Locus 405

Sequence ID	2L_DroMel_CAF1
Location	1,230,259 – 1,230,445
Length	186
Max. P	0.999967

overview

Window 2

Location	1,230,259 – 1,230,374
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.66
Mean single sequence MFE	-33.24
Consensus MFE	-27.26
Energy contribution	-27.02
Covariance contribution	-0.24
Combinations/Pair	1.23
Mean z-score	-2.44
Structure conservation index	0.82
SVM decision value	2.31
SVM RNA-class probability	0.992182
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1230259 115 + 22407834
UGCCGCCGGAGG---GAAAUUUAAGUGCCUUCGGCGACCAAACGAACCAAUUUUGUAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGUCCGGAAAA--AAAAAUGCUCAACAAAAU
...(((((((((---.(........).))))))))).............(((((((((((....((((..(((((....)))))...........)))).--.....))))..))))))) ( -31.22)
>DroSec_CAF1 7614 113 + 1
UGCCGCCGGAGG---GAAAUUUAAGUGCCCUCGGCGACCAAACGAACCAAUUUUGUAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGUCCGA--AA--AAAGAUGCCCAACAAAAU
...(((((.(((---(...........))))))))).............(((((((.(.(((........(((((....)))))......(((...--..--...))))))).))))))) ( -32.10)
>DroSim_CAF1 3410 113 + 1
UGCCGCCGGAGG---GAAAUUUAAGUGCCUUCGGCGACCAAACGAACCAAUUUUGUAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGUCCGA--AA--AAAGAUGCCCAGCAAAAU
...(((((((((---.(........).))))))))).............(((((((.(.(((........(((((....)))))......(((...--..--...))))))).))))))) ( -34.30)
>DroEre_CAF1 3573 113 + 1
UGUCGCCGGAGG---GAAAUUUAAGUGCCUCUGGCGACCAAGCGAACCAAUUUUGAAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGUCCGA--AA--AAAGAUGCCCAACAAAAU
.(((((((((((---.(........).)))))))))))...........((((((..(.(((........(((((....)))))......(((...--..--...)))))))..)))))) ( -37.10)
>DroYak_CAF1 3445 118 + 1
UGGCGCUGGGGGGCGGAAAUUUAAGUGCCUUCGGCGACCAAACGAACCAAUUUUGAAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGCCCGA--AAAAAAAGAUGCCCAACAAAAU
((((((((((((((..........)).))))))))).))).........((((((..(.((((......)(((((....)))))............--..........))))..)))))) ( -31.50)
>consensus
UGCCGCCGGAGG___GAAAUUUAAGUGCCUUCGGCGACCAAACGAACCAAUUUUGUAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGUCCGA__AA__AAAGAUGCCCAACAAAAU
...(((((((((...............))))))))).............(((((((.(.((((......)(((((....)))))........................)))).))))))) (-27.26 = -27.02 +  -0.24)

