Locus 1534

Sequence ID	X_DroMel_CAF1
Location	4,444,503 – 4,444,695
Length	192
Max. P	0.991398

overview

Window 3

Location	4,444,503 – 4,444,615
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.12
Mean single sequence MFE	-41.80
Consensus MFE	-28.09
Energy contribution	-29.68
Covariance contribution	1.59
Combinations/Pair	1.06
Mean z-score	-1.90
Structure conservation index	0.67
SVM decision value	0.12
SVM RNA-class probability	0.594049
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4444503 112 + 22224390
GUCUUUGGGCCCUGAGCCCUAGGCCGUGCCUUUAGCCAUCUACGGUUGCCAUCUUGACAAGACCUCGAGAG--------UCCGUAGCCCGUAGUUGGCCCAAAGCCAUUGGACACAUCAA
((((..((((.....)))).)))).(((......((((.((((((((((..((((((.......)))))).--------...)))).)))))).))))((((.....)))).)))..... ( -39.50)
>DroSec_CAF1 46133 120 + 1
GUCUUUGGGCUUAGGGCCUUAGGUCUUGCCUCUAGCCAUCUACGGUUGCCAUCUUGACAAGACCUCGAGAGUCCGGGAGUCCGUAGCCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAA
((((...(((((.(((((..((((((((.(..(((((......))))).......).))))))))...((.((((((.........)))))).))))))).)))))...))))....... ( -50.90)
>DroSim_CAF1 47334 120 + 1
GUCUUUGGGCUUAGGGCCUUAGGCCUUGCCUCUAGCCAUCUACGGUUGCCAUCUUGACAAGACCUCGAGAGUCCGGGAGUCCGUAGCCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAA
((((...(((((.(((((...(((...(((..(((....))).))).))).((((((.......)))))).((((((.........))))))...))))).)))))...))))....... ( -47.50)
>DroEre_CAF1 47986 103 + 1
GUC--UGGGCCCUGAGCCUUA-------------GCCAUCUACGGUUGCCAUCUUGACAAGACCUCGAGA--CCGGGAGUCCGUAGCCUGGAGUUGGCCCAAAGCCAUUGGACACAUCAA
(((--(.(((..((.(((...-------------.(((.((((((((.((.((((((.......))))))--..)).)).))))))..)))....))).))..)))...))))....... ( -37.70)
>DroYak_CAF1 46775 118 + 1
GUCUUUGGGCCCUGAGCCUUAGACCUUGCCACUAGCCAUCUACGGUUGCCAUCUAGACAAGAACUCGAGA--CCAGGAGUCCGUAACCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAA
(.((((((((((((.(.(((((..((((...((((.((.(....).))....)))).))))..)).))).--))))((.((((.....)))).))))))))))).).............. ( -33.40)
>consensus
GUCUUUGGGCCCUGAGCCUUAGGCCUUGCCUCUAGCCAUCUACGGUUGCCAUCUUGACAAGACCUCGAGAG_CCGGGAGUCCGUAGCCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAA
(.(((((((((..(.((...((((...))))...)))..((((((...((.((((((.......)))))).....))...)))))).........))))))))).).............. (-28.09 = -29.68 +   1.59)

