Locus 8185

Sequence ID	X_DroMel_CAF1
Location	20,347,370 – 20,347,637
Length	267
Max. P	0.999683

overview

Window 0

Location	20,347,370 – 20,347,490
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.39
Mean single sequence MFE	-31.42
Consensus MFE	-28.24
Energy contribution	-28.04
Covariance contribution	-0.20
Combinations/Pair	1.19
Mean z-score	-1.17
Structure conservation index	0.90
SVM decision value	0.11
SVM RNA-class probability	0.587943
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20347370 120 - 22224390
ACCCGAAGAGUGAGUGAAAAAUCGCAACCACAUAGGGCACGGCCGCCCGCCCAUCGACGAAAAUAUACAAAAAAAAUUUCCUACAGGGCGGUGCUAAAUACUUGCUUGGGUUUUUCGGCU
((((((.(((((.((((....)))).(((.....((((......))))((((......((((..............)))).....)))))))......)))))..))))))......... ( -32.44)
>DroSec_CAF1 15217 118 - 1
ACCCGAAGAGUGAGUAAAAAUUCGCAACCACAUAGGGCACGGCCGCCCGCCCAUCGACGAAAAUAUACAAA--AAAUUCCCUACAGGGCGGUGCUAAAUACUUGCUUAGGUUUUUCGGCU
..(((((((((((((....)))))).(((......(((...)))((((((((......(((..........--...)))......)))))).))..............)))))))))).. ( -32.22)
>DroSim_CAF1 16981 118 - 1
ACCCGAAGAGUGAGUGAAAAAUCGCAACCACAUAGGGCACGGCCGCCCGCCCAUCGACGAAAAUAUACAAA--AAAUUCCCUACAGGGCGGUGCUAAAUACUUGCUUGGGUUUUUCGGCU
((((((.(((((.((((....)))).(((.....((((......))))((((......(((..........--...)))......)))))))......)))))..))))))......... ( -32.02)
>DroEre_CAF1 11976 120 - 1
ACCCGAAGAAUGAGUGAAAAAUCGCAACCACAUAGGGCACAGCCGUCCGCCCAUCGACGAAAAUGUACAAAAAAAAUUCCCUACAGGGCGGUGCUAAAUACUUCCUCCGGUUUUUCGGUU
..((((((((((((.(((.....(((.((.....((((......))))((((.((...))...((((..............))))))))))))).......))))))..))))))))).. ( -29.74)
>DroYak_CAF1 15802 119 - 1
AGCCGAAGAAUGAGUGAAAAAUCGCAACCACACAGGGCACAGUCGCCCGCCCACCGAUGAAAAUAUACAAAA-AAAUUCCCUACAGGGCGGUGCUAAAUACUUCCUUGGGUUUUACGGUU
(((((.(((((..((((....))))..(((....((((......))))...(((((((....))........-.....(((....)))))))).............)))))))).))))) ( -30.70)
>consensus
ACCCGAAGAGUGAGUGAAAAAUCGCAACCACAUAGGGCACGGCCGCCCGCCCAUCGACGAAAAUAUACAAAA_AAAUUCCCUACAGGGCGGUGCUAAAUACUUGCUUGGGUUUUUCGGCU
..(((((((((((((((......(((.((.....((((......))))((((......(((...............)))......))))))))).......)))))))..)))))))).. (-28.24 = -28.04 +  -0.20)