alignment

secondary structure

dotplot

Window 3

Location	1,230,259 – 1,230,374
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.66
Mean single sequence MFE	-35.68
Consensus MFE	-28.47
Energy contribution	-28.87
Covariance contribution	0.40
Combinations/Pair	1.11
Mean z-score	-1.94
Structure conservation index	0.80
SVM decision value	1.06
SVM RNA-class probability	0.908407
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1230259 115 - 22407834
AUUUUGUUGAGCAUUUUU--UUUUCCGGACUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUACAAAAUUGGUUCGUUUGGUCGCCGAAGGCACUUAAAUUUC---CCUCCGGCGGCA
........((((...(((--(.(..(((...((((.(((((....)))))..))))...)))..).))))...)))).....(((((((.(((............---))).))))))). ( -35.00)
>DroSec_CAF1 7614 113 - 1
AUUUUGUUGGGCAUCUUU--UU--UCGGACUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUACAAAAUUGGUUCGUUUGGUCGCCGAGGGCACUUAAAUUUC---CCUCCGGCGGCA
(((((((.((((......--((--((((........(((((....)))))))))))..))).).)))))))...........(((((((((((...........)---))).))))))). ( -38.40)
>DroSim_CAF1 3410 113 - 1
AUUUUGCUGGGCAUCUUU--UU--UCGGACUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUACAAAAUUGGUUCGUUUGGUCGCCGAAGGCACUUAAAUUUC---CCUCCGGCGGCA
((((((..((((......--((--((((........(((((....)))))))))))..))).)..))))))...........(((((((.(((............---))).))))))). ( -34.10)
>DroEre_CAF1 3573 113 - 1
AUUUUGUUGGGCAUCUUU--UU--UCGGACUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUUCAAAAUUGGUUCGCUUGGUCGCCAGAGGCACUUAAAUUUC---CCUCCGGCGACA
..................--..--.((((((.(((((((((...((((.........)))))))))))))..))))))....((((((.((((............---)))).)))))). ( -36.40)
>DroYak_CAF1 3445 118 - 1
AUUUUGUUGGGCAUCUUUUUUU--UCGGGCUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUUCAAAAUUGGUUCGUUUGGUCGCCGAAGGCACUUAAAUUUCCGCCCCCCAGCGCCA
.....((((((...........--..((((..(((((((((...((((.........)))))))))))))..((...(((((((.(((...))))).)))))..)))))))))))).... ( -34.51)
>consensus
AUUUUGUUGGGCAUCUUU__UU__UCGGACUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUACAAAAUUGGUUCGUUUGGUCGCCGAAGGCACUUAAAUUUC___CCUCCGGCGGCA
........((((.............(((.(((((..(((((....)))))..)))).).)))...........)))).....(((((((.(((...............))).))))))). (-28.47 = -28.87 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	1,230,296 – 1,230,414
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.34
Mean single sequence MFE	-33.83
Consensus MFE	-30.92
Energy contribution	-30.96
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-3.20
Structure conservation index	0.91
SVM decision value	4.99
SVM RNA-class probability	0.999967
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1230296 118 + 22407834
AACGAACCAAUUUUGUAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGUCCGGAAAA--AAAAAUGCUCAACAAAAUGAAGCGGCAUGAAGUUAAUGCCGCAGACUCUGCACGGCCA
.(((((.....)))))...((((.......(((((....)))))......((.((((...--........(((......))).(((((((.......)))))))....)))).)))))). ( -36.20)
>DroSec_CAF1 7651 116 + 1
AACGAACCAAUUUUGUAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGUCCGA--AA--AAAGAUGCCCAACAAAAUGAAGCGGCAUGAAGUUAAUGCCGCAGACUCUGCACGGCCA
.(((((.....)))))...((((....((((((((....))))).....((((...--..--.........((......))..(((((((.......))))))).)))))))...)))). ( -34.00)
>DroSim_CAF1 3447 116 + 1
AACGAACCAAUUUUGUAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGUCCGA--AA--AAAGAUGCCCAGCAAAAUGAAGCGGCAUGAAGUUAAUGCCGCAGACUCUGCACGGCCA
.(((((.....)))))...((((....((((((((....))))).....((((...--..--.....(((...))).......(((((((.......))))))).)))))))...)))). ( -36.00)
>DroEre_CAF1 3610 112 + 1
AGCGAACCAAUUUUGAAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGUCCGA--AA--AAAGAUGCCCAACAAAAUGAAGCGGUAUGAAGUUAAUGCCGCAGACU----ACGGCCA
.((..............))((((.......(((((....))))).....((((...--..--.........((......))..(((((((.......))))))).))))----..)))). ( -31.44)
>DroYak_CAF1 3485 114 + 1
AACGAACCAAUUUUGAAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGCCCGA--AAAAAAAGAUGCCCAACAAAAUGAAGCGGCAUGAAGUUAAUGCCGCAGACU----GCGGCCA
...................((((....((((((((....)))))............--.........................(((((((.......)))))))...))----).)))). ( -31.50)
>consensus
AACGAACCAAUUUUGUAGCGGCCAUUUCAGGGAGCCAAAGCUCCAAAAAAGUCCGA__AA__AAAGAUGCCCAACAAAAUGAAGCGGCAUGAAGUUAAUGCCGCAGACUCUGCACGGCCA
...................((((.......(((((....))))).....((((..................((......))..(((((((.......))))))).))))......)))). (-30.92 = -30.96 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	1,230,296 – 1,230,414
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.34
Mean single sequence MFE	-36.82
Consensus MFE	-32.96
Energy contribution	-33.04
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-2.54
Structure conservation index	0.90
SVM decision value	3.86
SVM RNA-class probability	0.999666
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1230296 118 - 22407834
UGGCCGUGCAGAGUCUGCGGCAUUAACUUCAUGCCGCUUCAUUUUGUUGAGCAUUUUU--UUUUCCGGACUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUACAAAAUUGGUUCGUU
.((((((.(((((((((((((((.......)))))))((((......)))).......--......))))).....(((((....))))))))..))))))((((......))))..... ( -38.20)
>DroSec_CAF1 7651 116 - 1
UGGCCGUGCAGAGUCUGCGGCAUUAACUUCAUGCCGCUUCAUUUUGUUGGGCAUCUUU--UU--UCGGACUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUACAAAAUUGGUUCGUU
..(((..(((((((..(((((((.......)))))))...)))))))..)))......--..--.((((((.(((((.(((...((((.........))))))).)))))..)))))).. ( -38.50)
>DroSim_CAF1 3447 116 - 1
UGGCCGUGCAGAGUCUGCGGCAUUAACUUCAUGCCGCUUCAUUUUGCUGGGCAUCUUU--UU--UCGGACUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUACAAAAUUGGUUCGUU
((.(((.(((((((..(((((((.......)))))))...)))))))))).)).....--..--.((((((.(((((.(((...((((.........))))))).)))))..)))))).. ( -40.20)
>DroEre_CAF1 3610 112 - 1
UGGCCGU----AGUCUGCGGCAUUAACUUCAUACCGCUUCAUUUUGUUGGGCAUCUUU--UU--UCGGACUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUUCAAAAUUGGUUCGCU
..(((((----.....)))))..............(((.((......)))))......--..--.((((((.(((((((((...((((.........)))))))))))))..)))))).. ( -30.80)
>DroYak_CAF1 3485 114 - 1
UGGCCGC----AGUCUGCGGCAUUAACUUCAUGCCGCUUCAUUUUGUUGGGCAUCUUUUUUU--UCGGGCUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUUCAAAAUUGGUUCGUU
((.((((----((...(((((((.......)))))))......))).))).)).........--.((((((.(((((((((...((((.........)))))))))))))..)))))).. ( -36.40)
>consensus
UGGCCGUGCAGAGUCUGCGGCAUUAACUUCAUGCCGCUUCAUUUUGUUGGGCAUCUUU__UU__UCGGACUUUUUUGGAGCUUUGGCUCCCUGAAAUGGCCGCUACAAAAUUGGUUCGUU
.((((((....((((((((((((.......)))))))((((......))))...............)))))(((..(((((....)))))..)))))))))................... (-32.96 = -33.04 +   0.08)