alignment

secondary structure

dotplot

Window 4

Location	4,444,503 – 4,444,615
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.12
Mean single sequence MFE	-44.84
Consensus MFE	-35.14
Energy contribution	-37.98
Covariance contribution	2.84
Combinations/Pair	1.14
Mean z-score	-2.04
Structure conservation index	0.78
SVM decision value	1.01
SVM RNA-class probability	0.900430
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4444503 112 - 22224390
UUGAUGUGUCCAAUGGCUUUGGGCCAACUACGGGCUACGGA--------CUCUCGAGGUCUUGUCAAGAUGGCAACCGUAGAUGGCUAAAGGCACGGCCUAGGGCUCAGGGCCCAAAGAC
....((.((((...(((((((((((..((((((.....(((--------((.....)))))((((.....)))).))))))...((.....))..)))))))))))..)))).))..... ( -43.20)
>DroSec_CAF1 46133 120 - 1
UUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGCUACGGACUCCCGGACUCUCGAGGUCUUGUCAAGAUGGCAACCGUAGAUGGCUAGAGGCAAGACCUAAGGCCCUAAGCCCAAAGAC
.......(((....(((((.(((((...(((((((....)...))))))......((((((((((....((((...........))))..))))))))))..))))).)))))....))) ( -50.20)
>DroSim_CAF1 47334 120 - 1
UUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGCUACGGACUCCCGGACUCUCGAGGUCUUGUCAAGAUGGCAACCGUAGAUGGCUAGAGGCAAGGCCUAAGGCCCUAAGCCCAAAGAC
.......(((....(((((.(((((...(((((((....)...))))))......((((((((((....((((...........))))..))))))))))..))))).)))))....))) ( -49.60)
>DroEre_CAF1 47986 103 - 1
UUGAUGUGUCCAAUGGCUUUGGGCCAACUCCAGGCUACGGACUCCCGG--UCUCGAGGUCUUGUCAAGAUGGCAACCGUAGAUGGC-------------UAAGGCUCAGGGCCCA--GAC
.......(((....(((((((((((....(((..((((((......(.--.(....)..)(((((.....))))))))))).))).-------------...)))))))))))..--))) ( -39.10)
>DroYak_CAF1 46775 118 - 1
UUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGUUACGGACUCCUGG--UCUCGAGUUCUUGUCUAGAUGGCAACCGUAGAUGGCUAGUGGCAAGGUCUAAGGCUCAGGGCCCAAAGAC
................(((((((((...((((.....))))...((((--(((..((..((((((....((((...........))))..))))))..)).)))).)))))))))))).. ( -42.10)
>consensus
UUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGCUACGGACUCCCGG_CUCUCGAGGUCUUGUCAAGAUGGCAACCGUAGAUGGCUAGAGGCAAGGCCUAAGGCUCAGGGCCCAAAGAC
.......(((....(((((((((((.....((((...(((....)))....))))((((((((((....((((...........))))..))))))))))..)))))))))))....))) (-35.14 = -37.98 +   2.84)

alignment

secondary structure

dotplot

Window 5

Location	4,444,543 – 4,444,655
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.31
Mean single sequence MFE	-45.70
Consensus MFE	-38.16
Energy contribution	-40.24
Covariance contribution	2.08
Combinations/Pair	1.05
Mean z-score	-2.25
Structure conservation index	0.84
SVM decision value	2.27
SVM RNA-class probability	0.991398
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4444543 112 + 22224390
UACGGUUGCCAUCUUGACAAGACCUCGAGAG--------UCCGUAGCCCGUAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAUGGCAUGGCCUGCAGGAAAAUCCGGGGGGUAG
(((((......((((((.......)))))).--------.)))))((((...((.((((....(((((((..((((....)))).)))))))..)))).)).((.....))...)))).. ( -42.10)
>DroSec_CAF1 46173 120 + 1
UACGGUUGCCAUCUUGACAAGACCUCGAGAGUCCGGGAGUCCGUAGCCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAUGGCAUGGGCUGCAGGAAAAUCCGGGUGGUAG
......(((((((((((.......)))))).((((((..((((((((((((.(....)))...(((((((..((((....)))).)))))))..))))))).)))...))))))))))). ( -52.80)
>DroSim_CAF1 47374 120 + 1
UACGGUUGCCAUCUUGACAAGACCUCGAGAGUCCGGGAGUCCGUAGCCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAUGGCAUGGGCUGCAGGAAAAUCCGGGUGGUAG
......(((((((((((.......)))))).((((((..((((((((((((.(....)))...(((((((..((((....)))).)))))))..))))))).)))...))))))))))). ( -52.80)
>DroEre_CAF1 48011 118 + 1
UACGGUUGCCAUCUUGACAAGACCUCGAGA--CCGGGAGUCCGUAGCCUGGAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAAGGCAUGGUCUACAGGAAAAUGCGGGGGGUAG
......((((.(((((......(((..(((--((((((.((((.....)))).)...)))...(((.(((..((((....)))).))).)))..)))))..)))......))))))))). ( -37.20)
>DroYak_CAF1 46815 118 + 1
UACGGUUGCCAUCUAGACAAGAACUCGAGA--CCAGGAGUCCGUAACCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAUGGCACGGGCUGCAGGAAAAUCCGGGGGGUAG
(((((...((.(((.((.......)).)))--...))...))))).((((((.(((((((...(((((((..((((....)))).)))))))..)))))....))...))))))...... ( -43.60)
>consensus
UACGGUUGCCAUCUUGACAAGACCUCGAGAG_CCGGGAGUCCGUAGCCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAUGGCAUGGGCUGCAGGAAAAUCCGGGGGGUAG
......((((.((((((.......))))))..((.(((.((((((((((((.(....)))...(((((((..((((....)))).)))))))..))))))).)))...))).)).)))). (-38.16 = -40.24 +   2.08)

