGU----CUUCAGAGGCCUUAU----------GCCUAUU--UUUGUAACAUUAUUUUCGAGACGAGCCUCGC-UAAGUGAU--GUUGGGU---CACUGGAGA
....---------((((..((----..((..((((.....----------))))...--....(((((((((((.((((......)))).-.)))))))--)))))).---.))..)))) ( -28.50)
>DroYak_CAF1 5639 102 + 1
CAUA---------UCUCUGCU----CUCGAGGGGCUUUAUGUUUUGAGGUGCCUAUU--UUUGUAACAUUAUUUUCGAGACGAGCCUCGUUUAAGUGAUGUGUUGGGU---CACUGGAGA
....---------((((((((----(...(((.((((((.....)))))).)))...--......(((((((((.((((......))))...)))))))))...))))---....))))) ( -29.00)
>consensus
CAUA_________UCUCUGGU____CUUCAGGGGCUUUAU__________GCCUAUU__UUUGUAACAUUAUUUUCGAGACGAGCCUCGUUUAAGUGAU__GUUGGGU___CACUGGAGA
.........................((((((((((...............)))).........(((((((((((.((((......))))...)))))))..))))........)))))). (-14.71 = -13.74 +  -0.96)

alignment

secondary structure

dotplot

Window 7

Location	3,416,166 – 3,416,286
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.20
Mean single sequence MFE	-35.40
Consensus MFE	-23.63
Energy contribution	-26.26
Covariance contribution	2.63
Combinations/Pair	1.11
Mean z-score	-1.76
Structure conservation index	0.67
SVM decision value	0.50
SVM RNA-class probability	0.760030
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3416166 120 + 22407834
UAUAUGCACAUGGGGCUUGCGUGUCAGUUGGUCAAGUGGACAGAGGUGAAACAUUUCGGUUUUAAACACUCUGUCUAAUGACUUGGGAUCAGCCAAGCCAAGAGACUCUGUGACCUACGA
......((((.((((((((.(((((....(((((..(((((((((.((((((......))))))....))))))))).)))))...)))..))))))))......)).))))........ ( -38.50)
>DroSec_CAF1 5122 104 + 1
--------------GCUUGCGUGUCAGUUGGUCAAGUGGACAGAGGUGAAACAUUUCGGUUUUAAACACUCCGUCUAAUGGCUUGGGAUCACCCAAGCCAA--GUCUCUGUGACCUAAGA
--------------...............(((((..(((((.(((.((((((......))))))....))).))))).(((((((((....))))))))).--.......)))))..... ( -36.50)
>DroSim_CAF1 5345 110 + 1
UACAU--------GGCUUGCGUGUCAGUUGGUCAAGUGGACAGAGGUGAAACAUUUCGGUUUUAAACACUCCGUCUAAUGGCUUGGGAUCAGCCAAGCCAA--GACUCUGUGACCUAAGA
....(--------(((......))))...(((((..(((((.(((.((((((......))))))....))).))))).((((((((......)))))))).--.......)))))..... ( -37.00)
>DroEre_CAF1 5281 112 + 1
UACC------UGACGCUUGCGUGUCAGUUGGUCAAGUGGCCAGAGGUGAAACAUUUCGGCUUUAAACAUUCUGCCUGCUGGCUUGGGAUCAGCCAAGCCAC--GACUUUGUGGCCCAUGA
...(------((((((....)))))))....(((.(.((((((((((..........(((............)))((.((((((((......)))))))))--)))))).)))))).))) ( -40.00)
>DroYak_CAF1 5741 95 + 1
UACUU-----UGGGGUUUGCGUGUCAGUUGGUCAAGUGGCCAGAGGUGAAACAUUUCGGUUUUAAACAUACUG--------CUUGGGAUCAG------------ACUUGGUGACCUCUGA
.....-----.((((((..((.(((...(((((....)))))((((((...))))))((((((((.(.....)--------.)))))))).)------------)).))..))))))... ( -25.00)
>consensus
UACAU_____UG_GGCUUGCGUGUCAGUUGGUCAAGUGGACAGAGGUGAAACAUUUCGGUUUUAAACACUCUGUCUAAUGGCUUGGGAUCAGCCAAGCCAA__GACUCUGUGACCUAAGA
.............................(((((..(((((((((.((((((......))))))....))))))))).((((((((......))))))))..........)))))..... (-23.63 = -26.26 +   2.63)