alignment

secondary structure

dotplot

Window 6

Location	1,230,336 – 1,230,445
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.34
Mean single sequence MFE	-26.62
Consensus MFE	-22.26
Energy contribution	-21.98
Covariance contribution	-0.28
Combinations/Pair	1.13
Mean z-score	-1.49
Structure conservation index	0.84
SVM decision value	0.50
SVM RNA-class probability	0.760555
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1230336 109 + 22407834
CUCCAAAAAAGUCCGGAAAA--AAAAAUGCUCAACAAAAUGAAGCGGCAUGAAGUUAAUGCCGCAGACUCUGCACGGCCAUGUGCUU---------CACGAGACAGCGGAUGCCAAAAAG
..........((.((((...--........(((......))).(((((((.......)))))))....)))).))(((.((.(((((---------(....)).)))).)))))...... ( -28.40)
>DroSec_CAF1 7691 107 + 1
CUCCAAAAAAGUCCGA--AA--AAAGAUGCCCAACAAAAUGAAGCGGCAUGAAGUUAAUGCCGCAGACUCUGCACGGCCAUGUGCUC---------CACGAGACAGCGGAUGCCAAAAAG
..........(((((.--..--.....................(((((((.......)))))))...(((.(((((....)))))..---------...)))....)))))......... ( -27.00)
>DroSim_CAF1 3487 107 + 1
CUCCAAAAAAGUCCGA--AA--AAAGAUGCCCAGCAAAAUGAAGCGGCAUGAAGUUAAUGCCGCAGACUCUGCACGGCCAUGUGCUC---------CACGAGACAGCGGAUGCCAAAAAG
..........(((((.--..--......(((..(((.......(((((((.......)))))))......)))..)))..(((.(((---------...)))))).)))))......... ( -27.12)
>DroEre_CAF1 3650 103 + 1
CUCCAAAAAAGUCCGA--AA--AAAGAUGCCCAACAAAAUGAAGCGGUAUGAAGUUAAUGCCGCAGACU----ACGGCCAUGUGCUC---------CACGAGACAGCGGAUGCCAAAAAG
..........(((((.--..--......(((((......))..(((((((.......))))))).....----..)))..(((.(((---------...)))))).)))))......... ( -22.50)
>DroYak_CAF1 3525 114 + 1
CUCCAAAAAAGCCCGA--AAAAAAAGAUGCCCAACAAAAUGAAGCGGCAUGAAGUUAAUGCCGCAGACU----GCGGCCAUGUGCUCCAUGUGCUUCACGAGACAGCGGAUGCCAAAAAG
..........(((((.--.........((.....))...(((((((.((((.(((....(((((.....----))))).....))).)))))))))))........)))..))....... ( -28.10)
>consensus
CUCCAAAAAAGUCCGA__AA__AAAGAUGCCCAACAAAAUGAAGCGGCAUGAAGUUAAUGCCGCAGACUCUGCACGGCCAUGUGCUC_________CACGAGACAGCGGAUGCCAAAAAG
..........(((((.............(((((......))..(((((((.......)))))))...........)))..(((.(((............)))))).)))))......... (-22.26 = -21.98 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:12 2006