Locus 1191

Sequence ID	3R_DroMel_CAF1
Location	3,586,841 – 3,587,092
Length	251
Max. P	0.999659

overview

Window 0

Location	3,586,841 – 3,586,937
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	93.01
Mean single sequence MFE	-16.83
Consensus MFE	-13.84
Energy contribution	-14.08
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-1.79
Structure conservation index	0.82
SVM decision value	1.11
SVM RNA-class probability	0.916418
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3586841 96 - 27905053
AUCCCAACUACUUUGCGUGUUGAUUUCAUCUUCUGGGAUAUUUCCCACCAAUUUUAAUAAGAAAUUUCACAGCUUAUUUAAUAAGAACGCGUCUUU
..............(((((((((((((......(((((....)))))....((.....))))))))......(((((...)))))))))))).... ( -15.30)
>DroSec_CAF1 37374 96 - 1
AUCCCAACUACUUUGCGUGUUGAUUUCAUCUUCUGGGAUAUUUCCCACCAAUCUUAAUAAGAAGAUUCACAGCUUAUUCAAUAAGAACGCGUCUUU
..............(((((((......(((((((((((....)))).............)))))))......(((((...)))))))))))).... ( -17.91)
>DroSim_CAF1 38176 96 - 1
AUCCCAACUACUUUGCGUGUUGAUUUCAUCUUCUGGGAUAUUUCCCACCAAUCUUAAUAAGAAGAUUCACAGCUUAUUCAAUAAGAACGCGUCUUU
..............(((((((......(((((((((((....)))).............)))))))......(((((...)))))))))))).... ( -17.91)
>DroEre_CAF1 42977 94 - 1
AUCCCAACUACUUUGCGUGUUGACUUCAUCUUCUGGGAUAUUUCCCACGAAUCUUAAUAAUAAAUUUCACAGCUUAUUAA--AAGAACGCGUCUUU
..............(((((((.........((((((((....))))).)))..(((((((.............)))))))--...))))))).... ( -16.42)
>DroYak_CAF1 60617 94 - 1
AUCCCAACUACUUUGCGUGUUGACUUCAUCUUCUGGGAUAUUUCCCACAAGUCUUAAUAAUAAAUUUCACAGCUUGUUAA--CAGAACGCGUCUUU
..............((((.(((............((((....))))((((((...................))))))...--))).))))...... ( -16.61)
>consensus
AUCCCAACUACUUUGCGUGUUGAUUUCAUCUUCUGGGAUAUUUCCCACCAAUCUUAAUAAGAAAUUUCACAGCUUAUUAAAUAAGAACGCGUCUUU
..............(((((((............(((((....)))))........((((((...........)))))).......))))))).... (-13.84 = -14.08 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	3,586,869 – 3,586,977
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	94.91
Mean single sequence MFE	-30.43
Consensus MFE	-27.90
Energy contribution	-28.10
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.40
Structure conservation index	0.92
SVM decision value	3.85
SVM RNA-class probability	0.999659
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3586869 108 - 27905053
UUGUAGAACGGUGAAAGGCAGCAGGCAGGUGGCCAAAAAAAUCCCAACUACUUUGCGUGUUGAUUUCAUCUUCUGGGAUAUUUCCCACCAAUUUUAAUAAGAAAUUUC
....((((.(((((((..(((((.((((((((...............)))).)))).))))).)))))))))))((((....))))...................... ( -30.46)
>DroSec_CAF1 37402 108 - 1
UUGUAGAACGGUGAAAGGCAGCAGGCAGGUGGCCAAAAAAAUCCCAACUACUUUGCGUGUUGAUUUCAUCUUCUGGGAUAUUUCCCACCAAUCUUAAUAAGAAGAUUC
....((((.(((((((..(((((.((((((((...............)))).)))).))))).)))))))))))((((....))))...((((((......)))))). ( -32.96)
>DroSim_CAF1 38204 108 - 1
UUGUAGAACGGUGAAAGGCAGCAGGCAGGUGGCCAAAAAAAUCCCAACUACUUUGCGUGUUGAUUUCAUCUUCUGGGAUAUUUCCCACCAAUCUUAAUAAGAAGAUUC
....((((.(((((((..(((((.((((((((...............)))).)))).))))).)))))))))))((((....))))...((((((......)))))). ( -32.96)
>DroEre_CAF1 43003 108 - 1