alignment

secondary structure

dotplot

Window 6

Location	4,444,543 – 4,444,655
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.31
Mean single sequence MFE	-39.90
Consensus MFE	-30.98
Energy contribution	-32.62
Covariance contribution	1.64
Combinations/Pair	1.03
Mean z-score	-1.78
Structure conservation index	0.78
SVM decision value	0.50
SVM RNA-class probability	0.758919
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4444543 112 - 22224390
CUACCCCCCGGAUUUUCCUGCAGGCCAUGCCAUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUACGGGCUACGGA--------CUCUCGAGGUCUUGUCAAGAUGGCAACCGUA
......(((((.....))....((((..(((((((.((((....))))..)))))))....))))......))).(((((.--------((....))...(((((.....)))))))))) ( -37.40)
>DroSec_CAF1 46173 120 - 1
CUACCACCCGGAUUUUCCUGCAGCCCAUGCCAUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGCUACGGACUCCCGGACUCUCGAGGUCUUGUCAAGAUGGCAACCGUA
......((((((......((..(((((.(((((((.((((....))))..)))))))..)))))))..)))))).(((((......(((((.....)))))((((.....)))).))))) ( -43.30)
>DroSim_CAF1 47374 120 - 1
CUACCACCCGGAUUUUCCUGCAGCCCAUGCCAUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGCUACGGACUCCCGGACUCUCGAGGUCUUGUCAAGAUGGCAACCGUA
......((((((......((..(((((.(((((((.((((....))))..)))))))..)))))))..)))))).(((((......(((((.....)))))((((.....)))).))))) ( -43.30)
>DroEre_CAF1 48011 118 - 1
CUACCCCCCGCAUUUUCCUGUAGACCAUGCCUUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUCCAGGCUACGGACUCCCGG--UCUCGAGGUCUUGUCAAGAUGGCAACCGUA
.........((((..((.....))..))))..((((((..((((((.((((((.....)))))))..(((.((((..(((....))))--))).))).....)))))..))))))..... ( -33.40)
>DroYak_CAF1 46815 118 - 1
CUACCCCCCGGAUUUUCCUGCAGCCCGUGCCAUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGUUACGGACUCCUGG--UCUCGAGUUCUUGUCUAGAUGGCAACCGUA
......((((((......((..(((((.(((((((.((((....))))..)))))))..)))))))..)))))).(((((((((....--....))))..(((((.....)))))))))) ( -42.10)
>consensus
CUACCCCCCGGAUUUUCCUGCAGCCCAUGCCAUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGCUACGGACUCCCGG_CUCUCGAGGUCUUGUCAAGAUGGCAACCGUA
......((((((......((..(((((.(((((((.((((....))))..)))))))..)))))))..)))))).(((((.(((..........)))...(((((.....)))))))))) (-30.98 = -32.62 +   1.64)