alignment

secondary structure

dotplot

Window 8

Location	3,416,166 – 3,416,286
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.20
Mean single sequence MFE	-30.70
Consensus MFE	-19.75
Energy contribution	-21.78
Covariance contribution	2.03
Combinations/Pair	1.12
Mean z-score	-1.84
Structure conservation index	0.64
SVM decision value	0.57
SVM RNA-class probability	0.785758
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3416166 120 - 22407834
UCGUAGGUCACAGAGUCUCUUGGCUUGGCUGAUCCCAAGUCAUUAGACAGAGUGUUUAAAACCGAAAUGUUUCACCUCUGUCCACUUGACCAACUGACACGCAAGCCCCAUGUGCAUAUA
..((.(((((.((.......((((((((......))))))))...(((((((.((...((((......)))).)))))))))..))))))).))......(((.........)))..... ( -31.60)
>DroSec_CAF1 5122 104 - 1
UCUUAGGUCACAGAGAC--UUGGCUUGGGUGAUCCCAAGCCAUUAGACGGAGUGUUUAAAACCGAAAUGUUUCACCUCUGUCCACUUGACCAACUGACACGCAAGC--------------
.....(((((.((....--.(((((((((....)))))))))...(((((((.((...((((......)))).)))))))))..)))))))........(....).-------------- ( -35.90)
>DroSim_CAF1 5345 110 - 1
UCUUAGGUCACAGAGUC--UUGGCUUGGCUGAUCCCAAGCCAUUAGACGGAGUGUUUAAAACCGAAAUGUUUCACCUCUGUCCACUUGACCAACUGACACGCAAGCC--------AUGUA
.....(((((.((....--.((((((((......))))))))...(((((((.((...((((......)))).)))))))))..))))))).....((((....)..--------.))). ( -32.30)
>DroEre_CAF1 5281 112 - 1
UCAUGGGCCACAAAGUC--GUGGCUUGGCUGAUCCCAAGCCAGCAGGCAGAAUGUUUAAAGCCGAAAUGUUUCACCUCUGGCCACUUGACCAACUGACACGCAAGCGUCA------GGUA
(((..(((((.......--.((((((((......))))))))(.(((..((((((((.......))))))))..)))))))))...)))....(((((.(....).))))------)... ( -39.70)
>DroYak_CAF1 5741 95 - 1
UCAGAGGUCACCAAGU------------CUGAUCCCAAG--------CAGUAUGUUUAAAACCGAAAUGUUUCACCUCUGGCCACUUGACCAACUGACACGCAAACCCCA-----AAGUA
((((.(((((....((------------(.((....(((--------((...((........))...)))))....)).)))....)))))..)))).............-----..... ( -14.00)
>consensus
UCAUAGGUCACAGAGUC__UUGGCUUGGCUGAUCCCAAGCCAUUAGACAGAGUGUUUAAAACCGAAAUGUUUCACCUCUGUCCACUUGACCAACUGACACGCAAGCC_CA_____AUGUA
.....(((((..........((((((((......))))))))...(((((((.((...((((......)))).)))))))))....)))))............................. (-19.75 = -21.78 +   2.03)

alignment

secondary structure

dotplot

Window 9

Location	3,416,206 – 3,416,326
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.96
Mean single sequence MFE	-31.84
Consensus MFE	-16.56
Energy contribution	-18.60
Covariance contribution	2.04
Combinations/Pair	1.18
Mean z-score	-1.97
Structure conservation index	0.52
SVM decision value	0.01
SVM RNA-class probability	0.537593
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3416206 120 - 22407834
CAAAUUCUGAAAUCUAAUUUAGAUUCUUAAGUCCUAGGAGUCGUAGGUCACAGAGUCUCUUGGCUUGGCUGAUCCCAAGUCAUUAGACAGAGUGUUUAAAACCGAAAUGUUUCACCUCUG
.....((((..(((((.....((((((((.....)))))))).)))))..))))((((..((((((((......))))))))..))))((((.((...((((......)))).)))))). ( -36.00)
>DroSec_CAF1 5148 117 - 1
-AAAUUCUGAAAUCUAAUUUAGGUUCUUAAGCCCUAGGAGUCUUAGGUCACAGAGAC--UUGGCUUGGGUGAUCCCAAGCCAUUAGACGGAGUGUUUAAAACCGAAAUGUUUCACCUCUG
-......((((((...((((.((((.((((((.((....((((.(((((.....)))--))((((((((....))))))))...))))..)).)))))))))).))))))))))...... ( -36.70)
>DroSim_CAF1 5377 117 - 1
-AAAUUCUGAAAUCUAAUUUAGGUCCUUAAGCCCUAGGAGUCUUAGGUCACAGAGUC--UUGGCUUGGCUGAUCCCAAGCCAUUAGACGGAGUGUUUAAAACCGAAAUGUUUCACCUCUG
-....((((..((((((....(.((((........)))).).))))))..))))(((--(((((((((......))))))))..))))((((.((...((((......)))).)))))). ( -32.70)
>DroEre_CAF1 5315 117 - 1
-AAAUUCAACCAUCAAACUUGGUGUCUUAAGCACUAGGAGUCAUGGGCCACAAAGUC--GUGGCUUGGCUGAUCCCAAGCCAGCAGGCAGAAUGUUUAAAGCCGAAAUGUUUCACCUCUG
-........((((.(..((((((((.....))))))))..).))))(((((......--)))))..((((.......))))((.(((..((((((((.......))))))))..))))). ( -33.60)
>DroYak_CAF1 5776 99 - 1
-AAAAUCAGCCAUCUAACUUGGGCUCUUAAGCCCUAGGAGUCAGAGGUCACCAAGU------------CUGAUCCCAAG--------CAGUAUGUUUAAAACCGAAAUGUUUCACCUCUG
-................((.(((((....))))).))....(((((((......(.------------.((....))..--------)...............(((....)))))))))) ( -20.20)
>consensus
_AAAUUCUGAAAUCUAAUUUAGGUUCUUAAGCCCUAGGAGUCAUAGGUCACAGAGUC__UUGGCUUGGCUGAUCCCAAGCCAUUAGACAGAGUGUUUAAAACCGAAAUGUUUCACCUCUG
....(((..............((((((((.....))))))))...((((((...(((...((((((((......))))))))...)))...)))......)))))).............. (-16.56 = -18.60 +   2.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:37 2006