alignment

secondary structure

dotplot

Window 1

Location	20,347,450 – 20,347,570
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.50
Mean single sequence MFE	-40.14
Consensus MFE	-34.00
Energy contribution	-34.16
Covariance contribution	0.16
Combinations/Pair	1.09
Mean z-score	-1.95
Structure conservation index	0.85
SVM decision value	1.61
SVM RNA-class probability	0.967342
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20347450 120 - 22224390
AAGCCAGGGCGAAAGAGAUGGCAUCUGCGUGCGAGAAAGAGAGCGCCAAUGUCUUGUGGCUGCCAUUUGCGGCGAAGAAAACCCGAAGAGUGAGUGAAAAAUCGCAACCACAUAGGGCAC
..((((...(....)...))))...((.((((..........)))))).((((((((((((((.....)))))................((((.(....).)))).....))))))))). ( -36.60)
>DroSec_CAF1 15295 120 - 1
AAGCCAGGGCGAAAGAGAUGGCCUCUGCGCGCGAGAAAGAGAGCGCCAAUGUCUUGUGGCUGCCAUUUGCGGCCAAGAAAACCCGAAGAGUGAGUAAAAAUUCGCAACCACAUAGGGCAC
..(((.(((...((((.(((((((((.(.(....)...))))).))).)).)))).(((((((.....)))))))......))).....((((((....))))))..........))).. ( -42.70)
>DroSim_CAF1 17059 120 - 1
AAGCCAGGGCGAAAGAGAUGGCCUCUGCGCGCGAGAAAGAGAGCGCCAAUGUCUUGUGGCUGCCAUUUGCGGCCAAGAAAACCCGAAGAGUGAGUGAAAAAUCGCAACCACAUAGGGCAC
..(((.(((...((((.(((((((((.(.(....)...))))).))).)).)))).(((((((.....)))))))......))).....(((.((((....))))...)))....))).. ( -42.10)
>DroEre_CAF1 12056 120 - 1
AAGCCAGGGCGAAAGAGAUGGCCUCUGCGUGGGCGAAAGAGAGCGCCGAUGUCUUGUGGCUGCCAUUUGCGGCCAAGAAAACCCGAAGAAUGAGUGAAAAAUCGCAACCACAUAGGGCAC
..(((.(((...((((.(((((((((.((....))....)))).))).)).)))).(((((((.....)))))))......))).........((((....))))..........))).. ( -39.40)
>DroYak_CAF1 15881 120 - 1
AAGCCAGGGCGAAAGAGACGGCCUCUGCGUGCGAGAAAGAGAGCGCCGAUGUCUUGUGGCUGCCAUUUGCGGCCAAGAAAAGCCGAAGAAUGAGUGAAAAAUCGCAACCACACAGGGCAC
..(((..(((..((((.(((((((((.(..........))))).)))).).)))).(((((((.....)))))))......))).........((((....))))..........))).. ( -39.90)
>consensus
AAGCCAGGGCGAAAGAGAUGGCCUCUGCGUGCGAGAAAGAGAGCGCCAAUGUCUUGUGGCUGCCAUUUGCGGCCAAGAAAACCCGAAGAGUGAGUGAAAAAUCGCAACCACAUAGGGCAC
..(((.(((...((((.(((((((((.(.(....)...))))).)))).).)))).(((((((.....)))))))......))).........((((....))))..........))).. (-34.00 = -34.16 +   0.16)

alignment

secondary structure

dotplot

Window 2

Location	20,347,490 – 20,347,610
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.33
Mean single sequence MFE	-34.62
Consensus MFE	-31.62
Energy contribution	-31.98
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.62
Structure conservation index	0.91
SVM decision value	1.37
SVM RNA-class probability	0.947750
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20347490 120 + 22224390
UUUCUUCGCCGCAAAUGGCAGCCACAAGACAUUGGCGCUCUCUUUCUCGCACGCAGAUGCCAUCUCUUUCGCCCUGGCUUACCAAUUCCUGGUUUGCCACAAAGCCGCGUCUCCAACGCU
......(((.((..((((((((((........))))((..........)).......))))))...........((((..((((.....))))..))))....)).)))........... ( -31.40)
>DroSec_CAF1 15335 120 + 1
UUUCUUGGCCGCAAAUGGCAGCCACAAGACAUUGGCGCUCUCUUUCUCGCGCGCAGAGGCCAUCUCUUUCGCCCUGGCUUACCAAUUCCUGGUUUGCCACAAAGCCGCGUCUCCAACGCU
..(((((((.((.....)).))))..)))....(((..............(((.((((.....))))..)))..((((..((((.....))))..))))....)))((((.....)))). ( -35.50)
>DroSim_CAF1 17099 120 + 1
UUUCUUGGCCGCAAAUGGCAGCCACAAGACAUUGGCGCUCUCUUUCUCGCGCGCAGAGGCCAUCUCUUUCGCCCUGGCUUACCAAUUCCUGGUUUGCCACAAAGCCGCGUCUCCAACGCU
..(((((((.((.....)).))))..)))....(((..............(((.((((.....))))..)))..((((..((((.....))))..))))....)))((((.....)))). ( -35.50)
>DroEre_CAF1 12096 120 + 1
UUUCUUGGCCGCAAAUGGCAGCCACAAGACAUCGGCGCUCUCUUUCGCCCACGCAGAGGCCAUCUCUUUCGCCCUGGCUUACCAAUUCCUGGUUUGCCACAAAGCCGCGUCUCCAACGCU
.....((((.((.....)).))))..((((..((((((.((((...((....))))))))..............((((..((((.....))))..))))....)))).))))........ ( -35.30)
>DroYak_CAF1 15921 120 + 1
UUUCUUGGCCGCAAAUGGCAGCCACAAGACAUCGGCGCUCUCUUUCUCGCACGCAGAGGCCGUCUCUUUCGCCCUGGCUUACCAAUUCCUGGUUUGCCACAAAGCCGCGUCUCCAACGCU
.....((((.((.....)).)))).((((...((((.(((((..........).))))))))..))))..((..((((..((((.....))))..))))....)).((((.....)))). ( -35.40)
>consensus
UUUCUUGGCCGCAAAUGGCAGCCACAAGACAUUGGCGCUCUCUUUCUCGCACGCAGAGGCCAUCUCUUUCGCCCUGGCUUACCAAUUCCUGGUUUGCCACAAAGCCGCGUCUCCAACGCU
.....((((.((.....)).)))).((((...((((.(((((..........).))))))))..))))..((..((((..((((.....))))..))))....)).((((.....)))). (-31.62 = -31.98 +   0.36)