UUGUAGAACGGUGAAAGGCAGCAGGCAGGUGGUCAAGAAAAUCCCAACUACUUUGCGUGUUGACUUCAUCUUCUGGGAUAUUUCCCACGAAUCUUAAUAAUAAAUUUC
((((((((.((((((...(((((.(((((((((...(.....)...))))).)))).)))))..))))))))))((((....)))))))).................. ( -31.80)
>DroYak_CAF1 60643 108 - 1
UUGUAGAACGGUGAAAGGCAGAAGGCAGGUGGCCCAAAAAAUCCCAACUACUUUGCGUGUUGACUUCAUCUUCUGGGAUAUUUCCCACAAGUCUUAAUAAUAAAUUUC
((((((((.((((((...(((.(.((((((((...............)))).)))).).)))..))))))))))((((....)))))))).................. ( -23.96)
>consensus
UUGUAGAACGGUGAAAGGCAGCAGGCAGGUGGCCAAAAAAAUCCCAACUACUUUGCGUGUUGAUUUCAUCUUCUGGGAUAUUUCCCACCAAUCUUAAUAAGAAAUUUC
....((((.((((((...(((((.((((((((...............)))).)))).)))))..))))))))))((((....))))...................... (-27.90 = -28.10 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	3,586,977 – 3,587,092
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.54
Mean single sequence MFE	-30.44
Consensus MFE	-18.76
Energy contribution	-20.87
Covariance contribution	2.11
Combinations/Pair	1.04
Mean z-score	-1.92
Structure conservation index	0.62
SVM decision value	0.22
SVM RNA-class probability	0.641061
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3586977 115 + 27905053
AAUGUUGCGGCACAAGGAAGUAAGUACCGAGCUAUAAAUAUGUGAUUCACUCAGAGCUGACUCAUUAAUUGAGACCGGUACUUAUCCGU---GUUAAGCGCAAUAGCUUAACAGAA--UU
......((((.........((((((((((((((........(((...)))....))))..((((.....))))..))))))))))))))---(((((((......)))))))....--.. ( -33.40)
>DroSec_CAF1 37510 115 + 1
AAUGUUGCGGCCCAAGGAAGUAAGUACCGAGCUAUAAAUAUGUGAUUCACUCAGAGCUGACUCAUUAAUUGAGACCGGUACUUAUCCGU---GUUAAGCGCAAUAGCUUAGCAGAA--UU
......((((.........((((((((((((((........(((...)))....))))..((((.....))))..))))))))))))))---(((((((......)))))))....--.. ( -33.40)
>DroSim_CAF1 38312 115 + 1
AAUGUUGCGGCCCAAGGAAGUAAGUACCGCGCUAUAAAUAUGUGAUUCACUCAGAGCUGACUCAUUAAUUGAGACCGGUACUUAUCCGU---GUUAAGCGCAAUAGCUUAGCAGAA--UU
......((((.........((((((((((.(((........(((...)))....)))...((((.....))))..))))))))))))))---(((((((......)))))))....--.. ( -31.50)
>DroEre_CAF1 43111 115 + 1
AAUGUUGGGGCCCAAGGAAGUAAGUACCGAGCUAUAAACGUGUGAUUCACUCAGAGCUGACUCAUUAAUUGAGACCGGUACUUAUACUG---GUUAAGCGCAAUAGCUUAACAGAA--AU
..(.((((...)))).)..((((((((((((((......(((.....)))....))))..((((.....))))..)))))))))).(((---.((((((......)))))))))..--.. ( -34.60)
>DroYak_CAF1 60751 115 + 1
AAUGUUGAGGCCCAAGGAAGUAAGUACCCAGCUAUAAAUAUGUGAUUCACUCCGAGCUGACUCAUUAAUUGAGACCGGUACUUAGACUC---GUUAAGCGCAACAGCUUAACAGAA--AU
......(((.((...))...(((((((((((((........(((...)))....))))).((((.....))))...))))))))..)))---(((((((......)))))))....--.. ( -32.00)
>DroAna_CAF1 34402 111 + 1
ACAGUUCAAGCCCAACAAAGUUAGUACA----UCUUAAAACCUGAAUCACCCAGCACUGACUCAUGAUCAGUAGCCGGCAGCUAUCGACGUCAUUAAGGGAA-----UUAACAGAGAGUU
...(((....(((.....(((((((...----.........(((.......))).))))))).((((((.(((((.....))))).))..))))...)))..-----..)))........ ( -17.72)
>consensus
AAUGUUGCGGCCCAAGGAAGUAAGUACCGAGCUAUAAAUAUGUGAUUCACUCAGAGCUGACUCAUUAAUUGAGACCGGUACUUAUCCGU___GUUAAGCGCAAUAGCUUAACAGAA__UU
...................((((((((((..((........((((.(((........))).))))......))..)))))))))).......(((((((......)))))))........ (-18.76 = -20.87 +   2.11)