alignment

secondary structure

dotplot

Window 7

Location	4,444,575 – 4,444,695
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.58
Mean single sequence MFE	-42.62
Consensus MFE	-38.12
Energy contribution	-38.80
Covariance contribution	0.68
Combinations/Pair	1.05
Mean z-score	-1.35
Structure conservation index	0.89
SVM decision value	0.47
SVM RNA-class probability	0.749943
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4444575 120 + 22224390
CCGUAGCCCGUAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAUGGCAUGGCCUGCAGGAAAAUCCGGGGGGUAGCAACGUAUGUGGGGUGUCUCUAUGCGACAAUUUCCUGUUU
..((.((((...((.((((....(((((((..((((....)))).)))))))..)))).)).((.....))...)))).))..((((((.(((....))))))))).............. ( -41.30)
>DroSec_CAF1 46213 120 + 1
CCGUAGCCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAUGGCAUGGGCUGCAGGAAAAUCCGGGUGGUAGCAACGUAUGUGGGGUGUCUCUAUGCGACAAUUUCCUGUUU
..(((((((((.(....)))...(((((((..((((....)))).)))))))..)))))))((((((.((((.(((((....)).))).)))).((((.......)))).)))))).... ( -45.00)
>DroSim_CAF1 47414 120 + 1
CCGUAGCCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAUGGCAUGGGCUGCAGGAAAAUCCGGGUGGUAGCAACGUAUGUGGGGUGUCUCUAUGCGACAAUUUCCUGUUU
..(((((((((.(....)))...(((((((..((((....)))).)))))))..)))))))((((((.((((.(((((....)).))).)))).((((.......)))).)))))).... ( -45.00)
>DroEre_CAF1 48049 120 + 1
CCGUAGCCUGGAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAAGGCAUGGUCUACAGGAAAAUGCGGGGGGUAGCAACGUAUGUGGGGUGUCUCUAUGCGACAAUUUCCUGUUU
((((.((((((.(....)))...(((((..((....))...)))))..))))))))...((((((((.(((........))).((((((.(((....)))))))))....)))))))).. ( -38.10)
>DroYak_CAF1 46853 120 + 1
CCGUAACCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAUGGCACGGGCUGCAGGAAAAUCCGGGGGGUAGCAACGUAUGUGGGGUGUCUCUAUGCGACAAUUUCCUGUUU
(((.....)))....(((((...(((((((..((((....)))).)))))))..)))))((((((((((((...)))).....((((((.(((....)))))))))....)))))))).. ( -43.70)
>consensus
CCGUAGCCCGGAGUUGGCCCAAAGCCAUUGGACACAUCAAUGUGGCAAUGGCAUGGGCUGCAGGAAAAUCCGGGGGGUAGCAACGUAUGUGGGGUGUCUCUAUGCGACAAUUUCCUGUUU
(((((((((((.(....)))...(((((((..((((....)))).)))))))..))))))).))......((((..((.(...((((((.(((....))))))))).).))..))))... (-38.12 = -38.80 +   0.68)

alignment

secondary structure

dotplot

Window 8

Location	4,444,575 – 4,444,695
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.58
Mean single sequence MFE	-35.98
Consensus MFE	-30.46
Energy contribution	-30.94
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-1.36
Structure conservation index	0.85
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4444575 120 - 22224390
AAACAGGAAAUUGUCGCAUAGAGACACCCCACAUACGUUGCUACCCCCCGGAUUUUCCUGCAGGCCAUGCCAUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUACGGGCUACGG
...(((((((.((((.......)))).................((....))..)))))))..((((..(((((((.((((....))))..)))))))....)))).....((.....)). ( -35.50)
>DroSec_CAF1 46213 120 - 1
AAACAGGAAAUUGUCGCAUAGAGACACCCCACAUACGUUGCUACCACCCGGAUUUUCCUGCAGCCCAUGCCAUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGCUACGG
...(((((((.((((.......)))).................((....))..)))))))..(((((.(((((((.((((....))))..)))))))..))))).....(((.....))) ( -38.10)
>DroSim_CAF1 47414 120 - 1
AAACAGGAAAUUGUCGCAUAGAGACACCCCACAUACGUUGCUACCACCCGGAUUUUCCUGCAGCCCAUGCCAUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGCUACGG
...(((((((.((((.......)))).................((....))..)))))))..(((((.(((((((.((((....))))..)))))))..))))).....(((.....))) ( -38.10)
>DroEre_CAF1 48049 120 - 1
AAACAGGAAAUUGUCGCAUAGAGACACCCCACAUACGUUGCUACCCCCCGCAUUUUCCUGUAGACCAUGCCUUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUCCAGGCUACGG
..((((((((.((((.......))))............(((........))).))))))))...(((.(((.(((.((((....))))..))).)))..)))(((.......)))..... ( -31.40)
>DroYak_CAF1 46853 120 - 1
AAACAGGAAAUUGUCGCAUAGAGACACCCCACAUACGUUGCUACCCCCCGGAUUUUCCUGCAGCCCGUGCCAUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGUUACGG
...(((((((.((((.......)))).................((....))..)))))))..(((((.(((((((.((((....))))..)))))))..))))).....(((.....))) ( -36.80)
>consensus
AAACAGGAAAUUGUCGCAUAGAGACACCCCACAUACGUUGCUACCCCCCGGAUUUUCCUGCAGCCCAUGCCAUUGCCACAUUGAUGUGUCCAAUGGCUUUGGGCCAACUCCGGGCUACGG
.....((....((((.......))))..)).....(((.(((.......((.....))....(((((.(((((((.((((....))))..)))))))..)))))........))).))). (-30.46 = -30.94 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:40 2006