alignment

secondary structure

dotplot

Window 3

Location	20,347,490 – 20,347,610
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.33
Mean single sequence MFE	-46.64
Consensus MFE	-44.04
Energy contribution	-44.16
Covariance contribution	0.12
Combinations/Pair	1.05
Mean z-score	-2.51
Structure conservation index	0.94
SVM decision value	3.88
SVM RNA-class probability	0.999683
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20347490 120 - 22224390
AGCGUUGGAGACGCGGCUUUGUGGCAAACCAGGAAUUGGUAAGCCAGGGCGAAAGAGAUGGCAUCUGCGUGCGAGAAAGAGAGCGCCAAUGUCUUGUGGCUGCCAUUUGCGGCGAAGAAA
...........(((.((...((((((..((((((((((((..((((...(....)...))))....((...(......)...)))))))).))))).)..))))))..)).)))...... ( -44.40)
>DroSec_CAF1 15335 120 - 1
AGCGUUGGAGACGCGGCUUUGUGGCAAACCAGGAAUUGGUAAGCCAGGGCGAAAGAGAUGGCCUCUGCGCGCGAGAAAGAGAGCGCCAAUGUCUUGUGGCUGCCAUUUGCGGCCAAGAAA
.(((((...)))))((((..((((((..((((((((((((..((((...(....)...))))((((...(....)..))))...)))))).))))).)..))))))....))))...... ( -49.20)
>DroSim_CAF1 17099 120 - 1
AGCGUUGGAGACGCGGCUUUGUGGCAAACCAGGAAUUGGUAAGCCAGGGCGAAAGAGAUGGCCUCUGCGCGCGAGAAAGAGAGCGCCAAUGUCUUGUGGCUGCCAUUUGCGGCCAAGAAA
.(((((...)))))((((..((((((..((((((((((((..((((...(....)...))))((((...(....)..))))...)))))).))))).)..))))))....))))...... ( -49.20)
>DroEre_CAF1 12096 120 - 1
AGCGUUGGAGACGCGGCUUUGUGGCAAACCAGGAAUUGGUAAGCCAGGGCGAAAGAGAUGGCCUCUGCGUGGGCGAAAGAGAGCGCCGAUGUCUUGUGGCUGCCAUUUGCGGCCAAGAAA
.(((((...)))))((((..((((((..((((((((((((..((((...(....)...))))((((.((....))..))))...)))))).))))).)..))))))....))))...... ( -47.10)
>DroYak_CAF1 15921 120 - 1
AGCGUUGGAGACGCGGCUUUGUGGCAAACCAGGAAUUGGUAAGCCAGGGCGAAAGAGACGGCCUCUGCGUGCGAGAAAGAGAGCGCCGAUGUCUUGUGGCUGCCAUUUGCGGCCAAGAAA
.(((((...))))).((((..((((..(((((...)))))..))))))))..((((.(((((((((.(..........))))).)))).).)))).(((((((.....)))))))..... ( -43.30)
>consensus
AGCGUUGGAGACGCGGCUUUGUGGCAAACCAGGAAUUGGUAAGCCAGGGCGAAAGAGAUGGCCUCUGCGUGCGAGAAAGAGAGCGCCAAUGUCUUGUGGCUGCCAUUUGCGGCCAAGAAA
.(((((...)))))((((..((((((..((((((((((((..((((...(....)...))))((((...(....)..))))...)))))).))))).)..))))))....))))...... (-44.04 = -44.16 +   0.12)