alignment

secondary structure

dotplot

Window 3

Location	3,586,977 – 3,587,092
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.54
Mean single sequence MFE	-30.92
Consensus MFE	-17.25
Energy contribution	-19.28
Covariance contribution	2.03
Combinations/Pair	1.27
Mean z-score	-2.07
Structure conservation index	0.56
SVM decision value	0.02
SVM RNA-class probability	0.541750
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3586977 115 - 27905053
AA--UUCUGUUAAGCUAUUGCGCUUAAC---ACGGAUAAGUACCGGUCUCAAUUAAUGAGUCAGCUCUGAGUGAAUCACAUAUUUAUAGCUCGGUACUUACUUCCUUGUGCCGCAACAUU
..--...((((((((......)))))))---).(((((((((((((.((((.....)))).)((((.((((((.......)))))).)))))))))))))..))).(((......))).. ( -34.20)
>DroSec_CAF1 37510 115 - 1
AA--UUCUGCUAAGCUAUUGCGCUUAAC---ACGGAUAAGUACCGGUCUCAAUUAAUGAGUCAGCUCUGAGUGAAUCACAUAUUUAUAGCUCGGUACUUACUUCCUUGGGCCGCAACAUU
..--...(((...((....))((((((.---..(((((((((((((.((((.....)))).)((((.((((((.......)))))).)))))))))))))..))))))))).)))..... ( -32.90)
>DroSim_CAF1 38312 115 - 1
AA--UUCUGCUAAGCUAUUGCGCUUAAC---ACGGAUAAGUACCGGUCUCAAUUAAUGAGUCAGCUCUGAGUGAAUCACAUAUUUAUAGCGCGGUACUUACUUCCUUGGGCCGCAACAUU
..--...(((...((....))((((((.---..(((((((((((((.((((.....)))).).(((.((((((.......)))))).))).)))))))))..))))))))).)))..... ( -32.90)
>DroEre_CAF1 43111 115 - 1
AU--UUCUGUUAAGCUAUUGCGCUUAAC---CAGUAUAAGUACCGGUCUCAAUUAAUGAGUCAGCUCUGAGUGAAUCACACGUUUAUAGCUCGGUACUUACUUCCUUGGGCCCCAACAUU
..--..(((((((((......)))))).---)))..((((((((((.((((.....)))).)((((.((((((.....)))..))).))))))))))))).....((((...)))).... ( -29.70)
>DroYak_CAF1 60751 115 - 1
AU--UUCUGUUAAGCUGUUGCGCUUAAC---GAGUCUAAGUACCGGUCUCAAUUAAUGAGUCAGCUCGGAGUGAAUCACAUAUUUAUAGCUGGGUACUUACUUCCUUGGGCCUCAACAUU
..--...........(((((.((((((.---(((..((((((((...((((.....)))).(((((..(((((.......)))))..))))))))))))).))).))))))..))))).. ( -31.00)
>DroAna_CAF1 34402 111 - 1
AACUCUCUGUUAA-----UUCCCUUAAUGACGUCGAUAGCUGCCGGCUACUGAUCAUGAGUCAGUGCUGGGUGAUUCAGGUUUUAAGA----UGUACUAACUUUGUUGGGCUUGAACUGU
.............-----...(((.(((.((((.....))..(((((.((((((.....))))))))))))).))).))).((((((.----....(((((...))))).)))))).... ( -24.80)
>consensus
AA__UUCUGUUAAGCUAUUGCGCUUAAC___ACGGAUAAGUACCGGUCUCAAUUAAUGAGUCAGCUCUGAGUGAAUCACAUAUUUAUAGCUCGGUACUUACUUCCUUGGGCCGCAACAUU
........(((((((......))))))).....(((((((((((((.((((.....)))).).(((.((((((.......)))))).))).)))))))))..)))............... (-17.25 = -19.28 +   2.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:17 2006