alignment

secondary structure

dotplot

Window 4

Location	20,347,530 – 20,347,637
Length	107
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	96.42
Mean single sequence MFE	-26.90
Consensus MFE	-23.08
Energy contribution	-23.07
Covariance contribution	-0.00
Combinations/Pair	1.04
Mean z-score	-2.88
Structure conservation index	0.86
SVM decision value	1.03
SVM RNA-class probability	0.904105
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20347530 107 + 22224390
UCUUUCUCGCACGCAGAUGCCAUCUCUUUCGCCCUGGCUUACCAAUUCCUGGUUUGCCACAAAGCCGCGUCUCCAACGCUUUGCUUUCGCUUGGAUUUUUCUUCUUU
........(.((((((((...)))).....((..((((..((((.....))))..))))....)).)))))(((((.((.........)))))))............ ( -22.20)
>DroSec_CAF1 15375 107 + 1
UCUUUCUCGCGCGCAGAGGCCAUCUCUUUCGCCCUGGCUUACCAAUUCCUGGUUUGCCACAAAGCCGCGUCUCCAACGCUUUGCUUUCGCUUGGAUUUUUCUUCGUU
.......((((.((((.(((.(......).)))))(((..((((.....))))..))).....))))))..(((((.((.........)))))))............ ( -28.70)
>DroSim_CAF1 17139 107 + 1
UCUUUCUCGCGCGCAGAGGCCAUCUCUUUCGCCCUGGCUUACCAAUUCCUGGUUUGCCACAAAGCCGCGUCUCCAACGCUUUGCUUUCGCUUGGAUUUUUCUUCGUU
.......((((.((((.(((.(......).)))))(((..((((.....))))..))).....))))))..(((((.((.........)))))))............ ( -28.70)
>DroEre_CAF1 12136 107 + 1
UCUUUCGCCCACGCAGAGGCCAUCUCUUUCGCCCUGGCUUACCAAUUCCUGGUUUGCCACAAAGCCGCGUCUCCAACGCUUUGCUUUUGCUUGCAUUUUUCUUCUUU
......((....((((((((..........((..((((..((((.....))))..))))....)).((((.....))))...))))))))..))............. ( -28.00)
>consensus
UCUUUCUCGCACGCAGAGGCCAUCUCUUUCGCCCUGGCUUACCAAUUCCUGGUUUGCCACAAAGCCGCGUCUCCAACGCUUUGCUUUCGCUUGGAUUUUUCUUCGUU
.........((.((.(((((..........((..((((..((((.....))))..))))....)).((((.....))))...))))).)).)).............. (-23.08 = -23.07 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	20,347,530 – 20,347,637
Length	107
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	96.42
Mean single sequence MFE	-32.05
Consensus MFE	-28.54
Energy contribution	-28.35
Covariance contribution	-0.19
Combinations/Pair	1.08
Mean z-score	-2.91
Structure conservation index	0.89
SVM decision value	1.42
SVM RNA-class probability	0.952397
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20347530 107 - 22224390
AAAGAAGAAAAAUCCAAGCGAAAGCAAAGCGUUGGAGACGCGGCUUUGUGGCAAACCAGGAAUUGGUAAGCCAGGGCGAAAGAGAUGGCAUCUGCGUGCGAGAAAGA
.............((..((....))...(((((...)))))))((((.(.(((.(((((...)))))..((((...(....)...)))).......))).).)))). ( -31.40)
>DroSec_CAF1 15375 107 - 1
AACGAAGAAAAAUCCAAGCGAAAGCAAAGCGUUGGAGACGCGGCUUUGUGGCAAACCAGGAAUUGGUAAGCCAGGGCGAAAGAGAUGGCCUCUGCGCGCGAGAAAGA
.((((((..........((....))...(((((...)))))..))))))(((..(((((...)))))..))).(.(((..((((.....)))).))).)........ ( -32.80)
>DroSim_CAF1 17139 107 - 1
AACGAAGAAAAAUCCAAGCGAAAGCAAAGCGUUGGAGACGCGGCUUUGUGGCAAACCAGGAAUUGGUAAGCCAGGGCGAAAGAGAUGGCCUCUGCGCGCGAGAAAGA
.((((((..........((....))...(((((...)))))..))))))(((..(((((...)))))..))).(.(((..((((.....)))).))).)........ ( -32.80)
>DroEre_CAF1 12136 107 - 1
AAAGAAGAAAAAUGCAAGCAAAAGCAAAGCGUUGGAGACGCGGCUUUGUGGCAAACCAGGAAUUGGUAAGCCAGGGCGAAAGAGAUGGCCUCUGCGUGGGCGAAAGA
............(((..((....(((((((..((....))..))))))).(((.(((((...)))))..((((...(....)...))))...)))))..)))..... ( -31.20)
>consensus
AAAGAAGAAAAAUCCAAGCGAAAGCAAAGCGUUGGAGACGCGGCUUUGUGGCAAACCAGGAAUUGGUAAGCCAGGGCGAAAGAGAUGGCCUCUGCGCGCGAGAAAGA
.................(((...(((((((..((....))..))))))).(((.(((((...)))))..((((...(....)...))))...))).)))........ (-28.54 = -28.35 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:57:57 2006